Citrus Sinensis ID: 002040

---

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-------800-------810-------820-------830-------840-------850-------860-------870-------880-------890-------900-------910-------920-------930-------940-------950-------960-------970------
Protein Sequence
MAHSHRDRDREKEKEKHREKSRRSEREQSTDSDEDKHDKEKEKDKHRDRDRRRDRDRDRDREKEREEKRERAREKEREREKRDREREDRERERERERERRERDREREKRERERDRDKEKDRERKSRDREKRRKVESDDSDEDKDRDRKRRRRHDDDHKERVRERSLSRSNRHRDENDESPREKLVEDDSDKKEKKTREEELEDEQRKLDEEMEKRRRRVQEWQELKRKKEESERENRGDANVEEPKAGRNWTLDREDSDDEEVPQTGKSETDMDADEEPKPSENQVGDAMLVDSDGGSAAPALQIGAAEDEDIDPLDAFMNSMVLPEVEKLKNTVEPSFTDGNNVESKKMDRKGDRRSNGEQPKKSSNKSLGRIIPGEDSDSDYGDLENDEKPLEDEDDDEFMKRVKKTKAEKLSIVDHSKIDYQPFRKNFYIEVKEIARMTPEEVSAYRKQLELKIHGKDVPKPIKTWHQTGLTSKIMETIRKLNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMGFEPQITRIVQNIRPDRQTVLFSATFPRQVEILARKVLNKPVEIQVGGRSVVNKDITQLVEVRPESDRFLRLLELLGEWYEKGKILIFVHSQEKCDALFRDLLKHGYPCLSLHGAKDQTDRESTISDFKSNVCNLLIATSVAARGLDVKELELVINFDAPNHYEDYVHRVGRTGRAGRKGCAITFISEEDAKYSPDLVKALELSEQVVPDDLKALADSFMAKVNQGLEQAHGTGYGGSGFKFNEEEDEKRKAAKKAQAKEYGFEEDKSDSDDEDEGIRKAGGDISQQDALAKISAIRKLYLFIEGPTEQSVKRAKAELKRVLEDFTNQALSLPGGAQPGRYSVV
Secondary Structure (PSIPRED)
ccccccHHHHHHHHHHHHHHHccccccccccccccccccHHHcccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccHHHHHHHHcccccHHHHHHHHHcccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHccccccccccHHHHHHHcccHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHccccccccccccccccccccccccHHHHcccHHHHHHHHHHcccEEEcccccccccccccccccHHHHHHHHHcccccccHHHHHHHHHHHccccEEEEcccccHHHHHHHHHHHHHHHcccccccccccEEEEEcccHHHHHHHHHHHHHHHHHcccEEEEEEccccHHHHHHHHHccccEEEEcccHHHHHHHHccccEEEcccccEEEEcccccccccccHHHHHHHHHcccccccEEEEEccccHHHHHHHHHHHcccEEEEEccccccccccEEEEEEccccHHHHHHHHHHHHHcccccEEEEEcccHHHHHHHHHHHHcccccEEccccccHHHHHHHHHHHccccccEEEEEcccccccccccccEEEEcccccccccccccccccccccccEEEEEEEcccccccHHHHHHHHHHccccccHHHHHHHHHHHHHHccccccccccccccccccccHHHHHHHHHHHHHHHHHccccccccccccHHHHHHccccccHHHHHHHHHHHHHHHHHcccccccHHHHHHHHHHHHHHHHHHHHHccccccccccccccc
Secondary Structure Prediction (SSPRO)
cccccccccccccccccccccccccHcccccccHHHHHHHHHccccccccccccHHHccccccHHHHHccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccHHHHHHccccccccccccccccccccHHHHHHHHccccccHHHHHHcccccccccccccccccccccccccccHHcccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccHHcccccccccccccccccccccccccHccccHHHHHHHHHccHHHHHHccccccccccccccccccccEcccccccccHHHHccccccccEcccccccHHcccHHHccccccHccccccHHHHHHcccccccccccccccccccccccEcccHHHHHccHHHHHHHHHHccEEEEccccccccccHHHccccHHHHHHHHHcccccccHHHHcHHHHHHccccEEEEEEccccHHHHHHHHHHHHHHcccccccccccEEEEEccHHHHHHHHHHHHHHHHHHcccEEEEEEcccccHHHHHHHHcccEEEEEcccHHHHHHHcccccEEcHHHEEEEEHHHHHHHHHccccHHHHHHHHcccccccEEEEEcccHHHHHHHHHHHHcccEEEEEccccHHcccEEEEEEEcccHHHHHHHHHHHHHHHccccEEEEEccHHHHHHHHHHHHHccccEEEEEccccHHHHHHHHHHHHcccccEEEEEcHHHcccccccEEEEEEEcccccccHEEEEEccccccccccEEEEEEcccHHHHHHHHHHHHHHccccccHHHHHHHHHHHHHHHccccEEcccccccccccccHHHHHHHHHHHHHHHHHHcccccccccHHHHHHHHHHcccHHcccccccccccccEEEEcccccHHHHHHHHHHHHHHHHHHHHHHcccccccccccEEEc
Coil and Loop (DISEMBL)
mahshrdrdrekEKEKHREKsrrsereqstdsdedkhdkekekdkhrdrdrrrdrdrdrDREKEREEKRERAREKEREREKRDREREDRERERERERERRERDREREKRERERDRDKEKDRErksrdrekrrkvesddsdedkdrdrkrrrrhdddhkERVRERSLsrsnrhrdendespreklveddsdkkeKKTREEELEDEQRKLDEEMEKRRRRVQEWQELKRKKEESerenrgdanveepkagrnwtldredsddeevpqtgksetdmdadeepkpsenqvgdamlvdsdggsaapalqigaaededidpldafmnsmvlpeveklkntvepsftdgnnveskkmdrkgdrrsngeqpkkssnkslgriipgedsdsdygdlendekplededdDEFMKRVKKTkaeklsivdhskidyqpfrKNFYIEVKEIARMTPEEVSAYRKQLELKihgkdvpkpiktwhqtglTSKIMETIRKLnyekpmpiqaqalpvimsgrdcigvaktgsgktlAFVLPMlrhikdqppvaagdgpvglimaPTRELVQQIHSDIRKFAKVMGvrcvpvyggsgvAQQISElkrgteivvctpgrMIDILCtsggkitnlrrVTYLVMDEADrmfdmgfepqITRIVqnirpdrqtvlfsatFPRQVEILARKVlnkpveiqvggrsvvnkDITQLVEVRPESDRFLRLLELLGEWYEKGKILIFVHSQEKCDALFRDLLkhgypclslhgakdqtdrestisDFKSNVCNLLIATSVaargldvkeLELVInfdapnhyedyvhrvgrtgragrkgcaitfiseedakyspDLVKALELSEQVVPDDLKALADSFMAKVNQGleqahgtgyggsgfkfneEEDEKRKAAKKAQAKeygfeedksdsddedegirkaggdisQQDALAKISAIRKLYLFIEGPTEQSVKRAKAELKRVLEDFTNqalslpggaqpgrysvv
Flexible Loop (DISEMBL)
mahshrdrdrekekekhreksrrsereqstdsdedkhdkekekdkhrdrdrrrdrdrdrdrekereekrerarekererekrdreredrerererererrerdrerekrererdrdkekdrerksrdrekrrkvesddsdedkdrdrkrrrrhdddhkervrerslsrsnrhrdendespreklveddsdkkekktreeeledeqrkldeemekrrrrvqewqelkrkkeeserenrgdanveepkagrnwtldredsddeevpqtgksetdmdadeepkPSENQVGDAMLVDSDGGSAAPALQIGAAEDEDIDPLDAFMNSMVLPEVEklkntvepsftdgnnveskkmdrkgdrrsngeqpkkssnkslgriipgedsdsdygdlendekplededddefMKRVKktkaeklsivdhskidyqpfrkNFYIEVKEIARMTPEEVSAYRKQLElkihgkdvpkpiktwhqtgltsKIMETIRKLNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGsgvaqqiselkrgteivvctPGRMIDIlctsggkitnlrrVTYLVMDEADRMFDMGFEPQITRIVQNIRPDRQTVLFSATFPRQVEILarkvlnkpveiqvggrsvvnkditqlvevrpesdrFLRLLELLGEWYEKGKILIFVHSQEKCDALFRDLLKHGYPCLSLHGAKDQTDRESTISDFKSNVCNLLIATSVAARGLDVKELELVINfdapnhyedYVHRvgrtgragrKGCAITFISEEDAKYSPDLVKALELSEQVVPDDLKALADSFMAKVNQGLEQAHGTGYGGSGFKFNEEEDEKRKAAKkaqakeygfeedksdsddeDEGIRkaggdisqqdALAKISAIRKLYLfiegpteqsVKRAKAELKRVLEDFtnqalslpggaqpgrysvv
Low Complexity Region (SEG)
MAHShrdrdrekekekhreksrrsereQSTdsdedkhdkekekdkhrdrdrrrdrdrdrdrekereekrerarekererekrdreredrerererererrerdrerekrererdrdkekdrerksrdrekrrkvesddsdedkdrdrkrrrrhdddhkervrerSLSRSNRHRDENDESPReklveddsdkkekktreeeledeqrkldeeMEKRRRRVQEWQelkrkkeeserenrGDANVEEPKAGRNWTLDREDSDDEEVPQTGKSETDMDADEEPKPSENQVGDAMLVDSDGGSAAPALQIGAAEDEDIDPLDAFMNSMVLPEVEKLKNTVEPSFTDGNNVESKKMDRKGDRRSNGEQPKKSSNKSLGRIIPGEDSDSDYGdlendekplededddeFMKRVKKTKAEKLSIVDHSKIDYQPFRKNFYIEVKEIARMTPEEVSAYRKQLELKIHGKDVPKPIKTWHQTGLTSKIMETIRKLNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMGFEPQITRIVQNIRPDRQTVLFSATFPRQVEILARKVLNKPVEIQVGGRSVVNKDITQLVEVRPESDRFLRLLELLGEWYEKGKILIFVHSQEKCDALFRDLLKHGYPCLSLHGAKDQTDRESTISDFKSNVCNLLIATSVAARGLDVKELELVINFDAPNHYEDYVHRVGRTGRAGRKGCAITFISEEDAKYSPDLVKALELSEQVVPDDLKALADSFMAKVNQGLEQAHGTGYGGSGFKFNeeedekrkaakkaqakeYGFeedksdsddedeGIRKAGGDISQQDALAKISAIRKLYLFIEGPTEQSVKRAKAELKRVLEDFTNQALSLPGGAQPGRYSVV
Disordered region (IsUnstruct)
*****************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************LSIVDHSKIDYQPFRKNFYIEVKEIARMTPEEVSAYRKQLELKIHGKDVPKPIKTWHQTGLTSKIMETIRKLNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMGFEPQITRIVQNIRPDRQTVLFSATFPRQVEILARKVLNKPVEIQVGGRSVVNKDITQLVEVRPESDRFLRLLELLGEWYEKGKILIFVHSQEKCDALFRDLLKHGYPCLSLHGAK*******TISDFKSNVCNLLIATSVAARGLDVKELELVINFDAPNHYEDYVHRVGRTGRAGRKGCAITFISEEDAKYSPDLVKALELSEQVVPDDLKALADSFMAKV*****************************************************************ALAKISAIRKLYLFIEG***************************************
Disordered Region (DISOPRED)
*************************************************************************************************************************************************************************************************************************************************************************************************************************DPLDAFMNS*********************************************************************************************IVDHSKIDYQPFRKNFYIEVKEIARMTPEEVSAYRKQLELKIHGKDVPKPIKTWHQTGLTSKIMETIRKLNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMGFEPQITRIVQNIRPDRQTVLFSATFPRQVEILARKVLNKPVEIQVGGRSVVNKDITQLVEVRPESDRFLRLLELLGEWYEKGKILIFVHSQEKCDALFRDLLKHGYPCLSLHGAKDQTDRESTISDFKSNVCNLLIATSVAARGLDVKELELVINFDAPNHYEDYVHRVGRTGRAGRKGCAITFISEEDAKYSPDLVKALELSEQVVPDDLK***********************************************************************************************************************************
Disordered Region (DISEMBL)
**************************************************************************************************************************************************************************************************************KLDEEMEKRRRRVQEWQE********************PKAGRNWTL******************************NQVGDAMLVDSDGGSAAPALQIGAAEDEDIDPLDAFMNSMVLPEVEKLKNTVEPSFTDGNN**************************LGRIIPGEDSDSDYGDLENDEKPLEDEDDDEFMKRVKKTKAEKLSIVDHSKIDYQPFRKNFYIEVKEIARMTPEEVSAYRKQLELKIHGKDVPKPIKTWHQTGLTSKIMETIRKLNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMGFEPQITRIVQNIRPDRQTVLFSATFPRQVEILARKVLNKPVEIQVGGRSVVNKDITQLVEVRPESDRFLRLLELLGEWYEKGKILIFVHSQEKCDALFRDLLKHGYPCLSLHGA*********ISDFKSNVCNLLIATSVAARGLDVKELELVINFDAPNHYEDYVHRVGRTGRAGRKGCAITFISEEDAKYSPDLVKALELSEQVVPDDLKALADSFMAKVNQGLEQAHGTGYGGSGFKFN*********************************IRKAGGDISQQDALAKISAIRKLYLFIEGPTEQSVKRAKAELKRVLEDFTNQALSLPGGAQPGRYSVV
Disordered Region (DISPRO)
*******************************************************************************************************************************************************************************************************ELEDEQRKLDEEMEKRRRRVQEWQELKRKKE********************************************************************************EDIDPLDAFMNSMVLPEV********************************************************G******KPLEDEDDDEFMKRVKKTKAEKLSIVDHSKIDYQPFRKNFYIEVKEIARMTPEEVSAYRKQLELKIHGKDVPKPIKTWHQTGLTSKIMETIRKLNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMGFEPQITRIVQNIRPDRQTVLFSATFPRQVEILARKVLNKPVEIQVGGRSVVNKDITQLVEVRPESDRFLRLLELLGEWYEKGKILIFVHSQEKCDALFRDLLKHGYPCLSLHGAKDQTDRESTISDFKSNVCNLLIATSVAARGLDVKELELVINFDAPNHYEDYVHRVGRTGRAGRKGCAITFISEEDAKYSPDLVKALELSEQVVPDDLKALADSFMAKVNQGLEQAHGTGYGGSGFKFNEEEDEKRKAAKKA*****GF*********EDEGIRKAGGDISQ*DALAKISAIRKLYLFIEGPTEQSVKRAKAELKRVLEDFTNQALSLPGGA****YS**
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MAHSHRDRDREKEKEKHREKSRRSEREQSTDSDEDKHDKEKEKDKHRDRDRRRDRDRxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxEKDRERKSRDREKRRKVESDDSDEDKDRDRKRRRRHDDDHKERVRERSLSRSNRHRDENDESPREKLVEDDSDxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxERENRGDANVEEPKAGRNWTLDREDSDDEEVPQTGKSETDMDADEEPKPSENQVGDAMLVDSDGGSAAPALQIGAAEDEDIDPLDAFMNSMVLPEVEKLKNTVEPSFTDGNNVESKKMDRKGDRRSNGEQPKKSSNKSLGRIIPGEDSDSDYGDLENDEKPLEDEDDDEFMKRVKKTKAEKLSIVDHSKIDYQPFRKNFYIEVKEIARMTPEEVSAYRKQLELKIHGKDVPKPIKTWHQTGLTSKIMETIRKLNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMGFEPQITRIVQNIRPDRQTVLFSATFPRQVEILARKVLNKPVEIQVGGRSVVNKDITQLVEVRPESDRFLRLLELLGEWYEKGKILIFVHSQEKCDALFRDLLKHGYPCLSLHGAKDQTDRESTISDFKSNVCNLLIATSVAARGLDVKELELVINFDAPNHYEDYVHRVGRTGRAGRKGCAITFISEEDAKYSPDLVKALELSEQVVPDDLKALADSFMAKVNQGLEQAHGTGYGGSGFKFNEEEDEKRKAAKKAQAKEYGFEEDKSDSDDEDEGIRKAGGDISQQDALAKISAIRKLYLFIEGPTxxxxxxxxxxxxxxxxxxxxxALSLPGGAQPGRYSVV
Positional Conservation
no confident homologs detected

---

Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	976	2.2.26 [Sep-21-2011]
Q8H0U8	1166	DEAD-box ATP-dependent RN	yes	no	0.794	0.664	0.775	0.0
Q9SF41	989	DEAD-box ATP-dependent RN	no	no	0.693	0.684	0.739	0.0
Q0J7Y8	947	DEAD-box ATP-dependent RN	yes	no	0.700	0.722	0.679	0.0
Q4TVV3	1018	Probable ATP-dependent RN	yes	no	0.672	0.644	0.488	0.0
Q1DHB2	1197	Pre-mRNA-processing ATP-d	N/A	no	0.569	0.464	0.533	0.0
Q569Z5	1032	Probable ATP-dependent RN	yes	no	0.664	0.628	0.488	0.0
Q62780	1032	Probable ATP-dependent RN	yes	no	0.664	0.628	0.486	0.0
Q7L014	1031	Probable ATP-dependent RN	yes	no	0.664	0.629	0.486	1e-180
Q5R6D8	1032	Probable ATP-dependent RN	yes	no	0.664	0.628	0.485	1e-180
Q2U2J6	1186	Pre-mRNA-processing ATP-d	yes	no	0.581	0.478	0.504	1e-178

>sp|Q8H0U8|RH42_ARATH DEAD-box ATP-dependent RNA helicase 42 OS=Arabidopsis thaliana GN=RH42 PE=1 SV=2

 Score = 1189 bits (3076), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 615/793 (77%), Positives = 697/793 (87%), Gaps = 18/793 (2%)

Query: 134 VESDDSDEDKDRDRKRRRRHDDDHKERVRERSLSRSNRHRDENDESPREKLVEDDSDKKE 193
           V +++SD+D  RD KRRR+   + KE+ RE+S+ RS+RH D    SP+ K VED+ +KKE
Sbjct: 205 VGNEESDDDVKRDLKRRRKEGGERKEKEREKSVGRSSRHED----SPKRKSVEDNGEKKE 260

Query: 194 KKTREEELEDEQRKLDEEMEKRRRRVQEWQELKRKKEESERENRGDANVEEPKAGRNWTL 253
           KKTREEELEDEQ+KLDEE+EKRRRRVQEWQELKRKKEE+E E++GDA+  EPKAG+ WTL
Sbjct: 261 KKTREEELEDEQKKLDEEVEKRRRRVQEWQELKRKKEEAESESKGDADGNEPKAGKAWTL 320

Query: 254 DREDSDDEEVPQTGKSETDMDADEEPKPSENQVGDAMLVDSDGGSAAPALQI---GAAED 310
           + E SDDEE     KSET+MD DEE KP  +  GDA +VD +  +AA   +    GA ++
Sbjct: 321 EGE-SDDEEGHPEEKSETEMDVDEETKPEND--GDAKMVDLENETAATVSESGGDGAVDE 377

Query: 311 EDIDPLDAFMNSMVLPEVEKLKNTV-EPSFTDGNNVESKKMDRKGDRRSNGEQPKKSSNK 369
           E+IDPLDAFMN+MVLPEVEK  N    P+  DG       +D K + + +G++PKK  NK
Sbjct: 378 EEIDPLDAFMNTMVLPEVEKFCNGAPPPAVNDGT------LDSKMNGKESGDRPKKGFNK 431

Query: 370 SLGRIIPGEDSDSDYGDLENDEKPLEDEDDDEFMKRVKKTKAEKLSIVDHSKIDYQPFRK 429
           +LGRII GEDSDSDY + +ND+ P  DEDD+EFMKRVKKTKAEKLS+VDHSKI+Y+PFRK
Sbjct: 432 ALGRIIQGEDSDSDYSEPKNDDDPSLDEDDEEFMKRVKKTKAEKLSLVDHSKIEYEPFRK 491

Query: 430 NFYIEVKEIARMTPEEVSAYRKQLELKIHGKDVPKPIKTWHQTGLTSKIMETIRKLNYEK 489
           NFYIEVK+I+RMT EEV+ YRK+LELK+HGKDVP+PIK WHQTGLTSKI++T++KLNYEK
Sbjct: 492 NFYIEVKDISRMTQEEVNTYRKELELKVHGKDVPRPIKFWHQTGLTSKILDTMKKLNYEK 551

Query: 490 PMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPT 549
           PMPIQ QALP+IMSGRDCIGVAKTGSGKTL FVLPMLRHIKDQPPV AGDGP+GL+MAPT
Sbjct: 552 PMPIQTQALPIIMSGRDCIGVAKTGSGKTLGFVLPMLRHIKDQPPVEAGDGPIGLVMAPT 611

Query: 550 RELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSG 609
           RELVQQIHSDIRKF+K +G+RCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTS 
Sbjct: 612 RELVQQIHSDIRKFSKPLGIRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSS 671

Query: 610 GKITNLRRVTYLVMDEADRMFDMGFEPQITRIVQNIRPDRQTVLFSATFPRQVEILARKV 669
           GKITNLRRVT+LVMDEADRMFDMGFEPQITRI+QNIRP+RQTVLFSATFPRQVE LARKV
Sbjct: 672 GKITNLRRVTFLVMDEADRMFDMGFEPQITRIIQNIRPERQTVLFSATFPRQVETLARKV 731

Query: 670 LNKPVEIQVGGRSVVNKDITQLVEVRPESDRFLRLLELLGEWYEKGKILIFVHSQEKCDA 729
           LNKPVEIQVGGRSVVNKDITQLVEVRPESDRFLRLLELLGEW EKGKIL+FV SQEKCDA
Sbjct: 732 LNKPVEIQVGGRSVVNKDITQLVEVRPESDRFLRLLELLGEWSEKGKILVFVQSQEKCDA 791

Query: 730 LFRDLLKHGYPCLSLHGAKDQTDRESTISDFKSNVCNLLIATSVAARGLDVKELELVINF 789
           L+RD++K  YPCLSLHG KDQTDRESTISDFK++VCNLLIATSVAARGLDVKELELV+NF
Sbjct: 792 LYRDMIKSSYPCLSLHGGKDQTDRESTISDFKNDVCNLLIATSVAARGLDVKELELVVNF 851

Query: 790 DAPNHYEDYVHRVGRTGRAGRKGCAITFISEEDAKYSPDLVKALELSEQVVPDDLKALAD 849
           DAPNHYEDYVHRVGRTGRAGRKGCA+TFISE+DAKY+PDLVKALELSEQ VPDDLKALAD
Sbjct: 852 DAPNHYEDYVHRVGRTGRAGRKGCAVTFISEDDAKYAPDLVKALELSEQPVPDDLKALAD 911

Query: 850 SFMAKVNQGLEQAHGTGYGGSGFKFNEEEDEKRKAAKKAQAKEYGFEEDKSDSDDEDEGI 909
            FM KV QG+EQAHGTGYGGSGFKFNEEE+E RKAAKKAQAKEYGFEEDKSDS+DE++ +
Sbjct: 912 GFMVKVKQGIEQAHGTGYGGSGFKFNEEEEEVRKAAKKAQAKEYGFEEDKSDSEDENDVV 971

Query: 910 RKA-GGDISQQDA 921
           RKA GG+ISQQ A
Sbjct: 972 RKAGGGEISQQQA 984

Arabidopsis thaliana (taxid: 3702)
EC: 3EC: .EC: 6EC: .EC: 4EC: .EC: 1EC: 3

>sp|Q9SF41|RH45_ARATH DEAD-box ATP-dependent RNA helicase 45 OS=Arabidopsis thaliana GN=RH45 PE=2 SV=1

 Score = 1030 bits (2662), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 543/734 (73%), Positives = 620/734 (84%), Gaps = 57/734 (7%)

Query: 190 DKKEKKTREEELEDEQRKLDEEMEKRRRRVQEWQELKRKKEESERENRGDANVEEPKAGR 249
           D  EKKTR+E++EDEQ++L EE+EKRRRRVQEWQELKR+ EE++ E++G      P+ G+
Sbjct: 139 DDVEKKTRDEQVEDEQKQLAEEVEKRRRRVQEWQELKRQNEEAQIESKG------PETGK 192

Query: 250 NWTLDREDSDDEEVPQTGKSETDMDADEEPKPSENQVGDAMLVDSDGGSAAPALQIG--- 306
            WTLD E SDDE      KS+++MD D + K  EN  GDA +V S+  +A    + G   
Sbjct: 193 AWTLDGE-SDDEV-----KSDSEMDVDRDTK-LENG-GDAKMVASENETAVTVSENGGDR 244

Query: 307 AAEDEDIDPLDAFMNSMVLPEVEKLKNTVEPSFTDGNNVESKKMDRKGDRRSNGEQPKKS 366
           AA++++IDPLDAFMN+MVLPEVEKL N V     DG       +D K + +  G+Q KK 
Sbjct: 245 AADEDEIDPLDAFMNTMVLPEVEKLSNIV----IDG------ILDFKMNGKETGDQAKKG 294

Query: 367 SNKS-LGRIIPGEDSDSDYGDLENDEKPLEDEDDDEFMKRVKKTKAEKLSIVDHSKIDYQ 425
            NK+ LGRII GEDSDSDY + ++D+ P  DEDD+EFMKRVKKTKAEKLS+VDHSKI+Y+
Sbjct: 295 FNKAALGRIIQGEDSDSDYSEPKSDDDPSLDEDDEEFMKRVKKTKAEKLSLVDHSKIEYE 354

Query: 426 PFRKNFYIEVKEIARMTPEEVSAYRKQLELKIHGKDVPKPIKTWHQTGLTSKIMETIRKL 485
           PFRKNFYIEVK+I+RMT + V+AYRK+LELK+HGKDVP+PI+ WHQTGLTSKI++T++KL
Sbjct: 355 PFRKNFYIEVKDISRMTQDAVNAYRKELELKVHGKDVPRPIQFWHQTGLTSKILDTLKKL 414

Query: 486 NYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLI 545
           NYEKPMPIQAQALP+IMSGRDCIGVAKTGSGKTL FVLPMLRHIKDQPPV AGDGP+GL+
Sbjct: 415 NYEKPMPIQAQALPIIMSGRDCIGVAKTGSGKTLGFVLPMLRHIKDQPPVEAGDGPIGLV 474

Query: 546 MAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDIL 605
           MAPTRELVQQI+SDIRKF+K +G+ CVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDIL
Sbjct: 475 MAPTRELVQQIYSDIRKFSKALGIICVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDIL 534

Query: 606 CTSGGKITNLRRVTYLVMDEADRMFDMGFEPQITRIVQNIRPDRQTVLFSATFPRQVEIL 665
           CTS GKITNLRRVTYLVMDEADRMFDMGFEPQITRIVQNIRPDRQTVLFSATFPRQVE L
Sbjct: 535 CTSSGKITNLRRVTYLVMDEADRMFDMGFEPQITRIVQNIRPDRQTVLFSATFPRQVETL 594

Query: 666 ARKVLNKPVEIQVGGRSVVNKDITQLVEVRPESDRFLRLLELLGEWYEKGKILIFVHSQE 725
           ARKVLNKPVEIQVGGRSVVNKDITQLVE+RPES+RF RLLELLGEWYEKGK+L+FV SQE
Sbjct: 595 ARKVLNKPVEIQVGGRSVVNKDITQLVEIRPESERFSRLLELLGEWYEKGKVLVFVRSQE 654

Query: 726 KCDALFRDLLKHGYPCLSLHGAKDQTDRESTISDFKSNVCNLLIATSVAARGLDVKELEL 785
           K                             +ISDFKS+VCNLLIATSVAARGLDVKELEL
Sbjct: 655 K-----------------------------SISDFKSDVCNLLIATSVAARGLDVKELEL 685

Query: 786 VINFDAPNHYEDYVHRVGRTGRAGRKGCAITFISEEDAKYSPDLVKALELSEQVVPDDLK 845
           V+NFDAPNHYEDYVHRVGRTGRAGRKGCA+TFISE+DAKY+PDLVKALELSEQ VPDD+K
Sbjct: 686 VVNFDAPNHYEDYVHRVGRTGRAGRKGCAVTFISEDDAKYAPDLVKALELSEQPVPDDVK 745

Query: 846 ALADSFMAKVNQGLEQAHGTGYGGSGFKFNEEEDEKRKAAKKAQAKEYGFEEDKSDSDDE 905
           A+A+ FMAKV QG+EQAHGTGYGGSGFKFNEEEDE RKAAKKAQAKEYGFEE+KSDS+DE
Sbjct: 746 AVAEGFMAKVKQGIEQAHGTGYGGSGFKFNEEEDEVRKAAKKAQAKEYGFEEEKSDSEDE 805

Query: 906 DEGIRKAGGDISQQ 919
           ++ +RKAGGDISQQ
Sbjct: 806 NDVVRKAGGDISQQ 819

Arabidopsis thaliana (taxid: 3702)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q0J7Y8|RH45_ORYSJ DEAD-box ATP-dependent RNA helicase 45 OS=Oryza sativa subsp. japonica GN=Os08g0154200 PE=3 SV=2

 Score =  958 bits (2476), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 499/734 (67%), Positives = 579/734 (78%), Gaps = 50/734 (6%)

Query: 197 REEELEDEQRKLDEEMEKRRRRVQEWQELKRKKEESER------------ENRGDANVEE 244
           R++ +E+E+++LDEEME RRRRV+EWQE KR +EE  +                     +
Sbjct: 19  RQKMIEEEKKRLDEEMELRRRRVKEWQEQKRLEEEEAKRREQEAAAGAGTPAAAAGADGD 78

Query: 245 PKAGRNWTLDREDSDDEEVPQTGKSETDMDADEEPKPSENQVGDAMLVDSDGGSAAPALQ 304
             AG+ WTLD E+SD+E   +  ++  D        PSE          +D   AAP   
Sbjct: 79  SNAGKKWTLDGEESDEEGYKEDSQNAEDDGGITADLPSEV---------NDANVAAPM-- 127

Query: 305 IGAAEDEDIDPLDAFMNSMVLPEVEKLKNTVEPS-FTDGNNVESKKMDRKGDRRSNGEQP 363
               E+++IDPLDAFM+SMVLPEV KL+  V        +N+  K      D  SNG+  
Sbjct: 128 ----EEDEIDPLDAFMSSMVLPEVAKLETAVASMESMPASNMGDKNGKSAKDAVSNGD-- 181

Query: 364 KKSSNKSLGRIIPGEDSDSDYGDLENDEKPLEDEDDDEFMKRVKKTKAEKLSIVDHSKID 423
           KK   K++GRI+ G+DSDSDY D ++DE   +DEDD+EFMKRVKKTK EKL+IVDHSKI+
Sbjct: 182 KKGQKKAMGRIMQGDDSDSDYDDDDDDEGGSKDEDDEEFMKRVKKTKVEKLAIVDHSKIE 241

Query: 424 YQPFRKNFYIEVKEIARMTPEEVSAYRKQLELKIHGKDVPKPIKTWHQTGLTSKIMETIR 483
           YQPFRKN YIEVK+I  MT EEV+ YRK LELK+HGKDVPKPIKTW Q+GLTSK+++TI+
Sbjct: 242 YQPFRKNLYIEVKDITMMTGEEVATYRKNLELKVHGKDVPKPIKTWVQSGLTSKLLDTIK 301

Query: 484 KLNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVG 543
           KL +EKPMPIQAQALP+IMSGRDCIG+AKTGSGKTLAFVLPMLRH+KDQPPV  GDGP+G
Sbjct: 302 KLGFEKPMPIQAQALPIIMSGRDCIGIAKTGSGKTLAFVLPMLRHVKDQPPVVPGDGPIG 361

Query: 544 LIMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMID 603
           LIMAPTRELV QIHSDI+KFAK +G+ CV +YGGSGVAQQISELKRG EIVVCTPGRMID
Sbjct: 362 LIMAPTRELVVQIHSDIKKFAKSLGINCVAIYGGSGVAQQISELKRGAEIVVCTPGRMID 421

Query: 604 ILCTSGGKITNLRRVTYLVMDEADRMFDMGFEPQITRIVQNIRPDRQTVLFSATFPRQVE 663
           ILCTS GKITNLRRVT+LVMDEADRMFDMGFEPQITRIVQN RPDRQTVLFSA FPRQVE
Sbjct: 422 ILCTSSGKITNLRRVTFLVMDEADRMFDMGFEPQITRIVQNTRPDRQTVLFSAIFPRQVE 481

Query: 664 ILARKVLNKPVEIQVGGRSVVNKDITQLVEVRPESDRFLRLLELLGEWYEKGKILIFVHS 723
           ILARKVL KPVEIQVGGRSVVNKDITQLVEVRPE++RFLRLLELLGEW+++GKIL+FVHS
Sbjct: 482 ILARKVLTKPVEIQVGGRSVVNKDITQLVEVRPENERFLRLLELLGEWFDRGKILVFVHS 541

Query: 724 QEKCDALFRDLLKHGYPCLSLHGAKDQTDRESTISDFKSNVCNLLIATSVAARGLDVKEL 783
           Q+KCD+L +DL + GYPCLSLHG KDQTDREST++DFKSN                   L
Sbjct: 542 QDKCDSLLKDLFQRGYPCLSLHGGKDQTDRESTLADFKSN-------------------L 582

Query: 784 ELVINFDAPNHYEDYVHRVGRTGRAGRKGCAITFISEEDAKYSPDLVKALELSEQVVPDD 843
           ELV+N+D PNHYEDYVHRVGRTG AGRKG A+TFIS+E+ +Y+PDL KALELSEQ VP D
Sbjct: 583 ELVVNYDVPNHYEDYVHRVGRTGHAGRKGFAVTFISDEEERYAPDLAKALELSEQAVPQD 642

Query: 844 LKALADSFMAKVNQGLEQAHGTGYGGSGFKFNEEEDEKRKAAKKAQAKEYGFEEDKSDSD 903
           LK LAD FMAKV QG EQAHGTGYGGSGFKFNEEEDE R++AKKAQA+EYG+EEDKSDSD
Sbjct: 643 LKGLADRFMAKVKQGTEQAHGTGYGGSGFKFNEEEDEARRSAKKAQAREYGYEEDKSDSD 702

Query: 904 -DEDEGIRKAGGDI 916
            DE+ G+RKAGGD+
Sbjct: 703 SDEEGGVRKAGGDL 716

Oryza sativa subsp. japonica (taxid: 39947)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q4TVV3|DDX46_DANRE Probable ATP-dependent RNA helicase DDX46 OS=Danio rerio GN=ddx46 PE=2 SV=1

 Score =  656 bits (1693), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 347/710 (48%), Positives = 456/710 (64%), Gaps = 54/710 (7%)

Query: 204 EQRKLDEEMEKRRRRVQEWQELKRKKEESERENRGDAN--VEEPKAGRNWTLDREDSDDE 261
           +Q  L+EEM KR+ RV++W+E +RK   +  EN G+    +EE K G+ W+L  ED D+E
Sbjct: 120 DQNTLEEEMRKRKERVEKWREEQRK---TAMENIGEIKKELEEMKQGKKWSL--EDDDEE 174

Query: 262 EVPQTGKSETDMDADEEPKPSENQVGDAMLVDSDGGSAAPALQIGAAEDEDIDPLDAFMN 321
           +                              D    +            E++DPLDA+M 
Sbjct: 175 Q------------------------------DKAAEAEESERMEEEEVGEEVDPLDAYME 204

Query: 322 SMVLPEVEKLKNTVEPSFTDGNNVESKKMDRKGDRRSNGEQPKKSSNKSLGRIIPGEDSD 381
             V  EV+K           G N +   M           +    + K  G ++   ++D
Sbjct: 205 E-VKEEVKKFNMGT----MKGANDKKGGMSVTKVVTVVKTKKMPHATKKKGELM---END 256

Query: 382 SDYGDLENDEKPLEDEDDDEFMKRVKKTKAEKLSIVDHSKIDYQPFRKNFYIEVKEIARM 441
            D  +  ++E   E+ D    +   +  + + L  VDH KI Y+PFRKNFY+EV E+ARM
Sbjct: 257 QDAMEYSSEE---EEVDLQTALTGFQTKQRKVLEPVDHQKIQYEPFRKNFYVEVPELARM 313

Query: 442 TPEEVSAYRKQLE-LKIHGKDVPKPIKTWHQTGLTSKIMETIRKLNYEKPMPIQAQALPV 500
           +PEEVS YR +LE + + GK  PKPIKTW Q G++ K++  ++K NYEKP PIQAQA+P 
Sbjct: 314 SPEEVSEYRLELEGISVKGKGCPKPIKTWVQCGISMKVLNALKKHNYEKPTPIQAQAIPA 373

Query: 501 IMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDI 560
           IMSGRD IG+AKTGSGKT+AF+LPM RHI DQ PV   +GP+ +IM PTREL  QI  + 
Sbjct: 374 IMSGRDLIGIAKTGSGKTIAFLLPMFRHILDQRPVGEAEGPLAVIMTPTRELALQITKEC 433

Query: 561 RKFAKVMGVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTY 620
           +KF+K + +R V VYGG+G+++QI+ELKRG EI+VCTPGRMID+L  + G++TNLRRVTY
Sbjct: 434 KKFSKSLALRVVCVYGGTGISEQIAELKRGAEIIVCTPGRMIDMLGANNGRVTNLRRVTY 493

Query: 621 LVMDEADRMFDMGFEPQITRIVQNIRPDRQTVLFSATFPRQVEILARKVLNKPVEIQVGG 680
           +V+DEADRMFDMGFEPQ+ RIV N+RPDRQTV+FSATFPR +E LAR++L+KPVE+QVGG
Sbjct: 494 VVIDEADRMFDMGFEPQVMRIVDNVRPDRQTVMFSATFPRTMEALARRILSKPVEVQVGG 553

Query: 681 RSVVNKDITQLVEVRPESDRFLRLLELLGEWYEKGKILIFVHSQEKCDALFRDLLKHGYP 740
           RSVV  D+ Q V V  E  +FL+LLE+LG + EKG ++IFV  QE  D L +DL+K  YP
Sbjct: 554 RSVVCSDVEQHVIVIEEEKKFLKLLEILGHYQEKGSVIIFVDKQEHADGLLKDLMKASYP 613

Query: 741 CLSLHGAKDQTDRESTISDFKSNVCNLLIATSVAARGLDVKELELVINFDAPNHYEDYVH 800
           C+SLHG  DQ DR+S I+DFK+  C LL+ATSVAARGLDVK+L LV+N+  PNHYEDYVH
Sbjct: 614 CMSLHGGIDQYDRDSIINDFKNGACRLLVATSVAARGLDVKQLILVVNYSCPNHYEDYVH 673

Query: 801 RVGRTGRAGRKGCAITFISEEDAKYSPDLVKALELSEQVVPDDLKALADSFMAKVN-QGL 859
           R GRTGRAG KG A TFI+E  A+YS D++KALELS   VP +L+ L  +F  +   +G 
Sbjct: 674 RAGRTGRAGNKGYAYTFITEGQARYSGDILKALELSGSSVPAELEQLWTNFKEQQKAEGK 733

Query: 860 EQAHGTGYGGSGFKFNEEEDEKRKAAKKAQAKEYGFEEDKSDSDDEDEGI 909
                +G+ G GFKF+E E       KK Q    G      DSDDED  +
Sbjct: 734 IIKSSSGFSGKGFKFDETEHALANERKKLQKWALGLH----DSDDEDTAL 779

Plays an essential role in splicing, either prior to, or during A complex formation.

Danio rerio (taxid: 7955)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q1DHB2|PRP5_COCIM Pre-mRNA-processing ATP-dependent RNA helicase PRP5 OS=Coccidioides immitis (strain RS) GN=PRP5 PE=3 SV=1

 Score =  644 bits (1661), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 322/604 (53%), Positives = 422/604 (69%), Gaps = 48/604 (7%)

Query: 297 GSAAPALQIGAAEDEDIDPLDAFMNSMVLPEVEKLKNTVEPSFTDGNNVESKKMDRKGDR 356
           GSA P   +   ++E+IDPLDAFM+         LK++V         V++ K       
Sbjct: 425 GSAEP---MDVEDEEEIDPLDAFMSG--------LKDSV--------TVDASKY------ 459

Query: 357 RSNGEQPKKSSNKSLGRIIPGEDSDSDYGDLENDEKPLEDEDDDEFMKRVKKTKAEK-LS 415
           R N  +PK             ++ ++ +GD ++ +    D + D+F+    KT+ +K L 
Sbjct: 460 RKNVSKPK-------------QEPEAIFGDEDDVDLKAMDFEADDFLAITSKTRKKKDLP 506

Query: 416 IVDHSKIDYQPFRKNFYIEVKEIARMTPEEVSAYRKQLE-LKIHGKDVPKPIKTWHQTGL 474
            V+H  IDY+PFRK+FY E  ++A +  EEV+A R +L+ +K+ G DVPKP++ W Q GL
Sbjct: 507 TVNHETIDYEPFRKSFYTEPVDLAELNDEEVAALRLELDGIKVRGVDVPKPVQKWSQCGL 566

Query: 475 TSKIMETIRKLNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPP 534
             + ++ IRKL YE+P  IQ+QA+P IMSGRD IGVAKTGSGKT+AF+LPM RHIKDQ P
Sbjct: 567 GVQTLDVIRKLGYEQPTSIQSQAIPAIMSGRDVIGVAKTGSGKTIAFLLPMFRHIKDQRP 626

Query: 535 VAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQISELKRGTEIV 594
           +   +GPVGLIM PTREL  QIH + + F K + +R V  YGG+ +  QI+ELKRG EI+
Sbjct: 627 LENMEGPVGLIMTPTRELATQIHKECKPFLKALNLRAVCAYGGAPIKDQIAELKRGAEII 686

Query: 595 VCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMGFEPQITRIVQNIRPDRQTVLF 654
           VCTPGRMID+L  + G++TNLRRVTY+V+DEADRMFDMGFEPQ+ +I+ NIRP RQTVLF
Sbjct: 687 VCTPGRMIDLLAANSGRVTNLRRVTYVVLDEADRMFDMGFEPQVMKIISNIRPSRQTVLF 746

Query: 655 SATFPRQVEILARKVLNKPVEIQVGGRSVVNKDITQLVEVRPESDRFLRLLELLGEWY-- 712
           SATFPR +E LARK L KPVEI VGGRSVV ++ITQ+VEVRPE+ +F+RLLELLG  Y  
Sbjct: 747 SATFPRNMEALARKTLTKPVEIIVGGRSVVAQEITQIVEVRPENTKFVRLLELLGNLYSD 806

Query: 713 ---EKGKILIFVHSQEKCDALFRDLLKHGYPCLSLHGAKDQTDRESTISDFKSNVCNLLI 769
              E  + LIFV  QE  D L RDL++ GYPC+S+HG KDQ DR+STI DFK+ +  +LI
Sbjct: 807 DNNEDARALIFVDRQEAADGLLRDLMRKGYPCMSIHGGKDQVDRDSTIDDFKAGIFPVLI 866

Query: 770 ATSVAARGLDVKELELVINFDAPNHYEDYVHRVGRTGRAGRKGCAITFISEEDAKYSPDL 829
           ATSVAARGLDVK+L+LVIN+DAPNH EDYVHR GRTGRAG  G A+TF++EE  +YS D+
Sbjct: 867 ATSVAARGLDVKQLKLVINYDAPNHLEDYVHRAGRTGRAGNTGTAVTFLTEEQERYSVDI 926

Query: 830 VKALELSEQVVPDDLKALADSFMAKVNQGLEQAHGTGYGGSGFKFNEEEDEKRKAAKKAQ 889
            KAL+ S Q VP+ ++ + DSF+ KV  G E+A  +G+GG G    E  D++R AA+  +
Sbjct: 927 AKALKQSGQSVPEAVQKMVDSFLEKVKSGKEKASASGFGGKGL---ERLDQERDAARNRE 983

Query: 890 AKEY 893
            K Y
Sbjct: 984 RKTY 987

ATP-dependent RNA helicase involved spliceosome assembly and in nuclear splicing. Catalyzes an ATP-dependent conformational change of U2 snRNP. Bridges U1 and U2 snRNPs and enables stable U2 snRNP association with intron RNA.

Coccidioides immitis (strain RS) (taxid: 246410)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q569Z5|DDX46_MOUSE Probable ATP-dependent RNA helicase DDX46 OS=Mus musculus GN=Ddx46 PE=1 SV=2

 Score =  639 bits (1647), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 350/717 (48%), Positives = 469/717 (65%), Gaps = 68/717 (9%)

Query: 204 EQRKLDEEMEKRRRRVQEWQELKRKKEESERENRGDAN--VEEPKAGRNWTLDREDSDDE 261
           +Q KL+EEM KR+ RV++W+E +RKK     EN G+    +EE K G+ W+L+ +D D++
Sbjct: 152 DQNKLEEEMRKRKERVEKWREEQRKKA---MENIGELKKEIEEMKQGKKWSLEDDDDDED 208

Query: 262 EVPQTGKSETDMDADEEPKPSENQVGDAMLVDSDGGSAAPALQIGAAEDEDIDPLDAFMN 321
           +  +  K  T+M                                   EDE++DPLDA+M 
Sbjct: 209 DPAEAEKEGTEM-----------------------------------EDEELDPLDAYME 233

Query: 322 SMVLPEVEKLKNTVEPSFTDGNNVESKKMDRKGDRRSNGEQPKKSSNKSLGRIIPGEDSD 381
             V  EV+K             N+ S K     +++S     K  +  +  +     D+D
Sbjct: 234 E-VKEEVKKF------------NMRSVKGGAGNEKKSGPTVTKVVTVVTTKK--AVVDAD 278

Query: 382 SDYGDL-ENDEKPLE-----DEDDDEFMKRVKKTKAEKL-SIVDHSKIDYQPFRKNFYIE 434
              G+L END+  +E     +E D +      +TK  KL   VDH KI+Y+PFRKNFY+E
Sbjct: 279 KKKGELMENDQDAMEYSSEEEEVDLQTALTGYQTKQRKLLEPVDHGKIEYEPFRKNFYVE 338

Query: 435 VKEIARMTPEEVSAYRKQLE-LKIHGKDVPKPIKTWHQTGLTSKIMETIRKLNYEKPMPI 493
           V E+A+M+ EEV+ +R ++E + + GK  PKPIK+W Q G++ KI+ +++K  YEKP PI
Sbjct: 339 VPELAKMSQEEVNVFRLEMEGITVKGKGCPKPIKSWVQCGISMKILNSLKKHGYEKPTPI 398

Query: 494 QAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELV 553
           Q QA+P IMSGRD IG+AKTGSGKT+AF+LPM RHI DQ  +  G+GP+ +IM PTREL 
Sbjct: 399 QTQAIPAIMSGRDLIGIAKTGSGKTIAFLLPMFRHIMDQRSLEEGEGPIAVIMTPTRELA 458

Query: 554 QQIHSDIRKFAKVMGVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGGKIT 613
            QI  + +KF+K +G+R V VYGG+G+++QI+ELKRG EI+VCTPGRMID+L  + G++T
Sbjct: 459 LQITKECKKFSKTLGLRVVCVYGGTGISEQIAELKRGAEIIVCTPGRMIDMLAANSGRVT 518

Query: 614 NLRRVTYLVMDEADRMFDMGFEPQITRIVQNIRPDRQTVLFSATFPRQVEILARKVLNKP 673
           NLRRVTY+V+DEADRMFDMGFEPQ+ RIV N+RPDRQTV+FSATFPR +E LAR++L+KP
Sbjct: 519 NLRRVTYVVLDEADRMFDMGFEPQVMRIVDNVRPDRQTVMFSATFPRAMEALARRILSKP 578

Query: 674 VEIQVGGRSVVNKDITQLVEVRPESDRFLRLLELLGEWYEKGKILIFVHSQEKCDALFRD 733
           +E+QVGGRSVV  D+ Q V V  E  +FL+LLELLG + E G ++IFV  QE  D L +D
Sbjct: 579 IEVQVGGRSVVCSDVEQQVIVIEEEKKFLKLLELLGHYQESGSVIIFVDKQEHADGLLKD 638

Query: 734 LLKHGYPCLSLHGAKDQTDRESTISDFKSNVCNLLIATSVAARGLDVKELELVINFDAPN 793
           L++  YPC+SLHG  DQ DR+S I+DFK+  C LL+ATSVAARGLDVK L LV+N+  PN
Sbjct: 639 LMRASYPCMSLHGGIDQYDRDSIINDFKNGTCKLLVATSVAARGLDVKHLILVVNYSCPN 698

Query: 794 HYEDYVHRVGRTGRAGRKGCAITFISEEDAKYSPDLVKALELSEQVVPDDLKALADSFM- 852
           HYEDYVHR GRTGRAG KG A TFI+E+ A+Y+ D++KALELS   VP DL+ L   F  
Sbjct: 699 HYEDYVHRAGRTGRAGNKGYAYTFITEDQARYAGDIIKALELSGTAVPPDLEKLWSDFKD 758

Query: 853 AKVNQGLEQAHGTGYGGSGFKFNEEEDEKRKAAKKAQAKEYGFEEDKSDSDDEDEGI 909
            +  +G      +G+ G GFKF+E E       KK Q    G +    DSDDED  +
Sbjct: 759 QQKAEGKIIKKSSGFSGKGFKFDETEQALANERKKLQKAALGLQ----DSDDEDAAV 811

Plays an essential role in splicing, either prior to, or during A complex formation.

Mus musculus (taxid: 10090)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q62780|DDX46_RAT Probable ATP-dependent RNA helicase DDX46 OS=Rattus norvegicus GN=Ddx46 PE=1 SV=1

 Score =  636 bits (1640), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 349/717 (48%), Positives = 468/717 (65%), Gaps = 68/717 (9%)

Query: 204 EQRKLDEEMEKRRRRVQEWQELKRKKEESERENRGDAN--VEEPKAGRNWTLDREDSDDE 261
           +Q KL+EEM KR+ RV++W+E +RKK     EN G+    +EE K G+ W+L+ +D D++
Sbjct: 152 DQNKLEEEMRKRKERVEKWREEQRKKA---MENIGELKKEIEEMKQGKKWSLEDDDDDED 208

Query: 262 EVPQTGKSETDMDADEEPKPSENQVGDAMLVDSDGGSAAPALQIGAAEDEDIDPLDAFMN 321
           +  +  K   +M                                   EDE++DPLDA+M 
Sbjct: 209 DPAEAEKEGNEM-----------------------------------EDEELDPLDAYME 233

Query: 322 SMVLPEVEKLKNTVEPSFTDGNNVESKKMDRKGDRRSNGEQPKKSSNKSLGRIIPGEDSD 381
             V  EV+K             N+ S K     +++S     K  +  +  +     D+D
Sbjct: 234 E-VKEEVKKF------------NMRSVKGGAGNEKKSGPTVTKVVTVVTTKK--AVVDAD 278

Query: 382 SDYGDL-ENDEKPLE-----DEDDDEFMKRVKKTKAEKL-SIVDHSKIDYQPFRKNFYIE 434
              G+L END+  +E     +E D +      +TK  KL   VDH KI+Y+PFRKNFY+E
Sbjct: 279 KKKGELMENDQDAMEYSSEEEEVDLQTALTGYQTKQRKLLEPVDHGKIEYEPFRKNFYVE 338

Query: 435 VKEIARMTPEEVSAYRKQLE-LKIHGKDVPKPIKTWHQTGLTSKIMETIRKLNYEKPMPI 493
           V E+A+M+ EEV+ +R ++E + + GK  PKPIK+W Q G++ KI+ +++K  YEKP PI
Sbjct: 339 VPELAKMSQEEVNVFRLEMEGITVKGKGCPKPIKSWVQCGISMKILNSLKKHGYEKPTPI 398

Query: 494 QAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELV 553
           Q QA+P IMSGRD IG+AKTGSGKT+AF+LPM RHI DQ  +  G+GP+ +IM PTREL 
Sbjct: 399 QTQAIPAIMSGRDLIGIAKTGSGKTIAFLLPMFRHIMDQRSLEEGEGPIAVIMTPTRELA 458

Query: 554 QQIHSDIRKFAKVMGVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGGKIT 613
            QI  + +KF+K +G+R V VYGG+G+++QI+ELKRG EI+VCTPGRMID+L  + G++T
Sbjct: 459 LQITKECKKFSKTLGLRVVCVYGGTGISEQIAELKRGAEIIVCTPGRMIDMLAANSGRVT 518

Query: 614 NLRRVTYLVMDEADRMFDMGFEPQITRIVQNIRPDRQTVLFSATFPRQVEILARKVLNKP 673
           NLRRVTY+V+DEADRMFDMGFEPQ+ RIV N+RPDRQTV+FSATFPR +E LAR++L+KP
Sbjct: 519 NLRRVTYVVLDEADRMFDMGFEPQVMRIVDNVRPDRQTVMFSATFPRAMEALARRILSKP 578

Query: 674 VEIQVGGRSVVNKDITQLVEVRPESDRFLRLLELLGEWYEKGKILIFVHSQEKCDALFRD 733
           +E+QVGGRSVV  D+ Q V V  E  +FL+LLELLG + E G ++IFV  QE  D L +D
Sbjct: 579 IEVQVGGRSVVCSDVEQQVIVIEEEKKFLKLLELLGHYQESGSVIIFVDKQEHADGLLKD 638

Query: 734 LLKHGYPCLSLHGAKDQTDRESTISDFKSNVCNLLIATSVAARGLDVKELELVINFDAPN 793
           L++  YPC+SLHG  DQ DR+S I+DFK+  C LL+ATSVAARGLDVK L LV+N+  PN
Sbjct: 639 LMRASYPCMSLHGGIDQYDRDSIINDFKNGTCKLLVATSVAARGLDVKHLILVVNYSCPN 698

Query: 794 HYEDYVHRVGRTGRAGRKGCAITFISEEDAKYSPDLVKALELSEQVVPDDLKALADSFM- 852
           HYEDYVHR GRTGRAG KG A TFI+E+ A+Y+ D++KALELS   VP DL+ L   F  
Sbjct: 699 HYEDYVHRAGRTGRAGNKGYAYTFITEDQARYAGDIIKALELSGTAVPPDLEKLWSDFKD 758

Query: 853 AKVNQGLEQAHGTGYGGSGFKFNEEEDEKRKAAKKAQAKEYGFEEDKSDSDDEDEGI 909
            +  +G      +G+ G GFKF+E E       KK Q    G +    DSDDED  +
Sbjct: 759 QQKAEGKIIKKSSGFSGKGFKFDETEQALANERKKLQKAALGLQ----DSDDEDAAV 811

Plays an essential role in splicing, either prior to, or during A complex formation.

Rattus norvegicus (taxid: 10116)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q7L014|DDX46_HUMAN Probable ATP-dependent RNA helicase DDX46 OS=Homo sapiens GN=DDX46 PE=1 SV=2

 Score =  634 bits (1635), Expect = e-180,   Method: Compositional matrix adjust.
 Identities = 349/717 (48%), Positives = 468/717 (65%), Gaps = 68/717 (9%)

Query: 204 EQRKLDEEMEKRRRRVQEWQELKRKKEESERENRGDAN--VEEPKAGRNWTLDREDSDDE 261
           +Q KL+EEM KR+ RV++W+E +RKK     EN G+    +EE K G+ W+L+ +D D++
Sbjct: 152 DQNKLEEEMRKRKERVEKWREEQRKKA---MENIGELKKEIEEMKQGKKWSLEDDDDDED 208

Query: 262 EVPQTGKSETDMDADEEPKPSENQVGDAMLVDSDGGSAAPALQIGAAEDEDIDPLDAFMN 321
           +  +  K   +M                                   E E++DPLDA+M 
Sbjct: 209 DPAEAEKEGNEM-----------------------------------EGEELDPLDAYME 233

Query: 322 SMVLPEVEKLKNTVEPSFTDGNNVESKKMDRKGDRRSNGEQPKKSSNKSLGRIIPGEDSD 381
             V  EV+K             N+ S K     +++S     K  +  +  + +   DSD
Sbjct: 234 E-VKEEVKKF------------NMRSVKGGGGNEKKSGPTVTKVVTVVTTKKAV--VDSD 278

Query: 382 SDYGDL-ENDEKPLE-----DEDDDEFMKRVKKTKAEKL-SIVDHSKIDYQPFRKNFYIE 434
              G+L END+  +E     +E D +      +TK  KL   VDH KI+Y+PFRKNFY+E
Sbjct: 279 KKKGELMENDQDAMEYSSEEEEVDLQTALTGYQTKQRKLLEPVDHGKIEYEPFRKNFYVE 338

Query: 435 VKEIARMTPEEVSAYRKQLE-LKIHGKDVPKPIKTWHQTGLTSKIMETIRKLNYEKPMPI 493
           V E+A+M+ EEV+ +R ++E + + GK  PKPIK+W Q G++ KI+ +++K  YEKP PI
Sbjct: 339 VPELAKMSQEEVNVFRLEMEGITVKGKGCPKPIKSWVQCGISMKILNSLKKHGYEKPTPI 398

Query: 494 QAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELV 553
           Q QA+P IMSGRD IG+AKTGSGKT+AF+LPM RHI DQ  +  G+GP+ +IM PTREL 
Sbjct: 399 QTQAIPAIMSGRDLIGIAKTGSGKTIAFLLPMFRHIMDQRSLEEGEGPIAVIMTPTRELA 458

Query: 554 QQIHSDIRKFAKVMGVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGGKIT 613
            QI  + +KF+K +G+R V VYGG+G+++QI+ELKRG EI+VCTPGRMID+L  + G++T
Sbjct: 459 LQITKECKKFSKTLGLRVVCVYGGTGISEQIAELKRGAEIIVCTPGRMIDMLAANSGRVT 518

Query: 614 NLRRVTYLVMDEADRMFDMGFEPQITRIVQNIRPDRQTVLFSATFPRQVEILARKVLNKP 673
           NLRRVTY+V+DEADRMFDMGFEPQ+ RIV N+RPDRQTV+FSATFPR +E LAR++L+KP
Sbjct: 519 NLRRVTYVVLDEADRMFDMGFEPQVMRIVDNVRPDRQTVMFSATFPRAMEALARRILSKP 578

Query: 674 VEIQVGGRSVVNKDITQLVEVRPESDRFLRLLELLGEWYEKGKILIFVHSQEKCDALFRD 733
           +E+QVGGRSVV  D+ Q V V  E  +FL+LLELLG + E G ++IFV  QE  D L +D
Sbjct: 579 IEVQVGGRSVVCSDVEQQVIVIEEEKKFLKLLELLGHYQESGSVIIFVDKQEHADGLLKD 638

Query: 734 LLKHGYPCLSLHGAKDQTDRESTISDFKSNVCNLLIATSVAARGLDVKELELVINFDAPN 793
           L++  YPC+SLHG  DQ DR+S I+DFK+  C LL+ATSVAARGLDVK L LV+N+  PN
Sbjct: 639 LMRASYPCMSLHGGIDQYDRDSIINDFKNGTCKLLVATSVAARGLDVKHLILVVNYSCPN 698

Query: 794 HYEDYVHRVGRTGRAGRKGCAITFISEEDAKYSPDLVKALELSEQVVPDDLKALADSFM- 852
           HYEDYVHR GRTGRAG KG A TFI+E+ A+Y+ D++KALELS   VP DL+ L   F  
Sbjct: 699 HYEDYVHRAGRTGRAGNKGYAYTFITEDQARYAGDIIKALELSGTAVPPDLEKLWSDFKD 758

Query: 853 AKVNQGLEQAHGTGYGGSGFKFNEEEDEKRKAAKKAQAKEYGFEEDKSDSDDEDEGI 909
            +  +G      +G+ G GFKF+E E       KK Q    G +    DSDDED  +
Sbjct: 759 QQKAEGKIIKKSSGFSGKGFKFDETEQALANERKKLQKAALGLQ----DSDDEDAAV 811

Plays an essential role in splicing, either prior to, or during splicing A complex formation.

Homo sapiens (taxid: 9606)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q5R6D8|DDX46_PONAB Probable ATP-dependent RNA helicase DDX46 OS=Pongo abelii GN=DDX46 PE=2 SV=1

 Score =  632 bits (1630), Expect = e-180,   Method: Compositional matrix adjust.
 Identities = 348/717 (48%), Positives = 466/717 (64%), Gaps = 68/717 (9%)

Query: 204 EQRKLDEEMEKRRRRVQEWQELKRKKEESERENRGDAN--VEEPKAGRNWTLDREDSDDE 261
           +Q KL+EEM KR+ RV++W+E +RKK     EN G+    +EE K G+ W+L+ +D D++
Sbjct: 152 DQNKLEEEMRKRKERVEKWREEQRKKA---MENIGELKKEIEEMKQGKKWSLEDDDDDED 208

Query: 262 EVPQTGKSETDMDADEEPKPSENQVGDAMLVDSDGGSAAPALQIGAAEDEDIDPLDAFMN 321
           +  +  K   +M                                   E E++DPLDA+M 
Sbjct: 209 DPAEAEKEGNEM-----------------------------------EGEELDPLDAYME 233

Query: 322 SMVLPEVEKLKNTVEPSFTDGNNVESKKMDRKGDRRSNGEQPKKSSNKSLGRIIPGEDSD 381
             V  EV+K             N+ S K     +++S     K  +  +  +     DSD
Sbjct: 234 E-VKEEVKKF------------NMRSVKGGGGNEKKSGPTVTKVVTVVTTKK--AVVDSD 278

Query: 382 SDYGDL-ENDEKPLE-----DEDDDEFMKRVKKTKAEKL-SIVDHSKIDYQPFRKNFYIE 434
              G+L END+  +E     +E D +      +TK  KL   VDH KI+Y+PFRKNFY+E
Sbjct: 279 KKKGELMENDQDAMEYSSEEEEVDLQTALTGYQTKQRKLLEPVDHGKIEYEPFRKNFYVE 338

Query: 435 VKEIARMTPEEVSAYRKQLE-LKIHGKDVPKPIKTWHQTGLTSKIMETIRKLNYEKPMPI 493
           V E+A+M+ EEV+ +R ++E + + GK  PKPIK+W Q G++ KI+ +++K  YEKP PI
Sbjct: 339 VPELAKMSQEEVNVFRLEMEGITVKGKGCPKPIKSWVQCGISMKILNSLKKHGYEKPTPI 398

Query: 494 QAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELV 553
           Q QA+P IMSGRD IG+AKTGSGKT+AF+LPM RHI DQ  +  G+GP+ +IM PTREL 
Sbjct: 399 QTQAIPAIMSGRDLIGIAKTGSGKTIAFLLPMFRHIMDQRSLEEGEGPIAVIMTPTRELA 458

Query: 554 QQIHSDIRKFAKVMGVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGGKIT 613
            QI  + +KF+K +G+R V VYGG+G+++QI+ELKRG EI+VCTPGRMID+L  + G++T
Sbjct: 459 LQITKECKKFSKTLGLRVVCVYGGTGISEQIAELKRGAEIIVCTPGRMIDMLAANSGRVT 518

Query: 614 NLRRVTYLVMDEADRMFDMGFEPQITRIVQNIRPDRQTVLFSATFPRQVEILARKVLNKP 673
           NLRRVTY+V+DEADRMFDMGFEPQ+ RIV N+RPDRQTV+FSATFPR +E L R++L+KP
Sbjct: 519 NLRRVTYVVLDEADRMFDMGFEPQVMRIVDNVRPDRQTVMFSATFPRAMEALVRRILSKP 578

Query: 674 VEIQVGGRSVVNKDITQLVEVRPESDRFLRLLELLGEWYEKGKILIFVHSQEKCDALFRD 733
           +E+QVGGRSVV  D+ Q V V  E  +FL+LLELLG + E G ++IFV  QE  D L +D
Sbjct: 579 IEVQVGGRSVVCSDVEQQVIVIEEEKKFLKLLELLGHYQESGSVIIFVDKQEHADGLLKD 638

Query: 734 LLKHGYPCLSLHGAKDQTDRESTISDFKSNVCNLLIATSVAARGLDVKELELVINFDAPN 793
           L++  YPC+SLHG  DQ DR+S I+DFK+  C LL+ATSVAARGLDVK L LV+N+  PN
Sbjct: 639 LMRASYPCMSLHGGIDQYDRDSIINDFKNGTCKLLVATSVAARGLDVKHLILVVNYSCPN 698

Query: 794 HYEDYVHRVGRTGRAGRKGCAITFISEEDAKYSPDLVKALELSEQVVPDDLKALADSFM- 852
           HYEDYVHR GRTGRAG KG A TFI+E+ A+Y+ D++KALELS   VP DL+ L   F  
Sbjct: 699 HYEDYVHRAGRTGRAGNKGYAYTFITEDQARYAGDIIKALELSGTAVPPDLEKLWSDFKD 758

Query: 853 AKVNQGLEQAHGTGYGGSGFKFNEEEDEKRKAAKKAQAKEYGFEEDKSDSDDEDEGI 909
            +  +G      +G+ G GFKF+E E       KK Q    G +    DSDDED  +
Sbjct: 759 QQKAEGKIIKKSSGFSGKGFKFDETEQALANERKKLQKAALGLQ----DSDDEDAAV 811

Plays an essential role in splicing, either prior to, or during A complex formation.

Pongo abelii (taxid: 9601)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q2U2J6|PRP5_ASPOR Pre-mRNA-processing ATP-dependent RNA helicase prp5 OS=Aspergillus oryzae (strain ATCC 42149 / RIB 40) GN=prp5 PE=3 SV=1

 Score =  627 bits (1618), Expect = e-178,   Method: Compositional matrix adjust.
 Identities = 311/616 (50%), Positives = 416/616 (67%), Gaps = 48/616 (7%)

Query: 287 GDAMLVDSDGGSAAPALQIGAAEDEDIDPLDAFMNSMVLPEVEKLKNTVEPSFTDGNNVE 346
           GD  + D+    A   +++ A E+E++DPLDAFM+ +                       
Sbjct: 406 GDVQMSDASNQKAPDKMEVDAQEEEEVDPLDAFMSEL----------------------- 442

Query: 347 SKKMDRKGDRRSNGEQPKKSSNKSLGRIIPGEDSDSDYGDLENDE--KPLEDEDDDEFMK 404
                      +    PKK++     +  P +  ++ +GD END     + D D D+F+ 
Sbjct: 443 -----------AESAPPKKTAGAKFAKAKP-QQPEALFGD-ENDMDMTAVGDGDADDFLA 489

Query: 405 RVKKTKAEK-LSIVDHSKIDYQPFRKNFYIEVKEIARMTPEEVSAYRKQLE-LKIHGKDV 462
              K K +K +  VDH K++Y+PFRK FY E  ++A M+ EE ++ R +L+ +K+ G +V
Sbjct: 490 IANKAKKKKDIPTVDHKKVEYEPFRKKFYTEPSDLAAMSEEEAASLRLELDGIKVRGVEV 549

Query: 463 PKPIKTWHQTGLTSKIMETIRKLNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFV 522
           P+P+  W Q GL  + ++ I +L Y  P  IQAQA+P IMSGRD IGVAKTGSGKT+AF+
Sbjct: 550 PRPVSKWSQCGLGVQTLDVIDRLGYSAPTSIQAQAIPAIMSGRDVIGVAKTGSGKTIAFL 609

Query: 523 LPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQ 582
           +PM RHIKDQ P+   +GPVGLIM PTREL  QIH D + F K + +R V  YGG+ +  
Sbjct: 610 IPMFRHIKDQRPLENMEGPVGLIMTPTRELATQIHKDCKPFLKALNLRAVCAYGGAPIKD 669

Query: 583 QISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMGFEPQITRIV 642
           QI++LKRG EI+VCTPGRMID+L  + G++TNLRRVTY+V+DEADRMFDMGFEPQ+ +I+
Sbjct: 670 QIADLKRGAEIIVCTPGRMIDLLAANAGRVTNLRRVTYVVLDEADRMFDMGFEPQVMKIL 729

Query: 643 QNIRPDRQTVLFSATFPRQVEILARKVLNKPVEIQVGGRSVVNKDITQLVEVRPESDRFL 702
            N+RPD+QTVLFSATFPR +E LARK LNKPVEI VGGRSVV  +ITQ+VEVR E  +F+
Sbjct: 730 ANVRPDKQTVLFSATFPRNMEALARKTLNKPVEIVVGGRSVVAPEITQIVEVRSEDKKFI 789

Query: 703 RLLELLGEWY-----EKGKILIFVHSQEKCDALFRDLLKHGYPCLSLHGAKDQTDRESTI 757
           RLLELLG  Y     E  + LIFV  QE  D L R+L++ GYPC+S+HG KDQ DR+STI
Sbjct: 790 RLLELLGNLYSTDENEDARALIFVERQEGADTLLRELMRKGYPCMSIHGGKDQIDRDSTI 849

Query: 758 SDFKSNVCNLLIATSVAARGLDVKELELVINFDAPNHYEDYVHRVGRTGRAGRKGCAITF 817
            DFK+ +  +LIATSVAARGLDVK+L+LV+N+DAPNH EDYVHR GRTGRAG  G A+TF
Sbjct: 850 EDFKAGIFPVLIATSVAARGLDVKQLKLVVNYDAPNHLEDYVHRAGRTGRAGNTGTAVTF 909

Query: 818 ISEEDAKYSPDLVKALELSEQVVPDDLKALADSFMAKVNQGLEQAHGTGYGGSGFKFNEE 877
           ++E+  +YS D+ KAL+ S Q VP+ ++ + DSF+ KV  G E+A  +G+GG G    E 
Sbjct: 910 LTEDQERYSVDIAKALKQSGQSVPEPVQKMVDSFLEKVKAGKEKASASGFGGKGL---ER 966

Query: 878 EDEKRKAAKKAQAKEY 893
            D++R AA+  + K Y
Sbjct: 967 LDQERDAARMRERKTY 982

ATP-dependent RNA helicase involved spliceosome assembly and in nuclear splicing. Catalyzes an ATP-dependent conformational change of U2 snRNP. Bridges U1 and U2 snRNPs and enables stable U2 snRNP association with intron RNA.

Aspergillus oryzae (strain ATCC 42149 / RIB 40) (taxid: 510516)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

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	976
255578793	1173	dead box ATP-dependent RNA helicase, put	0.781	0.650	0.835	0.0
356497367	1104	PREDICTED: DEAD-box ATP-dependent RNA he	0.913	0.807	0.715	0.0
356538821	1107	PREDICTED: DEAD-box ATP-dependent RNA he	0.819	0.722	0.794	0.0
357445503	1148	DEAD box ATP-dependent RNA helicase [Med	0.802	0.682	0.783	0.0
449439147	1118	PREDICTED: DEAD-box ATP-dependent RNA he	0.880	0.768	0.713	0.0
449439149	1040	PREDICTED: DEAD-box ATP-dependent RNA he	0.857	0.804	0.747	0.0
224065635	1112	predicted protein [Populus trichocarpa]	0.760	0.667	0.776	0.0
224083374	895	predicted protein [Populus trichocarpa]	0.722	0.787	0.835	0.0
15218071	1166	DEAD-box ATP-dependent RNA helicase 42 [	0.794	0.664	0.775	0.0
449525702	1098	PREDICTED: LOW QUALITY PROTEIN: DEAD-box	0.859	0.764	0.688	0.0

>gi|255578793|ref|XP_002530253.1| dead box ATP-dependent RNA helicase, putative [Ricinus communis] gi|223530219|gb|EEF32123.1| dead box ATP-dependent RNA helicase, putative [Ricinus communis]

 Score = 1268 bits (3280), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 651/779 (83%), Positives = 705/779 (90%), Gaps = 16/779 (2%)

Query: 161 VRERSLSRSNRHRDENDESPREKLVEDDSDKKEKKTREEELEDEQRKLDEEMEKRRRRVQ 220
            RE+S SRS+RHRDE+D SPR+K  ED+ DKKEKKTREEELEDEQ++LDEEMEKRRRRVQ
Sbjct: 224 AREQSTSRSSRHRDESDGSPRKKSGEDELDKKEKKTREEELEDEQKRLDEEMEKRRRRVQ 283

Query: 221 EWQELKRKKEESERENRGDA-NVEEPKAGRNWTLDREDSDDEEVPQTGKSETDMDADEEP 279
           EWQEL+RKKEESERE  G+A N +EP+ G+ WTL+ E SDDEE P  GKSET+MD DE  
Sbjct: 284 EWQELRRKKEESEREKHGEASNADEPQTGKTWTLEGE-SDDEEAPLAGKSETNMDLDENA 342

Query: 280 KPSENQVGDAMLVDSDGGSAAPALQIG---AAEDEDIDPLDAFMNSMVLPEVEKLKNTVE 336
           KP E ++GDAM+VDS  G+A    + G     EDE+IDPLDAFMNSMVLPEVEKL N V 
Sbjct: 343 KPDE-EIGDAMVVDSYNGTATS--ENGDNDVIEDEEIDPLDAFMNSMVLPEVEKLNNAV- 398

Query: 337 PSFTDGNNVESKKMDRKGDRRSNGEQPKKSSNKSLGRIIPGEDSDSDYGDLENDEKPLED 396
              T+  +    ++ +K +  + GE+ KK SNKSLGRIIPGEDSDSDYGDLENDE PL+D
Sbjct: 399 --ITETVDENKVELKKKKEEGNEGEKLKKGSNKSLGRIIPGEDSDSDYGDLENDEGPLDD 456

Query: 397 EDDDEFMKRVKKTKAEKLSIVDHSKIDYQPFRKNFYIEVKEIARMTPEEVSAYRKQLELK 456
           EDDDEFMKRVKKTKAEKLS+VDHSKIDY+PFRKNFYIEVKEI+RM PEEV+AYRKQLELK
Sbjct: 457 EDDDEFMKRVKKTKAEKLSVVDHSKIDYKPFRKNFYIEVKEISRMAPEEVAAYRKQLELK 516

Query: 457 IHGKDVPKPIKTWHQTGLTSKIMETIRKLNYEKPMPIQAQALPVIMSGRDCIGVAKTGSG 516
           IHGKDVPKP+KTWHQTGL SKI+ETI+KLNYEKPMPIQAQALP+IMSGRDCIG+AKTGSG
Sbjct: 517 IHGKDVPKPVKTWHQTGLASKILETIKKLNYEKPMPIQAQALPIIMSGRDCIGIAKTGSG 576

Query: 517 KTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVMGVRCVPVYG 576
           KTLAFVLPMLRHIKDQP V AGDGP+GLIMAPTRELVQQIHSDI+KFAKV+G+RCVPVYG
Sbjct: 577 KTLAFVLPMLRHIKDQPLVEAGDGPIGLIMAPTRELVQQIHSDIKKFAKVLGIRCVPVYG 636

Query: 577 GSGVAQQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMGFEP 636
           GSGVAQQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMGFEP
Sbjct: 637 GSGVAQQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMGFEP 696

Query: 637 QITRIVQNIRPDRQTVLFSATFPRQVEILARKVLNKPVEIQVGGRSVVNKDITQLVEVRP 696
           QITRIVQNIRPDRQTVLFSATFPRQVEILARKVLNKPVEIQVGGRSVVNKDITQLVEVRP
Sbjct: 697 QITRIVQNIRPDRQTVLFSATFPRQVEILARKVLNKPVEIQVGGRSVVNKDITQLVEVRP 756

Query: 697 ESDRFLRLLELLGEWYEKGKILIFVHSQEKCDALFRDLLKHGYPCLSLHGAKDQTDREST 756
           ES+RFLRLLELLGEW EKGKILIFV SQ+KCDALFRDLLKHGYPCLSLHGAKDQTDREST
Sbjct: 757 ESERFLRLLELLGEWNEKGKILIFVQSQDKCDALFRDLLKHGYPCLSLHGAKDQTDREST 816

Query: 757 ISDFKSNVCNLLIATSVAARGLDVKELELVINFDAPNHYEDYVHRVGRTGRAGRKGCAIT 816
           ISDFKSNVCNLLIATS+AARGLDVKEL+LV+NFD PNHYEDYVHRVGRTGRAGRKGCAIT
Sbjct: 817 ISDFKSNVCNLLIATSIAARGLDVKELDLVVNFDVPNHYEDYVHRVGRTGRAGRKGCAIT 876

Query: 817 FISEEDAKYSPDLVKALELSEQVVPDDLKALADSFMAKVNQGLEQAHGTGYGGSGFKFNE 876
           FISEEDA+Y+PDLVKALELSEQVVP+DLKALAD FM KVNQGLEQAHGTGYGGSGFKFNE
Sbjct: 877 FISEEDARYAPDLVKALELSEQVVPEDLKALADGFMVKVNQGLEQAHGTGYGGSGFKFNE 936

Query: 877 EEDEKRKAAKKAQAKEYGFEEDKSDSDDEDEGIRKAGGDISQQDA-----LAKISAIRK 930
           EEDEKR AAKKAQAKEYGFEEDKSDS+DEDEGIRKAGGDIS+ +A     L  I+A  K
Sbjct: 937 EEDEKRIAAKKAQAKEYGFEEDKSDSEDEDEGIRKAGGDISRHNAALAQQLVAIAAASK 995

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356497367|ref|XP_003517532.1| PREDICTED: DEAD-box ATP-dependent RNA helicase 42-like [Glycine max]

 Score = 1262 bits (3266), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 681/952 (71%), Positives = 781/952 (82%), Gaps = 60/952 (6%)

Query: 33  DEDKHDKEKEKDKHRDRDRRR---DRDRDRDREKEREEKRERAREKEREREKRDREREDR 89
           DE KH   KE  + +D D +R   DRDR  +R K++ + R R REK     +R       
Sbjct: 2   DEGKHKSRKENHEVKDGDSKRSHRDRDRTGERGKDKNDGRHRDREKRDRESRRPERERST 61

Query: 90  ERERERERERRERDREREKRERERDRDKEKDRER-------------------------- 123
           + E   +R+R +R  + +  +RER RDK+++R+R                          
Sbjct: 62  DSEDRYDRDREKRKDKDKDVDRERSRDKKRERDRTDRVREKERERERKEDKERIRERERE 121

Query: 124 ------------------KSRDREKRRKVESDDSD-EDKDRDRKRRRRHDDDHKERVRER 164
                             + R REKRR+V+SD SD E K++DRKR R+ D D+K R RER
Sbjct: 122 RERRDHEREKEKERERGRRVRGREKRREVDSDCSDGESKEQDRKRHRKEDGDYK-RERER 180

Query: 165 SLSRSNRHRDENDESPREKLVEDDSDKKE---KKTREEELEDEQRKLDEEMEKRRRRVQE 221
           S+S+ +R  +E++ SPR+K  EDDSD K+   K TREEE+EDEQ++LDEEMEKRRRRVQE
Sbjct: 181 SVSKPSRKSEEHEGSPRKKSGEDDSDTKDEEKKPTREEEMEDEQKRLDEEMEKRRRRVQE 240

Query: 222 WQELKRKKEESERENRGDANVEEPKAGRNWTLDREDSDDEEVPQTGKSETDMDADEEPKP 281
           WQEL+RKKEE+ERE +G+A+  EP++G+ WTL+ E SDDEE   TGK +T MD DE+ KP
Sbjct: 241 WQELRRKKEEAEREKQGEASANEPESGKTWTLEGE-SDDEEGLGTGK-QTGMDVDEDDKP 298

Query: 282 SENQVGDAMLVDSDGGSAAPALQ---IGAAEDEDIDPLDAFMNSMVLPEVEKLKNTVEPS 338
           ++ +  D M+VD+D G+ A  LQ    GA EDE+IDPLDAFMNSMVLPEVEKL N V  S
Sbjct: 299 ADEEPKDVMVVDTDNGTIASDLQDGTAGAPEDEEIDPLDAFMNSMVLPEVEKLNNAVTSS 358

Query: 339 FTDGNNVESKKMDRKGDRRSNGEQPKKSSNKSLGRIIPGEDSDSDYGDLENDEKPLEDED 398
            +D   ++ K  D KG+ ++ G Q +K SNKS+GRIIPGE+SDSDY D E ++ PL DED
Sbjct: 359 LSD-KAIDVKPKD-KGNGQNRGAQSRKGSNKSIGRIIPGEESDSDYADDEVEKDPL-DED 415

Query: 399 DDEFMKRVKKTKAEKLSIVDHSKIDYQPFRKNFYIEVKEIARMTPEEVSAYRKQLELKIH 458
           DDEFMKRVKKTKAEKLS+VDHSKIDY+PF+KNFYIEVKEI++MTPEE + YRKQLELKIH
Sbjct: 416 DDEFMKRVKKTKAEKLSLVDHSKIDYEPFKKNFYIEVKEISKMTPEEAAVYRKQLELKIH 475

Query: 459 GKDVPKPIKTWHQTGLTSKIMETIRKLNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKT 518
           GKDVPKPIK+WHQTGL SKI+ETI+K+N+E PMPIQAQALPVIMSGRDCIG+AKTGSGKT
Sbjct: 476 GKDVPKPIKSWHQTGLPSKILETIKKMNFEMPMPIQAQALPVIMSGRDCIGIAKTGSGKT 535

Query: 519 LAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGS 578
           LAFVLPMLRHIKDQPPV AGDGP+GLIMAPTRELVQQIHSDI+KFAKV+G+RCVPVYGGS
Sbjct: 536 LAFVLPMLRHIKDQPPVVAGDGPIGLIMAPTRELVQQIHSDIKKFAKVLGLRCVPVYGGS 595

Query: 579 GVAQQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMGFEPQI 638
           GVAQQISELKRG EIVVCTPGRMIDILCTS GKITNLRRVTYLVMDEADRMFDMGFEPQI
Sbjct: 596 GVAQQISELKRGAEIVVCTPGRMIDILCTSSGKITNLRRVTYLVMDEADRMFDMGFEPQI 655

Query: 639 TRIVQNIRPDRQTVLFSATFPRQVEILARKVLNKPVEIQVGGRSVVNKDITQLVEVRPES 698
           TRIVQNIRPDRQTVLFSATFPRQVEILARKVLNKPVEIQVGGRSVVNKDITQLVEVRP++
Sbjct: 656 TRIVQNIRPDRQTVLFSATFPRQVEILARKVLNKPVEIQVGGRSVVNKDITQLVEVRPDN 715

Query: 699 DRFLRLLELLGEWYEKGKILIFVHSQEKCDALFRDLLKHGYPCLSLHGAKDQTDRESTIS 758
           +RFLRLLE+LGEWYEKGKILIFVHSQEKCD+LF+DLL+HGYPCLSLHGAKDQTDRESTIS
Sbjct: 716 ERFLRLLEILGEWYEKGKILIFVHSQEKCDSLFKDLLRHGYPCLSLHGAKDQTDRESTIS 775

Query: 759 DFKSNVCNLLIATSVAARGLDVKELELVINFDAPNHYEDYVHRVGRTGRAGRKGCAITFI 818
           DFKSNVCNLL+ATS+AARGLDVKELELVINFD PNHYEDYVHRVGRTGRAGRKGCAITFI
Sbjct: 776 DFKSNVCNLLVATSIAARGLDVKELELVINFDVPNHYEDYVHRVGRTGRAGRKGCAITFI 835

Query: 819 SEEDAKYSPDLVKALELSEQVVPDDLKALADSFMAKVNQGLEQAHGTGYGGSGFKFNEEE 878
           SEE+A+Y+PDL+KALELSEQ+VP+DLKALA SFMAKVNQGLEQAHGTGYGGSGFKFNEEE
Sbjct: 836 SEEEARYAPDLLKALELSEQIVPNDLKALAGSFMAKVNQGLEQAHGTGYGGSGFKFNEEE 895

Query: 879 DEKRKAAKKAQAKEYGFEEDKSDSDDEDEGIRKAGGDISQQDALAKISAIRK 930
           DE RKAAKKAQAKEYGFEE+KSDS+DEDEGIRKAGGDISQ  A A+I A  K
Sbjct: 896 DEVRKAAKKAQAKEYGFEEEKSDSEDEDEGIRKAGGDISQHSAFAQIIAATK 947

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356538821|ref|XP_003537899.1| PREDICTED: DEAD-box ATP-dependent RNA helicase 42-like [Glycine max]

 Score = 1238 bits (3204), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 646/813 (79%), Positives = 726/813 (89%), Gaps = 13/813 (1%)

Query: 125 SRDREKRRKVESDDSD-EDKDRDRKRRRRHDDDHKERVRERSLSRSNRHRDENDESPREK 183
           +R REKRR+V+SD SD E K+RDRKR R+ D D+K R RERS+S+S+R  +E++ SPR+K
Sbjct: 144 ARGREKRREVDSDCSDGESKERDRKRHRKEDGDYK-RERERSVSKSSRKSEEHEGSPRKK 202

Query: 184 LVEDDSDKKE---KKTREEELEDEQRKLDEEMEKRRRRVQEWQELKRKKEESERENRGDA 240
              DDSD K+   K TREEE+EDEQ++LDEEMEKRRRRVQEWQEL+RK+EE+ERE  G+A
Sbjct: 203 SGGDDSDTKDEEKKPTREEEMEDEQKRLDEEMEKRRRRVQEWQELRRKREEAEREKHGEA 262

Query: 241 NVEEPKAGRNWTLDREDSDDEEVPQTGKSETDMDADEEPKPSENQVGDAMLVDSDGGSAA 300
           +  EP++G+ WTL+ E SDDEE P TGK +T MD DE+ KP++ +  D M+VD+  G+ A
Sbjct: 263 SANEPESGKTWTLEGE-SDDEEGPGTGK-QTGMDVDEDDKPADKEPKDVMVVDTVNGTIA 320

Query: 301 PALQ---IGAAEDEDIDPLDAFMNSMVLPEVEKLKNTVEPSFTDGNNVESKKMDRKGDRR 357
             LQ    GA EDE+IDPLDAFMNSMVLPEVEKL N V  S + G  ++ K  D KG+ +
Sbjct: 321 SDLQDGPAGAPEDEEIDPLDAFMNSMVLPEVEKLNNAVTSSLS-GKAIDVKPKD-KGNEQ 378

Query: 358 SNGEQPKKSSNKSLGRIIPGEDSDSDYGDLENDEKPLEDEDDDEFMKRVKKTKAEKLSIV 417
           + G Q +K SNKS+GRIIPGE+SDSDY D E ++ PL DEDDDEFMKRVKKTKAEKLS+V
Sbjct: 379 NRGAQSRKVSNKSIGRIIPGEESDSDYADDEVEKDPL-DEDDDEFMKRVKKTKAEKLSLV 437

Query: 418 DHSKIDYQPFRKNFYIEVKEIARMTPEEVSAYRKQLELKIHGKDVPKPIKTWHQTGLTSK 477
           DHSKI Y+PF+KNFYIEVKE+++MTPEE + YRKQLELKIHGKDVPKPIK+WHQTGL SK
Sbjct: 438 DHSKIVYEPFKKNFYIEVKEVSKMTPEESAVYRKQLELKIHGKDVPKPIKSWHQTGLASK 497

Query: 478 IMETIRKLNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAA 537
           I+ETI+K+N+EKPMPIQAQALPVIMSGRDCIG+AKTGSGKTLAFVLPMLRHIKDQPPV A
Sbjct: 498 ILETIKKMNFEKPMPIQAQALPVIMSGRDCIGIAKTGSGKTLAFVLPMLRHIKDQPPVVA 557

Query: 538 GDGPVGLIMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQISELKRGTEIVVCT 597
           GDGP+GLIMAPTRELVQQIHSDI+KFAKV+G+RCVPVYGGSGVAQQISELKRG EIVVCT
Sbjct: 558 GDGPIGLIMAPTRELVQQIHSDIKKFAKVLGLRCVPVYGGSGVAQQISELKRGAEIVVCT 617

Query: 598 PGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMGFEPQITRIVQNIRPDRQTVLFSAT 657
           PGRMIDILCTS GKITNL RVTYLVMDEADRMFDMGFEPQITRIVQNIRPDRQTVLFSAT
Sbjct: 618 PGRMIDILCTSSGKITNLHRVTYLVMDEADRMFDMGFEPQITRIVQNIRPDRQTVLFSAT 677

Query: 658 FPRQVEILARKVLNKPVEIQVGGRSVVNKDITQLVEVRPESDRFLRLLELLGEWYEKGKI 717
           FPRQVEILARKVLNKPVEIQVGGRSVVNKDITQLVEVRP+++RFLRLLE+LGEWYEKGKI
Sbjct: 678 FPRQVEILARKVLNKPVEIQVGGRSVVNKDITQLVEVRPDNERFLRLLEILGEWYEKGKI 737

Query: 718 LIFVHSQEKCDALFRDLLKHGYPCLSLHGAKDQTDRESTISDFKSNVCNLLIATSVAARG 777
           LIFVHSQEKCD+LF+DLL+HGYPCLSLHGAKDQTDRESTISDFKSNVCNLL+ATS+AARG
Sbjct: 738 LIFVHSQEKCDSLFKDLLRHGYPCLSLHGAKDQTDRESTISDFKSNVCNLLVATSIAARG 797

Query: 778 LDVKELELVINFDAPNHYEDYVHRVGRTGRAGRKGCAITFISEEDAKYSPDLVKALELSE 837
           LDVKELELVINFD PNHYEDYVHRVGRTGRAGRKGCAITFISEE+A+Y+PDL+KALELSE
Sbjct: 798 LDVKELELVINFDVPNHYEDYVHRVGRTGRAGRKGCAITFISEEEARYAPDLLKALELSE 857

Query: 838 QVVPDDLKALADSFMAKVNQGLEQAHGTGYGGSGFKFNEEEDEKRKAAKKAQAKEYGFEE 897
           Q VP+DLKALA SFMAKVNQGLEQAHGTGYGGSGFKFNEEEDE RKAAKKAQAKEYGFEE
Sbjct: 858 QTVPNDLKALAGSFMAKVNQGLEQAHGTGYGGSGFKFNEEEDEVRKAAKKAQAKEYGFEE 917

Query: 898 DKSDSDDEDEGIRKAGGDISQQDALAKISAIRK 930
           +KSDS+DEDEGIRKAGGDISQ  A A+I A  K
Sbjct: 918 EKSDSEDEDEGIRKAGGDISQHSAFAQIIAATK 950

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357445503|ref|XP_003593029.1| DEAD box ATP-dependent RNA helicase [Medicago truncatula] gi|355482077|gb|AES63280.1| DEAD box ATP-dependent RNA helicase [Medicago truncatula]

 Score = 1233 bits (3189), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 625/798 (78%), Positives = 705/798 (88%), Gaps = 15/798 (1%)

Query: 130 KRRKVESDDSD-EDKDRDRKRRRRHDDDHKERVRERSLSRSNRHRDENDESPREKLVEDD 188
           K R V+S++SD E ++R+RKR ++ DDD+K R +E+S  +S+R  +  D SPR K   DD
Sbjct: 195 KHRDVDSENSDGELRERNRKRHKKDDDDYKRREKEKSSGKSSRKIEVVDGSPRRKSDGDD 254

Query: 189 SDKKEK---KTREEELEDEQRKLDEEMEKRRRRVQEWQELKRKKEESERENRGDANVEEP 245
           SD KEK   +TREEE+E+EQ++LD+EMEKRRR+VQ WQEL+R +EE++R+ +G+A+V E 
Sbjct: 255 SDSKEKAKKQTREEEMEEEQKRLDDEMEKRRRKVQAWQELRRLEEEAQRKKQGEASVVEA 314

Query: 246 KAGRNWTLDREDSDDEEVPQTGKSETDMDADEEPKPSENQVGDAMLVDSDGGSAAPALQ- 304
           ++G+ WTLD E+SDDE+   TGK  T MD DE+ KP++N+  D+M VD D G+ A  LQ 
Sbjct: 315 ESGKKWTLDGEESDDED--GTGK-HTSMDIDEDDKPADNEPTDSMAVDVDKGTVASDLQN 371

Query: 305 --IGAAEDEDIDPLDAFMNSMVLPEVEKLKNTVEPSFTD-GNNVESKKMDRKGDRRSNGE 361
              GA  +++IDPLDAFMNSMVLPEVEKL N V  +  D  +++  K    KG    NG 
Sbjct: 372 GDAGAPAEDEIDPLDAFMNSMVLPEVEKLNNAVNSAPPDKASDLNPKD---KGAESRNGG 428

Query: 362 QPKKSSNKSLGRIIPGEDSDSDYGDLENDEKPLEDEDDDEFMKRVKKTKAEKLSIVDHSK 421
           Q +K SNKS+GRIIPGE+SDSDY D E +  PL DEDDDEFMKRVKKTKAEKLSIVDHSK
Sbjct: 429 QSRKGSNKSIGRIIPGEESDSDYADPEVEGDPL-DEDDDEFMKRVKKTKAEKLSIVDHSK 487

Query: 422 IDYQPFRKNFYIEVKEIARMTPEEVSAYRKQLELKIHGKDVPKPIKTWHQTGLTSKIMET 481
           IDY PFRKNFYIEVKE+++MT EEV+ YRKQLELKIHGKDVPKP+K+W+QTGLTSKI++T
Sbjct: 488 IDYIPFRKNFYIEVKEVSKMTVEEVAFYRKQLELKIHGKDVPKPVKSWNQTGLTSKILDT 547

Query: 482 IRKLNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGP 541
           I+K N+EKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPV  GDGP
Sbjct: 548 IKKANFEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVVVGDGP 607

Query: 542 VGLIMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRM 601
           +GLIMAPTRELVQQIHSDIRKF KVMG+RCVPVYGGSGVAQQISELKRGTEIVVCTPGRM
Sbjct: 608 IGLIMAPTRELVQQIHSDIRKFTKVMGIRCVPVYGGSGVAQQISELKRGTEIVVCTPGRM 667

Query: 602 IDILCTSGGKITNLRRVTYLVMDEADRMFDMGFEPQITRIVQNIRPDRQTVLFSATFPRQ 661
           IDILCTS GKITNLRRVTYLVMDEADRMFDMGFEPQITRIVQNIRPDRQTVLFSATFPRQ
Sbjct: 668 IDILCTSSGKITNLRRVTYLVMDEADRMFDMGFEPQITRIVQNIRPDRQTVLFSATFPRQ 727

Query: 662 VEILARKVLNKPVEIQVGGRSVVNKDITQLVEVRPESDRFLRLLELLGEWYEKGKILIFV 721
           VEILARKVLNKPVEIQVGGRSVVNKDI QLVEVRPE++RFLRLLELLGEWYEKGKIL+FV
Sbjct: 728 VEILARKVLNKPVEIQVGGRSVVNKDIAQLVEVRPENERFLRLLELLGEWYEKGKILVFV 787

Query: 722 HSQEKCDALFRDLLKHGYPCLSLHGAKDQTDRESTISDFKSNVCNLLIATSVAARGLDVK 781
           HSQ+KCDALF+DL+KHGYPCLSLHGAKDQTDRESTISDFKSNVCNLL+ATS+AARGLDVK
Sbjct: 788 HSQDKCDALFKDLMKHGYPCLSLHGAKDQTDRESTISDFKSNVCNLLVATSIAARGLDVK 847

Query: 782 ELELVINFDAPNHYEDYVHRVGRTGRAGRKGCAITFISEEDAKYSPDLVKALELSEQVVP 841
           ELELVINFD PNHYEDYVHRVGRTGRAGRKGCAITFISEEDA+Y+PDLVKALELSEQ+VP
Sbjct: 848 ELELVINFDVPNHYEDYVHRVGRTGRAGRKGCAITFISEEDARYAPDLVKALELSEQIVP 907

Query: 842 DDLKALADSFMAKVNQGLEQAHGTGYGGSGFKFNEEEDEKRKAAKKAQAKEYGFEEDKSD 901
           DDLK+LA+ FMAKV QGLEQAHGTGYGG+GFKFNEEEDE R+AAKKAQAKEYGFEEDKSD
Sbjct: 908 DDLKSLAEGFMAKVTQGLEQAHGTGYGGTGFKFNEEEDEVRRAAKKAQAKEYGFEEDKSD 967

Query: 902 SDDEDEGIRKAGGDISQQ 919
           S+DEDEGIRKAGGDISQ 
Sbjct: 968 SEDEDEGIRKAGGDISQH 985

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449439147|ref|XP_004137349.1| PREDICTED: DEAD-box ATP-dependent RNA helicase 42-like isoform 1 [Cucumis sativus]

 Score = 1209 bits (3129), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 665/932 (71%), Positives = 747/932 (80%), Gaps = 73/932 (7%)

Query: 38  DKEKEKDKHRDRDRRRDRDRDRDREKEREEKRERAREKEREREKRDRER-----EDRERE 92
           D ++ K  HR+RDR RD++R+ DR               R++EKRDRER     E  + E
Sbjct: 12  DLDEPKKSHRERDRERDKERNGDRG--------------RDKEKRDRERSYDSEELVQHE 57

Query: 93  RERERERRERDR----EREKRERERDRDKEKDRERKSRDREKRRK--------------- 133
           RE+E+ RR++D+    + E+      R +      K+RD+EKR +               
Sbjct: 58  REKEKPRRDKDKTRNRDDERDRGRDRRKERDRAREKTRDKEKRERAREKERDKRDRDRDR 117

Query: 134 ----------------------VESDDSDEDKDRDRKRRRRHDDDHKERVRERSLSRSNR 171
                                 V S+ SDED     ++RRR DDD        S SR N+
Sbjct: 118 ERRERERDREKERDKDRRKRREVVSEYSDEDSTEHGRKRRRRDDDDHRA--HESNSRINK 175

Query: 172 HRDENDESPREKLVEDDSDKKEKK-TREEELEDEQRKLDEEMEKRRRRVQEWQELKRKKE 230
            RD  DESPREK  ED  DK E K TREEELE+EQ++LDEEMEKRRRRVQEWQ+ +R KE
Sbjct: 176 QRDHVDESPREKSEEDAFDKNETKPTREEELENEQKRLDEEMEKRRRRVQEWQKSRRLKE 235

Query: 231 ESERENRGDANVEEPKAGRNWTLDREDSDDEEVPQTGKSETDMDADEEPKPSENQVGDAM 290
           E++ + +G+ N +EPK+G+ WTL+ E  D+ E      +ETDMD DE  KP  +  G+ +
Sbjct: 236 EADGDKQGELNADEPKSGKTWTLEGESDDEYE--NARPTETDMDVDENSKPLVD--GEQI 291

Query: 291 LVDSDGGSAA----PALQIGA-AEDEDIDPLDAFMNSMVLPEVEKLKNTVEPSFTDGNNV 345
            V+ + G+ A    P   IG  A D++IDPLDAFMNSMVLPEVEKL     P+  D   V
Sbjct: 292 AVNFNNGNEAAASPPQDSIGGDAADDEIDPLDAFMNSMVLPEVEKLNKVEVPTVNDDKIV 351

Query: 346 ESKKMDRKGDRRSNGEQPKKSSNKSLGRIIPGEDSDSDYGDLENDEKPLEDEDDDEFMKR 405
           E K  D+  D+ S G+  ++ SNKS+GRIIPGEDSD+DYGDLEND   LEDEDDDEFMKR
Sbjct: 352 ELKSRDKPSDQ-SGGKAQRRISNKSMGRIIPGEDSDTDYGDLENDGDTLEDEDDDEFMKR 410

Query: 406 VKKTKAEKLSIVDHSKIDYQPFRKNFYIEVKEIARMTPEEVSAYRKQLELKIHGKDVPKP 465
           VKKTKAEKLSIVDHSK+DYQPFRKNFYIEVKEI+RMT EEV+AYRKQLELKIHGKDVPKP
Sbjct: 411 VKKTKAEKLSIVDHSKMDYQPFRKNFYIEVKEISRMTLEEVAAYRKQLELKIHGKDVPKP 470

Query: 466 IKTWHQTGLTSKIMETIRKLNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPM 525
           +KTWHQTGLTSKI+ETI+KLNYEKPMPIQAQALP++MSGRDCIG+AKTGSGKTLAFVLPM
Sbjct: 471 VKTWHQTGLTSKILETIKKLNYEKPMPIQAQALPIVMSGRDCIGIAKTGSGKTLAFVLPM 530

Query: 526 LRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQIS 585
           LRHIKDQ PV  GDGP+GLIMAPTRELVQQIHSDI+KF+KVMG+RCVPVYGGSGVAQQIS
Sbjct: 531 LRHIKDQSPVVPGDGPIGLIMAPTRELVQQIHSDIKKFSKVMGLRCVPVYGGSGVAQQIS 590

Query: 586 ELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMGFEPQITRIVQNI 645
           ELKRG EIVVCTPGRMIDILCTS GKITNLRRVTYLVMDEADRMFDMGFEPQITRIVQNI
Sbjct: 591 ELKRGAEIVVCTPGRMIDILCTSAGKITNLRRVTYLVMDEADRMFDMGFEPQITRIVQNI 650

Query: 646 RPDRQTVLFSATFPRQVEILARKVLNKPVEIQVGGRSVVNKDITQLVEVRPESDRFLRLL 705
           RPDRQTVLFSATFPRQVEILARKVLNKPVE+QVGGRSVVNKDI QLVEVRPE++RFLRLL
Sbjct: 651 RPDRQTVLFSATFPRQVEILARKVLNKPVEVQVGGRSVVNKDIAQLVEVRPENERFLRLL 710

Query: 706 ELLGEWYEKGKILIFVHSQEKCDALFRDLLKHGYPCLSLHGAKDQTDRESTISDFKSNVC 765
           ELLGEWYEKGKILIFVHSQEKCDALFRDLLKHGYPCLSLHGAKDQTDRESTISDFKSNVC
Sbjct: 711 ELLGEWYEKGKILIFVHSQEKCDALFRDLLKHGYPCLSLHGAKDQTDRESTISDFKSNVC 770

Query: 766 NLLIATSVAARGLDVKELELVINFDAPNHYEDYVHRVGRTGRAGRKGCAITFISEEDAKY 825
           NLLIATS+AARGLDVKELELVINFD PNHYEDYVHRVGRTGRAGRKGCAITFI+EED++Y
Sbjct: 771 NLLIATSIAARGLDVKELELVINFDVPNHYEDYVHRVGRTGRAGRKGCAITFIAEEDSRY 830

Query: 826 SPDLVKALELSEQVVPDDLKALADSFMAKVNQGLEQAHGTGYGGSGFKFNEEEDEKRKAA 885
           +PDLVKALELSEQVVPDDL+ALADSFMAKVNQGLEQAHGTGYGGSGFKFNEEEDE R+AA
Sbjct: 831 APDLVKALELSEQVVPDDLRALADSFMAKVNQGLEQAHGTGYGGSGFKFNEEEDEVRRAA 890

Query: 886 KKAQAKEYGFEEDKSDSDDEDEGIRKAGGDIS 917
           KKAQAKEYGFEEDKSDS+DED+G+RKAGGDIS
Sbjct: 891 KKAQAKEYGFEEDKSDSEDEDDGVRKAGGDIS 922

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449439149|ref|XP_004137350.1| PREDICTED: DEAD-box ATP-dependent RNA helicase 42-like isoform 2 [Cucumis sativus]

 Score = 1197 bits (3098), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 638/854 (74%), Positives = 716/854 (83%), Gaps = 17/854 (1%)

Query: 70  ERAREKEREREKRDREREDRERERERERERRERDREREKRERERDRDKEKDRERKSRDRE 129
           E  R K R  +  + ++  RER+RER++ER        +R       +++  + + + RE
Sbjct: 2   EEGRSKSRRDDLDEPKKSHRERDRERDKERNGDRDRDRERRERERDREKERDKDRRKRRE 61

Query: 130 KRRKVESDDSDEDKDRDRKRRRRHDDDHKERVRERSLSRSNRHRDENDESPREKLVEDDS 189
              +   +DS E   + R+R       H+      S SR N+ RD  DESPREK  ED  
Sbjct: 62  VVSEYSDEDSTEHGRKRRRRDDDDHRAHE------SNSRINKQRDHVDESPREKSEEDAF 115

Query: 190 DKKEKK-TREEELEDEQRKLDEEMEKRRRRVQEWQELKRKKEESERENRGDANVEEPKAG 248
           DK E K TREEELE+EQ++LDEEMEKRRRRVQEWQ+ +R KEE++ + +G+ N +EPK+G
Sbjct: 116 DKNETKPTREEELENEQKRLDEEMEKRRRRVQEWQKSRRLKEEADGDKQGELNADEPKSG 175

Query: 249 RNWTLDREDSDDEEVPQTGKSETDMDADEEPKPSENQVGDAMLVDSDGGSAA----PALQ 304
           + WTL+ E  D+ E      +ETDMD DE  KP  +  G+ + V+ + G+ A    P   
Sbjct: 176 KTWTLEGESDDEYE--NARPTETDMDVDENSKPLVD--GEQIAVNFNNGNEAAASPPQDS 231

Query: 305 IGA-AEDEDIDPLDAFMNSMVLPEVEKLKNTVEPSFTDGNNVESKKMDRKGDRRSNGEQP 363
           IG  A D++IDPLDAFMNSMVLPEVEKL     P+  D   VE K  D+  D+ S G+  
Sbjct: 232 IGGDAADDEIDPLDAFMNSMVLPEVEKLNKVEVPTVNDDKIVELKSRDKPSDQ-SGGKAQ 290

Query: 364 KKSSNKSLGRIIPGEDSDSDYGDLENDEKPLEDEDDDEFMKRVKKTKAEKLSIVDHSKID 423
           ++ SNKS+GRIIPGEDSD+DYGDLEND   LEDEDDDEFMKRVKKTKAEKLSIVDHSK+D
Sbjct: 291 RRISNKSMGRIIPGEDSDTDYGDLENDGDTLEDEDDDEFMKRVKKTKAEKLSIVDHSKMD 350

Query: 424 YQPFRKNFYIEVKEIARMTPEEVSAYRKQLELKIHGKDVPKPIKTWHQTGLTSKIMETIR 483
           YQPFRKNFYIEVKEI+RMT EEV+AYRKQLELKIHGKDVPKP+KTWHQTGLTSKI+ETI+
Sbjct: 351 YQPFRKNFYIEVKEISRMTLEEVAAYRKQLELKIHGKDVPKPVKTWHQTGLTSKILETIK 410

Query: 484 KLNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVG 543
           KLNYEKPMPIQAQALP++MSGRDCIG+AKTGSGKTLAFVLPMLRHIKDQ PV  GDGP+G
Sbjct: 411 KLNYEKPMPIQAQALPIVMSGRDCIGIAKTGSGKTLAFVLPMLRHIKDQSPVVPGDGPIG 470

Query: 544 LIMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMID 603
           LIMAPTRELVQQIHSDI+KF+KVMG+RCVPVYGGSGVAQQISELKRG EIVVCTPGRMID
Sbjct: 471 LIMAPTRELVQQIHSDIKKFSKVMGLRCVPVYGGSGVAQQISELKRGAEIVVCTPGRMID 530

Query: 604 ILCTSGGKITNLRRVTYLVMDEADRMFDMGFEPQITRIVQNIRPDRQTVLFSATFPRQVE 663
           ILCTS GKITNLRRVTYLVMDEADRMFDMGFEPQITRIVQNIRPDRQTVLFSATFPRQVE
Sbjct: 531 ILCTSAGKITNLRRVTYLVMDEADRMFDMGFEPQITRIVQNIRPDRQTVLFSATFPRQVE 590

Query: 664 ILARKVLNKPVEIQVGGRSVVNKDITQLVEVRPESDRFLRLLELLGEWYEKGKILIFVHS 723
           ILARKVLNKPVE+QVGGRSVVNKDI QLVEVRPE++RFLRLLELLGEWYEKGKILIFVHS
Sbjct: 591 ILARKVLNKPVEVQVGGRSVVNKDIAQLVEVRPENERFLRLLELLGEWYEKGKILIFVHS 650

Query: 724 QEKCDALFRDLLKHGYPCLSLHGAKDQTDRESTISDFKSNVCNLLIATSVAARGLDVKEL 783
           QEKCDALFRDLLKHGYPCLSLHGAKDQTDRESTISDFKSNVCNLLIATS+AARGLDVKEL
Sbjct: 651 QEKCDALFRDLLKHGYPCLSLHGAKDQTDRESTISDFKSNVCNLLIATSIAARGLDVKEL 710

Query: 784 ELVINFDAPNHYEDYVHRVGRTGRAGRKGCAITFISEEDAKYSPDLVKALELSEQVVPDD 843
           ELVINFD PNHYEDYVHRVGRTGRAGRKGCAITFI+EED++Y+PDLVKALELSEQVVPDD
Sbjct: 711 ELVINFDVPNHYEDYVHRVGRTGRAGRKGCAITFIAEEDSRYAPDLVKALELSEQVVPDD 770

Query: 844 LKALADSFMAKVNQGLEQAHGTGYGGSGFKFNEEEDEKRKAAKKAQAKEYGFEEDKSDSD 903
           L+ALADSFMAKVNQGLEQAHGTGYGGSGFKFNEEEDE R+AAKKAQAKEYGFEEDKSDS+
Sbjct: 771 LRALADSFMAKVNQGLEQAHGTGYGGSGFKFNEEEDEVRRAAKKAQAKEYGFEEDKSDSE 830

Query: 904 DEDEGIRKAGGDIS 917
           DED+G+RKAGGDIS
Sbjct: 831 DEDDGVRKAGGDIS 844

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224065635|ref|XP_002301895.1| predicted protein [Populus trichocarpa] gi|222843621|gb|EEE81168.1| predicted protein [Populus trichocarpa]

 Score = 1197 bits (3096), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 605/779 (77%), Positives = 662/779 (84%), Gaps = 37/779 (4%)

Query: 199 EELEDEQRKLDEEMEKRRRRVQEWQELKRKKEESERENRGD-ANVEEPKAGRNWTLDRED 257
           E LE EQ+KLDEEMEKRRRRVQEWQEL+RKKEE+ERE  G+ A+V EPK G+ WTL+ E 
Sbjct: 232 ERLEQEQKKLDEEMEKRRRRVQEWQELRRKKEETEREKHGEEADVNEPKTGKTWTLEGE- 290

Query: 258 SDDEEVPQTGKSETDMDADEEPKPSENQVGDAMLVDSDGGSAAPALQIGAAEDEDIDPLD 317
           SDDEE P TGKSETDMD +E  KP E                           E+IDPLD
Sbjct: 291 SDDEEAPPTGKSETDMDLEENAKPDE---------------------------EEIDPLD 323

Query: 318 AFMNSMVLPEVEKLKNTVEPSFTDGNNVESKKMDRKGDRRSNGEQPKKSSNKSLGRIIPG 377
           AFMNSMVLPEVEKL +T+     D N  + K  D+K + R NGEQ KK S+KSLGRI+PG
Sbjct: 324 AFMNSMVLPEVEKLNSTLVTHTADDNKTDLKNKDKK-EERINGEQRKKGSHKSLGRIVPG 382

Query: 378 EDSDSDYGDLENDEKPLEDEDDDEFMKRVKKTKAEKLSIVDHSKIDYQPFRKNFYIEVKE 437
           EDSDSDYGDLEN E PLE+EDDDEFMKRVKKTKAEKLSIVDHSKIDY PFRKNFYIEVKE
Sbjct: 383 EDSDSDYGDLENGEDPLEEEDDDEFMKRVKKTKAEKLSIVDHSKIDYNPFRKNFYIEVKE 442

Query: 438 IARMTPEEVSAYRKQLELKIHGKDVPKPIKTWHQTGLTSKIMETIRKLNYEKPMPIQAQA 497
           I+RMTPEEV A RK+LELK+HGKDVPKPIKTWHQTGLTSKI+ETI+KLNYEKPM IQAQA
Sbjct: 443 ISRMTPEEVVACRKELELKLHGKDVPKPIKTWHQTGLTSKILETIKKLNYEKPMTIQAQA 502

Query: 498 LPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIH 557
           LP+IMSGRDCIG+AKTGSGKTLAFVLPMLRHIKDQPPV AG+GP+GL+MAPTRELVQQIH
Sbjct: 503 LPIIMSGRDCIGIAKTGSGKTLAFVLPMLRHIKDQPPVEAGEGPIGLVMAPTRELVQQIH 562

Query: 558 SDIRKFAKVMGVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRR 617
           SDI+KFAK + +RCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRR
Sbjct: 563 SDIKKFAKALSIRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRR 622

Query: 618 VTYLVMDEADRMFDMGFEPQITRIVQNIRPDRQTVLFSATFPRQVEILARKVLNKPVEIQ 677
           VTYLVMDEADRMFDMGFEPQITRIVQNIRPDRQTVLFSATFPRQVE LARKVLNKPVEIQ
Sbjct: 623 VTYLVMDEADRMFDMGFEPQITRIVQNIRPDRQTVLFSATFPRQVETLARKVLNKPVEIQ 682

Query: 678 VGGRSVVNKDITQLVEVRPESDRFLRLLELLGEWYEKGKILIFVHSQEKCDALFRDLLKH 737
           VGGRSVVNKDITQLVE+R E  R+LRLLELLGEWY+KGKILIFV SQ+KCD+LFR+LLK 
Sbjct: 683 VGGRSVVNKDITQLVELRTEDQRWLRLLELLGEWYQKGKILIFVQSQDKCDSLFRNLLKF 742

Query: 738 GYPCLSLHGAKDQTDRESTISDFKSNVCNLLIATSVAARGLDVKELELVINFDAPNHYED 797
           GYPCLSLHGAKDQTDRESTISDFK+NVCNL+IATSVAARGLDVK+LELVIN+DAPNHYED
Sbjct: 743 GYPCLSLHGAKDQTDRESTISDFKTNVCNLMIATSVAARGLDVKDLELVINYDAPNHYED 802

Query: 798 YVHRVGRTGRAGRKGCAITFISEEDAKYSPDLVKALELSEQVVPDDLKALADSFMAKVNQ 857
           YVHRVGRTGRAGRKGCAITFISE+DA+Y+PDLVKALELSEQVVP DLKALAD FMAKVNQ
Sbjct: 803 YVHRVGRTGRAGRKGCAITFISEDDARYAPDLVKALELSEQVVPQDLKALADGFMAKVNQ 862

Query: 858 GLEQAHGTGYGGSGFKFNEEEDEKRKAAKKAQAKEYGFEEDKSDSDDEDEGIRKAGGDIS 917
           GLEQAHGTGYGGSGFKFNEEEDEKR AAKKAQAKEYG+E++KSDS+DEDE +RK+ GD+S
Sbjct: 863 GLEQAHGTGYGGSGFKFNEEEDEKRMAAKKAQAKEYGYEDEKSDSEDEDEVVRKSVGDVS 922

Query: 918 QQDALAKISAIRKLYLFIEGPTEQSVKRAKAELKRVLEDFTNQALSLPGGAQPGRYSVV 976
           QQ ALA+  A       +  P    +  + A+L       +N  L +P    P   SV 
Sbjct: 923 QQTALAQQIAALAAVSKVPMPA-PPISHSVAQL------LSNGGLPVPPNPGPAVVSVT 974

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224083374|ref|XP_002307002.1| predicted protein [Populus trichocarpa] gi|222856451|gb|EEE93998.1| predicted protein [Populus trichocarpa]

 Score = 1193 bits (3086), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 593/710 (83%), Positives = 638/710 (89%), Gaps = 5/710 (0%)

Query: 212 MEKRRRRVQEWQELKRKKEESERENRGD-ANVEEPKAGRNWTLDREDSDDEEVPQTGKSE 270
           MEKRRRRVQEWQEL+RKKEE+E E  G+ ANV+E K+G+ WTL+ E SDDEE P TGKS+
Sbjct: 1   MEKRRRRVQEWQELRRKKEETESEKGGEEANVDESKSGKTWTLEGE-SDDEEAPPTGKSD 59

Query: 271 TDMDADEEPKPSENQVGDAMLVDSDGGSAAPALQIGAAE-DEDIDPLDAFMNSMVLPEVE 329
            D+D +E   P + + GDAM+VD++   +AP  ++ A   DE+IDPLDAFMNSMVLPEVE
Sbjct: 60  MDIDQEENAIP-DKEAGDAMVVDTENDISAPQSEVDAVNGDEEIDPLDAFMNSMVLPEVE 118

Query: 330 KLKNTVEPSFTDGNNVESKKMDRKGDRRSNGEQPKKSSNKSLGRIIPGEDSDSDYGDLEN 389
            L N V     D N  +SKK D K D   NG Q KK S+KSLGRIIPGEDSDSD+GDLEN
Sbjct: 119 MLNNAVVTQTADDNKADSKKKD-KNDEGINGGQRKKGSHKSLGRIIPGEDSDSDHGDLEN 177

Query: 390 DEKPLEDEDDDEFMKRVKKTKAEKLSIVDHSKIDYQPFRKNFYIEVKEIARMTPEEVSAY 449
            E PLEDEDDDEFMKRVKKTKAEKLSIVDHSKIDY PFRKNFYIEVKEI RMTPEEV+AY
Sbjct: 178 SEVPLEDEDDDEFMKRVKKTKAEKLSIVDHSKIDYSPFRKNFYIEVKEILRMTPEEVTAY 237

Query: 450 RKQLELKIHGKDVPKPIKTWHQTGLTSKIMETIRKLNYEKPMPIQAQALPVIMSGRDCIG 509
           RK LELKIHGKDVPKPIKTWHQTGLTSKI+ETI+KLNYEKPM IQAQALP+IMSGRDCIG
Sbjct: 238 RKLLELKIHGKDVPKPIKTWHQTGLTSKILETIKKLNYEKPMTIQAQALPIIMSGRDCIG 297

Query: 510 VAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVMGV 569
           +AKTGSGKTLAFVLPMLRHIKDQPPV AG+GP+GLIMAPTRELVQQIHSDIRKF K +G+
Sbjct: 298 IAKTGSGKTLAFVLPMLRHIKDQPPVEAGEGPIGLIMAPTRELVQQIHSDIRKFTKALGI 357

Query: 570 RCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRM 629
           RCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRM
Sbjct: 358 RCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRM 417

Query: 630 FDMGFEPQITRIVQNIRPDRQTVLFSATFPRQVEILARKVLNKPVEIQVGGRSVVNKDIT 689
           FDMGFEPQITRIVQNIRPD QTVLFSATFPRQVE LARKVLNKPVEIQVGGRSVVNKDI 
Sbjct: 418 FDMGFEPQITRIVQNIRPDHQTVLFSATFPRQVETLARKVLNKPVEIQVGGRSVVNKDIN 477

Query: 690 QLVEVRPESDRFLRLLELLGEWYEKGKILIFVHSQEKCDALFRDLLKHGYPCLSLHGAKD 749
           QLVEVRPE +R+ RLLELLG W EKGKIL+FV SQ+KCDALFRDLLK G+PCLSLHGAKD
Sbjct: 478 QLVEVRPEGERWFRLLELLGVWSEKGKILVFVQSQDKCDALFRDLLKFGHPCLSLHGAKD 537

Query: 750 QTDRESTISDFKSNVCNLLIATSVAARGLDVKELELVINFDAPNHYEDYVHRVGRTGRAG 809
           QTDRESTISDFKSNVCNLLIATSVAARGLDVK+LELVIN+D PNHYEDYVHRVGRTGRAG
Sbjct: 538 QTDRESTISDFKSNVCNLLIATSVAARGLDVKDLELVINYDVPNHYEDYVHRVGRTGRAG 597

Query: 810 RKGCAITFISEEDAKYSPDLVKALELSEQVVPDDLKALADSFMAKVNQGLEQAHGTGYGG 869
           RKGCAITF SE+DA+Y+PDLVKALELSEQVVP DLKALAD FM KVNQGLEQAHGTGYGG
Sbjct: 598 RKGCAITFFSEDDARYAPDLVKALELSEQVVPQDLKALADGFMVKVNQGLEQAHGTGYGG 657

Query: 870 SGFKFNEEEDEKRKAAKKAQAKEYGFEEDKSDSDDEDEGIRKAGGDISQQ 919
           SGFKFNEEEDEKR AAKKAQA+EYGFEE+KSDS+DEDE +RKAGGDISQQ
Sbjct: 658 SGFKFNEEEDEKRMAAKKAQAREYGFEEEKSDSEDEDEVVRKAGGDISQQ 707

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|15218071|ref|NP_173516.1| DEAD-box ATP-dependent RNA helicase 42 [Arabidopsis thaliana] gi|108861895|sp|Q8H0U8.2|RH42_ARATH RecName: Full=DEAD-box ATP-dependent RNA helicase 42 gi|4836896|gb|AAD30599.1|AC007369_9 Similar to RNA helicases [Arabidopsis thaliana] gi|332191919|gb|AEE30040.1| DEAD-box ATP-dependent RNA helicase 42 [Arabidopsis thaliana]

 Score = 1189 bits (3076), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 615/793 (77%), Positives = 697/793 (87%), Gaps = 18/793 (2%)

Query: 134 VESDDSDEDKDRDRKRRRRHDDDHKERVRERSLSRSNRHRDENDESPREKLVEDDSDKKE 193
           V +++SD+D  RD KRRR+   + KE+ RE+S+ RS+RH D    SP+ K VED+ +KKE
Sbjct: 205 VGNEESDDDVKRDLKRRRKEGGERKEKEREKSVGRSSRHED----SPKRKSVEDNGEKKE 260

Query: 194 KKTREEELEDEQRKLDEEMEKRRRRVQEWQELKRKKEESERENRGDANVEEPKAGRNWTL 253
           KKTREEELEDEQ+KLDEE+EKRRRRVQEWQELKRKKEE+E E++GDA+  EPKAG+ WTL
Sbjct: 261 KKTREEELEDEQKKLDEEVEKRRRRVQEWQELKRKKEEAESESKGDADGNEPKAGKAWTL 320

Query: 254 DREDSDDEEVPQTGKSETDMDADEEPKPSENQVGDAMLVDSDGGSAAPALQI---GAAED 310
           + E SDDEE     KSET+MD DEE KP  +  GDA +VD +  +AA   +    GA ++
Sbjct: 321 EGE-SDDEEGHPEEKSETEMDVDEETKPEND--GDAKMVDLENETAATVSESGGDGAVDE 377

Query: 311 EDIDPLDAFMNSMVLPEVEKLKNTV-EPSFTDGNNVESKKMDRKGDRRSNGEQPKKSSNK 369
           E+IDPLDAFMN+MVLPEVEK  N    P+  DG       +D K + + +G++PKK  NK
Sbjct: 378 EEIDPLDAFMNTMVLPEVEKFCNGAPPPAVNDGT------LDSKMNGKESGDRPKKGFNK 431

Query: 370 SLGRIIPGEDSDSDYGDLENDEKPLEDEDDDEFMKRVKKTKAEKLSIVDHSKIDYQPFRK 429
           +LGRII GEDSDSDY + +ND+ P  DEDD+EFMKRVKKTKAEKLS+VDHSKI+Y+PFRK
Sbjct: 432 ALGRIIQGEDSDSDYSEPKNDDDPSLDEDDEEFMKRVKKTKAEKLSLVDHSKIEYEPFRK 491

Query: 430 NFYIEVKEIARMTPEEVSAYRKQLELKIHGKDVPKPIKTWHQTGLTSKIMETIRKLNYEK 489
           NFYIEVK+I+RMT EEV+ YRK+LELK+HGKDVP+PIK WHQTGLTSKI++T++KLNYEK
Sbjct: 492 NFYIEVKDISRMTQEEVNTYRKELELKVHGKDVPRPIKFWHQTGLTSKILDTMKKLNYEK 551

Query: 490 PMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPT 549
           PMPIQ QALP+IMSGRDCIGVAKTGSGKTL FVLPMLRHIKDQPPV AGDGP+GL+MAPT
Sbjct: 552 PMPIQTQALPIIMSGRDCIGVAKTGSGKTLGFVLPMLRHIKDQPPVEAGDGPIGLVMAPT 611

Query: 550 RELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSG 609
           RELVQQIHSDIRKF+K +G+RCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTS 
Sbjct: 612 RELVQQIHSDIRKFSKPLGIRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSS 671

Query: 610 GKITNLRRVTYLVMDEADRMFDMGFEPQITRIVQNIRPDRQTVLFSATFPRQVEILARKV 669
           GKITNLRRVT+LVMDEADRMFDMGFEPQITRI+QNIRP+RQTVLFSATFPRQVE LARKV
Sbjct: 672 GKITNLRRVTFLVMDEADRMFDMGFEPQITRIIQNIRPERQTVLFSATFPRQVETLARKV 731

Query: 670 LNKPVEIQVGGRSVVNKDITQLVEVRPESDRFLRLLELLGEWYEKGKILIFVHSQEKCDA 729
           LNKPVEIQVGGRSVVNKDITQLVEVRPESDRFLRLLELLGEW EKGKIL+FV SQEKCDA
Sbjct: 732 LNKPVEIQVGGRSVVNKDITQLVEVRPESDRFLRLLELLGEWSEKGKILVFVQSQEKCDA 791

Query: 730 LFRDLLKHGYPCLSLHGAKDQTDRESTISDFKSNVCNLLIATSVAARGLDVKELELVINF 789
           L+RD++K  YPCLSLHG KDQTDRESTISDFK++VCNLLIATSVAARGLDVKELELV+NF
Sbjct: 792 LYRDMIKSSYPCLSLHGGKDQTDRESTISDFKNDVCNLLIATSVAARGLDVKELELVVNF 851

Query: 790 DAPNHYEDYVHRVGRTGRAGRKGCAITFISEEDAKYSPDLVKALELSEQVVPDDLKALAD 849
           DAPNHYEDYVHRVGRTGRAGRKGCA+TFISE+DAKY+PDLVKALELSEQ VPDDLKALAD
Sbjct: 852 DAPNHYEDYVHRVGRTGRAGRKGCAVTFISEDDAKYAPDLVKALELSEQPVPDDLKALAD 911

Query: 850 SFMAKVNQGLEQAHGTGYGGSGFKFNEEEDEKRKAAKKAQAKEYGFEEDKSDSDDEDEGI 909
            FM KV QG+EQAHGTGYGGSGFKFNEEE+E RKAAKKAQAKEYGFEEDKSDS+DE++ +
Sbjct: 912 GFMVKVKQGIEQAHGTGYGGSGFKFNEEEEEVRKAAKKAQAKEYGFEEDKSDSEDENDVV 971

Query: 910 RKA-GGDISQQDA 921
           RKA GG+ISQQ A
Sbjct: 972 RKAGGGEISQQQA 984

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449525702|ref|XP_004169855.1| PREDICTED: LOW QUALITY PROTEIN: DEAD-box ATP-dependent RNA helicase 42-like [Cucumis sativus]

 Score = 1142 bits (2955), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 642/932 (68%), Positives = 725/932 (77%), Gaps = 93/932 (9%)

Query: 38  DKEKEKDKHRDRDRRRDRDRDRDREKEREEKRERAREKEREREKRDRER-----EDRERE 92
           D ++ K  HR+RDR RD++R+ DR               R++EKRDRER     E  + E
Sbjct: 12  DLDEPKKSHRERDRERDKERNGDRG--------------RDKEKRDRERSYDSEELVQHE 57

Query: 93  RERERERRERDR----EREKRERERDRDKEKDRERKSRDREKRRK--------------- 133
           RE+E+ RR++D+    + E+      R +      K+RD+EKR +               
Sbjct: 58  REKEKPRRDKDKTRNRDDERDRGRDRRKERDRAREKTRDKEKRERAREKERDKRDRDRDR 117

Query: 134 ----------------------VESDDSDEDKDRDRKRRRRHDDDHKERVRERSLSRSNR 171
                                 V S+ SDED     ++RRR DDD        S SR N+
Sbjct: 118 ERRERERDREKERDKDRRKRREVVSEYSDEDSTEHGRKRRRRDDDDHRA--HESNSRINK 175

Query: 172 HRDENDESPREKLVEDDSDKKEKK-TREEELEDEQRKLDEEMEKRRRRVQEWQELKRKKE 230
            RD  DESP  K  ED  DK E K TREEELE+EQ++LDEEMEKRRRRVQEWQ+ +R KE
Sbjct: 176 QRDHVDESPXRKSEEDAFDKNEXKPTREEELENEQKRLDEEMEKRRRRVQEWQKSRRLKE 235

Query: 231 ESERENRGDANVEEPKAGRNWTLDREDSDDEEVPQTGKSETDMDADEEPKPSENQVGDAM 290
           E++ + +G+ N +EPK+G+ WTL+ E  D+ E      +ETDMD DE  KP  +  G+ +
Sbjct: 236 EADGDKQGELNADEPKSGKTWTLEGESDDEYE--NARPTETDMDVDENSKPLVD--GEQI 291

Query: 291 LVDSDGGSAA----PALQIGA-AEDEDIDPLDAFMNSMVLPEVEKLKNTVEPSFTDGNNV 345
            V+ + G+ A    P   IG  A D++IDPLDAFMNSMVLPEVEKL     P+  D   V
Sbjct: 292 AVNFNNGNEAAASPPQDSIGGDAADDEIDPLDAFMNSMVLPEVEKLNKVEVPTVNDDKIV 351

Query: 346 ESKKMDRKGDRRSNGEQPKKSSNKSLGRIIPGEDSDSDYGDLENDEKPLEDEDDDEFMKR 405
           E K  D+  D +S G+  ++ SNKS+GRIIPGEDSD+DYGDLEND   LEDEDDDEFMKR
Sbjct: 352 ELKSRDKPSD-QSGGKAQRRISNKSMGRIIPGEDSDTDYGDLENDGDTLEDEDDDEFMKR 410

Query: 406 VKKTKAEKLSIVDHSKIDYQPFRKNFYIEVKEIARMTPEEVSAYRKQLELKIHGKDVPKP 465
           VKKTKAEKLSIVDHSK+DYQPFRKNFYIEVKEI+RMT EEV+AYRKQLELKIHGKDVPKP
Sbjct: 411 VKKTKAEKLSIVDHSKMDYQPFRKNFYIEVKEISRMTLEEVAAYRKQLELKIHGKDVPKP 470

Query: 466 IKTWHQTGLTSKIMETIRKLNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPM 525
           +KTWHQTGLTSKI+ETI+KLNYEKPMPIQAQALP++MSGRDCIG+AKTGSGKTLAFVLPM
Sbjct: 471 VKTWHQTGLTSKILETIKKLNYEKPMPIQAQALPIVMSGRDCIGIAKTGSGKTLAFVLPM 530

Query: 526 LRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQIS 585
           LRHIKDQ PV  GDGP+GLIMAPTRELVQQIHSDI+KF+KVMG+RCVPVYGGSGVAQQIS
Sbjct: 531 LRHIKDQSPVVPGDGPIGLIMAPTRELVQQIHSDIKKFSKVMGLRCVPVYGGSGVAQQIS 590

Query: 586 ELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMGFEPQITRIVQNI 645
           ELKRG EIVVCTPGRMIDILCTS GKITNLRRVTYLVMDEADRMFDMGFEPQITRIVQNI
Sbjct: 591 ELKRGAEIVVCTPGRMIDILCTSAGKITNLRRVTYLVMDEADRMFDMGFEPQITRIVQNI 650

Query: 646 RPDRQTVLFSATFPRQVEILARKVLNKPVEIQVGGRSVVNKDITQLVEVRPESDRFLRLL 705
           RPDRQTVLFSATFPRQVEILARKVLNKPVE+QVGGRSVVNKDI QLVEVRPE++RFLRLL
Sbjct: 651 RPDRQTVLFSATFPRQVEILARKVLNKPVEVQVGGRSVVNKDIAQLVEVRPENERFLRLL 710

Query: 706 ELLGEWYEKGKILIFVHSQEKCDALFRDLLKHGYPCLSLHGAKDQTDRESTISDFKSNVC 765
           ELLGEWYEKGKILIFVHSQEK                    +KDQTDRESTISDFKSNVC
Sbjct: 711 ELLGEWYEKGKILIFVHSQEK--------------------SKDQTDRESTISDFKSNVC 750

Query: 766 NLLIATSVAARGLDVKELELVINFDAPNHYEDYVHRVGRTGRAGRKGCAITFISEEDAKY 825
           NLLIATS+AARGLDVKELELVINFD PNHYEDYVHRVGRTGRAGRKGCAITFI+EED++Y
Sbjct: 751 NLLIATSIAARGLDVKELELVINFDVPNHYEDYVHRVGRTGRAGRKGCAITFIAEEDSRY 810

Query: 826 SPDLVKALELSEQVVPDDLKALADSFMAKVNQGLEQAHGTGYGGSGFKFNEEEDEKRKAA 885
           +PDLVKALELSEQVVPDDL+ALADSFMAKVNQGLEQAHGTGYGGSGFKFNEEEDE R+AA
Sbjct: 811 APDLVKALELSEQVVPDDLRALADSFMAKVNQGLEQAHGTGYGGSGFKFNEEEDEVRRAA 870

Query: 886 KKAQAKEYGFEEDKSDSDDEDEGIRKAGGDIS 917
           KKAQAKEYGFEEDKSDS+DED+G+RKAGGDIS
Sbjct: 871 KKAQAKEYGFEEDKSDSEDEDDGVRKAGGDIS 902

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	976
TAIR|locus:2037416	1166	RCF1 "regulator of CBF gene ex	0.770	0.644	0.703	1.7e-297
TAIR|locus:2074899	989	AT3G09620 [Arabidopsis thalian	0.487	0.481	0.724	2.4e-268
MGI|MGI:1920895	1032	Ddx46 "DEAD (Asp-Glu-Ala-Asp)	0.588	0.556	0.522	9.2e-174
RGD|708480	1032	Ddx46 "DEAD (Asp-Glu-Ala-Asp)	0.588	0.556	0.522	3.1e-173
UNIPROTKB|Q62780	1032	Ddx46 "Probable ATP-dependent	0.588	0.556	0.522	3.1e-173
UNIPROTKB|F1PK90	1032	DDX46 "Uncharacterized protein	0.588	0.556	0.522	1.7e-172
UNIPROTKB|Q7L014	1031	DDX46 "Probable ATP-dependent	0.588	0.556	0.522	1.7e-172
UNIPROTKB|I3LR20	1032	DDX46 "Uncharacterized protein	0.588	0.556	0.522	2.8e-172
UNIPROTKB|F1MX40	1032	DDX46 "Uncharacterized protein	0.588	0.556	0.522	2.8e-172
FB|FBgn0030631	1224	CG6227 [Drosophila melanogaste	0.475	0.379	0.605	2.4e-171

TAIR|locus:2037416 RCF1 "regulator of CBF gene expression 1" [Arabidopsis thaliana (taxid:3702)]

 Score = 2694 (953.4 bits), Expect = 1.7e-297, Sum P(2) = 1.7e-297
 Identities = 541/769 (70%), Positives = 602/769 (78%)

Query:   165 SLSRSNRHRDENDESPRXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXMEKRRRRVQEWQX 224
             S+ RS+RH D    SP+                              +EKRRRRVQEWQ 
Sbjct:   236 SVGRSSRHED----SPKRKSVEDNGEKKEKKTREEELEDEQKKLDEEVEKRRRRVQEWQE 291

Query:   225 XXXXXXXXXXXXXGDANVEEPKAGRNWTLDREDSDDEEVPQTGKSETDMDADEEPKPSEN 284
                          GDA+  EPKAG+ WTL+ E SDDEE     KSET+MD DEE KP EN
Sbjct:   292 LKRKKEEAESESKGDADGNEPKAGKAWTLEGE-SDDEEGHPEEKSETEMDVDEETKP-EN 349

Query:   285 QVGDAMLVDSDGGSAAPALQIG---AAEDEDIDPLDAFMNSMVLPEVEKLKNTVEPSFTD 341
               GDA +VD +  +AA   + G   A ++E+IDPLDAFMN+MVLPEVEK  N   P   +
Sbjct:   350 D-GDAKMVDLENETAATVSESGGDGAVDEEEIDPLDAFMNTMVLPEVEKFCNGAPPPAVN 408

Query:   342 GNNVESKKMDRKGDRRSNGEQPKKSSNKSLGRIIPGEDSDSDYGXXXXXXXXXXXXXXXX 401
                ++SK M+ K     +G++PKK  NK+LGRII GEDSDSDY                 
Sbjct:   409 DGTLDSK-MNGK----ESGDRPKKGFNKALGRIIQGEDSDSDYSEPKNDDDPSLDEDDEE 463

Query:   402 FMKRVKKTKAEKLSIVDHSKIDYQPFRKNFYIEVKEIARMTPEEVSAYRKQLELKIHGKD 461
             FMKRVKKTKAEKLS+VDHSKI+Y+PFRKNFYIEVK+I+RMT EEV+ YRK+LELK+HGKD
Sbjct:   464 FMKRVKKTKAEKLSLVDHSKIEYEPFRKNFYIEVKDISRMTQEEVNTYRKELELKVHGKD 523

Query:   462 VPKPIKTWHQTGLTSKIMETIRKLNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAF 521
             VP+PIK WHQTGLTSKI++T++KLNYEKPMPIQ QALP+IMSGRDCIGVAKTGSGKTL F
Sbjct:   524 VPRPIKFWHQTGLTSKILDTMKKLNYEKPMPIQTQALPIIMSGRDCIGVAKTGSGKTLGF 583

Query:   522 VLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVA 581
             VLPMLRHIKDQPPV AGDGP+GL+MAPTRELVQQIHSDIRKF+K +G+RCVPVYGGSGVA
Sbjct:   584 VLPMLRHIKDQPPVEAGDGPIGLVMAPTRELVQQIHSDIRKFSKPLGIRCVPVYGGSGVA 643

Query:   582 QQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMGFEPQITRI 641
             QQISELKRGTEIVVCTPGRMIDILCTS GKITNLRRVT+LVMDEADRMFDMGFEPQITRI
Sbjct:   644 QQISELKRGTEIVVCTPGRMIDILCTSSGKITNLRRVTFLVMDEADRMFDMGFEPQITRI 703

Query:   642 VQNIRPDRQTVLFSATFPRQVEILARKVLNKPVEIQVGGRSVVNKDITQLVEVRPESDRF 701
             +QNIRP+RQTVLFSATFPRQVE LARKVLNKPVEIQVGGRSVVNKDITQLVEVRPESDRF
Sbjct:   704 IQNIRPERQTVLFSATFPRQVETLARKVLNKPVEIQVGGRSVVNKDITQLVEVRPESDRF 763

Query:   702 LRLLELLGEWYEKGKILIFVHSQEKCDALFRDLLKHGYPCLSLHGAKDQTDRESTISDFK 761
             LRLLELLGEW EKGKIL+FV SQEKCDAL+RD++K  YPCLSLHG KDQTDRESTISDFK
Sbjct:   764 LRLLELLGEWSEKGKILVFVQSQEKCDALYRDMIKSSYPCLSLHGGKDQTDRESTISDFK 823

Query:   762 SNVCNLLIATSVAARGLDVKELELVINFDAPNHYEDYVHRVGRTGRAGRKGCAITFISEE 821
             ++VCNLLIATSVAARGLDVKELELV+NFDAPNHYEDYVHRVGRTGRAGRKGCA+TFISE+
Sbjct:   824 NDVCNLLIATSVAARGLDVKELELVVNFDAPNHYEDYVHRVGRTGRAGRKGCAVTFISED 883

Query:   822 DAKYSPDLVKALELSEQVVPDDLKALADSFMAKVNQGLEQAHGTGYGGSGFKFNXXXXXX 881
             DAKY+PDLVKALELSEQ VPDDLKALAD FM KV QG+EQAHGTGYGGSGFKFN      
Sbjct:   884 DAKYAPDLVKALELSEQPVPDDLKALADGFMVKVKQGIEQAHGTGYGGSGFKFNEEEEEV 943

Query:   882 XXXXXXXXXXXYGFXXXXXXXXXXXXGIRKAGG-DISQQDA-LAKISAI 928
                        YGF             +RKAGG +ISQQ A  A+I+AI
Sbjct:   944 RKAAKKAQAKEYGFEEDKSDSEDENDVVRKAGGGEISQQQATFAQIAAI 992

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0004386 "helicase activity" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISM

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

TAIR|locus:2074899 AT3G09620 [Arabidopsis thaliana (taxid:3702)]

 Score = 1785 (633.4 bits), Expect = 2.4e-268, Sum P(3) = 2.4e-268
 Identities = 362/500 (72%), Positives = 412/500 (82%)

Query:   239 DANVEE--PKAGRNWTLDREDSDDEEVPQTGKSETDMDADEEPKPSENQVGDAMLVDSDG 296
             +A +E   P+ G+ WTLD E SDDE      KS+++MD D + K  EN  GDA +V S+ 
Sbjct:   180 EAQIESKGPETGKAWTLDGE-SDDEV-----KSDSEMDVDRDTK-LENG-GDAKMVASEN 231

Query:   297 GSAAPALQIG---AAEDEDIDPLDAFMNSMVLPEVEKLKNTVEPSFTDGNNVESKKMDRK 353
              +A    + G   AA++++IDPLDAFMN+MVLPEVEKL N V     DG       +D K
Sbjct:   232 ETAVTVSENGGDRAADEDEIDPLDAFMNTMVLPEVEKLSNIV----IDGI------LDFK 281

Query:   354 GDRRSNGEQPKKSSNKS-LGRIIPGEDSDSDYGXXXXXXXXXXXXXXXXFMKRVKKTKAE 412
              + +  G+Q KK  NK+ LGRII GEDSDSDY                 FMKRVKKTKAE
Sbjct:   282 MNGKETGDQAKKGFNKAALGRIIQGEDSDSDYSEPKSDDDPSLDEDDEEFMKRVKKTKAE 341

Query:   413 KLSIVDHSKIDYQPFRKNFYIEVKEIARMTPEEVSAYRKQLELKIHGKDVPKPIKTWHQT 472
             KLS+VDHSKI+Y+PFRKNFYIEVK+I+RMT + V+AYRK+LELK+HGKDVP+PI+ WHQT
Sbjct:   342 KLSLVDHSKIEYEPFRKNFYIEVKDISRMTQDAVNAYRKELELKVHGKDVPRPIQFWHQT 401

Query:   473 GLTSKIMETIRKLNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQ 532
             GLTSKI++T++KLNYEKPMPIQAQALP+IMSGRDCIGVAKTGSGKTL FVLPMLRHIKDQ
Sbjct:   402 GLTSKILDTLKKLNYEKPMPIQAQALPIIMSGRDCIGVAKTGSGKTLGFVLPMLRHIKDQ 461

Query:   533 PPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQISELKRGTE 592
             PPV AGDGP+GL+MAPTRELVQQI+SDIRKF+K +G+ CVPVYGGSGVAQQISELKRGTE
Sbjct:   462 PPVEAGDGPIGLVMAPTRELVQQIYSDIRKFSKALGIICVPVYGGSGVAQQISELKRGTE 521

Query:   593 IVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMGFEPQITRIVQNIRPDRQTV 652
             IVVCTPGRMIDILCTS GKITNLRRVTYLVMDEADRMFDMGFEPQITRIVQNIRPDRQTV
Sbjct:   522 IVVCTPGRMIDILCTSSGKITNLRRVTYLVMDEADRMFDMGFEPQITRIVQNIRPDRQTV 581

Query:   653 LFSATFPRQVEILARKVLNKPVEIQVGGRSVVNKDITQLVEVRPESDRFLRLLELLGEWY 712
             LFSATFPRQVE LARKVLNKPVEIQVGGRSVVNKDITQLVE+RPES+RF RLLELLGEWY
Sbjct:   582 LFSATFPRQVETLARKVLNKPVEIQVGGRSVVNKDITQLVEIRPESERFSRLLELLGEWY 641

Query:   713 EKGKILIFVHSQEKCDALFR 732
             EKGK+L+FV SQEK  + F+
Sbjct:   642 EKGKVLVFVRSQEKSISDFK 661

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0004386 "helicase activity" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISM

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

MGI|MGI:1920895 Ddx46 "DEAD (Asp-Glu-Ala-Asp) box polypeptide 46" [Mus musculus (taxid:10090)]

 Score = 1544 (548.6 bits), Expect = 9.2e-174, Sum P(3) = 9.2e-174
 Identities = 307/587 (52%), Positives = 403/587 (68%)

Query:   293 DSDGGSAAPALQIGAA-EDEDIDPLDAFMNSMVLPEVEKLKNTVEPSFTDGNNVESKKMD 351
             D D    A A + G   EDE++DPLDA+M   V  EV+K  N        GN  +S    
Sbjct:   204 DDDEDDPAEAEKEGTEMEDEELDPLDAYMEE-VKEEVKKF-NMRSVKGGAGNEKKSGPTV 261

Query:   352 RKGDRRSNGEQPKKSSNKSLGRIIPGEDSDSDYGXXXXXXXXXXXXXXXXFMKRVKKTKA 411
              K       ++    ++K  G ++  +    +Y                       +TK 
Sbjct:   262 TKVVTVVTTKKAVVDADKKKGELMENDQDAMEYSSEEEEVDLQTALTGY-------QTKQ 314

Query:   412 EKL-SIVDHSKIDYQPFRKNFYIEVKEIARMTPEEVSAYRKQLE-LKIHGKDVPKPIKTW 469
              KL   VDH KI+Y+PFRKNFY+EV E+A+M+ EEV+ +R ++E + + GK  PKPIK+W
Sbjct:   315 RKLLEPVDHGKIEYEPFRKNFYVEVPELAKMSQEEVNVFRLEMEGITVKGKGCPKPIKSW 374

Query:   470 HQTGLTSKIMETIRKLNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHI 529
              Q G++ KI+ +++K  YEKP PIQ QA+P IMSGRD IG+AKTGSGKT+AF+LPM RHI
Sbjct:   375 VQCGISMKILNSLKKHGYEKPTPIQTQAIPAIMSGRDLIGIAKTGSGKTIAFLLPMFRHI 434

Query:   530 KDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQISELKR 589
              DQ  +  G+GP+ +IM PTREL  QI  + +KF+K +G+R V VYGG+G+++QI+ELKR
Sbjct:   435 MDQRSLEEGEGPIAVIMTPTRELALQITKECKKFSKTLGLRVVCVYGGTGISEQIAELKR 494

Query:   590 GTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMGFEPQITRIVQNIRPDR 649
             G EI+VCTPGRMID+L  + G++TNLRRVTY+V+DEADRMFDMGFEPQ+ RIV N+RPDR
Sbjct:   495 GAEIIVCTPGRMIDMLAANSGRVTNLRRVTYVVLDEADRMFDMGFEPQVMRIVDNVRPDR 554

Query:   650 QTVLFSATFPRQVEILARKVLNKPVEIQVGGRSVVNKDITQLVEVRPESDRFLRLLELLG 709
             QTV+FSATFPR +E LAR++L+KP+E+QVGGRSVV  D+ Q V V  E  +FL+LLELLG
Sbjct:   555 QTVMFSATFPRAMEALARRILSKPIEVQVGGRSVVCSDVEQQVIVIEEEKKFLKLLELLG 614

Query:   710 EWYEKGKILIFVHSQEKCDALFRDLLKHGYPCLSLHGAKDQTDRESTISDFKSNVCNLLI 769
              + E G ++IFV  QE  D L +DL++  YPC+SLHG  DQ DR+S I+DFK+  C LL+
Sbjct:   615 HYQESGSVIIFVDKQEHADGLLKDLMRASYPCMSLHGGIDQYDRDSIINDFKNGTCKLLV 674

Query:   770 ATSVAARGLDVKELELVINFDAPNHYEDYVHRVGRTGRAGRKGCAITFISEEDAKYSPDL 829
             ATSVAARGLDVK L LV+N+  PNHYEDYVHR GRTGRAG KG A TFI+E+ A+Y+ D+
Sbjct:   675 ATSVAARGLDVKHLILVVNYSCPNHYEDYVHRAGRTGRAGNKGYAYTFITEDQARYAGDI 734

Query:   830 VKALELSEQVVPDDLKALADSFMAKVN-QGLEQAHGTGYGGSGFKFN 875
             +KALELS   VP DL+ L   F  +   +G      +G+ G GFKF+
Sbjct:   735 IKALELSGTAVPPDLEKLWSDFKDQQKAEGKIIKKSSGFSGKGFKFD 781

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0004386 "helicase activity" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISO

GO:0006397 "mRNA processing" evidence=IEA

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

GO:0008380 "RNA splicing" evidence=IEA

GO:0016787 "hydrolase activity" evidence=IEA

RGD|708480 Ddx46 "DEAD (Asp-Glu-Ala-Asp) box polypeptide 46" [Rattus norvegicus (taxid:10116)]

 Score = 1543 (548.2 bits), Expect = 3.1e-173, Sum P(3) = 3.1e-173
 Identities = 307/587 (52%), Positives = 403/587 (68%)

Query:   293 DSDGGSAAPALQIG-AAEDEDIDPLDAFMNSMVLPEVEKLKNTVEPSFTDGNNVESKKMD 351
             D D    A A + G   EDE++DPLDA+M   V  EV+K  N        GN  +S    
Sbjct:   204 DDDEDDPAEAEKEGNEMEDEELDPLDAYMEE-VKEEVKKF-NMRSVKGGAGNEKKSGPTV 261

Query:   352 RKGDRRSNGEQPKKSSNKSLGRIIPGEDSDSDYGXXXXXXXXXXXXXXXXFMKRVKKTKA 411
              K       ++    ++K  G ++  +    +Y                       +TK 
Sbjct:   262 TKVVTVVTTKKAVVDADKKKGELMENDQDAMEYSSEEEEVDLQTALTGY-------QTKQ 314

Query:   412 EKL-SIVDHSKIDYQPFRKNFYIEVKEIARMTPEEVSAYRKQLE-LKIHGKDVPKPIKTW 469
              KL   VDH KI+Y+PFRKNFY+EV E+A+M+ EEV+ +R ++E + + GK  PKPIK+W
Sbjct:   315 RKLLEPVDHGKIEYEPFRKNFYVEVPELAKMSQEEVNVFRLEMEGITVKGKGCPKPIKSW 374

Query:   470 HQTGLTSKIMETIRKLNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHI 529
              Q G++ KI+ +++K  YEKP PIQ QA+P IMSGRD IG+AKTGSGKT+AF+LPM RHI
Sbjct:   375 VQCGISMKILNSLKKHGYEKPTPIQTQAIPAIMSGRDLIGIAKTGSGKTIAFLLPMFRHI 434

Query:   530 KDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQISELKR 589
              DQ  +  G+GP+ +IM PTREL  QI  + +KF+K +G+R V VYGG+G+++QI+ELKR
Sbjct:   435 MDQRSLEEGEGPIAVIMTPTRELALQITKECKKFSKTLGLRVVCVYGGTGISEQIAELKR 494

Query:   590 GTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMGFEPQITRIVQNIRPDR 649
             G EI+VCTPGRMID+L  + G++TNLRRVTY+V+DEADRMFDMGFEPQ+ RIV N+RPDR
Sbjct:   495 GAEIIVCTPGRMIDMLAANSGRVTNLRRVTYVVLDEADRMFDMGFEPQVMRIVDNVRPDR 554

Query:   650 QTVLFSATFPRQVEILARKVLNKPVEIQVGGRSVVNKDITQLVEVRPESDRFLRLLELLG 709
             QTV+FSATFPR +E LAR++L+KP+E+QVGGRSVV  D+ Q V V  E  +FL+LLELLG
Sbjct:   555 QTVMFSATFPRAMEALARRILSKPIEVQVGGRSVVCSDVEQQVIVIEEEKKFLKLLELLG 614

Query:   710 EWYEKGKILIFVHSQEKCDALFRDLLKHGYPCLSLHGAKDQTDRESTISDFKSNVCNLLI 769
              + E G ++IFV  QE  D L +DL++  YPC+SLHG  DQ DR+S I+DFK+  C LL+
Sbjct:   615 HYQESGSVIIFVDKQEHADGLLKDLMRASYPCMSLHGGIDQYDRDSIINDFKNGTCKLLV 674

Query:   770 ATSVAARGLDVKELELVINFDAPNHYEDYVHRVGRTGRAGRKGCAITFISEEDAKYSPDL 829
             ATSVAARGLDVK L LV+N+  PNHYEDYVHR GRTGRAG KG A TFI+E+ A+Y+ D+
Sbjct:   675 ATSVAARGLDVKHLILVVNYSCPNHYEDYVHRAGRTGRAGNKGYAYTFITEDQARYAGDI 734

Query:   830 VKALELSEQVVPDDLKALADSFMAKVN-QGLEQAHGTGYGGSGFKFN 875
             +KALELS   VP DL+ L   F  +   +G      +G+ G GFKF+
Sbjct:   735 IKALELSGTAVPPDLEKLWSDFKDQQKAEGKIIKKSSGFSGKGFKFD 781

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISO;IDA

GO:0005730 "nucleolus" evidence=IEA;ISO

GO:0006397 "mRNA processing" evidence=IEA

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

GO:0008380 "RNA splicing" evidence=IEA

GO:0015030 "Cajal body" evidence=IEA

GO:0016607 "nuclear speck" evidence=IEA

UNIPROTKB|Q62780 Ddx46 "Probable ATP-dependent RNA helicase DDX46" [Rattus norvegicus (taxid:10116)]

 Score = 1543 (548.2 bits), Expect = 3.1e-173, Sum P(3) = 3.1e-173
 Identities = 307/587 (52%), Positives = 403/587 (68%)

Query:   293 DSDGGSAAPALQIG-AAEDEDIDPLDAFMNSMVLPEVEKLKNTVEPSFTDGNNVESKKMD 351
             D D    A A + G   EDE++DPLDA+M   V  EV+K  N        GN  +S    
Sbjct:   204 DDDEDDPAEAEKEGNEMEDEELDPLDAYMEE-VKEEVKKF-NMRSVKGGAGNEKKSGPTV 261

Query:   352 RKGDRRSNGEQPKKSSNKSLGRIIPGEDSDSDYGXXXXXXXXXXXXXXXXFMKRVKKTKA 411
              K       ++    ++K  G ++  +    +Y                       +TK 
Sbjct:   262 TKVVTVVTTKKAVVDADKKKGELMENDQDAMEYSSEEEEVDLQTALTGY-------QTKQ 314

Query:   412 EKL-SIVDHSKIDYQPFRKNFYIEVKEIARMTPEEVSAYRKQLE-LKIHGKDVPKPIKTW 469
              KL   VDH KI+Y+PFRKNFY+EV E+A+M+ EEV+ +R ++E + + GK  PKPIK+W
Sbjct:   315 RKLLEPVDHGKIEYEPFRKNFYVEVPELAKMSQEEVNVFRLEMEGITVKGKGCPKPIKSW 374

Query:   470 HQTGLTSKIMETIRKLNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHI 529
              Q G++ KI+ +++K  YEKP PIQ QA+P IMSGRD IG+AKTGSGKT+AF+LPM RHI
Sbjct:   375 VQCGISMKILNSLKKHGYEKPTPIQTQAIPAIMSGRDLIGIAKTGSGKTIAFLLPMFRHI 434

Query:   530 KDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQISELKR 589
              DQ  +  G+GP+ +IM PTREL  QI  + +KF+K +G+R V VYGG+G+++QI+ELKR
Sbjct:   435 MDQRSLEEGEGPIAVIMTPTRELALQITKECKKFSKTLGLRVVCVYGGTGISEQIAELKR 494

Query:   590 GTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMGFEPQITRIVQNIRPDR 649
             G EI+VCTPGRMID+L  + G++TNLRRVTY+V+DEADRMFDMGFEPQ+ RIV N+RPDR
Sbjct:   495 GAEIIVCTPGRMIDMLAANSGRVTNLRRVTYVVLDEADRMFDMGFEPQVMRIVDNVRPDR 554

Query:   650 QTVLFSATFPRQVEILARKVLNKPVEIQVGGRSVVNKDITQLVEVRPESDRFLRLLELLG 709
             QTV+FSATFPR +E LAR++L+KP+E+QVGGRSVV  D+ Q V V  E  +FL+LLELLG
Sbjct:   555 QTVMFSATFPRAMEALARRILSKPIEVQVGGRSVVCSDVEQQVIVIEEEKKFLKLLELLG 614

Query:   710 EWYEKGKILIFVHSQEKCDALFRDLLKHGYPCLSLHGAKDQTDRESTISDFKSNVCNLLI 769
              + E G ++IFV  QE  D L +DL++  YPC+SLHG  DQ DR+S I+DFK+  C LL+
Sbjct:   615 HYQESGSVIIFVDKQEHADGLLKDLMRASYPCMSLHGGIDQYDRDSIINDFKNGTCKLLV 674

Query:   770 ATSVAARGLDVKELELVINFDAPNHYEDYVHRVGRTGRAGRKGCAITFISEEDAKYSPDL 829
             ATSVAARGLDVK L LV+N+  PNHYEDYVHR GRTGRAG KG A TFI+E+ A+Y+ D+
Sbjct:   675 ATSVAARGLDVKHLILVVNYSCPNHYEDYVHRAGRTGRAGNKGYAYTFITEDQARYAGDI 734

Query:   830 VKALELSEQVVPDDLKALADSFMAKVN-QGLEQAHGTGYGGSGFKFN 875
             +KALELS   VP DL+ L   F  +   +G      +G+ G GFKF+
Sbjct:   735 IKALELSGTAVPPDLEKLWSDFKDQQKAEGKIIKKSSGFSGKGFKFD 781

GO:0005524 "ATP binding" evidence=IEA

UNIPROTKB|F1PK90 DDX46 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 1540 (547.2 bits), Expect = 1.7e-172, Sum P(3) = 1.7e-172
 Identities = 307/587 (52%), Positives = 402/587 (68%)

Query:   293 DSDGGSAAPALQIG-AAEDEDIDPLDAFMNSMVLPEVEKLKNTVEPSFTDGNNVESKKMD 351
             D D    A A + G   E E++DPLDA+M   V  EV+K  N        GN  +S    
Sbjct:   204 DDDEDDPAEAEKEGNEMEGEELDPLDAYMEE-VKEEVKKF-NMRSVKGGGGNEKKSGPTV 261

Query:   352 RKGDRRSNGEQPKKSSNKSLGRIIPGEDSDSDYGXXXXXXXXXXXXXXXXFMKRVKKTKA 411
              K       ++    S+K  G ++  +    +Y                       +TK 
Sbjct:   262 TKVVTVVTTKKAVVDSDKKKGELMENDQDAMEYSSEEEEVDLQTALTGY-------QTKQ 314

Query:   412 EKL-SIVDHSKIDYQPFRKNFYIEVKEIARMTPEEVSAYRKQLE-LKIHGKDVPKPIKTW 469
              KL   VDH KI+Y+PFRKNFY+EV E+A+M+ EEV+ +R ++E + + GK  PKPIK+W
Sbjct:   315 RKLLEPVDHGKIEYEPFRKNFYVEVPELAKMSQEEVNVFRLEMEGITVKGKGCPKPIKSW 374

Query:   470 HQTGLTSKIMETIRKLNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHI 529
              Q G++ KI+ +++K  YEKP PIQ QA+P IMSGRD IG+AKTGSGKT+AF+LPM RHI
Sbjct:   375 VQCGISMKILNSLKKHGYEKPTPIQTQAIPAIMSGRDLIGIAKTGSGKTIAFLLPMFRHI 434

Query:   530 KDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQISELKR 589
              DQ  +  G+GP+ +IM PTREL  QI  + +KF+K +G+R V VYGG+G+++QI+ELKR
Sbjct:   435 MDQRSLEEGEGPIAVIMTPTRELALQITKECKKFSKTLGLRVVCVYGGTGISEQIAELKR 494

Query:   590 GTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMGFEPQITRIVQNIRPDR 649
             G EI+VCTPGRMID+L  + G++TNLRRVTY+V+DEADRMFDMGFEPQ+ RIV N+RPDR
Sbjct:   495 GAEIIVCTPGRMIDMLAANSGRVTNLRRVTYVVLDEADRMFDMGFEPQVMRIVDNVRPDR 554

Query:   650 QTVLFSATFPRQVEILARKVLNKPVEIQVGGRSVVNKDITQLVEVRPESDRFLRLLELLG 709
             QTV+FSATFPR +E LAR++L+KP+E+QVGGRSVV  D+ Q V V  E  +FL+LLELLG
Sbjct:   555 QTVMFSATFPRAMEALARRILSKPIEVQVGGRSVVCSDVEQQVIVIEEEKKFLKLLELLG 614

Query:   710 EWYEKGKILIFVHSQEKCDALFRDLLKHGYPCLSLHGAKDQTDRESTISDFKSNVCNLLI 769
              + E G ++IFV  QE  D L +DL++  YPC+SLHG  DQ DR+S I+DFK+  C LL+
Sbjct:   615 HYQESGSVIIFVDKQEHADGLLKDLMRASYPCMSLHGGIDQYDRDSIINDFKNGTCKLLV 674

Query:   770 ATSVAARGLDVKELELVINFDAPNHYEDYVHRVGRTGRAGRKGCAITFISEEDAKYSPDL 829
             ATSVAARGLDVK L LV+N+  PNHYEDYVHR GRTGRAG KG A TFI+E+ A+Y+ D+
Sbjct:   675 ATSVAARGLDVKHLILVVNYSCPNHYEDYVHRAGRTGRAGNKGYAYTFITEDQARYAGDI 734

Query:   830 VKALELSEQVVPDDLKALADSFMAKVN-QGLEQAHGTGYGGSGFKFN 875
             +KALELS   VP DL+ L   F  +   +G      +G+ G GFKF+
Sbjct:   735 IKALELSGTAVPPDLEKLWSDFKDQQKAEGKIIKKSSGFSGKGFKFD 781

GO:0005524 "ATP binding" evidence=IEA

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

GO:0003676 "nucleic acid binding" evidence=IEA

UNIPROTKB|Q7L014 DDX46 "Probable ATP-dependent RNA helicase DDX46" [Homo sapiens (taxid:9606)]

 Score = 1540 (547.2 bits), Expect = 1.7e-172, Sum P(3) = 1.7e-172
 Identities = 307/587 (52%), Positives = 402/587 (68%)

Query:   293 DSDGGSAAPALQIG-AAEDEDIDPLDAFMNSMVLPEVEKLKNTVEPSFTDGNNVESKKMD 351
             D D    A A + G   E E++DPLDA+M   V  EV+K  N        GN  +S    
Sbjct:   204 DDDEDDPAEAEKEGNEMEGEELDPLDAYMEE-VKEEVKKF-NMRSVKGGGGNEKKSGPTV 261

Query:   352 RKGDRRSNGEQPKKSSNKSLGRIIPGEDSDSDYGXXXXXXXXXXXXXXXXFMKRVKKTKA 411
              K       ++    S+K  G ++  +    +Y                       +TK 
Sbjct:   262 TKVVTVVTTKKAVVDSDKKKGELMENDQDAMEYSSEEEEVDLQTALTGY-------QTKQ 314

Query:   412 EKL-SIVDHSKIDYQPFRKNFYIEVKEIARMTPEEVSAYRKQLE-LKIHGKDVPKPIKTW 469
              KL   VDH KI+Y+PFRKNFY+EV E+A+M+ EEV+ +R ++E + + GK  PKPIK+W
Sbjct:   315 RKLLEPVDHGKIEYEPFRKNFYVEVPELAKMSQEEVNVFRLEMEGITVKGKGCPKPIKSW 374

Query:   470 HQTGLTSKIMETIRKLNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHI 529
              Q G++ KI+ +++K  YEKP PIQ QA+P IMSGRD IG+AKTGSGKT+AF+LPM RHI
Sbjct:   375 VQCGISMKILNSLKKHGYEKPTPIQTQAIPAIMSGRDLIGIAKTGSGKTIAFLLPMFRHI 434

Query:   530 KDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQISELKR 589
              DQ  +  G+GP+ +IM PTREL  QI  + +KF+K +G+R V VYGG+G+++QI+ELKR
Sbjct:   435 MDQRSLEEGEGPIAVIMTPTRELALQITKECKKFSKTLGLRVVCVYGGTGISEQIAELKR 494

Query:   590 GTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMGFEPQITRIVQNIRPDR 649
             G EI+VCTPGRMID+L  + G++TNLRRVTY+V+DEADRMFDMGFEPQ+ RIV N+RPDR
Sbjct:   495 GAEIIVCTPGRMIDMLAANSGRVTNLRRVTYVVLDEADRMFDMGFEPQVMRIVDNVRPDR 554

Query:   650 QTVLFSATFPRQVEILARKVLNKPVEIQVGGRSVVNKDITQLVEVRPESDRFLRLLELLG 709
             QTV+FSATFPR +E LAR++L+KP+E+QVGGRSVV  D+ Q V V  E  +FL+LLELLG
Sbjct:   555 QTVMFSATFPRAMEALARRILSKPIEVQVGGRSVVCSDVEQQVIVIEEEKKFLKLLELLG 614

Query:   710 EWYEKGKILIFVHSQEKCDALFRDLLKHGYPCLSLHGAKDQTDRESTISDFKSNVCNLLI 769
              + E G ++IFV  QE  D L +DL++  YPC+SLHG  DQ DR+S I+DFK+  C LL+
Sbjct:   615 HYQESGSVIIFVDKQEHADGLLKDLMRASYPCMSLHGGIDQYDRDSIINDFKNGTCKLLV 674

Query:   770 ATSVAARGLDVKELELVINFDAPNHYEDYVHRVGRTGRAGRKGCAITFISEEDAKYSPDL 829
             ATSVAARGLDVK L LV+N+  PNHYEDYVHR GRTGRAG KG A TFI+E+ A+Y+ D+
Sbjct:   675 ATSVAARGLDVKHLILVVNYSCPNHYEDYVHRAGRTGRAGNKGYAYTFITEDQARYAGDI 734

Query:   830 VKALELSEQVVPDDLKALADSFMAKVN-QGLEQAHGTGYGGSGFKFN 875
             +KALELS   VP DL+ L   F  +   +G      +G+ G GFKF+
Sbjct:   735 IKALELSGTAVPPDLEKLWSDFKDQQKAEGKIIKKSSGFSGKGFKFD 781

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

GO:0003723 "RNA binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0006397 "mRNA processing" evidence=IEA

GO:0008380 "RNA splicing" evidence=IEA

GO:0015030 "Cajal body" evidence=IEA

GO:0016607 "nuclear speck" evidence=IEA

GO:0005634 "nucleus" evidence=IDA

GO:0005730 "nucleolus" evidence=IDA

UNIPROTKB|I3LR20 DDX46 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 1541 (547.5 bits), Expect = 2.8e-172, Sum P(3) = 2.8e-172
 Identities = 307/587 (52%), Positives = 402/587 (68%)

Query:   293 DSDGGSAAPALQIG-AAEDEDIDPLDAFMNSMVLPEVEKLKNTVEPSFTDGNNVESKKMD 351
             D D    A A + G   E E++DPLDA+M   V  EV+K  N        GN  +S    
Sbjct:   204 DDDEDDPAEAEKEGNEVEGEELDPLDAYMEE-VKEEVKKF-NMRSVKGGGGNEKKSGPTV 261

Query:   352 RKGDRRSNGEQPKKSSNKSLGRIIPGEDSDSDYGXXXXXXXXXXXXXXXXFMKRVKKTKA 411
              K       ++    S+K  G ++  +    +Y                       +TK 
Sbjct:   262 TKVVTVVTTKKAVVDSDKKKGELMENDQDAMEYSSEEEEVDLQTALTGY-------QTKQ 314

Query:   412 EKL-SIVDHSKIDYQPFRKNFYIEVKEIARMTPEEVSAYRKQLE-LKIHGKDVPKPIKTW 469
              KL   VDH KI+Y+PFRKNFY+EV E+A+M+ EEV+ +R ++E + + GK  PKPIK+W
Sbjct:   315 RKLLEPVDHGKIEYEPFRKNFYVEVPELAKMSQEEVNVFRLEMEGITVKGKGCPKPIKSW 374

Query:   470 HQTGLTSKIMETIRKLNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHI 529
              Q G++ KI+ +++K  YEKP PIQ QA+P IMSGRD IG+AKTGSGKT+AF+LPM RHI
Sbjct:   375 VQCGISMKILNSLKKHGYEKPTPIQTQAIPAIMSGRDLIGIAKTGSGKTIAFLLPMFRHI 434

Query:   530 KDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQISELKR 589
              DQ  +  G+GP+ +IM PTREL  QI  + +KF+K +G+R V VYGG+G+++QI+ELKR
Sbjct:   435 MDQRSLEEGEGPIAVIMTPTRELALQITKECKKFSKTLGLRVVCVYGGTGISEQIAELKR 494

Query:   590 GTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMGFEPQITRIVQNIRPDR 649
             G EI+VCTPGRMID+L  + G++TNLRRVTY+V+DEADRMFDMGFEPQ+ RIV N+RPDR
Sbjct:   495 GAEIIVCTPGRMIDMLAANSGRVTNLRRVTYVVLDEADRMFDMGFEPQVMRIVDNVRPDR 554

Query:   650 QTVLFSATFPRQVEILARKVLNKPVEIQVGGRSVVNKDITQLVEVRPESDRFLRLLELLG 709
             QTV+FSATFPR +E LAR++L+KP+E+QVGGRSVV  D+ Q V V  E  +FL+LLELLG
Sbjct:   555 QTVMFSATFPRAMEALARRILSKPIEVQVGGRSVVCSDVEQQVIVIEEEKKFLKLLELLG 614

Query:   710 EWYEKGKILIFVHSQEKCDALFRDLLKHGYPCLSLHGAKDQTDRESTISDFKSNVCNLLI 769
              + E G ++IFV  QE  D L +DL++  YPC+SLHG  DQ DR+S I+DFK+  C LL+
Sbjct:   615 HYQESGSVIIFVDKQEHADGLLKDLMRASYPCMSLHGGIDQYDRDSIINDFKNGTCKLLV 674

Query:   770 ATSVAARGLDVKELELVINFDAPNHYEDYVHRVGRTGRAGRKGCAITFISEEDAKYSPDL 829
             ATSVAARGLDVK L LV+N+  PNHYEDYVHR GRTGRAG KG A TFI+E+ A+Y+ D+
Sbjct:   675 ATSVAARGLDVKHLILVVNYSCPNHYEDYVHRAGRTGRAGNKGYAYTFITEDQARYAGDI 734

Query:   830 VKALELSEQVVPDDLKALADSFMAKVN-QGLEQAHGTGYGGSGFKFN 875
             +KALELS   VP DL+ L   F  +   +G      +G+ G GFKF+
Sbjct:   735 IKALELSGTAVPPDLEKLWSDFKDQQKAEGKIIKKSSGFSGKGFKFD 781

GO:0005730 "nucleolus" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

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

GO:0003676 "nucleic acid binding" evidence=IEA

UNIPROTKB|F1MX40 DDX46 "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 1538 (546.5 bits), Expect = 2.8e-172, Sum P(3) = 2.8e-172
 Identities = 307/587 (52%), Positives = 402/587 (68%)

Query:   293 DSDGGSAAPALQIG-AAEDEDIDPLDAFMNSMVLPEVEKLKNTVEPSFTDGNNVESKKMD 351
             D D    A A + G   E E++DPLDA+M   V  EV+K  N        GN  +S    
Sbjct:   204 DDDEDDPAEAEKEGNEMEGEELDPLDAYMEE-VKEEVKKF-NMRSVKGGGGNEKKSGPTV 261

Query:   352 RKGDRRSNGEQPKKSSNKSLGRIIPGEDSDSDYGXXXXXXXXXXXXXXXXFMKRVKKTKA 411
              K       ++    S+K  G ++  +    +Y                       +TK 
Sbjct:   262 TKVVTVVTTKKAVVDSDKKKGELMENDQDAMEYSSEEEEVDLQTALTGY-------QTKQ 314

Query:   412 EKL-SIVDHSKIDYQPFRKNFYIEVKEIARMTPEEVSAYRKQLE-LKIHGKDVPKPIKTW 469
              KL   VDH KI+Y+PFRKNFY+EV E+A+M+ EEV+ +R ++E + + GK  PKPIK+W
Sbjct:   315 RKLLEPVDHGKIEYEPFRKNFYVEVPELAKMSLEEVNVFRLEMEGITVKGKGCPKPIKSW 374

Query:   470 HQTGLTSKIMETIRKLNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHI 529
              Q G++ KI+ +++K  YEKP PIQ QA+P IMSGRD IG+AKTGSGKT+AF+LPM RHI
Sbjct:   375 VQCGISMKILNSLKKHGYEKPTPIQTQAIPAIMSGRDLIGIAKTGSGKTIAFLLPMFRHI 434

Query:   530 KDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQISELKR 589
              DQ  +  G+GP+ +IM PTREL  QI  + +KF+K +G+R V VYGG+G+++QI+ELKR
Sbjct:   435 MDQRSLEEGEGPIAVIMTPTRELALQITKECKKFSKTLGLRVVCVYGGTGISEQIAELKR 494

Query:   590 GTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMGFEPQITRIVQNIRPDR 649
             G EI+VCTPGRMID+L  + G++TNLRRVTY+V+DEADRMFDMGFEPQ+ RIV N+RPDR
Sbjct:   495 GAEIIVCTPGRMIDMLAANSGRVTNLRRVTYVVLDEADRMFDMGFEPQVMRIVDNVRPDR 554

Query:   650 QTVLFSATFPRQVEILARKVLNKPVEIQVGGRSVVNKDITQLVEVRPESDRFLRLLELLG 709
             QTV+FSATFPR +E LAR++L+KP+E+QVGGRSVV  D+ Q V V  E  +FL+LLELLG
Sbjct:   555 QTVMFSATFPRAMEALARRILSKPIEVQVGGRSVVCSDVEQQVIVIEEEKKFLKLLELLG 614

Query:   710 EWYEKGKILIFVHSQEKCDALFRDLLKHGYPCLSLHGAKDQTDRESTISDFKSNVCNLLI 769
              + E G ++IFV  QE  D L +DL++  YPC+SLHG  DQ DR+S I+DFK+  C LL+
Sbjct:   615 HYQESGSVIIFVDKQEHADGLLKDLMRASYPCMSLHGGIDQYDRDSIINDFKNGTCKLLV 674

Query:   770 ATSVAARGLDVKELELVINFDAPNHYEDYVHRVGRTGRAGRKGCAITFISEEDAKYSPDL 829
             ATSVAARGLDVK L LV+N+  PNHYEDYVHR GRTGRAG KG A TFI+E+ A+Y+ D+
Sbjct:   675 ATSVAARGLDVKHLILVVNYSCPNHYEDYVHRAGRTGRAGNKGYAYTFITEDQARYAGDI 734

Query:   830 VKALELSEQVVPDDLKALADSFMAKVN-QGLEQAHGTGYGGSGFKFN 875
             +KALELS   VP DL+ L   F  +   +G      +G+ G GFKF+
Sbjct:   735 IKALELSGTAVPPDLEKLWSDFKDQQKAEGKIIKKSSGFSGKGFKFD 781

GO:0005730 "nucleolus" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

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

GO:0003676 "nucleic acid binding" evidence=IEA

FB|FBgn0030631 CG6227 [Drosophila melanogaster (taxid:7227)]

 Score = 1511 (537.0 bits), Expect = 2.4e-171, Sum P(4) = 2.4e-171
 Identities = 282/466 (60%), Positives = 361/466 (77%)

Query:   412 EKLSIVDHSKIDYQPFRKNFYIEVKEIARMTPEEVSAYRKQLE-LKIHGKDVPKPIKTWH 470
             ++L+ +DHS + Y PFRKNFY+EV E+ RMT  +V  YR  LE +++ GK  PKPIKTW 
Sbjct:   454 KELAKIDHSSVTYAPFRKNFYVEVPELTRMTAADVEKYRSDLEGIQVKGKGCPKPIKTWA 513

Query:   471 QTGLTSKIMETIRKLNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIK 530
             Q G++ K ME +R+L +EKP PIQ QA+P IMSGRD IG+AKTGSGKTLAF+LPM RHI 
Sbjct:   514 QCGVSKKEMEVLRRLGFEKPTPIQCQAIPAIMSGRDLIGIAKTGSGKTLAFILPMFRHIL 573

Query:   531 DQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQISELKRG 590
             DQP +  GDG + +IMAPTREL  QI  DIRKF+K +G+R V VYGG+G+++QI+ELKRG
Sbjct:   574 DQPSMEDGDGAIAIIMAPTRELCMQIGKDIRKFSKSLGLRPVCVYGGTGISEQIAELKRG 633

Query:   591 TEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMGFEPQITRIVQNIRPDRQ 650
              EI+VCTPGRMID+L  + G++TNLRRVTY+V+DEADRMFDMGFEPQ+ RI+ N+RPDRQ
Sbjct:   634 AEIIVCTPGRMIDMLAANSGRVTNLRRVTYVVLDEADRMFDMGFEPQVMRIIDNVRPDRQ 693

Query:   651 TVLFSATFPRQVEILARKVLNKPVEIQVGGRSVVNKDITQLVEVRPESDRFLRLLELLGE 710
             TV+FSATFPRQ+E LAR++L KP+E+ VGGRSVV K++ Q V +  +  +F +LLELLG 
Sbjct:   694 TVMFSATFPRQMEALARRILKKPIEVIVGGRSVVCKEVEQHVVILNDDAKFFKLLELLGI 753

Query:   711 WYEKGKILIFVHSQEKCDALFRDLLKHGYPCLSLHGAKDQTDRESTISDFKSNVCNLLIA 770
             + E G I++FV  QE  D L RDL+K  YPC+SLHG  DQ DR+STI DFKS    LLIA
Sbjct:   754 YQEAGSIIVFVDKQENADILLRDLMKASYPCMSLHGGIDQFDRDSTIIDFKSGKVRLLIA 813

Query:   771 TSVAARGLDVKELELVINFDAPNHYEDYVHRVGRTGRAGRKGCAITFISEEDAKYSPDLV 830
             TSVAARGLDVK+L LV+N+D PNHYEDYVHR GRTGRAG+KG A TFI+ E ++Y+ D++
Sbjct:   814 TSVAARGLDVKDLILVVNYDVPNHYEDYVHRCGRTGRAGKKGSAYTFITPEQSRYAGDII 873

Query:   831 KALELSEQVVPDDLKALADSFMAKVNQGLEQAH-GTGYGGSGFKFN 875
             +A++LS  ++P +L+AL   + A      +  H G G+ G GFKF+
Sbjct:   874 RAMDLSGTLIPAELQALWTEYKALQEAEGKTVHTGGGFSGKGFKFD 919

GO:0003729 "mRNA binding" evidence=ISS

GO:0004004 "ATP-dependent RNA helicase activity" evidence=ISS

GO:0003724 "RNA helicase activity" evidence=ISS

GO:0005681 "spliceosomal complex" evidence=ISS

GO:0000398 "mRNA splicing, via spliceosome" evidence=ISS

GO:0005524 "ATP binding" evidence=IEA

GO:0000381 "regulation of alternative mRNA splicing, via spliceosome" evidence=IMP

GO:0005634 "nucleus" evidence=IC

---

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)
Q0J7Y8	RH45_ORYSJ	3, ., 6, ., 4, ., 1, 3	0.6798	0.7008	0.7222	yes	no
Q8H0U8	RH42_ARATH	3, ., 6, ., 4, ., 1, 3	0.7755	0.7940	0.6646	yes	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

Prediction Level	EC number	Confidence of Prediction
3rd Layer	3.6.4.13	0.946
3rd Layer	3.6.4	0.963

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	976
PTZ00110	545	PTZ00110, PTZ00110, helicase; Provisional	1e-146
COG0513	513	COG0513, SrmB, Superfamily II DNA and RNA helicase	1e-120
cd00268	203	cd00268, DEADc, DEAD-box helicases	5e-91
PRK11776	460	PRK11776, PRK11776, ATP-dependent RNA helicase Dbp	9e-89
PRK10590	456	PRK10590, PRK10590, ATP-dependent RNA helicase Rhl	1e-78
PLN00206	518	PLN00206, PLN00206, DEAD-box ATP-dependent RNA hel	8e-70
PRK11192	434	PRK11192, PRK11192, ATP-dependent RNA helicase Srm	3e-69
PRK04837	423	PRK04837, PRK04837, ATP-dependent RNA helicase Rhl	9e-66
PRK01297	475	PRK01297, PRK01297, ATP-dependent RNA helicase Rhl	2e-65
PRK11634	629	PRK11634, PRK11634, ATP-dependent RNA helicase Dea	4e-65
pfam00270	169	pfam00270, DEAD, DEAD/DEAH box helicase	2e-61
PTZ00424	401	PTZ00424, PTZ00424, helicase 45; Provisional	1e-60
PRK04537	572	PRK04537, PRK04537, ATP-dependent RNA helicase Rhl	4e-60
smart00487	201	smart00487, DEXDc, DEAD-like helicases superfamily	3e-54
cd00046	144	cd00046, DEXDc, DEAD-like helicases superfamily	7e-41
cd00079	131	cd00079, HELICc, Helicase superfamily c-terminal d	6e-35
pfam00271	78	pfam00271, Helicase_C, Helicase conserved C-termin	2e-25
smart00490	82	smart00490, HELICc, helicase superfamily c-termina	5e-22
PRK12678	672	PRK12678, PRK12678, transcription termination fact	2e-20
PRK12678	672	PRK12678, PRK12678, transcription termination fact	4e-17
TIGR01642	509	TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, la	1e-16
TIGR01642	509	TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, la	2e-15
TIGR01642	509	TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, la	3e-15
PRK12678	672	PRK12678, PRK12678, transcription termination fact	2e-14
TIGR01642	509	TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, la	4e-14
COG1201	814	COG1201, Lhr, Lhr-like helicases [General function	8e-14
TIGR01642	509	TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, la	2e-13
TIGR00614	470	TIGR00614, recQ_fam, ATP-dependent DNA helicase, R	7e-13
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	1e-11
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	1e-11
pfam10243	506	pfam10243, MIP-T3, Microtubule-binding protein MIP	1e-10
pfam10243	506	pfam10243, MIP-T3, Microtubule-binding protein MIP	1e-10
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	2e-10
COG0514	590	COG0514, RecQ, Superfamily II DNA helicase [DNA re	2e-10
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	4e-10
COG1111	542	COG1111, MPH1, ERCC4-like helicases [DNA replicati	4e-10
TIGR01622	457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	4e-10
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	5e-10
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	7e-10
TIGR01642	509	TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, la	1e-09
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	1e-09
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	1e-09
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	3e-09
TIGR01622	457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	3e-09
TIGR01622	457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	3e-09
PRK12678	672	PRK12678, PRK12678, transcription termination fact	4e-09
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	4e-09
PRK10811	1068	PRK10811, rne, ribonuclease E; Reviewed	4e-09
PRK10811	1068	PRK10811, rne, ribonuclease E; Reviewed	4e-09
PRK02224	880	PRK02224, PRK02224, chromosome segregation protein	4e-09
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	5e-09
pfam10243	506	pfam10243, MIP-T3, Microtubule-binding protein MIP	6e-09
TIGR02168	1179	TIGR02168, SMC_prok_B, chromosome segregation prot	1e-08
TIGR02169	1164	TIGR02169, SMC_prok_A, chromosome segregation prot	2e-08
pfam13868	349	pfam13868, Trichoplein, Tumour suppressor, Mitosta	2e-08
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	4e-08
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	4e-08
TIGR01622	457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	4e-08
TIGR00927	1096	TIGR00927, 2A1904, K+-dependent Na+/Ca+ exchanger	4e-08
TIGR01389	591	TIGR01389, recQ, ATP-dependent DNA helicase RecQ	4e-08
TIGR02169	1164	TIGR02169, SMC_prok_A, chromosome segregation prot	5e-08
pfam08648	158	pfam08648, DUF1777, Protein of unknown function (D	5e-08
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	6e-08
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	8e-08
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	9e-08
TIGR01642	509	TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, la	1e-07
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	1e-07
TIGR01622	457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	3e-07
TIGR02169	1164	TIGR02169, SMC_prok_A, chromosome segregation prot	3e-07
TIGR01642	509	TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, la	4e-07
PRK02224	880	PRK02224, PRK02224, chromosome segregation protein	4e-07
pfam08648	158	pfam08648, DUF1777, Protein of unknown function (D	4e-07
PRK03918	880	PRK03918, PRK03918, chromosome segregation protein	5e-07
pfam02463	1162	pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	6e-07
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	8e-07
COG1205	851	COG1205, COG1205, Distinct helicase family with a	8e-07
TIGR02169	1164	TIGR02169, SMC_prok_A, chromosome segregation prot	1e-06
pfam13868	349	pfam13868, Trichoplein, Tumour suppressor, Mitosta	1e-06
pfam08648	158	pfam08648, DUF1777, Protein of unknown function (D	1e-06
pfam02029	431	pfam02029, Caldesmon, Caldesmon	1e-06
pfam10243	506	pfam10243, MIP-T3, Microtubule-binding protein MIP	2e-06
TIGR00927	1096	TIGR00927, 2A1904, K+-dependent Na+/Ca+ exchanger	2e-06
pfam08648	158	pfam08648, DUF1777, Protein of unknown function (D	2e-06
pfam08648	158	pfam08648, DUF1777, Protein of unknown function (D	2e-06
pfam08648	158	pfam08648, DUF1777, Protein of unknown function (D	2e-06
COG0419	908	COG0419, SbcC, ATPase involved in DNA repair [DNA	2e-06
COG0419	908	COG0419, SbcC, ATPase involved in DNA repair [DNA	2e-06
TIGR02168	1179	TIGR02168, SMC_prok_B, chromosome segregation prot	3e-06
pfam13868	349	pfam13868, Trichoplein, Tumour suppressor, Mitosta	3e-06
pfam02463	1162	pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	3e-06
COG1203	733	COG1203, COG1203, CRISPR-associated helicase Cas3	3e-06
pfam07767	387	pfam07767, Nop53, Nop53 (60S ribosomal biogenesis)	3e-06
PRK05306	746	PRK05306, infB, translation initiation factor IF-2	4e-06
COG5271	4600	COG5271, MDN1, AAA ATPase containing von Willebran	5e-06
pfam13868	349	pfam13868, Trichoplein, Tumour suppressor, Mitosta	6e-06
COG5271	4600	COG5271, MDN1, AAA ATPase containing von Willebran	6e-06
PTZ00108	1388	PTZ00108, PTZ00108, DNA topoisomerase 2-like prote	6e-06
pfam03154	979	pfam03154, Atrophin-1, Atrophin-1 family	6e-06
PRK05306	746	PRK05306, infB, translation initiation factor IF-2	7e-06
COG2433	652	COG2433, COG2433, Uncharacterized conserved protei	7e-06
COG0419	908	COG0419, SbcC, ATPase involved in DNA repair [DNA	9e-06
COG0419	908	COG0419, SbcC, ATPase involved in DNA repair [DNA	9e-06
PRK12678	672	PRK12678, PRK12678, transcription termination fact	1e-05
PRK02224	880	PRK02224, PRK02224, chromosome segregation protein	1e-05
TIGR02169	1164	TIGR02169, SMC_prok_A, chromosome segregation prot	1e-05
pfam02463	1162	pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	1e-05
pfam03154	979	pfam03154, Atrophin-1, Atrophin-1 family	1e-05
pfam09507	427	pfam09507, CDC27, DNA polymerase subunit Cdc27	1e-05
pfam02724	583	pfam02724, CDC45, CDC45-like protein	1e-05
pfam10243	506	pfam10243, MIP-T3, Microtubule-binding protein MIP	2e-05
TIGR02168	1179	TIGR02168, SMC_prok_B, chromosome segregation prot	2e-05
PRK13766	773	PRK13766, PRK13766, Hef nuclease; Provisional	2e-05
PTZ00266	1021	PTZ00266, PTZ00266, NIMA-related protein kinase; P	2e-05
TIGR00934	800	TIGR00934, 2a38euk, potassium uptake protein, Trk	2e-05
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	3e-05
pfam02029	431	pfam02029, Caldesmon, Caldesmon	3e-05
COG0419	908	COG0419, SbcC, ATPase involved in DNA repair [DNA	3e-05
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	4e-05
PRK00247	429	PRK00247, PRK00247, putative inner membrane protei	4e-05
PRK02224	880	PRK02224, PRK02224, chromosome segregation protein	6e-05
COG1204	766	COG1204, COG1204, Superfamily II helicase [General	6e-05
pfam13904	261	pfam13904, DUF4207, Domain of unknown function (DU	6e-05
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	7e-05
COG0419	908	COG0419, SbcC, ATPase involved in DNA repair [DNA	7e-05
PRK03918	880	PRK03918, PRK03918, chromosome segregation protein	8e-05
pfam03154	979	pfam03154, Atrophin-1, Atrophin-1 family	8e-05
pfam04147	809	pfam04147, Nop14, Nop14-like family	9e-05
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	1e-04
PRK02224	880	PRK02224, PRK02224, chromosome segregation protein	1e-04
COG1202	830	COG1202, COG1202, Superfamily II helicase, archaea	1e-04
pfam03344	715	pfam03344, Daxx, Daxx Family	1e-04
PRK02224	880	PRK02224, PRK02224, chromosome segregation protein	2e-04
TIGR02169	1164	TIGR02169, SMC_prok_A, chromosome segregation prot	2e-04
TIGR00927	1096	TIGR00927, 2A1904, K+-dependent Na+/Ca+ exchanger	2e-04
pfam02463	1162	pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	2e-04
COG2433	652	COG2433, COG2433, Uncharacterized conserved protei	2e-04
TIGR04121	803	TIGR04121, DEXH_lig_assoc, DEXH box helicase, DNA	2e-04
TIGR02680	1353	TIGR02680, TIGR02680, TIGR02680 family protein	2e-04
COG0419	908	COG0419, SbcC, ATPase involved in DNA repair [DNA	3e-04
COG4372	499	COG4372, COG4372, Uncharacterized protein conserve	3e-04
COG1269	660	COG1269, NtpI, Archaeal/vacuolar-type H+-ATPase su	3e-04
PHA02896	616	PHA02896, PHA02896, A-type inclusion like protein;	3e-04
PHA02896	616	PHA02896, PHA02896, A-type inclusion like protein;	3e-04
pfam04615	728	pfam04615, Utp14, Utp14 protein	3e-04
COG2433	652	COG2433, COG2433, Uncharacterized conserved protei	4e-04
pfam07946	322	pfam07946, DUF1682, Protein of unknown function (D	4e-04
pfam02463	1162	pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	5e-04
COG2433	652	COG2433, COG2433, Uncharacterized conserved protei	5e-04
PTZ00266	1021	PTZ00266, PTZ00266, NIMA-related protein kinase; P	5e-04
pfam07946	322	pfam07946, DUF1682, Protein of unknown function (D	5e-04
PRK12585	197	PRK12585, PRK12585, putative monovalent cation/H+	5e-04
COG2268	548	COG2268, COG2268, Uncharacterized protein conserve	5e-04
pfam11671	146	pfam11671, Apis_Csd, Complementary sex determiner	6e-04
PRK05035	695	PRK05035, PRK05035, electron transport complex pro	7e-04
pfam03879	105	pfam03879, Cgr1, Cgr1 family	7e-04
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	8e-04
COG0419	908	COG0419, SbcC, ATPase involved in DNA repair [DNA	8e-04
pfam09507	427	pfam09507, CDC27, DNA polymerase subunit Cdc27	8e-04
pfam02724	583	pfam02724, CDC45, CDC45-like protein	8e-04
pfam12037	276	pfam12037, DUF3523, Domain of unknown function (DU	8e-04
pfam04615	728	pfam04615, Utp14, Utp14 protein	9e-04
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	0.001
PRK10811	1068	PRK10811, rne, ribonuclease E; Reviewed	0.001
TIGR02168	1179	TIGR02168, SMC_prok_B, chromosome segregation prot	0.001
TIGR02169	1164	TIGR02169, SMC_prok_A, chromosome segregation prot	0.001
TIGR00927	1096	TIGR00927, 2A1904, K+-dependent Na+/Ca+ exchanger	0.001
PRK03918	880	PRK03918, PRK03918, chromosome segregation protein	0.001
PRK12705	508	PRK12705, PRK12705, hypothetical protein; Provisio	0.001
pfam06375	561	pfam06375, BLVR, Bovine leukaemia virus receptor (	0.001
pfam09756	189	pfam09756, DDRGK, DDRGK domain	0.001
pfam09756	189	pfam09756, DDRGK, DDRGK domain	0.001
TIGR01554	384	TIGR01554, major_cap_HK97, phage major capsid prot	0.001
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	0.002
PRK02224	880	PRK02224, PRK02224, chromosome segregation protein	0.002
pfam07767	387	pfam07767, Nop53, Nop53 (60S ribosomal biogenesis)	0.002
COG5271	4600	COG5271, MDN1, AAA ATPase containing von Willebran	0.002
TIGR02680	1353	TIGR02680, TIGR02680, TIGR02680 family protein	0.002
TIGR02680	1353	TIGR02680, TIGR02680, TIGR02680 family protein	0.002
pfam05262	489	pfam05262, Borrelia_P83, Borrelia P83/100 protein	0.002
pfam04889	241	pfam04889, Cwf_Cwc_15, Cwf15/Cwc15 cell cycle cont	0.002
pfam05793	528	pfam05793, TFIIF_alpha, Transcription initiation f	0.002
pfam12871	97	pfam12871, PRP38_assoc, Pre-mRNA-splicing factor 3	0.002
COG1061	442	COG1061, SSL2, DNA or RNA helicases of superfamily	0.002
COG5296	521	COG5296, COG5296, Transcription factor involved in	0.002
pfam09736	141	pfam09736, Bud13, Pre-mRNA-splicing factor of RES	0.002
pfam02463	1162	pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	0.003
pfam03154	979	pfam03154, Atrophin-1, Atrophin-1 family	0.003
PRK12705	508	PRK12705, PRK12705, hypothetical protein; Provisio	0.003
pfam06375	561	pfam06375, BLVR, Bovine leukaemia virus receptor (	0.003
pfam04006	613	pfam04006, Mpp10, Mpp10 protein	0.003
TIGR00643	630	TIGR00643, recG, ATP-dependent DNA helicase RecG	0.003
PRK04195	482	PRK04195, PRK04195, replication factor C large sub	0.003
TIGR03319	514	TIGR03319, RNase_Y, ribonuclease Y	0.003
PRK03918	880	PRK03918, PRK03918, chromosome segregation protein	0.004
COG0419	908	COG0419, SbcC, ATPase involved in DNA repair [DNA	0.004
pfam09756	189	pfam09756, DDRGK, DDRGK domain	0.004
pfam04514	363	pfam04514, BTV_NS2, Bluetongue virus non-structura	0.004
TIGR02794	346	TIGR02794, tolA_full, TolA protein	0.004
pfam06991	277	pfam06991, Prp19_bind, Splicing factor, Prp19-bind	0.004

>gnl|CDD|240273 PTZ00110, PTZ00110, helicase; Provisional

 Score =  445 bits (1146), Expect = e-146
 Identities = 207/463 (44%), Positives = 298/463 (64%), Gaps = 11/463 (2%)

Query: 413 KLSIVDHSKIDYQPFRKNFYIEVKEIARMTPEEVSAYRKQLELKI-HGKDVPKPIKTWHQ 471
           +L  +D   I+  PF KNFY E  E++ ++ +EV   RK+ E+ I  G++VPKP+ ++  
Sbjct: 75  RLQPIDWKSINLVPFEKNFYKEHPEVSALSSKEVDEIRKEKEITIIAGENVPKPVVSFEY 134

Query: 472 TGLTSKIMETIRKLNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKD 531
           T     I+++++   + +P PIQ Q  P+ +SGRD IG+A+TGSGKTLAF+LP + HI  
Sbjct: 135 TSFPDYILKSLKNAGFTEPTPIQVQGWPIALSGRDMIGIAETGSGKTLAFLLPAIVHINA 194

Query: 532 QPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQISELKRGT 591
           QP +  GDGP+ L++APTREL +QI     KF     +R    YGG     QI  L+RG 
Sbjct: 195 QPLLRYGDGPIVLVLAPTRELAEQIREQCNKFGASSKIRNTVAYGGVPKRGQIYALRRGV 254

Query: 592 EIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMGFEPQITRIVQNIRPDRQT 651
           EI++  PGR+ID L ++   +TNLRRVTYLV+DEADRM DMGFEPQI +IV  IRPDRQT
Sbjct: 255 EILIACPGRLIDFLESN---VTNLRRVTYLVLDEADRMLDMGFEPQIRKIVSQIRPDRQT 311

Query: 652 VLFSATFPRQVEILARKVL-NKPVEIQVGGRSV-VNKDITQLVEVRPESDRFLRLLELLG 709
           +++SAT+P++V+ LAR +   +PV + VG   +    +I Q V V  E ++  +L  LL 
Sbjct: 312 LMWSATWPKEVQSLARDLCKEEPVHVNVGSLDLTACHNIKQEVFVVEEHEKRGKLKMLLQ 371

Query: 710 EWYEKG-KILIFVHSQEKCDALFRDLLKHGYPCLSLHGAKDQTDRESTISDFKSNVCNLL 768
                G KILIFV +++  D L ++L   G+P L +HG K Q +R   +++FK+    ++
Sbjct: 372 RIMRDGDKILIFVETKKGADFLTKELRLDGWPALCIHGDKKQEERTWVLNEFKTGKSPIM 431

Query: 769 IATSVAARGLDVKELELVINFDAPNHYEDYVHRVGRTGRAGRKGCAITFISEEDAKYSPD 828
           IAT VA+RGLDVK+++ VINFD PN  EDYVHR+GRTGRAG KG + TF++ +  + + D
Sbjct: 432 IATDVASRGLDVKDVKYVINFDFPNQIEDYVHRIGRTGRAGAKGASYTFLTPDKYRLARD 491

Query: 829 LVKALELSEQVVPDDLKALADSFMAKVNQGLEQAHGTGYGGSG 871
           LVK L  ++Q VP +L+ L++      + G E+    GYG   
Sbjct: 492 LVKVLREAKQPVPPELEKLSNE----RSNGTERRRWGGYGRFS 530

Length = 545

>gnl|CDD|223587 COG0513, SrmB, Superfamily II DNA and RNA helicases [DNA replication, recombination, and repair / Transcription / Translation, ribosomal structure and biogenesis]

 Score =  375 bits (964), Expect = e-120
 Identities = 173/457 (37%), Positives = 252/457 (55%), Gaps = 20/457 (4%)

Query: 450 RKQLELKIHGKDVPKPIKTWHQTGLTSKIMETIRKLNYEKPMPIQAQALPVIMSGRDCIG 509
            K        +   K    +   GL+ ++++ ++ L +E+P PIQ  A+P+I++GRD +G
Sbjct: 12  LKSAHNVALSRGEEKTPPEFASLGLSPELLQALKDLGFEEPTPIQLAAIPLILAGRDVLG 71

Query: 510 VAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVM-G 568
            A+TG+GKT AF+LP+L+ I              LI+APTREL  QI  ++RK  K + G
Sbjct: 72  QAQTGTGKTAAFLLPLLQKILKSVER---KYVSALILAPTRELAVQIAEELRKLGKNLGG 128

Query: 569 VRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADR 628
           +R   VYGG  + +QI  LKRG +IVV TPGR++D++        +L  V  LV+DEADR
Sbjct: 129 LRVAVVYGGVSIRKQIEALKRGVDIVVATPGRLLDLI---KRGKLDLSGVETLVLDEADR 185

Query: 629 MFDMGFEPQITRIVQNIRPDRQTVLFSATFPRQVEILARKVLNKPVEIQVGGR--SVVNK 686
           M DMGF   I +I++ + PDRQT+LFSAT P  +  LAR+ LN PVEI+V         K
Sbjct: 186 MLDMGFIDDIEKILKALPPDRQTLLFSATMPDDIRELARRYLNDPVEIEVSVEKLERTLK 245

Query: 687 DITQ-LVEVRPESDRFLRLLELLGEWYEKGKILIFVHSQEKCDALFRDLLKHGYPCLSLH 745
            I Q  +EV  E ++   LL+LL +  ++G++++FV ++   + L   L K G+   +LH
Sbjct: 246 KIKQFYLEVESEEEKLELLLKLLKD-EDEGRVIVFVRTKRLVEELAESLRKRGFKVAALH 304

Query: 746 GAKDQTDRESTISDFKSNVCNLLIATSVAARGLDVKELELVINFDAPNHYEDYVHRVGRT 805
           G   Q +R+  +  FK     +L+AT VAARGLD+ ++  VIN+D P   EDYVHR+GRT
Sbjct: 305 GDLPQEERDRALEKFKDGELRVLVATDVAARGLDIPDVSHVINYDLPLDPEDYVHRIGRT 364

Query: 806 GRAGRKGCAITFI-SEEDAKYSPDLVKALELSEQVVPDDLKALADSFMAKVNQGLEQAHG 864
           GRAGRKG AI+F+  EE+ K    + K LE         L          +         
Sbjct: 365 GRAGRKGVAISFVTEEEEVKKLKRIEKRLERKLP-SAVLLPLDEPEDAKLLKTTRP---- 419

Query: 865 TGYGGSGFKFNEEEDEKRKAAKKAQAKEYGFEEDKSD 901
              G        +E +K K++KKA  +  G     S 
Sbjct: 420 ---GLEEESDISDEIKKLKSSKKALLRGLGVRFTLSK 453

Length = 513

>gnl|CDD|238167 cd00268, DEADc, DEAD-box helicases

 Score =  287 bits (738), Expect = 5e-91
 Identities = 106/208 (50%), Positives = 143/208 (68%), Gaps = 6/208 (2%)

Query: 469 WHQTGLTSKIMETIRKLNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRH 528
           + + GL+ +++  I  L +EKP PIQA+A+P ++SGRD IG A+TGSGKT AF++P+L  
Sbjct: 1   FEELGLSPELLRGIYALGFEKPTPIQARAIPPLLSGRDVIGQAQTGSGKTAAFLIPILEK 60

Query: 529 IKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQISELK 588
           +   P     DGP  LI+APTREL  QI    RK  K   ++ V +YGG+ + +QI +LK
Sbjct: 61  LDPSPKK---DGPQALILAPTRELALQIAEVARKLGKHTNLKVVVIYGGTSIDKQIRKLK 117

Query: 589 RGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMGFEPQITRIVQNIRPD 648
           RG  IVV TPGR++D+L    GK+ +L +V YLV+DEADRM DMGFE QI  I++ +  D
Sbjct: 118 RGPHIVVATPGRLLDLL--ERGKL-DLSKVKYLVLDEADRMLDMGFEDQIREILKLLPKD 174

Query: 649 RQTVLFSATFPRQVEILARKVLNKPVEI 676
           RQT+LFSAT P++V  LARK L  PV I
Sbjct: 175 RQTLLFSATMPKEVRDLARKFLRNPVRI 202

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. Length = 203

>gnl|CDD|236977 PRK11776, PRK11776, ATP-dependent RNA helicase DbpA; Provisional

 Score =  291 bits (747), Expect = 9e-89
 Identities = 140/381 (36%), Positives = 223/381 (58%), Gaps = 23/381 (6%)

Query: 474 LTSKIMETIRKLNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIK-DQ 532
           L   ++  + +L Y +  PIQAQ+LP I++G+D I  AKTGSGKT AF L +L+ +   +
Sbjct: 11  LPPALLANLNELGYTEMTPIQAQSLPAILAGKDVIAQAKTGSGKTAAFGLGLLQKLDVKR 70

Query: 533 PPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVM-GVRCVPVYGGSGVAQQISELKRGT 591
             V A      L++ PTREL  Q+  +IR+ A+ +  ++ + + GG  +  QI  L+ G 
Sbjct: 71  FRVQA------LVLCPTRELADQVAKEIRRLARFIPNIKVLTLCGGVPMGPQIDSLEHGA 124

Query: 592 EIVVCTPGRMIDILCTSGGKIT-NLRRVTYLVMDEADRMFDMGFEPQITRIVQNIRPDRQ 650
            I+V TPGR++D L     K T +L  +  LV+DEADRM DMGF+  I  I++     RQ
Sbjct: 125 HIIVGTPGRILDHL----RKGTLDLDALNTLVLDEADRMLDMGFQDAIDAIIRQAPARRQ 180

Query: 651 TVLFSATFPRQVEILARKVLNKPVEIQVGGRSVVNKDITQLV-EVRPESDRFLRLLELLG 709
           T+LFSAT+P  +  ++++    PVE++V     +   I Q   EV P+ +R   L  LL 
Sbjct: 181 TLLFSATYPEGIAAISQRFQRDPVEVKVESTHDLPA-IEQRFYEVSPD-ERLPALQRLLL 238

Query: 710 EWYEKGKILIFVHSQEKCDALFRDLLKHGYPCLSLHGAKDQTDRESTISDFKSNVCNLLI 769
             ++    ++F +++++C  +   L   G+  L+LHG  +Q DR+  +  F +  C++L+
Sbjct: 239 H-HQPESCVVFCNTKKECQEVADALNAQGFSALALHGDLEQRDRDQVLVRFANRSCSVLV 297

Query: 770 ATSVAARGLDVKELELVINFDAPNHYEDYVHRVGRTGRAGRKGCAITFISEEDAKYSPDL 829
           AT VAARGLD+K LE VIN++     E +VHR+GRTGRAG KG A++ ++ E+ +     
Sbjct: 298 ATDVAARGLDIKALEAVINYELARDPEVHVHRIGRTGRAGSKGLALSLVAPEEMQ----R 353

Query: 830 VKALE--LSEQVVPDDLKALA 848
             A+E  L  ++  + L +L+
Sbjct: 354 ANAIEDYLGRKLNWEPLPSLS 374

Length = 460

>gnl|CDD|236722 PRK10590, PRK10590, ATP-dependent RNA helicase RhlE; Provisional

 Score =  263 bits (674), Expect = 1e-78
 Identities = 143/366 (39%), Positives = 221/366 (60%), Gaps = 11/366 (3%)

Query: 473 GLTSKIMETIRKLNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQ 532
           GL+  I+  + +  Y +P PIQ QA+P ++ GRD +  A+TG+GKT  F LP+L+H+  +
Sbjct: 7   GLSPDILRAVAEQGYREPTPIQQQAIPAVLEGRDLMASAQTGTGKTAGFTLPLLQHLITR 66

Query: 533 PPVAAGDGPV-GLIMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQISELKRGT 591
            P A G  PV  LI+ PTREL  QI  ++R ++K + +R + V+GG  +  Q+ +L+ G 
Sbjct: 67  QPHAKGRRPVRALILTPTRELAAQIGENVRDYSKYLNIRSLVVFGGVSINPQMMKLRGGV 126

Query: 592 EIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMGFEPQITRIVQNIRPDRQT 651
           +++V TPGR++D+          L +V  LV+DEADRM DMGF   I R++  +   RQ 
Sbjct: 127 DVLVATPGRLLDL---EHQNAVKLDQVEILVLDEADRMLDMGFIHDIRRVLAKLPAKRQN 183

Query: 652 VLFSATFPRQVEILARKVLNKPVEIQVGGRSVVNKDITQLVEVRPESDRFLRLLELL--- 708
           +LFSATF   ++ LA K+L+ P+EI+V  R+  ++ +TQ V    +  R   LL  +   
Sbjct: 184 LLFSATFSDDIKALAEKLLHNPLEIEVARRNTASEQVTQHVHF-VDKKRKRELLSQMIGK 242

Query: 709 GEWYEKGKILIFVHSQEKCDALFRDLLKHGYPCLSLHGAKDQTDRESTISDFKSNVCNLL 768
           G W +   +L+F  ++   + L   L K G    ++HG K Q  R   ++DFKS    +L
Sbjct: 243 GNWQQ---VLVFTRTKHGANHLAEQLNKDGIRSAAIHGNKSQGARTRALADFKSGDIRVL 299

Query: 769 IATSVAARGLDVKELELVINFDAPNHYEDYVHRVGRTGRAGRKGCAITFISEEDAKYSPD 828
           +AT +AARGLD++EL  V+N++ PN  EDYVHR+GRTGRA   G A++ +  ++ K   D
Sbjct: 300 VATDIAARGLDIEELPHVVNYELPNVPEDYVHRIGRTGRAAATGEALSLVCVDEHKLLRD 359

Query: 829 LVKALE 834
           + K L+
Sbjct: 360 IEKLLK 365

Length = 456

>gnl|CDD|215103 PLN00206, PLN00206, DEAD-box ATP-dependent RNA helicase; Provisional

 Score =  241 bits (616), Expect = 8e-70
 Identities = 146/465 (31%), Positives = 237/465 (50%), Gaps = 25/465 (5%)

Query: 396 DEDDDE---------FMKRVKKTKAEKLSIVDHSKIDYQPFR-KNFYIEVKEI-ARMTPE 444
           DE DD+          ++RV K++      V   K    P   + FY+      + ++  
Sbjct: 43  DETDDDICSLECKQALLRRVAKSRVA----VGAPKPKRLPATDECFYVRDPGSTSGLSSS 98

Query: 445 EVSAYRKQLELKIHGKDVPKPIKTWHQTGLTSKIMETIRKLNYEKPMPIQAQALPVIMSG 504
           +    R++LE+ + G+ VP PI ++   GL  K++  +    YE P PIQ QA+P  +SG
Sbjct: 99  QAELLRRKLEIHVKGEAVPPPILSFSSCGLPPKLLLNLETAGYEFPTPIQMQAIPAALSG 158

Query: 505 RDCIGVAKTGSGKTLAFVLPMLRH---IKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIR 561
           R  +  A TGSGKT +F++P++     I+   P +    P+ +++ PTREL  Q+    +
Sbjct: 159 RSLLVSADTGSGKTASFLVPIISRCCTIRSGHP-SEQRNPLAMVLTPTRELCVQVEDQAK 217

Query: 562 KFAKVMGVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYL 621
              K +  +   V GG  + QQ+  +++G E++V TPGR+ID+L         L  V+ L
Sbjct: 218 VLGKGLPFKTALVVGGDAMPQQLYRIQQGVELIVGTPGRLIDLLSKHD---IELDNVSVL 274

Query: 622 VMDEADRMFDMGFEPQITRIVQNIRPDRQTVLFSATFPRQVEILARKVLNKPVEIQVGGR 681
           V+DE D M + GF  Q+ +I Q +    Q +LFSAT   +VE  A  +    + I +G  
Sbjct: 275 VLDEVDCMLERGFRDQVMQIFQAL-SQPQVLLFSATVSPEVEKFASSLAKDIILISIGNP 333

Query: 682 SVVNKDITQLVEVRPESDRFLRLLELL-GEWYEKGKILIFVHSQEKCDALFRDLLK-HGY 739
           +  NK + QL        +  +L ++L  + + K   ++FV S+   D L   +    G 
Sbjct: 334 NRPNKAVKQLAIWVETKQKKQKLFDILKSKQHFKPPAVVFVSSRLGADLLANAITVVTGL 393

Query: 740 PCLSLHGAKDQTDRESTISDFKSNVCNLLIATSVAARGLDVKELELVINFDAPNHYEDYV 799
             LS+HG K   +R   +  F      +++AT V  RG+D+  +  VI FD PN  ++Y+
Sbjct: 394 KALSIHGEKSMKERREVMKSFLVGEVPVIVATGVLGRGVDLLRVRQVIIFDMPNTIKEYI 453

Query: 800 HRVGRTGRAGRKGCAITFISEEDAKYSPDLVKALELSEQVVPDDL 844
           H++GR  R G KG AI F++EED    P+LV  L+ S   +P +L
Sbjct: 454 HQIGRASRMGEKGTAIVFVNEEDRNLFPELVALLKSSGAAIPREL 498

Length = 518

>gnl|CDD|236877 PRK11192, PRK11192, ATP-dependent RNA helicase SrmB; Provisional

 Score =  237 bits (607), Expect = 3e-69
 Identities = 144/437 (32%), Positives = 213/437 (48%), Gaps = 19/437 (4%)

Query: 467 KTWHQTGLTSKIMETIRKLNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPML 526
            T+ +  L   ++E ++   Y +P  IQA+A+P  + GRD +G A TG+GKT AF+LP L
Sbjct: 1   TTFSELELDESLLEALQDKGYTRPTAIQAEAIPPALDGRDVLGSAPTGTGKTAAFLLPAL 60

Query: 527 RHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQISE 586
           +H+ D P   +G  P  LI+ PTREL  Q+    R+ AK   +    + GG         
Sbjct: 61  QHLLDFPRRKSGP-PRILILTPTRELAMQVADQARELAKHTHLDIATITGGVAYMNHAEV 119

Query: 587 LKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMGFEPQITRIVQNIR 646
                +IVV TPGR++  +        + R V  L++DEADRM DMGF   I  I    R
Sbjct: 120 FSENQDIVVATPGRLLQYIKEEN---FDCRAVETLILDEADRMLDMGFAQDIETIAAETR 176

Query: 647 PDRQTVLFSATFP-RQVEILARKVLNKPVEIQVGGRSVVNKDITQLVEVRPESDRFLRLL 705
             +QT+LFSAT     V+  A ++LN PVE++        K I Q      + +    LL
Sbjct: 177 WRKQTLLFSATLEGDAVQDFAERLLNDPVEVEAEPSRRERKKIHQWYYRADDLEHKTALL 236

Query: 706 ELLGEWYEKGKILIFVHSQEKCDALFRDLLKHGYPCLSLHGAKDQTDRESTISDFKSNVC 765
             L +  E  + ++FV ++E+   L   L K G  C  L G   Q  R   I        
Sbjct: 237 CHLLKQPEVTRSIVFVRTRERVHELAGWLRKAGINCCYLEGEMVQAKRNEAIKRLTDGRV 296

Query: 766 NLLIATSVAARGLDVKELELVINFDAPNHYEDYVHRVGRTGRAGRKGCAITFISEEDAKY 825
           N+L+AT VAARG+D+ ++  VINFD P   + Y+HR+GRTGRAGRKG AI+ +   D   
Sbjct: 297 NVLVATDVAARGIDIDDVSHVINFDMPRSADTYLHRIGRTGRAGRKGTAISLVEAHDHLL 356

Query: 826 SPDLVKALELSEQVVPDDLKALADSFMAKVNQGLEQAHGTGYGGSGFKFNEEEDEKRKAA 885
                  L   E+ + + LK       A+V   L             K +++   KR   
Sbjct: 357 -------LGKIERYIEEPLK-------ARVIDELRPKTKAPSEKKTGKPSKKVLAKRAEK 402

Query: 886 KKAQAKEYGFEEDKSDS 902
           K+ + ++   ++   D+
Sbjct: 403 KEKEKEKPKVKKRHRDT 419

Length = 434

>gnl|CDD|235314 PRK04837, PRK04837, ATP-dependent RNA helicase RhlB; Provisional

 Score =  227 bits (580), Expect = 9e-66
 Identities = 126/364 (34%), Positives = 193/364 (53%), Gaps = 26/364 (7%)

Query: 473 GLTSKIMETIRKLNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQ 532
            L  +++E + K  +    PIQA ALP+ ++GRD  G A+TG+GKT+AF+     ++   
Sbjct: 14  ALHPQVVEALEKKGFHNCTPIQALALPLTLAGRDVAGQAQTGTGKTMAFLTATFHYLL-S 72

Query: 533 PPVAAG---DGPVGLIMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQISELKR 589
            P       + P  LIMAPTREL  QIH+D    A+  G++    YGG G  +Q+  L+ 
Sbjct: 73  HPAPEDRKVNQPRALIMAPTRELAVQIHADAEPLAQATGLKLGLAYGGDGYDKQLKVLES 132

Query: 590 GTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMGFEPQITRIVQNIR--- 646
           G +I++ T GR+ID          NL  +  +V+DEADRMFD+GF       +++IR   
Sbjct: 133 GVDILIGTTGRLIDYA---KQNHINLGAIQVVVLDEADRMFDLGF-------IKDIRWLF 182

Query: 647 ---PD---RQTVLFSATFPRQVEILARKVLNKPVEIQVGGRSVVNKDITQLVEVRPESDR 700
              P    R  +LFSAT   +V  LA + +N P  ++V         I + +      ++
Sbjct: 183 RRMPPANQRLNMLFSATLSYRVRELAFEHMNNPEYVEVEPEQKTGHRIKEELFYPSNEEK 242

Query: 701 FLRLLELLGE-WYEKGKILIFVHSQEKCDALFRDLLKHGYPCLSLHGAKDQTDRESTISD 759
              L  L+ E W ++   +IF +++ +C+ ++  L   G+    L G   Q  R   + +
Sbjct: 243 MRLLQTLIEEEWPDRA--IIFANTKHRCEEIWGHLAADGHRVGLLTGDVAQKKRLRILEE 300

Query: 760 FKSNVCNLLIATSVAARGLDVKELELVINFDAPNHYEDYVHRVGRTGRAGRKGCAITFIS 819
           F     ++L+AT VAARGL +  +  V N+D P+  EDYVHR+GRTGRAG  G +I+   
Sbjct: 301 FTRGDLDILVATDVAARGLHIPAVTHVFNYDLPDDCEDYVHRIGRTGRAGASGHSISLAC 360

Query: 820 EEDA 823
           EE A
Sbjct: 361 EEYA 364

Length = 423

>gnl|CDD|234938 PRK01297, PRK01297, ATP-dependent RNA helicase RhlB; Provisional

 Score =  227 bits (581), Expect = 2e-65
 Identities = 138/393 (35%), Positives = 216/393 (54%), Gaps = 18/393 (4%)

Query: 463 PKPIKT-WHQTGLTSKIMETIRKLNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAF 521
           P+  KT +H   L  ++M  I  L +    PIQAQ L   ++G D IG A+TG+GKT AF
Sbjct: 82  PQEGKTRFHDFNLAPELMHAIHDLGFPYCTPIQAQVLGYTLAGHDAIGRAQTGTGKTAAF 141

Query: 522 VLPMLRHIKDQPPVAA---GDGPVGLIMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGS 578
           ++ ++  +   PP      G+ P  LI+APTRELV QI  D     K  G+  +   GG 
Sbjct: 142 LISIINQLLQTPPPKERYMGE-PRALIIAPTRELVVQIAKDAAALTKYTGLNVMTFVGGM 200

Query: 579 GVAQQISELK-RGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMGFEPQ 637
              +Q+ +L+ R  +I+V TPGR++D    +     +L  V  +V+DEADRM DMGF PQ
Sbjct: 201 DFDKQLKQLEARFCDILVATPGRLLDF---NQRGEVHLDMVEVMVLDEADRMLDMGFIPQ 257

Query: 638 ITRIVQNIRP--DRQTVLFSATFPRQVEILARKVLNKPVEIQVGGRSVVNKDITQLVEVR 695
           + +I++      +RQT+LFSATF   V  LA++    P  +++   +V +  + Q V   
Sbjct: 258 VRQIIRQTPRKEERQTLLFSATFTDDVMNLAKQWTTDPAIVEIEPENVASDTVEQHVYAV 317

Query: 696 PESDRFLRLLELLGE--WYEKGKILIFVHSQEKCDALFRDLLKHGYPCLSLHGAKDQTDR 753
             SD++  L  L+ +  W    ++++F + +++   +   L+K G     L G   Q  R
Sbjct: 318 AGSDKYKLLYNLVTQNPW---ERVMVFANRKDEVRRIEERLVKDGINAAQLSGDVPQHKR 374

Query: 754 ESTISDFKSNVCNLLIATSVAARGLDVKELELVINFDAPNHYEDYVHRVGRTGRAGRKGC 813
             T+  F+     +L+AT VA RG+ +  +  VINF  P   +DYVHR+GRTGRAG  G 
Sbjct: 375 IKTLEGFREGKIRVLVATDVAGRGIHIDGISHVINFTLPEDPDDYVHRIGRTGRAGASGV 434

Query: 814 AITFISEEDAKYSPDLVKAL--ELSEQVVPDDL 844
           +I+F  E+DA   P++ + L  ++S ++ P +L
Sbjct: 435 SISFAGEDDAFQLPEIEELLGRKISCEMPPAEL 467

Length = 475

>gnl|CDD|236941 PRK11634, PRK11634, ATP-dependent RNA helicase DeaD; Provisional

 Score =  230 bits (589), Expect = 4e-65
 Identities = 152/397 (38%), Positives = 230/397 (57%), Gaps = 21/397 (5%)

Query: 473 GLTSKIMETIRKLNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQ 532
           GL + I+E +  L YEKP PIQA+ +P +++GRD +G+A+TGSGKT AF LP+L ++   
Sbjct: 12  GLKAPILEALNDLGYEKPSPIQAECIPHLLNGRDVLGMAQTGSGKTAAFSLPLLHNLD-- 69

Query: 533 PPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVM-GVRCVPVYGGSGVAQQISELKRGT 591
           P + A   P  L++APTREL  Q+   +  F+K M GV  V +YGG     Q+  L++G 
Sbjct: 70  PELKA---PQILVLAPTRELAVQVAEAMTDFSKHMRGVNVVALYGGQRYDVQLRALRQGP 126

Query: 592 EIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMGFEPQITRIVQNIRPDRQT 651
           +IVV TPGR++D L      ++ L     LV+DEAD M  MGF   +  I+  I    QT
Sbjct: 127 QIVVGTPGRLLDHLKRGTLDLSKLSG---LVLDEADEMLRMGFIEDVETIMAQIPEGHQT 183

Query: 652 VLFSATFPRQVEILARKVLNKPVEIQVGGRSVVNKDITQ---LVEVRPESDRFLRLLELL 708
            LFSAT P  +  + R+ + +P E+++        DI+Q    V    +++  +R LE  
Sbjct: 184 ALFSATMPEAIRRITRRFMKEPQEVRIQSSVTTRPDISQSYWTVWGMRKNEALVRFLE-- 241

Query: 709 GEWYEKGKILIFVHSQEKCDALFRDLLKHGYPCLSLHGAKDQTDRESTISDFKSNVCNLL 768
            E ++    +IFV ++     +   L ++GY   +L+G  +Q  RE T+   K    ++L
Sbjct: 242 AEDFDAA--IIFVRTKNATLEVAEALERNGYNSAALNGDMNQALREQTLERLKDGRLDIL 299

Query: 769 IATSVAARGLDVKELELVINFDAPNHYEDYVHRVGRTGRAGRKGCAITFISEEDAKYSPD 828
           IAT VAARGLDV+ + LV+N+D P   E YVHR+GRTGRAGR G A+ F+   + +   +
Sbjct: 300 IATDVAARGLDVERISLVVNYDIPMDSESYVHRIGRTGRAGRAGRALLFVENRERRLLRN 359

Query: 829 LVKALELS--EQVVPD-DL--KALADSFMAKVNQGLE 860
           + + ++L+  E  +P+ +L  K   + F AKV Q LE
Sbjct: 360 IERTMKLTIPEVELPNAELLGKRRLEKFAAKVQQQLE 396

Length = 629

>gnl|CDD|215832 pfam00270, DEAD, DEAD/DEAH box helicase

 Score =  205 bits (525), Expect = 2e-61
 Identities = 79/175 (45%), Positives = 119/175 (68%), Gaps = 8/175 (4%)

Query: 492 PIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRE 551
           PIQAQA+P I+SG+D +  A TGSGKTLAF+LP+L+ +  +       GP  L++APTRE
Sbjct: 2   PIQAQAIPAILSGKDVLVQAPTGSGKTLAFLLPILQALLPKK-----GGPQALVLAPTRE 56

Query: 552 LVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQISELKRGT-EIVVCTPGRMIDILCTSGG 610
           L +QI+ +++K  K++G+R   + GG+ + +Q  +LK+G  +I+V TPGR++D+L    G
Sbjct: 57  LAEQIYEELKKLFKILGLRVALLTGGTSLKEQARKLKKGKADILVGTPGRLLDLL--RRG 114

Query: 611 KITNLRRVTYLVMDEADRMFDMGFEPQITRIVQNIRPDRQTVLFSATFPRQVEIL 665
           K+  L+ +  LV+DEA R+ DMGF   +  I+  + PDRQ +L SAT PR +E L
Sbjct: 115 KLKLLKNLKLLVLDEAHRLLDMGFGDDLEEILSRLPPDRQILLLSATLPRNLEDL 169

Members of this family include the DEAD and DEAH box helicases. 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. Length = 169

>gnl|CDD|185609 PTZ00424, PTZ00424, helicase 45; Provisional

 Score =  212 bits (541), Expect = 1e-60
 Identities = 127/354 (35%), Positives = 194/354 (54%), Gaps = 16/354 (4%)

Query: 473 GLTSKIMETIRKLNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQ 532
            L   ++  I    +EKP  IQ + +  I+ G D IG A++G+GKT  FV+  L+ I   
Sbjct: 34  KLNEDLLRGIYSYGFEKPSAIQQRGIKPILDGYDTIGQAQSGTGKTATFVIAALQLI--D 91

Query: 533 PPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQISELKRGTE 592
             + A      LI+APTREL QQI   +      + VRC    GG+ V   I++LK G  
Sbjct: 92  YDLNACQA---LILAPTRELAQQIQKVVLALGDYLKVRCHACVGGTVVRDDINKLKAGVH 148

Query: 593 IVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMGFEPQITRIVQNIRPDRQTV 652
           +VV TPGR+ D++     ++ +L+     ++DEAD M   GF+ QI  + + + PD Q  
Sbjct: 149 MVVGTPGRVYDMIDKRHLRVDDLK---LFILDEADEMLSRGFKGQIYDVFKKLPPDVQVA 205

Query: 653 LFSATFPRQVEILARKVLNKPVEIQVGGRSVVNKDITQL-VEVRPESDRFLRLLELLGEW 711
           LFSAT P ++  L  K +  P  I V    +  + I Q  V V  E  +F  L +L    
Sbjct: 206 LFSATMPNEILELTTKFMRDPKRILVKKDELTLEGIRQFYVAVEKEEWKFDTLCDL---- 261

Query: 712 YEKGKI---LIFVHSQEKCDALFRDLLKHGYPCLSLHGAKDQTDRESTISDFKSNVCNLL 768
           YE   I   +I+ +++ K D L + + +  +    +HG  DQ DR+  + +F+S    +L
Sbjct: 262 YETLTITQAIIYCNTRRKVDYLTKKMHERDFTVSCMHGDMDQKDRDLIMREFRSGSTRVL 321

Query: 769 IATSVAARGLDVKELELVINFDAPNHYEDYVHRVGRTGRAGRKGCAITFISEED 822
           I T + ARG+DV+++ LVIN+D P   E+Y+HR+GR+GR GRKG AI F++ +D
Sbjct: 322 ITTDLLARGIDVQQVSLVINYDLPASPENYIHRIGRSGRFGRKGVAINFVTPDD 375

Length = 401

>gnl|CDD|235307 PRK04537, PRK04537, ATP-dependent RNA helicase RhlB; Provisional

 Score =  215 bits (549), Expect = 4e-60
 Identities = 135/354 (38%), Positives = 203/354 (57%), Gaps = 7/354 (1%)

Query: 492 PIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVA--AGDGPVGLIMAPT 549
           PIQA  LPV + G D  G A+TG+GKTLAF++ ++  +  +P +A    + P  LI+APT
Sbjct: 34  PIQALTLPVALPGGDVAGQAQTGTGKTLAFLVAVMNRLLSRPALADRKPEDPRALILAPT 93

Query: 550 RELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSG 609
           REL  QIH D  KF   +G+R   VYGG    +Q   L++G ++++ TPGR+ID +    
Sbjct: 94  RELAIQIHKDAVKFGADLGLRFALVYGGVDYDKQRELLQQGVDVIIATPGRLIDYV--KQ 151

Query: 610 GKITNLRRVTYLVMDEADRMFDMGFEPQITRIVQNI--RPDRQTVLFSATFPRQVEILAR 667
            K+ +L      V+DEADRMFD+GF   I  +++ +  R  RQT+LFSAT   +V  LA 
Sbjct: 152 HKVVSLHACEICVLDEADRMFDLGFIKDIRFLLRRMPERGTRQTLLFSATLSHRVLELAY 211

Query: 668 KVLNKPVEIQVGGRSVVNKDITQLVEVRPESDRFLRLLELLGEWYEKGKILIFVHSQEKC 727
           + +N+P ++ V   ++    + Q +    + ++   LL LL    E  + ++FV+++   
Sbjct: 212 EHMNEPEKLVVETETITAARVRQRIYFPADEEKQTLLLGLLSR-SEGARTMVFVNTKAFV 270

Query: 728 DALFRDLLKHGYPCLSLHGAKDQTDRESTISDFKSNVCNLLIATSVAARGLDVKELELVI 787
           + + R L +HGY    L G   Q  RES ++ F+     +L+AT VAARGL +  ++ V 
Sbjct: 271 ERVARTLERHGYRVGVLSGDVPQKKRESLLNRFQKGQLEILVATDVAARGLHIDGVKYVY 330

Query: 788 NFDAPNHYEDYVHRVGRTGRAGRKGCAITFISEEDAKYSPDLVKALELSEQVVP 841
           N+D P   EDYVHR+GRT R G +G AI+F  E  A   PD+   +E    V P
Sbjct: 331 NYDLPFDAEDYVHRIGRTARLGEEGDAISFACERYAMSLPDIEAYIEQKIPVEP 384

Length = 572

>gnl|CDD|214692 smart00487, DEXDc, DEAD-like helicases superfamily

 Score =  186 bits (475), Expect = 3e-54
 Identities = 77/211 (36%), Positives = 119/211 (56%), Gaps = 13/211 (6%)

Query: 482 IRKLNYEKPMPIQAQALPVIMSG-RDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDG 540
           I K  +E   P Q +A+  ++SG RD I  A TGSGKTLA +LP L  +K         G
Sbjct: 1   IEKFGFEPLRPYQKEAIEALLSGLRDVILAAPTGSGKTLAALLPALEALKRGK------G 54

Query: 541 PVGLIMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQISELKRG-TEIVVCTPG 599
              L++ PTREL +Q   +++K    +G++ V +YGG    +Q+ +L+ G T+I+V TPG
Sbjct: 55  GRVLVLVPTRELAEQWAEELKKLGPSLGLKVVGLYGGDSKREQLRKLESGKTDILVTTPG 114

Query: 600 RMIDILCTSGGKITNLRRVTYLVMDEADRMFDMGFEPQITRIVQNIRPDRQTVLFSATFP 659
           R++D+L        +L  V  +++DEA R+ D GF  Q+ ++++ +  + Q +L SAT P
Sbjct: 115 RLLDLLEN---DKLSLSNVDLVILDEAHRLLDGGFGDQLEKLLKLLPKNVQLLLLSATPP 171

Query: 660 RQVEILARKVLNKPVEIQVGGRSVVNKDITQ 690
            ++E L    LN PV I VG      + I Q
Sbjct: 172 EEIENLLELFLNDPVFIDVGFT--PLEPIEQ 200

Length = 201

>gnl|CDD|238005 cd00046, DEXDc, DEAD-like helicases superfamily

 Score =  146 bits (371), Expect = 7e-41
 Identities = 55/154 (35%), Positives = 85/154 (55%), Gaps = 10/154 (6%)

Query: 505 RDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFA 564
           RD +  A TGSGKTLA +LP+L  +          G   L++APTREL  Q+   +++  
Sbjct: 1   RDVLLAAPTGSGKTLAALLPILELLDSL------KGGQVLVLAPTRELANQVAERLKELF 54

Query: 565 KVMGVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMD 624
              G++   + GG+ + QQ   L   T+IVV TPGR++D L        +L+++  L++D
Sbjct: 55  GE-GIKVGYLIGGTSIKQQEKLLSGKTDIVVGTPGRLLDEL---ERLKLSLKKLDLLILD 110

Query: 625 EADRMFDMGFEPQITRIVQNIRPDRQTVLFSATF 658
           EA R+ + GF     +I+  +  DRQ +L SAT 
Sbjct: 111 EAHRLLNQGFGLLGLKILLKLPKDRQVLLLSATP 144

A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. Length = 144

>gnl|CDD|238034 cd00079, HELICc, Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may not be an autonomously folding unit, but an integral part of the helicase; 4 helicase superfamilies at present according to the organization of their signature motifs; all helicases share the ability to unwind nucleic acid duplexes with a distinct directional polarity; they utilize the free energy from nucleoside triphosphate hydrolysis to fuel their translocation along DNA, unwinding the duplex in the process

 Score =  129 bits (326), Expect = 6e-35
 Identities = 53/132 (40%), Positives = 74/132 (56%), Gaps = 2/132 (1%)

Query: 687 DITQLVEVRPESDRFLRLLELL-GEWYEKGKILIFVHSQEKCDALFRDLLKHGYPCLSLH 745
            I Q V +  E ++   LLELL     + GK+LIF  S++  D L   L K G    +LH
Sbjct: 1   PIKQYV-LPVEDEKLEALLELLKEHLKKGGKVLIFCPSKKMLDELAELLRKPGIKVAALH 59

Query: 746 GAKDQTDRESTISDFKSNVCNLLIATSVAARGLDVKELELVINFDAPNHYEDYVHRVGRT 805
           G   Q +RE  + DF+     +L+AT V ARG+D+  + +VIN+D P     Y+ R+GR 
Sbjct: 60  GDGSQEEREEVLKDFREGEIVVLVATDVIARGIDLPNVSVVINYDLPWSPSSYLQRIGRA 119

Query: 806 GRAGRKGCAITF 817
           GRAG+KG AI  
Sbjct: 120 GRAGQKGTAILL 131

Length = 131

>gnl|CDD|201125 pfam00271, Helicase_C, Helicase conserved C-terminal domain

 Score =   99 bits (250), Expect = 2e-25
 Identities = 33/76 (43%), Positives = 47/76 (61%)

Query: 734 LLKHGYPCLSLHGAKDQTDRESTISDFKSNVCNLLIATSVAARGLDVKELELVINFDAPN 793
           L K G     LHG   Q +RE  + DF++    +L+AT VA RG+D+ ++ LVIN+D P 
Sbjct: 3   LRKPGIKVARLHGGLSQEEREEILEDFRNGKSKVLVATDVAGRGIDLPDVNLVINYDLPW 62

Query: 794 HYEDYVHRVGRTGRAG 809
           +   Y+ R+GR GRAG
Sbjct: 63  NPASYIQRIGRAGRAG 78

The Prosite family is restricted to DEAD/H helicases, whereas this domain family is found in a wide variety of helicases and helicase related proteins. It may be that this is not an autonomously folding unit, but an integral part of the helicase. Length = 78

>gnl|CDD|197757 smart00490, HELICc, helicase superfamily c-terminal domain

 Score = 90.7 bits (226), Expect = 5e-22
 Identities = 32/82 (39%), Positives = 45/82 (54%)

Query: 728 DALFRDLLKHGYPCLSLHGAKDQTDRESTISDFKSNVCNLLIATSVAARGLDVKELELVI 787
           + L   L + G     LHG   Q +RE  +  F +    +L+AT VA RGLD+  ++LVI
Sbjct: 1   EELAELLKELGIKVARLHGGLSQEEREEILDKFNNGKIKVLVATDVAERGLDLPGVDLVI 60

Query: 788 NFDAPNHYEDYVHRVGRTGRAG 809
            +D P     Y+ R+GR GRAG
Sbjct: 61  IYDLPWSPASYIQRIGRAGRAG 82

Length = 82

>gnl|CDD|237171 PRK12678, PRK12678, transcription termination factor Rho; Provisional

 Score = 96.9 bits (242), Expect = 2e-20
 Identities = 42/182 (23%), Positives = 69/182 (37%), Gaps = 8/182 (4%)

Query: 2   AHSHRDRDREKEKEKHREKSRRSEREQSTDSDEDKHDKEKEKDKHR-DRDRRRDRDRDRD 60
           A          +  + RE+   + R  +  + E       E      +R    +RD  R 
Sbjct: 115 AAEAASAPEAAQARERRERGEAARRGAARKAGEGGEQPATEARADAAERTEEEERDERRR 174

Query: 61  REKEREEKRERAREKEREREKRDREREDRERERERERERRERDREREKRERERDRDKEKD 120
           R    + + E  R +   RE+R R+ +DR+R   RE+  R  +R R      R R + +D
Sbjct: 175 RGDREDRQAEAERGERGRREERGRDGDDRDRRDRREQGDRREERGRRDGGDRRGRRRRRD 234

Query: 121 RERKSRDREKRRKVESDDSDEDKDRDRKRRRRHDDDHKERVRERSLSRSNRHRDENDESP 180
           R     D  +  + + D  D +    R+ RR  D       R+R   R     +E +   
Sbjct: 235 RRDARGDDNREDRGDRDGDDGEGRGGRRGRRFRD-------RDRRGRRGGDGGNEREPEL 287

Query: 181 RE 182
           RE
Sbjct: 288 RE 289

Length = 672

>gnl|CDD|237171 PRK12678, PRK12678, transcription termination factor Rho; Provisional

 Score = 86.1 bits (214), Expect = 4e-17
 Identities = 34/201 (16%), Positives = 65/201 (32%), Gaps = 2/201 (0%)

Query: 6   RDRDREKEKEKHREKSRRSEREQSTDSDEDKHDKEKEKDKHRDRDRRRDRDRDRDREKER 65
           R  ++   +    +         +  +  +     +       R+R     R   R+   
Sbjct: 88  RQAEQPAAEAAAAKAEAAPAARAAAAAAAEAASAPEAAQARERRERGEAARRGAARKAGE 147

Query: 66  EEKRERAREKEREREKRDREREDRERERERERERRERDREREKRERERDRDKEKDRERKS 125
             ++     +    E+ + E  D  R R    +R+      E+  RE       DR+R+ 
Sbjct: 148 GGEQPATEARADAAERTEEEERDERRRRGDREDRQAEAERGERGRREERGRDGDDRDRRD 207

Query: 126 RDREKRRKVESDDSDEDKDRDRKRRRRHDDDHKERVRERSLSRSNRHRDENDESPREKLV 185
           R  +  R+ E    D    R R+RRR   D   +  RE    R     +        +  
Sbjct: 208 RREQGDRREERGRRDGGDRRGRRRRRDRRDARGDDNREDRGDRDGDDGEGRGGRRGRR-- 265

Query: 186 EDDSDKKEKKTREEELEDEQR 206
             D D++ ++  +   E E  
Sbjct: 266 FRDRDRRGRRGGDGGNEREPE 286

Length = 672

>gnl|CDD|233503 TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, large subunit, splicing factor

 Score = 83.8 bits (207), Expect = 1e-16
 Identities = 42/129 (32%), Positives = 58/129 (44%), Gaps = 18/129 (13%)

Query: 53  RDRDRDRDREKEREEKRERAREKEREREKRDREREDRERERERERERRERDREREKRERE 112
           RD + DR+REK R   R+R+ E+ R R         R+R R R+R RR R+R   +  R 
Sbjct: 1   RDEEPDREREKSRGRDRDRSSERPRRRS--------RDRSRFRDRHRRSRERSYREDSRP 52

Query: 113 RDRDKEKDRERKSRDREKRRKVESDDSDEDKDRDRKRRRRHDDDHKERVRERSLSRSNRH 172
           RDR +   R  +S      R          + RDR RRR       E+ R R   RS  +
Sbjct: 53  RDRRRYDSRSPRSLRYSSVR----------RSRDRPRRRSRSVRSIEQHRRRLRDRSPSN 102

Query: 173 RDENDESPR 181
           +   D+  R
Sbjct: 103 QWRKDDKKR 111

These splicing factors consist of an N-terminal arginine-rich low complexity domain followed by three tandem RNA recognition motifs (pfam00076). The well-characterized members of this family are auxilliary components of the U2 small nuclear ribonuclearprotein splicing factor (U2AF). These proteins are closely related to the CC1-like subfamily of splicing factors (TIGR01622). Members of this subfamily are found in plants, metazoa and fungi. Length = 509

>gnl|CDD|233503 TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, large subunit, splicing factor

 Score = 79.6 bits (196), Expect = 2e-15
 Identities = 35/111 (31%), Positives = 61/111 (54%), Gaps = 2/111 (1%)

Query: 41  KEKDKHRDRDRRRDRDRDRDREKEREEKRERAREKEREREKRDRER--EDRERERERERE 98
           ++++  R+R++ R RDRDR  E+ R   R+R+R ++R R  R+R    + R R+R R   
Sbjct: 1   RDEEPDREREKSRGRDRDRSSERPRRRSRDRSRFRDRHRRSRERSYREDSRPRDRRRYDS 60

Query: 99  RRERDREREKRERERDRDKEKDRERKSRDREKRRKVESDDSDEDKDRDRKR 149
           R  R        R RDR + + R  +S ++ +RR  +   S++ +  D+KR
Sbjct: 61  RSPRSLRYSSVRRSRDRPRRRSRSVRSIEQHRRRLRDRSPSNQWRKDDKKR 111

These splicing factors consist of an N-terminal arginine-rich low complexity domain followed by three tandem RNA recognition motifs (pfam00076). The well-characterized members of this family are auxilliary components of the U2 small nuclear ribonuclearprotein splicing factor (U2AF). These proteins are closely related to the CC1-like subfamily of splicing factors (TIGR01622). Members of this subfamily are found in plants, metazoa and fungi. Length = 509

>gnl|CDD|233503 TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, large subunit, splicing factor

 Score = 79.6 bits (196), Expect = 3e-15
 Identities = 34/117 (29%), Positives = 53/117 (45%), Gaps = 10/117 (8%)

Query: 18  REKSRRSEREQSTDSDEDKHDKEKEKDKHRDRDRRRDRDRDRDRE----KEREEKRERAR 73
           R++    ERE+S        D+++  ++ R R R R R RDR R       RE+ R R R
Sbjct: 1   RDEEPDREREKSRG-----RDRDRSSERPRRRSRDRSRFRDRHRRSRERSYREDSRPRDR 55

Query: 74  EKEREREKRDREREDRERERERERERRERDREREKRERERDRDKEKDRERKSRDREK 130
            +   R  R        R R+R R RR R     ++ R R RD+    + +  D+++
Sbjct: 56  RRYDSRSPRSLRYSSVRRSRDRPR-RRSRSVRSIEQHRRRLRDRSPSNQWRKDDKKR 111

These splicing factors consist of an N-terminal arginine-rich low complexity domain followed by three tandem RNA recognition motifs (pfam00076). The well-characterized members of this family are auxilliary components of the U2 small nuclear ribonuclearprotein splicing factor (U2AF). These proteins are closely related to the CC1-like subfamily of splicing factors (TIGR01622). Members of this subfamily are found in plants, metazoa and fungi. Length = 509

>gnl|CDD|237171 PRK12678, PRK12678, transcription termination factor Rho; Provisional

 Score = 77.3 bits (191), Expect = 2e-14
 Identities = 42/243 (17%), Positives = 70/243 (28%), Gaps = 30/243 (12%)

Query: 4   SHRDRDREKEKEKHREKSRRSEREQSTDSDEDKHDKEKEKDKHRDRDRRRDRDRDRDREK 63
           +     R   +     +       ++  +  +     +                     +
Sbjct: 72  APAAAARRAARAAAAARQAEQPAAEAAAAKAEAAPAARAAAAAAAEAASAPEAAQARERR 131

Query: 64  EREEKRERAREKEREREKRDREREDRERERER-ERERRERDREREKRERERDRDKEKDRE 122
           ER E   R   ++          E R    ER E E R+  R R  RE  +   +  +R 
Sbjct: 132 ERGEAARRGAARKAGEGGEQPATEARADAAERTEEEERDERRRRGDREDRQAEAERGERG 191

Query: 123 RKSRDREKRRKVESDDSDEDKDRDRKRRRRHDDDHKERVRERSLSRSNRHRDENDESPRE 182
           R+          +  D  E  DR  +R RR   D + R R R   R +   D+N E   +
Sbjct: 192 RREERGRDGDDRDRRDRREQGDRREERGRRDGGDRRGRRRRR--DRRDARGDDNREDRGD 249

Query: 183 KLVEDDSDKKEKKTREEELEDEQRKLDEEMEKRRRRVQEWQELKRKKEESERENRGDANV 242
           +  +D                     +    +R RR        R ++   R      N 
Sbjct: 250 RDGDDG--------------------EGRGGRRGRR-------FRDRDRRGRRGGDGGNE 282

Query: 243 EEP 245
            EP
Sbjct: 283 REP 285

Length = 672

>gnl|CDD|233503 TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, large subunit, splicing factor

 Score = 75.7 bits (186), Expect = 4e-14
 Identities = 36/120 (30%), Positives = 53/120 (44%), Gaps = 9/120 (7%)

Query: 43  KDKHRDRDRRRDRDRDRDREKEREEKRERAREKEREREKRDREREDRERERERERERRER 102
           +D+  DR+R + R RDRDR  ER  +R R R + R+R    R   +R   RE  R R  R
Sbjct: 1   RDEEPDREREKSRGRDRDRSSERPRRRSRDRSRFRDR---HRRSRERSY-REDSRPRDRR 56

Query: 103 DREREKRERERDRDKEKDRERKSRDREKRRKVESDDSDEDKDRDRKRRRRHDDDHKERVR 162
             +         R       R+SRDR +RR       ++ + R R R   +     ++ R
Sbjct: 57  RYDSRSP-----RSLRYSSVRRSRDRPRRRSRSVRSIEQHRRRLRDRSPSNQWRKDDKKR 111

These splicing factors consist of an N-terminal arginine-rich low complexity domain followed by three tandem RNA recognition motifs (pfam00076). The well-characterized members of this family are auxilliary components of the U2 small nuclear ribonuclearprotein splicing factor (U2AF). These proteins are closely related to the CC1-like subfamily of splicing factors (TIGR01622). Members of this subfamily are found in plants, metazoa and fungi. Length = 509

>gnl|CDD|224122 COG1201, Lhr, Lhr-like helicases [General function prediction only]

 Score = 75.4 bits (186), Expect = 8e-14
 Identities = 85/347 (24%), Positives = 140/347 (40%), Gaps = 39/347 (11%)

Query: 484 KLNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVG 543
           K  +    P Q  A+P I SG + + +A TGSGKT A  LP++  +         DG   
Sbjct: 17  KRKFTSLTPPQRYAIPEIHSGENVLIIAPTGSGKTEAAFLPVINELLSLGKGKLEDGIYA 76

Query: 544 LIMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQISE-LKRGTEIVVCTPGRMI 602
           L ++P + L   I   + +  + +G+  V V  G     +  + LK    I++ TP   +
Sbjct: 77  LYISPLKALNNDIRRRLEEPLRELGIE-VAVRHGDTPQSEKQKMLKNPPHILITTP-ESL 134

Query: 603 DILCTSGGKITNLRRVTYLVMDEADRMFD--------MGFEPQITRIVQNIRPDRQTVLF 654
            IL  S      LR V Y+++DE   + +        +  E    R+ + +  D Q +  
Sbjct: 135 AILLNSPKFRELLRDVRYVIVDEIHALAESKRGVQLALSLE----RL-RELAGDFQRIGL 189

Query: 655 SAT-------------FPRQVEILARKVLNKPVEIQVGGRSVVNKDITQLVEVRPESDRF 701
           SAT             F    EI+      K +EI+V   S V   I            +
Sbjct: 190 SATVGPPEEVAKFLVGFGDPCEIV-DVSAAKKLEIKV--ISPVEDLIYDEELWA---ALY 243

Query: 702 LRLLELLGEWYEKGKILIFVHSQEKCDALFRDLLK-HGYPCLSLHGAKDQTDRESTISDF 760
            R+ EL+    +    LIF +++   + L   L K         HG+  +  R       
Sbjct: 244 ERIAELVK---KHRTTLIFTNTRSGAERLAFRLKKLGPDIIEVHHGSLSRELRLEVEERL 300

Query: 761 KSNVCNLLIATSVAARGLDVKELELVINFDAPNHYEDYVHRVGRTGR 807
           K      ++ATS    G+D+ +++LVI   +P     ++ R+GR G 
Sbjct: 301 KEGELKAVVATSSLELGIDIGDIDLVIQLGSPKSVNRFLQRIGRAGH 347

Length = 814

>gnl|CDD|233503 TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, large subunit, splicing factor

 Score = 73.8 bits (181), Expect = 2e-13
 Identities = 31/115 (26%), Positives = 48/115 (41%), Gaps = 6/115 (5%)

Query: 34  EDKHDKEKEKDKHRDRDRRRDRDRDRDREKEREEKRERAREKEREREKRDREREDRERER 93
           E   ++EK + + RDR   R R R RDR + R+  R   R +ER   +  R    R+R R
Sbjct: 4   EPDREREKSRGRDRDRSSERPRRRSRDRSRFRDRHR---RSRERSYREDSR---PRDRRR 57

Query: 94  ERERERRERDREREKRERERDRDKEKDRERKSRDREKRRKVESDDSDEDKDRDRK 148
              R  R       +R R+R R + +      + R + R     +     D+ R 
Sbjct: 58  YDSRSPRSLRYSSVRRSRDRPRRRSRSVRSIEQHRRRLRDRSPSNQWRKDDKKRS 112

These splicing factors consist of an N-terminal arginine-rich low complexity domain followed by three tandem RNA recognition motifs (pfam00076). The well-characterized members of this family are auxilliary components of the U2 small nuclear ribonuclearprotein splicing factor (U2AF). These proteins are closely related to the CC1-like subfamily of splicing factors (TIGR01622). Members of this subfamily are found in plants, metazoa and fungi. Length = 509

>gnl|CDD|129701 TIGR00614, recQ_fam, ATP-dependent DNA helicase, RecQ family

 Score = 71.7 bits (176), Expect = 7e-13
 Identities = 77/354 (21%), Positives = 141/354 (39%), Gaps = 46/354 (12%)

Query: 487 YEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIM 546
                P+Q + +  ++ GRDC  V  TG GK+L + LP           A     + L++
Sbjct: 9   LSSFRPVQLEVINAVLLGRDCFVVMPTGGGKSLCYQLP-----------ALCSDGITLVI 57

Query: 547 APTREL----VQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQ---ISELKRGT-EIVVCTP 598
           +P   L    V Q+        K  G+    +       QQ   +++LK G  +++  TP
Sbjct: 58  SPLISLMEDQVLQL--------KASGIPATFLNSSQSKEQQKNVLTDLKDGKIKLLYVTP 109

Query: 599 GRMIDILCTSGGKITNL---RRVTYLVMDEADRMFDMG--FEPQITR--IVQNIRPDRQT 651
            +       S   +  L   + +T + +DEA  +   G  F P       ++   P+   
Sbjct: 110 EK----CSASNRLLQTLEERKGITLIAVDEAHCISQWGHDFRPDYKALGSLKQKFPNVPI 165

Query: 652 VLFSATFPRQV--EILARKVLNKPVEIQVGGRSVVNKDITQLVEVRPESDRFLR-LLELL 708
           +  +AT    V  +IL +  L  P +I        N       EVR ++ + L  LL  +
Sbjct: 166 MALTATASPSVREDILRQLNLKNP-QIFCTSFDRPN----LYYEVRRKTPKILEDLLRFI 220

Query: 709 GEWYEKGKILIFVHSQEKCDALFRDLLKHGYPCLSLHGAKDQTDRESTISDFKSNVCNLL 768
            + ++    +I+  S++K + +   L   G    + H   + + R+     F+ +   ++
Sbjct: 221 RKEFKGKSGIIYCPSRKKSEQVTASLQNLGIAAGAYHAGLEISARDDVHHKFQRDEIQVV 280

Query: 769 IATSVAARGLDVKELELVINFDAPNHYEDYVHRVGRTGRAGRKGCAITFISEED 822
           +AT     G++  ++  VI++  P   E Y    GR GR G       F +  D
Sbjct: 281 VATVAFGMGINKPDVRFVIHYSLPKSMESYYQESGRAGRDGLPSECHLFYAPAD 334

All proteins in this family for which functions are known are 3'-5' DNA-DNA helicases. These proteins are used for recombination, recombinational repair, and possibly maintenance of chromosome stability. 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 = 470

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 68.6 bits (167), Expect = 1e-11
 Identities = 50/277 (18%), Positives = 124/277 (44%), Gaps = 4/277 (1%)

Query: 10   REKEKEKHREKSRRSEREQSTDSDEDKHDKEKEKDKHRDRDRRRDRDRDRDREKEREEKR 69
            R+ E  K  E  +++E  +    +  K ++E+  ++ R  +  R     R +   + E+ 
Sbjct: 1218 RKAEDAKKAEAVKKAEEAKKDAEEAKKAEEERNNEEIRKFEEARMAHFARRQAAIKAEEA 1277

Query: 70   ERAREKEREREKRDREREDRERERERERERRERDREREKRE---RERDRDKEKDRERKSR 126
             +A E ++  EK+  +   +  E+++  E +++  E +K +   ++ +  K+K    K +
Sbjct: 1278 RKADELKKAEEKKKADEAKKAEEKKKADEAKKKAEEAKKADEAKKKAEEAKKKADAAKKK 1337

Query: 127  DREKRRKVESDDSDEDKDRDRKRRRRHDDDHKERVRERSLSRSNRHRDENDESPREKLVE 186
              E ++  E+  ++ +   D         +  E+ +E +  +++  + + +E  +    +
Sbjct: 1338 AEEAKKAAEAAKAEAEAAADEAEAAEEKAEAAEKKKEEAKKKADAAKKKAEEKKKADEAK 1397

Query: 187  DDSDKKEKKTREEELEDEQRKLDEEMEKRRRRVQEWQELKRKKEESERENRGDANVEEPK 246
              +++ +KK  E +     +K  +E +K+    ++  E K+K EE+++ +      EE K
Sbjct: 1398 KKAEEDKKKADELKKAAAAKKKADEAKKKAEEKKKADEAKKKAEEAKKADEAKKKAEEAK 1457

Query: 247  AGRNWTLDREDSDDEEVPQTGKSETDMDADEEPKPSE 283
                     E++   +  +  K+E    ADE  K +E
Sbjct: 1458 KAEEAKKKAEEAKKADEAKK-KAEEAKKADEAKKKAE 1493

Length = 2084

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 68.6 bits (167), Expect = 1e-11
 Identities = 42/260 (16%), Positives = 122/260 (46%)

Query: 11   EKEKEKHREKSRRSEREQSTDSDEDKHDKEKEKDKHRDRDRRRDRDRDRDREKEREEKRE 70
            E+ K+K  E  + +E ++  D  +   + +K  +  +  + ++  +  +  EK++ ++ +
Sbjct: 1493 EEAKKKADEAKKAAEAKKKADEAKKAEEAKKADEAKKAEEAKKADEAKKAEEKKKADELK 1552

Query: 71   RAREKEREREKRDREREDRERERERERERRERDREREKRERERDRDKEKDRERKSRDREK 130
            +A E ++  EK+  E   +  E +    R+  + ++ +  R  +  K  + E+K +  E 
Sbjct: 1553 KAEELKKAEEKKKAEEAKKAEEDKNMALRKAEEAKKAEEARIEEVMKLYEEEKKMKAEEA 1612

Query: 131  RRKVESDDSDEDKDRDRKRRRRHDDDHKERVRERSLSRSNRHRDENDESPREKLVEDDSD 190
            ++  E+    E+  +  + +++ +   K+   E+  +   +  +E ++    +  +   +
Sbjct: 1613 KKAEEAKIKAEELKKAEEEKKKVEQLKKKEAEEKKKAEELKKAEEENKIKAAEEAKKAEE 1672

Query: 191  KKEKKTREEELEDEQRKLDEEMEKRRRRVQEWQELKRKKEESERENRGDANVEEPKAGRN 250
             K+K    ++ E++++K  E ++K     ++ +ELK+K+ E +++       EE    + 
Sbjct: 1673 DKKKAEEAKKAEEDEKKAAEALKKEAEEAKKAEELKKKEAEEKKKAEELKKAEEENKIKA 1732

Query: 251  WTLDREDSDDEEVPQTGKSE 270
                +E  +D++  +  K +
Sbjct: 1733 EEAKKEAEEDKKKAEEAKKD 1752

Length = 2084

>gnl|CDD|220648 pfam10243, MIP-T3, Microtubule-binding protein MIP-T3

 Score = 64.9 bits (158), Expect = 1e-10
 Identities = 42/167 (25%), Positives = 73/167 (43%), Gaps = 3/167 (1%)

Query: 7   DRDREKEKEKHREKSRRSEREQSTDSDEDKHDKEKEKDKHRDRDRRRDRDRDRDREKERE 66
           ++ ++KEK K   K R+ + E        + +KEKEK     RDR  ++ R+R R K R 
Sbjct: 116 EKKKKKEKPKEEPKDRKPKEEAKEKRPPKEKEKEKEKKVEEPRDREEEKKRERVRAKSRP 175

Query: 67  EKRERAREKEREREKRDREREDRERERERERERRERDREREKRERERDRDKEKDRERKSR 126
           +K  + +   +++E  + E   ++R+  RE  + + +      ERE++ D  KDRE  + 
Sbjct: 176 KKPPKKKPPNKKKEPPEEE---KQRQAAREAVKGKPEEPDVNEEREKEEDDGKDRETTTS 232

Query: 127 DREKRRKVESDDSDEDKDRDRKRRRRHDDDHKERVRERSLSRSNRHR 173
             E+    +S +         K+            RE S     R R
Sbjct: 233 PMEEDESRQSSEISRRSSSSLKKPDPSPSMASPETRESSKRTETRPR 279

This protein, which interacts with both microtubules and TRAF3 (tumour necrosis factor receptor-associated factor 3), is conserved from worms to humans. The N-terminal region is the microtubule binding domain and is well-conserved; the C-terminal 100 residues, also well-conserved, constitute the coiled-coil region which binds to TRAF3. The central region of the protein is rich in lysine and glutamic acid and carries KKE motifs which may also be necessary for tubulin-binding, but this region is the least well-conserved. Length = 506

>gnl|CDD|220648 pfam10243, MIP-T3, Microtubule-binding protein MIP-T3

 Score = 64.9 bits (158), Expect = 1e-10
 Identities = 31/152 (20%), Positives = 79/152 (51%), Gaps = 2/152 (1%)

Query: 9   DREKEKEKHREKSRRSEREQSTDSDEDKH-DKEKEKDKHRDRDRRRDRDRDRDREKEREE 67
            +E+EKEK + K  + ++++    +      KE+ K+K   +++ +++++  +  ++REE
Sbjct: 103 GKEEEKEKEQVKEEKKKKKEKPKEEPKDRKPKEEAKEKRPPKEKEKEKEKKVEEPRDREE 162

Query: 68  KRERAREKEREREKRDREREDRERERERERERRERDREREKRER-ERDRDKEKDRERKSR 126
           +++R R + + R K+  +++   +++E   E ++R   RE  +    + D  ++RE++  
Sbjct: 163 EKKRERVRAKSRPKKPPKKKPPNKKKEPPEEEKQRQAAREAVKGKPEEPDVNEEREKEED 222

Query: 127 DREKRRKVESDDSDEDKDRDRKRRRRHDDDHK 158
           D + R    S   +++  +  +  RR     K
Sbjct: 223 DGKDRETTTSPMEEDESRQSSEISRRSSSSLK 254

This protein, which interacts with both microtubules and TRAF3 (tumour necrosis factor receptor-associated factor 3), is conserved from worms to humans. The N-terminal region is the microtubule binding domain and is well-conserved; the C-terminal 100 residues, also well-conserved, constitute the coiled-coil region which binds to TRAF3. The central region of the protein is rich in lysine and glutamic acid and carries KKE motifs which may also be necessary for tubulin-binding, but this region is the least well-conserved. Length = 506

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 65.2 bits (158), Expect = 2e-10
 Identities = 44/284 (15%), Positives = 127/284 (44%), Gaps = 10/284 (3%)

Query: 6    RDRDREKEKEKHREKSRRSEREQSTDSDEDKHDKEKEKDKHRDRDRRRDRDRDRDREKER 65
                 + E E   +++  +E +      + +  K+K     +  + ++  D  + + +E 
Sbjct: 1344 AAEAAKAEAEAAADEAEAAEEKAEAAEKKKEEAKKKADAAKKKAEEKKKADEAKKKAEED 1403

Query: 66   EEKRERAREKEREREKRDREREDRERERERERERRERDREREKRERERDRDKEKDRERKS 125
            ++K +  ++    ++K D  ++  E +++ +  +++ +  ++  E ++  ++ K  E   
Sbjct: 1404 KKKADELKKAAAAKKKADEAKKKAEEKKKADEAKKKAEEAKKADEAKKKAEEAKKAEEAK 1463

Query: 126  RDREKRRKVESDDSDEDKDRDRKRRRRHDDDHKERVRERSLSRSNRHRDENDESPREKLV 185
            +  E+ +K +      ++ +     ++  ++ K++  E   +   + + +  +   E   
Sbjct: 1464 KKAEEAKKADEAKKKAEEAKKADEAKKKAEEAKKKADEAKKAAEAKKKADEAKKAEEAKK 1523

Query: 186  EDDSDKKEKKTREEELED-EQRKLDEEMEKRR--RRVQEWQELKRKKEESERENRGDANV 242
             D++ K E+  + +E +  E++K  +E++K    ++ +E ++ +  K+  E +N      
Sbjct: 1524 ADEAKKAEEAKKADEAKKAEEKKKADELKKAEELKKAEEKKKAEEAKKAEEDKNMALRKA 1583

Query: 243  EEPKAGRNWTLDREDSDDEEVPQTGKSETDMDADEEPKPSENQV 286
            EE K         E++  EEV +  + E  M A+E  K  E ++
Sbjct: 1584 EEAKKA-------EEARIEEVMKLYEEEKKMKAEEAKKAEEAKI 1620

Length = 2084

>gnl|CDD|223588 COG0514, RecQ, Superfamily II DNA helicase [DNA replication, recombination, and repair]

 Score = 64.2 bits (157), Expect = 2e-10
 Identities = 75/346 (21%), Positives = 146/346 (42%), Gaps = 46/346 (13%)

Query: 494 QAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELV 553
           Q + +  ++SG+D + V  TG GK+L + +P L            +G   L+++P   L+
Sbjct: 22  QQEIIDALLSGKDTLVVMPTGGGKSLCYQIPAL----------LLEGLT-LVVSPLISLM 70

Query: 554 Q-QIHSDIRKFAKVMGVRCVPVYGGSGVAQQISE----LKRGT-EIVVCTP-----GRMI 602
           + Q+        +  G+R   +   +   ++  +    LK G  +++  +P      R +
Sbjct: 71  KDQVDQ-----LEAAGIRAAYL-NSTLSREERQQVLNQLKSGQLKLLYISPERLMSPRFL 124

Query: 603 DILCTSGGKITNLRRVTYLVMDEADRMFDMG--FEPQITRIVQNIR--PDRQTVLFSATF 658
           ++L            ++ + +DEA  +   G  F P   R+ +     P+   +  +AT 
Sbjct: 125 ELLKRL--------PISLVAIDEAHCISQWGHDFRPDYRRLGRLRAGLPNPPVLALTATA 176

Query: 659 PRQVEILARKVLN-KPVEIQVGGRSVVNKDITQLVEVRPESDRFLRLLELLGEWYEKGKI 717
             +V    R+ L  +   I  G  S    ++   ++V  + +   +L  L     +  K 
Sbjct: 177 TPRVRDDIREQLGLQDANIFRG--SFDRPNL--ALKVVEKGEPSDQLAFLATVLPQLSKS 232

Query: 718 -LIFVHSQEKCDALFRDLLKHGYPCLSLHGAKDQTDRESTISDFKSNVCNLLIATSVAAR 776
            +I+  +++K + L   L K+G    + H      +RE     F ++   +++AT+    
Sbjct: 233 GIIYCLTRKKVEELAEWLRKNGISAGAYHAGLSNEERERVQQAFLNDEIKVMVATNAFGM 292

Query: 777 GLDVKELELVINFDAPNHYEDYVHRVGRTGRAGRKGCAITFISEED 822
           G+D  ++  VI++D P   E Y    GR GR G    AI   S ED
Sbjct: 293 GIDKPDVRFVIHYDLPGSIESYYQETGRAGRDGLPAEAILLYSPED 338

Length = 590

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 64.0 bits (155), Expect = 4e-10
 Identities = 48/278 (17%), Positives = 110/278 (39%), Gaps = 4/278 (1%)

Query: 10   REKEKEKHREKSRRSEREQSTDSDEDKHDKEKEKDKHRDRDRRRDRDRDRDREKEREEKR 69
            R+ E+ +  E ++++E  +  +      +  K +D  +    R+  +  +  E  + E  
Sbjct: 1164 RKAEEARKAEDAKKAEAARKAEEVRKAEELRKAEDARKAEAARKAEEERKAEEARKAEDA 1223

Query: 70   ERAREKEREREKRDREREDRERERERERERRERDREREKRERERDRDKEKDRERKSRDR- 128
            ++A   ++  E +    E ++ E ER  E   +  E       R +   K  E +  D  
Sbjct: 1224 KKAEAVKKAEEAKKDAEEAKKAEEERNNEEIRKFEEARMAHFARRQAAIKAEEARKADEL 1283

Query: 129  ---EKRRKVESDDSDEDKDRDRKRRRRHDDDHKERVRERSLSRSNRHRDENDESPREKLV 185
               E+++K +     E+K +  + +++ ++  K    ++    + +  D   +   E   
Sbjct: 1284 KKAEEKKKADEAKKAEEKKKADEAKKKAEEAKKADEAKKKAEEAKKKADAAKKKAEEAKK 1343

Query: 186  EDDSDKKEKKTREEELEDEQRKLDEEMEKRRRRVQEWQELKRKKEESERENRGDANVEEP 245
              ++ K E +   +E E  + K +   +K+    ++    K+K EE ++ +      EE 
Sbjct: 1344 AAEAAKAEAEAAADEAEAAEEKAEAAEKKKEEAKKKADAAKKKAEEKKKADEAKKKAEED 1403

Query: 246  KAGRNWTLDREDSDDEEVPQTGKSETDMDADEEPKPSE 283
            K   +       +  +      K+E    ADE  K +E
Sbjct: 1404 KKKADELKKAAAAKKKADEAKKKAEEKKKADEAKKKAE 1441

Length = 2084

>gnl|CDD|224036 COG1111, MPH1, ERCC4-like helicases [DNA replication, recombination, and repair]

 Score = 63.1 bits (154), Expect = 4e-10
 Identities = 38/147 (25%), Positives = 68/147 (46%), Gaps = 13/147 (8%)

Query: 690 QLVEVRPESDRFLRLLELLGEWYEKG---KILIFVHSQEKCDALFRDLLKHGYPCLSL-- 744
           +  E   E  +  +L E+L E  EK    ++++F   ++  + +   L K G        
Sbjct: 339 RADESGVEHPKLEKLREILKEQLEKNGDSRVIVFTEYRDTAEEIVNFLKKIGIKARVRFI 398

Query: 745 -HGAKD------QTDRESTISDFKSNVCNLLIATSVAARGLDVKELELVINFDAPNHYED 797
              +++      Q +++  I  F+    N+L+ATSV   GLD+ E++LVI ++       
Sbjct: 399 GQASREGDKGMSQKEQKEIIDQFRKGEYNVLVATSVGEEGLDIPEVDLVIFYEPVPSEIR 458

Query: 798 YVHRVGRTGRAGRKGCAITFISEEDAK 824
            + R GRTGR  RKG  +  ++E    
Sbjct: 459 SIQRKGRTGR-KRKGRVVVLVTEGTRD 484

Length = 542

>gnl|CDD|233496 TIGR01622, SF-CC1, splicing factor, CC1-like family

 Score = 63.0 bits (153), Expect = 4e-10
 Identities = 31/104 (29%), Positives = 48/104 (46%), Gaps = 14/104 (13%)

Query: 45  KHRDRDRRRDRDRDRDREKEREEKRERAREKEREREKRDREREDRERERERERERRERDR 104
           ++RDR+R R R+  R  +K RE  R R+R ++R R         R R+R+  R RR R R
Sbjct: 1   RYRDRERGRLRNDTRRSDKGRERSRRRSRSRDRSR---------RRRDRDYYRGRRGRSR 51

Query: 105 EREKRERERDRDKEKDRERKSRDREKRRKVESDDSDEDKDRDRK 148
            R      R R       R  R  ++R    + +   + +RD +
Sbjct: 52  SRSPNRYYRPRGD-----RSYRRDDRRSGRNTKEPLTEAERDDR 90

This model represents a subfamily of RNA splicing factors including the Pad-1 protein (N. crassa), CAPER (M. musculus) and CC1.3 (H.sapiens). These proteins are characterized by an N-terminal arginine-rich, low complexity domain followed by three (or in the case of 4 H. sapiens paralogs, two) RNA recognition domains (rrm: pfam00706). These splicing factors are closely related to the U2AF splicing factor family (TIGR01642). A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the seed. Length = 457

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 63.6 bits (154), Expect = 5e-10
 Identities = 72/417 (17%), Positives = 174/417 (41%), Gaps = 21/417 (5%)

Query: 10   REKEKEKHREKSRRSEREQSTDSDEDKHDKEKEKDKHRDRDRRRDRDRDRDREKEREEKR 69
            ++ ++ K  E+ ++++  +  +  +   +K+K ++  +  + +    R  +  K+ EE R
Sbjct: 1534 KKADEAKKAEEKKKADELKKAEELKKAEEKKKAEEAKKAEEDKNMALRKAEEAKKAEEAR 1593

Query: 70   ERAREKEREREKRDREREDRERERERERERRERDREREKRERERDRDKEKDRERKSRDRE 129
                 K  E EK+ +  E ++ E  + +    +  E EK++ E+ + KE + ++K+ + +
Sbjct: 1594 IEEVMKLYEEEKKMKAEEAKKAEEAKIKAEELKKAEEEKKKVEQLKKKEAEEKKKAEELK 1653

Query: 130  KRRKVESDDSDEDKDRDRKRRRRHDDDHKERVRERSLSRSNRHRDENDESPREKLVEDDS 189
            K  +     + E+  +  + +++ ++  K    E+  + + +   E  E+ + + ++   
Sbjct: 1654 KAEEENKIKAAEEAKKAEEDKKKAEEAKKAEEDEKKAAEALKKEAE--EAKKAEELKKKE 1711

Query: 190  DKKEKKTREEELEDEQRKLDEEMEKRRRRVQEWQELKRKKEESERENRGDAN-VEEPKAG 248
             +++KK  E +  +E+ K+  E  K+        E  +KK E  +++  +   +   K  
Sbjct: 1712 AEEKKKAEELKKAEEENKIKAEEAKKE------AEEDKKKAEEAKKDEEEKKKIAHLKKE 1765

Query: 249  RNWTLDREDSDDEEVPQTGKSETDMDADEEPKPSENQVGDAMLVDSDGGSAAPALQIGAA 308
                 +    + E V +    E D     E       + D      +GG     +   + 
Sbjct: 1766 EEKKAEEIRKEKEAVIEEELDEEDEKRRMEVDKKIKDIFDNFANIIEGGKEGNLVINDSK 1825

Query: 309  EDEDIDPLDAFMNS-MVLPEVEKL------KNTVEPSFTDGNNVESKKMDRKGDRRSNGE 361
            E ED    +   +  M L E +        KN       +     +K+ D K D     E
Sbjct: 1826 EMEDSAIKEVADSKNMQLEEADAFEKHKFNKNNENGEDGNKEADFNKEKDLKEDDEEEIE 1885

Query: 362  QPKKSSNKSLGR-IIPGEDSDSDYGDLENDEKPLEDEDDDEFMKR-VKKTKAEKLSI 416
            +  +   + + +  I  E  +++    +N++   +  D DE++KR  ++T+ E + I
Sbjct: 1886 EADE--IEKIDKDDIEREIPNNNMAG-KNNDIIDDKLDKDEYIKRDAEETREEIIKI 1939

Length = 2084

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 62.9 bits (152), Expect = 7e-10
 Identities = 46/280 (16%), Positives = 133/280 (47%), Gaps = 6/280 (2%)

Query: 7    DRDREKEKEKHREKSRRSEREQSTDSDEDKHDKEKEKDKHRDRDRRRDRDRDRDREKERE 66
            D  ++K +EK +    + + E++  +DE K   E+ K     + +  +  +  + +K+ E
Sbjct: 1421 DEAKKKAEEKKKADEAKKKAEEAKKADEAKKKAEEAKKAEEAKKKAEEAKKADEAKKKAE 1480

Query: 67   EKRERAREKEREREKRDREREDRERERERERERRERDREREKRERERDRDKEKDRERKSR 126
            E ++    K++  E + +  E ++    +++    +  E  K+  E  + +E  +  +++
Sbjct: 1481 EAKKADEAKKKAEEAKKKADEAKKAAEAKKKADEAKKAEEAKKADEAKKAEEAKKADEAK 1540

Query: 127  DREKRRKVESDDSDEDKDRDRKRRRRHDDDHKERVRERSLSRSNRHRDENDESPREKLVE 186
              E+++K +     E+  +  ++++  +    E  +  +L ++   + + +E+  E++++
Sbjct: 1541 KAEEKKKADELKKAEELKKAEEKKKAEEAKKAEEDKNMALRKAEEAK-KAEEARIEEVMK 1599

Query: 187  DDSDKKEKKTREEELEDEQRKLDEEMEKRRRRVQEWQELKRKKEESERENRGDANVEEPK 246
               ++K+ K  E +  +E +   EE++K     ++ ++LK+K+ E +++       EE  
Sbjct: 1600 LYEEEKKMKAEEAKKAEEAKIKAEELKKAEEEKKKVEQLKKKEAEEKKKAEELKKAEEEN 1659

Query: 247  AGRNWTLDREDSDDEEVPQTGKSETDMDADEEPKPSENQV 286
              +     ++  +D++     K+E    A+E+ K +   +
Sbjct: 1660 KIKAAEEAKKAEEDKK-----KAEEAKKAEEDEKKAAEAL 1694

Length = 2084

>gnl|CDD|233503 TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, large subunit, splicing factor

 Score = 61.8 bits (150), Expect = 1e-09
 Identities = 33/112 (29%), Positives = 47/112 (41%), Gaps = 4/112 (3%)

Query: 100 RERDREREK-RERERDRDKEKDRER-KSRDREKRRKVESDDSDEDKDRDRKRRRRHDDDH 157
            E DREREK R R+RDR  E+ R R + R R + R   S +    +D  R R RR  D  
Sbjct: 3   EEPDREREKSRGRDRDRSSERPRRRSRDRSRFRDRHRRSRERSYRED-SRPRDRRRYDSR 61

Query: 158 KERVRERSLSRSNRHRDENDESPREKLV-EDDSDKKEKKTREEELEDEQRKL 208
             R    S  R +R R          +       +    + +   +D++R L
Sbjct: 62  SPRSLRYSSVRRSRDRPRRRSRSVRSIEQHRRRLRDRSPSNQWRKDDKKRSL 113

These splicing factors consist of an N-terminal arginine-rich low complexity domain followed by three tandem RNA recognition motifs (pfam00076). The well-characterized members of this family are auxilliary components of the U2 small nuclear ribonuclearprotein splicing factor (U2AF). These proteins are closely related to the CC1-like subfamily of splicing factors (TIGR01622). Members of this subfamily are found in plants, metazoa and fungi. Length = 509

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 62.5 bits (151), Expect = 1e-09
 Identities = 47/278 (16%), Positives = 123/278 (44%), Gaps = 5/278 (1%)

Query: 10   REKEKEKHREKSRRSEREQSTDSDEDKHDKEKEKDKHRDRDRRRDRDRDRDREKEREEKR 69
            + +E +K  E+++++E E++ +      +        R    + +  R  D  K+ EEK+
Sbjct: 1231 KAEEAKKDAEEAKKAEEERNNEEIRKFEEARMAHFARRQAAIKAEEARKADELKKAEEKK 1290

Query: 70   ERAREKEREREKRDREREDRERERERERERRERDREREKRERERDRDKEKDRERKSRDRE 129
             +A E ++  EK+  +   ++ E  ++ +  ++  E  K++ +  + K ++ ++ +   +
Sbjct: 1291 -KADEAKKAEEKKKADEAKKKAEEAKKADEAKKKAEEAKKKADAAKKKAEEAKKAAEAAK 1349

Query: 130  KRRKVESDDSDEDKDRDRKRRRRHDDDHKERVRERSLSRSNRHRDENDESPRE--KLVED 187
               +  +D+++  +++     ++ ++  K+    +  +   +  DE  +   E  K  ++
Sbjct: 1350 AEAEAAADEAEAAEEKAEAAEKKKEEAKKKADAAKKKAEEKKKADEAKKKAEEDKKKADE 1409

Query: 188  DSDKKEKKTREEELED--EQRKLDEEMEKRRRRVQEWQELKRKKEESERENRGDANVEEP 245
                   K + +E +   E++K  +E +K+    ++  E K+K EE+++        EE 
Sbjct: 1410 LKKAAAAKKKADEAKKKAEEKKKADEAKKKAEEAKKADEAKKKAEEAKKAEEAKKKAEEA 1469

Query: 246  KAGRNWTLDREDSDDEEVPQTGKSETDMDADEEPKPSE 283
            K         E++   +  +    E    ADE  K +E
Sbjct: 1470 KKADEAKKKAEEAKKADEAKKKAEEAKKKADEAKKAAE 1507

Length = 2084

>gnl|CDD|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and chromosome partitioning]

 Score = 62.0 bits (151), Expect = 1e-09
 Identities = 41/245 (16%), Positives = 92/245 (37%), Gaps = 10/245 (4%)

Query: 8   RDREKEKEKHREKSRRSEREQSTDSDEDKHDKEKEKDKHRDRDRRRDRDRDRDREKEREE 67
            + EKE E+ + +      E     +E    KE+ ++   +    R+R  + + E E  E
Sbjct: 263 EEAEKEIEELKSELEELREELEELQEELLELKEEIEELEGEISLLRERLEELENELEELE 322

Query: 68  KRERAREKEREREKRDRERE---DRERERERERERRERDREREKRERERDRDKEKDRERK 124
           +R    +++ E  K + E       E E+        ++   EK     +  +E     +
Sbjct: 323 ERLEELKEKIEALKEELEERETLLEELEQLLAELEEAKEELEEKLSALLEELEELFEALR 382

Query: 125 SRDREKRRKVESDDSD-----EDKDRDRKRRRRHDDDHKERVRERSLSRSNRHRDENDES 179
               E   ++    ++      + +   +R  R  +  ++   E     +    +E    
Sbjct: 383 EELAELEAELAEIRNELEELKREIESLEERLERLSERLEDLKEELKELEAEL--EELQTE 440

Query: 180 PREKLVEDDSDKKEKKTREEELEDEQRKLDEEMEKRRRRVQEWQELKRKKEESERENRGD 239
             E   E +  +++ +   + L++ +R+L E  E+ +R  +E   L+ + +  E E R  
Sbjct: 441 LEELNEELEELEEQLEELRDRLKELERELAELQEELQRLEKELSSLEARLDRLEAEQRAS 500

Query: 240 ANVEE 244
             V  
Sbjct: 501 QGVRA 505

Length = 1163

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 61.3 bits (148), Expect = 3e-09
 Identities = 50/285 (17%), Positives = 124/285 (43%), Gaps = 11/285 (3%)

Query: 10   REKEKEKHREKSRRSEREQSTDSDEDKHDKEKEKDKHRDRDRRRDRDRDRDREKEREEKR 69
            ++K +E  +    + + E++  +DE K   E+ K K  +  +  +  +  D  K+ EE +
Sbjct: 1463 KKKAEEAKKADEAKKKAEEAKKADEAKKKAEEAKKKADEAKKAAEAKKKADEAKKAEEAK 1522

Query: 70   --ERAREKEREREKRDREREDRERERERERERRERDREREKRERERDRDKEKDRERKSRD 127
              + A++ E  ++  + ++ + +++ +  ++  E  +  EK++ E  +  E+D+    R 
Sbjct: 1523 KADEAKKAEEAKKADEAKKAEEKKKADELKKAEELKKAEEKKKAEEAKKAEEDKNMALRK 1582

Query: 128  REKRRKVESDDSDEDKDRDRKRRRRHDDDHKERVRERSLSRSNRHRDENDESPRE--KLV 185
             E+ +K E    +E      + ++   ++ K+    +  +   +  +E  +   +  K  
Sbjct: 1583 AEEAKKAEEARIEEVMKLYEEEKKMKAEEAKKAEEAKIKAEELKKAEEEKKKVEQLKKKE 1642

Query: 186  EDDSDKKEKKTREEEL-----EDEQRKLDEEMEKRRRRVQEWQELKRKKEESERENRGDA 240
             ++  K E+  + EE       +E +K +E+ +K     +  ++ K+  E  ++E     
Sbjct: 1643 AEEKKKAEELKKAEEENKIKAAEEAKKAEEDKKKAEEAKKAEEDEKKAAEALKKEAEEAK 1702

Query: 241  NVEEPKAGRNWTLDREDS--DDEEVPQTGKSETDMDADEEPKPSE 283
              EE K        + +     EE  +    E   +A+E+ K +E
Sbjct: 1703 KAEELKKKEAEEKKKAEELKKAEEENKIKAEEAKKEAEEDKKKAE 1747

Length = 2084

>gnl|CDD|233496 TIGR01622, SF-CC1, splicing factor, CC1-like family

 Score = 60.3 bits (146), Expect = 3e-09
 Identities = 30/94 (31%), Positives = 42/94 (44%), Gaps = 5/94 (5%)

Query: 71  RAREKEREREKRDREREDRERERERERERRERDREREKRERERDRDKEKDRERKSRDREK 130
           R R++ER R + D  R D+ RER R R R      R++  R RDRD  + R  +SR R  
Sbjct: 1   RYRDRERGRLRNDTRRSDKGRERSRRRSR-----SRDRSRRRRDRDYYRGRRGRSRSRSP 55

Query: 131 RRKVESDDSDEDKDRDRKRRRRHDDDHKERVRER 164
            R          +  DR+  R   +   E  R+ 
Sbjct: 56  NRYYRPRGDRSYRRDDRRSGRNTKEPLTEAERDD 89

This model represents a subfamily of RNA splicing factors including the Pad-1 protein (N. crassa), CAPER (M. musculus) and CC1.3 (H.sapiens). These proteins are characterized by an N-terminal arginine-rich, low complexity domain followed by three (or in the case of 4 H. sapiens paralogs, two) RNA recognition domains (rrm: pfam00706). These splicing factors are closely related to the U2AF splicing factor family (TIGR01642). A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the seed. Length = 457

>gnl|CDD|233496 TIGR01622, SF-CC1, splicing factor, CC1-like family

 Score = 60.3 bits (146), Expect = 3e-09
 Identities = 27/87 (31%), Positives = 40/87 (45%), Gaps = 4/87 (4%)

Query: 39  KEKEKDKHRDRDRRRD--RDRDRDREKEREE-KRERAREKEREREKRDREREDRERERER 95
           +++E+ + R+  RR D  R+R R R + R+  +R R R+  R R  R R R      R R
Sbjct: 3   RDRERGRLRNDTRRSDKGRERSRRRSRSRDRSRRRRDRDYYRGRRGRSRSRSPNRYYRPR 62

Query: 96  ERERRERDREREKRER-ERDRDKEKDR 121
                 RD  R  R   E   + E+D 
Sbjct: 63  GDRSYRRDDRRSGRNTKEPLTEAERDD 89

This model represents a subfamily of RNA splicing factors including the Pad-1 protein (N. crassa), CAPER (M. musculus) and CC1.3 (H.sapiens). These proteins are characterized by an N-terminal arginine-rich, low complexity domain followed by three (or in the case of 4 H. sapiens paralogs, two) RNA recognition domains (rrm: pfam00706). These splicing factors are closely related to the U2AF splicing factor family (TIGR01642). A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the seed. Length = 457

>gnl|CDD|237171 PRK12678, PRK12678, transcription termination factor Rho; Provisional

 Score = 59.9 bits (146), Expect = 4e-09
 Identities = 35/204 (17%), Positives = 64/204 (31%), Gaps = 8/204 (3%)

Query: 39  KEKEKDKHRDRDRRRDRDRDRDREKEREEKRERAREKEREREKRDREREDRERERERERE 98
                       RR  R     R+ E+      A + E     R       E     E  
Sbjct: 66  AAATPAAPAAAARRAARAAAAARQAEQPAAEAAAAKAEAAPAARAAAAAAAEAASAPEAA 125

Query: 99  RRERDREREKRERERDRDKEKDRERKSRDREKRRKVESDDSDEDKDRDRKRRRR---HDD 155
           +    RER +  R     K  +   +     +     +D ++  ++ +R  RRR    +D
Sbjct: 126 QARERRERGEAARRGAARKAGEGGEQPATEAR-----ADAAERTEEEERDERRRRGDRED 180

Query: 156 DHKERVRERSLSRSNRHRDENDESPREKLVEDDSDKKEKKTREEELEDEQRKLDEEMEKR 215
              E  R     R  R RD +D   R++  + D  ++  +    +    +R+ D    + 
Sbjct: 181 RQAEAERGERGRREERGRDGDDRDRRDRREQGDRREERGRRDGGDRRGRRRRRDRRDARG 240

Query: 216 RRRVQEWQELKRKKEESERENRGD 239
               ++  +      E     RG 
Sbjct: 241 DDNREDRGDRDGDDGEGRGGRRGR 264

Length = 672

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 60.5 bits (146), Expect = 4e-09
 Identities = 59/299 (19%), Positives = 130/299 (43%), Gaps = 20/299 (6%)

Query: 1    MAHSHRDRDREKEKEKHR-EKSRRSEREQSTDSDEDKHDKEKEKDKHRDRDRRRDRDRDR 59
            MAH  R +   K +E  + ++ +++E ++  D  +   +K+K  +  +  +  +  D  +
Sbjct: 1262 MAHFARRQAAIKAEEARKADELKKAEEKKKADEAKKAEEKKKADEAKKKAEEAKKADEAK 1321

Query: 60   DREKEREEKRERAREKEREREKRD----REREDRERERERERERRERDREREKRERERDR 115
             + +E ++K + A++K  E +K       E E    E E   E+ E   ++++  +++  
Sbjct: 1322 KKAEEAKKKADAAKKKAEEAKKAAEAAKAEAEAAADEAEAAEEKAEAAEKKKEEAKKKAD 1381

Query: 116  DKEKDRERKSRDREKRRKVESDDSDEDKDRDRKRRRRHDDDHKERVRERSLSRSNRHRDE 175
              +K  E K +  E ++K E D    D+ +     ++  D+ K++  E+  +   + + E
Sbjct: 1382 AAKKKAEEKKKADEAKKKAEEDKKKADELKKAAAAKKKADEAKKKAEEKKKADEAKKKAE 1441

Query: 176  NDESPRE--------KLVEDDSDKKEKKTREEELE---DEQRKLDEEMEKRRRRVQEWQE 224
              +   E        K  E+   K E+  + +E +   +E +K DE  +K     ++  E
Sbjct: 1442 EAKKADEAKKKAEEAKKAEEAKKKAEEAKKADEAKKKAEEAKKADEAKKKAEEAKKKADE 1501

Query: 225  LKRKKEESERENRGDANVEEPKAGRNWTLDREDSDDEEVPQTGKSETDMDADEEPKPSE 283
             K+  E  ++ +      E  KA       ++  + ++  +  K+E    ADE  K  E
Sbjct: 1502 AKKAAEAKKKADEAKKAEEAKKADEA----KKAEEAKKADEAKKAEEKKKADELKKAEE 1556

Length = 2084

>gnl|CDD|236766 PRK10811, rne, ribonuclease E; Reviewed

 Score = 60.4 bits (147), Expect = 4e-09
 Identities = 49/226 (21%), Positives = 94/226 (41%), Gaps = 34/226 (15%)

Query: 11  EKEKEKHREKS-RRSEREQSTDSDEDKHDKEKEKDKHRDRDRRRDRDRDRDREKEREEKR 69
           E+   K   K  R+ +R +              ++  RDR+ RRD  RD    +E  E R
Sbjct: 590 EQPAPKAEAKPERQQDRRKP------------RQNNRRDRNERRD-TRDNRTRREGRENR 636

Query: 70  ERAREKEREREKRDREREDRERERERERERRERDREREKR-ERERDRDKEKDRERKSRDR 128
           E  R   R+ +++  E  + ++    E+ R + ++++  R ER+R R+ EK   R+++  
Sbjct: 637 EENRRNRRQAQQQTAETRESQQAEVTEKARTQDEQQQAPRRERQRRRNDEK---RQAQQE 693

Query: 129 EKRRKVESDDSDEDKDRDRK-----RRRRHDDDHKERVRERSLSRSNRHRDENDES---- 179
            K   VE     E +  +R      RR++   + K R+ +     +     E   +    
Sbjct: 694 AKALNVEEQSVQETEQEERVQQVQPRRKQRQLNQKVRIEQSVAEEAVAPVVEETVAAEPV 753

Query: 180 ------PREKLVEDDSDK-KEKKTREEELEDEQRKLDEEMEKRRRR 218
                 PR +LV+       +    ++E  + + + +  M +R RR
Sbjct: 754 VQEVPAPRTELVKVPLPVVAQTAPEQDEENNAENRDNNGMPRRSRR 799

Length = 1068

>gnl|CDD|236766 PRK10811, rne, ribonuclease E; Reviewed

 Score = 60.4 bits (147), Expect = 4e-09
 Identities = 42/228 (18%), Positives = 90/228 (39%), Gaps = 28/228 (12%)

Query: 62  EKEREEKRERAREKEREREKRDREREDRERERERERERRERDREREKRERERDRDKEKDR 121
            K +E+   +A  K   ++ R + R++  R+R   R+ R+    RE RE  R+ ++   R
Sbjct: 586 TKPQEQPAPKAEAKPERQQDRRKPRQNNRRDRNERRDTRDNRTRREGRE-NREENRRNRR 644

Query: 122 ERKSRDREKRRKVESDDSDEDKDRDRKRRRRHDDDHKERVRERSLSRSNRHRDENDESPR 181
           + + +  E R   +++ +++ + +D +++    +            R  R  DE  ++ +
Sbjct: 645 QAQQQTAETRESQQAEVTEKARTQDEQQQAPRRE------------RQRRRNDEKRQAQQ 692

Query: 182 EKLVEDDSDKKEKKTREEELEDEQRKLDEEMEKRRRRVQEWQELKRKKEESERENRGDAN 241
           E               EE+   E  + +   + + RR Q     K + E+S  E      
Sbjct: 693 EAKAL---------NVEEQSVQETEQEERVQQVQPRRKQRQLNQKVRIEQSVAEEAVAPV 743

Query: 242 VEEPKAGRNWTLDREDSDDEEVPQTGKSETDMDADEEPKPSENQVGDA 289
           VEE  A            +   P+T   +  +    +  P +++  +A
Sbjct: 744 VEETVA------AEPVVQEVPAPRTELVKVPLPVVAQTAPEQDEENNA 785

Length = 1068

>gnl|CDD|179385 PRK02224, PRK02224, chromosome segregation protein; Provisional

 Score = 60.4 bits (147), Expect = 4e-09
 Identities = 51/241 (21%), Positives = 98/241 (40%), Gaps = 12/241 (4%)

Query: 9   DREKEKEKHREKSRRSEREQSTDSDEDKHDKEKEKDKHRDRDRRRDRDRDRDREKEREEK 68
           +  +  E+        + E+  +  E++ ++ ++  +  DR  R   +R  D E+   E+
Sbjct: 472 EDRERVEELEA--ELEDLEEEVEEVEERLERAEDLVEAEDRIERL-EERREDLEELIAER 528

Query: 69  RERAREKEREREKRDREREDRERERERERERRERDREREKRERERDRDKEKDRERKSRDR 128
           RE   EK    E+      + E E E +RE      E  +  RE   +            
Sbjct: 529 RETIEEKRERAEELRERAAELEAEAEEKREAAAEAEEEAEEAREEVAELNSKLAELKERI 588

Query: 129 EKRRKVESDDSD-EDKDRDRKRRRRHDDDHKER---VRERSLSRSNRHRDENDESPREKL 184
           E   ++ +  +   D + + +R R   +   E     RER   +  R R+   E    ++
Sbjct: 589 ESLERIRTLLAAIADAEDEIERLREKREALAELNDERRERLAEKRERKRELEAEFDEARI 648

Query: 185 VEDDSDKKEKKTREEELEDEQRKLDEEMEKRRRRV----QEWQELKRKKEESER-ENRGD 239
            E   DK+  +   E++E++  +L EE +  +  +     E +EL+  +E  E  ENR +
Sbjct: 649 EEAREDKERAEEYLEQVEEKLDELREERDDLQAEIGAVENELEELEELRERREALENRVE 708

Query: 240 A 240
           A
Sbjct: 709 A 709

Length = 880

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 60.5 bits (146), Expect = 5e-09
 Identities = 52/275 (18%), Positives = 122/275 (44%), Gaps = 1/275 (0%)

Query: 10   REKEKEKHREKSRRSEREQSTDSDEDKHDKEKEKDKHRDRDRRRDRDRDRDREKEREEKR 69
            R+ E+ +  E +R++E  +  + +    +  K +D  +    ++  +  +D E+ ++ + 
Sbjct: 1188 RKAEELRKAEDARKAEAARKAEEERKAEEARKAEDAKKAEAVKKAEEAKKDAEEAKKAEE 1247

Query: 70   ERAREKEREREKRDREREDRERERERERERRERDREREKRERERDRDKEKDRERKSRDRE 129
            ER  E+ R+ E+       R +   +  E R+ D  ++  E+++  + +K  E+K  D  
Sbjct: 1248 ERNNEEIRKFEEARMAHFARRQAAIKAEEARKADELKKAEEKKKADEAKKAEEKKKADEA 1307

Query: 130  KRRKVESDDSDEDKDRDRKRRRRHDDDHKERVRERSLSRSNRHRDENDESPREKLVEDDS 189
            K++  E+  +DE K +  + +++ D   K+    +  + + +   E      E   E   
Sbjct: 1308 KKKAEEAKKADEAKKKAEEAKKKADAAKKKAEEAKKAAEAAKAEAEAAADEAEAAEEKAE 1367

Query: 190  DKKEKKTREEELEDEQRKLDEEMEKRRRRVQEWQELKRKKEESERENRGDANVEEPKAGR 249
              ++KK   ++  D  +K  EE +K     ++ +E K+K +E ++        +E K  +
Sbjct: 1368 AAEKKKEEAKKKADAAKKKAEEKKKADEAKKKAEEDKKKADELKKAAAAKKKADEAKK-K 1426

Query: 250  NWTLDREDSDDEEVPQTGKSETDMDADEEPKPSEN 284
                 + D   ++  +  K++      EE K +E 
Sbjct: 1427 AEEKKKADEAKKKAEEAKKADEAKKKAEEAKKAEE 1461

Length = 2084

>gnl|CDD|220648 pfam10243, MIP-T3, Microtubule-binding protein MIP-T3

 Score = 59.5 bits (144), Expect = 6e-09
 Identities = 43/249 (17%), Positives = 93/249 (37%), Gaps = 13/249 (5%)

Query: 23  RSEREQSTDSDEDKHDKEKEKDKHRDRDRRRDRDRDRDREKEREEKRERAREKEREREKR 82
            + + +     +++  KE+EK+K + ++ ++   + +++ KE  + R+   E + +R  +
Sbjct: 88  PAAKTKPAKEPKNESGKEEEKEKEQVKEEKK---KKKEKPKEEPKDRKPKEEAKEKRPPK 144

Query: 83  DREREDRERERERERERRERDREREKRERERDRDKEKDRERKSRDREKR--------RKV 134
           ++E+E  ++  E      E+ RER + +    +  +K    K ++  +           V
Sbjct: 145 EKEKEKEKKVEEPRDREEEKKRERVRAKSRPKKPPKKKPPNKKKEPPEEEKQRQAAREAV 204

Query: 135 ESDDSDEDKDRDRKRRRRHDDDHKERVRERSLSRSNRHRDENDESPREKLVEDDSDKKEK 194
           +    + D + +R++      D +          S +  + +  S       D S     
Sbjct: 205 KGKPEEPDVNEEREKEEDDGKDRETTTSPMEEDESRQSSEISRRSSSSLKKPDPSPSMAS 264

Query: 195 K-TREEELEDEQRKLDEEMEKRRRRVQEWQELKRKKEESERENRGDANVEEPKAGRNWTL 253
             TRE     E R          R         R K +       DA     K   N  L
Sbjct: 265 PETRESSKRTETRPRTSLRPPSARPASARPAPPRVKRKEIVTVLQDAQGVG-KIVSNVIL 323

Query: 254 DREDSDDEE 262
           + + S+DE+
Sbjct: 324 EGKKSEDED 332

This protein, which interacts with both microtubules and TRAF3 (tumour necrosis factor receptor-associated factor 3), is conserved from worms to humans. The N-terminal region is the microtubule binding domain and is well-conserved; the C-terminal 100 residues, also well-conserved, constitute the coiled-coil region which binds to TRAF3. The central region of the protein is rich in lysine and glutamic acid and carries KKE motifs which may also be necessary for tubulin-binding, but this region is the least well-conserved. Length = 506

>gnl|CDD|233757 TIGR02168, SMC_prok_B, chromosome segregation protein SMC, common bacterial type

 Score = 58.9 bits (143), Expect = 1e-08
 Identities = 54/274 (19%), Positives = 105/274 (38%), Gaps = 12/274 (4%)

Query: 8   RDREKEKEKHREKSRRSEREQSTDSDEDKHDKEKEKDKHRDRDRRRDRDRDRDREKEREE 67
           R   +E E+  E+ R+   E S      + D  + + +    + R  +       KE  E
Sbjct: 704 RKELEELEEELEQLRKELEELSRQISALRKDLARLEAEVEQLEERIAQ-----LSKELTE 758

Query: 68  KRERAREKEREREKRDREREDRERERERERERRERDREREKRERERDRDKEKDRERKSRD 127
                 E E   E+ + E  + E E E    + E+ +E  K  RE   +    R   +  
Sbjct: 759 LEAEIEELEERLEEAEEELAEAEAEIEELEAQIEQLKEELKALREALDEL---RAELTLL 815

Query: 128 REKRRKVESDDSDEDKDRDRKRRRRHDDDHKERVRERSLSRSNRHRDENDESPREKLVED 187
            E+   +       ++      RR  D + +       +       +E +E   E   E 
Sbjct: 816 NEEAANLRERLESLERRIAATERRLEDLEEQIEELSEDIESLAAEIEELEELIEELESEL 875

Query: 188 DSDKKEKKTREEELEDEQRKLDEEMEKRRRRVQEWQELKRKKEES-ERENRGDANVEEPK 246
           ++   E+ + EE L   + +L+E  E+ R    +  EL+R+ EE  E+  + +  +E  +
Sbjct: 876 EALLNERASLEEALALLRSELEELSEELRELESKRSELRRELEELREKLAQLELRLEGLE 935

Query: 247 AGRNWTLDR---EDSDDEEVPQTGKSETDMDADE 277
              +   +R   E S   E  +  +++ + D +E
Sbjct: 936 VRIDNLQERLSEEYSLTLEEAEALENKIEDDEEE 969

SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]. Length = 1179

>gnl|CDD|233758 TIGR02169, SMC_prok_A, chromosome segregation protein SMC, primarily archaeal type

 Score = 58.2 bits (141), Expect = 2e-08
 Identities = 39/237 (16%), Positives = 83/237 (35%), Gaps = 16/237 (6%)

Query: 14  KEKHREKSRRSEREQSTDSDEDKHDKEKEKDKHRDRDRRRDRDRDRDREKEREEKRE-RA 72
             +      RSE  +     E     ++E    +   RR +   D   ++  +  R+   
Sbjct: 661 APRGGILFSRSEPAELQRLRERLEGLKRELSSLQSELRRIENRLDELSQELSDASRKIGE 720

Query: 73  REKEREREKRDREREDRERERERERERRERDREREKRERERDRDKEKDRERKSRDREKRR 132
            EKE E+ +++ E+  +ER  E E +    ++E E  + E   + E   E    D  K  
Sbjct: 721 IEKEIEQLEQEEEKL-KERLEELEEDLSSLEQEIENVKSELK-ELEARIEELEEDLHKLE 778

Query: 133 KVESDDSDEDKDRDRKRRRRHDDDHKERVRERSLSRSNRHRDENDESPREKLVED----- 187
           +  +D             +      +E V           +  N  +  ++ +E      
Sbjct: 779 EALNDLEARLSHSRIPEIQAELSKLEEEVSRIEARLREIEQKLNRLTLEKEYLEKEIQEL 838

Query: 188 -------DSDKKEKKTREEELEDEQRKLDEEMEKRRRRVQEWQELKRKKEESERENR 237
                      K  +   E L  ++ +L+EE+E+    +++ +  +    + ER+  
Sbjct: 839 QEQRIDLKEQIKSIEKEIENLNGKKEELEEELEELEAALRDLES-RLGDLKKERDEL 894

SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]. Length = 1164

>gnl|CDD|206039 pfam13868, Trichoplein, Tumour suppressor, Mitostatin

 Score = 56.8 bits (138), Expect = 2e-08
 Identities = 53/237 (22%), Positives = 125/237 (52%), Gaps = 15/237 (6%)

Query: 6   RDRDREKEKEKHREKSRRSEREQSTDSDEDKHDKEKEKDKHRDRDRRRDRDRDRDREKER 65
            + +RE+++++ R + R   +EQ  + ++ + ++ +E+ + R++          + E E 
Sbjct: 57  EEEERERKRKEERREGRAVLQEQIEEREKRRQEEYEERLQEREQMDEIIERIQEEDEAEA 116

Query: 66  EEKRERAREKERE-----REKRDREREDRERERERERERRERDREREKRERERDRDKEKD 120
           +EKRE+ ++   E      E+ +R+ E++ERERE E +  E  RE+ +RE ER+ ++ + 
Sbjct: 117 QEKREKQKKLREEIDEFNEERIERKEEEKEREREEELKILEYQREKAEREEEREAERRER 176

Query: 121 RERKSRDREKRRKVESDDSDEDKDRDRKRRRRHDDDHKERVRERSLSRSNRHRDENDESP 180
           +E K R+  + R  + +  DE ++ D  R   + ++++ + R++          E +E+ 
Sbjct: 177 KEEKEREVARLRAQQEEAEDEREELDELRADLYQEEYERKERQK----------EKEEAE 226

Query: 181 REKLVEDDSDKKEKKTREEELEDEQRKLDEEMEKRRRRVQEWQELKRKKEESERENR 237
           + +  + +  +  ++  EE+ E  Q +  EE  +R R +++  E +  ++E+  + R
Sbjct: 227 KRRRQKQELQRAREEQIEEKEERLQEERAEEEAERERMLEKQAEDEELEQENAEKRR 283

Trichoplein or mitostatin, was first defined as a meiosis-specific nuclear structural protein. It has since been linked with mitochondrial movement. It is associated with the mitochondrial outer membrane, and over-expression leads to reduction in mitochondrial motility whereas lack of it enhances mitochondrial movement. The activity appears to be mediated through binding the mitochondria to the actin intermediate filaments (IFs). Length = 349

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 57.1 bits (137), Expect = 4e-08
 Identities = 51/277 (18%), Positives = 120/277 (43%), Gaps = 6/277 (2%)

Query: 10   REKEKEKHREKSRRSEREQSTDSDEDKHDKEKEKDKHRDRDRRRDRDRDRDREKEREEKR 69
            R+ E  +  E +R++E E+  +      D +K +   +  + ++D +  +  E+ER  + 
Sbjct: 1194 RKAEDARKAEAARKAEEERKAEEARKAEDAKKAEAVKKAEEAKKDAEEAKKAEEERNNEE 1253

Query: 70   ERAREKEREREKRDREREDRERERERERERRERDREREKRERERDRDKEKDRERKSRDRE 129
             R  E+ R      R+   +  E  +  E ++ + +++  E ++  +K+K  E K +  E
Sbjct: 1254 IRKFEEARMAHFARRQAAIKAEEARKADELKKAEEKKKADEAKKAEEKKKADEAKKKAEE 1313

Query: 130  KRRKVESDDSDEDKDRDRKRRRRHDDDHKERVRERSLSRSNRHRDENDESPREKLVEDDS 189
              +K +      ++ + +    +   +  ++  E + + +    DE + +  EK    + 
Sbjct: 1314 A-KKADEAKKKAEEAKKKADAAKKKAEEAKKAAEAAKAEAEAAADEAEAA-EEKAEAAEK 1371

Query: 190  DKKEKKTREEELE---DEQRKLDEEMEKRRRRVQEWQELKRKKEESERENRGDANVEEPK 246
             K+E K + +  +   +E++K DE  +K     ++  ELK+     ++ +      EE K
Sbjct: 1372 KKEEAKKKADAAKKKAEEKKKADEAKKKAEEDKKKADELKKAAAAKKKADEAKKKAEEKK 1431

Query: 247  AGRNWTLDREDSDDEEVPQTGKSETDMDADEEPKPSE 283
                     E++   +  +  K+E    A+E  K +E
Sbjct: 1432 KADEAKKKAEEAKKADEAKK-KAEEAKKAEEAKKKAE 1467

Length = 2084

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 57.1 bits (137), Expect = 4e-08
 Identities = 67/376 (17%), Positives = 159/376 (42%), Gaps = 17/376 (4%)

Query: 1    MAHSHRDRDREKEKEKHREKSRRSEREQSTDSDEDKHDKEKEKDKHRDRDRRRDRDRDRD 60
            MA    +  ++ E+ +  E  +  E E+   ++E K  +E +      +    ++ +   
Sbjct: 1578 MALRKAEEAKKAEEARIEEVMKLYEEEKKMKAEEAKKAEEAKIKAEELKKAEEEKKKVEQ 1637

Query: 61   REKEREEKRERAREKEREREKRDREREDRERERERERERRERDREREKRERERDRDKEKD 120
             +K+  E++++A E ++  E+   +  +  ++ E ++++ E  ++ E+ E++     +K+
Sbjct: 1638 LKKKEAEEKKKAEELKKAEEENKIKAAEEAKKAEEDKKKAEEAKKAEEDEKKAAEALKKE 1697

Query: 121  RERKSRDREKRRKVESDDSDEDKDRDRKRRRRHDDDHKERVRERSLSRSNRHRDENDESP 180
             E   +  E ++K   +    ++ +  +   +   +  ++  E    ++   + + +E  
Sbjct: 1698 AEEAKKAEELKKKEAEEKKKAEELKKAEEENKIKAEEAKKEAEEDKKKAEEAKKDEEEKK 1757

Query: 181  REKLVEDDSDKKEKKTREEELEDEQRKLDEEMEKRRRRVQEWQELKRKKEESERENRGDA 240
            +   ++ + +KK ++ R+E+    + +LDEE EKRR  V    + K K       N  + 
Sbjct: 1758 KIAHLKKEEEKKAEEIRKEKEAVIEEELDEEDEKRRMEV----DKKIKDIFDNFANIIEG 1813

Query: 241  NVEEPKAGRNWTLDREDSDDEEVPQTGKSE-TDMDADEEPKPSENQVGDAMLVDSDGGSA 299
              +E     N + + EDS  +EV  +   +  + DA E+ K ++N        +     A
Sbjct: 1814 G-KEGNLVINDSKEMEDSAIKEVADSKNMQLEEADAFEKHKFNKNNENG----EDGNKEA 1868

Query: 300  APALQIGAAEDEDIDPLDAFMNSMVLPEVEKLKNTVEPSFTDGNNVESKKMDRKGDRRSN 359
                +    ED++ +  +A          EK+           NN+  K  D   D+   
Sbjct: 1869 DFNKEKDLKEDDEEEIEEADEI-------EKIDKDDIEREIPNNNMAGKNNDIIDDKLDK 1921

Query: 360  GEQPKKSSNKSLGRII 375
             E  K+ + ++   II
Sbjct: 1922 DEYIKRDAEETREEII 1937

Length = 2084

>gnl|CDD|233496 TIGR01622, SF-CC1, splicing factor, CC1-like family

 Score = 56.4 bits (136), Expect = 4e-08
 Identities = 21/88 (23%), Positives = 36/88 (40%), Gaps = 1/88 (1%)

Query: 6  RDRDREKEKEKHREKSRRSEREQSTDSDEDKHDKEKEKDKHRDRDRRRDRDRDRDREKER 65
          RDR+R + +   R   +  ER +      D+  + +++D +R R R R R R  +R    
Sbjct: 3  RDRERGRLRNDTRRSDKGRERSRRRSRSRDRSRRRRDRDYYRGR-RGRSRSRSPNRYYRP 61

Query: 66 EEKRERAREKEREREKRDREREDRERER 93
             R   R+  R          + ER+ 
Sbjct: 62 RGDRSYRRDDRRSGRNTKEPLTEAERDD 89

This model represents a subfamily of RNA splicing factors including the Pad-1 protein (N. crassa), CAPER (M. musculus) and CC1.3 (H.sapiens). These proteins are characterized by an N-terminal arginine-rich, low complexity domain followed by three (or in the case of 4 H. sapiens paralogs, two) RNA recognition domains (rrm: pfam00706). These splicing factors are closely related to the U2AF splicing factor family (TIGR01642). A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the seed. Length = 457

>gnl|CDD|233191 TIGR00927, 2A1904, K+-dependent Na+/Ca+ exchanger

 Score = 57.3 bits (138), Expect = 4e-08
 Identities = 48/228 (21%), Positives = 95/228 (41%), Gaps = 9/228 (3%)

Query: 11  EKEKEKHREKSRRSEREQSTDSDEDKHDKEKEKDKHRDRDRRRDRDRDRDREKEREEKRE 70
           E E E      R+ E+E   + +  + D + E +               + E E E   E
Sbjct: 678 ENESEGEIPAERKGEQEGEGEIEAKEADHKGETEAEEVEHEGETEAEGTEDEGEIETGEE 737

Query: 71  -RAREKEREREKRDREREDRERERERERERRERDREREKRERERDRDKEKDRERKSRDRE 129
               E E E E   +   + E +R+      E + E ++ E E +    +D E K  +  
Sbjct: 738 GEEVEDEGEGEAEGKHEVETEGDRKETEHEGETEAEGKEDEDEGEIQAGEDGEMKGDEGA 797

Query: 130 KRR---KVESDDSDEDKDRDRKRRRRHDDDHKERVRERSLSRSNRHRDENDESPREKLVE 186
           + +   + E++  ++D+   +   +  D + K+   E+ L+  N+   + DE   +    
Sbjct: 798 EGKVEHEGETEAGEKDEHEGQSETQADDTEVKDETGEQELNAENQGEAKQDEKGVDGGGG 857

Query: 187 DD-----SDKKEKKTREEELEDEQRKLDEEMEKRRRRVQEWQELKRKK 229
            D      +++E++  EEE E+E+ + +EE E       EW E ++K+
Sbjct: 858 SDGGDSEEEEEEEEEEEEEEEEEEEEEEEEEENEEPLSLEWPETRQKQ 905

[Transport and binding proteins, Cations and iron carrying compounds]. Length = 1096

>gnl|CDD|130456 TIGR01389, recQ, ATP-dependent DNA helicase RecQ

 Score = 56.6 bits (137), Expect = 4e-08
 Identities = 78/373 (20%), Positives = 143/373 (38%), Gaps = 54/373 (14%)

Query: 487 YEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIM 546
           Y+   P Q + +  ++ GRD + V  TG GK+L + +P L               + +++
Sbjct: 11  YDDFRPGQEEIISHVLDGRDVLVVMPTGGGKSLCYQVPALLL-----------KGLTVVI 59

Query: 547 APTREL----VQQIHSDIRKFAKVMGVRCVPVYGGSGV-AQQISELKRGTEIVVCTPGRM 601
           +P   L    V Q+           GV     Y  S + A++  ++++         G  
Sbjct: 60  SPLISLMKDQVDQLR--------AAGVAAA--YLNSTLSAKEQQDIEKA-----LVNGE- 103

Query: 602 IDILCTSGGKITN------LRRVT--YLVMDEADRMFDMG--FEPQITRIVQ--NIRPDR 649
           + +L  +  ++        L+R+    + +DEA  +   G  F P+  R+       P  
Sbjct: 104 LKLLYVAPERLEQDYFLNMLQRIPIALVAVDEAHCVSQWGHDFRPEYQRLGSLAERFPQV 163

Query: 650 QTVLFSATFPRQV--EILARKVLNKPVEIQVGGRSVVNKDITQLV-EVRPESDRFLRLLE 706
             +  +AT   +   +I     L    E       + + D   L   V  ++++   LL+
Sbjct: 164 PRIALTATADAETRQDIRELLRLADANEF------ITSFDRPNLRFSVVKKNNKQKFLLD 217

Query: 707 LLGEWYEKGKILIFVHSQEKCDALFRDLLKHGYPCLSLHGAKDQTDRESTISDFKSNVCN 766
            L +   +  I I+  S++K + L   L   G   L+ H       R     DF  +   
Sbjct: 218 YLKKHRGQSGI-IYASSRKKVEELAERLESQGISALAYHAGLSNKVRAENQEDFLYDDVK 276

Query: 767 LLIATSVAARGLDVKELELVINFDAPNHYEDYVHRVGRTGRAGRKGCAITFISEEDAKYS 826
           +++AT+    G+D   +  VI++D P + E Y    GR GR G    AI   S  D    
Sbjct: 277 VMVATNAFGMGIDKPNVRFVIHYDMPGNLESYYQEAGRAGRDGLPAEAILLYSPADIALL 336

Query: 827 PDLVKALELSEQV 839
              ++  E  +  
Sbjct: 337 KRRIEQSEADDDY 349

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 [DNA metabolism, DNA replication, recombination, and repair]. Length = 591

>gnl|CDD|233758 TIGR02169, SMC_prok_A, chromosome segregation protein SMC, primarily archaeal type

 Score = 57.0 bits (138), Expect = 5e-08
 Identities = 52/234 (22%), Positives = 101/234 (43%), Gaps = 7/234 (2%)

Query: 7   DRDREKEKEKHREKSRRSEREQSTDSDEDKHDKEKEKDKHRDRDRRRDRDRDRDREKERE 66
           DR +EK  E+  E     ER       ++K  + +   + R++  R        RE E  
Sbjct: 169 DRKKEKALEELEEVEENIERLDLII--DEKRQQLERLRREREKAERYQALLKEKREYEGY 226

Query: 67  EKRERAREKEREREKRDREREDRERERE-RERERRERDREREKRERERD----RDKEKDR 121
           E  +     ER++E  +R+    E E E    E  E ++  E+ E+  +    + K+   
Sbjct: 227 ELLKEKEALERQKEAIERQLASLEEELEKLTEEISELEKRLEEIEQLLEELNKKIKDLGE 286

Query: 122 ERKSRDREKRRKVESDDSDEDKDRDRKRRRRHDDDHKERVRERSLSRSNRHRDENDESPR 181
           E + R +EK  ++E++ +  ++    K R   D + +    E  + +     +E +    
Sbjct: 287 EEQLRVKEKIGELEAEIASLERSIAEKERELEDAEERLAKLEAEIDKLLAEIEELEREIE 346

Query: 182 EKLVEDDSDKKEKKTREEELEDEQRKLDEEMEKRRRRVQEWQELKRKKEESERE 235
           E+    D   +E    +EELED + +L+E  ++      E ++ + K E+ +RE
Sbjct: 347 EERKRRDKLTEEYAELKEELEDLRAELEEVDKEFAETRDELKDYREKLEKLKRE 400

SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]. Length = 1164

>gnl|CDD|219953 pfam08648, DUF1777, Protein of unknown function (DUF1777)

 Score = 53.0 bits (127), Expect = 5e-08
 Identities = 38/99 (38%), Positives = 50/99 (50%), Gaps = 4/99 (4%)

Query: 47  RDRDRRRDRDRDRDREKEREEKRERAREKEREREKRDREREDRERERERERERRERDRER 106
           R R R   R R R R + R+ +RER RE+ R RE RDR R  R R   R R  R   R R
Sbjct: 3   RSRSRSPRRSRRRGRSRSRD-RRERRRERSRSRE-RDRRRRSRSRSPHRSRRSRSPRRHR 60

Query: 107 EKRERERDRDKEKDRERKSRDREKR-RKVESDDSDEDKD 144
             R R   R +++ RER    RE + R+ +    +ED +
Sbjct: 61  S-RSRSPSRRRDRKRERDKDAREPKKRERQKLIKEEDLE 98

This is a family of eukaryotic proteins of unknown function. Some of the proteins in this family are putative nucleic acid binding proteins. Length = 158

>gnl|CDD|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and chromosome partitioning]

 Score = 56.6 bits (137), Expect = 6e-08
 Identities = 54/271 (19%), Positives = 125/271 (46%), Gaps = 15/271 (5%)

Query: 7   DRDREKEKEKHREKSRRSEREQSTDSDEDKHDKEKEKDKHRDRDRR------RDRDRDRD 60
           + + + EK +   KS ++E     D  E+   + +E ++  +  +R       + ++ + 
Sbjct: 678 ELEAQLEKLEEELKSLKNELRSLEDLLEELRRQLEELERQLEELKRELAALEEELEQLQS 737

Query: 61  REKEREEKRERAREKEREREKRDREREDRERERERERERRERDREREKRERERDRDKEKD 120
           R +E EE+ E   E+  E ++R  E E+     E    + + + E  + +R+  +++ ++
Sbjct: 738 RLEELEEELEELEEELEELQERLEELEEELESLEEALAKLKEEIEELEEKRQALQEELEE 797

Query: 121 RERKSRDREKR-RKVESDDSDEDKDRDRKRRRRHDDDHKERVRERSLSRSNRHRDENDES 179
            E +  + E+R   +E +    ++ R+R  +   + + +    E  L       +E ++ 
Sbjct: 798 LEEELEEAERRLDALERELESLEQRRERLEQEIEELEEEIEELEEKLDELEEELEELEKE 857

Query: 180 PREKLVEDDSDKKEKKTREEEL---EDEQRKLDEEMEKRRRRV----QEWQELKRKKEES 232
             E   E +  + EK+  E+EL   E+E+ +L+EE+ +    +    +E ++L+ + EE 
Sbjct: 858 LEELKEELEELEAEKEELEDELKELEEEKEELEEELRELESELAELKEEIEKLRERLEEL 917

Query: 233 ERENRGDANVEEPKAGRNWTLDREDSDDEEV 263
           E +      VE P+       + ED+ + E+
Sbjct: 918 EAKLE-RLEVELPELEEELEEEYEDTLETEL 947

Length = 1163

>gnl|CDD|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and chromosome partitioning]

 Score = 56.3 bits (136), Expect = 8e-08
 Identities = 50/219 (22%), Positives = 95/219 (43%), Gaps = 3/219 (1%)

Query: 17  HREKSRRSEREQSTDSDEDKHDKEKEKDKHRDRDRRRDRDRDRDREKEREEKRERAREKE 76
            R K     +++     E++  + + + +  + + +  ++  R  E   EE R +  E E
Sbjct: 656 SRNKRSSLAQKRELKELEEELAELEAQLEKLEEELKSLKNELRSLEDLLEELRRQLEELE 715

Query: 77  REREKRDREREDRERERERERERRERDREREKRERERDRDKEKDRERKSRDREKRRKVES 136
           R+ E+  RE    E E E+ + R E   E E+   E + + E+ +ER     E+   +E 
Sbjct: 716 RQLEELKRELAALEEELEQLQSRLE---ELEEELEELEEELEELQERLEELEEELESLEE 772

Query: 137 DDSDEDKDRDRKRRRRHDDDHKERVRERSLSRSNRHRDENDESPREKLVEDDSDKKEKKT 196
             +   ++ +    +R     +    E  L  + R  D  +          +  ++E + 
Sbjct: 773 ALAKLKEEIEELEEKRQALQEELEELEEELEEAERRLDALERELESLEQRRERLEQEIEE 832

Query: 197 REEELEDEQRKLDEEMEKRRRRVQEWQELKRKKEESERE 235
            EEE+E+ + KLDE  E+     +E +ELK + EE E E
Sbjct: 833 LEEEIEELEEKLDELEEELEELEKELEELKEELEELEAE 871

Length = 1163

>gnl|CDD|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and chromosome partitioning]

 Score = 56.3 bits (136), Expect = 9e-08
 Identities = 46/282 (16%), Positives = 114/282 (40%), Gaps = 2/282 (0%)

Query: 10  REKEKEKHREKSRRSEREQSTDSDEDKHDKEKEKDKHRDRDRRRDRDRDRDREKEREEKR 69
            E EK+  + + +  + E+  +   +  + E      + ++ R++ +   +     EE+ 
Sbjct: 196 EELEKQLEKLERQAEKAERYQELKAELRELELALLLAKLKELRKELEELEEELSRLEEEL 255

Query: 70  ERAREKEREREKR-DREREDRERERERERERRERDREREKRERERDRDKEKDRERKSRDR 128
           E  +E+  E EK  +  + + E  RE   E +E   E ++   E + +    RER     
Sbjct: 256 EELQEELEEAEKEIEELKSELEELREELEELQEELLELKEEIEELEGEISLLRERLEELE 315

Query: 129 EKRRKVESDDSDEDKDRDRKRRRRHDDDHKERVRERSLSRSNRHRDENDESPREKLVEDD 188
            +  ++E    +  +  +  +    + +      E+ L+     ++E +E     L E +
Sbjct: 316 NELEELEERLEELKEKIEALKEELEERETLLEELEQLLAELEEAKEELEEKLSALLEELE 375

Query: 189 SDKKEKKTREEELEDEQRKLDEEMEKRRRRVQEWQELKRKKEESERENRGDANVEEPKAG 248
              +  +    ELE E  ++  E+E+ +R ++  +E   +  E   + + +    E +  
Sbjct: 376 ELFEALREELAELEAELAEIRNELEELKREIESLEERLERLSERLEDLKEELKELEAELE 435

Query: 249 RNWTLDREDSDDEEVPQTGKSETDMDADEEPKPSENQVGDAM 290
              T + E+ ++E      + E   D  +E +    ++ + +
Sbjct: 436 ELQT-ELEELNEELEELEEQLEELRDRLKELERELAELQEEL 476

Length = 1163

>gnl|CDD|233503 TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, large subunit, splicing factor

 Score = 55.3 bits (133), Expect = 1e-07
 Identities = 30/116 (25%), Positives = 47/116 (40%), Gaps = 16/116 (13%)

Query: 4   SHRDRDREKEKEKHREKSRRSEREQSTDSDEDKHDKEKEKDKHRDRDRRRDRDRDRDREK 63
           S R R R +++ + R++ RRS RE+S   D               R R R R   R    
Sbjct: 21  SERPRRRSRDRSRFRDRHRRS-RERSYRED--------------SRPRDRRRYDSRSPRS 65

Query: 64  EREEKRERAREKEREREKRDREREDRERERERERERRERDREREKRERERDRDKEK 119
            R     R+R++ R R  R     ++ R R R+R    + R+ +K+    D     
Sbjct: 66  LRYSSVRRSRDRPRRRS-RSVRSIEQHRRRLRDRSPSNQWRKDDKKRSLWDIKPPG 120

These splicing factors consist of an N-terminal arginine-rich low complexity domain followed by three tandem RNA recognition motifs (pfam00076). The well-characterized members of this family are auxilliary components of the U2 small nuclear ribonuclearprotein splicing factor (U2AF). These proteins are closely related to the CC1-like subfamily of splicing factors (TIGR01622). Members of this subfamily are found in plants, metazoa and fungi. Length = 509

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 55.9 bits (134), Expect = 1e-07
 Identities = 50/284 (17%), Positives = 120/284 (42%), Gaps = 3/284 (1%)

Query: 6    RDRDREKEKEKHREKSRRSEREQSTDSDEDKHDKEKEKDKHRDRDRRRDRDRDRDREKER 65
            R  +  +E     E+++++E  ++ ++ + +  K+K +D  +  + R+  D  +  E  +
Sbjct: 1088 RADEATEEAFGKAEEAKKTETGKAEEARKAEEAKKKAEDARKAEEARKAEDARKAEEARK 1147

Query: 66   EEKRERAREKEREREKRDREREDRERERERERERRERDREREKRERERDRDKEKDRERKS 125
             E  +R     +  + R +  E R+ E  ++ E   +  E  K E  R  +  +  E   
Sbjct: 1148 AEDAKRVEIARKAEDAR-KAEEARKAEDAKKAEAARKAEEVRKAEELRKAEDARKAEAAR 1206

Query: 126  RDREKRRKVESDDSDEDKDRDRKRRRRHDDDHKERVRERSLSRSNRHRDENDESPREKLV 185
            +  E+R+  E+  +++ K  +  ++        E  ++    R+N    + +E+      
Sbjct: 1207 KAEEERKAEEARKAEDAKKAEAVKKAEEAKKDAEEAKKAEEERNNEEIRKFEEARMAHFA 1266

Query: 186  EDDSD-KKEKKTREEELEDEQRKLDEEMEKRRRRVQEWQELKRKKEESERENRGDANVEE 244
               +  K E+  + +EL+  + K   +  K+    ++  E K+K EE+++ +      EE
Sbjct: 1267 RRQAAIKAEEARKADELKKAEEKKKADEAKKAEEKKKADEAKKKAEEAKKADEAKKKAEE 1326

Query: 245  PKAGRNWTLDREDSDDEEVPQTGKSETDMDADEEPKPSENQVGD 288
             K   +    ++  + ++  +  K+E +  ADE     E     
Sbjct: 1327 AKKKAD-AAKKKAEEAKKAAEAAKAEAEAAADEAEAAEEKAEAA 1369

Length = 2084

>gnl|CDD|233496 TIGR01622, SF-CC1, splicing factor, CC1-like family

 Score = 53.7 bits (129), Expect = 3e-07
 Identities = 35/119 (29%), Positives = 49/119 (41%), Gaps = 33/119 (27%)

Query: 89  RERERERERERRERDREREK-RERERDRDKEKDRERKSRDREKRRKVESDDSDEDKDRDR 147
           R R+RER R  R   R  +K RER R R + +DR R+ RDR             D  R R
Sbjct: 1   RYRDRERGRL-RNDTRRSDKGRERSRRRSRSRDRSRRRRDR-------------DYYRGR 46

Query: 148 KRRRRHDDDHKERVRERSLSRSNRHRDENDESPREKLVEDDSDKKEKKTREEELEDEQR 206
           +             R RS S +  +R   D S R        D++  +  +E L + +R
Sbjct: 47  RG------------RSRSRSPNRYYRPRGDRSYR------RDDRRSGRNTKEPLTEAER 87

This model represents a subfamily of RNA splicing factors including the Pad-1 protein (N. crassa), CAPER (M. musculus) and CC1.3 (H.sapiens). These proteins are characterized by an N-terminal arginine-rich, low complexity domain followed by three (or in the case of 4 H. sapiens paralogs, two) RNA recognition domains (rrm: pfam00706). These splicing factors are closely related to the U2AF splicing factor family (TIGR01642). A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the seed. Length = 457

>gnl|CDD|233758 TIGR02169, SMC_prok_A, chromosome segregation protein SMC, primarily archaeal type

 Score = 54.3 bits (131), Expect = 3e-07
 Identities = 51/283 (18%), Positives = 103/283 (36%), Gaps = 18/283 (6%)

Query: 6   RDRDREKEKEKHREKSRRSEREQSTDSDEDKHDKEKEKDKHRDRDRRRDR-DRDRDREKE 64
           R+R    ++E    +S     E   D    +      K    + ++  ++ +++ ++ KE
Sbjct: 680 RERLEGLKRELSSLQSELRRIENRLDELSQELSDASRK--IGEIEKEIEQLEQEEEKLKE 737

Query: 65  R-EEKRERAREKEREREKRDREREDRERERERERERRERDRERE---KRERERDRDKEKD 120
           R EE  E     E+E E    E ++ E   E   E   +  E     +      R  E  
Sbjct: 738 RLEELEEDLSSLEQEIENVKSELKELEARIEELEEDLHKLEEALNDLEARLSHSRIPEIQ 797

Query: 121 RERKSRDREKRRKVESDDSDEDKDRDRKRRRRHDDDHKERVRERSLSRSNRHRDENDESP 180
            E    + E  R        E K       + + +   + ++E+          E  +S 
Sbjct: 798 AELSKLEEEVSRIEARLREIEQKLNRLTLEKEYLEKEIQELQEQ-----RIDLKEQIKSI 852

Query: 181 REKLVEDDSDKKEKKTREEELEDEQRKLDEEM----EKRRRRVQEWQELKRKKEESERE- 235
            +++   +  K+E +   EELE   R L+  +    ++R     + +EL+RK EE E + 
Sbjct: 853 EKEIENLNGKKEELEEELEELEAALRDLESRLGDLKKERDELEAQLRELERKIEELEAQI 912

Query: 236 NRGDANVEEPKAGRNWTLDREDSDDEEVPQTGKSETDMDADEE 278
            +    + E KA      +     ++   +  +   + +   E
Sbjct: 913 EKKRKRLSELKAKLEALEEELSEIEDPKGE-DEEIPEEELSLE 954

SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]. Length = 1164

>gnl|CDD|233503 TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, large subunit, splicing factor

 Score = 53.4 bits (128), Expect = 4e-07
 Identities = 33/120 (27%), Positives = 50/120 (41%), Gaps = 14/120 (11%)

Query: 115 RDKEKDRER-KSRDREKRRKVESDDSDEDKDRDRKRRRRHDDDHKERVRERSLSRSNRHR 173
           RD+E DRER KSR R++       D   ++ R R R R    D   R RERS    +R R
Sbjct: 1   RDEEPDREREKSRGRDR-------DRSSERPRRRSRDRSRFRDRHRRSRERSYREDSRPR 53

Query: 174 DENDESPREKLVEDDSDKKEKKTREEELEDEQRKLDEEMEKRRRR----VQEWQELKRKK 229
           D      R            +++R+      +     E  +RR R      +W++  +K+
Sbjct: 54  DRRRYDSRS--PRSLRYSSVRRSRDRPRRRSRSVRSIEQHRRRLRDRSPSNQWRKDDKKR 111

These splicing factors consist of an N-terminal arginine-rich low complexity domain followed by three tandem RNA recognition motifs (pfam00076). The well-characterized members of this family are auxilliary components of the U2 small nuclear ribonuclearprotein splicing factor (U2AF). These proteins are closely related to the CC1-like subfamily of splicing factors (TIGR01622). Members of this subfamily are found in plants, metazoa and fungi. Length = 509

>gnl|CDD|179385 PRK02224, PRK02224, chromosome segregation protein; Provisional

 Score = 53.9 bits (130), Expect = 4e-07
 Identities = 46/177 (25%), Positives = 71/177 (40%), Gaps = 5/177 (2%)

Query: 66  EEKRERAREKEREREKRDREREDRERERERERERRERDREREKRERERDRDKEKDRERKS 125
           EE RER  E E E E  + E E+ E   ER  +  E +   E+ E  R+  +E   ER+ 
Sbjct: 471 EEDRERVEELEAELEDLEEEVEEVEERLERAEDLVEAEDRIERLEERREDLEELIAERRE 530

Query: 126 RDREKRRKVESDDSDEDKDRDRKRRRRHDDDHKERVRERSLSRS---NRHRDENDESPR- 181
              EKR + E       +       +R      E   E +       N    E  E    
Sbjct: 531 TIEEKRERAEELRERAAELEAEAEEKREAAAEAEEEAEEAREEVAELNSKLAELKERIES 590

Query: 182 -EKLVEDDSDKKEKKTREEELEDEQRKLDEEMEKRRRRVQEWQELKRKKEESERENR 237
            E++    +   + +   E L +++  L E  ++RR R+ E +E KR+ E    E R
Sbjct: 591 LERIRTLLAAIADAEDEIERLREKREALAELNDERRERLAEKRERKRELEAEFDEAR 647

Length = 880

>gnl|CDD|219953 pfam08648, DUF1777, Protein of unknown function (DUF1777)

 Score = 50.6 bits (121), Expect = 4e-07
 Identities = 32/88 (36%), Positives = 47/88 (53%), Gaps = 1/88 (1%)

Query: 61  REKEREEKRERAREKEREREKRDREREDRERERERERERRERDREREKRERERDRDKEKD 120
           R + R  +R R R + R R++R+R RE R R RER+R RR R R   +  R R   + + 
Sbjct: 3   RSRSRSPRRSRRRGRSRSRDRRERRRE-RSRSRERDRRRRSRSRSPHRSRRSRSPRRHRS 61

Query: 121 RERKSRDREKRRKVESDDSDEDKDRDRK 148
           R R    R  R++    D+ E K R+R+
Sbjct: 62  RSRSPSRRRDRKRERDKDAREPKKRERQ 89

This is a family of eukaryotic proteins of unknown function. Some of the proteins in this family are putative nucleic acid binding proteins. Length = 158

>gnl|CDD|235175 PRK03918, PRK03918, chromosome segregation protein; Provisional

 Score = 53.5 bits (129), Expect = 5e-07
 Identities = 42/184 (22%), Positives = 80/184 (43%), Gaps = 5/184 (2%)

Query: 56  DRDRDREKEREEKRERAREKEREREKRDREREDRERERERERERRERDREREKRERERDR 115
           +  +++EKE EE      E   E  +   E E  E+E +   E +E   E EK     + 
Sbjct: 193 ELIKEKEKELEEVLREINEISSELPELREELEKLEKEVKELEELKEEIEELEKELESLEG 252

Query: 116 DKEKDRERKSRDREKRRKVESDDSDEDKDRDRKRRRRHDDDHKERVRE-----RSLSRSN 170
            K K  E+     E+  +++ +  + ++     +  +   +   ++ E         R  
Sbjct: 253 SKRKLEEKIRELEERIEELKKEIEELEEKVKELKELKEKAEEYIKLSEFYEEYLDELREI 312

Query: 171 RHRDENDESPREKLVEDDSDKKEKKTREEELEDEQRKLDEEMEKRRRRVQEWQELKRKKE 230
             R    E     + E   + +EK+ R EEL+ + ++L++ +E+   R + ++E K KKE
Sbjct: 313 EKRLSRLEEEINGIEERIKELEEKEERLEELKKKLKELEKRLEELEERHELYEEAKAKKE 372

Query: 231 ESER 234
           E ER
Sbjct: 373 ELER 376

Length = 880

>gnl|CDD|217051 pfam02463, SMC_N, RecF/RecN/SMC N terminal domain

 Score = 53.4 bits (128), Expect = 6e-07
 Identities = 48/285 (16%), Positives = 109/285 (38%), Gaps = 10/285 (3%)

Query: 1   MAHSHRDRDREKEKEKHREKSRRSEREQSTDSDEDKHDKEKEKDKHRDRDRRRDRDRDRD 60
            A S   R +++  +K  E++           +  K  + K K      ++ +       
Sbjct: 163 AAGSREKRKKKERLKKLIEETENLAELIIDLEEL-KLQELKLK------EQAKKALEYYQ 215

Query: 61  REKEREEKRERAREKEREREKRDREREDRERERERERERRERDREREKRERERDRDKEKD 120
            +++ E + E     +  +   +R    +E  R+ + E     +E EK E    +  +++
Sbjct: 216 LKEKLELEEENLLYLDYLKLNEERIDLLQELLRDEQEEIESSKQELEKEEEILAQVLKEN 275

Query: 121 RERKSRDREKRRKVESDDSDEDKDRDRKRRRRHDDDHKERVRERSLSRSNRHRDENDESP 180
           +E +   + +  +++    +E++ +    +        E   + S     +   E  +  
Sbjct: 276 KEEEKEKKLQEEELKLLAKEEEELKSELLKLERRKVDDEEKLKESEKELKKLEKELKKE- 334

Query: 181 REKLVEDDSDKKEKKTREEELEDEQRKLDEEMEKRRRRVQEWQELKRKKEESERENRGDA 240
           +E++ E + + KE + + E  E+E+ +L++  EK  +  +E   L +KK ESER +    
Sbjct: 335 KEEIEELEKELKELEIKREAEEEEEEQLEKLQEKLEQLEEE--LLAKKKLESERLSSAAK 392

Query: 241 NVEEPKAGRNWTLDREDSDDEEVPQTGKSETDMDADEEPKPSENQ 285
             EE    +N          E   Q      +   +E     E +
Sbjct: 393 LKEEELELKNEEEKEAKLLLELSEQEEDLLKEEKKEELKIVEELE 437

This domain is found at the N terminus of SMC proteins. The SMC (structural maintenance of chromosomes) superfamily proteins have ATP-binding domains at the N- and C-termini, and two extended coiled-coil domains separated by a hinge in the middle. The eukaryotic SMC proteins form two kind of heterodimers: the SMC1/SMC3 and the SMC2/SMC4 types. These heterodimers constitute an essential part of higher order complexes, which are involved in chromatin and DNA dynamics. This family also includes the RecF and RecN proteins that are involved in DNA metabolism and recombination. Length = 1162

>gnl|CDD|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and chromosome partitioning]

 Score = 52.8 bits (127), Expect = 8e-07
 Identities = 50/258 (19%), Positives = 111/258 (43%), Gaps = 29/258 (11%)

Query: 6    RDRDREKEKEKHREKSRRSEREQSTDSDEDKHDKEKEKDKHRDRDRRRDRDRDRDREKER 65
            ++R  E E+E    +   ++ ++  +  E+K    +E+ +  + +      R    E+E 
Sbjct: 757  QERLEELEEELESLEEALAKLKEEIEELEEKRQALQEELEELEEELEEAERRLDALEREL 816

Query: 66   EEKRERAREKEREREKRDRERED------------RERERERERERRERDREREKRERER 113
            E   +R    E+E E+ + E E+             E E+E E  + E +    ++E   
Sbjct: 817  ESLEQRRERLEQEIEELEEEIEELEEKLDELEEELEELEKELEELKEELEELEAEKEELE 876

Query: 114  DRDKEKDRERKSRDREKRRKVESDDSDEDKDRDRKRRRRHDDDHKERVRERSLSRSNRHR 173
            D  KE + E++  + E  R++ES+ ++  ++ ++ R R  + + K    E  L       
Sbjct: 877  DELKELEEEKEELEEEL-RELESELAELKEEIEKLRERLEELEAKLERLEVELPELEEEL 935

Query: 174  DENDESPREKLVEDDSDKKEKKTR----------------EEELEDEQRKLDEEMEKRRR 217
            +E  E   E  +E + ++ E++                  EE  E+ + + ++  E + +
Sbjct: 936  EEEYEDTLETELEREIERLEEEIEALGPVNLRAIEEYEEVEERYEELKSQREDLEEAKEK 995

Query: 218  RVQEWQELKRKKEESERE 235
             ++  +EL ++K E  +E
Sbjct: 996  LLEVIEELDKEKRERFKE 1013

Length = 1163

>gnl|CDD|224126 COG1205, COG1205, Distinct helicase family with a unique C-terminal domain including a metal-binding cysteine cluster [General function prediction only]

 Score = 52.8 bits (127), Expect = 8e-07
 Identities = 80/357 (22%), Positives = 132/357 (36%), Gaps = 60/357 (16%)

Query: 494 QAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELV 553
           Q  AL +I  GR+ +    TGSGKT +F+LP+L H+  + P A       L++ PT  L 
Sbjct: 75  QVDALRLIREGRNVVVTTGTGSGKTESFLLPILDHLL-RDPSA-----RALLLYPTNALA 128

Query: 554 QQIHSDIRKFAKVMGVRCVP-VYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGGK- 611
                 +R+    +  +     Y G    ++   + R    ++ T   M+  L       
Sbjct: 129 NDQAERLRELISDLPGKVTFGRYTGDTPPEERRAIIRNPPDILLTNPDMLHYLLLRNHDA 188

Query: 612 -ITNLRRVTYLVMDEA---------------DRMFDM-GFEPQITRIVQNIRPDRQTVLF 654
            +  LR + YLV+DE                 R+                     Q +  
Sbjct: 189 WLWLLRNLKYLVVDELHTYRGVQGSEVALLLRRLLRRLRRYGS----------PLQIICT 238

Query: 655 SATFPRQVEILARKVLNKPVEIQV-------GGRSVV--NKDITQLVE-VRPESDRFLRL 704
           SAT     E  A ++  +  E+ V       G R  V     I +L E +R  +   L  
Sbjct: 239 SATLANPGE-FAEELFGRDFEVPVDEDGSPRGLRYFVRREPPIRELAESIRRSALAELAT 297

Query: 705 L--ELLGEWYEKGKILIFVHSQEK--------CDALFRDLLKHGYPCLSLHGAKDQTDRE 754
           L   L+       + L+F  S+++           L R+  K      +      + +R 
Sbjct: 298 LAALLVRNGI---QTLVFFRSRKQVELLYLSPRRRLVREGGKLLDAVSTYRAGLHREERR 354

Query: 755 STISDFKSNVCNLLIATSVAARGLDVKELELVINFDAPNH-YEDYVHRVGRTGRAGR 810
              ++FK      +IAT+    G+D+  L+ VI +  P      +  R GR GR G+
Sbjct: 355 RIEAEFKEGELLGVIATNALELGIDIGSLDAVIAYGYPGVSVLSFRQRAGRAGRRGQ 411

Length = 851

>gnl|CDD|233758 TIGR02169, SMC_prok_A, chromosome segregation protein SMC, primarily archaeal type

 Score = 52.4 bits (126), Expect = 1e-06
 Identities = 40/222 (18%), Positives = 87/222 (39%), Gaps = 17/222 (7%)

Query: 3   HSHRDRDREKEKEKHREKSRRSEREQSTDSDEDKHDKEKEKDKHRDRDRRRDRDRDRDRE 62
            +          EK RE     ER    +++ DK   E E+ +    + R+ RD+  +  
Sbjct: 300 EAEIASLERSIAEKERELEDAEERLAKLEAEIDKLLAEIEELEREIEEERKRRDKLTEEY 359

Query: 63  KEREEKRERAREKEREREKRDREREDRERERERERERRERDREREKRERERDRDKEKDRE 122
            E +E+ E  R +  E +K   E  D  ++   + E  +  RE  + +RE DR +E+ + 
Sbjct: 360 AELKEELEDLRAELEEVDKEFAETRDELKDYREKLE--KLKREINELKRELDRLQEELQR 417

Query: 123 RKSRDREKRRKVESDDSDEDKDRDRKRRRRHDDDHKERVRERSLSRSNRHRDENDESPRE 182
                 +    +   ++  ++  + K      +D    +++         ++   E    
Sbjct: 418 LSEELADLNAAIAGIEAKINELEEEK------EDKALEIKK---------QEWKLEQLAA 462

Query: 183 KLVEDDSDKKEKKTREEELEDEQRKLDEEMEKRRRRVQEWQE 224
            L + + +  + K   + +E E  KL  E+ +   + +  +E
Sbjct: 463 DLSKYEQELYDLKEEYDRVEKELSKLQRELAEAEAQARASEE 504

SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]. Length = 1164

>gnl|CDD|206039 pfam13868, Trichoplein, Tumour suppressor, Mitostatin

 Score = 51.1 bits (123), Expect = 1e-06
 Identities = 54/237 (22%), Positives = 120/237 (50%), Gaps = 11/237 (4%)

Query: 5   HRDRDREKEKEKHREKSRRSEREQSTDSDEDKHDKEKEKDKHRDRDRRRDRDRDRDREKE 64
            + R + +EKE+ R      E E           +E+E+++ R  +RR  R   +++ +E
Sbjct: 28  EKKRIKAEEKEEERRIDEMMEEE-----RLKALAEEEERERKRKEERREGRAVLQEQIEE 82

Query: 65  REEKRERARE-KEREREKRDR-----EREDRERERERERERRERDREREKRERERDRDKE 118
           RE++R+   E + +ERE+ D      + ED    +E+  ++++   E ++   ER   KE
Sbjct: 83  REKRRQEEYEERLQEREQMDEIIERIQEEDEAEAQEKREKQKKLREEIDEFNEERIERKE 142

Query: 119 KDRERKSRDREKRRKVESDDSDEDKDRDRKRRRRHDDDHKERVRERSLSRSNRHRDENDE 178
           +++ER+  +  K  + + + ++ +++R+ +RR R ++  +E  R R+         E  +
Sbjct: 143 EEKEREREEELKILEYQREKAEREEEREAERRERKEEKEREVARLRAQQEEAEDEREELD 202

Query: 179 SPREKLVEDDSDKKEKKTREEELEDEQRKLDEEMEKRRRRVQEWQELKRKKEESERE 235
             R  L +++ ++KE++  +EE E  +R+  E    R  +++E +E  +++   E  
Sbjct: 203 ELRADLYQEEYERKERQKEKEEAEKRRRQKQELQRAREEQIEEKEERLQEERAEEEA 259

Trichoplein or mitostatin, was first defined as a meiosis-specific nuclear structural protein. It has since been linked with mitochondrial movement. It is associated with the mitochondrial outer membrane, and over-expression leads to reduction in mitochondrial motility whereas lack of it enhances mitochondrial movement. The activity appears to be mediated through binding the mitochondria to the actin intermediate filaments (IFs). Length = 349

>gnl|CDD|219953 pfam08648, DUF1777, Protein of unknown function (DUF1777)

 Score = 49.1 bits (117), Expect = 1e-06
 Identities = 35/105 (33%), Positives = 49/105 (46%), Gaps = 4/105 (3%)

Query: 75  KEREREKRDREREDRERERERERERRERDREREKRERERDRDKEKDRERKSRDREKRRKV 134
           + R R  R   R  R R R+R   RRER R RE+  R R R +   R R+SR   + R  
Sbjct: 3   RSRSRSPRRSRRRGRSRSRDRRERRRERSRSRERDRRRRSRSRSPHRSRRSRSPRRHR-- 60

Query: 135 ESDDSDEDKDRDRKRRRRHDDDH-KERVRERSLSRSNRHRDENDE 178
            S      + RDRKR R  D    K+R R++ +   +     ++E
Sbjct: 61  -SRSRSPSRRRDRKRERDKDAREPKKRERQKLIKEEDLEGKSDEE 104

This is a family of eukaryotic proteins of unknown function. Some of the proteins in this family are putative nucleic acid binding proteins. Length = 158

>gnl|CDD|202096 pfam02029, Caldesmon, Caldesmon

 Score = 52.0 bits (124), Expect = 1e-06
 Identities = 57/283 (20%), Positives = 112/283 (39%), Gaps = 25/283 (8%)

Query: 9   DREKEKEKHREKSRRSEREQSTDSDED------------KHDKEKEKDKHRDRDRRRDRD 56
           D E+E  + R +  R E+ +    +              ++    E+ K    D     +
Sbjct: 2   DDEEEAARERRRREREEQLRQKQEEGSLGQVTTQVEVNSQNSVPDEESKTSTDDEAALLE 61

Query: 57  RDRDREKEREEKRERAREKEREREKRDRE---REDRERERERERERRERDREREKRERER 113
           R   RE+ R+E+   A E+++E +    +    E   R +E      E   E EK E   
Sbjct: 62  RLARREERRDERFSEALERQKEFKPTSTDQSLSEPSRRMQEDSGAENETVEEEEKEESRE 121

Query: 114 DRDKEKDRERKSRDREKRRKVESDDSDEDKDRDRKRRRRHDDDHKERVRERS----LSRS 169
           +R++ ++ E  ++  +K          E+  ++ K     +++  +R             
Sbjct: 122 EREEVEETEGVTKSEQK----NDWRDAEECQKEEKEPEPEEEEKPKRGSLEENNGEFMTH 177

Query: 170 NRHRDENDESPREKLVEDDSDKKEKKTREEELEDEQRKLDEEMEKR--RRRVQEWQELKR 227
                EN  S            KE +  +++ ++   +L+E  +KR  RR+V E +E +R
Sbjct: 178 KLKHTENTFSRGGAEGAQVEAGKEFEKLKQKQQEAALELEELKKKREERRKVLEEEEQRR 237

Query: 228 KKEESERENRGDANVEEPKAGRNWTLDREDSDDEEVPQTGKSE 270
           K+EE++R++R +      K              ++VP+ G SE
Sbjct: 238 KQEEADRKSREEEEKRRLKEEIERRRAEAAEKRQKVPEDGLSE 280

Length = 431

>gnl|CDD|220648 pfam10243, MIP-T3, Microtubule-binding protein MIP-T3

 Score = 51.0 bits (122), Expect = 2e-06
 Identities = 51/302 (16%), Positives = 119/302 (39%), Gaps = 22/302 (7%)

Query: 24  SEREQSTDSDEDKHDKEKEKDKHRDRDRRRDRDRDRDREKE-REEKRERAREKEREREKR 82
           +E + S+D    + +K   K         ++   +  +E+E  +E+ +  ++K++E+ K 
Sbjct: 67  AESKLSSDEAVKRVEKGGSKGPAAKTKPAKEPKNESGKEEEKEKEQVKEEKKKKKEKPKE 126

Query: 83  DREREDRERERERERERRERDREREKRERERDRDKEKDRER---------KSRDREKRRK 133
           + +    + E + +R  +E+++E+EK+  E  RD+E++++R         K   ++K   
Sbjct: 127 EPKDRKPKEEAKEKRPPKEKEKEKEKK-VEEPRDREEEKKRERVRAKSRPKKPPKKKPPN 185

Query: 134 VESDDSDEDKDRDRKRRRRHDDDHKERVRERSLSRSNRHRDENDESPREKLVEDDSDKKE 193
            + +  +E+K R   R        +  V E      +  +D   E+    + ED+S +  
Sbjct: 186 KKKEPPEEEKQRQAAREAVKGKPEEPDVNEEREKEEDDGKDR--ETTTSPMEEDESRQSS 243

Query: 194 KKTREEELEDEQRKLDEEMEKRRRRVQEWQELKRKKEESERENRGDANVEEPKAGRNWTL 253
           + +R      ++      M     R    +   R +      +        P + R    
Sbjct: 244 EISRRSSSSLKKPDPSPSMASPETRESSKRTETRPRTSLRPPSAR------PASARPAPP 297

Query: 254 DREDSDDEEVPQTGK--SETDMDADEEPKPSENQVGDAMLVDSDGGSAAPALQIGA-AED 310
             +  +   V Q  +   +   +   E K SE++  +  +V++   +          AED
Sbjct: 298 RVKRKEIVTVLQDAQGVGKIVSNVILEGKKSEDEDDENFVVEAAAQAPDIVAGGEDEAED 357

Query: 311 ED 312
            +
Sbjct: 358 GE 359

This protein, which interacts with both microtubules and TRAF3 (tumour necrosis factor receptor-associated factor 3), is conserved from worms to humans. The N-terminal region is the microtubule binding domain and is well-conserved; the C-terminal 100 residues, also well-conserved, constitute the coiled-coil region which binds to TRAF3. The central region of the protein is rich in lysine and glutamic acid and carries KKE motifs which may also be necessary for tubulin-binding, but this region is the least well-conserved. Length = 506

>gnl|CDD|233191 TIGR00927, 2A1904, K+-dependent Na+/Ca+ exchanger

 Score = 51.5 bits (123), Expect = 2e-06
 Identities = 47/249 (18%), Positives = 97/249 (38%), Gaps = 3/249 (1%)

Query: 35  DKHDKEKEKDKHRDRDRRRDRDRDRDREKEREEKRERAREKEREREKRDREREDRERERE 94
           ++  +E E+    + +   +   + ++E E E K E   E E   E++  E+E  E E E
Sbjct: 643 ERTGEEGERPTEAEGENGEESGGEAEQEGETETKGENESEGEIPAERKG-EQEG-EGEIE 700

Query: 95  RERERRERDREREKRERERDRDKEKDRERKSRDREKRRKVESDDSDEDKDRDRKRRRRHD 154
            +    + + E E+ E E + + E   +    +  +  +   D+ + + +   +     D
Sbjct: 701 AKEADHKGETEAEEVEHEGETEAEGTEDEGEIETGEEGEEVEDEGEGEAEGKHEVETEGD 760

Query: 155 DDHKERVRERSLSRSNRHRDENDESPREKLVEDDSDKKEKKTREEELEDEQRKLDEEMEK 214
               E   E   +      DE +    E       +  E K   E   +   K + E + 
Sbjct: 761 RKETEHEGETE-AEGKEDEDEGEIQAGEDGEMKGDEGAEGKVEHEGETEAGEKDEHEGQS 819

Query: 215 RRRRVQEWQELKRKKEESERENRGDANVEEPKAGRNWTLDREDSDDEEVPQTGKSETDMD 274
             +      + +  ++E   EN+G+A  +E         D  DS++EE  +  + E + +
Sbjct: 820 ETQADDTEVKDETGEQELNAENQGEAKQDEKGVDGGGGSDGGDSEEEEEEEEEEEEEEEE 879

Query: 275 ADEEPKPSE 283
            +EE +  E
Sbjct: 880 EEEEEEEEE 888

[Transport and binding proteins, Cations and iron carrying compounds]. Length = 1096

>gnl|CDD|219953 pfam08648, DUF1777, Protein of unknown function (DUF1777)

 Score = 48.7 bits (116), Expect = 2e-06
 Identities = 31/94 (32%), Positives = 41/94 (43%), Gaps = 3/94 (3%)

Query: 89  RERERERERERRE---RDREREKRERERDRDKEKDRERKSRDREKRRKVESDDSDEDKDR 145
           R R R   R RR    R R+R +R RER R +E+DR R+SR R   R   S      + R
Sbjct: 3   RSRSRSPRRSRRRGRSRSRDRRERRRERSRSRERDRRRRSRSRSPHRSRRSRSPRRHRSR 62

Query: 146 DRKRRRRHDDDHKERVRERSLSRSNRHRDENDES 179
            R   RR D   +     R   +  R +   +E 
Sbjct: 63  SRSPSRRRDRKRERDKDAREPKKRERQKLIKEED 96

This is a family of eukaryotic proteins of unknown function. Some of the proteins in this family are putative nucleic acid binding proteins. Length = 158

>gnl|CDD|219953 pfam08648, DUF1777, Protein of unknown function (DUF1777)

 Score = 48.7 bits (116), Expect = 2e-06
 Identities = 36/103 (34%), Positives = 50/103 (48%), Gaps = 3/103 (2%)

Query: 26  REQSTDSDEDKHDKEKEKDKHRDRDRRRDRDRDRDR-EKEREEKRERAREKEREREKRDR 84
           R +S      +          R+R R R R R+RDR  + R     R+R     R  R R
Sbjct: 3   RSRSRSPRRSRRRGRSRSRDRRERRRERSRSRERDRRRRSRSRSPHRSRRSRSPRRHRSR 62

Query: 85  EREDRERERERERERRERDREREKRERERDRDKEKDRERKSRD 127
            R    R R+R+RER +  RE +KRER++   KE+D E KS +
Sbjct: 63  SR-SPSRRRDRKRERDKDAREPKKRERQKL-IKEEDLEGKSDE 103

This is a family of eukaryotic proteins of unknown function. Some of the proteins in this family are putative nucleic acid binding proteins. Length = 158

>gnl|CDD|219953 pfam08648, DUF1777, Protein of unknown function (DUF1777)

 Score = 48.3 bits (115), Expect = 2e-06
 Identities = 36/104 (34%), Positives = 53/104 (50%), Gaps = 3/104 (2%)

Query: 38  DKEKEKDKHRDRDRRRDRDRDRDREKEREEKRERAREKEREREKRDREREDRERERERER 97
            +   + + R R R RDR R+R RE+ R  +R+R R        R R      R R R R
Sbjct: 6   SRSPRRSRRRGRSRSRDR-RERRRERSRSRERDRRRRSRSRSPHRSRRSRSPRRHRSRSR 64

Query: 98  ERRERDREREKRERERDRDKEKDRERKSRDREKRRKVESDDSDE 141
               R R+R KRER++D  + K RER+   +E+  + +SD+  E
Sbjct: 65  S-PSRRRDR-KRERDKDAREPKKRERQKLIKEEDLEGKSDEEVE 106

This is a family of eukaryotic proteins of unknown function. Some of the proteins in this family are putative nucleic acid binding proteins. Length = 158

>gnl|CDD|223496 COG0419, SbcC, ATPase involved in DNA repair [DNA replication, recombination, and repair]

 Score = 51.7 bits (124), Expect = 2e-06
 Identities = 42/247 (17%), Positives = 104/247 (42%), Gaps = 13/247 (5%)

Query: 7   DRDREKEKEKHREKSRRSEREQSTDS----DEDKHDKEKEKDKHRDRDRRRDRDRDRDRE 62
           +   E+   +  E   R E E+        +E+  +  + ++  ++    +    +   E
Sbjct: 484 EELEEELSREKEEAELREEIEELEKELRELEEELIELLELEEALKEELEEKLEKLENLLE 543

Query: 63  KEREEKR----ERAREKEREREKRDREREDRERERERERERRERDREREKRERERDRDKE 118
           +  E K     ++ +E+ R+ E R +E ++   E    R R+E   E  +R +E  +  +
Sbjct: 544 ELEELKEKLQLQQLKEELRQLEDRLQELKELLEELRLLRTRKEELEELRERLKELKKKLK 603

Query: 119 KDRERKSRDREKRRKVESDDSDEDKDRDRKRRRRHDDDHKERVRERSLSRSNRHRDEND- 177
           +  ER S+  E  + +E  +++ + +   +          E++  ++           + 
Sbjct: 604 ELEERLSQLEELLQSLELSEAENELEEAEEELE----SELEKLNLQAELEELLQAALEEL 659

Query: 178 ESPREKLVEDDSDKKEKKTREEELEDEQRKLDEEMEKRRRRVQEWQELKRKKEESERENR 237
           E   E+L  +   + ++   EE+LE++  +L++  E+  +  +E +EL +K  E E+   
Sbjct: 660 EEKVEELEAEIRRELQRIENEEQLEEKLEELEQLEEELEQLREELEELLKKLGEIEQLIE 719

Query: 238 GDANVEE 244
              + + 
Sbjct: 720 ELESRKA 726

Length = 908

>gnl|CDD|223496 COG0419, SbcC, ATPase involved in DNA repair [DNA replication, recombination, and repair]

 Score = 51.3 bits (123), Expect = 2e-06
 Identities = 51/245 (20%), Positives = 92/245 (37%), Gaps = 11/245 (4%)

Query: 6   RDRDREKEKEKHREKSRRSEREQSTDSDEDKHDKEKEKDKHRDRDRRRDRDRDRDREKER 65
             ++  KE +   E+      E   D ++     E+E  + +  +  ++   + + E+E 
Sbjct: 175 LLKEVIKEAKAKIEELEGQLSELLEDIEDLLEALEEELKELKKLEEIQEEQEEEELEQEI 234

Query: 66  EEKRERAREKEREREKRDREREDRERERERERERRERDREREKRERERDRDKEKDRERKS 125
           E   ER  E E E+E+ +  +         E E  +    RE+  RE +R  E+  E+  
Sbjct: 235 EALEERLAELEEEKERLEELKARLLEIESLELEALKI---REEELRELERLLEELEEKIE 291

Query: 126 RDREKRRKVESDDSDEDKDRDRKRRRRHDDDHKERVRERSLSRSN------RHRDENDES 179
           R  E  R++E  + + +  R          +  + + ER               +E  E 
Sbjct: 292 RLEELEREIEELEEELEGLRALLEELEELLEKLKSLEERLEKLEEKLEKLESELEELAEE 351

Query: 180 PREKLVEDDSDKKEKKTREEELEDEQRKLDEEMEKRRRRVQEWQELKRKKEESERENRGD 239
             E     +   KE + R EELE E  K  E +++    +QE    +   E S       
Sbjct: 352 KNELAKLLEERLKELEERLEELEKELEKALERLKQLEEAIQEL--KEELAELSAALEEIQ 409

Query: 240 ANVEE 244
             +EE
Sbjct: 410 EELEE 414

Length = 908

>gnl|CDD|233757 TIGR02168, SMC_prok_B, chromosome segregation protein SMC, common bacterial type

 Score = 51.2 bits (123), Expect = 3e-06
 Identities = 45/233 (19%), Positives = 88/233 (37%), Gaps = 19/233 (8%)

Query: 10  REKEKEKHREKSRRSEREQSTDSDEDKHDKEKEKDKHRD-RDRRRDRDRDRDREKEREEK 68
           R +E E+  EK    E        E   + EK   + R   +   +      +E E   +
Sbjct: 675 RRREIEELEEKIEELE--------EKIAELEKALAELRKELEELEEELEQLRKELEELSR 726

Query: 69  RERAREKEREREKRDREREDRERERERERERRERDREREKRERERDRDKEKDRERKSRDR 128
           +  A  K+  R + + E+   ER  +  +E  E + E E+ E       E+  E  +   
Sbjct: 727 QISALRKDLARLEAEVEQL-EERIAQLSKELTELEAEIEELEERL----EEAEEELAEAE 781

Query: 129 EKRRKVESDDSDEDKDRDRKRRRRHDDDHKERVRERSLSRSNRHRDENDE----SPREKL 184
            +  ++E    ++ K+  +  R   D+   E       + + R R E+ E    +   +L
Sbjct: 782 AEIEELE-AQIEQLKEELKALREALDELRAELTLLNEEAANLRERLESLERRIAATERRL 840

Query: 185 VEDDSDKKEKKTREEELEDEQRKLDEEMEKRRRRVQEWQELKRKKEESERENR 237
            + +   +E     E L  E  +L+E +E+    ++     +   EE+    R
Sbjct: 841 EDLEEQIEELSEDIESLAAEIEELEELIEELESELEALLNERASLEEALALLR 893

SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]. Length = 1179

>gnl|CDD|206039 pfam13868, Trichoplein, Tumour suppressor, Mitostatin

 Score = 49.9 bits (120), Expect = 3e-06
 Identities = 66/228 (28%), Positives = 126/228 (55%), Gaps = 8/228 (3%)

Query: 6   RDRDREKEKEKHREKSRRSEREQSTDSDEDKHDKEKEKDKHRDRDRRRDRDRDRDREKER 65
           + + RE+  E + E+  R E E+  + +E+    E +++K    + R    R+R  EKER
Sbjct: 123 QKKLREEIDEFNEERIERKEEEKEREREEELKILEYQREKAEREEEREAERRERKEEKER 182

Query: 66  EEKRERAREKEREREKRDREREDRERERERERERRERDREREKRERERDRDKEKDRERKS 125
           E  R RA+++E E E+ + + E R    + E ER+ER +E+E+ E+ R + +E  R R+ 
Sbjct: 183 EVARLRAQQEEAEDEREELD-ELRADLYQEEYERKERQKEKEEAEKRRRQKQELQRAREE 241

Query: 126 RDREKRRKVESDDSDEDKDRDRKRRRRHDDDHKERVR-ERSLSRSNRHRDENDESPREKL 184
           +  EK  +++ + ++E+ +R+R   ++ +D+  E+   E+   +   HR E ++   EK 
Sbjct: 242 QIEEKEERLQEERAEEEAERERMLEKQAEDEELEQENAEKRRMKRLEHRRELEQQIEEK- 300

Query: 185 VEDDSDKKEKKTREEELEDEQRKLDEEMEKRRRRVQEWQELKRKKEES 232
                +++    REEELE+ +R  +EE E++ R  +E Q L ++  E+
Sbjct: 301 -----EERRAAEREEELEEGERLREEEAERQARIEEERQRLLKEHAEA 343

Trichoplein or mitostatin, was first defined as a meiosis-specific nuclear structural protein. It has since been linked with mitochondrial movement. It is associated with the mitochondrial outer membrane, and over-expression leads to reduction in mitochondrial motility whereas lack of it enhances mitochondrial movement. The activity appears to be mediated through binding the mitochondria to the actin intermediate filaments (IFs). Length = 349

>gnl|CDD|217051 pfam02463, SMC_N, RecF/RecN/SMC N terminal domain

 Score = 50.7 bits (121), Expect = 3e-06
 Identities = 38/248 (15%), Positives = 99/248 (39%), Gaps = 8/248 (3%)

Query: 13  EKEKHREKSRRSEREQSTDSDEDKHDKEKEKDKHRDRDRRRDRDRDRDREKEREEKRERA 72
           E+     +    + ++  +S + + +KE+E      ++ + +    + +E+E +   +  
Sbjct: 237 EERIDLLQELLRDEQEEIESSKQELEKEEEILAQVLKENKEEEKEKKLQEEELKLLAKEE 296

Query: 73  REKEREREKRDREREDRERERERERERRERDREREKRERERDRDKEKDRERKSRDREKRR 132
            E + E  K +R + D E + +   +  ++  +  K+E+E   + EK+ +     RE   
Sbjct: 297 EELKSELLKLERRKVDDEEKLKESEKELKKLEKELKKEKEEIEELEKELKELEIKREAEE 356

Query: 133 KVESDDSDEDKDRDRKRRRRHDDDHKERVRERSLSRSNRHRDENDESPREKLVEDDSDKK 192
           + E    ++ +    K  +  ++   ++  E     S     E +   + +  ++     
Sbjct: 357 EEE----EQLEKLQEKLEQLEEELLAKKKLESERLSSAAKLKEEELELKNEEEKEAKLLL 412

Query: 193 EKKTREE----ELEDEQRKLDEEMEKRRRRVQEWQELKRKKEESERENRGDANVEEPKAG 248
           E   +EE    E + E+ K+ EE+E+     Q     ++++ E +        +E  K+ 
Sbjct: 413 ELSEQEEDLLKEEKKEELKIVEELEESLETKQGKLTEEKEELEKQALKLLKDKLELKKSE 472

Query: 249 RNWTLDRE 256
                 + 
Sbjct: 473 DLLKETKL 480

This domain is found at the N terminus of SMC proteins. The SMC (structural maintenance of chromosomes) superfamily proteins have ATP-binding domains at the N- and C-termini, and two extended coiled-coil domains separated by a hinge in the middle. The eukaryotic SMC proteins form two kind of heterodimers: the SMC1/SMC3 and the SMC2/SMC4 types. These heterodimers constitute an essential part of higher order complexes, which are involved in chromatin and DNA dynamics. This family also includes the RecF and RecN proteins that are involved in DNA metabolism and recombination. Length = 1162

>gnl|CDD|224124 COG1203, COG1203, CRISPR-associated helicase Cas3 [Defense mechanisms]

 Score = 50.9 bits (122), Expect = 3e-06
 Identities = 72/352 (20%), Positives = 138/352 (39%), Gaps = 34/352 (9%)

Query: 511 AKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVMGVR 570
           A TG GKT A ++  L  + ++           + + P R +++ ++   ++   +  V 
Sbjct: 221 APTGYGKTEASLILALALLDEK----IKLKSRVIYVLPFRTIIEDMYRRAKEIFGLFSVI 276

Query: 571 CVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILC--------------TSGGKITNLR 616
                  S     + E  +   + + T      +L                 G K   L 
Sbjct: 277 -GKSLHSSSKEPLLLEPDQDILLTLTTNDSYKKLLLALIVVTPIQILIFSVKGFKFEFLA 335

Query: 617 RVTY--LVMDEADRMFDMGFEPQITRIVQNIRPDRQTVLF-SATFPRQVEILARKVLNKP 673
            +    +++DE     D      +  +++ +      VL  SAT P  ++   +K L K 
Sbjct: 336 LLLTSLVILDEVHLYADETMLAALLALLEALAEAGVPVLLMSATLPPFLKEKLKKALGKG 395

Query: 674 VEIQVGGRSVVNKDITQLVEVRPESD---RFLRLLELLGEWYEKG-KILIFVHSQEKCDA 729
            E+    +    +D   L               L+EL+ E  ++G K+L+ V++ ++   
Sbjct: 396 REVVENAKFCPKEDEPGLKRKERVDVEDGPQEELIELISEEVKEGKKVLVIVNTVDRAIE 455

Query: 730 LFRDLLKHGYPCLSLHG---AKDQTDRESTISD-FKSNVCNLLIATSVAARGLDVKELEL 785
           L+  L + G   L LH     KD+ ++E  +   FK N   +++AT V   G+D+ + ++
Sbjct: 456 LYEKLKEKGPKVLLLHSRFTLKDREEKERELKKLFKQNEGFIVVATQVIEAGVDI-DFDV 514

Query: 786 VINFDAPNHYEDYVHRVGRTGRAGRKGCAITFISEEDAKYSPDLVKALELSE 837
           +I   AP      + R GR  R G+K     ++   D +  P L  + E  E
Sbjct: 515 LITELAPID--SLIQRAGRVNRHGKKENGKIYV-YNDEERGPYLKYSYEKLE 563

Length = 733

>gnl|CDD|219563 pfam07767, Nop53, Nop53 (60S ribosomal biogenesis)

 Score = 50.1 bits (120), Expect = 3e-06
 Identities = 25/147 (17%), Positives = 61/147 (41%), Gaps = 7/147 (4%)

Query: 9   DREKEKEKHREKSRRSEREQ---STDSDEDKHDKEKEKDKHRDRDRRRDRDRDRDREKER 65
           ++E + EK R++  R E ++            +  +   +  D D   + D +   E   
Sbjct: 204 EKEVKAEKKRQELERVEEKKLEKMAPEASRLDEMSEGLLEESDDDGEEESDDESAWEGFE 263

Query: 66  EEKRERAREKEREREKRDREREDRERERERERERRERDREREKRERERDRDKEKDRERKS 125
            E     +    +R+ +      R +E+ R+   RE   E++ +++     + K+  ++ 
Sbjct: 264 SEYEPINKPVRPKRKTK----AQRNKEKRRKELEREAKEEKQLKKKLAQLARLKEIAKEV 319

Query: 126 RDREKRRKVESDDSDEDKDRDRKRRRR 152
             +EK R  + +   E  ++ + +RR+
Sbjct: 320 AQKEKARARKKEQRKERGEKKKLKRRK 346

This nucleolar family of proteins are involved in 60S ribosomal biogenesis. They are specifically involved in the processing beyond the 27S stage of 25S rRNA maturation. This family contains sequences that bear similarity to the glioma tumour suppressor candidate region gene 2 protein (p60). This protein has been found to interact with herpes simplex type 1 regulatory proteins. Length = 387

>gnl|CDD|235401 PRK05306, infB, translation initiation factor IF-2; Validated

 Score = 50.2 bits (121), Expect = 4e-06
 Identities = 27/130 (20%), Positives = 50/130 (38%), Gaps = 1/130 (0%)

Query: 4   SHRDRDREKEKEKHREKSRRSEREQSTDSDEDKHDKEKEKDKHRDRDRRRDRDRDRDREK 63
           SH     E+E  K  E  R +E E   +++E    + +E+ K          +       
Sbjct: 33  SHSSTVEEEEARK-EEAKREAEEEAKAEAEEAAAAEAEEEAKAEAAAAAPAEEAAEAAAA 91

Query: 64  EREEKRERAREKEREREKRDREREDRERERERERERRERDREREKRERERDRDKEKDRER 123
                R    E  R  E   R  + ++  ++++  + ++ + + K  R   R K     R
Sbjct: 92  AEAAARPAEDEAARPAEAAARRPKAKKAAKKKKGPKPKKKKPKRKAARGGKRGKGGKGRR 151

Query: 124 KSRDREKRRK 133
           + R R +RRK
Sbjct: 152 RRRGRRRRRK 161

Length = 746

>gnl|CDD|227596 COG5271, MDN1, AAA ATPase containing von Willebrand factor type A (vWA) domain [General function prediction only]

 Score = 50.4 bits (120), Expect = 5e-06
 Identities = 58/299 (19%), Positives = 104/299 (34%), Gaps = 35/299 (11%)

Query: 28   QSTDSDEDKHDKEKEKDKHRDRDRRRDRDRDRDREKEREEKRERAREKEREREKRDRERE 87
            +   +  ++ D  +E     D   + D D    RE E +           E E  D E E
Sbjct: 3825 EDITNTLNEDDDLEELANEEDTANQSDLDESEARELESDMNGVTKDSVVSENENSDSEEE 3884

Query: 88   DRERERE----RERERRERDRE--REKRERERDRDKEKDRERKSRDREKRRKVESDDSDE 141
            +++ + E     E      + +   E  E +    ++K  E+ + + E     + DD+  
Sbjct: 3885 NQDLDEEVNDIPEDLSNSLNEKLWDEPNEEDLLETEQKSNEQSAANNESDLVSKEDDNKA 3944

Query: 142  DKDRDRKRRRRHDDDHKERVRERSLSRSNRHRDENDESPREKLVEDDSDKKEKKTREEEL 201
             +D+DR+ +    +D +E                +D    +++  D  +   +   E E 
Sbjct: 3945 LEDKDRQEK----EDEEE--------------MSDDVGIDDEIQPDIQENNSQPPPENED 3986

Query: 202  ED--EQRKLDEEMEKRRRRVQ----EWQELKRKKEESERENRGDANVEEPKAGRNWTLDR 255
             D  E  KLDE+     +       + +     KEE++ E       E+P    N TLD 
Sbjct: 3987 LDLPEDLKLDEKEGDVSKDSDLEDMDMEAADENKEEADAEKDEPMQDEDPLEENN-TLDE 4045

Query: 256  EDSDDEEVPQTGKSETDMDADEEPKPSENQVGDAMLVDSDGGSAAPALQIGAAEDEDID 314
            +   D+          D +   E    EN   +    +    S     Q    ED+ ID
Sbjct: 4046 DIQQDDFSDLA----EDDEKMNEDGFEENVQENEESTEDGVKSDEELEQGEVPEDQAID 4100

Length = 4600

>gnl|CDD|206039 pfam13868, Trichoplein, Tumour suppressor, Mitostatin

 Score = 49.1 bits (118), Expect = 6e-06
 Identities = 57/216 (26%), Positives = 102/216 (47%), Gaps = 30/216 (13%)

Query: 33  DEDKHDKEKEKDKHRDRDRRRDRD--RDRDREKEREEKRERAREKEREREKRDREREDRE 90
           D    +K++ K + ++ +RR D     +R +    EE+RER R++ER   +   + +  E
Sbjct: 23  DAQIEEKKRIKAEEKEEERRIDEMMEEERLKALAEEEERERKRKEERREGRAVLQEQIEE 82

Query: 91  RERERERERRERDREREKRERERDRDKEKDRERKSRDREKRRKV--ESDDSDEDKDRDRK 148
           RE+ R+ E  ER +ERE+ +   +R +E+D       REK++K+  E D+ +E++   ++
Sbjct: 83  REKRRQEEYEERLQEREQMDEIIERIQEEDEAEAQEKREKQKKLREEIDEFNEERIERKE 142

Query: 149 RRRRHDDDHKERVRERSLSRSNRHRDENDESPREKLVEDDSDKKEKKTREEELEDEQRKL 208
             +  + + + ++ E                            +EK  REEE E E+R+ 
Sbjct: 143 EEKEREREEELKILEYQ--------------------------REKAEREEEREAERRER 176

Query: 209 DEEMEKRRRRVQEWQELKRKKEESERENRGDANVEE 244
            EE E+   R++  QE    + E   E R D   EE
Sbjct: 177 KEEKEREVARLRAQQEEAEDEREELDELRADLYQEE 212

Trichoplein or mitostatin, was first defined as a meiosis-specific nuclear structural protein. It has since been linked with mitochondrial movement. It is associated with the mitochondrial outer membrane, and over-expression leads to reduction in mitochondrial motility whereas lack of it enhances mitochondrial movement. The activity appears to be mediated through binding the mitochondria to the actin intermediate filaments (IFs). Length = 349

>gnl|CDD|227596 COG5271, MDN1, AAA ATPase containing von Willebrand factor type A (vWA) domain [General function prediction only]

 Score = 50.4 bits (120), Expect = 6e-06
 Identities = 81/435 (18%), Positives = 161/435 (37%), Gaps = 38/435 (8%)

Query: 7    DRDREKEKEKHREKSRRSEREQSTDSDEDKHDKEKEKDKHRDRDRRRDRDRDRDREKERE 66
            + D E+E +   E+      + S   +E   D E  ++   + +++ +     + E +  
Sbjct: 3878 NSDSEEENQDLDEEVNDIPEDLSNSLNEKLWD-EPNEEDLLETEQKSNEQSAANNESDLV 3936

Query: 67   EKRE--RAREKEREREKRDREREDRERERERERERRERDREREKRERERDRDKEKDRERK 124
             K +  +A E +  +EK D E    +   + E +   ++   +      D D  +D +  
Sbjct: 3937 SKEDDNKALEDKDRQEKEDEEEMSDDVGIDDEIQPDIQENNSQPPPENEDLDLPEDLKLD 3996

Query: 125  SRDREKRRKVESDDSDEDKDRDRKRRRRHDDDHKERVRERSLSRSNRHRDENDESPRE-K 183
             ++ +  +  +SD  D D +   + +   D +  E +++      N   DE+ +      
Sbjct: 3997 EKEGDVSK--DSDLEDMDMEAADENKEEADAEKDEPMQDEDPLEENNTLDEDIQQDDFSD 4054

Query: 184  LVEDDSDKKEKKTREEELEDEQR-----KLDEEMEKRRRRVQEWQELKRKKEESERENRG 238
            L EDD    E    E   E+E+      K DEE+E+    V E Q +    +   +    
Sbjct: 4055 LAEDDEKMNEDGFEENVQENEESTEDGVKSDEELEQ--GEVPEDQAIDNHPKMDAKSTFA 4112

Query: 239  DANVEEPKAGRNWTLDREDSDDEE-VPQTGKSETDMDADEE----PKPSEN-------QV 286
             A  +E    +    + E+  +E+ V   G ++ + +  +E    PK + +        +
Sbjct: 4113 SAEADEENTDKGIVGENEELGEEDGVRGNGTADGEFEQVQEDTSTPKEAMSEADRQYQSL 4172

Query: 287  GDAMLVDSDGGSAAPALQIGAAEDEDIDPLDAFMNSMVLPEVEKLKNTVEPSFTDGNNVE 346
            GD +           A +I   ED       AF +S    E   +K   E       N E
Sbjct: 4173 GDHL------REWQQANRIHEWEDLTESQSQAFDDS----EFMHVKEDEEEDLQALGNAE 4222

Query: 347  SKKMDRKGDRRSNGEQPKKSSNKSLGRIIPGEDSD---SDYGDLENDEKPLEDEDDDEFM 403
              ++       S  + P   ++ ++      E  D    D  D+ + ++  ED    EF 
Sbjct: 4223 KDQIKSIDRDESANQNPDSMNSTNIAEDEADEVGDKQLQDGQDISDIKQTGEDTLPTEFG 4282

Query: 404  KRVKKTKAEKLSIVD 418
               +  K  +LS  +
Sbjct: 4283 SINQSEKVFELSEDE 4297

Length = 4600

>gnl|CDD|240271 PTZ00108, PTZ00108, DNA topoisomerase 2-like protein; Provisional

 Score = 50.0 bits (120), Expect = 6e-06
 Identities = 60/402 (14%), Positives = 122/402 (30%), Gaps = 66/402 (16%)

Query: 7    DRDREKEKEKHREKSRRSEREQSTDSDEDKHDKEKEKDKHRDRDRRRD-------RDRDR 59
             R ++  K+K  + +   E     D + D  D E+E       D           +++  
Sbjct: 1046 VRFKDIIKKKSEKITAEEEEGAEEDDEADDEDDEEELGAAVSYDYLLSMPIWSLTKEKVE 1105

Query: 60   DREKEREEKRERAREKEREREKRDREREDRERERERERERRERDREREKRERERDRDKEK 119
                E E+K E+  EK +    +D   ED ++  E   E +E   E+E  + +R + K K
Sbjct: 1106 KLNAELEKK-EKELEKLKNTTPKDMWLEDLDKFEE-ALEEQEEVEEKEIAKEQRLKSKTK 1163

Query: 120  DRERKSRDREKRRKVESDDSDEDKDRDRKRRRRHDDDHKERVRERSLSRSNRHRDENDES 179
             +  K R  + ++K +                  D   K  V   S    +  + + D+ 
Sbjct: 1164 GKASKLRKPKLKKKEKKKKKSSA-----------DKSKKASVVGNSKRVDSDEKRKLDDK 1212

Query: 180  PREKLVEDDSDKKEKKTREEELEDEQRKLDEEMEKRRRRVQEWQELKRKKEESERENRGD 239
            P  K        +E               DEE + + ++    +   +K   S+      
Sbjct: 1213 PDNKKSNSSGSDQED--------------DEEQKTKPKKSSVKRLKSKKNNSSKS----- 1253

Query: 240  ANVEEPKAGRNWTLDREDSDDEEVPQTGKSETDMDADEEPKPSENQVGDAMLVDSDGGSA 299
            +   +  +  + + + +  +  +     +      +      S                 
Sbjct: 1254 SEDNDEFSSDDLSKEGKPKNAPKRVSAVQYSPPPPSKRPDGESN---------------- 1297

Query: 300  APALQIGAAEDEDIDPLDAFMNSMVLPEVEKLKNTVEPSFTDGNNVESKKMDRKGDRRSN 359
                  G+                +   +  LK   +         +SK   ++     +
Sbjct: 1298 -----GGSKPSSPTKKKV---KKRLEGSLAALKKKKKSEKKTARKKKSKTRVKQASASQS 1349

Query: 360  GEQPKKSSNKSLGRIIPGEDSDSDYGDLENDEKPLEDEDDDE 401
                ++   K        ED D    D   DE   ED++DD+
Sbjct: 1350 SRLLRRPRKKKSDSSS--EDDDDSEVDDSEDEDD-EDDEDDD 1388

Length = 1388

>gnl|CDD|217393 pfam03154, Atrophin-1, Atrophin-1 family

 Score = 50.1 bits (119), Expect = 6e-06
 Identities = 24/49 (48%), Positives = 36/49 (73%), Gaps = 4/49 (8%)

Query: 63  KEREEKRERAREKEREREKRDREREDRERERERERERRERDREREKRER 111
           K+REE  E+A+   RE E++ RE  +RE+E+E+ERE RER+RE E+  +
Sbjct: 579 KKREEAVEKAK---REAEQKAREEREREKEKEKERE-REREREAERAAK 623

Atrophin-1 is the protein product of the dentatorubral-pallidoluysian atrophy (DRPLA) gene. DRPLA OMIM:125370 is a progressive neurodegenerative disorder. It is caused by the expansion of a CAG repeat in the DRPLA gene on chromosome 12p. This results in an extended polyglutamine region in atrophin-1, that is thought to confer toxicity to the protein, possibly through altering its interactions with other proteins. The expansion of a CAG repeat is also the underlying defect in six other neurodegenerative disorders, including Huntington's disease. One interaction of expanded polyglutamine repeats that is thought to be pathogenic is that with the short glutamine repeat in the transcriptional coactivator CREB binding protein, CBP. This interaction draws CBP away from its usual nuclear location to the expanded polyglutamine repeat protein aggregates that are characteristic of the polyglutamine neurodegenerative disorders. This interferes with CBP-mediated transcription and causes cytotoxicity. Length = 979

>gnl|CDD|235401 PRK05306, infB, translation initiation factor IF-2; Validated

 Score = 49.8 bits (120), Expect = 7e-06
 Identities = 24/136 (17%), Positives = 44/136 (32%), Gaps = 8/136 (5%)

Query: 60  DREKEREEKRERAREKEREREKRDREREDRERERER--------ERERRERDREREKRER 111
           + E  +EE +  A E+ +   +     E  E  +          E        E   R  
Sbjct: 40  EEEARKEEAKREAEEEAKAEAEEAAAAEAEEEAKAEAAAAAPAEEAAEAAAAAEAAARPA 99

Query: 112 ERDRDKEKDRERKSRDREKRRKVESDDSDEDKDRDRKRRRRHDDDHKERVRERSLSRSNR 171
           E +  +  +   +    +K  K +     + K   RK  R        + R R   R  R
Sbjct: 100 EDEAARPAEAAARRPKAKKAAKKKKGPKPKKKKPKRKAARGGKRGKGGKGRRRRRGRRRR 159

Query: 172 HRDENDESPREKLVED 187
            + +  + P EK+  +
Sbjct: 160 RKKKKKQKPTEKIPRE 175

Length = 746

>gnl|CDD|225288 COG2433, COG2433, Uncharacterized conserved protein [Function unknown]

 Score = 49.7 bits (119), Expect = 7e-06
 Identities = 48/251 (19%), Positives = 112/251 (44%), Gaps = 14/251 (5%)

Query: 11  EKEKEKHREKSRRSEREQSTDSDEDKHDKEKEKDKHRDRDRRRDRDRDRDREKEREEKRE 70
           E+ +EK   +          +    K ++  E+ +  + + +R+ +  +   ++ E + E
Sbjct: 401 ERPREKEGTEEEERREITVYEKRIKKLEETVERLEEENSELKRELEELKREIEKLESELE 460

Query: 71  RAREKEREREKRDREREDRERERER-ERERRERDREREKRERERDRDKEKDRERKSRDRE 129
           R R + R++ ++DRE   R+R  ER E+E  E+ +  E+ ER+    ++  +   S    
Sbjct: 461 RFRREVRDKVRKDREIRARDRRIERLEKELEEKKKRVEELERKLAELRKMRKLELSGKGT 520

Query: 130 KRRKVESDDSDEDKDRDRKRRRRHDDDHKERVRERSLSRSNRHRDENDESPREKLVEDD- 188
             + VE    +  ++ + +   +  D     V + S   +    +  D+ PR  +  ++ 
Sbjct: 521 PVKVVEKLTLEAIEEAEEEYGIKEGD--VILVEDPSGGGARTAEELIDKKPRAIIRGEEM 578

Query: 189 SDKKEKKTREEEL------EDEQRKLDE----EMEKRRRRVQEWQELKRKKEESERENRG 238
           S    ++  + E+      + +  +LDE    + E+ RR ++EW++   ++E  ++E   
Sbjct: 579 SHAAAEEFFKNEIPVLPEGDVQIIRLDEFAVVDSEELRRAIEEWKKRFEERERRQKEEDI 638

Query: 239 DANVEEPKAGR 249
              +EE +  R
Sbjct: 639 LRIIEEYRRER 649

Length = 652

>gnl|CDD|223496 COG0419, SbcC, ATPase involved in DNA repair [DNA replication, recombination, and repair]

 Score = 49.4 bits (118), Expect = 9e-06
 Identities = 44/234 (18%), Positives = 94/234 (40%), Gaps = 16/234 (6%)

Query: 6   RDRDREKEKEKHREKSRRSEREQSTDSDEDKHDKEKEKDKHRDRDRRRDRDRDRDREKER 65
            +   E E+ K + + ++ + E     D  +  KE  ++    R R+ + +  R+R KE 
Sbjct: 539 ENLLEELEELKEKLQLQQLKEELRQLEDRLQELKELLEELRLLRTRKEELEELRERLKEL 598

Query: 66  EEKRERAREKEREREKRDREREDRERERERERERRERDREREKRERERDRDKEKDRERKS 125
           ++K +   E+  + E+  +  E  E E E E    E + E EK   + + ++      + 
Sbjct: 599 KKKLKELEERLSQLEELLQSLELSEAENELEEAEEELESELEKLNLQAELEELLQAALEE 658

Query: 126 RDREKRRKVESDDSDEDKDRDRKRRRRHDDDHKERVRERSLSRSNRHRDENDESPREKLV 185
            + +          +  +  + ++     ++ ++   E              E  RE+L 
Sbjct: 659 LEEKVEELEAEIRRELQRIENEEQLEEKLEELEQLEEEL-------------EQLREELE 705

Query: 186 EDDSDKKEKKTREEELED---EQRKLDEEMEKRRRRVQEWQELKRKKEESEREN 236
           E      E +   EELE    E  +L +E+EK  + ++  +EL+ K  ++    
Sbjct: 706 ELLKKLGEIEQLIEELESRKAELEELKKELEKLEKALELLEELREKLGKAGLRA 759

Length = 908

>gnl|CDD|223496 COG0419, SbcC, ATPase involved in DNA repair [DNA replication, recombination, and repair]

 Score = 49.4 bits (118), Expect = 9e-06
 Identities = 54/255 (21%), Positives = 91/255 (35%), Gaps = 16/255 (6%)

Query: 6   RDRDREKEKEKHREKSRRSEREQSTDSDEDKHDKEKEKDKHRDRDRRRDRDRDRDREKER 65
           R+ +  +E+ K  E+       +     E     EK     ++     +++     E E 
Sbjct: 424 RELEELEEEIKKLEEQINQLESKELMIAELAGAGEKCPVCGQELPEEHEKELLELYELEL 483

Query: 66  EEKRERAREKEREREKRDREREDRERERERERERRERDREREKRERERDRDKEKDRERKS 125
           EE  E    ++ E E R+   E  +  RE E E  E     E  + E +   EK      
Sbjct: 484 EELEEELSREKEEAELREEIEELEKELRELEEELIELLELEEALKEELEEKLEKLENLLE 543

Query: 126 RDREKRRKVESDDSDEDKDRDRKRRRRHDDDHKERVRER---SLSRSNRHRDENDESPRE 182
              E + K++     E+  +   R +   +  +E    R         R R +  +   +
Sbjct: 544 ELEELKEKLQLQQLKEELRQLEDRLQELKELLEELRLLRTRKEELEELRERLKELKKKLK 603

Query: 183 KL-------------VEDDSDKKEKKTREEELEDEQRKLDEEMEKRRRRVQEWQELKRKK 229
           +L             +E    + E +  EEELE E  KL+ + E         +EL+ K 
Sbjct: 604 ELEERLSQLEELLQSLELSEAENELEEAEEELESELEKLNLQAELEELLQAALEELEEKV 663

Query: 230 EESERENRGDANVEE 244
           EE E E R +    E
Sbjct: 664 EELEAEIRRELQRIE 678

Length = 908

>gnl|CDD|237171 PRK12678, PRK12678, transcription termination factor Rho; Provisional

 Score = 49.1 bits (118), Expect = 1e-05
 Identities = 34/215 (15%), Positives = 61/215 (28%), Gaps = 12/215 (5%)

Query: 63  KEREEKRERAREKEREREKRDREREDRERERERERERRERDREREKRERERDRDKEKDRE 122
           KE       A             R  R     R+ E+   +    K E            
Sbjct: 56  KEARGGGAAAAAATPAAPAAAARRAARAAAAARQAEQPAAEAAAAKAEAAPAARAAAAAA 115

Query: 123 RKSRDREKRRKVESDDSDEDKDRDRKRRRRHDDDHKERVRERSLSRSNRHRDENDESPRE 182
            ++    +  +        +  R    R+  +   +     R+       R E +E    
Sbjct: 116 AEAASAPEAAQARERRERGEAARRGAARKAGEGGEQPATEARA---DAAERTEEEERDER 172

Query: 183 KLVEDDSDKKEKKTREEELEDEQRKLDEEMEKRRRRVQEWQELKRKKEESERENRGDANV 242
           +   D  D++ +  R E    E+R  D +   RR R +         +   RE RG  + 
Sbjct: 173 RRRGDREDRQAEAERGERGRREERGRDGDDRDRRDRRE---------QGDRREERGRRDG 223

Query: 243 EEPKAGRNWTLDREDSDDEEVPQTGKSETDMDADE 277
            + +  R     R+   D+     G  + D     
Sbjct: 224 GDRRGRRRRRDRRDARGDDNREDRGDRDGDDGEGR 258

Length = 672

>gnl|CDD|179385 PRK02224, PRK02224, chromosome segregation protein; Provisional

 Score = 49.3 bits (118), Expect = 1e-05
 Identities = 54/228 (23%), Positives = 93/228 (40%), Gaps = 19/228 (8%)

Query: 11  EKEKEKHREK-----SRRSEREQSTDSDEDKHDKEKEKDKHRDRDRRRDRDRDRDREKER 65
           E   E+  E+        +ER ++ +   ++ ++ +E+    + +    R+   + E+E 
Sbjct: 508 EDRIERLEERREDLEELIAERRETIEEKRERAEELRERAAELEAEAEEKREAAAEAEEEA 567

Query: 66  EEKRERAREKEREREKRDREREDRERERERERERRERDREREKRERERDRDKEKDRERKS 125
           EE RE   E   +  +     E  ER R       + + E E+   +R+   E + ER+ 
Sbjct: 568 EEAREEVAELNSKLAELKERIESLERIRTLLAAIADAEDEIERLREKREALAELNDERRE 627

Query: 126 RDREKRRKVESDDSDEDKDRDRKRRRRHDDDHKERVRERSLSRSNRHRDENDESPREKLV 185
           R  EKR            +R R+     D+   E  RE    R+  + ++ +E   E   
Sbjct: 628 RLAEKR------------ERKRELEAEFDEARIEEARED-KERAEEYLEQVEEKLDELRE 674

Query: 186 EDDSDKKEKKTREEELEDEQRKLDEEMEKRRRRVQEWQELKRKKEESE 233
           E D  + E    E ELE E  +L E  E    RV+  + L  + EE E
Sbjct: 675 ERDDLQAEIGAVENELE-ELEELRERREALENRVEALEALYDEAEELE 721

Length = 880

>gnl|CDD|233758 TIGR02169, SMC_prok_A, chromosome segregation protein SMC, primarily archaeal type

 Score = 49.3 bits (118), Expect = 1e-05
 Identities = 45/232 (19%), Positives = 92/232 (39%), Gaps = 9/232 (3%)

Query: 11  EKEKEKHREKSRRSEREQSTD---SDEDKHDKEKEKDKHRDRDRRRDRDRDRDREKEREE 67
           E EK     +    E  +       +E    KEK  +   +         +++RE E  E
Sbjct: 262 ELEKRLEEIEQLLEELNKKIKDLGEEEQLRVKEKIGELEAEIASLERSIAEKERELEDAE 321

Query: 68  KRERAREKEREREKRDREREDRERERERERERRERDREREKRERERDRDKEKDRERKSRD 127
           +R    E E ++   + E  +RE E ER+R  +  +   E +E   D   E +   K   
Sbjct: 322 ERLAKLEAEIDKLLAEIEELEREIEEERKRRDKLTEEYAELKEELEDLRAELEEVDKEFA 381

Query: 128 REKRRKVESDDSDEDKDRDRKRRRRHDDDHKERVRERSLSRSNRHRDENDESPREKLVED 187
             +    +  +  E   R+    +R  D  +E ++  S   ++ +          K+ E 
Sbjct: 382 ETRDELKDYREKLEKLKREINELKRELDRLQEELQRLSEELADLNAAI--AGIEAKINEL 439

Query: 188 DSDKKEK----KTREEELEDEQRKLDEEMEKRRRRVQEWQELKRKKEESERE 235
           + +K++K    K +E +LE     L +  ++     +E+  ++++  + +RE
Sbjct: 440 EEEKEDKALEIKKQEWKLEQLAADLSKYEQELYDLKEEYDRVEKELSKLQRE 491

SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]. Length = 1164

>gnl|CDD|217051 pfam02463, SMC_N, RecF/RecN/SMC N terminal domain

 Score = 49.2 bits (117), Expect = 1e-05
 Identities = 43/254 (16%), Positives = 104/254 (40%), Gaps = 13/254 (5%)

Query: 8   RDREKEKEKHREKS---RRSEREQSTDSDEDKHDKEKEKDKHRDRDRRRDRDRDRDREKE 64
           ++ EKE+E   +     +  E+E+    +E K   ++E++   +  +   R  D + + +
Sbjct: 259 QELEKEEEILAQVLKENKEEEKEKKLQEEELKLLAKEEEELKSELLKLERRKVDDEEKLK 318

Query: 65  REEKRERAREKEREREKRDREREDRE-------RERERERERRERDREREKRERERDRDK 117
             EK  +  EKE ++EK + E  ++E       RE E E E +    + +  + E +   
Sbjct: 319 ESEKELKKLEKELKKEKEEIEELEKELKELEIKREAEEEEEEQLEKLQEKLEQLEEELLA 378

Query: 118 EKDRERKSRDREKRRKVES---DDSDEDKDRDRKRRRRHDDDHKERVRERSLSRSNRHRD 174
           +K  E +      + K E     + +E + +        ++D  +  ++  L       +
Sbjct: 379 KKKLESERLSSAAKLKEEELELKNEEEKEAKLLLELSEQEEDLLKEEKKEELKIVEELEE 438

Query: 175 ENDESPREKLVEDDSDKKEKKTREEELEDEQRKLDEEMEKRRRRVQEWQELKRKKEESER 234
             +    +   E +  +K+     ++  + ++  D   E +  ++ E  EL   +++ E 
Sbjct: 439 SLETKQGKLTEEKEELEKQALKLLKDKLELKKSEDLLKETKLVKLLEQLELLLLRQKLEE 498

Query: 235 ENRGDANVEEPKAG 248
            ++ ++   E  A 
Sbjct: 499 ASQKESKAREGLAV 512

This domain is found at the N terminus of SMC proteins. The SMC (structural maintenance of chromosomes) superfamily proteins have ATP-binding domains at the N- and C-termini, and two extended coiled-coil domains separated by a hinge in the middle. The eukaryotic SMC proteins form two kind of heterodimers: the SMC1/SMC3 and the SMC2/SMC4 types. These heterodimers constitute an essential part of higher order complexes, which are involved in chromatin and DNA dynamics. This family also includes the RecF and RecN proteins that are involved in DNA metabolism and recombination. Length = 1162

>gnl|CDD|217393 pfam03154, Atrophin-1, Atrophin-1 family

 Score = 49.3 bits (117), Expect = 1e-05
 Identities = 27/65 (41%), Positives = 38/65 (58%), Gaps = 11/65 (16%)

Query: 67  EKRERAREKEREREKRDREREDRERERERERERRERDREREKRERERDRDKEKDRERKSR 126
           +KRE A EK + RE   + RE+RERE+E+E+ER          ERER+R+ E+  +  S 
Sbjct: 579 KKREEAVEKAK-REAEQKAREEREREKEKEKER----------EREREREAERAAKASSS 627

Query: 127 DREKR 131
             E R
Sbjct: 628 SHESR 632

Atrophin-1 is the protein product of the dentatorubral-pallidoluysian atrophy (DRPLA) gene. DRPLA OMIM:125370 is a progressive neurodegenerative disorder. It is caused by the expansion of a CAG repeat in the DRPLA gene on chromosome 12p. This results in an extended polyglutamine region in atrophin-1, that is thought to confer toxicity to the protein, possibly through altering its interactions with other proteins. The expansion of a CAG repeat is also the underlying defect in six other neurodegenerative disorders, including Huntington's disease. One interaction of expanded polyglutamine repeats that is thought to be pathogenic is that with the short glutamine repeat in the transcriptional coactivator CREB binding protein, CBP. This interaction draws CBP away from its usual nuclear location to the expanded polyglutamine repeat protein aggregates that are characteristic of the polyglutamine neurodegenerative disorders. This interferes with CBP-mediated transcription and causes cytotoxicity. Length = 979

>gnl|CDD|220271 pfam09507, CDC27, DNA polymerase subunit Cdc27

 Score = 48.3 bits (115), Expect = 1e-05
 Identities = 32/127 (25%), Positives = 54/127 (42%), Gaps = 8/127 (6%)

Query: 12  KEKEKHREKSRRSEREQSTDSDEDKHDKEKEKDKHRDRDRRRDRDRDRDREKEREEKRER 71
           KEK++  E + + E E+ +   +   + E  +    D D   D  +      ER +  E 
Sbjct: 230 KEKKEASESTVKEESEEESGKRDVILEDESAEPTGLDEDEDEDEPKPSG---ERSDSEEE 286

Query: 72  AREKEREREKRDREREDRERERERERERRERDREREKRER-----ERDRDKEKDRERKSR 126
             EKE+E+ KR ++  + E E E      E   E E+ E         +++EK+    S 
Sbjct: 287 TEEKEKEKRKRLKKMMEDEDEDEEMEIVPESPVEEEESEEPEPPPLPKKEEEKEEVTVSP 346

Query: 127 DREKRRK 133
           D  +RR 
Sbjct: 347 DGGRRRG 353

This protein forms the C subunit of DNA polymerase delta. It carries the essential residues for binding to the Pol1 subunit of polymerase alpha, from residues 293-332, which are characterized by the motif D--G--VT, referred to as the DPIM motif. The first 160 residues of the protein form the minimal domain for binding to the B subunit, Cdc1, of polymerase delta, the final 10 C-terminal residues, 362-372, being the DNA sliding clamp, PCNA, binding motif. Length = 427

>gnl|CDD|217203 pfam02724, CDC45, CDC45-like protein

 Score = 48.4 bits (116), Expect = 1e-05
 Identities = 27/83 (32%), Positives = 42/83 (50%), Gaps = 1/83 (1%)

Query: 35  DKHDKEKEKDK-HRDRDRRRDRDRDRDREKEREEKRERAREKEREREKRDREREDRERER 93
           D  D E+E     R  D  RD + D D ++E +E+ E + + E + +  D + +D    R
Sbjct: 102 DDGDIEEELQDEPRYDDAYRDLEEDDDDDEESDEEDEESSKSEDDEDDDDDDDDDDIATR 161

Query: 94  ERERERRERDREREKRERERDRD 116
           ER  ERR R RE E++  E +  
Sbjct: 162 ERSLERRRRRREWEEKRAELEFY 184

CDC45 is an essential gene required for initiation of DNA replication in S. cerevisiae, forming a complex with MCM5/CDC46. Homologues of CDC45 have been identified in human, mouse and smut fungus among others. Length = 583

>gnl|CDD|220648 pfam10243, MIP-T3, Microtubule-binding protein MIP-T3

 Score = 48.0 bits (114), Expect = 2e-05
 Identities = 32/204 (15%), Positives = 75/204 (36%), Gaps = 4/204 (1%)

Query: 5   HRDRDREKEKEKHREKSRRSEREQSTDSDEDKHDKEKEKDKHRDRDRRRDRDRDRDREKE 64
             ++ RE+ + K R K    ++  +    ++  ++EK++   R+  + +  + D + E+E
Sbjct: 161 EEEKKRERVRAKSRPKKPPKKKPPN--KKKEPPEEEKQRQAAREAVKGKPEEPDVNEERE 218

Query: 65  REEKRERAREKEREREKRDREREDRERERERERERRERDREREKRERERDRDKEKDRERK 124
           +EE   + RE      + D  R+  E  R R     ++            R+  K  E +
Sbjct: 219 KEEDDGKDRETTTSPMEEDESRQSSEISR-RSSSSLKKPDPSPSMASPETRESSKRTETR 277

Query: 125 SRDREKRRKVESDDSDEDKDRDRKRRRRHDD-DHKERVRERSLSRSNRHRDENDESPREK 183
            R   +        +     R +++       D +   +  S       + E+++     
Sbjct: 278 PRTSLRPPSARPASARPAPPRVKRKEIVTVLQDAQGVGKIVSNVILEGKKSEDEDDENFV 337

Query: 184 LVEDDSDKKEKKTREEELEDEQRK 207
           +             E+E ED +++
Sbjct: 338 VEAAAQAPDIVAGGEDEAEDGEQQ 361

This protein, which interacts with both microtubules and TRAF3 (tumour necrosis factor receptor-associated factor 3), is conserved from worms to humans. The N-terminal region is the microtubule binding domain and is well-conserved; the C-terminal 100 residues, also well-conserved, constitute the coiled-coil region which binds to TRAF3. The central region of the protein is rich in lysine and glutamic acid and carries KKE motifs which may also be necessary for tubulin-binding, but this region is the least well-conserved. Length = 506

>gnl|CDD|233757 TIGR02168, SMC_prok_B, chromosome segregation protein SMC, common bacterial type

 Score = 48.5 bits (116), Expect = 2e-05
 Identities = 39/255 (15%), Positives = 88/255 (34%), Gaps = 20/255 (7%)

Query: 16  KHREKSRRSEREQST--DSDEDKHDKEKEKDKHRDRDRRRDRDRDR--DREKEREEKRER 71
           +  E     E  Q        +    E++K   R+R    +R  +    + +E E K + 
Sbjct: 275 EVSELEEEIEELQKELYALANEISRLEQQKQILRERLANLERQLEELEAQLEELESKLDE 334

Query: 72  AREKEREREKR----------DREREDRERERERERERRERDREREKRERERDRDKEKDR 121
             E+  E E++               +       E E R  + E +         + + +
Sbjct: 335 LAEELAELEEKLEELKEELESLEAELEELEAELEELESRLEELEEQLETLRSKVAQLELQ 394

Query: 122 ERKSRDREKRRKVESDDSDEDKDRDRKRRRRHDDDHKERVRERSLSRSNRHRDENDESPR 181
                +  +R +   +  ++ ++R ++         +E   +   +      +E      
Sbjct: 395 IASLNNEIERLEARLERLEDRRERLQQEIEELLKKLEEAELKELQAELEELEEE-----L 449

Query: 182 EKLVEDDSDKKEKKTR-EEELEDEQRKLDEEMEKRRRRVQEWQELKRKKEESERENRGDA 240
           E+L E+    +E      EELE+ ++ LD    +  +       L+R +E  E  + G  
Sbjct: 450 EELQEELERLEEALEELREELEEAEQALDAAERELAQLQARLDSLERLQENLEGFSEGVK 509

Query: 241 NVEEPKAGRNWTLDR 255
            + + ++G +  L  
Sbjct: 510 ALLKNQSGLSGILGV 524

SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]. Length = 1179

>gnl|CDD|237496 PRK13766, PRK13766, Hef nuclease; Provisional

 Score = 48.7 bits (117), Expect = 2e-05
 Identities = 38/157 (24%), Positives = 69/157 (43%), Gaps = 30/157 (19%)

Query: 684 VNKDITQLVEVRPESDRFLRLLELLGEWYEKG---KILIFVHSQEKCDALFRDLLKHGYP 740
             K + +  E+  E  +  +L E++ E   K    +I++F   ++  + +   L K G  
Sbjct: 332 FRKAVRKAKELDIEHPKLEKLREIVKEQLGKNPDSRIIVFTQYRDTAEKIVDLLEKEGIK 391

Query: 741 CLSLHGAKDQTDRES-----------TISDFKSNVCNLLIATSVAARGLDVKELELVINF 789
            +   G   Q  ++             +  F++   N+L++TSVA  GLD+  ++LVI F
Sbjct: 392 AVRFVG---QASKDGDKGMSQKEQIEILDKFRAGEFNVLVSTSVAEEGLDIPSVDLVI-F 447

Query: 790 DAPNHYED------YVHRVGRTGRAGRKGCAITFISE 820
                YE        + R GRTGR   +G  +  I++
Sbjct: 448 -----YEPVPSEIRSIQRKGRTGR-QEEGRVVVLIAK 478

Length = 773

>gnl|CDD|173502 PTZ00266, PTZ00266, NIMA-related protein kinase; Provisional

 Score = 48.6 bits (115), Expect = 2e-05
 Identities = 40/100 (40%), Positives = 52/100 (52%), Gaps = 3/100 (3%)

Query: 52  RRDRDRDRDREKEREEKRERAREKEREREKRDREREDRERERERERERRERDREREKRER 111
           R D+D       E+E    +A E  +  EK+  ER +RE     ERER ER  ERE+ ER
Sbjct: 429 RVDKDHAERARIEKENAHRKALEM-KILEKKRIERLEREERERLERERMER-IERERLER 486

Query: 112 ERDRDKEKDRERKSRDREKRRKVESDDSDEDKDRDRKRRR 151
           ER   +  +R+R  RDR  R + E  D  E +DR  K RR
Sbjct: 487 ERLERERLERDRLERDRLDRLERERVDRLE-RDRLEKARR 525

Length = 1021

>gnl|CDD|130009 TIGR00934, 2a38euk, potassium uptake protein, Trk family

 Score = 48.1 bits (114), Expect = 2e-05
 Identities = 56/259 (21%), Positives = 87/259 (33%), Gaps = 17/259 (6%)

Query: 3   HSHRDRDREKEKEKHREKSRRSEREQ-STDSDEDKHDKEKEKDKHRDRDRRRDRDRDRDR 61
           H    R   ++K    E  +R E +Q S D   D    E   D   ++  +R   RD D 
Sbjct: 174 HGSAKRRDFQDKLFSGEFVKRDEPDQNSPDVKSDTRADESISDLEFEKFAKRRGSRDVDP 233

Query: 62  EKEREEKRERAREKEREREKRDREREDRERERERERERRER-----DREREKRERER--D 114
           E             ER REK        ER  E  +E+ ER     D ER  +   R  D
Sbjct: 234 EDLYRSIMMLQGIHERIREKSSANSRSDERSSESIQEQVERRPSTSDIERNSQSLTRRYD 293

Query: 115 RDKEKDRERKSRDREKRRKVESDDSDEDKDRDRKRRRRHDDDHKERVRERSLSRSNRHRD 174
                   R  R +   R    D  + D+ +D +  +   D+ K   R++   R    R 
Sbjct: 294 DKSFDKAVRLRRSKTIDRAEACDLEELDRAKDFE--KMTYDNWKAHHRKKKNFRP---RG 348

Query: 175 ENDESPREKLVEDDSDKKEKKTREEELEDEQRKLDEEMEKRRRRVQEWQELKRKKEESER 234
            N +  +      DSD+   +     L        EE              K++++    
Sbjct: 349 WNLKFRKASRFPKDSDRNY-EDNGNHLSASSSFGSEEPSLSSEENLYPTYNKKREDSRHT 407

Query: 235 ENRGDAN---VEEPKAGRN 250
            ++  +      +P  GRN
Sbjct: 408 LSKTMSTNYLSWQPTIGRN 426

The proteins of the Trk family are derived from Gram-negative and Gram-positive bacteria, yeast and wheat. The proteins of E. coli K12 TrkH and TrkG as well as several yeast proteins have been functionally characterized.The E. coli TrkH and TrkG proteins are complexed to two peripheral membrane proteins, TrkA, an NAD-binding protein, and TrkE, an ATP-binding protein. This complex forms the potassium uptake system. This family is specific for the eukaryotic Trk system [Transport and binding proteins, Cations and iron carrying compounds]. Length = 800

>gnl|CDD|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and chromosome partitioning]

 Score = 48.2 bits (115), Expect = 3e-05
 Identities = 33/205 (16%), Positives = 72/205 (35%), Gaps = 18/205 (8%)

Query: 3   HSHRDRDREKEKEKHREKSRRSEREQSTDSDEDKHDKEKEKDKHRDRDRRRDRDRDRDRE 62
               + +  +E+ +  ++   + +E+  + +    + E+   +  +     +        
Sbjct: 313 ELENELEELEERLEELKEKIEALKEELEERETLLEELEQLLAELEEAKEELEEKLSA-LL 371

Query: 63  KEREEKRERAREKEREREKRDREREDRERERERERERRERDREREKRERERDRDKEKDRE 122
           +E EE  E  RE+  E      E E  E   E E  +RE +   E+ ER  +R ++   E
Sbjct: 372 EELEELFEALREELAE-----LEAELAEIRNELEELKREIESLEERLERLSERLEDLKEE 426

Query: 123 RKSRDREKRRKVESDDSDEDKDRDRKRRRRHDDDHKERVRERSLSRSNRHRDENDESPRE 182
            K  + E       ++   + +   +     ++  +E               + +    E
Sbjct: 427 LKELEAEL------EELQTELEELNEELEELEEQLEELRDRLKELERELAELQEELQRLE 480

Query: 183 KLVEDDSDKKEKKTREEELEDEQRK 207
           K +         + R + LE EQR 
Sbjct: 481 KEL------SSLEARLDRLEAEQRA 499

Length = 1163

>gnl|CDD|202096 pfam02029, Caldesmon, Caldesmon

 Score = 47.3 bits (112), Expect = 3e-05
 Identities = 40/142 (28%), Positives = 69/142 (48%), Gaps = 4/142 (2%)

Query: 6   RDRDREKEKEKHREKSRRSEREQSTDSDEDKHDKEKEKDKHRDRDRRRDRDRDRDRE--K 63
                E +KE+   +    E+ +    +E+  +    K KH +    R        E  K
Sbjct: 141 WRDAEECQKEEKEPEPEEEEKPKRGSLEENNGEFMTHKLKHTENTFSRGGAEGAQVEAGK 200

Query: 64  EREEKRERAREKEREREKRDREREDRERERERERERRERDR-EREKRERERD-RDKEKDR 121
           E E+ +++ +E   E E+  ++RE+R +  E E +RR+++  +R+ RE E   R KE+  
Sbjct: 201 EFEKLKQKQQEAALELEELKKKREERRKVLEEEEQRRKQEEADRKSREEEEKRRLKEEIE 260

Query: 122 ERKSRDREKRRKVESDDSDEDK 143
            R++   EKR+KV  D   EDK
Sbjct: 261 RRRAEAAEKRQKVPEDGLSEDK 282

Length = 431

>gnl|CDD|223496 COG0419, SbcC, ATPase involved in DNA repair [DNA replication, recombination, and repair]

 Score = 47.4 bits (113), Expect = 3e-05
 Identities = 44/222 (19%), Positives = 91/222 (40%), Gaps = 10/222 (4%)

Query: 20  KSRRSERE----QSTDSDEDKHDKEKEKDKHRDRDRRRDRDRDRDRE-KEREEKRERARE 74
           KS+  ER+    +    ++ +   E  K+  ++   + +    +  E  E  E    A E
Sbjct: 150 KSKPKERKEILDELFGLEKYEKLSELLKEVIKEAKAKIEELEGQLSELLEDIEDLLEALE 209

Query: 75  KEREREKRDREREDRERERERERE-----RRERDREREKRERERDRDKEKDRERKSRDRE 129
           +E +  K+  E ++ + E E E+E      R  + E EK   E  + +  + E    +  
Sbjct: 210 EELKELKKLEEIQEEQEEEELEQEIEALEERLAELEEEKERLEELKARLLEIESLELEAL 269

Query: 130 KRRKVESDDSDEDKDRDRKRRRRHDDDHKERVRERSLSRSNRHRDENDESPREKLVEDDS 189
           K R+ E  + +   +   ++  R ++  +E           R   E  E   EKL   + 
Sbjct: 270 KIREEELRELERLLEELEEKIERLEELEREIEELEEELEGLRALLEELEELLEKLKSLEE 329

Query: 190 DKKEKKTREEELEDEQRKLDEEMEKRRRRVQEWQELKRKKEE 231
             ++ + + E+LE E  +L EE  +  + ++E  +   ++ E
Sbjct: 330 RLEKLEEKLEKLESELEELAEEKNELAKLLEERLKELEERLE 371

Length = 908

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 47.4 bits (112), Expect = 4e-05
 Identities = 52/286 (18%), Positives = 113/286 (39%), Gaps = 16/286 (5%)

Query: 11   EKEKEKHREKSRRSEREQSTDSDEDKHDKEKEKDKHRDRDRR------------RDRDRD 58
            E+  E         E++   +  +  H+ + E   H  +D              ++ +R 
Sbjct: 1030 EELTEYGNNDDVLKEKDIIDEDIDGNHEGKAEAKAHVGQDEGLKPSYKDFDFDAKEDNRA 1089

Query: 59   RDREKEREEKRERAREKEREREKRDREREDRERERERERERRERDREREKRERERDRDKE 118
             +  +E   K E A++ E  + +  R+ E+ +++ E  R+  E  +  + R+ E  R  E
Sbjct: 1090 DEATEEAFGKAEEAKKTETGKAEEARKAEEAKKKAEDARKAEEARKAEDARKAEEARKAE 1149

Query: 119  KDRERK-SRDREKRRKVESDDSDEDKDRDRKRRRRHDDDHKERVRERSLSRSNRHRDEND 177
              +  + +R  E  RK E     ED  +    R+  +    E +R+   +   R  +   
Sbjct: 1150 DAKRVEIARKAEDARKAEEARKAEDAKKAEAARKAEEVRKAEELRK---AEDARKAEAAR 1206

Query: 178  ESPREKLVEDDSDKKEKKTREEELEDEQRKLDEEMEKRRRRVQEWQELKRKKEESERENR 237
            ++  E+  E+    ++ K  E   + E+ K D E  K+    +  +E+++ +E       
Sbjct: 1207 KAEEERKAEEARKAEDAKKAEAVKKAEEAKKDAEEAKKAEEERNNEEIRKFEEARMAHFA 1266

Query: 238  GDANVEEPKAGRNWTLDREDSDDEEVPQTGKSETDMDADEEPKPSE 283
                  + +  R     ++  + ++  +  K+E    ADE  K +E
Sbjct: 1267 RRQAAIKAEEARKADELKKAEEKKKADEAKKAEEKKKADEAKKKAE 1312

Length = 2084

>gnl|CDD|178945 PRK00247, PRK00247, putative inner membrane protein translocase component YidC; Validated

 Score = 46.8 bits (111), Expect = 4e-05
 Identities = 22/138 (15%), Positives = 50/138 (36%), Gaps = 17/138 (12%)

Query: 35  DKHDKEKEKDKHRDRDRRRDRDR----------------DRDREKEREEKRERAREKERE 78
            ++ +++++ K      RR+R R                +  + +  E+   +AR+KE  
Sbjct: 292 AQYREKQKEKKAFLWTLRRNRLRMIITPWRAPELHAENAEIKKTRTAEKNEAKARKKEIA 351

Query: 79  REKRDRERE-DRERERERERERRERDREREKRERERDRDKEKDRERKSRDREKRRKVESD 137
           +++R  ERE +RE  +ER          R   + ++    +      +    +  K    
Sbjct: 352 QKRRAAEREINREARQERAAAMARARARRAAVKAKKKGLIDASPNEDTPSENEESKGSPP 411

Query: 138 DSDEDKDRDRKRRRRHDD 155
             +     +  R    +D
Sbjct: 412 QVEATTTAEPNREPSQED 429

Length = 429

>gnl|CDD|179385 PRK02224, PRK02224, chromosome segregation protein; Provisional

 Score = 46.6 bits (111), Expect = 6e-05
 Identities = 59/244 (24%), Positives = 92/244 (37%), Gaps = 37/244 (15%)

Query: 9   DREKEKEKHREKSRRSEREQSTDSDEDKHDKEKEKDKHRDRDRRRDRDRDRDREKEREEK 68
            R +E E   E+ R    E    +     + E              R+   D E+  EE 
Sbjct: 314 ARREELEDRDEELRDRLEECRVAAQAHNEEAE------------SLREDADDLEERAEEL 361

Query: 69  RERAREKEREREKRDREREDRERERERERERRERDRER-----EKRERERDRDKEKDRER 123
           RE A E E E E+     EDR  E E   E  E  RER            D   E+ RE 
Sbjct: 362 REEAAELESELEEAREAVEDRREEIEELEEEIEELRERFGDAPVDLGNAEDF-LEELREE 420

Query: 124 KSRDREKRRKVESDDSDEDKDRDRKRRRR------------HDDDHKERVRERSLSRSNR 171
           +   RE+  ++E+      +  +                      H E + E       R
Sbjct: 421 RDELREREAELEATLRTARERVEEAEALLEAGKCPECGQPVEGSPHVETIEED------R 474

Query: 172 HRDENDESPREKLVEDDSDKKEKKTREEELEDEQRKLDEEMEKRRRRVQEWQELKRKKEE 231
            R E  E+  E L E+  + +E+  R E+L + + ++ E +E+RR  ++E    +R+  E
Sbjct: 475 ERVEELEAELEDLEEEVEEVEERLERAEDLVEAEDRI-ERLEERREDLEELIAERRETIE 533

Query: 232 SERE 235
            +RE
Sbjct: 534 EKRE 537

Length = 880

>gnl|CDD|224125 COG1204, COG1204, Superfamily II helicase [General function prediction only]

 Score = 46.6 bits (111), Expect = 6e-05
 Identities = 32/135 (23%), Positives = 57/135 (42%), Gaps = 14/135 (10%)

Query: 492 PIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRE 551
           P Q      ++S  + +  A TGSGKTL  +L +L  + +      G G V  I  P + 
Sbjct: 35  PQQEAVEKGLLSDENVLISAPTGSGKTLIALLAILSTLLE------GGGKVVYI-VPLKA 87

Query: 552 LVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGGK 611
           L ++ + +  +  + +G+R     G         E     +++V TP ++ D L      
Sbjct: 88  LAEEKYEEFSRLEE-LGIRVGISTGDY---DLDDERLARYDVIVTTPEKL-DSLTRKRPS 142

Query: 612 ITNLRRVTYLVMDEA 626
              +  V  +V+DE 
Sbjct: 143 W--IEEVDLVVIDEI 155

Length = 766

>gnl|CDD|222447 pfam13904, DUF4207, Domain of unknown function (DUF4207)

 Score = 45.5 bits (108), Expect = 6e-05
 Identities = 35/153 (22%), Positives = 74/153 (48%), Gaps = 25/153 (16%)

Query: 75  KEREREKRDREREDRERERERERERRER-DREREKRER--ERDRDKEKDRERKSRDREKR 131
           K+ +R+K+ ++  + ++++ERE+ER E   R+R  +E+  E  R K +    K R  + +
Sbjct: 96  KQAQRQKKLQKLLEEKQKQEREKEREEAELRQRLAKEKYEEWCRQKAQQ-AAKQRTPKHK 154

Query: 132 RKVESDDSDEDKDRDRKRRRRHDDDHKERVRERSLSRSNRHRDENDESPREKLVEDDSDK 191
           ++     S       +  R    ++ K+R+                E   +KL      K
Sbjct: 155 KEAAESASSSLSGSAKPERNVSQEEAKKRL---------------QEWELKKL------K 193

Query: 192 KEKKTREEELEDEQRKLDEEMEKRRRRVQEWQE 224
           ++++ REEE   +++K  EE E++++  + WQ+
Sbjct: 194 QQQQKREEERRKQRKKQQEEEERKQKAEEAWQK 226

This family is found in eukaryotes; it has several conserved tryptophan residues. The function is not known. Length = 261

>gnl|CDD|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and chromosome partitioning]

 Score = 46.6 bits (111), Expect = 7e-05
 Identities = 46/228 (20%), Positives = 94/228 (41%), Gaps = 5/228 (2%)

Query: 13  EKEKHREKSRRSEREQSTDSDEDK-HDKEKEKDKHRDRDRRRDRDRDRDREKEREEKRER 71
           ++ K   + +    E++ +  ED   + EK+ +K   +  + +R ++   E    E    
Sbjct: 171 KERKEEAERKLERTEENLERLEDLLEELEKQLEKLERQAEKAERYQELKAELRELELALL 230

Query: 72  AREKEREREKRDREREDRERERERERERRERDREREKRERERDRDKEKDRERKSRDREKR 131
             + +  R++ +   E+  R  E   E +E   E EK   E   + E+ RE     +E+ 
Sbjct: 231 LAKLKELRKELEELEEELSRLEEELEELQEELEEAEKEIEELKSELEELREELEELQEEL 290

Query: 132 RKVESDDSDEDKDRDR-KRRRRHDDDHKERVRERSLSRSNRH--RDENDESPREKLVEDD 188
            +++ +  + + +    + R    ++  E + ER      +     E  E     L E +
Sbjct: 291 LELKEEIEELEGEISLLRERLEELENELEELEERLEELKEKIEALKEELEERETLLEELE 350

Query: 189 SDKKEKKTREEELEDEQRKLDEEMEKR-RRRVQEWQELKRKKEESERE 235
               E +  +EELE++   L EE+E+      +E  EL+ +  E   E
Sbjct: 351 QLLAELEEAKEELEEKLSALLEELEELFEALREELAELEAELAEIRNE 398

Length = 1163

>gnl|CDD|223496 COG0419, SbcC, ATPase involved in DNA repair [DNA replication, recombination, and repair]

 Score = 46.7 bits (111), Expect = 7e-05
 Identities = 51/240 (21%), Positives = 98/240 (40%), Gaps = 13/240 (5%)

Query: 3   HSHRDRDREKEKEKHREKSRRSEREQSTDSDEDKHDKEKEKDKHRDRDRRRDRDRDRDRE 62
               + ++E E  + R      E+E+  +      + E  + +         R+ +R   
Sbjct: 225 QEEEELEQEIEALEERLAELEEEKERLEELKARLLEIESLELEALKIREEELRELER-LL 283

Query: 63  KEREEKRERAREKEREREKRDREREDRERERERERERRERDREREKRERERDRDKEKDRE 122
           +E EEK ER  E ERE E      E  E          E +   EK +   +R ++ + +
Sbjct: 284 EELEEKIERLEELEREIE------ELEEELEGLRALLEELEELLEKLKSLEERLEKLEEK 337

Query: 123 RKSRDREKRRKVESDDSDEDKDRDRKRRRRHDDDHKERVRERSLSRSNRHRDENDESPRE 182
            +  + E     E  +       +R +      +  E+  E++L R  +  +   E  +E
Sbjct: 338 LEKLESELEELAEEKNELAKLLEERLKELEERLEELEKELEKALERLKQLEEAIQE-LKE 396

Query: 183 KLVEDDSD----KKEKKTREEELEDEQRKLDEEMEKRRRRVQEWQELKRKKEESERENRG 238
           +L E  +     ++E +  E+ELE+ +R+L EE+E+  ++++E       KE    E  G
Sbjct: 397 ELAELSAALEEIQEELEELEKELEELEREL-EELEEEIKKLEEQINQLESKELMIAELAG 455

Length = 908

>gnl|CDD|235175 PRK03918, PRK03918, chromosome segregation protein; Provisional

 Score = 46.2 bits (110), Expect = 8e-05
 Identities = 59/278 (21%), Positives = 120/278 (43%), Gaps = 46/278 (16%)

Query: 6   RDRDREKEKEKHREKSRRSEREQSTDSDEDKHDKEKEKDKHRDRDRRRDRDRDRDREKER 65
            D  RE EK   R +   +  E+     E+K ++ +E  K     + ++ ++  +  +ER
Sbjct: 306 LDELREIEKRLSRLEEEINGIEERIKELEEKEERLEELKK-----KLKELEKRLEELEER 360

Query: 66  EEKRERAREKEREREKRDREREDRERERERERERRERDREREKRERERDRDKEKDRERKS 125
            E  E A+ K+ E E+  +       E + E+E  E ++ +E+ E E  +   +  E K 
Sbjct: 361 HELYEEAKAKKEELERLKKRLTGLTPE-KLEKELEELEKAKEEIEEEISKITARIGELKK 419

Query: 126 RDREKRRKVE-----------------------------------SDDSDEDKDRDRKRR 150
             +E ++ +E                                     +  E ++++RK R
Sbjct: 420 EIKELKKAIEELKKAKGKCPVCGRELTEEHRKELLEEYTAELKRIEKELKEIEEKERKLR 479

Query: 151 RRHDDDHKERVRERSLSRSNRHRDENDESPREKLVEDDSDKKEKKTRE-EELEDEQRKLD 209
           +   +  K   +E  L +  +   E  +   EKL + + ++ EKK  E E+L+++  KL 
Sbjct: 480 KELRELEKVLKKESELIK-LKELAEQLKELEEKLKKYNLEELEKKAEEYEKLKEKLIKLK 538

Query: 210 EEMEKRRRRVQEWQELKRKKEESERENRGDANVEEPKA 247
            E++  ++ +++ +ELK+K  E E++      +EE  A
Sbjct: 539 GEIKSLKKELEKLEELKKKLAELEKKLD---ELEEELA 573

Length = 880

>gnl|CDD|217393 pfam03154, Atrophin-1, Atrophin-1 family

 Score = 46.2 bits (109), Expect = 8e-05
 Identities = 25/48 (52%), Positives = 34/48 (70%), Gaps = 3/48 (6%)

Query: 55  RDRDRDREKEREEKRERAREKEREREKRDREREDRERERERERERRER 102
           + R+   EK + E  ++ARE EREREK ++E+E RERERERE ER  +
Sbjct: 579 KKREEAVEKAKREAEQKARE-EREREK-EKEKE-REREREREAERAAK 623

Atrophin-1 is the protein product of the dentatorubral-pallidoluysian atrophy (DRPLA) gene. DRPLA OMIM:125370 is a progressive neurodegenerative disorder. It is caused by the expansion of a CAG repeat in the DRPLA gene on chromosome 12p. This results in an extended polyglutamine region in atrophin-1, that is thought to confer toxicity to the protein, possibly through altering its interactions with other proteins. The expansion of a CAG repeat is also the underlying defect in six other neurodegenerative disorders, including Huntington's disease. One interaction of expanded polyglutamine repeats that is thought to be pathogenic is that with the short glutamine repeat in the transcriptional coactivator CREB binding protein, CBP. This interaction draws CBP away from its usual nuclear location to the expanded polyglutamine repeat protein aggregates that are characteristic of the polyglutamine neurodegenerative disorders. This interferes with CBP-mediated transcription and causes cytotoxicity. Length = 979

>gnl|CDD|217927 pfam04147, Nop14, Nop14-like family

 Score = 46.1 bits (110), Expect = 9e-05
 Identities = 58/292 (19%), Positives = 121/292 (41%), Gaps = 31/292 (10%)

Query: 18  REKSRRSEREQSTDSDEDKHDKEKEKDKHRDR----DRRRDRDRDRDREKEREEKRERAR 73
           RE+ R+S+++   + ++D  D+++    H  +      + D  RD D   + +     + 
Sbjct: 92  RERQRQSKKKSMFNLEDD--DEDEFVLTHLGQSLSEIDKDDDVRDDDDFDDDDLGDLASD 149

Query: 74  EKEREREKRDREREDRERERERERERRERDRE---REKRER-ERDRDKEKDRERKSRDRE 129
           ++       + + ED E + ER++ ++E  +E   + K  + ER + KE+D +     RE
Sbjct: 150 DRAAHFGGGEDDEEDEEEQPERKKSKKEVMKEVIAKSKFYKAERQKAKEEDED----LRE 205

Query: 130 KRRKVESDDSDEDKDRDRKRRRRHDDDHKERVRERSLSRSNRHRDENDESPREKLVEDDS 189
           +      D     +      +     + K+              DE D+  RE   +  +
Sbjct: 206 ELDDDFKDLMSLLRTVKPPPKPPMTPEEKD--------------DEYDQRVRELTFDRRA 251

Query: 190 DKKEK-KTREEELEDEQRKLDEEMEKRRRRVQEWQELKRKKEESER--ENRGDANVEEPK 246
              ++ KT EE  ++E  +L +   +R RR++  +E   ++E+S+   ++  D    +  
Sbjct: 252 QPTDRTKTEEELAKEEAERLKKLEAERLRRMRGEEEDDEEEEDSKESADDLDDEFEPDDD 311

Query: 247 AGRNWTLDREDSDDEEVPQTGKSETDMDADEEPKPSENQVGDAMLVDSDGGS 298
                    ED ++EE     + E D D D E +  +  + D    + D  S
Sbjct: 312 DNFGLGQGEEDEEEEEDGVDDEDEEDDDDDLEEEEEDVDLSDEEEDEEDEDS 363

Emg1 and Nop14 are novel proteins whose interaction is required for the maturation of the 18S rRNA and for 40S ribosome production. Length = 809

>gnl|CDD|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and chromosome partitioning]

 Score = 46.2 bits (110), Expect = 1e-04
 Identities = 48/205 (23%), Positives = 92/205 (44%), Gaps = 19/205 (9%)

Query: 59  RDREKEREEKRERAREKEREREKRDREREDR----ERERERERERRERDREREKRE---- 110
           ++R++E E K ER  E     E    E E +    ER+ E+    +E   E  + E    
Sbjct: 171 KERKEEAERKLERTEENLERLEDLLEELEKQLEKLERQAEKAERYQELKAELRELELALL 230

Query: 111 ----RERDRDKEKDRERKSRDREKRRKVESDDSDEDKDRDRKRRRRHD-DDHKERVRERS 165
               +E  ++ E+  E  SR  E+  +++ +  + +K+ +  +    +  +  E ++E  
Sbjct: 231 LAKLKELRKELEELEEELSRLEEELEELQEELEEAEKEIEELKSELEELREELEELQEEL 290

Query: 166 LSRSNRHRD--ENDESPREKLVEDDSDKKEKKTREEELEDEQRKLDEEMEKRRRRVQEWQ 223
           L       +        RE+L E +++ +E + R EEL+++   L EE+E+R   ++E +
Sbjct: 291 LELKEEIEELEGEISLLRERLEELENELEELEERLEELKEKIEALKEELEERETLLEELE 350

Query: 224 ----ELKRKKEESERENRGDANVEE 244
               EL+  KEE E +        E
Sbjct: 351 QLLAELEEAKEELEEKLSALLEELE 375

Length = 1163

>gnl|CDD|179385 PRK02224, PRK02224, chromosome segregation protein; Provisional

 Score = 45.8 bits (109), Expect = 1e-04
 Identities = 63/231 (27%), Positives = 101/231 (43%), Gaps = 16/231 (6%)

Query: 23  RSEREQSTDSDEDKHDKEKEKDKHRDRDRRRDRDRDRDREKER-EEKRERAREKEREREK 81
            S++  S D  + + ++++EKD H   +       + D E ER EE+RE+ARE   E ++
Sbjct: 182 LSDQRGSLDQLKAQIEEKEEKDLHERLNGLESELAELDEEIERYEEQREQARETRDEADE 241

Query: 82  RDREREDRERERERERERRERDREREKRERERDRDKEKDRERKSRDR---------EKRR 132
              E E+R RE     E    D      E ER+R++  +  R  R+R         +   
Sbjct: 242 VLEEHEER-REELETLEAEIEDLRETIAETEREREELAEEVRDLRERLEELEEERDDLLA 300

Query: 133 KVESDDSDEDKDRDRKRRRRHDDDHKERVRERSLSRSNRHRDENDESPREKLVEDDSDKK 192
           +   DD+D +    R+      D+      E     +  H  E  ES RE   + +   +
Sbjct: 301 EAGLDDADAEAVEARREELEDRDEELRDRLEECRVAAQAHN-EEAESLREDADDLEERAE 359

Query: 193 EKKTREEELEDEQRKLDEEMEKRRRRVQEWQELKRKKEESERENRGDANVE 243
           E +    ELE E  +  E +E RR  ++E +E    + E  RE  GDA V+
Sbjct: 360 ELREEAAELESELEEAREAVEDRREEIEELEE----EIEELRERFGDAPVD 406

Length = 880

>gnl|CDD|224123 COG1202, COG1202, Superfamily II helicase, archaea-specific [General function prediction only]

 Score = 45.9 bits (109), Expect = 1e-04
 Identities = 80/360 (22%), Positives = 147/360 (40%), Gaps = 48/360 (13%)

Query: 477 KIMETIRKLNYEKPMPIQAQALPV-IMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPV 535
           K    +++   E+ +P+Q  A+   ++ G + + V+ T SGKTL   L  +       P 
Sbjct: 204 KFKRMLKREGIEELLPVQVLAVEAGLLEGENLLVVSATASGKTLIGELAGI-------PR 256

Query: 536 AAGDGPVGLIMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQISELKRGT---- 591
               G   L + P   L  Q + D ++    +G++ V +  G    +   E         
Sbjct: 257 LLSGGKKMLFLVPLVALANQKYEDFKERYSKLGLK-VAIRVGMSRIKTREEPVVVDTSPD 315

Query: 592 -EIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMGFEPQITRIVQNIR---P 647
            +I+V T    ID L  +G  + ++  V   V+DE   + D    P++  ++  +R   P
Sbjct: 316 ADIIVGTY-EGIDYLLRTGKDLGDIGTV---VIDEIHTLEDEERGPRLDGLIGRLRYLFP 371

Query: 648 DRQTVLFSATFPRQVEILARKVLNKPVEIQVGGRSVVNKDITQ-LVEVRPESDRFLRLLE 706
             Q +  SAT     E LA+K+  K V      R V    + + LV  R ES+++  +  
Sbjct: 372 GAQFIYLSATVGNPEE-LAKKLGAKLVLYD--ERPV---PLERHLVFARNESEKWDIIAR 425

Query: 707 LLGEWYE-------KGKILIFVHSQEKCDALFRDLLKHGYPCLSLHGAKDQTDRESTISD 759
           L+   +        +G+ ++F +S+ +C  L   L   G      H      +R+S    
Sbjct: 426 LVKREFSTESSKGYRGQTIVFTYSRRRCHELADALTGKGLKAAPYHAGLPYKERKSVERA 485

Query: 760 FKSNVCNLLIATSVAARGLD-------VKELELVINFDAPNHYEDYVHRVGRTGRAGRKG 812
           F +     ++ T+  A G+D        + L + I + +   ++  +      GRAGR  
Sbjct: 486 FAAQELAAVVTTAALAAGVDFPASQVIFESLAMGIEWLSVREFQQML------GRAGRPD 539

Length = 830

>gnl|CDD|217503 pfam03344, Daxx, Daxx Family

 Score = 45.7 bits (108), Expect = 1e-04
 Identities = 42/173 (24%), Positives = 71/173 (41%), Gaps = 16/173 (9%)

Query: 35  DKHDK--EKEKDKHRDRDRRRDRDRDRDREKEREEKRE---RAREKEREREKRDREREDR 89
            K D   E+E+ K ++R+R+    R  D  K      E    A ++  E E  + E E+ 
Sbjct: 393 MKQDDTEEEERRKRQERERQGTSSRSSDPSKASSTSGESPSMASQESEEEESVEEEEEEE 452

Query: 90  ERERERERERRERDREREKRERERDRDKEKDRERKSRDREKRRKVESDDSDEDKDRDRKR 149
           E E E E+E  E + E E+ E E + D   + E +           S + D D +   + 
Sbjct: 453 EEEEEEEQESEEEEGEDEEEEEEVEADNGSEEEMEG----------SSEGDGDGEEPEED 502

Query: 150 RRRHDDDHKERVRERSLSRSNRHRDENDESPREKLVEDDSDKKEKKTREEELE 202
             R + +    +   S  +  R      ESP+E+ ++ +S   E    E + E
Sbjct: 503 AERRNSEMAG-ISRMSEGQQPRGSSVQPESPQEEPLQPESMDAESVGEESDEE 554

The Daxx protein (also known as the Fas-binding protein) is thought to play a role in apoptosis, but precise role played by Daxx remains to be determined. Daxx forms a complex with Axin. Length = 715

>gnl|CDD|179385 PRK02224, PRK02224, chromosome segregation protein; Provisional

 Score = 45.4 bits (108), Expect = 2e-04
 Identities = 47/212 (22%), Positives = 87/212 (41%), Gaps = 13/212 (6%)

Query: 7   DRDREKEKEKHREKSR-RSEREQSTDSDEDKHDK-EKEKDKHRDRDRRRDRDRDRDREKE 64
           +  RE+ +E     +   +E E+  ++  +  ++ E+ +++  + + +    ++R    E
Sbjct: 533 EEKRERAEELRERAAELEAEAEEKREAAAEAEEEAEEAREEVAELNSKLAELKERIESLE 592

Query: 65  REEKRERAREKEREREKRDREREDRERERERERERRERDREREKRERERDRDKEKDRERK 124
           R      A     +  +R RE+ +   E   ER    R+R  EKRER+R+ + E D  R 
Sbjct: 593 RIRTLLAAIADAEDEIERLREKREALAELNDER----RERLAEKRERKRELEAEFDEARI 648

Query: 125 SRDREKRRKVESDDSDEDKDRDRKRRRRHDDDHKERVRERSLSRSNRHRDENDESPREKL 184
              RE + + E      ++  D  R  R D   +    E  L      R+  +       
Sbjct: 649 EEAREDKERAEEYLEQVEEKLDELREERDDLQAEIGAVENELEELEELRERREA------ 702

Query: 185 VEDDSDKKEKKTRE-EELEDEQRKLDEEMEKR 215
           +E+  +  E    E EELE     L  E+ +R
Sbjct: 703 LENRVEALEALYDEAEELESMYGDLRAELRQR 734

Length = 880

>gnl|CDD|233758 TIGR02169, SMC_prok_A, chromosome segregation protein SMC, primarily archaeal type

 Score = 45.1 bits (107), Expect = 2e-04
 Identities = 41/210 (19%), Positives = 78/210 (37%), Gaps = 25/210 (11%)

Query: 51  RRRDRDRDRDREKEREEKRERAREKEREREKRDREREDRERERER----------ERERR 100
           R         R +  E +R R R +  +RE    + E R  E              R+  
Sbjct: 660 RAPRGGILFSRSEPAELQRLRERLEGLKRELSSLQSELRRIENRLDELSQELSDASRKIG 719

Query: 101 ERDREREKRERERDRDKEKDRERKSRDREKRRKVESDDSDEDKDRDRKRRR--------- 151
           E ++E E+ E+E ++ KE+  E +       +++E+  S+  +   R             
Sbjct: 720 EIEKEIEQLEQEEEKLKERLEELEEDLSSLEQEIENVKSELKELEARIEELEEDLHKLEE 779

Query: 152 ------RHDDDHKERVRERSLSRSNRHRDENDESPREKLVEDDSDKKEKKTREEELEDEQ 205
                       +    +  LS+        +   RE   + +    EK+  E+E+++ Q
Sbjct: 780 ALNDLEARLSHSRIPEIQAELSKLEEEVSRIEARLREIEQKLNRLTLEKEYLEKEIQELQ 839

Query: 206 RKLDEEMEKRRRRVQEWQELKRKKEESERE 235
            +  +  E+ +   +E + L  KKEE E E
Sbjct: 840 EQRIDLKEQIKSIEKEIENLNGKKEELEEE 869

SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]. Length = 1164

>gnl|CDD|233191 TIGR00927, 2A1904, K+-dependent Na+/Ca+ exchanger

 Score = 45.4 bits (107), Expect = 2e-04
 Identities = 51/262 (19%), Positives = 100/262 (38%), Gaps = 25/262 (9%)

Query: 9   DREKEKEKHREKSRRSEREQSTDSDEDKHDKEKEKDKHRDRDRRRDRDRDRDREKEREEK 68
             E E+    E     E     + + +   K + + +      R+        E E E K
Sbjct: 646 GEEGERPTEAEGENGEESGGEAEQEGETETKGENESEGEIPAERKGEQEG---EGEIEAK 702

Query: 69  RERAR-EKEREREKRDREREDRERERERERERRERDREREKRERERDRDKEKDRERKSRD 127
               + E E E  + + E E    E E E E  E   E E  E E + + + + E +   
Sbjct: 703 EADHKGETEAEEVEHEGETEAEGTEDEGEIETGEEGEEVED-EGEGEAEGKHEVETEGDR 761

Query: 128 REKRRKVESDDSDEDKDRDRKRRRRHDDDHK--ERVRERSLSRSNRHRDENDESPREKLV 185
           +E   + E++   ++ + + + +   D + K  E    +          E DE   +   
Sbjct: 762 KETEHEGETEAEGKEDEDEGEIQAGEDGEMKGDEGAEGKVEHEGETEAGEKDEHEGQSET 821

Query: 186 EDDSDKKEKKTREEEL--------EDEQRKLD----------EEMEKRRRRVQEWQELKR 227
           + D  + + +T E+EL        + +++ +D          EE E+     +E +E + 
Sbjct: 822 QADDTEVKDETGEQELNAENQGEAKQDEKGVDGGGGSDGGDSEEEEEEEEEEEEEEEEEE 881

Query: 228 KKEESERENRGDANVEEPKAGR 249
           ++EE E EN    ++E P+  +
Sbjct: 882 EEEEEEEENEEPLSLEWPETRQ 903

[Transport and binding proteins, Cations and iron carrying compounds]. Length = 1096

>gnl|CDD|217051 pfam02463, SMC_N, RecF/RecN/SMC N terminal domain

 Score = 45.0 bits (106), Expect = 2e-04
 Identities = 35/239 (14%), Positives = 93/239 (38%), Gaps = 2/239 (0%)

Query: 9    DREKEKEKHREKSRRSEREQSTDSDEDKHDKEKEKDKHRDRDRRRDRDRDRDREKEREEK 68
            + E+   +  EK +  E E+     +++   EK  ++  +R        +  +E   +E+
Sbjct: 819  EEEQLLIEQEEKIKEEELEELALELKEEQKLEKLAEEELERLEEEITKEELLQELLLKEE 878

Query: 69   RERAREKEREREKRDREREDRERERERERERRERDREREKRERERDRDKEKDRERKSRDR 128
                ++ + E E ++ + ++ ++E E E ++     E+E    ER  ++     +   + 
Sbjct: 879  ELEEQKLKDELESKEEKEKEEKKELEEESQKDNLLEEKENEIEERIAEEAIILLKYESEP 938

Query: 129  EKRRKVESDDSDEDKDRDRKRRRRHDDDHKERVRERSLSRSNRHRDENDESPREKLVEDD 188
            E+    E+D+ ++++D   +   R+      +    +++       E  E    K     
Sbjct: 939  EELLLEEADEKEKEEDNKEEEEERNKRLLLAKEELGNVNLMAIAEFEEKEERYNKDELKK 998

Query: 189  SDKKEKKTR--EEELEDEQRKLDEEMEKRRRRVQEWQELKRKKEESERENRGDANVEEP 245
               +E+K     E +E+  ++  E +E      +   ++    E          + ++P
Sbjct: 999  ERLEEEKKELLREIIEETCQRFKEFLELFVSINRGLNKVFFYLELGGSAELRLEDSDDP 1057

This domain is found at the N terminus of SMC proteins. The SMC (structural maintenance of chromosomes) superfamily proteins have ATP-binding domains at the N- and C-termini, and two extended coiled-coil domains separated by a hinge in the middle. The eukaryotic SMC proteins form two kind of heterodimers: the SMC1/SMC3 and the SMC2/SMC4 types. These heterodimers constitute an essential part of higher order complexes, which are involved in chromatin and DNA dynamics. This family also includes the RecF and RecN proteins that are involved in DNA metabolism and recombination. Length = 1162

>gnl|CDD|225288 COG2433, COG2433, Uncharacterized conserved protein [Function unknown]

 Score = 45.1 bits (107), Expect = 2e-04
 Identities = 31/113 (27%), Positives = 55/113 (48%), Gaps = 5/113 (4%)

Query: 39  KEKEKDKHRDRDRRRDRDRDRDREKEREEKRERAREKEREREKRDREREDRERERERERE 98
           K KE+++ R+++   + +R      E+  K+     +  E E  + +RE  E +RE E+ 
Sbjct: 396 KVKEEERPREKEGTEEEERREITVYEKRIKKLEETVERLEEENSELKRELEELKREIEKL 455

Query: 99  RRERDREREKRERERDRDKEKDRERKSRDREKRRKVESDDSDEDKDRDRKRRR 151
             E +R R    RE      KDRE ++RDR   R +E +  ++ K  +   R+
Sbjct: 456 ESELERFR----REVRDKVRKDREIRARDRRIER-LEKELEEKKKRVEELERK 503

Length = 652

>gnl|CDD|234478 TIGR04121, DEXH_lig_assoc, DEXH box helicase, DNA ligase-associated

 Score = 45.2 bits (108), Expect = 2e-04
 Identities = 81/357 (22%), Positives = 144/357 (40%), Gaps = 41/357 (11%)

Query: 489 KPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAP 548
            P P Q +     + GR  + +A TGSGKTLA  LP L  I    P     G   L + P
Sbjct: 13  TPRPFQLEMWAAALEGRSGLLIAPTGSGKTLAGFLPSL--IDLAGPEKPKKGLHTLYITP 70

Query: 549 TRELVQQIHSDIRKFAKVMG--VRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILC 606
            R L   I  +++   + +G  +R     G +  +++  + K+  +I++ TP  +  +L 
Sbjct: 71  LRALAVDIARNLQAPIEELGLPIRVETRTGDTSSSERARQRKKPPDILLTTPESLALLLS 130

Query: 607 TSGGK--ITNLRRVTYLVMDEADRMFDMG------FEPQITRIVQNIRPDRQTVLFSATF 658
                    +LR V   V+DE   +   G       E  + R+ + + P  +    SAT 
Sbjct: 131 YPDAARLFKDLRCV---VVDEWHEL--AGSKRGDQLELALARL-RRLAPGLRRWGLSATI 184

Query: 659 PRQVEILARKVLNKPVEIQVGGRSVVNKDITQLVEVR----PESDRF-------LRLL-E 706
               E  AR+VL   + +      +V   + + + V        +RF       LR L E
Sbjct: 185 GNLEE--ARRVL---LGVGGAPAVLVRGKLPKAIPVISLLPESEERFPWAGHLGLRALPE 239

Query: 707 LLGEWYEKGKILIFVHSQEKCDALFRDLLKHGYPCLSL-----HGAKDQTDRESTISDFK 761
           +  E  +    L+F +++ + +  F+ L +   P  +L     HG+ D+  R    +   
Sbjct: 240 VYAEIDQARTTLVFTNTRSQAELWFQALWEA-NPEFALPIALHHGSLDREQRRWVEAAMA 298

Query: 762 SNVCNLLIATSVAARGLDVKELELVINFDAPNHYEDYVHRVGRTGRAGRKGCAITFI 818
           +     ++ TS    G+D   ++LVI   +P      + R GR+     +      +
Sbjct: 299 AGRLRAVVCTSSLDLGVDFGPVDLVIQIGSPKGVARLLQRAGRSNHRPGEPSRALLV 355

Members of this protein family are DEAD/DEAH box helicases found associated with a bacterial ATP-dependent DNA ligase, part of a four-gene system that occurs in about 12 % of prokaryotic reference genomes. The actual motif in this family is DE[VILW]H. Length = 803

>gnl|CDD|233973 TIGR02680, TIGR02680, TIGR02680 family protein

 Score = 44.8 bits (106), Expect = 2e-04
 Identities = 38/214 (17%), Positives = 58/214 (27%), Gaps = 2/214 (0%)

Query: 44  DKHRDRDRRRDRDRDRDREKEREEKRERAREKEREREKRDREREDRERERERERERRERD 103
            + R    R+    D       +     A  +  E E++    E       R+       
Sbjct: 763 RELRALGARQRALADELAGAPSDRSLRAAHRRAAEAERQAESAERELARAARKAAAAAAA 822

Query: 104 REREKRERERDRDKEKDRERKSRDREKRRKVESDDSDEDKDRDRKRRRRHDDDHKERVRE 163
            ++ +RE ERD                   ++             R  RH        R 
Sbjct: 823 WKQARRELERDAADLDLPTDPDALEAVGLALKRFGDHLHTLEVAVRELRHAATRAAEQRA 882

Query: 164 RSLSRSNRHRDENDESPREKLVEDDSDKKEKKTREEEL-EDEQRKLDEEMEKRRRRVQEW 222
           R  +R+     E  E   E   E +      +T EE +            E R       
Sbjct: 883 R-AARAESDAREAAEDAAEARAEAEEASLRLRTLEESVGAMVDEIRARLAETRAALASGG 941

Query: 223 QELKRKKEESERENRGDANVEEPKAGRNWTLDRE 256
           +EL R  E            EE +A  + TLD  
Sbjct: 942 RELPRLAEALATAEEARGRAEEKRAEADATLDER 975

Members of this protein family belong to a conserved gene four-gene neighborhood found sporadically in a phylogenetically broad range of bacteria: Nocardia farcinica, Symbiobacterium thermophilum, and Streptomyces avermitilis (Actinobacteria), Geobacillus kaustophilus (Firmicutes), Azoarcus sp. EbN1 and Ralstonia solanacearum (Betaproteobacteria). Proteins in this family average over 1400 amino acids in length [Hypothetical proteins, Conserved]. Length = 1353

>gnl|CDD|223496 COG0419, SbcC, ATPase involved in DNA repair [DNA replication, recombination, and repair]

 Score = 44.8 bits (106), Expect = 3e-04
 Identities = 53/244 (21%), Positives = 102/244 (41%), Gaps = 17/244 (6%)

Query: 10  REKEKEKHREKSRRSEREQSTDSDEDKHDKEKEKDKHRDRDRRRDRDRDRDREKEREEKR 69
            +  +E+ RE  R  E  +      ++ ++E E+ +      R   +   +  ++ +   
Sbjct: 269 LKIREEELRELERLLEELEEKIERLEELEREIEELEEELEGLRALLEELEELLEKLKSLE 328

Query: 70  ERAREKEREREKRDRERED-RERERERERERRERDREREKRERERDRDKEKDRERKSRDR 128
           ER  + E + EK + E E+  E + E  +   ER +E E+R  E +++ EK  ER  +  
Sbjct: 329 ERLEKLEEKLEKLESELEELAEEKNELAKLLEERLKELEERLEELEKELEKALERL-KQL 387

Query: 129 EKRRKVESDDSDEDKDRDRKRRRRHDDDHKERVR-ERSLSRSNRH-----RDENDESPRE 182
           E+  +   ++  E      + +   ++  KE    ER L              N    +E
Sbjct: 388 EEAIQELKEELAELSAALEEIQEELEELEKELEELERELEELEEEIKKLEEQINQLESKE 447

Query: 183 KLVEDDSDKKEK---------KTREEELEDEQRKLDEEMEKRRRRVQEWQELKRKKEESE 233
            ++ + +   EK         +  E+EL +      EE+E+   R +E  EL+ + EE E
Sbjct: 448 LMIAELAGAGEKCPVCGQELPEEHEKELLELYELELEELEEELSREKEEAELREEIEELE 507

Query: 234 RENR 237
           +E R
Sbjct: 508 KELR 511

Length = 908

>gnl|CDD|226809 COG4372, COG4372, Uncharacterized protein conserved in bacteria with the myosin-like domain [Function unknown]

 Score = 44.2 bits (104), Expect = 3e-04
 Identities = 29/217 (13%), Positives = 91/217 (41%), Gaps = 8/217 (3%)

Query: 23  RSEREQSTDSDEDKHDKEKEKDKHRDRDRRRDRDRDRDREKEREEKRERAREKEREREKR 82
           R+ R +   +  +K   E E++  R   ++  ++R+  R++    ++  A+ ++      
Sbjct: 84  RALRTELGTAQGEKRAAETEREAARSELQKARQEREAVRQELAAARQNLAKAQQELARLT 143

Query: 83  DREREDRERERERERERRERDREREKRERERDRDKEKDRERKSRDREKRRKVESDDSDED 142
            + ++ + R +    +RR+ + + +  +  + + +    + KS+  + + +       E 
Sbjct: 144 KQAQDLQTRLKTLAEQRRQLEAQAQSLQASQKQLQASATQLKSQVLDLKLRSA---QIEQ 200

Query: 143 KDRDRKRRRRHDDDHKERVRERSLSRSNR-----HRDENDESPREKLVEDDSDKKEKKTR 197
           + ++   R        E +  R+ +          RD       +++       +E++ +
Sbjct: 201 EAQNLATRANAAQARTEELARRAAAAQQTAQAIQQRDAQISQKAQQIAARAEQIRERERQ 260

Query: 198 EEELEDEQRKLDEEMEKRRRRVQEWQELKRKKEESER 234
            + LE  Q +L++E+ +     Q +  L+++   ++R
Sbjct: 261 LQRLETAQARLEQEVAQLEAYYQAYVRLRQQAAATQR 297

Length = 499

>gnl|CDD|224188 COG1269, NtpI, Archaeal/vacuolar-type H+-ATPase subunit I [Energy production and conversion]

 Score = 44.3 bits (105), Expect = 3e-04
 Identities = 37/254 (14%), Positives = 80/254 (31%), Gaps = 32/254 (12%)

Query: 6   RDRDREKEKEKHREKSRRSEREQSTDSDEDKHDKEKEKDKHRDRDRRRDRDRDRDREKER 65
            D +  ++  K  EK + +E  Q + S       +  +       R        +  ++ 
Sbjct: 34  EDLEEGEKGLKELEKLKVAEVAQISLSSLLSEVLDYLRSVKGLEGRLFI---LPEEVEKL 90

Query: 66  EEKRERAREKEREREKRDREREDRERERERERERRERDREREKRERERDR--------DK 117
           E + +   E  +  EK   E E+  R+ E ER     +   +  +   +         D 
Sbjct: 91  EAELKSLEEVIKPAEKFSSEVEELTRKLE-ERLSELDEELEDLEDLLEELEPLAYLDFDL 149

Query: 118 EKDRERK-----------SRDREKRRKVESDDSDEDKDRDRKRRRR--HDDDHKERVRE- 163
              R  K            +       +E + +   ++ +        H  +  ++V + 
Sbjct: 150 SLLRGLKFLLVRLGLVRREKLEALVGVIEDEVALYGENVEASVVIVVAHGAEDLDKVSKI 209

Query: 164 -RSLSRSNRHRDENDESPREKLVEDDSDKKEKKTREEELEDEQRKLDEEMEKRRRRVQEW 222
              L        E D  P E +      ++     ++ELE  + +L+   EK    +   
Sbjct: 210 LNELGFELYEVPEFDGGPSELI---SELEEVIAEIQDELESLRSELEALAEKIAEELLAV 266

Query: 223 QELKRKKEESEREN 236
           +E    + E    +
Sbjct: 267 RE--ILEIEKALGD 278

Length = 660

>gnl|CDD|165222 PHA02896, PHA02896, A-type inclusion like protein; Provisional

 Score = 44.3 bits (104), Expect = 3e-04
 Identities = 34/162 (20%), Positives = 68/162 (41%), Gaps = 11/162 (6%)

Query: 5   HRDRDREKEKEKHREKSRRSER-EQSTDSDEDKHDKEKEKDKHRDRDRRRDRDRDRDREK 63
           H   D + +K  HR K+ + +  +  +   + K D   + D + D      +  + +  K
Sbjct: 421 HGQMDDKYDKRDHRYKNNKYDIYDDESPRYKYKDDDYDDNDDNDDDHIIPKKANNLEDAK 480

Query: 64  EREEKRERAREKEREREKRDREREDRERERERERERRERDREREKRERERDRDKEKDRER 123
           + E++   A   +    K  R R +    ++ +R   +R          R+   EKD E+
Sbjct: 481 DFEDEMMDAIADDDYTPKSIRNRRNGYLLKDEDRYYYDRGH--------RNLGAEKDPEK 532

Query: 124 KSRDREKRRKVESDDSDEDK--DRDRKRRRRHDDDHKERVRE 163
              D+++    + D SD+D+  D D+  R+   D   +R R+
Sbjct: 533 PHPDKDEEYPEDKDKSDDDRLNDADKAMRKLEADGFGDRYRK 574

Length = 616

>gnl|CDD|165222 PHA02896, PHA02896, A-type inclusion like protein; Provisional

 Score = 44.3 bits (104), Expect = 3e-04
 Identities = 49/277 (17%), Positives = 108/277 (38%), Gaps = 35/277 (12%)

Query: 7   DRDREKEKEKHREKSRRSEREQSTDSDEDKHDKEK-------EKDKHRDRDRRRDRDRDR 59
           D D+    +   ++ RR +  +    D  + DK K         ++  D D+  + + D 
Sbjct: 342 DDDKHPSYDYSNDRERRPKDYKEYYIDNFECDKMKNCPSTNGTLNRDEDEDKIEEDNDDY 401

Query: 60  DREKEREEKRERA---REKEREREKRDREREDRERERERERERRERDREREKRERERDRD 116
           + + E +  ++ A     +  + + +  +R+ R +  + +    E  R + K +   D D
Sbjct: 402 NNDDEDDLIKDEAPILNRRHGQMDDKYDKRDHRYKNNKYDIYDDESPRYKYKDDDYDDND 461

Query: 117 KEKDRE---RKSRDREKRRKVESDDSDEDKDRD------RKRRRRH----------DDDH 157
              D     +K+ + E  +  E +  D   D D      R RR  +          D  H
Sbjct: 462 DNDDDHIIPKKANNLEDAKDFEDEMMDAIADDDYTPKSIRNRRNGYLLKDEDRYYYDRGH 521

Query: 158 KERVRERSLSRSNRHRDENDESPREKLVED---DSDKKEKKTREEELEDEQRKLDEEMEK 214
           +    E+   + +  +DE     ++K  +D   D+DK  +K   +   D  RK+ E+M+ 
Sbjct: 522 RNLGAEKDPEKPHPDKDEEYPEDKDKSDDDRLNDADKAMRKLEADGFGDRYRKIKEKMD- 580

Query: 215 RRRRVQEWQELKRKKEESERENRGDANVEEPKAGRNW 251
                 ++ +L++   E  ++    +   +    ++W
Sbjct: 581 --NLEDDYDDLRKHAIELPKKLDNQSGNGDRDEDKSW 615

Length = 616

>gnl|CDD|218177 pfam04615, Utp14, Utp14 protein

 Score = 44.3 bits (105), Expect = 3e-04
 Identities = 51/272 (18%), Positives = 103/272 (37%), Gaps = 18/272 (6%)

Query: 18  REKSRRSEREQSTDSDEDKHDKEKEKDKHRDRDRRRDRDRDRDREKEREEKRERAREKER 77
           +  S   E E S   +ED+ D E + D     +      +   + KE E+  E +     
Sbjct: 321 KSVSEEDEDEDSDSEEEDEDDDEDDDDG----ENPWMLRKKLGKLKEGEDDEENSGLLSM 376

Query: 78  EREKRDREREDRERERERERERRERDREREKRERERDRDKEKDRERKSRDREKRRKVESD 137
           +  +R   R+  E + E E  RRE + E E  E E +   +K+  R+    E   K    
Sbjct: 377 KFMQRAEARKKEENDAEIEELRRELEGEEESDEEENEEPSKKNVGRRKFGPENGEKEAES 436

Query: 138 DSDEDKDRDRKRRRRHDDDHKERVRERSLSRSNRHRDENDESPREKLVEDDSDKKEKKTR 197
              + ++++  + ++  D+                 +E         +   S+K +K+  
Sbjct: 437 KKLKKENKNEFKEKKESDE----------EEELEDEEEAKVEKVANKLLKRSEKAQKEEE 486

Query: 198 EEELEDEQRKLDEEMEKRRRRVQEWQELKRKKEESERENRGDAN----VEEPKAGRNWTL 253
           EEEL++E   L       +   ++  + K   +  +  N+         ++ K  ++  L
Sbjct: 487 EEELDEENPWLKTTSSVGKSAKKQDSKKKSSSKLDKAANKISKAAVKVKKKKKKEKSIDL 546

Query: 254 DREDSDDEEVPQTGKSETDMDADEEPKPSENQ 285
           D +  D+E+  +    + + + DEE      Q
Sbjct: 547 DDDLIDEEDSIKLDVDDEEDEDDEELPFLFKQ 578

This protein is found to be part of a large ribonucleoprotein complex containing the U3 snoRNA. Depletion of the Utp proteins impedes production of the 18S rRNA, indicating that they are part of the active pre-rRNA processing complex. This large RNP complex has been termed the small subunit (SSU) processome. Length = 728

>gnl|CDD|225288 COG2433, COG2433, Uncharacterized conserved protein [Function unknown]

 Score = 43.9 bits (104), Expect = 4e-04
 Identities = 30/103 (29%), Positives = 50/103 (48%), Gaps = 3/103 (2%)

Query: 52  RRDRDRDRDREKEREEKRERAREKEREREKRDREREDRERERER---ERERRERDREREK 108
            + ++ +R REKE  E+ ER      E+  +  E      E E    +RE  E  RE EK
Sbjct: 395 SKVKEEERPREKEGTEEEERREITVYEKRIKKLEETVERLEEENSELKRELEELKREIEK 454

Query: 109 RERERDRDKEKDRERKSRDREKRRKVESDDSDEDKDRDRKRRR 151
            E E +R + + R++  +DRE R +    +  E +  ++K+R 
Sbjct: 455 LESELERFRREVRDKVRKDREIRARDRRIERLEKELEEKKKRV 497

Length = 652

>gnl|CDD|219655 pfam07946, DUF1682, Protein of unknown function (DUF1682)

 Score = 43.4 bits (103), Expect = 4e-04
 Identities = 14/57 (24%), Positives = 30/57 (52%), Gaps = 3/57 (5%)

Query: 49  RDRRRDRDRDRDREKEREEKRERAREKEREREKRDREREDRERER---ERERERRER 102
           R+   ++      E+ +EE +E+  EK++E  +    +   E +R   E+ER+++ R
Sbjct: 265 REEEEEKILKAAEEERQEEAQEKKEEKKKEEREAKLAKLSPEEQRKLEEKERKKQAR 321

The members of this family are all hypothetical eukaryotic proteins of unknown function. One member is described as being an adipocyte-specific protein, but no evidence of this was found. Length = 322

>gnl|CDD|217051 pfam02463, SMC_N, RecF/RecN/SMC N terminal domain

 Score = 43.8 bits (103), Expect = 5e-04
 Identities = 42/258 (16%), Positives = 97/258 (37%), Gaps = 9/258 (3%)

Query: 6   RDRDREKEKEKHREKSRRSEREQSTDSDEDKHDKEKEKDKHRDRDRRRDRDRDRDREKER 65
            D  R K  E   + +  ++  +S  + E    K    ++              +  KE 
Sbjct: 618 EDDKRAKVVEGILKDTELTKLLESAKAKESGLRKGVSLEEGLAEKSELKA-SLSELTKEL 676

Query: 66  EEKRERAREKEREREKRDREREDRERERERERERRERDREREKRERERDRDKEKDRERKS 125
             ++E   + E E  K +  R   E +++ +R + E  + + ++E       ++ +++ +
Sbjct: 677 LAEQELQEKAESELAKNEILRRQEEIKKKEQRIKEELKKLKLEKEELLADKVQEAQDKIN 736

Query: 126 RDREKRRKVESDDSDEDKDRDRKRRRRHDDDHKERVRERSLSRSNRHRDENDESPREKLV 185
            + +   +   +  +E++    K+        +E   +  LS   +   E +E   +  V
Sbjct: 737 EELKLLEQKIKEKEEEEEKSRLKKE-------EEEEEKSELSLKEKELAEEEEKTEKLKV 789

Query: 186 EDDSDKKEKKTREEELEDEQRKLDEEMEKRRRRVQEWQELKRKKEESERENRGDANVEEP 245
           E++ ++K K   EEEL   + +L EE E         ++ ++ KEE   E   +   E+ 
Sbjct: 790 EEEKEEKLKAQ-EEELRALEEELKEEAELLEEEQLLIEQEEKIKEEELEELALELKEEQK 848

Query: 246 KAGRNWTLDREDSDDEEV 263
                        ++   
Sbjct: 849 LEKLAEEELERLEEEITK 866

This domain is found at the N terminus of SMC proteins. The SMC (structural maintenance of chromosomes) superfamily proteins have ATP-binding domains at the N- and C-termini, and two extended coiled-coil domains separated by a hinge in the middle. The eukaryotic SMC proteins form two kind of heterodimers: the SMC1/SMC3 and the SMC2/SMC4 types. These heterodimers constitute an essential part of higher order complexes, which are involved in chromatin and DNA dynamics. This family also includes the RecF and RecN proteins that are involved in DNA metabolism and recombination. Length = 1162

>gnl|CDD|225288 COG2433, COG2433, Uncharacterized conserved protein [Function unknown]

 Score = 43.5 bits (103), Expect = 5e-04
 Identities = 31/137 (22%), Positives = 55/137 (40%), Gaps = 19/137 (13%)

Query: 70  ERAREKEREREKRDREREDRERERERERERRERDREREKRERERDRDKEKDRERKSRDRE 129
            + +E+ER REK   E E+R      E+  ++ +   E+ E E         E K    E
Sbjct: 395 SKVKEEERPREKEGTEEEERREITVYEKRIKKLEETVERLEEEN-------SELKRELEE 447

Query: 130 KRRKVESDDSDEDKDRDRKRRRRHDDDHKERVRERSLSRSNRHRDENDESPREKLVEDDS 189
            +R++E     + +    + RR   D  ++        R  R RD   E   ++L E   
Sbjct: 448 LKREIE-----KLESELERFRREVRDKVRKD-------REIRARDRRIERLEKELEEKKK 495

Query: 190 DKKEKKTREEELEDEQR 206
             +E + +  EL   ++
Sbjct: 496 RVEELERKLAELRKMRK 512

Length = 652

>gnl|CDD|173502 PTZ00266, PTZ00266, NIMA-related protein kinase; Provisional

 Score = 43.6 bits (102), Expect = 5e-04
 Identities = 35/94 (37%), Positives = 54/94 (57%), Gaps = 4/94 (4%)

Query: 23  RSEREQSTDSDEDKHDKEKE-KDKHRDRDRRRDRDRDRDREKEREEKRERAR-EKER-ER 79
           +   E++    E+ H K  E K   + R  R +R+     E+ER E+ ER R E+ER ER
Sbjct: 432 KDHAERARIEKENAHRKALEMKILEKKRIERLEREERERLERERMERIERERLERERLER 491

Query: 80  EKRDREREDRERERERERERRERDREREKRERER 113
           E+ +R+R +R+R    ERER +R  ER++ E+ R
Sbjct: 492 ERLERDRLERDRLDRLERERVDR-LERDRLEKAR 524

Length = 1021

>gnl|CDD|219655 pfam07946, DUF1682, Protein of unknown function (DUF1682)

 Score = 43.0 bits (102), Expect = 5e-04
 Identities = 17/60 (28%), Positives = 39/60 (65%)

Query: 50  DRRRDRDRDRDREKEREEKRERAREKEREREKRDREREDRERERERERERRERDREREKR 109
           D+ R+ + ++  +   EE++E A+EK+ E++K +RE +  +   E +R+  E++R+++ R
Sbjct: 262 DKTREEEEEKILKAAEEERQEEAQEKKEEKKKEEREAKLAKLSPEEQRKLEEKERKKQAR 321

The members of this family are all hypothetical eukaryotic proteins of unknown function. One member is described as being an adipocyte-specific protein, but no evidence of this was found. Length = 322

>gnl|CDD|183610 PRK12585, PRK12585, putative monovalent cation/H+ antiporter subunit G; Reviewed

 Score = 42.0 bits (98), Expect = 5e-04
 Identities = 30/98 (30%), Positives = 55/98 (56%), Gaps = 2/98 (2%)

Query: 53  RDRDRDRDREKEREEKRERAREKEREREKRDREREDRERERERERERRERDREREKRERE 112
           R RD+ R  +K+  +K++    ++ + EK  +ERE+ E   E ER   + D   ++ E+E
Sbjct: 102 RIRDQLRSVKKDDIKKKKSLIIRQEQIEKARQEREELEERMEWERREEKIDEREDQEEQE 161

Query: 113 RDRDKEKDRERKSRDREKRRKVESDDSDEDKDRDRKRR 150
           R+R+ E+  E +S D E    +E D+S+ + D D+  +
Sbjct: 162 RERE-EQTIEEQSDDSE-HEIIEQDESETESDDDKTEK 197

Length = 197

>gnl|CDD|225177 COG2268, COG2268, Uncharacterized protein conserved in bacteria [Function unknown]

 Score = 43.7 bits (103), Expect = 5e-04
 Identities = 35/217 (16%), Positives = 70/217 (32%), Gaps = 28/217 (12%)

Query: 75  KEREREKRDREREDRERERERERERRERDREREKRERERDRDKEKDRERKSRDREKRRKV 134
           +   +  +D E  + E E+E E    E +R+ +  E E ++        ++R+ +     
Sbjct: 214 RRIAQVLQDAEIAENEAEKETEIAIAEANRDAKLVELEVEQQPAGKTAEQTREVKIILAE 273

Query: 135 ESDDSDEDKDRDRKRRRRHDDDHKERVRERSLSRSN-----RHRDENDESPREKLVEDDS 189
              +    K      RR  +       +     ++      +H    +   RE  V    
Sbjct: 274 TEAEVAAWKAE---TRREAEQAEILAEQAIQEEKAQAEQEVQHAKALEA--REMRVGLIE 328

Query: 190 DKKEK----KTREEELEDEQRKLDEEMEKRRR-----RVQEWQELKRKKEESERENRGDA 240
            +KE     + R   +   QR+  EE +           Q    ++  +E  E E    A
Sbjct: 329 RQKETELEPQERSYFINAAQRQAQEEAKAAANIAEAIGAQAEAAVETARETEEAERAEQA 388

Query: 241 NVEEPKAGRNWTLDREDSDDEEVPQTGKSETDMDADE 277
            +             E ++ E+V    ++E      E
Sbjct: 389 ALVAA---------AEAAEQEQVEIAVRAEAAKAEAE 416

Length = 548

>gnl|CDD|152107 pfam11671, Apis_Csd, Complementary sex determiner protein

 Score = 40.9 bits (95), Expect = 6e-04
 Identities = 19/40 (47%), Positives = 27/40 (67%), Gaps = 1/40 (2%)

Query: 71  RAREKEREREKRDRE-REDRERERERERERRERDREREKR 109
           R+RE+E++  K +   RE RE  RER R+R ER+R RE +
Sbjct: 8   RSREREQKSYKNENSYREYRETSRERSRDRTERERSREHK 47

This family of proteins represents the complementary sex determiner in the honeybee. In the honeybee, the mechanism of sex determination depends on the csd gene which produces an SR-type protein. Males are homozygous while females are homozygous for the csd gene. Heterozygosity generates an active protein which initiates female development. Length = 146

>gnl|CDD|235334 PRK05035, PRK05035, electron transport complex protein RnfC; Provisional

 Score = 43.0 bits (102), Expect = 7e-04
 Identities = 45/213 (21%), Positives = 78/213 (36%), Gaps = 27/213 (12%)

Query: 57  RDRDREKER-EEKRER--AREKEREREKRDREREDRERERERERERRERDREREKRERER 113
           R  ++EK++ EE + R  AR+   EREK  RE     R ++    R  +D++       R
Sbjct: 439 RAIEQEKKKAEEAKARFEARQARLEREKAARE----ARHKKAAEARAAKDKDAVAAALAR 494

Query: 114 DRDKEKDRERKSRDREKRRKVESDDSDEDKDRDRKRRRR--------HDDDHKERVRERS 165
            + K+    +    +   R   S      + R  + R R          D  K  V   +
Sbjct: 495 VKAKKAAATQPIVIKAGARPDNSAVIAAREARKAQARARQAEKQAAAAADPKKAAV-AAA 553

Query: 166 LSRSNRHRDENDESPREKLVEDDSDK----------KEKKTREEELEDEQRKLDEEMEKR 215
           ++R+   +     +  E   E D  K          K KK  ++    E  +   E++ +
Sbjct: 554 IARAKAKKAAQQAANAEAEEEVDPKKAAVAAAIARAKAKKAAQQAASAEPEEQVAEVDPK 613

Query: 216 RRRVQEWQE-LKRKKEESERENRGDANVEEPKA 247
           +  V       K KK E +     +  V+  KA
Sbjct: 614 KAAVAAAIARAKAKKAEQQANAEPEEPVDPRKA 646

Length = 695

>gnl|CDD|146486 pfam03879, Cgr1, Cgr1 family

 Score = 39.7 bits (93), Expect = 7e-04
 Identities = 26/73 (35%), Positives = 41/73 (56%), Gaps = 1/73 (1%)

Query: 62  EKEREEKRERAREKEREREKRDREREDRERERERERERRERDREREKRERERDRDKEKDR 121
           EK  E++ E+   K RE+E +D +  +R+R  +  +ERR    E+E+ E+   +   K  
Sbjct: 31  EKRMEKRLEQQAIKAREKELKDEKEAERQRRIQAIKERRAAKEEKERYEKMAAKMHAKKV 90

Query: 122 ERKSRDREKRRKV 134
           ER  R REKR K+
Sbjct: 91  ERLKR-REKRNKL 102

Members of this family are coiled-coil proteins that are involved in pre-rRNA processing. Length = 105

>gnl|CDD|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and chromosome partitioning]

 Score = 43.2 bits (102), Expect = 8e-04
 Identities = 51/243 (20%), Positives = 98/243 (40%), Gaps = 20/243 (8%)

Query: 6   RDRDREKEKEKHREKSRRSEREQSTDSDEDKHDKEKEKDKHRDRDRRRDRDRDRDREKER 65
           + R  E E+E    +    E ++  +  E++ +  +E       +     ++ +  ++E 
Sbjct: 736 QSRLEELEEELEELEEELEELQERLEELEEELESLEEALAKLKEEIEELEEKRQALQEEL 795

Query: 66  EEKRERAREKEREREKRDREREDRERERERERERRERDREREKRERERDRDKEKDRERKS 125
           EE  E   E ER  +  +RE E  E+ RER  +      E E+ E E +  +EK  E + 
Sbjct: 796 EELEEELEEAERRLDALERELESLEQRRERLEQ------EIEELEEEIEELEEKLDELEE 849

Query: 126 RDREKRRKVESDDSDEDKDRDRKRRRRHDDDHKERVRERSLSRSNRHRDENDESPREKLV 185
              E  +++E    + ++    K     +    E  +E          +E       +L 
Sbjct: 850 ELEELEKELEELKEELEELEAEKEELEDELKELEEEKEE--------LEEELRELESELA 901

Query: 186 EDDSDKKEKKTREEELEDEQRKLDEEMEKRRRRVQEW------QELKRKKEESERENRGD 239
           E   + ++ + R EELE +  +L+ E+ +    ++E        EL+R+ E  E E    
Sbjct: 902 ELKEEIEKLRERLEELEAKLERLEVELPELEEELEEEYEDTLETELEREIERLEEEIEAL 961

Query: 240 ANV 242
             V
Sbjct: 962 GPV 964

Length = 1163

>gnl|CDD|223496 COG0419, SbcC, ATPase involved in DNA repair [DNA replication, recombination, and repair]

 Score = 43.2 bits (102), Expect = 8e-04
 Identities = 45/259 (17%), Positives = 103/259 (39%), Gaps = 20/259 (7%)

Query: 11  EKEKEKHREKSRRSEREQSTDSDEDKHD--KEKEKDKHRDRDRRRDRDRDRDREKEREEK 68
             E+ K R     S   ++    E++    +   ++     +R  + +R+ +  +E  E 
Sbjct: 250 RLEELKARLLEIESLELEALKIREEELRELERLLEELEEKIERLEELEREIEELEEELEG 309

Query: 69  RERAREKEREREKRDREREDRERERERERERRERDREREKRERERDRDKEKDRERKSRDR 128
                E+  E  ++ +  E+R  + E + E+ E + E    E+       ++R ++  +R
Sbjct: 310 LRALLEELEELLEKLKSLEERLEKLEEKLEKLESELEELAEEKNELAKLLEERLKELEER 369

Query: 129 EKRRKVESDDSDEDKDRDRKRRRRHDDDHKERVRERSLSRSNRHRDENDESPREKLVEDD 188
            +  + E + + E   +  +          + ++E     S    +      +E+L E +
Sbjct: 370 LEELEKELEKALERLKQLEEAI--------QELKEELAELSAALEEI-----QEELEELE 416

Query: 189 SDKKEKKTREEELEDEQRKLDEEMEKRRRRVQEWQELKRKKEE-----SERENRGDANVE 243
            + +E +   EELE+E +KL+E++ +   +     EL    E+      E     +  + 
Sbjct: 417 KELEELERELEELEEEIKKLEEQINQLESKELMIAELAGAGEKCPVCGQELPEEHEKELL 476

Query: 244 EPKAGRNWTLDREDSDDEE 262
           E        L+ E S ++E
Sbjct: 477 ELYELELEELEEELSREKE 495

Length = 908

>gnl|CDD|220271 pfam09507, CDC27, DNA polymerase subunit Cdc27

 Score = 42.5 bits (100), Expect = 8e-04
 Identities = 30/140 (21%), Positives = 57/140 (40%), Gaps = 10/140 (7%)

Query: 14  KEKHREKSRRSEREQSTDSDEDKHDKEKEKDKHRDRDRRR------DRDRDRDREKEREE 67
           K K  +K++ + +E +T+  E K   +    K     +         +     +EK+   
Sbjct: 177 KVKSAKKTQDTSKETTTEKTEGKTSVKAASLKRNPPKKSNIMSSFFKKKTKEKKEKKEAS 236

Query: 68  KRERAREKEREREKRDREREDRERERERERERRERDREREKRERERDRDKEKDRERKSRD 127
           +     E E E  KRD   ED   E        E + E E +      D E++ E K ++
Sbjct: 237 ESTVKEESEEESGKRDVILED---ESAEPTGLDEDEDEDEPKPSGERSDSEEETEEKEKE 293

Query: 128 REKR-RKVESDDSDEDKDRD 146
           + KR +K+  D+ ++++   
Sbjct: 294 KRKRLKKMMEDEDEDEEMEI 313

This protein forms the C subunit of DNA polymerase delta. It carries the essential residues for binding to the Pol1 subunit of polymerase alpha, from residues 293-332, which are characterized by the motif D--G--VT, referred to as the DPIM motif. The first 160 residues of the protein form the minimal domain for binding to the B subunit, Cdc1, of polymerase delta, the final 10 C-terminal residues, 362-372, being the DNA sliding clamp, PCNA, binding motif. Length = 427

>gnl|CDD|217203 pfam02724, CDC45, CDC45-like protein

 Score = 42.7 bits (101), Expect = 8e-04
 Identities = 25/94 (26%), Positives = 41/94 (43%), Gaps = 12/94 (12%)

Query: 7   DRDREKEKE-KHREKSRRSEREQSTDSDEDKHDKEKEKDKHRDRDRRRDRDRDRDREKER 65
           D + E + E ++ +  R  E +   D + D+ D+E  K          D D D D + + 
Sbjct: 105 DIEEELQDEPRYDDAYRDLEEDDDDDEESDEEDEESSK-------SEDDEDDDDDDDDDD 157

Query: 66  EEKRERAREKEREREKRDREREDRERERERERER 99
              RER+ E+ R R    RE E++  E E    +
Sbjct: 158 IATRERSLERRRRR----REWEEKRAELEFYYYQ 187

CDC45 is an essential gene required for initiation of DNA replication in S. cerevisiae, forming a complex with MCM5/CDC46. Homologues of CDC45 have been identified in human, mouse and smut fungus among others. Length = 583

>gnl|CDD|221389 pfam12037, DUF3523, Domain of unknown function (DUF3523)

 Score = 42.1 bits (99), Expect = 8e-04
 Identities = 31/127 (24%), Positives = 62/127 (48%), Gaps = 3/127 (2%)

Query: 7   DRDREKEKEKHREKSRRSEREQSTDSDEDKHDKEKEKDKHRDRDRRRDRDRDRDREK-ER 65
           +R R + +E+ +    ++++EQ     +D+  +++ + +   + R+ +       E   R
Sbjct: 85  ERARVEAEERRKTLQEQTQQEQQRAQYQDELARKRYQKELEQQRRQNEELLKMQEESVLR 144

Query: 66  EEKRERAREKEREREKRDREREDRERERERERER-RERDREREKRERE-RDRDKEKDRER 123
           +E   RA E+E    +R+   E+ E ERE  R +     R R K ERE  D ++E  + +
Sbjct: 145 QEAMRRATEEEILEMRRETIEEEAELERENIRAKIEAEARGRAKEERENEDINREMLKLK 204

Query: 124 KSRDREK 130
            + +RE 
Sbjct: 205 ANEERET 211

This presumed domain is functionally uncharacterized. This domain is found in eukaryotes. This domain is typically between 257 to 277 amino acids in length. This domain is found associated with pfam00004. This domain has a conserved LER sequence motif. Length = 276

>gnl|CDD|218177 pfam04615, Utp14, Utp14 protein

 Score = 42.7 bits (101), Expect = 9e-04
 Identities = 51/269 (18%), Positives = 95/269 (35%), Gaps = 32/269 (11%)

Query: 61  REKEREEKRERAREKEREREKRDREREDRERERERER------------------ERRER 102
           +EK +EE +E     + + E    E E  ER R  ER                   R + 
Sbjct: 237 KEKLKEELKEFEELVKADPEAALEELEKLERRRAEERMTLKHKNTSKWAKSMLKTGRAKY 296

Query: 103 DREREKRERERDRDKEKDRERK--SRDREKRRKVESDDSDEDKDRDRKRRRRHDDDHKER 160
           D E  K   E+ R  E+ R +       E+    +SD  +ED+D D       D ++   
Sbjct: 297 DEEARKALEEQLRQGEELRRKIEGKSVSEEDEDEDSDSEEEDEDDDEDDD---DGENPWM 353

Query: 161 VRERSLSRSNRHRDENDESPREKLVEDDSDKKEKKTREEELEDEQRKLDEEMEKRRRRVQ 220
           +R+    +  + ++  D+     L+     ++ +  ++EE + E  +L  E+E      +
Sbjct: 354 LRK----KLGKLKEGEDDEENSGLLSMKFMQRAEARKKEENDAEIEELRRELEGEEESDE 409

Query: 221 EWQELKRKKEESER-----ENRGDANVEEPKAGRNWTLDREDSDDEEVPQTGKSETDMDA 275
           E  E   KK    R         +A  ++ K         +   DEE     + E  ++ 
Sbjct: 410 EENEEPSKKNVGRRKFGPENGEKEAESKKLKKENKNEFKEKKESDEEEELEDEEEAKVEK 469

Query: 276 DEEPKPSENQVGDAMLVDSDGGSAAPALQ 304
                   ++       + +     P L+
Sbjct: 470 VANKLLKRSEKAQKEEEEEELDEENPWLK 498

This protein is found to be part of a large ribonucleoprotein complex containing the U3 snoRNA. Depletion of the Utp proteins impedes production of the 18S rRNA, indicating that they are part of the active pre-rRNA processing complex. This large RNP complex has been termed the small subunit (SSU) processome. Length = 728

>gnl|CDD|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and chromosome partitioning]

 Score = 42.4 bits (100), Expect = 0.001
 Identities = 46/215 (21%), Positives = 97/215 (45%), Gaps = 21/215 (9%)

Query: 45  KHRDRDRRRDRDRDRDREKEREEKRERAREKEREREKRDREREDRERERERERER----- 99
           K R  +  R  +R  +  +  E+  E   EK+ E+ +R  E+ +R +E + E        
Sbjct: 171 KERKEEAERKLERTEENLERLEDLLEE-LEKQLEKLERQAEKAERYQELKAELRELELAL 229

Query: 100 -----RERDREREKRERERDRDKEKDRERKSRDREKRRKVESDDSDEDKDRDRKRRRRHD 154
                +E  +E E+ E E  R +E+  E +    E  +++E   S+ ++ R+     + +
Sbjct: 230 LLAKLKELRKELEELEEELSRLEEELEELQEELEEAEKEIEELKSELEELREELEELQEE 289

Query: 155 DDHKERVRERSLSRSNRHRDENDESPREKLVEDDSDKKEKKTREEELEDEQRKLDEEMEK 214
               +   E      +  R+  +E         +++ +E + R EEL+++   L EE+E+
Sbjct: 290 LLELKEEIEELEGEISLLRERLEEL--------ENELEELEERLEELKEKIEALKEELEE 341

Query: 215 RRRRVQEWQELK--RKKEESERENRGDANVEEPKA 247
           R   ++E ++L    ++ + E E +  A +EE + 
Sbjct: 342 RETLLEELEQLLAELEEAKEELEEKLSALLEELEE 376

Length = 1163

>gnl|CDD|236766 PRK10811, rne, ribonuclease E; Reviewed

 Score = 42.7 bits (101), Expect = 0.001
 Identities = 26/101 (25%), Positives = 57/101 (56%), Gaps = 6/101 (5%)

Query: 6   RDRDREKEKEKHREKSRRSERE---QSTDSDEDKHDKEKEKDKHRDRDRRRDRDRDRDRE 62
           RD    +E  ++RE++RR+ R+   Q+ ++ E +  +  EK + +D  ++  R R+R R 
Sbjct: 624 RDNRTRREGRENREENRRNRRQAQQQTAETRESQQAEVTEKARTQDEQQQAPR-RERQRR 682

Query: 63  KEREEKRERARE-KEREREKRDREREDRERERERERERRER 102
           +  +EKR+  +E K    E++  +  ++E   ++ + RR++
Sbjct: 683 RN-DEKRQAQQEAKALNVEEQSVQETEQEERVQQVQPRRKQ 722

Length = 1068

>gnl|CDD|233757 TIGR02168, SMC_prok_B, chromosome segregation protein SMC, common bacterial type

 Score = 42.7 bits (101), Expect = 0.001
 Identities = 36/189 (19%), Positives = 75/189 (39%), Gaps = 4/189 (2%)

Query: 50  DRRRDRDRDRDREKEREEKRERAREKEREREKRDRE---REDRERERERERERRERDRER 106
           D   + +R     + + EK ER +E + E  + +         E   E E  + E     
Sbjct: 193 DILNELERQLKSLERQAEKAERYKELKAELRELELALLVLRLEELREELEELQEELKEAE 252

Query: 107 EKRERERDRDKEKDRERKSRDREKRRKVESDDSDEDKDRDRKRRRRHDDDHKERVRERSL 166
           E+ E      +E + E+    R +  ++E +  +  K+           + ++++    L
Sbjct: 253 EELEELTAELQELE-EKLEELRLEVSELEEEIEELQKELYALANEISRLEQQKQILRERL 311

Query: 167 SRSNRHRDENDESPREKLVEDDSDKKEKKTREEELEDEQRKLDEEMEKRRRRVQEWQELK 226
           +   R  +E +    E   + D   +E    EE+LE+ + +L+    +      E +EL+
Sbjct: 312 ANLERQLEELEAQLEELESKLDELAEELAELEEKLEELKEELESLEAELEELEAELEELE 371

Query: 227 RKKEESERE 235
            + EE E +
Sbjct: 372 SRLEELEEQ 380

SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]. Length = 1179

>gnl|CDD|233758 TIGR02169, SMC_prok_A, chromosome segregation protein SMC, primarily archaeal type

 Score = 42.4 bits (100), Expect = 0.001
 Identities = 46/250 (18%), Positives = 105/250 (42%), Gaps = 22/250 (8%)

Query: 9    DREKEKEKHREKSRRSEREQSTDSDEDKHDKEKEKDKHRDRDRRRDRDRDRDREKEREEK 68
            + E++  K  E     E   S     +   +  + ++   R   R R+ ++ +      +
Sbjct: 769  ELEEDLHKLEEALNDLEARLSHSRIPEIQAELSKLEEEVSRIEARLREIEQ-KLNRLTLE 827

Query: 69   RERAREKEREREKRDREREDRERERERE--------RERRERDREREKRERERDRDKEKD 120
            +E   ++ +E +++  + +++ +  E+E         E  E   E E   R+ +      
Sbjct: 828  KEYLEKEIQELQEQRIDLKEQIKSIEKEIENLNGKKEELEEELEELEAALRDLESRLGDL 887

Query: 121  RERKSRDREKRRKVESDDSDEDKDRDRKRRRRHDDDHKERVRERSLSRSNRHRDENDESP 180
            ++ +     + R++E    + +   ++KR+R  +   K    E  LS     + E++E P
Sbjct: 888  KKERDELEAQLRELERKIEELEAQIEKKRKRLSELKAKLEALEEELSEIEDPKGEDEEIP 947

Query: 181  REKLVEDD-SDKKEKKTRE------------EELEDEQRKLDEEMEKRRRRVQEWQELKR 227
             E+L  +D   + ++   E            +E E+  ++LDE  EKR +  +E + +  
Sbjct: 948  EEELSLEDVQAELQRVEEEIRALEPVNMLAIQEYEEVLKRLDELKEKRAKLEEERKAILE 1007

Query: 228  KKEESERENR 237
            + EE E++ R
Sbjct: 1008 RIEEYEKKKR 1017

SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]. Length = 1164

>gnl|CDD|233191 TIGR00927, 2A1904, K+-dependent Na+/Ca+ exchanger

 Score = 42.3 bits (99), Expect = 0.001
 Identities = 49/229 (21%), Positives = 89/229 (38%), Gaps = 16/229 (6%)

Query: 177 DESPREKLVEDDSDKKEKKTREEELEDEQRKLDE---EMEKRRRRVQEWQELKRKKEESE 233
           +ES  E   E +++ K +   E E+  E++   E   E+E +    +   E +  + E E
Sbjct: 661 EESGGEAEQEGETETKGENESEGEIPAERKGEQEGEGEIEAKEADHKGETEAEEVEHEGE 720

Query: 234 RENRGDANVEEPKAGRNWTLDREDSDDEEVPQTGKSETDMDADEEPKPSENQVGDAMLVD 293
            E  G  +  E + G       E  D+ E    GK E + + D +    E +       D
Sbjct: 721 TEAEGTEDEGEIETGEE---GEEVEDEGEGEAEGKHEVETEGDRKETEHEGETEAEGKED 777

Query: 294 SDGGSAAPALQIGAAEDEDIDPLDAFMNSMVLPEVEKLKNTVEPSFTDGNNVESKKM-DR 352
            D G      +I A ED ++   +     +      +     E         +  ++ D 
Sbjct: 778 EDEG------EIQAGEDGEMKGDEGAEGKVEHEGETEAGEKDEHEGQSETQADDTEVKDE 831

Query: 353 KGDRRSNGEQPKKSSNKSLGRIIPGEDSDSDYGDLENDEKPLEDEDDDE 401
            G++  N E   ++     G  + G    SD GD E +E+  E+E+++E
Sbjct: 832 TGEQELNAENQGEAKQDEKG--VDGGGG-SDGGDSEEEEEEEEEEEEEE 877

[Transport and binding proteins, Cations and iron carrying compounds]. Length = 1096

>gnl|CDD|235175 PRK03918, PRK03918, chromosome segregation protein; Provisional

 Score = 42.7 bits (101), Expect = 0.001
 Identities = 48/211 (22%), Positives = 96/211 (45%), Gaps = 6/211 (2%)

Query: 11  EKEKEKHREKSRRSEREQSTDSDEDKHDKEKEKDKHRDRDRRRDRDRDRDREKEREEKRE 70
            +E EK +EK  + + E  +   E +  K +E  K      ++  + + +  +  +E  E
Sbjct: 524 AEEYEKLKEKLIKLKGEIKSLKKELE--KLEELKKKLAELEKKLDELEEELAELLKELEE 581

Query: 71  RAREKEREREKRDREREDRERE----RERERERRERDREREKRERERDRDKEKDRERKSR 126
              E   E E+R +E E    E    ++ E+E    ++E +K E E D+  E+  E + R
Sbjct: 582 LGFESVEELEERLKELEPFYNEYLELKDAEKELEREEKELKKLEEELDKAFEELAETEKR 641

Query: 127 DREKRRKVESDDSDEDKDRDRKRRRRHDDDHKERVRERSLSRSNRHRDENDESPREKLVE 186
             E R+++E  +    ++   + R  + +  +E    R+       R E  +   EKL E
Sbjct: 642 LEELRKELEELEKKYSEEEYEELREEYLELSRELAGLRAELEELEKRREEIKKTLEKLKE 701

Query: 187 DDSDKKEKKTREEELEDEQRKLDEEMEKRRR 217
           +  ++++ K   E+LE    +++E  EK ++
Sbjct: 702 ELEEREKAKKELEKLEKALERVEELREKVKK 732

Length = 880

>gnl|CDD|237178 PRK12705, PRK12705, hypothetical protein; Provisional

 Score = 42.4 bits (100), Expect = 0.001
 Identities = 39/186 (20%), Positives = 81/186 (43%), Gaps = 32/186 (17%)

Query: 52  RRDRDRDRDREKEREEKRERAREKEREREKRDREREDRERERERERERRERDREREKRER 111
           ++ +   ++ E+  +E ++ A EK        +E   RER ++R+  RRE  RE  +RE 
Sbjct: 26  KKRQRLAKEAERILQEAQKEAEEKLEAALLEAKELLLRERNQQRQEARRE--REELQREE 83

Query: 112 ERDRDKEKDRERKSRDREKRRKVESDDSDEDKDRDRKRRRRHDDDHKERVRERSLSRSNR 171
           ER   KE+  + +           ++  D  +++  +             RE++LS    
Sbjct: 84  ERLVQKEEQLDAR-----------AEKLDNLENQLEE-------------REKALSAREL 119

Query: 172 HRDENDESPREKLVEDDSDKKEKKTREEELEDEQRKLDEEMEKRRRRVQEWQELKRKKEE 231
             +E ++    +L        E + R+  L+    +L+EE  +R ++++E         E
Sbjct: 120 ELEELEKQLDNELYRVAGLTPE-QARKLLLKLLDAELEEEKAQRVKKIEE-----EADLE 173

Query: 232 SERENR 237
           +ER+ +
Sbjct: 174 AERKAQ 179

Length = 508

>gnl|CDD|115057 pfam06375, BLVR, Bovine leukaemia virus receptor (BLVR)

 Score = 42.4 bits (99), Expect = 0.001
 Identities = 53/251 (21%), Positives = 103/251 (41%), Gaps = 15/251 (5%)

Query: 81  KRDREREDRERERERERERRERDREREKRERERDRDKEKDRERKSRDR-----EKRRKVE 135
           K + ER  R+R  + +RE+++R++E+  R R      E D +           E+  +  
Sbjct: 83  KLEEERRHRQRLEKDKREKKKREKEKRGRRRHHSLGTESDEDIAPAQMVDIVTEEMPENA 142

Query: 136 SDDSDEDKDRDRKRRRRHDDDHKERVRERSLSRSNRHRDENDESPREK---LVEDDSDKK 192
               ++DKD +   R    D  K       L        E  +SP +     VE  S K 
Sbjct: 143 LPSDEDDKDPNDPYRALDIDLDKPLADSEKLPVQKHRNAETSKSPEKGDVPAVEKKSKKP 202

Query: 193 EKKTREEELEDEQRKLDEEMEKRRRRVQEWQELKRKK----EESERENRGDANVEEPKAG 248
           +KK ++E+ ++  +   +E+E  +  +    +         E  E       +   P + 
Sbjct: 203 KKKEKKEKEKERDKDKKKEVEGFKSLLLALDDSPASAASVAEADEASLANTVSGTAPDSE 262

Query: 249 RNWTLDREDSDDEEVPQTGKSETDMDADEEPKPSENQVGDAMLVDSDGGSAAPALQIGAA 308
            +   D E  + ++ P+  K +   + +E+ K  ++         SDGG+  P +Q GA 
Sbjct: 263 PDEPKDAEAEETKKSPKHKKKKQRKEKEEKKKKKKHH--HHRCHHSDGGAEQP-VQNGAV 319

Query: 309 EDEDIDPLDAF 319
           E+E + P+ ++
Sbjct: 320 EEEPLPPMSSY 330

This family consists of several bovine specific leukaemia virus receptors which are thought to function as transmembrane proteins, although their exact function is unknown. Length = 561

>gnl|CDD|220383 pfam09756, DDRGK, DDRGK domain

 Score = 40.8 bits (96), Expect = 0.001
 Identities = 20/67 (29%), Positives = 40/67 (59%)

Query: 67  EKRERAREKEREREKRDREREDRERERERERERRERDREREKRERERDRDKEKDRERKSR 126
             ++RA+ +E++  ++ RE E+ ERE  ++ E +     +E+ E E +R+K+K+ E +  
Sbjct: 4   GAKKRAKLEEKQARRQQREAEEEEREERKKLEEKREGERKEEEELEEEREKKKEEEERKE 63

Query: 127 DREKRRK 133
             E+ RK
Sbjct: 64  REEQARK 70

This is a family of proteins of approximately 300 residues, found in plants and vertebrates. They contain a highly conserved DDRGK motif. Length = 189

>gnl|CDD|220383 pfam09756, DDRGK, DDRGK domain

 Score = 40.5 bits (95), Expect = 0.001
 Identities = 20/74 (27%), Positives = 46/74 (62%)

Query: 57  RDRDREKEREEKRERAREKEREREKRDREREDRERERERERERRERDREREKRERERDRD 116
           + R + +E++ +R++   +E ERE+R +  E RE ER+ E E  E   ++++ E  ++R+
Sbjct: 6   KKRAKLEEKQARRQQREAEEEEREERKKLEEKREGERKEEEELEEEREKKKEEEERKERE 65

Query: 117 KEKDRERKSRDREK 130
           ++  +E++  ++ K
Sbjct: 66  EQARKEQEEYEKLK 79

This is a family of proteins of approximately 300 residues, found in plants and vertebrates. They contain a highly conserved DDRGK motif. Length = 189

>gnl|CDD|233467 TIGR01554, major_cap_HK97, phage major capsid protein, HK97 family

 Score = 41.6 bits (98), Expect = 0.001
 Identities = 18/85 (21%), Positives = 35/85 (41%)

Query: 61  REKEREEKRERAREKEREREKRDREREDRERERERERERRERDREREKRERERDRDKEKD 120
           R+   +EK   A E++ E +    E +  + E +R  E  +    +     E    +E++
Sbjct: 16  RKLTEDEKLAEAEEEKAEYDALKEEIDKLDAEIDRLEELLDELEAKPAASGEGGGGEEEE 75

Query: 121 RERKSRDREKRRKVESDDSDEDKDR 145
            E K+   E R  +   D    ++R
Sbjct: 76  EEAKAEAAEFRAYLRGGDDALAEER 100

This model family represents the major capsid protein component of the heads (capsids) of bacteriophage HK97, phi-105, P27, and related phage. This model represents one of several analogous families lacking detectable sequence similarity. The gene encoding this component is typically located in an operon encoding the small and large terminase subunits, the portal protein and the prohead or maturation protease [Mobile and extrachromosomal element functions, Prophage functions]. Length = 384

>gnl|CDD|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and chromosome partitioning]

 Score = 42.0 bits (99), Expect = 0.002
 Identities = 31/149 (20%), Positives = 60/149 (40%), Gaps = 3/149 (2%)

Query: 4   SHRDRDREKEKEKHREKSRRSEREQSTDSDEDKHDKEKEKDKHRDRDRRRDRDRDRDREK 63
           S    + E+  E  RE+    E E + +   +  + ++E +   +R   R  +R  D ++
Sbjct: 368 SALLEELEELFEALREELAELEAELA-EIRNELEELKREIESLEER-LERLSERLEDLKE 425

Query: 64  EREEKRERAREKEREREKRDREREDRERERERERERRERDREREKRERERDRDKEKDRER 123
           E +E      E + E E+ + E E+ E + E  R+R + + ERE  E + +  + +    
Sbjct: 426 ELKELEAELEELQTELEELNEELEELEEQLEELRDRLK-ELERELAELQEELQRLEKELS 484

Query: 124 KSRDREKRRKVESDDSDEDKDRDRKRRRR 152
               R  R + E   S   +         
Sbjct: 485 SLEARLDRLEAEQRASQGVRAVLEALESG 513

Length = 1163

>gnl|CDD|179385 PRK02224, PRK02224, chromosome segregation protein; Provisional

 Score = 41.6 bits (98), Expect = 0.002
 Identities = 72/300 (24%), Positives = 118/300 (39%), Gaps = 34/300 (11%)

Query: 11  EKEKEKHREKSRRSEREQSTDSDEDKHDKEKEKDKHRDRDRRRDR------------DRD 58
           E E E  RE    +ERE+   ++E +  +E+ ++   +RD                  R 
Sbjct: 257 EAEIEDLRETIAETEREREELAEEVRDLRERLEELEEERDDLLAEAGLDDADAEAVEARR 316

Query: 59  RDREKEREEKRERAREK----EREREKRDREREDRERERERERERRERDREREKRERERD 114
            + E   EE R+R  E     +   E+ +  RED +   ER  E RE   E E    E  
Sbjct: 317 EELEDRDEELRDRLEECRVAAQAHNEEAESLREDADDLEERAEELREEAAELESELEEAR 376

Query: 115 RDKEKDRERKSRDREKRRKVESDDSDEDKDRDRKRRRRHD-DDHKERVRER--SLSRSNR 171
              E  RE      E+  ++     D   D         +  + ++ +RER   L  + R
Sbjct: 377 EAVEDRREEIEELEEEIEELRERFGDAPVDLGNAEDFLEELREERDELREREAELEATLR 436

Query: 172 HRDENDESPREKL-----------VEDDSDK---KEKKTREEELEDEQRKLDEEMEKRRR 217
              E  E     L           VE        +E + R EELE E   L+EE+E+   
Sbjct: 437 TARERVEEAEALLEAGKCPECGQPVEGSPHVETIEEDRERVEELEAELEDLEEEVEEVEE 496

Query: 218 RVQEWQELKRKKEESERENRGDANVEEPKAGRNWTLDREDSDDEEVPQTGKSETDMDADE 277
           R++  ++L   ++  ER      ++EE  A R  T++ E  +  E  +   +E + +A+E
Sbjct: 497 RLERAEDLVEAEDRIERLEERREDLEELIAERRETIE-EKRERAEELRERAAELEAEAEE 555

Length = 880

>gnl|CDD|219563 pfam07767, Nop53, Nop53 (60S ribosomal biogenesis)

 Score = 41.6 bits (98), Expect = 0.002
 Identities = 20/108 (18%), Positives = 50/108 (46%), Gaps = 1/108 (0%)

Query: 7   DRDREKEKEKHREKSRRSEREQSTDSDEDKHDKEKEKDKHRDRDRRRDRDRDRDREKERE 66
           +   E+  +   E+S      +  +S+ +  +K     +     R +++ R     + +E
Sbjct: 239 EGLLEESDDDGEEESDDESAWEGFESEYEPINKPVRPKRKTKAQRNKEKRRKELEREAKE 298

Query: 67  EKRERAREKEREREKRDRER-EDRERERERERERRERDREREKRERER 113
           EK+ + +  +  R K   +    +E+ R R++E+R+   E++K +R +
Sbjct: 299 EKQLKKKLAQLARLKEIAKEVAQKEKARARKKEQRKERGEKKKLKRRK 346

This nucleolar family of proteins are involved in 60S ribosomal biogenesis. They are specifically involved in the processing beyond the 27S stage of 25S rRNA maturation. This family contains sequences that bear similarity to the glioma tumour suppressor candidate region gene 2 protein (p60). This protein has been found to interact with herpes simplex type 1 regulatory proteins. Length = 387

>gnl|CDD|227596 COG5271, MDN1, AAA ATPase containing von Willebrand factor type A (vWA) domain [General function prediction only]

 Score = 41.9 bits (98), Expect = 0.002
 Identities = 45/268 (16%), Positives = 107/268 (39%), Gaps = 30/268 (11%)

Query: 24   SEREQSTDSDEDKHD-KEKEKDKHRD-RDRRRDRDRDRDREKEREEKRERAREKER---- 77
            +E + +  SD D+ + +E E D +   +D     + + D E+E ++  E   +       
Sbjct: 3842 NEEDTANQSDLDESEARELESDMNGVTKDSVVSENENSDSEEENQDLDEEVNDIPEDLSN 3901

Query: 78   ---EREKRDREREDRERERERERERRERDREREKRERERDRDKEKDRERKSRDREKRRKV 134
               E+   +   ED     ++  E+   + E +   +E D    +D++R+ ++ E+    
Sbjct: 3902 SLNEKLWDEPNEEDLLETEQKSNEQSAANNESDLVSKEDDNKALEDKDRQEKEDEEEMSD 3961

Query: 135  ESDDSDEDKD-------------------RDRKRRRRHDDDHKER-VRERSLSRSNRHRD 174
            +    DE +                     D K   +  D  K+  + +  +  ++ +++
Sbjct: 3962 DVGIDDEIQPDIQENNSQPPPENEDLDLPEDLKLDEKEGDVSKDSDLEDMDMEAADENKE 4021

Query: 175  ENDESPREKLVEDDSDKKEKKTREEELEDEQRKLDEEMEKRRRRVQEWQELKRKKEESER 234
            E D    E + ++D  ++     E+  +D+   L E+ EK      E + ++  +E +E 
Sbjct: 4022 EADAEKDEPMQDEDPLEENNTLDEDIQQDDFSDLAEDDEKMNEDGFE-ENVQENEESTED 4080

Query: 235  ENRGDANVEEPKAGRNWTLDREDSDDEE 262
              + D  +E+ +   +  +D     D +
Sbjct: 4081 GVKSDEELEQGEVPEDQAIDNHPKMDAK 4108

Length = 4600

>gnl|CDD|233973 TIGR02680, TIGR02680, TIGR02680 family protein

 Score = 42.1 bits (99), Expect = 0.002
 Identities = 45/231 (19%), Positives = 78/231 (33%), Gaps = 15/231 (6%)

Query: 2   AHSHRDRDREKEKEKHREKSRRSEREQSTDSDEDKHDKEKEKDKHRDRDRRRDRDRDRDR 61
           A +  D+          E     E E+  D+  +  ++E        R R          
Sbjct: 274 AQTQYDQLSRDLGRARDELETAREEERELDARTEALERE----ADALRTRLEALQGSPAY 329

Query: 62  EKEREEKRERAREKEREREKRDREREDRERERERERERRERDREREKRERERDRDKEKDR 121
           +   E +R RA  +  +    D  +  RE E   E ERR R  E   R  + +R+    R
Sbjct: 330 QDAEELERARADAEALQAAAADARQAIREAESRLEEERR-RLDEEAGRLDDAERELRAAR 388

Query: 122 ERKSRDREK--------RRKVESDDSDEDKDRDRKRRRRHDDDHKERVRERSLSRSNRHR 173
           E+ +R  E+             +  + E ++      RR D D     R   ++   R  
Sbjct: 389 EQLARAAERAGLSPAHTAEPDAALAAQELQELGALDARRQDADRVIAQRSEQVALLRRRD 448

Query: 174 DENDESPREKLVEDDSDKKEKKTREEELEDEQRKLDEEMEKRRRRVQEWQE 224
           D  D +  E        ++++   E E    + +L +E   R      W +
Sbjct: 449 DVADRA--EATHAAARARRDELDEEAEQAAARAELADEAVHREGARLAWVD 497

Members of this protein family belong to a conserved gene four-gene neighborhood found sporadically in a phylogenetically broad range of bacteria: Nocardia farcinica, Symbiobacterium thermophilum, and Streptomyces avermitilis (Actinobacteria), Geobacillus kaustophilus (Firmicutes), Azoarcus sp. EbN1 and Ralstonia solanacearum (Betaproteobacteria). Proteins in this family average over 1400 amino acids in length [Hypothetical proteins, Conserved]. Length = 1353

>gnl|CDD|233973 TIGR02680, TIGR02680, TIGR02680 family protein

 Score = 42.1 bits (99), Expect = 0.002
 Identities = 40/203 (19%), Positives = 56/203 (27%), Gaps = 9/203 (4%)

Query: 48  DRDRRRDRDRDRDREKEREEKRERAREKEREREKRDREREDRERERERERERRERDRERE 107
           D +        R     +    +       +R  R   R   E ER+ E   RE  R   
Sbjct: 755 DDELAELARELRALGARQRALADELAGAPSDRSLRAAHRRAAEAERQAESAERELARAAR 814

Query: 108 KRERERDRDKEKDRERKSRDREKRRKVESDDSDEDKDRDRKRRRRHDDDHKERVRERSLS 167
           K        K+  RE   RD          D+ E      KR   H    +  VRE    
Sbjct: 815 KAAAAAAAWKQARREL-ERDAADLDLPTDPDALEAVGLALKRFGDHLHTLEVAVREL--- 870

Query: 168 RSNRHRDENDESPREKLVEDDSDKKEKKTREEELEDEQRKLDEEMEKRRRRV-QEWQELK 226
              RH        R +    +SD +E      E   E  +    +      V     E+ 
Sbjct: 871 ---RHAATRAAEQRARAARAESDAREAAEDAAEARAEAEEASLRLRTLEESVGAMVDEI- 926

Query: 227 RKKEESERENRGDANVEEPKAGR 249
           R +    R        E P+   
Sbjct: 927 RARLAETRAALASGGRELPRLAE 949

Members of this protein family belong to a conserved gene four-gene neighborhood found sporadically in a phylogenetically broad range of bacteria: Nocardia farcinica, Symbiobacterium thermophilum, and Streptomyces avermitilis (Actinobacteria), Geobacillus kaustophilus (Firmicutes), Azoarcus sp. EbN1 and Ralstonia solanacearum (Betaproteobacteria). Proteins in this family average over 1400 amino acids in length [Hypothetical proteins, Conserved]. Length = 1353

>gnl|CDD|114011 pfam05262, Borrelia_P83, Borrelia P83/100 protein

 Score = 41.9 bits (98), Expect = 0.002
 Identities = 31/162 (19%), Positives = 75/162 (46%), Gaps = 8/162 (4%)

Query: 8   RDREKEKEKHREKSRRSEREQSTDSDEDKHDKEKEKDKHRDRDRRRDRDRDRDREKEREE 67
           RD    KE+  ++  +  ++   + D+ + D +K + K        D+ RD  R+K++E 
Sbjct: 198 RDMTDLKERESQEDAKRAQQLKEELDKKQIDADKAQQKADFAQDNADKQRDEVRQKQQEA 257

Query: 68  KR-------ERAREKEREREKRDREREDRERERERERERRERDREREKRERERD-RDKEK 119
           K           +E ++  E + RE E  + E ++  E   + ++ +  + +++ +  EK
Sbjct: 258 KNLPKPADTSSPKEDKQVAENQKREIEKAQIEIKKNDEEALKAKDHKAFDLKQESKASEK 317

Query: 120 DRERKSRDREKRRKVESDDSDEDKDRDRKRRRRHDDDHKERV 161
           + E K  + +K+R+  ++D  + K +   +    ++D  +  
Sbjct: 318 EAEDKELEAQKKREPVAEDLQKTKPQVEAQPTSLNEDAIDSS 359

This family consists of several Borrelia P83/P100 antigen proteins. Length = 489

>gnl|CDD|218312 pfam04889, Cwf_Cwc_15, Cwf15/Cwc15 cell cycle control protein

 Score = 40.9 bits (96), Expect = 0.002
 Identities = 27/115 (23%), Positives = 53/115 (46%), Gaps = 6/115 (5%)

Query: 10  REKEKEKHREKSRRSEREQSTDSDEDKHDKEKEKDKHRDRDRRRDRDRDRDREKEREEKR 69
            +KE +   E + +S    +++  ++  D+E E  + R  +  R+ D D        +  
Sbjct: 72  SKKENKLAIEDADKSTNLDASNEGDEDDDEEDEIKRKRIEEDARNSDADDSDSSSDSD-- 129

Query: 70  ERAREKEREREKRDREREDRERERERERERRERDREREKRERERDRDKEKDRERK 124
                 + + +  D E E     RE E+ ++ER  E+E+ E E+  ++EK RE +
Sbjct: 130 ----SSDDDSDDDDSEDETAALLRELEKIKKERAEEKEREEEEKAAEEEKAREEE 180

This family represents Cwf15/Cwc15 (from Schizosaccharomyces pombe and Saccharomyces cerevisiae respectively) and their homologues. The function of these proteins is unknown, but they form part of the spliceosome and are thus thought to be involved in mRNA splicing. Length = 241

>gnl|CDD|218752 pfam05793, TFIIF_alpha, Transcription initiation factor IIF, alpha subunit (TFIIF-alpha)

 Score = 41.9 bits (98), Expect = 0.002
 Identities = 42/252 (16%), Positives = 89/252 (35%), Gaps = 30/252 (11%)

Query: 51  RRRDRDRDRDREKEREEKRERAREKEREREKRDREREDRERERERERERRERDREREKRE 110
            +  ++       E EE         R ++ + ++ E  + +   E ++   D + EK +
Sbjct: 183 MKAAKNGPAAFGDEDEETEGEKGGGGRGKDLKIKDLEGDDEDDGDESDKGGEDGDEEKSK 242

Query: 111 RERDRDKEKDRERKSRDREKRRKVESDDSDEDKDRDRKRRRRHDDDHKERVRERSLSRSN 170
           +++ +     + +K  D +K+ K   DD  ++ D D       ++D+           S+
Sbjct: 243 KKKKK---LAKNKKKLDDDKKGKRGGDDDADEYDSDDGDDEGREEDYI----------SD 289

Query: 171 RHRDENDESPREK-LVEDDSDKKEKKTREEELEDEQRKLDEEMEKRRRRVQEWQELKRKK 229
                ND   RE  L  +   K E +  E+  E E+ K +EE    ++  +  +   +K 
Sbjct: 290 SSASGNDPEEREDKLSPEIPAKPEIEQDEDSEESEEEKNEEEGGLSKKGKKLKKLKGKKN 349

Query: 230 EESERENRGDANVEEPKAGRNWTLDREDSDDEEVPQTGKSETDMDADEEPKPSENQVGDA 289
              + ++                   +DSDD ++             ++    E  V   
Sbjct: 350 GLDKDDSD----------------SGDDSDDSDIDGEDSVSLVTAKKQKEPKKEEPVDSN 393

Query: 290 MLVDSDGGSAAP 301
                + G A P
Sbjct: 394 PSSPGNSGPARP 405

Transcription initiation factor IIF, alpha subunit (TFIIF-alpha) or RNA polymerase II-associating protein 74 (RAP74) is the large subunit of transcription factor IIF (TFIIF), which is essential for accurate initiation and stimulates elongation by RNA polymerase II. Length = 528

>gnl|CDD|221821 pfam12871, PRP38_assoc, Pre-mRNA-splicing factor 38-associated hydrophilic C-term

 Score = 38.6 bits (90), Expect = 0.002
 Identities = 34/92 (36%), Positives = 57/92 (61%), Gaps = 1/92 (1%)

Query: 33  DEDKHDKEKEKDKHRDRDRRRDRDRDRDREKEREEKRERAREKEREREKRDREREDRERE 92
           +ED  ++E+ +++  D + RR  +RD DR +    +R R R + R+R ++ R R  R+R+
Sbjct: 7   EEDLDEEEESEEEEDDEEIRRKAERDVDRGRRSPRRRTRRRSRRRKRSRKRRRRR-RDRD 65

Query: 93  RERERERRERDREREKRERERDRDKEKDRERK 124
           R R R+R +RDR+R  R R R R + +DR R+
Sbjct: 66  RARYRDRDDRDRDRYDRSRSRSRSRSRDRRRR 97

This domain is a hydrophilic region found at the C-terminus of plant and metazoan pre-mRNA-splicing factor 38 proteins. The function is not known. Length = 97

>gnl|CDD|223989 COG1061, SSL2, DNA or RNA helicases of superfamily II [Transcription / DNA replication, recombination, and repair]

 Score = 41.7 bits (98), Expect = 0.002
 Identities = 66/388 (17%), Positives = 125/388 (32%), Gaps = 91/388 (23%)

Query: 489 KPMPIQAQALPVIMSGRDCIG----VAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGL 544
           +  P Q +AL  ++  R        V  TG+GKT+     +   +K             L
Sbjct: 36  ELRPYQEEALDALVKNRRTERRGVIVLPTGAGKTVVAAEAI-AELKRST----------L 84

Query: 545 IMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDI 604
           ++ PT+EL+ Q    ++KF  +     + +YGG        +     ++ V T    +  
Sbjct: 85  VLVPTKELLDQWAEALKKFLLLNDE--IGIYGGG------EKELEPAKVTVAT----VQT 132

Query: 605 LCTSGGKITNL--RRVTYLVMDEADRMFDMGFEPQITRIVQNIRPDRQTVL-FSATFPRQ 661
           L      +          ++ DE   +    +     R +  +       L  +AT  R+
Sbjct: 133 L-ARRQLLDEFLGNEFGLIIFDEVHHLPAPSY-----RRILELLSAAYPRLGLTATPERE 186

Query: 662 ---------------------VEILARKVLNKPVEIQVGGRSVVNKDITQLVEVRPESDR 700
                                 E++    L     +++     V     +  E   ES R
Sbjct: 187 DGGRIGDLFDLIGPIVYEVSLKELIDEGYLAPYKYVEI----KVTLTEDEEREYAKESAR 242

Query: 701 FLRLLELLGEWYEKG---------------------------KILIFVHSQEKCDALFRD 733
           F  LL   G    +                            K LIF    E    + + 
Sbjct: 243 FRELLRARGTLRAENEARRIAIASERKIAAVRGLLLKHARGDKTLIFASDVEHAYEIAKL 302

Query: 734 LLKHGYPCLSLHGAKDQTDRESTISDFKSNVCNLLIATSVAARGLDVKELELVINFDAPN 793
            L  G     + G   + +RE+ +  F++    +L+   V   G+D+ + +++I      
Sbjct: 303 FLAPGIVEA-ITGETPKEEREAILERFRTGGIKVLVTVKVLDEGVDIPDADVLIILRPTG 361

Query: 794 HYEDYVHRVGRTGRA--GRKGCAITFIS 819
               ++ R+GR  R   G++       S
Sbjct: 362 SRRLFIQRLGRGLRPAEGKEDTLALDYS 389

Length = 442

>gnl|CDD|227615 COG5296, COG5296, Transcription factor involved in TATA site selection and in elongation by RNA polymerase II [Transcription]

 Score = 41.6 bits (97), Expect = 0.002
 Identities = 39/194 (20%), Positives = 81/194 (41%), Gaps = 10/194 (5%)

Query: 24  SEREQSTDSDEDKHDKEKEKDKHRDRDRRRDRDRDRDREKEREEKRERAREKEREREKRD 83
           S R+++ D  +D      ++D + + D   +   + + + E E+ +   R + + +++ D
Sbjct: 21  SNRKRAHDDLDDVLSSSSDEDNNENVDYAEESGGEGNEKSEEEKFKNPYRLEGKFKDEAD 80

Query: 84  REREDRERERERERERRERDREREK-RERERDRDKEKDRERKSR----DREKRRKVESDD 138
           R +     E ERE    ER+ E  K  ER     + + + R S      R  R +  +  
Sbjct: 81  RAKIMAMTEIERESILFEREEEISKLMERRELAIRMEQQHRSSGCTDTRRSTRYEPLTSA 140

Query: 139 SDEDKDR---DRKRRRRHDDDHKERVRERSLSRSNRHRDENDESPREKLVEDDSDKKEKK 195
           ++E K +    +K R R +  + ER  E    +  +  +E+++  +E+     S  +E  
Sbjct: 141 AEEKKKKLLELKKTREREERLYSERHIELQRFKDYKELEESEQGLQEEY--TPSYAEEAV 198

Query: 196 TREEELEDEQRKLD 209
                 +D     D
Sbjct: 199 EDISRTDDFAELYD 212

Length = 521

>gnl|CDD|220371 pfam09736, Bud13, Pre-mRNA-splicing factor of RES complex

 Score = 39.2 bits (92), Expect = 0.002
 Identities = 23/85 (27%), Positives = 44/85 (51%), Gaps = 7/85 (8%)

Query: 46  HRDRD-RRRDRDRDRDREKEREEKRERAREKEREREKRDREREDRERERERERERRERDR 104
           +RD+  R  D +  R+ ++  +E++ER  EKE+E  K   ++E+RE+  E        ++
Sbjct: 4   YRDKSGRIIDIEEKREEKEREKEEKERKEEKEKEWGKGLVQKEEREKRLEEL------EK 57

Query: 105 EREKRERERDRDKEKDRERKSRDRE 129
            + K       D++ D E K ++R 
Sbjct: 58  AKNKPLARYADDEDYDEELKEQERW 82

This entry is characterized by proteins with alternating conserved and low-complexity regions. Bud13 together with Snu17p and a newly identified factor, Pml1p/Ylr016c, form a novel trimeric complex. called The RES complex, pre-mRNA retention and splicing complex. Subunits of this complex are not essential for viability of yeasts but they are required for efficient splicing in vitro and in vivo. Furthermore, inactivation of this complex causes pre-mRNA leakage from the nucleus. Bud13 contains a unique, phylogenetically conserved C-terminal region of unknown function. Length = 141

>gnl|CDD|217051 pfam02463, SMC_N, RecF/RecN/SMC N terminal domain

 Score = 41.1 bits (96), Expect = 0.003
 Identities = 33/203 (16%), Positives = 72/203 (35%), Gaps = 5/203 (2%)

Query: 9   DREKEKEKHREKSRRSEREQSTDSDEDKHDKEKEKDKHRDRDRRRDRDRDRDREKEREEK 68
           + EKE ++   K  R   E+  +  E   +K ++ ++     ++ + +R     K +EE+
Sbjct: 340 ELEKELKELEIK--REAEEEEEEQLEKLQEKLEQLEEELLAKKKLESERLSSAAKLKEEE 397

Query: 69  RERAREKEREREKRDREREDRERERERERERRERDREREKRERERDRDKEKDRERKSRDR 128
            E   E+E+E +      E  E   + E++   +  E  +   E  + K  + + +    
Sbjct: 398 LELKNEEEKEAKLLLELSEQEEDLLKEEKKEELKIVEELEESLETKQGKLTEEKEE---L 454

Query: 129 EKRRKVESDDSDEDKDRDRKRRRRHDDDHKERVRERSLSRSNRHRDENDESPREKLVEDD 188
           EK+      D  E K  +   +        E++    L +      + +   RE L    
Sbjct: 455 EKQALKLLKDKLELKKSEDLLKETKLVKLLEQLELLLLRQKLEEASQKESKAREGLAVLL 514

Query: 189 SDKKEKKTREEELEDEQRKLDEE 211
           +  K+           +      
Sbjct: 515 ALIKDGVGLRIISAAGRGGDLGV 537

This domain is found at the N terminus of SMC proteins. The SMC (structural maintenance of chromosomes) superfamily proteins have ATP-binding domains at the N- and C-termini, and two extended coiled-coil domains separated by a hinge in the middle. The eukaryotic SMC proteins form two kind of heterodimers: the SMC1/SMC3 and the SMC2/SMC4 types. These heterodimers constitute an essential part of higher order complexes, which are involved in chromatin and DNA dynamics. This family also includes the RecF and RecN proteins that are involved in DNA metabolism and recombination. Length = 1162

>gnl|CDD|217393 pfam03154, Atrophin-1, Atrophin-1 family

 Score = 41.2 bits (96), Expect = 0.003
 Identities = 24/63 (38%), Positives = 33/63 (52%), Gaps = 9/63 (14%)

Query: 47  RDRDRRRDRDRDRDREKEREEKRERAREKEREREKRDREREDRERERERERERRERDRER 106
           + R+   ++ +    +K REE RER +EKE+ERE        RERERE ER  +      
Sbjct: 579 KKREEAVEKAKREAEQKAREE-REREKEKEKERE--------REREREAERAAKASSSSH 629

Query: 107 EKR 109
           E R
Sbjct: 630 ESR 632

Atrophin-1 is the protein product of the dentatorubral-pallidoluysian atrophy (DRPLA) gene. DRPLA OMIM:125370 is a progressive neurodegenerative disorder. It is caused by the expansion of a CAG repeat in the DRPLA gene on chromosome 12p. This results in an extended polyglutamine region in atrophin-1, that is thought to confer toxicity to the protein, possibly through altering its interactions with other proteins. The expansion of a CAG repeat is also the underlying defect in six other neurodegenerative disorders, including Huntington's disease. One interaction of expanded polyglutamine repeats that is thought to be pathogenic is that with the short glutamine repeat in the transcriptional coactivator CREB binding protein, CBP. This interaction draws CBP away from its usual nuclear location to the expanded polyglutamine repeat protein aggregates that are characteristic of the polyglutamine neurodegenerative disorders. This interferes with CBP-mediated transcription and causes cytotoxicity. Length = 979

>gnl|CDD|237178 PRK12705, PRK12705, hypothetical protein; Provisional

 Score = 40.8 bits (96), Expect = 0.003
 Identities = 28/139 (20%), Positives = 61/139 (43%), Gaps = 3/139 (2%)

Query: 111 RERDRDKEKDRERKSRDREKRRKVESDDSDEDKDRDRKRRRRHDDDHKERVRERSLSRSN 170
           + +   KE +R  +   +E   K+E+   +  +   R+R ++  +  +ER   +      
Sbjct: 27  KRQRLAKEAERILQEAQKEAEEKLEAALLEAKELLLRERNQQRQEARREREELQREEERL 86

Query: 171 RHRDENDESPREKLVEDDSDKKEKKTREEELEDEQRKLDEEMEKRRRRVQEWQELKRKKE 230
             ++E  ++  EKL   D+ + + + RE+ L   + +L+E  ++    +     L  ++ 
Sbjct: 87  VQKEEQLDARAEKL---DNLENQLEEREKALSARELELEELEKQLDNELYRVAGLTPEQA 143

Query: 231 ESERENRGDANVEEPKAGR 249
                   DA +EE KA R
Sbjct: 144 RKLLLKLLDAELEEEKAQR 162

Length = 508

>gnl|CDD|115057 pfam06375, BLVR, Bovine leukaemia virus receptor (BLVR)

 Score = 40.8 bits (95), Expect = 0.003
 Identities = 36/213 (16%), Positives = 84/213 (39%), Gaps = 1/213 (0%)

Query: 5   HRDR-DREKEKEKHREKSRRSEREQSTDSDEDKHDKEKEKDKHRDRDRRRDRDRDRDREK 63
           HR R +++K ++K REK +R  R   +   E   D    +      +   +     D + 
Sbjct: 90  HRQRLEKDKREKKKREKEKRGRRRHHSLGTESDEDIAPAQMVDIVTEEMPENALPSDEDD 149

Query: 64  EREEKRERAREKEREREKRDREREDRERERERERERRERDREREKRERERDRDKEKDRER 123
           +      RA + + ++   D E+   ++ R  E  +     +    E++  + K+K+++ 
Sbjct: 150 KDPNDPYRALDIDLDKPLADSEKLPVQKHRNAETSKSPEKGDVPAVEKKSKKPKKKEKKE 209

Query: 124 KSRDREKRRKVESDDSDEDKDRDRKRRRRHDDDHKERVRERSLSRSNRHRDENDESPREK 183
           K ++R+K +K E +                    +      + + S    D   + P++ 
Sbjct: 210 KEKERDKDKKKEVEGFKSLLLALDDSPASAASVAEADEASLANTVSGTAPDSEPDEPKDA 269

Query: 184 LVEDDSDKKEKKTREEELEDEQRKLDEEMEKRR 216
             E+     + K +++  E E++K  ++    R
Sbjct: 270 EAEETKKSPKHKKKKQRKEKEEKKKKKKHHHHR 302

This family consists of several bovine specific leukaemia virus receptors which are thought to function as transmembrane proteins, although their exact function is unknown. Length = 561

>gnl|CDD|217840 pfam04006, Mpp10, Mpp10 protein

 Score = 41.1 bits (96), Expect = 0.003
 Identities = 42/257 (16%), Positives = 87/257 (33%), Gaps = 21/257 (8%)

Query: 11  EKEKEKHREKSRRSEREQSTDSDEDKHDKEKEKDKHRDRDRRRDRDRDRDREKEREEKRE 70
               ++H     + +  +S +   D  D + E     + +   D   + +   + +E   
Sbjct: 81  FLINKEHIRVLAKLQDSESHEDGSDGSDMDSEDSADDEEEEEEDESLEDEMIDDEDEADL 140

Query: 71  RAREKEREREKRDREREDRERERERERERRERDREREKRERERDRDK-----------EK 119
               +    +  D E ED E ++  E E  E     E+  RE+  DK           E 
Sbjct: 141 FNESESSLEDLSDDETEDDEEKKMEEEEAGEEKESVEQATREKKFDKSGVDDKFFKLDEM 200

Query: 120 DRERKSRDREKRRKVESDDSDEDKDRDRKRRRRHD----------DDHKERVRERSLSRS 169
           +   ++ + E+   +  +D  ED  +D     + D          DD +  +        
Sbjct: 201 NEFLEATEAEEEAALGDEDDFEDYFQDDSEDGKDDEDFGSGEDEEDDEEGNIEYEDFFDP 260

Query: 170 NRHRDENDESPREKLVEDDSDKKEKKTREEELEDEQRKLDEEMEKRRRRVQEWQELKRKK 229
                + D     +L +D+ DK+  K   +   +E+ + D+E E  +   +  +    K 
Sbjct: 261 KEKDKKKDAGDDAELEDDEPDKEAVKKEADSKPEEEDEEDDEQEDDQDEEEPPEAAMDKV 320

Query: 230 EESERENRGDANVEEPK 246
           +  E    G       +
Sbjct: 321 KLDEPVLEGVDLESPKE 337

This family includes proteins related to Mpp10 (M phase phosphoprotein 10). The U3 small nucleolar ribonucleoprotein (snoRNP) is required for three cleavage events that generate the mature 18S rRNA from the pre-rRNA. In Saccharomyces cerevisiae, depletion of Mpp10, a U3 snoRNP-specific protein, halts 18S rRNA production and impairs cleavage at the three U3 snoRNP-dependent sites. Length = 613

>gnl|CDD|233069 TIGR00643, recG, ATP-dependent DNA helicase RecG

 Score = 40.8 bits (96), Expect = 0.003
 Identities = 73/321 (22%), Positives = 128/321 (39%), Gaps = 51/321 (15%)

Query: 514 GSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVMGVRCVP 573
           GSGKTL   L ML  I+    VA        +MAPT  L +Q ++ +R     +G+    
Sbjct: 266 GSGKTLVAALAMLAAIEAGYQVA--------LMAPTEILAEQHYNSLRNLLAPLGIEVAL 317

Query: 574 VYG---GSGVAQQISELKRGT-EIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRM 629
           + G   G    + +  +  G   +VV T   + +            +R+  +++DE  R 
Sbjct: 318 LTGSLKGKRRKELLETIASGQIHLVVGTHALIQEK--------VEFKRLALVIIDEQHRF 369

Query: 630 FDMGFEPQITRIVQNIRPDRQTVLFSAT-FPRQVEILARKVLNKPVEIQV-----GGRSV 683
                +    +      P    ++ SAT  PR + +     +   ++  +      GR  
Sbjct: 370 GVEQRKKLREKGQGGFTPH--VLVMSATPIPRTLAL----TVYGDLDTSIIDELPPGRKP 423

Query: 684 VNKDITQLVEVRPESDRFLRLLELLGEWYEKGKILIFV----HSQEKCD-----ALFRDL 734
           +    T L++     D    + E + E   KG+    V       EK D     AL+  L
Sbjct: 424 I---TTVLIKH----DEKDIVYEFIEEEIAKGRQAYVVYPLIEESEKLDLKAAEALYERL 476

Query: 735 LKH--GYPCLSLHGAKDQTDRESTISDFKSNVCNLLIATSVAARGLDVKELELVINFDAP 792
            K    Y    LHG     ++E+ + +F+    ++L+AT+V   G+DV    +++  DA 
Sbjct: 477 KKAFPKYNVGLLHGRMKSDEKEAVMEEFREGEVDILVATTVIEVGVDVPNATVMVIEDAE 536

Query: 793 NHYEDYVHRV-GRTGRAGRKG 812
                 +H++ GR GR   + 
Sbjct: 537 RFGLSQLHQLRGRVGRGDHQS 557

[DNA metabolism, DNA replication, recombination, and repair]. Length = 630

>gnl|CDD|235250 PRK04195, PRK04195, replication factor C large subunit; Provisional

 Score = 40.7 bits (96), Expect = 0.003
 Identities = 19/61 (31%), Positives = 36/61 (59%)

Query: 59  RDREKEREEKRERAREKEREREKRDREREDRERERERERERRERDREREKRERERDRDKE 118
              EK+REE+++  ++K    +K++ E E+ + ++E E+E  E + E EK E E  + K+
Sbjct: 417 EKAEKKREEEKKEKKKKAFAGKKKEEEEEEEKEKKEEEKEEEEEEAEEEKEEEEEKKKKQ 476

Query: 119 K 119
            
Sbjct: 477 A 477

Length = 482

>gnl|CDD|188306 TIGR03319, RNase_Y, ribonuclease Y

 Score = 40.7 bits (96), Expect = 0.003
 Identities = 32/129 (24%), Positives = 57/129 (44%), Gaps = 10/129 (7%)

Query: 89  RERERERERERRERDREREKRERERD---RDKEKDRERKSRDREKRRKVESDDSDEDKDR 145
           R+R  E++    E   +R   E +++     KE   E K    + R ++E +  +   + 
Sbjct: 19  RKRIAEKKLGSAEELAKRIIEEAKKEAETLKKEALLEAKEEVHKLRAELERELKERRNEL 78

Query: 146 DRKRRRRHDDDHKERVRERSLSRSNRHRDENDESPREKLVEDDSDKKEKKTREEELEDEQ 205
            R  RR          RE +L R     D+ +E+  +K  E  + +K    +EEELE+  
Sbjct: 79  QRLERRL-------LQREETLDRKMESLDKKEENLEKKEKELSNKEKNLDEKEEELEELI 131

Query: 206 RKLDEEMEK 214
            +  EE+E+
Sbjct: 132 AEQREELER 140

Members of this family are RNase Y, an endoribonuclease. The member from Bacillus subtilis, YmdA, has been shown to be involved in turnover of yitJ riboswitch [Transcription, Degradation of RNA]. Length = 514

>gnl|CDD|235175 PRK03918, PRK03918, chromosome segregation protein; Provisional

 Score = 40.8 bits (96), Expect = 0.004
 Identities = 38/231 (16%), Positives = 96/231 (41%), Gaps = 16/231 (6%)

Query: 8   RDREKEKEKHREKSRRSEREQSTDSDEDKHDKEKEKDKHRDRDRRRDRDRDRDREKEREE 67
                E  +  EK  +  +E       ++  +E E+ +         + +  ++ +E EE
Sbjct: 213 SSELPELREELEKLEKEVKEL------EELKEEIEELEKELESLEGSKRKLEEKIRELEE 266

Query: 68  KRERAREKEREREKRDREREDRERERERERERRERDREREKRERERDRDKEKDRERKSRD 127
           + E  +++  E E++ +E ++ + + E   +  E   E     RE ++   +  E  +  
Sbjct: 267 RIEELKKEIEELEEKVKELKELKEKAEEYIKLSEFYEEYLDELREIEKRLSRLEEEINGI 326

Query: 128 REKRRKVESDDS-----DEDKDRDRKRRRRHDDDHKERVRERSL-SRSNRHRDENDESPR 181
            E+ +++E  +       +      KR    ++ H+     ++      R +        
Sbjct: 327 EERIKELEEKEERLEELKKKLKELEKRLEELEERHELYEEAKAKKEELERLKKRLTGLTP 386

Query: 182 EKLVED-DSDKKEKKTREEELE---DEQRKLDEEMEKRRRRVQEWQELKRK 228
           EKL ++ +  +K K+  EEE+        +L +E+++ ++ ++E ++ K K
Sbjct: 387 EKLEKELEELEKAKEEIEEEISKITARIGELKKEIKELKKAIEELKKAKGK 437

Length = 880

>gnl|CDD|223496 COG0419, SbcC, ATPase involved in DNA repair [DNA replication, recombination, and repair]

 Score = 40.5 bits (95), Expect = 0.004
 Identities = 39/249 (15%), Positives = 95/249 (38%), Gaps = 16/249 (6%)

Query: 3   HSHRDRDREKEKEKHREKSRRSEREQSTDSDEDKHDKEKEKDKHRDRDRRRDRDRDRDRE 62
               ++  E+ K+         E      +  ++  +E E+ +    +  R+ +   +  
Sbjct: 374 EKELEKALERLKQLEEAIQELKEELAELSAALEEIQEELEELEKELEELERELEELEEEI 433

Query: 63  KEREEKRERAREKEREREK-RDREREDRERERERERERRERDREREKRERERDRDKEKDR 121
           K+ EE+  +   KE    +      +     +E   E  +   E  + E E   ++    
Sbjct: 434 KKLEEQINQLESKELMIAELAGAGEKCPVCGQELPEEHEKELLELYELELEELEEELSRE 493

Query: 122 ERKSRDREKRRKVESDDSDEDKDRDRKRRRRHDDDHKERVRERSLSRSNRHRDENDESPR 181
           + ++  RE+  ++E +  + +++                  E +L      + E  E+  
Sbjct: 494 KEEAELREEIEELEKELRELEEELIELL-----------ELEEALKEELEEKLEKLENLL 542

Query: 182 EKLVEDDSDKKEKKTREE--ELEDEQRKLDEEMEKRR--RRVQEWQELKRKKEESERENR 237
           E+L E     + ++ +EE  +LED  ++L E +E+ R  R  +E  E  R++ +  ++  
Sbjct: 543 EELEELKEKLQLQQLKEELRQLEDRLQELKELLEELRLLRTRKEELEELRERLKELKKKL 602

Query: 238 GDANVEEPK 246
            +      +
Sbjct: 603 KELEERLSQ 611

Length = 908

>gnl|CDD|220383 pfam09756, DDRGK, DDRGK domain

 Score = 39.3 bits (92), Expect = 0.004
 Identities = 20/83 (24%), Positives = 43/83 (51%)

Query: 61  REKEREEKRERAREKEREREKRDREREDRERERERERERRERDREREKRERERDRDKEKD 120
           R ++RE + E   E+++  EKR+ ER++ E   E   +++E +  +E+ E+ R   +E +
Sbjct: 17  RRQQREAEEEEREERKKLEEKREGERKEEEELEEEREKKKEEEERKEREEQARKEQEEYE 76

Query: 121 RERKSRDREKRRKVESDDSDEDK 143
           + + S   E+    +    +E  
Sbjct: 77  KLKSSFVVEEEGTDKLSADEESN 99

This is a family of proteins of approximately 300 residues, found in plants and vertebrates. They contain a highly conserved DDRGK motif. Length = 189

>gnl|CDD|113290 pfam04514, BTV_NS2, Bluetongue virus non-structural protein NS2

 Score = 40.6 bits (95), Expect = 0.004
 Identities = 24/111 (21%), Positives = 47/111 (42%)

Query: 7   DRDREKEKEKHREKSRRSEREQSTDSDEDKHDKEKEKDKHRDRDRRRDRDRDRDREKERE 66
           +R++EKE++  +   +        DSDED++  ++E         ++D+  +R    ER 
Sbjct: 164 EREKEKEEQPMKPAFKPERWMGGPDSDEDENPLDEEAPDMTPETSKQDQKEERRAAVERR 223

Query: 67  EKRERAREKEREREKRDREREDRERERERERERRERDREREKRERERDRDK 117
                        E+R   R+++E E   ER+  + D   E  E    + +
Sbjct: 224 LAELVEMINWNLEERRRDLRKEQELEENVERDSDDEDEHGEDSEDGETKPE 274

This family includes NS2 proteins from other members of the Orbivirus genus. NS2 is a non-specific single-stranded RNA-binding protein that forms large homomultimers and accumulates in viral inclusion bodies of infected cells. Three RNA binding regions have been identified in Bluetongue virus serotype 17 at residues 2-11, 153-166 and 274-286. NS2 multimers also possess nucleotidyl phosphatase activity. The precise function of NS2 is not known, but it may be involved in the transport and condensation of viral mRNAs. Length = 363

>gnl|CDD|234017 TIGR02794, tolA_full, TolA protein

 Score = 40.2 bits (94), Expect = 0.004
 Identities = 21/146 (14%), Positives = 62/146 (42%), Gaps = 4/146 (2%)

Query: 9   DREKEKEKHREKSRRSEREQSTDSDEDKHDKEKEKDKHRDRDRRRDRDRDRDREKEREEK 68
            + +++ +  EK R +E+ +  + ++    ++  K   +   +  ++ +  +  K ++  
Sbjct: 71  KKLEQQAEEAEKQRAAEQARQKELEQRAAAEKAAKQAEQAAKQAEEKQKQAEEAKAKQAA 130

Query: 69  RERAREKEREREKRDREREDRERERERERERRE---RDREREKRERERDRDKEKDRERKS 125
            E   + E E EK+ +E   ++ E E + +      +     K++ E +   + + + K+
Sbjct: 131 -EAKAKAEAEAEKKAKEEAKKQAEEEAKAKAAAEAKKKAAEAKKKAEAEAKAKAEAKAKA 189

Query: 126 RDREKRRKVESDDSDEDKDRDRKRRR 151
           +  E + K E+  +    +   K   
Sbjct: 190 KAEEAKAKAEAAKAKAAAEAAAKAEA 215

TolA couples the inner membrane complex of itself with TolQ and TolR to the outer membrane complex of TolB and OprL (also called Pal). Most of the length of the protein consists of low-complexity sequence that may differ in both length and composition from one species to another, complicating efforts to discriminate TolA (the most divergent gene in the tol-pal system) from paralogs such as TonB. Selection of members of the seed alignment and criteria for setting scoring cutoffs are based largely conserved operon struction. //The Tol-Pal complex is required for maintaining outer membrane integrity. Also involved in transport (uptake) of colicins and filamentous DNA, and implicated in pathogenesis. Transport is energized by the proton motive force. TolA is an inner membrane protein that interacts with periplasmic TolB and with outer membrane porins ompC, phoE and lamB [Transport and binding proteins, Other, Cellular processes, Pathogenesis]. Length = 346

>gnl|CDD|219256 pfam06991, Prp19_bind, Splicing factor, Prp19-binding domain

 Score = 39.9 bits (93), Expect = 0.004
 Identities = 45/188 (23%), Positives = 84/188 (44%), Gaps = 20/188 (10%)

Query: 11  EKEKEKHREKSRRSEREQSTDSDEDKHDKEKEK-DKHRDRDRRRDRDRDRDREKEREEKR 69
           E+E E   E+   SE E+ TDS++D   + K    + +DR   ++R+R+  +EK  EE+ 
Sbjct: 8   EEEDESGEEEEEESEEEEETDSEDDMEPRLKPVFTRKKDRITIQEREREAAKEKALEEEA 67

Query: 70  ERAREKEREREKRDREREDRERERERERERRER--------DREREKRERE--------- 112
           +R  E+ +    +  E E ++    ++R             D E E+ E E         
Sbjct: 68  KRKAEERKRETLKIVEEEVKKELELKKRNTLLEANIDDVDTDDENEEEEYEAWKLRELKR 127

Query: 113 --RDRDKEKDRERKSRDREKRRKVESDDSDEDKDRDRKRRRRHDDDHKERVRERSLSRSN 170
             RDR++ ++ ER+  + EK R +  ++   +  ++ K         K +  ++   R  
Sbjct: 128 IKRDREEREEMEREKAEIEKMRNMTEEERRAELRKNPKVSTNKAKKGKYKFLQKYYHRGA 187

Query: 171 RHRDENDE 178
             +DE DE
Sbjct: 188 FFQDEEDE 195

This family represents the C-terminus (approximately 300 residues) of proteins that are involved as binding partners for Prp19 as part of the nuclear pore complex. The family in Drosophila is necessary for pre-mRNA splicing, and the human protein has been found in purifications of the spliceosome. In the past this family was thought, erroneously, to be associated with microfibrillin. Length = 277

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	976
KOG0334	997	consensus RNA helicase [RNA processing and modific	100.0
KOG0339	731	consensus ATP-dependent RNA helicase [RNA processi	100.0
KOG0331	519	consensus ATP-dependent RNA helicase [RNA processi	100.0
KOG0336	629	consensus ATP-dependent RNA helicase [RNA processi	100.0
KOG0333	673	consensus U5 snRNP-like RNA helicase subunit [RNA	100.0
KOG0341	610	consensus DEAD-box protein abstrakt [RNA processin	100.0
PTZ00110	545	helicase; Provisional	100.0
KOG0330	476	consensus ATP-dependent RNA helicase [RNA processi	100.0
PLN00206	518	DEAD-box ATP-dependent RNA helicase; Provisional	100.0
COG0513	513	SrmB Superfamily II DNA and RNA helicases [DNA rep	100.0
KOG0338	691	consensus ATP-dependent RNA helicase [RNA processi	100.0
KOG0335	482	consensus ATP-dependent RNA helicase [RNA processi	100.0
KOG0328	400	consensus Predicted ATP-dependent RNA helicase FAL	100.0
KOG0342	543	consensus ATP-dependent RNA helicase pitchoune [RN	100.0
KOG0340	442	consensus ATP-dependent RNA helicase [RNA processi	100.0
PRK04837	423	ATP-dependent RNA helicase RhlB; Provisional	100.0
KOG0345	567	consensus ATP-dependent RNA helicase [RNA processi	100.0
KOG0326	459	consensus ATP-dependent RNA helicase [RNA processi	100.0
KOG0343	758	consensus RNA Helicase [RNA processing and modific	100.0
PRK11634	629	ATP-dependent RNA helicase DeaD; Provisional	100.0
PRK04537	572	ATP-dependent RNA helicase RhlB; Provisional	100.0
PRK10590	456	ATP-dependent RNA helicase RhlE; Provisional	100.0
PRK11776	460	ATP-dependent RNA helicase DbpA; Provisional	100.0
KOG0348	708	consensus ATP-dependent RNA helicase [RNA processi	100.0
PRK11192	434	ATP-dependent RNA helicase SrmB; Provisional	100.0
KOG0347	731	consensus RNA helicase [RNA processing and modific	100.0
KOG0346	569	consensus RNA helicase [RNA processing and modific	100.0
PRK01297	475	ATP-dependent RNA helicase RhlB; Provisional	100.0
PTZ00424	401	helicase 45; Provisional	100.0
KOG0344	593	consensus ATP-dependent RNA helicase [RNA processi	100.0
KOG0337	529	consensus ATP-dependent RNA helicase [RNA processi	100.0
KOG0332	477	consensus ATP-dependent RNA helicase [RNA processi	100.0
KOG0327	397	consensus Translation initiation factor 4F, helica	100.0
KOG4284	980	consensus DEAD box protein [Transcription]	100.0
KOG0350	620	consensus DEAD-box ATP-dependent RNA helicase [RNA	100.0
TIGR03817	742	DECH_helic helicase/secretion neighborhood putativ	100.0
PLN03137	1195	ATP-dependent DNA helicase; Q4-like; Provisional	100.0
TIGR00580	926	mfd transcription-repair coupling factor (mfd). Al	100.0
PRK10689	1147	transcription-repair coupling factor; Provisional	100.0
TIGR00614	470	recQ_fam ATP-dependent DNA helicase, RecQ family.	100.0
PRK11057	607	ATP-dependent DNA helicase RecQ; Provisional	100.0
KOG0924	1042	consensus mRNA splicing factor ATP-dependent RNA h	100.0
PRK10917	681	ATP-dependent DNA helicase RecG; Provisional	100.0
TIGR00643	630	recG ATP-dependent DNA helicase RecG.	100.0
PRK13767	876	ATP-dependent helicase; Provisional	100.0
PRK02362	737	ski2-like helicase; Provisional	100.0
TIGR01389	591	recQ ATP-dependent DNA helicase RecQ. The ATP-depe	100.0
TIGR02621	844	cas3_GSU0051 CRISPR-associated helicase Cas3, Anae	100.0
PRK00254	720	ski2-like helicase; Provisional	100.0
KOG0329	387	consensus ATP-dependent RNA helicase [RNA processi	100.0
PRK01172	674	ski2-like helicase; Provisional	100.0
PHA02653	675	RNA helicase NPH-II; Provisional	100.0
TIGR01970	819	DEAH_box_HrpB ATP-dependent helicase HrpB. This mo	100.0
PRK11664	812	ATP-dependent RNA helicase HrpB; Provisional	100.0
PRK09401	1176	reverse gyrase; Reviewed	100.0
KOG0349	725	consensus Putative DEAD-box RNA helicase DDX1 [RNA	100.0
COG1200	677	RecG RecG-like helicase [DNA replication, recombin	100.0
COG0514	590	RecQ Superfamily II DNA helicase [DNA replication,	100.0
COG1201	814	Lhr Lhr-like helicases [General function predictio	100.0
PRK12898	656	secA preprotein translocase subunit SecA; Reviewed	100.0
PRK09751	1490	putative ATP-dependent helicase Lhr; Provisional	100.0
PRK14701	1638	reverse gyrase; Provisional	100.0
COG1197	1139	Mfd Transcription-repair coupling factor (superfam	100.0
COG1111	542	MPH1 ERCC4-like helicases [DNA replication, recomb	100.0
TIGR01587	358	cas3_core CRISPR-associated helicase Cas3. This mo	100.0
PHA02558	501	uvsW UvsW helicase; Provisional	100.0
PRK09200	790	preprotein translocase subunit SecA; Reviewed	100.0
TIGR03714	762	secA2 accessory Sec system translocase SecA2. Memb	100.0
TIGR01054	1171	rgy reverse gyrase. Generally, these gyrases are e	100.0
TIGR00963	745	secA preprotein translocase, SecA subunit. The pro	100.0
COG1202	830	Superfamily II helicase, archaea-specific [General	100.0
PRK13766	773	Hef nuclease; Provisional	100.0
PRK11131	1294	ATP-dependent RNA helicase HrpA; Provisional	100.0
KOG0352	641	consensus ATP-dependent DNA helicase [Replication,	100.0
COG1204	766	Superfamily II helicase [General function predicti	100.0
TIGR01967	1283	DEAH_box_HrpA ATP-dependent helicase HrpA. This mo	100.0
KOG0351	941	consensus ATP-dependent DNA helicase [Replication,	100.0
TIGR03158	357	cas3_cyano CRISPR-associated helicase, Cyano-type.	100.0
KOG0354	746	consensus DEAD-box like helicase [General function	100.0
TIGR00603	732	rad25 DNA repair helicase rad25. All proteins in t	100.0
COG1205	851	Distinct helicase family with a unique C-terminal	100.0
PRK04914	956	ATP-dependent helicase HepA; Validated	99.98
KOG0952	1230	consensus DNA/RNA helicase MER3/SLH1, DEAD-box sup	99.98
KOG0353	695	consensus ATP-dependent DNA helicase [General func	99.97
KOG0922	674	consensus DEAH-box RNA helicase [RNA processing an	99.97
KOG0923	902	consensus mRNA splicing factor ATP-dependent RNA h	99.97
PRK05580	679	primosome assembly protein PriA; Validated	99.97
PRK12899	970	secA preprotein translocase subunit SecA; Reviewed	99.97
PRK13104	896	secA preprotein translocase subunit SecA; Reviewed	99.97
COG1643	845	HrpA HrpA-like helicases [DNA replication, recombi	99.97
PRK09694	878	helicase Cas3; Provisional	99.96
PRK12906	796	secA preprotein translocase subunit SecA; Reviewed	99.96
PRK12904	830	preprotein translocase subunit SecA; Reviewed	99.96
PLN03142	1033	Probable chromatin-remodeling complex ATPase chain	99.96
cd00268	203	DEADc DEAD-box helicases. A diverse family of prot	99.96
KOG0951	1674	consensus RNA helicase BRR2, DEAD-box superfamily	99.96
COG1061	442	SSL2 DNA or RNA helicases of superfamily II [Trans	99.96
TIGR00595	505	priA primosomal protein N'. All proteins in this f	99.95
KOG0385	971	consensus Chromatin remodeling complex WSTF-ISWI,	99.95
PRK13107	908	preprotein translocase subunit SecA; Reviewed	99.94
KOG0947	1248	consensus Cytoplasmic exosomal RNA helicase SKI2,	99.94
PRK11448	1123	hsdR type I restriction enzyme EcoKI subunit R; Pr	99.94
KOG0926	1172	consensus DEAH-box RNA helicase [RNA processing an	99.94
COG4098	441	comFA Superfamily II DNA/RNA helicase required for	99.94
KOG0384	1373	consensus Chromodomain-helicase DNA-binding protei	99.94
KOG0920	924	consensus ATP-dependent RNA helicase A [RNA proces	99.93
COG4581	1041	Superfamily II RNA helicase [DNA replication, reco	99.93
KOG0948	1041	consensus Nuclear exosomal RNA helicase MTR4, DEAD	99.93
KOG0387	923	consensus Transcription-coupled repair protein CSB	99.92
KOG0925	699	consensus mRNA splicing factor ATP-dependent RNA h	99.91
PF00270	169	DEAD: DEAD/DEAH box helicase; InterPro: IPR011545	99.91
KOG0950	1008	consensus DNA polymerase theta/eta, DEAD-box super	99.91
PRK12900	1025	secA preprotein translocase subunit SecA; Reviewed	99.89
TIGR00631	655	uvrb excinuclease ABC, B subunit. This family is b	99.89
KOG2340	698	consensus Uncharacterized conserved protein [Funct	99.89
COG1203	733	CRISPR-associated helicase Cas3 [Defense mechanism	99.88
KOG0392	1549	consensus SNF2 family DNA-dependent ATPase domain-	99.88
PRK12326	764	preprotein translocase subunit SecA; Reviewed	99.88
KOG1002	791	consensus Nucleotide excision repair protein RAD16	99.88
COG0556	663	UvrB Helicase subunit of the DNA excision repair c	99.87
COG1110	1187	Reverse gyrase [DNA replication, recombination, an	99.87
KOG0389	941	consensus SNF2 family DNA-dependent ATPase [Chroma	99.87
KOG0390	776	consensus DNA repair protein, SNF2 family [Replica	99.87
PRK13103	913	secA preprotein translocase subunit SecA; Reviewed	99.86
TIGR01407	850	dinG_rel DnaQ family exonuclease/DinG family helic	99.86
TIGR00348	667	hsdR type I site-specific deoxyribonuclease, HsdR	99.85
COG1198	730	PriA Primosomal protein N' (replication factor Y)	99.85
PRK05298	652	excinuclease ABC subunit B; Provisional	99.84
PF06862	442	DUF1253: Protein of unknown function (DUF1253); In	99.84
KOG1000	689	consensus Chromatin remodeling protein HARP/SMARCA	99.83
PRK12903	925	secA preprotein translocase subunit SecA; Reviewed	99.83
COG4096	875	HsdR Type I site-specific restriction-modification	99.83
KOG1123	776	consensus RNA polymerase II transcription initiati	99.81
smart00487	201	DEXDc DEAD-like helicases superfamily.	99.8
KOG0386	1157	consensus Chromatin remodeling complex SWI/SNF, co	99.8
KOG0391	1958	consensus SNF2 family DNA-dependent ATPase [Genera	99.79
PRK07246	820	bifunctional ATP-dependent DNA helicase/DNA polyme	99.79
CHL00122	870	secA preprotein translocase subunit SecA; Validate	99.78
KOG0949	1330	consensus Predicted helicase, DEAD-box superfamily	99.77
KOG0388	1185	consensus SNF2 family DNA-dependent ATPase [Replic	99.76
PRK12902	939	secA preprotein translocase subunit SecA; Reviewed	99.74
COG4889	1518	Predicted helicase [General function prediction on	99.74
KOG4150	1034	consensus Predicted ATP-dependent RNA helicase [RN	99.72
cd00079	131	HELICc Helicase superfamily c-terminal domain; ass	99.72
PRK08074	928	bifunctional ATP-dependent DNA helicase/DNA polyme	99.7
TIGR03117	636	cas_csf4 CRISPR-associated DEAD/DEAH-box helicase	99.7
KOG4439	901	consensus RNA polymerase II transcription terminat	99.66
KOG0953	700	consensus Mitochondrial RNA helicase SUV3, DEAD-bo	99.65
PF00271	78	Helicase_C: Helicase conserved C-terminal domain;	99.64
PRK12901	1112	secA preprotein translocase subunit SecA; Reviewed	99.63
cd00046	144	DEXDc DEAD-like helicases superfamily. A diverse f	99.62
COG0553	866	HepA Superfamily II DNA/RNA helicases, SNF2 family	99.6
KOG1015	1567	consensus Transcription regulator XNP/ATRX, DEAD-b	99.6
KOG0951	1674	consensus RNA helicase BRR2, DEAD-box superfamily	99.58
PF04851	184	ResIII: Type III restriction enzyme, res subunit;	99.57
TIGR00604	705	rad3 DNA repair helicase (rad3). All proteins in t	99.56
COG1199	654	DinG Rad3-related DNA helicases [Transcription / D	99.56
PRK11747	697	dinG ATP-dependent DNA helicase DinG; Provisional	99.55
PRK14873	665	primosome assembly protein PriA; Provisional	99.52
TIGR02562	1110	cas3_yersinia CRISPR-associated helicase Cas3. The	99.52
smart00490	82	HELICc helicase superfamily c-terminal domain.	99.47
COG0610	962	Type I site-specific restriction-modification syst	99.42
KOG0921	1282	consensus Dosage compensation complex, subunit MLE	99.4
PF02399	824	Herpes_ori_bp: Origin of replication binding prote	99.38
COG0653	822	SecA Preprotein translocase subunit SecA (ATPase,	99.28
PF00176	299	SNF2_N: SNF2 family N-terminal domain; InterPro: I	99.27
PF07652	148	Flavi_DEAD: Flavivirus DEAD domain ; InterPro: IPR	99.18
KOG1016	1387	consensus Predicted DNA helicase, DEAD-box superfa	99.12
PF07517	266	SecA_DEAD: SecA DEAD-like domain; InterPro: IPR011	99.0
PRK15483	986	type III restriction-modification system StyLTI en	98.98
smart00489	289	DEXDc3 DEAD-like helicases superfamily.	98.98
smart00488	289	DEXDc2 DEAD-like helicases superfamily.	98.98
KOG1001	674	consensus Helicase-like transcription factor HLTF/	98.65
TIGR00596	814	rad1 DNA repair protein (rad1). This family is bas	98.54
COG3587	985	Restriction endonuclease [Defense mechanisms]	98.49
KOG0952	1230	consensus DNA/RNA helicase MER3/SLH1, DEAD-box sup	98.37
KOG1802	935	consensus RNA helicase nonsense mRNA reducing fact	98.24
KOG1131	755	consensus RNA polymerase II transcription initiati	98.24
PF13086	236	AAA_11: AAA domain; PDB: 2XZL_A 2XZO_A 2WJY_A 2WJV	98.23
PF13872	303	AAA_34: P-loop containing NTP hydrolase pore-1	98.19
PF02562	205	PhoH: PhoH-like protein; InterPro: IPR003714 PhoH	98.13
PF13604	196	AAA_30: AAA domain; PDB: 1W36_G 3K70_G 3UPU_B 3GPL	98.08
KOG0383	696	consensus Predicted helicase [General function pre	98.07
TIGR00376	637	DNA helicase, putative. The gene product may repre	98.06
PF13307	167	Helicase_C_2: Helicase C-terminal domain; PDB: 4A1	98.01
PF12340	229	DUF3638: Protein of unknown function (DUF3638); In	98.0
PRK10536	262	hypothetical protein; Provisional	97.96
TIGR01447	586	recD exodeoxyribonuclease V, alpha subunit. This f	97.81
PRK10875	615	recD exonuclease V subunit alpha; Provisional	97.75
PF09848	352	DUF2075: Uncharacterized conserved protein (DUF207	97.67
KOG1803	649	consensus DNA helicase [Replication, recombination	97.63
TIGR01448	720	recD_rel helicase, putative, RecD/TraA family. Thi	97.63
PRK12723	388	flagellar biosynthesis regulator FlhF; Provisional	97.62
KOG1132	945	consensus Helicase of the DEAD superfamily [Replic	97.56
COG3421	812	Uncharacterized protein conserved in bacteria [Fun	97.55
KOG1805	1100	consensus DNA replication helicase [Replication, r	97.43
COG1419	407	FlhF Flagellar GTP-binding protein [Cell motility	97.42
PF13245	76	AAA_19: Part of AAA domain	97.32
PRK08181	269	transposase; Validated	97.32
PRK13889	988	conjugal transfer relaxase TraA; Provisional	97.28
PRK14722	374	flhF flagellar biosynthesis regulator FlhF; Provis	97.27
TIGR02768	744	TraA_Ti Ti-type conjugative transfer relaxase TraA	97.26
PRK06526	254	transposase; Provisional	97.24
PRK05703	424	flhF flagellar biosynthesis regulator FlhF; Valida	97.2
PRK14974	336	cell division protein FtsY; Provisional	97.2
PRK11889	436	flhF flagellar biosynthesis regulator FlhF; Provis	97.18
PRK11773	721	uvrD DNA-dependent helicase II; Provisional	97.15
PF13401	131	AAA_22: AAA domain; PDB: 2QBY_B 1FNN_B 1W5T_A 1W5S	97.14
PF00448	196	SRP54: SRP54-type protein, GTPase domain; InterPro	97.1
PF00580	315	UvrD-helicase: UvrD/REP helicase N-terminal domain	97.09
PRK04296	190	thymidine kinase; Provisional	97.08
COG1875	436	NYN ribonuclease and ATPase of PhoH family domains	97.02
TIGR01073	726	pcrA ATP-dependent DNA helicase PcrA. Designed to	96.98
PF13871	278	Helicase_C_4: Helicase_C-like	96.95
KOG0298	1394	consensus DEAD box-containing helicase-like transc	96.94
PRK13826	1102	Dtr system oriT relaxase; Provisional	96.91
TIGR01074	664	rep ATP-dependent DNA helicase Rep. Designed to id	96.91
PF05970	364	PIF1: PIF1-like helicase; InterPro: IPR010285 This	96.85
TIGR02760	1960	TraI_TIGR conjugative transfer relaxase protein Tr	96.85
PRK08116	268	hypothetical protein; Validated	96.79
PRK06835	329	DNA replication protein DnaC; Validated	96.78
smart00492	141	HELICc3 helicase superfamily c-terminal domain.	96.76
PRK12727	559	flagellar biosynthesis regulator FlhF; Provisional	96.73
PRK06921	266	hypothetical protein; Provisional	96.72
cd00009	151	AAA The AAA+ (ATPases Associated with a wide varie	96.67
PRK12726	407	flagellar biosynthesis regulator FlhF; Provisional	96.59
PRK07952	244	DNA replication protein DnaC; Validated	96.56
smart00491	142	HELICc2 helicase superfamily c-terminal domain.	96.44
PF14617	252	CMS1: U3-containing 90S pre-ribosomal complex subu	96.44
PRK14723	767	flhF flagellar biosynthesis regulator FlhF; Provis	96.41
PF03354	477	Terminase_1: Phage Terminase ; InterPro: IPR005021	96.37
PRK06731	270	flhF flagellar biosynthesis regulator FlhF; Valida	96.36
PHA02533	534	17 large terminase protein; Provisional	96.28
TIGR01547	396	phage_term_2 phage terminase, large subunit, PBSX	96.26
PRK12724	432	flagellar biosynthesis regulator FlhF; Provisional	96.24
smart00382	148	AAA ATPases associated with a variety of cellular	96.19
PRK14721	420	flhF flagellar biosynthesis regulator FlhF; Provis	96.19
PRK12377	248	putative replication protein; Provisional	96.16
COG2805	353	PilT Tfp pilus assembly protein, pilus retraction	96.15
KOG0670	752	consensus U4/U6-associated splicing factor PRP4 [R	96.1
PRK09183	259	transposase/IS protein; Provisional	96.06
PRK00771	437	signal recognition particle protein Srp54; Provisi	96.03
PRK06995	484	flhF flagellar biosynthesis regulator FlhF; Valida	96.02
cd01120	165	RecA-like_NTPases RecA-like NTPases. This family i	96.01
PF01695	178	IstB_IS21: IstB-like ATP binding protein; InterPro	96.0
PRK05642	234	DNA replication initiation factor; Validated	95.95
TIGR01075	715	uvrD DNA helicase II. Designed to identify uvrD me	95.93
cd01124	187	KaiC KaiC is a circadian clock protein primarily f	95.82
PRK06893	229	DNA replication initiation factor; Validated	95.82
PF05127	177	Helicase_RecD: Helicase; InterPro: IPR007807 This	95.76
KOG1133	821	consensus Helicase of the DEAD superfamily [Replic	95.74
PRK10867	433	signal recognition particle protein; Provisional	95.71
COG1484	254	DnaC DNA replication protein [DNA replication, rec	95.69
PRK11054	684	helD DNA helicase IV; Provisional	95.63
COG1444	758	Predicted P-loop ATPase fused to an acetyltransfer	95.59
TIGR00064	272	ftsY signal recognition particle-docking protein F	95.57
PTZ00293	211	thymidine kinase; Provisional	95.55
PRK08084	235	DNA replication initiation factor; Provisional	95.53
PRK14712	1623	conjugal transfer nickase/helicase TraI; Provision	95.52
TIGR01425	429	SRP54_euk signal recognition particle protein SRP5	95.51
PRK13709	1747	conjugal transfer nickase/helicase TraI; Provision	95.5
KOG0989	346	consensus Replication factor C, subunit RFC4 [Repl	95.46
PHA03333	752	putative ATPase subunit of terminase; Provisional	95.46
PRK08727	233	hypothetical protein; Validated	95.42
TIGR03420	226	DnaA_homol_Hda DnaA regulatory inactivator Hda. Me	95.41
PF05621	302	TniB: Bacterial TniB protein; InterPro: IPR008868	95.39
PRK05707	328	DNA polymerase III subunit delta'; Validated	95.36
PRK14087	450	dnaA chromosomal replication initiation protein; P	95.33
PRK08903	227	DnaA regulatory inactivator Hda; Validated	95.26
PRK07003	830	DNA polymerase III subunits gamma and tau; Validat	95.26
PF05496	233	RuvB_N: Holliday junction DNA helicase ruvB N-term	95.25
PRK10919	672	ATP-dependent DNA helicase Rep; Provisional	95.17
TIGR00959	428	ffh signal recognition particle protein. This mode	95.15
PRK12323	700	DNA polymerase III subunits gamma and tau; Provisi	95.12
PRK12422	445	chromosomal replication initiation protein; Provis	95.11
PRK00149	450	dnaA chromosomal replication initiation protein; R	95.1
TIGR03499	282	FlhF flagellar biosynthetic protein FlhF.	95.08
PRK10917	681	ATP-dependent DNA helicase RecG; Provisional	95.08
COG0552	340	FtsY Signal recognition particle GTPase [Intracell	95.06
COG2256	436	MGS1 ATPase related to the helicase subunit of the	95.05
PHA02544	316	44 clamp loader, small subunit; Provisional	94.99
TIGR00362	405	DnaA chromosomal replication initiator protein Dna	94.93
PRK08939	306	primosomal protein DnaI; Reviewed	94.91
PRK14086	617	dnaA chromosomal replication initiation protein; P	94.89
TIGR02785	1232	addA_Gpos recombination helicase AddA, Firmicutes	94.82
PRK05580	679	primosome assembly protein PriA; Validated	94.81
COG1435	201	Tdk Thymidine kinase [Nucleotide transport and met	94.74
PRK11331	459	5-methylcytosine-specific restriction enzyme subun	94.74
PRK07764	824	DNA polymerase III subunits gamma and tau; Validat	94.59
PRK12402	337	replication factor C small subunit 2; Reviewed	94.58
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	94.53
PRK08769	319	DNA polymerase III subunit delta'; Validated	94.52
COG3973	747	Superfamily I DNA and RNA helicases [General funct	94.52
COG4626	546	Phage terminase-like protein, large subunit [Gener	94.51
TIGR02760	1960	TraI_TIGR conjugative transfer relaxase protein Tr	94.44
PF13173	128	AAA_14: AAA domain	94.43
cd03115	173	SRP The signal recognition particle (SRP) mediates	94.43
cd00561	159	CobA_CobO_BtuR ATP:corrinoid adenosyltransferase B	94.4
PRK07994	647	DNA polymerase III subunits gamma and tau; Validat	94.37
PTZ00112	1164	origin recognition complex 1 protein; Provisional	94.36
PRK14088	440	dnaA chromosomal replication initiation protein; P	94.34
TIGR02640	262	gas_vesic_GvpN gas vesicle protein GvpN. Members o	94.33
TIGR00643	630	recG ATP-dependent DNA helicase RecG.	94.27
TIGR00595	505	priA primosomal protein N'. All proteins in this f	94.25
TIGR02881	261	spore_V_K stage V sporulation protein K. Members o	94.24
PRK14960	702	DNA polymerase III subunits gamma and tau; Provisi	94.22
KOG2036	1011	consensus Predicted P-loop ATPase fused to an acet	94.19
PRK10416	318	signal recognition particle-docking protein FtsY;	94.19
PRK14956	484	DNA polymerase III subunits gamma and tau; Provisi	94.18
PRK08691	709	DNA polymerase III subunits gamma and tau; Validat	94.14
PRK05986	191	cob(I)alamin adenolsyltransferase/cobinamide ATP-d	94.13
PRK00411	394	cdc6 cell division control protein 6; Reviewed	94.09
KOG0298	1394	consensus DEAD box-containing helicase-like transc	94.03
COG1474	366	CDC6 Cdc6-related protein, AAA superfamily ATPase	94.03
PRK08533	230	flagellar accessory protein FlaH; Reviewed	94.0
TIGR03689	512	pup_AAA proteasome ATPase. In the Actinobacteria,	93.99
PRK14964	491	DNA polymerase III subunits gamma and tau; Provisi	93.96
PRK04195	482	replication factor C large subunit; Provisional	93.94
KOG2028	554	consensus ATPase related to the helicase subunit o	93.92
cd01122	271	GP4d_helicase GP4d_helicase is a homohexameric 5'-	93.89
TIGR00708	173	cobA cob(I)alamin adenosyltransferase. Alternate n	93.88
PF00308	219	Bac_DnaA: Bacterial dnaA protein; InterPro: IPR013	93.8
PRK14958	509	DNA polymerase III subunits gamma and tau; Provisi	93.77
PRK13342	413	recombination factor protein RarA; Reviewed	93.75
KOG0733	802	consensus Nuclear AAA ATPase (VCP subfamily) [Post	93.74
PRK06645	507	DNA polymerase III subunits gamma and tau; Validat	93.73
TIGR03015	269	pepcterm_ATPase putative secretion ATPase, PEP-CTE	93.73
PF00004	132	AAA: ATPase family associated with various cellula	93.71
TIGR00580	926	mfd transcription-repair coupling factor (mfd). Al	93.62
TIGR03877	237	thermo_KaiC_1 KaiC domain protein, Ph0284 family.	93.59
PRK09111	598	DNA polymerase III subunits gamma and tau; Validat	93.54
PRK13833	323	conjugal transfer protein TrbB; Provisional	93.52
PRK14873	665	primosome assembly protein PriA; Provisional	93.51
KOG0738	491	consensus AAA+-type ATPase [Posttranslational modi	93.49
PLN03025	319	replication factor C subunit; Provisional	93.47
PRK13341	725	recombination factor protein RarA/unknown domain f	93.44
cd00984	242	DnaB_C DnaB helicase C terminal domain. The hexame	93.39
PRK14949	944	DNA polymerase III subunits gamma and tau; Provisi	93.37
PF05876	557	Terminase_GpA: Phage terminase large subunit (GpA)	93.33
PF02456	369	Adeno_IVa2: Adenovirus IVa2 protein; InterPro: IPR	93.32
PHA03368	738	DNA packaging terminase subunit 1; Provisional	93.17
PRK14961	363	DNA polymerase III subunits gamma and tau; Provisi	93.14
PRK13894	319	conjugal transfer ATPase TrbB; Provisional	93.09
COG3972	660	Superfamily I DNA and RNA helicases [General funct	93.06
COG0541	451	Ffh Signal recognition particle GTPase [Intracellu	93.02
PRK07471	365	DNA polymerase III subunit delta'; Validated	92.99
PF03969	362	AFG1_ATPase: AFG1-like ATPase; InterPro: IPR005654	92.96
PHA00729	226	NTP-binding motif containing protein	92.93
PRK14955	397	DNA polymerase III subunits gamma and tau; Provisi	92.93
PRK14952	584	DNA polymerase III subunits gamma and tau; Provisi	92.92
TIGR02928	365	orc1/cdc6 family replication initiation protein. M	92.9
PF13177	162	DNA_pol3_delta2: DNA polymerase III, delta subunit	92.9
PRK14959	624	DNA polymerase III subunits gamma and tau; Provisi	92.89
PF00265	176	TK: Thymidine kinase; InterPro: IPR001267 Thymidin	92.89
PF02572	172	CobA_CobO_BtuR: ATP:corrinoid adenosyltransferase	92.87
PRK14951	618	DNA polymerase III subunits gamma and tau; Provisi	92.81
COG0593	408	DnaA ATPase involved in DNA replication initiation	92.78
PTZ00454	398	26S protease regulatory subunit 6B-like protein; P	92.77
PRK14957	546	DNA polymerase III subunits gamma and tau; Provisi	92.76
PF05707	193	Zot: Zonular occludens toxin (Zot); InterPro: IPR0	92.66
TIGR03878	259	thermo_KaiC_2 KaiC domain protein, AF_0795 family.	92.65
PRK07940	394	DNA polymerase III subunit delta'; Validated	92.65
COG2255	332	RuvB Holliday junction resolvasome, helicase subun	92.63
CHL00181	287	cbbX CbbX; Provisional	92.61
PRK14969	527	DNA polymerase III subunits gamma and tau; Provisi	92.58
PF06745	226	KaiC: KaiC; InterPro: IPR014774 This entry represe	92.56
PRK09112	351	DNA polymerase III subunit delta'; Validated	92.47
PRK06964	342	DNA polymerase III subunit delta'; Validated	92.47
PRK14965	576	DNA polymerase III subunits gamma and tau; Provisi	92.37
PRK14963	504	DNA polymerase III subunits gamma and tau; Provisi	92.2
PRK11823	446	DNA repair protein RadA; Provisional	92.18
TIGR02782	299	TrbB_P P-type conjugative transfer ATPase TrbB. Th	92.13
PRK05563	559	DNA polymerase III subunits gamma and tau; Validat	92.1
COG2909	894	MalT ATP-dependent transcriptional regulator [Tran	92.09
COG2109	198	BtuR ATP:corrinoid adenosyltransferase [Coenzyme m	92.08
PRK11034	758	clpA ATP-dependent Clp protease ATP-binding subuni	92.06
PRK06871	325	DNA polymerase III subunit delta'; Validated	91.99
PRK08699	325	DNA polymerase III subunit delta'; Validated	91.96
PRK14962	472	DNA polymerase III subunits gamma and tau; Provisi	91.95
PRK05896	605	DNA polymerase III subunits gamma and tau; Validat	91.91
KOG1513	1300	consensus Nuclear helicase MOP-3/SNO (DEAD-box sup	91.89
COG4962	355	CpaF Flp pilus assembly protein, ATPase CpaF [Intr	91.88
COG0470	325	HolB ATPase involved in DNA replication [DNA repli	91.8
KOG0739	439	consensus AAA+-type ATPase [Posttranslational modi	91.74
COG1110	1187	Reverse gyrase [DNA replication, recombination, an	91.73
KOG1133	821	consensus Helicase of the DEAD superfamily [Replic	91.73
PF10593	239	Z1: Z1 domain; InterPro: IPR018310 This entry repr	91.63
KOG0741	744	consensus AAA+-type ATPase [Posttranslational modi	91.62
TIGR02880	284	cbbX_cfxQ probable Rubsico expression protein CbbX	91.6
COG2804	500	PulE Type II secretory pathway, ATPase PulE/Tfp pi	91.6
TIGR02639	731	ClpA ATP-dependent Clp protease ATP-binding subuni	91.51
PRK14950	585	DNA polymerase III subunits gamma and tau; Provisi	91.5
PF05872	502	DUF853: Bacterial protein of unknown function (DUF	91.49
cd03239	178	ABC_SMC_head The structural maintenance of chromos	91.41
PF03237	384	Terminase_6: Terminase-like family; InterPro: IPR0	91.33
TIGR00767	415	rho transcription termination factor Rho. Members	91.32
PRK06067	234	flagellar accessory protein FlaH; Validated	91.29
KOG0670	752	consensus U4/U6-associated splicing factor PRP4 [R	91.28
PRK10689	1147	transcription-repair coupling factor; Provisional	91.26
KOG2543	438	consensus Origin recognition complex, subunit 5 [R	91.23
COG1198	730	PriA Primosomal protein N' (replication factor Y)	91.23
PRK04841	903	transcriptional regulator MalT; Provisional	91.22
TIGR02524	358	dot_icm_DotB Dot/Icm secretion system ATPase DotB.	91.05
KOG0344	593	consensus ATP-dependent RNA helicase [RNA processi	91.02
KOG0339	731	consensus ATP-dependent RNA helicase [RNA processi	90.92
PRK03992	389	proteasome-activating nucleotidase; Provisional	90.88
TIGR03346	852	chaperone_ClpB ATP-dependent chaperone ClpB. Membe	90.74
PRK04328	249	hypothetical protein; Provisional	90.64
TIGR03880	224	KaiC_arch_3 KaiC domain protein, AF_0351 family. T	90.64
cd01121	372	Sms Sms (bacterial radA) DNA repair protein. This	90.63
PRK08451	535	DNA polymerase III subunits gamma and tau; Validat	90.52
TIGR02688	449	conserved hypothetical protein TIGR02688. Members	90.47
PRK00440	319	rfc replication factor C small subunit; Reviewed	90.32
KOG0991	333	consensus Replication factor C, subunit RFC2 [Repl	90.27
PRK14948	620	DNA polymerase III subunits gamma and tau; Provisi	90.24
TIGR03600	421	phage_DnaB phage replicative helicase, DnaB family	90.23
PRK14954	620	DNA polymerase III subunits gamma and tau; Provisi	90.21
PHA00350	399	putative assembly protein	90.21
PRK07413	382	hypothetical protein; Validated	90.16
COG1200	677	RecG RecG-like helicase [DNA replication, recombin	90.13
KOG0740	428	consensus AAA+-type ATPase [Posttranslational modi	90.11
PRK06090	319	DNA polymerase III subunit delta'; Validated	90.1
PRK07993	334	DNA polymerase III subunit delta'; Validated	90.05
TIGR02525	372	plasmid_TraJ plasmid transfer ATPase TraJ. Members	90.05
KOG0742	630	consensus AAA+-type ATPase [Posttranslational modi	90.0
PF05729	166	NACHT: NACHT domain	89.99
TIGR00635	305	ruvB Holliday junction DNA helicase, RuvB subunit.	89.94
KOG0058	716	consensus Peptide exporter, ABC superfamily [Intra	89.9
PRK07414	178	cob(I)yrinic acid a,c-diamide adenosyltransferase;	89.9
TIGR03345	852	VI_ClpV1 type VI secretion ATPase, ClpV1 family. M	89.88
KOG0701	1606	consensus dsRNA-specific nuclease Dicer and relate	89.82
PRK07413	382	hypothetical protein; Validated	89.75
PRK09376	416	rho transcription termination factor Rho; Provisio	89.69
PRK07133	725	DNA polymerase III subunits gamma and tau; Validat	89.67
COG1222	406	RPT1 ATP-dependent 26S proteasome regulatory subun	89.66
KOG0734	752	consensus AAA+-type ATPase containing the peptidas	89.63
TIGR00665	434	DnaB replicative DNA helicase. This model describe	89.55
COG1485	367	Predicted ATPase [General function prediction only	89.54
PRK13851	344	type IV secretion system protein VirB11; Provision	89.39
TIGR02012	321	tigrfam_recA protein RecA. This model describes or	89.34
TIGR01243	733	CDC48 AAA family ATPase, CDC48 subfamily. This sub	89.33
PF03266	168	NTPase_1: NTPase; InterPro: IPR004948 This entry r	89.2
TIGR01243	733	CDC48 AAA family ATPase, CDC48 subfamily. This sub	89.17
COG0513	513	SrmB Superfamily II DNA and RNA helicases [DNA rep	89.13
TIGR01241	495	FtsH_fam ATP-dependent metalloprotease FtsH. HflB(	89.12
KOG1132	945	consensus Helicase of the DEAD superfamily [Replic	89.09
PRK10865	857	protein disaggregation chaperone; Provisional	89.04
PRK06647	563	DNA polymerase III subunits gamma and tau; Validat	89.01
TIGR00678	188	holB DNA polymerase III, delta' subunit. At positi	88.91
PF01443	234	Viral_helicase1: Viral (Superfamily 1) RNA helicas	88.9
PF12846	304	AAA_10: AAA-like domain	88.77
PRK13900	332	type IV secretion system ATPase VirB11; Provisiona	88.76
TIGR02858	270	spore_III_AA stage III sporulation protein AA. Mem	88.74
PRK06904	472	replicative DNA helicase; Validated	88.69
PRK14953	486	DNA polymerase III subunits gamma and tau; Provisi	88.61
cd01128	249	rho_factor Transcription termination factor rho is	88.56
CHL00095	821	clpC Clp protease ATP binding subunit	88.55
PRK00080	328	ruvB Holliday junction DNA helicase RuvB; Reviewed	88.53
CHL00176	638	ftsH cell division protein; Validated	88.45
TIGR03881	229	KaiC_arch_4 KaiC domain protein, PAE1156 family. M	88.38
PRK13764	602	ATPase; Provisional	88.35
KOG1513	1300	consensus Nuclear helicase MOP-3/SNO (DEAD-box sup	88.34
PF03796	259	DnaB_C: DnaB-like helicase C terminal domain; Inte	88.32
TIGR00614	470	recQ_fam ATP-dependent DNA helicase, RecQ family.	88.21
cd01129	264	PulE-GspE PulE/GspE The type II secretory pathway	88.18
PRK05416	288	glmZ(sRNA)-inactivating NTPase; Provisional	88.17
TIGR00763	775	lon ATP-dependent protease La. This protein is ind	88.09
TIGR01242	364	26Sp45 26S proteasome subunit P45 family. Many pro	88.0
COG5008	375	PilU Tfp pilus assembly protein, ATPase PilU [Cell	87.99
COG1618	179	Predicted nucleotide kinase [Nucleotide transport	87.93
cd00983	325	recA RecA is a bacterial enzyme which has roles in	87.81
PRK14971	614	DNA polymerase III subunits gamma and tau; Provisi	87.8
KOG0333	673	consensus U5 snRNP-like RNA helicase subunit [RNA	87.75
COG3598	402	RepA RecA-family ATPase [DNA replication, recombin	87.74
TIGR02868	529	CydC thiol reductant ABC exporter, CydC subunit. T	87.69
PRK09354	349	recA recombinase A; Provisional	87.66
PHA00012	361	I assembly protein	87.61
cd03221	144	ABCF_EF-3 ABCF_EF-3 Elongation factor 3 (EF-3) is	87.58
TIGR02237	209	recomb_radB DNA repair and recombination protein R	87.53
PF01637	234	Arch_ATPase: Archaeal ATPase; InterPro: IPR011579	87.51
PRK06305	451	DNA polymerase III subunits gamma and tau; Validat	87.42
PRK07004	460	replicative DNA helicase; Provisional	87.4
COG1219	408	ClpX ATP-dependent protease Clp, ATPase subunit [P	87.35
TIGR02655	484	circ_KaiC circadian clock protein KaiC. Members of	87.35
KOG0737	386	consensus AAA+-type ATPase [Posttranslational modi	87.08
PRK09435	332	membrane ATPase/protein kinase; Provisional	87.0
KOG0060	659	consensus Long-chain acyl-CoA transporter, ABC sup	86.97
PRK08506	472	replicative DNA helicase; Provisional	86.95
PRK10436	462	hypothetical protein; Provisional	86.94
cd01125	239	repA Hexameric Replicative Helicase RepA. RepA is	86.9
PHA03372	668	DNA packaging terminase subunit 1; Provisional	86.89
PF02534	469	T4SS-DNA_transf: Type IV secretory system Conjugat	86.86
cd01126	384	TraG_VirD4 The TraG/TraD/VirD4 family are bacteria	86.68
TIGR01420	343	pilT_fam pilus retraction protein PilT. This model	86.62
PRK05595	444	replicative DNA helicase; Provisional	86.61
cd03289	275	ABCC_CFTR2 The CFTR subfamily domain 2. The cystic	86.53
KOG0780	483	consensus Signal recognition particle, subunit Srp	86.51
TIGR02533	486	type_II_gspE general secretory pathway protein E.	86.4
PRK14701	1638	reverse gyrase; Provisional	86.37
KOG0733	802	consensus Nuclear AAA ATPase (VCP subfamily) [Post	86.18

>KOG0334 consensus RNA helicase [RNA processing and modification]

Probab=100.00  E-value=2.7e-101  Score=897.03  Aligned_cols=732  Identities=57%  Similarity=0.885  Sum_probs=626.9

Q ss_pred             HHHHHhhhhHHHHHHHHHHHHHHHHHHhHHHHHHhhcCCCCCCCCccCCCCccCCCCCcCccCccCC-CCCCCCCCCCCC
Q 002040          201 LEDEQRKLDEEMEKRRRRVQEWQELKRKKEESERENRGDANVEEPKAGRNWTLDREDSDDEEVPQTG-KSETDMDADEEP  279 (976)
Q Consensus       201 ~e~~~~~~~ee~~kr~~~~~e~~~~~~~~e~~e~e~~~~~~~~~~~~~r~~~~~~e~~de~~~~~~~-~~e~~~~~~e~~  279 (976)
                      ....+.++.+++.+++++++.|.+.+++.+.+...+..+.....+...+.|+++++++++..+|... .++.+...    
T Consensus       139 ~~~~~~~l~e~l~~rr~~~e~~~e~k~k~e~~~~~t~~~~~~~~~~s~k~~~l~~~~d~~~~~~~~~~~s~q~~~~----  214 (997)
T KOG0334|consen  139 YGSIQARLAEELRKRRERVEKWKELKRKEEKEKVVTLMLNVSDEKNSKKLWELEDEDDDDSANPAELGWSEQDVPE----  214 (997)
T ss_pred             cchhhhhHHHHHHHHHHHHHHHHHhhhcchHHhhhhhhcccccccccccceEecCCCCccccCccccchhhccchh----
Confidence            3456678899999999999999999999888887776666667778889999999988777554321 11111000    


Q ss_pred             CCCCccccccccccCCCCCCChhhhcCCCCCCCCChhHHHHhcccchhHHhhhccCCCCCCCCCccccccccccCCCCCC
Q 002040          280 KPSENQVGDAMLVDSDGGSAAPALQIGAAEDEDIDPLDAFMNSMVLPEVEKLKNTVEPSFTDGNNVESKKMDRKGDRRSN  359 (976)
Q Consensus       280 ~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~e~d~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~k~~~~~~~~~~~  359 (976)
                        .|    ..|              ..-..++++||+|+||..++.+.+..+... .+.  +..            ....
T Consensus       215 --~~----~~p--------------~~~~~dd~~d~ld~~m~~~~~~~~~~~~~~-~~~--~~~------------~~~~  259 (997)
T KOG0334|consen  215 --LM----KAP--------------NLMLVDDEEDPLDAFMEQMVGKVLAKFSNS-SHS--KAQ------------VVEV  259 (997)
T ss_pred             --hc----cCc--------------cccccccccchHHHHHHHHHHHHHHHhcCC-Ccc--ccc------------cccc
Confidence              00    000              012346789999999999765444332111 010  000            0011


Q ss_pred             CCCCCccc-ccccCCCCCCCCCCcccCCcccCCCCCCCcchHHHHHHHHHHhhccCCcCCCcccccCcccccccccchhh
Q 002040          360 GEQPKKSS-NKSLGRIIPGEDSDSDYGDLENDEKPLEDEDDDEFMKRVKKTKAEKLSIVDHSKIDYQPFRKNFYIEVKEI  438 (976)
Q Consensus       360 ~~~~~~~~-~~~~~~~~~~~d~~~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~~~~~~~~~~~  438 (976)
                      +....+.. .+..+.+++..+...|..+.+.+++    ++....++..+.+..+.+..++||.+.|.||+++||++..++
T Consensus       260 s~~~~~~~~~~~~g~v~e~~~~~~D~~e~~~~~~----~d~~~~~~~~~~~~~~~~~~~~~S~~~~epFRknfy~e~~di  335 (997)
T KOG0334|consen  260 SKDARKGLNPKLSGFVIEPGLVNGDNEEVELNGS----FDNRNAAKNMNLKAKKNLIQVDHSKISYEPFRKNFYIEVRDI  335 (997)
T ss_pred             chhhhccCCccccceeccCCcCCcchhhhhhccc----cchHHHHHHhccccccceeecccccccchhhhhcccccchhH
Confidence            22222332 2355677777666666554444333    445566666666666788999999999999999999999999


Q ss_pred             hcCCHHHHHHHHhhcC-ceeccCCCCCcccccccCCCCHHHHHHHHHcCCCCCcHHHHHHHHHHhcCCCEEEEcCCCCch
Q 002040          439 ARMTPEEVSAYRKQLE-LKIHGKDVPKPIKTWHQTGLTSKIMETIRKLNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGK  517 (976)
Q Consensus       439 ~~~~~~~~~~~~~~~~-i~~~g~~~p~pi~~~~~~~l~~~l~~~l~~~~~~~p~~~Q~~~i~~il~g~d~i~~a~TGsGK  517 (976)
                      ..|+.+++..|+..+. |.+.|..+|.|+.+|.++|++..++..++++||.+|+|||.+|||+|++|+|||++|.|||||
T Consensus       336 ~~ms~~eV~~yr~~l~~i~v~g~~~pkpv~sW~q~gl~~~il~tlkkl~y~k~~~IQ~qAiP~ImsGrdvIgvakTgSGK  415 (997)
T KOG0334|consen  336 KRMSAAEVDEYRCELDGIKVKGKECPKPVTSWTQCGLSSKILETLKKLGYEKPTPIQAQAIPAIMSGRDVIGVAKTGSGK  415 (997)
T ss_pred             HHHHHHHHHHhhcCccceeeccCCCCcccchHhhCCchHHHHHHHHHhcCCCCcchhhhhcchhccCcceEEeeccCCcc
Confidence            9999999999999998 999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHHHHhhcCcEEEEeeCCCChHHHHHHHhcCCeEEEeC
Q 002040          518 TLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQISELKRGTEIVVCT  597 (976)
Q Consensus       518 T~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~~~~~~~~~~~~~~gg~~~~~~~~~l~~~~~Iiv~T  597 (976)
                      |++|++||+.|++.+++...+.||.+||||||++||.||+.++.+|++.+++.++|+|||..+.+++..+++++.|+|||
T Consensus       416 T~af~LPmirhi~dQr~~~~gdGPi~li~aPtrela~QI~r~~~kf~k~l~ir~v~vygg~~~~~qiaelkRg~eIvV~t  495 (997)
T KOG0334|consen  416 TLAFLLPMIRHIKDQRPLEEGDGPIALILAPTRELAMQIHREVRKFLKLLGIRVVCVYGGSGISQQIAELKRGAEIVVCT  495 (997)
T ss_pred             chhhhcchhhhhhcCCChhhCCCceEEEEcCCHHHHHHHHHHHHHHHhhcCceEEEecCCccHHHHHHHHhcCCceEEec
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             chhHHHHHHhcCCcccccCCceEEEecCcccccccCCchHHHHHHHhcCCCCcEEEEeccCcHHHHHHHHHHcCCCeEEE
Q 002040          598 PGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMGFEPQITRIVQNIRPDRQTVLFSATFPRQVEILARKVLNKPVEIQ  677 (976)
Q Consensus       598 p~~L~~~l~~~~~~~~~l~~~~~vVlDEah~~~~~~f~~~i~~il~~~~~~~q~i~~SAT~~~~~~~l~~~~l~~~~~i~  677 (976)
                      ||+++++++.+.+++++|.++.|||+||||+|++++|.|++..|+.++++++|+++||||+|..+..++...+..|+.+.
T Consensus       496 pGRmiD~l~~n~grvtnlrR~t~lv~deaDrmfdmgfePq~~~Ii~nlrpdrQtvlfSatfpr~m~~la~~vl~~Pveii  575 (997)
T KOG0334|consen  496 PGRMIDILCANSGRVTNLRRVTYLVLDEADRMFDMGFEPQITRILQNLRPDRQTVLFSATFPRSMEALARKVLKKPVEII  575 (997)
T ss_pred             cchhhhhHhhcCCccccccccceeeechhhhhheeccCcccchHHhhcchhhhhhhhhhhhhHHHHHHHHHhhcCCeeEE
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eCCcccccCCceEEEEecC-cchHHHHHHHHHHhhhcCCcEEEEecCHHHHHHHHHHHHHCCCCceeccCCCCHHHHHHH
Q 002040          678 VGGRSVVNKDITQLVEVRP-ESDRFLRLLELLGEWYEKGKILIFVHSQEKCDALFRDLLKHGYPCLSLHGAKDQTDREST  756 (976)
Q Consensus       678 ~~~~~~~~~~i~q~~~~~~-~~~k~~~l~~~l~~~~~~~kvLIF~~s~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~  756 (976)
                      +++.++++..+.|.+.++. ...||..|+++|..+...+++||||.++..|+.|...|.+.||+|..|||+.++.+|..+
T Consensus       576 v~~~svV~k~V~q~v~V~~~e~eKf~kL~eLl~e~~e~~~tiiFv~~qe~~d~l~~~L~~ag~~~~slHGgv~q~dR~st  655 (997)
T KOG0334|consen  576 VGGRSVVCKEVTQVVRVCAIENEKFLKLLELLGERYEDGKTIIFVDKQEKADALLRDLQKAGYNCDSLHGGVDQHDRSST  655 (997)
T ss_pred             EccceeEeccceEEEEEecCchHHHHHHHHHHHHHhhcCCEEEEEcCchHHHHHHHHHHhcCcchhhhcCCCchHHHHhH
Confidence            9999999999999999988 899999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHhccCCccEEEecCcccccCCCCCCcEEEEeCCCCCHHHHHHHhcccCCCCCccEEEEEecCCCcCchHHHHHHHhhc
Q 002040          757 ISDFKSNVCNLLIATSVAARGLDVKELELVINFDAPNHYEDYVHRVGRTGRAGRKGCAITFISEEDAKYSPDLVKALELS  836 (976)
Q Consensus       757 ~~~F~~g~~~vLVaT~v~~~GlDi~~v~~VI~~d~p~s~~~y~Qr~GR~gR~g~~g~~~~~~~~~d~~~~~~i~~~l~~~  836 (976)
                      +..|++|.+.+||||+++++|||++.+.+||||++|+++.+|+||+||+||+|.+|.||+|+++.+..++.+|+++|..+
T Consensus       656 i~dfK~~~~~LLvaTsvvarGLdv~~l~Lvvnyd~pnh~edyvhR~gRTgragrkg~AvtFi~p~q~~~a~dl~~al~~~  735 (997)
T KOG0334|consen  656 IEDFKNGVVNLLVATSVVARGLDVKELILVVNYDFPNHYEDYVHRVGRTGRAGRKGAAVTFITPDQLKYAGDLCKALELS  735 (997)
T ss_pred             HHHHhccCceEEEehhhhhcccccccceEEEEcccchhHHHHHHHhcccccCCccceeEEEeChHHhhhHHHHHHHHHhc
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCCChHHHHHHHHHHHHHhhhhhhccCCC-CCCCCcccchhHHHHHHHHHHHHHHHcCCCCCCCCCCccccccccc---
Q 002040          837 EQVVPDDLKALADSFMAKVNQGLEQAHGTG-YGGSGFKFNEEEDEKRKAAKKAQAKEYGFEEDKSDSDDEDEGIRKA---  912 (976)
Q Consensus       837 ~~~vp~~l~~l~~~~~~~~~~~~~~~~~~~-~~g~g~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~---  912 (976)
                      ++++|..|.+|+..|+++.+.+....+++| |+|+||.|.+...+.++..+.++...+|+.+...+++........+   
T Consensus       736 ~~~~P~~l~~l~~~f~~~~~~~~s~~~~~Gg~~G~g~~~~~~~~~~~~~~ke~q~~~~g~~~~d~e~d~~~~~~~~~~~~  815 (997)
T KOG0334|consen  736 KQPVPKLLQALSERFKAKQKAGGSQVHGGGGFGGKGLKFDEVEEELRQERKEAQRKDLGLKEGDNESDIEVDNSDKASQP  815 (997)
T ss_pred             cCCCchHHHHHHHHHHhhhhcccccccccCcccCCcccccHHHHHHHHHHhhccccCcCCCCCCcccccccccchhhccc
Confidence            999999999999999999999988888888 9999999998888899999999999999987666543322210000   


Q ss_pred             -------------CCC--------------------------------Cc------------------------------
Q 002040          913 -------------GGD--------------------------------IS------------------------------  917 (976)
Q Consensus       913 -------------~~~--------------------------------~~------------------------------  917 (976)
                                   +..                                ++                              
T Consensus       816 ~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~a~~~A~~~~~~l~~~~~~~s~d~~~~  895 (997)
T KOG0334|consen  816 RESIQNPTFLQVEAESKTQEKTLLLGGELNAARPMVPYPVPGTAEFQVIAARDDAEIKALLLNAQLNYQLIDTSSDLILQ  895 (997)
T ss_pred             cccccCcccccccccccchhhhhhcccccccccccccccccccccccccchhhhHHHHHhhccccceeecccCCcccccc
Confidence                         000                                00                              


Q ss_pred             ------------HHHH---------HHHhh----------------------hccceeeeecCCcHHHHHHHHHHHHHHH
Q 002040          918 ------------QQDA---------LAKIS----------------------AIRKLYLFIEGPTEQSVKRAKAELKRVL  954 (976)
Q Consensus       918 ------------~~~~---------~~~~~----------------------~~~~~~~~~~~~~~~~~~~~~~~~~~~~  954 (976)
                                  ||.+         |..|.                      +++||||||||.++.+|+.|+.+|.++|
T Consensus       896 ~~y~~~~~inD~Pq~~r~~vt~~~~L~~i~e~~~~~it~rg~f~~~gk~p~~gErklyl~ve~~~e~~vqra~~e~~r~l  975 (997)
T KOG0334|consen  896 FIYEAELEINDFPQNARWRVTYKEALLRISEPTAAGITTRGKFNPPGKEPKPGERKLYLLVEGPDELSVQRAIEELERLL  975 (997)
T ss_pred             ceeeeeccccccchhcceeeechhhhhhccCccccceeeccccCCCCCCCCCcchhhhhhhhcchhHHHHHHHHHHHHHH
Confidence                        1111         22222                      2889999999999999999999999999


Q ss_pred             HHHHHHhhc-CCCCCCCcceeeC
Q 002040          955 EDFTNQALS-LPGGAQPGRYSVV  976 (976)
Q Consensus       955 ~~~~~~~~~-~~~~~~~~~~~~~  976 (976)
                      ++++.++.. ...+. +|||.||
T Consensus       976 ~e~~~~~~~~~~~~~-~~~y~~~  997 (997)
T KOG0334|consen  976 EEEVVNLFSSLQPSC-KGRYLVV  997 (997)
T ss_pred             HHHHHHHHhccCCCc-cceeecC
Confidence            999999985 44444 8999986

>KOG0339 consensus ATP-dependent RNA helicase [RNA processing and modification]

Probab=100.00  E-value=9.2e-83  Score=680.40  Aligned_cols=441  Identities=49%  Similarity=0.807  Sum_probs=426.2

Q ss_pred             HHHhhccCCcCCCcccccCcccccccccchhhhcCCHHHHHHHHhhcCceeccCCCCCcccccccCCCCHHHHHHHHHcC
Q 002040          407 KKTKAEKLSIVDHSKIDYQPFRKNFYIEVKEIARMTPEEVSAYRKQLELKIHGKDVPKPIKTWHQTGLTSKIMETIRKLN  486 (976)
Q Consensus       407 ~~~~~~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~g~~~p~pi~~~~~~~l~~~l~~~l~~~~  486 (976)
                      .+++.+++++++|+.+.|.||.++||.++..|..++..++..++..+++++.|..+|+|+++|.+||+...|+.++.+..
T Consensus       163 ~kr~idpl~~idhs~i~y~p~~kdfy~e~esI~gl~~~d~~~~r~~Lnlrv~g~s~~rpvtsfeh~gfDkqLm~airk~E  242 (731)
T KOG0339|consen  163 DKRQIDPLPPIDHSEIDYEPFNKDFYEEHESIEGLTKMDVIDLRLTLNLRVSGSSPPRPVTSFEHFGFDKQLMTAIRKSE  242 (731)
T ss_pred             ccccCCCCCCcchhhccccccccccccChhhhhccccccchhhHhhhcceeccCCCCCCcchhhhcCchHHHHHHHhhhh
Confidence            45678899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCcHHHHHHHHHHhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHHHHhh
Q 002040          487 YEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKV  566 (976)
Q Consensus       487 ~~~p~~~Q~~~i~~il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~~~~~  566 (976)
                      |.+|||+|+++||..++|+++|.+|.||||||.+|++|++-|+++++.+..++||..||||||++||.|++.++++|++.
T Consensus       243 y~kptpiq~qalptalsgrdvigIAktgSgktaAfi~pm~~himdq~eL~~g~gPi~vilvPTrela~Qi~~eaKkf~K~  322 (731)
T KOG0339|consen  243 YEKPTPIQCQALPTALSGRDVIGIAKTGSGKTAAFIWPMIVHIMDQPELKPGEGPIGVILVPTRELASQIFSEAKKFGKA  322 (731)
T ss_pred             cccCCcccccccccccccccchheeeccCcchhHHHHHHHHHhcchhhhcCCCCCeEEEEeccHHHHHHHHHHHHHhhhh
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCcEEEEeeCCCChHHHHHHHhcCCeEEEeCchhHHHHHHhcCCcccccCCceEEEecCcccccccCCchHHHHHHHhcC
Q 002040          567 MGVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMGFEPQITRIVQNIR  646 (976)
Q Consensus       567 ~~~~~~~~~gg~~~~~~~~~l~~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDEah~~~~~~f~~~i~~il~~~~  646 (976)
                      +|++++++|||.+..+|+..|+.++.||||||++|++++...   .++|.+++|||||||++|+++||.+++..|..+++
T Consensus       323 ygl~~v~~ygGgsk~eQ~k~Lk~g~EivVaTPgRlid~VkmK---atn~~rvS~LV~DEadrmfdmGfe~qVrSI~~hir  399 (731)
T KOG0339|consen  323 YGLRVVAVYGGGSKWEQSKELKEGAEIVVATPGRLIDMVKMK---ATNLSRVSYLVLDEADRMFDMGFEPQVRSIKQHIR  399 (731)
T ss_pred             ccceEEEeecCCcHHHHHHhhhcCCeEEEechHHHHHHHHhh---cccceeeeEEEEechhhhhccccHHHHHHHHhhcC
Confidence            999999999999999999999999999999999999999764   47899999999999999999999999999999999


Q ss_pred             CCCcEEEEeccCcHHHHHHHHHHcCCCeEEEeCCcccccCCceEEEEecCc-chHHHHHHHHHHhhhcCCcEEEEecCHH
Q 002040          647 PDRQTVLFSATFPRQVEILARKVLNKPVEIQVGGRSVVNKDITQLVEVRPE-SDRFLRLLELLGEWYEKGKILIFVHSQE  725 (976)
Q Consensus       647 ~~~q~i~~SAT~~~~~~~l~~~~l~~~~~i~~~~~~~~~~~i~q~~~~~~~-~~k~~~l~~~l~~~~~~~kvLIF~~s~~  725 (976)
                      |++|+|+|||||+..++.+++.+|.+|+.+..+.....+..|+|.+.+++. ..|+.+|+..|..+...|++|||+....
T Consensus       400 pdrQtllFsaTf~~kIe~lard~L~dpVrvVqg~vgean~dITQ~V~V~~s~~~Kl~wl~~~L~~f~S~gkvlifVTKk~  479 (731)
T KOG0339|consen  400 PDRQTLLFSATFKKKIEKLARDILSDPVRVVQGEVGEANEDITQTVSVCPSEEKKLNWLLRHLVEFSSEGKVLIFVTKKA  479 (731)
T ss_pred             CcceEEEeeccchHHHHHHHHHHhcCCeeEEEeehhccccchhheeeeccCcHHHHHHHHHHhhhhccCCcEEEEEeccC
Confidence            999999999999999999999999999999988888889999999987765 5789999999999999999999999999


Q ss_pred             HHHHHHHHHHHCCCCceeccCCCCHHHHHHHHHHhccCCccEEEecCcccccCCCCCCcEEEEeCCCCCHHHHHHHhccc
Q 002040          726 KCDALFRDLLKHGYPCLSLHGAKDQTDRESTISDFKSNVCNLLIATSVAARGLDVKELELVINFDAPNHYEDYVHRVGRT  805 (976)
Q Consensus       726 ~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLVaT~v~~~GlDi~~v~~VI~~d~p~s~~~y~Qr~GR~  805 (976)
                      .++.++..|.-.+|.|..+||+|.|.+|..++..|+.+.+.|||||+++++||||+.+.+|||||+-.++..|.||+||+
T Consensus       480 ~~e~i~a~Lklk~~~v~llhgdkdqa~rn~~ls~fKkk~~~VlvatDvaargldI~~ikTVvnyD~ardIdththrigrt  559 (731)
T KOG0339|consen  480 DAEEIAANLKLKGFNVSLLHGDKDQAERNEVLSKFKKKRKPVLVATDVAARGLDIPSIKTVVNYDFARDIDTHTHRIGRT  559 (731)
T ss_pred             CHHHHHHHhccccceeeeecCchhhHHHHHHHHHHhhcCCceEEEeeHhhcCCCccccceeecccccchhHHHHHHhhhc
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCCccEEEEEecCCCcCchHHHHHHHhhccCCCChHHHHHHHH
Q 002040          806 GRAGRKGCAITFISEEDAKYSPDLVKALELSEQVVPDDLKALADS  850 (976)
Q Consensus       806 gR~g~~g~~~~~~~~~d~~~~~~i~~~l~~~~~~vp~~l~~l~~~  850 (976)
                      ||+|.+|.+|+|+|+.|..++..|++.|+.++|.||+.|..|+-.
T Consensus       560 gRag~kGvayTlvTeKDa~fAG~LVnnLe~agQnVP~~l~dlamk  604 (731)
T KOG0339|consen  560 GRAGEKGVAYTLVTEKDAEFAGHLVNNLEGAGQNVPDELMDLAMK  604 (731)
T ss_pred             ccccccceeeEEechhhHHHhhHHHHHHhhccccCChHHHHHHhh
Confidence            999999999999999999999999999999999999999766643

>KOG0331 consensus ATP-dependent RNA helicase [RNA processing and modification]

Probab=100.00  E-value=1.4e-75  Score=653.61  Aligned_cols=427  Identities=47%  Similarity=0.851  Sum_probs=394.6

Q ss_pred             cccCcccccccccchhhhcCCHHHHHHHHhhcCceeccCC-CCCcccccc-----------------------------c
Q 002040          422 IDYQPFRKNFYIEVKEIARMTPEEVSAYRKQLELKIHGKD-VPKPIKTWH-----------------------------Q  471 (976)
Q Consensus       422 ~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~g~~-~p~pi~~~~-----------------------------~  471 (976)
                      ..+.+|.++||.+++........+...++....+.+.+.. +|.|+.+|.                             .
T Consensus        16 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~v~~~~~~p~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~~   95 (519)
T KOG0331|consen   16 LDLSPFDKNFYKEHPSVKKRGSAEVERKRKKNEITVKGGDSVPKPVKSFEESGFPAKVLEEIPKLSRSSGESDSSAAFQE   95 (519)
T ss_pred             cccCcccccccccccccccccccccccccCcceeeccCCCCCCCCccchhcccCCccccccccccccccccCCcchhhhc
Confidence            4677899999998888877777777777777777777755 677666554                             4


Q ss_pred             CCCCHHHHHHHHHcCCCCCcHHHHHHHHHHhcCCCEEEEcCCCCchHHHHHHHHHHHHhc-CCCCCCCCCCeEEEEccCH
Q 002040          472 TGLTSKIMETIRKLNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKD-QPPVAAGDGPVGLIMAPTR  550 (976)
Q Consensus       472 ~~l~~~l~~~l~~~~~~~p~~~Q~~~i~~il~g~d~i~~a~TGsGKT~~~~l~il~~l~~-~~~~~~~~~~~vLIl~Ptr  550 (976)
                      ++|+..+...|+..||..|||||+++||.+++|+|+|++|.||||||++|++|++.|+.. ++....+.+|+||||+|||
T Consensus        96 ~~ls~~~~~~lk~~g~~~PtpIQaq~wp~~l~GrD~v~iA~TGSGKTLay~lP~i~~l~~~~~~~~~~~~P~vLVL~PTR  175 (519)
T KOG0331|consen   96 LGLSEELMKALKEQGFEKPTPIQAQGWPIALSGRDLVGIARTGSGKTLAYLLPAIVHLNNEQGKLSRGDGPIVLVLAPTR  175 (519)
T ss_pred             ccccHHHHHHHHhcCCCCCchhhhcccceeccCCceEEEeccCCcchhhhhhHHHHHHHhccccccCCCCCeEEEEcCcH
Confidence            556666777778999999999999999999999999999999999999999999999998 6777788899999999999


Q ss_pred             HHHHHHHHHHHHHHhhcCcEEEEeeCCCChHHHHHHHhcCCeEEEeCchhHHHHHHhcCCcccccCCceEEEecCccccc
Q 002040          551 ELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMF  630 (976)
Q Consensus       551 ~La~Q~~~~~~~~~~~~~~~~~~~~gg~~~~~~~~~l~~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDEah~~~  630 (976)
                      +||.|+...+..|+..++++++|+|||.+...|+..+..+++|+|+|||+|++++....   .+|++++|+||||||+|+
T Consensus       176 ELA~QV~~~~~~~~~~~~~~~~cvyGG~~~~~Q~~~l~~gvdiviaTPGRl~d~le~g~---~~l~~v~ylVLDEADrMl  252 (519)
T KOG0331|consen  176 ELAVQVQAEAREFGKSLRLRSTCVYGGAPKGPQLRDLERGVDVVIATPGRLIDLLEEGS---LNLSRVTYLVLDEADRML  252 (519)
T ss_pred             HHHHHHHHHHHHHcCCCCccEEEEeCCCCccHHHHHHhcCCcEEEeCChHHHHHHHcCC---ccccceeEEEeccHHhhh
Confidence            99999999999999999999999999999999999999999999999999999998754   789999999999999999


Q ss_pred             ccCCchHHHHHHHhc-CCCCcEEEEeccCcHHHHHHHHHHcCCCeEEEeCCcc--cccCCceEEEEecCcchHHHHHHHH
Q 002040          631 DMGFEPQITRIVQNI-RPDRQTVLFSATFPRQVEILARKVLNKPVEIQVGGRS--VVNKDITQLVEVRPESDRFLRLLEL  707 (976)
Q Consensus       631 ~~~f~~~i~~il~~~-~~~~q~i~~SAT~~~~~~~l~~~~l~~~~~i~~~~~~--~~~~~i~q~~~~~~~~~k~~~l~~~  707 (976)
                      +|||.+++..|+..+ ++.+|+|++|||||..+..++..|+.+|+.+.++...  ..+.+|.|++.++....|...|..+
T Consensus       253 dmGFe~qI~~Il~~i~~~~rQtlm~saTwp~~v~~lA~~fl~~~~~i~ig~~~~~~a~~~i~qive~~~~~~K~~~l~~l  332 (519)
T KOG0331|consen  253 DMGFEPQIRKILSQIPRPDRQTLMFSATWPKEVRQLAEDFLNNPIQINVGNKKELKANHNIRQIVEVCDETAKLRKLGKL  332 (519)
T ss_pred             ccccHHHHHHHHHhcCCCcccEEEEeeeccHHHHHHHHHHhcCceEEEecchhhhhhhcchhhhhhhcCHHHHHHHHHHH
Confidence            999999999999999 7778999999999999999999999999999988654  5677899999999999999999999


Q ss_pred             HHhhh--cCCcEEEEecCHHHHHHHHHHHHHCCCCceeccCCCCHHHHHHHHHHhccCCccEEEecCcccccCCCCCCcE
Q 002040          708 LGEWY--EKGKILIFVHSQEKCDALFRDLLKHGYPCLSLHGAKDQTDRESTISDFKSNVCNLLIATSVAARGLDVKELEL  785 (976)
Q Consensus       708 l~~~~--~~~kvLIF~~s~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLVaT~v~~~GlDi~~v~~  785 (976)
                      |..+.  ..+++||||+|+..|+.|+..|...++++.+|||+++|.+|..+++.|++|++.|||||++|+||||||+|++
T Consensus       333 L~~~~~~~~~KvIIFc~tkr~~~~l~~~l~~~~~~a~~iHGd~sQ~eR~~~L~~FreG~~~vLVATdVAaRGLDi~dV~l  412 (519)
T KOG0331|consen  333 LEDISSDSEGKVIIFCETKRTCDELARNLRRKGWPAVAIHGDKSQSERDWVLKGFREGKSPVLVATDVAARGLDVPDVDL  412 (519)
T ss_pred             HHHHhccCCCcEEEEecchhhHHHHHHHHHhcCcceeeecccccHHHHHHHHHhcccCCcceEEEcccccccCCCccccE
Confidence            99886  5679999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEEeCCCCCHHHHHHHhcccCCCCCccEEEEEecCCCcCchHHHHHHHhhccCCCChHHHHHHHHH
Q 002040          786 VINFDAPNHYEDYVHRVGRTGRAGRKGCAITFISEEDAKYSPDLVKALELSEQVVPDDLKALADSF  851 (976)
Q Consensus       786 VI~~d~p~s~~~y~Qr~GR~gR~g~~g~~~~~~~~~d~~~~~~i~~~l~~~~~~vp~~l~~l~~~~  851 (976)
                      |||||+|.+.++|+||+|||||+|++|.+++|++..+...+..+++.+....+.+|+.|..+...-
T Consensus       413 VInydfP~~vEdYVHRiGRTGRa~~~G~A~tfft~~~~~~a~~l~~~l~e~~q~v~~~l~~~~~~~  478 (519)
T KOG0331|consen  413 VINYDFPNNVEDYVHRIGRTGRAGKKGTAITFFTSDNAKLARELIKVLREAGQTVPPDLLEYARVS  478 (519)
T ss_pred             EEeCCCCCCHHHHHhhcCccccCCCCceEEEEEeHHHHHHHHHHHHHHHHccCCCChHHHHHHhhc
Confidence            999999999999999999999999999999999999999999999999999999999887776543

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

Probab=100.00  E-value=3.3e-73  Score=592.71  Aligned_cols=436  Identities=42%  Similarity=0.709  Sum_probs=402.0

Q ss_pred             cCCCcccccCcccccccccchhhhcCCHHHHHHHHhhcC-ceec------cCCCCCccccccc-CCCCHHHHHHHHHcCC
Q 002040          416 IVDHSKIDYQPFRKNFYIEVKEIARMTPEEVSAYRKQLE-LKIH------GKDVPKPIKTWHQ-TGLTSKIMETIRKLNY  487 (976)
Q Consensus       416 ~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~-i~~~------g~~~p~pi~~~~~-~~l~~~l~~~l~~~~~  487 (976)
                      ..+..|...+|..++||.+..+.+.|+..++..++++.. |.+.      ...+|+|..+|++ |...+.++..+.+.||
T Consensus       161 ~e~~kW~~lpPi~knfYke~~e~s~ls~~q~~~~r~en~~it~dd~K~gekrpIPnP~ctFddAFq~~pevmenIkK~GF  240 (629)
T KOG0336|consen  161 DEKFKWAKLPPIKKNFYKESNETSNLSKEQLQEWRKENFNITCDDLKEGEKRPIPNPVCTFDDAFQCYPEVMENIKKTGF  240 (629)
T ss_pred             hhhcccccCCchhhhhhhcCchhccCCHHHHHHHHHcCCcEEecccccCCcccCCCCcCcHHHHHhhhHHHHHHHHhccC
Confidence            345567788999999999999999999999999998655 6543      2457999999987 6778999999999999


Q ss_pred             CCCcHHHHHHHHHHhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCC-CCCCCCeEEEEccCHHHHHHHHHHHHHHHhh
Q 002040          488 EKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPV-AAGDGPVGLIMAPTRELVQQIHSDIRKFAKV  566 (976)
Q Consensus       488 ~~p~~~Q~~~i~~il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~-~~~~~~~vLIl~Ptr~La~Q~~~~~~~~~~~  566 (976)
                      .+|||||.||||.+++|.|+|++|.||+|||++|++|.+-|+..++.. ...++|.+|+++||++||.|+.-++.++. .
T Consensus       241 qKPtPIqSQaWPI~LQG~DliGVAQTgtgKtL~~L~pg~ihi~aqp~~~~qr~~p~~lvl~ptreLalqie~e~~kys-y  319 (629)
T KOG0336|consen  241 QKPTPIQSQAWPILLQGIDLIGVAQTGTGKTLAFLLPGFIHIDAQPKRREQRNGPGVLVLTPTRELALQIEGEVKKYS-Y  319 (629)
T ss_pred             CCCCcchhcccceeecCcceEEEEecCCCcCHHHhccceeeeeccchhhhccCCCceEEEeccHHHHHHHHhHHhHhh-h
Confidence            999999999999999999999999999999999999999998877543 23468999999999999999988888764 4


Q ss_pred             cCcEEEEeeCCCChHHHHHHHhcCCeEEEeCchhHHHHHHhcCCcccccCCceEEEecCcccccccCCchHHHHHHHhcC
Q 002040          567 MGVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMGFEPQITRIVQNIR  646 (976)
Q Consensus       567 ~~~~~~~~~gg~~~~~~~~~l~~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDEah~~~~~~f~~~i~~il~~~~  646 (976)
                      .|+..+|+|||.+..+++..++.+.+|+|+||++|.++...+   ..+|..++||||||||+|++|||.+++..|+-.++
T Consensus       320 ng~ksvc~ygggnR~eqie~lkrgveiiiatPgrlndL~~~n---~i~l~siTYlVlDEADrMLDMgFEpqIrkilldiR  396 (629)
T KOG0336|consen  320 NGLKSVCVYGGGNRNEQIEDLKRGVEIIIATPGRLNDLQMDN---VINLASITYLVLDEADRMLDMGFEPQIRKILLDIR  396 (629)
T ss_pred             cCcceEEEecCCCchhHHHHHhcCceEEeeCCchHhhhhhcC---eeeeeeeEEEEecchhhhhcccccHHHHHHhhhcC
Confidence            689999999999999999999999999999999999988654   47899999999999999999999999999999999


Q ss_pred             CCCcEEEEeccCcHHHHHHHHHHcCCCeEEEeCCccc-ccCCceEEEEecCcchHHHHHHHHHHhhhcCCcEEEEecCHH
Q 002040          647 PDRQTVLFSATFPRQVEILARKVLNKPVEIQVGGRSV-VNKDITQLVEVRPESDRFLRLLELLGEWYEKGKILIFVHSQE  725 (976)
Q Consensus       647 ~~~q~i~~SAT~~~~~~~l~~~~l~~~~~i~~~~~~~-~~~~i~q~~~~~~~~~k~~~l~~~l~~~~~~~kvLIF~~s~~  725 (976)
                      |++|++++|||||..+..|+..|+..|+.+.++.... ....+.|.+.+.....|+..+..++....+..++||||..+.
T Consensus       397 PDRqtvmTSATWP~~VrrLa~sY~Kep~~v~vGsLdL~a~~sVkQ~i~v~~d~~k~~~~~~f~~~ms~ndKvIiFv~~K~  476 (629)
T KOG0336|consen  397 PDRQTVMTSATWPEGVRRLAQSYLKEPMIVYVGSLDLVAVKSVKQNIIVTTDSEKLEIVQFFVANMSSNDKVIIFVSRKV  476 (629)
T ss_pred             CcceeeeecccCchHHHHHHHHhhhCceEEEecccceeeeeeeeeeEEecccHHHHHHHHHHHHhcCCCceEEEEEechh
Confidence            9999999999999999999999999999998887654 455788999888888888877777777777889999999999


Q ss_pred             HHHHHHHHHHHCCCCceeccCCCCHHHHHHHHHHhccCCccEEEecCcccccCCCCCCcEEEEeCCCCCHHHHHHHhccc
Q 002040          726 KCDALFRDLLKHGYPCLSLHGAKDQTDRESTISDFKSNVCNLLIATSVAARGLDVKELELVINFDAPNHYEDYVHRVGRT  805 (976)
Q Consensus       726 ~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLVaT~v~~~GlDi~~v~~VI~~d~p~s~~~y~Qr~GR~  805 (976)
                      .++.|...|.-.|+.+..|||+-.|.+|+..+..|++|.++|||||+++++|||++++++|+|||+|.+++.|+||+||+
T Consensus       477 ~AD~LSSd~~l~gi~~q~lHG~r~Q~DrE~al~~~ksG~vrILvaTDlaSRGlDv~DiTHV~NyDFP~nIeeYVHRvGrt  556 (629)
T KOG0336|consen  477 MADHLSSDFCLKGISSQSLHGNREQSDREMALEDFKSGEVRILVATDLASRGLDVPDITHVYNYDFPRNIEEYVHRVGRT  556 (629)
T ss_pred             hhhhccchhhhcccchhhccCChhhhhHHHHHHhhhcCceEEEEEechhhcCCCchhcceeeccCCCccHHHHHHHhccc
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCCccEEEEEecCCCcCchHHHHHHHhhccCCCChHHHHHHHHHHHHH
Q 002040          806 GRAGRKGCAITFISEEDAKYSPDLVKALELSEQVVPDDLKALADSFMAKV  855 (976)
Q Consensus       806 gR~g~~g~~~~~~~~~d~~~~~~i~~~l~~~~~~vp~~l~~l~~~~~~~~  855 (976)
                      ||+|.+|++++|++-.|...+..|++.|+.+.|.||+.|..|+..|..+.
T Consensus       557 GRaGr~G~sis~lt~~D~~~a~eLI~ILe~aeQevPdeL~~mAeryk~~q  606 (629)
T KOG0336|consen  557 GRAGRTGTSISFLTRNDWSMAEELIQILERAEQEVPDELVRMAERYKLKQ  606 (629)
T ss_pred             ccCCCCcceEEEEehhhHHHHHHHHHHHHHhhhhCcHHHHHHHHHHHhhh
Confidence            99999999999999999999999999999999999999999999998874

>KOG0333 consensus U5 snRNP-like RNA helicase subunit [RNA processing and modification]

Probab=100.00  E-value=4.1e-71  Score=595.02  Aligned_cols=407  Identities=42%  Similarity=0.727  Sum_probs=382.4

Q ss_pred             chhhhcCCHHHHHHHHhhcCceeccCCCCCcccccccCCCCHHHHHHHHHcCCCCCcHHHHHHHHHHhcCCCEEEEcCCC
Q 002040          435 VKEIARMTPEEVSAYRKQLELKIHGKDVPKPIKTWHQTGLTSKIMETIRKLNYEKPMPIQAQALPVIMSGRDCIGVAKTG  514 (976)
Q Consensus       435 ~~~~~~~~~~~~~~~~~~~~i~~~g~~~p~pi~~~~~~~l~~~l~~~l~~~~~~~p~~~Q~~~i~~il~g~d~i~~a~TG  514 (976)
                      ...+..|++..|..|+..++|.+.|..+|.|+.+|.+.+||..++..+...||..|+|||.++||..++++|+|++|+||
T Consensus       213 ~k~l~Em~~rdwri~redynis~kg~~lpnplrnwEE~~~P~e~l~~I~~~~y~eptpIqR~aipl~lQ~rD~igvaETg  292 (673)
T KOG0333|consen  213 EKVLAEMTERDWRIFREDYNISIKGGRLPNPLRNWEESGFPLELLSVIKKPGYKEPTPIQRQAIPLGLQNRDPIGVAETG  292 (673)
T ss_pred             hhhHHhcCCccceeeecceeeeecCCCCCccccChhhcCCCHHHHHHHHhcCCCCCchHHHhhccchhccCCeeeEEecc
Confidence            34567889999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CchHHHHHHHHHHHHhcCCCCCC----CCCCeEEEEccCHHHHHHHHHHHHHHHhhcCcEEEEeeCCCChHHHHHHHhcC
Q 002040          515 SGKTLAFVLPMLRHIKDQPPVAA----GDGPVGLIMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQISELKRG  590 (976)
Q Consensus       515 sGKT~~~~l~il~~l~~~~~~~~----~~~~~vLIl~Ptr~La~Q~~~~~~~~~~~~~~~~~~~~gg~~~~~~~~~l~~~  590 (976)
                      ||||++|++|++..|...|+...    ..||.++||+|||+||.|+..+-.+|++.+|++++.++||.+..++--.+..|
T Consensus       293 sGktaaf~ipLl~~IsslP~~~~~en~~~gpyaiilaptReLaqqIeeEt~kf~~~lg~r~vsvigg~s~EEq~fqls~g  372 (673)
T KOG0333|consen  293 SGKTAAFLIPLLIWISSLPPMARLENNIEGPYAIILAPTRELAQQIEEETNKFGKPLGIRTVSVIGGLSFEEQGFQLSMG  372 (673)
T ss_pred             CCccccchhhHHHHHHcCCCcchhhhcccCceeeeechHHHHHHHHHHHHHHhcccccceEEEEecccchhhhhhhhhcc
Confidence            99999999999999998876543    35899999999999999999999999999999999999999999998899999


Q ss_pred             CeEEEeCchhHHHHHHhcCCcccccCCceEEEecCcccccccCCchHHHHHHHhcCCC----------------------
Q 002040          591 TEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMGFEPQITRIVQNIRPD----------------------  648 (976)
Q Consensus       591 ~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDEah~~~~~~f~~~i~~il~~~~~~----------------------  648 (976)
                      |+|+|+|||+|++.|.+.   .+-|..+.|||+|||++|++|||.+++..||.+++..                      
T Consensus       373 ceiviatPgrLid~Lenr---~lvl~qctyvvldeadrmiDmgfE~dv~~iL~~mPssn~k~~tde~~~~~~~~~~~~~~  449 (673)
T KOG0333|consen  373 CEIVIATPGRLIDSLENR---YLVLNQCTYVVLDEADRMIDMGFEPDVQKILEQMPSSNAKPDTDEKEGEERVRKNFSSS  449 (673)
T ss_pred             ceeeecCchHHHHHHHHH---HHHhccCceEeccchhhhhcccccHHHHHHHHhCCccccCCCccchhhHHHHHhhcccc
Confidence            999999999999999774   3678899999999999999999999999999887531                      


Q ss_pred             ---CcEEEEeccCcHHHHHHHHHHcCCCeEEEeCCcccccCCceEEEEecCcchHHHHHHHHHHhhhcCCcEEEEecCHH
Q 002040          649 ---RQTVLFSATFPRQVEILARKVLNKPVEIQVGGRSVVNKDITQLVEVRPESDRFLRLLELLGEWYEKGKILIFVHSQE  725 (976)
Q Consensus       649 ---~q~i~~SAT~~~~~~~l~~~~l~~~~~i~~~~~~~~~~~i~q~~~~~~~~~k~~~l~~~l~~~~~~~kvLIF~~s~~  725 (976)
                         +|+++||||+|+.+..++..||..|+.++++..+.+...+.|.+.....+.++..|.++|... ...++|||+|+++
T Consensus       450 k~yrqT~mftatm~p~verlar~ylr~pv~vtig~~gk~~~rveQ~v~m~~ed~k~kkL~eil~~~-~~ppiIIFvN~kk  528 (673)
T KOG0333|consen  450 KKYRQTVMFTATMPPAVERLARSYLRRPVVVTIGSAGKPTPRVEQKVEMVSEDEKRKKLIEILESN-FDPPIIIFVNTKK  528 (673)
T ss_pred             cceeEEEEEecCCChHHHHHHHHHhhCCeEEEeccCCCCccchheEEEEecchHHHHHHHHHHHhC-CCCCEEEEEechh
Confidence               799999999999999999999999999999999999999999999999999999999999876 4569999999999


Q ss_pred             HHHHHHHHHHHCCCCceeccCCCCHHHHHHHHHHhccCCccEEEecCcccccCCCCCCcEEEEeCCCCCHHHHHHHhccc
Q 002040          726 KCDALFRDLLKHGYPCLSLHGAKDQTDRESTISDFKSNVCNLLIATSVAARGLDVKELELVINFDAPNHYEDYVHRVGRT  805 (976)
Q Consensus       726 ~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLVaT~v~~~GlDi~~v~~VI~~d~p~s~~~y~Qr~GR~  805 (976)
                      .|+.|++.|.+.||.|..|||+.++++|+.++..|++|...|||||+++++|||||+|.+|||||++.++.+|+||||||
T Consensus       529 ~~d~lAk~LeK~g~~~~tlHg~k~qeQRe~aL~~fr~~t~dIlVaTDvAgRGIDIpnVSlVinydmaksieDYtHRIGRT  608 (673)
T KOG0333|consen  529 GADALAKILEKAGYKVTTLHGGKSQEQRENALADFREGTGDILVATDVAGRGIDIPNVSLVINYDMAKSIEDYTHRIGRT  608 (673)
T ss_pred             hHHHHHHHHhhccceEEEeeCCccHHHHHHHHHHHHhcCCCEEEEecccccCCCCCccceeeecchhhhHHHHHHHhccc
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCCccEEEEEecCCCcCchHHHHHHHh-hccCCCChHHH
Q 002040          806 GRAGRKGCAITFISEEDAKYSPDLVKALE-LSEQVVPDDLK  845 (976)
Q Consensus       806 gR~g~~g~~~~~~~~~d~~~~~~i~~~l~-~~~~~vp~~l~  845 (976)
                      ||+|+.|++++|+++.+...+++|...|- ......|+.|.
T Consensus       609 gRAGk~GtaiSflt~~dt~v~ydLkq~l~es~~s~~P~Ela  649 (673)
T KOG0333|consen  609 GRAGKSGTAISFLTPADTAVFYDLKQALRESVKSHCPPELA  649 (673)
T ss_pred             cccccCceeEEEeccchhHHHHHHHHHHHHhhhccCChhhc
Confidence            99999999999999999999999998876 44556676654

>KOG0341 consensus DEAD-box protein abstrakt [RNA processing and modification]

Probab=100.00  E-value=1.6e-72  Score=583.86  Aligned_cols=452  Identities=39%  Similarity=0.667  Sum_probs=413.1

Q ss_pred             cccCcccccccccchhhhcCCHHHHHHHHhhcCceeccCCCCCcccccccCCCCHHHHHHHHHcCCCCCcHHHHHHHHHH
Q 002040          422 IDYQPFRKNFYIEVKEIARMTPEEVSAYRKQLELKIHGKDVPKPIKTWHQTGLTSKIMETIRKLNYEKPMPIQAQALPVI  501 (976)
Q Consensus       422 ~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~g~~~p~pi~~~~~~~l~~~l~~~l~~~~~~~p~~~Q~~~i~~i  501 (976)
                      +.|..--+..|.++--+..|+.++.+..++.|.|.+.|..+|+||.+|.++.++..++..|++.|+..|||||.|.||.+
T Consensus       125 i~Y~ePi~T~WkPP~hir~mS~e~~e~vRk~~~I~veGd~ipPPIksF~eMKFP~~~L~~lk~KGI~~PTpIQvQGlPvv  204 (610)
T KOG0341|consen  125 ITYEEPIKTAWKPPRHIRKMSEEQRELVRKQLHILVEGDDIPPPIKSFKEMKFPKPLLRGLKKKGIVHPTPIQVQGLPVV  204 (610)
T ss_pred             CcccCcchhccCCcHHHHHhhHHHHHHHHHhheEEeeCCCCCCchhhhhhccCCHHHHHHHHhcCCCCCCceeecCcceE
Confidence            45655556678888889999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hcCCCEEEEcCCCCchHHHHHHHHHHHHhcC---CCCCCCCCCeEEEEccCHHHHHHHHHHHHHHHhhc------CcEEE
Q 002040          502 MSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQ---PPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVM------GVRCV  572 (976)
Q Consensus       502 l~g~d~i~~a~TGsGKT~~~~l~il~~l~~~---~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~~~~~~------~~~~~  572 (976)
                      ++|+|+|++|-||||||++|.+|++...+.+   -++..+.||..|||||+|+||.|++..+..|+..+      .+++.
T Consensus       205 LsGRDmIGIAfTGSGKTlvFvLP~imf~LeqE~~lPf~~~EGP~gLiicPSRELArQt~~iie~~~~~L~e~g~P~lRs~  284 (610)
T KOG0341|consen  205 LSGRDMIGIAFTGSGKTLVFVLPVIMFALEQEMMLPFARGEGPYGLIICPSRELARQTHDIIEQYVAALQEAGYPELRSL  284 (610)
T ss_pred             eecCceeeEEeecCCceEEEeHHHHHHHHHHHhcCccccCCCCeeEEEcCcHHHHHHHHHHHHHHHHHHHhcCChhhhhh
Confidence            9999999999999999999999998877654   35667889999999999999999999999887654      36788


Q ss_pred             EeeCCCChHHHHHHHhcCCeEEEeCchhHHHHHHhcCCcccccCCceEEEecCcccccccCCchHHHHHHHhcCCCCcEE
Q 002040          573 PVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMGFEPQITRIVQNIRPDRQTV  652 (976)
Q Consensus       573 ~~~gg~~~~~~~~~l~~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDEah~~~~~~f~~~i~~il~~~~~~~q~i  652 (976)
                      ++.||.+..++...++.|.+|+|+|||+|.++|..   +..+|.-+.|+++||||+|+++||...+..|+.++...+|++
T Consensus       285 LciGG~~v~eql~~v~~GvHivVATPGRL~DmL~K---K~~sLd~CRyL~lDEADRmiDmGFEddir~iF~~FK~QRQTL  361 (610)
T KOG0341|consen  285 LCIGGVPVREQLDVVRRGVHIVVATPGRLMDMLAK---KIMSLDACRYLTLDEADRMIDMGFEDDIRTIFSFFKGQRQTL  361 (610)
T ss_pred             hhhcCccHHHHHHHHhcCeeEEEcCcchHHHHHHH---hhccHHHHHHhhhhhHHHHhhccchhhHHHHHHHHhhhhhee
Confidence            89999999999999999999999999999999976   457888899999999999999999999999999999999999


Q ss_pred             EEeccCcHHHHHHHHHHcCCCeEEEeCCcccccCCceEEEEecCcchHHHHHHHHHHhhhcCCcEEEEecCHHHHHHHHH
Q 002040          653 LFSATFPRQVEILARKVLNKPVEIQVGGRSVVNKDITQLVEVRPESDRFLRLLELLGEWYEKGKILIFVHSQEKCDALFR  732 (976)
Q Consensus       653 ~~SAT~~~~~~~l~~~~l~~~~~i~~~~~~~~~~~i~q~~~~~~~~~k~~~l~~~l~~~~~~~kvLIF~~s~~~~~~l~~  732 (976)
                      +||||||..+..++...+-.|+.++++..+..+.++.|.+.++....|+.+|++.|++.  ..++||||..+.+++.+..
T Consensus       362 LFSATMP~KIQ~FAkSALVKPvtvNVGRAGAAsldViQevEyVkqEaKiVylLeCLQKT--~PpVLIFaEkK~DVD~IhE  439 (610)
T KOG0341|consen  362 LFSATMPKKIQNFAKSALVKPVTVNVGRAGAASLDVIQEVEYVKQEAKIVYLLECLQKT--SPPVLIFAEKKADVDDIHE  439 (610)
T ss_pred             eeeccccHHHHHHHHhhcccceEEecccccccchhHHHHHHHHHhhhhhhhHHHHhccC--CCceEEEeccccChHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999875  5689999999999999999


Q ss_pred             HHHHCCCCceeccCCCCHHHHHHHHHHhccCCccEEEecCcccccCCCCCCcEEEEeCCCCCHHHHHHHhcccCCCCCcc
Q 002040          733 DLLKHGYPCLSLHGAKDQTDRESTISDFKSNVCNLLIATSVAARGLDVKELELVINFDAPNHYEDYVHRVGRTGRAGRKG  812 (976)
Q Consensus       733 ~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLVaT~v~~~GlDi~~v~~VI~~d~p~s~~~y~Qr~GR~gR~g~~g  812 (976)
                      ||.-.|+.++.|||+.+|++|...+..|+.|+.+|||||++++.|||+|++.+|||||+|..+++|+|||||+||.|++|
T Consensus       440 YLLlKGVEavaIHGGKDQedR~~ai~afr~gkKDVLVATDVASKGLDFp~iqHVINyDMP~eIENYVHRIGRTGRsg~~G  519 (610)
T KOG0341|consen  440 YLLLKGVEAVAIHGGKDQEDRHYAIEAFRAGKKDVLVATDVASKGLDFPDIQHVINYDMPEEIENYVHRIGRTGRSGKTG  519 (610)
T ss_pred             HHHHccceeEEeecCcchhHHHHHHHHHhcCCCceEEEecchhccCCCccchhhccCCChHHHHHHHHHhcccCCCCCcc
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEEEEecCC-CcCchHHHHHHHhhccCCCChHHHHHHHHHHHHHhhhhhhccCCCC-CCCCcccchhH
Q 002040          813 CAITFISEE-DAKYSPDLVKALELSEQVVPDDLKALADSFMAKVNQGLEQAHGTGY-GGSGFKFNEEE  878 (976)
Q Consensus       813 ~~~~~~~~~-d~~~~~~i~~~l~~~~~~vp~~l~~l~~~~~~~~~~~~~~~~~~~~-~g~g~~~~~~~  878 (976)
                      .+.+|+... +...+.+|...|....|.+|+.|..|+...-..--.+.....|+.| ||-|+.+.++.
T Consensus       520 iATTfINK~~~esvLlDLK~LL~EakQ~vP~~L~~L~~~~E~~~~a~~~~~kGCayCgGLGHRItdCP  587 (610)
T KOG0341|consen  520 IATTFINKNQEESVLLDLKHLLQEAKQEVPPVLAELAGPMEEETIADAGGEKGCAYCGGLGHRITDCP  587 (610)
T ss_pred             eeeeeecccchHHHHHHHHHHHHHhhccCCHHHHHhCCCccccccccCCCccccccccCCCcccccCc
Confidence            999999975 5567778888889999999999988876544322223444456665 66799998774

>PTZ00110 helicase; Provisional

Probab=100.00  E-value=3e-69  Score=637.91  Aligned_cols=436  Identities=46%  Similarity=0.785  Sum_probs=404.1

Q ss_pred             cCCcCCCcccccCcccccccccchhhhcCCHHHHHHHHhhcCcee-ccCCCCCcccccccCCCCHHHHHHHHHcCCCCCc
Q 002040          413 KLSIVDHSKIDYQPFRKNFYIEVKEIARMTPEEVSAYRKQLELKI-HGKDVPKPIKTWHQTGLTSKIMETIRKLNYEKPM  491 (976)
Q Consensus       413 ~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~-~g~~~p~pi~~~~~~~l~~~l~~~l~~~~~~~p~  491 (976)
                      .+..++|....+.||.++||.+++.+..++..++..++....+.+ .|..+|+|+.+|.+++|++.+++.|..+||..||
T Consensus        75 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~g~~~p~p~~~f~~~~l~~~l~~~l~~~g~~~pt  154 (545)
T PTZ00110         75 RLQPIDWKSINLVPFEKNFYKEHPEVSALSSKEVDEIRKEKEITIIAGENVPKPVVSFEYTSFPDYILKSLKNAGFTEPT  154 (545)
T ss_pred             ccCCCCCccccccchhhhcccCChhhhcCCHHHHHHHHHhcCcEEecCCCCCcccCCHhhcCCCHHHHHHHHHCCCCCCC
Confidence            456788888889999999999999999999999999999988875 7999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHHHHhhcCcEE
Q 002040          492 PIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVMGVRC  571 (976)
Q Consensus       492 ~~Q~~~i~~il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~~~~~~~~~~  571 (976)
                      |+|.++||.+++|+|+|++|+||||||++|++|++.++..++....+.+|.+|||+||++||.|++..+..|+...++.+
T Consensus       155 ~iQ~~aip~~l~G~dvI~~ApTGSGKTlaylLP~l~~i~~~~~~~~~~gp~~LIL~PTreLa~Qi~~~~~~~~~~~~i~~  234 (545)
T PTZ00110        155 PIQVQGWPIALSGRDMIGIAETGSGKTLAFLLPAIVHINAQPLLRYGDGPIVLVLAPTRELAEQIREQCNKFGASSKIRN  234 (545)
T ss_pred             HHHHHHHHHHhcCCCEEEEeCCCChHHHHHHHHHHHHHHhcccccCCCCcEEEEECChHHHHHHHHHHHHHHhcccCccE
Confidence            99999999999999999999999999999999999999877655566789999999999999999999999999899999


Q ss_pred             EEeeCCCChHHHHHHHhcCCeEEEeCchhHHHHHHhcCCcccccCCceEEEecCcccccccCCchHHHHHHHhcCCCCcE
Q 002040          572 VPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMGFEPQITRIVQNIRPDRQT  651 (976)
Q Consensus       572 ~~~~gg~~~~~~~~~l~~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDEah~~~~~~f~~~i~~il~~~~~~~q~  651 (976)
                      .+++||.....+...+..+++|||+||++|++++...   ..+|.++.+|||||||+|++++|.+++..|+..+++++|+
T Consensus       235 ~~~~gg~~~~~q~~~l~~~~~IlVaTPgrL~d~l~~~---~~~l~~v~~lViDEAd~mld~gf~~~i~~il~~~~~~~q~  311 (545)
T PTZ00110        235 TVAYGGVPKRGQIYALRRGVEILIACPGRLIDFLESN---VTNLRRVTYLVLDEADRMLDMGFEPQIRKIVSQIRPDRQT  311 (545)
T ss_pred             EEEeCCCCHHHHHHHHHcCCCEEEECHHHHHHHHHcC---CCChhhCcEEEeehHHhhhhcchHHHHHHHHHhCCCCCeE
Confidence            9999999999998889999999999999999999754   3578899999999999999999999999999999999999


Q ss_pred             EEEeccCcHHHHHHHHHHcC-CCeEEEeCCcc-cccCCceEEEEecCcchHHHHHHHHHHhhh-cCCcEEEEecCHHHHH
Q 002040          652 VLFSATFPRQVEILARKVLN-KPVEIQVGGRS-VVNKDITQLVEVRPESDRFLRLLELLGEWY-EKGKILIFVHSQEKCD  728 (976)
Q Consensus       652 i~~SAT~~~~~~~l~~~~l~-~~~~i~~~~~~-~~~~~i~q~~~~~~~~~k~~~l~~~l~~~~-~~~kvLIF~~s~~~~~  728 (976)
                      |+||||+|..+..++..++. .++.+.++... .....+.+.+.+.....|...|..+|.... ...++||||+++..|+
T Consensus       312 l~~SAT~p~~v~~l~~~l~~~~~v~i~vg~~~l~~~~~i~q~~~~~~~~~k~~~L~~ll~~~~~~~~k~LIF~~t~~~a~  391 (545)
T PTZ00110        312 LMWSATWPKEVQSLARDLCKEEPVHVNVGSLDLTACHNIKQEVFVVEEHEKRGKLKMLLQRIMRDGDKILIFVETKKGAD  391 (545)
T ss_pred             EEEEeCCCHHHHHHHHHHhccCCEEEEECCCccccCCCeeEEEEEEechhHHHHHHHHHHHhcccCCeEEEEecChHHHH
Confidence            99999999999999998886 57777776543 334567788888888888888888887765 5679999999999999


Q ss_pred             HHHHHHHHCCCCceeccCCCCHHHHHHHHHHhccCCccEEEecCcccccCCCCCCcEEEEeCCCCCHHHHHHHhcccCCC
Q 002040          729 ALFRDLLKHGYPCLSLHGAKDQTDRESTISDFKSNVCNLLIATSVAARGLDVKELELVINFDAPNHYEDYVHRVGRTGRA  808 (976)
Q Consensus       729 ~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLVaT~v~~~GlDi~~v~~VI~~d~p~s~~~y~Qr~GR~gR~  808 (976)
                      .|+..|...++.+..+||++++.+|..+++.|++|.+.|||||+++++|||||+|++||+||+|.++..|+||+||+||+
T Consensus       392 ~l~~~L~~~g~~~~~ihg~~~~~eR~~il~~F~~G~~~ILVaTdv~~rGIDi~~v~~VI~~d~P~s~~~yvqRiGRtGR~  471 (545)
T PTZ00110        392 FLTKELRLDGWPALCIHGDKKQEERTWVLNEFKTGKSPIMIATDVASRGLDVKDVKYVINFDFPNQIEDYVHRIGRTGRA  471 (545)
T ss_pred             HHHHHHHHcCCcEEEEECCCcHHHHHHHHHHHhcCCCcEEEEcchhhcCCCcccCCEEEEeCCCCCHHHHHHHhcccccC
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCccEEEEEecCCCcCchHHHHHHHhhccCCCChHHHHHHHHH
Q 002040          809 GRKGCAITFISEEDAKYSPDLVKALELSEQVVPDDLKALADSF  851 (976)
Q Consensus       809 g~~g~~~~~~~~~d~~~~~~i~~~l~~~~~~vp~~l~~l~~~~  851 (976)
                      |..|.|++|+++.+...+..|++.|..+.+.+|++|..|+...
T Consensus       472 G~~G~ai~~~~~~~~~~~~~l~~~l~~~~q~vp~~l~~~~~~~  514 (545)
T PTZ00110        472 GAKGASYTFLTPDKYRLARDLVKVLREAKQPVPPELEKLSNER  514 (545)
T ss_pred             CCCceEEEEECcchHHHHHHHHHHHHHccCCCCHHHHHHHHHh
Confidence            9999999999999999999999999999999999999887654

>KOG0330 consensus ATP-dependent RNA helicase [RNA processing and modification]

Probab=100.00  E-value=6e-68  Score=553.17  Aligned_cols=365  Identities=36%  Similarity=0.616  Sum_probs=346.8

Q ss_pred             cccccccCCCCHHHHHHHHHcCCCCCcHHHHHHHHHHhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEE
Q 002040          465 PIKTWHQTGLTSKIMETIRKLNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGL  544 (976)
Q Consensus       465 pi~~~~~~~l~~~l~~~l~~~~~~~p~~~Q~~~i~~il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vL  544 (976)
                      ...+|.++++.+.+++++...+|..||++|.++||.++.|+|||+.|+||||||.+|++|++++|+..+.     .+.+|
T Consensus        59 ~~~sf~dLgv~~~L~~ac~~l~~~~PT~IQ~~aiP~~L~g~dvIglAeTGSGKT~afaLPIl~~LL~~p~-----~~~~l  133 (476)
T KOG0330|consen   59 SFKSFADLGVHPELLEACQELGWKKPTKIQSEAIPVALGGRDVIGLAETGSGKTGAFALPILQRLLQEPK-----LFFAL  133 (476)
T ss_pred             hhcchhhcCcCHHHHHHHHHhCcCCCchhhhhhcchhhCCCcEEEEeccCCCchhhhHHHHHHHHHcCCC-----CceEE
Confidence            3468999999999999999999999999999999999999999999999999999999999999998753     48899


Q ss_pred             EEccCHHHHHHHHHHHHHHHhhcCcEEEEeeCCCChHHHHHHHhcCCeEEEeCchhHHHHHHhcCCcccccCCceEEEec
Q 002040          545 IMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMD  624 (976)
Q Consensus       545 Il~Ptr~La~Q~~~~~~~~~~~~~~~~~~~~gg~~~~~~~~~l~~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlD  624 (976)
                      ||+|||+||.||...|..+...+|+.+.+++||.+...+...+.+.++|||||||+|.+++.+.  +.++|..+.|+|+|
T Consensus       134 VLtPtRELA~QI~e~fe~Lg~~iglr~~~lvGG~~m~~q~~~L~kkPhilVaTPGrL~dhl~~T--kgf~le~lk~LVlD  211 (476)
T KOG0330|consen  134 VLTPTRELAQQIAEQFEALGSGIGLRVAVLVGGMDMMLQANQLSKKPHILVATPGRLWDHLENT--KGFSLEQLKFLVLD  211 (476)
T ss_pred             EecCcHHHHHHHHHHHHHhccccCeEEEEEecCchHHHHHHHhhcCCCEEEeCcHHHHHHHHhc--cCccHHHhHHHhhc
Confidence            9999999999999999999999999999999999999999999999999999999999999865  34788999999999


Q ss_pred             CcccccccCCchHHHHHHHhcCCCCcEEEEeccCcHHHHHHHHHHcCCCeEEEeCCcccccCCceEEEEecCcchHHHHH
Q 002040          625 EADRMFDMGFEPQITRIVQNIRPDRQTVLFSATFPRQVEILARKVLNKPVEIQVGGRSVVNKDITQLVEVRPESDRFLRL  704 (976)
Q Consensus       625 Eah~~~~~~f~~~i~~il~~~~~~~q~i~~SAT~~~~~~~l~~~~l~~~~~i~~~~~~~~~~~i~q~~~~~~~~~k~~~l  704 (976)
                      |||++++++|.+.+..|+..++..+|+++||||||..+..+....+.+|+.+.+.........+.|.|.+.+...|..+|
T Consensus       212 EADrlLd~dF~~~ld~ILk~ip~erqt~LfsATMt~kv~kL~rasl~~p~~v~~s~ky~tv~~lkQ~ylfv~~k~K~~yL  291 (476)
T KOG0330|consen  212 EADRLLDMDFEEELDYILKVIPRERQTFLFSATMTKKVRKLQRASLDNPVKVAVSSKYQTVDHLKQTYLFVPGKDKDTYL  291 (476)
T ss_pred             hHHhhhhhhhHHHHHHHHHhcCccceEEEEEeecchhhHHHHhhccCCCeEEeccchhcchHHhhhheEeccccccchhH
Confidence            99999999999999999999999999999999999999999999999999999888888888999999999999999999


Q ss_pred             HHHHHhhhcCCcEEEEecCHHHHHHHHHHHHHCCCCceeccCCCCHHHHHHHHHHhccCCccEEEecCcccccCCCCCCc
Q 002040          705 LELLGEWYEKGKILIFVHSQEKCDALFRDLLKHGYPCLSLHGAKDQTDRESTISDFKSNVCNLLIATSVAARGLDVKELE  784 (976)
Q Consensus       705 ~~~l~~~~~~~kvLIF~~s~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLVaT~v~~~GlDi~~v~  784 (976)
                      +.+|... .++.+||||++...+..++-.|...|+.+..+||.|++..|.-+++.|++|.+.|||||++++||||||.|+
T Consensus       292 V~ll~e~-~g~s~iVF~~t~~tt~~la~~L~~lg~~a~~LhGqmsq~~Rlg~l~~Fk~~~r~iLv~TDVaSRGLDip~Vd  370 (476)
T KOG0330|consen  292 VYLLNEL-AGNSVIVFCNTCNTTRFLALLLRNLGFQAIPLHGQMSQSKRLGALNKFKAGARSILVCTDVASRGLDIPHVD  370 (476)
T ss_pred             HHHHHhh-cCCcEEEEEeccchHHHHHHHHHhcCcceecccchhhHHHHHHHHHHHhccCCcEEEecchhcccCCCCCce
Confidence            9999875 458999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEEEeCCCCCHHHHHHHhcccCCCCCccEEEEEecCCCcCchHHHHHHHhhcc
Q 002040          785 LVINFDAPNHYEDYVHRVGRTGRAGRKGCAITFISEEDAKYSPDLVKALELSE  837 (976)
Q Consensus       785 ~VI~~d~p~s~~~y~Qr~GR~gR~g~~g~~~~~~~~~d~~~~~~i~~~l~~~~  837 (976)
                      +|||||+|.+..+|+||+||+||+|..|.+++|++..|...+..|...+....
T Consensus       371 ~VVNyDiP~~skDYIHRvGRtaRaGrsG~~ItlVtqyDve~~qrIE~~~gkkl  423 (476)
T KOG0330|consen  371 VVVNYDIPTHSKDYIHRVGRTARAGRSGKAITLVTQYDVELVQRIEHALGKKL  423 (476)
T ss_pred             EEEecCCCCcHHHHHHHcccccccCCCcceEEEEehhhhHHHHHHHHHHhcCC
Confidence            99999999999999999999999999999999999999888888888876554

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

Probab=100.00  E-value=9.3e-65  Score=598.33  Aligned_cols=433  Identities=31%  Similarity=0.539  Sum_probs=393.4

Q ss_pred             ccCCcCCCccccc-Ccccccccccchhhhc-CCHHHHHHHHhhcCceeccCCCCCcccccccCCCCHHHHHHHHHcCCCC
Q 002040          412 EKLSIVDHSKIDY-QPFRKNFYIEVKEIAR-MTPEEVSAYRKQLELKIHGKDVPKPIKTWHQTGLTSKIMETIRKLNYEK  489 (976)
Q Consensus       412 ~~~~~~~~~~~~~-~~f~~~~~~~~~~~~~-~~~~~~~~~~~~~~i~~~g~~~p~pi~~~~~~~l~~~l~~~l~~~~~~~  489 (976)
                      .....++|+...+ .+|.++||...+.... ++..++..+++.++|.+.|..+|.|+.+|.+++|++.+++.|...||..
T Consensus        64 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~i~~~g~~~p~pi~~f~~~~l~~~l~~~L~~~g~~~  143 (518)
T PLN00206         64 KSRVAVGAPKPKRLPATDECFYVRDPGSTSGLSSSQAELLRRKLEIHVKGEAVPPPILSFSSCGLPPKLLLNLETAGYEF  143 (518)
T ss_pred             hccCCcCCCchhhcCCcCCcCCccCcchhccCCHHHHHHHHHHCCCEecCCCCCchhcCHHhCCCCHHHHHHHHHcCCCC
Confidence            3456678876665 7789999998887755 9999999999999999999999999999999999999999999999999


Q ss_pred             CcHHHHHHHHHHhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCC--CCCCCCCeEEEEccCHHHHHHHHHHHHHHHhhc
Q 002040          490 PMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPP--VAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVM  567 (976)
Q Consensus       490 p~~~Q~~~i~~il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~--~~~~~~~~vLIl~Ptr~La~Q~~~~~~~~~~~~  567 (976)
                      |||+|.++||.+++|+|+|++|+||||||++|++|++.++.....  .....++++|||+||++||.|++..+..++..+
T Consensus       144 ptpiQ~~aip~il~g~dviv~ApTGSGKTlayllPil~~l~~~~~~~~~~~~~~~aLIL~PTreLa~Qi~~~~~~l~~~~  223 (518)
T PLN00206        144 PTPIQMQAIPAALSGRSLLVSADTGSGKTASFLVPIISRCCTIRSGHPSEQRNPLAMVLTPTRELCVQVEDQAKVLGKGL  223 (518)
T ss_pred             CCHHHHHHHHHHhcCCCEEEEecCCCCccHHHHHHHHHHHHhhccccccccCCceEEEEeCCHHHHHHHHHHHHHHhCCC
Confidence            999999999999999999999999999999999999998865321  122367899999999999999999999999888


Q ss_pred             CcEEEEeeCCCChHHHHHHHhcCCeEEEeCchhHHHHHHhcCCcccccCCceEEEecCcccccccCCchHHHHHHHhcCC
Q 002040          568 GVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMGFEPQITRIVQNIRP  647 (976)
Q Consensus       568 ~~~~~~~~gg~~~~~~~~~l~~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDEah~~~~~~f~~~i~~il~~~~~  647 (976)
                      ++.+++++||.....++..+..+++|||+||++|++++...   ...+.++.+|||||||+|++++|..++..++..+ +
T Consensus       224 ~~~~~~~~gG~~~~~q~~~l~~~~~IiV~TPgrL~~~l~~~---~~~l~~v~~lViDEad~ml~~gf~~~i~~i~~~l-~  299 (518)
T PLN00206        224 PFKTALVVGGDAMPQQLYRIQQGVELIVGTPGRLIDLLSKH---DIELDNVSVLVLDEVDCMLERGFRDQVMQIFQAL-S  299 (518)
T ss_pred             CceEEEEECCcchHHHHHHhcCCCCEEEECHHHHHHHHHcC---CccchheeEEEeecHHHHhhcchHHHHHHHHHhC-C
Confidence            99999999999999988888889999999999999998764   3578899999999999999999999999999888 5


Q ss_pred             CCcEEEEeccCcHHHHHHHHHHcCCCeEEEeCCcccccCCceEEEEecCcchHHHHHHHHHHhhhc-CCcEEEEecCHHH
Q 002040          648 DRQTVLFSATFPRQVEILARKVLNKPVEIQVGGRSVVNKDITQLVEVRPESDRFLRLLELLGEWYE-KGKILIFVHSQEK  726 (976)
Q Consensus       648 ~~q~i~~SAT~~~~~~~l~~~~l~~~~~i~~~~~~~~~~~i~q~~~~~~~~~k~~~l~~~l~~~~~-~~kvLIF~~s~~~  726 (976)
                      ..|+|+||||+++.+..++..++.+++.+.++........+.+.+.+.....+...|..+|..... .+++||||+++..
T Consensus       300 ~~q~l~~SATl~~~v~~l~~~~~~~~~~i~~~~~~~~~~~v~q~~~~~~~~~k~~~l~~~l~~~~~~~~~~iVFv~s~~~  379 (518)
T PLN00206        300 QPQVLLFSATVSPEVEKFASSLAKDIILISIGNPNRPNKAVKQLAIWVETKQKKQKLFDILKSKQHFKPPAVVFVSSRLG  379 (518)
T ss_pred             CCcEEEEEeeCCHHHHHHHHHhCCCCEEEEeCCCCCCCcceeEEEEeccchhHHHHHHHHHHhhcccCCCEEEEcCCchh
Confidence            689999999999999999999999999988887777777788888888877888888888765432 3589999999999


Q ss_pred             HHHHHHHHHH-CCCCceeccCCCCHHHHHHHHHHhccCCccEEEecCcccccCCCCCCcEEEEeCCCCCHHHHHHHhccc
Q 002040          727 CDALFRDLLK-HGYPCLSLHGAKDQTDRESTISDFKSNVCNLLIATSVAARGLDVKELELVINFDAPNHYEDYVHRVGRT  805 (976)
Q Consensus       727 ~~~l~~~L~~-~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLVaT~v~~~GlDi~~v~~VI~~d~p~s~~~y~Qr~GR~  805 (976)
                      ++.|+..|.. .++.+..+||+|++.+|..+++.|++|.++|||||+++++|||||++++||+||+|.++..|+||+|||
T Consensus       380 a~~l~~~L~~~~g~~~~~~Hg~~~~~eR~~il~~Fr~G~~~ILVaTdvl~rGiDip~v~~VI~~d~P~s~~~yihRiGRa  459 (518)
T PLN00206        380 ADLLANAITVVTGLKALSIHGEKSMKERREVMKSFLVGEVPVIVATGVLGRGVDLLRVRQVIIFDMPNTIKEYIHQIGRA  459 (518)
T ss_pred             HHHHHHHHhhccCcceEEeeCCCCHHHHHHHHHHHHCCCCCEEEEecHhhccCCcccCCEEEEeCCCCCHHHHHHhcccc
Confidence            9999999975 589999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCCccEEEEEecCCCcCchHHHHHHHhhccCCCChHHHHHH
Q 002040          806 GRAGRKGCAITFISEEDAKYSPDLVKALELSEQVVPDDLKALA  848 (976)
Q Consensus       806 gR~g~~g~~~~~~~~~d~~~~~~i~~~l~~~~~~vp~~l~~l~  848 (976)
                      ||.|..|.|++|+++.+...+..|++.|..+++.+|++|..+.
T Consensus       460 GR~g~~G~ai~f~~~~~~~~~~~l~~~l~~~~~~vp~~l~~~~  502 (518)
T PLN00206        460 SRMGEKGTAIVFVNEEDRNLFPELVALLKSSGAAIPRELANSR  502 (518)
T ss_pred             ccCCCCeEEEEEEchhHHHHHHHHHHHHHHcCCCCCHHHHhCh
Confidence            9999999999999999999999999999999999999887644

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

Probab=100.00  E-value=1.3e-62  Score=575.72  Aligned_cols=363  Identities=44%  Similarity=0.740  Sum_probs=336.3

Q ss_pred             cccccCCCCHHHHHHHHHcCCCCCcHHHHHHHHHHhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEE
Q 002040          467 KTWHQTGLTSKIMETIRKLNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIM  546 (976)
Q Consensus       467 ~~~~~~~l~~~l~~~l~~~~~~~p~~~Q~~~i~~il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl  546 (976)
                      ..|..++|+..++++|...||..|||||.++||.++.|+|++++|+||||||++|++|++..+.....  ....+ +|||
T Consensus        29 ~~F~~l~l~~~ll~~l~~~gf~~pt~IQ~~~IP~~l~g~Dvi~~A~TGsGKT~Af~lP~l~~l~~~~~--~~~~~-aLil  105 (513)
T COG0513          29 PEFASLGLSPELLQALKDLGFEEPTPIQLAAIPLILAGRDVLGQAQTGTGKTAAFLLPLLQKILKSVE--RKYVS-ALIL  105 (513)
T ss_pred             CCHhhcCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHHhcccc--cCCCc-eEEE
Confidence            78999999999999999999999999999999999999999999999999999999999999774311  11112 9999


Q ss_pred             ccCHHHHHHHHHHHHHHHhhc-CcEEEEeeCCCChHHHHHHHhcCCeEEEeCchhHHHHHHhcCCcccccCCceEEEecC
Q 002040          547 APTRELVQQIHSDIRKFAKVM-GVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDE  625 (976)
Q Consensus       547 ~Ptr~La~Q~~~~~~~~~~~~-~~~~~~~~gg~~~~~~~~~l~~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDE  625 (976)
                      +|||+||.|+++.+..++... ++.+++++||.+...+...+..+++|||+|||+|++++...   ..++..+.++||||
T Consensus       106 ~PTRELA~Qi~~~~~~~~~~~~~~~~~~i~GG~~~~~q~~~l~~~~~ivVaTPGRllD~i~~~---~l~l~~v~~lVlDE  182 (513)
T COG0513         106 APTRELAVQIAEELRKLGKNLGGLRVAVVYGGVSIRKQIEALKRGVDIVVATPGRLLDLIKRG---KLDLSGVETLVLDE  182 (513)
T ss_pred             CCCHHHHHHHHHHHHHHHhhcCCccEEEEECCCCHHHHHHHHhcCCCEEEECccHHHHHHHcC---CcchhhcCEEEecc
Confidence            999999999999999999998 79999999999999999999999999999999999999875   47899999999999


Q ss_pred             cccccccCCchHHHHHHHhcCCCCcEEEEeccCcHHHHHHHHHHcCCCeEEEeCCccc--ccCCceEEEEecCcch-HHH
Q 002040          626 ADRMFDMGFEPQITRIVQNIRPDRQTVLFSATFPRQVEILARKVLNKPVEIQVGGRSV--VNKDITQLVEVRPESD-RFL  702 (976)
Q Consensus       626 ah~~~~~~f~~~i~~il~~~~~~~q~i~~SAT~~~~~~~l~~~~l~~~~~i~~~~~~~--~~~~i~q~~~~~~~~~-k~~  702 (976)
                      ||+|+++||...+..|+..++.++|+++||||+|..+..++..++.+|..+.+.....  ....|.|.+..+.... |+.
T Consensus       183 ADrmLd~Gf~~~i~~I~~~~p~~~qtllfSAT~~~~i~~l~~~~l~~p~~i~v~~~~~~~~~~~i~q~~~~v~~~~~k~~  262 (513)
T COG0513         183 ADRMLDMGFIDDIEKILKALPPDRQTLLFSATMPDDIRELARRYLNDPVEIEVSVEKLERTLKKIKQFYLEVESEEEKLE  262 (513)
T ss_pred             HhhhhcCCCHHHHHHHHHhCCcccEEEEEecCCCHHHHHHHHHHccCCcEEEEccccccccccCceEEEEEeCCHHHHHH
Confidence            9999999999999999999999999999999999999999999999999888875444  7788999998888765 888


Q ss_pred             HHHHHHHhhhcCCcEEEEecCHHHHHHHHHHHHHCCCCceeccCCCCHHHHHHHHHHhccCCccEEEecCcccccCCCCC
Q 002040          703 RLLELLGEWYEKGKILIFVHSQEKCDALFRDLLKHGYPCLSLHGAKDQTDRESTISDFKSNVCNLLIATSVAARGLDVKE  782 (976)
Q Consensus       703 ~l~~~l~~~~~~~kvLIF~~s~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLVaT~v~~~GlDi~~  782 (976)
                      .|..+|... ...++||||+++..|+.|+..|...|+.+..|||+|+|.+|..++..|++|.+.|||||++++||||||+
T Consensus       263 ~L~~ll~~~-~~~~~IVF~~tk~~~~~l~~~l~~~g~~~~~lhG~l~q~~R~~~l~~F~~g~~~vLVaTDvaaRGiDi~~  341 (513)
T COG0513         263 LLLKLLKDE-DEGRVIVFVRTKRLVEELAESLRKRGFKVAALHGDLPQEERDRALEKFKDGELRVLVATDVAARGLDIPD  341 (513)
T ss_pred             HHHHHHhcC-CCCeEEEEeCcHHHHHHHHHHHHHCCCeEEEecCCCCHHHHHHHHHHHHcCCCCEEEEechhhccCCccc
Confidence            888888764 3457999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CcEEEEeCCCCCHHHHHHHhcccCCCCCccEEEEEecCC-CcCchHHHHHHHhhc
Q 002040          783 LELVINFDAPNHYEDYVHRVGRTGRAGRKGCAITFISEE-DAKYSPDLVKALELS  836 (976)
Q Consensus       783 v~~VI~~d~p~s~~~y~Qr~GR~gR~g~~g~~~~~~~~~-d~~~~~~i~~~l~~~  836 (976)
                      +.+|||||+|.+++.|+||+|||||+|..|.+++|+++. +...+..|.+.+...
T Consensus       342 v~~VinyD~p~~~e~yvHRiGRTgRaG~~G~ai~fv~~~~e~~~l~~ie~~~~~~  396 (513)
T COG0513         342 VSHVINYDLPLDPEDYVHRIGRTGRAGRKGVAISFVTEEEEVKKLKRIEKRLERK  396 (513)
T ss_pred             cceeEEccCCCCHHHheeccCccccCCCCCeEEEEeCcHHHHHHHHHHHHHHhcc
Confidence            999999999999999999999999999999999999986 888888888887555

>KOG0338 consensus ATP-dependent RNA helicase [RNA processing and modification]

Probab=100.00  E-value=1.9e-63  Score=533.38  Aligned_cols=383  Identities=35%  Similarity=0.535  Sum_probs=344.1

Q ss_pred             ccccccCCCCHHHHHHHHHcCCCCCcHHHHHHHHHHhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEE
Q 002040          466 IKTWHQTGLTSKIMETIRKLNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLI  545 (976)
Q Consensus       466 i~~~~~~~l~~~l~~~l~~~~~~~p~~~Q~~~i~~il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLI  545 (976)
                      ..+|.++.|+..|+.+|..+||..|||||..+||..+-|+|++.||.||||||.+|++|+|..|+-.|..  ....+|||
T Consensus       180 ~~sF~~mNLSRPlLka~~~lGy~~PTpIQ~a~IPvallgkDIca~A~TGsGKTAAF~lPiLERLlYrPk~--~~~TRVLV  257 (691)
T KOG0338|consen  180 NESFQSMNLSRPLLKACSTLGYKKPTPIQVATIPVALLGKDICACAATGSGKTAAFALPILERLLYRPKK--VAATRVLV  257 (691)
T ss_pred             hhhHHhcccchHHHHHHHhcCCCCCCchhhhcccHHhhcchhhheecccCCchhhhHHHHHHHHhcCccc--CcceeEEE
Confidence            4589999999999999999999999999999999999999999999999999999999999999876643  23568999


Q ss_pred             EccCHHHHHHHHHHHHHHHhhcCcEEEEeeCCCChHHHHHHHhcCCeEEEeCchhHHHHHHhcCCcccccCCceEEEecC
Q 002040          546 MAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDE  625 (976)
Q Consensus       546 l~Ptr~La~Q~~~~~~~~~~~~~~~~~~~~gg~~~~~~~~~l~~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDE  625 (976)
                      |||||+||.|++..+++++.+..+.|++++||.+...|-..|...++|||+|||+|+++|.+..  .++|+++.++||||
T Consensus       258 L~PTRELaiQv~sV~~qlaqFt~I~~~L~vGGL~lk~QE~~LRs~PDIVIATPGRlIDHlrNs~--sf~ldsiEVLvlDE  335 (691)
T KOG0338|consen  258 LVPTRELAIQVHSVTKQLAQFTDITVGLAVGGLDLKAQEAVLRSRPDIVIATPGRLIDHLRNSP--SFNLDSIEVLVLDE  335 (691)
T ss_pred             EeccHHHHHHHHHHHHHHHhhccceeeeeecCccHHHHHHHHhhCCCEEEecchhHHHHhccCC--CccccceeEEEech
Confidence            9999999999999999999999999999999999999999999999999999999999997754  36899999999999


Q ss_pred             cccccccCCchHHHHHHHhcCCCCcEEEEeccCcHHHHHHHHHHcCCCeEEEeCCcccccCCceEEEEecC---cchHHH
Q 002040          626 ADRMFDMGFEPQITRIVQNIRPDRQTVLFSATFPRQVEILARKVLNKPVEIQVGGRSVVNKDITQLVEVRP---ESDRFL  702 (976)
Q Consensus       626 ah~~~~~~f~~~i~~il~~~~~~~q~i~~SAT~~~~~~~l~~~~l~~~~~i~~~~~~~~~~~i~q~~~~~~---~~~k~~  702 (976)
                      ||+|++.+|..++..|+..++.++|+++|||||+..+..|+...|..|+.|.+.........+.|.|...-   ...+-.
T Consensus       336 ADRMLeegFademnEii~lcpk~RQTmLFSATMteeVkdL~slSL~kPvrifvd~~~~~a~~LtQEFiRIR~~re~dRea  415 (691)
T KOG0338|consen  336 ADRMLEEGFADEMNEIIRLCPKNRQTMLFSATMTEEVKDLASLSLNKPVRIFVDPNKDTAPKLTQEFIRIRPKREGDREA  415 (691)
T ss_pred             HHHHHHHHHHHHHHHHHHhccccccceeehhhhHHHHHHHHHhhcCCCeEEEeCCccccchhhhHHHheeccccccccHH
Confidence            99999999999999999999999999999999999999999999999999999888777777777665332   234445


Q ss_pred             HHHHHHHhhhcCCcEEEEecCHHHHHHHHHHHHHCCCCceeccCCCCHHHHHHHHHHhccCCccEEEecCcccccCCCCC
Q 002040          703 RLLELLGEWYEKGKILIFVHSQEKCDALFRDLLKHGYPCLSLHGAKDQTDRESTISDFKSNVCNLLIATSVAARGLDVKE  782 (976)
Q Consensus       703 ~l~~~l~~~~~~~kvLIF~~s~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLVaT~v~~~GlDi~~  782 (976)
                      .|..++...+ ...+|||+.++..|..|.-.|--.|+.+.-+||.++|.+|-..+..|+++.++|||||+++++||||++
T Consensus       416 ~l~~l~~rtf-~~~~ivFv~tKk~AHRl~IllGLlgl~agElHGsLtQ~QRlesL~kFk~~eidvLiaTDvAsRGLDI~g  494 (691)
T KOG0338|consen  416 MLASLITRTF-QDRTIVFVRTKKQAHRLRILLGLLGLKAGELHGSLTQEQRLESLEKFKKEEIDVLIATDVASRGLDIEG  494 (691)
T ss_pred             HHHHHHHHhc-ccceEEEEehHHHHHHHHHHHHHhhchhhhhcccccHHHHHHHHHHHHhccCCEEEEechhhccCCccc
Confidence            5556665554 678999999999999999999889999999999999999999999999999999999999999999999


Q ss_pred             CcEEEEeCCCCCHHHHHHHhcccCCCCCccEEEEEecCCCcCchHHHHHHHh-----hccCCCChHHHHHHHHHHH
Q 002040          783 LELVINFDAPNHYEDYVHRVGRTGRAGRKGCAITFISEEDAKYSPDLVKALE-----LSEQVVPDDLKALADSFMA  853 (976)
Q Consensus       783 v~~VI~~d~p~s~~~y~Qr~GR~gR~g~~g~~~~~~~~~d~~~~~~i~~~l~-----~~~~~vp~~l~~l~~~~~~  853 (976)
                      |.+||||++|.++..|+||+||+.|+|+.|.+++|+.+.+...+..|++.-.     +.+-.||+....-+...+.
T Consensus       495 V~tVINy~mP~t~e~Y~HRVGRTARAGRaGrsVtlvgE~dRkllK~iik~~~~a~~klk~R~i~~~~Iek~~~~ie  570 (691)
T KOG0338|consen  495 VQTVINYAMPKTIEHYLHRVGRTARAGRAGRSVTLVGESDRKLLKEIIKSSTKAGSKLKNRNIPPEVIEKFRKKIE  570 (691)
T ss_pred             eeEEEeccCchhHHHHHHHhhhhhhcccCcceEEEeccccHHHHHHHHhhhhhcccchhhcCCCHHHHHHHHHHHH
Confidence            9999999999999999999999999999999999999999999999998743     2344566654443333333

>KOG0335 consensus ATP-dependent RNA helicase [RNA processing and modification]

Probab=100.00  E-value=6.5e-63  Score=542.05  Aligned_cols=391  Identities=42%  Similarity=0.711  Sum_probs=365.8

Q ss_pred             ceeccCCCCCcccccccCCCCHHHHHHHHHcCCCCCcHHHHHHHHHHhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCC
Q 002040          455 LKIHGKDVPKPIKTWHQTGLTSKIMETIRKLNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPP  534 (976)
Q Consensus       455 i~~~g~~~p~pi~~~~~~~l~~~l~~~l~~~~~~~p~~~Q~~~i~~il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~  534 (976)
                      +.+.|..+|.++.+|..-.+...+...+...+|..|||+|+.+||.|..|+++++||+||||||.+|++|++.+++....
T Consensus        62 v~~~G~~~p~~i~~f~~~~l~~~l~~ni~~~~~~~ptpvQk~sip~i~~Grdl~acAqTGsGKT~aFLiPii~~~~~~~~  141 (482)
T KOG0335|consen   62 VKVSGRDVPPHIPTFDEAILGEALAGNIKRSGYTKPTPVQKYSIPIISGGRDLMACAQTGSGKTAAFLIPIISYLLDEGP  141 (482)
T ss_pred             eeccCCccCCCcccccccchhHHHhhccccccccCCCcceeeccceeecCCceEEEccCCCcchHHHHHHHHHHHHhcCc
Confidence            46789999999999999899999999999999999999999999999999999999999999999999999999987643


Q ss_pred             CCC-----CCCCeEEEEccCHHHHHHHHHHHHHHHhhcCcEEEEeeCCCChHHHHHHHhcCCeEEEeCchhHHHHHHhcC
Q 002040          535 VAA-----GDGPVGLIMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSG  609 (976)
Q Consensus       535 ~~~-----~~~~~vLIl~Ptr~La~Q~~~~~~~~~~~~~~~~~~~~gg~~~~~~~~~l~~~~~Iiv~Tp~~L~~~l~~~~  609 (976)
                      ...     +..|.+|||+|||+||.|+++++.+|....++.++.+|||.+...+...+..+|+|+|||||+|.+++... 
T Consensus       142 ~~~~~~~~~~~P~~lIlapTReL~~Qi~nea~k~~~~s~~~~~~~ygg~~~~~q~~~~~~gcdIlvaTpGrL~d~~e~g-  220 (482)
T KOG0335|consen  142 EDRGESGGGVYPRALILAPTRELVDQIYNEARKFSYLSGMKSVVVYGGTDLGAQLRFIKRGCDILVATPGRLKDLIERG-  220 (482)
T ss_pred             ccCcccCCCCCCceEEEeCcHHHhhHHHHHHHhhcccccceeeeeeCCcchhhhhhhhccCccEEEecCchhhhhhhcc-
Confidence            221     13599999999999999999999999999999999999999999999999999999999999999999764 


Q ss_pred             CcccccCCceEEEecCcccccc-cCCchHHHHHHHhcCC----CCcEEEEeccCcHHHHHHHHHHcCC-CeEEEeCCccc
Q 002040          610 GKITNLRRVTYLVMDEADRMFD-MGFEPQITRIVQNIRP----DRQTVLFSATFPRQVEILARKVLNK-PVEIQVGGRSV  683 (976)
Q Consensus       610 ~~~~~l~~~~~vVlDEah~~~~-~~f~~~i~~il~~~~~----~~q~i~~SAT~~~~~~~l~~~~l~~-~~~i~~~~~~~  683 (976)
                        ...|..+.||||||||+|++ ++|.++|..|+.+...    .+|+++||||+|..+..++..++.+ ++.+.++....
T Consensus       221 --~i~l~~~k~~vLDEADrMlD~mgF~p~Ir~iv~~~~~~~~~~~qt~mFSAtfp~~iq~l~~~fl~~~yi~laV~rvg~  298 (482)
T KOG0335|consen  221 --KISLDNCKFLVLDEADRMLDEMGFEPQIRKIVEQLGMPPKNNRQTLLFSATFPKEIQRLAADFLKDNYIFLAVGRVGS  298 (482)
T ss_pred             --eeehhhCcEEEecchHHhhhhccccccHHHHhcccCCCCccceeEEEEeccCChhhhhhHHHHhhccceEEEEeeecc
Confidence              36789999999999999999 9999999999988754    6899999999999999999999886 88888988889


Q ss_pred             ccCCceEEEEecCcchHHHHHHHHHHhhh---cCC-----cEEEEecCHHHHHHHHHHHHHCCCCceeccCCCCHHHHHH
Q 002040          684 VNKDITQLVEVRPESDRFLRLLELLGEWY---EKG-----KILIFVHSQEKCDALFRDLLKHGYPCLSLHGAKDQTDRES  755 (976)
Q Consensus       684 ~~~~i~q~~~~~~~~~k~~~l~~~l~~~~---~~~-----kvLIF~~s~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~  755 (976)
                      ...++.|.+.++....|...|+.+|....   ..+     +++|||.++..|+.|+.+|...++++..|||..++.+|..
T Consensus       299 ~~~ni~q~i~~V~~~~kr~~Lldll~~~~~~~~~~~~~~e~tlvFvEt~~~~d~l~~~l~~~~~~~~sIhg~~tq~er~~  378 (482)
T KOG0335|consen  299 TSENITQKILFVNEMEKRSKLLDLLNKDDGPPSDGEPKWEKTLVFVETKRGADELAAFLSSNGYPAKSIHGDRTQIEREQ  378 (482)
T ss_pred             ccccceeEeeeecchhhHHHHHHHhhcccCCcccCCcccceEEEEeeccchhhHHHHHHhcCCCCceeecchhhhhHHHH
Confidence            99999999999999999999999998655   344     8999999999999999999999999999999999999999


Q ss_pred             HHHHhccCCccEEEecCcccccCCCCCCcEEEEeCCCCCHHHHHHHhcccCCCCCccEEEEEecCCCcCchHHHHHHHhh
Q 002040          756 TISDFKSNVCNLLIATSVAARGLDVKELELVINFDAPNHYEDYVHRVGRTGRAGRKGCAITFISEEDAKYSPDLVKALEL  835 (976)
Q Consensus       756 ~~~~F~~g~~~vLVaT~v~~~GlDi~~v~~VI~~d~p~s~~~y~Qr~GR~gR~g~~g~~~~~~~~~d~~~~~~i~~~l~~  835 (976)
                      ++..|++|.+.|||||+|+++|||||+|++|||||+|.+..+|+||||||||.|+.|.++.|+...+......|++.|..
T Consensus       379 al~~Fr~g~~pvlVaT~VaaRGlDi~~V~hVInyDmP~d~d~YvHRIGRTGR~Gn~G~atsf~n~~~~~i~~~L~~~l~e  458 (482)
T KOG0335|consen  379 ALNDFRNGKAPVLVATNVAARGLDIPNVKHVINYDMPADIDDYVHRIGRTGRVGNGGRATSFFNEKNQNIAKALVEILTE  458 (482)
T ss_pred             HHHHhhcCCcceEEEehhhhcCCCCCCCceeEEeecCcchhhHHHhccccccCCCCceeEEEeccccchhHHHHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccCCCChHHHHHH
Q 002040          836 SEQVVPDDLKALA  848 (976)
Q Consensus       836 ~~~~vp~~l~~l~  848 (976)
                      +++.+|.+|.+++
T Consensus       459 a~q~vP~wl~~~~  471 (482)
T KOG0335|consen  459 ANQEVPQWLSELS  471 (482)
T ss_pred             hcccCcHHHHhhh
Confidence            9999999998743

>KOG0328 consensus Predicted ATP-dependent RNA helicase FAL1, involved in rRNA maturation, DEAD-box superfamily [Translation, ribosomal structure and biogenesis]

Probab=100.00  E-value=1.1e-61  Score=485.06  Aligned_cols=375  Identities=34%  Similarity=0.579  Sum_probs=346.2

Q ss_pred             CCCCcccccccCCCCHHHHHHHHHcCCCCCcHHHHHHHHHHhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCC
Q 002040          461 DVPKPIKTWHQTGLTSKIMETIRKLNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDG  540 (976)
Q Consensus       461 ~~p~pi~~~~~~~l~~~l~~~l~~~~~~~p~~~Q~~~i~~il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~  540 (976)
                      .-..++.+|+++||...++..+...||.+|+.+|+.||+.|+.|+|+|+++..|+|||.+|.+.++..+.-.     ...
T Consensus        21 ~~~~v~~~F~~Mgl~edlLrgiY~yGfekPS~IQqrAi~~IlkGrdViaQaqSGTGKTa~~si~vlq~~d~~-----~r~   95 (400)
T KOG0328|consen   21 EKVKVIPTFDDMGLKEDLLRGIYAYGFEKPSAIQQRAIPQILKGRDVIAQAQSGTGKTATFSISVLQSLDIS-----VRE   95 (400)
T ss_pred             cCcccccchhhcCchHHHHHHHHHhccCCchHHHhhhhhhhhcccceEEEecCCCCceEEEEeeeeeecccc-----cce
Confidence            335678899999999999999999999999999999999999999999999999999999998888665432     224


Q ss_pred             CeEEEEccCHHHHHHHHHHHHHHHhhcCcEEEEeeCCCChHHHHHHHhcCCeEEEeCchhHHHHHHhcCCcccccCCceE
Q 002040          541 PVGLIMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTY  620 (976)
Q Consensus       541 ~~vLIl~Ptr~La~Q~~~~~~~~~~~~~~~~~~~~gg~~~~~~~~~l~~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~  620 (976)
                      .++|||.|||+||.|+.+.+..++..+++.+..+.||.+..+.+..+..|.++|.+|||++++++....   ..-..+.+
T Consensus        96 tQ~lilsPTRELa~Qi~~vi~alg~~mnvq~hacigg~n~gedikkld~G~hvVsGtPGrv~dmikr~~---L~tr~vkm  172 (400)
T KOG0328|consen   96 TQALILSPTRELAVQIQKVILALGDYMNVQCHACIGGKNLGEDIKKLDYGQHVVSGTPGRVLDMIKRRS---LRTRAVKM  172 (400)
T ss_pred             eeEEEecChHHHHHHHHHHHHHhcccccceEEEEecCCccchhhhhhcccceEeeCCCchHHHHHHhcc---ccccceeE
Confidence            689999999999999999999999999999999999999999999999999999999999999998754   45677999


Q ss_pred             EEecCcccccccCCchHHHHHHHhcCCCCcEEEEeccCcHHHHHHHHHHcCCCeEEEeCCcccccCCceEEEEecCcc-h
Q 002040          621 LVMDEADRMFDMGFEPQITRIVQNIRPDRQTVLFSATFPRQVEILARKVLNKPVEIQVGGRSVVNKDITQLVEVRPES-D  699 (976)
Q Consensus       621 vVlDEah~~~~~~f~~~i~~il~~~~~~~q~i~~SAT~~~~~~~l~~~~l~~~~~i~~~~~~~~~~~i~q~~~~~~~~-~  699 (976)
                      |||||||.|++.||..++..|+..++|+.|++++|||+|..+.....+|+.+|+.+.+.....+...|.|++.-.... .
T Consensus       173 lVLDEaDemL~kgfk~Qiydiyr~lp~~~Qvv~~SATlp~eilemt~kfmtdpvrilvkrdeltlEgIKqf~v~ve~Eew  252 (400)
T KOG0328|consen  173 LVLDEADEMLNKGFKEQIYDIYRYLPPGAQVVLVSATLPHEILEMTEKFMTDPVRILVKRDELTLEGIKQFFVAVEKEEW  252 (400)
T ss_pred             EEeccHHHHHHhhHHHHHHHHHHhCCCCceEEEEeccCcHHHHHHHHHhcCCceeEEEecCCCchhhhhhheeeechhhh
Confidence            999999999999999999999999999999999999999999999999999999999998888888899888666554 4


Q ss_pred             HHHHHHHHHHhhhcCCcEEEEecCHHHHHHHHHHHHHCCCCceeccCCCCHHHHHHHHHHhccCCccEEEecCcccccCC
Q 002040          700 RFLRLLELLGEWYEKGKILIFVHSQEKCDALFRDLLKHGYPCLSLHGAKDQTDRESTISDFKSNVCNLLIATSVAARGLD  779 (976)
Q Consensus       700 k~~~l~~~l~~~~~~~kvLIF~~s~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLVaT~v~~~GlD  779 (976)
                      |+..|..+... +.-.+++|||||+..++.|.+.+...++.+.++||+|++.+|+.++..|++|..+|||+|++.++|+|
T Consensus       253 KfdtLcdLYd~-LtItQavIFcnTk~kVdwLtekm~~~nftVssmHGDm~qkERd~im~dFRsg~SrvLitTDVwaRGiD  331 (400)
T KOG0328|consen  253 KFDTLCDLYDT-LTITQAVIFCNTKRKVDWLTEKMREANFTVSSMHGDMEQKERDKIMNDFRSGKSRVLITTDVWARGID  331 (400)
T ss_pred             hHhHHHHHhhh-hehheEEEEecccchhhHHHHHHHhhCceeeeccCCcchhHHHHHHHHhhcCCceEEEEechhhccCC
Confidence            88888877654 34568999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCcEEEEeCCCCCHHHHHHHhcccCCCCCccEEEEEecCCCcCchHHHHHHHhhccCCCChHH
Q 002040          780 VKELELVINFDAPNHYEDYVHRVGRTGRAGRKGCAITFISEEDAKYSPDLVKALELSEQVVPDDL  844 (976)
Q Consensus       780 i~~v~~VI~~d~p~s~~~y~Qr~GR~gR~g~~g~~~~~~~~~d~~~~~~i~~~l~~~~~~vp~~l  844 (976)
                      +|.|++|||||.|.+.+.|+||+||.||.|++|.++-|+..++-..+.+|.+.+.......|..+
T Consensus       332 v~qVslviNYDLP~nre~YIHRIGRSGRFGRkGvainFVk~~d~~~lrdieq~yst~i~emp~nv  396 (400)
T KOG0328|consen  332 VQQVSLVINYDLPNNRELYIHRIGRSGRFGRKGVAINFVKSDDLRILRDIEQYYSTQIDEMPMNV  396 (400)
T ss_pred             cceeEEEEecCCCccHHHHhhhhccccccCCcceEEEEecHHHHHHHHHHHHHHhhhcccccchh
Confidence            99999999999999999999999999999999999999999999999999999888777777543

>KOG0342 consensus ATP-dependent RNA helicase pitchoune [RNA processing and modification]

Probab=100.00  E-value=3.4e-60  Score=509.95  Aligned_cols=373  Identities=33%  Similarity=0.562  Sum_probs=339.9

Q ss_pred             cccccccCCCCHHHHHHHHHcCCCCCcHHHHHHHHHHhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEE
Q 002040          465 PIKTWHQTGLTSKIMETIRKLNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGL  544 (976)
Q Consensus       465 pi~~~~~~~l~~~l~~~l~~~~~~~p~~~Q~~~i~~il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vL  544 (976)
                      +...|....|++..+.+|+.+||..+|++|..+|+.++.|+|+|+.|.||+|||++|++|+++++.+.+... .++..||
T Consensus        80 ~~~~f~~~~LS~~t~kAi~~~GF~~MT~VQ~~ti~pll~gkDvl~~AKTGtGKTlAFLiPaie~l~k~~~~~-r~~~~vl  158 (543)
T KOG0342|consen   80 TTFRFEEGSLSPLTLKAIKEMGFETMTPVQQKTIPPLLEGKDVLAAAKTGTGKTLAFLLPAIELLRKLKFKP-RNGTGVL  158 (543)
T ss_pred             hhhHhhccccCHHHHHHHHhcCccchhHHHHhhcCccCCCccceeeeccCCCceeeehhHHHHHHHhcccCC-CCCeeEE
Confidence            345678889999999999999999999999999999999999999999999999999999999999876543 3677899


Q ss_pred             EEccCHHHHHHHHHHHHHHHhhc-CcEEEEeeCCCChHHHHHHHhcCCeEEEeCchhHHHHHHhcCCcccccCCceEEEe
Q 002040          545 IMAPTRELVQQIHSDIRKFAKVM-GVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVM  623 (976)
Q Consensus       545 Il~Ptr~La~Q~~~~~~~~~~~~-~~~~~~~~gg~~~~~~~~~l~~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVl  623 (976)
                      ||||||+||.|++.+++.+.+.. ++.+..+.||+........+..+++|+|+|||+|+++|.+..+.  .+..+.++||
T Consensus       159 Ii~PTRELA~Q~~~eak~Ll~~h~~~~v~~viGG~~~~~e~~kl~k~~niliATPGRLlDHlqNt~~f--~~r~~k~lvl  236 (543)
T KOG0342|consen  159 IICPTRELAMQIFAEAKELLKYHESITVGIVIGGNNFSVEADKLVKGCNILIATPGRLLDHLQNTSGF--LFRNLKCLVL  236 (543)
T ss_pred             EecccHHHHHHHHHHHHHHHhhCCCcceEEEeCCccchHHHHHhhccccEEEeCCchHHhHhhcCCcc--hhhccceeEe
Confidence            99999999999999999999988 99999999999988888888889999999999999999887653  3455689999


Q ss_pred             cCcccccccCCchHHHHHHHhcCCCCcEEEEeccCcHHHHHHHHHHcCC-CeEEEeCC--cccccCCceEEEEecCcchH
Q 002040          624 DEADRMFDMGFEPQITRIVQNIRPDRQTVLFSATFPRQVEILARKVLNK-PVEIQVGG--RSVVNKDITQLVEVRPESDR  700 (976)
Q Consensus       624 DEah~~~~~~f~~~i~~il~~~~~~~q~i~~SAT~~~~~~~l~~~~l~~-~~~i~~~~--~~~~~~~i~q~~~~~~~~~k  700 (976)
                      ||||+++++||...+..|+..++..+|+++||||.|+.+..++...+.. |+++.+..  .......+.|.+.+.+...+
T Consensus       237 DEADrlLd~GF~~di~~Ii~~lpk~rqt~LFSAT~~~kV~~l~~~~L~~d~~~v~~~d~~~~~The~l~Qgyvv~~~~~~  316 (543)
T KOG0342|consen  237 DEADRLLDIGFEEDVEQIIKILPKQRQTLLFSATQPSKVKDLARGALKRDPVFVNVDDGGERETHERLEQGYVVAPSDSR  316 (543)
T ss_pred             ecchhhhhcccHHHHHHHHHhccccceeeEeeCCCcHHHHHHHHHhhcCCceEeecCCCCCcchhhcccceEEeccccch
Confidence            9999999999999999999999999999999999999999999988866 77776644  34456678899999999999


Q ss_pred             HHHHHHHHHhhhcCCcEEEEecCHHHHHHHHHHHHHCCCCceeccCCCCHHHHHHHHHHhccCCccEEEecCcccccCCC
Q 002040          701 FLRLLELLGEWYEKGKILIFVHSQEKCDALFRDLLKHGYPCLSLHGAKDQTDRESTISDFKSNVCNLLIATSVAARGLDV  780 (976)
Q Consensus       701 ~~~l~~~l~~~~~~~kvLIF~~s~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLVaT~v~~~GlDi  780 (976)
                      |..++.+|.+.....++||||+|...+..++..|....++|..|||+++|..|..++..|.+.+..|||||+|++||+|+
T Consensus       317 f~ll~~~LKk~~~~~KiiVF~sT~~~vk~~~~lL~~~dlpv~eiHgk~~Q~kRT~~~~~F~kaesgIL~cTDVaARGlD~  396 (543)
T KOG0342|consen  317 FSLLYTFLKKNIKRYKIIVFFSTCMSVKFHAELLNYIDLPVLEIHGKQKQNKRTSTFFEFCKAESGILVCTDVAARGLDI  396 (543)
T ss_pred             HHHHHHHHHHhcCCceEEEEechhhHHHHHHHHHhhcCCchhhhhcCCcccccchHHHHHhhcccceEEecchhhccCCC
Confidence            99999999998777899999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCcEEEEeCCCCCHHHHHHHhcccCCCCCccEEEEEecCCCcCchHHHHHHHhhccCCCC
Q 002040          781 KELELVINFDAPNHYEDYVHRVGRTGRAGRKGCAITFISEEDAKYSPDLVKALELSEQVVP  841 (976)
Q Consensus       781 ~~v~~VI~~d~p~s~~~y~Qr~GR~gR~g~~g~~~~~~~~~d~~~~~~i~~~l~~~~~~vp  841 (976)
                      |+|++||.||+|.++.+||||+|||||.|..|.+++|+.+++..++..|. .+.+.....|
T Consensus       397 P~V~~VvQ~~~P~d~~~YIHRvGRTaR~gk~G~alL~l~p~El~Flr~LK-~lpl~~~e~~  456 (543)
T KOG0342|consen  397 PDVDWVVQYDPPSDPEQYIHRVGRTAREGKEGKALLLLAPWELGFLRYLK-KLPLEEFEFP  456 (543)
T ss_pred             CCceEEEEeCCCCCHHHHHHHhccccccCCCceEEEEeChhHHHHHHHHh-hCCCcccCCC
Confidence            99999999999999999999999999999999999999999888877776 4444444444

>KOG0340 consensus ATP-dependent RNA helicase [RNA processing and modification]

Probab=100.00  E-value=5.8e-60  Score=487.86  Aligned_cols=366  Identities=36%  Similarity=0.575  Sum_probs=335.0

Q ss_pred             ccccccCCCCHHHHHHHHHcCCCCCcHHHHHHHHHHhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEE
Q 002040          466 IKTWHQTGLTSKIMETIRKLNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLI  545 (976)
Q Consensus       466 i~~~~~~~l~~~l~~~l~~~~~~~p~~~Q~~~i~~il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLI  545 (976)
                      ...|..+||++++.+.|+.+|+.+|||+|..|||.|+.|+|+|++|.||||||++|.+|+++.+...|     +|..+||
T Consensus         6 ~~~F~~LGl~~Wlve~l~~l~i~~pTpiQ~~cIpkILeGrdcig~AkTGsGKT~AFaLPil~rLsedP-----~giFalv   80 (442)
T KOG0340|consen    6 AKPFSILGLSPWLVEQLKALGIKKPTPIQQACIPKILEGRDCIGCAKTGSGKTAAFALPILNRLSEDP-----YGIFALV   80 (442)
T ss_pred             cCchhhcCccHHHHHHHHHhcCCCCCchHhhhhHHHhcccccccccccCCCcchhhhHHHHHhhccCC-----CcceEEE
Confidence            46799999999999999999999999999999999999999999999999999999999999998764     5788999


Q ss_pred             EccCHHHHHHHHHHHHHHHhhcCcEEEEeeCCCChHHHHHHHhcCCeEEEeCchhHHHHHHhcCCc-ccccCCceEEEec
Q 002040          546 MAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGGK-ITNLRRVTYLVMD  624 (976)
Q Consensus       546 l~Ptr~La~Q~~~~~~~~~~~~~~~~~~~~gg~~~~~~~~~l~~~~~Iiv~Tp~~L~~~l~~~~~~-~~~l~~~~~vVlD  624 (976)
                      ++|||+||.|+.+.|.-+.+.+++++.+++||...-.+...|....+|||+|||+|.+++..+.+. ...+.++.|+|||
T Consensus        81 lTPTrELA~QiaEQF~alGk~l~lK~~vivGG~d~i~qa~~L~~rPHvVvatPGRlad~l~sn~~~~~~~~~rlkflVlD  160 (442)
T KOG0340|consen   81 LTPTRELALQIAEQFIALGKLLNLKVSVIVGGTDMIMQAAILSDRPHVVVATPGRLADHLSSNLGVCSWIFQRLKFLVLD  160 (442)
T ss_pred             ecchHHHHHHHHHHHHHhcccccceEEEEEccHHHhhhhhhcccCCCeEecCccccccccccCCccchhhhhceeeEEec
Confidence            999999999999999999999999999999999999998899999999999999999999776332 3457899999999


Q ss_pred             CcccccccCCchHHHHHHHhcCCCCcEEEEeccCcHHHHHHHHHHcCCC--eEEEeCCcccccCCceEEEEecCcchHHH
Q 002040          625 EADRMFDMGFEPQITRIVQNIRPDRQTVLFSATFPRQVEILARKVLNKP--VEIQVGGRSVVNKDITQLVEVRPESDRFL  702 (976)
Q Consensus       625 Eah~~~~~~f~~~i~~il~~~~~~~q~i~~SAT~~~~~~~l~~~~l~~~--~~i~~~~~~~~~~~i~q~~~~~~~~~k~~  702 (976)
                      ||++|++.+|...+..++..++..+|+++||||++..+..+.......+  ..+.......+...+.|.+.+++...+-.
T Consensus       161 EADrvL~~~f~d~L~~i~e~lP~~RQtLlfSATitd~i~ql~~~~i~k~~a~~~e~~~~vstvetL~q~yI~~~~~vkda  240 (442)
T KOG0340|consen  161 EADRVLAGCFPDILEGIEECLPKPRQTLLFSATITDTIKQLFGCPITKSIAFELEVIDGVSTVETLYQGYILVSIDVKDA  240 (442)
T ss_pred             chhhhhccchhhHHhhhhccCCCccceEEEEeehhhHHHHhhcCCcccccceEEeccCCCCchhhhhhheeecchhhhHH
Confidence            9999999999999999999999999999999999999887766555553  33333334445667888899999999999


Q ss_pred             HHHHHHHhhhc--CCcEEEEecCHHHHHHHHHHHHHCCCCceeccCCCCHHHHHHHHHHhccCCccEEEecCcccccCCC
Q 002040          703 RLLELLGEWYE--KGKILIFVHSQEKCDALFRDLLKHGYPCLSLHGAKDQTDRESTISDFKSNVCNLLIATSVAARGLDV  780 (976)
Q Consensus       703 ~l~~~l~~~~~--~~kvLIF~~s~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLVaT~v~~~GlDi  780 (976)
                      +|+.+|..+..  .+.++||+++..+|+.|+..|...++.++.+||.|+|.+|...+..|+++..+|||||+++++||||
T Consensus       241 YLv~~Lr~~~~~~~~simIFvnttr~cQ~l~~~l~~le~r~~~lHs~m~Q~eR~~aLsrFrs~~~~iliaTDVAsRGLDI  320 (442)
T KOG0340|consen  241 YLVHLLRDFENKENGSIMIFVNTTRECQLLSMTLKNLEVRVVSLHSQMPQKERLAALSRFRSNAARILIATDVASRGLDI  320 (442)
T ss_pred             HHHHHHhhhhhccCceEEEEeehhHHHHHHHHHHhhhceeeeehhhcchHHHHHHHHHHHhhcCccEEEEechhhcCCCC
Confidence            99999988776  6799999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCcEEEEeCCCCCHHHHHHHhcccCCCCCccEEEEEecCCCcCchHHHHHHHhhc
Q 002040          781 KELELVINFDAPNHYEDYVHRVGRTGRAGRKGCAITFISEEDAKYSPDLVKALELS  836 (976)
Q Consensus       781 ~~v~~VI~~d~p~s~~~y~Qr~GR~gR~g~~g~~~~~~~~~d~~~~~~i~~~l~~~  836 (976)
                      |.|.+|||||.|.+|.+|+||+||+.|+|+.|.++.|+++.|...+..|...+...
T Consensus       321 P~V~LVvN~diPr~P~~yiHRvGRtARAGR~G~aiSivt~rDv~l~~aiE~~igkK  376 (442)
T KOG0340|consen  321 PTVELVVNHDIPRDPKDYIHRVGRTARAGRKGMAISIVTQRDVELLQAIEEEIGKK  376 (442)
T ss_pred             CceeEEEecCCCCCHHHHHHhhcchhcccCCcceEEEechhhHHHHHHHHHHHhcc
Confidence            99999999999999999999999999999999999999999998888888876544

>PRK04837 ATP-dependent RNA helicase RhlB; Provisional

Probab=100.00  E-value=2.6e-58  Score=533.98  Aligned_cols=368  Identities=34%  Similarity=0.561  Sum_probs=331.4

Q ss_pred             ccccccCCCCHHHHHHHHHcCCCCCcHHHHHHHHHHhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCC--CCCCCeE
Q 002040          466 IKTWHQTGLTSKIMETIRKLNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVA--AGDGPVG  543 (976)
Q Consensus       466 i~~~~~~~l~~~l~~~l~~~~~~~p~~~Q~~~i~~il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~--~~~~~~v  543 (976)
                      -.+|.+++|++.++++|..+||..|||+|.++||.+++|+|+|++||||||||++|++|++..+...+...  ...++++
T Consensus         7 ~~~f~~~~l~~~l~~~l~~~g~~~pt~iQ~~aip~il~g~dvi~~ApTGsGKTla~llp~l~~l~~~~~~~~~~~~~~~~   86 (423)
T PRK04837          7 EQKFSDFALHPQVVEALEKKGFHNCTPIQALALPLTLAGRDVAGQAQTGTGKTMAFLTATFHYLLSHPAPEDRKVNQPRA   86 (423)
T ss_pred             CCCHhhCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCcEEEECCCCchHHHHHHHHHHHHHHhcccccccccCCceE
Confidence            36899999999999999999999999999999999999999999999999999999999999987654321  1346899


Q ss_pred             EEEccCHHHHHHHHHHHHHHHhhcCcEEEEeeCCCChHHHHHHHhcCCeEEEeCchhHHHHHHhcCCcccccCCceEEEe
Q 002040          544 LIMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVM  623 (976)
Q Consensus       544 LIl~Ptr~La~Q~~~~~~~~~~~~~~~~~~~~gg~~~~~~~~~l~~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVl  623 (976)
                      |||+||++||.|++..+..++..+++.+.+++||.....+...+..+++||||||++|.+++...   ...+..+.+|||
T Consensus        87 lil~PtreLa~Qi~~~~~~l~~~~~~~v~~~~gg~~~~~~~~~l~~~~~IlV~TP~~l~~~l~~~---~~~l~~v~~lVi  163 (423)
T PRK04837         87 LIMAPTRELAVQIHADAEPLAQATGLKLGLAYGGDGYDKQLKVLESGVDILIGTTGRLIDYAKQN---HINLGAIQVVVL  163 (423)
T ss_pred             EEECCcHHHHHHHHHHHHHHhccCCceEEEEECCCCHHHHHHHhcCCCCEEEECHHHHHHHHHcC---CcccccccEEEE
Confidence            99999999999999999999999999999999999988888888888999999999999998653   357889999999


Q ss_pred             cCcccccccCCchHHHHHHHhcCC--CCcEEEEeccCcHHHHHHHHHHcCCCeEEEeCCcccccCCceEEEEecCcchHH
Q 002040          624 DEADRMFDMGFEPQITRIVQNIRP--DRQTVLFSATFPRQVEILARKVLNKPVEIQVGGRSVVNKDITQLVEVRPESDRF  701 (976)
Q Consensus       624 DEah~~~~~~f~~~i~~il~~~~~--~~q~i~~SAT~~~~~~~l~~~~l~~~~~i~~~~~~~~~~~i~q~~~~~~~~~k~  701 (976)
                      ||||+|++++|...+..++..++.  .+++++||||++..+..++..++.+|..+.+.........+.+.+.+.....|.
T Consensus       164 DEad~l~~~~f~~~i~~i~~~~~~~~~~~~~l~SAT~~~~~~~~~~~~~~~p~~i~v~~~~~~~~~i~~~~~~~~~~~k~  243 (423)
T PRK04837        164 DEADRMFDLGFIKDIRWLFRRMPPANQRLNMLFSATLSYRVRELAFEHMNNPEYVEVEPEQKTGHRIKEELFYPSNEEKM  243 (423)
T ss_pred             ecHHHHhhcccHHHHHHHHHhCCCccceeEEEEeccCCHHHHHHHHHHCCCCEEEEEcCCCcCCCceeEEEEeCCHHHHH
Confidence            999999999999999999998874  567899999999999999999999998887766555556677777777677788


Q ss_pred             HHHHHHHHhhhcCCcEEEEecCHHHHHHHHHHHHHCCCCceeccCCCCHHHHHHHHHHhccCCccEEEecCcccccCCCC
Q 002040          702 LRLLELLGEWYEKGKILIFVHSQEKCDALFRDLLKHGYPCLSLHGAKDQTDRESTISDFKSNVCNLLIATSVAARGLDVK  781 (976)
Q Consensus       702 ~~l~~~l~~~~~~~kvLIF~~s~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLVaT~v~~~GlDi~  781 (976)
                      ..|..++... ...++||||+++..|+.|+..|...|+.+..+||+|++.+|..+++.|++|.++|||||+++++|||||
T Consensus       244 ~~l~~ll~~~-~~~~~lVF~~t~~~~~~l~~~L~~~g~~v~~lhg~~~~~~R~~~l~~F~~g~~~vLVaTdv~~rGiDip  322 (423)
T PRK04837        244 RLLQTLIEEE-WPDRAIIFANTKHRCEEIWGHLAADGHRVGLLTGDVAQKKRLRILEEFTRGDLDILVATDVAARGLHIP  322 (423)
T ss_pred             HHHHHHHHhc-CCCeEEEEECCHHHHHHHHHHHHhCCCcEEEecCCCChhHHHHHHHHHHcCCCcEEEEechhhcCCCcc
Confidence            7777777653 457899999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCcEEEEeCCCCCHHHHHHHhcccCCCCCccEEEEEecCCCcCchHHHHHHHhhcc
Q 002040          782 ELELVINFDAPNHYEDYVHRVGRTGRAGRKGCAITFISEEDAKYSPDLVKALELSE  837 (976)
Q Consensus       782 ~v~~VI~~d~p~s~~~y~Qr~GR~gR~g~~g~~~~~~~~~d~~~~~~i~~~l~~~~  837 (976)
                      ++++||+||+|.++..|+||+||+||.|+.|.|++|+++.+...+..|.+.+....
T Consensus       323 ~v~~VI~~d~P~s~~~yiqR~GR~gR~G~~G~ai~~~~~~~~~~~~~i~~~~~~~~  378 (423)
T PRK04837        323 AVTHVFNYDLPDDCEDYVHRIGRTGRAGASGHSISLACEEYALNLPAIETYIGHSI  378 (423)
T ss_pred             ccCEEEEeCCCCchhheEeccccccCCCCCeeEEEEeCHHHHHHHHHHHHHhCCCC
Confidence            99999999999999999999999999999999999999988888888877665553

>KOG0345 consensus ATP-dependent RNA helicase [RNA processing and modification]

Probab=100.00  E-value=8.6e-59  Score=495.05  Aligned_cols=359  Identities=34%  Similarity=0.563  Sum_probs=322.3

Q ss_pred             cccccCC--CCHHHHHHHHHcCCCCCcHHHHHHHHHHhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEE
Q 002040          467 KTWHQTG--LTSKIMETIRKLNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGL  544 (976)
Q Consensus       467 ~~~~~~~--l~~~l~~~l~~~~~~~p~~~Q~~~i~~il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vL  544 (976)
                      ..|..++  |+++|++++..+||...||+|..+||.++.++|+++.++||||||++|++|++..+............-+|
T Consensus         4 ~~~~~l~~~L~~~l~~~l~~~GF~~mTpVQa~tIPlll~~KDVvveavTGSGKTlAFllP~le~i~rr~~~~~~~~vgal   83 (567)
T KOG0345|consen    4 KSFSSLAPPLSPWLLEALDESGFEKMTPVQAATIPLLLKNKDVVVEAVTGSGKTLAFLLPMLEIIYRREAKTPPGQVGAL   83 (567)
T ss_pred             cchhhcCCCccHHHHHHHHhcCCcccCHHHHhhhHHHhcCCceEEEcCCCCCchhhHHHHHHHHHHhhccCCCccceeEE
Confidence            4566665  45999999999999999999999999999999999999999999999999999999654322221124689


Q ss_pred             EEccCHHHHHHHHHHHHHHHhh-cCcEEEEeeCCCChHHHHHHHhc-CCeEEEeCchhHHHHHHhcCCcccccCCceEEE
Q 002040          545 IMAPTRELVQQIHSDIRKFAKV-MGVRCVPVYGGSGVAQQISELKR-GTEIVVCTPGRMIDILCTSGGKITNLRRVTYLV  622 (976)
Q Consensus       545 Il~Ptr~La~Q~~~~~~~~~~~-~~~~~~~~~gg~~~~~~~~~l~~-~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vV  622 (976)
                      ||+|||+||.||.+.+..|... .++++.+++||....+.+..++. +++|+|||||+|.+++..... .+++.++.++|
T Consensus        84 IIsPTRELa~QI~~V~~~F~~~l~~l~~~l~vGG~~v~~Di~~fkee~~nIlVgTPGRL~di~~~~~~-~l~~rsLe~LV  162 (567)
T KOG0345|consen   84 IISPTRELARQIREVAQPFLEHLPNLNCELLVGGRSVEEDIKTFKEEGPNILVGTPGRLLDILQREAE-KLSFRSLEILV  162 (567)
T ss_pred             EecCcHHHHHHHHHHHHHHHHhhhccceEEEecCccHHHHHHHHHHhCCcEEEeCchhHHHHHhchhh-hccccccceEE
Confidence            9999999999999999999887 68999999999999999888775 678999999999999977442 24567999999


Q ss_pred             ecCcccccccCCchHHHHHHHhcCCCCcEEEEeccCcHHHHHHHHHHcCCCeEEEeCCccc--ccCCceEEEEecCcchH
Q 002040          623 MDEADRMFDMGFEPQITRIVQNIRPDRQTVLFSATFPRQVEILARKVLNKPVEIQVGGRSV--VNKDITQLVEVRPESDR  700 (976)
Q Consensus       623 lDEah~~~~~~f~~~i~~il~~~~~~~q~i~~SAT~~~~~~~l~~~~l~~~~~i~~~~~~~--~~~~i~q~~~~~~~~~k  700 (976)
                      |||||++++|||..++..|+..++.++.+=+||||....+..++...+.+|+.+.+.....  .+..+...+.++.+..|
T Consensus       163 LDEADrLldmgFe~~~n~ILs~LPKQRRTGLFSATq~~~v~dL~raGLRNpv~V~V~~k~~~~tPS~L~~~Y~v~~a~eK  242 (567)
T KOG0345|consen  163 LDEADRLLDMGFEASVNTILSFLPKQRRTGLFSATQTQEVEDLARAGLRNPVRVSVKEKSKSATPSSLALEYLVCEADEK  242 (567)
T ss_pred             ecchHhHhcccHHHHHHHHHHhcccccccccccchhhHHHHHHHHhhccCceeeeecccccccCchhhcceeeEecHHHH
Confidence            9999999999999999999999999999999999999999999999999999999887765  66667788889999999


Q ss_pred             HHHHHHHHHhhhcCCcEEEEecCHHHHHHHHHHHHHC--CCCceeccCCCCHHHHHHHHHHhccCCccEEEecCcccccC
Q 002040          701 FLRLLELLGEWYEKGKILIFVHSQEKCDALFRDLLKH--GYPCLSLHGAKDQTDRESTISDFKSNVCNLLIATSVAARGL  778 (976)
Q Consensus       701 ~~~l~~~l~~~~~~~kvLIF~~s~~~~~~l~~~L~~~--~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLVaT~v~~~Gl  778 (976)
                      +..|+.+|.. ....++|||++|...++.....|...  ++.++.+||.|.+..|..++..|.+..-.||+||++++|||
T Consensus       243 ~~~lv~~L~~-~~~kK~iVFF~TCasVeYf~~~~~~~l~~~~i~~iHGK~~q~~R~k~~~~F~~~~~~vl~~TDVaARGl  321 (567)
T KOG0345|consen  243 LSQLVHLLNN-NKDKKCIVFFPTCASVEYFGKLFSRLLKKREIFSIHGKMSQKARAKVLEAFRKLSNGVLFCTDVAARGL  321 (567)
T ss_pred             HHHHHHHHhc-cccccEEEEecCcchHHHHHHHHHHHhCCCcEEEecchhcchhHHHHHHHHHhccCceEEeehhhhccC
Confidence            9999999987 35679999999999999988888764  67899999999999999999999998889999999999999


Q ss_pred             CCCCCcEEEEeCCCCCHHHHHHHhcccCCCCCccEEEEEecCCCcCchH
Q 002040          779 DVKELELVINFDAPNHYEDYVHRVGRTGRAGRKGCAITFISEEDAKYSP  827 (976)
Q Consensus       779 Di~~v~~VI~~d~p~s~~~y~Qr~GR~gR~g~~g~~~~~~~~~d~~~~~  827 (976)
                      |||+|++||+||+|.++..|+||+|||||+|+.|.+++|+.+.+..|..
T Consensus       322 Dip~iD~VvQ~DpP~~~~~FvHR~GRTaR~gr~G~Aivfl~p~E~aYve  370 (567)
T KOG0345|consen  322 DIPGIDLVVQFDPPKDPSSFVHRCGRTARAGREGNAIVFLNPREEAYVE  370 (567)
T ss_pred             CCCCceEEEecCCCCChhHHHhhcchhhhccCccceEEEecccHHHHHH
Confidence            9999999999999999999999999999999999999999986655544

>KOG0326 consensus ATP-dependent RNA helicase [RNA processing and modification]

Probab=100.00  E-value=5.2e-60  Score=480.38  Aligned_cols=368  Identities=31%  Similarity=0.576  Sum_probs=346.0

Q ss_pred             cccccCCCCHHHHHHHHHcCCCCCcHHHHHHHHHHhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEE
Q 002040          467 KTWHQTGLTSKIMETIRKLNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIM  546 (976)
Q Consensus       467 ~~~~~~~l~~~l~~~l~~~~~~~p~~~Q~~~i~~il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl  546 (976)
                      ..|++++|...++..+...||..|+|+|.++||.+++|+|+|+-|..|+|||.+|++|+++.+...     .+.-+++|+
T Consensus        85 ~efEd~~Lkr~LLmgIfe~G~ekPSPiQeesIPiaLtGrdiLaRaKNGTGKT~a~~IP~Lekid~~-----~~~IQ~~il  159 (459)
T KOG0326|consen   85 NEFEDYCLKRELLMGIFEKGFEKPSPIQEESIPIALTGRDILARAKNGTGKTAAYCIPVLEKIDPK-----KNVIQAIIL  159 (459)
T ss_pred             ccHHHhhhhHHHHHHHHHhccCCCCCccccccceeecchhhhhhccCCCCCccceechhhhhcCcc-----ccceeEEEE
Confidence            569999999999999999999999999999999999999999999999999999999999987643     345689999


Q ss_pred             ccCHHHHHHHHHHHHHHHhhcCcEEEEeeCCCChHHHHHHHhcCCeEEEeCchhHHHHHHhcCCcccccCCceEEEecCc
Q 002040          547 APTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEA  626 (976)
Q Consensus       547 ~Ptr~La~Q~~~~~~~~~~~~~~~~~~~~gg~~~~~~~~~l~~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDEa  626 (976)
                      +|||+||.|+...++.+++.+++.+.+.+||++....+-.+..+++++|+|||++++++..   .+..++++.++|+|||
T Consensus       160 VPtrelALQtSqvc~~lskh~~i~vmvttGGT~lrDDI~Rl~~~VH~~vgTPGRIlDL~~K---gVa~ls~c~~lV~DEA  236 (459)
T KOG0326|consen  160 VPTRELALQTSQVCKELSKHLGIKVMVTTGGTSLRDDIMRLNQTVHLVVGTPGRILDLAKK---GVADLSDCVILVMDEA  236 (459)
T ss_pred             eecchhhHHHHHHHHHHhcccCeEEEEecCCcccccceeeecCceEEEEcCChhHHHHHhc---ccccchhceEEEechh
Confidence            9999999999999999999999999999999999999999999999999999999999865   4567899999999999


Q ss_pred             ccccccCCchHHHHHHHhcCCCCcEEEEeccCcHHHHHHHHHHcCCCeEEEeCCcccccCCceEEEEecCcchHHHHHHH
Q 002040          627 DRMFDMGFEPQITRIVQNIRPDRQTVLFSATFPRQVEILARKVLNKPVEIQVGGRSVVNKDITQLVEVRPESDRFLRLLE  706 (976)
Q Consensus       627 h~~~~~~f~~~i~~il~~~~~~~q~i~~SAT~~~~~~~l~~~~l~~~~~i~~~~~~~~~~~i~q~~~~~~~~~k~~~l~~  706 (976)
                      |.+++..|.+.+..++..++..+|++++|||||-.+..+...++.+|..|++- .......+.|++.++.+..|+..|-.
T Consensus       237 DKlLs~~F~~~~e~li~~lP~~rQillySATFP~tVk~Fm~~~l~kPy~INLM-~eLtl~GvtQyYafV~e~qKvhCLnt  315 (459)
T KOG0326|consen  237 DKLLSVDFQPIVEKLISFLPKERQILLYSATFPLTVKGFMDRHLKKPYEINLM-EELTLKGVTQYYAFVEERQKVHCLNT  315 (459)
T ss_pred             hhhhchhhhhHHHHHHHhCCccceeeEEecccchhHHHHHHHhccCcceeehh-hhhhhcchhhheeeechhhhhhhHHH
Confidence            99999999999999999999999999999999999999999999999998875 34566789999999999999988888


Q ss_pred             HHHhhhcCCcEEEEecCHHHHHHHHHHHHHCCCCceeccCCCCHHHHHHHHHHhccCCccEEEecCcccccCCCCCCcEE
Q 002040          707 LLGEWYEKGKILIFVHSQEKCDALFRDLLKHGYPCLSLHGAKDQTDRESTISDFKSNVCNLLIATSVAARGLDVKELELV  786 (976)
Q Consensus       707 ~l~~~~~~~kvLIF~~s~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLVaT~v~~~GlDi~~v~~V  786 (976)
                      ++..+ .-.+.|||||+...++.|+..+.+.||+|..+|+.|.|..|..++..|++|.++.||||+.+.+||||+.+++|
T Consensus       316 LfskL-qINQsIIFCNS~~rVELLAkKITelGyscyyiHakM~Q~hRNrVFHdFr~G~crnLVctDL~TRGIDiqavNvV  394 (459)
T KOG0326|consen  316 LFSKL-QINQSIIFCNSTNRVELLAKKITELGYSCYYIHAKMAQEHRNRVFHDFRNGKCRNLVCTDLFTRGIDIQAVNVV  394 (459)
T ss_pred             HHHHh-cccceEEEeccchHhHHHHHHHHhccchhhHHHHHHHHhhhhhhhhhhhccccceeeehhhhhcccccceeeEE
Confidence            77764 45689999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEeCCCCCHHHHHHHhcccCCCCCccEEEEEecCCCcCchHHHHHHHhhccCCCChHH
Q 002040          787 INFDAPNHYEDYVHRVGRTGRAGRKGCAITFISEEDAKYSPDLVKALELSEQVVPDDL  844 (976)
Q Consensus       787 I~~d~p~s~~~y~Qr~GR~gR~g~~g~~~~~~~~~d~~~~~~i~~~l~~~~~~vp~~l  844 (976)
                      ||||+|.+.++|+||+||.||.|..|.++.|++-+|...+..|...|.....++|..+
T Consensus       395 INFDfpk~aEtYLHRIGRsGRFGhlGlAInLityedrf~L~~IE~eLGtEI~pip~~i  452 (459)
T KOG0326|consen  395 INFDFPKNAETYLHRIGRSGRFGHLGLAINLITYEDRFNLYRIEQELGTEIKPIPSNI  452 (459)
T ss_pred             EecCCCCCHHHHHHHccCCccCCCcceEEEEEehhhhhhHHHHHHHhccccccCCCcC
Confidence            9999999999999999999999999999999999999999999999999989998643

>KOG0343 consensus RNA Helicase [RNA processing and modification]

Probab=100.00  E-value=1.3e-58  Score=500.27  Aligned_cols=364  Identities=32%  Similarity=0.533  Sum_probs=333.2

Q ss_pred             CcccccccCCCCHHHHHHHHHcCCCCCcHHHHHHHHHHhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeE
Q 002040          464 KPIKTWHQTGLTSKIMETIRKLNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVG  543 (976)
Q Consensus       464 ~pi~~~~~~~l~~~l~~~l~~~~~~~p~~~Q~~~i~~il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~v  543 (976)
                      ..+..|.+|+|+...+..|+..+|..||.+|.++||..++|+|+|+.|.||||||++|++|+|.+|.... +....|.-|
T Consensus        66 ~~~~kF~dlpls~~t~kgLke~~fv~~teiQ~~~Ip~aL~G~DvlGAAkTGSGKTLAFlvPvlE~L~r~k-Ws~~DGlGa  144 (758)
T KOG0343|consen   66 TTIKKFADLPLSQKTLKGLKEAKFVKMTEIQRDTIPMALQGHDVLGAAKTGSGKTLAFLVPVLEALYRLK-WSPTDGLGA  144 (758)
T ss_pred             hhhhhHHhCCCchHHHHhHhhcCCccHHHHHHhhcchhccCcccccccccCCCceeeehHHHHHHHHHcC-CCCCCCcee
Confidence            3457899999999999999999999999999999999999999999999999999999999999997542 345678889


Q ss_pred             EEEccCHHHHHHHHHHHHHHHhhcCcEEEEeeCCCChHHHHHHHhcCCeEEEeCchhHHHHHHhcCCcccccCCceEEEe
Q 002040          544 LIMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVM  623 (976)
Q Consensus       544 LIl~Ptr~La~Q~~~~~~~~~~~~~~~~~~~~gg~~~~~~~~~l~~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVl  623 (976)
                      |||.|||+||.|++..+.++++..++.+.++.||.........+. +++|+|||||+|+.++..+.  .++..++.++||
T Consensus       145 lIISPTRELA~QtFevL~kvgk~h~fSaGLiiGG~~~k~E~eRi~-~mNILVCTPGRLLQHmde~~--~f~t~~lQmLvL  221 (758)
T KOG0343|consen  145 LIISPTRELALQTFEVLNKVGKHHDFSAGLIIGGKDVKFELERIS-QMNILVCTPGRLLQHMDENP--NFSTSNLQMLVL  221 (758)
T ss_pred             EEecchHHHHHHHHHHHHHHhhccccccceeecCchhHHHHHhhh-cCCeEEechHHHHHHhhhcC--CCCCCcceEEEe
Confidence            999999999999999999999999999999999998877766665 48999999999999997653  255678899999


Q ss_pred             cCcccccccCCchHHHHHHHhcCCCCcEEEEeccCcHHHHHHHHHHcCCCeEEEeCCc--ccccCCceEEEEecCcchHH
Q 002040          624 DEADRMFDMGFEPQITRIVQNIRPDRQTVLFSATFPRQVEILARKVLNKPVEIQVGGR--SVVNKDITQLVEVRPESDRF  701 (976)
Q Consensus       624 DEah~~~~~~f~~~i~~il~~~~~~~q~i~~SAT~~~~~~~l~~~~l~~~~~i~~~~~--~~~~~~i~q~~~~~~~~~k~  701 (976)
                      ||||+|++|||...+..|+.++++.+|+++||||.+..+..+++..+.+|.+|.+...  ...+..+.|.|.+++...|+
T Consensus       222 DEADR~LDMGFk~tL~~Ii~~lP~~RQTLLFSATqt~svkdLaRLsL~dP~~vsvhe~a~~atP~~L~Q~y~~v~l~~Ki  301 (758)
T KOG0343|consen  222 DEADRMLDMGFKKTLNAIIENLPKKRQTLLFSATQTKSVKDLARLSLKDPVYVSVHENAVAATPSNLQQSYVIVPLEDKI  301 (758)
T ss_pred             ccHHHHHHHhHHHHHHHHHHhCChhheeeeeecccchhHHHHHHhhcCCCcEEEEeccccccChhhhhheEEEEehhhHH
Confidence            9999999999999999999999999999999999999999999999999988887632  45677899999999999999


Q ss_pred             HHHHHHHHhhhcCCcEEEEecCHHHHHHHHHHHHHC--CCCceeccCCCCHHHHHHHHHHhccCCccEEEecCcccccCC
Q 002040          702 LRLLELLGEWYEKGKILIFVHSQEKCDALFRDLLKH--GYPCLSLHGAKDQTDRESTISDFKSNVCNLLIATSVAARGLD  779 (976)
Q Consensus       702 ~~l~~~l~~~~~~~kvLIF~~s~~~~~~l~~~L~~~--~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLVaT~v~~~GlD  779 (976)
                      ..|..+|..+. ..++|||+.|.+.+..++..|...  |+++.++||.|+|..|..++..|......||+||++++||||
T Consensus       302 ~~L~sFI~shl-k~K~iVF~SscKqvkf~~e~F~rlrpg~~l~~L~G~~~Q~~R~ev~~~F~~~~~~vLF~TDv~aRGLD  380 (758)
T KOG0343|consen  302 DMLWSFIKSHL-KKKSIVFLSSCKQVKFLYEAFCRLRPGIPLLALHGTMSQKKRIEVYKKFVRKRAVVLFCTDVAARGLD  380 (758)
T ss_pred             HHHHHHHHhcc-ccceEEEEehhhHHHHHHHHHHhcCCCCceeeeccchhHHHHHHHHHHHHHhcceEEEeehhhhccCC
Confidence            99999998754 678999999999999999999875  899999999999999999999999999999999999999999


Q ss_pred             CCCCcEEEEeCCCCCHHHHHHHhcccCCCCCccEEEEEecCCC-cCchHHHHHH
Q 002040          780 VKELELVINFDAPNHYEDYVHRVGRTGRAGRKGCAITFISEED-AKYSPDLVKA  832 (976)
Q Consensus       780 i~~v~~VI~~d~p~s~~~y~Qr~GR~gR~g~~g~~~~~~~~~d-~~~~~~i~~~  832 (976)
                      +|.|++||.||+|.+..+|+||+||+.|.+..|.+++|+++.+ +.++..|.+.
T Consensus       381 FpaVdwViQ~DCPedv~tYIHRvGRtAR~~~~G~sll~L~psEeE~~l~~Lq~k  434 (758)
T KOG0343|consen  381 FPAVDWVIQVDCPEDVDTYIHRVGRTARYKERGESLLMLTPSEEEAMLKKLQKK  434 (758)
T ss_pred             CcccceEEEecCchhHHHHHHHhhhhhcccCCCceEEEEcchhHHHHHHHHHHc
Confidence            9999999999999999999999999999999999999999987 5555555554

>PRK11634 ATP-dependent RNA helicase DeaD; Provisional

Probab=100.00  E-value=3.5e-57  Score=539.08  Aligned_cols=363  Identities=38%  Similarity=0.640  Sum_probs=332.6

Q ss_pred             ccccccCCCCHHHHHHHHHcCCCCCcHHHHHHHHHHhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEE
Q 002040          466 IKTWHQTGLTSKIMETIRKLNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLI  545 (976)
Q Consensus       466 i~~~~~~~l~~~l~~~l~~~~~~~p~~~Q~~~i~~il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLI  545 (976)
                      ..+|.+++|++.++++|..+||..|+|+|.++||.++.++|+|++|+||||||++|++|++..+...     ..++++||
T Consensus         5 ~~~f~~l~L~~~ll~al~~~G~~~ptpiQ~~ai~~ll~g~dvl~~ApTGsGKT~af~lpll~~l~~~-----~~~~~~LI   79 (629)
T PRK11634          5 ETTFADLGLKAPILEALNDLGYEKPSPIQAECIPHLLNGRDVLGMAQTGSGKTAAFSLPLLHNLDPE-----LKAPQILV   79 (629)
T ss_pred             cCCHhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHcCCCEEEEcCCCCcHHHHHHHHHHHHhhhc-----cCCCeEEE
Confidence            3569999999999999999999999999999999999999999999999999999999999887542     24689999


Q ss_pred             EccCHHHHHHHHHHHHHHHhhc-CcEEEEeeCCCChHHHHHHHhcCCeEEEeCchhHHHHHHhcCCcccccCCceEEEec
Q 002040          546 MAPTRELVQQIHSDIRKFAKVM-GVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMD  624 (976)
Q Consensus       546 l~Ptr~La~Q~~~~~~~~~~~~-~~~~~~~~gg~~~~~~~~~l~~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlD  624 (976)
                      ||||++||.|++..+..|...+ ++.++.+|||.....++..+..+++|||+||++|++++...   ...|+++.+||||
T Consensus        80 L~PTreLa~Qv~~~l~~~~~~~~~i~v~~~~gG~~~~~q~~~l~~~~~IVVgTPgrl~d~l~r~---~l~l~~l~~lVlD  156 (629)
T PRK11634         80 LAPTRELAVQVAEAMTDFSKHMRGVNVVALYGGQRYDVQLRALRQGPQIVVGTPGRLLDHLKRG---TLDLSKLSGLVLD  156 (629)
T ss_pred             EeCcHHHHHHHHHHHHHHHhhcCCceEEEEECCcCHHHHHHHhcCCCCEEEECHHHHHHHHHcC---CcchhhceEEEec
Confidence            9999999999999999998775 79999999999999998889889999999999999998754   2568899999999


Q ss_pred             CcccccccCCchHHHHHHHhcCCCCcEEEEeccCcHHHHHHHHHHcCCCeEEEeCCcccccCCceEEEEecCcchHHHHH
Q 002040          625 EADRMFDMGFEPQITRIVQNIRPDRQTVLFSATFPRQVEILARKVLNKPVEIQVGGRSVVNKDITQLVEVRPESDRFLRL  704 (976)
Q Consensus       625 Eah~~~~~~f~~~i~~il~~~~~~~q~i~~SAT~~~~~~~l~~~~l~~~~~i~~~~~~~~~~~i~q~~~~~~~~~k~~~l  704 (976)
                      |||.|++++|...+..|+..++...|+++||||+|..+..++..++.+|..+.+.........+.+.+.......|...|
T Consensus       157 EAd~ml~~gf~~di~~Il~~lp~~~q~llfSAT~p~~i~~i~~~~l~~~~~i~i~~~~~~~~~i~q~~~~v~~~~k~~~L  236 (629)
T PRK11634        157 EADEMLRMGFIEDVETIMAQIPEGHQTALFSATMPEAIRRITRRFMKEPQEVRIQSSVTTRPDISQSYWTVWGMRKNEAL  236 (629)
T ss_pred             cHHHHhhcccHHHHHHHHHhCCCCCeEEEEEccCChhHHHHHHHHcCCCeEEEccCccccCCceEEEEEEechhhHHHHH
Confidence            99999999999999999999999999999999999999999999999998888776666667788888777777888888


Q ss_pred             HHHHHhhhcCCcEEEEecCHHHHHHHHHHHHHCCCCceeccCCCCHHHHHHHHHHhccCCccEEEecCcccccCCCCCCc
Q 002040          705 LELLGEWYEKGKILIFVHSQEKCDALFRDLLKHGYPCLSLHGAKDQTDRESTISDFKSNVCNLLIATSVAARGLDVKELE  784 (976)
Q Consensus       705 ~~~l~~~~~~~kvLIF~~s~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLVaT~v~~~GlDi~~v~  784 (976)
                      ..+|... ...++||||+++..+..|+..|...|+.+..+||+|++.+|..+++.|++|.++|||||+++++|||||+|+
T Consensus       237 ~~~L~~~-~~~~~IVF~~tk~~a~~l~~~L~~~g~~~~~lhgd~~q~~R~~il~~Fr~G~~~ILVATdv~arGIDip~V~  315 (629)
T PRK11634        237 VRFLEAE-DFDAAIIFVRTKNATLEVAEALERNGYNSAALNGDMNQALREQTLERLKDGRLDILIATDVAARGLDVERIS  315 (629)
T ss_pred             HHHHHhc-CCCCEEEEeccHHHHHHHHHHHHhCCCCEEEeeCCCCHHHHHHHHHHHhCCCCCEEEEcchHhcCCCcccCC
Confidence            8887653 456899999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEEEeCCCCCHHHHHHHhcccCCCCCccEEEEEecCCCcCchHHHHHHHhhcc
Q 002040          785 LVINFDAPNHYEDYVHRVGRTGRAGRKGCAITFISEEDAKYSPDLVKALELSE  837 (976)
Q Consensus       785 ~VI~~d~p~s~~~y~Qr~GR~gR~g~~g~~~~~~~~~d~~~~~~i~~~l~~~~  837 (976)
                      +|||||+|.++..|+||+|||||+|+.|.|++|+++.+...+..|.+.+....
T Consensus       316 ~VI~~d~P~~~e~yvqRiGRtGRaGr~G~ai~~v~~~e~~~l~~ie~~~~~~i  368 (629)
T PRK11634        316 LVVNYDIPMDSESYVHRIGRTGRAGRAGRALLFVENRERRLLRNIERTMKLTI  368 (629)
T ss_pred             EEEEeCCCCCHHHHHHHhccccCCCCcceEEEEechHHHHHHHHHHHHhCCCc
Confidence            99999999999999999999999999999999999988888888887765543

>PRK04537 ATP-dependent RNA helicase RhlB; Provisional

Probab=100.00  E-value=1.7e-57  Score=539.38  Aligned_cols=368  Identities=36%  Similarity=0.598  Sum_probs=331.3

Q ss_pred             ccccccCCCCHHHHHHHHHcCCCCCcHHHHHHHHHHhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCC--CCCCCeE
Q 002040          466 IKTWHQTGLTSKIMETIRKLNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVA--AGDGPVG  543 (976)
Q Consensus       466 i~~~~~~~l~~~l~~~l~~~~~~~p~~~Q~~~i~~il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~--~~~~~~v  543 (976)
                      ..+|.+++|++.|++.|..+||..|||+|.++||.++.|+|+|++||||||||++|++|++..+...+...  ...++++
T Consensus         8 ~~~f~~l~l~~~l~~~L~~~g~~~ptpiQ~~~ip~~l~G~Dvi~~ApTGSGKTlafllpil~~l~~~~~~~~~~~~~~ra   87 (572)
T PRK04537          8 DLTFSSFDLHPALLAGLESAGFTRCTPIQALTLPVALPGGDVAGQAQTGTGKTLAFLVAVMNRLLSRPALADRKPEDPRA   87 (572)
T ss_pred             CCChhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEEcCCCCcHHHHHHHHHHHHHHhcccccccccCCceE
Confidence            34799999999999999999999999999999999999999999999999999999999999987543221  1235899


Q ss_pred             EEEccCHHHHHHHHHHHHHHHhhcCcEEEEeeCCCChHHHHHHHhcCCeEEEeCchhHHHHHHhcCCcccccCCceEEEe
Q 002040          544 LIMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVM  623 (976)
Q Consensus       544 LIl~Ptr~La~Q~~~~~~~~~~~~~~~~~~~~gg~~~~~~~~~l~~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVl  623 (976)
                      |||+||++||.|++..+..|+..+++.+..++||.....+...+..+++|||+||++|++++...  ....+..+.+|||
T Consensus        88 LIl~PTreLa~Qi~~~~~~l~~~~~i~v~~l~Gg~~~~~q~~~l~~~~dIiV~TP~rL~~~l~~~--~~~~l~~v~~lVi  165 (572)
T PRK04537         88 LILAPTRELAIQIHKDAVKFGADLGLRFALVYGGVDYDKQRELLQQGVDVIIATPGRLIDYVKQH--KVVSLHACEICVL  165 (572)
T ss_pred             EEEeCcHHHHHHHHHHHHHHhccCCceEEEEECCCCHHHHHHHHhCCCCEEEECHHHHHHHHHhc--cccchhheeeeEe
Confidence            99999999999999999999999999999999999998888888888999999999999988653  2356788999999


Q ss_pred             cCcccccccCCchHHHHHHHhcCC--CCcEEEEeccCcHHHHHHHHHHcCCCeEEEeCCcccccCCceEEEEecCcchHH
Q 002040          624 DEADRMFDMGFEPQITRIVQNIRP--DRQTVLFSATFPRQVEILARKVLNKPVEIQVGGRSVVNKDITQLVEVRPESDRF  701 (976)
Q Consensus       624 DEah~~~~~~f~~~i~~il~~~~~--~~q~i~~SAT~~~~~~~l~~~~l~~~~~i~~~~~~~~~~~i~q~~~~~~~~~k~  701 (976)
                      ||||+|++++|...+..|+..++.  .+|+|+||||++..+..++..++..|..+.+.........+.+.+.+.....++
T Consensus       166 DEAh~lld~gf~~~i~~il~~lp~~~~~q~ll~SATl~~~v~~l~~~~l~~p~~i~v~~~~~~~~~i~q~~~~~~~~~k~  245 (572)
T PRK04537        166 DEADRMFDLGFIKDIRFLLRRMPERGTRQTLLFSATLSHRVLELAYEHMNEPEKLVVETETITAARVRQRIYFPADEEKQ  245 (572)
T ss_pred             cCHHHHhhcchHHHHHHHHHhcccccCceEEEEeCCccHHHHHHHHHHhcCCcEEEeccccccccceeEEEEecCHHHHH
Confidence            999999999999999999998876  789999999999999999999999987777666555666778888877777888


Q ss_pred             HHHHHHHHhhhcCCcEEEEecCHHHHHHHHHHHHHCCCCceeccCCCCHHHHHHHHHHhccCCccEEEecCcccccCCCC
Q 002040          702 LRLLELLGEWYEKGKILIFVHSQEKCDALFRDLLKHGYPCLSLHGAKDQTDRESTISDFKSNVCNLLIATSVAARGLDVK  781 (976)
Q Consensus       702 ~~l~~~l~~~~~~~kvLIF~~s~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLVaT~v~~~GlDi~  781 (976)
                      ..|+.+|.. ....++||||+++..|+.|+..|...++.+..|||+|++.+|..+++.|++|.++|||||+++++|||||
T Consensus       246 ~~L~~ll~~-~~~~k~LVF~nt~~~ae~l~~~L~~~g~~v~~lhg~l~~~eR~~il~~Fr~G~~~VLVaTdv~arGIDip  324 (572)
T PRK04537        246 TLLLGLLSR-SEGARTMVFVNTKAFVERVARTLERHGYRVGVLSGDVPQKKRESLLNRFQKGQLEILVATDVAARGLHID  324 (572)
T ss_pred             HHHHHHHhc-ccCCcEEEEeCCHHHHHHHHHHHHHcCCCEEEEeCCCCHHHHHHHHHHHHcCCCeEEEEehhhhcCCCcc
Confidence            888777754 3456899999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCcEEEEeCCCCCHHHHHHHhcccCCCCCccEEEEEecCCCcCchHHHHHHHhhc
Q 002040          782 ELELVINFDAPNHYEDYVHRVGRTGRAGRKGCAITFISEEDAKYSPDLVKALELS  836 (976)
Q Consensus       782 ~v~~VI~~d~p~s~~~y~Qr~GR~gR~g~~g~~~~~~~~~d~~~~~~i~~~l~~~  836 (976)
                      +|++|||||+|+++..|+||+||+||.|..|.|++|+++.+...+..|.+.+...
T Consensus       325 ~V~~VInyd~P~s~~~yvqRiGRaGR~G~~G~ai~~~~~~~~~~l~~i~~~~~~~  379 (572)
T PRK04537        325 GVKYVYNYDLPFDAEDYVHRIGRTARLGEEGDAISFACERYAMSLPDIEAYIEQK  379 (572)
T ss_pred             CCCEEEEcCCCCCHHHHhhhhcccccCCCCceEEEEecHHHHHHHHHHHHHHcCC
Confidence            9999999999999999999999999999999999999988887888887776544

>PRK10590 ATP-dependent RNA helicase RhlE; Provisional

Probab=100.00  E-value=3.3e-57  Score=528.13  Aligned_cols=365  Identities=38%  Similarity=0.674  Sum_probs=329.0

Q ss_pred             ccccCCCCHHHHHHHHHcCCCCCcHHHHHHHHHHhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCC-CCCCeEEEE
Q 002040          468 TWHQTGLTSKIMETIRKLNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAA-GDGPVGLIM  546 (976)
Q Consensus       468 ~~~~~~l~~~l~~~l~~~~~~~p~~~Q~~~i~~il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~-~~~~~vLIl  546 (976)
                      +|..++|++.++..|..+||..|||+|.++||.++.|+|+|+++|||||||++|++|++..+........ ...+++|||
T Consensus         2 ~f~~l~l~~~l~~~l~~~g~~~pt~iQ~~ai~~il~g~dvlv~apTGsGKTla~~lpil~~l~~~~~~~~~~~~~~aLil   81 (456)
T PRK10590          2 SFDSLGLSPDILRAVAEQGYREPTPIQQQAIPAVLEGRDLMASAQTGTGKTAGFTLPLLQHLITRQPHAKGRRPVRALIL   81 (456)
T ss_pred             CHHHcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCCcHHHHHHHHHHHHhhhcccccccCCCceEEEE
Confidence            6899999999999999999999999999999999999999999999999999999999999875432211 234589999


Q ss_pred             ccCHHHHHHHHHHHHHHHhhcCcEEEEeeCCCChHHHHHHHhcCCeEEEeCchhHHHHHHhcCCcccccCCceEEEecCc
Q 002040          547 APTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEA  626 (976)
Q Consensus       547 ~Ptr~La~Q~~~~~~~~~~~~~~~~~~~~gg~~~~~~~~~l~~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDEa  626 (976)
                      +||++||.|+++.+..++..+++.+..++||.+...+...+..+++||||||++|++++....   ..++.+.+||||||
T Consensus        82 ~PtreLa~Qi~~~~~~~~~~~~~~~~~~~gg~~~~~~~~~l~~~~~IiV~TP~rL~~~~~~~~---~~l~~v~~lViDEa  158 (456)
T PRK10590         82 TPTRELAAQIGENVRDYSKYLNIRSLVVFGGVSINPQMMKLRGGVDVLVATPGRLLDLEHQNA---VKLDQVEILVLDEA  158 (456)
T ss_pred             eCcHHHHHHHHHHHHHHhccCCCEEEEEECCcCHHHHHHHHcCCCcEEEEChHHHHHHHHcCC---cccccceEEEeecH
Confidence            999999999999999999999999999999999998888888889999999999999886532   56889999999999


Q ss_pred             ccccccCCchHHHHHHHhcCCCCcEEEEeccCcHHHHHHHHHHcCCCeEEEeCCcccccCCceEEEEecCcchHHHHHHH
Q 002040          627 DRMFDMGFEPQITRIVQNIRPDRQTVLFSATFPRQVEILARKVLNKPVEIQVGGRSVVNKDITQLVEVRPESDRFLRLLE  706 (976)
Q Consensus       627 h~~~~~~f~~~i~~il~~~~~~~q~i~~SAT~~~~~~~l~~~~l~~~~~i~~~~~~~~~~~i~q~~~~~~~~~k~~~l~~  706 (976)
                      |+|++++|...+..++..++...|+|+||||++..+..++..++.+|..+.+.........+.+.+.+.....+...|..
T Consensus       159 h~ll~~~~~~~i~~il~~l~~~~q~l~~SAT~~~~~~~l~~~~~~~~~~i~~~~~~~~~~~i~~~~~~~~~~~k~~~l~~  238 (456)
T PRK10590        159 DRMLDMGFIHDIRRVLAKLPAKRQNLLFSATFSDDIKALAEKLLHNPLEIEVARRNTASEQVTQHVHFVDKKRKRELLSQ  238 (456)
T ss_pred             HHHhccccHHHHHHHHHhCCccCeEEEEeCCCcHHHHHHHHHHcCCCeEEEEecccccccceeEEEEEcCHHHHHHHHHH
Confidence            99999999999999999999999999999999999999999999999888776666666677787777776666655555


Q ss_pred             HHHhhhcCCcEEEEecCHHHHHHHHHHHHHCCCCceeccCCCCHHHHHHHHHHhccCCccEEEecCcccccCCCCCCcEE
Q 002040          707 LLGEWYEKGKILIFVHSQEKCDALFRDLLKHGYPCLSLHGAKDQTDRESTISDFKSNVCNLLIATSVAARGLDVKELELV  786 (976)
Q Consensus       707 ~l~~~~~~~kvLIF~~s~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLVaT~v~~~GlDi~~v~~V  786 (976)
                      ++.. ....++||||+++..++.|+..|...++.+..+||+|++.+|..+++.|++|.++|||||+++++|||||+|++|
T Consensus       239 l~~~-~~~~~~lVF~~t~~~~~~l~~~L~~~g~~~~~lhg~~~~~~R~~~l~~F~~g~~~iLVaTdv~~rGiDip~v~~V  317 (456)
T PRK10590        239 MIGK-GNWQQVLVFTRTKHGANHLAEQLNKDGIRSAAIHGNKSQGARTRALADFKSGDIRVLVATDIAARGLDIEELPHV  317 (456)
T ss_pred             HHHc-CCCCcEEEEcCcHHHHHHHHHHHHHCCCCEEEEECCCCHHHHHHHHHHHHcCCCcEEEEccHHhcCCCcccCCEE
Confidence            5543 344689999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEeCCCCCHHHHHHHhcccCCCCCccEEEEEecCCCcCchHHHHHHHhhc
Q 002040          787 INFDAPNHYEDYVHRVGRTGRAGRKGCAITFISEEDAKYSPDLVKALELS  836 (976)
Q Consensus       787 I~~d~p~s~~~y~Qr~GR~gR~g~~g~~~~~~~~~d~~~~~~i~~~l~~~  836 (976)
                      |+|++|.++..|+||+||+||+|..|.|++|++..+...+..|.+.+...
T Consensus       318 I~~~~P~~~~~yvqR~GRaGR~g~~G~ai~l~~~~d~~~~~~ie~~l~~~  367 (456)
T PRK10590        318 VNYELPNVPEDYVHRIGRTGRAAATGEALSLVCVDEHKLLRDIEKLLKKE  367 (456)
T ss_pred             EEeCCCCCHHHhhhhccccccCCCCeeEEEEecHHHHHHHHHHHHHhcCC
Confidence            99999999999999999999999999999999999888888888876544

>PRK11776 ATP-dependent RNA helicase DbpA; Provisional

Probab=100.00  E-value=7.4e-57  Score=527.55  Aligned_cols=359  Identities=36%  Similarity=0.619  Sum_probs=327.7

Q ss_pred             cccccCCCCHHHHHHHHHcCCCCCcHHHHHHHHHHhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEE
Q 002040          467 KTWHQTGLTSKIMETIRKLNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIM  546 (976)
Q Consensus       467 ~~~~~~~l~~~l~~~l~~~~~~~p~~~Q~~~i~~il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl  546 (976)
                      .+|..++|++.++.+|..+||..|||+|.+|||.++.|+|+|++||||||||++|++|++..+...     ..++++|||
T Consensus         4 ~~f~~l~l~~~l~~~l~~~g~~~~t~iQ~~ai~~~l~g~dvi~~a~TGsGKT~a~~lpil~~l~~~-----~~~~~~lil   78 (460)
T PRK11776          4 TAFSTLPLPPALLANLNELGYTEMTPIQAQSLPAILAGKDVIAQAKTGSGKTAAFGLGLLQKLDVK-----RFRVQALVL   78 (460)
T ss_pred             CChhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhcCCCEEEECCCCCcHHHHHHHHHHHHhhhc-----cCCceEEEE
Confidence            579999999999999999999999999999999999999999999999999999999999988542     235689999


Q ss_pred             ccCHHHHHHHHHHHHHHHhhc-CcEEEEeeCCCChHHHHHHHhcCCeEEEeCchhHHHHHHhcCCcccccCCceEEEecC
Q 002040          547 APTRELVQQIHSDIRKFAKVM-GVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDE  625 (976)
Q Consensus       547 ~Ptr~La~Q~~~~~~~~~~~~-~~~~~~~~gg~~~~~~~~~l~~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDE  625 (976)
                      |||++||.|+...+..++..+ ++.+..++||.+...+...+..+++|+||||++|.+++....   ..+.++.+|||||
T Consensus        79 ~PtreLa~Q~~~~~~~~~~~~~~~~v~~~~Gg~~~~~~~~~l~~~~~IvV~Tp~rl~~~l~~~~---~~l~~l~~lViDE  155 (460)
T PRK11776         79 CPTRELADQVAKEIRRLARFIPNIKVLTLCGGVPMGPQIDSLEHGAHIIVGTPGRILDHLRKGT---LDLDALNTLVLDE  155 (460)
T ss_pred             eCCHHHHHHHHHHHHHHHhhCCCcEEEEEECCCChHHHHHHhcCCCCEEEEChHHHHHHHHcCC---ccHHHCCEEEEEC
Confidence            999999999999999988765 789999999999999998999999999999999999987532   5678899999999


Q ss_pred             cccccccCCchHHHHHHHhcCCCCcEEEEeccCcHHHHHHHHHHcCCCeEEEeCCcccccCCceEEEEecCcchHHHHHH
Q 002040          626 ADRMFDMGFEPQITRIVQNIRPDRQTVLFSATFPRQVEILARKVLNKPVEIQVGGRSVVNKDITQLVEVRPESDRFLRLL  705 (976)
Q Consensus       626 ah~~~~~~f~~~i~~il~~~~~~~q~i~~SAT~~~~~~~l~~~~l~~~~~i~~~~~~~~~~~i~q~~~~~~~~~k~~~l~  705 (976)
                      ||+|++++|...+..++..+++.+|+|+||||+|+.+..++..++.+|..+.+.... ....+.+.+.......++..|.
T Consensus       156 ad~~l~~g~~~~l~~i~~~~~~~~q~ll~SAT~~~~~~~l~~~~~~~~~~i~~~~~~-~~~~i~~~~~~~~~~~k~~~l~  234 (460)
T PRK11776        156 ADRMLDMGFQDAIDAIIRQAPARRQTLLFSATYPEGIAAISQRFQRDPVEVKVESTH-DLPAIEQRFYEVSPDERLPALQ  234 (460)
T ss_pred             HHHHhCcCcHHHHHHHHHhCCcccEEEEEEecCcHHHHHHHHHhcCCCEEEEECcCC-CCCCeeEEEEEeCcHHHHHHHH
Confidence            999999999999999999999999999999999999999999999999888776543 3445778887777777888888


Q ss_pred             HHHHhhhcCCcEEEEecCHHHHHHHHHHHHHCCCCceeccCCCCHHHHHHHHHHhccCCccEEEecCcccccCCCCCCcE
Q 002040          706 ELLGEWYEKGKILIFVHSQEKCDALFRDLLKHGYPCLSLHGAKDQTDRESTISDFKSNVCNLLIATSVAARGLDVKELEL  785 (976)
Q Consensus       706 ~~l~~~~~~~kvLIF~~s~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLVaT~v~~~GlDi~~v~~  785 (976)
                      .+|... ..+++||||+++..++.++..|...++.+..+||+|++.+|..++..|++|.++|||||+++++|||||++++
T Consensus       235 ~ll~~~-~~~~~lVF~~t~~~~~~l~~~L~~~~~~v~~~hg~~~~~eR~~~l~~F~~g~~~vLVaTdv~~rGiDi~~v~~  313 (460)
T PRK11776        235 RLLLHH-QPESCVVFCNTKKECQEVADALNAQGFSALALHGDLEQRDRDQVLVRFANRSCSVLVATDVAARGLDIKALEA  313 (460)
T ss_pred             HHHHhc-CCCceEEEECCHHHHHHHHHHHHhCCCcEEEEeCCCCHHHHHHHHHHHHcCCCcEEEEecccccccchhcCCe
Confidence            877643 4578999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEEeCCCCCHHHHHHHhcccCCCCCccEEEEEecCCCcCchHHHHHHHhh
Q 002040          786 VINFDAPNHYEDYVHRVGRTGRAGRKGCAITFISEEDAKYSPDLVKALEL  835 (976)
Q Consensus       786 VI~~d~p~s~~~y~Qr~GR~gR~g~~g~~~~~~~~~d~~~~~~i~~~l~~  835 (976)
                      ||+|++|.++..|+||+|||||+|..|.|++|+++.+...+..|.+.+..
T Consensus       314 VI~~d~p~~~~~yiqR~GRtGR~g~~G~ai~l~~~~e~~~~~~i~~~~~~  363 (460)
T PRK11776        314 VINYELARDPEVHVHRIGRTGRAGSKGLALSLVAPEEMQRANAIEDYLGR  363 (460)
T ss_pred             EEEecCCCCHhHhhhhcccccCCCCcceEEEEEchhHHHHHHHHHHHhCC
Confidence            99999999999999999999999999999999999887777777776654

>KOG0348 consensus ATP-dependent RNA helicase [RNA processing and modification]

Probab=100.00  E-value=9.5e-57  Score=484.66  Aligned_cols=367  Identities=34%  Similarity=0.572  Sum_probs=321.2

Q ss_pred             CcccccccCCCCHHHHHHHH-HcCCCCCcHHHHHHHHHHhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCC-CCCCCCCC
Q 002040          464 KPIKTWHQTGLTSKIMETIR-KLNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQP-PVAAGDGP  541 (976)
Q Consensus       464 ~pi~~~~~~~l~~~l~~~l~-~~~~~~p~~~Q~~~i~~il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~-~~~~~~~~  541 (976)
                      -.-..|..+||.+.+...|. .+++..||.+|.++||.|++|+|++|.++||||||++|++|++.+|.... .+....|+
T Consensus       133 fts~~f~~LGL~~~lv~~L~~~m~i~~pTsVQkq~IP~lL~grD~lV~aQTGSGKTLAYllPiVq~Lq~m~~ki~Rs~G~  212 (708)
T KOG0348|consen  133 FTSAAFASLGLHPHLVSHLNTKMKISAPTSVQKQAIPVLLEGRDALVRAQTGSGKTLAYLLPIVQSLQAMEPKIQRSDGP  212 (708)
T ss_pred             cccccchhcCCCHHHHHHHHHHhccCccchHhhcchhhhhcCcceEEEcCCCCcccHHHHHHHHHHHHhcCccccccCCc
Confidence            33457999999999999998 59999999999999999999999999999999999999999999998654 34566899


Q ss_pred             eEEEEccCHHHHHHHHHHHHHHHhhcC-cEEEEeeCCCChHHHHHHHhcCCeEEEeCchhHHHHHHhcCCcccccCCceE
Q 002040          542 VGLIMAPTRELVQQIHSDIRKFAKVMG-VRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTY  620 (976)
Q Consensus       542 ~vLIl~Ptr~La~Q~~~~~~~~~~~~~-~~~~~~~gg~~~~~~~~~l~~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~  620 (976)
                      .+|||||||+||.|+|+.+.++.+.+. +..+.+.||.........|.+|++|+|+|||+|+++|.+.  ..+.++.+.+
T Consensus       213 ~ALVivPTREL~~Q~y~~~qKLl~~~hWIVPg~lmGGEkkKSEKARLRKGiNILIgTPGRLvDHLknT--~~i~~s~LRw  290 (708)
T KOG0348|consen  213 YALVIVPTRELALQIYETVQKLLKPFHWIVPGVLMGGEKKKSEKARLRKGINILIGTPGRLVDHLKNT--KSIKFSRLRW  290 (708)
T ss_pred             eEEEEechHHHHHHHHHHHHHHhcCceEEeeceeecccccccHHHHHhcCceEEEcCchHHHHHHhcc--chheeeeeeE
Confidence            999999999999999999999987654 4445678999888888999999999999999999999765  3456788999


Q ss_pred             EEecCcccccccCCchHHHHHHHhcC-------------CCCcEEEEeccCcHHHHHHHHHHcCCCeEEEeCC-------
Q 002040          621 LVMDEADRMFDMGFEPQITRIVQNIR-------------PDRQTVLFSATFPRQVEILARKVLNKPVEIQVGG-------  680 (976)
Q Consensus       621 vVlDEah~~~~~~f~~~i~~il~~~~-------------~~~q~i~~SAT~~~~~~~l~~~~l~~~~~i~~~~-------  680 (976)
                      ||+||||+++++||...|..|+..+.             +..|.+++|||++..+..|+...+.+|+.|....       
T Consensus       291 lVlDEaDrlleLGfekdit~Il~~v~~~~~~e~~~~~lp~q~q~mLlSATLtd~V~rLa~~sLkDpv~I~ld~s~~~~~p  370 (708)
T KOG0348|consen  291 LVLDEADRLLELGFEKDITQILKAVHSIQNAECKDPKLPHQLQNMLLSATLTDGVNRLADLSLKDPVYISLDKSHSQLNP  370 (708)
T ss_pred             EEecchhHHHhccchhhHHHHHHHHhhccchhcccccccHHHHhHhhhhhhHHHHHHHhhccccCceeeeccchhhhcCc
Confidence            99999999999999999999988762             2368899999999999999999999999887211       


Q ss_pred             ------------------cccccCCceEEEEecCcchHHHHHHHHHHhhh---cCCcEEEEecCHHHHHHHHHHHHHC--
Q 002040          681 ------------------RSVVNKDITQLVEVRPESDRFLRLLELLGEWY---EKGKILIFVHSQEKCDALFRDLLKH--  737 (976)
Q Consensus       681 ------------------~~~~~~~i~q~~~~~~~~~k~~~l~~~l~~~~---~~~kvLIF~~s~~~~~~l~~~L~~~--  737 (976)
                                        ....+..+.|.|.++++.-++..|..+|....   ...++|||+.+...++.-+..|...  
T Consensus       371 ~~~a~~ev~~~~~~~~l~~~~iPeqL~qry~vVPpKLRLV~Laa~L~~~~k~~~~qk~iVF~S~~d~VeFHy~lf~~~l~  450 (708)
T KOG0348|consen  371 KDKAVQEVDDGPAGDKLDSFAIPEQLLQRYTVVPPKLRLVALAALLLNKVKFEEKQKMIVFFSCSDSVEFHYSLFSEALL  450 (708)
T ss_pred             chhhhhhcCCcccccccccccCcHHhhhceEecCCchhHHHHHHHHHHHhhhhhhceeEEEEechhHHHHHHHHHHhhhh
Confidence                              01234456788889999889888888887644   3458999999999999888777643  


Q ss_pred             --------------------CCCceeccCCCCHHHHHHHHHHhccCCccEEEecCcccccCCCCCCcEEEEeCCCCCHHH
Q 002040          738 --------------------GYPCLSLHGAKDQTDRESTISDFKSNVCNLLIATSVAARGLDVKELELVINFDAPNHYED  797 (976)
Q Consensus       738 --------------------~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLVaT~v~~~GlDi~~v~~VI~~d~p~s~~~  797 (976)
                                          +..+..+||+|.|.+|..+++.|......||+||+|++||||+|.|.+||.||+|.++++
T Consensus       451 ~~~e~~s~~~~s~g~~~l~~~~k~~rLHGsm~QeeRts~f~~Fs~~~~~VLLcTDVAaRGLDlP~V~~vVQYd~P~s~ad  530 (708)
T KOG0348|consen  451 SHLEGSSGAPDSEGLPPLFMDLKFYRLHGSMEQEERTSVFQEFSHSRRAVLLCTDVAARGLDLPHVGLVVQYDPPFSTAD  530 (708)
T ss_pred             cccccccCCcccCCChhhhhcceEEEecCchhHHHHHHHHHhhccccceEEEehhhhhccCCCCCcCeEEEeCCCCCHHH
Confidence                                356889999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHhcccCCCCCccEEEEEecCCCcCchHHHHHH
Q 002040          798 YVHRVGRTGRAGRKGCAITFISEEDAKYSPDLVKA  832 (976)
Q Consensus       798 y~Qr~GR~gR~g~~g~~~~~~~~~d~~~~~~i~~~  832 (976)
                      |+||+||+.|+|.+|.+++|+.|.+..|+..|...
T Consensus       531 ylHRvGRTARaG~kG~alLfL~P~Eaey~~~l~~~  565 (708)
T KOG0348|consen  531 YLHRVGRTARAGEKGEALLFLLPSEAEYVNYLKKH  565 (708)
T ss_pred             HHHHhhhhhhccCCCceEEEecccHHHHHHHHHhh
Confidence            99999999999999999999999988877666554

>PRK11192 ATP-dependent RNA helicase SrmB; Provisional

Probab=100.00  E-value=3.2e-55  Score=510.56  Aligned_cols=362  Identities=36%  Similarity=0.586  Sum_probs=323.0

Q ss_pred             ccccCCCCHHHHHHHHHcCCCCCcHHHHHHHHHHhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEc
Q 002040          468 TWHQTGLTSKIMETIRKLNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMA  547 (976)
Q Consensus       468 ~~~~~~l~~~l~~~l~~~~~~~p~~~Q~~~i~~il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~  547 (976)
                      +|.+++|++.+++.|..+||..|+++|.++|+.++.|+|+|++||||+|||++|++|++.++...+.. ...++++|||+
T Consensus         2 ~f~~l~l~~~l~~~l~~~g~~~p~~iQ~~ai~~~~~g~d~l~~apTGsGKT~~~~lp~l~~l~~~~~~-~~~~~~~lil~   80 (434)
T PRK11192          2 TFSELELDESLLEALQDKGYTRPTAIQAEAIPPALDGRDVLGSAPTGTGKTAAFLLPALQHLLDFPRR-KSGPPRILILT   80 (434)
T ss_pred             CHhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHHhhcccc-CCCCceEEEEC
Confidence            68999999999999999999999999999999999999999999999999999999999998764321 23357899999


Q ss_pred             cCHHHHHHHHHHHHHHHhhcCcEEEEeeCCCChHHHHHHHhcCCeEEEeCchhHHHHHHhcCCcccccCCceEEEecCcc
Q 002040          548 PTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEAD  627 (976)
Q Consensus       548 Ptr~La~Q~~~~~~~~~~~~~~~~~~~~gg~~~~~~~~~l~~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDEah  627 (976)
                      ||++||.|+++.+..++..+++.+..++||.....+...+..+++|||+||++|++++....   ..+..+.+|||||||
T Consensus        81 Pt~eLa~Q~~~~~~~l~~~~~~~v~~~~gg~~~~~~~~~l~~~~~IlV~Tp~rl~~~~~~~~---~~~~~v~~lViDEah  157 (434)
T PRK11192         81 PTRELAMQVADQARELAKHTHLDIATITGGVAYMNHAEVFSENQDIVVATPGRLLQYIKEEN---FDCRAVETLILDEAD  157 (434)
T ss_pred             CcHHHHHHHHHHHHHHHccCCcEEEEEECCCCHHHHHHHhcCCCCEEEEChHHHHHHHHcCC---cCcccCCEEEEECHH
Confidence            99999999999999999999999999999999988888888889999999999999986543   567889999999999


Q ss_pred             cccccCCchHHHHHHHhcCCCCcEEEEeccCcH-HHHHHHHHHcCCCeEEEeCCcccccCCceEEEEecCc-chHHHHHH
Q 002040          628 RMFDMGFEPQITRIVQNIRPDRQTVLFSATFPR-QVEILARKVLNKPVEIQVGGRSVVNKDITQLVEVRPE-SDRFLRLL  705 (976)
Q Consensus       628 ~~~~~~f~~~i~~il~~~~~~~q~i~~SAT~~~-~~~~l~~~~l~~~~~i~~~~~~~~~~~i~q~~~~~~~-~~k~~~l~  705 (976)
                      +|++++|...+..+...++...|+++||||++. .+..+...++.+|+.+.+.........+.+.+..... ..+...|.
T Consensus       158 ~~l~~~~~~~~~~i~~~~~~~~q~~~~SAT~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~  237 (434)
T PRK11192        158 RMLDMGFAQDIETIAAETRWRKQTLLFSATLEGDAVQDFAERLLNDPVEVEAEPSRRERKKIHQWYYRADDLEHKTALLC  237 (434)
T ss_pred             HHhCCCcHHHHHHHHHhCccccEEEEEEeecCHHHHHHHHHHHccCCEEEEecCCcccccCceEEEEEeCCHHHHHHHHH
Confidence            999999999999999999999999999999985 5788888889999888776655556667777665553 45555555


Q ss_pred             HHHHhhhcCCcEEEEecCHHHHHHHHHHHHHCCCCceeccCCCCHHHHHHHHHHhccCCccEEEecCcccccCCCCCCcE
Q 002040          706 ELLGEWYEKGKILIFVHSQEKCDALFRDLLKHGYPCLSLHGAKDQTDRESTISDFKSNVCNLLIATSVAARGLDVKELEL  785 (976)
Q Consensus       706 ~~l~~~~~~~kvLIF~~s~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLVaT~v~~~GlDi~~v~~  785 (976)
                      .++.. ...+++||||++...|..|+..|...++.+..+||+|++.+|..++..|++|.++|||||+++++|||||++++
T Consensus       238 ~l~~~-~~~~~~lVF~~s~~~~~~l~~~L~~~~~~~~~l~g~~~~~~R~~~l~~f~~G~~~vLVaTd~~~~GiDip~v~~  316 (434)
T PRK11192        238 HLLKQ-PEVTRSIVFVRTRERVHELAGWLRKAGINCCYLEGEMVQAKRNEAIKRLTDGRVNVLVATDVAARGIDIDDVSH  316 (434)
T ss_pred             HHHhc-CCCCeEEEEeCChHHHHHHHHHHHhCCCCEEEecCCCCHHHHHHHHHHHhCCCCcEEEEccccccCccCCCCCE
Confidence            55543 34579999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEEeCCCCCHHHHHHHhcccCCCCCccEEEEEecCCCcCchHHHHHHHh
Q 002040          786 VINFDAPNHYEDYVHRVGRTGRAGRKGCAITFISEEDAKYSPDLVKALE  834 (976)
Q Consensus       786 VI~~d~p~s~~~y~Qr~GR~gR~g~~g~~~~~~~~~d~~~~~~i~~~l~  834 (976)
                      ||+|++|.+...|+||+||+||+|..|.|++|++..+...+..|.+.+.
T Consensus       317 VI~~d~p~s~~~yiqr~GR~gR~g~~g~ai~l~~~~d~~~~~~i~~~~~  365 (434)
T PRK11192        317 VINFDMPRSADTYLHRIGRTGRAGRKGTAISLVEAHDHLLLGKIERYIE  365 (434)
T ss_pred             EEEECCCCCHHHHhhcccccccCCCCceEEEEecHHHHHHHHHHHHHHh
Confidence            9999999999999999999999999999999999888777777766543

>KOG0347 consensus RNA helicase [RNA processing and modification]

Probab=100.00  E-value=8.6e-57  Score=486.34  Aligned_cols=373  Identities=32%  Similarity=0.525  Sum_probs=321.1

Q ss_pred             CCcccccccCCCCHHHHHHHHHcCCCCCcHHHHHHHHHHhcC-CCEEEEcCCCCchHHHHHHHHHHHHhcCCCC------
Q 002040          463 PKPIKTWHQTGLTSKIMETIRKLNYEKPMPIQAQALPVIMSG-RDCIGVAKTGSGKTLAFVLPMLRHIKDQPPV------  535 (976)
Q Consensus       463 p~pi~~~~~~~l~~~l~~~l~~~~~~~p~~~Q~~~i~~il~g-~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~------  535 (976)
                      +..++.|.+|+|+..++.+|..+||..||+||.-.||+++.| .|+|+.|.||||||++|.+||+..+......      
T Consensus       177 ~~DvsAW~~l~lp~~iL~aL~~~gFs~Pt~IQsl~lp~ai~gk~DIlGaAeTGSGKTLAFGIPiv~~l~~~s~~s~e~~~  256 (731)
T KOG0347|consen  177 KVDVSAWKNLFLPMEILRALSNLGFSRPTEIQSLVLPAAIRGKVDILGAAETGSGKTLAFGIPIVERLLESSDDSQELSN  256 (731)
T ss_pred             ccChHHHhcCCCCHHHHHHHHhcCCCCCccchhhcccHhhccchhcccccccCCCceeeecchhhhhhhhccchHhhhhh
Confidence            566889999999999999999999999999999999999999 7999999999999999999999955432111      


Q ss_pred             --CCCCCCeEEEEccCHHHHHHHHHHHHHHHhhcCcEEEEeeCCCChHHHHHHHhcCCeEEEeCchhHHHHHHhcCCccc
Q 002040          536 --AAGDGPVGLIMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGGKIT  613 (976)
Q Consensus       536 --~~~~~~~vLIl~Ptr~La~Q~~~~~~~~~~~~~~~~~~~~gg~~~~~~~~~l~~~~~Iiv~Tp~~L~~~l~~~~~~~~  613 (976)
                        .....|.+||++|||+||.|+.+.|..++...++.+..++||.....|-..|....+|||+|||+|..++......+.
T Consensus       257 ~~~k~~k~~~LV~tPTRELa~QV~~Hl~ai~~~t~i~v~si~GGLavqKQqRlL~~~p~IVVATPGRlweli~e~n~~l~  336 (731)
T KOG0347|consen  257 TSAKYVKPIALVVTPTRELAHQVKQHLKAIAEKTQIRVASITGGLAVQKQQRLLNQRPDIVVATPGRLWELIEEDNTHLG  336 (731)
T ss_pred             HHhccCcceeEEecChHHHHHHHHHHHHHhccccCeEEEEeechhHHHHHHHHHhcCCCEEEecchHHHHHHHhhhhhhh
Confidence              111234599999999999999999999999999999999999999999888888899999999999999988776677


Q ss_pred             ccCCceEEEecCcccccccCCchHHHHHHHhcC-----CCCcEEEEeccCcHH---------------------HHHHHH
Q 002040          614 NLRRVTYLVMDEADRMFDMGFEPQITRIVQNIR-----PDRQTVLFSATFPRQ---------------------VEILAR  667 (976)
Q Consensus       614 ~l~~~~~vVlDEah~~~~~~f~~~i~~il~~~~-----~~~q~i~~SAT~~~~---------------------~~~l~~  667 (976)
                      ++..+.++||||||+|+..|+...+..|+..+.     ..+|+++||||++-.                     ++.+..
T Consensus       337 ~~k~vkcLVlDEaDRmvekghF~Els~lL~~L~e~~~~~qrQTlVFSATlt~~~~~~~~~~~k~~~k~~~~~~kiq~Lmk  416 (731)
T KOG0347|consen  337 NFKKVKCLVLDEADRMVEKGHFEELSKLLKHLNEEQKNRQRQTLVFSATLTLVLQQPLSSSRKKKDKEDELNAKIQHLMK  416 (731)
T ss_pred             hhhhceEEEEccHHHHhhhccHHHHHHHHHHhhhhhcccccceEEEEEEeehhhcChhHHhhhccchhhhhhHHHHHHHH
Confidence            899999999999999999998888888887765     568999999997422                     333333


Q ss_pred             H--HcCCCeEEEeCCcccccCCceEEEEecCcchHHHHHHHHHHhhhcCCcEEEEecCHHHHHHHHHHHHHCCCCceecc
Q 002040          668 K--VLNKPVEIQVGGRSVVNKDITQLVEVRPESDRFLRLLELLGEWYEKGKILIFVHSQEKCDALFRDLLKHGYPCLSLH  745 (976)
Q Consensus       668 ~--~l~~~~~i~~~~~~~~~~~i~q~~~~~~~~~k~~~l~~~l~~~~~~~kvLIF~~s~~~~~~l~~~L~~~~~~~~~lh  745 (976)
                      .  +..+|.+|.+.....+...+....+.|+...|-.+|+.+|..+  +|++|||||++..+..|+-+|...+++.+.||
T Consensus       417 ~ig~~~kpkiiD~t~q~~ta~~l~Es~I~C~~~eKD~ylyYfl~ry--PGrTlVF~NsId~vKRLt~~L~~L~i~p~~LH  494 (731)
T KOG0347|consen  417 KIGFRGKPKIIDLTPQSATASTLTESLIECPPLEKDLYLYYFLTRY--PGRTLVFCNSIDCVKRLTVLLNNLDIPPLPLH  494 (731)
T ss_pred             HhCccCCCeeEecCcchhHHHHHHHHhhcCCccccceeEEEEEeec--CCceEEEechHHHHHHHHHHHhhcCCCCchhh
Confidence            3  3355666665554444444444444556666666666666654  79999999999999999999999999999999


Q ss_pred             CCCCHHHHHHHHHHhccCCccEEEecCcccccCCCCCCcEEEEeCCCCCHHHHHHHhcccCCCCCccEEEEEecCCCcCc
Q 002040          746 GAKDQTDRESTISDFKSNVCNLLIATSVAARGLDVKELELVINFDAPNHYEDYVHRVGRTGRAGRKGCAITFISEEDAKY  825 (976)
Q Consensus       746 g~~~~~~R~~~~~~F~~g~~~vLVaT~v~~~GlDi~~v~~VI~~d~p~s~~~y~Qr~GR~gR~g~~g~~~~~~~~~d~~~  825 (976)
                      +.|.|.+|-..++.|++....|||||+||+||||||+|.+||||-.|.+.+.|+||.||++|++..|..++|+.|.+...
T Consensus       495 A~M~QKqRLknLEkF~~~~~~VLiaTDVAARGLDIp~V~HVIHYqVPrtseiYVHRSGRTARA~~~Gvsvml~~P~e~~~  574 (731)
T KOG0347|consen  495 ASMIQKQRLKNLEKFKQSPSGVLIATDVAARGLDIPGVQHVIHYQVPRTSEIYVHRSGRTARANSEGVSVMLCGPQEVGP  574 (731)
T ss_pred             HHHHHHHHHHhHHHHhcCCCeEEEeehhhhccCCCCCcceEEEeecCCccceeEecccccccccCCCeEEEEeChHHhHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999888


Q ss_pred             hHHHHHHHhhcc
Q 002040          826 SPDLVKALELSE  837 (976)
Q Consensus       826 ~~~i~~~l~~~~  837 (976)
                      +..|++-|....
T Consensus       575 ~~KL~ktL~k~~  586 (731)
T KOG0347|consen  575 LKKLCKTLKKKE  586 (731)
T ss_pred             HHHHHHHHhhcc
Confidence            889998886553

>KOG0346 consensus RNA helicase [RNA processing and modification]

Probab=100.00  E-value=4.2e-55  Score=462.45  Aligned_cols=367  Identities=31%  Similarity=0.519  Sum_probs=329.2

Q ss_pred             cccccCCCCHHHHHHHHHcCCCCCcHHHHHHHHHHhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCC-CCCCCCeEEE
Q 002040          467 KTWHQTGLTSKIMETIRKLNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPV-AAGDGPVGLI  545 (976)
Q Consensus       467 ~~~~~~~l~~~l~~~l~~~~~~~p~~~Q~~~i~~il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~-~~~~~~~vLI  545 (976)
                      .+|++++|.+.|++++.++||.+||-+|..|||.++.|+|+++.|.||||||.+|++|+++.|...... ....+|.++|
T Consensus        19 ktFe~~gLD~RllkAi~~lG~ekpTlIQs~aIplaLEgKDvvarArTGSGKT~AYliPllqkll~~k~t~~~e~~~sa~i   98 (569)
T KOG0346|consen   19 KTFEEFGLDSRLLKAITKLGWEKPTLIQSSAIPLALEGKDVVARARTGSGKTAAYLIPLLQKLLAEKKTNDGEQGPSAVI   98 (569)
T ss_pred             ccHHHhCCCHHHHHHHHHhCcCCcchhhhcccchhhcCcceeeeeccCCCchHHHHHHHHHHHHHhhhcccccccceeEE
Confidence            689999999999999999999999999999999999999999999999999999999999999876544 3446899999


Q ss_pred             EccCHHHHHHHHHHHHHHHhhcC--cEEEEeeCCCChHHHHHHHhcCCeEEEeCchhHHHHHHhcCCcccccCCceEEEe
Q 002040          546 MAPTRELVQQIHSDIRKFAKVMG--VRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVM  623 (976)
Q Consensus       546 l~Ptr~La~Q~~~~~~~~~~~~~--~~~~~~~gg~~~~~~~~~l~~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVl  623 (976)
                      |+||++||.|+|+.+.++....+  ++++.+....+.......|...++|||+||+.|+.++....  ...+..+.++||
T Consensus        99 LvPTkEL~qQvy~viekL~~~c~k~lr~~nl~s~~sdsv~~~~L~d~pdIvV~TP~~ll~~~~~~~--~~~~~~l~~LVv  176 (569)
T KOG0346|consen   99 LVPTKELAQQVYKVIEKLVEYCSKDLRAINLASSMSDSVNSVALMDLPDIVVATPAKLLRHLAAGV--LEYLDSLSFLVV  176 (569)
T ss_pred             EechHHHHHHHHHHHHHHHHHHHHhhhhhhhhcccchHHHHHHHccCCCeEEeChHHHHHHHhhcc--chhhhheeeEEe
Confidence            99999999999999998876653  55566665555555556777789999999999999987643  356788999999


Q ss_pred             cCcccccccCCchHHHHHHHhcCCCCcEEEEeccCcHHHHHHHHHHcCCCeEEEeCCcccc-cCCceEEEEecCcchHHH
Q 002040          624 DEADRMFDMGFEPQITRIVQNIRPDRQTVLFSATFPRQVEILARKVLNKPVEIQVGGRSVV-NKDITQLVEVRPESDRFL  702 (976)
Q Consensus       624 DEah~~~~~~f~~~i~~il~~~~~~~q~i~~SAT~~~~~~~l~~~~l~~~~~i~~~~~~~~-~~~i~q~~~~~~~~~k~~  702 (976)
                      ||||.++..||...+..+...+++..|.++||||+...+..+-..++++|+.+.+.....+ +..+.|+...+...+|+.
T Consensus       177 DEADLllsfGYeedlk~l~~~LPr~~Q~~LmSATl~dDv~~LKkL~l~nPviLkl~e~el~~~dqL~Qy~v~cse~DKfl  256 (569)
T KOG0346|consen  177 DEADLLLSFGYEEDLKKLRSHLPRIYQCFLMSATLSDDVQALKKLFLHNPVILKLTEGELPNPDQLTQYQVKCSEEDKFL  256 (569)
T ss_pred             chhhhhhhcccHHHHHHHHHhCCchhhheeehhhhhhHHHHHHHHhccCCeEEEeccccCCCcccceEEEEEeccchhHH
Confidence            9999999999999999999999999999999999999999999999999999888766554 456788888888999999


Q ss_pred             HHHHHHHhhhcCCcEEEEecCHHHHHHHHHHHHHCCCCceeccCCCCHHHHHHHHHHhccCCccEEEecC----------
Q 002040          703 RLLELLGEWYEKGKILIFVHSQEKCDALFRDLLKHGYPCLSLHGAKDQTDRESTISDFKSNVCNLLIATS----------  772 (976)
Q Consensus       703 ~l~~~l~~~~~~~kvLIF~~s~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLVaT~----------  772 (976)
                      .++.+|.-..-.|++|||+|++..|..|.-.|...|+..++++|.||...|-.++..|+.|-++|||||+          
T Consensus       257 llyallKL~LI~gKsliFVNtIdr~YrLkLfLeqFGiksciLNseLP~NSR~Hii~QFNkG~YdivIAtD~s~~~~~~ee  336 (569)
T KOG0346|consen  257 LLYALLKLRLIRGKSLIFVNTIDRCYRLKLFLEQFGIKSCILNSELPANSRCHIIEQFNKGLYDIVIATDDSADGDKLEE  336 (569)
T ss_pred             HHHHHHHHHHhcCceEEEEechhhhHHHHHHHHHhCcHhhhhcccccccchhhHHHHhhCcceeEEEEccCccchhhhhc
Confidence            9999998877889999999999999999999999999999999999999999999999999999999998          


Q ss_pred             -------------------------cccccCCCCCCcEEEEeCCCCCHHHHHHHhcccCCCCCccEEEEEecCCCcCchH
Q 002040          773 -------------------------VAARGLDVKELELVINFDAPNHYEDYVHRVGRTGRAGRKGCAITFISEEDAKYSP  827 (976)
Q Consensus       773 -------------------------v~~~GlDi~~v~~VI~~d~p~s~~~y~Qr~GR~gR~g~~g~~~~~~~~~d~~~~~  827 (976)
                                               -++||||+.+|.+|||||+|.+...|+||+|||+|++++|++++|+.+.+.....
T Consensus       337 e~kgk~~e~~~kndkkskkK~D~E~GVsRGIDF~~V~~VlNFD~P~t~~sYIHRvGRTaRg~n~GtalSfv~P~e~~g~~  416 (569)
T KOG0346|consen  337 EVKGKSDEKNPKNDKKSKKKLDKESGVSRGIDFHHVSNVLNFDFPETVTSYIHRVGRTARGNNKGTALSFVSPKEEFGKE  416 (569)
T ss_pred             cccccccccCCCCccccccccCchhchhccccchheeeeeecCCCCchHHHHHhccccccCCCCCceEEEecchHHhhhh
Confidence                                     1358999999999999999999999999999999999999999999998777555


Q ss_pred             HHHHHHhh
Q 002040          828 DLVKALEL  835 (976)
Q Consensus       828 ~i~~~l~~  835 (976)
                      .|...+..
T Consensus       417 ~le~~~~d  424 (569)
T KOG0346|consen  417 SLESILKD  424 (569)
T ss_pred             HHHHHHhh
Confidence            55555543

>PRK01297 ATP-dependent RNA helicase RhlB; Provisional

Probab=100.00  E-value=8.2e-54  Score=503.02  Aligned_cols=369  Identities=35%  Similarity=0.577  Sum_probs=328.5

Q ss_pred             cccccccCCCCHHHHHHHHHcCCCCCcHHHHHHHHHHhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCC--CCCCCe
Q 002040          465 PIKTWHQTGLTSKIMETIRKLNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVA--AGDGPV  542 (976)
Q Consensus       465 pi~~~~~~~l~~~l~~~l~~~~~~~p~~~Q~~~i~~il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~--~~~~~~  542 (976)
                      ....|..++|++.+.++|..+||..|+++|.++|+.++.|+|+|++++||||||++|++|++..+...+...  ....++
T Consensus        85 ~~~~f~~~~l~~~l~~~l~~~g~~~~~~iQ~~ai~~~~~G~dvi~~apTGSGKTlay~lpil~~l~~~~~~~~~~~~~~~  164 (475)
T PRK01297         85 GKTRFHDFNLAPELMHAIHDLGFPYCTPIQAQVLGYTLAGHDAIGRAQTGTGKTAAFLISIINQLLQTPPPKERYMGEPR  164 (475)
T ss_pred             CCCCHhHCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHHHhcCcccccccCCce
Confidence            346789999999999999999999999999999999999999999999999999999999999987653211  112579


Q ss_pred             EEEEccCHHHHHHHHHHHHHHHhhcCcEEEEeeCCCChHHHHHHHhc-CCeEEEeCchhHHHHHHhcCCcccccCCceEE
Q 002040          543 GLIMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQISELKR-GTEIVVCTPGRMIDILCTSGGKITNLRRVTYL  621 (976)
Q Consensus       543 vLIl~Ptr~La~Q~~~~~~~~~~~~~~~~~~~~gg~~~~~~~~~l~~-~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~v  621 (976)
                      +|||+||++||.|++..+..++..+++.+..++||.....+...+.. .++|||+||++|+.++...   ...|.++.+|
T Consensus       165 aLil~PtreLa~Q~~~~~~~l~~~~~~~v~~~~gg~~~~~~~~~~~~~~~~Iiv~TP~~Ll~~~~~~---~~~l~~l~~l  241 (475)
T PRK01297        165 ALIIAPTRELVVQIAKDAAALTKYTGLNVMTFVGGMDFDKQLKQLEARFCDILVATPGRLLDFNQRG---EVHLDMVEVM  241 (475)
T ss_pred             EEEEeCcHHHHHHHHHHHHHhhccCCCEEEEEEccCChHHHHHHHhCCCCCEEEECHHHHHHHHHcC---CcccccCceE
Confidence            99999999999999999999999899999999999888877777654 5899999999998877543   2568889999


Q ss_pred             EecCcccccccCCchHHHHHHHhcCC--CCcEEEEeccCcHHHHHHHHHHcCCCeEEEeCCcccccCCceEEEEecCcch
Q 002040          622 VMDEADRMFDMGFEPQITRIVQNIRP--DRQTVLFSATFPRQVEILARKVLNKPVEIQVGGRSVVNKDITQLVEVRPESD  699 (976)
Q Consensus       622 VlDEah~~~~~~f~~~i~~il~~~~~--~~q~i~~SAT~~~~~~~l~~~~l~~~~~i~~~~~~~~~~~i~q~~~~~~~~~  699 (976)
                      ||||||.+++++|...+..++..+..  ..|+|+||||++..+..++..++.++..+.+.........+.+.+.......
T Consensus       242 ViDEah~l~~~~~~~~l~~i~~~~~~~~~~q~i~~SAT~~~~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~  321 (475)
T PRK01297        242 VLDEADRMLDMGFIPQVRQIIRQTPRKEERQTLLFSATFTDDVMNLAKQWTTDPAIVEIEPENVASDTVEQHVYAVAGSD  321 (475)
T ss_pred             EechHHHHHhcccHHHHHHHHHhCCCCCCceEEEEEeecCHHHHHHHHHhccCCEEEEeccCcCCCCcccEEEEEecchh
Confidence            99999999999999999999998854  5799999999999999999999999988877666666666777777777777


Q ss_pred             HHHHHHHHHHhhhcCCcEEEEecCHHHHHHHHHHHHHCCCCceeccCCCCHHHHHHHHHHhccCCccEEEecCcccccCC
Q 002040          700 RFLRLLELLGEWYEKGKILIFVHSQEKCDALFRDLLKHGYPCLSLHGAKDQTDRESTISDFKSNVCNLLIATSVAARGLD  779 (976)
Q Consensus       700 k~~~l~~~l~~~~~~~kvLIF~~s~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLVaT~v~~~GlD  779 (976)
                      +...|..++... ...++||||+++..++.++..|...++.+..+||++++.+|..+++.|++|.+.|||||+++++|||
T Consensus       322 k~~~l~~ll~~~-~~~~~IVF~~s~~~~~~l~~~L~~~~~~~~~~~g~~~~~~R~~~~~~Fr~G~~~vLvaT~~l~~GID  400 (475)
T PRK01297        322 KYKLLYNLVTQN-PWERVMVFANRKDEVRRIEERLVKDGINAAQLSGDVPQHKRIKTLEGFREGKIRVLVATDVAGRGIH  400 (475)
T ss_pred             HHHHHHHHHHhc-CCCeEEEEeCCHHHHHHHHHHHHHcCCCEEEEECCCCHHHHHHHHHHHhCCCCcEEEEccccccCCc
Confidence            777777776542 3468999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCcEEEEeCCCCCHHHHHHHhcccCCCCCccEEEEEecCCCcCchHHHHHHHhhcc
Q 002040          780 VKELELVINFDAPNHYEDYVHRVGRTGRAGRKGCAITFISEEDAKYSPDLVKALELSE  837 (976)
Q Consensus       780 i~~v~~VI~~d~p~s~~~y~Qr~GR~gR~g~~g~~~~~~~~~d~~~~~~i~~~l~~~~  837 (976)
                      |+++++||+|++|.+...|+||+||+||.|..|.+++|++..|..++..+.+.+....
T Consensus       401 i~~v~~VI~~~~P~s~~~y~Qr~GRaGR~g~~g~~i~~~~~~d~~~~~~~~~~~~~~~  458 (475)
T PRK01297        401 IDGISHVINFTLPEDPDDYVHRIGRTGRAGASGVSISFAGEDDAFQLPEIEELLGRKI  458 (475)
T ss_pred             ccCCCEEEEeCCCCCHHHHHHhhCccCCCCCCceEEEEecHHHHHHHHHHHHHhCCCC
Confidence            9999999999999999999999999999999999999999988888888888776654

>PTZ00424 helicase 45; Provisional

Probab=100.00  E-value=2.4e-52  Score=482.77  Aligned_cols=368  Identities=33%  Similarity=0.570  Sum_probs=322.8

Q ss_pred             cccccccCCCCHHHHHHHHHcCCCCCcHHHHHHHHHHhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEE
Q 002040          465 PIKTWHQTGLTSKIMETIRKLNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGL  544 (976)
Q Consensus       465 pi~~~~~~~l~~~l~~~l~~~~~~~p~~~Q~~~i~~il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vL  544 (976)
                      .+.+|.++++++.+.++|..+||..|+|+|.++|+.++.|+|+|++||||||||++|++|++.++...     ..++++|
T Consensus        26 ~~~~~~~l~l~~~~~~~l~~~~~~~~~~~Q~~ai~~i~~~~d~ii~apTGsGKT~~~~l~~l~~~~~~-----~~~~~~l  100 (401)
T PTZ00424         26 IVDSFDALKLNEDLLRGIYSYGFEKPSAIQQRGIKPILDGYDTIGQAQSGTGKTATFVIAALQLIDYD-----LNACQAL  100 (401)
T ss_pred             ccCCHhhCCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHhcCC-----CCCceEE
Confidence            35789999999999999999999999999999999999999999999999999999999999887532     2467899


Q ss_pred             EEccCHHHHHHHHHHHHHHHhhcCcEEEEeeCCCChHHHHHHHhcCCeEEEeCchhHHHHHHhcCCcccccCCceEEEec
Q 002040          545 IMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMD  624 (976)
Q Consensus       545 Il~Ptr~La~Q~~~~~~~~~~~~~~~~~~~~gg~~~~~~~~~l~~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlD  624 (976)
                      ||+||++||.|+...+..++...++.+..++||.....++..+..+++|+|+||++|.+++....   ..+.++++||||
T Consensus       101 il~Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~Ivv~Tp~~l~~~l~~~~---~~l~~i~lvViD  177 (401)
T PTZ00424        101 ILAPTRELAQQIQKVVLALGDYLKVRCHACVGGTVVRDDINKLKAGVHMVVGTPGRVYDMIDKRH---LRVDDLKLFILD  177 (401)
T ss_pred             EECCCHHHHHHHHHHHHHHhhhcCceEEEEECCcCHHHHHHHHcCCCCEEEECcHHHHHHHHhCC---cccccccEEEEe
Confidence            99999999999999999999888899999999998888888888889999999999998886543   468889999999


Q ss_pred             CcccccccCCchHHHHHHHhcCCCCcEEEEeccCcHHHHHHHHHHcCCCeEEEeCCcccccCCceEEEEecCc-chHHHH
Q 002040          625 EADRMFDMGFEPQITRIVQNIRPDRQTVLFSATFPRQVEILARKVLNKPVEIQVGGRSVVNKDITQLVEVRPE-SDRFLR  703 (976)
Q Consensus       625 Eah~~~~~~f~~~i~~il~~~~~~~q~i~~SAT~~~~~~~l~~~~l~~~~~i~~~~~~~~~~~i~q~~~~~~~-~~k~~~  703 (976)
                      |||++++.+|...+..++..+++..|+|++|||+|+.+..+...++..|..+.+.........+.+.+..... ..+...
T Consensus       178 Eah~~~~~~~~~~~~~i~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  257 (401)
T PTZ00424        178 EADEMLSRGFKGQIYDVFKKLPPDVQVALFSATMPNEILELTTKFMRDPKRILVKKDELTLEGIRQFYVAVEKEEWKFDT  257 (401)
T ss_pred             cHHHHHhcchHHHHHHHHhhCCCCcEEEEEEecCCHHHHHHHHHHcCCCEEEEeCCCCcccCCceEEEEecChHHHHHHH
Confidence            9999999999999999999999999999999999999988888999888777665555455556665554443 334444


Q ss_pred             HHHHHHhhhcCCcEEEEecCHHHHHHHHHHHHHCCCCceeccCCCCHHHHHHHHHHhccCCccEEEecCcccccCCCCCC
Q 002040          704 LLELLGEWYEKGKILIFVHSQEKCDALFRDLLKHGYPCLSLHGAKDQTDRESTISDFKSNVCNLLIATSVAARGLDVKEL  783 (976)
Q Consensus       704 l~~~l~~~~~~~kvLIF~~s~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLVaT~v~~~GlDi~~v  783 (976)
                      +..++.. ....++||||+++..++.++..|...++.+..+||+|++.+|..+++.|++|.++|||||+++++|||+|++
T Consensus       258 l~~~~~~-~~~~~~ivF~~t~~~~~~l~~~l~~~~~~~~~~h~~~~~~~R~~i~~~f~~g~~~vLvaT~~l~~GiDip~v  336 (401)
T PTZ00424        258 LCDLYET-LTITQAIIYCNTRRKVDYLTKKMHERDFTVSCMHGDMDQKDRDLIMREFRSGSTRVLITTDLLARGIDVQQV  336 (401)
T ss_pred             HHHHHHh-cCCCeEEEEecCcHHHHHHHHHHHHCCCcEEEEeCCCCHHHHHHHHHHHHcCCCCEEEEcccccCCcCcccC
Confidence            5544433 345689999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cEEEEeCCCCCHHHHHHHhcccCCCCCccEEEEEecCCCcCchHHHHHHHhhccCCCC
Q 002040          784 ELVINFDAPNHYEDYVHRVGRTGRAGRKGCAITFISEEDAKYSPDLVKALELSEQVVP  841 (976)
Q Consensus       784 ~~VI~~d~p~s~~~y~Qr~GR~gR~g~~g~~~~~~~~~d~~~~~~i~~~l~~~~~~vp  841 (976)
                      ++||+|++|.+...|+||+||+||.|..|.|++|+++.+...+..+.+.+.......|
T Consensus       337 ~~VI~~~~p~s~~~y~qr~GRagR~g~~G~~i~l~~~~~~~~~~~~e~~~~~~~~~~~  394 (401)
T PTZ00424        337 SLVINYDLPASPENYIHRIGRSGRFGRKGVAINFVTPDDIEQLKEIERHYNTQIEEMP  394 (401)
T ss_pred             CEEEEECCCCCHHHEeecccccccCCCCceEEEEEcHHHHHHHHHHHHHHCCcccccC
Confidence            9999999999999999999999999999999999999888777777776655444443

>KOG0344 consensus ATP-dependent RNA helicase [RNA processing and modification]

Probab=100.00  E-value=9e-52  Score=455.65  Aligned_cols=401  Identities=33%  Similarity=0.547  Sum_probs=348.4

Q ss_pred             HHHHHhhcCceeccCCCCCccccccc----CCCCHHHHHHHHHcCCCCCcHHHHHHHHHHhcCCCEEEEcCCCCchHHHH
Q 002040          446 VSAYRKQLELKIHGKDVPKPIKTWHQ----TGLTSKIMETIRKLNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAF  521 (976)
Q Consensus       446 ~~~~~~~~~i~~~g~~~p~pi~~~~~----~~l~~~l~~~l~~~~~~~p~~~Q~~~i~~il~g~d~i~~a~TGsGKT~~~  521 (976)
                      ....|+.+.+.+.|..+|+|+.+|.+    +.+...+++.+...+|..|+|+|.+|||.++.+++++.|||||||||++|
T Consensus       111 ~~~~Rk~~k~~v~G~~~~~~l~~f~~lt~~~~~~~~ll~nl~~~~F~~Pt~iq~~aipvfl~~r~~lAcapTGsgKtlaf  190 (593)
T KOG0344|consen  111 LLGIRKSNKINVDGFHLPPPLLSFSDLTYDYSMNKRLLENLQELGFDEPTPIQKQAIPVFLEKRDVLACAPTGSGKTLAF  190 (593)
T ss_pred             cccchhcceeeccCCCCCCccccccccchhhhhcHHHHHhHhhCCCCCCCcccchhhhhhhcccceEEeccCCCcchhhh
Confidence            44567788899999999999999997    67899999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHHHH--hhcCcEEEEeeCCCChHHHH-HHHhcCCeEEEeCc
Q 002040          522 VLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFA--KVMGVRCVPVYGGSGVAQQI-SELKRGTEIVVCTP  598 (976)
Q Consensus       522 ~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~~~--~~~~~~~~~~~gg~~~~~~~-~~l~~~~~Iiv~Tp  598 (976)
                      ++|++.+|..........|-+++|+.||++||.|++.++.++.  ...++.+..+.......... ......++|+|+||
T Consensus       191 ~~Pil~~L~~~~~~~~~~gl~a~Il~ptreLa~Qi~re~~k~~~~~~t~~~a~~~~~~~~~~qk~a~~~~~k~dili~TP  270 (593)
T KOG0344|consen  191 NLPILQHLKDLSQEKHKVGLRALILSPTRELAAQIYREMRKYSIDEGTSLRAAQFSKPAYPSQKPAFLSDEKYDILISTP  270 (593)
T ss_pred             hhHHHHHHHHhhcccCccceEEEEecchHHHHHHHHHHHHhcCCCCCCchhhhhcccccchhhccchhHHHHHHHHhcCH
Confidence            9999999987643333557899999999999999999999998  55555554433322111111 11122479999999


Q ss_pred             hhHHHHHHhcCCcccccCCceEEEecCccccccc-CCchHHHHHHHhcC-CCCcEEEEeccCcHHHHHHHHHHcCCCeEE
Q 002040          599 GRMIDILCTSGGKITNLRRVTYLVMDEADRMFDM-GFEPQITRIVQNIR-PDRQTVLFSATFPRQVEILARKVLNKPVEI  676 (976)
Q Consensus       599 ~~L~~~l~~~~~~~~~l~~~~~vVlDEah~~~~~-~f~~~i~~il~~~~-~~~q~i~~SAT~~~~~~~l~~~~l~~~~~i  676 (976)
                      .+|..++.... ....|..+.++|+||||+++.. .|..|+..|+..+. ++..+-+||||++..++.++...+.+++.+
T Consensus       271 ~ri~~~~~~~~-~~idl~~V~~lV~dEaD~lfe~~~f~~Qla~I~sac~s~~i~~a~FSat~~~~VEE~~~~i~~~~~~v  349 (593)
T KOG0344|consen  271 MRIVGLLGLGK-LNIDLSKVEWLVVDEADLLFEPEFFVEQLADIYSACQSPDIRVALFSATISVYVEEWAELIKSDLKRV  349 (593)
T ss_pred             HHHHHHhcCCC-ccchhheeeeEeechHHhhhChhhHHHHHHHHHHHhcCcchhhhhhhccccHHHHHHHHHhhccceeE
Confidence            99988885532 2247889999999999999998 89999999988775 556677899999999999999999999999


Q ss_pred             EeCCcccccCCceEEE-EecCcchHHHHHHHHHHhhhcCCcEEEEecCHHHHHHHHHHH-HHCCCCceeccCCCCHHHHH
Q 002040          677 QVGGRSVVNKDITQLV-EVRPESDRFLRLLELLGEWYEKGKILIFVHSQEKCDALFRDL-LKHGYPCLSLHGAKDQTDRE  754 (976)
Q Consensus       677 ~~~~~~~~~~~i~q~~-~~~~~~~k~~~l~~~l~~~~~~~kvLIF~~s~~~~~~l~~~L-~~~~~~~~~lhg~~~~~~R~  754 (976)
                      .++..+.....|.|.. .+.....|+..+.+++.... ..++|||+++.+.|..|+..| .-.++.+.+|||..++.+|.
T Consensus       350 ivg~~~sa~~~V~QelvF~gse~~K~lA~rq~v~~g~-~PP~lIfVQs~eRak~L~~~L~~~~~i~v~vIh~e~~~~qrd  428 (593)
T KOG0344|consen  350 IVGLRNSANETVDQELVFCGSEKGKLLALRQLVASGF-KPPVLIFVQSKERAKQLFEELEIYDNINVDVIHGERSQKQRD  428 (593)
T ss_pred             EEecchhHhhhhhhhheeeecchhHHHHHHHHHhccC-CCCeEEEEecHHHHHHHHHHhhhccCcceeeEecccchhHHH
Confidence            9998888777777765 45567789999999888753 569999999999999999999 66789999999999999999


Q ss_pred             HHHHHhccCCccEEEecCcccccCCCCCCcEEEEeCCCCCHHHHHHHhcccCCCCCccEEEEEecCCCcCchHHHHHHHh
Q 002040          755 STISDFKSNVCNLLIATSVAARGLDVKELELVINFDAPNHYEDYVHRVGRTGRAGRKGCAITFISEEDAKYSPDLVKALE  834 (976)
Q Consensus       755 ~~~~~F~~g~~~vLVaT~v~~~GlDi~~v~~VI~~d~p~s~~~y~Qr~GR~gR~g~~g~~~~~~~~~d~~~~~~i~~~l~  834 (976)
                      .++..|+.|++.|||||+++++|||+.++++|||||+|.+...|+||+||+||+|+.|.||+||+..+..++..|...+.
T Consensus       429 e~~~~FR~g~IwvLicTdll~RGiDf~gvn~VInyD~p~s~~syihrIGRtgRag~~g~Aitfytd~d~~~ir~iae~~~  508 (593)
T KOG0344|consen  429 ETMERFRIGKIWVLICTDLLARGIDFKGVNLVINYDFPQSDLSYIHRIGRTGRAGRSGKAITFYTDQDMPRIRSIAEVME  508 (593)
T ss_pred             HHHHHHhccCeeEEEehhhhhccccccCcceEEecCCCchhHHHHHHhhccCCCCCCcceEEEeccccchhhhhHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hccCCCChHHHHHH
Q 002040          835 LSEQVVPDDLKALA  848 (976)
Q Consensus       835 ~~~~~vp~~l~~l~  848 (976)
                      .++..||.++..+.
T Consensus       509 ~sG~evpe~~m~~~  522 (593)
T KOG0344|consen  509 QSGCEVPEKIMGIK  522 (593)
T ss_pred             HcCCcchHHHHhhh
Confidence            99999999876555

>KOG0337 consensus ATP-dependent RNA helicase [RNA processing and modification]

Probab=100.00  E-value=2.6e-52  Score=439.56  Aligned_cols=363  Identities=33%  Similarity=0.553  Sum_probs=341.9

Q ss_pred             ccccccCCCCHHHHHHHHHcCCCCCcHHHHHHHHHHhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEE
Q 002040          466 IKTWHQTGLTSKIMETIRKLNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLI  545 (976)
Q Consensus       466 i~~~~~~~l~~~l~~~l~~~~~~~p~~~Q~~~i~~il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLI  545 (976)
                      --.|..+||...++.+|.+.||..|||+|...||.|+.+++++..+-||||||.+|++||+.++....    ..|.++||
T Consensus        20 ~g~fqsmgL~~~v~raI~kkg~~~ptpiqRKTipliLe~~dvv~martgsgktaaf~ipm~e~Lk~~s----~~g~Rali   95 (529)
T KOG0337|consen   20 SGGFQSMGLDYKVLRAIHKKGFNTPTPIQRKTIPLILEGRDVVGMARTGSGKTAAFLIPMIEKLKSHS----QTGLRALI   95 (529)
T ss_pred             CCCccccCCCHHHHHHHHHhhcCCCCchhcccccceeeccccceeeecCCcchhhHHHHHHHHHhhcc----ccccceee
Confidence            45799999999999999999999999999999999999999999999999999999999999998752    45789999


Q ss_pred             EccCHHHHHHHHHHHHHHHhhcCcEEEEeeCCCChHHHHHHHhcCCeEEEeCchhHHHHHHhcCCcccccCCceEEEecC
Q 002040          546 MAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDE  625 (976)
Q Consensus       546 l~Ptr~La~Q~~~~~~~~~~~~~~~~~~~~gg~~~~~~~~~l~~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDE  625 (976)
                      +.||++||.|....++.++...++++++++||....+++..+..+.+||++||++++.+....   ...|+.+.|||+||
T Consensus        96 lsptreLa~qtlkvvkdlgrgt~lr~s~~~ggD~~eeqf~~l~~npDii~ATpgr~~h~~vem---~l~l~sveyVVfdE  172 (529)
T KOG0337|consen   96 LSPTRELALQTLKVVKDLGRGTKLRQSLLVGGDSIEEQFILLNENPDIIIATPGRLLHLGVEM---TLTLSSVEYVVFDE  172 (529)
T ss_pred             ccCcHHHHHHHHHHHHHhccccchhhhhhcccchHHHHHHHhccCCCEEEecCceeeeeehhe---eccccceeeeeehh
Confidence            999999999999999999999999999999999999999999989999999999997765432   25788999999999


Q ss_pred             cccccccCCchHHHHHHHhcCCCCcEEEEeccCcHHHHHHHHHHcCCCeEEEeCCcccccCCceEEEEecCcchHHHHHH
Q 002040          626 ADRMFDMGFEPQITRIVQNIRPDRQTVLFSATFPRQVEILARKVLNKPVEIQVGGRSVVNKDITQLVEVRPESDRFLRLL  705 (976)
Q Consensus       626 ah~~~~~~f~~~i~~il~~~~~~~q~i~~SAT~~~~~~~l~~~~l~~~~~i~~~~~~~~~~~i~q~~~~~~~~~k~~~l~  705 (976)
                      |++++.|||.+++..++..++..+|+++||||+|..+..+++..+.+|+.+.+...+-+...+...+..+...+|...|+
T Consensus       173 adrlfemgfqeql~e~l~rl~~~~QTllfSatlp~~lv~fakaGl~~p~lVRldvetkise~lk~~f~~~~~a~K~aaLl  252 (529)
T KOG0337|consen  173 ADRLFEMGFQEQLHEILSRLPESRQTLLFSATLPRDLVDFAKAGLVPPVLVRLDVETKISELLKVRFFRVRKAEKEAALL  252 (529)
T ss_pred             hhHHHhhhhHHHHHHHHHhCCCcceEEEEeccCchhhHHHHHccCCCCceEEeehhhhcchhhhhheeeeccHHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999998888888888888888899999999999


Q ss_pred             HHHHhhhcCCcEEEEecCHHHHHHHHHHHHHCCCCceeccCCCCHHHHHHHHHHhccCCccEEEecCcccccCCCCCCcE
Q 002040          706 ELLGEWYEKGKILIFVHSQEKCDALFRDLLKHGYPCLSLHGAKDQTDRESTISDFKSNVCNLLIATSVAARGLDVKELEL  785 (976)
Q Consensus       706 ~~l~~~~~~~kvLIF~~s~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLVaT~v~~~GlDi~~v~~  785 (976)
                      .++.......+++|||.+...++.+...|...|+.+..++|.|++.-|...+..|..++..+||.|+++++|+|||.+..
T Consensus       253 ~il~~~~~~~~t~vf~~tk~hve~~~~ll~~~g~~~s~iysslD~~aRk~~~~~F~~~k~~~lvvTdvaaRG~diplldn  332 (529)
T KOG0337|consen  253 SILGGRIKDKQTIVFVATKHHVEYVRGLLRDFGGEGSDIYSSLDQEARKINGRDFRGRKTSILVVTDVAARGLDIPLLDN  332 (529)
T ss_pred             HHHhccccccceeEEecccchHHHHHHHHHhcCCCccccccccChHhhhhccccccCCccceEEEehhhhccCCCccccc
Confidence            99998877778999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEEeCCCCCHHHHHHHhcccCCCCCccEEEEEecCCCcCchHHHHHHHhh
Q 002040          786 VINFDAPNHYEDYVHRVGRTGRAGRKGCAITFISEEDAKYSPDLVKALEL  835 (976)
Q Consensus       786 VI~~d~p~s~~~y~Qr~GR~gR~g~~g~~~~~~~~~d~~~~~~i~~~l~~  835 (976)
                      |||||+|.....|+||+||+.|+|..|.+|.|+.+.+..++-+|.-++..
T Consensus       333 vinyd~p~~~klFvhRVgr~aragrtg~aYs~V~~~~~~yl~DL~lflgr  382 (529)
T KOG0337|consen  333 VINYDFPPDDKLFVHRVGRVARAGRTGRAYSLVASTDDPYLLDLQLFLGR  382 (529)
T ss_pred             cccccCCCCCceEEEEecchhhccccceEEEEEecccchhhhhhhhhcCC
Confidence            99999999999999999999999999999999999999998888877644

>KOG0332 consensus ATP-dependent RNA helicase [RNA processing and modification]

Probab=100.00  E-value=6e-51  Score=423.23  Aligned_cols=374  Identities=30%  Similarity=0.521  Sum_probs=322.9

Q ss_pred             CCCcccccccCCCCHHHHHHHHHcCCCCCcHHHHHHHHHHhcC--CCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCC
Q 002040          462 VPKPIKTWHQTGLTSKIMETIRKLNYEKPMPIQAQALPVIMSG--RDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGD  539 (976)
Q Consensus       462 ~p~pi~~~~~~~l~~~l~~~l~~~~~~~p~~~Q~~~i~~il~g--~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~  539 (976)
                      +.-.+++|.+++|.+.+++.|..++|.+|+.||..|+|.++..  +++|.++..|+|||.+|.|.||..+.-.     .-
T Consensus        85 PlyS~ksFeeL~LkPellkgly~M~F~kPskIQe~aLPlll~~Pp~nlIaQsqsGtGKTaaFvL~MLsrvd~~-----~~  159 (477)
T KOG0332|consen   85 PLYSAKSFEELRLKPELLKGLYAMKFQKPSKIQETALPLLLAEPPQNLIAQSQSGTGKTAAFVLTMLSRVDPD-----VV  159 (477)
T ss_pred             CccccccHHhhCCCHHHHhHHHHhccCCcchHHHhhcchhhcCCchhhhhhhcCCCchhHHHHHHHHHhcCcc-----cc
Confidence            3456789999999999999999999999999999999999976  7999999999999999999999886532     23


Q ss_pred             CCeEEEEccCHHHHHHHHHHHHHHHhhcCcEEEEeeCCCChHHHHHHHhcCCeEEEeCchhHHHHHHhcCCcccccCCce
Q 002040          540 GPVGLIMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVT  619 (976)
Q Consensus       540 ~~~vLIl~Ptr~La~Q~~~~~~~~~~~~~~~~~~~~gg~~~~~~~~~l~~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~  619 (976)
                      .|+++.|+||++||.|+.+.+.+.++..++.+...+.|.....   .-.-..+|+|+|||.+.+++..-  +...+..+.
T Consensus       160 ~PQ~iCLaPtrELA~Q~~eVv~eMGKf~~ita~yair~sk~~r---G~~i~eqIviGTPGtv~Dlm~kl--k~id~~kik  234 (477)
T KOG0332|consen  160 VPQCICLAPTRELAPQTGEVVEEMGKFTELTASYAIRGSKAKR---GNKLTEQIVIGTPGTVLDLMLKL--KCIDLEKIK  234 (477)
T ss_pred             CCCceeeCchHHHHHHHHHHHHHhcCceeeeEEEEecCccccc---CCcchhheeeCCCccHHHHHHHH--HhhChhhce
Confidence            6889999999999999999999999888888888777761110   00112589999999999998652  346788899


Q ss_pred             EEEecCccccccc-CCchHHHHHHHhcCCCCcEEEEeccCcHHHHHHHHHHcCCCeEEEeCCcccccCCceEEEEecC-c
Q 002040          620 YLVMDEADRMFDM-GFEPQITRIVQNIRPDRQTVLFSATFPRQVEILARKVLNKPVEIQVGGRSVVNKDITQLVEVRP-E  697 (976)
Q Consensus       620 ~vVlDEah~~~~~-~f~~~i~~il~~~~~~~q~i~~SAT~~~~~~~l~~~~l~~~~~i~~~~~~~~~~~i~q~~~~~~-~  697 (976)
                      ++|+|||+.|++. ||..+-..|...++++.|+|+||||+...+..++..++.++..+.+........+|.|.+..+. .
T Consensus       235 vfVlDEAD~Mi~tqG~~D~S~rI~~~lP~~~QllLFSATf~e~V~~Fa~kivpn~n~i~Lk~eel~L~~IkQlyv~C~~~  314 (477)
T KOG0332|consen  235 VFVLDEADVMIDTQGFQDQSIRIMRSLPRNQQLLLFSATFVEKVAAFALKIVPNANVIILKREELALDNIKQLYVLCACR  314 (477)
T ss_pred             EEEecchhhhhhcccccccchhhhhhcCCcceEEeeechhHHHHHHHHHHhcCCCceeeeehhhccccchhhheeeccch
Confidence            9999999988875 6999999999999999999999999999999999999999999999888888889999886665 5


Q ss_pred             chHHHHHHHHHHhhhcCCcEEEEecCHHHHHHHHHHHHHCCCCceeccCCCCHHHHHHHHHHhccCCccEEEecCccccc
Q 002040          698 SDRFLRLLELLGEWYEKGKILIFVHSQEKCDALFRDLLKHGYPCLSLHGAKDQTDRESTISDFKSNVCNLLIATSVAARG  777 (976)
Q Consensus       698 ~~k~~~l~~~l~~~~~~~kvLIF~~s~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLVaT~v~~~G  777 (976)
                      .+|+..|.. |.....-|+.||||.++..+..|+..|...|+.+.++||.|...+|..++..|+.|..+|||+|++++||
T Consensus       315 ~~K~~~l~~-lyg~~tigqsiIFc~tk~ta~~l~~~m~~~Gh~V~~l~G~l~~~~R~~ii~~Fr~g~~kVLitTnV~ARG  393 (477)
T KOG0332|consen  315 DDKYQALVN-LYGLLTIGQSIIFCHTKATAMWLYEEMRAEGHQVSLLHGDLTVEQRAAIIDRFREGKEKVLITTNVCARG  393 (477)
T ss_pred             hhHHHHHHH-HHhhhhhhheEEEEeehhhHHHHHHHHHhcCceeEEeeccchhHHHHHHHHHHhcCcceEEEEechhhcc
Confidence            678888888 4444566899999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCCCcEEEEeCCCC------CHHHHHHHhcccCCCCCccEEEEEecCC-CcCchHHHHHHHhhcc-CCCChHHHH
Q 002040          778 LDVKELELVINFDAPN------HYEDYVHRVGRTGRAGRKGCAITFISEE-DAKYSPDLVKALELSE-QVVPDDLKA  846 (976)
Q Consensus       778 lDi~~v~~VI~~d~p~------s~~~y~Qr~GR~gR~g~~g~~~~~~~~~-d~~~~~~i~~~l~~~~-~~vp~~l~~  846 (976)
                      ||++.|++|||||+|.      +++.|+||+||+||.|++|.++.|+... ....+..|.+.+.... ...|+++..
T Consensus       394 iDv~qVs~VvNydlP~~~~~~pD~etYlHRiGRtGRFGkkG~a~n~v~~~~s~~~mn~iq~~F~~~i~~~~~~d~~E  470 (477)
T KOG0332|consen  394 IDVAQVSVVVNYDLPVKYTGEPDYETYLHRIGRTGRFGKKGLAINLVDDKDSMNIMNKIQKHFNMKIKRLDPDDLDE  470 (477)
T ss_pred             cccceEEEEEecCCccccCCCCCHHHHHHHhcccccccccceEEEeecccCcHHHHHHHHHHHhhcceecCCccHHH
Confidence            9999999999999996      5899999999999999999999999754 4455557777664432 344554443

>KOG0327 consensus Translation initiation factor 4F, helicase subunit (eIF-4A) and related helicases [Translation, ribosomal structure and biogenesis]

Probab=100.00  E-value=1.2e-50  Score=426.43  Aligned_cols=367  Identities=34%  Similarity=0.579  Sum_probs=337.8

Q ss_pred             ccccccCCCCHHHHHHHHHcCCCCCcHHHHHHHHHHhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEE
Q 002040          466 IKTWHQTGLTSKIMETIRKLNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLI  545 (976)
Q Consensus       466 i~~~~~~~l~~~l~~~l~~~~~~~p~~~Q~~~i~~il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLI  545 (976)
                      +.+|++++|+..|+..+..+||.+|+.+|+.||+.+..|.|+++.+++|+|||.+|+++++.++.-.     ....+|||
T Consensus        25 vdsfddm~L~e~LLrgiy~yGFekPSaIQqraI~p~i~G~dv~~qaqsgTgKt~af~i~iLq~iD~~-----~ke~qali   99 (397)
T KOG0327|consen   25 VDSFDDMNLKESLLRGIYAYGFEKPSAIQQRAILPCIKGHDVIAQAQSGTGKTAAFLISILQQIDMS-----VKETQALI   99 (397)
T ss_pred             hhhhhhcCCCHHHHhHHHhhccCCchHHHhccccccccCCceeEeeeccccchhhhHHHHHhhcCcc-----hHHHHHHH
Confidence            4589999999999999999999999999999999999999999999999999999999999887421     23567999


Q ss_pred             EccCHHHHHHHHHHHHHHHhhcCcEEEEeeCCCChHHHHHHHhc-CCeEEEeCchhHHHHHHhcCCcccccCCceEEEec
Q 002040          546 MAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQISELKR-GTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMD  624 (976)
Q Consensus       546 l~Ptr~La~Q~~~~~~~~~~~~~~~~~~~~gg~~~~~~~~~l~~-~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlD  624 (976)
                      ++||++||.|+......+...+++.+..++||.....+...++. +.+|+|+|||++.+++...   ......+.++|+|
T Consensus       100 laPtreLa~qi~~v~~~lg~~~~~~v~~~igg~~~~~~~~~i~~~~~hivvGTpgrV~dml~~~---~l~~~~iKmfvlD  176 (397)
T KOG0327|consen  100 LAPTRELAQQIQKVVRALGDHMDVSVHACIGGTNVRREDQALLKDKPHIVVGTPGRVFDMLNRG---SLSTDGIKMFVLD  176 (397)
T ss_pred             hcchHHHHHHHHHHHHhhhcccceeeeeecCcccchhhhhhhhccCceeecCCchhHHHhhccc---cccccceeEEeec
Confidence            99999999999999999999999999999999988866655554 5899999999999998654   2456779999999


Q ss_pred             CcccccccCCchHHHHHHHhcCCCCcEEEEeccCcHHHHHHHHHHcCCCeEEEeCCcccccCCceEEEEecCcchHHHHH
Q 002040          625 EADRMFDMGFEPQITRIVQNIRPDRQTVLFSATFPRQVEILARKVLNKPVEIQVGGRSVVNKDITQLVEVRPESDRFLRL  704 (976)
Q Consensus       625 Eah~~~~~~f~~~i~~il~~~~~~~q~i~~SAT~~~~~~~l~~~~l~~~~~i~~~~~~~~~~~i~q~~~~~~~~~k~~~l  704 (976)
                      ||+.|+..||..++..|+..++++.|++++|||+|.++..+...|+.+|+.+.+.........+.|.+.......|+..|
T Consensus       177 EaDEmLs~gfkdqI~~if~~lp~~vQv~l~SAT~p~~vl~vt~~f~~~pv~i~vkk~~ltl~gikq~~i~v~k~~k~~~l  256 (397)
T KOG0327|consen  177 EADEMLSRGFKDQIYDIFQELPSDVQVVLLSATMPSDVLEVTKKFMREPVRILVKKDELTLEGIKQFYINVEKEEKLDTL  256 (397)
T ss_pred             chHhhhccchHHHHHHHHHHcCcchhheeecccCcHHHHHHHHHhccCceEEEecchhhhhhheeeeeeeccccccccHH
Confidence            99999999999999999999999999999999999999999999999999999998888888899999888777899888


Q ss_pred             HHHHHhhhcCCcEEEEecCHHHHHHHHHHHHHCCCCceeccCCCCHHHHHHHHHHhccCCccEEEecCcccccCCCCCCc
Q 002040          705 LELLGEWYEKGKILIFVHSQEKCDALFRDLLKHGYPCLSLHGAKDQTDRESTISDFKSNVCNLLIATSVAARGLDVKELE  784 (976)
Q Consensus       705 ~~~l~~~~~~~kvLIF~~s~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLVaT~v~~~GlDi~~v~  784 (976)
                      ..+..   .-.+.+||||+...+..|...|..+++.+.++||.|.+.+|..++..|+.|..+|||.|+.+++|+||..+.
T Consensus       257 ~dl~~---~~~q~~if~nt~r~v~~l~~~L~~~~~~~s~~~~d~~q~~R~~~~~ef~~gssrvlIttdl~argidv~~~s  333 (397)
T KOG0327|consen  257 CDLYR---RVTQAVIFCNTRRKVDNLTDKLRAHGFTVSAIHGDMEQNERDTLMREFRSGSSRVLITTDLLARGIDVQQVS  333 (397)
T ss_pred             HHHHH---hhhcceEEecchhhHHHHHHHHhhCCceEEEeecccchhhhhHHHHHhhcCCceEEeeccccccccchhhcc
Confidence            88877   457899999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEEEeCCCCCHHHHHHHhcccCCCCCccEEEEEecCCCcCchHHHHHHHhhccCCCChH
Q 002040          785 LVINFDAPNHYEDYVHRVGRTGRAGRKGCAITFISEEDAKYSPDLVKALELSEQVVPDD  843 (976)
Q Consensus       785 ~VI~~d~p~s~~~y~Qr~GR~gR~g~~g~~~~~~~~~d~~~~~~i~~~l~~~~~~vp~~  843 (976)
                      .||||+.|.+..+|+||+||+||.|.+|.++.|++..+...+.++.+++.......|..
T Consensus       334 lvinydlP~~~~~yihR~gr~gr~grkg~~in~v~~~d~~~lk~ie~~y~~~i~e~p~~  392 (397)
T KOG0327|consen  334 LVVNYDLPARKENYIHRIGRAGRFGRKGVAINFVTEEDVRDLKDIEKFYNTPIEELPSN  392 (397)
T ss_pred             eeeeeccccchhhhhhhcccccccCCCceeeeeehHhhHHHHHhHHHhcCCcceecccc
Confidence            99999999999999999999999999999999999999999999998887666666653

>KOG4284 consensus DEAD box protein [Transcription]

Probab=100.00  E-value=3.4e-50  Score=440.77  Aligned_cols=352  Identities=30%  Similarity=0.514  Sum_probs=316.2

Q ss_pred             CCCcccccccCCCCHHHHHHHHHcCCCCCcHHHHHHHHHHhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCC
Q 002040          462 VPKPIKTWHQTGLTSKIMETIRKLNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGP  541 (976)
Q Consensus       462 ~p~pi~~~~~~~l~~~l~~~l~~~~~~~p~~~Q~~~i~~il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~  541 (976)
                      .|.-...|.++.|...++..|...+|..||++|..|||.++++.|+||++..|+|||++|.+.++..+.-     ....+
T Consensus        20 ~~~~~~~fe~l~l~r~vl~glrrn~f~~ptkiQaaAIP~~~~kmDliVQaKSGTGKTlVfsv~av~sl~~-----~~~~~   94 (980)
T KOG4284|consen   20 QSNCTPGFEQLALWREVLLGLRRNAFALPTKIQAAAIPAIFSKMDLIVQAKSGTGKTLVFSVLAVESLDS-----RSSHI   94 (980)
T ss_pred             ccCCCCCHHHHHHHHHHHHHHHhhcccCCCchhhhhhhhhhcccceEEEecCCCCceEEEEeeeehhcCc-----ccCcc
Confidence            3556678999999999999999999999999999999999999999999999999999999888876653     34578


Q ss_pred             eEEEEccCHHHHHHHHHHHHHHHhhc-CcEEEEeeCCCChHHHHHHHhcCCeEEEeCchhHHHHHHhcCCcccccCCceE
Q 002040          542 VGLIMAPTRELVQQIHSDIRKFAKVM-GVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTY  620 (976)
Q Consensus       542 ~vLIl~Ptr~La~Q~~~~~~~~~~~~-~~~~~~~~gg~~~~~~~~~l~~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~  620 (976)
                      ++|||+|||++|.|+...+..++..+ |++|.+++||+........|+. +.|+|+|||+|..++...   ..+.+++.+
T Consensus        95 q~~Iv~PTREiaVQI~~tv~~v~~sf~g~~csvfIGGT~~~~d~~rlk~-~rIvIGtPGRi~qL~el~---~~n~s~vrl  170 (980)
T KOG4284|consen   95 QKVIVTPTREIAVQIKETVRKVAPSFTGARCSVFIGGTAHKLDLIRLKQ-TRIVIGTPGRIAQLVELG---AMNMSHVRL  170 (980)
T ss_pred             eeEEEecchhhhhHHHHHHHHhcccccCcceEEEecCchhhhhhhhhhh-ceEEecCchHHHHHHHhc---CCCccceeE
Confidence            89999999999999999999999754 8999999999999988888775 899999999999998764   478899999


Q ss_pred             EEecCccccccc-CCchHHHHHHHhcCCCCcEEEEeccCcHHHHHHHHHHcCCCeEEEeCCcccccCCceEEEEecCcch
Q 002040          621 LVMDEADRMFDM-GFEPQITRIVQNIRPDRQTVLFSATFPRQVEILARKVLNKPVEIQVGGRSVVNKDITQLVEVRPESD  699 (976)
Q Consensus       621 vVlDEah~~~~~-~f~~~i~~il~~~~~~~q~i~~SAT~~~~~~~l~~~~l~~~~~i~~~~~~~~~~~i~q~~~~~~~~~  699 (976)
                      +||||||.+++. .|..+|..|+..++..+|++.||||-|..+..++.+||.+|..+...........|.|++.......
T Consensus       171 fVLDEADkL~~t~sfq~~In~ii~slP~~rQv~a~SATYp~nLdn~Lsk~mrdp~lVr~n~~d~~L~GikQyv~~~~s~n  250 (980)
T KOG4284|consen  171 FVLDEADKLMDTESFQDDINIIINSLPQIRQVAAFSATYPRNLDNLLSKFMRDPALVRFNADDVQLFGIKQYVVAKCSPN  250 (980)
T ss_pred             EEeccHHhhhchhhHHHHHHHHHHhcchhheeeEEeccCchhHHHHHHHHhcccceeecccCCceeechhheeeeccCCc
Confidence            999999999884 5999999999999999999999999999999999999999999998888888888999887655432


Q ss_pred             --------HHHHHHHHHHhhhcCCcEEEEecCHHHHHHHHHHHHHCCCCceeccCCCCHHHHHHHHHHhccCCccEEEec
Q 002040          700 --------RFLRLLELLGEWYEKGKILIFVHSQEKCDALFRDLLKHGYPCLSLHGAKDQTDRESTISDFKSNVCNLLIAT  771 (976)
Q Consensus       700 --------k~~~l~~~l~~~~~~~kvLIF~~s~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLVaT  771 (976)
                              |+..|..++.. .+-.++||||+.+..|+-++.+|...|+.|.+|.|.|+|.+|..++..+++-.++|||+|
T Consensus       251 nsveemrlklq~L~~vf~~-ipy~QAlVF~~~~sra~~~a~~L~ssG~d~~~ISgaM~Q~~Rl~a~~~lr~f~~rILVsT  329 (980)
T KOG4284|consen  251 NSVEEMRLKLQKLTHVFKS-IPYVQALVFCDQISRAEPIATHLKSSGLDVTFISGAMSQKDRLLAVDQLRAFRVRILVST  329 (980)
T ss_pred             chHHHHHHHHHHHHHHHhh-CchHHHHhhhhhhhhhhHHHHHhhccCCCeEEeccccchhHHHHHHHHhhhceEEEEEec
Confidence                    33444444433 234589999999999999999999999999999999999999999999999999999999


Q ss_pred             CcccccCCCCCCcEEEEeCCCCCHHHHHHHhcccCCCCCccEEEEEecCCCc
Q 002040          772 SVAARGLDVKELELVINFDAPNHYEDYVHRVGRTGRAGRKGCAITFISEEDA  823 (976)
Q Consensus       772 ~v~~~GlDi~~v~~VI~~d~p~s~~~y~Qr~GR~gR~g~~g~~~~~~~~~d~  823 (976)
                      +..+||||-+.+++|||.|+|.+..+|.||||||||.|..|.+++|+....+
T Consensus       330 DLtaRGIDa~~vNLVVNiD~p~d~eTY~HRIGRAgRFG~~G~aVT~~~~~~e  381 (980)
T KOG4284|consen  330 DLTARGIDADNVNLVVNIDAPADEETYFHRIGRAGRFGAHGAAVTLLEDERE  381 (980)
T ss_pred             chhhccCCccccceEEecCCCcchHHHHHHhhhcccccccceeEEEeccchh
Confidence            9999999999999999999999999999999999999999999999976543

>KOG0350 consensus DEAD-box ATP-dependent RNA helicase [RNA processing and modification]

Probab=100.00  E-value=7.1e-49  Score=421.52  Aligned_cols=361  Identities=28%  Similarity=0.477  Sum_probs=297.5

Q ss_pred             CHHHHHHHHHcCCCCCcHHHHHHHHHHh---------cCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEE
Q 002040          475 TSKIMETIRKLNYEKPMPIQAQALPVIM---------SGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLI  545 (976)
Q Consensus       475 ~~~l~~~l~~~~~~~p~~~Q~~~i~~il---------~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLI  545 (976)
                      ...+.+.|.++++...+|+|..++|+++         ..+|+.|.||||||||++|.+||++.+...+.    +..++||
T Consensus       145 ea~~~q~l~k~~is~~FPVQ~aVlp~ll~~~~~p~~~r~rDIcV~ApTGSGKTLaY~iPIVQ~L~~R~v----~~LRavV  220 (620)
T KOG0350|consen  145 EATIDQLLVKMAISRLFPVQYAVLPSLLEEIRSPPPSRPRDICVNAPTGSGKTLAYVIPIVQLLSSRPV----KRLRAVV  220 (620)
T ss_pred             HHHHHHHHHHhhcccccchHHHHHHHHHHhhcCCCCCCCCceEEecCCCCCceeeehhHHHHHHccCCc----cceEEEE
Confidence            3455677899999999999999999996         25799999999999999999999999887532    3468999


Q ss_pred             EccCHHHHHHHHHHHHHHHhhcCcEEEEeeCCCChHHHHHHHhcC-----CeEEEeCchhHHHHHHhcCCcccccCCceE
Q 002040          546 MAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQISELKRG-----TEIVVCTPGRMIDILCTSGGKITNLRRVTY  620 (976)
Q Consensus       546 l~Ptr~La~Q~~~~~~~~~~~~~~~~~~~~gg~~~~~~~~~l~~~-----~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~  620 (976)
                      |+||++|+.|++..|..++...|+.|+.+.|..+......+|...     .+|+|+|||+|+++|.+.  +-++|.++.|
T Consensus       221 ivPtr~L~~QV~~~f~~~~~~tgL~V~~~sgq~sl~~E~~qL~~~~~~~~~DIlVaTPGRLVDHl~~~--k~f~Lk~Lrf  298 (620)
T KOG0350|consen  221 IVPTRELALQVYDTFKRLNSGTGLAVCSLSGQNSLEDEARQLASDPPECRIDILVATPGRLVDHLNNT--KSFDLKHLRF  298 (620)
T ss_pred             EeeHHHHHHHHHHHHHHhccCCceEEEecccccchHHHHHHHhcCCCccccceEEcCchHHHHhccCC--CCcchhhceE
Confidence            999999999999999999999999999999988887777776652     389999999999999753  4478999999


Q ss_pred             EEecCcccccccCCchHHHHHHHhc----------------------------------CCCCcEEEEeccCcHHHHHHH
Q 002040          621 LVMDEADRMFDMGFEPQITRIVQNI----------------------------------RPDRQTVLFSATFPRQVEILA  666 (976)
Q Consensus       621 vVlDEah~~~~~~f~~~i~~il~~~----------------------------------~~~~q~i~~SAT~~~~~~~l~  666 (976)
                      +||||||||++..|..-+-.++..+                                  .+..+.++||||++.....+.
T Consensus       299 LVIDEADRll~qsfQ~Wl~~v~~~~~~~k~~~~~~nii~~~~~~~pt~~~e~~t~~~~~~~~l~kL~~satLsqdP~Kl~  378 (620)
T KOG0350|consen  299 LVIDEADRLLDQSFQEWLDTVMSLCKTMKRVACLDNIIRQRQAPQPTVLSELLTKLGKLYPPLWKLVFSATLSQDPSKLK  378 (620)
T ss_pred             EEechHHHHHHHHHHHHHHHHHHHhCCchhhcChhhhhhhcccCCchhhHHHHhhcCCcCchhHhhhcchhhhcChHHHh
Confidence            9999999998765433322222111                                  122347889999887777788


Q ss_pred             HHHcCCCeEEEeC----CcccccCCceEEEEecCcchHHHHHHHHHHhhhcCCcEEEEecCHHHHHHHHHHHH----HCC
Q 002040          667 RKVLNKPVEIQVG----GRSVVNKDITQLVEVRPESDRFLRLLELLGEWYEKGKILIFVHSQEKCDALFRDLL----KHG  738 (976)
Q Consensus       667 ~~~l~~~~~i~~~----~~~~~~~~i~q~~~~~~~~~k~~~l~~~l~~~~~~~kvLIF~~s~~~~~~l~~~L~----~~~  738 (976)
                      ..-++.|..+.+.    +....+..+.+...+....-+...+..+|..+ .-.++|||+++...+..|+..|.    ..+
T Consensus       379 ~l~l~~Prl~~v~~~~~~ryslp~~l~~~~vv~~~~~kpl~~~~lI~~~-k~~r~lcf~~S~~sa~Rl~~~L~v~~~~~~  457 (620)
T KOG0350|consen  379 DLTLHIPRLFHVSKPLIGRYSLPSSLSHRLVVTEPKFKPLAVYALITSN-KLNRTLCFVNSVSSANRLAHVLKVEFCSDN  457 (620)
T ss_pred             hhhcCCCceEEeecccceeeecChhhhhceeecccccchHhHHHHHHHh-hcceEEEEecchHHHHHHHHHHHHHhcccc
Confidence            8788888544443    34445556666666666666777777777654 45699999999999999999887    235


Q ss_pred             CCceeccCCCCHHHHHHHHHHhccCCccEEEecCcccccCCCCCCcEEEEeCCCCCHHHHHHHhcccCCCCCccEEEEEe
Q 002040          739 YPCLSLHGAKDQTDRESTISDFKSNVCNLLIATSVAARGLDVKELELVINFDAPNHYEDYVHRVGRTGRAGRKGCAITFI  818 (976)
Q Consensus       739 ~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLVaT~v~~~GlDi~~v~~VI~~d~p~s~~~y~Qr~GR~gR~g~~g~~~~~~  818 (976)
                      +.+-.+.|+++...|...+..|..|.+.|||||++++||+||.++++|||||+|.+...|+||+||++|+|+.|+||+++
T Consensus       458 ~~~s~~t~~l~~k~r~k~l~~f~~g~i~vLIcSD~laRGiDv~~v~~VINYd~P~~~ktyVHR~GRTARAgq~G~a~tll  537 (620)
T KOG0350|consen  458 FKVSEFTGQLNGKRRYKMLEKFAKGDINVLICSDALARGIDVNDVDNVINYDPPASDKTYVHRAGRTARAGQDGYAITLL  537 (620)
T ss_pred             chhhhhhhhhhHHHHHHHHHHHhcCCceEEEehhhhhcCCcccccceEeecCCCchhhHHHHhhcccccccCCceEEEee
Confidence            67777999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCCcCchHHHHHHHhh----ccCCCCh
Q 002040          819 SEEDAKYSPDLVKALEL----SEQVVPD  842 (976)
Q Consensus       819 ~~~d~~~~~~i~~~l~~----~~~~vp~  842 (976)
                      +..+...+..+++....    ..+++|.
T Consensus       538 ~~~~~r~F~klL~~~~~~d~~~i~~~e~  565 (620)
T KOG0350|consen  538 DKHEKRLFSKLLKKTNLWDGVEIQPIEY  565 (620)
T ss_pred             ccccchHHHHHHHHhcccCCcceeecCc
Confidence            99999988888887654    3455554

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

Probab=100.00  E-value=3.8e-47  Score=461.80  Aligned_cols=347  Identities=20%  Similarity=0.261  Sum_probs=274.4

Q ss_pred             CCCHHHHHHHHHcCCCCCcHHHHHHHHHHhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHH
Q 002040          473 GLTSKIMETIRKLNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTREL  552 (976)
Q Consensus       473 ~l~~~l~~~l~~~~~~~p~~~Q~~~i~~il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~L  552 (976)
                      .|++.+.+.|...||..|+++|.++|+.++.|+|+|+++|||||||++|++|++..+...      .++++|||+||++|
T Consensus        20 ~l~~~l~~~L~~~g~~~p~~~Q~~ai~~il~G~nvvv~apTGSGKTla~~LPiL~~l~~~------~~~~aL~l~PtraL   93 (742)
T TIGR03817        20 WAHPDVVAALEAAGIHRPWQHQARAAELAHAGRHVVVATGTASGKSLAYQLPVLSALADD------PRATALYLAPTKAL   93 (742)
T ss_pred             cCCHHHHHHHHHcCCCcCCHHHHHHHHHHHCCCCEEEECCCCCcHHHHHHHHHHHHHhhC------CCcEEEEEcChHHH
Confidence            478999999999999999999999999999999999999999999999999999998753      25789999999999


Q ss_pred             HHHHHHHHHHHHhhcCcEEEEeeCCCChHHHHHHHhcCCeEEEeCchhHHHHHHhc-CCcccccCCceEEEecCcccccc
Q 002040          553 VQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTS-GGKITNLRRVTYLVMDEADRMFD  631 (976)
Q Consensus       553 a~Q~~~~~~~~~~~~~~~~~~~~gg~~~~~~~~~l~~~~~Iiv~Tp~~L~~~l~~~-~~~~~~l~~~~~vVlDEah~~~~  631 (976)
                      |.|++..+..+. ..++.+..+.|+.+. .+...+..+++|||+||++|...+... ......|+++.+|||||||.|.+
T Consensus        94 a~q~~~~l~~l~-~~~i~v~~~~Gdt~~-~~r~~i~~~~~IivtTPd~L~~~~L~~~~~~~~~l~~l~~vViDEah~~~g  171 (742)
T TIGR03817        94 AADQLRAVRELT-LRGVRPATYDGDTPT-EERRWAREHARYVLTNPDMLHRGILPSHARWARFLRRLRYVVIDECHSYRG  171 (742)
T ss_pred             HHHHHHHHHHhc-cCCeEEEEEeCCCCH-HHHHHHhcCCCEEEEChHHHHHhhccchhHHHHHHhcCCEEEEeChhhccC
Confidence            999999999987 457888777777664 444566677999999999986533221 11112478899999999999876


Q ss_pred             cCCchHHHHHHHh-------cCCCCcEEEEeccCcHHHHHHHHHHcCCCeEEEeCCcccccCCceEEEEecCc-------
Q 002040          632 MGFEPQITRIVQN-------IRPDRQTVLFSATFPRQVEILARKVLNKPVEIQVGGRSVVNKDITQLVEVRPE-------  697 (976)
Q Consensus       632 ~~f~~~i~~il~~-------~~~~~q~i~~SAT~~~~~~~l~~~~l~~~~~i~~~~~~~~~~~i~q~~~~~~~-------  697 (976)
                       .|..++..++..       ....+|+|+||||+++... ++..++..++.+ +.....+.... +.+.+.+.       
T Consensus       172 -~fg~~~~~il~rL~ri~~~~g~~~q~i~~SATi~n~~~-~~~~l~g~~~~~-i~~~~~~~~~~-~~~~~~p~~~~~~~~  247 (742)
T TIGR03817       172 -VFGSHVALVLRRLRRLCARYGASPVFVLASATTADPAA-AASRLIGAPVVA-VTEDGSPRGAR-TVALWEPPLTELTGE  247 (742)
T ss_pred             -ccHHHHHHHHHHHHHHHHhcCCCCEEEEEecCCCCHHH-HHHHHcCCCeEE-ECCCCCCcCce-EEEEecCCccccccc
Confidence             377665555443       3567899999999998865 567777777544 32222222222 22211111       


Q ss_pred             ----------chHHHHHHHHHHhhhcCCcEEEEecCHHHHHHHHHHHHHC--------CCCceeccCCCCHHHHHHHHHH
Q 002040          698 ----------SDRFLRLLELLGEWYEKGKILIFVHSQEKCDALFRDLLKH--------GYPCLSLHGAKDQTDRESTISD  759 (976)
Q Consensus       698 ----------~~k~~~l~~~l~~~~~~~kvLIF~~s~~~~~~l~~~L~~~--------~~~~~~lhg~~~~~~R~~~~~~  759 (976)
                                ..+...+..++.   ...++||||+|+..++.++..|...        +..+..+||++++.+|..+++.
T Consensus       248 ~~~~~r~~~~~~~~~~l~~l~~---~~~~~IVF~~sr~~ae~l~~~l~~~l~~~~~~l~~~v~~~hgg~~~~eR~~ie~~  324 (742)
T TIGR03817       248 NGAPVRRSASAEAADLLADLVA---EGARTLTFVRSRRGAELVAAIARRLLGEVDPDLAERVAAYRAGYLPEDRRELERA  324 (742)
T ss_pred             cccccccchHHHHHHHHHHHHH---CCCCEEEEcCCHHHHHHHHHHHHHHHHhhccccccchhheecCCCHHHHHHHHHH
Confidence                      123333333333   3579999999999999999988763        5688999999999999999999


Q ss_pred             hccCCccEEEecCcccccCCCCCCcEEEEeCCCCCHHHHHHHhcccCCCCCccEEEEEecC--CCcCchHHHHHHHh
Q 002040          760 FKSNVCNLLIATSVAARGLDVKELELVINFDAPNHYEDYVHRVGRTGRAGRKGCAITFISE--EDAKYSPDLVKALE  834 (976)
Q Consensus       760 F~~g~~~vLVaT~v~~~GlDi~~v~~VI~~d~p~s~~~y~Qr~GR~gR~g~~g~~~~~~~~--~d~~~~~~i~~~l~  834 (976)
                      |++|.++|||||+++++||||+++++||+|++|.+...|+||+|||||.|+.|.+++|++.  .|..++..+.+.+.
T Consensus       325 f~~G~i~vLVaTd~lerGIDI~~vd~VI~~~~P~s~~~y~qRiGRaGR~G~~g~ai~v~~~~~~d~~~~~~~~~~~~  401 (742)
T TIGR03817       325 LRDGELLGVATTNALELGVDISGLDAVVIAGFPGTRASLWQQAGRAGRRGQGALVVLVARDDPLDTYLVHHPEALFD  401 (742)
T ss_pred             HHcCCceEEEECchHhccCCcccccEEEEeCCCCCHHHHHHhccccCCCCCCcEEEEEeCCChHHHHHHhCHHHHhc
Confidence            9999999999999999999999999999999999999999999999999999999999863  35555555555554

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.

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

Probab=100.00  E-value=1.8e-46  Score=449.61  Aligned_cols=345  Identities=20%  Similarity=0.310  Sum_probs=268.5

Q ss_pred             cccc--CCCCHHHHHHHHH-cCCCCCcHHHHHHHHHHhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEE
Q 002040          468 TWHQ--TGLTSKIMETIRK-LNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGL  544 (976)
Q Consensus       468 ~~~~--~~l~~~l~~~l~~-~~~~~p~~~Q~~~i~~il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vL  544 (976)
                      .|..  ++....+...++. +||..|+|+|.++|+.++.|+|+|+++|||+|||++|++|++..           ++.+|
T Consensus       436 ~W~~~~fpw~~~L~~~lk~~FG~~sFRp~Q~eaI~aiL~GrDVLVimPTGSGKSLcYQLPAL~~-----------~GiTL  504 (1195)
T PLN03137        436 KWSSRNFPWTKKLEVNNKKVFGNHSFRPNQREIINATMSGYDVFVLMPTGGGKSLTYQLPALIC-----------PGITL  504 (1195)
T ss_pred             cccccCCCchHHHHHHHHHHcCCCCCCHHHHHHHHHHHcCCCEEEEcCCCccHHHHHHHHHHHc-----------CCcEE
Confidence            4664  4455666666654 89999999999999999999999999999999999999999843           35799


Q ss_pred             EEccCHHHHHHHHHHHHHHHhhcCcEEEEeeCCCChHHHHHHHh------cCCeEEEeCchhHHH--HHHhcCCcccccC
Q 002040          545 IMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQISELK------RGTEIVVCTPGRMID--ILCTSGGKITNLR  616 (976)
Q Consensus       545 Il~Ptr~La~Q~~~~~~~~~~~~~~~~~~~~gg~~~~~~~~~l~------~~~~Iiv~Tp~~L~~--~l~~~~~~~~~l~  616 (976)
                      ||+|+++|+.++...+..    .++.+..+.++....++...+.      ..++|||+||++|..  .+......+....
T Consensus       505 VISPLiSLmqDQV~~L~~----~GI~Aa~L~s~~s~~eq~~ilr~l~s~~g~~~ILyvTPERL~~~d~ll~~L~~L~~~~  580 (1195)
T PLN03137        505 VISPLVSLIQDQIMNLLQ----ANIPAASLSAGMEWAEQLEILQELSSEYSKYKLLYVTPEKVAKSDSLLRHLENLNSRG  580 (1195)
T ss_pred             EEeCHHHHHHHHHHHHHh----CCCeEEEEECCCCHHHHHHHHHHHHhcCCCCCEEEEChHHhhcchHHHHHHHhhhhcc
Confidence            999999999855444433    5899999999988776654433      357999999999852  2221111112234


Q ss_pred             CceEEEecCcccccccC--CchHHHHH--HHhcCCCCcEEEEeccCcHHHHHHHHHHcCCCeEEEeCCcccccCCceEEE
Q 002040          617 RVTYLVMDEADRMFDMG--FEPQITRI--VQNIRPDRQTVLFSATFPRQVEILARKVLNKPVEIQVGGRSVVNKDITQLV  692 (976)
Q Consensus       617 ~~~~vVlDEah~~~~~~--f~~~i~~i--l~~~~~~~q~i~~SAT~~~~~~~l~~~~l~~~~~i~~~~~~~~~~~i~q~~  692 (976)
                      .+.+|||||||++++||  |.+.+..+  +....+..++++||||+++.+...+...+.....+.+ ..++...++... 
T Consensus       581 ~LslIVIDEAHcVSqWGhDFRpdYr~L~~Lr~~fp~vPilALTATAT~~V~eDI~~~L~l~~~~vf-r~Sf~RpNL~y~-  658 (1195)
T PLN03137        581 LLARFVIDEAHCVSQWGHDFRPDYQGLGILKQKFPNIPVLALTATATASVKEDVVQALGLVNCVVF-RQSFNRPNLWYS-  658 (1195)
T ss_pred             ccceeccCcchhhhhcccchHHHHHHHHHHHHhCCCCCeEEEEecCCHHHHHHHHHHcCCCCcEEe-ecccCccceEEE-
Confidence            58899999999999998  77776653  5555577899999999999887766555543221111 122333344322 


Q ss_pred             EecCcch-HHHHHHHHHHhhhcCCcEEEEecCHHHHHHHHHHHHHCCCCceeccCCCCHHHHHHHHHHhccCCccEEEec
Q 002040          693 EVRPESD-RFLRLLELLGEWYEKGKILIFVHSQEKCDALFRDLLKHGYPCLSLHGAKDQTDRESTISDFKSNVCNLLIAT  771 (976)
Q Consensus       693 ~~~~~~~-k~~~l~~~l~~~~~~~kvLIF~~s~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLVaT  771 (976)
                       +..... .+..+..+|.........||||.++..|+.|+..|...|+.+..+||+|++.+|..+++.|..|.++|||||
T Consensus       659 -Vv~k~kk~le~L~~~I~~~~~~esgIIYC~SRke~E~LAe~L~~~Gika~~YHAGLs~eeR~~vqe~F~~Gei~VLVAT  737 (1195)
T PLN03137        659 -VVPKTKKCLEDIDKFIKENHFDECGIIYCLSRMDCEKVAERLQEFGHKAAFYHGSMDPAQRAFVQKQWSKDEINIICAT  737 (1195)
T ss_pred             -EeccchhHHHHHHHHHHhcccCCCceeEeCchhHHHHHHHHHHHCCCCeeeeeCCCCHHHHHHHHHHHhcCCCcEEEEe
Confidence             222222 234566666554445688999999999999999999999999999999999999999999999999999999


Q ss_pred             CcccccCCCCCCcEEEEeCCCCCHHHHHHHhcccCCCCCccEEEEEecCCCcCchHHHH
Q 002040          772 SVAARGLDVKELELVINFDAPNHYEDYVHRVGRTGRAGRKGCAITFISEEDAKYSPDLV  830 (976)
Q Consensus       772 ~v~~~GlDi~~v~~VI~~d~p~s~~~y~Qr~GR~gR~g~~g~~~~~~~~~d~~~~~~i~  830 (976)
                      +++++|||+|+|++||||++|.+++.|+|++|||||.|..|.|++||+..|...+..++
T Consensus       738 dAFGMGIDkPDVR~VIHydlPkSiEsYyQriGRAGRDG~~g~cILlys~~D~~~~~~lI  796 (1195)
T PLN03137        738 VAFGMGINKPDVRFVIHHSLPKSIEGYHQECGRAGRDGQRSSCVLYYSYSDYIRVKHMI  796 (1195)
T ss_pred             chhhcCCCccCCcEEEEcCCCCCHHHHHhhhcccCCCCCCceEEEEecHHHHHHHHHHH
Confidence            99999999999999999999999999999999999999999999999887765555554

>TIGR00580 mfd transcription-repair coupling factor (mfd)

Probab=100.00  E-value=2.7e-45  Score=448.52  Aligned_cols=367  Identities=19%  Similarity=0.205  Sum_probs=282.5

Q ss_pred             HHHHHHH-HHcCCCCCcHHHHHHHHHHhcC------CCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEcc
Q 002040          476 SKIMETI-RKLNYEKPMPIQAQALPVIMSG------RDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAP  548 (976)
Q Consensus       476 ~~l~~~l-~~~~~~~p~~~Q~~~i~~il~g------~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~P  548 (976)
                      ..+...+ ..++|. |||+|.+||+.|+.+      +|+|++|+||||||++|++|++..+..        +++++||||
T Consensus       438 ~~~~~~~~~~~~f~-~T~~Q~~aI~~I~~d~~~~~~~d~Ll~adTGsGKT~val~a~l~al~~--------g~qvlvLvP  508 (926)
T TIGR00580       438 LEWQQEFEDSFPFE-ETPDQLKAIEEIKADMESPRPMDRLVCGDVGFGKTEVAMRAAFKAVLD--------GKQVAVLVP  508 (926)
T ss_pred             HHHHHHHHHhCCCC-CCHHHHHHHHHHHhhhcccCcCCEEEECCCCccHHHHHHHHHHHHHHh--------CCeEEEEeC
Confidence            3444444 457884 999999999999975      799999999999999999999988753        578999999


Q ss_pred             CHHHHHHHHHHHHHHHhhcCcEEEEeeCCCChHHH---HHHHhc-CCeEEEeCchhHHHHHHhcCCcccccCCceEEEec
Q 002040          549 TRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQ---ISELKR-GTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMD  624 (976)
Q Consensus       549 tr~La~Q~~~~~~~~~~~~~~~~~~~~gg~~~~~~---~~~l~~-~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlD  624 (976)
                      |++||.|++..|.+++..+++.+..++|+.+..+.   +..+.. .++|||+||..|    .    ....+.++++||||
T Consensus       509 T~~LA~Q~~~~f~~~~~~~~i~v~~Lsg~~~~~e~~~~~~~l~~g~~dIVIGTp~ll----~----~~v~f~~L~llVID  580 (926)
T TIGR00580       509 TTLLAQQHFETFKERFANFPVTIELLSRFRSAKEQNEILKELASGKIDILIGTHKLL----Q----KDVKFKDLGLLIID  580 (926)
T ss_pred             cHHHHHHHHHHHHHHhccCCcEEEEEeccccHHHHHHHHHHHHcCCceEEEchHHHh----h----CCCCcccCCEEEee
Confidence            99999999999999998889999999888765443   344544 489999999432    2    12467889999999


Q ss_pred             CcccccccCCchHHHHHHHhcCCCCcEEEEeccCcHHHHHHHHHHcCCCeEEEeCCcccccCCceEEEEecCcchHHHHH
Q 002040          625 EADRMFDMGFEPQITRIVQNIRPDRQTVLFSATFPRQVEILARKVLNKPVEIQVGGRSVVNKDITQLVEVRPESDRFLRL  704 (976)
Q Consensus       625 Eah~~~~~~f~~~i~~il~~~~~~~q~i~~SAT~~~~~~~l~~~~l~~~~~i~~~~~~~~~~~i~q~~~~~~~~~k~~~l  704 (976)
                      |+|++     .......+..+.++.|+|+||||+++....++...+.++..+.....  ....+.+.+.......-... 
T Consensus       581 Eahrf-----gv~~~~~L~~~~~~~~vL~~SATpiprtl~~~l~g~~d~s~I~~~p~--~R~~V~t~v~~~~~~~i~~~-  652 (926)
T TIGR00580       581 EEQRF-----GVKQKEKLKELRTSVDVLTLSATPIPRTLHMSMSGIRDLSIIATPPE--DRLPVRTFVMEYDPELVREA-  652 (926)
T ss_pred             ccccc-----chhHHHHHHhcCCCCCEEEEecCCCHHHHHHHHhcCCCcEEEecCCC--CccceEEEEEecCHHHHHHH-
Confidence            99984     44556677778888999999999888766565555556655543221  12234333322221111112 


Q ss_pred             HHHHHhhhcCCcEEEEecCHHHHHHHHHHHHHC--CCCceeccCCCCHHHHHHHHHHhccCCccEEEecCcccccCCCCC
Q 002040          705 LELLGEWYEKGKILIFVHSQEKCDALFRDLLKH--GYPCLSLHGAKDQTDRESTISDFKSNVCNLLIATSVAARGLDVKE  782 (976)
Q Consensus       705 ~~~l~~~~~~~kvLIF~~s~~~~~~l~~~L~~~--~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLVaT~v~~~GlDi~~  782 (976)
                        ++.....+++++|||+++..++.++..|...  ++.+..+||+|++.+|..++..|.+|+++|||||+++++|||||+
T Consensus       653 --i~~el~~g~qv~if~n~i~~~e~l~~~L~~~~p~~~v~~lHG~m~~~eRe~im~~F~~Gk~~ILVaT~iie~GIDIp~  730 (926)
T TIGR00580       653 --IRRELLRGGQVFYVHNRIESIEKLATQLRELVPEARIAIAHGQMTENELEEVMLEFYKGEFQVLVCTTIIETGIDIPN  730 (926)
T ss_pred             --HHHHHHcCCeEEEEECCcHHHHHHHHHHHHhCCCCeEEEecCCCCHHHHHHHHHHHHcCCCCEEEECChhhccccccc
Confidence              2233345789999999999999999999885  789999999999999999999999999999999999999999999


Q ss_pred             CcEEEEeCCCC-CHHHHHHHhcccCCCCCccEEEEEecCCCcCchHHHHHHHhhccCCCChHHHHHHHHHHHHHhhhhhh
Q 002040          783 LELVINFDAPN-HYEDYVHRVGRTGRAGRKGCAITFISEEDAKYSPDLVKALELSEQVVPDDLKALADSFMAKVNQGLEQ  861 (976)
Q Consensus       783 v~~VI~~d~p~-s~~~y~Qr~GR~gR~g~~g~~~~~~~~~d~~~~~~i~~~l~~~~~~vp~~l~~l~~~~~~~~~~~~~~  861 (976)
                      +++||++++|. ....|+|++||+||.|..|+||+|++...... ..-.+.           |..        +    ..
T Consensus       731 v~~VIi~~a~~~gls~l~Qr~GRvGR~g~~g~aill~~~~~~l~-~~~~~R-----------L~~--------~----~~  786 (926)
T TIGR00580       731 ANTIIIERADKFGLAQLYQLRGRVGRSKKKAYAYLLYPHQKALT-EDAQKR-----------LEA--------I----QE  786 (926)
T ss_pred             CCEEEEecCCCCCHHHHHHHhcCCCCCCCCeEEEEEECCcccCC-HHHHHH-----------HHH--------H----HH
Confidence            99999999976 57799999999999999999999987643210 111111           111        1    11


Q ss_pred             ccCCCCCCCCcccchhHHHHHHHHHHHHHHHcCCC
Q 002040          862 AHGTGYGGSGFKFNEEEDEKRKAAKKAQAKEYGFE  896 (976)
Q Consensus       862 ~~~~~~~g~g~~~~~~~~~~~~~~~~~~~~~~g~~  896 (976)
                         ..-.|+||.+++.++++||+|..+|..|+|+-
T Consensus       787 ---~~~~g~gf~ia~~Dl~~Rg~G~~lG~~QsG~~  818 (926)
T TIGR00580       787 ---FSELGAGFKIALHDLEIRGAGNLLGEEQSGHI  818 (926)
T ss_pred             ---hhcchhhHHHHHHHHHhcCCcCCCCCcccCch
Confidence               11237899999999999999999999999964

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.

>PRK10689 transcription-repair coupling factor; Provisional

Probab=100.00  E-value=3.7e-45  Score=456.57  Aligned_cols=365  Identities=18%  Similarity=0.183  Sum_probs=286.3

Q ss_pred             HHHHHHHcCCCCCcHHHHHHHHHHhcC------CCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHH
Q 002040          478 IMETIRKLNYEKPMPIQAQALPVIMSG------RDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRE  551 (976)
Q Consensus       478 l~~~l~~~~~~~p~~~Q~~~i~~il~g------~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~  551 (976)
                      .......++| .||++|.+||+.++.+      .|+|++|+||+|||.+|+.+++..+.        .+++|||||||++
T Consensus       590 ~~~~~~~~~~-~~T~~Q~~aI~~il~d~~~~~~~d~Ll~a~TGsGKT~val~aa~~~~~--------~g~qvlvLvPT~e  660 (1147)
T PRK10689        590 YQLFCDSFPF-ETTPDQAQAINAVLSDMCQPLAMDRLVCGDVGFGKTEVAMRAAFLAVE--------NHKQVAVLVPTTL  660 (1147)
T ss_pred             HHHHHHhCCC-CCCHHHHHHHHHHHHHhhcCCCCCEEEEcCCCcCHHHHHHHHHHHHHH--------cCCeEEEEeCcHH
Confidence            3455677898 6999999999999987      89999999999999999988876653        3678999999999


Q ss_pred             HHHHHHHHHHHHHhhcCcEEEEeeCCCChHHHHHHH---h-cCCeEEEeCchhHHHHHHhcCCcccccCCceEEEecCcc
Q 002040          552 LVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQISEL---K-RGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEAD  627 (976)
Q Consensus       552 La~Q~~~~~~~~~~~~~~~~~~~~gg~~~~~~~~~l---~-~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDEah  627 (976)
                      ||.|++..|..++..+++.+.+++|+.+..++...+   . ..++|||+||+.|.    .    ...+.++++|||||+|
T Consensus       661 LA~Q~~~~f~~~~~~~~v~i~~l~g~~s~~e~~~il~~l~~g~~dIVVgTp~lL~----~----~v~~~~L~lLVIDEah  732 (1147)
T PRK10689        661 LAQQHYDNFRDRFANWPVRIEMLSRFRSAKEQTQILAEAAEGKIDILIGTHKLLQ----S----DVKWKDLGLLIVDEEH  732 (1147)
T ss_pred             HHHHHHHHHHHhhccCCceEEEEECCCCHHHHHHHHHHHHhCCCCEEEECHHHHh----C----CCCHhhCCEEEEechh
Confidence            999999999998887889999999988877765443   3 35899999997431    1    1456789999999999


Q ss_pred             cccccCCchHHHHHHHhcCCCCcEEEEeccCcHHHHHHHHHHcCCCeEEEeCCcccccCCceEEEEecCcchHHHHHHHH
Q 002040          628 RMFDMGFEPQITRIVQNIRPDRQTVLFSATFPRQVEILARKVLNKPVEIQVGGRSVVNKDITQLVEVRPESDRFLRLLEL  707 (976)
Q Consensus       628 ~~~~~~f~~~i~~il~~~~~~~q~i~~SAT~~~~~~~l~~~~l~~~~~i~~~~~~~~~~~i~q~~~~~~~~~k~~~l~~~  707 (976)
                      ++   |+  ....++..++++.|+|+||||+++.+..++...+.++..+......  ...+.+.+.......   ....+
T Consensus       733 rf---G~--~~~e~lk~l~~~~qvLl~SATpiprtl~l~~~gl~d~~~I~~~p~~--r~~v~~~~~~~~~~~---~k~~i  802 (1147)
T PRK10689        733 RF---GV--RHKERIKAMRADVDILTLTATPIPRTLNMAMSGMRDLSIIATPPAR--RLAVKTFVREYDSLV---VREAI  802 (1147)
T ss_pred             hc---ch--hHHHHHHhcCCCCcEEEEcCCCCHHHHHHHHhhCCCcEEEecCCCC--CCCceEEEEecCcHH---HHHHH
Confidence            96   33  3356677788899999999999888877888888888766543221  223444333222211   12233


Q ss_pred             HHhhhcCCcEEEEecCHHHHHHHHHHHHHC--CCCceeccCCCCHHHHHHHHHHhccCCccEEEecCcccccCCCCCCcE
Q 002040          708 LGEWYEKGKILIFVHSQEKCDALFRDLLKH--GYPCLSLHGAKDQTDRESTISDFKSNVCNLLIATSVAARGLDVKELEL  785 (976)
Q Consensus       708 l~~~~~~~kvLIF~~s~~~~~~l~~~L~~~--~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLVaT~v~~~GlDi~~v~~  785 (976)
                      +..+..+++++|||+++..++.++..|...  ++.+..+||+|++.+|..++..|.+|+++|||||+++++|||||++++
T Consensus       803 l~el~r~gqv~vf~n~i~~ie~la~~L~~~~p~~~v~~lHG~m~q~eRe~im~~Fr~Gk~~VLVaTdIierGIDIP~v~~  882 (1147)
T PRK10689        803 LREILRGGQVYYLYNDVENIQKAAERLAELVPEARIAIGHGQMRERELERVMNDFHHQRFNVLVCTTIIETGIDIPTANT  882 (1147)
T ss_pred             HHHHhcCCeEEEEECCHHHHHHHHHHHHHhCCCCcEEEEeCCCCHHHHHHHHHHHHhcCCCEEEECchhhcccccccCCE
Confidence            444445789999999999999999999887  789999999999999999999999999999999999999999999999


Q ss_pred             EEEeCCC-CCHHHHHHHhcccCCCCCccEEEEEecCCCcCchHHHHHHHhhccCCCChHHHHHHHHHHHHHhhhhhhccC
Q 002040          786 VINFDAP-NHYEDYVHRVGRTGRAGRKGCAITFISEEDAKYSPDLVKALELSEQVVPDDLKALADSFMAKVNQGLEQAHG  864 (976)
Q Consensus       786 VI~~d~p-~s~~~y~Qr~GR~gR~g~~g~~~~~~~~~d~~~~~~i~~~l~~~~~~vp~~l~~l~~~~~~~~~~~~~~~~~  864 (976)
                      ||+.+++ .+...|+|++||+||.|..|+||+++.......                    ..+..-+..+    ..   
T Consensus       883 VIi~~ad~fglaq~~Qr~GRvGR~g~~g~a~ll~~~~~~~~--------------------~~~~~rl~~~----~~---  935 (1147)
T PRK10689        883 IIIERADHFGLAQLHQLRGRVGRSHHQAYAWLLTPHPKAMT--------------------TDAQKRLEAI----AS---  935 (1147)
T ss_pred             EEEecCCCCCHHHHHHHhhccCCCCCceEEEEEeCCCcccC--------------------HHHHHHHHHH----HH---
Confidence            9976664 356789999999999999999998875432111                    1111111111    11   


Q ss_pred             CCCCCCCcccchhHHHHHHHHHHHHHHHcCCC
Q 002040          865 TGYGGSGFKFNEEEDEKRKAAKKAQAKEYGFE  896 (976)
Q Consensus       865 ~~~~g~g~~~~~~~~~~~~~~~~~~~~~~g~~  896 (976)
                      ..-.|+||.+++.|+++||+|..+|..|+|+-
T Consensus       936 ~~~lg~gf~~a~~dl~~rg~g~~~g~~q~g~~  967 (1147)
T PRK10689        936 LEDLGAGFALATHDLEIRGAGELLGEEQSGQM  967 (1147)
T ss_pred             hcCCcchHHHHHHHHHhcCCccCCCCccCCCc
Confidence            12238899999999999999999999999964

>TIGR00614 recQ_fam ATP-dependent DNA helicase, RecQ family

Probab=100.00  E-value=1.4e-44  Score=423.09  Aligned_cols=328  Identities=20%  Similarity=0.334  Sum_probs=259.7

Q ss_pred             HcCCCCCcHHHHHHHHHHhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHHH
Q 002040          484 KLNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKF  563 (976)
Q Consensus       484 ~~~~~~p~~~Q~~~i~~il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~~  563 (976)
                      .+||..|+|+|.++|+.++.|+|+++++|||+|||++|++|++..           ++.+|||+||++|+.|++..+.. 
T Consensus         6 ~~g~~~~r~~Q~~ai~~~l~g~dvlv~apTGsGKTl~y~lp~l~~-----------~~~~lVi~P~~~L~~dq~~~l~~-   73 (470)
T TIGR00614         6 VFGLSSFRPVQLEVINAVLLGRDCFVVMPTGGGKSLCYQLPALCS-----------DGITLVISPLISLMEDQVLQLKA-   73 (470)
T ss_pred             hcCCCCCCHHHHHHHHHHHcCCCEEEEcCCCCcHhHHHHHHHHHc-----------CCcEEEEecHHHHHHHHHHHHHH-
Confidence            589999999999999999999999999999999999999998842           45689999999999998887765 


Q ss_pred             HhhcCcEEEEeeCCCChHHHH---HHHhc-CCeEEEeCchhHHHHHHhcCCcccccCCceEEEecCcccccccC--CchH
Q 002040          564 AKVMGVRCVPVYGGSGVAQQI---SELKR-GTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMG--FEPQ  637 (976)
Q Consensus       564 ~~~~~~~~~~~~gg~~~~~~~---~~l~~-~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDEah~~~~~~--f~~~  637 (976)
                         +|+.+..+.++....+..   ..+.. ..+|+|+||+.|........ .+..+..+.+|||||||++++||  |.+.
T Consensus        74 ---~gi~~~~l~~~~~~~~~~~i~~~~~~~~~~il~~TPe~l~~~~~~~~-~l~~~~~i~~iViDEaH~i~~~g~~fr~~  149 (470)
T TIGR00614        74 ---SGIPATFLNSSQSKEQQKNVLTDLKDGKIKLLYVTPEKCSASNRLLQ-TLEERKGITLIAVDEAHCISQWGHDFRPD  149 (470)
T ss_pred             ---cCCcEEEEeCCCCHHHHHHHHHHHhcCCCCEEEECHHHHcCchhHHH-HHHhcCCcCEEEEeCCcccCccccccHHH
Confidence               578888887777655332   22333 47999999998753220000 01145779999999999999987  6666


Q ss_pred             HHHH--HHhcCCCCcEEEEeccCcHHHHHHHHHHc--CCCeEEEeCCcccccCCceEEEEecCcchHHHHHHHHHHhhhc
Q 002040          638 ITRI--VQNIRPDRQTVLFSATFPRQVEILARKVL--NKPVEIQVGGRSVVNKDITQLVEVRPESDRFLRLLELLGEWYE  713 (976)
Q Consensus       638 i~~i--l~~~~~~~q~i~~SAT~~~~~~~l~~~~l--~~~~~i~~~~~~~~~~~i~q~~~~~~~~~k~~~l~~~l~~~~~  713 (976)
                      +..+  +....++.++++||||+++.+.......+  ..|..+..   .....++...+.. .....+..++.+|.....
T Consensus       150 ~~~l~~l~~~~~~~~~l~lTAT~~~~~~~di~~~l~l~~~~~~~~---s~~r~nl~~~v~~-~~~~~~~~l~~~l~~~~~  225 (470)
T TIGR00614       150 YKALGSLKQKFPNVPIMALTATASPSVREDILRQLNLKNPQIFCT---SFDRPNLYYEVRR-KTPKILEDLLRFIRKEFK  225 (470)
T ss_pred             HHHHHHHHHHcCCCceEEEecCCCHHHHHHHHHHcCCCCCcEEeC---CCCCCCcEEEEEe-CCccHHHHHHHHHHHhcC
Confidence            6544  33344778999999999998766555554  34443322   1222333322222 222455566777765445


Q ss_pred             CCcEEEEecCHHHHHHHHHHHHHCCCCceeccCCCCHHHHHHHHHHhccCCccEEEecCcccccCCCCCCcEEEEeCCCC
Q 002040          714 KGKILIFVHSQEKCDALFRDLLKHGYPCLSLHGAKDQTDRESTISDFKSNVCNLLIATSVAARGLDVKELELVINFDAPN  793 (976)
Q Consensus       714 ~~kvLIF~~s~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLVaT~v~~~GlDi~~v~~VI~~d~p~  793 (976)
                      ...+||||+++..++.++..|...|+.+..+||+|++.+|..+++.|.+|.++|||||+++++|||+|+|++||+|++|.
T Consensus       226 ~~~~IIF~~s~~~~e~la~~L~~~g~~~~~~H~~l~~~eR~~i~~~F~~g~~~vLVaT~~~~~GID~p~V~~VI~~~~P~  305 (470)
T TIGR00614       226 GKSGIIYCPSRKKSEQVTASLQNLGIAAGAYHAGLEISARDDVHHKFQRDEIQVVVATVAFGMGINKPDVRFVIHYSLPK  305 (470)
T ss_pred             CCceEEEECcHHHHHHHHHHHHhcCCCeeEeeCCCCHHHHHHHHHHHHcCCCcEEEEechhhccCCcccceEEEEeCCCC
Confidence            55679999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CHHHHHHHhcccCCCCCccEEEEEecCCCcCchHHHHH
Q 002040          794 HYEDYVHRVGRTGRAGRKGCAITFISEEDAKYSPDLVK  831 (976)
Q Consensus       794 s~~~y~Qr~GR~gR~g~~g~~~~~~~~~d~~~~~~i~~  831 (976)
                      ++..|+|++||+||.|..|.|++|+++.+...+..++.
T Consensus       306 s~~~y~Qr~GRaGR~G~~~~~~~~~~~~d~~~~~~~~~  343 (470)
T TIGR00614       306 SMESYYQESGRAGRDGLPSECHLFYAPADINRLRRLLM  343 (470)
T ss_pred             CHHHHHhhhcCcCCCCCCceEEEEechhHHHHHHHHHh
Confidence            99999999999999999999999999988766666554

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

>PRK11057 ATP-dependent DNA helicase RecQ; Provisional

Probab=100.00  E-value=6.3e-43  Score=419.48  Aligned_cols=328  Identities=20%  Similarity=0.338  Sum_probs=257.0

Q ss_pred             HHHHH-HcCCCCCcHHHHHHHHHHhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHH
Q 002040          479 METIR-KLNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIH  557 (976)
Q Consensus       479 ~~~l~-~~~~~~p~~~Q~~~i~~il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~  557 (976)
                      ...|+ .+||..|+|+|.++|+.++.|+|+|+++|||+|||++|++|++..           +..+|||+|+++|+.|+.
T Consensus        14 ~~~l~~~fG~~~~r~~Q~~ai~~il~g~dvlv~apTGsGKTl~y~lpal~~-----------~g~tlVisPl~sL~~dqv   82 (607)
T PRK11057         14 KQVLQETFGYQQFRPGQQEIIDAVLSGRDCLVVMPTGGGKSLCYQIPALVL-----------DGLTLVVSPLISLMKDQV   82 (607)
T ss_pred             HHHHHHHcCCCCCCHHHHHHHHHHHcCCCEEEEcCCCchHHHHHHHHHHHc-----------CCCEEEEecHHHHHHHHH
Confidence            34444 389999999999999999999999999999999999999999843           346899999999999998


Q ss_pred             HHHHHHHhhcCcEEEEeeCCCChHHHHHH---Hh-cCCeEEEeCchhHHHHHHhcCCcccccCCceEEEecCcccccccC
Q 002040          558 SDIRKFAKVMGVRCVPVYGGSGVAQQISE---LK-RGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMG  633 (976)
Q Consensus       558 ~~~~~~~~~~~~~~~~~~gg~~~~~~~~~---l~-~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDEah~~~~~~  633 (976)
                      ..+..    .|+.+.++.++.........   +. ...+|+|+||++|.......   .....++++|||||||++++||
T Consensus        83 ~~l~~----~gi~~~~~~s~~~~~~~~~~~~~~~~g~~~il~~tPe~l~~~~~~~---~l~~~~l~~iVIDEaH~i~~~G  155 (607)
T PRK11057         83 DQLLA----NGVAAACLNSTQTREQQLEVMAGCRTGQIKLLYIAPERLMMDNFLE---HLAHWNPALLAVDEAHCISQWG  155 (607)
T ss_pred             HHHHH----cCCcEEEEcCCCCHHHHHHHHHHHhCCCCcEEEEChHHhcChHHHH---HHhhCCCCEEEEeCcccccccc
Confidence            88775    47888888777766554322   22 24689999999986322111   1234468999999999999987


Q ss_pred             --CchHHHHH--HHhcCCCCcEEEEeccCcHHHHHHHHHHc--CCCeEEEeCCcccccCCceEEEEecCcchHHHHHHHH
Q 002040          634 --FEPQITRI--VQNIRPDRQTVLFSATFPRQVEILARKVL--NKPVEIQVGGRSVVNKDITQLVEVRPESDRFLRLLEL  707 (976)
Q Consensus       634 --f~~~i~~i--l~~~~~~~q~i~~SAT~~~~~~~l~~~~l--~~~~~i~~~~~~~~~~~i~q~~~~~~~~~k~~~l~~~  707 (976)
                        |.+.+..+  +....+..++|+||||++..+...+...+  .+|..+ +..  ....++.  +.+.........++..
T Consensus       156 ~~fr~~y~~L~~l~~~~p~~~~v~lTAT~~~~~~~di~~~l~l~~~~~~-~~~--~~r~nl~--~~v~~~~~~~~~l~~~  230 (607)
T PRK11057        156 HDFRPEYAALGQLRQRFPTLPFMALTATADDTTRQDIVRLLGLNDPLIQ-ISS--FDRPNIR--YTLVEKFKPLDQLMRY  230 (607)
T ss_pred             CcccHHHHHHHHHHHhCCCCcEEEEecCCChhHHHHHHHHhCCCCeEEE-ECC--CCCCcce--eeeeeccchHHHHHHH
Confidence              66665544  33334678999999999988765444433  344432 221  2222332  2222223344555555


Q ss_pred             HHhhhcCCcEEEEecCHHHHHHHHHHHHHCCCCceeccCCCCHHHHHHHHHHhccCCccEEEecCcccccCCCCCCcEEE
Q 002040          708 LGEWYEKGKILIFVHSQEKCDALFRDLLKHGYPCLSLHGAKDQTDRESTISDFKSNVCNLLIATSVAARGLDVKELELVI  787 (976)
Q Consensus       708 l~~~~~~~kvLIF~~s~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLVaT~v~~~GlDi~~v~~VI  787 (976)
                      +.. ....++||||+++..|+.++..|...|+.+..+||+|++.+|..+++.|..|.++|||||+++++|||+|+|++||
T Consensus       231 l~~-~~~~~~IIFc~tr~~~e~la~~L~~~g~~v~~~Ha~l~~~~R~~i~~~F~~g~~~VLVaT~a~~~GIDip~V~~VI  309 (607)
T PRK11057        231 VQE-QRGKSGIIYCNSRAKVEDTAARLQSRGISAAAYHAGLDNDVRADVQEAFQRDDLQIVVATVAFGMGINKPNVRFVV  309 (607)
T ss_pred             HHh-cCCCCEEEEECcHHHHHHHHHHHHhCCCCEEEecCCCCHHHHHHHHHHHHCCCCCEEEEechhhccCCCCCcCEEE
Confidence            543 3457899999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EeCCCCCHHHHHHHhcccCCCCCccEEEEEecCCCcCchHHHH
Q 002040          788 NFDAPNHYEDYVHRVGRTGRAGRKGCAITFISEEDAKYSPDLV  830 (976)
Q Consensus       788 ~~d~p~s~~~y~Qr~GR~gR~g~~g~~~~~~~~~d~~~~~~i~  830 (976)
                      +|++|.+...|+|++|||||.|.+|.|++||++.|...+..++
T Consensus       310 ~~d~P~s~~~y~Qr~GRaGR~G~~~~~ill~~~~d~~~~~~~~  352 (607)
T PRK11057        310 HFDIPRNIESYYQETGRAGRDGLPAEAMLFYDPADMAWLRRCL  352 (607)
T ss_pred             EeCCCCCHHHHHHHhhhccCCCCCceEEEEeCHHHHHHHHHHH
Confidence            9999999999999999999999999999999988765544443

>KOG0924 consensus mRNA splicing factor ATP-dependent RNA helicase [RNA processing and modification]

Probab=100.00  E-value=1.3e-44  Score=398.85  Aligned_cols=497  Identities=20%  Similarity=0.254  Sum_probs=369.2

Q ss_pred             CCCCccCCCCCcCccCccCCCCCCCCCCCCCCCCCCccccccccccCCCCCCChhhhcCCCCCCCCChhHHHHhcccchh
Q 002040          248 GRNWTLDREDSDDEEVPQTGKSETDMDADEEPKPSENQVGDAMLVDSDGGSAAPALQIGAAEDEDIDPLDAFMNSMVLPE  327 (976)
Q Consensus       248 ~r~~~~~~e~~de~~~~~~~~~e~~~~~~e~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~e~d~~~~~~~~~~~~~  327 (976)
                      +|.||+.+++.|+.++||+.-+.+ .        ...+.+..++.|++.|+.+.+.+||++..-|+.+  .|... ...+
T Consensus       169 dR~WYdnde~~d~~~npf~~~~~E-~--------~l~~~~~ki~~dn~~we~nrl~~sgvv~~~e~~~--~f~~~-e~~~  236 (1042)
T KOG0924|consen  169 DREWYDNDEGGDEVHNPFSELSRE-A--------ELLEKIQKINNDNALWETNRLLTSGVVQRMEVIS--DFLSD-EARE  236 (1042)
T ss_pred             chhhhhcCCccccccCchhcchhH-H--------HHHHHHHhhcchhhhhhhhcccchhhhhcccccC--ccchh-hHHH
Confidence            599999999999999999864411 1        1222334489999999999999999999888876  56554 3333


Q ss_pred             HHhhhccCCCCCCCCCccccccccccCCCCCCCCCCCcccccccCCCCCCCCCCcccCCcccCCCCCCCcchHHHHHHHH
Q 002040          328 VEKLKNTVEPSFTDGNNVESKKMDRKGDRRSNGEQPKKSSNKSLGRIIPGEDSDSDYGDLENDEKPLEDEDDDEFMKRVK  407 (976)
Q Consensus       328 ~~~~~~~~~~~~~d~~~~~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~d~~~~~~~~~~~~~~~~~~~~~~~~  407 (976)
                        +|||+++|+|+||..+++|+..+                     +++..|.++|++..++.++.+        +...+
T Consensus       237 --llv~~i~~~fld~r~~~~k~~~~---------------------v~pv~d~~sd~a~~a~~gs~l--------v~~~r  285 (1042)
T KOG0924|consen  237 --LLVHNIVPPFLDGREVFTKQAEP---------------------VIPVRDPTSDLAISARRGSKL--------VRERR  285 (1042)
T ss_pred             --hhhhcccCCccccceeeeccccc---------------------ccccCCCchhhhhhhhccccH--------HHHHH
Confidence              99999999999999999999766                     899999999999998888865        66677


Q ss_pred             HHhhccCCcCCCcccccCcccccccccchhhhcCCHHHHHHHHhhcCceeccCCCCCcccccccCCCCHHHHHHHHHcCC
Q 002040          408 KTKAEKLSIVDHSKIDYQPFRKNFYIEVKEIARMTPEEVSAYRKQLELKIHGKDVPKPIKTWHQTGLTSKIMETIRKLNY  487 (976)
Q Consensus       408 ~~~~~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~g~~~p~pi~~~~~~~l~~~l~~~l~~~~~  487 (976)
                      .+...+.+..+||.+.++.++..+.++.+.-    .....+|+.......+.+.. .....|.   ....+.   ....+
T Consensus       286 ~~~~~~k~~~~~~~~~~~~lgn~~glek~~~----ed~~~~~~~~~~~a~h~k~~-~a~~~fa---~~k~i~---eqrq~  354 (1042)
T KOG0924|consen  286 EKEERKKAQKKHWKLAGTALGNVMGLEKKND----EDGKVAYRGSVKFASHMKKS-EAVSEFA---SKKSIR---EQRQY  354 (1042)
T ss_pred             HhhhhhhhhhhhhhhcchhhccccccccCcc----cccccccccchhhhhccccc-ccccccc---ccchHH---HHHhh
Confidence            7778888889999999999988887765432    11111122111111111100 0111111   111122   22344


Q ss_pred             CCCcHHHHHHHHHHhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHHHHhhc
Q 002040          488 EKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVM  567 (976)
Q Consensus       488 ~~p~~~Q~~~i~~il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~~~~~~  567 (976)
                      ...+.++.+.+..|..++-+||+|+||||||++....++..=       .+++..+.+..|.|..|+.+   .+.++..+
T Consensus       355 LPvf~~R~~ll~~ir~n~vvvivgETGSGKTTQl~QyL~edG-------Y~~~GmIGcTQPRRvAAiSV---AkrVa~EM  424 (1042)
T KOG0924|consen  355 LPVFACRDQLLSVIRENQVVVIVGETGSGKTTQLAQYLYEDG-------YADNGMIGCTQPRRVAAISV---AKRVAEEM  424 (1042)
T ss_pred             cchHHHHHHHHHHHhhCcEEEEEecCCCCchhhhHHHHHhcc-------cccCCeeeecCchHHHHHHH---HHHHHHHh
Confidence            455678889999999999999999999999998655554331       12334566677999998855   55566678


Q ss_pred             CcEEEEeeCCCChHHHHHHHhcCCeEEEeCchhHHHHHHhcCCcccccCCceEEEecCcc-cccccCCchHHHHHHHhcC
Q 002040          568 GVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEAD-RMFDMGFEPQITRIVQNIR  646 (976)
Q Consensus       568 ~~~~~~~~gg~~~~~~~~~l~~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDEah-~~~~~~f~~~i~~il~~~~  646 (976)
                      ++.+.+-+|.+..++....  ..+.|-++|.|.|+......    ..|..+++||||||| +.++.+....+...+..-+
T Consensus       425 ~~~lG~~VGYsIRFEdvT~--~~T~IkymTDGiLLrEsL~d----~~L~kYSviImDEAHERslNtDilfGllk~~larR  498 (1042)
T KOG0924|consen  425 GVTLGDTVGYSIRFEDVTS--EDTKIKYMTDGILLRESLKD----RDLDKYSVIIMDEAHERSLNTDILFGLLKKVLARR  498 (1042)
T ss_pred             CCccccccceEEEeeecCC--CceeEEEeccchHHHHHhhh----hhhhheeEEEechhhhcccchHHHHHHHHHHHHhh
Confidence            8888888888777766433  55789999999998766543    478899999999999 8888888888888888888


Q ss_pred             CCCcEEEEeccCcHHHHHHHHHHcCCCeEEEeCCcccccCCceEEEEecCcchHHHHHHHHHHhhh---cCCcEEEEecC
Q 002040          647 PDRQTVLFSATFPRQVEILARKVLNKPVEIQVGGRSVVNKDITQLVEVRPESDRFLRLLELLGEWY---EKGKILIFVHS  723 (976)
Q Consensus       647 ~~~q~i~~SAT~~~~~~~l~~~~l~~~~~i~~~~~~~~~~~i~q~~~~~~~~~k~~~l~~~l~~~~---~~~kvLIF~~s  723 (976)
                      .+.++|++||||...  .+ ..|+++...+++.+++++..   ..+...+-.+.+.+.+......+   ..|.+|||++.
T Consensus       499 rdlKliVtSATm~a~--kf-~nfFgn~p~f~IpGRTyPV~---~~~~k~p~eDYVeaavkq~v~Ihl~~~~GdilIfmtG  572 (1042)
T KOG0924|consen  499 RDLKLIVTSATMDAQ--KF-SNFFGNCPQFTIPGRTYPVE---IMYTKTPVEDYVEAAVKQAVQIHLSGPPGDILIFMTG  572 (1042)
T ss_pred             ccceEEEeeccccHH--HH-HHHhCCCceeeecCCccceE---EEeccCchHHHHHHHHhhheEeeccCCCCCEEEecCC
Confidence            899999999999543  34 45556555567777776643   23333444555555444333322   35789999999


Q ss_pred             HHHHHHHHHHHHHC----------CCCceeccCCCCHHHHHHHHHHhccCCccEEEecCcccccCCCCCCcEEEEeCC--
Q 002040          724 QEKCDALFRDLLKH----------GYPCLSLHGAKDQTDRESTISDFKSNVCNLLIATSVAARGLDVKELELVINFDA--  791 (976)
Q Consensus       724 ~~~~~~l~~~L~~~----------~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLVaT~v~~~GlDi~~v~~VI~~d~--  791 (976)
                      +..++..+..+...          ++.++.|++.|++..+.++++....|..+|||||++|++.|.||++.+||+.++  
T Consensus       573 qediE~t~~~i~~~l~ql~~~~~~~L~vlpiYSQLp~dlQ~kiFq~a~~~vRK~IvATNIAETSLTi~gI~yVID~Gy~K  652 (1042)
T KOG0924|consen  573 QEDIECTCDIIKEKLEQLDSAPTTDLAVLPIYSQLPADLQAKIFQKAEGGVRKCIVATNIAETSLTIPGIRYVIDTGYCK  652 (1042)
T ss_pred             CcchhHHHHHHHHHHHhhhcCCCCceEEEeehhhCchhhhhhhcccCCCCceeEEEeccchhhceeecceEEEEecCcee
Confidence            98877766666542          678999999999999999999999999999999999999999999999997433  


Q ss_pred             ----------------CCCHHHHHHHhcccCCCCCccEEEEEecCC
Q 002040          792 ----------------PNHYEDYVHRVGRTGRAGRKGCAITFISEE  821 (976)
Q Consensus       792 ----------------p~s~~~y~Qr~GR~gR~g~~g~~~~~~~~~  821 (976)
                                      |.|.++..||.|||||+| +|+||.+||..
T Consensus       653 ~kvyn~~~G~D~L~~~pIS~AnA~QRaGRAGRt~-pG~cYRlYTe~  697 (1042)
T KOG0924|consen  653 LKVYNPRIGMDALQIVPISQANADQRAGRAGRTG-PGTCYRLYTED  697 (1042)
T ss_pred             eeecccccccceeEEEechhccchhhccccCCCC-Ccceeeehhhh
Confidence                            678888999999999998 99999999874

>PRK10917 ATP-dependent DNA helicase RecG; Provisional

Probab=100.00  E-value=8.5e-43  Score=422.51  Aligned_cols=360  Identities=18%  Similarity=0.266  Sum_probs=271.0

Q ss_pred             HHHHHHcCCCCCcHHHHHHHHHHhcC------CCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHH
Q 002040          479 METIRKLNYEKPMPIQAQALPVIMSG------RDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTREL  552 (976)
Q Consensus       479 ~~~l~~~~~~~p~~~Q~~~i~~il~g------~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~L  552 (976)
                      ...+..++| .||++|.++|+.|..+      .++|++|+||||||++|++|++..+.        +|+++|||+||++|
T Consensus       252 ~~~~~~l~f-~lt~~Q~~ai~~I~~d~~~~~~~~~Ll~~~TGSGKT~va~~~il~~~~--------~g~q~lilaPT~~L  322 (681)
T PRK10917        252 KKFLASLPF-ELTGAQKRVVAEILADLASPKPMNRLLQGDVGSGKTVVAALAALAAIE--------AGYQAALMAPTEIL  322 (681)
T ss_pred             HHHHHhCCC-CCCHHHHHHHHHHHHhhhccCCceEEEECCCCCcHHHHHHHHHHHHHH--------cCCeEEEEeccHHH
Confidence            334556888 5999999999999976      47999999999999999999998764        36789999999999


Q ss_pred             HHHHHHHHHHHHhhcCcEEEEeeCCCChHH---HHHHHhcC-CeEEEeCchhHHHHHHhcCCcccccCCceEEEecCccc
Q 002040          553 VQQIHSDIRKFAKVMGVRCVPVYGGSGVAQ---QISELKRG-TEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADR  628 (976)
Q Consensus       553 a~Q~~~~~~~~~~~~~~~~~~~~gg~~~~~---~~~~l~~~-~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDEah~  628 (976)
                      |.|++..+.+++..+|+.+.+++|+.+..+   .+..+..| ++||||||+.|.+.        ..+.++++|||||+|+
T Consensus       323 A~Q~~~~l~~l~~~~~i~v~ll~G~~~~~~r~~~~~~l~~g~~~IvVgT~~ll~~~--------v~~~~l~lvVIDE~Hr  394 (681)
T PRK10917        323 AEQHYENLKKLLEPLGIRVALLTGSLKGKERREILEAIASGEADIVIGTHALIQDD--------VEFHNLGLVIIDEQHR  394 (681)
T ss_pred             HHHHHHHHHHHHhhcCcEEEEEcCCCCHHHHHHHHHHHhCCCCCEEEchHHHhccc--------chhcccceEEEechhh
Confidence            999999999999999999999999998544   34455554 89999999877432        3577899999999998


Q ss_pred             ccccCCchHHHHHHHhcCCCCcEEEEeccCcHHHHHHHHHHcCCCeEEEeCCcccccCCceEEEEecCcchHHHHHHHHH
Q 002040          629 MFDMGFEPQITRIVQNIRPDRQTVLFSATFPRQVEILARKVLNKPVEIQVGGRSVVNKDITQLVEVRPESDRFLRLLELL  708 (976)
Q Consensus       629 ~~~~~f~~~i~~il~~~~~~~q~i~~SAT~~~~~~~l~~~~l~~~~~i~~~~~~~~~~~i~q~~~~~~~~~k~~~l~~~l  708 (976)
                      +.     ......+.......++|+||||+.+....+.  .+.......+...+.....+.+.+...   .....++..+
T Consensus       395 fg-----~~qr~~l~~~~~~~~iL~~SATp~prtl~~~--~~g~~~~s~i~~~p~~r~~i~~~~~~~---~~~~~~~~~i  464 (681)
T PRK10917        395 FG-----VEQRLALREKGENPHVLVMTATPIPRTLAMT--AYGDLDVSVIDELPPGRKPITTVVIPD---SRRDEVYERI  464 (681)
T ss_pred             hh-----HHHHHHHHhcCCCCCEEEEeCCCCHHHHHHH--HcCCCceEEEecCCCCCCCcEEEEeCc---ccHHHHHHHH
Confidence            53     2334444455556899999999877654333  233322222222222223344333322   2223344444


Q ss_pred             Hhhh-cCCcEEEEecCH--------HHHHHHHHHHHHC--CCCceeccCCCCHHHHHHHHHHhccCCccEEEecCccccc
Q 002040          709 GEWY-EKGKILIFVHSQ--------EKCDALFRDLLKH--GYPCLSLHGAKDQTDRESTISDFKSNVCNLLIATSVAARG  777 (976)
Q Consensus       709 ~~~~-~~~kvLIF~~s~--------~~~~~l~~~L~~~--~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLVaT~v~~~G  777 (976)
                      .... ...+++|||+.+        ..+..++..|...  ++.+..+||+|++.+|..+++.|.+|.++|||||+++++|
T Consensus       465 ~~~~~~g~q~~v~~~~ie~s~~l~~~~~~~~~~~L~~~~~~~~v~~lHG~m~~~eR~~i~~~F~~g~~~ILVaT~vie~G  544 (681)
T PRK10917        465 REEIAKGRQAYVVCPLIEESEKLDLQSAEETYEELQEAFPELRVGLLHGRMKPAEKDAVMAAFKAGEIDILVATTVIEVG  544 (681)
T ss_pred             HHHHHcCCcEEEEEcccccccchhHHHHHHHHHHHHHHCCCCcEEEEeCCCCHHHHHHHHHHHHcCCCCEEEECcceeeC
Confidence            4333 456999999964        3456677777765  5789999999999999999999999999999999999999


Q ss_pred             CCCCCCcEEEEeCCCCC-HHHHHHHhcccCCCCCccEEEEEecCCCcCchHHHHHHHhhccCCCChHHHHHHHHHHHHHh
Q 002040          778 LDVKELELVINFDAPNH-YEDYVHRVGRTGRAGRKGCAITFISEEDAKYSPDLVKALELSEQVVPDDLKALADSFMAKVN  856 (976)
Q Consensus       778 lDi~~v~~VI~~d~p~s-~~~y~Qr~GR~gR~g~~g~~~~~~~~~d~~~~~~i~~~l~~~~~~vp~~l~~l~~~~~~~~~  856 (976)
                      ||||++++||+|++|.. .+.|.|++||+||.|..|+|+++++.........-++.              |.        
T Consensus       545 iDip~v~~VIi~~~~r~gls~lhQ~~GRvGR~g~~g~~ill~~~~~~~~~~~rl~~--------------~~--------  602 (681)
T PRK10917        545 VDVPNATVMVIENAERFGLAQLHQLRGRVGRGAAQSYCVLLYKDPLSETARERLKI--------------MR--------  602 (681)
T ss_pred             cccCCCcEEEEeCCCCCCHHHHHHHhhcccCCCCceEEEEEECCCCChhHHHHHHH--------------HH--------
Confidence            99999999999999974 67888999999999999999999963211111111111              11        


Q ss_pred             hhhhhccCCCCCCCCcccchhHHHHHHHHHHHHHHHcCCCC
Q 002040          857 QGLEQAHGTGYGGSGFKFNEEEDEKRKAAKKAQAKEYGFEE  897 (976)
Q Consensus       857 ~~~~~~~~~~~~g~g~~~~~~~~~~~~~~~~~~~~~~g~~~  897 (976)
                      +          ...||.+++.++.+|+.+..++..|+|+..
T Consensus       603 ~----------~~dgf~iae~dl~~rg~g~~~g~~q~g~~~  633 (681)
T PRK10917        603 E----------TNDGFVIAEKDLELRGPGELLGTRQSGLPE  633 (681)
T ss_pred             H----------hcchHHHHHHhHhhCCCccccCceecCCCC
Confidence            0          145789999999999999999999999654

>TIGR00643 recG ATP-dependent DNA helicase RecG

Probab=100.00  E-value=3.5e-42  Score=414.70  Aligned_cols=363  Identities=21%  Similarity=0.275  Sum_probs=267.5

Q ss_pred             HHHHHHHHcCCCCCcHHHHHHHHHHhcC------CCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCH
Q 002040          477 KIMETIRKLNYEKPMPIQAQALPVIMSG------RDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTR  550 (976)
Q Consensus       477 ~l~~~l~~~~~~~p~~~Q~~~i~~il~g------~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr  550 (976)
                      .+...+..++| .||++|..||+.|+.+      .++|++|+||||||++|++|++..+.        +|++++||+||+
T Consensus       224 ~~~~~~~~lpf-~lt~~Q~~ai~~I~~~~~~~~~~~~Ll~g~TGSGKT~va~l~il~~~~--------~g~qvlilaPT~  294 (630)
T TIGR00643       224 LLTKFLASLPF-KLTRAQKRVVKEILQDLKSDVPMNRLLQGDVGSGKTLVAALAMLAAIE--------AGYQVALMAPTE  294 (630)
T ss_pred             HHHHHHHhCCC-CCCHHHHHHHHHHHHHhccCCCccEEEECCCCCcHHHHHHHHHHHHHH--------cCCcEEEECCHH
Confidence            34556778999 6999999999999876      36899999999999999999998765        367899999999


Q ss_pred             HHHHHHHHHHHHHHhhcCcEEEEeeCCCChHH---HHHHHhc-CCeEEEeCchhHHHHHHhcCCcccccCCceEEEecCc
Q 002040          551 ELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQ---QISELKR-GTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEA  626 (976)
Q Consensus       551 ~La~Q~~~~~~~~~~~~~~~~~~~~gg~~~~~---~~~~l~~-~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDEa  626 (976)
                      +||.|++..+.+++..+|+.+.+++|+.....   .+..+.. .++|||+||+.|.+.        ..+.++++|||||+
T Consensus       295 ~LA~Q~~~~~~~l~~~~gi~v~lltg~~~~~~r~~~~~~i~~g~~~IiVgT~~ll~~~--------~~~~~l~lvVIDEa  366 (630)
T TIGR00643       295 ILAEQHYNSLRNLLAPLGIEVALLTGSLKGKRRKELLETIASGQIHLVVGTHALIQEK--------VEFKRLALVIIDEQ  366 (630)
T ss_pred             HHHHHHHHHHHHHhcccCcEEEEEecCCCHHHHHHHHHHHhCCCCCEEEecHHHHhcc--------ccccccceEEEech
Confidence            99999999999999989999999999987665   3344443 479999999876432        35778999999999


Q ss_pred             ccccccCCchHHHHHHHhcC--CCCcEEEEeccCcHHHHHHHHHHcCCCeEEEeCCcccccCCceEEEEecCcchHHHHH
Q 002040          627 DRMFDMGFEPQITRIVQNIR--PDRQTVLFSATFPRQVEILARKVLNKPVEIQVGGRSVVNKDITQLVEVRPESDRFLRL  704 (976)
Q Consensus       627 h~~~~~~f~~~i~~il~~~~--~~~q~i~~SAT~~~~~~~l~~~~l~~~~~i~~~~~~~~~~~i~q~~~~~~~~~k~~~l  704 (976)
                      |++...    +...+.....  ..+++|+||||+.+....+.  .+.......+...+.....+...+.  .... ...+
T Consensus       367 H~fg~~----qr~~l~~~~~~~~~~~~l~~SATp~prtl~l~--~~~~l~~~~i~~~p~~r~~i~~~~~--~~~~-~~~~  437 (630)
T TIGR00643       367 HRFGVE----QRKKLREKGQGGFTPHVLVMSATPIPRTLALT--VYGDLDTSIIDELPPGRKPITTVLI--KHDE-KDIV  437 (630)
T ss_pred             hhccHH----HHHHHHHhcccCCCCCEEEEeCCCCcHHHHHH--hcCCcceeeeccCCCCCCceEEEEe--Ccch-HHHH
Confidence            985321    2222222222  26789999999876543332  2222211111111111223333222  2222 2444


Q ss_pred             HHHHHhhh-cCCcEEEEecCH--------HHHHHHHHHHHHC--CCCceeccCCCCHHHHHHHHHHhccCCccEEEecCc
Q 002040          705 LELLGEWY-EKGKILIFVHSQ--------EKCDALFRDLLKH--GYPCLSLHGAKDQTDRESTISDFKSNVCNLLIATSV  773 (976)
Q Consensus       705 ~~~l~~~~-~~~kvLIF~~s~--------~~~~~l~~~L~~~--~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLVaT~v  773 (976)
                      +..+.... ...+++|||+..        ..+..++..|...  ++.|..+||+|++.+|..+++.|++|.++|||||++
T Consensus       438 ~~~i~~~l~~g~q~~v~~~~i~~s~~~~~~~a~~~~~~L~~~~~~~~v~~lHG~m~~~eR~~i~~~F~~g~~~ILVaT~v  517 (630)
T TIGR00643       438 YEFIEEEIAKGRQAYVVYPLIEESEKLDLKAAEALYERLKKAFPKYNVGLLHGRMKSDEKEAVMEEFREGEVDILVATTV  517 (630)
T ss_pred             HHHHHHHHHhCCcEEEEEccccccccchHHHHHHHHHHHHhhCCCCcEEEEeCCCCHHHHHHHHHHHHcCCCCEEEECce
Confidence            55554433 456899999876        4566677777653  788999999999999999999999999999999999


Q ss_pred             ccccCCCCCCcEEEEeCCCC-CHHHHHHHhcccCCCCCccEEEEEecCCCcCchHHHHHHHhhccCCCChHHHHHHHHHH
Q 002040          774 AARGLDVKELELVINFDAPN-HYEDYVHRVGRTGRAGRKGCAITFISEEDAKYSPDLVKALELSEQVVPDDLKALADSFM  852 (976)
Q Consensus       774 ~~~GlDi~~v~~VI~~d~p~-s~~~y~Qr~GR~gR~g~~g~~~~~~~~~d~~~~~~i~~~l~~~~~~vp~~l~~l~~~~~  852 (976)
                      +++|||+|++++||+|++|. ..+.|.|++||+||.|.+|.|++++...........              |.       
T Consensus       518 ie~GvDiP~v~~VIi~~~~r~gls~lhQ~~GRvGR~g~~g~~il~~~~~~~~~~~~r--------------l~-------  576 (630)
T TIGR00643       518 IEVGVDVPNATVMVIEDAERFGLSQLHQLRGRVGRGDHQSYCLLVYKNPKSESAKKR--------------LR-------  576 (630)
T ss_pred             eecCcccCCCcEEEEeCCCcCCHHHHHHHhhhcccCCCCcEEEEEECCCCCHHHHHH--------------HH-------
Confidence            99999999999999999997 577888999999999999999999843211110000              00       


Q ss_pred             HHHhhhhhhccCCCCCCCCcccchhHHHHHHHHHHHHHHHcCCCC
Q 002040          853 AKVNQGLEQAHGTGYGGSGFKFNEEEDEKRKAAKKAQAKEYGFEE  897 (976)
Q Consensus       853 ~~~~~~~~~~~~~~~~g~g~~~~~~~~~~~~~~~~~~~~~~g~~~  897 (976)
                       .+..          ...||.+++.++++|+.+..++.+|+|+..
T Consensus       577 -~~~~----------~~dgf~iae~dl~~Rg~g~~~g~~QsG~~~  610 (630)
T TIGR00643       577 -VMAD----------TLDGFVIAEEDLELRGPGDLLGTKQSGYPE  610 (630)
T ss_pred             -HHHh----------hcccHHHHHHHHhcCCCcccCCCcccCCCc
Confidence             1100          145788999999999999999999999654

>PRK13767 ATP-dependent helicase; Provisional

Probab=100.00  E-value=1e-41  Score=422.59  Aligned_cols=343  Identities=22%  Similarity=0.316  Sum_probs=251.8

Q ss_pred             CCHHHHHHHHHcCCCCCcHHHHHHHHHHhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCC-CCCCCCeEEEEccCHHH
Q 002040          474 LTSKIMETIRKLNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPV-AAGDGPVGLIMAPTREL  552 (976)
Q Consensus       474 l~~~l~~~l~~~~~~~p~~~Q~~~i~~il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~-~~~~~~~vLIl~Ptr~L  552 (976)
                      |++.+...+.. +|..|+|+|.++|+.+++|+|+|++||||||||++|++|++.++...... ....++.+|||+||++|
T Consensus        18 l~~~v~~~~~~-~~~~~tpiQ~~Ai~~il~g~nvli~APTGSGKTlaa~Lpil~~l~~~~~~~~~~~~~~~LyIsPtraL   96 (876)
T PRK13767         18 LRPYVREWFKE-KFGTFTPPQRYAIPLIHEGKNVLISSPTGSGKTLAAFLAIIDELFRLGREGELEDKVYCLYVSPLRAL   96 (876)
T ss_pred             cCHHHHHHHHH-ccCCCCHHHHHHHHHHHcCCCEEEECCCCCcHHHHHHHHHHHHHHhhccccCCCCCeEEEEEcCHHHH
Confidence            45556555554 78899999999999999999999999999999999999999988753211 11346789999999999


Q ss_pred             HHHHHHHHHH-------HHh----hc-CcEEEEeeCCCChHHHHHHHhcCCeEEEeCchhHHHHHHhcCCcccccCCceE
Q 002040          553 VQQIHSDIRK-------FAK----VM-GVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTY  620 (976)
Q Consensus       553 a~Q~~~~~~~-------~~~----~~-~~~~~~~~gg~~~~~~~~~l~~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~  620 (976)
                      |.|++..+..       ++.    .+ ++.+.+++|+.+.......+...++|+||||++|..++... .....|.++.+
T Consensus        97 a~di~~~L~~~l~~i~~~~~~~g~~~~~i~v~v~~Gdt~~~~r~~~l~~~p~IlVtTPE~L~~ll~~~-~~~~~l~~l~~  175 (876)
T PRK13767         97 NNDIHRNLEEPLTEIREIAKERGEELPEIRVAIRTGDTSSYEKQKMLKKPPHILITTPESLAILLNSP-KFREKLRTVKW  175 (876)
T ss_pred             HHHHHHHHHHHHHHHHHHHHhcCCCcCCeeEEEEcCCCCHHHHHHHHhCCCCEEEecHHHHHHHhcCh-hHHHHHhcCCE
Confidence            9999886653       221    22 67888899999888877777778999999999997766432 11235788999


Q ss_pred             EEecCcccccccCCchHHHHHH----HhcCCCCcEEEEeccCcHHHHHHHHHHcCC-----C--eEEEeCCcccccCCce
Q 002040          621 LVMDEADRMFDMGFEPQITRIV----QNIRPDRQTVLFSATFPRQVEILARKVLNK-----P--VEIQVGGRSVVNKDIT  689 (976)
Q Consensus       621 vVlDEah~~~~~~f~~~i~~il----~~~~~~~q~i~~SAT~~~~~~~l~~~~l~~-----~--~~i~~~~~~~~~~~i~  689 (976)
                      |||||||.+++..+..++..++    ....+..|+|+||||+++. ..++..+...     +  +.+ +.........+.
T Consensus       176 VVIDE~H~l~~~~RG~~l~~~L~rL~~l~~~~~q~IglSATl~~~-~~va~~L~~~~~~~~~r~~~i-v~~~~~k~~~i~  253 (876)
T PRK13767        176 VIVDEIHSLAENKRGVHLSLSLERLEELAGGEFVRIGLSATIEPL-EEVAKFLVGYEDDGEPRDCEI-VDARFVKPFDIK  253 (876)
T ss_pred             EEEechhhhccCccHHHHHHHHHHHHHhcCCCCeEEEEecccCCH-HHHHHHhcCccccCCCCceEE-EccCCCccceEE
Confidence            9999999998776665544333    3334678999999999763 2333332221     1  111 111111111111


Q ss_pred             EEEE-----ecCcchHHHHHHHHHHhhh-cCCcEEEEecCHHHHHHHHHHHHHC------CCCceeccCCCCHHHHHHHH
Q 002040          690 QLVE-----VRPESDRFLRLLELLGEWY-EKGKILIFVHSQEKCDALFRDLLKH------GYPCLSLHGAKDQTDRESTI  757 (976)
Q Consensus       690 q~~~-----~~~~~~k~~~l~~~l~~~~-~~~kvLIF~~s~~~~~~l~~~L~~~------~~~~~~lhg~~~~~~R~~~~  757 (976)
                      ....     ..........+...|.... ..+++||||+|+..|+.++..|...      +..+..+||+|++.+|..++
T Consensus       254 v~~p~~~l~~~~~~~~~~~l~~~L~~~i~~~~~~LVF~nTr~~ae~la~~L~~~~~~~~~~~~i~~hHg~ls~~~R~~ve  333 (876)
T PRK13767        254 VISPVDDLIHTPAEEISEALYETLHELIKEHRTTLIFTNTRSGAERVLYNLRKRFPEEYDEDNIGAHHSSLSREVRLEVE  333 (876)
T ss_pred             EeccCccccccccchhHHHHHHHHHHHHhcCCCEEEEeCCHHHHHHHHHHHHHhchhhccccceeeeeCCCCHHHHHHHH
Confidence            0000     0111112223333333332 3578999999999999999999873      46899999999999999999


Q ss_pred             HHhccCCccEEEecCcccccCCCCCCcEEEEeCCCCCHHHHHHHhcccCCC-CCccEEEEEecC
Q 002040          758 SDFKSNVCNLLIATSVAARGLDVKELELVINFDAPNHYEDYVHRVGRTGRA-GRKGCAITFISE  820 (976)
Q Consensus       758 ~~F~~g~~~vLVaT~v~~~GlDi~~v~~VI~~d~p~s~~~y~Qr~GR~gR~-g~~g~~~~~~~~  820 (976)
                      +.|++|.++|||||+++++|||||++++||+|++|.+...|+||+||+||. |..+.++++++.
T Consensus       334 ~~fk~G~i~vLVaTs~Le~GIDip~Vd~VI~~~~P~sv~~ylQRiGRaGR~~g~~~~g~ii~~~  397 (876)
T PRK13767        334 EKLKRGELKVVVSSTSLELGIDIGYIDLVVLLGSPKSVSRLLQRIGRAGHRLGEVSKGRIIVVD  397 (876)
T ss_pred             HHHHcCCCeEEEECChHHhcCCCCCCcEEEEeCCCCCHHHHHHhcccCCCCCCCCCcEEEEEcC
Confidence            999999999999999999999999999999999999999999999999986 444445555443

>PRK02362 ski2-like helicase; Provisional

Probab=100.00  E-value=5.3e-42  Score=421.84  Aligned_cols=335  Identities=24%  Similarity=0.370  Sum_probs=258.2

Q ss_pred             ccccCCCCHHHHHHHHHcCCCCCcHHHHHHHHH-HhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEE
Q 002040          468 TWHQTGLTSKIMETIRKLNYEKPMPIQAQALPV-IMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIM  546 (976)
Q Consensus       468 ~~~~~~l~~~l~~~l~~~~~~~p~~~Q~~~i~~-il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl  546 (976)
                      .|.+++|++.+.+.+...||..|+|+|.+|++. +++|+|+|++||||||||++|.+|++.++..        +.++|||
T Consensus         2 ~~~~l~lp~~~~~~l~~~g~~~l~p~Q~~ai~~~~~~g~nvlv~APTGSGKTlia~lail~~l~~--------~~kal~i   73 (737)
T PRK02362          2 KIAELPLPEGVIEFYEAEGIEELYPPQAEAVEAGLLDGKNLLAAIPTASGKTLIAELAMLKAIAR--------GGKALYI   73 (737)
T ss_pred             ChhhcCCCHHHHHHHHhCCCCcCCHHHHHHHHHHHhCCCcEEEECCCcchHHHHHHHHHHHHHhc--------CCcEEEE
Confidence            578899999999999999999999999999998 7799999999999999999999999998752        5689999


Q ss_pred             ccCHHHHHHHHHHHHHHHhhcCcEEEEeeCCCChHHHHHHHhcCCeEEEeCchhHHHHHHhcCCcccccCCceEEEecCc
Q 002040          547 APTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEA  626 (976)
Q Consensus       547 ~Ptr~La~Q~~~~~~~~~~~~~~~~~~~~gg~~~~~~~~~l~~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDEa  626 (976)
                      +||++||.|++..|..+.. +|+++..++|+......   ....++|+||||+++..++....   ..+..+++|||||+
T Consensus        74 ~P~raLa~q~~~~~~~~~~-~g~~v~~~tGd~~~~~~---~l~~~~IiV~Tpek~~~llr~~~---~~l~~v~lvViDE~  146 (737)
T PRK02362         74 VPLRALASEKFEEFERFEE-LGVRVGISTGDYDSRDE---WLGDNDIIVATSEKVDSLLRNGA---PWLDDITCVVVDEV  146 (737)
T ss_pred             eChHHHHHHHHHHHHHhhc-CCCEEEEEeCCcCcccc---ccCCCCEEEECHHHHHHHHhcCh---hhhhhcCEEEEECc
Confidence            9999999999999998653 58999999998754432   22457999999999988776432   34678999999999


Q ss_pred             ccccccCCchHHHHHHHhc---CCCCcEEEEeccCcHHHHHHHHHHcCC-------CeEEEeC--CcccccCCceEE-EE
Q 002040          627 DRMFDMGFEPQITRIVQNI---RPDRQTVLFSATFPRQVEILARKVLNK-------PVEIQVG--GRSVVNKDITQL-VE  693 (976)
Q Consensus       627 h~~~~~~f~~~i~~il~~~---~~~~q~i~~SAT~~~~~~~l~~~~l~~-------~~~i~~~--~~~~~~~~i~q~-~~  693 (976)
                      |.+.+.++++.+..++..+   .+..|+|+||||+++. ..++..+...       |+.+..+  ..........+. +.
T Consensus       147 H~l~d~~rg~~le~il~rl~~~~~~~qii~lSATl~n~-~~la~wl~~~~~~~~~rpv~l~~~v~~~~~~~~~~~~~~~~  225 (737)
T PRK02362        147 HLIDSANRGPTLEVTLAKLRRLNPDLQVVALSATIGNA-DELADWLDAELVDSEWRPIDLREGVFYGGAIHFDDSQREVE  225 (737)
T ss_pred             cccCCCcchHHHHHHHHHHHhcCCCCcEEEEcccCCCH-HHHHHHhCCCcccCCCCCCCCeeeEecCCeeccccccccCC
Confidence            9999888888887776554   5788999999999864 2233322111       1111100  000000000000 00


Q ss_pred             ecCcchHHHHHHHHHHhhhcCCcEEEEecCHHHHHHHHHHHHHC------------------------------------
Q 002040          694 VRPESDRFLRLLELLGEWYEKGKILIFVHSQEKCDALFRDLLKH------------------------------------  737 (976)
Q Consensus       694 ~~~~~~k~~~l~~~l~~~~~~~kvLIF~~s~~~~~~l~~~L~~~------------------------------------  737 (976)
                      .......+..+...+   ..++++||||+++..|..++..|...                                    
T Consensus       226 ~~~~~~~~~~~~~~~---~~~~~~LVF~~sr~~~~~~a~~L~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~L~~~l  302 (737)
T PRK02362        226 VPSKDDTLNLVLDTL---EEGGQCLVFVSSRRNAEGFAKRAASALKKTLTAAERAELAELAEEIREVSDTETSKDLADCV  302 (737)
T ss_pred             CccchHHHHHHHHHH---HcCCCeEEEEeCHHHHHHHHHHHHHHhhhcCCHHHHHHHHHHHHHHHhccCccccHHHHHHH
Confidence            000111222222222   25689999999999999998887643                                    


Q ss_pred             CCCceeccCCCCHHHHHHHHHHhccCCccEEEecCcccccCCCCCCcEEEE----eC-----CCCCHHHHHHHhcccCCC
Q 002040          738 GYPCLSLHGAKDQTDRESTISDFKSNVCNLLIATSVAARGLDVKELELVIN----FD-----APNHYEDYVHRVGRTGRA  808 (976)
Q Consensus       738 ~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLVaT~v~~~GlDi~~v~~VI~----~d-----~p~s~~~y~Qr~GR~gR~  808 (976)
                      ...+..+||+|++.+|..++..|++|.++|||||+++++|||+|.+.+||+    |+     .|.+..+|+||+|||||.
T Consensus       303 ~~gva~hHagl~~~eR~~ve~~Fr~G~i~VLvaT~tla~GvnlPa~~VVI~~~~~yd~~~g~~~~s~~~y~Qm~GRAGR~  382 (737)
T PRK02362        303 AKGAAFHHAGLSREHRELVEDAFRDRLIKVISSTPTLAAGLNLPARRVIIRDYRRYDGGAGMQPIPVLEYHQMAGRAGRP  382 (737)
T ss_pred             HhCEEeecCCCCHHHHHHHHHHHHcCCCeEEEechhhhhhcCCCceEEEEecceeecCCCCceeCCHHHHHHHhhcCCCC
Confidence            136788999999999999999999999999999999999999999999997    76     588999999999999999


Q ss_pred             CCc--cEEEEEecCC
Q 002040          809 GRK--GCAITFISEE  821 (976)
Q Consensus       809 g~~--g~~~~~~~~~  821 (976)
                      |..  |.|++++...
T Consensus       383 g~d~~G~~ii~~~~~  397 (737)
T PRK02362        383 GLDPYGEAVLLAKSY  397 (737)
T ss_pred             CCCCCceEEEEecCc
Confidence            865  8999988654

>TIGR01389 recQ ATP-dependent DNA helicase RecQ

Probab=100.00  E-value=5.5e-42  Score=412.88  Aligned_cols=326  Identities=22%  Similarity=0.350  Sum_probs=259.7

Q ss_pred             HHH-HcCCCCCcHHHHHHHHHHhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHH
Q 002040          481 TIR-KLNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSD  559 (976)
Q Consensus       481 ~l~-~~~~~~p~~~Q~~~i~~il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~  559 (976)
                      .|+ .+||..|+|+|.++|+.++.|+|+++++|||+|||++|++|++..           +..+|||+|+++|+.|++..
T Consensus         4 ~l~~~fg~~~fr~~Q~~~i~~il~g~dvlv~~PTG~GKTl~y~lpal~~-----------~g~~lVisPl~sL~~dq~~~   72 (591)
T TIGR01389         4 VLKRTFGYDDFRPGQEEIISHVLDGRDVLVVMPTGGGKSLCYQVPALLL-----------KGLTVVISPLISLMKDQVDQ   72 (591)
T ss_pred             HHHHhcCCCCCCHHHHHHHHHHHcCCCEEEEcCCCccHhHHHHHHHHHc-----------CCcEEEEcCCHHHHHHHHHH
Confidence            344 399999999999999999999999999999999999999998842           33589999999999998887


Q ss_pred             HHHHHhhcCcEEEEeeCCCChHHHHH---HHh-cCCeEEEeCchhHHHHHHhcCCcccccCCceEEEecCcccccccC--
Q 002040          560 IRKFAKVMGVRCVPVYGGSGVAQQIS---ELK-RGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMG--  633 (976)
Q Consensus       560 ~~~~~~~~~~~~~~~~gg~~~~~~~~---~l~-~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDEah~~~~~~--  633 (976)
                      +..    +|+.+..+.++....+...   .+. ...+|+++||++|.......   ......+++|||||||++..||  
T Consensus        73 l~~----~gi~~~~~~s~~~~~~~~~~~~~l~~~~~~il~~tpe~l~~~~~~~---~l~~~~l~~iViDEaH~i~~~g~~  145 (591)
T TIGR01389        73 LRA----AGVAAAYLNSTLSAKEQQDIEKALVNGELKLLYVAPERLEQDYFLN---MLQRIPIALVAVDEAHCVSQWGHD  145 (591)
T ss_pred             HHH----cCCcEEEEeCCCCHHHHHHHHHHHhCCCCCEEEEChhHhcChHHHH---HHhcCCCCEEEEeCCcccccccCc
Confidence            776    4788888888876655432   222 35799999999986432221   1345679999999999999887  


Q ss_pred             CchHHHHHHHh--cCCCCcEEEEeccCcHHHHHHHHHHcC--CCeEEEeCCcccccCCceEEEEecCcchHHHHHHHHHH
Q 002040          634 FEPQITRIVQN--IRPDRQTVLFSATFPRQVEILARKVLN--KPVEIQVGGRSVVNKDITQLVEVRPESDRFLRLLELLG  709 (976)
Q Consensus       634 f~~~i~~il~~--~~~~~q~i~~SAT~~~~~~~l~~~~l~--~~~~i~~~~~~~~~~~i~q~~~~~~~~~k~~~l~~~l~  709 (976)
                      |.+.+..+...  .-+..++|+||||+++.+...+...+.  .+..+. .  .....++.  +.+.....+...+...|.
T Consensus       146 frp~y~~l~~l~~~~~~~~vi~lTAT~~~~~~~~i~~~l~~~~~~~~~-~--~~~r~nl~--~~v~~~~~~~~~l~~~l~  220 (591)
T TIGR01389       146 FRPEYQRLGSLAERFPQVPRIALTATADAETRQDIRELLRLADANEFI-T--SFDRPNLR--FSVVKKNNKQKFLLDYLK  220 (591)
T ss_pred             cHHHHHHHHHHHHhCCCCCEEEEEeCCCHHHHHHHHHHcCCCCCCeEe-c--CCCCCCcE--EEEEeCCCHHHHHHHHHH
Confidence            66666554332  224556999999999988766666554  333221 1  22223332  223334456667777776


Q ss_pred             hhhcCCcEEEEecCHHHHHHHHHHHHHCCCCceeccCCCCHHHHHHHHHHhccCCccEEEecCcccccCCCCCCcEEEEe
Q 002040          710 EWYEKGKILIFVHSQEKCDALFRDLLKHGYPCLSLHGAKDQTDRESTISDFKSNVCNLLIATSVAARGLDVKELELVINF  789 (976)
Q Consensus       710 ~~~~~~kvLIF~~s~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLVaT~v~~~GlDi~~v~~VI~~  789 (976)
                      .. ...++||||+++..|+.++..|...|+.+..+||+|+..+|..+++.|.+|.++|||||+++++|||+|++++||+|
T Consensus       221 ~~-~~~~~IIf~~sr~~~e~la~~L~~~g~~~~~~H~~l~~~~R~~i~~~F~~g~~~vlVaT~a~~~GID~p~v~~VI~~  299 (591)
T TIGR01389       221 KH-RGQSGIIYASSRKKVEELAERLESQGISALAYHAGLSNKVRAENQEDFLYDDVKVMVATNAFGMGIDKPNVRFVIHY  299 (591)
T ss_pred             hc-CCCCEEEEECcHHHHHHHHHHHHhCCCCEEEEECCCCHHHHHHHHHHHHcCCCcEEEEechhhccCcCCCCCEEEEc
Confidence            53 35789999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCCHHHHHHHhcccCCCCCccEEEEEecCCCcCchHHHH
Q 002040          790 DAPNHYEDYVHRVGRTGRAGRKGCAITFISEEDAKYSPDLV  830 (976)
Q Consensus       790 d~p~s~~~y~Qr~GR~gR~g~~g~~~~~~~~~d~~~~~~i~  830 (976)
                      ++|.++..|+|++||+||.|..|.|++||++.+...+..++
T Consensus       300 ~~p~s~~~y~Q~~GRaGR~G~~~~~il~~~~~d~~~~~~~i  340 (591)
T TIGR01389       300 DMPGNLESYYQEAGRAGRDGLPAEAILLYSPADIALLKRRI  340 (591)
T ss_pred             CCCCCHHHHhhhhccccCCCCCceEEEecCHHHHHHHHHHH
Confidence            99999999999999999999999999999987765555444

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.

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

Probab=100.00  E-value=7.3e-42  Score=405.94  Aligned_cols=317  Identities=20%  Similarity=0.277  Sum_probs=249.0

Q ss_pred             cCCCCCcHHHHHHHHHHhcCC-CEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEE-EccCHHHHHHHHHHHHH
Q 002040          485 LNYEKPMPIQAQALPVIMSGR-DCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLI-MAPTRELVQQIHSDIRK  562 (976)
Q Consensus       485 ~~~~~p~~~Q~~~i~~il~g~-d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLI-l~Ptr~La~Q~~~~~~~  562 (976)
                      .||. |||||.++|+.++.|+ ++++++|||||||.+|+++++.. ..     ....|+.|| ++|||+||.|+++.+.+
T Consensus        12 ~G~~-PtpiQ~~~i~~il~G~~~v~~~apTGSGKTaa~aafll~~-~~-----~~~~~~rLv~~vPtReLa~Qi~~~~~~   84 (844)
T TIGR02621        12 HGYS-PFPWQLSLAERFVAGQPPESCSTPTGLGKTSIIAAWLLAV-EI-----GAKVPRRLVYVVNRRTVVDQVTEEAEK   84 (844)
T ss_pred             hCCC-CCHHHHHHHHHHHcCCCcceEecCCCCcccHHHHHhhccc-cc-----cccccceEEEeCchHHHHHHHHHHHHH
Confidence            5887 9999999999999998 57778999999999776555532 11     123566666 66999999999999999


Q ss_pred             HHhhc-----------------------CcEEEEeeCCCChHHHHHHHhcCCeEEEeCchhHHHHHHhcCC---------
Q 002040          563 FAKVM-----------------------GVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGG---------  610 (976)
Q Consensus       563 ~~~~~-----------------------~~~~~~~~gg~~~~~~~~~l~~~~~Iiv~Tp~~L~~~l~~~~~---------  610 (976)
                      +++.+                       ++.+.+++||.+...++..+..+++|||+|+    +++.+...         
T Consensus        85 ~~k~l~~~~~~~~~~~~~~~~~~~~~~~~l~v~~l~GG~~~~~q~~~l~~~p~IIVgT~----D~i~sr~L~~gYg~~~~  160 (844)
T TIGR02621        85 IGERLPDVPEVEAALWALCSTRPEKKDRPLAISTLRGQFADNDEWMLDPHRPAVIVGTV----DMIGSRLLFSGYGCGFK  160 (844)
T ss_pred             HHHHhcccchhhhhhhhhhccccccccCCeEEEEEECCCChHHHHHhcCCCCcEEEECH----HHHcCCccccccccccc
Confidence            98865                       4889999999999999999999999999995    44433211         


Q ss_pred             ----cccccCCceEEEecCcccccccCCchHHHHHHHhc--CCC---CcEEEEeccCcHHHHHHHHHHcCCCeEEEeCCc
Q 002040          611 ----KITNLRRVTYLVMDEADRMFDMGFEPQITRIVQNI--RPD---RQTVLFSATFPRQVEILARKVLNKPVEIQVGGR  681 (976)
Q Consensus       611 ----~~~~l~~~~~vVlDEah~~~~~~f~~~i~~il~~~--~~~---~q~i~~SAT~~~~~~~l~~~~l~~~~~i~~~~~  681 (976)
                          ....|.++.+|||||||  ++++|...+..|+..+  ++.   +|+++||||++..+..++..++.++..+.+...
T Consensus       161 ~~pi~ag~L~~v~~LVLDEAD--Ld~gF~~~l~~Il~~l~rp~~~rprQtLLFSAT~p~ei~~l~~~~~~~p~~i~V~~~  238 (844)
T TIGR02621       161 SRPLHAGFLGQDALIVHDEAH--LEPAFQELLKQIMNEQQRPPDFLPLRVVELTATSRTDGPDRTTLLSAEDYKHPVLKK  238 (844)
T ss_pred             cccchhhhhccceEEEEehhh--hccccHHHHHHHHHhcccCcccccceEEEEecCCCccHHHHHHHHccCCceeecccc
Confidence                00126789999999999  6799999999999975  332   699999999999888888888878876666544


Q ss_pred             ccccCCceEEEEecCcchHHHHHHHHHHhh--hcCCcEEEEecCHHHHHHHHHHHHHCCCCceeccCCCCHHHHH-----
Q 002040          682 SVVNKDITQLVEVRPESDRFLRLLELLGEW--YEKGKILIFVHSQEKCDALFRDLLKHGYPCLSLHGAKDQTDRE-----  754 (976)
Q Consensus       682 ~~~~~~i~q~~~~~~~~~k~~~l~~~l~~~--~~~~kvLIF~~s~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~-----  754 (976)
                      ......+.+.+. .....++..++..|...  ...+++||||||+..|..|+..|...++  ..|||.|++.+|.     
T Consensus       239 ~l~a~ki~q~v~-v~~e~Kl~~lv~~L~~ll~e~g~~vLVF~NTv~~Aq~L~~~L~~~g~--~lLHG~m~q~dR~~~~~~  315 (844)
T TIGR02621       239 RLAAKKIVKLVP-PSDEKFLSTMVKELNLLMKDSGGAILVFCRTVKHVRKVFAKLPKEKF--ELLTGTLRGAERDDLVKK  315 (844)
T ss_pred             cccccceEEEEe-cChHHHHHHHHHHHHHHHhhCCCcEEEEECCHHHHHHHHHHHHhcCC--eEeeCCCCHHHHhhHHHH
Confidence            444445555433 23334444444333222  2357899999999999999999998876  8999999999999     


Q ss_pred             HHHHHhcc----CC-------ccEEEecCcccccCCCCCCcEEEEeCCCCCHHHHHHHhcccCCCCCc-cEEEEEecC
Q 002040          755 STISDFKS----NV-------CNLLIATSVAARGLDVKELELVINFDAPNHYEDYVHRVGRTGRAGRK-GCAITFISE  820 (976)
Q Consensus       755 ~~~~~F~~----g~-------~~vLVaT~v~~~GlDi~~v~~VI~~d~p~s~~~y~Qr~GR~gR~g~~-g~~~~~~~~  820 (976)
                      .+++.|++    |.       ..|||||+++++||||+. ++||++..|  .+.|+||+||+||.|.. +..+++++.
T Consensus       316 ~il~~Fk~~~~~g~~~~~~~g~~ILVATdVaerGLDId~-d~VI~d~aP--~esyIQRiGRtgR~G~~~~~~i~vv~~  390 (844)
T TIGR02621       316 EIFNRFLPQMLSGSRARPQQGTVYLVCTSAGEVGVNISA-DHLVCDLAP--FESMQQRFGRVNRFGELQACQIAVVHL  390 (844)
T ss_pred             HHHHHHhccccccccccccccceEEeccchhhhcccCCc-ceEEECCCC--HHHHHHHhcccCCCCCCCCceEEEEee
Confidence            88999987    54       689999999999999986 888888777  68999999999999985 344555543

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.

>PRK00254 ski2-like helicase; Provisional

Probab=100.00  E-value=8.3e-41  Score=410.24  Aligned_cols=338  Identities=20%  Similarity=0.278  Sum_probs=260.9

Q ss_pred             ccccCCCCHHHHHHHHHcCCCCCcHHHHHHHHH-HhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEE
Q 002040          468 TWHQTGLTSKIMETIRKLNYEKPMPIQAQALPV-IMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIM  546 (976)
Q Consensus       468 ~~~~~~l~~~l~~~l~~~~~~~p~~~Q~~~i~~-il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl  546 (976)
                      +|.++++++.+.+.|...||..|+|+|.++++. +++|+++|+++|||||||++|.+|++.++..       .+.++|||
T Consensus         2 ~~~~l~l~~~~~~~l~~~g~~~l~~~Q~~ai~~~~~~g~nvlv~apTGsGKT~~~~l~il~~l~~-------~~~~~l~l   74 (720)
T PRK00254          2 KVDELRVDERIKRVLKERGIEELYPPQAEALKSGVLEGKNLVLAIPTASGKTLVAEIVMVNKLLR-------EGGKAVYL   74 (720)
T ss_pred             cHHHcCCCHHHHHHHHhCCCCCCCHHHHHHHHHHHhCCCcEEEECCCCcHHHHHHHHHHHHHHHh-------cCCeEEEE
Confidence            577889999999999999999999999999986 7899999999999999999999999988764       25689999


Q ss_pred             ccCHHHHHHHHHHHHHHHhhcCcEEEEeeCCCChHHHHHHHhcCCeEEEeCchhHHHHHHhcCCcccccCCceEEEecCc
Q 002040          547 APTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEA  626 (976)
Q Consensus       547 ~Ptr~La~Q~~~~~~~~~~~~~~~~~~~~gg~~~~~~~~~l~~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDEa  626 (976)
                      +|+++||.|++..|..+. .+|+.+..++|+......   ....++|+|+||+++..++....   ..++++++|||||+
T Consensus        75 ~P~~aLa~q~~~~~~~~~-~~g~~v~~~~Gd~~~~~~---~~~~~~IiV~Tpe~~~~ll~~~~---~~l~~l~lvViDE~  147 (720)
T PRK00254         75 VPLKALAEEKYREFKDWE-KLGLRVAMTTGDYDSTDE---WLGKYDIIIATAEKFDSLLRHGS---SWIKDVKLVVADEI  147 (720)
T ss_pred             eChHHHHHHHHHHHHHHh-hcCCEEEEEeCCCCCchh---hhccCCEEEEcHHHHHHHHhCCc---hhhhcCCEEEEcCc
Confidence            999999999999998864 478999999998765432   22458999999999987775432   34788999999999


Q ss_pred             ccccccCCchHHHHHHHhcCCCCcEEEEeccCcHHHHHHHHHHcCCCeEEEeCCcccccC-C-ceEEEEecCcc--hHH-
Q 002040          627 DRMFDMGFEPQITRIVQNIRPDRQTVLFSATFPRQVEILARKVLNKPVEIQVGGRSVVNK-D-ITQLVEVRPES--DRF-  701 (976)
Q Consensus       627 h~~~~~~f~~~i~~il~~~~~~~q~i~~SAT~~~~~~~l~~~~l~~~~~i~~~~~~~~~~-~-i~q~~~~~~~~--~k~-  701 (976)
                      |.+.+.++...+..++..+....|+|+||||+++. ..++. |+...... ....+.+.. . +.+.+......  .++ 
T Consensus       148 H~l~~~~rg~~le~il~~l~~~~qiI~lSATl~n~-~~la~-wl~~~~~~-~~~rpv~l~~~~~~~~~~~~~~~~~~~~~  224 (720)
T PRK00254        148 HLIGSYDRGATLEMILTHMLGRAQILGLSATVGNA-EELAE-WLNAELVV-SDWRPVKLRKGVFYQGFLFWEDGKIERFP  224 (720)
T ss_pred             CccCCccchHHHHHHHHhcCcCCcEEEEEccCCCH-HHHHH-HhCCcccc-CCCCCCcceeeEecCCeeeccCcchhcch
Confidence            99998899999999999998899999999999864 44444 44433211 111111110 0 11111111111  111 


Q ss_pred             HHHHHHHHhh-hcCCcEEEEecCHHHHHHHHHHHHHC---------------------------------CCCceeccCC
Q 002040          702 LRLLELLGEW-YEKGKILIFVHSQEKCDALFRDLLKH---------------------------------GYPCLSLHGA  747 (976)
Q Consensus       702 ~~l~~~l~~~-~~~~kvLIF~~s~~~~~~l~~~L~~~---------------------------------~~~~~~lhg~  747 (976)
                      ..+...+... ..++++||||+++..|..++..|...                                 ...+.++||+
T Consensus       225 ~~~~~~~~~~i~~~~~vLVF~~sr~~~~~~a~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~~l~~gv~~hHag  304 (720)
T PRK00254        225 NSWESLVYDAVKKGKGALVFVNTRRSAEKEALELAKKIKRFLTKPELRALKELADSLEENPTNEKLKKALRGGVAFHHAG  304 (720)
T ss_pred             HHHHHHHHHHHHhCCCEEEEEcChHHHHHHHHHHHHHHHHhcCchhHHHHHHHHHHHhcCCCcHHHHHHHhhCEEEeCCC
Confidence            1111222221 23679999999999998877666421                                 2358899999


Q ss_pred             CCHHHHHHHHHHhccCCccEEEecCcccccCCCCCCcEEEE-------eCCCC-CHHHHHHHhcccCCCC--CccEEEEE
Q 002040          748 KDQTDRESTISDFKSNVCNLLIATSVAARGLDVKELELVIN-------FDAPN-HYEDYVHRVGRTGRAG--RKGCAITF  817 (976)
Q Consensus       748 ~~~~~R~~~~~~F~~g~~~vLVaT~v~~~GlDi~~v~~VI~-------~d~p~-s~~~y~Qr~GR~gR~g--~~g~~~~~  817 (976)
                      |++.+|..+...|++|.++|||||+++++|||+|.+.+||.       ++.|. ....|+||+|||||.|  ..|.|++|
T Consensus       305 l~~~eR~~ve~~F~~G~i~VLvaT~tLa~Gvnipa~~vVI~~~~~~~~~~~~~~~~~~~~Qm~GRAGR~~~d~~G~~ii~  384 (720)
T PRK00254        305 LGRTERVLIEDAFREGLIKVITATPTLSAGINLPAFRVIIRDTKRYSNFGWEDIPVLEIQQMMGRAGRPKYDEVGEAIIV  384 (720)
T ss_pred             CCHHHHHHHHHHHHCCCCeEEEeCcHHhhhcCCCceEEEECCceEcCCCCceeCCHHHHHHhhhccCCCCcCCCceEEEE
Confidence            99999999999999999999999999999999999999994       45444 4679999999999965  57999999


Q ss_pred             ecCCC
Q 002040          818 ISEED  822 (976)
Q Consensus       818 ~~~~d  822 (976)
                      ++..+
T Consensus       385 ~~~~~  389 (720)
T PRK00254        385 ATTEE  389 (720)
T ss_pred             ecCcc
Confidence            87644

>KOG0329 consensus ATP-dependent RNA helicase [RNA processing and modification]

Probab=100.00  E-value=3.5e-42  Score=340.19  Aligned_cols=334  Identities=31%  Similarity=0.523  Sum_probs=287.0

Q ss_pred             ccccccCCCCHHHHHHHHHcCCCCCcHHHHHHHHHHhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEE
Q 002040          466 IKTWHQTGLTSKIMETIRKLNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLI  545 (976)
Q Consensus       466 i~~~~~~~l~~~l~~~l~~~~~~~p~~~Q~~~i~~il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLI  545 (976)
                      .+.|.++-|.+.++.++-..||..|+.+|.++||...-|.|+|.+|..|.|||.+|.+..++.+.--     .....+||
T Consensus        41 ssgfrdfllkpellraivdcgfehpsevqhecipqailgmdvlcqaksgmgktavfvl~tlqqiepv-----~g~vsvlv  115 (387)
T KOG0329|consen   41 SSGFRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQIEPV-----DGQVSVLV  115 (387)
T ss_pred             ccchhhhhcCHHHHHHHHhccCCCchHhhhhhhhHHhhcchhheecccCCCceeeeehhhhhhcCCC-----CCeEEEEE
Confidence            3568889999999999999999999999999999999999999999999999999999888776532     22456899


Q ss_pred             EccCHHHHHHHHHHHHHHHhhc-CcEEEEeeCCCChHHHHHHHhcCCeEEEeCchhHHHHHHhcCCcccccCCceEEEec
Q 002040          546 MAPTRELVQQIHSDIRKFAKVM-GVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMD  624 (976)
Q Consensus       546 l~Ptr~La~Q~~~~~~~~~~~~-~~~~~~~~gg~~~~~~~~~l~~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlD  624 (976)
                      +|.||+||.|+.+++.+|++++ ++++.++|||..+......++.-++|+|+|||+++.+....   ..+|+++..+|||
T Consensus       116 mchtrelafqi~~ey~rfskymP~vkvaVFfGG~~Ikkdee~lk~~PhivVgTPGrilALvr~k---~l~lk~vkhFvlD  192 (387)
T KOG0329|consen  116 MCHTRELAFQISKEYERFSKYMPSVKVSVFFGGLFIKKDEELLKNCPHIVVGTPGRILALVRNR---SLNLKNVKHFVLD  192 (387)
T ss_pred             EeccHHHHHHHHHHHHHHHhhCCCceEEEEEcceeccccHHHHhCCCeEEEcCcHHHHHHHHhc---cCchhhcceeehh
Confidence            9999999999999999999987 58899999999998888888887899999999999888764   3788999999999


Q ss_pred             Cccccccc-CCchHHHHHHHhcCCCCcEEEEeccCcHHHHHHHHHHcCCCeEEEeCCccc-ccCCceEEEEecCcchHHH
Q 002040          625 EADRMFDM-GFEPQITRIVQNIRPDRQTVLFSATFPRQVEILARKVLNKPVEIQVGGRSV-VNKDITQLVEVRPESDRFL  702 (976)
Q Consensus       625 Eah~~~~~-~f~~~i~~il~~~~~~~q~i~~SAT~~~~~~~l~~~~l~~~~~i~~~~~~~-~~~~i~q~~~~~~~~~k~~  702 (976)
                      ||+.|+.+ +....+..|+...+...|+.+||||++..+.....+|+.+|..|.+..... ....+.|++.......|..
T Consensus       193 Ecdkmle~lDMrRDvQEifr~tp~~KQvmmfsatlskeiRpvC~kFmQdPmEi~vDdE~KLtLHGLqQ~YvkLke~eKNr  272 (387)
T KOG0329|consen  193 ECDKMLEQLDMRRDVQEIFRMTPHEKQVMMFSATLSKEIRPVCHKFMQDPMEIFVDDEAKLTLHGLQQYYVKLKENEKNR  272 (387)
T ss_pred             hHHHHHHHHHHHHHHHHHhhcCcccceeeeeeeecchhhHHHHHhhhcCchhhhccchhhhhhhhHHHHHHhhhhhhhhh
Confidence            99988653 457788899999999999999999999999999999999999988876543 4455677777777778887


Q ss_pred             HHHHHHHhhhcCCcEEEEecCHHHHHHHHHHHHHCCCCceeccCCCCHHHHHHHHHHhccCCccEEEecCcccccCCCCC
Q 002040          703 RLLELLGEWYEKGKILIFVHSQEKCDALFRDLLKHGYPCLSLHGAKDQTDRESTISDFKSNVCNLLIATSVAARGLDVKE  782 (976)
Q Consensus       703 ~l~~~l~~~~~~~kvLIF~~s~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLVaT~v~~~GlDi~~  782 (976)
                      .+..+|..+ .-++++||+.+...+.                               |   ..+ ||||+++++|+||..
T Consensus       273 kl~dLLd~L-eFNQVvIFvKsv~Rl~-------------------------------f---~kr-~vat~lfgrgmdier  316 (387)
T KOG0329|consen  273 KLNDLLDVL-EFNQVVIFVKSVQRLS-------------------------------F---QKR-LVATDLFGRGMDIER  316 (387)
T ss_pred             hhhhhhhhh-hhcceeEeeehhhhhh-------------------------------h---hhh-hHHhhhhccccCccc
Confidence            877777653 4679999999876510                               2   122 899999999999999


Q ss_pred             CcEEEEeCCCCCHHHHHHHhcccCCCCCccEEEEEecC-CCcCchHHHHHHHhhccCCCChH
Q 002040          783 LELVINFDAPNHYEDYVHRVGRTGRAGRKGCAITFISE-EDAKYSPDLVKALELSEQVVPDD  843 (976)
Q Consensus       783 v~~VI~~d~p~s~~~y~Qr~GR~gR~g~~g~~~~~~~~-~d~~~~~~i~~~l~~~~~~vp~~  843 (976)
                      ++.|||||.|.+..+|+||+|||||.|.+|.+++|++. ++...+..+...+......+|+.
T Consensus       317 vNi~~NYdmp~~~DtYlHrv~rAgrfGtkglaitfvs~e~da~iLn~vqdRf~v~i~eLpde  378 (387)
T KOG0329|consen  317 VNIVFNYDMPEDSDTYLHRVARAGRFGTKGLAITFVSDENDAKILNPVQDRFEVNIKELPDE  378 (387)
T ss_pred             ceeeeccCCCCCchHHHHHhhhhhccccccceeehhcchhhHHHhchhhHhhhccHhhcCcc
Confidence            99999999999999999999999999999999999974 57777777777777776677764

>PRK01172 ski2-like helicase; Provisional

Probab=100.00  E-value=1.2e-38  Score=389.73  Aligned_cols=331  Identities=18%  Similarity=0.266  Sum_probs=251.5

Q ss_pred             ccccCCCCHHHHHHHHHcCCCCCcHHHHHHHHHHhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEc
Q 002040          468 TWHQTGLTSKIMETIRKLNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMA  547 (976)
Q Consensus       468 ~~~~~~l~~~l~~~l~~~~~~~p~~~Q~~~i~~il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~  547 (976)
                      .|.+++|++.+.+.+...+|. |+|+|.++++.+.+++++|+++|||||||++|.++++.++..        +.++|||+
T Consensus         2 ~~~~~~l~~~~~~~~~~~~~~-l~~~Q~~ai~~l~~~~nvlv~apTGSGKTl~a~lail~~l~~--------~~k~v~i~   72 (674)
T PRK01172          2 KISDLGYDDEFLNLFTGNDFE-LYDHQRMAIEQLRKGENVIVSVPTAAGKTLIAYSAIYETFLA--------GLKSIYIV   72 (674)
T ss_pred             cHhhcCCCHHHHHHHhhCCCC-CCHHHHHHHHHHhcCCcEEEECCCCchHHHHHHHHHHHHHHh--------CCcEEEEe
Confidence            467889999999999999987 999999999999999999999999999999999999988753        45789999


Q ss_pred             cCHHHHHHHHHHHHHHHhhcCcEEEEeeCCCChHHHHHHHhcCCeEEEeCchhHHHHHHhcCCcccccCCceEEEecCcc
Q 002040          548 PTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEAD  627 (976)
Q Consensus       548 Ptr~La~Q~~~~~~~~~~~~~~~~~~~~gg~~~~~~~~~l~~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDEah  627 (976)
                      |+++||.|+++.|.++. .+|+.+..++|+......   +...++|+|+||+++..++....   ..+.++++|||||||
T Consensus        73 P~raLa~q~~~~~~~l~-~~g~~v~~~~G~~~~~~~---~~~~~dIiv~Tpek~~~l~~~~~---~~l~~v~lvViDEaH  145 (674)
T PRK01172         73 PLRSLAMEKYEELSRLR-SLGMRVKISIGDYDDPPD---FIKRYDVVILTSEKADSLIHHDP---YIINDVGLIVADEIH  145 (674)
T ss_pred             chHHHHHHHHHHHHHHh-hcCCeEEEEeCCCCCChh---hhccCCEEEECHHHHHHHHhCCh---hHHhhcCEEEEecch
Confidence            99999999999999864 478889888887654322   22458999999999977775432   357889999999999


Q ss_pred             cccccCCchHHHHHHH---hcCCCCcEEEEeccCcHHHHHHHHHHcCCCeEEEeCCcccccCCceEEE------EecCcc
Q 002040          628 RMFDMGFEPQITRIVQ---NIRPDRQTVLFSATFPRQVEILARKVLNKPVEIQVGGRSVVNKDITQLV------EVRPES  698 (976)
Q Consensus       628 ~~~~~~f~~~i~~il~---~~~~~~q~i~~SAT~~~~~~~l~~~~l~~~~~i~~~~~~~~~~~i~q~~------~~~~~~  698 (976)
                      .+.+.++++.+..++.   .+++..|+|+||||+++. ..++. |+..... .....+.   .+...+      ......
T Consensus       146 ~l~d~~rg~~le~ll~~~~~~~~~~riI~lSATl~n~-~~la~-wl~~~~~-~~~~r~v---pl~~~i~~~~~~~~~~~~  219 (674)
T PRK01172        146 IIGDEDRGPTLETVLSSARYVNPDARILALSATVSNA-NELAQ-WLNASLI-KSNFRPV---PLKLGILYRKRLILDGYE  219 (674)
T ss_pred             hccCCCccHHHHHHHHHHHhcCcCCcEEEEeCccCCH-HHHHH-HhCCCcc-CCCCCCC---CeEEEEEecCeeeecccc
Confidence            9988888877776654   456788999999999764 33444 3332221 1111111   111100      110111


Q ss_pred             hHHHHHHHHHHhh-hcCCcEEEEecCHHHHHHHHHHHHHC-------------------------CCCceeccCCCCHHH
Q 002040          699 DRFLRLLELLGEW-YEKGKILIFVHSQEKCDALFRDLLKH-------------------------GYPCLSLHGAKDQTD  752 (976)
Q Consensus       699 ~k~~~l~~~l~~~-~~~~kvLIF~~s~~~~~~l~~~L~~~-------------------------~~~~~~lhg~~~~~~  752 (976)
                      .....+..++... ..++++||||+++..|..++..|...                         ...+..+||+|++.+
T Consensus       220 ~~~~~~~~~i~~~~~~~~~vLVF~~sr~~~~~~a~~L~~~~~~~~~~~~~~~~~~~~~~~L~~~l~~gv~~~hagl~~~e  299 (674)
T PRK01172        220 RSQVDINSLIKETVNDGGQVLVFVSSRKNAEDYAEMLIQHFPEFNDFKVSSENNNVYDDSLNEMLPHGVAFHHAGLSNEQ  299 (674)
T ss_pred             cccccHHHHHHHHHhCCCcEEEEeccHHHHHHHHHHHHHhhhhcccccccccccccccHHHHHHHhcCEEEecCCCCHHH
Confidence            1111133333332 34679999999999999999888653                         124778999999999


Q ss_pred             HHHHHHHhccCCccEEEecCcccccCCCCCCcEEEEeCC---------CCCHHHHHHHhcccCCCCC--ccEEEEEecCC
Q 002040          753 RESTISDFKSNVCNLLIATSVAARGLDVKELELVINFDA---------PNHYEDYVHRVGRTGRAGR--KGCAITFISEE  821 (976)
Q Consensus       753 R~~~~~~F~~g~~~vLVaT~v~~~GlDi~~v~~VI~~d~---------p~s~~~y~Qr~GR~gR~g~--~g~~~~~~~~~  821 (976)
                      |..+++.|++|.++|||||+++++|||+|+..+|| ++.         |.+..+|.||+|||||.|.  .|.+++|+...
T Consensus       300 R~~ve~~f~~g~i~VLvaT~~la~Gvnipa~~VII-~~~~~~~~~~~~~~s~~~~~Qm~GRAGR~g~d~~g~~~i~~~~~  378 (674)
T PRK01172        300 RRFIEEMFRNRYIKVIVATPTLAAGVNLPARLVIV-RDITRYGNGGIRYLSNMEIKQMIGRAGRPGYDQYGIGYIYAASP  378 (674)
T ss_pred             HHHHHHHHHcCCCeEEEecchhhccCCCcceEEEE-cCceEeCCCCceeCCHHHHHHHhhcCCCCCCCCcceEEEEecCc
Confidence            99999999999999999999999999999865444 432         5678899999999999984  57788776543

>PHA02653 RNA helicase NPH-II; Provisional

Probab=100.00  E-value=1.5e-38  Score=376.94  Aligned_cols=310  Identities=16%  Similarity=0.215  Sum_probs=233.5

Q ss_pred             HHHHHHHHHHhcCCCEEEEcCCCCchHHH---------HHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHH
Q 002040          492 PIQAQALPVIMSGRDCIGVAKTGSGKTLA---------FVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRK  562 (976)
Q Consensus       492 ~~Q~~~i~~il~g~d~i~~a~TGsGKT~~---------~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~  562 (976)
                      .+|.++++.+++|+++|++|+||||||++         |++|.+..+....  ....+++++|++||++||.|+...+..
T Consensus       167 ~iQ~qil~~i~~gkdvIv~A~TGSGKTtqvPq~l~~~~flf~~l~~l~~~~--~~~~~~~ilvt~PrreLa~qi~~~i~~  244 (675)
T PHA02653        167 DVQLKIFEAWISRKPVVLTGGTGVGKTSQVPKLLLWFNYLFGGFDNLDKID--PNFIERPIVLSLPRVALVRLHSITLLK  244 (675)
T ss_pred             HHHHHHHHHHHhCCCEEEECCCCCCchhHHHHHHHHhhhccchhhhhhhcc--cccCCcEEEEECcHHHHHHHHHHHHHH
Confidence            58999999999999999999999999997         3334444332110  022356899999999999999999887


Q ss_pred             HHhh---cCcEEEEeeCCCChHHHHHHHhcCCeEEEeCchhHHHHHHhcCCcccccCCceEEEecCcccccccCCchHHH
Q 002040          563 FAKV---MGVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMGFEPQIT  639 (976)
Q Consensus       563 ~~~~---~~~~~~~~~gg~~~~~~~~~l~~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDEah~~~~~~f~~~i~  639 (976)
                      ....   .++.+.+.+||... .+......+.+|+|+|++..          ...|.++++|||||||.+..++  ..+.
T Consensus       245 ~vg~~~~~g~~v~v~~Gg~~~-~~~~t~~k~~~Ilv~T~~L~----------l~~L~~v~~VVIDEaHEr~~~~--DllL  311 (675)
T PHA02653        245 SLGFDEIDGSPISLKYGSIPD-ELINTNPKPYGLVFSTHKLT----------LNKLFDYGTVIIDEVHEHDQIG--DIII  311 (675)
T ss_pred             HhCccccCCceEEEEECCcch-HHhhcccCCCCEEEEeCccc----------ccccccCCEEEccccccCccch--hHHH
Confidence            5543   36678889999873 22222233679999997631          1357889999999999877655  3455


Q ss_pred             HHHHhcC-CCCcEEEEeccCcHHHHHHHHHHcCCCeEEEeCCcccccCCceEEEEecCc---------chHHHHHHHHHH
Q 002040          640 RIVQNIR-PDRQTVLFSATFPRQVEILARKVLNKPVEIQVGGRSVVNKDITQLVEVRPE---------SDRFLRLLELLG  709 (976)
Q Consensus       640 ~il~~~~-~~~q~i~~SAT~~~~~~~l~~~~l~~~~~i~~~~~~~~~~~i~q~~~~~~~---------~~k~~~l~~~l~  709 (976)
                      .++..+. ..+|+|+||||++..+..+ ..++.+|..+.+.+..  ...+.+.+.....         ......++..+.
T Consensus       312 ~llk~~~~~~rq~ILmSATl~~dv~~l-~~~~~~p~~I~I~grt--~~pV~~~yi~~~~~~~~~~~y~~~~k~~~l~~L~  388 (675)
T PHA02653        312 AVARKHIDKIRSLFLMTATLEDDRDRI-KEFFPNPAFVHIPGGT--LFPISEVYVKNKYNPKNKRAYIEEEKKNIVTALK  388 (675)
T ss_pred             HHHHHhhhhcCEEEEEccCCcHhHHHH-HHHhcCCcEEEeCCCc--CCCeEEEEeecCcccccchhhhHHHHHHHHHHHH
Confidence            5555443 3359999999999888776 5788888888776432  2345554432211         111122333343


Q ss_pred             hhh--cCCcEEEEecCHHHHHHHHHHHHHC--CCCceeccCCCCHHHHHHHHHHh-ccCCccEEEecCcccccCCCCCCc
Q 002040          710 EWY--EKGKILIFVHSQEKCDALFRDLLKH--GYPCLSLHGAKDQTDRESTISDF-KSNVCNLLIATSVAARGLDVKELE  784 (976)
Q Consensus       710 ~~~--~~~kvLIF~~s~~~~~~l~~~L~~~--~~~~~~lhg~~~~~~R~~~~~~F-~~g~~~vLVaT~v~~~GlDi~~v~  784 (976)
                      ...  ..+.+||||+++..|+.++..|...  ++.+..+||+|++.  ++++..| ++|..+|||||++|++|||||+|.
T Consensus       389 ~~~~~~~g~iLVFlpg~~ei~~l~~~L~~~~~~~~v~~LHG~Lsq~--eq~l~~ff~~gk~kILVATdIAERGIDIp~V~  466 (675)
T PHA02653        389 KYTPPKGSSGIVFVASVSQCEEYKKYLEKRLPIYDFYIIHGKVPNI--DEILEKVYSSKNPSIIISTPYLESSVTIRNAT  466 (675)
T ss_pred             HhhcccCCcEEEEECcHHHHHHHHHHHHhhcCCceEEeccCCcCHH--HHHHHHHhccCceeEEeccChhhccccccCee
Confidence            322  3468999999999999999999887  79999999999975  4667777 789999999999999999999999


Q ss_pred             EEEEeC---CCC---------CHHHHHHHhcccCCCCCccEEEEEecCCC
Q 002040          785 LVINFD---APN---------HYEDYVHRVGRTGRAGRKGCAITFISEED  822 (976)
Q Consensus       785 ~VI~~d---~p~---------s~~~y~Qr~GR~gR~g~~g~~~~~~~~~d  822 (976)
                      +||+++   .|.         |.+.|+||+|||||. ++|.||.|+++.+
T Consensus       467 ~VID~G~~k~p~~~~g~~~~iSkasa~QRaGRAGR~-~~G~c~rLyt~~~  515 (675)
T PHA02653        467 HVYDTGRVYVPEPFGGKEMFISKSMRTQRKGRVGRV-SPGTYVYFYDLDL  515 (675)
T ss_pred             EEEECCCccCCCcccCcccccCHHHHHHhccCcCCC-CCCeEEEEECHHH
Confidence            999998   554         888999999999999 7999999999765

>TIGR01970 DEAH_box_HrpB ATP-dependent helicase HrpB

Probab=100.00  E-value=2.1e-38  Score=384.51  Aligned_cols=303  Identities=20%  Similarity=0.272  Sum_probs=239.2

Q ss_pred             HHHHHHHHHhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHH-HHhhcCcEE
Q 002040          493 IQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRK-FAKVMGVRC  571 (976)
Q Consensus       493 ~Q~~~i~~il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~-~~~~~~~~~  571 (976)
                      +-.+.+..|.+++++|++|+||||||++|.++++..+.        .++++||++|||++|.|++..+.. +....|..|
T Consensus         6 ~~~~i~~~l~~~~~vIi~a~TGSGKTT~vpl~lL~~~~--------~~~~ilvlqPrR~aA~qiA~rva~~~~~~~g~~V   77 (819)
T TIGR01970         6 VLPALRDALAAHPQVVLEAPPGAGKSTAVPLALLDAPG--------IGGKIIMLEPRRLAARSAAQRLASQLGEAVGQTV   77 (819)
T ss_pred             HHHHHHHHHHcCCcEEEECCCCCCHHHHHHHHHHHhhc--------cCCeEEEEeCcHHHHHHHHHHHHHHhCCCcCcEE
Confidence            34566777788999999999999999999999997752        246899999999999999998854 333456666


Q ss_pred             EEeeCCCChHHHHHHHhcCCeEEEeCchhHHHHHHhcCCcccccCCceEEEecCcc-cccccCCchHH-HHHHHhcCCCC
Q 002040          572 VPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEAD-RMFDMGFEPQI-TRIVQNIRPDR  649 (976)
Q Consensus       572 ~~~~gg~~~~~~~~~l~~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDEah-~~~~~~f~~~i-~~il~~~~~~~  649 (976)
                      .+.+++..      .+...+.|+|+|||+|++++...    ..|.++++||||||| ++++.+|...+ ..+...++++.
T Consensus        78 Gy~vr~~~------~~s~~t~I~v~T~G~Llr~l~~d----~~L~~v~~VIiDEaHER~L~~Dl~L~ll~~i~~~lr~dl  147 (819)
T TIGR01970        78 GYRVRGEN------KVSRRTRLEVVTEGILTRMIQDD----PELDGVGALIFDEFHERSLDADLGLALALDVQSSLREDL  147 (819)
T ss_pred             EEEEcccc------ccCCCCcEEEECCcHHHHHHhhC----cccccCCEEEEeccchhhhccchHHHHHHHHHHhcCCCc
Confidence            66655542      23456899999999999988653    468999999999999 78888776544 34556678899


Q ss_pred             cEEEEeccCcHHHHHHHHHHcCCCeEEEeCCcccccCCceEEEEecCcchHHH-----HHHHHHHhhhcCCcEEEEecCH
Q 002040          650 QTVLFSATFPRQVEILARKVLNKPVEIQVGGRSVVNKDITQLVEVRPESDRFL-----RLLELLGEWYEKGKILIFVHSQ  724 (976)
Q Consensus       650 q~i~~SAT~~~~~~~l~~~~l~~~~~i~~~~~~~~~~~i~q~~~~~~~~~k~~-----~l~~~l~~~~~~~kvLIF~~s~  724 (976)
                      |+|+||||++...   +..++.++..+.+.+...+   +.+.+.......++.     .+..++..  ..+.+||||+++
T Consensus       148 qlIlmSATl~~~~---l~~~l~~~~vI~~~gr~~p---Ve~~y~~~~~~~~~~~~v~~~l~~~l~~--~~g~iLVFlpg~  219 (819)
T TIGR01970       148 KILAMSATLDGER---LSSLLPDAPVVESEGRSFP---VEIRYLPLRGDQRLEDAVSRAVEHALAS--ETGSILVFLPGQ  219 (819)
T ss_pred             eEEEEeCCCCHHH---HHHHcCCCcEEEecCccee---eeeEEeecchhhhHHHHHHHHHHHHHHh--cCCcEEEEECCH
Confidence            9999999998763   3567776666666555432   444444333333332     22222222  358999999999


Q ss_pred             HHHHHHHHHHHH---CCCCceeccCCCCHHHHHHHHHHhccCCccEEEecCcccccCCCCCCcEEEEeCCCC--------
Q 002040          725 EKCDALFRDLLK---HGYPCLSLHGAKDQTDRESTISDFKSNVCNLLIATSVAARGLDVKELELVINFDAPN--------  793 (976)
Q Consensus       725 ~~~~~l~~~L~~---~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLVaT~v~~~GlDi~~v~~VI~~d~p~--------  793 (976)
                      .++..++..|..   .++.++.+||+|++.+|..++..|.+|..+|||||+++++|||||+|++||+++.|.        
T Consensus       220 ~eI~~l~~~L~~~~~~~~~v~pLHg~L~~~eq~~~~~~~~~G~rkVlVATnIAErgItIp~V~~VID~Gl~r~~~yd~~~  299 (819)
T TIGR01970       220 AEIRRVQEQLAERLDSDVLICPLYGELSLAAQDRAIKPDPQGRRKVVLATNIAETSLTIEGIRVVIDSGLARVARFDPKT  299 (819)
T ss_pred             HHHHHHHHHHHhhcCCCcEEEEecCCCCHHHHHHHHhhcccCCeEEEEecchHhhcccccCceEEEEcCccccccccccc
Confidence            999999999987   478999999999999999999999999999999999999999999999999999874        


Q ss_pred             ----------CHHHHHHHhcccCCCCCccEEEEEecCCC
Q 002040          794 ----------HYEDYVHRVGRTGRAGRKGCAITFISEED  822 (976)
Q Consensus       794 ----------s~~~y~Qr~GR~gR~g~~g~~~~~~~~~d  822 (976)
                                |.++|+||+|||||. .+|.||.||++.+
T Consensus       300 g~~~L~~~~iSkasa~QR~GRAGR~-~~G~cyrL~t~~~  337 (819)
T TIGR01970       300 GITRLETVRISQASATQRAGRAGRL-EPGVCYRLWSEEQ  337 (819)
T ss_pred             CCceeeEEEECHHHHHhhhhhcCCC-CCCEEEEeCCHHH
Confidence                      345699999999999 6999999998753

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.

>PRK11664 ATP-dependent RNA helicase HrpB; Provisional

Probab=100.00  E-value=6.6e-38  Score=381.21  Aligned_cols=305  Identities=19%  Similarity=0.289  Sum_probs=237.7

Q ss_pred             HHHHHHHHHhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHHH-HhhcCcEE
Q 002040          493 IQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKF-AKVMGVRC  571 (976)
Q Consensus       493 ~Q~~~i~~il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~~-~~~~~~~~  571 (976)
                      +-.+.+..+.+++++|++|+||||||++|.++++....        .++++||++|||++|.|++..+... ....|..+
T Consensus         9 ~~~~i~~~l~~~~~vvv~A~TGSGKTt~~pl~lL~~~~--------~~~~ilvlqPrR~aA~qia~rva~~l~~~~g~~V   80 (812)
T PRK11664          9 VLPELLTALKTAPQVLLKAPTGAGKSTWLPLQLLQHGG--------INGKIIMLEPRRLAARNVAQRLAEQLGEKPGETV   80 (812)
T ss_pred             HHHHHHHHHHhCCCEEEEcCCCCCHHHHHHHHHHHcCC--------cCCeEEEECChHHHHHHHHHHHHHHhCcccCceE
Confidence            34566777788999999999999999999999886521        1347999999999999999988643 34457777


Q ss_pred             EEeeCCCChHHHHHHHhcCCeEEEeCchhHHHHHHhcCCcccccCCceEEEecCcc-cccccCCchH-HHHHHHhcCCCC
Q 002040          572 VPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEAD-RMFDMGFEPQ-ITRIVQNIRPDR  649 (976)
Q Consensus       572 ~~~~gg~~~~~~~~~l~~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDEah-~~~~~~f~~~-i~~il~~~~~~~  649 (976)
                      ...+++...      ....+.|+|+|||+|++++...    ..|.++++||||||| ++++.++... +..++..++++.
T Consensus        81 Gy~vr~~~~------~~~~t~I~v~T~G~Llr~l~~d----~~L~~v~~IIlDEaHER~l~~Dl~L~ll~~i~~~lr~~l  150 (812)
T PRK11664         81 GYRMRAESK------VGPNTRLEVVTEGILTRMIQRD----PELSGVGLVILDEFHERSLQADLALALLLDVQQGLRDDL  150 (812)
T ss_pred             EEEecCccc------cCCCCcEEEEChhHHHHHHhhC----CCcCcCcEEEEcCCCccccccchHHHHHHHHHHhCCccc
Confidence            777776532      2345789999999999988653    468999999999999 4666654333 345667788899


Q ss_pred             cEEEEeccCcHHHHHHHHHHcCCCeEEEeCCcccccCCceEEEEecCcchHHHH-HHHHHHhhh--cCCcEEEEecCHHH
Q 002040          650 QTVLFSATFPRQVEILARKVLNKPVEIQVGGRSVVNKDITQLVEVRPESDRFLR-LLELLGEWY--EKGKILIFVHSQEK  726 (976)
Q Consensus       650 q~i~~SAT~~~~~~~l~~~~l~~~~~i~~~~~~~~~~~i~q~~~~~~~~~k~~~-l~~~l~~~~--~~~kvLIF~~s~~~  726 (976)
                      |+|+||||++..   ....++.++..+.+.+..+   .+.+.+.......++.. +...|....  ..+.+||||+++.+
T Consensus       151 qlilmSATl~~~---~l~~~~~~~~~I~~~gr~~---pV~~~y~~~~~~~~~~~~v~~~l~~~l~~~~g~iLVFlpg~~e  224 (812)
T PRK11664        151 KLLIMSATLDND---RLQQLLPDAPVIVSEGRSF---PVERRYQPLPAHQRFDEAVARATAELLRQESGSLLLFLPGVGE  224 (812)
T ss_pred             eEEEEecCCCHH---HHHHhcCCCCEEEecCccc---cceEEeccCchhhhHHHHHHHHHHHHHHhCCCCEEEEcCCHHH
Confidence            999999999875   2356676666666655433   35555544444444431 111222221  35899999999999


Q ss_pred             HHHHHHHHHH---CCCCceeccCCCCHHHHHHHHHHhccCCccEEEecCcccccCCCCCCcEEEEeCCCC----------
Q 002040          727 CDALFRDLLK---HGYPCLSLHGAKDQTDRESTISDFKSNVCNLLIATSVAARGLDVKELELVINFDAPN----------  793 (976)
Q Consensus       727 ~~~l~~~L~~---~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLVaT~v~~~GlDi~~v~~VI~~d~p~----------  793 (976)
                      +..++..|..   .++.+..+||+|++.+|..++..|.+|..+|||||+++++||||++|++||+++.+.          
T Consensus       225 i~~l~~~L~~~~~~~~~v~~Lhg~l~~~eq~~~~~~~~~G~rkVlvATnIAErsLtIp~V~~VID~Gl~r~~~yd~~~g~  304 (812)
T PRK11664        225 IQRVQEQLASRVASDVLLCPLYGALSLAEQQKAILPAPAGRRKVVLATNIAETSLTIEGIRLVVDSGLERVARFDPKTGL  304 (812)
T ss_pred             HHHHHHHHHHhccCCceEEEeeCCCCHHHHHHHhccccCCCeEEEEecchHHhcccccCceEEEECCCcccccccccCCc
Confidence            9999999987   578899999999999999999999999999999999999999999999999977664          


Q ss_pred             --------CHHHHHHHhcccCCCCCccEEEEEecCCC
Q 002040          794 --------HYEDYVHRVGRTGRAGRKGCAITFISEED  822 (976)
Q Consensus       794 --------s~~~y~Qr~GR~gR~g~~g~~~~~~~~~d  822 (976)
                              |.++|+||+||+||. .+|.||.||++.+
T Consensus       305 ~~L~~~~iSkasa~QR~GRaGR~-~~G~cyrL~t~~~  340 (812)
T PRK11664        305 TRLVTQRISQASMTQRAGRAGRL-EPGICLHLYSKEQ  340 (812)
T ss_pred             ceeEEEeechhhhhhhccccCCC-CCcEEEEecCHHH
Confidence                    336899999999999 5999999999753

>PRK09401 reverse gyrase; Reviewed

Probab=100.00  E-value=1.1e-37  Score=390.45  Aligned_cols=296  Identities=24%  Similarity=0.309  Sum_probs=241.7

Q ss_pred             cCCCCCcHHHHHHHHHHhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHHHH
Q 002040          485 LNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFA  564 (976)
Q Consensus       485 ~~~~~p~~~Q~~~i~~il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~~~  564 (976)
                      +|+ .|+++|..++|.++.|+|++++||||||||+ |+++++..+..       .++++|||+||++||.|++..++.++
T Consensus        77 ~G~-~pt~iQ~~~i~~il~g~dv~i~ApTGsGKT~-f~l~~~~~l~~-------~g~~alIL~PTreLa~Qi~~~l~~l~  147 (1176)
T PRK09401         77 TGS-KPWSLQRTWAKRLLLGESFAIIAPTGVGKTT-FGLVMSLYLAK-------KGKKSYIIFPTRLLVEQVVEKLEKFG  147 (1176)
T ss_pred             cCC-CCcHHHHHHHHHHHCCCcEEEEcCCCCCHHH-HHHHHHHHHHh-------cCCeEEEEeccHHHHHHHHHHHHHHh
Confidence            576 7999999999999999999999999999996 55665555432       37889999999999999999999999


Q ss_pred             hhcCcEEEEeeCCCCh-----HHHHHHHhc-CCeEEEeCchhHHHHHHhcCCcccccCCceEEEecCcccccc-------
Q 002040          565 KVMGVRCVPVYGGSGV-----AQQISELKR-GTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFD-------  631 (976)
Q Consensus       565 ~~~~~~~~~~~gg~~~-----~~~~~~l~~-~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDEah~~~~-------  631 (976)
                      ...++.+.+++|+.+.     ..+...+.. +++|+|+||++|.+++..     ..+..+++|||||||+|++       
T Consensus       148 ~~~~~~~~~~~g~~~~~~~ek~~~~~~l~~~~~~IlV~Tp~rL~~~~~~-----l~~~~~~~lVvDEaD~~L~~~k~id~  222 (1176)
T PRK09401        148 EKVGCGVKILYYHSSLKKKEKEEFLERLKEGDFDILVTTSQFLSKNFDE-----LPKKKFDFVFVDDVDAVLKSSKNIDK  222 (1176)
T ss_pred             hhcCceEEEEEccCCcchhHHHHHHHHHhcCCCCEEEECHHHHHHHHHh-----ccccccCEEEEEChHHhhhcccchhh
Confidence            9889888888877642     333445554 589999999999988752     3456699999999999986       


Q ss_pred             ----cCCc-hHHHHHHHhcCC------------------------CCcEEEEeccCcHH-HHHHHHHHcCCCeEEEeCCc
Q 002040          632 ----MGFE-PQITRIVQNIRP------------------------DRQTVLFSATFPRQ-VEILARKVLNKPVEIQVGGR  681 (976)
Q Consensus       632 ----~~f~-~~i~~il~~~~~------------------------~~q~i~~SAT~~~~-~~~l~~~~l~~~~~i~~~~~  681 (976)
                          +||. ..+..++..++.                        ..|+|+||||+++. +..   .++..+..+.++..
T Consensus       223 ~l~~lGF~~~~i~~i~~~i~~~~~~~~~~~~i~~l~~~i~~~~~~~~q~ilfSAT~~~~~~~~---~l~~~ll~~~v~~~  299 (1176)
T PRK09401        223 LLYLLGFSEEDIEKAMELIRLKRKYEEIYEKIRELEEKIAELKDKKGVLVVSSATGRPRGNRV---KLFRELLGFEVGSP  299 (1176)
T ss_pred             HHHhCCCCHHHHHHHHHhcccccccchhhhHHHHHHHhhhhcccCCceEEEEeCCCCccchHH---HHhhccceEEecCc
Confidence                6785 567777777654                        68999999999874 332   23445555666666


Q ss_pred             ccccCCceEEEEecCcchHHHHHHHHHHhhhcCCcEEEEecCHHH---HHHHHHHHHHCCCCceeccCCCCHHHHHHHHH
Q 002040          682 SVVNKDITQLVEVRPESDRFLRLLELLGEWYEKGKILIFVHSQEK---CDALFRDLLKHGYPCLSLHGAKDQTDRESTIS  758 (976)
Q Consensus       682 ~~~~~~i~q~~~~~~~~~k~~~l~~~l~~~~~~~kvLIF~~s~~~---~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~  758 (976)
                      .....+|.+.+....  .+...|..++...  +.++||||++...   ++.|+.+|...|+.+..+||+|     ...++
T Consensus       300 ~~~~rnI~~~yi~~~--~k~~~L~~ll~~l--~~~~LIFv~t~~~~~~ae~l~~~L~~~gi~v~~~hg~l-----~~~l~  370 (1176)
T PRK09401        300 VFYLRNIVDSYIVDE--DSVEKLVELVKRL--GDGGLIFVPSDKGKEYAEELAEYLEDLGINAELAISGF-----ERKFE  370 (1176)
T ss_pred             ccccCCceEEEEEcc--cHHHHHHHHHHhc--CCCEEEEEecccChHHHHHHHHHHHHCCCcEEEEeCcH-----HHHHH
Confidence            556667877776554  5677777777654  3579999999776   9999999999999999999999     33469


Q ss_pred             HhccCCccEEEe----cCcccccCCCCC-CcEEEEeCCCC------CHHHHHHHhcccC
Q 002040          759 DFKSNVCNLLIA----TSVAARGLDVKE-LELVINFDAPN------HYEDYVHRVGRTG  806 (976)
Q Consensus       759 ~F~~g~~~vLVa----T~v~~~GlDi~~-v~~VI~~d~p~------s~~~y~Qr~GR~g  806 (976)
                      .|++|+++||||    |++++||||+|+ |.+||||+.|.      ....|.|++||+-
T Consensus       371 ~F~~G~~~VLVatas~tdv~aRGIDiP~~IryVI~y~vP~~~~~~~~~~~~~~~~~r~~  429 (1176)
T PRK09401        371 KFEEGEVDVLVGVASYYGVLVRGIDLPERIRYAIFYGVPKFKFSLEEELAPPFLLLRLL  429 (1176)
T ss_pred             HHHCCCCCEEEEecCCCCceeecCCCCcceeEEEEeCCCCEEEeccccccCHHHHHHHH
Confidence            999999999999    699999999999 89999999999      5678999999985

>KOG0349 consensus Putative DEAD-box RNA helicase DDX1 [RNA processing and modification]

Probab=100.00  E-value=2.5e-39  Score=340.64  Aligned_cols=317  Identities=32%  Similarity=0.548  Sum_probs=250.7

Q ss_pred             CeEEEEccCHHHHHHHHHHHHHHHhhc---CcEEEEeeCCCChHHHHHHHhcCCeEEEeCchhHHHHHHhcCCcccccCC
Q 002040          541 PVGLIMAPTRELVQQIHSDIRKFAKVM---GVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRR  617 (976)
Q Consensus       541 ~~vLIl~Ptr~La~Q~~~~~~~~~~~~---~~~~~~~~gg~~~~~~~~~l~~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~  617 (976)
                      |.+||+-|.++||.|.++.|.+|-..+   .++..++.||.-...|...++.|++|||+||++|.+.+...   +..|.+
T Consensus       287 p~avivepsrelaEqt~N~i~~Fk~h~~np~~r~lLmiggv~~r~Q~~ql~~g~~ivvGtpgRl~~~is~g---~~~lt~  363 (725)
T KOG0349|consen  287 PEAVIVEPSRELAEQTHNQIEEFKMHTSNPEVRSLLMIGGVLKRTQCKQLKDGTHIVVGTPGRLLQPISKG---LVTLTH  363 (725)
T ss_pred             cceeEecCcHHHHHHHHhhHHHHHhhcCChhhhhhhhhhhHHhHHHHHHhhcCceeeecCchhhhhhhhcc---ceeeee
Confidence            788999999999999999888775443   45666889999999999999999999999999999998653   367889


Q ss_pred             ceEEEecCcccccccCCchHHHHHHHhcCC------CCcEEEEeccCcH-HHHHHHHHHcCCCeEEEeCCcccccCCceE
Q 002040          618 VTYLVMDEADRMFDMGFEPQITRIVQNIRP------DRQTVLFSATFPR-QVEILARKVLNKPVEIQVGGRSVVNKDITQ  690 (976)
Q Consensus       618 ~~~vVlDEah~~~~~~f~~~i~~il~~~~~------~~q~i~~SAT~~~-~~~~l~~~~l~~~~~i~~~~~~~~~~~i~q  690 (976)
                      +.++|+|||+.++..++...|..+..+++.      ..|.++.|||+.. .+..+...+++.|..+.+.+...++..+.+
T Consensus       364 crFlvlDead~lL~qgy~d~I~r~h~qip~~tsdg~rlq~~vCsatlh~feVkk~~ervmhfptwVdLkgeD~vpetvHh  443 (725)
T KOG0349|consen  364 CRFLVLDEADLLLGQGYDDKIYRFHGQIPHMTSDGFRLQSPVCSATLHIFEVKKVGERVMHFPTWVDLKGEDLVPETVHH  443 (725)
T ss_pred             eEEEEecchhhhhhcccHHHHHHHhccchhhhcCCcccccceeeeEEeEEEeeehhhhhccCceeEecccccccchhhcc
Confidence            999999999999998998888888877753      3689999999754 455677888999999888888777776666


Q ss_pred             EEEecCcc--hHHHHH----------------------------HHHHHh--------hhcCCcEEEEecCHHHHHHHHH
Q 002040          691 LVEVRPES--DRFLRL----------------------------LELLGE--------WYEKGKILIFVHSQEKCDALFR  732 (976)
Q Consensus       691 ~~~~~~~~--~k~~~l----------------------------~~~l~~--------~~~~~kvLIF~~s~~~~~~l~~  732 (976)
                      .+....+.  .-+..|                            ..+|.-        .+...++||||.++.+|+.|..
T Consensus       444 vv~lv~p~~d~sw~~lr~~i~td~vh~kdn~~pg~~Spe~~s~a~kilkgEy~v~ai~~h~mdkaiifcrtk~dcDnLer  523 (725)
T KOG0349|consen  444 VVKLVCPSVDGSWCDLRQFIETDKVHTKDNLLPGQVSPENPSSATKILKGEYGVVAIRRHAMDKAIIFCRTKQDCDNLER  523 (725)
T ss_pred             ceeecCCccCccHHHHhhhhccCCcccccccccccCCCCChhhhhHHhcCchhhhhhhhhccCceEEEEeccccchHHHH
Confidence            55432221  111111                            111110        1123589999999999999999


Q ss_pred             HHHHCC---CCceeccCCCCHHHHHHHHHHhccCCccEEEecCcccccCCCCCCcEEEEeCCCCCHHHHHHHhcccCCCC
Q 002040          733 DLLKHG---YPCLSLHGAKDQTDRESTISDFKSNVCNLLIATSVAARGLDVKELELVINFDAPNHYEDYVHRVGRTGRAG  809 (976)
Q Consensus       733 ~L~~~~---~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLVaT~v~~~GlDi~~v~~VI~~d~p~s~~~y~Qr~GR~gR~g  809 (976)
                      ++.+.|   |.|+++||+..+.+|...++.|+.+.+++||||+++++||||.++-+|||..+|..-.+|+|||||+||+.
T Consensus       524 ~~~qkgg~~~scvclhgDrkP~Erk~nle~Fkk~dvkflictdvaargldi~g~p~~invtlpd~k~nyvhrigrvgrae  603 (725)
T KOG0349|consen  524 MMNQKGGKHYSCVCLHGDRKPDERKANLESFKKFDVKFLICTDVAARGLDITGLPFMINVTLPDDKTNYVHRIGRVGRAE  603 (725)
T ss_pred             HHHHcCCccceeEEEecCCChhHHHHHHHhhhhcCeEEEEEehhhhccccccCCceEEEEecCcccchhhhhhhccchhh
Confidence            999864   78999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CccEEEEEecCCCcC--------------------------------chHHHHHHHhhccCCCChHHHHHHHHHHHHHhh
Q 002040          810 RKGCAITFISEEDAK--------------------------------YSPDLVKALELSEQVVPDDLKALADSFMAKVNQ  857 (976)
Q Consensus       810 ~~g~~~~~~~~~d~~--------------------------------~~~~i~~~l~~~~~~vp~~l~~l~~~~~~~~~~  857 (976)
                      +-|.++.++....++                                .+..+...|....++|...+.-..+.|-.++-.
T Consensus       604 rmglaislvat~~ekvwyh~c~srgr~c~nt~l~e~~gc~iwyne~~llaeve~hln~ti~qv~~~~~vpv~~fdgkv~y  683 (725)
T KOG0349|consen  604 RMGLAISLVATVPEKVWYHWCKSRGRSCNNTNLTEVRGCCIWYNEPNLLAEVEDHLNITIQQVDKTMDVPVNDFDGKVVY  683 (725)
T ss_pred             hcceeEEEeeccchheeehhhhccCCcccCCccccccceEEEeCchhHHHHHHHhhcceeeeeCCCCCCcccccCCeEEe
Confidence            899999887543332                                344455555555555555555555555555544


Q ss_pred             hhh
Q 002040          858 GLE  860 (976)
Q Consensus       858 ~~~  860 (976)
                      +..
T Consensus       684 gqk  686 (725)
T KOG0349|consen  684 GQK  686 (725)
T ss_pred             ccc
Confidence            433

>COG1200 RecG RecG-like helicase [DNA replication, recombination, and repair / Transcription]

Probab=100.00  E-value=1.6e-37  Score=352.41  Aligned_cols=362  Identities=20%  Similarity=0.282  Sum_probs=282.4

Q ss_pred             HHHHHHcCCCCCcHHHHHHHHHHhcC------CCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHH
Q 002040          479 METIRKLNYEKPMPIQAQALPVIMSG------RDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTREL  552 (976)
Q Consensus       479 ~~~l~~~~~~~p~~~Q~~~i~~il~g------~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~L  552 (976)
                      ...+..++|. ||..|..++..|...      .+-|++|..|||||++++++|+..+..        |.++.+|+||--|
T Consensus       253 ~~~~~~LPF~-LT~aQ~~vi~EI~~Dl~~~~~M~RLlQGDVGSGKTvVA~laml~ai~~--------G~Q~ALMAPTEIL  323 (677)
T COG1200         253 AKFLAALPFK-LTNAQKRVIKEILADLASPVPMNRLLQGDVGSGKTVVALLAMLAAIEA--------GYQAALMAPTEIL  323 (677)
T ss_pred             HHHHHhCCCC-ccHHHHHHHHHHHhhhcCchhhHHHhccCcCCCHHHHHHHHHHHHHHc--------CCeeEEeccHHHH
Confidence            3445678875 999999999999854      468999999999999999999988653        7889999999999


Q ss_pred             HHHHHHHHHHHHhhcCcEEEEeeCCCChH---HHHHHHhcC-CeEEEeCchhHHHHHHhcCCcccccCCceEEEecCccc
Q 002040          553 VQQIHSDIRKFAKVMGVRCVPVYGGSGVA---QQISELKRG-TEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADR  628 (976)
Q Consensus       553 a~Q~~~~~~~~~~~~~~~~~~~~gg~~~~---~~~~~l~~~-~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDEah~  628 (976)
                      |.|++..+.+++..+|+.|..++|...-.   .....+..| .+|||+|+.-+.+-        ..++++.+||+||-||
T Consensus       324 A~QH~~~~~~~l~~~~i~V~lLtG~~kgk~r~~~l~~l~~G~~~ivVGTHALiQd~--------V~F~~LgLVIiDEQHR  395 (677)
T COG1200         324 AEQHYESLRKWLEPLGIRVALLTGSLKGKARKEILEQLASGEIDIVVGTHALIQDK--------VEFHNLGLVIIDEQHR  395 (677)
T ss_pred             HHHHHHHHHHHhhhcCCeEEEeecccchhHHHHHHHHHhCCCCCEEEEcchhhhcc--------eeecceeEEEEecccc
Confidence            99999999999999999999999976543   345566666 79999998766443        4688899999999999


Q ss_pred             ccccCCchHHHHHHHhcCC-CCcEEEEeccCcHHHHHHHHHHcCCCeEEEeCCcccccCCceEEEEecCcchHHHHHHHH
Q 002040          629 MFDMGFEPQITRIVQNIRP-DRQTVLFSATFPRQVEILARKVLNKPVEIQVGGRSVVNKDITQLVEVRPESDRFLRLLEL  707 (976)
Q Consensus       629 ~~~~~f~~~i~~il~~~~~-~~q~i~~SAT~~~~~~~l~~~~l~~~~~i~~~~~~~~~~~i~q~~~~~~~~~k~~~l~~~  707 (976)
                           |+-.....+..... .+.+|+|||||-|..  ++...+++.....+...+.....|...+..   ..+...+++.
T Consensus       396 -----FGV~QR~~L~~KG~~~Ph~LvMTATPIPRT--LAlt~fgDldvS~IdElP~GRkpI~T~~i~---~~~~~~v~e~  465 (677)
T COG1200         396 -----FGVHQRLALREKGEQNPHVLVMTATPIPRT--LALTAFGDLDVSIIDELPPGRKPITTVVIP---HERRPEVYER  465 (677)
T ss_pred             -----ccHHHHHHHHHhCCCCCcEEEEeCCCchHH--HHHHHhccccchhhccCCCCCCceEEEEec---cccHHHHHHH
Confidence                 66677777777777 789999999987764  555566665444444444444455443332   2344455555


Q ss_pred             HHhh-hcCCcEEEEecCHH--------HHHHHHHHHHHC--CCCceeccCCCCHHHHHHHHHHhccCCccEEEecCcccc
Q 002040          708 LGEW-YEKGKILIFVHSQE--------KCDALFRDLLKH--GYPCLSLHGAKDQTDRESTISDFKSNVCNLLIATSVAAR  776 (976)
Q Consensus       708 l~~~-~~~~kvLIF~~s~~--------~~~~l~~~L~~~--~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLVaT~v~~~  776 (976)
                      +... ..+.++.|.|+-++        .+..++..|...  ++.+..+||.|+..+++.+|..|++|+++|||||.+++.
T Consensus       466 i~~ei~~GrQaY~VcPLIeESE~l~l~~a~~~~~~L~~~~~~~~vgL~HGrm~~~eKd~vM~~Fk~~e~~ILVaTTVIEV  545 (677)
T COG1200         466 IREEIAKGRQAYVVCPLIEESEKLELQAAEELYEELKSFLPELKVGLVHGRMKPAEKDAVMEAFKEGEIDILVATTVIEV  545 (677)
T ss_pred             HHHHHHcCCEEEEEeccccccccchhhhHHHHHHHHHHHcccceeEEEecCCChHHHHHHHHHHHcCCCcEEEEeeEEEe
Confidence            5443 34568999999765        445666677643  667999999999999999999999999999999999999


Q ss_pred             cCCCCCCcEEEEeCCCCC-HHHHHHHhcccCCCCCccEEEEEecCCCcCchHHHHHHHhhccCCCChHHHHHHHHHHHHH
Q 002040          777 GLDVKELELVINFDAPNH-YEDYVHRVGRTGRAGRKGCAITFISEEDAKYSPDLVKALELSEQVVPDDLKALADSFMAKV  855 (976)
Q Consensus       777 GlDi~~v~~VI~~d~p~s-~~~y~Qr~GR~gR~g~~g~~~~~~~~~d~~~~~~i~~~l~~~~~~vp~~l~~l~~~~~~~~  855 (976)
                      |||+|+++++|++++-.. .++.-|--||+||.+.+++|++++.+........-+              ..|.       
T Consensus       546 GVdVPnATvMVIe~AERFGLaQLHQLRGRVGRG~~qSyC~Ll~~~~~~~~a~~RL--------------~im~-------  604 (677)
T COG1200         546 GVDVPNATVMVIENAERFGLAQLHQLRGRVGRGDLQSYCVLLYKPPLSEVAKQRL--------------KIMR-------  604 (677)
T ss_pred             cccCCCCeEEEEechhhhhHHHHHHhccccCCCCcceEEEEEeCCCCChhHHHHH--------------HHHH-------
Confidence            999999999999999876 455666679999999999999999764322211111              1111       


Q ss_pred             hhhhhhccCCCCCCCCcccchhHHHHHHHHHHHHHHHcCCCCCC
Q 002040          856 NQGLEQAHGTGYGGSGFKFNEEEDEKRKAAKKAQAKEYGFEEDK  899 (976)
Q Consensus       856 ~~~~~~~~~~~~~g~g~~~~~~~~~~~~~~~~~~~~~~g~~~~~  899 (976)
                                 -+..||.+++.|+++||.|..++.+|+|+.+..
T Consensus       605 -----------~t~DGF~IAE~DLklRGpGe~lG~rQSG~~~f~  637 (677)
T COG1200         605 -----------ETTDGFVIAEEDLKLRGPGELLGTRQSGLPEFR  637 (677)
T ss_pred             -----------hcCCcceehhhhHhccCCccccCCcccCCcceE
Confidence                       136799999999999999999999999976543

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

Probab=100.00  E-value=1.6e-37  Score=354.72  Aligned_cols=329  Identities=23%  Similarity=0.373  Sum_probs=259.3

Q ss_pred             HHHH-HcCCCCCcHHHHHHHHHHhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHH
Q 002040          480 ETIR-KLNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHS  558 (976)
Q Consensus       480 ~~l~-~~~~~~p~~~Q~~~i~~il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~  558 (976)
                      ..|+ -+||..+.|-|.++|..+++|+|+|++.|||.||+++|.+|++-.          .| .+|||.|..+|......
T Consensus         7 ~~L~~~fGy~~FR~gQ~evI~~~l~g~d~lvvmPTGgGKSlCyQiPAll~----------~G-~TLVVSPLiSLM~DQV~   75 (590)
T COG0514           7 QVLKQVFGYASFRPGQQEIIDALLSGKDTLVVMPTGGGKSLCYQIPALLL----------EG-LTLVVSPLISLMKDQVD   75 (590)
T ss_pred             HHHHHHhCccccCCCHHHHHHHHHcCCcEEEEccCCCCcchHhhhHHHhc----------CC-CEEEECchHHHHHHHHH
Confidence            3454 389999999999999999999999999999999999999999843          23 68999999999876666


Q ss_pred             HHHHHHhhcCcEEEEeeCCCChHHHH---HHHhcC-CeEEEeCchhHHHHHHhcCCcccccCCceEEEecCcccccccC-
Q 002040          559 DIRKFAKVMGVRCVPVYGGSGVAQQI---SELKRG-TEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMG-  633 (976)
Q Consensus       559 ~~~~~~~~~~~~~~~~~gg~~~~~~~---~~l~~~-~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDEah~~~~~~-  633 (976)
                      .+..    .|+.+.++.+..+..+..   ..+..| .+|++.+|++|..-.....   ..-..+.+|||||||++.+|| 
T Consensus        76 ~l~~----~Gi~A~~lnS~l~~~e~~~v~~~l~~g~~klLyisPErl~~~~f~~~---L~~~~i~l~vIDEAHCiSqWGh  148 (590)
T COG0514          76 QLEA----AGIRAAYLNSTLSREERQQVLNQLKSGQLKLLYISPERLMSPRFLEL---LKRLPISLVAIDEAHCISQWGH  148 (590)
T ss_pred             HHHH----cCceeehhhcccCHHHHHHHHHHHhcCceeEEEECchhhcChHHHHH---HHhCCCceEEechHHHHhhcCC
Confidence            6665    688888888887666553   344444 6999999999854322110   123458899999999999998 


Q ss_pred             -CchHHHHHHHhc--CCCCcEEEEeccCcHHHHHHHHHHcCCCe-EEEeCCcccccCCceEEEEecC-cchHHHHHHHHH
Q 002040          634 -FEPQITRIVQNI--RPDRQTVLFSATFPRQVEILARKVLNKPV-EIQVGGRSVVNKDITQLVEVRP-ESDRFLRLLELL  708 (976)
Q Consensus       634 -f~~~i~~il~~~--~~~~q~i~~SAT~~~~~~~l~~~~l~~~~-~i~~~~~~~~~~~i~q~~~~~~-~~~k~~~l~~~l  708 (976)
                       |.+.+..+-...  -++..++.||||.++.+...+...|.-.. .+.+.  ++..++|...+.... ...++.    +|
T Consensus       149 dFRP~Y~~lg~l~~~~~~~p~~AlTATA~~~v~~DI~~~L~l~~~~~~~~--sfdRpNi~~~v~~~~~~~~q~~----fi  222 (590)
T COG0514         149 DFRPDYRRLGRLRAGLPNPPVLALTATATPRVRDDIREQLGLQDANIFRG--SFDRPNLALKVVEKGEPSDQLA----FL  222 (590)
T ss_pred             ccCHhHHHHHHHHhhCCCCCEEEEeCCCChHHHHHHHHHhcCCCcceEEe--cCCCchhhhhhhhcccHHHHHH----HH
Confidence             999888764433  24788999999999988766665554322 22222  233333332222211 222222    33


Q ss_pred             Hh--hhcCCcEEEEecCHHHHHHHHHHHHHCCCCceeccCCCCHHHHHHHHHHhccCCccEEEecCcccccCCCCCCcEE
Q 002040          709 GE--WYEKGKILIFVHSQEKCDALFRDLLKHGYPCLSLHGAKDQTDRESTISDFKSNVCNLLIATSVAARGLDVKELELV  786 (976)
Q Consensus       709 ~~--~~~~~kvLIF~~s~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLVaT~v~~~GlDi~~v~~V  786 (976)
                      ..  ....+..||||.|+..++.++..|...|+.+..+||+|+..+|..+.+.|..+.++|||||.++++|||-|+|.+|
T Consensus       223 ~~~~~~~~~~GIIYc~sRk~~E~ia~~L~~~g~~a~~YHaGl~~~eR~~~q~~f~~~~~~iiVAT~AFGMGIdKpdVRfV  302 (590)
T COG0514         223 ATVLPQLSKSGIIYCLTRKKVEELAEWLRKNGISAGAYHAGLSNEERERVQQAFLNDEIKVMVATNAFGMGIDKPDVRFV  302 (590)
T ss_pred             HhhccccCCCeEEEEeeHHhHHHHHHHHHHCCCceEEecCCCCHHHHHHHHHHHhcCCCcEEEEeccccCccCCCCceEE
Confidence            32  2345678999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEeCCCCCHHHHHHHhcccCCCCCccEEEEEecCCCcCchHHHHHH
Q 002040          787 INFDAPNHYEDYVHRVGRTGRAGRKGCAITFISEEDAKYSPDLVKA  832 (976)
Q Consensus       787 I~~d~p~s~~~y~Qr~GR~gR~g~~g~~~~~~~~~d~~~~~~i~~~  832 (976)
                      |||++|.+++.|+|-+|||||.|.+..|++||++.|......++..
T Consensus       303 iH~~lP~s~EsYyQE~GRAGRDG~~a~aill~~~~D~~~~~~~i~~  348 (590)
T COG0514         303 IHYDLPGSIESYYQETGRAGRDGLPAEAILLYSPEDIRWQRYLIEQ  348 (590)
T ss_pred             EEecCCCCHHHHHHHHhhccCCCCcceEEEeeccccHHHHHHHHHh
Confidence            9999999999999999999999999999999999987766666554

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

Probab=100.00  E-value=4.1e-37  Score=363.50  Aligned_cols=340  Identities=24%  Similarity=0.333  Sum_probs=267.2

Q ss_pred             CCHHHHHHHHHcCCCCCcHHHHHHHHHHhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHH
Q 002040          474 LTSKIMETIRKLNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELV  553 (976)
Q Consensus       474 l~~~l~~~l~~~~~~~p~~~Q~~~i~~il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La  553 (976)
                      |++.+.+.+... |..|||.|.+|||.|.+|+++|++||||||||+++.+|++..|..........+-.||+|+|.++|.
T Consensus         8 l~~~v~~~~~~~-~~~~t~~Q~~a~~~i~~G~nvLiiAPTGsGKTeAAfLpil~~l~~~~~~~~~~~i~~lYIsPLkALn   86 (814)
T COG1201           8 LDPRVREWFKRK-FTSLTPPQRYAIPEIHSGENVLIIAPTGSGKTEAAFLPVINELLSLGKGKLEDGIYALYISPLKALN   86 (814)
T ss_pred             cCHHHHHHHHHh-cCCCCHHHHHHHHHHhCCCceEEEcCCCCChHHHHHHHHHHHHHhccCCCCCCceEEEEeCcHHHHH
Confidence            577788888877 9999999999999999999999999999999999999999999886322234567899999999999


Q ss_pred             HHHHHHHHHHHhhcCcEEEEeeCCCChHHHHHHHhcCCeEEEeCchhHHHHHHhcCCcccccCCceEEEecCcccccccC
Q 002040          554 QQIHSDIRKFAKVMGVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMG  633 (976)
Q Consensus       554 ~Q~~~~~~~~~~~~~~~~~~~~gg~~~~~~~~~l~~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDEah~~~~~~  633 (976)
                      ..+...+..+...+|+.+.+-+|.++..+....+++.++|+|+||+.|.-+|... .....|.++.+|||||+|.+....
T Consensus        87 ~Di~~rL~~~~~~~G~~v~vRhGDT~~~er~r~~~~PPdILiTTPEsL~lll~~~-~~r~~l~~vr~VIVDEiHel~~sK  165 (814)
T COG1201          87 NDIRRRLEEPLRELGIEVAVRHGDTPQSEKQKMLKNPPHILITTPESLAILLNSP-KFRELLRDVRYVIVDEIHALAESK  165 (814)
T ss_pred             HHHHHHHHHHHHHcCCccceecCCCChHHhhhccCCCCcEEEeChhHHHHHhcCH-HHHHHhcCCcEEEeehhhhhhccc
Confidence            9999999999999999999999999988888888888999999999997666442 233568899999999999887655


Q ss_pred             CchHHHHH---HHhcCCCCcEEEEeccCcHHHHHHHHHHcCC--CeEEEeCCcccccCCceEEEEecC-------cchHH
Q 002040          634 FEPQITRI---VQNIRPDRQTVLFSATFPRQVEILARKVLNK--PVEIQVGGRSVVNKDITQLVEVRP-------ESDRF  701 (976)
Q Consensus       634 f~~~i~~i---l~~~~~~~q~i~~SAT~~~~~~~l~~~~l~~--~~~i~~~~~~~~~~~i~q~~~~~~-------~~~k~  701 (976)
                      -+.++.--   +..+.++.|.|++|||..+.. .+++.+.+.  +..|... .......+.-......       ....+
T Consensus       166 RG~~Lsl~LeRL~~l~~~~qRIGLSATV~~~~-~varfL~g~~~~~~Iv~~-~~~k~~~i~v~~p~~~~~~~~~~~~~~~  243 (814)
T COG1201         166 RGVQLALSLERLRELAGDFQRIGLSATVGPPE-EVAKFLVGFGDPCEIVDV-SAAKKLEIKVISPVEDLIYDEELWAALY  243 (814)
T ss_pred             cchhhhhhHHHHHhhCcccEEEeehhccCCHH-HHHHHhcCCCCceEEEEc-ccCCcceEEEEecCCccccccchhHHHH
Confidence            44443322   333344899999999987543 345544444  3333211 1111111211111111       11223


Q ss_pred             HHHHHHHHhhhcCCcEEEEecCHHHHHHHHHHHHHCC-CCceeccCCCCHHHHHHHHHHhccCCccEEEecCcccccCCC
Q 002040          702 LRLLELLGEWYEKGKILIFVHSQEKCDALFRDLLKHG-YPCLSLHGAKDQTDRESTISDFKSNVCNLLIATSVAARGLDV  780 (976)
Q Consensus       702 ~~l~~~l~~~~~~~kvLIF~~s~~~~~~l~~~L~~~~-~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLVaT~v~~~GlDi  780 (976)
                      ..+.+++.+   ...+|||+||+..++.|+..|.+.+ ..+..+||.++...|..+.+.|++|..+++|||+.++-||||
T Consensus       244 ~~i~~~v~~---~~ttLIF~NTR~~aE~l~~~L~~~~~~~i~~HHgSlSre~R~~vE~~lk~G~lravV~TSSLELGIDi  320 (814)
T COG1201         244 ERIAELVKK---HRTTLIFTNTRSGAERLAFRLKKLGPDIIEVHHGSLSRELRLEVEERLKEGELKAVVATSSLELGIDI  320 (814)
T ss_pred             HHHHHHHhh---cCcEEEEEeChHHHHHHHHHHHHhcCCceeeecccccHHHHHHHHHHHhcCCceEEEEccchhhcccc
Confidence            333444433   3589999999999999999999886 899999999999999999999999999999999999999999


Q ss_pred             CCCcEEEEeCCCCCHHHHHHHhcccCC-CCCccEEEEEecC
Q 002040          781 KELELVINFDAPNHYEDYVHRVGRTGR-AGRKGCAITFISE  820 (976)
Q Consensus       781 ~~v~~VI~~d~p~s~~~y~Qr~GR~gR-~g~~g~~~~~~~~  820 (976)
                      .+++.||+|+.|.+...++||+||+|. .|....++++...
T Consensus       321 G~vdlVIq~~SP~sV~r~lQRiGRsgHr~~~~Skg~ii~~~  361 (814)
T COG1201         321 GDIDLVIQLGSPKSVNRFLQRIGRAGHRLGEVSKGIIIAED  361 (814)
T ss_pred             CCceEEEEeCCcHHHHHHhHhccccccccCCcccEEEEecC
Confidence            999999999999999999999999996 4555666665544

>PRK12898 secA preprotein translocase subunit SecA; Reviewed

Probab=100.00  E-value=4.3e-37  Score=358.18  Aligned_cols=322  Identities=21%  Similarity=0.236  Sum_probs=249.5

Q ss_pred             cCCCCCcHHHHHHHHHHhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHHHH
Q 002040          485 LNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFA  564 (976)
Q Consensus       485 ~~~~~p~~~Q~~~i~~il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~~~  564 (976)
                      +|+ .|+|+|..+++.++.|+  |+.+.||+|||++|++|++.++.        .|+.|+||+||++||.|.+.++..++
T Consensus       100 lg~-~p~~VQ~~~~~~ll~G~--Iae~~TGeGKTla~~lp~~~~al--------~G~~v~VvTptreLA~qdae~~~~l~  168 (656)
T PRK12898        100 LGQ-RHFDVQLMGGLALLSGR--LAEMQTGEGKTLTATLPAGTAAL--------AGLPVHVITVNDYLAERDAELMRPLY  168 (656)
T ss_pred             hCC-CCChHHHHHHHHHhCCC--eeeeeCCCCcHHHHHHHHHHHhh--------cCCeEEEEcCcHHHHHHHHHHHHHHH
Confidence            565 58999999999999999  99999999999999999998754        36789999999999999999999999


Q ss_pred             hhcCcEEEEeeCCCChHHHHHHHhcCCeEEEeCchhH-HHHHHhcCC----------------------cccccCCceEE
Q 002040          565 KVMGVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRM-IDILCTSGG----------------------KITNLRRVTYL  621 (976)
Q Consensus       565 ~~~~~~~~~~~gg~~~~~~~~~l~~~~~Iiv~Tp~~L-~~~l~~~~~----------------------~~~~l~~~~~v  621 (976)
                      ..+|+.+.+++||.+..  ...+..+++|+|+|..-| .++|..+-.                      .......+.|+
T Consensus       169 ~~lGlsv~~i~gg~~~~--~r~~~y~~dIvygT~~e~~FDyLrd~~~~~~~~~~~~~~~~~l~~~~~~~~~~v~r~~~~a  246 (656)
T PRK12898        169 EALGLTVGCVVEDQSPD--ERRAAYGADITYCTNKELVFDYLRDRLALGQRASDARLALESLHGRSSRSTQLLLRGLHFA  246 (656)
T ss_pred             hhcCCEEEEEeCCCCHH--HHHHHcCCCEEEECCCchhhhhccccccccccccchhhhhhhhccccCchhhhccccccee
Confidence            99999999999998654  344556799999999987 455543310                      01124567899


Q ss_pred             EecCccccc-cc----------------------------------CCc---------------hHHHHH----------
Q 002040          622 VMDEADRMF-DM----------------------------------GFE---------------PQITRI----------  641 (976)
Q Consensus       622 VlDEah~~~-~~----------------------------------~f~---------------~~i~~i----------  641 (976)
                      ||||+|.++ |.                                  .|.               ..+..+          
T Consensus       247 IvDEvDSiLiDeartpliis~~~~~~~~~~~y~~~~~~~~~l~~~~~y~~d~~~~~v~lt~~g~~~~e~~~~~l~~~~~~  326 (656)
T PRK12898        247 IVDEADSVLIDEARTPLIISAPAKEADEAEVYRQALELAAQLKEGEDYTIDAAEKRIELTEAGRARIAELAESLPPAWRG  326 (656)
T ss_pred             EeecccceeeccCCCceEEECCCCCCchhHHHHHHHHHHHhcCCCCceEEECCCCeEEEcHHHHHHHHHHhCcchhhccc
Confidence            999999652 10                                  000               000000          


Q ss_pred             --------HHhc------CCC-----------------------------------------------------------
Q 002040          642 --------VQNI------RPD-----------------------------------------------------------  648 (976)
Q Consensus       642 --------l~~~------~~~-----------------------------------------------------------  648 (976)
                              ...+      ..+                                                           
T Consensus       327 ~~~~~~~i~~Al~A~~l~~~d~dYiV~d~~V~ivD~~TGR~~~gr~w~~GLhQaieaKE~v~i~~e~~t~a~It~q~~Fr  406 (656)
T PRK12898        327 AVRREELVRQALSALHLFRRDEHYIVRDGKVVIVDEFTGRVMPDRSWEDGLHQMIEAKEGCELTDPRETLARITYQRFFR  406 (656)
T ss_pred             chHHHHHHHHHHHHHHHHhcCCceEEECCeEEEEECCCCeECCCCCcChHHHHHHHHhcCCCCCcCceeeeeehHHHHHH
Confidence                    0000      000                                                           


Q ss_pred             --CcEEEEeccCcHHHHHHHHHHcCCCeEEEeCCcccccCCceEEEEecCcchHHHHHHHHHHhhhc-CCcEEEEecCHH
Q 002040          649 --RQTVLFSATFPRQVEILARKVLNKPVEIQVGGRSVVNKDITQLVEVRPESDRFLRLLELLGEWYE-KGKILIFVHSQE  725 (976)
Q Consensus       649 --~q~i~~SAT~~~~~~~l~~~~l~~~~~i~~~~~~~~~~~i~q~~~~~~~~~k~~~l~~~l~~~~~-~~kvLIF~~s~~  725 (976)
                        .++.+||||.+.....+...|..+++.|......  .....+.+.+.....|+..|...+..... +.++||||+|+.
T Consensus       407 ~Y~kl~GmTGTa~~~~~El~~~y~l~vv~IPt~kp~--~r~~~~~~v~~t~~~K~~aL~~~i~~~~~~~~pvLIft~t~~  484 (656)
T PRK12898        407 RYLRLAGMTGTAREVAGELWSVYGLPVVRIPTNRPS--QRRHLPDEVFLTAAAKWAAVAARVRELHAQGRPVLVGTRSVA  484 (656)
T ss_pred             hhHHHhcccCcChHHHHHHHHHHCCCeEEeCCCCCc--cceecCCEEEeCHHHHHHHHHHHHHHHHhcCCCEEEEeCcHH
Confidence              2367999999988888888887777655433222  11233444556677899999998877542 468999999999


Q ss_pred             HHHHHHHHHHHCCCCceeccCCCCHHHHHHHHHHhccCCccEEEecCcccccCCCC---CCc-----EEEEeCCCCCHHH
Q 002040          726 KCDALFRDLLKHGYPCLSLHGAKDQTDRESTISDFKSNVCNLLIATSVAARGLDVK---ELE-----LVINFDAPNHYED  797 (976)
Q Consensus       726 ~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLVaT~v~~~GlDi~---~v~-----~VI~~d~p~s~~~  797 (976)
                      .++.|+..|...|+++..|||.++  .++..+..|..+...|||||++++||+||+   +|.     +||+|+.|.+...
T Consensus       485 ~se~L~~~L~~~gi~~~~Lhg~~~--~rE~~ii~~ag~~g~VlVATdmAgRGtDI~l~~~V~~~GGLhVI~~d~P~s~r~  562 (656)
T PRK12898        485 ASERLSALLREAGLPHQVLNAKQD--AEEAAIVARAGQRGRITVATNMAGRGTDIKLEPGVAARGGLHVILTERHDSARI  562 (656)
T ss_pred             HHHHHHHHHHHCCCCEEEeeCCcH--HHHHHHHHHcCCCCcEEEEccchhcccCcCCccchhhcCCCEEEEcCCCCCHHH
Confidence            999999999999999999999865  455556666666667999999999999999   665     9999999999999


Q ss_pred             HHHHhcccCCCCCccEEEEEecCCCc
Q 002040          798 YVHRVGRTGRAGRKGCAITFISEEDA  823 (976)
Q Consensus       798 y~Qr~GR~gR~g~~g~~~~~~~~~d~  823 (976)
                      |+|++|||||.|.+|.|++|++.+|.
T Consensus       563 y~hr~GRTGRqG~~G~s~~~is~eD~  588 (656)
T PRK12898        563 DRQLAGRCGRQGDPGSYEAILSLEDD  588 (656)
T ss_pred             HHHhcccccCCCCCeEEEEEechhHH
Confidence            99999999999999999999998664

>PRK09751 putative ATP-dependent helicase Lhr; Provisional

Probab=100.00  E-value=8.4e-37  Score=382.44  Aligned_cols=307  Identities=21%  Similarity=0.261  Sum_probs=227.2

Q ss_pred             EEcCCCCchHHHHHHHHHHHHhcCCCC-----CCCCCCeEEEEccCHHHHHHHHHHHHHHHh------------hcCcEE
Q 002040          509 GVAKTGSGKTLAFVLPMLRHIKDQPPV-----AAGDGPVGLIMAPTRELVQQIHSDIRKFAK------------VMGVRC  571 (976)
Q Consensus       509 ~~a~TGsGKT~~~~l~il~~l~~~~~~-----~~~~~~~vLIl~Ptr~La~Q~~~~~~~~~~------------~~~~~~  571 (976)
                      |++|||||||++|.+|++..+...+..     ....+.++|||+|+++|+.|+++.++..+.            .+++.+
T Consensus         1 V~APTGSGKTLAA~LpaL~~Ll~~~~~~~~~~~~~~~~raLYISPLKALa~Dv~~~L~~pl~~i~~~~~~~g~~~~~i~V   80 (1490)
T PRK09751          1 VIAPTGSGKTLAAFLYALDRLFREGGEDTREAHKRKTSRILYISPIKALGTDVQRNLQIPLKGIADERRRRGETEVNLRV   80 (1490)
T ss_pred             CcCCCCcHHHHHHHHHHHHHHHhcccccccccccCCCCEEEEEeChHHHHHHHHHHHHHHHHhhhhhhhhcccccCceEE
Confidence            579999999999999999998764311     112468999999999999999998875321            247889


Q ss_pred             EEeeCCCChHHHHHHHhcCCeEEEeCchhHHHHHHhcCCcccccCCceEEEecCcccccccCCchH----HHHHHHhcCC
Q 002040          572 VPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMGFEPQ----ITRIVQNIRP  647 (976)
Q Consensus       572 ~~~~gg~~~~~~~~~l~~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDEah~~~~~~f~~~----i~~il~~~~~  647 (976)
                      ..++|+++..++...++..++|||+||++|..+|.+.  ....|+++.+|||||+|.|++..++.+    +..+...+..
T Consensus        81 ~vrtGDt~~~eR~rll~~ppdILVTTPEsL~~LLtsk--~r~~L~~Vr~VIVDE~H~L~g~kRG~~Lel~LeRL~~l~~~  158 (1490)
T PRK09751         81 GIRTGDTPAQERSKLTRNPPDILITTPESLYLMLTSR--ARETLRGVETVIIDEVHAVAGSKRGAHLALSLERLDALLHT  158 (1490)
T ss_pred             EEEECCCCHHHHHHHhcCCCCEEEecHHHHHHHHhhh--hhhhhccCCEEEEecHHHhcccccccHHHHHHHHHHHhCCC
Confidence            9999999998887777778999999999998877542  224689999999999999987654444    4445455567


Q ss_pred             CCcEEEEeccCcHHHHHHHHHHcC-CCeEEEeCCcccccCCceEEEEecCc------------------c-hHHHHH-HH
Q 002040          648 DRQTVLFSATFPRQVEILARKVLN-KPVEIQVGGRSVVNKDITQLVEVRPE------------------S-DRFLRL-LE  706 (976)
Q Consensus       648 ~~q~i~~SAT~~~~~~~l~~~~l~-~~~~i~~~~~~~~~~~i~q~~~~~~~------------------~-~k~~~l-~~  706 (976)
                      ..|+|+||||+++. ..++..+.. .++.+.. ........+...+.....                  . .....+ ..
T Consensus       159 ~~QrIgLSATI~n~-eevA~~L~g~~pv~Iv~-~~~~r~~~l~v~vp~~d~~~~~~~~~~~~~~~~~~r~~~i~~~v~~~  236 (1490)
T PRK09751        159 SAQRIGLSATVRSA-SDVAAFLGGDRPVTVVN-PPAMRHPQIRIVVPVANMDDVSSVASGTGEDSHAGREGSIWPYIETG  236 (1490)
T ss_pred             CCeEEEEEeeCCCH-HHHHHHhcCCCCEEEEC-CCCCcccceEEEEecCchhhccccccccccccchhhhhhhhHHHHHH
Confidence            78999999999874 455544333 3444422 211112222221211110                  0 000111 12


Q ss_pred             HHHhhhcCCcEEEEecCHHHHHHHHHHHHHCC---------------------------------CCceeccCCCCHHHH
Q 002040          707 LLGEWYEKGKILIFVHSQEKCDALFRDLLKHG---------------------------------YPCLSLHGAKDQTDR  753 (976)
Q Consensus       707 ~l~~~~~~~kvLIF~~s~~~~~~l~~~L~~~~---------------------------------~~~~~lhg~~~~~~R  753 (976)
                      ++.......++||||||+..|+.++..|.+..                                 +.+..+||+|++.+|
T Consensus       237 il~~i~~~~stLVFvNSR~~AE~La~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ia~~HHGsLSkeeR  316 (1490)
T PRK09751        237 ILDEVLRHRSTIVFTNSRGLAEKLTARLNELYAARLQRSPSIAVDAAHFESTSGATSNRVQSSDVFIARSHHGSVSKEQR  316 (1490)
T ss_pred             HHHHHhcCCCEEEECCCHHHHHHHHHHHHHhhhhhccccccccchhhhhhhccccchhccccccceeeeeccccCCHHHH
Confidence            33333446789999999999999999997631                                 125689999999999


Q ss_pred             HHHHHHhccCCccEEEecCcccccCCCCCCcEEEEeCCCCCHHHHHHHhcccCCC-CCccEEEEEec
Q 002040          754 ESTISDFKSNVCNLLIATSVAARGLDVKELELVINFDAPNHYEDYVHRVGRTGRA-GRKGCAITFIS  819 (976)
Q Consensus       754 ~~~~~~F~~g~~~vLVaT~v~~~GlDi~~v~~VI~~d~p~s~~~y~Qr~GR~gR~-g~~g~~~~~~~  819 (976)
                      ..+++.|++|.++|||||+++++||||+.+++||+|+.|.+...|+||+||+||. |..+.++++..
T Consensus       317 ~~IE~~fK~G~LrvLVATssLELGIDIg~VDlVIq~gsP~sVas~LQRiGRAGR~~gg~s~gli~p~  383 (1490)
T PRK09751        317 AITEQALKSGELRCVVATSSLELGIDMGAVDLVIQVATPLSVASGLQRIGRAGHQVGGVSKGLFFPR  383 (1490)
T ss_pred             HHHHHHHHhCCceEEEeCcHHHccCCcccCCEEEEeCCCCCHHHHHHHhCCCCCCCCCccEEEEEeC
Confidence            9999999999999999999999999999999999999999999999999999996 33445554333

>PRK14701 reverse gyrase; Provisional

Probab=100.00  E-value=8e-37  Score=389.73  Aligned_cols=322  Identities=20%  Similarity=0.239  Sum_probs=251.1

Q ss_pred             HHHHHHH-cCCCCCcHHHHHHHHHHhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHH
Q 002040          478 IMETIRK-LNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQI  556 (976)
Q Consensus       478 l~~~l~~-~~~~~p~~~Q~~~i~~il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~  556 (976)
                      +.+.++. +|| .|+++|.++|+.+++|+|++++||||+|||++++++++....        .++++|||+||++|+.|+
T Consensus        68 ~~~~f~~~~G~-~pt~iQ~~~i~~il~G~d~li~APTGsGKTl~~~~~al~~~~--------~g~~aLVl~PTreLa~Qi  138 (1638)
T PRK14701         68 FEEFFEKITGF-EFWSIQKTWAKRILRGKSFSIVAPTGMGKSTFGAFIALFLAL--------KGKKCYIILPTTLLVKQT  138 (1638)
T ss_pred             HHHHHHHhhCC-CCCHHHHHHHHHHHcCCCEEEEEcCCCCHHHHHHHHHHHHHh--------cCCeEEEEECHHHHHHHH
Confidence            3455655 899 699999999999999999999999999999965655554321        367899999999999999


Q ss_pred             HHHHHHHHhhc--CcEEEEeeCCCChHHHH---HHHhcC-CeEEEeCchhHHHHHHhcCCcccccCCceEEEecCccccc
Q 002040          557 HSDIRKFAKVM--GVRCVPVYGGSGVAQQI---SELKRG-TEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMF  630 (976)
Q Consensus       557 ~~~~~~~~~~~--~~~~~~~~gg~~~~~~~---~~l~~~-~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDEah~~~  630 (976)
                      +..+..++..+  ++.+.+++||.+..++.   ..+..+ ++|+|+||++|.+.+...    . ..++++|||||||+|+
T Consensus       139 ~~~l~~l~~~~~~~v~v~~~~g~~s~~e~~~~~~~l~~g~~dILV~TPgrL~~~~~~l----~-~~~i~~iVVDEAD~ml  213 (1638)
T PRK14701        139 VEKIESFCEKANLDVRLVYYHSNLRKKEKEEFLERIENGDFDILVTTAQFLARNFPEM----K-HLKFDFIFVDDVDAFL  213 (1638)
T ss_pred             HHHHHHHHhhcCCceeEEEEeCCCCHHHHHHHHHHHhcCCCCEEEECCchhHHhHHHH----h-hCCCCEEEEECceecc
Confidence            99999998875  46677888998877663   345554 899999999998776431    1 2678999999999998


Q ss_pred             c-----------cCCchHHHH----HHH----------------------hcCCCCc-EEEEeccCcHHHHHHHHHHcCC
Q 002040          631 D-----------MGFEPQITR----IVQ----------------------NIRPDRQ-TVLFSATFPRQVEILARKVLNK  672 (976)
Q Consensus       631 ~-----------~~f~~~i~~----il~----------------------~~~~~~q-~i~~SAT~~~~~~~l~~~~l~~  672 (976)
                      .           +||.+.+..    |+.                      .++...| ++++|||+++...  ...++..
T Consensus       214 ~~~knid~~L~llGF~~e~~~~~~~il~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~ll~~SAT~~~r~~--~~~l~~~  291 (1638)
T PRK14701        214 KASKNIDRSLQLLGFYEEIIEKAWKIIYLKKQGNIEDAMEKREILNKEIEKIGNKIGCLIVASATGKAKGD--RVKLYRE  291 (1638)
T ss_pred             ccccccchhhhcCCChHHHHHHHHHhhhcccccccchhhhhhhhhhhhhhhcCCCccEEEEEecCCCchhH--HHHHhhc
Confidence            6           588887764    332                      2334455 6779999986422  1234566


Q ss_pred             CeEEEeCCcccccCCceEEEEecCcchHHHHHHHHHHhhhcCCcEEEEecCHHH---HHHHHHHHHHCCCCceeccCCCC
Q 002040          673 PVEIQVGGRSVVNKDITQLVEVRPESDRFLRLLELLGEWYEKGKILIFVHSQEK---CDALFRDLLKHGYPCLSLHGAKD  749 (976)
Q Consensus       673 ~~~i~~~~~~~~~~~i~q~~~~~~~~~k~~~l~~~l~~~~~~~kvLIF~~s~~~---~~~l~~~L~~~~~~~~~lhg~~~  749 (976)
                      +..+.++.......++.+.+.......+ ..|+.+|...  +.++||||++...   |+.|+..|...|+.+..+||+  
T Consensus       292 ~l~f~v~~~~~~lr~i~~~yi~~~~~~k-~~L~~ll~~~--g~~gIVF~~t~~~~e~ae~la~~L~~~Gi~a~~~h~~--  366 (1638)
T PRK14701        292 LLGFEVGSGRSALRNIVDVYLNPEKIIK-EHVRELLKKL--GKGGLIFVPIDEGAEKAEEIEKYLLEDGFKIELVSAK--  366 (1638)
T ss_pred             CeEEEecCCCCCCCCcEEEEEECCHHHH-HHHHHHHHhC--CCCeEEEEeccccchHHHHHHHHHHHCCCeEEEecch--
Confidence            7777777666566677777766554444 4677777654  4578999999775   589999999999999999995  


Q ss_pred             HHHHHHHHHHhccCCccEEEec----CcccccCCCCC-CcEEEEeCCCC---CHHHHHHHh-------------cccCCC
Q 002040          750 QTDRESTISDFKSNVCNLLIAT----SVAARGLDVKE-LELVINFDAPN---HYEDYVHRV-------------GRTGRA  808 (976)
Q Consensus       750 ~~~R~~~~~~F~~g~~~vLVaT----~v~~~GlDi~~-v~~VI~~d~p~---s~~~y~Qr~-------------GR~gR~  808 (976)
                         |..+++.|++|.++|||||    ++++||||+|+ |.+|||||+|.   +...|.|-.             ||+||.
T Consensus       367 ---R~~~l~~F~~G~~~VLVaT~s~~gvaaRGIDiP~~Vryvi~~~~Pk~~~~~e~~~~~~~~~~~~~~~~~~~~~a~~~  443 (1638)
T PRK14701        367 ---NKKGFDLFEEGEIDYLIGVATYYGTLVRGLDLPERIRFAVFYGVPKFRFRVDLEDPTIYRILGLLSEILKIEEELKE  443 (1638)
T ss_pred             ---HHHHHHHHHcCCCCEEEEecCCCCeeEecCccCCccCEEEEeCCCCCCcchhhcccchhhhhcchHHHHHhhhhccc
Confidence               8899999999999999999    58999999999 99999999999   777666554             999999


Q ss_pred             CCccEEEEEecCCCc
Q 002040          809 GRKGCAITFISEEDA  823 (976)
Q Consensus       809 g~~g~~~~~~~~~d~  823 (976)
                      |.++.+++.+...+.
T Consensus       444 g~~~~~~~~~~~~~~  458 (1638)
T PRK14701        444 GIPIEGVLDVFPEDV  458 (1638)
T ss_pred             CCcchhHHHhHHHHH
Confidence            988777654444433

>COG1197 Mfd Transcription-repair coupling factor (superfamily II helicase) [DNA replication, recombination, and repair / Transcription]

Probab=100.00  E-value=1.5e-36  Score=362.33  Aligned_cols=361  Identities=20%  Similarity=0.246  Sum_probs=287.6

Q ss_pred             HHcCCCCCcHHHHHHHHHHhc----C--CCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHH
Q 002040          483 RKLNYEKPMPIQAQALPVIMS----G--RDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQI  556 (976)
Q Consensus       483 ~~~~~~~p~~~Q~~~i~~il~----g--~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~  556 (976)
                      ..|+|. .||-|..||..|..    +  .|-||||..|.|||.+++-+++..++        +|++|.|||||.-||.|+
T Consensus       589 ~~FPye-ET~DQl~AI~eVk~DM~~~kpMDRLiCGDVGFGKTEVAmRAAFkAV~--------~GKQVAvLVPTTlLA~QH  659 (1139)
T COG1197         589 ASFPYE-ETPDQLKAIEEVKRDMESGKPMDRLICGDVGFGKTEVAMRAAFKAVM--------DGKQVAVLVPTTLLAQQH  659 (1139)
T ss_pred             hcCCCc-CCHHHHHHHHHHHHHhccCCcchheeecCcCCcHHHHHHHHHHHHhc--------CCCeEEEEcccHHhHHHH
Confidence            356765 79999999999874    3  58999999999999999999998865        478999999999999999


Q ss_pred             HHHHHHHHhhcCcEEEEeeCCCChHHHH---HHHhcC-CeEEEeCchhHHHHHHhcCCcccccCCceEEEecCccccccc
Q 002040          557 HSDIRKFAKVMGVRCVPVYGGSGVAQQI---SELKRG-TEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDM  632 (976)
Q Consensus       557 ~~~~~~~~~~~~~~~~~~~gg~~~~~~~---~~l~~~-~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDEah~~~~~  632 (976)
                      ++.|+.-+..+++++..+..-.+..++.   ..++.| .+|||+|+-.|    .    +...+.++++|||||-|+    
T Consensus       660 y~tFkeRF~~fPV~I~~LSRF~s~kE~~~il~~la~G~vDIvIGTHrLL----~----kdv~FkdLGLlIIDEEqR----  727 (1139)
T COG1197         660 YETFKERFAGFPVRIEVLSRFRSAKEQKEILKGLAEGKVDIVIGTHRLL----S----KDVKFKDLGLLIIDEEQR----  727 (1139)
T ss_pred             HHHHHHHhcCCCeeEEEecccCCHHHHHHHHHHHhcCCccEEEechHhh----C----CCcEEecCCeEEEechhh----
Confidence            9999999999999999988877777664   444444 69999997644    2    225788899999999998    


Q ss_pred             CCchHHHHHHHhcCCCCcEEEEeccCcHHHHHHHHHHcCCCeEEEeCCcccccCCceEEEEecCcchHHHHHHHHHHhhh
Q 002040          633 GFEPQITRIVQNIRPDRQTVLFSATFPRQVEILARKVLNKPVEIQVGGRSVVNKDITQLVEVRPESDRFLRLLELLGEWY  712 (976)
Q Consensus       633 ~f~~~i~~il~~~~~~~q~i~~SAT~~~~~~~l~~~~l~~~~~i~~~~~~~~~~~i~q~~~~~~~~~k~~~l~~~l~~~~  712 (976)
                       |+-.....+..++.+..+|.|||||-|..-.++...+.+...|..  .+.....|..++.-.   +-...-..++.+..
T Consensus       728 -FGVk~KEkLK~Lr~~VDvLTLSATPIPRTL~Msm~GiRdlSvI~T--PP~~R~pV~T~V~~~---d~~~ireAI~REl~  801 (1139)
T COG1197         728 -FGVKHKEKLKELRANVDVLTLSATPIPRTLNMSLSGIRDLSVIAT--PPEDRLPVKTFVSEY---DDLLIREAILRELL  801 (1139)
T ss_pred             -cCccHHHHHHHHhccCcEEEeeCCCCcchHHHHHhcchhhhhccC--CCCCCcceEEEEecC---ChHHHHHHHHHHHh
Confidence             677778889999999999999999988777777666665544332  122222333222222   22222234445556


Q ss_pred             cCCcEEEEecCHHHHHHHHHHHHHC--CCCceeccCCCCHHHHHHHHHHhccCCccEEEecCcccccCCCCCCcEEEEeC
Q 002040          713 EKGKILIFVHSQEKCDALFRDLLKH--GYPCLSLHGAKDQTDRESTISDFKSNVCNLLIATSVAARGLDVKELELVINFD  790 (976)
Q Consensus       713 ~~~kvLIF~~s~~~~~~l~~~L~~~--~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLVaT~v~~~GlDi~~v~~VI~~d  790 (976)
                      .+|++...+|.++.+..++..|...  ...+++.||.|+..+-+.+|..|.+|.++|||||.+++.|||||+++++|+.+
T Consensus       802 RgGQvfYv~NrV~~Ie~~~~~L~~LVPEarI~vaHGQM~e~eLE~vM~~F~~g~~dVLv~TTIIEtGIDIPnANTiIIe~  881 (1139)
T COG1197         802 RGGQVFYVHNRVESIEKKAERLRELVPEARIAVAHGQMRERELEEVMLDFYNGEYDVLVCTTIIETGIDIPNANTIIIER  881 (1139)
T ss_pred             cCCEEEEEecchhhHHHHHHHHHHhCCceEEEEeecCCCHHHHHHHHHHHHcCCCCEEEEeeeeecCcCCCCCceEEEec
Confidence            6899999999999999999999886  56789999999999999999999999999999999999999999999999988


Q ss_pred             CCCC-HHHHHHHhcccCCCCCccEEEEEecCCCcCchHHHHHHHhhccCCCChHHHHHHHHHHHHHhhhhhhccCCCCCC
Q 002040          791 APNH-YEDYVHRVGRTGRAGRKGCAITFISEEDAKYSPDLVKALELSEQVVPDDLKALADSFMAKVNQGLEQAHGTGYGG  869 (976)
Q Consensus       791 ~p~s-~~~y~Qr~GR~gR~g~~g~~~~~~~~~d~~~~~~i~~~l~~~~~~vp~~l~~l~~~~~~~~~~~~~~~~~~~~~g  869 (976)
                      .... .++..|.-||+||..+.++||.+|.+...                    |...+..-+..+++       ...-|
T Consensus       882 AD~fGLsQLyQLRGRVGRS~~~AYAYfl~p~~k~--------------------lT~~A~kRL~aI~~-------~~~LG  934 (1139)
T COG1197         882 ADKFGLAQLYQLRGRVGRSNKQAYAYFLYPPQKA--------------------LTEDAEKRLEAIAS-------FTELG  934 (1139)
T ss_pred             cccccHHHHHHhccccCCccceEEEEEeecCccc--------------------cCHHHHHHHHHHHh-------hhhcC
Confidence            8775 67888999999999999999999976432                    22233333333321       22348


Q ss_pred             CCcccchhHHHHHHHHHHHHHHHcCCCC
Q 002040          870 SGFKFNEEEDEKRKAAKKAQAKEYGFEE  897 (976)
Q Consensus       870 ~g~~~~~~~~~~~~~~~~~~~~~~g~~~  897 (976)
                      +||.++.+|+++||+|..+|..|+|+-.
T Consensus       935 aGf~lA~~DLeIRGaGNlLG~eQSG~I~  962 (1139)
T COG1197         935 AGFKLAMHDLEIRGAGNLLGEEQSGHIE  962 (1139)
T ss_pred             chHHHHhcchhccccccccCccccCchh
Confidence            9999999999999999999999999754

>COG1111 MPH1 ERCC4-like helicases [DNA replication, recombination, and repair]

Probab=100.00  E-value=4e-35  Score=319.37  Aligned_cols=323  Identities=23%  Similarity=0.292  Sum_probs=238.2

Q ss_pred             CCCCcHHHHHHHHHHhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHHHHhh
Q 002040          487 YEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKV  566 (976)
Q Consensus       487 ~~~p~~~Q~~~i~~il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~~~~~  566 (976)
                      ...++.+|.......+.+ ++|++.|||.|||+++++.|.+.+...      .+ ++|+|+||+.|+.|++..|.+++..
T Consensus        13 ~ie~R~YQ~~i~a~al~~-NtLvvlPTGLGKT~IA~~V~~~~l~~~------~~-kvlfLAPTKPLV~Qh~~~~~~v~~i   84 (542)
T COG1111          13 TIEPRLYQLNIAAKALFK-NTLVVLPTGLGKTFIAAMVIANRLRWF------GG-KVLFLAPTKPLVLQHAEFCRKVTGI   84 (542)
T ss_pred             cccHHHHHHHHHHHHhhc-CeEEEecCCccHHHHHHHHHHHHHHhc------CC-eEEEecCCchHHHHHHHHHHHHhCC
Confidence            346788999888887765 999999999999999999998887764      23 8999999999999999999998776


Q ss_pred             cCcEEEEeeCCCChHHHHHHHhcCCeEEEeCchhHHHHHHhcCCcccccCCceEEEecCcccccccCCchHHHHHHHhcC
Q 002040          567 MGVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMGFEPQITRIVQNIR  646 (976)
Q Consensus       567 ~~~~~~~~~gg~~~~~~~~~l~~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDEah~~~~~~f~~~i~~il~~~~  646 (976)
                      ....++.++|.....+....+ ....|+|+||..+.+-|..+   ..++.++.+||+||||+-....-...+...+....
T Consensus        85 p~~~i~~ltGev~p~~R~~~w-~~~kVfvaTPQvveNDl~~G---rid~~dv~~lifDEAHRAvGnyAYv~Va~~y~~~~  160 (542)
T COG1111          85 PEDEIAALTGEVRPEEREELW-AKKKVFVATPQVVENDLKAG---RIDLDDVSLLIFDEAHRAVGNYAYVFVAKEYLRSA  160 (542)
T ss_pred             ChhheeeecCCCChHHHHHHH-hhCCEEEeccHHHHhHHhcC---ccChHHceEEEechhhhccCcchHHHHHHHHHHhc
Confidence            666788888887776654444 44799999999998877653   37889999999999997543221222333333344


Q ss_pred             CCCcEEEEeccCcHHHHHH---HHHHcCCCeEEEe---------------------------------------------
Q 002040          647 PDRQTVLFSATFPRQVEIL---ARKVLNKPVEIQV---------------------------------------------  678 (976)
Q Consensus       647 ~~~q~i~~SAT~~~~~~~l---~~~~l~~~~~i~~---------------------------------------------  678 (976)
                      .++.+|++||||....+.+   +..+.-..+.+..                                             
T Consensus       161 k~~~ilgLTASPGs~~ekI~eV~~nLgIe~vevrTE~d~DV~~Yv~~~kve~ikV~lp~e~~~ir~~l~~~l~~~Lk~L~  240 (542)
T COG1111         161 KNPLILGLTASPGSDLEKIQEVVENLGIEKVEVRTEEDPDVRPYVKKIKVEWIKVDLPEEIKEIRDLLRDALKPRLKPLK  240 (542)
T ss_pred             cCceEEEEecCCCCCHHHHHHHHHhCCcceEEEecCCCccHHHhhccceeEEEeccCcHHHHHHHHHHHHHHHHHHHHHH
Confidence            5677999999974432211   1111000000000                                             


Q ss_pred             ------CCcccccC--------------C---------------------------------------------------
Q 002040          679 ------GGRSVVNK--------------D---------------------------------------------------  687 (976)
Q Consensus       679 ------~~~~~~~~--------------~---------------------------------------------------  687 (976)
                            ........              .                                                   
T Consensus       241 ~~g~~~~~~~~~~kdl~~~~~~~~~~a~~~~~~~~~~l~~~a~~~kl~~a~elletqGi~~~~~Yl~~l~e~~~~~~sk~  320 (542)
T COG1111         241 ELGVIESSSPVSKKDLLELRQIRLIMAKNEDSDKFRLLSVLAEAIKLAHALELLETQGIRPFYQYLEKLEEEATKGGSKA  320 (542)
T ss_pred             HcCceeccCcccHhHHHHHHHHHHHhccCccHHHHHHHHHHHHHHHHHHHHHHHHhhChHHHHHHHHHHHHHhcccchHH
Confidence                  00000000              0                                                   


Q ss_pred             ----------------ceEEEEecCcchHHHHHHHHHHhhhc---CCcEEEEecCHHHHHHHHHHHHHCCCCce-ecc--
Q 002040          688 ----------------ITQLVEVRPESDRFLRLLELLGEWYE---KGKILIFVHSQEKCDALFRDLLKHGYPCL-SLH--  745 (976)
Q Consensus       688 ----------------i~q~~~~~~~~~k~~~l~~~l~~~~~---~~kvLIF~~s~~~~~~l~~~L~~~~~~~~-~lh--  745 (976)
                                      ............|+..+..++...+.   ..++|||++.+.+++.+.++|...+..+. .+-  
T Consensus       321 a~~l~~d~~~~~al~~~~~~~~~~v~HPKl~~l~eilke~~~k~~~~RvIVFT~yRdTae~i~~~L~~~~~~~~~rFiGQ  400 (542)
T COG1111         321 AKSLLADPYFKRALRLLIRADESGVEHPKLEKLREILKEQLEKNGDSRVIVFTEYRDTAEEIVNFLKKIGIKARVRFIGQ  400 (542)
T ss_pred             HHHHhcChhhHHHHHHHHHhccccCCCccHHHHHHHHHHHHhcCCCceEEEEehhHhHHHHHHHHHHhcCCcceeEEeec
Confidence                            00000011123355555666665552   34899999999999999999999887774 333  


Q ss_pred             ------CCCCHHHHHHHHHHhccCCccEEEecCcccccCCCCCCcEEEEeCCCCCHHHHHHHhcccCCCCCccEEEEEec
Q 002040          746 ------GAKDQTDRESTISDFKSNVCNLLIATSVAARGLDVKELELVINFDAPNHYEDYVHRVGRTGRAGRKGCAITFIS  819 (976)
Q Consensus       746 ------g~~~~~~R~~~~~~F~~g~~~vLVaT~v~~~GlDi~~v~~VI~~d~p~s~~~y~Qr~GR~gR~g~~g~~~~~~~  819 (976)
                            .||+|.++..++..|++|.++|||||++++.|||||.+++||+|++..|+..++||.|||||. +.|.+|+|++
T Consensus       401 a~r~~~~GMsQkeQ~eiI~~Fr~Ge~nVLVaTSVgEEGLDIp~vDlVifYEpvpSeIR~IQR~GRTGR~-r~Grv~vLvt  479 (542)
T COG1111         401 ASREGDKGMSQKEQKEIIDQFRKGEYNVLVATSVGEEGLDIPEVDLVIFYEPVPSEIRSIQRKGRTGRK-RKGRVVVLVT  479 (542)
T ss_pred             cccccccccCHHHHHHHHHHHhcCCceEEEEcccccccCCCCcccEEEEecCCcHHHHHHHhhCccccC-CCCeEEEEEe
Confidence                  479999999999999999999999999999999999999999999999999999999999998 7999999999


Q ss_pred             CCC
Q 002040          820 EED  822 (976)
Q Consensus       820 ~~d  822 (976)
                      ...
T Consensus       480 ~gt  482 (542)
T COG1111         480 EGT  482 (542)
T ss_pred             cCc
Confidence            873

>TIGR01587 cas3_core CRISPR-associated helicase Cas3

Probab=100.00  E-value=9.3e-36  Score=338.81  Aligned_cols=304  Identities=21%  Similarity=0.239  Sum_probs=214.1

Q ss_pred             CEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHHHHhhcCcEEEEeeCCCChH----
Q 002040          506 DCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVA----  581 (976)
Q Consensus       506 d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~~~~~~~~~~~~~~gg~~~~----  581 (976)
                      +++++||||||||++|++|++..+...      .+.+++|++|+++|+.|++..+..++.   ..+..++|+....    
T Consensus         1 ~vvi~apTGsGKT~~~~~~~l~~~~~~------~~~~ii~v~P~~~L~~q~~~~l~~~f~---~~~~~~~~~~~~~~~~~   71 (358)
T TIGR01587         1 LLVIEAPTGYGKTEAALLWALHSIKSQ------KADRVIIALPTRATINAMYRRAKELFG---SNLGLLHSSSSFKRIKE   71 (358)
T ss_pred             CEEEEeCCCCCHHHHHHHHHHHHHhhC------CCCeEEEEeehHHHHHHHHHHHHHHhC---cccEEeeccHHHHHHhc
Confidence            589999999999999999999876532      356899999999999999999998753   2344444433211    


Q ss_pred             -------HH-HHHHh------cCCeEEEeCchhHHHHHHhcCC-cccccC--CceEEEecCcccccccCCchHHHHHHHh
Q 002040          582 -------QQ-ISELK------RGTEIVVCTPGRMIDILCTSGG-KITNLR--RVTYLVMDEADRMFDMGFEPQITRIVQN  644 (976)
Q Consensus       582 -------~~-~~~l~------~~~~Iiv~Tp~~L~~~l~~~~~-~~~~l~--~~~~vVlDEah~~~~~~f~~~i~~il~~  644 (976)
                             .. ...+.      ...+|+|+||+.++..+..... ....+.  ..++|||||||.++.+++.. +..++..
T Consensus        72 ~~~~~~~~~~~~~~~~~~~~~~~~~I~v~T~~~l~~~~~~~~~~~~~~~~~~~~~~iViDE~h~~~~~~~~~-l~~~l~~  150 (358)
T TIGR01587        72 MGDSEEFEHLFPLYIHSNDKLFLDPITVCTIDQVLKSVFGEFGHYEFTLASIANSLLIFDEVHFYDEYTLAL-ILAVLEV  150 (358)
T ss_pred             cCCchhHHHHHHHHhhchhhhhhCCeeeCCHHHHHHHHhcccchHHHHHHHhcCCEEEEeCCCCCCHHHHHH-HHHHHHH
Confidence                   01 01111      1368999999999887754211 111111  23799999999998765443 5555554


Q ss_pred             cC-CCCcEEEEeccCcHHHHHHHHHHcCCCeEEEeCCcccccCCceEEEE--ecCcchHHHHHHHHHHhhhcCCcEEEEe
Q 002040          645 IR-PDRQTVLFSATFPRQVEILARKVLNKPVEIQVGGRSVVNKDITQLVE--VRPESDRFLRLLELLGEWYEKGKILIFV  721 (976)
Q Consensus       645 ~~-~~~q~i~~SAT~~~~~~~l~~~~l~~~~~i~~~~~~~~~~~i~q~~~--~~~~~~k~~~l~~~l~~~~~~~kvLIF~  721 (976)
                      +. .+.|+|+||||+|..+..++..+...+....+...... ....+.+.  ......+...+..++.....++++||||
T Consensus       151 l~~~~~~~i~~SATlp~~l~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~l~~l~~~~~~~~~~lVf~  229 (358)
T TIGR01587       151 LKDNDVPILLMSATLPKFLKEYAEKIGYVEFNEPLDLKEER-RFERHRFIKIESDKVGEISSLERLLEFIKKGGKIAIIV  229 (358)
T ss_pred             HHHcCCCEEEEecCchHHHHHHHhcCCCcccccCCCCcccc-ccccccceeeccccccCHHHHHHHHHHhhCCCeEEEEE
Confidence            43 57899999999998776666555433221111111100 00112221  1122344555555555545578999999


Q ss_pred             cCHHHHHHHHHHHHHCCC--CceeccCCCCHHHHHHH----HHHhccCCccEEEecCcccccCCCCCCcEEEEeCCCCCH
Q 002040          722 HSQEKCDALFRDLLKHGY--PCLSLHGAKDQTDREST----ISDFKSNVCNLLIATSVAARGLDVKELELVINFDAPNHY  795 (976)
Q Consensus       722 ~s~~~~~~l~~~L~~~~~--~~~~lhg~~~~~~R~~~----~~~F~~g~~~vLVaT~v~~~GlDi~~v~~VI~~d~p~s~  795 (976)
                      +++..|+.++..|.+.+.  .+..+||++++.+|..+    +..|++|...|||||+++++||||+ +++||++..|  +
T Consensus       230 ~t~~~~~~~~~~L~~~~~~~~~~~~h~~~~~~~r~~~~~~~~~~f~~~~~~ilvaT~~~~~GiDi~-~~~vi~~~~~--~  306 (358)
T TIGR01587       230 NTVDRAQEFYQQLKENAPEEEIMLLHSRFTEKDRAKKEAELLEEMKKNEKFVIVATQVIEASLDIS-ADVMITELAP--I  306 (358)
T ss_pred             CCHHHHHHHHHHHHhhcCCCeEEEEECCCCHHHHHHHHHHHHHHhcCCCCeEEEECcchhceeccC-CCEEEEcCCC--H
Confidence            999999999999988766  49999999999999764    8999999999999999999999995 8899988776  7


Q ss_pred             HHHHHHhcccCCCCCc----cEEEEEecCCCc
Q 002040          796 EDYVHRVGRTGRAGRK----GCAITFISEEDA  823 (976)
Q Consensus       796 ~~y~Qr~GR~gR~g~~----g~~~~~~~~~d~  823 (976)
                      ..|+||+||+||.|..    |.+|+|....+.
T Consensus       307 ~~~iqr~GR~gR~g~~~~~~~~~~v~~~~~~~  338 (358)
T TIGR01587       307 DSLIQRLGRLHRYGRKNGENFEVYIITIAPEG  338 (358)
T ss_pred             HHHHHHhccccCCCCCCCCCCeEEEEeecCCC
Confidence            8999999999998754    367777765444

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.

>PHA02558 uvsW UvsW helicase; Provisional

Probab=100.00  E-value=2.6e-35  Score=346.64  Aligned_cols=301  Identities=16%  Similarity=0.148  Sum_probs=221.6

Q ss_pred             CCCCcHHHHHHHHHHhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHHHHhh
Q 002040          487 YEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKV  566 (976)
Q Consensus       487 ~~~p~~~Q~~~i~~il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~~~~~  566 (976)
                      ...|+++|.++++.++.+.++|+++|||+|||++++..+...+..       ...++||||||++|+.||.+.|.+++..
T Consensus       112 ~~~~r~~Q~~av~~~l~~~~~il~apTGsGKT~i~~~l~~~~~~~-------~~~~vLilvpt~eL~~Q~~~~l~~~~~~  184 (501)
T PHA02558        112 KIEPHWYQYDAVYEGLKNNRRLLNLPTSAGKSLIQYLLSRYYLEN-------YEGKVLIIVPTTSLVTQMIDDFVDYRLF  184 (501)
T ss_pred             cCCCCHHHHHHHHHHHhcCceEEEeCCCCCHHHHHHHHHHHHHhc-------CCCeEEEEECcHHHHHHHHHHHHHhccc
Confidence            457999999999999999999999999999999765433222222       1347999999999999999999998754


Q ss_pred             cCcEEEEeeCCCChHHHHHHHhcCCeEEEeCchhHHHHHHhcCCcccccCCceEEEecCcccccccCCchHHHHHHHhcC
Q 002040          567 MGVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMGFEPQITRIVQNIR  646 (976)
Q Consensus       567 ~~~~~~~~~gg~~~~~~~~~l~~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDEah~~~~~~f~~~i~~il~~~~  646 (976)
                      ....+..+++|....       .+.+|+|+||++|.....      ..+.++++|||||||++..    ..+..++..++
T Consensus       185 ~~~~~~~i~~g~~~~-------~~~~I~VaT~qsl~~~~~------~~~~~~~~iIvDEaH~~~~----~~~~~il~~~~  247 (501)
T PHA02558        185 PREAMHKIYSGTAKD-------TDAPIVVSTWQSAVKQPK------EWFDQFGMVIVDECHLFTG----KSLTSIITKLD  247 (501)
T ss_pred             cccceeEEecCcccC-------CCCCEEEeeHHHHhhchh------hhccccCEEEEEchhcccc----hhHHHHHHhhh
Confidence            445566677776432       347999999999865431      2467899999999999864    45667777777


Q ss_pred             CCCcEEEEeccCcHHHHH-H-HHHHcCCCeEEEeCCcccc------cCCceEEEE---------------------ecCc
Q 002040          647 PDRQTVLFSATFPRQVEI-L-ARKVLNKPVEIQVGGRSVV------NKDITQLVE---------------------VRPE  697 (976)
Q Consensus       647 ~~~q~i~~SAT~~~~~~~-l-~~~~l~~~~~i~~~~~~~~------~~~i~q~~~---------------------~~~~  697 (976)
                      +.+++|+||||++..... + ...+++ |+...+......      ...+.....                     +...
T Consensus       248 ~~~~~lGLTATp~~~~~~~~~~~~~fG-~i~~~v~~~~li~~g~l~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~l~~~  326 (501)
T PHA02558        248 NCKFKFGLTGSLRDGKANILQYVGLFG-DIFKPVTTSQLMEEGQVTDLKINSIFLRYPDEDRVKLKGEDYQEEIKYITSH  326 (501)
T ss_pred             ccceEEEEeccCCCccccHHHHHHhhC-CceEEecHHHHHhCCCcCCceEEEEeccCCHHHhhhhcccchHHHHHHHhcc
Confidence            778999999999753221 1 111222 222222111000      000000000                     0111


Q ss_pred             chHHHHHHHHHHhhh-cCCcEEEEecCHHHHHHHHHHHHHCCCCceeccCCCCHHHHHHHHHHhccCCccEEEec-Cccc
Q 002040          698 SDRFLRLLELLGEWY-EKGKILIFVHSQEKCDALFRDLLKHGYPCLSLHGAKDQTDRESTISDFKSNVCNLLIAT-SVAA  775 (976)
Q Consensus       698 ~~k~~~l~~~l~~~~-~~~kvLIF~~s~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLVaT-~v~~  775 (976)
                      ..+...+..++..+. .+.++||||++...++.|+..|...|+++..+||+|++.+|..+++.|++|...||||| ++++
T Consensus       327 ~~Rn~~I~~~~~~~~~~~~~~lV~~~~~~h~~~L~~~L~~~g~~v~~i~G~~~~~eR~~i~~~~~~~~~~vLvaT~~~l~  406 (501)
T PHA02558        327 TKRNKWIANLALKLAKKGENTFVMFKYVEHGKPLYEMLKKVYDKVYYVSGEVDTEDRNEMKKIAEGGKGIIIVASYGVFS  406 (501)
T ss_pred             HHHHHHHHHHHHHHHhcCCCEEEEEEEHHHHHHHHHHHHHcCCCEEEEeCCCCHHHHHHHHHHHhCCCCeEEEEEcceec
Confidence            122233333333332 34689999999999999999999999999999999999999999999999999999998 8999


Q ss_pred             ccCCCCCCcEEEEeCCCCCHHHHHHHhcccCCCCCcc
Q 002040          776 RGLDVKELELVINFDAPNHYEDYVHRVGRTGRAGRKG  812 (976)
Q Consensus       776 ~GlDi~~v~~VI~~d~p~s~~~y~Qr~GR~gR~g~~g  812 (976)
                      +|+|+|++++||++.++.+...|+|++||++|.+..+
T Consensus       407 eG~Dip~ld~vIl~~p~~s~~~~~QriGR~~R~~~~K  443 (501)
T PHA02558        407 TGISIKNLHHVIFAHPSKSKIIVLQSIGRVLRKHGSK  443 (501)
T ss_pred             cccccccccEEEEecCCcchhhhhhhhhccccCCCCC
Confidence            9999999999999999999999999999999986544

>PRK09200 preprotein translocase subunit SecA; Reviewed

Probab=100.00  E-value=3.5e-35  Score=349.34  Aligned_cols=325  Identities=20%  Similarity=0.250  Sum_probs=243.7

Q ss_pred             HcCCCCCcHHHHHHHHHHhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHHH
Q 002040          484 KLNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKF  563 (976)
Q Consensus       484 ~~~~~~p~~~Q~~~i~~il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~~  563 (976)
                      .+|+ .|+++|..+++.++.|+  |+.+.||+|||++|++|++.....        |+.|+||+||+.||.|.+.++..+
T Consensus        74 ~~g~-~p~~vQl~~~~~l~~G~--Iaem~TGeGKTL~a~lp~~l~al~--------G~~v~VvTpt~~LA~qd~e~~~~l  142 (790)
T PRK09200         74 VLGM-RPYDVQLIGALVLHEGN--IAEMQTGEGKTLTATMPLYLNALE--------GKGVHLITVNDYLAKRDAEEMGQV  142 (790)
T ss_pred             HhCC-CCchHHHHhHHHHcCCc--eeeecCCCcchHHHHHHHHHHHHc--------CCCeEEEeCCHHHHHHHHHHHHHH
Confidence            3676 69999999999998876  999999999999999999866553        678999999999999999999999


Q ss_pred             HhhcCcEEEEeeCCCChHHHHHHHhcCCeEEEeCchhH-HHHHHhcC---CcccccCCceEEEecCccccc-ccC-----
Q 002040          564 AKVMGVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRM-IDILCTSG---GKITNLRRVTYLVMDEADRMF-DMG-----  633 (976)
Q Consensus       564 ~~~~~~~~~~~~gg~~~~~~~~~l~~~~~Iiv~Tp~~L-~~~l~~~~---~~~~~l~~~~~vVlDEah~~~-~~~-----  633 (976)
                      +..+|+.+.+++||.+...+... ..+++|+||||+.| .++|..+-   .....+..+.++||||||.|+ +..     
T Consensus       143 ~~~lGl~v~~i~g~~~~~~~r~~-~y~~dIvygT~~~l~fDyLrd~~~~~~~~~~~r~~~~~IvDEaDsiLiDea~tpli  221 (790)
T PRK09200        143 YEFLGLTVGLNFSDIDDASEKKA-IYEADIIYTTNSELGFDYLRDNLADSKEDKVQRPLNYAIIDEIDSILLDEAQTPLI  221 (790)
T ss_pred             HhhcCCeEEEEeCCCCcHHHHHH-hcCCCEEEECCccccchhHHhccccchhhhcccccceEEEeccccceeccCCCcee
Confidence            99999999999999984333333 34699999999999 56554421   111346788999999999873 100     


Q ss_pred             ----------CchHHHHHHHhcCCC-------------------------------------------------------
Q 002040          634 ----------FEPQITRIVQNIRPD-------------------------------------------------------  648 (976)
Q Consensus       634 ----------f~~~i~~il~~~~~~-------------------------------------------------------  648 (976)
                                +...+..++..+...                                                       
T Consensus       222 isg~~~~~~~~y~~~~~~~~~l~~~~dy~~d~~~~~~~lt~~g~~~~e~~~~i~~l~~~~~~~~~~~i~~Al~A~~~~~~  301 (790)
T PRK09200        222 ISGKPRVQSNLYHIAAKFVKTLEEDVDYEFDEEKKEVWLTDQGIEKAESYFGIDNLYSLEHQVLYRHIILALRAHVLFKR  301 (790)
T ss_pred             eeCCCccccHHHHHHHHHHHhcccCCCeEEecCCCeEEecHhHHHHHHHhcCCccccChhhhHHHHHHHHHHHHHHHhhc
Confidence                      000111111111000                                                       


Q ss_pred             --------------------------------------------------------------CcEEEEeccCcHHHHHHH
Q 002040          649 --------------------------------------------------------------RQTVLFSATFPRQVEILA  666 (976)
Q Consensus       649 --------------------------------------------------------------~q~i~~SAT~~~~~~~l~  666 (976)
                                                                                    ..+.+||+|....-..+ 
T Consensus       302 d~dYiV~~~~v~ivD~~TGr~~~gr~~s~GlhQaieaKe~v~i~~e~~t~a~It~q~~fr~Y~kl~GmTGTa~t~~~e~-  380 (790)
T PRK09200        302 DVDYIVYDGEIVLVDRFTGRVLPGRKLQDGLHQAIEAKEGVEITEENRTMASITIQNLFRMFPKLSGMTGTAKTEEKEF-  380 (790)
T ss_pred             CCcEEEECCEEEEEECCCCcCCCCCccChHHHHHHHHhcCCCcCCCceehhhhhHHHHHHHhHHHhccCCCChHHHHHH-
Confidence                                                                          12456666654433333 


Q ss_pred             HHHcCCCeEEEeCCcccccCCceEEEEecCcchHHHHHHHHHHhhh-cCCcEEEEecCHHHHHHHHHHHHHCCCCceecc
Q 002040          667 RKVLNKPVEIQVGGRSVVNKDITQLVEVRPESDRFLRLLELLGEWY-EKGKILIFVHSQEKCDALFRDLLKHGYPCLSLH  745 (976)
Q Consensus       667 ~~~l~~~~~i~~~~~~~~~~~i~q~~~~~~~~~k~~~l~~~l~~~~-~~~kvLIF~~s~~~~~~l~~~L~~~~~~~~~lh  745 (976)
                      ...++-.+...+...+....... ...+.....|+..|+..+.... ...++||||+|+..++.|+..|...|+++..+|
T Consensus       381 ~~~Y~l~v~~IPt~kp~~r~d~~-~~i~~~~~~K~~al~~~i~~~~~~~~pvLIf~~t~~~se~l~~~L~~~gi~~~~L~  459 (790)
T PRK09200        381 FEVYNMEVVQIPTNRPIIRIDYP-DKVFVTLDEKYKAVIEEVKERHETGRPVLIGTGSIEQSETFSKLLDEAGIPHNLLN  459 (790)
T ss_pred             HHHhCCcEEECCCCCCcccccCC-CeEEcCHHHHHHHHHHHHHHHHhcCCCEEEEeCcHHHHHHHHHHHHHCCCCEEEec
Confidence            23333333322222222222221 1234455778888988887643 456999999999999999999999999999999


Q ss_pred             CCCCHHHHHHHHHHhccCCccEEEecCcccccCCC---CCCc-----EEEEeCCCCCHHHHHHHhcccCCCCCccEEEEE
Q 002040          746 GAKDQTDRESTISDFKSNVCNLLIATSVAARGLDV---KELE-----LVINFDAPNHYEDYVHRVGRTGRAGRKGCAITF  817 (976)
Q Consensus       746 g~~~~~~R~~~~~~F~~g~~~vLVaT~v~~~GlDi---~~v~-----~VI~~d~p~s~~~y~Qr~GR~gR~g~~g~~~~~  817 (976)
                      |.+.+.++..+...+..|  .|||||++++||+||   ++|.     +||+|++|.+...|+|++||+||.|.+|.+++|
T Consensus       460 ~~~~~~e~~~i~~ag~~g--~VlIATdmAgRG~DI~l~~~V~~~GGL~VI~~d~p~s~r~y~qr~GRtGR~G~~G~s~~~  537 (790)
T PRK09200        460 AKNAAKEAQIIAEAGQKG--AVTVATNMAGRGTDIKLGEGVHELGGLAVIGTERMESRRVDLQLRGRSGRQGDPGSSQFF  537 (790)
T ss_pred             CCccHHHHHHHHHcCCCC--eEEEEccchhcCcCCCcccccccccCcEEEeccCCCCHHHHHHhhccccCCCCCeeEEEE
Confidence            999998888888777766  699999999999999   6898     999999999999999999999999999999999


Q ss_pred             ecCCCcC
Q 002040          818 ISEEDAK  824 (976)
Q Consensus       818 ~~~~d~~  824 (976)
                      ++..|..
T Consensus       538 is~eD~l  544 (790)
T PRK09200        538 ISLEDDL  544 (790)
T ss_pred             EcchHHH
Confidence            9986553

>TIGR03714 secA2 accessory Sec system translocase SecA2

Probab=100.00  E-value=6.6e-35  Score=343.49  Aligned_cols=321  Identities=20%  Similarity=0.241  Sum_probs=232.0

Q ss_pred             cHHHHHHHHHHhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHHHHhhcCcE
Q 002040          491 MPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVMGVR  570 (976)
Q Consensus       491 ~~~Q~~~i~~il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~~~~~~~~~  570 (976)
                      +|+|.|++..+..++..|+.++||+|||++|++|++.+++.        ++.|+||+||+.||.|+++++..++..+|+.
T Consensus        70 rpydVQlig~l~l~~G~Iaem~TGeGKTLta~Lpa~l~aL~--------g~~V~VVTpn~yLA~Rdae~m~~l~~~LGLs  141 (762)
T TIGR03714        70 FPYDVQVLGAIVLHQGNIAEMKTGEGKTLTATMPLYLNALT--------GKGAMLVTTNDYLAKRDAEEMGPVYEWLGLT  141 (762)
T ss_pred             CccHHHHHHHHHhcCCceeEecCCcchHHHHHHHHHHHhhc--------CCceEEeCCCHHHHHHHHHHHHHHHhhcCCc
Confidence            45555555555555558999999999999999998776553        4569999999999999999999999999999


Q ss_pred             EEEeeCCCC---hHHHHHHHhcCCeEEEeCchhH-HHHHHhc---CCcccccCCceEEEecCcccccc-cCC--------
Q 002040          571 CVPVYGGSG---VAQQISELKRGTEIVVCTPGRM-IDILCTS---GGKITNLRRVTYLVMDEADRMFD-MGF--------  634 (976)
Q Consensus       571 ~~~~~gg~~---~~~~~~~l~~~~~Iiv~Tp~~L-~~~l~~~---~~~~~~l~~~~~vVlDEah~~~~-~~f--------  634 (976)
                      +.+++++..   ..........+++|+||||+.| .++|..+   ......+..+.++||||||.|+- ...        
T Consensus       142 v~~~~~~s~~~~~~~~~rr~~y~~dIvygTp~~LgfDyLrD~l~~~~~~~~~r~l~~~IVDEaDsILiDeartpliisg~  221 (762)
T TIGR03714       142 VSLGVVDDPDEEYDANEKRKIYNSDIVYTTNSALGFDYLIDNLASNKEGKFLRPFNYVIVDEVDSVLLDSAQTPLVISGA  221 (762)
T ss_pred             EEEEECCCCccccCHHHHHHhCCCCEEEECchhhhhhHHHHHhhcchhhcccccCcEEEEecHhhHhhccCcCCeeeeCC
Confidence            999887632   2222233345799999999999 5655432   11123467899999999998731 100        


Q ss_pred             -------chHHHHHHHhcCCC-----------------------------------------------------------
Q 002040          635 -------EPQITRIVQNIRPD-----------------------------------------------------------  648 (976)
Q Consensus       635 -------~~~i~~il~~~~~~-----------------------------------------------------------  648 (976)
                             ...+..++..+...                                                           
T Consensus       222 ~~~~~~~y~~~~~~v~~l~~~~dy~~d~~~~~v~lt~~G~~~~e~~~~~~~l~~~~~~~~~~~i~~al~A~~~~~~d~dY  301 (762)
T TIGR03714       222 PRVQSNLYHIADTFVRTLKEDVDYIFKKDKKEVWLTDKGIEKAEQYFKIDNLYSEEYFELVRHINLALRAHYLFKRNKDY  301 (762)
T ss_pred             CccchHHHHHHHHHHHhcCCCCCeEEEcCCCeeeecHhHHHHHHHHcCCCccCChhhHHHHHHHHHHHHHHHHHhcCCce
Confidence                   00011111111110                                                           


Q ss_pred             ----------------------------------------------------------CcEEEEeccCcHHHHHHHHHHc
Q 002040          649 ----------------------------------------------------------RQTVLFSATFPRQVEILARKVL  670 (976)
Q Consensus       649 ----------------------------------------------------------~q~i~~SAT~~~~~~~l~~~~l  670 (976)
                                                                                .++.+||+|.......+. ..+
T Consensus       302 iV~~~~v~ivD~~TGr~~~gr~~~~GLhQaieaKE~v~i~~e~~t~a~It~qn~Fr~Y~kl~GmTGTa~~~~~Ef~-~iY  380 (762)
T TIGR03714       302 VVTNGEVVLLDRITGRLLEGTKLQSGIHQAIEAKEHVELSKETRAMASITYQNLFKMFNKLSGMTGTGKVAEKEFI-ETY  380 (762)
T ss_pred             EEECCEEEEEECCCCcCCCCCCcchHHHHHHHhhcCCCCCCCceeeeeeeHHHHHhhCchhcccCCCChhHHHHHH-HHh
Confidence                                                                      124566666544334443 233


Q ss_pred             CCCeEEEeCCcccccCCceEEEEecCcchHHHHHHHHHHhhh-cCCcEEEEecCHHHHHHHHHHHHHCCCCceeccCCCC
Q 002040          671 NKPVEIQVGGRSVVNKDITQLVEVRPESDRFLRLLELLGEWY-EKGKILIFVHSQEKCDALFRDLLKHGYPCLSLHGAKD  749 (976)
Q Consensus       671 ~~~~~i~~~~~~~~~~~i~q~~~~~~~~~k~~~l~~~l~~~~-~~~kvLIF~~s~~~~~~l~~~L~~~~~~~~~lhg~~~  749 (976)
                      +-.+...+...+...... ....+.....|+..++..+.... ...++||||+++..++.|+..|...|+++..+||.+.
T Consensus       381 ~l~v~~IPt~kp~~r~d~-~d~i~~~~~~K~~ai~~~i~~~~~~~~pvLIft~s~~~se~ls~~L~~~gi~~~~L~a~~~  459 (762)
T TIGR03714       381 SLSVVKIPTNKPIIRIDY-PDKIYATLPEKLMATLEDVKEYHETGQPVLLITGSVEMSEIYSELLLREGIPHNLLNAQNA  459 (762)
T ss_pred             CCCEEEcCCCCCeeeeeC-CCeEEECHHHHHHHHHHHHHHHhhCCCCEEEEECcHHHHHHHHHHHHHCCCCEEEecCCCh
Confidence            333332222222221111 11344556778998988887653 4569999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHhccCCccEEEecCcccccCCCC---------CCcEEEEeCCCCCHHHHHHHhcccCCCCCccEEEEEecC
Q 002040          750 QTDRESTISDFKSNVCNLLIATSVAARGLDVK---------ELELVINFDAPNHYEDYVHRVGRTGRAGRKGCAITFISE  820 (976)
Q Consensus       750 ~~~R~~~~~~F~~g~~~vLVaT~v~~~GlDi~---------~v~~VI~~d~p~s~~~y~Qr~GR~gR~g~~g~~~~~~~~  820 (976)
                      +.++..+...|+.|  .|+|||++++||+||+         ++.+||+|++|....+ +|++|||||.|.+|.+++|++.
T Consensus       460 ~~E~~ii~~ag~~g--~VlIATdmAgRGtDI~l~~~v~~~GGL~vIit~~~ps~rid-~qr~GRtGRqG~~G~s~~~is~  536 (762)
T TIGR03714       460 AKEAQIIAEAGQKG--AVTVATSMAGRGTDIKLGKGVAELGGLAVIGTERMENSRVD-LQLRGRSGRQGDPGSSQFFVSL  536 (762)
T ss_pred             HHHHHHHHHcCCCC--eEEEEccccccccCCCCCccccccCCeEEEEecCCCCcHHH-HHhhhcccCCCCceeEEEEEcc
Confidence            99988888777777  6999999999999999         9999999999998766 9999999999999999999998


Q ss_pred             CCcC
Q 002040          821 EDAK  824 (976)
Q Consensus       821 ~d~~  824 (976)
                      .|..
T Consensus       537 eD~l  540 (762)
T TIGR03714       537 EDDL  540 (762)
T ss_pred             chhh
Confidence            7553

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.

>TIGR01054 rgy reverse gyrase

Probab=100.00  E-value=7e-35  Score=365.89  Aligned_cols=290  Identities=22%  Similarity=0.338  Sum_probs=226.4

Q ss_pred             HHHHHcCCCCCcHHHHHHHHHHhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHH
Q 002040          480 ETIRKLNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSD  559 (976)
Q Consensus       480 ~~l~~~~~~~p~~~Q~~~i~~il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~  559 (976)
                      +.+.......|+++|..+++.++.|++++++||||||||+ |++|++..+..       .++++|||+||++||.|++..
T Consensus        69 ~~f~~~~g~~p~~iQ~~~i~~il~G~d~vi~ApTGsGKT~-f~l~~~~~l~~-------~g~~vLIL~PTreLa~Qi~~~  140 (1171)
T TIGR01054        69 EFFKKAVGSEPWSIQKMWAKRVLRGDSFAIIAPTGVGKTT-FGLAMSLFLAK-------KGKRCYIILPTTLLVIQVAEK  140 (1171)
T ss_pred             HHHHHhcCCCCcHHHHHHHHHHhCCCeEEEECCCCCCHHH-HHHHHHHHHHh-------cCCeEEEEeCHHHHHHHHHHH
Confidence            3444434457999999999999999999999999999997 66777666543       268899999999999999999


Q ss_pred             HHHHHhhcCcEEE---EeeCCCChHHH---HHHHhc-CCeEEEeCchhHHHHHHhcCCcccccCCceEEEecCcccccc-
Q 002040          560 IRKFAKVMGVRCV---PVYGGSGVAQQ---ISELKR-GTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFD-  631 (976)
Q Consensus       560 ~~~~~~~~~~~~~---~~~gg~~~~~~---~~~l~~-~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDEah~~~~-  631 (976)
                      +..++..+++.+.   +++||.+..++   +..+.. +++|||+||++|.+.+...     .. ++.+|||||||+|++ 
T Consensus       141 l~~l~~~~~i~~~~i~~~~Gg~~~~e~~~~~~~l~~~~~dIlV~Tp~rL~~~~~~l-----~~-~~~~iVvDEaD~~L~~  214 (1171)
T TIGR01054       141 ISSLAEKAGVGTVNIGAYHSRLPTKEKKEFMERIENGDFDILITTTMFLSKNYDEL-----GP-KFDFIFVDDVDALLKA  214 (1171)
T ss_pred             HHHHHHhcCCceeeeeeecCCCCHHHHHHHHHHHhcCCCCEEEECHHHHHHHHHHh-----cC-CCCEEEEeChHhhhhc
Confidence            9999988776654   46788877654   334444 4899999999998877531     11 799999999999998 


Q ss_pred             ----------cCCchH-HHHHH----------------------HhcCCCCc--EEEEecc-CcHHHHHHHHHHcCCCeE
Q 002040          632 ----------MGFEPQ-ITRIV----------------------QNIRPDRQ--TVLFSAT-FPRQVEILARKVLNKPVE  675 (976)
Q Consensus       632 ----------~~f~~~-i~~il----------------------~~~~~~~q--~i~~SAT-~~~~~~~l~~~~l~~~~~  675 (976)
                                +||... +..++                      ..++..+|  +++|||| +|..+.   ..++..+..
T Consensus       215 ~k~vd~il~llGF~~e~i~~il~~~~~~~~~~~~~~~~~~~~~~~~~~~~~q~~li~~SAT~~p~~~~---~~l~r~ll~  291 (1171)
T TIGR01054       215 SKNVDKLLKLLGFSEELIEKAWKLIRLRLKLYRALHAKKRLELLEAIPGKKRGCLIVSSATGRPRGKR---AKLFRELLG  291 (1171)
T ss_pred             cccHHHHHHHcCCCHHHHHHHHHHhhhccccchHHHHHHHHHHHHhhhhccCcEEEEEeCCCCccccH---HHHcccccc
Confidence                      788774 44443                      23444455  5779999 565433   234556666


Q ss_pred             EEeCCcccccCCceEEEEecCcchHHHHHHHHHHhhhcCCcEEEEecCH---HHHHHHHHHHHHCCCCceeccCCCCHHH
Q 002040          676 IQVGGRSVVNKDITQLVEVRPESDRFLRLLELLGEWYEKGKILIFVHSQ---EKCDALFRDLLKHGYPCLSLHGAKDQTD  752 (976)
Q Consensus       676 i~~~~~~~~~~~i~q~~~~~~~~~k~~~l~~~l~~~~~~~kvLIF~~s~---~~~~~l~~~L~~~~~~~~~lhg~~~~~~  752 (976)
                      +.++.......++.+.+.....  +...|..+|...  +.++||||++.   +.|+.|+..|...|+.+..+||++++  
T Consensus       292 ~~v~~~~~~~r~I~~~~~~~~~--~~~~L~~ll~~l--~~~~IVFv~t~~~~~~a~~l~~~L~~~g~~a~~lhg~~~~--  365 (1171)
T TIGR01054       292 FEVGGGSDTLRNVVDVYVEDED--LKETLLEIVKKL--GTGGIVYVSIDYGKEKAEEIAEFLENHGVKAVAYHATKPK--  365 (1171)
T ss_pred             eEecCccccccceEEEEEeccc--HHHHHHHHHHHc--CCCEEEEEeccccHHHHHHHHHHHHhCCceEEEEeCCCCH--
Confidence            6776665556677777654432  245566666554  35799999999   99999999999999999999999973  


Q ss_pred             HHHHHHHhccCCccEEEe----cCcccccCCCCC-CcEEEEeCCCCC
Q 002040          753 RESTISDFKSNVCNLLIA----TSVAARGLDVKE-LELVINFDAPNH  794 (976)
Q Consensus       753 R~~~~~~F~~g~~~vLVa----T~v~~~GlDi~~-v~~VI~~d~p~s  794 (976)
                        .+++.|++|+++||||    |++++||||||+ |++|||||+|..
T Consensus       366 --~~l~~Fr~G~~~vLVata~~tdv~aRGIDip~~V~~vI~~~~P~~  410 (1171)
T TIGR01054       366 --EDYEKFAEGEIDVLIGVASYYGTLVRGLDLPERVRYAVFLGVPKF  410 (1171)
T ss_pred             --HHHHHHHcCCCCEEEEeccccCcccccCCCCccccEEEEECCCCE
Confidence              7899999999999999    589999999999 899999999973

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.

>TIGR00963 secA preprotein translocase, SecA subunit

Probab=100.00  E-value=2.2e-34  Score=336.76  Aligned_cols=323  Identities=22%  Similarity=0.288  Sum_probs=246.4

Q ss_pred             cCCCCCcHHHHHHHHHHhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHHHH
Q 002040          485 LNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFA  564 (976)
Q Consensus       485 ~~~~~p~~~Q~~~i~~il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~~~  564 (976)
                      +|+ .|+++|..+++.+..|+  |+.++||+|||++|++|++.....        |..|+||+||..||.|.++++..++
T Consensus        53 lg~-~p~~vQlig~~~l~~G~--Iaem~TGeGKTLva~lpa~l~aL~--------G~~V~VvTpt~~LA~qdae~~~~l~  121 (745)
T TIGR00963        53 LGM-RPFDVQLIGGIALHKGK--IAEMKTGEGKTLTATLPAYLNALT--------GKGVHVVTVNDYLAQRDAEWMGQVY  121 (745)
T ss_pred             hCC-CccchHHhhhhhhcCCc--eeeecCCCccHHHHHHHHHHHHHh--------CCCEEEEcCCHHHHHHHHHHHHHHh
Confidence            564 48899999888887776  999999999999999999644432        4469999999999999999999999


Q ss_pred             hhcCcEEEEeeCCCChHHHHHHHhcCCeEEEeCchhH-HHHHHhcCC---cccccCCceEEEecCcccccc-c-------
Q 002040          565 KVMGVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRM-IDILCTSGG---KITNLRRVTYLVMDEADRMFD-M-------  632 (976)
Q Consensus       565 ~~~~~~~~~~~gg~~~~~~~~~l~~~~~Iiv~Tp~~L-~~~l~~~~~---~~~~l~~~~~vVlDEah~~~~-~-------  632 (976)
                      ..+|+.+.+++||.+.......+  .++|+|+||++| +++|..+..   ....+..+.++||||+|+|+- .       
T Consensus       122 ~~LGLsv~~i~g~~~~~~r~~~y--~~dIvyGT~~rlgfDyLrd~~~~~~~~~~~r~l~~aIIDEaDs~LIDeaRtpLii  199 (745)
T TIGR00963       122 RFLGLSVGLILSGMSPEERREAY--ACDITYGTNNELGFDYLRDNMAHSKEEKVQRPFHFAIIDEVDSILIDEARTPLII  199 (745)
T ss_pred             ccCCCeEEEEeCCCCHHHHHHhc--CCCEEEECCCchhhHHHhcccccchhhhhccccceeEeecHHHHhHHhhhhHHhh
Confidence            99999999999998876654443  489999999999 888865421   123578899999999998731 0       


Q ss_pred             -C------------------------Cc------------h---HHHHH------------------HHhc------CCC
Q 002040          633 -G------------------------FE------------P---QITRI------------------VQNI------RPD  648 (976)
Q Consensus       633 -~------------------------f~------------~---~i~~i------------------l~~~------~~~  648 (976)
                       |                        |.            .   .+..+                  ...+      ..+
T Consensus       200 sg~~~~~~~ly~~a~~i~r~L~~~~dy~~de~~k~v~Lt~~G~~~~e~~~~~~~ly~~~~~~~~~~i~~Al~A~~l~~~d  279 (745)
T TIGR00963       200 SGPAEKSTELYLQANRFAKALEKEVHYEVDEKNRAVLLTEKGIKKAEDLLGVDNLYDLENSPLIHYINNALKAKELFEKD  279 (745)
T ss_pred             cCCCCCchHHHHHHHHHHHhhccCCCeEEecCCCceeECHHHHHHHHHHcCCccccChhhhHHHHHHHHHHHHHHHHhcC
Confidence             0                        00            0   00000                  0000      000


Q ss_pred             -------------------------------------------------------------CcEEEEeccCcHHHHHHHH
Q 002040          649 -------------------------------------------------------------RQTVLFSATFPRQVEILAR  667 (976)
Q Consensus       649 -------------------------------------------------------------~q~i~~SAT~~~~~~~l~~  667 (976)
                                                                                   ..+.+||+|.......+..
T Consensus       280 ~dYiV~d~~V~ivD~~TGR~~~gr~ws~GLhQaiEaKE~v~i~~e~~t~a~It~qn~Fr~Y~kl~GmTGTa~te~~E~~~  359 (745)
T TIGR00963       280 VDYIVRDGEVVIVDEFTGRIMEGRRWSDGLHQAIEAKEGVEIQNENQTLATITYQNFFRLYEKLSGMTGTAKTEEEEFEK  359 (745)
T ss_pred             CcEEEECCEEEEEECCCCcCCCCCccchHHHHHHHHhcCCCcCCCceeeeeeeHHHHHhhCchhhccCCCcHHHHHHHHH
Confidence                                                                         2356777777655444433


Q ss_pred             HHcCCCeEEEeCCcccccCCceEEEEecCcchHHHHHHHHHHhhh-cCCcEEEEecCHHHHHHHHHHHHHCCCCceeccC
Q 002040          668 KVLNKPVEIQVGGRSVVNKDITQLVEVRPESDRFLRLLELLGEWY-EKGKILIFVHSQEKCDALFRDLLKHGYPCLSLHG  746 (976)
Q Consensus       668 ~~l~~~~~i~~~~~~~~~~~i~q~~~~~~~~~k~~~l~~~l~~~~-~~~kvLIF~~s~~~~~~l~~~L~~~~~~~~~lhg  746 (976)
                       .++-++...+...+....... ...+.....|+..++..+.... .+.++||||+++..++.|+..|...|+++..+||
T Consensus       360 -iY~l~vv~IPtnkp~~R~d~~-d~i~~t~~~k~~ai~~~i~~~~~~grpvLV~t~si~~se~ls~~L~~~gi~~~~Lna  437 (745)
T TIGR00963       360 -IYNLEVVVVPTNRPVIRKDLS-DLVYKTEEEKWKAVVDEIKERHAKGQPVLVGTTSVEKSELLSNLLKERGIPHNVLNA  437 (745)
T ss_pred             -HhCCCEEEeCCCCCeeeeeCC-CeEEcCHHHHHHHHHHHHHHHHhcCCCEEEEeCcHHHHHHHHHHHHHcCCCeEEeeC
Confidence             334444333333332222211 2234556678888887775554 3559999999999999999999999999999999


Q ss_pred             CCCHHHHHHHHHHhccCCccEEEecCcccccCCCCC-------CcEEEEeCCCCCHHHHHHHhcccCCCCCccEEEEEec
Q 002040          747 AKDQTDRESTISDFKSNVCNLLIATSVAARGLDVKE-------LELVINFDAPNHYEDYVHRVGRTGRAGRKGCAITFIS  819 (976)
Q Consensus       747 ~~~~~~R~~~~~~F~~g~~~vLVaT~v~~~GlDi~~-------v~~VI~~d~p~s~~~y~Qr~GR~gR~g~~g~~~~~~~  819 (976)
                      .  +..|+..+..|..+...|+|||++|+||+||+.       ..+||+++.|.|...|.|++||+||.|.+|.+..|++
T Consensus       438 ~--q~~rEa~ii~~ag~~g~VtIATnmAgRGtDI~l~~V~~~GGl~VI~t~~p~s~ri~~q~~GRtGRqG~~G~s~~~ls  515 (745)
T TIGR00963       438 K--NHEREAEIIAQAGRKGAVTIATNMAGRGTDIKLEEVKELGGLYVIGTERHESRRIDNQLRGRSGRQGDPGSSRFFLS  515 (745)
T ss_pred             C--hHHHHHHHHHhcCCCceEEEEeccccCCcCCCccchhhcCCcEEEecCCCCcHHHHHHHhccccCCCCCcceEEEEe
Confidence            8  889999999999999999999999999999998       5699999999999999999999999999999999999


Q ss_pred             CCCcC
Q 002040          820 EEDAK  824 (976)
Q Consensus       820 ~~d~~  824 (976)
                      ..|.-
T Consensus       516 ~eD~l  520 (745)
T TIGR00963       516 LEDNL  520 (745)
T ss_pred             ccHHH
Confidence            87654

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.

>COG1202 Superfamily II helicase, archaea-specific [General function prediction only]

Probab=100.00  E-value=2e-34  Score=314.23  Aligned_cols=338  Identities=21%  Similarity=0.290  Sum_probs=272.2

Q ss_pred             ccccCCCCHHHHHHHHHcCCCCCcHHHHHHHHH-HhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEE
Q 002040          468 TWHQTGLTSKIMETIRKLNYEKPMPIQAQALPV-IMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIM  546 (976)
Q Consensus       468 ~~~~~~l~~~l~~~l~~~~~~~p~~~Q~~~i~~-il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl  546 (976)
                      ....+.++.++...|+..|+..++|+|.-++.. ++.|.|.+++++|+||||++.-++-+..++.       .|.+.|+|
T Consensus       195 ~vdeLdipe~fk~~lk~~G~~eLlPVQ~laVe~GLLeG~nllVVSaTasGKTLIgElAGi~~~l~-------~g~KmlfL  267 (830)
T COG1202         195 PVDELDIPEKFKRMLKREGIEELLPVQVLAVEAGLLEGENLLVVSATASGKTLIGELAGIPRLLS-------GGKKMLFL  267 (830)
T ss_pred             cccccCCcHHHHHHHHhcCcceecchhhhhhhhccccCCceEEEeccCCCcchHHHhhCcHHHHh-------CCCeEEEE
Confidence            456788999999999999999999999999987 6799999999999999999988887777664       36789999


Q ss_pred             ccCHHHHHHHHHHHHHHHhhcCcEEEEeeCCCChHHHH----HHHhcCCeEEEeCchhHHHHHHhcCCcccccCCceEEE
Q 002040          547 APTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQI----SELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLV  622 (976)
Q Consensus       547 ~Ptr~La~Q~~~~~~~~~~~~~~~~~~~~gg~~~~~~~----~~l~~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vV  622 (976)
                      ||..+||+|-|..|+.-...+|+.+.+-+|-.-+...-    ......++|||+|++.+-.+|...    ..+.+++.||
T Consensus       268 vPLVALANQKy~dF~~rYs~LglkvairVG~srIk~~~~pv~~~t~~dADIIVGTYEGiD~lLRtg----~~lgdiGtVV  343 (830)
T COG1202         268 VPLVALANQKYEDFKERYSKLGLKVAIRVGMSRIKTREEPVVVDTSPDADIIVGTYEGIDYLLRTG----KDLGDIGTVV  343 (830)
T ss_pred             ehhHHhhcchHHHHHHHhhcccceEEEEechhhhcccCCccccCCCCCCcEEEeechhHHHHHHcC----CcccccceEE
Confidence            99999999999999998888999998877765333221    112235799999999986666543    4788999999


Q ss_pred             ecCcccccccCCchH---HHHHHHhcCCCCcEEEEeccCcHHHHHHHHHHcCCCeEEEeCCcccccCCceEEEEecCcch
Q 002040          623 MDEADRMFDMGFEPQ---ITRIVQNIRPDRQTVLFSATFPRQVEILARKVLNKPVEIQVGGRSVVNKDITQLVEVRPESD  699 (976)
Q Consensus       623 lDEah~~~~~~f~~~---i~~il~~~~~~~q~i~~SAT~~~~~~~l~~~~l~~~~~i~~~~~~~~~~~i~q~~~~~~~~~  699 (976)
                      |||+|.+-+...++.   +..-+..+-+..|+|++|||..+.. .++..+...++.+.  .++++  --.+.+.......
T Consensus       344 IDEiHtL~deERG~RLdGLI~RLr~l~~~AQ~i~LSATVgNp~-elA~~l~a~lV~y~--~RPVp--lErHlvf~~~e~e  418 (830)
T COG1202         344 IDEIHTLEDEERGPRLDGLIGRLRYLFPGAQFIYLSATVGNPE-ELAKKLGAKLVLYD--ERPVP--LERHLVFARNESE  418 (830)
T ss_pred             eeeeeeccchhcccchhhHHHHHHHhCCCCeEEEEEeecCChH-HHHHHhCCeeEeec--CCCCC--hhHeeeeecCchH
Confidence            999998776554444   4445566678999999999987654 47777766665443  22222  2234455556788


Q ss_pred             HHHHHHHHHHhhh-------cCCcEEEEecCHHHHHHHHHHHHHCCCCceeccCCCCHHHHHHHHHHhccCCccEEEecC
Q 002040          700 RFLRLLELLGEWY-------EKGKILIFVHSQEKCDALFRDLLKHGYPCLSLHGAKDQTDRESTISDFKSNVCNLLIATS  772 (976)
Q Consensus       700 k~~~l~~~l~~~~-------~~~kvLIF~~s~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLVaT~  772 (976)
                      |+..+..+...-.       -.|++|||++|+..|..|+.+|...|+.+.++|++|+..+|..+...|.++.+.++|+|-
T Consensus       419 K~~ii~~L~k~E~~~~sskg~rGQtIVFT~SRrr~h~lA~~L~~kG~~a~pYHaGL~y~eRk~vE~~F~~q~l~~VVTTA  498 (830)
T COG1202         419 KWDIIARLVKREFSTESSKGYRGQTIVFTYSRRRCHELADALTGKGLKAAPYHAGLPYKERKSVERAFAAQELAAVVTTA  498 (830)
T ss_pred             HHHHHHHHHHHHHhhhhccCcCCceEEEecchhhHHHHHHHhhcCCcccccccCCCcHHHHHHHHHHHhcCCcceEeehh
Confidence            8877777665432       247999999999999999999999999999999999999999999999999999999999


Q ss_pred             cccccCCCCCCcEEE----EeCCCCCHHHHHHHhcccCCCCC--ccEEEEEecCC
Q 002040          773 VAARGLDVKELELVI----NFDAPNHYEDYVHRVGRTGRAGR--KGCAITFISEE  821 (976)
Q Consensus       773 v~~~GlDi~~v~~VI----~~d~p~s~~~y~Qr~GR~gR~g~--~g~~~~~~~~~  821 (976)
                      +++.|+|+|.-.+|+    +-.-+.++..|.|++|||||.+-  .|.+|+++-+.
T Consensus       499 AL~AGVDFPASQVIFEsLaMG~~WLs~~EF~QM~GRAGRp~yHdrGkVyllvepg  553 (830)
T COG1202         499 ALAAGVDFPASQVIFESLAMGIEWLSVREFQQMLGRAGRPDYHDRGKVYLLVEPG  553 (830)
T ss_pred             hhhcCCCCchHHHHHHHHHcccccCCHHHHHHHhcccCCCCcccCceEEEEecCC
Confidence            999999999755443    23446689999999999999764  69999998764

>PRK13766 Hef nuclease; Provisional

Probab=100.00  E-value=3.7e-33  Score=347.89  Aligned_cols=323  Identities=23%  Similarity=0.312  Sum_probs=241.0

Q ss_pred             CCCCcHHHHHHHHHHhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHHHHhh
Q 002040          487 YEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKV  566 (976)
Q Consensus       487 ~~~p~~~Q~~~i~~il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~~~~~  566 (976)
                      ...|+++|.+++..++.+ ++|+++|||+|||++++++++..+..       .+.++||||||++|+.||...+..++..
T Consensus        13 ~~~~r~yQ~~~~~~~l~~-n~lv~~ptG~GKT~~a~~~i~~~l~~-------~~~~vLvl~Pt~~L~~Q~~~~~~~~~~~   84 (773)
T PRK13766         13 TIEARLYQQLLAATALKK-NTLVVLPTGLGKTAIALLVIAERLHK-------KGGKVLILAPTKPLVEQHAEFFRKFLNI   84 (773)
T ss_pred             cCCccHHHHHHHHHHhcC-CeEEEcCCCccHHHHHHHHHHHHHHh-------CCCeEEEEeCcHHHHHHHHHHHHHHhCC
Confidence            346899999999988877 99999999999999999998887742       2568999999999999999999998755


Q ss_pred             cCcEEEEeeCCCChHHHHHHHhcCCeEEEeCchhHHHHHHhcCCcccccCCceEEEecCcccccccCCchHHHHHHHhcC
Q 002040          567 MGVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMGFEPQITRIVQNIR  646 (976)
Q Consensus       567 ~~~~~~~~~gg~~~~~~~~~l~~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDEah~~~~~~f~~~i~~il~~~~  646 (976)
                      .+..++.++|+...... ..+..+++|+|+||+.|...+...   ...+..+++|||||||++........+...+....
T Consensus        85 ~~~~v~~~~g~~~~~~r-~~~~~~~~iiv~T~~~l~~~l~~~---~~~~~~~~liVvDEaH~~~~~~~~~~i~~~~~~~~  160 (773)
T PRK13766         85 PEEKIVVFTGEVSPEKR-AELWEKAKVIVATPQVIENDLIAG---RISLEDVSLLIFDEAHRAVGNYAYVYIAERYHEDA  160 (773)
T ss_pred             CCceEEEEeCCCCHHHH-HHHHhCCCEEEECHHHHHHHHHcC---CCChhhCcEEEEECCccccccccHHHHHHHHHhcC
Confidence            45577778887766543 344456899999999998776543   24677899999999998765433333444444555


Q ss_pred             CCCcEEEEeccCcHHH---HHHHHHHcCCCeEE--------------------EeCCc----------------------
Q 002040          647 PDRQTVLFSATFPRQV---EILARKVLNKPVEI--------------------QVGGR----------------------  681 (976)
Q Consensus       647 ~~~q~i~~SAT~~~~~---~~l~~~~l~~~~~i--------------------~~~~~----------------------  681 (976)
                      +..++++||||+....   ..+...+....+.+                    .+...                      
T Consensus       161 ~~~~il~lTaTP~~~~~~i~~~~~~L~i~~v~~~~~~~~~v~~~~~~~~v~~~~v~l~~~~~~i~~~l~~~~~~~l~~l~  240 (773)
T PRK13766        161 KNPLVLGLTASPGSDEEKIKEVCENLGIEHVEVRTEDDPDVKPYVHKVKIEWVRVELPEELKEIRDLLNEALKDRLKKLK  240 (773)
T ss_pred             CCCEEEEEEcCCCCCHHHHHHHHHhCCceEEEEcCCCChhHHhhhccceeEEEEeCCcHHHHHHHHHHHHHHHHHHHHHH
Confidence            6678999999974221   11111111000000                    00000                      


Q ss_pred             --ccc--cC-------------Cce-------------------------------------------------------
Q 002040          682 --SVV--NK-------------DIT-------------------------------------------------------  689 (976)
Q Consensus       682 --~~~--~~-------------~i~-------------------------------------------------------  689 (976)
                        ...  ..             .+.                                                       
T Consensus       241 ~~~~~~~~~~~~~~~~l~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~l~~~~~~l~~~~~~~~~~y~~~l~~~~~~~~~~  320 (773)
T PRK13766        241 ELGVIVSISPDVSKKELLGLQKKLQQEIANDDSEGYEAISILAEAMKLRHAVELLETQGVEALRRYLERLREEARSSGGS  320 (773)
T ss_pred             HCCCcccCCCCcCHHHHHHHHHHHHHHhhcCchHHHHHHHHHHHHHHHHHHHHHHHHhCHHHHHHHHHHHHhhccccCCc
Confidence              000  00             000                                                       


Q ss_pred             -----------------EEEEecCcchHHHHHHHHHHhhh---cCCcEEEEecCHHHHHHHHHHHHHCCCCceeccCC--
Q 002040          690 -----------------QLVEVRPESDRFLRLLELLGEWY---EKGKILIFVHSQEKCDALFRDLLKHGYPCLSLHGA--  747 (976)
Q Consensus       690 -----------------q~~~~~~~~~k~~~l~~~l~~~~---~~~kvLIF~~s~~~~~~l~~~L~~~~~~~~~lhg~--  747 (976)
                                       ....+.....|+..|..+|....   ..+++||||++...|..|+.+|...++.+..+||.  
T Consensus       321 ~~~~~l~~~~~~~~~~~~~~~~~~~~pK~~~L~~il~~~~~~~~~~kvlIF~~~~~t~~~L~~~L~~~~~~~~~~~g~~~  400 (773)
T PRK13766        321 KASKRLVEDPRFRKAVRKAKELDIEHPKLEKLREIVKEQLGKNPDSRIIVFTQYRDTAEKIVDLLEKEGIKAVRFVGQAS  400 (773)
T ss_pred             HHHHHHHhCHHHHHHHHHHHhcccCChHHHHHHHHHHHHHhcCCCCeEEEEeCcHHHHHHHHHHHHhCCCceEEEEcccc
Confidence                             00001122345666666666543   45799999999999999999999999999999986  


Q ss_pred             ------CCHHHHHHHHHHhccCCccEEEecCcccccCCCCCCcEEEEeCCCCCHHHHHHHhcccCCCCCccEEEEEecCC
Q 002040          748 ------KDQTDRESTISDFKSNVCNLLIATSVAARGLDVKELELVINFDAPNHYEDYVHRVGRTGRAGRKGCAITFISEE  821 (976)
Q Consensus       748 ------~~~~~R~~~~~~F~~g~~~vLVaT~v~~~GlDi~~v~~VI~~d~p~s~~~y~Qr~GR~gR~g~~g~~~~~~~~~  821 (976)
                            |++.+|..++..|++|.++|||||+++++|+|+|.+++||+||+|+++..|+||+||+||.| .|.+|+|++..
T Consensus       401 ~~~~~~~~~~~r~~~~~~F~~g~~~vLvaT~~~~eGldi~~~~~VI~yd~~~s~~r~iQR~GR~gR~~-~~~v~~l~~~~  479 (773)
T PRK13766        401 KDGDKGMSQKEQIEILDKFRAGEFNVLVSTSVAEEGLDIPSVDLVIFYEPVPSEIRSIQRKGRTGRQE-EGRVVVLIAKG  479 (773)
T ss_pred             ccccCCCCHHHHHHHHHHHHcCCCCEEEECChhhcCCCcccCCEEEEeCCCCCHHHHHHHhcccCcCC-CCEEEEEEeCC
Confidence                  99999999999999999999999999999999999999999999999999999999999987 58899888765


Q ss_pred             C
Q 002040          822 D  822 (976)
Q Consensus       822 d  822 (976)
                      .
T Consensus       480 t  480 (773)
T PRK13766        480 T  480 (773)
T ss_pred             C
Confidence            3

>PRK11131 ATP-dependent RNA helicase HrpA; Provisional

Probab=100.00  E-value=1.2e-33  Score=348.03  Aligned_cols=302  Identities=23%  Similarity=0.297  Sum_probs=213.3

Q ss_pred             HHHHHHHHHHhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccC----HHHHHHHHHHHHHHHhhc
Q 002040          492 PIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPT----RELVQQIHSDIRKFAKVM  567 (976)
Q Consensus       492 ~~Q~~~i~~il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Pt----r~La~Q~~~~~~~~~~~~  567 (976)
                      .+..+.+..|..++.+||+|+||||||++  +|.+.....     .+....+++..|.    ++||.++..++..-   +
T Consensus        77 ~~r~~Il~ai~~~~VviI~GeTGSGKTTq--lPq~lle~g-----~g~~g~I~~TQPRRlAArsLA~RVA~El~~~---l  146 (1294)
T PRK11131         77 QKKQDILEAIRDHQVVIVAGETGSGKTTQ--LPKICLELG-----RGVKGLIGHTQPRRLAARTVANRIAEELETE---L  146 (1294)
T ss_pred             HHHHHHHHHHHhCCeEEEECCCCCCHHHH--HHHHHHHcC-----CCCCCceeeCCCcHHHHHHHHHHHHHHHhhh---h
Confidence            34456667777788889999999999994  664433221     1112234455575    46666666655531   2


Q ss_pred             CcEEEEeeCCCChHHHHHHHhcCCeEEEeCchhHHHHHHhcCCcccccCCceEEEecCcc-cccccCCchHHHHHHHhcC
Q 002040          568 GVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEAD-RMFDMGFEPQITRIVQNIR  646 (976)
Q Consensus       568 ~~~~~~~~gg~~~~~~~~~l~~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDEah-~~~~~~f~~~i~~il~~~~  646 (976)
                      |..+.+-+...      .....++.|+|||||+|++.+...    ..|..+++||||||| ++++++|...+..-+...+
T Consensus       147 G~~VGY~vrf~------~~~s~~t~I~v~TpG~LL~~l~~d----~~Ls~~~~IIIDEAHERsLn~DfLLg~Lk~lL~~r  216 (1294)
T PRK11131        147 GGCVGYKVRFN------DQVSDNTMVKLMTDGILLAEIQQD----RLLMQYDTIIIDEAHERSLNIDFILGYLKELLPRR  216 (1294)
T ss_pred             cceeceeecCc------cccCCCCCEEEEChHHHHHHHhcC----CccccCcEEEecCccccccccchHHHHHHHhhhcC
Confidence            32222211111      122457899999999999998653    358999999999999 7999998765433333345


Q ss_pred             CCCcEEEEeccCcHHHHHHHHHHcCCCeEEEeCCcccccCCceEEEEecCc------chHHHHHHHHHHhh--hcCCcEE
Q 002040          647 PDRQTVLFSATFPRQVEILARKVLNKPVEIQVGGRSVVNKDITQLVEVRPE------SDRFLRLLELLGEW--YEKGKIL  718 (976)
Q Consensus       647 ~~~q~i~~SAT~~~~~~~l~~~~l~~~~~i~~~~~~~~~~~i~q~~~~~~~------~~k~~~l~~~l~~~--~~~~kvL  718 (976)
                      ++.|+|+||||++..  .+...|.+.|+ +.+.+...+   +.+.+.....      .+.+..++..+...  ...|.+|
T Consensus       217 pdlKvILmSATid~e--~fs~~F~~apv-I~V~Gr~~p---Vei~y~p~~~~~~~~~~d~l~~ll~~V~~l~~~~~GdIL  290 (1294)
T PRK11131        217 PDLKVIITSATIDPE--RFSRHFNNAPI-IEVSGRTYP---VEVRYRPIVEEADDTERDQLQAIFDAVDELGREGPGDIL  290 (1294)
T ss_pred             CCceEEEeeCCCCHH--HHHHHcCCCCE-EEEcCcccc---ceEEEeecccccchhhHHHHHHHHHHHHHHhcCCCCCEE
Confidence            788999999999753  45555555554 566555433   3333332221      12333444433322  2457899


Q ss_pred             EEecCHHHHHHHHHHHHHCCCC---ceeccCCCCHHHHHHHHHHhccCCccEEEecCcccccCCCCCCcEEEEeCC----
Q 002040          719 IFVHSQEKCDALFRDLLKHGYP---CLSLHGAKDQTDRESTISDFKSNVCNLLIATSVAARGLDVKELELVINFDA----  791 (976)
Q Consensus       719 IF~~s~~~~~~l~~~L~~~~~~---~~~lhg~~~~~~R~~~~~~F~~g~~~vLVaT~v~~~GlDi~~v~~VI~~d~----  791 (976)
                      |||++..+++.++..|...++.   +..+||+|++.+|..+++.  .|..+|||||+++++|||||+|.+||+++.    
T Consensus       291 VFLpg~~EIe~lae~L~~~~~~~~~VlpLhg~Ls~~eQ~~Vf~~--~g~rkIIVATNIAEtSITIpgI~yVID~Gl~k~~  368 (1294)
T PRK11131        291 IFMSGEREIRDTADALNKLNLRHTEILPLYARLSNSEQNRVFQS--HSGRRIVLATNVAETSLTVPGIKYVIDPGTARIS  368 (1294)
T ss_pred             EEcCCHHHHHHHHHHHHhcCCCcceEeecccCCCHHHHHHHhcc--cCCeeEEEeccHHhhccccCcceEEEECCCcccc
Confidence            9999999999999999988765   6789999999999999886  478999999999999999999999999862    


Q ss_pred             --------------CCCHHHHHHHhcccCCCCCccEEEEEecCCC
Q 002040          792 --------------PNHYEDYVHRVGRTGRAGRKGCAITFISEED  822 (976)
Q Consensus       792 --------------p~s~~~y~Qr~GR~gR~g~~g~~~~~~~~~d  822 (976)
                                    |.|.++|+||+|||||. .+|.||.||++.+
T Consensus       369 ~Yd~~~~~~~Lp~~~iSkasa~QRaGRAGR~-~~G~c~rLyte~d  412 (1294)
T PRK11131        369 RYSYRTKVQRLPIEPISQASANQRKGRCGRV-SEGICIRLYSEDD  412 (1294)
T ss_pred             ccccccCcccCCeeecCHhhHhhhccccCCC-CCcEEEEeCCHHH
Confidence                          34568999999999999 5999999999754

>KOG0352 consensus ATP-dependent DNA helicase [Replication, recombination and repair]

Probab=100.00  E-value=2.7e-33  Score=295.42  Aligned_cols=334  Identities=21%  Similarity=0.351  Sum_probs=248.7

Q ss_pred             HHHHHHH-cCCCCC-cHHHHHHHHHHhcC-CCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHH
Q 002040          478 IMETIRK-LNYEKP-MPIQAQALPVIMSG-RDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQ  554 (976)
Q Consensus       478 l~~~l~~-~~~~~p-~~~Q~~~i~~il~g-~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~  554 (976)
                      +..+|++ ||+.++ ++.|.+|+..+..+ +||.|++|||+||+++|.||+|.+           +.+.||+.|..+|+.
T Consensus         7 VreaLKK~FGh~kFKs~LQE~A~~c~VK~k~DVyVsMPTGaGKSLCyQLPaL~~-----------~gITIV~SPLiALIk   75 (641)
T KOG0352|consen    7 VREALKKLFGHKKFKSRLQEQAINCIVKRKCDVYVSMPTGAGKSLCYQLPALVH-----------GGITIVISPLIALIK   75 (641)
T ss_pred             HHHHHHHHhCchhhcChHHHHHHHHHHhccCcEEEeccCCCchhhhhhchHHHh-----------CCeEEEehHHHHHHH
Confidence            4455654 676654 79999999998865 699999999999999999999865           348899999999987


Q ss_pred             HHHHHHHHHHhhcCcEEEEeeCCCChHHH---H---HHHhcCCeEEEeCchhH-----HHHHHhcCCcccccCCceEEEe
Q 002040          555 QIHSDIRKFAKVMGVRCVPVYGGSGVAQQ---I---SELKRGTEIVVCTPGRM-----IDILCTSGGKITNLRRVTYLVM  623 (976)
Q Consensus       555 Q~~~~~~~~~~~~~~~~~~~~gg~~~~~~---~---~~l~~~~~Iiv~Tp~~L-----~~~l~~~~~~~~~l~~~~~vVl  623 (976)
                      .....+.+    +.+.+..+....+..+.   +   ...+....|++.||+.-     ..+|..    +.+-.-+.||||
T Consensus        76 DQiDHL~~----LKVp~~SLNSKlSt~ER~ri~~DL~~ekp~~K~LYITPE~AAt~~FQ~lLn~----L~~r~~L~Y~vV  147 (641)
T KOG0352|consen   76 DQIDHLKR----LKVPCESLNSKLSTVERSRIMGDLAKEKPTIKMLYITPEGAATDGFQKLLNG----LANRDVLRYIVV  147 (641)
T ss_pred             HHHHHHHh----cCCchhHhcchhhHHHHHHHHHHHHhcCCceeEEEEchhhhhhhhHHHHHHH----HhhhceeeeEEe
Confidence            66666665    34445444444433332   2   23344679999999873     333322    123345789999


Q ss_pred             cCcccccccC--CchHHHHHH--HhcCCCCcEEEEeccCcHHHHHH--HHHHcCCCeEEEeCCcccccCCceEEEEe-cC
Q 002040          624 DEADRMFDMG--FEPQITRIV--QNIRPDRQTVLFSATFPRQVEIL--ARKVLNKPVEIQVGGRSVVNKDITQLVEV-RP  696 (976)
Q Consensus       624 DEah~~~~~~--f~~~i~~il--~~~~~~~q~i~~SAT~~~~~~~l--~~~~l~~~~~i~~~~~~~~~~~i~q~~~~-~~  696 (976)
                      ||||+..+||  |.+.+..+-  ...-+...-|.+|||.++.+..-  +...+.+|+.+.-.  +....++...+.+ ..
T Consensus       148 DEAHCVSQWGHDFRPDYL~LG~LRS~~~~vpwvALTATA~~~VqEDi~~qL~L~~PVAiFkT--P~FR~NLFYD~~~K~~  225 (641)
T KOG0352|consen  148 DEAHCVSQWGHDFRPDYLTLGSLRSVCPGVPWVALTATANAKVQEDIAFQLKLRNPVAIFKT--PTFRDNLFYDNHMKSF  225 (641)
T ss_pred             chhhhHhhhccccCcchhhhhhHHhhCCCCceEEeecccChhHHHHHHHHHhhcCcHHhccC--cchhhhhhHHHHHHHH
Confidence            9999999997  888887663  33446677899999999988654  34456777654321  1111111100000 00


Q ss_pred             cchHHHHHHHHHHhhhc------------CCcEEEEecCHHHHHHHHHHHHHCCCCceeccCCCCHHHHHHHHHHhccCC
Q 002040          697 ESDRFLRLLELLGEWYE------------KGKILIFVHSQEKCDALFRDLLKHGYPCLSLHGAKDQTDRESTISDFKSNV  764 (976)
Q Consensus       697 ~~~k~~~l~~~l~~~~~------------~~kvLIF~~s~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~  764 (976)
                      -.+-+..|..+....+.            .|-.||||.|+..|+.++-.|...|+++..+|.++...+|..+-+.|++|+
T Consensus       226 I~D~~~~LaDF~~~~LG~~~~~~~~~K~~~GCGIVYCRTR~~cEq~AI~l~~~Gi~A~AYHAGLK~~ERTeVQe~WM~~~  305 (641)
T KOG0352|consen  226 ITDCLTVLADFSSSNLGKHEKASQNKKTFTGCGIVYCRTRNECEQVAIMLEIAGIPAMAYHAGLKKKERTEVQEKWMNNE  305 (641)
T ss_pred             hhhHhHhHHHHHHHhcCChhhhhcCCCCcCcceEEEeccHHHHHHHHHHhhhcCcchHHHhcccccchhHHHHHHHhcCC
Confidence            11222333333222211            246799999999999999999999999999999999999999999999999


Q ss_pred             ccEEEecCcccccCCCCCCcEEEEeCCCCCHHHHHHHhcccCCCCCccEEEEEecCCCcCchHHHHHH
Q 002040          765 CNLLIATSVAARGLDVKELELVINFDAPNHYEDYVHRVGRTGRAGRKGCAITFISEEDAKYSPDLVKA  832 (976)
Q Consensus       765 ~~vLVaT~v~~~GlDi~~v~~VI~~d~p~s~~~y~Qr~GR~gR~g~~g~~~~~~~~~d~~~~~~i~~~  832 (976)
                      +.||+||..+++|+|-|+|.+||++++|.|++.|.|-.||+||.|...+|.+||+.+|...+..|+..
T Consensus       306 ~PvI~AT~SFGMGVDKp~VRFViHW~~~qn~AgYYQESGRAGRDGk~SyCRLYYsR~D~~~i~FLi~~  373 (641)
T KOG0352|consen  306 IPVIAATVSFGMGVDKPDVRFVIHWSPSQNLAGYYQESGRAGRDGKRSYCRLYYSRQDKNALNFLVSG  373 (641)
T ss_pred             CCEEEEEeccccccCCcceeEEEecCchhhhHHHHHhccccccCCCccceeeeecccchHHHHHHHhh
Confidence            99999999999999999999999999999999999999999999999999999999988777766653

>COG1204 Superfamily II helicase [General function prediction only]

Probab=100.00  E-value=1.3e-32  Score=330.53  Aligned_cols=332  Identities=22%  Similarity=0.266  Sum_probs=247.6

Q ss_pred             CCCHHHHHHHHHcCCCCCcHHHHHHHHHHh-cCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHH
Q 002040          473 GLTSKIMETIRKLNYEKPMPIQAQALPVIM-SGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRE  551 (976)
Q Consensus       473 ~l~~~l~~~l~~~~~~~p~~~Q~~~i~~il-~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~  551 (976)
                      .+...+...+...++..++|.|+.++...+ .+.|+|+++|||||||+++++.|++.+.+.       +.++|+|||+++
T Consensus        15 ~~~~~v~~i~~~~~~~el~~~qq~av~~~~~~~~N~li~aPTgsGKTlIA~lai~~~l~~~-------~~k~vYivPlkA   87 (766)
T COG1204          15 KLDDRVLEILKGDGIDELFNPQQEAVEKGLLSDENVLISAPTGSGKTLIALLAILSTLLEG-------GGKVVYIVPLKA   87 (766)
T ss_pred             cccHHHHHHhccCChHHhhHHHHHHhhccccCCCcEEEEcCCCCchHHHHHHHHHHHHHhc-------CCcEEEEeChHH
Confidence            356677777788888788888888887655 569999999999999999999999998864       567999999999


Q ss_pred             HHHHHHHHHHHHHhhcCcEEEEeeCCCChHHHHHHHhcCCeEEEeCchhHHHHHHhcCCcccccCCceEEEecCcccccc
Q 002040          552 LVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFD  631 (976)
Q Consensus       552 La~Q~~~~~~~~~~~~~~~~~~~~gg~~~~~~~~~l~~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDEah~~~~  631 (976)
                      ||.+.+.+|+ .+..+|++|...+|+......   ...+++|||+||+.+-.++.+...   .+..+++|||||+|.+.+
T Consensus        88 La~Ek~~~~~-~~~~~GirV~~~TgD~~~~~~---~l~~~~ViVtT~EK~Dsl~R~~~~---~~~~V~lvViDEiH~l~d  160 (766)
T COG1204          88 LAEEKYEEFS-RLEELGIRVGISTGDYDLDDE---RLARYDVIVTTPEKLDSLTRKRPS---WIEEVDLVVIDEIHLLGD  160 (766)
T ss_pred             HHHHHHHHhh-hHHhcCCEEEEecCCcccchh---hhccCCEEEEchHHhhHhhhcCcc---hhhcccEEEEeeeeecCC
Confidence            9999999999 456789999999998864431   224599999999999777665432   566899999999998877


Q ss_pred             cCCchHHHHHHHhc---CCCCcEEEEeccCcHHHHHHHHHHcCCCeEEEeCCcc-cccCCceEEEEecCcch------H-
Q 002040          632 MGFEPQITRIVQNI---RPDRQTVLFSATFPRQVEILARKVLNKPVEIQVGGRS-VVNKDITQLVEVRPESD------R-  700 (976)
Q Consensus       632 ~~f~~~i~~il~~~---~~~~q~i~~SAT~~~~~~~l~~~~l~~~~~i~~~~~~-~~~~~i~q~~~~~~~~~------k-  700 (976)
                      ...++.+..|+...   ....|+|++|||+|+..+ ++...-.+++.......+ .......+.+.......      . 
T Consensus       161 ~~RG~~lE~iv~r~~~~~~~~rivgLSATlpN~~e-vA~wL~a~~~~~~~rp~~l~~~v~~~~~~~~~~~~~k~~~~~~~  239 (766)
T COG1204         161 RTRGPVLESIVARMRRLNELIRIVGLSATLPNAEE-VADWLNAKLVESDWRPVPLRRGVPYVGAFLGADGKKKTWPLLID  239 (766)
T ss_pred             cccCceehhHHHHHHhhCcceEEEEEeeecCCHHH-HHHHhCCcccccCCCCcccccCCccceEEEEecCccccccccch
Confidence            75666666665544   445799999999987644 555554444411111111 11112223333222222      1 


Q ss_pred             HHHHHHHHHhhhcCCcEEEEecCHHHHHHHHHHHHHC-------------------------------------CCCcee
Q 002040          701 FLRLLELLGEWYEKGKILIFVHSQEKCDALFRDLLKH-------------------------------------GYPCLS  743 (976)
Q Consensus       701 ~~~l~~~l~~~~~~~kvLIF~~s~~~~~~l~~~L~~~-------------------------------------~~~~~~  743 (976)
                      ...+...+.....++++||||+++..+...+..|...                                     -..+..
T Consensus       240 ~~~~~~v~~~~~~~~qvLvFv~sR~~a~~~A~~l~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~l~e~v~~Gvaf  319 (766)
T COG1204         240 NLALELVLESLAEGGQVLVFVHSRKEAEKTAKKLRIKMSATLSDDEKIVLDEGASPILIPETPTSEDEELAELVLRGVAF  319 (766)
T ss_pred             HHHHHHHHHHHhcCCeEEEEEecCchHHHHHHHHHHHHhhcCChhhhhhccccccccccccccccchHHHHHHHHhCccc
Confidence            2223333333345779999999999999888888731                                     124678


Q ss_pred             ccCCCCHHHHHHHHHHhccCCccEEEecCcccccCCCCCCcEEE----EeC-----CCCCHHHHHHHhcccCCCCC--cc
Q 002040          744 LHGAKDQTDRESTISDFKSNVCNLLIATSVAARGLDVKELELVI----NFD-----APNHYEDYVHRVGRTGRAGR--KG  812 (976)
Q Consensus       744 lhg~~~~~~R~~~~~~F~~g~~~vLVaT~v~~~GlDi~~v~~VI----~~d-----~p~s~~~y~Qr~GR~gR~g~--~g  812 (976)
                      +|++++..+|..+...|+.|.++|||||+.++.|+|+|.-.+||    .|+     .+.+..+|+|++|||||.|-  .|
T Consensus       320 HhAGL~~~~R~~vE~~Fr~g~ikVlv~TpTLA~GVNLPA~~VIIk~~~~y~~~~g~~~i~~~dv~QM~GRAGRPg~d~~G  399 (766)
T COG1204         320 HHAGLPREDRQLVEDAFRKGKIKVLVSTPTLAAGVNLPARTVIIKDTRRYDPKGGIVDIPVLDVLQMAGRAGRPGYDDYG  399 (766)
T ss_pred             cccCCCHHHHHHHHHHHhcCCceEEEechHHhhhcCCcceEEEEeeeEEEcCCCCeEECchhhHhhccCcCCCCCcCCCC
Confidence            99999999999999999999999999999999999999877777    377     56678899999999999875  46


Q ss_pred             EEEEEec
Q 002040          813 CAITFIS  819 (976)
Q Consensus       813 ~~~~~~~  819 (976)
                      .++++.+
T Consensus       400 ~~~i~~~  406 (766)
T COG1204         400 EAIILAT  406 (766)
T ss_pred             cEEEEec
Confidence            6666663

>TIGR01967 DEAH_box_HrpA ATP-dependent helicase HrpA

Probab=100.00  E-value=5.8e-33  Score=343.47  Aligned_cols=303  Identities=24%  Similarity=0.307  Sum_probs=219.5

Q ss_pred             HHHHHHHhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHHHHhhcCcEEEEe
Q 002040          495 AQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVMGVRCVPV  574 (976)
Q Consensus       495 ~~~i~~il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~~~~~~~~~~~~~  574 (976)
                      .+.+..|..++.+||+|+||||||++  +|.+..-..     .+....++++.|.|..|..+...+   +..+|..+...
T Consensus        73 ~~Il~~l~~~~vvii~g~TGSGKTTq--lPq~lle~~-----~~~~~~I~~tQPRRlAA~svA~Rv---A~elg~~lG~~  142 (1283)
T TIGR01967        73 EDIAEAIAENQVVIIAGETGSGKTTQ--LPKICLELG-----RGSHGLIGHTQPRRLAARTVAQRI---AEELGTPLGEK  142 (1283)
T ss_pred             HHHHHHHHhCceEEEeCCCCCCcHHH--HHHHHHHcC-----CCCCceEecCCccHHHHHHHHHHH---HHHhCCCcceE
Confidence            35666677778889999999999995  454432211     112235666779988877665444   44456666666


Q ss_pred             eCCCChHHHHHHHhcCCeEEEeCchhHHHHHHhcCCcccccCCceEEEecCcc-cccccCCchHHHHHHHhcCCCCcEEE
Q 002040          575 YGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEAD-RMFDMGFEPQITRIVQNIRPDRQTVL  653 (976)
Q Consensus       575 ~gg~~~~~~~~~l~~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDEah-~~~~~~f~~~i~~il~~~~~~~q~i~  653 (976)
                      +|+......  ....++.|+|||+|+|+..+...    ..|..+++||||||| ++++.+|...+..-+...+++.|+|+
T Consensus       143 VGY~vR~~~--~~s~~T~I~~~TdGiLLr~l~~d----~~L~~~~~IIIDEaHERsL~~D~LL~lLk~il~~rpdLKlIl  216 (1283)
T TIGR01967       143 VGYKVRFHD--QVSSNTLVKLMTDGILLAETQQD----RFLSRYDTIIIDEAHERSLNIDFLLGYLKQLLPRRPDLKIII  216 (1283)
T ss_pred             EeeEEcCCc--ccCCCceeeeccccHHHHHhhhC----cccccCcEEEEcCcchhhccchhHHHHHHHHHhhCCCCeEEE
Confidence            665322221  23456899999999999988654    358899999999999 79999988764443444567899999


Q ss_pred             EeccCcHHHHHHHHHHcCCCeEEEeCCcccccCCceEEEEecCc------chHHHHHHHHHHhhh--cCCcEEEEecCHH
Q 002040          654 FSATFPRQVEILARKVLNKPVEIQVGGRSVVNKDITQLVEVRPE------SDRFLRLLELLGEWY--EKGKILIFVHSQE  725 (976)
Q Consensus       654 ~SAT~~~~~~~l~~~~l~~~~~i~~~~~~~~~~~i~q~~~~~~~------~~k~~~l~~~l~~~~--~~~kvLIF~~s~~  725 (976)
                      ||||++.  ..++..|...|+ +.+.+...+   +...+.....      ..+...++..+....  ..|.+||||++..
T Consensus       217 mSATld~--~~fa~~F~~apv-I~V~Gr~~P---Vev~Y~~~~~~~~~~~~~~~~~i~~~I~~l~~~~~GdILVFLpg~~  290 (1283)
T TIGR01967       217 TSATIDP--ERFSRHFNNAPI-IEVSGRTYP---VEVRYRPLVEEQEDDDLDQLEAILDAVDELFAEGPGDILIFLPGER  290 (1283)
T ss_pred             EeCCcCH--HHHHHHhcCCCE-EEECCCccc---ceeEEecccccccchhhhHHHHHHHHHHHHHhhCCCCEEEeCCCHH
Confidence            9999975  345555544554 556555443   2222221111      123444444444332  4589999999999


Q ss_pred             HHHHHHHHHHHCC---CCceeccCCCCHHHHHHHHHHhccCCccEEEecCcccccCCCCCCcEEEEeCC-----------
Q 002040          726 KCDALFRDLLKHG---YPCLSLHGAKDQTDRESTISDFKSNVCNLLIATSVAARGLDVKELELVINFDA-----------  791 (976)
Q Consensus       726 ~~~~l~~~L~~~~---~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLVaT~v~~~GlDi~~v~~VI~~d~-----------  791 (976)
                      ++..++..|...+   +.+..+||.|++.++..++..+  +..+|||||+++++|||||+|.+||+++.           
T Consensus       291 EI~~l~~~L~~~~~~~~~VlpLhg~Ls~~eQ~~vf~~~--~~rkIVLATNIAEtSLTIpgV~yVIDsGl~r~~~yd~~~~  368 (1283)
T TIGR01967       291 EIRDAAEILRKRNLRHTEILPLYARLSNKEQQRVFQPH--SGRRIVLATNVAETSLTVPGIHYVIDTGTARISRYSYRTK  368 (1283)
T ss_pred             HHHHHHHHHHhcCCCCcEEEeccCCCCHHHHHHHhCCC--CCceEEEeccHHHhccccCCeeEEEeCCCccccccccccC
Confidence            9999999998864   4588999999999999997654  34789999999999999999999999884           


Q ss_pred             -------CCCHHHHHHHhcccCCCCCccEEEEEecCCC
Q 002040          792 -------PNHYEDYVHRVGRTGRAGRKGCAITFISEED  822 (976)
Q Consensus       792 -------p~s~~~y~Qr~GR~gR~g~~g~~~~~~~~~d  822 (976)
                             |.|.++|+||+|||||.| +|.||.||++.+
T Consensus       369 ~~~L~~~~ISkasa~QRaGRAGR~~-~G~cyRLyte~~  405 (1283)
T TIGR01967       369 VQRLPIEPISQASANQRKGRCGRVA-PGICIRLYSEED  405 (1283)
T ss_pred             ccccCCccCCHHHHHHHhhhhCCCC-CceEEEecCHHH
Confidence                   346689999999999998 999999998654

This model represents HrpA, one of two related but uncharacterized DEAH-box ATP-dependent helicases in many Proteobacteria and a few high-GC Gram-positive bacteria. HrpA is about 1300 amino acids long, while its paralog HrpB, also uncharacterized, is about 800 amino acids long. Related characterized eukarotic proteins are RNA helicases associated with pre-mRNA processing.

>KOG0351 consensus ATP-dependent DNA helicase [Replication, recombination and repair]

Probab=100.00  E-value=6.4e-33  Score=334.61  Aligned_cols=332  Identities=22%  Similarity=0.340  Sum_probs=269.8

Q ss_pred             HHHHcCCCCCcHHHHHHHHHHhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHH
Q 002040          481 TIRKLNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDI  560 (976)
Q Consensus       481 ~l~~~~~~~p~~~Q~~~i~~il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~  560 (976)
                      ....+|+..++|-|.++|..++.|+|+++.+|||.||+++|.+|++-.           ++.+|||.|..+|..-+   +
T Consensus       256 l~~~Fg~~~FR~~Q~eaI~~~l~Gkd~fvlmpTG~GKSLCYQlPA~l~-----------~gitvVISPL~SLm~DQ---v  321 (941)
T KOG0351|consen  256 LKEVFGHKGFRPNQLEAINATLSGKDCFVLMPTGGGKSLCYQLPALLL-----------GGVTVVISPLISLMQDQ---V  321 (941)
T ss_pred             HHHHhccccCChhHHHHHHHHHcCCceEEEeecCCceeeEeecccccc-----------CCceEEeccHHHHHHHH---H
Confidence            344699999999999999999999999999999999999999998733           45889999999997644   4


Q ss_pred             HHHHhhcCcEEEEeeCCCChHHHH---HHHhcC---CeEEEeCchhHHHHHHhcCCcccccCC---ceEEEecCcccccc
Q 002040          561 RKFAKVMGVRCVPVYGGSGVAQQI---SELKRG---TEIVVCTPGRMIDILCTSGGKITNLRR---VTYLVMDEADRMFD  631 (976)
Q Consensus       561 ~~~~~~~~~~~~~~~gg~~~~~~~---~~l~~~---~~Iiv~Tp~~L~~~l~~~~~~~~~l~~---~~~vVlDEah~~~~  631 (976)
                      ..+ ...++...++.++....++.   ..+..+   ++|++.||+.+...-... .....|..   +.++||||||+...
T Consensus       322 ~~L-~~~~I~a~~L~s~q~~~~~~~i~q~l~~~~~~ikilYvtPE~v~~~~~l~-~~~~~L~~~~~lal~vIDEAHCVSq  399 (941)
T KOG0351|consen  322 THL-SKKGIPACFLSSIQTAAERLAILQKLANGNPIIKILYVTPEKVVASEGLL-ESLADLYARGLLALFVIDEAHCVSQ  399 (941)
T ss_pred             Hhh-hhcCcceeeccccccHHHHHHHHHHHhCCCCeEEEEEeCHHHhhcccchh-hHHHhccCCCeeEEEEecHHHHhhh
Confidence            444 34689999999988876543   344443   699999999875422110 01234445   88999999999999


Q ss_pred             cC--CchHHHHHHH--hcCCCCcEEEEeccCcHHHHHHHHHHcC--CCeEEEeCCcccccCCceEEEEecCcchHHHHHH
Q 002040          632 MG--FEPQITRIVQ--NIRPDRQTVLFSATFPRQVEILARKVLN--KPVEIQVGGRSVVNKDITQLVEVRPESDRFLRLL  705 (976)
Q Consensus       632 ~~--f~~~i~~il~--~~~~~~q~i~~SAT~~~~~~~l~~~~l~--~~~~i~~~~~~~~~~~i~q~~~~~~~~~k~~~l~  705 (976)
                      ||  |.+.+..+..  ...+...+|.+|||.+..+..-+...|+  ++..   ....+...++...|...........++
T Consensus       400 WgHdFRp~Yk~l~~l~~~~~~vP~iALTATAT~~v~~DIi~~L~l~~~~~---~~~sfnR~NL~yeV~~k~~~~~~~~~~  476 (941)
T KOG0351|consen  400 WGHDFRPSYKRLGLLRIRFPGVPFIALTATATERVREDVIRSLGLRNPEL---FKSSFNRPNLKYEVSPKTDKDALLDIL  476 (941)
T ss_pred             hcccccHHHHHHHHHHhhCCCCCeEEeehhccHHHHHHHHHHhCCCCcce---ecccCCCCCceEEEEeccCccchHHHH
Confidence            97  8888876543  3334578999999998887665555544  4442   235566667766555555456666777


Q ss_pred             HHHHhhhcCCcEEEEecCHHHHHHHHHHHHHCCCCceeccCCCCHHHHHHHHHHhccCCccEEEecCcccccCCCCCCcE
Q 002040          706 ELLGEWYEKGKILIFVHSQEKCDALFRDLLKHGYPCLSLHGAKDQTDRESTISDFKSNVCNLLIATSVAARGLDVKELEL  785 (976)
Q Consensus       706 ~~l~~~~~~~kvLIF~~s~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLVaT~v~~~GlDi~~v~~  785 (976)
                      ..+..+.+.+.+||||.++.+|+.++..|...|+.+..||++|+..+|..+-..|..++++|+|||=++++|||.|+|..
T Consensus       477 ~~~~~~~~~~s~IIYC~sr~~ce~vs~~L~~~~~~a~~YHAGl~~~~R~~Vq~~w~~~~~~VivATVAFGMGIdK~DVR~  556 (941)
T KOG0351|consen  477 EESKLRHPDQSGIIYCLSRKECEQVSAVLRSLGKSAAFYHAGLPPKERETVQKAWMSDKIRVIVATVAFGMGIDKPDVRF  556 (941)
T ss_pred             HHhhhcCCCCCeEEEeCCcchHHHHHHHHHHhchhhHhhhcCCCHHHHHHHHHHHhcCCCeEEEEEeeccCCCCCCceeE
Confidence            77788888899999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEEeCCCCCHHHHHHHhcccCCCCCccEEEEEecCCCcCchHHHHH
Q 002040          786 VINFDAPNHYEDYVHRVGRTGRAGRKGCAITFISEEDAKYSPDLVK  831 (976)
Q Consensus       786 VI~~d~p~s~~~y~Qr~GR~gR~g~~g~~~~~~~~~d~~~~~~i~~  831 (976)
                      ||||..|.+++.|.|-+|||||.|....|++||...|...+..++.
T Consensus       557 ViH~~lPks~E~YYQE~GRAGRDG~~s~C~l~y~~~D~~~l~~ll~  602 (941)
T KOG0351|consen  557 VIHYSLPKSFEGYYQEAGRAGRDGLPSSCVLLYGYADISELRRLLT  602 (941)
T ss_pred             EEECCCchhHHHHHHhccccCcCCCcceeEEecchhHHHHHHHHHH
Confidence            9999999999999999999999999999999999876655544443

>TIGR03158 cas3_cyano CRISPR-associated helicase, Cyano-type

Probab=100.00  E-value=5.4e-32  Score=304.85  Aligned_cols=292  Identities=19%  Similarity=0.224  Sum_probs=202.9

Q ss_pred             HHHHHHHHHhcCCC--EEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHHHHhhc---
Q 002040          493 IQAQALPVIMSGRD--CIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVM---  567 (976)
Q Consensus       493 ~Q~~~i~~il~g~d--~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~~~~~~---  567 (976)
                      +|.++++.+..+.+  +++++|||||||++|++|++..           +.++++++|+++|+.|+++.+..++..+   
T Consensus         1 hQ~~~~~~~~~~~~~~~~i~apTGsGKT~~~~~~~l~~-----------~~~~~~~~P~~aL~~~~~~~~~~~~~~~~~~   69 (357)
T TIGR03158         1 HQVATFEALQSKDADIIFNTAPTGAGKTLAWLTPLLHG-----------ENDTIALYPTNALIEDQTEAIKEFVDVFKPE   69 (357)
T ss_pred             CHHHHHHHHHcCCCCEEEEECCCCCCHHHHHHHHHHHc-----------CCCEEEEeChHHHHHHHHHHHHHHHHhcCCC
Confidence            59999999998874  7889999999999999998842           3357999999999999999999988544   


Q ss_pred             -CcEEEEeeCCCChH--HHH-----------------HHH-hcCCeEEEeCchhHHHHHHhcCC-----cccccCCceEE
Q 002040          568 -GVRCVPVYGGSGVA--QQI-----------------SEL-KRGTEIVVCTPGRMIDILCTSGG-----KITNLRRVTYL  621 (976)
Q Consensus       568 -~~~~~~~~gg~~~~--~~~-----------------~~l-~~~~~Iiv~Tp~~L~~~l~~~~~-----~~~~l~~~~~v  621 (976)
                       ++.+..+.|.....  ...                 ..+ ...+.|+++||+.|..++.....     ....+..+++|
T Consensus        70 ~~~~v~~~~g~~~~d~~~~~~~~~~~~~g~~~~~~~r~~~~~~~p~illT~p~~l~~llr~~~~~~~~~~~~~~~~~~~i  149 (357)
T TIGR03158        70 RDVNLLHVSKATLKDIKEYANDKVGSSKGEKLYNLLRNPIGTSTPIILLTNPDIFVYLTRFAYIDRGDIAAGFYTKFSTV  149 (357)
T ss_pred             CCceEEEecCCchHHHHHhhhhhcccCccchhhhhHHHHHhcCCCCEEEecHHHHHHHHhhhccCcccchhhhhcCCCEE
Confidence             45555555542211  000                 011 12568888889888655432110     01125789999


Q ss_pred             EecCcccccccC-----CchHHHHHHHhcCCCCcEEEEeccCcHHHHHHHHHH--cCCCeEEEeCCccc-----------
Q 002040          622 VMDEADRMFDMG-----FEPQITRIVQNIRPDRQTVLFSATFPRQVEILARKV--LNKPVEIQVGGRSV-----------  683 (976)
Q Consensus       622 VlDEah~~~~~~-----f~~~i~~il~~~~~~~q~i~~SAT~~~~~~~l~~~~--l~~~~~i~~~~~~~-----------  683 (976)
                      ||||+|.+..++     |......++.......++|++|||+++.+.......  ++.++... .+...           
T Consensus       150 V~DE~H~~~~~~~~~~~~~l~~~~~~~~~~~~~~~i~lSAT~~~~~~~~l~~~~~~~~~~~~v-~g~~~~~~~~~~~~~~  228 (357)
T TIGR03158       150 IFDEFHLYDAKQLVGMLFLLAYMQLIRFFECRRKFVFLSATPDPALILRLQNAKQAGVKIAPI-DGEKYQFPDNPELEAD  228 (357)
T ss_pred             EEecccccCcccchhhhhhhHHHHHHHhhhcCCcEEEEecCCCHHHHHHHHhccccCceeeee-cCcccccCCChhhhcc
Confidence            999999865433     222334444444445799999999999877766654  44444322 22200           


Q ss_pred             --------ccCCceEEEEecCcchHHHH---HHHHHHhhh---cCCcEEEEecCHHHHHHHHHHHHHCC--CCceeccCC
Q 002040          684 --------VNKDITQLVEVRPESDRFLR---LLELLGEWY---EKGKILIFVHSQEKCDALFRDLLKHG--YPCLSLHGA  747 (976)
Q Consensus       684 --------~~~~i~q~~~~~~~~~k~~~---l~~~l~~~~---~~~kvLIF~~s~~~~~~l~~~L~~~~--~~~~~lhg~  747 (976)
                              +.+.+.+.+.. ....+...   ++..+.+..   ..+++||||+++..++.++..|...+  +.+..+||.
T Consensus       229 ~~~~~~~~~~~~i~~~~~~-~~~~~~~~l~~l~~~i~~~~~~~~~~k~LIf~nt~~~~~~l~~~L~~~~~~~~~~~l~g~  307 (357)
T TIGR03158       229 NKTQSFRPVLPPVELELIP-APDFKEEELSELAEEVIERFRQLPGERGAIILDSLDEVNRLSDLLQQQGLGDDIGRITGF  307 (357)
T ss_pred             ccccccceeccceEEEEEe-CCchhHHHHHHHHHHHHHHHhccCCCeEEEEECCHHHHHHHHHHHhhhCCCceEEeeecC
Confidence                    00234443333 22233322   333333322   45699999999999999999999864  578899999


Q ss_pred             CCHHHHHHHHHHhccCCccEEEecCcccccCCCCCCcEEEEeCCCCCHHHHHHHhcccC
Q 002040          748 KDQTDRESTISDFKSNVCNLLIATSVAARGLDVKELELVINFDAPNHYEDYVHRVGRTG  806 (976)
Q Consensus       748 ~~~~~R~~~~~~F~~g~~~vLVaT~v~~~GlDi~~v~~VI~~d~p~s~~~y~Qr~GR~g  806 (976)
                      +++..|..+      +...|||||+++++||||+.+ +|| ++ |.++..|+||+||+|
T Consensus       308 ~~~~~R~~~------~~~~iLVaTdv~~rGiDi~~~-~vi-~~-p~~~~~yiqR~GR~g  357 (357)
T TIGR03158       308 APKKDRERA------MQFDILLGTSTVDVGVDFKRD-WLI-FS-ARDAAAFWQRLGRLG  357 (357)
T ss_pred             CCHHHHHHh------ccCCEEEEecHHhcccCCCCc-eEE-EC-CCCHHHHhhhcccCC
Confidence            999998765      378899999999999999987 666 55 889999999999997

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.

>KOG0354 consensus DEAD-box like helicase [General function prediction only]

Probab=100.00  E-value=1.6e-32  Score=316.38  Aligned_cols=320  Identities=24%  Similarity=0.300  Sum_probs=227.4

Q ss_pred             CCCcHHHHHHHHHHhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHHHHhhc
Q 002040          488 EKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVM  567 (976)
Q Consensus       488 ~~p~~~Q~~~i~~il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~~~~~~  567 (976)
                      ..++.+|.+.+...| |+++||++|||+|||++++..|++|+...+      ..++|+++||+.|+.|....+..++.. 
T Consensus        61 ~~lR~YQ~eivq~AL-gkNtii~lPTG~GKTfIAa~Vm~nh~rw~p------~~KiVF~aP~~pLv~QQ~a~~~~~~~~-  132 (746)
T KOG0354|consen   61 LELRNYQEELVQPAL-GKNTIIALPTGSGKTFIAAVIMKNHFEWRP------KGKVVFLAPTRPLVNQQIACFSIYLIP-  132 (746)
T ss_pred             ccccHHHHHHhHHhh-cCCeEEEeecCCCccchHHHHHHHHHhcCC------cceEEEeeCCchHHHHHHHHHhhccCc-
Confidence            468899999999999 999999999999999999999999988764      368999999999999998777766543 


Q ss_pred             CcEEEEeeCCCChHHHHHHHhcCCeEEEeCchhHHHHHHhcCCcccccCCceEEEecCcccccccC-CchHHHHHHHhcC
Q 002040          568 GVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMG-FEPQITRIVQNIR  646 (976)
Q Consensus       568 ~~~~~~~~gg~~~~~~~~~l~~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDEah~~~~~~-f~~~i~~il~~~~  646 (976)
                       ..+....||.........+-...+|+|+||..|.+.|.....  ..|+.|.+|||||||+-.... |...+..++....
T Consensus       133 -~~~T~~l~~~~~~~~r~~i~~s~~vff~TpQil~ndL~~~~~--~~ls~fs~iv~DE~Hra~kn~~Y~~Vmr~~l~~k~  209 (746)
T KOG0354|consen  133 -YSVTGQLGDTVPRSNRGEIVASKRVFFRTPQILENDLKSGLH--DELSDFSLIVFDECHRTSKNHPYNNIMREYLDLKN  209 (746)
T ss_pred             -ccceeeccCccCCCchhhhhcccceEEeChHhhhhhcccccc--cccceEEEEEEcccccccccccHHHHHHHHHHhhh
Confidence             455555666333222334555689999999999988865432  237889999999999765433 3334435554444


Q ss_pred             CCCcEEEEeccCcHHHHHHHHHHcCCCeEEEe------------------------------------------------
Q 002040          647 PDRQTVLFSATFPRQVEILARKVLNKPVEIQV------------------------------------------------  678 (976)
Q Consensus       647 ~~~q~i~~SAT~~~~~~~l~~~~l~~~~~i~~------------------------------------------------  678 (976)
                      ...|+|++|||+...+.....-..+-.+.+.+                                                
T Consensus       210 ~~~qILgLTASpG~~~~~v~~~I~~L~asldvr~~ssi~~~y~~lr~~~~i~v~~~~~~~~~~~~f~~~i~p~l~~l~~~  289 (746)
T KOG0354|consen  210 QGNQILGLTASPGSKLEQVQNVIDNLCASLDVRTESSIKSNYEELREHVQIPVDLSLCERDIEDPFGMIIEPLLQQLQEE  289 (746)
T ss_pred             ccccEEEEecCCCccHHHHHHHHHhhheecccchhhhhhhhHHHHhccCcccCcHHHhhhhhhhhHHHHHHHHHHHHHhc
Confidence            45599999999865433221111000000000                                                


Q ss_pred             -------CC------------cccccCCceEE--------------------EE--------------------------
Q 002040          679 -------GG------------RSVVNKDITQL--------------------VE--------------------------  693 (976)
Q Consensus       679 -------~~------------~~~~~~~i~q~--------------------~~--------------------------  693 (976)
                             ..            .......-.+.                    +.                          
T Consensus       290 ~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~q~~~f~~~~~~~~~~~ll~~~gir~~~~l~~~~~f~~e~~~~k~~~~~~e  369 (746)
T KOG0354|consen  290 GLIEISDKSTSYEQWVVQAEKAAAPNGPENQRNCFYALHLRKYNLALLISDGIRFVDALDYLEDFYEEVALKKYLKLELE  369 (746)
T ss_pred             CccccccccccccchhhhhhhhhccCCCccchhhHHHHHHHHHHHHHHhhcchhhHHHHhhhhhhccccchhHHHHHHhc
Confidence                   00            00000000000                    00                          


Q ss_pred             ------------------ec--CcchHHHHHHHHHHhhhc---CCcEEEEecCHHHHHHHHHHHHHC---CCCceecc--
Q 002040          694 ------------------VR--PESDRFLRLLELLGEWYE---KGKILIFVHSQEKCDALFRDLLKH---GYPCLSLH--  745 (976)
Q Consensus       694 ------------------~~--~~~~k~~~l~~~l~~~~~---~~kvLIF~~s~~~~~~l~~~L~~~---~~~~~~lh--  745 (976)
                                        ..  ....|+..|.+.|...+.   ..++||||.++..|..|..+|...   |+....+-  
T Consensus       370 ~~~~~~~~~~m~~~~~l~~~~~~~npkle~l~~~l~e~f~~~~dsR~IIFve~R~sa~~l~~~l~~~~~~~ir~~~fiGq  449 (746)
T KOG0354|consen  370 ARLIRNFTENMNELEHLSLDPPKENPKLEKLVEILVEQFEQNPDSRTIIFVETRESALALKKWLLQLHELGIKAEIFIGQ  449 (746)
T ss_pred             chhhHHHHHHHHhhhhhhcCCCccChhHHHHHHHHHHHhhcCCCccEEEEEehHHHHHHHHHHHHhhhhcccccceeeec
Confidence                              00  012344445555544432   348999999999999999999832   33333333  


Q ss_pred             ------CCCCHHHHHHHHHHhccCCccEEEecCcccccCCCCCCcEEEEeCCCCCHHHHHHHhcccCCCCCccEEEEEec
Q 002040          746 ------GAKDQTDRESTISDFKSNVCNLLIATSVAARGLDVKELELVINFDAPNHYEDYVHRVGRTGRAGRKGCAITFIS  819 (976)
Q Consensus       746 ------g~~~~~~R~~~~~~F~~g~~~vLVaT~v~~~GlDi~~v~~VI~~d~p~s~~~y~Qr~GR~gR~g~~g~~~~~~~  819 (976)
                            .+|++.++..+++.|++|.++|||||+|++.||||+.|++||.||...|+...+||+|| ||+ ..|.|+++++
T Consensus       450 ~~s~~~~gmtqk~Q~evl~~Fr~G~~NvLVATSV~EEGLDI~ec~lVIcYd~~snpIrmIQrrGR-gRa-~ns~~vll~t  527 (746)
T KOG0354|consen  450 GKSTQSTGMTQKEQKEVLDKFRDGEINVLVATSVAEEGLDIGECNLVICYDYSSNPIRMVQRRGR-GRA-RNSKCVLLTT  527 (746)
T ss_pred             cccccccccCHHHHHHHHHHHhCCCccEEEEecchhccCCcccccEEEEecCCccHHHHHHHhcc-ccc-cCCeEEEEEc
Confidence                  37999999999999999999999999999999999999999999999999999999999 998 4788998888


Q ss_pred             C
Q 002040          820 E  820 (976)
Q Consensus       820 ~  820 (976)
                      .
T Consensus       528 ~  528 (746)
T KOG0354|consen  528 G  528 (746)
T ss_pred             c
Confidence            4

>TIGR00603 rad25 DNA repair helicase rad25

Probab=100.00  E-value=1.7e-31  Score=314.94  Aligned_cols=309  Identities=17%  Similarity=0.197  Sum_probs=212.5

Q ss_pred             CCCcHHHHHHHHHHhc-C--CCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHHHH
Q 002040          488 EKPMPIQAQALPVIMS-G--RDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFA  564 (976)
Q Consensus       488 ~~p~~~Q~~~i~~il~-g--~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~~~  564 (976)
                      ..|+|+|.+++..++. |  +..|+++|||+|||++.+..+.. +          +..+|||||+..|+.||.++|.+|+
T Consensus       254 ~~LRpYQ~eAl~~~~~~gr~r~GIIvLPtGaGKTlvai~aa~~-l----------~k~tLILvps~~Lv~QW~~ef~~~~  322 (732)
T TIGR00603       254 TQIRPYQEKSLSKMFGNGRARSGIIVLPCGAGKSLVGVTAACT-V----------KKSCLVLCTSAVSVEQWKQQFKMWS  322 (732)
T ss_pred             CCcCHHHHHHHHHHHhcCCCCCcEEEeCCCCChHHHHHHHHHH-h----------CCCEEEEeCcHHHHHHHHHHHHHhc
Confidence            3589999999999884 3  37899999999999997755543 2          2358999999999999999999987


Q ss_pred             hhcCcEEEEeeCCCChHHHHHHHhcCCeEEEeCchhHHHHHHhcCC-----cccccCCceEEEecCcccccccCCchHHH
Q 002040          565 KVMGVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGG-----KITNLRRVTYLVMDEADRMFDMGFEPQIT  639 (976)
Q Consensus       565 ~~~~~~~~~~~gg~~~~~~~~~l~~~~~Iiv~Tp~~L~~~l~~~~~-----~~~~l~~~~~vVlDEah~~~~~~f~~~i~  639 (976)
                      ......+..++|+....     +.....|+|+|+..+.........     ..+.-..|++||+||||++..    ..+.
T Consensus       323 ~l~~~~I~~~tg~~k~~-----~~~~~~VvVtTYq~l~~~~~r~~~~~~~l~~l~~~~~gLII~DEvH~lpA----~~fr  393 (732)
T TIGR00603       323 TIDDSQICRFTSDAKER-----FHGEAGVVVSTYSMVAHTGKRSYESEKVMEWLTNREWGLILLDEVHVVPA----AMFR  393 (732)
T ss_pred             CCCCceEEEEecCcccc-----cccCCcEEEEEHHHhhcccccchhhhHHHHHhccccCCEEEEEccccccH----HHHH
Confidence            54455566666653221     112368999999877432111000     011224689999999998753    4555


Q ss_pred             HHHHhcCCCCcEEEEeccCcHHHHH--HHHHHcCCCeEEEeCCcccccC----Cce-EEEE-------------------
Q 002040          640 RIVQNIRPDRQTVLFSATFPRQVEI--LARKVLNKPVEIQVGGRSVVNK----DIT-QLVE-------------------  693 (976)
Q Consensus       640 ~il~~~~~~~q~i~~SAT~~~~~~~--l~~~~l~~~~~i~~~~~~~~~~----~i~-q~~~-------------------  693 (976)
                      .++..+. ....|+|||||...-..  ....+++ |..+...-......    .+. ..+.                   
T Consensus       394 ~il~~l~-a~~RLGLTATP~ReD~~~~~L~~LiG-P~vye~~~~eLi~~G~LA~~~~~ev~v~~t~~~~~~yl~~~~~~k  471 (732)
T TIGR00603       394 RVLTIVQ-AHCKLGLTATLVREDDKITDLNFLIG-PKLYEANWMELQKKGFIANVQCAEVWCPMTPEFYREYLRENSRKR  471 (732)
T ss_pred             HHHHhcC-cCcEEEEeecCcccCCchhhhhhhcC-CeeeecCHHHHHhCCccccceEEEEEecCCHHHHHHHHHhcchhh
Confidence            5666653 34579999998643211  1222222 32222211111000    000 0000                   


Q ss_pred             ---ecCcchHHHHHHHHHHhhh-cCCcEEEEecCHHHHHHHHHHHHHCCCCceeccCCCCHHHHHHHHHHhccC-CccEE
Q 002040          694 ---VRPESDRFLRLLELLGEWY-EKGKILIFVHSQEKCDALFRDLLKHGYPCLSLHGAKDQTDRESTISDFKSN-VCNLL  768 (976)
Q Consensus       694 ---~~~~~~k~~~l~~~l~~~~-~~~kvLIF~~s~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g-~~~vL  768 (976)
                         ......|+..+..+|..+. .+.++||||.+...+..++..|     .+..|||.+++.+|..+++.|++| .+++|
T Consensus       472 ~~l~~~np~K~~~~~~Li~~he~~g~kiLVF~~~~~~l~~~a~~L-----~~~~I~G~ts~~ER~~il~~Fr~~~~i~vL  546 (732)
T TIGR00603       472 MLLYVMNPNKFRACQFLIRFHEQRGDKIIVFSDNVFALKEYAIKL-----GKPFIYGPTSQQERMQILQNFQHNPKVNTI  546 (732)
T ss_pred             hHHhhhChHHHHHHHHHHHHHhhcCCeEEEEeCCHHHHHHHHHHc-----CCceEECCCCHHHHHHHHHHHHhCCCccEE
Confidence               1112234444444554332 4569999999999999888877     356799999999999999999865 88999


Q ss_pred             EecCcccccCCCCCCcEEEEeCCCC-CHHHHHHHhcccCCCCCccEE-------EEEecCCCc
Q 002040          769 IATSVAARGLDVKELELVINFDAPN-HYEDYVHRVGRTGRAGRKGCA-------ITFISEEDA  823 (976)
Q Consensus       769 VaT~v~~~GlDi~~v~~VI~~d~p~-s~~~y~Qr~GR~gR~g~~g~~-------~~~~~~~d~  823 (976)
                      |+|+++.+|||+|++++||++++|. |...|+||+||++|.+..|.+       |+|++....
T Consensus       547 v~SkVgdeGIDlP~a~vvI~~s~~~gS~~q~iQRlGRilR~~~~~~~~~~~A~fY~lVs~dT~  609 (732)
T TIGR00603       547 FLSKVGDTSIDLPEANVLIQISSHYGSRRQEAQRLGRILRAKKGSDAEEYNAFFYSLVSKDTQ  609 (732)
T ss_pred             EEecccccccCCCCCCEEEEeCCCCCCHHHHHHHhcccccCCCCCccccccceEEEEecCCch
Confidence            9999999999999999999999985 999999999999998766554       888887643

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).

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

Probab=100.00  E-value=3.5e-31  Score=322.79  Aligned_cols=336  Identities=22%  Similarity=0.340  Sum_probs=261.6

Q ss_pred             CHHHHHHHHHcCCCCCcHHHHHHHHHHhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHH
Q 002040          475 TSKIMETIRKLNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQ  554 (976)
Q Consensus       475 ~~~l~~~l~~~~~~~p~~~Q~~~i~~il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~  554 (976)
                      ...+...|.+.|+..|++||.+|+..+.+|+++||+.+||||||.+|++||+.++...+.      .++|+|.||.+||+
T Consensus        56 ~~~l~~~l~~~g~~~lY~HQ~~A~~~~~~G~~vvVtTgTgSGKTe~FllPIld~~l~~~~------a~AL~lYPtnALa~  129 (851)
T COG1205          56 DESLKSALVKAGIERLYSHQVDALRLIREGRNVVVTTGTGSGKTESFLLPILDHLLRDPS------ARALLLYPTNALAN  129 (851)
T ss_pred             hhHHHHHHHHhccccccHHHHHHHHHHHCCCCEEEECCCCCchhHHHHHHHHHHHhhCcC------ccEEEEechhhhHh
Confidence            344577888899999999999999999999999999999999999999999999997642      27899999999999


Q ss_pred             HHHHHHHHHHhhcC--cEEEEeeCCCChHHHHHHHhcCCeEEEeCchhHHHHHHh-cCCcccccCCceEEEecCcccccc
Q 002040          555 QIHSDIRKFAKVMG--VRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCT-SGGKITNLRRVTYLVMDEADRMFD  631 (976)
Q Consensus       555 Q~~~~~~~~~~~~~--~~~~~~~gg~~~~~~~~~l~~~~~Iiv~Tp~~L~~~l~~-~~~~~~~l~~~~~vVlDEah~~~~  631 (976)
                      ...+.|.++...++  +.+....|.+...+....+...++||++||.+|-.++.. .......+.++.||||||+|..- 
T Consensus       130 DQ~~rl~~~~~~~~~~v~~~~y~Gdt~~~~r~~~~~~pp~IllTNpdMLh~~llr~~~~~~~~~~~Lk~lVvDElHtYr-  208 (851)
T COG1205         130 DQAERLRELISDLPGKVTFGRYTGDTPPEERRAIIRNPPDILLTNPDMLHYLLLRNHDAWLWLLRNLKYLVVDELHTYR-  208 (851)
T ss_pred             hHHHHHHHHHHhCCCcceeeeecCCCChHHHHHHHhCCCCEEEeCHHHHHHHhccCcchHHHHHhcCcEEEEecceecc-
Confidence            99999999999888  777777777777666566778899999999999764443 33334557789999999999532 


Q ss_pred             cCCchHHHHHH-------HhcCCCCcEEEEeccCcHHHHHHHHHHcCCCeEEEeCCcccccCCceEEEEecC--------
Q 002040          632 MGFEPQITRIV-------QNIRPDRQTVLFSATFPRQVEILARKVLNKPVEIQVGGRSVVNKDITQLVEVRP--------  696 (976)
Q Consensus       632 ~~f~~~i~~il-------~~~~~~~q~i~~SAT~~~~~~~l~~~~l~~~~~i~~~~~~~~~~~i~q~~~~~~--------  696 (976)
                      -.|+..+..++       ...+...|+|++|||+....+ ++..+++......+.....+....... ...+        
T Consensus       209 Gv~GS~vA~llRRL~~~~~~~~~~~q~i~~SAT~~np~e-~~~~l~~~~f~~~v~~~g~~~~~~~~~-~~~p~~~~~~~~  286 (851)
T COG1205         209 GVQGSEVALLLRRLLRRLRRYGSPLQIICTSATLANPGE-FAEELFGRDFEVPVDEDGSPRGLRYFV-RREPPIRELAES  286 (851)
T ss_pred             ccchhHHHHHHHHHHHHHhccCCCceEEEEeccccChHH-HHHHhcCCcceeeccCCCCCCCceEEE-EeCCcchhhhhh
Confidence            22444443333       333457899999999876544 666777666655444444443333322 2222        


Q ss_pred             -cchHHHHHHHHHHhhh-cCCcEEEEecCHHHHHHHH----HHHHHCC----CCceeccCCCCHHHHHHHHHHhccCCcc
Q 002040          697 -ESDRFLRLLELLGEWY-EKGKILIFVHSQEKCDALF----RDLLKHG----YPCLSLHGAKDQTDRESTISDFKSNVCN  766 (976)
Q Consensus       697 -~~~k~~~l~~~l~~~~-~~~kvLIF~~s~~~~~~l~----~~L~~~~----~~~~~lhg~~~~~~R~~~~~~F~~g~~~  766 (976)
                       ...+...+..++.... .+-++|+|+.+...++.+.    ..+...+    ..+..++|+|...+|..+...|+.|+..
T Consensus       287 ~r~s~~~~~~~~~~~~~~~~~~tL~F~~sr~~~e~~~~~~~~~~~~~~~~l~~~v~~~~~~~~~~er~~ie~~~~~g~~~  366 (851)
T COG1205         287 IRRSALAELATLAALLVRNGIQTLVFFRSRKQVELLYLSPRRRLVREGGKLLDAVSTYRAGLHREERRRIEAEFKEGELL  366 (851)
T ss_pred             cccchHHHHHHHHHHHHHcCceEEEEEehhhhhhhhhhchhHHHhhcchhhhhheeeccccCCHHHHHHHHHHHhcCCcc
Confidence             1133333333333333 3459999999999999987    4444445    5688999999999999999999999999


Q ss_pred             EEEecCcccccCCCCCCcEEEEeCCCC-CHHHHHHHhcccCCCCCccEEEEEec
Q 002040          767 LLIATSVAARGLDVKELELVINFDAPN-HYEDYVHRVGRTGRAGRKGCAITFIS  819 (976)
Q Consensus       767 vLVaT~v~~~GlDi~~v~~VI~~d~p~-s~~~y~Qr~GR~gR~g~~g~~~~~~~  819 (976)
                      ++|+|++++.|+||-++..||+++.|. +...++|+.||+||.++.+..++++.
T Consensus       367 ~~~st~AlelgidiG~ldavi~~g~P~~s~~~~~Q~~GRaGR~~~~~l~~~v~~  420 (851)
T COG1205         367 GVIATNALELGIDIGSLDAVIAYGYPGVSVLSFRQRAGRAGRRGQESLVLVVLR  420 (851)
T ss_pred             EEecchhhhhceeehhhhhHhhcCCCCchHHHHHHhhhhccCCCCCceEEEEeC
Confidence            999999999999999999999999999 89999999999999997776666654

>PRK04914 ATP-dependent helicase HepA; Validated

Probab=99.98  E-value=2.7e-30  Score=315.24  Aligned_cols=332  Identities=15%  Similarity=0.167  Sum_probs=219.6

Q ss_pred             CCcHHHHHHHHHHhcC--CCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHHHHhh
Q 002040          489 KPMPIQAQALPVIMSG--RDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKV  566 (976)
Q Consensus       489 ~p~~~Q~~~i~~il~g--~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~~~~~  566 (976)
                      .|.|||..++..++..  ..+|++.++|.|||+.+++.+...+...      ....+|||||+ .|+.||..++.+.+  
T Consensus       152 ~l~pHQl~~~~~vl~~~~~R~LLADEvGLGKTIeAglil~~l~~~g------~~~rvLIVvP~-sL~~QW~~El~~kF--  222 (956)
T PRK04914        152 SLIPHQLYIAHEVGRRHAPRVLLADEVGLGKTIEAGMIIHQQLLTG------RAERVLILVPE-TLQHQWLVEMLRRF--  222 (956)
T ss_pred             CCCHHHHHHHHHHhhccCCCEEEEeCCcCcHHHHHHHHHHHHHHcC------CCCcEEEEcCH-HHHHHHHHHHHHHh--
Confidence            5889999998887654  4799999999999999877666554432      23469999997 79999999987653  


Q ss_pred             cCcEEEEeeCCCChHHHHH--HHhcCCeEEEeCchhHHHHHHhcCCcccccCCceEEEecCcccccccC-CchHHHHHHH
Q 002040          567 MGVRCVPVYGGSGVAQQIS--ELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMG-FEPQITRIVQ  643 (976)
Q Consensus       567 ~~~~~~~~~gg~~~~~~~~--~l~~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDEah~~~~~~-f~~~i~~il~  643 (976)
                       ++.+.++.++........  ......+++|||++.|...-...  ....-..|++|||||||++-+.. ........+.
T Consensus       223 -~l~~~i~~~~~~~~~~~~~~~pf~~~~~vI~S~~~l~~~~~~~--~~l~~~~wdlvIvDEAH~lk~~~~~~s~~y~~v~  299 (956)
T PRK04914        223 -NLRFSLFDEERYAEAQHDADNPFETEQLVICSLDFLRRNKQRL--EQALAAEWDLLVVDEAHHLVWSEEAPSREYQVVE  299 (956)
T ss_pred             -CCCeEEEcCcchhhhcccccCccccCcEEEEEHHHhhhCHHHH--HHHhhcCCCEEEEechhhhccCCCCcCHHHHHHH
Confidence             455444333221110000  01113689999998775411000  00112368999999999986321 1111122333


Q ss_pred             hc-CCCCcEEEEeccCcHH-H------------------HHH-------------HH-----------------HHcCC-
Q 002040          644 NI-RPDRQTVLFSATFPRQ-V------------------EIL-------------AR-----------------KVLNK-  672 (976)
Q Consensus       644 ~~-~~~~q~i~~SAT~~~~-~------------------~~l-------------~~-----------------~~l~~-  672 (976)
                      .+ .....+|++||||-.. .                  ..+             +.                 .++.. 
T Consensus       300 ~La~~~~~~LLLTATP~q~~~~e~falL~lLdP~~f~~~~~F~~e~~~~~~~a~~v~~l~~~~~~~~~~~~~l~~ll~~~  379 (956)
T PRK04914        300 QLAEVIPGVLLLTATPEQLGQESHFARLRLLDPDRFHDYEAFVEEQQQYRPVADAVQALLAGEKLSDDALNALGELLGEQ  379 (956)
T ss_pred             HHhhccCCEEEEEcCcccCCcHHHHHhhhhhCCCcCCCHHHHHHHHHhhHHHHHHHHHHhcCCcCCHHHHHHHHHHhccc
Confidence            33 2345789999997320 0                  000             00                 00000 


Q ss_pred             ----------------------------------CeEEEeCC---cccccCCceEEEEe---------------------
Q 002040          673 ----------------------------------PVEIQVGG---RSVVNKDITQLVEV---------------------  694 (976)
Q Consensus       673 ----------------------------------~~~i~~~~---~~~~~~~i~q~~~~---------------------  694 (976)
                                                        .+.+.-..   ..++ ....+.+.+                     
T Consensus       380 ~~~~l~~~~~~~~~~~~~~~~~~i~~L~d~hg~~rvm~RntR~~v~~fp-~R~~~~~~l~~~~~y~~~~~~~~~~~~~~~  458 (956)
T PRK04914        380 DIEPLLQAANSDSEEAQAARQELISELLDRHGTGRVLFRNTRAAVKGFP-KRELHPIPLPLPEQYQTAIKVSLEARARDM  458 (956)
T ss_pred             chhHHHhhhcccccccHHHHHHHHHHHHhhcCcceEEEeccHHhhcCCC-cCceeEeecCCCHHHHHHHHHhHHHHHHhh
Confidence                                              00000000   0000 001111111                     


Q ss_pred             ----------------cCcchHHHHHHHHHHhhhcCCcEEEEecCHHHHHHHHHHH-HHCCCCceeccCCCCHHHHHHHH
Q 002040          695 ----------------RPESDRFLRLLELLGEWYEKGKILIFVHSQEKCDALFRDL-LKHGYPCLSLHGAKDQTDRESTI  757 (976)
Q Consensus       695 ----------------~~~~~k~~~l~~~l~~~~~~~kvLIF~~s~~~~~~l~~~L-~~~~~~~~~lhg~~~~~~R~~~~  757 (976)
                                      ...+.|+..|+.+|... ...++||||+++..+..|+..| ...|+.+..|||+|++.+|..++
T Consensus       459 l~pe~~~~~~~~~~~~~~~d~Ki~~L~~~L~~~-~~~KvLVF~~~~~t~~~L~~~L~~~~Gi~~~~ihG~~s~~eR~~~~  537 (956)
T PRK04914        459 LYPEQIYQEFEDNATWWNFDPRVEWLIDFLKSH-RSEKVLVICAKAATALQLEQALREREGIRAAVFHEGMSIIERDRAA  537 (956)
T ss_pred             cCHHHHHHHHhhhhhccccCHHHHHHHHHHHhc-CCCeEEEEeCcHHHHHHHHHHHhhccCeeEEEEECCCCHHHHHHHH
Confidence                            11233555666666543 3579999999999999999999 46799999999999999999999


Q ss_pred             HHhccC--CccEEEecCcccccCCCCCCcEEEEeCCCCCHHHHHHHhcccCCCCCccEEEEEecCCCcCchHHHHHHHh
Q 002040          758 SDFKSN--VCNLLIATSVAARGLDVKELELVINFDAPNHYEDYVHRVGRTGRAGRKGCAITFISEEDAKYSPDLVKALE  834 (976)
Q Consensus       758 ~~F~~g--~~~vLVaT~v~~~GlDi~~v~~VI~~d~p~s~~~y~Qr~GR~gR~g~~g~~~~~~~~~d~~~~~~i~~~l~  834 (976)
                      ..|+++  .+.|||||+++++|+|++.+++|||||+||||..|+||+||+||.|+++.+.+++..........|...+.
T Consensus       538 ~~F~~~~~~~~VLIsTdvgseGlNlq~a~~VInfDlP~nP~~~eQRIGR~~RiGQ~~~V~i~~~~~~~t~~e~i~~~~~  616 (956)
T PRK04914        538 AYFADEEDGAQVLLCSEIGSEGRNFQFASHLVLFDLPFNPDLLEQRIGRLDRIGQKHDIQIHVPYLEGTAQERLFRWYH  616 (956)
T ss_pred             HHHhcCCCCccEEEechhhccCCCcccccEEEEecCCCCHHHHHHHhcccccCCCCceEEEEEccCCCCHHHHHHHHHh
Confidence            999974  69999999999999999999999999999999999999999999999999888876655555555555443

>KOG0952 consensus DNA/RNA helicase MER3/SLH1, DEAD-box superfamily [RNA processing and modification]

Probab=99.98  E-value=9.6e-31  Score=303.34  Aligned_cols=362  Identities=22%  Similarity=0.291  Sum_probs=258.7

Q ss_pred             HcCCCCCcHHHHHHHHHHh-cCCCEEEEcCCCCchHHHHHHHHHHHHhcC--CCCCCCCCCeEEEEccCHHHHHHHHHHH
Q 002040          484 KLNYEKPMPIQAQALPVIM-SGRDCIGVAKTGSGKTLAFVLPMLRHIKDQ--PPVAAGDGPVGLIMAPTRELVQQIHSDI  560 (976)
Q Consensus       484 ~~~~~~p~~~Q~~~i~~il-~g~d~i~~a~TGsGKT~~~~l~il~~l~~~--~~~~~~~~~~vLIl~Ptr~La~Q~~~~~  560 (976)
                      -++|..+..+|..++|.+. ++.|+|||||||||||.+|+|.||+.+..+  +.....++.++++|+|+++||..++..|
T Consensus       105 ~f~f~~fN~iQS~vFp~aY~SneNMLIcAPTGsGKT~la~L~ILr~ik~~~~~~~i~k~~fKiVYIaPmKALa~Em~~~~  184 (1230)
T KOG0952|consen  105 FFSFEEFNRIQSEVFPVAYKSNENMLICAPTGSGKTVLAELCILRTIKEHEEQGDIAKDDFKIVYIAPMKALAAEMVDKF  184 (1230)
T ss_pred             cccHHHHHHHHHHhhhhhhcCCCCEEEECCCCCCchHHHHHHHHHHHHhhccccccccCCceEEEEechHHHHHHHHHHH
Confidence            4778889999999999987 567999999999999999999999998852  2223345789999999999999999999


Q ss_pred             HHHHhhcCcEEEEeeCCCChHHHHHHHhcCCeEEEeCchhHHHHHHhc-CCcccccCCceEEEecCcccccccCCchHHH
Q 002040          561 RKFAKVMGVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTS-GGKITNLRRVTYLVMDEADRMFDMGFEPQIT  639 (976)
Q Consensus       561 ~~~~~~~~~~~~~~~gg~~~~~~~~~l~~~~~Iiv~Tp~~L~~~l~~~-~~~~~~l~~~~~vVlDEah~~~~~~f~~~i~  639 (976)
                      .+-+..+|+.|..++|.+.....-  + ..++|||+||+.+ |.+.+. .+....+..+.+|||||+|. +....++.+.
T Consensus       185 ~kkl~~~gi~v~ELTGD~ql~~te--i-~~tqiiVTTPEKw-DvvTRk~~~d~~l~~~V~LviIDEVHl-Lhd~RGpvlE  259 (1230)
T KOG0952|consen  185 SKKLAPLGISVRELTGDTQLTKTE--I-ADTQIIVTTPEKW-DVVTRKSVGDSALFSLVRLVIIDEVHL-LHDDRGPVLE  259 (1230)
T ss_pred             hhhcccccceEEEecCcchhhHHH--H-HhcCEEEecccce-eeeeeeeccchhhhhheeeEEeeeehh-hcCcccchHH
Confidence            988888999999999988554432  2 3499999999987 444332 22233467799999999994 4555677777


Q ss_pred             HHHHhc-------CCCCcEEEEeccCcHHHHHHHHHHcCCC-eEEEeCCcccccCCceEEEEecCcc-----------hH
Q 002040          640 RIVQNI-------RPDRQTVLFSATFPRQVEILARKVLNKP-VEIQVGGRSVVNKDITQLVEVRPES-----------DR  700 (976)
Q Consensus       640 ~il~~~-------~~~~q~i~~SAT~~~~~~~l~~~~l~~~-~~i~~~~~~~~~~~i~q~~~~~~~~-----------~k  700 (976)
                      .|+...       ....++|++|||+|+-.. ++..+-.+| .-+......+.+..+.+.+.-....           ..
T Consensus       260 tiVaRtlr~vessqs~IRivgLSATlPN~eD-vA~fL~vn~~~glfsFd~~yRPvpL~~~~iG~k~~~~~~~~~~~d~~~  338 (1230)
T KOG0952|consen  260 TIVARTLRLVESSQSMIRIVGLSATLPNYED-VARFLRVNPYAGLFSFDQRYRPVPLTQGFIGIKGKKNRQQKKNIDEVC  338 (1230)
T ss_pred             HHHHHHHHHHHhhhhheEEEEeeccCCCHHH-HHHHhcCCCccceeeecccccccceeeeEEeeecccchhhhhhHHHHH
Confidence            776543       345689999999997644 554444432 2233233334444555555433322           11


Q ss_pred             HHHHHHHHHhhhcCCcEEEEecCHHHHHHHHHHHHHC-----------------------CCCceeccCCCCHHHHHHHH
Q 002040          701 FLRLLELLGEWYEKGKILIFVHSQEKCDALFRDLLKH-----------------------GYPCLSLHGAKDQTDRESTI  757 (976)
Q Consensus       701 ~~~l~~~l~~~~~~~kvLIF~~s~~~~~~l~~~L~~~-----------------------~~~~~~lhg~~~~~~R~~~~  757 (976)
                      +..+.+.+   ..+.+++|||.++......+..|.+.                       ...+...|++|.-.+|..+.
T Consensus       339 ~~kv~e~~---~~g~qVlvFvhsR~~Ti~tA~~l~~~a~~~g~~~~f~~~~~~k~l~elf~~g~~iHhAGm~r~DR~l~E  415 (1230)
T KOG0952|consen  339 YDKVVEFL---QEGHQVLVFVHSRNETIRTAKKLRERAETNGEKDLFLPSPRNKQLKELFQQGMGIHHAGMLRSDRQLVE  415 (1230)
T ss_pred             HHHHHHHH---HcCCeEEEEEecChHHHHHHHHHHHHHHhcCcccccCCChhhHHHHHHHHhhhhhcccccchhhHHHHH
Confidence            22222332   34669999999999888888888653                       13467789999999999999


Q ss_pred             HHhccCCccEEEecCcccccCCCCCCcEEEE----eCCCC------CHHHHHHHhcccCCC--CCccEEEEEecCCCcCc
Q 002040          758 SDFKSNVCNLLIATSVAARGLDVKELELVIN----FDAPN------HYEDYVHRVGRTGRA--GRKGCAITFISEEDAKY  825 (976)
Q Consensus       758 ~~F~~g~~~vLVaT~v~~~GlDi~~v~~VI~----~d~p~------s~~~y~Qr~GR~gR~--g~~g~~~~~~~~~d~~~  825 (976)
                      ..|..|.++||+||..++.|+|+|.--++|-    ||.-.      ...+.+|..|||||.  +..|.++++.+.+...+
T Consensus       416 ~~F~~G~i~vL~cTaTLAwGVNLPA~aViIKGT~~ydsskg~f~dlgilDVlQifGRAGRPqFd~~G~giIiTt~dkl~~  495 (1230)
T KOG0952|consen  416 KEFKEGHIKVLCCTATLAWGVNLPAYAVIIKGTQVYDSSKGSFVDLGILDVLQIFGRAGRPQFDSSGEGIIITTRDKLDH  495 (1230)
T ss_pred             HHHhcCCceEEEecceeeeccCCcceEEEecCCcccccccCceeeehHHHHHHHHhccCCCCCCCCceEEEEecccHHHH
Confidence            9999999999999999999999997766662    44433      356789999999995  45688887766543333


Q ss_pred             hHHHHHHHhhccCCCChHHHHHHHHHHHHHhh
Q 002040          826 SPDLVKALELSEQVVPDDLKALADSFMAKVNQ  857 (976)
Q Consensus       826 ~~~i~~~l~~~~~~vp~~l~~l~~~~~~~~~~  857 (976)
                         .+..|......-...+..|++.+.+.+..
T Consensus       496 ---Y~sLl~~~~piES~~~~~L~dnLnAEi~L  524 (1230)
T KOG0952|consen  496 ---YESLLTGQNPIESQLLPCLIDNLNAEISL  524 (1230)
T ss_pred             ---HHHHHcCCChhHHHHHHHHHHhhhhheee
Confidence               33333333222234456777777666543

>KOG0353 consensus ATP-dependent DNA helicase [General function prediction only]

Probab=99.97  E-value=1.5e-30  Score=270.29  Aligned_cols=337  Identities=19%  Similarity=0.325  Sum_probs=260.4

Q ss_pred             cCCCCHHHHHHHH-HcCCCCCcHHHHHHHHHHhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccC
Q 002040          471 QTGLTSKIMETIR-KLNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPT  549 (976)
Q Consensus       471 ~~~l~~~l~~~l~-~~~~~~p~~~Q~~~i~~il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Pt  549 (976)
                      .|+.+....+.|+ .+.+.+++|.|..+|++.|.|.+++++.|||.||+++|.+|+|..           ...+|||||.
T Consensus        75 ~fpws~e~~~ilk~~f~lekfrplq~~ain~~ma~ed~~lil~tgggkslcyqlpal~a-----------dg~alvi~pl  143 (695)
T KOG0353|consen   75 DFPWSDEAKDILKEQFHLEKFRPLQLAAINATMAGEDAFLILPTGGGKSLCYQLPALCA-----------DGFALVICPL  143 (695)
T ss_pred             CCCCchHHHHHHHHHhhHHhcChhHHHHhhhhhccCceEEEEeCCCccchhhhhhHHhc-----------CCceEeechh
Confidence            4556666666666 477889999999999999999999999999999999999999843           4578999999


Q ss_pred             HHHHHHHHHHHHHHHhhcCcEEEEeeCCCChHHHH---HHH---hcCCeEEEeCchhHHHH--HHhcCCcccccCCceEE
Q 002040          550 RELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQI---SEL---KRGTEIVVCTPGRMIDI--LCTSGGKITNLRRVTYL  621 (976)
Q Consensus       550 r~La~Q~~~~~~~~~~~~~~~~~~~~gg~~~~~~~---~~l---~~~~~Iiv~Tp~~L~~~--l~~~~~~~~~l~~~~~v  621 (976)
                      ..|.....-.++.    +|+....+...++..+..   ..+   .....+|+.||+.+...  +.+.-.+......+.+|
T Consensus       144 islmedqil~lkq----lgi~as~lnansske~~k~v~~~i~nkdse~kliyvtpekiaksk~~mnkleka~~~~~~~~i  219 (695)
T KOG0353|consen  144 ISLMEDQILQLKQ----LGIDASMLNANSSKEEAKRVEAAITNKDSEFKLIYVTPEKIAKSKKFMNKLEKALEAGFFKLI  219 (695)
T ss_pred             HHHHHHHHHHHHH----hCcchhhccCcccHHHHHHHHHHHcCCCceeEEEEecHHHHHHHHHHHHHHHHHhhcceeEEE
Confidence            9998766555555    577776666555544321   111   12358999999987421  11111122345678899


Q ss_pred             EecCcccccccC--CchHHH--HHHHhcCCCCcEEEEeccCcHHHHHHHHHHcCCCeEEEeCCcccccCCceEEEEecC-
Q 002040          622 VMDEADRMFDMG--FEPQIT--RIVQNIRPDRQTVLFSATFPRQVEILARKVLNKPVEIQVGGRSVVNKDITQLVEVRP-  696 (976)
Q Consensus       622 VlDEah~~~~~~--f~~~i~--~il~~~~~~~q~i~~SAT~~~~~~~l~~~~l~~~~~i~~~~~~~~~~~i~q~~~~~~-  696 (976)
                      -|||+|+-..||  |.+.+.  .|+..--+...+|+++||.++.+..-+...+.-...+++ ..++..+++...+...+ 
T Consensus       220 aidevhccsqwghdfr~dy~~l~ilkrqf~~~~iigltatatn~vl~d~k~il~ie~~~tf-~a~fnr~nl~yev~qkp~  298 (695)
T KOG0353|consen  220 AIDEVHCCSQWGHDFRPDYKALGILKRQFKGAPIIGLTATATNHVLDDAKDILCIEAAFTF-RAGFNRPNLKYEVRQKPG  298 (695)
T ss_pred             eecceeehhhhCcccCcchHHHHHHHHhCCCCceeeeehhhhcchhhHHHHHHhHHhhhee-ecccCCCCceeEeeeCCC
Confidence            999999998887  777654  455555577889999999998887777766654332222 13344455554443333 


Q ss_pred             -cchHHHHHHHHHHhhhcCCcEEEEecCHHHHHHHHHHHHHCCCCceeccCCCCHHHHHHHHHHhccCCccEEEecCccc
Q 002040          697 -ESDRFLRLLELLGEWYEKGKILIFVHSQEKCDALFRDLLKHGYPCLSLHGAKDQTDRESTISDFKSNVCNLLIATSVAA  775 (976)
Q Consensus       697 -~~~k~~~l~~~l~~~~~~~kvLIF~~s~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLVaT~v~~  775 (976)
                       ..+-+..+..+|..-+.+...||||-++.+|+.++..|..+|+.+..+|..|.+.++.-+-+.|..|++.|+|||-+++
T Consensus       299 n~dd~~edi~k~i~~~f~gqsgiiyc~sq~d~ekva~alkn~gi~a~~yha~lep~dks~~hq~w~a~eiqvivatvafg  378 (695)
T KOG0353|consen  299 NEDDCIEDIAKLIKGDFAGQSGIIYCFSQKDCEKVAKALKNHGIHAGAYHANLEPEDKSGAHQGWIAGEIQVIVATVAFG  378 (695)
T ss_pred             ChHHHHHHHHHHhccccCCCcceEEEeccccHHHHHHHHHhcCccccccccccCccccccccccccccceEEEEEEeeec
Confidence             2345556666666656666789999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccCCCCCCcEEEEeCCCCCHHHHHH-------------------------------------------HhcccCCCCCcc
Q 002040          776 RGLDVKELELVINFDAPNHYEDYVH-------------------------------------------RVGRTGRAGRKG  812 (976)
Q Consensus       776 ~GlDi~~v~~VI~~d~p~s~~~y~Q-------------------------------------------r~GR~gR~g~~g  812 (976)
                      +|||-|+|.+||+..+|.++++|.|                                           -.||+||.|.+.
T Consensus       379 mgidkpdvrfvihhsl~ksienyyqasarillrmtkqknksdtggstqinilevctnfkiffavfsekesgragrd~~~a  458 (695)
T KOG0353|consen  379 MGIDKPDVRFVIHHSLPKSIENYYQASARILLRMTKQKNKSDTGGSTQINILEVCTNFKIFFAVFSEKESGRAGRDDMKA  458 (695)
T ss_pred             ccCCCCCeeEEEecccchhHHHHHHHHHHHHHHHhhhcccccCCCcceeehhhhhccceeeeeeecchhccccccCCCcc
Confidence            9999999999999999999999999                                           679999999999


Q ss_pred             EEEEEecCCCc
Q 002040          813 CAITFISEEDA  823 (976)
Q Consensus       813 ~~~~~~~~~d~  823 (976)
                      .|++||.-.|.
T Consensus       459 ~cilyy~~~di  469 (695)
T KOG0353|consen  459 DCILYYGFADI  469 (695)
T ss_pred             cEEEEechHHH
Confidence            99999875443

>KOG0922 consensus DEAH-box RNA helicase [RNA processing and modification]

Probab=99.97  E-value=1.2e-29  Score=285.25  Aligned_cols=309  Identities=20%  Similarity=0.244  Sum_probs=237.1

Q ss_pred             HHHHHHHHHHhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHHHHhhcCcEE
Q 002040          492 PIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVMGVRC  571 (976)
Q Consensus       492 ~~Q~~~i~~il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~~~~~~~~~~  571 (976)
                      .+-.+.+..+..++-+||+|+||||||++.-..++..-..       ....+.+.-|.|..|..+   .++++..++..+
T Consensus        54 ~~r~~il~~ve~nqvlIviGeTGsGKSTQipQyL~eaG~~-------~~g~I~~TQPRRVAavsl---A~RVAeE~~~~l  123 (674)
T KOG0922|consen   54 KYRDQILYAVEDNQVLIVIGETGSGKSTQIPQYLAEAGFA-------SSGKIACTQPRRVAAVSL---AKRVAEEMGCQL  123 (674)
T ss_pred             HHHHHHHHHHHHCCEEEEEcCCCCCccccHhHHHHhcccc-------cCCcEEeecCchHHHHHH---HHHHHHHhCCCc
Confidence            3445777888889999999999999999754444433221       223378888999988855   455555666666


Q ss_pred             EEeeCCCChHHHHHHHhcCCeEEEeCchhHHHHHHhcCCcccccCCceEEEecCcc-cccccCCchHHHHHHHhcCCCCc
Q 002040          572 VPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEAD-RMFDMGFEPQITRIVQNIRPDRQ  650 (976)
Q Consensus       572 ~~~~gg~~~~~~~~~l~~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDEah-~~~~~~f~~~i~~il~~~~~~~q  650 (976)
                      ...+|....++..  ....+.|.++|.|.|+..+...    ..|..+++||||||| |.+..+....+.+-+...+++.+
T Consensus       124 G~~VGY~IRFed~--ts~~TrikymTDG~LLRE~l~D----p~LskYsvIIlDEAHERsl~TDiLlGlLKki~~~R~~Lk  197 (674)
T KOG0922|consen  124 GEEVGYTIRFEDS--TSKDTRIKYMTDGMLLREILKD----PLLSKYSVIILDEAHERSLHTDILLGLLKKILKKRPDLK  197 (674)
T ss_pred             CceeeeEEEeccc--CCCceeEEEecchHHHHHHhcC----CccccccEEEEechhhhhhHHHHHHHHHHHHHhcCCCce
Confidence            6666665554442  2235899999999999888654    578999999999999 77777766666666667778899


Q ss_pred             EEEEeccCcHHHHHHHHHHcCCCeEEEeCCcccccCCceEEEEecCcchHHHHHHHHHHhh---hcCCcEEEEecCHHHH
Q 002040          651 TVLFSATFPRQVEILARKVLNKPVEIQVGGRSVVNKDITQLVEVRPESDRFLRLLELLGEW---YEKGKILIFVHSQEKC  727 (976)
Q Consensus       651 ~i~~SAT~~~~~~~l~~~~l~~~~~i~~~~~~~~~~~i~q~~~~~~~~~k~~~l~~~l~~~---~~~~kvLIF~~s~~~~  727 (976)
                      +|+||||+...   .+..|+.+...+.+.++.++.   ...+...+..+.+...+..+.+.   .+.|.+|||.++++++
T Consensus       198 lIimSATlda~---kfS~yF~~a~i~~i~GR~fPV---ei~y~~~p~~dYv~a~~~tv~~Ih~~E~~GDILvFLtGqeEI  271 (674)
T KOG0922|consen  198 LIIMSATLDAE---KFSEYFNNAPILTIPGRTFPV---EILYLKEPTADYVDAALITVIQIHLTEPPGDILVFLTGQEEI  271 (674)
T ss_pred             EEEEeeeecHH---HHHHHhcCCceEeecCCCCce---eEEeccCCchhhHHHHHHHHHHHHccCCCCCEEEEeCCHHHH
Confidence            99999999754   566677776667777776653   33344445555555544443333   3678999999999999


Q ss_pred             HHHHHHHHHC----C--C--CceeccCCCCHHHHHHHHHHhccCCccEEEecCcccccCCCCCCcEEEEe--------CC
Q 002040          728 DALFRDLLKH----G--Y--PCLSLHGAKDQTDRESTISDFKSNVCNLLIATSVAARGLDVKELELVINF--------DA  791 (976)
Q Consensus       728 ~~l~~~L~~~----~--~--~~~~lhg~~~~~~R~~~~~~F~~g~~~vLVaT~v~~~GlDi~~v~~VI~~--------d~  791 (976)
                      +.++..|.+.    +  .  -++++||.++..++..++..-..|..+|+|||+++++.|.|+++.+||+-        ++
T Consensus       272 e~~~~~l~e~~~~~~~~~~~~~lply~aL~~e~Q~rvF~p~p~g~RKvIlsTNIAETSlTI~GI~YVVDsG~vK~~~y~p  351 (674)
T KOG0922|consen  272 EAACELLRERAKSLPEDCPELILPLYGALPSEEQSRVFDPAPPGKRKVILSTNIAETSLTIDGIRYVVDSGFVKQKKYNP  351 (674)
T ss_pred             HHHHHHHHHHhhhccccCcceeeeecccCCHHHhhccccCCCCCcceEEEEcceeeeeEEecceEEEEcCCceEEEeecc
Confidence            9999999875    1  1  25789999999999999999999999999999999999999999999973        33


Q ss_pred             ----------CCCHHHHHHHhcccCCCCCccEEEEEecCCCc
Q 002040          792 ----------PNHYEDYVHRVGRTGRAGRKGCAITFISEEDA  823 (976)
Q Consensus       792 ----------p~s~~~y~Qr~GR~gR~g~~g~~~~~~~~~d~  823 (976)
                                |.|.+...||.|||||.| +|.||.+|++.+.
T Consensus       352 ~~g~~~L~v~~ISkasA~QRaGRAGRt~-pGkcyRLYte~~~  392 (674)
T KOG0922|consen  352 RTGLDSLIVVPISKASANQRAGRAGRTG-PGKCYRLYTESAY  392 (674)
T ss_pred             ccCccceeEEechHHHHhhhcccCCCCC-CceEEEeeeHHHH
Confidence                      668889999999999997 9999999997643

>KOG0923 consensus mRNA splicing factor ATP-dependent RNA helicase [RNA processing and modification]

Probab=99.97  E-value=4.4e-30  Score=284.33  Aligned_cols=309  Identities=19%  Similarity=0.242  Sum_probs=244.7

Q ss_pred             cHHHHHHHHHHhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHHHHhhcCcE
Q 002040          491 MPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVMGVR  570 (976)
Q Consensus       491 ~~~Q~~~i~~il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~~~~~~~~~  570 (976)
                      +++-.+.|.+|..++-+||.|+||||||++.-..+...=+      ...|.++-+..|.|..|+.+   ..+++..+|++
T Consensus       267 y~ykdell~av~e~QVLiI~GeTGSGKTTQiPQyL~EaGy------tk~gk~IgcTQPRRVAAmSV---AaRVA~EMgvk  337 (902)
T KOG0923|consen  267 YPYKDELLKAVKEHQVLIIVGETGSGKTTQIPQYLYEAGY------TKGGKKIGCTQPRRVAAMSV---AARVAEEMGVK  337 (902)
T ss_pred             hhhHHHHHHHHHhCcEEEEEcCCCCCccccccHHHHhccc------ccCCceEeecCcchHHHHHH---HHHHHHHhCcc
Confidence            4677888999999999999999999999873333332211      12244578888999999855   45566678888


Q ss_pred             EEEeeCCCChHHHHHHHhcCCeEEEeCchhHHHHHHhcCCcccccCCceEEEecCcc-cccccCCchHHHHHHHhcCCCC
Q 002040          571 CVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEAD-RMFDMGFEPQITRIVQNIRPDR  649 (976)
Q Consensus       571 ~~~~~gg~~~~~~~~~l~~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDEah-~~~~~~f~~~i~~il~~~~~~~  649 (976)
                      ...-+|.+..++.+..  ..+-|-++|.|.|+..+...    ..|.++++||||||| +-+..+....+..-+..++|+.
T Consensus       338 LG~eVGYsIRFEdcTS--ekTvlKYMTDGmLlREfL~e----pdLasYSViiiDEAHERTL~TDILfgLvKDIar~RpdL  411 (902)
T KOG0923|consen  338 LGHEVGYSIRFEDCTS--EKTVLKYMTDGMLLREFLSE----PDLASYSVIIVDEAHERTLHTDILFGLVKDIARFRPDL  411 (902)
T ss_pred             cccccceEEEeccccC--cceeeeeecchhHHHHHhcc----ccccceeEEEeehhhhhhhhhhHHHHHHHHHHhhCCcc
Confidence            8777888777766433  45789999999999888665    689999999999999 7777777777777778889999


Q ss_pred             cEEEEeccCcHHHHHHHHHHcCCCeEEEeCCcccccCCceEEEEecCcchHHHHHHHHHHhhh---cCCcEEEEecCHHH
Q 002040          650 QTVLFSATFPRQVEILARKVLNKPVEIQVGGRSVVNKDITQLVEVRPESDRFLRLLELLGEWY---EKGKILIFVHSQEK  726 (976)
Q Consensus       650 q~i~~SAT~~~~~~~l~~~~l~~~~~i~~~~~~~~~~~i~q~~~~~~~~~k~~~l~~~l~~~~---~~~kvLIF~~s~~~  726 (976)
                      ++|+.|||+...   -+..|+.+...+.+.++-++   +...+...++.+.+...+..+.+.+   +.|.||||...+..
T Consensus       412 KllIsSAT~DAe---kFS~fFDdapIF~iPGRRyP---Vdi~Yt~~PEAdYldAai~tVlqIH~tqp~GDILVFltGQeE  485 (902)
T KOG0923|consen  412 KLLISSATMDAE---KFSAFFDDAPIFRIPGRRYP---VDIFYTKAPEADYLDAAIVTVLQIHLTQPLGDILVFLTGQEE  485 (902)
T ss_pred             eEEeeccccCHH---HHHHhccCCcEEeccCcccc---eeeecccCCchhHHHHHHhhheeeEeccCCccEEEEeccHHH
Confidence            999999999654   45566666555555555443   3445566677777777666665543   46899999999999


Q ss_pred             HHHHHHHHHHC---------CCCceeccCCCCHHHHHHHHHHhccCCccEEEecCcccccCCCCCCcEEEEeCC------
Q 002040          727 CDALFRDLLKH---------GYPCLSLHGAKDQTDRESTISDFKSNVCNLLIATSVAARGLDVKELELVINFDA------  791 (976)
Q Consensus       727 ~~~l~~~L~~~---------~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLVaT~v~~~GlDi~~v~~VI~~d~------  791 (976)
                      ++.....|...         .+-+++||+.++...+..|++.-..|..+|++||++|++.|.|++|.+||+-++      
T Consensus       486 IEt~~e~l~~~~~~LGski~eliv~PiYaNLPselQakIFePtP~gaRKVVLATNIAETSlTIdgI~yViDpGf~K~nsy  565 (902)
T KOG0923|consen  486 IETVKENLKERCRRLGSKIRELIVLPIYANLPSELQAKIFEPTPPGARKVVLATNIAETSLTIDGIKYVIDPGFVKQNSY  565 (902)
T ss_pred             HHHHHHHHHHHHHHhccccceEEEeeccccCChHHHHhhcCCCCCCceeEEEeecchhhceeecCeEEEecCccccccCc
Confidence            98888877653         356889999999999999999999999999999999999999999999997443      


Q ss_pred             ------------CCCHHHHHHHhcccCCCCCccEEEEEecCC
Q 002040          792 ------------PNHYEDYVHRVGRTGRAGRKGCAITFISEE  821 (976)
Q Consensus       792 ------------p~s~~~y~Qr~GR~gR~g~~g~~~~~~~~~  821 (976)
                                  |.|-++..||.||+||+| +|.||.+|+.+
T Consensus       566 nprtGmesL~v~piSKAsA~QRaGRAGRtg-PGKCfRLYt~~  606 (902)
T KOG0923|consen  566 NPRTGMESLLVTPISKASANQRAGRAGRTG-PGKCFRLYTAW  606 (902)
T ss_pred             CCCcCceeEEEeeechhhhhhhccccCCCC-CCceEEeechh
Confidence                        567788899999999998 99999999854

>PRK05580 primosome assembly protein PriA; Validated

Probab=99.97  E-value=8.2e-29  Score=299.31  Aligned_cols=309  Identities=20%  Similarity=0.264  Sum_probs=219.7

Q ss_pred             CCcHHHHHHHHHHhcC---CCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHHHHh
Q 002040          489 KPMPIQAQALPVIMSG---RDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAK  565 (976)
Q Consensus       489 ~p~~~Q~~~i~~il~g---~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~~~~  565 (976)
                      .|++.|.+++..+..+   +++++.|+||||||.+|+.++...+..        |.++|||+||++|+.|++..++..  
T Consensus       144 ~Lt~~Q~~ai~~i~~~~~~~~~Ll~~~TGSGKT~v~l~~i~~~l~~--------g~~vLvLvPt~~L~~Q~~~~l~~~--  213 (679)
T PRK05580        144 TLNPEQAAAVEAIRAAAGFSPFLLDGVTGSGKTEVYLQAIAEVLAQ--------GKQALVLVPEIALTPQMLARFRAR--  213 (679)
T ss_pred             CCCHHHHHHHHHHHhccCCCcEEEECCCCChHHHHHHHHHHHHHHc--------CCeEEEEeCcHHHHHHHHHHHHHH--
Confidence            5899999999999974   789999999999999998887766543        568999999999999999988875  


Q ss_pred             hcCcEEEEeeCCCChHHHHH---HHh-cCCeEEEeCchhHHHHHHhcCCcccccCCceEEEecCcccccccCC-ch--HH
Q 002040          566 VMGVRCVPVYGGSGVAQQIS---ELK-RGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMGF-EP--QI  638 (976)
Q Consensus       566 ~~~~~~~~~~gg~~~~~~~~---~l~-~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDEah~~~~~~f-~~--~i  638 (976)
                       +|..+..++|+.+..+...   .+. ...+|||+|++.+.          ..+.++++|||||+|.....+. .+  ..
T Consensus       214 -fg~~v~~~~s~~s~~~r~~~~~~~~~g~~~IVVgTrsal~----------~p~~~l~liVvDEeh~~s~~~~~~p~y~~  282 (679)
T PRK05580        214 -FGAPVAVLHSGLSDGERLDEWRKAKRGEAKVVIGARSALF----------LPFKNLGLIIVDEEHDSSYKQQEGPRYHA  282 (679)
T ss_pred             -hCCCEEEEECCCCHHHHHHHHHHHHcCCCCEEEeccHHhc----------ccccCCCEEEEECCCccccccCcCCCCcH
Confidence             4678899999987765433   233 34799999998762          3567899999999997543321 11  11


Q ss_pred             H--HHHHhcCCCCcEEEEeccCcHHHHHHHHHHcCCCeEEEeCCccccc-CCceEEEEecCc------chHHHHHHHHHH
Q 002040          639 T--RIVQNIRPDRQTVLFSATFPRQVEILARKVLNKPVEIQVGGRSVVN-KDITQLVEVRPE------SDRFLRLLELLG  709 (976)
Q Consensus       639 ~--~il~~~~~~~q~i~~SAT~~~~~~~l~~~~l~~~~~i~~~~~~~~~-~~i~q~~~~~~~------~~k~~~l~~~l~  709 (976)
                      .  .++.....+.++|++|||++......+..  +....+.+....... ......+.....      ..-...++..+.
T Consensus       283 r~va~~ra~~~~~~~il~SATps~~s~~~~~~--g~~~~~~l~~r~~~~~~p~v~~id~~~~~~~~~~~~ls~~l~~~i~  360 (679)
T PRK05580        283 RDLAVVRAKLENIPVVLGSATPSLESLANAQQ--GRYRLLRLTKRAGGARLPEVEIIDMRELLRGENGSFLSPPLLEAIK  360 (679)
T ss_pred             HHHHHHHhhccCCCEEEEcCCCCHHHHHHHhc--cceeEEEeccccccCCCCeEEEEechhhhhhcccCCCCHHHHHHHH
Confidence            1  23444557889999999988665433322  222222222221100 011111111110      001134555565


Q ss_pred             hhhcCC-cEEEEecCH------------------------------------------------------------HHHH
Q 002040          710 EWYEKG-KILIFVHSQ------------------------------------------------------------EKCD  728 (976)
Q Consensus       710 ~~~~~~-kvLIF~~s~------------------------------------------------------------~~~~  728 (976)
                      +....+ ++|||+|.+                                                            ..++
T Consensus       361 ~~l~~g~qvll~~nrrGy~~~~~C~~Cg~~~~C~~C~~~l~~h~~~~~l~Ch~Cg~~~~~~~~Cp~Cg~~~l~~~g~G~e  440 (679)
T PRK05580        361 QRLERGEQVLLFLNRRGYAPFLLCRDCGWVAECPHCDASLTLHRFQRRLRCHHCGYQEPIPKACPECGSTDLVPVGPGTE  440 (679)
T ss_pred             HHHHcCCeEEEEEcCCCCCCceEhhhCcCccCCCCCCCceeEECCCCeEECCCCcCCCCCCCCCCCCcCCeeEEeeccHH
Confidence            555444 899998752                                                            1345


Q ss_pred             HHHHHHHHC--CCCceeccCCCCH--HHHHHHHHHhccCCccEEEecCcccccCCCCCCcEEEEeCCC--CC--------
Q 002040          729 ALFRDLLKH--GYPCLSLHGAKDQ--TDRESTISDFKSNVCNLLIATSVAARGLDVKELELVINFDAP--NH--------  794 (976)
Q Consensus       729 ~l~~~L~~~--~~~~~~lhg~~~~--~~R~~~~~~F~~g~~~vLVaT~v~~~GlDi~~v~~VI~~d~p--~s--------  794 (976)
                      .+++.|...  ++++..+|+++.+  .+++.++..|.+|+++|||+|+++++|+|+|++++|++++.+  .+        
T Consensus       441 ~~~e~l~~~fp~~~v~~~~~d~~~~~~~~~~~l~~f~~g~~~ILVgT~~iakG~d~p~v~lV~il~aD~~l~~pdfra~E  520 (679)
T PRK05580        441 RLEEELAELFPEARILRIDRDTTRRKGALEQLLAQFARGEADILIGTQMLAKGHDFPNVTLVGVLDADLGLFSPDFRASE  520 (679)
T ss_pred             HHHHHHHHhCCCCcEEEEeccccccchhHHHHHHHHhcCCCCEEEEChhhccCCCCCCcCEEEEEcCchhccCCccchHH
Confidence            677777765  7889999999874  578999999999999999999999999999999999766554  22        


Q ss_pred             --HHHHHHHhcccCCCCCccEEEEEecC
Q 002040          795 --YEDYVHRVGRTGRAGRKGCAITFISE  820 (976)
Q Consensus       795 --~~~y~Qr~GR~gR~g~~g~~~~~~~~  820 (976)
                        ...|+|++||+||.+..|.|++....
T Consensus       521 r~~~~l~q~~GRagR~~~~g~viiqT~~  548 (679)
T PRK05580        521 RTFQLLTQVAGRAGRAEKPGEVLIQTYH  548 (679)
T ss_pred             HHHHHHHHHHhhccCCCCCCEEEEEeCC
Confidence              36789999999999999999876543

>PRK12899 secA preprotein translocase subunit SecA; Reviewed

Probab=99.97  E-value=2.2e-28  Score=289.04  Aligned_cols=183  Identities=17%  Similarity=0.248  Sum_probs=143.5

Q ss_pred             hhhhcCCHHHHHHHHhhcCcee-ccCCCCCcccccccCCCCHHHHHHHH-----HcCCCCC---cHHHHHHHHHHhcCCC
Q 002040          436 KEIARMTPEEVSAYRKQLELKI-HGKDVPKPIKTWHQTGLTSKIMETIR-----KLNYEKP---MPIQAQALPVIMSGRD  506 (976)
Q Consensus       436 ~~~~~~~~~~~~~~~~~~~i~~-~g~~~p~pi~~~~~~~l~~~l~~~l~-----~~~~~~p---~~~Q~~~i~~il~g~d  506 (976)
                      +.+..++.+++......+...+ .|..+ .. .-...|++...+...+.     ..||..|   +|+|.|+||.++.+++
T Consensus        32 ~~~~~lsd~eL~~kt~~~k~~l~~~~~l-d~-~l~eafal~re~~~r~lg~~~~~~G~~~p~~~tp~qvQ~I~~i~l~~g  109 (970)
T PRK12899         32 EKFSSLSDDELRNKTAELKQRYQDGESL-DK-LLPEAYGVVKNVCRRLAGTPVEVSGYHQQWDMVPYDVQILGAIAMHKG  109 (970)
T ss_pred             HHHHcCCHHHHHHHHHHHHHHHHcCCch-HH-HHHHHhCCCHHHHHHHhccccccccccCCCCCChHHHHHhhhhhcCCC
Confidence            4566777777665444443222 22211 11 11356888888887766     6899988   9999999999999999


Q ss_pred             EEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHHHHhhcCcEEEEeeCCCChHHHHHH
Q 002040          507 CIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQISE  586 (976)
Q Consensus       507 ~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~~~~~~~~~~~~~~gg~~~~~~~~~  586 (976)
                      +|+.++||+|||++|++|++..+...        ..++||+||++||.|+++++..++..+|+++.+++||.+...+...
T Consensus       110 vIAeaqTGeGKTLAf~LP~l~~aL~g--------~~v~IVTpTrELA~Qdae~m~~L~k~lGLsV~~i~GG~~~~eq~~~  181 (970)
T PRK12899        110 FITEMQTGEGKTLTAVMPLYLNALTG--------KPVHLVTVNDYLAQRDCEWVGSVLRWLGLTTGVLVSGSPLEKRKEI  181 (970)
T ss_pred             eEEEeCCCCChHHHHHHHHHHHHhhc--------CCeEEEeCCHHHHHHHHHHHHHHHhhcCCeEEEEeCCCCHHHHHHH
Confidence            99999999999999999999887642        2389999999999999999999999999999999999999988766


Q ss_pred             HhcCCeEEEeCchhH-HHHHHhcCCccc----ccCCceEEEecCccccc
Q 002040          587 LKRGTEIVVCTPGRM-IDILCTSGGKIT----NLRRVTYLVMDEADRMF  630 (976)
Q Consensus       587 l~~~~~Iiv~Tp~~L-~~~l~~~~~~~~----~l~~~~~vVlDEah~~~  630 (976)
                      +  +++|+||||++| +++|..+.....    -...+.++||||||.|+
T Consensus       182 y--~~DIVygTPgRLgfDyLrd~~~~~~~~~~vqr~~~~~IIDEADsmL  228 (970)
T PRK12899        182 Y--QCDVVYGTASEFGFDYLRDNSIATRKEEQVGRGFYFAIIDEVDSIL  228 (970)
T ss_pred             c--CCCEEEECCChhHHHHhhCCCCCcCHHHhhcccccEEEEechhhhh
Confidence            5  499999999999 999876421111    12356899999999874

>PRK13104 secA preprotein translocase subunit SecA; Reviewed

Probab=99.97  E-value=2.3e-28  Score=289.88  Aligned_cols=321  Identities=20%  Similarity=0.233  Sum_probs=231.2

Q ss_pred             cCCCCCcHHHHHHHHHHhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHHHH
Q 002040          485 LNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFA  564 (976)
Q Consensus       485 ~~~~~p~~~Q~~~i~~il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~~~  564 (976)
                      +|. .|++.|..+--++  +..-|+.++||+|||++|++|++..+..        |..|+||+||+.||.|.++++..++
T Consensus        79 lg~-~~ydvQliGg~~L--h~G~Iaem~TGeGKTL~a~Lpa~~~al~--------G~~V~VvTpn~yLA~qd~e~m~~l~  147 (896)
T PRK13104         79 LGL-RHFDVQLIGGMVL--HEGNIAEMRTGEGKTLVATLPAYLNAIS--------GRGVHIVTVNDYLAKRDSQWMKPIY  147 (896)
T ss_pred             cCC-CcchHHHhhhhhh--ccCccccccCCCCchHHHHHHHHHHHhc--------CCCEEEEcCCHHHHHHHHHHHHHHh
Confidence            554 3666666555444  4556899999999999999999977653        3468999999999999999999999


Q ss_pred             hhcCcEEEEeeCCCChHHHHHHHhcCCeEEEeCchhH-HHHHHhcCCccccc-----CCceEEEecCccccc-ccC----
Q 002040          565 KVMGVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRM-IDILCTSGGKITNL-----RRVTYLVMDEADRMF-DMG----  633 (976)
Q Consensus       565 ~~~~~~~~~~~gg~~~~~~~~~l~~~~~Iiv~Tp~~L-~~~l~~~~~~~~~l-----~~~~~vVlDEah~~~-~~~----  633 (976)
                      ..+|+.+.+++||.+.......+  .++|+|+||+.| .++|..+.  ...+     ..+.++||||||.|+ |..    
T Consensus       148 ~~lGLtv~~i~gg~~~~~r~~~y--~~dIvygT~grlgfDyLrd~~--~~~~~~~v~r~l~~~IvDEaDsiLIDeArtPL  223 (896)
T PRK13104        148 EFLGLTVGVIYPDMSHKEKQEAY--KADIVYGTNNEYGFDYLRDNM--AFSLTDKVQRELNFAIVDEVDSILIDEARTPL  223 (896)
T ss_pred             cccCceEEEEeCCCCHHHHHHHh--CCCEEEECChhhhHHHHhcCC--ccchHhhhccccceEEeccHhhhhhhccCCce
Confidence            99999999999999887765554  589999999999 89987542  1223     578999999999873 110    


Q ss_pred             -----------CchHHHHHHHhcCCC--------------Cc--------------------------------------
Q 002040          634 -----------FEPQITRIVQNIRPD--------------RQ--------------------------------------  650 (976)
Q Consensus       634 -----------f~~~i~~il~~~~~~--------------~q--------------------------------------  650 (976)
                                 +...+..++..+...              .+                                      
T Consensus       224 IISg~~~~~~~~y~~~~~~v~~l~~~~~~~~~~dy~idek~~~v~Lte~G~~~~e~~~~~~~il~~~~~l~~~~~~~~~~  303 (896)
T PRK13104        224 IISGAAEDSSELYIKINSLIPQLKKQEEEGDEGDYTIDEKQKQAHLTDAGHLHIEELLTKAKLLDPGESLYHASNIMLMH  303 (896)
T ss_pred             eeeCCCccchHHHHHHHHHHHHHHhccccCCCCCEEEEcCCCceEEchHHHHHHHHHHHhCCccCCcccccCchhhhHHH
Confidence                       011111122222111              11                                      


Q ss_pred             ------------------------------------------------------------------------------EE
Q 002040          651 ------------------------------------------------------------------------------TV  652 (976)
Q Consensus       651 ------------------------------------------------------------------------------~i  652 (976)
                                                                                                    +-
T Consensus       304 ~i~~aL~A~~lf~~d~dYiV~dg~V~iVDe~TGR~m~grr~s~GLHQaiEaKE~v~i~~e~~t~AsIT~Qn~Fr~Y~kLs  383 (896)
T PRK13104        304 HVNAALKAHAMFHRDIDYIVKDNQVVIVDEHTGRTMPGRRWSEGLHQAVEAKEGVPIQNENQTLASITFQNFFRMYNKLS  383 (896)
T ss_pred             HHHHHHHHHHHhcCCCceEEECCEEEEEECCCCCcCCCCCcChHHHHHHHHHcCCCCCCCceeeeeehHHHHHHhcchhc
Confidence                                                                                          22


Q ss_pred             EEeccCcHHHHHHHHHHcCCCeEEEeCCcccccCCceEEEEecCcchHHHHHHHHHHhhhc-CCcEEEEecCHHHHHHHH
Q 002040          653 LFSATFPRQVEILARKVLNKPVEIQVGGRSVVNKDITQLVEVRPESDRFLRLLELLGEWYE-KGKILIFVHSQEKCDALF  731 (976)
Q Consensus       653 ~~SAT~~~~~~~l~~~~l~~~~~i~~~~~~~~~~~i~q~~~~~~~~~k~~~l~~~l~~~~~-~~kvLIF~~s~~~~~~l~  731 (976)
                      +||+|.......+.. +++-.+...+...+...... ....+.....|+..++..+...+. +.|+||||+|+..++.|+
T Consensus       384 GMTGTa~te~~Ef~~-iY~l~Vv~IPtnkp~~R~d~-~d~v~~t~~~k~~av~~~i~~~~~~g~PVLVgt~Sie~sE~ls  461 (896)
T PRK13104        384 GMTGTADTEAYEFQQ-IYNLEVVVIPTNRSMIRKDE-ADLVYLTQADKFQAIIEDVRECGVRKQPVLVGTVSIEASEFLS  461 (896)
T ss_pred             cCCCCChhHHHHHHH-HhCCCEEECCCCCCcceecC-CCeEEcCHHHHHHHHHHHHHHHHhCCCCEEEEeCcHHHHHHHH
Confidence            233332222211111 11111111111111111111 112344556788888888876654 459999999999999999


Q ss_pred             HHHHHCCCCceeccCCCCHHHHHHHHHHhccCCccEEEecCcccccCCCCC-----------------------------
Q 002040          732 RDLLKHGYPCLSLHGAKDQTDRESTISDFKSNVCNLLIATSVAARGLDVKE-----------------------------  782 (976)
Q Consensus       732 ~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLVaT~v~~~GlDi~~-----------------------------  782 (976)
                      ..|...|+++..||+.+.+.++..+...|+.|.  |+|||++|+||+||.=                             
T Consensus       462 ~~L~~~gi~h~vLnak~~q~Ea~iia~Ag~~G~--VtIATNmAGRGtDI~Lggn~~~~~~~~~~~~~~~~~~~~~~~~~~  539 (896)
T PRK13104        462 QLLKKENIKHQVLNAKFHEKEAQIIAEAGRPGA--VTIATNMAGRGTDIVLGGSLAADLANLPADASEQEKEAVKKEWQK  539 (896)
T ss_pred             HHHHHcCCCeEeecCCCChHHHHHHHhCCCCCc--EEEeccCccCCcceecCCchhhhhhccccchhhHHHHHHHHHhhh
Confidence            999999999999999999999999999999995  9999999999999972                             


Q ss_pred             ---------CcEEEEeCCCCCHHHHHHHhcccCCCCCccEEEEEecCCCcC
Q 002040          783 ---------LELVINFDAPNHYEDYVHRVGRTGRAGRKGCAITFISEEDAK  824 (976)
Q Consensus       783 ---------v~~VI~~d~p~s~~~y~Qr~GR~gR~g~~g~~~~~~~~~d~~  824 (976)
                               =-+||--..+.|----.|-.||+||.|.+|.+..|++-+|.-
T Consensus       540 ~~~~V~~~GGL~VIgTerhesrRID~QLrGRaGRQGDPGss~f~lSleD~l  590 (896)
T PRK13104        540 RHDEVIAAGGLRIIGSERHESRRIDNQLRGRAGRQGDPGSSRFYLSLEDNL  590 (896)
T ss_pred             hhhHHHHcCCCEEEeeccCchHHHHHHhccccccCCCCCceEEEEEcCcHH
Confidence                     236777778888888899999999999999999999977653

>COG1643 HrpA HrpA-like helicases [DNA replication, recombination, and repair]

Probab=99.97  E-value=1.6e-28  Score=293.27  Aligned_cols=322  Identities=21%  Similarity=0.252  Sum_probs=242.2

Q ss_pred             HHHHHHHHHHhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHHHHhhcCcEE
Q 002040          492 PIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVMGVRC  571 (976)
Q Consensus       492 ~~Q~~~i~~il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~~~~~~~~~~  571 (976)
                      ....+.+.+|.+++-+||+|+||||||++.-..++....       +.+..+.++-|.|..|..+   ..+++..++..+
T Consensus        53 ~~~~~i~~ai~~~~vvii~getGsGKTTqlP~~lle~g~-------~~~g~I~~tQPRRlAArsv---A~RvAeel~~~~  122 (845)
T COG1643          53 AVRDEILKAIEQNQVVIIVGETGSGKTTQLPQFLLEEGL-------GIAGKIGCTQPRRLAARSV---AERVAEELGEKL  122 (845)
T ss_pred             HHHHHHHHHHHhCCEEEEeCCCCCChHHHHHHHHHhhhc-------ccCCeEEecCchHHHHHHH---HHHHHHHhCCCc
Confidence            445566777788889999999999999975555554432       2345678888999777655   445555667666


Q ss_pred             EEeeCCCChHHHHHHHhcCCeEEEeCchhHHHHHHhcCCcccccCCceEEEecCcc-cccccCCchHHHHH-HHhcCCCC
Q 002040          572 VPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEAD-RMFDMGFEPQITRI-VQNIRPDR  649 (976)
Q Consensus       572 ~~~~gg~~~~~~~~~l~~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDEah-~~~~~~f~~~i~~i-l~~~~~~~  649 (976)
                      ...+|.....+.  .....+.|.|+|.|.|+..+...    ..|+.+++||||||| +.++.+|.-.+..- +..++++.
T Consensus       123 G~~VGY~iRfe~--~~s~~Trik~mTdGiLlrei~~D----~~Ls~ys~vIiDEaHERSl~tDilLgllk~~~~~rr~DL  196 (845)
T COG1643         123 GETVGYSIRFES--KVSPRTRIKVMTDGILLREIQND----PLLSGYSVVIIDEAHERSLNTDILLGLLKDLLARRRDDL  196 (845)
T ss_pred             CceeeEEEEeec--cCCCCceeEEeccHHHHHHHhhC----cccccCCEEEEcchhhhhHHHHHHHHHHHHHHhhcCCCc
Confidence            666666655443  33456899999999999999765    468999999999999 88888877666554 66666689


Q ss_pred             cEEEEeccCcHHHHHHHHHHcCCCeEEEeCCcccccCCceEEEEecC-cch-HHHHHHHHHHhhh--cCCcEEEEecCHH
Q 002040          650 QTVLFSATFPRQVEILARKVLNKPVEIQVGGRSVVNKDITQLVEVRP-ESD-RFLRLLELLGEWY--EKGKILIFVHSQE  725 (976)
Q Consensus       650 q~i~~SAT~~~~~~~l~~~~l~~~~~i~~~~~~~~~~~i~q~~~~~~-~~~-k~~~l~~~l~~~~--~~~kvLIF~~s~~  725 (976)
                      ++|+||||+...   .+..++++...+.+.++.++..   ..|.... ... -...+...+....  ..|.+|||.+.+.
T Consensus       197 KiIimSATld~~---rfs~~f~~apvi~i~GR~fPVe---i~Y~~~~~~d~~l~~ai~~~v~~~~~~~~GdILvFLpG~~  270 (845)
T COG1643         197 KLIIMSATLDAE---RFSAYFGNAPVIEIEGRTYPVE---IRYLPEAEADYILLDAIVAAVDIHLREGSGSILVFLPGQR  270 (845)
T ss_pred             eEEEEecccCHH---HHHHHcCCCCEEEecCCccceE---EEecCCCCcchhHHHHHHHHHHHhccCCCCCEEEECCcHH
Confidence            999999999765   4566677666677777776532   2231111 222 2233333333332  3689999999999


Q ss_pred             HHHHHHHHHHH----CCCCceeccCCCCHHHHHHHHHHhccCCccEEEecCcccccCCCCCCcEEEEeCC----------
Q 002040          726 KCDALFRDLLK----HGYPCLSLHGAKDQTDRESTISDFKSNVCNLLIATSVAARGLDVKELELVINFDA----------  791 (976)
Q Consensus       726 ~~~~l~~~L~~----~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLVaT~v~~~GlDi~~v~~VI~~d~----------  791 (976)
                      ++..++..|.+    ..+.++++||.++..++.++++.-..|..+|++||+|++++|+|++|.+||+-+.          
T Consensus       271 EI~~~~~~L~~~~l~~~~~i~PLy~~L~~~eQ~rvF~p~~~~~RKVVlATNIAETSLTI~gIr~VIDsG~ak~~~y~~~~  350 (845)
T COG1643         271 EIERTAEWLEKAELGDDLEILPLYGALSAEEQVRVFEPAPGGKRKVVLATNIAETSLTIPGIRYVIDSGLAKEKRYDPRT  350 (845)
T ss_pred             HHHHHHHHHHhccccCCcEEeeccccCCHHHHHhhcCCCCCCcceEEEEccccccceeeCCeEEEecCCccccccccccc
Confidence            99999999998    3477999999999999999999888898889999999999999999999997332          


Q ss_pred             --------CCCHHHHHHHhcccCCCCCccEEEEEecCCCcCchHHHHHHHhhccCCCChHHH
Q 002040          792 --------PNHYEDYVHRVGRTGRAGRKGCAITFISEEDAKYSPDLVKALELSEQVVPDDLK  845 (976)
Q Consensus       792 --------p~s~~~y~Qr~GR~gR~g~~g~~~~~~~~~d~~~~~~i~~~l~~~~~~vp~~l~  845 (976)
                              |.|-++..||.|||||.+ +|.||-+|++.+.         .....+..|+.|.
T Consensus       351 g~~~L~~~~ISqAsA~QRaGRAGR~~-pGicyRLyse~~~---------~~~~~~t~PEIlr  402 (845)
T COG1643         351 GLTRLETEPISKASADQRAGRAGRTG-PGICYRLYSEEDF---------LAFPEFTLPEILR  402 (845)
T ss_pred             CceeeeEEEechhhhhhhccccccCC-CceEEEecCHHHH---------HhcccCCChhhhh
Confidence                    567889999999999997 9999999997432         2334456777664

>PRK09694 helicase Cas3; Provisional

Probab=99.96  E-value=2.2e-27  Score=288.11  Aligned_cols=313  Identities=20%  Similarity=0.228  Sum_probs=205.4

Q ss_pred             CCCCCcHHHHHHHHHHhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHHHHh
Q 002040          486 NYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAK  565 (976)
Q Consensus       486 ~~~~p~~~Q~~~i~~il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~~~~  565 (976)
                      +...|+|+|..+........-+||.||||+|||.++++++...+..      +....++|++||+++++|++..+..++.
T Consensus       283 ~~~~p~p~Q~~~~~~~~~pgl~ileApTGsGKTEAAL~~A~~l~~~------~~~~gi~~aLPT~Atan~m~~Rl~~~~~  356 (878)
T PRK09694        283 NGYQPRQLQTLVDALPLQPGLTIIEAPTGSGKTEAALAYAWRLIDQ------GLADSIIFALPTQATANAMLSRLEALAS  356 (878)
T ss_pred             CCCCChHHHHHHHhhccCCCeEEEEeCCCCCHHHHHHHHHHHHHHh------CCCCeEEEECcHHHHHHHHHHHHHHHHH
Confidence            3458999999886554456678999999999999987766654432      2245789999999999999999987654


Q ss_pred             hc--CcEEEEeeCCCChHHHHH--------------------HHh----c---CCeEEEeCchhHHHHHHhcCCcccccC
Q 002040          566 VM--GVRCVPVYGGSGVAQQIS--------------------ELK----R---GTEIVVCTPGRMIDILCTSGGKITNLR  616 (976)
Q Consensus       566 ~~--~~~~~~~~gg~~~~~~~~--------------------~l~----~---~~~Iiv~Tp~~L~~~l~~~~~~~~~l~  616 (976)
                      .+  ...+.+++|.........                    .+.    +   -.+|+|||+..++..+.....  ..+.
T Consensus       357 ~~f~~~~v~L~Hg~a~l~~~~~~~~~~~~~~~~~~~~~~~~~~w~~~~~kr~llapi~V~TiDQlL~a~l~~kh--~~lR  434 (878)
T PRK09694        357 KLFPSPNLILAHGNSRFNHLFQSLKSRAATEQGQEEAWVQCCEWLSQSNKRVFLGQIGVCTIDQVLISVLPVKH--RFIR  434 (878)
T ss_pred             HhcCCCceEeecCcchhhhhhhhhhcccccccccchhhhHHHHHHhhhhhhhhcCCEEEcCHHHHHHHHHccch--HHHH
Confidence            32  345667776654221100                    111    1   269999999988755433211  1222


Q ss_pred             Cc----eEEEecCcccccccCCchHHHHHHHhc-CCCCcEEEEeccCcHHHHHH-HHHHcCC-Ce-------EEE-eCCc
Q 002040          617 RV----TYLVMDEADRMFDMGFEPQITRIVQNI-RPDRQTVLFSATFPRQVEIL-ARKVLNK-PV-------EIQ-VGGR  681 (976)
Q Consensus       617 ~~----~~vVlDEah~~~~~~f~~~i~~il~~~-~~~~q~i~~SAT~~~~~~~l-~~~~l~~-~~-------~i~-~~~~  681 (976)
                      .+    ++|||||+|.+ +......+..++..+ .....+|+||||+|..+... ...+-.. ++       .++ ....
T Consensus       435 ~~~La~svvIiDEVHAy-D~ym~~lL~~~L~~l~~~g~~vIllSATLP~~~r~~L~~a~~~~~~~~~~~~YPlvt~~~~~  513 (878)
T PRK09694        435 GFGLGRSVLIVDEVHAY-DAYMYGLLEAVLKAQAQAGGSVILLSATLPATLKQKLLDTYGGHDPVELSSAYPLITWRGVN  513 (878)
T ss_pred             HHhhccCeEEEechhhC-CHHHHHHHHHHHHHHHhcCCcEEEEeCCCCHHHHHHHHHHhccccccccccccccccccccc
Confidence            22    48999999965 222233444444443 23567999999999876543 3332111 10       000 0000


Q ss_pred             ---cccc------CCceEEEEe--c--CcchHHHHHHHHHHh-hhcCCcEEEEecCHHHHHHHHHHHHHCC---CCceec
Q 002040          682 ---SVVN------KDITQLVEV--R--PESDRFLRLLELLGE-WYEKGKILIFVHSQEKCDALFRDLLKHG---YPCLSL  744 (976)
Q Consensus       682 ---~~~~------~~i~q~~~~--~--~~~~k~~~l~~~l~~-~~~~~kvLIF~~s~~~~~~l~~~L~~~~---~~~~~l  744 (976)
                         ....      ......+.+  .  ........++..|.. ...++++||||||+..|..++..|...+   +.+..+
T Consensus       514 ~~~~~~~~~~~~~~~~~~~v~v~~~~~~~~~~~~~~l~~i~~~~~~g~~vLVf~NTV~~Aq~ly~~L~~~~~~~~~v~ll  593 (878)
T PRK09694        514 GAQRFDLSAHPEQLPARFTIQLEPICLADMLPDLTLLQRMIAAANAGAQVCLICNLVDDAQKLYQRLKELNNTQVDIDLF  593 (878)
T ss_pred             cceeeeccccccccCcceEEEEEeeccccccCHHHHHHHHHHHHhcCCEEEEEECCHHHHHHHHHHHHhhCCCCceEEEE
Confidence               0000      001111111  1  100111233333333 3346789999999999999999999764   679999


Q ss_pred             cCCCCHHHH----HHHHHHh-ccCC---ccEEEecCcccccCCCCCCcEEEEeCCCCCHHHHHHHhcccCCCCC
Q 002040          745 HGAKDQTDR----ESTISDF-KSNV---CNLLIATSVAARGLDVKELELVINFDAPNHYEDYVHRVGRTGRAGR  810 (976)
Q Consensus       745 hg~~~~~~R----~~~~~~F-~~g~---~~vLVaT~v~~~GlDi~~v~~VI~~d~p~s~~~y~Qr~GR~gR~g~  810 (976)
                      ||.++..+|    ..+++.| ++|.   ..|||||+++++|||| ++++||...+|  ...++||+||+||.+.
T Consensus       594 Hsrf~~~dR~~~E~~vl~~fgk~g~r~~~~ILVaTQViE~GLDI-d~DvlItdlaP--idsLiQRaGR~~R~~~  664 (878)
T PRK09694        594 HARFTLNDRREKEQRVIENFGKNGKRNQGRILVATQVVEQSLDL-DFDWLITQLCP--VDLLFQRLGRLHRHHR  664 (878)
T ss_pred             eCCCCHHHHHHHHHHHHHHHHhcCCcCCCeEEEECcchhheeec-CCCeEEECCCC--HHHHHHHHhccCCCCC
Confidence            999999999    4678888 6776   4799999999999999 57999998888  6799999999999875

>PRK12906 secA preprotein translocase subunit SecA; Reviewed

Probab=99.96  E-value=1.2e-27  Score=282.90  Aligned_cols=323  Identities=21%  Similarity=0.265  Sum_probs=233.2

Q ss_pred             cCCCCCcHHHHHHHHHHhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHHHH
Q 002040          485 LNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFA  564 (976)
Q Consensus       485 ~~~~~p~~~Q~~~i~~il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~~~  564 (976)
                      +|+ .|++.|.-+.-++..|+  |..+.||+|||+++++|++.....        |..|-||+||--||.|.+.++..++
T Consensus        77 ~g~-~~~dvQlig~l~l~~G~--iaEm~TGEGKTLvA~l~a~l~al~--------G~~v~vvT~neyLA~Rd~e~~~~~~  145 (796)
T PRK12906         77 LGL-RPFDVQIIGGIVLHEGN--IAEMKTGEGKTLTATLPVYLNALT--------GKGVHVVTVNEYLSSRDATEMGELY  145 (796)
T ss_pred             hCC-CCchhHHHHHHHHhcCC--cccccCCCCCcHHHHHHHHHHHHc--------CCCeEEEeccHHHHHhhHHHHHHHH
Confidence            564 48888888777766665  999999999999999999877664        6678999999999999999999999


Q ss_pred             hhcCcEEEEeeCCCChHHHHHHHhcCCeEEEeCchhHH-HHHHhcC---CcccccCCceEEEecCccccc-ccC------
Q 002040          565 KVMGVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMI-DILCTSG---GKITNLRRVTYLVMDEADRMF-DMG------  633 (976)
Q Consensus       565 ~~~~~~~~~~~gg~~~~~~~~~l~~~~~Iiv~Tp~~L~-~~l~~~~---~~~~~l~~~~~vVlDEah~~~-~~~------  633 (976)
                      ..+|+.|.++.|+.+..+....+  .++|++||...|. ++|..+-   ........+.+.||||+|.|+ +..      
T Consensus       146 ~~LGl~vg~i~~~~~~~~r~~~y--~~dI~Y~t~~e~gfDyLRD~m~~~~~~~v~r~~~~aIvDEvDSiLiDeartPLii  223 (796)
T PRK12906        146 RWLGLTVGLNLNSMSPDEKRAAY--NCDITYSTNSELGFDYLRDNMVVYKEQMVQRPLNYAIVDEVDSILIDEARTPLII  223 (796)
T ss_pred             HhcCCeEEEeCCCCCHHHHHHHh--cCCCeecCCccccccchhhccccchhhhhccCcceeeeccchheeeccCCCceec
Confidence            99999999999887766654444  4899999998763 4443321   011124568899999999763 110      


Q ss_pred             ---------CchHHHHHHHhcCCC--------------------------------------------------------
Q 002040          634 ---------FEPQITRIVQNIRPD--------------------------------------------------------  648 (976)
Q Consensus       634 ---------f~~~i~~il~~~~~~--------------------------------------------------------  648 (976)
                               +...+..++..+...                                                        
T Consensus       224 sg~~~~~~~~y~~~~~~v~~l~~~~~~~~~~~~~~~dy~id~~~k~v~lte~G~~~~e~~~~i~~l~~~~~~~~~~~i~~  303 (796)
T PRK12906        224 SGQAEKATDLYIRADRFVKTLIKDEAEDGDDDEDTGDYKIDEKTKTISLTEQGIRKAEKLFGLDNLYDSENTALAHHIDQ  303 (796)
T ss_pred             CCCCCcchHHHHHHHHHHHHHHhhhhccccccCCCCceEEEcccCceeecHHHHHHHHHHcCCccccCchhhhHHHHHHH
Confidence                     000111111111100                                                        


Q ss_pred             ------------------------------------------------------------------------CcEEEEec
Q 002040          649 ------------------------------------------------------------------------RQTVLFSA  656 (976)
Q Consensus       649 ------------------------------------------------------------------------~q~i~~SA  656 (976)
                                                                                              .++.+||+
T Consensus       304 Al~A~~l~~~d~dYiV~d~~V~ivD~~TGR~~~gr~ws~GLHQaieaKe~v~i~~e~~t~a~It~qnfFr~Y~kl~GmTG  383 (796)
T PRK12906        304 ALRANYIMLKDIDYVVQDGEVLIVDEFTGRVMEGRRYSDGLHQAIEAKEGVKIQEENQTLATITYQNFFRMYKKLSGMTG  383 (796)
T ss_pred             HHHHHHHHhcCCcEEEECCEEEEEeCCCCCcCCCCccChHHHHHHHHhcCCCcCCCceeeeeehHHHHHHhcchhhccCC
Confidence                                                                                    11334444


Q ss_pred             cCcHHHHHHHHHHcCCCeEEEeCCcccccCCceEEEEecCcchHHHHHHHHHHhhh-cCCcEEEEecCHHHHHHHHHHHH
Q 002040          657 TFPRQVEILARKVLNKPVEIQVGGRSVVNKDITQLVEVRPESDRFLRLLELLGEWY-EKGKILIFVHSQEKCDALFRDLL  735 (976)
Q Consensus       657 T~~~~~~~l~~~~l~~~~~i~~~~~~~~~~~i~q~~~~~~~~~k~~~l~~~l~~~~-~~~kvLIF~~s~~~~~~l~~~L~  735 (976)
                      |.......+ ...++-++...+...+...... ....+.....|+..++..+.... .+.++||||+|+..++.|+..|.
T Consensus       384 Ta~~e~~Ef-~~iY~l~vv~IPtnkp~~r~d~-~d~i~~t~~~K~~al~~~i~~~~~~g~pvLI~t~si~~se~ls~~L~  461 (796)
T PRK12906        384 TAKTEEEEF-REIYNMEVITIPTNRPVIRKDS-PDLLYPTLDSKFNAVVKEIKERHAKGQPVLVGTVAIESSERLSHLLD  461 (796)
T ss_pred             CCHHHHHHH-HHHhCCCEEEcCCCCCeeeeeC-CCeEEcCHHHHHHHHHHHHHHHHhCCCCEEEEeCcHHHHHHHHHHHH
Confidence            443332222 2222222222211111111111 11234455678888888886544 45699999999999999999999


Q ss_pred             HCCCCceeccCCCCHHHHHHHHHHhccCCccEEEecCcccccCCCC---CCc-----EEEEeCCCCCHHHHHHHhcccCC
Q 002040          736 KHGYPCLSLHGAKDQTDRESTISDFKSNVCNLLIATSVAARGLDVK---ELE-----LVINFDAPNHYEDYVHRVGRTGR  807 (976)
Q Consensus       736 ~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLVaT~v~~~GlDi~---~v~-----~VI~~d~p~s~~~y~Qr~GR~gR  807 (976)
                      +.|+++..+||.+.+.++..+...++.|.  |+|||++|+||+||+   +|.     +||+++.|.+...|.|++||+||
T Consensus       462 ~~gi~~~~Lna~~~~~Ea~ii~~ag~~g~--VtIATnmAGRGtDI~l~~~V~~~GGLhVI~te~pes~ri~~Ql~GRtGR  539 (796)
T PRK12906        462 EAGIPHAVLNAKNHAKEAEIIMNAGQRGA--VTIATNMAGRGTDIKLGPGVKELGGLAVIGTERHESRRIDNQLRGRSGR  539 (796)
T ss_pred             HCCCCeeEecCCcHHHHHHHHHhcCCCce--EEEEeccccCCCCCCCCcchhhhCCcEEEeeecCCcHHHHHHHhhhhcc
Confidence            99999999999999888888888877777  999999999999995   788     99999999999999999999999


Q ss_pred             CCCccEEEEEecCCCcC
Q 002040          808 AGRKGCAITFISEEDAK  824 (976)
Q Consensus       808 ~g~~g~~~~~~~~~d~~  824 (976)
                      .|.+|.+..|++.+|.-
T Consensus       540 qG~~G~s~~~~sleD~l  556 (796)
T PRK12906        540 QGDPGSSRFYLSLEDDL  556 (796)
T ss_pred             CCCCcceEEEEeccchH
Confidence            99999999999987653

>PRK12904 preprotein translocase subunit SecA; Reviewed

Probab=99.96  E-value=1.4e-27  Score=283.30  Aligned_cols=323  Identities=22%  Similarity=0.247  Sum_probs=238.7

Q ss_pred             cCCCCCcHHHHHHHHHHhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHHHH
Q 002040          485 LNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFA  564 (976)
Q Consensus       485 ~~~~~p~~~Q~~~i~~il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~~~  564 (976)
                      +|+ .|++.|.-+.-.+..|  .|+.+.||+|||++|++|++.....        |..|-||+||..||.|.++++..++
T Consensus        78 lg~-~~~dvQlig~l~L~~G--~Iaem~TGeGKTLva~lpa~l~aL~--------G~~V~IvTpn~yLA~rd~e~~~~l~  146 (830)
T PRK12904         78 LGM-RHFDVQLIGGMVLHEG--KIAEMKTGEGKTLVATLPAYLNALT--------GKGVHVVTVNDYLAKRDAEWMGPLY  146 (830)
T ss_pred             hCC-CCCccHHHhhHHhcCC--chhhhhcCCCcHHHHHHHHHHHHHc--------CCCEEEEecCHHHHHHHHHHHHHHH
Confidence            564 4788888777666655  5999999999999999999644332        3357799999999999999999999


Q ss_pred             hhcCcEEEEeeCCCChHHHHHHHhcCCeEEEeCchhH-HHHHHhcCCc---ccccCCceEEEecCccccc-ccC------
Q 002040          565 KVMGVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRM-IDILCTSGGK---ITNLRRVTYLVMDEADRMF-DMG------  633 (976)
Q Consensus       565 ~~~~~~~~~~~gg~~~~~~~~~l~~~~~Iiv~Tp~~L-~~~l~~~~~~---~~~l~~~~~vVlDEah~~~-~~~------  633 (976)
                      ..+|+.+.+++|+.+..++...+  .++|+|+||+.| .++|..+...   ...+..+.++||||||.|+ +..      
T Consensus       147 ~~LGlsv~~i~~~~~~~er~~~y--~~dI~ygT~~elgfDyLrd~~~~~~~~~~~r~~~~aIvDEaDsiLIDeArtpLii  224 (830)
T PRK12904        147 EFLGLSVGVILSGMSPEERREAY--AADITYGTNNEFGFDYLRDNMVFSLEERVQRGLNYAIVDEVDSILIDEARTPLII  224 (830)
T ss_pred             hhcCCeEEEEcCCCCHHHHHHhc--CCCeEEECCcchhhhhhhcccccchhhhcccccceEEEechhhheeccCCCceee
Confidence            99999999999999888776665  389999999999 8888654211   1236788999999999873 100      


Q ss_pred             ---------CchHHHHHHHhcCCC--------------------------------------------------------
Q 002040          634 ---------FEPQITRIVQNIRPD--------------------------------------------------------  648 (976)
Q Consensus       634 ---------f~~~i~~il~~~~~~--------------------------------------------------------  648 (976)
                               +...+..++..+..+                                                        
T Consensus       225 Sg~~~~~~~~y~~~~~~v~~l~~~~dy~vde~~~~v~lte~G~~~~e~~~~~~~ly~~~~~~~~~~i~~AL~A~~l~~~d  304 (830)
T PRK12904        225 SGPAEDSSELYKRANKIVPTLEKEGDYTVDEKSRTVGLTEEGIEKAEKLLGIENLYDPENIALVHHLNQALRAHELFKRD  304 (830)
T ss_pred             ECCCCcccHHHHHHHHHHHhcCCCCCeEEEcCCCeeeECHHHHHHHHHHhCCccccChhhhHHHHHHHHHHHHHHHHhcC
Confidence                     011111111111110                                                        


Q ss_pred             -------------------------------------------------------------CcEEEEeccCcHHHHHHHH
Q 002040          649 -------------------------------------------------------------RQTVLFSATFPRQVEILAR  667 (976)
Q Consensus       649 -------------------------------------------------------------~q~i~~SAT~~~~~~~l~~  667 (976)
                                                                                   .++.+||+|.......+..
T Consensus       305 ~dYiV~dg~V~ivDe~TGR~~~gr~ws~GLHQaiEaKE~v~i~~e~~t~a~It~qn~Fr~Y~kl~GmTGTa~te~~E~~~  384 (830)
T PRK12904        305 VDYIVKDGEVVIVDEFTGRLMPGRRYSDGLHQAIEAKEGVKIQNENQTLASITFQNYFRMYEKLAGMTGTADTEAEEFRE  384 (830)
T ss_pred             CcEEEECCEEEEEECCCCccCCCCccchHHHHHHHHhcCCCCCCCceeeeeeeHHHHHHhcchhcccCCCcHHHHHHHHH
Confidence                                                                         1245666665544433333


Q ss_pred             HHcCCCeEEEeCCcccccCCceEEEEecCcchHHHHHHHHHHhhhc-CCcEEEEecCHHHHHHHHHHHHHCCCCceeccC
Q 002040          668 KVLNKPVEIQVGGRSVVNKDITQLVEVRPESDRFLRLLELLGEWYE-KGKILIFVHSQEKCDALFRDLLKHGYPCLSLHG  746 (976)
Q Consensus       668 ~~l~~~~~i~~~~~~~~~~~i~q~~~~~~~~~k~~~l~~~l~~~~~-~~kvLIF~~s~~~~~~l~~~L~~~~~~~~~lhg  746 (976)
                      .| +-.+...+...+...... ....+.....|+..+...+..... +.++||||+|+..++.|+..|...|+++..|||
T Consensus       385 iY-~l~vv~IPtnkp~~r~d~-~d~i~~t~~~K~~aI~~~I~~~~~~grpVLIft~Si~~se~Ls~~L~~~gi~~~vLna  462 (830)
T PRK12904        385 IY-NLDVVVIPTNRPMIRIDH-PDLIYKTEKEKFDAVVEDIKERHKKGQPVLVGTVSIEKSELLSKLLKKAGIPHNVLNA  462 (830)
T ss_pred             Hh-CCCEEEcCCCCCeeeeeC-CCeEEECHHHHHHHHHHHHHHHHhcCCCEEEEeCcHHHHHHHHHHHHHCCCceEeccC
Confidence            32 333322222222211111 112344566789999988876443 459999999999999999999999999999999


Q ss_pred             CCCHHHHHHHHHHhccCCccEEEecCcccccCCCCCC--------------------------------------cEEEE
Q 002040          747 AKDQTDRESTISDFKSNVCNLLIATSVAARGLDVKEL--------------------------------------ELVIN  788 (976)
Q Consensus       747 ~~~~~~R~~~~~~F~~g~~~vLVaT~v~~~GlDi~~v--------------------------------------~~VI~  788 (976)
                      .  +.+|+..+..|..+...|+|||++|+||+||+--                                      -+||-
T Consensus       463 k--q~eREa~Iia~Ag~~g~VtIATNmAGRGtDI~LgGn~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~GGLhVig  540 (830)
T PRK12904        463 K--NHEREAEIIAQAGRPGAVTIATNMAGRGTDIKLGGNPEMLAAALLEEETEEQIAKIKAEWQEEHEEVLEAGGLHVIG  540 (830)
T ss_pred             c--hHHHHHHHHHhcCCCceEEEecccccCCcCccCCCchhhhhhhhhhhhhhHHHHHHHHHHhhhhhhHHHcCCCEEEe
Confidence            5  8899999999999999999999999999999643                                      36887


Q ss_pred             eCCCCCHHHHHHHhcccCCCCCccEEEEEecCCCcC
Q 002040          789 FDAPNHYEDYVHRVGRTGRAGRKGCAITFISEEDAK  824 (976)
Q Consensus       789 ~d~p~s~~~y~Qr~GR~gR~g~~g~~~~~~~~~d~~  824 (976)
                      ...|.|----.|-.||+||.|.+|.+..|++-+|.-
T Consensus       541 TerhesrRid~QlrGRagRQGdpGss~f~lSleD~l  576 (830)
T PRK12904        541 TERHESRRIDNQLRGRSGRQGDPGSSRFYLSLEDDL  576 (830)
T ss_pred             cccCchHHHHHHhhcccccCCCCCceeEEEEcCcHH
Confidence            888889888999999999999999999999877653

>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional

Probab=99.96  E-value=2.5e-27  Score=290.01  Aligned_cols=317  Identities=22%  Similarity=0.291  Sum_probs=216.4

Q ss_pred             CCcHHHHHHHHHHh----cCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHHHH
Q 002040          489 KPMPIQAQALPVIM----SGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFA  564 (976)
Q Consensus       489 ~p~~~Q~~~i~~il----~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~~~  564 (976)
                      .+.|||.+++.+++    .|.++|++.+||.|||++++.. +.++....    +....+|||||. .|+.||..+|.+|+
T Consensus       169 ~Lr~YQleGlnWLi~l~~~g~gGILADEMGLGKTlQaIal-L~~L~~~~----~~~gp~LIVvP~-SlL~nW~~Ei~kw~  242 (1033)
T PLN03142        169 KMRDYQLAGLNWLIRLYENGINGILADEMGLGKTLQTISL-LGYLHEYR----GITGPHMVVAPK-STLGNWMNEIRRFC  242 (1033)
T ss_pred             chHHHHHHHHHHHHHHHhcCCCEEEEeCCCccHHHHHHHH-HHHHHHhc----CCCCCEEEEeCh-HHHHHHHHHHHHHC
Confidence            58899999999986    5788999999999999985544 44443321    122347999996 56689999999997


Q ss_pred             hhcCcEEEEeeCCCChHHHHH-H-H-hcCCeEEEeCchhHHHHHHhcCCcccccCCceEEEecCcccccccCCchHHHHH
Q 002040          565 KVMGVRCVPVYGGSGVAQQIS-E-L-KRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMGFEPQITRI  641 (976)
Q Consensus       565 ~~~~~~~~~~~gg~~~~~~~~-~-l-~~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDEah~~~~~~f~~~i~~i  641 (976)
                      .  .+.++.++|.......+. . + ....+|||+|+..+......     ..--.+.+|||||||++-+.  ...+..+
T Consensus       243 p--~l~v~~~~G~~~eR~~~~~~~~~~~~~dVvITSYe~l~~e~~~-----L~k~~W~~VIvDEAHrIKN~--~Sklska  313 (1033)
T PLN03142        243 P--VLRAVKFHGNPEERAHQREELLVAGKFDVCVTSFEMAIKEKTA-----LKRFSWRYIIIDEAHRIKNE--NSLLSKT  313 (1033)
T ss_pred             C--CCceEEEeCCHHHHHHHHHHHhcccCCCcceecHHHHHHHHHH-----hccCCCCEEEEcCccccCCH--HHHHHHH
Confidence            5  345555665443222211 1 1 23579999999988654322     12235789999999998653  3345555


Q ss_pred             HHhcCCCCcEEEEeccCcHH-HHH---HHHHH------------------------------------------------
Q 002040          642 VQNIRPDRQTVLFSATFPRQ-VEI---LARKV------------------------------------------------  669 (976)
Q Consensus       642 l~~~~~~~q~i~~SAT~~~~-~~~---l~~~~------------------------------------------------  669 (976)
                      +..+.. ...|++||||-.+ +..   ++..+                                                
T Consensus       314 lr~L~a-~~RLLLTGTPlqNnl~ELwsLL~FL~P~~f~s~~~F~~~f~~~~~~~~~e~i~~L~~~L~pf~LRR~KsdV~~  392 (1033)
T PLN03142        314 MRLFST-NYRLLITGTPLQNNLHELWALLNFLLPEIFSSAETFDEWFQISGENDQQEVVQQLHKVLRPFLLRRLKSDVEK  392 (1033)
T ss_pred             HHHhhc-CcEEEEecCCCCCCHHHHHHHHhcCCCCcCCCHHHHHHHHccccccchHHHHHHHHHHhhHHHhhhhHHHHhh
Confidence            555543 3468899996321 111   10000                                                


Q ss_pred             -cCCCeE--EEeCCcc--------c-------ccC--------C-------------ceEE----------EEecCcchH
Q 002040          670 -LNKPVE--IQVGGRS--------V-------VNK--------D-------------ITQL----------VEVRPESDR  700 (976)
Q Consensus       670 -l~~~~~--i~~~~~~--------~-------~~~--------~-------------i~q~----------~~~~~~~~k  700 (976)
                       +.....  +.+.-..        .       ...        .             +...          -.+...+.|
T Consensus       393 ~LPpK~e~iv~v~LS~~Qk~lY~~ll~k~~~~l~~g~~~~~LlnilmqLRk~cnHP~L~~~~ep~~~~~~~e~lie~SgK  472 (1033)
T PLN03142        393 GLPPKKETILKVGMSQMQKQYYKALLQKDLDVVNAGGERKRLLNIAMQLRKCCNHPYLFQGAEPGPPYTTGEHLVENSGK  472 (1033)
T ss_pred             hCCCceeEEEeeCCCHHHHHHHHHHHHHHHHHHhccccHHHHHHHHHHHHHHhCCHHhhhcccccCcccchhHHhhhhhH
Confidence             000000  0000000        0       000        0             0000          001122456


Q ss_pred             HHHHHHHHHhhhc-CCcEEEEecCHHHHHHHHHHHHHCCCCceeccCCCCHHHHHHHHHHhccC---CccEEEecCcccc
Q 002040          701 FLRLLELLGEWYE-KGKILIFVHSQEKCDALFRDLLKHGYPCLSLHGAKDQTDRESTISDFKSN---VCNLLIATSVAAR  776 (976)
Q Consensus       701 ~~~l~~~l~~~~~-~~kvLIF~~s~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g---~~~vLVaT~v~~~  776 (976)
                      +..|..+|..+.. +.+|||||+....++.|..+|...|+.++.|||+++..+|..++..|++.   .+.|||+|.+++.
T Consensus       473 l~lLdkLL~~Lk~~g~KVLIFSQft~~LdiLed~L~~~g~~y~rIdGsts~~eRq~~Id~Fn~~~s~~~VfLLSTrAGGl  552 (1033)
T PLN03142        473 MVLLDKLLPKLKERDSRVLIFSQMTRLLDILEDYLMYRGYQYCRIDGNTGGEDRDASIDAFNKPGSEKFVFLLSTRAGGL  552 (1033)
T ss_pred             HHHHHHHHHHHHhcCCeEEeehhHHHHHHHHHHHHHHcCCcEEEECCCCCHHHHHHHHHHhccccCCceEEEEecccccc
Confidence            6666666666543 45999999999999999999999999999999999999999999999753   3568999999999


Q ss_pred             cCCCCCCcEEEEeCCCCCHHHHHHHhcccCCCCCccEEEE--EecCC
Q 002040          777 GLDVKELELVINFDAPNHYEDYVHRVGRTGRAGRKGCAIT--FISEE  821 (976)
Q Consensus       777 GlDi~~v~~VI~~d~p~s~~~y~Qr~GR~gR~g~~g~~~~--~~~~~  821 (976)
                      |||+..+++||+||+||||..+.|++||++|.|++..|++  |++..
T Consensus       553 GINLt~Ad~VIiyD~dWNP~~d~QAidRaHRIGQkk~V~VyRLIt~g  599 (1033)
T PLN03142        553 GINLATADIVILYDSDWNPQVDLQAQDRAHRIGQKKEVQVFRFCTEY  599 (1033)
T ss_pred             CCchhhCCEEEEeCCCCChHHHHHHHHHhhhcCCCceEEEEEEEeCC
Confidence            9999999999999999999999999999999999866554  45543

>cd00268 DEADc DEAD-box helicases

Probab=99.96  E-value=1.3e-27  Score=249.50  Aligned_cols=202  Identities=51%  Similarity=0.867  Sum_probs=183.7

Q ss_pred             cccCCCCHHHHHHHHHcCCCCCcHHHHHHHHHHhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEcc
Q 002040          469 WHQTGLTSKIMETIRKLNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAP  548 (976)
Q Consensus       469 ~~~~~l~~~l~~~l~~~~~~~p~~~Q~~~i~~il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~P  548 (976)
                      |.++++++.+.+.|..+|+..|+++|.++++.+++|+++|+++|||+|||++|++|++.++....   ...++++||++|
T Consensus         1 ~~~~~~~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~TG~GKT~~~~~~~l~~~~~~~---~~~~~~viii~p   77 (203)
T cd00268           1 FEELGLSPELLRGIYALGFEKPTPIQARAIPPLLSGRDVIGQAQTGSGKTAAFLIPILEKLDPSP---KKDGPQALILAP   77 (203)
T ss_pred             CCcCCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhcCCcEEEECCCCCcHHHHHHHHHHHHHHhhc---ccCCceEEEEcC
Confidence            67899999999999999999999999999999999999999999999999999999999988642   135789999999


Q ss_pred             CHHHHHHHHHHHHHHHhhcCcEEEEeeCCCChHHHHHHHhcCCeEEEeCchhHHHHHHhcCCcccccCCceEEEecCccc
Q 002040          549 TRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADR  628 (976)
Q Consensus       549 tr~La~Q~~~~~~~~~~~~~~~~~~~~gg~~~~~~~~~l~~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDEah~  628 (976)
                      |++|+.|+...+..+....++.+.+++|+.........+..+++|+||||+.|..++....   ..+..+.+|||||||.
T Consensus        78 ~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iiv~T~~~l~~~l~~~~---~~~~~l~~lIvDE~h~  154 (203)
T cd00268          78 TRELALQIAEVARKLGKHTNLKVVVIYGGTSIDKQIRKLKRGPHIVVATPGRLLDLLERGK---LDLSKVKYLVLDEADR  154 (203)
T ss_pred             CHHHHHHHHHHHHHHhccCCceEEEEECCCCHHHHHHHhcCCCCEEEEChHHHHHHHHcCC---CChhhCCEEEEeChHH
Confidence            9999999999999998888899999999998877777776689999999999999887543   5678899999999999


Q ss_pred             ccccCCchHHHHHHHhcCCCCcEEEEeccCcHHHHHHHHHHcCCCeEE
Q 002040          629 MFDMGFEPQITRIVQNIRPDRQTVLFSATFPRQVEILARKVLNKPVEI  676 (976)
Q Consensus       629 ~~~~~f~~~i~~il~~~~~~~q~i~~SAT~~~~~~~l~~~~l~~~~~i  676 (976)
                      +.+.+|...+..++..+....|+++||||+++.+..++..++.+|+.+
T Consensus       155 ~~~~~~~~~~~~~~~~l~~~~~~~~~SAT~~~~~~~~~~~~~~~~~~~  202 (203)
T cd00268         155 MLDMGFEDQIREILKLLPKDRQTLLFSATMPKEVRDLARKFLRNPVRI  202 (203)
T ss_pred             hhccChHHHHHHHHHhCCcccEEEEEeccCCHHHHHHHHHHCCCCEEe
Confidence            998889999999999999999999999999999999999999998865

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.

>KOG0951 consensus RNA helicase BRR2, DEAD-box superfamily [RNA processing and modification]

Probab=99.96  E-value=1.7e-27  Score=279.17  Aligned_cols=362  Identities=23%  Similarity=0.320  Sum_probs=261.0

Q ss_pred             cCCCCCcHHHHHHHHHHhcC-CCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCC---CCCeEEEEccCHHHHHHHHHHH
Q 002040          485 LNYEKPMPIQAQALPVIMSG-RDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAG---DGPVGLIMAPTRELVQQIHSDI  560 (976)
Q Consensus       485 ~~~~~p~~~Q~~~i~~il~g-~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~---~~~~vLIl~Ptr~La~Q~~~~~  560 (976)
                      +|...+.++|..+.++.+.+ .++++|||||+|||.++++-||+.+........+   ...++++++|..+|+..|...|
T Consensus       305 ~g~~sLNrIQS~v~daAl~~~EnmLlCAPTGaGKTNVAvLtiLqel~~h~r~dgs~nl~~fKIVYIAPmKaLvqE~Vgsf  384 (1674)
T KOG0951|consen  305 FGKQSLNRIQSKVYDAALRGDENMLLCAPTGAGKTNVAVLTILQELGNHLREDGSVNLAPFKIVYIAPMKALVQEMVGSF  384 (1674)
T ss_pred             ccchhhhHHHHHHHHHHhcCcCcEEEeccCCCCchHHHHHHHHHHHhcccccccceecccceEEEEeeHHHHHHHHHHHH
Confidence            45566889999999998866 5899999999999999999999998765432222   1348999999999999999999


Q ss_pred             HHHHhhcCcEEEEeeCCCChHHHHHHHhcCCeEEEeCchhHHHHHHhcCCcccccCCceEEEecCcccccccCCchHHHH
Q 002040          561 RKFAKVMGVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMGFEPQITR  640 (976)
Q Consensus       561 ~~~~~~~~~~~~~~~gg~~~~~~~~~l~~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDEah~~~~~~f~~~i~~  640 (976)
                      .+....+|+.|.-++|......+  .+ .+++||||||+.. +.+....+.....+-+.++|+||.|. +....++.+..
T Consensus       385 SkRla~~GI~V~ElTgD~~l~~~--qi-eeTqVIV~TPEK~-DiITRk~gdraY~qlvrLlIIDEIHL-LhDdRGpvLES  459 (1674)
T KOG0951|consen  385 SKRLAPLGITVLELTGDSQLGKE--QI-EETQVIVTTPEKW-DIITRKSGDRAYEQLVRLLIIDEIHL-LHDDRGPVLES  459 (1674)
T ss_pred             HhhccccCcEEEEecccccchhh--hh-hcceeEEeccchh-hhhhcccCchhHHHHHHHHhhhhhhh-cccccchHHHH
Confidence            99999999999999998654322  12 3589999999987 56666555555566688999999994 44456777766


Q ss_pred             HHHhc-------CCCCcEEEEeccCcHHHHHHHHHHcCCCeEEEeCCcccccCCceEEEEecCc---chHHH----HHHH
Q 002040          641 IVQNI-------RPDRQTVLFSATFPRQVEILARKVLNKPVEIQVGGRSVVNKDITQLVEVRPE---SDRFL----RLLE  706 (976)
Q Consensus       641 il~~~-------~~~~q~i~~SAT~~~~~~~l~~~~l~~~~~i~~~~~~~~~~~i~q~~~~~~~---~~k~~----~l~~  706 (976)
                      |+...       .....++++|||+|+-.. .+..+..++--+...+.++.+.++.|.++-...   ..++.    ...+
T Consensus       460 IVaRt~r~ses~~e~~RlVGLSATLPNy~D-V~~Fl~v~~~glf~fd~syRpvPL~qq~Igi~ek~~~~~~qamNe~~ye  538 (1674)
T KOG0951|consen  460 IVARTFRRSESTEEGSRLVGLSATLPNYED-VASFLRVDPEGLFYFDSSYRPVPLKQQYIGITEKKPLKRFQAMNEACYE  538 (1674)
T ss_pred             HHHHHHHHhhhcccCceeeeecccCCchhh-hHHHhccCcccccccCcccCcCCccceEeccccCCchHHHHHHHHHHHH
Confidence            65443       235789999999998654 344444444444444555555666666543332   22332    2334


Q ss_pred             HHHhhhcCCcEEEEecCHHHHHHHHHHHHHC-------------------------------------CCCceeccCCCC
Q 002040          707 LLGEWYEKGKILIFVHSQEKCDALFRDLLKH-------------------------------------GYPCLSLHGAKD  749 (976)
Q Consensus       707 ~l~~~~~~~kvLIF~~s~~~~~~l~~~L~~~-------------------------------------~~~~~~lhg~~~  749 (976)
                      .+.+....+++|||+.++++....++.++..                                     .+.++++|+||+
T Consensus       539 KVm~~agk~qVLVFVHsRkET~ktA~aIRd~~le~dtls~fmre~s~s~eilrtea~~~kn~dLkdLLpygfaIHhAGl~  618 (1674)
T KOG0951|consen  539 KVLEHAGKNQVLVFVHSRKETAKTARAIRDKALEEDTLSRFMREDSASREILRTEAGQAKNPDLKDLLPYGFAIHHAGLN  618 (1674)
T ss_pred             HHHHhCCCCcEEEEEEechHHHHHHHHHHHHHhhhhHHHHHHhcccchhhhhhhhhhcccChhHHHHhhccceeeccCCC
Confidence            4444455689999999998887777776521                                     467899999999


Q ss_pred             HHHHHHHHHHhccCCccEEEecCcccccCCCCCCcEEEE----eCC------CCCHHHHHHHhcccCCCCCc--cEEEEE
Q 002040          750 QTDRESTISDFKSNVCNLLIATSVAARGLDVKELELVIN----FDA------PNHYEDYVHRVGRTGRAGRK--GCAITF  817 (976)
Q Consensus       750 ~~~R~~~~~~F~~g~~~vLVaT~v~~~GlDi~~v~~VI~----~d~------p~s~~~y~Qr~GR~gR~g~~--g~~~~~  817 (976)
                      ..+|..+...|.+|.++|||+|-.++.|+|+|+-+++|-    ||+      +.++.+.+|++||+||.+-.  |..++.
T Consensus       619 R~dR~~~EdLf~~g~iqvlvstatlawgvnlpahtViikgtqvy~pekg~w~elsp~dv~qmlgragrp~~D~~gegiii  698 (1674)
T KOG0951|consen  619 RKDRELVEDLFADGHIQVLVSTATLAWGVNLPAHTVIIKGTQVYDPEKGRWTELSPLDVMQMLGRAGRPQYDTCGEGIII  698 (1674)
T ss_pred             cchHHHHHHHHhcCceeEEEeehhhhhhcCCCcceEEecCccccCcccCccccCCHHHHHHHHhhcCCCccCcCCceeec
Confidence            999999999999999999999999999999998777773    665      44789999999999997543  444433


Q ss_pred             ecCCCcCchHHHHHHHhhccCCCC---hHHHHHHHHHHHHHhhh
Q 002040          818 ISEEDAKYSPDLVKALELSEQVVP---DDLKALADSFMAKVNQG  858 (976)
Q Consensus       818 ~~~~d~~~~~~i~~~l~~~~~~vp---~~l~~l~~~~~~~~~~~  858 (976)
                      -...+..+      .+...++.+|   ..+..+++.+.+.+-.|
T Consensus       699 t~~se~qy------yls~mn~qLpiesq~~~rl~d~lnaeiv~G  736 (1674)
T KOG0951|consen  699 TDHSELQY------YLSLMNQQLPIESQFVSRLADCLNAEIVLG  736 (1674)
T ss_pred             cCchHhhh------hHHhhhhcCCChHHHHHHhhhhhhhhhhcc
Confidence            33333222      3333344444   23466666666665443

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

Probab=99.96  E-value=3.1e-27  Score=272.72  Aligned_cols=298  Identities=20%  Similarity=0.273  Sum_probs=204.5

Q ss_pred             CCCcHHHHHHHHHHhc----CCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHHH
Q 002040          488 EKPMPIQAQALPVIMS----GRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKF  563 (976)
Q Consensus       488 ~~p~~~Q~~~i~~il~----g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~~  563 (976)
                      ..|+++|.+|+..+..    ++.+++++|||+|||++++..+...           +..+||||||.+|+.||.+.+..+
T Consensus        35 ~~lr~yQ~~al~a~~~~~~~~~~gvivlpTGaGKT~va~~~~~~~-----------~~~~Lvlv~~~~L~~Qw~~~~~~~  103 (442)
T COG1061          35 FELRPYQEEALDALVKNRRTERRGVIVLPTGAGKTVVAAEAIAEL-----------KRSTLVLVPTKELLDQWAEALKKF  103 (442)
T ss_pred             CCCcHHHHHHHHHHHhhcccCCceEEEeCCCCCHHHHHHHHHHHh-----------cCCEEEEECcHHHHHHHHHHHHHh
Confidence            4589999999999998    8899999999999999876655533           223899999999999998777665


Q ss_pred             HhhcCcEEEEeeCCCChHHHHHHHhcCCeEEEeCchhHHHHHHhcCCcccccCCceEEEecCcccccccCCchHHHHHHH
Q 002040          564 AKVMGVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMGFEPQITRIVQ  643 (976)
Q Consensus       564 ~~~~~~~~~~~~gg~~~~~~~~~l~~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDEah~~~~~~f~~~i~~il~  643 (976)
                      +... . .+..+||....     +.. ..|+|+|...+......   .......+++|||||||++....    ...++.
T Consensus       104 ~~~~-~-~~g~~~~~~~~-----~~~-~~i~vat~qtl~~~~~l---~~~~~~~~~liI~DE~Hh~~a~~----~~~~~~  168 (442)
T COG1061         104 LLLN-D-EIGIYGGGEKE-----LEP-AKVTVATVQTLARRQLL---DEFLGNEFGLIIFDEVHHLPAPS----YRRILE  168 (442)
T ss_pred             cCCc-c-ccceecCceec-----cCC-CcEEEEEhHHHhhhhhh---hhhcccccCEEEEEccccCCcHH----HHHHHH
Confidence            4321 1 23334443221     111 46999999988664100   11233479999999999976433    344444


Q ss_pred             hcCCCCcEEEEeccCcHHHHH---HHHHHcCCCeEEEeCCccccc-----CCceEEEEe-c-------------------
Q 002040          644 NIRPDRQTVLFSATFPRQVEI---LARKVLNKPVEIQVGGRSVVN-----KDITQLVEV-R-------------------  695 (976)
Q Consensus       644 ~~~~~~q~i~~SAT~~~~~~~---l~~~~l~~~~~i~~~~~~~~~-----~~i~q~~~~-~-------------------  695 (976)
                      .+.....+|+||||++..-..   ....+++ ++.+.+.......     +.....+.+ .                   
T Consensus       169 ~~~~~~~~LGLTATp~R~D~~~~~~l~~~~g-~~vy~~~~~~li~~g~Lap~~~~~i~~~~t~~~~~~~~~~~~~~~~~~  247 (442)
T COG1061         169 LLSAAYPRLGLTATPEREDGGRIGDLFDLIG-PIVYEVSLKELIDEGYLAPYKYVEIKVTLTEDEEREYAKESARFRELL  247 (442)
T ss_pred             hhhcccceeeeccCceeecCCchhHHHHhcC-CeEeecCHHHHHhCCCccceEEEEEEeccchHHHHHhhhhhhhhhhhh
Confidence            443333389999998743211   1111111 3333322211111     000000000 0                   


Q ss_pred             -----------------CcchHHHHHHHHHHhhhcCCcEEEEecCHHHHHHHHHHHHHCCCCceeccCCCCHHHHHHHHH
Q 002040          696 -----------------PESDRFLRLLELLGEWYEKGKILIFVHSQEKCDALFRDLLKHGYPCLSLHGAKDQTDRESTIS  758 (976)
Q Consensus       696 -----------------~~~~k~~~l~~~l~~~~~~~kvLIF~~s~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~  758 (976)
                                       ....++..+..++.......++||||.+...+..++..|...++ +..+.|.++..+|..+++
T Consensus       248 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lif~~~~~~a~~i~~~~~~~~~-~~~it~~t~~~eR~~il~  326 (442)
T COG1061         248 RARGTLRAENEARRIAIASERKIAAVRGLLLKHARGDKTLIFASDVEHAYEIAKLFLAPGI-VEAITGETPKEEREAILE  326 (442)
T ss_pred             hhhhhhhHHHHHHHHhhccHHHHHHHHHHHHHhcCCCcEEEEeccHHHHHHHHHHhcCCCc-eEEEECCCCHHHHHHHHH
Confidence                             00112222223332222345999999999999999999988887 899999999999999999


Q ss_pred             HhccCCccEEEecCcccccCCCCCCcEEEEeCCCCCHHHHHHHhcccCC-CCCccE
Q 002040          759 DFKSNVCNLLIATSVAARGLDVKELELVINFDAPNHYEDYVHRVGRTGR-AGRKGC  813 (976)
Q Consensus       759 ~F~~g~~~vLVaT~v~~~GlDi~~v~~VI~~d~p~s~~~y~Qr~GR~gR-~g~~g~  813 (976)
                      .|+.|.+++||++.++..|+|+|+++++|...+..|+..|+||+||+-| ...++.
T Consensus       327 ~fr~g~~~~lv~~~vl~EGvDiP~~~~~i~~~~t~S~~~~~Q~lGR~LR~~~~k~~  382 (442)
T COG1061         327 RFRTGGIKVLVTVKVLDEGVDIPDADVLIILRPTGSRRLFIQRLGRGLRPAEGKED  382 (442)
T ss_pred             HHHcCCCCEEEEeeeccceecCCCCcEEEEeCCCCcHHHHHHHhhhhccCCCCCCc
Confidence            9999999999999999999999999999999999999999999999999 333443

>TIGR00595 priA primosomal protein N'

Probab=99.95  E-value=5.3e-27  Score=273.84  Aligned_cols=288  Identities=18%  Similarity=0.232  Sum_probs=197.0

Q ss_pred             EEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHHHHhhcCcEEEEeeCCCChHHHH---
Q 002040          508 IGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQI---  584 (976)
Q Consensus       508 i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~~~~~~~~~~~~~~gg~~~~~~~---  584 (976)
                      |+.|+||||||.+|+..+...+.        .|.++|||+|+++|+.|++..|+..   ++..+..++++.+..+..   
T Consensus         1 LL~g~TGsGKT~v~l~~i~~~l~--------~g~~vLvlvP~i~L~~Q~~~~l~~~---f~~~v~vlhs~~~~~er~~~~   69 (505)
T TIGR00595         1 LLFGVTGSGKTEVYLQAIEKVLA--------LGKSVLVLVPEIALTPQMIQRFKYR---FGSQVAVLHSGLSDSEKLQAW   69 (505)
T ss_pred             CccCCCCCCHHHHHHHHHHHHHH--------cCCeEEEEeCcHHHHHHHHHHHHHH---hCCcEEEEECCCCHHHHHHHH
Confidence            57899999999998766555443        2568999999999999999988875   467788888887765543   


Q ss_pred             HHHhc-CCeEEEeCchhHHHHHHhcCCcccccCCceEEEecCcccccccCC-chH--H--HHHHHhcCCCCcEEEEeccC
Q 002040          585 SELKR-GTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMGF-EPQ--I--TRIVQNIRPDRQTVLFSATF  658 (976)
Q Consensus       585 ~~l~~-~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDEah~~~~~~f-~~~--i--~~il~~~~~~~q~i~~SAT~  658 (976)
                      ..+.. .++|||+|+..|.          ..+.++++|||||+|....++. .+.  .  ..++.....+.++|++|||+
T Consensus        70 ~~~~~g~~~IVVGTrsalf----------~p~~~l~lIIVDEeh~~sykq~~~p~y~ar~~a~~ra~~~~~~vil~SATP  139 (505)
T TIGR00595        70 RKVKNGEILVVIGTRSALF----------LPFKNLGLIIVDEEHDSSYKQEEGPRYHARDVAVYRAKKFNCPVVLGSATP  139 (505)
T ss_pred             HHHHcCCCCEEECChHHHc----------CcccCCCEEEEECCCccccccccCCCCcHHHHHHHHHHhcCCCEEEEeCCC
Confidence            33333 4799999998662          3577899999999997653331 111  1  23344445678999999998


Q ss_pred             cHHHHHHHHHHcCCCeEEEeCCcccc-cCCceEEEEecCcc---hHHHHHHHHHHhhhc-CCcEEEEecCHHH-------
Q 002040          659 PRQVEILARKVLNKPVEIQVGGRSVV-NKDITQLVEVRPES---DRFLRLLELLGEWYE-KGKILIFVHSQEK-------  726 (976)
Q Consensus       659 ~~~~~~l~~~~l~~~~~i~~~~~~~~-~~~i~q~~~~~~~~---~k~~~l~~~l~~~~~-~~kvLIF~~s~~~-------  726 (976)
                      +......+.  .+....+.+...... .......+......   .--..|+..|..... ++++|||+|++..       
T Consensus       140 sles~~~~~--~g~~~~~~l~~r~~~~~~p~v~vid~~~~~~~~~ls~~l~~~i~~~l~~g~qvLvflnrrGya~~~~C~  217 (505)
T TIGR00595       140 SLESYHNAK--QKAYRLLVLTRRVSGRKPPEVKLIDMRKEPRQSFLSPELITAIEQTLAAGEQSILFLNRRGYSKNLLCR  217 (505)
T ss_pred             CHHHHHHHh--cCCeEEeechhhhcCCCCCeEEEEecccccccCCccHHHHHHHHHHHHcCCcEEEEEeCCcCCCeeEhh
Confidence            765433332  122222222211110 01111111111111   111345556655554 4589999776532       


Q ss_pred             -----------------------------------------------------HHHHHHHHHHC--CCCceeccCCCCHH
Q 002040          727 -----------------------------------------------------CDALFRDLLKH--GYPCLSLHGAKDQT  751 (976)
Q Consensus       727 -----------------------------------------------------~~~l~~~L~~~--~~~~~~lhg~~~~~  751 (976)
                                                                           .+.+...|.+.  +.++..+|++++..
T Consensus       218 ~Cg~~~~C~~C~~~l~~h~~~~~l~Ch~Cg~~~~~~~~Cp~C~s~~l~~~g~Gte~~~e~l~~~fp~~~v~~~d~d~~~~  297 (505)
T TIGR00595       218 SCGYILCCPNCDVSLTYHKKEGKLRCHYCGYQEPIPKTCPQCGSEDLVYKGYGTEQVEEELAKLFPGARIARIDSDTTSR  297 (505)
T ss_pred             hCcCccCCCCCCCceEEecCCCeEEcCCCcCcCCCCCCCCCCCCCeeEeecccHHHHHHHHHhhCCCCcEEEEecccccC
Confidence                                                                 36777777765  78899999999877


Q ss_pred             HH--HHHHHHhccCCccEEEecCcccccCCCCCCcEEEEeCCCC------------CHHHHHHHhcccCCCCCccEEEEE
Q 002040          752 DR--ESTISDFKSNVCNLLIATSVAARGLDVKELELVINFDAPN------------HYEDYVHRVGRTGRAGRKGCAITF  817 (976)
Q Consensus       752 ~R--~~~~~~F~~g~~~vLVaT~v~~~GlDi~~v~~VI~~d~p~------------s~~~y~Qr~GR~gR~g~~g~~~~~  817 (976)
                      .+  ..++..|.+|+++|||+|++++.|+|+|++++|+.+|...            ....|+|++||+||.+..|.+++.
T Consensus       298 ~~~~~~~l~~f~~g~~~ILVgT~~i~kG~d~~~v~lV~vl~aD~~l~~pd~ra~E~~~~ll~q~~GRagR~~~~g~viiq  377 (505)
T TIGR00595       298 KGAHEALLNQFANGKADILIGTQMIAKGHHFPNVTLVGVLDADSGLHSPDFRAAERGFQLLTQVAGRAGRAEDPGQVIIQ  377 (505)
T ss_pred             ccHHHHHHHHHhcCCCCEEEeCcccccCCCCCcccEEEEEcCcccccCcccchHHHHHHHHHHHHhccCCCCCCCEEEEE
Confidence            65  8999999999999999999999999999999987554432            146789999999999999998864


Q ss_pred             e
Q 002040          818 I  818 (976)
Q Consensus       818 ~  818 (976)
                      .
T Consensus       378 t  378 (505)
T TIGR00595       378 T  378 (505)
T ss_pred             e
Confidence            4

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).

>KOG0385 consensus Chromatin remodeling complex WSTF-ISWI, small subunit [Transcription]

Probab=99.95  E-value=8.9e-27  Score=262.46  Aligned_cols=314  Identities=22%  Similarity=0.329  Sum_probs=222.4

Q ss_pred             CCcHHHHHHHHHHh----cCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHHHH
Q 002040          489 KPMPIQAQALPVIM----SGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFA  564 (976)
Q Consensus       489 ~p~~~Q~~~i~~il----~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~~~  564 (976)
                      .+.++|.++++|+.    +|-++|+..+||.|||++ .++++.+|....   ...||. ||+||...| ..|.++|.+|+
T Consensus       167 ~lr~YQveGlnWLi~l~engingILaDEMGLGKTlQ-tIs~l~yl~~~~---~~~GPf-LVi~P~StL-~NW~~Ef~rf~  240 (971)
T KOG0385|consen  167 ELRDYQLEGLNWLISLYENGINGILADEMGLGKTLQ-TISLLGYLKGRK---GIPGPF-LVIAPKSTL-DNWMNEFKRFT  240 (971)
T ss_pred             ccchhhhccHHHHHHHHhcCcccEeehhcccchHHH-HHHHHHHHHHhc---CCCCCe-EEEeeHhhH-HHHHHHHHHhC
Confidence            57899999999987    577899999999999998 455555555432   123554 999999888 66889999998


Q ss_pred             hhcCcEEEEeeCCCChHHHH-HHH--hcCCeEEEeCchhHHHHHHhcCCcccccCCceEEEecCcccccccCCchHHHHH
Q 002040          565 KVMGVRCVPVYGGSGVAQQI-SEL--KRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMGFEPQITRI  641 (976)
Q Consensus       565 ~~~~~~~~~~~gg~~~~~~~-~~l--~~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDEah~~~~~~f~~~i~~i  641 (976)
                      .  ++.+++++|.......+ ..+  ....+|+|+|++..+.--.     ...--.|.||||||||++-+..  ..+..+
T Consensus       241 P--~l~~~~~~Gdk~eR~~~~r~~~~~~~fdV~iTsYEi~i~dk~-----~lk~~~W~ylvIDEaHRiKN~~--s~L~~~  311 (971)
T KOG0385|consen  241 P--SLNVVVYHGDKEERAALRRDIMLPGRFDVCITSYEIAIKDKS-----FLKKFNWRYLVIDEAHRIKNEK--SKLSKI  311 (971)
T ss_pred             C--CcceEEEeCCHHHHHHHHHHhhccCCCceEeehHHHHHhhHH-----HHhcCCceEEEechhhhhcchh--hHHHHH
Confidence            5  56777777765332221 111  2257999999998765321     1222358999999999987653  344456


Q ss_pred             HHhcCCCCcEEEEeccCcH-HHHH--------------------------------------------------------
Q 002040          642 VQNIRPDRQTVLFSATFPR-QVEI--------------------------------------------------------  664 (976)
Q Consensus       642 l~~~~~~~q~i~~SAT~~~-~~~~--------------------------------------------------------  664 (976)
                      +..+.... -|++|+||-. ++..                                                        
T Consensus       312 lr~f~~~n-rLLlTGTPLQNNL~ELWaLLnFllPdiF~~~e~F~swF~~~~~~~~~e~v~~Lh~vL~pFlLRR~K~dVe~  390 (971)
T KOG0385|consen  312 LREFKTDN-RLLLTGTPLQNNLHELWALLNFLLPDIFNSAEDFDSWFDFTNCEGDQELVSRLHKVLRPFLLRRIKSDVEK  390 (971)
T ss_pred             HHHhcccc-eeEeeCCcccccHHHHHHHHHhhchhhccCHHHHHHHHcccccccCHHHHHHHHhhhhHHHHHHHHHhHhh
Confidence            66654433 3566666411 1100                                                        


Q ss_pred             -------------------------------------------------HHHHHcCCCeEEEeCCcccccCCceEEEEec
Q 002040          665 -------------------------------------------------LARKVLNKPVEIQVGGRSVVNKDITQLVEVR  695 (976)
Q Consensus       665 -------------------------------------------------l~~~~l~~~~~i~~~~~~~~~~~i~q~~~~~  695 (976)
                                                                       ..++.++.|..+... .+.  +.....-.++
T Consensus       391 sLppKkE~~iyvgms~mQkk~Y~~iL~kdl~~~n~~~~~~k~kL~NI~mQLRKccnHPYLF~g~-ePg--~pyttdehLv  467 (971)
T KOG0385|consen  391 SLPPKKELIIYVGMSSMQKKWYKAILMKDLDALNGEGKGEKTKLQNIMMQLRKCCNHPYLFDGA-EPG--PPYTTDEHLV  467 (971)
T ss_pred             cCCCcceeeEeccchHHHHHHHHHHHHhcchhhcccccchhhHHHHHHHHHHHhcCCccccCCC-CCC--CCCCcchHHH
Confidence                                                             011122222211110 000  0001111123


Q ss_pred             CcchHHHHHHHHHHhhhcC-CcEEEEecCHHHHHHHHHHHHHCCCCceeccCCCCHHHHHHHHHHhccC---CccEEEec
Q 002040          696 PESDRFLRLLELLGEWYEK-GKILIFVHSQEKCDALFRDLLKHGYPCLSLHGAKDQTDRESTISDFKSN---VCNLLIAT  771 (976)
Q Consensus       696 ~~~~k~~~l~~~l~~~~~~-~kvLIF~~s~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g---~~~vLVaT  771 (976)
                      ..+.|+..|-.+|..+... .+||||.+...+.+.|..|+.-.+|.++.|.|.++..+|...|+.|...   .+-+|++|
T Consensus       468 ~nSGKm~vLDkLL~~Lk~~GhRVLIFSQmt~mLDILeDyc~~R~y~ycRiDGSt~~eeR~~aI~~fn~~~s~~FiFlLST  547 (971)
T KOG0385|consen  468 TNSGKMLVLDKLLPKLKEQGHRVLIFSQMTRMLDILEDYCMLRGYEYCRLDGSTSHEEREDAIEAFNAPPSEKFIFLLST  547 (971)
T ss_pred             hcCcceehHHHHHHHHHhCCCeEEEeHHHHHHHHHHHHHHHhcCceeEeecCCCCcHHHHHHHHhcCCCCcceEEEEEec
Confidence            3456777777787777655 4999999999999999999999999999999999999999999999844   46789999


Q ss_pred             CcccccCCCCCCcEEEEeCCCCCHHHHHHHhcccCCCCCccEEEE--EecCC
Q 002040          772 SVAARGLDVKELELVINFDAPNHYEDYVHRVGRTGRAGRKGCAIT--FISEE  821 (976)
Q Consensus       772 ~v~~~GlDi~~v~~VI~~d~p~s~~~y~Qr~GR~gR~g~~g~~~~--~~~~~  821 (976)
                      .+++.|||+..+++||.||..|||..-+|.+.||+|.||+..|.+  |+|..
T Consensus       548 RAGGLGINL~aADtVIlyDSDWNPQ~DLQAmDRaHRIGQ~K~V~V~RLiten  599 (971)
T KOG0385|consen  548 RAGGLGINLTAADTVILYDSDWNPQVDLQAMDRAHRIGQKKPVVVYRLITEN  599 (971)
T ss_pred             cccccccccccccEEEEecCCCCchhhhHHHHHHHhhCCcCceEEEEEeccc
Confidence            999999999999999999999999999999999999999766555  56654

>PRK13107 preprotein translocase subunit SecA; Reviewed

Probab=99.94  E-value=1e-25  Score=266.33  Aligned_cols=322  Identities=18%  Similarity=0.220  Sum_probs=228.9

Q ss_pred             cCCCCCcHHHHHHHHHHhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHHHH
Q 002040          485 LNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFA  564 (976)
Q Consensus       485 ~~~~~p~~~Q~~~i~~il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~~~  564 (976)
                      +|. .|++.|.-+--.+  ...-|+.++||.|||++|++|++..++.        |..|.||+|+..||.|..+++..++
T Consensus        79 lgm-~~ydVQliGgl~L--~~G~IaEm~TGEGKTL~a~lp~~l~al~--------g~~VhIvT~ndyLA~RD~e~m~~l~  147 (908)
T PRK13107         79 FEM-RHFDVQLLGGMVL--DSNRIAEMRTGEGKTLTATLPAYLNALT--------GKGVHVITVNDYLARRDAENNRPLF  147 (908)
T ss_pred             hCC-CcCchHHhcchHh--cCCccccccCCCCchHHHHHHHHHHHhc--------CCCEEEEeCCHHHHHHHHHHHHHHH
Confidence            554 3667776554444  4556899999999999999999877654        4459999999999999999999999


Q ss_pred             hhcCcEEEEeeCCCChHHHHHHHhcCCeEEEeCchhH-HHHHHhcCCc---ccccCCceEEEecCccccccc-CC-----
Q 002040          565 KVMGVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRM-IDILCTSGGK---ITNLRRVTYLVMDEADRMFDM-GF-----  634 (976)
Q Consensus       565 ~~~~~~~~~~~gg~~~~~~~~~l~~~~~Iiv~Tp~~L-~~~l~~~~~~---~~~l~~~~~vVlDEah~~~~~-~f-----  634 (976)
                      ..+|+.|.+++++.+.......  -+++|+|+||+.| +++|..+-..   ......+.++||||||.|+-. ..     
T Consensus       148 ~~lGlsv~~i~~~~~~~~r~~~--Y~~dI~YgT~~e~gfDyLrdnm~~~~~~~vqr~~~~aIvDEvDsiLiDEArtPLII  225 (908)
T PRK13107        148 EFLGLTVGINVAGLGQQEKKAA--YNADITYGTNNEFGFDYLRDNMAFSPQERVQRPLHYALIDEVDSILIDEARTPLII  225 (908)
T ss_pred             HhcCCeEEEecCCCCHHHHHhc--CCCCeEEeCCCcccchhhhccCccchhhhhccccceeeecchhhhccccCCCceee
Confidence            9999999999999886443222  2689999999999 8888665110   112367889999999976421 10     


Q ss_pred             ----------chHHHHHHHhcCC-------------------CCc-----------------------------------
Q 002040          635 ----------EPQITRIVQNIRP-------------------DRQ-----------------------------------  650 (976)
Q Consensus       635 ----------~~~i~~il~~~~~-------------------~~q-----------------------------------  650 (976)
                                ...+..++..+..                   ..+                                   
T Consensus       226 Sg~~~~~~~~y~~~~~~v~~L~~~~~~~~~~~~~~~dy~idek~~~v~LTe~G~~~~e~~l~~~~~~~~~~~l~~~~~~~  305 (908)
T PRK13107        226 SGAAEDSSELYIKINTLIPNLIRQDKEDTEEYVGEGDYSIDEKAKQVHFTERGQEKVENLLIERGMLAEGDSLYSAANIS  305 (908)
T ss_pred             cCCCccchHHHHHHHHHHHHHHhhhhccccccCCCCCEEEecCCCeeeechHHHHHHHHHHHhCCcccCcccccCchhhH
Confidence                      0011111111110                   011                                   


Q ss_pred             --------------------------------------------------------------------------------
Q 002040          651 --------------------------------------------------------------------------------  650 (976)
Q Consensus       651 --------------------------------------------------------------------------------  650 (976)
                                                                                                      
T Consensus       306 ~~~~i~~aL~A~~lf~~d~dYiV~dg~V~IVDe~TGRim~grrwsdGLHQaIEaKE~v~I~~e~~t~AsIT~QnfFr~Y~  385 (908)
T PRK13107        306 LLHHVNAALRAHTLFEKDVDYIVQDNEVIIVDEHTGRTMPGRRWSEGLHQAVEAKEGVHIQNENQTLASITFQNYFRQYE  385 (908)
T ss_pred             HHHHHHHHHHHHHHHhcCCceEEECCEEEEEECCCCCCCCCCccchHHHHHHHHhcCCCCCCCceeeeeehHHHHHHhhh
Confidence                                                                                            


Q ss_pred             -EEEEeccCcHHHHHHHHHHcCCCeEEEeCCcccccCCceEEEEecCcchHHHHHHHHHHhhhcC-CcEEEEecCHHHHH
Q 002040          651 -TVLFSATFPRQVEILARKVLNKPVEIQVGGRSVVNKDITQLVEVRPESDRFLRLLELLGEWYEK-GKILIFVHSQEKCD  728 (976)
Q Consensus       651 -~i~~SAT~~~~~~~l~~~~l~~~~~i~~~~~~~~~~~i~q~~~~~~~~~k~~~l~~~l~~~~~~-~kvLIF~~s~~~~~  728 (976)
                       +.+||+|.......|... ++-.+...+...+....... ...+.....|+..++..+...+.. .++||||+|+..++
T Consensus       386 kL~GMTGTa~te~~Ef~~i-Y~l~Vv~IPTnkp~~R~d~~-d~iy~t~~~K~~Aii~ei~~~~~~GrpVLV~t~sv~~se  463 (908)
T PRK13107        386 KLAGMTGTADTEAFEFQHI-YGLDTVVVPTNRPMVRKDMA-DLVYLTADEKYQAIIKDIKDCRERGQPVLVGTVSIEQSE  463 (908)
T ss_pred             HhhcccCCChHHHHHHHHH-hCCCEEECCCCCCccceeCC-CcEEeCHHHHHHHHHHHHHHHHHcCCCEEEEeCcHHHHH
Confidence             222333322222211111 11111111111111111111 123345577888888888776654 49999999999999


Q ss_pred             HHHHHHHHCCCCceeccCCCCHHHHHHHHHHhccCCccEEEecCcccccCCCC---------------------------
Q 002040          729 ALFRDLLKHGYPCLSLHGAKDQTDRESTISDFKSNVCNLLIATSVAARGLDVK---------------------------  781 (976)
Q Consensus       729 ~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLVaT~v~~~GlDi~---------------------------  781 (976)
                      .|+..|...|+++..+|+.+++.++..+...|+.|.  |+|||++|+||+||.                           
T Consensus       464 ~ls~~L~~~gi~~~vLnak~~~~Ea~ii~~Ag~~G~--VtIATnmAGRGTDIkLggn~~~~~~~~~~~~~~~~~~~~~~~  541 (908)
T PRK13107        464 LLARLMVKEKIPHEVLNAKFHEREAEIVAQAGRTGA--VTIATNMAGRGTDIVLGGNWNMEIEALENPTAEQKAKIKADW  541 (908)
T ss_pred             HHHHHHHHCCCCeEeccCcccHHHHHHHHhCCCCCc--EEEecCCcCCCcceecCCchHHhhhhhcchhhHHHHHHHHHH
Confidence            999999999999999999999999999999999999  999999999999997                           


Q ss_pred             ----------CCcEEEEeCCCCCHHHHHHHhcccCCCCCccEEEEEecCCCc
Q 002040          782 ----------ELELVINFDAPNHYEDYVHRVGRTGRAGRKGCAITFISEEDA  823 (976)
Q Consensus       782 ----------~v~~VI~~d~p~s~~~y~Qr~GR~gR~g~~g~~~~~~~~~d~  823 (976)
                                +=-+||-...+.|----.|-.||+||.|.+|.+..|++-+|.
T Consensus       542 ~~~~~~V~~~GGL~VIgTerheSrRID~QLrGRaGRQGDPGss~f~lSlED~  593 (908)
T PRK13107        542 QIRHDEVVAAGGLHILGTERHESRRIDNQLRGRAGRQGDAGSSRFYLSMEDS  593 (908)
T ss_pred             HhhHHHHHHcCCCEEEecccCchHHHHhhhhcccccCCCCCceeEEEEeCcH
Confidence                      234788888888888889999999999999999999997765

>KOG0947 consensus Cytoplasmic exosomal RNA helicase SKI2, DEAD-box superfamily [RNA processing and modification]

Probab=99.94  E-value=9.5e-26  Score=258.89  Aligned_cols=324  Identities=19%  Similarity=0.244  Sum_probs=234.3

Q ss_pred             HHcCCCCCcHHHHHHHHHHhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHH
Q 002040          483 RKLNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRK  562 (976)
Q Consensus       483 ~~~~~~~p~~~Q~~~i~~il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~  562 (976)
                      ..++|. |-++|.+||-.+..|..|+|.|+|.+|||+++-.++...        ..++.++++..|-.+|-+|-+..|+.
T Consensus       292 ~~~pFe-lD~FQk~Ai~~lerg~SVFVAAHTSAGKTvVAEYAiala--------q~h~TR~iYTSPIKALSNQKfRDFk~  362 (1248)
T KOG0947|consen  292 LIYPFE-LDTFQKEAIYHLERGDSVFVAAHTSAGKTVVAEYAIALA--------QKHMTRTIYTSPIKALSNQKFRDFKE  362 (1248)
T ss_pred             hhCCCC-ccHHHHHHHHHHHcCCeEEEEecCCCCcchHHHHHHHHH--------HhhccceEecchhhhhccchHHHHHH
Confidence            345654 889999999999999999999999999999965554432        12466899999999999999999887


Q ss_pred             HHhhcCcEEEEeeCCCChHHHHHHHhcCCeEEEeCchhHHHHHHhcCCcccccCCceEEEecCcccccccCCchHHHHHH
Q 002040          563 FAKVMGVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMGFEPQITRIV  642 (976)
Q Consensus       563 ~~~~~~~~~~~~~gg~~~~~~~~~l~~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDEah~~~~~~f~~~i~~il  642 (976)
                      -+...|    +++|..       ++...+.++|||.+.|..+|.++.   .-++++.+||+||+|.+-|...+..+..++
T Consensus       363 tF~Dvg----LlTGDv-------qinPeAsCLIMTTEILRsMLYrga---dliRDvE~VIFDEVHYiND~eRGvVWEEVi  428 (1248)
T KOG0947|consen  363 TFGDVG----LLTGDV-------QINPEASCLIMTTEILRSMLYRGA---DLIRDVEFVIFDEVHYINDVERGVVWEEVI  428 (1248)
T ss_pred             hccccc----eeecce-------eeCCCcceEeehHHHHHHHHhccc---chhhccceEEEeeeeecccccccccceeee
Confidence            665444    677766       556678999999999999998765   346779999999999988887778888899


Q ss_pred             HhcCCCCcEEEEeccCcHHHHHHHHHHc-CCCeEEEeCCcccccCCceEEEEecC-------------------------
Q 002040          643 QNIRPDRQTVLFSATFPRQVEILARKVL-NKPVEIQVGGRSVVNKDITQLVEVRP-------------------------  696 (976)
Q Consensus       643 ~~~~~~~q~i~~SAT~~~~~~~l~~~~l-~~~~~i~~~~~~~~~~~i~q~~~~~~-------------------------  696 (976)
                      -.+++..++|++|||.|+..+ ++..+. ...-.|.+......+-.+.+++....                         
T Consensus       429 IMlP~HV~~IlLSATVPN~~E-FA~WIGRtK~K~IyViST~kRPVPLEh~l~t~~~l~kiidq~g~fl~~~~~~a~~~~~  507 (1248)
T KOG0947|consen  429 IMLPRHVNFILLSATVPNTLE-FADWIGRTKQKTIYVISTSKRPVPLEHYLYTKKSLFKIIDQNGIFLLKGIKDAKDSLK  507 (1248)
T ss_pred             eeccccceEEEEeccCCChHH-HHHHhhhccCceEEEEecCCCccceEEEEEeccceehhhcccchhhhhcchhhhhhhc
Confidence            999999999999999998876 443332 11111222111111111111111000                         


Q ss_pred             --------------------------------------cchHH--HHHHHHHHhhhc--CCcEEEEecCHHHHHHHHHHH
Q 002040          697 --------------------------------------ESDRF--LRLLELLGEWYE--KGKILIFVHSQEKCDALFRDL  734 (976)
Q Consensus       697 --------------------------------------~~~k~--~~l~~~l~~~~~--~~kvLIF~~s~~~~~~l~~~L  734 (976)
                                                            ...+.  ...+.+|.....  --|+||||-++..|+..+.+|
T Consensus       508 ~~ak~~~~~~~~~~~~rgs~~~ggk~~~~~g~~r~~~~~~nrr~~~~~l~lin~L~k~~lLP~VvFvFSkkrCde~a~~L  587 (1248)
T KOG0947|consen  508 KEAKFVDVEKSDARGGRGSQKRGGKTNYHNGGSRGSGIGKNRRKQPTWLDLINHLRKKNLLPVVVFVFSKKRCDEYADYL  587 (1248)
T ss_pred             ccccccccccccccccccccccCCcCCCCCCCcccccccccccccchHHHHHHHHhhcccCceEEEEEccccHHHHHHHH
Confidence                                                  00011  113333333222  238999999999999999999


Q ss_pred             HHCC---------------------------------------CCceeccCCCCHHHHHHHHHHhccCCccEEEecCccc
Q 002040          735 LKHG---------------------------------------YPCLSLHGAKDQTDRESTISDFKSNVCNLLIATSVAA  775 (976)
Q Consensus       735 ~~~~---------------------------------------~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLVaT~v~~  775 (976)
                      ...+                                       -.++++||++-+--++-+.-.|..|-++||+||..++
T Consensus       588 ~~~nL~~~~EKseV~lfl~k~~~rLk~~DR~LPQvl~m~~ll~RGiaVHH~GlLPivKE~VE~LFqrGlVKVLFATETFA  667 (1248)
T KOG0947|consen  588 TNLNLTDSKEKSEVHLFLSKAVARLKGEDRNLPQVLSMRSLLLRGIAVHHGGLLPIVKEVVELLFQRGLVKVLFATETFA  667 (1248)
T ss_pred             hccCcccchhHHHHHHHHHHHHHhcChhhccchHHHHHHHHHhhcchhhcccchHHHHHHHHHHHhcCceEEEeehhhhh
Confidence            6541                                       1367799999999999999999999999999999999


Q ss_pred             ccCCCCCCcEEEEe----CC----CCCHHHHHHHhcccCCCCC--ccEEEEEecCCCcCchHHHHH
Q 002040          776 RGLDVKELELVINF----DA----PNHYEDYVHRVGRTGRAGR--KGCAITFISEEDAKYSPDLVK  831 (976)
Q Consensus       776 ~GlDi~~v~~VI~~----d~----p~s~~~y~Qr~GR~gR~g~--~g~~~~~~~~~d~~~~~~i~~  831 (976)
                      +|+|.|.-.+|+.-    |-    -..|-.|.|++|||||-|-  +|+++++.... ......+.+
T Consensus       668 MGVNMPARtvVF~Sl~KhDG~efR~L~PGEytQMAGRAGRRGlD~tGTVii~~~~~-vp~~a~l~~  732 (1248)
T KOG0947|consen  668 MGVNMPARTVVFSSLRKHDGNEFRELLPGEYTQMAGRAGRRGLDETGTVIIMCKDS-VPSAATLKR  732 (1248)
T ss_pred             hhcCCCceeEEeeehhhccCcceeecCChhHHhhhccccccccCcCceEEEEecCC-CCCHHHHhh
Confidence            99999987777641    11    2257799999999999874  68888777644 233334443

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

Probab=99.94  E-value=2e-25  Score=278.81  Aligned_cols=306  Identities=17%  Similarity=0.219  Sum_probs=198.4

Q ss_pred             CCCcHHHHHHHHHHh----c-CCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHH
Q 002040          488 EKPMPIQAQALPVIM----S-GRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRK  562 (976)
Q Consensus       488 ~~p~~~Q~~~i~~il----~-g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~  562 (976)
                      ..|+++|.+||..+.    . .+.+|++++||||||.+++..+ ..+...     +...+||||||+.+|+.|+...|..
T Consensus       412 ~~lR~YQ~~AI~ai~~a~~~g~r~~Ll~maTGSGKT~tai~li-~~L~~~-----~~~~rVLfLvDR~~L~~Qa~~~F~~  485 (1123)
T PRK11448        412 LGLRYYQEDAIQAVEKAIVEGQREILLAMATGTGKTRTAIALM-YRLLKA-----KRFRRILFLVDRSALGEQAEDAFKD  485 (1123)
T ss_pred             CCCCHHHHHHHHHHHHHHHhccCCeEEEeCCCCCHHHHHHHHH-HHHHhc-----CccCeEEEEecHHHHHHHHHHHHHh
Confidence            358999999998876    2 3679999999999998855444 344332     2246899999999999999999988


Q ss_pred             HHhhcCcEEEEeeCCCChHHHHHHHhcCCeEEEeCchhHHHHHHhcCC--cccccCCceEEEecCcccccc---------
Q 002040          563 FAKVMGVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGG--KITNLRRVTYLVMDEADRMFD---------  631 (976)
Q Consensus       563 ~~~~~~~~~~~~~gg~~~~~~~~~l~~~~~Iiv~Tp~~L~~~l~~~~~--~~~~l~~~~~vVlDEah~~~~---------  631 (976)
                      +....+..+..+++.......  .......|+|+|+..|...+.....  ....+..+++|||||||+...         
T Consensus       486 ~~~~~~~~~~~i~~i~~L~~~--~~~~~~~I~iaTiQtl~~~~~~~~~~~~~~~~~~fdlIIiDEaHRs~~~d~~~~~~~  563 (1123)
T PRK11448        486 TKIEGDQTFASIYDIKGLEDK--FPEDETKVHVATVQGMVKRILYSDDPMDKPPVDQYDCIIVDEAHRGYTLDKEMSEGE  563 (1123)
T ss_pred             cccccccchhhhhchhhhhhh--cccCCCCEEEEEHHHHHHhhhccccccccCCCCcccEEEEECCCCCCccccccccch
Confidence            632222122222222111111  1123579999999998776533211  113467889999999998531         


Q ss_pred             cC------CchHHHHHHHhcCCCCcEEEEeccCcHHHHHHHHHHcCCCeEEEeCCc----ccc-----cCCceEE-----
Q 002040          632 MG------FEPQITRIVQNIRPDRQTVLFSATFPRQVEILARKVLNKPVEIQVGGR----SVV-----NKDITQL-----  691 (976)
Q Consensus       632 ~~------f~~~i~~il~~~~~~~q~i~~SAT~~~~~~~l~~~~l~~~~~i~~~~~----~~~-----~~~i~q~-----  691 (976)
                      .+      +...+..++.++  +...|+|||||....    ..+++.|+....-..    +..     +..+...     
T Consensus       564 ~~~~~~~~~~~~yr~iL~yF--dA~~IGLTATP~r~t----~~~FG~pv~~Ysl~eAI~DG~Lv~~~~p~~i~t~~~~~g  637 (1123)
T PRK11448        564 LQFRDQLDYVSKYRRVLDYF--DAVKIGLTATPALHT----TEIFGEPVYTYSYREAVIDGYLIDHEPPIRIETRLSQEG  637 (1123)
T ss_pred             hccchhhhHHHHHHHHHhhc--CccEEEEecCCccch----hHHhCCeeEEeeHHHHHhcCCcccCcCCEEEEEEecccc
Confidence            01      134566777765  356899999986532    223333332110000    000     0000000     


Q ss_pred             ------------------E--EecCc---------------chHHHHHHHHHHhhh---cCCcEEEEecCHHHHHHHHHH
Q 002040          692 ------------------V--EVRPE---------------SDRFLRLLELLGEWY---EKGKILIFVHSQEKCDALFRD  733 (976)
Q Consensus       692 ------------------~--~~~~~---------------~~k~~~l~~~l~~~~---~~~kvLIF~~s~~~~~~l~~~  733 (976)
                                        +  ...+.               ......++..|..+.   ..+++||||.+...|+.++..
T Consensus       638 i~~~~~e~~~~~~~~~~~i~~~~l~d~~~~~~~~~~~~vi~~~~~~~i~~~l~~~l~~~~~~KtiIF~~s~~HA~~i~~~  717 (1123)
T PRK11448        638 IHFEKGEEVEVINTQTGEIDLATLEDEVDFEVEDFNRRVITESFNRVVCEELAKYLDPTGEGKTLIFAATDAHADMVVRL  717 (1123)
T ss_pred             ccccccchhhhcchhhhhhhhccCcHHHhhhHHHHHHHHhhHHHHHHHHHHHHHHHhccCCCcEEEEEcCHHHHHHHHHH
Confidence                              0  00000               000111122222222   237999999999999999888


Q ss_pred             HHHC------CC---CceeccCCCCHHHHHHHHHHhccCCc-cEEEecCcccccCCCCCCcEEEEeCCCCCHHHHHHHhc
Q 002040          734 LLKH------GY---PCLSLHGAKDQTDRESTISDFKSNVC-NLLIATSVAARGLDVKELELVINFDAPNHYEDYVHRVG  803 (976)
Q Consensus       734 L~~~------~~---~~~~lhg~~~~~~R~~~~~~F~~g~~-~vLVaT~v~~~GlDi~~v~~VI~~d~p~s~~~y~Qr~G  803 (976)
                      |...      ++   .|..+||.++  .+..++..|+++.. .|||+++++.+|+|+|.|.+||++.++.|...|+|++|
T Consensus       718 L~~~f~~~~~~~~~~~v~~itg~~~--~~~~li~~Fk~~~~p~IlVsvdmL~TG~DvP~v~~vVf~rpvkS~~lf~QmIG  795 (1123)
T PRK11448        718 LKEAFKKKYGQVEDDAVIKITGSID--KPDQLIRRFKNERLPNIVVTVDLLTTGIDVPSICNLVFLRRVRSRILYEQMLG  795 (1123)
T ss_pred             HHHHHHhhcCCcCccceEEEeCCcc--chHHHHHHHhCCCCCeEEEEecccccCCCcccccEEEEecCCCCHHHHHHHHh
Confidence            7653      22   4567899886  46789999999887 69999999999999999999999999999999999999


Q ss_pred             ccCCCC
Q 002040          804 RTGRAG  809 (976)
Q Consensus       804 R~gR~g  809 (976)
                      |+.|..
T Consensus       796 RgtR~~  801 (1123)
T PRK11448        796 RATRLC  801 (1123)
T ss_pred             hhccCC
Confidence            999963

>KOG0926 consensus DEAH-box RNA helicase [RNA processing and modification; Translation, ribosomal structure and biogenesis]

Probab=99.94  E-value=3.3e-26  Score=257.76  Aligned_cols=307  Identities=20%  Similarity=0.257  Sum_probs=210.1

Q ss_pred             HHHHHHHHhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHHHHhhcCcEEEE
Q 002040          494 QAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVMGVRCVP  573 (976)
Q Consensus       494 Q~~~i~~il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~~~~~~~~~~~~  573 (976)
                      .++++.+|..+--+||||.||||||++.-..++..=+.....  .++..+-|.-|.|..|..+...+..-+..+|-.|..
T Consensus       261 Eq~IMEaIn~n~vvIIcGeTGsGKTTQvPQFLYEAGf~s~~~--~~~gmIGITqPRRVAaiamAkRVa~EL~~~~~eVsY  338 (1172)
T KOG0926|consen  261 EQRIMEAINENPVVIICGETGSGKTTQVPQFLYEAGFASEQS--SSPGMIGITQPRRVAAIAMAKRVAFELGVLGSEVSY  338 (1172)
T ss_pred             HHHHHHHhhcCCeEEEecCCCCCccccchHHHHHcccCCccC--CCCCeeeecCchHHHHHHHHHHHHHHhccCccceeE
Confidence            355667777777899999999999997544444443332221  124477889999999987765554332224434433


Q ss_pred             e--eCCCChHHHHHHHhcCCeEEEeCchhHHHHHHhcCCcccccCCceEEEecCcc-cccccCCchHHHHHHHhcC----
Q 002040          574 V--YGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEAD-RMFDMGFEPQITRIVQNIR----  646 (976)
Q Consensus       574 ~--~gg~~~~~~~~~l~~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDEah-~~~~~~f~~~i~~il~~~~----  646 (976)
                      .  |.|+        +...+.|.++|.|.|+..+.+.    +.|..+++||||||| +..+.+..-.+..-+-.++    
T Consensus       339 qIRfd~t--------i~e~T~IkFMTDGVLLrEi~~D----flL~kYSvIIlDEAHERSvnTDILiGmLSRiV~LR~k~~  406 (1172)
T KOG0926|consen  339 QIRFDGT--------IGEDTSIKFMTDGVLLREIEND----FLLTKYSVIILDEAHERSVNTDILIGMLSRIVPLRQKYY  406 (1172)
T ss_pred             EEEeccc--------cCCCceeEEecchHHHHHHHHh----HhhhhceeEEechhhhccchHHHHHHHHHHHHHHHHHHh
Confidence            2  3332        3346899999999999998765    678999999999999 6655553333332222221    


Q ss_pred             ------CCCcEEEEeccCcHHHHHHH--HHHcC-CCeEEEeCCcccccCCceEEEEecCcchHHHHHHH---HHHhhhcC
Q 002040          647 ------PDRQTVLFSATFPRQVEILA--RKVLN-KPVEIQVGGRSVVNKDITQLVEVRPESDRFLRLLE---LLGEWYEK  714 (976)
Q Consensus       647 ------~~~q~i~~SAT~~~~~~~l~--~~~l~-~~~~i~~~~~~~~~~~i~q~~~~~~~~~k~~~l~~---~l~~~~~~  714 (976)
                            ...++|+||||+-  +..+.  ..++. .|..|.+..+.++   +..+|....+.+.+.....   .|.+.++.
T Consensus       407 ke~~~~kpLKLIIMSATLR--VsDFtenk~LFpi~pPlikVdARQfP---VsIHF~krT~~DYi~eAfrKtc~IH~kLP~  481 (1172)
T KOG0926|consen  407 KEQCQIKPLKLIIMSATLR--VSDFTENKRLFPIPPPLIKVDARQFP---VSIHFNKRTPDDYIAEAFRKTCKIHKKLPP  481 (1172)
T ss_pred             hhhcccCceeEEEEeeeEE--ecccccCceecCCCCceeeeecccCc---eEEEeccCCCchHHHHHHHHHHHHhhcCCC
Confidence                  1356899999972  22222  12222 2234454444333   4444544444443332222   23344578


Q ss_pred             CcEEEEecCHHHHHHHHHHHHHC---------------------------------------------------------
Q 002040          715 GKILIFVHSQEKCDALFRDLLKH---------------------------------------------------------  737 (976)
Q Consensus       715 ~kvLIF~~s~~~~~~l~~~L~~~---------------------------------------------------------  737 (976)
                      |.||||+..+.+++.|+..|++.                                                         
T Consensus       482 G~ILVFvTGQqEV~qL~~kLRK~~p~~f~~~k~~k~~k~~~e~k~~~s~~~~~~k~~dfe~Ed~~~~~ed~d~~~~~~~~  561 (1172)
T KOG0926|consen  482 GGILVFVTGQQEVDQLCEKLRKRFPESFGGVKMKKNVKAFKELKENPSDIGDSNKTDDFEEEDMYESDEDIDQELVDSGF  561 (1172)
T ss_pred             CcEEEEEeChHHHHHHHHHHHhhCccccccchhhhhhhhccccccchhhhccCcccccchhcccccchhhhhhhhhcccc
Confidence            99999999999999999999753                                                         


Q ss_pred             ------------------------------------------CCCceeccCCCCHHHHHHHHHHhccCCccEEEecCccc
Q 002040          738 ------------------------------------------GYPCLSLHGAKDQTDRESTISDFKSNVCNLLIATSVAA  775 (976)
Q Consensus       738 ------------------------------------------~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLVaT~v~~  775 (976)
                                                                .+-|++|++-++...+.+++..-..|..-|+|||++|+
T Consensus       562 ~~~raa~~~~~De~~~~nge~e~d~~e~~~E~~~~~~~~~~~pLyvLPLYSLLs~~~Q~RVF~~~p~g~RLcVVaTNVAE  641 (1172)
T KOG0926|consen  562 ASLRAAFNALADENGSVNGEPEKDESEEGQEAEQGKGKFSPGPLYVLPLYSLLSTEKQMRVFDEVPKGERLCVVATNVAE  641 (1172)
T ss_pred             hhhhhhhhccccccccccCCcccchhhhchhhhhccCCCCCCceEEeehhhhcCHHHhhhhccCCCCCceEEEEeccchh
Confidence                                                      12367788888889999999999999999999999999


Q ss_pred             ccCCCCCCcEEEE--------eCCC----------CCHHHHHHHhcccCCCCCccEEEEEecC
Q 002040          776 RGLDVKELELVIN--------FDAP----------NHYEDYVHRVGRTGRAGRKGCAITFISE  820 (976)
Q Consensus       776 ~GlDi~~v~~VI~--------~d~p----------~s~~~y~Qr~GR~gR~g~~g~~~~~~~~  820 (976)
                      +.|+||+|.+||+        ||.-          .|.++.-||+|||||+| +|+||.+|+.
T Consensus       642 TSLTIPgIkYVVD~Gr~K~R~Yd~~TGV~~FeV~wiSkASadQRAGRAGRtg-pGHcYRLYSS  703 (1172)
T KOG0926|consen  642 TSLTIPGIKYVVDCGRVKERLYDSKTGVSSFEVDWISKASADQRAGRAGRTG-PGHCYRLYSS  703 (1172)
T ss_pred             cccccCCeeEEEeccchhhhccccccCceeEEEEeeeccccchhccccCCCC-CCceeehhhh
Confidence            9999999999997        4432          24555679999999998 9999999975

>COG4098 comFA Superfamily II DNA/RNA helicase required for DNA uptake (late competence protein) [DNA replication, recombination, and repair]

Probab=99.94  E-value=1.8e-24  Score=224.19  Aligned_cols=299  Identities=19%  Similarity=0.230  Sum_probs=209.3

Q ss_pred             CCcHHHHHHHHHHh----cCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHHHH
Q 002040          489 KPMPIQAQALPVIM----SGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFA  564 (976)
Q Consensus       489 ~p~~~Q~~~i~~il----~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~~~  564 (976)
                      +++|.|..+-..++    +..+.|++|-||+|||.. +.+.+..+..+       |..+.|..|....|..++..++.-+
T Consensus        97 ~Ls~~Q~~as~~l~q~i~~k~~~lv~AV~GaGKTEM-if~~i~~al~~-------G~~vciASPRvDVclEl~~Rlk~aF  168 (441)
T COG4098          97 TLSPGQKKASNQLVQYIKQKEDTLVWAVTGAGKTEM-IFQGIEQALNQ-------GGRVCIASPRVDVCLELYPRLKQAF  168 (441)
T ss_pred             ccChhHHHHHHHHHHHHHhcCcEEEEEecCCCchhh-hHHHHHHHHhc-------CCeEEEecCcccchHHHHHHHHHhh
Confidence            68899987766554    668999999999999986 55555555543       7789999999999999998888754


Q ss_pred             hhcCcEEEEeeCCCChHHHHHHHhcCCeEEEeCchhHHHHHHhcCCcccccCCceEEEecCcccccccCCchHHHHHHHh
Q 002040          565 KVMGVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMGFEPQITRIVQN  644 (976)
Q Consensus       565 ~~~~~~~~~~~gg~~~~~~~~~l~~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDEah~~~~~~f~~~i~~il~~  644 (976)
                        .++.+.++||++....       ...+||||...|+.+-.          .+++|||||+|.+.-..-......+-..
T Consensus       169 --~~~~I~~Lyg~S~~~f-------r~plvVaTtHQLlrFk~----------aFD~liIDEVDAFP~~~d~~L~~Av~~a  229 (441)
T COG4098         169 --SNCDIDLLYGDSDSYF-------RAPLVVATTHQLLRFKQ----------AFDLLIIDEVDAFPFSDDQSLQYAVKKA  229 (441)
T ss_pred             --ccCCeeeEecCCchhc-------cccEEEEehHHHHHHHh----------hccEEEEeccccccccCCHHHHHHHHHh
Confidence              3578889999885432       27899999888876542          3789999999976432222223334445


Q ss_pred             cCCCCcEEEEeccCcHHHHHHHHHHcCCCeEEEeCCcccccC-CceEEEEecCcchHH------HHHHHHHHhhhc-CCc
Q 002040          645 IRPDRQTVLFSATFPRQVEILARKVLNKPVEIQVGGRSVVNK-DITQLVEVRPESDRF------LRLLELLGEWYE-KGK  716 (976)
Q Consensus       645 ~~~~~q~i~~SAT~~~~~~~l~~~~l~~~~~i~~~~~~~~~~-~i~q~~~~~~~~~k~------~~l~~~l~~~~~-~~k  716 (976)
                      .....-+|++|||++..++.-+..  ++...+.+..+.-..+ .+...+-+.....++      ..|..+|..... +.+
T Consensus       230 rk~~g~~IylTATp~k~l~r~~~~--g~~~~~klp~RfH~~pLpvPkf~w~~~~~k~l~r~kl~~kl~~~lekq~~~~~P  307 (441)
T COG4098         230 RKKEGATIYLTATPTKKLERKILK--GNLRILKLPARFHGKPLPVPKFVWIGNWNKKLQRNKLPLKLKRWLEKQRKTGRP  307 (441)
T ss_pred             hcccCceEEEecCChHHHHHHhhh--CCeeEeecchhhcCCCCCCCceEEeccHHHHhhhccCCHHHHHHHHHHHhcCCc
Confidence            566778999999999875543322  1222223322211111 122222233333333      245566655443 459


Q ss_pred             EEEEecCHHHHHHHHHHHHH-CCC-CceeccCCCCHHHHHHHHHHhccCCccEEEecCcccccCCCCCCcEEEEeCCC--
Q 002040          717 ILIFVHSQEKCDALFRDLLK-HGY-PCLSLHGAKDQTDRESTISDFKSNVCNLLIATSVAARGLDVKELELVINFDAP--  792 (976)
Q Consensus       717 vLIF~~s~~~~~~l~~~L~~-~~~-~~~~lhg~~~~~~R~~~~~~F~~g~~~vLVaT~v~~~GlDi~~v~~VI~~d~p--  792 (976)
                      +|||++++...+.++..|.. .+. .+..+|+..  ..|...++.|++|.+.|||+|.+++||+++|+|+++|.-.-.  
T Consensus       308 ~liF~p~I~~~eq~a~~lk~~~~~~~i~~Vhs~d--~~R~EkV~~fR~G~~~lLiTTTILERGVTfp~vdV~Vlgaeh~v  385 (441)
T COG4098         308 VLIFFPEIETMEQVAAALKKKLPKETIASVHSED--QHRKEKVEAFRDGKITLLITTTILERGVTFPNVDVFVLGAEHRV  385 (441)
T ss_pred             EEEEecchHHHHHHHHHHHhhCCccceeeeeccC--ccHHHHHHHHHcCceEEEEEeehhhcccccccceEEEecCCccc
Confidence            99999999999999999954 333 346778753  468888999999999999999999999999999998753332  


Q ss_pred             CCHHHHHHHhcccCCCC--CccEEEEEe
Q 002040          793 NHYEDYVHRVGRTGRAG--RKGCAITFI  818 (976)
Q Consensus       793 ~s~~~y~Qr~GR~gR~g--~~g~~~~~~  818 (976)
                      .+-+..+|.+||+||.-  ..|.++.|-
T Consensus       386 fTesaLVQIaGRvGRs~~~PtGdv~FFH  413 (441)
T COG4098         386 FTESALVQIAGRVGRSLERPTGDVLFFH  413 (441)
T ss_pred             ccHHHHHHHhhhccCCCcCCCCcEEEEe
Confidence            46788999999999952  346665553

>KOG0384 consensus Chromodomain-helicase DNA-binding protein [Transcription]

Probab=99.94  E-value=3.5e-26  Score=269.46  Aligned_cols=373  Identities=18%  Similarity=0.274  Sum_probs=241.1

Q ss_pred             cccccccccchhhhcCCHHHHHHHHhhcCce---eccCCCCCcccccccCCCCHHHHHHHHHcCCCCCcHHHHHHHHHHh
Q 002040          426 PFRKNFYIEVKEIARMTPEEVSAYRKQLELK---IHGKDVPKPIKTWHQTGLTSKIMETIRKLNYEKPMPIQAQALPVIM  502 (976)
Q Consensus       426 ~f~~~~~~~~~~~~~~~~~~~~~~~~~~~i~---~~g~~~p~pi~~~~~~~l~~~l~~~l~~~~~~~p~~~Q~~~i~~il  502 (976)
                      |+....|.....+......++..|...-...   -.+...-++...|..+...+..+.     | ..++.+|.+++++++
T Consensus       310 pY~e~TWE~~~~I~~~~~~~~~~~~~Re~sk~~p~~~~~~~~~rp~~~Kle~qp~~~~-----g-~~LRdyQLeGlNWl~  383 (1373)
T KOG0384|consen  310 PYEECTWEDAEDIAKKAQEEIEEFQSRENSKTLPNKGCKYRPQRPRFRKLEKQPEYKG-----G-NELRDYQLEGLNWLL  383 (1373)
T ss_pred             CcccccccchhhhhhhHHHHHHHHhhhhccccCCCCccccCccchhHHHhhcCccccc-----c-chhhhhhcccchhHH
Confidence            4455667666666666666666655443211   112222233344555544444332     2 678999999999987


Q ss_pred             ----cCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHHHHhhcCcEEEEeeCCC
Q 002040          503 ----SGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGS  578 (976)
Q Consensus       503 ----~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~~~~~~~~~~~~~~gg~  578 (976)
                          .++++|++.++|.|||++.+ .+|..|....   ...||. |||||...+ ..|..+|..++   .+++++++|..
T Consensus       384 ~~W~~~~n~ILADEmgLgktvqti-~fl~~l~~~~---~~~gpf-lvvvplst~-~~W~~ef~~w~---~mn~i~y~g~~  454 (1373)
T KOG0384|consen  384 YSWYKRNNCILADEMGLGKTVQTI-TFLSYLFHSL---QIHGPF-LVVVPLSTI-TAWEREFETWT---DMNVIVYHGNL  454 (1373)
T ss_pred             HHHHhcccceehhhcCCCcchHHH-HHHHHHHHhh---hccCCe-EEEeehhhh-HHHHHHHHHHh---hhceeeeecch
Confidence                67899999999999998833 3444444321   124564 899998766 45667777765   67788777776


Q ss_pred             ChHHHHHHHh----c-----CCeEEEeCchhHHHHHHhcCCcccccCCceEEEecCcccccccCCchHHHHHHHhcCCCC
Q 002040          579 GVAQQISELK----R-----GTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMGFEPQITRIVQNIRPDR  649 (976)
Q Consensus       579 ~~~~~~~~l~----~-----~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDEah~~~~~~f~~~i~~il~~~~~~~  649 (976)
                      ...+.+....    .     ..+++++|+..++.--.    . ..--.+.+++|||||++-+.  ...+...+..+..+.
T Consensus       455 ~sr~~i~~ye~~~~~~~~~lkf~~lltTye~~LkDk~----~-L~~i~w~~~~vDeahrLkN~--~~~l~~~l~~f~~~~  527 (1373)
T KOG0384|consen  455 ESRQLIRQYEFYHSSNTKKLKFNALLTTYEIVLKDKA----E-LSKIPWRYLLVDEAHRLKND--ESKLYESLNQFKMNH  527 (1373)
T ss_pred             hHHHHHHHHHheecCCccccccceeehhhHHHhccHh----h-hccCCcceeeecHHhhcCch--HHHHHHHHHHhcccc
Confidence            6555554432    1     36899999987743221    1 11124779999999998654  334444455554443


Q ss_pred             cEEEEeccCc-HHHHHHHHHH-cCCCeEEEe---------------------------------CCcccccCCceEEE--
Q 002040          650 QTVLFSATFP-RQVEILARKV-LNKPVEIQV---------------------------------GGRSVVNKDITQLV--  692 (976)
Q Consensus       650 q~i~~SAT~~-~~~~~l~~~~-l~~~~~i~~---------------------------------~~~~~~~~~i~q~~--  692 (976)
                       -|++|+||- +.+..|...+ +..|-.+..                                 ......+....+++  
T Consensus       528 -rllitgTPlQNsikEL~sLl~Fl~P~kf~~~~~f~~~~~~~~e~~~~~L~~~L~P~~lRr~kkdvekslp~k~E~IlrV  606 (1373)
T KOG0384|consen  528 -RLLITGTPLQNSLKELWSLLHFLMPGKFDSWDEFLEEFDEETEEQVRKLQQILKPFLLRRLKKDVEKSLPPKEETILRV  606 (1373)
T ss_pred             -eeeecCCCccccHHHHHHHhcccCCCCCCcHHHHHHhhcchhHHHHHHHHHHhhHHHHHHHHhhhccCCCCCcceEEEe
Confidence             466666642 2333332111 000000000                                 00000000000110  


Q ss_pred             -----------------------------------------------Eec-----------------------CcchHHH
Q 002040          693 -----------------------------------------------EVR-----------------------PESDRFL  702 (976)
Q Consensus       693 -----------------------------------------------~~~-----------------------~~~~k~~  702 (976)
                                                                     .+.                       ..+.|+.
T Consensus       607 els~lQk~yYk~ILtkN~~~LtKG~~g~~~~lLNimmELkKccNHpyLi~gaee~~~~~~~~~~~d~~L~~lI~sSGKlV  686 (1373)
T KOG0384|consen  607 ELSDLQKQYYKAILTKNFSALTKGAKGSTPSLLNIMMELKKCCNHPYLIKGAEEKILGDFRDKMRDEALQALIQSSGKLV  686 (1373)
T ss_pred             ehhHHHHHHHHHHHHhhHHHHhccCCCCCchHHHHHHHHHHhcCCccccCcHHHHHHHhhhhcchHHHHHHHHHhcCcEE
Confidence                                                           000                       1122223


Q ss_pred             HHHHHHHhhhcC-CcEEEEecCHHHHHHHHHHHHHCCCCceeccCCCCHHHHHHHHHHhc---cCCccEEEecCcccccC
Q 002040          703 RLLELLGEWYEK-GKILIFVHSQEKCDALFRDLLKHGYPCLSLHGAKDQTDRESTISDFK---SNVCNLLIATSVAARGL  778 (976)
Q Consensus       703 ~l~~~l~~~~~~-~kvLIF~~s~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~---~g~~~vLVaT~v~~~Gl  778 (976)
                      .|-.+|..+... .+||||.+.+.+++.|+.||...+|++..|.|.+....|..+|..|.   +..+.||+||.+++.||
T Consensus       687 LLDKLL~rLk~~GHrVLIFSQMVRmLDIL~eYL~~r~ypfQRLDGsvrgelRq~AIDhFnap~SddFvFLLSTRAGGLGI  766 (1373)
T KOG0384|consen  687 LLDKLLPRLKEGGHRVLIFSQMVRMLDILAEYLSLRGYPFQRLDGSVRGELRQQAIDHFNAPDSDDFVFLLSTRAGGLGI  766 (1373)
T ss_pred             eHHHHHHHHhcCCceEEEhHHHHHHHHHHHHHHHHcCCcceeccCCcchHHHHHHHHhccCCCCCceEEEEecccCcccc
Confidence            333444444444 49999999999999999999999999999999999999999999998   45689999999999999


Q ss_pred             CCCCCcEEEEeCCCCCHHHHHHHhcccCCCCCccE--EEEEecCC
Q 002040          779 DVKELELVINFDAPNHYEDYVHRVGRTGRAGRKGC--AITFISEE  821 (976)
Q Consensus       779 Di~~v~~VI~~d~p~s~~~y~Qr~GR~gR~g~~g~--~~~~~~~~  821 (976)
                      |+..+++||+||..|||.+-+|+..||+|+||+..  +|.|+|..
T Consensus       767 NLatADTVIIFDSDWNPQNDLQAqARaHRIGQkk~VnVYRLVTk~  811 (1373)
T KOG0384|consen  767 NLATADTVIIFDSDWNPQNDLQAQARAHRIGQKKHVNVYRLVTKN  811 (1373)
T ss_pred             cccccceEEEeCCCCCcchHHHHHHHHHhhcccceEEEEEEecCC
Confidence            99999999999999999999999999999999765  56678765

>KOG0920 consensus ATP-dependent RNA helicase A [RNA processing and modification]

Probab=99.93  E-value=1.5e-24  Score=257.65  Aligned_cols=313  Identities=20%  Similarity=0.276  Sum_probs=238.5

Q ss_pred             CcHHHHHHHHHHhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHH-HHhhcC
Q 002040          490 PMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRK-FAKVMG  568 (976)
Q Consensus       490 p~~~Q~~~i~~il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~-~~~~~~  568 (976)
                      .+..+.+.|.+|.+++.++|.|+||+|||++.-..++.+.....     ....+++..|.|--|.-+++.+.. .+...|
T Consensus       174 a~~~r~~Il~~i~~~qVvvIsGeTGcGKTTQvpQfiLd~~~~~~-----~~~~IicTQPRRIsAIsvAeRVa~ER~~~~g  248 (924)
T KOG0920|consen  174 AYKMRDTILDAIEENQVVVISGETGCGKTTQVPQFILDEAIESG-----AACNIICTQPRRISAISVAERVAKERGESLG  248 (924)
T ss_pred             cHHHHHHHHHHHHhCceEEEeCCCCCCchhhhhHHHHHHHHhcC-----CCCeEEecCCchHHHHHHHHHHHHHhccccC
Confidence            45778899999999999999999999999998888888776542     345578888999888888776653 233344


Q ss_pred             cEEEEeeCCCChHHHHHHHhcCCeEEEeCchhHHHHHHhcCCcccccCCceEEEecCcc-cccccCCchHHHHHHHhcCC
Q 002040          569 VRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEAD-RMFDMGFEPQITRIVQNIRP  647 (976)
Q Consensus       569 ~~~~~~~gg~~~~~~~~~l~~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDEah-~~~~~~f~~~i~~il~~~~~  647 (976)
                      -.|..-++..+      .....+.+++||.|.|+..|...    ..+..+++||+||+| +-.+.+|.-.+...+-..+|
T Consensus       249 ~~VGYqvrl~~------~~s~~t~L~fcTtGvLLr~L~~~----~~l~~vthiivDEVHER~i~~DflLi~lk~lL~~~p  318 (924)
T KOG0920|consen  249 EEVGYQVRLES------KRSRETRLLFCTTGVLLRRLQSD----PTLSGVTHIIVDEVHERSINTDFLLILLKDLLPRNP  318 (924)
T ss_pred             CeeeEEEeeec------ccCCceeEEEecHHHHHHHhccC----cccccCceeeeeeEEEccCCcccHHHHHHHHhhhCC
Confidence            44444333321      12234899999999999998763    578899999999999 77888898888888888899


Q ss_pred             CCcEEEEeccCcHHHHHHHHHHcCCCeEEEeCCcccccCC----------------ceEE------------EEecCc--
Q 002040          648 DRQTVLFSATFPRQVEILARKVLNKPVEIQVGGRSVVNKD----------------ITQL------------VEVRPE--  697 (976)
Q Consensus       648 ~~q~i~~SAT~~~~~~~l~~~~l~~~~~i~~~~~~~~~~~----------------i~q~------------~~~~~~--  697 (976)
                      +.++|+||||+...   ++..|++....+.+.+.+++...                ..+.            +.+...  
T Consensus       319 ~LkvILMSAT~dae---~fs~YF~~~pvi~i~grtfpV~~~fLEDil~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i  395 (924)
T KOG0920|consen  319 DLKVILMSATLDAE---LFSDYFGGCPVITIPGRTFPVKEYFLEDILSKTGYVSEDDSARSGPERSQLRLARLKLWEPEI  395 (924)
T ss_pred             CceEEEeeeecchH---HHHHHhCCCceEeecCCCcchHHHHHHHHHHHhcccccccccccccccCccccccchhccccc
Confidence            99999999999743   66777777777777776654221                0000            000011  


Q ss_pred             -chHHHHHHHHHHhhhcCCcEEEEecCHHHHHHHHHHHHHC-------CCCceeccCCCCHHHHHHHHHHhccCCccEEE
Q 002040          698 -SDRFLRLLELLGEWYEKGKILIFVHSQEKCDALFRDLLKH-------GYPCLSLHGAKDQTDRESTISDFKSNVCNLLI  769 (976)
Q Consensus       698 -~~k~~~l~~~l~~~~~~~kvLIF~~s~~~~~~l~~~L~~~-------~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLV  769 (976)
                       ..-+..|+..|......|.||||.++...+..+.+.|...       .+-+.++|+.|+..++..++.....|..+||+
T Consensus       396 d~~Li~~li~~I~~~~~~GaILVFLPG~~eI~~~~~~L~~~~~f~~~~~~~ilplHs~~~s~eQ~~VF~~pp~g~RKIIl  475 (924)
T KOG0920|consen  396 DYDLIEDLIEYIDEREFEGAILVFLPGWEEILQLKELLEVNLPFADSLKFAILPLHSSIPSEEQQAVFKRPPKGTRKIIL  475 (924)
T ss_pred             cHHHHHHHHHhcccCCCCceEEEEcCCHHHHHHHHHHhhhccccccccceEEEeccccCChHHHHHhcCCCCCCcchhhh
Confidence             1122333444444334689999999999999999999652       36688999999999999999999999999999


Q ss_pred             ecCcccccCCCCCCcEEEE--------eCCCC----------CHHHHHHHhcccCCCCCccEEEEEecCC
Q 002040          770 ATSVAARGLDVKELELVIN--------FDAPN----------HYEDYVHRVGRTGRAGRKGCAITFISEE  821 (976)
Q Consensus       770 aT~v~~~GlDi~~v~~VI~--------~d~p~----------s~~~y~Qr~GR~gR~g~~g~~~~~~~~~  821 (976)
                      ||++|+++|.|++|-+||+        ||+-.          +-++..||.|||||. +.|.||.+|+..
T Consensus       476 aTNIAETSITIdDVvyVIDsG~~Ke~~yD~~~~~s~l~~~wvSkAna~QR~GRAGRv-~~G~cy~L~~~~  544 (924)
T KOG0920|consen  476 ATNIAETSITIDDVVYVIDSGLVKEKSYDPERKVSCLLLSWVSKANAKQRRGRAGRV-RPGICYHLYTRS  544 (924)
T ss_pred             hhhhHhhcccccCeEEEEecCeeeeeeecccCCcchhheeeccccchHHhcccccCc-cCCeeEEeechh
Confidence            9999999999999999997        55533          455667999999998 699999999864

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

Probab=99.93  E-value=2.9e-24  Score=257.73  Aligned_cols=315  Identities=20%  Similarity=0.261  Sum_probs=230.6

Q ss_pred             HHcCCCCCcHHHHHHHHHHhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHH
Q 002040          483 RKLNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRK  562 (976)
Q Consensus       483 ~~~~~~~p~~~Q~~~i~~il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~  562 (976)
                      ..++|. |-++|++++..|..|.+|+++||||+|||+++-.++...+..        |.++++++|..+|.+|.+..|..
T Consensus       114 ~~~~F~-LD~fQ~~a~~~Ler~esVlV~ApTssGKTvVaeyAi~~al~~--------~qrviYTsPIKALsNQKyrdl~~  184 (1041)
T COG4581         114 REYPFE-LDPFQQEAIAILERGESVLVCAPTSSGKTVVAEYAIALALRD--------GQRVIYTSPIKALSNQKYRDLLA  184 (1041)
T ss_pred             HhCCCC-cCHHHHHHHHHHhCCCcEEEEccCCCCcchHHHHHHHHHHHc--------CCceEeccchhhhhhhHHHHHHH
Confidence            446664 889999999999999999999999999999977776665543        45699999999999999999887


Q ss_pred             HHhhcCcEEEEeeCCCChHHHHHHHhcCCeEEEeCchhHHHHHHhcCCcccccCCceEEEecCcccccccCCchHHHHHH
Q 002040          563 FAKVMGVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMGFEPQITRIV  642 (976)
Q Consensus       563 ~~~~~~~~~~~~~gg~~~~~~~~~l~~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDEah~~~~~~f~~~i~~il  642 (976)
                      .+...--.+.+++|..       .+..++.++|+|.+.|.+++....   ..+..+.+||+||+|.|.+..-+..+..++
T Consensus       185 ~fgdv~~~vGL~TGDv-------~IN~~A~clvMTTEILRnMlyrg~---~~~~~i~~ViFDEvHyi~D~eRG~VWEE~I  254 (1041)
T COG4581         185 KFGDVADMVGLMTGDV-------SINPDAPCLVMTTEILRNMLYRGS---ESLRDIEWVVFDEVHYIGDRERGVVWEEVI  254 (1041)
T ss_pred             Hhhhhhhhccceecce-------eeCCCCceEEeeHHHHHHHhccCc---ccccccceEEEEeeeeccccccchhHHHHH
Confidence            6543322245566655       345678999999999999987764   567889999999999999998888999999


Q ss_pred             HhcCCCCcEEEEeccCcHHHHHHHHHHc---CCCeEEEeCCcccccCCceEEEEe-------cCcchH------------
Q 002040          643 QNIRPDRQTVLFSATFPRQVEILARKVL---NKPVEIQVGGRSVVNKDITQLVEV-------RPESDR------------  700 (976)
Q Consensus       643 ~~~~~~~q~i~~SAT~~~~~~~l~~~~l---~~~~~i~~~~~~~~~~~i~q~~~~-------~~~~~k------------  700 (976)
                      -.++...++|+||||+|+..+ +...+.   ..|+.+...  ...+.++.+++..       .....+            
T Consensus       255 i~lP~~v~~v~LSATv~N~~E-F~~Wi~~~~~~~~~vv~t--~~RpvPL~~~~~~~~~l~~lvde~~~~~~~~~~~a~~~  331 (1041)
T COG4581         255 ILLPDHVRFVFLSATVPNAEE-FAEWIQRVHSQPIHVVST--EHRPVPLEHFVYVGKGLFDLVDEKKKFNAENFPSANRS  331 (1041)
T ss_pred             HhcCCCCcEEEEeCCCCCHHH-HHHHHHhccCCCeEEEee--cCCCCCeEEEEecCCceeeeecccccchhhcchhhhhh
Confidence            999999999999999998754 333222   233332221  1111122222211       111110            


Q ss_pred             -----------------------------------HHHHHHHHHhhhcCCcEEEEecCHHHHHHHHHHHHHC--------
Q 002040          701 -----------------------------------FLRLLELLGEWYEKGKILIFVHSQEKCDALFRDLLKH--------  737 (976)
Q Consensus       701 -----------------------------------~~~l~~~l~~~~~~~kvLIF~~s~~~~~~l~~~L~~~--------  737 (976)
                                                         ...++..|.. ...-++|+||-++..|+.++..|...        
T Consensus       332 l~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~iv~~l~~-~~~lP~I~F~FSr~~Ce~~a~~~~~ldl~~~~~~  410 (1041)
T COG4581         332 LSCFSEKVRETDDGDVGRYARRTKALRGSAKGPAGRPEIVNKLDK-DNLLPAIVFSFSRRGCEEAAQILSTLDLVLTEEK  410 (1041)
T ss_pred             hhccchhccccCccccccccccccccCCcccccccchHHHhhhhh-hcCCceEEEEEchhhHHHHHHHhcccccccCCcH
Confidence                                               0111111111 11238999999999998888776521        


Q ss_pred             --------------------CCC-------------ceeccCCCCHHHHHHHHHHhccCCccEEEecCcccccCCCCCCc
Q 002040          738 --------------------GYP-------------CLSLHGAKDQTDRESTISDFKSNVCNLLIATSVAARGLDVKELE  784 (976)
Q Consensus       738 --------------------~~~-------------~~~lhg~~~~~~R~~~~~~F~~g~~~vLVaT~v~~~GlDi~~v~  784 (976)
                                          +++             ++++|++|=+..+..+...|..|-++||+||.+++.|+|.|.-+
T Consensus       411 e~~i~~ii~~~i~~L~~ed~~lp~~~~~~~~~L~RGiavHH~GlLP~~K~~vE~Lfq~GLvkvvFaTeT~s~GiNmPart  490 (1041)
T COG4581         411 ERAIREIIDHAIGDLAEEDRELPLQILEISALLLRGIAVHHAGLLPAIKELVEELFQEGLVKVVFATETFAIGINMPART  490 (1041)
T ss_pred             HHHHHHHHHHHHhhcChhhhcCcccHHHHHHHHhhhhhhhccccchHHHHHHHHHHhccceeEEeehhhhhhhcCCcccc
Confidence                                221             45789999999999999999999999999999999999999776


Q ss_pred             EEEE----eC----CCCCHHHHHHHhcccCCCCC--ccEEEEEecC
Q 002040          785 LVIN----FD----APNHYEDYVHRVGRTGRAGR--KGCAITFISE  820 (976)
Q Consensus       785 ~VI~----~d----~p~s~~~y~Qr~GR~gR~g~--~g~~~~~~~~  820 (976)
                      +|+-    ++    .+-++..|.|+.|||||.|.  .|.+++.-.+
T Consensus       491 vv~~~l~K~dG~~~r~L~~gEy~QmsGRAGRRGlD~~G~vI~~~~~  536 (1041)
T COG4581         491 VVFTSLSKFDGNGHRWLSPGEYTQMSGRAGRRGLDVLGTVIVIEPP  536 (1041)
T ss_pred             eeeeeeEEecCCceeecChhHHHHhhhhhccccccccceEEEecCC
Confidence            6662    22    24468899999999999886  4888777443

>KOG0948 consensus Nuclear exosomal RNA helicase MTR4, DEAD-box superfamily [RNA processing and modification]

Probab=99.93  E-value=3.1e-25  Score=248.82  Aligned_cols=308  Identities=20%  Similarity=0.284  Sum_probs=229.9

Q ss_pred             CCcHHHHHHHHHHhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHHHHhhcC
Q 002040          489 KPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVMG  568 (976)
Q Consensus       489 ~p~~~Q~~~i~~il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~~~~~~~  568 (976)
                      .+-|+|.++|..|-.+..+|+.|.|.+|||.++-.+|...+..        ..+|++..|-.+|.+|-|.++..-++..|
T Consensus       129 ~LDpFQ~~aI~Cidr~eSVLVSAHTSAGKTVVAeYAIA~sLr~--------kQRVIYTSPIKALSNQKYREl~~EF~DVG  200 (1041)
T KOG0948|consen  129 TLDPFQSTAIKCIDRGESVLVSAHTSAGKTVVAEYAIAMSLRE--------KQRVIYTSPIKALSNQKYRELLEEFKDVG  200 (1041)
T ss_pred             ccCchHhhhhhhhcCCceEEEEeecCCCcchHHHHHHHHHHHh--------cCeEEeeChhhhhcchhHHHHHHHhcccc
Confidence            4779999999999999999999999999999977777666554        45799999999999999999887665544


Q ss_pred             cEEEEeeCCCChHHHHHHHhcCCeEEEeCchhHHHHHHhcCCcccccCCceEEEecCcccccccCCchHHHHHHHhcCCC
Q 002040          569 VRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMGFEPQITRIVQNIRPD  648 (976)
Q Consensus       569 ~~~~~~~gg~~~~~~~~~l~~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDEah~~~~~~f~~~i~~il~~~~~~  648 (976)
                          +.+|...       +...+-.+|+|.+.|..+|.+++   --+..+.+||+||+|.|-+...+-.+...+-.++.+
T Consensus       201 ----LMTGDVT-------InP~ASCLVMTTEILRsMLYRGS---EvmrEVaWVIFDEIHYMRDkERGVVWEETIIllP~~  266 (1041)
T KOG0948|consen  201 ----LMTGDVT-------INPDASCLVMTTEILRSMLYRGS---EVMREVAWVIFDEIHYMRDKERGVVWEETIILLPDN  266 (1041)
T ss_pred             ----eeeccee-------eCCCCceeeeHHHHHHHHHhccc---hHhheeeeEEeeeehhccccccceeeeeeEEecccc
Confidence                4556553       34557889999999999998765   346779999999999998887777777777788999


Q ss_pred             CcEEEEeccCcHHHHHHHHHHc---CCCeEEEeCCcccccCCceEEE---------EecCc-----chHHHHHHHHHHhh
Q 002040          649 RQTVLFSATFPRQVEILARKVL---NKPVEIQVGGRSVVNKDITQLV---------EVRPE-----SDRFLRLLELLGEW  711 (976)
Q Consensus       649 ~q~i~~SAT~~~~~~~l~~~~l---~~~~~i~~~~~~~~~~~i~q~~---------~~~~~-----~~k~~~l~~~l~~~  711 (976)
                      .+.+++|||+|+..+ ++.+.+   ..|..+.+  ..+.+.++.+++         .+++.     .+.|......|...
T Consensus       267 vr~VFLSATiPNA~q-FAeWI~~ihkQPcHVVY--TdyRPTPLQHyifP~ggdGlylvVDek~~FrednF~~am~~l~~~  343 (1041)
T KOG0948|consen  267 VRFVFLSATIPNARQ-FAEWICHIHKQPCHVVY--TDYRPTPLQHYIFPAGGDGLYLVVDEKGKFREDNFQKAMSVLRKA  343 (1041)
T ss_pred             ceEEEEeccCCCHHH-HHHHHHHHhcCCceEEe--ecCCCCcceeeeecCCCCeeEEEEecccccchHHHHHHHHHhhcc
Confidence            999999999998765 444332   34433222  122222222221         11111     12233333222211


Q ss_pred             -----------------------------------h--cCCcEEEEecCHHHHHHHHHHHHHCC----------------
Q 002040          712 -----------------------------------Y--EKGKILIFVHSQEKCDALFRDLLKHG----------------  738 (976)
Q Consensus       712 -----------------------------------~--~~~kvLIF~~s~~~~~~l~~~L~~~~----------------  738 (976)
                                                         .  .-.++|||+-++++|+.++-.+.+..                
T Consensus       344 ~~~~~~~~~~~k~~kG~~~~~~~~~s~i~kiVkmi~~~~~~PVIvFSFSkkeCE~~Alqm~kldfN~deEk~~V~~iF~n  423 (1041)
T KOG0948|consen  344 GESDGKKKANKKGRKGGTGGKGPGDSDIYKIVKMIMERNYLPVIVFSFSKKECEAYALQMSKLDFNTDEEKELVETIFNN  423 (1041)
T ss_pred             CCCccccccccccccCCcCCCCCCcccHHHHHHHHHhhcCCceEEEEecHhHHHHHHHhhccCcCCChhHHHHHHHHHHH
Confidence                                               1  12489999999999999988775541                


Q ss_pred             -----------------------CCceeccCCCCHHHHHHHHHHhccCCccEEEecCcccccCCCCCCcEEEE----eCC
Q 002040          739 -----------------------YPCLSLHGAKDQTDRESTISDFKSNVCNLLIATSVAARGLDVKELELVIN----FDA  791 (976)
Q Consensus       739 -----------------------~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLVaT~v~~~GlDi~~v~~VI~----~d~  791 (976)
                                             -.++++|||+-+-.++-+.-.|+.|-++||+||..++.|||.|.-++|+-    ||-
T Consensus       424 Ai~~LseeDr~LPqie~iLPLL~RGIGIHHsGLLPIlKE~IEILFqEGLvKvLFATETFsiGLNMPAkTVvFT~~rKfDG  503 (1041)
T KOG0948|consen  424 AIDQLSEEDRELPQIENILPLLRRGIGIHHSGLLPILKEVIEILFQEGLVKVLFATETFSIGLNMPAKTVVFTAVRKFDG  503 (1041)
T ss_pred             HHHhcChhhccchHHHHHHHHHHhccccccccchHHHHHHHHHHHhccHHHHHHhhhhhhhccCCcceeEEEeeccccCC
Confidence                                   13678999999999999999999999999999999999999997766663    222


Q ss_pred             ----CCCHHHHHHHhcccCCCCC--ccEEEEEecCC
Q 002040          792 ----PNHYEDYVHRVGRTGRAGR--KGCAITFISEE  821 (976)
Q Consensus       792 ----p~s~~~y~Qr~GR~gR~g~--~g~~~~~~~~~  821 (976)
                          +.+.-.|+|+.|||||-|-  .|.|++++++.
T Consensus       504 ~~fRwissGEYIQMSGRAGRRG~DdrGivIlmiDek  539 (1041)
T KOG0948|consen  504 KKFRWISSGEYIQMSGRAGRRGIDDRGIVILMIDEK  539 (1041)
T ss_pred             cceeeecccceEEecccccccCCCCCceEEEEecCc
Confidence                2356689999999999885  59999998753

>KOG0387 consensus Transcription-coupled repair protein CSB/RAD26 (contains SNF2 family DNA-dependent ATPase domain) [Transcription; Replication, recombination and repair]

Probab=99.92  E-value=4.7e-24  Score=242.10  Aligned_cols=328  Identities=20%  Similarity=0.287  Sum_probs=220.4

Q ss_pred             CCcHHHHHHHHHHh----cCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHHHH
Q 002040          489 KPMPIQAQALPVIM----SGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFA  564 (976)
Q Consensus       489 ~p~~~Q~~~i~~il----~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~~~  564 (976)
                      .++|+|..++.|+.    ++...|+..+||.|||++. +..|..|.....+    ...+|||||. .+..||.++|..|.
T Consensus       205 ~Lf~yQreGV~WL~~L~~q~~GGILgDeMGLGKTIQi-isFLaaL~~S~k~----~~paLIVCP~-Tii~qW~~E~~~w~  278 (923)
T KOG0387|consen  205 KLFPYQREGVQWLWELYCQRAGGILGDEMGLGKTIQI-ISFLAALHHSGKL----TKPALIVCPA-TIIHQWMKEFQTWW  278 (923)
T ss_pred             HhhHHHHHHHHHHHHHHhccCCCeecccccCccchhH-HHHHHHHhhcccc----cCceEEEccH-HHHHHHHHHHHHhC
Confidence            47799999999986    5667899999999999983 3444444433211    2458999996 46689999999987


Q ss_pred             hhcCcEEEEeeCCCCh--------HHHH-----HHHhcCCeEEEeCchhHHHHHHhcCCcccccCCceEEEecCcccccc
Q 002040          565 KVMGVRCVPVYGGSGV--------AQQI-----SELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFD  631 (976)
Q Consensus       565 ~~~~~~~~~~~gg~~~--------~~~~-----~~l~~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDEah~~~~  631 (976)
                      ..  ++|.+++|....        ....     ........|+|+|+..|.-.    . ....-..|.|+|+||.|++-+
T Consensus       279 p~--~rv~ilh~t~s~~r~~~~~~~~~~~~~L~r~~~~~~~ilitty~~~r~~----~-d~l~~~~W~y~ILDEGH~IrN  351 (923)
T KOG0387|consen  279 PP--FRVFILHGTGSGARYDASHSSHKKDKLLIRKVATDGGILITTYDGFRIQ----G-DDLLGILWDYVILDEGHRIRN  351 (923)
T ss_pred             cc--eEEEEEecCCcccccccchhhhhhhhhheeeecccCcEEEEehhhhccc----C-cccccccccEEEecCcccccC
Confidence            54  566666665442        0111     11122467999998876321    1 112234589999999999876


Q ss_pred             cCCchHHHHHHHhcCCCCcEEEEeccCc-HHHHHHHHHH---c----------CC--CeEEEeCCcccc-----------
Q 002040          632 MGFEPQITRIVQNIRPDRQTVLFSATFP-RQVEILARKV---L----------NK--PVEIQVGGRSVV-----------  684 (976)
Q Consensus       632 ~~f~~~i~~il~~~~~~~q~i~~SAT~~-~~~~~l~~~~---l----------~~--~~~i~~~~~~~~-----------  684 (976)
                      ..  .++...+..++. .+-|++|+||- +.+..|...|   +          ..  ...|.+++....           
T Consensus       352 pn--s~islackki~T-~~RiILSGTPiQNnL~ELwsLfDFv~PG~Lgt~~~F~~~f~~pI~~GgyaNAs~~qv~~aykc  428 (923)
T KOG0387|consen  352 PN--SKISLACKKIRT-VHRIILSGTPIQNNLTELWSLFDFVFPGKLGTLPVFQQNFEHPINRGGYANASPRQVQTAYKC  428 (923)
T ss_pred             Cc--cHHHHHHHhccc-cceEEeeCccccchHHHHHHHhhhccCCcccchHHHHhhhhhheeccccCCCCHHHHHHHHHH
Confidence            53  344444445533 44566677742 2222211100   0          00  001111110000           


Q ss_pred             -------------------------cCCceEEE-----------------------------------------------
Q 002040          685 -------------------------NKDITQLV-----------------------------------------------  692 (976)
Q Consensus       685 -------------------------~~~i~q~~-----------------------------------------------  692 (976)
                                               +..-.+++                                               
T Consensus       429 a~~Lr~lI~PylLRR~K~dv~~~~Lp~K~E~VlfC~LT~~QR~~Y~~fl~s~~v~~i~ng~~~~l~Gi~iLrkICnHPdl  508 (923)
T KOG0387|consen  429 AVALRDLISPYLLRRMKSDVKGLKLPKKEEIVLFCRLTKLQRRLYQRFLNSSEVNKILNGKRNCLSGIDILRKICNHPDL  508 (923)
T ss_pred             HHHHHHHhHHHHHHHHHHHhhhccCCCccceEEEEeccHHHHHHHHHHhhhHHHHHHHcCCccceechHHHHhhcCCccc
Confidence                                     00000000                                               


Q ss_pred             ---------------EecCcchHHHHHHHHHHhhhcCC-cEEEEecCHHHHHHHHHHHH-HCCCCceeccCCCCHHHHHH
Q 002040          693 ---------------EVRPESDRFLRLLELLGEWYEKG-KILIFVHSQEKCDALFRDLL-KHGYPCLSLHGAKDQTDRES  755 (976)
Q Consensus       693 ---------------~~~~~~~k~~~l~~~l~~~~~~~-kvLIF~~s~~~~~~l~~~L~-~~~~~~~~lhg~~~~~~R~~  755 (976)
                                     -....+.|+..+..+|..|...| ++|+|.+++.+++.|...|. ..||.++.+.|.++...|..
T Consensus       509 l~~~~~~~~~~~D~~g~~k~sGKm~vl~~ll~~W~kqg~rvllFsqs~~mLdilE~fL~~~~~ysylRmDGtT~~~~R~~  588 (923)
T KOG0387|consen  509 LDRRDEDEKQGPDYEGDPKRSGKMKVLAKLLKDWKKQGDRVLLFSQSRQMLDILESFLRRAKGYSYLRMDGTTPAALRQK  588 (923)
T ss_pred             ccCcccccccCCCcCCChhhcchHHHHHHHHHHHhhCCCEEEEehhHHHHHHHHHHHHHhcCCceEEEecCCCccchhhH
Confidence                           01112457888888888888654 99999999999999999999 57999999999999999999


Q ss_pred             HHHHhccCC--ccEEEecCcccccCCCCCCcEEEEeCCCCCHHHHHHHhcccCCCCCccEEE--EEecCC---CcCchHH
Q 002040          756 TISDFKSNV--CNLLIATSVAARGLDVKELELVINFDAPNHYEDYVHRVGRTGRAGRKGCAI--TFISEE---DAKYSPD  828 (976)
Q Consensus       756 ~~~~F~~g~--~~vLVaT~v~~~GlDi~~v~~VI~~d~p~s~~~y~Qr~GR~gR~g~~g~~~--~~~~~~---d~~~~~~  828 (976)
                      ++..|+++.  .-+|++|.|++-|||+.+++-||+|||.|||++-.|..-|+.|.||+..|+  .|++..   +..|..+
T Consensus       589 lVd~Fne~~s~~VFLLTTrvGGLGlNLTgAnRVIIfDPdWNPStD~QAreRawRiGQkkdV~VYRL~t~gTIEEkiY~rQ  668 (923)
T KOG0387|consen  589 LVDRFNEDESIFVFLLTTRVGGLGLNLTGANRVIIFDPDWNPSTDNQARERAWRIGQKKDVVVYRLMTAGTIEEKIYHRQ  668 (923)
T ss_pred             HHHhhcCCCceEEEEEEecccccccccccCceEEEECCCCCCccchHHHHHHHhhcCccceEEEEEecCCcHHHHHHHHH
Confidence            999999775  458899999999999999999999999999999999999999999976554  455542   3344555


Q ss_pred             HHHH
Q 002040          829 LVKA  832 (976)
Q Consensus       829 i~~~  832 (976)
                      |.+.
T Consensus       669 I~Kq  672 (923)
T KOG0387|consen  669 IFKQ  672 (923)
T ss_pred             HHHH
Confidence            5554

>KOG0925 consensus mRNA splicing factor ATP-dependent RNA helicase [RNA processing and modification]

Probab=99.91  E-value=2.7e-23  Score=223.44  Aligned_cols=329  Identities=19%  Similarity=0.258  Sum_probs=237.1

Q ss_pred             cccccccCCCCHHHHHHHHHcCCCCCcHHHHHHHHHHhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEE
Q 002040          465 PIKTWHQTGLTSKIMETIRKLNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGL  544 (976)
Q Consensus       465 pi~~~~~~~l~~~l~~~l~~~~~~~p~~~Q~~~i~~il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vL  544 (976)
                      .+..|...+.++...+.|++..-...+..+...+..+.+++-++++|+||||||++.-..++......       ...|.
T Consensus        23 ~~Npf~~~p~s~rY~~ilk~R~~LPvw~~k~~F~~~l~~nQ~~v~vGetgsGKttQiPq~~~~~~~~~-------~~~v~   95 (699)
T KOG0925|consen   23 AINPFNGKPYSQRYYDILKKRRELPVWEQKEEFLKLLLNNQIIVLVGETGSGKTTQIPQFVLEYELSH-------LTGVA   95 (699)
T ss_pred             hcCCCCCCcCcHHHHHHHHHHhcCchHHhHHHHHHHHhcCceEEEEecCCCCccccCcHHHHHHHHhh-------cccee
Confidence            36778888889888888887554444566666777777888999999999999987544445444432       13456


Q ss_pred             EEccCHHHHHHHHHHHHHHHhhcCcEEEEeeCCCChHHHHHHHhcCCeEEEeCchhHHHHHHhcCCcccccCCceEEEec
Q 002040          545 IMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMD  624 (976)
Q Consensus       545 Il~Ptr~La~Q~~~~~~~~~~~~~~~~~~~~gg~~~~~~~~~l~~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlD  624 (976)
                      ...|.|..|+++   ..+++..+.+.+.--+|.+...+.+..  ..+-+-+||.+.|+......    ..|..+++||+|
T Consensus        96 CTQprrvaamsv---a~RVadEMDv~lG~EVGysIrfEdC~~--~~T~Lky~tDgmLlrEams~----p~l~~y~viiLD  166 (699)
T KOG0925|consen   96 CTQPRRVAAMSV---AQRVADEMDVTLGEEVGYSIRFEDCTS--PNTLLKYCTDGMLLREAMSD----PLLGRYGVIILD  166 (699)
T ss_pred             ecCchHHHHHHH---HHHHHHHhccccchhccccccccccCC--hhHHHHHhcchHHHHHHhhC----cccccccEEEec
Confidence            777999988866   455666788888777787766665321  22445689999988766544    468899999999


Q ss_pred             Ccc-cccccCCchHHHHHHHhcCCCCcEEEEeccCcHHHHHHHHHHcCCCeEEEeCCcccccCCceEEEEecCcchHHHH
Q 002040          625 EAD-RMFDMGFEPQITRIVQNIRPDRQTVLFSATFPRQVEILARKVLNKPVEIQVGGRSVVNKDITQLVEVRPESDRFLR  703 (976)
Q Consensus       625 Eah-~~~~~~f~~~i~~il~~~~~~~q~i~~SAT~~~~~~~l~~~~l~~~~~i~~~~~~~~~~~i~q~~~~~~~~~k~~~  703 (976)
                      ||| +.+..+....+.+-+..-+|+.++|+||||+-..   .+..|+.++..+.+.+.    ..+..++.-....+.+..
T Consensus       167 eahERtlATDiLmGllk~v~~~rpdLk~vvmSatl~a~---Kfq~yf~n~Pll~vpg~----~PvEi~Yt~e~erDylEa  239 (699)
T KOG0925|consen  167 EAHERTLATDILMGLLKEVVRNRPDLKLVVMSATLDAE---KFQRYFGNAPLLAVPGT----HPVEIFYTPEPERDYLEA  239 (699)
T ss_pred             hhhhhhHHHHHHHHHHHHHHhhCCCceEEEeecccchH---HHHHHhCCCCeeecCCC----CceEEEecCCCChhHHHH
Confidence            999 6555554444444444456899999999997543   45667777766666652    123333444445566666


Q ss_pred             HHHHHHhhh---cCCcEEEEecCHHHHHHHHHHHHHC---------CCCceeccCCCCHHHHHHHHHHhc---cC--Ccc
Q 002040          704 LLELLGEWY---EKGKILIFVHSQEKCDALFRDLLKH---------GYPCLSLHGAKDQTDRESTISDFK---SN--VCN  766 (976)
Q Consensus       704 l~~~l~~~~---~~~kvLIF~~s~~~~~~l~~~L~~~---------~~~~~~lhg~~~~~~R~~~~~~F~---~g--~~~  766 (976)
                      .+..+.+.+   ..|.+|||.++.++++..|..+...         .+.|+.+|    +.++..+++...   +|  ..+
T Consensus       240 airtV~qih~~ee~GDilvFLtgeeeIe~aC~~i~re~~~L~~~~g~l~v~PLy----P~~qq~iFep~p~~~~~~~~Rk  315 (699)
T KOG0925|consen  240 AIRTVLQIHMCEEPGDILVFLTGEEEIEDACRKISREVDNLGPQVGPLKVVPLY----PAQQQRIFEPAPEKRNGAYGRK  315 (699)
T ss_pred             HHHHHHHHHhccCCCCEEEEecCHHHHHHHHHHHHHHHHhhccccCCceEEecC----chhhccccCCCCcccCCCccce
Confidence            665555443   4689999999999999999888742         35678888    444555555443   23  357


Q ss_pred             EEEecCcccccCCCCCCcEEEEeCC------------------CCCHHHHHHHhcccCCCCCccEEEEEecCC
Q 002040          767 LLIATSVAARGLDVKELELVINFDA------------------PNHYEDYVHRVGRTGRAGRKGCAITFISEE  821 (976)
Q Consensus       767 vLVaT~v~~~GlDi~~v~~VI~~d~------------------p~s~~~y~Qr~GR~gR~g~~g~~~~~~~~~  821 (976)
                      |+|+|++++..|.|++|.+||+.++                  |.|..+..||.||+||+ .+|.|+.+|++.
T Consensus       316 vVvstniaetsltidgiv~VIDpGf~kqkVYNPRIRvesllv~PISkasA~qR~gragrt-~pGkcfrLYte~  387 (699)
T KOG0925|consen  316 VVVSTNIAETSLTIDGIVFVIDPGFSKQKVYNPRIRVESLLVSPISKASAQQRAGRAGRT-RPGKCFRLYTEE  387 (699)
T ss_pred             EEEEecchheeeeeccEEEEecCchhhhcccCcceeeeeeeeccchHhHHHHHhhhccCC-CCCceEEeecHH
Confidence            9999999999999999999997443                  77888899999999998 599999999864

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

Probab=99.91  E-value=2.2e-23  Score=210.76  Aligned_cols=165  Identities=36%  Similarity=0.619  Sum_probs=141.2

Q ss_pred             cHHHHHHHHHHhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHHHHhhcCcE
Q 002040          491 MPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVMGVR  570 (976)
Q Consensus       491 ~~~Q~~~i~~il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~~~~~~~~~  570 (976)
                      ||+|.++|+.+.+++++|++||||+|||++|+++++..+...      ....+||++|+++|+.|++..+..++...++.
T Consensus         1 t~~Q~~~~~~i~~~~~~li~aptGsGKT~~~~~~~l~~~~~~------~~~~~lii~P~~~l~~q~~~~~~~~~~~~~~~   74 (169)
T PF00270_consen    1 TPLQQEAIEAIISGKNVLISAPTGSGKTLAYILPALNRLQEG------KDARVLIIVPTRALAEQQFERLRKFFSNTNVR   74 (169)
T ss_dssp             -HHHHHHHHHHHTTSEEEEECSTTSSHHHHHHHHHHHHHHTT------SSSEEEEEESSHHHHHHHHHHHHHHTTTTTSS
T ss_pred             CHHHHHHHHHHHcCCCEEEECCCCCccHHHHHHHHHhhhccC------CCceEEEEeecccccccccccccccccccccc
Confidence            699999999999999999999999999999999999988763      23489999999999999999999998888889


Q ss_pred             EEEeeCCCChH-HHHHHHhcCCeEEEeCchhHHHHHHhcCCcccccCCceEEEecCcccccccCCchHHHHHHHhcCC--
Q 002040          571 CVPVYGGSGVA-QQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMGFEPQITRIVQNIRP--  647 (976)
Q Consensus       571 ~~~~~gg~~~~-~~~~~l~~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDEah~~~~~~f~~~i~~il~~~~~--  647 (976)
                      +..++|+.... .....+..+++|+|+||+.|..++...  .. ++.++++|||||+|.+..+++...+..++..+..  
T Consensus        75 ~~~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~~--~~-~~~~~~~iViDE~h~l~~~~~~~~~~~i~~~~~~~~  151 (169)
T PF00270_consen   75 VVLLHGGQSISEDQREVLSNQADILVTTPEQLLDLISNG--KI-NISRLSLIVIDEAHHLSDETFRAMLKSILRRLKRFK  151 (169)
T ss_dssp             EEEESTTSCHHHHHHHHHHTTSSEEEEEHHHHHHHHHTT--SS-TGTTESEEEEETHHHHHHTTHHHHHHHHHHHSHTTT
T ss_pred             cccccccccccccccccccccccccccCcchhhcccccc--cc-ccccceeeccCcccccccccHHHHHHHHHHHhcCCC
Confidence            99999999866 444455567999999999999998762  22 5666999999999999988888888888888733  


Q ss_pred             CCcEEEEeccCcHHHHH
Q 002040          648 DRQTVLFSATFPRQVEI  664 (976)
Q Consensus       648 ~~q~i~~SAT~~~~~~~  664 (976)
                      ..++|++|||+++.++.
T Consensus       152 ~~~~i~~SAT~~~~~~~  168 (169)
T PF00270_consen  152 NIQIILLSATLPSNVEK  168 (169)
T ss_dssp             TSEEEEEESSSTHHHHH
T ss_pred             CCcEEEEeeCCChhHhh
Confidence            58999999999976654

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 ....

>KOG0950 consensus DNA polymerase theta/eta, DEAD-box superfamily [General function prediction only]

Probab=99.91  E-value=1.2e-23  Score=244.23  Aligned_cols=348  Identities=22%  Similarity=0.250  Sum_probs=242.0

Q ss_pred             cccCCCCHHHHHHHHHcCCCCCcHHHHHHH--HHHhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEE
Q 002040          469 WHQTGLTSKIMETIRKLNYEKPMPIQAQAL--PVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIM  546 (976)
Q Consensus       469 ~~~~~l~~~l~~~l~~~~~~~p~~~Q~~~i--~~il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl  546 (976)
                      +...+++....-.....|+.+++.+|.+++  |.++.++++|+.+||+.|||+++-+-|+..+.-.       ...++++
T Consensus       203 ~a~~~~~k~~~~~~~~kgi~~~fewq~ecls~~~~~e~~nliys~Pts~gktlvaeilml~~~l~~-------rr~~lli  275 (1008)
T KOG0950|consen  203 FAKRLPTKVSHLYAKDKGILKLFEWQAECLSLPRLLERKNLIYSLPTSAGKTLVAEILMLREVLCR-------RRNVLLI  275 (1008)
T ss_pred             hhhcCchHHHHHHHHhhhHHHHHHHHHHHhcchhhhcccceEEeCCCccchHHHHHHHHHHHHHHH-------hhceeEe
Confidence            333334444444456789999999999997  6688999999999999999999999888877643       3468999


Q ss_pred             ccCHHHHHHHHHHHHHHHhhcCcEEEEeeCCCChHHHHHHHhcCCeEEEeCchhHHHHHHhcCCcccccCCceEEEecCc
Q 002040          547 APTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEA  626 (976)
Q Consensus       547 ~Ptr~La~Q~~~~~~~~~~~~~~~~~~~~gg~~~~~~~~~l~~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDEa  626 (976)
                      .|....+..-...+..|+..+|+.+-+.+|..+....    .....|.|||.+.-..++...- ....+..+++|||||.
T Consensus       276 lp~vsiv~Ek~~~l~~~~~~~G~~ve~y~g~~~p~~~----~k~~sv~i~tiEkanslin~li-e~g~~~~~g~vvVdEl  350 (1008)
T KOG0950|consen  276 LPYVSIVQEKISALSPFSIDLGFPVEEYAGRFPPEKR----RKRESVAIATIEKANSLINSLI-EQGRLDFLGMVVVDEL  350 (1008)
T ss_pred             cceeehhHHHHhhhhhhccccCCcchhhcccCCCCCc----ccceeeeeeehHhhHhHHHHHH-hcCCccccCcEEEeee
Confidence            9999888888888889999999999888876554322    2336899999987543332210 1135777999999999


Q ss_pred             ccccccCCchHHHHHHHhc-----CCCCcEEEEeccCcHHHHHHHHHHcCCCeEEEeCCcccccC-CceEEEEecCc-ch
Q 002040          627 DRMFDMGFEPQITRIVQNI-----RPDRQTVLFSATFPRQVEILARKVLNKPVEIQVGGRSVVNK-DITQLVEVRPE-SD  699 (976)
Q Consensus       627 h~~~~~~f~~~i~~il~~~-----~~~~q~i~~SAT~~~~~~~l~~~~l~~~~~i~~~~~~~~~~-~i~q~~~~~~~-~~  699 (976)
                      |.+.+.+.+..+..++..+     ....|+|+||||+|+.-  +...++..-++..- .++++.. .+..-..+... ..
T Consensus       351 hmi~d~~rg~~lE~~l~k~~y~~~~~~~~iIGMSATi~N~~--lL~~~L~A~~y~t~-fRPv~L~E~ik~G~~i~~~~r~  427 (1008)
T KOG0950|consen  351 HMIGDKGRGAILELLLAKILYENLETSVQIIGMSATIPNNS--LLQDWLDAFVYTTR-FRPVPLKEYIKPGSLIYESSRN  427 (1008)
T ss_pred             eeeeccccchHHHHHHHHHHHhccccceeEeeeecccCChH--HHHHHhhhhheecc-cCcccchhccCCCcccccchhh
Confidence            9999888777666655432     33467999999998752  33333332222110 0111000 00000000000 00


Q ss_pred             HH-----------------HHHHHHHHhhhcCC-cEEEEecCHHHHHHHHHHHHHC------------------------
Q 002040          700 RF-----------------LRLLELLGEWYEKG-KILIFVHSQEKCDALFRDLLKH------------------------  737 (976)
Q Consensus       700 k~-----------------~~l~~~l~~~~~~~-kvLIF~~s~~~~~~l~~~L~~~------------------------  737 (976)
                      +.                 ..++.++.+..+.+ .+||||+++..|+.++..+...                        
T Consensus       428 ~~lr~ia~l~~~~~g~~dpD~~v~L~tet~~e~~~~lvfc~sk~~ce~~a~~~~~~vpk~~~~e~~~~~~~~~s~s~~lr  507 (1008)
T KOG0950|consen  428 KVLREIANLYSSNLGDEDPDHLVGLCTETAPEGSSVLVFCPSKKNCENVASLIAKKVPKHIKSEKRLGLWELLSISNLLR  507 (1008)
T ss_pred             HHHHHhhhhhhhhcccCCCcceeeehhhhhhcCCeEEEEcCcccchHHHHHHHHHHhhHhhhhhhhhhHHHHHHHHhHhh
Confidence            00                 12223333333334 5999999999999888665321                        


Q ss_pred             --------------CCCceeccCCCCHHHHHHHHHHhccCCccEEEecCcccccCCCCCCcEEEEe----CCCCCHHHHH
Q 002040          738 --------------GYPCLSLHGAKDQTDRESTISDFKSNVCNLLIATSVAARGLDVKELELVINF----DAPNHYEDYV  799 (976)
Q Consensus       738 --------------~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLVaT~v~~~GlDi~~v~~VI~~----d~p~s~~~y~  799 (976)
                                    .+.+..+|.+++..+|..+-..|++|.+.||+||+.++.|+|+|...++|-+    ....+...|.
T Consensus       508 ~~~~~ld~Vl~~ti~~GvAyHhaGLT~eER~~iE~afr~g~i~vl~aTSTlaaGVNLPArRVIiraP~~g~~~l~~~~Yk  587 (1008)
T KOG0950|consen  508 RIPGILDPVLAKTIPYGVAYHHAGLTSEEREIIEAAFREGNIFVLVATSTLAAGVNLPARRVIIRAPYVGREFLTRLEYK  587 (1008)
T ss_pred             cCCcccchHHheeccccceecccccccchHHHHHHHHHhcCeEEEEecchhhccCcCCcceeEEeCCccccchhhhhhHH
Confidence                          3567889999999999999999999999999999999999999998888843    2244678999


Q ss_pred             HHhcccCCCCC--ccEEEEEecCCCcCchHHHHH
Q 002040          800 HRVGRTGRAGR--KGCAITFISEEDAKYSPDLVK  831 (976)
Q Consensus       800 Qr~GR~gR~g~--~g~~~~~~~~~d~~~~~~i~~  831 (976)
                      |++|||||+|-  .|.+++.+.+.+......++.
T Consensus       588 QM~GRAGR~gidT~GdsiLI~k~~e~~~~~~lv~  621 (1008)
T KOG0950|consen  588 QMVGRAGRTGIDTLGDSILIIKSSEKKRVRELVN  621 (1008)
T ss_pred             hhhhhhhhcccccCcceEEEeeccchhHHHHHHh
Confidence            99999999874  588999998877655555544

>PRK12900 secA preprotein translocase subunit SecA; Reviewed

Probab=99.89  E-value=5.7e-22  Score=235.38  Aligned_cols=128  Identities=23%  Similarity=0.304  Sum_probs=114.1

Q ss_pred             cCcchHHHHHHHHHHhhh-cCCcEEEEecCHHHHHHHHHHHHHCCCCceeccCCCCHHHHHHHHHHhccCCccEEEecCc
Q 002040          695 RPESDRFLRLLELLGEWY-EKGKILIFVHSQEKCDALFRDLLKHGYPCLSLHGAKDQTDRESTISDFKSNVCNLLIATSV  773 (976)
Q Consensus       695 ~~~~~k~~~l~~~l~~~~-~~~kvLIF~~s~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLVaT~v  773 (976)
                      .....|+..++..|.... .+.++||||+|+..++.|+..|...|+++..||+  .+.+|+..+..|..+...|+|||++
T Consensus       578 ~t~~eK~~Ali~~I~~~~~~grpVLIft~Sve~sE~Ls~~L~~~gI~h~vLna--kq~~REa~Iia~AG~~g~VtIATNM  655 (1025)
T PRK12900        578 KTRREKYNAIVLKVEELQKKGQPVLVGTASVEVSETLSRMLRAKRIAHNVLNA--KQHDREAEIVAEAGQKGAVTIATNM  655 (1025)
T ss_pred             cCHHHHHHHHHHHHHHHhhCCCCEEEEeCcHHHHHHHHHHHHHcCCCceeecC--CHHHhHHHHHHhcCCCCeEEEeccC
Confidence            344568888888886654 3569999999999999999999999999999997  6889999999999999999999999


Q ss_pred             ccccCCCC---CCc-----EEEEeCCCCCHHHHHHHhcccCCCCCccEEEEEecCCCcC
Q 002040          774 AARGLDVK---ELE-----LVINFDAPNHYEDYVHRVGRTGRAGRKGCAITFISEEDAK  824 (976)
Q Consensus       774 ~~~GlDi~---~v~-----~VI~~d~p~s~~~y~Qr~GR~gR~g~~g~~~~~~~~~d~~  824 (976)
                      |+||+||+   +|.     +||++..|.+...|+|++||+||.|.+|.+++|++.+|..
T Consensus       656 AGRGtDIkl~~~V~~vGGL~VIgterhes~Rid~Ql~GRtGRqGdpGsS~ffvSleD~L  714 (1025)
T PRK12900        656 AGRGTDIKLGEGVRELGGLFILGSERHESRRIDRQLRGRAGRQGDPGESVFYVSLEDEL  714 (1025)
T ss_pred             cCCCCCcCCccchhhhCCceeeCCCCCchHHHHHHHhhhhhcCCCCcceEEEechhHHH
Confidence            99999999   453     4588999999999999999999999999999999987654

>TIGR00631 uvrb excinuclease ABC, B subunit

Probab=99.89  E-value=5.7e-21  Score=228.26  Aligned_cols=130  Identities=21%  Similarity=0.332  Sum_probs=117.3

Q ss_pred             cCcchHHHHHHHHHHhhhc-CCcEEEEecCHHHHHHHHHHHHHCCCCceeccCCCCHHHHHHHHHHhccCCccEEEecCc
Q 002040          695 RPESDRFLRLLELLGEWYE-KGKILIFVHSQEKCDALFRDLLKHGYPCLSLHGAKDQTDRESTISDFKSNVCNLLIATSV  773 (976)
Q Consensus       695 ~~~~~k~~~l~~~l~~~~~-~~kvLIF~~s~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLVaT~v  773 (976)
                      .+...++..|+..|..+.. +.++||||+++..++.|+.+|...|+.+..+||++++.+|..++..|+.|.+.|||||++
T Consensus       422 ~~~~~qi~~Ll~eI~~~~~~g~~vLIf~~tk~~ae~L~~~L~~~gi~~~~lh~~~~~~eR~~~l~~fr~G~i~VLV~t~~  501 (655)
T TIGR00631       422 RPTDGQVDDLLSEIRQRVARNERVLVTTLTKKMAEDLTDYLKELGIKVRYLHSEIDTLERVEIIRDLRLGEFDVLVGINL  501 (655)
T ss_pred             eeccchHHHHHHHHHHHHcCCCEEEEEECCHHHHHHHHHHHhhhccceeeeeCCCCHHHHHHHHHHHhcCCceEEEEcCh
Confidence            3445677788888877654 458999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccccCCCCCCcEEEEeC-----CCCCHHHHHHHhcccCCCCCccEEEEEecCCCcCc
Q 002040          774 AARGLDVKELELVINFD-----APNHYEDYVHRVGRTGRAGRKGCAITFISEEDAKY  825 (976)
Q Consensus       774 ~~~GlDi~~v~~VI~~d-----~p~s~~~y~Qr~GR~gR~g~~g~~~~~~~~~d~~~  825 (976)
                      +++|+|+|.+++||+++     .|.+...|+|++|||||. ..|.|++|++..+..+
T Consensus       502 L~rGfDiP~v~lVvi~DadifG~p~~~~~~iqriGRagR~-~~G~vi~~~~~~~~~~  557 (655)
T TIGR00631       502 LREGLDLPEVSLVAILDADKEGFLRSERSLIQTIGRAARN-VNGKVIMYADKITDSM  557 (655)
T ss_pred             hcCCeeeCCCcEEEEeCcccccCCCCHHHHHHHhcCCCCC-CCCEEEEEEcCCCHHH
Confidence            99999999999999988     799999999999999998 5899999998765443

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

>KOG2340 consensus Uncharacterized conserved protein [Function unknown]

Probab=99.89  E-value=8.8e-23  Score=221.90  Aligned_cols=346  Identities=19%  Similarity=0.215  Sum_probs=249.8

Q ss_pred             CCCCCcHHHHHHHHHHhcCCCEEEEc-CCCCch--HHHHHHHHHHHHhcCCCCCCCC-----------------------
Q 002040          486 NYEKPMPIQAQALPVIMSGRDCIGVA-KTGSGK--TLAFVLPMLRHIKDQPPVAAGD-----------------------  539 (976)
Q Consensus       486 ~~~~p~~~Q~~~i~~il~g~d~i~~a-~TGsGK--T~~~~l~il~~l~~~~~~~~~~-----------------------  539 (976)
                      .-..+|+.|.+.+..+.+++|++..- ..+.|+  +-+|++++|+|+.+.+....++                       
T Consensus       213 ~s~pltalQ~~L~~~m~~YrDl~y~~~s~kn~~e~R~lYclH~lNHi~K~r~~IL~Nn~r~~Sqk~g~~~~~~frDQG~t  292 (698)
T KOG2340|consen  213 KSEPLTALQKELFKIMFNYRDLLYPTRSQKNGEEYRSLYCLHALNHILKTRDLILGNNRRLASQKEGENPDESFRDQGFT  292 (698)
T ss_pred             ccCcchHHHHHHHHHHHhhhhhccccccccccchhhhhHHHHHHHHHHHHHHHHhcchHhhhhhhcCCCCchhhhhcCCC
Confidence            34578999999999999999998763 345565  5679999999998653322221                       


Q ss_pred             CCeEEEEccCHHHHHHHHHHHHHHHhhcCc---------EEEE---------------------eeCCCChHHHHHH---
Q 002040          540 GPVGLIMAPTRELVQQIHSDIRKFAKVMGV---------RCVP---------------------VYGGSGVAQQISE---  586 (976)
Q Consensus       540 ~~~vLIl~Ptr~La~Q~~~~~~~~~~~~~~---------~~~~---------------------~~gg~~~~~~~~~---  586 (976)
                      .|+||||||+|+.|..+.+.+..++....-         ++..                     ++.|+........   
T Consensus       293 RpkVLivvpfRe~A~riVn~lis~l~G~~q~k~~V~Nk~RF~~eys~~te~~~~~~~kP~D~~~lf~GNtDD~FriGl~f  372 (698)
T KOG2340|consen  293 RPKVLIVVPFRESAYRIVNLLISLLSGDDQGKSEVWNKKRFEGEYSGPTELPPPRAKKPEDFEELFSGNTDDAFRIGLAF  372 (698)
T ss_pred             CceEEEEecchHHHHHHHHHHHHHhcCccccchhhhhhhhhchhcCCCcccCCCCCCCchhHHHHhcCCCcchhhhhHHH
Confidence            389999999999999999988887422211         0111                     1222222211111   


Q ss_pred             ------Hh---cCCeEEEeCchhHHHHHHhcCCcc---cccCCceEEEecCcccccccCCchHHHHHHHhcCCC------
Q 002040          587 ------LK---RGTEIVVCTPGRMIDILCTSGGKI---TNLRRVTYLVMDEADRMFDMGFEPQITRIVQNIRPD------  648 (976)
Q Consensus       587 ------l~---~~~~Iiv~Tp~~L~~~l~~~~~~~---~~l~~~~~vVlDEah~~~~~~f~~~i~~il~~~~~~------  648 (976)
                            |-   ...+|+||+|-.|..+|...+.+.   ..|+++.++|||.||.|+ ++.|..+..|+.+++..      
T Consensus       373 tkKtikLys~fy~SDIlVaSPLGLRmil~n~gdkkrd~dfLSSIEl~iIDQa~~~l-~QNwEhl~~ifdHLn~~P~k~h~  451 (698)
T KOG2340|consen  373 TKKTIKLYSKFYKSDILVASPLGLRMILGNTGDKKRDFDFLSSIELLIIDQADIML-MQNWEHLLHIFDHLNLQPSKQHD  451 (698)
T ss_pred             HHHHHHHHhhhcccCeEEecchhhhhhhcCCCcccccchhhhhhhhhhhhhHHHHH-HhhHHHHHHHHHHhhcCcccccC
Confidence                  11   157999999999988887444332   347889999999999776 56788888888876432      


Q ss_pred             ------------------CcEEEEeccCcHHHHHHHHHHcCCCeE----EEeCC---cccccCCceEEE---E----ecC
Q 002040          649 ------------------RQTVLFSATFPRQVEILARKVLNKPVE----IQVGG---RSVVNKDITQLV---E----VRP  696 (976)
Q Consensus       649 ------------------~q~i~~SAT~~~~~~~l~~~~l~~~~~----i~~~~---~~~~~~~i~q~~---~----~~~  696 (976)
                                        +|+|+||+-..+.+..++..++.+..-    -.+..   ...+...+.|.+   .    ...
T Consensus       452 ~DfSRVR~wyL~~qsr~~rQtl~Fs~y~~~~~nS~fn~~c~N~~Gkv~~~~~~~~gsi~~v~~~l~Qvf~ri~~~si~~~  531 (698)
T KOG2340|consen  452 VDFSRVRMWYLDGQSRYFRQTLLFSRYSHPLFNSLFNQYCQNMAGKVKARNLQSGGSISNVGIPLCQVFQRIEVKSIIET  531 (698)
T ss_pred             CChhheehheeccHHHHHHHHHHHHhhccHHHHHHHHHhhhhhcceeeeccccCCCchhhccchhhhhhhheeccCcccC
Confidence                              589999999888888888877765421    11111   111122233333   2    223


Q ss_pred             cchHHHHHHHHHHhhhc---CCcEEEEecCHHHHHHHHHHHHHCCCCceeccCCCCHHHHHHHHHHhccCCccEEEecCc
Q 002040          697 ESDRFLRLLELLGEWYE---KGKILIFVHSQEKCDALFRDLLKHGYPCLSLHGAKDQTDRESTISDFKSNVCNLLIATSV  773 (976)
Q Consensus       697 ~~~k~~~l~~~l~~~~~---~~kvLIF~~s~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLVaT~v  773 (976)
                      .+.+|..++..|...+.   ...+|||+|+.-+...+.+++++.++.++.||.+.+...-.++...|..|...||+.|.-
T Consensus       532 ~D~RFkyFv~~ImPq~~k~t~s~~LiyIPSYfDFVRvRNy~K~e~i~F~~i~EYssk~~vsRAR~lF~qgr~~vlLyTER  611 (698)
T KOG2340|consen  532 PDARFKYFVDKIMPQLIKRTESGILIYIPSYFDFVRVRNYMKKEEISFVMINEYSSKSKVSRARELFFQGRKSVLLYTER  611 (698)
T ss_pred             chHHHHHHHHhhchhhcccccCceEEEecchhhHHHHHHHhhhhhcchHHHhhhhhHhhhhHHHHHHHhcCceEEEEehh
Confidence            46678777766543332   247899999999999999999999999999999999999999999999999999999997


Q ss_pred             cc--ccCCCCCCcEEEEeCCCCCHHHHHHHhcccCCC---C----CccEEEEEecCCCcCchHHHHHH
Q 002040          774 AA--RGLDVKELELVINFDAPNHYEDYVHRVGRTGRA---G----RKGCAITFISEEDAKYSPDLVKA  832 (976)
Q Consensus       774 ~~--~GlDi~~v~~VI~~d~p~s~~~y~Qr~GR~gR~---g----~~g~~~~~~~~~d~~~~~~i~~~  832 (976)
                      +.  +..+|.+|..||+|.+|.+|..|...+--.+|+   |    ..-+|.++|+..|...+..|+-.
T Consensus       612 ~hffrR~~ikGVk~vVfYqpP~~P~FYsEiinm~~k~~~~gn~d~d~~t~~ilytKyD~i~Le~ivGt  679 (698)
T KOG2340|consen  612 AHFFRRYHIKGVKNVVFYQPPNNPHFYSEIINMSDKTTSQGNTDLDIFTVRILYTKYDRIRLENIVGT  679 (698)
T ss_pred             hhhhhhheecceeeEEEecCCCCcHHHHHHHhhhhhhhccCCccccceEEEEEeechhhHHHHHhhhH
Confidence            76  889999999999999999999997665433332   2    23589999999888777777643

>COG1203 CRISPR-associated helicase Cas3 [Defense mechanisms]

Probab=99.88  E-value=9.8e-22  Score=240.22  Aligned_cols=337  Identities=20%  Similarity=0.237  Sum_probs=220.8

Q ss_pred             CCcHHHHHHHHHHhcC---C-CEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHHHH
Q 002040          489 KPMPIQAQALPVIMSG---R-DCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFA  564 (976)
Q Consensus       489 ~p~~~Q~~~i~~il~g---~-d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~~~  564 (976)
                      .+++.|..++..++..   . .+++.||||+|||++.+++++..+...    ....++++++.|++.++.+++..+..++
T Consensus       195 ~~~~~~~~~~~~~~~~~~~~~~~vl~aPTG~GKT~asl~~a~~~~~~~----~~~~~r~i~vlP~~t~ie~~~~r~~~~~  270 (733)
T COG1203         195 EGYELQEKALELILRLEKRSLLVVLEAPTGYGKTEASLILALALLDEK----IKLKSRVIYVLPFRTIIEDMYRRAKEIF  270 (733)
T ss_pred             hhhHHHHHHHHHHHhcccccccEEEEeCCCCChHHHHHHHHHHHhhcc----ccccceEEEEccHHHHHHHHHHHHHhhh
Confidence            3478999999888754   4 688999999999999999988777653    1257889999999999999999999877


Q ss_pred             hhcCcEEEEeeCCCChHHHHHH-----H---------hcCCeEEEeCchhHHHHHHhcCCcc-cccCCceEEEecCcccc
Q 002040          565 KVMGVRCVPVYGGSGVAQQISE-----L---------KRGTEIVVCTPGRMIDILCTSGGKI-TNLRRVTYLVMDEADRM  629 (976)
Q Consensus       565 ~~~~~~~~~~~gg~~~~~~~~~-----l---------~~~~~Iiv~Tp~~L~~~l~~~~~~~-~~l~~~~~vVlDEah~~  629 (976)
                      ...++....+.|..........     +         .....++++||-.+........... ..+-..+++|+||+|.+
T Consensus       271 ~~~~~~~~~~h~~~~~~~~~~~~~~~~~~~~~~ds~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~S~vIlDE~h~~  350 (733)
T COG1203         271 GLFSVIGKSLHSSSKEPLLLEPDQDILLTLTTNDSYKKLLLALIVVTPIQILIFSVKGFKFEFLALLLTSLVILDEVHLY  350 (733)
T ss_pred             cccccccccccccccchhhhccccccceeEEecccccceeccccccCHhHhhhhhccccchHHHHHHHhhchhhccHHhh
Confidence            6554433322332221111000     0         0013455555554433211111111 00112468999999977


Q ss_pred             cccCCchHHHHHHHhc-CCCCcEEEEeccCcHHHHHHHHHHcCCCeEEEeCCccc---ccCCceEEEEecCcchH-HHHH
Q 002040          630 FDMGFEPQITRIVQNI-RPDRQTVLFSATFPRQVEILARKVLNKPVEIQVGGRSV---VNKDITQLVEVRPESDR-FLRL  704 (976)
Q Consensus       630 ~~~~f~~~i~~il~~~-~~~~q~i~~SAT~~~~~~~l~~~~l~~~~~i~~~~~~~---~~~~i~q~~~~~~~~~k-~~~l  704 (976)
                      ....-...+..++..+ ..+..+|+||||+|+.+.......+.....+.......   ....+.+.......... ...+
T Consensus       351 ~~~~~~~~l~~~i~~l~~~g~~ill~SATlP~~~~~~l~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~  430 (733)
T COG1203         351 ADETMLAALLALLEALAEAGVPVLLMSATLPPFLKEKLKKALGKGREVVENAKFCPKEDEPGLKRKERVDVEDGPQEELI  430 (733)
T ss_pred             cccchHHHHHHHHHHHHhCCCCEEEEecCCCHHHHHHHHHHHhcccceeccccccccccccccccccchhhhhhhhHhhh
Confidence            6653333344444333 34678999999999999888888877665444321100   01111111000000000 1112


Q ss_pred             HHHHHhhhcCCcEEEEecCHHHHHHHHHHHHHCCCCceeccCCCCHHHHHHHHHHh----ccCCccEEEecCcccccCCC
Q 002040          705 LELLGEWYEKGKILIFVHSQEKCDALFRDLLKHGYPCLSLHGAKDQTDRESTISDF----KSNVCNLLIATSVAARGLDV  780 (976)
Q Consensus       705 ~~~l~~~~~~~kvLIF~~s~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F----~~g~~~vLVaT~v~~~GlDi  780 (976)
                      .........+++++|.|||+..|..++..|+..+..++.|||.+...+|...+..+    +.+...|+|||++++.||||
T Consensus       431 ~~~~~~~~~~~kvlvI~NTV~~Aie~Y~~Lk~~~~~v~LlHSRf~~~dR~~ke~~l~~~~~~~~~~IvVaTQVIEagvDi  510 (733)
T COG1203         431 ELISEEVKEGKKVLVIVNTVDRAIELYEKLKEKGPKVLLLHSRFTLKDREEKERELKKLFKQNEGFIVVATQVIEAGVDI  510 (733)
T ss_pred             hcchhhhccCCcEEEEEecHHHHHHHHHHHHhcCCCEEEEecccchhhHHHHHHHHHHHHhccCCeEEEEeeEEEEEecc
Confidence            22222333467999999999999999999999877899999999999999888754    45678899999999999999


Q ss_pred             CCCcEEEEeCCCCCHHHHHHHhcccCCCC--CccEEEEEecCCCcCchHHHHHH
Q 002040          781 KELELVINFDAPNHYEDYVHRVGRTGRAG--RKGCAITFISEEDAKYSPDLVKA  832 (976)
Q Consensus       781 ~~v~~VI~~d~p~s~~~y~Qr~GR~gR~g--~~g~~~~~~~~~d~~~~~~i~~~  832 (976)
                      . .+++|-=  +..+...+||+||++|-|  ..|.++++.......+.......
T Consensus       511 d-fd~mITe--~aPidSLIQR~GRv~R~g~~~~~~~~v~~~~~~~~~~~~~~~~  561 (733)
T COG1203         511 D-FDVLITE--LAPIDSLIQRAGRVNRHGKKENGKIYVYNDEERGPYLKYSYEK  561 (733)
T ss_pred             c-cCeeeec--CCCHHHHHHHHHHHhhcccccCCceeEeecccCCCchhhhhhc
Confidence            5 7777633  344778999999999999  67888888776655555444443

>KOG0392 consensus SNF2 family DNA-dependent ATPase domain-containing protein [Transcription]

Probab=99.88  E-value=1.3e-21  Score=229.96  Aligned_cols=321  Identities=20%  Similarity=0.277  Sum_probs=213.7

Q ss_pred             CCcHHHHHHHHHHh---c-CCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCC-eEEEEccCHHHHHHHHHHHHHH
Q 002040          489 KPMPIQAQALPVIM---S-GRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGP-VGLIMAPTRELVQQIHSDIRKF  563 (976)
Q Consensus       489 ~p~~~Q~~~i~~il---~-g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~-~vLIl~Ptr~La~Q~~~~~~~~  563 (976)
                      .++.||+++++|+.   . +-+.|+|..||.|||++.+..+.......+.......+ -.|||||. .|+--|..++.+|
T Consensus       975 ~LRkYQqEGVnWLaFLnky~LHGILcDDMGLGKTLQticilAsd~y~r~s~~~e~~~~PSLIVCPs-TLtGHW~~E~~kf 1053 (1549)
T KOG0392|consen  975 KLRKYQQEGVNWLAFLNKYKLHGILCDDMGLGKTLQTICILASDHYKRRSESSEFNRLPSLIVCPS-TLTGHWKSEVKKF 1053 (1549)
T ss_pred             HHHHHHHhccHHHHHHHHhcccceeeccccccHHHHHHHHHHHHHHhhcccchhhccCCeEEECCc-hhhhHHHHHHHHh
Confidence            35679999999875   2 34899999999999999766655554443211111223 37999995 6999999999999


Q ss_pred             HhhcCcEEEEeeCCCChHHHHHHHhcCCeEEEeCchhHHHHHHhcCCcccccCCceEEEecCcccccccCCchHHHHHHH
Q 002040          564 AKVMGVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMGFEPQITRIVQ  643 (976)
Q Consensus       564 ~~~~~~~~~~~~gg~~~~~~~~~l~~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDEah~~~~~~f~~~i~~il~  643 (976)
                      +..  +++...+|+......+..-.+.++|||+++..+.+-+..     ..-..|.|+|+||.|-|-+.  ...+...+.
T Consensus      1054 ~pf--L~v~~yvg~p~~r~~lR~q~~~~~iiVtSYDv~RnD~d~-----l~~~~wNYcVLDEGHVikN~--ktkl~kavk 1124 (1549)
T KOG0392|consen 1054 FPF--LKVLQYVGPPAERRELRDQYKNANIIVTSYDVVRNDVDY-----LIKIDWNYCVLDEGHVIKNS--KTKLTKAVK 1124 (1549)
T ss_pred             cch--hhhhhhcCChHHHHHHHhhccccceEEeeHHHHHHHHHH-----HHhcccceEEecCcceecch--HHHHHHHHH
Confidence            876  566666666554444444444689999999988644322     12235789999999977543  334555556


Q ss_pred             hcCCCCcEEEEeccCcH-HHHHH---HHHHcC--------------CC--------------------------------
Q 002040          644 NIRPDRQTVLFSATFPR-QVEIL---ARKVLN--------------KP--------------------------------  673 (976)
Q Consensus       644 ~~~~~~q~i~~SAT~~~-~~~~l---~~~~l~--------------~~--------------------------------  673 (976)
                      .++.+. -+++|+||-. ++..+   +..+|+              .|                                
T Consensus      1125 qL~a~h-RLILSGTPIQNnvleLWSLFdFLMPGfLGtEKqFqsrf~kpI~asRd~K~Sske~EaG~lAleaLHKqVLPF~ 1203 (1549)
T KOG0392|consen 1125 QLRANH-RLILSGTPIQNNVLELWSLFDFLMPGFLGTEKQFQSRFGKPILASRDPKSSSKEQEAGVLALEALHKQVLPFL 1203 (1549)
T ss_pred             HHhhcc-eEEeeCCCcccCHHHHHHHHHHhcccccCcHHHHHHHhcchhhhhcCcccchhHHHhhHHHHHHHHHHHHHHH
Confidence            665544 3566777521 11100   000000              00                                


Q ss_pred             ------------------------------------------eEEEeCCcccccC----CceEE------------EEe-
Q 002040          674 ------------------------------------------VEIQVGGRSVVNK----DITQL------------VEV-  694 (976)
Q Consensus       674 ------------------------------------------~~i~~~~~~~~~~----~i~q~------------~~~-  694 (976)
                                                                +...+.+......    .|.|.            +.. 
T Consensus      1204 LRRlKedVL~DLPpKIIQDyyCeLs~lQ~kLY~df~~~~k~~~~~~~d~~~~S~gt~~~HvFqaLqYlrKLcnHpaLvlt 1283 (1549)
T KOG0392|consen 1204 LRRLKEDVLKDLPPKIIQDYYCELSPLQKKLYRDFVKKAKQCVSSQIDGGEESLGTDKTHVFQALQYLRKLCNHPALVLT 1283 (1549)
T ss_pred             HHHHHHHHHhhCChhhhhheeeccCHHHHHHHHHHHHHhccccccccccchhccCcchHHHHHHHHHHHHhcCCcceeeC
Confidence                                                      0000000000000    00000            000 


Q ss_pred             ----------------------cCcchHHHHHHHHHHhhh---------------cCCcEEEEecCHHHHHHHHHHHHHC
Q 002040          695 ----------------------RPESDRFLRLLELLGEWY---------------EKGKILIFVHSQEKCDALFRDLLKH  737 (976)
Q Consensus       695 ----------------------~~~~~k~~~l~~~l~~~~---------------~~~kvLIF~~s~~~~~~l~~~L~~~  737 (976)
                                            .....|+.+|-++|....               .+.++||||+-+.+++.+.+.|.+.
T Consensus      1284 ~~hp~la~i~~~l~~~~~~LHdi~hspKl~AL~qLL~eCGig~~~~~~~g~~s~vsqHRiLIFcQlK~mlDlVekDL~k~ 1363 (1549)
T KOG0392|consen 1284 PVHPDLAAIVSHLAHFNSSLHDIQHSPKLSALKQLLSECGIGNNSDSEVGTPSDVSQHRILIFCQLKSMLDLVEKDLFKK 1363 (1549)
T ss_pred             CCcchHHHHHHHHHHhhhhHHHhhhchhHHHHHHHHHHhCCCCCCcccccCcchhccceeEEeeeHHHHHHHHHHHHhhh
Confidence                                  011335555666665442               1248999999999999999999775


Q ss_pred             ---CCCceeccCCCCHHHHHHHHHHhccC-CccEEE-ecCcccccCCCCCCcEEEEeCCCCCHHHHHHHhcccCCCCCcc
Q 002040          738 ---GYPCLSLHGAKDQTDRESTISDFKSN-VCNLLI-ATSVAARGLDVKELELVINFDAPNHYEDYVHRVGRTGRAGRKG  812 (976)
Q Consensus       738 ---~~~~~~lhg~~~~~~R~~~~~~F~~g-~~~vLV-aT~v~~~GlDi~~v~~VI~~d~p~s~~~y~Qr~GR~gR~g~~g  812 (976)
                         .+..+.+.|..++.+|.++...|+++ .++||+ +|.|++.|||+.++++||++.-.|||-.-+|.+.||+|.||+-
T Consensus      1364 ~mpsVtymRLDGSVpp~~R~kiV~~FN~DptIDvLlLTThVGGLGLNLTGADTVVFvEHDWNPMrDLQAMDRAHRIGQKr 1443 (1549)
T KOG0392|consen 1364 YMPSVTYMRLDGSVPPGDRQKIVERFNEDPTIDVLLLTTHVGGLGLNLTGADTVVFVEHDWNPMRDLQAMDRAHRIGQKR 1443 (1549)
T ss_pred             hcCceeEEEecCCCCcHHHHHHHHHhcCCCceeEEEEeeeccccccccCCCceEEEEecCCCchhhHHHHHHHHhhcCce
Confidence               45566899999999999999999999 788765 5679999999999999999999999999999999999999986


Q ss_pred             E--EEEEecC
Q 002040          813 C--AITFISE  820 (976)
Q Consensus       813 ~--~~~~~~~  820 (976)
                      .  +|.|++.
T Consensus      1444 vVNVyRlItr 1453 (1549)
T KOG0392|consen 1444 VVNVYRLITR 1453 (1549)
T ss_pred             eeeeeeehhc
Confidence            5  4556664

>PRK12326 preprotein translocase subunit SecA; Reviewed

Probab=99.88  E-value=1.1e-20  Score=218.79  Aligned_cols=321  Identities=18%  Similarity=0.200  Sum_probs=225.3

Q ss_pred             cCCCCCcHHHHHHHHHHhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHHHH
Q 002040          485 LNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFA  564 (976)
Q Consensus       485 ~~~~~p~~~Q~~~i~~il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~~~  564 (976)
                      +|+ .|++.|.-+.-.+++|  -|+.+.||+|||+++++|++.....        |..|.||+|+--||.|-++++..++
T Consensus        75 lg~-r~ydvQlig~l~Ll~G--~VaEM~TGEGKTLvA~l~a~l~AL~--------G~~VhvvT~NdyLA~RDae~m~~ly  143 (764)
T PRK12326         75 LGL-RPFDVQLLGALRLLAG--DVIEMATGEGKTLAGAIAAAGYALQ--------GRRVHVITVNDYLARRDAEWMGPLY  143 (764)
T ss_pred             cCC-CcchHHHHHHHHHhCC--CcccccCCCCHHHHHHHHHHHHHHc--------CCCeEEEcCCHHHHHHHHHHHHHHH
Confidence            564 4889999888888876  4778999999999999998877653        6678999999999999999999999


Q ss_pred             hhcCcEEEEeeCCCChHHHHHHHhcCCeEEEeCchhH-HHHHHhcC---CcccccCCceEEEecCccccc-ccC------
Q 002040          565 KVMGVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRM-IDILCTSG---GKITNLRRVTYLVMDEADRMF-DMG------  633 (976)
Q Consensus       565 ~~~~~~~~~~~gg~~~~~~~~~l~~~~~Iiv~Tp~~L-~~~l~~~~---~~~~~l~~~~~vVlDEah~~~-~~~------  633 (976)
                      ..+|+.|.++.++.+..+....+  .|+|+++|..-| .++|..+-   ........+.++||||+|.|+ |..      
T Consensus       144 ~~LGLsvg~i~~~~~~~err~aY--~~DItYgTn~e~gFDyLRDnm~~~~~~~v~R~~~faIVDEvDSiLIDeArtPLiI  221 (764)
T PRK12326        144 EALGLTVGWITEESTPEERRAAY--ACDVTYASVNEIGFDVLRDQLVTDVADLVSPNPDVAIIDEADSVLVDEALVPLVL  221 (764)
T ss_pred             HhcCCEEEEECCCCCHHHHHHHH--cCCCEEcCCcccccccchhhhccChHhhcCCccceeeecchhhheeccccCceee
Confidence            99999999999988766554444  489999998875 23332221   011234568899999999763 100      


Q ss_pred             --------CchHHHHHHHhcCCC---------------------------------------------------------
Q 002040          634 --------FEPQITRIVQNIRPD---------------------------------------------------------  648 (976)
Q Consensus       634 --------f~~~i~~il~~~~~~---------------------------------------------------------  648 (976)
                              ....+..++..+...                                                         
T Consensus       222 Sg~~~~~~~y~~~~~~v~~L~~~~dy~ide~~k~v~LTe~G~~~~e~~l~~~~ly~~~~~~~~~~~i~~AL~A~~l~~~d  301 (764)
T PRK12326        222 AGSTPGEAPRGEIAELVRRLREGKDYEIDDDGRNVHLTDKGARKVEKALGGIDLYSEEHVGTTLTQVNVALHAHALLQRD  301 (764)
T ss_pred             eCCCcchhHHHHHHHHHHhcCcCCcEEEEcCCCeeEecHHHHHHHHHHcCCccccCcchhHHHHHHHHHHHHHHHHHhcC
Confidence                    000111111111110                                                         


Q ss_pred             -------------------------------------------------------------CcEEEEeccCcHHHHHHHH
Q 002040          649 -------------------------------------------------------------RQTVLFSATFPRQVEILAR  667 (976)
Q Consensus       649 -------------------------------------------------------------~q~i~~SAT~~~~~~~l~~  667 (976)
                                                                                   ..+.+||+|.......+..
T Consensus       302 ~dYiV~dgeV~iVDe~TGRvm~grrwsdGLHQaIEaKE~v~i~~e~~t~AsIT~QnfFr~Y~kLsGMTGTa~t~~~Ef~~  381 (764)
T PRK12326        302 VHYIVRDGKVHLINASRGRIAQLQRWPDGLQAAVEAKEGLETTETGEVLDTITVQALIGRYPTVCGMTGTAVAAGEQLRQ  381 (764)
T ss_pred             CcEEEECCEEEEEECCCCCcCCCCccChHHHHHHHHHcCCCCCCCceeeehhhHHHHHHhcchheeecCCChhHHHHHHH
Confidence                                                                         1245666665544443333


Q ss_pred             HHcCCCeEEEeCCcccccCCceEEEEecCcchHHHHHHHHHHhhhc-CCcEEEEecCHHHHHHHHHHHHHCCCCceeccC
Q 002040          668 KVLNKPVEIQVGGRSVVNKDITQLVEVRPESDRFLRLLELLGEWYE-KGKILIFVHSQEKCDALFRDLLKHGYPCLSLHG  746 (976)
Q Consensus       668 ~~l~~~~~i~~~~~~~~~~~i~q~~~~~~~~~k~~~l~~~l~~~~~-~~kvLIF~~s~~~~~~l~~~L~~~~~~~~~lhg  746 (976)
                      .| +-++.+.+...+...... ....+.....|+..++..+...+. +.||||.|.++...+.|+..|.+.|+++..|++
T Consensus       382 iY-~l~Vv~IPtnkp~~R~d~-~d~iy~t~~~k~~Aii~ei~~~~~~GrPVLVgt~sI~~SE~ls~~L~~~gI~h~vLNA  459 (764)
T PRK12326        382 FY-DLGVSVIPPNKPNIREDE-ADRVYATAAEKNDAIVEHIAEVHETGQPVLVGTHDVAESEELAERLRAAGVPAVVLNA  459 (764)
T ss_pred             Hh-CCcEEECCCCCCceeecC-CCceEeCHHHHHHHHHHHHHHHHHcCCCEEEEeCCHHHHHHHHHHHHhCCCcceeecc
Confidence            33 323322222222211111 112344566788888888877654 459999999999999999999999999999998


Q ss_pred             CCCHHHHHHHHHHhccCC-ccEEEecCcccccCCCC---------------CCcEEEEeCCCCCHHHHHHHhcccCCCCC
Q 002040          747 AKDQTDRESTISDFKSNV-CNLLIATSVAARGLDVK---------------ELELVINFDAPNHYEDYVHRVGRTGRAGR  810 (976)
Q Consensus       747 ~~~~~~R~~~~~~F~~g~-~~vLVaT~v~~~GlDi~---------------~v~~VI~~d~p~s~~~y~Qr~GR~gR~g~  810 (976)
                      .-...+-..+-   ..|. -.|.|||++|+||.||.               +=-+||-...+.|--.-.|..||+||.|.
T Consensus       460 k~~~~EA~IIa---~AG~~gaVTIATNMAGRGTDIkLg~~~~~~~~~V~~~GGLhVIgTerheSrRID~QLrGRaGRQGD  536 (764)
T PRK12326        460 KNDAEEARIIA---EAGKYGAVTVSTQMAGRGTDIRLGGSDEADRDRVAELGGLHVIGTGRHRSERLDNQLRGRAGRQGD  536 (764)
T ss_pred             CchHhHHHHHH---hcCCCCcEEEEecCCCCccCeecCCCcccchHHHHHcCCcEEEeccCCchHHHHHHHhcccccCCC
Confidence            75544432222   2343 35999999999999997               33478888899999999999999999999


Q ss_pred             ccEEEEEecCCCc
Q 002040          811 KGCAITFISEEDA  823 (976)
Q Consensus       811 ~g~~~~~~~~~d~  823 (976)
                      +|.+..|++-+|.
T Consensus       537 pGss~f~lSleDd  549 (764)
T PRK12326        537 PGSSVFFVSLEDD  549 (764)
T ss_pred             CCceeEEEEcchh
Confidence            9999999987664

>KOG1002 consensus Nucleotide excision repair protein RAD16 [Replication, recombination and repair]

Probab=99.88  E-value=2.3e-21  Score=208.66  Aligned_cols=124  Identities=24%  Similarity=0.320  Sum_probs=106.0

Q ss_pred             chHHHHHHHHHHhhhcC---CcEEEEecCHHHHHHHHHHHHHCCCCceeccCCCCHHHHHHHHHHhccCC-c-cEEEecC
Q 002040          698 SDRFLRLLELLGEWYEK---GKILIFVHSQEKCDALFRDLLKHGYPCLSLHGAKDQTDRESTISDFKSNV-C-NLLIATS  772 (976)
Q Consensus       698 ~~k~~~l~~~l~~~~~~---~kvLIF~~s~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~-~-~vLVaT~  772 (976)
                      +.|+..|.+.|......   -+.|||.+...+.+.+...|.+.|+.|+.+.|+|++..|..+++.|++.- + -+||+-.
T Consensus       619 STKIEAL~EEl~~l~~rd~t~KsIVFSQFTSmLDLi~~rL~kaGfscVkL~GsMs~~ardatik~F~nd~~c~vfLvSLk  698 (791)
T KOG1002|consen  619 STKIEALVEELYFLRERDRTAKSIVFSQFTSMLDLIEWRLGKAGFSCVKLVGSMSPAARDATIKYFKNDIDCRVFLVSLK  698 (791)
T ss_pred             hhHHHHHHHHHHHHHHcccchhhhhHHHHHHHHHHHHHHhhccCceEEEeccCCChHHHHHHHHHhccCCCeEEEEEEec
Confidence            44666666666544433   37899999999999999999999999999999999999999999999764 3 3678889


Q ss_pred             cccccCCCCCCcEEEEeCCCCCHHHHHHHhcccCCCCCc--cEEEEEecCC
Q 002040          773 VAARGLDVKELELVINFDAPNHYEDYVHRVGRTGRAGRK--GCAITFISEE  821 (976)
Q Consensus       773 v~~~GlDi~~v~~VI~~d~p~s~~~y~Qr~GR~gR~g~~--g~~~~~~~~~  821 (976)
                      +++..||+..+..|+++||+||++.-.|...|++|.|+.  -.++.|+.+.
T Consensus       699 AGGVALNLteASqVFmmDPWWNpaVe~Qa~DRiHRIGQ~rPvkvvrf~iEn  749 (791)
T KOG1002|consen  699 AGGVALNLTEASQVFMMDPWWNPAVEWQAQDRIHRIGQYRPVKVVRFCIEN  749 (791)
T ss_pred             cCceEeeechhceeEeecccccHHHHhhhhhhHHhhcCccceeEEEeehhc
Confidence            999999999999999999999999999999999999974  4566676543

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

Probab=99.87  E-value=3.4e-20  Score=202.95  Aligned_cols=189  Identities=21%  Similarity=0.288  Sum_probs=142.2

Q ss_pred             CcEEEEeccCcHHHHHHHHHHcCCCeEEEeCCcccccCCceEEEEecCcchHHHHHHHHHHhhh-cCCcEEEEecCHHHH
Q 002040          649 RQTVLFSATFPRQVEILARKVLNKPVEIQVGGRSVVNKDITQLVEVRPESDRFLRLLELLGEWY-EKGKILIFVHSQEKC  727 (976)
Q Consensus       649 ~q~i~~SAT~~~~~~~l~~~~l~~~~~i~~~~~~~~~~~i~q~~~~~~~~~k~~~l~~~l~~~~-~~~kvLIF~~s~~~~  727 (976)
                      .|+|++||||.+.-....   -+..+.-.+...+.+    ...+.+.+....+..|+..|.... .+.++||-+-|++++
T Consensus       387 ~q~i~VSATPg~~E~e~s---~~~vveQiIRPTGLl----DP~ievRp~~~QvdDL~~EI~~r~~~~eRvLVTtLTKkmA  459 (663)
T COG0556         387 PQTIYVSATPGDYELEQS---GGNVVEQIIRPTGLL----DPEIEVRPTKGQVDDLLSEIRKRVAKNERVLVTTLTKKMA  459 (663)
T ss_pred             CCEEEEECCCChHHHHhc---cCceeEEeecCCCCC----CCceeeecCCCcHHHHHHHHHHHHhcCCeEEEEeehHHHH
Confidence            699999999876522221   112222222222222    233456677777888887777644 456999999999999


Q ss_pred             HHHHHHHHHCCCCceeccCCCCHHHHHHHHHHhccCCccEEEecCcccccCCCCCCcEEEEeCCC-----CCHHHHHHHh
Q 002040          728 DALFRDLLKHGYPCLSLHGAKDQTDRESTISDFKSNVCNLLIATSVAARGLDVKELELVINFDAP-----NHYEDYVHRV  802 (976)
Q Consensus       728 ~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLVaT~v~~~GlDi~~v~~VI~~d~p-----~s~~~y~Qr~  802 (976)
                      +.|..+|.+.|+.+..+|++.+.-+|..++..++.|.++|||.-+.+-.|||+|.|.+|.++|..     .|-.+.+|.+
T Consensus       460 EdLT~Yl~e~gikv~YlHSdidTlER~eIirdLR~G~~DvLVGINLLREGLDiPEVsLVAIlDADKeGFLRse~SLIQtI  539 (663)
T COG0556         460 EDLTEYLKELGIKVRYLHSDIDTLERVEIIRDLRLGEFDVLVGINLLREGLDLPEVSLVAILDADKEGFLRSERSLIQTI  539 (663)
T ss_pred             HHHHHHHHhcCceEEeeeccchHHHHHHHHHHHhcCCccEEEeehhhhccCCCcceeEEEEeecCccccccccchHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999998764     5778999999


Q ss_pred             cccCCCCCccEEEEEecCCCcCch---------HHHHHHHhhccCCCChHHH
Q 002040          803 GRTGRAGRKGCAITFISEEDAKYS---------PDLVKALELSEQVVPDDLK  845 (976)
Q Consensus       803 GR~gR~g~~g~~~~~~~~~d~~~~---------~~i~~~l~~~~~~vp~~l~  845 (976)
                      |||.|.- .|.+++|...-...+-         ..+.-.++.....+|..+.
T Consensus       540 GRAARN~-~GkvIlYAD~iT~sM~~Ai~ET~RRR~iQ~~yN~~hgItP~ti~  590 (663)
T COG0556         540 GRAARNV-NGKVILYADKITDSMQKAIDETERRREIQMAYNEEHGITPQTIK  590 (663)
T ss_pred             HHHhhcc-CCeEEEEchhhhHHHHHHHHHHHHHHHHHHHHHHhcCCCchhhh
Confidence            9999974 7899888754322221         2233344555566675543

>COG1110 Reverse gyrase [DNA replication, recombination, and repair]

Probab=99.87  E-value=1.6e-20  Score=219.09  Aligned_cols=280  Identities=23%  Similarity=0.358  Sum_probs=199.4

Q ss_pred             cCCCCCcHHHHHHHHHHhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHHHH
Q 002040          485 LNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFA  564 (976)
Q Consensus       485 ~~~~~p~~~Q~~~i~~il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~~~  564 (976)
                      .|+ .|+..|.--..-++.|+++-++||||.|||+- .+.|-.++..       .|.+++||+||..|+.|+++.+.+|+
T Consensus        79 ~G~-~~ws~QR~WakR~~rg~SFaiiAPTGvGKTTf-g~~~sl~~a~-------kgkr~yii~PT~~Lv~Q~~~kl~~~~  149 (1187)
T COG1110          79 TGF-RPWSAQRVWAKRLVRGKSFAIIAPTGVGKTTF-GLLMSLYLAK-------KGKRVYIIVPTTTLVRQVYERLKKFA  149 (1187)
T ss_pred             hCC-CchHHHHHHHHHHHcCCceEEEcCCCCchhHH-HHHHHHHHHh-------cCCeEEEEecCHHHHHHHHHHHHHHH
Confidence            454 79999999999999999999999999999974 4433333332       36789999999999999999999999


Q ss_pred             hhcC-cEEEEeeCCCC-h---HHHHHHHhc-CCeEEEeCchhHHHHHHhcCCcccccCCceEEEecCccccccc------
Q 002040          565 KVMG-VRCVPVYGGSG-V---AQQISELKR-GTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDM------  632 (976)
Q Consensus       565 ~~~~-~~~~~~~gg~~-~---~~~~~~l~~-~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDEah~~~~~------  632 (976)
                      ...+ ..+..+|.+.- .   .+....+.. +.+|+|+|..-|...+..-    .. -++++|++|.+|.++..      
T Consensus       150 e~~~~~~~~~~yh~~l~~~ekee~le~i~~gdfdIlitTs~FL~k~~e~L----~~-~kFdfifVDDVDA~LkaskNvDr  224 (1187)
T COG1110         150 EDAGSLDVLVVYHSALPTKEKEEALERIESGDFDILITTSQFLSKRFEEL----SK-LKFDFIFVDDVDAILKASKNVDR  224 (1187)
T ss_pred             hhcCCcceeeeeccccchHHHHHHHHHHhcCCccEEEEeHHHHHhhHHHh----cc-cCCCEEEEccHHHHHhccccHHH
Confidence            8776 55555566652 2   233445554 5799999988766555321    12 35899999999977543      


Q ss_pred             -----CCchHH-------HHHHHh------------------------cCCCCcEEEEeccCcHHH--HHHHHHHcCCCe
Q 002040          633 -----GFEPQI-------TRIVQN------------------------IRPDRQTVLFSATFPRQV--EILARKVLNKPV  674 (976)
Q Consensus       633 -----~f~~~i-------~~il~~------------------------~~~~~q~i~~SAT~~~~~--~~l~~~~l~~~~  674 (976)
                           ||...+       ..+...                        -....++|+.|||..+.-  ..+.+.+++.  
T Consensus       225 iL~LlGf~eE~i~~a~~~~~lr~~~~~~~~~~~~~e~~~~~e~~~~~~r~k~g~LvvsSATg~~rg~R~~LfReLlgF--  302 (1187)
T COG1110         225 LLRLLGFSEEVIESAYELIKLRRKLYGEKRAERVREELREVEREREKKRRKLGILVVSSATGKPRGSRLKLFRELLGF--  302 (1187)
T ss_pred             HHHHcCCCHHHHHHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHHHhccCCceEEEeeccCCCCCchHHHHHHHhCC--
Confidence                 233211       111111                        113357899999976532  2345555543  


Q ss_pred             EEEeCCcccccCCceEEEEecCcchHHHHHHHHHHhhhcCCcEEEEecC---HHHHHHHHHHHHHCCCCceeccCCCCHH
Q 002040          675 EIQVGGRSVVNKDITQLVEVRPESDRFLRLLELLGEWYEKGKILIFVHS---QEKCDALFRDLLKHGYPCLSLHGAKDQT  751 (976)
Q Consensus       675 ~i~~~~~~~~~~~i~q~~~~~~~~~k~~~l~~~l~~~~~~~kvLIF~~s---~~~~~~l~~~L~~~~~~~~~lhg~~~~~  751 (976)
                        .++.......+|...+...   .-...+++++..+  +...|||++.   .+.++.|+.+|..+|+++..+|+..   
T Consensus       303 --evG~~~~~LRNIvD~y~~~---~~~e~~~elvk~l--G~GgLIfV~~d~G~e~aeel~e~Lr~~Gi~a~~~~a~~---  372 (1187)
T COG1110         303 --EVGSGGEGLRNIVDIYVES---ESLEKVVELVKKL--GDGGLIFVPIDYGREKAEELAEYLRSHGINAELIHAEK---  372 (1187)
T ss_pred             --ccCccchhhhheeeeeccC---ccHHHHHHHHHHh--CCCeEEEEEcHHhHHHHHHHHHHHHhcCceEEEeeccc---
Confidence              3444444445565555544   3344455555554  3367999999   9999999999999999999999843   


Q ss_pred             HHHHHHHHhccCCccEEEec----CcccccCCCCC-CcEEEEeCCC
Q 002040          752 DRESTISDFKSNVCNLLIAT----SVAARGLDVKE-LELVINFDAP  792 (976)
Q Consensus       752 ~R~~~~~~F~~g~~~vLVaT----~v~~~GlDi~~-v~~VI~~d~p  792 (976)
                        ...++.|..|+++|||++    .++-||||+|. +.++|+|+.|
T Consensus       373 --~~~le~F~~GeidvLVGvAsyYG~lVRGlDLP~rirYaIF~GvP  416 (1187)
T COG1110         373 --EEALEDFEEGEVDVLVGVASYYGVLVRGLDLPHRIRYAVFYGVP  416 (1187)
T ss_pred             --hhhhhhhccCceeEEEEecccccceeecCCchhheeEEEEecCC
Confidence              678999999999999976    58889999998 8899999887

>KOG0389 consensus SNF2 family DNA-dependent ATPase [Chromatin structure and dynamics]

Probab=99.87  E-value=5.8e-21  Score=216.80  Aligned_cols=318  Identities=21%  Similarity=0.317  Sum_probs=215.6

Q ss_pred             CcHHHHHHHHHHh----cCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHHHHh
Q 002040          490 PMPIQAQALPVIM----SGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAK  565 (976)
Q Consensus       490 p~~~Q~~~i~~il----~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~~~~  565 (976)
                      +-++|.-+++|+.    .+-++|+..++|.|||++ +++.|.+|...    ...||. |||||...| ..|..+|.+||.
T Consensus       400 LkdYQlvGvNWL~Llyk~~l~gILADEMGLGKTiQ-vIaFlayLkq~----g~~gpH-LVVvPsSTl-eNWlrEf~kwCP  472 (941)
T KOG0389|consen  400 LKDYQLVGVNWLLLLYKKKLNGILADEMGLGKTIQ-VIAFLAYLKQI----GNPGPH-LVVVPSSTL-ENWLREFAKWCP  472 (941)
T ss_pred             ccchhhhhHHHHHHHHHccccceehhhccCcchhH-HHHHHHHHHHc----CCCCCc-EEEecchhH-HHHHHHHHHhCC
Confidence            6799999999975    456789999999999998 44555566553    123554 999999888 668899999986


Q ss_pred             hcCcEEEEeeCCCChHHHHHH-Hh---cCCeEEEeCchhHHHHHHhcCCcccccCCceEEEecCcccccccCCchHHHHH
Q 002040          566 VMGVRCVPVYGGSGVAQQISE-LK---RGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMGFEPQITRI  641 (976)
Q Consensus       566 ~~~~~~~~~~gg~~~~~~~~~-l~---~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDEah~~~~~~f~~~i~~i  641 (976)
                      .  +.|.+.||.......+.. +.   .+++|+|+|+.....--  ....++.-.++.|+|+||+|.+-+++ ...+..+
T Consensus       473 s--l~Ve~YyGSq~ER~~lR~~i~~~~~~ydVllTTY~la~~~k--dDRsflk~~~~n~viyDEgHmLKN~~-SeRy~~L  547 (941)
T KOG0389|consen  473 S--LKVEPYYGSQDERRELRERIKKNKDDYDVLLTTYNLAASSK--DDRSFLKNQKFNYVIYDEGHMLKNRT-SERYKHL  547 (941)
T ss_pred             c--eEEEeccCcHHHHHHHHHHHhccCCCccEEEEEeecccCCh--HHHHHHHhccccEEEecchhhhhccc-hHHHHHh
Confidence            4  677777887755444432 22   25799999987553110  00111223468899999999877664 2222222


Q ss_pred             HHhcCCCCcEEEEeccCcH-HHHHHHH-----------------------------------------------------
Q 002040          642 VQNIRPDRQTVLFSATFPR-QVEILAR-----------------------------------------------------  667 (976)
Q Consensus       642 l~~~~~~~q~i~~SAT~~~-~~~~l~~-----------------------------------------------------  667 (976)
                       ..++ ..+-|++|+||-. ++.+|..                                                     
T Consensus       548 -M~I~-An~RlLLTGTPLQNNL~ELiSLL~FvlP~vF~~~~~dl~~if~~k~~~d~d~e~~~l~qerIsrAK~im~PFIL  625 (941)
T KOG0389|consen  548 -MSIN-ANFRLLLTGTPLQNNLKELISLLAFVLPKVFDSSMEDLDVIFKAKKTSDGDIENALLSQERISRAKTIMKPFIL  625 (941)
T ss_pred             -cccc-ccceEEeeCCcccccHHHHHHHHHHHhhHhhhccchHHHHHHhccCCccchhhHHHHHHHHHHHHHHhhhHHHH
Confidence             2232 3346888888521 1111100                                                     


Q ss_pred             -----HHcCC-C---eEEEeCC-------------------cccccCC---------------------ceEEE------
Q 002040          668 -----KVLNK-P---VEIQVGG-------------------RSVVNKD---------------------ITQLV------  692 (976)
Q Consensus       668 -----~~l~~-~---~~i~~~~-------------------~~~~~~~---------------------i~q~~------  692 (976)
                           .++.. |   ..|....                   .+....+                     +.+.|      
T Consensus       626 RR~K~qVL~~LPpK~~~Ie~c~mse~Q~~~Y~~~~~~~~~~~~~~~~ns~~~~~~vlmqlRK~AnHPLL~R~~Y~de~L~  705 (941)
T KOG0389|consen  626 RRLKSQVLKQLPPKIQRIEYCEMSEKQKQLYDELIELYDVKLNEVSKNSELKSGNVLMQLRKAANHPLLFRSIYTDEKLR  705 (941)
T ss_pred             HHHHHHHHHhcCCccceeEeeecchHHHHHHHHHHHHHhhhccccccccccccchHHHHHHHHhcChhHHHHhccHHHHH
Confidence                 00000 0   0000000                   0000000                     00000      


Q ss_pred             ---------------------------------------------E----ecCcchHHHHHHHHHHhhhcC-CcEEEEec
Q 002040          693 ---------------------------------------------E----VRPESDRFLRLLELLGEWYEK-GKILIFVH  722 (976)
Q Consensus       693 ---------------------------------------------~----~~~~~~k~~~l~~~l~~~~~~-~kvLIF~~  722 (976)
                                                                   .    ....+.|+..|..+|...... .+||||.+
T Consensus       706 ~mak~il~e~ay~~~n~qyIfEDm~~msDfelHqLc~~f~~~~~f~L~d~~~mdSgK~r~L~~LLp~~k~~G~RVLiFSQ  785 (941)
T KOG0389|consen  706 KMAKRILNEPAYKKANEQYIFEDMEVMSDFELHQLCCQFRHLSKFQLKDDLWMDSGKCRKLKELLPKIKKKGDRVLIFSQ  785 (941)
T ss_pred             HHHHHHhCchhhhhcCHHHHHHHHHhhhHHHHHHHHHhcCCCcccccCCchhhhhhhHhHHHHHHHHHhhcCCEEEEeeH
Confidence                                                         0    001134666666677666554 59999999


Q ss_pred             CHHHHHHHHHHHHHCCCCceeccCCCCHHHHHHHHHHhccCC--ccEEEecCcccccCCCCCCcEEEEeCCCCCHHHHHH
Q 002040          723 SQEKCDALFRDLLKHGYPCLSLHGAKDQTDRESTISDFKSNV--CNLLIATSVAARGLDVKELELVINFDAPNHYEDYVH  800 (976)
Q Consensus       723 s~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~--~~vLVaT~v~~~GlDi~~v~~VI~~d~p~s~~~y~Q  800 (976)
                      ...+.+.|..+|...++.++.+.|.+.-.+|+.+|..|...+  +-+|++|.+++-|||+.++++||+||+..||-+-.|
T Consensus       786 FTqmLDILE~~L~~l~~~ylRLDGsTqV~~RQ~lId~Fn~d~difVFLLSTKAGG~GINLt~An~VIihD~dFNP~dD~Q  865 (941)
T KOG0389|consen  786 FTQMLDILEVVLDTLGYKYLRLDGSTQVNDRQDLIDEFNTDKDIFVFLLSTKAGGFGINLTCANTVIIHDIDFNPYDDKQ  865 (941)
T ss_pred             HHHHHHHHHHHHHhcCceEEeecCCccchHHHHHHHhhccCCceEEEEEeeccCcceecccccceEEEeecCCCCcccch
Confidence            999999999999999999999999999999999999999654  678999999999999999999999999999999999


Q ss_pred             HhcccCCCCCc--cEEEEEecCC
Q 002040          801 RVGRTGRAGRK--GCAITFISEE  821 (976)
Q Consensus       801 r~GR~gR~g~~--g~~~~~~~~~  821 (976)
                      .-.||+|.||.  -++|.||+..
T Consensus       866 AEDRcHRvGQtkpVtV~rLItk~  888 (941)
T KOG0389|consen  866 AEDRCHRVGQTKPVTVYRLITKS  888 (941)
T ss_pred             hHHHHHhhCCcceeEEEEEEecC
Confidence            99999999986  4566677764

>KOG0390 consensus DNA repair protein, SNF2 family [Replication, recombination and repair]

Probab=99.87  E-value=2.8e-20  Score=217.98  Aligned_cols=320  Identities=20%  Similarity=0.241  Sum_probs=205.1

Q ss_pred             CCcHHHHHHHHHHhc---C-------CCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHH
Q 002040          489 KPMPIQAQALPVIMS---G-------RDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHS  558 (976)
Q Consensus       489 ~p~~~Q~~~i~~il~---g-------~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~  558 (976)
                      .+.|+|.+++..+..   |       ..+|+...+|+|||++.+..|...+...|. ...--.++|||||. .|+..|++
T Consensus       238 ~LrPHQ~EG~~FL~knl~g~~~~~~~~GCImAd~~GlGKTlq~IsflwtlLrq~P~-~~~~~~k~lVV~P~-sLv~nWkk  315 (776)
T KOG0390|consen  238 ILRPHQREGFEFLYKNLAGLIRPKNSGGCIMADEPGLGKTLQCISFIWTLLRQFPQ-AKPLINKPLVVAPS-SLVNNWKK  315 (776)
T ss_pred             hcCchHHHHHHHHHhhhhcccccCCCCceEeeCCCCcchHHHHHHHHHHHHHhCcC-ccccccccEEEccH-HHHHHHHH
Confidence            467999999988752   2       358888999999999866555555554432 11122568999995 68899999


Q ss_pred             HHHHHHhhcCcEEEEeeCCCCh-H---HHHH---HHhcCCeEEEeCchhHHHHHHhcCCcccccCCceEEEecCcccccc
Q 002040          559 DIRKFAKVMGVRCVPVYGGSGV-A---QQIS---ELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFD  631 (976)
Q Consensus       559 ~~~~~~~~~~~~~~~~~gg~~~-~---~~~~---~l~~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDEah~~~~  631 (976)
                      +|.+|.....+....++|+... .   ..+.   .-....-|++.+++.+.+++..     ..+..+++||+||.|++-+
T Consensus       316 EF~KWl~~~~i~~l~~~~~~~~~w~~~~sil~~~~~~~~~~vli~sye~~~~~~~~-----il~~~~glLVcDEGHrlkN  390 (776)
T KOG0390|consen  316 EFGKWLGNHRINPLDFYSTKKSSWIKLKSILFLGYKQFTTPVLIISYETASDYCRK-----ILLIRPGLLVCDEGHRLKN  390 (776)
T ss_pred             HHHHhccccccceeeeecccchhhhhhHHHHHhhhhheeEEEEeccHHHHHHHHHH-----HhcCCCCeEEECCCCCccc
Confidence            9999876556777788888764 0   0011   1112357888899988766643     4567799999999998754


Q ss_pred             cCCchHHHHHHHhcCCCCcEEEEeccCcHH-H------------------------------------------------
Q 002040          632 MGFEPQITRIVQNIRPDRQTVLFSATFPRQ-V------------------------------------------------  662 (976)
Q Consensus       632 ~~f~~~i~~il~~~~~~~q~i~~SAT~~~~-~------------------------------------------------  662 (976)
                      .  ...+...+..+.- ..-|++|+|+-.+ +                                                
T Consensus       391 ~--~s~~~kaL~~l~t-~rRVLLSGTp~QNdl~EyFnlL~fvrP~~Lgs~~sf~k~~~~~i~~~~~~~~s~e~~~~~~rl  467 (776)
T KOG0390|consen  391 S--DSLTLKALSSLKT-PRRVLLTGTPIQNDLKEYFNLLDFVRPGFLGSISSFKKKFEIPILRGRDADASEEDREREERL  467 (776)
T ss_pred             h--hhHHHHHHHhcCC-CceEEeeCCcccccHHHHHHHHhhcChhhccchHHHHHHhhcccccccCCCcchhhhhhHHHH
Confidence            3  2234444444433 3346677774111 0                                                


Q ss_pred             ---HHHHHHH------------c-----------------------------------------------CCCeEEEeCC
Q 002040          663 ---EILARKV------------L-----------------------------------------------NKPVEIQVGG  680 (976)
Q Consensus       663 ---~~l~~~~------------l-----------------------------------------------~~~~~i~~~~  680 (976)
                         ..+...|            |                                               ..|..+....
T Consensus       468 ~eL~~~t~~fi~rrt~~il~k~LP~k~e~vv~~n~t~~Q~~~~~~l~~~~~~~~~~~~~l~~~~~L~k~cnhP~L~~~~~  547 (776)
T KOG0390|consen  468 QELRELTNKFILRRTGDILLKYLPGKYEYVVFCNPTPIQKELYKKLLDSMKMRTLKGYALELITKLKKLCNHPSLLLLCE  547 (776)
T ss_pred             HHHHHHHHhheeecccchhhhhCCCceeEEEEeCCcHHHHHHHHHHHHHHHhhhhhcchhhHHHHHHHHhcCHHhhcccc
Confidence               0111111            1                                               1110000000


Q ss_pred             cc-----cccCC-------ceEEEEecCcchHHHHHHHHHHhhhcC--CcEEEEecCHHHHHHHHHHHHHCCCCceeccC
Q 002040          681 RS-----VVNKD-------ITQLVEVRPESDRFLRLLELLGEWYEK--GKILIFVHSQEKCDALFRDLLKHGYPCLSLHG  746 (976)
Q Consensus       681 ~~-----~~~~~-------i~q~~~~~~~~~k~~~l~~~l~~~~~~--~kvLIF~~s~~~~~~l~~~L~~~~~~~~~lhg  746 (976)
                      ..     ..++.       ......-...+.++..|..+|......  ..+.+..|-....+.+...+.-.|+.++.+||
T Consensus       548 ~~~~e~~~~~~~~~~~~~~~~~~~~~~~ks~kl~~L~~ll~~~~ek~~~~~v~Isny~~tldl~e~~~~~~g~~~~rLdG  627 (776)
T KOG0390|consen  548 KTEKEKAFKNPALLLDPGKLKLDAGDGSKSGKLLVLVFLLEVIREKLLVKSVLISNYTQTLDLFEQLCRWRGYEVLRLDG  627 (776)
T ss_pred             cccccccccChHhhhcccccccccccchhhhHHHHHHHHHHHHhhhcceEEEEeccHHHHHHHHHHHHhhcCceEEEEcC
Confidence            00     00000       000000001133555555555333221  13444445555666666666667999999999


Q ss_pred             CCCHHHHHHHHHHhccCC---ccEEEecCcccccCCCCCCcEEEEeCCCCCHHHHHHHhcccCCCCCccEEEEEe
Q 002040          747 AKDQTDRESTISDFKSNV---CNLLIATSVAARGLDVKELELVINFDAPNHYEDYVHRVGRTGRAGRKGCAITFI  818 (976)
Q Consensus       747 ~~~~~~R~~~~~~F~~g~---~~vLVaT~v~~~GlDi~~v~~VI~~d~p~s~~~y~Qr~GR~gR~g~~g~~~~~~  818 (976)
                      .|+..+|+.++..|++-.   .-+|.+|.+.+.||++-+++.||+||++|||+.-.|+++|+.|.||+-.||+|-
T Consensus       628 ~~~~~qRq~~vd~FN~p~~~~~vfLlSsKAgg~GinLiGAsRlil~D~dWNPa~d~QAmaR~~RdGQKk~v~iYr  702 (776)
T KOG0390|consen  628 KTSIKQRQKLVDTFNDPESPSFVFLLSSKAGGEGLNLIGASRLILFDPDWNPAVDQQAMARAWRDGQKKPVYIYR  702 (776)
T ss_pred             CCchHHHHHHHHhccCCCCCceEEEEecccccCceeecccceEEEeCCCCCchhHHHHHHHhccCCCcceEEEEE
Confidence            999999999999998543   557889999999999999999999999999999999999999999988777653

>PRK13103 secA preprotein translocase subunit SecA; Reviewed

Probab=99.86  E-value=8.9e-20  Score=216.48  Aligned_cols=322  Identities=18%  Similarity=0.200  Sum_probs=220.7

Q ss_pred             cCCCCCcHHHHHHHHHHhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHHHH
Q 002040          485 LNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFA  564 (976)
Q Consensus       485 ~~~~~p~~~Q~~~i~~il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~~~  564 (976)
                      +|. .|++.|..+--.+  ...-|..+.||+|||+++++|++.....        |..|.||+||--||.|-+.++..++
T Consensus        79 lGm-~~ydVQliGg~~L--h~G~iaEM~TGEGKTLvA~l~a~l~al~--------G~~VhvvT~ndyLA~RD~e~m~~l~  147 (913)
T PRK13103         79 MGM-RHFDVQLIGGMTL--HEGKIAEMRTGEGKTLVGTLAVYLNALS--------GKGVHVVTVNDYLARRDANWMRPLY  147 (913)
T ss_pred             hCC-CcchhHHHhhhHh--ccCccccccCCCCChHHHHHHHHHHHHc--------CCCEEEEeCCHHHHHHHHHHHHHHh
Confidence            563 4667776554444  4567889999999999999999876553        6678999999999999999999999


Q ss_pred             hhcCcEEEEeeCCCChHHHHHHHhcCCeEEEeCchhH-HHHHHhcCC---cccccCCceEEEecCccccc-ccC------
Q 002040          565 KVMGVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRM-IDILCTSGG---KITNLRRVTYLVMDEADRMF-DMG------  633 (976)
Q Consensus       565 ~~~~~~~~~~~gg~~~~~~~~~l~~~~~Iiv~Tp~~L-~~~l~~~~~---~~~~l~~~~~vVlDEah~~~-~~~------  633 (976)
                      ..+|+.|.++.++.+..+....+.  ++|+|+|..-| .++|..+-.   .......+.|+||||+|.++ |..      
T Consensus       148 ~~lGl~v~~i~~~~~~~err~~Y~--~dI~YGT~~e~gFDYLrD~~~~~~~~~vqr~l~~aIVDEvDsiLIDEArtPLII  225 (913)
T PRK13103        148 EFLGLSVGIVTPFQPPEEKRAAYA--ADITYGTNNEFGFDYLRDNMAFSLDDKFQRELNFAVIDEVDSILIDEARTPLII  225 (913)
T ss_pred             cccCCEEEEECCCCCHHHHHHHhc--CCEEEEcccccccchhhccceechhhhcccccceeEechhhheeccccCCceee
Confidence            999999999998887766555444  89999999986 344432210   01124678999999999763 110      


Q ss_pred             ---------CchHHHHHHHhcCC---------------------------------------------------------
Q 002040          634 ---------FEPQITRIVQNIRP---------------------------------------------------------  647 (976)
Q Consensus       634 ---------f~~~i~~il~~~~~---------------------------------------------------------  647 (976)
                               +...+..++..+..                                                         
T Consensus       226 Sg~~~~~~~~y~~~~~~v~~L~~~~~~~~~~~~~~~~y~idek~~~v~LTe~G~~~~e~~~~~~~i~~~~~~ly~~~~~~  305 (913)
T PRK13103        226 SGQAEDSSKLYIEINRLIPRLKQHIEEVEGQVTQEGHFTIDEKTRQVELNEAGHQFIEEMLTQAGLLAEGESLYSAHNLG  305 (913)
T ss_pred             cCCCccchHHHHHHHHHHHHHHhhhhccccccCCCCCeEEEcCCCeeeechHHHHHHHHHhhhCCCcccchhccChhhhH
Confidence                     00001111111100                                                         


Q ss_pred             -----------------C-------------------------------------------------------------C
Q 002040          648 -----------------D-------------------------------------------------------------R  649 (976)
Q Consensus       648 -----------------~-------------------------------------------------------------~  649 (976)
                                       +                                                             .
T Consensus       306 ~~~~i~~AL~A~~lf~~d~dYiV~dg~V~IVDe~TGR~m~grrwsdGLHQaIEaKE~v~I~~e~~t~AsIT~QnfFr~Y~  385 (913)
T PRK13103        306 LLTHVYAGLRAHKLFHRNVEYIVQDGQVLLIDEHTGRTMPGRRLSEGLHQAIEAKENLNIQAESQTLASTTFQNYFRLYN  385 (913)
T ss_pred             HHHHHHHHHHHHHHHhcCCcEEEECCEEEEEECCCCCcCCCCccchHHHHHHHHHcCCCcCCCceeEEeehHHHHHHhcc
Confidence                             0                                                             1


Q ss_pred             cEEEEeccCcHHHHHHHHHHcCCCeEEEeCCcccccCCceEEEEecCcchHHHHHHHHHHhhhc-CCcEEEEecCHHHHH
Q 002040          650 QTVLFSATFPRQVEILARKVLNKPVEIQVGGRSVVNKDITQLVEVRPESDRFLRLLELLGEWYE-KGKILIFVHSQEKCD  728 (976)
Q Consensus       650 q~i~~SAT~~~~~~~l~~~~l~~~~~i~~~~~~~~~~~i~q~~~~~~~~~k~~~l~~~l~~~~~-~~kvLIF~~s~~~~~  728 (976)
                      ++.+||+|.......|. .+++-.+...+...+....... ...+.....|+..++..+...+. +.||||-|.|+...+
T Consensus       386 kLsGMTGTa~te~~Ef~-~iY~l~Vv~IPTnkP~~R~D~~-d~vy~t~~eK~~Ai~~ei~~~~~~GrPVLVGT~SVe~SE  463 (913)
T PRK13103        386 KLSGMTGTADTEAFEFR-QIYGLDVVVIPPNKPLARKDFN-DLVYLTAEEKYAAIITDIKECMALGRPVLVGTATIETSE  463 (913)
T ss_pred             hhccCCCCCHHHHHHHH-HHhCCCEEECCCCCCcccccCC-CeEEcCHHHHHHHHHHHHHHHHhCCCCEEEEeCCHHHHH
Confidence            13344444433332222 2222222222222222211111 12345567889999888887765 459999999999999


Q ss_pred             HHHHHHHHCCCCceeccCCCCHHHHHHHHHHhccCC-ccEEEecCcccccCCCC--------------------------
Q 002040          729 ALFRDLLKHGYPCLSLHGAKDQTDRESTISDFKSNV-CNLLIATSVAARGLDVK--------------------------  781 (976)
Q Consensus       729 ~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~-~~vLVaT~v~~~GlDi~--------------------------  781 (976)
                      .|+..|...|+++.+|+......+-..+-   ..|. -.|.|||++|+||.||.                          
T Consensus       464 ~ls~~L~~~gi~h~VLNAk~~~~EA~IIa---~AG~~GaVTIATNMAGRGTDIkLg~n~~~~~~~~~~~~~~~~~~~~~~  540 (913)
T PRK13103        464 HMSNLLKKEGIEHKVLNAKYHEKEAEIIA---QAGRPGALTIATNMAGRGTDILLGGNWEVEVAALENPTPEQIAQIKAD  540 (913)
T ss_pred             HHHHHHHHcCCcHHHhccccchhHHHHHH---cCCCCCcEEEeccCCCCCCCEecCCchHHHHHhhhhhhHHHHHHHHHH
Confidence            99999999999998888875544333332   3453 46999999999999995                          


Q ss_pred             -----------CCcEEEEeCCCCCHHHHHHHhcccCCCCCccEEEEEecCCCcC
Q 002040          782 -----------ELELVINFDAPNHYEDYVHRVGRTGRAGRKGCAITFISEEDAK  824 (976)
Q Consensus       782 -----------~v~~VI~~d~p~s~~~y~Qr~GR~gR~g~~g~~~~~~~~~d~~  824 (976)
                                 +=-+||--..+.|----.|-.||+||.|.+|.+..|++-+|..
T Consensus       541 ~~~~~e~V~e~GGLhVIgTerheSrRID~QLrGRaGRQGDPGsS~f~lSlED~L  594 (913)
T PRK13103        541 WQKRHQQVIEAGGLHVIASERHESRRIDNQLRGRAGRQGDPGSSRFYLSLEDSL  594 (913)
T ss_pred             HHhHHHHHHHcCCCEEEeeccCchHHHHHHhccccccCCCCCceEEEEEcCcHH
Confidence                       3347888888889888899999999999999999999876653

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

Probab=99.86  E-value=3.3e-19  Score=222.68  Aligned_cols=342  Identities=19%  Similarity=0.218  Sum_probs=214.8

Q ss_pred             HHHHHHHHHcCCCCCcHHHHHHHH----HHhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHH
Q 002040          476 SKIMETIRKLNYEKPMPIQAQALP----VIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRE  551 (976)
Q Consensus       476 ~~l~~~l~~~~~~~p~~~Q~~~i~----~il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~  551 (976)
                      +.+...+...||. ++|.|.+.+.    .+..++++++.|+||+|||++|++|++.++.        .+.++||.|||++
T Consensus       233 ~~~~~~~~~~~~~-~r~~Q~~~~~~i~~~~~~~~~~~~eA~TG~GKT~ayLlp~~~~~~--------~~~~vvi~t~t~~  303 (850)
T TIGR01407       233 SLFSKNIDRLGLE-YRPEQLKLAELVLDQLTHSEKSLIEAPTGTGKTLGYLLPALYYAI--------TEKPVVISTNTKV  303 (850)
T ss_pred             HHHHHhhhhcCCc-cCHHHHHHHHHHHHHhccCCcEEEECCCCCchhHHHHHHHHHHhc--------CCCeEEEEeCcHH
Confidence            3556666678886 7899998776    4557889999999999999999999987754        2447999999999


Q ss_pred             HHHHHHH-HHHHHHhhcC--cEEEEeeCCCChH---------------HH------------------------------
Q 002040          552 LVQQIHS-DIRKFAKVMG--VRCVPVYGGSGVA---------------QQ------------------------------  583 (976)
Q Consensus       552 La~Q~~~-~~~~~~~~~~--~~~~~~~gg~~~~---------------~~------------------------------  583 (976)
                      |..|+.. .+..+.+.++  ++++++.|+...-               ..                              
T Consensus       304 Lq~Ql~~~~~~~l~~~~~~~~~~~~~kG~~~ylcl~k~~~~l~~~~~~~~~~~~~~~~~~wl~~T~tGD~~el~~~~~~~  383 (850)
T TIGR01407       304 LQSQLLEKDIPLLNEILNFKINAALIKGKSNYLSLGKFSQILKDNTDNYEFNIFKMQVLVWLTETETGDLDELNLKGGNK  383 (850)
T ss_pred             HHHHHHHHHHHHHHHHcCCCceEEEEEcchhhccHHHHHHHHhcCCCcHHHHHHHHHHHHHhccCCccCHhhccCCCcch
Confidence            9999965 5666665555  7777777654220               00                              


Q ss_pred             --HHH------------------------HhcCCeEEEeCchhHHHHHHhcCCcccccCCceEEEecCcccccccC----
Q 002040          584 --ISE------------------------LKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMG----  633 (976)
Q Consensus       584 --~~~------------------------l~~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDEah~~~~~~----  633 (976)
                        +..                        ....++||||++..|+..+....   .-|....+|||||||++.+..    
T Consensus       384 ~~~~~i~~~~~l~~~c~~~~~Cf~~~ar~~a~~AdivItNHa~L~~~~~~~~---~ilp~~~~lIiDEAH~L~d~a~~~~  460 (850)
T TIGR01407       384 MFFAQVRHDGNLSKKDLFYEVDFYNRAQKNAEQAQILITNHAYLITRLVDNP---ELFPSFRDLIIDEAHHLPDIAENQL  460 (850)
T ss_pred             hhHHHhhcCCCCCCCCCCccccHHHHHHHHHhcCCEEEecHHHHHHHhhccc---ccCCCCCEEEEECcchHHHHHHHHh
Confidence              000                        01146899999998877764332   234566899999999874210    


Q ss_pred             ---C-----chH----------------------------------------------------------------HHHH
Q 002040          634 ---F-----EPQ----------------------------------------------------------------ITRI  641 (976)
Q Consensus       634 ---f-----~~~----------------------------------------------------------------i~~i  641 (976)
                         +     ...                                                                +...
T Consensus       461 ~~~ls~~~~~~~l~~l~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~l~~~l~~~~~~~~~~~~~l~~~  540 (850)
T TIGR01407       461 QEELDYADIKYQIDLIGKGENEQLLKRIQQLEKQEILEKLFDFETKDILKDLQAILDKLNKLLQIFSELSHKTVDQLRKF  540 (850)
T ss_pred             cceeCHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHhhhhhhhHHHHHHHHHHHHHHHHHHHHhhhhhhHHHHHHH
Confidence               0     000                                                                0000


Q ss_pred             HHh---------------------c---------------------------CCCCcEEEEeccCcH--HHHHHHHHHcC
Q 002040          642 VQN---------------------I---------------------------RPDRQTVLFSATFPR--QVEILARKVLN  671 (976)
Q Consensus       642 l~~---------------------~---------------------------~~~~q~i~~SAT~~~--~~~~l~~~~l~  671 (976)
                      +..                     .                           .....+|++|||++.  ....+ ...++
T Consensus       541 ~~~~~~~~~~l~~~~~~~~~~wi~~~~~~~~~~~~l~~~pl~~~~~l~~~~~~~~~~~il~SATL~~~~~~~~~-~~~lG  619 (850)
T TIGR01407       541 DLALKDDFKNIEQSLKEGHTSWISIENLQQKSTIRLYIKDYEVGDVLTKRLLPKFKSLIFTSATLKFSHSFESF-PQLLG  619 (850)
T ss_pred             HHHHHHHHHHHHHHhccCCeEEEEecCCCCCceEEEEeeeCcHHHHHHHHHhccCCeEEEEecccccCCChHHH-HHhcC
Confidence            000                     0                           001357899999863  22323 33333


Q ss_pred             C--CeEEEeCCccccc-CCceEEEEe---c-----CcchHHHHHHHHHHhhh--cCCcEEEEecCHHHHHHHHHHHHH--
Q 002040          672 K--PVEIQVGGRSVVN-KDITQLVEV---R-----PESDRFLRLLELLGEWY--EKGKILIFVHSQEKCDALFRDLLK--  736 (976)
Q Consensus       672 ~--~~~i~~~~~~~~~-~~i~q~~~~---~-----~~~~k~~~l~~~l~~~~--~~~kvLIF~~s~~~~~~l~~~L~~--  736 (976)
                      -  .....+...++.. ... ..+..   .     ........+...|....  ..|++||||++...++.++..|..  
T Consensus       620 l~~~~~~~~~~spf~~~~~~-~l~v~~d~~~~~~~~~~~~~~~ia~~i~~l~~~~~g~~LVlftS~~~l~~v~~~L~~~~  698 (850)
T TIGR01407       620 LTDVHFNTIEPTPLNYAENQ-RVLIPTDAPAIQNKSLEEYAQEIASYIIEITAITSPKILVLFTSYEMLHMVYDMLNELP  698 (850)
T ss_pred             CCccccceecCCCCCHHHcC-EEEecCCCCCCCCCChHHHHHHHHHHHHHHHHhcCCCEEEEeCCHHHHHHHHHHHhhhc
Confidence            2  1212221111111 111 11111   0     11122234444443332  457999999999999999999975  


Q ss_pred             --CCCCceeccCCCCHHHHHHHHHHhccCCccEEEecCcccccCCCCCCc--EEEEeCCCCC----H-------------
Q 002040          737 --HGYPCLSLHGAKDQTDRESTISDFKSNVCNLLIATSVAARGLDVKELE--LVINFDAPNH----Y-------------  795 (976)
Q Consensus       737 --~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLVaT~v~~~GlDi~~v~--~VI~~d~p~s----~-------------  795 (976)
                        .++.+  +..+.. ..|..+++.|++|...|||||+.+++|||+++..  +||+...|..    +             
T Consensus       699 ~~~~~~~--l~q~~~-~~r~~ll~~F~~~~~~iLlgt~sf~EGVD~~g~~l~~viI~~LPf~~p~dp~~~a~~~~~~~~g  775 (850)
T TIGR01407       699 EFEGYEV--LAQGIN-GSRAKIKKRFNNGEKAILLGTSSFWEGVDFPGNGLVCLVIPRLPFANPKHPLTKKYWQKLEQEG  775 (850)
T ss_pred             cccCceE--EecCCC-ccHHHHHHHHHhCCCeEEEEcceeecccccCCCceEEEEEeCCCCCCCCCHHHHHHHHHHHHhc
Confidence              23333  333333 5788999999999999999999999999999955  5677665531    1             


Q ss_pred             -------------HHHHHHhcccCCCCCccEEEEEecCC--CcCchHHHHHHHh
Q 002040          796 -------------EDYVHRVGRTGRAGRKGCAITFISEE--DAKYSPDLVKALE  834 (976)
Q Consensus       796 -------------~~y~Qr~GR~gR~g~~g~~~~~~~~~--d~~~~~~i~~~l~  834 (976)
                                   ..+.|.+||+-|......++++++..  ...|-..+.+.|.
T Consensus       776 ~~~f~~~~lP~A~~~l~Qa~GRlIRs~~D~G~v~ilD~R~~~~~Yg~~~~~sLp  829 (850)
T TIGR01407       776 KNPFYDYVLPMAIIRLRQALGRLIRRENDRGSIVILDRRLVGKRYGKRFEKSLP  829 (850)
T ss_pred             CCchHHhhHHHHHHHHHHhhccccccCCceEEEEEEccccccchHHHHHHHhCC
Confidence                         12359999999987665566666654  4456667766664

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.

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

Probab=99.85  E-value=1e-19  Score=220.21  Aligned_cols=301  Identities=18%  Similarity=0.189  Sum_probs=182.5

Q ss_pred             CcHHHHHHHHHHh----c------CCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHH
Q 002040          490 PMPIQAQALPVIM----S------GRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSD  559 (976)
Q Consensus       490 p~~~Q~~~i~~il----~------g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~  559 (976)
                      |.++|..|+..+.    .      .+..|++++||||||++++..+...+.      ...++++|||||+.+|..|+...
T Consensus       239 ~r~~Q~~av~~~~~~~~~~~~~~~~~~gli~~~TGsGKT~t~~~la~~l~~------~~~~~~vl~lvdR~~L~~Q~~~~  312 (667)
T TIGR00348       239 QRYMQYRAVKKIVESITRKTWGKDERGGLIWHTQGSGKTLTMLFAARKALE------LLKNPKVFFVVDRRELDYQLMKE  312 (667)
T ss_pred             hHHHHHHHHHHHHHHHHhcccCCCCceeEEEEecCCCccHHHHHHHHHHHh------hcCCCeEEEEECcHHHHHHHHHH
Confidence            6789999988764    2      257999999999999986655544432      12468999999999999999999


Q ss_pred             HHHHHhhcCcEEEEeeCCCChHHHHHHHhc-CCeEEEeCchhHHHHHHhcCCcccccCCceEEEecCcccccccCCchHH
Q 002040          560 IRKFAKVMGVRCVPVYGGSGVAQQISELKR-GTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMGFEPQI  638 (976)
Q Consensus       560 ~~~~~~~~~~~~~~~~gg~~~~~~~~~l~~-~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDEah~~~~~~f~~~i  638 (976)
                      |..+...      +..+..+.......+.. ...|+|+|...|...+.........-..--+||+||||+...    ..+
T Consensus       313 f~~~~~~------~~~~~~s~~~L~~~l~~~~~~iivtTiQk~~~~~~~~~~~~~~~~~~~lvIvDEaHrs~~----~~~  382 (667)
T TIGR00348       313 FQSLQKD------CAERIESIAELKRLLEKDDGGIIITTIQKFDKKLKEEEEKFPVDRKEVVVIFDEAHRSQY----GEL  382 (667)
T ss_pred             HHhhCCC------CCcccCCHHHHHHHHhCCCCCEEEEEhHHhhhhHhhhhhccCCCCCCEEEEEEcCccccc----hHH
Confidence            9886431      11111222222233332 368999999999764432111111101113899999998642    234


Q ss_pred             HHHHHhcCCCCcEEEEeccCcHHHHHHHHHHc----CCCeEEEeCCcccccCCceEEE--Ee------cC----------
Q 002040          639 TRIVQNIRPDRQTVLFSATFPRQVEILARKVL----NKPVEIQVGGRSVVNKDITQLV--EV------RP----------  696 (976)
Q Consensus       639 ~~il~~~~~~~q~i~~SAT~~~~~~~l~~~~l----~~~~~i~~~~~~~~~~~i~q~~--~~------~~----------  696 (976)
                      ..++...-++...|+|||||-..........+    +.++. ...-.......+...+  ..      ..          
T Consensus       383 ~~~l~~~~p~a~~lGfTaTP~~~~d~~t~~~f~~~fg~~i~-~Y~~~~AI~dG~~~~i~Y~~~~~~~~~~~~~l~~~~~~  461 (667)
T TIGR00348       383 AKNLKKALKNASFFGFTGTPIFKKDRDTSLTFAYVFGRYLH-RYFITDAIRDGLTVKIDYEDRLPEDHLDRKKLDAFFDE  461 (667)
T ss_pred             HHHHHhhCCCCcEEEEeCCCcccccccccccccCCCCCeEE-EeeHHHHhhcCCeeeEEEEecchhhccChHHHHHHHHH
Confidence            44444334567899999998542111111111    12221 1111111111100000  00      00          


Q ss_pred             -----------------------------cchHHHHHHHHHHhhh----c--CCcEEEEecCHHHHHHHHHHHHHC----
Q 002040          697 -----------------------------ESDRFLRLLELLGEWY----E--KGKILIFVHSQEKCDALFRDLLKH----  737 (976)
Q Consensus       697 -----------------------------~~~k~~~l~~~l~~~~----~--~~kvLIF~~s~~~~~~l~~~L~~~----  737 (976)
                                                   ....+..+...+..++    .  .++++|||.++..|..+...|.+.    
T Consensus       462 ~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~ia~~i~~h~~~~~~~~~~kamvv~~sr~~a~~~~~~l~~~~~~~  541 (667)
T TIGR00348       462 IFELLPERIREITKESLKEKLQKTKKILFNEDRLESIAKDIAEHYAKFKELFKFKAMVVAISRYACVEEKNALDEELNEK  541 (667)
T ss_pred             HHHhhhccccHHHHHHHHHHHHHHHhhhcChHHHHHHHHHHHHHHHHhhhcccCceeEEEecHHHHHHHHHHHHhhcccc
Confidence                                         0000111122222221    1  379999999999999999888664    


Q ss_pred             -CCCceeccCCCCHH---------------------HHHHHHHHhcc-CCccEEEecCcccccCCCCCCcEEEEeCCCCC
Q 002040          738 -GYPCLSLHGAKDQT---------------------DRESTISDFKS-NVCNLLIATSVAARGLDVKELELVINFDAPNH  794 (976)
Q Consensus       738 -~~~~~~lhg~~~~~---------------------~R~~~~~~F~~-g~~~vLVaT~v~~~GlDi~~v~~VI~~d~p~s  794 (976)
                       +..++.+++..+..                     ....++..|++ +.++|||+++.+.+|+|+|.+++++..-+-. 
T Consensus       542 ~~~~~vv~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Fk~~~~~~ilIVvdmllTGFDaP~l~tLyldKplk-  620 (667)
T TIGR00348       542 FEASAIVMTGKESDDAEIRDYNKHIRTKFDKSDGFEIYYKDLERFKKEENPKLLIVVDMLLTGFDAPILNTLYLDKPLK-  620 (667)
T ss_pred             cCCeeEEecCCccchhHHHHHHHHhccccccchhhhHHHHHHHHhcCCCCceEEEEEcccccccCCCccceEEEecccc-
Confidence             34556666654332                     12368889976 6889999999999999999999999555544 


Q ss_pred             HHHHHHHhcccCCC
Q 002040          795 YEDYVHRVGRTGRA  808 (976)
Q Consensus       795 ~~~y~Qr~GR~gR~  808 (976)
                      ...++|.+||+.|.
T Consensus       621 ~h~LlQai~R~nR~  634 (667)
T TIGR00348       621 YHGLLQAIARTNRI  634 (667)
T ss_pred             ccHHHHHHHHhccc
Confidence            45789999999994

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

>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]

Probab=99.85  E-value=4.7e-19  Score=209.47  Aligned_cols=309  Identities=19%  Similarity=0.274  Sum_probs=211.9

Q ss_pred             CCCcHHHHHHHHHHhcC----CCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHHH
Q 002040          488 EKPMPIQAQALPVIMSG----RDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKF  563 (976)
Q Consensus       488 ~~p~~~Q~~~i~~il~g----~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~~  563 (976)
                      ..+.+-|..++..|...    ...++.|.||||||.+|+-.+-..+..        |..+|||+|-..|..|+...|+..
T Consensus       197 ~~Ln~~Q~~a~~~i~~~~~~~~~~Ll~GvTGSGKTEvYl~~i~~~L~~--------GkqvLvLVPEI~Ltpq~~~rf~~r  268 (730)
T COG1198         197 LALNQEQQAAVEAILSSLGGFAPFLLDGVTGSGKTEVYLEAIAKVLAQ--------GKQVLVLVPEIALTPQLLARFKAR  268 (730)
T ss_pred             cccCHHHHHHHHHHHHhcccccceeEeCCCCCcHHHHHHHHHHHHHHc--------CCEEEEEeccccchHHHHHHHHHH
Confidence            35678999999999765    578999999999999988777766654        678999999999999998888876


Q ss_pred             HhhcCcEEEEeeCCCChHHHHH---HHh-cCCeEEEeCchhHHHHHHhcCCcccccCCceEEEecCccccccc-----CC
Q 002040          564 AKVMGVRCVPVYGGSGVAQQIS---ELK-RGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDM-----GF  634 (976)
Q Consensus       564 ~~~~~~~~~~~~gg~~~~~~~~---~l~-~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDEah~~~~~-----~f  634 (976)
                         +|..+.++++|.+..+...   ... ....|||||=..|          +..|.++++|||||-|-..-.     .+
T Consensus       269 ---Fg~~v~vlHS~Ls~~er~~~W~~~~~G~~~vVIGtRSAl----------F~Pf~~LGLIIvDEEHD~sYKq~~~prY  335 (730)
T COG1198         269 ---FGAKVAVLHSGLSPGERYRVWRRARRGEARVVIGTRSAL----------FLPFKNLGLIIVDEEHDSSYKQEDGPRY  335 (730)
T ss_pred             ---hCCChhhhcccCChHHHHHHHHHHhcCCceEEEEechhh----------cCchhhccEEEEeccccccccCCcCCCc
Confidence               4678888888887665533   333 3579999996544          257888999999999943211     13


Q ss_pred             chHHHHHHHhcCCCCcEEEEeccCcHHHHHHHHHHcCCCeEEEeCCccccc-CCceEEEEecCcchHH-----HHHHHHH
Q 002040          635 EPQITRIVQNIRPDRQTVLFSATFPRQVEILARKVLNKPVEIQVGGRSVVN-KDITQLVEVRPESDRF-----LRLLELL  708 (976)
Q Consensus       635 ~~~i~~il~~~~~~~q~i~~SAT~~~~~~~l~~~~l~~~~~i~~~~~~~~~-~~i~q~~~~~~~~~k~-----~~l~~~l  708 (976)
                      ...-..++.....++++|+-|||++-+  .+.+-.-+....+.+..+.... ..-.+.+.+.......     ..|+..|
T Consensus       336 hARdvA~~Ra~~~~~pvvLgSATPSLE--S~~~~~~g~y~~~~L~~R~~~a~~p~v~iiDmr~e~~~~~~~lS~~Ll~~i  413 (730)
T COG1198         336 HARDVAVLRAKKENAPVVLGSATPSLE--SYANAESGKYKLLRLTNRAGRARLPRVEIIDMRKEPLETGRSLSPALLEAI  413 (730)
T ss_pred             CHHHHHHHHHHHhCCCEEEecCCCCHH--HHHhhhcCceEEEEccccccccCCCcceEEeccccccccCccCCHHHHHHH
Confidence            333344555555678899999998644  3333333333333333332211 1112222222222222     4566666


Q ss_pred             Hhhhc-CCcEEEEecCHHHH------------------------------------------------------------
Q 002040          709 GEWYE-KGKILIFVHSQEKC------------------------------------------------------------  727 (976)
Q Consensus       709 ~~~~~-~~kvLIF~~s~~~~------------------------------------------------------------  727 (976)
                      .+... +.++|||.|.+..+                                                            
T Consensus       414 ~~~l~~geQ~llflnRRGys~~l~C~~Cg~v~~Cp~Cd~~lt~H~~~~~L~CH~Cg~~~~~p~~Cp~Cgs~~L~~~G~Gt  493 (730)
T COG1198         414 RKTLERGEQVLLFLNRRGYAPLLLCRDCGYIAECPNCDSPLTLHKATGQLRCHYCGYQEPIPQSCPECGSEHLRAVGPGT  493 (730)
T ss_pred             HHHHhcCCeEEEEEccCCccceeecccCCCcccCCCCCcceEEecCCCeeEeCCCCCCCCCCCCCCCCCCCeeEEecccH
Confidence            65554 45888888865433                                                            


Q ss_pred             HHHHHHHHHC--CCCceeccCCCCHH--HHHHHHHHhccCCccEEEecCcccccCCCCCCcEEEEeCCCC----------
Q 002040          728 DALFRDLLKH--GYPCLSLHGAKDQT--DRESTISDFKSNVCNLLIATSVAARGLDVKELELVINFDAPN----------  793 (976)
Q Consensus       728 ~~l~~~L~~~--~~~~~~lhg~~~~~--~R~~~~~~F~~g~~~vLVaT~v~~~GlDi~~v~~VI~~d~p~----------  793 (976)
                      +.+.+.|...  +..+..+.++....  .-...+..|.+|+.+|||.|.+++-|+|+|++++|...|...          
T Consensus       494 erieeeL~~~FP~~rv~r~d~Dtt~~k~~~~~~l~~~~~ge~dILiGTQmiaKG~~fp~vtLVgvl~aD~~L~~~DfRA~  573 (730)
T COG1198         494 ERIEEELKRLFPGARIIRIDSDTTRRKGALEDLLDQFANGEADILIGTQMIAKGHDFPNVTLVGVLDADTGLGSPDFRAS  573 (730)
T ss_pred             HHHHHHHHHHCCCCcEEEEccccccchhhHHHHHHHHhCCCCCeeecchhhhcCCCcccceEEEEEechhhhcCCCcchH
Confidence            2333333332  45666677766543  356789999999999999999999999999999988766543          


Q ss_pred             --CHHHHHHHhcccCCCCCccEEEEEec
Q 002040          794 --HYEDYVHRVGRTGRAGRKGCAITFIS  819 (976)
Q Consensus       794 --s~~~y~Qr~GR~gR~g~~g~~~~~~~  819 (976)
                        ...-+.|-.||+||++.+|.+++-.-
T Consensus       574 Er~fqll~QvaGRAgR~~~~G~VvIQT~  601 (730)
T COG1198         574 ERTFQLLMQVAGRAGRAGKPGEVVIQTY  601 (730)
T ss_pred             HHHHHHHHHHHhhhccCCCCCeEEEEeC
Confidence              23456799999999998998877543

>PRK05298 excinuclease ABC subunit B; Provisional

Probab=99.84  E-value=5.2e-19  Score=213.33  Aligned_cols=148  Identities=20%  Similarity=0.328  Sum_probs=129.7

Q ss_pred             cchHHHHHHHHHHhhhc-CCcEEEEecCHHHHHHHHHHHHHCCCCceeccCCCCHHHHHHHHHHhccCCccEEEecCccc
Q 002040          697 ESDRFLRLLELLGEWYE-KGKILIFVHSQEKCDALFRDLLKHGYPCLSLHGAKDQTDRESTISDFKSNVCNLLIATSVAA  775 (976)
Q Consensus       697 ~~~k~~~l~~~l~~~~~-~~kvLIF~~s~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLVaT~v~~  775 (976)
                      ...++..|+..|..+.. +.++||||++...++.|+..|...|+.+..+||++++.+|..++..|+.|.+.|||||++++
T Consensus       428 ~~~q~~~L~~~L~~~~~~g~~viIf~~t~~~ae~L~~~L~~~gi~~~~~h~~~~~~~R~~~l~~f~~g~i~vlV~t~~L~  507 (652)
T PRK05298        428 TKGQVDDLLSEIRKRVAKGERVLVTTLTKRMAEDLTDYLKELGIKVRYLHSDIDTLERVEIIRDLRLGEFDVLVGINLLR  507 (652)
T ss_pred             ccccHHHHHHHHHHHHhCCCEEEEEeCCHHHHHHHHHHHhhcceeEEEEECCCCHHHHHHHHHHHHcCCceEEEEeCHHh
Confidence            44567778888877654 45899999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccCCCCCCcEEEEeCC-----CCCHHHHHHHhcccCCCCCccEEEEEecC---------CCcCchHHHHHHHhhccCCCC
Q 002040          776 RGLDVKELELVINFDA-----PNHYEDYVHRVGRTGRAGRKGCAITFISE---------EDAKYSPDLVKALELSEQVVP  841 (976)
Q Consensus       776 ~GlDi~~v~~VI~~d~-----p~s~~~y~Qr~GR~gR~g~~g~~~~~~~~---------~d~~~~~~i~~~l~~~~~~vp  841 (976)
                      +|+|+|++++||+++.     |.+...|+||+||+||. ..|.|++|++.         .+......|...+......+|
T Consensus       508 rGfdlp~v~lVii~d~eifG~~~~~~~yiqr~GR~gR~-~~G~~i~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~  586 (652)
T PRK05298        508 EGLDIPEVSLVAILDADKEGFLRSERSLIQTIGRAARN-VNGKVILYADKITDSMQKAIDETERRREIQIAYNEEHGITP  586 (652)
T ss_pred             CCccccCCcEEEEeCCcccccCCCHHHHHHHhccccCC-CCCEEEEEecCCCHHHHHHHHHHHHHHHHHHHhhhccCCCC
Confidence            9999999999999875     78999999999999996 68999999984         355566677777778888888


Q ss_pred             hHHH
Q 002040          842 DDLK  845 (976)
Q Consensus       842 ~~l~  845 (976)
                      ..+.
T Consensus       587 ~~~~  590 (652)
T PRK05298        587 KTIK  590 (652)
T ss_pred             hhHH
Confidence            6553

>PF06862 DUF1253: Protein of unknown function (DUF1253); InterPro: IPR010678 This family is defined by a C-terminal region of approximately 500 residues, Digestive organ expansion factor (DEF) is thought to Regulate the p53 pathway to control the expansion growth of digestive organs and is required for the expansion growth of intestine, liver and exocrine pancreas, but not endocrine pancreas [, ]

Probab=99.84  E-value=2.8e-19  Score=200.03  Aligned_cols=293  Identities=17%  Similarity=0.205  Sum_probs=219.2

Q ss_pred             CCCeEEEEccCHHHHHHHHHHHHHHHhh-------------cCc-------------------EEEEeeCCCChHHHHHH
Q 002040          539 DGPVGLIMAPTRELVQQIHSDIRKFAKV-------------MGV-------------------RCVPVYGGSGVAQQISE  586 (976)
Q Consensus       539 ~~~~vLIl~Ptr~La~Q~~~~~~~~~~~-------------~~~-------------------~~~~~~gg~~~~~~~~~  586 (976)
                      ..|+||||||+|..|..+.+.+..++..             +|+                   ....+++|+..+.....
T Consensus        36 tRPkVLIL~P~R~~A~~~V~~Li~l~~~~~~~~nk~RF~~efg~~~~~~~~~~~~~~~~~kP~D~~~~F~GN~DD~FrlG  115 (442)
T PF06862_consen   36 TRPKVLILLPFRNSALRIVETLISLLPPGKQVENKKRFEEEFGLPEDEDDDEEPPEFKKSKPEDFKALFSGNNDDCFRLG  115 (442)
T ss_pred             CCceEEEEcccHHHHHHHHHHHHHHcCccchHHHHHHHHHHcCCCccccchhhhccccCCCchhHHHhcCCCccceEEEe
Confidence            3699999999999999998888776533             120                   00011122211111000


Q ss_pred             H------------hcCCeEEEeCchhHHHHHHhc---CCcccccCCceEEEecCcccccccCCchHHHHHHHhcCCC---
Q 002040          587 L------------KRGTEIVVCTPGRMIDILCTS---GGKITNLRRVTYLVMDEADRMFDMGFEPQITRIVQNIRPD---  648 (976)
Q Consensus       587 l------------~~~~~Iiv~Tp~~L~~~l~~~---~~~~~~l~~~~~vVlDEah~~~~~~f~~~i~~il~~~~~~---  648 (976)
                      +            -.++|||||+|-.|...+...   ......|++|.++|||.||.|+ |+.|.++..++.+++..   
T Consensus       116 ik~trk~ikLys~Fy~SDIIiASPLGLr~~i~~~~~~~~d~DFLSSIEv~iiD~ad~l~-MQNW~Hv~~v~~~lN~~P~~  194 (442)
T PF06862_consen  116 IKFTRKSIKLYSDFYSSDIIIASPLGLRMIIGEEGEKKRDYDFLSSIEVLIIDQADVLL-MQNWEHVLHVFEHLNLQPKK  194 (442)
T ss_pred             EEEecCeeeeecccccCCEEEEChHHHHHHhccccccccccchhheeeeEeechhhHHH-HhhHHHHHHHHHHhccCCCC
Confidence            0            015799999999998888752   2223458999999999999655 77788888888776422   


Q ss_pred             ---------------------CcEEEEeccCcHHHHHHHHHHcCCC---eEEEeCCc-----ccccCCceEEEEecC---
Q 002040          649 ---------------------RQTVLFSATFPRQVEILARKVLNKP---VEIQVGGR-----SVVNKDITQLVEVRP---  696 (976)
Q Consensus       649 ---------------------~q~i~~SAT~~~~~~~l~~~~l~~~---~~i~~~~~-----~~~~~~i~q~~~~~~---  696 (976)
                                           +|+|+||+...+.+..+....+.+.   +.+.....     ..+...+.|.+...+   
T Consensus       195 ~~~~DfsRVR~w~Ldg~a~~~RQtii~S~~~~pe~~slf~~~~~N~~G~v~~~~~~~~~g~i~~v~~~v~Q~F~r~~~~s  274 (442)
T PF06862_consen  195 SHDTDFSRVRPWYLDGQAKYYRQTIIFSSFQTPEINSLFNRHCQNYAGKVRLKPPYEASGVISQVVVQVRQVFQRFDCSS  274 (442)
T ss_pred             CCCCCHHHHHHHHHcCcchheeEeEEecCCCCHHHHHHHHhhCcCccceEEEeeccccceeeeccccCCceEEEEecCCC
Confidence                                 7999999999999999999977765   22222212     234456777776432   


Q ss_pred             ----cchHHHHHHHHH-Hhhh---cCCcEEEEecCHHHHHHHHHHHHHCCCCceeccCCCCHHHHHHHHHHhccCCccEE
Q 002040          697 ----ESDRFLRLLELL-GEWY---EKGKILIFVHSQEKCDALFRDLLKHGYPCLSLHGAKDQTDRESTISDFKSNVCNLL  768 (976)
Q Consensus       697 ----~~~k~~~l~~~l-~~~~---~~~kvLIF~~s~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vL  768 (976)
                          .+.++..+...+ ..+.   ..+.+|||+++.-+...|.++|.+.++.++.+|.++++.+-..+...|..|...||
T Consensus       275 ~~~~~d~Rf~yF~~~iLP~l~~~~~~~~~LIfIPSYfDfVRlRN~lk~~~~sF~~i~EYts~~~isRAR~~F~~G~~~iL  354 (442)
T PF06862_consen  275 PADDPDARFKYFTKKILPQLKRDSKMSGTLIFIPSYFDFVRLRNYLKKENISFVQISEYTSNSDISRARSQFFHGRKPIL  354 (442)
T ss_pred             cchhhhHHHHHHHHHHHHHhhhccCCCcEEEEecchhhhHHHHHHHHhcCCeEEEecccCCHHHHHHHHHHHHcCCceEE
Confidence                345666665533 3332   34689999999999999999999999999999999999999999999999999999


Q ss_pred             EecCccc--ccCCCCCCcEEEEeCCCCCHHHHHHHhcccCCCCC------ccEEEEEecCCCcCchHHHHHH
Q 002040          769 IATSVAA--RGLDVKELELVINFDAPNHYEDYVHRVGRTGRAGR------KGCAITFISEEDAKYSPDLVKA  832 (976)
Q Consensus       769 VaT~v~~--~GlDi~~v~~VI~~d~p~s~~~y~Qr~GR~gR~g~------~g~~~~~~~~~d~~~~~~i~~~  832 (976)
                      |.|.-+.  +-..|.++..||+|.+|.++..|...++-.+....      ...|.++|+..|...++.|+-.
T Consensus       355 L~TER~HFfrRy~irGi~~viFY~~P~~p~fY~El~n~~~~~~~~~~~~~~~~~~~lysk~D~~~LErIVGt  426 (442)
T PF06862_consen  355 LYTERFHFFRRYRIRGIRHVIFYGPPENPQFYSELLNMLDESSGGEVDAADATVTVLYSKYDALRLERIVGT  426 (442)
T ss_pred             EEEhHHhhhhhceecCCcEEEEECCCCChhHHHHHHhhhcccccccccccCceEEEEecHhHHHHHHHHhCH
Confidence            9999666  88999999999999999999999988876665433      5799999999998888877753

; GO: 0005634 nucleus

>KOG1000 consensus Chromatin remodeling protein HARP/SMARCAL1, DEAD-box superfamily [Chromatin structure and dynamics]

Probab=99.83  E-value=1.2e-18  Score=188.53  Aligned_cols=312  Identities=14%  Similarity=0.164  Sum_probs=213.9

Q ss_pred             CCCcHHHHHHHHHHh-cCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHHHHhh
Q 002040          488 EKPMPIQAQALPVIM-SGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKV  566 (976)
Q Consensus       488 ~~p~~~Q~~~i~~il-~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~~~~~  566 (976)
                      ..+.|+|.+++...+ .|..+|+..+||.|||++++..+..+...++         .|||||.. |-..|...+.+|+..
T Consensus       197 s~LlPFQreGv~faL~RgGR~llADeMGLGKTiQAlaIA~yyraEwp---------lliVcPAs-vrftWa~al~r~lps  266 (689)
T KOG1000|consen  197 SRLLPFQREGVIFALERGGRILLADEMGLGKTIQALAIARYYRAEWP---------LLIVCPAS-VRFTWAKALNRFLPS  266 (689)
T ss_pred             HhhCchhhhhHHHHHhcCCeEEEecccccchHHHHHHHHHHHhhcCc---------EEEEecHH-HhHHHHHHHHHhccc
Confidence            357899999998766 5778899999999999998877766655543         48999964 558899999998865


Q ss_pred             cCcEEEEeeCCCChHHHHHHHhcCCeEEEeCchhHHHHHHhcCCcccccCCceEEEecCcccccccCCchHHHHHHHhcC
Q 002040          567 MGVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMGFEPQITRIVQNIR  646 (976)
Q Consensus       567 ~~~~~~~~~gg~~~~~~~~~l~~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDEah~~~~~~f~~~i~~il~~~~  646 (976)
                      ... +.++.++.....   .+-....|.|.++..|..+-..     ..-..+.+||+||.|.+-+. -......++..+.
T Consensus       267 ~~p-i~vv~~~~D~~~---~~~t~~~v~ivSye~ls~l~~~-----l~~~~~~vvI~DEsH~Lk~s-ktkr~Ka~~dllk  336 (689)
T KOG1000|consen  267 IHP-IFVVDKSSDPLP---DVCTSNTVAIVSYEQLSLLHDI-----LKKEKYRVVIFDESHMLKDS-KTKRTKAATDLLK  336 (689)
T ss_pred             ccc-eEEEecccCCcc---ccccCCeEEEEEHHHHHHHHHH-----HhcccceEEEEechhhhhcc-chhhhhhhhhHHH
Confidence            433 445555553321   2223457999999887544321     22344899999999966443 2334555555555


Q ss_pred             CCCcEEEEeccCc----H---------------HHHHHHHHHcCCC---eEEEeCCccc---------------------
Q 002040          647 PDRQTVLFSATFP----R---------------QVEILARKVLNKP---VEIQVGGRSV---------------------  683 (976)
Q Consensus       647 ~~~q~i~~SAT~~----~---------------~~~~l~~~~l~~~---~~i~~~~~~~---------------------  683 (976)
                      ...++|++|+|+.    .               ..-.++..|+..-   +.+...+.+.                     
T Consensus       337 ~akhvILLSGTPavSRP~elytqi~avd~tlfp~f~efa~rYCd~k~vr~~~Dykg~tnl~EL~~lL~k~lMIRRlK~dv  416 (689)
T KOG1000|consen  337 VAKHVILLSGTPAVSRPSELYTQIRAVDHTLFPNFHEFAIRYCDGKQVRFCFDYKGCTNLEELAALLFKRLMIRRLKADV  416 (689)
T ss_pred             HhhheEEecCCcccCCchhhhhhhhhhcccccccHHHHHHHhcCccccceeeecCCCCCHHHHHHHHHHHHHHHHHHHHH
Confidence            5667999999962    1               1122333343221   1111111110                     


Q ss_pred             ---ccCCceEEEEecCc-------------------------------------chHHHHHHHHHHhh-----hcCCcEE
Q 002040          684 ---VNKDITQLVEVRPE-------------------------------------SDRFLRLLELLGEW-----YEKGKIL  718 (976)
Q Consensus       684 ---~~~~i~q~~~~~~~-------------------------------------~~k~~~l~~~l~~~-----~~~~kvL  718 (976)
                         .++.-.+.+.+...                                     ..|+..+.+.|...     .+..+.|
T Consensus       417 L~qLPpKrr~Vv~~~~gr~da~~~~lv~~a~~~t~~~~~e~~~~~l~l~y~~tgiaK~~av~eyi~~~~~l~d~~~~Kfl  496 (689)
T KOG1000|consen  417 LKQLPPKRREVVYVSGGRIDARMDDLVKAAADYTKVNSMERKHESLLLFYSLTGIAKAAAVCEYILENYFLPDAPPRKFL  496 (689)
T ss_pred             HhhCCccceEEEEEcCCccchHHHHHHHHhhhcchhhhhhhhhHHHHHHHHHhcccccHHHHHHHHhCcccccCCCceEE
Confidence               01111222222111                                     01222233333331     1234899


Q ss_pred             EEecCHHHHHHHHHHHHHCCCCceeccCCCCHHHHHHHHHHhccC-Ccc-EEEecCcccccCCCCCCcEEEEeCCCCCHH
Q 002040          719 IFVHSQEKCDALFRDLLKHGYPCLSLHGAKDQTDRESTISDFKSN-VCN-LLIATSVAARGLDVKELELVINFDAPNHYE  796 (976)
Q Consensus       719 IF~~s~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g-~~~-vLVaT~v~~~GlDi~~v~~VI~~d~p~s~~  796 (976)
                      |||..+...+.+...+.+.++..+.|.|.++...|....+.|+.. .+. -|++..++++||++..+.+||+...+|||.
T Consensus       497 VFaHH~~vLd~Iq~~~~~r~vg~IRIDGst~s~~R~ll~qsFQ~seev~VAvlsItA~gvGLt~tAa~~VVFaEL~wnPg  576 (689)
T KOG1000|consen  497 VFAHHQIVLDTIQVEVNKRKVGSIRIDGSTPSHRRTLLCQSFQTSEEVRVAVLSITAAGVGLTLTAASVVVFAELHWNPG  576 (689)
T ss_pred             EEehhHHHHHHHHHHHHHcCCCeEEecCCCCchhHHHHHHHhccccceEEEEEEEeecccceeeeccceEEEEEecCCCc
Confidence            999999999999999999999999999999999999999999954 444 456778999999999999999999999999


Q ss_pred             HHHHHhcccCCCCCccEEEEEec
Q 002040          797 DYVHRVGRTGRAGRKGCAITFIS  819 (976)
Q Consensus       797 ~y~Qr~GR~gR~g~~g~~~~~~~  819 (976)
                      -.+|.-.|++|.|++..+.++|.
T Consensus       577 vLlQAEDRaHRiGQkssV~v~yl  599 (689)
T KOG1000|consen  577 VLLQAEDRAHRIGQKSSVFVQYL  599 (689)
T ss_pred             eEEechhhhhhccccceeeEEEE
Confidence            99999999999999987766654

>PRK12903 secA preprotein translocase subunit SecA; Reviewed

Probab=99.83  E-value=2.8e-18  Score=201.45  Aligned_cols=322  Identities=20%  Similarity=0.243  Sum_probs=218.8

Q ss_pred             cCCCCCcHHHHHHHHHHhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHHHH
Q 002040          485 LNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFA  564 (976)
Q Consensus       485 ~~~~~p~~~Q~~~i~~il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~~~  564 (976)
                      +|+ .|++.|.-+.-.+..|  .|..+.||-|||+++++|++...+.        |..|-||+..--||..=..++..++
T Consensus        75 lG~-r~ydVQliGglvLh~G--~IAEMkTGEGKTLvAtLpayLnAL~--------GkgVhVVTvNdYLA~RDae~mg~vy  143 (925)
T PRK12903         75 LGK-RPYDVQIIGGIILDLG--SVAEMKTGEGKTITSIAPVYLNALT--------GKGVIVSTVNEYLAERDAEEMGKVF  143 (925)
T ss_pred             hCC-CcCchHHHHHHHHhcC--CeeeecCCCCccHHHHHHHHHHHhc--------CCceEEEecchhhhhhhHHHHHHHH
Confidence            565 4788888777666655  5889999999999999998765443        4457788888899999999999999


Q ss_pred             hhcCcEEEEeeCCCChHHHHHHHhcCCeEEEeCchhH-HHHHHhcCC---cccccCCceEEEecCccccc-ccC------
Q 002040          565 KVMGVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRM-IDILCTSGG---KITNLRRVTYLVMDEADRMF-DMG------  633 (976)
Q Consensus       565 ~~~~~~~~~~~gg~~~~~~~~~l~~~~~Iiv~Tp~~L-~~~l~~~~~---~~~~l~~~~~vVlDEah~~~-~~~------  633 (976)
                      ..+|+.|.++..+.........+  .|+|++||..-| .++|..+-.   .......+.|.||||+|.++ +..      
T Consensus       144 ~fLGLsvG~i~~~~~~~~rr~aY--~~DItYgTn~E~gFDYLRDnm~~~~~~~vqR~~~faIVDEVDSILIDEArTPLII  221 (925)
T PRK12903        144 NFLGLSVGINKANMDPNLKREAY--ACDITYSVHSELGFDYLRDNMVSSKEEKVQRGLNFCLIDEVDSILIDEAKTPLII  221 (925)
T ss_pred             HHhCCceeeeCCCCChHHHHHhc--cCCCeeecCcccchhhhhhcccccHHHhcCcccceeeeccchheeecccCCcccc
Confidence            99999999998887666554444  489999999876 345543211   11224678899999999763 111      


Q ss_pred             ---------CchHHHHHHHhcCCC--------------------------------------------------------
Q 002040          634 ---------FEPQITRIVQNIRPD--------------------------------------------------------  648 (976)
Q Consensus       634 ---------f~~~i~~il~~~~~~--------------------------------------------------------  648 (976)
                               +...+..++..+...                                                        
T Consensus       222 Sg~~~~~~~~Y~~~~~~v~~L~~~dy~iDek~k~v~LTe~G~~~~E~~l~i~nLy~~~n~~l~h~i~~AL~A~~lf~rd~  301 (925)
T PRK12903        222 SGGQSNDSNLYLAADQFVRTLKEDDYKIDEETKAISLTEKGIKKANKFFKLKNLYDIENSELVHRIQNALRAHKVMKEDV  301 (925)
T ss_pred             cCCCccchHHHHHHHHHHHhccccceEEecccceEEECHhHHHHHHHHcCCCcccChhhHHHHHHHHHHHHHHHHHhcCC
Confidence                     001111111111110                                                        


Q ss_pred             ------------------------------------------------------------CcEEEEeccCcHHHHHHHHH
Q 002040          649 ------------------------------------------------------------RQTVLFSATFPRQVEILARK  668 (976)
Q Consensus       649 ------------------------------------------------------------~q~i~~SAT~~~~~~~l~~~  668 (976)
                                                                                  .++.+||+|.......+.. 
T Consensus       302 dYiV~dg~V~IVDefTGR~m~gRrwsdGLHQaIEAKEgv~I~~e~~TlAsIT~QnfFr~Y~kLsGMTGTA~te~~Ef~~-  380 (925)
T PRK12903        302 EYIVRDGKIELVDQFTGRIMEGRSYSEGLQQAIQAKEMVEIEPETKTLATITYQNFFRLFKKLSGMTGTAKTEEQEFID-  380 (925)
T ss_pred             ceEEECCEEEEEECCCCCCCCCCccchHHHHHHHHHcCCCCCCCceeeeeehHHHHHHhcchhhccCCCCHHHHHHHHH-
Confidence                                                                        1233444444333333322 


Q ss_pred             HcCCCeEEEeCCcccccCCceEEEEecCcchHHHHHHHHHHhhhc-CCcEEEEecCHHHHHHHHHHHHHCCCCceeccCC
Q 002040          669 VLNKPVEIQVGGRSVVNKDITQLVEVRPESDRFLRLLELLGEWYE-KGKILIFVHSQEKCDALFRDLLKHGYPCLSLHGA  747 (976)
Q Consensus       669 ~l~~~~~i~~~~~~~~~~~i~q~~~~~~~~~k~~~l~~~l~~~~~-~~kvLIF~~s~~~~~~l~~~L~~~~~~~~~lhg~  747 (976)
                      .++-.+...+...+...... ....+.....|+..++..+...+. +.||||.|.++...+.|+..|...|+++..+++.
T Consensus       381 iY~l~Vv~IPTnkP~~R~D~-~d~iy~t~~~K~~Aii~ei~~~~~~gqPVLVgT~SIe~SE~ls~~L~~~gi~h~vLNAk  459 (925)
T PRK12903        381 IYNMRVNVVPTNKPVIRKDE-PDSIFGTKHAKWKAVVKEVKRVHKKGQPILIGTAQVEDSETLHELLLEANIPHTVLNAK  459 (925)
T ss_pred             HhCCCEEECCCCCCeeeeeC-CCcEEEcHHHHHHHHHHHHHHHHhcCCCEEEEeCcHHHHHHHHHHHHHCCCCceeeccc
Confidence            22222222211111111111 112344567888888888877654 4599999999999999999999999999999986


Q ss_pred             CCHHHHHHHHHHhccCC-ccEEEecCcccccCCCCCC--------cEEEEeCCCCCHHHHHHHhcccCCCCCccEEEEEe
Q 002040          748 KDQTDRESTISDFKSNV-CNLLIATSVAARGLDVKEL--------ELVINFDAPNHYEDYVHRVGRTGRAGRKGCAITFI  818 (976)
Q Consensus       748 ~~~~~R~~~~~~F~~g~-~~vLVaT~v~~~GlDi~~v--------~~VI~~d~p~s~~~y~Qr~GR~gR~g~~g~~~~~~  818 (976)
                      ....  +..+-. ..|. -.|.|||++|+||.||.--        -+||....|.|----.|..||+||.|.+|.+..|+
T Consensus       460 ~~e~--EA~IIa-~AG~~GaVTIATNMAGRGTDI~Lg~~V~~~GGLhVIgTerheSrRIDnQLrGRaGRQGDpGss~f~l  536 (925)
T PRK12903        460 QNAR--EAEIIA-KAGQKGAITIATNMAGRGTDIKLSKEVLELGGLYVLGTDKAESRRIDNQLRGRSGRQGDVGESRFFI  536 (925)
T ss_pred             chhh--HHHHHH-hCCCCCeEEEecccccCCcCccCchhHHHcCCcEEEecccCchHHHHHHHhcccccCCCCCcceEEE
Confidence            4433  322222 4564 4699999999999999743        28998999999888899999999999999999999


Q ss_pred             cCCCcC
Q 002040          819 SEEDAK  824 (976)
Q Consensus       819 ~~~d~~  824 (976)
                      +-+|..
T Consensus       537 SLeD~L  542 (925)
T PRK12903        537 SLDDQL  542 (925)
T ss_pred             ecchHH
Confidence            877653

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

Probab=99.83  E-value=2.9e-19  Score=206.30  Aligned_cols=298  Identities=19%  Similarity=0.241  Sum_probs=194.3

Q ss_pred             CCCcHHHHHHHHHHh----cCC-CEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHH
Q 002040          488 EKPMPIQAQALPVIM----SGR-DCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRK  562 (976)
Q Consensus       488 ~~p~~~Q~~~i~~il----~g~-d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~  562 (976)
                      ..|+.+|..||..+.    .|+ .+|+++.||+|||.+++. |+..|.+.     +.-.+||+|+-+..|+.|.+..+..
T Consensus       164 i~~RyyQ~~AI~rv~Eaf~~g~~raLlvMATGTGKTrTAia-ii~rL~r~-----~~~KRVLFLaDR~~Lv~QA~~af~~  237 (875)
T COG4096         164 IGPRYYQIIAIRRVIEAFSKGQNRALLVMATGTGKTRTAIA-IIDRLIKS-----GWVKRVLFLADRNALVDQAYGAFED  237 (875)
T ss_pred             ccchHHHHHHHHHHHHHHhcCCceEEEEEecCCCcceeHHH-HHHHHHhc-----chhheeeEEechHHHHHHHHHHHHH
Confidence            468899999998765    443 489999999999988554 44444432     3456899999999999999999888


Q ss_pred             HHhhcCcEEEEeeCCCChHHHHHHHhcCCeEEEeCchhHHHHHHhcCC--cccccCCceEEEecCcccccccCCchHHHH
Q 002040          563 FAKVMGVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGG--KITNLRRVTYLVMDEADRMFDMGFEPQITR  640 (976)
Q Consensus       563 ~~~~~~~~~~~~~gg~~~~~~~~~l~~~~~Iiv~Tp~~L~~~l~~~~~--~~~~l~~~~~vVlDEah~~~~~~f~~~i~~  640 (976)
                      +... +..+..+.+....        ..+.|.|+|+..|...+.....  ..+....+++||||||||-.    ......
T Consensus       238 ~~P~-~~~~n~i~~~~~~--------~s~~i~lsTyqt~~~~~~~~~~~~~~f~~g~FDlIvIDEaHRgi----~~~~~~  304 (875)
T COG4096         238 FLPF-GTKMNKIEDKKGD--------TSSEIYLSTYQTMTGRIEQKEDEYRRFGPGFFDLIVIDEAHRGI----YSEWSS  304 (875)
T ss_pred             hCCC-ccceeeeecccCC--------cceeEEEeehHHHHhhhhccccccccCCCCceeEEEechhhhhH----HhhhHH
Confidence            7653 3333333222211        1489999999999888865421  22334569999999999854    333345


Q ss_pred             HHHhcCCCCcEEEEeccCcHHHHHHHHHHc-CCCeEEEeCC-----cccccCCceEE-----------------------
Q 002040          641 IVQNIRPDRQTVLFSATFPRQVEILARKVL-NKPVEIQVGG-----RSVVNKDITQL-----------------------  691 (976)
Q Consensus       641 il~~~~~~~q~i~~SAT~~~~~~~l~~~~l-~~~~~i~~~~-----~~~~~~~i~q~-----------------------  691 (976)
                      |+.++..-  ++++||||...+..-.-.|+ +.|+..+--.     .-.++..+...                       
T Consensus       305 I~dYFdA~--~~gLTATP~~~~d~~T~~~F~g~Pt~~YsleeAV~DGfLvpy~vi~i~~~~~~~G~~~~~~serek~~g~  382 (875)
T COG4096         305 ILDYFDAA--TQGLTATPKETIDRSTYGFFNGEPTYAYSLEEAVEDGFLVPYKVIRIDTDFDLDGWKPDAGSEREKLQGE  382 (875)
T ss_pred             HHHHHHHH--HHhhccCcccccccccccccCCCcceeecHHHHhhccccCCCCceEEeeeccccCcCcCccchhhhhhcc
Confidence            65555433  34559998765544444444 4443321100     00000000000                       


Q ss_pred             --------EEecC------cchHHHHHHHHHHhhhc-------CCcEEEEecCHHHHHHHHHHHHHC-----CCCceecc
Q 002040          692 --------VEVRP------ESDRFLRLLELLGEWYE-------KGKILIFVHSQEKCDALFRDLLKH-----GYPCLSLH  745 (976)
Q Consensus       692 --------~~~~~------~~~k~~~l~~~l~~~~~-------~~kvLIF~~s~~~~~~l~~~L~~~-----~~~~~~lh  745 (976)
                              +...+      .......+...|..+..       -+++||||.+..+|+.+...|...     +--|..|.
T Consensus       383 ~i~~dd~~~~~~d~dr~~v~~~~~~~V~r~~~~~l~~~~~g~~~~KTIvFa~n~dHAe~i~~~~~~~ype~~~~~a~~IT  462 (875)
T COG4096         383 AIDEDDQNFEARDFDRTLVIPFRTETVARELTEYLKRGATGDEIGKTIVFAKNHDHAERIREALVNEYPEYNGRYAMKIT  462 (875)
T ss_pred             ccCcccccccccccchhccccchHHHHHHHHHHHhccccCCCccCceEEEeeCcHHHHHHHHHHHHhCccccCceEEEEe
Confidence                    00000      00111223333333322       258999999999999999999764     34467777


Q ss_pred             CCCCHHHHHHHHHHhcc--CCccEEEecCcccccCCCCCCcEEEEeCCCCCHHHHHHHhcccCCC
Q 002040          746 GAKDQTDRESTISDFKS--NVCNLLIATSVAARGLDVKELELVINFDAPNHYEDYVHRVGRTGRA  808 (976)
Q Consensus       746 g~~~~~~R~~~~~~F~~--g~~~vLVaT~v~~~GlDi~~v~~VI~~d~p~s~~~y~Qr~GR~gR~  808 (976)
                      |...+.+  ..+..|..  .-..|.|+.+++.+|||+|.|.++|++-.-.|..-|.|++||.-|.
T Consensus       463 ~d~~~~q--~~Id~f~~ke~~P~IaitvdlL~TGiDvpev~nlVF~r~VrSktkF~QMvGRGTRl  525 (875)
T COG4096         463 GDAEQAQ--ALIDNFIDKEKYPRIAITVDLLTTGVDVPEVVNLVFDRKVRSKTKFKQMVGRGTRL  525 (875)
T ss_pred             ccchhhH--HHHHHHHhcCCCCceEEehhhhhcCCCchheeeeeehhhhhhHHHHHHHhcCcccc
Confidence            7665443  34666654  3357888999999999999999999999999999999999999885

>KOG1123 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, 3'-5' helicase subunit SSL2 [Transcription; Replication, recombination and repair]

Probab=99.81  E-value=3.7e-19  Score=192.23  Aligned_cols=310  Identities=17%  Similarity=0.198  Sum_probs=203.8

Q ss_pred             CCCcHHHHHHHHHHhcC---CCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHHHH
Q 002040          488 EKPMPIQAQALPVIMSG---RDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFA  564 (976)
Q Consensus       488 ~~p~~~Q~~~i~~il~g---~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~~~  564 (976)
                      ..++|+|..++..++.+   +..||+.|+|+|||++-+.++...           ...|||||.+-..+.||...|+.|+
T Consensus       301 t~iRpYQEksL~KMFGNgRARSGiIVLPCGAGKtLVGvTAa~ti-----------kK~clvLcts~VSVeQWkqQfk~ws  369 (776)
T KOG1123|consen  301 TQIRPYQEKSLSKMFGNGRARSGIIVLPCGAGKTLVGVTAACTI-----------KKSCLVLCTSAVSVEQWKQQFKQWS  369 (776)
T ss_pred             cccCchHHHHHHHHhCCCcccCceEEEecCCCCceeeeeeeeee-----------cccEEEEecCccCHHHHHHHHHhhc
Confidence            46789999999999843   579999999999999855444321           3468999999999999999999998


Q ss_pred             hhcCcEEEEeeCCCChHHHHHHHhcCCeEEEeCchhHHHHHHhcCC-----cccccCCceEEEecCcccccccCCchHHH
Q 002040          565 KVMGVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGG-----KITNLRRVTYLVMDEADRMFDMGFEPQIT  639 (976)
Q Consensus       565 ~~~~~~~~~~~gg~~~~~~~~~l~~~~~Iiv~Tp~~L~~~l~~~~~-----~~~~l~~~~~vVlDEah~~~~~~f~~~i~  639 (976)
                      ..-+-.++.++.....     ....++.|+|+|+.++..--.+.+.     ....-..|+++||||+|.+...-|...+.
T Consensus       370 ti~d~~i~rFTsd~Ke-----~~~~~~gvvvsTYsMva~t~kRS~eaek~m~~l~~~EWGllllDEVHvvPA~MFRRVls  444 (776)
T KOG1123|consen  370 TIQDDQICRFTSDAKE-----RFPSGAGVVVTTYSMVAYTGKRSHEAEKIMDFLRGREWGLLLLDEVHVVPAKMFRRVLS  444 (776)
T ss_pred             ccCccceEEeeccccc-----cCCCCCcEEEEeeehhhhcccccHHHHHHHHHHhcCeeeeEEeehhccchHHHHHHHHH
Confidence            7666666666554422     2345789999999876321110000     00123568999999999776555555555


Q ss_pred             HHHHhcCCCCcEEEEeccCcHHHHHHHH-HHcCCC--------------eEEEeCCcccccC-------------CceEE
Q 002040          640 RIVQNIRPDRQTVLFSATFPRQVEILAR-KVLNKP--------------VEIQVGGRSVVNK-------------DITQL  691 (976)
Q Consensus       640 ~il~~~~~~~q~i~~SAT~~~~~~~l~~-~~l~~~--------------~~i~~~~~~~~~~-------------~i~q~  691 (976)
                      .+-.++     -|++|||+-++-..+.. .|+-.|              ..-.+....+..+             .-...
T Consensus       445 iv~aHc-----KLGLTATLvREDdKI~DLNFLIGPKlYEAnWmdL~~kGhIA~VqCaEVWCpMt~eFy~eYL~~~t~kr~  519 (776)
T KOG1123|consen  445 IVQAHC-----KLGLTATLVREDDKITDLNFLIGPKLYEANWMDLQKKGHIAKVQCAEVWCPMTPEFYREYLRENTRKRM  519 (776)
T ss_pred             HHHHHh-----hccceeEEeeccccccccceeecchhhhccHHHHHhCCceeEEeeeeeecCCCHHHHHHHHhhhhhhhh
Confidence            444444     48999997443211110 011111              0001110111100             01111


Q ss_pred             EEecCcchHHHHHHHHHHhhh-cCCcEEEEecCHHHHHHHHHHHHHCCCCceeccCCCCHHHHHHHHHHhc-cCCccEEE
Q 002040          692 VEVRPESDRFLRLLELLGEWY-EKGKILIFVHSQEKCDALFRDLLKHGYPCLSLHGAKDQTDRESTISDFK-SNVCNLLI  769 (976)
Q Consensus       692 ~~~~~~~~k~~~l~~~l~~~~-~~~kvLIF~~s~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~-~g~~~vLV  769 (976)
                      ........||...--+|.-+- .+.++|||..+.-.+..++-.|   |  --.|+|.+++.+|..|++.|+ +..++.|+
T Consensus       520 lLyvMNP~KFraCqfLI~~HE~RgDKiIVFsDnvfALk~YAikl---~--KpfIYG~Tsq~ERm~ILqnFq~n~~vNTIF  594 (776)
T KOG1123|consen  520 LLYVMNPNKFRACQFLIKFHERRGDKIIVFSDNVFALKEYAIKL---G--KPFIYGPTSQNERMKILQNFQTNPKVNTIF  594 (776)
T ss_pred             eeeecCcchhHHHHHHHHHHHhcCCeEEEEeccHHHHHHHHHHc---C--CceEECCCchhHHHHHHHhcccCCccceEE
Confidence            222334556665544544333 3459999999887776666555   3  346899999999999999999 55788899


Q ss_pred             ecCcccccCCCCCCcEEEEeCCCC-CHHHHHHHhcccCCCC------CccEEEEEecCCCc
Q 002040          770 ATSVAARGLDVKELELVINFDAPN-HYEDYVHRVGRTGRAG------RKGCAITFISEEDA  823 (976)
Q Consensus       770 aT~v~~~GlDi~~v~~VI~~d~p~-s~~~y~Qr~GR~gR~g------~~g~~~~~~~~~d~  823 (976)
                      ...++.+.||+|.++++|...... |--.-.||+||+-|+-      -....|.+++.+..
T Consensus       595 lSKVgDtSiDLPEAnvLIQISSH~GSRRQEAQRLGRILRAKk~~de~fnafFYSLVS~DTq  655 (776)
T KOG1123|consen  595 LSKVGDTSIDLPEANVLIQISSHGGSRRQEAQRLGRILRAKKRNDEEFNAFFYSLVSKDTQ  655 (776)
T ss_pred             EeeccCccccCCcccEEEEEcccccchHHHHHHHHHHHHHhhcCccccceeeeeeeecchH
Confidence            999999999999999999876643 4567789999998863      23456666766543

>smart00487 DEXDc DEAD-like helicases superfamily

Probab=99.80  E-value=2.2e-18  Score=178.10  Aligned_cols=188  Identities=39%  Similarity=0.646  Sum_probs=155.5

Q ss_pred             HcCCCCCcHHHHHHHHHHhcC-CCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHH
Q 002040          484 KLNYEKPMPIQAQALPVIMSG-RDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRK  562 (976)
Q Consensus       484 ~~~~~~p~~~Q~~~i~~il~g-~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~  562 (976)
                      .+++..|+++|.+++..++.. +.++++++||+|||++++.+++.++...+      ...+||++|+..++.|+...+..
T Consensus         3 ~~~~~~~~~~Q~~~~~~~~~~~~~~~i~~~~GsGKT~~~~~~~~~~~~~~~------~~~~l~~~p~~~~~~~~~~~~~~   76 (201)
T smart00487        3 KFGFEPLRPYQKEAIEALLSGLRDVILAAPTGSGKTLAALLPALEALKRGK------GKRVLVLVPTRELAEQWAEELKK   76 (201)
T ss_pred             ccCCCCCCHHHHHHHHHHHcCCCcEEEECCCCCchhHHHHHHHHHHhcccC------CCcEEEEeCCHHHHHHHHHHHHH
Confidence            356778999999999999998 99999999999999999999988876532      45799999999999999999998


Q ss_pred             HHhhcCcEEEEeeCCCChHHHHHHHhcCC-eEEEeCchhHHHHHHhcCCcccccCCceEEEecCcccccccCCchHHHHH
Q 002040          563 FAKVMGVRCVPVYGGSGVAQQISELKRGT-EIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMGFEPQITRI  641 (976)
Q Consensus       563 ~~~~~~~~~~~~~gg~~~~~~~~~l~~~~-~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDEah~~~~~~f~~~i~~i  641 (976)
                      ++..........+++......+..+..+. +|+++|++.|.+.+....   ..+..+.+|||||||.+....+...+..+
T Consensus        77 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~t~~~l~~~~~~~~---~~~~~~~~iIiDE~h~~~~~~~~~~~~~~  153 (201)
T smart00487       77 LGPSLGLKVVGLYGGDSKREQLRKLESGKTDILVTTPGRLLDLLENDL---LELSNVDLVILDEAHRLLDGGFGDQLEKL  153 (201)
T ss_pred             HhccCCeEEEEEeCCcchHHHHHHHhcCCCCEEEeChHHHHHHHHcCC---cCHhHCCEEEEECHHHHhcCCcHHHHHHH
Confidence            87655545566677766556666666666 999999999998886542   35667889999999988765678888888


Q ss_pred             HHhcCCCCcEEEEeccCcHHHHHHHHHHcCCCeEEEeCC
Q 002040          642 VQNIRPDRQTVLFSATFPRQVEILARKVLNKPVEIQVGG  680 (976)
Q Consensus       642 l~~~~~~~q~i~~SAT~~~~~~~l~~~~l~~~~~i~~~~  680 (976)
                      +..+.+..+++++|||++..+......++...+.+....
T Consensus       154 ~~~~~~~~~~v~~saT~~~~~~~~~~~~~~~~~~~~~~~  192 (201)
T smart00487      154 LKLLPKNVQLLLLSATPPEEIENLLELFLNDPVFIDVGP  192 (201)
T ss_pred             HHhCCccceEEEEecCCchhHHHHHHHhcCCCEEEeCCc
Confidence            888888899999999999999989999888777766543

>KOG0386 consensus Chromatin remodeling complex SWI/SNF, component SWI2 and related ATPases (DNA/RNA helicase superfamily) [Chromatin structure and dynamics; Transcription]

Probab=99.80  E-value=2.2e-19  Score=208.76  Aligned_cols=322  Identities=20%  Similarity=0.249  Sum_probs=207.1

Q ss_pred             CCcHHHHHHHHHHhc----CCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHHHH
Q 002040          489 KPMPIQAQALPVIMS----GRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFA  564 (976)
Q Consensus       489 ~p~~~Q~~~i~~il~----g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~~~  564 (976)
                      .+.+||..++.|+.+    +-+.|+..+||.|||++ .+.++.+++...   ...||. |||||+..|.+ |..+|..|+
T Consensus       394 ~Lk~YQl~GLqWmVSLyNNnLNGILADEMGLGKTIQ-tIsLitYLmE~K---~~~GP~-LvivPlstL~N-W~~Ef~kWa  467 (1157)
T KOG0386|consen  394 ELKEYQLHGLQWMVSLYNNNLNGILADEMGLGKTIQ-TISLITYLMEHK---QMQGPF-LIIVPLSTLVN-WSSEFPKWA  467 (1157)
T ss_pred             CCchhhhhhhHHHhhccCCCcccccchhcccchHHH-HHHHHHHHHHHc---ccCCCe-EEeccccccCC-chhhccccc
Confidence            567899999999863    34789999999999998 444555555432   335665 99999999854 667777765


Q ss_pred             hhcCcEEEEeeCCCChHHH--HH-HHhcCCeEEEeCchhHHHHHHhcCCcccccCCceEEEecCcccccccCCchHHHHH
Q 002040          565 KVMGVRCVPVYGGSGVAQQ--IS-ELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMGFEPQITRI  641 (976)
Q Consensus       565 ~~~~~~~~~~~gg~~~~~~--~~-~l~~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDEah~~~~~~f~~~i~~i  641 (976)
                      ..   -..++|-|++....  .. ......+|+++|+..++.-     ..+..--+|.|+||||.|+|-+..  ..+...
T Consensus       468 PS---v~~i~YkGtp~~R~~l~~qir~gKFnVLlTtyEyiikd-----k~lLsKI~W~yMIIDEGHRmKNa~--~KLt~~  537 (1157)
T KOG0386|consen  468 PS---VQKIQYKGTPQQRSGLTKQQRHGKFNVLLTTYEYIIKD-----KALLSKISWKYMIIDEGHRMKNAI--CKLTDT  537 (1157)
T ss_pred             cc---eeeeeeeCCHHHHhhHHHHHhcccceeeeeeHHHhcCC-----HHHHhccCCcceeecccccccchh--hHHHHH
Confidence            43   23344555533211  11 1123579999999877541     011122357899999999985421  111111


Q ss_pred             HHhcCCCCcEEEEeccC---------------------------------------------------------------
Q 002040          642 VQNIRPDRQTVLFSATF---------------------------------------------------------------  658 (976)
Q Consensus       642 l~~~~~~~q~i~~SAT~---------------------------------------------------------------  658 (976)
                      +........-+++|+|+                                                               
T Consensus       538 L~t~y~~q~RLLLTGTPLQN~LpELWaLLNFlLP~IFnS~~~FeqWFN~PFantGek~eLteEEtlLIIrRLHkVLRPFl  617 (1157)
T KOG0386|consen  538 LNTHYRAQRRLLLTGTPLQNNLPELWALLNFLLPNIFNSCKAFEQWFNQPFANTGEKVELTEEETLLIIRRLHKVLRPFL  617 (1157)
T ss_pred             hhccccchhhhhhcCChhhhccHHHHHHHHHhccchhhhHhHHHHHhhhhhhhcCCcccccchHHHHHHHHHHHhhhHHH
Confidence            11111111123333332                                                               


Q ss_pred             ------------cHHHHH------------------------------------------HHHHHcCCCeEEEeCCcccc
Q 002040          659 ------------PRQVEI------------------------------------------LARKVLNKPVEIQVGGRSVV  684 (976)
Q Consensus       659 ------------~~~~~~------------------------------------------l~~~~l~~~~~i~~~~~~~~  684 (976)
                                  |..++.                                          ..+++|+.|..+.-..    
T Consensus       618 LRRlKkeVE~~LPdKve~viKC~mSalQq~lY~~m~~~g~l~~d~~~g~~g~k~L~N~imqLRKiCNHP~lf~~ve----  693 (1157)
T KOG0386|consen  618 LRRLKKEVEQELPDKVEDVIKCDMSALQQSLYKQMQNKGQLLKDTAKGKKGYKPLFNTIMQLRKLCNHPYLFANVE----  693 (1157)
T ss_pred             HHhhhHHHhhhCchhhhHhhheehhhhhHhhhHHHHhCCCCCcCchhccccchhhhhHhHHHHHhcCCchhhhhhc----
Confidence                        100000                                          0111111111110000    


Q ss_pred             cCCceEE---EEecCcchHHHHHHHHHHhhhc-CCcEEEEecCHHHHHHHHHHHHHCCCCceeccCCCCHHHHHHHHHHh
Q 002040          685 NKDITQL---VEVRPESDRFLRLLELLGEWYE-KGKILIFVHSQEKCDALFRDLLKHGYPCLSLHGAKDQTDRESTISDF  760 (976)
Q Consensus       685 ~~~i~q~---~~~~~~~~k~~~l~~~l~~~~~-~~kvLIF~~s~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F  760 (976)
                       ..+...   ..+.-.+.|+..|-.+|.++.. +++||+||......+.+..+|.-.++..+.+.|.+...+|...+..|
T Consensus       694 -~~~~~~~~~~dL~R~sGKfELLDRiLPKLkatgHRVLlF~qMTrlmdimEdyL~~~~~kYlRLDG~TK~~eRg~ll~~F  772 (1157)
T KOG0386|consen  694 -NSYTLHYDIKDLVRVSGKFELLDRILPKLKATGHRVLLFSQMTRLMDILEDYLQIREYKYLRLDGQTKVEERGDLLEIF  772 (1157)
T ss_pred             -cccccccChhHHHHhccHHHHHHhhhHHHHhcCcchhhHHHHHHHHHHHHHHHhhhhhheeeecCCcchhhHHHHHHHh
Confidence             000000   0111224566666666665543 56999999999999999999999999999999999999999999999


Q ss_pred             ccC---CccEEEecCcccccCCCCCCcEEEEeCCCCCHHHHHHHhcccCCCCCccEEEEEecCCCcCchHHHHH
Q 002040          761 KSN---VCNLLIATSVAARGLDVKELELVINFDAPNHYEDYVHRVGRTGRAGRKGCAITFISEEDAKYSPDLVK  831 (976)
Q Consensus       761 ~~g---~~~vLVaT~v~~~GlDi~~v~~VI~~d~p~s~~~y~Qr~GR~gR~g~~g~~~~~~~~~d~~~~~~i~~  831 (976)
                      +.-   -+.||++|.+++.|||+..+++||+||..|+|..+.|+..|++|.|++..|.+|....-..+-..|+.
T Consensus       773 N~Pds~yf~FllstragglglNlQtadtviifdsdwnp~~d~qaqdrahrigq~~evRv~rl~tv~sveE~il~  846 (1157)
T KOG0386|consen  773 NAPDSPYFIFLLSTRAGGLGLNLQTADTVIIFDSDWNPHQDLQAQDRAHRIGQKKEVRVLRLITVNSVEEKILA  846 (1157)
T ss_pred             cCCCCceeeeeeeecccccccchhhcceEEEecCCCCchhHHHHHHHHHHhhchhheeeeeeehhhHHHHHHHH
Confidence            854   36789999999999999999999999999999999999999999999888777665443333333333

>KOG0391 consensus SNF2 family DNA-dependent ATPase [General function prediction only]

Probab=99.79  E-value=7.1e-18  Score=196.40  Aligned_cols=121  Identities=21%  Similarity=0.316  Sum_probs=103.4

Q ss_pred             HHHHHHHHHhhhc-CCcEEEEecCHHHHHHHHHHHHHCCCCceeccCCCCHHHHHHHHHHhccCC--ccEEEecCccccc
Q 002040          701 FLRLLELLGEWYE-KGKILIFVHSQEKCDALFRDLLKHGYPCLSLHGAKDQTDRESTISDFKSNV--CNLLIATSVAARG  777 (976)
Q Consensus       701 ~~~l~~~l~~~~~-~~kvLIF~~s~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~--~~vLVaT~v~~~G  777 (976)
                      +..|.-+|.++.. +.++|||++...+++.|..+|.-+||.++.|.|....++|+..|..|+...  +++|++|...+.|
T Consensus      1262 LQtLAiLLqQLk~eghRvLIfTQMtkmLDVLeqFLnyHgylY~RLDg~t~vEqRQaLmerFNaD~RIfcfILSTrSggvG 1341 (1958)
T KOG0391|consen 1262 LQTLAILLQQLKSEGHRVLIFTQMTKMLDVLEQFLNYHGYLYVRLDGNTSVEQRQALMERFNADRRIFCFILSTRSGGVG 1341 (1958)
T ss_pred             HHHHHHHHHHHHhcCceEEehhHHHHHHHHHHHHHhhcceEEEEecCCccHHHHHHHHHHhcCCCceEEEEEeccCCccc
Confidence            3333344444433 348999999999999999999999999999999999999999999999764  6899999999999


Q ss_pred             CCCCCCcEEEEeCCCCCHHHHHHHhcccCCCCCccEE--EEEecCC
Q 002040          778 LDVKELELVINFDAPNHYEDYVHRVGRTGRAGRKGCA--ITFISEE  821 (976)
Q Consensus       778 lDi~~v~~VI~~d~p~s~~~y~Qr~GR~gR~g~~g~~--~~~~~~~  821 (976)
                      ||+.++++||+||..||+.--.|.-.||+|+|+.-.+  |.||++.
T Consensus      1342 iNLtgADTVvFYDsDwNPtMDaQAQDrChRIGqtRDVHIYRLISe~ 1387 (1958)
T KOG0391|consen 1342 INLTGADTVVFYDSDWNPTMDAQAQDRCHRIGQTRDVHIYRLISER 1387 (1958)
T ss_pred             cccccCceEEEecCCCCchhhhHHHHHHHhhcCccceEEEEeeccc
Confidence            9999999999999999999999999999999987555  4456543

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

Probab=99.79  E-value=8.7e-17  Score=198.03  Aligned_cols=329  Identities=19%  Similarity=0.234  Sum_probs=204.7

Q ss_pred             cCCCCCcHHHHHHHHHHh----cCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHH-HHH
Q 002040          485 LNYEKPMPIQAQALPVIM----SGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQI-HSD  559 (976)
Q Consensus       485 ~~~~~p~~~Q~~~i~~il----~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~-~~~  559 (976)
                      .|| .+++-|.+.+..|.    .+..+++.|+||+|||++|++|++...         .+++|||++||++|+.|+ ...
T Consensus       242 ~~~-e~R~~Q~~ma~~V~~~l~~~~~~~~eA~tGtGKT~ayllp~l~~~---------~~~~vvI~t~T~~Lq~Ql~~~~  311 (820)
T PRK07246        242 LGL-EERPKQESFAKLVGEDFHDGPASFIEAQTGIGKTYGYLLPLLAQS---------DQRQIIVSVPTKILQDQIMAEE  311 (820)
T ss_pred             CCC-ccCHHHHHHHHHHHHHHhCCCcEEEECCCCCcHHHHHHHHHHHhc---------CCCcEEEEeCcHHHHHHHHHHH
Confidence            344 58899998665543    567899999999999999999988653         256899999999999999 477


Q ss_pred             HHHHHhhcCcEEEEeeCCCChH-----HH------------------------------------------HHHH-----
Q 002040          560 IRKFAKVMGVRCVPVYGGSGVA-----QQ------------------------------------------ISEL-----  587 (976)
Q Consensus       560 ~~~~~~~~~~~~~~~~gg~~~~-----~~------------------------------------------~~~l-----  587 (976)
                      +..+...+++.+.++.|+..+-     .+                                          +..+     
T Consensus       312 i~~l~~~~~~~~~~~kg~~~ylcl~k~~~~l~~~~~~~~~~~~~~~il~Wl~~T~tGD~~El~~~~~~~~~w~~i~~~~~  391 (820)
T PRK07246        312 VKAIQEVFHIDCHSLKGPQNYLKLDAFYDSLQQNDDNRLVNRYKMQLLVWLTETETGDLDEIKQKQRYAAYFDQLKHDGN  391 (820)
T ss_pred             HHHHHHhcCCcEEEEECCcccccHHHHHHHhhccCcchHHHHHHHHHHHHHhcCCCCCHhhccCCccccHHHHHhhccCC
Confidence            8888888888888777764320     00                                          0000     


Q ss_pred             -------------------hcCCeEEEeCchhHHHHHHhcCCcccccCCceEEEecCcccccccC-----Cc-------h
Q 002040          588 -------------------KRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMG-----FE-------P  636 (976)
Q Consensus       588 -------------------~~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDEah~~~~~~-----f~-------~  636 (976)
                                         ...++|||+.+..|+..+....    .+..+.+|||||||++.+..     ..       .
T Consensus       392 ~~~~cp~~~~cf~~~ar~~a~~AdivItNHall~~~~~~~~----~~p~~~~lIiDEAH~l~~~~~~~~~~~~~~~~~~~  467 (820)
T PRK07246        392 LSQSSLFYDYDFWKRSYEKAKTARLLITNHAYFLTRVQDDK----DFARNKVLVFDEAQKLMLQLEQLSRHQLNITSFLQ  467 (820)
T ss_pred             CCCCCCcchhhHHHHHHHHHHhCCEEEEchHHHHHHHhhcc----CCCCCCEEEEECcchhHHHHHHHhcceecHHHHHH
Confidence                               0146799999998877664331    35679999999999874211     00       0


Q ss_pred             HH-------------------------------------------------------------HHHHHh--------c--
Q 002040          637 QI-------------------------------------------------------------TRIVQN--------I--  645 (976)
Q Consensus       637 ~i-------------------------------------------------------------~~il~~--------~--  645 (976)
                      .+                                                             ..++..        .  
T Consensus       468 ~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~l~~~l~~l~~~~~~~~~~~~~~~~~~~W~e~~~  547 (820)
T PRK07246        468 TIQKALSGPLPLLQKRLLESISFELLQLSEQFYQGKERQLIHDSLSRLHQYFSELEVAGFQELQAFFATAEGDYWLESEK  547 (820)
T ss_pred             HHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCeEEEEecC
Confidence            00                                                             000000        0  


Q ss_pred             -----------------------CCCCcEEEEeccCc--HHHHHHHHHHcC-CCeEEEeCCcccccCCceEEEEec---C
Q 002040          646 -----------------------RPDRQTVLFSATFP--RQVEILARKVLN-KPVEIQVGGRSVVNKDITQLVEVR---P  696 (976)
Q Consensus       646 -----------------------~~~~q~i~~SAT~~--~~~~~l~~~~l~-~~~~i~~~~~~~~~~~i~q~~~~~---~  696 (976)
                                             .....+|++|||++  +... +...+.- ......+.   ..... .+.+.+.   +
T Consensus       548 ~~~~~~~~l~~~pl~v~~~~~~~~~~~~~i~tSATL~v~~~f~-~~~~lGl~~~~~~~~~---~~~~~-~~~~~i~~~~p  622 (820)
T PRK07246        548 QSEKRVTYLNSASKAFTHFSQLLPETCKTYFVSATLQISPRVS-LADLLGFEEYLFHKIE---KDKKQ-DQLVVVDQDMP  622 (820)
T ss_pred             CCCcceeEEEeeeCcHHHHHHHHhcCCeEEEEecccccCCCCc-HHHHcCCCccceecCC---CChHH-ccEEEeCCCCC
Confidence                                   00134788888885  2222 3222211 11111111   11110 1111111   1


Q ss_pred             ------cchHHHHHHHHHHhhh-cCCcEEEEecCHHHHHHHHHHHHHCCCCceeccCCCCHHHHHHHHHHhccCCccEEE
Q 002040          697 ------ESDRFLRLLELLGEWY-EKGKILIFVHSQEKCDALFRDLLKHGYPCLSLHGAKDQTDRESTISDFKSNVCNLLI  769 (976)
Q Consensus       697 ------~~~k~~~l~~~l~~~~-~~~kvLIF~~s~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLV  769 (976)
                            .......+...|.... .+|++|||++|...+..++..|....+.+ ...|...  .+..+++.|+.+...||+
T Consensus       623 ~~~~~~~~~~~~~~~~~i~~~~~~~g~~LVLFtS~~~l~~v~~~l~~~~~~~-l~Qg~~~--~~~~l~~~F~~~~~~vLl  699 (820)
T PRK07246        623 LVTETSDEVYAEEIAKRLEELKQLQQPILVLFNSKKHLLAVSDLLDQWQVSH-LAQEKNG--TAYNIKKRFDRGEQQILL  699 (820)
T ss_pred             CCCCCChHHHHHHHHHHHHHHHhcCCCEEEEECcHHHHHHHHHHHhhcCCcE-EEeCCCc--cHHHHHHHHHcCCCeEEE
Confidence                  1223334444443322 46899999999999999999997655544 4445322  245689999998889999


Q ss_pred             ecCcccccCCCCC--CcEEEEeCCCC----CH--------------------------HHHHHHhcccCCCCCccEEEEE
Q 002040          770 ATSVAARGLDVKE--LELVINFDAPN----HY--------------------------EDYVHRVGRTGRAGRKGCAITF  817 (976)
Q Consensus       770 aT~v~~~GlDi~~--v~~VI~~d~p~----s~--------------------------~~y~Qr~GR~gR~g~~g~~~~~  817 (976)
                      +|..+..|||+|+  ...||+...|.    +|                          ..+.|.+||+-|....--++++
T Consensus       700 G~~sFwEGVD~p~~~~~~viI~kLPF~~P~dP~~~a~~~~~~~~g~~~F~~~~lP~A~iklkQg~GRLIRs~~D~Gvv~i  779 (820)
T PRK07246        700 GLGSFWEGVDFVQADRMIEVITRLPFDNPEDPFVKKMNQYLLQEGKNPFYDYFLPMTILRLKQAIGRTMRREDQKSAVLI  779 (820)
T ss_pred             ecchhhCCCCCCCCCeEEEEEecCCCCCCCCHHHHHHHHHHHHhCCCchhheeHHHHHHHHHHHhcccccCCCCcEEEEE
Confidence            9999999999974  55667655542    21                          2235999999998754335555


Q ss_pred             ecCC--CcCchHHHHHHHhh
Q 002040          818 ISEE--DAKYSPDLVKALEL  835 (976)
Q Consensus       818 ~~~~--d~~~~~~i~~~l~~  835 (976)
                      ++..  ...|-..+++.|..
T Consensus       780 lD~R~~~k~Yg~~~l~sLP~  799 (820)
T PRK07246        780 LDRRILTKSYGKQILASLAE  799 (820)
T ss_pred             ECCcccccHHHHHHHHhCCC
Confidence            5543  44466677666643

>CHL00122 secA preprotein translocase subunit SecA; Validated

Probab=99.78  E-value=2.5e-17  Score=195.00  Aligned_cols=280  Identities=18%  Similarity=0.181  Sum_probs=182.6

Q ss_pred             cCCCCCcHHHHHHHHHHhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHHHH
Q 002040          485 LNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFA  564 (976)
Q Consensus       485 ~~~~~p~~~Q~~~i~~il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~~~  564 (976)
                      +|+. |++.|.-+.  +.-....|+.+.||.|||+++++|++...+.        |..|-||+++..||.+-++++..++
T Consensus        73 lG~r-~ydvQlig~--l~L~~G~IaEm~TGEGKTL~a~l~ayl~aL~--------G~~VhVvT~NdyLA~RD~e~m~pvy  141 (870)
T CHL00122         73 LGLR-HFDVQLIGG--LVLNDGKIAEMKTGEGKTLVATLPAYLNALT--------GKGVHIVTVNDYLAKRDQEWMGQIY  141 (870)
T ss_pred             hCCC-CCchHhhhh--HhhcCCccccccCCCCchHHHHHHHHHHHhc--------CCceEEEeCCHHHHHHHHHHHHHHH
Confidence            5654 677776554  4445678999999999999999998655432        5668999999999999999999999


Q ss_pred             hhcCcEEEEeeCCCChHHHHHHHhcCCeEEEeCchhHH-HHHHhcC---CcccccCCceEEEecCccccc-ccCC-----
Q 002040          565 KVMGVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMI-DILCTSG---GKITNLRRVTYLVMDEADRMF-DMGF-----  634 (976)
Q Consensus       565 ~~~~~~~~~~~gg~~~~~~~~~l~~~~~Iiv~Tp~~L~-~~l~~~~---~~~~~l~~~~~vVlDEah~~~-~~~f-----  634 (976)
                      ..+|+.|.++.++.+..+....+  .++|+++|..-|. ++|..+-   ........+.|+||||+|.|+ |...     
T Consensus       142 ~~LGLsvg~i~~~~~~~err~aY--~~DItYgTn~e~gFDyLRDnm~~~~~~~v~r~~~faIVDEvDSiLIDeArTPLiI  219 (870)
T CHL00122        142 RFLGLTVGLIQEGMSSEERKKNY--LKDITYVTNSELGFDYLRDNMALSLSDVVQRPFNYCIIDEVDSILIDEARTPLII  219 (870)
T ss_pred             HHcCCceeeeCCCCChHHHHHhc--CCCCEecCCccccccchhhccCcChHHhhccccceeeeecchhheeccCCCceec
Confidence            99999999999988776654444  4899999997552 3333221   011124668899999999762 1100     


Q ss_pred             ----------chHHHHHHHhcCCC--------------------------------------------------------
Q 002040          635 ----------EPQITRIVQNIRPD--------------------------------------------------------  648 (976)
Q Consensus       635 ----------~~~i~~il~~~~~~--------------------------------------------------------  648 (976)
                                ...+..++..+..+                                                        
T Consensus       220 Sg~~~~~~~~y~~~~~~v~~L~~~~dy~vdek~k~v~LTe~G~~~~e~~l~i~~ly~~~~~~~~~i~~AL~A~~lf~~d~  299 (870)
T CHL00122        220 SGQSKTNIDKYIVADELAKYLEKNVHYEVDEKNKNVILTEQGILFIEKILKIEDLYSANDPWIPYILNALKAKELFFKNV  299 (870)
T ss_pred             cCCCccchHHHHHHHHHHHhcCcCCCeEEEcCCCceEecHHHHHHHHHHcCCccccccccHHHHHHHHHHHHHHHHhcCC
Confidence                      00000111111000                                                        


Q ss_pred             ------------------------------------------------------------CcEEEEeccCcHHHHHHHHH
Q 002040          649 ------------------------------------------------------------RQTVLFSATFPRQVEILARK  668 (976)
Q Consensus       649 ------------------------------------------------------------~q~i~~SAT~~~~~~~l~~~  668 (976)
                                                                                  ..+.+||+|.......+ ..
T Consensus       300 dYiV~dgeV~iVDe~TGR~m~grrws~GLHQaiEaKEgv~It~e~~tlAsIT~QnfFr~Y~kL~GMTGTa~te~~Ef-~~  378 (870)
T CHL00122        300 HYIVRNNEIIIVDEFTGRIMPGRRWSDGLHQAIEAKENLPIRQETETLASITYQNFFLLYPKLSGMTGTAKTEELEF-EK  378 (870)
T ss_pred             cEEEECCEEEEEECCCCcCCCCCccchHHHHHHHhhcCCCCCCCceeeeeeeHHHHHHhCchhcccCCCCHHHHHHH-HH
Confidence                                                                        12456666654443333 33


Q ss_pred             HcCCCeEEEeCCcccccCCceEEEEecCcchHHHHHHHHHHhhhc-CCcEEEEecCHHHHHHHHHHHHHCCCCceeccCC
Q 002040          669 VLNKPVEIQVGGRSVVNKDITQLVEVRPESDRFLRLLELLGEWYE-KGKILIFVHSQEKCDALFRDLLKHGYPCLSLHGA  747 (976)
Q Consensus       669 ~l~~~~~i~~~~~~~~~~~i~q~~~~~~~~~k~~~l~~~l~~~~~-~~kvLIF~~s~~~~~~l~~~L~~~~~~~~~lhg~  747 (976)
                      .++-.+...+...+...... ....+.....|+..++..+...+. +.||||-|.|+...+.|+..|...|+++.++++.
T Consensus       379 iY~l~vv~IPtnkp~~R~d~-~d~v~~t~~~K~~AI~~ei~~~~~~grPVLIgT~SIe~SE~ls~~L~~~gi~h~vLNAk  457 (870)
T CHL00122        379 IYNLEVVCIPTHRPMLRKDL-PDLIYKDELSKWRAIADECLQMHQTGRPILIGTTTIEKSELLSQLLKEYRLPHQLLNAK  457 (870)
T ss_pred             HhCCCEEECCCCCCccceeC-CCeEEeCHHHHHHHHHHHHHHHHhcCCCEEEeeCCHHHHHHHHHHHHHcCCccceeeCC
Confidence            33333333222222222111 123345556788888877766554 4599999999999999999999999999999986


Q ss_pred             CCH-HHHHHHHHHhccCC-ccEEEecCcccccCCCC
Q 002040          748 KDQ-TDRESTISDFKSNV-CNLLIATSVAARGLDVK  781 (976)
Q Consensus       748 ~~~-~~R~~~~~~F~~g~-~~vLVaT~v~~~GlDi~  781 (976)
                      -.. ..=..++..  .|. -.|.|||++|+||.||.
T Consensus       458 ~~~~~~EA~IIA~--AG~~G~VTIATNMAGRGTDI~  491 (870)
T CHL00122        458 PENVRRESEIVAQ--AGRKGSITIATNMAGRGTDII  491 (870)
T ss_pred             CccchhHHHHHHh--cCCCCcEEEeccccCCCcCee
Confidence            422 222233322  444 46999999999999984

>KOG0949 consensus Predicted helicase, DEAD-box superfamily [General function prediction only]

Probab=99.77  E-value=2.6e-17  Score=190.30  Aligned_cols=163  Identities=19%  Similarity=0.227  Sum_probs=115.0

Q ss_pred             CCcHHHHHHHHHHhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHHHHh-hc
Q 002040          489 KPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAK-VM  567 (976)
Q Consensus       489 ~p~~~Q~~~i~~il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~~~~-~~  567 (976)
                      .|-.+|.+.+..+-.+..++|+|||.+|||.+-- .++..++..     .....||+++||.+|++|+...+...+. ..
T Consensus       511 ~Pd~WQ~elLDsvDr~eSavIVAPTSaGKTfisf-Y~iEKVLRe-----sD~~VVIyvaPtKaLVnQvsa~VyaRF~~~t  584 (1330)
T KOG0949|consen  511 CPDEWQRELLDSVDRNESAVIVAPTSAGKTFISF-YAIEKVLRE-----SDSDVVIYVAPTKALVNQVSANVYARFDTKT  584 (1330)
T ss_pred             CCcHHHHHHhhhhhcccceEEEeeccCCceeccH-HHHHHHHhh-----cCCCEEEEecchHHHhhhhhHHHHHhhccCc
Confidence            5778999999999999999999999999998633 334443332     2456799999999999999887776552 22


Q ss_pred             CcEEEEeeCCCChHHHHHHHhcCCeEEEeCchhHHHHHHhcCCcccccCCceEEEecCcccccccCCchHHHHHHHhcCC
Q 002040          568 GVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMGFEPQITRIVQNIRP  647 (976)
Q Consensus       568 ~~~~~~~~gg~~~~~~~~~l~~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDEah~~~~~~f~~~i~~il~~~~~  647 (976)
                      -...+.+.|......++..  -+|+|+|+-|+.|..+|...........++.|||+||+|.+.++.-...+..++..+  
T Consensus       585 ~~rg~sl~g~ltqEYsinp--~nCQVLITvPecleslLlspp~~q~~cerIRyiIfDEVH~iG~~ed~l~~Eqll~li--  660 (1330)
T KOG0949|consen  585 FLRGVSLLGDLTQEYSINP--WNCQVLITVPECLESLLLSPPHHQKFCERIRYIIFDEVHLIGNEEDGLLWEQLLLLI--  660 (1330)
T ss_pred             cccchhhHhhhhHHhcCCc--hhceEEEEchHHHHHHhcCchhhhhhhhcceEEEechhhhccccccchHHHHHHHhc--
Confidence            2333344444433333331  259999999999988886632223456789999999999987765444444444444  


Q ss_pred             CCcEEEEeccCcHH
Q 002040          648 DRQTVLFSATFPRQ  661 (976)
Q Consensus       648 ~~q~i~~SAT~~~~  661 (976)
                      .+.+|++|||+.+.
T Consensus       661 ~CP~L~LSATigN~  674 (1330)
T KOG0949|consen  661 PCPFLVLSATIGNP  674 (1330)
T ss_pred             CCCeeEEecccCCH
Confidence            36699999997543

>KOG0388 consensus SNF2 family DNA-dependent ATPase [Replication, recombination and repair]

Probab=99.76  E-value=1.7e-17  Score=185.36  Aligned_cols=124  Identities=21%  Similarity=0.389  Sum_probs=109.4

Q ss_pred             cchHHHHHHHHHHhhhcC-CcEEEEecCHHHHHHHHHHHHHCCCCceeccCCCCHHHHHHHHHHhccC-CccEEEecCcc
Q 002040          697 ESDRFLRLLELLGEWYEK-GKILIFVHSQEKCDALFRDLLKHGYPCLSLHGAKDQTDRESTISDFKSN-VCNLLIATSVA  774 (976)
Q Consensus       697 ~~~k~~~l~~~l~~~~~~-~kvLIF~~s~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g-~~~vLVaT~v~  774 (976)
                      .+.|+..|-.+|..+... .++|+|++...+++.+..||.-.+|..+.+.|.....+|..++..|+.. .+-+|++|.++
T Consensus      1026 dSgKL~~LDeLL~kLkaegHRvL~yfQMTkM~dl~EdYl~yr~Y~ylRLDGSsk~~dRrd~vrDwQ~sdiFvFLLSTRAG 1105 (1185)
T KOG0388|consen 1026 DSGKLVVLDELLPKLKAEGHRVLMYFQMTKMIDLIEDYLVYRGYTYLRLDGSSKASDRRDVVRDWQASDIFVFLLSTRAG 1105 (1185)
T ss_pred             cccceeeHHHHHHHhhcCCceEEehhHHHHHHHHHHHHHHhhccceEEecCcchhhHHHHHHhhccCCceEEEEEecccC
Confidence            355777777777776654 4999999999999999999999999999999999999999999999965 46789999999


Q ss_pred             cccCCCCCCcEEEEeCCCCCHHHHHHHhcccCCCCCccE--EEEEecC
Q 002040          775 ARGLDVKELELVINFDAPNHYEDYVHRVGRTGRAGRKGC--AITFISE  820 (976)
Q Consensus       775 ~~GlDi~~v~~VI~~d~p~s~~~y~Qr~GR~gR~g~~g~--~~~~~~~  820 (976)
                      +-|||+..+++||+||..|+|..-.|.+.||+|-|+.-.  +|.+++.
T Consensus      1106 GLGINLTAADTViFYdSDWNPT~D~QAMDRAHRLGQTrdvtvyrl~~r 1153 (1185)
T KOG0388|consen 1106 GLGINLTAADTVIFYDSDWNPTADQQAMDRAHRLGQTRDVTVYRLITR 1153 (1185)
T ss_pred             cccccccccceEEEecCCCCcchhhHHHHHHHhccCccceeeeeeccc
Confidence            999999999999999999999999999999999998654  5555554

>PRK12902 secA preprotein translocase subunit SecA; Reviewed

Probab=99.74  E-value=9e-16  Score=181.32  Aligned_cols=279  Identities=18%  Similarity=0.193  Sum_probs=180.0

Q ss_pred             cCCCCCcHHHHHHHHHHhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHHHH
Q 002040          485 LNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFA  564 (976)
Q Consensus       485 ~~~~~p~~~Q~~~i~~il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~~~  564 (976)
                      +|. .|++.|..+--++  ....|..+.||-|||+++.+|++...+.        |..|-||+++.-||..-++++..+.
T Consensus        82 lG~-r~ydVQliGgl~L--h~G~IAEM~TGEGKTL~atlpaylnAL~--------GkgVhVVTvNdYLA~RDae~m~~vy  150 (939)
T PRK12902         82 LGM-RHFDVQLIGGMVL--HEGQIAEMKTGEGKTLVATLPSYLNALT--------GKGVHVVTVNDYLARRDAEWMGQVH  150 (939)
T ss_pred             hCC-CcchhHHHhhhhh--cCCceeeecCCCChhHHHHHHHHHHhhc--------CCCeEEEeCCHHHHHhHHHHHHHHH
Confidence            454 3666665554444  5667999999999999999998866553        5568899999999999999999999


Q ss_pred             hhcCcEEEEeeCCCChHHHHHHHhcCCeEEEeCchhH-----HHHHHhcCCcccccCCceEEEecCccccc-ccCCc---
Q 002040          565 KVMGVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRM-----IDILCTSGGKITNLRRVTYLVMDEADRMF-DMGFE---  635 (976)
Q Consensus       565 ~~~~~~~~~~~gg~~~~~~~~~l~~~~~Iiv~Tp~~L-----~~~l~~~~~~~~~l~~~~~vVlDEah~~~-~~~f~---  635 (976)
                      ..+|+.|.++.++....+....  -.|+|++||+..|     .+.+...... .....+.|+||||+|.++ |....   
T Consensus       151 ~~LGLtvg~i~~~~~~~err~a--Y~~DItYgTn~e~gFDYLRDnm~~~~~~-~vqR~~~faIVDEvDSILIDEArTPLI  227 (939)
T PRK12902        151 RFLGLSVGLIQQDMSPEERKKN--YACDITYATNSELGFDYLRDNMATDISE-VVQRPFNYCVIDEVDSILIDEARTPLI  227 (939)
T ss_pred             HHhCCeEEEECCCCChHHHHHh--cCCCeEEecCCcccccchhhhhcccccc-cccCccceEEEecccceeeccCCCccc
Confidence            9999999999888766554333  3599999999987     4544432211 235678899999999763 21100   


Q ss_pred             ------------hHHHHHHHhcCC--------------CC----------------------------------------
Q 002040          636 ------------PQITRIVQNIRP--------------DR----------------------------------------  649 (976)
Q Consensus       636 ------------~~i~~il~~~~~--------------~~----------------------------------------  649 (976)
                                  .....+...+..              ..                                        
T Consensus       228 ISg~~~~~~~~y~~~~~~~~~L~~~~~~~~~~dy~idek~~~v~LTe~G~~~~e~~~~i~nLy~~~~~~~~~i~~AL~A~  307 (939)
T PRK12902        228 ISGQVERPQEKYQKAAEVAAALQRKDGIDPEGDYEVDEKQRNVLLTDEGFAKAEQLLGVSDLFDPQDPWAHYIFNALKAK  307 (939)
T ss_pred             ccCCCccchHHHHHHHHHHHHhhhhcccCCCCCeEEecCCCeeeEcHHHHHHHHHHhCchhhcCcccHHHHHHHHHHHHH
Confidence                        001111111111              01                                        


Q ss_pred             --------------------------------------------------------------------cEEEEeccCcHH
Q 002040          650 --------------------------------------------------------------------QTVLFSATFPRQ  661 (976)
Q Consensus       650 --------------------------------------------------------------------q~i~~SAT~~~~  661 (976)
                                                                                          ++.+||+|....
T Consensus       308 ~lf~~d~dYiV~dg~V~IVDe~TGR~m~grrws~GLHQaIEaKE~v~it~e~~tlAsIT~QnfFr~Y~kLsGMTGTa~te  387 (939)
T PRK12902        308 ELFIKDVNYIVRNGEVVIVDEFTGRVMPGRRWSDGLHQAIEAKEGVEIQPETQTLASITYQNFFLLYPKLAGMTGTAKTE  387 (939)
T ss_pred             HHHhcCCeEEEECCEEEEEECCCCCCCCCCccchHHHHHHHhhcCCCCCCCceeeeeeeHHHHHhhCchhcccCCCCHHH
Confidence                                                                                133444443322


Q ss_pred             HHHHHHHHcCCCeEEEeCCcccccCCceEEEEecCcchHHHHHHHHHHhhhc-CCcEEEEecCHHHHHHHHHHHHHCCCC
Q 002040          662 VEILARKVLNKPVEIQVGGRSVVNKDITQLVEVRPESDRFLRLLELLGEWYE-KGKILIFVHSQEKCDALFRDLLKHGYP  740 (976)
Q Consensus       662 ~~~l~~~~l~~~~~i~~~~~~~~~~~i~q~~~~~~~~~k~~~l~~~l~~~~~-~~kvLIF~~s~~~~~~l~~~L~~~~~~  740 (976)
                      ...+.. .++-++...+...+....... ...+.....|+..++..+...+. +.||||-|.|++..+.|+..|...|++
T Consensus       388 ~~Ef~~-iY~l~Vv~IPTnkP~~R~d~~-d~vy~t~~~K~~Ai~~ei~~~~~~GrPVLIgT~SVe~SE~ls~~L~~~gi~  465 (939)
T PRK12902        388 EVEFEK-TYKLEVTVIPTNRPRRRQDWP-DQVYKTEIAKWRAVANETAEMHKQGRPVLVGTTSVEKSELLSALLQEQGIP  465 (939)
T ss_pred             HHHHHH-HhCCcEEEcCCCCCeeeecCC-CeEEcCHHHHHHHHHHHHHHHHhCCCCEEEeeCCHHHHHHHHHHHHHcCCc
Confidence            222222 222222222111111111111 12344556788888887777664 459999999999999999999999999


Q ss_pred             ceeccCCC-CHHHHHHHHHHhccCC-ccEEEecCcccccCCCC
Q 002040          741 CLSLHGAK-DQTDRESTISDFKSNV-CNLLIATSVAARGLDVK  781 (976)
Q Consensus       741 ~~~lhg~~-~~~~R~~~~~~F~~g~-~~vLVaT~v~~~GlDi~  781 (976)
                      +.+++..- ....-..|+..  .|. -.|-|||++|+||.||.
T Consensus       466 h~vLNAk~~~~~~EA~IIa~--AG~~GaVTIATNMAGRGTDIk  506 (939)
T PRK12902        466 HNLLNAKPENVEREAEIVAQ--AGRKGAVTIATNMAGRGTDII  506 (939)
T ss_pred             hheeeCCCcchHhHHHHHHh--cCCCCcEEEeccCCCCCcCEe
Confidence            99999863 22222233322  454 35999999999999985

>COG4889 Predicted helicase [General function prediction only]

Probab=99.74  E-value=5.5e-18  Score=193.04  Aligned_cols=325  Identities=19%  Similarity=0.267  Sum_probs=193.2

Q ss_pred             ccccCCCCHHHHHHHHHcCCCCCcHHHHHHHHHHhcC----CCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeE
Q 002040          468 TWHQTGLTSKIMETIRKLNYEKPMPIQAQALPVIMSG----RDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVG  543 (976)
Q Consensus       468 ~~~~~~l~~~l~~~l~~~~~~~p~~~Q~~~i~~il~g----~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~v  543 (976)
                      .|..+.. ..+...|.-..-.+|+|+|++||...+.|    ...-+++.+|+|||++.+ -+...+..         .++
T Consensus       141 DW~~f~p-~e~~~nl~l~~~kk~R~hQq~Aid~a~~~F~~n~RGkLIMAcGTGKTfTsL-kisEala~---------~~i  209 (1518)
T COG4889         141 DWDIFDP-TELQDNLPLKKPKKPRPHQQTAIDAAKEGFSDNDRGKLIMACGTGKTFTSL-KISEALAA---------ARI  209 (1518)
T ss_pred             ChhhcCc-cccccccccCCCCCCChhHHHHHHHHHhhcccccCCcEEEecCCCccchHH-HHHHHHhh---------hhe
Confidence            4444433 23333444445568999999999998865    235667889999998854 34444432         478


Q ss_pred             EEEccCHHHHHHHHHHHHHHHhhcCcEEEEeeCCCChH-------------------HHH-HHH-----hcCCeEEEeCc
Q 002040          544 LIMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVA-------------------QQI-SEL-----KRGTEIVVCTP  598 (976)
Q Consensus       544 LIl~Ptr~La~Q~~~~~~~~~~~~~~~~~~~~gg~~~~-------------------~~~-~~l-----~~~~~Iiv~Tp  598 (976)
                      |+|||+..|..|...++..- +.+.+....++......                   ..+ ..+     ..+--||++|+
T Consensus       210 L~LvPSIsLLsQTlrew~~~-~~l~~~a~aVcSD~kvsrs~eDik~sdl~~p~sT~~~~il~~~~~~~k~~~~~vvFsTY  288 (1518)
T COG4889         210 LFLVPSISLLSQTLREWTAQ-KELDFRASAVCSDDKVSRSAEDIKASDLPIPVSTDLEDILSEMEHRQKANGLTVVFSTY  288 (1518)
T ss_pred             EeecchHHHHHHHHHHHhhc-cCccceeEEEecCccccccccccccccCCCCCcccHHHHHHHHHHhhccCCcEEEEEcc
Confidence            99999999999988777653 23455555444432111                   111 111     12557999999


Q ss_pred             hhHHHHHHhcCCcccccCCceEEEecCcccccccCCchHHHHHHHhcCC-----CCcEEEEeccCcHHH-----------
Q 002040          599 GRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMGFEPQITRIVQNIRP-----DRQTVLFSATFPRQV-----------  662 (976)
Q Consensus       599 ~~L~~~l~~~~~~~~~l~~~~~vVlDEah~~~~~~f~~~i~~il~~~~~-----~~q~i~~SAT~~~~~-----------  662 (976)
                      ..|..+-..+.   .-+..+++||+||||+.....+...-...+..+..     ..+.+.|||||.--.           
T Consensus       289 QSl~~i~eAQe---~G~~~fDliicDEAHRTtGa~~a~dd~saFt~vHs~~niKa~kRlYmTATPkiy~eS~K~kAkd~s  365 (1518)
T COG4889         289 QSLPRIKEAQE---AGLDEFDLIICDEAHRTTGATLAGDDKSAFTRVHSDQNIKAAKRLYMTATPKIYSESSKAKAKDHS  365 (1518)
T ss_pred             cchHHHHHHHH---cCCCCccEEEecchhccccceecccCcccceeecCcchhHHHHhhhcccCchhhchhhhhhhhhcc
Confidence            99877655443   34678999999999985422111111111111111     123578888862110           


Q ss_pred             ----------------------HHHHHHHcCCCeEEEeCC-cccccCCceEEEEecCc-------chHHHHHHHHHHhhh
Q 002040          663 ----------------------EILARKVLNKPVEIQVGG-RSVVNKDITQLVEVRPE-------SDRFLRLLELLGEWY  712 (976)
Q Consensus       663 ----------------------~~l~~~~l~~~~~i~~~~-~~~~~~~i~q~~~~~~~-------~~k~~~l~~~l~~~~  712 (976)
                                            +.+...+|.+.-++.+.. .......+ +.....+.       ..++.-...-|....
T Consensus       366 ~~l~SMDDe~~fGeef~rl~FgeAv~rdlLTDYKVmvlaVd~~~i~~~~-~~~~~~~~~~L~~dd~~kIvG~wnGlakr~  444 (1518)
T COG4889         366 AELSSMDDELTFGEEFHRLGFGEAVERDLLTDYKVMVLAVDKEVIAGVL-QSVLSGPSKGLALDDVSKIVGCWNGLAKRN  444 (1518)
T ss_pred             ceeeccchhhhhchhhhcccHHHHHHhhhhccceEEEEEechhhhhhhh-hhhccCcccccchhhhhhhhhhhhhhhhhc
Confidence                                  112223333332221111 11111111 11111111       112222222221111


Q ss_pred             --------------cCCcEEEEecCHHHHHHHHHHHHH---------------CCCCceeccCCCCHHHHHHHHH---Hh
Q 002040          713 --------------EKGKILIFVHSQEKCDALFRDLLK---------------HGYPCLSLHGAKDQTDRESTIS---DF  760 (976)
Q Consensus       713 --------------~~~kvLIF~~s~~~~~~l~~~L~~---------------~~~~~~~lhg~~~~~~R~~~~~---~F  760 (976)
                                    +..+.|-||.++++...++..+..               ..+.|..+.|.|...+|...+.   .|
T Consensus       445 g~~n~~~~~~~d~ap~~RAIaF~k~I~tSK~i~~sFe~Vve~Y~~Elk~d~~nL~iSi~HvDGtmNal~R~~l~~l~~~~  524 (1518)
T COG4889         445 GEDNDLKNIKADTAPMQRAIAFAKDIKTSKQIAESFETVVEAYDEELKKDFKNLKISIDHVDGTMNALERLDLLELKNTF  524 (1518)
T ss_pred             cccccccCCcCCchHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHhcCCCceEEeecccccccHHHHHHHHhccCCC
Confidence                          012678899988877776665532               1345667889999999965543   44


Q ss_pred             ccCCccEEEecCcccccCCCCCCcEEEEeCCCCCHHHHHHHhcccCCC
Q 002040          761 KSNVCNLLIATSVAARGLDVKELELVINFDAPNHYEDYVHRVGRTGRA  808 (976)
Q Consensus       761 ~~g~~~vLVaT~v~~~GlDi~~v~~VI~~d~p~s~~~y~Qr~GR~gR~  808 (976)
                      ....++||--..++..|+|||.++.||+|++-.++.+.+|.+||+.|-
T Consensus       525 ~~neckIlSNaRcLSEGVDVPaLDsViFf~pr~smVDIVQaVGRVMRK  572 (1518)
T COG4889         525 EPNECKILSNARCLSEGVDVPALDSVIFFDPRSSMVDIVQAVGRVMRK  572 (1518)
T ss_pred             CcchheeeccchhhhcCCCccccceEEEecCchhHHHHHHHHHHHHHh
Confidence            567899999999999999999999999999999999999999999994

>KOG4150 consensus Predicted ATP-dependent RNA helicase [RNA processing and modification]

Probab=99.72  E-value=8.3e-17  Score=176.06  Aligned_cols=345  Identities=14%  Similarity=0.100  Sum_probs=235.1

Q ss_pred             HHHHHcCCCCCcHHHHHHHHHHhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHH
Q 002040          480 ETIRKLNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSD  559 (976)
Q Consensus       480 ~~l~~~~~~~p~~~Q~~~i~~il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~  559 (976)
                      ..+..+.-.....+|.++|..+.+|+++++.-.|.+||.+++.+.....+...+      ....|++.|+.+++.....-
T Consensus       277 ~~~~~~~~E~~~~~~~~~~~~~~~G~~~~~~~~~~~GK~~~~~~~s~~~~~~~~------~s~~~~~~~~~~~~~~~~~~  350 (1034)
T KOG4150|consen  277 SLLNKNTGESGIAISLELLKFASEGRADGGNEARQAGKGTCPTSGSRKFQTLCH------ATNSLLPSEMVEHLRNGSKG  350 (1034)
T ss_pred             HHHhcccccchhhhhHHHHhhhhhcccccccchhhcCCccCcccchhhhhhcCc------ccceecchhHHHHhhccCCc
Confidence            445566667788999999999999999999999999999999988877765533      23468888999887643222


Q ss_pred             HHH---HHhhcCcEEEEeeCCCChHHHHHHHhcCCeEEEeCchhHHHHHHhcC-CcccccCCceEEEecCcccccccCCc
Q 002040          560 IRK---FAKVMGVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSG-GKITNLRRVTYLVMDEADRMFDMGFE  635 (976)
Q Consensus       560 ~~~---~~~~~~~~~~~~~gg~~~~~~~~~l~~~~~Iiv~Tp~~L~~~l~~~~-~~~~~l~~~~~vVlDEah~~~~~~f~  635 (976)
                      +.-   ..+...-.++-.+.|............+..++++.|..+...+..+. -....+-...++++||+|..+.. |.
T Consensus       351 ~~V~~~~I~~~K~A~V~~~D~~sE~~~~A~~R~~~~~~~s~~~~~~s~~L~~~~~~~~~~~~~~~~~~~~~~~Y~~~-~~  429 (1034)
T KOG4150|consen  351 QVVHVEVIKARKSAYVEMSDKLSETTKSALKRIGLNTLYSHQAEAISAALAKSLCYNVPVFEELCKDTNSCALYLFP-TK  429 (1034)
T ss_pred             eEEEEEehhhhhcceeecccCCCchhHHHHHhcCcceeecCHHHHHHHHhhhccccccHHHHHHHhcccceeeeecc-hh
Confidence            110   01112233455666666666666667789999999998766543321 11122334567899999954321 22


Q ss_pred             h----HHHHHHHhc-----CCCCcEEEEeccCcHHHHHHHHHHcCCC-eEEEeCCcccccCCceEEEEecCc--------
Q 002040          636 P----QITRIVQNI-----RPDRQTVLFSATFPRQVEILARKVLNKP-VEIQVGGRSVVNKDITQLVEVRPE--------  697 (976)
Q Consensus       636 ~----~i~~il~~~-----~~~~q~i~~SAT~~~~~~~l~~~~l~~~-~~i~~~~~~~~~~~i~q~~~~~~~--------  697 (976)
                      .    ++..++..+     ..+.|++-.|||....+......+.-+- ..+.+.+.+..   ....+.+.++        
T Consensus       430 ~~~~~~~R~L~~L~~~F~~~~~~~~~~~~~~~K~~~~~~~~~~~~~E~~Li~~DGSPs~---~K~~V~WNP~~~P~~~~~  506 (1034)
T KOG4150|consen  430 ALAQDQLRALSDLIKGFEASINMGVYDGDTPYKDRTRLRSELANLSELELVTIDGSPSS---EKLFVLWNPSAPPTSKSE  506 (1034)
T ss_pred             hHHHHHHHHHHHHHHHHHhhcCcceEeCCCCcCCHHHHHHHhcCCcceEEEEecCCCCc---cceEEEeCCCCCCcchhh
Confidence            2    222332222     3568899999999887765554443333 33444443322   2233333221        


Q ss_pred             -chHHHHHHHHHHhhhc-CCcEEEEecCHHHHHHHHHHHHH----CCC----CceeccCCCCHHHHHHHHHHhccCCccE
Q 002040          698 -SDRFLRLLELLGEWYE-KGKILIFVHSQEKCDALFRDLLK----HGY----PCLSLHGAKDQTDRESTISDFKSNVCNL  767 (976)
Q Consensus       698 -~~k~~~l~~~l~~~~~-~~kvLIF~~s~~~~~~l~~~L~~----~~~----~~~~lhg~~~~~~R~~~~~~F~~g~~~v  767 (976)
                       +.++.....++.+... +-++|-||+++..|+.|......    .+-    .+..+.|+....+|.++...+-.|+..-
T Consensus       507 ~~~~i~E~s~~~~~~i~~~~R~IAFC~~R~~CEL~~~~~R~I~~ET~~~LV~~i~SYRGGY~A~DRRKIE~~~F~G~L~g  586 (1034)
T KOG4150|consen  507 KSSKVVEVSHLFAEMVQHGLRCIAFCPSRKLCELVLCLTREILAETAPHLVEAITSYRGGYIAEDRRKIESDLFGGKLCG  586 (1034)
T ss_pred             hhhHHHHHHHHHHHHHHcCCcEEEeccHHHHHHHHHHHHHHHHHHhhHHHHHHHHhhcCccchhhHHHHHHHhhCCeeeE
Confidence             3345555555555443 44999999999999887655433    221    3567889999999999999999999999


Q ss_pred             EEecCcccccCCCCCCcEEEEeCCCCCHHHHHHHhcccCCCCCccEEEEEe--cCCCcCchHHHHHHHh
Q 002040          768 LIATSVAARGLDVKELELVINFDAPNHYEDYVHRVGRTGRAGRKGCAITFI--SEEDAKYSPDLVKALE  834 (976)
Q Consensus       768 LVaT~v~~~GlDi~~v~~VI~~d~p~s~~~y~Qr~GR~gR~g~~g~~~~~~--~~~d~~~~~~i~~~l~  834 (976)
                      +|||++++.||||.+++.|++.++|.+++++.|..||+||..+...++.+.  .+-|..|+..-...+.
T Consensus       587 iIaTNALELGIDIG~LDAVl~~GFP~S~aNl~QQ~GRAGRRNk~SLavyva~~~PVDQ~Y~~HP~~l~~  655 (1034)
T KOG4150|consen  587 IIATNALELGIDIGHLDAVLHLGFPGSIANLWQQAGRAGRRNKPSLAVYVAFLGPVDQYYMSHPDKLFG  655 (1034)
T ss_pred             EEecchhhhccccccceeEEEccCchhHHHHHHHhccccccCCCceEEEEEeccchhhHhhcCcHHHhC
Confidence            999999999999999999999999999999999999999998876655443  3556555554444443

>cd00079 HELICc Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may not be an autonomously folding unit, but an integral part of the helicase; 4 helicase superfamilies at present according to the organization of their signature motifs; all helicases share the ability to unwind nucleic acid duplexes with a distinct directional polarity; they utilize the free energy from nucleoside triphosphate hydrolysis to fuel their translocation along DNA, unwinding the duplex in the process

Probab=99.72  E-value=6.5e-17  Score=155.73  Aligned_cols=120  Identities=42%  Similarity=0.674  Sum_probs=112.2

Q ss_pred             chHHHHHHHHHHhhh-cCCcEEEEecCHHHHHHHHHHHHHCCCCceeccCCCCHHHHHHHHHHhccCCccEEEecCcccc
Q 002040          698 SDRFLRLLELLGEWY-EKGKILIFVHSQEKCDALFRDLLKHGYPCLSLHGAKDQTDRESTISDFKSNVCNLLIATSVAAR  776 (976)
Q Consensus       698 ~~k~~~l~~~l~~~~-~~~kvLIF~~s~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLVaT~v~~~  776 (976)
                      +.|+..+..++.... ..+++||||++...++.++..|...++.+..+||.++..++..++..|.+|...|||+|.++++
T Consensus        11 ~~k~~~i~~~i~~~~~~~~~~lvf~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~f~~~~~~ili~t~~~~~   90 (131)
T cd00079          11 DEKLEALLELLKEHLKKGGKVLIFCPSKKMLDELAELLRKPGIKVAALHGDGSQEEREEVLKDFREGEIVVLVATDVIAR   90 (131)
T ss_pred             HHHHHHHHHHHHhcccCCCcEEEEeCcHHHHHHHHHHHHhcCCcEEEEECCCCHHHHHHHHHHHHcCCCcEEEEcChhhc
Confidence            378888888887764 4679999999999999999999998999999999999999999999999999999999999999


Q ss_pred             cCCCCCCcEEEEeCCCCCHHHHHHHhcccCCCCCccEEEEE
Q 002040          777 GLDVKELELVINFDAPNHYEDYVHRVGRTGRAGRKGCAITF  817 (976)
Q Consensus       777 GlDi~~v~~VI~~d~p~s~~~y~Qr~GR~gR~g~~g~~~~~  817 (976)
                      |+|+|++++||++++|++...|+|++||+||.|+.|.|++|
T Consensus        91 G~d~~~~~~vi~~~~~~~~~~~~Q~~GR~~R~~~~~~~~~~  131 (131)
T cd00079          91 GIDLPNVSVVINYDLPWSPSSYLQRIGRAGRAGQKGTAILL  131 (131)
T ss_pred             CcChhhCCEEEEeCCCCCHHHheecccccccCCCCceEEeC
Confidence            99999999999999999999999999999999999988764

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

Probab=99.70  E-value=3.9e-15  Score=186.87  Aligned_cols=133  Identities=16%  Similarity=0.223  Sum_probs=94.8

Q ss_pred             HHHHHHHHhhh--cCCcEEEEecCHHHHHHHHHHHHHCCC--CceeccCCCCHHHHHHHHHHhccCCccEEEecCccccc
Q 002040          702 LRLLELLGEWY--EKGKILIFVHSQEKCDALFRDLLKHGY--PCLSLHGAKDQTDRESTISDFKSNVCNLLIATSVAARG  777 (976)
Q Consensus       702 ~~l~~~l~~~~--~~~kvLIF~~s~~~~~~l~~~L~~~~~--~~~~lhg~~~~~~R~~~~~~F~~g~~~vLVaT~v~~~G  777 (976)
                      ..+...|....  .+|++|||++|......++..|.....  .+..+.-+++...+..+++.|+.+.-.||++|..+..|
T Consensus       738 ~~la~~i~~l~~~~~g~~LVLFtSy~~l~~v~~~l~~~~~~~~~~ll~Qg~~~~~r~~l~~~F~~~~~~iLlG~~sFwEG  817 (928)
T PRK08074        738 EEVAAYIAKIAKATKGRMLVLFTSYEMLKKTYYNLKNEEELEGYVLLAQGVSSGSRARLTKQFQQFDKAILLGTSSFWEG  817 (928)
T ss_pred             HHHHHHHHHHHHhCCCCEEEEECCHHHHHHHHHHHhhcccccCceEEecCCCCCCHHHHHHHHHhcCCeEEEecCcccCc
Confidence            45555554433  468999999999999999999976422  12223224444567889999999888999999999999


Q ss_pred             CCCCC--CcEEEEeCCCC----CH--------------------------HHHHHHhcccCCCCCccEEEEEecCC--Cc
Q 002040          778 LDVKE--LELVINFDAPN----HY--------------------------EDYVHRVGRTGRAGRKGCAITFISEE--DA  823 (976)
Q Consensus       778 lDi~~--v~~VI~~d~p~----s~--------------------------~~y~Qr~GR~gR~g~~g~~~~~~~~~--d~  823 (976)
                      ||+|+  +.+||+...|.    ++                          ..+.|.+||+-|....-.++++++..  ..
T Consensus       818 VD~pg~~l~~viI~kLPF~~p~dp~~~a~~~~~~~~g~~~F~~~~lP~A~~~lkQg~GRlIRs~~D~G~v~ilD~R~~~k  897 (928)
T PRK08074        818 IDIPGDELSCLVIVRLPFAPPDQPVMEAKSEWAKEQGENPFQELSLPQAVLRFKQGFGRLIRTETDRGTVFVLDRRLTTT  897 (928)
T ss_pred             cccCCCceEEEEEecCCCCCCCCHHHHHHHHHHHHhCCCchhhhhhHHHHHHHHhhhhhhcccCCceEEEEEecCccccc
Confidence            99998  57888876554    21                          12259999999987654455566554  55


Q ss_pred             CchHHHHHHHh
Q 002040          824 KYSPDLVKALE  834 (976)
Q Consensus       824 ~~~~~i~~~l~  834 (976)
                      .|-..+++.|.
T Consensus       898 ~Yg~~~l~sLP  908 (928)
T PRK08074        898 SYGKYFLESLP  908 (928)
T ss_pred             hHHHHHHHhCC
Confidence            56677777764

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

Probab=99.70  E-value=1.3e-14  Score=171.11  Aligned_cols=107  Identities=20%  Similarity=0.172  Sum_probs=76.9

Q ss_pred             cCCcEEEEecCHHHHHHHHHHHHHCCCCceeccCCCCHHHHHHHHHHhcc----CCccEEEecCcccccCCC--------
Q 002040          713 EKGKILIFVHSQEKCDALFRDLLKHGYPCLSLHGAKDQTDRESTISDFKS----NVCNLLIATSVAARGLDV--------  780 (976)
Q Consensus       713 ~~~kvLIF~~s~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~----g~~~vLVaT~v~~~GlDi--------  780 (976)
                      ..|.+||.+.+...+..++..|...--..+.+.|..+  .+..+++.|+.    |...||++|..+..||||        
T Consensus       469 ~~G~~lvLfTS~~~~~~~~~~l~~~l~~~~l~qg~~~--~~~~l~~~f~~~~~~~~~~vL~gt~sfweGvDv~~~~~~p~  546 (636)
T TIGR03117       469 AQGGTLVLTTAFSHISAIGQLVELGIPAEIVIQSEKN--RLASAEQQFLALYANGIQPVLIAAGGAWTGIDLTHKPVSPD  546 (636)
T ss_pred             cCCCEEEEechHHHHHHHHHHHHhhcCCCEEEeCCCc--cHHHHHHHHHHhhcCCCCcEEEeCCccccccccCCccCCCC
Confidence            4789999999999999999999653223345566443  34567888876    478999999999999999        


Q ss_pred             CC--CcEEEEeCCCCCH-------------------------HHHHHHhcccCCCCCc--cEEEEEecCC
Q 002040          781 KE--LELVINFDAPNHY-------------------------EDYVHRVGRTGRAGRK--GCAITFISEE  821 (976)
Q Consensus       781 ~~--v~~VI~~d~p~s~-------------------------~~y~Qr~GR~gR~g~~--g~~~~~~~~~  821 (976)
                      |+  +.+||+...|..+                         ..+.|-+||.-|....  -.+++++.+.
T Consensus       547 ~G~~Ls~ViI~kLPF~~~dp~a~~~~~~~~g~~~f~~~p~a~i~lkQg~GRLIR~~~D~~~G~i~ilD~R  616 (636)
T TIGR03117       547 KDNLLTDLIITCAPFGLNRSLSMLKRIRKTSVRPWEIINESLMMLRQGLGRLVRHPDMPQNRRIHMLDGR  616 (636)
T ss_pred             CCCcccEEEEEeCCCCcCChHHHHHHHHhcCCChHhhhHHHHHHHHHhcCceeecCCCcCceEEEEEeCC
Confidence            34  8899986665311                         2235889999997654  3344445443

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.

>KOG4439 consensus RNA polymerase II transcription termination factor TTF2/lodestar, DEAD-box superfamily [Transcription; Replication, recombination and repair]

Probab=99.66  E-value=3e-15  Score=168.59  Aligned_cols=121  Identities=19%  Similarity=0.211  Sum_probs=103.1

Q ss_pred             cchHHHHHHHHHHhhh--cCCcEEEEecCHHHHHHHHHHHHHCCCCceeccCCCCHHHHHHHHHHhc--cC-CccEEEec
Q 002040          697 ESDRFLRLLELLGEWY--EKGKILIFVHSQEKCDALFRDLLKHGYPCLSLHGAKDQTDRESTISDFK--SN-VCNLLIAT  771 (976)
Q Consensus       697 ~~~k~~~l~~~l~~~~--~~~kvLIF~~s~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~--~g-~~~vLVaT  771 (976)
                      .+.|+..++..+...+  ...+++|..+-......+...|...|+.+..+||.....+|+.+++.|+  +| ....||+-
T Consensus       727 ~S~Ki~~~l~~le~i~~~skeK~viVSQwtsvLniv~~hi~~~g~~y~si~Gqv~vK~Rq~iv~~FN~~k~~~rVmLlSL  806 (901)
T KOG4439|consen  727 PSCKIAMVLEILETILTSSKEKVVIVSQWTSVLNIVRKHIQKGGHIYTSITGQVLVKDRQEIVDEFNQEKGGARVMLLSL  806 (901)
T ss_pred             chhHHHHHHHHHHHHhhcccceeeehhHHHHHHHHHHHHHhhCCeeeeeecCccchhHHHHHHHHHHhccCCceEEEEEE
Confidence            4456666666665542  3458888888889999999999999999999999999999999999997  34 44566778


Q ss_pred             CcccccCCCCCCcEEEEeCCCCCHHHHHHHhcccCCCCCccEEEEE
Q 002040          772 SVAARGLDVKELELVINFDAPNHYEDYVHRVGRTGRAGRKGCAITF  817 (976)
Q Consensus       772 ~v~~~GlDi~~v~~VI~~d~p~s~~~y~Qr~GR~gR~g~~g~~~~~  817 (976)
                      .+.+.|||+.+.+++|.+|+.|||+---|.+.|+.|.|++..++++
T Consensus       807 tAGGVGLNL~GaNHlilvDlHWNPaLEqQAcDRIYR~GQkK~V~Ih  852 (901)
T KOG4439|consen  807 TAGGVGLNLIGANHLILVDLHWNPALEQQACDRIYRMGQKKDVFIH  852 (901)
T ss_pred             ccCcceeeecccceEEEEecccCHHHHHHHHHHHHHhcccCceEEE
Confidence            8999999999999999999999999999999999999998776664

>KOG0953 consensus Mitochondrial RNA helicase SUV3, DEAD-box superfamily [RNA processing and modification]

Probab=99.65  E-value=1.5e-15  Score=167.21  Aligned_cols=266  Identities=22%  Similarity=0.268  Sum_probs=176.9

Q ss_pred             CCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHHHHhhcCcEEEEeeCCCChHHHH
Q 002040          505 RDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQI  584 (976)
Q Consensus       505 ~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~~~~~~~~~~~~~~gg~~~~~~~  584 (976)
                      +-++-+|||.||||.-++-    ++..        ...+++..|.|-||..+++.+..    .|+.|..++|.......-
T Consensus       192 kIi~H~GPTNSGKTy~ALq----rl~~--------aksGvycGPLrLLA~EV~~r~na----~gipCdL~TGeE~~~~~~  255 (700)
T KOG0953|consen  192 KIIMHVGPTNSGKTYRALQ----RLKS--------AKSGVYCGPLRLLAHEVYDRLNA----LGIPCDLLTGEERRFVLD  255 (700)
T ss_pred             eEEEEeCCCCCchhHHHHH----HHhh--------hccceecchHHHHHHHHHHHhhh----cCCCccccccceeeecCC
Confidence            4467789999999987543    3332        23468999999999999888776    688888888765333221


Q ss_pred             HHHhcCCeEEEeCchhHHHHHHhcCCcccccCCceEEEecCcccccccCCchHHHHHHHhcC-CCCcEEEEeccCcHHHH
Q 002040          585 SELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMGFEPQITRIVQNIR-PDRQTVLFSATFPRQVE  663 (976)
Q Consensus       585 ~~l~~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDEah~~~~~~f~~~i~~il~~~~-~~~q~i~~SAT~~~~~~  663 (976)
                      .  ...+..+-||.++.           .--..+++.||||++.|.+...+-.+.+.+--+. ...++.+   -  +.+-
T Consensus       256 ~--~~~a~hvScTVEM~-----------sv~~~yeVAViDEIQmm~Dp~RGwAWTrALLGl~AdEiHLCG---e--psvl  317 (700)
T KOG0953|consen  256 N--GNPAQHVSCTVEMV-----------SVNTPYEVAVIDEIQMMRDPSRGWAWTRALLGLAADEIHLCG---E--PSVL  317 (700)
T ss_pred             C--CCcccceEEEEEEe-----------ecCCceEEEEehhHHhhcCcccchHHHHHHHhhhhhhhhccC---C--chHH
Confidence            1  12357777886643           1123488999999999988776555555443322 1122221   1  1222


Q ss_pred             HHHHHHcC---CCeEEEeCCcccccCCceEEEEecCcchHHHHHHHHHHhhhcCCcEEEEecCHHHHHHHHHHHHHCCCC
Q 002040          664 ILARKVLN---KPVEIQVGGRSVVNKDITQLVEVRPESDRFLRLLELLGEWYEKGKILIFVHSQEKCDALFRDLLKHGYP  740 (976)
Q Consensus       664 ~l~~~~l~---~~~~i~~~~~~~~~~~i~q~~~~~~~~~k~~~l~~~l~~~~~~~kvLIF~~s~~~~~~l~~~L~~~~~~  740 (976)
                      .+...++.   +.+.+..             +....+-.-...++..|... ..|.+| .|-++..+-.+...+.+.|..
T Consensus       318 dlV~~i~k~TGd~vev~~-------------YeRl~pL~v~~~~~~sl~nl-k~GDCv-V~FSkk~I~~~k~kIE~~g~~  382 (700)
T KOG0953|consen  318 DLVRKILKMTGDDVEVRE-------------YERLSPLVVEETALGSLSNL-KPGDCV-VAFSKKDIFTVKKKIEKAGNH  382 (700)
T ss_pred             HHHHHHHhhcCCeeEEEe-------------ecccCcceehhhhhhhhccC-CCCCeE-EEeehhhHHHHHHHHHHhcCc
Confidence            34443332   2222221             11111111112333444333 345554 466777888888888888766


Q ss_pred             -ceeccCCCCHHHHHHHHHHhcc--CCccEEEecCcccccCCCCCCcEEEEeCC---------CCCHHHHHHHhcccCCC
Q 002040          741 -CLSLHGAKDQTDRESTISDFKS--NVCNLLIATSVAARGLDVKELELVINFDA---------PNHYEDYVHRVGRTGRA  808 (976)
Q Consensus       741 -~~~lhg~~~~~~R~~~~~~F~~--g~~~vLVaT~v~~~GlDi~~v~~VI~~d~---------p~s~~~y~Qr~GR~gR~  808 (976)
                       |.+|+|++++..|.+--..|++  +.++|||||+++++|||+ ++..||+|+.         |.......|.+|||||.
T Consensus       383 k~aVIYGsLPPeTr~aQA~~FNd~~~e~dvlVAsDAIGMGLNL-~IrRiiF~sl~Kysg~e~~~it~sqikQIAGRAGRf  461 (700)
T KOG0953|consen  383 KCAVIYGSLPPETRLAQAALFNDPSNECDVLVASDAIGMGLNL-NIRRIIFYSLIKYSGRETEDITVSQIKQIAGRAGRF  461 (700)
T ss_pred             ceEEEecCCCCchhHHHHHHhCCCCCccceEEeeccccccccc-ceeEEEEeecccCCcccceeccHHHHHHHhhccccc
Confidence             9999999999999999999996  899999999999999999 8999998876         34677889999999998


Q ss_pred             CC---ccEEEEEecC
Q 002040          809 GR---KGCAITFISE  820 (976)
Q Consensus       809 g~---~g~~~~~~~~  820 (976)
                      |.   .|.+.+|..+
T Consensus       462 ~s~~~~G~vTtl~~e  476 (700)
T KOG0953|consen  462 GSKYPQGEVTTLHSE  476 (700)
T ss_pred             ccCCcCceEEEeeHh
Confidence            64   4777777653

>PF00271 Helicase_C: Helicase conserved C-terminal domain; InterPro: IPR001650 The domain, which defines this group of proteins is found in a wide variety of helicases and helicase related proteins

Probab=99.64  E-value=4.5e-16  Score=135.46  Aligned_cols=78  Identities=35%  Similarity=0.623  Sum_probs=75.6

Q ss_pred             HHHHHCCCCceeccCCCCHHHHHHHHHHhccCCccEEEecCcccccCCCCCCcEEEEeCCCCCHHHHHHHhcccCCCC
Q 002040          732 RDLLKHGYPCLSLHGAKDQTDRESTISDFKSNVCNLLIATSVAARGLDVKELELVINFDAPNHYEDYVHRVGRTGRAG  809 (976)
Q Consensus       732 ~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLVaT~v~~~GlDi~~v~~VI~~d~p~s~~~y~Qr~GR~gR~g  809 (976)
                      ++|...++.+..+||++++.+|..+++.|.+|...|||||+++++|||+|.+++||+|++|+++..|.|++||+||.|
T Consensus         1 ~~L~~~~~~~~~i~~~~~~~~r~~~~~~f~~~~~~vli~t~~~~~Gid~~~~~~vi~~~~~~~~~~~~Q~~GR~~R~g   78 (78)
T PF00271_consen    1 KFLEKKGIKVAIIHGDMSQKERQEILKKFNSGEIRVLIATDILGEGIDLPDASHVIFYDPPWSPEEYIQRIGRAGRIG   78 (78)
T ss_dssp             HHHHHTTSSEEEESTTSHHHHHHHHHHHHHTTSSSEEEESCGGTTSSTSTTESEEEESSSESSHHHHHHHHTTSSTTT
T ss_pred             CChHHCCCcEEEEECCCCHHHHHHHHHHhhccCceEEEeeccccccccccccccccccccCCCHHHHHHHhhcCCCCC
Confidence            367888999999999999999999999999999999999999999999999999999999999999999999999986

It may be that this is not an autonomously folding unit, but an integral part of the helicase. The eukaryotic translation initiation factor 4A (eIF4A) is a member of the DEA(D/H)-box RNA helicase family This is a diverse group of proteins that couples an ATPase activity to RNA binding and unwinding. The structure of the carboxyl-terminal domain of eIF4A has been determined to 1.75 A resolution; it has a parallel alpha-beta topology that superimposes, with minor variations, on the structures and conserved motifs of the equivalent domain in other, distantly related helicases [].; GO: 0003676 nucleic acid binding, 0004386 helicase activity, 0005524 ATP binding; PDB: 2Z83_A 2JGN_C 2I4I_A 2BMF_A 2BHR_B 1WP9_E 2WAX_C 2WAY_C 3JUX_A 3DIN_B ....

>PRK12901 secA preprotein translocase subunit SecA; Reviewed

Probab=99.63  E-value=1.5e-14  Score=172.61  Aligned_cols=129  Identities=24%  Similarity=0.271  Sum_probs=105.3

Q ss_pred             ecCcchHHHHHHHHHHhhhcC-CcEEEEecCHHHHHHHHHHHHHCCCCceeccCCCCHHHHHHHHHHhccCCccEEEecC
Q 002040          694 VRPESDRFLRLLELLGEWYEK-GKILIFVHSQEKCDALFRDLLKHGYPCLSLHGAKDQTDRESTISDFKSNVCNLLIATS  772 (976)
Q Consensus       694 ~~~~~~k~~~l~~~l~~~~~~-~kvLIF~~s~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLVaT~  772 (976)
                      +.....|+..++..+...+.. .||||-|.|++..+.|+..|...|+++..|+......+-..+-+.=+.  -.|-|||+
T Consensus       607 y~t~~eK~~Aii~ei~~~~~~GrPVLVGT~SVe~SE~lS~~L~~~gI~H~VLNAK~h~~EAeIVA~AG~~--GaVTIATN  684 (1112)
T PRK12901        607 YKTKREKYNAVIEEITELSEAGRPVLVGTTSVEISELLSRMLKMRKIPHNVLNAKLHQKEAEIVAEAGQP--GTVTIATN  684 (1112)
T ss_pred             ecCHHHHHHHHHHHHHHHHHCCCCEEEEeCcHHHHHHHHHHHHHcCCcHHHhhccchhhHHHHHHhcCCC--CcEEEecc
Confidence            344567888888888777654 499999999999999999999999999999887654444443333233  35999999


Q ss_pred             cccccCCCC--------CCcEEEEeCCCCCHHHHHHHhcccCCCCCccEEEEEecCCCcC
Q 002040          773 VAARGLDVK--------ELELVINFDAPNHYEDYVHRVGRTGRAGRKGCAITFISEEDAK  824 (976)
Q Consensus       773 v~~~GlDi~--------~v~~VI~~d~p~s~~~y~Qr~GR~gR~g~~g~~~~~~~~~d~~  824 (976)
                      +|+||.||.        +=-+||--..+.|.--..|..||+||.|.+|.+..|++-+|..
T Consensus       685 MAGRGTDIkLg~~V~e~GGL~VIgTerheSrRID~QLrGRaGRQGDPGsS~f~lSLEDdL  744 (1112)
T PRK12901        685 MAGRGTDIKLSPEVKAAGGLAIIGTERHESRRVDRQLRGRAGRQGDPGSSQFYVSLEDNL  744 (1112)
T ss_pred             CcCCCcCcccchhhHHcCCCEEEEccCCCcHHHHHHHhcccccCCCCCcceEEEEcccHH
Confidence            999999997        4468888889999999999999999999999999999876653

>cd00046 DEXDc DEAD-like helicases superfamily

Probab=99.62  E-value=1.1e-14  Score=141.37  Aligned_cols=144  Identities=38%  Similarity=0.568  Sum_probs=110.5

Q ss_pred             CCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHHHHhhcCcEEEEeeCCCChHHHH
Q 002040          505 RDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQI  584 (976)
Q Consensus       505 ~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~~~~~~~~~~~~~~gg~~~~~~~  584 (976)
                      +++++.++||+|||++++.++...+..      ...+++||++|+..|+.|+...+..+... ++.+..+.++.......
T Consensus         1 ~~~~i~~~~G~GKT~~~~~~~~~~~~~------~~~~~~lv~~p~~~l~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~   73 (144)
T cd00046           1 RDVLLAAPTGSGKTLAALLPILELLDS------LKGGQVLVLAPTRELANQVAERLKELFGE-GIKVGYLIGGTSIKQQE   73 (144)
T ss_pred             CCEEEECCCCCchhHHHHHHHHHHHhc------ccCCCEEEEcCcHHHHHHHHHHHHHHhhC-CcEEEEEecCcchhHHH
Confidence            468999999999999988888776554      23568999999999999999998887765 67777777777666555


Q ss_pred             HHHhcCCeEEEeCchhHHHHHHhcCCcccccCCceEEEecCcccccccCCchHHHHHHHhcCCCCcEEEEeccC
Q 002040          585 SELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMGFEPQITRIVQNIRPDRQTVLFSATF  658 (976)
Q Consensus       585 ~~l~~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDEah~~~~~~f~~~i~~il~~~~~~~q~i~~SAT~  658 (976)
                      .....+.+|+|+|++.+...+....   .....+.+|||||+|.+....+...............+++++||||
T Consensus        74 ~~~~~~~~i~i~t~~~~~~~~~~~~---~~~~~~~~iiiDE~h~~~~~~~~~~~~~~~~~~~~~~~~i~~saTp  144 (144)
T cd00046          74 KLLSGKTDIVVGTPGRLLDELERLK---LSLKKLDLLILDEAHRLLNQGFGLLGLKILLKLPKDRQVLLLSATP  144 (144)
T ss_pred             HHhcCCCCEEEECcHHHHHHHHcCC---cchhcCCEEEEeCHHHHhhcchHHHHHHHHhhCCccceEEEEeccC
Confidence            4555678999999999887775432   2345688999999998876654444333445556778899999996

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

>COG0553 HepA Superfamily II DNA/RNA helicases, SNF2 family [Transcription / DNA replication, recombination, and repair]

Probab=99.60  E-value=7.2e-14  Score=178.35  Aligned_cols=121  Identities=25%  Similarity=0.315  Sum_probs=108.1

Q ss_pred             hHHHHHHHHH-HhhhcCC---cEEEEecCHHHHHHHHHHHHHCCCCceeccCCCCHHHHHHHHHHhccC--CccEEEecC
Q 002040          699 DRFLRLLELL-GEWYEKG---KILIFVHSQEKCDALFRDLLKHGYPCLSLHGAKDQTDRESTISDFKSN--VCNLLIATS  772 (976)
Q Consensus       699 ~k~~~l~~~l-~~~~~~~---kvLIF~~s~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g--~~~vLVaT~  772 (976)
                      .|...+..+| ......+   ++|||++.....+.+..+|...++.++.++|.++...|..++..|.++  ...+|++|.
T Consensus       692 ~k~~~l~~ll~~~~~~~~~~~kvlifsq~t~~l~il~~~l~~~~~~~~~ldG~~~~~~r~~~i~~f~~~~~~~v~lls~k  771 (866)
T COG0553         692 GKLQALDELLLDKLLEEGHYHKVLIFSQFTPVLDLLEDYLKALGIKYVRLDGSTPAKRRQELIDRFNADEEEKVFLLSLK  771 (866)
T ss_pred             hHHHHHHHHHHHHHHhhcccccEEEEeCcHHHHHHHHHHHHhcCCcEEEEeCCCChhhHHHHHHHhhcCCCCceEEEEec
Confidence            6777777888 4555444   799999999999999999999999999999999999999999999986  567888899


Q ss_pred             cccccCCCCCCcEEEEeCCCCCHHHHHHHhcccCCCCCccEEEEEec
Q 002040          773 VAARGLDVKELELVINFDAPNHYEDYVHRVGRTGRAGRKGCAITFIS  819 (976)
Q Consensus       773 v~~~GlDi~~v~~VI~~d~p~s~~~y~Qr~GR~gR~g~~g~~~~~~~  819 (976)
                      +++.|||+.++++||+||++|+++...|.+.|++|.|++..+.++-.
T Consensus       772 agg~glnLt~a~~vi~~d~~wnp~~~~Qa~dRa~RigQ~~~v~v~r~  818 (866)
T COG0553         772 AGGLGLNLTGADTVILFDPWWNPAVELQAIDRAHRIGQKRPVKVYRL  818 (866)
T ss_pred             ccccceeecccceEEEeccccChHHHHHHHHHHHHhcCcceeEEEEe
Confidence            99999999999999999999999999999999999999877666543

>KOG1015 consensus Transcription regulator XNP/ATRX, DEAD-box superfamily [Transcription]

Probab=99.60  E-value=3e-14  Score=164.06  Aligned_cols=119  Identities=24%  Similarity=0.257  Sum_probs=101.4

Q ss_pred             HHHHHHHHHHhhhc-CCcEEEEecCHHHHHHHHHHHHHC----------------------CCCceeccCCCCHHHHHHH
Q 002040          700 RFLRLLELLGEWYE-KGKILIFVHSQEKCDALFRDLLKH----------------------GYPCLSLHGAKDQTDREST  756 (976)
Q Consensus       700 k~~~l~~~l~~~~~-~~kvLIF~~s~~~~~~l~~~L~~~----------------------~~~~~~lhg~~~~~~R~~~  756 (976)
                      |+..|+.+|...-. +.++|||.++...++.+..+|.-.                      |.....|.|......|..+
T Consensus      1127 KmiLLleIL~mceeIGDKlLVFSQSL~SLdLIe~fLe~v~r~gk~~~d~~~~~~~eGkW~~GkDyyriDGst~s~~R~k~ 1206 (1567)
T KOG1015|consen 1127 KMILLLEILRMCEEIGDKLLVFSQSLISLDLIEDFLELVSREGKEDKDKPLIYKGEGKWLRGKDYYRLDGSTTSQSRKKW 1206 (1567)
T ss_pred             ceehHHHHHHHHHHhcceeEEeecccchhHHHHHHHHhhcccCccccccccccccccceecCCceEEecCcccHHHHHHH
Confidence            55556667665443 459999999999999999888642                      5567889999999999999


Q ss_pred             HHHhccCC----ccEEEecCcccccCCCCCCcEEEEeCCCCCHHHHHHHhcccCCCCCccEEEEEe
Q 002040          757 ISDFKSNV----CNLLIATSVAARGLDVKELELVINFDAPNHYEDYVHRVGRTGRAGRKGCAITFI  818 (976)
Q Consensus       757 ~~~F~~g~----~~vLVaT~v~~~GlDi~~v~~VI~~d~p~s~~~y~Qr~GR~gR~g~~g~~~~~~  818 (976)
                      ...|++-.    ..+||+|.+++.|||+-.++.||+||..|||+.-+|.|=|+.|.|+..-||+|-
T Consensus      1207 ~~~FNdp~NlRaRl~LISTRAGsLGiNLvAANRVIIfDasWNPSyDtQSIFRvyRfGQtKPvyiYR 1272 (1567)
T KOG1015|consen 1207 AEEFNDPTNLRARLFLISTRAGSLGINLVAANRVIIFDASWNPSYDTQSIFRVYRFGQTKPVYIYR 1272 (1567)
T ss_pred             HHHhcCcccceeEEEEEeeccCccccceeecceEEEEecccCCccchHHHHHHHhhcCcCceeehh
Confidence            99998542    358999999999999999999999999999999999999999999987777653

>KOG0951 consensus RNA helicase BRR2, DEAD-box superfamily [RNA processing and modification]

Probab=99.58  E-value=1.7e-14  Score=171.06  Aligned_cols=311  Identities=17%  Similarity=0.243  Sum_probs=206.5

Q ss_pred             cHHHHHHHHHHhcC-CCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHH-HHHhhcC
Q 002040          491 MPIQAQALPVIMSG-RDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIR-KFAKVMG  568 (976)
Q Consensus       491 ~~~Q~~~i~~il~g-~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~-~~~~~~~  568 (976)
                      .|+|.++++.+.+. .++++++|+|||||+++-++++.         ......+++++|.-+.+..++..|. +|....|
T Consensus      1145 n~iqtqVf~~~y~~nd~v~vga~~gsgkt~~ae~a~l~---------~~~~~~~vyi~p~~~i~~~~~~~w~~~f~~~~G 1215 (1674)
T KOG0951|consen 1145 NPIQTQVFTSLYNTNDNVLVGAPNGSGKTACAELALLR---------PDTIGRAVYIAPLEEIADEQYRDWEKKFSKLLG 1215 (1674)
T ss_pred             CCceEEEEeeeecccceEEEecCCCCchhHHHHHHhcC---------CccceEEEEecchHHHHHHHHHHHHHhhccccC
Confidence            78999999998855 56888899999999998887774         1234579999999999988877765 5666678


Q ss_pred             cEEEEeeCCCChHHHHHHHhcCCeEEEeCchhHHHHHHhcCCcccccCCceEEEecCcccccccC-----CchHHHHHHH
Q 002040          569 VRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMG-----FEPQITRIVQ  643 (976)
Q Consensus       569 ~~~~~~~gg~~~~~~~~~l~~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDEah~~~~~~-----f~~~i~~il~  643 (976)
                      ..++.+.|..+..-   .+....+|+|+||..+- ++.       ..+.+++.|+||+|.+....     ..-.+..|..
T Consensus      1216 ~~~~~l~ge~s~~l---kl~~~~~vii~tpe~~d-~lq-------~iQ~v~l~i~d~lh~igg~~g~v~evi~S~r~ia~ 1284 (1674)
T KOG0951|consen 1216 LRIVKLTGETSLDL---KLLQKGQVIISTPEQWD-LLQ-------SIQQVDLFIVDELHLIGGVYGAVYEVICSMRYIAS 1284 (1674)
T ss_pred             ceEEecCCccccch---HHhhhcceEEechhHHH-HHh-------hhhhcceEeeehhhhhcccCCceEEEEeeHHHHHH
Confidence            88888877766543   33345799999999983 331       45678999999999775221     1112556666


Q ss_pred             hcCCCCcEEEEeccCcHHHHHHHHHHcCCCeEEEeCCcccccCC--ceEEEEecCcchHHHHH----HHHHHh-hhcCCc
Q 002040          644 NIRPDRQTVLFSATFPRQVEILARKVLNKPVEIQVGGRSVVNKD--ITQLVEVRPESDRFLRL----LELLGE-WYEKGK  716 (976)
Q Consensus       644 ~~~~~~q~i~~SAT~~~~~~~l~~~~l~~~~~i~~~~~~~~~~~--i~q~~~~~~~~~k~~~l----~~~l~~-~~~~~k  716 (976)
                      ++-...+++.+|..+.+.-. +  .++...-.+++.....+.+.  -.|.+........+..+    +..+.. ...+.+
T Consensus      1285 q~~k~ir~v~ls~~lana~d-~--ig~s~~~v~Nf~p~~R~~Pl~i~i~~~~~~~~~~~~~am~~~~~~ai~~~a~~~k~ 1361 (1674)
T KOG0951|consen 1285 QLEKKIRVVALSSSLANARD-L--IGASSSGVFNFSPSVRPVPLEIHIQSVDISHFESRMLAMTKPTYTAIVRHAGNRKP 1361 (1674)
T ss_pred             HHHhheeEEEeehhhccchh-h--ccccccceeecCcccCCCceeEEEEEeccchhHHHHHHhhhhHHHHHHHHhcCCCC
Confidence            77777788888887654322 2  11122222222211111111  12222222222222221    222222 234568


Q ss_pred             EEEEecCHHHHHHHHHHHHHC----------------------CCCceeccCCCCHHHHHHHHHHhccCCccEEEecCcc
Q 002040          717 ILIFVHSQEKCDALFRDLLKH----------------------GYPCLSLHGAKDQTDRESTISDFKSNVCNLLIATSVA  774 (976)
Q Consensus       717 vLIF~~s~~~~~~l~~~L~~~----------------------~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLVaT~v~  774 (976)
                      .+||+++.+.|..++..|...                      .+++++-|.+++..+...+-..|..|.+.|+|...- 
T Consensus      1362 ~~vf~p~rk~~~~~a~~~~~~s~~~~~~~l~~~~e~~~~~l~e~l~~gvg~e~~s~~d~~iv~~l~e~g~i~v~v~s~~- 1440 (1674)
T KOG0951|consen 1362 AIVFLPTRKHARLVAVDLVTFSHADEPDYLLSELEECDETLRESLKHGVGHEGLSSNDQEIVQQLFEAGAIQVCVMSRD- 1440 (1674)
T ss_pred             eEEEeccchhhhhhhhccchhhccCcHHHHHHHHhcchHhhhhcccccccccccCcchHHHHHHHHhcCcEEEEEEEcc-
Confidence            999999999998777665432                      234444499999999999999999999999998766 


Q ss_pred             cccCCCCCCcEEEE----eCC------CCCHHHHHHHhcccCCCCCccEEEEEecCCCcCchHH
Q 002040          775 ARGLDVKELELVIN----FDA------PNHYEDYVHRVGRTGRAGRKGCAITFISEEDAKYSPD  828 (976)
Q Consensus       775 ~~GlDi~~v~~VI~----~d~------p~s~~~y~Qr~GR~gR~g~~g~~~~~~~~~d~~~~~~  828 (976)
                      ..|+-...--+||.    ||-      +..++...|++|+|.|   .|.|++++......++..
T Consensus      1441 ~~~~~~~~~lVvvmgt~~ydg~e~~~~~y~i~~ll~m~G~a~~---~~k~vi~~~~~~k~yykk 1501 (1674)
T KOG0951|consen 1441 CYGTKLKAHLVVVMGTQYYDGKEHSYEDYPIAELLQMVGLASG---AGKCVIMCHTPKKEYYKK 1501 (1674)
T ss_pred             cccccccceEEEEecceeecccccccccCchhHHHHHhhhhcC---CccEEEEecCchHHHHHH
Confidence            77777654444442    433      4457889999999988   567888887665555443

>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=99.57  E-value=1e-14  Score=149.30  Aligned_cols=156  Identities=19%  Similarity=0.171  Sum_probs=101.7

Q ss_pred             CCcHHHHHHHHHHhc-------CCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHH
Q 002040          489 KPMPIQAQALPVIMS-------GRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIR  561 (976)
Q Consensus       489 ~p~~~Q~~~i~~il~-------g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~  561 (976)
                      +|+++|.+++..+..       +..+++.++||||||.+++..+.....           ++||+||+..|+.|+...|.
T Consensus         3 ~lr~~Q~~ai~~i~~~~~~~~~~~~~ll~~~tGsGKT~~~~~~~~~l~~-----------~~l~~~p~~~l~~Q~~~~~~   71 (184)
T PF04851_consen    3 KLRPYQQEAIARIINSLENKKEERRVLLNAPTGSGKTIIALALILELAR-----------KVLIVAPNISLLEQWYDEFD   71 (184)
T ss_dssp             EE-HHHHHHHHHHHHHHHTTSGCSEEEEEESTTSSHHHHHHHHHHHHHC-----------EEEEEESSHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHHHHhcCCCCCEEEEECCCCCcChhhhhhhhcccc-----------ceeEecCHHHHHHHHHHHHH
Confidence            478999999999883       588999999999999987765555432           68999999999999999997


Q ss_pred             HHHhhcCcEEEE-----------eeCCCChHHHHHHHhcCCeEEEeCchhHHHHHHhcCC--------cccccCCceEEE
Q 002040          562 KFAKVMGVRCVP-----------VYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGG--------KITNLRRVTYLV  622 (976)
Q Consensus       562 ~~~~~~~~~~~~-----------~~gg~~~~~~~~~l~~~~~Iiv~Tp~~L~~~l~~~~~--------~~~~l~~~~~vV  622 (976)
                      .+..........           ...................|+++|...|...+.....        .......+.+||
T Consensus        72 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~vI  151 (184)
T PF04851_consen   72 DFGSEKYNFFEKSIKPAYDSKEFISIQDDISDKSESDNNDKDIILTTYQSLQSDIKEEKKIDESARRSYKLLKNKFDLVI  151 (184)
T ss_dssp             HHSTTSEEEEE--GGGCCE-SEEETTTTEEEHHHHHCBSS-SEEEEEHHHHHHHHHH---------GCHHGGGGSESEEE
T ss_pred             HhhhhhhhhcccccccccccccccccccccccccccccccccchhhHHHHHHhhcccccccccchhhhhhhccccCCEEE
Confidence            665432111111           0111111111122234578999999999877654211        112345678999


Q ss_pred             ecCcccccccCCchHHHHHHHhcCCCCcEEEEeccCcH
Q 002040          623 MDEADRMFDMGFEPQITRIVQNIRPDRQTVLFSATFPR  660 (976)
Q Consensus       623 lDEah~~~~~~f~~~i~~il~~~~~~~q~i~~SAT~~~  660 (976)
                      +||||++....   .+..++.  .+...+|+|||||++
T Consensus       152 ~DEaH~~~~~~---~~~~i~~--~~~~~~l~lTATp~r  184 (184)
T PF04851_consen  152 IDEAHHYPSDS---SYREIIE--FKAAFILGLTATPFR  184 (184)
T ss_dssp             EETGGCTHHHH---HHHHHHH--SSCCEEEEEESS-S-
T ss_pred             EehhhhcCCHH---HHHHHHc--CCCCeEEEEEeCccC
Confidence            99999865432   1444444  566779999999863

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 ....

>TIGR00604 rad3 DNA repair helicase (rad3)

Probab=99.56  E-value=1.8e-12  Score=159.42  Aligned_cols=74  Identities=23%  Similarity=0.364  Sum_probs=62.3

Q ss_pred             cCCCCCcHHHHHHHHHHh----cCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHH
Q 002040          485 LNYEKPMPIQAQALPVIM----SGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDI  560 (976)
Q Consensus       485 ~~~~~p~~~Q~~~i~~il----~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~  560 (976)
                      +.|..++|.|.+.+..+.    .+.++|+.+|||+|||++.+.|++.++...+     ..+++++++.|..-..|+.+++
T Consensus         6 FPy~~~y~~Q~~~m~~v~~~l~~~~~~llEsPTGtGKTlslL~~aL~~~~~~~-----~~~kIiy~sRThsQl~q~i~El   80 (705)
T TIGR00604         6 FPYEKIYPEQRSYMRDLKRSLDRGDEAILEMPSGTGKTISLLSLILAYQQEKP-----EVRKIIYASRTHSQLEQATEEL   80 (705)
T ss_pred             cCCCCCCHHHHHHHHHHHHHhccCCceEEeCCCCCCccHHHHHHHHHHHHhcc-----ccccEEEEcccchHHHHHHHHH
Confidence            567778999998887654    6789999999999999999999998876532     3468999999998889999999


Q ss_pred             HHH
Q 002040          561 RKF  563 (976)
Q Consensus       561 ~~~  563 (976)
                      ++.
T Consensus        81 k~~   83 (705)
T TIGR00604        81 RKL   83 (705)
T ss_pred             Hhh
Confidence            884

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).

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

Probab=99.56  E-value=1.7e-12  Score=159.55  Aligned_cols=117  Identities=21%  Similarity=0.260  Sum_probs=82.6

Q ss_pred             HHHHHHHHHhhh--cCCcEEEEecCHHHHHHHHHHHHHCCCC-ceeccCCCCHHHHHHHHHHhccCCc-cEEEecCcccc
Q 002040          701 FLRLLELLGEWY--EKGKILIFVHSQEKCDALFRDLLKHGYP-CLSLHGAKDQTDRESTISDFKSNVC-NLLIATSVAAR  776 (976)
Q Consensus       701 ~~~l~~~l~~~~--~~~kvLIF~~s~~~~~~l~~~L~~~~~~-~~~lhg~~~~~~R~~~~~~F~~g~~-~vLVaT~v~~~  776 (976)
                      ...+...|....  .++++|||++|...+..+...|...... .+..+|..+.   ..+++.|..+.- .|||+|..++.
T Consensus       464 ~~~~~~~i~~~~~~~~~~~lvlF~Sy~~l~~~~~~~~~~~~~~~v~~q~~~~~---~~~l~~f~~~~~~~~lv~~gsf~E  540 (654)
T COG1199         464 LAKLAAYLREILKASPGGVLVLFPSYEYLKRVAERLKDERSTLPVLTQGEDER---EELLEKFKASGEGLILVGGGSFWE  540 (654)
T ss_pred             HHHHHHHHHHHHhhcCCCEEEEeccHHHHHHHHHHHhhcCccceeeecCCCcH---HHHHHHHHHhcCCeEEEeeccccC
Confidence            333444443332  3568999999999999999999876542 4455555443   377888876554 89999999999


Q ss_pred             cCCCCC--CcEEEEeCCCCC------------------------------HHHHHHHhcccCCCCCccEEEEEecC
Q 002040          777 GLDVKE--LELVINFDAPNH------------------------------YEDYVHRVGRTGRAGRKGCAITFISE  820 (976)
Q Consensus       777 GlDi~~--v~~VI~~d~p~s------------------------------~~~y~Qr~GR~gR~g~~g~~~~~~~~  820 (976)
                      |||+++  +.+||+...|.-                              +....|.+||+-|.-....++++++.
T Consensus       541 GVD~~g~~l~~vvI~~lPfp~p~dp~~~~r~~~~~~~g~~~f~~~~l~~A~~~l~QavGRlIR~~~D~G~ivllD~  616 (654)
T COG1199         541 GVDFPGDALRLVVIVGLPFPNPDDPLLKARLEFLKRLGGDPFEEFYLPPAVIKLRQAVGRLIRSEDDRGVIVLLDK  616 (654)
T ss_pred             cccCCCCCeeEEEEEecCCCCCCCHHHHHHHHHHHHhcCCCceEeehHHHHHHHHHhhccccccCCCceEEEEecc
Confidence            999998  577888776642                              23346999999997555444445544

>PRK11747 dinG ATP-dependent DNA helicase DinG; Provisional

Probab=99.55  E-value=3.3e-12  Score=155.81  Aligned_cols=116  Identities=22%  Similarity=0.296  Sum_probs=82.2

Q ss_pred             CCcEEEEecCHHHHHHHHHHHHHC-CCCceeccCCCCHHHHHHHHHHhc----cCCccEEEecCcccccCCCCC--CcEE
Q 002040          714 KGKILIFVHSQEKCDALFRDLLKH-GYPCLSLHGAKDQTDRESTISDFK----SNVCNLLIATSVAARGLDVKE--LELV  786 (976)
Q Consensus       714 ~~kvLIF~~s~~~~~~l~~~L~~~-~~~~~~lhg~~~~~~R~~~~~~F~----~g~~~vLVaT~v~~~GlDi~~--v~~V  786 (976)
                      .+.+|||++|...+..++..|... ++. +.++|..   .+..++..|+    .|...||++|..+..|||+|+  +.+|
T Consensus       534 ~gg~LVlFtSy~~l~~v~~~l~~~~~~~-ll~Q~~~---~~~~ll~~f~~~~~~~~~~VL~g~~sf~EGVD~pGd~l~~v  609 (697)
T PRK11747        534 HKGSLVLFASRRQMQKVADLLPRDLRLM-LLVQGDQ---PRQRLLEKHKKRVDEGEGSVLFGLQSFAEGLDLPGDYLTQV  609 (697)
T ss_pred             CCCEEEEeCcHHHHHHHHHHHHHhcCCc-EEEeCCc---hHHHHHHHHHHHhccCCCeEEEEeccccccccCCCCceEEE
Confidence            557999999999999999998743 333 4456643   4667776665    467789999999999999998  7889


Q ss_pred             EEeCCCC----CHH--------------------------HHHHHhcccCCCCCccEEEEEecCC--CcCchHHHHHHH
Q 002040          787 INFDAPN----HYE--------------------------DYVHRVGRTGRAGRKGCAITFISEE--DAKYSPDLVKAL  833 (976)
Q Consensus       787 I~~d~p~----s~~--------------------------~y~Qr~GR~gR~g~~g~~~~~~~~~--d~~~~~~i~~~l  833 (976)
                      |+...|.    ++.                          .+.|.+||+-|....-.+++++++.  ...|-..+++.|
T Consensus       610 II~kLPF~~p~dp~~~ar~~~~~~~g~~~F~~~~lP~A~~kl~Qg~GRlIRs~~D~G~i~ilD~R~~~~~Yg~~~l~sL  688 (697)
T PRK11747        610 IITKIPFAVPDSPVEATLAEWLKSRGGNPFMEISVPDASFKLIQAVGRLIRSEQDRGRVTILDRRLLTKRYGKRLLDAL  688 (697)
T ss_pred             EEEcCCCCCCCCHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHhccccccCCceEEEEEEcccccchhHHHHHHHhC
Confidence            9877653    221                          1248899999986554455555543  334555665554

>PRK14873 primosome assembly protein PriA; Provisional

Probab=99.52  E-value=1.3e-12  Score=156.21  Aligned_cols=272  Identities=11%  Similarity=0.122  Sum_probs=165.3

Q ss_pred             cCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHHHHhhcCcEEEEeeCCCChHHHH---HHH
Q 002040          511 AKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQI---SEL  587 (976)
Q Consensus       511 a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~~~~~~~~~~~~~~gg~~~~~~~---~~l  587 (976)
                      +-+|||||.+|+-.+-..+..        |..+|||+|...|+.|+...|+..+.  +..++.++++.+..+..   ..+
T Consensus       167 ~~~GSGKTevyl~~i~~~l~~--------Gk~vLvLvPEi~lt~q~~~rl~~~f~--~~~v~~lhS~l~~~~R~~~w~~~  236 (665)
T PRK14873        167 ALPGEDWARRLAAAAAATLRA--------GRGALVVVPDQRDVDRLEAALRALLG--AGDVAVLSAGLGPADRYRRWLAV  236 (665)
T ss_pred             cCCCCcHHHHHHHHHHHHHHc--------CCeEEEEecchhhHHHHHHHHHHHcC--CCcEEEECCCCCHHHHHHHHHHH
Confidence            336999999988777666553        66799999999999999998887642  26688888888766553   333


Q ss_pred             hcC-CeEEEeCchhHHHHHHhcCCcccccCCceEEEecCcccccc-cC----CchHHHHHHHhcCCCCcEEEEeccCcHH
Q 002040          588 KRG-TEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFD-MG----FEPQITRIVQNIRPDRQTVLFSATFPRQ  661 (976)
Q Consensus       588 ~~~-~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDEah~~~~-~~----f~~~i~~il~~~~~~~q~i~~SAT~~~~  661 (976)
                      ..| ..|||+|-..+          +..+.++++|||||-|--.. .+    |...-..++.....+..+|+.|||++-.
T Consensus       237 ~~G~~~IViGtRSAv----------FaP~~~LgLIIvdEEhd~sykq~~~p~yhaRdvA~~Ra~~~~~~lvLgSaTPSle  306 (665)
T PRK14873        237 LRGQARVVVGTRSAV----------FAPVEDLGLVAIWDDGDDLLAEPRAPYPHAREVALLRAHQHGCALLIGGHARTAE  306 (665)
T ss_pred             hCCCCcEEEEcceeE----------EeccCCCCEEEEEcCCchhhcCCCCCCccHHHHHHHHHHHcCCcEEEECCCCCHH
Confidence            444 68999996654          25788899999999994321 11    1222223344445678899999999766


Q ss_pred             HHHHHHHHcCCCeEEEeCCccc--ccCCceEEEEecC------cch----HHHHHHHHHHhhhcCCcEEEEecCHHHHHH
Q 002040          662 VEILARKVLNKPVEIQVGGRSV--VNKDITQLVEVRP------ESD----RFLRLLELLGEWYEKGKILIFVHSQEKCDA  729 (976)
Q Consensus       662 ~~~l~~~~l~~~~~i~~~~~~~--~~~~i~q~~~~~~------~~~----k~~~l~~~l~~~~~~~kvLIF~~s~~~~~~  729 (976)
                      ....+...  ....+.......  ..+.+ ..+....      ...    --..++..|.+....|++|||+|.+..+-.
T Consensus       307 s~~~~~~g--~~~~~~~~~~~~~~~~P~v-~~vd~~~~~~~~~~~~~g~~ls~~l~~~i~~~L~~gqvll~lnRrGyap~  383 (665)
T PRK14873        307 AQALVESG--WAHDLVAPRPVVRARAPRV-RALGDSGLALERDPAARAARLPSLAFRAARDALEHGPVLVQVPRRGYVPS  383 (665)
T ss_pred             HHHHHhcC--cceeeccccccccCCCCeE-EEEeCchhhhccccccccCccCHHHHHHHHHHHhcCcEEEEecCCCCCCe
Confidence            54433321  111111110000  00111 1111100      000    113466667766666799999997654322


Q ss_pred             HH-----------------------------------------------------------HHHHHC--CCCceeccCCC
Q 002040          730 LF-----------------------------------------------------------RDLLKH--GYPCLSLHGAK  748 (976)
Q Consensus       730 l~-----------------------------------------------------------~~L~~~--~~~~~~lhg~~  748 (976)
                      |.                                                           +.|...  +.++..+    
T Consensus       384 l~C~~Cg~~~~C~~C~~~L~~h~~~~~l~Ch~CG~~~~p~~Cp~Cgs~~l~~~g~Gter~eeeL~~~FP~~~V~r~----  459 (665)
T PRK14873        384 LACARCRTPARCRHCTGPLGLPSAGGTPRCRWCGRAAPDWRCPRCGSDRLRAVVVGARRTAEELGRAFPGVPVVTS----  459 (665)
T ss_pred             eEhhhCcCeeECCCCCCceeEecCCCeeECCCCcCCCcCccCCCCcCCcceeeeccHHHHHHHHHHHCCCCCEEEE----
Confidence            11                                                           111110  1111111    


Q ss_pred             CHHHHHHHHHHhccCCccEEEecC----cccccCCCCCCcEEEEeCCCC------------CHHHHHHHhcccCCCCCcc
Q 002040          749 DQTDRESTISDFKSNVCNLLIATS----VAARGLDVKELELVINFDAPN------------HYEDYVHRVGRTGRAGRKG  812 (976)
Q Consensus       749 ~~~~R~~~~~~F~~g~~~vLVaT~----v~~~GlDi~~v~~VI~~d~p~------------s~~~y~Qr~GR~gR~g~~g  812 (976)
                         +++.++..|. ++.+|||+|.    ++.     +++.+|+++|...            ...-+.|.+||+||.+..|
T Consensus       460 ---d~d~~l~~~~-~~~~IlVGTqgaepm~~-----g~~~lV~ildaD~~L~~pDfRA~Er~~qll~qvagragr~~~~G  530 (665)
T PRK14873        460 ---GGDQVVDTVD-AGPALVVATPGAEPRVE-----GGYGAALLLDAWALLGRQDLRAAEDTLRRWMAAAALVRPRADGG  530 (665)
T ss_pred             ---ChHHHHHhhc-cCCCEEEECCCCccccc-----CCceEEEEEcchhhhcCCCcChHHHHHHHHHHHHHhhcCCCCCC
Confidence               2345778886 5899999998    555     3667777766532            1344578899999998899


Q ss_pred             EEEEEe
Q 002040          813 CAITFI  818 (976)
Q Consensus       813 ~~~~~~  818 (976)
                      .+++..
T Consensus       531 ~V~iq~  536 (665)
T PRK14873        531 QVVVVA  536 (665)
T ss_pred             EEEEEe
Confidence            998864

>TIGR02562 cas3_yersinia CRISPR-associated helicase Cas3

Probab=99.52  E-value=5.5e-13  Score=160.30  Aligned_cols=313  Identities=22%  Similarity=0.238  Sum_probs=178.0

Q ss_pred             CCCcHHHHHHHHHHhc--------CCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHH
Q 002040          488 EKPMPIQAQALPVIMS--------GRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSD  559 (976)
Q Consensus       488 ~~p~~~Q~~~i~~il~--------g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~  559 (976)
                      ...+.+|-.|+..+..        |-=+|-.|.||||||++=+-.|. .|..     ...|.+..|..-.|.|..|.-..
T Consensus       407 ~~rF~WQdkA~d~a~~~r~~~~~~GfF~vNMASTGcGKT~aNARImy-aLsd-----~~~g~RfsiALGLRTLTLQTGda  480 (1110)
T TIGR02562       407 HPRFRWQNKAFNLAQKLRQKSPEQGAFGVNMASTGCGKTLANARAMY-ALRD-----DKQGARFAIALGLRSLTLQTGHA  480 (1110)
T ss_pred             CCCcchHHHHHHHHHHHHhhcccCCeEEEEecCCCcchHHHHHHHHH-HhCC-----CCCCceEEEEccccceeccchHH
Confidence            3456789999988764        12255569999999987443333 3332     23466777777888888888777


Q ss_pred             HHHHHhhcCcEEEEeeCCCChHHHHH-------------------------------------------HHhc-------
Q 002040          560 IRKFAKVMGVRCVPVYGGSGVAQQIS-------------------------------------------ELKR-------  589 (976)
Q Consensus       560 ~~~~~~~~~~~~~~~~gg~~~~~~~~-------------------------------------------~l~~-------  589 (976)
                      ++.-...-.-.+.+++||....+...                                           .+..       
T Consensus       481 ~r~rL~L~~ddLAVlIGs~Av~~L~e~~~~~~~~~~~~GSeS~e~l~~e~~~~~~~~~~g~l~~~~l~~~l~~~~k~~rl  560 (1110)
T TIGR02562       481 LKTRLNLSDDDLAVLIGGTAVQTLFDLSKEKIEQVDEDGSESAPIFLAEGQDCNLPDWDGPLDTIELLGRLSLDDKEKTL  560 (1110)
T ss_pred             HHHhcCCCccceEEEECHHHHHHHHHHHhhhccccccCCCccchhhhcccCcCCeeeccCCccchhhhhhhccChhhhhh
Confidence            77654433444555555433221110                                           0000       


Q ss_pred             -CCeEEEeCchhHHHHHHhcC--CcccccC--CceEEEecCcccccccCCchHHHHHHHhc-CCCCcEEEEeccCcHHHH
Q 002040          590 -GTEIVVCTPGRMIDILCTSG--GKITNLR--RVTYLVMDEADRMFDMGFEPQITRIVQNI-RPDRQTVLFSATFPRQVE  663 (976)
Q Consensus       590 -~~~Iiv~Tp~~L~~~l~~~~--~~~~~l~--~~~~vVlDEah~~~~~~f~~~i~~il~~~-~~~~q~i~~SAT~~~~~~  663 (976)
                       ...|+|||+..++.......  .....+-  .-+.|||||+|.+-... ...+..++..+ .....+|+||||+|+.+.
T Consensus       561 l~apv~V~TIDQlL~a~~~~r~~~~~l~ll~La~svlVlDEVHaYD~~~-~~~L~rlL~w~~~lG~~VlLmSATLP~~l~  639 (1110)
T TIGR02562       561 LAAPVLVCTIDHLIPATESHRGGHHIAPMLRLMSSDLILDEPDDYEPED-LPALLRLVQLAGLLGSRVLLSSATLPPALV  639 (1110)
T ss_pred             hcCCeEEecHHHHHHHhhhcccchhHHHHHHhcCCCEEEECCccCCHHH-HHHHHHHHHHHHHcCCCEEEEeCCCCHHHH
Confidence             25799999999887663221  1111111  12579999999642211 12233333311 235679999999999764


Q ss_pred             HH-HHH----------HcCC---CeEEEe---CCcccc--------------------------cCCc---eEEEEecCc
Q 002040          664 IL-ARK----------VLNK---PVEIQV---GGRSVV--------------------------NKDI---TQLVEVRPE  697 (976)
Q Consensus       664 ~l-~~~----------~l~~---~~~i~~---~~~~~~--------------------------~~~i---~q~~~~~~~  697 (976)
                      .. ...          ..+.   ++.|..   ......                          ...+   -..+.+...
T Consensus       640 ~~L~~Ay~~G~~~~q~~~g~~~~~~~i~CaW~DE~~~~~~~~~~~~~F~~~H~~Fv~~R~~~L~~~p~~R~a~i~~~~~~  719 (1110)
T TIGR02562       640 KTLFRAYEAGRQMYQALYGQPKKPLNICCAWVDEPQVWQADCNQKSEFIQRHQDFLRDRAVQLAKKPVRRLAELLSLSSL  719 (1110)
T ss_pred             HHHHHHHHHHHHHHHHhcCCCCCCcceeEEeecccCchhhhhcCHHHHHHHHHHHHHHHHHHHhcCcccceEEEeecCCc
Confidence            32 222          2222   111110   000000                          0001   111111111


Q ss_pred             c----hHHHHHHHHH----Hhhh-------c-CCc----EEEEecCHHHHHHHHHHHHHC------CCCceeccCCCCHH
Q 002040          698 S----DRFLRLLELL----GEWY-------E-KGK----ILIFVHSQEKCDALFRDLLKH------GYPCLSLHGAKDQT  751 (976)
Q Consensus       698 ~----~k~~~l~~~l----~~~~-------~-~~k----vLIF~~s~~~~~~l~~~L~~~------~~~~~~lhg~~~~~  751 (976)
                      .    .....+...|    ...+       + .++    .||-+.++..+..++..|...      .+.+++||+..+..
T Consensus       720 ~~~~~~~~~~~a~~i~~~~~~LH~~h~~~~~~sgk~VSfGliR~anI~p~V~~A~~L~~~~~~~~~~i~~~~yHSr~~l~  799 (1110)
T TIGR02562       720 PRENESTYLALAQSLLEGALRLHQAHAQTDPKSEKKVSVGLIRVANIDPLIRLAQFLYALLAEEKYQIHLCCYHAQDPLL  799 (1110)
T ss_pred             ccchhHHHHHHHHHHHHHHHHHHHHhCccCCCCCeEEEEEEEEEcCchHHHHHHHHHHhhccccCCceeEEEecccChHH
Confidence            1    1222222222    1111       1 122    478888888888888888754      24578899999888


Q ss_pred             HHHHHHHHh----------------------cc----CCccEEEecCcccccCCCCCCcEEEEeCCCCCHHHHHHHhccc
Q 002040          752 DRESTISDF----------------------KS----NVCNLLIATSVAARGLDVKELELVINFDAPNHYEDYVHRVGRT  805 (976)
Q Consensus       752 ~R~~~~~~F----------------------~~----g~~~vLVaT~v~~~GlDi~~v~~VI~~d~p~s~~~y~Qr~GR~  805 (976)
                      .|..+.+..                      .+    +...|+|||++++.|+|+. .+++|  .-|.++...+|++||+
T Consensus       800 ~Rs~~E~~Ld~~L~R~~~~~~~~~~~i~~~l~~~~~~~~~~i~v~Tqv~E~g~D~d-fd~~~--~~~~~~~sliQ~aGR~  876 (1110)
T TIGR02562       800 LRSYIERRLDQLLTRHKPEQLFQDDEIIDLMQNSPALNHLFIVLATPVEEVGRDHD-YDWAI--ADPSSMRSIIQLAGRV  876 (1110)
T ss_pred             HHHHHHHHHHHHhcccChhhhhchHHHHHHHhcccccCCCeEEEEeeeEEEEeccc-CCeee--eccCcHHHHHHHhhcc
Confidence            777655442                      12    4668999999999999994 55554  3456688999999999


Q ss_pred             CCCCC
Q 002040          806 GRAGR  810 (976)
Q Consensus       806 gR~g~  810 (976)
                      .|.|.
T Consensus       877 ~R~~~  881 (1110)
T TIGR02562       877 NRHRL  881 (1110)
T ss_pred             ccccc
Confidence            99764

The helicase in many CRISPR-associated (cas) gene clusters is designated Cas3, and most Cas3 proteins are described by model TIGR01587. Members of this family are considerably larger, show a number of motifs in common with TIGR01587 sequences, and replace Cas3 in some CRISPR/cas loci in a number of Proteobacteria, including Yersinia pestis, Chromobacterium violaceum, Erwinia carotovora subsp. atroseptica SCRI1043, Photorhabdus luminescens subsp. laumondii TTO1, Legionella pneumophila, etc.

>smart00490 HELICc helicase superfamily c-terminal domain

Probab=99.47  E-value=1.3e-13  Score=120.73  Aligned_cols=81  Identities=40%  Similarity=0.651  Sum_probs=77.4

Q ss_pred             HHHHHHHHCCCCceeccCCCCHHHHHHHHHHhccCCccEEEecCcccccCCCCCCcEEEEeCCCCCHHHHHHHhcccCCC
Q 002040          729 ALFRDLLKHGYPCLSLHGAKDQTDRESTISDFKSNVCNLLIATSVAARGLDVKELELVINFDAPNHYEDYVHRVGRTGRA  808 (976)
Q Consensus       729 ~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLVaT~v~~~GlDi~~v~~VI~~d~p~s~~~y~Qr~GR~gR~  808 (976)
                      .++..|...++.+..+||.++..++..++..|..|...|||+|++++.|+|++.+++||++++|+++..|.|++||++|.
T Consensus         2 ~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vli~t~~~~~Gi~~~~~~~vi~~~~~~~~~~~~Q~~gR~~R~   81 (82)
T smart00490        2 ELAELLKELGIKVARLHGGLSQEEREEILEKFNNGKIKVLVATDVAERGLDLPGVDLVIIYDLPWSPASYIQRIGRAGRA   81 (82)
T ss_pred             HHHHHHHHCCCeEEEEECCCCHHHHHHHHHHHHcCCCeEEEECChhhCCcChhcCCEEEEeCCCCCHHHHHHhhcccccC
Confidence            46777888899999999999999999999999999999999999999999999999999999999999999999999997


Q ss_pred             C
Q 002040          809 G  809 (976)
Q Consensus       809 g  809 (976)
                      |
T Consensus        82 g   82 (82)
T smart00490       82 G   82 (82)
T ss_pred             C
Confidence            6

>COG0610 Type I site-specific restriction-modification system, R (restriction) subunit and related helicases [Defense mechanisms]

Probab=99.42  E-value=4.9e-11  Score=149.12  Aligned_cols=308  Identities=19%  Similarity=0.253  Sum_probs=177.4

Q ss_pred             CCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHHHHhhcCcEEEEeeCCCChHHHH
Q 002040          505 RDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQI  584 (976)
Q Consensus       505 ~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~~~~~~~~~~~~~~gg~~~~~~~  584 (976)
                      +..+|+.-||||||++.+..+ ..+...     ...|.|+|||-++.|-.|+.++|..+........    ...+.....
T Consensus       274 ~~G~IWHtqGSGKTlTm~~~A-~~l~~~-----~~~~~v~fvvDR~dLd~Q~~~~f~~~~~~~~~~~----~~~s~~~Lk  343 (962)
T COG0610         274 KGGYIWHTQGSGKTLTMFKLA-RLLLEL-----PKNPKVLFVVDRKDLDDQTSDEFQSFGKVAFNDP----KAESTSELK  343 (962)
T ss_pred             CceEEEeecCCchHHHHHHHH-HHHHhc-----cCCCeEEEEechHHHHHHHHHHHHHHHHhhhhcc----cccCHHHHH
Confidence            469999999999999854443 333332     3578999999999999999999999876543222    233344444


Q ss_pred             HHHhcC-CeEEEeCchhHHHHHHhcCCcccccCCceEEEecCcccccccCCchHHHHHHHhcCCCCcEEEEeccCcHHHH
Q 002040          585 SELKRG-TEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMGFEPQITRIVQNIRPDRQTVLFSATFPRQVE  663 (976)
Q Consensus       585 ~~l~~~-~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDEah~~~~~~f~~~i~~il~~~~~~~q~i~~SAT~~~~~~  663 (976)
                      ..+..+ ..|||+|-..|...+...... ..-..--+||+|||||.-   ++.....+-..+ ++...++||+||--.-.
T Consensus       344 ~~l~~~~~~ii~TTIQKf~~~~~~~~~~-~~~~~~ivvI~DEaHRSQ---~G~~~~~~~~~~-~~a~~~gFTGTPi~~~d  418 (962)
T COG0610         344 ELLEDGKGKIIVTTIQKFNKAVKEDELE-LLKRKNVVVIIDEAHRSQ---YGELAKLLKKAL-KKAIFIGFTGTPIFKED  418 (962)
T ss_pred             HHHhcCCCcEEEEEecccchhhhccccc-ccCCCcEEEEEechhhcc---ccHHHHHHHHHh-ccceEEEeeCCcccccc
Confidence            445444 489999999998777543111 112223478999999853   343333333333 44779999999743322


Q ss_pred             HH-HHHHcCCCeEEEeCCcccccCCceEEEEecC-------cc--------------------h----------------
Q 002040          664 IL-ARKVLNKPVEIQVGGRSVVNKDITQLVEVRP-------ES--------------------D----------------  699 (976)
Q Consensus       664 ~l-~~~~l~~~~~i~~~~~~~~~~~i~q~~~~~~-------~~--------------------~----------------  699 (976)
                      .. ....++.++.............+...+....       ..                    .                
T Consensus       419 ~~tt~~~fg~ylh~Y~i~daI~Dg~vl~i~y~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~~~~~~  498 (962)
T COG0610         419 KDTTKDVFGDYLHTYTITDAIRDGAVLPVYYENRVELELIEESIKEEAEELDERIEEITEDILEKIKKKTKNLEFLAMLA  498 (962)
T ss_pred             ccchhhhhcceeEEEecchhhccCceeeEEEeecccccccccchhhhhhhhHHHHhhhHHHHHHHHHHHHhhhhHHhcch
Confidence            22 2334444443332222111111111110000       00                    0                


Q ss_pred             -HHHH----HHHHHHh-hhcCCcEEEEecCHHHHHHHHHHHHHC-----------C--------C----CceeccCCCCH
Q 002040          700 -RFLR----LLELLGE-WYEKGKILIFVHSQEKCDALFRDLLKH-----------G--------Y----PCLSLHGAKDQ  750 (976)
Q Consensus       700 -k~~~----l~~~l~~-~~~~~kvLIF~~s~~~~~~l~~~L~~~-----------~--------~----~~~~lhg~~~~  750 (976)
                       +...    +...+.. .....++++.|.+...|..+.+.+...           +        +    .....|... .
T Consensus       499 ~r~~~~a~~i~~~f~~~~~~~~kam~V~~sr~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~-~  577 (962)
T COG0610         499 VRLIRAAKDIYDHFKKEEVFDLKAMVVASSRKVAVELYEAEIAARLDWHSKESLEGAIKDYNTEFETDFDKKQSHAKL-K  577 (962)
T ss_pred             HHHHHHHHHHHHHHHhhcccCceEEEEEechHHHHHhHHHHhhhhhhhhhhhhhhhHHHHHHhhcccchhhhhhhHHH-H
Confidence             0000    0111111 112357888888887555555443321           0        0    000001111 1


Q ss_pred             HHHHHHHHHh--ccCCccEEEecCcccccCCCCCCcEEEEeCCCCCHHHHHHHhcccCCC--C--CccEEEEEecCCCcC
Q 002040          751 TDRESTISDF--KSNVCNLLIATSVAARGLDVKELELVINFDAPNHYEDYVHRVGRTGRA--G--RKGCAITFISEEDAK  824 (976)
Q Consensus       751 ~~R~~~~~~F--~~g~~~vLVaT~v~~~GlDi~~v~~VI~~d~p~s~~~y~Qr~GR~gR~--g--~~g~~~~~~~~~d~~  824 (976)
                      .........|  .....+|||.++.+-+|+|.|.++++. +|-|.-....+|.+.|+.|.  +  ..|.++.|+.     
T Consensus       578 ~~~~~~~~r~~~~~d~~kilIV~dmlLTGFDaP~L~TmY-vDK~Lk~H~L~QAisRtNR~~~~~K~~G~IVDf~g-----  651 (962)
T COG0610         578 DEKKDLIKRFKLKDDPLDLLIVVDMLLTGFDAPCLNTLY-VDKPLKYHNLIQAISRTNRVFPGKKKFGLIVDFRG-----  651 (962)
T ss_pred             HHHhhhhhhhcCcCCCCCEEEEEccccccCCccccceEE-eccccccchHHHHHHHhccCCCCCCCCcEEEECcc-----
Confidence            2223334443  456789999999999999999999888 78888889999999999995  3  2355555554     


Q ss_pred             chHHHHHHHh
Q 002040          825 YSPDLVKALE  834 (976)
Q Consensus       825 ~~~~i~~~l~  834 (976)
                      ....+.+++.
T Consensus       652 l~e~l~~Al~  661 (962)
T COG0610         652 LKEALKKALK  661 (962)
T ss_pred             hHHHHHHHHH
Confidence            4555556554

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

Probab=99.40  E-value=1.3e-12  Score=150.55  Aligned_cols=307  Identities=22%  Similarity=0.312  Sum_probs=192.8

Q ss_pred             HHHHHHHhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHHHHhhcCcEEEEe
Q 002040          495 AQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVMGVRCVPV  574 (976)
Q Consensus       495 ~~~i~~il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~~~~~~~~~~~~~  574 (976)
                      ...+..+..+.-+++-+.||+|||.++...+|..+.....   +-...+.+..|++..+.-+.+.+..   .-+-.+.-.
T Consensus       384 ~~i~q~v~dn~v~~I~getgcgk~tq~aq~iLe~~~~ns~---g~~~na~v~qprrisaisiaerva~---er~e~~g~t  457 (1282)
T KOG0921|consen  384 SEILQAVAENRVVIIKGETGCGKSTQVAQFLLESFLENSN---GASFNAVVSQPRRISAISLAERVAN---ERGEEVGET  457 (1282)
T ss_pred             HHHHHHHhcCceeeEeecccccchhHHHHHHHHHHhhccc---cccccceeccccccchHHHHHHHHH---hhHHhhccc
Confidence            3444555566778888999999999999999988876531   2223456777998887766554432   222222223


Q ss_pred             eCCCChHHHHHHHhc-CCeEEEeCchhHHHHHHhcCCcccccCCceEEEecCcccc-cccCCchHHHHHHHhcCCCCcEE
Q 002040          575 YGGSGVAQQISELKR-GTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRM-FDMGFEPQITRIVQNIRPDRQTV  652 (976)
Q Consensus       575 ~gg~~~~~~~~~l~~-~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDEah~~-~~~~f~~~i~~il~~~~~~~q~i  652 (976)
                      +|.+....  ..+.. ---|.+||-+.|+..+.+      -+..+.++|+||.|.. .+..|...+.+-+....++..++
T Consensus       458 vgy~vRf~--Sa~prpyg~i~fctvgvllr~~e~------glrg~sh~i~deiherdv~~dfll~~lr~m~~ty~dl~v~  529 (1282)
T KOG0921|consen  458 CGYNVRFD--SATPRPYGSIMFCTVGVLLRMMEN------GLRGISHVIIDEIHERDVDTDFVLIVLREMISTYRDLRVV  529 (1282)
T ss_pred             cccccccc--ccccccccceeeeccchhhhhhhh------cccccccccchhhhhhccchHHHHHHHHhhhccchhhhhh
Confidence            33332221  11222 236889999999888865      3566889999999932 33345544444444444555666


Q ss_pred             EEeccCcHHHHHHHHHHcCCCeEEEeCCcccccC-----CceEEE--------------------------------E--
Q 002040          653 LFSATFPRQVEILARKVLNKPVEIQVGGRSVVNK-----DITQLV--------------------------------E--  693 (976)
Q Consensus       653 ~~SAT~~~~~~~l~~~~l~~~~~i~~~~~~~~~~-----~i~q~~--------------------------------~--  693 (976)
                      +||||+...   ++..++.....+.+.+..++..     .+.+..                                .  
T Consensus       530 lmsatIdTd---~f~~~f~~~p~~~~~grt~pvq~F~led~~~~~~~vp~~~~~~k~k~~~~~~~~~~ddK~~n~n~~~d  606 (1282)
T KOG0921|consen  530 LMSATIDTD---LFTNFFSSIPDVTVHGRTFPVQSFFLEDIIQMTQFVPSEPSQKKRKKDDDEEDEEVDDKGRNMNILCD  606 (1282)
T ss_pred             hhhcccchh---hhhhhhccccceeeccccccHHHHHHHHhhhhhhccCCCcCccchhhcccccCchhhhcccccccccC
Confidence            666665433   2222222222222211111100     000000                                0  


Q ss_pred             ------------ecCcchHHHHHHHHHHhhh----cCCcEEEEecCHHHHHHHHHHHHHC-------CCCceeccCCCCH
Q 002040          694 ------------VRPESDRFLRLLELLGEWY----EKGKILIFVHSQEKCDALFRDLLKH-------GYPCLSLHGAKDQ  750 (976)
Q Consensus       694 ------------~~~~~~k~~~l~~~l~~~~----~~~kvLIF~~s~~~~~~l~~~L~~~-------~~~~~~lhg~~~~  750 (976)
                                  ..........|++.|....    -.+-|+||.+.-..+..|+..|..+       .+.++.+|+.+..
T Consensus       607 d~~~~~~~~am~~~se~d~~f~l~Eal~~~i~s~~i~gailvflpgwa~i~~L~~~ll~~~~fg~~~~y~ilp~Hsq~~~  686 (1282)
T KOG0921|consen  607 PSYNESTRTAMSRLSEKDIPFGLIEALLNDIASRNIDGAVLVFLPGWAEIMTLCNRLLEHQEFGQANKYEILPLHSQLTS  686 (1282)
T ss_pred             hhhcchhhhhhhcchhhcchhHHHHHHHhhhcccCCccceeeecCchHHhhhhhhhhhhhhhhccchhcccccchhhccc
Confidence                        0000011112233322221    2467999999999999999998765       4789999999999


Q ss_pred             HHHHHHHHHhccCCccEEEecCcccccCCCCCCcEEEEeCC------------------CCCHHHHHHHhcccCCCCCcc
Q 002040          751 TDRESTISDFKSNVCNLLIATSVAARGLDVKELELVINFDA------------------PNHYEDYVHRVGRTGRAGRKG  812 (976)
Q Consensus       751 ~~R~~~~~~F~~g~~~vLVaT~v~~~GlDi~~v~~VI~~d~------------------p~s~~~y~Qr~GR~gR~g~~g  812 (976)
                      .+..+++.....|..++|++|+++...+.|.++.+||+.+.                  +.+..+.+|+.||+||. ++|
T Consensus       687 ~eqrkvf~~~p~gv~kii~stniaetsiTidd~v~vid~cka~~~~~~s~nn~~~~Atvw~sktn~eqr~gr~grv-R~G  765 (1282)
T KOG0921|consen  687 QEQRKVFEPVPEGVTKIILSTNIAETSITIDDVVYVIDSCKAKEKLFTSHNNMTHYATVWASKTNLEQRKGRAGRV-RPG  765 (1282)
T ss_pred             HhhhhccCcccccccccccccceeeEeeeecceeEEEeeeeeeeeeeccccceeeeeeecccccchHhhcccCcee-ccc
Confidence            99999999999999999999999999999999888886332                  33456678999999997 588


Q ss_pred             EEEEEec
Q 002040          813 CAITFIS  819 (976)
Q Consensus       813 ~~~~~~~  819 (976)
                      .|+.+++
T Consensus       766 ~~f~lcs  772 (1282)
T KOG0921|consen  766 FCFHLCS  772 (1282)
T ss_pred             ccccccH
Confidence            8888764

>PF02399 Herpes_ori_bp: Origin of replication binding protein; InterPro: IPR003450 This entry represents replication origin binding protein

Probab=99.38  E-value=5.3e-11  Score=140.17  Aligned_cols=326  Identities=16%  Similarity=0.194  Sum_probs=191.4

Q ss_pred             CEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHHHHhhcCcEEEEeeCCCChHHHHH
Q 002040          506 DCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQIS  585 (976)
Q Consensus       506 d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~~~~~~~~~~~~~~gg~~~~~~~~  585 (976)
                      -.+|.+|+|||||.+.+-++-..+. .      ....+|+|+..+.|+.++...++..    ++.-...|......    
T Consensus        51 V~vVRSpMGTGKTtaLi~wLk~~l~-~------~~~~VLvVShRrSL~~sL~~rf~~~----~l~gFv~Y~d~~~~----  115 (824)
T PF02399_consen   51 VLVVRSPMGTGKTTALIRWLKDALK-N------PDKSVLVVSHRRSLTKSLAERFKKA----GLSGFVNYLDSDDY----  115 (824)
T ss_pred             eEEEECCCCCCcHHHHHHHHHHhcc-C------CCCeEEEEEhHHHHHHHHHHHHhhc----CCCcceeeeccccc----
Confidence            3577799999999875444433322 1      2567999999999999998887753    22111122211110    


Q ss_pred             HHh-cCCeEEEeCchhHHHHHHhcCCcccccCCceEEEecCcccccccCCchHHH------H-HHHhcCCCCcEEEEecc
Q 002040          586 ELK-RGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMGFEPQIT------R-IVQNIRPDRQTVLFSAT  657 (976)
Q Consensus       586 ~l~-~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDEah~~~~~~f~~~i~------~-il~~~~~~~q~i~~SAT  657 (976)
                      .+. ...+-++++...|..+..      ..+.++++|||||+-..+..-|.+.+.      . +...++....+|++-||
T Consensus       116 ~i~~~~~~rLivqIdSL~R~~~------~~l~~yDvVIIDEv~svL~qL~S~Tm~~~~~v~~~L~~lI~~ak~VI~~DA~  189 (824)
T PF02399_consen  116 IIDGRPYDRLIVQIDSLHRLDG------SLLDRYDVVIIDEVMSVLNQLFSPTMRQREEVDNLLKELIRNAKTVIVMDAD  189 (824)
T ss_pred             cccccccCeEEEEehhhhhccc------ccccccCEEEEehHHHHHHHHhHHHHhhHHHHHHHHHHHHHhCCeEEEecCC
Confidence            011 124566667666644421      246779999999998665443332222      2 23345666789999999


Q ss_pred             CcHHHHHHHHHHcCCC-eEEEeCCcccccCCceEEEEe------------c-----------------------CcchHH
Q 002040          658 FPRQVEILARKVLNKP-VEIQVGGRSVVNKDITQLVEV------------R-----------------------PESDRF  701 (976)
Q Consensus       658 ~~~~~~~l~~~~l~~~-~~i~~~~~~~~~~~i~q~~~~------------~-----------------------~~~~k~  701 (976)
                      +...+-.++..+.+.. +.+.+..-..+...-.+.+..            .                       ......
T Consensus       190 ln~~tvdFl~~~Rp~~~i~vI~n~y~~~~fs~R~~~~~~~l~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  269 (824)
T PF02399_consen  190 LNDQTVDFLASCRPDENIHVIVNTYASPGFSNRRCTFLRSLGTDTLAAALNPEDENADTSPTPKHSPDPTATAAISNDET  269 (824)
T ss_pred             CCHHHHHHHHHhCCCCcEEEEEeeeecCCcccceEEEecccCcHHHHHHhCCcccccccCCCcCCCCccccccccccchh
Confidence            9998888888776543 333322111100000000000            0                       001111


Q ss_pred             HHHHHHHHhhhcCCcEEEEecCHHHHHHHHHHHHHCCCCceeccCCCCHHHHHHHHHHhccCCccEEEecCcccccCCCC
Q 002040          702 LRLLELLGEWYEKGKILIFVHSQEKCDALFRDLLKHGYPCLSLHGAKDQTDRESTISDFKSNVCNLLIATSVAARGLDVK  781 (976)
Q Consensus       702 ~~l~~~l~~~~~~~kvLIF~~s~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLVaT~v~~~GlDi~  781 (976)
                      ..+-.++..+..+.+|-||+.|...++.++......+..++.++|..+..+..    .  =++++|||.|+++..||++.
T Consensus       270 tF~~~L~~~L~~gknIcvfsSt~~~~~~v~~~~~~~~~~Vl~l~s~~~~~dv~----~--W~~~~VviYT~~itvG~Sf~  343 (824)
T PF02399_consen  270 TFFSELLARLNAGKNICVFSSTVSFAEIVARFCARFTKKVLVLNSTDKLEDVE----S--WKKYDVVIYTPVITVGLSFE  343 (824)
T ss_pred             hHHHHHHHHHhCCCcEEEEeChHHHHHHHHHHHHhcCCeEEEEcCCCCccccc----c--ccceeEEEEeceEEEEeccc
Confidence            22223333444566888999999999999999998889999999877766332    2  25689999999999999997


Q ss_pred             CC--cEEEEeCCC----CCHHHHHHHhcccCCCCCccEEEEEecCC----CcCchHHHHHHHhhccCCCChHH----HHH
Q 002040          782 EL--ELVINFDAP----NHYEDYVHRVGRTGRAGRKGCAITFISEE----DAKYSPDLVKALELSEQVVPDDL----KAL  847 (976)
Q Consensus       782 ~v--~~VI~~d~p----~s~~~y~Qr~GR~gR~g~~g~~~~~~~~~----d~~~~~~i~~~l~~~~~~vp~~l----~~l  847 (976)
                      ..  +-|+-|=-|    .++.+..|++||+-.. .....++++...    +.-+.+-|++..-.....=|...    ..+
T Consensus       344 ~~HF~~~f~yvk~~~~gpd~~s~~Q~lgRvR~l-~~~ei~v~~d~~~~~~~~~~tpmlLNh~i~~~~~Wp~~~~~vtn~l  422 (824)
T PF02399_consen  344 EKHFDSMFAYVKPMSYGPDMVSVYQMLGRVRSL-LDNEIYVYIDASGARSEPIFTPMLLNHVIPSCGGWPAQFSQVTNLL  422 (824)
T ss_pred             hhhceEEEEEecCCCCCCcHHHHHHHHHHHHhh-ccCeEEEEEecccccCCCCCCcchhcccccCCCCCChhHHHHHHHH
Confidence            64  334444223    2355689999999544 366777777653    22233333332222222334333    445


Q ss_pred             HHHHHHHHhhhh
Q 002040          848 ADSFMAKVNQGL  859 (976)
Q Consensus       848 ~~~~~~~~~~~~  859 (976)
                      ...|..+.....
T Consensus       423 c~~Fr~rC~~a~  434 (824)
T PF02399_consen  423 CCDFRRRCAPAF  434 (824)
T ss_pred             HHHHHHhhhhhh
Confidence            556666655444

It functions as a docking protein to recruit essential components of the viral replication machinery to viral DNA origins. In the presence of the major DNA-binding protein, it opens dsDNA which leads to a conformational change in the origin that facilitates DNA unwinding and subsequent replication [].; GO: 0003688 DNA replication origin binding, 0005524 ATP binding, 0006260 DNA replication

>COG0653 SecA Preprotein translocase subunit SecA (ATPase, RNA helicase) [Intracellular trafficking and secretion]

Probab=99.28  E-value=9.4e-11  Score=139.10  Aligned_cols=316  Identities=22%  Similarity=0.244  Sum_probs=196.2

Q ss_pred             HHHHHHHHHHhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHHHHhhcCcEE
Q 002040          492 PIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVMGVRC  571 (976)
Q Consensus       492 ~~Q~~~i~~il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~~~~~~~~~~  571 (976)
                      |+-.|.|-.+..+...|.-+.||-|||+++.+|+.-..+.        |..|.|++..-=||.--..++..+...+|+.+
T Consensus        81 ~~dVQliG~i~lh~g~iaEM~TGEGKTL~atlp~ylnaL~--------gkgVhvVTvNdYLA~RDae~m~~l~~~LGlsv  152 (822)
T COG0653          81 HFDVQLLGGIVLHLGDIAEMRTGEGKTLVATLPAYLNALA--------GKGVHVVTVNDYLARRDAEWMGPLYEFLGLSV  152 (822)
T ss_pred             hhhHHHhhhhhhcCCceeeeecCCchHHHHHHHHHHHhcC--------CCCcEEeeehHHhhhhCHHHHHHHHHHcCCce
Confidence            4446666677777778999999999999999998765443        44577888888899999999999999999999


Q ss_pred             EEeeCCCChHHHHHHHhcCCeEEEeCchhH-HHHHHhcC---CcccccCCceEEEecCccccc-cc--------C---C-
Q 002040          572 VPVYGGSGVAQQISELKRGTEIVVCTPGRM-IDILCTSG---GKITNLRRVTYLVMDEADRMF-DM--------G---F-  634 (976)
Q Consensus       572 ~~~~gg~~~~~~~~~l~~~~~Iiv~Tp~~L-~~~l~~~~---~~~~~l~~~~~vVlDEah~~~-~~--------~---f-  634 (976)
                      .+...+.+..+....+.  |+|.++|...| .++|..+-   ..-..+..+.|.|+||++.++ +.        |   . 
T Consensus       153 G~~~~~m~~~ek~~aY~--~DItY~TnnElGFDYLRDNm~~~~ee~vqr~~~faIvDEvDSILIDEARtPLiISG~~~~~  230 (822)
T COG0653         153 GVILAGMSPEEKRAAYA--CDITYGTNNELGFDYLRDNMVTSQEEKVQRGLNFAIVDEVDSILIDEARTPLIISGPAEDS  230 (822)
T ss_pred             eeccCCCChHHHHHHHh--cCceeccccccCcchhhhhhhccHHHhhhccCCeEEEcchhheeeeccccceeeecccccC
Confidence            99999998777665554  89999998775 23332210   000123457899999999652 10        1   1 


Q ss_pred             ---chHHHHHHHhcCCC--------CcEEEEec-----------------------------------------------
Q 002040          635 ---EPQITRIVQNIRPD--------RQTVLFSA-----------------------------------------------  656 (976)
Q Consensus       635 ---~~~i~~il~~~~~~--------~q~i~~SA-----------------------------------------------  656 (976)
                         ...+..++..+...        .+.|.||-                                               
T Consensus       231 ~~~Y~~~~~~v~~l~~~~d~~iDek~k~v~lte~G~~kae~~f~~~~Ly~~en~~~~h~~~~alrA~~l~~~D~dYIVrd  310 (822)
T COG0653         231 SELYKKVDDLVRLLSEDEDFTIDEKSKNVSLTESGLEKAEELLGIENLYDLENVNLVHHLNQALRAHILFFRDVDYIVRD  310 (822)
T ss_pred             chHHHHHHHHHHHhccccceeecchhcccccchhhHHHHHHHhCcccccchhhHHHHhhHHHHHHHHHHhhcCCeeEEec
Confidence               11122222222111        01111111                                               


Q ss_pred             --------------------------------------------------------------cCcHHHHHHHHHHcCCCe
Q 002040          657 --------------------------------------------------------------TFPRQVEILARKVLNKPV  674 (976)
Q Consensus       657 --------------------------------------------------------------T~~~~~~~l~~~~l~~~~  674 (976)
                                                                                    |.-.....+...| +.-+
T Consensus       311 ~ev~IvD~ftGR~m~gRr~s~GLhQAiEAKEgv~i~~e~~tlatITfQn~fR~y~kl~gmTGTa~te~~EF~~iY-~l~v  389 (822)
T COG0653         311 GEVVIVDEFTGRMMEGRRWSDGLHQAIEAKEGVEIQEENQTLATITFQNLFRLYPKLAGMTGTADTEEEEFDVIY-GLDV  389 (822)
T ss_pred             CeEEEEecccCCcccCcCCCchhHHHHHHhcCCcccccceeehhhhHHHHHhhhhhhcCCCCcchhhhhhhhhcc-CCce
Confidence                                                                          1000000000000 0000


Q ss_pred             EEEeCCcccccCCceEEEEecCcchHHHHHHHHHHhhhc-CCcEEEEecCHHHHHHHHHHHHHCCCCceeccCCCCHHHH
Q 002040          675 EIQVGGRSVVNKDITQLVEVRPESDRFLRLLELLGEWYE-KGKILIFVHSQEKCDALFRDLLKHGYPCLSLHGAKDQTDR  753 (976)
Q Consensus       675 ~i~~~~~~~~~~~i~q~~~~~~~~~k~~~l~~~l~~~~~-~~kvLIF~~s~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R  753 (976)
                      .+.+...+....+.. -..+.....|+..++..+...+. +.|+||-+.+++..+.+...|.+.|++...+...-...+-
T Consensus       390 v~iPTnrp~~R~D~~-D~vy~t~~~K~~Aiv~~I~~~~~~gqPvLvgT~sie~SE~ls~~L~~~~i~h~VLNAk~h~~EA  468 (822)
T COG0653         390 VVIPTNRPIIRLDEP-DLVYKTEEEKFKAIVEDIKERHEKGQPVLVGTVSIEKSELLSKLLRKAGIPHNVLNAKNHAREA  468 (822)
T ss_pred             eeccCCCcccCCCCc-cccccchHHHHHHHHHHHHHHHhcCCCEEEcCcceecchhHHHHHHhcCCCceeeccccHHHHH
Confidence            000000100000000 01233446688888887776664 5599999999999999999999999999888877664444


Q ss_pred             HHHHHHhccCC-ccEEEecCcccccCCCCCCc-----------EEEEeCCCCCHHHHHHHhcccCCCCCccEEEEEecCC
Q 002040          754 ESTISDFKSNV-CNLLIATSVAARGLDVKELE-----------LVINFDAPNHYEDYVHRVGRTGRAGRKGCAITFISEE  821 (976)
Q Consensus       754 ~~~~~~F~~g~-~~vLVaT~v~~~GlDi~~v~-----------~VI~~d~p~s~~~y~Qr~GR~gR~g~~g~~~~~~~~~  821 (976)
                      ..+..   .|. --|-|||++|++|-||.--.           +||--.--.|----.|.-||+||.|-+|....|++-+
T Consensus       469 ~Iia~---AG~~gaVTiATNMAGRGTDIkLg~~~~~V~~lGGL~VIgTERhESRRIDnQLRGRsGRQGDpG~S~F~lSle  545 (822)
T COG0653         469 EIIAQ---AGQPGAVTIATNMAGRGTDIKLGGNPEFVMELGGLHVIGTERHESRRIDNQLRGRAGRQGDPGSSRFYLSLE  545 (822)
T ss_pred             HHHhh---cCCCCccccccccccCCcccccCCCHHHHHHhCCcEEEecccchhhHHHHHhhcccccCCCcchhhhhhhhH
Confidence            33332   333 34889999999999986433           2333333333444458999999999999888777754


Q ss_pred             C
Q 002040          822 D  822 (976)
Q Consensus       822 d  822 (976)
                      |
T Consensus       546 D  546 (822)
T COG0653         546 D  546 (822)
T ss_pred             H
Confidence            3

>PF00176 SNF2_N: SNF2 family N-terminal domain; InterPro: IPR000330 This domain is found in proteins involved in a variety of processes including transcription regulation (e

Probab=99.27  E-value=1.8e-11  Score=135.78  Aligned_cols=161  Identities=19%  Similarity=0.211  Sum_probs=94.8

Q ss_pred             HHHHHHHHHh-------------cCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHH
Q 002040          493 IQAQALPVIM-------------SGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSD  559 (976)
Q Consensus       493 ~Q~~~i~~il-------------~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~  559 (976)
                      +|..++.+++             ..+.+|++.++|+|||++++..+. .+......  ..-..+|||||. .+..||..+
T Consensus         1 ~Q~~~v~~m~~~~~~~~~~~~~~~~~g~lL~de~GlGKT~~~i~~~~-~l~~~~~~--~~~~~~LIv~P~-~l~~~W~~E   76 (299)
T PF00176_consen    1 HQLEAVRWMLDRELVEEYPNSESPPRGGLLADEMGLGKTITAIALIS-YLKNEFPQ--RGEKKTLIVVPS-SLLSQWKEE   76 (299)
T ss_dssp             HHHHHHHHHHHHH----TTSSSTTT-EEEE---TTSSHHHHHHHHHH-HHHHCCTT--SS-S-EEEEE-T-TTHHHHHHH
T ss_pred             CHHHHHHHHHHHhhhhcccccccCCCCEEEEECCCCCchhhhhhhhh-hhhhcccc--ccccceeEeecc-chhhhhhhh
Confidence            5888888774             335789999999999998665554 33332111  111248999999 777999999


Q ss_pred             HHHHHhhcCcEEEEeeCCCChHHHHHHHhcCCeEEEeCchhHHHHHHhcCCcccccCCceEEEecCcccccccCCchHHH
Q 002040          560 IRKFAKVMGVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMGFEPQIT  639 (976)
Q Consensus       560 ~~~~~~~~~~~~~~~~gg~~~~~~~~~l~~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDEah~~~~~~f~~~i~  639 (976)
                      +.+++....+.+..+.|...............+|+|+|+..+.............--.+.+|||||+|.+-+  ......
T Consensus        77 ~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~vvi~ty~~~~~~~~~~~~~~l~~~~~~~vIvDEaH~~k~--~~s~~~  154 (299)
T PF00176_consen   77 IEKWFDPDSLRVIIYDGDSERRRLSKNQLPKYDVVITTYETLRKARKKKDKEDLKQIKWDRVIVDEAHRLKN--KDSKRY  154 (299)
T ss_dssp             HHHHSGT-TS-EEEESSSCHHHHTTSSSCCCSSEEEEEHHHHH--TSTHTTHHHHTSEEEEEEETTGGGGTT--TTSHHH
T ss_pred             hccccccccccccccccccccccccccccccceeeeccccccccccccccccccccccceeEEEeccccccc--cccccc
Confidence            999986556666666655512222222234579999999998711000000011113489999999998843  334455


Q ss_pred             HHHHhcCCCCcEEEEeccCcH
Q 002040          640 RIVQNIRPDRQTVLFSATFPR  660 (976)
Q Consensus       640 ~il~~~~~~~q~i~~SAT~~~  660 (976)
                      ..+..+. ....+++||||..
T Consensus       155 ~~l~~l~-~~~~~lLSgTP~~  174 (299)
T PF00176_consen  155 KALRKLR-ARYRWLLSGTPIQ  174 (299)
T ss_dssp             HHHHCCC-ECEEEEE-SS-SS
T ss_pred             ccccccc-cceEEeecccccc
Confidence            5555565 5668999999743

g., SNF2, STH1, brahma, MOT1), DNA repair (e.g., ERCC6, RAD16, RAD5), DNA recombination (e.g., RAD54), and chromatin unwinding (e.g., ISWI) as well as a variety of other proteins with little functional information (e.g., lodestar, ETL1) [, ]. SNF2 functions as the ATPase component of the SNF2/SWI multisubunit complex, which utilises energy derived from ATP hydrolysis to disrupt histone-DNA interactions, resulting in the increased accessibility of DNA to transcription factors. Proteins that contain this domain appear to be distantly related to the DEAX box helicases IPR001410 from INTERPRO, however no helicase activity has ever been demonstrated for these proteins. ; GO: 0003677 DNA binding, 0005524 ATP binding; PDB: 1Z63_B 1Z3I_X 3DMQ_A 3MWY_W.

>PF07652 Flavi_DEAD: Flavivirus DEAD domain ; InterPro: IPR011492 This is the Flavivirus DEAD domain

Probab=99.18  E-value=6.7e-11  Score=111.59  Aligned_cols=135  Identities=18%  Similarity=0.190  Sum_probs=79.9

Q ss_pred             CCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHHHHhhcCcEEEEeeCCCChHHH
Q 002040          504 GRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQ  583 (976)
Q Consensus       504 g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~~~~~~~~~~~~~~gg~~~~~~  583 (976)
                      |.-.++-..+|+|||.-.+.-++.....       .+.++|||.|||.++..+++.++.    .++++....-+.     
T Consensus         4 g~~~~~d~hpGaGKTr~vlp~~~~~~i~-------~~~rvLvL~PTRvva~em~~aL~~----~~~~~~t~~~~~-----   67 (148)
T PF07652_consen    4 GELTVLDLHPGAGKTRRVLPEIVREAIK-------RRLRVLVLAPTRVVAEEMYEALKG----LPVRFHTNARMR-----   67 (148)
T ss_dssp             TEEEEEE--TTSSTTTTHHHHHHHHHHH-------TT--EEEEESSHHHHHHHHHHTTT----SSEEEESTTSS------
T ss_pred             CceeEEecCCCCCCcccccHHHHHHHHH-------ccCeEEEecccHHHHHHHHHHHhc----CCcccCceeeec-----
Confidence            4446778899999998766655554443       266899999999999888776653    444443222211     


Q ss_pred             HHHHhcCCeEEEeCchhHHHHHHhcCCcccccCCceEEEecCcccccccCCchHHHHHHHhc--CCCCcEEEEeccCcHH
Q 002040          584 ISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMGFEPQITRIVQNI--RPDRQTVLFSATFPRQ  661 (976)
Q Consensus       584 ~~~l~~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDEah~~~~~~f~~~i~~il~~~--~~~~q~i~~SAT~~~~  661 (976)
                        ....+.-|-|+|++.+...+...    ..+.+|++||+||||-+ |..-. .....+..+  .....+|++|||+|..
T Consensus        68 --~~~g~~~i~vMc~at~~~~~~~p----~~~~~yd~II~DEcH~~-Dp~sI-A~rg~l~~~~~~g~~~~i~mTATPPG~  139 (148)
T PF07652_consen   68 --THFGSSIIDVMCHATYGHFLLNP----CRLKNYDVIIMDECHFT-DPTSI-AARGYLRELAESGEAKVIFMTATPPGS  139 (148)
T ss_dssp             -----SSSSEEEEEHHHHHHHHHTS----SCTTS-SEEEECTTT---SHHHH-HHHHHHHHHHHTTS-EEEEEESS-TT-
T ss_pred             --cccCCCcccccccHHHHHHhcCc----ccccCccEEEEeccccC-CHHHH-hhheeHHHhhhccCeeEEEEeCCCCCC
Confidence              12345688899999998887653    34678999999999953 21101 111122222  2335799999999876


Q ss_pred             H
Q 002040          662 V  662 (976)
Q Consensus       662 ~  662 (976)
                      .
T Consensus       140 ~  140 (148)
T PF07652_consen  140 E  140 (148)
T ss_dssp             -
T ss_pred             C
Confidence            4

The domain is related to the DEAD/DEAH box helicase domain which is found in a large family of ATPases.; GO: 0005524 ATP binding, 0008026 ATP-dependent helicase activity, 0019079 viral genome replication; PDB: 2QEQ_A 2V6J_A 2V6I_A 8OHM_A 4A92_B 1JR6_A 1HEI_A 1ONB_A 1A1V_A 1YMF_A ....

>KOG1016 consensus Predicted DNA helicase, DEAD-box superfamily [General function prediction only]

Probab=99.12  E-value=3.4e-09  Score=120.75  Aligned_cols=115  Identities=25%  Similarity=0.290  Sum_probs=96.5

Q ss_pred             CcEEEEecCHHHHHHHHHHHHHCC------------------CCceeccCCCCHHHHHHHHHHhccC---CccEEEecCc
Q 002040          715 GKILIFVHSQEKCDALFRDLLKHG------------------YPCLSLHGAKDQTDRESTISDFKSN---VCNLLIATSV  773 (976)
Q Consensus       715 ~kvLIF~~s~~~~~~l~~~L~~~~------------------~~~~~lhg~~~~~~R~~~~~~F~~g---~~~vLVaT~v  773 (976)
                      .++|||.++...++.|...|.+..                  ...+.+.|..+..+|++.|+.|++-   ..-||++|.+
T Consensus       720 ~kil~fSq~l~~Ld~ieeil~krq~pc~~gdnG~~aqkW~~n~sy~rldG~t~a~~rekLinqfN~e~~lsWlfllstra  799 (1387)
T KOG1016|consen  720 EKILIFSQNLTALDMIEEILKKRQIPCKDGDNGCPAQKWEKNRSYLRLDGTTSAADREKLINQFNSEPGLSWLFLLSTRA  799 (1387)
T ss_pred             ceEEEeecchhHHHHHHHHHhcccccCCCCCCCCchhhhhhccceecccCCcccchHHHHHHhccCCCCceeeeeehhcc
Confidence            389999999999999999997752                  3456788999999999999999853   2468999999


Q ss_pred             ccccCCCCCCcEEEEeCCCCCHHHHHHHhcccCCCCCccEEEEEecCCCcCchHHH
Q 002040          774 AARGLDVKELELVINFDAPNHYEDYVHRVGRTGRAGRKGCAITFISEEDAKYSPDL  829 (976)
Q Consensus       774 ~~~GlDi~~v~~VI~~d~p~s~~~y~Qr~GR~gR~g~~g~~~~~~~~~d~~~~~~i  829 (976)
                      ...|||+-+++.+|+|++.|++..-.|.+-|+-|.|++.-||+|-.-.|...-..|
T Consensus       800 g~lGinLIsanr~~ifda~wnpchdaqavcRvyrYGQ~KpcfvYRlVmD~~lEkkI  855 (1387)
T KOG1016|consen  800 GSLGINLISANRCIIFDACWNPCHDAQAVCRVYRYGQQKPCFVYRLVMDNSLEKKI  855 (1387)
T ss_pred             ccccceeeccceEEEEEeecCccccchhhhhhhhhcCcCceeEEeehhhhhhHHHH
Confidence            99999999999999999999999999999999999999888887654444433333

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

Probab=99.00  E-value=1.3e-08  Score=108.38  Aligned_cols=133  Identities=21%  Similarity=0.291  Sum_probs=98.5

Q ss_pred             cCCCCCcHHHHHHHHHHhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHHHH
Q 002040          485 LNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFA  564 (976)
Q Consensus       485 ~~~~~p~~~Q~~~i~~il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~~~  564 (976)
                      +|+ .|++.|..++-.+..|+  |+...||-|||++..+|++.+.+.        |..|=|++.+.-||..=++++..|+
T Consensus        74 ~g~-~p~~vQll~~l~L~~G~--laEm~TGEGKTli~~l~a~~~AL~--------G~~V~vvT~NdyLA~RD~~~~~~~y  142 (266)
T PF07517_consen   74 LGL-RPYDVQLLGALALHKGR--LAEMKTGEGKTLIAALPAALNALQ--------GKGVHVVTSNDYLAKRDAEEMRPFY  142 (266)
T ss_dssp             TS-----HHHHHHHHHHHTTS--EEEESTTSHHHHHHHHHHHHHHTT--------SS-EEEEESSHHHHHHHHHHHHHHH
T ss_pred             cCC-cccHHHHhhhhhcccce--eEEecCCCCcHHHHHHHHHHHHHh--------cCCcEEEeccHHHhhccHHHHHHHH
Confidence            454 58888988887776665  999999999999988887766553        5568899999999999999999999


Q ss_pred             hhcCcEEEEeeCCCChHHHHHHHhcCCeEEEeCchhHH-HHHHhcCCc---ccccCCceEEEecCccccc
Q 002040          565 KVMGVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMI-DILCTSGGK---ITNLRRVTYLVMDEADRMF  630 (976)
Q Consensus       565 ~~~~~~~~~~~gg~~~~~~~~~l~~~~~Iiv~Tp~~L~-~~l~~~~~~---~~~l~~~~~vVlDEah~~~  630 (976)
                      ..+|+.+.+++++.+.........  ++|+++|...|. ++|..+...   ......+.++||||||.|+
T Consensus       143 ~~LGlsv~~~~~~~~~~~r~~~Y~--~dI~Y~t~~~~~fD~Lrd~~~~~~~~~~~r~~~~~ivDEvDs~L  210 (266)
T PF07517_consen  143 EFLGLSVGIITSDMSSEERREAYA--ADIVYGTNSEFGFDYLRDNLALSKNEQVQRGFDFAIVDEVDSIL  210 (266)
T ss_dssp             HHTT--EEEEETTTEHHHHHHHHH--SSEEEEEHHHHHHHHHHHTT-SSGGG--SSSSSEEEECTHHHHT
T ss_pred             HHhhhccccCccccCHHHHHHHHh--CcccccccchhhHHHHHHHHhhccchhccCCCCEEEEeccceEE
Confidence            999999999999988665444444  789999999874 455443211   1124678899999999653

SecA protein achieves this translocation, in association with SecY protein, in an ATP-dependent manner [,]. This domain represents the N-terminal ATP-dependent helicase domain, which is related to the IPR0011545 from INTERPRO.; GO: 0005524 ATP binding, 0017038 protein import, 0016020 membrane; PDB: 1NL3_B 1NKT_B 3DIN_B 3JUX_A 2FSG_B 2VDA_A 2FSH_A 2FSF_A 2FSI_A 3BXZ_A ....

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

Probab=98.98  E-value=2.2e-07  Score=113.41  Aligned_cols=73  Identities=15%  Similarity=0.261  Sum_probs=55.9

Q ss_pred             CccEEEecCcccccCCCCCCcEEEEeCCCCCHHHHHHHhcccCCC-----CC----ccEEE-EEecCCCcCchHHHHHHH
Q 002040          764 VCNLLIATSVAARGLDVKELELVINFDAPNHYEDYVHRVGRTGRA-----GR----KGCAI-TFISEEDAKYSPDLVKAL  833 (976)
Q Consensus       764 ~~~vLVaT~v~~~GlDi~~v~~VI~~d~p~s~~~y~Qr~GR~gR~-----g~----~g~~~-~~~~~~d~~~~~~i~~~l  833 (976)
                      ...+|++-+++..|+|.|++-++..+....|...-.|.+||.-|.     |.    ..... ++++.....++..|++.+
T Consensus       501 ~~~fifs~~al~egwd~~~~~~~~~l~~~~s~~~~~q~~gr~lr~~vnq~G~R~~~~~~~LTvianesy~dFa~~LQ~EI  580 (986)
T PRK15483        501 TRRFLFSKWTLREGWDNPNVFQIAKLRSSGSETSKLQEVGRGLRLPVDENGHRVSQEEFRLNYLIDYDEKDFASKLVGEI  580 (986)
T ss_pred             CeEEEEEhHHhhhcCCCCCeEEEEEeccCCchHHHHHHhccceeccccccCccccCccEEEEEEeCccHHHHHHHHHHHH
Confidence            578999999999999999999999999888988999999999883     21    12222 234555566777777776


Q ss_pred             hhc
Q 002040          834 ELS  836 (976)
Q Consensus       834 ~~~  836 (976)
                      ...
T Consensus       581 ~~~  583 (986)
T PRK15483        581 NSD  583 (986)
T ss_pred             Hhh
Confidence            544

>smart00489 DEXDc3 DEAD-like helicases superfamily

Probab=98.98  E-value=5.9e-09  Score=114.07  Aligned_cols=76  Identities=26%  Similarity=0.372  Sum_probs=59.4

Q ss_pred             cCCCCCcHHHHHHHH----HHhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHH
Q 002040          485 LNYEKPMPIQAQALP----VIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDI  560 (976)
Q Consensus       485 ~~~~~p~~~Q~~~i~----~il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~  560 (976)
                      |+|. |+|.|.+.+.    .+..|.++|+.||||+|||+++++|++.++......  ..+.+++|+++|..+..|....+
T Consensus         5 FPy~-~r~~Q~~~m~~v~~~~~~~~~~~~eapTGtGKTl~~L~~al~~~~~~~~~--~~~~kvi~~t~T~~~~~q~i~~l   81 (289)
T smart00489        5 FPYE-PYPIQYEFMEELKRVLDRGKIGILESPTGTGKTLSLLCLTLTWLRSFPER--IQKIKLIYLSRTVSEIEKRLEEL   81 (289)
T ss_pred             CCCC-CCHHHHHHHHHHHHHHHcCCcEEEECCCCcchhHHHHHHHHHHHHhCccc--ccccceeEEeccHHHHHHHHHHH
Confidence            4554 6999999554    455788999999999999999999999887653211  02347899999999999887777


Q ss_pred             HHH
Q 002040          561 RKF  563 (976)
Q Consensus       561 ~~~  563 (976)
                      +++
T Consensus        82 ~~~   84 (289)
T smart00489       82 RKL   84 (289)
T ss_pred             Hhc
Confidence            665

>smart00488 DEXDc2 DEAD-like helicases superfamily

Probab=98.98  E-value=5.9e-09  Score=114.07  Aligned_cols=76  Identities=26%  Similarity=0.372  Sum_probs=59.4

Q ss_pred             cCCCCCcHHHHHHHH----HHhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHH
Q 002040          485 LNYEKPMPIQAQALP----VIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDI  560 (976)
Q Consensus       485 ~~~~~p~~~Q~~~i~----~il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~  560 (976)
                      |+|. |+|.|.+.+.    .+..|.++|+.||||+|||+++++|++.++......  ..+.+++|+++|..+..|....+
T Consensus         5 FPy~-~r~~Q~~~m~~v~~~~~~~~~~~~eapTGtGKTl~~L~~al~~~~~~~~~--~~~~kvi~~t~T~~~~~q~i~~l   81 (289)
T smart00488        5 FPYE-PYPIQYEFMEELKRVLDRGKIGILESPTGTGKTLSLLCLTLTWLRSFPER--IQKIKLIYLSRTVSEIEKRLEEL   81 (289)
T ss_pred             CCCC-CCHHHHHHHHHHHHHHHcCCcEEEECCCCcchhHHHHHHHHHHHHhCccc--ccccceeEEeccHHHHHHHHHHH
Confidence            4554 6999999554    455788999999999999999999999887653211  02347899999999999887777


Q ss_pred             HHH
Q 002040          561 RKF  563 (976)
Q Consensus       561 ~~~  563 (976)
                      +++
T Consensus        82 ~~~   84 (289)
T smart00488       82 RKL   84 (289)
T ss_pred             Hhc
Confidence            665

>KOG1001 consensus Helicase-like transcription factor HLTF/DNA helicase RAD5, DEAD-box superfamily [Transcription; Replication, recombination and repair]

Probab=98.65  E-value=1.4e-07  Score=112.77  Aligned_cols=118  Identities=19%  Similarity=0.209  Sum_probs=98.9

Q ss_pred             hHHHHHHHHHHhhhc-C-CcEEEEecCHHHHHHHHHHHHHCCCCceeccCCCCHHHHHHHHHHhccCC-c-cEEEecCcc
Q 002040          699 DRFLRLLELLGEWYE-K-GKILIFVHSQEKCDALFRDLLKHGYPCLSLHGAKDQTDRESTISDFKSNV-C-NLLIATSVA  774 (976)
Q Consensus       699 ~k~~~l~~~l~~~~~-~-~kvLIF~~s~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~-~-~vLVaT~v~  774 (976)
                      .++..++.+|..... . .++|||++....+..++-.|...++.+..+.|.|+...|...+..|..+. . ..|++..++
T Consensus       522 ~ki~~~~~~l~~~~~s~~~kiiifsq~~~~l~l~~~~l~~~~~~~~~~~g~~~~~~r~~s~~~~~~~~~~~vll~Slkag  601 (674)
T KOG1001|consen  522 SKIYAFLKILQAKEMSEQPKIVIFSQLIWGLALVCLRLFFKGFVFLRYDGEMLMKIRTKSFTDFPCDPLVTALLMSLKAG  601 (674)
T ss_pred             hhhHHHHHHHhhccCCCCCceeeehhHHHHHHHhhhhhhhcccccchhhhhhHHHHHHhhhcccccCccHHHHHHHHHHh
Confidence            344445555542211 1 38999999999999999999999999999999999999999999999554 2 356688999


Q ss_pred             cccCCCCCCcEEEEeCCCCCHHHHHHHhcccCCCCCccEEEE
Q 002040          775 ARGLDVKELELVINFDAPNHYEDYVHRVGRTGRAGRKGCAIT  816 (976)
Q Consensus       775 ~~GlDi~~v~~VI~~d~p~s~~~y~Qr~GR~gR~g~~g~~~~  816 (976)
                      +.|||+..+.+||..|+.||+..--|.+-|++|.|+.-.+.+
T Consensus       602 ~~glnlt~a~~v~~~d~~wnp~~eeQaidR~hrigq~k~v~v  643 (674)
T KOG1001|consen  602 KVGLNLTAASHVLLMDPWWNPAVEEQAIDRAHRIGQTKPVKV  643 (674)
T ss_pred             hhhhchhhhhHHHhhchhcChHHHHHHHHHHHHhcccceeee
Confidence            999999999999999999999999999999999998766655

>TIGR00596 rad1 DNA repair protein (rad1)

Probab=98.54  E-value=1.6e-06  Score=106.04  Aligned_cols=68  Identities=21%  Similarity=0.132  Sum_probs=54.0

Q ss_pred             cCCeEEEeCchhHHHHHHhcCCcccccCCceEEEecCcccccccCCchHHHHHHHhcCCCCcEEEEeccCc
Q 002040          589 RGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMGFEPQITRIVQNIRPDRQTVLFSATFP  659 (976)
Q Consensus       589 ~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDEah~~~~~~f~~~i~~il~~~~~~~q~i~~SAT~~  659 (976)
                      ....|+++||..|..-|..+   ..++..|+.|||||||++....-...+..++...++..-+.+|||.|.
T Consensus         6 ~~ggi~~~T~rIl~~DlL~~---ri~~~~itgiiv~~Ahr~~~~~~eaFI~rlyr~~n~~gfIkafSdsP~   73 (814)
T TIGR00596         6 LEGGIFSITSRILVVDLLTG---IIPPELITGILVLRADRIIESSQEAFILRLYRQKNKTGFIKAFSDNPE   73 (814)
T ss_pred             hcCCEEEEechhhHhHHhcC---CCCHHHccEEEEeecccccccccHHHHHHHHHHhCCCcceEEecCCCc
Confidence            34689999999987666543   367889999999999998766666667777777777788999999863

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

>COG3587 Restriction endonuclease [Defense mechanisms]

Probab=98.49  E-value=9.6e-06  Score=95.41  Aligned_cols=74  Identities=14%  Similarity=0.208  Sum_probs=57.2

Q ss_pred             CCccEEEecCcccccCCCCCCcEEEEeCCCCCHHHHHHHhcccCCC--CCcc-----------EEEEEecCCCcCchHHH
Q 002040          763 NVCNLLIATSVAARGLDVKELELVINFDAPNHYEDYVHRVGRTGRA--GRKG-----------CAITFISEEDAKYSPDL  829 (976)
Q Consensus       763 g~~~vLVaT~v~~~GlDi~~v~~VI~~d~p~s~~~y~Qr~GR~gR~--g~~g-----------~~~~~~~~~d~~~~~~i  829 (976)
                      ...++|++-.++-.|+|=|+|-+++-+....|..+=.|.+||.-|.  .+.|           .-.+|+......++..|
T Consensus       482 ~plRFIFS~waLrEGWDNPNVFtIckL~~S~SeiSK~QeVGRGLRLaVNe~G~RV~~~~~~~n~L~vlv~~sek~Fv~~L  561 (985)
T COG3587         482 EPLRFIFSKWALREGWDNPNVFTICKLRSSGSEISKLQEVGRGLRLAVNENGERVTKDFDFPNELTVLVNESEKDFVKAL  561 (985)
T ss_pred             CcceeeeehhHHhhcCCCCCeeEEEEecCCCcchHHHHHhccceeeeeccccceecccccccceEEEEecccHHHHHHHH
Confidence            3478999999999999999999999999999999999999999883  2222           23345555666677777


Q ss_pred             HHHHhhc
Q 002040          830 VKALELS  836 (976)
Q Consensus       830 ~~~l~~~  836 (976)
                      ++.+...
T Consensus       562 qkEI~~~  568 (985)
T COG3587         562 QKEINDE  568 (985)
T ss_pred             HHHHHHh
Confidence            7766444

>KOG0952 consensus DNA/RNA helicase MER3/SLH1, DEAD-box superfamily [RNA processing and modification]

Probab=98.37  E-value=1.3e-07  Score=112.65  Aligned_cols=260  Identities=21%  Similarity=0.237  Sum_probs=153.4

Q ss_pred             CcHHHHHHHHHHh-cCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHHHHhhcC
Q 002040          490 PMPIQAQALPVIM-SGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVMG  568 (976)
Q Consensus       490 p~~~Q~~~i~~il-~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~~~~~~~  568 (976)
                      ..|+|.+.+..+. ...++++.+|||+|||++|-++++..+...|      +.++++++|-.+|+..-.+.+.......|
T Consensus       928 fn~~q~~if~~~y~td~~~~~g~ptgsgkt~~ae~a~~~~~~~~p------~~kvvyIap~kalvker~~Dw~~r~~~~g 1001 (1230)
T KOG0952|consen  928 FNPIQTQIFHCLYHTDLNFLLGAPTGSGKTVVAELAIFRALSYYP------GSKVVYIAPDKALVKERSDDWSKRDELPG 1001 (1230)
T ss_pred             cCCccceEEEEEeecchhhhhcCCccCcchhHHHHHHHHHhccCC------CccEEEEcCCchhhcccccchhhhcccCC
Confidence            3356666555444 3457888899999999999999988776653      46899999999999887777776655558


Q ss_pred             cEEEEeeCCCChHHHHHHHhcCCeEEEeCchhHHHHHHhcCCcccccCCceEEEecCcccccccCCchHHHHHHH-----
Q 002040          569 VRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMGFEPQITRIVQ-----  643 (976)
Q Consensus       569 ~~~~~~~gg~~~~~~~~~l~~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDEah~~~~~~f~~~i~~il~-----  643 (976)
                      ++++-+.|.....  ...+ ..++|+|+||.....+..+ |.....+++++++|+||.|.+. .+..+.+..+..     
T Consensus      1002 ~k~ie~tgd~~pd--~~~v-~~~~~~ittpek~dgi~Rs-w~~r~~v~~v~~iv~de~hllg-~~rgPVle~ivsr~n~~ 1076 (1230)
T KOG0952|consen 1002 IKVIELTGDVTPD--VKAV-READIVITTPEKWDGISRS-WQTRKYVQSVSLIVLDEIHLLG-EDRGPVLEVIVSRMNYI 1076 (1230)
T ss_pred             ceeEeccCccCCC--hhhe-ecCceEEcccccccCcccc-ccchhhhccccceeeccccccc-CCCcceEEEEeeccccC
Confidence            9999988877554  2222 3479999999998766543 4455678899999999999654 344444333322     


Q ss_pred             --hcCCCCcEEEEeccCcHHHHHHHHHHcCCCeEEEeCCcccccC-CceEEE-------EecCcchHHHHHHHHHHhhhc
Q 002040          644 --NIRPDRQTVLFSATFPRQVEILARKVLNKPVEIQVGGRSVVNK-DITQLV-------EVRPESDRFLRLLELLGEWYE  713 (976)
Q Consensus       644 --~~~~~~q~i~~SAT~~~~~~~l~~~~l~~~~~i~~~~~~~~~~-~i~q~~-------~~~~~~~k~~~l~~~l~~~~~  713 (976)
                        ...+..+++++|.-+. +...++.. ++....+  +..+.+.+ .+...+       .+.-...+.......+....+
T Consensus      1077 s~~t~~~vr~~glsta~~-na~dla~w-l~~~~~~--nf~~svrpvp~~~~i~gfp~~~~cprm~smnkpa~qaik~~sp 1152 (1230)
T KOG0952|consen 1077 SSQTEEPVRYLGLSTALA-NANDLADW-LNIKDMY--NFRPSVRPVPLEVHIDGFPGQHYCPRMMSMNKPAFQAIKTHSP 1152 (1230)
T ss_pred             ccccCcchhhhhHhhhhh-ccHHHHHH-hCCCCcC--CCCcccccCCceEeecCCCchhcchhhhhcccHHHHHHhcCCC
Confidence              2223345555543332 22223333 2222111  11111111 111111       111111223345566777777


Q ss_pred             CCcEEEEecCHHHHHHHHHHHHH----CCCCceeccCCCCHHHHHHHHHHhccCCcc
Q 002040          714 KGKILIFVHSQEKCDALFRDLLK----HGYPCLSLHGAKDQTDRESTISDFKSNVCN  766 (976)
Q Consensus       714 ~~kvLIF~~s~~~~~~l~~~L~~----~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~  766 (976)
                      ..++|||+.+......-+..|..    ..-+...++  |+..+-+.++....+...+
T Consensus      1153 ~~p~lifv~srrqtrlta~~li~~~~~~~~p~~fl~--~de~e~e~~~~~~~d~~Lk 1207 (1230)
T KOG0952|consen 1153 IKPVLIFVSSRRQTRLTALDLIASCATEDNPKQFLN--MDELELEIIMSKVRDTNLK 1207 (1230)
T ss_pred             CCceEEEeecccccccchHhHHhhccCCCCchhccC--CCHHHHHHHHHHhcccchh
Confidence            88999999987755444433322    122223333  3455666666666655443

>KOG1802 consensus RNA helicase nonsense mRNA reducing factor (pNORF1) [RNA processing and modification]

Probab=98.24  E-value=1.6e-05  Score=90.79  Aligned_cols=84  Identities=23%  Similarity=0.295  Sum_probs=67.2

Q ss_pred             HHHHcCCCCCcHHHHHHHHHHhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHH
Q 002040          481 TIRKLNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDI  560 (976)
Q Consensus       481 ~l~~~~~~~p~~~Q~~~i~~il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~  560 (976)
                      .+...++.++..-|..|+..+++..-.||+||+|+|||.+.. .|+.|+..+      ....|||++|+-..+.|+...|
T Consensus       402 ~~s~~~lpkLN~SQ~~AV~~VL~rplsLIQGPPGTGKTvtsa-~IVyhl~~~------~~~~VLvcApSNiAVDqLaeKI  474 (935)
T KOG1802|consen  402 RFSVPNLPKLNASQSNAVKHVLQRPLSLIQGPPGTGKTVTSA-TIVYHLARQ------HAGPVLVCAPSNIAVDQLAEKI  474 (935)
T ss_pred             hhcCCCchhhchHHHHHHHHHHcCCceeeecCCCCCceehhH-HHHHHHHHh------cCCceEEEcccchhHHHHHHHH
Confidence            455678889999999999999999999999999999998744 445555443      2456899999999999998888


Q ss_pred             HHHHhhcCcEEEEee
Q 002040          561 RKFAKVMGVRCVPVY  575 (976)
Q Consensus       561 ~~~~~~~~~~~~~~~  575 (976)
                      .+    .|++|+-+.
T Consensus       475 h~----tgLKVvRl~  485 (935)
T KOG1802|consen  475 HK----TGLKVVRLC  485 (935)
T ss_pred             Hh----cCceEeeee
Confidence            77    567776543

>KOG1131 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, 5'-3' helicase subunit RAD3 [Transcription; Replication, recombination and repair]

Probab=98.24  E-value=0.00025  Score=79.17  Aligned_cols=149  Identities=16%  Similarity=0.239  Sum_probs=84.1

Q ss_pred             CCcEEEEecCHHHHHHHHHHHHHCCCC------ceeccCCCCHHHHHHHHHHh----ccCCccEEE--ecCcccccCCCC
Q 002040          714 KGKILIFVHSQEKCDALFRDLLKHGYP------CLSLHGAKDQTDRESTISDF----KSNVCNLLI--ATSVAARGLDVK  781 (976)
Q Consensus       714 ~~kvLIF~~s~~~~~~l~~~L~~~~~~------~~~lhg~~~~~~R~~~~~~F----~~g~~~vLV--aT~v~~~GlDi~  781 (976)
                      ++.+++|+++.--.+.+.......|+-      -+.+-+.-+..+-.-++...    -+|.-.||+  |-.-...|+|+.
T Consensus       530 pdG~v~ff~sylYmesiv~~w~~~gil~ei~k~KL~fIetpD~~ETs~al~ny~~aC~~gRGavl~sVargkVsEgidF~  609 (755)
T KOG1131|consen  530 PDGIVCFFPSYLYMESIVSRWYEQGILDEIMKYKLLFIETPDFRETSLALANYRYACDNGRGAVLLSVARGKVSEGIDFD  609 (755)
T ss_pred             CCceEEEEehHHHHHHHHHHHHHHhHHHHHhhCceEEEeCCchhhhHHHHHHHHHHhcCCCCceEEEEecCccccCcccc
Confidence            357889999988777776665554431      12222322222223333322    356666664  556778999998


Q ss_pred             CCc--EEEEeCCCCCHHH------------------------------HHHHhcccCCCCCccEEEEEe-cCC----Cc-
Q 002040          782 ELE--LVINFDAPNHYED------------------------------YVHRVGRTGRAGRKGCAITFI-SEE----DA-  823 (976)
Q Consensus       782 ~v~--~VI~~d~p~s~~~------------------------------y~Qr~GR~gR~g~~g~~~~~~-~~~----d~-  823 (976)
                      +-.  .||+++.|..+..                              ..|..||+-|. +.-+...++ ++.    |. 
T Consensus       610 hhyGR~ViM~gIP~qytesriLkarle~Lrd~~~irE~dflTFDAmRhaAQC~GrvLr~-K~dYg~mI~aDkRf~R~dKR  688 (755)
T KOG1131|consen  610 HHYGREVIMEGIPYQYTESRILKARLEYLRDQFQIRENDFLTFDAMRHAAQCLGRVLRG-KTDYGLMIFADKRFSRGDKR  688 (755)
T ss_pred             cccCceEEEEeccchhhHHHHHHHHHHHHHHHhcccccceechHhHHHHHHHHHHHHhc-cccceeeEeeehhhccccch
Confidence            866  8999999874321                              13788999886 344444444 322    21 


Q ss_pred             -CchHHHHHHHhhccCCCChH-HHHHHHHHHHHHhhhhhhcc
Q 002040          824 -KYSPDLVKALELSEQVVPDD-LKALADSFMAKVNQGLEQAH  863 (976)
Q Consensus       824 -~~~~~i~~~l~~~~~~vp~~-l~~l~~~~~~~~~~~~~~~~  863 (976)
                       +.-.+|...+......+..+ -..++..|+...++-+....
T Consensus       689 ~klp~wi~~~l~~~~~nlstd~a~~varrflR~maQp~~k~d  730 (755)
T KOG1131|consen  689 SKLPKWIRNHLFDAKLNLSTDMANQVARRFLRLMAQPFDKED  730 (755)
T ss_pred             hhhhHHHHhhhhhhccCCCcchhHHHHHHHHHHhcCCCCccc
Confidence             12234444444444444332 25666777777766554433

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

Probab=98.23  E-value=1.1e-05  Score=85.55  Aligned_cols=72  Identities=19%  Similarity=0.310  Sum_probs=50.5

Q ss_pred             CcHHHHHHHHHHhcCCC-EEEEcCCCCchHHHHHHHHHHHHhcC-CCCCCCCCCeEEEEccCHHHHHHHHHHHHH
Q 002040          490 PMPIQAQALPVIMSGRD-CIGVAKTGSGKTLAFVLPMLRHIKDQ-PPVAAGDGPVGLIMAPTRELVQQIHSDIRK  562 (976)
Q Consensus       490 p~~~Q~~~i~~il~g~d-~i~~a~TGsGKT~~~~l~il~~l~~~-~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~  562 (976)
                      +.+.|..||..+++... .+|+||.|+|||.+ +..++..+... .......+..+||++||...+.++...+.+
T Consensus         2 ln~~Q~~Ai~~~~~~~~~~~i~GpPGTGKT~~-l~~~i~~~~~~~~~~~~~~~~~il~~~~sN~avd~~~~~l~~   75 (236)
T PF13086_consen    2 LNESQREAIQSALSSNGITLIQGPPGTGKTTT-LASIIAQLLQRFKSRSADRGKKILVVSPSNAAVDNILERLKK   75 (236)
T ss_dssp             --HHHHHHHHHHCTSSE-EEEE-STTSSHHHH-HHHHHHHH-------HCCCSS-EEEEESSHHHHHHHHHHHHC
T ss_pred             CCHHHHHHHHHHHcCCCCEEEECCCCCChHHH-HHHHHHHhccchhhhhhhccccceeecCCchhHHHHHHHHHh
Confidence            56899999999999998 99999999999965 33444444210 001123467899999999999998888777

>PF13872 AAA_34: P-loop containing NTP hydrolase pore-1

Probab=98.19  E-value=9.3e-06  Score=86.78  Aligned_cols=173  Identities=14%  Similarity=0.140  Sum_probs=104.6

Q ss_pred             cCCCCHHHHHHHHHcCCCCCcHHHHHHHHHHh----------cCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCC
Q 002040          471 QTGLTSKIMETIRKLNYEKPMPIQAQALPVIM----------SGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDG  540 (976)
Q Consensus       471 ~~~l~~~l~~~l~~~~~~~p~~~Q~~~i~~il----------~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~  540 (976)
                      .+.|+..+...      ..++..|.+++-...          ....+++-..||.||.-+..-.|+.++...       .
T Consensus        25 ~~~lp~~~~~~------g~LS~~QLEaV~yA~q~h~~~Lp~~~R~Gf~lGDGtGvGKGR~iAgiI~~n~l~G-------r   91 (303)
T PF13872_consen   25 RLHLPEEVIDS------GLLSALQLEAVIYACQRHEQILPGGSRAGFFLGDGTGVGKGRQIAGIILENWLRG-------R   91 (303)
T ss_pred             ccCCCHHHHhc------ccccHHHHHHHHHHHHHHHhhcccccCcEEEeccCCCcCccchhHHHHHHHHHcC-------C
Confidence            34667665542      346788988886654          234577778999999987666666665542       2


Q ss_pred             CeEEEEccCHHHHHHHHHHHHHHHhhcCcEEEEeeCCCChHHHHHHHhcCCeEEEeCchhHHHHHHhcCCccccc-----
Q 002040          541 PVGLIMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGGKITNL-----  615 (976)
Q Consensus       541 ~~vLIl~Ptr~La~Q~~~~~~~~~~~~~~~~~~~~gg~~~~~~~~~l~~~~~Iiv~Tp~~L~~~l~~~~~~~~~l-----  615 (976)
                      .++|++..+-.|.......+..+... .+.+..+..-. ..   ........||++|+..|+..-.........|     
T Consensus        92 ~r~vwvS~s~dL~~Da~RDl~DIG~~-~i~v~~l~~~~-~~---~~~~~~~GvlF~TYs~L~~~~~~~~~~~sRl~ql~~  166 (303)
T PF13872_consen   92 KRAVWVSVSNDLKYDAERDLRDIGAD-NIPVHPLNKFK-YG---DIIRLKEGVLFSTYSTLISESQSGGKYRSRLDQLVD  166 (303)
T ss_pred             CceEEEECChhhhhHHHHHHHHhCCC-cccceechhhc-cC---cCCCCCCCccchhHHHHHhHHhccCCccchHHHHHH
Confidence            36899999999988887877775432 23333222100 00   0011235799999999877653221111111     


Q ss_pred             ----CCceEEEecCcccccccCCc--------hHHHHHHHhcCCCCcEEEEeccCcHHH
Q 002040          616 ----RRVTYLVMDEADRMFDMGFE--------PQITRIVQNIRPDRQTVLFSATFPRQV  662 (976)
Q Consensus       616 ----~~~~~vVlDEah~~~~~~f~--------~~i~~il~~~~~~~q~i~~SAT~~~~~  662 (976)
                          ..=.+||+||||.+.+..-.        ..+..+-..+ |+.++|++|||.....
T Consensus       167 W~g~dfdgvivfDEcH~akn~~~~~~~~sk~g~avl~LQ~~L-P~ARvvY~SATgasep  224 (303)
T PF13872_consen  167 WCGEDFDGVIVFDECHKAKNLSSGSKKPSKTGIAVLELQNRL-PNARVVYASATGASEP  224 (303)
T ss_pred             HHhcCCCceEEeccchhcCCCCccCccccHHHHHHHHHHHhC-CCCcEEEecccccCCC
Confidence                11248999999988665321        1222333334 6677999999975543

>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=98.13  E-value=5.5e-06  Score=84.90  Aligned_cols=146  Identities=16%  Similarity=0.247  Sum_probs=75.6

Q ss_pred             CCCcHHHHHHHHHHhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHH-------HHHH
Q 002040          488 EKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQI-------HSDI  560 (976)
Q Consensus       488 ~~p~~~Q~~~i~~il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~-------~~~~  560 (976)
                      ...++.|..++.+++...-+++.|+.|||||+.++..++..+...      .-.+++|+-|+.+....+       .+.+
T Consensus         3 ~p~~~~Q~~~~~al~~~~~v~~~G~AGTGKT~LA~a~Al~~v~~g------~~~kiii~Rp~v~~~~~lGflpG~~~eK~   76 (205)
T PF02562_consen    3 KPKNEEQKFALDALLNNDLVIVNGPAGTGKTFLALAAALELVKEG------EYDKIIITRPPVEAGEDLGFLPGDLEEKM   76 (205)
T ss_dssp             ---SHHHHHHHHHHHH-SEEEEE--TTSSTTHHHHHHHHHHHHTT------S-SEEEEEE-S--TT----SS--------
T ss_pred             cCCCHHHHHHHHHHHhCCeEEEECCCCCcHHHHHHHHHHHHHHhC------CCcEEEEEecCCCCccccccCCCCHHHHH
Confidence            345789999999999888889999999999999999998888752      234677777876431111       0000


Q ss_pred             HHHHhhcCcEEEEeeCCCChHHHHHHHhcCCeEEEeCchhHHHHHHhcCCcccccCCceEEEecCcccccccCCchHHHH
Q 002040          561 RKFAKVMGVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMGFEPQITR  640 (976)
Q Consensus       561 ~~~~~~~~~~~~~~~gg~~~~~~~~~l~~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDEah~~~~~~f~~~i~~  640 (976)
                      .-++..+--....+++..    .+..+.....|-+.++.-+.       +  ..|. -.+||||||+.+.    ..++..
T Consensus        77 ~p~~~p~~d~l~~~~~~~----~~~~~~~~~~Ie~~~~~~iR-------G--rt~~-~~~iIvDEaQN~t----~~~~k~  138 (205)
T PF02562_consen   77 EPYLRPIYDALEELFGKE----KLEELIQNGKIEIEPLAFIR-------G--RTFD-NAFIIVDEAQNLT----PEELKM  138 (205)
T ss_dssp             -TTTHHHHHHHTTTS-TT----CHHHHHHTTSEEEEEGGGGT-------T----B--SEEEEE-SGGG------HHHHHH
T ss_pred             HHHHHHHHHHHHHHhChH----hHHHHhhcCeEEEEehhhhc-------C--cccc-ceEEEEecccCCC----HHHHHH
Confidence            000000000000001111    12233334566666654331       1  2233 3899999999764    557888


Q ss_pred             HHHhcCCCCcEEEEecc
Q 002040          641 IVQNIRPDRQTVLFSAT  657 (976)
Q Consensus       641 il~~~~~~~q~i~~SAT  657 (976)
                      ++..+..+.++|++.-+
T Consensus       139 ilTR~g~~skii~~GD~  155 (205)
T PF02562_consen  139 ILTRIGEGSKIIITGDP  155 (205)
T ss_dssp             HHTTB-TT-EEEEEE--
T ss_pred             HHcccCCCcEEEEecCc
Confidence            88888888887776554

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

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

Probab=98.08  E-value=1.2e-05  Score=82.96  Aligned_cols=125  Identities=17%  Similarity=0.241  Sum_probs=72.3

Q ss_pred             CcHHHHHHHHHHhcCC--CEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHHHHhhc
Q 002040          490 PMPIQAQALPVIMSGR--DCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVM  567 (976)
Q Consensus       490 p~~~Q~~~i~~il~g~--d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~~~~~~  567 (976)
                      +++-|..++..++...  -++++|+.|+|||.+ +..+...+..       .+..+++++||...+..+...       .
T Consensus         2 L~~~Q~~a~~~~l~~~~~~~~l~G~aGtGKT~~-l~~~~~~~~~-------~g~~v~~~apT~~Aa~~L~~~-------~   66 (196)
T PF13604_consen    2 LNEEQREAVRAILTSGDRVSVLQGPAGTGKTTL-LKALAEALEA-------AGKRVIGLAPTNKAAKELREK-------T   66 (196)
T ss_dssp             S-HHHHHHHHHHHHCTCSEEEEEESTTSTHHHH-HHHHHHHHHH-------TT--EEEEESSHHHHHHHHHH-------H
T ss_pred             CCHHHHHHHHHHHhcCCeEEEEEECCCCCHHHH-HHHHHHHHHh-------CCCeEEEECCcHHHHHHHHHh-------h
Confidence            6789999999997543  467779999999975 4445555554       257899999999887765443       2


Q ss_pred             CcEEEEeeCCCChHHHHHHHhcCCeEEEeCchhHHHHHHhcC-CcccccCCceEEEecCcccccccCCchHHHHHHHhcC
Q 002040          568 GVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSG-GKITNLRRVTYLVMDEADRMFDMGFEPQITRIVQNIR  646 (976)
Q Consensus       568 ~~~~~~~~gg~~~~~~~~~l~~~~~Iiv~Tp~~L~~~l~~~~-~~~~~l~~~~~vVlDEah~~~~~~f~~~i~~il~~~~  646 (976)
                      ++.+.                        |-..++....... .....+...++||||||-.+.    ...+..++..+.
T Consensus        67 ~~~a~------------------------Ti~~~l~~~~~~~~~~~~~~~~~~vliVDEasmv~----~~~~~~ll~~~~  118 (196)
T PF13604_consen   67 GIEAQ------------------------TIHSFLYRIPNGDDEGRPELPKKDVLIVDEASMVD----SRQLARLLRLAK  118 (196)
T ss_dssp             TS-EE------------------------EHHHHTTEECCEECCSSCC-TSTSEEEESSGGG-B----HHHHHHHHHHS-
T ss_pred             Ccchh------------------------hHHHHHhcCCcccccccccCCcccEEEEecccccC----HHHHHHHHHHHH
Confidence            22222                        2111111100000 000114556899999999653    446677777776


Q ss_pred             C-CCcEEEEecc
Q 002040          647 P-DRQTVLFSAT  657 (976)
Q Consensus       647 ~-~~q~i~~SAT  657 (976)
                      . ..++|++.-+
T Consensus       119 ~~~~klilvGD~  130 (196)
T PF13604_consen  119 KSGAKLILVGDP  130 (196)
T ss_dssp             T-T-EEEEEE-T
T ss_pred             hcCCEEEEECCc
Confidence            6 5667766655

>KOG0383 consensus Predicted helicase [General function prediction only]

Probab=98.07  E-value=7.8e-07  Score=105.04  Aligned_cols=79  Identities=25%  Similarity=0.357  Sum_probs=66.6

Q ss_pred             chHHHHHHHHHHhhhcC-CcEEEEecCHHHHHHHHHHHHHCCCCceeccCCCCHHHHHHHHHHhc---cCCccEEEecCc
Q 002040          698 SDRFLRLLELLGEWYEK-GKILIFVHSQEKCDALFRDLLKHGYPCLSLHGAKDQTDRESTISDFK---SNVCNLLIATSV  773 (976)
Q Consensus       698 ~~k~~~l~~~l~~~~~~-~kvLIF~~s~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~---~g~~~vLVaT~v  773 (976)
                      ..|+..|...+...... .+||||.+.+.+.+.|..++...+ ....+.|......|+.++..|+   ...+.+|++|.+
T Consensus       614 ~~k~~~l~~~~~~l~~~ghrvl~~~q~~~~ldlled~~~~~~-~~~r~dG~~~~~~rq~ai~~~n~~~~~~~cfllstra  692 (696)
T KOG0383|consen  614 SGKLTLLLKMLKKLKSSGHRVLIFSQMIHMLDLLEDYLTYEG-KYERIDGPITGPERQAAIDRFNAPGSNQFCFLLSTRA  692 (696)
T ss_pred             HHHHHHHHHHHHHHHhcchhhHHHHHHHHHHHHhHHHHhccC-cceeccCCccchhhhhhccccCCCCccceEEEeeccc
Confidence            34556666666666554 499999999999999999998888 8999999999999999999998   446889999999


Q ss_pred             cccc
Q 002040          774 AARG  777 (976)
Q Consensus       774 ~~~G  777 (976)
                      .+.|
T Consensus       693 ~g~g  696 (696)
T KOG0383|consen  693 GGLG  696 (696)
T ss_pred             ccCC
Confidence            8876

>TIGR00376 DNA helicase, putative

Probab=98.06  E-value=0.0002  Score=86.87  Aligned_cols=67  Identities=21%  Similarity=0.269  Sum_probs=52.3

Q ss_pred             CCCcHHHHHHHHHHhcC-CCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHH
Q 002040          488 EKPMPIQAQALPVIMSG-RDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRK  562 (976)
Q Consensus       488 ~~p~~~Q~~~i~~il~g-~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~  562 (976)
                      ..+.+.|..|+..++.. ..+||.||+|+|||.+.+ .++.++..       .|++|||++||...+.++.+.+..
T Consensus       156 ~~ln~~Q~~Av~~~l~~~~~~lI~GpPGTGKT~t~~-~ii~~~~~-------~g~~VLv~a~sn~Avd~l~e~l~~  223 (637)
T TIGR00376       156 PNLNESQKEAVSFALSSKDLFLIHGPPGTGKTRTLV-ELIRQLVK-------RGLRVLVTAPSNIAVDNLLERLAL  223 (637)
T ss_pred             CCCCHHHHHHHHHHhcCCCeEEEEcCCCCCHHHHHH-HHHHHHHH-------cCCCEEEEcCcHHHHHHHHHHHHh
Confidence            45789999999999876 567889999999997644 34444333       256899999999999988877765

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.

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

Probab=98.01  E-value=1.9e-05  Score=79.29  Aligned_cols=105  Identities=19%  Similarity=0.274  Sum_probs=72.1

Q ss_pred             CCcEEEEecCHHHHHHHHHHHHHCCC--CceeccCCCCHHHHHHHHHHhccCCccEEEecC--cccccCCCCC--CcEEE
Q 002040          714 KGKILIFVHSQEKCDALFRDLLKHGY--PCLSLHGAKDQTDRESTISDFKSNVCNLLIATS--VAARGLDVKE--LELVI  787 (976)
Q Consensus       714 ~~kvLIF~~s~~~~~~l~~~L~~~~~--~~~~lhg~~~~~~R~~~~~~F~~g~~~vLVaT~--v~~~GlDi~~--v~~VI  787 (976)
                      ++.+|||++|...++.+...|.....  .+..+..  .......+++.|+.+...||+|+.  .+..|||+++  +.+||
T Consensus         9 ~g~~lv~f~Sy~~l~~~~~~~~~~~~~~~~~v~~q--~~~~~~~~l~~~~~~~~~il~~v~~g~~~EGiD~~~~~~r~vi   86 (167)
T PF13307_consen    9 PGGVLVFFPSYRRLEKVYERLKERLEEKGIPVFVQ--GSKSRDELLEEFKRGEGAILLAVAGGSFSEGIDFPGDLLRAVI   86 (167)
T ss_dssp             SSEEEEEESSHHHHHHHHTT-TSS-E-ETSCEEES--TCCHHHHHHHHHCCSSSEEEEEETTSCCGSSS--ECESEEEEE
T ss_pred             CCCEEEEeCCHHHHHHHHHHHHhhcccccceeeec--CcchHHHHHHHHHhccCeEEEEEecccEEEeecCCCchhheee
Confidence            58999999999999999999876531  1222222  355778999999999999999998  9999999997  77899


Q ss_pred             EeCCCCC----HH--------------------------HHHHHhcccCCCCCccEEEEEecC
Q 002040          788 NFDAPNH----YE--------------------------DYVHRVGRTGRAGRKGCAITFISE  820 (976)
Q Consensus       788 ~~d~p~s----~~--------------------------~y~Qr~GR~gR~g~~g~~~~~~~~  820 (976)
                      +...|..    +.                          ...|.+||+-|....-.++++++.
T Consensus        87 i~glPfp~~~d~~~~~~~~~~~~~~~~~~~~~~~~~a~~~l~Qa~GR~iR~~~D~g~i~llD~  149 (167)
T PF13307_consen   87 IVGLPFPPPSDPLVQAKREYLDKQGKNPFRDWYLPPAIRKLKQAIGRLIRSEDDYGVIILLDS  149 (167)
T ss_dssp             EES-----TTCHHHHHHHHHHHHCCTTCHHHHTHHHHHHHHHHHHHCC--STT-EEEEEEESG
T ss_pred             ecCCCCCCCCCHHHHHHHHHHHHHhccchhhHhhHHHHHHHhhhcCcceeccCCcEEEEEEcC
Confidence            9888752    11                          114999999998765445555543

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

Probab=98.00  E-value=9.5e-05  Score=76.46  Aligned_cols=154  Identities=20%  Similarity=0.337  Sum_probs=95.6

Q ss_pred             ccccCCCCHHHHHHHHHcCCCCCcHHHHHHHHHHhc---CCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEE
Q 002040          468 TWHQTGLTSKIMETIRKLNYEKPMPIQAQALPVIMS---GRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGL  544 (976)
Q Consensus       468 ~~~~~~l~~~l~~~l~~~~~~~p~~~Q~~~i~~il~---g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vL  544 (976)
                      +|.....|..++=.+. .++ -.++.|.+.+..+++   |.+.+.+.-||.|||.+ ++||+..+...      ....|.
T Consensus         4 ~w~p~~~P~wLl~E~e-~~i-liR~~Q~~ia~~mi~~~~~~n~v~QlnMGeGKTsV-I~Pmla~~LAd------g~~Lvr   74 (229)
T PF12340_consen    4 NWDPMEYPDWLLFEIE-SNI-LIRPVQVEIAREMISPPSGKNSVMQLNMGEGKTSV-IVPMLALALAD------GSRLVR   74 (229)
T ss_pred             CCCchhChHHHHHHHH-cCc-eeeHHHHHHHHHHhCCCCCCCeEeeecccCCccch-HHHHHHHHHcC------CCcEEE
Confidence            5666666666653322 232 478999999999885   57899999999999987 78888777653      234677


Q ss_pred             EEccCHHHHHHHHHHHHHHHh-hcCcEEEE--eeCCCChH----HHH----HHHhcCCeEEEeCchhHHHHHHhcC----
Q 002040          545 IMAPTRELVQQIHSDIRKFAK-VMGVRCVP--VYGGSGVA----QQI----SELKRGTEIVVCTPGRMIDILCTSG----  609 (976)
Q Consensus       545 Il~Ptr~La~Q~~~~~~~~~~-~~~~~~~~--~~gg~~~~----~~~----~~l~~~~~Iiv~Tp~~L~~~l~~~~----  609 (976)
                      ++|| ..|..|.++.+...+. .++-.+..  +.-.....    ..+    ........|+++||+.++.+....-    
T Consensus        75 viVp-k~Ll~q~~~~L~~~lg~l~~r~i~~lpFsR~~~~~~~~~~~~~~l~~~~~~~~gill~~PEhilSf~L~~le~l~  153 (229)
T PF12340_consen   75 VIVP-KALLEQMRQMLRSRLGGLLNRRIYHLPFSRSTPLTPETLEKIRQLLEECMRSGGILLATPEHILSFKLKGLERLQ  153 (229)
T ss_pred             EEcC-HHHHHHHHHHHHHHHHHHhCCeeEEecccCCCCCCHHHHHHHHHHHHHHHHcCCEEEeChHHHHHHHHHHHHHHH
Confidence            8888 5788999988876443 33433332  22222211    111    1222345799999998765432211    


Q ss_pred             -Ccc----------cccCCceEEEecCcccccc
Q 002040          610 -GKI----------TNLRRVTYLVMDEADRMFD  631 (976)
Q Consensus       610 -~~~----------~~l~~~~~vVlDEah~~~~  631 (976)
                       +..          .-|.....=|+||+|.++.
T Consensus       154 ~~~~~~~~~l~~~q~~l~~~~rdilDEsDe~L~  186 (229)
T PF12340_consen  154 DGKPEEARELLKIQKWLDEHSRDILDESDEILS  186 (229)
T ss_pred             hcCHHHHHHHHHHHHHHHhcCCeEeECchhccC
Confidence             010          0133445578999997653

There are two conserved sequence motifs: LLE and NMG.

>PRK10536 hypothetical protein; Provisional

Probab=97.96  E-value=0.00012  Score=77.18  Aligned_cols=143  Identities=13%  Similarity=0.119  Sum_probs=82.7

Q ss_pred             cCCCCCcHHHHHHHHHHhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHH-----------
Q 002040          485 LNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELV-----------  553 (976)
Q Consensus       485 ~~~~~p~~~Q~~~i~~il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La-----------  553 (976)
                      .++...+..|..++.++.++..+++.|++|+|||+.++..++..+...      .-.+++|.-|+....           
T Consensus        55 ~~i~p~n~~Q~~~l~al~~~~lV~i~G~aGTGKT~La~a~a~~~l~~~------~~~kIiI~RP~v~~ge~LGfLPG~~~  128 (262)
T PRK10536         55 SPILARNEAQAHYLKAIESKQLIFATGEAGCGKTWISAAKAAEALIHK------DVDRIIVTRPVLQADEDLGFLPGDIA  128 (262)
T ss_pred             ccccCCCHHHHHHHHHHhcCCeEEEECCCCCCHHHHHHHHHHHHHhcC------CeeEEEEeCCCCCchhhhCcCCCCHH
Confidence            445567789999999999988889999999999998777777666442      123455555664321           


Q ss_pred             HHHHHHHHHHHhhcCcEEEEeeCCCChHHHHHHH-h-cCCeEEEeCchhHHHHHHhcCCcccccCCceEEEecCcccccc
Q 002040          554 QQIHSDIRKFAKVMGVRCVPVYGGSGVAQQISEL-K-RGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFD  631 (976)
Q Consensus       554 ~Q~~~~~~~~~~~~~~~~~~~~gg~~~~~~~~~l-~-~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDEah~~~~  631 (976)
                      .-+.-++.-+...+..    +.|.    ..+..+ . ....|.|+...    ++..     ..|. -++||||||+.+. 
T Consensus       129 eK~~p~~~pi~D~L~~----~~~~----~~~~~~~~~~~~~Iei~~l~----ymRG-----rtl~-~~~vIvDEaqn~~-  189 (262)
T PRK10536        129 EKFAPYFRPVYDVLVR----RLGA----SFMQYCLRPEIGKVEIAPFA----YMRG-----RTFE-NAVVILDEAQNVT-  189 (262)
T ss_pred             HHHHHHHHHHHHHHHH----HhCh----HHHHHHHHhccCcEEEecHH----HhcC-----Cccc-CCEEEEechhcCC-
Confidence            1111112222111111    1111    111211 1 12345555433    2321     1232 3799999999753 


Q ss_pred             cCCchHHHHHHHhcCCCCcEEEEe
Q 002040          632 MGFEPQITRIVQNIRPDRQTVLFS  655 (976)
Q Consensus       632 ~~f~~~i~~il~~~~~~~q~i~~S  655 (976)
                         ..++..++..+..+.++|++.
T Consensus       190 ---~~~~k~~ltR~g~~sk~v~~G  210 (262)
T PRK10536        190 ---AAQMKMFLTRLGENVTVIVNG  210 (262)
T ss_pred             ---HHHHHHHHhhcCCCCEEEEeC
Confidence               467788888888777766654

>TIGR01447 recD exodeoxyribonuclease V, alpha subunit

Probab=97.81  E-value=0.00015  Score=86.71  Aligned_cols=146  Identities=21%  Similarity=0.265  Sum_probs=89.4

Q ss_pred             cHHHHHHHHHHhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHHHHhhcCcE
Q 002040          491 MPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVMGVR  570 (976)
Q Consensus       491 ~~~Q~~~i~~il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~~~~~~~~~  570 (976)
                      .+.|..|+..++.++-++|.|+.|+|||++ +..++..+.....  ....+.+++++||--.|..+.+.+......++..
T Consensus       147 ~~~Qk~A~~~al~~~~~vitGgpGTGKTt~-v~~ll~~l~~~~~--~~~~~~I~l~APTGkAA~rL~e~~~~~~~~l~~~  223 (586)
T TIGR01447       147 QNWQKVAVALALKSNFSLITGGPGTGKTTT-VARLLLALVKQSP--KQGKLRIALAAPTGKAAARLAESLRKAVKNLAAA  223 (586)
T ss_pred             cHHHHHHHHHHhhCCeEEEEcCCCCCHHHH-HHHHHHHHHHhcc--ccCCCcEEEECCcHHHHHHHHHHHHhhhcccccc
Confidence            379999999999999999999999999986 3344444432211  0113578999999988887777665533222110


Q ss_pred             EEEeeCCCChHHHHHHHhcCCeEEEeCchhHHHHHHhcCC---cccccCCceEEEecCcccccccCCchHHHHHHHhcCC
Q 002040          571 CVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGG---KITNLRRVTYLVMDEADRMFDMGFEPQITRIVQNIRP  647 (976)
Q Consensus       571 ~~~~~gg~~~~~~~~~l~~~~~Iiv~Tp~~L~~~l~~~~~---~~~~l~~~~~vVlDEah~~~~~~f~~~i~~il~~~~~  647 (976)
                                .    .+.....+-..|-.+|+........   ...+...+++||||||-.+ +   ...+..++..+++
T Consensus       224 ----------~----~~~~~~~~~a~TiHrlLg~~~~~~~~~~~~~~~l~~dvlIiDEaSMv-d---~~l~~~ll~al~~  285 (586)
T TIGR01447       224 ----------E----ALIAALPSEAVTIHRLLGIKPDTKRFRHHERNPLPLDVLVVDEASMV-D---LPLMAKLLKALPP  285 (586)
T ss_pred             ----------h----hhhhccccccchhhhhhcccCCcchhhhcccCCCcccEEEEcccccC-C---HHHHHHHHHhcCC
Confidence                      0    0011112223444444322111000   0012335789999999843 2   4567788888998


Q ss_pred             CCcEEEEecc
Q 002040          648 DRQTVLFSAT  657 (976)
Q Consensus       648 ~~q~i~~SAT  657 (976)
                      ..++|++.=.
T Consensus       286 ~~rlIlvGD~  295 (586)
T TIGR01447       286 NTKLILLGDK  295 (586)
T ss_pred             CCEEEEECCh
Confidence            9998887655

This family describes the exodeoxyribonuclease V alpha subunit, RecD. RecD is part of a RecBCD complex. A related family in the Gram-positive bacteria separates in a phylogenetic tree, has an additional N-terminal extension of about 200 residues, and is not supported as a member of a RecBCD complex by neighboring genes. The related family is consequently described by a different model.

>PRK10875 recD exonuclease V subunit alpha; Provisional

Probab=97.75  E-value=0.00015  Score=86.96  Aligned_cols=146  Identities=21%  Similarity=0.252  Sum_probs=89.7

Q ss_pred             CcHHHHHHHHHHhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHHHHhhcCc
Q 002040          490 PMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVMGV  569 (976)
Q Consensus       490 p~~~Q~~~i~~il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~~~~~~~~  569 (976)
                      ..+.|..|+...+.++-+||.|++|+|||++ +..++..+....   ......+++++||-..|..+.+.+......+++
T Consensus       153 ~~d~Qk~Av~~a~~~~~~vItGgpGTGKTt~-v~~ll~~l~~~~---~~~~~~i~l~APTgkAA~rL~e~~~~~~~~~~~  228 (615)
T PRK10875        153 EVDWQKVAAAVALTRRISVISGGPGTGKTTT-VAKLLAALIQLA---DGERCRIRLAAPTGKAAARLTESLGKALRQLPL  228 (615)
T ss_pred             CCHHHHHHHHHHhcCCeEEEEeCCCCCHHHH-HHHHHHHHHHhc---CCCCcEEEEECCcHHHHHHHHHHHHhhhhcccc
Confidence            3589999999999999999999999999986 333343333211   112356889999999998887776654333221


Q ss_pred             EEEEeeCCCChHHHHHHHhcCCeEEEeCchhHHHHHHhcC---CcccccCCceEEEecCcccccccCCchHHHHHHHhcC
Q 002040          570 RCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSG---GKITNLRRVTYLVMDEADRMFDMGFEPQITRIVQNIR  646 (976)
Q Consensus       570 ~~~~~~gg~~~~~~~~~l~~~~~Iiv~Tp~~L~~~l~~~~---~~~~~l~~~~~vVlDEah~~~~~~f~~~i~~il~~~~  646 (976)
                      .-              .+......-..|-.+|+.......   ....+.-.+++||||||-.+ +   ...+..++..++
T Consensus       229 ~~--------------~~~~~~~~~a~TiHrlLg~~~~~~~~~~~~~~~l~~dvlIvDEaSMv-d---~~lm~~ll~al~  290 (615)
T PRK10875        229 TD--------------EQKKRIPEEASTLHRLLGAQPGSQRLRYHAGNPLHLDVLVVDEASMV-D---LPMMARLIDALP  290 (615)
T ss_pred             ch--------------hhhhcCCCchHHHHHHhCcCCCccchhhccccCCCCCeEEEChHhcc-c---HHHHHHHHHhcc
Confidence            10              000001111233333322111000   00112335689999999843 2   567778889999


Q ss_pred             CCCcEEEEecc
Q 002040          647 PDRQTVLFSAT  657 (976)
Q Consensus       647 ~~~q~i~~SAT  657 (976)
                      +..++|++.-.
T Consensus       291 ~~~rlIlvGD~  301 (615)
T PRK10875        291 PHARVIFLGDR  301 (615)
T ss_pred             cCCEEEEecch
Confidence            99998888765

>PF09848 DUF2075: Uncharacterized conserved protein (DUF2075); InterPro: IPR018647 This domain, found in putative ATP/GTP binding proteins, has no known function

Probab=97.67  E-value=0.00014  Score=82.47  Aligned_cols=108  Identities=16%  Similarity=0.242  Sum_probs=66.0

Q ss_pred             CEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHHHHhhcCcEEEEeeCCCChHHHHH
Q 002040          506 DCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQIS  585 (976)
Q Consensus       506 d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~~~~~~~~~~~~~~gg~~~~~~~~  585 (976)
                      -+||.|..|||||++++ .++..+..     ...+..++++|+...|...+...+....          ..         
T Consensus         3 v~~I~G~aGTGKTvla~-~l~~~l~~-----~~~~~~~~~l~~n~~l~~~l~~~l~~~~----------~~---------   57 (352)
T PF09848_consen    3 VILITGGAGTGKTVLAL-NLAKELQN-----SEEGKKVLYLCGNHPLRNKLREQLAKKY----------NP---------   57 (352)
T ss_pred             EEEEEecCCcCHHHHHH-HHHHHhhc-----cccCCceEEEEecchHHHHHHHHHhhhc----------cc---------
Confidence            36888999999998744 34444311     1246678999999999887777776532          00         


Q ss_pred             HHhcCCeEEEeCchhHHHHHHhcCCcccccCCceEEEecCcccccccC-------CchHHHHHHHh
Q 002040          586 ELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMG-------FEPQITRIVQN  644 (976)
Q Consensus       586 ~l~~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDEah~~~~~~-------f~~~i~~il~~  644 (976)
                         ......+..+..++..+.   ........+++|||||||+|...+       ...++..++..
T Consensus        58 ---~~~~~~~~~~~~~i~~~~---~~~~~~~~~DviivDEAqrl~~~~~~~~~~~~~~~L~~i~~~  117 (352)
T PF09848_consen   58 ---KLKKSDFRKPTSFINNYS---ESDKEKNKYDVIIVDEAQRLRTKGDQYNNFSEPNQLDEIIKR  117 (352)
T ss_pred             ---chhhhhhhhhHHHHhhcc---cccccCCcCCEEEEehhHhhhhccccccccccHHHHHHHHhc
Confidence               001223344444443332   011345678999999999987631       23556666555

It is found in some proteins described as Schlafen family members, which may have a role in hematopoeitic cell differentiation [].

>KOG1803 consensus DNA helicase [Replication, recombination and repair]

Probab=97.63  E-value=0.00015  Score=83.03  Aligned_cols=65  Identities=23%  Similarity=0.273  Sum_probs=51.5

Q ss_pred             CCCcHHHHHHHHHHhcCCC-EEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHH
Q 002040          488 EKPMPIQAQALPVIMSGRD-CIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDI  560 (976)
Q Consensus       488 ~~p~~~Q~~~i~~il~g~d-~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~  560 (976)
                      ..+.+-|..|+...++.++ .++.||+|+|||.+....+.+.+..        +.+|||++||...+..+.+.+
T Consensus       184 ~~ln~SQk~Av~~~~~~k~l~~I~GPPGTGKT~TlvEiI~qlvk~--------~k~VLVcaPSn~AVdNiverl  249 (649)
T KOG1803|consen  184 KNLNSSQKAAVSFAINNKDLLIIHGPPGTGKTRTLVEIISQLVKQ--------KKRVLVCAPSNVAVDNIVERL  249 (649)
T ss_pred             ccccHHHHHHHHHHhccCCceEeeCCCCCCceeeHHHHHHHHHHc--------CCeEEEEcCchHHHHHHHHHh
Confidence            3567889999999998865 5677999999998866655555543        568999999999988887753

>TIGR01448 recD_rel helicase, putative, RecD/TraA family

Probab=97.63  E-value=0.0004  Score=85.59  Aligned_cols=131  Identities=17%  Similarity=0.166  Sum_probs=80.4

Q ss_pred             CCCcHHHHHHHHHHhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHHHHhhc
Q 002040          488 EKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVM  567 (976)
Q Consensus       488 ~~p~~~Q~~~i~~il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~~~~~~  567 (976)
                      ..+++.|..|+..+..++-+++.|+.|+|||++ +..++..+...     +....+++++||-..|..+.+.       .
T Consensus       322 ~~l~~~Q~~Ai~~~~~~~~~iitGgpGTGKTt~-l~~i~~~~~~~-----~~~~~v~l~ApTg~AA~~L~e~-------~  388 (720)
T TIGR01448       322 KGLSEEQKQALDTAIQHKVVILTGGPGTGKTTI-TRAIIELAEEL-----GGLLPVGLAAPTGRAAKRLGEV-------T  388 (720)
T ss_pred             CCCCHHHHHHHHHHHhCCeEEEECCCCCCHHHH-HHHHHHHHHHc-----CCCceEEEEeCchHHHHHHHHh-------c
Confidence            468999999999999989999999999999975 34444444332     1114678899998777644322       2


Q ss_pred             CcEEEEeeCCCChHHHHHHHhcCCeEEEeCchhHHHHHHhcCCcccccCCceEEEecCcccccccCCchHHHHHHHhcCC
Q 002040          568 GVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMGFEPQITRIVQNIRP  647 (976)
Q Consensus       568 ~~~~~~~~gg~~~~~~~~~l~~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDEah~~~~~~f~~~i~~il~~~~~  647 (976)
                      |....      .+...   +..       .++.+...      ........++||||||+.+.    ...+..++..+++
T Consensus       389 g~~a~------Tih~l---L~~-------~~~~~~~~------~~~~~~~~~llIvDEaSMvd----~~~~~~Ll~~~~~  442 (720)
T TIGR01448       389 GLTAS------TIHRL---LGY-------GPDTFRHN------HLEDPIDCDLLIVDESSMMD----TWLALSLLAALPD  442 (720)
T ss_pred             CCccc------cHHHH---hhc-------cCCccchh------hhhccccCCEEEEeccccCC----HHHHHHHHHhCCC
Confidence            22111      11111   000       00000000      00122357899999999653    3456777888888


Q ss_pred             CCcEEEEecc
Q 002040          648 DRQTVLFSAT  657 (976)
Q Consensus       648 ~~q~i~~SAT  657 (976)
                      ..++|++.-+
T Consensus       443 ~~rlilvGD~  452 (720)
T TIGR01448       443 HARLLLVGDT  452 (720)
T ss_pred             CCEEEEECcc
Confidence            8888887655

This model describes a family similar to RecD, the exodeoxyribonuclease V alpha chain of TIGR01447. Members of this family, however, are not found in a context of RecB and RecC and are longer by about 200 amino acids at the amino end. Chlamydia muridarum has both a member of this family and a RecD.

>PRK12723 flagellar biosynthesis regulator FlhF; Provisional

Probab=97.62  E-value=0.0017  Score=73.58  Aligned_cols=171  Identities=14%  Similarity=0.108  Sum_probs=90.5

Q ss_pred             CCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeE-EEEccC-HHHHHHHHHHHHHHHhhcCcEEEEeeCCCChH
Q 002040          504 GRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVG-LIMAPT-RELVQQIHSDIRKFAKVMGVRCVPVYGGSGVA  581 (976)
Q Consensus       504 g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~v-LIl~Pt-r~La~Q~~~~~~~~~~~~~~~~~~~~gg~~~~  581 (976)
                      ...++++|+||+|||++..-.+..+....    ...+..| ||-+-| |.-+.   .++..++..+|+.+.+.       
T Consensus       174 ~~vi~lvGptGvGKTTT~aKLA~~~~~~~----~~~g~~V~lit~Dt~R~aa~---eQL~~~a~~lgvpv~~~-------  239 (388)
T PRK12723        174 KRVFILVGPTGVGKTTTIAKLAAIYGINS----DDKSLNIKIITIDNYRIGAK---KQIQTYGDIMGIPVKAI-------  239 (388)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHhhh----ccCCCeEEEEeccCccHHHH---HHHHHHhhcCCcceEee-------
Confidence            35688899999999987544333322211    0123334 444443 44443   22556666566654322       


Q ss_pred             HHHHHHhcCCeEEEeCchhHHHHHHhcCCcccccCCceEEEecCcccccccC-CchHHHHHHHhcCCC-CcEEEEeccCc
Q 002040          582 QQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMG-FEPQITRIVQNIRPD-RQTVLFSATFP  659 (976)
Q Consensus       582 ~~~~~l~~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDEah~~~~~~-f~~~i~~il~~~~~~-~q~i~~SAT~~  659 (976)
                                    .++..+...+.       .+.++++||||.+.++.... ....+..++..+.+. .-++++|||..
T Consensus       240 --------------~~~~~l~~~L~-------~~~~~DlVLIDTaGr~~~~~~~l~el~~~l~~~~~~~e~~LVlsat~~  298 (388)
T PRK12723        240 --------------ESFKDLKEEIT-------QSKDFDLVLVDTIGKSPKDFMKLAEMKELLNACGRDAEFHLAVSSTTK  298 (388)
T ss_pred             --------------CcHHHHHHHHH-------HhCCCCEEEEcCCCCCccCHHHHHHHHHHHHhcCCCCeEEEEEcCCCC
Confidence                          13333433332       34568999999999765211 123444555555544 45688999986


Q ss_pred             HH-HHHHHHHHcCCCeEEEeCCcccccCCceEEEEecCcchHHHHHHHHHHhhhcCCcEEEEecCH
Q 002040          660 RQ-VEILARKVLNKPVEIQVGGRSVVNKDITQLVEVRPESDRFLRLLELLGEWYEKGKILIFVHSQ  724 (976)
Q Consensus       660 ~~-~~~l~~~~l~~~~~i~~~~~~~~~~~i~q~~~~~~~~~k~~~l~~~l~~~~~~~kvLIF~~s~  724 (976)
                      .. +...+..|-..++.             .-.+...+...+.-.++.++...  +-|+..++..+
T Consensus       299 ~~~~~~~~~~~~~~~~~-------------~~I~TKlDet~~~G~~l~~~~~~--~~Pi~yit~Gq  349 (388)
T PRK12723        299 TSDVKEIFHQFSPFSYK-------------TVIFTKLDETTCVGNLISLIYEM--RKEVSYVTDGQ  349 (388)
T ss_pred             HHHHHHHHHHhcCCCCC-------------EEEEEeccCCCcchHHHHHHHHH--CCCEEEEeCCC
Confidence            43 44444444221110             11234455566667777776553  34555555544

>KOG1132 consensus Helicase of the DEAD superfamily [Replication, recombination and repair]

Probab=97.56  E-value=0.00034  Score=83.17  Aligned_cols=76  Identities=18%  Similarity=0.302  Sum_probs=52.1

Q ss_pred             CCcHHHHHHHHHHh----cCCCEEEEcCCCCchHHHHHHHHHHHHhcCC-------------------CCC-C-------
Q 002040          489 KPMPIQAQALPVIM----SGRDCIGVAKTGSGKTLAFVLPMLRHIKDQP-------------------PVA-A-------  537 (976)
Q Consensus       489 ~p~~~Q~~~i~~il----~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~-------------------~~~-~-------  537 (976)
                      +|+|.|...+..++    ...++++-.|||+|||++.+...|.+...+.                   +.. .       
T Consensus        21 qpY~~Q~a~M~rvl~~L~~~q~~llESPTGTGKSLsLLCS~LAW~q~~k~~~~~~~~s~~~~~~~p~~~s~~~g~~s~e~  100 (945)
T KOG1132|consen   21 QPYPTQLAFMTRVLSCLDRKQNGLLESPTGTGKSLSLLCSTLAWQQHLKSRKPKGKISERKAGFIPTQPSDSGGEKSEEA  100 (945)
T ss_pred             CcchHHHHHHHHHHHHHHHhhhhhccCCCCCCccHHHHHHHHHHHHHhhccccccchhhhhccccCCCCccCCCCchhhh
Confidence            47899987776655    5678999999999999987666655543221                   000 0       


Q ss_pred             -------CCCCeEEEEccCHHHHHHHHHHHHHHH
Q 002040          538 -------GDGPVGLIMAPTRELVQQIHSDIRKFA  564 (976)
Q Consensus       538 -------~~~~~vLIl~Ptr~La~Q~~~~~~~~~  564 (976)
                             ...|++.+-.-|..-..|+..++.+..
T Consensus       101 ~e~~~~~~~ipkIyyaSRTHsQltQvvrElrrT~  134 (945)
T KOG1132|consen  101 GEPIACYTGIPKIYYASRTHSQLTQVVRELRRTG  134 (945)
T ss_pred             cCccccccCCceEEEecchHHHHHHHHHHHhhcC
Confidence                   013666777777777788888888764

>COG3421 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=97.55  E-value=0.00038  Score=79.21  Aligned_cols=146  Identities=18%  Similarity=0.174  Sum_probs=72.7

Q ss_pred             EEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHH-HHhhcCcEEEEeeCCCChHHH----
Q 002040          509 GVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRK-FAKVMGVRCVPVYGGSGVAQQ----  583 (976)
Q Consensus       509 ~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~-~~~~~~~~~~~~~gg~~~~~~----  583 (976)
                      ..+.||||||++++..||....+      |. ...|+.|..-.........|.. +...+-..-.+.+++..+.-.    
T Consensus         2 f~matgsgkt~~ma~lil~~y~k------gy-r~flffvnq~nilekt~~nftd~~s~kylf~e~i~~~d~~i~ikkvn~   74 (812)
T COG3421           2 FEMATGSGKTLVMAGLILECYKK------GY-RNFLFFVNQANILEKTKLNFTDSVSSKYLFSENININDENIEIKKVNN   74 (812)
T ss_pred             cccccCCChhhHHHHHHHHHHHh------ch-hhEEEEecchhHHHHHHhhcccchhhhHhhhhhhhcCCceeeeeeecc
Confidence            45789999999866555544332      11 2346666654444433222211 111010111122233222110    


Q ss_pred             HHHHhcCCeEEEeCchhHHHHHHhcCCccc---ccCCce-EEEecCcccccccC------------CchHHHHHHHhcCC
Q 002040          584 ISELKRGTEIVVCTPGRMIDILCTSGGKIT---NLRRVT-YLVMDEADRMFDMG------------FEPQITRIVQNIRP  647 (976)
Q Consensus       584 ~~~l~~~~~Iiv~Tp~~L~~~l~~~~~~~~---~l~~~~-~vVlDEah~~~~~~------------f~~~i~~il~~~~~  647 (976)
                      ......+..|+++|...|...+.+......   +|.+.. +++-||||++-...            .+..+..+...-++
T Consensus        75 fsehnd~iei~fttiq~l~~d~~~~ken~itledl~~~klvfl~deahhln~~tkkk~~de~~~~~~we~~v~la~~~nk  154 (812)
T COG3421          75 FSEHNDAIEIYFTTIQGLFSDFTRAKENAITLEDLKDQKLVFLADEAHHLNTETKKKLNDEASEKRNWESVVKLALEQNK  154 (812)
T ss_pred             cCccCCceEEEEeehHHHHHHHHhhccccccHhhHhhCceEEEechhhhhhhhhhhhcccHHHHHhhHHHHHHHHHhcCC
Confidence            111223578999999999777755433222   344444 46779999873211            11111112222345


Q ss_pred             CCcEEEEeccCcHH
Q 002040          648 DRQTVLFSATFPRQ  661 (976)
Q Consensus       648 ~~q~i~~SAT~~~~  661 (976)
                      +.-++.||||+|..
T Consensus       155 d~~~lef~at~~k~  168 (812)
T COG3421         155 DNLLLEFSATIPKE  168 (812)
T ss_pred             CceeehhhhcCCcc
Confidence            55678899999843

>KOG1805 consensus DNA replication helicase [Replication, recombination and repair]

Probab=97.43  E-value=0.00069  Score=81.32  Aligned_cols=145  Identities=21%  Similarity=0.244  Sum_probs=89.2

Q ss_pred             CCcccccccCCCCHHHHHHHHHcCCCCCcHHHHHHHHHHhcCCC-EEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCC
Q 002040          463 PKPIKTWHQTGLTSKIMETIRKLNYEKPMPIQAQALPVIMSGRD-CIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGP  541 (976)
Q Consensus       463 p~pi~~~~~~~l~~~l~~~l~~~~~~~p~~~Q~~~i~~il~g~d-~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~  541 (976)
                      |+.........+.+.+...    -+..+...|.+|+-.++.-.| .||.|=+|+|||++.. .++..|..       .|.
T Consensus       647 pP~f~~~~~~~~~p~~~~~----~~~~LN~dQr~A~~k~L~aedy~LI~GMPGTGKTTtI~-~LIkiL~~-------~gk  714 (1100)
T KOG1805|consen  647 PPKFVDALSKVLIPKIKKI----ILLRLNNDQRQALLKALAAEDYALILGMPGTGKTTTIS-LLIKILVA-------LGK  714 (1100)
T ss_pred             CchhhcccccccCchhhHH----HHhhcCHHHHHHHHHHHhccchheeecCCCCCchhhHH-HHHHHHHH-------cCC
Confidence            3333444445555665553    223466899999999887766 5777999999998633 33333332       367


Q ss_pred             eEEEEccCHHHHHHHHHHHHHHHhhcCcEEEEeeCCCChHHH-----------------HHHHhcCCeEEEeCchhHHHH
Q 002040          542 VGLIMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQ-----------------ISELKRGTEIVVCTPGRMIDI  604 (976)
Q Consensus       542 ~vLIl~Ptr~La~Q~~~~~~~~~~~~~~~~~~~~gg~~~~~~-----------------~~~l~~~~~Iiv~Tp~~L~~~  604 (976)
                      +||+.+=|...+..+.-.+..    +++.+.-+-.+..+..+                 +..+...+.||.||--.+.+.
T Consensus       715 kVLLtsyThsAVDNILiKL~~----~~i~~lRLG~~~kih~~v~e~~~~~~~s~ks~~~l~~~~~~~~IVa~TClgi~~p  790 (1100)
T KOG1805|consen  715 KVLLTSYTHSAVDNILIKLKG----FGIYILRLGSEEKIHPDVEEFTLTNETSEKSYADLKKFLDQTSIVACTCLGINHP  790 (1100)
T ss_pred             eEEEEehhhHHHHHHHHHHhc----cCcceeecCCccccchHHHHHhcccccchhhHHHHHHHhCCCcEEEEEccCCCch
Confidence            889998888777655433333    34443322222222222                 223334678999997666554


Q ss_pred             HHhcCCcccccCCceEEEecCccccc
Q 002040          605 LCTSGGKITNLRRVTYLVMDEADRMF  630 (976)
Q Consensus       605 l~~~~~~~~~l~~~~~vVlDEah~~~  630 (976)
                      |       +....|+|+|||||-.|+
T Consensus       791 l-------f~~R~FD~cIiDEASQI~  809 (1100)
T KOG1805|consen  791 L-------FVNRQFDYCIIDEASQIL  809 (1100)
T ss_pred             h-------hhccccCEEEEccccccc
Confidence            4       455679999999999775

>COG1419 FlhF Flagellar GTP-binding protein [Cell motility and secretion]

Probab=97.42  E-value=0.0041  Score=69.43  Aligned_cols=174  Identities=19%  Similarity=0.225  Sum_probs=97.3

Q ss_pred             hcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHHHHhhcCcEEEEeeCCCChH
Q 002040          502 MSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVA  581 (976)
Q Consensus       502 l~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~~~~~~~~~~~~~~gg~~~~  581 (976)
                      ..++.+.++||||.|||++.+=.+..+++.     .+....+||.+-|--...  +++++.++..+++.+.+++      
T Consensus       201 ~~~~vi~LVGPTGVGKTTTlAKLAar~~~~-----~~~~kVaiITtDtYRIGA--~EQLk~Ya~im~vp~~vv~------  267 (407)
T COG1419         201 EQKRVIALVGPTGVGKTTTLAKLAARYVML-----KKKKKVAIITTDTYRIGA--VEQLKTYADIMGVPLEVVY------  267 (407)
T ss_pred             ccCcEEEEECCCCCcHHHHHHHHHHHHHhh-----ccCcceEEEEeccchhhH--HHHHHHHHHHhCCceEEec------
Confidence            347889999999999998744433333311     123345677776643332  3667777777777665443      


Q ss_pred             HHHHHHhcCCeEEEeCchhHHHHHHhcCCcccccCCceEEEecCccccc-ccCCchHHHHHHHhcCCCCcEEEEeccCcH
Q 002040          582 QQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMF-DMGFEPQITRIVQNIRPDRQTVLFSATFPR  660 (976)
Q Consensus       582 ~~~~~l~~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDEah~~~-~~~f~~~i~~il~~~~~~~q~i~~SAT~~~  660 (976)
                                     +|.-|...+       ..|.++++|.||=|-+.. |......+..++....+.--.|++|||...
T Consensus       268 ---------------~~~el~~ai-------~~l~~~d~ILVDTaGrs~~D~~~i~el~~~~~~~~~i~~~Lvlsat~K~  325 (407)
T COG1419         268 ---------------SPKELAEAI-------EALRDCDVILVDTAGRSQYDKEKIEELKELIDVSHSIEVYLVLSATTKY  325 (407)
T ss_pred             ---------------CHHHHHHHH-------HHhhcCCEEEEeCCCCCccCHHHHHHHHHHHhccccceEEEEEecCcch
Confidence                           444444444       345566777777666432 112344455555555555567889999765


Q ss_pred             H-HHHHHHHHcCCCeEEEeCCcccccCCceEEEEecCcchHHHHHHHHHHhhhcCCcEEEEecCHH
Q 002040          661 Q-VEILARKVLNKPVEIQVGGRSVVNKDITQLVEVRPESDRFLRLLELLGEWYEKGKILIFVHSQE  725 (976)
Q Consensus       661 ~-~~~l~~~~l~~~~~i~~~~~~~~~~~i~q~~~~~~~~~k~~~l~~~l~~~~~~~kvLIF~~s~~  725 (976)
                      . +..+...|-.-++.-             .++...++...+-.++.++...  .-|+..|++.+.
T Consensus       326 ~dlkei~~~f~~~~i~~-------------~I~TKlDET~s~G~~~s~~~e~--~~PV~YvT~GQ~  376 (407)
T COG1419         326 EDLKEIIKQFSLFPIDG-------------LIFTKLDETTSLGNLFSLMYET--RLPVSYVTNGQR  376 (407)
T ss_pred             HHHHHHHHHhccCCcce-------------eEEEcccccCchhHHHHHHHHh--CCCeEEEeCCCC
Confidence            4 455555554333211             1123344444555566666543  345666665554

>PF13245 AAA_19: Part of AAA domain

Probab=97.32  E-value=0.00088  Score=57.45  Aligned_cols=53  Identities=19%  Similarity=0.315  Sum_probs=37.2

Q ss_pred             CCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHH
Q 002040          504 GRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDI  560 (976)
Q Consensus       504 g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~  560 (976)
                      +.-++|.|+.|||||.+.+-.+...+....   .. +..+||++||+.++..+.+.+
T Consensus        10 ~~~~vv~g~pGtGKT~~~~~~i~~l~~~~~---~~-~~~vlv~a~t~~aa~~l~~rl   62 (76)
T PF13245_consen   10 SPLFVVQGPPGTGKTTTLAARIAELLAARA---DP-GKRVLVLAPTRAAADELRERL   62 (76)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHHHHHhc---CC-CCeEEEECCCHHHHHHHHHHH
Confidence            334556999999999775555554443211   12 567999999999998887766

>PRK08181 transposase; Validated

Probab=97.32  E-value=0.0035  Score=67.72  Aligned_cols=110  Identities=15%  Similarity=0.159  Sum_probs=60.3

Q ss_pred             HHhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHHHHhhcCcEEEEeeCCCC
Q 002040          500 VIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSG  579 (976)
Q Consensus       500 ~il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~~~~~~~~~~~~~~gg~~  579 (976)
                      ++-.+.+++++||+|+|||..+.. +...+...       |..|++ ++...|+.++.....               .  
T Consensus       102 ~~~~~~nlll~Gp~GtGKTHLa~A-ia~~a~~~-------g~~v~f-~~~~~L~~~l~~a~~---------------~--  155 (269)
T PRK08181        102 WLAKGANLLLFGPPGGGKSHLAAA-IGLALIEN-------GWRVLF-TRTTDLVQKLQVARR---------------E--  155 (269)
T ss_pred             HHhcCceEEEEecCCCcHHHHHHH-HHHHHHHc-------CCceee-eeHHHHHHHHHHHHh---------------C--
Confidence            556788999999999999975443 33333321       334444 344455544321100               0  


Q ss_pred             hHHHHHHHhcCCeEEEeCchhHHHHHHhcCCcccccCCceEEEecCcccccccCC-chHHHHHHHhcCCCCcEEEEeccC
Q 002040          580 VAQQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMGF-EPQITRIVQNIRPDRQTVLFSATF  658 (976)
Q Consensus       580 ~~~~~~~l~~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDEah~~~~~~f-~~~i~~il~~~~~~~q~i~~SAT~  658 (976)
                                      .+...++.          .+..+++|||||.+.+....+ ...+..++........+|+.|-..
T Consensus       156 ----------------~~~~~~l~----------~l~~~dLLIIDDlg~~~~~~~~~~~Lf~lin~R~~~~s~IiTSN~~  209 (269)
T PRK08181        156 ----------------LQLESAIA----------KLDKFDLLILDDLAYVTKDQAETSVLFELISARYERRSILITANQP  209 (269)
T ss_pred             ----------------CcHHHHHH----------HHhcCCEEEEeccccccCCHHHHHHHHHHHHHHHhCCCEEEEcCCC
Confidence                            11111211          234578999999996543222 234556666554445667766666


Q ss_pred             cHH
Q 002040          659 PRQ  661 (976)
Q Consensus       659 ~~~  661 (976)
                      +..
T Consensus       210 ~~~  212 (269)
T PRK08181        210 FGE  212 (269)
T ss_pred             HHH
Confidence            554

>PRK13889 conjugal transfer relaxase TraA; Provisional

Probab=97.28  E-value=0.0017  Score=81.52  Aligned_cols=123  Identities=20%  Similarity=0.140  Sum_probs=76.4

Q ss_pred             CCcHHHHHHHHHHhcCCC-EEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHHHHhhc
Q 002040          489 KPMPIQAQALPVIMSGRD-CIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVM  567 (976)
Q Consensus       489 ~p~~~Q~~~i~~il~g~d-~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~~~~~~  567 (976)
                      .+++-|.+|+..++++.+ ++|.|..|+|||++ +-+++..+..       .|..|++++||-..|..+..       ..
T Consensus       346 ~Ls~eQr~Av~~il~s~~v~vv~G~AGTGKTT~-l~~~~~~~e~-------~G~~V~~~ApTGkAA~~L~e-------~t  410 (988)
T PRK13889        346 VLSGEQADALAHVTDGRDLGVVVGYAGTGKSAM-LGVAREAWEA-------AGYEVRGAALSGIAAENLEG-------GS  410 (988)
T ss_pred             CCCHHHHHHHHHHhcCCCeEEEEeCCCCCHHHH-HHHHHHHHHH-------cCCeEEEecCcHHHHHHHhh-------cc
Confidence            589999999999998664 67889999999986 4444444332       36789999999766644321       12


Q ss_pred             CcEEEEeeCCCChHHHHHHHhcCCeEEEeCchhHHHHHHhcCCcccccCCceEEEecCcccccccCCchHHHHHHHhc-C
Q 002040          568 GVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMGFEPQITRIVQNI-R  646 (976)
Q Consensus       568 ~~~~~~~~gg~~~~~~~~~l~~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDEah~~~~~~f~~~i~~il~~~-~  646 (976)
                      |+..                        .|...|+.-+..   ....+...++||||||-.+.    ..++..++... .
T Consensus       411 Gi~a------------------------~TI~sll~~~~~---~~~~l~~~~vlIVDEASMv~----~~~m~~LL~~a~~  459 (988)
T PRK13889        411 GIAS------------------------RTIASLEHGWGQ---GRDLLTSRDVLVIDEAGMVG----TRQLERVLSHAAD  459 (988)
T ss_pred             Ccch------------------------hhHHHHHhhhcc---cccccccCcEEEEECcccCC----HHHHHHHHHhhhh
Confidence            2211                        121122111111   11245667899999999543    33455666544 4


Q ss_pred             CCCcEEEEecc
Q 002040          647 PDRQTVLFSAT  657 (976)
Q Consensus       647 ~~~q~i~~SAT  657 (976)
                      ...++|++.=+
T Consensus       460 ~garvVLVGD~  470 (988)
T PRK13889        460 AGAKVVLVGDP  470 (988)
T ss_pred             CCCEEEEECCH
Confidence            56777777665

>PRK14722 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=97.27  E-value=0.0029  Score=71.21  Aligned_cols=178  Identities=19%  Similarity=0.199  Sum_probs=88.6

Q ss_pred             cCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHHHHhhcCcEEEEeeCCCChHH
Q 002040          503 SGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQ  582 (976)
Q Consensus       503 ~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~~~~~~~~~~~~~~gg~~~~~  582 (976)
                      .|..++++||||+|||+.+...+...+...     +....++|.+.+--  .--.+.+..|+..+++.+..+        
T Consensus       136 ~g~ii~lvGptGvGKTTtiakLA~~~~~~~-----G~~~V~lit~D~~R--~ga~EqL~~~a~~~gv~~~~~--------  200 (374)
T PRK14722        136 RGGVFALMGPTGVGKTTTTAKLAARCVMRF-----GASKVALLTTDSYR--IGGHEQLRIFGKILGVPVHAV--------  200 (374)
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHHHHhc-----CCCeEEEEeccccc--ccHHHHHHHHHHHcCCceEec--------
Confidence            456789999999999987555444433321     11122333333311  112245555665566544332        


Q ss_pred             HHHHHhcCCeEEEeCchhHHHHHHhcCCcccccCCceEEEecCcccccccC-CchHHHHHHHhcCCCCcEEEEeccCcHH
Q 002040          583 QISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMG-FEPQITRIVQNIRPDRQTVLFSATFPRQ  661 (976)
Q Consensus       583 ~~~~l~~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDEah~~~~~~-f~~~i~~il~~~~~~~q~i~~SAT~~~~  661 (976)
                                   .+++.+...+       ..+.++++|+||.+-+..... ....+..+.....+...+|++|||....
T Consensus       201 -------------~~~~~l~~~l-------~~l~~~DlVLIDTaG~~~~d~~l~e~La~L~~~~~~~~~lLVLsAts~~~  260 (374)
T PRK14722        201 -------------KDGGDLQLAL-------AELRNKHMVLIDTIGMSQRDRTVSDQIAMLHGADTPVQRLLLLNATSHGD  260 (374)
T ss_pred             -------------CCcccHHHHH-------HHhcCCCEEEEcCCCCCcccHHHHHHHHHHhccCCCCeEEEEecCccChH
Confidence                         3333333333       234557889999997532111 1222222222223344578899998654


Q ss_pred             H-HHHHHHHcCC---CeEEEeCCcccccCCc-eEEEEecCcchHHHHHHHHHHhhhcCCcEEEEecCHH
Q 002040          662 V-EILARKVLNK---PVEIQVGGRSVVNKDI-TQLVEVRPESDRFLRLLELLGEWYEKGKILIFVHSQE  725 (976)
Q Consensus       662 ~-~~l~~~~l~~---~~~i~~~~~~~~~~~i-~q~~~~~~~~~k~~~l~~~l~~~~~~~kvLIF~~s~~  725 (976)
                      . ...+..|...   |..-.        ..+ .-++...++..++-.++.++...  +-++..+++.+.
T Consensus       261 ~l~evi~~f~~~~~~p~~~~--------~~~~~~I~TKlDEt~~~G~~l~~~~~~--~lPi~yvt~Gq~  319 (374)
T PRK14722        261 TLNEVVQAYRSAAGQPKAAL--------PDLAGCILTKLDEASNLGGVLDTVIRY--KLPVHYVSTGQK  319 (374)
T ss_pred             HHHHHHHHHHHhhccccccc--------CCCCEEEEeccccCCCccHHHHHHHHH--CcCeEEEecCCC
Confidence            3 4444444322   11000        001 12234455666677777776654  345665555543

>TIGR02768 TraA_Ti Ti-type conjugative transfer relaxase TraA

Probab=97.26  E-value=0.0032  Score=78.09  Aligned_cols=124  Identities=16%  Similarity=0.148  Sum_probs=74.3

Q ss_pred             CCCcHHHHHHHHHHhcC-CCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHHHHhh
Q 002040          488 EKPMPIQAQALPVIMSG-RDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKV  566 (976)
Q Consensus       488 ~~p~~~Q~~~i~~il~g-~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~~~~~  566 (976)
                      ..+++-|..|+..++.+ +-++|.|+.|+|||++ +-.++..+..       .|..+++++||-..|..+..       .
T Consensus       351 ~~Ls~~Q~~Av~~i~~s~~~~il~G~aGTGKTtl-l~~i~~~~~~-------~g~~V~~~ApTg~Aa~~L~~-------~  415 (744)
T TIGR02768       351 YRLSEEQYEAVRHVTGSGDIAVVVGRAGTGKSTM-LKAAREAWEA-------AGYRVIGAALSGKAAEGLQA-------E  415 (744)
T ss_pred             CCCCHHHHHHHHHHhcCCCEEEEEecCCCCHHHH-HHHHHHHHHh-------CCCeEEEEeCcHHHHHHHHh-------c
Confidence            35889999999999874 5678899999999975 3334444332       26678999999766654421       1


Q ss_pred             cCcEEEEeeCCCChHHHHHHHhcCCeEEEeCchhHHHHHHhcCCcccccCCceEEEecCcccccccCCchHHHHHHHh-c
Q 002040          567 MGVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMGFEPQITRIVQN-I  645 (976)
Q Consensus       567 ~~~~~~~~~gg~~~~~~~~~l~~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDEah~~~~~~f~~~i~~il~~-~  645 (976)
                      .|+...                        |-.+++..+..   ....+...++||||||-.+.    ...+..++.. .
T Consensus       416 ~g~~a~------------------------Ti~~~~~~~~~---~~~~~~~~~llIvDEasMv~----~~~~~~Ll~~~~  464 (744)
T TIGR02768       416 SGIESR------------------------TLASLEYAWAN---GRDLLSDKDVLVIDEAGMVG----SRQMARVLKEAE  464 (744)
T ss_pred             cCCcee------------------------eHHHHHhhhcc---CcccCCCCcEEEEECcccCC----HHHHHHHHHHHH
Confidence            232211                        11111111111   11235678999999999543    2234445542 2


Q ss_pred             CCCCcEEEEecc
Q 002040          646 RPDRQTVLFSAT  657 (976)
Q Consensus       646 ~~~~q~i~~SAT  657 (976)
                      ....++|++.=+
T Consensus       465 ~~~~kliLVGD~  476 (744)
T TIGR02768       465 EAGAKVVLVGDP  476 (744)
T ss_pred             hcCCEEEEECCh
Confidence            356667766633

This protein contains domains distinctive of a single strand exonuclease (N-terminus, MobA/MobL, pfam03389) as well as a helicase domain (central region, homologous to the corresponding region of the F-type relaxase TraI, TIGR02760). This protein likely fills the same role as TraI(F), nicking (at the oriT site) and unwinding the coiled plasmid prior to conjugative transfer.

>PRK06526 transposase; Provisional

Probab=97.24  E-value=0.0021  Score=69.02  Aligned_cols=29  Identities=17%  Similarity=0.211  Sum_probs=22.2

Q ss_pred             HHHHhcCCCEEEEcCCCCchHHHHHHHHH
Q 002040          498 LPVIMSGRDCIGVAKTGSGKTLAFVLPML  526 (976)
Q Consensus       498 i~~il~g~d~i~~a~TGsGKT~~~~l~il  526 (976)
                      ..++..+.+++++||+|+|||..+...+.
T Consensus        92 ~~fi~~~~nlll~Gp~GtGKThLa~al~~  120 (254)
T PRK06526         92 LDFVTGKENVVFLGPPGTGKTHLAIGLGI  120 (254)
T ss_pred             CchhhcCceEEEEeCCCCchHHHHHHHHH
Confidence            35566788999999999999987554333

>PRK05703 flhF flagellar biosynthesis regulator FlhF; Validated

Probab=97.20  E-value=0.014  Score=67.62  Aligned_cols=170  Identities=21%  Similarity=0.212  Sum_probs=86.1

Q ss_pred             cCCCEEEEcCCCCchHHHHHHHHHHHH-hcCCCCCCCCCCeEE-EEccC-HHHHHHHHHHHHHHHhhcCcEEEEeeCCCC
Q 002040          503 SGRDCIGVAKTGSGKTLAFVLPMLRHI-KDQPPVAAGDGPVGL-IMAPT-RELVQQIHSDIRKFAKVMGVRCVPVYGGSG  579 (976)
Q Consensus       503 ~g~d~i~~a~TGsGKT~~~~l~il~~l-~~~~~~~~~~~~~vL-Il~Pt-r~La~Q~~~~~~~~~~~~~~~~~~~~gg~~  579 (976)
                      .++.++++||||+|||++.+..+.... ..       .+.+|+ |-+-+ +.-+   ...+..++..+++.+..      
T Consensus       220 ~~~~i~~vGptGvGKTTt~~kLA~~~~~~~-------~g~~V~li~~D~~r~~a---~eqL~~~a~~~~vp~~~------  283 (424)
T PRK05703        220 QGGVVALVGPTGVGKTTTLAKLAARYALLY-------GKKKVALITLDTYRIGA---VEQLKTYAKIMGIPVEV------  283 (424)
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHHHHhc-------CCCeEEEEECCccHHHH---HHHHHHHHHHhCCceEc------
Confidence            356788899999999987554443332 22       133344 44433 3222   24455555445543322      


Q ss_pred             hHHHHHHHhcCCeEEEeCchhHHHHHHhcCCcccccCCceEEEecCcccccc-cCCchHHHHHHH-hcCCCCcEEEEecc
Q 002040          580 VAQQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFD-MGFEPQITRIVQ-NIRPDRQTVLFSAT  657 (976)
Q Consensus       580 ~~~~~~~l~~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDEah~~~~-~~f~~~i~~il~-~~~~~~q~i~~SAT  657 (976)
                                     +.++..|...+.       .+..+++||||-+-+... ......+..++. ...+...++++|||
T Consensus       284 ---------------~~~~~~l~~~l~-------~~~~~DlVlIDt~G~~~~d~~~~~~L~~ll~~~~~~~~~~LVl~a~  341 (424)
T PRK05703        284 ---------------VYDPKELAKALE-------QLRDCDVILIDTAGRSQRDKRLIEELKALIEFSGEPIDVYLVLSAT  341 (424)
T ss_pred             ---------------cCCHHhHHHHHH-------HhCCCCEEEEeCCCCCCCCHHHHHHHHHHHhccCCCCeEEEEEECC
Confidence                           233444444442       234578999998865321 112234445555 22344557889999


Q ss_pred             CcHH-HHHHHHHHcCCCeEEEeCCcccccCCceEEEEecCcchHHHHHHHHHHhhhcCCcEEEEecCHH
Q 002040          658 FPRQ-VEILARKVLNKPVEIQVGGRSVVNKDITQLVEVRPESDRFLRLLELLGEWYEKGKILIFVHSQE  725 (976)
Q Consensus       658 ~~~~-~~~l~~~~l~~~~~i~~~~~~~~~~~i~q~~~~~~~~~k~~~l~~~l~~~~~~~kvLIF~~s~~  725 (976)
                      .... +..++..|-..++.             .-++...+....+..++.++...  +-++..++..+.
T Consensus       342 ~~~~~l~~~~~~f~~~~~~-------------~vI~TKlDet~~~G~i~~~~~~~--~lPv~yit~Gq~  395 (424)
T PRK05703        342 TKYEDLKDIYKHFSRLPLD-------------GLIFTKLDETSSLGSILSLLIES--GLPISYLTNGQR  395 (424)
T ss_pred             CCHHHHHHHHHHhCCCCCC-------------EEEEecccccccccHHHHHHHHH--CCCEEEEeCCCC
Confidence            8753 44444444221110             11123334444555566666543  346666665554

>PRK14974 cell division protein FtsY; Provisional

Probab=97.20  E-value=0.0043  Score=69.08  Aligned_cols=132  Identities=23%  Similarity=0.273  Sum_probs=74.8

Q ss_pred             CCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEcc-C-H-HHHHHHHHHHHHHHhhcCcEEEEeeCCCChH
Q 002040          505 RDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAP-T-R-ELVQQIHSDIRKFAKVMGVRCVPVYGGSGVA  581 (976)
Q Consensus       505 ~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~P-t-r-~La~Q~~~~~~~~~~~~~~~~~~~~gg~~~~  581 (976)
                      .-++++|++|+|||++..-.+ ..+..       .+..++++.. | | ....|+    ..++..+|+.+.....|....
T Consensus       141 ~vi~~~G~~GvGKTTtiakLA-~~l~~-------~g~~V~li~~Dt~R~~a~eqL----~~~a~~lgv~v~~~~~g~dp~  208 (336)
T PRK14974        141 VVIVFVGVNGTGKTTTIAKLA-YYLKK-------NGFSVVIAAGDTFRAGAIEQL----EEHAERLGVKVIKHKYGADPA  208 (336)
T ss_pred             eEEEEEcCCCCCHHHHHHHHH-HHHHH-------cCCeEEEecCCcCcHHHHHHH----HHHHHHcCCceecccCCCCHH
Confidence            357788999999998643333 33332       2344555543 2 2 333343    444555666554332222111


Q ss_pred             HHHHHHhcCCeEEEeCchhHHHHHHhcCCcccccCCceEEEecCccccc-ccCCchHHHHHHHhcCCCCcEEEEeccCcH
Q 002040          582 QQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMF-DMGFEPQITRIVQNIRPDRQTVLFSATFPR  660 (976)
Q Consensus       582 ~~~~~l~~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDEah~~~-~~~f~~~i~~il~~~~~~~q~i~~SAT~~~  660 (976)
                      ..                 +.+.+..     .....+++||||.|.++. +..+...+..+...+.|+.-+++++||...
T Consensus       209 ~v-----------------~~~ai~~-----~~~~~~DvVLIDTaGr~~~~~~lm~eL~~i~~~~~pd~~iLVl~a~~g~  266 (336)
T PRK14974        209 AV-----------------AYDAIEH-----AKARGIDVVLIDTAGRMHTDANLMDELKKIVRVTKPDLVIFVGDALAGN  266 (336)
T ss_pred             HH-----------------HHHHHHH-----HHhCCCCEEEEECCCccCCcHHHHHHHHHHHHhhCCceEEEeeccccch
Confidence            10                 1122211     112346899999999875 234556677777777888888999999876


Q ss_pred             HHHHHHHHHc
Q 002040          661 QVEILARKVL  670 (976)
Q Consensus       661 ~~~~l~~~~l  670 (976)
                      .....+..|.
T Consensus       267 d~~~~a~~f~  276 (336)
T PRK14974        267 DAVEQAREFN  276 (336)
T ss_pred             hHHHHHHHHH
Confidence            6555555543

>PRK11889 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=97.18  E-value=0.011  Score=66.15  Aligned_cols=169  Identities=17%  Similarity=0.220  Sum_probs=88.2

Q ss_pred             CCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEE-Ec-cCH-HHHHHHHHHHHHHHhhcCcEEEEeeCCCCh
Q 002040          504 GRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLI-MA-PTR-ELVQQIHSDIRKFAKVMGVRCVPVYGGSGV  580 (976)
Q Consensus       504 g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLI-l~-Ptr-~La~Q~~~~~~~~~~~~~~~~~~~~gg~~~  580 (976)
                      .+.++++|+||+|||+.....+. .+..       .+..+++ -+ |.| ..+.|    +..++...++.+.        
T Consensus       241 ~~vI~LVGptGvGKTTTiaKLA~-~L~~-------~GkkVglI~aDt~RiaAvEQ----Lk~yae~lgipv~--------  300 (436)
T PRK11889        241 VQTIALIGPTGVGKTTTLAKMAW-QFHG-------KKKTVGFITTDHSRIGTVQQ----LQDYVKTIGFEVI--------  300 (436)
T ss_pred             CcEEEEECCCCCcHHHHHHHHHH-HHHH-------cCCcEEEEecCCcchHHHHH----HHHHhhhcCCcEE--------
Confidence            35688999999999987544443 3322       2344444 44 333 23333    3344443443332        


Q ss_pred             HHHHHHHhcCCeEEEeCchhHHHHHHhcCCcccccCCceEEEecCccccccc-CCchHHHHHHHhcCCCCcEEEEeccCc
Q 002040          581 AQQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDM-GFEPQITRIVQNIRPDRQTVLFSATFP  659 (976)
Q Consensus       581 ~~~~~~l~~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDEah~~~~~-~f~~~i~~il~~~~~~~q~i~~SAT~~  659 (976)
                                   ++.+|..|.+.+...    ....++++||||-+=+.... .....+..++....+..-++++|||..
T Consensus       301 -------------v~~d~~~L~~aL~~l----k~~~~~DvVLIDTaGRs~kd~~lm~EL~~~lk~~~PdevlLVLsATtk  363 (436)
T PRK11889        301 -------------AVRDEAAMTRALTYF----KEEARVDYILIDTAGKNYRASETVEEMIETMGQVEPDYICLTLSASMK  363 (436)
T ss_pred             -------------ecCCHHHHHHHHHHH----HhccCCCEEEEeCccccCcCHHHHHHHHHHHhhcCCCeEEEEECCccC
Confidence                         233566665555321    11124789999988764422 123334455555556655677999865


Q ss_pred             H-HHHHHHHHHcCCCeEEEeCCcccccCCceEEEEecCcchHHHHHHHHHHhhhcCCcEEEEecCH
Q 002040          660 R-QVEILARKVLNKPVEIQVGGRSVVNKDITQLVEVRPESDRFLRLLELLGEWYEKGKILIFVHSQ  724 (976)
Q Consensus       660 ~-~~~~l~~~~l~~~~~i~~~~~~~~~~~i~q~~~~~~~~~k~~~l~~~l~~~~~~~kvLIF~~s~  724 (976)
                      . .+...+..|-..++.             .-++...+...+.-.++.++...  +-|+..++..+
T Consensus       364 ~~d~~~i~~~F~~~~id-------------glI~TKLDET~k~G~iLni~~~~--~lPIsyit~GQ  414 (436)
T PRK11889        364 SKDMIEIITNFKDIHID-------------GIVFTKFDETASSGELLKIPAVS--SAPIVLMTDGQ  414 (436)
T ss_pred             hHHHHHHHHHhcCCCCC-------------EEEEEcccCCCCccHHHHHHHHH--CcCEEEEeCCC
Confidence            4 445555555321110             01233445555666666666553  34555555543

>PRK11773 uvrD DNA-dependent helicase II; Provisional

Probab=97.15  E-value=0.024  Score=70.68  Aligned_cols=71  Identities=15%  Similarity=0.123  Sum_probs=53.2

Q ss_pred             CCcHHHHHHHHHHhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHHHHh
Q 002040          489 KPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAK  565 (976)
Q Consensus       489 ~p~~~Q~~~i~~il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~~~~  565 (976)
                      .++|-|.+|+..  ....++|.|..|||||.+.+.-+...+....    -....+|+|+-|+..|..+.+.+..+..
T Consensus         9 ~Ln~~Q~~av~~--~~g~~lV~AgaGSGKT~vl~~Ria~Li~~~~----v~p~~IL~lTFT~kAA~Em~~Rl~~~~~   79 (721)
T PRK11773          9 SLNDKQREAVAA--PLGNMLVLAGAGSGKTRVLVHRIAWLMQVEN----ASPYSIMAVTFTNKAAAEMRHRIEQLLG   79 (721)
T ss_pred             hcCHHHHHHHhC--CCCCEEEEecCCCCHHHHHHHHHHHHHHcCC----CChhHeEeeeccHHHHHHHHHHHHHHhc
Confidence            478999998864  3468999999999999986555554443221    1234689999999999999888887653

>PF13401 AAA_22: AAA domain; PDB: 2QBY_B 1FNN_B 1W5T_A 1W5S_B

Probab=97.14  E-value=0.00096  Score=63.87  Aligned_cols=21  Identities=29%  Similarity=0.151  Sum_probs=13.7

Q ss_pred             CCCEEEEcCCCCchHHHHHHH
Q 002040          504 GRDCIGVAKTGSGKTLAFVLP  524 (976)
Q Consensus       504 g~d~i~~a~TGsGKT~~~~l~  524 (976)
                      ++.+++.|++|+|||.+....
T Consensus         4 ~~~~~i~G~~G~GKT~~~~~~   24 (131)
T PF13401_consen    4 QRILVISGPPGSGKTTLIKRL   24 (131)
T ss_dssp             ---EEEEE-TTSSHHHHHHHH
T ss_pred             CcccEEEcCCCCCHHHHHHHH
Confidence            456889999999999874433

>PF00448 SRP54: SRP54-type protein, GTPase domain; InterPro: IPR000897 The signal recognition particle (SRP) is a multimeric protein, which along with its conjugate receptor (SR), is involved in targeting secretory proteins to the rough endoplasmic reticulum (RER) membrane in eukaryotes, or to the plasma membrane in prokaryotes [, ]

Probab=97.10  E-value=0.0037  Score=64.45  Aligned_cols=172  Identities=19%  Similarity=0.168  Sum_probs=92.8

Q ss_pred             CEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEc-c-CHHHHHHHHHHHHHHHhhcCcEEEEeeCCCChHHH
Q 002040          506 DCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMA-P-TRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQ  583 (976)
Q Consensus       506 d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~-P-tr~La~Q~~~~~~~~~~~~~~~~~~~~gg~~~~~~  583 (976)
                      -++++||||+|||++..-.+......        +.++.+++ - .|.-|   .++++.++..+++.+....-.......
T Consensus         3 vi~lvGptGvGKTTt~aKLAa~~~~~--------~~~v~lis~D~~R~ga---~eQL~~~a~~l~vp~~~~~~~~~~~~~   71 (196)
T PF00448_consen    3 VIALVGPTGVGKTTTIAKLAARLKLK--------GKKVALISADTYRIGA---VEQLKTYAEILGVPFYVARTESDPAEI   71 (196)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHHHHT--------T--EEEEEESTSSTHH---HHHHHHHHHHHTEEEEESSTTSCHHHH
T ss_pred             EEEEECCCCCchHhHHHHHHHHHhhc--------cccceeecCCCCCccH---HHHHHHHHHHhccccchhhcchhhHHH
Confidence            36789999999998744433333222        23344444 3 34333   366777777788777654433322111


Q ss_pred             HHHHhcCCeEEEeCchhHHHHHHhcCCcccccCCceEEEecCcccccc-cCCchHHHHHHHhcCCCCcEEEEeccCcHHH
Q 002040          584 ISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFD-MGFEPQITRIVQNIRPDRQTVLFSATFPRQV  662 (976)
Q Consensus       584 ~~~l~~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDEah~~~~-~~f~~~i~~il~~~~~~~q~i~~SAT~~~~~  662 (976)
                                       +...+..     ....++++|+||=+-+... ......+..++..+.+..-++++|||.....
T Consensus        72 -----------------~~~~l~~-----~~~~~~D~vlIDT~Gr~~~d~~~~~el~~~~~~~~~~~~~LVlsa~~~~~~  129 (196)
T PF00448_consen   72 -----------------AREALEK-----FRKKGYDLVLIDTAGRSPRDEELLEELKKLLEALNPDEVHLVLSATMGQED  129 (196)
T ss_dssp             -----------------HHHHHHH-----HHHTTSSEEEEEE-SSSSTHHHHHHHHHHHHHHHSSSEEEEEEEGGGGGHH
T ss_pred             -----------------HHHHHHH-----HhhcCCCEEEEecCCcchhhHHHHHHHHHHhhhcCCccceEEEecccChHH
Confidence                             1112211     1223477888888865431 2234556677777777777899999987664


Q ss_pred             HHHHHHHcCC-CeEEEeCCcccccCCceEEEEecCcchHHHHHHHHHHhhhcCCcEEEEecCHH
Q 002040          663 EILARKVLNK-PVEIQVGGRSVVNKDITQLVEVRPESDRFLRLLELLGEWYEKGKILIFVHSQE  725 (976)
Q Consensus       663 ~~l~~~~l~~-~~~i~~~~~~~~~~~i~q~~~~~~~~~k~~~l~~~l~~~~~~~kvLIF~~s~~  725 (976)
                      ...+..++.. ++.             .-.+...++..++-.++.++...  +-|+-.+++.+.
T Consensus       130 ~~~~~~~~~~~~~~-------------~lIlTKlDet~~~G~~l~~~~~~--~~Pi~~it~Gq~  178 (196)
T PF00448_consen  130 LEQALAFYEAFGID-------------GLILTKLDETARLGALLSLAYES--GLPISYITTGQR  178 (196)
T ss_dssp             HHHHHHHHHHSSTC-------------EEEEESTTSSSTTHHHHHHHHHH--TSEEEEEESSSS
T ss_pred             HHHHHHHhhcccCc-------------eEEEEeecCCCCcccceeHHHHh--CCCeEEEECCCC
Confidence            4333333211 100             01134455566677777777654  345555555543

SRP recognises the signal sequence of the nascent polypeptide on the ribosome, retards its elongation, and docks the SRP-ribosome-polypeptide complex to the RER membrane via the SR receptor. Eukaryotic SRP consists of six polypeptides (SRP9, SRP14, SRP19, SRP54, SRP68 and SRP72) and a single 300 nucleotide 7S RNA molecule. The RNA component catalyses the interaction of SRP with its SR receptor []. In higher eukaryotes, the SRP complex consists of the Alu domain and the S domain linked by the SRP RNA. The Alu domain consists of a heterodimer of SRP9 and SRP14 bound to the 5' and 3' terminal sequences of SRP RNA. This domain is necessary for retarding the elongation of the nascent polypeptide chain, which gives SRP time to dock the ribosome-polypeptide complex to the RER membrane. In archaea, the SRP complex contains 7S RNA like its eukaryotic counterpart, yet only includes two of the six protein subunits found in the eukarytic complex: SRP19 and SRP54 []. This entry represents the GTPase domain of the 54 kDa SRP54 component, a GTP-binding protein that interacts with the signal sequence when it emerges from the ribosome. SRP54 of the signal recognition particle has a three-domain structure: an N-terminal helical bundle domain, a GTPase domain, and the M-domain that binds the 7s RNA and also binds the signal sequence. The extreme C-terminal region is glycine-rich and lower in complexity and poorly conserved between species. The GTPase domain is evolutionary related to P-loop NTPase domains found in a variety of other proteins []. These proteins include Escherichia coli and Bacillus subtilis ffh protein (P48), which seems to be the prokaryotic counterpart of SRP54; signal recognition particle receptor alpha subunit (docking protein), an integral membrane GTP-binding protein which ensures, in conjunction with SRP, the correct targeting of nascent secretory proteins to the endoplasmic reticulum membrane; bacterial FtsY protein, which is believed to play a similar role to that of the docking protein in eukaryotes; the pilA protein from Neisseria gonorrhoeae, the homologue of ftsY; and bacterial flagellar biosynthesis protein flhF.; GO: 0005525 GTP binding, 0006614 SRP-dependent cotranslational protein targeting to membrane; PDB: 2OG2_A 3B9Q_A 3DM9_B 3DMD_B 3E70_C 3DM5_B 2XXA_C 2J28_9 1ZU5_B 1ZU4_A ....

>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=97.09  E-value=0.0029  Score=70.40  Aligned_cols=125  Identities=16%  Similarity=0.111  Sum_probs=77.4

Q ss_pred             CcHHHHHHHHHHhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHHHHhhcCc
Q 002040          490 PMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVMGV  569 (976)
Q Consensus       490 p~~~Q~~~i~~il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~~~~~~~~  569 (976)
                      +++-|.++|..  ....++|.|..|||||.+.+.-++..+....    .....+|+|++|+.+|..+...+...+.....
T Consensus         1 l~~eQ~~~i~~--~~~~~lV~a~AGSGKT~~l~~ri~~ll~~~~----~~~~~Il~lTft~~aa~e~~~ri~~~l~~~~~   74 (315)
T PF00580_consen    1 LTDEQRRIIRS--TEGPLLVNAGAGSGKTTTLLERIAYLLYEGG----VPPERILVLTFTNAAAQEMRERIRELLEEEQQ   74 (315)
T ss_dssp             S-HHHHHHHHS---SSEEEEEE-TTSSHHHHHHHHHHHHHHTSS----STGGGEEEEESSHHHHHHHHHHHHHHHHHCCH
T ss_pred             CCHHHHHHHhC--CCCCEEEEeCCCCCchHHHHHHHHHhhcccc----CChHHheecccCHHHHHHHHHHHHHhcCcccc
Confidence            46889998888  6778999999999999987666666665432    23457999999999999999998886654321


Q ss_pred             EEEEeeCCCChHHHHHHHhcCCeEEEeCchhHHHHHHhcCCcccccCCceEEEecCcc
Q 002040          570 RCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEAD  627 (976)
Q Consensus       570 ~~~~~~gg~~~~~~~~~l~~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDEah  627 (976)
                      .      .............-..+.|+|...+...+.........+ .-.+-|+|+..
T Consensus        75 ~------~~~~~~~~~~~~~~~~~~i~T~hsf~~~ll~~~~~~~~~-~~~~~i~~~~~  125 (315)
T PF00580_consen   75 E------SSDNERLRRQLSNIDRIYISTFHSFCYRLLREYGYEIGI-DPNFEILDEEE  125 (315)
T ss_dssp             C------CTT-HHHHHHHHHCTTSEEEEHHHHHHHHHHHHHGGTTS-HTTTEEECHHH
T ss_pred             c------ccccccccccccccchheeehhhhhhhhhhhhhhhhhhc-cccceeecchh
Confidence            0      000011112223345788999888766544321111111 12356667766

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 ....

>PRK04296 thymidine kinase; Provisional

Probab=97.08  E-value=0.0013  Score=67.68  Aligned_cols=109  Identities=15%  Similarity=0.173  Sum_probs=58.3

Q ss_pred             CCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccC---HHHHHHHHHHHHHHHhhcCcEEEEeeCCCChH
Q 002040          505 RDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPT---RELVQQIHSDIRKFAKVMGVRCVPVYGGSGVA  581 (976)
Q Consensus       505 ~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Pt---r~La~Q~~~~~~~~~~~~~~~~~~~~gg~~~~  581 (976)
                      .-.++.|++|+|||+.++-.+.....        .+.+|+|+.|.   +....       .++..+|+.+..        
T Consensus         3 ~i~litG~~GsGKTT~~l~~~~~~~~--------~g~~v~i~k~~~d~~~~~~-------~i~~~lg~~~~~--------   59 (190)
T PRK04296          3 KLEFIYGAMNSGKSTELLQRAYNYEE--------RGMKVLVFKPAIDDRYGEG-------KVVSRIGLSREA--------   59 (190)
T ss_pred             EEEEEECCCCCHHHHHHHHHHHHHHH--------cCCeEEEEeccccccccCC-------cEecCCCCcccc--------
Confidence            34688999999999875555444422        25677888663   21111       111112211110        


Q ss_pred             HHHHHHhcCCeEEEeCchhHHHHHHhcCCcccccCCceEEEecCcccccccCCchHHHHHHHhcCCCCcEEEEecc
Q 002040          582 QQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMGFEPQITRIVQNIRPDRQTVLFSAT  657 (976)
Q Consensus       582 ~~~~~l~~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDEah~~~~~~f~~~i~~il~~~~~~~q~i~~SAT  657 (976)
                                 +.+..+..+...+..      .-..+.+|||||||.+.    ..++..++..+.+....+++++-
T Consensus        60 -----------~~~~~~~~~~~~~~~------~~~~~dvviIDEaq~l~----~~~v~~l~~~l~~~g~~vi~tgl  114 (190)
T PRK04296         60 -----------IPVSSDTDIFELIEE------EGEKIDCVLIDEAQFLD----KEQVVQLAEVLDDLGIPVICYGL  114 (190)
T ss_pred             -----------eEeCChHHHHHHHHh------hCCCCCEEEEEccccCC----HHHHHHHHHHHHHcCCeEEEEec
Confidence                       122344444444432      12357899999998532    23466666665555455555554

>COG1875 NYN ribonuclease and ATPase of PhoH family domains [General function prediction only]

Probab=97.02  E-value=0.0034  Score=68.17  Aligned_cols=144  Identities=16%  Similarity=0.147  Sum_probs=84.0

Q ss_pred             HcCCCCCcHHHHHHHHHHhcCC--CEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHH-----
Q 002040          484 KLNYEKPMPIQAQALPVIMSGR--DCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQI-----  556 (976)
Q Consensus       484 ~~~~~~p~~~Q~~~i~~il~g~--d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~-----  556 (976)
                      -+|+......|.-|+..++...  =|.+.|+-|||||+.++.+.+..++..+.     ..+++|.=|+..+-..+     
T Consensus       223 vwGi~prn~eQ~~ALdlLld~dI~lV~L~G~AGtGKTlLALaAgleqv~e~~~-----y~KiiVtRp~vpvG~dIGfLPG  297 (436)
T COG1875         223 VWGIRPRNAEQRVALDLLLDDDIDLVSLGGKAGTGKTLLALAAGLEQVLERKR-----YRKIIVTRPTVPVGEDIGFLPG  297 (436)
T ss_pred             hhccCcccHHHHHHHHHhcCCCCCeEEeeccCCccHhHHHHHHHHHHHHHHhh-----hceEEEecCCcCcccccCcCCC
Confidence            4677777788999999988654  36778999999999999998888876532     33566666775543211     


Q ss_pred             ------HHHHHHHHhhcCcEEEEeeCCCChHHHHHHHhcCCeEEEeCchhHHHHHHhcCCcccccC-------CceEEEe
Q 002040          557 ------HSDIRKFAKVMGVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGGKITNLR-------RVTYLVM  623 (976)
Q Consensus       557 ------~~~~~~~~~~~~~~~~~~~gg~~~~~~~~~l~~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~-------~~~~vVl  623 (976)
                            .-|++.++..                 +..+..   .-=|+.+.|..++......+..|.       .=.||||
T Consensus       298 ~eEeKm~PWmq~i~Dn-----------------LE~L~~---~~~~~~~~l~~~l~~~~iev~alt~IRGRSl~~~FiII  357 (436)
T COG1875         298 TEEEKMGPWMQAIFDN-----------------LEVLFS---PNEPGDRALEEILSRGRIEVEALTYIRGRSLPDSFIII  357 (436)
T ss_pred             chhhhccchHHHHHhH-----------------HHHHhc---ccccchHHHHHHHhccceeeeeeeeecccccccceEEE
Confidence                  1111111111                 111111   011122233222222211111111       1258999


Q ss_pred             cCcccccccCCchHHHHHHHhcCCCCcEEEEec
Q 002040          624 DEADRMFDMGFEPQITRIVQNIRPDRQTVLFSA  656 (976)
Q Consensus       624 DEah~~~~~~f~~~i~~il~~~~~~~q~i~~SA  656 (976)
                      |||+.+.    ..++..|+..+....++|++.-
T Consensus       358 DEaQNLT----pheikTiltR~G~GsKIVl~gd  386 (436)
T COG1875         358 DEAQNLT----PHELKTILTRAGEGSKIVLTGD  386 (436)
T ss_pred             ehhhccC----HHHHHHHHHhccCCCEEEEcCC
Confidence            9999864    4578889999888887776543

>TIGR01073 pcrA ATP-dependent DNA helicase PcrA

Probab=96.98  E-value=0.04  Score=68.88  Aligned_cols=71  Identities=18%  Similarity=0.161  Sum_probs=53.4

Q ss_pred             CCcHHHHHHHHHHhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHHHHh
Q 002040          489 KPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAK  565 (976)
Q Consensus       489 ~p~~~Q~~~i~~il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~~~~  565 (976)
                      .++|-|.+|+..  ....++|.|..|||||.+.+.-+...+....    -....+|+|+-|+..|..+...+..++.
T Consensus         4 ~Ln~~Q~~av~~--~~g~~lV~AgaGSGKT~~l~~ria~Li~~~~----i~P~~IL~lTFT~kAA~em~~Rl~~~~~   74 (726)
T TIGR01073         4 HLNPEQREAVKT--TEGPLLIMAGAGSGKTRVLTHRIAHLIAEKN----VAPWNILAITFTNKAAREMKERVEKLLG   74 (726)
T ss_pred             ccCHHHHHHHhC--CCCCEEEEeCCCCCHHHHHHHHHHHHHHcCC----CCHHHeeeeeccHHHHHHHHHHHHHHhc
Confidence            578999999875  3568999999999999986665555554321    1123689999999999998888877653

Designed to identify pcrA members of the uvrD/rep subfamily.

>PF13871 Helicase_C_4: Helicase_C-like

Probab=96.95  E-value=0.002  Score=68.97  Aligned_cols=81  Identities=15%  Similarity=0.347  Sum_probs=62.5

Q ss_pred             HHHHHhccCCccEEEecCcccccCCCCC--------CcEEEEeCCCCCHHHHHHHhcccCCCCCc-cEEEEEecCC---C
Q 002040          755 STISDFKSNVCNLLIATSVAARGLDVKE--------LELVINFDAPNHYEDYVHRVGRTGRAGRK-GCAITFISEE---D  822 (976)
Q Consensus       755 ~~~~~F~~g~~~vLVaT~v~~~GlDi~~--------v~~VI~~d~p~s~~~y~Qr~GR~gR~g~~-g~~~~~~~~~---d  822 (976)
                      ...+.|++|...|+|.|.++++||.+..        -.+.|.+.+||+....+|..||++|.||. .-.|.++...   +
T Consensus        52 ~e~~~F~~g~k~v~iis~AgstGiSlHAd~~~~nqr~Rv~i~le~pwsad~aiQ~~GR~hRsnQ~~~P~y~~l~t~~~gE  131 (278)
T PF13871_consen   52 AEKQAFMDGEKDVAIISDAGSTGISLHADRRVKNQRRRVHITLELPWSADKAIQQFGRTHRSNQVSAPEYRFLVTDLPGE  131 (278)
T ss_pred             HHHHHHhCCCceEEEEecccccccchhccccCCCCCceEEEEeeCCCCHHHHHHHhccccccccccCCEEEEeecCCHHH
Confidence            5577999999999999999999998864        34677799999999999999999999984 4455555433   4


Q ss_pred             cCchHHHHHHHhh
Q 002040          823 AKYSPDLVKALEL  835 (976)
Q Consensus       823 ~~~~~~i~~~l~~  835 (976)
                      ..++..+.+.|..
T Consensus       132 ~Rfas~va~rL~s  144 (278)
T PF13871_consen  132 RRFASTVARRLES  144 (278)
T ss_pred             HHHHHHHHHHHhh
Confidence            4555555555543

>KOG0298 consensus DEAD box-containing helicase-like transcription factor/DNA repair protein [Replication, recombination and repair]

Probab=96.94  E-value=0.0015  Score=80.67  Aligned_cols=158  Identities=16%  Similarity=0.154  Sum_probs=93.4

Q ss_pred             cCCCEEEEcCCCCchHHHHHHHHHHHHhcCCC----------CCCCCCCeEEEEccCHHHHHHHHHHHHHHHhhcCcEEE
Q 002040          503 SGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPP----------VAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVMGVRCV  572 (976)
Q Consensus       503 ~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~----------~~~~~~~~vLIl~Ptr~La~Q~~~~~~~~~~~~~~~~~  572 (976)
                      .|+.++++..+|+|||..-+...+.++-..-+          .......-+|||||. ++..||+.+|.+.+... +.+.
T Consensus       373 ~g~~~~~ade~~~qk~~~~l~~~l~~~~k~~~~~cS~~~~e~~n~~~tgaTLII~P~-aIl~QW~~EI~kH~~~~-lKv~  450 (1394)
T KOG0298|consen  373 HGKRVQCADEMGWQKTSEKLILELSDLPKLCPSCCSELVKEGENLVETGATLIICPN-AILMQWFEEIHKHISSL-LKVL  450 (1394)
T ss_pred             CCcceeehhhhhccchHHHHHHHHhcccccchhhhhHHHhcccceeecCceEEECcH-HHHHHHHHHHHHhcccc-ceEE
Confidence            45678888999999998866555544221100          011123567999997 56699999999987654 5665


Q ss_pred             EeeCCCChHHHHHHHhcCCeEEEeCchhHHHHHHhcC--Ccccc-------------cCCce--EEEecCcccccccCCc
Q 002040          573 PVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSG--GKITN-------------LRRVT--YLVMDEADRMFDMGFE  635 (976)
Q Consensus       573 ~~~gg~~~~~~~~~l~~~~~Iiv~Tp~~L~~~l~~~~--~~~~~-------------l~~~~--~vVlDEah~~~~~~f~  635 (976)
                      ...|-...........-.+|||++|+..|...+....  +...+             |-.+.  -||||||+.+-.  ..
T Consensus       451 ~Y~Girk~~~~~~~el~~yDIVlTtYdiLr~El~hte~~~~~R~lR~qsr~~~~~SPL~~v~wWRIclDEaQMves--ss  528 (1394)
T KOG0298|consen  451 LYFGIRKTFWLSPFELLQYDIVLTTYDILRNELYHTEDFGSDRQLRHQSRYMRPNSPLLMVNWWRICLDEAQMVES--SS  528 (1394)
T ss_pred             EEechhhhcccCchhhhccCEEEeehHHHHhHhhcccccCChhhhhcccCCCCCCCchHHHHHHHHhhhHHHhhcc--hH
Confidence            5555332211111222358999999999987665431  11111             11112  289999995432  23


Q ss_pred             hHHHHHHHhcCCCCcEEEEeccCcHHHHHH
Q 002040          636 PQITRIVQNIRPDRQTVLFSATFPRQVEIL  665 (976)
Q Consensus       636 ~~i~~il~~~~~~~q~i~~SAT~~~~~~~l  665 (976)
                      ......+..+ +....-++|+||-..+..+
T Consensus       529 S~~a~M~~rL-~~in~W~VTGTPiq~Iddl  557 (1394)
T KOG0298|consen  529 SAAAEMVRRL-HAINRWCVTGTPIQKIDDL  557 (1394)
T ss_pred             HHHHHHHHHh-hhhceeeecCCchhhhhhh
Confidence            3444444444 2334678999976554433

>PRK13826 Dtr system oriT relaxase; Provisional

Probab=96.91  E-value=0.0097  Score=75.37  Aligned_cols=124  Identities=17%  Similarity=0.131  Sum_probs=77.5

Q ss_pred             CCCcHHHHHHHHHHhc-CCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHHHHhh
Q 002040          488 EKPMPIQAQALPVIMS-GRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKV  566 (976)
Q Consensus       488 ~~p~~~Q~~~i~~il~-g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~~~~~  566 (976)
                      ..+++-|.+++..+.. ++-++|+|..|+|||++ +-++...+..       .|..|+.++||-..|..+.+       .
T Consensus       380 ~~Ls~eQ~~Av~~i~~~~r~~~v~G~AGTGKTt~-l~~~~~~~e~-------~G~~V~g~ApTgkAA~~L~e-------~  444 (1102)
T PRK13826        380 ARLSDEQKTAIEHVAGPARIAAVVGRAGAGKTTM-MKAAREAWEA-------AGYRVVGGALAGKAAEGLEK-------E  444 (1102)
T ss_pred             CCCCHHHHHHHHHHhccCCeEEEEeCCCCCHHHH-HHHHHHHHHH-------cCCeEEEEcCcHHHHHHHHH-------h
Confidence            3589999999998865 45678889999999976 4444444433       36788999999776654422       2


Q ss_pred             cCcEEEEeeCCCChHHHHHHHhcCCeEEEeCchhHHHHHHhcCCcccccCCceEEEecCcccccccCCchHHHHHHHhcC
Q 002040          567 MGVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMGFEPQITRIVQNIR  646 (976)
Q Consensus       567 ~~~~~~~~~gg~~~~~~~~~l~~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDEah~~~~~~f~~~i~~il~~~~  646 (976)
                      .|+....                        ...|+-.+  .. ....|...++||||||-.+.    ..++..++....
T Consensus       445 ~Gi~a~T------------------------Ias~ll~~--~~-~~~~l~~~~vlVIDEAsMv~----~~~m~~Ll~~~~  493 (1102)
T PRK13826        445 AGIQSRT------------------------LSSWELRW--NQ-GRDQLDNKTVFVLDEAGMVA----SRQMALFVEAVT  493 (1102)
T ss_pred             hCCCeee------------------------HHHHHhhh--cc-CccCCCCCcEEEEECcccCC----HHHHHHHHHHHH
Confidence            3333221                        11111000  00 11245667899999999543    345556666664


Q ss_pred             -CCCcEEEEecc
Q 002040          647 -PDRQTVLFSAT  657 (976)
Q Consensus       647 -~~~q~i~~SAT  657 (976)
                       ...++|++.=+
T Consensus       494 ~~garvVLVGD~  505 (1102)
T PRK13826        494 RAGAKLVLVGDP  505 (1102)
T ss_pred             hcCCEEEEECCH
Confidence             56778877665

>TIGR01074 rep ATP-dependent DNA helicase Rep

Probab=96.91  E-value=0.058  Score=66.92  Aligned_cols=70  Identities=19%  Similarity=0.158  Sum_probs=52.7

Q ss_pred             CcHHHHHHHHHHhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHHHHh
Q 002040          490 PMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAK  565 (976)
Q Consensus       490 p~~~Q~~~i~~il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~~~~  565 (976)
                      ++|-|.+++..  ...+++|.|..|||||.+.+.-+...+....    .....+|+|+.|+..|.++...+...+.
T Consensus         2 Ln~~Q~~av~~--~~~~~~V~Ag~GSGKT~~L~~ri~~ll~~~~----~~p~~IL~vTFt~~Aa~em~~Rl~~~l~   71 (664)
T TIGR01074         2 LNPQQQEAVEY--VTGPCLVLAGAGSGKTRVITNKIAYLIQNCG----YKARNIAAVTFTNKAAREMKERVAKTLG   71 (664)
T ss_pred             CCHHHHHHHhC--CCCCEEEEecCCCCHHHHHHHHHHHHHHhcC----CCHHHeEEEeccHHHHHHHHHHHHHHhC
Confidence            67889998764  4568999999999999986665655554321    1234689999999999999888877653

Designed to identify rep members of the uvrD/rep subfamily.

>PF05970 PIF1: PIF1-like helicase; InterPro: IPR010285 This entry represents PIF1 helicase and related proteins

Probab=96.85  E-value=0.0032  Score=71.69  Aligned_cols=59  Identities=19%  Similarity=0.284  Sum_probs=43.2

Q ss_pred             CcHHHHHHHHHH------hcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHH
Q 002040          490 PMPIQAQALPVI------MSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQI  556 (976)
Q Consensus       490 p~~~Q~~~i~~i------l~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~  556 (976)
                      +++-|..++..+      ..+..+++.|+-|+|||+. +-.+...+..       .+..+++++||-..|..+
T Consensus         2 Ln~eQ~~~~~~v~~~~~~~~~~~~fv~G~~GtGKs~l-~~~i~~~~~~-------~~~~~~~~a~tg~AA~~i   66 (364)
T PF05970_consen    2 LNEEQRRVFDTVIEAIENEEGLNFFVTGPAGTGKSFL-IKAIIDYLRS-------RGKKVLVTAPTGIAAFNI   66 (364)
T ss_pred             CCHHHHHHHHHHHHHHHccCCcEEEEEcCCCCChhHH-HHHHHHHhcc-------ccceEEEecchHHHHHhc
Confidence            567899998888      5778899999999999974 2233333322       356799999998776544

The PIF1 helicase inhibits telomerase activity and is cell cycle regulated [, ].

>TIGR02760 TraI_TIGR conjugative transfer relaxase protein TraI

Probab=96.85  E-value=0.042  Score=74.85  Aligned_cols=210  Identities=11%  Similarity=0.101  Sum_probs=115.0

Q ss_pred             CCcHHHHHHHHHHhcC--CCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHHHHhh
Q 002040          489 KPMPIQAQALPVIMSG--RDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKV  566 (976)
Q Consensus       489 ~p~~~Q~~~i~~il~g--~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~~~~~  566 (976)
                      .+++-|.+++..++..  +-+||.|..|+|||.+ +-.++..+..       .|..|++++||-..+..+.+.+..    
T Consensus       429 ~Ls~~Q~~Av~~il~s~~~v~ii~G~aGTGKTt~-l~~l~~~~~~-------~G~~V~~lAPTgrAA~~L~e~~g~----  496 (1960)
T TIGR02760       429 ALSPSNKDAVSTLFTSTKRFIIINGFGGTGSTEI-AQLLLHLASE-------QGYEIQIITAGSLSAQELRQKIPR----  496 (1960)
T ss_pred             CCCHHHHHHHHHHHhCCCCeEEEEECCCCCHHHH-HHHHHHHHHh-------cCCeEEEEeCCHHHHHHHHHHhcc----
Confidence            5789999999999875  5678889999999975 4444444333       367899999998777665443221    


Q ss_pred             cCcEEEEeeCCCChHHHHHHHhcCCeEEEeCchhHHHHHHhcCCcccccCCceEEEecCcccccccCCchHHHHHHHhc-
Q 002040          567 MGVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMGFEPQITRIVQNI-  645 (976)
Q Consensus       567 ~~~~~~~~~gg~~~~~~~~~l~~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDEah~~~~~~f~~~i~~il~~~-  645 (976)
                         ...      .+...+..+..  .....|...|+    .   ....|...++||||||-.+.    ...+..++... 
T Consensus       497 ---~A~------Ti~~~l~~l~~--~~~~~tv~~fl----~---~~~~l~~~~vlIVDEAsMl~----~~~~~~Ll~~a~  554 (1960)
T TIGR02760       497 ---LAS------TFITWVKNLFN--DDQDHTVQGLL----D---KSSPFSNKDIFVVDEANKLS----NNELLKLIDKAE  554 (1960)
T ss_pred             ---hhh------hHHHHHHhhcc--cccchhHHHhh----c---ccCCCCCCCEEEEECCCCCC----HHHHHHHHHHHh
Confidence               110      01111111111  11122322332    1   11345567899999999543    44566677655 


Q ss_pred             CCCCcEEEEecc--CcH----HHHHHHHHHcCCCeEEEeCCcccccCCceEEEEecCcchHHHHHHHHHHhhhc-CCcEE
Q 002040          646 RPDRQTVLFSAT--FPR----QVEILARKVLNKPVEIQVGGRSVVNKDITQLVEVRPESDRFLRLLELLGEWYE-KGKIL  718 (976)
Q Consensus       646 ~~~~q~i~~SAT--~~~----~~~~l~~~~l~~~~~i~~~~~~~~~~~i~q~~~~~~~~~k~~~l~~~l~~~~~-~~kvL  718 (976)
                      ..+.++|++.=+  +|+    .+..++... +-+.. .+.........+  .+.......++..+...+..... ...++
T Consensus       555 ~~garvVlvGD~~QL~sV~aG~~f~~L~~~-gv~t~-~l~~i~rq~~~v--~i~~~~~~~r~~~ia~~y~~L~~~r~~tl  630 (1960)
T TIGR02760       555 QHNSKLILLNDSAQRQGMSAGSAIDLLKEG-GVTTY-AWVDTKQQKASV--EISEAVDKLRVDYIASAWLDLTPDRQNSQ  630 (1960)
T ss_pred             hcCCEEEEEcChhhcCccccchHHHHHHHC-CCcEE-EeecccccCcce--eeeccCchHHHHHHHHHHHhcccccCceE
Confidence            467888888766  222    222233222 11211 111111111111  12222333444455555444443 33689


Q ss_pred             EEecCHHHHHHHHHHHHH
Q 002040          719 IFVHSQEKCDALFRDLLK  736 (976)
Q Consensus       719 IF~~s~~~~~~l~~~L~~  736 (976)
                      ||..+..+...|...++.
T Consensus       631 iv~~t~~dr~~Ln~~iR~  648 (1960)
T TIGR02760       631 VLATTHREQQDLTQIIRN  648 (1960)
T ss_pred             EEcCCcHHHHHHHHHHHH
Confidence            999998888887776643

This protein is a component of the relaxosome complex. In the process of conjugative plasmid transfer the realaxosome binds to the plasmid at the oriT (origin of transfer) site. The relaxase protein TraI mediates the single-strand nicking and ATP-dependent unwinding (relaxation, helicase activity) of the plasmid molecule. These two activities reside in separate domains of the protein.

>PRK08116 hypothetical protein; Validated

Probab=96.79  E-value=0.023  Score=61.66  Aligned_cols=48  Identities=13%  Similarity=0.200  Sum_probs=28.8

Q ss_pred             cCCceEEEecCccc--ccccCCchHHHHHHHhc-CCCCcEEEEeccCcHHHH
Q 002040          615 LRRVTYLVMDEADR--MFDMGFEPQITRIVQNI-RPDRQTVLFSATFPRQVE  663 (976)
Q Consensus       615 l~~~~~vVlDEah~--~~~~~f~~~i~~il~~~-~~~~q~i~~SAT~~~~~~  663 (976)
                      +..+++||||+++.  ..++ ....+..|+... .....+|+.|...|..+.
T Consensus       176 l~~~dlLviDDlg~e~~t~~-~~~~l~~iin~r~~~~~~~IiTsN~~~~eL~  226 (268)
T PRK08116        176 LVNADLLILDDLGAERDTEW-AREKVYNIIDSRYRKGLPTIVTTNLSLEELK  226 (268)
T ss_pred             hcCCCEEEEecccCCCCCHH-HHHHHHHHHHHHHHCCCCEEEECCCCHHHHH
Confidence            34578999999963  2222 233455566554 344567777776665543

>PRK06835 DNA replication protein DnaC; Validated

Probab=96.78  E-value=0.018  Score=64.09  Aligned_cols=48  Identities=8%  Similarity=0.176  Sum_probs=28.5

Q ss_pred             cCCceEEEecCcccccccCC-chHHHHHHHhcCC-CCcEEEEeccCcHHH
Q 002040          615 LRRVTYLVMDEADRMFDMGF-EPQITRIVQNIRP-DRQTVLFSATFPRQV  662 (976)
Q Consensus       615 l~~~~~vVlDEah~~~~~~f-~~~i~~il~~~~~-~~q~i~~SAT~~~~~  662 (976)
                      +..+++||||+.+......| ...+..|+..... ...+|+.|...|..+
T Consensus       244 l~~~DLLIIDDlG~e~~t~~~~~~Lf~iin~R~~~~k~tIiTSNl~~~el  293 (329)
T PRK06835        244 LINCDLLIIDDLGTEKITEFSKSELFNLINKRLLRQKKMIISTNLSLEEL  293 (329)
T ss_pred             hccCCEEEEeccCCCCCCHHHHHHHHHHHHHHHHCCCCEEEECCCCHHHH
Confidence            44578999999986543333 2345556555432 455666666555554

>smart00492 HELICc3 helicase superfamily c-terminal domain

Probab=96.76  E-value=0.0098  Score=57.71  Aligned_cols=78  Identities=21%  Similarity=0.230  Sum_probs=54.1

Q ss_pred             eeccCCCCHHHHHHHHHHhccCC-ccEEEecCcccccCCCCC--CcEEEEeCCCCC----H-------------------
Q 002040          742 LSLHGAKDQTDRESTISDFKSNV-CNLLIATSVAARGLDVKE--LELVINFDAPNH----Y-------------------  795 (976)
Q Consensus       742 ~~lhg~~~~~~R~~~~~~F~~g~-~~vLVaT~v~~~GlDi~~--v~~VI~~d~p~s----~-------------------  795 (976)
                      .++.-+.+..+...+++.|.... ..||++|..++.|||+++  +.+||+...|..    +                   
T Consensus        25 ~i~~e~~~~~~~~~~l~~f~~~~~~~iL~~~~~~~EGiD~~g~~~r~vii~glPfp~~~d~~~~~~~~~~~~~~~~~~~~  104 (141)
T smart00492       25 LLLVQGEDGKETGKLLEKYVEACENAILLATARFSEGVDFPGDYLRAVIIDGLPFPYPDSPILKARLELLRDKGQIRPFD  104 (141)
T ss_pred             eEEEeCCChhHHHHHHHHHHHcCCCEEEEEccceecceecCCCCeeEEEEEecCCCCCCCHHHHHHHHHHHHhCCCCchh
Confidence            33444455556788899998654 379999988999999998  578888776641    1                   


Q ss_pred             --------HHHHHHhcccCCCCCccEEEEEec
Q 002040          796 --------EDYVHRVGRTGRAGRKGCAITFIS  819 (976)
Q Consensus       796 --------~~y~Qr~GR~gR~g~~g~~~~~~~  819 (976)
                              ....|.+||+-|....-.++++++
T Consensus       105 ~~~~~~a~~~l~Qa~GR~iR~~~D~g~i~l~D  136 (141)
T smart00492      105 FVSLPDAMRTLAQCVGRLIRGANDYGVVVIAD  136 (141)
T ss_pred             HHHHHHHHHHHHHHhCccccCcCceEEEEEEe
Confidence                    112488899999865544444544

>PRK12727 flagellar biosynthesis regulator FlhF; Provisional

Probab=96.73  E-value=0.056  Score=63.01  Aligned_cols=170  Identities=15%  Similarity=0.180  Sum_probs=81.8

Q ss_pred             cCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEE-cc-CHHHHHHHHHHHHHHHhhcCcEEEEeeCCCCh
Q 002040          503 SGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIM-AP-TRELVQQIHSDIRKFAKVMGVRCVPVYGGSGV  580 (976)
Q Consensus       503 ~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl-~P-tr~La~Q~~~~~~~~~~~~~~~~~~~~gg~~~  580 (976)
                      .|..++++|+||+|||+.+...+.......      .+..+.++ +. .+..+.   ..+..+...+++.+..       
T Consensus       349 ~G~vIaLVGPtGvGKTTtaakLAa~la~~~------~gkkVaLIdtDtyRigA~---EQLk~ya~iLgv~v~~-------  412 (559)
T PRK12727        349 RGGVIALVGPTGAGKTTTIAKLAQRFAAQH------APRDVALVTTDTQRVGGR---EQLHSYGRQLGIAVHE-------  412 (559)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHHHHHHhc------CCCceEEEecccccccHH---HHHHHhhcccCceeEe-------
Confidence            466788899999999987544333332221      12233333 33 233222   2233333333432221       


Q ss_pred             HHHHHHHhcCCeEEEeCchhHHHHHHhcCCcccccCCceEEEecCccccccc-CCchHHHHHHHhcCCCCcEEEEeccCc
Q 002040          581 AQQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDM-GFEPQITRIVQNIRPDRQTVLFSATFP  659 (976)
Q Consensus       581 ~~~~~~l~~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDEah~~~~~-~f~~~i~~il~~~~~~~q~i~~SAT~~  659 (976)
                                    +.++..|...+.       .+.++++||||.+-++... .....+..+ ........+|+++++..
T Consensus       413 --------------a~d~~~L~~aL~-------~l~~~DLVLIDTaG~s~~D~~l~eeL~~L-~aa~~~a~lLVLpAtss  470 (559)
T PRK12727        413 --------------ADSAESLLDLLE-------RLRDYKLVLIDTAGMGQRDRALAAQLNWL-RAARQVTSLLVLPANAH  470 (559)
T ss_pred             --------------cCcHHHHHHHHH-------HhccCCEEEecCCCcchhhHHHHHHHHHH-HHhhcCCcEEEEECCCC
Confidence                          123334444442       2446789999999754211 111122222 22234456788888875


Q ss_pred             H-HHHHHHHHHcCCCeEEEeCCcccccCCceEEEEecCcchHHHHHHHHHHhhhcCCcEEEEecCHH
Q 002040          660 R-QVEILARKVLNKPVEIQVGGRSVVNKDITQLVEVRPESDRFLRLLELLGEWYEKGKILIFVHSQE  725 (976)
Q Consensus       660 ~-~~~~l~~~~l~~~~~i~~~~~~~~~~~i~q~~~~~~~~~k~~~l~~~l~~~~~~~kvLIF~~s~~  725 (976)
                      . .+..++..|....+             ..-++...+...++-.++.++...  +-++..+++++.
T Consensus       471 ~~Dl~eii~~f~~~~~-------------~gvILTKlDEt~~lG~aLsv~~~~--~LPI~yvt~GQ~  522 (559)
T PRK12727        471 FSDLDEVVRRFAHAKP-------------QGVVLTKLDETGRFGSALSVVVDH--QMPITWVTDGQR  522 (559)
T ss_pred             hhHHHHHHHHHHhhCC-------------eEEEEecCcCccchhHHHHHHHHh--CCCEEEEeCCCC
Confidence            3 44444444422110             011233344556666677766653  335555555443

>PRK06921 hypothetical protein; Provisional

Probab=96.72  E-value=0.02  Score=62.03  Aligned_cols=27  Identities=19%  Similarity=0.203  Sum_probs=19.5

Q ss_pred             cCCCEEEEcCCCCchHHHHHHHHHHHHh
Q 002040          503 SGRDCIGVAKTGSGKTLAFVLPMLRHIK  530 (976)
Q Consensus       503 ~g~d~i~~a~TGsGKT~~~~l~il~~l~  530 (976)
                      .+..++++|++|+|||..+ .++...+.
T Consensus       116 ~~~~l~l~G~~G~GKThLa-~aia~~l~  142 (266)
T PRK06921        116 RKNSIALLGQPGSGKTHLL-TAAANELM  142 (266)
T ss_pred             CCCeEEEECCCCCcHHHHH-HHHHHHHh
Confidence            3577999999999999753 34444444

>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=96.67  E-value=0.012  Score=56.70  Aligned_cols=25  Identities=16%  Similarity=0.268  Sum_probs=18.6

Q ss_pred             CCCEEEEcCCCCchHHHHHHHHHHHH
Q 002040          504 GRDCIGVAKTGSGKTLAFVLPMLRHI  529 (976)
Q Consensus       504 g~d~i~~a~TGsGKT~~~~l~il~~l  529 (976)
                      +..+++.|++|+|||.. +..++..+
T Consensus        19 ~~~v~i~G~~G~GKT~l-~~~i~~~~   43 (151)
T cd00009          19 PKNLLLYGPPGTGKTTL-ARAIANEL   43 (151)
T ss_pred             CCeEEEECCCCCCHHHH-HHHHHHHh
Confidence            67899999999999964 44444443

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.

>PRK12726 flagellar biosynthesis regulator FlhF; Provisional

Probab=96.59  E-value=0.049  Score=60.94  Aligned_cols=24  Identities=29%  Similarity=0.206  Sum_probs=18.2

Q ss_pred             cCCCEEEEcCCCCchHHHHHHHHH
Q 002040          503 SGRDCIGVAKTGSGKTLAFVLPML  526 (976)
Q Consensus       503 ~g~d~i~~a~TGsGKT~~~~l~il  526 (976)
                      .++.++++||+|+|||+.+.-.+.
T Consensus       205 ~~~ii~lvGptGvGKTTt~akLA~  228 (407)
T PRK12726        205 NHRIISLIGQTGVGKTTTLVKLGW  228 (407)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHH
Confidence            456788999999999987554443

>PRK07952 DNA replication protein DnaC; Validated

Probab=96.56  E-value=0.022  Score=60.71  Aligned_cols=48  Identities=25%  Similarity=0.339  Sum_probs=29.1

Q ss_pred             cCCceEEEecCcccccccCCch-HHHHHHHhcC-CCCcEEEEeccCcHHH
Q 002040          615 LRRVTYLVMDEADRMFDMGFEP-QITRIVQNIR-PDRQTVLFSATFPRQV  662 (976)
Q Consensus       615 l~~~~~vVlDEah~~~~~~f~~-~i~~il~~~~-~~~q~i~~SAT~~~~~  662 (976)
                      +..+++||||+++......+.. .+..|+.... ....+|+.|--.+..+
T Consensus       160 l~~~dlLvIDDig~~~~s~~~~~~l~~Ii~~Ry~~~~~tiitSNl~~~~l  209 (244)
T PRK07952        160 LSNVDLLVIDEIGVQTESRYEKVIINQIVDRRSSSKRPTGMLTNSNMEEM  209 (244)
T ss_pred             hccCCEEEEeCCCCCCCCHHHHHHHHHHHHHHHhCCCCEEEeCCCCHHHH
Confidence            3458899999999765444443 3444555432 3456777776655443

>smart00491 HELICc2 helicase superfamily c-terminal domain

Probab=96.44  E-value=0.015  Score=56.56  Aligned_cols=93  Identities=16%  Similarity=0.229  Sum_probs=57.6

Q ss_pred             HHHHHHHHHHCCC---CceeccCCCCHHHHHHHHHHhccCCc---cEEEecCc--ccccCCCCC--CcEEEEeCCCCC--
Q 002040          727 CDALFRDLLKHGY---PCLSLHGAKDQTDRESTISDFKSNVC---NLLIATSV--AARGLDVKE--LELVINFDAPNH--  794 (976)
Q Consensus       727 ~~~l~~~L~~~~~---~~~~lhg~~~~~~R~~~~~~F~~g~~---~vLVaT~v--~~~GlDi~~--v~~VI~~d~p~s--  794 (976)
                      .+.++..+...++   ...++.-+....+...++..|+...-   .||+++.-  ++.|||+++  +.+||+...|..  
T Consensus         4 m~~v~~~~~~~~~~~~~~~i~~e~~~~~~~~~~l~~f~~~~~~~g~iL~~v~~G~~~EGiD~~g~~~r~vii~glPfp~~   83 (142)
T smart00491        4 LEQVVEYWKENGILEINKPVFIEGKDSGETEELLEKYSAACEARGALLLAVARGKVSEGIDFPDDLGRAVIIVGIPFPNP   83 (142)
T ss_pred             HHHHHHHHHhcCccccCceEEEECCCCchHHHHHHHHHHhcCCCCEEEEEEeCCeeecceecCCCccEEEEEEecCCCCC
Confidence            3445555554432   12223323333344678888886433   68888876  999999998  678988777641  


Q ss_pred             --H---------------------------HHHHHHhcccCCCCCccEEEEEec
Q 002040          795 --Y---------------------------EDYVHRVGRTGRAGRKGCAITFIS  819 (976)
Q Consensus       795 --~---------------------------~~y~Qr~GR~gR~g~~g~~~~~~~  819 (976)
                        +                           ....|.+||+-|....-.+++|+.
T Consensus        84 ~d~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~Qa~GR~iR~~~D~g~i~l~D  137 (142)
T smart00491       84 DSPILRARLEYLDEKGGIRPFDEVYLFDAMRALAQAIGRAIRHKNDYGVVVLLD  137 (142)
T ss_pred             CCHHHHHHHHHHHHhcCCCcHHHHHHHHHHHHHHHHhCccccCccceEEEEEEe
Confidence              1                           112489999999875544555554

>PF14617 CMS1: U3-containing 90S pre-ribosomal complex subunit

Probab=96.44  E-value=0.0061  Score=64.56  Aligned_cols=86  Identities=20%  Similarity=0.345  Sum_probs=64.5

Q ss_pred             CCCCeEEEEccCHHHHHHHHHHHHHHHhhcCcEEEEeeCCC-ChHHHHHHHhc-CCeEEEeCchhHHHHHHhcCCccccc
Q 002040          538 GDGPVGLIMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGS-GVAQQISELKR-GTEIVVCTPGRMIDILCTSGGKITNL  615 (976)
Q Consensus       538 ~~~~~vLIl~Ptr~La~Q~~~~~~~~~~~~~~~~~~~~gg~-~~~~~~~~l~~-~~~Iiv~Tp~~L~~~l~~~~~~~~~l  615 (976)
                      ...|.+||||..---|..+...+..|.. -+..|+-++.-. ...+++..|.. .+.|.||||++|..++....   ..+
T Consensus       124 ~gsP~~lvvs~SalRa~dl~R~l~~~~~-k~~~v~KLFaKH~Kl~eqv~~L~~~~~~i~vGTP~Rl~kLle~~~---L~l  199 (252)
T PF14617_consen  124 KGSPHVLVVSSSALRAADLIRALRSFKG-KDCKVAKLFAKHIKLEEQVKLLKKTRVHIAVGTPGRLSKLLENGA---LSL  199 (252)
T ss_pred             CCCCEEEEEcchHHHHHHHHHHHHhhcc-CCchHHHHHHhhccHHHHHHHHHhCCceEEEeChHHHHHHHHcCC---CCc
Confidence            3478999999986667766666666521 124555556555 67888888875 57999999999999997653   578


Q ss_pred             CCceEEEecCcc
Q 002040          616 RRVTYLVMDEAD  627 (976)
Q Consensus       616 ~~~~~vVlDEah  627 (976)
                      +++.+||||=-|
T Consensus       200 ~~l~~ivlD~s~  211 (252)
T PF14617_consen  200 SNLKRIVLDWSY  211 (252)
T ss_pred             ccCeEEEEcCCc
Confidence            899999999876

>PRK14723 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=96.41  E-value=0.027  Score=68.63  Aligned_cols=23  Identities=30%  Similarity=0.156  Sum_probs=17.4

Q ss_pred             CCCEEEEcCCCCchHHHHHHHHH
Q 002040          504 GRDCIGVAKTGSGKTLAFVLPML  526 (976)
Q Consensus       504 g~d~i~~a~TGsGKT~~~~l~il  526 (976)
                      +.-++++||||+|||+++...+.
T Consensus       185 g~Vi~lVGpnGvGKTTTiaKLA~  207 (767)
T PRK14723        185 GGVLALVGPTGVGKTTTTAKLAA  207 (767)
T ss_pred             CeEEEEECCCCCcHHHHHHHHHh
Confidence            45678899999999987554443

>PF03354 Terminase_1: Phage Terminase ; InterPro: IPR005021 This entry is represented by Lactococcus phage bIL285, Orf41 (terminase)

Probab=96.37  E-value=0.0089  Score=70.73  Aligned_cols=151  Identities=17%  Similarity=0.137  Sum_probs=85.6

Q ss_pred             HHHHHHHHHHhc-----C----CCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHH
Q 002040          492 PIQAQALPVIMS-----G----RDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRK  562 (976)
Q Consensus       492 ~~Q~~~i~~il~-----g----~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~  562 (976)
                      |+|.-++-.|+.     |    +.+++.-+=|.|||......++.++.-.    ...++.++++++++.-|..+++.+..
T Consensus         1 PwQ~fi~~~i~G~~~~~g~rrf~~~~l~v~RkNGKS~l~a~i~ly~l~~~----g~~~~~i~~~A~~~~QA~~~f~~~~~   76 (477)
T PF03354_consen    1 PWQKFILRSIFGWRKDDGRRRFREVYLEVPRKNGKSTLAAAIALYMLFLD----GEPGAEIYCAANTRDQAKIVFDEAKK   76 (477)
T ss_pred             CcHHHHHHHHhceEcCCCCEEEEEEEEEEcCccCccHHHHHHHHHHHhcC----CccCceEEEEeCCHHHHHHHHHHHHH
Confidence            578877777762     2    2477788999999987666555555432    22478899999999999999999988


Q ss_pred             HHhhcCcEEEEeeCCCChHHHHHHHhcCCeEEEeCchhHHHHHHhcCCcccccCCceEEEecCcccccccCCchHHHHHH
Q 002040          563 FAKVMGVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMGFEPQITRIV  642 (976)
Q Consensus       563 ~~~~~~~~~~~~~gg~~~~~~~~~l~~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDEah~~~~~~f~~~i~~il  642 (976)
                      +....+...... ..     .+... ....|.+...+.++..+...... ..=.+..++|+||+|.+-+......+..-.
T Consensus        77 ~i~~~~~l~~~~-~~-----~~~~~-~~~~i~~~~~~s~~~~~s~~~~~-~dG~~~~~~i~DE~h~~~~~~~~~~l~~g~  148 (477)
T PF03354_consen   77 MIEASPELRKRK-KP-----KIIKS-NKKEIEFPKTGSFFKALSSDADS-LDGLNPSLAIFDELHAHKDDELYDALESGM  148 (477)
T ss_pred             HHHhChhhccch-hh-----hhhhh-hceEEEEcCCCcEEEEEecCCCC-ccCCCCceEEEeCCCCCCCHHHHHHHHhhh
Confidence            876532211100 00     00001 01233333333333333332222 222357899999999875433223333222


Q ss_pred             HhcCCCCcEEEEe
Q 002040          643 QNIRPDRQTVLFS  655 (976)
Q Consensus       643 ~~~~~~~q~i~~S  655 (976)
                      .. +++.+++++|
T Consensus       149 ~~-r~~pl~~~IS  160 (477)
T PF03354_consen  149 GA-RPNPLIIIIS  160 (477)
T ss_pred             cc-CCCceEEEEe
Confidence            22 4566666554

The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.

>PRK06731 flhF flagellar biosynthesis regulator FlhF; Validated

Probab=96.36  E-value=0.15  Score=55.17  Aligned_cols=170  Identities=16%  Similarity=0.209  Sum_probs=89.0

Q ss_pred             cCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEE-ccCH--HHHHHHHHHHHHHHhhcCcEEEEeeCCCC
Q 002040          503 SGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIM-APTR--ELVQQIHSDIRKFAKVMGVRCVPVYGGSG  579 (976)
Q Consensus       503 ~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl-~Ptr--~La~Q~~~~~~~~~~~~~~~~~~~~gg~~  579 (976)
                      .+..++++|++|+|||+.+.+.+... ..       .+..+.++ +.+.  ..+.||.    .++..+++.+...     
T Consensus        74 ~~~~i~~~G~~g~GKTtl~~~l~~~l-~~-------~~~~v~~i~~D~~ri~~~~ql~----~~~~~~~~~~~~~-----  136 (270)
T PRK06731         74 EVQTIALIGPTGVGKTTTLAKMAWQF-HG-------KKKTVGFITTDHSRIGTVQQLQ----DYVKTIGFEVIAV-----  136 (270)
T ss_pred             CCCEEEEECCCCCcHHHHHHHHHHHH-HH-------cCCeEEEEecCCCCHHHHHHHH----HHhhhcCceEEec-----
Confidence            34678889999999998765444332 21       13334444 4232  3444443    3433344333221     


Q ss_pred             hHHHHHHHhcCCeEEEeCchhHHHHHHhcCCcccccCCceEEEecCcccccc-cCCchHHHHHHHhcCCCCcEEEEeccC
Q 002040          580 VAQQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFD-MGFEPQITRIVQNIRPDRQTVLFSATF  658 (976)
Q Consensus       580 ~~~~~~~l~~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDEah~~~~-~~f~~~i~~il~~~~~~~q~i~~SAT~  658 (976)
                                      .++..|...+..-    .....+++||||-+=++.. ......+..++....++.-++++|||.
T Consensus       137 ----------------~~~~~l~~~l~~l----~~~~~~D~ViIDt~Gr~~~~~~~l~el~~~~~~~~~~~~~LVl~a~~  196 (270)
T PRK06731        137 ----------------RDEAAMTRALTYF----KEEARVDYILIDTAGKNYRASETVEEMIETMGQVEPDYICLTLSASM  196 (270)
T ss_pred             ----------------CCHHHHHHHHHHH----HhcCCCCEEEEECCCCCcCCHHHHHHHHHHHhhhCCCeEEEEEcCcc
Confidence                            2444444443211    1223578999999876532 122334455555566665577899987


Q ss_pred             cH-HHHHHHHHHcCCCeEEEeCCcccccCCceEEEEecCcchHHHHHHHHHHhhhcCCcEEEEecCH
Q 002040          659 PR-QVEILARKVLNKPVEIQVGGRSVVNKDITQLVEVRPESDRFLRLLELLGEWYEKGKILIFVHSQ  724 (976)
Q Consensus       659 ~~-~~~~l~~~~l~~~~~i~~~~~~~~~~~i~q~~~~~~~~~k~~~l~~~l~~~~~~~kvLIF~~s~  724 (976)
                      .. .+...+..|-.-++.             .-.+...+...+.-.++.++...  +-|+..++..+
T Consensus       197 ~~~d~~~~~~~f~~~~~~-------------~~I~TKlDet~~~G~~l~~~~~~--~~Pi~~it~Gq  248 (270)
T PRK06731        197 KSKDMIEIITNFKDIHID-------------GIVFTKFDETASSGELLKIPAVS--SAPIVLMTDGQ  248 (270)
T ss_pred             CHHHHHHHHHHhCCCCCC-------------EEEEEeecCCCCccHHHHHHHHH--CcCEEEEeCCC
Confidence            54 555666665321110             11233445555666666666553  34555555543

>PHA02533 17 large terminase protein; Provisional

Probab=96.28  E-value=0.027  Score=66.96  Aligned_cols=148  Identities=14%  Similarity=0.073  Sum_probs=85.8

Q ss_pred             CCcHHHHHHHHHHhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHHHHhhcC
Q 002040          489 KPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVMG  568 (976)
Q Consensus       489 ~p~~~Q~~~i~~il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~~~~~~~  568 (976)
                      .|.|+|...+..+..++-.++..+=..|||.+.+..++..+...      .+..+++++|+..-|..+++.++.+...++
T Consensus        59 ~L~p~Q~~i~~~~~~~R~~ii~~aRq~GKStl~a~~al~~a~~~------~~~~v~i~A~~~~QA~~vF~~ik~~ie~~P  132 (534)
T PHA02533         59 QMRDYQKDMLKIMHKNRFNACNLSRQLGKTTVVAIFLLHYVCFN------KDKNVGILAHKASMAAEVLDRTKQAIELLP  132 (534)
T ss_pred             CCcHHHHHHHHHHhcCeEEEEEEcCcCChHHHHHHHHHHHHHhC------CCCEEEEEeCCHHHHHHHHHHHHHHHHhCH
Confidence            47799999998876666667778888999998765555444422      256899999999999998888876655432


Q ss_pred             c--EEEEeeCCCChHHHHHHHhcCCeEEEeCchhHHHHHHhcCCcccccCCceEEEecCcccccccCCchHHHHHHHhcC
Q 002040          569 V--RCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMGFEPQITRIVQNIR  646 (976)
Q Consensus       569 ~--~~~~~~gg~~~~~~~~~l~~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDEah~~~~~~f~~~i~~il~~~~  646 (976)
                      .  ....... +   .....+..|+.|.+.|..         . ....-.++.++||||+|.+.+  +...+..+...+.
T Consensus       133 ~l~~~~i~~~-~---~~~I~l~NGS~I~~lss~---------~-~t~rG~~~~~liiDE~a~~~~--~~e~~~ai~p~la  196 (534)
T PHA02533        133 DFLQPGIVEW-N---KGSIELENGSKIGAYASS---------P-DAVRGNSFAMIYIDECAFIPN--FIDFWLAIQPVIS  196 (534)
T ss_pred             HHhhcceeec-C---ccEEEeCCCCEEEEEeCC---------C-CccCCCCCceEEEeccccCCC--HHHHHHHHHHHHH
Confidence            1  1100000 0   001122345555544422         1 001122456899999996533  2233333443333


Q ss_pred             C--CCcEEEEeccC
Q 002040          647 P--DRQTVLFSATF  658 (976)
Q Consensus       647 ~--~~q~i~~SAT~  658 (976)
                      .  ..+++++|.+.
T Consensus       197 sg~~~r~iiiSTp~  210 (534)
T PHA02533        197 SGRSSKIIITSTPN  210 (534)
T ss_pred             cCCCceEEEEECCC
Confidence            2  23455555553

>TIGR01547 phage_term_2 phage terminase, large subunit, PBSX family

Probab=96.26  E-value=0.015  Score=67.14  Aligned_cols=145  Identities=14%  Similarity=0.258  Sum_probs=85.2

Q ss_pred             CEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHH-HHHHHHHHHHHHHhhcCcEEEEeeCCCChHHHH
Q 002040          506 DCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRE-LVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQI  584 (976)
Q Consensus       506 d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~-La~Q~~~~~~~~~~~~~~~~~~~~gg~~~~~~~  584 (976)
                      -.++.|..|||||.++++-++..+...+     .+..+||+.|+.. |..-++..+......+|+....-....+.  .+
T Consensus         3 ~~i~~GgrgSGKS~~~~~~~~~~~~~~~-----~~~~~~~~r~~~~sl~~sv~~~l~~~i~~~g~~~~~~~~~~~~--~i   75 (396)
T TIGR01547         3 EIIAKGGRRSGKTFAIALKLVEKLAINK-----KQQNILAARKVQNSIRDSVFKDIENLLSIEGINYEFKKSKSSM--EI   75 (396)
T ss_pred             eEEEeCCCCcccHHHHHHHHHHHHHhcC-----CCcEEEEEehhhhHHHHHHHHHHHHHHHHcCChhheeecCCcc--EE
Confidence            3678899999999998888887777641     2467888889886 77777888887777777543222221110  01


Q ss_pred             HHHhc-CCeEEEeCc-hhHHHHHHhcCCcccccCCceEEEecCcccccccCCchHHHHHHHhcCC--CCcEEEEeccCcH
Q 002040          585 SELKR-GTEIVVCTP-GRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMGFEPQITRIVQNIRP--DRQTVLFSATFPR  660 (976)
Q Consensus       585 ~~l~~-~~~Iiv~Tp-~~L~~~l~~~~~~~~~l~~~~~vVlDEah~~~~~~f~~~i~~il~~~~~--~~q~i~~SAT~~~  660 (976)
                       .+.. |..|++..- ....        .+.....+.++++|||..+...    .+..++..++.  ....|++|.||+.
T Consensus        76 -~~~~~g~~i~f~g~~d~~~--------~ik~~~~~~~~~idEa~~~~~~----~~~~l~~rlr~~~~~~~i~~t~NP~~  142 (396)
T TIGR01547        76 -KILNTGKKFIFKGLNDKPN--------KLKSGAGIAIIWFEEASQLTFE----DIKELIPRLRETGGKKFIIFSSNPES  142 (396)
T ss_pred             -EecCCCeEEEeecccCChh--------HhhCcceeeeehhhhhhhcCHH----HHHHHHHHhhccCCccEEEEEcCcCC
Confidence             1122 455555443 2111        1123344789999999976422    34444444442  2224888888865


Q ss_pred             HHHHHHHHHc
Q 002040          661 QVEILARKVL  670 (976)
Q Consensus       661 ~~~~l~~~~l  670 (976)
                      ...-+...|+
T Consensus       143 ~~~w~~~~f~  152 (396)
T TIGR01547       143 PLHWVKKRFI  152 (396)
T ss_pred             CccHHHHHHH
Confidence            3333333333

This model detects members of a highly divergent family of the large subunit of phage terminase. All members are encoded by phage genomes or within prophage regions of bacterial genomes. This is a distinct family from pfam03354.

>PRK12724 flagellar biosynthesis regulator FlhF; Provisional

Probab=96.24  E-value=0.13  Score=58.49  Aligned_cols=167  Identities=16%  Similarity=0.155  Sum_probs=82.8

Q ss_pred             CCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEE-c-cCHHHHHHHHHHHHHHHhhcCcEEEEeeCCCChH
Q 002040          504 GRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIM-A-PTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVA  581 (976)
Q Consensus       504 g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl-~-Ptr~La~Q~~~~~~~~~~~~~~~~~~~~gg~~~~  581 (976)
                      +.-++++|++|+|||+++.-.+......       .|..|+++ + +.|..+.   ..+..++..+++.+...       
T Consensus       223 ~~vi~lvGptGvGKTTtaaKLA~~~~~~-------~G~~V~Lit~Dt~R~aA~---eQLk~yAe~lgvp~~~~-------  285 (432)
T PRK12724        223 RKVVFFVGPTGSGKTTSIAKLAAKYFLH-------MGKSVSLYTTDNYRIAAI---EQLKRYADTMGMPFYPV-------  285 (432)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHHh-------cCCeEEEecccchhhhHH---HHHHHHHHhcCCCeeeh-------
Confidence            3457788999999998865554433222       13344443 3 3344443   24555555555433211       


Q ss_pred             HHHHHHhcCCeEEEeCchhHHHHHHhcCCcccccCCceEEEecCccccc-ccCCchHHHHHHHhcC---CCCcEEEEecc
Q 002040          582 QQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMF-DMGFEPQITRIVQNIR---PDRQTVLFSAT  657 (976)
Q Consensus       582 ~~~~~l~~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDEah~~~-~~~f~~~i~~il~~~~---~~~q~i~~SAT  657 (976)
                                    ..+..+...+.        -..+++||||=+-++. +......+..++..+.   +...++++|||
T Consensus       286 --------------~~~~~l~~~l~--------~~~~D~VLIDTaGr~~rd~~~l~eL~~~~~~~~~~~~~e~~LVLsAt  343 (432)
T PRK12724        286 --------------KDIKKFKETLA--------RDGSELILIDTAGYSHRNLEQLERMQSFYSCFGEKDSVENLLVLSST  343 (432)
T ss_pred             --------------HHHHHHHHHHH--------hCCCCEEEEeCCCCCccCHHHHHHHHHHHHhhcCCCCCeEEEEEeCC
Confidence                          01122222321        1357889999766542 1112223344444432   23457889999


Q ss_pred             CcH-HHHHHHHHHcCCCeEEEeCCcccccCCceEEEEecCcchHHHHHHHHHHhhhcCCcEEEEecCH
Q 002040          658 FPR-QVEILARKVLNKPVEIQVGGRSVVNKDITQLVEVRPESDRFLRLLELLGEWYEKGKILIFVHSQ  724 (976)
Q Consensus       658 ~~~-~~~~l~~~~l~~~~~i~~~~~~~~~~~i~q~~~~~~~~~k~~~l~~~l~~~~~~~kvLIF~~s~  724 (976)
                      ... .+...+..|-.-++.             .-++...+...+.-.++.++...  +-|+..++..+
T Consensus       344 ~~~~~~~~~~~~f~~~~~~-------------glIlTKLDEt~~~G~il~i~~~~--~lPI~ylt~GQ  396 (432)
T PRK12724        344 SSYHHTLTVLKAYESLNYR-------------RILLTKLDEADFLGSFLELADTY--SKSFTYLSVGQ  396 (432)
T ss_pred             CCHHHHHHHHHHhcCCCCC-------------EEEEEcccCCCCccHHHHHHHHH--CCCEEEEecCC
Confidence            877 444444444211110             01233445555666666666543  34555555543

>smart00382 AAA ATPases associated with a variety of cellular activities

Probab=96.19  E-value=0.015  Score=55.63  Aligned_cols=19  Identities=37%  Similarity=0.335  Sum_probs=15.7

Q ss_pred             CCCEEEEcCCCCchHHHHH
Q 002040          504 GRDCIGVAKTGSGKTLAFV  522 (976)
Q Consensus       504 g~d~i~~a~TGsGKT~~~~  522 (976)
                      +..++++||+|+|||+.+.
T Consensus         2 ~~~~~l~G~~G~GKTtl~~   20 (148)
T smart00382        2 GEVILIVGPPGSGKTTLAR   20 (148)
T ss_pred             CCEEEEECCCCCcHHHHHH
Confidence            4678999999999998633

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.

>PRK14721 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=96.19  E-value=0.085  Score=60.48  Aligned_cols=173  Identities=17%  Similarity=0.175  Sum_probs=86.4

Q ss_pred             cCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHHHHhhcCcEEEEeeCCCChHH
Q 002040          503 SGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQ  582 (976)
Q Consensus       503 ~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~~~~~~~~~~~~~~gg~~~~~  582 (976)
                      .|.-+.++|+||+|||+.+...+...+...     +.....+|.+.+.-.+  ..+.+..++..+|+.+..++.      
T Consensus       190 ~g~vi~lvGpnG~GKTTtlakLA~~~~~~~-----~~~~v~~i~~d~~rig--alEQL~~~a~ilGvp~~~v~~------  256 (420)
T PRK14721        190 QGGVYALIGPTGVGKTTTTAKLAARAVIRH-----GADKVALLTTDSYRIG--GHEQLRIYGKLLGVSVRSIKD------  256 (420)
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHHHHhc-----CCCeEEEEecCCcchh--HHHHHHHHHHHcCCceecCCC------
Confidence            456688899999999987544333333221     1122356666663332  234455566666665543322      


Q ss_pred             HHHHHhcCCeEEEeCchhHHHHHHhcCCcccccCCceEEEecCcccccc-cCCchHHHHHHHhcCCCCcEEEEeccCcHH
Q 002040          583 QISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFD-MGFEPQITRIVQNIRPDRQTVLFSATFPRQ  661 (976)
Q Consensus       583 ~~~~l~~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDEah~~~~-~~f~~~i~~il~~~~~~~q~i~~SAT~~~~  661 (976)
                                     +..+...+       ..+..+.+|+||-+=+... ......+..+.....+...+|++|||....
T Consensus       257 ---------------~~dl~~al-------~~l~~~d~VLIDTaGrsqrd~~~~~~l~~l~~~~~~~~~~LVl~at~~~~  314 (420)
T PRK14721        257 ---------------IADLQLML-------HELRGKHMVLIDTVGMSQRDQMLAEQIAMLSQCGTQVKHLLLLNATSSGD  314 (420)
T ss_pred             ---------------HHHHHHHH-------HHhcCCCEEEecCCCCCcchHHHHHHHHHHhccCCCceEEEEEcCCCCHH
Confidence                           22222222       1344567777777532110 001122222222223445578899997554


Q ss_pred             -HHHHHHHHcCCCeEEEeCCcccccCCceEEEEecCcchHHHHHHHHHHhhhcCCcEEEEecCHH
Q 002040          662 -VEILARKVLNKPVEIQVGGRSVVNKDITQLVEVRPESDRFLRLLELLGEWYEKGKILIFVHSQE  725 (976)
Q Consensus       662 -~~~l~~~~l~~~~~i~~~~~~~~~~~i~q~~~~~~~~~k~~~l~~~l~~~~~~~kvLIF~~s~~  725 (976)
                       +...+..|-..++.             .-++...+...++-.++.++...  +-++..+++.+.
T Consensus       315 ~~~~~~~~f~~~~~~-------------~~I~TKlDEt~~~G~~l~~~~~~--~lPi~yvt~Gq~  364 (420)
T PRK14721        315 TLDEVISAYQGHGIH-------------GCIITKVDEAASLGIALDAVIRR--KLVLHYVTNGQK  364 (420)
T ss_pred             HHHHHHHHhcCCCCC-------------EEEEEeeeCCCCccHHHHHHHHh--CCCEEEEECCCC
Confidence             44444444322110             11234455566667777776653  346666666554

>PRK12377 putative replication protein; Provisional

Probab=96.16  E-value=0.037  Score=59.11  Aligned_cols=47  Identities=17%  Similarity=0.183  Sum_probs=26.8

Q ss_pred             cCCceEEEecCcccccccCC-chHHHHHHHhcCC-CCcEEEEeccCcHH
Q 002040          615 LRRVTYLVMDEADRMFDMGF-EPQITRIVQNIRP-DRQTVLFSATFPRQ  661 (976)
Q Consensus       615 l~~~~~vVlDEah~~~~~~f-~~~i~~il~~~~~-~~q~i~~SAT~~~~  661 (976)
                      +..+++|||||++......+ ...+..|+..... ...+|++|--.+..
T Consensus       161 l~~~dLLiIDDlg~~~~s~~~~~~l~~ii~~R~~~~~ptiitSNl~~~~  209 (248)
T PRK12377        161 LCKVDLLVLDEIGIQRETKNEQVVLNQIIDRRTASMRSVGMLTNLNHEA  209 (248)
T ss_pred             hcCCCEEEEcCCCCCCCCHHHHHHHHHHHHHHHhcCCCEEEEcCCCHHH
Confidence            45689999999964322222 2344455554433 45677776654433

>COG2805 PilT Tfp pilus assembly protein, pilus retraction ATPase PilT [Cell motility and secretion / Intracellular trafficking and secretion]

Probab=96.15  E-value=0.0073  Score=64.17  Aligned_cols=53  Identities=28%  Similarity=0.383  Sum_probs=40.5

Q ss_pred             CCCCCcccccccCCCCHHHHHHHHHcCCCCCcHHHHHHHHHHhcCC-CEEEEcCCCCchHHHHHHHHHHHHhcC
Q 002040          460 KDVPKPIKTWHQTGLTSKIMETIRKLNYEKPMPIQAQALPVIMSGR-DCIGVAKTGSGKTLAFVLPMLRHIKDQ  532 (976)
Q Consensus       460 ~~~p~pi~~~~~~~l~~~l~~~l~~~~~~~p~~~Q~~~i~~il~g~-d~i~~a~TGsGKT~~~~l~il~~l~~~  532 (976)
                      ..+|..+.+|.++++|+-+.+.+.                   ..+ =+||.||||||||++ +.+|+.++...
T Consensus        99 R~Ip~~i~~~e~LglP~i~~~~~~-------------------~~~GLILVTGpTGSGKSTT-lAamId~iN~~  152 (353)
T COG2805          99 RLIPSKIPTLEELGLPPIVRELAE-------------------SPRGLILVTGPTGSGKSTT-LAAMIDYINKH  152 (353)
T ss_pred             eccCccCCCHHHcCCCHHHHHHHh-------------------CCCceEEEeCCCCCcHHHH-HHHHHHHHhcc
Confidence            356888999999999988776322                   122 267789999999986 77888888765

>KOG0670 consensus U4/U6-associated splicing factor PRP4 [RNA processing and modification]

Probab=96.10  E-value=0.025  Score=64.02  Aligned_cols=47  Identities=23%  Similarity=0.486  Sum_probs=30.9

Q ss_pred             chHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHHHHhhcCcEEEEe
Q 002040          516 GKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVMGVRCVPV  574 (976)
Q Consensus       516 GKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~~~~~~~~~~~~~  574 (976)
                      +|--  |+-++.|++..       +..|||+-|   |.+.+.+.+++|....|+.+..+
T Consensus       492 dk~H--clrl~r~F~hk-------nHLClVFE~---LslNLRevLKKyG~nvGL~ikaV  538 (752)
T KOG0670|consen  492 DKFH--CLRLFRHFKHK-------NHLCLVFEP---LSLNLREVLKKYGRNVGLHIKAV  538 (752)
T ss_pred             hhhH--HHHHHHHhhhc-------ceeEEEehh---hhchHHHHHHHhCcccceeehHH
Confidence            4543  45566665542       456788777   67788888888887777665443

>PRK09183 transposase/IS protein; Provisional

Probab=96.06  E-value=0.056  Score=58.38  Aligned_cols=26  Identities=19%  Similarity=0.235  Sum_probs=20.5

Q ss_pred             HHHhcCCCEEEEcCCCCchHHHHHHH
Q 002040          499 PVIMSGRDCIGVAKTGSGKTLAFVLP  524 (976)
Q Consensus       499 ~~il~g~d~i~~a~TGsGKT~~~~l~  524 (976)
                      .++..+.+++++||+|+|||..+...
T Consensus        97 ~~i~~~~~v~l~Gp~GtGKThLa~al  122 (259)
T PRK09183         97 SFIERNENIVLLGPSGVGKTHLAIAL  122 (259)
T ss_pred             CchhcCCeEEEEeCCCCCHHHHHHHH
Confidence            34567889999999999999765443

>PRK00771 signal recognition particle protein Srp54; Provisional

Probab=96.03  E-value=0.07  Score=61.72  Aligned_cols=130  Identities=20%  Similarity=0.231  Sum_probs=67.7

Q ss_pred             CCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEc-cC-HHHHHHHHHHHHHHHhhcCcEEEEeeCCCChHH
Q 002040          505 RDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMA-PT-RELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQ  582 (976)
Q Consensus       505 ~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~-Pt-r~La~Q~~~~~~~~~~~~~~~~~~~~gg~~~~~  582 (976)
                      ..++++|++|+|||++..-.+ .++...       +..+++++ .+ +..+   +..+..++...++.+.......... 
T Consensus        96 ~vI~lvG~~GsGKTTtaakLA-~~L~~~-------g~kV~lV~~D~~R~aa---~eQL~~la~~~gvp~~~~~~~~d~~-  163 (437)
T PRK00771         96 QTIMLVGLQGSGKTTTAAKLA-RYFKKK-------GLKVGLVAADTYRPAA---YDQLKQLAEKIGVPFYGDPDNKDAV-  163 (437)
T ss_pred             eEEEEECCCCCcHHHHHHHHH-HHHHHc-------CCeEEEecCCCCCHHH---HHHHHHHHHHcCCcEEecCCccCHH-
Confidence            457889999999998754433 333331       33444444 33 3322   3445555555555433211111100 


Q ss_pred             HHHHHhcCCeEEEeCchhHHHHHHhcCCcccccCCceEEEecCcccccc-cCCchHHHHHHHhcCCCCcEEEEeccCcHH
Q 002040          583 QISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFD-MGFEPQITRIVQNIRPDRQTVLFSATFPRQ  661 (976)
Q Consensus       583 ~~~~l~~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDEah~~~~-~~f~~~i~~il~~~~~~~q~i~~SAT~~~~  661 (976)
                                      ..+...+..       +..+++||||.+-++.. ......+..+.....++.-+++++||....
T Consensus       164 ----------------~i~~~al~~-------~~~~DvVIIDTAGr~~~d~~lm~El~~l~~~~~pdevlLVvda~~gq~  220 (437)
T PRK00771        164 ----------------EIAKEGLEK-------FKKADVIIVDTAGRHALEEDLIEEMKEIKEAVKPDEVLLVIDATIGQQ  220 (437)
T ss_pred             ----------------HHHHHHHHH-------hhcCCEEEEECCCcccchHHHHHHHHHHHHHhcccceeEEEeccccHH
Confidence                            011122221       22348899999965421 122334455556667777788899988765


Q ss_pred             HHHHHHHH
Q 002040          662 VEILARKV  669 (976)
Q Consensus       662 ~~~l~~~~  669 (976)
                      ....+..|
T Consensus       221 av~~a~~F  228 (437)
T PRK00771        221 AKNQAKAF  228 (437)
T ss_pred             HHHHHHHH
Confidence            54444443

>PRK06995 flhF flagellar biosynthesis regulator FlhF; Validated

Probab=96.02  E-value=0.15  Score=59.47  Aligned_cols=172  Identities=16%  Similarity=0.200  Sum_probs=80.6

Q ss_pred             CCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHHHHhhcCcEEEEeeCCCChHHH
Q 002040          504 GRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQ  583 (976)
Q Consensus       504 g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~~~~~~~~~~~~~~gg~~~~~~  583 (976)
                      |.-++++|+||+|||++....+..+....     +....+||-+-+.-++  ..+.+..|+..+|+.+..........  
T Consensus       256 g~Vi~LvGpnGvGKTTTiaKLA~~~~~~~-----G~~kV~LI~~Dt~Rig--A~EQLr~~AeilGVpv~~~~~~~Dl~--  326 (484)
T PRK06995        256 GGVFALMGPTGVGKTTTTAKLAARCVMRH-----GASKVALLTTDSYRIG--GHEQLRIYGKILGVPVHAVKDAADLR--  326 (484)
T ss_pred             CcEEEEECCCCccHHHHHHHHHHHHHHhc-----CCCeEEEEeCCccchh--HHHHHHHHHHHhCCCeeccCCchhHH--
Confidence            55688899999999987554443332221     1112334444442222  23556666666665443332222111  


Q ss_pred             HHHHhcCCeEEEeCchhHHHHHHhcCCcccccCCceEEEecCcccccccCCchHHHHHHHhc-CCCCcEEEEeccCcHH-
Q 002040          584 ISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMGFEPQITRIVQNI-RPDRQTVLFSATFPRQ-  661 (976)
Q Consensus       584 ~~~l~~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDEah~~~~~~f~~~i~~il~~~-~~~~q~i~~SAT~~~~-  661 (976)
                                         ..+       ..+..+.+++||.+=+.............+... .+...+++++||.... 
T Consensus       327 -------------------~aL-------~~L~d~d~VLIDTaGr~~~d~~~~e~~~~l~~~~~p~e~~LVLdAt~~~~~  380 (484)
T PRK06995        327 -------------------LAL-------SELRNKHIVLIDTIGMSQRDRMVSEQIAMLHGAGAPVKRLLLLNATSHGDT  380 (484)
T ss_pred             -------------------HHH-------HhccCCCeEEeCCCCcChhhHHHHHHHHHHhccCCCCeeEEEEeCCCcHHH
Confidence                               111       234455677777754321110001111122222 1333567889887554 


Q ss_pred             HHHHHHHHcCCCeEEEeCCcccccCCceEEEEecCcchHHHHHHHHHHhhhcCCcEEEEecCHH
Q 002040          662 VEILARKVLNKPVEIQVGGRSVVNKDITQLVEVRPESDRFLRLLELLGEWYEKGKILIFVHSQE  725 (976)
Q Consensus       662 ~~~l~~~~l~~~~~i~~~~~~~~~~~i~q~~~~~~~~~k~~~l~~~l~~~~~~~kvLIF~~s~~  725 (976)
                      +...+..|-...+.             .-++...+...++-.++.++..+  +-++..++..+.
T Consensus       381 l~~i~~~f~~~~~~-------------g~IlTKlDet~~~G~~l~i~~~~--~lPI~yvt~GQ~  429 (484)
T PRK06995        381 LNEVVQAYRGPGLA-------------GCILTKLDEAASLGGALDVVIRY--KLPLHYVSNGQR  429 (484)
T ss_pred             HHHHHHHhccCCCC-------------EEEEeCCCCcccchHHHHHHHHH--CCCeEEEecCCC
Confidence            33334333221110             01233455566677777776654  345555555443

>cd01120 RecA-like_NTPases RecA-like NTPases

Probab=96.01  E-value=0.043  Score=54.21  Aligned_cols=20  Identities=35%  Similarity=0.308  Sum_probs=15.2

Q ss_pred             EEEEcCCCCchHHHHHHHHH
Q 002040          507 CIGVAKTGSGKTLAFVLPML  526 (976)
Q Consensus       507 ~i~~a~TGsGKT~~~~l~il  526 (976)
                      ++++|++|+|||+.+...+.
T Consensus         2 ~~i~G~~G~GKT~l~~~i~~   21 (165)
T cd01120           2 ILVFGPTGSGKTTLALQLAL   21 (165)
T ss_pred             eeEeCCCCCCHHHHHHHHHH
Confidence            67899999999986444433

This family includes the NTP binding domain of F1 and V1 H+ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.

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

Probab=96.00  E-value=0.0072  Score=61.30  Aligned_cols=48  Identities=23%  Similarity=0.233  Sum_probs=26.8

Q ss_pred             HHHhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHH
Q 002040          499 PVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQ  555 (976)
Q Consensus       499 ~~il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q  555 (976)
                      .++-.+.++++.|++|+|||..+...+. .+...       |..|++ +++..|...
T Consensus        42 ~~~~~~~~l~l~G~~G~GKThLa~ai~~-~~~~~-------g~~v~f-~~~~~L~~~   89 (178)
T PF01695_consen   42 EFIENGENLILYGPPGTGKTHLAVAIAN-EAIRK-------GYSVLF-ITASDLLDE   89 (178)
T ss_dssp             -S-SC--EEEEEESTTSSHHHHHHHHHH-HHHHT-------T--EEE-EEHHHHHHH
T ss_pred             CCcccCeEEEEEhhHhHHHHHHHHHHHH-HhccC-------CcceeE-eecCceecc
Confidence            3344678999999999999987544443 33332       344555 455556544

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.

>PRK05642 DNA replication initiation factor; Validated

Probab=95.95  E-value=0.022  Score=60.54  Aligned_cols=45  Identities=13%  Similarity=0.308  Sum_probs=28.4

Q ss_pred             CCceEEEecCccccccc-CCchHHHHHHHhcCCCCcEEEEeccCcH
Q 002040          616 RRVTYLVMDEADRMFDM-GFEPQITRIVQNIRPDRQTVLFSATFPR  660 (976)
Q Consensus       616 ~~~~~vVlDEah~~~~~-~f~~~i~~il~~~~~~~q~i~~SAT~~~  660 (976)
                      ..+++||||++|.+... .+...+..+++.+......+++++|.++
T Consensus        96 ~~~d~LiiDDi~~~~~~~~~~~~Lf~l~n~~~~~g~~ilits~~~p  141 (234)
T PRK05642         96 EQYELVCLDDLDVIAGKADWEEALFHLFNRLRDSGRRLLLAASKSP  141 (234)
T ss_pred             hhCCEEEEechhhhcCChHHHHHHHHHHHHHHhcCCEEEEeCCCCH
Confidence            34679999999976432 2344567777766554445666666444

>TIGR01075 uvrD DNA helicase II

Probab=95.93  E-value=0.02  Score=71.37  Aligned_cols=71  Identities=14%  Similarity=0.119  Sum_probs=53.1

Q ss_pred             CCCcHHHHHHHHHHhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHHHH
Q 002040          488 EKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFA  564 (976)
Q Consensus       488 ~~p~~~Q~~~i~~il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~~~  564 (976)
                      ..++|-|.+++..  ....++|.|..|||||.+.+.-+...+....    .....+|+|+.|+..|..+.+.+..+.
T Consensus         3 ~~Ln~~Q~~av~~--~~g~~lV~AgaGSGKT~~L~~Ria~Li~~~~----v~p~~IL~lTFTnkAA~em~~Rl~~~~   73 (715)
T TIGR01075         3 DGLNDKQREAVAA--PPGNLLVLAGAGSGKTRVLTHRIAWLLSVEN----ASPHSIMAVTFTNKAAAEMRHRIGALL   73 (715)
T ss_pred             cccCHHHHHHHcC--CCCCEEEEecCCCCHHHHHHHHHHHHHHcCC----CCHHHeEeeeccHHHHHHHHHHHHHHh
Confidence            3578999998864  3568999999999999985555554443221    123478999999999999988887764

Designed to identify uvrD members of the uvrD/rep subfamily.

>cd01124 KaiC KaiC is a circadian clock protein primarily found in cyanobacteria KaiC is a RecA-like ATPase, having both Walker A and Walker B motifs

Probab=95.82  E-value=0.066  Score=54.60  Aligned_cols=48  Identities=17%  Similarity=0.227  Sum_probs=31.5

Q ss_pred             EEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHHH
Q 002040          507 CIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKF  563 (976)
Q Consensus       507 ~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~~  563 (976)
                      +++.|++|+|||+..+-.+...+.        +|..|++++. .+...++...+..+
T Consensus         2 ~li~G~~G~GKT~l~~~~~~~~~~--------~g~~v~~~s~-e~~~~~~~~~~~~~   49 (187)
T cd01124           2 TLLSGGPGTGKTTFALQFLYAGLA--------RGEPGLYVTL-EESPEELIENAESL   49 (187)
T ss_pred             EEEEcCCCCCHHHHHHHHHHHHHH--------CCCcEEEEEC-CCCHHHHHHHHHHc
Confidence            688999999999876555555443        2556777764 34456665555543

A related protein is found in archaea.

>PRK06893 DNA replication initiation factor; Validated

Probab=95.82  E-value=0.025  Score=60.04  Aligned_cols=46  Identities=15%  Similarity=0.294  Sum_probs=29.2

Q ss_pred             CCceEEEecCccccccc-CCchHHHHHHHhcCC-CCcEEEEeccCcHH
Q 002040          616 RRVTYLVMDEADRMFDM-GFEPQITRIVQNIRP-DRQTVLFSATFPRQ  661 (976)
Q Consensus       616 ~~~~~vVlDEah~~~~~-~f~~~i~~il~~~~~-~~q~i~~SAT~~~~  661 (976)
                      .++++|||||+|.+... .+...+..++..+.. ..++|++|++.++.
T Consensus        90 ~~~dlLilDDi~~~~~~~~~~~~l~~l~n~~~~~~~~illits~~~p~  137 (229)
T PRK06893         90 EQQDLVCLDDLQAVIGNEEWELAIFDLFNRIKEQGKTLLLISADCSPH  137 (229)
T ss_pred             ccCCEEEEeChhhhcCChHHHHHHHHHHHHHHHcCCcEEEEeCCCChH
Confidence            45789999999977532 233345566665544 34567787776554

>PF05127 Helicase_RecD: Helicase; InterPro: IPR007807 This domain is about 350 amino acid residues long and appears to have a P-loop motif, suggesting this is an ATPase

Probab=95.76  E-value=0.0052  Score=61.55  Aligned_cols=124  Identities=23%  Similarity=0.246  Sum_probs=53.6

Q ss_pred             EEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHHHHhhcCcEEEEeeCCCChHHHHHHH
Q 002040          508 IGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQISEL  587 (976)
Q Consensus       508 i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~~~~~~~~~~~~~~gg~~~~~~~~~l  587 (976)
                      |+.|+-|-|||.+..+.+...+..       ....++|.+|+..-+..++..+...+..++++......+.   ......
T Consensus         1 VltA~RGRGKSa~lGl~~a~l~~~-------~~~~I~vtAP~~~~~~~lf~~~~~~l~~~~~~~~~~~~~~---~~~~~~   70 (177)
T PF05127_consen    1 VLTADRGRGKSAALGLAAAALIQK-------GKIRILVTAPSPENVQTLFEFAEKGLKALGYKEEKKKRIG---QIIKLR   70 (177)
T ss_dssp             -EEE-TTSSHHHHHHHCCCCSSS------------EEEE-SS--S-HHHHHCC---------------------------
T ss_pred             CccCCCCCCHHHHHHHHHHHHHHh-------cCceEEEecCCHHHHHHHHHHHHhhccccccccccccccc---cccccc
Confidence            578999999998765554332221       1246899999998887777666655544444331000000   000011


Q ss_pred             hcCCeEEEeCchhHHHHHHhcCCcccccCCceEEEecCcccccccCCchHHHHHHHhcCCCCcEEEEeccCc
Q 002040          588 KRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMGFEPQITRIVQNIRPDRQTVLFSATFP  659 (976)
Q Consensus       588 ~~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDEah~~~~~~f~~~i~~il~~~~~~~q~i~~SAT~~  659 (976)
                      ..+..|.+..|..+...          ....++||||||=.+.    .+.+..++...    ..++||.|..
T Consensus        71 ~~~~~i~f~~Pd~l~~~----------~~~~DlliVDEAAaIp----~p~L~~ll~~~----~~vv~stTi~  124 (177)
T PF05127_consen   71 FNKQRIEFVAPDELLAE----------KPQADLLIVDEAAAIP----LPLLKQLLRRF----PRVVFSTTIH  124 (177)
T ss_dssp             --CCC--B--HHHHCCT--------------SCEEECTGGGS-----HHHHHHHHCCS----SEEEEEEEBS
T ss_pred             cccceEEEECCHHHHhC----------cCCCCEEEEechhcCC----HHHHHHHHhhC----CEEEEEeecc
Confidence            12457777787755221          1235899999998653    44555554333    3678888864

This domain is often N-terminal to a GCN5-related N-acetyltransferase domain IPR000182 from INTERPRO and C-terminal to IPR013562 from INTERPRO.; PDB: 2ZPA_B.

>KOG1133 consensus Helicase of the DEAD superfamily [Replication, recombination and repair]

Probab=95.74  E-value=1.2  Score=52.73  Aligned_cols=122  Identities=13%  Similarity=0.184  Sum_probs=76.7

Q ss_pred             cCcchHHHHHHHHHHhhh--cCCcEEEEecCHHHHHHHHHHHHHCCCC-------ceeccCCCCHHHHHHHHHHhc----
Q 002040          695 RPESDRFLRLLELLGEWY--EKGKILIFVHSQEKCDALFRDLLKHGYP-------CLSLHGAKDQTDRESTISDFK----  761 (976)
Q Consensus       695 ~~~~~k~~~l~~~l~~~~--~~~kvLIF~~s~~~~~~l~~~L~~~~~~-------~~~lhg~~~~~~R~~~~~~F~----  761 (976)
                      .....-+..|...+..+.  -+|.|++|+++......+...+...|+.       .+.+-...+   -..++..|.    
T Consensus       608 R~s~~~l~~l~~~~~nL~~~VPgGvV~FfPSy~yL~~v~k~w~~~gil~ri~~kK~vF~E~k~~---~~dvl~~Ya~a~~  684 (821)
T KOG1133|consen  608 RESPEMIKDLGSSISNLSNAVPGGVVCFFPSYAYLGQVRKRWEQNGILARIVGKKKVFYEPKDT---VEDVLEGYAEAAE  684 (821)
T ss_pred             cCChHHHHHHHHHHHHHHhhCCCcEEEEeccHHHHHHHHHHHHhcchHHHhhccchhhccCccc---HHHHHHHHHHHhh
Confidence            333444444444444332  1488999999999999999998876542       222222222   344555554    


Q ss_pred             cCCccEEEec--CcccccCCCCC--CcEEEEeCCCCC--------------------------------HHHHHHHhccc
Q 002040          762 SNVCNLLIAT--SVAARGLDVKE--LELVINFDAPNH--------------------------------YEDYVHRVGRT  805 (976)
Q Consensus       762 ~g~~~vLVaT--~v~~~GlDi~~--v~~VI~~d~p~s--------------------------------~~~y~Qr~GR~  805 (976)
                      .|.-.||+|.  .-++.|||+.+  +..||.+++|..                                +-...|.||||
T Consensus       685 ~g~GaiLlaVVGGKlSEGINF~D~LgRaVvvVGlPyPN~~s~EL~er~k~l~~k~~~~gagke~yEnlCMkAVNQsIGRA  764 (821)
T KOG1133|consen  685 RGRGAILLAVVGGKLSEGINFSDDLGRAVVVVGLPYPNIQSVELQERMKHLDGKLPTPGAGKELYENLCMKAVNQSIGRA  764 (821)
T ss_pred             cCCCeEEEEEeccccccccccccccccEEEEeecCCCCCCCHHHHHHHHHhhhccCCCCchHHHHHHHHHHHHHHHHHHH
Confidence            4555677664  57889999987  778888877642                                11235999999


Q ss_pred             CCCCCccEEEEEec
Q 002040          806 GRAGRKGCAITFIS  819 (976)
Q Consensus       806 gR~g~~g~~~~~~~  819 (976)
                      -|.-+.--++++++
T Consensus       765 IRH~~DYA~i~LlD  778 (821)
T KOG1133|consen  765 IRHRKDYASIYLLD  778 (821)
T ss_pred             HhhhccceeEEEeh
Confidence            99765544555554

>PRK10867 signal recognition particle protein; Provisional

Probab=95.71  E-value=0.13  Score=59.47  Aligned_cols=59  Identities=20%  Similarity=0.221  Sum_probs=32.8

Q ss_pred             CEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEc--cCHHHHHHHHHHHHHHHhhcCcEEEEe
Q 002040          506 DCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMA--PTRELVQQIHSDIRKFAKVMGVRCVPV  574 (976)
Q Consensus       506 d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~--Ptr~La~Q~~~~~~~~~~~~~~~~~~~  574 (976)
                      -++++|++|+|||++..-.+.. +...      .|.+|++++  +.|..+.   ..+..++...++.+...
T Consensus       102 vI~~vG~~GsGKTTtaakLA~~-l~~~------~G~kV~lV~~D~~R~aa~---eQL~~~a~~~gv~v~~~  162 (433)
T PRK10867        102 VIMMVGLQGAGKTTTAGKLAKY-LKKK------KKKKVLLVAADVYRPAAI---EQLKTLGEQIGVPVFPS  162 (433)
T ss_pred             EEEEECCCCCcHHHHHHHHHHH-HHHh------cCCcEEEEEccccchHHH---HHHHHHHhhcCCeEEec
Confidence            4778899999999875444433 3221      134455444  3444333   33445555567665543

>COG1484 DnaC DNA replication protein [DNA replication, recombination, and repair]

Probab=95.69  E-value=0.065  Score=57.63  Aligned_cols=51  Identities=14%  Similarity=0.256  Sum_probs=33.6

Q ss_pred             HhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHH
Q 002040          501 IMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDI  560 (976)
Q Consensus       501 il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~  560 (976)
                      +.++.++++.|++|+|||..++..+...+ ..       |. -++++++.+|+.++...+
T Consensus       102 ~~~~~nl~l~G~~G~GKThLa~Ai~~~l~-~~-------g~-sv~f~~~~el~~~Lk~~~  152 (254)
T COG1484         102 FERGENLVLLGPPGVGKTHLAIAIGNELL-KA-------GI-SVLFITAPDLLSKLKAAF  152 (254)
T ss_pred             hccCCcEEEECCCCCcHHHHHHHHHHHHH-Hc-------CC-eEEEEEHHHHHHHHHHHH
Confidence            33778999999999999987554444443 31       33 355567777776654443

>PRK11054 helD DNA helicase IV; Provisional

Probab=95.63  E-value=0.043  Score=67.31  Aligned_cols=73  Identities=22%  Similarity=0.200  Sum_probs=53.1

Q ss_pred             cCCCCCcHHHHHHHHHHhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHHH
Q 002040          485 LNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKF  563 (976)
Q Consensus       485 ~~~~~p~~~Q~~~i~~il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~~  563 (976)
                      ..-..+++-|..|+-.  ...+++|.|..|||||.+.+.-+...+...    ...+..+|+|+.|+.+|..+.+.+...
T Consensus       192 ~e~~~L~~~Q~~av~~--~~~~~lV~agaGSGKT~vl~~r~ayLl~~~----~~~~~~IL~ltft~~AA~em~eRL~~~  264 (684)
T PRK11054        192 VESSPLNPSQARAVVN--GEDSLLVLAGAGSGKTSVLVARAGWLLARG----QAQPEQILLLAFGRQAAEEMDERIRER  264 (684)
T ss_pred             ccCCCCCHHHHHHHhC--CCCCeEEEEeCCCCHHHHHHHHHHHHHHhC----CCCHHHeEEEeccHHHHHHHHHHHHHh
Confidence            3445689999998853  345789999999999998555554444332    112457999999999999888877764

>COG1444 Predicted P-loop ATPase fused to an acetyltransferase [General function prediction only]

Probab=95.59  E-value=0.13  Score=62.44  Aligned_cols=149  Identities=19%  Similarity=0.206  Sum_probs=91.7

Q ss_pred             HHHcCCCCCcHHHHHHHHHHhcCC--CEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHH
Q 002040          482 IRKLNYEKPMPIQAQALPVIMSGR--DCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSD  559 (976)
Q Consensus       482 l~~~~~~~p~~~Q~~~i~~il~g~--d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~  559 (976)
                      |..+..+.+..-|.+.+..++...  -+++.|.-|=|||.+..+.+.......      ....++|.+|+.+-+..++..
T Consensus       207 l~~l~~T~dQ~~~l~~~~~l~~~~~~~~vlTAdRGRGKSA~lGi~~~~~~~~~------~~~~iiVTAP~~~nv~~Lf~f  280 (758)
T COG1444         207 LYELCLTEDQAEALEILERLLDAPKRALVLTADRGRGKSAALGIALAAAARLA------GSVRIIVTAPTPANVQTLFEF  280 (758)
T ss_pred             HhhhhcChhHHHHHHHHHHHHcCCCceEEEEcCCCCcHhHHHhHHHHHHHHhc------CCceEEEeCCCHHHHHHHHHH
Confidence            444444555555555666666554  578889999999998776663222211      134789999999998888888


Q ss_pred             HHHHHhhcCcEEEEeeCCCChHHHHHHHhcCCeEEEeCchhHHHHHHhcCCcccccCCceEEEecCcccccccCCchHHH
Q 002040          560 IRKFAKVMGVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMGFEPQIT  639 (976)
Q Consensus       560 ~~~~~~~~~~~~~~~~gg~~~~~~~~~l~~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDEah~~~~~~f~~~i~  639 (976)
                      +.+-+..+|+.-.+........  +..-.....|-+.+|....            . ..++||||||=.|.    .+.+.
T Consensus       281 a~~~l~~lg~~~~v~~d~~g~~--~~~~~~~~~i~y~~P~~a~------------~-~~DllvVDEAAaIp----lplL~  341 (758)
T COG1444         281 AGKGLEFLGYKRKVAPDALGEI--REVSGDGFRIEYVPPDDAQ------------E-EADLLVVDEAAAIP----LPLLH  341 (758)
T ss_pred             HHHhHHHhCCccccccccccce--eeecCCceeEEeeCcchhc------------c-cCCEEEEehhhcCC----hHHHH
Confidence            8777777775543322221000  0000112345566665331            1 15799999998653    55666


Q ss_pred             HHHHhcCCCCcEEEEeccCc
Q 002040          640 RIVQNIRPDRQTVLFSATFP  659 (976)
Q Consensus       640 ~il~~~~~~~q~i~~SAT~~  659 (976)
                      .++..+    +.++||.|+.
T Consensus       342 ~l~~~~----~rv~~sTTIh  357 (758)
T COG1444         342 KLLRRF----PRVLFSTTIH  357 (758)
T ss_pred             HHHhhc----CceEEEeeec
Confidence            666654    3689999974

>TIGR00064 ftsY signal recognition particle-docking protein FtsY

Probab=95.57  E-value=0.17  Score=55.09  Aligned_cols=174  Identities=18%  Similarity=0.207  Sum_probs=83.9

Q ss_pred             CCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEc-c-CHHHHHHHHHHHHHHHhhcCcEEEEeeCCCChHH
Q 002040          505 RDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMA-P-TRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQ  582 (976)
Q Consensus       505 ~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~-P-tr~La~Q~~~~~~~~~~~~~~~~~~~~gg~~~~~  582 (976)
                      +-++++|++|+|||++..-.+... ..       .+.+|+++. - .|.-+.   ..+..++...++.+.....+.....
T Consensus        73 ~vi~l~G~~G~GKTTt~akLA~~l-~~-------~g~~V~li~~D~~r~~a~---~ql~~~~~~~~i~~~~~~~~~dp~~  141 (272)
T TIGR00064        73 NVILFVGVNGVGKTTTIAKLANKL-KK-------QGKSVLLAAGDTFRAAAI---EQLEEWAKRLGVDVIKQKEGADPAA  141 (272)
T ss_pred             eEEEEECCCCCcHHHHHHHHHHHH-Hh-------cCCEEEEEeCCCCCHHHH---HHHHHHHHhCCeEEEeCCCCCCHHH
Confidence            457778999999998754444332 22       244555554 3 343332   3455555556655443222211111


Q ss_pred             HHHHHhcCCeEEEeCchhHHHHHHhcCCcccccCCceEEEecCcccccc-cCCchHHHHHHHhcC------CCCcEEEEe
Q 002040          583 QISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFD-MGFEPQITRIVQNIR------PDRQTVLFS  655 (976)
Q Consensus       583 ~~~~l~~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDEah~~~~-~~f~~~i~~il~~~~------~~~q~i~~S  655 (976)
                                       .+...+..     .....+++||||=+-++.. ......+..+...+.      ++.-+++++
T Consensus       142 -----------------~~~~~l~~-----~~~~~~D~ViIDT~G~~~~d~~~~~el~~~~~~~~~~~~~~~~~~~LVl~  199 (272)
T TIGR00064       142 -----------------VAFDAIQK-----AKARNIDVVLIDTAGRLQNKVNLMDELKKIKRVIKKVDKDAPDEVLLVLD  199 (272)
T ss_pred             -----------------HHHHHHHH-----HHHCCCCEEEEeCCCCCcchHHHHHHHHHHHHHHhcccCCCCceEEEEEE
Confidence                             01111111     1124467788887765431 112233444444444      566688899


Q ss_pred             ccCcHHHHHHHHHHcCCCeEEEeCCcccccCCceEEEEecCcchHHHHHHHHHHhhhcCCcEEEEecCHH
Q 002040          656 ATFPRQVEILARKVLNKPVEIQVGGRSVVNKDITQLVEVRPESDRFLRLLELLGEWYEKGKILIFVHSQE  725 (976)
Q Consensus       656 AT~~~~~~~l~~~~l~~~~~i~~~~~~~~~~~i~q~~~~~~~~~k~~~l~~~l~~~~~~~kvLIF~~s~~  725 (976)
                      ||........+..+....   .+         ..-.+...+...+.-.++.+....  +-|+..++..+.
T Consensus       200 a~~~~~~~~~~~~f~~~~---~~---------~g~IlTKlDe~~~~G~~l~~~~~~--~~Pi~~~~~Gq~  255 (272)
T TIGR00064       200 ATTGQNALEQAKVFNEAV---GL---------TGIILTKLDGTAKGGIILSIAYEL--KLPIKFIGVGEK  255 (272)
T ss_pred             CCCCHHHHHHHHHHHhhC---CC---------CEEEEEccCCCCCccHHHHHHHHH--CcCEEEEeCCCC
Confidence            997665444444443211   00         011123334455555566655543  345555554443

There is a weak division between FtsY and SRP54; both are GTPases. In E.coli, ftsY is an essential gene located in an operon with cell division genes ftsE and ftsX, but its apparent function is as the signal recognition particle docking protein.

>PTZ00293 thymidine kinase; Provisional

Probab=95.55  E-value=0.06  Score=55.55  Aligned_cols=38  Identities=16%  Similarity=0.116  Sum_probs=27.5

Q ss_pred             CCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccC
Q 002040          504 GRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPT  549 (976)
Q Consensus       504 g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Pt  549 (976)
                      |.-.++.|||+||||..++-.+.++...        +..++++-|.
T Consensus         4 G~i~vi~GpMfSGKTteLLr~i~~y~~a--------g~kv~~~kp~   41 (211)
T PTZ00293          4 GTISVIIGPMFSGKTTELMRLVKRFTYS--------EKKCVVIKYS   41 (211)
T ss_pred             eEEEEEECCCCChHHHHHHHHHHHHHHc--------CCceEEEEec
Confidence            4456789999999998766655555432        4568888885

>PRK08084 DNA replication initiation factor; Provisional

Probab=95.53  E-value=0.047  Score=58.13  Aligned_cols=18  Identities=11%  Similarity=0.167  Sum_probs=15.1

Q ss_pred             CCCEEEEcCCCCchHHHH
Q 002040          504 GRDCIGVAKTGSGKTLAF  521 (976)
Q Consensus       504 g~d~i~~a~TGsGKT~~~  521 (976)
                      +..++++||+|+|||..+
T Consensus        45 ~~~l~l~Gp~G~GKThLl   62 (235)
T PRK08084         45 SGYIYLWSREGAGRSHLL   62 (235)
T ss_pred             CCeEEEECCCCCCHHHHH
Confidence            357899999999999753

>PRK14712 conjugal transfer nickase/helicase TraI; Provisional

Probab=95.52  E-value=0.061  Score=70.57  Aligned_cols=62  Identities=24%  Similarity=0.320  Sum_probs=45.2

Q ss_pred             CCcHHHHHHHHHHhcC--CCEEEEcCCCCchHHHH--HHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHH
Q 002040          489 KPMPIQAQALPVIMSG--RDCIGVAKTGSGKTLAF--VLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQI  556 (976)
Q Consensus       489 ~p~~~Q~~~i~~il~g--~d~i~~a~TGsGKT~~~--~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~  556 (976)
                      .+++-|.+|+..++..  +-++|.|..|+|||+++  ++.++..+..      ..+..++.++||-..+..+
T Consensus       835 ~Lt~~Qr~Av~~iLts~dr~~~IqG~AGTGKTT~l~~i~~~~~~l~e------~~g~~V~glAPTgkAa~~L  900 (1623)
T PRK14712        835 KLTSGQRAATRMILETSDRFTVVQGYAGVGKTTQFRAVMSAVNMLPE------SERPRVVGLGPTHRAVGEM  900 (1623)
T ss_pred             ccCHHHHHHHHHHHhCCCceEEEEeCCCCCHHHHHHHHHHHHHHHhh------ccCceEEEEechHHHHHHH
Confidence            6899999999999965  66888999999999863  2222322221      2356788999998776655

>TIGR01425 SRP54_euk signal recognition particle protein SRP54

Probab=95.51  E-value=0.16  Score=58.41  Aligned_cols=131  Identities=15%  Similarity=0.150  Sum_probs=64.2

Q ss_pred             CEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEc--cCHHHHHHHHHHHHHHHhhcCcEEEEeeCCCChHHH
Q 002040          506 DCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMA--PTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQ  583 (976)
Q Consensus       506 d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~--Ptr~La~Q~~~~~~~~~~~~~~~~~~~~gg~~~~~~  583 (976)
                      -++++|++|+|||++..-.+. ++..       .|.+|++++  |.|..|.   .+++.++...++.+...+.+......
T Consensus       102 vi~lvG~~GvGKTTtaaKLA~-~l~~-------~G~kV~lV~~D~~R~aA~---eQLk~~a~~~~vp~~~~~~~~dp~~i  170 (429)
T TIGR01425       102 VIMFVGLQGSGKTTTCTKLAY-YYQR-------KGFKPCLVCADTFRAGAF---DQLKQNATKARIPFYGSYTESDPVKI  170 (429)
T ss_pred             EEEEECCCCCCHHHHHHHHHH-HHHH-------CCCCEEEEcCcccchhHH---HHHHHHhhccCCeEEeecCCCCHHHH
Confidence            467889999999987443333 3332       144555554  3454444   33444555566666554443321110


Q ss_pred             HHHHhcCCeEEEeCchhHHHHHHhcCCcccccCCceEEEecCccccccc-CCchHHHHHHHhcCCCCcEEEEeccCcHHH
Q 002040          584 ISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDM-GFEPQITRIVQNIRPDRQTVLFSATFPRQV  662 (976)
Q Consensus       584 ~~~l~~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDEah~~~~~-~f~~~i~~il~~~~~~~q~i~~SAT~~~~~  662 (976)
                      ..                 ..+..     ..-..+++||||=+-++... .....+..+.....|+.-+++++||.....
T Consensus       171 ~~-----------------~~l~~-----~~~~~~DvViIDTaGr~~~d~~lm~El~~i~~~~~p~e~lLVlda~~Gq~a  228 (429)
T TIGR01425       171 AS-----------------EGVEK-----FKKENFDIIIVDTSGRHKQEDSLFEEMLQVAEAIQPDNIIFVMDGSIGQAA  228 (429)
T ss_pred             HH-----------------HHHHH-----HHhCCCCEEEEECCCCCcchHHHHHHHHHHhhhcCCcEEEEEeccccChhH
Confidence            00                 00100     00123556666666543211 122334444455556666777888876554


Q ss_pred             HHHHHHH
Q 002040          663 EILARKV  669 (976)
Q Consensus       663 ~~l~~~~  669 (976)
                      ...+..|
T Consensus       229 ~~~a~~F  235 (429)
T TIGR01425       229 EAQAKAF  235 (429)
T ss_pred             HHHHHHH
Confidence            4444444

This model represents examples from the eukaryotic cytosol of the signal recognition particle protein component, SRP54. This GTP-binding protein is a component of the eukaryotic signal recognition particle, along with several other protein subunits and a 7S RNA. Some species, including Arabidopsis, have several closely related forms. The extreme C-terminal region is glycine-rich and lower in complexity, poorly conserved between species, and excluded from this model.

>PRK13709 conjugal transfer nickase/helicase TraI; Provisional

Probab=95.50  E-value=0.075  Score=70.70  Aligned_cols=65  Identities=20%  Similarity=0.236  Sum_probs=46.1

Q ss_pred             CCCcHHHHHHHHHHhcC--CCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHH
Q 002040          488 EKPMPIQAQALPVIMSG--RDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQI  556 (976)
Q Consensus       488 ~~p~~~Q~~~i~~il~g--~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~  556 (976)
                      ..+++.|.+|+..++..  +-++|.|..|+|||++ +-.++..+...   ....+..++.++||--.|..+
T Consensus       966 ~~Lt~~Q~~Av~~il~s~dr~~~I~G~AGTGKTT~-l~~v~~~~~~l---~~~~~~~V~glAPTgrAAk~L 1032 (1747)
T PRK13709        966 EGLTSGQRAATRMILESTDRFTVVQGYAGVGKTTQ-FRAVMSAVNTL---PESERPRVVGLGPTHRAVGEM 1032 (1747)
T ss_pred             CCCCHHHHHHHHHHHhCCCcEEEEEeCCCCCHHHH-HHHHHHHHHHh---hcccCceEEEECCcHHHHHHH
Confidence            35899999999999975  4688889999999986 33344333221   112356788999998776544

>KOG0989 consensus Replication factor C, subunit RFC4 [Replication, recombination and repair]

Probab=95.46  E-value=0.058  Score=57.69  Aligned_cols=44  Identities=14%  Similarity=0.292  Sum_probs=31.3

Q ss_pred             ccCCceEEEecCcccccccCCchHHHHHHHhcCCCCcEEEEeccC
Q 002040          614 NLRRVTYLVMDEADRMFDMGFEPQITRIVQNIRPDRQTVLFSATF  658 (976)
Q Consensus       614 ~l~~~~~vVlDEah~~~~~~f~~~i~~il~~~~~~~q~i~~SAT~  658 (976)
                      ....+.+|||||||.|.... +..+.+++........+|+.+..+
T Consensus       126 ~~~~fKiiIlDEcdsmtsda-q~aLrr~mE~~s~~trFiLIcnyl  169 (346)
T KOG0989|consen  126 PCPPFKIIILDECDSMTSDA-QAALRRTMEDFSRTTRFILICNYL  169 (346)
T ss_pred             CCCcceEEEEechhhhhHHH-HHHHHHHHhccccceEEEEEcCCh
Confidence            45668899999999886443 556677777766666677766654

>PHA03333 putative ATPase subunit of terminase; Provisional

Probab=95.46  E-value=0.25  Score=58.98  Aligned_cols=148  Identities=11%  Similarity=0.116  Sum_probs=83.3

Q ss_pred             CCCcHHHHHHHHHH---hcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHHHH
Q 002040          488 EKPMPIQAQALPVI---MSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFA  564 (976)
Q Consensus       488 ~~p~~~Q~~~i~~i---l~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~~~  564 (976)
                      ..|.|.-.+-|..+   +..+-.++.+|=|.|||.+..+.++..+..       .+..++|++|...-+.+++..+..++
T Consensus       168 ~~~~~~~~~~id~~~~~fkq~~tV~taPRqrGKS~iVgi~l~~La~f-------~Gi~IlvTAH~~~ts~evF~rv~~~l  240 (752)
T PHA03333        168 EAPSPRTLREIDRIFDEYGKCYTAATVPRRCGKTTIMAIILAAMISF-------LEIDIVVQAQRKTMCLTLYNRVETVV  240 (752)
T ss_pred             CCCChhhHHHHHHHHHHHhhcceEEEeccCCCcHHHHHHHHHHHHHh-------cCCeEEEECCChhhHHHHHHHHHHHH
Confidence            34444444444444   455678888999999998765554433321       25679999999999999999988888


Q ss_pred             hhcCc--------EEEEeeCCCChHHHHHHHhcCCeEEEeCchhHH------HHHHhcCCcccccCCceEEEecCccccc
Q 002040          565 KVMGV--------RCVPVYGGSGVAQQISELKRGTEIVVCTPGRMI------DILCTSGGKITNLRRVTYLVMDEADRMF  630 (976)
Q Consensus       565 ~~~~~--------~~~~~~gg~~~~~~~~~l~~~~~Iiv~Tp~~L~------~~l~~~~~~~~~l~~~~~vVlDEah~~~  630 (976)
                      ..++.        .+..+.||.            -.|.+..|....      ....+.... ..-..+++||||||+-+.
T Consensus       241 e~lg~~~~fp~~~~iv~vkgg~------------E~I~f~~p~gak~G~sti~F~Ars~~s-~RG~~~DLLIVDEAAfI~  307 (752)
T PHA03333        241 HAYQHKPWFPEEFKIVTLKGTD------------ENLEYISDPAAKEGKTTAHFLASSPNA-ARGQNPDLVIVDEAAFVN  307 (752)
T ss_pred             HHhccccccCCCceEEEeeCCe------------eEEEEecCcccccCcceeEEecccCCC-cCCCCCCEEEEECcccCC
Confidence            74431        111122221            123333221110      000000100 122356899999999764


Q ss_pred             ccCCchHHHHHHHhcC-CCCcEEEEeccCc
Q 002040          631 DMGFEPQITRIVQNIR-PDRQTVLFSATFP  659 (976)
Q Consensus       631 ~~~f~~~i~~il~~~~-~~~q~i~~SAT~~  659 (976)
                      .    ..+..++-.+. ...++|++|.+..
T Consensus       308 ~----~~l~aIlP~l~~~~~k~IiISS~~~  333 (752)
T PHA03333        308 P----GALLSVLPLMAVKGTKQIHISSPVD  333 (752)
T ss_pred             H----HHHHHHHHHHccCCCceEEEeCCCC
Confidence            3    34444544443 3566777777753

>PRK08727 hypothetical protein; Validated

Probab=95.42  E-value=0.063  Score=57.10  Aligned_cols=47  Identities=9%  Similarity=0.108  Sum_probs=26.0

Q ss_pred             CCceEEEecCcccccccC-CchHHHHHHHhcCC-CCcEEEEeccCcHHH
Q 002040          616 RRVTYLVMDEADRMFDMG-FEPQITRIVQNIRP-DRQTVLFSATFPRQV  662 (976)
Q Consensus       616 ~~~~~vVlDEah~~~~~~-f~~~i~~il~~~~~-~~q~i~~SAT~~~~~  662 (976)
                      ..+.+|||||+|.+.... ....+..++..+.. ..++|+.|..+|...
T Consensus        92 ~~~dlLiIDDi~~l~~~~~~~~~lf~l~n~~~~~~~~vI~ts~~~p~~l  140 (233)
T PRK08727         92 EGRSLVALDGLESIAGQREDEVALFDFHNRARAAGITLLYTARQMPDGL  140 (233)
T ss_pred             hcCCEEEEeCcccccCChHHHHHHHHHHHHHHHcCCeEEEECCCChhhh
Confidence            346799999999775432 22234445544432 334555555555443

>TIGR03420 DnaA_homol_Hda DnaA regulatory inactivator Hda

Probab=95.41  E-value=0.079  Score=55.93  Aligned_cols=20  Identities=25%  Similarity=0.205  Sum_probs=16.3

Q ss_pred             cCCCEEEEcCCCCchHHHHH
Q 002040          503 SGRDCIGVAKTGSGKTLAFV  522 (976)
Q Consensus       503 ~g~d~i~~a~TGsGKT~~~~  522 (976)
                      .+..+++.|++|+|||..+.
T Consensus        37 ~~~~lll~G~~G~GKT~la~   56 (226)
T TIGR03420        37 GDRFLYLWGESGSGKSHLLQ   56 (226)
T ss_pred             CCCeEEEECCCCCCHHHHHH
Confidence            35679999999999997643

Members of this protein family are Hda (Homologous to DnaA). These proteins are about half the length of DnaA and homologous over length of Hda. In the model species Escherichia coli, the initiation of DNA replication requires DnaA bound to ATP rather than ADP; Hda helps facilitate the conversion of DnaA-ATP to DnaA-ADP.

>PF05621 TniB: Bacterial TniB protein; InterPro: IPR008868 This family consists of several bacterial TniB NTP-binding proteins

Probab=95.39  E-value=0.072  Score=57.66  Aligned_cols=114  Identities=20%  Similarity=0.282  Sum_probs=58.7

Q ss_pred             CCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCC---CCCeEEEEccCHHHHHHHHHHHHHHHhhcCcEEEEeeCCCChH
Q 002040          505 RDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAG---DGPVGLIMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVA  581 (976)
Q Consensus       505 ~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~---~~~~vLIl~Ptr~La~Q~~~~~~~~~~~~~~~~~~~~gg~~~~  581 (976)
                      .+++++|+||.|||...--..-.|    +.....   .-|.++|-+|...-..-+|..|-.   .++..+..   .....
T Consensus        62 p~lLivG~snnGKT~Ii~rF~~~h----p~~~d~~~~~~PVv~vq~P~~p~~~~~Y~~IL~---~lgaP~~~---~~~~~  131 (302)
T PF05621_consen   62 PNLLIVGDSNNGKTMIIERFRRLH----PPQSDEDAERIPVVYVQMPPEPDERRFYSAILE---ALGAPYRP---RDRVA  131 (302)
T ss_pred             CceEEecCCCCcHHHHHHHHHHHC----CCCCCCCCccccEEEEecCCCCChHHHHHHHHH---HhCcccCC---CCCHH
Confidence            479999999999998532222222    221111   236777778876655555554433   23322110   11111


Q ss_pred             HHHHHHhcCCeEEEeCchhHHHHHHhcCCcccccCCceEEEecCcccccccCCchH--HHHHHHhcCCCCc
Q 002040          582 QQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMGFEPQ--ITRIVQNIRPDRQ  650 (976)
Q Consensus       582 ~~~~~l~~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDEah~~~~~~f~~~--i~~il~~~~~~~q  650 (976)
                      ..    .          .....+|..        -.+.+|||||+|.++......+  +...++.+....+
T Consensus       132 ~~----~----------~~~~~llr~--------~~vrmLIIDE~H~lLaGs~~~qr~~Ln~LK~L~NeL~  180 (302)
T PF05621_consen  132 KL----E----------QQVLRLLRR--------LGVRMLIIDEFHNLLAGSYRKQREFLNALKFLGNELQ  180 (302)
T ss_pred             HH----H----------HHHHHHHHH--------cCCcEEEeechHHHhcccHHHHHHHHHHHHHHhhccC
Confidence            10    0          011123322        2478999999999876543332  3445555555444

TniB is a probable ATP-binding protein [] which is involved in Tn5053 mercury resistance transposition [].

>PRK05707 DNA polymerase III subunit delta'; Validated

Probab=95.36  E-value=0.088  Score=58.82  Aligned_cols=37  Identities=14%  Similarity=0.003  Sum_probs=28.0

Q ss_pred             CcHHHHHHHHHHhcCC----CEEEEcCCCCchHHHHHHHHH
Q 002040          490 PMPIQAQALPVIMSGR----DCIGVAKTGSGKTLAFVLPML  526 (976)
Q Consensus       490 p~~~Q~~~i~~il~g~----d~i~~a~TGsGKT~~~~l~il  526 (976)
                      ++|+|...|..++...    -+|+.||.|.|||..+...+-
T Consensus         4 ~yPWl~~~~~~~~~~~r~~ha~Lf~G~~G~GK~~~A~~~A~   44 (328)
T PRK05707          4 IYPWQQSLWQQLAGRGRHPHAYLLHGPAGIGKRALAERLAA   44 (328)
T ss_pred             CCCCcHHHHHHHHHCCCcceeeeeECCCCCCHHHHHHHHHH
Confidence            4689999998887542    488999999999976544333

>PRK14087 dnaA chromosomal replication initiation protein; Provisional

Probab=95.33  E-value=0.092  Score=61.39  Aligned_cols=110  Identities=15%  Similarity=0.107  Sum_probs=57.8

Q ss_pred             CCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHHHHhhcCcEEEEeeCCCChHHHH
Q 002040          505 RDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQI  584 (976)
Q Consensus       505 ~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~~~~~~~~~~~~~~gg~~~~~~~  584 (976)
                      +.+++.|++|+|||.. +.++.+.+...     ..+..++++.+ ..+...+...+..-.                    
T Consensus       142 npl~i~G~~G~GKTHL-l~Ai~~~l~~~-----~~~~~v~yv~~-~~f~~~~~~~l~~~~--------------------  194 (450)
T PRK14087        142 NPLFIYGESGMGKTHL-LKAAKNYIESN-----FSDLKVSYMSG-DEFARKAVDILQKTH--------------------  194 (450)
T ss_pred             CceEEECCCCCcHHHH-HHHHHHHHHHh-----CCCCeEEEEEH-HHHHHHHHHHHHHhh--------------------
Confidence            4588999999999964 34445544432     12445555544 455544433332100                    


Q ss_pred             HHHhcCCeEEEeCchhHHHHHHhcCCcccccCCceEEEecCcccccccC-CchHHHHHHHhcCC-CCcEEEEeccCcHHH
Q 002040          585 SELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMG-FEPQITRIVQNIRP-DRQTVLFSATFPRQV  662 (976)
Q Consensus       585 ~~l~~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDEah~~~~~~-f~~~i~~il~~~~~-~~q~i~~SAT~~~~~  662 (976)
                                    +.+..+.       ..+..+++|||||+|.+.... ....+..+++.+.. ..|+|++|-..|..+
T Consensus       195 --------------~~~~~~~-------~~~~~~dvLiIDDiq~l~~k~~~~e~lf~l~N~~~~~~k~iIltsd~~P~~l  253 (450)
T PRK14087        195 --------------KEIEQFK-------NEICQNDVLIIDDVQFLSYKEKTNEIFFTIFNNFIENDKQLFFSSDKSPELL  253 (450)
T ss_pred             --------------hHHHHHH-------HHhccCCEEEEeccccccCCHHHHHHHHHHHHHHHHcCCcEEEECCCCHHHH
Confidence                          1111111       123457899999999764321 23345555555433 345555555554443

>PRK08903 DnaA regulatory inactivator Hda; Validated

Probab=95.26  E-value=0.077  Score=56.17  Aligned_cols=42  Identities=14%  Similarity=0.283  Sum_probs=25.2

Q ss_pred             ceEEEecCcccccccCCchHHHHHHHhcCCCCc-EEEEeccCcH
Q 002040          618 VTYLVMDEADRMFDMGFEPQITRIVQNIRPDRQ-TVLFSATFPR  660 (976)
Q Consensus       618 ~~~vVlDEah~~~~~~f~~~i~~il~~~~~~~q-~i~~SAT~~~  660 (976)
                      .++|||||+|.+... -...+..++..+..... +++++++.++
T Consensus        91 ~~~liiDdi~~l~~~-~~~~L~~~~~~~~~~~~~~vl~~~~~~~  133 (227)
T PRK08903         91 AELYAVDDVERLDDA-QQIALFNLFNRVRAHGQGALLVAGPAAP  133 (227)
T ss_pred             CCEEEEeChhhcCch-HHHHHHHHHHHHHHcCCcEEEEeCCCCH
Confidence            568999999976432 23334455554443333 5777777554

>PRK07003 DNA polymerase III subunits gamma and tau; Validated

Probab=95.26  E-value=0.089  Score=63.66  Aligned_cols=40  Identities=18%  Similarity=0.360  Sum_probs=24.3

Q ss_pred             CCceEEEecCcccccccCCchHHHHHHHhcCCCCcEEEEecc
Q 002040          616 RRVTYLVMDEADRMFDMGFEPQITRIVQNIRPDRQTVLFSAT  657 (976)
Q Consensus       616 ~~~~~vVlDEah~~~~~~f~~~i~~il~~~~~~~q~i~~SAT  657 (976)
                      ..+.+|||||+|.|....| ..+.+++..-+....+|+ ++|
T Consensus       118 gr~KVIIIDEah~LT~~A~-NALLKtLEEPP~~v~FIL-aTt  157 (830)
T PRK07003        118 ARFKVYMIDEVHMLTNHAF-NAMLKTLEEPPPHVKFIL-ATT  157 (830)
T ss_pred             CCceEEEEeChhhCCHHHH-HHHHHHHHhcCCCeEEEE-EEC
Confidence            3578999999998765433 334445555544444444 444

>PF05496 RuvB_N: Holliday junction DNA helicase ruvB N-terminus; InterPro: IPR008824 The RuvB protein makes up part of the RuvABC revolvasome which catalyses the resolution of Holliday junctions that arise during genetic recombination and DNA repair

Probab=95.25  E-value=0.067  Score=55.39  Aligned_cols=16  Identities=25%  Similarity=0.168  Sum_probs=14.1

Q ss_pred             CEEEEcCCCCchHHHH
Q 002040          506 DCIGVAKTGSGKTLAF  521 (976)
Q Consensus       506 d~i~~a~TGsGKT~~~  521 (976)
                      ++|++||+|+|||+.+
T Consensus        52 h~lf~GPPG~GKTTLA   67 (233)
T PF05496_consen   52 HMLFYGPPGLGKTTLA   67 (233)
T ss_dssp             EEEEESSTTSSHHHHH
T ss_pred             eEEEECCCccchhHHH
Confidence            6999999999999753

Branch migration is catalysed by the RuvB protein that is targeted to the Holliday junction by the structure specific RuvA protein []. This group of sequences contain this signature which is located in the N-terminal region of the proteins.; GO: 0009378 four-way junction helicase activity, 0006281 DNA repair, 0006310 DNA recombination; PDB: 1IQP_B 3PFI_B 1IXR_C 1HQC_B 1IXS_B.

>PRK10919 ATP-dependent DNA helicase Rep; Provisional

Probab=95.17  E-value=0.042  Score=67.74  Aligned_cols=71  Identities=18%  Similarity=0.168  Sum_probs=53.2

Q ss_pred             CCcHHHHHHHHHHhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHHHHh
Q 002040          489 KPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAK  565 (976)
Q Consensus       489 ~p~~~Q~~~i~~il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~~~~  565 (976)
                      .+++-|.+|+..  ....++|.|..|||||.+.+.-+...|....    .....+|+|+.|+..|..+...+..++.
T Consensus         2 ~Ln~~Q~~av~~--~~g~~lV~AgpGSGKT~vL~~Ria~Li~~~~----v~p~~IL~lTFT~kAA~em~~Rl~~~l~   72 (672)
T PRK10919          2 RLNPGQQQAVEF--VTGPCLVLAGAGSGKTRVITNKIAHLIRGCG----YQARHIAAVTFTNKAAREMKERVAQTLG   72 (672)
T ss_pred             CCCHHHHHHHhC--CCCCEEEEecCCCCHHHHHHHHHHHHHHhcC----CCHHHeeeEechHHHHHHHHHHHHHHhC
Confidence            367899998865  3567899999999999986665555554321    1234699999999999999888877643

>TIGR00959 ffh signal recognition particle protein

Probab=95.15  E-value=0.24  Score=57.21  Aligned_cols=60  Identities=20%  Similarity=0.182  Sum_probs=32.5

Q ss_pred             CEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEE-ccC-HHHHHHHHHHHHHHHhhcCcEEEEee
Q 002040          506 DCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIM-APT-RELVQQIHSDIRKFAKVMGVRCVPVY  575 (976)
Q Consensus       506 d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl-~Pt-r~La~Q~~~~~~~~~~~~~~~~~~~~  575 (976)
                      -++++|++|+|||+++.-.+......       .|.+|+++ |-+ |..|.   ..+..++...++.+....
T Consensus       101 vi~~vG~~GsGKTTtaakLA~~l~~~-------~g~kV~lV~~D~~R~~a~---~QL~~~a~~~gvp~~~~~  162 (428)
T TIGR00959       101 VILMVGLQGSGKTTTCGKLAYYLKKK-------QGKKVLLVACDLYRPAAI---EQLKVLGQQVGVPVFALG  162 (428)
T ss_pred             EEEEECCCCCcHHHHHHHHHHHHHHh-------CCCeEEEEeccccchHHH---HHHHHHHHhcCCceEecC
Confidence            47888999999998755444432211       13344444 433 33332   344455555666655433

This model represents Ffh (Fifty-Four Homolog), the protein component that forms the bacterial (and organellar) signal recognition particle together with a 4.5S RNA. Ffh is a GTPase homologous to eukaryotic SRP54 and also to the GTPase FtsY (TIGR00064) that is the receptor for the signal recognition particle.

>PRK12323 DNA polymerase III subunits gamma and tau; Provisional

Probab=95.12  E-value=0.049  Score=64.90  Aligned_cols=42  Identities=12%  Similarity=0.232  Sum_probs=25.6

Q ss_pred             cCCceEEEecCcccccccCCchHHHHHHHhcCCCCcEEEEecc
Q 002040          615 LRRVTYLVMDEADRMFDMGFEPQITRIVQNIRPDRQTVLFSAT  657 (976)
Q Consensus       615 l~~~~~vVlDEah~~~~~~f~~~i~~il~~~~~~~q~i~~SAT  657 (976)
                      ...+.++||||+|.|....| ..+.+++..-+....+|+.|.-
T Consensus       122 ~gr~KViIIDEah~Ls~~Aa-NALLKTLEEPP~~v~FILaTte  163 (700)
T PRK12323        122 AGRFKVYMIDEVHMLTNHAF-NAMLKTLEEPPEHVKFILATTD  163 (700)
T ss_pred             cCCceEEEEEChHhcCHHHH-HHHHHhhccCCCCceEEEEeCC
Confidence            34678999999998764443 2344455554455555555443

>PRK12422 chromosomal replication initiation protein; Provisional

Probab=95.11  E-value=0.13  Score=59.97  Aligned_cols=50  Identities=14%  Similarity=0.304  Sum_probs=29.2

Q ss_pred             CCceEEEecCcccccccC-CchHHHHHHHhcC-CCCcEEEEeccCcHHHHHH
Q 002040          616 RRVTYLVMDEADRMFDMG-FEPQITRIVQNIR-PDRQTVLFSATFPRQVEIL  665 (976)
Q Consensus       616 ~~~~~vVlDEah~~~~~~-f~~~i~~il~~~~-~~~q~i~~SAT~~~~~~~l  665 (976)
                      ..+++|||||+|.+.... ....+..+++.+. ...++|+.|.+.|..+..+
T Consensus       201 ~~~dvLiIDDiq~l~~k~~~qeelf~l~N~l~~~~k~IIlts~~~p~~l~~l  252 (445)
T PRK12422        201 RNVDALFIEDIEVFSGKGATQEEFFHTFNSLHTEGKLIVISSTCAPQDLKAM  252 (445)
T ss_pred             ccCCEEEEcchhhhcCChhhHHHHHHHHHHHHHCCCcEEEecCCCHHHHhhh
Confidence            457899999999875432 2233445554442 3456666665566655433

>PRK00149 dnaA chromosomal replication initiation protein; Reviewed

Probab=95.10  E-value=0.096  Score=61.61  Aligned_cols=26  Identities=19%  Similarity=0.100  Sum_probs=18.5

Q ss_pred             CCEEEEcCCCCchHHHHHHHHHHHHhc
Q 002040          505 RDCIGVAKTGSGKTLAFVLPMLRHIKD  531 (976)
Q Consensus       505 ~d~i~~a~TGsGKT~~~~l~il~~l~~  531 (976)
                      ..+++.|++|+|||.. +.++...+..
T Consensus       149 ~~l~l~G~~G~GKThL-~~ai~~~~~~  174 (450)
T PRK00149        149 NPLFIYGGVGLGKTHL-LHAIGNYILE  174 (450)
T ss_pred             CeEEEECCCCCCHHHH-HHHHHHHHHH
Confidence            4589999999999975 3444444443

>TIGR03499 FlhF flagellar biosynthetic protein FlhF

Probab=95.08  E-value=0.14  Score=55.98  Aligned_cols=24  Identities=29%  Similarity=0.216  Sum_probs=17.8

Q ss_pred             cCCCEEEEcCCCCchHHHHHHHHH
Q 002040          503 SGRDCIGVAKTGSGKTLAFVLPML  526 (976)
Q Consensus       503 ~g~d~i~~a~TGsGKT~~~~l~il  526 (976)
                      .+..++++||||+|||++....+.
T Consensus       193 ~~~vi~~vGptGvGKTTt~~kLa~  216 (282)
T TIGR03499       193 QGGVIALVGPTGVGKTTTLAKLAA  216 (282)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHH
Confidence            345688899999999987544433

>PRK10917 ATP-dependent DNA helicase RecG; Provisional

Probab=95.08  E-value=0.082  Score=65.40  Aligned_cols=94  Identities=17%  Similarity=0.223  Sum_probs=73.0

Q ss_pred             cCcchHHHH-HHHHHHhhhcCCcEEEEecCHHHHHHHHHHHHH----CCCCceeccCCCCHHHHHHHHHHhccCCccEEE
Q 002040          695 RPESDRFLR-LLELLGEWYEKGKILIFVHSQEKCDALFRDLLK----HGYPCLSLHGAKDQTDRESTISDFKSNVCNLLI  769 (976)
Q Consensus       695 ~~~~~k~~~-l~~~l~~~~~~~kvLIF~~s~~~~~~l~~~L~~----~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLV  769 (976)
                      ...+.|... ++.++.....+.+++|.+||..-+.+++..|..    .|+.+..+||+++..++..++..+.+|.+.|||
T Consensus       290 ~TGSGKT~va~~~il~~~~~g~q~lilaPT~~LA~Q~~~~l~~l~~~~~i~v~ll~G~~~~~~r~~~~~~l~~g~~~IvV  369 (681)
T PRK10917        290 DVGSGKTVVAALAALAAIEAGYQAALMAPTEILAEQHYENLKKLLEPLGIRVALLTGSLKGKERREILEAIASGEADIVI  369 (681)
T ss_pred             CCCCcHHHHHHHHHHHHHHcCCeEEEEeccHHHHHHHHHHHHHHHhhcCcEEEEEcCCCCHHHHHHHHHHHhCCCCCEEE
Confidence            334555443 333444444556899999999998888777654    478999999999999999999999999999999


Q ss_pred             ecCc-ccccCCCCCCcEEEE
Q 002040          770 ATSV-AARGLDVKELELVIN  788 (976)
Q Consensus       770 aT~v-~~~GlDi~~v~~VI~  788 (976)
                      +|.. +...+.+.++.+||.
T Consensus       370 gT~~ll~~~v~~~~l~lvVI  389 (681)
T PRK10917        370 GTHALIQDDVEFHNLGLVII  389 (681)
T ss_pred             chHHHhcccchhcccceEEE
Confidence            9974 445677889998885

>COG0552 FtsY Signal recognition particle GTPase [Intracellular trafficking and secretion]

Probab=95.06  E-value=0.46  Score=51.94  Aligned_cols=130  Identities=20%  Similarity=0.296  Sum_probs=70.9

Q ss_pred             CEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEcc--CHHHHHHHHHHHHHHHhhcCcEEEE-eeCCCChHH
Q 002040          506 DCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAP--TRELVQQIHSDIRKFAKVMGVRCVP-VYGGSGVAQ  582 (976)
Q Consensus       506 d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~P--tr~La~Q~~~~~~~~~~~~~~~~~~-~~gg~~~~~  582 (976)
                      -++++|-.|+|||++.. -+..++..       .|..||+.+.  .|+-|.   +++.-|+...|+.++. -+|+.+..-
T Consensus       141 Vil~vGVNG~GKTTTIa-KLA~~l~~-------~g~~VllaA~DTFRAaAi---EQL~~w~er~gv~vI~~~~G~DpAaV  209 (340)
T COG0552         141 VILFVGVNGVGKTTTIA-KLAKYLKQ-------QGKSVLLAAGDTFRAAAI---EQLEVWGERLGVPVISGKEGADPAAV  209 (340)
T ss_pred             EEEEEecCCCchHhHHH-HHHHHHHH-------CCCeEEEEecchHHHHHH---HHHHHHHHHhCCeEEccCCCCCcHHH
Confidence            47788999999998733 33333332       3666776664  344444   5566666668888776 334333222


Q ss_pred             HHHHHhcCCeEEEeCchhHHHHHHhcCCcccccCCceEEEecCcccccccC-CchHHHHHHHhcCCCC------cEEEEe
Q 002040          583 QISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMG-FEPQITRIVQNIRPDR------QTVLFS  655 (976)
Q Consensus       583 ~~~~l~~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDEah~~~~~~-f~~~i~~il~~~~~~~------q~i~~S  655 (976)
                      ..                  +.+..     ..-..+++|++|=|-||-+.. .-..+..|..-+.+..      -++++=
T Consensus       210 af------------------DAi~~-----Akar~~DvvliDTAGRLhnk~nLM~EL~KI~rV~~k~~~~ap~e~llvlD  266 (340)
T COG0552         210 AF------------------DAIQA-----AKARGIDVVLIDTAGRLHNKKNLMDELKKIVRVIKKDDPDAPHEILLVLD  266 (340)
T ss_pred             HH------------------HHHHH-----HHHcCCCEEEEeCcccccCchhHHHHHHHHHHHhccccCCCCceEEEEEE
Confidence            21                  22221     123446677777777665432 3344555555554443      234447


Q ss_pred             ccCcHHHHHHHHHH
Q 002040          656 ATFPRQVEILARKV  669 (976)
Q Consensus       656 AT~~~~~~~l~~~~  669 (976)
                      ||...+.-.-++.|
T Consensus       267 AttGqnal~QAk~F  280 (340)
T COG0552         267 ATTGQNALSQAKIF  280 (340)
T ss_pred             cccChhHHHHHHHH
Confidence            88776654444433

>COG2256 MGS1 ATPase related to the helicase subunit of the Holliday junction resolvase [DNA replication, recombination, and repair]

Probab=95.05  E-value=0.085  Score=58.59  Aligned_cols=19  Identities=32%  Similarity=0.261  Sum_probs=15.8

Q ss_pred             CCEEEEcCCCCchHHHHHH
Q 002040          505 RDCIGVAKTGSGKTLAFVL  523 (976)
Q Consensus       505 ~d~i~~a~TGsGKT~~~~l  523 (976)
                      .++|++||+|+|||+.+-+
T Consensus        49 ~SmIl~GPPG~GKTTlA~l   67 (436)
T COG2256          49 HSMILWGPPGTGKTTLARL   67 (436)
T ss_pred             ceeEEECCCCCCHHHHHHH
Confidence            3799999999999986543

>PHA02544 44 clamp loader, small subunit; Provisional

Probab=94.99  E-value=0.18  Score=56.38  Aligned_cols=40  Identities=10%  Similarity=0.157  Sum_probs=25.4

Q ss_pred             CceEEEecCcccccccCCchHHHHHHHhcCCCCcEEEEec
Q 002040          617 RVTYLVMDEADRMFDMGFEPQITRIVQNIRPDRQTVLFSA  656 (976)
Q Consensus       617 ~~~~vVlDEah~~~~~~f~~~i~~il~~~~~~~q~i~~SA  656 (976)
                      ...+|||||+|.+........+..++.......++|+.|.
T Consensus       100 ~~~vliiDe~d~l~~~~~~~~L~~~le~~~~~~~~Ilt~n  139 (316)
T PHA02544        100 GGKVIIIDEFDRLGLADAQRHLRSFMEAYSKNCSFIITAN  139 (316)
T ss_pred             CCeEEEEECcccccCHHHHHHHHHHHHhcCCCceEEEEcC
Confidence            4679999999987333233455566666666666555443

>TIGR00362 DnaA chromosomal replication initiator protein DnaA

Probab=94.93  E-value=0.1  Score=60.49  Aligned_cols=37  Identities=14%  Similarity=0.093  Sum_probs=23.5

Q ss_pred             CCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEc
Q 002040          505 RDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMA  547 (976)
Q Consensus       505 ~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~  547 (976)
                      ..+++.|++|+|||.. +.++.+.+...     ..+..++++.
T Consensus       137 n~l~l~G~~G~GKThL-~~ai~~~l~~~-----~~~~~v~yi~  173 (405)
T TIGR00362       137 NPLFIYGGVGLGKTHL-LHAIGNEILEN-----NPNAKVVYVS  173 (405)
T ss_pred             CeEEEECCCCCcHHHH-HHHHHHHHHHh-----CCCCcEEEEE
Confidence            4578999999999975 34455555432     1134556654

DnaA is involved in DNA biosynthesis; initiation of chromosome replication and can also be transcription regulator. The C-terminal of the family hits the pfam bacterial DnaA (bac_dnaA) domain family. For a review, see Kaguni (2006).

>PRK08939 primosomal protein DnaI; Reviewed

Probab=94.91  E-value=0.23  Score=54.99  Aligned_cols=26  Identities=12%  Similarity=0.170  Sum_probs=18.8

Q ss_pred             CCCEEEEcCCCCchHHHHHHHHHHHHh
Q 002040          504 GRDCIGVAKTGSGKTLAFVLPMLRHIK  530 (976)
Q Consensus       504 g~d~i~~a~TGsGKT~~~~l~il~~l~  530 (976)
                      ++.+++.|++|+|||..+. ++.+.+.
T Consensus       156 ~~gl~L~G~~G~GKThLa~-Aia~~l~  181 (306)
T PRK08939        156 VKGLYLYGDFGVGKSYLLA-AIANELA  181 (306)
T ss_pred             CCeEEEECCCCCCHHHHHH-HHHHHHH
Confidence            4679999999999997643 4444443

>PRK14086 dnaA chromosomal replication initiation protein; Provisional

Probab=94.89  E-value=0.15  Score=60.91  Aligned_cols=48  Identities=21%  Similarity=0.313  Sum_probs=29.9

Q ss_pred             CCceEEEecCcccccccC-CchHHHHHHHhcCC-CCcEEEEeccCcHHHH
Q 002040          616 RRVTYLVMDEADRMFDMG-FEPQITRIVQNIRP-DRQTVLFSATFPRQVE  663 (976)
Q Consensus       616 ~~~~~vVlDEah~~~~~~-f~~~i~~il~~~~~-~~q~i~~SAT~~~~~~  663 (976)
                      ..+++||||++|.+.... ....+..+++.+.. +.++|+.|-..|..+.
T Consensus       376 ~~~DLLlIDDIq~l~gke~tqeeLF~l~N~l~e~gk~IIITSd~~P~eL~  425 (617)
T PRK14086        376 REMDILLVDDIQFLEDKESTQEEFFHTFNTLHNANKQIVLSSDRPPKQLV  425 (617)
T ss_pred             hcCCEEEEehhccccCCHHHHHHHHHHHHHHHhcCCCEEEecCCChHhhh
Confidence            457899999999775433 22345556665544 4667766666555543

>TIGR02785 addA_Gpos recombination helicase AddA, Firmicutes type

Probab=94.82  E-value=0.14  Score=67.54  Aligned_cols=124  Identities=15%  Similarity=0.101  Sum_probs=81.5

Q ss_pred             CcHHHHHHHHHHhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHHHHhhcCc
Q 002040          490 PMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVMGV  569 (976)
Q Consensus       490 p~~~Q~~~i~~il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~~~~~~~~  569 (976)
                      +|+-|.++|.  ..+.+++|.|.-|||||.+.+--++..+...     ..-..+||||=|+..|..+...+.......-.
T Consensus         2 ~t~~Q~~ai~--~~~~~~lv~A~AGsGKT~~lv~r~~~~~~~~-----~~~~~il~~tFt~~aa~e~~~ri~~~l~~~~~   74 (1232)
T TIGR02785         2 WTDEQWQAIY--TRGQNILVSASAGSGKTAVLVERIIKKILRG-----VDIDRLLVVTFTNAAAREMKERIEEALQKALQ   74 (1232)
T ss_pred             CCHHHHHHHh--CCCCCEEEEecCCCcHHHHHHHHHHHHHhcC-----CCHhhEEEEeccHHHHHHHHHHHHHHHHHHHh
Confidence            5789999997  4688999999999999999777777776643     11235899999999999988888765432110


Q ss_pred             EEEEeeCCCChHH-HHHHHhcCCeEEEeCchhHHHHHHhcCCcccccCCceEEEecCccc
Q 002040          570 RCVPVYGGSGVAQ-QISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADR  628 (976)
Q Consensus       570 ~~~~~~gg~~~~~-~~~~l~~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDEah~  628 (976)
                             ..+... ....+..-...-|+|...|...+.........|. ..+=|+||...
T Consensus        75 -------~~p~~~~L~~q~~~~~~~~i~Tihsf~~~~~~~~~~~l~ld-P~F~i~de~e~  126 (1232)
T TIGR02785        75 -------QEPNSKHLRRQLALLNTANISTLHSFCLKVIRKHYYLLDLD-PSFRILTDTEQ  126 (1232)
T ss_pred             -------cCchhHHHHHHHhhccCCeEeeHHHHHHHHHHHhhhhcCCC-CCceeCCHHHH
Confidence                   011111 1122222245678999888766655443333332 34567888874

AddAB, also called RexAB, substitutes for RecBCD in several bacterial lineages. These DNA recombination proteins act before synapse and are particularly important for DNA repair of double-stranded breaks by homologous recombination. The term AddAB is used broadly, with AddA homologous between the Firmicutes (as modeled here) and the alphaproteobacteria, while the partner AddB proteins show no strong homology across the two groups of species.

>PRK05580 primosome assembly protein PriA; Validated

Probab=94.81  E-value=0.19  Score=62.08  Aligned_cols=93  Identities=19%  Similarity=0.223  Sum_probs=72.7

Q ss_pred             cchHHHHHHHHHHhhh-cCCcEEEEecCHHHHHHHHHHHHH-CCCCceeccCCCCHHHHHHHHHHhccCCccEEEecCcc
Q 002040          697 ESDRFLRLLELLGEWY-EKGKILIFVHSQEKCDALFRDLLK-HGYPCLSLHGAKDQTDRESTISDFKSNVCNLLIATSVA  774 (976)
Q Consensus       697 ~~~k~~~l~~~l~~~~-~~~kvLIF~~s~~~~~~l~~~L~~-~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLVaT~v~  774 (976)
                      .+.|....+..+.... .+.++||.++++..+.++...|.+ .|..+..+||+++..++..++..+..|..+|+|+|..+
T Consensus       172 GSGKT~v~l~~i~~~l~~g~~vLvLvPt~~L~~Q~~~~l~~~fg~~v~~~~s~~s~~~r~~~~~~~~~g~~~IVVgTrsa  251 (679)
T PRK05580        172 GSGKTEVYLQAIAEVLAQGKQALVLVPEIALTPQMLARFRARFGAPVAVLHSGLSDGERLDEWRKAKRGEAKVVIGARSA  251 (679)
T ss_pred             CChHHHHHHHHHHHHHHcCCeEEEEeCcHHHHHHHHHHHHHHhCCCEEEEECCCCHHHHHHHHHHHHcCCCCEEEeccHH
Confidence            3455555554444433 355899999999999999999976 47889999999999999999999999999999999744


Q ss_pred             cccCCCCCCcEEEEeC
Q 002040          775 ARGLDVKELELVINFD  790 (976)
Q Consensus       775 ~~GlDi~~v~~VI~~d  790 (976)
                      .. +.+.++.+||.-.
T Consensus       252 l~-~p~~~l~liVvDE  266 (679)
T PRK05580        252 LF-LPFKNLGLIIVDE  266 (679)
T ss_pred             hc-ccccCCCEEEEEC
Confidence            32 5677888888543

>COG1435 Tdk Thymidine kinase [Nucleotide transport and metabolism]

Probab=94.74  E-value=0.25  Score=49.83  Aligned_cols=89  Identities=20%  Similarity=0.140  Sum_probs=55.0

Q ss_pred             CCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHHHHhhcCcEEEEeeCCCChHHHH
Q 002040          505 RDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQI  584 (976)
Q Consensus       505 ~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~~~~~~~~~~~~~~gg~~~~~~~  584 (976)
                      +=.+++|||+||||...+..+.++..        .|.+++|..|-..-             .++...+...-|...    
T Consensus         5 ~l~~i~gpM~SGKT~eLl~r~~~~~~--------~g~~v~vfkp~iD~-------------R~~~~~V~Sr~G~~~----   59 (201)
T COG1435           5 WLEFIYGPMFSGKTEELLRRARRYKE--------AGMKVLVFKPAIDT-------------RYGVGKVSSRIGLSS----   59 (201)
T ss_pred             EEEEEEccCcCcchHHHHHHHHHHHH--------cCCeEEEEeccccc-------------ccccceeeeccCCcc----
Confidence            34678899999999976655555533        25678888884211             123333333333321    


Q ss_pred             HHHhcCCeEEEeCchhHHHHHHhcCCcccccCCceEEEecCccc
Q 002040          585 SELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADR  628 (976)
Q Consensus       585 ~~l~~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDEah~  628 (976)
                            .-++|-++..+.+.+....    ....+.+|.||||+-
T Consensus        60 ------~A~~i~~~~~i~~~i~~~~----~~~~~~~v~IDEaQF   93 (201)
T COG1435          60 ------EAVVIPSDTDIFDEIAALH----EKPPVDCVLIDEAQF   93 (201)
T ss_pred             ------cceecCChHHHHHHHHhcc----cCCCcCEEEEehhHh
Confidence                  3456667777777776532    222278999999994

>PRK11331 5-methylcytosine-specific restriction enzyme subunit McrB; Provisional

Probab=94.74  E-value=0.093  Score=60.16  Aligned_cols=33  Identities=21%  Similarity=0.211  Sum_probs=26.9

Q ss_pred             CcHHHHHHHHHHhcCCCEEEEcCCCCchHHHHH
Q 002040          490 PMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFV  522 (976)
Q Consensus       490 p~~~Q~~~i~~il~g~d~i~~a~TGsGKT~~~~  522 (976)
                      +-......+..+..++++|+.|++|+|||..+.
T Consensus       180 ~e~~le~l~~~L~~~~~iil~GppGtGKT~lA~  212 (459)
T PRK11331        180 PETTIETILKRLTIKKNIILQGPPGVGKTFVAR  212 (459)
T ss_pred             CHHHHHHHHHHHhcCCCEEEECCCCCCHHHHHH
Confidence            445566677788889999999999999998654

>PRK07764 DNA polymerase III subunits gamma and tau; Validated

Probab=94.59  E-value=0.13  Score=64.22  Aligned_cols=41  Identities=20%  Similarity=0.243  Sum_probs=26.6

Q ss_pred             CCceEEEecCcccccccCCchHHHHHHHhcCCCCcEEEEeccC
Q 002040          616 RRVTYLVMDEADRMFDMGFEPQITRIVQNIRPDRQTVLFSATF  658 (976)
Q Consensus       616 ~~~~~vVlDEah~~~~~~f~~~i~~il~~~~~~~q~i~~SAT~  658 (976)
                      ..+.+|||||||+|.... ...+.++|...+....+||++ |-
T Consensus       119 ~~~KV~IIDEad~lt~~a-~NaLLK~LEEpP~~~~fIl~t-t~  159 (824)
T PRK07764        119 SRYKIFIIDEAHMVTPQG-FNALLKIVEEPPEHLKFIFAT-TE  159 (824)
T ss_pred             CCceEEEEechhhcCHHH-HHHHHHHHhCCCCCeEEEEEe-CC
Confidence            568899999999886433 334556666655555555544 53

>PRK12402 replication factor C small subunit 2; Reviewed

Probab=94.58  E-value=0.17  Score=57.03  Aligned_cols=39  Identities=10%  Similarity=0.238  Sum_probs=23.9

Q ss_pred             CCceEEEecCcccccccCCchHHHHHHHhcCCCCcEEEEe
Q 002040          616 RRVTYLVMDEADRMFDMGFEPQITRIVQNIRPDRQTVLFS  655 (976)
Q Consensus       616 ~~~~~vVlDEah~~~~~~f~~~i~~il~~~~~~~q~i~~S  655 (976)
                      ....+|||||+|.+... ....+..++...+....+|+++
T Consensus       124 ~~~~vlilDe~~~l~~~-~~~~L~~~le~~~~~~~~Il~~  162 (337)
T PRK12402        124 ADYKTILLDNAEALRED-AQQALRRIMEQYSRTCRFIIAT  162 (337)
T ss_pred             CCCcEEEEeCcccCCHH-HHHHHHHHHHhccCCCeEEEEe
Confidence            45679999999976432 2334555666555555555443

>TIGR01642 U2AF_lg U2 snRNP auxilliary factor, large subunit, splicing factor

Probab=94.53  E-value=0.0045  Score=74.20  Aligned_cols=10  Identities=20%  Similarity=0.321  Sum_probs=4.4

Q ss_pred             ccEEEEEecC
Q 002040          811 KGCAITFISE  820 (976)
Q Consensus       811 ~g~~~~~~~~  820 (976)
                      .-.++.|+++
T Consensus       492 r~v~~~~~~~  501 (509)
T TIGR01642       492 RVVVAAFYGE  501 (509)
T ss_pred             eEEEEEEeCH
Confidence            3344445443

Members of this subfamily are found in plants, metazoa and fungi.

>PRK08769 DNA polymerase III subunit delta'; Validated

Probab=94.52  E-value=0.3  Score=54.21  Aligned_cols=42  Identities=21%  Similarity=0.279  Sum_probs=29.8

Q ss_pred             CCCcHHHHHHHHHHh----cCC---CEEEEcCCCCchHHHHHHHHHHHHh
Q 002040          488 EKPMPIQAQALPVIM----SGR---DCIGVAKTGSGKTLAFVLPMLRHIK  530 (976)
Q Consensus       488 ~~p~~~Q~~~i~~il----~g~---d~i~~a~TGsGKT~~~~l~il~~l~  530 (976)
                      ..++|+|..++..+.    +++   -+|+.|+.|+||+..+.. +...++
T Consensus         3 ~~~yPW~~~~~~~l~~~~~~~rl~HA~Lf~Gp~G~GK~~lA~~-lA~~Ll   51 (319)
T PRK08769          3 SAFSPWQQRAYDQTVAALDAGRLGHGLLICGPEGLGKRAVALA-LAEHVL   51 (319)
T ss_pred             ccccccHHHHHHHHHHHHHcCCcceeEeeECCCCCCHHHHHHH-HHHHHh
Confidence            457889998887765    343   488999999999976443 344443

>COG3973 Superfamily I DNA and RNA helicases [General function prediction only]

Probab=94.52  E-value=0.17  Score=58.82  Aligned_cols=68  Identities=18%  Similarity=0.165  Sum_probs=44.9

Q ss_pred             HHHHHHHHHhc--CCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHH
Q 002040          493 IQAQALPVIMS--GRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRK  562 (976)
Q Consensus       493 ~Q~~~i~~il~--g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~  562 (976)
                      +|.+==..|..  +.-+||+|..|||||++++--+...+...+..-.  +..|||+.|.+.++.-+.+.+-.
T Consensus       213 IQkEQneIIR~ek~~ilVVQGaAGSGKTtiALHRvAyLlY~~R~~l~--~k~vlvl~PN~vFleYis~VLPe  282 (747)
T COG3973         213 IQKEQNEIIRFEKNKILVVQGAAGSGKTTIALHRVAYLLYGYRGPLQ--AKPVLVLGPNRVFLEYISRVLPE  282 (747)
T ss_pred             hhHhHHHHHhccCCCeEEEecCCCCCchhHHHHHHHHHHhccccccc--cCceEEEcCcHHHHHHHHHhchh
Confidence            44444444443  4568889999999999877666666666543322  33499999999887655444433

>COG4626 Phage terminase-like protein, large subunit [General function prediction only]

Probab=94.51  E-value=0.24  Score=57.52  Aligned_cols=149  Identities=13%  Similarity=0.146  Sum_probs=85.6

Q ss_pred             CCcHHHHHHHHHHhc------C----CCEEEEcCCCCchHHHHH-HHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHH
Q 002040          489 KPMPIQAQALPVIMS------G----RDCIGVAKTGSGKTLAFV-LPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIH  557 (976)
Q Consensus       489 ~p~~~Q~~~i~~il~------g----~d~i~~a~TGsGKT~~~~-l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~  557 (976)
                      .+.|+|.-++..|+.      |    +..+|..|-|-|||..+. +.+...+...     ..+..+.|++|+.+-+.+.+
T Consensus        61 ~l~PwQkFiia~l~G~~~k~T~~rrf~e~fI~v~RkngKt~l~A~i~~~~~l~~~-----~~~~~~~i~A~s~~qa~~~F  135 (546)
T COG4626          61 SLEPWQKFIVAALFGFYDKQTGIRRFKEAFIFIPRKNGKSTLAAGIMMTALLLNW-----RSGAGIYILAPSVEQAANSF  135 (546)
T ss_pred             ccchHHHHHHHHHhceeecCCCceEEEEEEEEEecCCchHHHHHHHHHHHHHhhh-----hcCCcEEEEeccHHHHHHhh
Confidence            466999999998882      1    247777888899997654 3344444433     34677899999999998888


Q ss_pred             HHHHHHHhhcCcEEEEeeCCCChHHHHHHHhc-CCeEEEeCchhHHHHHHhcCCcccccCCceEEEecCcccccccCCch
Q 002040          558 SDIRKFAKVMGVRCVPVYGGSGVAQQISELKR-GTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMGFEP  636 (976)
Q Consensus       558 ~~~~~~~~~~~~~~~~~~gg~~~~~~~~~l~~-~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDEah~~~~~~f~~  636 (976)
                      +.++....... ....          ...+.. ...|++.--...+..+...... .+-.+..+.|+||.|...+.+  .
T Consensus       136 ~~ar~mv~~~~-~l~~----------~~~~q~~s~~i~~~~~~s~ik~~aa~~~~-~Dg~~~~~~I~DEih~f~~~~--~  201 (546)
T COG4626         136 NPARDMVKRDD-DLRD----------LCNVQTHSRTITHRKTDSTIKAVAADPNT-VDGLNSVGAIIDELHLFGKQE--D  201 (546)
T ss_pred             HHHHHHHHhCc-chhh----------hhccccceeEEEecccceeeeeeccCCCc-ccCCCcceEEEehhhhhcCHH--H
Confidence            88877654433 0000          001111 1112222222223333333222 234467899999999765432  3


Q ss_pred             HHHHHHHhc--CCCCcEEEEec
Q 002040          637 QITRIVQNI--RPDRQTVLFSA  656 (976)
Q Consensus       637 ~i~~il~~~--~~~~q~i~~SA  656 (976)
                      .+..+..-+  +++.+++..|.
T Consensus       202 ~~~~~~~g~~ar~~~l~~~ITT  223 (546)
T COG4626         202 MYSEAKGGLGARPEGLVVYITT  223 (546)
T ss_pred             HHHHHHhhhccCcCceEEEEec
Confidence            444443333  46677777665

>TIGR02760 TraI_TIGR conjugative transfer relaxase protein TraI

Probab=94.44  E-value=0.17  Score=69.26  Aligned_cols=62  Identities=29%  Similarity=0.316  Sum_probs=44.7

Q ss_pred             CCCcHHHHHHHHHHhcC--CCEEEEcCCCCchHHHHH---HHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHH
Q 002040          488 EKPMPIQAQALPVIMSG--RDCIGVAKTGSGKTLAFV---LPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQI  556 (976)
Q Consensus       488 ~~p~~~Q~~~i~~il~g--~d~i~~a~TGsGKT~~~~---l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~  556 (976)
                      ..+++.|.+|+..|+.+  +-++|.|..|+|||+++.   -++...+..       .+..++.++||-..|..+
T Consensus      1018 ~~Lt~~Q~~Ai~~il~~~~~~~~i~G~AGtGKTt~l~~~~~~i~~~~~~-------~g~~v~glApT~~Aa~~L 1084 (1960)
T TIGR02760      1018 ERLTHGQKQAIHLIISTKDRFVAVQGLAGVGKTTMLESRYKPVLQAFES-------EQLQVIGLAPTHEAVGEL 1084 (1960)
T ss_pred             CCCCHHHHHHHHHHHhCCCcEEEEEeCCCCCHHHhHHHHHHHHHHHHHh-------cCCeEEEEeChHHHHHHH
Confidence            36899999999999876  456778999999998641   223333222       356788999997776554

This protein is a component of the relaxosome complex. In the process of conjugative plasmid transfer the realaxosome binds to the plasmid at the oriT (origin of transfer) site. The relaxase protein TraI mediates the single-strand nicking and ATP-dependent unwinding (relaxation, helicase activity) of the plasmid molecule. These two activities reside in separate domains of the protein.

>PF13173 AAA_14: AAA domain

Probab=94.43  E-value=0.28  Score=46.77  Aligned_cols=38  Identities=21%  Similarity=0.395  Sum_probs=24.5

Q ss_pred             CceEEEecCcccccccCCchHHHHHHHhcCCCCcEEEEecc
Q 002040          617 RVTYLVMDEADRMFDMGFEPQITRIVQNIRPDRQTVLFSAT  657 (976)
Q Consensus       617 ~~~~vVlDEah~~~~~~f~~~i~~il~~~~~~~q~i~~SAT  657 (976)
                      .-.+|||||+|.+.  ++...+..++... ++.++|+++..
T Consensus        61 ~~~~i~iDEiq~~~--~~~~~lk~l~d~~-~~~~ii~tgS~   98 (128)
T PF13173_consen   61 GKKYIFIDEIQYLP--DWEDALKFLVDNG-PNIKIILTGSS   98 (128)
T ss_pred             CCcEEEEehhhhhc--cHHHHHHHHHHhc-cCceEEEEccc
Confidence            35789999999874  3456666666644 45555554443

>cd03115 SRP The signal recognition particle (SRP) mediates the transport to or across the plasma membrane in bacteria and the endoplasmic reticulum in eukaryotes

Probab=94.43  E-value=0.89  Score=45.72  Aligned_cols=53  Identities=17%  Similarity=0.305  Sum_probs=28.2

Q ss_pred             CceEEEecCccccc-ccCCchHHHHHHHhcCCCCcEEEEeccCcHHHHHHHHHH
Q 002040          617 RVTYLVMDEADRMF-DMGFEPQITRIVQNIRPDRQTVLFSATFPRQVEILARKV  669 (976)
Q Consensus       617 ~~~~vVlDEah~~~-~~~f~~~i~~il~~~~~~~q~i~~SAT~~~~~~~l~~~~  669 (976)
                      .+.+||+|....+. +......+..+.....++.-+++++|+.+......+..+
T Consensus        82 ~~d~viiDt~g~~~~~~~~l~~l~~l~~~~~~~~~~lVv~~~~~~~~~~~~~~~  135 (173)
T cd03115          82 NFDVVIVDTAGRLQIDENLMEELKKIKRVVKPDEVLLVVDAMTGQDAVNQAKAF  135 (173)
T ss_pred             CCCEEEEECcccchhhHHHHHHHHHHHhhcCCCeEEEEEECCCChHHHHHHHHH
Confidence            46788888887542 112233333333334455566777776555444444444

SRP recognizes N-terminal sighnal sequences of newly synthesized polypeptides at the ribosome. The SRP-polypeptide complex is then targeted to the membrane by an interaction between SRP and its cognated receptor (SR). In mammals, SRP consists of six protein subunits and a 7SL RNA. One of these subunits is a 54 kd protein (SRP54), which is a GTP-binding protein that interacts with the signal sequence when it emerges from the ribosome. SRP54 is a multidomain protein that consists of an N-terminal domain, followed by a central G (GTPase) domain and a C-terminal M domain.

>cd00561 CobA_CobO_BtuR ATP:corrinoid adenosyltransferase BtuR/CobO/CobP

Probab=94.40  E-value=0.48  Score=46.84  Aligned_cols=53  Identities=15%  Similarity=0.256  Sum_probs=40.5

Q ss_pred             cCCceEEEecCcccccccCCc--hHHHHHHHhcCCCCcEEEEeccCcHHHHHHHH
Q 002040          615 LRRVTYLVMDEADRMFDMGFE--PQITRIVQNIRPDRQTVLFSATFPRQVEILAR  667 (976)
Q Consensus       615 l~~~~~vVlDEah~~~~~~f~--~~i~~il~~~~~~~q~i~~SAT~~~~~~~l~~  667 (976)
                      ...+++|||||+-..++.++.  ..+..++...+...-+|+++-.+|+.+..++.
T Consensus        93 ~~~~dLlVLDEi~~a~~~gli~~~~v~~ll~~rp~~~evIlTGr~~p~~l~e~AD  147 (159)
T cd00561          93 SGEYDLVILDEINYALGYGLLDVEEVVDLLKAKPEDLELVLTGRNAPKELIEAAD  147 (159)
T ss_pred             cCCCCEEEEechHhHhhCCCCCHHHHHHHHHcCCCCCEEEEECCCCCHHHHHhCc
Confidence            456899999999987777754  45777788877777788888888888766543

This family consists of the BtuR, CobO, CobP proteins all of which are Cob(I)alamin (vitamin B12) adenosyltransferase, which is involved in cobalamin (vitamin B12) biosynthesis. This enzyme is a homodimer, which catalyzes the adenosylation reaction: ATP + cob(I)alamin + H2O <= phosphate + diphosphate + adenosylcobalamin.

>PRK07994 DNA polymerase III subunits gamma and tau; Validated

Probab=94.37  E-value=0.42  Score=57.91  Aligned_cols=19  Identities=26%  Similarity=0.160  Sum_probs=15.4

Q ss_pred             EEEEcCCCCchHHHHHHHH
Q 002040          507 CIGVAKTGSGKTLAFVLPM  525 (976)
Q Consensus       507 ~i~~a~TGsGKT~~~~l~i  525 (976)
                      +|+.|+.|+|||+++.+.+
T Consensus        41 yLf~Gp~GvGKTTlAr~lA   59 (647)
T PRK07994         41 YLFSGTRGVGKTTIARLLA   59 (647)
T ss_pred             EEEECCCCCCHHHHHHHHH
Confidence            6899999999998755443

>PTZ00112 origin recognition complex 1 protein; Provisional

Probab=94.36  E-value=0.35  Score=59.22  Aligned_cols=23  Identities=22%  Similarity=0.340  Sum_probs=16.5

Q ss_pred             EEEEcCCCCchHHHHHHHHHHHHh
Q 002040          507 CIGVAKTGSGKTLAFVLPMLRHIK  530 (976)
Q Consensus       507 ~i~~a~TGsGKT~~~~l~il~~l~  530 (976)
                      ++|.|+||+|||++ +..++..|.
T Consensus       784 LYIyG~PGTGKTAT-VK~VLrELq  806 (1164)
T PTZ00112        784 LYISGMPGTGKTAT-VYSVIQLLQ  806 (1164)
T ss_pred             EEEECCCCCCHHHH-HHHHHHHHH
Confidence            35899999999987 444455543

>PRK14088 dnaA chromosomal replication initiation protein; Provisional

Probab=94.34  E-value=0.34  Score=56.61  Aligned_cols=49  Identities=14%  Similarity=0.331  Sum_probs=27.3

Q ss_pred             CceEEEecCcccccccC-CchHHHHHHHhcCC-CCcEEEEeccCcHHHHHH
Q 002040          617 RVTYLVMDEADRMFDMG-FEPQITRIVQNIRP-DRQTVLFSATFPRQVEIL  665 (976)
Q Consensus       617 ~~~~vVlDEah~~~~~~-f~~~i~~il~~~~~-~~q~i~~SAT~~~~~~~l  665 (976)
                      .+++|||||+|.+.+.. ....+..++..+.. ..++|+.|...|..+..+
T Consensus       194 ~~dvLlIDDi~~l~~~~~~q~elf~~~n~l~~~~k~iIitsd~~p~~l~~l  244 (440)
T PRK14088        194 KVDVLLIDDVQFLIGKTGVQTELFHTFNELHDSGKQIVICSDREPQKLSEF  244 (440)
T ss_pred             cCCEEEEechhhhcCcHHHHHHHHHHHHHHHHcCCeEEEECCCCHHHHHHH
Confidence            36799999999775432 12334445544433 345555554555555443

>TIGR02640 gas_vesic_GvpN gas vesicle protein GvpN

Probab=94.33  E-value=0.33  Score=52.66  Aligned_cols=28  Identities=29%  Similarity=0.285  Sum_probs=22.8

Q ss_pred             HHHHHHHhcCCCEEEEcCCCCchHHHHH
Q 002040          495 AQALPVIMSGRDCIGVAKTGSGKTLAFV  522 (976)
Q Consensus       495 ~~~i~~il~g~d~i~~a~TGsGKT~~~~  522 (976)
                      ..++..+..+.++++.|++|+|||..+.
T Consensus        12 ~~~l~~l~~g~~vLL~G~~GtGKT~lA~   39 (262)
T TIGR02640        12 SRALRYLKSGYPVHLRGPAGTGKTTLAM   39 (262)
T ss_pred             HHHHHHHhcCCeEEEEcCCCCCHHHHHH
Confidence            4456667789999999999999998643

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).

>TIGR00643 recG ATP-dependent DNA helicase RecG

Probab=94.27  E-value=0.14  Score=62.78  Aligned_cols=92  Identities=18%  Similarity=0.252  Sum_probs=71.7

Q ss_pred             cchHHH-HHHHHHHhhhcCCcEEEEecCHHHHHHHHHHHHH----CCCCceeccCCCCHHHHHHHHHHhccCCccEEEec
Q 002040          697 ESDRFL-RLLELLGEWYEKGKILIFVHSQEKCDALFRDLLK----HGYPCLSLHGAKDQTDRESTISDFKSNVCNLLIAT  771 (976)
Q Consensus       697 ~~~k~~-~l~~~l~~~~~~~kvLIF~~s~~~~~~l~~~L~~----~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLVaT  771 (976)
                      .+.|.. .++.++.....+.+++|.+||..-+.+++..|..    .|+.+..+||+++...+..++..+.+|.+.|||+|
T Consensus       266 GSGKT~va~l~il~~~~~g~qvlilaPT~~LA~Q~~~~~~~l~~~~gi~v~lltg~~~~~~r~~~~~~i~~g~~~IiVgT  345 (630)
T TIGR00643       266 GSGKTLVAALAMLAAIEAGYQVALMAPTEILAEQHYNSLRNLLAPLGIEVALLTGSLKGKRRKELLETIASGQIHLVVGT  345 (630)
T ss_pred             CCcHHHHHHHHHHHHHHcCCcEEEECCHHHHHHHHHHHHHHHhcccCcEEEEEecCCCHHHHHHHHHHHhCCCCCEEEec
Confidence            344443 3334444444566999999999998888777664    37899999999999999999999999999999999


Q ss_pred             Cccc-ccCCCCCCcEEEE
Q 002040          772 SVAA-RGLDVKELELVIN  788 (976)
Q Consensus       772 ~v~~-~GlDi~~v~~VI~  788 (976)
                      ..+- ..+.+.++.+||.
T Consensus       346 ~~ll~~~~~~~~l~lvVI  363 (630)
T TIGR00643       346 HALIQEKVEFKRLALVII  363 (630)
T ss_pred             HHHHhccccccccceEEE
Confidence            8443 5677888888884

>TIGR00595 priA primosomal protein N'

Probab=94.25  E-value=0.22  Score=59.24  Aligned_cols=92  Identities=17%  Similarity=0.183  Sum_probs=71.9

Q ss_pred             cchHHHHHHHHHHhhhc-CCcEEEEecCHHHHHHHHHHHHHC-CCCceeccCCCCHHHHHHHHHHhccCCccEEEecCcc
Q 002040          697 ESDRFLRLLELLGEWYE-KGKILIFVHSQEKCDALFRDLLKH-GYPCLSLHGAKDQTDRESTISDFKSNVCNLLIATSVA  774 (976)
Q Consensus       697 ~~~k~~~l~~~l~~~~~-~~kvLIF~~s~~~~~~l~~~L~~~-~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLVaT~v~  774 (976)
                      .+.|....+.++..... ++++||.+|+..-+..++..|... +..+..+||+++..+|..++....+|..+|+|+|..+
T Consensus         7 GsGKT~v~l~~i~~~l~~g~~vLvlvP~i~L~~Q~~~~l~~~f~~~v~vlhs~~~~~er~~~~~~~~~g~~~IVVGTrsa   86 (505)
T TIGR00595         7 GSGKTEVYLQAIEKVLALGKSVLVLVPEIALTPQMIQRFKYRFGSQVAVLHSGLSDSEKLQAWRKVKNGEILVVIGTRSA   86 (505)
T ss_pred             CCCHHHHHHHHHHHHHHcCCeEEEEeCcHHHHHHHHHHHHHHhCCcEEEEECCCCHHHHHHHHHHHHcCCCCEEECChHH
Confidence            34555555555544433 458999999999999999988764 7789999999999999999999999999999999754


Q ss_pred             cccCCCCCCcEEEEe
Q 002040          775 ARGLDVKELELVINF  789 (976)
Q Consensus       775 ~~GlDi~~v~~VI~~  789 (976)
                      -. +.+.++.+||.-
T Consensus        87 lf-~p~~~l~lIIVD  100 (505)
T TIGR00595        87 LF-LPFKNLGLIIVD  100 (505)
T ss_pred             Hc-CcccCCCEEEEE
Confidence            32 456778888853

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).

>TIGR02881 spore_V_K stage V sporulation protein K

Probab=94.24  E-value=0.14  Score=55.39  Aligned_cols=18  Identities=28%  Similarity=0.200  Sum_probs=15.2

Q ss_pred             CCEEEEcCCCCchHHHHH
Q 002040          505 RDCIGVAKTGSGKTLAFV  522 (976)
Q Consensus       505 ~d~i~~a~TGsGKT~~~~  522 (976)
                      .++|+.||+|+|||+.+-
T Consensus        43 ~~vll~GppGtGKTtlA~   60 (261)
T TIGR02881        43 LHMIFKGNPGTGKTTVAR   60 (261)
T ss_pred             ceEEEEcCCCCCHHHHHH
Confidence            468999999999998643

Members of this protein family are the stage V sporulation protein K (SpoVK), a close homolog of the Rubisco expression protein CbbX (TIGR02880) and a members of the ATPase family associated with various cellular activities (pfam00004). Members are strictly limited to bacterial endospore-forming species, but are not universal in this group and are missing from the Clostridium group.

>PRK14960 DNA polymerase III subunits gamma and tau; Provisional

Probab=94.22  E-value=0.22  Score=59.71  Aligned_cols=40  Identities=15%  Similarity=0.284  Sum_probs=24.0

Q ss_pred             CCceEEEecCcccccccCCchHHHHHHHhcCCCCcEEEEecc
Q 002040          616 RRVTYLVMDEADRMFDMGFEPQITRIVQNIRPDRQTVLFSAT  657 (976)
Q Consensus       616 ~~~~~vVlDEah~~~~~~f~~~i~~il~~~~~~~q~i~~SAT  657 (976)
                      ..+.++||||+|+|....+ ..+..++...+....+| |++|
T Consensus       117 gk~KV~IIDEVh~LS~~A~-NALLKtLEEPP~~v~FI-LaTt  156 (702)
T PRK14960        117 GRFKVYLIDEVHMLSTHSF-NALLKTLEEPPEHVKFL-FATT  156 (702)
T ss_pred             CCcEEEEEechHhcCHHHH-HHHHHHHhcCCCCcEEE-EEEC
Confidence            4578999999997754332 34555555544444444 4445

>KOG2036 consensus Predicted P-loop ATPase fused to an acetyltransferase [General function prediction only]

Probab=94.19  E-value=0.82  Score=53.84  Aligned_cols=142  Identities=18%  Similarity=0.167  Sum_probs=76.1

Q ss_pred             cHHHHHHHHHHhc-------CCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHHH
Q 002040          491 MPIQAQALPVIMS-------GRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKF  563 (976)
Q Consensus       491 ~~~Q~~~i~~il~-------g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~~  563 (976)
                      |-.|..|+-.++.       .--+-+.|.-|-||+.+..+.+...+...       -..+.|..|.-+-...+++.+-+=
T Consensus       255 T~dQakav~~f~dai~eK~lr~~vsLtA~RGRGKSAALGlsiA~AVa~G-------ysnIyvtSPspeNlkTlFeFv~kG  327 (1011)
T KOG2036|consen  255 TLDQAKAVLTFFDAIVEKTLRSTVSLTASRGRGKSAALGLSIAGAVAFG-------YSNIYVTSPSPENLKTLFEFVFKG  327 (1011)
T ss_pred             hHHHHHHHHHHHHHHHHhhhcceEEEEecCCCCchhhhhHHHHHHHhcC-------cceEEEcCCChHHHHHHHHHHHcc
Confidence            5668777765542       23467789999999999888887776542       224677789877665555444332


Q ss_pred             HhhcCcEE----EEeeCCCChHHH-HH--HHhcC--CeEEEeCchhHHHHHHhcCCcccccCCceEEEecCcccccccCC
Q 002040          564 AKVMGVRC----VPVYGGSGVAQQ-IS--ELKRG--TEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMGF  634 (976)
Q Consensus       564 ~~~~~~~~----~~~~gg~~~~~~-~~--~l~~~--~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDEah~~~~~~f  634 (976)
                      +..++..-    -++..-++.... +.  .+.++  --|-+..|.           ....|....+||||||-.+.    
T Consensus       328 fDaL~Yqeh~Dy~iI~s~np~fkkaivRInifr~hrQtIQYi~P~-----------D~~kl~q~eLlVIDEAAAIP----  392 (1011)
T KOG2036|consen  328 FDALEYQEHVDYDIIQSTNPDFKKAIVRINIFREHRQTIQYISPH-----------DHQKLGQAELLVIDEAAAIP----  392 (1011)
T ss_pred             hhhhcchhhcchhhhhhcChhhhhhEEEEEEeccccceeEeeccc-----------hhhhccCCcEEEechhhcCC----
Confidence            22222111    011111100000 00  00000  012222221           11235678899999999764    


Q ss_pred             chHHHHHHHhcCCCCcEEEEeccCc
Q 002040          635 EPQITRIVQNIRPDRQTVLFSATFP  659 (976)
Q Consensus       635 ~~~i~~il~~~~~~~q~i~~SAT~~  659 (976)
                      .+.+..++     .+.+++|+.|+.
T Consensus       393 Lplvk~Li-----gPylVfmaSTin  412 (1011)
T KOG2036|consen  393 LPLVKKLI-----GPYLVFMASTIN  412 (1011)
T ss_pred             HHHHHHhh-----cceeEEEeeccc
Confidence            55565554     345788999874

>PRK10416 signal recognition particle-docking protein FtsY; Provisional

Probab=94.19  E-value=0.86  Score=50.71  Aligned_cols=133  Identities=19%  Similarity=0.232  Sum_probs=63.4

Q ss_pred             CCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEE-ccC-HHHHHHHHHHHHHHHhhcCcEEEEeeCCCChH
Q 002040          504 GRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIM-APT-RELVQQIHSDIRKFAKVMGVRCVPVYGGSGVA  581 (976)
Q Consensus       504 g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl-~Pt-r~La~Q~~~~~~~~~~~~~~~~~~~~gg~~~~  581 (976)
                      +.-++++|++|+|||+.+...+. .+..       .+..|+++ +.+ +..+.   ..+..++...++.++....+....
T Consensus       114 ~~vi~lvGpnGsGKTTt~~kLA~-~l~~-------~g~~V~Li~~D~~r~~a~---eql~~~a~~~~i~~~~~~~~~dpa  182 (318)
T PRK10416        114 PFVILVVGVNGVGKTTTIGKLAH-KYKA-------QGKKVLLAAGDTFRAAAI---EQLQVWGERVGVPVIAQKEGADPA  182 (318)
T ss_pred             CeEEEEECCCCCcHHHHHHHHHH-HHHh-------cCCeEEEEecCccchhhH---HHHHHHHHHcCceEEEeCCCCCHH
Confidence            44577889999999986443332 2222       23445554 444 33332   223333444555544332222111


Q ss_pred             HHHHHHhcCCeEEEeCchhHHHHHHhcCCcccccCCceEEEecCcccccccC-CchHHHHHHHh------cCCCCcEEEE
Q 002040          582 QQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMG-FEPQITRIVQN------IRPDRQTVLF  654 (976)
Q Consensus       582 ~~~~~l~~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDEah~~~~~~-f~~~i~~il~~------~~~~~q~i~~  654 (976)
                      .                 ...+.+..     .....+++||||=+-++.... ....+..+...      ..+..-++++
T Consensus       183 ~-----------------~v~~~l~~-----~~~~~~D~ViIDTaGr~~~~~~l~~eL~~~~~v~~~~~~~~p~~~~LVl  240 (318)
T PRK10416        183 S-----------------VAFDAIQA-----AKARGIDVLIIDTAGRLHNKTNLMEELKKIKRVIKKADPDAPHEVLLVL  240 (318)
T ss_pred             H-----------------HHHHHHHH-----HHhCCCCEEEEeCCCCCcCCHHHHHHHHHHHHHHhhhcCCCCceEEEEE
Confidence            0                 01111111     122457888888887653221 12233333332      2344457889


Q ss_pred             eccCcHHHHHHHHHH
Q 002040          655 SATFPRQVEILARKV  669 (976)
Q Consensus       655 SAT~~~~~~~l~~~~  669 (976)
                      +||........+..+
T Consensus       241 ~a~~g~~~~~~a~~f  255 (318)
T PRK10416        241 DATTGQNALSQAKAF  255 (318)
T ss_pred             ECCCChHHHHHHHHH
Confidence            999765443344444

>PRK14956 DNA polymerase III subunits gamma and tau; Provisional

Probab=94.18  E-value=0.12  Score=59.97  Aligned_cols=19  Identities=26%  Similarity=0.167  Sum_probs=15.4

Q ss_pred             EEEEcCCCCchHHHHHHHH
Q 002040          507 CIGVAKTGSGKTLAFVLPM  525 (976)
Q Consensus       507 ~i~~a~TGsGKT~~~~l~i  525 (976)
                      +|++||.|+|||.++.+.+
T Consensus        43 ~Lf~GP~GtGKTTlAriLA   61 (484)
T PRK14956         43 YIFFGPRGVGKTTIARILA   61 (484)
T ss_pred             EEEECCCCCCHHHHHHHHH
Confidence            7999999999998755443

>PRK08691 DNA polymerase III subunits gamma and tau; Validated

Probab=94.14  E-value=0.4  Score=58.02  Aligned_cols=40  Identities=10%  Similarity=0.204  Sum_probs=24.3

Q ss_pred             cCCceEEEecCcccccccCCchHHHHHHHhcCCCCcEEEEe
Q 002040          615 LRRVTYLVMDEADRMFDMGFEPQITRIVQNIRPDRQTVLFS  655 (976)
Q Consensus       615 l~~~~~vVlDEah~~~~~~f~~~i~~il~~~~~~~q~i~~S  655 (976)
                      +..+.+|||||+|.|....| ..+..++...+....+|+.|
T Consensus       117 ~gk~KVIIIDEad~Ls~~A~-NALLKtLEEPp~~v~fILaT  156 (709)
T PRK08691        117 AGKYKVYIIDEVHMLSKSAF-NAMLKTLEEPPEHVKFILAT  156 (709)
T ss_pred             hCCcEEEEEECccccCHHHH-HHHHHHHHhCCCCcEEEEEe
Confidence            34678999999997653222 33455555545555555544

>PRK05986 cob(I)alamin adenolsyltransferase/cobinamide ATP-dependent adenolsyltransferase; Validated

Probab=94.13  E-value=0.63  Score=47.30  Aligned_cols=147  Identities=14%  Similarity=0.082  Sum_probs=76.9

Q ss_pred             hcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHHHHhhcCcEEEEeeCCCChH
Q 002040          502 MSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVA  581 (976)
Q Consensus       502 l~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~~~~~~~~~~~~~~gg~~~~  581 (976)
                      +....+++...+|.|||.+++--++..+-        .|.+|+|+-=.+--.  -+.+...+....++.+..  .|.+..
T Consensus        20 ~~~g~v~v~~g~GkGKtt~a~g~a~ra~g--------~G~~V~ivQFlKg~~--~~GE~~~l~~l~~v~~~~--~g~~~~   87 (191)
T PRK05986         20 EEKGLLIVHTGNGKGKSTAAFGMALRAVG--------HGKKVGVVQFIKGAW--STGERNLLEFGGGVEFHV--MGTGFT   87 (191)
T ss_pred             ccCCeEEEECCCCCChHHHHHHHHHHHHH--------CCCeEEEEEEecCCC--ccCHHHHHhcCCCcEEEE--CCCCCc
Confidence            45568899999999999987777776643        366777765222110  011222221111333322  122110


Q ss_pred             HHHHHHhcCCeEEEeCchhHHHHHHhcCCcccccCCceEEEecCcccccccCCc--hHHHHHHHhcCCCCcEEEEeccCc
Q 002040          582 QQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMGFE--PQITRIVQNIRPDRQTVLFSATFP  659 (976)
Q Consensus       582 ~~~~~l~~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDEah~~~~~~f~--~~i~~il~~~~~~~q~i~~SAT~~  659 (976)
                      -.    ......-+......+....    ....-..+++|||||+-..++.++.  ..+..++...++..-+|++.-.+|
T Consensus        88 ~~----~~~~~e~~~~~~~~~~~a~----~~l~~~~ydlvVLDEi~~Al~~gli~~eevi~~L~~rp~~~evVlTGR~~p  159 (191)
T PRK05986         88 WE----TQDRERDIAAAREGWEEAK----RMLADESYDLVVLDELTYALKYGYLDVEEVLEALNARPGMQHVVITGRGAP  159 (191)
T ss_pred             cc----CCCcHHHHHHHHHHHHHHH----HHHhCCCCCEEEEehhhHHHHCCCccHHHHHHHHHcCCCCCEEEEECCCCC
Confidence            00    0000000000001111111    1122356899999999988888865  356777777666666777767788


Q ss_pred             HHHHHHHHH
Q 002040          660 RQVEILARK  668 (976)
Q Consensus       660 ~~~~~l~~~  668 (976)
                      +.+..++..
T Consensus       160 ~~Lie~ADl  168 (191)
T PRK05986        160 RELIEAADL  168 (191)
T ss_pred             HHHHHhCch
Confidence            877665543

>PRK00411 cdc6 cell division control protein 6; Reviewed

Probab=94.09  E-value=0.29  Score=56.51  Aligned_cols=26  Identities=19%  Similarity=0.369  Sum_probs=19.3

Q ss_pred             CCEEEEcCCCCchHHHHHHHHHHHHhc
Q 002040          505 RDCIGVAKTGSGKTLAFVLPMLRHIKD  531 (976)
Q Consensus       505 ~d~i~~a~TGsGKT~~~~l~il~~l~~  531 (976)
                      .+++|.|++|+|||.+ +..++..+..
T Consensus        56 ~~~lI~G~~GtGKT~l-~~~v~~~l~~   81 (394)
T PRK00411         56 LNVLIYGPPGTGKTTT-VKKVFEELEE   81 (394)
T ss_pred             CeEEEECCCCCCHHHH-HHHHHHHHHH
Confidence            5799999999999986 4445555443

>KOG0298 consensus DEAD box-containing helicase-like transcription factor/DNA repair protein [Replication, recombination and repair]

Probab=94.03  E-value=0.078  Score=66.17  Aligned_cols=96  Identities=23%  Similarity=0.200  Sum_probs=78.8

Q ss_pred             CCcEEEEecCHHHHHHHHHHHHHCCCCceeccCCCCHHHHHHHHHHhccCCccEEEecCcccccCCCCCCcEEEEeCCCC
Q 002040          714 KGKILIFVHSQEKCDALFRDLLKHGYPCLSLHGAKDQTDRESTISDFKSNVCNLLIATSVAARGLDVKELELVINFDAPN  793 (976)
Q Consensus       714 ~~kvLIF~~s~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLVaT~v~~~GlDi~~v~~VI~~d~p~  793 (976)
                      ..++|||+.-....+.+...|...++.+...-++   .+-...+..|++ --.+||-+...+-|+|+-++.+|+..+|-.
T Consensus      1221 qekvIvfsqws~~ldV~e~~~~~N~I~~~~~~~t---~d~~dc~~~fk~-I~clll~~~~~~~GLNL~eA~Hvfl~ePiL 1296 (1394)
T KOG0298|consen 1221 QEKVIVFSQWSVVLDVKELRYLMNLIKKQLDGET---EDFDDCIICFKS-IDCLLLFVSKGSKGLNLIEATHVFLVEPIL 1296 (1394)
T ss_pred             CceEEEEEehHHHHHHHHHHHHhhhhHhhhccCC---cchhhhhhhccc-ceEEEEEeccCcccccHHhhhhhheecccc
Confidence            3589999999998888888887777776655443   334556777776 445778899999999999999999999999


Q ss_pred             CHHHHHHHhcccCCCCCccE
Q 002040          794 HYEDYVHRVGRTGRAGRKGC  813 (976)
Q Consensus       794 s~~~y~Qr~GR~gR~g~~g~  813 (976)
                      ++..-.|.+||++|.|++--
T Consensus      1297 N~~~E~QAigRvhRiGQ~~p 1316 (1394)
T KOG0298|consen 1297 NPGDEAQAIGRVHRIGQKRP 1316 (1394)
T ss_pred             CchHHHhhhhhhhhcccccc
Confidence            99999999999999998643

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

Probab=94.03  E-value=0.43  Score=54.11  Aligned_cols=26  Identities=27%  Similarity=0.397  Sum_probs=19.3

Q ss_pred             CCEEEEcCCCCchHHHHHHHHHHHHhc
Q 002040          505 RDCIGVAKTGSGKTLAFVLPMLRHIKD  531 (976)
Q Consensus       505 ~d~i~~a~TGsGKT~~~~l~il~~l~~  531 (976)
                      .++++.|+||+|||.+ +..++..+..
T Consensus        43 ~n~~iyG~~GTGKT~~-~~~v~~~l~~   68 (366)
T COG1474          43 SNIIIYGPTGTGKTAT-VKFVMEELEE   68 (366)
T ss_pred             ccEEEECCCCCCHhHH-HHHHHHHHHh
Confidence            3699999999999976 4455555554

>PRK08533 flagellar accessory protein FlaH; Reviewed

Probab=94.00  E-value=0.32  Score=51.54  Aligned_cols=51  Identities=8%  Similarity=0.054  Sum_probs=30.7

Q ss_pred             cCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHH
Q 002040          503 SGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRK  562 (976)
Q Consensus       503 ~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~  562 (976)
                      .|.-+++.|++|+|||+.++..+...+.        .+..+++++.. +-..++...+..
T Consensus        23 ~g~~~~i~G~~G~GKTtl~~~~~~~~~~--------~g~~~~yi~~e-~~~~~~~~~~~~   73 (230)
T PRK08533         23 AGSLILIEGDESTGKSILSQRLAYGFLQ--------NGYSVSYVSTQ-LTTTEFIKQMMS   73 (230)
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHHHh--------CCCcEEEEeCC-CCHHHHHHHHHH
Confidence            4667899999999999864444443322        24567777743 223444444433

>TIGR03689 pup_AAA proteasome ATPase

Probab=93.99  E-value=0.3  Score=57.50  Aligned_cols=61  Identities=23%  Similarity=0.311  Sum_probs=32.0

Q ss_pred             cccccccCC-CCHHHHHHHHH--cCCCCCcHHHHHHHHHHhcCCCEEEEcCCCCchHHHHHHHHHHHH
Q 002040          465 PIKTWHQTG-LTSKIMETIRK--LNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHI  529 (976)
Q Consensus       465 pi~~~~~~~-l~~~l~~~l~~--~~~~~p~~~Q~~~i~~il~g~d~i~~a~TGsGKT~~~~l~il~~l  529 (976)
                      |-.+|.+++ +...+......  +.+..|.-+....++   ..+.+|+.||+|+|||+. +-.+...+
T Consensus       177 p~v~~~dIgGl~~~i~~i~~~v~lp~~~~~l~~~~gl~---~p~GILLyGPPGTGKT~L-AKAlA~eL  240 (512)
T TIGR03689       177 PDVTYADIGGLDSQIEQIRDAVELPFLHPELYREYDLK---PPKGVLLYGPPGCGKTLI-AKAVANSL  240 (512)
T ss_pred             CCCCHHHcCChHHHHHHHHHHHHHHhhCHHHHHhccCC---CCcceEEECCCCCcHHHH-HHHHHHhh
Confidence            346788876 44443322221  222222222222221   246799999999999975 33444443

In the Actinobacteria, as shown for Mycobacterium tuberculosis, some proteins are modified by ligation between an epsilon-amino group of a lysine side chain and the C-terminal carboxylate of the ubiquitin-like protein Pup. This modification leads to protein degradation by the archaeal-like proteasome found in the Actinobacteria. Members of this protein family belong to the AAA family of ATPases and tend to be clustered with the genes for Pup, the Pup ligase PafA, and structural components of the proteasome. This protein forms hexameric rings with ATPase activity.

>PRK14964 DNA polymerase III subunits gamma and tau; Provisional

Probab=93.96  E-value=0.35  Score=56.70  Aligned_cols=21  Identities=24%  Similarity=0.254  Sum_probs=16.8

Q ss_pred             CCEEEEcCCCCchHHHHHHHH
Q 002040          505 RDCIGVAKTGSGKTLAFVLPM  525 (976)
Q Consensus       505 ~d~i~~a~TGsGKT~~~~l~i  525 (976)
                      +.+|++||.|+|||+++.+.+
T Consensus        36 ha~Lf~Gp~G~GKTT~ArilA   56 (491)
T PRK14964         36 QSILLVGASGVGKTTCARIIS   56 (491)
T ss_pred             ceEEEECCCCccHHHHHHHHH
Confidence            368999999999998755443

>PRK04195 replication factor C large subunit; Provisional

Probab=93.94  E-value=0.3  Score=57.92  Aligned_cols=18  Identities=22%  Similarity=0.176  Sum_probs=15.3

Q ss_pred             CCCEEEEcCCCCchHHHH
Q 002040          504 GRDCIGVAKTGSGKTLAF  521 (976)
Q Consensus       504 g~d~i~~a~TGsGKT~~~  521 (976)
                      .+.+|+.||+|+|||..+
T Consensus        39 ~~~lLL~GppG~GKTtla   56 (482)
T PRK04195         39 KKALLLYGPPGVGKTSLA   56 (482)
T ss_pred             CCeEEEECCCCCCHHHHH
Confidence            467999999999999753

>KOG2028 consensus ATPase related to the helicase subunit of the Holliday junction resolvase [Replication, recombination and repair]

Probab=93.92  E-value=0.26  Score=53.82  Aligned_cols=17  Identities=29%  Similarity=0.202  Sum_probs=14.7

Q ss_pred             CEEEEcCCCCchHHHHH
Q 002040          506 DCIGVAKTGSGKTLAFV  522 (976)
Q Consensus       506 d~i~~a~TGsGKT~~~~  522 (976)
                      .+|++||.|+|||..+-
T Consensus       164 SmIlWGppG~GKTtlAr  180 (554)
T KOG2028|consen  164 SMILWGPPGTGKTTLAR  180 (554)
T ss_pred             ceEEecCCCCchHHHHH
Confidence            69999999999997543

>cd01122 GP4d_helicase GP4d_helicase is a homohexameric 5'-3' helicases

Probab=93.89  E-value=0.13  Score=56.10  Aligned_cols=40  Identities=28%  Similarity=0.122  Sum_probs=26.2

Q ss_pred             hcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEcc
Q 002040          502 MSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAP  548 (976)
Q Consensus       502 l~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~P  548 (976)
                      ..|.-+++.|++|+|||+..+..+...+..       .+..|+++.-
T Consensus        28 ~~g~~~~i~g~~G~GKT~l~~~~~~~~~~~-------~g~~vl~iS~   67 (271)
T cd01122          28 RKGELIILTAGTGVGKTTFLREYALDLITQ-------HGVRVGTISL   67 (271)
T ss_pred             cCCcEEEEEcCCCCCHHHHHHHHHHHHHHh-------cCceEEEEEc
Confidence            356778999999999997655444443322       2456777663

Helicases couple NTP hydrolysis to the unwinding of nucleic acid duplexes into their component strands.

>TIGR00708 cobA cob(I)alamin adenosyltransferase

Probab=93.88  E-value=0.16  Score=50.80  Aligned_cols=52  Identities=13%  Similarity=0.289  Sum_probs=40.1

Q ss_pred             CCceEEEecCcccccccCCch--HHHHHHHhcCCCCcEEEEeccCcHHHHHHHH
Q 002040          616 RRVTYLVMDEADRMFDMGFEP--QITRIVQNIRPDRQTVLFSATFPRQVEILAR  667 (976)
Q Consensus       616 ~~~~~vVlDEah~~~~~~f~~--~i~~il~~~~~~~q~i~~SAT~~~~~~~l~~  667 (976)
                      ..+++|||||+-..++.++.+  .+..++...++...+|++.-.+|+.+..++.
T Consensus        96 ~~~DlvVLDEi~~A~~~gli~~~~v~~lL~~rp~~~evVlTGR~~p~~l~e~AD  149 (173)
T TIGR00708        96 PELDLVLLDELTYALKYGYLDVEEVVEALQERPGHQHVIITGRGCPQDLLELAD  149 (173)
T ss_pred             CCCCEEEehhhHHHHHCCCcCHHHHHHHHHhCCCCCEEEEECCCCCHHHHHhCc
Confidence            568999999999888887553  5677787777777778777778888766554

Alternate name: corrinoid adenosyltransferase.

>PF00308 Bac_DnaA: Bacterial dnaA protein; InterPro: IPR013317 This entry represents the central domain of bacterial DnaA proteins [, , ] that play an important role in initiating and regulating chromosomal replication

Probab=93.80  E-value=0.14  Score=53.77  Aligned_cols=48  Identities=17%  Similarity=0.315  Sum_probs=30.0

Q ss_pred             cCCceEEEecCcccccccC-CchHHHHHHHhcC-CCCcEEEEeccCcHHH
Q 002040          615 LRRVTYLVMDEADRMFDMG-FEPQITRIVQNIR-PDRQTVLFSATFPRQV  662 (976)
Q Consensus       615 l~~~~~vVlDEah~~~~~~-f~~~i~~il~~~~-~~~q~i~~SAT~~~~~  662 (976)
                      +..+++||||.+|.+.... ....+..++..+. .+.++|+.|...|..+
T Consensus        95 ~~~~DlL~iDDi~~l~~~~~~q~~lf~l~n~~~~~~k~li~ts~~~P~~l  144 (219)
T PF00308_consen   95 LRSADLLIIDDIQFLAGKQRTQEELFHLFNRLIESGKQLILTSDRPPSEL  144 (219)
T ss_dssp             HCTSSEEEEETGGGGTTHHHHHHHHHHHHHHHHHTTSEEEEEESS-TTTT
T ss_pred             hhcCCEEEEecchhhcCchHHHHHHHHHHHHHHhhCCeEEEEeCCCCccc
Confidence            4468999999999876432 2334555555553 3456777776766553

DnaA is an ATP- and DNA-binding protein. It binds specifically to 9 bp nucleotide repeats known as dnaA boxes which are found in the chromosome origin of replication (oriC). DnaA is a protein of about 50 kDa that contains two conserved regions: the first is located in the N-terminal half and corresponds to the ATP-binding domain, the second is located in the C-terminal half and could be involved in DNA-binding. The protein may also bind the RNA polymerase beta subunit, the dnaB and dnaZ proteins, and the groE gene products (chaperonins) [].; PDB: 2KJQ_A 2Z4S_A 2Z4R_C 2HCB_B 3R8F_C 1L8Q_A 3SC3_B 3BOS_A.

>PRK14958 DNA polymerase III subunits gamma and tau; Provisional

Probab=93.77  E-value=0.25  Score=58.64  Aligned_cols=39  Identities=13%  Similarity=0.243  Sum_probs=24.7

Q ss_pred             CCceEEEecCcccccccCCchHHHHHHHhcCCCCcEEEEe
Q 002040          616 RRVTYLVMDEADRMFDMGFEPQITRIVQNIRPDRQTVLFS  655 (976)
Q Consensus       616 ~~~~~vVlDEah~~~~~~f~~~i~~il~~~~~~~q~i~~S  655 (976)
                      ..+.++||||||.|....| ..+..++...++...+|+.|
T Consensus       118 ~~~kV~iIDE~~~ls~~a~-naLLk~LEepp~~~~fIlat  156 (509)
T PRK14958        118 GRFKVYLIDEVHMLSGHSF-NALLKTLEEPPSHVKFILAT  156 (509)
T ss_pred             CCcEEEEEEChHhcCHHHH-HHHHHHHhccCCCeEEEEEE
Confidence            3578999999998764433 34445666655555555544

>PRK13342 recombination factor protein RarA; Reviewed

Probab=93.75  E-value=0.45  Score=55.32  Aligned_cols=17  Identities=29%  Similarity=0.202  Sum_probs=14.6

Q ss_pred             CEEEEcCCCCchHHHHH
Q 002040          506 DCIGVAKTGSGKTLAFV  522 (976)
Q Consensus       506 d~i~~a~TGsGKT~~~~  522 (976)
                      .+|+.||+|+|||+.+.
T Consensus        38 ~ilL~GppGtGKTtLA~   54 (413)
T PRK13342         38 SMILWGPPGTGKTTLAR   54 (413)
T ss_pred             eEEEECCCCCCHHHHHH
Confidence            68999999999997643

>KOG0733 consensus Nuclear AAA ATPase (VCP subfamily) [Posttranslational modification, protein turnover, chaperones]

Probab=93.74  E-value=0.2  Score=58.31  Aligned_cols=55  Identities=20%  Similarity=0.305  Sum_probs=34.6

Q ss_pred             CcccccccCCCCHHHHHHHHH---cCCCCCcHHHHHHHHHHhcCCCEEEEcCCCCchHHHH
Q 002040          464 KPIKTWHQTGLTSKIMETIRK---LNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAF  521 (976)
Q Consensus       464 ~pi~~~~~~~l~~~l~~~l~~---~~~~~p~~~Q~~~i~~il~g~d~i~~a~TGsGKT~~~  521 (976)
                      -|-.+|.+.|--..+...|.-   ..+..|--++.-.|.   .-..+|+|||+|+|||+.+
T Consensus       505 VPdVtW~dIGaL~~vR~eL~~aI~~PiK~pd~~k~lGi~---~PsGvLL~GPPGCGKTLlA  562 (802)
T KOG0733|consen  505 VPDVTWDDIGALEEVRLELNMAILAPIKRPDLFKALGID---APSGVLLCGPPGCGKTLLA  562 (802)
T ss_pred             cCCCChhhcccHHHHHHHHHHHHhhhccCHHHHHHhCCC---CCCceEEeCCCCccHHHHH
Confidence            356789999877777655542   233333333322221   2457999999999999853

>PRK06645 DNA polymerase III subunits gamma and tau; Validated

Probab=93.73  E-value=0.33  Score=57.35  Aligned_cols=20  Identities=20%  Similarity=0.154  Sum_probs=16.2

Q ss_pred             CEEEEcCCCCchHHHHHHHH
Q 002040          506 DCIGVAKTGSGKTLAFVLPM  525 (976)
Q Consensus       506 d~i~~a~TGsGKT~~~~l~i  525 (976)
                      .+|++||.|+|||+++.+.+
T Consensus        45 a~Lf~Gp~G~GKTT~ArilA   64 (507)
T PRK06645         45 GYLLTGIRGVGKTTSARIIA   64 (507)
T ss_pred             eEEEECCCCCCHHHHHHHHH
Confidence            68999999999998755443

>TIGR03015 pepcterm_ATPase putative secretion ATPase, PEP-CTERM locus subfamily

Probab=93.73  E-value=0.98  Score=48.99  Aligned_cols=33  Identities=18%  Similarity=0.195  Sum_probs=22.3

Q ss_pred             CcHHHHHHHHHHh----cCC-CEEEEcCCCCchHHHHH
Q 002040          490 PMPIQAQALPVIM----SGR-DCIGVAKTGSGKTLAFV  522 (976)
Q Consensus       490 p~~~Q~~~i~~il----~g~-d~i~~a~TGsGKT~~~~  522 (976)
                      +++.+.+++..+.    .+. .++++|++|+|||+.+.
T Consensus        24 ~~~~~~~~~~~l~~~~~~~~~~~~l~G~~G~GKTtl~~   61 (269)
T TIGR03015        24 PSKGHKRAMAYLEYGLSQREGFILITGEVGAGKTTLIR   61 (269)
T ss_pred             CCHHHHHHHHHHHHHHhcCCCEEEEEcCCCCCHHHHHH
Confidence            4555566665543    333 57889999999998633

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.

>PF00004 AAA: ATPase family associated with various cellular activities (AAA); InterPro: IPR003959 AAA ATPases (ATPases Associated with diverse cellular Activities) form a large protein family and play a number of roles in the cell including cell-cycle regulation, protein proteolysis and disaggregation, organelle biogenesis and intracellular transport

Probab=93.71  E-value=0.19  Score=47.68  Aligned_cols=14  Identities=29%  Similarity=0.316  Sum_probs=12.5

Q ss_pred             EEEEcCCCCchHHH
Q 002040          507 CIGVAKTGSGKTLA  520 (976)
Q Consensus       507 ~i~~a~TGsGKT~~  520 (976)
                      +|+.||+|+|||..
T Consensus         1 ill~G~~G~GKT~l   14 (132)
T PF00004_consen    1 ILLHGPPGTGKTTL   14 (132)
T ss_dssp             EEEESSTTSSHHHH
T ss_pred             CEEECcCCCCeeHH
Confidence            58999999999975

Some of them function as molecular chaperones, subunits of proteolytic complexes or independent proteases (FtsH, Lon). They also act as DNA helicases and transcription factors []. AAA ATPases belong to the AAA+ superfamily of ringshaped P-loop NTPases, which act via the energy-dependent unfolding of macromolecules [, ]. There are six major clades of AAA domains (proteasome subunits, metalloproteases, domains D1 and D2 of ATPases with two AAA domains, the MSP1/katanin/spastin group and BCS1 and it homologues), as well as a number of deeply branching minor clades []. They assemble into oligomeric assemblies (often hexamers) that form a ring-shaped structure with a central pore. These proteins produce a molecular motor that couples ATP binding and hydrolysis to changes in conformational states that act upon a target substrate, either translocating or remodelling it []. They are found in all living organisms and share the common feature of the presence of a highly conserved AAA domain called the AAA module. This domain is responsible for ATP binding and hydrolysis. It contains 200-250 residues, among them there are two classical motifs, Walker A (GX4GKT) and Walker B (HyDE) []. The functional variety seen between AAA ATPases is in part due to their extensive number of accessory domains and factors, and to their variable organisation within oligomeric assemblies, in addition to changes in key functional residues within the ATPase domain itself. More information about these proteins can be found at Protein of the Month: AAA ATPases [].; GO: 0005524 ATP binding; PDB: 3H4M_A 1NSF_A 1D2N_A 1HQY_E 1DO0_E 1DO2_C 1G4B_E 1HT1_F 1G4A_F 1HT2_G ....

>TIGR00580 mfd transcription-repair coupling factor (mfd)

Probab=93.62  E-value=0.23  Score=62.99  Aligned_cols=93  Identities=12%  Similarity=0.162  Sum_probs=72.3

Q ss_pred             CcchHHHHH-HHHHHhhhcCCcEEEEecCHHHHHHHHHHHHHC----CCCceeccCCCCHHHHHHHHHHhccCCccEEEe
Q 002040          696 PESDRFLRL-LELLGEWYEKGKILIFVHSQEKCDALFRDLLKH----GYPCLSLHGAKDQTDRESTISDFKSNVCNLLIA  770 (976)
Q Consensus       696 ~~~~k~~~l-~~~l~~~~~~~kvLIF~~s~~~~~~l~~~L~~~----~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLVa  770 (976)
                      ....|.... ..++.....+.+++|.+||..-|.+.+..|...    ++.+..++|..+..++..++..+.+|.++|||+
T Consensus       481 TGsGKT~val~a~l~al~~g~qvlvLvPT~~LA~Q~~~~f~~~~~~~~i~v~~Lsg~~~~~e~~~~~~~l~~g~~dIVIG  560 (926)
T TIGR00580       481 VGFGKTEVAMRAAFKAVLDGKQVAVLVPTTLLAQQHFETFKERFANFPVTIELLSRFRSAKEQNEILKELASGKIDILIG  560 (926)
T ss_pred             CCccHHHHHHHHHHHHHHhCCeEEEEeCcHHHHHHHHHHHHHHhccCCcEEEEEeccccHHHHHHHHHHHHcCCceEEEc
Confidence            344554433 233333345678999999999999988877653    677889999999999999999999999999999


Q ss_pred             cC-cccccCCCCCCcEEEE
Q 002040          771 TS-VAARGLDVKELELVIN  788 (976)
Q Consensus       771 T~-v~~~GlDi~~v~~VI~  788 (976)
                      |. .+...+.+.++.+||.
T Consensus       561 Tp~ll~~~v~f~~L~llVI  579 (926)
T TIGR00580       561 THKLLQKDVKFKDLGLLII  579 (926)
T ss_pred             hHHHhhCCCCcccCCEEEe
Confidence            97 4445678888998885

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.

>TIGR03877 thermo_KaiC_1 KaiC domain protein, Ph0284 family

Probab=93.59  E-value=0.22  Score=53.15  Aligned_cols=51  Identities=18%  Similarity=0.257  Sum_probs=34.4

Q ss_pred             CCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHHH
Q 002040          504 GRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKF  563 (976)
Q Consensus       504 g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~~  563 (976)
                      |..++|.|++|+|||+.++..++..+..        |..+++++ +-+-..|+.+.+..+
T Consensus        21 gs~~lI~G~pGsGKT~la~~~l~~~~~~--------ge~~lyvs-~ee~~~~i~~~~~~~   71 (237)
T TIGR03877        21 RNVVLLSGGPGTGKSIFSQQFLWNGLQM--------GEPGIYVA-LEEHPVQVRRNMAQF   71 (237)
T ss_pred             CeEEEEEcCCCCCHHHHHHHHHHHHHHc--------CCcEEEEE-eeCCHHHHHHHHHHh
Confidence            4678999999999998766666655532        45677776 344555666655543

Members of this family contain a single copy of the KaiC domain (pfam06745) that occurs in two copies of the circadian clock protein kinase KaiC itself. Members occur primarily in thermophilic archaea and in Thermotoga.

>PRK09111 DNA polymerase III subunits gamma and tau; Validated

Probab=93.54  E-value=0.31  Score=58.83  Aligned_cols=41  Identities=10%  Similarity=0.159  Sum_probs=25.5

Q ss_pred             ccCCceEEEecCcccccccCCchHHHHHHHhcCCCCcEEEEe
Q 002040          614 NLRRVTYLVMDEADRMFDMGFEPQITRIVQNIRPDRQTVLFS  655 (976)
Q Consensus       614 ~l~~~~~vVlDEah~~~~~~f~~~i~~il~~~~~~~q~i~~S  655 (976)
                      .+..+.+|||||+|.|.... ...+...+...++...+|+.+
T Consensus       129 ~~a~~KVvIIDEad~Ls~~a-~naLLKtLEePp~~~~fIl~t  169 (598)
T PRK09111        129 VSARYKVYIIDEVHMLSTAA-FNALLKTLEEPPPHVKFIFAT  169 (598)
T ss_pred             hcCCcEEEEEEChHhCCHHH-HHHHHHHHHhCCCCeEEEEEe
Confidence            34568899999999875432 234445555555555555544

>PRK13833 conjugal transfer protein TrbB; Provisional

Probab=93.52  E-value=0.25  Score=54.81  Aligned_cols=58  Identities=22%  Similarity=0.186  Sum_probs=38.8

Q ss_pred             CcHHHHHHHHHHh-cCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHH
Q 002040          490 PMPIQAQALPVIM-SGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELV  553 (976)
Q Consensus       490 p~~~Q~~~i~~il-~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La  553 (976)
                      +++.|...|..++ .+.++|++|+||||||+. +-.++..+...+     .+-+++++=.+.+|.
T Consensus       129 ~~~~~~~~L~~~v~~~~nilI~G~tGSGKTTl-l~aL~~~i~~~~-----~~~rivtiEd~~El~  187 (323)
T PRK13833        129 MTEAQASVIRSAIDSRLNIVISGGTGSGKTTL-ANAVIAEIVASA-----PEDRLVILEDTAEIQ  187 (323)
T ss_pred             CCHHHHHHHHHHHHcCCeEEEECCCCCCHHHH-HHHHHHHHhcCC-----CCceEEEecCCcccc
Confidence            4567776665554 567899999999999975 455666554322     133567777777763

>PRK14873 primosome assembly protein PriA; Provisional

Probab=93.51  E-value=0.39  Score=58.71  Aligned_cols=94  Identities=21%  Similarity=0.157  Sum_probs=77.0

Q ss_pred             cchHHHHHHHHHHhhhc-CCcEEEEecCHHHHHHHHHHHHHC-C-CCceeccCCCCHHHHHHHHHHhccCCccEEEecCc
Q 002040          697 ESDRFLRLLELLGEWYE-KGKILIFVHSQEKCDALFRDLLKH-G-YPCLSLHGAKDQTDRESTISDFKSNVCNLLIATSV  773 (976)
Q Consensus       697 ~~~k~~~l~~~l~~~~~-~~kvLIF~~s~~~~~~l~~~L~~~-~-~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLVaT~v  773 (976)
                      .+.|...++.++..... ++++||.++.+..+..+...|... | ..+..+|++++..+|...+....+|..+|+|.|-.
T Consensus       170 GSGKTevyl~~i~~~l~~Gk~vLvLvPEi~lt~q~~~rl~~~f~~~~v~~lhS~l~~~~R~~~w~~~~~G~~~IViGtRS  249 (665)
T PRK14873        170 GEDWARRLAAAAAATLRAGRGALVVVPDQRDVDRLEAALRALLGAGDVAVLSAGLGPADRYRRWLAVLRGQARVVVGTRS  249 (665)
T ss_pred             CCcHHHHHHHHHHHHHHcCCeEEEEecchhhHHHHHHHHHHHcCCCcEEEECCCCCHHHHHHHHHHHhCCCCcEEEEcce
Confidence            35777777887777665 458999999999999999999864 4 67999999999999999999999999999999975


Q ss_pred             ccccCCCCCCcEEEEeCC
Q 002040          774 AARGLDVKELELVINFDA  791 (976)
Q Consensus       774 ~~~GlDi~~v~~VI~~d~  791 (976)
                      +-- +-++++.+||..+-
T Consensus       250 AvF-aP~~~LgLIIvdEE  266 (665)
T PRK14873        250 AVF-APVEDLGLVAIWDD  266 (665)
T ss_pred             eEE-eccCCCCEEEEEcC
Confidence            442 45667788876443

>KOG0738 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=93.49  E-value=0.19  Score=55.36  Aligned_cols=16  Identities=38%  Similarity=0.598  Sum_probs=14.5

Q ss_pred             CCEEEEcCCCCchHHH
Q 002040          505 RDCIGVAKTGSGKTLA  520 (976)
Q Consensus       505 ~d~i~~a~TGsGKT~~  520 (976)
                      +.+|++||+|+|||+.
T Consensus       246 kgvLm~GPPGTGKTlL  261 (491)
T KOG0738|consen  246 KGVLMVGPPGTGKTLL  261 (491)
T ss_pred             ceeeeeCCCCCcHHHH
Confidence            6799999999999975

>PLN03025 replication factor C subunit; Provisional

Probab=93.47  E-value=0.55  Score=52.50  Aligned_cols=39  Identities=18%  Similarity=0.286  Sum_probs=22.6

Q ss_pred             CceEEEecCcccccccCCchHHHHHHHhcCCCCcEEEEecc
Q 002040          617 RVTYLVMDEADRMFDMGFEPQITRIVQNIRPDRQTVLFSAT  657 (976)
Q Consensus       617 ~~~~vVlDEah~~~~~~f~~~i~~il~~~~~~~q~i~~SAT  657 (976)
                      .+.+|||||||.|.... ...+..++........+ +|+++
T Consensus        99 ~~kviiiDE~d~lt~~a-q~aL~~~lE~~~~~t~~-il~~n  137 (319)
T PLN03025         99 RHKIVILDEADSMTSGA-QQALRRTMEIYSNTTRF-ALACN  137 (319)
T ss_pred             CeEEEEEechhhcCHHH-HHHHHHHHhcccCCceE-EEEeC
Confidence            47899999999875432 23344445544444444 44444

>PRK13341 recombination factor protein RarA/unknown domain fusion protein; Reviewed

Probab=93.44  E-value=0.46  Score=58.70  Aligned_cols=40  Identities=23%  Similarity=0.283  Sum_probs=24.0

Q ss_pred             CceEEEecCcccccccCCchHHHHHHHhcCCCCcEEEEeccCcHH
Q 002040          617 RVTYLVMDEADRMFDMGFEPQITRIVQNIRPDRQTVLFSATFPRQ  661 (976)
Q Consensus       617 ~~~~vVlDEah~~~~~~f~~~i~~il~~~~~~~q~i~~SAT~~~~  661 (976)
                      ...+|||||+|++..    .+...++..+ ...++++++||.++.
T Consensus       109 ~~~IL~IDEIh~Ln~----~qQdaLL~~l-E~g~IiLI~aTTenp  148 (725)
T PRK13341        109 KRTILFIDEVHRFNK----AQQDALLPWV-ENGTITLIGATTENP  148 (725)
T ss_pred             CceEEEEeChhhCCH----HHHHHHHHHh-cCceEEEEEecCCCh
Confidence            457899999998642    2222333333 235677878775443

>cd00984 DnaB_C DnaB helicase C terminal domain

Probab=93.39  E-value=0.25  Score=52.83  Aligned_cols=46  Identities=24%  Similarity=0.203  Sum_probs=28.9

Q ss_pred             cCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEc---cCHHHHHH
Q 002040          503 SGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMA---PTRELVQQ  555 (976)
Q Consensus       503 ~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~---Ptr~La~Q  555 (976)
                      .|.-++|.|++|+|||...+..++..+..       .+..+++++   |..+++..
T Consensus        12 ~G~l~lI~G~~G~GKT~~~~~~~~~~~~~-------~g~~vly~s~E~~~~~~~~r   60 (242)
T cd00984          12 PGDLIIIAARPSMGKTAFALNIAENIAKK-------QGKPVLFFSLEMSKEQLLQR   60 (242)
T ss_pred             CCeEEEEEeCCCCCHHHHHHHHHHHHHHh-------CCCceEEEeCCCCHHHHHHH
Confidence            45668889999999997644444444432       145677777   33444443

The hexameric helicase DnaB unwinds the DNA duplex at the chromosome replication fork. Although the mechanism by which DnaB both couples ATP hydrolysis to translocation along DNA and denatures the duplex is unknown, a change in the quaternary structure of the protein involving dimerization of the N-terminal domain has been observed and may occur during the enzymatic cycle. This C-terminal domain contains an ATP-binding site and is therefore probably the site of ATP hydrolysis.

>PRK14949 DNA polymerase III subunits gamma and tau; Provisional

Probab=93.37  E-value=0.53  Score=58.33  Aligned_cols=38  Identities=11%  Similarity=0.117  Sum_probs=22.5

Q ss_pred             CCceEEEecCcccccccCCchHHHHHHHhcCCCCcEEEE
Q 002040          616 RRVTYLVMDEADRMFDMGFEPQITRIVQNIRPDRQTVLF  654 (976)
Q Consensus       616 ~~~~~vVlDEah~~~~~~f~~~i~~il~~~~~~~q~i~~  654 (976)
                      ..+.+|||||||+|.... ...+.+++..-+....+|+.
T Consensus       118 gk~KViIIDEAh~LT~eA-qNALLKtLEEPP~~vrFILa  155 (944)
T PRK14949        118 GRFKVYLIDEVHMLSRSS-FNALLKTLEEPPEHVKFLLA  155 (944)
T ss_pred             CCcEEEEEechHhcCHHH-HHHHHHHHhccCCCeEEEEE
Confidence            357899999999875332 23444455554444444443

>PF05876 Terminase_GpA: Phage terminase large subunit (GpA); InterPro: IPR008866 This entry is represented by Bacteriophage lambda, GpA

Probab=93.33  E-value=0.16  Score=60.94  Aligned_cols=70  Identities=13%  Similarity=0.177  Sum_probs=49.6

Q ss_pred             CCcHHHHHHHHHHhcC--CCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHH-HHHHHHHh
Q 002040          489 KPMPIQAQALPVIMSG--RDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIH-SDIRKFAK  565 (976)
Q Consensus       489 ~p~~~Q~~~i~~il~g--~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~-~~~~~~~~  565 (976)
                      ..+|+|.+.+..+...  +.|+++.++-+|||.+.+..+...+...       ...+|++.||..+|..+. ..|..+..
T Consensus        16 ~~~Py~~eimd~~~~~~v~~Vv~~k~aQ~GkT~~~~n~~g~~i~~~-------P~~~l~v~Pt~~~a~~~~~~rl~Pmi~   88 (557)
T PF05876_consen   16 DRTPYLREIMDALSDPSVREVVVMKSAQVGKTELLLNWIGYSIDQD-------PGPMLYVQPTDDAAKDFSKERLDPMIR   88 (557)
T ss_pred             CCChhHHHHHHhcCCcCccEEEEEEcchhhHhHHHHhhceEEEEeC-------CCCEEEEEEcHHHHHHHHHHHHHHHHH
Confidence            5689999998888754  5788899999999996444443333322       234799999999998876 44444443

The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry consists of several phage terminase large subunit proteins as well as related sequences from several bacterial species. The DNA packaging enzyme of bacteriophage lambda, terminase, is a heteromultimer composed of a small subunit, gpNu1, and a large subunit, gpA, products of the Nu1 and A genes, respectively. Terminase is involved in the site-specific binding and cutting of the DNA in the initial stages of packaging. It is now known that gpA is actively involved in late stages of packaging, including DNA translocation, and that this enzyme contains separate functional domains for its early and late packaging activities [].

>PF02456 Adeno_IVa2: Adenovirus IVa2 protein; InterPro: IPR003389 Va2 protein can interact with the adenoviral packaging signal and this interaction involves DNA sequences that have previously been demonstrated to be required for packaging []

Probab=93.32  E-value=0.41  Score=51.35  Aligned_cols=39  Identities=18%  Similarity=0.247  Sum_probs=23.4

Q ss_pred             EEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHH
Q 002040          507 CIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRE  551 (976)
Q Consensus       507 ~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~  551 (976)
                      .+|.|||||||+- ++-.++..-+-+     ...-.|++|+|+..
T Consensus        90 ~~VYGPTG~GKSq-LlRNLis~~lI~-----P~PETVfFItP~~~  128 (369)
T PF02456_consen   90 GVVYGPTGSGKSQ-LLRNLISCQLIQ-----PPPETVFFITPQKD  128 (369)
T ss_pred             EEEECCCCCCHHH-HHHHhhhcCccc-----CCCCceEEECCCCC
Confidence            5677999999994 333333221111     12336899999864

During the course of lytic infection, the adenovirus major late promoter (MLP) is induced to high levels after replication of viral DNA has started. IVa2 is a transcriptional activator of the major late promoter [].; GO: 0019083 viral transcription

>PHA03368 DNA packaging terminase subunit 1; Provisional

Probab=93.17  E-value=0.48  Score=56.45  Aligned_cols=136  Identities=18%  Similarity=0.183  Sum_probs=79.4

Q ss_pred             hcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHHHHhhc-CcEEE-EeeCCCC
Q 002040          502 MSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVM-GVRCV-PVYGGSG  579 (976)
Q Consensus       502 l~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~~~~~~-~~~~~-~~~gg~~  579 (976)
                      +..+-.++..|=-.|||.... +++..+...     -.|-.+++++|....+..++.++..++..+ +-..+ .+.| ..
T Consensus       252 fkqk~tVflVPRR~GKTwivv-~iI~~ll~s-----~~Gi~IgytAH~~~ts~~vF~eI~~~le~~f~~~~v~~vkG-e~  324 (738)
T PHA03368        252 FRQRATVFLVPRRHGKTWFLV-PLIALALAT-----FRGIKIGYTAHIRKATEPVFEEIGARLRQWFGASRVDHVKG-ET  324 (738)
T ss_pred             hhccceEEEecccCCchhhHH-HHHHHHHHh-----CCCCEEEEEcCcHHHHHHHHHHHHHHHhhhcchhheeeecC-cE
Confidence            345667888888899998644 555544432     136789999999999999999999876543 11112 2222 21


Q ss_pred             hHHHHHHHhcC--CeEEEeCchhHHHHHHhcCCcccccCCceEEEecCcccccccCCchHHHHHHHhc-CCCCcEEEEec
Q 002040          580 VAQQISELKRG--TEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMGFEPQITRIVQNI-RPDRQTVLFSA  656 (976)
Q Consensus       580 ~~~~~~~l~~~--~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDEah~~~~~~f~~~i~~il~~~-~~~~q~i~~SA  656 (976)
                      +   .-.+..|  .-|.++|-        .+. ....-..+++||||||+-+-..    .+..++-.+ ..+.++|++|.
T Consensus       325 I---~i~f~nG~kstI~FaSa--------rnt-NsiRGqtfDLLIVDEAqFIk~~----al~~ilp~l~~~n~k~I~ISS  388 (738)
T PHA03368        325 I---SFSFPDGSRSTIVFASS--------HNT-NGIRGQDFNLLFVDEANFIRPD----AVQTIMGFLNQTNCKIIFVSS  388 (738)
T ss_pred             E---EEEecCCCccEEEEEec--------cCC-CCccCCcccEEEEechhhCCHH----HHHHHHHHHhccCccEEEEec
Confidence            1   0011222  24444421        110 0011236889999999966532    333333222 23788999998


Q ss_pred             cCcH
Q 002040          657 TFPR  660 (976)
Q Consensus       657 T~~~  660 (976)
                      |-+.
T Consensus       389 ~Ns~  392 (738)
T PHA03368        389 TNTG  392 (738)
T ss_pred             CCCC
Confidence            8654

>PRK14961 DNA polymerase III subunits gamma and tau; Provisional

Probab=93.14  E-value=0.65  Score=52.94  Aligned_cols=38  Identities=13%  Similarity=0.231  Sum_probs=22.0

Q ss_pred             CCceEEEecCcccccccCCchHHHHHHHhcCCCCcEEEE
Q 002040          616 RRVTYLVMDEADRMFDMGFEPQITRIVQNIRPDRQTVLF  654 (976)
Q Consensus       616 ~~~~~vVlDEah~~~~~~f~~~i~~il~~~~~~~q~i~~  654 (976)
                      ....+|||||||.|....+ ..+...+...++...+|+.
T Consensus       118 ~~~kviIIDEa~~l~~~a~-naLLk~lEe~~~~~~fIl~  155 (363)
T PRK14961        118 SRFKVYLIDEVHMLSRHSF-NALLKTLEEPPQHIKFILA  155 (363)
T ss_pred             CCceEEEEEChhhcCHHHH-HHHHHHHhcCCCCeEEEEE
Confidence            4578999999998754322 2234444444444444443

>PRK13894 conjugal transfer ATPase TrbB; Provisional

Probab=93.09  E-value=0.27  Score=54.62  Aligned_cols=64  Identities=22%  Similarity=0.225  Sum_probs=41.3

Q ss_pred             HHHHcCCCCCcHHHHHHHHH-HhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHH
Q 002040          481 TIRKLNYEKPMPIQAQALPV-IMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTREL  552 (976)
Q Consensus       481 ~l~~~~~~~p~~~Q~~~i~~-il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~L  552 (976)
                      .|...|+  +++.|...|.. +..+.+++++|+||||||+. +..++..+...+     ...++++|-.+.+|
T Consensus       126 ~l~~~g~--~~~~~~~~L~~~v~~~~~ilI~G~tGSGKTTl-l~aL~~~~~~~~-----~~~rivtIEd~~El  190 (319)
T PRK13894        126 QYVERGI--MTAAQREAIIAAVRAHRNILVIGGTGSGKTTL-VNAIINEMVIQD-----PTERVFIIEDTGEI  190 (319)
T ss_pred             HHHhcCC--CCHHHHHHHHHHHHcCCeEEEECCCCCCHHHH-HHHHHHhhhhcC-----CCceEEEEcCCCcc
Confidence            3444454  45677777765 44678899999999999964 555555443211     23466777777776

>COG3972 Superfamily I DNA and RNA helicases [General function prediction only]

Probab=93.06  E-value=0.13  Score=58.10  Aligned_cols=133  Identities=18%  Similarity=0.139  Sum_probs=72.9

Q ss_pred             CcHHHHHHHHHHhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHHHHhhc--
Q 002040          490 PMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVM--  567 (976)
Q Consensus       490 p~~~Q~~~i~~il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~~~~~~--  567 (976)
                      +-..|..+.-.+-.|.- .|.|-.|||||.+.++-+. +|...     +..-+++|.+-|+.|+.++...+.+|+-..  
T Consensus       163 fD~~Q~kaa~~~~~G~q-rIrGLAGSGKT~~La~Kaa-~lh~k-----nPd~~I~~Tfftk~L~s~~r~lv~~F~f~~~e  235 (660)
T COG3972         163 FDTDQTKAAFQSGFGKQ-RIRGLAGSGKTELLAHKAA-ELHSK-----NPDSRIAFTFFTKILASTMRTLVPEFFFMRVE  235 (660)
T ss_pred             ccchhheeeeecCCchh-hhhcccCCCchhHHHHHHH-HHhcC-----CCCceEEEEeehHHHHHHHHHHHHHHHHHHhh
Confidence            44567766655555554 6678899999987544433 33322     224578999999999999998888887322  


Q ss_pred             -----C-cEEEEeeCCCChHHHHHHHh---cCCeEEEeCchhHHHHHHhcC-CcccccCCceEEEecCcccc
Q 002040          568 -----G-VRCVPVYGGSGVAQQISELK---RGTEIVVCTPGRMIDILCTSG-GKITNLRRVTYLVMDEADRM  629 (976)
Q Consensus       568 -----~-~~~~~~~gg~~~~~~~~~l~---~~~~Iiv~Tp~~L~~~l~~~~-~~~~~l~~~~~vVlDEah~~  629 (976)
                           + +.+..-.||....-......   .-..|-++--|.-.+..+..- ....++.-+++|.|||++-+
T Consensus       236 ~~pdW~~~l~~h~wgG~t~~g~y~~~~~~~~~~~~~fsg~g~~F~~aC~eli~~~~~~~~yD~ilIDE~QDF  307 (660)
T COG3972         236 KQPDWGTKLFCHNWGGLTKEGFYGMYRYICHYYEIPFSGFGNGFDAACKELIADINNKKAYDYILIDESQDF  307 (660)
T ss_pred             cCCCccceEEEeccCCCCCCcchHHHHHHhcccccccCCCCcchHHHHHHHHHhhhccccccEEEecccccC
Confidence                 2 23333445554322211111   111222221111111111100 00123567899999999954

>COG0541 Ffh Signal recognition particle GTPase [Intracellular trafficking and secretion]

Probab=93.02  E-value=1.2  Score=50.41  Aligned_cols=131  Identities=20%  Similarity=0.250  Sum_probs=76.3

Q ss_pred             CEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEc-c-CHHHHHHHHHHHHHHHhhcCcEEEEeeCCCChHHH
Q 002040          506 DCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMA-P-TRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQ  583 (976)
Q Consensus       506 d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~-P-tr~La~Q~~~~~~~~~~~~~~~~~~~~gg~~~~~~  583 (976)
                      -++++|=-|||||+++.- +..++.+.       +.++++++ - .|..|.   ++++.++...++.+.....+.+.- .
T Consensus       102 vImmvGLQGsGKTTt~~K-LA~~lkk~-------~~kvllVaaD~~RpAA~---eQL~~La~q~~v~~f~~~~~~~Pv-~  169 (451)
T COG0541         102 VILMVGLQGSGKTTTAGK-LAKYLKKK-------GKKVLLVAADTYRPAAI---EQLKQLAEQVGVPFFGSGTEKDPV-E  169 (451)
T ss_pred             EEEEEeccCCChHhHHHH-HHHHHHHc-------CCceEEEecccCChHHH---HHHHHHHHHcCCceecCCCCCCHH-H
Confidence            378889999999987443 34444432       44555555 3 344443   667777777787776552222111 1


Q ss_pred             HHHHhcCCeEEEeCchhHHHHHHhcCCcccccCCceEEEecCccccc-ccCCchHHHHHHHhcCCCCcEEEEeccCcHHH
Q 002040          584 ISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMF-DMGFEPQITRIVQNIRPDRQTVLFSATFPRQV  662 (976)
Q Consensus       584 ~~~l~~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDEah~~~-~~~f~~~i~~il~~~~~~~q~i~~SAT~~~~~  662 (976)
                      +..                .-+..     .....+++||||=|-|+- +...-..+..|-..++|+--++++-|++....
T Consensus       170 Iak----------------~al~~-----ak~~~~DvvIvDTAGRl~ide~Lm~El~~Ik~~~~P~E~llVvDam~GQdA  228 (451)
T COG0541         170 IAK----------------AALEK-----AKEEGYDVVIVDTAGRLHIDEELMDELKEIKEVINPDETLLVVDAMIGQDA  228 (451)
T ss_pred             HHH----------------HHHHH-----HHHcCCCEEEEeCCCcccccHHHHHHHHHHHhhcCCCeEEEEEecccchHH
Confidence            110                11111     123346778888777542 22234456667777888887888888887766


Q ss_pred             HHHHHHH
Q 002040          663 EILARKV  669 (976)
Q Consensus       663 ~~l~~~~  669 (976)
                      ...+..|
T Consensus       229 ~~~A~aF  235 (451)
T COG0541         229 VNTAKAF  235 (451)
T ss_pred             HHHHHHH
Confidence            6666555

>PRK07471 DNA polymerase III subunit delta'; Validated

Probab=92.99  E-value=0.57  Score=53.19  Aligned_cols=43  Identities=14%  Similarity=0.127  Sum_probs=26.3

Q ss_pred             cCCceEEEecCcccccccCCchHHHHHHHhcCCCCcEEEEeccC
Q 002040          615 LRRVTYLVMDEADRMFDMGFEPQITRIVQNIRPDRQTVLFSATF  658 (976)
Q Consensus       615 l~~~~~vVlDEah~~~~~~f~~~i~~il~~~~~~~q~i~~SAT~  658 (976)
                      ...+.+|||||+|.|-. .-...+.+++...++...+|++|..+
T Consensus       139 ~~~~kVviIDead~m~~-~aanaLLK~LEepp~~~~~IL~t~~~  181 (365)
T PRK07471        139 EGGWRVVIVDTADEMNA-NAANALLKVLEEPPARSLFLLVSHAP  181 (365)
T ss_pred             cCCCEEEEEechHhcCH-HHHHHHHHHHhcCCCCeEEEEEECCc
Confidence            45678999999998742 22334555555544455555555543

>PF03969 AFG1_ATPase: AFG1-like ATPase; InterPro: IPR005654 ATPase family gene 1 (AFG1) ATPase is a 377 amino acid putative protein with an ATPase motif typical of the protein family including SEC18p PAS1, CDC48-VCP and TBP

Probab=92.96  E-value=1.2  Score=50.43  Aligned_cols=44  Identities=18%  Similarity=0.191  Sum_probs=27.4

Q ss_pred             CceEEEecCcccccccCCchHHHHHHHhc-CCCCcEEEEeccCcHH
Q 002040          617 RVTYLVMDEADRMFDMGFEPQITRIVQNI-RPDRQTVLFSATFPRQ  661 (976)
Q Consensus       617 ~~~~vVlDEah~~~~~~f~~~i~~il~~~-~~~~q~i~~SAT~~~~  661 (976)
                      ...+|++||+|- .|-+-...+..++..+ ....-+|++|-++|..
T Consensus       127 ~~~lLcfDEF~V-~DiaDAmil~rLf~~l~~~gvvlVaTSN~~P~~  171 (362)
T PF03969_consen  127 ESRLLCFDEFQV-TDIADAMILKRLFEALFKRGVVLVATSNRPPED  171 (362)
T ss_pred             cCCEEEEeeeec-cchhHHHHHHHHHHHHHHCCCEEEecCCCChHH
Confidence            467999999993 3333334445555544 3455667777777765

AFG1 also has substantial homology to these proteins outside the ATPase domain []. This family of proteins contains a P-loop motif.; GO: 0005524 ATP binding

>PHA00729 NTP-binding motif containing protein

Probab=92.93  E-value=0.68  Score=48.41  Aligned_cols=75  Identities=15%  Similarity=0.217  Sum_probs=38.3

Q ss_pred             CeEEEeCchhHHHHHHhcCCcccccCCceEEEecCccccccc-CCc----hHHHHHHHhcCCCCcEEEEeccCcHHHHHH
Q 002040          591 TEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDM-GFE----PQITRIVQNIRPDRQTVLFSATFPRQVEIL  665 (976)
Q Consensus       591 ~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDEah~~~~~-~f~----~~i~~il~~~~~~~q~i~~SAT~~~~~~~l  665 (976)
                      ...++.+...|+..+....   .....+.+||||++=.-+.. .|.    ..+..+...+++..+++.|...-|..+...
T Consensus        59 ~~~~fid~~~Ll~~L~~a~---~~~~~~dlLIIDd~G~~~~~~~wh~~~~~~yf~L~~aLrSR~~l~il~~ls~edL~~~  135 (226)
T PHA00729         59 QNSYFFELPDALEKIQDAI---DNDYRIPLIIFDDAGIWLSKYVWYEDYMKTFYKIYALIRTRVSAVIFTTPSPEDLAFY  135 (226)
T ss_pred             CcEEEEEHHHHHHHHHHHH---hcCCCCCEEEEeCCchhhcccchhhhccchHHHHHHHHHhhCcEEEEecCCHHHHHHH
Confidence            3455555555555553211   11234578999994311111 011    223345555555566777777766666555


Q ss_pred             HHH
Q 002040          666 ARK  668 (976)
Q Consensus       666 ~~~  668 (976)
                      +..
T Consensus       136 Lr~  138 (226)
T PHA00729        136 LRE  138 (226)
T ss_pred             HHh
Confidence            554

>PRK14955 DNA polymerase III subunits gamma and tau; Provisional

Probab=92.93  E-value=0.61  Score=53.87  Aligned_cols=20  Identities=30%  Similarity=0.129  Sum_probs=15.9

Q ss_pred             CEEEEcCCCCchHHHHHHHH
Q 002040          506 DCIGVAKTGSGKTLAFVLPM  525 (976)
Q Consensus       506 d~i~~a~TGsGKT~~~~l~i  525 (976)
                      .+|++||.|+|||+++.+.+
T Consensus        40 a~lf~Gp~G~GKtt~A~~~a   59 (397)
T PRK14955         40 GYIFSGLRGVGKTTAARVFA   59 (397)
T ss_pred             eEEEECCCCCCHHHHHHHHH
Confidence            48899999999998755443

>PRK14952 DNA polymerase III subunits gamma and tau; Provisional

Probab=92.92  E-value=0.66  Score=55.80  Aligned_cols=43  Identities=23%  Similarity=0.335  Sum_probs=25.5

Q ss_pred             cCCceEEEecCcccccccCCchHHHHHHHhcCCCCcEEEEeccCc
Q 002040          615 LRRVTYLVMDEADRMFDMGFEPQITRIVQNIRPDRQTVLFSATFP  659 (976)
Q Consensus       615 l~~~~~vVlDEah~~~~~~f~~~i~~il~~~~~~~q~i~~SAT~~  659 (976)
                      ...+.+|||||||.|....| ..+..++...+...-+|+.+ |-+
T Consensus       116 ~~~~KVvIIDEah~Lt~~A~-NALLK~LEEpp~~~~fIL~t-te~  158 (584)
T PRK14952        116 QSRYRIFIVDEAHMVTTAGF-NALLKIVEEPPEHLIFIFAT-TEP  158 (584)
T ss_pred             cCCceEEEEECCCcCCHHHH-HHHHHHHhcCCCCeEEEEEe-CCh
Confidence            35688999999998764432 23445555544444444444 543

>TIGR02928 orc1/cdc6 family replication initiation protein

Probab=92.90  E-value=0.46  Score=54.19  Aligned_cols=25  Identities=24%  Similarity=0.391  Sum_probs=18.9

Q ss_pred             CCEEEEcCCCCchHHHHHHHHHHHHh
Q 002040          505 RDCIGVAKTGSGKTLAFVLPMLRHIK  530 (976)
Q Consensus       505 ~d~i~~a~TGsGKT~~~~l~il~~l~  530 (976)
                      .+++|.||+|+|||.+ +..++..+.
T Consensus        41 ~~i~I~G~~GtGKT~l-~~~~~~~l~   65 (365)
T TIGR02928        41 SNVFIYGKTGTGKTAV-TKYVMKELE   65 (365)
T ss_pred             CcEEEECCCCCCHHHH-HHHHHHHHH
Confidence            5799999999999976 445555554

Members of this protein family are found exclusively in the archaea. This set of DNA binding proteins shows homology to the origin recognition complex subunit 1/cell division control protein 6 family in eukaryotes. Several members may be found in genome and interact with each other.

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

Probab=92.90  E-value=0.48  Score=47.23  Aligned_cols=43  Identities=12%  Similarity=0.267  Sum_probs=28.2

Q ss_pred             CCceEEEecCcccccccCCchHHHHHHHhcCCCCcEEEEeccCc
Q 002040          616 RRVTYLVMDEADRMFDMGFEPQITRIVQNIRPDRQTVLFSATFP  659 (976)
Q Consensus       616 ~~~~~vVlDEah~~~~~~f~~~i~~il~~~~~~~q~i~~SAT~~  659 (976)
                      ..+.++|||+||.|... -...+.+++..-+.+..+|++|..+.
T Consensus       101 ~~~KviiI~~ad~l~~~-a~NaLLK~LEepp~~~~fiL~t~~~~  143 (162)
T PF13177_consen  101 GKYKVIIIDEADKLTEE-AQNALLKTLEEPPENTYFILITNNPS  143 (162)
T ss_dssp             SSSEEEEEETGGGS-HH-HHHHHHHHHHSTTTTEEEEEEES-GG
T ss_pred             CCceEEEeehHhhhhHH-HHHHHHHHhcCCCCCEEEEEEECChH
Confidence            56889999999987533 34556666666666666666665543

...

>PRK14959 DNA polymerase III subunits gamma and tau; Provisional

Probab=92.89  E-value=0.43  Score=57.37  Aligned_cols=20  Identities=20%  Similarity=0.102  Sum_probs=16.2

Q ss_pred             CEEEEcCCCCchHHHHHHHH
Q 002040          506 DCIGVAKTGSGKTLAFVLPM  525 (976)
Q Consensus       506 d~i~~a~TGsGKT~~~~l~i  525 (976)
                      .+|+.|+.|+|||+++.+.+
T Consensus        40 a~Lf~GPpG~GKTtiArilA   59 (624)
T PRK14959         40 AYLFSGTRGVGKTTIARIFA   59 (624)
T ss_pred             eEEEECCCCCCHHHHHHHHH
Confidence            57889999999998765544

>PF00265 TK: Thymidine kinase; InterPro: IPR001267 Thymidine kinase (TK) (2

Probab=92.89  E-value=0.2  Score=50.64  Aligned_cols=35  Identities=20%  Similarity=0.188  Sum_probs=23.9

Q ss_pred             EEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccC
Q 002040          507 CIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPT  549 (976)
Q Consensus       507 ~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Pt  549 (976)
                      .++.|||+||||..++.-+.+. ..       .+.+++++-|.
T Consensus         4 ~~i~GpM~sGKS~eLi~~~~~~-~~-------~~~~v~~~kp~   38 (176)
T PF00265_consen    4 EFITGPMFSGKSTELIRRIHRY-EI-------AGKKVLVFKPA   38 (176)
T ss_dssp             EEEEESTTSSHHHHHHHHHHHH-HH-------TT-EEEEEEES
T ss_pred             EEEECCcCChhHHHHHHHHHHH-Hh-------CCCeEEEEEec
Confidence            5788999999998754444333 22       25678898885

7.1.21 from EC) is an ubiquitous enzyme that catalyzes the ATP-dependent phosphorylation of thymidine. Two different families of Thymidine kinase have been identified [, ] and are represented in this entry; one groups together Thymidine kinase from herpesviruses, as well as cytosolic thymidylate kinases and the second family groups Thymidine kinase from various sources that include, vertebrates, bacteria, the Bacteriophage T4, poxviruses, African swine fever virus (ASFV) and Fish lymphocystis disease virus (FLDV). The major capsid protein of insect iridescent viruses also belongs to this family.; GO: 0004797 thymidine kinase activity, 0005524 ATP binding; PDB: 1XX6_B 2J9R_A 2J87_B 3E2I_A 2JA1_A 2UZ3_B 2B8T_B 2WVJ_A 1W4R_F 1XBT_F ....

>PF02572 CobA_CobO_BtuR: ATP:corrinoid adenosyltransferase BtuR/CobO/CobP; InterPro: IPR003724 ATP:cob(I)alamin (or ATP:corrinoid) adenosyltransferases (2

Probab=92.87  E-value=0.8  Score=45.84  Aligned_cols=52  Identities=17%  Similarity=0.270  Sum_probs=33.3

Q ss_pred             cCCceEEEecCcccccccCCch--HHHHHHHhcCCCCcEEEEeccCcHHHHHHH
Q 002040          615 LRRVTYLVMDEADRMFDMGFEP--QITRIVQNIRPDRQTVLFSATFPRQVEILA  666 (976)
Q Consensus       615 l~~~~~vVlDEah~~~~~~f~~--~i~~il~~~~~~~q~i~~SAT~~~~~~~l~  666 (976)
                      -..+++|||||+-..++.++..  .+..++...++..-+|++.-.+|+.+..++
T Consensus        94 ~~~~dlvILDEi~~a~~~gll~~~~v~~~l~~rp~~~evVlTGR~~~~~l~e~A  147 (172)
T PF02572_consen   94 SGEYDLVILDEINYAVDYGLLSEEEVLDLLENRPESLEVVLTGRNAPEELIEAA  147 (172)
T ss_dssp             -TT-SEEEEETHHHHHHTTSS-HHHHHHHHHTS-TT-EEEEE-SS--HHHHHH-
T ss_pred             CCCCCEEEEcchHHHhHCCCccHHHHHHHHHcCCCCeEEEEECCCCCHHHHHhC
Confidence            3568999999999888888654  466777777677777777777887766554

5.1.17 from EC), catalyse the conversion of cobalamin (vitamin B12) into its coenzyme form, adenosylcobalamin (coenzyme B12) []. Adenosylcobalamin (AdoCbl) is required for the ativity of certain enzymes. AdoCbl contains an adenosyl moiety liganded to the cobalt ion of cobalamin via a covalent Co-C bond, and its synthesis is unique to certain prokaryotes. ATP:cob(I)alamin adenosyltransferases are classed into three groups: CobA-type [], EutT-type [] and PduO-type []. Each of the three enzyme types appears to be specialised for particular AdoCbl-dependent enzymes or for the de novo synthesis AdoCbl. PduO and EutT are distantly related, sharing short conserved motifs, while CobA is evolutionarily unrelated and is an example of convergent evolution. This entry represents the ATP:cob(I)alamin adenosyltransferases CobA (Salmonella typhimurium), CobO (Pseudomonas denitrificans), and ButR (Escherichia coli). There is a high degree of sequence identity between these proteins []. CobA is responsible for attaching the adenosyl moiety from ATP to the cobalt ion of the corrin ring, necessary for the convertion of cobalamin to adenosylcobalamin [, ]. ; GO: 0005524 ATP binding, 0008817 cob(I)yrinic acid a,c-diamide adenosyltransferase activity, 0009236 cobalamin biosynthetic process; PDB: 1G64_A 1G5T_A 1G5R_A.

>PRK14951 DNA polymerase III subunits gamma and tau; Provisional

Probab=92.81  E-value=0.23  Score=59.93  Aligned_cols=19  Identities=21%  Similarity=0.163  Sum_probs=15.5

Q ss_pred             EEEEcCCCCchHHHHHHHH
Q 002040          507 CIGVAKTGSGKTLAFVLPM  525 (976)
Q Consensus       507 ~i~~a~TGsGKT~~~~l~i  525 (976)
                      +|++|+.|+|||+++.+.+
T Consensus        41 ~Lf~Gp~GvGKTtlAr~lA   59 (618)
T PRK14951         41 YLFTGTRGVGKTTVSRILA   59 (618)
T ss_pred             EEEECCCCCCHHHHHHHHH
Confidence            6899999999998755543

>COG0593 DnaA ATPase involved in DNA replication initiation [DNA replication, recombination, and repair]

Probab=92.78  E-value=0.43  Score=54.24  Aligned_cols=47  Identities=15%  Similarity=0.240  Sum_probs=32.5

Q ss_pred             CceEEEecCccccccc-CCchHHHHHHHhcCCCC-cEEEEeccCcHHHH
Q 002040          617 RVTYLVMDEADRMFDM-GFEPQITRIVQNIRPDR-QTVLFSATFPRQVE  663 (976)
Q Consensus       617 ~~~~vVlDEah~~~~~-~f~~~i~~il~~~~~~~-q~i~~SAT~~~~~~  663 (976)
                      ++++|+||.++.+... .....+..+++.+.... |+|+.|..+|..+.
T Consensus       175 ~~dlllIDDiq~l~gk~~~qeefFh~FN~l~~~~kqIvltsdr~P~~l~  223 (408)
T COG0593         175 SLDLLLIDDIQFLAGKERTQEEFFHTFNALLENGKQIVLTSDRPPKELN  223 (408)
T ss_pred             ccCeeeechHhHhcCChhHHHHHHHHHHHHHhcCCEEEEEcCCCchhhc
Confidence            5889999999977654 23455666677665543 77777777777654

>PTZ00454 26S protease regulatory subunit 6B-like protein; Provisional

Probab=92.77  E-value=0.32  Score=55.82  Aligned_cols=54  Identities=22%  Similarity=0.246  Sum_probs=31.1

Q ss_pred             cccccccCCCCHHHHHHHHH---cCCCCCcHHHHHHHHHHhcCCCEEEEcCCCCchHHHH
Q 002040          465 PIKTWHQTGLTSKIMETIRK---LNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAF  521 (976)
Q Consensus       465 pi~~~~~~~l~~~l~~~l~~---~~~~~p~~~Q~~~i~~il~g~d~i~~a~TGsGKT~~~  521 (976)
                      |-.+|.+.+-.....+.|..   +.+..|.-++.-.+   ...+.+++.||+|+|||+.+
T Consensus       140 p~v~~~digGl~~~k~~l~~~v~~pl~~~~~~~~~Gl---~~pkgvLL~GppGTGKT~LA  196 (398)
T PTZ00454        140 PDVTYSDIGGLDIQKQEIREAVELPLTCPELYEQIGI---DPPRGVLLYGPPGTGKTMLA  196 (398)
T ss_pred             CCCCHHHcCCHHHHHHHHHHHHHHHhcCHHHHHhcCC---CCCceEEEECCCCCCHHHHH
Confidence            44567777665555544443   22332222222211   23578999999999999853

>PRK14957 DNA polymerase III subunits gamma and tau; Provisional

Probab=92.76  E-value=0.66  Score=55.29  Aligned_cols=40  Identities=10%  Similarity=0.095  Sum_probs=24.3

Q ss_pred             cCCceEEEecCcccccccCCchHHHHHHHhcCCCCcEEEEe
Q 002040          615 LRRVTYLVMDEADRMFDMGFEPQITRIVQNIRPDRQTVLFS  655 (976)
Q Consensus       615 l~~~~~vVlDEah~~~~~~f~~~i~~il~~~~~~~q~i~~S  655 (976)
                      .....+|||||||+|.... ...+..++...+....+|+.|
T Consensus       117 ~g~~kViIIDEa~~ls~~a-~naLLK~LEepp~~v~fIL~T  156 (546)
T PRK14957        117 QGRYKVYLIDEVHMLSKQS-FNALLKTLEEPPEYVKFILAT  156 (546)
T ss_pred             cCCcEEEEEechhhccHHH-HHHHHHHHhcCCCCceEEEEE
Confidence            3467899999999875433 234445555544444445444

>PF05707 Zot: Zonular occludens toxin (Zot); InterPro: IPR008900 This entry consists of bacterial and viral proteins which are very similar to the Zonular occludens toxin (Zot)

Probab=92.66  E-value=0.23  Score=51.06  Aligned_cols=50  Identities=22%  Similarity=0.353  Sum_probs=24.4

Q ss_pred             CceEEEecCcccccccCCc-----hHHHHHHHhcCCC-CcEEEEeccCcHHHHHHHH
Q 002040          617 RVTYLVMDEADRMFDMGFE-----PQITRIVQNIRPD-RQTVLFSATFPRQVEILAR  667 (976)
Q Consensus       617 ~~~~vVlDEah~~~~~~f~-----~~i~~il~~~~~~-~q~i~~SAT~~~~~~~l~~  667 (976)
                      .-++|||||||.+++....     +.+...+...+.. ..++++|-.+ ..+...++
T Consensus        79 ~~~liviDEa~~~~~~r~~~~~~~~~~~~~l~~hRh~g~diiliTQ~~-~~id~~ir  134 (193)
T PF05707_consen   79 KGSLIVIDEAQNFFPSRSWKGKKVPEIIEFLAQHRHYGWDIILITQSP-SQIDKFIR  134 (193)
T ss_dssp             TT-EEEETTGGGTSB---T-T----HHHHGGGGCCCTT-EEEEEES-G-GGB-HHHH
T ss_pred             CCcEEEEECChhhcCCCccccccchHHHHHHHHhCcCCcEEEEEeCCH-HHHhHHHH
Confidence            4579999999987765433     2233444444443 4455555554 34443333

Zot is elaborated by bacteriophage present in toxigenic strains of Vibrio cholerae. Zot is a single polypeptide chain of 44.8 kDa, with the ability to reversibly alter intestinal epithelial tight junctions, allowing the passage of macromolecules through mucosal barriers.; PDB: 2R2A_B.

>TIGR03878 thermo_KaiC_2 KaiC domain protein, AF_0795 family

Probab=92.65  E-value=0.71  Score=49.92  Aligned_cols=37  Identities=14%  Similarity=0.037  Sum_probs=25.3

Q ss_pred             cCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEc
Q 002040          503 SGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMA  547 (976)
Q Consensus       503 ~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~  547 (976)
                      .|.-++|.|++|+|||+..+..+.+.+.        .|..+++++
T Consensus        35 ~gs~~lI~G~pGtGKT~l~~qf~~~~a~--------~Ge~vlyis   71 (259)
T TIGR03878        35 AYSVINITGVSDTGKSLMVEQFAVTQAS--------RGNPVLFVT   71 (259)
T ss_pred             CCcEEEEEcCCCCCHHHHHHHHHHHHHh--------CCCcEEEEE
Confidence            3456889999999999865554454432        245677776

This KaiC domain-containing protein family occurs sporadically across a broad taxonomic range (Euryarchaeota, Aquificae, Dictyoglomi, Epsilonproteobacteria, and Firmicutes), but exclusively in thermophiles.

>PRK07940 DNA polymerase III subunit delta'; Validated

Probab=92.65  E-value=0.22  Score=57.13  Aligned_cols=44  Identities=23%  Similarity=0.373  Sum_probs=25.9

Q ss_pred             cCCceEEEecCcccccccCCchHHHHHHHhcCCCCcEEEEeccCcH
Q 002040          615 LRRVTYLVMDEADRMFDMGFEPQITRIVQNIRPDRQTVLFSATFPR  660 (976)
Q Consensus       615 l~~~~~vVlDEah~~~~~~f~~~i~~il~~~~~~~q~i~~SAT~~~  660 (976)
                      ...+.++||||||+|.... ...+..++..-++.. ++++++|-+.
T Consensus       115 ~~~~kViiIDead~m~~~a-anaLLk~LEep~~~~-~fIL~a~~~~  158 (394)
T PRK07940        115 TGRWRIVVIEDADRLTERA-ANALLKAVEEPPPRT-VWLLCAPSPE  158 (394)
T ss_pred             cCCcEEEEEechhhcCHHH-HHHHHHHhhcCCCCC-eEEEEECChH
Confidence            3467899999999985432 234555555544444 4445555333

>COG2255 RuvB Holliday junction resolvasome, helicase subunit [DNA replication, recombination, and repair]

Probab=92.63  E-value=0.3  Score=51.95  Aligned_cols=27  Identities=41%  Similarity=0.613  Sum_probs=20.1

Q ss_pred             CchhHHHHHHhcCCcccccCCceEEEecCccccc
Q 002040          597 TPGRMIDILCTSGGKITNLRRVTYLVMDEADRMF  630 (976)
Q Consensus       597 Tp~~L~~~l~~~~~~~~~l~~~~~vVlDEah~~~  630 (976)
                      -|+-|..+|       ++|..-+++.|||+|++.
T Consensus        90 K~gDlaaiL-------t~Le~~DVLFIDEIHrl~  116 (332)
T COG2255          90 KPGDLAAIL-------TNLEEGDVLFIDEIHRLS  116 (332)
T ss_pred             ChhhHHHHH-------hcCCcCCeEEEehhhhcC
Confidence            455566666       467777899999999974

>CHL00181 cbbX CbbX; Provisional

Probab=92.61  E-value=0.89  Score=49.91  Aligned_cols=21  Identities=24%  Similarity=0.189  Sum_probs=16.7

Q ss_pred             CCCEEEEcCCCCchHHHHHHH
Q 002040          504 GRDCIGVAKTGSGKTLAFVLP  524 (976)
Q Consensus       504 g~d~i~~a~TGsGKT~~~~l~  524 (976)
                      +.++++.|++|+|||+++...
T Consensus        59 ~~~ill~G~pGtGKT~lAr~l   79 (287)
T CHL00181         59 GLHMSFTGSPGTGKTTVALKM   79 (287)
T ss_pred             CceEEEECCCCCCHHHHHHHH
Confidence            456899999999999875443

>PRK14969 DNA polymerase III subunits gamma and tau; Provisional

Probab=92.58  E-value=0.8  Score=54.75  Aligned_cols=40  Identities=13%  Similarity=0.223  Sum_probs=24.3

Q ss_pred             cCCceEEEecCcccccccCCchHHHHHHHhcCCCCcEEEEe
Q 002040          615 LRRVTYLVMDEADRMFDMGFEPQITRIVQNIRPDRQTVLFS  655 (976)
Q Consensus       615 l~~~~~vVlDEah~~~~~~f~~~i~~il~~~~~~~q~i~~S  655 (976)
                      ...+.++||||+|.|....+ ..+...+...+....+|+.|
T Consensus       117 ~~~~kVvIIDEad~ls~~a~-naLLK~LEepp~~~~fIL~t  156 (527)
T PRK14969        117 RGRFKVYIIDEVHMLSKSAF-NAMLKTLEEPPEHVKFILAT  156 (527)
T ss_pred             cCCceEEEEcCcccCCHHHH-HHHHHHHhCCCCCEEEEEEe
Confidence            34678999999998764332 23444555544455455544

>PF06745 KaiC: KaiC; InterPro: IPR014774 This entry represents a domain within bacterial and archaeal proteins, most of which are hypothetical

Probab=92.56  E-value=0.28  Score=51.80  Aligned_cols=51  Identities=20%  Similarity=0.235  Sum_probs=32.2

Q ss_pred             CCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHH
Q 002040          504 GRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRK  562 (976)
Q Consensus       504 g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~  562 (976)
                      |..+++.|++|+|||+..+..+.+.+...       |..|++++- .+-..++.+.+..
T Consensus        19 gs~~li~G~~GsGKT~l~~q~l~~~~~~~-------ge~vlyvs~-ee~~~~l~~~~~s   69 (226)
T PF06745_consen   19 GSVVLISGPPGSGKTTLALQFLYNGLKNF-------GEKVLYVSF-EEPPEELIENMKS   69 (226)
T ss_dssp             TSEEEEEESTTSSHHHHHHHHHHHHHHHH-------T--EEEEES-SS-HHHHHHHHHT
T ss_pred             CcEEEEEeCCCCCcHHHHHHHHHHhhhhc-------CCcEEEEEe-cCCHHHHHHHHHH
Confidence            45789999999999987666666665540       335677663 3334555555554

More than one copy is sometimes found in each protein in this entry. These include KaiC, which is one of the Kai proteins among which direct protein-protein association may be a critical process in the generation of circadian rhythms in cyanobacteria []. The circadian clock protein KaiC, is encoded in the kaiABC operon that controls circadian rhythms and may be universal in Cyanobacteria. Each member contains two copies of this domain, which is also found in other proteins. KaiC performs autophosphorylation and acts as its own transcriptional repressor. RadA/Sms is a highly conserved eubacterial protein that shares sequence similarity with both RecA strand transferase and lon protease. The RadA/Sms family are probable ATP-dependent proteases involved in both DNA repair and degradation of proteins, peptides, glycopeptides. They are classified in as non-peptidase homologues and unassigned peptidases in MEROPS peptidase family S16 (lon protease family, clan SJ). RadA/Sms is involved in recombination and recombinational repair, most likely involving the stabilisation or processing of branched DNA molecules or blocked replication forks because of its genetic redundancy with RecG and RuvABC [].; PDB: 2W0M_A 2ZTS_C 4DUG_B 3K0E_B 3K09_B 3S1A_E 3JZM_E 2GBL_B 3DVL_A 1TF7_C ....

>PRK09112 DNA polymerase III subunit delta'; Validated

Probab=92.47  E-value=0.75  Score=51.97  Aligned_cols=41  Identities=17%  Similarity=0.157  Sum_probs=25.8

Q ss_pred             cCCceEEEecCcccccccCCchHHHHHHHhcCCCCcEEEEec
Q 002040          615 LRRVTYLVMDEADRMFDMGFEPQITRIVQNIRPDRQTVLFSA  656 (976)
Q Consensus       615 l~~~~~vVlDEah~~~~~~f~~~i~~il~~~~~~~q~i~~SA  656 (976)
                      ...+.+|||||||.|.... ...+..++...+....+|++|.
T Consensus       139 ~g~~rVviIDeAd~l~~~a-anaLLk~LEEpp~~~~fiLit~  179 (351)
T PRK09112        139 DGNWRIVIIDPADDMNRNA-ANAILKTLEEPPARALFILISH  179 (351)
T ss_pred             cCCceEEEEEchhhcCHHH-HHHHHHHHhcCCCCceEEEEEC
Confidence            3467899999999875332 3445566666444555555553

>PRK06964 DNA polymerase III subunit delta'; Validated

Probab=92.47  E-value=0.72  Score=51.70  Aligned_cols=35  Identities=14%  Similarity=0.054  Sum_probs=25.5

Q ss_pred             cHHHHHHHHHHhc--C---CCEEEEcCCCCchHHHHHHHH
Q 002040          491 MPIQAQALPVIMS--G---RDCIGVAKTGSGKTLAFVLPM  525 (976)
Q Consensus       491 ~~~Q~~~i~~il~--g---~d~i~~a~TGsGKT~~~~l~i  525 (976)
                      +|+|...+..+..  +   +-+|+.|+.|.|||..+...+
T Consensus         3 yPW~~~~~~~l~~~~~rl~ha~Lf~Gp~G~GK~~lA~~~A   42 (342)
T PRK06964          3 YPWQTDDWNRLQALRARLPHALLLHGQAGIGKLDFAQHLA   42 (342)
T ss_pred             CcccHHHHHHHHHhcCCcceEEEEECCCCCCHHHHHHHHH
Confidence            5777777777664  2   358899999999998654444

>PRK14965 DNA polymerase III subunits gamma and tau; Provisional

Probab=92.37  E-value=0.54  Score=56.88  Aligned_cols=43  Identities=14%  Similarity=0.245  Sum_probs=25.1

Q ss_pred             cCCceEEEecCcccccccCCchHHHHHHHhcCCCCcEEEEeccCc
Q 002040          615 LRRVTYLVMDEADRMFDMGFEPQITRIVQNIRPDRQTVLFSATFP  659 (976)
Q Consensus       615 l~~~~~vVlDEah~~~~~~f~~~i~~il~~~~~~~q~i~~SAT~~  659 (976)
                      ...+.++||||+|.|.... ...+..++..-++...+|+ .+|-+
T Consensus       117 ~~~~KVvIIdev~~Lt~~a-~naLLk~LEepp~~~~fIl-~t~~~  159 (576)
T PRK14965        117 RSRYKIFIIDEVHMLSTNA-FNALLKTLEEPPPHVKFIF-ATTEP  159 (576)
T ss_pred             cCCceEEEEEChhhCCHHH-HHHHHHHHHcCCCCeEEEE-EeCCh
Confidence            4568899999999775332 2344555555444444444 44533

>PRK14963 DNA polymerase III subunits gamma and tau; Provisional

Probab=92.20  E-value=0.59  Score=55.41  Aligned_cols=23  Identities=22%  Similarity=0.225  Sum_probs=16.7

Q ss_pred             EEEEcCCCCchHHHHHHHHHHHHh
Q 002040          507 CIGVAKTGSGKTLAFVLPMLRHIK  530 (976)
Q Consensus       507 ~i~~a~TGsGKT~~~~l~il~~l~  530 (976)
                      +|++||.|+|||+++.+ +...+.
T Consensus        39 ~Lf~GppGtGKTTlA~~-lA~~l~   61 (504)
T PRK14963         39 YLFSGPRGVGKTTTARL-IAMAVN   61 (504)
T ss_pred             EEEECCCCCCHHHHHHH-HHHHHh
Confidence            59999999999987543 344443

>PRK11823 DNA repair protein RadA; Provisional

Probab=92.18  E-value=0.68  Score=54.18  Aligned_cols=50  Identities=20%  Similarity=0.181  Sum_probs=31.0

Q ss_pred             CCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHH
Q 002040          504 GRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRK  562 (976)
Q Consensus       504 g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~  562 (976)
                      |.-+++.|++|+|||+..+..+.... .       .+.++|++.- .+-..|+...+..
T Consensus        80 Gs~~lI~G~pG~GKTtL~lq~a~~~a-~-------~g~~vlYvs~-Ees~~qi~~ra~r  129 (446)
T PRK11823         80 GSVVLIGGDPGIGKSTLLLQVAARLA-A-------AGGKVLYVSG-EESASQIKLRAER  129 (446)
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHHHH-h-------cCCeEEEEEc-cccHHHHHHHHHH
Confidence            45678899999999986544444332 2       2456778774 3444566554444

>TIGR02782 TrbB_P P-type conjugative transfer ATPase TrbB

Probab=92.13  E-value=0.51  Score=52.07  Aligned_cols=64  Identities=25%  Similarity=0.253  Sum_probs=40.0

Q ss_pred             HHHcCCCCCcHHHHHHHHHH-hcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHH
Q 002040          482 IRKLNYEKPMPIQAQALPVI-MSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELV  553 (976)
Q Consensus       482 l~~~~~~~p~~~Q~~~i~~i-l~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La  553 (976)
                      |...|.  +++.|...|..+ ..+.++|++|+||||||+. +-.++..+...+     ...+++++-.+.+|.
T Consensus       111 l~~~g~--~~~~~~~~L~~~v~~~~~ilI~G~tGSGKTTl-l~al~~~i~~~~-----~~~ri~tiEd~~El~  175 (299)
T TIGR02782       111 YVEAGI--MTAAQRDVLREAVLARKNILVVGGTGSGKTTL-ANALLAEIAKND-----PTDRVVIIEDTRELQ  175 (299)
T ss_pred             HHhcCC--CCHHHHHHHHHHHHcCCeEEEECCCCCCHHHH-HHHHHHHhhccC-----CCceEEEECCchhhc
Confidence            344443  345555555544 4567899999999999975 455555544321     134577777777763

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.

>PRK05563 DNA polymerase III subunits gamma and tau; Validated

Probab=92.10  E-value=0.49  Score=56.97  Aligned_cols=21  Identities=24%  Similarity=0.178  Sum_probs=16.3

Q ss_pred             CCEEEEcCCCCchHHHHHHHH
Q 002040          505 RDCIGVAKTGSGKTLAFVLPM  525 (976)
Q Consensus       505 ~d~i~~a~TGsGKT~~~~l~i  525 (976)
                      +-+|++||.|+|||.++-+.+
T Consensus        39 hayLf~Gp~GtGKTt~Ak~lA   59 (559)
T PRK05563         39 HAYLFSGPRGTGKTSAAKIFA   59 (559)
T ss_pred             eEEEEECCCCCCHHHHHHHHH
Confidence            347889999999998755444

>COG2909 MalT ATP-dependent transcriptional regulator [Transcription]

Probab=92.09  E-value=0.26  Score=59.71  Aligned_cols=44  Identities=18%  Similarity=0.280  Sum_probs=38.0

Q ss_pred             CceEEEecCcccccccCCchHHHHHHHhcCCCCcEEEEeccCcH
Q 002040          617 RVTYLVMDEADRMFDMGFEPQITRIVQNIRPDRQTVLFSATFPR  660 (976)
Q Consensus       617 ~~~~vVlDEah~~~~~~f~~~i~~il~~~~~~~q~i~~SAT~~~  660 (976)
                      ..-|+|||.-|++.+...-..+..++.+.+++.++|+.|-+-|+
T Consensus       129 ~pl~LVlDDyHli~~~~l~~~l~fLl~~~P~~l~lvv~SR~rP~  172 (894)
T COG2909         129 GPLYLVLDDYHLISDPALHEALRFLLKHAPENLTLVVTSRSRPQ  172 (894)
T ss_pred             CceEEEeccccccCcccHHHHHHHHHHhCCCCeEEEEEeccCCC
Confidence            34699999999999888788899999999999999999987554

>COG2109 BtuR ATP:corrinoid adenosyltransferase [Coenzyme metabolism]

Probab=92.08  E-value=0.84  Score=45.71  Aligned_cols=53  Identities=15%  Similarity=0.322  Sum_probs=38.9

Q ss_pred             CceEEEecCcccccccCCch--HHHHHHHhcCCCCcEEEEeccCcHHHHHHHHHH
Q 002040          617 RVTYLVMDEADRMFDMGFEP--QITRIVQNIRPDRQTVLFSATFPRQVEILARKV  669 (976)
Q Consensus       617 ~~~~vVlDEah~~~~~~f~~--~i~~il~~~~~~~q~i~~SAT~~~~~~~l~~~~  669 (976)
                      .+++||+||.--.+..++.+  .+..++...+....+|++.-..|+.+..++...
T Consensus       122 ~ydlviLDEl~~al~~g~l~~eeV~~~l~~kP~~~~vIiTGr~ap~~lie~ADlV  176 (198)
T COG2109         122 KYDLVILDELNYALRYGLLPLEEVVALLKARPEHTHVIITGRGAPPELIELADLV  176 (198)
T ss_pred             CCCEEEEehhhHHHHcCCCCHHHHHHHHhcCCCCcEEEEECCCCCHHHHHHHHHH
Confidence            58999999999888888654  466677766666666666666888877666543

>PRK11034 clpA ATP-dependent Clp protease ATP-binding subunit; Provisional

Probab=92.06  E-value=1.1  Score=55.85  Aligned_cols=45  Identities=11%  Similarity=0.237  Sum_probs=27.0

Q ss_pred             ceEEEecCcccccccCC----chHHHHHHHhcCCCCcEEEEeccCcHHH
Q 002040          618 VTYLVMDEADRMFDMGF----EPQITRIVQNIRPDRQTVLFSATFPRQV  662 (976)
Q Consensus       618 ~~~vVlDEah~~~~~~f----~~~i~~il~~~~~~~q~i~~SAT~~~~~  662 (976)
                      ..+|+|||+|.++..+-    ...+..++..+-....+.++.||-++..
T Consensus       279 ~~ILfIDEIh~L~g~g~~~~g~~d~~nlLkp~L~~g~i~vIgATt~~E~  327 (758)
T PRK11034        279 NSILFIDEIHTIIGAGAASGGQVDAANLIKPLLSSGKIRVIGSTTYQEF  327 (758)
T ss_pred             CCEEEeccHHHHhccCCCCCcHHHHHHHHHHHHhCCCeEEEecCChHHH
Confidence            35899999998876542    1223344444433455677777765553

>PRK06871 DNA polymerase III subunit delta'; Validated

Probab=91.99  E-value=1  Score=50.20  Aligned_cols=42  Identities=12%  Similarity=0.192  Sum_probs=26.2

Q ss_pred             cCCceEEEecCcccccccCCchHHHHHHHhcCCCCcEEEEecc
Q 002040          615 LRRVTYLVMDEADRMFDMGFEPQITRIVQNIRPDRQTVLFSAT  657 (976)
Q Consensus       615 l~~~~~vVlDEah~~~~~~f~~~i~~il~~~~~~~q~i~~SAT  657 (976)
                      ...+.++|||+||.|... -...+.+++..-++...+|++|..
T Consensus       105 ~g~~KV~iI~~a~~m~~~-AaNaLLKtLEEPp~~~~fiL~t~~  146 (325)
T PRK06871        105 QGGNKVVYIQGAERLTEA-AANALLKTLEEPRPNTYFLLQADL  146 (325)
T ss_pred             cCCceEEEEechhhhCHH-HHHHHHHHhcCCCCCeEEEEEECC
Confidence            356789999999988533 244555666664555544444443

>PRK08699 DNA polymerase III subunit delta'; Validated

Probab=91.96  E-value=1.3  Score=49.63  Aligned_cols=36  Identities=19%  Similarity=0.158  Sum_probs=26.4

Q ss_pred             cHHHHHHHHHHhcC-----CCEEEEcCCCCchHHHHHHHHH
Q 002040          491 MPIQAQALPVIMSG-----RDCIGVAKTGSGKTLAFVLPML  526 (976)
Q Consensus       491 ~~~Q~~~i~~il~g-----~d~i~~a~TGsGKT~~~~l~il  526 (976)
                      +|+|...|..+...     ..+|+.||.|+|||..+...+-
T Consensus         3 yPW~~~~w~~l~~~~~r~~hA~Lf~G~~G~GK~~la~~~a~   43 (325)
T PRK08699          3 YPWHQEQWRQIAEHWERRPNAWLFAGKKGIGKTAFARFAAQ   43 (325)
T ss_pred             CCccHHHHHHHHHhcCCcceEEEeECCCCCCHHHHHHHHHH
Confidence            57788888777632     2488999999999987554443

>PRK14962 DNA polymerase III subunits gamma and tau; Provisional

Probab=91.95  E-value=1  Score=53.00  Aligned_cols=18  Identities=28%  Similarity=0.289  Sum_probs=14.8

Q ss_pred             CEEEEcCCCCchHHHHHH
Q 002040          506 DCIGVAKTGSGKTLAFVL  523 (976)
Q Consensus       506 d~i~~a~TGsGKT~~~~l  523 (976)
                      .+|++||+|+|||+.+.+
T Consensus        38 ~~Lf~GPpGtGKTTlA~~   55 (472)
T PRK14962         38 AYIFAGPRGTGKTTVARI   55 (472)
T ss_pred             EEEEECCCCCCHHHHHHH
Confidence            379999999999986544

>PRK05896 DNA polymerase III subunits gamma and tau; Validated

Probab=91.91  E-value=0.72  Score=55.17  Aligned_cols=21  Identities=24%  Similarity=0.094  Sum_probs=16.2

Q ss_pred             CCEEEEcCCCCchHHHHHHHH
Q 002040          505 RDCIGVAKTGSGKTLAFVLPM  525 (976)
Q Consensus       505 ~d~i~~a~TGsGKT~~~~l~i  525 (976)
                      +.+|+.||.|+|||..+.+.+
T Consensus        39 hA~Lf~GP~GvGKTTlA~~lA   59 (605)
T PRK05896         39 HAYIFSGPRGIGKTSIAKIFA   59 (605)
T ss_pred             ceEEEECCCCCCHHHHHHHHH
Confidence            358899999999998754433

>KOG1513 consensus Nuclear helicase MOP-3/SNO (DEAD-box superfamily) [Transcription; Signal transduction mechanisms]

Probab=91.89  E-value=0.19  Score=59.68  Aligned_cols=80  Identities=18%  Similarity=0.270  Sum_probs=59.6

Q ss_pred             HHHhccCCccEEEecCcccccCCCCCCcEEE--------EeCCCCCHHHHHHHhcccCCCCCc-cEEEEEecC---CCcC
Q 002040          757 ISDFKSNVCNLLIATSVAARGLDVKELELVI--------NFDAPNHYEDYVHRVGRTGRAGRK-GCAITFISE---EDAK  824 (976)
Q Consensus       757 ~~~F~~g~~~vLVaT~v~~~GlDi~~v~~VI--------~~d~p~s~~~y~Qr~GR~gR~g~~-g~~~~~~~~---~d~~  824 (976)
                      -+.|+.|...|-|-..+++-||-+..-..|+        -+.+||+....+|..||++|..+- +--|+|+..   .+..
T Consensus       850 KqrFM~GeK~vAIISEAaSSGiSLQsDrRv~NqRRRvHiTLELPWSADrAIQQFGRTHRSNQVsaPEYvFlIseLAGErR  929 (1300)
T KOG1513|consen  850 KQRFMDGEKLVAIISEAASSGISLQSDRRVQNQRRRVHITLELPWSADRAIQQFGRTHRSNQVSAPEYVFLISELAGERR  929 (1300)
T ss_pred             HhhhccccceeeeeehhhccCceeecchhhhhhhheEEEEEECCcchhHHHHHhcccccccccCCCeEEEEehhhccchH
Confidence            4689999999999999999999998755554        488999999999999999998763 444555432   2445


Q ss_pred             chHHHHHHHhhc
Q 002040          825 YSPDLVKALELS  836 (976)
Q Consensus       825 ~~~~i~~~l~~~  836 (976)
                      ++..+.+.|+.-
T Consensus       930 FAS~VAKRLESL  941 (1300)
T KOG1513|consen  930 FASIVAKRLESL  941 (1300)
T ss_pred             HHHHHHHHHHhh
Confidence            555555555544

>COG4962 CpaF Flp pilus assembly protein, ATPase CpaF [Intracellular trafficking and secretion]

Probab=91.88  E-value=0.39  Score=52.75  Aligned_cols=60  Identities=22%  Similarity=0.166  Sum_probs=42.2

Q ss_pred             CCCCCcHHHHHHHHHHhcCC-CEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHH
Q 002040          486 NYEKPMPIQAQALPVIMSGR-DCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQ  554 (976)
Q Consensus       486 ~~~~p~~~Q~~~i~~il~g~-d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~  554 (976)
                      .|...++-|...+-.+...+ ++|++|.||||||+. +-+++.++-        ..-+++++--|.+|-.
T Consensus       154 ~~gt~~~~~a~~L~~av~~r~NILisGGTGSGKTTl-LNal~~~i~--------~~eRvItiEDtaELql  214 (355)
T COG4962         154 IFGTMIRRAAKFLRRAVGIRCNILISGGTGSGKTTL-LNALSGFID--------SDERVITIEDTAELQL  214 (355)
T ss_pred             HcCCcCHHHHHHHHHHHhhceeEEEeCCCCCCHHHH-HHHHHhcCC--------CcccEEEEeehhhhcc
Confidence            45578889998888877665 999999999999974 222322211        2237788888877744

>COG0470 HolB ATPase involved in DNA replication [DNA replication, recombination, and repair]

Probab=91.80  E-value=0.53  Score=52.62  Aligned_cols=26  Identities=19%  Similarity=0.200  Sum_probs=18.7

Q ss_pred             CC-EEEEcCCCCchHHHHHHHHHHHHhc
Q 002040          505 RD-CIGVAKTGSGKTLAFVLPMLRHIKD  531 (976)
Q Consensus       505 ~d-~i~~a~TGsGKT~~~~l~il~~l~~  531 (976)
                      .. +|+.||.|+|||.++. .+...+..
T Consensus        24 ~halL~~Gp~G~Gktt~a~-~lA~~l~~   50 (325)
T COG0470          24 PHALLFYGPPGVGKTTAAL-ALAKELLC   50 (325)
T ss_pred             CceeeeeCCCCCCHHHHHH-HHHHHHhC
Confidence            45 8999999999998744 44444443

>KOG0739 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=91.74  E-value=2.5  Score=45.27  Aligned_cols=127  Identities=16%  Similarity=0.261  Sum_probs=70.9

Q ss_pred             HHHHhcCC-----CEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHHHHhhcCcEEE
Q 002040          498 LPVIMSGR-----DCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVMGVRCV  572 (976)
Q Consensus       498 i~~il~g~-----d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~~~~~~~~~~~  572 (976)
                      +|.++.|+     .+|+.||+|+||+..+-  ++..-          ..-.++-+.+..|+..|.-+-.++.+.      
T Consensus       155 FPqlFtGkR~PwrgiLLyGPPGTGKSYLAK--AVATE----------AnSTFFSvSSSDLvSKWmGESEkLVkn------  216 (439)
T KOG0739|consen  155 FPQLFTGKRKPWRGILLYGPPGTGKSYLAK--AVATE----------ANSTFFSVSSSDLVSKWMGESEKLVKN------  216 (439)
T ss_pred             chhhhcCCCCcceeEEEeCCCCCcHHHHHH--HHHhh----------cCCceEEeehHHHHHHHhccHHHHHHH------
Confidence            45666664     58999999999996432  22210          113577778888887776554443221      


Q ss_pred             EeeCCCChHHHHHHHhcCCeEEEeCchhHHHHHHhcCCcccccCCceEEEecCcccccccCC---chHHHHH----HHhc
Q 002040          573 PVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMGF---EPQITRI----VQNI  645 (976)
Q Consensus       573 ~~~gg~~~~~~~~~l~~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDEah~~~~~~f---~~~i~~i----l~~~  645 (976)
                                                  |..+..        -+..++|.|||+|.+....-   .....+|    +.++
T Consensus       217 ----------------------------LFemAR--------e~kPSIIFiDEiDslcg~r~enEseasRRIKTEfLVQM  260 (439)
T KOG0739|consen  217 ----------------------------LFEMAR--------ENKPSIIFIDEIDSLCGSRSENESEASRRIKTEFLVQM  260 (439)
T ss_pred             ----------------------------HHHHHH--------hcCCcEEEeehhhhhccCCCCCchHHHHHHHHHHHHhh
Confidence                                        111211        12357899999997654321   1122222    2222


Q ss_pred             ----CCCCcEEEEeccCcHHH-HHHHHHHcCCCeEEEe
Q 002040          646 ----RPDRQTVLFSATFPRQV-EILARKVLNKPVEIQV  678 (976)
Q Consensus       646 ----~~~~q~i~~SAT~~~~~-~~l~~~~l~~~~~i~~  678 (976)
                          ..+--+|++.||-.|++ ...++.-+...++|.+
T Consensus       261 qGVG~d~~gvLVLgATNiPw~LDsAIRRRFekRIYIPL  298 (439)
T KOG0739|consen  261 QGVGNDNDGVLVLGATNIPWVLDSAIRRRFEKRIYIPL  298 (439)
T ss_pred             hccccCCCceEEEecCCCchhHHHHHHHHhhcceeccC
Confidence                23346899999976654 4445555555554443

>COG1110 Reverse gyrase [DNA replication, recombination, and repair]

Probab=91.73  E-value=0.42  Score=58.90  Aligned_cols=62  Identities=23%  Similarity=0.356  Sum_probs=53.0

Q ss_pred             cCCcEEEEecCHHHHHHHHHHHHHC----C-CCcee-ccCCCCHHHHHHHHHHhccCCccEEEecCcc
Q 002040          713 EKGKILIFVHSQEKCDALFRDLLKH----G-YPCLS-LHGAKDQTDRESTISDFKSNVCNLLIATSVA  774 (976)
Q Consensus       713 ~~~kvLIF~~s~~~~~~l~~~L~~~----~-~~~~~-lhg~~~~~~R~~~~~~F~~g~~~vLVaT~v~  774 (976)
                      .+.+++|.+||..-+.++++.|.+.    + +.+.. +||.|+..++..+++.|.+|.++|||+|+.+
T Consensus       124 kgkr~yii~PT~~Lv~Q~~~kl~~~~e~~~~~~~~~~yh~~l~~~ekee~le~i~~gdfdIlitTs~F  191 (1187)
T COG1110         124 KGKRVYIIVPTTTLVRQVYERLKKFAEDAGSLDVLVVYHSALPTKEKEEALERIESGDFDILITTSQF  191 (1187)
T ss_pred             cCCeEEEEecCHHHHHHHHHHHHHHHhhcCCcceeeeeccccchHHHHHHHHHHhcCCccEEEEeHHH
Confidence            4579999999999999999888765    2 44333 9999999999999999999999999999754

>KOG1133 consensus Helicase of the DEAD superfamily [Replication, recombination and repair]

Probab=91.73  E-value=0.23  Score=58.49  Aligned_cols=42  Identities=26%  Similarity=0.442  Sum_probs=35.8

Q ss_pred             CCcHHHHHHHHHHh----cCCCEEEEcCCCCchHHHHHHHHHHHHh
Q 002040          489 KPMPIQAQALPVIM----SGRDCIGVAKTGSGKTLAFVLPMLRHIK  530 (976)
Q Consensus       489 ~p~~~Q~~~i~~il----~g~d~i~~a~TGsGKT~~~~l~il~~l~  530 (976)
                      +|+.||.+.+..+.    .|+-.|+-.|||+|||+..+..++.+|.
T Consensus        15 ~PYdIQ~~lM~elyrvLe~GkIgIfESPTGTGKSLSLiCaaltWL~   60 (821)
T KOG1133|consen   15 TPYDIQEDLMRELYRVLEEGKIGIFESPTGTGKSLSLICAALTWLR   60 (821)
T ss_pred             CchhHHHHHHHHHHHHHhcCCeeeeeCCCCCCchHHHHHHHHHHHH
Confidence            68999999887765    6888999999999999998888777664

>PF10593 Z1: Z1 domain; InterPro: IPR018310 This entry represents the Z1 domain of unknown function that is found in a group of putative endonucleases

Probab=91.63  E-value=0.38  Score=51.13  Aligned_cols=87  Identities=14%  Similarity=0.288  Sum_probs=60.7

Q ss_pred             CCCceeccCCCCHHHHHHHHHHhccC----CccEEEecCcccccCCCCCCcEEEEeCCCCCHHHHHHHhcccC-CCCCcc
Q 002040          738 GYPCLSLHGAKDQTDRESTISDFKSN----VCNLLIATSVAARGLDVKELELVINFDAPNHYEDYVHRVGRTG-RAGRKG  812 (976)
Q Consensus       738 ~~~~~~lhg~~~~~~R~~~~~~F~~g----~~~vLVaT~v~~~GlDi~~v~~VI~~d~p~s~~~y~Qr~GR~g-R~g~~g  812 (976)
                      ++.+..++++.+...     -.|.++    ...|+|+-+.++|||+++++.+..+...+.+..++.|+.-=.| |.|-.+
T Consensus       110 ~~~v~~vNS~~~~~~-----ldy~~~~~~~~~~I~VGGn~LsRGlTleGL~vsYf~R~s~~~DTL~QmgRwFGYR~gY~d  184 (239)
T PF10593_consen  110 GIEVVVVNSGSSDDS-----LDYDDGENLGLNVIAVGGNKLSRGLTLEGLTVSYFLRNSKQYDTLMQMGRWFGYRPGYED  184 (239)
T ss_pred             CceEEEEeCCCcccc-----ccccccccCCceEEEECCccccCceeECCcEEEEecCCCchHHHHHHHhhcccCCccccc
Confidence            455555665443322     223333    3789999999999999999999999999998888888653233 777788


Q ss_pred             EEEEEecCCCcCchHHH
Q 002040          813 CAITFISEEDAKYSPDL  829 (976)
Q Consensus       813 ~~~~~~~~~d~~~~~~i  829 (976)
                      .|-+|+++.-...+..|
T Consensus       185 l~Ri~~~~~l~~~f~~i  201 (239)
T PF10593_consen  185 LCRIYMPEELYDWFRHI  201 (239)
T ss_pred             ceEEecCHHHHHHHHHH
Confidence            99999876543333333

This domain is found associated with a helicase domain of superfamily type II [].

>KOG0741 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=91.62  E-value=3.3  Score=47.81  Aligned_cols=69  Identities=20%  Similarity=0.160  Sum_probs=40.6

Q ss_pred             cCCCCHHHHHHHHHcCCCCCcHHHHHHHH----HHhcC--------CCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCC
Q 002040          471 QTGLTSKIMETIRKLNYEKPMPIQAQALP----VIMSG--------RDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAG  538 (976)
Q Consensus       471 ~~~l~~~l~~~l~~~~~~~p~~~Q~~~i~----~il~g--------~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~  538 (976)
                      .+|.+...+..+...|.-.-.|.-.+.+.    .+.+-        ..+|+.||.|||||..++-.++.          .
T Consensus       493 AFG~see~l~~~~~~Gmi~~g~~v~~il~~G~llv~qvk~s~~s~lvSvLl~Gp~~sGKTaLAA~iA~~----------S  562 (744)
T KOG0741|consen  493 AFGISEEDLERFVMNGMINWGPPVTRILDDGKLLVQQVKNSERSPLVSVLLEGPPGSGKTALAAKIALS----------S  562 (744)
T ss_pred             ccCCCHHHHHHHHhCCceeecccHHHHHhhHHHHHHHhhccccCcceEEEEecCCCCChHHHHHHHHhh----------c
Confidence            36777777776666555433333233322    22211        25899999999999765444331          2


Q ss_pred             CCCeEEEEccC
Q 002040          539 DGPVGLIMAPT  549 (976)
Q Consensus       539 ~~~~vLIl~Pt  549 (976)
                      .-|.+=|+.|.
T Consensus       563 ~FPFvKiiSpe  573 (744)
T KOG0741|consen  563 DFPFVKIISPE  573 (744)
T ss_pred             CCCeEEEeChH
Confidence            45777788884

>TIGR02880 cbbX_cfxQ probable Rubsico expression protein CbbX

Probab=91.60  E-value=0.59  Score=51.25  Aligned_cols=19  Identities=21%  Similarity=0.165  Sum_probs=16.1

Q ss_pred             CCCEEEEcCCCCchHHHHH
Q 002040          504 GRDCIGVAKTGSGKTLAFV  522 (976)
Q Consensus       504 g~d~i~~a~TGsGKT~~~~  522 (976)
                      +.++++.||+|+|||+++.
T Consensus        58 ~~~vll~G~pGTGKT~lA~   76 (284)
T TIGR02880        58 TLHMSFTGNPGTGKTTVAL   76 (284)
T ss_pred             CceEEEEcCCCCCHHHHHH
Confidence            4579999999999998753

Proteins in this family are now designated CbbX. Some previously were CfxQ (carbon fixation Q). Its gene is often found immmediately downstream of the Rubisco large and small chain genes, and it is suggested to be necessary for Rubisco expression. CbbX has been shown to be necessary for photoautotrophic growth. This protein belongs to the larger family of pfam00004, ATPase family Associated with various cellular Activities. Within that larger family, members of this family are most closely related to the stage V sporulation protein K, or SpoVK, in endospore-forming bacteria such as Bacillus subtilis.

>COG2804 PulE Type II secretory pathway, ATPase PulE/Tfp pilus assembly pathway, ATPase PilB [Cell motility and secretion / Intracellular trafficking and secretion]

Probab=91.60  E-value=0.32  Score=56.08  Aligned_cols=46  Identities=26%  Similarity=0.393  Sum_probs=31.6

Q ss_pred             HHHcCCCCCcHHHHHHHHHHhcCCC--EEEEcCCCCchHHHHHHHHHHHHhc
Q 002040          482 IRKLNYEKPMPIQAQALPVIMSGRD--CIGVAKTGSGKTLAFVLPMLRHIKD  531 (976)
Q Consensus       482 l~~~~~~~p~~~Q~~~i~~il~g~d--~i~~a~TGsGKT~~~~l~il~~l~~  531 (976)
                      |.++|+   ++.|...+..+++...  +|+.||||||||++ +..++..+..
T Consensus       237 l~~Lg~---~~~~~~~~~~~~~~p~GliLvTGPTGSGKTTT-LY~~L~~ln~  284 (500)
T COG2804         237 LEKLGM---SPFQLARLLRLLNRPQGLILVTGPTGSGKTTT-LYAALSELNT  284 (500)
T ss_pred             HHHhCC---CHHHHHHHHHHHhCCCeEEEEeCCCCCCHHHH-HHHHHHHhcC
Confidence            344454   5788888888776543  56779999999986 5555655543

>TIGR02639 ClpA ATP-dependent Clp protease ATP-binding subunit clpA

Probab=91.51  E-value=2.1  Score=53.69  Aligned_cols=21  Identities=24%  Similarity=0.112  Sum_probs=16.8

Q ss_pred             CCCEEEEcCCCCchHHHHHHH
Q 002040          504 GRDCIGVAKTGSGKTLAFVLP  524 (976)
Q Consensus       504 g~d~i~~a~TGsGKT~~~~l~  524 (976)
                      ..++|++|++|+|||..+-..
T Consensus       203 ~~n~lL~G~pG~GKT~l~~~l  223 (731)
T TIGR02639       203 KNNPLLVGEPGVGKTAIAEGL  223 (731)
T ss_pred             CCceEEECCCCCCHHHHHHHH
Confidence            358999999999999864433

>PRK14950 DNA polymerase III subunits gamma and tau; Provisional

Probab=91.50  E-value=2  Score=52.19  Aligned_cols=19  Identities=21%  Similarity=0.162  Sum_probs=15.1

Q ss_pred             CEEEEcCCCCchHHHHHHH
Q 002040          506 DCIGVAKTGSGKTLAFVLP  524 (976)
Q Consensus       506 d~i~~a~TGsGKT~~~~l~  524 (976)
                      .+|+.|+.|+|||+++.+.
T Consensus        40 a~Lf~Gp~G~GKTtlA~~l   58 (585)
T PRK14950         40 AYLFTGPRGVGKTSTARIL   58 (585)
T ss_pred             EEEEECCCCCCHHHHHHHH
Confidence            3689999999999875443

>PF05872 DUF853: Bacterial protein of unknown function (DUF853); InterPro: IPR008571 Members of this family have a P-loop containing nucleotide triphosphate hydrolases fold

Probab=91.49  E-value=0.38  Score=54.53  Aligned_cols=45  Identities=20%  Similarity=0.335  Sum_probs=30.4

Q ss_pred             ccCCceE-EEecCcccccccC---CchHHHHHHHhcCCC-CcEEEEeccC
Q 002040          614 NLRRVTY-LVMDEADRMFDMG---FEPQITRIVQNIRPD-RQTVLFSATF  658 (976)
Q Consensus       614 ~l~~~~~-vVlDEah~~~~~~---f~~~i~~il~~~~~~-~q~i~~SAT~  658 (976)
                      ++....+ +++||||.+|+..   +...|..++..++.. .-++++|-++
T Consensus       251 D~dkPklVfFfDEAHLLF~da~kall~~ieqvvrLIRSKGVGv~fvTQ~P  300 (502)
T PF05872_consen  251 DLDKPKLVFFFDEAHLLFNDAPKALLDKIEQVVRLIRSKGVGVYFVTQNP  300 (502)
T ss_pred             CCCCceEEEEEechhhhhcCCCHHHHHHHHHHHHHhhccCceEEEEeCCC
Confidence            4555565 5699999888654   666777777777654 4456666664

This family is restricted to bacterial proteins, none of which have currently been characterised.

>cd03239 ABC_SMC_head The structural maintenance of chromosomes (SMC) proteins are essential for successful chromosome transmission during replication and segregation of the genome in all organisms

Probab=91.41  E-value=0.18  Score=51.17  Aligned_cols=42  Identities=14%  Similarity=0.357  Sum_probs=29.4

Q ss_pred             CCceEEEecCcccccccCCchHHHHHHHhcCCC-CcEEEEecc
Q 002040          616 RRVTYLVMDEADRMFDMGFEPQITRIVQNIRPD-RQTVLFSAT  657 (976)
Q Consensus       616 ~~~~~vVlDEah~~~~~~f~~~i~~il~~~~~~-~q~i~~SAT  657 (976)
                      ....++|+||...-++......+..++..+... .++|+.|--
T Consensus       115 ~~p~llilDEp~~~LD~~~~~~i~~~L~~~~~~g~tiIiiSH~  157 (178)
T cd03239         115 KPSPFYVLDEIDAALDPTNRRRVSDMIKEMAKHTSQFIVITLK  157 (178)
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHHHHHHHhCCCEEEEEECC
Confidence            457899999999888776666666666655433 566666554

SMCs are generally present as single proteins in bacteria, and as at least six distinct proteins in eukaryotes. The proteins range in size from approximately 110 to 170 kDa, and each has five distinct domains: amino- and carboxy-terminal globular domains, which contain sequences characteristic of ATPases, two coiled-coil regions separating the terminal domains , and a central flexible hinge. SMC proteins function together with other proteins in a range of chromosomal transactions, including chromosome condensation, sister-chromatid cohesion, recombination, DNA repair, and epigenetic silencing of gene expression.

>PF03237 Terminase_6: Terminase-like family; InterPro: IPR004921 The terminase is a component of the molecular motor that translocates genomic DNA into empty capsids during DNA packaging []

Probab=91.33  E-value=1.8  Score=49.20  Aligned_cols=145  Identities=17%  Similarity=0.155  Sum_probs=61.8

Q ss_pred             EEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHH-HH---HHHHHHHhh-cCcEEEEeeCCCChHH
Q 002040          508 IGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQ-IH---SDIRKFAKV-MGVRCVPVYGGSGVAQ  582 (976)
Q Consensus       508 i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q-~~---~~~~~~~~~-~~~~~~~~~gg~~~~~  582 (976)
                      |+.++.|+|||.+.++.++.++...+.     ...++++ ||..-+.. +.   ..+..+... +.+...........  
T Consensus         1 ~i~~~r~~GKT~~~~~~~~~~~~~~~~-----~~~vi~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--   72 (384)
T PF03237_consen    1 LINGGRGSGKTTLIAIWFLWWALTRPP-----GRRVIIA-STYRQARDIFGRFWKGIIELLPSWFEIKFNEWNDRKII--   72 (384)
T ss_dssp             -EEE-SSS-HHHHHHHHHHHHHHSSSS-------EEEEE-ESSHHHHHHHHHHHHHHHHTS-TTTS--EEEE-SSEEE--
T ss_pred             CCcCCccccHHHHHHHHHHHHHhhCCC-----CcEEEEe-cCHHHHHHHHHHhHHHHHHHHHHhcCcccccCCCCcEE--
Confidence            577899999999988888887776431     2345555 66544443 22   223333322 12222211111100  


Q ss_pred             HHHHHhcCCeEEEeCchh--HHHHHHhcCCcccccCCceEEEecCcccccccCCchHHHHHHHhcCCCCcEEEEeccC--
Q 002040          583 QISELKRGTEIVVCTPGR--MIDILCTSGGKITNLRRVTYLVMDEADRMFDMGFEPQITRIVQNIRPDRQTVLFSATF--  658 (976)
Q Consensus       583 ~~~~l~~~~~Iiv~Tp~~--L~~~l~~~~~~~~~l~~~~~vVlDEah~~~~~~f~~~i~~il~~~~~~~q~i~~SAT~--  658 (976)
                          +..|..|.+++...  -..-+.        =..+++|||||+-.+.+..+...+...+..... ...+++|.|+  
T Consensus        73 ----~~nG~~i~~~~~~~~~~~~~~~--------G~~~~~i~iDE~~~~~~~~~~~~~~~~~~~~~~-~~~~~~s~p~~~  139 (384)
T PF03237_consen   73 ----LPNGSRIQFRGADSPDSGDNIR--------GFEYDLIIIDEAAKVPDDAFSELIRRLRATWGG-SIRMYISTPPNP  139 (384)
T ss_dssp             ----ETTS-EEEEES-----SHHHHH--------TS--SEEEEESGGGSTTHHHHHHHHHHHHCSTT---EEEEEE---S
T ss_pred             ----ecCceEEEEecccccccccccc--------ccccceeeeeecccCchHHHHHHHHhhhhcccC-cceEEeecCCCC
Confidence                13455666666332  111221        134789999998866443333333333222222 2222444443  


Q ss_pred             cHHHHHHHHHHcCCC
Q 002040          659 PRQVEILARKVLNKP  673 (976)
Q Consensus       659 ~~~~~~l~~~~l~~~  673 (976)
                      ...+..+........
T Consensus       140 ~~~~~~~~~~~~~~~  154 (384)
T PF03237_consen  140 GGWFYEIFQRNLDDD  154 (384)
T ss_dssp             SSHHHHHHHHHHCTS
T ss_pred             CCceeeeeehhhcCC
Confidence            234444555555444

The large subunit heterodimerises with the small terminase protein, which is docked on the capsid portal protein. The latter forms a ring through which genomic DNA is translocated into the capsid. The terminase protein may have or induce an endonuclease activity to cleave DNA after encapsidation. This entry represents a family of terminase large subunits found in a variety of the Caudovirales and prophage regions of bacterial genomes. Homologues are also found in Gene Transfer Agents (GTA) [], including ORFg2 (RCAP_rcc01683) of the GTA of Rhodobacter capsulatus (Rhodopseudomonas capsulata) [see Fig.1, in ].; PDB: 2O0K_A 3CPE_A 2O0J_A 2O0H_A 3C6H_A 3C6A_A.

>TIGR00767 rho transcription termination factor Rho

Probab=91.32  E-value=0.57  Score=53.07  Aligned_cols=28  Identities=25%  Similarity=0.294  Sum_probs=20.6

Q ss_pred             hcCCCEEEEcCCCCchHHHHHHHHHHHHh
Q 002040          502 MSGRDCIGVAKTGSGKTLAFVLPMLRHIK  530 (976)
Q Consensus       502 l~g~d~i~~a~TGsGKT~~~~l~il~~l~  530 (976)
                      -.|+-++|+|++|+|||+. +..+...+.
T Consensus       166 g~Gq~~~IvG~~g~GKTtL-~~~i~~~I~  193 (415)
T TIGR00767       166 GKGQRGLIVAPPKAGKTVL-LQKIAQAIT  193 (415)
T ss_pred             CCCCEEEEECCCCCChhHH-HHHHHHhhc
Confidence            3688899999999999975 333444443

Members of this family differ in the specificity of RNA binding.

>PRK06067 flagellar accessory protein FlaH; Validated

Probab=91.29  E-value=1.5  Score=46.49  Aligned_cols=50  Identities=10%  Similarity=0.110  Sum_probs=30.9

Q ss_pred             CCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHH
Q 002040          504 GRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRK  562 (976)
Q Consensus       504 g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~  562 (976)
                      |.-+++.|++|+|||+.++..++..+.        ++..|+++.-- +-..++...+..
T Consensus        25 g~~~~i~G~~GsGKt~l~~~~~~~~~~--------~g~~~~y~~~e-~~~~~~~~~~~~   74 (234)
T PRK06067         25 PSLILIEGDHGTGKSVLSQQFVYGALK--------QGKKVYVITTE-NTSKSYLKQMES   74 (234)
T ss_pred             CcEEEEECCCCCChHHHHHHHHHHHHh--------CCCEEEEEEcC-CCHHHHHHHHHH
Confidence            456888899999999875555554433        24566666643 223445455544

>KOG0670 consensus U4/U6-associated splicing factor PRP4 [RNA processing and modification]

Probab=91.28  E-value=0.17  Score=57.70  Aligned_cols=10  Identities=20%  Similarity=0.411  Sum_probs=5.5

Q ss_pred             HHHHHcCCCe
Q 002040          665 LARKVLNKPV  674 (976)
Q Consensus       665 l~~~~l~~~~  674 (976)
                      |+..|+..|-
T Consensus       596 LVSRFYRaPE  605 (752)
T KOG0670|consen  596 LVSRFYRAPE  605 (752)
T ss_pred             HHHHhccCcc
Confidence            5555555554

>PRK10689 transcription-repair coupling factor; Provisional

Probab=91.26  E-value=0.75  Score=59.84  Aligned_cols=76  Identities=12%  Similarity=0.211  Sum_probs=63.8

Q ss_pred             cCCcEEEEecCHHHHHHHHHHHHHC----CCCceeccCCCCHHHHHHHHHHhccCCccEEEecC-cccccCCCCCCcEEE
Q 002040          713 EKGKILIFVHSQEKCDALFRDLLKH----GYPCLSLHGAKDQTDRESTISDFKSNVCNLLIATS-VAARGLDVKELELVI  787 (976)
Q Consensus       713 ~~~kvLIF~~s~~~~~~l~~~L~~~----~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLVaT~-v~~~GlDi~~v~~VI  787 (976)
                      .+.++||.|||..-|.+++..|...    ++.+..++|..+..++..++..+.+|.++|||+|. .+...+.+..+.+||
T Consensus       648 ~g~qvlvLvPT~eLA~Q~~~~f~~~~~~~~v~i~~l~g~~s~~e~~~il~~l~~g~~dIVVgTp~lL~~~v~~~~L~lLV  727 (1147)
T PRK10689        648 NHKQVAVLVPTTLLAQQHYDNFRDRFANWPVRIEMLSRFRSAKEQTQILAEAAEGKIDILIGTHKLLQSDVKWKDLGLLI  727 (1147)
T ss_pred             cCCeEEEEeCcHHHHHHHHHHHHHhhccCCceEEEEECCCCHHHHHHHHHHHHhCCCCEEEECHHHHhCCCCHhhCCEEE
Confidence            4668999999999999988887653    46778899999999999999999999999999997 344456777888887


Q ss_pred             E
Q 002040          788 N  788 (976)
Q Consensus       788 ~  788 (976)
                      .
T Consensus       728 I  728 (1147)
T PRK10689        728 V  728 (1147)
T ss_pred             E
Confidence            5

>KOG2543 consensus Origin recognition complex, subunit 5 [Replication, recombination and repair]

Probab=91.23  E-value=1.3  Score=49.12  Aligned_cols=143  Identities=17%  Similarity=0.199  Sum_probs=72.4

Q ss_pred             cHHHHHHHHHHhcCCC------EEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHHHH
Q 002040          491 MPIQAQALPVIMSGRD------CIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFA  564 (976)
Q Consensus       491 ~~~Q~~~i~~il~g~d------~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~~~  564 (976)
                      ...|...+..++...+      +++.|.+|+|||.+ +..++.++          +-..++++|.-  |.-+.--+..++
T Consensus        11 Re~qi~~L~~Llg~~~~~~PS~~~iyG~sgTGKT~~-~r~~l~~~----------n~~~vw~n~~e--cft~~~lle~IL   77 (438)
T KOG2543|consen   11 RESQIRRLKSLLGNNSCTIPSIVHIYGHSGTGKTYL-VRQLLRKL----------NLENVWLNCVE--CFTYAILLEKIL   77 (438)
T ss_pred             hHHHHHHHHHHhCCCCcccceeEEEeccCCCchhHH-HHHHHhhc----------CCcceeeehHH--hccHHHHHHHHH
Confidence            4678888888887665      38889999999975 44444443          11234554421  111222222222


Q ss_pred             hhcCcEEEEeeCCCChHHHHHHHhcCCeEEEeCchhHHHHHHhcCCcccccCCceEEEecCcccccccC--CchHHHHHH
Q 002040          565 KVMGVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMG--FEPQITRIV  642 (976)
Q Consensus       565 ~~~~~~~~~~~gg~~~~~~~~~l~~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDEah~~~~~~--f~~~i~~il  642 (976)
                      ...+   .+-..|.........           -..++..+.+. ....+....-+||+|-|+.+-+++  ..+.+..+-
T Consensus        78 ~~~~---~~d~dg~~~~~~~en-----------~~d~i~~l~q~-~~~t~~d~~~~liLDnad~lrD~~a~ll~~l~~L~  142 (438)
T KOG2543|consen   78 NKSQ---LADKDGDKVEGDAEN-----------FSDFIYLLVQW-PAATNRDQKVFLILDNADALRDMDAILLQCLFRLY  142 (438)
T ss_pred             HHhc---cCCCchhhhhhHHHH-----------HHHHHHHHHhh-HHhhccCceEEEEEcCHHhhhccchHHHHHHHHHH
Confidence            2211   000011101000001           11122233221 111233456799999999988876  333444444


Q ss_pred             HhcCCCCcEEEEeccCcHH
Q 002040          643 QNIRPDRQTVLFSATFPRQ  661 (976)
Q Consensus       643 ~~~~~~~q~i~~SAT~~~~  661 (976)
                      ..++.+.-.|+||+++++.
T Consensus       143 el~~~~~i~iils~~~~e~  161 (438)
T KOG2543|consen  143 ELLNEPTIVIILSAPSCEK  161 (438)
T ss_pred             HHhCCCceEEEEeccccHH
Confidence            4555555568899998765

>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]

Probab=91.23  E-value=0.79  Score=56.05  Aligned_cols=94  Identities=20%  Similarity=0.222  Sum_probs=77.3

Q ss_pred             ecCcchHHHHHHHHHHhhhcCC-cEEEEecCHHHHHHHHHHHHH-CCCCceeccCCCCHHHHHHHHHHhccCCccEEEec
Q 002040          694 VRPESDRFLRLLELLGEWYEKG-KILIFVHSQEKCDALFRDLLK-HGYPCLSLHGAKDQTDRESTISDFKSNVCNLLIAT  771 (976)
Q Consensus       694 ~~~~~~k~~~l~~~l~~~~~~~-kvLIF~~s~~~~~~l~~~L~~-~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLVaT  771 (976)
                      -.+.+.|....++++......| .+||.+|-+.....+...|.. .|.++..+|+++++.+|........+|..+|+|.|
T Consensus       224 GvTGSGKTEvYl~~i~~~L~~GkqvLvLVPEI~Ltpq~~~rf~~rFg~~v~vlHS~Ls~~er~~~W~~~~~G~~~vVIGt  303 (730)
T COG1198         224 GVTGSGKTEVYLEAIAKVLAQGKQVLVLVPEIALTPQLLARFKARFGAKVAVLHSGLSPGERYRVWRRARRGEARVVIGT  303 (730)
T ss_pred             CCCCCcHHHHHHHHHHHHHHcCCEEEEEeccccchHHHHHHHHHHhCCChhhhcccCChHHHHHHHHHHhcCCceEEEEe
Confidence            3456778888888888877666 899999999888888877765 48899999999999999999999999999999999


Q ss_pred             CcccccCCCCCCcEEEE
Q 002040          772 SVAARGLDVKELELVIN  788 (976)
Q Consensus       772 ~v~~~GlDi~~v~~VI~  788 (976)
                      -.+-- +-++++.+||.
T Consensus       304 RSAlF-~Pf~~LGLIIv  319 (730)
T COG1198         304 RSALF-LPFKNLGLIIV  319 (730)
T ss_pred             chhhc-CchhhccEEEE
Confidence            74431 45667777775

>PRK04841 transcriptional regulator MalT; Provisional

Probab=91.22  E-value=1  Score=58.25  Aligned_cols=45  Identities=16%  Similarity=0.284  Sum_probs=34.4

Q ss_pred             CCceEEEecCcccccccCCchHHHHHHHhcCCCCcEEEEeccCcH
Q 002040          616 RRVTYLVMDEADRMFDMGFEPQITRIVQNIRPDRQTVLFSATFPR  660 (976)
Q Consensus       616 ~~~~~vVlDEah~~~~~~f~~~i~~il~~~~~~~q~i~~SAT~~~  660 (976)
                      ..--+||||.+|.+.+......+..++...++...+|+.|-+.|+
T Consensus       120 ~~~~~lvlDD~h~~~~~~~~~~l~~l~~~~~~~~~lv~~sR~~~~  164 (903)
T PRK04841        120 HQPLYLVIDDYHLITNPEIHEAMRFFLRHQPENLTLVVLSRNLPP  164 (903)
T ss_pred             CCCEEEEEeCcCcCCChHHHHHHHHHHHhCCCCeEEEEEeCCCCC
Confidence            344689999999875555556777888888888889888877544

>TIGR02524 dot_icm_DotB Dot/Icm secretion system ATPase DotB

Probab=91.05  E-value=0.5  Score=53.45  Aligned_cols=28  Identities=21%  Similarity=0.331  Sum_probs=20.8

Q ss_pred             cCCCEEEEcCCCCchHHHHHHHHHHHHhc
Q 002040          503 SGRDCIGVAKTGSGKTLAFVLPMLRHIKD  531 (976)
Q Consensus       503 ~g~d~i~~a~TGsGKT~~~~l~il~~l~~  531 (976)
                      .+.-++++||||||||+. +..++.++..
T Consensus       133 ~~glilI~GpTGSGKTTt-L~aLl~~i~~  160 (358)
T TIGR02524       133 QEGIVFITGATGSGKSTL-LAAIIRELAE  160 (358)
T ss_pred             cCCEEEEECCCCCCHHHH-HHHHHHHHhh
Confidence            456789999999999985 4556666543

Members of this protein family are the DotB component of Dot/Icm secretion systems, as found in obligate intracellular pathogens Legionella pneumophila and Coxiella burnetii. While this system resembles type IV secretion systems and has been called a form of type IV, the liturature now seems to favor calling this the Dot/Icm system. This family is most closely related to TraJ proteins of plasmid transfer, rather than to proteins of other type IV secretion systems.

>KOG0344 consensus ATP-dependent RNA helicase [RNA processing and modification]

Probab=91.02  E-value=3.7  Score=47.99  Aligned_cols=98  Identities=16%  Similarity=0.301  Sum_probs=73.2

Q ss_pred             CCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHHHHhhcCcEEEEeeCCCChHHH---HHHHh
Q 002040          512 KTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQ---ISELK  588 (976)
Q Consensus       512 ~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~~~~~~~~~~~~~~gg~~~~~~---~~~l~  588 (976)
                      -+++|++..-++++.+.+..      +-.|.+||.+-+.+-|.|++.++..   .-++.+.+++|..+..+.   +..+.
T Consensus       365 lvF~gse~~K~lA~rq~v~~------g~~PP~lIfVQs~eRak~L~~~L~~---~~~i~v~vIh~e~~~~qrde~~~~FR  435 (593)
T KOG0344|consen  365 LVFCGSEKGKLLALRQLVAS------GFKPPVLIFVQSKERAKQLFEELEI---YDNINVDVIHGERSQKQRDETMERFR  435 (593)
T ss_pred             heeeecchhHHHHHHHHHhc------cCCCCeEEEEecHHHHHHHHHHhhh---ccCcceeeEecccchhHHHHHHHHHh
Confidence            45788888878877777664      3467889999999999999888862   357888889998655443   34444


Q ss_pred             cC-CeEEEeCchhHHHHHHhcCCcccccCCceEEEecCcc
Q 002040          589 RG-TEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEAD  627 (976)
Q Consensus       589 ~~-~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDEah  627 (976)
                      .| ..|+|||     ++|.++    .+|..+.+||.+..-
T Consensus       436 ~g~IwvLicT-----dll~RG----iDf~gvn~VInyD~p  466 (593)
T KOG0344|consen  436 IGKIWVLICT-----DLLARG----IDFKGVNLVINYDFP  466 (593)
T ss_pred             ccCeeEEEeh-----hhhhcc----ccccCcceEEecCCC
Confidence            44 5899999     566554    689999999986655

>KOG0339 consensus ATP-dependent RNA helicase [RNA processing and modification]

Probab=90.92  E-value=1.1  Score=50.86  Aligned_cols=71  Identities=14%  Similarity=0.356  Sum_probs=52.7

Q ss_pred             CCcE-EEEecCHHHHHHHHHHHH----HCCCCceeccCCCCHHHHHHHHHHhccCCccEEEecC--cc----cccCCCCC
Q 002040          714 KGKI-LIFVHSQEKCDALFRDLL----KHGYPCLSLHGAKDQTDRESTISDFKSNVCNLLIATS--VA----ARGLDVKE  782 (976)
Q Consensus       714 ~~kv-LIF~~s~~~~~~l~~~L~----~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLVaT~--v~----~~GlDi~~  782 (976)
                      .|++ ||.|+|++-|.++....+    -+|+.++++||+++..++...++    -.+-|+|||+  ++    --++|+..
T Consensus       295 ~gPi~vilvPTrela~Qi~~eaKkf~K~ygl~~v~~ygGgsk~eQ~k~Lk----~g~EivVaTPgRlid~VkmKatn~~r  370 (731)
T KOG0339|consen  295 EGPIGVILVPTRELASQIFSEAKKFGKAYGLRVVAVYGGGSKWEQSKELK----EGAEIVVATPGRLIDMVKMKATNLSR  370 (731)
T ss_pred             CCCeEEEEeccHHHHHHHHHHHHHhhhhccceEEEeecCCcHHHHHHhhh----cCCeEEEechHHHHHHHHhhccccee
Confidence            3454 677899998877765544    35899999999999888776665    3467999997  22    25789988


Q ss_pred             CcEEEE
Q 002040          783 LELVIN  788 (976)
Q Consensus       783 v~~VI~  788 (976)
                      +.++|+
T Consensus       371 vS~LV~  376 (731)
T KOG0339|consen  371 VSYLVL  376 (731)
T ss_pred             eeEEEE
Confidence            888775

>PRK03992 proteasome-activating nucleotidase; Provisional

Probab=90.88  E-value=0.72  Score=53.08  Aligned_cols=16  Identities=31%  Similarity=0.486  Sum_probs=14.4

Q ss_pred             CCEEEEcCCCCchHHH
Q 002040          505 RDCIGVAKTGSGKTLA  520 (976)
Q Consensus       505 ~d~i~~a~TGsGKT~~  520 (976)
                      +.+|+.||+|+|||+.
T Consensus       166 ~gvLL~GppGtGKT~l  181 (389)
T PRK03992        166 KGVLLYGPPGTGKTLL  181 (389)
T ss_pred             CceEEECCCCCChHHH
Confidence            5799999999999975

>TIGR03346 chaperone_ClpB ATP-dependent chaperone ClpB

Probab=90.74  E-value=2.1  Score=54.45  Aligned_cols=20  Identities=20%  Similarity=0.195  Sum_probs=16.3

Q ss_pred             CCCEEEEcCCCCchHHHHHH
Q 002040          504 GRDCIGVAKTGSGKTLAFVL  523 (976)
Q Consensus       504 g~d~i~~a~TGsGKT~~~~l  523 (976)
                      ..+.|++||+|+|||..+-.
T Consensus       194 ~~n~lL~G~pGvGKT~l~~~  213 (852)
T TIGR03346       194 KNNPVLIGEPGVGKTAIVEG  213 (852)
T ss_pred             CCceEEEcCCCCCHHHHHHH
Confidence            35899999999999976443

Members of this protein family are the bacterial ATP-dependent chaperone ClpB. This protein belongs to the AAA family, ATPases associated with various cellular activities (pfam00004). This molecular chaperone does not act as a protease, but rather serves to disaggregate misfolded and aggregated proteins.

>PRK04328 hypothetical protein; Provisional

Probab=90.64  E-value=1  Score=48.46  Aligned_cols=51  Identities=20%  Similarity=0.285  Sum_probs=32.0

Q ss_pred             CCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHHH
Q 002040          504 GRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKF  563 (976)
Q Consensus       504 g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~~  563 (976)
                      |..+++.|++|+|||+..+..+...+..        |..+++++ +.+-..++...+..|
T Consensus        23 gs~ili~G~pGsGKT~l~~~fl~~~~~~--------ge~~lyis-~ee~~~~i~~~~~~~   73 (249)
T PRK04328         23 RNVVLLSGGPGTGKSIFSQQFLWNGLQM--------GEPGVYVA-LEEHPVQVRRNMRQF   73 (249)
T ss_pred             CcEEEEEcCCCCCHHHHHHHHHHHHHhc--------CCcEEEEE-eeCCHHHHHHHHHHc
Confidence            5678889999999998766555554432        44566665 333444555555443

>TIGR03880 KaiC_arch_3 KaiC domain protein, AF_0351 family

Probab=90.64  E-value=1.2  Score=46.91  Aligned_cols=51  Identities=18%  Similarity=0.242  Sum_probs=31.9

Q ss_pred             CCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHHH
Q 002040          504 GRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKF  563 (976)
Q Consensus       504 g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~~  563 (976)
                      |.-+++.|++|+|||+.++..+...+.        ++..|++++.. +-..++...+..+
T Consensus        16 g~~~li~G~~G~GKt~~~~~~~~~~~~--------~g~~~~y~s~e-~~~~~l~~~~~~~   66 (224)
T TIGR03880        16 GHVIVVIGEYGTGKTTFSLQFLYQGLK--------NGEKAMYISLE-EREERILGYAKSK   66 (224)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHh--------CCCeEEEEECC-CCHHHHHHHHHHc
Confidence            456888999999999765544544433        24456776653 3445665555543

This model represents a rather narrowly distributed archaeal protein family in which members have a single copy of the KaiC domain. This stands in contrast to the circadian clock protein KaiC itself, with two copies of the domain. Members are expected to have weak ATPase activity, by homology to the autokinase/autophosphorylase KaiC itself.

>cd01121 Sms Sms (bacterial radA) DNA repair protein

Probab=90.63  E-value=1.4  Score=50.06  Aligned_cols=50  Identities=20%  Similarity=0.171  Sum_probs=29.8

Q ss_pred             CCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHH
Q 002040          504 GRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRK  562 (976)
Q Consensus       504 g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~  562 (976)
                      |.-+++.|++|+|||+.++..+... ..       .+..+|++.-. +...|+...+..
T Consensus        82 GslvLI~G~pG~GKStLllq~a~~~-a~-------~g~~VlYvs~E-Es~~qi~~Ra~r  131 (372)
T cd01121          82 GSVILIGGDPGIGKSTLLLQVAARL-AK-------RGGKVLYVSGE-ESPEQIKLRADR  131 (372)
T ss_pred             CeEEEEEeCCCCCHHHHHHHHHHHH-Hh-------cCCeEEEEECC-cCHHHHHHHHHH
Confidence            4567888999999998654444333 22       23467777653 334555444443

This protein is not related to archael radA any more than is to other RecA-like NTPases. Sms has a role in recombination and recombinational repair and is responsible for the stabilization or processing of branched DNA molecules.

>PRK08451 DNA polymerase III subunits gamma and tau; Validated

Probab=90.52  E-value=1.7  Score=51.55  Aligned_cols=40  Identities=10%  Similarity=0.180  Sum_probs=25.7

Q ss_pred             cCCceEEEecCcccccccCCchHHHHHHHhcCCCCcEEEEe
Q 002040          615 LRRVTYLVMDEADRMFDMGFEPQITRIVQNIRPDRQTVLFS  655 (976)
Q Consensus       615 l~~~~~vVlDEah~~~~~~f~~~i~~il~~~~~~~q~i~~S  655 (976)
                      ...+.+|||||||.|.... ...+..++...++...+|+++
T Consensus       115 ~~~~KVvIIDEad~Lt~~A-~NALLK~LEEpp~~t~FIL~t  154 (535)
T PRK08451        115 MARFKIFIIDEVHMLTKEA-FNALLKTLEEPPSYVKFILAT  154 (535)
T ss_pred             cCCeEEEEEECcccCCHHH-HHHHHHHHhhcCCceEEEEEE
Confidence            4568899999999875432 234555566555555555554

>TIGR02688 conserved hypothetical protein TIGR02688

Probab=90.47  E-value=0.58  Score=53.22  Aligned_cols=27  Identities=22%  Similarity=0.452  Sum_probs=22.5

Q ss_pred             HHHHHhcCCCEEEEcCCCCchHHHHHH
Q 002040          497 ALPVIMSGRDCIGVAKTGSGKTLAFVL  523 (976)
Q Consensus       497 ~i~~il~g~d~i~~a~TGsGKT~~~~l  523 (976)
                      +++++-.+.|+|+.||+|+|||..|..
T Consensus       202 l~~fve~~~Nli~lGp~GTGKThla~~  228 (449)
T TIGR02688       202 LLPLVEPNYNLIELGPKGTGKSYIYNN  228 (449)
T ss_pred             hHHHHhcCCcEEEECCCCCCHHHHHHH
Confidence            347788899999999999999976553

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.

>PRK00440 rfc replication factor C small subunit; Reviewed

Probab=90.32  E-value=2.8  Score=46.60  Aligned_cols=39  Identities=15%  Similarity=0.275  Sum_probs=24.0

Q ss_pred             CceEEEecCcccccccCCchHHHHHHHhcCCCCcEEEEec
Q 002040          617 RVTYLVMDEADRMFDMGFEPQITRIVQNIRPDRQTVLFSA  656 (976)
Q Consensus       617 ~~~~vVlDEah~~~~~~f~~~i~~il~~~~~~~q~i~~SA  656 (976)
                      ...+|||||+|.+.... ...+..++....+...+|+.+.
T Consensus       102 ~~~vviiDe~~~l~~~~-~~~L~~~le~~~~~~~lIl~~~  140 (319)
T PRK00440        102 PFKIIFLDEADNLTSDA-QQALRRTMEMYSQNTRFILSCN  140 (319)
T ss_pred             CceEEEEeCcccCCHHH-HHHHHHHHhcCCCCCeEEEEeC
Confidence            35799999999874322 2345555665555565555443

>KOG0991 consensus Replication factor C, subunit RFC2 [Replication, recombination and repair]

Probab=90.27  E-value=0.84  Score=47.04  Aligned_cols=18  Identities=28%  Similarity=0.396  Sum_probs=15.4

Q ss_pred             CCEEEEcCCCCchHHHHH
Q 002040          505 RDCIGVAKTGSGKTLAFV  522 (976)
Q Consensus       505 ~d~i~~a~TGsGKT~~~~  522 (976)
                      -++|+.||+|+|||++..
T Consensus        49 P~liisGpPG~GKTTsi~   66 (333)
T KOG0991|consen   49 PNLIISGPPGTGKTTSIL   66 (333)
T ss_pred             CceEeeCCCCCchhhHHH
Confidence            379999999999998743

>PRK14948 DNA polymerase III subunits gamma and tau; Provisional

Probab=90.24  E-value=0.68  Score=56.31  Aligned_cols=21  Identities=19%  Similarity=0.169  Sum_probs=16.3

Q ss_pred             CCEEEEcCCCCchHHHHHHHH
Q 002040          505 RDCIGVAKTGSGKTLAFVLPM  525 (976)
Q Consensus       505 ~d~i~~a~TGsGKT~~~~l~i  525 (976)
                      ..+|+.|+.|+|||.++.+.+
T Consensus        39 ~a~Lf~Gp~G~GKttlA~~lA   59 (620)
T PRK14948         39 PAYLFTGPRGTGKTSSARILA   59 (620)
T ss_pred             ceEEEECCCCCChHHHHHHHH
Confidence            357999999999998754433

>TIGR03600 phage_DnaB phage replicative helicase, DnaB family, HK022 subfamily

Probab=90.23  E-value=1.1  Score=52.29  Aligned_cols=38  Identities=18%  Similarity=0.067  Sum_probs=23.5

Q ss_pred             cCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEc
Q 002040          503 SGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMA  547 (976)
Q Consensus       503 ~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~  547 (976)
                      .|.-+++.|.+|+|||..++-.+.+....       .+..|+|++
T Consensus       193 ~g~liviag~pg~GKT~~al~ia~~~a~~-------~g~~v~~fS  230 (421)
T TIGR03600       193 KGDLIVIGARPSMGKTTLALNIAENVALR-------EGKPVLFFS  230 (421)
T ss_pred             CCceEEEEeCCCCCHHHHHHHHHHHHHHh-------CCCcEEEEE
Confidence            35567888999999997544433333222       244567766

Members of this family are phage (or prophage-region) homologs of the bacterial homohexameric replicative helicase DnaB. Some phage may rely on host DnaB, while others encode their own verions. This model describes the largest phage-specific clade among the close homologs of DnaB, but there are, or course, other DnaB homologs from phage that fall outside the scope of this model.

>PRK14954 DNA polymerase III subunits gamma and tau; Provisional

Probab=90.21  E-value=2.2  Score=51.72  Aligned_cols=20  Identities=30%  Similarity=0.129  Sum_probs=16.1

Q ss_pred             CEEEEcCCCCchHHHHHHHH
Q 002040          506 DCIGVAKTGSGKTLAFVLPM  525 (976)
Q Consensus       506 d~i~~a~TGsGKT~~~~l~i  525 (976)
                      .+|++||.|+|||+++.+.+
T Consensus        40 a~Lf~Gp~GvGKttlA~~lA   59 (620)
T PRK14954         40 GYIFSGLRGVGKTTAARVFA   59 (620)
T ss_pred             eEEEECCCCCCHHHHHHHHH
Confidence            48899999999998755443

>PHA00350 putative assembly protein

Probab=90.21  E-value=1.1  Score=51.03  Aligned_cols=25  Identities=28%  Similarity=0.355  Sum_probs=18.3

Q ss_pred             EEEEcCCCCchHHHHHH-HHHHHHhc
Q 002040          507 CIGVAKTGSGKTLAFVL-PMLRHIKD  531 (976)
Q Consensus       507 ~i~~a~TGsGKT~~~~l-~il~~l~~  531 (976)
                      .|+.|..|||||+.++. .++..+..
T Consensus         4 ~l~tG~pGSGKT~~aV~~~i~palk~   29 (399)
T PHA00350          4 YAIVGRPGSYKSYEAVVYHIIPALKD   29 (399)
T ss_pred             EEEecCCCCchhHHHHHHHHHHHHHC
Confidence            57889999999988765 35555443

>PRK07413 hypothetical protein; Validated

Probab=90.16  E-value=1.7  Score=48.91  Aligned_cols=53  Identities=15%  Similarity=0.316  Sum_probs=41.1

Q ss_pred             CCceEEEecCcccccccCCch--HHHHHHHhcCCCCcEEEEeccCcHHHHHHHHH
Q 002040          616 RRVTYLVMDEADRMFDMGFEP--QITRIVQNIRPDRQTVLFSATFPRQVEILARK  668 (976)
Q Consensus       616 ~~~~~vVlDEah~~~~~~f~~--~i~~il~~~~~~~q~i~~SAT~~~~~~~l~~~  668 (976)
                      ..+++|||||+-..++.++.+  .+..++...++...+|++.-.+|+.+..++..
T Consensus       124 g~ydlvILDEi~~Al~~gll~~eevl~~L~~rP~~~evVLTGR~ap~~Lie~ADl  178 (382)
T PRK07413        124 GLYSVVVLDELNPVLDLGLLPVDEVVNTLKSRPEGLEIIITGRAAPQSLLDIADL  178 (382)
T ss_pred             CCCCEEEEehhHHHHHCCCccHHHHHHHHHhCCCCCEEEEeCCCCCHHHHHhCCe
Confidence            568999999999888888654  56777777777777788777888887766544

>COG1200 RecG RecG-like helicase [DNA replication, recombination, and repair / Transcription]

Probab=90.13  E-value=1.2  Score=53.01  Aligned_cols=89  Identities=17%  Similarity=0.218  Sum_probs=73.7

Q ss_pred             HHHHHHHHHHhhhcCCcEEEEecCHHHHH----HHHHHHHHCCCCceeccCCCCHHHHHHHHHHhccCCccEEEecCccc
Q 002040          700 RFLRLLELLGEWYEKGKILIFVHSQEKCD----ALFRDLLKHGYPCLSLHGAKDQTDRESTISDFKSNVCNLLIATSVAA  775 (976)
Q Consensus       700 k~~~l~~~l~~~~~~~kvLIF~~s~~~~~----~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLVaT~v~~  775 (976)
                      -+..++.++.....+.++.+-+||---|.    .+..+|...|+.+..+.|.+....|..++....+|.++|+|.|-++-
T Consensus       297 TvVA~laml~ai~~G~Q~ALMAPTEILA~QH~~~~~~~l~~~~i~V~lLtG~~kgk~r~~~l~~l~~G~~~ivVGTHALi  376 (677)
T COG1200         297 TVVALLAMLAAIEAGYQAALMAPTEILAEQHYESLRKWLEPLGIRVALLTGSLKGKARKEILEQLASGEIDIVVGTHALI  376 (677)
T ss_pred             HHHHHHHHHHHHHcCCeeEEeccHHHHHHHHHHHHHHHhhhcCCeEEEeecccchhHHHHHHHHHhCCCCCEEEEcchhh
Confidence            45666777776666779999999965554    45555666799999999999999999999999999999999998554


Q ss_pred             -ccCCCCCCcEEEE
Q 002040          776 -RGLDVKELELVIN  788 (976)
Q Consensus       776 -~GlDi~~v~~VI~  788 (976)
                       ..+.+.++-+||.
T Consensus       377 Qd~V~F~~LgLVIi  390 (677)
T COG1200         377 QDKVEFHNLGLVII  390 (677)
T ss_pred             hcceeecceeEEEE
Confidence             7899999998885

>KOG0740 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=90.11  E-value=1.1  Score=51.15  Aligned_cols=81  Identities=23%  Similarity=0.235  Sum_probs=46.2

Q ss_pred             cCCceEEEecCcccccccC------------CchHHHHHHHhcCCCCcEEEEecc-CcHHHHHHHHHHcCCCeEEEeCCc
Q 002040          615 LRRVTYLVMDEADRMFDMG------------FEPQITRIVQNIRPDRQTVLFSAT-FPRQVEILARKVLNKPVEIQVGGR  681 (976)
Q Consensus       615 l~~~~~vVlDEah~~~~~~------------f~~~i~~il~~~~~~~q~i~~SAT-~~~~~~~l~~~~l~~~~~i~~~~~  681 (976)
                      ....++|+|||+|.++..-            -...+..+.....++-++++++|| .|-.+...+...+..-++|     
T Consensus       243 ~~qPsvifidEidslls~Rs~~e~e~srr~ktefLiq~~~~~s~~~drvlvigaTN~P~e~Dea~~Rrf~kr~yi-----  317 (428)
T KOG0740|consen  243 SLQPSVIFIDEIDSLLSKRSDNEHESSRRLKTEFLLQFDGKNSAPDDRVLVIGATNRPWELDEAARRRFVKRLYI-----  317 (428)
T ss_pred             hcCCeEEEechhHHHHhhcCCcccccchhhhhHHHhhhccccCCCCCeEEEEecCCCchHHHHHHHHHhhceeee-----
Confidence            3457889999999876421            011223333444566689999999 4555655555544433322     


Q ss_pred             ccccCCceEEEEecCcchHHHHHHHHHHhh
Q 002040          682 SVVNKDITQLVEVRPESDRFLRLLELLGEW  711 (976)
Q Consensus       682 ~~~~~~i~q~~~~~~~~~k~~~l~~~l~~~  711 (976)
                                 .......+...+..+|...
T Consensus       318 -----------plPd~etr~~~~~~ll~~~  336 (428)
T KOG0740|consen  318 -----------PLPDYETRSLLWKQLLKEQ  336 (428)
T ss_pred             -----------cCCCHHHHHHHHHHHHHhC
Confidence                       2233455666666666653

>PRK06090 DNA polymerase III subunit delta'; Validated

Probab=90.10  E-value=1.7  Score=48.32  Aligned_cols=43  Identities=16%  Similarity=0.268  Sum_probs=27.0

Q ss_pred             ccCCceEEEecCcccccccCCchHHHHHHHhcCCCCcEEEEecc
Q 002040          614 NLRRVTYLVMDEADRMFDMGFEPQITRIVQNIRPDRQTVLFSAT  657 (976)
Q Consensus       614 ~l~~~~~vVlDEah~~~~~~f~~~i~~il~~~~~~~q~i~~SAT  657 (976)
                      ....+.++|||+||.|... -...+.+++..-+++..+|++|..
T Consensus       105 ~~~~~kV~iI~~ae~m~~~-AaNaLLKtLEEPp~~t~fiL~t~~  147 (319)
T PRK06090        105 QLNGYRLFVIEPADAMNES-ASNALLKTLEEPAPNCLFLLVTHN  147 (319)
T ss_pred             ccCCceEEEecchhhhCHH-HHHHHHHHhcCCCCCeEEEEEECC
Confidence            3456889999999988532 244555666664555545555544

>PRK07993 DNA polymerase III subunit delta'; Validated

Probab=90.05  E-value=1.2  Score=50.09  Aligned_cols=43  Identities=9%  Similarity=0.071  Sum_probs=26.1

Q ss_pred             ccCCceEEEecCcccccccCCchHHHHHHHhcCCCCcEEEEecc
Q 002040          614 NLRRVTYLVMDEADRMFDMGFEPQITRIVQNIRPDRQTVLFSAT  657 (976)
Q Consensus       614 ~l~~~~~vVlDEah~~~~~~f~~~i~~il~~~~~~~q~i~~SAT  657 (976)
                      ....+.++|||+||.|... -...+.+++..=++..-+|++|.-
T Consensus       105 ~~g~~kV~iI~~ae~m~~~-AaNaLLKtLEEPp~~t~fiL~t~~  147 (334)
T PRK07993        105 RLGGAKVVWLPDAALLTDA-AANALLKTLEEPPENTWFFLACRE  147 (334)
T ss_pred             ccCCceEEEEcchHhhCHH-HHHHHHHHhcCCCCCeEEEEEECC
Confidence            3456889999999988532 244455555554444444444443

>TIGR02525 plasmid_TraJ plasmid transfer ATPase TraJ

Probab=90.05  E-value=0.8  Score=51.96  Aligned_cols=27  Identities=22%  Similarity=0.291  Sum_probs=20.7

Q ss_pred             CCCEEEEcCCCCchHHHHHHHHHHHHhc
Q 002040          504 GRDCIGVAKTGSGKTLAFVLPMLRHIKD  531 (976)
Q Consensus       504 g~d~i~~a~TGsGKT~~~~l~il~~l~~  531 (976)
                      +..+|++|+||||||+. +..++.++..
T Consensus       149 ~GlilI~G~TGSGKTT~-l~al~~~i~~  175 (372)
T TIGR02525       149 AGLGLICGETGSGKSTL-AASIYQHCGE  175 (372)
T ss_pred             CCEEEEECCCCCCHHHH-HHHHHHHHHh
Confidence            44688999999999975 5667777654

Members of this protein family are predicted ATPases associated with plasmid transfer loci in bacteria. This family is most similar to the DotB ATPase of a type-IV secretion-like system of obligate intracellular pathogens Legionella pneumophila and Coxiella burnetii (TIGR02524).

>KOG0742 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=90.00  E-value=1.2  Score=49.47  Aligned_cols=16  Identities=31%  Similarity=0.484  Sum_probs=14.6

Q ss_pred             CCEEEEcCCCCchHHH
Q 002040          505 RDCIGVAKTGSGKTLA  520 (976)
Q Consensus       505 ~d~i~~a~TGsGKT~~  520 (976)
                      +|+++.||+|+|||+.
T Consensus       385 RNilfyGPPGTGKTm~  400 (630)
T KOG0742|consen  385 RNILFYGPPGTGKTMF  400 (630)
T ss_pred             hheeeeCCCCCCchHH
Confidence            6899999999999975

>PF05729 NACHT: NACHT domain

Probab=89.99  E-value=1.7  Score=42.86  Aligned_cols=25  Identities=16%  Similarity=0.216  Sum_probs=17.8

Q ss_pred             CEEEEcCCCCchHHHHHHHHHHHHhc
Q 002040          506 DCIGVAKTGSGKTLAFVLPMLRHIKD  531 (976)
Q Consensus       506 d~i~~a~TGsGKT~~~~l~il~~l~~  531 (976)
                      -++|.|+.|+|||+. +..++..+..
T Consensus         2 ~l~I~G~~G~GKStl-l~~~~~~~~~   26 (166)
T PF05729_consen    2 VLWISGEPGSGKSTL-LRKLAQQLAE   26 (166)
T ss_pred             EEEEECCCCCChHHH-HHHHHHHHHh
Confidence            368899999999986 4444545444

>TIGR00635 ruvB Holliday junction DNA helicase, RuvB subunit

Probab=89.94  E-value=0.79  Score=50.83  Aligned_cols=17  Identities=24%  Similarity=0.157  Sum_probs=14.5

Q ss_pred             CCEEEEcCCCCchHHHH
Q 002040          505 RDCIGVAKTGSGKTLAF  521 (976)
Q Consensus       505 ~d~i~~a~TGsGKT~~~  521 (976)
                      .+++++||+|+|||..+
T Consensus        31 ~~~ll~Gp~G~GKT~la   47 (305)
T TIGR00635        31 DHLLLYGPPGLGKTTLA   47 (305)
T ss_pred             CeEEEECCCCCCHHHHH
Confidence            46999999999999753

RuvA specifically binds Holliday junctions as a sandwich of two tetramers and maintains the configuration of the junction. It forms a complex with two hexameric rings of RuvB, the subunit that contains helicase activity. The complex drives ATP-dependent branch migration of the Holliday junction recombination intermediate. The endonuclease RuvC resolves junctions.

>KOG0058 consensus Peptide exporter, ABC superfamily [Intracellular trafficking, secretion, and vesicular transport]

Probab=89.90  E-value=0.59  Score=55.99  Aligned_cols=146  Identities=23%  Similarity=0.243  Sum_probs=77.9

Q ss_pred             HhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHHHHhhcCcEEE--------
Q 002040          501 IMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVMGVRCV--------  572 (976)
Q Consensus       501 il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~~~~~~~~~~~--------  572 (976)
                      |-.|..+-++||.|+|||++  +.++.++++     ...|...|==+|-+.+-..++.   +.....+-..+        
T Consensus       491 i~pGe~vALVGPSGsGKSTi--asLL~rfY~-----PtsG~IllDG~~i~~~~~~~lr---~~Ig~V~QEPvLFs~sI~e  560 (716)
T KOG0058|consen  491 IRPGEVVALVGPSGSGKSTI--ASLLLRFYD-----PTSGRILLDGVPISDINHKYLR---RKIGLVGQEPVLFSGSIRE  560 (716)
T ss_pred             eCCCCEEEEECCCCCCHHHH--HHHHHHhcC-----CCCCeEEECCeehhhcCHHHHH---HHeeeeeccceeecccHHH
Confidence            33578899999999999985  445555553     1223332333466665544433   21111111111        


Q ss_pred             -EeeCCC--------------ChHHHHHHHhcCCeEEEeCchhHHHHHHhcC--CcccccCCceEEEecCcccccccCCc
Q 002040          573 -PVYGGS--------------GVAQQISELKRGTEIVVCTPGRMIDILCTSG--GKITNLRRVTYLVMDEADRMFDMGFE  635 (976)
Q Consensus       573 -~~~gg~--------------~~~~~~~~l~~~~~Iiv~Tp~~L~~~l~~~~--~~~~~l~~~~~vVlDEah~~~~~~f~  635 (976)
                       +.||-.              +..+.+..+..|++-.|+.-|..+.==.++.  -....+++..++|+|||-.-+|..-+
T Consensus       561 NI~YG~~~~t~e~i~~AAk~ANah~FI~~~p~gY~T~VGEkG~qLSGGQKQRIAIARALlr~P~VLILDEATSALDaeSE  640 (716)
T KOG0058|consen  561 NIAYGLDNATDEEIEAAAKMANAHEFITNFPDGYNTVVGEKGSQLSGGQKQRIAIARALLRNPRVLILDEATSALDAESE  640 (716)
T ss_pred             HHhcCCCCCCHHHHHHHHHHhChHHHHHhCccccccccCCccccccchHHHHHHHHHHHhcCCCEEEEechhhhcchhhH
Confidence             112211              1112333444566666666654321000000  00013567889999999988888878


Q ss_pred             hHHHHHHHhcCCCCcEEEEecc
Q 002040          636 PQITRIVQNIRPDRQTVLFSAT  657 (976)
Q Consensus       636 ~~i~~il~~~~~~~q~i~~SAT  657 (976)
                      ..+...+..+..+ +++++=|-
T Consensus       641 ~lVq~aL~~~~~~-rTVlvIAH  661 (716)
T KOG0058|consen  641 YLVQEALDRLMQG-RTVLVIAH  661 (716)
T ss_pred             HHHHHHHHHhhcC-CeEEEEeh
Confidence            8888888777666 45554443

>PRK07414 cob(I)yrinic acid a,c-diamide adenosyltransferase; Validated

Probab=89.90  E-value=1.1  Score=45.06  Aligned_cols=51  Identities=18%  Similarity=0.381  Sum_probs=39.4

Q ss_pred             CCceEEEecCcccccccCCch--HHHHHHHhcCCCCcEEEEeccCcHHHHHHH
Q 002040          616 RRVTYLVMDEADRMFDMGFEP--QITRIVQNIRPDRQTVLFSATFPRQVEILA  666 (976)
Q Consensus       616 ~~~~~vVlDEah~~~~~~f~~--~i~~il~~~~~~~q~i~~SAT~~~~~~~l~  666 (976)
                      ..+++|||||+-..++.++.+  .+..++...++..-+|++.-.+|+.+..++
T Consensus       114 ~~~dlvVLDEi~~Al~~gli~~eeVl~~L~~rp~~~evILTGR~~p~~Lie~A  166 (178)
T PRK07414        114 GRYSLVVLDELSLAIQFGLIPETEVLEFLEKRPSHVDVILTGPEMPESLLAIA  166 (178)
T ss_pred             CCCCEEEEehhHHHHHCCCccHHHHHHHHHhCCCCCEEEEECCCCCHHHHHhC
Confidence            568999999999888888654  567778877777777777777888766554

>TIGR03345 VI_ClpV1 type VI secretion ATPase, ClpV1 family

Probab=89.88  E-value=2.8  Score=53.23  Aligned_cols=17  Identities=29%  Similarity=0.358  Sum_probs=15.1

Q ss_pred             CCEEEEcCCCCchHHHH
Q 002040          505 RDCIGVAKTGSGKTLAF  521 (976)
Q Consensus       505 ~d~i~~a~TGsGKT~~~  521 (976)
                      .++|++|+.|+|||...
T Consensus       209 ~n~lLvG~pGvGKTal~  225 (852)
T TIGR03345       209 NNPILTGEAGVGKTAVV  225 (852)
T ss_pred             CceeEECCCCCCHHHHH
Confidence            58999999999999764

Members of this protein family are homologs of ClpB, an ATPase associated with chaperone-related functions. These ClpB homologs, designated ClpV1, are a key component of the bacterial pathogenicity-associated type VI secretion system.

>KOG0701 consensus dsRNA-specific nuclease Dicer and related ribonucleases [RNA processing and modification]

Probab=89.82  E-value=0.22  Score=64.94  Aligned_cols=92  Identities=35%  Similarity=0.470  Sum_probs=74.7

Q ss_pred             EEEEecCHHHHHHHHHHHHHC-CCCceeccCCCCH-----------HHHHHHHHHhccCCccEEEecCcccccCCCCCCc
Q 002040          717 ILIFVHSQEKCDALFRDLLKH-GYPCLSLHGAKDQ-----------TDRESTISDFKSNVCNLLIATSVAARGLDVKELE  784 (976)
Q Consensus       717 vLIF~~s~~~~~~l~~~L~~~-~~~~~~lhg~~~~-----------~~R~~~~~~F~~g~~~vLVaT~v~~~GlDi~~v~  784 (976)
                      .||||+....+..++..+... .+.+..+.|.+.+           ..+..++..|....+++|++|.++..|+|++.++
T Consensus       295 ~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~k~~~~~~~~~~~~vl~~~~~~~ln~L~~~~~~~e~~d~~~~~  374 (1606)
T KOG0701|consen  295 GIIFVDQRYTAYVLLELLREIFSNDPLFVTGASGANLWKSFKNELELRQAEVLRRFHFHELNLLIATSVLEEGVDVPKCN  374 (1606)
T ss_pred             heeecccchHHHHHHHHHHHhhccCcceeeccccCccchhhHHHHHhhhHHHHHHHhhhhhhHHHHHHHHHhhcchhhhh
Confidence            489999888888888777654 2333334444322           2356889999999999999999999999999999


Q ss_pred             EEEEeCCCCCHHHHHHHhcccCCC
Q 002040          785 LVINFDAPNHYEDYVHRVGRTGRA  808 (976)
Q Consensus       785 ~VI~~d~p~s~~~y~Qr~GR~gR~  808 (976)
                      .||.++.|.....|+|..||+-..
T Consensus       375 ~~~~~~~~~~~~~~vq~~~r~~~~  398 (1606)
T KOG0701|consen  375 LVVLFDAPTYYRSYVQKKGRARAA  398 (1606)
T ss_pred             hheeccCcchHHHHHHhhcccccc
Confidence            999999999999999999998654

>PRK07413 hypothetical protein; Validated

Probab=89.75  E-value=0.54  Score=52.89  Aligned_cols=53  Identities=15%  Similarity=0.164  Sum_probs=38.8

Q ss_pred             CCceEEEecCcccccccCCch--HHHHHHHhcCCCCcEEEEecc-CcHHHHHHHHH
Q 002040          616 RRVTYLVMDEADRMFDMGFEP--QITRIVQNIRPDRQTVLFSAT-FPRQVEILARK  668 (976)
Q Consensus       616 ~~~~~vVlDEah~~~~~~f~~--~i~~il~~~~~~~q~i~~SAT-~~~~~~~l~~~  668 (976)
                      ..+++|||||+-..++.++.+  .+..++...++...+|++.-. +|+.+..++..
T Consensus       304 g~ydlvVLDEi~~Al~~gli~~eevi~~L~~rp~~~evVLTGR~~ap~~lie~ADl  359 (382)
T PRK07413        304 GLYKTIILDELNPTVDLELLPVEPIVQTLLRKPRDTEVIITGRCKNQPAYFDLASV  359 (382)
T ss_pred             CCCCEEEEechHHHHHCCCccHHHHHHHHHhCCCCCEEEEeCCCCCCHHHHHhCch
Confidence            468999999999888888765  577777776666666665555 77877666543

>PRK09376 rho transcription termination factor Rho; Provisional

Probab=89.69  E-value=0.78  Score=51.79  Aligned_cols=30  Identities=27%  Similarity=0.309  Sum_probs=21.9

Q ss_pred             HhcCCCEEEEcCCCCchHHHHHHHHHHHHhc
Q 002040          501 IMSGRDCIGVAKTGSGKTLAFVLPMLRHIKD  531 (976)
Q Consensus       501 il~g~d~i~~a~TGsGKT~~~~l~il~~l~~  531 (976)
                      |-.|+.++|+|+.|+|||+. +..+.+.+..
T Consensus       166 IGkGQR~lIvgppGvGKTTL-aK~Ian~I~~  195 (416)
T PRK09376        166 IGKGQRGLIVAPPKAGKTVL-LQNIANSITT  195 (416)
T ss_pred             cccCceEEEeCCCCCChhHH-HHHHHHHHHh
Confidence            34788999999999999975 4445555543

>PRK07133 DNA polymerase III subunits gamma and tau; Validated

Probab=89.67  E-value=0.55  Score=57.35  Aligned_cols=20  Identities=20%  Similarity=0.139  Sum_probs=15.7

Q ss_pred             CEEEEcCCCCchHHHHHHHH
Q 002040          506 DCIGVAKTGSGKTLAFVLPM  525 (976)
Q Consensus       506 d~i~~a~TGsGKT~~~~l~i  525 (976)
                      -+|++||.|+|||.++.+.+
T Consensus        42 AYLF~GP~GtGKTt~AriLA   61 (725)
T PRK07133         42 AYLFSGPRGTGKTSVAKIFA   61 (725)
T ss_pred             EEEEECCCCCcHHHHHHHHH
Confidence            36899999999998755443

>COG1222 RPT1 ATP-dependent 26S proteasome regulatory subunit [Posttranslational modification, protein turnover, chaperones]

Probab=89.66  E-value=1.6  Score=48.20  Aligned_cols=18  Identities=28%  Similarity=0.361  Sum_probs=15.4

Q ss_pred             CCCEEEEcCCCCchHHHH
Q 002040          504 GRDCIGVAKTGSGKTLAF  521 (976)
Q Consensus       504 g~d~i~~a~TGsGKT~~~  521 (976)
                      -+.+|+.||+|+|||+.+
T Consensus       185 PKGVLLYGPPGTGKTLLA  202 (406)
T COG1222         185 PKGVLLYGPPGTGKTLLA  202 (406)
T ss_pred             CCceEeeCCCCCcHHHHH
Confidence            367999999999999853

>KOG0734 consensus AAA+-type ATPase containing the peptidase M41 domain [Posttranslational modification, protein turnover, chaperones]

Probab=89.63  E-value=1.4  Score=50.73  Aligned_cols=45  Identities=11%  Similarity=0.180  Sum_probs=27.5

Q ss_pred             CceEEEecCcccccccCCc-------hHHHHHH---HhcCCCCcEEEEeccCcHH
Q 002040          617 RVTYLVMDEADRMFDMGFE-------PQITRIV---QNIRPDRQTVLFSATFPRQ  661 (976)
Q Consensus       617 ~~~~vVlDEah~~~~~~f~-------~~i~~il---~~~~~~~q~i~~SAT~~~~  661 (976)
                      -.++|.|||.|.+...-..       ..+..++   .-+.++--+|++.||-.+.
T Consensus       396 APcIIFIDEiDavG~kR~~~~~~y~kqTlNQLLvEmDGF~qNeGiIvigATNfpe  450 (752)
T KOG0734|consen  396 APCIIFIDEIDAVGGKRNPSDQHYAKQTLNQLLVEMDGFKQNEGIIVIGATNFPE  450 (752)
T ss_pred             CCeEEEEechhhhcccCCccHHHHHHHHHHHHHHHhcCcCcCCceEEEeccCChh
Confidence            3578999999977543211       1122232   3345667799999995544

>TIGR00665 DnaB replicative DNA helicase

Probab=89.55  E-value=1.6  Score=51.18  Aligned_cols=37  Identities=16%  Similarity=0.014  Sum_probs=22.6

Q ss_pred             CCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEc
Q 002040          504 GRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMA  547 (976)
Q Consensus       504 g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~  547 (976)
                      |.-++|.|++|+|||..++-.+.+.+..       .+..|++++
T Consensus       195 G~l~vi~g~pg~GKT~~~l~~a~~~a~~-------~g~~vl~~S  231 (434)
T TIGR00665       195 SDLIILAARPSMGKTAFALNIAENAAIK-------EGKPVAFFS  231 (434)
T ss_pred             CeEEEEEeCCCCChHHHHHHHHHHHHHh-------CCCeEEEEe
Confidence            4457888999999997544333333322       244566665

This model describes the helicase DnaB, a homohexameric protein required for DNA replication. The homohexamer can form a ring around a single strand of DNA near a replication fork. An intein of 400 residues is found at a conserved location in DnaB of Synechocystis PCC6803, Rhodothermus marinus (both experimentally confirmed), and Mycobacterium tuberculosis. The intein removes itself by a self-splicing reaction. The seed alignment contains inteins so that the model built from the seed alignment will model a low cost at common intein insertion sites.

>COG1485 Predicted ATPase [General function prediction only]

Probab=89.54  E-value=1.2  Score=48.96  Aligned_cols=109  Identities=17%  Similarity=0.205  Sum_probs=62.0

Q ss_pred             CCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHHHHhhcCcEEEEeeCCCChHHHH
Q 002040          505 RDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQI  584 (976)
Q Consensus       505 ~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~~~~~~~~~~~~~~gg~~~~~~~  584 (976)
                      +.+.++|+.|.|||.  ++-++.+.....         .-.-++.......+++.+..+.            |.      
T Consensus        66 ~GlYl~GgVGrGKT~--LMD~Fy~~lp~~---------~k~R~HFh~FM~~vH~~l~~l~------------g~------  116 (367)
T COG1485          66 RGLYLWGGVGRGKTM--LMDLFYESLPGE---------RKRRLHFHRFMARVHQRLHTLQ------------GQ------  116 (367)
T ss_pred             ceEEEECCCCccHHH--HHHHHHhhCCcc---------ccccccHHHHHHHHHHHHHHHc------------CC------
Confidence            679999999999996  444444432210         0133566666666666666642            11      


Q ss_pred             HHHhcCCeEEEeCchhHHHHHHhcCCcccccCCceEEEecCcccccccCCchHHHHHHHhc-CCCCcEEEEeccCcHHH
Q 002040          585 SELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMGFEPQITRIVQNI-RPDRQTVLFSATFPRQV  662 (976)
Q Consensus       585 ~~l~~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDEah~~~~~~f~~~i~~il~~~-~~~~q~i~~SAT~~~~~  662 (976)
                            .+.+    ..+..-         .+....+|++||+| +.|-+-.-.+..++..+ .....++.+|.|.|..+
T Consensus       117 ------~dpl----~~iA~~---------~~~~~~vLCfDEF~-VtDI~DAMiL~rL~~~Lf~~GV~lvaTSN~~P~~L  175 (367)
T COG1485         117 ------TDPL----PPIADE---------LAAETRVLCFDEFE-VTDIADAMILGRLLEALFARGVVLVATSNTAPDNL  175 (367)
T ss_pred             ------CCcc----HHHHHH---------HHhcCCEEEeeeee-ecChHHHHHHHHHHHHHHHCCcEEEEeCCCChHHh
Confidence                  1100    001111         13347899999999 33333333444555443 45677888899988763

>PRK13851 type IV secretion system protein VirB11; Provisional

Probab=89.39  E-value=0.61  Score=52.38  Aligned_cols=46  Identities=24%  Similarity=0.240  Sum_probs=30.9

Q ss_pred             HHHhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHH
Q 002040          499 PVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELV  553 (976)
Q Consensus       499 ~~il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La  553 (976)
                      .++..+.+++++|+||||||+. +-.++.++-        ....++.+-.+.+|.
T Consensus       157 ~~v~~~~nilI~G~tGSGKTTl-l~aLl~~i~--------~~~rivtiEd~~El~  202 (344)
T PRK13851        157 ACVVGRLTMLLCGPTGSGKTTM-SKTLISAIP--------PQERLITIEDTLELV  202 (344)
T ss_pred             HHHHcCCeEEEECCCCccHHHH-HHHHHcccC--------CCCCEEEECCCcccc
Confidence            3455788999999999999974 444444332        133566777777763

>TIGR02012 tigrfam_recA protein RecA

Probab=89.34  E-value=0.8  Score=50.77  Aligned_cols=42  Identities=19%  Similarity=0.162  Sum_probs=26.6

Q ss_pred             CCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHH
Q 002040          504 GRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELV  553 (976)
Q Consensus       504 g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La  553 (976)
                      |.-++|.|++|||||+.++..+. ....       .+..|+++..-..+.
T Consensus        55 G~iteI~G~~GsGKTtLaL~~~~-~~~~-------~g~~v~yId~E~~~~   96 (321)
T TIGR02012        55 GRIIEIYGPESSGKTTLALHAIA-EAQK-------AGGTAAFIDAEHALD   96 (321)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHH-HHHH-------cCCcEEEEcccchhH
Confidence            45688999999999986444444 4332       245667775544443

This model describes orthologs of the recA protein. RecA promotes hybridization of homolgous regions of DNA. A segment of ssDNA can be hybridized to another ssDNA region, or to a dsDNA region. ATP is hydrolyzed in the process. Part of the SOS respones, it is regulated by LexA via autocatalytic cleavage.

>TIGR01243 CDC48 AAA family ATPase, CDC48 subfamily

Probab=89.33  E-value=1.1  Score=56.26  Aligned_cols=54  Identities=20%  Similarity=0.371  Sum_probs=31.2

Q ss_pred             CcccccccCCCCHHHHHHHHHc---CCCCCcHHHHHHHHHHhcCCCEEEEcCCCCchHHH
Q 002040          464 KPIKTWHQTGLTSKIMETIRKL---NYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLA  520 (976)
Q Consensus       464 ~pi~~~~~~~l~~~l~~~l~~~---~~~~p~~~Q~~~i~~il~g~d~i~~a~TGsGKT~~  520 (976)
                      .|..+|.+.+....+...|...   .+..|.-++...   +...+.+|+.||+|+|||+.
T Consensus       447 ~~~~~~~di~g~~~~k~~l~~~v~~~~~~~~~~~~~g---~~~~~giLL~GppGtGKT~l  503 (733)
T TIGR01243       447 VPNVRWSDIGGLEEVKQELREAVEWPLKHPEIFEKMG---IRPPKGVLLFGPPGTGKTLL  503 (733)
T ss_pred             ccccchhhcccHHHHHHHHHHHHHhhhhCHHHHHhcC---CCCCceEEEECCCCCCHHHH
Confidence            3456788887777666655531   222111111110   11235689999999999975

This subfamily of the AAA family ATPases includes two members each from three archaeal species. It also includes yeast CDC48 (cell division control protein 48) and the human ortholog, transitional endoplasmic reticulum ATPase (valosin-containing protein). These proteins in eukaryotes are involved in the budding and transfer of membrane from the transitional endoplasmic reticulum to the Golgi apparatus.

>PF03266 NTPase_1: NTPase; InterPro: IPR004948 This entry represents a family of nucleoside-triphosphatases which have activity towards ATP, GTP, CTP, TTP and UTP and may hydrolyse nucleoside diphosphates with lower efficiency []

Probab=89.20  E-value=0.12  Score=51.90  Aligned_cols=119  Identities=17%  Similarity=0.207  Sum_probs=51.9

Q ss_pred             CEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHHHHhhcCcEEEEeeCCCChHHHHH
Q 002040          506 DCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQIS  585 (976)
Q Consensus       506 d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~~~~~~~~~~~~~~gg~~~~~~~~  585 (976)
                      ++++.|+.|+|||+. +.-++..+....      -+.+-+++|-.-          .-....|..++.+..|....  +.
T Consensus         1 ~i~iTG~pG~GKTTl-l~k~i~~l~~~~------~~v~Gf~t~evr----------~~g~r~GF~iv~l~~g~~~~--la   61 (168)
T PF03266_consen    1 HIFITGPPGVGKTTL-LKKVIEELKKKG------LPVGGFYTEEVR----------ENGRRIGFDIVDLNSGEEAI--LA   61 (168)
T ss_dssp             EEEEES-TTSSHHHH-HHHHHHHHHHTC------GGEEEEEEEEEE----------TTSSEEEEEEEET-TS-EEE--EE
T ss_pred             CEEEECcCCCCHHHH-HHHHHHHhhccC------CccceEEeeccc----------CCCceEEEEEEECcCCCccc--cc
Confidence            378999999999986 556666665421      123334443210          01111234444432221000  00


Q ss_pred             HHhcCCeEEEeCchhHHHHHHhcCCcccc--cCCceEEEecCcccccc--cCCchHHHHHHH
Q 002040          586 ELKRGTEIVVCTPGRMIDILCTSGGKITN--LRRVTYLVMDEADRMFD--MGFEPQITRIVQ  643 (976)
Q Consensus       586 ~l~~~~~Iiv~Tp~~L~~~l~~~~~~~~~--l~~~~~vVlDEah~~~~--~~f~~~i~~il~  643 (976)
                      .......+-++.+....+.+.........  +...++|||||+=.|--  .+|...+..++.
T Consensus        62 ~~~~~~~~~vgky~v~~e~fe~~~~~~L~~~~~~~~liviDEIG~mEl~~~~F~~~v~~~l~  123 (168)
T PF03266_consen   62 RVDFRSGPRVGKYFVDLESFEEIGLPALRNALSSSDLIVIDEIGKMELKSPGFREAVEKLLD  123 (168)
T ss_dssp             ETTSS-SCECTTCEE-HHHHHCCCCCCCHHHHHCCHEEEE---STTCCC-CHHHHHHHHHHC
T ss_pred             cccccccccCCCEEEcHHHHHHHHHHHHHhhcCCCCEEEEeccchhhhcCHHHHHHHHHHHc
Confidence            00011233444444443444332212222  35678999999997633  345555655555

It includes proteins from bacteria to human, and the function was determined first in a hyperthermophilic bacterium to be an NTPase []. The structure of one member-sequence represents a variation of the RecA fold, and implies that the function might be that of a DNA/RNA modifying enzyme []. The sequence carries both a Walker A and Walker B motif which together are characteristic of ATPases or GTPases. The protein exhibits an increased expression profile in human liver cholangiocarcinoma when compared to normal tissue [].; GO: 0005524 ATP binding, 0016740 transferase activity, 0019204 nucleotide phosphatase activity; PDB: 1YE8_A 2I3B_A.

>TIGR01243 CDC48 AAA family ATPase, CDC48 subfamily

Probab=89.17  E-value=0.74  Score=57.70  Aligned_cols=53  Identities=25%  Similarity=0.356  Sum_probs=29.0

Q ss_pred             cccccccCCCCHHHHHHHHHc---CCCCCcHHHHHHHHHHhcCCCEEEEcCCCCchHHH
Q 002040          465 PIKTWHQTGLTSKIMETIRKL---NYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLA  520 (976)
Q Consensus       465 pi~~~~~~~l~~~l~~~l~~~---~~~~p~~~Q~~~i~~il~g~d~i~~a~TGsGKT~~  520 (976)
                      |-.+|++++-....+..|..+   .+..|.-++...   +..++.+++.||+|+|||+.
T Consensus       173 ~~~~~~di~G~~~~~~~l~~~i~~~~~~~~~~~~~g---i~~~~giLL~GppGtGKT~l  228 (733)
T TIGR01243       173 PKVTYEDIGGLKEAKEKIREMVELPMKHPELFEHLG---IEPPKGVLLYGPPGTGKTLL  228 (733)
T ss_pred             CCCCHHHhcCHHHHHHHHHHHHHHHhhCHHHHHhcC---CCCCceEEEECCCCCChHHH
Confidence            345677776555554444331   222211111111   12357899999999999975

This subfamily of the AAA family ATPases includes two members each from three archaeal species. It also includes yeast CDC48 (cell division control protein 48) and the human ortholog, transitional endoplasmic reticulum ATPase (valosin-containing protein). These proteins in eukaryotes are involved in the budding and transfer of membrane from the transitional endoplasmic reticulum to the Golgi apparatus.

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

Probab=89.13  E-value=1.3  Score=52.91  Aligned_cols=68  Identities=21%  Similarity=0.344  Sum_probs=55.2

Q ss_pred             EEEEecCHHHHHHHHHHHHHC-----CCCceeccCCCCHHHHHHHHHHhccCCccEEEecC-----ccccc-CCCCCCcE
Q 002040          717 ILIFVHSQEKCDALFRDLLKH-----GYPCLSLHGAKDQTDRESTISDFKSNVCNLLIATS-----VAARG-LDVKELEL  785 (976)
Q Consensus       717 vLIF~~s~~~~~~l~~~L~~~-----~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLVaT~-----v~~~G-lDi~~v~~  785 (976)
                      +||++||++-|.++++.+...     ++.++.++|+++...+...+.   .| .+|||||+     .+.+| +++..+.+
T Consensus       102 aLil~PTRELA~Qi~~~~~~~~~~~~~~~~~~i~GG~~~~~q~~~l~---~~-~~ivVaTPGRllD~i~~~~l~l~~v~~  177 (513)
T COG0513         102 ALILAPTRELAVQIAEELRKLGKNLGGLRVAVVYGGVSIRKQIEALK---RG-VDIVVATPGRLLDLIKRGKLDLSGVET  177 (513)
T ss_pred             eEEECCCHHHHHHHHHHHHHHHhhcCCccEEEEECCCCHHHHHHHHh---cC-CCEEEECccHHHHHHHcCCcchhhcCE
Confidence            899999999999998887653     567899999998777665444   46 99999996     55566 89999999


Q ss_pred             EEE
Q 002040          786 VIN  788 (976)
Q Consensus       786 VI~  788 (976)
                      +|.
T Consensus       178 lVl  180 (513)
T COG0513         178 LVL  180 (513)
T ss_pred             EEe
Confidence            885

>TIGR01241 FtsH_fam ATP-dependent metalloprotease FtsH

Probab=89.12  E-value=0.98  Score=53.85  Aligned_cols=54  Identities=20%  Similarity=0.281  Sum_probs=29.0

Q ss_pred             CcccccccCCCCHHHHHHHHHcC--CCCCcHHHHHHHHHHhcCCCEEEEcCCCCchHHH
Q 002040          464 KPIKTWHQTGLTSKIMETIRKLN--YEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLA  520 (976)
Q Consensus       464 ~pi~~~~~~~l~~~l~~~l~~~~--~~~p~~~Q~~~i~~il~g~d~i~~a~TGsGKT~~  520 (976)
                      .|-.+|.+++....+...+...-  +..|..++...   +...+.+|+.||+|+|||+.
T Consensus        49 ~~~~~~~di~g~~~~k~~l~~~~~~l~~~~~~~~~g---~~~~~giLL~GppGtGKT~l  104 (495)
T TIGR01241        49 KPKVTFKDVAGIDEAKEELMEIVDFLKNPSKFTKLG---AKIPKGVLLVGPPGTGKTLL  104 (495)
T ss_pred             CCCCCHHHhCCHHHHHHHHHHHHHHHHCHHHHHhcC---CCCCCcEEEECCCCCCHHHH
Confidence            45567777765555544333210  11121121111   11235799999999999975

HflB(FtsH) is a pleiotropic protein required for correct cell division in bacteria. It has ATP-dependent zinc metalloprotease activity. It was formerly designated cell division protein FtsH.

>KOG1132 consensus Helicase of the DEAD superfamily [Replication, recombination and repair]

Probab=89.09  E-value=7.1  Score=47.91  Aligned_cols=104  Identities=17%  Similarity=0.210  Sum_probs=65.5

Q ss_pred             cEEEEecCHHHHHHHHHHHHHC-------CCCceeccCCCCHHHHHHHHHHhccC--------CccEEEecCcccccCCC
Q 002040          716 KILIFVHSQEKCDALFRDLLKH-------GYPCLSLHGAKDQTDRESTISDFKSN--------VCNLLIATSVAARGLDV  780 (976)
Q Consensus       716 kvLIF~~s~~~~~~l~~~L~~~-------~~~~~~lhg~~~~~~R~~~~~~F~~g--------~~~vLVaT~v~~~GlDi  780 (976)
                      .+|||++++...+.+...+...       ++.- .+.+--+...-..++..|.++        ..-+.||--.+++|||+
T Consensus       563 G~L~FfPSY~vmdk~~tfw~~~~~we~~~~vk~-l~vEPr~k~~f~e~m~~y~~~i~~pes~ga~~~aVcRGKVSEGlDF  641 (945)
T KOG1132|consen  563 GLLIFFPSYPVMDKLITFWQNRGLWERMEKVKK-LVVEPRSKSEFTEVMSRYYNAIADPESSGAVFFAVCRGKVSEGLDF  641 (945)
T ss_pred             ceEEeccchHHHHHHHHHHHcchHHHHhhcccC-ceeccCCccchHHHHHHHHHHhhCccccceEEEEEecccccCCCCc
Confidence            4999999999888885555432       1222 222222444445666666533        33455677788999999


Q ss_pred             CC--CcEEEEeCCCCC--------------------------------------HHHHHHHhcccCCCCCccEEEEEecC
Q 002040          781 KE--LELVINFDAPNH--------------------------------------YEDYVHRVGRTGRAGRKGCAITFISE  820 (976)
Q Consensus       781 ~~--v~~VI~~d~p~s--------------------------------------~~~y~Qr~GR~gR~g~~g~~~~~~~~  820 (976)
                      .+  ...||..+.|.-                                      .-...|.+||+-|.-+.=.+++|++.
T Consensus       642 sD~~~RaVI~tGlPyP~~~D~~V~lK~~y~D~~~~~~g~~s~~lsg~eWY~~qA~RAvNQAiGRviRHR~D~Gav~l~D~  721 (945)
T KOG1132|consen  642 SDDNGRAVIITGLPYPPVMDPRVKLKKQYLDENSSLKGAKSQLLSGQEWYSQQAYRAVNQAIGRVIRHRNDYGAVILCDD  721 (945)
T ss_pred             cccCCceeEEecCCCCCCCCHHHHHHHHhhhhhccccccccccccchHHHHhhHHHHHHHHHHHHHhhhcccceeeEeec
Confidence            76  667888777641                                      11235999999987555445556654

>PRK10865 protein disaggregation chaperone; Provisional

Probab=89.04  E-value=2.7  Score=53.41  Aligned_cols=19  Identities=21%  Similarity=0.282  Sum_probs=15.9

Q ss_pred             CCCEEEEcCCCCchHHHHH
Q 002040          504 GRDCIGVAKTGSGKTLAFV  522 (976)
Q Consensus       504 g~d~i~~a~TGsGKT~~~~  522 (976)
                      ..++|++|++|+|||...-
T Consensus       199 ~~n~lL~G~pGvGKT~l~~  217 (857)
T PRK10865        199 KNNPVLIGEPGVGKTAIVE  217 (857)
T ss_pred             cCceEEECCCCCCHHHHHH
Confidence            3589999999999998643

>PRK06647 DNA polymerase III subunits gamma and tau; Validated

Probab=89.01  E-value=3  Score=50.24  Aligned_cols=19  Identities=26%  Similarity=0.078  Sum_probs=15.3

Q ss_pred             CEEEEcCCCCchHHHHHHH
Q 002040          506 DCIGVAKTGSGKTLAFVLP  524 (976)
Q Consensus       506 d~i~~a~TGsGKT~~~~l~  524 (976)
                      -+|+.||.|+|||.++.+.
T Consensus        40 ayLf~Gp~G~GKTt~Ar~l   58 (563)
T PRK06647         40 AYIFSGPRGVGKTSSARAF   58 (563)
T ss_pred             EEEEECCCCCCHHHHHHHH
Confidence            4789999999999875443

>TIGR00678 holB DNA polymerase III, delta' subunit

Probab=88.91  E-value=2.9  Score=42.66  Aligned_cols=24  Identities=17%  Similarity=0.263  Sum_probs=17.1

Q ss_pred             CEEEEcCCCCchHHHHHHHHHHHHh
Q 002040          506 DCIGVAKTGSGKTLAFVLPMLRHIK  530 (976)
Q Consensus       506 d~i~~a~TGsGKT~~~~l~il~~l~  530 (976)
                      .+|+.|+.|+|||..+. .+...+.
T Consensus        16 ~~L~~G~~G~gkt~~a~-~~~~~l~   39 (188)
T TIGR00678        16 AYLFAGPEGVGKELLAL-ALAKALL   39 (188)
T ss_pred             EEEEECCCCCCHHHHHH-HHHHHHc
Confidence            48899999999997643 3444443

At position 126-127 of the seed alignment, this family lacks the HM motif of gamma/tau; at 132 it has a near-invariant A vs. an invariant F in gamma/tau.

>PF01443 Viral_helicase1: Viral (Superfamily 1) RNA helicase; InterPro: IPR000606 This entry includes RNA and DNA helicases

Probab=88.90  E-value=0.53  Score=49.82  Aligned_cols=19  Identities=26%  Similarity=0.359  Sum_probs=14.3

Q ss_pred             EEEEcCCCCchHHHHHHHHH
Q 002040          507 CIGVAKTGSGKTLAFVLPML  526 (976)
Q Consensus       507 ~i~~a~TGsGKT~~~~l~il  526 (976)
                      ++|.|..|||||.. +.-++
T Consensus         1 ~vv~G~pGsGKSt~-i~~~~   19 (234)
T PF01443_consen    1 IVVHGVPGSGKSTL-IKKLL   19 (234)
T ss_pred             CEEEcCCCCCHHHH-HHHHH
Confidence            47889999999985 44444

Some of the members are found in positive-strand single stranded RNA viruses. The helicase has multiple roles at different stages of viral RNA replication, as dissected by mutational analysis [].; GO: 0004386 helicase activity

>PF12846 AAA_10: AAA-like domain

Probab=88.77  E-value=1.2  Score=49.07  Aligned_cols=41  Identities=29%  Similarity=0.458  Sum_probs=28.8

Q ss_pred             CCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHH
Q 002040          505 RDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELV  553 (976)
Q Consensus       505 ~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La  553 (976)
                      .+++++|+||||||+.+. .++..+..       .++.++|+=|.-+..
T Consensus         2 ~h~~i~G~tGsGKT~~~~-~l~~~~~~-------~g~~~~i~D~~g~~~   42 (304)
T PF12846_consen    2 PHTLILGKTGSGKTTLLK-NLLEQLIR-------RGPRVVIFDPKGDYS   42 (304)
T ss_pred             CeEEEECCCCCcHHHHHH-HHHHHHHH-------cCCCEEEEcCCchHH
Confidence            578999999999998755 55544443       256778887765443

>PRK13900 type IV secretion system ATPase VirB11; Provisional

Probab=88.76  E-value=1.3  Score=49.57  Aligned_cols=45  Identities=27%  Similarity=0.277  Sum_probs=30.2

Q ss_pred             HHhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHH
Q 002040          500 VIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELV  553 (976)
Q Consensus       500 ~il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La  553 (976)
                      ++..+.+++++|+||||||+. +-+++.++-.        ..+++++=-+.+|.
T Consensus       156 ~v~~~~nili~G~tgSGKTTl-l~aL~~~ip~--------~~ri~tiEd~~El~  200 (332)
T PRK13900        156 AVISKKNIIISGGTSTGKTTF-TNAALREIPA--------IERLITVEDAREIV  200 (332)
T ss_pred             HHHcCCcEEEECCCCCCHHHH-HHHHHhhCCC--------CCeEEEecCCCccc
Confidence            344678999999999999974 4555555422        33566665666653

>TIGR02858 spore_III_AA stage III sporulation protein AA

Probab=88.74  E-value=1.7  Score=47.22  Aligned_cols=24  Identities=21%  Similarity=0.339  Sum_probs=17.9

Q ss_pred             HHHHHhc-C--CCEEEEcCCCCchHHH
Q 002040          497 ALPVIMS-G--RDCIGVAKTGSGKTLA  520 (976)
Q Consensus       497 ~i~~il~-g--~d~i~~a~TGsGKT~~  520 (976)
                      .++.+.. +  .++++.|++|+|||+.
T Consensus       101 ~l~~l~~~~~~~~~~i~g~~g~GKttl  127 (270)
T TIGR02858       101 LLPYLVRNNRVLNTLIISPPQCGKTTL  127 (270)
T ss_pred             HHHHHHhCCCeeEEEEEcCCCCCHHHH
Confidence            3555553 3  5789999999999974

Members of this protein are the stage III sporulation protein AA, encoded by one of several genes in the spoIIIA locus. It seems that this protein is found in a species if and only if that species is capable of endospore formation.

>PRK06904 replicative DNA helicase; Validated

Probab=88.69  E-value=3.9  Score=48.26  Aligned_cols=49  Identities=16%  Similarity=0.100  Sum_probs=27.0

Q ss_pred             CCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHH
Q 002040          504 GRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDI  560 (976)
Q Consensus       504 g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~  560 (976)
                      |.=+||.|.||.|||.. ++-+..++...      .+..|+|++.- .-..|+...+
T Consensus       221 G~LiiIaarPg~GKTaf-alnia~~~a~~------~g~~Vl~fSlE-Ms~~ql~~Rl  269 (472)
T PRK06904        221 SDLIIVAARPSMGKTTF-AMNLCENAAMA------SEKPVLVFSLE-MPAEQIMMRM  269 (472)
T ss_pred             CcEEEEEeCCCCChHHH-HHHHHHHHHHh------cCCeEEEEecc-CCHHHHHHHH
Confidence            34467778999999975 44444443321      13446666532 3334444443

>PRK14953 DNA polymerase III subunits gamma and tau; Provisional

Probab=88.61  E-value=2.1  Score=50.55  Aligned_cols=28  Identities=14%  Similarity=0.224  Sum_probs=24.2

Q ss_pred             ccceeeeecCCcHHHHHHHHHHHHHHHH
Q 002040          928 IRKLYLFIEGPTEQSVKRAKAELKRVLE  955 (976)
Q Consensus       928 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~  955 (976)
                      +-|+|+.||++.+...+.-+.-|+...-
T Consensus       416 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~  443 (486)
T PRK14953        416 EGKITIKVEKSEEDTLDLEIKSIKKYFP  443 (486)
T ss_pred             cCceEEEecccHHHHHHHHHHHHHHhCC
Confidence            8899999999999999888888887653

>cd01128 rho_factor Transcription termination factor rho is a bacterial ATP-dependent RNA/DNA helicase

Probab=88.56  E-value=1.7  Score=46.51  Aligned_cols=20  Identities=35%  Similarity=0.331  Sum_probs=17.3

Q ss_pred             HhcCCCEEEEcCCCCchHHH
Q 002040          501 IMSGRDCIGVAKTGSGKTLA  520 (976)
Q Consensus       501 il~g~d~i~~a~TGsGKT~~  520 (976)
                      +-.|+.+++.|+.|+|||+.
T Consensus        13 i~~Gqr~~I~G~~G~GKTTL   32 (249)
T cd01128          13 IGKGQRGLIVAPPKAGKTTL   32 (249)
T ss_pred             cCCCCEEEEECCCCCCHHHH
Confidence            45788999999999999964

It is a homohexamer. Each monomer consists of an N-terminal domain of the OB fold, which is responsible for binding to cysteine rich nucleotides. This alignment is of the C-terminal ATP binding domain.

>CHL00095 clpC Clp protease ATP binding subunit

Probab=88.55  E-value=2.7  Score=53.32  Aligned_cols=23  Identities=22%  Similarity=0.082  Sum_probs=17.6

Q ss_pred             CCCEEEEcCCCCchHHHHHHHHH
Q 002040          504 GRDCIGVAKTGSGKTLAFVLPML  526 (976)
Q Consensus       504 g~d~i~~a~TGsGKT~~~~l~il  526 (976)
                      ..++|++|++|+|||..+-..+.
T Consensus       200 ~~n~lL~G~pGvGKTal~~~la~  222 (821)
T CHL00095        200 KNNPILIGEPGVGKTAIAEGLAQ  222 (821)
T ss_pred             cCCeEEECCCCCCHHHHHHHHHH
Confidence            35899999999999987543333

>PRK00080 ruvB Holliday junction DNA helicase RuvB; Reviewed

Probab=88.53  E-value=0.83  Score=51.32  Aligned_cols=18  Identities=22%  Similarity=0.135  Sum_probs=15.2

Q ss_pred             CCEEEEcCCCCchHHHHH
Q 002040          505 RDCIGVAKTGSGKTLAFV  522 (976)
Q Consensus       505 ~d~i~~a~TGsGKT~~~~  522 (976)
                      ..+++.||+|+|||..+.
T Consensus        52 ~~~ll~GppG~GKT~la~   69 (328)
T PRK00080         52 DHVLLYGPPGLGKTTLAN   69 (328)
T ss_pred             CcEEEECCCCccHHHHHH
Confidence            479999999999997643

>CHL00176 ftsH cell division protein; Validated

Probab=88.45  E-value=1.2  Score=54.36  Aligned_cols=17  Identities=35%  Similarity=0.501  Sum_probs=14.8

Q ss_pred             CCEEEEcCCCCchHHHH
Q 002040          505 RDCIGVAKTGSGKTLAF  521 (976)
Q Consensus       505 ~d~i~~a~TGsGKT~~~  521 (976)
                      +.+|+.||+|+|||+.+
T Consensus       217 ~gVLL~GPpGTGKT~LA  233 (638)
T CHL00176        217 KGVLLVGPPGTGKTLLA  233 (638)
T ss_pred             ceEEEECCCCCCHHHHH
Confidence            57999999999999753

>TIGR03881 KaiC_arch_4 KaiC domain protein, PAE1156 family

Probab=88.38  E-value=3.5  Score=43.55  Aligned_cols=49  Identities=18%  Similarity=0.220  Sum_probs=28.7

Q ss_pred             cCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHH
Q 002040          503 SGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDI  560 (976)
Q Consensus       503 ~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~  560 (976)
                      .|..+++.|++|+|||+.++..+...+..        +..+++++. -..+.++...+
T Consensus        19 ~G~~~~i~G~~G~GKT~l~~~~~~~~~~~--------g~~~~~is~-e~~~~~i~~~~   67 (229)
T TIGR03881        19 RGFFVAVTGEPGTGKTIFCLHFAYKGLRD--------GDPVIYVTT-EESRESIIRQA   67 (229)
T ss_pred             CCeEEEEECCCCCChHHHHHHHHHHHHhc--------CCeEEEEEc-cCCHHHHHHHH
Confidence            35678999999999998655444444321        335566653 22334444433

Members of this protein family are archaeal single-domain KaiC_related proteins, homologous to the Cyanobacterial circadian clock cycle protein KaiC, an autokinase/autophosphorylase that has two copies of the domain.

>PRK13764 ATPase; Provisional

Probab=88.35  E-value=0.93  Score=54.43  Aligned_cols=27  Identities=11%  Similarity=0.166  Sum_probs=20.9

Q ss_pred             cCCCEEEEcCCCCchHHHHHHHHHHHHh
Q 002040          503 SGRDCIGVAKTGSGKTLAFVLPMLRHIK  530 (976)
Q Consensus       503 ~g~d~i~~a~TGsGKT~~~~l~il~~l~  530 (976)
                      .+.++|++|+||||||+. +.+++.++.
T Consensus       256 ~~~~ILIsG~TGSGKTTl-l~AL~~~i~  282 (602)
T PRK13764        256 RAEGILIAGAPGAGKSTF-AQALAEFYA  282 (602)
T ss_pred             cCCEEEEECCCCCCHHHH-HHHHHHHHh
Confidence            467899999999999975 555666654

>KOG1513 consensus Nuclear helicase MOP-3/SNO (DEAD-box superfamily) [Transcription; Signal transduction mechanisms]

Probab=88.34  E-value=1.1  Score=53.48  Aligned_cols=228  Identities=16%  Similarity=0.173  Sum_probs=113.2

Q ss_pred             CCCcHHHHHHHHHHhc--------CC--CEEEEc--CCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHH
Q 002040          488 EKPMPIQAQALPVIMS--------GR--DCIGVA--KTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQ  555 (976)
Q Consensus       488 ~~p~~~Q~~~i~~il~--------g~--d~i~~a--~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q  555 (976)
                      ..+...|.++|-...+        |.  .+||-.  ..|-|.|++. +.+-++|..        ..++|++.-+..|-..
T Consensus       263 g~lSALQLEav~YAcQ~He~llPsG~RaGfLiGDGAGVGKGRTvAg-iIfeNyLkG--------RKrAlW~SVSsDLKfD  333 (1300)
T KOG1513|consen  263 GHLSALQLEAVTYACQAHEVLLPSGQRAGFLIGDGAGVGKGRTVAG-IIFENYLKG--------RKRALWFSVSSDLKFD  333 (1300)
T ss_pred             cchhHHHHHHHHHHHhhhhhcCCCCccceeeeccCcccCCCceeEE-EEehhhhcc--------cceeEEEEeccccccc
Confidence            3566788888866553        22  244443  4555667653 323334332        3578999887777655


Q ss_pred             HHHHHHHHHhhcCcEEEEee----CCCChHHHHHHHhcCCeEEEeCchhHHHHHHhcCCcc-cc---c------CCceEE
Q 002040          556 IHSDIRKFAKVMGVRCVPVY----GGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGGKI-TN---L------RRVTYL  621 (976)
Q Consensus       556 ~~~~~~~~~~~~~~~~~~~~----gg~~~~~~~~~l~~~~~Iiv~Tp~~L~~~l~~~~~~~-~~---l------~~~~~v  621 (976)
                      .-..+..+. ..++.|..+.    +..+-.+. ...  .-.||+||+..|+-.-....++. ..   |      ..=++|
T Consensus       334 AERDL~Dig-A~~I~V~alnK~KYakIss~en-~n~--krGViFaTYtaLIGEs~~~~~kyrtR~rQllqW~Ge~feGvI  409 (1300)
T KOG1513|consen  334 AERDLRDIG-ATGIAVHALNKFKYAKISSKEN-TNT--KRGVIFATYTALIGESQGKGGKYRTRFRQLLQWCGEDFEGVI  409 (1300)
T ss_pred             hhhchhhcC-CCCccceehhhccccccccccc-CCc--cceeEEEeeHhhhhhccccCchHHHHHHHHHHHhhhccceeE
Confidence            555555432 2344443321    11100000 011  23799999988865433211111 11   1      112589


Q ss_pred             EecCcccccc---cC------CchHHHHHHHhcCCCCcEEEEeccC---cHHHHHHHHHHcCCCeEEEeCCcccccCCce
Q 002040          622 VMDEADRMFD---MG------FEPQITRIVQNIRPDRQTVLFSATF---PRQVEILARKVLNKPVEIQVGGRSVVNKDIT  689 (976)
Q Consensus       622 VlDEah~~~~---~~------f~~~i~~il~~~~~~~q~i~~SAT~---~~~~~~l~~~~l~~~~~i~~~~~~~~~~~i~  689 (976)
                      |+||||+.-+   ++      -+..+..+-.. -|+..+|.-|||-   |.++..+.+..+-        +...      
T Consensus       410 vfDECHkAKNL~p~~~~k~TKtG~tVLdLQk~-LP~ARVVYASATGAsEPrNMaYM~RLGlW--------Gegt------  474 (1300)
T KOG1513|consen  410 VFDECHKAKNLVPTAGAKSTKTGKTVLDLQKK-LPNARVVYASATGASEPRNMAYMVRLGLW--------GEGT------  474 (1300)
T ss_pred             EehhhhhhcccccccCCCcCcccHhHHHHHHh-CCCceEEEeeccCCCCcchhhhhhhhccc--------cCCC------
Confidence            9999996543   11      22334444344 4677899999984   4444333322211        1111      


Q ss_pred             EEEEecCcchHHHHHHHHHHhhhcCCcEEEEecCHHHHHHHHHHHHHCCCCceeccCCCCH
Q 002040          690 QLVEVRPESDRFLRLLELLGEWYEKGKILIFVHSQEKCDALFRDLLKHGYPCLSLHGAKDQ  750 (976)
Q Consensus       690 q~~~~~~~~~k~~~l~~~l~~~~~~~kvLIF~~s~~~~~~l~~~L~~~~~~~~~lhg~~~~  750 (976)
                             ...-|..++..+....-+.--||-+..+..-..|+..|.-.|+.+.+--=.|+.
T Consensus       475 -------af~eF~eFi~AvEkRGvGAMEIVAMDMK~rGmYiARQLSFkgVsFrieEv~ls~  528 (1300)
T KOG1513|consen  475 -------AFPEFEEFIHAVEKRGVGAMEIVAMDMKLRGMYIARQLSFKGVSFRIEEVPLSK  528 (1300)
T ss_pred             -------cCccHHHHHHHHHhcCCceeeeeehhhhhhhhhhhhhccccCceEEEEecccCH
Confidence                   111233444444332222234666666666677777776666655443333443

>PF03796 DnaB_C: DnaB-like helicase C terminal domain; InterPro: IPR007694 The hexameric helicase DnaB unwinds the DNA duplex at the Escherichia coli chromosome replication fork

Probab=88.32  E-value=1.1  Score=48.50  Aligned_cols=111  Identities=16%  Similarity=0.152  Sum_probs=55.4

Q ss_pred             CCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccC---HHHHHHHHHHHHHHHhhcCcEEEEeeCCCChH
Q 002040          505 RDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPT---RELVQQIHSDIRKFAKVMGVRCVPVYGGSGVA  581 (976)
Q Consensus       505 ~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Pt---r~La~Q~~~~~~~~~~~~~~~~~~~~gg~~~~  581 (976)
                      .=+++.|.||.|||..++-.+++.+...       +..|++++.-   .+++..+...+      .++....+..|....
T Consensus        20 ~L~vi~a~pg~GKT~~~l~ia~~~a~~~-------~~~vly~SlEm~~~~l~~R~la~~------s~v~~~~i~~g~l~~   86 (259)
T PF03796_consen   20 ELTVIAARPGVGKTAFALQIALNAALNG-------GYPVLYFSLEMSEEELAARLLARL------SGVPYNKIRSGDLSD   86 (259)
T ss_dssp             -EEEEEESTTSSHHHHHHHHHHHHHHTT-------SSEEEEEESSS-HHHHHHHHHHHH------HTSTHHHHHCCGCHH
T ss_pred             cEEEEEecccCCchHHHHHHHHHHHHhc-------CCeEEEEcCCCCHHHHHHHHHHHh------hcchhhhhhccccCH
Confidence            4477889999999976555455444432       4567777742   33333332222      222222222233222


Q ss_pred             HHHH-------HHhcCCeEE-EeCch----hHHHHHHhcCCcccccCCceEEEecCccccccc
Q 002040          582 QQIS-------ELKRGTEIV-VCTPG----RMIDILCTSGGKITNLRRVTYLVMDEADRMFDM  632 (976)
Q Consensus       582 ~~~~-------~l~~~~~Ii-v~Tp~----~L~~~l~~~~~~~~~l~~~~~vVlDEah~~~~~  632 (976)
                      ..+.       .+.. ..++ ..+|.    .|...+....   .....+.+||||=.|.|...
T Consensus        87 ~e~~~~~~~~~~l~~-~~l~i~~~~~~~~~~i~~~i~~~~---~~~~~~~~v~IDyl~ll~~~  145 (259)
T PF03796_consen   87 EEFERLQAAAEKLSD-LPLYIEDTPSLTIDDIESKIRRLK---REGKKVDVVFIDYLQLLKSE  145 (259)
T ss_dssp             HHHHHHHHHHHHHHT-SEEEEEESSS-BHHHHHHHHHHHH---HHSTTEEEEEEEEGGGSBTS
T ss_pred             HHHHHHHHHHHHHhh-CcEEEECCCCCCHHHHHHHHHHHH---hhccCCCEEEechHHHhcCC
Confidence            2222       2222 3344 34443    3433332210   12267899999999977653

Although the mechanism by which DnaB both couples ATP hydrolysis to translocation along DNA and denatures the duplex is unknown, a change in the quaternary structure of the protein involving dimerization of the N-terminal domain has been observed and may occur during the enzymatic cycle. This C-terminal domain contains an ATP-binding site and is therefore probably the site of ATP hydrolysis. ; GO: 0003678 DNA helicase activity, 0005524 ATP binding, 0006260 DNA replication; PDB: 1Q57_E 1E0K_D 1E0J_B 1CR2_A 1CR4_A 1CR1_A 1CR0_A 1MI8_A 2R6D_B 2R6C_C ....

>TIGR00614 recQ_fam ATP-dependent DNA helicase, RecQ family

Probab=88.21  E-value=2.1  Score=50.77  Aligned_cols=76  Identities=18%  Similarity=0.284  Sum_probs=63.1

Q ss_pred             cCCcEEEEecCHHHHHHHHHHHHHCCCCceeccCCCCHHHHHHHHHHhccCCccEEEecCc-ccc------cC-CCCCCc
Q 002040          713 EKGKILIFVHSQEKCDALFRDLLKHGYPCLSLHGAKDQTDRESTISDFKSNVCNLLIATSV-AAR------GL-DVKELE  784 (976)
Q Consensus       713 ~~~kvLIF~~s~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLVaT~v-~~~------Gl-Di~~v~  784 (976)
                      ..+.+||++|++.-+......|...|+.+..++|..+..++..++..+..|.++||++|+- +..      .+ ....+.
T Consensus        50 ~~~~~lVi~P~~~L~~dq~~~l~~~gi~~~~l~~~~~~~~~~~i~~~~~~~~~~il~~TPe~l~~~~~~~~~l~~~~~i~  129 (470)
T TIGR00614        50 SDGITLVISPLISLMEDQVLQLKASGIPATFLNSSQSKEQQKNVLTDLKDGKIKLLYVTPEKCSASNRLLQTLEERKGIT  129 (470)
T ss_pred             cCCcEEEEecHHHHHHHHHHHHHHcCCcEEEEeCCCCHHHHHHHHHHHhcCCCCEEEECHHHHcCchhHHHHHHhcCCcC
Confidence            4678999999999999888899999999999999999999999999999999999999972 222      12 455677


Q ss_pred             EEEE
Q 002040          785 LVIN  788 (976)
Q Consensus       785 ~VI~  788 (976)
                      +||+
T Consensus       130 ~iVi  133 (470)
T TIGR00614       130 LIAV  133 (470)
T ss_pred             EEEE
Confidence            7764

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

>cd01129 PulE-GspE PulE/GspE The type II secretory pathway is the main terminal branch of the general secretory pathway (GSP)

Probab=88.18  E-value=1.3  Score=47.88  Aligned_cols=37  Identities=22%  Similarity=0.308  Sum_probs=24.5

Q ss_pred             HHHHHHHHHHhc--CCCEEEEcCCCCchHHHHHHHHHHHH
Q 002040          492 PIQAQALPVIMS--GRDCIGVAKTGSGKTLAFVLPMLRHI  529 (976)
Q Consensus       492 ~~Q~~~i~~il~--g~d~i~~a~TGsGKT~~~~l~il~~l  529 (976)
                      +.|.+.|..++.  +..++++|+||||||+. +..++..+
T Consensus        66 ~~~~~~l~~~~~~~~GlilisG~tGSGKTT~-l~all~~i  104 (264)
T cd01129          66 PENLEIFRKLLEKPHGIILVTGPTGSGKTTT-LYSALSEL  104 (264)
T ss_pred             HHHHHHHHHHHhcCCCEEEEECCCCCcHHHH-HHHHHhhh
Confidence            455666655543  33578899999999985 44455554

It is responsible for the export the majority of Gram-negative bacterial exoenzymes and toxins. PulE is a cytoplasmic protein of the GSP, which contains an ATP binding site and a tetracysteine motif. This subgroup also includes PillB and HofB.

>PRK05416 glmZ(sRNA)-inactivating NTPase; Provisional

Probab=88.17  E-value=2.1  Score=46.91  Aligned_cols=26  Identities=23%  Similarity=0.252  Sum_probs=21.0

Q ss_pred             CHHHHHHHHHHHHHCCCCceeccCCCC
Q 002040          723 SQEKCDALFRDLLKHGYPCLSLHGAKD  749 (976)
Q Consensus       723 s~~~~~~l~~~L~~~~~~~~~lhg~~~  749 (976)
                      |+..++.|+..|. .++.+...|-++.
T Consensus       259 SV~~~e~l~~~l~-~~~~v~~~Hrd~~  284 (288)
T PRK05416        259 SVAIAERLAERLS-KGYNVQVRHRDLE  284 (288)
T ss_pred             HHHHHHHHHHHHh-CCCcEEEEeCccc
Confidence            5678899999994 6889999887764

>TIGR00763 lon ATP-dependent protease La

Probab=88.09  E-value=2.2  Score=53.75  Aligned_cols=17  Identities=35%  Similarity=0.255  Sum_probs=14.6

Q ss_pred             CCCEEEEcCCCCchHHH
Q 002040          504 GRDCIGVAKTGSGKTLA  520 (976)
Q Consensus       504 g~d~i~~a~TGsGKT~~  520 (976)
                      +..++++||+|+|||..
T Consensus       347 ~~~lll~GppG~GKT~l  363 (775)
T TIGR00763       347 GPILCLVGPPGVGKTSL  363 (775)
T ss_pred             CceEEEECCCCCCHHHH
Confidence            45689999999999975

This protein is induced by heat shock and other stresses in E. coli, B. subtilis, and other species. The yeast member, designated PIM1, is located in the mitochondrial matrix, required for mitochondrial function, and also induced by heat shock.

>TIGR01242 26Sp45 26S proteasome subunit P45 family

Probab=88.00  E-value=1.2  Score=50.91  Aligned_cols=17  Identities=29%  Similarity=0.427  Sum_probs=14.7

Q ss_pred             CCCEEEEcCCCCchHHH
Q 002040          504 GRDCIGVAKTGSGKTLA  520 (976)
Q Consensus       504 g~d~i~~a~TGsGKT~~  520 (976)
                      .+.+++.||+|+|||+.
T Consensus       156 p~gvLL~GppGtGKT~l  172 (364)
T TIGR01242       156 PKGVLLYGPPGTGKTLL  172 (364)
T ss_pred             CceEEEECCCCCCHHHH
Confidence            35699999999999975

Many proteins may score above the trusted cutoff because an internal

>COG5008 PilU Tfp pilus assembly protein, ATPase PilU [Cell motility and secretion / Intracellular trafficking and secretion]

Probab=87.99  E-value=0.42  Score=50.10  Aligned_cols=45  Identities=27%  Similarity=0.344  Sum_probs=29.9

Q ss_pred             CcccccccCCCCHHHHHHHHHcCCCCCcHHHHHHHHHHhcCC-CEEEEcCCCCchHHHHHHHHHHH
Q 002040          464 KPIKTWHQTGLTSKIMETIRKLNYEKPMPIQAQALPVIMSGR-DCIGVAKTGSGKTLAFVLPMLRH  528 (976)
Q Consensus       464 ~pi~~~~~~~l~~~l~~~l~~~~~~~p~~~Q~~~i~~il~g~-d~i~~a~TGsGKT~~~~l~il~~  528 (976)
                      ..|.+|+.++||+.+.+.                   .+..+ -+|++|+|||||++. +..|+.+
T Consensus       105 ~~IPt~eeL~LPevlk~l-------------------a~~kRGLviiVGaTGSGKSTt-mAaMi~y  150 (375)
T COG5008         105 TKIPTFEELKLPEVLKDL-------------------ALAKRGLVIIVGATGSGKSTT-MAAMIGY  150 (375)
T ss_pred             ccCCcHHhcCCcHHHHHh-------------------hcccCceEEEECCCCCCchhh-HHHHhcc
Confidence            345578888887766542                   12222 378889999999986 4555554

>COG1618 Predicted nucleotide kinase [Nucleotide transport and metabolism]

Probab=87.93  E-value=0.2  Score=48.77  Aligned_cols=119  Identities=18%  Similarity=0.251  Sum_probs=61.1

Q ss_pred             CEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHHHHhhcCcEEEEeeCCCChHHHHH
Q 002040          506 DCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQIS  585 (976)
Q Consensus       506 d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~~~~~~~~~~~~~~gg~~~~~~~~  585 (976)
                      .+++.|++|+|||+. ++-+...|....      -...-|+||-          +..-.+..|+.++.+..|...  +++
T Consensus         7 ki~ITG~PGvGKtTl-~~ki~e~L~~~g------~kvgGf~t~E----------VR~gGkR~GF~Ivdl~tg~~~--~la   67 (179)
T COG1618           7 KIFITGRPGVGKTTL-VLKIAEKLREKG------YKVGGFITPE----------VREGGKRIGFKIVDLATGEEG--ILA   67 (179)
T ss_pred             EEEEeCCCCccHHHH-HHHHHHHHHhcC------ceeeeEEeee----------eecCCeEeeeEEEEccCCceE--EEE
Confidence            578999999999975 666666665431      1123466663          233334456777666544311  000


Q ss_pred             HHhcCCeEEEeCchhHHHHHHhcCCc-c-cccCCceEEEecCcccccc--cCCchHHHHHHHh
Q 002040          586 ELKRGTEIVVCTPGRMIDILCTSGGK-I-TNLRRVTYLVMDEADRMFD--MGFEPQITRIVQN  644 (976)
Q Consensus       586 ~l~~~~~Iiv~Tp~~L~~~l~~~~~~-~-~~l~~~~~vVlDEah~~~~--~~f~~~i~~il~~  644 (976)
                      ... ....-|+-++...+.+..-... + .-+..-++|||||+--|-.  ..|...+..++..
T Consensus        68 ~~~-~~~~rvGkY~V~v~~le~i~~~al~rA~~~aDvIIIDEIGpMElks~~f~~~ve~vl~~  129 (179)
T COG1618          68 RVG-FSRPRVGKYGVNVEGLEEIAIPALRRALEEADVIIIDEIGPMELKSKKFREAVEEVLKS  129 (179)
T ss_pred             EcC-CCCcccceEEeeHHHHHHHhHHHHHHHhhcCCEEEEecccchhhccHHHHHHHHHHhcC
Confidence            000 1233444444444433211000 0 0133458999999996632  2355555555543

>cd00983 recA RecA is a bacterial enzyme which has roles in homologous recombination, DNA repair, and the induction of the SOS response

Probab=87.81  E-value=1.4  Score=48.99  Aligned_cols=43  Identities=19%  Similarity=0.099  Sum_probs=28.3

Q ss_pred             CCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHH
Q 002040          504 GRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQ  554 (976)
Q Consensus       504 g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~  554 (976)
                      |.-+.+.||+|||||+.++..+... ..       .+..|+++.+--.+-.
T Consensus        55 G~iteI~Gp~GsGKTtLal~~~~~~-~~-------~g~~~vyId~E~~~~~   97 (325)
T cd00983          55 GRIIEIYGPESSGKTTLALHAIAEA-QK-------LGGTVAFIDAEHALDP   97 (325)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHH-HH-------cCCCEEEECccccHHH
Confidence            4568899999999997644444443 32       2556788876555543

RecA couples ATP hydrolysis to DNA strand exchange.

>PRK14971 DNA polymerase III subunits gamma and tau; Provisional

Probab=87.80  E-value=4.3  Score=49.53  Aligned_cols=42  Identities=7%  Similarity=0.162  Sum_probs=25.0

Q ss_pred             ccCCceEEEecCcccccccCCchHHHHHHHhcCCCCcEEEEecc
Q 002040          614 NLRRVTYLVMDEADRMFDMGFEPQITRIVQNIRPDRQTVLFSAT  657 (976)
Q Consensus       614 ~l~~~~~vVlDEah~~~~~~f~~~i~~il~~~~~~~q~i~~SAT  657 (976)
                      .+..+.+|||||||.|.... ...+..++...+... +++|.+|
T Consensus       118 ~~~~~KVvIIdea~~Ls~~a-~naLLK~LEepp~~t-ifIL~tt  159 (614)
T PRK14971        118 QIGKYKIYIIDEVHMLSQAA-FNAFLKTLEEPPSYA-IFILATT  159 (614)
T ss_pred             ccCCcEEEEEECcccCCHHH-HHHHHHHHhCCCCCe-EEEEEeC
Confidence            34568899999999875422 234455555544433 4445555

>KOG0333 consensus U5 snRNP-like RNA helicase subunit [RNA processing and modification]

Probab=87.75  E-value=2.1  Score=49.16  Aligned_cols=71  Identities=17%  Similarity=0.335  Sum_probs=51.6

Q ss_pred             CCCeEEEEccCHHHHHHHHHHHHHHHhhcCcEEEEeeCCCChHHH---HHHHhc-CCeEEEeCchhHHHHHHhcCCcccc
Q 002040          539 DGPVGLIMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQ---ISELKR-GTEIVVCTPGRMIDILCTSGGKITN  614 (976)
Q Consensus       539 ~~~~vLIl~Ptr~La~Q~~~~~~~~~~~~~~~~~~~~gg~~~~~~---~~~l~~-~~~Iiv~Tp~~L~~~l~~~~~~~~~  614 (976)
                      ..|.++|.+.|..-|..++..+.+    .|+.++.++||.+..+.   +..+.. ..+|+|||.     ...    +-.+
T Consensus       516 ~~ppiIIFvN~kk~~d~lAk~LeK----~g~~~~tlHg~k~qeQRe~aL~~fr~~t~dIlVaTD-----vAg----RGID  582 (673)
T KOG0333|consen  516 FDPPIIIFVNTKKGADALAKILEK----AGYKVTTLHGGKSQEQRENALADFREGTGDILVATD-----VAG----RGID  582 (673)
T ss_pred             CCCCEEEEEechhhHHHHHHHHhh----ccceEEEeeCCccHHHHHHHHHHHHhcCCCEEEEec-----ccc----cCCC
Confidence            357789999998888776666655    68999999999887665   344555 469999994     222    2257


Q ss_pred             cCCceEEE
Q 002040          615 LRRVTYLV  622 (976)
Q Consensus       615 l~~~~~vV  622 (976)
                      +.++++||
T Consensus       583 IpnVSlVi  590 (673)
T KOG0333|consen  583 IPNVSLVI  590 (673)
T ss_pred             CCccceee
Confidence            77787776

>COG3598 RepA RecA-family ATPase [DNA replication, recombination, and repair]

Probab=87.74  E-value=3  Score=45.23  Aligned_cols=77  Identities=14%  Similarity=0.116  Sum_probs=43.5

Q ss_pred             HHHHHHHHHh-cCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCC--CCCCCeEEEEccCHHHHHHHHHHHHHHHhhcCc
Q 002040          493 IQAQALPVIM-SGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVA--AGDGPVGLIMAPTRELVQQIHSDIRKFAKVMGV  569 (976)
Q Consensus       493 ~Q~~~i~~il-~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~--~~~~~~vLIl~Ptr~La~Q~~~~~~~~~~~~~~  569 (976)
                      .|-+.|+.++ .|-.+|+.|+.|.|||++.+...+.......-+.  ..+..+||+|..--. -..+...++.++..+++
T Consensus        77 ~~P~lId~~fr~g~~~~~~gdsg~GKttllL~l~IalaaG~~lfG~~v~epGkvlyvslEl~-re~~L~Rl~~v~a~mgL  155 (402)
T COG3598          77 NSPQLIDEFFRKGYVSILYGDSGVGKTTLLLYLCIALAAGKNLFGNKVKEPGKVLYVSLELY-REDILERLEPVRARMGL  155 (402)
T ss_pred             cChhhhhHHhhcCeeEEEecCCcccHhHHHHHHHHHHHhhHHHhcccccCCCeEEEEEeccC-hHHHHHHHHHHHHHcCC
Confidence            4455666544 5667788899999999875544444333222111  223346677653211 13344667777776765


Q ss_pred             E
Q 002040          570 R  570 (976)
Q Consensus       570 ~  570 (976)
                      .
T Consensus       156 s  156 (402)
T COG3598         156 S  156 (402)
T ss_pred             C
Confidence            4

>TIGR02868 CydC thiol reductant ABC exporter, CydC subunit

Probab=87.69  E-value=1.3  Score=53.43  Aligned_cols=41  Identities=20%  Similarity=0.334  Sum_probs=29.0

Q ss_pred             cCCceEEEecCcccccccCCchHHHHHHHhcCCCCcEEEEe
Q 002040          615 LRRVTYLVMDEADRMFDMGFEPQITRIVQNIRPDRQTVLFS  655 (976)
Q Consensus       615 l~~~~~vVlDEah~~~~~~f~~~i~~il~~~~~~~q~i~~S  655 (976)
                      +.+-.++|+||+-.-+|......+...+..+.+++-+|+.|
T Consensus       486 l~~~~iliLDE~TSaLD~~te~~I~~~l~~~~~~~TvIiIt  526 (529)
T TIGR02868       486 LADAPILLLDEPTEHLDAGTESELLEDLLAALSGKTVVVIT  526 (529)
T ss_pred             hcCCCEEEEeCCcccCCHHHHHHHHHHHHHhcCCCEEEEEe
Confidence            56678899999987777766777777776665555555544

The gene pair cydCD encodes an ABC-family transporter in which each gene contains an N-terminal membrane-spanning domain (pfam00664) and a C-terminal ATP-binding domain (pfam00005). In E. coli these genes were discovered as mutants which caused the terminal heme-copper oxidase complex cytochrome bd to fail to assemble. Recent work has shown that the transporter is involved in export of redox-active thiol compounds such as cysteine and glutathione. The linkage to assembly of the cytochrome bd complex is further supported by the conserved operon structure found outside the gammaproteobacteria (cydABCD) containing both the transporter and oxidase genes components. The genes used as the seed members for this model are all either found in the gammproteobacterial context or the CydABCD context. All members of this family scoring above trusted at the time of its creation were from genomes which encode a cytochrome bd complex.

>PRK09354 recA recombinase A; Provisional

Probab=87.66  E-value=1.1  Score=50.18  Aligned_cols=42  Identities=19%  Similarity=0.144  Sum_probs=28.3

Q ss_pred             CCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHH
Q 002040          504 GRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELV  553 (976)
Q Consensus       504 g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La  553 (976)
                      |.-+.|.|++|||||+.++..+.+.. .       .+..|++|..--.+-
T Consensus        60 G~IteI~G~~GsGKTtLal~~~~~~~-~-------~G~~~~yId~E~s~~  101 (349)
T PRK09354         60 GRIVEIYGPESSGKTTLALHAIAEAQ-K-------AGGTAAFIDAEHALD  101 (349)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHH-H-------cCCcEEEECCccchH
Confidence            45688999999999986555444443 2       256677777655554

>PHA00012 I assembly protein

Probab=87.61  E-value=4.5  Score=44.43  Aligned_cols=25  Identities=28%  Similarity=0.357  Sum_probs=20.6

Q ss_pred             EEEEcCCCCchHHHHHHHHHHHHhc
Q 002040          507 CIGVAKTGSGKTLAFVLPMLRHIKD  531 (976)
Q Consensus       507 ~i~~a~TGsGKT~~~~l~il~~l~~  531 (976)
                      .++.|..|+|||+.++..|+..+..
T Consensus         4 ylITGkPGSGKSl~aV~~I~~~L~~   28 (361)
T PHA00012          4 YVVTGKLGAGKTLVAVSRIQDKLVK   28 (361)
T ss_pred             EEEecCCCCCchHHHHHHHHHHHHc
Confidence            5788999999999888777776654

>cd03221 ABCF_EF-3 ABCF_EF-3 Elongation factor 3 (EF-3) is a cytosolic protein required by fungal ribosomes for in vitro protein synthesis and for in vivo growth

Probab=87.58  E-value=2.4  Score=41.27  Aligned_cols=40  Identities=18%  Similarity=0.306  Sum_probs=27.1

Q ss_pred             cCCceEEEecCcccccccCCchHHHHHHHhcCCCCcEEEEecc
Q 002040          615 LRRVTYLVMDEADRMFDMGFEPQITRIVQNIRPDRQTVLFSAT  657 (976)
Q Consensus       615 l~~~~~vVlDEah~~~~~~f~~~i~~il~~~~~~~q~i~~SAT  657 (976)
                      +.+..++|+||.-.-+|......+..++..+.  . +|+++.-
T Consensus        86 ~~~p~illlDEP~~~LD~~~~~~l~~~l~~~~--~-til~~th  125 (144)
T cd03221          86 LENPNLLLLDEPTNHLDLESIEALEEALKEYP--G-TVILVSH  125 (144)
T ss_pred             hcCCCEEEEeCCccCCCHHHHHHHHHHHHHcC--C-EEEEEEC
Confidence            44568999999997777766666777776663  3 4444443

EF-3 stimulates the binding of the EF-1: GTP: aa-tRNA ternary complex to the ribosomal A site by facilitated release of the deacylated tRNA from the E site. The reaction requires ATP hydrolysis. EF-3 contains two ATP nucleotide binding sequence (NBS) motifs. NBSI is sufficient for the intrinsic ATPase activity. NBSII is essential for the ribosome-stimulated functions.

>TIGR02237 recomb_radB DNA repair and recombination protein RadB

Probab=87.53  E-value=2.6  Score=43.79  Aligned_cols=38  Identities=18%  Similarity=0.185  Sum_probs=24.9

Q ss_pred             CCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccC
Q 002040          504 GRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPT  549 (976)
Q Consensus       504 g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Pt  549 (976)
                      |.-+.+.|++|+|||...+..+.+.+.        .+..|+++.-.
T Consensus        12 g~i~~i~G~~GsGKT~l~~~~~~~~~~--------~g~~v~yi~~e   49 (209)
T TIGR02237        12 GTITQIYGPPGSGKTNICMILAVNAAR--------QGKKVVYIDTE   49 (209)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHh--------CCCeEEEEECC
Confidence            456889999999999875544444332        24456666653

This family consists exclusively of archaeal RadB protein, a homolog of bacterial RecA (TIGR02012), eukaryotic RAD51 (TIGR02239) and DMC1 (TIGR02238), and archaeal RadA (TIGR02236).

>PF01637 Arch_ATPase: Archaeal ATPase; InterPro: IPR011579 This domain has been found in a number of bacterial and archaeal proteins, all of which contain a conserved P-loop motif that is involved in binding ATP

Probab=87.51  E-value=0.39  Score=50.56  Aligned_cols=25  Identities=20%  Similarity=0.310  Sum_probs=18.1

Q ss_pred             CCCEEEEcCCCCchHHHHHHHHHHHH
Q 002040          504 GRDCIGVAKTGSGKTLAFVLPMLRHI  529 (976)
Q Consensus       504 g~d~i~~a~TGsGKT~~~~l~il~~l  529 (976)
                      +..++|.||.|+|||.. +..++..+
T Consensus        20 ~~~~~l~G~rg~GKTsL-l~~~~~~~   44 (234)
T PF01637_consen   20 SQHILLYGPRGSGKTSL-LKEFINEL   44 (234)
T ss_dssp             SSEEEEEESTTSSHHHH-HHHHHHHC
T ss_pred             CcEEEEEcCCcCCHHHH-HHHHHHHh
Confidence            36788889999999974 44455443

; GO: 0005524 ATP binding; PDB: 2FNA_A 2QEN_A.

>PRK06305 DNA polymerase III subunits gamma and tau; Validated

Probab=87.42  E-value=2.5  Score=49.64  Aligned_cols=20  Identities=20%  Similarity=0.101  Sum_probs=15.7

Q ss_pred             CEEEEcCCCCchHHHHHHHH
Q 002040          506 DCIGVAKTGSGKTLAFVLPM  525 (976)
Q Consensus       506 d~i~~a~TGsGKT~~~~l~i  525 (976)
                      .+|+.||.|+|||.++.+.+
T Consensus        41 a~Lf~Gp~G~GKtt~A~~lA   60 (451)
T PRK06305         41 AYLFSGIRGTGKTTLARIFA   60 (451)
T ss_pred             EEEEEcCCCCCHHHHHHHHH
Confidence            47899999999998754433

>PRK07004 replicative DNA helicase; Provisional

Probab=87.40  E-value=2.5  Score=49.68  Aligned_cols=23  Identities=22%  Similarity=0.013  Sum_probs=16.2

Q ss_pred             CCCEEEEcCCCCchHHHHHHHHH
Q 002040          504 GRDCIGVAKTGSGKTLAFVLPML  526 (976)
Q Consensus       504 g~d~i~~a~TGsGKT~~~~l~il  526 (976)
                      |.-+||.|.+|+|||..++-.+.
T Consensus       213 g~liviaarpg~GKT~~al~ia~  235 (460)
T PRK07004        213 GELIIVAGRPSMGKTAFSMNIGE  235 (460)
T ss_pred             CceEEEEeCCCCCccHHHHHHHH
Confidence            44577789999999975443333

>COG1219 ClpX ATP-dependent protease Clp, ATPase subunit [Posttranslational modification, protein turnover, chaperones]

Probab=87.35  E-value=0.42  Score=51.47  Aligned_cols=21  Identities=38%  Similarity=0.458  Sum_probs=17.0

Q ss_pred             hcCCCEEEEcCCCCchHHHHH
Q 002040          502 MSGRDCIGVAKTGSGKTLAFV  522 (976)
Q Consensus       502 l~g~d~i~~a~TGsGKT~~~~  522 (976)
                      ++.-|++++||||||||+.+.
T Consensus        95 L~KSNILLiGPTGsGKTlLAq  115 (408)
T COG1219          95 LSKSNILLIGPTGSGKTLLAQ  115 (408)
T ss_pred             eeeccEEEECCCCCcHHHHHH
Confidence            345689999999999998644

>TIGR02655 circ_KaiC circadian clock protein KaiC

Probab=87.35  E-value=2.8  Score=49.80  Aligned_cols=59  Identities=17%  Similarity=0.170  Sum_probs=38.9

Q ss_pred             HHHHHHhc-----CCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHHH
Q 002040          496 QALPVIMS-----GRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKF  563 (976)
Q Consensus       496 ~~i~~il~-----g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~~  563 (976)
                      ..+..++.     |.-+++.|++|+|||+..+..+...+.        +|.+|++++ +-+-..|+...+..+
T Consensus       250 ~~lD~~lgGG~~~gs~~li~G~~G~GKt~l~~~f~~~~~~--------~ge~~~y~s-~eEs~~~i~~~~~~l  313 (484)
T TIGR02655       250 VRLDEMCGGGFFKDSIILATGATGTGKTLLVSKFLENACA--------NKERAILFA-YEESRAQLLRNAYSW  313 (484)
T ss_pred             HhHHHHhcCCccCCcEEEEECCCCCCHHHHHHHHHHHHHH--------CCCeEEEEE-eeCCHHHHHHHHHHc
Confidence            34555554     456889999999999876655554433        255677776 445557777766654

Members of this family are the circadian clock protein KaiC, part of the kaiABC operon that controls circadian rhythm. It may be universal in Cyanobacteria. Each member has two copies of the KaiC domain (Pfam model pfam06745), which is also found in other proteins. KaiC performs autophosphorylation and acts as its own transcriptional repressor.

>KOG0737 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=87.08  E-value=2.7  Score=46.59  Aligned_cols=53  Identities=15%  Similarity=0.286  Sum_probs=31.5

Q ss_pred             cccccCCCCHHHHHHHHHcCCCCCcHHHHHHHH----HHhcCCCEEEEcCCCCchHHHHH
Q 002040          467 KTWHQTGLTSKIMETIRKLNYEKPMPIQAQALP----VIMSGRDCIGVAKTGSGKTLAFV  522 (976)
Q Consensus       467 ~~~~~~~l~~~l~~~l~~~~~~~p~~~Q~~~i~----~il~g~d~i~~a~TGsGKT~~~~  522 (976)
                      .+|.+.|-...+.+.|+..=+.   |.|.--+-    .+..-+.+++.||+|+|||.++-
T Consensus        89 v~f~DIggLe~v~~~L~e~Vil---Plr~pelF~~g~Ll~p~kGiLL~GPpG~GKTmlAK  145 (386)
T KOG0737|consen   89 VSFDDIGGLEEVKDALQELVIL---PLRRPELFAKGKLLRPPKGILLYGPPGTGKTMLAK  145 (386)
T ss_pred             eehhhccchHHHHHHHHHHHhh---cccchhhhcccccccCCccceecCCCCchHHHHHH
Confidence            4678877777777766653221   22211111    11123679999999999998643

>PRK09435 membrane ATPase/protein kinase; Provisional

Probab=87.00  E-value=11  Score=42.02  Aligned_cols=23  Identities=17%  Similarity=0.091  Sum_probs=15.4

Q ss_pred             EEEEcCCCCchHHHHHHHHHHHHh
Q 002040          507 CIGVAKTGSGKTLAFVLPMLRHIK  530 (976)
Q Consensus       507 ~i~~a~TGsGKT~~~~l~il~~l~  530 (976)
                      +-+.|+.|+|||+. +-.++..+.
T Consensus        59 igi~G~~GaGKSTl-~~~l~~~l~   81 (332)
T PRK09435         59 IGITGVPGVGKSTF-IEALGMHLI   81 (332)
T ss_pred             EEEECCCCCCHHHH-HHHHHHHHH
Confidence            56679999999974 444444443

>KOG0060 consensus Long-chain acyl-CoA transporter, ABC superfamily (involved in peroxisome organization and biogenesis) [Lipid transport and metabolism; General function prediction only]

Probab=86.97  E-value=0.71  Score=53.75  Aligned_cols=48  Identities=15%  Similarity=0.268  Sum_probs=30.8

Q ss_pred             EeCchhHHHHHHhcCCcccccCCceEEEecCcccccccCCchHHHHHHHhcC
Q 002040          595 VCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMGFEPQITRIVQNIR  646 (976)
Q Consensus       595 v~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDEah~~~~~~f~~~i~~il~~~~  646 (976)
                      |-+||-...+-...    .......+.|+|||-.-.+.+.+..+.++++...
T Consensus       570 vLS~GEqQRLa~AR----Lfy~kPk~AiLDE~TSAv~~dvE~~~Yr~~r~~g  617 (659)
T KOG0060|consen  570 VLSPGEQQRLAFAR----LFYHKPKFAILDECTSAVTEDVEGALYRKCREMG  617 (659)
T ss_pred             hcCHHHHHHHHHHH----HHhcCCceEEeechhhhccHHHHHHHHHHHHHcC
Confidence            44566544432211    2345678999999998777777777777776654

>PRK08506 replicative DNA helicase; Provisional

Probab=86.95  E-value=3.6  Score=48.57  Aligned_cols=48  Identities=17%  Similarity=0.081  Sum_probs=27.0

Q ss_pred             CCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHH
Q 002040          504 GRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDI  560 (976)
Q Consensus       504 g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~  560 (976)
                      |.-+|+.|.||.|||..++ -++.++..       .+..|+|++.- .-+.|+...+
T Consensus       192 G~LivIaarpg~GKT~fal-~ia~~~~~-------~g~~V~~fSlE-Ms~~ql~~Rl  239 (472)
T PRK08506        192 GDLIIIAARPSMGKTTLCL-NMALKALN-------QDKGVAFFSLE-MPAEQLMLRM  239 (472)
T ss_pred             CceEEEEcCCCCChHHHHH-HHHHHHHh-------cCCcEEEEeCc-CCHHHHHHHH
Confidence            3457778999999997544 44444432       24456666532 3334444443

>PRK10436 hypothetical protein; Provisional

Probab=86.94  E-value=1.1  Score=52.55  Aligned_cols=38  Identities=24%  Similarity=0.337  Sum_probs=25.3

Q ss_pred             HHHHHHHHHHhc--CCCEEEEcCCCCchHHHHHHHHHHHHh
Q 002040          492 PIQAQALPVIMS--GRDCIGVAKTGSGKTLAFVLPMLRHIK  530 (976)
Q Consensus       492 ~~Q~~~i~~il~--g~d~i~~a~TGsGKT~~~~l~il~~l~  530 (976)
                      +.|.+.|..++.  +.-+|++||||||||+. +..++.++.
T Consensus       204 ~~~~~~l~~~~~~~~GliLvtGpTGSGKTTt-L~a~l~~~~  243 (462)
T PRK10436        204 PAQLAQFRQALQQPQGLILVTGPTGSGKTVT-LYSALQTLN  243 (462)
T ss_pred             HHHHHHHHHHHHhcCCeEEEECCCCCChHHH-HHHHHHhhC
Confidence            555556655543  34578889999999986 345566543

>cd01125 repA Hexameric Replicative Helicase RepA

Probab=86.90  E-value=3.1  Score=44.30  Aligned_cols=61  Identities=13%  Similarity=0.136  Sum_probs=32.8

Q ss_pred             CEEEEcCCCCchHHHHHHHHHHHHhcCCCCC----CCCCCeEEEEccCHHHHHHHHHHHHHHHhhc
Q 002040          506 DCIGVAKTGSGKTLAFVLPMLRHIKDQPPVA----AGDGPVGLIMAPTRELVQQIHSDIRKFAKVM  567 (976)
Q Consensus       506 d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~----~~~~~~vLIl~Ptr~La~Q~~~~~~~~~~~~  567 (976)
                      -.+++|+.|+|||+.++..++......+-..    ...+..|||++--- =..++...+..+...+
T Consensus         3 ~~ll~g~~G~GKS~lal~la~~va~G~~~~g~~~~~~~~~~Vlyi~~Ed-~~~~i~~Rl~~i~~~~   67 (239)
T cd01125           3 VSALVAPGGTGKSSLLLVLALAMALGKNLFGGGLKVTEPGRVVYLSAED-PREEIHRRLEAILQHL   67 (239)
T ss_pred             eeEEEcCCCCCHHHHHHHHHHHHhcCccccCCccccCCCceEEEEECCC-CHHHHHHHHHHHHhhc
Confidence            4688999999999875555554333221111    12355788887211 1123444555554433

RepA is encoded by a plasmid, which is found in most Gram negative bacteria. RepA is a 5'-3' DNA helicase which can utilize ATP, GTP and CTP to a lesser extent.

>PHA03372 DNA packaging terminase subunit 1; Provisional

Probab=86.89  E-value=6  Score=46.93  Aligned_cols=134  Identities=13%  Similarity=0.142  Sum_probs=80.9

Q ss_pred             hcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHHHH-hhcCcEEEEeeCCCCh
Q 002040          502 MSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFA-KVMGVRCVPVYGGSGV  580 (976)
Q Consensus       502 l~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~~~-~~~~~~~~~~~gg~~~  580 (976)
                      +..+-.+..-|--.|||+ |+.|++..++..     -.|-.+.+++.-+..+.-++.++..-+ .+++-..+.-.     
T Consensus       200 FKQkaTVFLVPRRHGKTW-f~VpiIsllL~s-----~~gI~IGYvAHqKhvs~~Vf~EI~~~lrrwF~~~~vi~~-----  268 (668)
T PHA03372        200 FKQKATVFLVPRRHGKTW-FIIPIISFLLKN-----IIGISIGYVAHQKHVSQFVLKEVEFRCRRMFPRKHTIEN-----  268 (668)
T ss_pred             hhccceEEEecccCCcee-hHHHHHHHHHHh-----hcCceEEEEeeHHHHHHHHHHHHHHHHhhhcCccceeee-----
Confidence            344556667799999997 588888887763     247789999999999888888776433 33333222111     


Q ss_pred             HHHHHHHhcCCeEEEeCchhHHHH--HHhcCCcccccCCceEEEecCcccccccCCchHHHHHHHhcC-CCCcEEEEecc
Q 002040          581 AQQISELKRGTEIVVCTPGRMIDI--LCTSGGKITNLRRVTYLVMDEADRMFDMGFEPQITRIVQNIR-PDRQTVLFSAT  657 (976)
Q Consensus       581 ~~~~~~l~~~~~Iiv~Tp~~L~~~--l~~~~~~~~~l~~~~~vVlDEah~~~~~~f~~~i~~il~~~~-~~~q~i~~SAT  657 (976)
                              .+.-|.+.-|+.=...  +...+.....-+.+.+++|||||-+-    ...+..|+-.+. .+.++|+.|.|
T Consensus       269 --------k~~tI~~s~pg~Kst~~fasc~n~NsiRGQ~fnll~VDEA~FI~----~~a~~tilgfm~q~~~KiIfISS~  336 (668)
T PHA03372        269 --------KDNVISIDHRGAKSTALFASCYNTNSIRGQNFHLLLVDEAHFIK----KDAFNTILGFLAQNTTKIIFISST  336 (668)
T ss_pred             --------cCcEEEEecCCCcceeeehhhccCccccCCCCCEEEEehhhccC----HHHHHHhhhhhcccCceEEEEeCC
Confidence                    1223444444321110  11011111234568899999999442    334555655543 56789999988


Q ss_pred             C
Q 002040          658 F  658 (976)
Q Consensus       658 ~  658 (976)
                      -
T Consensus       337 N  337 (668)
T PHA03372        337 N  337 (668)
T ss_pred             C
Confidence            4

>PF02534 T4SS-DNA_transf: Type IV secretory system Conjugative DNA transfer; InterPro: IPR003688 This entry represents TraG proteins and their homologues

Probab=86.86  E-value=0.7  Score=54.74  Aligned_cols=56  Identities=27%  Similarity=0.387  Sum_probs=37.7

Q ss_pred             CCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHHHHhhcCcEEEEe
Q 002040          505 RDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVMGVRCVPV  574 (976)
Q Consensus       505 ~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~~~~~~~~~~~~~  574 (976)
                      .+++++|+||||||..+++|.+..   .       ..-+||+=|--+|+......+++    .|..|.++
T Consensus        45 ~h~lvig~tgSGKt~~~viP~ll~---~-------~~s~iV~D~KgEl~~~t~~~r~~----~G~~V~vl  100 (469)
T PF02534_consen   45 THVLVIGPTGSGKTTSFVIPNLLN---Y-------PGSMIVTDPKGELYEKTAGYRKK----RGYKVYVL  100 (469)
T ss_pred             eEEEEEeCCCCCccceeeHhHHHh---c-------cCCEEEEECCCcHHHHHHHHHHH----CCCEEEEe
Confidence            479999999999999999997632   1       11467777887886655443333    34444444

These proteins contain a P-loop and walker-B site for nucleotide binding. TraG is essential for DNA transfer in bacterial conjugation. These proteins are thought to mediate interactions between the DNA-processing (Dtr) and the mating pair formation (Mpf) systems [, ].; GO: 0009291 unidirectional conjugation, 0016020 membrane

>cd01126 TraG_VirD4 The TraG/TraD/VirD4 family are bacterial conjugation proteins involved in type IV secretion

Probab=86.68  E-value=0.62  Score=53.62  Aligned_cols=55  Identities=24%  Similarity=0.317  Sum_probs=36.3

Q ss_pred             CEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHHHHhhcCcEEEEe
Q 002040          506 DCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVMGVRCVPV  574 (976)
Q Consensus       506 d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~~~~~~~~~~~~~  574 (976)
                      +++++|+||||||.++++|.+..   .       +..+||+=|--++........+    ..|..|.++
T Consensus         1 H~lv~g~tGsGKt~~~viP~ll~---~-------~~s~vv~D~Kge~~~~t~~~r~----~~G~~V~v~   55 (384)
T cd01126           1 HVLVFAPTRSGKGVGFVIPNLLT---W-------PGSVVVLDPKGENFELTSEHRR----ALGRKVFVF   55 (384)
T ss_pred             CeeEecCCCCCCccEEEccchhc---C-------CCCEEEEccchhHHHHHHHHHH----HcCCeEEEE
Confidence            47899999999999988886632   1       2346777788777654433332    245555544

These proteins aid the transfer of DNA from the plasmid into the host bacterial chromosome. They contain an ATP binding domain. VirD4 is involved in DNA transfer to plant cells and is required for virulence.

>TIGR01420 pilT_fam pilus retraction protein PilT

Probab=86.62  E-value=1.7  Score=49.10  Aligned_cols=27  Identities=26%  Similarity=0.310  Sum_probs=19.5

Q ss_pred             cCCCEEEEcCCCCchHHHHHHHHHHHHh
Q 002040          503 SGRDCIGVAKTGSGKTLAFVLPMLRHIK  530 (976)
Q Consensus       503 ~g~d~i~~a~TGsGKT~~~~l~il~~l~  530 (976)
                      .+..++++||||||||+. +..++.++.
T Consensus       121 ~~g~ili~G~tGSGKTT~-l~al~~~i~  147 (343)
T TIGR01420       121 PRGLILVTGPTGSGKSTT-LASMIDYIN  147 (343)
T ss_pred             cCcEEEEECCCCCCHHHH-HHHHHHhhC
Confidence            356789999999999986 444555543

This model represents the PilT subfamily of proteins related to GspE, a protein involved in type II secretion (also called the General Secretion Pathway). PilT is an apparent cytosolic ATPase associated with type IV pilus systems. It is not required for pilin biogenesis, but is required for twitching motility and social gliding behaviors, shown in some species, powered by pilus retraction. Members of this family may be found in some species that type IV pili but have related structures for DNA uptake and natural transformation.

>PRK05595 replicative DNA helicase; Provisional

Probab=86.61  E-value=2.3  Score=49.98  Aligned_cols=157  Identities=11%  Similarity=0.081  Sum_probs=0.0

Q ss_pred             CCCCCcHHHHHHHHHHhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEc---cCHHHHHHHHHHHHH
Q 002040          486 NYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMA---PTRELVQQIHSDIRK  562 (976)
Q Consensus       486 ~~~~p~~~Q~~~i~~il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~---Ptr~La~Q~~~~~~~  562 (976)
                      |+...++.--..+.-+..|.-+||.|.||+|||..++-.+......+       |..|+|+.   +...|+..+      
T Consensus       183 gi~tg~~~ld~~~~G~~~g~liviaarpg~GKT~~al~ia~~~a~~~-------g~~vl~fSlEms~~~l~~R~------  249 (444)
T PRK05595        183 GVASGFRELDAKTSGFQKGDMILIAARPSMGKTTFALNIAEYAALRE-------GKSVAIFSLEMSKEQLAYKL------  249 (444)
T ss_pred             cccCChHHHHHhcCCCCCCcEEEEEecCCCChHHHHHHHHHHHHHHc-------CCcEEEEecCCCHHHHHHHH------


Q ss_pred             HHhhcCcEEEEeeCCCChHHHH-------HHHhcCCeEEEeCchhHHHHHHhcCCcccccCCceEEEecCcccccccCCc
Q 002040          563 FAKVMGVRCVPVYGGSGVAQQI-------SELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMGFE  635 (976)
Q Consensus       563 ~~~~~~~~~~~~~gg~~~~~~~-------~~l~~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDEah~~~~~~f~  635 (976)
                      ++...++....+..|.-....+       ..+....-.|.-+++.-+..+.........-..+++||||=.|.|...+..
T Consensus       250 ~a~~~~v~~~~~~~~~l~~~e~~~~~~~~~~l~~~~l~i~d~~~~t~~~i~~~~r~~~~~~~~~~vvIDylql~~~~~~~  329 (444)
T PRK05595        250 LCSEANVDMLRLRTGNLEDKDWENIARASGPLAAAKIFIDDTAGVSVMEMRSKCRRLKIEHGIDMILIDYLQLMSGGKGS  329 (444)
T ss_pred             HHHhcCCCHHHHhcCCCCHHHHHHHHHHHHHHhcCCEEEECCCCCCHHHHHHHHHHHHHhcCCCEEEEeHHHhccCCCCC


Q ss_pred             ----hHHHHHHHhcCC-----CCcEEEEe
Q 002040          636 ----PQITRIVQNIRP-----DRQTVLFS  655 (976)
Q Consensus       636 ----~~i~~il~~~~~-----~~q~i~~S  655 (976)
                          ..+..|...++.     ++.+|++|
T Consensus       330 ~~r~~~v~~is~~LK~lAke~~i~vi~ls  358 (444)
T PRK05595        330 ESRQQEVSEISRSIKALAKEMECPVIALS  358 (444)
T ss_pred             ccHHHHHHHHHHHHHHHHHHhCCeEEEee

>cd03289 ABCC_CFTR2 The CFTR subfamily domain 2

Probab=86.53  E-value=0.84  Score=49.78  Aligned_cols=149  Identities=17%  Similarity=0.205  Sum_probs=0.0

Q ss_pred             HhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCC-------------CeEEEEccCHHHHHHHHHHHHHHHhhc
Q 002040          501 IMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDG-------------PVGLIMAPTRELVQQIHSDIRKFAKVM  567 (976)
Q Consensus       501 il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~-------------~~vLIl~Ptr~La~Q~~~~~~~~~~~~  567 (976)
                      |..|.-+.|+|++|+|||+  ++-++.-+........-++             ..++|.-...-...-+.+.+.-+....
T Consensus        27 I~~Ge~~~IvG~nGsGKST--Ll~~L~gl~~~~G~I~i~g~~i~~~~~~~lr~~i~~v~q~~~lf~~tv~~nl~~~~~~~  104 (275)
T cd03289          27 ISPGQRVGLLGRTGSGKST--LLSAFLRLLNTEGDIQIDGVSWNSVPLQKWRKAFGVIPQKVFIFSGTFRKNLDPYGKWS  104 (275)
T ss_pred             EcCCCEEEEECCCCCCHHH--HHHHHhhhcCCCcEEEECCEEhhhCCHHHHhhhEEEECCCcccchhhHHHHhhhccCCC


Q ss_pred             CcEEEEeeCCCChHHHHHHHhcCCeEEE------eCchhHHHHHHhcCCcccccCCceEEEecCcccccccCCchHHHHH
Q 002040          568 GVRCVPVYGGSGVAQQISELKRGTEIVV------CTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMGFEPQITRI  641 (976)
Q Consensus       568 ~~~~~~~~gg~~~~~~~~~l~~~~~Iiv------~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDEah~~~~~~f~~~i~~i  641 (976)
                      .-.+..+.........+..+..+.+..|      .+.|....+....    ..+.+-.++|+||.-.-+|......+..+
T Consensus       105 ~~~~~~~l~~~gL~~~~~~~p~~l~~~~~~~g~~LS~G~~qrl~LaR----all~~p~illlDEpts~LD~~~~~~l~~~  180 (275)
T cd03289         105 DEEIWKVAEEVGLKSVIEQFPGQLDFVLVDGGCVLSHGHKQLMCLAR----SVLSKAKILLLDEPSAHLDPITYQVIRKT  180 (275)
T ss_pred             HHHHHHHHHHcCCHHHHHhCcccccceecCCCCCCCHHHHHHHHHHH----HHhcCCCEEEEECccccCCHHHHHHHHHH


Q ss_pred             HHhcCCCCcEEEEe
Q 002040          642 VQNIRPDRQTVLFS  655 (976)
Q Consensus       642 l~~~~~~~q~i~~S  655 (976)
                      +..+...+.+|+.|
T Consensus       181 l~~~~~~~tii~is  194 (275)
T cd03289         181 LKQAFADCTVILSE  194 (275)
T ss_pred             HHHhcCCCEEEEEE

The cystic fibrosis transmembrane regulator (CFTR), the product of the gene mutated in patients with cystic fibrosis, has adapted the ABC transporter structural motif to form a tightly regulated anion channel at the apical surface of many epithelia. Use of the term assembly of a functional ion channel implies the coming together of subunits or at least smaller not-yet functional components of the active whole. In fact, on the basis of current knowledge only the CFTR polypeptide itself is required to form an ATP- and protein kinase A-dependent low-conductance chloride channel of the type present in the apical membrane of many epithelial cells. CFTR displays the typical organization (IM-ABC)2 and carries a characteristic hydrophilic R-domain that separates IM1-ABC1 from IM2-ABC2.

>KOG0780 consensus Signal recognition particle, subunit Srp54 [Intracellular trafficking, secretion, and vesicular transport]

Probab=86.51  E-value=4.5  Score=44.97  Aligned_cols=132  Identities=15%  Similarity=0.147  Sum_probs=0.0

Q ss_pred             EEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHHHHhhcCcEEEEeeCCCChHHHHHH
Q 002040          507 CIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQISE  586 (976)
Q Consensus       507 ~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~~~~~~~~~~~~~~gg~~~~~~~~~  586 (976)
                      ++++|-.|+|||++..-.++.+        ...|.+++++|--.--|... ..++..+...++.+...|...........
T Consensus       104 imfVGLqG~GKTTtc~KlA~y~--------kkkG~K~~LvcaDTFRagAf-DQLkqnA~k~~iP~ygsyte~dpv~ia~e  174 (483)
T KOG0780|consen  104 IMFVGLQGSGKTTTCTKLAYYY--------KKKGYKVALVCADTFRAGAF-DQLKQNATKARVPFYGSYTEADPVKIASE  174 (483)
T ss_pred             EEEEeccCCCcceeHHHHHHHH--------HhcCCceeEEeecccccchH-HHHHHHhHhhCCeeEecccccchHHHHHH


Q ss_pred             HhcCCeEEEeCchhHHHHHHhcCCcccccCCceEEEecCcc-cccccCCchHHHHHHHhcCCCCcEEEEeccCcHHHHHH
Q 002040          587 LKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEAD-RMFDMGFEPQITRIVQNIRPDRQTVLFSATFPRQVEIL  665 (976)
Q Consensus       587 l~~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDEah-~~~~~~f~~~i~~il~~~~~~~q~i~~SAT~~~~~~~l  665 (976)
                      --..                      +.-.+|++||+|=.- +-.+.+.-..+..+...+.|+.-++++-|++....+..
T Consensus       175 gv~~----------------------fKke~fdvIIvDTSGRh~qe~sLfeEM~~v~~ai~Pd~vi~VmDasiGQaae~Q  232 (483)
T KOG0780|consen  175 GVDR----------------------FKKENFDVIIVDTSGRHKQEASLFEEMKQVSKAIKPDEIIFVMDASIGQAAEAQ  232 (483)
T ss_pred             HHHH----------------------HHhcCCcEEEEeCCCchhhhHHHHHHHHHHHhhcCCCeEEEEEeccccHhHHHH


Q ss_pred             HHHH
Q 002040          666 ARKV  669 (976)
Q Consensus       666 ~~~~  669 (976)
                      +..|
T Consensus       233 a~aF  236 (483)
T KOG0780|consen  233 ARAF  236 (483)
T ss_pred             HHHH

>TIGR02533 type_II_gspE general secretory pathway protein E

Probab=86.40  E-value=1.4  Score=52.04  Aligned_cols=54  Identities=19%  Similarity=0.246  Sum_probs=0.0

Q ss_pred             HHHcCCCCCcHHHHHHHHHHhcCCC--EEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEE
Q 002040          482 IRKLNYEKPMPIQAQALPVIMSGRD--CIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIM  546 (976)
Q Consensus       482 l~~~~~~~p~~~Q~~~i~~il~g~d--~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl  546 (976)
                      |..+||.   +.|.+.|..++....  ++++||||||||+. +..++..+...       +..++.+
T Consensus       221 l~~Lg~~---~~~~~~l~~~~~~~~GlilitGptGSGKTTt-L~a~L~~l~~~-------~~~iiTi  276 (486)
T TIGR02533       221 LETLGMS---PELLSRFERLIRRPHGIILVTGPTGSGKTTT-LYAALSRLNTP-------ERNILTV  276 (486)
T ss_pred             HHHcCCC---HHHHHHHHHHHhcCCCEEEEEcCCCCCHHHH-HHHHHhccCCC-------CCcEEEE

This family describes GspE, the E protein of the type II secretion system, also called the main terminal branch of the general secretion pathway. This model separates GspE from the PilB protein of type IV pilin biosynthesis.

>PRK14701 reverse gyrase; Provisional

Probab=86.37  E-value=2.9  Score=56.27  Aligned_cols=81  Identities=7%  Similarity=0.117  Sum_probs=0.0

Q ss_pred             EEEecCcchHHHHHHHHHHhhh--cCCcEEEEecCHHHHHHHHHHHHH------CCCCceeccCCCCHHHHHHHHHHhcc
Q 002040          691 LVEVRPESDRFLRLLELLGEWY--EKGKILIFVHSQEKCDALFRDLLK------HGYPCLSLHGAKDQTDRESTISDFKS  762 (976)
Q Consensus       691 ~~~~~~~~~k~~~l~~~l~~~~--~~~kvLIF~~s~~~~~~l~~~L~~------~~~~~~~lhg~~~~~~R~~~~~~F~~  762 (976)
                      .+.......|.. +...+....  .+.++||.+||+.-+.+++..|..      .++.+..+||+++..++..++..+.+
T Consensus        98 li~APTGsGKTl-~~~~~al~~~~~g~~aLVl~PTreLa~Qi~~~l~~l~~~~~~~v~v~~~~g~~s~~e~~~~~~~l~~  176 (1638)
T PRK14701         98 SIVAPTGMGKST-FGAFIALFLALKGKKCYIILPTTLLVKQTVEKIESFCEKANLDVRLVYYHSNLRKKEKEEFLERIEN  176 (1638)
T ss_pred             EEEEcCCCCHHH-HHHHHHHHHHhcCCeEEEEECHHHHHHHHHHHHHHHHhhcCCceeEEEEeCCCCHHHHHHHHHHHhc


Q ss_pred             CCccEEEecC
Q 002040          763 NVCNLLIATS  772 (976)
Q Consensus       763 g~~~vLVaT~  772 (976)
                      |..+|||+|+
T Consensus       177 g~~dILV~TP  186 (1638)
T PRK14701        177 GDFDILVTTA  186 (1638)
T ss_pred             CCCCEEEECC

>KOG0733 consensus Nuclear AAA ATPase (VCP subfamily) [Posttranslational modification, protein turnover, chaperones]

Probab=86.18  E-value=3.3  Score=48.67  Aligned_cols=144  Identities=14%  Similarity=0.227  Sum_probs=0.0

Q ss_pred             eccCCCCCcccccccCCCCHHHHHHHHH--cCCCCCcHHHHHHHHHHhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCC
Q 002040          457 IHGKDVPKPIKTWHQTGLTSKIMETIRK--LNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPP  534 (976)
Q Consensus       457 ~~g~~~p~pi~~~~~~~l~~~l~~~l~~--~~~~~p~~~Q~~~i~~il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~  534 (976)
                      +.+...|.+-.+|.++|=-...+..|..  ..+..|-.++.-.+..   -+.+|+.||+|+|||..              
T Consensus       177 ~~~~~~~~snv~f~diGG~d~~~~el~~li~~i~~Pe~~~~lGv~P---prGvLlHGPPGCGKT~l--------------  239 (802)
T KOG0733|consen  177 VEGLEFPESNVSFSDIGGLDKTLAELCELIIHIKHPEVFSSLGVRP---PRGVLLHGPPGCGKTSL--------------  239 (802)
T ss_pred             hcccCCCCCCcchhhccChHHHHHHHHHHHHHhcCchhHhhcCCCC---CCceeeeCCCCccHHHH--------------


Q ss_pred             CCCCCCCeEEEEccCHHHHHHHHHHHHHHHhhcCcEEEEeeCCCChHHHHHHHhcCCeEEEeCchhHHHHHHhcCCcccc
Q 002040          535 VAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGGKITN  614 (976)
Q Consensus       535 ~~~~~~~~vLIl~Ptr~La~Q~~~~~~~~~~~~~~~~~~~~gg~~~~~~~~~l~~~~~Iiv~Tp~~L~~~l~~~~~~~~~  614 (976)
                                               ...++..+++.+..+.+-..+          ..|.=-|-..+..++..     ..
T Consensus       240 -------------------------A~AiAgel~vPf~~isApeiv----------SGvSGESEkkiRelF~~-----A~  279 (802)
T KOG0733|consen  240 -------------------------ANAIAGELGVPFLSISAPEIV----------SGVSGESEKKIRELFDQ-----AK  279 (802)
T ss_pred             -------------------------HHHHhhhcCCceEeecchhhh----------cccCcccHHHHHHHHHH-----Hh


Q ss_pred             cCCceEEEecCcccccccC----------CchHHHHHHHhcCCC----CcEEEEecc
Q 002040          615 LRRVTYLVMDEADRMFDMG----------FEPQITRIVQNIRPD----RQTVLFSAT  657 (976)
Q Consensus       615 l~~~~~vVlDEah~~~~~~----------f~~~i~~il~~~~~~----~q~i~~SAT  657 (976)
                      -...++|+|||+|.+...-          ...++...+..+...    ..+|+..||
T Consensus       280 ~~aPcivFiDeIDAI~pkRe~aqreMErRiVaQLlt~mD~l~~~~~~g~~VlVIgAT  336 (802)
T KOG0733|consen  280 SNAPCIVFIDEIDAITPKREEAQREMERRIVAQLLTSMDELSNEKTKGDPVLVIGAT  336 (802)
T ss_pred             ccCCeEEEeecccccccchhhHHHHHHHHHHHHHHHhhhcccccccCCCCeEEEecC

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	976
2i4i_A	417	Crystal Structure Of Human Dead-Box Rna Helicase Dd		5e-82
2db3_A	434	Structural Basis For Rna Unwinding By The Dead-Box		5e-75
4a4d_A	253	Crystal Structure Of The N-Terminal Domain Of The H		2e-67
3fe2_A	242	Human Dead-Box Rna Helicase Ddx5 (P68), Conserved D		8e-63
2xb2_A	411	Crystal Structure Of The Core Mago-Y14-Eif4aiii-Bar		6e-56
2j0q_A	410	The Crystal Structure Of The Exon Junction Complex		6e-56
2hyi_C	413	Structure Of The Human Exon Junction Complex With A		7e-56
2hxy_A	391	Crystal Structure Of Human Apo-Eif4aiii Length = 39		1e-55
2j0u_A	374	The Crystal Structure Of Eif4aiii-Barentsz Complex		4e-55
1s2m_A	400	Crystal Structure Of The Dead Box Protein Dhh1p Len		3e-54
2j0u_B	374	The Crystal Structure Of Eif4aiii-Barentsz Complex		4e-54
1hv8_A	367	Crystal Structure Of A Dead Box Protein From The Hy		5e-52
2z0m_A	337	Crystal Structure Of Hypothetical Atp-Dependent Rna		2e-48
1xtk_A	390	Structure Of Decd To Dead Mutation Of Human Uap56 L		6e-47
1xti_A	391	Structure Of Wildtype Human Uap56 Length = 391		2e-46
1xtj_A	386	Structure Of Human Uap56 In Complex With Adp Length		2e-46
3eiq_A	414	Crystal Structure Of Pdcd4-eif4a Length = 414		3e-46
2zu6_A	388	Crystal Structure Of The Eif4a-Pdcd4 Complex Length		8e-46
3pey_A	395	S. Cerevisiae Dbp5 Bound To Rna And Adp Bef3 Length		3e-45
3pew_A	395	S. Cerevisiae Dbp5 L327v Bound To Rna And Adp Bef3		4e-45
3iuy_A	228	Crystal Structure Of Ddx53 Dead-Box Domain Length =		1e-40
1wrb_A	253	Crystal Structure Of The N-Terminal Reca-Like Domai		2e-39
2vso_A	395	Crystal Structure Of A Translation Initiation Compl		2e-39
3sqw_A	579	Structure Of Mss116p (Nte Deletion) Bound To Ssrna		2e-38
3i5x_A	563	Structure Of Mss116p Bound To Ssrna And Amp-Pnp Len		6e-38
3sqx_A	512	Structure Of Mss116p (Nte And C-Tail Double Deletio		1e-37
3ber_A	249	Human Dead-Box Rna-Helicase Ddx47, Conserved Domain		3e-37
3fho_B	508	Structure Of S. Pombe Dbp5 Length = 508		3e-37
1fuu_A	394	Yeast Initiation Factor 4a Length = 394		4e-37
2gxq_A	207	Hera N-Terminal Domain In Complex With Amp, Crystal		7e-37
3mwj_A	207	Q28e Mutant Of Hera N-Terminal Reca-Like Domain, Ap		2e-36
3fmp_B	479	Crystal Structure Of The Nucleoporin Nup214 In Comp		3e-36
3ews_A	445	Human Dead-Box Rna-Helicase Ddx19 In Complex With A		5e-36
3g0h_A	424	Human Dead-box Rna Helicase Ddx19, In Complex With		7e-36
3fht_A	412	Crystal Structure Of Human Dbp5 In Complex With Amp		8e-36
3dkp_A	245	Human Dead-Box Rna-Helicase Ddx52, Conserved Domain		2e-30
2jgn_A	185	Ddx3 Helicase Domain Length = 185		4e-29
2pl3_A	236	Human Dead-Box Rna Helicase Ddx10, Dead Domain In C		2e-27
3ly5_A	262	Ddx18 Dead-Domain Length = 262		1e-25
1vec_A	206	Crystal Structure Of The N-Terminal Domain Of RckP5		3e-25
3bor_A	237	Crystal Structure Of The Deadc Domain Of Human Tran		1e-24
2g9n_A	221	Structure Of The Dead Domain Of Human Eukaryotic In		3e-23
2hjv_A	163	Structure Of The Second Domain (Residues 207-368) O		6e-22
2p6n_A	191	Human Dead-box Rna Helicase Ddx41, Helicase Domain		1e-21
1t6n_A	220	Crystal Structure Of The N-Terminal Domain Of Human		8e-21
1t5i_A	172	Crystal Structure Of The C-Terminal Domain Of Uap56		1e-20
1qde_A	224	Crystal Structure Of The Atpase Domain Of Translati		1e-20
1qva_A	223	Yeast Initiation Factor 4a N-Terminal Domain Length		1e-20
1q0u_A	219	Crystal Structure Of The Bstdead N-Terminal Domain		6e-20
2kbe_A	226	Solution Structure Of Amino-Terminal Domain Of Dbp5		9e-20
2kbf_A	187	Solution Structure Of Carboxyl-Terminal Domain Of D		4e-19
3gfp_A	189	Structure Of The C-Terminal Domain Of The Dead-Box		1e-18
3peu_A	188	S. Cerevisiae Dbp5 L327v C-Terminal Domain Bound To		2e-18
2wax_A	193	Structure Of The Human Ddx6 C-Terminal Domain In Co		6e-18
2oxc_A	230	Human Dead-Box Rna Helicase Ddx20, Dead Domain In C		2e-17
3fmo_B	300	Crystal Structure Of The Nucleoporin Nup214 In Comp		3e-16
3fhc_B	235	Crystal Structure Of Human Dbp5 In Complex With Nup		7e-16
2yjt_D	170	Crystal Structure Of E. Coli Dead-Box Protein Srmb		2e-15
2rb4_A	175	Crystal Structure Of The Helicase Domain Of Human D		2e-14
4db4_A	256	Mss116p Dead-Box Helicase Domain 2 Bound To A Chima		3e-13
4db2_C	257	Mss116p Dead-Box Helicase Domain 2 Bound To An Rna		3e-13
4db2_A	257	Mss116p Dead-Box Helicase Domain 2 Bound To An Rna		3e-13
3i32_A	300	Dimeric Structure Of A Hera Helicase Fragment Inclu		5e-12
1fuk_A	165	Crystal Structure Of The Carboxy Terminal Domain Of		2e-11
3eaq_A	212	Novel Dimerization Motif In The Dead Box Rna Helica		2e-11
4f91_B	1724	Brr2 Helicase Region Length = 1724		5e-10
4f92_B	1724	Brr2 Helicase Region S1087l Length = 1724		6e-10
2v1x_A	591	Crystal Structure Of Human Recq-Like Dna Helicase L		4e-09
1oyy_A	523	Structure Of The Recq Catalytic Core Bound To Atp-G		2e-08
1oyw_A	523	Structure Of The Recq Catalytic Core Length = 523		7e-07
1wp9_A	494	Crystal Structure Of Pyrococcus Furiosus Hef Helica		1e-05
2ykg_A	696	Structural Insights Into Rna Recognition By Rig-I L		2e-04
3tmi_A	695	Structural Basis For Rna Recognition And Activation		3e-04
4ay2_A	687	Capturing 5' Tri-Phosphorylated Rna Duplex By Rig-I		3e-04
4gl2_A	699	Structural Basis For Dsrna Duplex Backbone Recognit		9e-04

>pdb|2I4I|A Chain A, Crystal Structure Of Human Dead-Box Rna Helicase Ddx3x Length = 417

Iteration: 1
 Score =  303 bits (775), Expect = 5e-82,   Method: Compositional matrix adjust.
 Identities = 171/408 (41%), Positives = 246/408 (60%), Gaps = 22/408 (5%)
Query: 459 GKDVPKPIKTWHQTGLTSKIMETIRKLNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKT 518
           G + P  I+++    +   IM  I    Y +P P+Q  A+P+I   RD +  A+TGSGKT
Sbjct: 7   GNNCPPHIESFSDVEMGEIIMGNIELTRYTRPTPVQKHAIPIIKEKRDLMACAQTGSGKT 66
Query: 519 LAFVLPMLRHIKDQPPVAAGDG-------------PVGLIMAPTRELVQQIHSDIRKFAK 565
            AF+LP+L  I    P  A                P+ L++APTREL  QI+ + RKF+ 
Sbjct: 67  AAFLLPILSQIYSDGPGEALRAMKENGRYGRRKQYPISLVLAPTRELAVQIYEEARKFSY 126
Query: 566 VMGVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDE 625
              VR   VYGG+ + QQI +L+RG  ++V TPGR++D++    GKI  L    YLV+DE
Sbjct: 127 RSRVRPCVVYGGADIGQQIRDLERGCHLLVATPGRLVDMM--ERGKI-GLDFCKYLVLDE 183
Query: 626 ADRMFDMGFEPQITRIV-QNIRPD---RQTVLFSATFPRQVEILARKVLNKPVEIQVGGR 681
           ADRM DMGFEPQI RIV Q+  P    R T++FSATFP+++++LAR  L++ + + VG  
Sbjct: 184 ADRMLDMGFEPQIRRIVEQDTMPPKGVRHTMMFSATFPKEIQMLARDFLDEYIFLAVGRV 243
Query: 682 SVVNKDITQLVEVRPESDRFLRLLELLGEWYEKGKILIFVHSQEKCDALFRDLLKH-GYP 740
              +++ITQ V    ESD+   LL+LL    +    L+FV +++  D+L  D L H GY 
Sbjct: 244 GSTSENITQKVVWVEESDKRSFLLDLLNATGKDSLTLVFVETKKGADSL-EDFLYHEGYA 302
Query: 741 CLSLHGAKDQTDRESTISDFKSNVCNLLIATSVAARGLDVKELELVINFDAPNHYEDYVH 800
           C S+HG + Q DRE  +  F+S    +L+AT+VAARGLD+  ++ VINFD P+  E+YVH
Sbjct: 303 CTSIHGDRSQRDREEALHQFRSGKSPILVATAVAARGLDISNVKHVINFDLPSDIEEYVH 362
Query: 801 RVGRTGRAGRKGCAITFISEEDAKYSPDLVKALELSEQVVPDDLKALA 848
           R+GRTGR G  G A +F +E +   + DL+  L  ++Q VP  L+ +A
Sbjct: 363 RIGRTGRVGNLGLATSFFNERNINITKDLLDLLVEAKQEVPSWLENMA 410

>pdb|2DB3|A Chain A, Structural Basis For Rna Unwinding By The Dead-Box Protein Drosophila Vasa Length = 434

Iteration: 1
 Score =  279 bits (714), Expect = 5e-75,   Method: Compositional matrix adjust.
 Identities = 158/399 (39%), Positives = 240/399 (60%), Gaps = 10/399 (2%)
Query: 452 QLELKIHGKDVPKPIKTWHQTGLTSKIMETIRKLNYEKPMPIQAQALPVIMSGRDCIGVA 511
            + +K+ G DVP+PI+ +    L   I++ + K  Y+ P PIQ  ++PVI SGRD +  A
Sbjct: 41  NIPVKVTGSDVPQPIQHFTSADLRDIIIDNVNKSGYKIPTPIQKCSIPVISSGRDLMACA 100
Query: 512 KTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVMGVRC 571
           +TGSGKT AF+LP+L  + + P       P  +I++PTREL  QI ++ RKFA    ++ 
Sbjct: 101 QTGSGKTAAFLLPILSKLLEDPHELELGRPQVVIVSPTRELAIQIFNEARKFAFESYLKI 160
Query: 572 VPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFD 631
             VYGG+    Q   + RG  +V+ TPGR++D +  +     + R   ++V+DEADRM D
Sbjct: 161 GIVYGGTSFRHQNECITRGCHVVIATPGRLLDFVDRTFITFEDTR---FVVLDEADRMLD 217
Query: 632 MGFEPQITRIVQNI--RPDRQTVLFSATFPRQVEILARKVLNKPVEIQVGGRSVVNKDIT 689
           MGF   + RI+ ++  RP+ QT++FSATFP +++ +A + L   V + +G       D+ 
Sbjct: 218 MGFSEDMRRIMTHVTMRPEHQTLMFSATFPEEIQRMAGEFLKNYVFVAIGIVGGACSDVK 277
Query: 690 QLV-EVRPESDRFLRLLELLGEWYEKGKILIFVHSQEKCDALFRDLLKHGYPCLSLHGAK 748
           Q + EV   + R  +L+E+L E  +    ++FV ++   D L   L +  +P  S+HG +
Sbjct: 278 QTIYEVNKYAKR-SKLIEILSE--QADGTIVFVETKRGADFLASFLSEKEFPTTSIHGDR 334
Query: 749 DQTDRESTISDFKSNVCNLLIATSVAARGLDVKELELVINFDAPNHYEDYVHRVGRTGRA 808
            Q+ RE  + DFK+    +LIATSVA+RGLD+K ++ VIN+D P+  +DYVHR+GRTGR 
Sbjct: 335 LQSQREQALRDFKNGSMKVLIATSVASRGLDIKNIKHVINYDMPSKIDDYVHRIGRTGRV 394
Query: 809 GRKGCAITFIS-EEDAKYSPDLVKALELSEQVVPDDLKA 846
           G  G A +F   E+D   + DLVK LE S Q VPD L+ 
Sbjct: 395 GNNGRATSFFDPEKDRAIAADLVKILEGSGQTVPDFLRT 433

>pdb|4A4D|A Chain A, Crystal Structure Of The N-Terminal Domain Of The Human Dead-Box Rna Helicase Ddx5 (P68) Length = 253

Iteration: 1
 Score =  254 bits (649), Expect = 2e-67,   Method: Compositional matrix adjust.
 Identities = 121/254 (47%), Positives = 171/254 (67%), Gaps = 3/254 (1%)
Query: 427 FRKNFYIEVKEIARMTPEEVSAYRKQLELKIHGKDVPKPIKTWHQTGLTSKIMETIRKLN 486
           F KNFY E  ++AR T +EV  YR+  E+ + G + PKP+  +++    + +M+ I + N
Sbjct: 3   FEKNFYQEHPDLARRTAQEVETYRRSKEITVRGHNCPKPVLNFYEANFPANVMDVIARQN 62
Query: 487 YEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIM 546
           + +P  IQAQ  PV +SG D +GVA+TGSGKTL+++LP + HI  QP +  GDGP+ L++
Sbjct: 63  FTEPTAIQAQGWPVALSGLDMVGVAQTGSGKTLSYLLPAIVHINHQPFLERGDGPICLVL 122
Query: 547 APTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILC 606
           APTREL QQ+     ++ +   ++   +YGG+    QI +L+RG EI + TPGR+ID L 
Sbjct: 123 APTRELAQQVQQVAAEYCRACRLKSTCIYGGAPKGPQIRDLERGVEICIATPGRLIDFL- 181
Query: 607 TSGGKITNLRRVTYLVMDEADRMFDMGFEPQITRIVQNIRPDRQTVLFSATFPRQVEILA 666
              GK TNLRR TYLV+DEADRM DMGFEPQI +IV  IRPDRQT+++SAT+P++V  LA
Sbjct: 182 -ECGK-TNLRRTTYLVLDEADRMLDMGFEPQIRKIVDQIRPDRQTLMWSATWPKEVRQLA 239
Query: 667 RKVLNKPVEIQVGG 680
              L   + I +G 
Sbjct: 240 EDFLKDYIHINIGA 253

>pdb|3FE2|A Chain A, Human Dead-Box Rna Helicase Ddx5 (P68), Conserved Domain I In Complex With Adp Length = 242

Iteration: 1
 Score =  238 bits (608), Expect = 8e-63,   Method: Compositional matrix adjust.
 Identities = 113/239 (47%), Positives = 161/239 (67%), Gaps = 3/239 (1%)
Query: 442 TPEEVSAYRKQLELKIHGKDVPKPIKTWHQTGLTSKIMETIRKLNYEKPMPIQAQALPVI 501
           T +EV  YR+  E+ + G + PKP+  +++    + +M+ I + N+ +P  IQAQ  PV 
Sbjct: 4   TAQEVETYRRSKEITVRGHNCPKPVLNFYEANFPANVMDVIARQNFTEPTAIQAQGWPVA 63
Query: 502 MSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIR 561
           +SG D +GVA+TGSGKTL+++LP + HI  QP +  GDGP+ L++APTREL QQ+     
Sbjct: 64  LSGLDMVGVAQTGSGKTLSYLLPAIVHINHQPFLERGDGPICLVLAPTRELAQQVQQVAA 123
Query: 562 KFAKVMGVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYL 621
           ++ +   ++   +YGG+    QI +L+RG EI + TPGR+ID L    GK TNLRR TYL
Sbjct: 124 EYCRACRLKSTCIYGGAPKGPQIRDLERGVEICIATPGRLIDFL--ECGK-TNLRRTTYL 180
Query: 622 VMDEADRMFDMGFEPQITRIVQNIRPDRQTVLFSATFPRQVEILARKVLNKPVEIQVGG 680
           V+DEADRM DMGFEPQI +IV  IRPDRQT+++SAT+P++V  LA   L   + I +G 
Sbjct: 181 VLDEADRMLDMGFEPQIRKIVDQIRPDRQTLMWSATWPKEVRQLAEDFLKDYIHINIGA 239

>pdb|2XB2|A Chain A, Crystal Structure Of The Core Mago-Y14-Eif4aiii-Barentsz- Upf3b Assembly Shows How The Ejc Is Bridged To The Nmd Machinery Length = 411

Iteration: 1
 Score =  216 bits (549), Expect = 6e-56,   Method: Compositional matrix adjust.
 Identities = 128/366 (34%), Positives = 197/366 (53%), Gaps = 16/366 (4%)
Query: 468 TWHQTGLTSKIMETIRKLNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLR 527
           T+   GL   ++  I    +EKP  IQ +A+  I+ GRD I  +++G+GKT  F + +L+
Sbjct: 39  TFDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSISVLQ 98
Query: 528 HIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQISEL 587
            +  Q           LI+APTREL  QI   +      M V+C    GG+ V + I +L
Sbjct: 99  CLDIQVRETQA-----LILAPTRELAVQIQKGLLALGDYMNVQCHACIGGTNVGEDIRKL 153
Query: 588 KRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMGFEPQITRIVQNIRP 647
             G  +V  TPGR+ D++     +    R +  LV+DEAD M + GF+ QI  + + + P
Sbjct: 154 DYGQHVVAGTPGRVFDMIRRRSLRT---RAIKMLVLDEADEMLNKGFKEQIYDVYRYLPP 210
Query: 648 DRQTVLFSATFPRQVEILARKVLNKPVEIQVGGRSVVNKDITQL-VEVRPESDRFLRLLE 706
             Q VL SAT P ++  +  K +  P+ I V    +  + I Q  V V  E  +F  L +
Sbjct: 211 ATQVVLISATLPHEILEMTNKFMTDPIRILVKRDELTLEGIKQFFVAVEREEWKFDTLCD 270
Query: 707 LLGEWYEKGKI---LIFVHSQEKCDALFRDLLKHGYPCLSLHGAKDQTDRESTISDFKSN 763
           L    Y+   I   +IF +++ K D L   + +  +   S+HG   Q +RES + +F+S 
Sbjct: 271 L----YDTLTITQAVIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSG 326
Query: 764 VCNLLIATSVAARGLDVKELELVINFDAPNHYEDYVHRVGRTGRAGRKGCAITFISEEDA 823
              +LI+T V ARGLDV ++ L+IN+D PN+ E Y+HR+GR+GR GRKG AI F+  +D 
Sbjct: 327 ASRVLISTDVWARGLDVPQVSLIINYDLPNNRELYIHRIGRSGRYGRKGVAINFVKNDDI 386
Query: 824 KYSPDL 829
           +   D+
Sbjct: 387 RILRDI 392

>pdb|2J0Q|A Chain A, The Crystal Structure Of The Exon Junction Complex At 3.2 A Resolution Length = 410

Iteration: 1
 Score =  216 bits (549), Expect = 6e-56,   Method: Compositional matrix adjust.
 Identities = 128/366 (34%), Positives = 197/366 (53%), Gaps = 16/366 (4%)
Query: 468 TWHQTGLTSKIMETIRKLNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLR 527
           T+   GL   ++  I    +EKP  IQ +A+  I+ GRD I  +++G+GKT  F + +L+
Sbjct: 38  TFDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSISVLQ 97
Query: 528 HIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQISEL 587
            +  Q           LI+APTREL  QI   +      M V+C    GG+ V + I +L
Sbjct: 98  CLDIQVRETQA-----LILAPTRELAVQIQKGLLALGDYMNVQCHACIGGTNVGEDIRKL 152
Query: 588 KRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMGFEPQITRIVQNIRP 647
             G  +V  TPGR+ D++     +    R +  LV+DEAD M + GF+ QI  + + + P
Sbjct: 153 DYGQHVVAGTPGRVFDMIRRRSLRT---RAIKMLVLDEADEMLNKGFKEQIYDVYRYLPP 209
Query: 648 DRQTVLFSATFPRQVEILARKVLNKPVEIQVGGRSVVNKDITQL-VEVRPESDRFLRLLE 706
             Q VL SAT P ++  +  K +  P+ I V    +  + I Q  V V  E  +F  L +
Sbjct: 210 ATQVVLISATLPHEILEMTNKFMTDPIRILVKRDELTLEGIKQFFVAVEREEWKFDTLCD 269
Query: 707 LLGEWYEKGKI---LIFVHSQEKCDALFRDLLKHGYPCLSLHGAKDQTDRESTISDFKSN 763
           L    Y+   I   +IF +++ K D L   + +  +   S+HG   Q +RES + +F+S 
Sbjct: 270 L----YDTLTITQAVIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSG 325
Query: 764 VCNLLIATSVAARGLDVKELELVINFDAPNHYEDYVHRVGRTGRAGRKGCAITFISEEDA 823
              +LI+T V ARGLDV ++ L+IN+D PN+ E Y+HR+GR+GR GRKG AI F+  +D 
Sbjct: 326 ASRVLISTDVWARGLDVPQVSLIINYDLPNNRELYIHRIGRSGRYGRKGVAINFVKNDDI 385
Query: 824 KYSPDL 829
           +   D+
Sbjct: 386 RILRDI 391

>pdb|2HYI|C Chain C, Structure Of The Human Exon Junction Complex With A Trapped Dead-Box Helicase Bound To Rna Length = 413

Iteration: 1
 Score =  216 bits (549), Expect = 7e-56,   Method: Compositional matrix adjust.
 Identities = 128/366 (34%), Positives = 197/366 (53%), Gaps = 16/366 (4%)
Query: 468 TWHQTGLTSKIMETIRKLNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLR 527
           T+   GL   ++  I    +EKP  IQ +A+  I+ GRD I  +++G+GKT  F + +L+
Sbjct: 39  TFDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSISVLQ 98
Query: 528 HIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQISEL 587
            +  Q           LI+APTREL  QI   +      M V+C    GG+ V + I +L
Sbjct: 99  CLDIQVRETQA-----LILAPTRELAVQIQKGLLALGDYMNVQCHACIGGTNVGEDIRKL 153
Query: 588 KRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMGFEPQITRIVQNIRP 647
             G  +V  TPGR+ D++     +    R +  LV+DEAD M + GF+ QI  + + + P
Sbjct: 154 DYGQHVVAGTPGRVFDMIRRRSLRT---RAIKMLVLDEADEMLNKGFKEQIYDVYRYLPP 210
Query: 648 DRQTVLFSATFPRQVEILARKVLNKPVEIQVGGRSVVNKDITQL-VEVRPESDRFLRLLE 706
             Q VL SAT P ++  +  K +  P+ I V    +  + I Q  V V  E  +F  L +
Sbjct: 211 ATQVVLISATLPHEILEMTNKFMTDPIRILVKRDELTLEGIKQFFVAVEREEWKFDTLCD 270
Query: 707 LLGEWYEKGKI---LIFVHSQEKCDALFRDLLKHGYPCLSLHGAKDQTDRESTISDFKSN 763
           L    Y+   I   +IF +++ K D L   + +  +   S+HG   Q +RES + +F+S 
Sbjct: 271 L----YDTLTITQAVIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSG 326
Query: 764 VCNLLIATSVAARGLDVKELELVINFDAPNHYEDYVHRVGRTGRAGRKGCAITFISEEDA 823
              +LI+T V ARGLDV ++ L+IN+D PN+ E Y+HR+GR+GR GRKG AI F+  +D 
Sbjct: 327 ASRVLISTDVWARGLDVPQVSLIINYDLPNNRELYIHRIGRSGRYGRKGVAINFVKNDDI 386
Query: 824 KYSPDL 829
           +   D+
Sbjct: 387 RILRDI 392

>pdb|2HXY|A Chain A, Crystal Structure Of Human Apo-Eif4aiii Length = 391

Iteration: 1
 Score =  215 bits (547), Expect = 1e-55,   Method: Compositional matrix adjust.
 Identities = 128/366 (34%), Positives = 197/366 (53%), Gaps = 16/366 (4%)
Query: 468 TWHQTGLTSKIMETIRKLNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLR 527
           T+   GL   ++  I    +EKP  IQ +A+  I+ GRD I  +++G+GKT  F + +L+
Sbjct: 17  TFDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSISVLQ 76
Query: 528 HIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQISEL 587
            +  Q           LI+APTREL  QI   +      M V+C    GG+ V + I +L
Sbjct: 77  CLDIQVRETQA-----LILAPTRELAVQIQKGLLALGDYMNVQCHACIGGTNVGEDIRKL 131
Query: 588 KRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMGFEPQITRIVQNIRP 647
             G  +V  TPGR+ D++     +    R +  LV+DEAD M + GF+ QI  + + + P
Sbjct: 132 DYGQHVVAGTPGRVFDMIRRRSLRT---RAIKMLVLDEADEMLNKGFKEQIYDVYRYLPP 188
Query: 648 DRQTVLFSATFPRQVEILARKVLNKPVEIQVGGRSVVNKDITQL-VEVRPESDRFLRLLE 706
             Q VL SAT P ++  +  K +  P+ I V    +  + I Q  V V  E  +F  L +
Sbjct: 189 ATQVVLISATLPHEILEMTNKFMTDPIRILVKRDELTLEGIKQFFVAVEREEWKFDTLCD 248
Query: 707 LLGEWYEKGKI---LIFVHSQEKCDALFRDLLKHGYPCLSLHGAKDQTDRESTISDFKSN 763
           L    Y+   I   +IF +++ K D L   + +  +   S+HG   Q +RES + +F+S 
Sbjct: 249 L----YDTLTITQAVIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSG 304
Query: 764 VCNLLIATSVAARGLDVKELELVINFDAPNHYEDYVHRVGRTGRAGRKGCAITFISEEDA 823
              +LI+T V ARGLDV ++ L+IN+D PN+ E Y+HR+GR+GR GRKG AI F+  +D 
Sbjct: 305 ASRVLISTDVWARGLDVPQVSLIINYDLPNNRELYIHRIGRSGRYGRKGVAINFVKNDDI 364
Query: 824 KYSPDL 829
           +   D+
Sbjct: 365 RILRDI 370

>pdb|2J0U|A Chain A, The Crystal Structure Of Eif4aiii-Barentsz Complex At 3.0 A Resolution Length = 374

Iteration: 1
 Score =  213 bits (542), Expect = 4e-55,   Method: Compositional matrix adjust.
 Identities = 126/366 (34%), Positives = 197/366 (53%), Gaps = 16/366 (4%)
Query: 468 TWHQTGLTSKIMETIRKLNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLR 527
           T+   GL   ++  I    +EKP  IQ +A+  I+ GRD I  +++G+GKT  F + +L+
Sbjct: 2   TFDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSVSVLQ 61
Query: 528 HIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQISEL 587
            +  Q           LI+APTREL  Q+   +      M V+C    GG+ V + I +L
Sbjct: 62  CLDIQVRETQA-----LILAPTRELAVQVQKGLLALGDYMNVQCHACIGGTNVGEDIRKL 116
Query: 588 KRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMGFEPQITRIVQNIRP 647
             G  +V  TPGR+ D++     +    R +  LV+DEAD M + GF+ QI  + + + P
Sbjct: 117 DYGQHVVAGTPGRVFDMIRRRSLRT---RAIKMLVLDEADEMLNKGFKEQIYDVYRYLPP 173
Query: 648 DRQTVLFSATFPRQVEILARKVLNKPVEIQVGGRSVVNKDITQL-VEVRPESDRFLRLLE 706
             Q VL SAT P ++  +  K +  P+ I V    +  + I Q  V V  E  +F  L +
Sbjct: 174 ATQVVLISATLPHEILEMTNKFMTDPIRILVKRDELTLEGIKQFFVAVEREEWKFDTLCD 233
Query: 707 LLGEWYEKGKI---LIFVHSQEKCDALFRDLLKHGYPCLSLHGAKDQTDRESTISDFKSN 763
           L    Y+   I   +IF +++ K D L   + +  +   S+HG   Q +RES + +F+S 
Sbjct: 234 L----YDTLTITQAVIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSG 289
Query: 764 VCNLLIATSVAARGLDVKELELVINFDAPNHYEDYVHRVGRTGRAGRKGCAITFISEEDA 823
              +LI+T V ARGLDV ++ L+IN+D PN+ E Y+HR+GR+GR GRKG A+ F+  +D 
Sbjct: 290 ASRVLISTDVWARGLDVPQVSLIINYDLPNNRELYIHRIGRSGRYGRKGVAVNFVKNDDI 349
Query: 824 KYSPDL 829
           +   D+
Sbjct: 350 RVLRDI 355

>pdb|1S2M|A Chain A, Crystal Structure Of The Dead Box Protein Dhh1p Length = 400

Iteration: 1
 Score =  210 bits (534), Expect = 3e-54,   Method: Compositional matrix adjust.
 Identities = 121/355 (34%), Positives = 186/355 (52%), Gaps = 10/355 (2%)
Query: 468 TWHQTGLTSKIMETIRKLNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLR 527
           T+    L  +++  I +  +EKP PIQ +A+PV ++GRD +  AK G+GKT AFV+P L 
Sbjct: 22  TFEDFYLKRELLMGIFEAGFEKPSPIQEEAIPVAITGRDILARAKNGTGKTAAFVIPTLE 81
Query: 528 HIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQISEL 587
            +K +      +    LIM PTREL  Q    +R   K  G+ C+   GG+ +   I  L
Sbjct: 82  KVKPKL-----NKIQALIMVPTRELALQTSQVVRTLGKHCGISCMVTTGGTNLRDDILRL 136
Query: 588 KRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMGFEPQITRIVQNIRP 647
                I+V TPGR++D+   +  K+ +L   +  +MDEAD+M    F+  I +I+  + P
Sbjct: 137 NETVHILVGTPGRVLDL---ASRKVADLSDCSLFIMDEADKMLSRDFKTIIEQILSFLPP 193
Query: 648 DRQTVLFSATFPRQVEILARKVLNKPVEIQVGGRSVVNKDITQLVEVRPESDRFLRLLEL 707
             Q++LFSATFP  V+    K L+KP EI +    +  K ITQ      E  + L  L  
Sbjct: 194 THQSLLFSATFPLTVKEFMVKHLHKPYEINLM-EELTLKGITQYYAFVEERQK-LHCLNT 251
Query: 708 LGEWYEKGKILIFVHSQEKCDALFRDLLKHGYPCLSLHGAKDQTDRESTISDFKSNVCNL 767
           L    +  + +IF +S  + + L + +   GY C   H    Q +R     +F+      
Sbjct: 252 LFSKLQINQAIIFCNSTNRVELLAKKITDLGYSCYYSHARMKQQERNKVFHEFRQGKVRT 311
Query: 768 LIATSVAARGLDVKELELVINFDAPNHYEDYVHRVGRTGRAGRKGCAITFISEED 822
           L+ + +  RG+D++ + +VINFD P   E Y+HR+GR+GR G  G AI  I+  D
Sbjct: 312 LVCSDLLTRGIDIQAVNVVINFDFPKTAETYLHRIGRSGRFGHLGLAINLINWND 366

>pdb|2J0U|B Chain B, The Crystal Structure Of Eif4aiii-Barentsz Complex At 3.0 A Resolution Length = 374

Iteration: 1
 Score =  209 bits (533), Expect = 4e-54,   Method: Compositional matrix adjust.
 Identities = 126/366 (34%), Positives = 196/366 (53%), Gaps = 16/366 (4%)
Query: 468 TWHQTGLTSKIMETIRKLNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLR 527
           T+   GL   ++  I    +EKP  IQ +A+  I+ GRD I  +++G+GKT  F + +L+
Sbjct: 2   TFDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSVSVLQ 61
Query: 528 HIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQISEL 587
            +  Q           LI+APTREL  Q+   +      M V+     GG+ V + I +L
Sbjct: 62  CLDIQVRETQA-----LILAPTRELAVQVQKGLLALGDYMNVQSHACIGGTNVGEDIRKL 116
Query: 588 KRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMGFEPQITRIVQNIRP 647
             G  +V  TPGR+ D++     +    R +  LV+DEAD M + GF+ QI  + + + P
Sbjct: 117 DYGQHVVAGTPGRVFDMIRRRSLRT---RAIKMLVLDEADEMLNKGFKEQIYDVYRYLPP 173
Query: 648 DRQTVLFSATFPRQVEILARKVLNKPVEIQVGGRSVVNKDITQL-VEVRPESDRFLRLLE 706
             Q VL SAT P +V  +  K +  P+ I V    +  + I Q  V V  E  +F  L +
Sbjct: 174 ATQVVLISATLPHEVLEMTNKFMTDPIRILVKRDELTLEGIKQFFVAVEREEWKFDTLCD 233
Query: 707 LLGEWYEKGKI---LIFVHSQEKCDALFRDLLKHGYPCLSLHGAKDQTDRESTISDFKSN 763
           L    Y+   I   +IF +++ K D L   + +  +   S+HG   Q +RES + +F+S 
Sbjct: 234 L----YDTLTITQAVIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSG 289
Query: 764 VCNLLIATSVAARGLDVKELELVINFDAPNHYEDYVHRVGRTGRAGRKGCAITFISEEDA 823
              +LI+T V ARGLDV ++ L+IN+D PN+ E Y+HR+GR+GR GRKG A+ F+  +D 
Sbjct: 290 ASRVLISTDVWARGLDVPQVSLIINYDLPNNRELYIHRIGRSGRYGRKGVAVNFVKNDDI 349
Query: 824 KYSPDL 829
           +   D+
Sbjct: 350 RVLRDI 355

>pdb|1HV8|A Chain A, Crystal Structure Of A Dead Box Protein From The Hyperthermophile Methanococcus Jannaschii Length = 367

Iteration: 1
 Score =  202 bits (515), Expect = 5e-52,   Method: Compositional matrix adjust.
 Identities = 124/361 (34%), Positives = 194/361 (53%), Gaps = 23/361 (6%)
Query: 468 TWHQTGLTSKIMETIRKLNYEKPMPIQAQALPVIMSGR-DCIGVAKTGSGKTLAFVLPML 526
            +++  L+  I+  IR   +EKP  IQ + +P+ ++   + +  A+TGSGKT +F +P++
Sbjct: 7   NFNELNLSDNILNAIRNKGFEKPTDIQXKVIPLFLNDEYNIVAQARTGSGKTASFAIPLI 66
Query: 527 RHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQISE 586
             + +   + A      +I+ PTREL  Q+  +I        ++   +YGG  +  QI  
Sbjct: 67  ELVNENNGIEA------IILTPTRELAIQVADEIESLKGNKNLKIAKIYGGKAIYPQIKA 120
Query: 587 LKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMGFEPQITRIVQNIR 646
           LK    IVV TPGR++D +        NL+ V Y ++DEAD   + GF   + +I+    
Sbjct: 121 LKNAN-IVVGTPGRILDHINRG---TLNLKNVKYFILDEADEXLNXGFIKDVEKILNACN 176
Query: 647 PDRQTVLFSATFPRQVEILARKVLNKPVEIQVGGRSVVNKDITQ-LVEVRPESDRFLRLL 705
            D++ +LFSAT PR++  LA+K       I    ++ +N +I Q  VEV  E++RF  L 
Sbjct: 177 KDKRILLFSATXPREILNLAKKYXGDYSFI----KAKINANIEQSYVEVN-ENERFEALC 231
Query: 706 ELLG--EWYEKGKILIFVHSQEKCDALFRDLLKHGYPCLSLHGAKDQTDRESTISDFKSN 763
            LL   E+Y     L+F  ++     L   L   G+   ++HG   Q+ RE  I  FK  
Sbjct: 232 RLLKNKEFYG----LVFCKTKRDTKELASXLRDIGFKAGAIHGDLSQSQREKVIRLFKQK 287
Query: 764 VCNLLIATSVAARGLDVKELELVINFDAPNHYEDYVHRVGRTGRAGRKGCAITFISEEDA 823
              +LIAT V +RG+DV +L  VIN+  P + E Y HR+GRTGRAG+KG AI+ I+  + 
Sbjct: 288 KIRILIATDVXSRGIDVNDLNCVINYHLPQNPESYXHRIGRTGRAGKKGKAISIINRREY 347
Query: 824 K 824
           K
Sbjct: 348 K 348

>pdb|2Z0M|A Chain A, Crystal Structure Of Hypothetical Atp-Dependent Rna Helicase From Sulfolobus Tokodaii Length = 337

Iteration: 1
 Score =  191 bits (485), Expect = 2e-48,   Method: Compositional matrix adjust.
 Identities = 124/350 (35%), Positives = 194/350 (55%), Gaps = 29/350 (8%)
Query: 474 LTSKIMETIRKLNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQP 533
           +  KI + IR++ ++    +Q++ +P+++ G++ +  AKTGSGKT A+ +P+L       
Sbjct: 1   MNEKIEQAIREMGFKNFTEVQSKTIPLMLQGKNVVVRAKTGSGKTAAYAIPILEL----- 55
Query: 534 PVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQISELKRGTEI 593
                 G   L++ PTREL +Q+ S IR   + M  +   VYGG     QI+ + R  +I
Sbjct: 56  ------GMKSLVVTPTRELTRQVASHIRDIGRYMDTKVAEVYGGMPYKAQINRV-RNADI 108
Query: 594 VVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMGFEPQITRIVQNIRPDRQTVL 653
           VV TPGR++D L + G  + +L     +++DEAD MF+MGF   I  I+      + T L
Sbjct: 109 VVATPGRLLD-LWSKG--VIDLSSFEIVIIDEADLMFEMGFIDDIKIILAQTSNRKITGL 165
Query: 654 FSATFPRQVEILARKVLNKPVEIQ--VGGRSVVNKDITQLVEVRPESDRFLRLLELLGEW 711
           FSAT P ++  + +  +    EI+  +G  +V +K     V V+   D +   ++ L E 
Sbjct: 166 FSATIPEEIRKVVKDFITNYEEIEACIGLANVEHK----FVHVK---DDWRSKVQALREN 218
Query: 712 YEKGKILIFVHSQEKCDALFRDLLKHGYPCLSLHGAKDQTDRESTISDFKSNVCNLLIAT 771
            +KG +++FV ++ +   L R L  +    + L G   Q+ R   I  F+    ++LI T
Sbjct: 219 KDKG-VIVFVRTRNRVAKLVR-LFDN---AIELRGDLPQSVRNRNIDAFREGEYDMLITT 273
Query: 772 SVAARGLDVKELELVINFDAPNHYEDYVHRVGRTGRAGRKGCAITFISEE 821
            VA+RGLD+  +E VINFDAP     Y+HR+GRTGR GRKG AITFI  E
Sbjct: 274 DVASRGLDIPLVEKVINFDAPQDLRTYIHRIGRTGRMGRKGEAITFILNE 323

>pdb|1XTK|A Chain A, Structure Of Decd To Dead Mutation Of Human Uap56 Length = 390

Iteration: 1
 Score =  186 bits (472), Expect = 6e-47,   Method: Compositional matrix adjust.
 Identities = 121/387 (31%), Positives = 205/387 (52%), Gaps = 14/387 (3%)
Query: 463 PKPIKTWHQTGLTSKIMETIRKLNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFV 522
           P  +  +    L  +++  I    +E P  +Q + +P  + G D +  AK+G GKT  FV
Sbjct: 3   PGHMSGFRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFV 62
Query: 523 LPMLRHIKDQPPVAAGDGPVG-LIMAPTRELVQQIHSDIRKFAKVM-GVRCVPVYGGSGV 580
           L  L+ ++   PV    G V  L+M  TREL  QI  +  +F+K M  V+    +GG  +
Sbjct: 63  LATLQQLE---PVT---GQVSVLVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLSI 116
Query: 581 AQQISELKRGT-EIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFD-MGFEPQI 638
            +    LK+    IVV TPGR   IL  +  K  NL+ + + ++DEAD+M + +     +
Sbjct: 117 KKDEEVLKKNCPHIVVGTPGR---ILALARNKSLNLKHIKHFILDEADKMLEQLDMRRDV 173
Query: 639 TRIVQNIRPDRQTVLFSATFPRQVEILARKVLNKPVEIQVGGRSVVNKDITQLVEVRPES 698
             I +    ++Q ++FSAT  +++  + RK +  P+EI V   + +     Q   V+ + 
Sbjct: 174 QEIFRMTPHEKQVMMFSATLSKEIRPVCRKFMQDPMEIFVDDETKLTLHGLQQYYVKLKD 233
Query: 699 DRFLRLLELLGEWYEKGKILIFVHSQEKCDALFRDLLKHGYPCLSLHGAKDQTDRESTIS 758
           +   R L  L +  E  +++IFV S ++C AL + L++  +P +++H    Q +R S   
Sbjct: 234 NEKNRKLFDLLDVLEFNQVVIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQEERLSRYQ 293
Query: 759 DFKSNVCNLLIATSVAARGLDVKELELVINFDAPNHYEDYVHRVGRTGRAGRKGCAITFI 818
            FK     +L+AT++  RG+D++ + +  N+D P   + Y+HRV R GR G KG AITF+
Sbjct: 294 QFKDFQRRILVATNLFGRGMDIERVNIAFNYDMPEDSDTYLHRVARAGRFGTKGLAITFV 353
Query: 819 SEE-DAKYSPDLVKALELSEQVVPDDL 844
           S+E DAK   D+    E++   +PD++
Sbjct: 354 SDENDAKILNDVQDRFEVNISELPDEI 380

>pdb|1XTI|A Chain A, Structure Of Wildtype Human Uap56 Length = 391

Iteration: 1
 Score =  184 bits (467), Expect = 2e-46,   Method: Compositional matrix adjust.
 Identities = 119/376 (31%), Positives = 201/376 (53%), Gaps = 14/376 (3%)
Query: 474 LTSKIMETIRKLNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQP 533
           L  +++  I    +E P  +Q + +P  + G D +  AK+G GKT  FVL  L+ ++   
Sbjct: 15  LKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQLE--- 71
Query: 534 PVAAGDGPVG-LIMAPTRELVQQIHSDIRKFAKVM-GVRCVPVYGGSGVAQQISELKRGT 591
           PV    G V  L+M  TREL  QI  +  +F+K M  V+    +GG  + +    LK+  
Sbjct: 72  PVT---GQVSVLVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLKKNC 128
Query: 592 -EIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFD-MGFEPQITRIVQNIRPDR 649
             IVV TPGR   IL  +  K  NL+ + + ++DE D+M + +     +  I +    ++
Sbjct: 129 PHIVVGTPGR---ILALARNKSLNLKHIKHFILDECDKMLEQLDMRRDVQEIFRMTPHEK 185
Query: 650 QTVLFSATFPRQVEILARKVLNKPVEIQVGGRSVVNKDITQLVEVRPESDRFLRLLELLG 709
           Q ++FSAT  +++  + RK +  P+EI V   + +     Q   V+ + +   R L  L 
Sbjct: 186 QVMMFSATLSKEIRPVCRKFMQDPMEIFVDDETKLTLHGLQQYYVKLKDNEKNRKLFDLL 245
Query: 710 EWYEKGKILIFVHSQEKCDALFRDLLKHGYPCLSLHGAKDQTDRESTISDFKSNVCNLLI 769
           +  E  +++IFV S ++C AL + L++  +P +++H    Q +R S    FK     +L+
Sbjct: 246 DVLEFNQVVIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQEERLSRYQQFKDFQRRILV 305
Query: 770 ATSVAARGLDVKELELVINFDAPNHYEDYVHRVGRTGRAGRKGCAITFISEE-DAKYSPD 828
           AT++  RG+D++ + +  N+D P   + Y+HRV R GR G KG AITF+S+E DAK   D
Sbjct: 306 ATNLFGRGMDIERVNIAFNYDMPEDSDTYLHRVARAGRFGTKGLAITFVSDENDAKILND 365
Query: 829 LVKALELSEQVVPDDL 844
           +    E++   +PD++
Sbjct: 366 VQDRFEVNISELPDEI 381

>pdb|1XTJ|A Chain A, Structure Of Human Uap56 In Complex With Adp Length = 386

Iteration: 1
 Score =  184 bits (467), Expect = 2e-46,   Method: Compositional matrix adjust.
 Identities = 119/376 (31%), Positives = 201/376 (53%), Gaps = 14/376 (3%)
Query: 474 LTSKIMETIRKLNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQP 533
           L  +++  I    +E P  +Q + +P  + G D +  AK+G GKT  FVL  L+ ++   
Sbjct: 15  LKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQLE--- 71
Query: 534 PVAAGDGPVG-LIMAPTRELVQQIHSDIRKFAKVM-GVRCVPVYGGSGVAQQISELKRGT 591
           PV    G V  L+M  TREL  QI  +  +F+K M  V+    +GG  + +    LK+  
Sbjct: 72  PVT---GQVSVLVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLKKNC 128
Query: 592 -EIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFD-MGFEPQITRIVQNIRPDR 649
             IVV TPGR   IL  +  K  NL+ + + ++DE D+M + +     +  I +    ++
Sbjct: 129 PHIVVGTPGR---ILALARNKSLNLKHIKHFILDECDKMLEQLDMRRDVQEIFRMTPHEK 185
Query: 650 QTVLFSATFPRQVEILARKVLNKPVEIQVGGRSVVNKDITQLVEVRPESDRFLRLLELLG 709
           Q ++FSAT  +++  + RK +  P+EI V   + +     Q   V+ + +   R L  L 
Sbjct: 186 QVMMFSATLSKEIRPVCRKFMQDPMEIFVDDETKLTLHGLQQYYVKLKDNEKNRKLFDLL 245
Query: 710 EWYEKGKILIFVHSQEKCDALFRDLLKHGYPCLSLHGAKDQTDRESTISDFKSNVCNLLI 769
           +  E  +++IFV S ++C AL + L++  +P +++H    Q +R S    FK     +L+
Sbjct: 246 DVLEFNQVVIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQEERLSRYQQFKDFQRRILV 305
Query: 770 ATSVAARGLDVKELELVINFDAPNHYEDYVHRVGRTGRAGRKGCAITFISEE-DAKYSPD 828
           AT++  RG+D++ + +  N+D P   + Y+HRV R GR G KG AITF+S+E DAK   D
Sbjct: 306 ATNLFGRGMDIERVNIAFNYDMPEDSDTYLHRVARAGRFGTKGLAITFVSDENDAKILND 365
Query: 829 LVKALELSEQVVPDDL 844
           +    E++   +PD++
Sbjct: 366 VQDRFEVNISELPDEI 381

>pdb|3EIQ|A Chain A, Crystal Structure Of Pdcd4-eif4a Length = 414

Iteration: 1
 Score =  184 bits (466), Expect = 3e-46,   Method: Compositional matrix adjust.
 Identities = 123/370 (33%), Positives = 198/370 (53%), Gaps = 19/370 (5%)
Query: 466 IKTWHQTGLTSKIMETIRKLNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPM 525
           + ++    L+  ++  I    +EKP  IQ +A+   + G D I  A++G+GKT  F + +
Sbjct: 39  VDSFDDMNLSESLLRGIYAYGFEKPSAIQQRAILPCIKGYDVIAQAQSGTGKTATFAISI 98
Query: 526 LRHIK-DQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQI 584
           L+ I+ D     A      L++APTREL QQI   +      MG  C    GG+ V  ++
Sbjct: 99  LQQIELDLKATQA------LVLAPTRELAQQIQKVVMALGDYMGASCHACIGGTNVRAEV 152
Query: 585 SELK-RGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMGFEPQITRIVQ 643
            +L+     I+V TPGR+ D+L     +  + + +   V+DEAD M   GF+ QI  I Q
Sbjct: 153 QKLQMEAPHIIVGTPGRVFDML---NRRYLSPKYIKMFVLDEADEMLSRGFKDQIYDIFQ 209
Query: 644 NIRPDRQTVLFSATFPRQVEILARKVLNKPVEIQVGGRSVVNKDITQL-VEVRPESDRFL 702
            +  + Q VL SAT P  V  + +K +  P+ I V    +  + I Q  + V  E  +  
Sbjct: 210 KLNSNTQVVLLSATMPSDVLEVTKKFMRDPIRILVKKEELTLEGIRQFYINVEREEWK-- 267
Query: 703 RLLELLGEWYEKGKI---LIFVHSQEKCDALFRDLLKHGYPCLSLHGAKDQTDRESTISD 759
             L+ L + YE   I   +IF++++ K D L   +    +   ++HG  DQ +R+  + +
Sbjct: 268 --LDTLCDLYETLTITQAVIFINTRRKVDWLTEKMHARDFTVSAMHGDMDQKERDVIMRE 325
Query: 760 FKSNVCNLLIATSVAARGLDVKELELVINFDAPNHYEDYVHRVGRTGRAGRKGCAITFIS 819
           F+S    +LI T + ARG+DV+++ LVIN+D P + E+Y+HR+GR GR GRKG AI  ++
Sbjct: 326 FRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTNRENYIHRIGRGGRFGRKGVAINMVT 385
Query: 820 EEDAKYSPDL 829
           EED +   D+
Sbjct: 386 EEDKRTLRDI 395

>pdb|2ZU6|A Chain A, Crystal Structure Of The Eif4a-Pdcd4 Complex Length = 388

Iteration: 1
 Score =  182 bits (462), Expect = 8e-46,   Method: Compositional matrix adjust.
 Identities = 123/370 (33%), Positives = 198/370 (53%), Gaps = 19/370 (5%)
Query: 466 IKTWHQTGLTSKIMETIRKLNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPM 525
           + ++    L+  ++  I    +EKP  IQ +A+   + G D I  A++G+GKT  F + +
Sbjct: 13  VDSFDDMNLSESLLRGIYAYGFEKPSAIQQRAILPCIKGYDVIAQAQSGTGKTATFAISI 72
Query: 526 LRHIK-DQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQI 584
           L+ I+ D     A      L++APTREL QQI   +      MG  C    GG+ V  ++
Sbjct: 73  LQQIELDLKATQA------LVLAPTRELAQQIQKVVMALGDYMGASCHACIGGTNVRAEV 126
Query: 585 SELK-RGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMGFEPQITRIVQ 643
            +L+     I+V TPGR+ D+L     +  + + +   V+DEAD M   GF+ QI  I Q
Sbjct: 127 QKLQMEAPHIIVGTPGRVFDML---NRRYLSPKYIKMFVLDEADEMLSRGFKDQIYDIFQ 183
Query: 644 NIRPDRQTVLFSATFPRQVEILARKVLNKPVEIQVGGRSVVNKDITQL-VEVRPESDRFL 702
            +  + Q VL SAT P  V  + +K +  P+ I V    +  + I Q  + V  E  +  
Sbjct: 184 KLNSNTQVVLLSATMPSDVLEVTKKFMRDPIRILVKKEELTLEGIRQFYINVEREEWK-- 241
Query: 703 RLLELLGEWYEKGKI---LIFVHSQEKCDALFRDLLKHGYPCLSLHGAKDQTDRESTISD 759
             L+ L + YE   I   +IF++++ K D L   +    +   ++HG  DQ +R+  + +
Sbjct: 242 --LDTLCDLYETLTITQAVIFINTRRKVDWLTEKMHARDFTVSAMHGDMDQKERDVIMRE 299
Query: 760 FKSNVCNLLIATSVAARGLDVKELELVINFDAPNHYEDYVHRVGRTGRAGRKGCAITFIS 819
           F+S    +LI T + ARG+DV+++ LVIN+D P + E+Y+HR+GR GR GRKG AI  ++
Sbjct: 300 FRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTNRENYIHRIGRGGRFGRKGVAINMVT 359
Query: 820 EEDAKYSPDL 829
           EED +   D+
Sbjct: 360 EEDKRTLRDI 369

>pdb|3PEY|A Chain A, S. Cerevisiae Dbp5 Bound To Rna And Adp Bef3 Length = 395

Iteration: 1
 Score =  180 bits (457), Expect = 3e-45,   Method: Compositional matrix adjust.
 Identities = 121/370 (32%), Positives = 204/370 (55%), Gaps = 29/370 (7%)
Query: 467 KTWHQTGLTSKIMETIRKLNYEKPMPIQAQALPVIMSG--RDCIGVAKTGSGKTLAFVLP 524
           K++ + GL  ++++ I  + ++KP  IQ +ALP+++    R+ I  +++G+GKT AF L 
Sbjct: 5   KSFDELGLAPELLKGIYAMKFQKPSKIQERALPLLLHNPPRNMIAQSQSGTGKTAAFSLT 64
Query: 525 MLRHIKDQPPVAAGDGPVGLIMAPTRELVQQ---IHSDIRKFAKVMGVRCVPVYGGSGVA 581
           ML  +   P  A+   P  + +AP+REL +Q   +  ++ KF K+     VP        
Sbjct: 65  MLTRV--NPEDAS---PQAICLAPSRELARQTLEVVQEMGKFTKITSQLIVP--DSFEKN 117
Query: 582 QQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDM-GFEPQITR 640
           +QI+      +++V TPG ++D++     K+  L+++   V+DEAD M D  G   Q  R
Sbjct: 118 KQIN-----AQVIVGTPGTVLDLM---RRKLMQLQKIKIFVLDEADNMLDQQGLGDQCIR 169
Query: 641 IVQNIRPDRQTVLFSATFPRQVEILARKVLNKPVEIQVGGRSVVNKDITQL-VEVRPESD 699
           + + +  D Q VLFSATF   V   A+K++     +++    V    I QL ++ + E+D
Sbjct: 170 VKRFLPKDTQLVLFSATFADAVRQYAKKIVPNANTLELQTNEVNVDAIKQLYMDCKNEAD 229
Query: 700 RFLRLLELLGEWYEKGKILIFVHSQEKCDALFRDLLKHGYPCLSLHGAKDQTDRESTISD 759
           +F  L EL G     G  +IFV +++  + L+  L   G+    LHG     +R+  I D
Sbjct: 230 KFDVLTELYG-LMTIGSSIIFVATKKTANVLYGKLKSEGHEVSILHGDLQTQERDRLIDD 288
Query: 760 FKSNVCNLLIATSVAARGLDVKELELVINFDAP---NHYED---YVHRVGRTGRAGRKGC 813
           F+     +LI T+V ARG+D+  + +V+N+D P   N   D   Y+HR+GRTGR GRKG 
Sbjct: 289 FREGRSKVLITTNVLARGIDIPTVSMVVNYDLPTLANGQADPATYIHRIGRTGRFGRKGV 348
Query: 814 AITFISEEDA 823
           AI+F+ ++++
Sbjct: 349 AISFVHDKNS 358

>pdb|3PEW|A Chain A, S. Cerevisiae Dbp5 L327v Bound To Rna And Adp Bef3 Length = 395

Iteration: 1
 Score =  180 bits (456), Expect = 4e-45,   Method: Compositional matrix adjust.
 Identities = 119/370 (32%), Positives = 202/370 (54%), Gaps = 29/370 (7%)
Query: 467 KTWHQTGLTSKIMETIRKLNYEKPMPIQAQALPVIMSG--RDCIGVAKTGSGKTLAFVLP 524
           K++ + GL  ++++ I  + ++KP  IQ +ALP+++    R+ I  +++G+GKT AF L 
Sbjct: 5   KSFDELGLAPELLKGIYAMKFQKPSKIQERALPLLLHNPPRNMIAQSQSGTGKTAAFSLT 64
Query: 525 MLRHIKDQPPVAAGDGPVGLIMAPTRELVQQ---IHSDIRKFAKVMGVRCVPVYGGSGVA 581
           ML  +  +        P  + +AP+REL +Q   +  ++ KF K+     VP        
Sbjct: 65  MLTRVNPEDA-----SPQAICLAPSRELARQTLEVVQEMGKFTKITSQLIVP--DSFEKN 117
Query: 582 QQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDM-GFEPQITR 640
           +QI+      +++V TPG ++D++     K+  L+++   V+DEAD M D  G   Q  R
Sbjct: 118 KQIN-----AQVIVGTPGTVLDLM---RRKLMQLQKIKIFVLDEADNMLDQQGLGDQCIR 169
Query: 641 IVQNIRPDRQTVLFSATFPRQVEILARKVLNKPVEIQVGGRSVVNKDITQL-VEVRPESD 699
           + + +  D Q VLFSATF   V   A+K++     +++    V    I QL ++ + E+D
Sbjct: 170 VKRFLPKDTQLVLFSATFADAVRQYAKKIVPNANTLELQTNEVNVDAIKQLYMDCKNEAD 229
Query: 700 RFLRLLELLGEWYEKGKILIFVHSQEKCDALFRDLLKHGYPCLSLHGAKDQTDRESTISD 759
           +F  L EL G     G  +IFV +++  + L+  L   G+    LHG     +R+  I D
Sbjct: 230 KFDVLTELYG-VMTIGSSIIFVATKKTANVLYGKLKSEGHEVSILHGDLQTQERDRLIDD 288
Query: 760 FKSNVCNLLIATSVAARGLDVKELELVINFDAP---NHYED---YVHRVGRTGRAGRKGC 813
           F+     +LI T+V ARG+D+  + +V+N+D P   N   D   Y+HR+GRTGR GRKG 
Sbjct: 289 FREGRSKVLITTNVLARGIDIPTVSMVVNYDLPTLANGQADPATYIHRIGRTGRFGRKGV 348
Query: 814 AITFISEEDA 823
           AI+F+ ++++
Sbjct: 349 AISFVHDKNS 358

>pdb|3IUY|A Chain A, Crystal Structure Of Ddx53 Dead-Box Domain Length = 228

Iteration: 1
 Score =  165 bits (418), Expect = 1e-40,   Method: Compositional matrix adjust.
 Identities = 84/202 (41%), Positives = 132/202 (65%), Gaps = 5/202 (2%)
Query: 478 IMETIRKLNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQP-PVA 536
           ++++I ++   KP PIQ+QA P+I+ G D I VA+TG+GKTL++++P   H+  QP    
Sbjct: 31  LLKSIIRVGILKPTPIQSQAWPIILQGIDLIVVAQTGTGKTLSYLMPGFIHLDSQPISRE 90
Query: 537 AGDGPVGLIMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQISELKRGTEIVVC 596
             +GP  L++ PTREL   + ++  K++   G++ + +YGG     QI ++ +G +I++ 
Sbjct: 91  QRNGPGMLVLTPTRELALHVEAECSKYS-YKGLKSICIYGGRNRNGQIEDISKGVDIIIA 149
Query: 597 TPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMGFEPQITRIVQNIRPDRQTVLFSA 656
           TPGR+ D+   +     NLR +TYLV+DEAD+M DM FEPQI +I+ ++RPDRQTV+ SA
Sbjct: 150 TPGRLNDLQMNNS---VNLRSITYLVIDEADKMLDMEFEPQIRKILLDVRPDRQTVMTSA 206
Query: 657 TFPRQVEILARKVLNKPVEIQV 678
           T+P  V  LA   L  P+ + V
Sbjct: 207 TWPDTVRQLALSYLKDPMIVYV 228

>pdb|1WRB|A Chain A, Crystal Structure Of The N-Terminal Reca-Like Domain Of Djvlgb, A Pranarian Vasa-Like Rna Helicase Length = 253

Iteration: 1
 Score =  161 bits (408), Expect = 2e-39,   Method: Compositional matrix adjust.
 Identities = 89/222 (40%), Positives = 134/222 (60%), Gaps = 11/222 (4%)
Query: 466 IKTWHQTGLTSKIMETIRKLNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPM 525
           I+ + +  L   I   I   +Y++P PIQ  A+P I+  RD +  A+TGSGKT AF++P+
Sbjct: 22  IENFDELKLDPTIRNNILLASYQRPTPIQKNAIPAILEHRDIMACAQTGSGKTAAFLIPI 81
Query: 526 LRHIK----DQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVA 581
           + H+     +Q   +    P  LI+APTREL  QI S+ +KF+    +R   VYGG+   
Sbjct: 82  INHLVCQDLNQQRYSKTAYPKCLILAPTRELAIQILSESQKFSLNTPLRSCVVYGGADTH 141
Query: 582 QQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMGFEPQITRI 641
            QI E++ G  ++V TPGR++D +     KI+ L    Y+V+DEADRM DMGFEPQI +I
Sbjct: 142 SQIREVQMGCHLLVATPGRLVDFI--EKNKIS-LEFCKYIVLDEADRMLDMGFEPQIRKI 198
Query: 642 VQNIRP----DRQTVLFSATFPRQVEILARKVLNKPVEIQVG 679
           ++        +RQT++FSATFP++++ LA   L   + + VG
Sbjct: 199 IEESNMPSGINRQTLMFSATFPKEIQKLAADFLYNYIFMTVG 240

>pdb|2VSO|A Chain A, Crystal Structure Of A Translation Initiation Complex Length = 395

Iteration: 1
 Score =  161 bits (408), Expect = 2e-39,   Method: Compositional matrix adjust.
 Identities = 121/397 (30%), Positives = 199/397 (50%), Gaps = 31/397 (7%)
Query: 464 KPIKTWHQTGLTSKIMETIRKLNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVL 523
           K +  +    L   ++  +    +E+P  IQ +A+  I+ G D +  A++G+GKT  F +
Sbjct: 19  KVVYKFDDMELDENLLRGVFGYGFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFSI 78
Query: 524 PMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQ 583
             L+ I       +   P  L++APTREL  QI   +   A  M ++     GG+   + 
Sbjct: 79  AALQRID-----TSVKAPQALMLAPTRELALQIQKVVMALAFHMDIKVHACIGGTSFVED 133
Query: 584 ISELKRGTEIVVCTPGRMIDILCTSGGKITNLRR-------VTYLVMDEADRMFDMGFEP 636
            +E  R  +IVV TPGR+ D          N++R       +   ++DEAD M   GF+ 
Sbjct: 134 -AEGLRDAQIVVGTPGRVFD----------NIQRRRFRTDKIKMFILDEADEMLSSGFKE 182
Query: 637 QITRIVQNIRPDRQTVLFSATFPRQVEILARKVLNKPVEIQVGGRSVVNKDITQL-VEVR 695
           QI +I   + P  Q VL SAT P  V  +  K +  PV I V    +  + I Q  V V 
Sbjct: 183 QIYQIFTLLPPTTQVVLLSATMPNDVLEVTTKFMRNPVRILVKKDELTLEGIKQFYVNVE 242
Query: 696 PESDRFLRLLELLGEWYEKGKI---LIFVHSQEKCDALFRDLLKHGYPCLSLHGAKDQTD 752
            E  ++    E L + Y+   +   +IF +++ K + L   L    +   +++    Q +
Sbjct: 243 EEEYKY----ECLTDLYDSISVTQAVIFCNTRRKVEELTTKLRNDKFTVSAIYSDLPQQE 298
Query: 753 RESTISDFKSNVCNLLIATSVAARGLDVKELELVINFDAPNHYEDYVHRVGRTGRAGRKG 812
           R++ + +F+S    +LI+T + ARG+DV+++ LVIN+D P + E+Y+HR+GR GR GRKG
Sbjct: 299 RDTIMKEFRSGSSRILISTDLLARGIDVQQVSLVINYDLPANKENYIHRIGRGGRFGRKG 358
Query: 813 CAITFISEEDAKYSPDLVKALELSEQVVPDDLKALAD 849
            AI F++ ED     +L K      + +P D+  L +
Sbjct: 359 VAINFVTNEDVGAMRELEKFYSTQIEELPSDIATLLN 395

>pdb|3SQW|A Chain A, Structure Of Mss116p (Nte Deletion) Bound To Ssrna And Amp-Pnp Length = 579

Iteration: 1
 Score =  158 bits (399), Expect = 2e-38,   Method: Compositional matrix adjust.
 Identities = 119/404 (29%), Positives = 205/404 (50%), Gaps = 55/404 (13%)
Query: 474 LTSKIMETIRKLNYEKPMPIQAQALPVIMSG--RDCIGVAKTGSGKTLAFVLPMLRHIKD 531
           L  +I + I ++ +    P+Q + +  I+S    D I  AKTG+GKT AF++P+ +H+ +
Sbjct: 28  LDKEIHKAITRMEFPGLTPVQQKTIKPILSSEDHDVIARAKTGTGKTFAFLIPIFQHLIN 87
Query: 532 -----QPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKV-MGVR---CVPVYGGSGVAQ 582
                Q  V A      +I+APTR+L  QI ++++K   +  G++   CV + GG+    
Sbjct: 88  TKFDSQYMVKA------VIVAPTRDLALQIEAEVKKIHDMNYGLKKYACVSLVGGTDFRA 141
Query: 583 QISEL-KRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMGFEPQITRI 641
            ++++ K    IV+ TPGR+ID+L     K    R V Y V+DEADR+ ++GF   +  I
Sbjct: 142 AMNKMNKLRPNIVIATPGRLIDVLEKYSNKF--FRFVDYKVLDEADRLLEIGFRDDLETI 199
Query: 642 --VQNIRPDR-----QTVLFSATFPRQVEILARKVLNKPVEIQVGGRSVVNKD------- 687
             + N +  +     +T+LFSAT   +V+ LA  ++NK    +      V+K+       
Sbjct: 200 SGILNEKNSKSADNIKTLLFSATLDDKVQKLANNIMNKK---ECLFLDTVDKNEPEAHER 256
Query: 688 ITQLVEVRPESDRFLRLLELLGEWYEKG--------KILIF---VHSQEKCDALFRDLLK 736
           I Q V +   S++F   +    E  +K         K +IF   V       ++ ++  K
Sbjct: 257 IDQSVVI---SEKFANSIFAAVEHIKKQIKERDSNYKAIIFAPTVKFTSFLCSILKNEFK 313
Query: 737 HGYPCLSLHGAKDQTDRESTISDFKSNVCNLLIATSVAARGLDVKELELVINFDAPNHYE 796
              P L  HG   Q  R S +  FK +   +L+ T V ARG+D   +  V+    P+   
Sbjct: 314 KDLPILEFHGKITQNKRTSLVKRFKKDESGILVCTDVGARGMDFPNVHEVLQIGVPSELA 373
Query: 797 DYVHRVGRTGRAGRKGCAITFISEEDAKYSPDLVKALELSEQVV 840
           +Y+HR+GRT R+G++G ++ FI +++  +    V+ LE ++ +V
Sbjct: 374 NYIHRIGRTARSGKEGSSVLFICKDELPF----VRELEDAKNIV 413

>pdb|3I5X|A Chain A, Structure Of Mss116p Bound To Ssrna And Amp-Pnp Length = 563

Iteration: 1
 Score =  156 bits (394), Expect = 6e-38,   Method: Compositional matrix adjust.
 Identities = 119/404 (29%), Positives = 205/404 (50%), Gaps = 55/404 (13%)
Query: 474 LTSKIMETIRKLNYEKPMPIQAQALPVIMSG--RDCIGVAKTGSGKTLAFVLPMLRHIKD 531
           L  +I + I ++ +    P+Q + +  I+S    D I  AKTG+GKT AF++P+ +H+ +
Sbjct: 79  LDKEIHKAITRMEFPGLTPVQQKTIKPILSSEDHDVIARAKTGTGKTFAFLIPIFQHLIN 138
Query: 532 -----QPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKV-MGVR---CVPVYGGSGVAQ 582
                Q  V A      +I+APTR+L  QI ++++K   +  G++   CV + GG+    
Sbjct: 139 TKFDSQYMVKA------VIVAPTRDLALQIEAEVKKIHDMNYGLKKYACVSLVGGTDFRA 192
Query: 583 QISEL-KRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMGFEPQITRI 641
            ++++ K    IV+ TPGR+ID+L     K    R V Y V+DEADR+ ++GF   +  I
Sbjct: 193 AMNKMNKLRPNIVIATPGRLIDVLEKYSNKF--FRFVDYKVLDEADRLLEIGFRDDLETI 250
Query: 642 --VQNIRPDR-----QTVLFSATFPRQVEILARKVLNKPVEIQVGGRSVVNKD------- 687
             + N +  +     +T+LFSAT   +V+ LA  ++NK    +      V+K+       
Sbjct: 251 SGILNEKNSKSADNIKTLLFSATLDDKVQKLANNIMNKK---ECLFLDTVDKNEPEAHER 307
Query: 688 ITQLVEVRPESDRFLRLLELLGEWYEKG--------KILIF---VHSQEKCDALFRDLLK 736
           I Q V +   S++F   +    E  +K         K +IF   V       ++ ++  K
Sbjct: 308 IDQSVVI---SEKFANSIFAAVEHIKKQIKERDSNYKAIIFAPTVKFTSFLCSILKNEFK 364
Query: 737 HGYPCLSLHGAKDQTDRESTISDFKSNVCNLLIATSVAARGLDVKELELVINFDAPNHYE 796
              P L  HG   Q  R S +  FK +   +L+ T V ARG+D   +  V+    P+   
Sbjct: 365 KDLPILEFHGKITQNKRTSLVKRFKKDESGILVCTDVGARGMDFPNVHEVLQIGVPSELA 424
Query: 797 DYVHRVGRTGRAGRKGCAITFISEEDAKYSPDLVKALELSEQVV 840
           +Y+HR+GRT R+G++G ++ FI +++  +    V+ LE ++ +V
Sbjct: 425 NYIHRIGRTARSGKEGSSVLFICKDELPF----VRELEDAKNIV 464

>pdb|3SQX|A Chain A, Structure Of Mss116p (Nte And C-Tail Double Deletion) Bound To Ssrna And Amp-Pnp Length = 512

Iteration: 1
 Score =  155 bits (392), Expect = 1e-37,   Method: Compositional matrix adjust.
 Identities = 119/404 (29%), Positives = 205/404 (50%), Gaps = 55/404 (13%)
Query: 474 LTSKIMETIRKLNYEKPMPIQAQALPVIMSG--RDCIGVAKTGSGKTLAFVLPMLRHIKD 531
           L  +I + I ++ +    P+Q + +  I+S    D I  AKTG+GKT AF++P+ +H+ +
Sbjct: 28  LDKEIHKAITRMEFPGLTPVQQKTIKPILSSEDHDVIARAKTGTGKTFAFLIPIFQHLIN 87
Query: 532 -----QPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKV-MGVR---CVPVYGGSGVAQ 582
                Q  V A      +I+APTR+L  QI ++++K   +  G++   CV + GG+    
Sbjct: 88  TKFDSQYMVKA------VIVAPTRDLALQIEAEVKKIHDMNYGLKKYACVSLVGGTDFRA 141
Query: 583 QISEL-KRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMGFEPQITRI 641
            ++++ K    IV+ TPGR+ID+L     K    R V Y V+DEADR+ ++GF   +  I
Sbjct: 142 AMNKMNKLRPNIVIATPGRLIDVLEKYSNKF--FRFVDYKVLDEADRLLEIGFRDDLETI 199
Query: 642 --VQNIRPDR-----QTVLFSATFPRQVEILARKVLNKPVEIQVGGRSVVNKD------- 687
             + N +  +     +T+LFSAT   +V+ LA  ++NK    +      V+K+       
Sbjct: 200 SGILNEKNSKSADNIKTLLFSATLDDKVQKLANNIMNKK---ECLFLDTVDKNEPEAHER 256
Query: 688 ITQLVEVRPESDRFLRLLELLGEWYEKG--------KILIF---VHSQEKCDALFRDLLK 736
           I Q V +   S++F   +    E  +K         K +IF   V       ++ ++  K
Sbjct: 257 IDQSVVI---SEKFANSIFAAVEHIKKQIKERDSNYKAIIFAPTVKFTSFLCSILKNEFK 313
Query: 737 HGYPCLSLHGAKDQTDRESTISDFKSNVCNLLIATSVAARGLDVKELELVINFDAPNHYE 796
              P L  HG   Q  R S +  FK +   +L+ T V ARG+D   +  V+    P+   
Sbjct: 314 KDLPILEFHGKITQNKRTSLVKRFKKDESGILVCTDVGARGMDFPNVHEVLQIGVPSELA 373
Query: 797 DYVHRVGRTGRAGRKGCAITFISEEDAKYSPDLVKALELSEQVV 840
           +Y+HR+GRT R+G++G ++ FI +++  +    V+ LE ++ +V
Sbjct: 374 NYIHRIGRTARSGKEGSSVLFICKDELPF----VRELEDAKNIV 413

>pdb|3BER|A Chain A, Human Dead-Box Rna-Helicase Ddx47, Conserved Domain I In Complex With Amp Length = 249

Iteration: 1
 Score =  154 bits (389), Expect = 3e-37,   Method: Compositional matrix adjust.
 Identities = 85/212 (40%), Positives = 122/212 (57%), Gaps = 7/212 (3%)
Query: 467 KTWHQTGLTSKIMETIRKLNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPML 526
           KT+   G+T  + E   +L + KP  IQ +A+P+ + GRD IG+A+TGSGKT AF LP+L
Sbjct: 43  KTFKDLGVTDVLCEACDQLGWTKPTKIQIEAIPLALQGRDIIGLAETGSGKTGAFALPIL 102
Query: 527 RHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQISE 586
             + + P          L++ PTREL  QI          +GV+   + GG     Q   
Sbjct: 103 NALLETP-----QRLFALVLTPTRELAFQISEQFEALGSSIGVQSAVIVGGIDSMSQSLA 157
Query: 587 LKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMGFEPQITRIVQNIR 646
           L +   I++ TPGR+ID L  + G   NLR + YLVMDEADR+ +M FE ++ +I++ I 
Sbjct: 158 LAKKPHIIIATPGRLIDHLENTKG--FNLRALKYLVMDEADRILNMDFETEVDKILKVIP 215
Query: 647 PDRQTVLFSATFPRQVEILARKVLNKPVEIQV 678
            DR+T LFSAT  ++V+ L R  L  PV+  V
Sbjct: 216 RDRKTFLFSATMTKKVQKLQRAALKNPVKCAV 247

>pdb|1FUU|A Chain A, Yeast Initiation Factor 4a Length = 394

Iteration: 1
 Score =  153 bits (387), Expect = 4e-37,   Method: Compositional matrix adjust.
 Identities = 119/397 (29%), Positives = 194/397 (48%), Gaps = 31/397 (7%)
Query: 464 KPIKTWHQTGLTSKIMETIRKLNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVL 523
           K +  +    L   ++  +    +E+P  IQ +A+  I+ G D +  A++G+GKT  F +
Sbjct: 18  KVVYKFDDXELDENLLRGVFGYGFEEPSAIQQRAIXPIIEGHDVLAQAQSGTGKTGTFSI 77
Query: 524 PMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQ 583
             L+ I       +   P  L +APTREL  QI   +   A    ++     GG+   + 
Sbjct: 78  AALQRID-----TSVKAPQALXLAPTRELALQIQKVVXALAFHXDIKVHACIGGTSFVED 132
Query: 584 ISELKRGTEIVVCTPGRMIDILCTSGGKITNLRR-------VTYLVMDEADRMFDMGFEP 636
            +E  R  +IVV TPGR+ D          N++R       +   ++DEAD     GF+ 
Sbjct: 133 -AEGLRDAQIVVGTPGRVFD----------NIQRRRFRTDKIKXFILDEADEXLSSGFKE 181
Query: 637 QITRIVQNIRPDRQTVLFSATFPRQVEILARKVLNKPVEIQVGGRSVVNKDITQL-VEVR 695
           QI +I   + P  Q VL SAT P  V  +  K    PV I V    +  + I Q  V V 
Sbjct: 182 QIYQIFTLLPPTTQVVLLSATXPNDVLEVTTKFXRNPVRILVKKDELTLEGIKQFYVNVE 241
Query: 696 PESDRFLRLLELLGEWYEKGKI---LIFVHSQEKCDALFRDLLKHGYPCLSLHGAKDQTD 752
            E  ++    E L + Y+   +   +IF +++ K + L   L    +   +++    Q +
Sbjct: 242 EEEYKY----ECLTDLYDSISVTQAVIFCNTRRKVEELTTKLRNDKFTVSAIYSDLPQQE 297
Query: 753 RESTISDFKSNVCNLLIATSVAARGLDVKELELVINFDAPNHYEDYVHRVGRTGRAGRKG 812
           R++   +F+S    +LI+T + ARG+DV+++ LVIN+D P + E+Y+HR+GR GR GRKG
Sbjct: 298 RDTIXKEFRSGSSRILISTDLLARGIDVQQVSLVINYDLPANKENYIHRIGRGGRFGRKG 357
Query: 813 CAITFISEEDAKYSPDLVKALELSEQVVPDDLKALAD 849
            AI F++ ED     +L K      + +P D+  L +
Sbjct: 358 VAINFVTNEDVGAXRELEKFYSTQIEELPSDIATLLN 394

>pdb|2GXQ|A Chain A, Hera N-Terminal Domain In Complex With Amp, Crystal Form 1 Length = 207

Iteration: 1
 Score =  152 bits (385), Expect = 7e-37,   Method: Compositional matrix adjust.
 Identities = 85/205 (41%), Positives = 117/205 (57%), Gaps = 7/205 (3%)
Query: 474 LTSKIMETIRKLNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQP 533
           L  +I+E +       P PIQA ALP+ + G+D IG A+TG+GKTLAF LP+   +   P
Sbjct: 8   LKPEILEALHGRGLTTPTPIQAAALPLALEGKDLIGQARTGTGKTLAFALPIAERLA--P 65
Query: 534 PVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQISELKRGTEI 593
               G  P  L++ PTREL  Q+ S++   A    ++ V VYGG+G  +Q   L RG + 
Sbjct: 66  SQERGRKPRALVLTPTRELALQVASELTAVAP--HLKVVAVYGGTGYGKQKEALLRGADA 123
Query: 594 VVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMGFEPQITRIVQNIRPDRQTVL 653
           VV TPGR +D L      + +L RV   V+DEAD M  MGFE ++  ++    P RQT+L
Sbjct: 124 VVATPGRALDYLRQG---VLDLSRVEVAVLDEADEMLSMGFEEEVEALLSATPPSRQTLL 180
Query: 654 FSATFPRQVEILARKVLNKPVEIQV 678
           FSAT P   + LA + +  PV I V
Sbjct: 181 FSATLPSWAKRLAERYMKNPVLINV 205

>pdb|3MWJ|A Chain A, Q28e Mutant Of Hera N-Terminal Reca-Like Domain, Apo Form Length = 207

Iteration: 1
 Score =  151 bits (381), Expect = 2e-36,   Method: Compositional matrix adjust.
 Identities = 84/205 (40%), Positives = 117/205 (57%), Gaps = 7/205 (3%)
Query: 474 LTSKIMETIRKLNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQP 533
           L  +I+E +       P PI+A ALP+ + G+D IG A+TG+GKTLAF LP+   +   P
Sbjct: 8   LKPEILEALHGRGLTTPTPIEAAALPLALEGKDLIGQARTGTGKTLAFALPIAERLA--P 65
Query: 534 PVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQISELKRGTEI 593
               G  P  L++ PTREL  Q+ S++   A    ++ V VYGG+G  +Q   L RG + 
Sbjct: 66  SQERGRKPRALVLTPTRELALQVASELTAVAP--HLKVVAVYGGTGYGKQKEALLRGADA 123
Query: 594 VVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMGFEPQITRIVQNIRPDRQTVL 653
           VV TPGR +D L      + +L RV   V+DEAD M  MGFE ++  ++    P RQT+L
Sbjct: 124 VVATPGRALDYLRQG---VLDLSRVEVAVLDEADEMLSMGFEEEVEALLSATPPSRQTLL 180
Query: 654 FSATFPRQVEILARKVLNKPVEIQV 678
           FSAT P   + LA + +  PV I V
Sbjct: 181 FSATLPSWAKRLAERYMKNPVLINV 205

>pdb|3FMP|B Chain B, Crystal Structure Of The Nucleoporin Nup214 In Complex With The Dead- Box Helicase Ddx19 Length = 479

Iteration: 1
 Score =  150 bits (379), Expect = 3e-36,   Method: Compositional matrix adjust.
 Identities = 113/382 (29%), Positives = 195/382 (51%), Gaps = 29/382 (7%)
Query: 466 IKTWHQTGLTSKIMETIRKLNYEKPMPIQAQALPVIMSG--RDCIGVAKTGSGKTLAFVL 523
           +K++ +  L  ++++ +  + + +P  IQ  ALP++++   ++ I  +++G+GKT AFVL
Sbjct: 91  VKSFEELRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVL 150
Query: 524 PMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVM-GVRCVPVYGGSGV-- 580
            ML  ++      A   P  L ++PT EL  Q    I +  K    ++      G+ +  
Sbjct: 151 AMLSQVE-----PANKYPQCLCLSPTYELALQTGKVIEQMGKFYPELKLAYAVRGNKLER 205
Query: 581 AQQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMF-DMGFEPQIT 639
            Q+ISE     +IV+ TPG ++D    S  K  + +++   V+DEAD M    G + Q  
Sbjct: 206 GQKISE-----QIVIGTPGTVLD--WCSKLKFIDPKKIKVFVLDEADVMIATQGHQDQSI 258
Query: 640 RIVQNIRPDRQTVLFSATFPRQVEILARKVLNKPVEIQVGGRSVVNKDITQL-VEVRPES 698
           RI + +  + Q +LFSATF   V   A+KV+  P  I++         I Q  V      
Sbjct: 259 RIQRMLPRNCQMLLFSATFEDSVWKFAQKVVPDPNVIKLKREEETLDTIKQYYVLCSSRD 318
Query: 699 DRFLRLLELLGEWYEKGKILIFVHSQEKCDALFRDLLKHGYPCLSLHGAKDQTDRESTIS 758
           ++F  L  L G      + +IF H+++    L  +L K G+    L G      R + I 
Sbjct: 319 EKFQALCNLYGA-ITIAQAMIFCHTRKTASWLAAELSKEGHQVALLSGEMMVEQRAAVIE 377
Query: 759 DFKSNVCNLLIATSVAARGLDVKELELVINFDAP------NHYEDYVHRVGRTGRAGRKG 812
            F+     +L+ T+V ARG+DV+++ +VINFD P         E Y+HR+GRTGR G++G
Sbjct: 378 RFREGKEKVLVTTNVCARGIDVEQVSVVINFDLPVDKDGNPDNETYLHRIGRTGRFGKRG 437
Query: 813 CAITFISEEDAKYSPDLVKALE 834
            A+  +   D+K+S +++  ++
Sbjct: 438 LAVNMV---DSKHSMNILNRIQ 456

>pdb|3EWS|A Chain A, Human Dead-Box Rna-Helicase Ddx19 In Complex With Adp Length = 445

Iteration: 1
 Score =  149 bits (377), Expect = 5e-36,   Method: Compositional matrix adjust.
 Identities = 113/382 (29%), Positives = 195/382 (51%), Gaps = 29/382 (7%)
Query: 466 IKTWHQTGLTSKIMETIRKLNYEKPMPIQAQALPVIMSG--RDCIGVAKTGSGKTLAFVL 523
           +K++ +  L  ++++ +  + + +P  IQ  ALP++++   ++ I  +++G+GKT AFVL
Sbjct: 61  VKSFEELRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVL 120
Query: 524 PMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVM-GVRCVPVYGGSGV-- 580
            ML  ++      A   P  L ++PT EL  Q    I +  K    ++      G+ +  
Sbjct: 121 AMLSQVE-----PANKYPQCLCLSPTYELALQTGKVIEQMGKFYPELKLAYAVRGNKLER 175
Query: 581 AQQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMF-DMGFEPQIT 639
            Q+ISE     +IV+ TPG ++D    S  K  + +++   V+DEAD M    G + Q  
Sbjct: 176 GQKISE-----QIVIGTPGTVLD--WCSKLKFIDPKKIKVFVLDEADVMIATQGHQDQSI 228
Query: 640 RIVQNIRPDRQTVLFSATFPRQVEILARKVLNKPVEIQVGGRSVVNKDITQL-VEVRPES 698
           RI + +  + Q +LFSATF   V   A+KV+  P  I++         I Q  V      
Sbjct: 229 RIQRMLPRNCQMLLFSATFEDSVWKFAQKVVPDPNVIKLKREEETLDTIKQYYVLCSSRD 288
Query: 699 DRFLRLLELLGEWYEKGKILIFVHSQEKCDALFRDLLKHGYPCLSLHGAKDQTDRESTIS 758
           ++F  L  L G      + +IF H+++    L  +L K G+    L G      R + I 
Sbjct: 289 EKFQALCNLYGA-ITIAQAMIFCHTRKTASWLAAELSKEGHQVALLSGEMMVEQRAAVIE 347
Query: 759 DFKSNVCNLLIATSVAARGLDVKELELVINFDAP------NHYEDYVHRVGRTGRAGRKG 812
            F+     +L+ T+V ARG+DV+++ +VINFD P         E Y+HR+GRTGR G++G
Sbjct: 348 RFREGKEKVLVTTNVCARGIDVEQVSVVINFDLPVDKDGNPDNETYLHRIGRTGRFGKRG 407
Query: 813 CAITFISEEDAKYSPDLVKALE 834
            A+  +   D+K+S +++  ++
Sbjct: 408 LAVNMV---DSKHSMNILNRIQ 426

>pdb|3G0H|A Chain A, Human Dead-box Rna Helicase Ddx19, In Complex With An Atp-analogue And Rna Length = 424

Iteration: 1
 Score =  149 bits (376), Expect = 7e-36,   Method: Compositional matrix adjust.
 Identities = 113/382 (29%), Positives = 195/382 (51%), Gaps = 29/382 (7%)
Query: 466 IKTWHQTGLTSKIMETIRKLNYEKPMPIQAQALPVIMSG--RDCIGVAKTGSGKTLAFVL 523
           +K++ +  L  ++++ +  + + +P  IQ  ALP++++   ++ I  +++G+GKT AFVL
Sbjct: 40  VKSFEELRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVL 99
Query: 524 PMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVM-GVRCVPVYGGSGV-- 580
            ML  ++      A   P  L ++PT EL  Q    I +  K    ++      G+ +  
Sbjct: 100 AMLSQVE-----PANKYPQCLCLSPTYELALQTGKVIEQMGKFYPELKLAYAVRGNKLER 154
Query: 581 AQQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMF-DMGFEPQIT 639
            Q+ISE     +IV+ TPG ++D    S  K  + +++   V+DEAD M    G + Q  
Sbjct: 155 GQKISE-----QIVIGTPGTVLD--WCSKLKFIDPKKIKVFVLDEADVMIATQGHQDQSI 207
Query: 640 RIVQNIRPDRQTVLFSATFPRQVEILARKVLNKPVEIQVGGRSVVNKDITQL-VEVRPES 698
           RI + +  + Q +LFSATF   V   A+KV+  P  I++         I Q  V      
Sbjct: 208 RIQRMLPRNCQMLLFSATFEDSVWKFAQKVVPDPNVIKLKREEETLDTIKQYYVLCSSRD 267
Query: 699 DRFLRLLELLGEWYEKGKILIFVHSQEKCDALFRDLLKHGYPCLSLHGAKDQTDRESTIS 758
           ++F  L  L G      + +IF H+++    L  +L K G+    L G      R + I 
Sbjct: 268 EKFQALCNLYGA-ITIAQAMIFCHTRKTASWLAAELSKEGHQVALLSGEMMVEQRAAVIE 326
Query: 759 DFKSNVCNLLIATSVAARGLDVKELELVINFDAP------NHYEDYVHRVGRTGRAGRKG 812
            F+     +L+ T+V ARG+DV+++ +VINFD P         E Y+HR+GRTGR G++G
Sbjct: 327 RFREGKEKVLVTTNVCARGIDVEQVSVVINFDLPVDKDGNPDNETYLHRIGRTGRFGKRG 386
Query: 813 CAITFISEEDAKYSPDLVKALE 834
            A+  +   D+K+S +++  ++
Sbjct: 387 LAVNMV---DSKHSMNILNRIQ 405

>pdb|3FHT|A Chain A, Crystal Structure Of Human Dbp5 In Complex With Amppnp And Rna Length = 412

Iteration: 1
 Score =  149 bits (376), Expect = 8e-36,   Method: Compositional matrix adjust.
 Identities = 113/382 (29%), Positives = 195/382 (51%), Gaps = 29/382 (7%)
Query: 466 IKTWHQTGLTSKIMETIRKLNYEKPMPIQAQALPVIMSG--RDCIGVAKTGSGKTLAFVL 523
           +K++ +  L  ++++ +  + + +P  IQ  ALP++++   ++ I  +++G+GKT AFVL
Sbjct: 24  VKSFEELRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVL 83
Query: 524 PMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVM-GVRCVPVYGGSGV-- 580
            ML  ++      A   P  L ++PT EL  Q    I +  K    ++      G+ +  
Sbjct: 84  AMLSQVE-----PANKYPQCLCLSPTYELALQTGKVIEQMGKFYPELKLAYAVRGNKLER 138
Query: 581 AQQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMF-DMGFEPQIT 639
            Q+ISE     +IV+ TPG ++D    S  K  + +++   V+DEAD M    G + Q  
Sbjct: 139 GQKISE-----QIVIGTPGTVLD--WCSKLKFIDPKKIKVFVLDEADVMIATQGHQDQSI 191
Query: 640 RIVQNIRPDRQTVLFSATFPRQVEILARKVLNKPVEIQVGGRSVVNKDITQL-VEVRPES 698
           RI + +  + Q +LFSATF   V   A+KV+  P  I++         I Q  V      
Sbjct: 192 RIQRMLPRNCQMLLFSATFEDSVWKFAQKVVPDPNVIKLKREEETLDTIKQYYVLCSSRD 251
Query: 699 DRFLRLLELLGEWYEKGKILIFVHSQEKCDALFRDLLKHGYPCLSLHGAKDQTDRESTIS 758
           ++F  L  L G      + +IF H+++    L  +L K G+    L G      R + I 
Sbjct: 252 EKFQALCNLYGA-ITIAQAMIFCHTRKTASWLAAELSKEGHQVALLSGEMMVEQRAAVIE 310
Query: 759 DFKSNVCNLLIATSVAARGLDVKELELVINFDAP------NHYEDYVHRVGRTGRAGRKG 812
            F+     +L+ T+V ARG+DV+++ +VINFD P         E Y+HR+GRTGR G++G
Sbjct: 311 RFREGKEKVLVTTNVCARGIDVEQVSVVINFDLPVDKDGNPDNETYLHRIGRTGRFGKRG 370
Query: 813 CAITFISEEDAKYSPDLVKALE 834
            A+  +   D+K+S +++  ++
Sbjct: 371 LAVNMV---DSKHSMNILNRIQ 389

>pdb|3DKP|A Chain A, Human Dead-Box Rna-Helicase Ddx52, Conserved Domain I In Complex With Adp Length = 245

Iteration: 1
 Score =  131 bits (329), Expect = 2e-30,   Method: Compositional matrix adjust.
 Identities = 81/247 (32%), Positives = 139/247 (56%), Gaps = 14/247 (5%)
Query: 445 EVSAYRKQLELKIHGKDVPKPIKTWHQTG----LTSKIMETIRKLNYEKPMPIQAQALPV 500
           +++  R + ++ + G D+P PI T+ Q      + S++++ I    ++ P PIQ QA+PV
Sbjct: 3   KINFLRNKHKIHVQGTDLPDPIATFQQLDQEYKINSRLLQNILDAGFQMPTPIQMQAIPV 62
Query: 501 IMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDI 560
           ++ GR+ +  A TGSGKTLAF +P+L  +K QP   A  G   LI++PTREL  QIH ++
Sbjct: 63  MLHGRELLASAPTGSGKTLAFSIPILMQLK-QP---ANKGFRALIISPTRELASQIHREL 118
Query: 561 RKFAKVMGVRCVPVYGGSGVAQQIS-ELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVT 619
            K ++  G R   ++  +  A++   +  +  +I+V TP R+I +L      I +L  V 
Sbjct: 119 IKISEGTGFRIHMIHKAAVAAKKFGPKSSKKFDILVTTPNRLIYLLKQDPPGI-DLASVE 177
Query: 620 YLVMDEADRMFD---MGFEPQITRIVQNIRPDR-QTVLFSATFPRQVEILARKVLNKPVE 675
           +LV+DE+D++F+    GF  Q+  I       + +  +FSATF   VE   +  L+  + 
Sbjct: 178 WLVVDESDKLFEDGKTGFRDQLASIFLACTSHKVRRAMFSATFAYDVEQWCKLNLDNVIS 237
Query: 676 IQVGGRS 682
           + +G R+
Sbjct: 238 VSIGARN 244

>pdb|2JGN|A Chain A, Ddx3 Helicase Domain Length = 185

Iteration: 1
 Score =  127 bits (318), Expect = 4e-29,   Method: Compositional matrix adjust.
 Identities = 70/165 (42%), Positives = 103/165 (62%), Gaps = 2/165 (1%)
Query: 685 NKDITQLVEVRPESDRFLRLLELLGEWYEKGKILIFVHSQEKCDALFRDLLKH-GYPCLS 743
           +++ITQ V    ESD+   LL+LL    +    L+FV +++  D+L  D L H GY C S
Sbjct: 17  SENITQKVVWVEESDKRSFLLDLLNATGKDSLTLVFVETKKGADSL-EDFLYHEGYACTS 75
Query: 744 LHGAKDQTDRESTISDFKSNVCNLLIATSVAARGLDVKELELVINFDAPNHYEDYVHRVG 803
           +HG + Q DRE  +  F+S    +L+AT+VAARGLD+  ++ VINFD P+  E+YVHR+G
Sbjct: 76  IHGDRSQRDREEALHQFRSGKSPILVATAVAARGLDISNVKHVINFDLPSDIEEYVHRIG 135
Query: 804 RTGRAGRKGCAITFISEEDAKYSPDLVKALELSEQVVPDDLKALA 848
           RTGR G  G A +F +E +   + DL+  L  ++Q VP  L+ +A
Sbjct: 136 RTGRVGNLGLATSFFNERNINITKDLLDLLVEAKQEVPSWLENMA 180

>pdb|2PL3|A Chain A, Human Dead-Box Rna Helicase Ddx10, Dead Domain In Complex With Adp Length = 236

Iteration: 1
 Score =  121 bits (303), Expect = 2e-27,   Method: Compositional matrix adjust.
 Identities = 75/206 (36%), Positives = 116/206 (56%), Gaps = 6/206 (2%)
Query: 474 LTSKIMETIRKLNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQP 533
           L+ K ++ +++  Y     IQ Q + + + G+D +G AKTGSGKTLAF++P+L  +  + 
Sbjct: 32  LSKKTLKGLQEAQYRLVTEIQKQTIGLALQGKDVLGAAKTGSGKTLAFLVPVLEALY-RL 90
Query: 534 PVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQISELKRGTEI 593
              + DG   LI++PTREL  Q    +RK  K        + GG  +  + +E      I
Sbjct: 91  QWTSTDGLGVLIISPTRELAYQTFEVLRKVGKNHDFSAGLIIGGKDLKHE-AERINNINI 149
Query: 594 VVCTPGRMIDILC-TSGGKITNLRRVTYLVMDEADRMFDMGFEPQITRIVQNIRPDRQTV 652
           +VCTPGR++  +  T     T+L+    LV+DEADR+ DMGF   +  +++N+   RQT+
Sbjct: 150 LVCTPGRLLQHMDETVSFHATDLQ---MLVLDEADRILDMGFADTMNAVIENLPKKRQTL 206
Query: 653 LFSATFPRQVEILARKVLNKPVEIQV 678
           LFSAT  + V+ LAR  L  P  + V
Sbjct: 207 LFSATQTKSVKDLARLSLKNPEYVWV 232

>pdb|3LY5|A Chain A, Ddx18 Dead-Domain Length = 262

Iteration: 1
 Score =  115 bits (288), Expect = 1e-25,   Method: Compositional matrix adjust.
 Identities = 69/197 (35%), Positives = 115/197 (58%), Gaps = 9/197 (4%)
Query: 479 METIRKLNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLP---MLRHIKDQPPV 535
           ++ I+++ +     IQ +++  ++ GRD +  AKTGSGKTLAF++P   ++  ++  P  
Sbjct: 66  LKAIKEMGFTNMTEIQHKSIRPLLEGRDLLAAAKTGSGKTLAFLIPAVELIVKLRFMPRN 125
Query: 536 AAGDGPVGLIMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQISELKRGTEIVV 595
             G     LI++PTREL  Q    +++           + GGS  + +  +L  G  I+V
Sbjct: 126 GTGV----LILSPTRELAMQTFGVLKELMTHHVHTYGLIMGGSNRSAEAQKLGNGINIIV 181
Query: 596 CTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMGFEPQITRIVQNIRPDRQTVLFS 655
            TPGR++D +  + G +   + +  LV+DEADR+ D+GFE ++ +I++ +   RQT+LFS
Sbjct: 182 ATPGRLLDHMQNTPGFM--YKNLQCLVIDEADRILDVGFEEELKQIIKLLPTRRQTMLFS 239
Query: 656 ATFPRQVEILARKVLNK 672
           AT  R+VE LAR  L K
Sbjct: 240 ATQTRKVEDLARISLKK 256

>pdb|1VEC|A Chain A, Crystal Structure Of The N-Terminal Domain Of RckP54, A Human Dead-Box Protein Length = 206

Iteration: 1
 Score =  114 bits (285), Expect = 3e-25,   Method: Compositional matrix adjust.
 Identities = 64/204 (31%), Positives = 112/204 (54%), Gaps = 9/204 (4%)
Query: 474 LTSKIMETIRKLNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQP 533
           L  +++  I ++ +EKP PIQ +++P+ +SGRD +  AK G+GK+ A+++P+L  +    
Sbjct: 10  LKRELLMGIFEMGWEKPSPIQEESIPIALSGRDILARAKNGTGKSGAYLIPLLERLD--- 66
Query: 534 PVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVM-GVRCVPVYGGSGVAQQISELKRGTE 592
                D    +++ PTREL  Q+     + +K M G + +   GG+ +   I  L     
Sbjct: 67  --LKKDNIQAMVIVPTRELALQVSQICIQVSKHMGGAKVMATTGGTNLRDDIMRLDDTVH 124
Query: 593 IVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMGFEPQITRIVQNIRPDRQTV 652
           +V+ TPGR++D++     K+ +   V  +V+DEAD++    F   +  I+  +  +RQ +
Sbjct: 125 VVIATPGRILDLIKKGVAKVDH---VQMIVLDEADKLLSQDFVQIMEDIILTLPKNRQIL 181
Query: 653 LFSATFPRQVEILARKVLNKPVEI 676
           L+SATFP  V+      L KP EI
Sbjct: 182 LYSATFPLSVQKFMNSHLEKPYEI 205

>pdb|3BOR|A Chain A, Crystal Structure Of The Deadc Domain Of Human Translation Initiation Factor 4a-2 Length = 237

Iteration: 1
 Score =  112 bits (279), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 69/206 (33%), Positives = 104/206 (50%), Gaps = 9/206 (4%)
Query: 474 LTSKIMETIRKLNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQP 533
           L   ++  I    +EKP  IQ +A+   + G D I  A++G+GKT  F + +L+ ++ + 
Sbjct: 37  LKESLLRGIYAYGFEKPSAIQQRAIIPCIKGYDVIAQAQSGTGKTATFAISILQQLEIEF 96
Query: 534 PVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQISELK-RGTE 592
                     L++APTREL QQI   I      MG  C    GG+ V  ++ +L+     
Sbjct: 97  KETQA-----LVLAPTRELAQQIQKVILALGDYMGATCHACIGGTNVRNEMQKLQAEAPH 151
Query: 593 IVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMGFEPQITRIVQNIRPDRQTV 652
           IVV TPGR+ D+L     +  + + +   V+DEAD M   GF+ QI  I Q +    Q V
Sbjct: 152 IVVGTPGRVFDML---NRRYLSPKWIKMFVLDEADEMLSRGFKDQIYEIFQKLNTSIQVV 208
Query: 653 LFSATFPRQVEILARKVLNKPVEIQV 678
           L SAT P  V  + +K +  P+ I V
Sbjct: 209 LLSATMPTDVLEVTKKFMRDPIRILV 234

>pdb|2G9N|A Chain A, Structure Of The Dead Domain Of Human Eukaryotic Initiation Factor 4a, Eif4a Length = 221

Iteration: 1
 Score =  107 bits (267), Expect = 3e-23,   Method: Composition-based stats.
 Identities = 67/215 (31%), Positives = 103/215 (47%), Gaps = 11/215 (5%)
Query: 466 IKTWHQTGLTSKIMETIRKLNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPM 525
           + ++    L+  ++  I    +E P  IQ +A+   + G D I  A++G+G T  F + +
Sbjct: 14  VDSFDDMNLSESLLRGIYAYGFEXPSAIQQRAILPCIXGYDVIAQAQSGTGXTATFAISI 73
Query: 526 LRHIK-DQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQI 584
           L+ I+ D     A      L++APTREL QQI   +      MG  C    GG+ V  ++
Sbjct: 74  LQQIELDLXATQA------LVLAPTRELAQQIQXVVMALGDYMGASCHACIGGTNVRAEV 127
Query: 585 SELK-RGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMGFEPQITRIVQ 643
             L+     I+V TPGR+ D+L     +  +   +   V+DEAD M   GF  QI  I Q
Sbjct: 128 QXLQMEAPHIIVGTPGRVFDML---NRRYLSPXYIXMFVLDEADEMLSRGFXDQIYDIFQ 184
Query: 644 NIRPDRQTVLFSATFPRQVEILARKVLNKPVEIQV 678
            +  + Q VL SAT P  V  +    +  P+ I V
Sbjct: 185 XLNSNTQVVLLSATMPSDVLEVTXXFMRDPIRILV 219

>pdb|2HJV|A Chain A, Structure Of The Second Domain (Residues 207-368) Of The Bacillus Subtilis Yxin Protein Length = 163

Iteration: 1
 Score =  103 bits (256), Expect = 6e-22,   Method: Compositional matrix adjust.
 Identities = 49/112 (43%), Positives = 71/112 (63%)
Query: 718 LIFVHSQEKCDALFRDLLKHGYPCLSLHGAKDQTDRESTISDFKSNVCNLLIATSVAARG 777
           +IF  ++E  + L  +L   GYPC  +HG   Q DR   +++FK      L+AT VAARG
Sbjct: 39  IIFCRTKEHVNQLTDELDDLGYPCDKIHGGMIQEDRFDVMNEFKRGEYRYLVATDVAARG 98
Query: 778 LDVKELELVINFDAPNHYEDYVHRVGRTGRAGRKGCAITFISEEDAKYSPDL 829
           +D++ + LVIN+D P   E YVHR GRTGRAG KG AI+F++  + ++  D+
Sbjct: 99  IDIENISLVINYDLPLEKESYVHRTGRTGRAGNKGKAISFVTAFEKRFLADI 150

>pdb|2P6N|A Chain A, Human Dead-box Rna Helicase Ddx41, Helicase Domain Length = 191

Iteration: 1
 Score =  102 bits (253), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 62/162 (38%), Positives = 90/162 (55%), Gaps = 3/162 (1%)
Query: 687 DITQLVEVRPESDRFLRLLELLGEWYEKGKILIFVHSQEKCDALFRDLLKHGYPCLSLHG 746
           D+ Q VE   E  + + LLE L +      +LIF   +   DA+   LL  G   +++HG
Sbjct: 29  DVIQEVEYVKEEAKMVYLLECLQKT--PPPVLIFAEKKADVDAIHEYLLLKGVEAVAIHG 86
Query: 747 AKDQTDRESTISDFKSNVCNLLIATSVAARGLDVKELELVINFDAPNHYEDYVHRVGRTG 806
            KDQ +R   I  F+    ++L+AT VA++GLD   ++ VIN+D P   E+YVHR+GRTG
Sbjct: 87  GKDQEERTKAIEAFREGKKDVLVATDVASKGLDFPAIQHVINYDMPEEIENYVHRIGRTG 146
Query: 807 RAGRKGCAITFISEE-DAKYSPDLVKALELSEQVVPDDLKAL 847
            +G  G A TFI++  D     DL   L  ++Q VP  L+ L
Sbjct: 147 CSGNTGIATTFINKACDESVLMDLKALLLEAKQKVPPVLQVL 188

>pdb|1T6N|A Chain A, Crystal Structure Of The N-Terminal Domain Of Human Uap56 Length = 220

Iteration: 1
 Score = 99.8 bits (247), Expect = 8e-21,   Method: Compositional matrix adjust.
 Identities = 71/229 (31%), Positives = 116/229 (50%), Gaps = 18/229 (7%)
Query: 459 GKDVPKPIKTWHQTG-----LTSKIMETIRKLNYEKPMPIQAQALPVIMSGRDCIGVAKT 513
           G DV     + H +G     L  +++  I    +E P  +Q + +P  + G D +  AK+
Sbjct: 1   GSDVKGSYVSIHSSGFRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKS 60
Query: 514 GSGKTLAFVLPMLRHIKDQPPVAAGDGPVG-LIMAPTRELVQQIHSDIRKFAKVM-GVRC 571
           G GKT  FVL  L+ ++   PV    G V  L+M  TREL  QI  +  +F+K M  V+ 
Sbjct: 61  GMGKTAVFVLATLQQLE---PVT---GQVSVLVMCHTRELAFQISKEYERFSKYMPNVKV 114
Query: 572 VPVYGGSGVAQQISELKRGT-EIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMF 630
              +GG  + +    LK+    IVV TPGR   IL  +  K  NL+ + + ++DE D+M 
Sbjct: 115 AVFFGGLSIKKDEEVLKKNCPHIVVGTPGR---ILALARNKSLNLKHIKHFILDECDKML 171
Query: 631 D-MGFEPQITRIVQNIRPDRQTVLFSATFPRQVEILARKVLNKPVEIQV 678
           + +     +  I +    ++Q ++FSAT  +++  + RK +  P+EI V
Sbjct: 172 EQLDMRRDVQEIFRMTPHEKQVMMFSATLSKEIRPVCRKFMQDPMEIFV 220

>pdb|1T5I|A Chain A, Crystal Structure Of The C-Terminal Domain Of Uap56 Length = 172

Iteration: 1
 Score = 99.0 bits (245), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 51/143 (35%), Positives = 87/143 (60%), Gaps = 2/143 (1%)
Query: 703 RLLELLGEWYEKGKILIFVHSQEKCDALFRDLLKHGYPCLSLHGAKDQTDRESTISDFKS 762
           +L +LL +  E  +++IFV S ++C AL + L++  +P +++H    Q +R S    FK 
Sbjct: 21  KLFDLL-DVLEFNQVVIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQEERLSRYQQFKD 79
Query: 763 NVCNLLIATSVAARGLDVKELELVINFDAPNHYEDYVHRVGRTGRAGRKGCAITFISEE- 821
               +L+AT++  RG+D++ + +  N+D P   + Y+HRV R GR G KG AITF+S+E 
Sbjct: 80  FQRRILVATNLFGRGMDIERVNIAFNYDMPEDSDTYLHRVARAGRFGTKGLAITFVSDEN 139
Query: 822 DAKYSPDLVKALELSEQVVPDDL 844
           DAK   D+    E++   +PD++
Sbjct: 140 DAKILNDVQDRFEVNISELPDEI 162

>pdb|1QDE|A Chain A, Crystal Structure Of The Atpase Domain Of Translation Initiation Factor 4a From Saccharomyces Cerevisiae-The Prototype Of The Dead Box Protein Family Length = 224

Iteration: 1
 Score = 99.0 bits (245), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 68/222 (30%), Positives = 105/222 (47%), Gaps = 23/222 (10%)
Query: 464 KPIKTWHQTGLTSKIMETIRKLNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVL 523
           K +  +    L   ++  +    +E+P  IQ +A+  I+ G D +  A++G+GKT  F +
Sbjct: 11  KVVYKFDDMELDENLLRGVFGYGFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFSI 70
Query: 524 PMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQ 583
             L+ I       +   P  L++APTREL  QI   +   A  M ++     GG+   + 
Sbjct: 71  AALQRID-----TSVKAPQALMLAPTRELALQIQKVVMALAFHMDIKVHACIGGTSFVED 125
Query: 584 ISELKRGTEIVVCTPGRMIDILCTSGGKITNLRR-------VTYLVMDEADRMFDMGFEP 636
            +E  R  +IVV TPGR+ D          N++R       +   ++DEAD M   GF+ 
Sbjct: 126 -AEGLRDAQIVVGTPGRVFD----------NIQRRRFRTDKIKMFILDEADEMLSSGFKE 174
Query: 637 QITRIVQNIRPDRQTVLFSATFPRQVEILARKVLNKPVEIQV 678
           QI +I   + P  Q VL SAT P  V  +  K +  PV I V
Sbjct: 175 QIYQIFTLLPPTTQVVLLSATMPNDVLEVTTKFMRNPVRILV 216

>pdb|1QVA|A Chain A, Yeast Initiation Factor 4a N-Terminal Domain Length = 223

Iteration: 1
 Score = 99.0 bits (245), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 68/222 (30%), Positives = 106/222 (47%), Gaps = 23/222 (10%)
Query: 464 KPIKTWHQTGLTSKIMETIRKLNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVL 523
           K +  +    L  +++  +    +E+P  IQ +A+  I+ G D +  A++G+GKT  F +
Sbjct: 18  KVVYKFDDMELDEQLLRGVFGYGFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFSI 77
Query: 524 PMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQ 583
             L+ I       +   P  L++APTREL  QI   +   A  M ++     GG+   + 
Sbjct: 78  AALQRID-----TSVKAPQALMLAPTRELALQIQKVVMALAFHMDIKVHACIGGTSFVED 132
Query: 584 ISELKRGTEIVVCTPGRMIDILCTSGGKITNLRR-------VTYLVMDEADRMFDMGFEP 636
            +E  R  +IVV TPGR+ D          N++R       +   ++DEAD M   GF+ 
Sbjct: 133 -AEGLRDAQIVVGTPGRVFD----------NIQRRRFRTDKIKMFILDEADEMLSSGFKE 181
Query: 637 QITRIVQNIRPDRQTVLFSATFPRQVEILARKVLNKPVEIQV 678
           QI +I   + P  Q VL SAT P  V  +  K +  PV I V
Sbjct: 182 QIYQIFTLLPPTTQVVLLSATMPNDVLEVTTKFMRNPVRILV 223

>pdb|1Q0U|A Chain A, Crystal Structure Of The Bstdead N-Terminal Domain Length = 219

Iteration: 1
 Score = 96.7 bits (239), Expect = 6e-20,   Method: Composition-based stats.
 Identities = 66/208 (31%), Positives = 105/208 (50%), Gaps = 18/208 (8%)
Query: 478 IMETIRKLNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIK-DQPPVA 536
           I+E I+ L + KP  IQ + +P  + G   +G ++TG+GKT A++LP+   IK ++  V 
Sbjct: 15  IIEAIKTLRFYKPTEIQERIIPGALRGESXVGQSQTGTGKTHAYLLPIXEKIKPERAEVQ 74
Query: 537 AGDGPVGLIMAPTRELVQQIHSDIRKFAK------VMGVRCVPVYGGSGVAQQISELKRG 590
           A      +I APTREL  QI+ +  K  K       +  RC  + GG+   + + +L   
Sbjct: 75  A------VITAPTRELATQIYHETLKITKFCPKDRXIVARC--LIGGTDKQKALEKLNVQ 126
Query: 591 TEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMGFEPQITRIVQNIRPDRQ 650
             IV+ TPGR+ D +        ++     LV+DEAD   D GF   + +I      D Q
Sbjct: 127 PHIVIGTPGRINDFIREQA---LDVHTAHILVVDEADLXLDXGFITDVDQIAARXPKDLQ 183
Query: 651 TVLFSATFPRQVEILARKVLNKPVEIQV 678
            ++FSAT P +++   +K    P  + V
Sbjct: 184 XLVFSATIPEKLKPFLKKYXENPTFVHV 211

>pdb|2KBE|A Chain A, Solution Structure Of Amino-Terminal Domain Of Dbp5p Length = 226

Iteration: 1
 Score = 95.9 bits (237), Expect = 9e-20,   Method: Compositional matrix adjust.
 Identities = 65/210 (30%), Positives = 114/210 (54%), Gaps = 21/210 (10%)
Query: 467 KTWHQTGLTSKIMETIRKLNYEKPMPIQAQALPVIMSG--RDCIGVAKTGSGKTLAFVLP 524
           K++ + GL  ++++ I  + ++KP  IQ +ALP+++    R+ I  +++G+GKT AF L 
Sbjct: 22  KSFDELGLAPELLKGIYAMKFQKPSKIQERALPLLLHNPPRNMIAQSQSGTGKTAAFSLT 81
Query: 525 MLRHIKDQPPVAAGDGPVGLIMAPTRELVQQ---IHSDIRKFAKVMGVRCVPVYGGSGVA 581
           ML  +  +        P  + +AP+REL +Q   +  ++ KF K+     VP        
Sbjct: 82  MLTRVNPE-----DASPQAICLAPSRELARQTLEVVQEMGKFTKITSQLIVP--DSFEKN 134
Query: 582 QQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFD-MGFEPQITR 640
           +QI+      +++V TPG ++D++     K+  L+++   V+DEAD M D  G   Q  R
Sbjct: 135 KQIN-----AQVIVGTPGTVLDLM---RRKLMQLQKIKIFVLDEADNMLDQQGLGDQCIR 186
Query: 641 IVQNIRPDRQTVLFSATFPRQVEILARKVL 670
           + + +  D Q VLFSATF   V   A+K++
Sbjct: 187 VKRFLPKDTQLVLFSATFADAVRQYAKKIV 216

>pdb|2KBF|A Chain A, Solution Structure Of Carboxyl-Terminal Domain Of Dbp5p Length = 187

Iteration: 1
 Score = 93.6 bits (231), Expect = 4e-19,   Method: Compositional matrix adjust.
 Identities = 56/148 (37%), Positives = 87/148 (58%), Gaps = 9/148 (6%)
Query: 684 VNKD-ITQL-VEVRPESDRFLRLLELLGEWYEKGKILIFVHSQEKCDALFRDLLKHGYPC 741
           VN D I QL ++ + E+D+F  L EL G     G  +IFV +++  + L+  L   G+  
Sbjct: 4   VNVDAIKQLYMDCKNEADKFDVLTELYG-LMTIGSSIIFVATKKTANVLYGKLKSEGHEV 62
Query: 742 LSLHGAKDQTDRESTISDFKSNVCNLLIATSVAARGLDVKELELVINFDAP---NHYED- 797
             LHG     +R+  I DF+     +LI T+V ARG+D+  + +V+N+D P   N   D 
Sbjct: 63  SILHGDLQTQERDRLIDDFREGRSKVLITTNVLARGIDIPTVSMVVNYDLPTLANGQADP 122
Query: 798 --YVHRVGRTGRAGRKGCAITFISEEDA 823
             Y+HR+GRTGR GRKG AI+F+ ++++
Sbjct: 123 ATYIHRIGRTGRFGRKGVAISFVHDKNS 150

>pdb|3GFP|A Chain A, Structure Of The C-Terminal Domain Of The Dead-Box Protein Dbp5 Length = 189

Iteration: 1
 Score = 92.0 bits (227), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 57/153 (37%), Positives = 87/153 (56%), Gaps = 9/153 (5%)
Query: 679 GGRSVVNKD-ITQLV-EVRPESDRFLRLLELLGEWYEKGKILIFVHSQEKCDALFRDLLK 736
           G  + VN D I QL  + + E+D+F  L EL G     G  +IFV +++  + L+  L  
Sbjct: 1   GATNEVNVDAIKQLYXDCKNEADKFDVLTELYG-LXTIGSSIIFVATKKTANVLYGKLKS 59
Query: 737 HGYPCLSLHGAKDQTDRESTISDFKSNVCNLLIATSVAARGLDVKELELVINFDAP---N 793
            G+    LHG     +R+  I DF+     +LI T+V ARG+D+  +  V+N+D P   N
Sbjct: 60  EGHEVSILHGDLQTQERDRLIDDFREGRSKVLITTNVLARGIDIPTVSXVVNYDLPTLAN 119
Query: 794 HYED---YVHRVGRTGRAGRKGCAITFISEEDA 823
              D   Y+HR+GRTGR GRKG AI+F+ ++++
Sbjct: 120 GQADPATYIHRIGRTGRFGRKGVAISFVHDKNS 152

>pdb|3PEU|A Chain A, S. Cerevisiae Dbp5 L327v C-Terminal Domain Bound To Gle1 H337r And Ip6 Length = 188

Iteration: 1
 Score = 91.7 bits (226), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 57/152 (37%), Positives = 87/152 (57%), Gaps = 9/152 (5%)
Query: 680 GRSVVNKD-ITQLV-EVRPESDRFLRLLELLGEWYEKGKILIFVHSQEKCDALFRDLLKH 737
           G + VN D I QL  + + E+D+F  L EL G     G  +IFV +++  + L+  L   
Sbjct: 1   GANEVNVDAIKQLYXDCKNEADKFDVLTELYG-VXTIGSSIIFVATKKTANVLYGKLKSE 59
Query: 738 GYPCLSLHGAKDQTDRESTISDFKSNVCNLLIATSVAARGLDVKELELVINFDAP---NH 794
           G+    LHG     +R+  I DF+     +LI T+V ARG+D+  +  V+N+D P   N 
Sbjct: 60  GHEVSILHGDLQTQERDRLIDDFREGRSKVLITTNVLARGIDIPTVSXVVNYDLPTLANG 119
Query: 795 YED---YVHRVGRTGRAGRKGCAITFISEEDA 823
             D   Y+HR+GRTGR GRKG AI+F+ ++++
Sbjct: 120 QADPATYIHRIGRTGRFGRKGVAISFVHDKNS 151

>pdb|2WAX|A Chain A, Structure Of The Human Ddx6 C-Terminal Domain In Complex With An Edc3-Fdf Peptide Length = 193

Iteration: 1
 Score = 90.1 bits (222), Expect = 6e-18,   Method: Compositional matrix adjust.
 Identities = 44/137 (32%), Positives = 73/137 (53%), Gaps = 1/137 (0%)
Query: 686 KDITQLVEVRPESDRFLRLLELLGEWYEKGKILIFVHSQEKCDALFRDLLKHGYPCLSLH 745
           K +TQ      E  + +  L  L    +  + +IF +S ++ + L + + + GY C  +H
Sbjct: 17  KGVTQYYAYVTERQK-VHCLNTLFSRLQINQSIIFCNSSQRVELLAKKISQLGYSCFYIH 75
Query: 746 GAKDQTDRESTISDFKSNVCNLLIATSVAARGLDVKELELVINFDAPNHYEDYVHRVGRT 805
               Q  R     DF++ +C  L+ T +  RG+D++ + +VINFD P   E Y+HR+GR+
Sbjct: 76  AKMRQEHRNRVFHDFRNGLCRNLVCTDLFTRGIDIQAVNVVINFDFPKLAETYLHRIGRS 135
Query: 806 GRAGRKGCAITFISEED 822
           GR G  G AI  I+ +D
Sbjct: 136 GRFGHLGLAINLITYDD 152

>pdb|2OXC|A Chain A, Human Dead-Box Rna Helicase Ddx20, Dead Domain In Complex With Adp Length = 230

Iteration: 1
 Score = 88.2 bits (217), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 63/207 (30%), Positives = 106/207 (51%), Gaps = 11/207 (5%)
Query: 474 LTSKIMETIRKLNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQP 533
           L+  ++E +R   +E+P P+Q +A+P+   G D I  AK+G+GKT  F    L  +    
Sbjct: 31  LSRPVLEGLRAAGFERPSPVQLKAIPLGRCGLDLIVQAKSGTGKTCVFSTIALDSL---- 86
Query: 534 PVAAGDGPVGLIMAPTRELVQQIHSDIRKFA-KVMGVRCVPVYGGSGVAQQISELKRGTE 592
            V        LI+APTRE+  QIHS I     K+ G+ C    GG+ ++Q  + LK+   
Sbjct: 87  -VLENLSTQILILAPTREIAVQIHSVITAIGIKMEGLECHVFIGGTPLSQDKTRLKK-CH 144
Query: 593 IVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMG-FEPQITRIVQNIRPDRQT 651
           I V +PGR+  ++        N   +   ++DEAD++ + G F+ QI  I  ++   +Q 
Sbjct: 145 IAVGSPGRIKQLIELD---YLNPGSIRLFILDEADKLLEEGSFQEQINWIYSSLPASKQM 201
Query: 652 VLFSATFPRQVEILARKVLNKPVEIQV 678
           +  SAT+P  +     K +  P  +++
Sbjct: 202 LAVSATYPEFLANALTKYMRDPTFVRL 228

>pdb|3FMO|B Chain B, Crystal Structure Of The Nucleoporin Nup214 In Complex With The Dead- Box Helicase Ddx19 Length = 300

Iteration: 1
 Score = 84.3 bits (207), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 65/219 (29%), Positives = 115/219 (52%), Gaps = 18/219 (8%)
Query: 466 IKTWHQTGLTSKIMETIRKLNYEKPMPIQAQALPVIMS--GRDCIGVAKTGSGKTLAFVL 523
           +K++ +  L  ++++ +  + + +P  IQ  ALP++++   ++ I  +++G+GKT AFVL
Sbjct: 91  VKSFEELRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVL 150
Query: 524 PMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVMG-VRCVPVYGGSGV-- 580
            ML  ++      A   P  L ++PT EL  Q    I +  K    ++      G+ +  
Sbjct: 151 AMLSQVE-----PANKYPQCLCLSPTYELALQTGKVIEQMGKFYPELKLAYAVRGNKLER 205
Query: 581 AQQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMF-DMGFEPQIT 639
            Q+ISE     +IV+ TPG ++D    S  K  + +++   V+DEAD M    G + Q  
Sbjct: 206 GQKISE-----QIVIGTPGTVLD--WCSKLKFIDPKKIKVFVLDEADVMIATQGHQDQSI 258
Query: 640 RIVQNIRPDRQTVLFSATFPRQVEILARKVLNKPVEIQV 678
           RI + +  + Q +LFSATF   V   A+KV+  P  I++
Sbjct: 259 RIQRMLPRNCQMLLFSATFEDSVWKFAQKVVPDPNVIKL 297

>pdb|3FHC|B Chain B, Crystal Structure Of Human Dbp5 In Complex With Nup214 Length = 235

Iteration: 1
 Score = 83.2 bits (204), Expect = 7e-16,   Method: Compositional matrix adjust.
 Identities = 65/219 (29%), Positives = 115/219 (52%), Gaps = 18/219 (8%)
Query: 466 IKTWHQTGLTSKIMETIRKLNYEKPMPIQAQALPVIMS--GRDCIGVAKTGSGKTLAFVL 523
           +K++ +  L  ++++ +  + + +P  IQ  ALP++++   ++ I  +++G+GKT AFVL
Sbjct: 24  VKSFEELRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVL 83
Query: 524 PMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVMG-VRCVPVYGGSGV-- 580
            ML  ++      A   P  L ++PT EL  Q    I +  K    ++      G+ +  
Sbjct: 84  AMLSQVE-----PANKYPQCLCLSPTYELALQTGKVIEQMGKFYPELKLAYAVRGNKLER 138
Query: 581 AQQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMF-DMGFEPQIT 639
            Q+ISE     +IV+ TPG ++D    S  K  + +++   V+DEAD M    G + Q  
Sbjct: 139 GQKISE-----QIVIGTPGTVLD--WCSKLKFIDPKKIKVFVLDEADVMIATQGHQDQSI 191
Query: 640 RIVQNIRPDRQTVLFSATFPRQVEILARKVLNKPVEIQV 678
           RI + +  + Q +LFSATF   V   A+KV+  P  I++
Sbjct: 192 RIQRMLPRNCQMLLFSATFEDSVWKFAQKVVPDPNVIKL 230

>pdb|2YJT|D Chain D, Crystal Structure Of E. Coli Dead-Box Protein Srmb Bound To Regulator Of Ribonuclease Activity A (Rraa) Length = 170

Iteration: 1
 Score = 81.6 bits (200), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 42/110 (38%), Positives = 59/110 (53%)
Query: 713 EKGKILIFVHSQEKCDALFRDLLKHGYPCLSLHGAKDQTDRESTISDFKSNVCNLLIATS 772
           E  + ++FV  +E+   L   L + G     L G   Q  R   I        N+L+AT 
Sbjct: 29  EATRSIVFVRKRERVHELANWLREAGINNCYLEGEMVQGKRNEAIKRLTEGRVNVLVATD 88
Query: 773 VAARGLDVKELELVINFDAPNHYEDYVHRVGRTGRAGRKGCAITFISEED 822
           VAARG+D+ ++  V NFD P   + Y+HR+GRT RAGRKG AI+ +   D
Sbjct: 89  VAARGIDIPDVSHVFNFDMPRSGDTYLHRIGRTARAGRKGTAISLVEAHD 138

>pdb|2RB4|A Chain A, Crystal Structure Of The Helicase Domain Of Human Ddx25 Rna Helicase Length = 175

Iteration: 1
 Score = 78.6 bits (192), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 47/139 (33%), Positives = 73/139 (52%), Gaps = 10/139 (7%)
Query: 699 DRFLRLLELLGEWYEKGKILIFVHSQEKCDALFRDLLKHGYPCLSLHGAKDQTDRESTIS 758
           D++  L  + G     G+ +IF  ++     L  ++++ G+    L G      R S I 
Sbjct: 20  DKYQALCNIYGS-ITIGQAIIFCQTRRNAKWLTVEMIQDGHQVSLLSGELTVEQRASIIQ 78
Query: 759 DFKSNVCNLLIATSVAARGLDVKELELVINFDAPNH------YEDYVHRVGRTGRAGRKG 812
            F+     +LI T+V ARG+DVK++ +V+NFD P        YE Y+HR+GRTGR G+KG
Sbjct: 79  RFRDGKEKVLITTNVCARGIDVKQVTIVVNFDLPVKQGEEPDYETYLHRIGRTGRFGKKG 138
Query: 813 CAITFISEEDAKYSPDLVK 831
            A   I  ++    P L+K
Sbjct: 139 LAFNMIEVDEL---PSLMK 154

>pdb|4DB4|A Chain A, Mss116p Dead-Box Helicase Domain 2 Bound To A Chimaeric Rna-Dna Duplex Length = 256

Iteration: 1
 Score = 74.3 bits (181), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 34/112 (30%), Positives = 62/112 (55%), Gaps = 4/112 (3%)
Query: 729 ALFRDLLKHGYPCLSLHGAKDQTDRESTISDFKSNVCNLLIATSVAARGLDVKELELVIN 788
           ++ ++  K   P L  HG   Q  R S +  FK +   +L+ T V ARG+D   +  V+ 
Sbjct: 51  SILKNEFKKDLPILEFHGKITQNKRTSLVKRFKKDESGILVCTDVGARGMDFPNVHEVLQ 110
Query: 789 FDAPNHYEDYVHRVGRTGRAGRKGCAITFISEEDAKYSPDLVKALELSEQVV 840
              P+   +Y+HR+GRT R+G++G ++ FI +++  +    V+ LE ++ +V
Sbjct: 111 IGVPSELANYIHRIGRTARSGKEGSSVLFICKDELPF----VRELEDAKNIV 158

>pdb|4DB2|C Chain C, Mss116p Dead-Box Helicase Domain 2 Bound To An Rna Duplex Length = 257

Iteration: 1
 Score = 74.3 bits (181), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 34/112 (30%), Positives = 62/112 (55%), Gaps = 4/112 (3%)
Query: 729 ALFRDLLKHGYPCLSLHGAKDQTDRESTISDFKSNVCNLLIATSVAARGLDVKELELVIN 788
           ++ ++  K   P L  HG   Q  R S +  FK +   +L+ T V ARG+D   +  V+ 
Sbjct: 51  SILKNEFKKDLPILEFHGKITQNKRTSLVKRFKKDESGILVCTDVGARGMDFPNVHEVLQ 110
Query: 789 FDAPNHYEDYVHRVGRTGRAGRKGCAITFISEEDAKYSPDLVKALELSEQVV 840
              P+   +Y+HR+GRT R+G++G ++ FI +++  +    V+ LE ++ +V
Sbjct: 111 IGVPSELANYIHRIGRTARSGKEGSSVLFICKDELPF----VRELEDAKNIV 158

>pdb|4DB2|A Chain A, Mss116p Dead-Box Helicase Domain 2 Bound To An Rna Duplex Length = 257

Iteration: 1
 Score = 74.3 bits (181), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 34/112 (30%), Positives = 62/112 (55%), Gaps = 4/112 (3%)
Query: 729 ALFRDLLKHGYPCLSLHGAKDQTDRESTISDFKSNVCNLLIATSVAARGLDVKELELVIN 788
           ++ ++  K   P L  HG   Q  R S +  FK +   +L+ T V ARG+D   +  V+ 
Sbjct: 51  SILKNEFKKDLPILEFHGKITQNKRTSLVKRFKKDESGILVCTDVGARGMDFPNVHEVLQ 110
Query: 789 FDAPNHYEDYVHRVGRTGRAGRKGCAITFISEEDAKYSPDLVKALELSEQVV 840
              P+   +Y+HR+GRT R+G++G ++ FI +++  +    V+ LE ++ +V
Sbjct: 111 IGVPSELANYIHRIGRTARSGKEGSSVLFICKDELPF----VRELEDAKNIV 158

>pdb|3I32|A Chain A, Dimeric Structure Of A Hera Helicase Fragment Including The C-Terminal Reca Domain, The Dimerization Domain, And The Rna Binding Domain Length = 300

Iteration: 1
 Score = 70.5 bits (171), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 28/85 (32%), Positives = 53/85 (62%)
Query: 716 KILIFVHSQEKCDALFRDLLKHGYPCLSLHGAKDQTDRESTISDFKSNVCNLLIATSVAA 775
           + ++F  ++ + + + + LL+ G+P  +LHG   Q +RE  +  F+     +L+AT VAA
Sbjct: 30  RAMVFTRTKAETEEIAQGLLRLGHPAQALHGDMSQGERERVMGAFRQGEVRVLVATDVAA 89
Query: 776 RGLDVKELELVINFDAPNHYEDYVH 800
           RGLD+ +++LV+++  P+  E Y H
Sbjct: 90  RGLDIPQVDLVVHYRMPDRAEAYQH 114

>pdb|1FUK|A Chain A, Crystal Structure Of The Carboxy Terminal Domain Of Yeast Eif4a Length = 165

Iteration: 1
 Score = 68.6 bits (166), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 45/130 (34%), Positives = 78/130 (60%)
Query: 718 LIFVHSQEKCDALFRDLLKHGYPCLSLHGAKDQTDRESTISDFKSNVCNLLIATSVAARG 777
           +IF +++ K + L   L    +   +++    Q +R++ + +F+S    +LI+T + ARG
Sbjct: 34  VIFCNTRRKVEELTTKLRNDKFTVSAIYSDLPQQERDTIMKEFRSGSSRILISTDLLARG 93
Query: 778 LDVKELELVINFDAPNHYEDYVHRVGRTGRAGRKGCAITFISEEDAKYSPDLVKALELSE 837
           +DV+++ LVIN+D P + E+Y+HR+GR GR GRKG AI F++ ED     +L K      
Sbjct: 94  IDVQQVSLVINYDLPANKENYIHRIGRGGRFGRKGVAINFVTNEDVGAMRELEKFYSTQI 153
Query: 838 QVVPDDLKAL 847
           + +P D+  L
Sbjct: 154 EELPSDIATL 163

>pdb|3EAQ|A Chain A, Novel Dimerization Motif In The Dead Box Rna Helicase Hera Form 2, Complete Dimer, Symmetric Length = 212

Iteration: 1
 Score = 68.2 bits (165), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 28/85 (32%), Positives = 53/85 (62%)
Query: 716 KILIFVHSQEKCDALFRDLLKHGYPCLSLHGAKDQTDRESTISDFKSNVCNLLIATSVAA 775
           + ++F  ++ + + + + LL+ G+P  +LHG   Q +RE  +  F+     +L+AT VAA
Sbjct: 33  RAMVFTRTKAETEEIAQGLLRLGHPAQALHGDLSQGERERVLGAFRQGEVRVLVATDVAA 92
Query: 776 RGLDVKELELVINFDAPNHYEDYVH 800
           RGLD+ +++LV+++  P+  E Y H
Sbjct: 93  RGLDIPQVDLVVHYRLPDRAEAYQH 117

>pdb|4F91|B Chain B, Brr2 Helicase Region Length = 1724

Iteration: 1
 Score = 63.5 bits (153), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 98/440 (22%), Positives = 174/440 (39%), Gaps = 91/440 (20%)
Query: 506 DCIGVAKTGSGKTLAFVLPMLR----HIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIR 561
           + +  A TG+GKT   ++ MLR    HI     +   D  + + +AP R LVQ++   + 
Sbjct: 97  NLLLCAPTGAGKTNVALMCMLREIGKHINMDGTINVDDFKI-IYIAPMRSLVQEM---VG 152
Query: 562 KFAKVMGVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYL 621
            F K +    + V   +G  Q   E    T+I+VCTP +  DI+   GG+ T  + V  +
Sbjct: 153 SFGKRLATYGITVAELTGDHQLCKEEISATQIIVCTPEKW-DIITRKGGERTYTQLVRLI 211
Query: 622 VMDEADRMFD---MGFEPQITRIVQNI---RPDRQTVLFSATFPRQVEILARKVLN---- 671
           ++DE   + D      E  + R ++NI   + D + +  SAT P   ++     ++    
Sbjct: 212 ILDEIHLLHDDRGPVLEALVARAIRNIEMTQEDVRLIGLSATLPNYEDVATFLRVDPAKG 271
Query: 672 --------KPVEIQVGGRSVVNKDITQLVEVRPESDRFLRLLELLGEWYEKGKILIFVHS 723
                   +PV ++     +  K   +  ++  E   + +++E  G    K ++L+FVHS
Sbjct: 272 LFYFDNSFRPVPLEQTYVGITEKKAIKRFQIMNEI-VYEKIMEHAG----KNQVLVFVHS 326
Query: 724 Q--------------------------------------EKCDAL-FRDLLKHGYPCLSL 744
           +                                      E+C  L  +DLL +G+     
Sbjct: 327 RKETGKTARAIRDMCLEKDTLGLFLREGSASTEVLRTEAEQCKNLELKDLLPYGFAI--H 384
Query: 745 HGAKDQTDRESTISDFKSNVCNLLIATSVAARGLDVKELELVINFDAPNHYE-------- 796
           H    + DR      F      +L++T+  A G+++    ++I        E        
Sbjct: 385 HAGMTRVDRTLVEDLFADKHIQVLVSTATLAWGVNLPAHTVIIKGTQVYSPEKGRWTELG 444
Query: 797 --DYVHRVGRTGR--AGRKGCAITFISEEDAKYSPDLV-KALELSEQVV---PDDLKALA 848
             D +  +GR GR     KG  I   S  + +Y   L+ + L +  Q+V   PD L   A
Sbjct: 445 ALDILQMLGRAGRPQYDTKGEGILITSHGELQYYLSLLNQQLPIESQMVSKLPDMLN--A 502
Query: 849 DSFMAKVNQGLEQAHGTGYG 868
           +  +  V    +  +  GY 
Sbjct: 503 EIVLGNVQNAKDAVNWLGYA 522

>pdb|4F92|B Chain B, Brr2 Helicase Region S1087l Length = 1724

Iteration: 1
 Score = 63.2 bits (152), Expect = 6e-10,   Method: Compositional matrix adjust.
 Identities = 98/440 (22%), Positives = 174/440 (39%), Gaps = 91/440 (20%)
Query: 506 DCIGVAKTGSGKTLAFVLPMLR----HIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIR 561
           + +  A TG+GKT   ++ MLR    HI     +   D  + + +AP R LVQ++   + 
Sbjct: 97  NLLLCAPTGAGKTNVALMCMLREIGKHINMDGTINVDDFKI-IYIAPMRSLVQEM---VG 152
Query: 562 KFAKVMGVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYL 621
            F K +    + V   +G  Q   E    T+I+VCTP +  DI+   GG+ T  + V  +
Sbjct: 153 SFGKRLATYGITVAELTGDHQLCKEEISATQIIVCTPEKW-DIITRKGGERTYTQLVRLI 211
Query: 622 VMDEADRMFD---MGFEPQITRIVQNI---RPDRQTVLFSATFPRQVEILARKVLN---- 671
           ++DE   + D      E  + R ++NI   + D + +  SAT P   ++     ++    
Sbjct: 212 ILDEIHLLHDDRGPVLEALVARAIRNIEMTQEDVRLIGLSATLPNYEDVATFLRVDPAKG 271
Query: 672 --------KPVEIQVGGRSVVNKDITQLVEVRPESDRFLRLLELLGEWYEKGKILIFVHS 723
                   +PV ++     +  K   +  ++  E   + +++E  G    K ++L+FVHS
Sbjct: 272 LFYFDNSFRPVPLEQTYVGITEKKAIKRFQIMNEI-VYEKIMEHAG----KNQVLVFVHS 326
Query: 724 Q--------------------------------------EKCDAL-FRDLLKHGYPCLSL 744
           +                                      E+C  L  +DLL +G+     
Sbjct: 327 RKETGKTARAIRDMCLEKDTLGLFLREGSASTEVLRTEAEQCKNLELKDLLPYGFAI--H 384
Query: 745 HGAKDQTDRESTISDFKSNVCNLLIATSVAARGLDVKELELVINFDAPNHYE-------- 796
           H    + DR      F      +L++T+  A G+++    ++I        E        
Sbjct: 385 HAGMTRVDRTLVEDLFADKHIQVLVSTATLAWGVNLPAHTVIIKGTQVYSPEKGRWTELG 444
Query: 797 --DYVHRVGRTGR--AGRKGCAITFISEEDAKYSPDLV-KALELSEQVV---PDDLKALA 848
             D +  +GR GR     KG  I   S  + +Y   L+ + L +  Q+V   PD L   A
Sbjct: 445 ALDILQMLGRAGRPQYDTKGEGILITSHGELQYYLSLLNQQLPIESQMVSKLPDMLN--A 502
Query: 849 DSFMAKVNQGLEQAHGTGYG 868
           +  +  V    +  +  GY 
Sbjct: 503 EIVLGNVQNAKDAVNWLGYA 522

>pdb|2V1X|A Chain A, Crystal Structure Of Human Recq-Like Dna Helicase Length = 591

Iteration: 1
 Score = 60.8 bits (146), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 81/365 (22%), Positives = 150/365 (41%), Gaps = 42/365 (11%)
Query: 472 TGLTSKIMETIRKLNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKD 531
           +G    I++ + KL  EK  P+Q + + V M+G++   V  TG GK+L + LP L     
Sbjct: 29  SGKVKDILQNVFKL--EKFRPLQLETINVTMAGKEVFLVMPTGGGKSLCYQLPAL----- 81
Query: 532 QPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSG----------VA 581
                  DG   L++ P   L++    D     K +G+    +   S           + 
Sbjct: 82  -----CSDG-FTLVICPLISLME----DQLMVLKQLGISATMLNASSSKEHVKWVHAEMV 131
Query: 582 QQISELKRGTEIVVCTPGRMID--ILCTSGGKITNLRRVTYLVMDEADRMFDMG--FEP- 636
            + SELK    ++  TP ++    +  +   K    RR T + +DE       G  F P 
Sbjct: 132 NKNSELK----LIYVTPEKIAKSKMFMSRLEKAYEARRFTRIAVDEVHCCSQWGHDFRPD 187
Query: 637 -QITRIVQNIRPDRQTVLFSATFPRQVEILARKVLNKPVEIQVGGRSVVNK-DITQLVEV 694
            +   I++   P+   +  +AT    V   A+K+L   +E      +  N+ ++   V  
Sbjct: 188 YKALGILKRQFPNASLIGLTATATNHVLTDAQKIL--CIEKCFTFTASFNRPNLYYEVRQ 245
Query: 695 RPES--DRFLRLLELLGEWYEKGKILIFVHSQEKCDALFRDLLKHGYPCLSLHGAKDQTD 752
           +P +  D    +++L+   Y+    +I+  SQ+  + +   L   G    + H   +  D
Sbjct: 246 KPSNTEDFIEDIVKLINGRYKGQSGIIYCFSQKDSEQVTVSLQNLGIHAGAYHANLEPED 305
Query: 753 RESTISDFKSNVCNLLIATSVAARGLDVKELELVINFDAPNHYEDYVHRVGRTGRAGRKG 812
           + +    + +N   +++AT     G+D  ++  VI+       E+Y    GR GR   K 
Sbjct: 306 KTTVHRKWSANEIQVVVATVAFGMGIDKPDVRFVIHHSMSKSMENYYQESGRAGRDDMKA 365
Query: 813 CAITF 817
             I +
Sbjct: 366 DCILY 370

>pdb|1OYY|A Chain A, Structure Of The Recq Catalytic Core Bound To Atp-Gamma-S Length = 523

Iteration: 1
 Score = 58.2 bits (139), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 84/378 (22%), Positives = 146/378 (38%), Gaps = 63/378 (16%)
Query: 471 QTGLTSKIMETIRKLNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAF--------- 521
           ++G    + ET     Y++  P Q + +  ++SGRDC+ V  TG GK+L +         
Sbjct: 10  ESGAKQVLQET---FGYQQFRPGQEEIIDTVLSGRDCLVVMPTGGGKSLCYQIPALLLNG 66
Query: 522 ----VLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGG 577
               V P++  +KDQ      +G     +  T+   QQ+                 V  G
Sbjct: 67  LTVVVSPLISLMKDQVDQLQANGVAAACLNSTQTREQQLE----------------VMTG 110
Query: 578 SGVAQQISELKRGTEIVVCTPGR-MIDILCTSGGKITNLRRVTYLVMDEADRMFDMG--F 634
               Q          ++   P R M+D           +     L +DEA  +   G  F
Sbjct: 111 CRTGQ--------IRLLYIAPERLMLDNFLEHLAHWNPV----LLAVDEAHCISQWGHDF 158
Query: 635 EPQITRIVQNIRPDRQTVLFSATFP------RQVEILARKVLNKPVEIQVGGRSVVNKDI 688
            P+   + Q +R    T+ F A         RQ +I+    LN P+ IQ+      N   
Sbjct: 159 RPEYAALGQ-LRQRFPTLPFMALTATADDTTRQ-DIVRLLGLNDPL-IQISSFDRPNIRY 215
Query: 689 TQLVEVRPESDRFLRLLELLGEWYEKGKI-LIFVHSQEKCDALFRDLLKHGYPCLSLHGA 747
             + + +P  D+ +R ++      ++GK  +I+ +S+ K +     L   G    + H  
Sbjct: 216 MLMEKFKP-LDQLMRYVQ-----EQRGKSGIIYCNSRAKVEDTAARLQSKGISAAAYHAG 269
Query: 748 KDQTDRESTISDFKSNVCNLLIATSVAARGLDVKELELVINFDAPNHYEDYVHRVGRTGR 807
            +   R      F+ +   +++AT     G++   +  V++FD P + E Y    GR GR
Sbjct: 270 LENNVRADVQEKFQRDDLQIVVATVAFGMGINKPNVRFVVHFDIPRNIESYYQETGRAGR 329
Query: 808 AGRKGCAITFISEEDAKY 825
            G    A+ F    D  +
Sbjct: 330 DGLPAEAMLFYDPADMAW 347

>pdb|1OYW|A Chain A, Structure Of The Recq Catalytic Core Length = 523

Iteration: 1
 Score = 53.1 bits (126), Expect = 7e-07,   Method: Compositional matrix adjust.
 Identities = 83/378 (21%), Positives = 142/378 (37%), Gaps = 63/378 (16%)
Query: 471 QTGLTSKIMETIRKLNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAF--------- 521
           ++G    + ET     Y++  P Q + +  ++SGRDC+ V  TG GK+L +         
Sbjct: 10  ESGAKQVLQET---FGYQQFRPGQEEIIDTVLSGRDCLVVXPTGGGKSLCYQIPALLLNG 66
Query: 522 ----VLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGG 577
               V P++   KDQ      +G     +  T+   QQ+                 V  G
Sbjct: 67  LTVVVSPLISLXKDQVDQLQANGVAAACLNSTQTREQQLE----------------VXTG 110
Query: 578 SGVAQQISELKRGTEIVVCTPGRM-IDILCTSGGKITNLRRVTYLVMDEADRMFDMG--F 634
               Q          ++   P R+ +D           +     L +DEA  +   G  F
Sbjct: 111 CRTGQ--------IRLLYIAPERLXLDNFLEHLAHWNPV----LLAVDEAHCISQWGHDF 158
Query: 635 EPQITRIVQNIRPDRQTVLFSATFP------RQVEILARKVLNKPVEIQVGGRSVVNKDI 688
            P+   + Q +R    T+ F A         RQ +I+    LN P+ IQ+      N   
Sbjct: 159 RPEYAALGQ-LRQRFPTLPFXALTATADDTTRQ-DIVRLLGLNDPL-IQISSFDRPNIRY 215
Query: 689 TQLVEVRPESDRFLRLLELLGEWYEKGKI-LIFVHSQEKCDALFRDLLKHGYPCLSLHGA 747
               + +P  D+  R ++      ++GK  +I+ +S+ K +     L   G    + H  
Sbjct: 216 XLXEKFKP-LDQLXRYVQ-----EQRGKSGIIYCNSRAKVEDTAARLQSKGISAAAYHAG 269
Query: 748 KDQTDRESTISDFKSNVCNLLIATSVAARGLDVKELELVINFDAPNHYEDYVHRVGRTGR 807
            +   R      F+ +   +++AT     G++   +  V++FD P + E Y    GR GR
Sbjct: 270 LENNVRADVQEKFQRDDLQIVVATVAFGXGINKPNVRFVVHFDIPRNIESYYQETGRAGR 329
Query: 808 AGRKGCAITFISEEDAKY 825
            G    A  F    D  +
Sbjct: 330 DGLPAEAXLFYDPADXAW 347

>pdb|1WP9|A Chain A, Crystal Structure Of Pyrococcus Furiosus Hef Helicase Domain Length = 494

Iteration: 1
 Score = 48.9 bits (115), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 37/138 (26%), Positives = 66/138 (47%), Gaps = 14/138 (10%)
Query: 684 VNKDITQLVEVR------PESDRFLRLLELLGEWYEKGKILIFVHSQEKCDALFRDLLKH 737
           + K I+ LV+ +      P+ D+   ++    +  +  KI++F + +E    +  +L+K 
Sbjct: 325 MKKAISLLVQAKEIGLDHPKMDKLKEIIREQLQRKQNSKIIVFTNYRETAKKIVNELVKD 384
Query: 738 GYPCLSLHG-AKDQTDR-------ESTISDFKSNVCNLLIATSVAARGLDVKELELVINF 789
           G       G A  + DR       +  + +F     N+L+ATSV   GLDV E++LV+ +
Sbjct: 385 GIKAKRFVGQASKENDRGLSQREQKLILDEFARGEFNVLVATSVGEEGLDVPEVDLVVFY 444
Query: 790 DAPNHYEDYVHRVGRTGR 807
           +        + R GRTGR
Sbjct: 445 EPVPSAIRSIQRRGRTGR 462

>pdb|2YKG|A Chain A, Structural Insights Into Rna Recognition By Rig-I Length = 696

Iteration: 1
 Score = 44.7 bits (104), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 37/139 (26%), Positives = 61/139 (43%), Gaps = 7/139 (5%)
Query: 489 KPMPIQAQ-ALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMA 547
           KP   Q + ALP  M G++ I  A TG GKT   +L    H+K  P    G     +  A
Sbjct: 13  KPRNYQLELALPA-MKGKNTIICAPTGCGKTFVSLLICEHHLKKFP---QGQKGKVVFFA 68
Query: 548 PTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCT 607
               + +Q  S   K+ +  G R   + G +     + ++    +I++ TP  +++ L  
Sbjct: 69  NQIPVYEQNKSVFSKYFERHGYRVTGISGATAENVPVEQIVENNDIIILTPQILVNNL-- 126
Query: 608 SGGKITNLRRVTYLVMDEA 626
             G I +L   T ++ DE 
Sbjct: 127 KKGTIPSLSIFTLMIFDEC 145

>pdb|3TMI|A Chain A, Structural Basis For Rna Recognition And Activation Of Rig-I Length = 695

Iteration: 1
 Score = 44.7 bits (104), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 37/139 (26%), Positives = 61/139 (43%), Gaps = 7/139 (5%)
Query: 489 KPMPIQAQ-ALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMA 547
           KP   Q + ALP  M G++ I  A TG GKT   +L    H+K  P    G     +  A
Sbjct: 12  KPRNYQLELALPA-MKGKNTIICAPTGCGKTFVSLLICEHHLKKFP---QGQKGKVVFFA 67
Query: 548 PTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCT 607
               + +Q  S   K+ +  G R   + G +     + ++    +I++ TP  +++ L  
Sbjct: 68  NQIPVYEQQKSVFSKYFERHGYRVTGISGATAENVPVEQIVENNDIIILTPQILVNNL-- 125
Query: 608 SGGKITNLRRVTYLVMDEA 626
             G I +L   T ++ DE 
Sbjct: 126 KKGTIPSLSIFTLMIFDEC 144

>pdb|4AY2|A Chain A, Capturing 5' Tri-Phosphorylated Rna Duplex By Rig-I Length = 687

Iteration: 1
 Score = 44.7 bits (104), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 37/139 (26%), Positives = 61/139 (43%), Gaps = 7/139 (5%)
Query: 489 KPMPIQAQ-ALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMA 547
           KP   Q + ALP  M G++ I  A TG GKT   +L    H+K  P    G     +  A
Sbjct: 4   KPRNYQLELALPA-MKGKNTIICAPTGCGKTFVSLLICEHHLKKFP---QGQKGKVVFFA 59
Query: 548 PTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCT 607
               + +Q  S   K+ +  G R   + G +     + ++    +I++ TP  +++ L  
Sbjct: 60  NQIPVYEQNKSVFSKYFERHGYRVTGISGATAENVPVEQIVENNDIIILTPQILVNNL-- 117
Query: 608 SGGKITNLRRVTYLVMDEA 626
             G I +L   T ++ DE 
Sbjct: 118 KKGTIPSLSIFTLMIFDEC 136

>pdb|4GL2|A Chain A, Structural Basis For Dsrna Duplex Backbone Recognition By Mda5 Length = 699

Iteration: 1
 Score = 42.7 bits (99), Expect = 9e-04,   Method: Compositional matrix adjust.
 Identities = 19/40 (47%), Positives = 28/40 (70%)
Query: 750 QTDRESTISDFKSNVCNLLIATSVAARGLDVKELELVINF 789
           Q +++  IS F++   NLLIAT+VA  GLD+KE  +VI +
Sbjct: 450 QNEQKEVISKFRTGKINLLIATTVAEEGLDIKECNIVIRY 489

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	976
2db3_A	434	ATP-dependent RNA helicase VASA; DEAD-BOX, protein	0.0
2i4i_A	417	ATP-dependent RNA helicase DDX3X; DEAD, structural	0.0
3fe2_A	242	Probable ATP-dependent RNA helicase DDX5; DEAD, AD	1e-149
3iuy_A	228	Probable ATP-dependent RNA helicase DDX53; REC-A-l	1e-131
3dkp_A	245	Probable ATP-dependent RNA helicase DDX52; DEAD, A	1e-122
2j0s_A	410	ATP-dependent RNA helicase DDX48; mRNA processing,	1e-121
1fuu_A	394	Yeast initiation factor 4A; IF4A, helicase, DEAD-b	1e-120
1s2m_A	400	Putative ATP-dependent RNA helicase DHH1; ATP-bind	1e-119
3eiq_A	414	Eukaryotic initiation factor 4A-I; PDCD4, anti-onc	1e-119
1wrb_A	253	DJVLGB; RNA helicase, DEAD BOX, VASA, structural g	1e-117
1hv8_A	367	Putative ATP-dependent RNA helicase MJ0669; RNA-bi	1e-116
2z0m_A	337	337AA long hypothetical ATP-dependent RNA helicase	1e-115
3fho_A	508	ATP-dependent RNA helicase DBP5; mRNA export, ATPa	1e-115
3fht_A	412	ATP-dependent RNA helicase DDX19B; DBP5, DEAD-box	1e-111
3i5x_A	563	ATP-dependent RNA helicase MSS116; protein-RNA com	1e-110
1xti_A	391	Probable ATP-dependent RNA helicase P47; alpha-bet	1e-109
3pey_A	395	ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, A	1e-108
3fmp_B	479	ATP-dependent RNA helicase DDX19B; nuclear porin,	1e-107
3sqw_A	579	ATP-dependent RNA helicase MSS116, mitochondrial;	1e-107
3oiy_A	414	Reverse gyrase helicase domain; topoisomerase, DNA	9e-98
3ber_A	249	Probable ATP-dependent RNA helicase DDX47; DEAD, A	1e-81
2pl3_A	236	Probable ATP-dependent RNA helicase DDX10; DEAD, s	3e-77
2gxq_A	207	Heat resistant RNA dependent ATPase; RNA helicase,	9e-75
1vec_A	206	ATP-dependent RNA helicase P54; DEAD-box protein,	3e-74
1q0u_A	219	Bstdead; DEAD protein, RNA binding protein; 1.85A	5e-74
3ly5_A	262	ATP-dependent RNA helicase DDX18; alpha-beta, stru	3e-69
3bor_A	237	Human initiation factor 4A-II; translation initiat	4e-69
1qde_A	224	EIF4A, translation initiation factor 4A; DEAD box	3e-68
1t6n_A	220	Probable ATP-dependent RNA helicase; RECA-like fol	4e-67
2jgn_A	185	DBX, DDX3, ATP-dependent RNA helicase DDX3X; phosp	1e-66
2oxc_A	230	Probable ATP-dependent RNA helicase DDX20; DEAD, s	2e-65
2p6n_A	191	ATP-dependent RNA helicase DDX41; DEAD, structural	4e-62
3fmo_B	300	ATP-dependent RNA helicase DDX19B; nuclear porin,	9e-62
2yjt_D	170	ATP-dependent RNA helicase SRMB, regulator of ribo	5e-42
2hjv_A	163	ATP-dependent RNA helicase DBPA; parallel alpha-be	6e-41
1t5i_A	172	C_terminal domain of A probable ATP-dependent RNA	1e-40
1fuk_A	165	Eukaryotic initiation factor 4A; helicase, DEAD-bo	2e-40
2rb4_A	175	ATP-dependent RNA helicase DDX25; rossmann fold, s	5e-39
3eaq_A	212	Heat resistant RNA dependent ATPase; DEAD box RNA	2e-35
3i32_A	300	Heat resistant RNA dependent ATPase; RNA helicase,	9e-33
3o8b_A	666	HCV NS3 protease/helicase; ntpase, RNA, translocat	2e-21
1wp9_A	494	ATP-dependent RNA helicase, putative; ATPase, DNA	6e-21
1wp9_A	494	ATP-dependent RNA helicase, putative; ATPase, DNA	5e-17
2zj8_A	720	DNA helicase, putative SKI2-type helicase; RECA fo	2e-16
2p6r_A	702	Afuhel308 helicase; protein-DNA complex, SF2 helic	4e-16
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	9e-16
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	4e-15
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	8e-15
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	1e-14
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	1e-14
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	2e-13
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	4e-12
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	3e-11
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	3e-10
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	3e-09
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	2e-07
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	4e-07
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	4e-05
3b6e_A	216	Interferon-induced helicase C domain-containing P;	3e-14
1i84_S	1184	Smooth muscle myosin heavy chain; muscle protein,	3e-13
1i84_S	1184	Smooth muscle myosin heavy chain; muscle protein,	2e-12
1i84_S	1184	Smooth muscle myosin heavy chain; muscle protein,	4e-12
1i84_S	1184	Smooth muscle myosin heavy chain; muscle protein,	5e-12
1i84_S	1184	Smooth muscle myosin heavy chain; muscle protein,	8e-12
1i84_S	1184	Smooth muscle myosin heavy chain; muscle protein,	4e-11
1i84_S	1184	Smooth muscle myosin heavy chain; muscle protein,	3e-08
1yks_A	440	Genome polyprotein [contains: flavivirin protease	7e-13
2dfs_A	1080	Myosin-5A; myosin-V, inhibited state, cryoelectron	7e-13
2dfs_A	1080	Myosin-5A; myosin-V, inhibited state, cryoelectron	6e-12
2dfs_A	1080	Myosin-5A; myosin-V, inhibited state, cryoelectron	2e-11
2dfs_A	1080	Myosin-5A; myosin-V, inhibited state, cryoelectron	1e-08
2dfs_A	1080	Myosin-5A; myosin-V, inhibited state, cryoelectron	7e-05
2dfs_A	1080	Myosin-5A; myosin-V, inhibited state, cryoelectron	2e-04
2dfs_A	1080	Myosin-5A; myosin-V, inhibited state, cryoelectron	3e-04
2va8_A	715	SSO2462, SKI2-type helicase; hydrolase, DNA repair	1e-12
4a2q_A	797	RIG-I, retinoic acid inducible protein I; hydrolas	2e-12
4a2q_A	797	RIG-I, retinoic acid inducible protein I; hydrolas	6e-07
2zuo_A	861	MVP, major vault protein; repeat domains, protein-	2e-12
2zuo_A	861	MVP, major vault protein; repeat domains, protein-	3e-09
2zuo_A	861	MVP, major vault protein; repeat domains, protein-	5e-08
4a2p_A	556	RIG-I, retinoic acid inducible protein I; hydrolas	3e-12
4a2p_A	556	RIG-I, retinoic acid inducible protein I; hydrolas	6e-09
1g8x_A	1010	Myosin II heavy chain fused to alpha-actinin 3; mo	5e-12
1g8x_A	1010	Myosin II heavy chain fused to alpha-actinin 3; mo	6e-10
1g8x_A	1010	Myosin II heavy chain fused to alpha-actinin 3; mo	2e-08
2ykg_A	696	Probable ATP-dependent RNA helicase DDX58; hydrola	1e-11
2ykg_A	696	Probable ATP-dependent RNA helicase DDX58; hydrola	3e-08
3tbk_A	555	RIG-I helicase domain; DECH helicase, ATP binding,	2e-11
3tbk_A	555	RIG-I helicase domain; DECH helicase, ATP binding,	6e-09
2jlq_A	451	Serine protease subunit NS3; ribonucleoprotein, nu	7e-11
4a2w_A	936	RIG-I, retinoic acid inducible protein I; hydrolas	3e-10
4a2w_A	936	RIG-I, retinoic acid inducible protein I; hydrolas	6e-08
2ycu_A	995	Non muscle myosin 2C, alpha-actinin; motor protein	4e-09
2v6i_A	431	RNA helicase; membrane, hydrolase, transmembrane,	5e-09
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	8e-09
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	2e-06
3dmq_A	968	RNA polymerase-associated protein RAPA; SWF2/SNF2,	1e-08
1gku_B	1054	Reverse gyrase, TOP-RG; topoisomerase, DNA superco	3e-08
2whx_A	618	Serine protease/ntpase/helicase NS3; transcription	4e-08
2z83_A	459	Helicase/nucleoside triphosphatase; hydrolase, mem	7e-08
3lvg_D	190	LCB, clathrin light chain B; SELF assembly, coated	3e-07
3lvg_D	190	LCB, clathrin light chain B; SELF assembly, coated	6e-07
3lvg_D	190	LCB, clathrin light chain B; SELF assembly, coated	2e-06
3lvg_D	190	LCB, clathrin light chain B; SELF assembly, coated	3e-05
3lvg_D	190	LCB, clathrin light chain B; SELF assembly, coated	6e-05
3lvg_D	190	LCB, clathrin light chain B; SELF assembly, coated	6e-05
3lvg_D	190	LCB, clathrin light chain B; SELF assembly, coated	6e-04
2fwr_A	472	DNA repair protein RAD25; DNA unwinding, XPB, DNA	6e-07
2oca_A	510	DAR protein, ATP-dependent DNA helicase UVSW; ATP-	6e-07
2qag_B	427	Septin-6, protein NEDD5; cell cycle, cell division	2e-06
2wv9_A	673	Flavivirin protease NS2B regulatory subunit, FLAV	3e-06
2a6h_D	1524	DNA-directed RNA polymerase beta' chain; RNA polym	1e-05
2a6h_D	1524	DNA-directed RNA polymerase beta' chain; RNA polym	6e-05
1w1w_A	430	Structural maintenance of chromosome 1; cohesin, c	4e-05
1f5n_A	592	Interferon-induced guanylate-binding protein 1; GB	1e-04
1f5n_A	592	Interferon-induced guanylate-binding protein 1; GB	5e-04
1f5n_A	592	Interferon-induced guanylate-binding protein 1; GB	7e-04
2qag_C	418	Septin-7; cell cycle, cell division, GTP-binding,	2e-04
3auy_A	371	DNA double-strand break repair RAD50 ATPase; DNA r	4e-04
3mwy_W	800	Chromo domain-containing protein 1; SWI2/SNF2 ATPa	5e-04

>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} Length = 434

 Score =  644 bits (1663), Expect = 0.0
 Identities = 159/431 (36%), Positives = 241/431 (55%), Gaps = 16/431 (3%)

Query: 426 PFRKNFYIEVKEIARMTPEEVSAYRK--------QLELKIHGKDVPKPIKTWHQTGLTSK 477
            F   FYI  +          S             + +K+ G DVP+PI+ +    L   
Sbjct: 7   EFPGEFYIPPEPSNDAIEIFSSGIASGIHFSKYNNIPVKVTGSDVPQPIQHFTSADLRDI 66

Query: 478 IMETIRKLNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAA 537
           I++ + K  Y+ P PIQ  ++PVI SGRD +  A+TGSGKT AF+LP+L  + + P    
Sbjct: 67  IIDNVNKSGYKIPTPIQKCSIPVISSGRDLMACAQTGSGKTAAFLLPILSKLLEDPHELE 126

Query: 538 GDGPVGLIMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQISELKRGTEIVVCT 597
              P  +I++PTREL  QI ++ RKFA    ++   VYGG+    Q   + RG  +V+ T
Sbjct: 127 LGRPQVVIVSPTRELAIQIFNEARKFAFESYLKIGIVYGGTSFRHQNECITRGCHVVIAT 186

Query: 598 PGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMGFEPQITRIVQNI--RPDRQTVLFS 655
           PGR++D +              ++V+DEADRM DMGF   + RI+ ++  RP+ QT++FS
Sbjct: 187 PGRLLDFV---DRTFITFEDTRFVVLDEADRMLDMGFSEDMRRIMTHVTMRPEHQTLMFS 243

Query: 656 ATFPRQVEILARKVLNKPVEIQVGGRSVVNKDITQLVEVRPESDRFLRLLELLGEWYEKG 715
           ATFP +++ +A + L   V + +G       D+ Q +    +  +  +L+E+L E  +  
Sbjct: 244 ATFPEEIQRMAGEFLKNYVFVAIGIVGGACSDVKQTIYEVNKYAKRSKLIEILSE--QAD 301

Query: 716 KILIFVHSQEKCDALFRDLLKHGYPCLSLHGAKDQTDRESTISDFKSNVCNLLIATSVAA 775
             ++FV ++   D L   L +  +P  S+HG + Q+ RE  + DFK+    +LIATSVA+
Sbjct: 302 GTIVFVETKRGADFLASFLSEKEFPTTSIHGDRLQSQREQALRDFKNGSMKVLIATSVAS 361

Query: 776 RGLDVKELELVINFDAPNHYEDYVHRVGRTGRAGRKGCAITFIS-EEDAKYSPDLVKALE 834
           RGLD+K ++ VIN+D P+  +DYVHR+GRTGR G  G A +F   E+D   + DLVK LE
Sbjct: 362 RGLDIKNIKHVINYDMPSKIDDYVHRIGRTGRVGNNGRATSFFDPEKDRAIAADLVKILE 421

Query: 835 LSEQVVPDDLK 845
            S Q VPD L+
Sbjct: 422 GSGQTVPDFLR 432

>2i4i_A ATP-dependent RNA helicase DDX3X; DEAD, structural genomics, SGC, structural GE consortium, hydrolase; HET: AMP; 2.20A {Homo sapiens} Length = 417

 Score =  630 bits (1628), Expect = 0.0
 Identities = 165/414 (39%), Positives = 243/414 (58%), Gaps = 20/414 (4%)

Query: 454 ELKIHGKDVPKPIKTWHQTGLTSKIMETIRKLNYEKPMPIQAQALPVIMSGRDCIGVAKT 513
            ++  G + P  I+++    +   IM  I    Y +P P+Q  A+P+I   RD +  A+T
Sbjct: 2   MVEATGNNCPPHIESFSDVEMGEIIMGNIELTRYTRPTPVQKHAIPIIKEKRDLMACAQT 61

Query: 514 GSGKTLAFVLPMLRHIKDQPPVAA-------------GDGPVGLIMAPTRELVQQIHSDI 560
           GSGKT AF+LP+L  I    P  A                P+ L++APTREL  QI+ + 
Sbjct: 62  GSGKTAAFLLPILSQIYSDGPGEALRAMKENGRYGRRKQYPISLVLAPTRELAVQIYEEA 121

Query: 561 RKFAKVMGVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTY 620
           RKF+    VR   VYGG+ + QQI +L+RG  ++V TPGR++D++         L    Y
Sbjct: 122 RKFSYRSRVRPCVVYGGADIGQQIRDLERGCHLLVATPGRLVDMM---ERGKIGLDFCKY 178

Query: 621 LVMDEADRMFDMGFEPQITRIVQ--NIRPD--RQTVLFSATFPRQVEILARKVLNKPVEI 676
           LV+DEADRM DMGFEPQI RIV+   + P   R T++FSATFP+++++LAR  L++ + +
Sbjct: 179 LVLDEADRMLDMGFEPQIRRIVEQDTMPPKGVRHTMMFSATFPKEIQMLARDFLDEYIFL 238

Query: 677 QVGGRSVVNKDITQLVEVRPESDRFLRLLELLGEWYEKGKILIFVHSQEKCDALFRDLLK 736
            VG     +++ITQ V    ESD+   LL+LL    +    L+FV +++  D+L   L  
Sbjct: 239 AVGRVGSTSENITQKVVWVEESDKRSFLLDLLNATGKDSLTLVFVETKKGADSLEDFLYH 298

Query: 737 HGYPCLSLHGAKDQTDRESTISDFKSNVCNLLIATSVAARGLDVKELELVINFDAPNHYE 796
            GY C S+HG + Q DRE  +  F+S    +L+AT+VAARGLD+  ++ VINFD P+  E
Sbjct: 299 EGYACTSIHGDRSQRDREEALHQFRSGKSPILVATAVAARGLDISNVKHVINFDLPSDIE 358

Query: 797 DYVHRVGRTGRAGRKGCAITFISEEDAKYSPDLVKALELSEQVVPDDLKALADS 850
           +YVHR+GRTGR G  G A +F +E +   + DL+  L  ++Q VP  L+ +A  
Sbjct: 359 EYVHRIGRTGRVGNLGLATSFFNERNINITKDLLDLLVEAKQEVPSWLENMAYE 412

>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} Length = 242

 Score =  442 bits (1139), Expect = e-149
 Identities = 111/245 (45%), Positives = 161/245 (65%), Gaps = 3/245 (1%)

Query: 439 ARMTPEEVSAYRKQLELKIHGKDVPKPIKTWHQTGLTSKIMETIRKLNYEKPMPIQAQAL 498
           +  T +EV  YR+  E+ + G + PKP+  +++    + +M+ I + N+ +P  IQAQ  
Sbjct: 1   SMRTAQEVETYRRSKEITVRGHNCPKPVLNFYEANFPANVMDVIARQNFTEPTAIQAQGW 60

Query: 499 PVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHS 558
           PV +SG D +GVA+TGSGKTL+++LP + HI  QP +  GDGP+ L++APTREL QQ+  
Sbjct: 61  PVALSGLDMVGVAQTGSGKTLSYLLPAIVHINHQPFLERGDGPICLVLAPTRELAQQVQQ 120

Query: 559 DIRKFAKVMGVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRV 618
              ++ +   ++   +YGG+    QI +L+RG EI + TPGR+ID L       TNLRR 
Sbjct: 121 VAAEYCRACRLKSTCIYGGAPKGPQIRDLERGVEICIATPGRLIDFLEC---GKTNLRRT 177

Query: 619 TYLVMDEADRMFDMGFEPQITRIVQNIRPDRQTVLFSATFPRQVEILARKVLNKPVEIQV 678
           TYLV+DEADRM DMGFEPQI +IV  IRPDRQT+++SAT+P++V  LA   L   + I +
Sbjct: 178 TYLVLDEADRMLDMGFEPQIRKIVDQIRPDRQTLMWSATWPKEVRQLAEDFLKDYIHINI 237

Query: 679 GGRSV 683
           G   +
Sbjct: 238 GALEL 242

>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} Length = 228

 Score =  394 bits (1015), Expect = e-131
 Identities = 87/223 (39%), Positives = 137/223 (61%), Gaps = 6/223 (2%)

Query: 458 HGKDVPKPIKTWHQT-GLTSKIMETIRKLNYEKPMPIQAQALPVIMSGRDCIGVAKTGSG 516
             + +PKP   +         ++++I ++   KP PIQ+QA P+I+ G D I VA+TG+G
Sbjct: 10  EKRLIPKPTCRFKDAFQQYPDLLKSIIRVGILKPTPIQSQAWPIILQGIDLIVVAQTGTG 69

Query: 517 KTLAFVLPMLRHIKDQP-PVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVMGVRCVPVY 575
           KTL++++P   H+  QP      +GP  L++ PTREL   + ++  K++   G++ + +Y
Sbjct: 70  KTLSYLMPGFIHLDSQPISREQRNGPGMLVLTPTRELALHVEAECSKYSY-KGLKSICIY 128

Query: 576 GGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMGFE 635
           GG     QI ++ +G +I++ TPGR+ D+         NLR +TYLV+DEAD+M DM FE
Sbjct: 129 GGRNRNGQIEDISKGVDIIIATPGRLNDLQ---MNNSVNLRSITYLVIDEADKMLDMEFE 185

Query: 636 PQITRIVQNIRPDRQTVLFSATFPRQVEILARKVLNKPVEIQV 678
           PQI +I+ ++RPDRQTV+ SAT+P  V  LA   L  P+ + V
Sbjct: 186 PQIRKILLDVRPDRQTVMTSATWPDTVRQLALSYLKDPMIVYV 228

>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} Length = 245

 Score =  370 bits (953), Expect = e-122
 Identities = 78/248 (31%), Positives = 135/248 (54%), Gaps = 14/248 (5%)

Query: 444 EEVSAYRKQLELKIHGKDVPKPIKTWHQT----GLTSKIMETIRKLNYEKPMPIQAQALP 499
            +++  R + ++ + G D+P PI T+ Q      + S++++ I    ++ P PIQ QA+P
Sbjct: 2   MKINFLRNKHKIHVQGTDLPDPIATFQQLDQEYKINSRLLQNILDAGFQMPTPIQMQAIP 61

Query: 500 VIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSD 559
           V++ GR+ +  A TGSGKTLAF +P+L  +K         G   LI++PTREL  QIH +
Sbjct: 62  VMLHGRELLASAPTGSGKTLAFSIPILMQLKQPA----NKGFRALIISPTRELASQIHRE 117

Query: 560 IRKFAKVMGVRCVPVYGGSGVAQQIS-ELKRGTEIVVCTPGRMIDILCTSGGKITNLRRV 618
           + K ++  G R   ++  +  A++   +  +  +I+V TP R+I +L      I +L  V
Sbjct: 118 LIKISEGTGFRIHMIHKAAVAAKKFGPKSSKKFDILVTTPNRLIYLLKQDPPGI-DLASV 176

Query: 619 TYLVMDEADRMFD---MGFEPQITRIVQNIRPD-RQTVLFSATFPRQVEILARKVLNKPV 674
            +LV+DE+D++F+    GF  Q+  I         +  +FSATF   VE   +  L+  +
Sbjct: 177 EWLVVDESDKLFEDGKTGFRDQLASIFLACTSHKVRRAMFSATFAYDVEQWCKLNLDNVI 236

Query: 675 EIQVGGRS 682
            + +G R+
Sbjct: 237 SVSIGARN 244

>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 Length = 410

 Score =  374 bits (962), Expect = e-121
 Identities = 125/364 (34%), Positives = 194/364 (53%), Gaps = 10/364 (2%)

Query: 463 PKPIKTWHQTGLTSKIMETIRKLNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFV 522
                T+   GL   ++  I    +EKP  IQ +A+  I+ GRD I  +++G+GKT  F 
Sbjct: 33  VDVTPTFDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFS 92

Query: 523 LPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQ 582
           + +L+ +  Q           LI+APTREL  QI   +      M V+C    GG+ V +
Sbjct: 93  ISVLQCLDIQVR-----ETQALILAPTRELAVQIQKGLLALGDYMNVQCHACIGGTNVGE 147

Query: 583 QISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMGFEPQITRIV 642
            I +L  G  +V  TPGR+ D++     +    R +  LV+DEAD M + GF+ QI  + 
Sbjct: 148 DIRKLDYGQHVVAGTPGRVFDMI---RRRSLRTRAIKMLVLDEADEMLNKGFKEQIYDVY 204

Query: 643 QNIRPDRQTVLFSATFPRQVEILARKVLNKPVEIQVGGRSVVNKDITQL-VEVRPESDRF 701
           + + P  Q VL SAT P ++  +  K +  P+ I V    +  + I Q  V V  E  +F
Sbjct: 205 RYLPPATQVVLISATLPHEILEMTNKFMTDPIRILVKRDELTLEGIKQFFVAVEREEWKF 264

Query: 702 LRLLELLGEWYEKGKILIFVHSQEKCDALFRDLLKHGYPCLSLHGAKDQTDRESTISDFK 761
             L +L  +     + +IF +++ K D L   + +  +   S+HG   Q +RES + +F+
Sbjct: 265 DTLCDLY-DTLTITQAVIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFR 323

Query: 762 SNVCNLLIATSVAARGLDVKELELVINFDAPNHYEDYVHRVGRTGRAGRKGCAITFISEE 821
           S    +LI+T V ARGLDV ++ L+IN+D PN+ E Y+HR+GR+GR GRKG AI F+  +
Sbjct: 324 SGASRVLISTDVWARGLDVPQVSLIINYDLPNNRELYIHRIGRSGRYGRKGVAINFVKND 383

Query: 822 DAKY 825
           D + 
Sbjct: 384 DIRI 387

>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* Length = 394

 Score =  372 bits (958), Expect = e-120
 Identities = 112/360 (31%), Positives = 185/360 (51%), Gaps = 11/360 (3%)

Query: 464 KPIKTWHQTGLTSKIMETIRKLNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVL 523
           K +  +    L   ++  +    +E+P  IQ +A+  I+ G D +  A++G+GKT  F +
Sbjct: 18  KVVYKFDDMELDENLLRGVFGYGFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFSI 77

Query: 524 PMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQ 583
             L+ I           P  L++APTREL  QI   +   A  M ++     GG+   + 
Sbjct: 78  AALQRIDTSVK-----APQALMLAPTRELALQIQKVVMALAFHMDIKVHACIGGTSFVED 132

Query: 584 ISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMGFEPQITRIVQ 643
              L+   +IVV TPGR+ D +     +     ++   ++DEAD M   GF+ QI +I  
Sbjct: 133 AEGLR-DAQIVVGTPGRVFDNI---QRRRFRTDKIKMFILDEADEMLSSGFKEQIYQIFT 188

Query: 644 NIRPDRQTVLFSATFPRQVEILARKVLNKPVEIQVGGRSVVNKDITQL-VEVRPESDRFL 702
            + P  Q VL SAT P  V  +  K +  PV I V    +  + I Q  V V  E  ++ 
Sbjct: 189 LLPPTTQVVLLSATMPNDVLEVTTKFMRNPVRILVKKDELTLEGIKQFYVNVEEEEYKYE 248

Query: 703 RLLELLGEWYEKGKILIFVHSQEKCDALFRDLLKHGYPCLSLHGAKDQTDRESTISDFKS 762
            L +L  +     + +IF +++ K + L   L    +   +++    Q +R++ + +F+S
Sbjct: 249 CLTDLY-DSISVTQAVIFCNTRRKVEELTTKLRNDKFTVSAIYSDLPQQERDTIMKEFRS 307

Query: 763 NVCNLLIATSVAARGLDVKELELVINFDAPNHYEDYVHRVGRTGRAGRKGCAITFISEED 822
               +LI+T + ARG+DV+++ LVIN+D P + E+Y+HR+GR GR GRKG AI F++ ED
Sbjct: 308 GSSRILISTDLLARGIDVQQVSLVINYDLPANKENYIHRIGRGGRFGRKGVAINFVTNED 367

>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 Length = 400

 Score =  368 bits (948), Expect = e-119
 Identities = 120/354 (33%), Positives = 182/354 (51%), Gaps = 12/354 (3%)

Query: 473 GLTSKIMETIRKLNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQ 532
            L  +++  I +  +EKP PIQ +A+PV ++GRD +  AK G+GKT AFV+P L  +K +
Sbjct: 27  YLKRELLMGIFEAGFEKPSPIQEEAIPVAITGRDILARAKNGTGKTAAFVIPTLEKVKPK 86

Query: 533 PPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQISELKRGTE 592
                      LIM PTREL  Q    +R   K  G+ C+   GG+ +   I  L     
Sbjct: 87  LNK-----IQALIMVPTRELALQTSQVVRTLGKHCGISCMVTTGGTNLRDDILRLNETVH 141

Query: 593 IVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMGFEPQITRIVQNIRPDRQTV 652
           I+V TPGR++D+      K+ +L   +  +MDEAD+M    F+  I +I+  + P  Q++
Sbjct: 142 ILVGTPGRVLDLA---SRKVADLSDCSLFIMDEADKMLSRDFKTIIEQILSFLPPTHQSL 198

Query: 653 LFSATFPRQVEILARKVLNKPVEIQVGGRSVVNKDITQL-VEVRPESDRFLRLLELLGEW 711
           LFSATFP  V+    K L+KP EI +    +  K ITQ    V  E  +   L  L    
Sbjct: 199 LFSATFPLTVKEFMVKHLHKPYEINLM-EELTLKGITQYYAFVE-ERQKLHCLNTLF-SK 255

Query: 712 YEKGKILIFVHSQEKCDALFRDLLKHGYPCLSLHGAKDQTDRESTISDFKSNVCNLLIAT 771
            +  + +IF +S  + + L + +   GY C   H    Q +R     +F+      L+ +
Sbjct: 256 LQINQAIIFCNSTNRVELLAKKITDLGYSCYYSHARMKQQERNKVFHEFRQGKVRTLVCS 315

Query: 772 SVAARGLDVKELELVINFDAPNHYEDYVHRVGRTGRAGRKGCAITFISEEDAKY 825
            +  RG+D++ + +VINFD P   E Y+HR+GR+GR G  G AI  I+  D   
Sbjct: 316 DLLTRGIDIQAVNVVINFDFPKTAETYLHRIGRSGRFGHLGLAINLINWNDRFN 369

>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} Length = 414

 Score =  368 bits (948), Expect = e-119
 Identities = 118/364 (32%), Positives = 193/364 (53%), Gaps = 11/364 (3%)

Query: 464 KPIKTWHQTGLTSKIMETIRKLNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVL 523
           + + ++    L+  ++  I    +EKP  IQ +A+   + G D I  A++G+GKT  F +
Sbjct: 37  EIVDSFDDMNLSESLLRGIYAYGFEKPSAIQQRAILPCIKGYDVIAQAQSGTGKTATFAI 96

Query: 524 PMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQ 583
            +L+ I+             L++APTREL QQI   +      MG  C    GG+ V  +
Sbjct: 97  SILQQIELDLK-----ATQALVLAPTRELAQQIQKVVMALGDYMGASCHACIGGTNVRAE 151

Query: 584 ISELKR-GTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMGFEPQITRIV 642
           + +L+     I+V TPGR+ D+L     +  + + +   V+DEAD M   GF+ QI  I 
Sbjct: 152 VQKLQMEAPHIIVGTPGRVFDML---NRRYLSPKYIKMFVLDEADEMLSRGFKDQIYDIF 208

Query: 643 QNIRPDRQTVLFSATFPRQVEILARKVLNKPVEIQVGGRSVVNKDITQL-VEVRPESDRF 701
           Q +  + Q VL SAT P  V  + +K +  P+ I V    +  + I Q  + V  E  + 
Sbjct: 209 QKLNSNTQVVLLSATMPSDVLEVTKKFMRDPIRILVKKEELTLEGIRQFYINVEREEWKL 268

Query: 702 LRLLELLGEWYEKGKILIFVHSQEKCDALFRDLLKHGYPCLSLHGAKDQTDRESTISDFK 761
             L +L  E     + +IF++++ K D L   +    +   ++HG  DQ +R+  + +F+
Sbjct: 269 DTLCDLY-ETLTITQAVIFINTRRKVDWLTEKMHARDFTVSAMHGDMDQKERDVIMREFR 327

Query: 762 SNVCNLLIATSVAARGLDVKELELVINFDAPNHYEDYVHRVGRTGRAGRKGCAITFISEE 821
           S    +LI T + ARG+DV+++ LVIN+D P + E+Y+HR+GR GR GRKG AI  ++EE
Sbjct: 328 SGSSRVLITTDLLARGIDVQQVSLVINYDLPTNRENYIHRIGRGGRFGRKGVAINMVTEE 387

Query: 822 DAKY 825
           D + 
Sbjct: 388 DKRT 391

>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 Length = 253

 Score =  357 bits (919), Expect = e-117
 Identities = 91/250 (36%), Positives = 141/250 (56%), Gaps = 13/250 (5%)

Query: 453 LELKIHGKD--VPKPIKTWHQTGLTSKIMETIRKLNYEKPMPIQAQALPVIMSGRDCIGV 510
           + + + G D      I+ + +  L   I   I   +Y++P PIQ  A+P I+  RD +  
Sbjct: 7   IPVSVTGPDYSATNVIENFDELKLDPTIRNNILLASYQRPTPIQKNAIPAILEHRDIMAC 66

Query: 511 AKTGSGKTLAFVLPMLRHI----KDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKV 566
           A+TGSGKT AF++P++ H+     +Q   +    P  LI+APTREL  QI S+ +KF+  
Sbjct: 67  AQTGSGKTAAFLIPIINHLVCQDLNQQRYSKTAYPKCLILAPTRELAIQILSESQKFSLN 126

Query: 567 MGVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEA 626
             +R   VYGG+    QI E++ G  ++V TPGR++D +        +L    Y+V+DEA
Sbjct: 127 TPLRSCVVYGGADTHSQIREVQMGCHLLVATPGRLVDFI---EKNKISLEFCKYIVLDEA 183

Query: 627 DRMFDMGFEPQITRIVQNIRP----DRQTVLFSATFPRQVEILARKVLNKPVEIQVGGRS 682
           DRM DMGFEPQI +I++        +RQT++FSATFP++++ LA   L   + + VG   
Sbjct: 184 DRMLDMGFEPQIRKIIEESNMPSGINRQTLMFSATFPKEIQKLAADFLYNYIFMTVGRVG 243

Query: 683 VVNKDITQLV 692
             +  I Q +
Sbjct: 244 STSDSIKQEI 253

>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 Length = 367

 Score =  358 bits (922), Expect = e-116
 Identities = 120/351 (34%), Positives = 188/351 (53%), Gaps = 23/351 (6%)

Query: 473 GLTSKIMETIRKLNYEKPMPIQAQALPVIMSGR-DCIGVAKTGSGKTLAFVLPMLRHIKD 531
            L+  I+  IR   +EKP  IQ + +P+ ++   + +  A+TGSGKT +F +P++  + +
Sbjct: 12  NLSDNILNAIRNKGFEKPTDIQMKVIPLFLNDEYNIVAQARTGSGKTASFAIPLIELVNE 71

Query: 532 QPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQISELKRGT 591
                  +G   +I+ PTREL  Q+  +I        ++   +YGG  +  QI  LK   
Sbjct: 72  N------NGIEAIILTPTRELAIQVADEIESLKGNKNLKIAKIYGGKAIYPQIKALKNA- 124

Query: 592 EIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMGFEPQITRIVQNIRPDRQT 651
            IVV TPGR++D +        NL+ V Y ++DEAD M +MGF   + +I+     D++ 
Sbjct: 125 NIVVGTPGRILDHI---NRGTLNLKNVKYFILDEADEMLNMGFIKDVEKILNACNKDKRI 181

Query: 652 VLFSATFPRQVEILARKVLNKPVEIQVGGRSVVNKDITQLVEVRPESDRF---LRLLELL 708
           +LFSAT PR++  LA+K +     I+       N +I Q      E++RF    RLL+  
Sbjct: 182 LLFSATMPREILNLAKKYMGDYSFIKAKI----NANIEQSYVEVNENERFEALCRLLK-- 235

Query: 709 GEWYEKGKILIFVHSQEKCDALFRDLLKHGYPCLSLHGAKDQTDRESTISDFKSNVCNLL 768
               ++   L+F  ++     L   L   G+   ++HG   Q+ RE  I  FK     +L
Sbjct: 236 ---NKEFYGLVFCKTKRDTKELASMLRDIGFKAGAIHGDLSQSQREKVIRLFKQKKIRIL 292

Query: 769 IATSVAARGLDVKELELVINFDAPNHYEDYVHRVGRTGRAGRKGCAITFIS 819
           IAT V +RG+DV +L  VIN+  P + E Y+HR+GRTGRAG+KG AI+ I+
Sbjct: 293 IATDVMSRGIDVNDLNCVINYHLPQNPESYMHRIGRTGRAGKKGKAISIIN 343

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

 Score =  357 bits (918), Expect = e-115
 Identities = 113/350 (32%), Positives = 185/350 (52%), Gaps = 29/350 (8%)

Query: 474 LTSKIMETIRKLNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPML-RHIKDQ 532
           +  KI + IR++ ++    +Q++ +P+++ G++ +  AKTGSGKT A+ +P+L   +K  
Sbjct: 1   MNEKIEQAIREMGFKNFTEVQSKTIPLMLQGKNVVVRAKTGSGKTAAYAIPILELGMK-- 58

Query: 533 PPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQISELKRGTE 592
                      L++ PTREL +Q+ S IR   + M  +   VYGG     QI+ + R  +
Sbjct: 59  ----------SLVVTPTRELTRQVASHIRDIGRYMDTKVAEVYGGMPYKAQINRV-RNAD 107

Query: 593 IVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMGFEPQITRIVQNIRPDRQTV 652
           IVV TPGR++D+       + +L     +++DEAD MF+MGF   I  I+      + T 
Sbjct: 108 IVVATPGRLLDLW---SKGVIDLSSFEIVIIDEADLMFEMGFIDDIKIILAQTSNRKITG 164

Query: 653 LFSATFPRQVEILARKVLNKPVEIQVGGRSVVNKDITQ-LVEVRPESDRFLRLLELLGEW 711
           LFSAT P ++  + +  +    EI+     +   ++    V V+ +    ++ L      
Sbjct: 165 LFSATIPEEIRKVVKDFITNYEEIEA---CIGLANVEHKFVHVKDDWRSKVQALRE---- 217

Query: 712 YEKGKILIFVHSQEKCDALFRDLLKHGYPCLSLHGAKDQTDRESTISDFKSNVCNLLIAT 771
            +   +++FV ++ +       L++     + L G   Q+ R   I  F+    ++LI T
Sbjct: 218 NKDKGVIVFVRTRNRVA----KLVRLFDNAIELRGDLPQSVRNRNIDAFREGEYDMLITT 273

Query: 772 SVAARGLDVKELELVINFDAPNHYEDYVHRVGRTGRAGRKGCAITFISEE 821
            VA+RGLD+  +E VINFDAP     Y+HR+GRTGR GRKG AITFI  E
Sbjct: 274 DVASRGLDIPLVEKVINFDAPQDLRTYIHRIGRTGRMGRKGEAITFILNE 323

>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 Length = 412

 Score =  349 bits (898), Expect = e-111
 Identities = 107/383 (27%), Positives = 188/383 (49%), Gaps = 25/383 (6%)

Query: 454 ELKIHGKDVPKP---IKTWHQTGLTSKIMETIRKLNYEKPMPIQAQALPVIMSG--RDCI 508
           ++++  +D   P   +K++ +  L  ++++ +  + + +P  IQ  ALP++++   ++ I
Sbjct: 9   QVEVLQRDPNSPLYSVKSFEELRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLI 68

Query: 509 GVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVM- 567
             +++G+GKT AFVL ML  ++          P  L ++PT EL  Q    I +  K   
Sbjct: 69  AQSQSGTGKTAAFVLAMLSQVEPANK-----YPQCLCLSPTYELALQTGKVIEQMGKFYP 123

Query: 568 GVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEAD 627
            ++      G+ + +     K   +IV+ TPG ++D    S  K  + +++   V+DEAD
Sbjct: 124 ELKLAYAVRGNKLERG---QKISEQIVIGTPGTVLDWC--SKLKFIDPKKIKVFVLDEAD 178

Query: 628 RMFD-MGFEPQITRIVQNIRPDRQTVLFSATFPRQVEILARKVLNKPVEIQVGGRSVVNK 686
            M    G + Q  RI + +  + Q +LFSATF   V   A+KV+  P  I++        
Sbjct: 179 VMIATQGHQDQSIRIQRMLPRNCQMLLFSATFEDSVWKFAQKVVPDPNVIKLKREEETLD 238

Query: 687 DITQL-VEVRPESDRFLRLLELLGEWYEKGKILIFVHSQEKCDALFRDLLKHGYPCLSLH 745
            I Q  V      ++F  L  L        + +IF H+++    L  +L K G+    L 
Sbjct: 239 TIKQYYVLCSSRDEKFQALCNLY-GAITIAQAMIFCHTRKTASWLAAELSKEGHQVALLS 297

Query: 746 GAKDQTDRESTISDFKSNVCNLLIATSVAARGLDVKELELVINFDAPN------HYEDYV 799
           G      R + I  F+     +L+ T+V ARG+DV+++ +VINFD P         E Y+
Sbjct: 298 GEMMVEQRAAVIERFREGKEKVLVTTNVCARGIDVEQVSVVINFDLPVDKDGNPDNETYL 357

Query: 800 HRVGRTGRAGRKGCAITFISEED 822
           HR+GRTGR G++G A+  +  + 
Sbjct: 358 HRIGRTGRFGKRGLAVNMVDSKH 380

>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* Length = 563

 Score =  351 bits (901), Expect = e-110
 Identities = 113/498 (22%), Positives = 219/498 (43%), Gaps = 41/498 (8%)

Query: 396 DEDDDEFMKRVKKTKAEKLSIVDHSKIDYQPFRKNFYIEVKEIARMTPEEVSAYRKQLEL 455
           + D   F +  +   + +      +       R        +      +   +    +  
Sbjct: 8   NRDQRNFGRNQRNNNSNRYRNSRFNS------RPRTRSREDDDEVHFDKTTFSKLIHVPK 61

Query: 456 KIHGKDVPKPIKTWHQTGLTSKIMETIRKLNYEKPMPIQAQALPVIMSG--RDCIGVAKT 513
           + + K+V        +  L  +I + I ++ +    P+Q + +  I+S    D I  AKT
Sbjct: 62  EDNSKEVTLD-SLLEEGVLDKEIHKAITRMEFPGLTPVQQKTIKPILSSEDHDVIARAKT 120

Query: 514 GSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAK----VMGV 569
           G+GKT AF++P+ +H+       +      +I+APTR+L  QI ++++K       +   
Sbjct: 121 GTGKTFAFLIPIFQHL-INTKFDSQYMVKAVIVAPTRDLALQIEAEVKKIHDMNYGLKKY 179

Query: 570 RCVPVYGGSGVAQQISEL-KRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADR 628
            CV + GG+     ++++ K    IV+ TPGR+ID+L          R V Y V+DEADR
Sbjct: 180 ACVSLVGGTDFRAAMNKMNKLRPNIVIATPGRLIDVL--EKYSNKFFRFVDYKVLDEADR 237

Query: 629 MFDMGFEPQITRIVQNI-------RPDRQTVLFSATFPRQVEILARKVLNKPVEIQVG-- 679
           + ++GF   +  I   +         + +T+LFSAT   +V+ LA  ++NK   + +   
Sbjct: 238 LLEIGFRDDLETISGILNEKNSKSADNIKTLLFSATLDDKVQKLANNIMNKKECLFLDTV 297

Query: 680 --GRSVVNKDITQLVEVRPESDRFLRLLEL-----LGEWYEKGKILIFVHSQEKCDAL-- 730
                  ++ I Q V +  +    +          + E     K +IF  + +    L  
Sbjct: 298 DKNEPEAHERIDQSVVISEKFANSIFAAVEHIKKQIKERDSNYKAIIFAPTVKFTSFLCS 357

Query: 731 -FRDLLKHGYPCLSLHGAKDQTDRESTISDFKSNVCNLLIATSVAARGLDVKELELVINF 789
             ++  K   P L  HG   Q  R S +  FK +   +L+ T V ARG+D   +  V+  
Sbjct: 358 ILKNEFKKDLPILEFHGKITQNKRTSLVKRFKKDESGILVCTDVGARGMDFPNVHEVLQI 417

Query: 790 DAPNHYEDYVHRVGRTGRAGRKGCAITFISEEDAKYSPDL--VKALELSEQVVP---DDL 844
             P+   +Y+HR+GRT R+G++G ++ FI +++  +  +L   K + +++Q      +++
Sbjct: 418 GVPSELANYIHRIGRTARSGKEGSSVLFICKDELPFVRELEDAKNIVIAKQEKYEPSEEI 477

Query: 845 KALADSFMAKVNQGLEQA 862
           K+     + +  + +   
Sbjct: 478 KSEVLEAVTEEPEDISDI 495

>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 Length = 391

 Score =  343 bits (881), Expect = e-109
 Identities = 106/355 (29%), Positives = 192/355 (54%), Gaps = 15/355 (4%)

Query: 473 GLTSKIMETIRKLNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQ 532
            L  +++  I    +E P  +Q + +P  + G D +  AK+G GKT  FVL  L+ ++  
Sbjct: 14  LLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQLEPV 73

Query: 533 PPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVM-GVRCVPVYGGSGVAQQISELKRGT 591
                      L+M  TREL  QI  +  +F+K M  V+    +GG  + +    LK+  
Sbjct: 74  TG-----QVSVLVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLKKNC 128

Query: 592 E-IVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFD-MGFEPQITRIVQNIRPDR 649
             IVV TPGR++ +      K  NL+ + + ++DE D+M + +     +  I +    ++
Sbjct: 129 PHIVVGTPGRILALA---RNKSLNLKHIKHFILDECDKMLEQLDMRRDVQEIFRMTPHEK 185

Query: 650 QTVLFSATFPRQVEILARKVLNKPVEIQVGGRS-VVNKDITQL-VEVRPESDRFLRLLEL 707
           Q ++FSAT  +++  + RK +  P+EI V   + +    + Q  V+++ ++++  +L +L
Sbjct: 186 QVMMFSATLSKEIRPVCRKFMQDPMEIFVDDETKLTLHGLQQYYVKLK-DNEKNRKLFDL 244

Query: 708 LGEWYEKGKILIFVHSQEKCDALFRDLLKHGYPCLSLHGAKDQTDRESTISDFKSNVCNL 767
           L +  E  +++IFV S ++C AL + L++  +P +++H    Q +R S    FK     +
Sbjct: 245 L-DVLEFNQVVIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQEERLSRYQQFKDFQRRI 303

Query: 768 LIATSVAARGLDVKELELVINFDAPNHYEDYVHRVGRTGRAGRKGCAITFISEED 822
           L+AT++  RG+D++ + +  N+D P   + Y+HRV R GR G KG AITF+S+E+
Sbjct: 304 LVATNLFGRGMDIERVNIAFNYDMPEDSDTYLHRVARAGRFGTKGLAITFVSDEN 358

>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* Length = 395

 Score =  340 bits (875), Expect = e-108
 Identities = 113/368 (30%), Positives = 194/368 (52%), Gaps = 25/368 (6%)

Query: 466 IKTWHQTGLTSKIMETIRKLNYEKPMPIQAQALPVIMSG--RDCIGVAKTGSGKTLAFVL 523
            K++ + GL  ++++ I  + ++KP  IQ +ALP+++    R+ I  +++G+GKT AF L
Sbjct: 4   AKSFDELGLAPELLKGIYAMKFQKPSKIQERALPLLLHNPPRNMIAQSQSGTGKTAAFSL 63

Query: 524 PMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVMGVRCV-PVYGGSGVAQ 582
            ML  +  +        P  + +AP+REL +Q    +++  K   +     V       +
Sbjct: 64  TMLTRVNPEDA-----SPQAICLAPSRELARQTLEVVQEMGKFTKITSQLIVPDSFEKNK 118

Query: 583 QISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDM-GFEPQITRI 641
           QI       +++V TPG ++D++     K+  L+++   V+DEAD M D  G   Q  R+
Sbjct: 119 QI-----NAQVIVGTPGTVLDLM---RRKLMQLQKIKIFVLDEADNMLDQQGLGDQCIRV 170

Query: 642 VQNIRPDRQTVLFSATFPRQVEILARKVLNKPVEIQVGGRSVVNKDITQL-VEVRPESDR 700
            + +  D Q VLFSATF   V   A+K++     +++    V    I QL ++ + E+D+
Sbjct: 171 KRFLPKDTQLVLFSATFADAVRQYAKKIVPNANTLELQTNEVNVDAIKQLYMDCKNEADK 230

Query: 701 FLRLLELLGEWYEKGKILIFVHSQEKCDALFRDLLKHGYPCLSLHGAKDQTDRESTISDF 760
           F  L EL       G  +IFV +++  + L+  L   G+    LHG     +R+  I DF
Sbjct: 231 FDVLTELY-GLMTIGSSIIFVATKKTANVLYGKLKSEGHEVSILHGDLQTQERDRLIDDF 289

Query: 761 KSNVCNLLIATSVAARGLDVKELELVINFDAPNH------YEDYVHRVGRTGRAGRKGCA 814
           +     +LI T+V ARG+D+  + +V+N+D P           Y+HR+GRTGR GRKG A
Sbjct: 290 REGRSKVLITTNVLARGIDIPTVSMVVNYDLPTLANGQADPATYIHRIGRTGRFGRKGVA 349

Query: 815 ITFISEED 822
           I+F+ +++
Sbjct: 350 ISFVHDKN 357

>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} Length = 479

 Score =  341 bits (877), Expect = e-107
 Identities = 115/458 (25%), Positives = 205/458 (44%), Gaps = 35/458 (7%)

Query: 379 DSDSDYGDLENDEKPLEDEDDDEFMKRVKKTKAEKLSIVDHSKIDYQPFRKNFYIEVKEI 438
           D      +  ++    E++   +    V KT A      +  K D             + 
Sbjct: 11  DEQEAAAESLSNLHLKEEKIKPDTNGAVVKTNANAEKTDEEEKED----------RAAQS 60

Query: 439 ARMTPEEVSAYRKQLELKIHGKDVPKP---IKTWHQTGLTSKIMETIRKLNYEKPMPIQA 495
                   +      ++++  +D   P   +K++ +  L  ++++ +  + + +P  IQ 
Sbjct: 61  LLNKLIRSNLVDNTNQVEVLQRDPNSPLYSVKSFEELRLKPQLLQGVYAMGFNRPSKIQE 120

Query: 496 QALPVIMSG--RDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELV 553
            ALP++++   ++ I  +++G+GKT AFVL ML  ++          P  L ++PT EL 
Sbjct: 121 NALPLMLAEPPQNLIAQSQSGTGKTAAFVLAMLSQVEPANKY-----PQCLCLSPTYELA 175

Query: 554 QQIHSDIRKFAKVM-GVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGGKI 612
            Q    I +  K    ++      G+ + +     K   +IV+ TPG ++D    S  K 
Sbjct: 176 LQTGKVIEQMGKFYPELKLAYAVRGNKLERG---QKISEQIVIGTPGTVLDWC--SKLKF 230

Query: 613 TNLRRVTYLVMDEADRMFD-MGFEPQITRIVQNIRPDRQTVLFSATFPRQVEILARKVLN 671
            + +++   V+DEAD M    G + Q  RI + +  + Q +LFSATF   V   A+KV+ 
Sbjct: 231 IDPKKIKVFVLDEADVMIATQGHQDQSIRIQRMLPRNCQMLLFSATFEDSVWKFAQKVVP 290

Query: 672 KPVEIQVGGRSVVNKDITQL-VEVRPESDRFLRLLELLGEWYEKGKILIFVHSQEKCDAL 730
            P  I++         I Q  V      ++F  L  L        + +IF H+++    L
Sbjct: 291 DPNVIKLKREEETLDTIKQYYVLCSSRDEKFQALCNLY-GAITIAQAMIFCHTRKTASWL 349

Query: 731 FRDLLKHGYPCLSLHGAKDQTDRESTISDFKSNVCNLLIATSVAARGLDVKELELVINFD 790
             +L K G+    L G      R + I  F+     +L+ T+V ARG+DV+++ +VINFD
Sbjct: 350 AAELSKEGHQVALLSGEMMVEQRAAVIERFREGKEKVLVTTNVCARGIDVEQVSVVINFD 409

Query: 791 APN------HYEDYVHRVGRTGRAGRKGCAITFISEED 822
            P         E Y+HR+GRTGR G++G A+  +  + 
Sbjct: 410 LPVDKDGNPDNETYLHRIGRTGRFGKRGLAVNMVDSKH 447

>3sqw_A ATP-dependent RNA helicase MSS116, mitochondrial; RECA fold, RNA dependent ATPase, RNA helicase; HET: ANP; 1.91A {Saccharomyces cerevisiae S288C} Length = 579

 Score =  344 bits (883), Expect = e-107
 Identities = 114/454 (25%), Positives = 209/454 (46%), Gaps = 35/454 (7%)

Query: 473 GLTSKIMETIRKLNYEKPMPIQAQALPVIMSG--RDCIGVAKTGSGKTLAFVLPMLRHIK 530
            L  +I + I ++ +    P+Q + +  I+S    D I  AKTG+GKT AF++P+ +H+ 
Sbjct: 27  VLDKEIHKAITRMEFPGLTPVQQKTIKPILSSEDHDVIARAKTGTGKTFAFLIPIFQHL- 85

Query: 531 DQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAK----VMGVRCVPVYGGSGVAQQISE 586
                 +      +I+APTR+L  QI ++++K       +    CV + GG+     +++
Sbjct: 86  INTKFDSQYMVKAVIVAPTRDLALQIEAEVKKIHDMNYGLKKYACVSLVGGTDFRAAMNK 145

Query: 587 L-KRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMGFEPQITRIVQNI 645
           + K    IV+ TPGR+ID+L          R V Y V+DEADR+ ++GF   +  I   +
Sbjct: 146 MNKLRPNIVIATPGRLIDVL--EKYSNKFFRFVDYKVLDEADRLLEIGFRDDLETISGIL 203

Query: 646 -------RPDRQTVLFSATFPRQVEILARKVLNKPVEIQVG----GRSVVNKDITQ-LVE 693
                    + +T+LFSAT   +V+ LA  ++NK   + +          ++ I Q +V 
Sbjct: 204 NEKNSKSADNIKTLLFSATLDDKVQKLANNIMNKKECLFLDTVDKNEPEAHERIDQSVVI 263

Query: 694 VRPESDRFLRLLEL----LGEWYEKGKILIFVHSQEKCDAL---FRDLLKHGYPCLSLHG 746
               ++     +E     + E     K +IF  + +    L    ++  K   P L  HG
Sbjct: 264 SEKFANSIFAAVEHIKKQIKERDSNYKAIIFAPTVKFTSFLCSILKNEFKKDLPILEFHG 323

Query: 747 AKDQTDRESTISDFKSNVCNLLIATSVAARGLDVKELELVINFDAPNHYEDYVHRVGRTG 806
              Q  R S +  FK +   +L+ T V ARG+D   +  V+    P+   +Y+HR+GRT 
Sbjct: 324 KITQNKRTSLVKRFKKDESGILVCTDVGARGMDFPNVHEVLQIGVPSELANYIHRIGRTA 383

Query: 807 RAGRKGCAITFISEEDAKYSPDL--VKALELSEQVVP---DDLKALADSFMAKVNQGLEQ 861
           R+G++G ++ FI +++  +  +L   K + +++Q      +++K+     + +  + +  
Sbjct: 384 RSGKEGSSVLFICKDELPFVRELEDAKNIVIAKQEKYEPSEEIKSEVLEAVTEEPEDISD 443

Query: 862 AHGTGYGGSGFKFNEEEDEKRKAAKKAQAKEYGF 895
                   S     +E     +      A  YG 
Sbjct: 444 IV-ISLISSYRSCIKEYRFSERRILPEIASTYGV 476

>3oiy_A Reverse gyrase helicase domain; topoisomerase, DNA supercoiling, archaea, isomeras; 2.35A {Thermotoga maritima} PDB: 3p4y_A 3p4x_A* Length = 414

 Score =  313 bits (803), Expect = 9e-98
 Identities = 73/419 (17%), Positives = 144/419 (34%), Gaps = 59/419 (14%)

Query: 474 LTSKIMETIRKLNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQP 533
                    +K   +     Q      I+ G+    VA TG GKT   ++  L   +   
Sbjct: 6   EYEDFRSFFKKKFGKDLTGYQRLWAKRIVQGKSFTMVAPTGVGKTTFGMMTALWLARKGK 65

Query: 534 PVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQISELKR---- 589
                      ++ PT  LV+Q    ++K A    V+    Y      ++    K     
Sbjct: 66  KS--------ALVFPTVTLVKQTLERLQKLAD-EKVKIFGFYSSMKKEEKEKFEKSFEED 116

Query: 590 GTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMGFEPQITRIVQNIRPDR 649
              I+V +   +         K+ + +R  ++ +D+ D +           ++  I  + 
Sbjct: 117 DYHILVFSTQFVSKNR----EKL-SQKRFDFVFVDDVDAVLKASRNIDTLLMMVGIPEEI 171

Query: 650 QTVLFSATFPRQVEILARKV---------------------LNKPVEIQVGGRSVVNKDI 688
               FS     ++    + +                         +   VG    V ++I
Sbjct: 172 IRKAFSTIKQGKIYERPKNLKPGILVVSSATAKPRGIRPLLFRDLLNFTVGRLVSVARNI 231

Query: 689 TQLVEVRPESDRFLRLLELLGEWYEKGKILIFVHSQEKCDALFRDLLKHGYPCLSLHGAK 748
           T +       ++ + LLE+  +      ILIF  ++E+   L+  L +  +         
Sbjct: 232 THVRISSRSKEKLVELLEIFRD-----GILIFAQTEEEGKELYEYLKRFKFNVGETWS-- 284

Query: 749 DQTDRESTISDFKSNVCNLLIATSV----AARGLDVKE-LELVINFDAPNH--YEDYVHR 801
              + E    DFK    N+LI          RG+D+ E ++ VI +  P+      Y+  
Sbjct: 285 ---EFEKNFEDFKVGKINILIGVQAYYGKLTRGVDLPERIKYVIFWGTPSGPDVYTYIQA 341

Query: 802 VGRTGRAGRKGC--AITFISEEDAKYSPDLVKALE-LSEQVVPDDLKALADSFMAKVNQ 857
            GR+ R         ++ I EED +    L   L  ++E+ + ++ +A     + +V +
Sbjct: 342 SGRSSRILNGVLVKGVSVIFEEDEEIFESLKTRLLLIAEEEIIEEAEANWKELVHEVEE 400

>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} Length = 249

 Score =  264 bits (676), Expect = 1e-81
 Identities = 85/216 (39%), Positives = 122/216 (56%), Gaps = 7/216 (3%)

Query: 463 PKPIKTWHQTGLTSKIMETIRKLNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFV 522
            +  KT+   G+T  + E   +L + KP  IQ +A+P+ + GRD IG+A+TGSGKT AF 
Sbjct: 39  EEETKTFKDLGVTDVLCEACDQLGWTKPTKIQIEAIPLALQGRDIIGLAETGSGKTGAFA 98

Query: 523 LPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQ 582
           LP+L  + + P          L++ PTREL  QI          +GV+   + GG     
Sbjct: 99  LPILNALLETPQ-----RLFALVLTPTRELAFQISEQFEALGSSIGVQSAVIVGGIDSMS 153

Query: 583 QISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMGFEPQITRIV 642
           Q   L +   I++ TPGR+ID L     K  NLR + YLVMDEADR+ +M FE ++ +I+
Sbjct: 154 QSLALAKKPHIIIATPGRLIDHL--ENTKGFNLRALKYLVMDEADRILNMDFETEVDKIL 211

Query: 643 QNIRPDRQTVLFSATFPRQVEILARKVLNKPVEIQV 678
           + I  DR+T LFSAT  ++V+ L R  L  PV+  V
Sbjct: 212 KVIPRDRKTFLFSATMTKKVQKLQRAALKNPVKCAV 247

>2pl3_A Probable ATP-dependent RNA helicase DDX10; DEAD, structural genomics, structural genomic consortium, SGC, hydrolase; HET: ADP; 2.15A {Homo sapiens} Length = 236

 Score =  251 bits (642), Expect = 3e-77
 Identities = 76/235 (32%), Positives = 120/235 (51%), Gaps = 9/235 (3%)

Query: 444 EEVSAYRKQLELKIHGKDVPKPIKTWHQTGLTSKIMETIRKLNYEKPMPIQAQALPVIMS 503
           E +S   +  E     K     I  +    L+ K ++ +++  Y     IQ Q + + + 
Sbjct: 7   ESISRLMQNYE-----KINVNEITRFSDFPLSKKTLKGLQEAQYRLVTEIQKQTIGLALQ 61

Query: 504 GRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKF 563
           G+D +G AKTGSGKTLAF++P+L  +      +  DG   LI++PTREL  Q    +RK 
Sbjct: 62  GKDVLGAAKTGSGKTLAFLVPVLEALYRLQWTST-DGLGVLIISPTRELAYQTFEVLRKV 120

Query: 564 AKVMGVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVM 623
            K        + GG  +  +   +     I+VCTPGR++  +  +     +   +  LV+
Sbjct: 121 GKNHDFSAGLIIGGKDLKHEAERIN-NINILVCTPGRLLQHMDETVS--FHATDLQMLVL 177

Query: 624 DEADRMFDMGFEPQITRIVQNIRPDRQTVLFSATFPRQVEILARKVLNKPVEIQV 678
           DEADR+ DMGF   +  +++N+   RQT+LFSAT  + V+ LAR  L  P  + V
Sbjct: 178 DEADRILDMGFADTMNAVIENLPKKRQTLLFSATQTKSVKDLARLSLKNPEYVWV 232

>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 Length = 207

 Score =  243 bits (623), Expect = 9e-75
 Identities = 85/206 (41%), Positives = 117/206 (56%), Gaps = 7/206 (3%)

Query: 473 GLTSKIMETIRKLNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQ 532
            L  +I+E +       P PIQA ALP+ + G+D IG A+TG+GKTLAF LP+   +   
Sbjct: 7   PLKPEILEALHGRGLTTPTPIQAAALPLALEGKDLIGQARTGTGKTLAFALPIAERL--A 64

Query: 533 PPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQISELKRGTE 592
           P    G  P  L++ PTREL  Q+ S++   A    ++ V VYGG+G  +Q   L RG +
Sbjct: 65  PSQERGRKPRALVLTPTRELALQVASELTAVAP--HLKVVAVYGGTGYGKQKEALLRGAD 122

Query: 593 IVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMGFEPQITRIVQNIRPDRQTV 652
            VV TPGR +D L      + +L RV   V+DEAD M  MGFE ++  ++    P RQT+
Sbjct: 123 AVVATPGRALDYL---RQGVLDLSRVEVAVLDEADEMLSMGFEEEVEALLSATPPSRQTL 179

Query: 653 LFSATFPRQVEILARKVLNKPVEIQV 678
           LFSAT P   + LA + +  PV I V
Sbjct: 180 LFSATLPSWAKRLAERYMKNPVLINV 205

>1vec_A ATP-dependent RNA helicase P54; DEAD-box protein, RNA binding protein; HET: TLA; 2.01A {Homo sapiens} SCOP: c.37.1.19 Length = 206

 Score =  242 bits (619), Expect = 3e-74
 Identities = 63/205 (30%), Positives = 111/205 (54%), Gaps = 9/205 (4%)

Query: 473 GLTSKIMETIRKLNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQ 532
            L  +++  I ++ +EKP PIQ +++P+ +SGRD +  AK G+GK+ A+++P+L  +   
Sbjct: 9   CLKRELLMGIFEMGWEKPSPIQEESIPIALSGRDILARAKNGTGKSGAYLIPLLERLD-- 66

Query: 533 PPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVM-GVRCVPVYGGSGVAQQISELKRGT 591
                 D    +++ PTREL  Q+     + +K M G + +   GG+ +   I  L    
Sbjct: 67  ---LKKDNIQAMVIVPTRELALQVSQICIQVSKHMGGAKVMATTGGTNLRDDIMRLDDTV 123

Query: 592 EIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMGFEPQITRIVQNIRPDRQT 651
            +V+ TPGR++D++      +  +  V  +V+DEAD++    F   +  I+  +  +RQ 
Sbjct: 124 HVVIATPGRILDLI---KKGVAKVDHVQMIVLDEADKLLSQDFVQIMEDIILTLPKNRQI 180

Query: 652 VLFSATFPRQVEILARKVLNKPVEI 676
           +L+SATFP  V+      L KP EI
Sbjct: 181 LLYSATFPLSVQKFMNSHLEKPYEI 205

>1q0u_A Bstdead; DEAD protein, RNA binding protein; 1.85A {Geobacillus stearothermophilus} SCOP: c.37.1.19 Length = 219

 Score =  241 bits (618), Expect = 5e-74
 Identities = 64/210 (30%), Positives = 105/210 (50%), Gaps = 12/210 (5%)

Query: 473 GLTSKIMETIRKLNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQ 532
                I+E I+ L + KP  IQ + +P  + G   +G ++TG+GKT A++LP++  IK  
Sbjct: 10  PFQPFIIEAIKTLRFYKPTEIQERIIPGALRGESMVGQSQTGTGKTHAYLLPIMEKIK-- 67

Query: 533 PPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVM----GVRCVPVYGGSGVAQQISELK 588
                      +I APTREL  QI+ +  K  K       +    + GG+   + + +L 
Sbjct: 68  ---PERAEVQAVITAPTRELATQIYHETLKITKFCPKDRMIVARCLIGGTDKQKALEKLN 124

Query: 589 RGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMGFEPQITRIVQNIRPD 648
               IV+ TPGR+ D +     +  ++     LV+DEAD M DMGF   + +I   +  D
Sbjct: 125 VQPHIVIGTPGRINDFI---REQALDVHTAHILVVDEADLMLDMGFITDVDQIAARMPKD 181

Query: 649 RQTVLFSATFPRQVEILARKVLNKPVEIQV 678
            Q ++FSAT P +++   +K +  P  + V
Sbjct: 182 LQMLVFSATIPEKLKPFLKKYMENPTFVHV 211

>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} Length = 262

 Score =  230 bits (589), Expect = 3e-69
 Identities = 70/204 (34%), Positives = 116/204 (56%), Gaps = 4/204 (1%)

Query: 474 LTSKIMETIRKLNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQP 533
           +    ++ I+++ +     IQ +++  ++ GRD +  AKTGSGKTLAF++P +  I    
Sbjct: 61  VNENTLKAIKEMGFTNMTEIQHKSIRPLLEGRDLLAAAKTGSGKTLAFLIPAVELIVKLR 120

Query: 534 PVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQISELKRGTEI 593
                +G   LI++PTREL  Q    +++           + GGS  + +  +L  G  I
Sbjct: 121 F-MPRNGTGVLILSPTRELAMQTFGVLKELMTHHVHTYGLIMGGSNRSAEAQKLGNGINI 179

Query: 594 VVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMGFEPQITRIVQNIRPDRQTVL 653
           +V TPGR++D +  + G     + +  LV+DEADR+ D+GFE ++ +I++ +   RQT+L
Sbjct: 180 IVATPGRLLDHMQNTPG--FMYKNLQCLVIDEADRILDVGFEEELKQIIKLLPTRRQTML 237

Query: 654 FSATFPRQVEILARKVLNK-PVEI 676
           FSAT  R+VE LAR  L K P+ +
Sbjct: 238 FSATQTRKVEDLARISLKKEPLYV 261

>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* Length = 237

 Score =  229 bits (586), Expect = 4e-69
 Identities = 69/216 (31%), Positives = 107/216 (49%), Gaps = 9/216 (4%)

Query: 464 KPIKTWHQTGLTSKIMETIRKLNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVL 523
           + +  +    L   ++  I    +EKP  IQ +A+   + G D I  A++G+GKT  F +
Sbjct: 27  EIVDNFDDMNLKESLLRGIYAYGFEKPSAIQQRAIIPCIKGYDVIAQAQSGTGKTATFAI 86

Query: 524 PMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQ 583
            +L+ ++ +           L++APTREL QQI   I      MG  C    GG+ V  +
Sbjct: 87  SILQQLEIEFK-----ETQALVLAPTRELAQQIQKVILALGDYMGATCHACIGGTNVRNE 141

Query: 584 ISELK-RGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMGFEPQITRIV 642
           + +L+     IVV TPGR+ D+L     +  + + +   V+DEAD M   GF+ QI  I 
Sbjct: 142 MQKLQAEAPHIVVGTPGRVFDML---NRRYLSPKWIKMFVLDEADEMLSRGFKDQIYEIF 198

Query: 643 QNIRPDRQTVLFSATFPRQVEILARKVLNKPVEIQV 678
           Q +    Q VL SAT P  V  + +K +  P+ I V
Sbjct: 199 QKLNTSIQVVLLSATMPTDVLEVTKKFMRDPIRILV 234

>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 Length = 224

 Score =  226 bits (578), Expect = 3e-68
 Identities = 66/215 (30%), Positives = 102/215 (47%), Gaps = 9/215 (4%)

Query: 464 KPIKTWHQTGLTSKIMETIRKLNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVL 523
           K +  +    L   ++  +    +E+P  IQ +A+  I+ G D +  A++G+GKT  F +
Sbjct: 11  KVVYKFDDMELDENLLRGVFGYGFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFSI 70

Query: 524 PMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQ 583
             L+ I           P  L++APTREL  QI   +   A  M ++     GG+   + 
Sbjct: 71  AALQRIDTSVK-----APQALMLAPTRELALQIQKVVMALAFHMDIKVHACIGGTSFVED 125

Query: 584 ISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMGFEPQITRIVQ 643
              L R  +IVV TPGR+ D +     +     ++   ++DEAD M   GF+ QI +I  
Sbjct: 126 AEGL-RDAQIVVGTPGRVFDNI---QRRRFRTDKIKMFILDEADEMLSSGFKEQIYQIFT 181

Query: 644 NIRPDRQTVLFSATFPRQVEILARKVLNKPVEIQV 678
            + P  Q VL SAT P  V  +  K +  PV I V
Sbjct: 182 LLPPTTQVVLLSATMPNDVLEVTTKFMRNPVRILV 216

>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 Length = 220

 Score =  222 bits (569), Expect = 4e-67
 Identities = 60/209 (28%), Positives = 105/209 (50%), Gaps = 11/209 (5%)

Query: 473 GLTSKIMETIRKLNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQ 532
            L  +++  I    +E P  +Q + +P  + G D +  AK+G GKT  FVL  L+ ++  
Sbjct: 20  LLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQLEPV 79

Query: 533 PPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVM-GVRCVPVYGGSGVAQQISELKRGT 591
                      L+M  TREL  QI  +  +F+K M  V+    +GG  + +    LK+  
Sbjct: 80  TG-----QVSVLVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLKKNC 134

Query: 592 E-IVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFD-MGFEPQITRIVQNIRPDR 649
             IVV TPGR++ +      K  NL+ + + ++DE D+M + +     +  I +    ++
Sbjct: 135 PHIVVGTPGRILALA---RNKSLNLKHIKHFILDECDKMLEQLDMRRDVQEIFRMTPHEK 191

Query: 650 QTVLFSATFPRQVEILARKVLNKPVEIQV 678
           Q ++FSAT  +++  + RK +  P+EI V
Sbjct: 192 QVMMFSATLSKEIRPVCRKFMQDPMEIFV 220

>2jgn_A DBX, DDX3, ATP-dependent RNA helicase DDX3X; phosphorylation, nucleotide-binding, hydrolase, RNA-binding, ATP-binding, DNA-binding, nuclear protein; 1.91A {Homo sapiens} Length = 185

 Score =  220 bits (563), Expect = 1e-66
 Identities = 68/177 (38%), Positives = 103/177 (58%)

Query: 674 VEIQVGGRSVVNKDITQLVEVRPESDRFLRLLELLGEWYEKGKILIFVHSQEKCDALFRD 733
               +  +   +++ITQ V    ESD+   LL+LL    +    L+FV +++  D+L   
Sbjct: 6   HHENLYFQGSTSENITQKVVWVEESDKRSFLLDLLNATGKDSLTLVFVETKKGADSLEDF 65

Query: 734 LLKHGYPCLSLHGAKDQTDRESTISDFKSNVCNLLIATSVAARGLDVKELELVINFDAPN 793
           L   GY C S+HG + Q DRE  +  F+S    +L+AT+VAARGLD+  ++ VINFD P+
Sbjct: 66  LYHEGYACTSIHGDRSQRDREEALHQFRSGKSPILVATAVAARGLDISNVKHVINFDLPS 125

Query: 794 HYEDYVHRVGRTGRAGRKGCAITFISEEDAKYSPDLVKALELSEQVVPDDLKALADS 850
             E+YVHR+GRTGR G  G A +F +E +   + DL+  L  ++Q VP  L+ +A  
Sbjct: 126 DIEEYVHRIGRTGRVGNLGLATSFFNERNINITKDLLDLLVEAKQEVPSWLENMAYE 182

>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* Length = 230

 Score =  218 bits (557), Expect = 2e-65
 Identities = 62/208 (29%), Positives = 104/208 (50%), Gaps = 11/208 (5%)

Query: 473 GLTSKIMETIRKLNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQ 532
            L+  ++E +R   +E+P P+Q +A+P+   G D I  AK+G+GKT  F    L  +   
Sbjct: 30  LLSRPVLEGLRAAGFERPSPVQLKAIPLGRCGLDLIVQAKSGTGKTCVFSTIALDSLV-- 87

Query: 533 PPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVM-GVRCVPVYGGSGVAQQISELKRGT 591
                      LI+APTRE+  QIHS I      M G+ C    GG+ ++Q  + LK+  
Sbjct: 88  ---LENLSTQILILAPTREIAVQIHSVITAIGIKMEGLECHVFIGGTPLSQDKTRLKKC- 143

Query: 592 EIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMG-FEPQITRIVQNIRPDRQ 650
            I V +PGR+  ++        N   +   ++DEAD++ + G F+ QI  I  ++   +Q
Sbjct: 144 HIAVGSPGRIKQLI---ELDYLNPGSIRLFILDEADKLLEEGSFQEQINWIYSSLPASKQ 200

Query: 651 TVLFSATFPRQVEILARKVLNKPVEIQV 678
            +  SAT+P  +     K +  P  +++
Sbjct: 201 MLAVSATYPEFLANALTKYMRDPTFVRL 228

>2p6n_A ATP-dependent RNA helicase DDX41; DEAD, structural genomics, structural genomic consortium, SGC, hydrolase; 2.60A {Homo sapiens} Length = 191

 Score =  208 bits (531), Expect = 4e-62
 Identities = 63/182 (34%), Positives = 93/182 (51%), Gaps = 3/182 (1%)

Query: 668 KVLNKPVEIQVGGRSVVNKDITQLVEVRPESDRFLRLLELLGEWYEKGKILIFVHSQEKC 727
            V      +        + D+ Q VE   E  + + LLE L +      +LIF   +   
Sbjct: 10  GVDLGTENLYFQSMGAASLDVIQEVEYVKEEAKMVYLLECLQK--TPPPVLIFAEKKADV 67

Query: 728 DALFRDLLKHGYPCLSLHGAKDQTDRESTISDFKSNVCNLLIATSVAARGLDVKELELVI 787
           DA+   LL  G   +++HG KDQ +R   I  F+    ++L+AT VA++GLD   ++ VI
Sbjct: 68  DAIHEYLLLKGVEAVAIHGGKDQEERTKAIEAFREGKKDVLVATDVASKGLDFPAIQHVI 127

Query: 788 NFDAPNHYEDYVHRVGRTGRAGRKGCAITFISEE-DAKYSPDLVKALELSEQVVPDDLKA 846
           N+D P   E+YVHR+GRTG +G  G A TFI++  D     DL   L  ++Q VP  L+ 
Sbjct: 128 NYDMPEEIENYVHRIGRTGCSGNTGIATTFINKACDESVLMDLKALLLEAKQKVPPVLQV 187

Query: 847 LA 848
           L 
Sbjct: 188 LH 189

>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} Length = 300

 Score =  211 bits (538), Expect = 9e-62
 Identities = 61/219 (27%), Positives = 111/219 (50%), Gaps = 14/219 (6%)

Query: 464 KPIKTWHQTGLTSKIMETIRKLNYEKPMPIQAQALPVIMSG--RDCIGVAKTGSGKTLAF 521
             +K++ +  L  ++++ +  + + +P  IQ  ALP++++   ++ I  +++G+GKT AF
Sbjct: 89  YSVKSFEELRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAF 148

Query: 522 VLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVM-GVRCVPVYGGSGV 580
           VL ML  ++          P  L ++PT EL  Q    I +  K    ++      G+ +
Sbjct: 149 VLAMLSQVEPANKY-----PQCLCLSPTYELALQTGKVIEQMGKFYPELKLAYAVRGNKL 203

Query: 581 AQQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFD-MGFEPQIT 639
            +     K   +IV+ TPG ++D    S  K  + +++   V+DEAD M    G + Q  
Sbjct: 204 ERG---QKISEQIVIGTPGTVLDWC--SKLKFIDPKKIKVFVLDEADVMIATQGHQDQSI 258

Query: 640 RIVQNIRPDRQTVLFSATFPRQVEILARKVLNKPVEIQV 678
           RI + +  + Q +LFSATF   V   A+KV+  P  I++
Sbjct: 259 RIQRMLPRNCQMLLFSATFEDSVWKFAQKVVPDPNVIKL 297

>2yjt_D ATP-dependent RNA helicase SRMB, regulator of ribonuclease activity A; hydrolase inhibitor-hydrolase complex, DEAD box RNA helicase; 2.90A {Escherichia coli} Length = 170

 Score =  150 bits (381), Expect = 5e-42
 Identities = 48/140 (34%), Positives = 68/140 (48%)

Query: 686 KDITQLVEVRPESDRFLRLLELLGEWYEKGKILIFVHSQEKCDALFRDLLKHGYPCLSLH 745
           K I Q      + +    LL  L +  E  + ++FV  +E+   L   L + G     L 
Sbjct: 2   KKIHQWYYRADDLEHKTALLVHLLKQPEATRSIVFVRKRERVHELANWLREAGINNCYLE 61

Query: 746 GAKDQTDRESTISDFKSNVCNLLIATSVAARGLDVKELELVINFDAPNHYEDYVHRVGRT 805
           G   Q  R   I        N+L+AT VAARG+D+ ++  V NFD P   + Y+HR+GRT
Sbjct: 62  GEMVQGKRNEAIKRLTEGRVNVLVATDVAARGIDIPDVSHVFNFDMPRSGDTYLHRIGRT 121

Query: 806 GRAGRKGCAITFISEEDAKY 825
            RAGRKG AI+ +   D   
Sbjct: 122 ARAGRKGTAISLVEAHDHLL 141

>2hjv_A ATP-dependent RNA helicase DBPA; parallel alpha-beta, hydrolase; 1.95A {Bacillus subtilis} Length = 163

 Score =  147 bits (373), Expect = 6e-41
 Identities = 55/139 (39%), Positives = 83/139 (59%), Gaps = 3/139 (2%)

Query: 688 ITQ-LVEVRPESDRFLRLLELLGEWYEKGKILIFVHSQEKCDALFRDLLKHGYPCLSLHG 746
           I   +++VR E ++F  L ++L         +IF  ++E  + L  +L   GYPC  +HG
Sbjct: 10  IEHAVIQVR-EENKFSLLKDVL-MTENPDSCIIFCRTKEHVNQLTDELDDLGYPCDKIHG 67

Query: 747 AKDQTDRESTISDFKSNVCNLLIATSVAARGLDVKELELVINFDAPNHYEDYVHRVGRTG 806
              Q DR   +++FK      L+AT VAARG+D++ + LVIN+D P   E YVHR GRTG
Sbjct: 68  GMIQEDRFDVMNEFKRGEYRYLVATDVAARGIDIENISLVINYDLPLEKESYVHRTGRTG 127

Query: 807 RAGRKGCAITFISEEDAKY 825
           RAG KG AI+F++  + ++
Sbjct: 128 RAGNKGKAISFVTAFEKRF 146

>1t5i_A C_terminal domain of A probable ATP-dependent RNA helicase; RECA-like fold, PRE-mRNA processing protein; 1.90A {Homo sapiens} SCOP: c.37.1.19 Length = 172

 Score =  146 bits (370), Expect = 1e-40
 Identities = 53/159 (33%), Positives = 95/159 (59%), Gaps = 4/159 (2%)

Query: 688 ITQL-VEVRPESDRFLRLLELLGEWYEKGKILIFVHSQEKCDALFRDLLKHGYPCLSLHG 746
           + Q  V+++ ++++  +L +LL    E  +++IFV S ++C AL + L++  +P +++H 
Sbjct: 6   LQQYYVKLK-DNEKNRKLFDLLDV-LEFNQVVIFVKSVQRCIALAQLLVEQNFPAIAIHR 63

Query: 747 AKDQTDRESTISDFKSNVCNLLIATSVAARGLDVKELELVINFDAPNHYEDYVHRVGRTG 806
              Q +R S    FK     +L+AT++  RG+D++ + +  N+D P   + Y+HRV R G
Sbjct: 64  GMPQEERLSRYQQFKDFQRRILVATNLFGRGMDIERVNIAFNYDMPEDSDTYLHRVARAG 123

Query: 807 RAGRKGCAITFIS-EEDAKYSPDLVKALELSEQVVPDDL 844
           R G KG AITF+S E DAK   D+    E++   +PD++
Sbjct: 124 RFGTKGLAITFVSDENDAKILNDVQDRFEVNISELPDEI 162

>1fuk_A Eukaryotic initiation factor 4A; helicase, DEAD-box protein, translation; 1.75A {Saccharomyces cerevisiae} SCOP: c.37.1.19 Length = 165

 Score =  145 bits (368), Expect = 2e-40
 Identities = 47/139 (33%), Positives = 81/139 (58%), Gaps = 2/139 (1%)

Query: 688 ITQL-VEVRPESDRFLRLLELLGEWYEKGKILIFVHSQEKCDALFRDLLKHGYPCLSLHG 746
           I Q  V V  E  ++  L +L  +     + +IF +++ K + L   L    +   +++ 
Sbjct: 4   IKQFYVNVEEEEYKYECLTDLY-DSISVTQAVIFCNTRRKVEELTTKLRNDKFTVSAIYS 62

Query: 747 AKDQTDRESTISDFKSNVCNLLIATSVAARGLDVKELELVINFDAPNHYEDYVHRVGRTG 806
              Q +R++ + +F+S    +LI+T + ARG+DV+++ LVIN+D P + E+Y+HR+GR G
Sbjct: 63  DLPQQERDTIMKEFRSGSSRILISTDLLARGIDVQQVSLVINYDLPANKENYIHRIGRGG 122

Query: 807 RAGRKGCAITFISEEDAKY 825
           R GRKG AI F++ ED   
Sbjct: 123 RFGRKGVAINFVTNEDVGA 141

>2rb4_A ATP-dependent RNA helicase DDX25; rossmann fold, structural genomics, structural consortium, SGC, alternative initiation, ATP-binding, devel protein; 2.80A {Homo sapiens} Length = 175

 Score =  141 bits (359), Expect = 5e-39
 Identities = 46/145 (31%), Positives = 71/145 (48%), Gaps = 8/145 (5%)

Query: 688 ITQL-VEVRPESDRFLRLLELLGEWYEKGKILIFVHSQEKCDALFRDLLKHGYPCLSLHG 746
           I Q  V      D++  L  +       G+ +IF  ++     L  ++++ G+    L G
Sbjct: 8   IRQYYVLCEHRKDKYQALCNIY-GSITIGQAIIFCQTRRNAKWLTVEMIQDGHQVSLLSG 66

Query: 747 AKDQTDRESTISDFKSNVCNLLIATSVAARGLDVKELELVINFDAPN------HYEDYVH 800
                 R S I  F+     +LI T+V ARG+DVK++ +V+NFD P        YE Y+H
Sbjct: 67  ELTVEQRASIIQRFRDGKEKVLITTNVCARGIDVKQVTIVVNFDLPVKQGEEPDYETYLH 126

Query: 801 RVGRTGRAGRKGCAITFISEEDAKY 825
           R+GRTGR G+KG A   I  ++   
Sbjct: 127 RIGRTGRFGKKGLAFNMIEVDELPS 151

>3eaq_A Heat resistant RNA dependent ATPase; DEAD box RNA helicase, dimer, ATP-binding, helicase, hydrolase, nucleotide-binding; 2.30A {Thermus thermophilus} PDB: 3ear_A 3eas_A Length = 212

 Score =  132 bits (335), Expect = 2e-35
 Identities = 43/132 (32%), Positives = 71/132 (53%), Gaps = 1/132 (0%)

Query: 688 ITQLVEVRPESDRFLRLLELLGEWYEKGKILIFVHSQEKCDALFRDLLKHGYPCLSLHGA 747
             +     P   R   L +LL       + ++F  ++ + + + + LL+ G+P  +LHG 
Sbjct: 6   YEEEAVPAPVRGRLEVLSDLL-YVASPDRAMVFTRTKAETEEIAQGLLRLGHPAQALHGD 64

Query: 748 KDQTDRESTISDFKSNVCNLLIATSVAARGLDVKELELVINFDAPNHYEDYVHRVGRTGR 807
             Q +RE  +  F+     +L+AT VAARGLD+ +++LV+++  P+  E Y HR GRTGR
Sbjct: 65  LSQGERERVLGAFRQGEVRVLVATDVAARGLDIPQVDLVVHYRLPDRAEAYQHRSGRTGR 124

Query: 808 AGRKGCAITFIS 819
           AGR G  +    
Sbjct: 125 AGRGGRVVLLYG 136

>3i32_A Heat resistant RNA dependent ATPase; RNA helicase, dimer, RNA recognition motif, ATP-BIND helicase, nucleotide-binding; 2.80A {Thermus thermophilus} Length = 300

 Score =  128 bits (323), Expect = 9e-33
 Identities = 43/132 (32%), Positives = 71/132 (53%), Gaps = 1/132 (0%)

Query: 688 ITQLVEVRPESDRFLRLLELLGEWYEKGKILIFVHSQEKCDALFRDLLKHGYPCLSLHGA 747
             +     P   R   L +LL       + ++F  ++ + + + + LL+ G+P  +LHG 
Sbjct: 3   YEEEAVPAPVRGRLEVLSDLL-YVASPDRAMVFTRTKAETEEIAQGLLRLGHPAQALHGD 61

Query: 748 KDQTDRESTISDFKSNVCNLLIATSVAARGLDVKELELVINFDAPNHYEDYVHRVGRTGR 807
             Q +RE  +  F+     +L+AT VAARGLD+ +++LV+++  P+  E Y HR GRTGR
Sbjct: 62  MSQGERERVMGAFRQGEVRVLVATDVAARGLDIPQVDLVVHYRMPDRAEAYQHRSGRTGR 121

Query: 808 AGRKGCAITFIS 819
           AGR G  +    
Sbjct: 122 AGRGGRVVLLYG 133

>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* 4a92_A* 1cu1_A 2zjo_A* 1a1v_A* 1hei_A 3kqn_A* 3kql_A* 3kqu_A* 3kqh_A 3kqk_A 8ohm_A 2f55_A 1jr6_A 1onb_A Length = 666

 Score = 99.3 bits (247), Expect = 2e-21
 Identities = 63/380 (16%), Positives = 106/380 (27%), Gaps = 82/380 (21%)

Query: 479 METIRKLNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAG 538
           +E++            +    V  S +     A TGSGK+          +   P   A 
Sbjct: 207 VESMETTMRSPVFTDNSSPPAVPQSFQVAHLHAPTGSGKS--------TKV---PAAYAA 255

Query: 539 DGPVGLIMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQISELKRGTEIVVCTP 598
            G   L++ P+        + + K                 +   +  +  G  +   T 
Sbjct: 256 QGYKVLVLNPSVAATLGFGAYMSK----------AHGIDPNIRTGVRTITTGAPVTYSTY 305

Query: 599 GR-MIDILCTSGGKITNLRRVTYLVMDEADRM---FDMGFEPQITRIVQNIRPDRQTVLF 654
           G+ + D  C       +      ++ DE         +G               R  VL 
Sbjct: 306 GKFLADGGC-------SGGAYDIIICDECHSTDSTTILGIG--TVLDQAETAGARLVVLA 356

Query: 655 SATFPRQVEILARKVLNKPVEIQVGGRSVVNKDITQLVEVRPESDRFLRLLELLGEWYEK 714
           +AT P  V +      N                    +    E   + + + +  E    
Sbjct: 357 TATPPGSVTV---PHPNIEEVA---------------LSNTGEIPFYGKAIPI--EAIRG 396

Query: 715 GKILIFVHSQEKCDALFRDLLKHGYPCLSLHGAKDQTDRESTISDFKSNVCNLLIATSVA 774
           G+ LIF HS++KCD L   L   G   ++ +   D +   +            ++AT   
Sbjct: 397 GRHLIFCHSKKKCDELAAKLSGLGINAVAYYRGLDVSVIPTIGDVV-------VVATDAL 449

Query: 775 ARGL--DVK-------ELELVINFDAPNH-----------YEDYVHRVGRTGRAGRKGCA 814
             G   D          +   ++F                      R GRTGR GR+G  
Sbjct: 450 MTGYTGDFDSVIDCNTCVTQTVDFSLDPTFTIETTTVPQDAVSRSQRRGRTGR-GRRGIY 508

Query: 815 ITFISEEDAKYSPDLVKALE 834
                 E      D     E
Sbjct: 509 RFVTPGERPSGMFDSSVLCE 528

>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 Length = 494

 Score = 96.4 bits (239), Expect = 6e-21
 Identities = 44/228 (19%), Positives = 91/228 (39%), Gaps = 27/228 (11%)

Query: 606 CTSGGKITNLRRVTYLVMDEADRMFDMGFEPQITRIVQNIRPDRQTVLFSATFPRQVEIL 665
                +   L     L +  A  + +      +   ++ +  + +     A+     EI 
Sbjct: 265 GNHDLRGLLLYHAMALKLHHAIELLETQGLSALRAYIKKLYEEAKAGSTKASK----EIF 320

Query: 666 ARKVLNKPVEIQVGGRSVVNKDITQLVEVRPESDRFLRLLELLGEWYEKG---KILIFVH 722
           + K + K + +           + Q  E+  +  +  +L E++ E  ++    KI++F +
Sbjct: 321 SDKRMKKAISL-----------LVQAKEIGLDHPKMDKLKEIIREQLQRKQNSKIIVFTN 369

Query: 723 SQEKCDALFRDLLKHGYPCLSLHGAK--------DQTDRESTISDFKSNVCNLLIATSVA 774
            +E    +  +L+K G       G           Q +++  + +F     N+L+ATSV 
Sbjct: 370 YRETAKKIVNELVKDGIKAKRFVGQASKENDRGLSQREQKLILDEFARGEFNVLVATSVG 429

Query: 775 ARGLDVKELELVINFDAPNHYEDYVHRVGRTGRAGRKGCAITFISEED 822
             GLDV E++LV+ ++        + R GRTGR    G  I  +++  
Sbjct: 430 EEGLDVPEVDLVVFYEPVPSAIRSIQRRGRTGRH-MPGRVIILMAKGT 476

>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 Length = 494

 Score = 84.5 bits (208), Expect = 5e-17
 Identities = 45/231 (19%), Positives = 87/231 (37%), Gaps = 13/231 (5%)

Query: 489 KPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAP 548
           +P   Q           +C+ V  TG GKTL  ++     +              L++AP
Sbjct: 9   QPRIYQEVIYAKCK-ETNCLIVLPTGLGKTLIAMMIAEYRLTKYGGKV-------LMLAP 60

Query: 549 TRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTS 608
           T+ LV Q     R+   +   + V + G     ++ S+     +++V TP  + + L   
Sbjct: 61  TKPLVLQHAESFRRLFNLPPEKIVALTGEKSPEER-SKAWARAKVIVATPQTIENDLLA- 118

Query: 609 GGKITNLRRVTYLVMDEADRMFDMGFEPQITRIVQNIRPDRQTVLFSATFPRQVEILARK 668
                +L  V+ +V DEA R         I R  +    +   +  +A+     E +  +
Sbjct: 119 --GRISLEDVSLIVFDEAHRAVGNYAYVFIAREYKRQAKNPLVIGLTASPGSTPEKI-ME 175

Query: 669 VLNKPVEIQVGGRSVVNKDITQLVEVRPESDRFLRLLELLGEWYEKGKILI 719
           V+N      +  RS  + D+   V+        + L E+  E  +  + ++
Sbjct: 176 VINNLGIEHIEYRSENSPDVRPYVKGIRFEWVRVDLPEIYKEVRKLLREML 226

>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* Length = 720

 Score = 83.0 bits (205), Expect = 2e-16
 Identities = 80/405 (19%), Positives = 144/405 (35%), Gaps = 74/405 (18%)

Query: 473 GLTSKIMETIRKLNYEKPMPIQAQALP-VIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKD 531
            +  +I  T+++   E   P QA+AL   I+ G++ +    T SGKTL   + M+  I  
Sbjct: 7   RVDERIKSTLKERGIESFYPPQAEALKSGILEGKNALISIPTASGKTLIAEIAMVHRILT 66

Query: 532 QPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQISELKRGT 591
           Q       G    I  P + L ++   + + + K +G+R     G         E     
Sbjct: 67  Q------GGKAVYI-VPLKALAEEKFQEFQDWEK-IGLRVAMATGDYDSK---DEWLGKY 115

Query: 592 EIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMGFEPQITRIVQNIRPDRQT 651
           +I++ T  +  D L   G     ++ V  LV DE   +        +  I+ ++    Q 
Sbjct: 116 DIIIATAEKF-DSLLRHGSSW--IKDVKILVADEIHLIGSRDRGATLEVILAHMLGKAQI 172

Query: 652 VLFSATFPRQVEIL----ARKVLNK--PVEIQVGGRSVVNKDITQLVEVRPESDRFLRLL 705
           +  SAT     E+     A  +++   PV+++   R V  +    +       DRF    
Sbjct: 173 IGLSATIGNPEELAEWLNAELIVSDWRPVKLR---RGVFYQGF--VTWEDGSIDRFSSWE 227

Query: 706 ELLGEWYEKGK-ILIFVHSQEKCDALFRDLLKHGY------------------------- 739
           EL+ +   K K  LIFV+ + K + +  +L K                            
Sbjct: 228 ELVYDAIRKKKGALIFVNMRRKAERVALELSKKVKSLLTKPEIRALNELADSLEENPTNE 287

Query: 740 ---PCLSL-----HGAKDQTDRESTISDFKSNVCNLLIATSVAARGLDVKELELVINFDA 791
                +       H    + +R     +F+  +   ++AT   + G++      VI    
Sbjct: 288 KLAKAIRGGVAFHHAGLGRDERVLVEENFRKGIIKAVVATPTLSAGINTPA-FRVI-IRD 345

Query: 792 PNHYEDYVHR----------VGRTGRAG--RKGCAITFISEEDAK 824
              Y D+             +GR GR      G  I   + +D +
Sbjct: 346 IWRYSDFGMERIPIIEVHQMLGRAGRPKYDEVGEGIIVSTSDDPR 390

>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 Length = 702

 Score = 82.2 bits (203), Expect = 4e-16
 Identities = 79/407 (19%), Positives = 151/407 (37%), Gaps = 82/407 (20%)

Query: 455 LKIHGKDVPKPIKTWHQTGLTSKIMETIRKLNYEKPMPIQAQALPVIMSGRDCIGVAKTG 514
           +K+   ++ + I ++    L  +    I +L      P QA+A+  + SG++ +    T 
Sbjct: 1   MKVE--ELAESISSYAVGILKEE---GIEELF-----PPQAEAVEKVFSGKNLLLAMPTA 50

Query: 515 SGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVMGVRCVPV 574
           +GKTL   + M+R                L + P R L  + +   +K+ K +G+R    
Sbjct: 51  AGKTLLAEMAMVREAIKGGKS--------LYVVPLRALAGEKYESFKKWEK-IGLRIGIS 101

Query: 575 YGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDE----ADRMF 630
            G     +   E     +I+V T  +  D L  +      ++ V+ LV+DE         
Sbjct: 102 TGDY---ESRDEHLGDCDIIVTTSEKA-DSLIRNRASW--IKAVSCLVVDEIHLLDSE-- 153

Query: 631 DMGF--EPQITRIVQNIRPDRQTVLFSATFPRQVEI---LARKVLNK---PVEIQVGGRS 682
             G   E  +T++ + +    + +  SAT P   EI   L          PV +  G   
Sbjct: 154 KRGATLEILVTKMRR-MNKALRVIGLSATAPNVTEIAEWLDADYYVSDWRPVPLVEG--- 209

Query: 683 VVNKDITQLVEVRPESDRFLRLLELLGEWYEKGK-ILIFVHSQEKC-------------- 727
           V+ +   +L +    + R ++  EL+ E   +   +L+F  ++                 
Sbjct: 210 VLCEGTLELFDGAFSTSRRVKFEELVEECVAENGGVLVFESTRRGAEKTAVKLSAITAKY 269

Query: 728 ---DALFRDLLKHGYPCLS-------------LHGAKDQTDRESTISDFKSNVCNLLIAT 771
              + L + +L+     +S              H       R      F+     +++AT
Sbjct: 270 VENEGLEKAILEENEGEMSRKLAECVRKGAAFHHAGLLNGQRRVVEDAFRRGNIKVVVAT 329

Query: 772 SVAARGLDVKELELVINFDAPNHYEDYVHRVGRT------GRAGRKG 812
              A G+++     VI   +   ++ Y  R+  +      GRAGR G
Sbjct: 330 PTLAAGVNLPA-RRVI-VRSLYRFDGYSKRIKVSEYKQMAGRAGRPG 374

>3pgw_S U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 3cw1_K 2l5i_A 2l5j_A* Length = 437

 Score = 79.9 bits (196), Expect = 9e-16
 Identities = 38/198 (19%), Positives = 74/198 (37%)

Query: 3   HSHRDRDREKEKEKHREKSRRSEREQSTDSDEDKHDKEKEKDKHRDRDRRRDRDRDRDRE 62
                  R++++++ RE+  RS              +++ +         R R R+R ++
Sbjct: 224 GPSPLPHRDRDRDRERERRERSRERDKERERRRSRSRDRRRRSRSRDKEERRRSRERSKD 283

Query: 63  KEREEKRERAREKEREREKRDREREDRERERERERERRERDREREKRERERDRDKEKDRE 122
           K+R+ KR  +R +ER R +R+R+ E R    +        D   +            D  
Sbjct: 284 KDRDRKRRSSRSRERARRERERKEELRGGGGDMAEPSEAGDAPPDDGPPGELGPDGPDGP 343

Query: 123 RKSRDREKRRKVESDDSDEDKDRDRKRRRRHDDDHKERVRERSLSRSNRHRDENDESPRE 182
            +      R +  S  S+ ++ RDR R R  D +HK   R     R         +    
Sbjct: 344 EEKGRDRDRERRRSHRSERERRRDRDRDRDRDREHKRGERGSERGRDEARGGGGGQDNGL 403

Query: 183 KLVEDDSDKKEKKTREEE 200
           + + +DS     ++   +
Sbjct: 404 EGLGNDSRDMYMESEGGD 421

>3pgw_S U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 3cw1_K 2l5i_A 2l5j_A* Length = 437

 Score = 78.0 bits (191), Expect = 4e-15
 Identities = 38/195 (19%), Positives = 75/195 (38%)

Query: 3   HSHRDRDREKEKEKHREKSRRSEREQSTDSDEDKHDKEKEKDKHRDRDRRRDRDRDRDRE 62
              R+R+R +   +  ++  R            +   ++E+ + R+R + +DRDR R   
Sbjct: 234 DRDRERERRERSRERDKERERRRSRSRDRRRRSRSRDKEERRRSRERSKDKDRDRKRRSS 293

Query: 63  KEREEKRERAREKEREREKRDREREDRERERERERERRERDREREKRERERDRDKEKDRE 122
           + RE  R     KE  R       E  E       +    +   +  +   ++ +++DRE
Sbjct: 294 RSRERARRERERKEELRGGGGDMAEPSEAGDAPPDDGPPGELGPDGPDGPEEKGRDRDRE 353

Query: 123 RKSRDREKRRKVESDDSDEDKDRDRKRRRRHDDDHKERVRERSLSRSNRHRDENDESPRE 182
           R+   R +R +    D D D+DR+ KR  R  +  ++  R     + N      ++S   
Sbjct: 354 RRRSHRSERERRRDRDRDRDRDREHKRGERGSERGRDEARGGGGGQDNGLEGLGNDSRDM 413

Query: 183 KLVEDDSDKKEKKTR 197
            +  +  D       
Sbjct: 414 YMESEGGDGYLAPEN 428

>3pgw_S U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 3cw1_K 2l5i_A 2l5j_A* Length = 437

 Score = 77.2 bits (189), Expect = 8e-15
 Identities = 45/215 (20%), Positives = 82/215 (38%), Gaps = 1/215 (0%)

Query: 3   HSHRDRDREKEKEKHREKSRRSEREQSTDSDEDKHDKEKEKDKHRDRDRRRDRDRDRDRE 62
            S  D         HR++ R  ERE+   S E   ++E+ + + RDR RR       +R 
Sbjct: 216 TSRYDERPGPSPLPHRDRDRDRERERRERSRERDKERERRRSRSRDRRRRSRSRDKEERR 275

Query: 63  KEREEKRERAREKEREREK-RDREREDRERERERERERRERDREREKRERERDRDKEKDR 121
           + RE  +++ R+++R   + R+R R +RER+ E      +     E  +   D     + 
Sbjct: 276 RSRERSKDKDRDRKRRSSRSRERARRERERKEELRGGGGDMAEPSEAGDAPPDDGPPGEL 335

Query: 122 ERKSRDREKRRKVESDDSDEDKDRDRKRRRRHDDDHKERVRERSLSRSNRHRDENDESPR 181
                D  + +  + D       R  + RRR  D  ++R RE         R  ++    
Sbjct: 336 GPDGPDGPEEKGRDRDRERRRSHRSERERRRDRDRDRDRDREHKRGERGSERGRDEARGG 395

Query: 182 EKLVEDDSDKKEKKTREEELEDEQRKLDEEMEKRR 216
               ++  +     +R+  +E E        E   
Sbjct: 396 GGGQDNGLEGLGNDSRDMYMESEGGDGYLAPENGY 430

>3pgw_S U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 3cw1_K 2l5i_A 2l5j_A* Length = 437

 Score = 76.4 bits (187), Expect = 1e-14
 Identities = 37/232 (15%), Positives = 80/232 (34%)

Query: 1   MAHSHRDRDREKEKEKHREKSRRSEREQSTDSDEDKHDKEKEKDKHRDRDRRRDRDRDRD 60
                      +   +            S     D+    + + + R R+R ++R+R R 
Sbjct: 198 GTRRGGADVNIRHSGRDDTSRYDERPGPSPLPHRDRDRDRERERRERSRERDKERERRRS 257

Query: 61  REKEREEKRERAREKEREREKRDREREDRERERERERERRERDREREKRERERDRDKEKD 120
           R ++R  +     ++ER R +   + +DR+R+R   R R    RERE++E  R    +  
Sbjct: 258 RSRDRRRRSRSRDKEERRRSRERSKDKDRDRKRRSSRSRERARRERERKEELRGGGGDMA 317

Query: 121 RERKSRDREKRRKVESDDSDEDKDRDRKRRRRHDDDHKERVRERSLSRSNRHRDENDESP 180
              ++ D         +   +  D   ++ R  D + +   R     R +R RD + +  
Sbjct: 318 EPSEAGDAPPDDGPPGELGPDGPDGPEEKGRDRDRERRRSHRSERERRRDRDRDRDRDRE 377

Query: 181 REKLVEDDSDKKEKKTREEELEDEQRKLDEEMEKRRRRVQEWQELKRKKEES 232
            ++        +++       +D   +      +      E  +     E  
Sbjct: 378 HKRGERGSERGRDEARGGGGGQDNGLEGLGNDSRDMYMESEGGDGYLAPENG 429

>3pgw_S U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 3cw1_K 2l5i_A 2l5j_A* Length = 437

 Score = 76.4 bits (187), Expect = 1e-14
 Identities = 34/180 (18%), Positives = 61/180 (33%)

Query: 3   HSHRDRDREKEKEKHREKSRRSEREQSTDSDEDKHDKEKEKDKHRDRDRRRDRDRDRDRE 62
            S   R R + ++K   +  R   +      + +  + +E+ +     +   R    D  
Sbjct: 258 RSRDRRRRSRSRDKEERRRSRERSKDKDRDRKRRSSRSRERARRERERKEELRGGGGDMA 317

Query: 63  KEREEKRERAREKEREREKRDREREDRERERERERERRERDREREKRERERDRDKEKDRE 122
           +  E       +        D      E+ R+R+RERR   R   +R R+RDRD+++DRE
Sbjct: 318 EPSEAGDAPPDDGPPGELGPDGPDGPEEKGRDRDRERRRSHRSERERRRDRDRDRDRDRE 377

Query: 123 RKSRDREKRRKVESDDSDEDKDRDRKRRRRHDDDHKERVRERSLSRSNRHRDENDESPRE 182
            K  +R   R  +          +      +D        E              E+  E
Sbjct: 378 HKRGERGSERGRDEARGGGGGQDNGLEGLGNDSRDMYMESEGGDGYLAPENGYLMEAAPE 437

>3pgw_S U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 3cw1_K 2l5i_A 2l5j_A* Length = 437

 Score = 72.2 bits (176), Expect = 2e-13
 Identities = 43/242 (17%), Positives = 76/242 (31%)

Query: 8   RDREKEKEKHREKSRRSEREQSTDSDEDKHDKEKEKDKHRDRDRRRDRDRDRDREKEREE 67
             R         +       + +  D+     E+          R        RE+ RE 
Sbjct: 189 PRRLGGGLGGTRRGGADVNIRHSGRDDTSRYDERPGPSPLPHRDRDRDRERERRERSRER 248

Query: 68  KRERAREKEREREKRDREREDRERERERERERRERDREREKRERERDRDKEKDRERKSRD 127
            +ER R + R R++R R R   + ER R RER +      KR   R R++ +    +  +
Sbjct: 249 DKERERRRSRSRDRRRRSRSRDKEERRRSRERSKDKDRDRKRRSSRSRERARRERERKEE 308

Query: 128 REKRRKVESDDSDEDKDRDRKRRRRHDDDHKERVRERSLSRSNRHRDENDESPREKLVED 187
                   ++ S+                      E      +R R  +  S RE+  + 
Sbjct: 309 LRGGGGDMAEPSEAGDAPPDDGPPGELGPDGPDGPEEKGRDRDRERRRSHRSERERRRDR 368

Query: 188 DSDKKEKKTREEELEDEQRKLDEEMEKRRRRVQEWQELKRKKEESERENRGDANVEEPKA 247
           D D+   +  +      +R  DE       +    + L     +   E+ G      P+ 
Sbjct: 369 DRDRDRDREHKRGERGSERGRDEARGGGGGQDNGLEGLGNDSRDMYMESEGGDGYLAPEN 428

Query: 248 GR 249
           G 
Sbjct: 429 GY 430

>3pgw_S U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 3cw1_K 2l5i_A 2l5j_A* Length = 437

 Score = 68.7 bits (167), Expect = 4e-12
 Identities = 48/244 (19%), Positives = 92/244 (37%), Gaps = 3/244 (1%)

Query: 8   RDREKEKEKHREKSRRSEREQSTDSDEDKHDKEKEKDKHRDRDRRRDRDRDRDREKEREE 67
               + +                +      D     D+         RDRDRDRE+ER E
Sbjct: 184 VKGWRPRRLGGGLGGTRRGGADVNIRHSGRDDTSRYDERPGPSPLPHRDRDRDRERERRE 243

Query: 68  KRERAREKEREREKRDREREDRERERERERERRERDREREKRERERDRDKEKDRERKSRD 127
           +     ++   R  R R+R  R R R++E  RR R+R ++ ++R+R R   + RER  R+
Sbjct: 244 RSRERDKERERRRSRSRDRRRRSRSRDKEERRRSRERSKD-KDRDRKRRSSRSRERARRE 302

Query: 128 REKRRKVESDDSDEDKDRDRKRRRRHDDDHKERVRERSLSRSNRHRDENDESPREKLVED 187
           RE++ ++     D  +  +       D    E   +       + RD + E  R      
Sbjct: 303 RERKEELRGGGGDMAEPSEAGDAPPDDGPPGELGPDGPDGPEEKGRDRDRERRRSH--RS 360

Query: 188 DSDKKEKKTREEELEDEQRKLDEEMEKRRRRVQEWQELKRKKEESERENRGDANVEEPKA 247
           + +++  + R+ + + E ++ +   E+ R   +     +    E    +  D  +E    
Sbjct: 361 ERERRRDRDRDRDRDREHKRGERGSERGRDEARGGGGGQDNGLEGLGNDSRDMYMESEGG 420

Query: 248 GRNW 251
               
Sbjct: 421 DGYL 424

>3pgw_S U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 3cw1_K 2l5i_A 2l5j_A* Length = 437

 Score = 65.6 bits (159), Expect = 3e-11
 Identities = 42/239 (17%), Positives = 78/239 (32%)

Query: 3   HSHRDRDREKEKEKHREKSRRSEREQSTDSDEDKHDKEKEKDKHRDRDRRRDRDRDRDRE 62
              R     +     +    R        +     D         D  R  +R       
Sbjct: 170 DGRRVLVDVERGRTVKGWRPRRLGGGLGGTRRGGADVNIRHSGRDDTSRYDERPGPSPLP 229

Query: 63  KEREEKRERAREKEREREKRDREREDRERERERERERRERDREREKRERERDRDKEKDRE 122
               ++      +ER RE+       R R R+R R  R RD+E  +R RER +DK++DR+
Sbjct: 230 HRDRDRDRERERRERSRERDKERERRRSRSRDRRRRSRSRDKEERRRSRERSKDKDRDRK 289

Query: 123 RKSRDREKRRKVESDDSDEDKDRDRKRRRRHDDDHKERVRERSLSRSNRHRDENDESPRE 182
           R+S    +R + E +  +E +          +                   D  +E  R+
Sbjct: 290 RRSSRSRERARRERERKEELRGGGGDMAEPSEAGDAPPDDGPPGELGPDGPDGPEEKGRD 349

Query: 183 KLVEDDSDKKEKKTREEELEDEQRKLDEEMEKRRRRVQEWQELKRKKEESERENRGDAN 241
           +  E     + ++ R  + + ++ +  E     R   +   E +      +    G  N
Sbjct: 350 RDRERRRSHRSERERRRDRDRDRDRDREHKRGERGSERGRDEARGGGGGQDNGLEGLGN 408

>3pgw_S U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 3cw1_K 2l5i_A 2l5j_A* Length = 437

 Score = 62.6 bits (151), Expect = 3e-10
 Identities = 43/256 (16%), Positives = 82/256 (32%), Gaps = 1/256 (0%)

Query: 12  KEKEKHREKSRRSEREQSTDSDEDKHDKEKEKDKHRDRDRRRDRDRDRDREKEREEKRER 71
               +     +     +             + +          R  +R        +   
Sbjct: 175 LVDVERGRTVKGWRPRRLGGGLGGTRRGGADVNIRHSGRDDTSRYDERPGPSPLPHRDRD 234

Query: 72  AREKEREREKRDREREDRERERERERERRERDREREKRERERDRDKEKDRERKSRDREKR 131
              +   RE+     ++RER R R R+RR R R R+K ER R R++ KD++R  + R  R
Sbjct: 235 RDRERERRERSRERDKERERRRSRSRDRRRRSRSRDKEERRRSRERSKDKDRDRKRRSSR 294

Query: 132 RKVESDDSDEDKDRDRKRRRRHDDDHKERVRERSLSRSNRHRDENDESPREKLVEDDSDK 191
            +  +    E K+  R        +  E                +     E+   D   +
Sbjct: 295 SRERARRERERKEELR-GGGGDMAEPSEAGDAPPDDGPPGELGPDGPDGPEEKGRDRDRE 353

Query: 192 KEKKTREEELEDEQRKLDEEMEKRRRRVQEWQELKRKKEESERENRGDANVEEPKAGRNW 251
           + +  R E      R  D + ++  +R +   E  R +       + +         R+ 
Sbjct: 354 RRRSHRSERERRRDRDRDRDRDREHKRGERGSERGRDEARGGGGGQDNGLEGLGNDSRDM 413

Query: 252 TLDREDSDDEEVPQTG 267
            ++ E  D    P+ G
Sbjct: 414 YMESEGGDGYLAPENG 429

>3pgw_S U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 3cw1_K 2l5i_A 2l5j_A* Length = 437

 Score = 59.5 bits (143), Expect = 3e-09
 Identities = 38/266 (14%), Positives = 78/266 (29%)

Query: 3   HSHRDRDREKEKEKHREKSRRSEREQSTDSDEDKHDKEKEKDKHRDRDRRRDRDRDRDRE 62
                  +  + +K   +    + E+       +  +         R       R   R+
Sbjct: 155 RDMHSAYKHADGKKIDGRRVLVDVERGRTVKGWRPRRLGGGLGGTRRGGADVNIRHSGRD 214

Query: 63  KEREEKRERAREKEREREKRDREREDRERERERERERRERDREREKRERERDRDKEKDRE 122
                           R++      +R        + RER R R +  R R R ++K+  
Sbjct: 215 DTSRYDERPGPSPLPHRDRDRDRERERRERSRERDKERERRRSRSRDRRRRSRSRDKEER 274

Query: 123 RKSRDREKRRKVESDDSDEDKDRDRKRRRRHDDDHKERVRERSLSRSNRHRDENDESPRE 182
           R+SR+R K +  +            +R R   ++ +    + +          +D  P E
Sbjct: 275 RRSRERSKDKDRDRKRRSSRSRERARRERERKEELRGGGGDMAEPSEAGDAPPDDGPPGE 334

Query: 183 KLVEDDSDKKEKKTREEELEDEQRKLDEEMEKRRRRVQEWQELKRKKEESERENRGDANV 242
              +     +EK    +       + + E  + R R ++     ++ E      R +A  
Sbjct: 335 LGPDGPDGPEEKGRDRDRERRRSHRSERERRRDRDRDRDRDREHKRGERGSERGRDEARG 394

Query: 243 EEPKAGRNWTLDREDSDDEEVPQTGK 268
                         DS D  +   G 
Sbjct: 395 GGGGQDNGLEGLGNDSRDMYMESEGG 420

>3pgw_S U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 3cw1_K 2l5i_A 2l5j_A* Length = 437

 Score = 53.7 bits (128), Expect = 2e-07
 Identities = 43/267 (16%), Positives = 84/267 (31%), Gaps = 1/267 (0%)

Query: 13  EKEKHREKSRRSEREQSTDSDEDKHDKEKEKDKHRDRDRRRDRDRDRDREKEREEKRERA 72
           E E  R+     +       D  +   + E+ +     R R         +         
Sbjct: 150 EYEHERDMHSAYKHADGKKIDGRRVLVDVERGRTVKGWRPRRLGGGLGGTRRGGADVNIR 209

Query: 73  REKEREREKRDREREDRERERERERERRERDREREKRERERDRDKEKDRERKSRDREKRR 132
                +  + D                RER+R    RER+++R++ + R R  R R + R
Sbjct: 210 HSGRDDTSRYDERPGPSPLPHRDRDRDRERERRERSRERDKERERRRSRSRDRRRRSRSR 269

Query: 133 KVESDDSDEDKDRDRKRRR-RHDDDHKERVRERSLSRSNRHRDENDESPREKLVEDDSDK 191
             E      ++ +D+ R R R     +ER R     +        D +   +  +   D 
Sbjct: 270 DKEERRRSRERSKDKDRDRKRRSSRSRERARRERERKEELRGGGGDMAEPSEAGDAPPDD 329

Query: 192 KEKKTREEELEDEQRKLDEEMEKRRRRVQEWQELKRKKEESERENRGDANVEEPKAGRNW 251
                   +  D   +   + ++ RRR    +  +R+  + +R+   +    E  + R  
Sbjct: 330 GPPGELGPDGPDGPEEKGRDRDRERRRSHRSERERRRDRDRDRDRDREHKRGERGSERGR 389

Query: 252 TLDREDSDDEEVPQTGKSETDMDADEE 278
              R     ++    G      D   E
Sbjct: 390 DEARGGGGGQDNGLEGLGNDSRDMYME 416

>3pgw_S U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 3cw1_K 2l5i_A 2l5j_A* Length = 437

 Score = 52.5 bits (125), Expect = 4e-07
 Identities = 36/251 (14%), Positives = 71/251 (28%)

Query: 35  DKHDKEKEKDKHRDRDRRRDRDRDRDREKEREEKRERAREKEREREKRDREREDRERERE 94
           D      + ++ R     R R         R    +         +    +         
Sbjct: 170 DGRRVLVDVERGRTVKGWRPRRLGGGLGGTRRGGADVNIRHSGRDDTSRYDERPGPSPLP 229

Query: 95  RERERRERDREREKRERERDRDKEKDRERKSRDREKRRKVESDDSDEDKDRDRKRRRRHD 154
                R+R+RER +R RERD+++E+ R R    R + R  + ++    ++R + + R   
Sbjct: 230 HRDRDRDRERERRERSRERDKERERRRSRSRDRRRRSRSRDKEERRRSRERSKDKDRDRK 289

Query: 155 DDHKERVRERSLSRSNRHRDENDESPREKLVEDDSDKKEKKTREEELEDEQRKLDEEMEK 214
                        R  +           +  E      +     E   D     +E+   
Sbjct: 290 RRSSRSRERARRERERKEELRGGGGDMAEPSEAGDAPPDDGPPGELGPDGPDGPEEKGRD 349

Query: 215 RRRRVQEWQELKRKKEESERENRGDANVEEPKAGRNWTLDREDSDDEEVPQTGKSETDMD 274
           R R  +     +R++      +R      +     +     E          G      D
Sbjct: 350 RDRERRRSHRSERERRRDRDRDRDRDREHKRGERGSERGRDEARGGGGGQDNGLEGLGND 409

Query: 275 ADEEPKPSENQ 285
           + +    SE  
Sbjct: 410 SRDMYMESEGG 420

>3pgw_S U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 3cw1_K 2l5i_A 2l5j_A* Length = 437

 Score = 46.4 bits (109), Expect = 4e-05
 Identities = 36/262 (13%), Positives = 69/262 (26%), Gaps = 1/262 (0%)

Query: 25  EREQSTDSDEDKHDKEKEKDKHRDRDRRRDRDRDRDREKEREEKRERAREKEREREKRDR 84
           E E   D        + +K   R      +R R     + R         +    +   R
Sbjct: 150 EYEHERDMHSAYKHADGKKIDGRRVLVDVERGRTVKGWRPRRLGGGLGGTRRGGADVNIR 209

Query: 85  EREDRERERERERERRERDREREKRERERDRDKEKDRERKSRDREKRRKVESDDSDEDKD 144
                +  R  ER        R++        +E+ RER      +R +           
Sbjct: 210 HSGRDDTSRYDERPGPSPLPHRDRDRDRERERRERSRERDKERERRRSRSRDRRRRSRSR 269

Query: 145 RDRKRRR-RHDDDHKERVRERSLSRSNRHRDENDESPREKLVEDDSDKKEKKTREEELED 203
              +RRR R     K+R R+R  SRS        E   E         +  +  +   +D
Sbjct: 270 DKEERRRSRERSKDKDRDRKRRSSRSRERARRERERKEELRGGGGDMAEPSEAGDAPPDD 329

Query: 204 EQRKLDEEMEKRRRRVQEWQELKRKKEESERENRGDANVEEPKAGRNWTLDREDSDDEEV 263
                           +     + ++     E     + +  +         E   +   
Sbjct: 330 GPPGELGPDGPDGPEEKGRDRDRERRRSHRSERERRRDRDRDRDRDREHKRGERGSERGR 389

Query: 264 PQTGKSETDMDADEEPKPSENQ 285
            +        D   E   ++++
Sbjct: 390 DEARGGGGGQDNGLEGLGNDSR 411

>3b6e_A Interferon-induced helicase C domain-containing P; DECH, DEXD/H RNA-binding helicase, innate immunity, IFIH1, S genomics; 1.60A {Homo sapiens} Length = 216

 Score = 71.8 bits (176), Expect = 3e-14
 Identities = 26/155 (16%), Positives = 56/155 (36%), Gaps = 5/155 (3%)

Query: 475 TSKIMETIRKLNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPP 534
              +          +  P Q +     + G++ I    TGSGKT   V     H+  +  
Sbjct: 19  EENVAARASPEPELQLRPYQMEVAQPALEGKNIIICLPTGSGKTRVAVYIAKDHLDKKKK 78

Query: 535 VAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQISELKRGTEIV 594
            +   G V +++     LV+Q+     +       R + + G + +     E+ +  +I+
Sbjct: 79  ASEP-GKV-IVLVNKVLLVEQLFRKEFQPFLKKWYRVIGLSGDTQLKISFPEVVKSCDII 136

Query: 595 VCTPGRMIDILCTSGG---KITNLRRVTYLVMDEA 626
           + T   + + L            L   + +++DE 
Sbjct: 137 ISTAQILENSLLNLENGEDAGVQLSDFSLIIIDEC 171

>1i84_S Smooth muscle myosin heavy chain; muscle protein, myosin subfragment 2, heavy meromyosin, essential light chain, motor protein; HET: MLY; 20.00A {Gallus gallus} SCOP: i.15.1.1 PDB: 3j04_A 3dtp_B 3dtp_A Length = 1184

 Score = 73.3 bits (180), Expect = 3e-13
 Identities = 39/228 (17%), Positives = 93/228 (40%), Gaps = 10/228 (4%)

Query: 8    RDREKEKEKHREKSRRSEREQSTDSDEDKHDKEKEKDKHRDRDRRRDRDRDRDREKEREE 67
            R  E+ + K  E  R  ER+Q  +++  + +++  +        +     + +   E EE
Sbjct: 854  RQEEEMQAKDEELQRTKERQQKAEAELKELEQKHTQLCEEKNLLQEKLQAETELYAEAEE 913

Query: 68   KRERAREKEREREKRDREREDRERERERERERRERDREREKRERERDRDKEKDRERKSRD 127
             R R   K++E E+   E E R  E E   ++ + ++++ +++     ++ ++ E   + 
Sbjct: 914  MRVRLAAKKQELEEILHEMEARIEEEEERSQQLQAEKKKMQQQMLDLEEQLEEEEAARQK 973

Query: 128  REKRRKVESDDSDEDKDRDRKRRRRHDDDHKERVRERSLSRSNRHRDENDESPREKLVED 187
             +  +        + +D       +++   KER          +  +E        L E+
Sbjct: 974  LQLEKVTADGKIKKMEDDILIMEDQNNKLTKER----------KLLEERVSDLTTNLAEE 1023

Query: 188  DSDKKEKKTREEELEDEQRKLDEEMEKRRRRVQEWQELKRKKEESERE 235
            +   K     + + E    +L+  ++K  +  QE +++KRK E    +
Sbjct: 1024 EEKAKNLTKLKNKHESMISELEVRLKKEEKSRQELEKIKRKLEGESSD 1071

>1i84_S Smooth muscle myosin heavy chain; muscle protein, myosin subfragment 2, heavy meromyosin, essential light chain, motor protein; HET: MLY; 20.00A {Gallus gallus} SCOP: i.15.1.1 PDB: 3j04_A 3dtp_B 3dtp_A Length = 1184

 Score = 70.6 bits (173), Expect = 2e-12
 Identities = 37/240 (15%), Positives = 99/240 (41%), Gaps = 2/240 (0%)

Query: 6    RDRDREKEKEKHREKSRRSEREQSTDSDEDKHDKEKEKDKHRDRDRRRDRDRDRDREKER 65
            ++R ++ E E    + + ++  +  +  ++K   E E     +  R R   + ++ E+  
Sbjct: 870  KERQQKAEAELKELEQKHTQLCEEKNLLQEKLQAETELYAEAEEMRVRLAAKKQELEEIL 929

Query: 66   EEKRERAREKEREREKRDREREDRERE-RERERERRERDREREKRERERDRDKEKDRERK 124
             E   R  E+E   ++   E++  +++  + E +  E +  R+K + E+     K ++ +
Sbjct: 930  HEMEARIEEEEERSQQLQAEKKKMQQQMLDLEEQLEEEEAARQKLQLEKVTADGKIKKME 989

Query: 125  SRDREKRRKVESDDSDEDKDRDRKRRRRHDDDHKERVRERSLSRSNRHRDENDESPREKL 184
                    +       E K  + +      +  +E  + ++L++     +        +L
Sbjct: 990  DDILIMEDQNNKLTK-ERKLLEERVSDLTTNLAEEEEKAKNLTKLKNKHESMISELEVRL 1048

Query: 185  VEDDSDKKEKKTREEELEDEQRKLDEEMEKRRRRVQEWQELKRKKEESERENRGDANVEE 244
             +++  ++E +  + +LE E   L E++ + + ++ E +    KKEE  +        E 
Sbjct: 1049 KKEEKSRQELEKIKRKLEGESSDLHEQIAELQAQIAELKAQLAKKEEELQAALARLEDET 1108

>1i84_S Smooth muscle myosin heavy chain; muscle protein, myosin subfragment 2, heavy meromyosin, essential light chain, motor protein; HET: MLY; 20.00A {Gallus gallus} SCOP: i.15.1.1 PDB: 3j04_A 3dtp_B 3dtp_A Length = 1184

 Score = 69.5 bits (170), Expect = 4e-12
 Identities = 38/236 (16%), Positives = 105/236 (44%), Gaps = 11/236 (4%)

Query: 4    SHRDRDREKEKEKHREKSRRSEREQSTDSDEDKHDKEKEKDKHRDRDRRRDRDRDRDREK 63
            +  +   E E+ + R  +++ E E+     E + ++E+E+ +    ++++ + +  D E+
Sbjct: 903  AETELYAEAEEMRVRLAAKKQELEEILHEMEARIEEEEERSQQLQAEKKKMQQQMLDLEE 962

Query: 64   ---EREEKRERAREKEREREKRDREREDRERERERERERRERDREREKRERERDRDKEKD 120
               E E  R++ + ++   + + ++ ED     E +  +  ++R+  +           +
Sbjct: 963  QLEEEEAARQKLQLEKVTADGKIKKMEDDILIMEDQNNKLTKERKLLEERVSDLTTNLAE 1022

Query: 121  RERKSRDREKRR-KVESDDSDEDKDRDRKRRRRHDDDHKERVRERSLSRSNRHRDENDES 179
             E K+++  K + K ES  S+ +    ++ + R + +  +R  E   S  +    E    
Sbjct: 1023 EEEKAKNLTKLKNKHESMISELEVRLKKEEKSRQELEKIKRKLEGESSDLHEQIAELQA- 1081

Query: 180  PREKLVEDDSDKKEKKTREEELEDEQRKLDEEMEKRRRRVQEWQELKRKKEESERE 235
                  +    K +   +EEEL+    +L++E  ++   +++ +EL+    + + +
Sbjct: 1082 ------QIAELKAQLAKKEEELQAALARLEDETSQKNNALKKIRELESHISDLQED 1131

>1i84_S Smooth muscle myosin heavy chain; muscle protein, myosin subfragment 2, heavy meromyosin, essential light chain, motor protein; HET: MLY; 20.00A {Gallus gallus} SCOP: i.15.1.1 PDB: 3j04_A 3dtp_B 3dtp_A Length = 1184

 Score = 69.5 bits (170), Expect = 5e-12
 Identities = 33/225 (14%), Positives = 88/225 (39%), Gaps = 7/225 (3%)

Query: 11   EKEKEKHREKSRRSEREQSTDSDEDKHDKEKEKDKHRDRDRRRDRDRDRDREKEREEKRE 70
            E+E  + + +  +   +      ED     ++++    ++R+   +R  D      E+ E
Sbjct: 966  EEEAARQKLQLEKVTADGKIKKMEDDILIMEDQNNKLTKERKLLEERVSDLTTNLAEEEE 1025

Query: 71   RAREKEREREKRDREREDRERERERERERRERDREREKRERERDRDKEKDRERKSRDREK 130
            +A+   + + K +    + E   ++E + R+ + E+ KR+ E     E     +     +
Sbjct: 1026 KAKNLTKLKNKHESMISELEVRLKKEEKSRQ-ELEKIKRKLE----GESSDLHEQIAELQ 1080

Query: 131  RRKVESDDSDEDKDRDRKRRRRHDDDHKERVRERSLSRSNRHRDENDESPREKLVEDDSD 190
             +  E       K+ + +      +D   + +  +L +         +  +E L  + + 
Sbjct: 1081 AQIAELKAQLAKKEEELQAALARLEDETSQ-KNNALKKIRELESHISD-LQEDLESEKAA 1138

Query: 191  KKEKKTREEELEDEQRKLDEEMEKRRRRVQEWQELKRKKEESERE 235
            + + + ++ +L +E   L  E+E         QEL+    + + +
Sbjct: 1139 RNKAEKQKRDLSEELEALKTELEDTLDTTATQQELRGSDYKDDDD 1183

>1i84_S Smooth muscle myosin heavy chain; muscle protein, myosin subfragment 2, heavy meromyosin, essential light chain, motor protein; HET: MLY; 20.00A {Gallus gallus} SCOP: i.15.1.1 PDB: 3j04_A 3dtp_B 3dtp_A Length = 1184

 Score = 68.7 bits (168), Expect = 8e-12
 Identities = 43/260 (16%), Positives = 97/260 (37%), Gaps = 24/260 (9%)

Query: 1    MAHSHRDRDREKEKEKHREKSRRSEREQSTDSDEDKHDKEKEKDKHRDR---DRRRDRDR 57
             A +   R R   K++  E+       +  + +E     + EK K + +      +  + 
Sbjct: 908  YAEAEEMRVRLAAKKQELEEILHEMEARIEEEEERSQQLQAEKKKMQQQMLDLEEQLEEE 967

Query: 58   DRDREKEREEKR----------ERAREKEREREKRDREREDRERE--------RERERER 99
            +  R+K + EK           +     E +  K  +ER+  E           E E + 
Sbjct: 968  EAARQKLQLEKVTADGKIKKMEDDILIMEDQNNKLTKERKLLEERVSDLTTNLAEEEEKA 1027

Query: 100  RERDREREKRERERDRDKEK-DRERKSRD--REKRRKVESDDSDEDKDRDRKRRRRHDDD 156
            +   + + K E      + +  +E KSR    + +RK+E + SD  +     + +  +  
Sbjct: 1028 KNLTKLKNKHESMISELEVRLKKEEKSRQELEKIKRKLEGESSDLHEQIAELQAQIAELK 1087

Query: 157  HKERVRERSLSRSNRHRDENDESPREKLVEDDSDKKEKKTREEELEDEQRKLDEEMEKRR 216
             +   +E  L  +    ++        L +    +      +E+LE E+   ++  +++R
Sbjct: 1088 AQLAKKEEELQAALARLEDETSQKNNALKKIRELESHISDLQEDLESEKAARNKAEKQKR 1147

Query: 217  RRVQEWQELKRKKEESEREN 236
               +E + LK + E++    
Sbjct: 1148 DLSEELEALKTELEDTLDTT 1167

>1i84_S Smooth muscle myosin heavy chain; muscle protein, myosin subfragment 2, heavy meromyosin, essential light chain, motor protein; HET: MLY; 20.00A {Gallus gallus} SCOP: i.15.1.1 PDB: 3j04_A 3dtp_B 3dtp_A Length = 1184

 Score = 66.4 bits (162), Expect = 4e-11
 Identities = 36/225 (16%), Positives = 92/225 (40%), Gaps = 12/225 (5%)

Query: 20   KSRRSEREQSTDSDEDKHDKEKEKDKHRDRDRRRDRDRDRDREKEREEKRERAREKERER 79
            K  R E E     +E +  KE+++    +      +      EK   +++ +A E E   
Sbjct: 851  KVTRQEEEMQAKDEELQRTKERQQKAEAELKELEQKHTQLCEEKNLLQEKLQA-ETELYA 909

Query: 80   EKRDREREDRERERERERERRERDREREKRERERDRDKEKDRERKSRDREKRRKVESDDS 139
            E  +       +++E E    E +   E+ E    + + + ++ + +  +   ++E    
Sbjct: 910  EAEEMRVRLAAKKQELEEILHEMEARIEEEEERSQQLQAEKKKMQQQMLDLEEQLE---- 965

Query: 140  DEDKDRDRKRRRRHDDDHKERVRERSLS---RSNRHRDENDESPREKLVEDDSDKKEKKT 196
            +E+  R + +  +   D K +  E  +      N    +  +   E++ +  ++  E++ 
Sbjct: 966  EEEAARQKLQLEKVTADGKIKKMEDDILIMEDQNNKLTKERKLLEERVSDLTTNLAEEEE 1025

Query: 197  REEELEDEQRKLDEEMEKRRRRVQE----WQELKRKKEESERENR 237
            + + L   + K +  + +   R+++     QEL++ K + E E+ 
Sbjct: 1026 KAKNLTKLKNKHESMISELEVRLKKEEKSRQELEKIKRKLEGESS 1070

>1i84_S Smooth muscle myosin heavy chain; muscle protein, myosin subfragment 2, heavy meromyosin, essential light chain, motor protein; HET: MLY; 20.00A {Gallus gallus} SCOP: i.15.1.1 PDB: 3j04_A 3dtp_B 3dtp_A Length = 1184

 Score = 57.2 bits (138), Expect = 3e-08
 Identities = 16/181 (8%), Positives = 70/181 (38%), Gaps = 4/181 (2%)

Query: 61   REKEREEKRERAREKEREREKRDREREDRERERERERERRERDREREKRERERDRDKEKD 120
                             +  +++ E + ++ E +R +ER+++     K   ++     ++
Sbjct: 834  VXHWPWMXLFFXIXPLLKVTRQEEEMQAKDEELQRTKERQQKAEAELKELEQKHTQLCEE 893

Query: 121  RERKSRDREKRRKVESDDSDEDKDRDRKRRRRHDDDHKERVRERSLSRSNRHRDENDESP 180
            +       +   ++ ++  +       K++   +  H+   R       ++      +  
Sbjct: 894  KNLLQEKLQAETELYAEAEEMRVRLAAKKQELEEILHEMEARIEEEEERSQQLQAEKKKM 953

Query: 181  REKLVEDDSDKKEKKTREEELEDEQRKLDEEMEKRRRRVQEWQE----LKRKKEESEREN 236
            ++++++ +   +E++   ++L+ E+   D +++K    +   ++    L ++++  E   
Sbjct: 954  QQQMLDLEEQLEEEEAARQKLQLEKVTADGKIKKMEDDILIMEDQNNKLTKERKLLEERV 1013

Query: 237  R 237
             
Sbjct: 1014 S 1014

>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* Length = 440

 Score = 71.0 bits (174), Expect = 7e-13
 Identities = 47/357 (13%), Positives = 94/357 (26%), Gaps = 84/357 (23%)

Query: 500 VIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSD 559
           ++  G   +     G+GKT  F+  +L         A       L++APTR ++ ++   
Sbjct: 4   MLKKGMTTVLDFHPGAGKTRRFLPQILAE------CARRRLRT-LVLAPTRVVLSEMKEA 56

Query: 560 IRKFAKVMGVRCVPVYGGSGVAQQISELKRGTEIVVCTPG---RMIDILCTSGGKITNLR 616
                     +    +G                I           +        + T + 
Sbjct: 57  FHGLDVKFHTQAFSAHGSGR-----------EVIDAMCHATLTYRML-------EPTRVV 98

Query: 617 RVTYLVMDE-----ADRMFDMGFEPQITRIVQNIRPDRQTVLFSATFP---RQVEILARK 668
               ++MDE        +   G+     R       +  T+L +AT P    +      +
Sbjct: 99  NWEVIIMDEAHFLDPASIAARGWAAHRAR-----ANESATILMTATPPGTSDEFPHSNGE 153

Query: 669 VLNKPVEIQVGGRSVVNKDITQLVEVRPESDRFLRLLELLGEWYEKGKILIFVHSQEKCD 728
           + +   +I     +  +  I                        +K     F+ S    +
Sbjct: 154 IEDVQTDIPSEPWNTGHDWILA----------------------DKRPTAWFLPSIRAAN 191

Query: 729 ALFRDLLKHGYPCLSLHGAKDQTDRESTISDFKSNVCNLLIATSVAARGL--DVK----- 781
            +   L K G   + L+    + +        K    + ++AT +A  G    V+     
Sbjct: 192 VMAASLRKAGKSVVVLNRKTFERE----YPTIKQKKPDFILATDIAEMGANLCVERVLDC 247

Query: 782 ELELVINFDAPNHY--------EDYVHRVGRTGRAGRK--GCAITFISEEDAKYSPD 828
                                         R GR GR       ++   E    +  
Sbjct: 248 RTAFKPVLVDEGRKVAIKGPLRISASSAAQRRGRIGRNPNRDGDSYYYSEPTSENNA 304

>2dfs_A Myosin-5A; myosin-V, inhibited state, cryoelectron tomograp contractIle protein-transport protein complex; 24.00A {Gallus gallus} Length = 1080

 Score = 72.1 bits (177), Expect = 7e-13
 Identities = 32/228 (14%), Positives = 86/228 (37%), Gaps = 6/228 (2%)

Query: 10   REKEKEKHREKSRRSEREQSTDSDEDKHDKEKEKDKHRDRDRRRDRDRDRDREKEREEKR 69
             + +      KS   ++          + +  +   +     RR   + R+ +K + E R
Sbjct: 856  NKYQMMLREHKSIIIQKHVRGWLARVHYHRTLKAIVYLQCCYRRMMAK-RELKKLKIEAR 914

Query: 70   ERAREKEREREKRDREREDRERERERERERRERDREREKRERERDRDKEKDRERKSRDRE 129
               R K+      ++  + + +  E+ +E +    +    E     + EK R    R R 
Sbjct: 915  SVERYKKLHIGLENKIMQLQRKIDEQNKEYKSLLEKMNNLEITYSTETEKLRSDVERLRM 974

Query: 130  KRRKVESDDSDEDKDRDRKRRRRHDDDHKERVRERSLSRSNRHRDENDESPREKLVEDDS 189
               + ++  +     ++   + R +    +  ++     +++++ E ++   E   ++  
Sbjct: 975  SEEEAKNATNRVLSLQEEIAKLRKELHQTQTEKKTIEEWADKYKHETEQLVSELKEQNTL 1034

Query: 190  DKKEKKTREEELEDEQRKLDEEMEKRRRRVQEWQELKRKKEESERENR 237
             K EK+     + D+ +++ E MEK+       +E K+ + +   E  
Sbjct: 1035 LKTEKEELNRRIHDQAKEITETMEKKLV-----EETKQLELDLNDERL 1077

>2dfs_A Myosin-5A; myosin-V, inhibited state, cryoelectron tomograp contractIle protein-transport protein complex; 24.00A {Gallus gallus} Length = 1080

 Score = 69.0 bits (169), Expect = 6e-12
 Identities = 32/212 (15%), Positives = 78/212 (36%), Gaps = 7/212 (3%)

Query: 10   REKEKEKHREKSRRSEREQSTDSDEDKHDKEKEKDKHRDRDRRRDRDRDRDREKEREEKR 69
            R      H  ++ ++               ++E  K +   R  +R +      E +  +
Sbjct: 875  RGWLARVHYHRTLKAIVYLQCCYRRMM--AKRELKKLKIEARSVERYKKLHIGLENKIMQ 932

Query: 70   ERAREKEREREKRDREREDRERERERERERRE-RDREREKRERERDRDKEKDRERKSRDR 128
             + +  E+ +E +    +    E     E  + R      R  E +     +R    ++ 
Sbjct: 933  LQRKIDEQNKEYKSLLEKMNNLEITYSTETEKLRSDVERLRMSEEEAKNATNRVLSLQEE 992

Query: 129  EKRRKVESDDSDEDKDRDRKRRRRHDDDHKERVRERSLSRSNRHRDENDESPREKLVEDD 188
              + + E   +  +K    +   ++  + ++ V E    ++   + E +E  R      D
Sbjct: 993  IAKLRKELHQTQTEKKTIEEWADKYKHETEQLVSELK-EQNTLLKTEKEELNRRI---HD 1048

Query: 189  SDKKEKKTREEELEDEQRKLDEEMEKRRRRVQ 220
              K+  +T E++L +E ++L+ ++   R R Q
Sbjct: 1049 QAKEITETMEKKLVEETKQLELDLNDERLRYQ 1080

>2dfs_A Myosin-5A; myosin-V, inhibited state, cryoelectron tomograp contractIle protein-transport protein complex; 24.00A {Gallus gallus} Length = 1080

 Score = 67.4 bits (165), Expect = 2e-11
 Identities = 31/245 (12%), Positives = 80/245 (32%), Gaps = 8/245 (3%)

Query: 6    RDRDREKEKEKHREKSRRSE-REQSTDSDEDKHDKEKEKDKHRDRDRRRDRDRDRDREKE 64
            R +         +   R    R +      +      +K       R       +     
Sbjct: 834  RYQCMRDATIALQALLRGYLVRNKYQMMLREHKSIIIQKHVRGWLARVHYHRTLKAIVYL 893

Query: 65   REEKRERAREKEREREKRDREREDRERERERERERRERDREREKRERERDRDKEKDRERK 124
            +   R    ++E ++ K +    +R ++     E +    +R+  E+ ++  K    +  
Sbjct: 894  QCCYRRMMAKRELKKLKIEARSVERYKKLHIGLENKIMQLQRKIDEQNKEY-KSLLEKMN 952

Query: 125  SRDREKRRKVESDDSDEDKDRDRKRRRRHDDDHKERVRERSLSRSNRHRDENDESPREKL 184
            + +     + E   SD +           +  ++    +  +++  +   +     +   
Sbjct: 953  NLEITYSTETEKLRSDVE-RLRMSEEEAKNATNRVLSLQEEIAKLRKELHQTQTEKKTIE 1011

Query: 185  VEDDSDKKEKKTREEELEDEQRKLDEEMEKRRRRVQE-----WQELKRKKEESERENRGD 239
               D  K E +    EL+++   L  E E+  RR+ +      + +++K  E  ++   D
Sbjct: 1012 EWADKYKHETEQLVSELKEQNTLLKTEKEELNRRIHDQAKEITETMEKKLVEETKQLELD 1071

Query: 240  ANVEE 244
             N E 
Sbjct: 1072 LNDER 1076

>2dfs_A Myosin-5A; myosin-V, inhibited state, cryoelectron tomograp contractIle protein-transport protein complex; 24.00A {Gallus gallus} Length = 1080

 Score = 58.6 bits (142), Expect = 1e-08
 Identities = 31/209 (14%), Positives = 73/209 (34%), Gaps = 13/209 (6%)

Query: 49   RDRRRDRDRDRDRE-KEREEKRERAREKEREREKRDREREDRERERERERERRERDRERE 107
            + +R    R R +  ++     +        R K      + +    ++  R    R   
Sbjct: 824  KFQRMYVVRKRYQCMRDATIALQALLRGYLVRNKYQMMLREHKSIIIQKHVRGWLARVHY 883

Query: 108  KRERERDRDKEKD-RERKSRDREKRRKVESDDSDEDK-------DRDRKRRRRHDDDHKE 159
             R  +     +   R   ++   K+ K+E+   +  K       ++  + +R+ D+ +KE
Sbjct: 884  HRTLKAIVYLQCCYRRMMAKRELKKLKIEARSVERYKKLHIGLENKIMQLQRKIDEQNKE 943

Query: 160  RVRE----RSLSRSNRHRDENDESPREKLVEDDSDKKEKKTREEELEDEQRKLDEEMEKR 215
                     +L  +     E   S  E+L   + + K    R   L++E  KL +E+ + 
Sbjct: 944  YKSLLEKMNNLEITYSTETEKLRSDVERLRMSEEEAKNATNRVLSLQEEIAKLRKELHQT 1003

Query: 216  RRRVQEWQELKRKKEESERENRGDANVEE 244
            +   +  +E   K +    +   +   + 
Sbjct: 1004 QTEKKTIEEWADKYKHETEQLVSELKEQN 1032

>2dfs_A Myosin-5A; myosin-V, inhibited state, cryoelectron tomograp contractIle protein-transport protein complex; 24.00A {Gallus gallus} Length = 1080

 Score = 45.9 bits (109), Expect = 7e-05
 Identities = 21/175 (12%), Positives = 52/175 (29%)

Query: 61  REKEREEKRERAREKEREREKRDREREDRERERERERERRERDREREKRERERDRDKEKD 120
           R      +R RA    ++ ++    R+  +  R+     +   R    R + +   +E  
Sbjct: 807 RCYATFLRRTRAAIIIQKFQRMYVVRKRYQCMRDATIALQALLRGYLVRNKYQMMLREHK 866

Query: 121 RERKSRDREKRRKVESDDSDEDKDRDRKRRRRHDDDHKERVRERSLSRSNRHRDENDESP 180
                +                     +   R     +E  + +  +RS     +     
Sbjct: 867 SIIIQKHVRGWLARVHYHRTLKAIVYLQCCYRRMMAKRELKKLKIEARSVERYKKLHIGL 926

Query: 181 REKLVEDDSDKKEKKTREEELEDEQRKLDEEMEKRRRRVQEWQELKRKKEESERE 235
             K+++      E+    + L ++   L+        +++   E  R  EE  + 
Sbjct: 927 ENKIMQLQRKIDEQNKEYKSLLEKMNNLEITYSTETEKLRSDVERLRMSEEEAKN 981

>2dfs_A Myosin-5A; myosin-V, inhibited state, cryoelectron tomograp contractIle protein-transport protein complex; 24.00A {Gallus gallus} Length = 1080

 Score = 44.3 bits (105), Expect = 2e-04
 Identities = 18/110 (16%), Positives = 40/110 (36%), Gaps = 2/110 (1%)

Query: 7    DRDREKEKEKHREKSRRSEREQSTDS-DEDKHDKEKEKDKHRDRDRRRDRDRDRDREKER 65
            +R R  E+E     +R    ++      ++ H  + EK K  +    + +        E 
Sbjct: 970  ERLRMSEEEAKNATNRVLSLQEEIAKLRKELHQTQTEK-KTIEEWADKYKHETEQLVSEL 1028

Query: 66   EEKRERAREKEREREKRDREREDRERERERERERRERDREREKRERERDR 115
            +E+    + ++ E  +R  ++     E   ++   E  +       ER R
Sbjct: 1029 KEQNTLLKTEKEELNRRIHDQAKEITETMEKKLVEETKQLELDLNDERLR 1078

>2dfs_A Myosin-5A; myosin-V, inhibited state, cryoelectron tomograp contractIle protein-transport protein complex; 24.00A {Gallus gallus} Length = 1080

 Score = 43.6 bits (103), Expect = 3e-04
 Identities = 34/180 (18%), Positives = 62/180 (34%), Gaps = 27/180 (15%)

Query: 69  RERAREKERER-----EKRDREREDRERERERERERRERDREREKRERERDRDKEKDRER 123
           R  A    R R     +K  R    R+R +   R+     +   +    R++ +   RE 
Sbjct: 807 RCYATFLRRTRAAIIIQKFQRMYVVRKRYQCM-RDATIALQALLRGYLVRNKYQMMLREH 865

Query: 124 KSRDREKRRKVESDDSDEDKDRDRKRRRRHDDDHKERVRERSLSRSNRHRDENDESPREK 183
           KS   +K              R    R  +    K  V  +   R    + E      +K
Sbjct: 866 KSIIIQKHV------------RGWLARVHYHRTLKAIVYLQCCYRRMMAKRE-----LKK 908

Query: 184 LVEDDSDKKEKKTREEELEDE----QRKLDEEMEKRRRRVQEWQELKRKKEESERENRGD 239
           L  +    +  K     LE++    QRK+DE+ ++ +  +++   L+        + R D
Sbjct: 909 LKIEARSVERYKKLHIGLENKIMQLQRKIDEQNKEYKSLLEKMNNLEITYSTETEKLRSD 968

>2va8_A SSO2462, SKI2-type helicase; hydrolase, DNA repair, ATP-bindin nucleotide-binding; 2.30A {Sulfolobus solfataricus} Length = 715

 Score = 70.5 bits (173), Expect = 1e-12
 Identities = 58/327 (17%), Positives = 118/327 (36%), Gaps = 47/327 (14%)

Query: 463 PKPIKTWHQTGLTSKIMETIRKLNYEKPMPIQAQALP-VIMSGRDCIGVAKTGSGKTLAF 521
             PI+      L S ++E I+K   +K  P Q +A+   ++ G   +  + TGSGKTL  
Sbjct: 7   WMPIEDL---KLPSNVIEIIKKRGIKKLNPPQTEAVKKGLLEGNRLLLTSPTGSGKTLIA 63

Query: 522 VLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVA 581
            + ++  +         +G   + + P R L  + +   + +   +G +     G     
Sbjct: 64  EMGIISFLLK-------NGGKAIYVTPLRALTNEKYLTFKDWEL-IGFKVAMTSGDY--- 112

Query: 582 QQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDE------ADRMFDMG-- 633
                  +  +I++ T  ++ D L     +   L  V Y V+DE       +R    G  
Sbjct: 113 DTDDAWLKNYDIIITTYEKL-DSLWRHRPEW--LNEVNYFVLDELHYLNDPER----GPV 165

Query: 634 FEPQITRIVQNIRPDRQTVLFSATFPRQVEI---LARKVLNK---PVEIQVG--GRSVVN 685
            E    R  +     R  +  SAT     +I   L  + +     PV +  G        
Sbjct: 166 VESVTIRAKR-----RNLLALSATISNYKQIAKWLGAEPVATNWRPVPLIEGVIYPERKK 220

Query: 686 KDITQLVEVRPESDRFL--RLLELLGEWYEKGK-ILIFVHSQEKCDALFRDLLKH-GYPC 741
           K+   + +            ++    +   K   +L+F +S++  ++    +  +  +  
Sbjct: 221 KEYNVIFKDNTTKKVHGDDAIIAYTLDSLSKNGQVLVFRNSRKMAESTALKIANYMNFVS 280

Query: 742 LSLHGAKDQTDRESTISDFKSNVCNLL 768
           L  +   +   +   I +  S+   LL
Sbjct: 281 LDENALSEILKQLDDIEEGGSDEKELL 307

>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} Length = 797

 Score = 70.0 bits (170), Expect = 2e-12
 Identities = 47/360 (13%), Positives = 110/360 (30%), Gaps = 21/360 (5%)

Query: 391 EKPLEDEDDDEFMKRVKKTKAEKLSIVDHSKIDYQPFRKNFYIEVKEIARMTPEEVSAYR 450
           E     + +                         +   K+   E+ + +    E    Y 
Sbjct: 158 ECLCRSDKEHWPKSLQLALDTTGYYRASELWDIREDNAKDVDSEMTDASEDCLEASMTYS 217

Query: 451 KQLELKIHGKDVPKPIKTWHQTGLTSKIMETIRKLNYEKPMPIQAQALPVIMSGRDCIGV 510
           ++ E   +  +                  +  R          Q +     ++G++ +  
Sbjct: 218 EEAEPDDNLSENLGSAAEGIGKPPPVYETKKAR--------SYQIELAQPAINGKNALIC 269

Query: 511 AKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVMGVR 570
           A TGSGKT   +L    H ++ P   AG     + +A    + +Q  +  +   +  G  
Sbjct: 270 APTGSGKTFVSILICEHHFQNMP---AGRKAKVVFLATKVPVYEQQKNVFKHHFERQGYS 326

Query: 571 CVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMF 630
              + G +     + ++   ++I+V TP  +++      G +T+L   T ++ DE     
Sbjct: 327 VQGISGENFSNVSVEKVIEDSDIIVVTPQILVNSFED--GTLTSLSIFTLMIFDECHNTT 384

Query: 631 DMGFEPQITRIVQNIRPDRQTVLF-----SATFPRQVEILARKVLNKPVEIQVGGRSVVN 685
                  +       + +  + L      +A+          + +     +         
Sbjct: 385 GNHPYNVLMTRYLEQKFNSASQLPQILGLTASVGVGNAKNIEETIEHICSLCSYLDI--- 441

Query: 686 KDITQLVEVRPESDRFLRLLELLGEWYEKGKILIFVHSQEKCDALFRDLLKHGYPCLSLH 745
           + I+ + E   E  RF+   E+     ++     F        +    L++  Y   +L 
Sbjct: 442 QAISTVRENIQELQRFMNKPEIDVRLVKRRIHNPFAAIISNLMSETEALMRTIYSVDTLS 501

>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} Length = 797

 Score = 52.7 bits (125), Expect = 6e-07
 Identities = 36/177 (20%), Positives = 70/177 (39%), Gaps = 17/177 (9%)

Query: 697 ESDRFLRLLELLGEWYEKG---KILIFVHSQEKCDALFRDLLKH------------GYPC 741
           E+ +   L+ +L + Y      + L+F  ++    AL + + ++            G   
Sbjct: 611 ENPKLEELVCILDDAYRYNPQTRTLLFAKTRALVSALKKCMEENPILNYIKPGVLMGRGR 670

Query: 742 LSLHGAKDQTDRESTISDFKSNVCN-LLIATSVAARGLDVKELELVINFDAPNHYEDYVH 800
                      ++  +  FK++  N LLIATSVA  G+D+ +  LV+ ++   +    + 
Sbjct: 671 RDQTTGMTLPSQKGVLDAFKTSKDNRLLIATSVADEGIDIVQCNLVVLYEYSGNVTKMIQ 730

Query: 801 RVGRTGRAGRKGCAITFISEEDAKYSPDLVKALELSEQVVPDDLKALADSFMAKVNQ 857
             GR GRA    C +     E  +         E+  + V    K   ++F  K++ 
Sbjct: 731 VRGR-GRAAGSKCILVTSKTEVVENEKCNRYKEEMMNKAVEKIQKWDEETFAKKIHN 786

>2zuo_A MVP, major vault protein; repeat domains, protein-protein complex, cytoplasm, ribonucleoprotein, structural protein; 3.50A {Rattus norvegicus} PDB: 2zv4_N 2zv5_a 2qzv_A Length = 861

 Score = 70.2 bits (171), Expect = 2e-12
 Identities = 28/218 (12%), Positives = 60/218 (27%), Gaps = 1/218 (0%)

Query: 3   HSHRDRDREKEKEKHREKSRRSEREQSTDSDEDKHDKEKEKDKHRDRDRRRDRDRDRDRE 62
               D   +              +     S  D    E    + RD  +R  +       
Sbjct: 607 EMSEDTGPDGTLLPKARDQAVFPQNGLVVSSVDVQSVEPVDQRTRDALQRSVQLAIEITT 666

Query: 63  KEREEKRERAREKEREREKRDREREDRERERERERERRERDREREKRERERDRDKEKDRE 122
             +E   +   ++  +  +   ER+    + E E+ R+E                 K  E
Sbjct: 667 NSQEAAAKHEAQRLEQEARGRLERQKILDQSEAEKARKELLELEAMSMAVESTGNAK-AE 725

Query: 123 RKSRDREKRRKVESDDSDEDKDRDRKRRRRHDDDHKERVRERSLSRSNRHRDENDESPRE 182
            +SR    R + E                   +  + +          R + E + S  +
Sbjct: 726 AESRAEAARIEGEGSVLQAKLKAQALAIETEAELERVKKVREMELIYARAQLELEVSKAQ 785

Query: 183 KLVEDDSDKKEKKTREEELEDEQRKLDEEMEKRRRRVQ 220
           +L   ++ K ++ T        +       E + + +Q
Sbjct: 786 QLANVEAKKFKEMTEALGPGTIRDLAVAGPEMQVKLLQ 823

>2zuo_A MVP, major vault protein; repeat domains, protein-protein complex, cytoplasm, ribonucleoprotein, structural protein; 3.50A {Rattus norvegicus} PDB: 2zv4_N 2zv5_a 2qzv_A Length = 861

 Score = 60.2 bits (145), Expect = 3e-09
 Identities = 20/141 (14%), Positives = 50/141 (35%)

Query: 1   MAHSHRDRDREKEKEKHREKSRRSEREQSTDSDEDKHDKEKEKDKHRDRDRRRDRDRDRD 60
             +S     + + +   +E   R ER++  D  E +  +++  +              + 
Sbjct: 665 TTNSQEAAAKHEAQRLEQEARGRLERQKILDQSEAEKARKELLELEAMSMAVESTGNAKA 724

Query: 61  REKEREEKRERAREKEREREKRDREREDRERERERERERRERDREREKRERERDRDKEKD 120
             + R E      E    + K   +    E E E ER ++ R+ E      + + +  K 
Sbjct: 725 EAESRAEAARIEGEGSVLQAKLKAQALAIETEAELERVKKVREMELIYARAQLELEVSKA 784

Query: 121 RERKSRDREKRRKVESDDSDE 141
           ++  + + +K +++       
Sbjct: 785 QQLANVEAKKFKEMTEALGPG 805

>2zuo_A MVP, major vault protein; repeat domains, protein-protein complex, cytoplasm, ribonucleoprotein, structural protein; 3.50A {Rattus norvegicus} PDB: 2zv4_N 2zv5_a 2qzv_A Length = 861

 Score = 56.0 bits (134), Expect = 5e-08
 Identities = 34/235 (14%), Positives = 67/235 (28%), Gaps = 31/235 (13%)

Query: 1   MAHSHRDRDREKEKEKHREKSRRSEREQSTDSDEDKHDKEKEKDKHRDRDRRRDRDRDRD 60
               H++  R         +         T   + +      ++               D
Sbjct: 588 FDDFHKNSARIIRMAVFGFEMSEDTGPDGTLLPKARDQAVFPQNGLVVSSVDVQSVEPVD 647

Query: 61  REKEREEKRERAREKEREREKRDREREDRERERERERERRERDREREKRERERDRDKEKD 120
           +      +R      E     ++   +  E +R  +  R   +R++   + E     EK 
Sbjct: 648 QRTRDALQRSVQLAIEITTNSQEAAAK-HEAQRLEQEARGRLERQKILDQSEA----EKA 702

Query: 121 RERKSRDREKRRKVESDDSDEDKDRDRKRRRRHDDDHKERVRERSLSRSNRHRDENDESP 180
           R+           VES                         +  + SR+   R E + S 
Sbjct: 703 RKELLELEAMSMAVES---------------------TGNAKAEAESRAEAARIEGEGSV 741

Query: 181 REKLVEDDSDKKEKKTREEELEDEQRKLDEEMEKRRRRVQEWQELKRKKEESERE 235
            +  ++      +    E E E E+ K   EME    R Q   E+ + ++ +  E
Sbjct: 742 LQAKLK-----AQALAIETEAELERVKKVREMELIYARAQLELEVSKAQQLANVE 791

>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* Length = 556

 Score = 69.2 bits (168), Expect = 3e-12
 Identities = 41/262 (15%), Positives = 93/262 (35%), Gaps = 13/262 (4%)

Query: 489 KPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAP 548
           K    Q +     ++G++ +  A TGSGKT   +L    H ++ P   AG     + +A 
Sbjct: 7   KARSYQIELAQPAINGKNALICAPTGSGKTFVSILICEHHFQNMP---AGRKAKVVFLAT 63

Query: 549 TRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTS 608
              + +Q  +  +   +  G     + G +     + ++   ++I+V TP  +++     
Sbjct: 64  KVPVYEQQKNVFKHHFERQGYSVQGISGENFSNVSVEKVIEDSDIIVVTPQILVNSFED- 122

Query: 609 GGKITNLRRVTYLVMDEADRMFDMGFEPQITRIVQNIRPDRQTVLF-----SATFPRQVE 663
            G +T+L   T ++ DE            +       + +  + L      +A+      
Sbjct: 123 -GTLTSLSIFTLMIFDECHNTTGNHPYNVLMTRYLEQKFNSASQLPQILGLTASVGVGNA 181

Query: 664 ILARKVLNKPVEIQVGGRSVVNKDITQLVEVRPESDRFLRLLELLGEWYEKGKILIFVHS 723
               + +     +      +  + I+ + E   E  RF+   E+     ++     F   
Sbjct: 182 KNIEETIEHICSLC---SYLDIQAISTVRENIQELQRFMNKPEIDVRLVKRRIHNPFAAI 238

Query: 724 QEKCDALFRDLLKHGYPCLSLH 745
                +    L++  Y   +L 
Sbjct: 239 ISNLMSETEALMRTIYSVDTLS 260

>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* Length = 556

 Score = 58.8 bits (141), Expect = 6e-09
 Identities = 31/155 (20%), Positives = 63/155 (40%), Gaps = 15/155 (9%)

Query: 693 EVRPESDRFLRLLELLGEWYEKGKILIFVHSQEKCDALFRDLLKH----GYPCLSLHGAK 748
              P+ +  + +L+    +  + + L+F  ++    AL + + ++          L G  
Sbjct: 369 NENPKLEELVCILDDAYRYNPQTRTLLFAKTRALVSALKKCMEENPILNYIKPGVLMGRG 428

Query: 749 --------DQTDRESTISDFKSNVCN-LLIATSVAARGLDVKELELVINFDAPNHYEDYV 799
                       ++  +  FK++  N LLIATSVA  G+D+ +  LV+ ++   +    +
Sbjct: 429 RRDQTTGMTLPSQKGVLDAFKTSKDNRLLIATSVADEGIDIVQCNLVVLYEYSGNVTKMI 488

Query: 800 HRVGRTGRAGRKGCAITFISEEDAKYSPDLVKALE 834
              GR GRA      I   S+ +   +    +  E
Sbjct: 489 QVRGR-GRA-AGSKCILVTSKTEVVENEKCNRYKE 521

>1g8x_A Myosin II heavy chain fused to alpha-actinin 3; motor, lever ARM, protein engineering, structural protein; HET: ADP; 2.80A {Dictyostelium discoideum} SCOP: k.1.1.1 Length = 1010

 Score = 69.3 bits (170), Expect = 5e-12
 Identities = 22/203 (10%), Positives = 57/203 (28%), Gaps = 1/203 (0%)

Query: 5    HRDRDREKEKEKHREKSRRSEREQSTDSDEDKHDKEKEKDKHRDRDRRRDRDRDRDREKE 64
            H++  + ++  K +E S       S  +      +E             D       + E
Sbjct: 808  HKEYKKTEKPPKGQEVSELEAIYNSLQTKLRLIKREPFVAPAGLTPNEIDSTWSALEKAE 867

Query: 65   REEKRERAREKEREREKRDREREDRERERERERERRERDREREKRERERDRDKEKDRERK 124
            +E       E +R+++     ++     ++ E     +       E        + + + 
Sbjct: 868  QEHAEALRIELKRQKKIAVLLQKYNRILKKLENWATTKSVYLGSNETGDSITAVQAKLKN 927

Query: 125  SRDREKRRKVESDDSDEDKDRDRKRRRRHDDDHKERVRERSLSRSNRHRDENDESPREKL 184
                +   +     S+ D      +    + +    + ER        +    +S  E  
Sbjct: 928  LEAFDGECQSLEGQSNSDLLSILAQLTELNYNGVPELTER-KDTFFAQQWTGVKSSAETY 986

Query: 185  VEDDSDKKEKKTREEELEDEQRK 207
                  + E+  + E+L      
Sbjct: 987  KNTLLAELERLQKIEDLHHHHHH 1009

>1g8x_A Myosin II heavy chain fused to alpha-actinin 3; motor, lever ARM, protein engineering, structural protein; HET: ADP; 2.80A {Dictyostelium discoideum} SCOP: k.1.1.1 Length = 1010

 Score = 62.4 bits (152), Expect = 6e-10
 Identities = 17/207 (8%), Positives = 57/207 (27%), Gaps = 30/207 (14%)

Query: 49   RDRRRDRDRDRDREKEREEKRERAREKEREREKRD------------------------R 84
            ++ ++     + +E    E    + + +    KR+                        +
Sbjct: 809  KEYKKTEKPPKGQEVSELEAIYNSLQTKLRLIKREPFVAPAGLTPNEIDSTWSALEKAEQ 868

Query: 85   EREDRERERERERERRERDREREKRERERDRDKEKDRERKSRDREKRRKVESDDSDEDKD 144
            E  +  R   + +++     ++  R  ++  +    +       E    + +  +     
Sbjct: 869  EHAEALRIELKRQKKIAVLLQKYNRILKKLENWATTKSVYLGSNETGDSITAVQAKLKNL 928

Query: 145  RDRKRRRRHDDDHKERVRERSLSRSNRHRDENDESPREKLVEDDSDKKEKKTREEELEDE 204
                   +  +          L++             E+   D    ++    +   E  
Sbjct: 929  EAFDGECQSLEGQSNSDLLSILAQLTELNYNGVPELTERK--DTFFAQQWTGVKSSAETY 986

Query: 205  QRKLDEEMEKRRRRVQEWQELKRKKEE 231
            +  L  E+E+    +Q+ ++L      
Sbjct: 987  KNTLLAELER----LQKIEDLHHHHHH 1009

>1g8x_A Myosin II heavy chain fused to alpha-actinin 3; motor, lever ARM, protein engineering, structural protein; HET: ADP; 2.80A {Dictyostelium discoideum} SCOP: k.1.1.1 Length = 1010

 Score = 57.4 bits (139), Expect = 2e-08
 Identities = 17/237 (7%), Positives = 68/237 (28%), Gaps = 24/237 (10%)

Query: 62  EKEREEKRERA-------------REKEREREKRDREREDRER---ERERERERRERDR- 104
           E+ RE++                  +   +++     R+  +     +      +E  + 
Sbjct: 755 EEAREQRLGSEQTKSDYLKRANELVQWINDKQASLESRDFGDSIESVQSFMNAHKEYKKT 814

Query: 105 EREKRERERDRDKEKDRERKSRDREKRRKVESDDSDEDKDRDRKRRRRHDDDHKERVRER 164
           E+  + +E    +      +++ R  +R+     +    +             ++  +E 
Sbjct: 815 EKPPKGQEVSELEAIYNSLQTKLRLIKREPFVAPAGLTPNEIDSTWSA----LEKAEQEH 870

Query: 165 SLSRSNRHRDENDESPREKLVEDDSDKKEKKTREEELEDEQRKLDEEMEKRRRRVQEWQE 224
           + +     + +   +   +       K E     + +     +  + +   + +++  + 
Sbjct: 871 AEALRIELKRQKKIAVLLQKYNRILKKLENWATTKSVYLGSNETGDSITAVQAKLKNLEA 930

Query: 225 LKRKKEESERENRGD---ANVEEPKAGRNWTLDREDSDDEEVPQTGKSETDMDADEE 278
              + +  E ++  D      +  +   N   +  +  D    Q            +
Sbjct: 931 FDGECQSLEGQSNSDLLSILAQLTELNYNGVPELTERKDTFFAQQWTGVKSSAETYK 987

>2ykg_A Probable ATP-dependent RNA helicase DDX58; hydrolase, innate immunity; 2.50A {Homo sapiens} PDB: 3tmi_A* Length = 696

 Score = 67.3 bits (163), Expect = 1e-11
 Identities = 35/152 (23%), Positives = 59/152 (38%), Gaps = 5/152 (3%)

Query: 489 KPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAP 548
           KP   Q +     M G++ I  A TG GKT   +L    H+K  P    G     +  A 
Sbjct: 13  KPRNYQLELALPAMKGKNTIICAPTGCGKTFVSLLICEHHLKKFP---QGQKGKVVFFAN 69

Query: 549 TRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTS 608
              + +Q  S   K+ +  G R   + G +     + ++    +I++ TP  +++ L   
Sbjct: 70  QIPVYEQNKSVFSKYFERHGYRVTGISGATAENVPVEQIVENNDIIILTPQILVNNL--K 127

Query: 609 GGKITNLRRVTYLVMDEADRMFDMGFEPQITR 640
            G I +L   T ++ DE            I  
Sbjct: 128 KGTIPSLSIFTLMIFDECHNTSKQHPYNMIMF 159

>2ykg_A Probable ATP-dependent RNA helicase DDX58; hydrolase, innate immunity; 2.50A {Homo sapiens} PDB: 3tmi_A* Length = 696

 Score = 56.9 bits (136), Expect = 3e-08
 Identities = 27/143 (18%), Positives = 53/143 (37%), Gaps = 15/143 (10%)

Query: 693 EVRPESDRFLRLLELLGEWYEKGKILIFVHSQEKCDALFRDLLKH------------GYP 740
              P+ +    +L+       +   ++FV ++   DAL   +  +            G  
Sbjct: 377 NENPKLEDLCFILQEEYHLNPETITILFVKTRALVDALKNWIEGNPKLSFLKPGILTGRG 436

Query: 741 CLSLHGAKDQTDRESTISDFKSN-VCNLLIATSVAARGLDVKELELVINFDAPNHYEDYV 799
             + +       ++  +  FK++   N+LIATSVA  G+D+ +  LVI ++   +    +
Sbjct: 437 KTNQNTGMTLPAQKCILDAFKASGDHNILIATSVADEGIDIAQCNLVILYEYVGNVIKMI 496

Query: 800 HRVGRTGRAGRKGCAITFISEED 822
              GR     R        S   
Sbjct: 497 QTRGRGRA--RGSKCFLLTSNAG 517

>3tbk_A RIG-I helicase domain; DECH helicase, ATP binding, hydrolase; HET: ANP; 2.14A {Mus musculus} Length = 555

 Score = 66.8 bits (162), Expect = 2e-11
 Identities = 28/136 (20%), Positives = 55/136 (40%), Gaps = 5/136 (3%)

Query: 494 QAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELV 553
           Q +       G++ I  A TG GKT   +L    H+K  P    G     +  A    + 
Sbjct: 9   QLELALPAKKGKNTIICAPTGCGKTFVSLLICEHHLKKFP---CGQKGKVVFFANQIPVY 65

Query: 554 QQIHSDIRKFAKVMGVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGGKIT 613
           +Q  +   ++ + +G     + G +  +  +  +    +I++ TP  +++ L    G I 
Sbjct: 66  EQQATVFSRYFERLGYNIASISGATSDSVSVQHIIEDNDIIILTPQILVNNLNN--GAIP 123

Query: 614 NLRRVTYLVMDEADRM 629
           +L   T ++ DE    
Sbjct: 124 SLSVFTLMIFDECHNT 139

>3tbk_A RIG-I helicase domain; DECH helicase, ATP binding, hydrolase; HET: ANP; 2.14A {Mus musculus} Length = 555

 Score = 58.8 bits (141), Expect = 6e-09
 Identities = 35/151 (23%), Positives = 60/151 (39%), Gaps = 18/151 (11%)

Query: 690 QLVEVRPESDRFLRLLELLGEWYEKGK---ILIFVHSQEKCDALFRDLLKH----GYPCL 742
              +   E+ +   L  +L E Y        ++FV ++   DAL + + ++         
Sbjct: 362 VSRDPSNENPKLRDLYLVLQEEYHLKPETKTILFVKTRALVDALKKWIEENPALSFLKPG 421

Query: 743 SLHG--------AKDQTDRESTISDFKSN-VCNLLIATSVAARGLDVKELELVINFDAPN 793
            L G              ++  +  F+++   N+LIATSVA  G+D+ E  LVI ++   
Sbjct: 422 ILTGRGRTNRATGMTLPAQKCVLEAFRASGDNNILIATSVADEGIDIAECNLVILYEYVG 481

Query: 794 HYEDYVHRVGRTGRAGRKGCAITFISEEDAK 824
           +    +   GR GRA R        S  D  
Sbjct: 482 NVIKMIQTRGR-GRA-RDSKCFLLTSSADVI 510

>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 Length = 451

 Score = 64.5 bits (157), Expect = 7e-11
 Identities = 56/341 (16%), Positives = 94/341 (27%), Gaps = 73/341 (21%)

Query: 492 PIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRE 551
           P       +    R  I     G+GKT   +  ++R                LI+APTR 
Sbjct: 7   PDYEVDEDIFRKKRLTIMDLHPGAGKTKRILPSIVRE------ALLRRLRT-LILAPTRV 59

Query: 552 LVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGGK 611
           +  ++   +R     + +R       S              + +           T    
Sbjct: 60  VAAEMEEALRG----LPIRYQTPAVKSDH-------TGREIVDLMCHA----TFTTRLLS 104

Query: 612 ITNLRRVTYLVMDEA-----DRMFDMGFEPQITRIVQNIRPDRQTVLFSATFP-RQVEIL 665
            T +     +VMDEA       +   G+             +   +  +AT P       
Sbjct: 105 STRVPNYNLIVMDEAHFTDPCSVAARGYISTRVE-----MGEAAAIFMTATPPGSTDPFP 159

Query: 666 ARKVLNKPVEIQVGGRSVVNKDITQLVEVRPESDRFLRLLELLGEWYEKGKILIFVHSQE 725
                N P+E                +E       +    + + +   +GK + FV S +
Sbjct: 160 QS---NSPIED---------------IEREIPERSWNTGFDWITD--YQGKTVWFVPSIK 199

Query: 726 KCDALFRDLLKHGYPCLSLHGAKDQTDRESTISDFKSNVCNLLIATSVAARGL--DVK-- 781
             + +   L K G   + L      T+   T       V    + T ++  G        
Sbjct: 200 AGNDIANCLRKSGKRVIQLSRKTFDTEYPKTKLTDWDFV----VTTDISEMGANFRAGRV 255

Query: 782 -----ELELVINFDAPNHYE-------DYVHRVGRTGRAGR 810
                 L+ VI  D P                  R GR GR
Sbjct: 256 IDPRRCLKPVILTDGPERVILAGPIPVTPASAAQRRGRIGR 296

>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} Length = 936

 Score = 63.4 bits (153), Expect = 3e-10
 Identities = 36/264 (13%), Positives = 83/264 (31%), Gaps = 13/264 (4%)

Query: 391 EKPLEDEDDDEFMKRVKKTKAEKLSIVDHSKIDYQPFRKNFYIEVKEIARMTPEEVSAYR 450
           E     + +                         +   K+   E+ + +    E    Y 
Sbjct: 158 ECLCRSDKEHWPKSLQLALDTTGYYRASELWDIREDNAKDVDSEMTDASEDCLEASMTYS 217

Query: 451 KQLELKIHGKDVPKPIKTWHQTGLTSKIMETIRKLNYEKPMPIQAQALPVIMSGRDCIGV 510
           ++ E   +  +                  +  R          Q +     ++G++ +  
Sbjct: 218 EEAEPDDNLSENLGSAAEGIGKPPPVYETKKAR--------SYQIELAQPAINGKNALIC 269

Query: 511 AKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVMGVR 570
           A TGSGKT   +L    H ++ P   AG     + +A    + +Q  +  +   +  G  
Sbjct: 270 APTGSGKTFVSILICEHHFQNMP---AGRKAKVVFLATKVPVYEQQKNVFKHHFERQGYS 326

Query: 571 CVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMF 630
              + G +     + ++   ++I+V TP  +++      G +T+L   T ++ DE     
Sbjct: 327 VQGISGENFSNVSVEKVIEDSDIIVVTPQILVNSFED--GTLTSLSIFTLMIFDECHNTT 384

Query: 631 DMGFEPQITRIVQNIRPDRQTVLF 654
                  +       + +  + L 
Sbjct: 385 GNHPYNVLMTRYLEQKFNSASQLP 408

>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} Length = 936

 Score = 55.7 bits (133), Expect = 6e-08
 Identities = 28/155 (18%), Positives = 59/155 (38%), Gaps = 19/155 (12%)

Query: 684 VNKDITQLVEVRPESDRFLRLLELLGEWYEKG---KILIFVHSQEKCDALFRDLLKH--- 737
             + I    +   E+ +   L+ +L + Y      + L+F  ++    AL + + ++   
Sbjct: 598 EPELIALSKDETNENPKLEELVCILDDAYRYNPQTRTLLFAKTRALVSALKKCMEENPIL 657

Query: 738 ---------GYPCLSLHGAKDQTDRESTISDFKSNVCN-LLIATSVAARGLDVKELELVI 787
                    G              ++  +  FK++  N LLIATSVA  G+D+ +  LV+
Sbjct: 658 NYIKPGVLMGRGRRDQTTGMTLPSQKGVLDAFKTSKDNRLLIATSVADEGIDIVQCNLVV 717

Query: 788 NFDAPNHYEDYVHRVGRTGRAGRKGCAITFISEED 822
            ++   +    +      GR    G     ++ + 
Sbjct: 718 LYEYSGNVTKMIQVR---GRGRAAGSKCILVTSKT 749

>2ycu_A Non muscle myosin 2C, alpha-actinin; motor protein; HET: AOV; 2.25A {Homo sapiens} PDB: 1br1_A* 1br4_A* 1br2_A* Length = 995

 Score = 59.7 bits (145), Expect = 4e-09
 Identities = 20/200 (10%), Positives = 55/200 (27%), Gaps = 3/200 (1%)

Query: 2   AHSHRDRDREKEKEKHREKSRRSEREQSTDSDEDKHDKEKEKDKHRDRDRRRDRDRDRDR 61
           AH    +  +  K +   +         T     K +           +           
Sbjct: 799 AHKEYKKTEKPPKGQEVSELEAIYNSLQTKLRLIKREPFVAPAGLTPNEIDSTWSALEKA 858

Query: 62  EKEREEKRERAREKEREREKRDREREDRERERERERERRERDREREKRERERDRDKEKDR 121
           E+E  E      +++++     ++     ++ E     +       +        + K +
Sbjct: 859 EQEHAEALRIELKRQKKIAVLLQKYNRILKKLENWATTKSVYLGSNETGDSITAVQAKLK 918

Query: 122 ERKSRDREKRRKVESDDSDEDKDRDRKRRRRHDDDHKERVRERSLSRSNRHRDENDESPR 181
             ++ D E +      +SD      +     ++   +   R+ +            +S  
Sbjct: 919 NLEAFDGECQSLEGQSNSDLLSILAQLTELNYNGVPELTERKDTFFAQQW---TGVKSSA 975

Query: 182 EKLVEDDSDKKEKKTREEEL 201
           E        + E+  + E+L
Sbjct: 976 ETYKNTLLAELERLQKIEDL 995

>2v6i_A RNA helicase; membrane, hydrolase, transmembrane, RNA replication, viral replication, nucleotide-binding; 2.10A {Kokobera virus} PDB: 2v6j_A Length = 431

 Score = 58.7 bits (142), Expect = 5e-09
 Identities = 47/347 (13%), Positives = 93/347 (26%), Gaps = 86/347 (24%)

Query: 510 VAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVMGV 569
               G+GKT   +  ++R                +I+APTR +  ++        + +  
Sbjct: 8   DLHPGAGKTRRVLPQLVREA------VKKRLRT-VILAPTRVVASEM-------YEALRG 53

Query: 570 RCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEA--- 626
             +  Y    V  + +       +                 +   +      +MDEA   
Sbjct: 54  EPI-RYMTPAVQSERT---GNEIVDFMCHS----TFTMKLLQGVRVPNYNLYIMDEAHFL 105

Query: 627 --DRMFDMGFEPQITRIVQNIRPDRQTVLFSATFP---RQVEILARKVLNKPVEIQVGGR 681
               +   G+             D   +  +AT P            ++++   I     
Sbjct: 106 DPASVAARGYIETRVS-----MGDAGAIFMTATPPGTTEAFPPSNSPIIDEETRIPDKAW 160

Query: 682 SVVNKDITQLVEVRPESDRFLRLLELLGEWYEKGKILIFVHSQEKCDALFRDLLKHGYPC 741
           +   + IT+                        G+ + FVHS ++   +   L K G   
Sbjct: 161 NSGYEWITE----------------------FDGRTVWFVHSIKQGAEIGTCLQKAGKKV 198

Query: 742 LSLHGAKDQTDRESTISDFKSNVCNLLIATSVAARGL--DVKELELVINFDAPNHYEDYV 799
           L L+    +++     S+    V    I T ++  G          VI  D     +  +
Sbjct: 199 LYLNRKTFESEYPKCKSEKWDFV----ITTDISEMGANFKAD---RVI--DPRKTIKPIL 249

Query: 800 HRVG----------------RTGRAGRK--GCAITFISEEDAKYSPD 828
                               R GR GR        +    +     +
Sbjct: 250 LDGRVSMQGPIAITPASAAQRRGRIGRNPEKLGDIYAYSGNVSSDNE 296

>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 = 58.7 bits (141), Expect = 8e-09
 Identities = 82/632 (12%), Positives = 183/632 (28%), Gaps = 191/632 (30%)

Query: 381 DSDYGDLENDEKP-LEDEDDDEFMK---------------RVKKTKAEKLSIVDHSKIDY 424
           + D  D+++  K  L  E+ D  +                  K+ +  +  + +  +I+Y
Sbjct: 32  NFDCKDVQDMPKSILSKEEIDHIIMSKDAVSGTLRLFWTLLSKQEEMVQKFVEEVLRINY 91

Query: 425 QPFRKNFYIEVKEIARMTPEEVSAYRKQL--ELKIHGK-DVPKPIKTWHQTGLTSKIMET 481
           +        E ++ + MT   +   R +L  + ++  K +V +            +    
Sbjct: 92  KFLMSPIKTEQRQPSMMTRMYIE-QRDRLYNDNQVFAKYNVSRL-----------QPYLK 139

Query: 482 IRKLNYE-KPMPIQAQALPVIMSGRDCIGVAKTGSGKT-LAFVLPMLRHIKDQPPVAAGD 539
           +R+   E +P         V++ G         GSGKT +A  L +             D
Sbjct: 140 LRQALLELRPAKN------VLIDG-------VLGSGKTWVA--LDVCL---SYKVQCKMD 181

Query: 540 GPV-----------GLIMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQISELK 588
             +             ++   ++L+ QI  +                  S +  +I  ++
Sbjct: 182 FKIFWLNLKNCNSPETVLEMLQKLLYQIDPNW----------TSRSDHSSNIKLRIHSIQ 231

Query: 589 RGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMGFEPQITRIVQNIRPD 648
                       +  +L +   +         LV+                  VQ    +
Sbjct: 232 A----------ELRRLLKSKPYEN------CLLVLLN----------------VQ----N 255

Query: 649 RQTVLFSATFPRQVEILA--RKVLNKPVEIQVGGRSVVNKDITQLVEV--RPESDRFLRL 704
            +       F    +IL   R    K V   +   +  +  +          E       
Sbjct: 256 AKAW---NAFNLSCKILLTTR---FKQVTDFLSAATTTHISLDHHSMTLTPDEV------ 303

Query: 705 LELLGEWYEKGKILIFVHSQEKCDALFRDLLKHGYP-CLSLHGAKDQTDRESTISDFKSN 763
             LL ++ +            +   L R++L    P  LS+     + D  +T  ++K  
Sbjct: 304 KSLLLKYLD-----------CRPQDLPREVLT-TNPRRLSIIAESIR-DGLATWDNWKHV 350

Query: 764 VCNLL---IATSVAARGLDVKELELVINFDAPNHYEDYVHRVGRTGRAGRKGCAITFISE 820
            C+ L   I +S+    L+  E            ++                 ++ F   
Sbjct: 351 NCDKLTTIIESSLNV--LEPAEYR--------KMFDR---------------LSV-F--P 382

Query: 821 EDAKYSPDLVKAL--ELSEQVVPDDLKALADSFMAK--VNQGLEQAHGTGYGGSGFKFNE 876
             A     L+  +  ++ +  V   +  L    + +    +         Y     +   
Sbjct: 383 PSAHIPTILLSLIWFDVIKSDVMVVVNKLHKYSLVEKQPKESTISIPS-IY----LELKV 437

Query: 877 EEDEKRKAAKKAQAKEYGFEEDKSDSDD-----EDEGIRKAGGD-ISQQDALAKISAIRK 930
           + + +    +      Y       DSDD      D+      G  +   +   +++  R 
Sbjct: 438 KLENEYALHRSIVDH-YNI-PKTFDSDDLIPPYLDQYFYSHIGHHLKNIEHPERMTLFRM 495

Query: 931 LYL---FIEGP--TEQSVKRAKAELKRVLEDF 957
           ++L   F+E     + +   A   +   L+  
Sbjct: 496 VFLDFRFLEQKIRHDSTAWNASGSILNTLQQL 527

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

 Score = 51.0 bits (121), Expect = 2e-06
 Identities = 79/598 (13%), Positives = 156/598 (26%), Gaps = 178/598 (29%)

Query: 3   HSHRDRDREKEKEKHREKSRRSEREQSTDSDEDKHDKEKEKDKHRDRDRRRDRDRDRD-- 60
           H H   D E  + +++ K   S  E +   + D  D +       D  +      + D  
Sbjct: 2   HHHHHMDFETGEHQYQYKDILSVFEDAFVDNFDCKDVQ-------DMPKSILSKEEIDHI 54

Query: 61  -REKEREEKRERA----REKEREREKR---DRERED--------RERERERERERRERDR 104
              K+      R       K+ E  ++   +  R +        +  +R+     R    
Sbjct: 55  IMSKDAVSGTLRLFWTLLSKQEEMVQKFVEEVLRINYKFLMSPIKTEQRQPSMMTRMYIE 114

Query: 105 EREKRERERDRDKEKDRERKSRDREKRRKVESDDSDED----------KD-------RDR 147
           +R++   +     + +  R     + R+ +      ++          K           
Sbjct: 115 QRDRLYNDNQVFAKYNVSRLQPYLKLRQALLELRPAKNVLIDGVLGSGKTWVALDVCLSY 174

Query: 148 KRRRRHDD---------DHKERVRERSLSRSNRHRDENDESPREKLVEDDSDKKEKKTRE 198
           K + + D           +        L +     D N  S        D      K R 
Sbjct: 175 KVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQIDPNWTS------RSDHSSNI-KLRI 227

Query: 199 EELEDEQRKLDEEMEKRR-----RRVQEWQELK------------RKKEESERENRGDAN 241
             ++ E R+L +             VQ  +               R         +   +
Sbjct: 228 HSIQAELRRLLKSKPYENCLLVLLNVQNAKAWNAFNLSCKILLTTR--------FKQVTD 279

Query: 242 VEEPKAGRNWTLDRED---SDDEEVPQTGKSETDMDADEEPKPSENQVGDAMLVDSDGGS 298
                   + +LD      + DE      K   D    + P+  E    +   +      
Sbjct: 280 FLSAATTTHISLDHHSMTLTPDEVKSLLLKY-LDCRPQDLPR--EVLTTNPRRL------ 330

Query: 299 AAPALQIGAAEDEDIDPLDAFMNSMVLPEVEKLKNTVEPSFTDGNNVESKKMDRKGDRRS 358
              ++ I  +  + +   D + +       +KL   +E S       E +KM        
Sbjct: 331 ---SI-IAESIRDGLATWDNWKH----VNCDKLTTIIESSLNVLEPAEYRKM-------- 374

Query: 359 NGEQPKKSSNKSLGRIIPGEDSDSDYGDLE---NDEKPLEDEDD-DEFMKR---VKKTKA 411
                       L  + P   +      L     D    +     ++  K     K+ K 
Sbjct: 375 ---------FDRLS-VFP-PSAHIPTILLSLIWFDVIKSDVMVVVNKLHKYSLVEKQPKE 423

Query: 412 EKLSIVD---------------HSKI--DYQPFRKN---------------FYI--EVKE 437
             +SI                 H  I   Y   +                  +I   +K 
Sbjct: 424 STISIPSIYLELKVKLENEYALHRSIVDHYNIPKTFDSDDLIPPYLDQYFYSHIGHHLKN 483

Query: 438 IARMTPEEVSAYRKQ------LELKIHGKDVPKPIKTWHQTGLTSKIMETIRKLNYEK 489
           I    PE ++ +R        LE KI           W+ +G     ++ ++   Y+ 
Sbjct: 484 IEH--PERMTLFRMVFLDFRFLEQKIRHDSTA-----WNASGSILNTLQQLKF--YKP 532

>3dmq_A RNA polymerase-associated protein RAPA; SWF2/SNF2, transcription factor, RNA polymerase recycling, activator, ATP-binding, DNA-binding; 3.20A {Escherichia coli K12} Length = 968

 Score = 57.8 bits (139), Expect = 1e-08
 Identities = 37/235 (15%), Positives = 76/235 (32%), Gaps = 15/235 (6%)

Query: 698 SDRFLRLLELLGEWYEKGKILIFVHSQEKCDALFRDLLKH-GYPCLSLHGAKDQTDREST 756
             R   L+  L     + K+L+          L + L +  G      H      +R+  
Sbjct: 488 DPRVEWLMGYLTSHRSQ-KVLVICAKAATALQLEQVLREREGIRAAVFHEGMSIIERDRA 546

Query: 757 ISDFKSN--VCNLLIATSVAARGLDVKELELVINFDAPNHYEDYVHRVGRTGRAG-RKGC 813
            + F        +L+ + + + G + +    ++ FD P + +    R+GR  R G     
Sbjct: 547 AAWFAEEDTGAQVLLCSEIGSEGRNFQFASHMVMFDLPFNPDLLEQRIGRLDRIGQAHDI 606

Query: 814 AITFISEE---DAKYSPDLVKALELSEQVVPDDLKALADSFMAKVNQGLEQAHGTGYGGS 870
            I     E    +       + L+  E   P        +    V   L     +     
Sbjct: 607 QIHVPYLEKTAQSVLVRWYHEGLDAFEHTCPT-----GRTIYDSVYNDLINYLASPDQTE 661

Query: 871 GFKFNEEEDEKRKAAKKAQAKEY--GFEEDKSDSDDEDEGIRKAGGDISQQDALA 923
           GF    +   ++  A KAQ ++      E  S+  ++ + + ++  +      L 
Sbjct: 662 GFDDLIKNCREQHEALKAQLEQGRDRLLEIHSNGGEKAQALAESIEEQDDDTNLI 716

>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* Length = 1054

 Score = 57.0 bits (138), Expect = 3e-08
 Identities = 53/290 (18%), Positives = 103/290 (35%), Gaps = 48/290 (16%)

Query: 510 VAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVMGV 569
            A TG GKT +F L M   +       A  G    ++ PT  LV Q    IRK+A+  GV
Sbjct: 77  TAPTGVGKT-SFGLAMSLFL-------ALKGKRCYVIFPTSLLVIQAAETIRKYAEKAGV 128

Query: 570 RCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGG----KITNLRRVTYLVMDE 625
               +     +      + +  +       R   I+ T+          L    ++ +D+
Sbjct: 129 GTENL-----IGYYHGRIPKREKENFMQNLRNFKIVITTTQFLSKHYRELGHFDFIFVDD 183

Query: 626 AD----------RMFD-MGFEPQITRIVQNIRPDRQTVLFSATFPRQVEILA-RKVLNKP 673
            D          ++   +GF   +             ++ +AT  +  +    R++LN  
Sbjct: 184 VDAILKASKNVDKLLHLLGFHYDLKTKSWVGEARGCLMVSTATAKKGKKAELFRQLLN-- 241

Query: 674 VEIQVGGRSVVNKDITQLVEVRPESDRFLRLLELLGEWYEKGKILIFVHSQEKCDALFRD 733
               +G   +  +++  +            +LE LG     G  +I+  + E+ + ++ +
Sbjct: 242 --FDIGSSRITVRNVEDVAVNDESISTLSSILEKLG----TG-GIIYARTGEEAEEIY-E 293

Query: 734 LLKHGYPCLSLHGAKDQTDRESTISDFKSNVCNLLIATS----VAARGLD 779
            LK+ +    +        ++     F     + LI T+       RGLD
Sbjct: 294 SLKNKFRIGIVT-----ATKKGDYEKFVEGEIDHLIGTAHYYGTLVRGLD 338

>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 Length = 618

 Score = 56.1 bits (135), Expect = 4e-08
 Identities = 56/343 (16%), Positives = 93/343 (27%), Gaps = 71/343 (20%)

Query: 489 KPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAP 548
              P       +    R  I     G+GKT   +  ++R                LI+AP
Sbjct: 171 IGEPDYEVDEDIFRKKRLTIMDLHPGAGKTKRILPSIVREA------LKRRLRT-LILAP 223

Query: 549 TRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTS 608
           TR +  ++   +R             Y    V    S+      + +         L +S
Sbjct: 224 TRVVAAEMEEALRG--------LPIRYQTPAV---KSDHTGREIVDLMCHATFTTRLLSS 272

Query: 609 GGKITNLRRVTYLVMDE-----ADRMFDMGFEPQITRIVQNIRPDRQTVLFSATFPRQVE 663
                 +     +VMDE        +   G+             +   +  +AT P    
Sbjct: 273 TR----VPNYNLIVMDEAHFTDPCSVAARGYISTRVE-----MGEAAAIFMTATPP--GS 321

Query: 664 ILARKVLNKPVEIQVGGRSVVNKDITQLVEVRPESDRFLRLLELLGEWYEKGKILIFVHS 723
                  N P+E                +E       +    + + +   +GK + FV S
Sbjct: 322 TDPFPQSNSPIED---------------IEREIPERSWNTGFDWITD--YQGKTVWFVPS 364

Query: 724 QEKCDALFRDLLKHGYPCLSLHGAKDQTDRESTISDFKSNVCNLLIATSVAARGL--DVK 781
            +  + +   L K G   + L      T+   T       V      T ++  G      
Sbjct: 365 IKAGNDIANCLRKSGKRVIQLSRKTFDTEYPKTKLTDWDFVV----TTDISEMGANFRAG 420

Query: 782 -------ELELVINFDAPNHYE-------DYVHRVGRTGRAGR 810
                   L+ VI  D P                  R GR GR
Sbjct: 421 RVIDPRRCLKPVILTDGPERVILAGPIPVTPASAAQRRGRIGR 463

>2z83_A Helicase/nucleoside triphosphatase; hydrolase, membrane, nucleotide-binding, RNA replication, transmembrane, viral protein; 1.80A {Japanese encephalitis virus} PDB: 2v8o_A 2qeq_A Length = 459

 Score = 55.2 bits (133), Expect = 7e-08
 Identities = 45/339 (13%), Positives = 84/339 (24%), Gaps = 69/339 (20%)

Query: 510 VAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVMGV 569
               GSGKT   +  +++        A        ++APTR +  ++         + G+
Sbjct: 27  DLHPGSGKTRKILPQIIKD-------AIQQRLRTAVLAPTRVVAAEM------AEALRGL 73

Query: 570 RCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRM 629
                      +    E +    + V         L         +      VMDEA   
Sbjct: 74  PV-----RYQTSAVQREHQGNEIVDVMCHA----TLTHRLMSPNRVPNYNLFVMDEAHFT 124

Query: 630 FDMGFEPQITRIVQNIRPDRQTVLFSATFP-RQVEILARK--VLNKPVEIQVGGRSVVNK 686
                  +     +    +   +  +AT P            + +   EI     S   +
Sbjct: 125 DPASIAARGYIATKVELGEAAAIFMTATPPGTTDPFPDSNAPIHDLQDEIPDRAWSSGYE 184

Query: 687 DITQLVEVRPESDRFLRLLELLGEWYEKGKILIFVHSQEKCDALFRDLLKHGYPCLSLHG 746
            IT+                        GK + FV S +  + +   L + G   + L+ 
Sbjct: 185 WITE----------------------YAGKTVWFVASVKMGNEIAMCLQRAGKKVIQLNR 222

Query: 747 AKDQTDRESTISDFKSNVCNLLIATSVAARGL--DVK-------ELELVINFDAPNHYE- 796
               T+     +     V      T ++  G              ++  I  +       
Sbjct: 223 KSYDTEYPKCKNGDWDFVI----TTDISEMGANFGASRVIDCRKSVKPTILEEGEGRVIL 278

Query: 797 ------DYVHRVGRTGRAGRK--GCAITFISEEDAKYSP 827
                        R GR GR        +          
Sbjct: 279 GNPSPITSASAAQRRGRVGRNPNQVGDEYHYGGATSEDD 317

>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic vesicle, membrane, Ca structural protein; 7.94A {Bos taurus} Length = 190

 Score = 50.5 bits (120), Expect = 3e-07
 Identities = 15/76 (19%), Positives = 37/76 (48%), Gaps = 7/76 (9%)

Query: 60  DREKEREEKRERAREKERER-EKRDREREDRERERERERERRERD----REREKRERERD 114
           DR  +  E   + RE++R+R ++ D        +  RE+ +++ +    R+ E+ E+ + 
Sbjct: 78  DRLTQEPESIRKWREEQRKRLQELD-AASKVMEQEWREKAKKDLEEWNQRQSEQVEKNKI 136

Query: 115 RDKEKDRE-RKSRDRE 129
            ++  D+   +  D +
Sbjct: 137 NNRIADKAFYQQPDAD 152

>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic vesicle, membrane, Ca structural protein; 7.94A {Bos taurus} Length = 190

 Score = 49.8 bits (118), Expect = 6e-07
 Identities = 15/78 (19%), Positives = 34/78 (43%), Gaps = 3/78 (3%)

Query: 62  EKEREEKRERAREKEREREKRDREREDRERERERERERRERDREREKRERERDRDKEKDR 121
           ++  +E  E  R+   E+ KR +E  D   +   +  R +  ++ E+  + +    EK++
Sbjct: 78  DRLTQEP-ESIRKWREEQRKRLQEL-DAASKVMEQEWREKAKKDLEEWNQRQSEQVEKNK 135

Query: 122 ERKSRDREKRRKVESDDS 139
              +R  +K    + D  
Sbjct: 136 IN-NRIADKAFYQQPDAD 152

>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic vesicle, membrane, Ca structural protein; 7.94A {Bos taurus} Length = 190

 Score = 48.2 bits (114), Expect = 2e-06
 Identities = 16/85 (18%), Positives = 37/85 (43%), Gaps = 7/85 (8%)

Query: 32  SDEDKHDKEKEKDKHRDRDRRRDRDRDRDREKEREEKRERAREKEREREKRDREREDRER 91
           +  D+  +E E         R+ R+  R R +E +   +   ++ RE+ K+D E  ++ +
Sbjct: 75  AQADRLTQEPES-------IRKWREEQRKRLQELDAASKVMEQEWREKAKKDLEEWNQRQ 127

Query: 92  ERERERERRERDREREKRERERDRD 116
             + E+ +       +   ++ D D
Sbjct: 128 SEQVEKNKINNRIADKAFYQQPDAD 152

>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic vesicle, membrane, Ca structural protein; 7.94A {Bos taurus} Length = 190

 Score = 45.1 bits (106), Expect = 3e-05
 Identities = 13/75 (17%), Positives = 39/75 (52%), Gaps = 2/75 (2%)

Query: 74  EKEREREKRDREREDRERERERERERRERDREREKRERERDRDKEKDRERKSRDREKRRK 133
           + +R  ++ +  R+ RE +R+R +E     +  E+  RE+ +   ++  ++  ++ ++ K
Sbjct: 76  QADRLTQEPESIRKWREEQRKRLQELDAASKVMEQEWREKAKKDLEEWNQRQSEQVEKNK 135

Query: 134 VESDDSDED--KDRD 146
           + +  +D+   +  D
Sbjct: 136 INNRIADKAFYQQPD 150

>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic vesicle, membrane, Ca structural protein; 7.94A {Bos taurus} Length = 190

 Score = 44.0 bits (103), Expect = 6e-05
 Identities = 15/84 (17%), Positives = 37/84 (44%), Gaps = 15/84 (17%)

Query: 159 ERVRERSLSRSNRHRDENDESPREKLVEDDSDKKEKKTREEELEDEQRKLDEEMEKRRRR 218
           E +R+         R+E  +  +E       D   K   +E  E  ++ L+E  +++  +
Sbjct: 85  ESIRKW--------REEQRKRLQEL------DAASKVMEQEWREKAKKDLEEWNQRQSEQ 130

Query: 219 VQEWQELKRKKEESERENRGDANV 242
           V++ +   R  +++  +   DA++
Sbjct: 131 VEKNKINNRIADKAFYQQP-DADI 153

>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic vesicle, membrane, Ca structural protein; 7.94A {Bos taurus} Length = 190

 Score = 44.0 bits (103), Expect = 6e-05
 Identities = 14/83 (16%), Positives = 36/83 (43%), Gaps = 10/83 (12%)

Query: 83  DREREDRERERERERERRERDREREKRERERDRDKEKDRERKSRDREKRRKVESDDSDED 142
           DR  ++ E  R+    R E+ +  ++ +      +++ RE+  +D E+  + +     E 
Sbjct: 78  DRLTQEPESIRKW---REEQRKRLQELDAASKVMEQEWREKAKKDLEEWNQRQ----SEQ 130

Query: 143 KDRDRKRRRRHDDDHKERVRERS 165
            ++++   R  D   K   ++  
Sbjct: 131 VEKNKINNRIAD---KAFYQQPD 150

>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic vesicle, membrane, Ca structural protein; 7.94A {Bos taurus} Length = 190

 Score = 40.9 bits (95), Expect = 6e-04
 Identities = 15/88 (17%), Positives = 37/88 (42%), Gaps = 11/88 (12%)

Query: 4   SHRDRDREKEKEKHRE-KSRRSEREQSTDSDEDKHDKEKEKDKHRDRDRRRDRDRDRDRE 62
           +  DR  + E E  R+ +  + +R Q  D+     ++E  +   +D +         +  
Sbjct: 75  AQADRLTQ-EPESIRKWREEQRKRLQELDAASKVMEQEWREKAKKDLE---------EWN 124

Query: 63  KEREEKRERAREKEREREKRDREREDRE 90
           + + E+ E+ +   R  +K   ++ D +
Sbjct: 125 QRQSEQVEKNKINNRIADKAFYQQPDAD 152

>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* Length = 472

 Score = 52.1 bits (125), Expect = 6e-07
 Identities = 60/356 (16%), Positives = 103/356 (28%), Gaps = 94/356 (26%)

Query: 492 PIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRE 551
             Q +AL   +  +    V  TGSGKT   +   +  +           P  LI+ PT  
Sbjct: 96  DYQEKALERWLVDKRGCIVLPTGSGKTHVAMA-AINELS---------TPT-LIVVPTLA 144

Query: 552 LVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGGK 611
           L +Q    +  F    G   V  + G         +K    + V T     D    +  K
Sbjct: 145 LAEQWKERLGIF----GEEYVGEFSG--------RIKELKPLTVST----YDSAYVNAEK 188

Query: 612 ITNLRRVTYLVMDEADRMFDMGFEPQITRIVQNIR------PDR----QTVLFSA----T 657
           + N  R   L+ DE   +    +       +   R       +R      +L        
Sbjct: 189 LGN--RFMLLIFDEVHHLPAESYVQIAQMSIAPFRLGLTATFEREDGRHEILKEVVGGKV 246

Query: 658 FPRQVEILARKVLNKPVEIQV--------------------------GGRSVVNKDITQL 691
           F    + LA K L K    ++                          G      +D  ++
Sbjct: 247 FELFPDSLAGKHLAKYTIKRIFVPLAEDERVEYEKREKVYKQFLRARGITLRRAEDFNKI 306

Query: 692 VEVRPESDRFLRLLELLGEWYE-----KGKI---------------LIFVHSQEKCDALF 731
           V      +R    L    E        K KI               +IF    E    + 
Sbjct: 307 VMASGYDERAYEALRAWEEARRIAFNSKNKIRKLREILERHRKDKIIIFTRHNELVYRIS 366

Query: 732 RDLLKHGYPCLSLHGAKDQTDRESTISDFKSNVCNLLIATSVAARGLDVKELELVI 787
           +  L              + +RE  +  F++     ++++ V   G+DV +  + +
Sbjct: 367 KVFLIPAI-----THRTSREEREEILEGFRTGRFRAIVSSQVLDEGIDVPDANVGV 417

>2oca_A DAR protein, ATP-dependent DNA helicase UVSW; ATP-dependant helicase, T4-bacteriophage, recombination, hydrolase; 2.70A {Enterobacteria phage T4} Length = 510

 Score = 52.2 bits (124), Expect = 6e-07
 Identities = 45/338 (13%), Positives = 102/338 (30%), Gaps = 28/338 (8%)

Query: 489 KPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAP 548
           +P   Q  A+   +  R  I    T +G++L   L    ++++            LI+ P
Sbjct: 113 EPHWYQKDAVFEGLVNRRRILNLPTSAGRSLIQALLARYYLENYEGKI-------LIIVP 165

Query: 549 TRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRM------- 601
           T  L  Q+  D   +          + GG+    +             T  +        
Sbjct: 166 TTALTTQMADDFVDYRLFSHAMIKKIGGGASKDDKYKNDAPVVVGTWQTVVKQPKEWFSQ 225

Query: 602 IDILCTSGGKITNLRRVTYLVMDEADRMFDMGFEPQITRIVQNI-----------RPDRQ 650
             ++      +   + ++ ++    + MF  G    +     NI           +P   
Sbjct: 226 FGMMMNDECHLATGKSISSIISGLNNCMFKFGLSGSLRDGKANIMQYVGMFGEIFKPVTT 285

Query: 651 TVLFSATFPRQVEILARKVLNKPVEIQVGGRSVVNKDITQLVEVRPESDRFLRLLELLGE 710
           + L       +++I +  +                ++I  +  +   +    +L   L +
Sbjct: 286 SKLMEDGQVTELKINSIFLRYPDEFTTKLKGKTYQEEIKIITGLSKRNKWIAKLAIKLAQ 345

Query: 711 WYEKGKILIFVHSQEKCDALFRDLLKHGYPCLSLHGAKDQTDRESTISDFKSNVCNLLIA 770
                   +         A+F  +         + G  D   R    +  ++    +++A
Sbjct: 346 K--DENAFVMFKHVSHGKAIFDLIKNEYDKVYYVSGEVDTETRNIMKTLAENGKGIIIVA 403

Query: 771 T-SVAARGLDVKELELVINFDAPNHYEDYVHRVGRTGR 807
           +  V + G+ VK L  V+           +  +GR  R
Sbjct: 404 SYGVFSTGISVKNLHHVVLAHGVKSKIIVLQTIGRVLR 441

>2qag_B Septin-6, protein NEDD5; cell cycle, cell division, GTP-binding, nucleotide-binding, phosphorylation, acetylation, alternative splicing, coiled coil; HET: GDP GTP; 4.00A {Homo sapiens} Length = 427

 Score = 50.1 bits (119), Expect = 2e-06
 Identities = 27/148 (18%), Positives = 65/148 (43%), Gaps = 1/148 (0%)

Query: 3   HSHRDRDREKEKEKHREKSRRSEREQSTDSDEDKHDKEKEKDKHRDRDRRRDRDRDRDRE 62
             + +  RE+   +H E  RR + E+    D D   K     +  +  R       + +E
Sbjct: 280 RVNMEDLREQTHTRHYELYRRCKLEEMGFKDTDPDSKPFSLQETYEAKRNEFLGELQKKE 339

Query: 63  KEREEKRERAREKEREREKRDREREDRERERERERERRERDREREKRERERDRDKEKDRE 122
           +E  +   + R KE+E E ++ E+E  E+    ++  ++  ++ E +++  D +    ++
Sbjct: 340 EEMRQMFVQ-RVKEKEAELKEAEKELHEKFDRLKKLHQDEKKKLEDKKKSLDDEVNAFKQ 398

Query: 123 RKSRDREKRRKVESDDSDEDKDRDRKRR 150
           RK+     + +       +   RD++++
Sbjct: 399 RKTAAELLQSQGSQAGGSQTLKRDKEKK 426

>2wv9_A Flavivirin protease NS2B regulatory subunit, FLAV protease NS3 catalytic subunit; nucleotide-binding, capsid protein; 2.75A {Murray valley encephalitis virus} Length = 673

 Score = 50.3 bits (120), Expect = 3e-06
 Identities = 47/360 (13%), Positives = 92/360 (25%), Gaps = 79/360 (21%)

Query: 494 QAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELV 553
           +A    ++   +  +     G+GKT   +  +++                 ++APTR + 
Sbjct: 231 EAYNPEMLKKRQLTVLDLHPGAGKTRRILPQIIKDA------IQKRLRT-AVLAPTRVVA 283

Query: 554 QQIHSDIRKFAKVMGVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGGKIT 613
            ++   +R     + VR +                    + V     +   L +      
Sbjct: 284 AEMAEALRG----LPVRYLTPAVQREH-------SGNEIVDVMCHATLTHRLMSP----L 328

Query: 614 NLRRVTYLVMDE-----ADRMFDMGFEPQITRIVQNIRPDRQTVLFSATFP-RQVEILAR 667
            +      VMDE        +   G+             +   +  +AT P         
Sbjct: 329 RVPNYNLFVMDEAHFTDPASIAARGYIATRVE-----AGEAAAIFMTATPPGTSDPFPDT 383

Query: 668 K--VLNKPVEIQVGGRSVVNKDITQLVEVRPESDRFLRLLELLGEWYEKGKILIFVHSQE 725
              V +   EI     S   + IT                         GK + FV S +
Sbjct: 384 NSPVHDVSSEIPDRAWSSGFEWITD----------------------YAGKTVWFVASVK 421

Query: 726 KCDALFRDLLKHGYPCLSLHGAKDQTDRESTISDFKSNVCNLLIATSVAARGL--DVK-- 781
             + + + L + G   + L+     T+     +     V      T ++  G        
Sbjct: 422 MSNEIAQCLQRAGKRVIQLNRKSYDTEYPKCKNGDWDFVI----TTDISEMGANFGASRV 477

Query: 782 -----ELELVINFDAPNHYEDYVH-------RVGRTGRAGRK--GCAITFISEEDAKYSP 827
                 ++  I  +        V           R GR GR        +          
Sbjct: 478 IDCRKSVKPTILDEGEGRVILSVPSAITSASAAQRRGRVGRNPSQIGDEYHYGGGTSEDD 537

>2a6h_D DNA-directed RNA polymerase beta' chain; RNA polymerase holoenzyme, streptolydigin, antibiotic, transcription regulation; HET: STD; 2.40A {Thermus thermophilus} SCOP: e.29.1.2 PDB: 1smy_D* 1zyr_D* 1iw7_D* 2a69_D* 2a6e_D 2a68_D* 2be5_D* 2cw0_D 2o5i_D 2o5j_D* 2ppb_D* 3aoh_D* 3aoi_D* 3dxj_D* 3eql_D* 1ynj_D* 1l9z_D 1l9u_D* 1ynn_D* 2auj_D Length = 1524

 Score = 48.6 bits (116), Expect = 1e-05
 Identities = 24/224 (10%), Positives = 65/224 (29%), Gaps = 5/224 (2%)

Query: 8   RDREKEKEKHREKSRRSEREQSTDSDEDKHDKEKEKDKHRDRDRRRDRDRDRDREKEREE 67
             R +++                  +  +  +   + K   R  R+ R    + E+E E 
Sbjct: 271 VLRREDEPVATYFLPVGMTPLVVHGEIVEKGQPLAEAKGLLRMPRQVRAAQVEAEEEGET 330

Query: 68  KRERAREKEREREKRDREREDRERERERERERRERDREREKRERERDRDKEKDRERKSRD 127
                   E    K  R +                D+     + E +   E +      +
Sbjct: 331 VYLTL-FLEWTEPKDYRVQPHMNVVVPEGARVEAGDKIVAAIDPEEEVIAEAEGVVHLHE 389

Query: 128 REKRRKVESDDSDEDKDRDRKRRRRHDDDHKERVRERSLSRSNRHRDENDESPREKLVED 187
                 V++     + D +     R      + + +    +S+ +     +  R  +   
Sbjct: 390 PASILVVKARVYPFEDDVEVSTGDRVAP--GDVLADGGKVKSDVYGRVEVDLVRNVVRVV 447

Query: 188 DSDKKEKKTREEELED--EQRKLDEEMEKRRRRVQEWQELKRKK 229
           +S   + +   E ++   ++  L+   ++    ++     +R K
Sbjct: 448 ESYDIDARMGAEAIQQLLKELDLEALEKELLEEMKHPSRARRAK 491

>2a6h_D DNA-directed RNA polymerase beta' chain; RNA polymerase holoenzyme, streptolydigin, antibiotic, transcription regulation; HET: STD; 2.40A {Thermus thermophilus} SCOP: e.29.1.2 PDB: 1smy_D* 1zyr_D* 1iw7_D* 2a69_D* 2a6e_D 2a68_D* 2be5_D* 2cw0_D 2o5i_D 2o5j_D* 2ppb_D* 3aoh_D* 3aoi_D* 3dxj_D* 3eql_D* 1ynj_D* 1l9z_D 1l9u_D* 1ynn_D* 2auj_D Length = 1524

 Score = 45.9 bits (109), Expect = 6e-05
 Identities = 32/310 (10%), Positives = 72/310 (23%), Gaps = 18/310 (5%)

Query: 27  EQSTDSDEDKHDKEKEKDKHRDRDRRRDRDRDRDREKEREEKRERAREKEREREKRDRER 86
               +    +  +    +++R+    +          +   K      K +E       R
Sbjct: 139 GAILNGVPVEKRQLLTDEEYRELRYGKQETYPLPPGVDALVKDGEEVVKGQELAPGVVSR 198

Query: 87  EDRERERERERERRERDREREKRERERDRDKEKDRERKSRDRE--KRRKVESDDSDE--- 141
            D        R  R    ++E+    R        +   +  E             E   
Sbjct: 199 LDGVALYRFPRRVRVEYVKKERAGL-RLPLAAWVEKEAYKPGEILAELPEPYLFRAEEEG 257

Query: 142 -----DKDRDRKRRRRHDDDHKERVRERSLSRSNRHRDENDESPREKLVEDDSDKKEKKT 196
                + +       R +D+                  E  E  +         +  ++ 
Sbjct: 258 VVELKELEEGAFLVLRREDEPVATYFLPVGMTPLVVHGEIVEKGQPLAEAKGLLRMPRQV 317

Query: 197 REEELEDEQRK-------LDEEMEKRRRRVQEWQELKRKKEESERENRGDANVEEPKAGR 249
           R  ++E E+           E  E +  RVQ    +   +              +P+   
Sbjct: 318 RAAQVEAEEEGETVYLTLFLEWTEPKDYRVQPHMNVVVPEGARVEAGDKIVAAIDPEEEV 377

Query: 250 NWTLDREDSDDEEVPQTGKSETDMDADEEPKPSENQVGDAMLVDSDGGSAAPALQIGAAE 309
               +      E              +++ + S         V +DGG     +      
Sbjct: 378 IAEAEGVVHLHEPASILVVKARVYPFEDDVEVSTGDRVAPGDVLADGGKVKSDVYGRVEV 437

Query: 310 DEDIDPLDAF 319
           D   + +   
Sbjct: 438 DLVRNVVRVV 447

>1w1w_A Structural maintenance of chromosome 1; cohesin, chromosome segregation, cell adhesion, kleisin, MIT cell cycle; HET: ATG; 2.90A {Saccharomyces cerevisiae} SCOP: c.37.1.12 Length = 430

 Score = 46.2 bits (110), Expect = 4e-05
 Identities = 15/146 (10%), Positives = 48/146 (32%), Gaps = 1/146 (0%)

Query: 70  ERAREKEREREKRDREREDRERERERERERRERDREREKRERERDRDKEKDRERKSRDRE 129
           +    K+      +     + +     +   E+   +   E  R   +E     + +   
Sbjct: 124 KTVSYKDYSIFLENENILIKAKNFLVFQGDVEQIAAQSPVELSR-MFEEVSGSIQYKKEY 182

Query: 130 KRRKVESDDSDEDKDRDRKRRRRHDDDHKERVRERSLSRSNRHRDENDESPREKLVEDDS 189
           +  K + +   +      K RRR   + K              R    +    +    ++
Sbjct: 183 EELKEKIEKLSKSATESIKNRRRIHGELKTYKSPGLEVLFQGPRGSRYDEAEGRFEVINN 242

Query: 190 DKKEKKTREEELEDEQRKLDEEMEKR 215
           + ++ K  E+++ ++  K+ ++ ++ 
Sbjct: 243 ETEQLKAEEKKILNQFLKIKKKRKEL 268

>1f5n_A Interferon-induced guanylate-binding protein 1; GBP, GTP hydrolysis, GDP, GMP, dynamin related, large GTPase family. GMPPNP, GPPNHP.; HET: GNP; 1.70A {Homo sapiens} SCOP: a.114.1.1 c.37.1.8 PDB: 1dg3_A* 2b8w_A* 2b92_A* 2bc9_A* 2d4h_A* Length = 592

 Score = 44.6 bits (104), Expect = 1e-04
 Identities = 28/228 (12%), Positives = 82/228 (35%), Gaps = 7/228 (3%)

Query: 9   DREKEKEKHREKSRRSEREQSTDSDEDKHDKEKEKDKHRDRDRRRDRDRDRDREKEREEK 68
             ++  + HR+  R +       S +D     +++   +   +R D  +           
Sbjct: 349 SLQELLDLHRDSEREAIEVFIRSSFKDVDHLFQKELAAQLEKKRDDFCKQNQEASSDRCS 408

Query: 69  RERAREKEREREKRDREREDRERERERERERRERDREREKRERERDRDKEKDRERKSRDR 128
                      E+       +        ++ +  +++   E  +    E+  +   + +
Sbjct: 409 GLLQVIFSPLEEEVKAGIYSKPGGYRLFVQKLQDLKKKYYEEPRKGIQAEEILQTYLKSK 468

Query: 129 EKRRKVESDDSDEDKDRDRKRRRRHDDDHKERVRERSLSRSNRHRDENDESPREKLVEDD 188
           E    +       D+    K +    +  K    + S    +  + +N++   +K   + 
Sbjct: 469 ES---MTDAILQTDQTLTEKEKEIEVERVKAESAQASAKMLHEMQRKNEQMMEQK---ER 522

Query: 189 SDKKEKKTREEELEDEQRKLDEEMEKRR-RRVQEWQELKRKKEESERE 235
           S ++  K   E++E+++ +L +E E+    ++QE ++L ++  + E  
Sbjct: 523 SYQEHLKQLTEKMENDRVQLLKEQERTLALKLQEQEQLLKEGFQKESR 570

>1f5n_A Interferon-induced guanylate-binding protein 1; GBP, GTP hydrolysis, GDP, GMP, dynamin related, large GTPase family. GMPPNP, GPPNHP.; HET: GNP; 1.70A {Homo sapiens} SCOP: a.114.1.1 c.37.1.8 PDB: 1dg3_A* 2b8w_A* 2b92_A* 2bc9_A* 2d4h_A* Length = 592

 Score = 42.6 bits (99), Expect = 5e-04
 Identities = 27/235 (11%), Positives = 83/235 (35%), Gaps = 11/235 (4%)

Query: 11  EKEKEKHREKSRRSEREQSTDSDEDKHDKEKEKDKHRDRDRRRDRDRDRDREKEREEKRE 70
                    ++       S    +    KE      + RD    ++++   ++     + 
Sbjct: 354 LDLHRDSEREAIEVFIRSSFKDVDHLFQKELAAQLEKKRDDFCKQNQEASSDRCSGLLQV 413

Query: 71  RAREKEREREKRDREREDRERERERERERRERDREREKRER-ERDRDKEKDRERKSRDRE 129
                E E +     +    R   ++ +  ++    E R+  + +   +   + K    +
Sbjct: 414 IFSPLEEEVKAGIYSKPGGYRLFVQKLQDLKKKYYEEPRKGIQAEEILQTYLKSKESMTD 473

Query: 130 KRRKVESDDSDEDKDRDRKRRRRHDDDHKERVRERSLSRSNRHRDENDESPREKLVE-DD 188
              + +   ++++K+ + +R +        ++      ++ +  ++ + S +E L +  +
Sbjct: 474 AILQTDQTLTEKEKEIEVERVKAESAQASAKMLHEMQRKNEQMMEQKERSYQEHLKQLTE 533

Query: 189 SDKKEKKTREEELED-------EQRKLDEE--MEKRRRRVQEWQELKRKKEESER 234
             + ++    +E E        EQ +L +E   ++ R    E Q+L+ K    + 
Sbjct: 534 KMENDRVQLLKEQERTLALKLQEQEQLLKEGFQKESRIMKNEIQDLQTKMRRRKA 588

>1f5n_A Interferon-induced guanylate-binding protein 1; GBP, GTP hydrolysis, GDP, GMP, dynamin related, large GTPase family. GMPPNP, GPPNHP.; HET: GNP; 1.70A {Homo sapiens} SCOP: a.114.1.1 c.37.1.8 PDB: 1dg3_A* 2b8w_A* 2b92_A* 2bc9_A* 2d4h_A* Length = 592

 Score = 42.2 bits (98), Expect = 7e-04
 Identities = 34/204 (16%), Positives = 67/204 (32%), Gaps = 21/204 (10%)

Query: 8   RDREKEKEKHREKSRRSEREQSTDSDEDKHDKEKEKDKHRDRDRRRDRDRDRDREKEREE 67
            DR     +        E +    S    +    +K +   +    +  +    E+  + 
Sbjct: 404 SDRCSGLLQVIFSPLEEEVKAGIYSKPGGYRLFVQKLQDLKKKYYEEPRKGIQAEEILQT 463

Query: 68  KRERAREKEREREKRDREREDRERERERERERRERDREREKRERERDRDKEKDRERKSRD 127
             +          + D+   ++E+E E ER + E  +   K   E  R  E+  E+K R 
Sbjct: 464 YLKSKESMTDAILQTDQTLTEKEKEIEVERVKAESAQASAKMLHEMQRKNEQMMEQKERS 523

Query: 128 REKRRKVESDDSDEDKDRDRKRRRRHDDDHKERVRERSLSRSNRHRDENDESPREKLVED 187
            ++  K       E  + DR +  +     +ER     L    +   E            
Sbjct: 524 YQEHLK----QLTEKMENDRVQLLKE----QERTLALKLQEQEQLLKEGF---------- 565

Query: 188 DSDKKEKKTREEELEDEQRKLDEE 211
              +KE +  + E++D Q K+   
Sbjct: 566 ---QKESRIMKNEIQDLQTKMRRR 586

>2qag_C Septin-7; cell cycle, cell division, GTP-binding, nucleotide-binding, phosphorylation, acetylation, alternative splicing, coiled coil; HET: GDP GTP; 4.00A {Homo sapiens} Length = 418

 Score = 44.0 bits (103), Expect = 2e-04
 Identities = 25/147 (17%), Positives = 61/147 (41%), Gaps = 2/147 (1%)

Query: 1   MAHSHRDRDREKEKEKHREKSRRSEREQSTDSDEDKHDKEKEKDKHRDRDRRRDRDRDRD 60
           +  +H    ++     H E  R  +    T +  D +  + +  K        +R     
Sbjct: 270 LIRTHMQDLKDVTNNVHYENYRSRKLAAVTYNGVDNNKNKGQLTKSPLAQMEEERREHVA 329

Query: 61  REKEREEKRERARE-KEREREKRDREREDRERERERERERRERDREREKRERERDRDKEK 119
           + K+ E + E+  E K +E+ ++ ++ E   + R  + ++    + +E  E+ R  + EK
Sbjct: 330 KMKKMEMEMEQVFEMKVKEKVQKLKDSEAELQRRHEQMKKNLEAQHKELEEKRRQFEDEK 389

Query: 120 DR-ERKSRDREKRRKVESDDSDEDKDR 145
              E + R  E++    + + ++ K +
Sbjct: 390 ANWEAQQRILEQQNSSRTLEKNKKKGK 416

>3auy_A DNA double-strand break repair RAD50 ATPase; DNA repair, ABC transporter ATPase domain-like; HET: DNA ADP; 2.70A {Methanocaldococcus jannaschii} PDB: 3aux_A* 3av0_B* Length = 371

 Score = 42.9 bits (101), Expect = 4e-04
 Identities = 20/139 (14%), Positives = 46/139 (33%), Gaps = 5/139 (3%)

Query: 18  REKSRRSEREQSTDSDEDKHDKEKEKDKHRDRDRRRDRDRDR--DREKEREEKRERAREK 75
           +   +     +    DE +   +K  +  ++ ++R +R       +E+  + + +     
Sbjct: 144 KPSEKLETVAKLLGIDEFEKCYQKMGEIVKEYEKRLERIEGELNYKEESLKARLKEMSNL 203

Query: 76  EREREKRDREREDRERERERERERRERDREREKRERERDRDKEKDRERKSRDREKRRKVE 135
           E+E+EK  +  E  ++ R           +   RE+     ++   E  S        VE
Sbjct: 204 EKEKEKLTKFVEYLDKVRRIFGRNGF---QAYLREKYVPLIQKYLNEAFSEFDLPYSFVE 260

Query: 136 SDDSDEDKDRDRKRRRRHD 154
                E +          D
Sbjct: 261 LTKDFEVRVHAPNGVLTID 279

>3mwy_W Chromo domain-containing protein 1; SWI2/SNF2 ATPase, double chromodomains, hydrolase; HET: ATG; 3.70A {Saccharomyces cerevisiae} Length = 800

 Score = 42.8 bits (101), Expect = 5e-04
 Identities = 35/204 (17%), Positives = 72/204 (35%), Gaps = 14/204 (6%)

Query: 62  EKEREEKRERAREKEREREKRDREREDRERERER---ERERRERDREREKRERERDRDKE 118
           E E +   E A  +E   E     + +     +     R +   +  +   +   D +  
Sbjct: 9   ESEDDYGSEEALSEENVHEASANPQPEDFHGIDIVINHRLKTSLEEGKVLEKTVPDLNNC 68

Query: 119 KDRER---KSRDREKRRKV-ESDDSDEDKDRDRKRRRRHDDDHKERVRERSLSRSNRHRD 174
           K+      K  D        E+ +S       ++         K+ + E    R + +  
Sbjct: 69  KENYEFLIKWTDESHLHNTWETYESIGQVRGLKRLDNYC----KQFIIEDQQVRLDPYVT 124

Query: 175 ENDESPREKLVEDDSDKKEKKTREEELEDEQRKLDEEMEKRRRRVQEWQELKRKKEESER 234
             D    +   E   D+ E+    E + D QR   E+   + + + +W+ L    +E+  
Sbjct: 125 AEDIEIMDMERERRLDEFEEFHVPERIIDSQRASLEDGTSQLQYLVKWRRLNY--DEATW 182

Query: 235 ENRGDANVEEPKAGRNWTLDREDS 258
           EN  D     P+  +++  +RE+S
Sbjct: 183 ENATDIVKLAPEQVKHF-QNRENS 205

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	976
2db3_A	434	ATP-dependent RNA helicase VASA; DEAD-BOX, protein	100.0
2i4i_A	417	ATP-dependent RNA helicase DDX3X; DEAD, structural	100.0
2j0s_A	410	ATP-dependent RNA helicase DDX48; mRNA processing,	100.0
3eiq_A	414	Eukaryotic initiation factor 4A-I; PDCD4, anti-onc	100.0
1s2m_A	400	Putative ATP-dependent RNA helicase DHH1; ATP-bind	100.0
1xti_A	391	Probable ATP-dependent RNA helicase P47; alpha-bet	100.0
1hv8_A	367	Putative ATP-dependent RNA helicase MJ0669; RNA-bi	100.0
3fht_A	412	ATP-dependent RNA helicase DDX19B; DBP5, DEAD-box	100.0
3pey_A	395	ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, A	100.0
1fuu_A	394	Yeast initiation factor 4A; IF4A, helicase, DEAD-b	100.0
3sqw_A	579	ATP-dependent RNA helicase MSS116, mitochondrial;	100.0
3i5x_A	563	ATP-dependent RNA helicase MSS116; protein-RNA com	100.0
3fmp_B	479	ATP-dependent RNA helicase DDX19B; nuclear porin,	100.0
2z0m_A	337	337AA long hypothetical ATP-dependent RNA helicase	100.0
2v1x_A	591	ATP-dependent DNA helicase Q1; DNA strand annealin	100.0
3fho_A	508	ATP-dependent RNA helicase DBP5; mRNA export, ATPa	100.0
3oiy_A	414	Reverse gyrase helicase domain; topoisomerase, DNA	100.0
1oyw_A	523	RECQ helicase, ATP-dependent DNA helicase; winged	100.0
1tf5_A	844	Preprotein translocase SECA subunit; ATPase, helic	100.0
3l9o_A	1108	ATP-dependent RNA helicase DOB1; REC-A fold, winge	100.0
4a2p_A	556	RIG-I, retinoic acid inducible protein I; hydrolas	100.0
2va8_A	715	SSO2462, SKI2-type helicase; hydrolase, DNA repair	100.0
3tbk_A	555	RIG-I helicase domain; DECH helicase, ATP binding,	100.0
2fsf_A	853	Preprotein translocase SECA subunit; ATPase, DNA-R	100.0
2ykg_A	696	Probable ATP-dependent RNA helicase DDX58; hydrola	100.0
2zj8_A	720	DNA helicase, putative SKI2-type helicase; RECA fo	100.0
4a2q_A	797	RIG-I, retinoic acid inducible protein I; hydrolas	100.0
4ddu_A	1104	Reverse gyrase; topoisomerase, DNA supercoiling, a	100.0
2p6r_A	702	Afuhel308 helicase; protein-DNA complex, SF2 helic	100.0
2eyq_A	1151	TRCF, transcription-repair coupling factor; MFD, S	100.0
1nkt_A	922	Preprotein translocase SECA 1 subunit; preprotein	100.0
1wp9_A	494	ATP-dependent RNA helicase, putative; ATPase, DNA	100.0
1gku_B	1054	Reverse gyrase, TOP-RG; topoisomerase, DNA superco	100.0
1gm5_A	780	RECG; helicase, replication restart; HET: DNA ADP;	100.0
2xgj_A	1010	ATP-dependent RNA helicase DOB1; hydrolase-RNA com	100.0
4a2w_A	936	RIG-I, retinoic acid inducible protein I; hydrolas	100.0
4gl2_A	699	Interferon-induced helicase C domain-containing P;	100.0
4a4z_A	997	Antiviral helicase SKI2; hydrolase, ATPase, mRNA d	100.0
2whx_A	618	Serine protease/ntpase/helicase NS3; transcription	100.0
3fe2_A	242	Probable ATP-dependent RNA helicase DDX5; DEAD, AD	100.0
4f92_B	1724	U5 small nuclear ribonucleoprotein 200 kDa helica;	100.0
2xau_A	773	PRE-mRNA-splicing factor ATP-dependent RNA helica;	100.0
2jlq_A	451	Serine protease subunit NS3; ribonucleoprotein, nu	100.0
2oca_A	510	DAR protein, ATP-dependent DNA helicase UVSW; ATP-	100.0
4f92_B	1724	U5 small nuclear ribonucleoprotein 200 kDa helica;	100.0
1yks_A	440	Genome polyprotein [contains: flavivirin protease	100.0
2fwr_A	472	DNA repair protein RAD25; DNA unwinding, XPB, DNA	100.0
2wv9_A	673	Flavivirin protease NS2B regulatory subunit, FLAV	100.0
3o8b_A	666	HCV NS3 protease/helicase; ntpase, RNA, translocat	100.0
2z83_A	459	Helicase/nucleoside triphosphatase; hydrolase, mem	100.0
2v6i_A	431	RNA helicase; membrane, hydrolase, transmembrane,	100.0
1wrb_A	253	DJVLGB; RNA helicase, DEAD BOX, VASA, structural g	100.0
3h1t_A	590	Type I site-specific restriction-modification syst	100.0
3dmq_A	968	RNA polymerase-associated protein RAPA; SWF2/SNF2,	100.0
3iuy_A	228	Probable ATP-dependent RNA helicase DDX53; REC-A-l	100.0
3rc3_A	677	ATP-dependent RNA helicase SUPV3L1, mitochondrial;	100.0
3ber_A	249	Probable ATP-dependent RNA helicase DDX47; DEAD, A	100.0
1z63_A	500	Helicase of the SNF2/RAD54 hamily; protein-DNA com	100.0
3dkp_A	245	Probable ATP-dependent RNA helicase DDX52; DEAD, A	100.0
3bor_A	237	Human initiation factor 4A-II; translation initiat	100.0
3fmo_B	300	ATP-dependent RNA helicase DDX19B; nuclear porin,	100.0
3jux_A	822	Protein translocase subunit SECA; protein transloc	100.0
2pl3_A	236	Probable ATP-dependent RNA helicase DDX10; DEAD, s	100.0
2oxc_A	230	Probable ATP-dependent RNA helicase DDX20; DEAD, s	100.0
1qde_A	224	EIF4A, translation initiation factor 4A; DEAD box	100.0
1q0u_A	219	Bstdead; DEAD protein, RNA binding protein; 1.85A	100.0
3mwy_W	800	Chromo domain-containing protein 1; SWI2/SNF2 ATPa	100.0
1vec_A	206	ATP-dependent RNA helicase P54; DEAD-box protein,	100.0
1z3i_X	644	Similar to RAD54-like; recombination ATPase helica	99.98
2gxq_A	207	Heat resistant RNA dependent ATPase; RNA helicase,	99.98
3ly5_A	262	ATP-dependent RNA helicase DDX18; alpha-beta, stru	99.98
1t6n_A	220	Probable ATP-dependent RNA helicase; RECA-like fol	99.97
2w00_A	1038	HSDR, R.ECOR124I; ATP-binding, DNA-binding, restri	99.97
2ipc_A	997	Preprotein translocase SECA subunit; nucleotide bi	99.96
1c4o_A	664	DNA nucleotide excision repair enzyme UVRB; uvrabc	99.95
2p6n_A	191	ATP-dependent RNA helicase DDX41; DEAD, structural	99.95
2jgn_A	185	DBX, DDX3, ATP-dependent RNA helicase DDX3X; phosp	99.94
2d7d_A	661	Uvrabc system protein B; helicase, protein-DNA-ADP	99.94
2hjv_A	163	ATP-dependent RNA helicase DBPA; parallel alpha-be	99.93
1t5i_A	172	C_terminal domain of A probable ATP-dependent RNA	99.92
1fuk_A	165	Eukaryotic initiation factor 4A; helicase, DEAD-bo	99.92
2rb4_A	175	ATP-dependent RNA helicase DDX25; rossmann fold, s	99.91
3eaq_A	212	Heat resistant RNA dependent ATPase; DEAD box RNA	99.91
3i32_A	300	Heat resistant RNA dependent ATPase; RNA helicase,	99.9
2yjt_D	170	ATP-dependent RNA helicase SRMB, regulator of ribo	99.79
3b6e_A	216	Interferon-induced helicase C domain-containing P;	99.87
2vl7_A	540	XPD; helicase, unknown function; 2.25A {Sulfolobus	99.86
3crv_A	551	XPD/RAD3 related DNA helicase; XPD helicase DNA re	99.85
3llm_A	235	ATP-dependent RNA helicase A; alpha-beta-alpha, st	99.85
1rif_A	282	DAR protein, DNA helicase UVSW; bacteriophage, REC	99.83
4a15_A	620	XPD helicase, ATP-dependent DNA helicase TA0057; h	99.77
1z5z_A	271	Helicase of the SNF2/RAD54 family; hydrolase, reco	99.75
2fz4_A	237	DNA repair protein RAD25; RECA-like domain, DNA da	99.74
1w36_D	608	RECD, exodeoxyribonuclease V alpha chain; recombin	98.72
2gk6_A	624	Regulator of nonsense transcripts 1; UPF1, helicas	98.32
4b3f_X	646	DNA-binding protein smubp-2; hydrolase, helicase;	98.26
3hgt_A	328	HDA1 complex subunit 3; RECA-like domain, SWI2/SNF	98.26
3lfu_A	647	DNA helicase II; SF1 helicase, ATP-binding, DNA da	98.21
3upu_A	459	ATP-dependent DNA helicase DDA; RECA-like domain,	98.19
2xzl_A	802	ATP-dependent helicase NAM7; hydrolase-RNA complex	98.19
2wjy_A	800	Regulator of nonsense transcripts 1; nonsense medi	98.15
3e1s_A	574	Exodeoxyribonuclease V, subunit RECD; alpha and be	98.03
1uaa_A	673	REP helicase, protein (ATP-dependent DNA helicase	97.45
1pjr_A	724	PCRA; DNA repair, DNA replication, SOS response, h	97.34
2o0j_A	385	Terminase, DNA packaging protein GP17; nucleotide-	97.32
3cpe_A	592	Terminase, DNA packaging protein GP17; large termi	96.69
2orw_A	184	Thymidine kinase; TMTK, TP4A, transferase; HET: 4T	96.64
3ec2_A	180	DNA replication protein DNAC; helicase loader, rep	96.63
1xx6_A	191	Thymidine kinase; NESG, northeast structural genom	96.53
3kl4_A	433	SRP54, signal recognition 54 kDa protein; signal r	96.15
2j9r_A	214	Thymidine kinase; TK1, DNK, lasso, transferase, AT	96.04
2b8t_A	223	Thymidine kinase; deoxyribonucleoside kinase, zinc	96.0
3vkw_A	446	Replicase large subunit; alpha/beta domain, helica	95.74
3e2i_A	219	Thymidine kinase; Zn-binding, ATP-binding, DNA syn	95.73
3dm5_A	443	SRP54, signal recognition 54 kDa protein; protein-	95.66
3te6_A	318	Regulatory protein SIR3; heterochromatin, gene sil	95.64
1w4r_A	195	Thymidine kinase; type II, human, cytosolic, phosp	95.61
2kjq_A	149	DNAA-related protein; solution structure, NESG, st	95.6
2w58_A	202	DNAI, primosome component (helicase loader); ATP-b	95.53
2qgz_A	308	Helicase loader, putative primosome component; str	95.52
2orv_A	234	Thymidine kinase; TP4A (P1-(5'-adenosyl)P4-(5'- (2	95.51
2p65_A	187	Hypothetical protein PF08_0063; CLPB, malaria, str	95.49
1l8q_A	324	Chromosomal replication initiator protein DNAA; AA	95.45
2zpa_A	671	Uncharacterized protein YPFI; RNA modification enz	95.36
1jbk_A	195	CLPB protein; beta barrel, chaperone; 1.80A {Esche	95.21
3u4q_A	1232	ATP-dependent helicase/nuclease subunit A; helicas	95.19
1d2n_A	272	N-ethylmaleimide-sensitive fusion protein; hexamer	94.9
4b4t_M	434	26S protease regulatory subunit 6A; hydrolase, AAA	94.86
1a5t_A	334	Delta prime, HOLB; zinc finger, DNA replication; 2	94.77
3h4m_A	285	Proteasome-activating nucleotidase; ATPase, PAN, A	94.76
2z4s_A	440	Chromosomal replication initiator protein DNAA; AA	94.73
4b4t_J	405	26S protease regulatory subunit 8 homolog; hydrola	94.63
1gm5_A	780	RECG; helicase, replication restart; HET: DNA ADP;	94.54
1g5t_A	196	COB(I)alamin adenosyltransferase; P-loop protein,	94.5
3cf0_A	301	Transitional endoplasmic reticulum ATPase; AAA, P9	94.36
3n70_A	145	Transport activator; sigma-54, ntpase, PSI, MCSG,	94.22
2chg_A	226	Replication factor C small subunit; DNA-binding pr	93.89
4b4t_L	437	26S protease subunit RPT4; hydrolase, AAA-atpases,	93.86
2qby_B	384	CDC6 homolog 3, cell division control protein 6 ho	93.84
2v1u_A	387	Cell division control protein 6 homolog; DNA repli	93.83
3bos_A	242	Putative DNA replication factor; P-loop containing	93.78
3eie_A	322	Vacuolar protein sorting-associated protein 4; AAA	93.78
4b4t_I	437	26S protease regulatory subunit 4 homolog; hydrola	93.64
4b4t_K	428	26S protease regulatory subunit 6B homolog; hydrol	93.62
3syl_A	309	Protein CBBX; photosynthesis, rubisco activase, AA	93.59
3u61_B	324	DNA polymerase accessory protein 44; AAA+, ATP hyd	93.3
3oiy_A	414	Reverse gyrase helicase domain; topoisomerase, DNA	93.15
1njg_A	250	DNA polymerase III subunit gamma; rossman-like fol	93.14
3vfd_A	389	Spastin; ATPase, microtubule severing, hydrolase;	93.09
1fnn_A	389	CDC6P, cell division control protein 6; ORC1, AAA	92.96
1sxj_E	354	Activator 1 40 kDa subunit; clamp loader, processi	92.96
3pfi_A	338	Holliday junction ATP-dependent DNA helicase RUVB;	92.68
4b4t_H	467	26S protease regulatory subunit 7 homolog; hydrola	92.56
3b9p_A	297	CG5977-PA, isoform A; AAA ATPase, ATP-binding, nuc	92.5
1xwi_A	322	SKD1 protein; VPS4B, AAA ATPase, protein transport	92.48
2qby_A	386	CDC6 homolog 1, cell division control protein 6 ho	92.27
2qp9_X	355	Vacuolar protein sorting-associated protein 4; ATP	92.11
1lv7_A	257	FTSH; alpha/beta domain, four helix bundle, hydrol	91.54
1ls1_A	295	Signal recognition particle protein; FFH, SRP54, S	91.54
2r6a_A	454	DNAB helicase, replicative helicase; replication,	91.52
1iqp_A	327	RFCS; clamp loader, extended AAA-ATPase domain, co	91.26
3pvs_A	447	Replication-associated recombination protein A; ma	91.06
3uk6_A	368	RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding	91.06
1jr3_A	373	DNA polymerase III subunit gamma; processivity, pr	90.9
2p6n_A	191	ATP-dependent RNA helicase DDX41; DEAD, structural	90.61
2qz4_A	262	Paraplegin; AAA+, SPG7, protease, ADP, structural	90.34
1ofh_A	310	ATP-dependent HSL protease ATP-binding subunit HSL	90.33
1sxj_D	353	Activator 1 41 kDa subunit; clamp loader, processi	90.03
2w0m_A	235	SSO2452; RECA, SSPF, unknown FUN; 2.0A {Sulfolobus	89.88
4ddu_A	1104	Reverse gyrase; topoisomerase, DNA supercoiling, a	89.73
1hqc_A	324	RUVB; extended AAA-ATPase domain, complex with nuc	89.71
1vma_A	306	Cell division protein FTSY; TM0570, structural gen	89.7
3e70_C	328	DPA, signal recognition particle receptor; FTSY, S	89.64
2q6t_A	444	DNAB replication FORK helicase; hydrolase; 2.90A {	89.55
2dr3_A	247	UPF0273 protein PH0284; RECA superfamily ATPase, h	89.53
2zan_A	444	Vacuolar protein sorting-associating protein 4B; S	89.36
2eyq_A	1151	TRCF, transcription-repair coupling factor; MFD, S	89.31
2ehv_A	251	Hypothetical protein PH0186; KAIC, RECA ATPase, un	89.2
1sxj_A	516	Activator 1 95 kDa subunit; clamp loader, processi	89.19
2gno_A	305	DNA polymerase III, gamma subunit-related protein;	88.91
2hjv_A	163	ATP-dependent RNA helicase DBPA; parallel alpha-be	88.91
3lda_A	400	DNA repair protein RAD51; DNA binding protein, ATP	88.75
2ffh_A	425	Protein (FFH); SRP54, signal recognition particle,	88.74
3d8b_A	357	Fidgetin-like protein 1; AAA+, ATPase, ADP, SGC, s	88.61
1nlf_A	279	Regulatory protein REPA; replicative DNA helicase	88.48
3hu3_A	489	Transitional endoplasmic reticulum ATPase; VCP, tr	88.41
1sxj_B	323	Activator 1 37 kDa subunit; clamp loader, processi	88.25
3t15_A	293	Ribulose bisphosphate carboxylase/oxygenase activ	88.24
4a1f_A	338	DNAB helicase, replicative DNA helicase; hydrolase	88.05
1qvr_A	854	CLPB protein; coiled coil, AAA ATPase, chaperone;	87.95
2ce7_A	476	Cell division protein FTSH; metalloprotease; HET:	87.72
1cr0_A	296	DNA primase/helicase; RECA-type protein fold, tran	87.71
2rb4_A	175	ATP-dependent RNA helicase DDX25; rossmann fold, s	87.63
1t6n_A	220	Probable ATP-dependent RNA helicase; RECA-like fol	87.56
1fuk_A	165	Eukaryotic initiation factor 4A; helicase, DEAD-bo	87.05
2cvh_A	220	DNA repair and recombination protein RADB; filamen	87.0
3k1j_A	604	LON protease, ATP-dependent protease LON; ATP-bind	86.58
3eaq_A	212	Heat resistant RNA dependent ATPase; DEAD box RNA	86.41
2yhs_A	503	FTSY, cell division protein FTSY; cell cycle, prot	86.39
3hjh_A	483	Transcription-repair-coupling factor; MFD, mutatio	86.27
2xxa_A	433	Signal recognition particle protein; protein trans	86.26
2jgn_A	185	DBX, DDX3, ATP-dependent RNA helicase DDX3X; phosp	85.96
2v1x_A	591	ATP-dependent DNA helicase Q1; DNA strand annealin	85.66
3cmu_A	2050	Protein RECA, recombinase A; homologous recombinat	85.45
3ber_A	249	Probable ATP-dependent RNA helicase DDX47; DEAD, A	85.31
1w5s_A	412	Origin recognition complex subunit 2 ORC2; replica	85.17
2v3c_C	432	SRP54, signal recognition 54 kDa protein; nucleoti	85.02
1t5i_A	172	C_terminal domain of A probable ATP-dependent RNA	84.66
1oyw_A	523	RECQ helicase, ATP-dependent DNA helicase; winged	84.6
1j8m_F	297	SRP54, signal recognition 54 kDa protein; signalin	84.5
3fe2_A	242	Probable ATP-dependent RNA helicase DDX5; DEAD, AD	84.47
2zts_A	251	Putative uncharacterized protein PH0186; KAIC like	84.37
1um8_A	376	ATP-dependent CLP protease ATP-binding subunit CL;	84.36
2j37_W	504	Signal recognition particle 54 kDa protein (SRP54)	83.93
3i5x_A	563	ATP-dependent RNA helicase MSS116; protein-RNA com	83.93
1xp8_A	366	RECA protein, recombinase A; recombination, radior	83.46
3cf2_A	806	TER ATPase, transitional endoplasmic reticulum ATP	83.4
2fna_A	357	Conserved hypothetical protein; structural genomic	83.02
1r6b_X	758	CLPA protein; AAA+, N-terminal domain, CLPS, cryst	82.93
2pl3_A	236	Probable ATP-dependent RNA helicase DDX10; DEAD, s	82.43
3bh0_A	315	DNAB-like replicative helicase; ATPase, replicatio	82.34
2oxc_A	230	Probable ATP-dependent RNA helicase DDX20; DEAD, s	82.32
1n0w_A	243	DNA repair protein RAD51 homolog 1; DNA repair, ho	82.31
2i4i_A	417	ATP-dependent RNA helicase DDX3X; DEAD, structural	82.21
3sqw_A	579	ATP-dependent RNA helicase MSS116, mitochondrial;	82.0
3i32_A	300	Heat resistant RNA dependent ATPase; RNA helicase,	81.51
3cf2_A	806	TER ATPase, transitional endoplasmic reticulum ATP	81.43
2px0_A	296	Flagellar biosynthesis protein FLHF; SRP GTPase, f	81.39
1wrb_A	253	DJVLGB; RNA helicase, DEAD BOX, VASA, structural g	81.36
2z43_A	324	DNA repair and recombination protein RADA; archaea	81.36
3co5_A	143	Putative two-component system transcriptional RES	81.29
3bgw_A	444	DNAB-like replicative helicase; ATPase, replicatio	81.15
3hr8_A	356	Protein RECA; alpha and beta proteins (A/B, A+B),	80.46
3bor_A	237	Human initiation factor 4A-II; translation initiat	80.14
3iuy_A	228	Probable ATP-dependent RNA helicase DDX53; REC-A-l	80.02

>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=100.00  E-value=1.6e-63  Score=579.88  Aligned_cols=389  Identities=39%  Similarity=0.659  Sum_probs=360.7

Q ss_pred             cCceeccCCCCCcccccccCCCCHHHHHHHHHcCCCCCcHHHHHHHHHHhcCCCEEEEcCCCCchHHHHHHHHHHHHhcC
Q 002040          453 LELKIHGKDVPKPIKTWHQTGLTSKIMETIRKLNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQ  532 (976)
Q Consensus       453 ~~i~~~g~~~p~pi~~~~~~~l~~~l~~~l~~~~~~~p~~~Q~~~i~~il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~  532 (976)
                      ..+.+.|.++|.|+.+|.+++|++.+++.|..+||..|+|+|.++||.+++|+|+|++|+||||||++|++|++.++...
T Consensus        42 ~~~~~~~~~~p~~~~~f~~~~l~~~l~~~l~~~g~~~pt~iQ~~ai~~i~~g~d~i~~a~TGsGKT~a~~lpil~~l~~~  121 (434)
T 2db3_A           42 IPVKVTGSDVPQPIQHFTSADLRDIIIDNVNKSGYKIPTPIQKCSIPVISSGRDLMACAQTGSGKTAAFLLPILSKLLED  121 (434)
T ss_dssp             SCEEEESSSCCCCCCCGGGSCCCHHHHHHHHHTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHHHHHS
T ss_pred             ceeEecCCCCCCCcCChhhcCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhcCCCEEEECCCCCCchHHHHHHHHHHHHhc
Confidence            34678899999999999999999999999999999999999999999999999999999999999999999999999876


Q ss_pred             CCCCCCCCCeEEEEccCHHHHHHHHHHHHHHHhhcCcEEEEeeCCCChHHHHHHHhcCCeEEEeCchhHHHHHHhcCCcc
Q 002040          533 PPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGGKI  612 (976)
Q Consensus       533 ~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~~~~~~~~~~~~~~gg~~~~~~~~~l~~~~~Iiv~Tp~~L~~~l~~~~~~~  612 (976)
                      +......++++|||+||++||.|++..+.+++...++.+.+++||.....+...+..+++|+|+||++|.+++....   
T Consensus       122 ~~~~~~~~~~~lil~PtreLa~Q~~~~~~~~~~~~~~~~~~~~gg~~~~~~~~~l~~~~~Ivv~Tp~~l~~~l~~~~---  198 (434)
T 2db3_A          122 PHELELGRPQVVIVSPTRELAIQIFNEARKFAFESYLKIGIVYGGTSFRHQNECITRGCHVVIATPGRLLDFVDRTF---  198 (434)
T ss_dssp             CCCCCTTCCSEEEECSSHHHHHHHHHHHHHHTTTSSCCCCEECTTSCHHHHHHHHTTCCSEEEECHHHHHHHHHTTS---
T ss_pred             ccccccCCccEEEEecCHHHHHHHHHHHHHHhccCCcEEEEEECCCCHHHHHHHhhcCCCEEEEChHHHHHHHHhCC---
Confidence            54334457899999999999999999999999888999999999999998888888899999999999999987542   


Q ss_pred             cccCCceEEEecCcccccccCCchHHHHHHHhc--CCCCcEEEEeccCcHHHHHHHHHHcCCCeEEEeCCcccccCCceE
Q 002040          613 TNLRRVTYLVMDEADRMFDMGFEPQITRIVQNI--RPDRQTVLFSATFPRQVEILARKVLNKPVEIQVGGRSVVNKDITQ  690 (976)
Q Consensus       613 ~~l~~~~~vVlDEah~~~~~~f~~~i~~il~~~--~~~~q~i~~SAT~~~~~~~l~~~~l~~~~~i~~~~~~~~~~~i~q  690 (976)
                      ..+.++.+|||||||+|++++|...+..++..+  ++.+|+|+||||+|..+..++..++.+++.+.++........+.+
T Consensus       199 ~~l~~~~~lVlDEah~~~~~gf~~~~~~i~~~~~~~~~~q~l~~SAT~~~~~~~~~~~~l~~~~~i~~~~~~~~~~~i~~  278 (434)
T 2db3_A          199 ITFEDTRFVVLDEADRMLDMGFSEDMRRIMTHVTMRPEHQTLMFSATFPEEIQRMAGEFLKNYVFVAIGIVGGACSDVKQ  278 (434)
T ss_dssp             CCCTTCCEEEEETHHHHTSTTTHHHHHHHHHCTTSCSSCEEEEEESCCCHHHHHHHHTTCSSCEEEEESSTTCCCTTEEE
T ss_pred             cccccCCeEEEccHhhhhccCcHHHHHHHHHhcCCCCCceEEEEeccCCHHHHHHHHHhccCCEEEEeccccccccccce
Confidence            568899999999999999999999999999875  678999999999999999999999999999988877777778899


Q ss_pred             EEEecCcchHHHHHHHHHHhhhcCCcEEEEecCHHHHHHHHHHHHHCCCCceeccCCCCHHHHHHHHHHhccCCccEEEe
Q 002040          691 LVEVRPESDRFLRLLELLGEWYEKGKILIFVHSQEKCDALFRDLLKHGYPCLSLHGAKDQTDRESTISDFKSNVCNLLIA  770 (976)
Q Consensus       691 ~~~~~~~~~k~~~l~~~l~~~~~~~kvLIF~~s~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLVa  770 (976)
                      .+.......+...|+.+|...  ..++||||+++..|+.++..|...|+.+..+||++++.+|..+++.|++|.++||||
T Consensus       279 ~~~~~~~~~k~~~l~~~l~~~--~~~~lVF~~t~~~a~~l~~~L~~~~~~~~~lhg~~~~~~R~~~l~~F~~g~~~vLva  356 (434)
T 2db3_A          279 TIYEVNKYAKRSKLIEILSEQ--ADGTIVFVETKRGADFLASFLSEKEFPTTSIHGDRLQSQREQALRDFKNGSMKVLIA  356 (434)
T ss_dssp             EEEECCGGGHHHHHHHHHHHC--CTTEEEECSSHHHHHHHHHHHHHTTCCEEEESTTSCHHHHHHHHHHHHTSSCSEEEE
T ss_pred             EEEEeCcHHHHHHHHHHHHhC--CCCEEEEEeCcHHHHHHHHHHHhCCCCEEEEeCCCCHHHHHHHHHHHHcCCCcEEEE
Confidence            988888889999999988775  345999999999999999999999999999999999999999999999999999999


Q ss_pred             cCcccccCCCCCCcEEEEeCCCCCHHHHHHHhcccCCCCCccEEEEEecC-CCcCchHHHHHHHhhccCCCChHHHH
Q 002040          771 TSVAARGLDVKELELVINFDAPNHYEDYVHRVGRTGRAGRKGCAITFISE-EDAKYSPDLVKALELSEQVVPDDLKA  846 (976)
Q Consensus       771 T~v~~~GlDi~~v~~VI~~d~p~s~~~y~Qr~GR~gR~g~~g~~~~~~~~-~d~~~~~~i~~~l~~~~~~vp~~l~~  846 (976)
                      |+++++|||||++++||+||+|+++..|+||+||+||.|+.|.|++|+++ .+...+..|++.|..+.+.+|++|..
T Consensus       357 T~v~~rGlDi~~v~~VI~~d~p~~~~~y~qriGR~gR~g~~G~a~~~~~~~~~~~~~~~l~~~l~~~~~~vp~~l~~  433 (434)
T 2db3_A          357 TSVASRGLDIKNIKHVINYDMPSKIDDYVHRIGRTGRVGNNGRATSFFDPEKDRAIAADLVKILEGSGQTVPDFLRT  433 (434)
T ss_dssp             CGGGTSSCCCTTCCEEEESSCCSSHHHHHHHHTTSSCTTCCEEEEEEECTTTCGGGHHHHHHHHHHTTCCCCGGGC-
T ss_pred             chhhhCCCCcccCCEEEEECCCCCHHHHHHHhcccccCCCCCEEEEEEeccccHHHHHHHHHHHHHcCCCCCHHHHh
Confidence            99999999999999999999999999999999999999999999999995 57788999999999999999998754

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

Probab=100.00  E-value=2e-57  Score=526.84  Aligned_cols=392  Identities=42%  Similarity=0.694  Sum_probs=353.5

Q ss_pred             ceeccCCCCCcccccccCCCCHHHHHHHHHcCCCCCcHHHHHHHHHHhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCC
Q 002040          455 LKIHGKDVPKPIKTWHQTGLTSKIMETIRKLNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPP  534 (976)
Q Consensus       455 i~~~g~~~p~pi~~~~~~~l~~~l~~~l~~~~~~~p~~~Q~~~i~~il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~  534 (976)
                      +.+.|..+|.|+.+|.+++|++.+.+.|..+||..|+|+|.++|+.++.++++|+++|||||||++|++|++..+.....
T Consensus         3 ~~~~~~~~p~~~~~f~~~~l~~~l~~~l~~~~~~~~~~~Q~~~i~~i~~~~~~lv~a~TGsGKT~~~~~~~l~~~~~~~~   82 (417)
T 2i4i_A            3 VEATGNNCPPHIESFSDVEMGEIIMGNIELTRYTRPTPVQKHAIPIIKEKRDLMACAQTGSGKTAAFLLPILSQIYSDGP   82 (417)
T ss_dssp             EEEESTTCCCCCSSGGGSCCCHHHHHHHHHHTCCSCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHHHHCC
T ss_pred             cccCCCcCCcccCCHhhCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHccCCCEEEEcCCCCHHHHHHHHHHHHHHHhccc
Confidence            45778899999999999999999999999999999999999999999999999999999999999999999988865321


Q ss_pred             C-------------CCCCCCeEEEEccCHHHHHHHHHHHHHHHhhcCcEEEEeeCCCChHHHHHHHhcCCeEEEeCchhH
Q 002040          535 V-------------AAGDGPVGLIMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRM  601 (976)
Q Consensus       535 ~-------------~~~~~~~vLIl~Ptr~La~Q~~~~~~~~~~~~~~~~~~~~gg~~~~~~~~~l~~~~~Iiv~Tp~~L  601 (976)
                      .             ....++++|||+||++||.|++..+..++...++.+..++||.....+...+..+++|+|+||++|
T Consensus        83 ~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~I~v~Tp~~l  162 (417)
T 2i4i_A           83 GEALRAMKENGRYGRRKQYPISLVLAPTRELAVQIYEEARKFSYRSRVRPCVVYGGADIGQQIRDLERGCHLLVATPGRL  162 (417)
T ss_dssp             CHHHHHHHHCBTTBSCSBCCSEEEECSSHHHHHHHHHHHHHHHTTSSCCEEEECSSSCHHHHHHHHTTCCSEEEECHHHH
T ss_pred             cchhhccccccccccccCCccEEEECCcHHHHHHHHHHHHHHhCcCCceEEEEECCCCHHHHHHHhhCCCCEEEEChHHH
Confidence            1             112357899999999999999999999998889999999999999988888888999999999999


Q ss_pred             HHHHHhcCCcccccCCceEEEecCcccccccCCchHHHHHHHh--cCC--CCcEEEEeccCcHHHHHHHHHHcCCCeEEE
Q 002040          602 IDILCTSGGKITNLRRVTYLVMDEADRMFDMGFEPQITRIVQN--IRP--DRQTVLFSATFPRQVEILARKVLNKPVEIQ  677 (976)
Q Consensus       602 ~~~l~~~~~~~~~l~~~~~vVlDEah~~~~~~f~~~i~~il~~--~~~--~~q~i~~SAT~~~~~~~l~~~~l~~~~~i~  677 (976)
                      ..++....   ..+..+++|||||||++++++|...+..++..  +++  ..|+|+||||+++.+..++..++..+..+.
T Consensus       163 ~~~l~~~~---~~~~~~~~iViDEah~~~~~~~~~~~~~i~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~  239 (417)
T 2i4i_A          163 VDMMERGK---IGLDFCKYLVLDEADRMLDMGFEPQIRRIVEQDTMPPKGVRHTMMFSATFPKEIQMLARDFLDEYIFLA  239 (417)
T ss_dssp             HHHHHTTS---BCCTTCCEEEESSHHHHHHTTCHHHHHHHHTSSSCCCBTTBEEEEEESCCCHHHHHHHHHHCSSCEEEE
T ss_pred             HHHHHcCC---cChhhCcEEEEEChhHhhccCcHHHHHHHHHhccCCCcCCcEEEEEEEeCCHHHHHHHHHHcCCCEEEE
Confidence            99887642   46788999999999999999999999999874  332  679999999999999999999999998888


Q ss_pred             eCCcccccCCceEEEEecCcchHHHHHHHHHHhhhcCCcEEEEecCHHHHHHHHHHHHHCCCCceeccCCCCHHHHHHHH
Q 002040          678 VGGRSVVNKDITQLVEVRPESDRFLRLLELLGEWYEKGKILIFVHSQEKCDALFRDLLKHGYPCLSLHGAKDQTDRESTI  757 (976)
Q Consensus       678 ~~~~~~~~~~i~q~~~~~~~~~k~~~l~~~l~~~~~~~kvLIF~~s~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~  757 (976)
                      +.........+.+.+.......+...+..++......+++||||+++..++.++..|...++.+..+||++++.+|..++
T Consensus       240 ~~~~~~~~~~i~~~~~~~~~~~~~~~l~~~l~~~~~~~~~lVf~~~~~~~~~l~~~L~~~~~~~~~~h~~~~~~~r~~~~  319 (417)
T 2i4i_A          240 VGRVGSTSENITQKVVWVEESDKRSFLLDLLNATGKDSLTLVFVETKKGADSLEDFLYHEGYACTSIHGDRSQRDREEAL  319 (417)
T ss_dssp             EC----CCSSEEEEEEECCGGGHHHHHHHHHHTCCTTCEEEEECSSHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHH
T ss_pred             eCCCCCCccCceEEEEEeccHhHHHHHHHHHHhcCCCCeEEEEECCHHHHHHHHHHHHHCCCCeeEecCCCCHHHHHHHH
Confidence            87766677788888888888889999999888766678999999999999999999999999999999999999999999


Q ss_pred             HHhccCCccEEEecCcccccCCCCCCcEEEEeCCCCCHHHHHHHhcccCCCCCccEEEEEecCCCcCchHHHHHHHhhcc
Q 002040          758 SDFKSNVCNLLIATSVAARGLDVKELELVINFDAPNHYEDYVHRVGRTGRAGRKGCAITFISEEDAKYSPDLVKALELSE  837 (976)
Q Consensus       758 ~~F~~g~~~vLVaT~v~~~GlDi~~v~~VI~~d~p~s~~~y~Qr~GR~gR~g~~g~~~~~~~~~d~~~~~~i~~~l~~~~  837 (976)
                      +.|++|.++|||||+++++|||+|++++||+|++|+++..|+||+||+||.|+.|.|++|+++.+...+..|++.+....
T Consensus       320 ~~f~~g~~~vlvaT~~~~~Gidip~v~~Vi~~~~p~s~~~~~Qr~GR~gR~g~~g~~~~~~~~~~~~~~~~l~~~~~~~~  399 (417)
T 2i4i_A          320 HQFRSGKSPILVATAVAARGLDISNVKHVINFDLPSDIEEYVHRIGRTGRVGNLGLATSFFNERNINITKDLLDLLVEAK  399 (417)
T ss_dssp             HHHHHTSSCEEEECHHHHTTSCCCCEEEEEESSCCSSHHHHHHHHTTBCC--CCEEEEEEECGGGGGGHHHHHHHHHHTT
T ss_pred             HHHHcCCCCEEEECChhhcCCCcccCCEEEEEcCCCCHHHHHHhcCccccCCCCceEEEEEccccHHHHHHHHHHHHHhc
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCChHHHHHHH
Q 002040          838 QVVPDDLKALAD  849 (976)
Q Consensus       838 ~~vp~~l~~l~~  849 (976)
                      +.+|.+|..++.
T Consensus       400 ~~~~~~l~~~~~  411 (417)
T 2i4i_A          400 QEVPSWLENMAY  411 (417)
T ss_dssp             CCCCHHHHHHHT
T ss_pred             CcCCHHHHHHHH
Confidence            999998877653

>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=100.00  E-value=2.6e-54  Score=499.67  Aligned_cols=373  Identities=33%  Similarity=0.565  Sum_probs=336.3

Q ss_pred             CCCCcccccccCCCCHHHHHHHHHcCCCCCcHHHHHHHHHHhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCC
Q 002040          461 DVPKPIKTWHQTGLTSKIMETIRKLNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDG  540 (976)
Q Consensus       461 ~~p~pi~~~~~~~l~~~l~~~l~~~~~~~p~~~Q~~~i~~il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~  540 (976)
                      ..+.+..+|.+++|++.++..|..+||..|+|+|.++|+.++.|+++|++++||||||++|++|++..+...     ..+
T Consensus        31 ~~~~~~~~f~~~~l~~~l~~~l~~~g~~~~~~~Q~~ai~~i~~~~~~lv~a~TGsGKT~~~~~~~~~~l~~~-----~~~  105 (410)
T 2j0s_A           31 EEVDVTPTFDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSISVLQCLDIQ-----VRE  105 (410)
T ss_dssp             TTCCCCCSGGGGCCCHHHHHHHHHHTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHTCCTT-----SCS
T ss_pred             CCccCCCCHhhcCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCEEEECCCCCCchHHHHHHHHHHHhhc-----cCC
Confidence            345667889999999999999999999999999999999999999999999999999999999999876432     246


Q ss_pred             CeEEEEccCHHHHHHHHHHHHHHHhhcCcEEEEeeCCCChHHHHHHHhcCCeEEEeCchhHHHHHHhcCCcccccCCceE
Q 002040          541 PVGLIMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTY  620 (976)
Q Consensus       541 ~~vLIl~Ptr~La~Q~~~~~~~~~~~~~~~~~~~~gg~~~~~~~~~l~~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~  620 (976)
                      +++|||+||++|+.||+..+..++...++.+..++||.....+...+..+++|+|+||++|.+++....   ..+..+++
T Consensus       106 ~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~ivv~Tp~~l~~~l~~~~---~~~~~~~~  182 (410)
T 2j0s_A          106 TQALILAPTRELAVQIQKGLLALGDYMNVQCHACIGGTNVGEDIRKLDYGQHVVAGTPGRVFDMIRRRS---LRTRAIKM  182 (410)
T ss_dssp             CCEEEECSSHHHHHHHHHHHHHHTTTTTCCEEEECTTSCHHHHHHHHHHCCSEEEECHHHHHHHHHTTS---SCCTTCCE
T ss_pred             ceEEEEcCcHHHHHHHHHHHHHHhccCCeEEEEEECCCCHHHHHHHhhcCCCEEEcCHHHHHHHHHhCC---ccHhheeE
Confidence            789999999999999999999999889999999999999998888888889999999999999887642   45778999


Q ss_pred             EEecCcccccccCCchHHHHHHHhcCCCCcEEEEeccCcHHHHHHHHHHcCCCeEEEeCCcccccCCceEEEEecCcc-h
Q 002040          621 LVMDEADRMFDMGFEPQITRIVQNIRPDRQTVLFSATFPRQVEILARKVLNKPVEIQVGGRSVVNKDITQLVEVRPES-D  699 (976)
Q Consensus       621 vVlDEah~~~~~~f~~~i~~il~~~~~~~q~i~~SAT~~~~~~~l~~~~l~~~~~i~~~~~~~~~~~i~q~~~~~~~~-~  699 (976)
                      |||||||++++++|...+..++..+++..|+|+||||+++.+..+...++.+|..+.+.........+.+.+...... .
T Consensus       183 vViDEah~~~~~~~~~~~~~i~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  262 (410)
T 2j0s_A          183 LVLDEADEMLNKGFKEQIYDVYRYLPPATQVVLISATLPHEILEMTNKFMTDPIRILVKRDELTLEGIKQFFVAVEREEW  262 (410)
T ss_dssp             EEEETHHHHTSTTTHHHHHHHHTTSCTTCEEEEEESCCCHHHHTTGGGTCSSCEEECCCGGGCSCTTEEEEEEEESSTTH
T ss_pred             EEEccHHHHHhhhhHHHHHHHHHhCccCceEEEEEcCCCHHHHHHHHHHcCCCEEEEecCccccCCCceEEEEEeCcHHh
Confidence            999999999999999999999999999999999999999998888888999998887776666667777777655544 4


Q ss_pred             HHHHHHHHHHhhhcCCcEEEEecCHHHHHHHHHHHHHCCCCceeccCCCCHHHHHHHHHHhccCCccEEEecCcccccCC
Q 002040          700 RFLRLLELLGEWYEKGKILIFVHSQEKCDALFRDLLKHGYPCLSLHGAKDQTDRESTISDFKSNVCNLLIATSVAARGLD  779 (976)
Q Consensus       700 k~~~l~~~l~~~~~~~kvLIF~~s~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLVaT~v~~~GlD  779 (976)
                      ++..+..++... ..+++||||+++..++.++..|...++.+..+||++++.+|..+++.|++|.++|||||+++++|||
T Consensus       263 k~~~l~~~~~~~-~~~~~lVf~~~~~~~~~l~~~L~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gid  341 (410)
T 2j0s_A          263 KFDTLCDLYDTL-TITQAVIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWARGLD  341 (410)
T ss_dssp             HHHHHHHHHHHH-TSSEEEEECSSHHHHHHHHHHHHHTTCCCEEECTTSCHHHHHHHHHHHHHTSSCEEEECGGGSSSCC
T ss_pred             HHHHHHHHHHhc-CCCcEEEEEcCHHHHHHHHHHHHhCCCceEEeeCCCCHHHHHHHHHHHHCCCCCEEEECChhhCcCC
Confidence            777777777654 4679999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCcEEEEeCCCCCHHHHHHHhcccCCCCCccEEEEEecCCCcCchHHHHHHHhhccCCCCh
Q 002040          780 VKELELVINFDAPNHYEDYVHRVGRTGRAGRKGCAITFISEEDAKYSPDLVKALELSEQVVPD  842 (976)
Q Consensus       780 i~~v~~VI~~d~p~s~~~y~Qr~GR~gR~g~~g~~~~~~~~~d~~~~~~i~~~l~~~~~~vp~  842 (976)
                      +|++++||+|++|+++..|+||+||+||.|+.|.|++|+++.+...+..|.+.+......+|.
T Consensus       342 i~~v~~Vi~~~~p~s~~~~~Qr~GR~gR~g~~g~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~  404 (410)
T 2j0s_A          342 VPQVSLIINYDLPNNRELYIHRIGRSGRYGRKGVAINFVKNDDIRILRDIEQYYSTQIDEMPM  404 (410)
T ss_dssp             CTTEEEEEESSCCSSHHHHHHHHTTSSGGGCCEEEEEEEEGGGHHHHHHHHHHTTCCCEECCS
T ss_pred             cccCCEEEEECCCCCHHHHHHhcccccCCCCceEEEEEecHHHHHHHHHHHHHhCCCceeccc
Confidence            999999999999999999999999999999999999999999988888888888766555553

>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=100.00  E-value=1.9e-53  Score=492.79  Aligned_cols=379  Identities=31%  Similarity=0.544  Sum_probs=324.1

Q ss_pred             CCCCCcccccccCCCCHHHHHHHHHcCCCCCcHHHHHHHHHHhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCC
Q 002040          460 KDVPKPIKTWHQTGLTSKIMETIRKLNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGD  539 (976)
Q Consensus       460 ~~~p~pi~~~~~~~l~~~l~~~l~~~~~~~p~~~Q~~~i~~il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~  539 (976)
                      ...+..+.+|..+++++.+.+.|..+||..|+|+|.++|+.++.|+++|++++||||||++|++|++..+...     ..
T Consensus        33 ~~~~~~~~~f~~~~l~~~~~~~l~~~~~~~~~~~Q~~~i~~~~~~~~~lv~a~TGsGKT~~~~~~~~~~~~~~-----~~  107 (414)
T 3eiq_A           33 SNWNEIVDSFDDMNLSESLLRGIYAYGFEKPSAIQQRAILPCIKGYDVIAQAQSGTGKTATFAISILQQIELD-----LK  107 (414)
T ss_dssp             CCCCCCCCCGGGGCCCHHHHHHHHHTTCCSCCHHHHHHHHHHHTTCCEEECCCSCSSSHHHHHHHHHHHCCTT-----SC
T ss_pred             CCccchhcCHhhCCCCHHHHHHHHHcCCCCCCHHHHHHhHHHhCCCCEEEECCCCCcccHHHHHHHHHHHhhc-----CC
Confidence            3445677899999999999999999999999999999999999999999999999999999999999887542     24


Q ss_pred             CCeEEEEccCHHHHHHHHHHHHHHHhhcCcEEEEeeCCCChHHHHHHHh-cCCeEEEeCchhHHHHHHhcCCcccccCCc
Q 002040          540 GPVGLIMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQISELK-RGTEIVVCTPGRMIDILCTSGGKITNLRRV  618 (976)
Q Consensus       540 ~~~vLIl~Ptr~La~Q~~~~~~~~~~~~~~~~~~~~gg~~~~~~~~~l~-~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~  618 (976)
                      ++++|||+||++|+.|++..+..++...++.+..++||.........+. .+++|+||||++|.+++....   ..+..+
T Consensus       108 ~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iiv~T~~~l~~~l~~~~---~~~~~~  184 (414)
T 3eiq_A          108 ATQALVLAPTRELAQQIQKVVMALGDYMGASCHACIGGTNVRAEVQKLQMEAPHIIVGTPGRVFDMLNRRY---LSPKYI  184 (414)
T ss_dssp             SCCEEEECSSHHHHHHHHHHHHHHGGGSCCCEEECCCCTTHHHHHHHHTTTCCSEEEECHHHHHHHHHHTS---SCSTTC
T ss_pred             ceeEEEEeChHHHHHHHHHHHHHHhcccCceEEEEECCcchHHHHHHHhcCCCCEEEECHHHHHHHHHcCC---cccccC
Confidence            6789999999999999999999999999999999999999888877776 578999999999999987643   456789


Q ss_pred             eEEEecCcccccccCCchHHHHHHHhcCCCCcEEEEeccCcHHHHHHHHHHcCCCeEEEeCCcccccCCceEEEEecCcc
Q 002040          619 TYLVMDEADRMFDMGFEPQITRIVQNIRPDRQTVLFSATFPRQVEILARKVLNKPVEIQVGGRSVVNKDITQLVEVRPES  698 (976)
Q Consensus       619 ~~vVlDEah~~~~~~f~~~i~~il~~~~~~~q~i~~SAT~~~~~~~l~~~~l~~~~~i~~~~~~~~~~~i~q~~~~~~~~  698 (976)
                      ++|||||||++.+++|...+..++..+++..|+|+||||++..+..+...++.++..+.+.........+.+.+......
T Consensus       185 ~~vViDEah~~~~~~~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  264 (414)
T 3eiq_A          185 KMFVLDEADEMLSRGFKDQIYDIFQKLNSNTQVVLLSATMPSDVLEVTKKFMRDPIRILVKKEELTLEGIRQFYINVERE  264 (414)
T ss_dssp             CEEEECSHHHHHHTTTHHHHHHHHTTSCTTCEEEEECSCCCHHHHHHHTTTCSSCEEECCCCCCCCTTSCCEEEEECSSS
T ss_pred             cEEEEECHHHhhccCcHHHHHHHHHhCCCCCeEEEEEEecCHHHHHHHHHHcCCCEEEEecCCccCCCCceEEEEEeChH
Confidence            99999999999999999999999999999999999999999999999999999998888777666666777766655544


Q ss_pred             -hHHHHHHHHHHhhhcCCcEEEEecCHHHHHHHHHHHHHCCCCceeccCCCCHHHHHHHHHHhccCCccEEEecCccccc
Q 002040          699 -DRFLRLLELLGEWYEKGKILIFVHSQEKCDALFRDLLKHGYPCLSLHGAKDQTDRESTISDFKSNVCNLLIATSVAARG  777 (976)
Q Consensus       699 -~k~~~l~~~l~~~~~~~kvLIF~~s~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLVaT~v~~~G  777 (976)
                       .+...+..++... ..+++||||+++..++.++..|...++.+..+||+|++.+|..+++.|++|.++|||||+++++|
T Consensus       265 ~~~~~~l~~~~~~~-~~~~~lvf~~~~~~~~~l~~~l~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~G  343 (414)
T 3eiq_A          265 EWKLDTLCDLYETL-TITQAVIFINTRRKVDWLTEKMHARDFTVSAMHGDMDQKERDVIMREFRSGSSRVLITTDLLARG  343 (414)
T ss_dssp             TTHHHHHHHHHHSS-CCSSCEEECSCHHHHHHHHHHHHTTTCCCEEC---CHHHHHHHHHHHHSCC---CEEECSSCC--
T ss_pred             HhHHHHHHHHHHhC-CCCcEEEEeCCHHHHHHHHHHHHhcCCeEEEecCCCCHHHHHHHHHHHHcCCCcEEEECCccccC
Confidence             4777777776654 56799999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCCCcEEEEeCCCCCHHHHHHHhcccCCCCCccEEEEEecCCCcCchHHHHHHHhhccCCCChHHHHH
Q 002040          778 LDVKELELVINFDAPNHYEDYVHRVGRTGRAGRKGCAITFISEEDAKYSPDLVKALELSEQVVPDDLKAL  847 (976)
Q Consensus       778 lDi~~v~~VI~~d~p~s~~~y~Qr~GR~gR~g~~g~~~~~~~~~d~~~~~~i~~~l~~~~~~vp~~l~~l  847 (976)
                      ||+|++++||+|++|+++..|+||+||+||.|+.|.|++|+++.+...+..|...+......+|..+.++
T Consensus       344 idip~v~~Vi~~~~p~s~~~~~Qr~GR~gR~g~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l  413 (414)
T 3eiq_A          344 IDVQQVSLVINYDLPTNRENYIHRIGRGGRFGRKGVAINMVTEEDKRTLRDIETFYNTSIEEMPLNVADL  413 (414)
T ss_dssp             CCGGGCSCEEESSCCSSTHHHHHHSCCC-------CEEEEECSTHHHHHHHHHHHTTCCCEECCC-----
T ss_pred             CCccCCCEEEEeCCCCCHHHhhhhcCcccCCCCCceEEEEEcHHHHHHHHHHHHHHcCCccccChhhhhc
Confidence            9999999999999999999999999999999999999999999999999999999888888888766544

>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=100.00  E-value=1.5e-52  Score=483.08  Aligned_cols=371  Identities=33%  Similarity=0.554  Sum_probs=330.8

Q ss_pred             CCcccccccCCCCHHHHHHHHHcCCCCCcHHHHHHHHHHhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCe
Q 002040          463 PKPIKTWHQTGLTSKIMETIRKLNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPV  542 (976)
Q Consensus       463 p~pi~~~~~~~l~~~l~~~l~~~~~~~p~~~Q~~~i~~il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~  542 (976)
                      +.+..+|.+++|++.+.+.|..+||..|+|+|.++++.++.++++|+++|||+|||++|++|++.++...     ..+++
T Consensus        17 ~~~~~~f~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~i~~~~~~li~a~TGsGKT~~~~~~~~~~~~~~-----~~~~~   91 (400)
T 1s2m_A           17 NTKGNTFEDFYLKRELLMGIFEAGFEKPSPIQEEAIPVAITGRDILARAKNGTGKTAAFVIPTLEKVKPK-----LNKIQ   91 (400)
T ss_dssp             ----CCGGGGCCCHHHHHHHHHTTCCSCCHHHHHHHHHHHHTCCEEEECCTTSCHHHHHHHHHHHHCCTT-----SCSCC
T ss_pred             ccccCChhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhcCCCEEEECCCCcHHHHHHHHHHHHHHhhc-----cCCcc
Confidence            3456789999999999999999999999999999999999999999999999999999999999887542     24678


Q ss_pred             EEEEccCHHHHHHHHHHHHHHHhhcCcEEEEeeCCCChHHHHHHHhcCCeEEEeCchhHHHHHHhcCCcccccCCceEEE
Q 002040          543 GLIMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLV  622 (976)
Q Consensus       543 vLIl~Ptr~La~Q~~~~~~~~~~~~~~~~~~~~gg~~~~~~~~~l~~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vV  622 (976)
                      +||++||++|+.|+++.+..++...++.+..++|+.....+...+..+++|+||||++|..++....   ..+.++++||
T Consensus        92 ~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~Ivv~T~~~l~~~~~~~~---~~~~~~~~vI  168 (400)
T 1s2m_A           92 ALIMVPTRELALQTSQVVRTLGKHCGISCMVTTGGTNLRDDILRLNETVHILVGTPGRVLDLASRKV---ADLSDCSLFI  168 (400)
T ss_dssp             EEEECSSHHHHHHHHHHHHHHTTTTTCCEEEECSSSCHHHHHHHTTSCCSEEEECHHHHHHHHHTTC---SCCTTCCEEE
T ss_pred             EEEEcCCHHHHHHHHHHHHHHhcccCceEEEEeCCcchHHHHHHhcCCCCEEEEchHHHHHHHHhCC---cccccCCEEE
Confidence            9999999999999999999999888999999999998888777777789999999999998886543   4578899999


Q ss_pred             ecCcccccccCCchHHHHHHHhcCCCCcEEEEeccCcHHHHHHHHHHcCCCeEEEeCCcccccCCceEEEEecCcchHHH
Q 002040          623 MDEADRMFDMGFEPQITRIVQNIRPDRQTVLFSATFPRQVEILARKVLNKPVEIQVGGRSVVNKDITQLVEVRPESDRFL  702 (976)
Q Consensus       623 lDEah~~~~~~f~~~i~~il~~~~~~~q~i~~SAT~~~~~~~l~~~~l~~~~~i~~~~~~~~~~~i~q~~~~~~~~~k~~  702 (976)
                      |||||++++.+|...+..++..+++..|+|+||||++..+..+...++..+..+.+... .....+.+.+.......+..
T Consensus       169 iDEaH~~~~~~~~~~~~~i~~~~~~~~~~i~lSAT~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~k~~  247 (400)
T 1s2m_A          169 MDEADKMLSRDFKTIIEQILSFLPPTHQSLLFSATFPLTVKEFMVKHLHKPYEINLMEE-LTLKGITQYYAFVEERQKLH  247 (400)
T ss_dssp             EESHHHHSSHHHHHHHHHHHTTSCSSCEEEEEESCCCHHHHHHHHHHCSSCEEESCCSS-CBCTTEEEEEEECCGGGHHH
T ss_pred             EeCchHhhhhchHHHHHHHHHhCCcCceEEEEEecCCHHHHHHHHHHcCCCeEEEeccc-cccCCceeEEEEechhhHHH
Confidence            99999999888888899999999889999999999999999999999998877655432 34456777777777778888


Q ss_pred             HHHHHHHhhhcCCcEEEEecCHHHHHHHHHHHHHCCCCceeccCCCCHHHHHHHHHHhccCCccEEEecCcccccCCCCC
Q 002040          703 RLLELLGEWYEKGKILIFVHSQEKCDALFRDLLKHGYPCLSLHGAKDQTDRESTISDFKSNVCNLLIATSVAARGLDVKE  782 (976)
Q Consensus       703 ~l~~~l~~~~~~~kvLIF~~s~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLVaT~v~~~GlDi~~  782 (976)
                      .+..++... ..+++||||++...++.++..|...++.+..+||+|++.+|..+++.|++|.++|||||+++++|||+|+
T Consensus       248 ~l~~~~~~~-~~~~~lVf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vLv~T~~~~~Gidip~  326 (400)
T 1s2m_A          248 CLNTLFSKL-QINQAIIFCNSTNRVELLAKKITDLGYSCYYSHARMKQQERNKVFHEFRQGKVRTLVCSDLLTRGIDIQA  326 (400)
T ss_dssp             HHHHHHHHS-CCSEEEEECSSHHHHHHHHHHHHHHTCCEEEECTTSCHHHHHHHHHHHHTTSSSEEEESSCSSSSCCCTT
T ss_pred             HHHHHHhhc-CCCcEEEEEecHHHHHHHHHHHHhcCCCeEEecCCCCHHHHHHHHHHHhcCCCcEEEEcCccccCCCccC
Confidence            777777653 5679999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CcEEEEeCCCCCHHHHHHHhcccCCCCCccEEEEEecCCCcCchHHHHHHHhhccCCCChH
Q 002040          783 LELVINFDAPNHYEDYVHRVGRTGRAGRKGCAITFISEEDAKYSPDLVKALELSEQVVPDD  843 (976)
Q Consensus       783 v~~VI~~d~p~s~~~y~Qr~GR~gR~g~~g~~~~~~~~~d~~~~~~i~~~l~~~~~~vp~~  843 (976)
                      +++||+|++|+++..|+||+||+||.|+.|.|++|+++.+...+..|.+.+....+.+|..
T Consensus       327 ~~~Vi~~~~p~s~~~~~Qr~GR~gR~g~~g~~~~l~~~~~~~~~~~i~~~~~~~~~~~~~~  387 (400)
T 1s2m_A          327 VNVVINFDFPKTAETYLHRIGRSGRFGHLGLAINLINWNDRFNLYKIEQELGTEIAAIPAT  387 (400)
T ss_dssp             EEEEEESSCCSSHHHHHHHHCBSSCTTCCEEEEEEECGGGHHHHHHHHHHHTCCCEECCSS
T ss_pred             CCEEEEeCCCCCHHHHHHhcchhcCCCCCceEEEEeccchHHHHHHHHHHhCCCccccccc
Confidence            9999999999999999999999999999999999999999888889988887776666653

>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=100.00  E-value=2.4e-51  Score=471.41  Aligned_cols=367  Identities=30%  Similarity=0.549  Sum_probs=322.4

Q ss_pred             cccccCCCCHHHHHHHHHcCCCCCcHHHHHHHHHHhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEE
Q 002040          467 KTWHQTGLTSKIMETIRKLNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIM  546 (976)
Q Consensus       467 ~~~~~~~l~~~l~~~l~~~~~~~p~~~Q~~~i~~il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl  546 (976)
                      .+|.+++|++.+.+.|..+||..|+|+|.++|+.++.++++|+++|||+|||++|++|++..+...     ..++++||+
T Consensus         8 ~~f~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~lv~a~TGsGKT~~~~~~~~~~l~~~-----~~~~~~lil   82 (391)
T 1xti_A            8 SGFRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQLEPV-----TGQVSVLVM   82 (391)
T ss_dssp             -CGGGGCCCHHHHHHHHHHSCCSCCHHHHHHHHHHTTTCCEEEECSSCSSHHHHHHHHHHHHCCCC-----TTCCCEEEE
T ss_pred             CChhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhcCCcEEEECCCCCcHHHHHHHHHHHhhccc-----CCCeeEEEE
Confidence            569999999999999999999999999999999999999999999999999999999999887542     246789999


Q ss_pred             ccCHHHHHHHHHHHHHHHhhc-CcEEEEeeCCCChHHHHHHHhcC-CeEEEeCchhHHHHHHhcCCcccccCCceEEEec
Q 002040          547 APTRELVQQIHSDIRKFAKVM-GVRCVPVYGGSGVAQQISELKRG-TEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMD  624 (976)
Q Consensus       547 ~Ptr~La~Q~~~~~~~~~~~~-~~~~~~~~gg~~~~~~~~~l~~~-~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlD  624 (976)
                      |||++|+.||+..+..++..+ ++.+..++||.........+..+ ++|+|+||++|..++....   ..+..+++||||
T Consensus        83 ~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~iiv~T~~~l~~~~~~~~---~~~~~~~~vViD  159 (391)
T 1xti_A           83 CHTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLKKNCPHIVVGTPGRILALARNKS---LNLKHIKHFILD  159 (391)
T ss_dssp             CSCHHHHHHHHHHHHHHTTTCTTCCEEEECTTSCHHHHHHHHHHSCCSEEEECHHHHHHHHHTTS---SCCTTCSEEEEC
T ss_pred             CCCHHHHHHHHHHHHHHHhhCCCeEEEEEeCCCCHHHHHHHHhcCCCCEEEECHHHHHHHHHcCC---ccccccCEEEEe
Confidence            999999999999999998776 78999999999887776666554 7999999999998886542   457889999999


Q ss_pred             Cccccccc-CCchHHHHHHHhcCCCCcEEEEeccCcHHHHHHHHHHcCCCeEEEeCCcc-cccCCceEEEEecCcchHHH
Q 002040          625 EADRMFDM-GFEPQITRIVQNIRPDRQTVLFSATFPRQVEILARKVLNKPVEIQVGGRS-VVNKDITQLVEVRPESDRFL  702 (976)
Q Consensus       625 Eah~~~~~-~f~~~i~~il~~~~~~~q~i~~SAT~~~~~~~l~~~~l~~~~~i~~~~~~-~~~~~i~q~~~~~~~~~k~~  702 (976)
                      |||++.++ +|...+..++..+++..|+|+||||+++.+..++..++..|..+.+.... .....+.+.+.......+..
T Consensus       160 EaH~~~~~~~~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  239 (391)
T 1xti_A          160 ECDKMLEQLDMRRDVQEIFRMTPHEKQVMMFSATLSKEIRPVCRKFMQDPMEIFVDDETKLTLHGLQQYYVKLKDNEKNR  239 (391)
T ss_dssp             SHHHHTSSHHHHHHHHHHHHTSCSSSEEEEEESSCCSTHHHHHHHHCSSCEEEECCCCCCCCCTTCEEEEEECCGGGHHH
T ss_pred             CHHHHhhccchHHHHHHHHhhCCCCceEEEEEeeCCHHHHHHHHHHcCCCeEEEecCccccCcccceEEEEEcCchhHHH
Confidence            99998874 77888888998888899999999999999999999999999877765433 33456677777777788888


Q ss_pred             HHHHHHHhhhcCCcEEEEecCHHHHHHHHHHHHHCCCCceeccCCCCHHHHHHHHHHhccCCccEEEecCcccccCCCCC
Q 002040          703 RLLELLGEWYEKGKILIFVHSQEKCDALFRDLLKHGYPCLSLHGAKDQTDRESTISDFKSNVCNLLIATSVAARGLDVKE  782 (976)
Q Consensus       703 ~l~~~l~~~~~~~kvLIF~~s~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLVaT~v~~~GlDi~~  782 (976)
                      .+..++... ..+++||||+++..+..++..|...|+.+..+||++++.+|..+++.|++|..+|||||+++++|||+|+
T Consensus       240 ~l~~~l~~~-~~~~~lvf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~T~~~~~Gidi~~  318 (391)
T 1xti_A          240 KLFDLLDVL-EFNQVVIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQEERLSRYQQFKDFQRRILVATNLFGRGMDIER  318 (391)
T ss_dssp             HHHHHHHHS-CCSEEEEECSCHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHTTCCSEEEESCCCSSCBCCTT
T ss_pred             HHHHHHHhc-CCCcEEEEeCcHHHHHHHHHHHHhCCCcEEEEeCCCCHHHHHHHHHHHhcCCCcEEEECChhhcCCCccc
Confidence            888888764 5689999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CcEEEEeCCCCCHHHHHHHhcccCCCCCccEEEEEecCC-CcCchHHHHHHHhhccCCCCh
Q 002040          783 LELVINFDAPNHYEDYVHRVGRTGRAGRKGCAITFISEE-DAKYSPDLVKALELSEQVVPD  842 (976)
Q Consensus       783 v~~VI~~d~p~s~~~y~Qr~GR~gR~g~~g~~~~~~~~~-d~~~~~~i~~~l~~~~~~vp~  842 (976)
                      +++||+|++|+++..|+||+||+||.|+.|.|++|+++. +..++..+.+.+......+|.
T Consensus       319 ~~~Vi~~~~p~s~~~~~Qr~GR~~R~g~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  379 (391)
T 1xti_A          319 VNIAFNYDMPEDSDTYLHRVARAGRFGTKGLAITFVSDENDAKILNDVQDRFEVNISELPD  379 (391)
T ss_dssp             EEEEEESSCCSSHHHHHHHHCBCSSSCCCCEEEEEECSHHHHHHHHHHHHHTTCCCEECCS
T ss_pred             CCEEEEeCCCCCHHHHHHhcccccCCCCceEEEEEEcccchHHHHHHHHHHhcCChhhCCc
Confidence            999999999999999999999999999999999999876 445566677666665555554

>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=100.00  E-value=2e-50  Score=459.12  Aligned_cols=357  Identities=34%  Similarity=0.588  Sum_probs=320.8

Q ss_pred             ccccccCCCCHHHHHHHHHcCCCCCcHHHHHHHHHHhcC-CCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEE
Q 002040          466 IKTWHQTGLTSKIMETIRKLNYEKPMPIQAQALPVIMSG-RDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGL  544 (976)
Q Consensus       466 i~~~~~~~l~~~l~~~l~~~~~~~p~~~Q~~~i~~il~g-~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vL  544 (976)
                      ..+|.+++|++.+...|..+||..|+|+|.++|+.++.+ +++|+++|||+|||++|++|++..+...      .++++|
T Consensus         5 ~~~f~~~~l~~~~~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~~l~~~~TGsGKT~~~~~~~~~~~~~~------~~~~~l   78 (367)
T 1hv8_A            5 YMNFNELNLSDNILNAIRNKGFEKPTDIQMKVIPLFLNDEYNIVAQARTGSGKTASFAIPLIELVNEN------NGIEAI   78 (367)
T ss_dssp             CCCGGGSSCCHHHHHHHHHHTCCSCCHHHHHHHHHHHHTCSEEEEECCSSSSHHHHHHHHHHHHSCSS------SSCCEE
T ss_pred             cCchhhcCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCCEEEECCCCChHHHHHHHHHHHHhccc------CCCcEE
Confidence            457999999999999999999999999999999999988 6999999999999999999999876532      467899


Q ss_pred             EEccCHHHHHHHHHHHHHHHhhcCcEEEEeeCCCChHHHHHHHhcCCeEEEeCchhHHHHHHhcCCcccccCCceEEEec
Q 002040          545 IMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMD  624 (976)
Q Consensus       545 Il~Ptr~La~Q~~~~~~~~~~~~~~~~~~~~gg~~~~~~~~~l~~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlD  624 (976)
                      |++||++|+.||++.+..++...++.+..++||.....+...+. +++|+|+||+.|...+....   ..+..+++||||
T Consensus        79 il~P~~~L~~q~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~-~~~iiv~T~~~l~~~~~~~~---~~~~~~~~iIiD  154 (367)
T 1hv8_A           79 ILTPTRELAIQVADEIESLKGNKNLKIAKIYGGKAIYPQIKALK-NANIVVGTPGRILDHINRGT---LNLKNVKYFILD  154 (367)
T ss_dssp             EECSCHHHHHHHHHHHHHHHCSSCCCEEEECTTSCHHHHHHHHH-TCSEEEECHHHHHHHHHTTC---SCTTSCCEEEEE
T ss_pred             EEcCCHHHHHHHHHHHHHHhCCCCceEEEEECCcchHHHHhhcC-CCCEEEecHHHHHHHHHcCC---cccccCCEEEEe
Confidence            99999999999999999998888899999999998887766665 68999999999998886542   457889999999


Q ss_pred             CcccccccCCchHHHHHHHhcCCCCcEEEEeccCcHHHHHHHHHHcCCCeEEEeCCcccccCCceEEEEecCcchHHHHH
Q 002040          625 EADRMFDMGFEPQITRIVQNIRPDRQTVLFSATFPRQVEILARKVLNKPVEIQVGGRSVVNKDITQLVEVRPESDRFLRL  704 (976)
Q Consensus       625 Eah~~~~~~f~~~i~~il~~~~~~~q~i~~SAT~~~~~~~l~~~~l~~~~~i~~~~~~~~~~~i~q~~~~~~~~~k~~~l  704 (976)
                      |||.+.+++|...+..++..+++..++|+||||+++.+..+...++.++..+....    ...+.+.+.......++..+
T Consensus       155 Eah~~~~~~~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~~~~~~~~~~l  230 (367)
T 1hv8_A          155 EADEMLNMGFIKDVEKILNACNKDKRILLFSATMPREILNLAKKYMGDYSFIKAKI----NANIEQSYVEVNENERFEAL  230 (367)
T ss_dssp             THHHHHTTTTHHHHHHHHHTSCSSCEEEEECSSCCHHHHHHHHHHCCSEEEEECCS----SSSSEEEEEECCGGGHHHHH
T ss_pred             CchHhhhhchHHHHHHHHHhCCCCceEEEEeeccCHHHHHHHHHHcCCCeEEEecC----CCCceEEEEEeChHHHHHHH
Confidence            99999999999999999999999999999999999999888888888876654432    23566777777788888888


Q ss_pred             HHHHHhhhcCCcEEEEecCHHHHHHHHHHHHHCCCCceeccCCCCHHHHHHHHHHhccCCccEEEecCcccccCCCCCCc
Q 002040          705 LELLGEWYEKGKILIFVHSQEKCDALFRDLLKHGYPCLSLHGAKDQTDRESTISDFKSNVCNLLIATSVAARGLDVKELE  784 (976)
Q Consensus       705 ~~~l~~~~~~~kvLIF~~s~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLVaT~v~~~GlDi~~v~  784 (976)
                      ..++..  ..+++||||+++..+..++..|...++.+..+||+++..+|..+++.|++|..+|||||+++++|||+|+++
T Consensus       231 ~~~l~~--~~~~~lvf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~T~~~~~Gid~~~~~  308 (367)
T 1hv8_A          231 CRLLKN--KEFYGLVFCKTKRDTKELASMLRDIGFKAGAIHGDLSQSQREKVIRLFKQKKIRILIATDVMSRGIDVNDLN  308 (367)
T ss_dssp             HHHHCS--TTCCEEEECSSHHHHHHHHHHHHHTTCCEEEECSSSCHHHHHHHHHHHHTTSSSEEEECTTHHHHCCCSCCS
T ss_pred             HHHHhc--CCCcEEEEECCHHHHHHHHHHHHhcCCCeEEeeCCCCHHHHHHHHHHHHcCCCeEEEECChhhcCCCcccCC
Confidence            888763  467899999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEEEeCCCCCHHHHHHHhcccCCCCCccEEEEEecCCCcCchHHHHHHHhhccC
Q 002040          785 LVINFDAPNHYEDYVHRVGRTGRAGRKGCAITFISEEDAKYSPDLVKALELSEQ  838 (976)
Q Consensus       785 ~VI~~d~p~s~~~y~Qr~GR~gR~g~~g~~~~~~~~~d~~~~~~i~~~l~~~~~  838 (976)
                      +||+|++|+++..|+||+||+||.|++|.|++|+++.+...+..|.+.+.....
T Consensus       309 ~Vi~~~~~~s~~~~~Q~~GR~~R~g~~g~~~~~~~~~~~~~~~~i~~~~~~~~~  362 (367)
T 1hv8_A          309 CVINYHLPQNPESYMHRIGRTGRAGKKGKAISIINRREYKKLRYIERAMKLKIK  362 (367)
T ss_dssp             EEEESSCCSCHHHHHHHSTTTCCSSSCCEEEEEECTTSHHHHHHHHHHHTCCCC
T ss_pred             EEEEecCCCCHHHhhhcccccccCCCccEEEEEEcHHHHHHHHHHHHHhCCCCc
Confidence            999999999999999999999999999999999999998888888887765533

>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=100.00  E-value=8.4e-51  Score=470.11  Aligned_cols=369  Identities=28%  Similarity=0.468  Sum_probs=318.0

Q ss_pred             CCCcccccccCCCCHHHHHHHHHcCCCCCcHHHHHHHHHHhcC--CCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCC
Q 002040          462 VPKPIKTWHQTGLTSKIMETIRKLNYEKPMPIQAQALPVIMSG--RDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGD  539 (976)
Q Consensus       462 ~p~pi~~~~~~~l~~~l~~~l~~~~~~~p~~~Q~~~i~~il~g--~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~  539 (976)
                      .+.++.+|.++++++.+++.|..+||..|+|+|.++|+.++.+  +++|+++|||+|||++|++|++..+...     ..
T Consensus        20 ~~~~~~~f~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~~~lv~apTGsGKT~~~~~~~~~~~~~~-----~~   94 (412)
T 3fht_A           20 PLYSVKSFEELRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLAMLSQVEPA-----NK   94 (412)
T ss_dssp             TTCCSSCTGGGTCCHHHHHHHHHTTCCSCCHHHHHHHHHHHSSSCCCEEEECCTTSCHHHHHHHHHHHHCCTT-----SC
T ss_pred             CccccCCHhhCCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhcCCCCeEEEECCCCchHHHHHHHHHHHHhhhc-----CC
Confidence            3466889999999999999999999999999999999999987  9999999999999999999999887643     34


Q ss_pred             CCeEEEEccCHHHHHHHHHHHHHHHhhc-CcEEEEeeCCCChHHHHHHHhcCCeEEEeCchhHHHHHHhcCCcccccCCc
Q 002040          540 GPVGLIMAPTRELVQQIHSDIRKFAKVM-GVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRV  618 (976)
Q Consensus       540 ~~~vLIl~Ptr~La~Q~~~~~~~~~~~~-~~~~~~~~gg~~~~~~~~~l~~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~  618 (976)
                      ++++|||+||++||.|++..+..+...+ ++.+.+.+++......   ...+++|+|+||++|..++...  ....+.++
T Consensus        95 ~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~ivv~T~~~l~~~~~~~--~~~~~~~~  169 (412)
T 3fht_A           95 YPQCLCLSPTYELALQTGKVIEQMGKFYPELKLAYAVRGNKLERG---QKISEQIVIGTPGTVLDWCSKL--KFIDPKKI  169 (412)
T ss_dssp             SCCEEEECSSHHHHHHHHHHHHHHTTTSTTCCEEEECTTCCCCTT---CCCCCSEEEECHHHHHHHHTTS--CSSCGGGC
T ss_pred             CCCEEEECCCHHHHHHHHHHHHHHHhhcccceEEEeecCcchhhh---hcCCCCEEEECchHHHHHHHhc--CCcChhhC
Confidence            6789999999999999999999988764 6777777877654322   1345799999999999888543  23467889


Q ss_pred             eEEEecCcccccc-cCCchHHHHHHHhcCCCCcEEEEeccCcHHHHHHHHHHcCCCeEEEeCCcccccCCceEEEEecCc
Q 002040          619 TYLVMDEADRMFD-MGFEPQITRIVQNIRPDRQTVLFSATFPRQVEILARKVLNKPVEIQVGGRSVVNKDITQLVEVRPE  697 (976)
Q Consensus       619 ~~vVlDEah~~~~-~~f~~~i~~il~~~~~~~q~i~~SAT~~~~~~~l~~~~l~~~~~i~~~~~~~~~~~i~q~~~~~~~  697 (976)
                      ++|||||||++++ .+|...+..++..+++..|+|+||||+++.+..++..++.++..+.+.........+.+.+.....
T Consensus       170 ~~iViDEah~~~~~~~~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  249 (412)
T 3fht_A          170 KVFVLDEADVMIATQGHQDQSIRIQRMLPRNCQMLLFSATFEDSVWKFAQKVVPDPNVIKLKREEETLDTIKQYYVLCSS  249 (412)
T ss_dssp             CEEEEETHHHHHSTTTTHHHHHHHHHTSCTTCEEEEEESCCCHHHHHHHHHHSSSCEEECCCGGGSSCTTEEEEEEECSS
T ss_pred             cEEEEeCHHHHhhcCCcHHHHHHHHhhCCCCceEEEEEeecCHHHHHHHHHhcCCCeEEeeccccccccCceEEEEEcCC
Confidence            9999999999887 678888999999999999999999999999999999999999988877766666777777665554


Q ss_pred             -chHHHHHHHHHHhhhcCCcEEEEecCHHHHHHHHHHHHHCCCCceeccCCCCHHHHHHHHHHhccCCccEEEecCcccc
Q 002040          698 -SDRFLRLLELLGEWYEKGKILIFVHSQEKCDALFRDLLKHGYPCLSLHGAKDQTDRESTISDFKSNVCNLLIATSVAAR  776 (976)
Q Consensus       698 -~~k~~~l~~~l~~~~~~~kvLIF~~s~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLVaT~v~~~  776 (976)
                       ..++..+..++.. ...+++||||+++..+..++..|...++.+..+||+|++.+|..+++.|++|.++|||||+++++
T Consensus       250 ~~~~~~~l~~~~~~-~~~~~~lvf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~  328 (412)
T 3fht_A          250 RDEKFQALCNLYGA-ITIAQAMIFCHTRKTASWLAAELSKEGHQVALLSGEMMVEQRAAVIERFREGKEKVLVTTNVCAR  328 (412)
T ss_dssp             HHHHHHHHHHHHHH-HSSSEEEEECSSHHHHHHHHHHHHHTTCCCEEECTTSCHHHHHHHHHHHHTTSCSEEEECGGGTS
T ss_pred             hHHHHHHHHHHHhh-cCCCCEEEEeCCHHHHHHHHHHHHhCCCeEEEecCCCCHHHHHHHHHHHHCCCCcEEEEcCcccc
Confidence             4566666666654 35679999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCCCCCcEEEEeCCCC------CHHHHHHHhcccCCCCCccEEEEEecCCC-cCchHHHHHHHhhccCCCC
Q 002040          777 GLDVKELELVINFDAPN------HYEDYVHRVGRTGRAGRKGCAITFISEED-AKYSPDLVKALELSEQVVP  841 (976)
Q Consensus       777 GlDi~~v~~VI~~d~p~------s~~~y~Qr~GR~gR~g~~g~~~~~~~~~d-~~~~~~i~~~l~~~~~~vp  841 (976)
                      |||+|++++||+|++|+      +...|+||+||+||.|+.|.|++|+++.+ ..++..|.+.+......++
T Consensus       329 Gidip~~~~Vi~~~~p~~~~~~~s~~~~~Qr~GR~gR~g~~g~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~  400 (412)
T 3fht_A          329 GIDVEQVSVVINFDLPVDKDGNPDNETYLHRIGRTGRFGKRGLAVNMVDSKHSMNILNRIQEHFNKKIERLD  400 (412)
T ss_dssp             SCCCTTEEEEEESSCCBCSSSSBCHHHHHHHHTTSSCTTCCEEEEEEECSHHHHHHHHHHHHHHTCCCEEC-
T ss_pred             CCCccCCCEEEEECCCCCCCCCcchheeecccCcccCCCCCceEEEEEcChhhHHHHHHHHHHHCCccccCC
Confidence            99999999999999995      66899999999999999999999998754 6667777777765544444

>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=100.00  E-value=1.1e-50  Score=465.96  Aligned_cols=358  Identities=31%  Similarity=0.547  Sum_probs=310.4

Q ss_pred             CcccccccCCCCHHHHHHHHHcCCCCCcHHHHHHHHHHhcC--CCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCC
Q 002040          464 KPIKTWHQTGLTSKIMETIRKLNYEKPMPIQAQALPVIMSG--RDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGP  541 (976)
Q Consensus       464 ~pi~~~~~~~l~~~l~~~l~~~~~~~p~~~Q~~~i~~il~g--~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~  541 (976)
                      +...+|.+++|++.+++.|..+||..|+|+|.++|+.++.+  +++|+++|||+|||++|++|++.++...     ..++
T Consensus         2 ~~~~~f~~~~l~~~l~~~l~~~~~~~~~~~Q~~~i~~~~~~~~~~~lv~a~TGsGKT~~~~~~~~~~~~~~-----~~~~   76 (395)
T 3pey_A            2 AMAKSFDELGLAPELLKGIYAMKFQKPSKIQERALPLLLHNPPRNMIAQSQSGTGKTAAFSLTMLTRVNPE-----DASP   76 (395)
T ss_dssp             --CCSSTTSCCCHHHHHHHHHTTCCSCCHHHHHHHHHHHCSSCCCEEEECCTTSCHHHHHHHHHHHHCCTT-----CCSC
T ss_pred             ccccCHhhCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHcCCCCeEEEECCCCCcHHHHHHHHHHHHhccC-----CCCc
Confidence            34678999999999999999999999999999999999998  8999999999999999999999887542     3467


Q ss_pred             eEEEEccCHHHHHHHHHHHHHHHhhcCcEEEEeeCCCChHHHHHHHhcCCeEEEeCchhHHHHHHhcCCcccccCCceEE
Q 002040          542 VGLIMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYL  621 (976)
Q Consensus       542 ~vLIl~Ptr~La~Q~~~~~~~~~~~~~~~~~~~~gg~~~~~~~~~l~~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~v  621 (976)
                      ++|||+||++|+.|++..+..++...++.+..++++.....    ...+++|+|+||+.|..++...   ...+.++++|
T Consensus        77 ~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~iiv~T~~~l~~~~~~~---~~~~~~~~~i  149 (395)
T 3pey_A           77 QAICLAPSRELARQTLEVVQEMGKFTKITSQLIVPDSFEKN----KQINAQVIVGTPGTVLDLMRRK---LMQLQKIKIF  149 (395)
T ss_dssp             CEEEECSSHHHHHHHHHHHHHHTTTSCCCEEEESTTSSCTT----SCBCCSEEEECHHHHHHHHHTT---CBCCTTCCEE
T ss_pred             cEEEECCCHHHHHHHHHHHHHHhcccCeeEEEEecCchhhh----ccCCCCEEEEcHHHHHHHHHcC---CcccccCCEE
Confidence            89999999999999999999999888888888888764322    1236899999999999888653   2467889999


Q ss_pred             EecCcccccc-cCCchHHHHHHHhcCCCCcEEEEeccCcHHHHHHHHHHcCCCeEEEeCCcccccCCceEEEEecCc-ch
Q 002040          622 VMDEADRMFD-MGFEPQITRIVQNIRPDRQTVLFSATFPRQVEILARKVLNKPVEIQVGGRSVVNKDITQLVEVRPE-SD  699 (976)
Q Consensus       622 VlDEah~~~~-~~f~~~i~~il~~~~~~~q~i~~SAT~~~~~~~l~~~~l~~~~~i~~~~~~~~~~~i~q~~~~~~~-~~  699 (976)
                      ||||||++.+ ++|...+..++..+++..|+|+||||+++.+..++..++..+..+.+.........+.+.+..... ..
T Consensus       150 IiDEah~~~~~~~~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  229 (395)
T 3pey_A          150 VLDEADNMLDQQGLGDQCIRVKRFLPKDTQLVLFSATFADAVRQYAKKIVPNANTLELQTNEVNVDAIKQLYMDCKNEAD  229 (395)
T ss_dssp             EEETHHHHHHSTTHHHHHHHHHHTSCTTCEEEEEESCCCHHHHHHHHHHSCSCEEECCCGGGCSCTTEEEEEEECSSHHH
T ss_pred             EEEChhhhcCccccHHHHHHHHHhCCCCcEEEEEEecCCHHHHHHHHHhCCCCeEEEccccccccccccEEEEEcCchHH
Confidence            9999999887 678888999999999999999999999999999999999999888777666666677776665544 44


Q ss_pred             HHHHHHHHHHhhhcCCcEEEEecCHHHHHHHHHHHHHCCCCceeccCCCCHHHHHHHHHHhccCCccEEEecCcccccCC
Q 002040          700 RFLRLLELLGEWYEKGKILIFVHSQEKCDALFRDLLKHGYPCLSLHGAKDQTDRESTISDFKSNVCNLLIATSVAARGLD  779 (976)
Q Consensus       700 k~~~l~~~l~~~~~~~kvLIF~~s~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLVaT~v~~~GlD  779 (976)
                      +...+..++.. ...+++||||+++..++.++..|...++.+..+||+|++.+|..+++.|++|.++|||||+++++|||
T Consensus       230 ~~~~l~~~~~~-~~~~~~lvf~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gid  308 (395)
T 3pey_A          230 KFDVLTELYGL-MTIGSSIIFVATKKTANVLYGKLKSEGHEVSILHGDLQTQERDRLIDDFREGRSKVLITTNVLARGID  308 (395)
T ss_dssp             HHHHHHHHHTT-TTSSEEEEECSCHHHHHHHHHHHHHTTCCCEEECTTSCHHHHHHHHHHHHTTSCCEEEECGGGSSSCC
T ss_pred             HHHHHHHHHHh-ccCCCEEEEeCCHHHHHHHHHHHHhcCCcEEEeCCCCCHHHHHHHHHHHHCCCCCEEEECChhhcCCC
Confidence            55555555543 45689999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCcEEEEeCCCC------CHHHHHHHhcccCCCCCccEEEEEecCCC-cCchHHHHHHHh
Q 002040          780 VKELELVINFDAPN------HYEDYVHRVGRTGRAGRKGCAITFISEED-AKYSPDLVKALE  834 (976)
Q Consensus       780 i~~v~~VI~~d~p~------s~~~y~Qr~GR~gR~g~~g~~~~~~~~~d-~~~~~~i~~~l~  834 (976)
                      +|++++||+|++|+      ++..|+||+||+||.|+.|.|++|++..+ ...+..+.+.+.
T Consensus       309 ip~~~~Vi~~~~p~~~~~~~s~~~~~Qr~GR~gR~g~~g~~~~~~~~~~~~~~~~~i~~~~~  370 (395)
T 3pey_A          309 IPTVSMVVNYDLPTLANGQADPATYIHRIGRTGRFGRKGVAISFVHDKNSFNILSAIQKYFG  370 (395)
T ss_dssp             CTTEEEEEESSCCBCTTSSBCHHHHHHHHTTSSCTTCCEEEEEEECSHHHHHHHHHHHHHTT
T ss_pred             cccCCEEEEcCCCCCCcCCCCHHHhhHhccccccCCCCceEEEEEechHHHHHHHHHHHHhC
Confidence            99999999999999      99999999999999999999999998654 344445555444

>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=100.00  E-value=1.9e-52  Score=480.85  Aligned_cols=374  Identities=30%  Similarity=0.521  Sum_probs=189.6

Q ss_pred             CCCcccccccCCCCHHHHHHHHHcCCCCCcHHHHHHHHHHhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCC
Q 002040          462 VPKPIKTWHQTGLTSKIMETIRKLNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGP  541 (976)
Q Consensus       462 ~p~pi~~~~~~~l~~~l~~~l~~~~~~~p~~~Q~~~i~~il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~  541 (976)
                      ...++.+|.+++|++.+...|..+||..|+|+|.++++.++.++++++++|||+|||++|++|++..+...     ..++
T Consensus        16 ~~~~~~~f~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~i~~~~~~lv~~~TGsGKT~~~~~~~~~~l~~~-----~~~~   90 (394)
T 1fuu_A           16 YDKVVYKFDDMELDENLLRGVFGYGFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFSIAALQRIDTS-----VKAP   90 (394)
T ss_dssp             SCCCCCSSGGGCCCHHHHHHHHHHTCCSCCHHHHHHHHHHHHTCCEEECCCSSHHHHHHHHHHHHHHCCTT-----CCSC
T ss_pred             cccccCChhhcCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHhhcc-----CCCC
Confidence            45677889999999999999999999999999999999999999999999999999999999999887542     3467


Q ss_pred             eEEEEccCHHHHHHHHHHHHHHHhhcCcEEEEeeCCCChHHHHHHHhcCCeEEEeCchhHHHHHHhcCCcccccCCceEE
Q 002040          542 VGLIMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYL  621 (976)
Q Consensus       542 ~vLIl~Ptr~La~Q~~~~~~~~~~~~~~~~~~~~gg~~~~~~~~~l~~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~v  621 (976)
                      ++||+|||++|+.|++..+..++...++.+..++|+.........+. +++|+|+||+.|...+....   ..+..+++|
T Consensus        91 ~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~-~~~i~v~T~~~l~~~~~~~~---~~~~~~~~v  166 (394)
T 1fuu_A           91 QALMLAPTRELALQIQKVVMALAFHMDIKVHACIGGTSFVEDAEGLR-DAQIVVGTPGRVFDNIQRRR---FRTDKIKMF  166 (394)
T ss_dssp             CEEEECSSHHHHHHHHHHHHHHTTTSCCCEEEECSSCCHHHHHHHHH-HCSEEEECHHHHHHHHHTTS---SCCTTCCEE
T ss_pred             CEEEEcCCHHHHHHHHHHHHHHhccCCeeEEEEeCCCchHHHHhhcC-CCCEEEECHHHHHHHHHhCC---cchhhCcEE
Confidence            89999999999999999999999888999999999998877665555 58999999999998886532   456789999


Q ss_pred             EecCcccccccCCchHHHHHHHhcCCCCcEEEEeccCcHHHHHHHHHHcCCCeEEEeCCcccccCCceEEEEecCcc-hH
Q 002040          622 VMDEADRMFDMGFEPQITRIVQNIRPDRQTVLFSATFPRQVEILARKVLNKPVEIQVGGRSVVNKDITQLVEVRPES-DR  700 (976)
Q Consensus       622 VlDEah~~~~~~f~~~i~~il~~~~~~~q~i~~SAT~~~~~~~l~~~~l~~~~~i~~~~~~~~~~~i~q~~~~~~~~-~k  700 (976)
                      ||||||++.+++|...+..++..+++..|+|+||||+++.+..+...++..|..+.+.........+.+.+...... .+
T Consensus       167 IiDEah~~~~~~~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  246 (394)
T 1fuu_A          167 ILDEADEMLSSGFKEQIYQIFTLLPPTTQVVLLSATMPNDVLEVTTKFMRNPVRILVKKDELTLEGIKQFYVNVEEEEYK  246 (394)
T ss_dssp             EEETHHHHHHTTCHHHHHHHHHHSCTTCEEEEECSSCCHHHHHHHHHHCCSCEEEEECC---------------------
T ss_pred             EEEChHHhhCCCcHHHHHHHHHhCCCCceEEEEEEecCHHHHHHHHHhcCCCeEEEecCccccCCCceEEEEEcCchhhH
Confidence            99999999999999999999999999999999999999999889999999998887766555555555554433333 35


Q ss_pred             HHHHHHHHHhhhcCCcEEEEecCHHHHHHHHHHHHHCCCCceeccCCCCHHHHHHHHHHhccCCccEEEecCcccccCCC
Q 002040          701 FLRLLELLGEWYEKGKILIFVHSQEKCDALFRDLLKHGYPCLSLHGAKDQTDRESTISDFKSNVCNLLIATSVAARGLDV  780 (976)
Q Consensus       701 ~~~l~~~l~~~~~~~kvLIF~~s~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLVaT~v~~~GlDi  780 (976)
                      ...+..++.. ...+++||||+++..+..++..|...++.+..+||++++.+|..+++.|++|..+|||||+++++|||+
T Consensus       247 ~~~l~~~~~~-~~~~~~lVf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~T~~~~~Gldi  325 (394)
T 1fuu_A          247 YECLTDLYDS-ISVTQAVIFCNTRRKVEELTTKLRNDKFTVSAIYSDLPQQERDTIMKEFRSGSSRILISTDLLARGIDV  325 (394)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             HHHHHHHHhc-CCCCcEEEEECCHHHHHHHHHHHHHcCCeEEEeeCCCCHHHHHHHHHHHHCCCCcEEEECChhhcCCCc
Confidence            5555555544 346799999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCcEEEEeCCCCCHHHHHHHhcccCCCCCccEEEEEecCCCcCchHHHHHHHhhccCCCChHHH
Q 002040          781 KELELVINFDAPNHYEDYVHRVGRTGRAGRKGCAITFISEEDAKYSPDLVKALELSEQVVPDDLK  845 (976)
Q Consensus       781 ~~v~~VI~~d~p~s~~~y~Qr~GR~gR~g~~g~~~~~~~~~d~~~~~~i~~~l~~~~~~vp~~l~  845 (976)
                      |++++||+|++|+++..|+||+||+||.|++|.|++|+++.+...+..|.+.+......+|..+.
T Consensus       326 ~~~~~Vi~~~~p~s~~~~~Qr~GR~~R~g~~g~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~  390 (394)
T 1fuu_A          326 QQVSLVINYDLPANKENYIHRIGRGGRFGRKGVAINFVTNEDVGAMRELEKFYSTQIEELPSDIA  390 (394)
T ss_dssp             -----------------------------------------------------------------
T ss_pred             ccCCEEEEeCCCCCHHHHHHHcCcccCCCCCceEEEEEchhHHHHHHHHHHHhCCcccccCcchh
Confidence            99999999999999999999999999999999999999999988888888887776666665443

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

Probab=100.00  E-value=1.1e-50  Score=489.39  Aligned_cols=358  Identities=29%  Similarity=0.527  Sum_probs=303.8

Q ss_pred             CCHHHHHHHHHcCCCCCcHHHHHHHHHHh--cCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHH
Q 002040          474 LTSKIMETIRKLNYEKPMPIQAQALPVIM--SGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRE  551 (976)
Q Consensus       474 l~~~l~~~l~~~~~~~p~~~Q~~~i~~il--~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~  551 (976)
                      |++.++.+|..+||..|+|+|.++|+.++  .++++|++||||+|||++|++|++..+..... ....++++|||+||++
T Consensus        28 l~~~l~~~l~~~g~~~~~~~Q~~~i~~il~~~~~dvlv~apTGsGKTl~~~lpil~~l~~~~~-~~~~~~~~lvl~Ptr~  106 (579)
T 3sqw_A           28 LDKEIHKAITRMEFPGLTPVQQKTIKPILSSEDHDVIARAKTGTGKTFAFLIPIFQHLINTKF-DSQYMVKAVIVAPTRD  106 (579)
T ss_dssp             SCHHHHHHHHTTTCSSCCHHHHHHHHHHHCSSSEEEEEECCTTSCHHHHHHHHHHHHHHHTTT-SSTTSCCEEEECSSHH
T ss_pred             CCHHHHHHHHHCCCCCCCHHHHHHHHHHHccCCCeEEEEcCCCcHHHHHHHHHHHHHHHhccc-cccCCCeEEEEcchHH
Confidence            99999999999999999999999999999  78899999999999999999999999876532 2234679999999999


Q ss_pred             HHHHHHHHHHHHHhh----cCcEEEEeeCCCChHHHHHHHhc-CCeEEEeCchhHHHHHHhcCCcccccCCceEEEecCc
Q 002040          552 LVQQIHSDIRKFAKV----MGVRCVPVYGGSGVAQQISELKR-GTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEA  626 (976)
Q Consensus       552 La~Q~~~~~~~~~~~----~~~~~~~~~gg~~~~~~~~~l~~-~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDEa  626 (976)
                      ||.|++..+..++..    ..+.+..++||.....++..+.. +++|+||||++|.+++...  ....+..+.+||||||
T Consensus       107 La~Q~~~~~~~~~~~~~~~~~~~~~~~~gg~~~~~~~~~l~~~~~~IlV~Tp~~l~~~l~~~--~~~~~~~~~~lViDEa  184 (579)
T 3sqw_A          107 LALQIEAEVKKIHDMNYGLKKYACVSLVGGTDFRAAMNKMNKLRPNIVIATPGRLIDVLEKY--SNKFFRFVDYKVLDEA  184 (579)
T ss_dssp             HHHHHHHHHHHHHHHCGGGTTSCEEEECTTSCHHHHHHHHHHHCCSEEEECHHHHHHHHHHH--HHHHCTTCCEEEEETH
T ss_pred             HHHHHHHHHHHHHhhcccccceEEEEEECCccHHHHHHHHhcCCCCEEEECHHHHHHHHHhc--cccccccCCEEEEECh
Confidence            999999999998743    35678889999998888777754 7899999999999988653  1245788999999999


Q ss_pred             ccccccCCchHHHHHHHhcC-------CCCcEEEEeccCcHHHHHHHHHHcCCCeEEEeCCc----ccccCCceEEEEec
Q 002040          627 DRMFDMGFEPQITRIVQNIR-------PDRQTVLFSATFPRQVEILARKVLNKPVEIQVGGR----SVVNKDITQLVEVR  695 (976)
Q Consensus       627 h~~~~~~f~~~i~~il~~~~-------~~~q~i~~SAT~~~~~~~l~~~~l~~~~~i~~~~~----~~~~~~i~q~~~~~  695 (976)
                      |+|++++|...+..|+..++       +..|+|+||||+++.+..++..++..+..+.+...    ......+.+.+...
T Consensus       185 h~l~~~gf~~~~~~i~~~l~~~~~~~~~~~~~l~~SAT~~~~v~~~~~~~l~~~~~~~~~~~~~~~~~~~~~i~~~~~~~  264 (579)
T 3sqw_A          185 DRLLEIGFRDDLETISGILNEKNSKSADNIKTLLFSATLDDKVQKLANNIMNKKECLFLDTVDKNEPEAHERIDQSVVIS  264 (579)
T ss_dssp             HHHTSTTTHHHHHHHHHHHHHHCSSCTTCCEEEEEESSCCTHHHHHTTTTCCSSEEEEEESSCSSSCSSCTTEEEEEEEE
T ss_pred             HHhhcCCCHHHHHHHHHHhhhhhcccccCceEEEEeccCChHHHHHHHHHcCCCceEEEeecCccccccccccceEEEEe
Confidence            99999999999988877653       36799999999999999999999998876655432    22333455555444


Q ss_pred             Cc-chHHHHHH----HHHHhhhcCCcEEEEecCHHHHHHHHHHHHHC---CCCceeccCCCCHHHHHHHHHHhccCCccE
Q 002040          696 PE-SDRFLRLL----ELLGEWYEKGKILIFVHSQEKCDALFRDLLKH---GYPCLSLHGAKDQTDRESTISDFKSNVCNL  767 (976)
Q Consensus       696 ~~-~~k~~~l~----~~l~~~~~~~kvLIF~~s~~~~~~l~~~L~~~---~~~~~~lhg~~~~~~R~~~~~~F~~g~~~v  767 (976)
                      .. ..+...++    ..+.......++||||+++..|+.++..|...   ++.+..+||+|++.+|..++..|++|.++|
T Consensus       265 ~~~~~~~~~~~~~l~~~~~~~~~~~~~iVF~~t~~~~~~l~~~L~~~~~~~~~v~~~hg~~~~~~R~~~~~~F~~g~~~v  344 (579)
T 3sqw_A          265 EKFANSIFAAVEHIKKQIKERDSNYKAIIFAPTVKFTSFLCSILKNEFKKDLPILEFHGKITQNKRTSLVKRFKKDESGI  344 (579)
T ss_dssp             SSTTHHHHHHHHHHHHHHHHTTTCCEEEEECSSHHHHHHHHHHHHHHHTTTSCEEEESTTSCHHHHHHHHHHHHHCSSEE
T ss_pred             cchhhhHHHHHHHHHHHHhhcCCCCcEEEECCcHHHHHHHHHHHHHhhcCCCcEEEecCCCCHHHHHHHHHHhhcCCCeE
Confidence            33 33333333    33333344679999999999999999999887   899999999999999999999999999999


Q ss_pred             EEecCcccccCCCCCCcEEEEeCCCCCHHHHHHHhcccCCCCCccEEEEEecCCCcCchHHHHHHHh
Q 002040          768 LIATSVAARGLDVKELELVINFDAPNHYEDYVHRVGRTGRAGRKGCAITFISEEDAKYSPDLVKALE  834 (976)
Q Consensus       768 LVaT~v~~~GlDi~~v~~VI~~d~p~s~~~y~Qr~GR~gR~g~~g~~~~~~~~~d~~~~~~i~~~l~  834 (976)
                      ||||+++++|||+|++++||+|++|.++..|+||+|||||.|+.|.|++|+++.+..++..|.+...
T Consensus       345 LVaT~~~~~GiDip~v~~VI~~~~p~s~~~y~Qr~GRagR~g~~g~~i~~~~~~e~~~~~~l~~~~~  411 (579)
T 3sqw_A          345 LVCTDVGARGMDFPNVHEVLQIGVPSELANYIHRIGRTARSGKEGSSVLFICKDELPFVRELEDAKN  411 (579)
T ss_dssp             EEECGGGTSSCCCTTCCEEEEESCCSSTTHHHHHHTTSSCTTCCEEEEEEEEGGGHHHHHHHHHHHC
T ss_pred             EEEcchhhcCCCcccCCEEEEcCCCCCHHHhhhhccccccCCCCceEEEEEcccHHHHHHHHHHHhC
Confidence            9999999999999999999999999999999999999999999999999999998888888877654

>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=100.00  E-value=5.6e-50  Score=482.71  Aligned_cols=358  Identities=29%  Similarity=0.521  Sum_probs=302.2

Q ss_pred             CCHHHHHHHHHcCCCCCcHHHHHHHHHHh--cCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHH
Q 002040          474 LTSKIMETIRKLNYEKPMPIQAQALPVIM--SGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRE  551 (976)
Q Consensus       474 l~~~l~~~l~~~~~~~p~~~Q~~~i~~il--~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~  551 (976)
                      |++.++..|..+||..|+|+|.++|+.++  .++++|++||||||||++|++|++.++...... ...++++|||+||++
T Consensus        79 l~~~l~~~l~~~g~~~~~~~Q~~~i~~~l~~~~~~~lv~apTGsGKTl~~~lpil~~l~~~~~~-~~~~~~~lil~Ptr~  157 (563)
T 3i5x_A           79 LDKEIHKAITRMEFPGLTPVQQKTIKPILSSEDHDVIARAKTGTGKTFAFLIPIFQHLINTKFD-SQYMVKAVIVAPTRD  157 (563)
T ss_dssp             SCHHHHHHHHTTCCSSCCHHHHHHHHHHHSSSSEEEEEECCTTSCHHHHHHHHHHHHHHHTTTS-STTSCCEEEECSSHH
T ss_pred             CCHHHHHHHHHCCCCCCCHHHHHHHHHHhcCCCCeEEEECCCCCCccHHHHHHHHHHHHhcccc-ccCCeeEEEEcCcHH
Confidence            99999999999999999999999999999  678999999999999999999999998875421 234678999999999


Q ss_pred             HHHHHHHHHHHHHhh----cCcEEEEeeCCCChHHHHHHHh-cCCeEEEeCchhHHHHHHhcCCcccccCCceEEEecCc
Q 002040          552 LVQQIHSDIRKFAKV----MGVRCVPVYGGSGVAQQISELK-RGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEA  626 (976)
Q Consensus       552 La~Q~~~~~~~~~~~----~~~~~~~~~gg~~~~~~~~~l~-~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDEa  626 (976)
                      ||.|++..+..++..    .++.+..++||.....++..+. .+++|+||||++|.+++...  ....+..+.+||||||
T Consensus       158 La~Q~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~Iiv~Tp~~l~~~l~~~--~~~~~~~~~~lViDEa  235 (563)
T 3i5x_A          158 LALQIEAEVKKIHDMNYGLKKYACVSLVGGTDFRAAMNKMNKLRPNIVIATPGRLIDVLEKY--SNKFFRFVDYKVLDEA  235 (563)
T ss_dssp             HHHHHHHHHHHHHHHCGGGTTSCEEEECTTSCHHHHHHHHHHHCCSEEEECHHHHHHHHHHH--HHHHCTTCCEEEEETH
T ss_pred             HHHHHHHHHHHHHhhccccCceeEEEEECCcCHHHHHHHHhcCCCCEEEECcHHHHHHHHhc--cccccccceEEEEeCH
Confidence            999999999998653    2467888999998888776664 47899999999999988653  1235788999999999


Q ss_pred             ccccccCCchHHHHHHHhc-------CCCCcEEEEeccCcHHHHHHHHHHcCCCeEEEeCCc----ccccCCceEEEEec
Q 002040          627 DRMFDMGFEPQITRIVQNI-------RPDRQTVLFSATFPRQVEILARKVLNKPVEIQVGGR----SVVNKDITQLVEVR  695 (976)
Q Consensus       627 h~~~~~~f~~~i~~il~~~-------~~~~q~i~~SAT~~~~~~~l~~~~l~~~~~i~~~~~----~~~~~~i~q~~~~~  695 (976)
                      |+|++++|.+.+..++..+       .+..|+|+||||+++.+..++..++..+..+.+...    ......+.+.+...
T Consensus       236 h~l~~~~f~~~~~~i~~~l~~~~~~~~~~~~~l~~SAT~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  315 (563)
T 3i5x_A          236 DRLLEIGFRDDLETISGILNEKNSKSADNIKTLLFSATLDDKVQKLANNIMNKKECLFLDTVDKNEPEAHERIDQSVVIS  315 (563)
T ss_dssp             HHHTSTTTHHHHHHHHHHHHHHCSSCTTCCEEEEEESSCCTHHHHHTTTTCCSSEEEEEESSCSSSCSSCTTEEEEEEEE
T ss_pred             HHHhccchHHHHHHHHHhhhhccccCccCceEEEEEccCCHHHHHHHHHhcCCCceEEEeccCCCCccccccCceEEEEC
Confidence            9999999999998887665       236799999999999999999999988866655322    22233455555444


Q ss_pred             Cc-chHHHHHHH----HHHhhhcCCcEEEEecCHHHHHHHHHHHHHC---CCCceeccCCCCHHHHHHHHHHhccCCccE
Q 002040          696 PE-SDRFLRLLE----LLGEWYEKGKILIFVHSQEKCDALFRDLLKH---GYPCLSLHGAKDQTDRESTISDFKSNVCNL  767 (976)
Q Consensus       696 ~~-~~k~~~l~~----~l~~~~~~~kvLIF~~s~~~~~~l~~~L~~~---~~~~~~lhg~~~~~~R~~~~~~F~~g~~~v  767 (976)
                      .. ..++..++.    .+......+++||||+++..|+.++..|...   ++.+..+||+|++.+|..+++.|++|.++|
T Consensus       316 ~~~~~~~~~~~~~l~~~~~~~~~~~~~iVF~~s~~~~~~l~~~L~~~~~~~~~v~~~h~~~~~~~R~~~~~~f~~g~~~v  395 (563)
T 3i5x_A          316 EKFANSIFAAVEHIKKQIKERDSNYKAIIFAPTVKFTSFLCSILKNEFKKDLPILEFHGKITQNKRTSLVKRFKKDESGI  395 (563)
T ss_dssp             SSTTHHHHHHHHHHHHHHHHTTTCCEEEEECSCHHHHHHHHHHHHHHHTTTSCEEEESTTSCHHHHHHHHHHHHHCSSEE
T ss_pred             chhHhhHHHHHHHHHHHHhhcCCCCcEEEEcCcHHHHHHHHHHHHHhccCCceEEEecCCCCHHHHHHHHHHHhcCCCCE
Confidence            33 333333333    3333345679999999999999999999886   899999999999999999999999999999


Q ss_pred             EEecCcccccCCCCCCcEEEEeCCCCCHHHHHHHhcccCCCCCccEEEEEecCCCcCchHHHHHHHh
Q 002040          768 LIATSVAARGLDVKELELVINFDAPNHYEDYVHRVGRTGRAGRKGCAITFISEEDAKYSPDLVKALE  834 (976)
Q Consensus       768 LVaT~v~~~GlDi~~v~~VI~~d~p~s~~~y~Qr~GR~gR~g~~g~~~~~~~~~d~~~~~~i~~~l~  834 (976)
                      ||||+++++|||+|++++||+|++|.++..|+||+|||||.|+.|.|++|+++.+..++..|.+.+.
T Consensus       396 LvaT~~~~~GiDip~v~~VI~~~~p~s~~~y~Qr~GRagR~g~~g~~i~~~~~~e~~~~~~l~~~~~  462 (563)
T 3i5x_A          396 LVCTDVGARGMDFPNVHEVLQIGVPSELANYIHRIGRTARSGKEGSSVLFICKDELPFVRELEDAKN  462 (563)
T ss_dssp             EEECGGGTSSCCCTTCCEEEEESCCSSTTHHHHHHTTSSCTTCCEEEEEEEEGGGHHHHHHHHHHHC
T ss_pred             EEEcchhhcCCCcccCCEEEEECCCCchhhhhhhcCccccCCCCceEEEEEchhHHHHHHHHHHHhC
Confidence            9999999999999999999999999999999999999999999999999999988888888777654

>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=100.00  E-value=7e-52  Score=489.13  Aligned_cols=366  Identities=28%  Similarity=0.476  Sum_probs=178.0

Q ss_pred             CcccccccCCCCHHHHHHHHHcCCCCCcHHHHHHHHHHhcC--CCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCC
Q 002040          464 KPIKTWHQTGLTSKIMETIRKLNYEKPMPIQAQALPVIMSG--RDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGP  541 (976)
Q Consensus       464 ~pi~~~~~~~l~~~l~~~l~~~~~~~p~~~Q~~~i~~il~g--~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~  541 (976)
                      .++.+|..++|++.++..|..+||..|+|+|.++|+.++.+  +++|++|+||||||++|++|++..+...     ..++
T Consensus        89 ~~~~~f~~~~l~~~l~~~l~~~g~~~p~~~Q~~ai~~il~~~~~~~l~~a~TGsGKT~~~~l~il~~l~~~-----~~~~  163 (479)
T 3fmp_B           89 YSVKSFEELRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLAMLSQVEPA-----NKYP  163 (479)
T ss_dssp             CCCCCSGGGTCCHHHHHHHHHTTCCSCCHHHHHHHHHHTSBSCCEEEEECCSSSSHHHHHHHHHHTTCCTT-----SCSC
T ss_pred             cCcCCHHHcCCCHHHHHHHHHcCCCCCCHHHHHHHHHHHcCCCCcEEEEcCCCCchhHHHHHHHHHHHhhc-----CCCC
Confidence            34678999999999999999999999999999999999987  8999999999999999999999876542     3467


Q ss_pred             eEEEEccCHHHHHHHHHHHHHHHhhc-CcEEEEeeCCCChHHHHHHHhcCCeEEEeCchhHHHHHHhcCCcccccCCceE
Q 002040          542 VGLIMAPTRELVQQIHSDIRKFAKVM-GVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTY  620 (976)
Q Consensus       542 ~vLIl~Ptr~La~Q~~~~~~~~~~~~-~~~~~~~~gg~~~~~~~~~l~~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~  620 (976)
                      ++|||+||++||.|++..+..+.... ++.+.+.+++......   ...+++|+||||++|.+++...  ....+.++++
T Consensus       164 ~~lil~Pt~~La~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~Ivv~Tp~~l~~~l~~~--~~~~~~~~~~  238 (479)
T 3fmp_B          164 QCLCLSPTYELALQTGKVIEQMGKFYPELKLAYAVRGNKLERG---QKISEQIVIGTPGTVLDWCSKL--KFIDPKKIKV  238 (479)
T ss_dssp             CEEEECSSHHHHHHHHHHHHHHHTTSTTCCEEEESTTCCCCTT---CCCCCSEEEECHHHHHHHHTTS--CCCCGGGCCE
T ss_pred             cEEEEeChHHHHHHHHHHHHHHHhhCCCceEEEEeCCcccccc---ccCCCCEEEECchHHHHHHHhc--CCcCcccCCE
Confidence            89999999999999999999988754 5677777777654321   1335799999999999988553  2356789999


Q ss_pred             EEecCcccccc-cCCchHHHHHHHhcCCCCcEEEEeccCcHHHHHHHHHHcCCCeEEEeCCcccccCCceEEEEecCc-c
Q 002040          621 LVMDEADRMFD-MGFEPQITRIVQNIRPDRQTVLFSATFPRQVEILARKVLNKPVEIQVGGRSVVNKDITQLVEVRPE-S  698 (976)
Q Consensus       621 vVlDEah~~~~-~~f~~~i~~il~~~~~~~q~i~~SAT~~~~~~~l~~~~l~~~~~i~~~~~~~~~~~i~q~~~~~~~-~  698 (976)
                      |||||||+|++ .+|...+..++..+++.+|+|+||||++..+..++..++.++..+.+.........+.+.+..... .
T Consensus       239 iViDEah~~~~~~~~~~~~~~i~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~  318 (479)
T 3fmp_B          239 FVLDEADVMIATQGHQDQSIRIQRMLPRNCQMLLFSATFEDSVWKFAQKVVPDPNVIKLKREEETLDTIKQYYVLCSSRD  318 (479)
T ss_dssp             EEECCHHHHHTSTTHHHHHHHHHTTSCTTSEEEEEESCCCHHHHHHHHHHSSSEEEEEEC--------------------
T ss_pred             EEEECHHHHhhcCCcHHHHHHHHhhCCccceEEEEeCCCCHHHHHHHHHHcCCCeEEeccccccCcCCceEEEEEeCCHH
Confidence            99999999987 678888889999999999999999999999999999999999888887766666666666655443 4


Q ss_pred             hHHHHHHHHHHhhhcCCcEEEEecCHHHHHHHHHHHHHCCCCceeccCCCCHHHHHHHHHHhccCCccEEEecCcccccC
Q 002040          699 DRFLRLLELLGEWYEKGKILIFVHSQEKCDALFRDLLKHGYPCLSLHGAKDQTDRESTISDFKSNVCNLLIATSVAARGL  778 (976)
Q Consensus       699 ~k~~~l~~~l~~~~~~~kvLIF~~s~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLVaT~v~~~Gl  778 (976)
                      .++..|..++... ..+++||||+++..|..++..|...++.+..+||+|++.+|..+++.|++|.++|||||+++++||
T Consensus       319 ~~~~~l~~~~~~~-~~~~~lvF~~s~~~~~~l~~~L~~~~~~v~~lh~~~~~~~R~~~~~~f~~g~~~iLv~T~~~~~Gl  397 (479)
T 3fmp_B          319 EKFQALCNLYGAI-TIAQAMIFCHTRKTASWLAAELSKEGHQVALLSGEMMVEQRAAVIERFREGKEKVLVTTNVCARGI  397 (479)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             HHHHHHHHHHhhc-cCCceEEEeCcHHHHHHHHHHHHhCCccEEEecCCCCHHHHHHHHHHHHcCCCcEEEEccccccCC
Confidence            5666666665543 457999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCCcEEEEeCCCC------CHHHHHHHhcccCCCCCccEEEEEecCCC-cCchHHHHHHHhhccCCC
Q 002040          779 DVKELELVINFDAPN------HYEDYVHRVGRTGRAGRKGCAITFISEED-AKYSPDLVKALELSEQVV  840 (976)
Q Consensus       779 Di~~v~~VI~~d~p~------s~~~y~Qr~GR~gR~g~~g~~~~~~~~~d-~~~~~~i~~~l~~~~~~v  840 (976)
                      |+|++++||+||+|+      +...|+||+||+||.|+.|.|++|+++.+ ..++..|.+.+......+
T Consensus       398 Dip~v~~VI~~d~p~~~~~~~s~~~~~Qr~GRagR~g~~G~~i~~~~~~~~~~~~~~i~~~~~~~~~~l  466 (479)
T 3fmp_B          398 DVEQVSVVINFDLPVDKDGNPDNETYLHRIGRTGRFGKRGLAVNMVDSKHSMNILNRIQEHFNKKIERL  466 (479)
T ss_dssp             ---------------------------------------------------------------------
T ss_pred             ccccCCEEEEecCCCCCccCCCHHHHHHHhcccccCCCCceEEEEEcCcchHHHHHHHHHHhCCCceEC
Confidence            999999999999995      56899999999999999999999998654 666667766665444333

>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=100.00  E-value=8.1e-48  Score=432.40  Aligned_cols=334  Identities=34%  Similarity=0.584  Sum_probs=287.1

Q ss_pred             CCHHHHHHHHHcCCCCCcHHHHHHHHHHhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHH
Q 002040          474 LTSKIMETIRKLNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELV  553 (976)
Q Consensus       474 l~~~l~~~l~~~~~~~p~~~Q~~~i~~il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La  553 (976)
                      |++.|.+.|..+||..|+|+|.++++.+++++++++++|||+|||++|++|++..           ++++||++||++|+
T Consensus         1 l~~~i~~~l~~~g~~~l~~~Q~~~i~~i~~~~~~lv~~~TGsGKT~~~~~~~~~~-----------~~~~liv~P~~~L~   69 (337)
T 2z0m_A            1 MNEKIEQAIREMGFKNFTEVQSKTIPLMLQGKNVVVRAKTGSGKTAAYAIPILEL-----------GMKSLVVTPTRELT   69 (337)
T ss_dssp             CCHHHHHHHHHTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHH-----------TCCEEEECSSHHHH
T ss_pred             CCHHHHHHHHHcCCCCCCHHHHHHHHHHhcCCCEEEEcCCCCcHHHHHHHHHHhh-----------cCCEEEEeCCHHHH
Confidence            5678999999999999999999999999999999999999999999999998864           56799999999999


Q ss_pred             HHHHHHHHHHHhhcCcEEEEeeCCCChHHHHHHHhcCCeEEEeCchhHHHHHHhcCCcccccCCceEEEecCcccccccC
Q 002040          554 QQIHSDIRKFAKVMGVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMG  633 (976)
Q Consensus       554 ~Q~~~~~~~~~~~~~~~~~~~~gg~~~~~~~~~l~~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDEah~~~~~~  633 (976)
                      .||+..+..++..+++.+..++|+.....+...+.. ++|+|+||+.|..++....   ..+..+++|||||||++.+++
T Consensus        70 ~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~i~v~T~~~l~~~~~~~~---~~~~~~~~iViDEah~~~~~~  145 (337)
T 2z0m_A           70 RQVASHIRDIGRYMDTKVAEVYGGMPYKAQINRVRN-ADIVVATPGRLLDLWSKGV---IDLSSFEIVIIDEADLMFEMG  145 (337)
T ss_dssp             HHHHHHHHHHTTTSCCCEEEECTTSCHHHHHHHHTT-CSEEEECHHHHHHHHHTTS---CCGGGCSEEEEESHHHHHHTT
T ss_pred             HHHHHHHHHHhhhcCCcEEEEECCcchHHHHhhcCC-CCEEEECHHHHHHHHHcCC---cchhhCcEEEEEChHHhhccc
Confidence            999999999988889999999999988877666654 8999999999998876532   457789999999999999999


Q ss_pred             CchHHHHHHHhcCCCCcEEEEeccCcHHHHHHHHHHcCCCeEEEeCCcccccCCceEEEEecCcchHHHHHHHHHHhhhc
Q 002040          634 FEPQITRIVQNIRPDRQTVLFSATFPRQVEILARKVLNKPVEIQVGGRSVVNKDITQLVEVRPESDRFLRLLELLGEWYE  713 (976)
Q Consensus       634 f~~~i~~il~~~~~~~q~i~~SAT~~~~~~~l~~~~l~~~~~i~~~~~~~~~~~i~q~~~~~~~~~k~~~l~~~l~~~~~  713 (976)
                      |...+..++..++...++++||||+++.+..+...++..+..+...   .....+.+.+.......+  ..+..+.. ..
T Consensus       146 ~~~~~~~~~~~~~~~~~~~~~SAT~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~--~~~~~~~~-~~  219 (337)
T 2z0m_A          146 FIDDIKIILAQTSNRKITGLFSATIPEEIRKVVKDFITNYEEIEAC---IGLANVEHKFVHVKDDWR--SKVQALRE-NK  219 (337)
T ss_dssp             CHHHHHHHHHHCTTCSEEEEEESCCCHHHHHHHHHHSCSCEEEECS---GGGGGEEEEEEECSSSSH--HHHHHHHT-CC
T ss_pred             cHHHHHHHHhhCCcccEEEEEeCcCCHHHHHHHHHhcCCceeeecc---cccCCceEEEEEeChHHH--HHHHHHHh-CC
Confidence            9999999999999999999999999999998999999888766432   223344454444433322  22333333 35


Q ss_pred             CCcEEEEecCHHHHHHHHHHHHHCCCCceeccCCCCHHHHHHHHHHhccCCccEEEecCcccccCCCCCCcEEEEeCCCC
Q 002040          714 KGKILIFVHSQEKCDALFRDLLKHGYPCLSLHGAKDQTDRESTISDFKSNVCNLLIATSVAARGLDVKELELVINFDAPN  793 (976)
Q Consensus       714 ~~kvLIF~~s~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLVaT~v~~~GlDi~~v~~VI~~d~p~  793 (976)
                      .+++||||++...++.++..|.    .+..+||+++..+|..+++.|++|.++|||||+++++|||+|++++||+|++|+
T Consensus       220 ~~~~lvf~~~~~~~~~l~~~l~----~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~T~~~~~Gid~~~~~~Vi~~~~~~  295 (337)
T 2z0m_A          220 DKGVIVFVRTRNRVAKLVRLFD----NAIELRGDLPQSVRNRNIDAFREGEYDMLITTDVASRGLDIPLVEKVINFDAPQ  295 (337)
T ss_dssp             CSSEEEECSCHHHHHHHHTTCT----TEEEECTTSCHHHHHHHHHHHHTTSCSEEEECHHHHTTCCCCCBSEEEESSCCS
T ss_pred             CCcEEEEEcCHHHHHHHHHHhh----hhhhhcCCCCHHHHHHHHHHHHcCCCcEEEEcCccccCCCccCCCEEEEecCCC
Confidence            6799999999999999998885    688999999999999999999999999999999999999999999999999999


Q ss_pred             CHHHHHHHhcccCCCCCccEEEEEecCCCcCchHHHHHHH
Q 002040          794 HYEDYVHRVGRTGRAGRKGCAITFISEEDAKYSPDLVKAL  833 (976)
Q Consensus       794 s~~~y~Qr~GR~gR~g~~g~~~~~~~~~d~~~~~~i~~~l  833 (976)
                      ++..|+||+||+||.|+.|.|++|++ .+..++..|.+.+
T Consensus       296 s~~~~~Q~~GR~gR~g~~g~~~~~~~-~~~~~~~~i~~~~  334 (337)
T 2z0m_A          296 DLRTYIHRIGRTGRMGRKGEAITFIL-NEYWLEKEVKKVS  334 (337)
T ss_dssp             SHHHHHHHHTTBCGGGCCEEEEEEES-SCHHHHHHHC---
T ss_pred             CHHHhhHhcCccccCCCCceEEEEEe-CcHHHHHHHHHHh
Confidence            99999999999999999999999999 6666666665554

>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=100.00  E-value=1.4e-47  Score=458.79  Aligned_cols=346  Identities=21%  Similarity=0.328  Sum_probs=284.8

Q ss_pred             CCccccccc--CCCCHHHHHHHHH-cCCCCCcHHHHHHHHHHhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCC
Q 002040          463 PKPIKTWHQ--TGLTSKIMETIRK-LNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGD  539 (976)
Q Consensus       463 p~pi~~~~~--~~l~~~l~~~l~~-~~~~~p~~~Q~~~i~~il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~  539 (976)
                      +.....|..  +++++.+...|+. +||..|+|+|.++|+.++.|+++|+++|||+|||++|++|++..           
T Consensus        15 ~~~~~~w~~~~~~l~~~l~~~L~~~fg~~~~rp~Q~~~i~~il~g~d~lv~~pTGsGKTl~~~lpal~~-----------   83 (591)
T 2v1x_A           15 DSSPAAWNKEDFPWSGKVKDILQNVFKLEKFRPLQLETINVTMAGKEVFLVMPTGGGKSLCYQLPALCS-----------   83 (591)
T ss_dssp             -CCGGGGCCSCSTTHHHHHHHHHHTSCCCSCCTTHHHHHHHHHTTCCEEEECCTTSCTTHHHHHHHHTS-----------
T ss_pred             CcchhccccccCCCCHHHHHHHHHHhCCCCCCHHHHHHHHHHHcCCCEEEEECCCChHHHHHHHHHHHc-----------
Confidence            344556654  7888999999998 79999999999999999999999999999999999999999742           


Q ss_pred             CCeEEEEccCHHHHHHHHHHHHHHHhhcCcEEEEeeCCCChHHHHHH---H---hcCCeEEEeCchhHH------HHHHh
Q 002040          540 GPVGLIMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQISE---L---KRGTEIVVCTPGRMI------DILCT  607 (976)
Q Consensus       540 ~~~vLIl~Ptr~La~Q~~~~~~~~~~~~~~~~~~~~gg~~~~~~~~~---l---~~~~~Iiv~Tp~~L~------~~l~~  607 (976)
                      ++.+|||+||++|+.|++..+..+    |+.+..++|+.........   +   ..+++|+|+||++|.      +.+..
T Consensus        84 ~g~~lVisP~~~L~~q~~~~l~~~----gi~~~~l~~~~~~~~~~~~~~~l~~~~~~~~Ilv~Tpe~L~~~~~~~~~l~~  159 (591)
T 2v1x_A           84 DGFTLVICPLISLMEDQLMVLKQL----GISATMLNASSSKEHVKWVHAEMVNKNSELKLIYVTPEKIAKSKMFMSRLEK  159 (591)
T ss_dssp             SSEEEEECSCHHHHHHHHHHHHHH----TCCEEECCSSCCHHHHHHHHHHHHCTTCCCCEEEECHHHHHSCHHHHHHHHH
T ss_pred             CCcEEEEeCHHHHHHHHHHHHHhc----CCcEEEEeCCCCHHHHHHHHHHhhcccCCCCEEEEChhHhhccHHHHHHHHh
Confidence            458999999999999999998875    8889999999877655322   2   346899999999874      22221


Q ss_pred             cCCcccccCCceEEEecCcccccccC--CchHHHH--HHHhcCCCCcEEEEeccCcHHHHHHHHHHcCCCeEEEeCCccc
Q 002040          608 SGGKITNLRRVTYLVMDEADRMFDMG--FEPQITR--IVQNIRPDRQTVLFSATFPRQVEILARKVLNKPVEIQVGGRSV  683 (976)
Q Consensus       608 ~~~~~~~l~~~~~vVlDEah~~~~~~--f~~~i~~--il~~~~~~~q~i~~SAT~~~~~~~l~~~~l~~~~~i~~~~~~~  683 (976)
                          ...+..+.+|||||||++++||  |.+.+..  ++....+..++|+||||+++.+...+..++..+..+.+.. ..
T Consensus       160 ----~~~~~~i~~iViDEAH~is~~g~dfr~~~~~l~~l~~~~~~~~ii~lSAT~~~~v~~~i~~~l~~~~~~~~~~-~~  234 (591)
T 2v1x_A          160 ----AYEARRFTRIAVDEVHCCSQWGHDFRPDYKALGILKRQFPNASLIGLTATATNHVLTDAQKILCIEKCFTFTA-SF  234 (591)
T ss_dssp             ----HHHTTCEEEEEEETGGGGSTTCTTCCGGGGGGGHHHHHCTTSEEEEEESSCCHHHHHHHHHHTTCCSCEEEEC-CC
T ss_pred             ----hhhccCCcEEEEECcccccccccccHHHHHHHHHHHHhCCCCcEEEEecCCCHHHHHHHHHHhCCCCcEEEec-CC
Confidence                2456789999999999999988  8887665  5556667899999999999998887777776553332221 23


Q ss_pred             ccCCceEEEEecCc--chHHHHHHHHHHhhhcCCcEEEEecCHHHHHHHHHHHHHCCCCceeccCCCCHHHHHHHHHHhc
Q 002040          684 VNKDITQLVEVRPE--SDRFLRLLELLGEWYEKGKILIFVHSQEKCDALFRDLLKHGYPCLSLHGAKDQTDRESTISDFK  761 (976)
Q Consensus       684 ~~~~i~q~~~~~~~--~~k~~~l~~~l~~~~~~~kvLIF~~s~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~  761 (976)
                      ...++...+.....  ..++..|+.+|......+++||||+++..++.++..|...|+.+..+||+|++.+|..+++.|.
T Consensus       235 ~r~nl~~~v~~~~~~~~~~~~~l~~~l~~~~~~~~~IVf~~sr~~~e~la~~L~~~g~~~~~~h~~l~~~~R~~~~~~F~  314 (591)
T 2v1x_A          235 NRPNLYYEVRQKPSNTEDFIEDIVKLINGRYKGQSGIIYCFSQKDSEQVTVSLQNLGIHAGAYHANLEPEDKTTVHRKWS  314 (591)
T ss_dssp             CCTTEEEEEEECCSSHHHHHHHHHHHHTTTTTTCEEEEECSSHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHH
T ss_pred             CCcccEEEEEeCCCcHHHHHHHHHHHHHHhccCCCeEEEeCcHHHHHHHHHHHHHCCCCEEEecCCCCHHHHHHHHHHHH
Confidence            33444433333322  3455667777765556789999999999999999999999999999999999999999999999


Q ss_pred             cCCccEEEecCcccccCCCCCCcEEEEeCCCCCHHHHHHHhcccCCCCCccEEEEEecCCCcCchHH
Q 002040          762 SNVCNLLIATSVAARGLDVKELELVINFDAPNHYEDYVHRVGRTGRAGRKGCAITFISEEDAKYSPD  828 (976)
Q Consensus       762 ~g~~~vLVaT~v~~~GlDi~~v~~VI~~d~p~s~~~y~Qr~GR~gR~g~~g~~~~~~~~~d~~~~~~  828 (976)
                      +|.++|||||+++++|||+|+|++||+|++|.++..|+|++||+||.|.+|.|++||++.|...+..
T Consensus       315 ~g~~~VlVAT~a~~~GID~p~V~~VI~~~~p~s~~~y~Qr~GRaGR~G~~g~~i~l~~~~D~~~~~~  381 (591)
T 2v1x_A          315 ANEIQVVVATVAFGMGIDKPDVRFVIHHSMSKSMENYYQESGRAGRDDMKADCILYYGFGDIFRISS  381 (591)
T ss_dssp             TTSSSEEEECTTSCTTCCCSCEEEEEESSCCSSHHHHHHHHTTSCTTSSCEEEEEEECHHHHHHHHH
T ss_pred             cCCCeEEEEechhhcCCCcccccEEEEeCCCCCHHHHHHHhccCCcCCCCceEEEEEChHHHHHHHH
Confidence            9999999999999999999999999999999999999999999999999999999998766544333

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

Probab=100.00  E-value=4.3e-46  Score=431.37  Aligned_cols=324  Identities=25%  Similarity=0.334  Sum_probs=266.9

Q ss_pred             HHHHHH-cCCCCCcHHHHHHHHHHhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHH
Q 002040          479 METIRK-LNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIH  557 (976)
Q Consensus       479 ~~~l~~-~~~~~p~~~Q~~~i~~il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~  557 (976)
                      .+.++. ++| .|+|+|.++|+.++.|+++|+++|||||||++|++|++..+.        .++++|||+||++||.|++
T Consensus        11 ~~~l~~~~~~-~~~~~Q~~~i~~i~~~~~~lv~apTGsGKT~~~l~~~~~~~~--------~~~~~lil~Pt~~L~~q~~   81 (414)
T 3oiy_A           11 RSFFKKKFGK-DLTGYQRLWAKRIVQGKSFTMVAPTGVGKTTFGMMTALWLAR--------KGKKSALVFPTVTLVKQTL   81 (414)
T ss_dssp             HHHHHHHHSS-CCCHHHHHHHHHHTTTCCEECCSCSSSSHHHHHHHHHHHHHT--------TTCCEEEEESSHHHHHHHH
T ss_pred             HHHHHHhcCC-CCCHHHHHHHHHHhcCCCEEEEeCCCCCHHHHHHHHHHHHhc--------CCCEEEEEECCHHHHHHHH
Confidence            344554 566 799999999999999999999999999999999999887652        3678999999999999999


Q ss_pred             HHHHHHHhhcCcEEEEeeCCCCh---HHHHHHHhcC-CeEEEeCchhHHHHHHhcCCcccccCCceEEEecCccccc---
Q 002040          558 SDIRKFAKVMGVRCVPVYGGSGV---AQQISELKRG-TEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMF---  630 (976)
Q Consensus       558 ~~~~~~~~~~~~~~~~~~gg~~~---~~~~~~l~~~-~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDEah~~~---  630 (976)
                      ..+..++. .++.+..++||.+.   ..++..+..+ ++|+|+||++|.+++..     ..+.++++|||||||++.   
T Consensus        82 ~~~~~~~~-~~~~v~~~~g~~~~~~~~~~~~~l~~~~~~Iiv~Tp~~l~~~l~~-----~~~~~~~~iViDEaH~~~~~~  155 (414)
T 3oiy_A           82 ERLQKLAD-EKVKIFGFYSSMKKEEKEKFEKSFEEDDYHILVFSTQFVSKNREK-----LSQKRFDFVFVDDVDAVLKAS  155 (414)
T ss_dssp             HHHHHHCC-SSCCEEECCTTSCHHHHHHHHHHHHHTCCSEEEEEHHHHHHCHHH-----HTTCCCSEEEESCHHHHHHCH
T ss_pred             HHHHHHcc-CCceEEEEECCCChhhHHHHHHHhhcCCCCEEEECHHHHHHHHHH-----hccccccEEEEeChHhhhhcc
Confidence            99999888 89999999999988   5566677666 89999999999887753     456789999999998654   


Q ss_pred             -------c-cCCchH-HHHHHHhcC-----------CCCcEEEEecc-CcHHHH-HHHHHHcCCCeEEEeCCcccccCCc
Q 002040          631 -------D-MGFEPQ-ITRIVQNIR-----------PDRQTVLFSAT-FPRQVE-ILARKVLNKPVEIQVGGRSVVNKDI  688 (976)
Q Consensus       631 -------~-~~f~~~-i~~il~~~~-----------~~~q~i~~SAT-~~~~~~-~l~~~~l~~~~~i~~~~~~~~~~~i  688 (976)
                             + ++|.+. +..++..++           +..|+|+|||| +|..+. .+...++.    +.+.........+
T Consensus       156 ~~~d~~l~~~~~~~~~~~~i~~~~~~~~~~~~l~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~----~~~~~~~~~~~~i  231 (414)
T 3oiy_A          156 RNIDTLLMMVGIPEEIIRKAFSTIKQGKIYERPKNLKPGILVVSSATAKPRGIRPLLFRDLLN----FTVGRLVSVARNI  231 (414)
T ss_dssp             HHHHHHHHHTTCCHHHHHHHHHHHHHTCCCCCCTTCCCCEEEESSCCSSCCSSTTHHHHHHHS----CCSSCCCCCCCSE
T ss_pred             chhhhHHhhcCCcHHHHHHHHHhcccchhhhhcccCCCceEEEEecCCCcchhHHHHHHHhhc----cCcCccccccccc
Confidence                   4 788888 788888876           88999999999 554433 23333333    2223333444556


Q ss_pred             eEEEEecCcchHHHHHHHHHHhhhcCCcEEEEecCHHHHHHHHHHHHHCCCCce-eccCCCCHHHHHHHHHHhccCCccE
Q 002040          689 TQLVEVRPESDRFLRLLELLGEWYEKGKILIFVHSQEKCDALFRDLLKHGYPCL-SLHGAKDQTDRESTISDFKSNVCNL  767 (976)
Q Consensus       689 ~q~~~~~~~~~k~~~l~~~l~~~~~~~kvLIF~~s~~~~~~l~~~L~~~~~~~~-~lhg~~~~~~R~~~~~~F~~g~~~v  767 (976)
                      .+.+...   .+...|..+|..  .++++||||+++..|+.++..|...|+.+. .+||.    +|.  +..|++|.++|
T Consensus       232 ~~~~~~~---~~~~~l~~~l~~--~~~~~lVF~~~~~~~~~l~~~L~~~~~~~~~~~h~~----~r~--~~~f~~g~~~v  300 (414)
T 3oiy_A          232 THVRISS---RSKEKLVELLEI--FRDGILIFAQTEEEGKELYEYLKRFKFNVGETWSEF----EKN--FEDFKVGKINI  300 (414)
T ss_dssp             EEEEESS---CCHHHHHHHHHH--HCSSEEEEESSHHHHHHHHHHHHHTTCCEEESSSCH----HHH--HHHHHTTSCSE
T ss_pred             hheeecc---CHHHHHHHHHHH--cCCCEEEEECCHHHHHHHHHHHHHcCCceehhhcCc----chH--HHHHhCCCCeE
Confidence            6666554   455566666666  358999999999999999999999999998 99995    444  99999999999


Q ss_pred             EEe----cCcccccCCCCC-CcEEEEeCCC--CCHHHHHHHhcccCCCC----CccEEEEEecCCCcCchHHHHHHHh
Q 002040          768 LIA----TSVAARGLDVKE-LELVINFDAP--NHYEDYVHRVGRTGRAG----RKGCAITFISEEDAKYSPDLVKALE  834 (976)
Q Consensus       768 LVa----T~v~~~GlDi~~-v~~VI~~d~p--~s~~~y~Qr~GR~gR~g----~~g~~~~~~~~~d~~~~~~i~~~l~  834 (976)
                      |||    |+++++|||+|+ +++||+|++|  .++..|+||+||+||.|    ..|.|++|+  .+...+..|.+.+.
T Consensus       301 Lvat~s~T~~~~~GiDip~~v~~VI~~~~p~~~~~~~y~qr~GR~gR~g~~~~~~g~~i~~~--~~~~~~~~l~~~~~  376 (414)
T 3oiy_A          301 LIGVQAYYGKLTRGVDLPERIKYVIFWGTPSGPDVYTYIQASGRSSRILNGVLVKGVSVIFE--EDEEIFESLKTRLL  376 (414)
T ss_dssp             EEEECCTTCCCCCCCCCTTTCCEEEEESCCTTTCHHHHHHHHGGGCCEETTEECCEEEEEEC--CCHHHHHHHHHHHH
T ss_pred             EEEecCcCchhhccCccccccCEEEEECCCCCCCHHHHHHHhCccccCCCCCCcceEEEEEE--ccHHHHHHHHHHhc
Confidence            999    999999999999 9999999999  99999999999999987    489999999  55666667776665

>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=100.00  E-value=2.8e-45  Score=434.62  Aligned_cols=341  Identities=20%  Similarity=0.321  Sum_probs=277.2

Q ss_pred             cccccCCCCHHHHHHHHH-cCCCCCcHHHHHHHHHHhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEE
Q 002040          467 KTWHQTGLTSKIMETIRK-LNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLI  545 (976)
Q Consensus       467 ~~~~~~~l~~~l~~~l~~-~~~~~p~~~Q~~~i~~il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLI  545 (976)
                      .+|+.++|++.+...|.. +||..|+|+|.++|+.++.|+++|+++|||+|||++|++|++..           ++.+||
T Consensus         2 ~~fe~l~L~~~~~~~l~~~~g~~~~r~~Q~~~i~~il~g~d~lv~apTGsGKTl~~~lp~l~~-----------~g~~lv   70 (523)
T 1oyw_A            2 AQAEVLNLESGAKQVLQETFGYQQFRPGQEEIIDTVLSGRDCLVVMPTGGGKSLCYQIPALLL-----------NGLTVV   70 (523)
T ss_dssp             CCCCCSSHHHHHHHHHHHTTCCSSCCTTHHHHHHHHHTTCCEEEECSCHHHHHHHHHHHHHHS-----------SSEEEE
T ss_pred             CChhhCCCCHHHHHHHHHHhCCCCCCHHHHHHHHHHHcCCCEEEECCCCcHHHHHHHHHHHHh-----------CCCEEE
Confidence            578999999999999998 99999999999999999999999999999999999999998842           347899


Q ss_pred             EccCHHHHHHHHHHHHHHHhhcCcEEEEeeCCCChHHHHH---HH-hcCCeEEEeCchhHHHHHHhcCCcccccCCceEE
Q 002040          546 MAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQIS---EL-KRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYL  621 (976)
Q Consensus       546 l~Ptr~La~Q~~~~~~~~~~~~~~~~~~~~gg~~~~~~~~---~l-~~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~v  621 (976)
                      |+|+++|+.|++..+..    +|+.+..++++........   .+ ...++|+|+||++|.......   ......+.+|
T Consensus        71 i~P~~aL~~q~~~~l~~----~gi~~~~l~~~~~~~~~~~~~~~~~~~~~~ilv~Tpe~l~~~~~~~---~l~~~~~~~v  143 (523)
T 1oyw_A           71 VSPLISLMKDQVDQLQA----NGVAAACLNSTQTREQQLEVMTGCRTGQIRLLYIAPERLMLDNFLE---HLAHWNPVLL  143 (523)
T ss_dssp             ECSCHHHHHHHHHHHHH----TTCCEEEECTTSCHHHHHHHHHHHHHTCCSEEEECHHHHTSTTHHH---HHTTSCEEEE
T ss_pred             ECChHHHHHHHHHHHHH----cCCcEEEEeCCCCHHHHHHHHHHHhcCCCCEEEECHHHHhChHHHH---HHhhCCCCEE
Confidence            99999999999998876    4788888888887655432   22 235899999999985321110   1234678999


Q ss_pred             EecCcccccccC--CchHHHHH--HHhcCCCCcEEEEeccCcHHHHHHHHHHc--CCCeEEEeCCcccccCCceEEEEec
Q 002040          622 VMDEADRMFDMG--FEPQITRI--VQNIRPDRQTVLFSATFPRQVEILARKVL--NKPVEIQVGGRSVVNKDITQLVEVR  695 (976)
Q Consensus       622 VlDEah~~~~~~--f~~~i~~i--l~~~~~~~q~i~~SAT~~~~~~~l~~~~l--~~~~~i~~~~~~~~~~~i~q~~~~~  695 (976)
                      ||||||++.+||  |.+.+..+  +....+..++|+||||+++.+...+...+  ..+..+ +..  ....++.  +.+.
T Consensus       144 ViDEaH~i~~~g~~fr~~~~~l~~l~~~~~~~~~i~lSAT~~~~~~~~i~~~l~~~~~~~~-~~~--~~r~~l~--~~v~  218 (523)
T 1oyw_A          144 AVDEAHCISQWGHDFRPEYAALGQLRQRFPTLPFMALTATADDTTRQDIVRLLGLNDPLIQ-ISS--FDRPNIR--YMLM  218 (523)
T ss_dssp             EESSGGGGCTTSSCCCHHHHGGGGHHHHCTTSCEEEEESCCCHHHHHHHHHHHTCCSCEEE-ECC--CCCTTEE--EEEE
T ss_pred             EEeCccccCcCCCccHHHHHHHHHHHHhCCCCCEEEEeCCCCHHHHHHHHHHhCCCCCeEE-eCC--CCCCceE--EEEE
Confidence            999999999987  66665543  22334678999999999988755444433  344433 222  2233343  2333


Q ss_pred             CcchHHHHHHHHHHhhhcCCcEEEEecCHHHHHHHHHHHHHCCCCceeccCCCCHHHHHHHHHHhccCCccEEEecCccc
Q 002040          696 PESDRFLRLLELLGEWYEKGKILIFVHSQEKCDALFRDLLKHGYPCLSLHGAKDQTDRESTISDFKSNVCNLLIATSVAA  775 (976)
Q Consensus       696 ~~~~k~~~l~~~l~~~~~~~kvLIF~~s~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLVaT~v~~  775 (976)
                      ....+...++.+|... ..+++||||+++..++.++..|...|+.+..+||+|++.+|..+++.|.+|.++|||||++++
T Consensus       219 ~~~~~~~~l~~~l~~~-~~~~~IVf~~sr~~~e~l~~~L~~~g~~~~~~h~~l~~~~R~~~~~~f~~g~~~vlVaT~a~~  297 (523)
T 1oyw_A          219 EKFKPLDQLMRYVQEQ-RGKSGIIYCNSRAKVEDTAARLQSKGISAAAYHAGLENNVRADVQEKFQRDDLQIVVATVAFG  297 (523)
T ss_dssp             ECSSHHHHHHHHHHHT-TTCCEEEECSSHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEECTTSC
T ss_pred             eCCCHHHHHHHHHHhc-CCCcEEEEeCCHHHHHHHHHHHHHCCCCEEEecCCCCHHHHHHHHHHHHcCCCeEEEEechhh
Confidence            3456677788877654 456999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccCCCCCCcEEEEeCCCCCHHHHHHHhcccCCCCCccEEEEEecCCCcCchHHHHH
Q 002040          776 RGLDVKELELVINFDAPNHYEDYVHRVGRTGRAGRKGCAITFISEEDAKYSPDLVK  831 (976)
Q Consensus       776 ~GlDi~~v~~VI~~d~p~s~~~y~Qr~GR~gR~g~~g~~~~~~~~~d~~~~~~i~~  831 (976)
                      +|||+|++++||+|++|.++..|+|++||+||.|.+|.|++|+++.+...+..++.
T Consensus       298 ~GiD~p~v~~VI~~~~p~s~~~y~Qr~GRaGR~g~~~~~~l~~~~~d~~~~~~~~~  353 (523)
T 1oyw_A          298 MGINKPNVRFVVHFDIPRNIESYYQETGRAGRDGLPAEAMLFYDPADMAWLRRCLE  353 (523)
T ss_dssp             TTTCCTTCCEEEESSCCSSHHHHHHHHTTSCTTSSCEEEEEEECHHHHHHHHHHHH
T ss_pred             CCCCccCccEEEEECCCCCHHHHHHHhccccCCCCCceEEEEeCHHHHHHHHHHHh
Confidence            99999999999999999999999999999999999999999999877655555443

>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=100.00  E-value=4.5e-45  Score=435.57  Aligned_cols=373  Identities=18%  Similarity=0.231  Sum_probs=288.5

Q ss_pred             cCcccccccccchhhhcCCHHHHHHHHhhcCcee-ccCCCCCcccccccCCCCHHHHHHHH--------HcCCCCCcHHH
Q 002040          424 YQPFRKNFYIEVKEIARMTPEEVSAYRKQLELKI-HGKDVPKPIKTWHQTGLTSKIMETIR--------KLNYEKPMPIQ  494 (976)
Q Consensus       424 ~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~-~g~~~p~pi~~~~~~~l~~~l~~~l~--------~~~~~~p~~~Q  494 (976)
                      +.++-+.++...+.+..++.+++......+...+ .|..       +.+     .+..++.        .+|| .|||+|
T Consensus        22 ~~~~~~~in~~~~~~~~lsd~el~~~t~~~~~~~~~g~~-------ld~-----~l~ea~a~vrea~~r~lG~-~pt~VQ   88 (844)
T 1tf5_A           22 YEKIANDIDAIRGDYENLSDDALKHKTIEFKERLEKGAT-------TDD-----LLVEAFAVVREASRRVTGM-FPFKVQ   88 (844)
T ss_dssp             HHHHHHHHHHTTHHHHTCCHHHHHHHHHHHHHHHHTTCC-------HHH-----HHHHHHHHHHHHHHHHHSC-CCCHHH
T ss_pred             HHHHHHHHHhhhHHHHhCCHHHHHHHHHHHHHHHhcCCC-------hHH-----HHHHHHHHHHHHHHHHcCC-CCcHHH
Confidence            4556666777788899999999988777766443 2321       111     1222222        5899 999999


Q ss_pred             HHHHHHHhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHHHHhhcCcEEEEe
Q 002040          495 AQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVMGVRCVPV  574 (976)
Q Consensus       495 ~~~i~~il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~~~~~~~~~~~~~  574 (976)
                      ..++|.++.|+  |+.++||+|||++|++|++.+..        .|+.|+|||||++||.|++.++..++..+|+++.++
T Consensus        89 ~~~ip~ll~G~--Iaea~TGeGKTlaf~LP~~l~aL--------~g~~vlVltptreLA~qd~e~~~~l~~~lgl~v~~i  158 (844)
T 1tf5_A           89 LMGGVALHDGN--IAEMKTGEGKTLTSTLPVYLNAL--------TGKGVHVVTVNEYLASRDAEQMGKIFEFLGLTVGLN  158 (844)
T ss_dssp             HHHHHHHHTTS--EEECCTTSCHHHHHHHHHHHHHT--------TSSCEEEEESSHHHHHHHHHHHHHHHHHTTCCEEEC
T ss_pred             HHhhHHHhCCC--EEEccCCcHHHHHHHHHHHHHHH--------cCCCEEEEeCCHHHHHHHHHHHHHHHhhcCCeEEEE
Confidence            99999999998  99999999999999999985543        256799999999999999999999999999999999


Q ss_pred             eCCCChHHHHHHHhcCCeEEEeCchhH-HHHHHhcCC---cccccCCceEEEecCccccc-ccC---------------C
Q 002040          575 YGGSGVAQQISELKRGTEIVVCTPGRM-IDILCTSGG---KITNLRRVTYLVMDEADRMF-DMG---------------F  634 (976)
Q Consensus       575 ~gg~~~~~~~~~l~~~~~Iiv~Tp~~L-~~~l~~~~~---~~~~l~~~~~vVlDEah~~~-~~~---------------f  634 (976)
                      +||.+...+..  ..+++|+|+||++| +++|..+-.   ....+..+.++||||||+|+ +++               |
T Consensus       159 ~gg~~~~~r~~--~~~~dIv~gTpgrlgfD~L~D~m~~~~~~l~lr~~~~lVlDEaD~mLiDea~tplIisg~~~~~~~~  236 (844)
T 1tf5_A          159 LNSMSKDEKRE--AYAADITYSTNNELGFDYLRDNMVLYKEQMVQRPLHFAVIDEVDSILIDEARTPLIISGQAAKSTKL  236 (844)
T ss_dssp             CTTSCHHHHHH--HHHSSEEEEEHHHHHHHHHHHTTCSSGGGCCCCCCCEEEEETHHHHHTTTTTCEEEEEEEEECCCHH
T ss_pred             eCCCCHHHHHH--hcCCCEEEECchhhhHHHHHHhhhcchhhhcccCCCEEEECchhhhhhhccccchhhcCCcccchhH
Confidence            99998765433  34699999999999 777765421   23457889999999999988 775               4


Q ss_pred             chHHHHHHHhcCC---------CCcEE-----------------EEeccCcHHHHHH-----HHHHcC-CCeEEE-----
Q 002040          635 EPQITRIVQNIRP---------DRQTV-----------------LFSATFPRQVEIL-----ARKVLN-KPVEIQ-----  677 (976)
Q Consensus       635 ~~~i~~il~~~~~---------~~q~i-----------------~~SAT~~~~~~~l-----~~~~l~-~~~~i~-----  677 (976)
                      ...+..|+..+++         .+|++                 +||||++..+..+     +..++. +..++.     
T Consensus       237 ~~~i~~iv~~l~~~~~y~vd~k~rq~~lt~~g~~~~e~~~~i~~Lfsat~~~~~~~i~~al~A~~l~~~d~dYiv~dg~v  316 (844)
T 1tf5_A          237 YVQANAFVRTLKAEKDYTYDIKTKAVQLTEEGMTKAEKAFGIDNLFDVKHVALNHHINQALKAHVAMQKDVDYVVEDGQV  316 (844)
T ss_dssp             HHHHHHHHTTCCSSSSBCCCSSSCCCCBCHHHHHHHHHHTTCSCTTSGGGHHHHHHHHHHHHHHHTCCBTTTEEEETTEE
T ss_pred             HHHHHHHHHhCcccccceeccccceEEecHHHHHHHHHHhCccccCCCccchhHHHHHHHHHHHHHhhcCCceEEecCee
Confidence            5678889988873         67887                 8999987533322     222332 111110     


Q ss_pred             --eC-----------------------------CcccccCCce-------------------------------------
Q 002040          678 --VG-----------------------------GRSVVNKDIT-------------------------------------  689 (976)
Q Consensus       678 --~~-----------------------------~~~~~~~~i~-------------------------------------  689 (976)
                        +.                             ........|.                                     
T Consensus       317 ~ivDe~tgr~m~grr~sdGLhqaieake~v~I~~e~~t~a~It~q~~fr~y~kl~GmTGTa~te~~e~~~iY~l~vv~IP  396 (844)
T 1tf5_A          317 VIVDSFTGRLMKGRRYSEGLHQAIEAKEGLEIQNESMTLATITFQNYFRMYEKLAGMTGTAKTEEEEFRNIYNMQVVTIP  396 (844)
T ss_dssp             EEBCTTTCCBCTTCCCSTTHHHHHHHHTTCCCCCCEEEEEEEEHHHHHTTSSEEEEEESCCGGGHHHHHHHHCCCEEECC
T ss_pred             EEeecccccccCCCccchhhHHHHhhcccceecccccccceeeHHHHHHHHhhhccCCcccchhHHHHHHHhCCceEEec
Confidence              00                             0000000000                                     


Q ss_pred             ----------EEEEecCcchHHHHHHHHHHhhh-cCCcEEEEecCHHHHHHHHHHHHHCCCCceeccCCCCHHHHHHHHH
Q 002040          690 ----------QLVEVRPESDRFLRLLELLGEWY-EKGKILIFVHSQEKCDALFRDLLKHGYPCLSLHGAKDQTDRESTIS  758 (976)
Q Consensus       690 ----------q~~~~~~~~~k~~~l~~~l~~~~-~~~kvLIF~~s~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~  758 (976)
                                +.+.+.....|+..|+..|.... ...++||||+|+..++.|+..|...|+++..|||++.+.++..+..
T Consensus       397 tn~p~~r~d~~d~v~~~~~~K~~al~~~i~~~~~~~~pvLVft~s~~~se~Ls~~L~~~gi~~~vLhg~~~~rEr~ii~~  476 (844)
T 1tf5_A          397 TNRPVVRDDRPDLIYRTMEGKFKAVAEDVAQRYMTGQPVLVGTVAVETSELISKLLKNKGIPHQVLNAKNHEREAQIIEE  476 (844)
T ss_dssp             CSSCCCCEECCCEEESSHHHHHHHHHHHHHHHHHHTCCEEEEESCHHHHHHHHHHHHTTTCCCEEECSSCHHHHHHHHTT
T ss_pred             CCCCcccccCCcEEEeCHHHHHHHHHHHHHHHHhcCCcEEEEECCHHHHHHHHHHHHHCCCCEEEeeCCccHHHHHHHHH
Confidence                      11234456778888888887643 4568999999999999999999999999999999998888876666


Q ss_pred             HhccCCccEEEecCcccccCCCC--------CCcEEEEeCCCCCHHHHHHHhcccCCCCCccEEEEEecCCCc
Q 002040          759 DFKSNVCNLLIATSVAARGLDVK--------ELELVINFDAPNHYEDYVHRVGRTGRAGRKGCAITFISEEDA  823 (976)
Q Consensus       759 ~F~~g~~~vLVaT~v~~~GlDi~--------~v~~VI~~d~p~s~~~y~Qr~GR~gR~g~~g~~~~~~~~~d~  823 (976)
                      .|+.|  .|||||++|+||+||+        ++.+||+|+.|.+...|+||+||+||+|.+|.+++|++..|.
T Consensus       477 ag~~g--~VlIATdmAgRG~DI~l~~~V~~~ggl~VIn~d~p~s~r~y~hr~GRTGRqG~~G~s~~~vs~eD~  547 (844)
T 1tf5_A          477 AGQKG--AVTIATNMAGRGTDIKLGEGVKELGGLAVVGTERHESRRIDNQLRGRSGRQGDPGITQFYLSMEDE  547 (844)
T ss_dssp             TTSTT--CEEEEETTSSTTCCCCCCTTSGGGTSEEEEESSCCSSHHHHHHHHTTSSGGGCCEEEEEEEETTSS
T ss_pred             cCCCC--eEEEeCCccccCcCccccchhhhcCCcEEEEecCCCCHHHHHhhcCccccCCCCCeEEEEecHHHH
Confidence            66665  6999999999999999        889999999999999999999999999999999999998875

>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=100.00  E-value=8.5e-45  Score=460.83  Aligned_cols=329  Identities=18%  Similarity=0.223  Sum_probs=259.1

Q ss_pred             ccccCCCCHHHHHHHHHcCCCCCcHHHHHHHHHHhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEc
Q 002040          468 TWHQTGLTSKIMETIRKLNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMA  547 (976)
Q Consensus       468 ~~~~~~l~~~l~~~l~~~~~~~p~~~Q~~~i~~il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~  547 (976)
                      .|..++++..+...+...++..|+|+|.++|+.|+.|+++|++|+||||||++|++|++..+..        ++++||++
T Consensus       163 ~~~~~~l~~~~~~~~~~~~~f~ltp~Q~~AI~~i~~g~dvLV~ApTGSGKTlva~l~i~~~l~~--------g~rvlvl~  234 (1108)
T 3l9o_A          163 NYDYTPIAEHKRVNEARTYPFTLDPFQDTAISCIDRGESVLVSAHTSAGKTVVAEYAIAQSLKN--------KQRVIYTS  234 (1108)
T ss_dssp             CCCSSTTTTTCCCSCSSCCSSCCCHHHHHHHHHHTTTCCEEEECCSSSHHHHHHHHHHHHHHHT--------TCEEEEEE
T ss_pred             CcccCCCChhhhHHHHHhCCCCCCHHHHHHHHHHHcCCCEEEECCCCCChHHHHHHHHHHHHhc--------CCeEEEEc
Confidence            5666666666655556666678999999999999999999999999999999999999988743        67899999


Q ss_pred             cCHHHHHHHHHHHHHHHhhcCcEEEEeeCCCChHHHHHHHhcCCeEEEeCchhHHHHHHhcCCcccccCCceEEEecCcc
Q 002040          548 PTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEAD  627 (976)
Q Consensus       548 Ptr~La~Q~~~~~~~~~~~~~~~~~~~~gg~~~~~~~~~l~~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDEah  627 (976)
                      ||++|+.|++..|..++.    .+.+++|+...       ..+++|+||||++|.+++....   ..+.++++|||||||
T Consensus       235 PtraLa~Q~~~~l~~~~~----~VglltGd~~~-------~~~~~IlV~Tpe~L~~~L~~~~---~~l~~l~lVVIDEaH  300 (1108)
T 3l9o_A          235 PIKALSNQKYRELLAEFG----DVGLMTGDITI-------NPDAGCLVMTTEILRSMLYRGS---EVMREVAWVIFDEVH  300 (1108)
T ss_dssp             SSHHHHHHHHHHHHHHTS----SEEEECSSCBC-------CCSCSEEEEEHHHHHHHHHHCS---SHHHHEEEEEEETGG
T ss_pred             CcHHHHHHHHHHHHHHhC----CccEEeCcccc-------CCCCCEEEeChHHHHHHHHcCc---cccccCCEEEEhhhh
Confidence            999999999999998754    56678888753       3568999999999999887653   347789999999999


Q ss_pred             cccccCCchHHHHHHHhcCCCCcEEEEeccCcHH--HHHHHHHHcCCCeEEEeCCcccccCCceEEEEecC---------
Q 002040          628 RMFDMGFEPQITRIVQNIRPDRQTVLFSATFPRQ--VEILARKVLNKPVEIQVGGRSVVNKDITQLVEVRP---------  696 (976)
Q Consensus       628 ~~~~~~f~~~i~~il~~~~~~~q~i~~SAT~~~~--~~~l~~~~l~~~~~i~~~~~~~~~~~i~q~~~~~~---------  696 (976)
                      +|.+++|...+..++..+++..|+|+||||+|+.  +..++..+...+..+......  +..+.+.+....         
T Consensus       301 ~l~d~~rg~~~e~ii~~l~~~~qvl~lSATipn~~e~a~~l~~~~~~~~~vi~~~~r--p~pl~~~~~~~~~~~~~~~vd  378 (1108)
T 3l9o_A          301 YMRDKERGVVWEETIILLPDKVRYVFLSATIPNAMEFAEWICKIHSQPCHIVYTNFR--PTPLQHYLFPAHGDGIYLVVD  378 (1108)
T ss_dssp             GTTSHHHHHHHHHHHHHSCTTSEEEEEECSCSSCHHHHHHHHHHTCSCEEEEEECCC--SSCEEEEEEETTSSCCEEEEE
T ss_pred             hccccchHHHHHHHHHhcCCCceEEEEcCCCCCHHHHHHHHHhhcCCCeEEEecCCC--cccceEEEeecCCcceeeeec
Confidence            9999999999999999999999999999999875  335555666666544432211  111222111100         


Q ss_pred             c----------------------------------------------chHHHHHHHHHHhhhcCCcEEEEecCHHHHHHH
Q 002040          697 E----------------------------------------------SDRFLRLLELLGEWYEKGKILIFVHSQEKCDAL  730 (976)
Q Consensus       697 ~----------------------------------------------~~k~~~l~~~l~~~~~~~kvLIF~~s~~~~~~l  730 (976)
                      .                                              ...+..++..+.. ...+++||||+++..|+.+
T Consensus       379 ~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~li~~l~~-~~~~~vIVF~~sr~~~e~l  457 (1108)
T 3l9o_A          379 EKSTFREENFQKAMASISNQIGDDPNSTDSRGKKGQTYKGGSAKGDAKGDIYKIVKMIWK-KKYNPVIVFSFSKRDCEEL  457 (1108)
T ss_dssp             TTTEECHHHHHHHHTTC-----------------------------CHHHHHHHHHHHHH-TTCCCEEEEESCHHHHHHH
T ss_pred             cccchhhhhHHHHHHHHHhhhcccccccccccccccccccccccccchhHHHHHHHHHHh-cCCCCEEEEeCcHHHHHHH
Confidence            0                                              1222333333333 2346999999999999999


Q ss_pred             HHHHHHCCCC---------------------------------------ceeccCCCCHHHHHHHHHHhccCCccEEEec
Q 002040          731 FRDLLKHGYP---------------------------------------CLSLHGAKDQTDRESTISDFKSNVCNLLIAT  771 (976)
Q Consensus       731 ~~~L~~~~~~---------------------------------------~~~lhg~~~~~~R~~~~~~F~~g~~~vLVaT  771 (976)
                      +..|...++.                                       +..+||+|++.+|..++..|.+|.++|||||
T Consensus       458 a~~L~~~~~~~~~e~~~i~~~~~~~~~~l~~~d~~l~~~~~l~~~l~~gV~~~Hg~l~~~~R~~v~~~F~~G~ikVLVAT  537 (1108)
T 3l9o_A          458 ALKMSKLDFNSDDEKEALTKIFNNAIALLPETDRELPQIKHILPLLRRGIGIHHSGLLPILKEVIEILFQEGFLKVLFAT  537 (1108)
T ss_dssp             HHHTCSHHHHCC----CHHHHGGGSCTHHHHHTTCCHHHHHHTHHHHHTEEEECSCSCHHHHHHHHHHHHHTCCCEEEEE
T ss_pred             HHHHHhccCCCHHHHHHHHHHHHHHHhhcchhhhhhhhHHHHHHhhhcCeeeecCCCCHHHHHHHHHHHhCCCCeEEEEC
Confidence            9988543222                                       6889999999999999999999999999999


Q ss_pred             CcccccCCCCCCcEEEEeCCC--------CCHHHHHHHhcccCCCC--CccEEEEEecCC
Q 002040          772 SVAARGLDVKELELVINFDAP--------NHYEDYVHRVGRTGRAG--RKGCAITFISEE  821 (976)
Q Consensus       772 ~v~~~GlDi~~v~~VI~~d~p--------~s~~~y~Qr~GR~gR~g--~~g~~~~~~~~~  821 (976)
                      +++++|||+|++++||+++.|        .++..|+||+|||||.|  ..|.||+++++.
T Consensus       538 ~vla~GIDiP~v~~VI~~~~~~d~~~~r~iS~~eyiQr~GRAGR~G~d~~G~~ill~~~~  597 (1108)
T 3l9o_A          538 ETFSIGLNMPAKTVVFTSVRKWDGQQFRWVSGGEYIQMSGRAGRRGLDDRGIVIMMIDEK  597 (1108)
T ss_dssp             SCCCSCCCC--CEEEESCSEEESSSCEEECCHHHHHHHHHHSCCSSSCSSEEEEEEECCC
T ss_pred             cHHhcCCCCCCceEEEecCcccCccccccCCHHHHHHhhcccCCCCCCCceEEEEEecCC
Confidence            999999999999999977663        46778999999999999  689999998765

>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=100.00  E-value=3.2e-43  Score=423.03  Aligned_cols=331  Identities=20%  Similarity=0.267  Sum_probs=205.9

Q ss_pred             CCCCCcHHHHHHHHHHhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHHHHh
Q 002040          486 NYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAK  565 (976)
Q Consensus       486 ~~~~p~~~Q~~~i~~il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~~~~  565 (976)
                      +...|+|+|.++|+.++.++++|+++|||||||++|++|++..+...+   .+.++++||||||++|+.||+..+..++.
T Consensus         4 ~~~~~~~~Q~~~i~~~~~~~~~l~~~~tGsGKT~~~~~~~~~~~~~~~---~~~~~~~lil~P~~~L~~q~~~~~~~~~~   80 (556)
T 4a2p_A            4 ETKKARSYQIELAQPAINGKNALICAPTGSGKTFVSILICEHHFQNMP---AGRKAKVVFLATKVPVYEQQKNVFKHHFE   80 (556)
T ss_dssp             ----CCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHHTCC---SSCCCCEEEECSSHHHHHHHHHHHHHHHG
T ss_pred             CCCCCCHHHHHHHHHHHcCCCEEEEcCCCChHHHHHHHHHHHHHHhCc---ccCCCeEEEEeCCHHHHHHHHHHHHHHhc
Confidence            345799999999999999999999999999999999999999887653   23367899999999999999999999999


Q ss_pred             hcCcEEEEeeCCCChHHHHHHHhcCCeEEEeCchhHHHHHHhcCCcccccCCceEEEecCcccccccCCchHHH-HHHHh
Q 002040          566 VMGVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMGFEPQIT-RIVQN  644 (976)
Q Consensus       566 ~~~~~~~~~~gg~~~~~~~~~l~~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDEah~~~~~~f~~~i~-~il~~  644 (976)
                      ..++.+..++|+.....+...+..+++|+|+||++|.+++....  ...+..+++|||||||++.++++...+. .++..
T Consensus        81 ~~~~~~~~~~g~~~~~~~~~~~~~~~~i~v~T~~~l~~~~~~~~--~~~~~~~~~vViDEah~~~~~~~~~~~~~~~~~~  158 (556)
T 4a2p_A           81 RQGYSVQGISGENFSNVSVEKVIEDSDIIVVTPQILVNSFEDGT--LTSLSIFTLMIFDECHNTTGNHPYNVLMTRYLEQ  158 (556)
T ss_dssp             GGTCCEEECCCC-----CHHHHHHHCSEEEECHHHHHHHHHSSS--CCCSTTCSEEEEETGGGCSTTSHHHHHHHHHHHH
T ss_pred             ccCceEEEEeCCCCcchhHHHhhCCCCEEEECHHHHHHHHHhCc--ccccccCCEEEEECCcccCCcchHHHHHHHHHHh
Confidence            88999999999998777777777779999999999999886532  2367889999999999998776433332 22221


Q ss_pred             ----cCCCCcEEEEeccCcH-----------HHHHHHHHH------------------cCCCeEEEeCCcccccCC----
Q 002040          645 ----IRPDRQTVLFSATFPR-----------QVEILARKV------------------LNKPVEIQVGGRSVVNKD----  687 (976)
Q Consensus       645 ----~~~~~q~i~~SAT~~~-----------~~~~l~~~~------------------l~~~~~i~~~~~~~~~~~----  687 (976)
                          ..+..++|+||||++.           .+..+...+                  ...|....+.........    
T Consensus       159 ~~~~~~~~~~~l~lSAT~~~~~~~~~~~~~~~i~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  238 (556)
T 4a2p_A          159 KFNSASQLPQILGLTASVGVGNAKNIEETIEHICSLCSYLDIQAISTVRENIQELQRFMNKPEIDVRLVKRRIHNPFAAI  238 (556)
T ss_dssp             HHCC---CCEEEEEESCCCCTTCSSHHHHHHHHHHHHHHHTCSEEECCCTTHHHHHHHTCCCCEEEEECCCCSCCHHHHH
T ss_pred             hhcccCCCCeEEEEeCCcccCchhhHHHHHHHHHHHHHhcCCeEecchhcchHHHHhcCCCCceEEEEcCCCcCChHHHH
Confidence                1466899999999853           122222211                  111111110000000000    


Q ss_pred             -----------------ceEEE----------------------------------------------------------
Q 002040          688 -----------------ITQLV----------------------------------------------------------  692 (976)
Q Consensus       688 -----------------i~q~~----------------------------------------------------------  692 (976)
                                       +....                                                          
T Consensus       239 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~  318 (556)
T 4a2p_A          239 ISNLMSETEALMRTIYSVDTLSQNSKKDFGTQNYEHWIVVTQRKCRLLQLEDKEEESRICRALFICTEHLRKYNDALIIS  318 (556)
T ss_dssp             HHHHHHHHHHHHHHHCC---------CCCSSHHHHHHHHHHHHHHHHC---CHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHhhhhhhhcccccccchhhHHHHHHHHHHHHHhhcccccchhHHHHHHHHHHHHHHHHHHHHHHHh
Confidence                             00000                                                          


Q ss_pred             -----------------------------------------------EecCcchHHHHHHHHHHhh---hcCCcEEEEec
Q 002040          693 -----------------------------------------------EVRPESDRFLRLLELLGEW---YEKGKILIFVH  722 (976)
Q Consensus       693 -----------------------------------------------~~~~~~~k~~~l~~~l~~~---~~~~kvLIF~~  722 (976)
                                                                     .......|+..|..+|...   ....++||||+
T Consensus       319 ~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~K~~~L~~~l~~~~~~~~~~k~lVF~~  398 (556)
T 4a2p_A          319 EDARIIDALSYLTEFFTNVKNGPYTELEQHLTAKFQEKEPELIALSKDETNENPKLEELVCILDDAYRYNPQTRTLLFAK  398 (556)
T ss_dssp             HHSCHHHHHHHHHHHHHHHHHSCCCHHHHHHHHHHHTTHHHHHHHHHCSSSCCHHHHHHHHHHHHHHHHCTTCCEEEEES
T ss_pred             hhhhHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHhhHHHHhhhhccCCCCCChHHHHHHHHHHHHhcCCCCceEEEEEc
Confidence                                                           0001245666777777654   34579999999


Q ss_pred             CHHHHHHHHHHHHHC------------CCCceeccCCCCHHHHHHHHHHhcc-CCccEEEecCcccccCCCCCCcEEEEe
Q 002040          723 SQEKCDALFRDLLKH------------GYPCLSLHGAKDQTDRESTISDFKS-NVCNLLIATSVAARGLDVKELELVINF  789 (976)
Q Consensus       723 s~~~~~~l~~~L~~~------------~~~~~~lhg~~~~~~R~~~~~~F~~-g~~~vLVaT~v~~~GlDi~~v~~VI~~  789 (976)
                      ++..++.|+..|...            |..+..+||+|++.+|..+++.|++ |.++|||||+++++|||+|+|++||+|
T Consensus       399 ~~~~~~~l~~~L~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~R~~~~~~F~~~g~~~vLvaT~~~~~GiDip~v~~VI~~  478 (556)
T 4a2p_A          399 TRALVSALKKCMEENPILNYIKPGVLMGRGRRDQTTGMTLPSQKGVLDAFKTSKDNRLLIATSVADEGIDIVQCNLVVLY  478 (556)
T ss_dssp             SHHHHHHHHHHHTTCSGGGSCCEEC------------------------------CCEEEEEC-----------CEEEEE
T ss_pred             cHHHHHHHHHHHHhCCCcceeeeeEEEccCCcccccccCHHHHHHHHHHhcccCceEEEEEcCchhcCCCchhCCEEEEe
Confidence            999999999999875            5556677888999999999999999 999999999999999999999999999


Q ss_pred             CCCCCHHHHHHHhcccCCCCCccEEEEEecCCCc
Q 002040          790 DAPNHYEDYVHRVGRTGRAGRKGCAITFISEEDA  823 (976)
Q Consensus       790 d~p~s~~~y~Qr~GR~gR~g~~g~~~~~~~~~d~  823 (976)
                      |+|+|+..|+||+|| ||. +.|.||+|++..+.
T Consensus       479 d~p~s~~~~~Qr~GR-gR~-~~g~~~~l~~~~~~  510 (556)
T 4a2p_A          479 EYSGNVTKMIQVRGR-GRA-AGSKCILVTSKTEV  510 (556)
T ss_dssp             TCCSCHHHHHHC----------CCEEEEESCHHH
T ss_pred             CCCCCHHHHHHhcCC-CCC-CCceEEEEEeCcch
Confidence            999999999999999 999 79999999987543

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

Probab=100.00  E-value=2.2e-42  Score=427.53  Aligned_cols=336  Identities=20%  Similarity=0.303  Sum_probs=265.1

Q ss_pred             ccccccCCCCHHHHHHHHHcCCCCCcHHHHHHHHH-HhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEE
Q 002040          466 IKTWHQTGLTSKIMETIRKLNYEKPMPIQAQALPV-IMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGL  544 (976)
Q Consensus       466 i~~~~~~~l~~~l~~~l~~~~~~~p~~~Q~~~i~~-il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vL  544 (976)
                      ..+|.+++|++.+...+..+||..|+|+|.++|+. +..++++|++||||||||++|.++++..+...       +.++|
T Consensus         7 ~~~~~~l~l~~~~~~~l~~~g~~~l~~~Q~~~i~~~~~~~~~~lv~apTGsGKT~~~~l~il~~~~~~-------~~~il   79 (715)
T 2va8_A            7 WMPIEDLKLPSNVIEIIKKRGIKKLNPPQTEAVKKGLLEGNRLLLTSPTGSGKTLIAEMGIISFLLKN-------GGKAI   79 (715)
T ss_dssp             CCBGGGSSSCHHHHHHHHTTSCCBCCHHHHHHHHTTTTTTCCEEEECCTTSCHHHHHHHHHHHHHHHS-------CSEEE
T ss_pred             cCcHHHcCCCHHHHHHHHhCCCCCCCHHHHHHHHHHhcCCCcEEEEcCCCCcHHHHHHHHHHHHHHHC-------CCeEE
Confidence            35799999999999999999999999999999999 78999999999999999999999999887642       56899


Q ss_pred             EEccCHHHHHHHHHHHHHHHhhcCcEEEEeeCCCChHHHHHHHhcCCeEEEeCchhHHHHHHhcCCcccccCCceEEEec
Q 002040          545 IMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMD  624 (976)
Q Consensus       545 Il~Ptr~La~Q~~~~~~~~~~~~~~~~~~~~gg~~~~~~~~~l~~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlD  624 (976)
                      |++|+++||.|++..+..+ ..+|+.+..++|+.......  + ..++|+||||++|..++....   ..+.++++||||
T Consensus        80 ~i~P~r~La~q~~~~~~~~-~~~g~~v~~~~G~~~~~~~~--~-~~~~Iiv~Tpe~l~~~~~~~~---~~l~~~~~vIiD  152 (715)
T 2va8_A           80 YVTPLRALTNEKYLTFKDW-ELIGFKVAMTSGDYDTDDAW--L-KNYDIIITTYEKLDSLWRHRP---EWLNEVNYFVLD  152 (715)
T ss_dssp             EECSCHHHHHHHHHHHGGG-GGGTCCEEECCSCSSSCCGG--G-GGCSEEEECHHHHHHHHHHCC---GGGGGEEEEEEC
T ss_pred             EEeCcHHHHHHHHHHHHHh-hcCCCEEEEEeCCCCCchhh--c-CCCCEEEEcHHHHHHHHhCCh---hHhhccCEEEEe
Confidence            9999999999999999644 45689999999987654431  2 368999999999998887642   347889999999


Q ss_pred             CcccccccCCchHHHHHHHhcCCCCcEEEEeccCcHHHHHHHHHHcCCCeEEEeCCcccccC---------CceEEEEec
Q 002040          625 EADRMFDMGFEPQITRIVQNIRPDRQTVLFSATFPRQVEILARKVLNKPVEIQVGGRSVVNK---------DITQLVEVR  695 (976)
Q Consensus       625 Eah~~~~~~f~~~i~~il~~~~~~~q~i~~SAT~~~~~~~l~~~~l~~~~~i~~~~~~~~~~---------~i~q~~~~~  695 (976)
                      |||.+.+.++...+..++..++ +.|+|+||||+++. ..++. ++..+. +.....+.+..         .....+.+.
T Consensus       153 E~H~l~~~~~~~~l~~i~~~~~-~~~ii~lSATl~n~-~~~~~-~l~~~~-~~~~~r~~~l~~~~~~~~~~~~~~~~~~~  228 (715)
T 2va8_A          153 ELHYLNDPERGPVVESVTIRAK-RRNLLALSATISNY-KQIAK-WLGAEP-VATNWRPVPLIEGVIYPERKKKEYNVIFK  228 (715)
T ss_dssp             SGGGGGCTTTHHHHHHHHHHHH-TSEEEEEESCCTTH-HHHHH-HHTCEE-EECCCCSSCEEEEEEEECSSTTEEEEEET
T ss_pred             chhhcCCcccchHHHHHHHhcc-cCcEEEEcCCCCCH-HHHHH-HhCCCc-cCCCCCCCCceEEEEecCCcccceeeecC
Confidence            9999988888888888887776 78999999999853 44444 343322 12211111100         000011111


Q ss_pred             C--------cchHHHHHHHHHHhhhcCCcEEEEecCHHHHHHHHHHHHHCC-----------------------------
Q 002040          696 P--------ESDRFLRLLELLGEWYEKGKILIFVHSQEKCDALFRDLLKHG-----------------------------  738 (976)
Q Consensus       696 ~--------~~~k~~~l~~~l~~~~~~~kvLIF~~s~~~~~~l~~~L~~~~-----------------------------  738 (976)
                      .        ....+..+...+   ..++++||||+++..++.++..|....                             
T Consensus       229 ~~~~~~~~~~~~~~~~~~~~~---~~~~~~LVF~~s~~~~~~~a~~L~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~  305 (715)
T 2va8_A          229 DNTTKKVHGDDAIIAYTLDSL---SKNGQVLVFRNSRKMAESTALKIANYMNFVSLDENALSEILKQLDDIEEGGSDEKE  305 (715)
T ss_dssp             TSCEEEEESSSHHHHHHHHHH---TTTCCEEEECSSHHHHHHHHHHHHHTTTSSCCCHHHHHHHHHHHHTCCSSCHHHHH
T ss_pred             cchhhhcccchHHHHHHHHHH---hcCCCEEEEECCHHHHHHHHHHHHHHHhhccCChHHHHHHHHHHHHhhhccccccH
Confidence            1        123333343433   246899999999999999999998642                             


Q ss_pred             -------CCceeccCCCCHHHHHHHHHHhccCCccEEEecCcccccCCCCCCcEEEE----eC-------CCCCHHHHHH
Q 002040          739 -------YPCLSLHGAKDQTDRESTISDFKSNVCNLLIATSVAARGLDVKELELVIN----FD-------APNHYEDYVH  800 (976)
Q Consensus       739 -------~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLVaT~v~~~GlDi~~v~~VI~----~d-------~p~s~~~y~Q  800 (976)
                             +.+..+||+|++.+|..+++.|.+|.++|||||+++++|||+|++.+||+    ||       .|.+..+|+|
T Consensus       306 ~l~~~~~~~v~~~h~~l~~~~r~~v~~~f~~g~~~vlvaT~~l~~Gidip~~~~VI~~~~~~d~~~~~~~~~~s~~~~~Q  385 (715)
T 2va8_A          306 LLKSLISKGVAYHHAGLSKALRDLIEEGFRQRKIKVIVATPTLAAGVNLPARTVIIGDIYRFNKKIAGYYDEIPIMEYKQ  385 (715)
T ss_dssp             HHHHHHTTTEEEECTTSCHHHHHHHHHHHHTTCSCEEEECGGGGGSSCCCBSEEEECCC--------------CHHHHHH
T ss_pred             HHHHHHhcCEEEECCCCCHHHHHHHHHHHHcCCCeEEEEChHHhcccCCCceEEEEeCCeeccccCCCCCCcCCHHHHHH
Confidence                   35889999999999999999999999999999999999999999999999    99       8999999999


Q ss_pred             HhcccCCCC--CccEEEEEecCCC
Q 002040          801 RVGRTGRAG--RKGCAITFISEED  822 (976)
Q Consensus       801 r~GR~gR~g--~~g~~~~~~~~~d  822 (976)
                      |+|||||.|  ..|.||+|++..+
T Consensus       386 r~GRaGR~g~~~~G~~~~l~~~~~  409 (715)
T 2va8_A          386 MSGRAGRPGFDQIGESIVVVRDKE  409 (715)
T ss_dssp             HHTTBCCTTTCSCEEEEEECSCGG
T ss_pred             HhhhcCCCCCCCCceEEEEeCCch
Confidence            999999988  4799999998754

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

Probab=100.00  E-value=1.2e-42  Score=417.65  Aligned_cols=331  Identities=23%  Similarity=0.289  Sum_probs=233.2

Q ss_pred             CCCcHHHHHHHHHHhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHHHHhhc
Q 002040          488 EKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVM  567 (976)
Q Consensus       488 ~~p~~~Q~~~i~~il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~~~~~~  567 (976)
                      ..|+|+|.++|+.++.|+++|++++||+|||++|++|++..+...+   ...++++||||||++|+.||+..+..++...
T Consensus         3 ~~~~~~Q~~~i~~~~~~~~~l~~~~tGsGKT~~~~~~~~~~~~~~~---~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~   79 (555)
T 3tbk_A            3 LKPRNYQLELALPAKKGKNTIICAPTGCGKTFVSLLICEHHLKKFP---CGQKGKVVFFANQIPVYEQQATVFSRYFERL   79 (555)
T ss_dssp             CCCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHHTCC---SSCCCCEEEECSSHHHHHHHHHHHHHHHHTT
T ss_pred             CCCcHHHHHHHHHHhCCCCEEEEeCCCChHHHHHHHHHHHHHHhcc---cCCCCEEEEEeCCHHHHHHHHHHHHHHhccC
Confidence            3699999999999999999999999999999999999999988653   2347789999999999999999999999988


Q ss_pred             CcEEEEeeCCCChHHHHHHHhcCCeEEEeCchhHHHHHHhcCCcccccCCceEEEecCcccccccCC-chHHHHHHHhc-
Q 002040          568 GVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMGF-EPQITRIVQNI-  645 (976)
Q Consensus       568 ~~~~~~~~gg~~~~~~~~~l~~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDEah~~~~~~f-~~~i~~il~~~-  645 (976)
                      ++.+..++|+.....+...+..+++|+|+||++|..++....  ...+..+.+|||||||++.+.+. ...+..++... 
T Consensus        80 ~~~~~~~~g~~~~~~~~~~~~~~~~i~v~T~~~l~~~~~~~~--~~~~~~~~~vViDEah~~~~~~~~~~~~~~~~~~~~  157 (555)
T 3tbk_A           80 GYNIASISGATSDSVSVQHIIEDNDIIILTPQILVNNLNNGA--IPSLSVFTLMIFDECHNTSKNHPYNQIMFRYLDHKL  157 (555)
T ss_dssp             TCCEEEECTTTGGGSCHHHHHHHCSEEEECHHHHHHHHHTSS--SCCGGGCSEEEETTGGGCSTTCHHHHHHHHHHHHHT
T ss_pred             CcEEEEEcCCCcchhhHHHHhcCCCEEEECHHHHHHHHhcCc--ccccccCCEEEEECccccCCcchHHHHHHHHHHhhh
Confidence            999999999997776666676779999999999999886542  22677899999999999987652 22222333322 


Q ss_pred             ----CCCCcEEEEeccCcHH-----------HHHHHHHHcCCCeEEEeCCc-----ccccCCceEEEEec----------
Q 002040          646 ----RPDRQTVLFSATFPRQ-----------VEILARKVLNKPVEIQVGGR-----SVVNKDITQLVEVR----------  695 (976)
Q Consensus       646 ----~~~~q~i~~SAT~~~~-----------~~~l~~~~l~~~~~i~~~~~-----~~~~~~i~q~~~~~----------  695 (976)
                          .+..++|+||||++..           +..+. ..+..+........     ............+.          
T Consensus       158 ~~~~~~~~~~l~lSAT~~~~~~~~~~~~~~~~~~l~-~~l~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~  236 (555)
T 3tbk_A          158 GESRDPLPQVVGLTASVGVGDAKTAEEAMQHICKLC-AALDASVIATVRDNVAELEQVVYKPQKISRKVASRTSNTFKCI  236 (555)
T ss_dssp             SSCCSCCCEEEEEESCCCCTTCCSHHHHHHHHHHHH-HHTTCSEEECCCSCHHHHHTTCCCCCEEEEECCCCSCCHHHHH
T ss_pred             ccccCCCCeEEEEecCcccCccccHHHHHHHHHHHH-HhcCCeeeeccccCHHHHHhhcCCCceEEEEecCcccChHHHH
Confidence                2567999999999542           11111 11221111111100     00000000000000          


Q ss_pred             --------------------------------------------------------------------------------
Q 002040          696 --------------------------------------------------------------------------------  695 (976)
Q Consensus       696 --------------------------------------------------------------------------------  695 (976)
                                                                                                      
T Consensus       237 ~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~  316 (555)
T 3tbk_A          237 ISQLMKETEKLAKDVSEELGKLFQIQNREFGTQKYEQWIVGVHKACSVFQMADKEEESRVCKALFLYTSHLRKYNDALII  316 (555)
T ss_dssp             HHHHHHHHHHHHHTSCHHHHGGGGCCSCCSSSHHHHHHHHHHHHHHHTCCCSSHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHhhhhhhhcccccccchhhhHHHHHHHHHhhhhhccchhhHHHHHHHHHHHHHHHHHHHHHHhh
Confidence                                                                                            


Q ss_pred             ---------------------------------------------------CcchHHHHHHHHHHhhh---cCCcEEEEe
Q 002040          696 ---------------------------------------------------PESDRFLRLLELLGEWY---EKGKILIFV  721 (976)
Q Consensus       696 ---------------------------------------------------~~~~k~~~l~~~l~~~~---~~~kvLIF~  721 (976)
                                                                         ....|+..|..+|....   ..+++||||
T Consensus       317 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~l~~~l~~~~~~~~~~k~lVF~  396 (555)
T 3tbk_A          317 SEDAQMTDALNYLKAFFHDVREAAFDETERELTRRFEEKLEELEKVSRDPSNENPKLRDLYLVLQEEYHLKPETKTILFV  396 (555)
T ss_dssp             HHHSCHHHHHHHHHHHHHHHCC-----HHHHHHHHHHTTHHHHHHHHHCGGGCCHHHHHHHHHHHHHHHHCTTCCEEEEC
T ss_pred             hhhhhHHHHHHHHHHHHHHHhhcccchHHHHHHHHHhhhhhhhhhhccCCCcCCHHHHHHHHHHHHHhccCCCceEEEEe
Confidence                                                               12456666777776543   457999999


Q ss_pred             cCHHHHHHHHHHHHHCC------------CCceeccCCCCHHHHHHHHHHhcc-CCccEEEecCcccccCCCCCCcEEEE
Q 002040          722 HSQEKCDALFRDLLKHG------------YPCLSLHGAKDQTDRESTISDFKS-NVCNLLIATSVAARGLDVKELELVIN  788 (976)
Q Consensus       722 ~s~~~~~~l~~~L~~~~------------~~~~~lhg~~~~~~R~~~~~~F~~-g~~~vLVaT~v~~~GlDi~~v~~VI~  788 (976)
                      ++...++.|+..|...+            ..+..+||+|++.+|..++..|++ |.++|||||+++++|||+|+|++||+
T Consensus       397 ~~~~~~~~l~~~L~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~R~~~~~~F~~~g~~~vLvaT~~~~~GlDlp~v~~VI~  476 (555)
T 3tbk_A          397 KTRALVDALKKWIEENPALSFLKPGILTGRGRTNRATGMTLPAQKCVLEAFRASGDNNILIATSVADEGIDIAECNLVIL  476 (555)
T ss_dssp             SSHHHHHHHHHHHHHCGGGTTCCEEECCC--------------------------CCSEEEECCCTTCCEETTSCSEEEE
T ss_pred             CcHHHHHHHHHHHhhCcCcCceeeeEEEecCCcccccccCHHHHHHHHHHHhcCCCeeEEEEcchhhcCCccccCCEEEE
Confidence            99999999999999864            344556679999999999999999 99999999999999999999999999


Q ss_pred             eCCCCCHHHHHHHhcccCCCCCccEEEEEecCCCcCch
Q 002040          789 FDAPNHYEDYVHRVGRTGRAGRKGCAITFISEEDAKYS  826 (976)
Q Consensus       789 ~d~p~s~~~y~Qr~GR~gR~g~~g~~~~~~~~~d~~~~  826 (976)
                      ||+|+|+..|+||+|| ||. ..|.||+|+++.+....
T Consensus       477 ~d~p~s~~~~~Qr~GR-gR~-~~g~~~~l~~~~~~~~~  512 (555)
T 3tbk_A          477 YEYVGNVIKMIQTRGR-GRA-RDSKCFLLTSSADVIEK  512 (555)
T ss_dssp             ESCCSSCCCEECSSCC-CTT-TSCEEEEEESCHHHHHH
T ss_pred             eCCCCCHHHHHHhcCc-CcC-CCceEEEEEcCCCHHHH
Confidence            9999999999999999 998 79999999987655433

>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=100.00  E-value=1.3e-42  Score=412.94  Aligned_cols=368  Identities=19%  Similarity=0.226  Sum_probs=255.0

Q ss_pred             chhhhcCCHHHHHHHHhhcCceeccCCCCCcccccccCCCCHHHHHH-----HHHcCCCCCcHHHHHHHHHHhcCCCEEE
Q 002040          435 VKEIARMTPEEVSAYRKQLELKIHGKDVPKPIKTWHQTGLTSKIMET-----IRKLNYEKPMPIQAQALPVIMSGRDCIG  509 (976)
Q Consensus       435 ~~~~~~~~~~~~~~~~~~~~i~~~g~~~p~pi~~~~~~~l~~~l~~~-----l~~~~~~~p~~~Q~~~i~~il~g~d~i~  509 (976)
                      .+.+..++.+++......+...+....      ++.++ | +.....     ...+|. .|+|+|..++|.+++|+  |+
T Consensus        24 e~~~~~lsd~eL~~kt~~fk~rl~~g~------~ld~~-l-peafA~vrea~~R~lg~-~p~~VQ~~~i~~ll~G~--Ia   92 (853)
T 2fsf_A           24 EPEMEKLSDEELKGKTAEFRARLEKGE------VLENL-I-PEAFAVVREASKRVFGM-RHFDVQLLGGMVLNERC--IA   92 (853)
T ss_dssp             HHHHHHSCHHHHHHHHHHHHHHHHTTC------CHHHH-H-HHHHHHHHHHHHHHHSC-CCCHHHHHHHHHHHSSE--EE
T ss_pred             HHHHHhCCHHHHHHHHHHHHHHHHcCC------Chhhh-h-HHHHHHHHHHHHHHcCC-CCChHHHhhcccccCCe--ee
Confidence            456778888888776665553332211      12221 1 222221     223675 79999999999999998  99


Q ss_pred             EcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHHHHhhcCcEEEEeeCCCChHHHHHHHhc
Q 002040          510 VAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQISELKR  589 (976)
Q Consensus       510 ~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~~~~~~~~~~~~~~gg~~~~~~~~~l~~  589 (976)
                      .++||+|||++|++|++....        .++.|+|||||++||.|++.++..++..+|+++.+++||.+...  ..+..
T Consensus        93 em~TGsGKTlaf~LP~l~~~l--------~g~~vlVltPTreLA~Q~~e~~~~l~~~lgl~v~~i~GG~~~~~--r~~~~  162 (853)
T 2fsf_A           93 EMRTGEGKTLTATLPAYLNAL--------TGKGVHVVTVNDYLAQRDAENNRPLFEFLGLTVGINLPGMPAPA--KREAY  162 (853)
T ss_dssp             ECCTTSCHHHHHHHHHHHHHT--------TSSCCEEEESSHHHHHHHHHHHHHHHHHTTCCEEECCTTCCHHH--HHHHH
T ss_pred             eecCCchHHHHHHHHHHHHHH--------cCCcEEEEcCCHHHHHHHHHHHHHHHHhcCCeEEEEeCCCCHHH--HHHhc
Confidence            999999999999999986543        25679999999999999999999999999999999999998653  34445


Q ss_pred             CCeEEEeCchhH-HHHHHhcCC---cccccCCceEEEecCccccc-ccC---------------CchHHHHHHHhcCC--
Q 002040          590 GTEIVVCTPGRM-IDILCTSGG---KITNLRRVTYLVMDEADRMF-DMG---------------FEPQITRIVQNIRP--  647 (976)
Q Consensus       590 ~~~Iiv~Tp~~L-~~~l~~~~~---~~~~l~~~~~vVlDEah~~~-~~~---------------f~~~i~~il~~~~~--  647 (976)
                      +++|+||||++| +++|..+..   ....++.+.++||||||+|+ +++               |...+..|+..++.  
T Consensus       163 ~~dIvvgTpgrl~fDyLrd~~~~~~~~~~~~~l~~lVlDEaD~mLiD~a~tpLIiSg~~~~~~~~y~~i~~iv~~L~~~~  242 (853)
T 2fsf_A          163 AADITYGTNNEYGFDYLRDNMAFSPEERVQRKLHYALVDEVDSILIDEARTPLIISGPAEDSSEMYKRVNKIIPHLIRQE  242 (853)
T ss_dssp             HSSEEEEEHHHHHHHHHHHTTCSSGGGCCCCSCCEEEESCHHHHTTTTTTCEEEEEEC----------------------
T ss_pred             CCCEEEECCchhhHHHHHhhhhccHhHhcccCCcEEEECchHHHHHhcCcccccccCCCccchhHHHHHHHHHHhchhhh
Confidence            699999999999 788875421   12457889999999999998 544               55677788877764  


Q ss_pred             ------------------CCcEE------------------------EEeccCcHHHHHH-----HHHHcC---------
Q 002040          648 ------------------DRQTV------------------------LFSATFPRQVEIL-----ARKVLN---------  671 (976)
Q Consensus       648 ------------------~~q~i------------------------~~SAT~~~~~~~l-----~~~~l~---------  671 (976)
                                        .+|++                        +||||++..+..+     +..++.         
T Consensus       243 ~~~~~~~~~~~dy~vdek~rqv~lte~g~~~~e~~l~~~~l~~~~~~Lfsat~~~~~~~i~~al~A~~l~~~d~dYiV~d  322 (853)
T 2fsf_A          243 KEDSETFQGEGHFSVDEKSRQVNLTERGLVLIEELLVKEGIMDEGESLYSPANIMLMHHVTAALRAHALFTRDVDYIVKD  322 (853)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             ccccccccccccceeccccceEEEcHHHHHHHHHHHHhCCcccccccccCcccchHHHHHHHHHHHHHHhhcCccceeec
Confidence                              45654                        8999976432211     111111         


Q ss_pred             ------------------------CC----eEEEeCCcccccCCce----------------------------------
Q 002040          672 ------------------------KP----VEIQVGGRSVVNKDIT----------------------------------  689 (976)
Q Consensus       672 ------------------------~~----~~i~~~~~~~~~~~i~----------------------------------  689 (976)
                                              .+    ..+.+.........|.                                  
T Consensus       323 ~~vviVde~tgR~m~grr~sdGLhQaieake~v~I~~e~~tla~It~qnyfr~Y~kl~GmTGTa~te~~ef~~iY~l~vv  402 (853)
T 2fsf_A          323 GEVIIVDEHTGRTMQGRRWSDGLHQAVEAKEGVQIQNENQTLASITFQNYFRLYEKLAGMTGTADTEAFEFSSIYKLDTV  402 (853)
T ss_dssp             ----------------------------------CCCCCEEEEEEEHHHHHTTSSEEEEEECTTCCCHHHHHHHHCCEEE
T ss_pred             CcEEEEecccCcccCCCccchhhhHHHHhcccceecccccccceeehHHHHhhhhhhhcCCCCchhHHHHHHHHhCCcEE
Confidence                                    01    0111111110001111                                  


Q ss_pred             -------------EEEEecCcchHHHHHHHHHHhhh-cCCcEEEEecCHHHHHHHHHHHHHCCCCceeccCCCCHHHHHH
Q 002040          690 -------------QLVEVRPESDRFLRLLELLGEWY-EKGKILIFVHSQEKCDALFRDLLKHGYPCLSLHGAKDQTDRES  755 (976)
Q Consensus       690 -------------q~~~~~~~~~k~~~l~~~l~~~~-~~~kvLIF~~s~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~  755 (976)
                                   +.+.+.....|+..|+..|.... .+.++||||+|+..++.|+..|...|+++.+|||.+.+.++..
T Consensus       403 ~IPtn~p~~R~d~~d~v~~~~~~K~~al~~~i~~~~~~gqpvLVft~sie~se~Ls~~L~~~gi~~~vLnak~~~rEa~i  482 (853)
T 2fsf_A          403 VVPTNRPMIRKDLPDLVYMTEAEKIQAIIEDIKERTAKGQPVLVGTISIEKSELVSNELTKAGIKHNVLNAKFHANEAAI  482 (853)
T ss_dssp             ECCCSSCCCCEECCCEEESSHHHHHHHHHHHHHHHHTTTCCEEEEESSHHHHHHHHHHHHHTTCCCEECCTTCHHHHHHH
T ss_pred             EcCCCCCceeecCCcEEEeCHHHHHHHHHHHHHHHhcCCCCEEEEECcHHHHHHHHHHHHHCCCCEEEecCChhHHHHHH
Confidence                         11234556778999998887654 3568999999999999999999999999999999999888888


Q ss_pred             HHHHhccCCccEEEecCcccccCCCCCC-------------------------------------cEEEEeCCCCCHHHH
Q 002040          756 TISDFKSNVCNLLIATSVAARGLDVKEL-------------------------------------ELVINFDAPNHYEDY  798 (976)
Q Consensus       756 ~~~~F~~g~~~vLVaT~v~~~GlDi~~v-------------------------------------~~VI~~d~p~s~~~y  798 (976)
                      +...|+.|  .|+|||++|+||+||+..                                     .+||+|+.|.+...|
T Consensus       483 ia~agr~G--~VtIATnmAgRGtDI~l~gn~~~~~~~~~~~~~~~~~~~~~~~~~~~~~V~~~GGl~VI~te~pes~riy  560 (853)
T 2fsf_A          483 VAQAGYPA--AVTIATNMAGRGTDIVLGGSWQAEVAALENPTAEQIEKIKADWQVRHDAVLEAGGLHIIGTERHESRRID  560 (853)
T ss_dssp             HHTTTSTT--CEEEEESCCSSCSCCCTTCCHHHHHHHCSSCCSSHHHHHHHHHHHHHHHHHHTTSEEEEESSCCSSHHHH
T ss_pred             HHhcCCCC--eEEEecccccCCcCccCCCchHhhhhhcccchhHHHHHHHHHhhhhhhHHHhcCCcEEEEccCCCCHHHH
Confidence            88899988  599999999999999974                                     699999999999999


Q ss_pred             HHHhcccCCCCCccEEEEEecCCCcCc
Q 002040          799 VHRVGRTGRAGRKGCAITFISEEDAKY  825 (976)
Q Consensus       799 ~Qr~GR~gR~g~~g~~~~~~~~~d~~~  825 (976)
                      +|++||+||.|.+|.+++|++..|..+
T Consensus       561 ~qr~GRTGRqGd~G~s~~fls~eD~l~  587 (853)
T 2fsf_A          561 NQLRGRSGRQGDAGSSRFYLSMEDALM  587 (853)
T ss_dssp             HHHHTTSSGGGCCEEEEEEEETTSGGG
T ss_pred             HhhccccccCCCCeeEEEEecccHHHH
Confidence            999999999999999999999877543

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

Probab=100.00  E-value=2.5e-43  Score=435.65  Aligned_cols=338  Identities=22%  Similarity=0.279  Sum_probs=224.8

Q ss_pred             HHHHHcCCCCCcHHHHHHHHHHhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHH
Q 002040          480 ETIRKLNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSD  559 (976)
Q Consensus       480 ~~l~~~~~~~p~~~Q~~~i~~il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~  559 (976)
                      ..+..+||..|+|+|.++|++++.|+++|+++|||+|||++|++|++.++...+   .+.++++|||+||++|+.||+..
T Consensus         4 ~~l~~~g~~~lr~~Q~~~i~~~l~g~~~iv~~~TGsGKTl~~~~~i~~~l~~~~---~~~~~~~lvl~Pt~~L~~Q~~~~   80 (696)
T 2ykg_A            4 SDTNLYSPFKPRNYQLELALPAMKGKNTIICAPTGCGKTFVSLLICEHHLKKFP---QGQKGKVVFFANQIPVYEQNKSV   80 (696)
T ss_dssp             ---CTTC--CCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHHHHHSC---TTCCCCEEEECSSHHHHHHHHHH
T ss_pred             CcccccCCCCccHHHHHHHHHHHcCCCEEEEcCCCchHHHHHHHHHHHHHHhCc---cCCCCeEEEEECCHHHHHHHHHH
Confidence            456789999999999999999999999999999999999999999999887653   12346899999999999999999


Q ss_pred             HHHHHhhcCcEEEEeeCCCChHHHHHHHhcCCeEEEeCchhHHHHHHhcCCcccccCCceEEEecCcccccccC-CchHH
Q 002040          560 IRKFAKVMGVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMG-FEPQI  638 (976)
Q Consensus       560 ~~~~~~~~~~~~~~~~gg~~~~~~~~~l~~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDEah~~~~~~-f~~~i  638 (976)
                      +.+++...++.+..++||.....+...+..+++|+||||++|.+.+....  ...+..+++|||||||++.+.. +...+
T Consensus        81 ~~~~~~~~~~~v~~~~g~~~~~~~~~~~~~~~~Iiv~Tp~~L~~~l~~~~--~~~l~~~~~vViDEaH~~~~~~~~~~i~  158 (696)
T 2ykg_A           81 FSKYFERHGYRVTGISGATAENVPVEQIVENNDIIILTPQILVNNLKKGT--IPSLSIFTLMIFDECHNTSKQHPYNMIM  158 (696)
T ss_dssp             HHHHTTTTTCCEEEECSSSCSSSCHHHHHHTCSEEEECHHHHHHHHHTTS--SCCGGGCSEEEEETGGGCSTTCHHHHHH
T ss_pred             HHHHhccCCceEEEEeCCccccccHHHhccCCCEEEECHHHHHHHHhcCc--ccccccccEEEEeCCCcccCcccHHHHH
Confidence            99999888999999999987666666666789999999999999886532  2257889999999999987554 11222


Q ss_pred             HHHHHh-----cCCCCcEEEEeccCc-------HH-HHHHHHH---------------------HcCCCeEEEeCCcc--
Q 002040          639 TRIVQN-----IRPDRQTVLFSATFP-------RQ-VEILARK---------------------VLNKPVEIQVGGRS--  682 (976)
Q Consensus       639 ~~il~~-----~~~~~q~i~~SAT~~-------~~-~~~l~~~---------------------~l~~~~~i~~~~~~--  682 (976)
                      ...+..     ..+..++|+||||+.       .. +..+...                     +...|.........  
T Consensus       159 ~~~l~~~~~~~~~~~~~il~LTATp~~~~~~~~~~~~~~i~~~~~~l~~~~~~~~~~~~~~l~~~~~~p~~~~~~~~~~~  238 (696)
T 2ykg_A          159 FNYLDQKLGGSSGPLPQVIGLTASVGVGDAKTTDEALDYICKLCASLDASVIATVKHNLEELEQVVYKPQKFFRKVESRI  238 (696)
T ss_dssp             HHHHHHHHTTCCSCCCEEEEEESCCCCSSCCSHHHHHHHHHHHHHHTTCCEEECCCTTHHHHHHHSCCCEEEEEECCCCS
T ss_pred             HHHHHHhhcccCCCCCeEEEEeCccccCccccHHHHHHHHHHHHHhcCCceEeecccchHHHHhhcCCCceeEEecCccc
Confidence            222222     246789999999986       11 2222111                     11112111000000  


Q ss_pred             c-------c-----------------------------------------------------------------------
Q 002040          683 V-------V-----------------------------------------------------------------------  684 (976)
Q Consensus       683 ~-------~-----------------------------------------------------------------------  684 (976)
                      .       .                                                                       
T Consensus       239 ~~~fs~~~~~l~~~i~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~l~~  318 (696)
T 2ykg_A          239 SDKFKYIIAQLMRDTESLAKRICKDLENLSQIQNREFGTQKYEQWIVTVQKACMVFQMPDKDEESRICKALFLYTSHLRK  318 (696)
T ss_dssp             CCHHHHHHHHHHHHHHHHHHHHSTTGGGSSSCCSCCSSSHHHHHHHHHHHHTSCC------CCHHHHHHHHHHHHHHHHH
T ss_pred             CChHHHHHHHHHHHHHHHHHHHHHHHHHhhccccccccchhHHHHHHHHHHHHHHhhcccchhhhHHHHHHHHHHHHHHH
Confidence            0       0                                                                       


Q ss_pred             -------------------------------cCCceEEEE----------------ecCcchHHHHHHHHHHhhh---cC
Q 002040          685 -------------------------------NKDITQLVE----------------VRPESDRFLRLLELLGEWY---EK  714 (976)
Q Consensus       685 -------------------------------~~~i~q~~~----------------~~~~~~k~~~l~~~l~~~~---~~  714 (976)
                                                     ...+.+.+.                ......|+..|..+|....   ..
T Consensus       319 ~~~~~~i~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~k~~~L~~ll~~~~~~~~~  398 (696)
T 2ykg_A          319 YNDALIISEHARMKDALDYLKDFFSNVRAAGFDEIEQDLTQRFEEKLQELESVSRDPSNENPKLEDLCFILQEEYHLNPE  398 (696)
T ss_dssp             HHHHHHHHHHSCHHHHHHHHHHHHHHHHTTCCCHHHHHHHHHHHTTHHHHHHHHHCGGGCCHHHHHHHHHHHHHHTTCTT
T ss_pred             HhHHHhccchhhHHHHHHHHHHHHHHHhhcccchHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHhccCCC
Confidence                                           000000000                0013457777777777653   45


Q ss_pred             CcEEEEecCHHHHHHHHHHHHHCC----CCceec--------cCCCCHHHHHHHHHHhcc-CCccEEEecCcccccCCCC
Q 002040          715 GKILIFVHSQEKCDALFRDLLKHG----YPCLSL--------HGAKDQTDRESTISDFKS-NVCNLLIATSVAARGLDVK  781 (976)
Q Consensus       715 ~kvLIF~~s~~~~~~l~~~L~~~~----~~~~~l--------hg~~~~~~R~~~~~~F~~-g~~~vLVaT~v~~~GlDi~  781 (976)
                      +++||||+++..++.|+..|...+    +.+..+        ||+|++.+|..+++.|++ |.++|||||+++++|||||
T Consensus       399 ~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~~~~l~G~~~~~~h~~~~~~eR~~v~~~F~~~g~~~vLVaT~v~~~GiDip  478 (696)
T 2ykg_A          399 TITILFVKTRALVDALKNWIEGNPKLSFLKPGILTGRGKTNQNTGMTLPAQKCILDAFKASGDHNILIATSVADEGIDIA  478 (696)
T ss_dssp             CCEEEECSCHHHHHHHHHHHHHCTTCCSCCEEC-----------------------------CCSCSEEEESSCCC---C
T ss_pred             CcEEEEeCcHHHHHHHHHHHHhCCCccccceeEEEccCCCccccCCCHHHHHHHHHHHHhcCCccEEEEechhhcCCcCc
Confidence            799999999999999999999988    888888        559999999999999998 9999999999999999999


Q ss_pred             CCcEEEEeCCCCCHHHHHHHhcccCCCCCccEEEEEecCCCcC
Q 002040          782 ELELVINFDAPNHYEDYVHRVGRTGRAGRKGCAITFISEEDAK  824 (976)
Q Consensus       782 ~v~~VI~~d~p~s~~~y~Qr~GR~gR~g~~g~~~~~~~~~d~~  824 (976)
                      ++++||+||+|+++..|+||+|| ||. +.|.|++|++..+..
T Consensus       479 ~v~~VI~~d~p~s~~~~~Qr~GR-GR~-~~g~~~~l~~~~~~~  519 (696)
T 2ykg_A          479 QCNLVILYEYVGNVIKMIQTRGR-GRA-RGSKCFLLTSNAGVI  519 (696)
T ss_dssp             CCSEEEEESCC--CCCC-----------CCCEEEEEESCHHHH
T ss_pred             cCCEEEEeCCCCCHHHHHHhhcc-CcC-CCceEEEEecCCCHH
Confidence            99999999999999999999999 998 689999999876543

>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=100.00  E-value=1.8e-42  Score=428.29  Aligned_cols=332  Identities=21%  Similarity=0.285  Sum_probs=268.8

Q ss_pred             ccccCCCCHHHHHHHHHcCCCCCcHHHHHHHHH-HhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEE
Q 002040          468 TWHQTGLTSKIMETIRKLNYEKPMPIQAQALPV-IMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIM  546 (976)
Q Consensus       468 ~~~~~~l~~~l~~~l~~~~~~~p~~~Q~~~i~~-il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl  546 (976)
                      +|.+++|++.+.+.+..+||..|+|+|.++|+. +..++++|++||||||||++|.+|++..+...       +.++||+
T Consensus         2 ~f~~l~l~~~~~~~l~~~g~~~l~~~Q~~~i~~~~~~~~~~lv~apTGsGKT~~~~l~il~~~~~~-------~~~~l~i   74 (720)
T 2zj8_A            2 RVDELRVDERIKSTLKERGIESFYPPQAEALKSGILEGKNALISIPTASGKTLIAEIAMVHRILTQ-------GGKAVYI   74 (720)
T ss_dssp             BGGGCCSCHHHHHHHHHTTCCBCCHHHHHHHTTTGGGTCEEEEECCGGGCHHHHHHHHHHHHHHHH-------CSEEEEE
T ss_pred             cHhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhcCCCcEEEEcCCccHHHHHHHHHHHHHHHhC-------CCEEEEE
Confidence            588999999999999999999999999999998 88999999999999999999999999887642       5689999


Q ss_pred             ccCHHHHHHHHHHHHHHHhhcCcEEEEeeCCCChHHHHHHHhcCCeEEEeCchhHHHHHHhcCCcccccCCceEEEecCc
Q 002040          547 APTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEA  626 (976)
Q Consensus       547 ~Ptr~La~Q~~~~~~~~~~~~~~~~~~~~gg~~~~~~~~~l~~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDEa  626 (976)
                      +|+++||.|++..+..+. .+|+.+..++|+......   ....++|+||||++|..++....   ..+.++++||||||
T Consensus        75 ~P~raLa~q~~~~~~~l~-~~g~~v~~~~G~~~~~~~---~~~~~~Iiv~Tpe~l~~~~~~~~---~~l~~~~~vIiDE~  147 (720)
T 2zj8_A           75 VPLKALAEEKFQEFQDWE-KIGLRVAMATGDYDSKDE---WLGKYDIIIATAEKFDSLLRHGS---SWIKDVKILVADEI  147 (720)
T ss_dssp             CSSGGGHHHHHHHTGGGG-GGTCCEEEECSCSSCCCG---GGGGCSEEEECHHHHHHHHHHTC---TTGGGEEEEEEETG
T ss_pred             cCcHHHHHHHHHHHHHHH-hcCCEEEEecCCCCcccc---ccCCCCEEEECHHHHHHHHHcCh---hhhhcCCEEEEECC
Confidence            999999999999997554 468999999997654332   12368999999999988876632   34778999999999


Q ss_pred             ccccccCCchHHHHHHHhcCCCCcEEEEeccCcHHHHHHHHHHcCCCeEEEeCCcccccCCceEEE------EecC----
Q 002040          627 DRMFDMGFEPQITRIVQNIRPDRQTVLFSATFPRQVEILARKVLNKPVEIQVGGRSVVNKDITQLV------EVRP----  696 (976)
Q Consensus       627 h~~~~~~f~~~i~~il~~~~~~~q~i~~SAT~~~~~~~l~~~~l~~~~~i~~~~~~~~~~~i~q~~------~~~~----  696 (976)
                      |.+.++++...+..++..++...|+|+||||+++. ..++. ++..+. +.....+.+   +...+      .+..    
T Consensus       148 H~l~~~~r~~~~~~ll~~l~~~~~ii~lSATl~n~-~~~~~-~l~~~~-~~~~~rp~~---l~~~~~~~~~~~~~~~~~~  221 (720)
T 2zj8_A          148 HLIGSRDRGATLEVILAHMLGKAQIIGLSATIGNP-EELAE-WLNAEL-IVSDWRPVK---LRRGVFYQGFVTWEDGSID  221 (720)
T ss_dssp             GGGGCTTTHHHHHHHHHHHBTTBEEEEEECCCSCH-HHHHH-HTTEEE-EECCCCSSE---EEEEEEETTEEEETTSCEE
T ss_pred             cccCCCcccHHHHHHHHHhhcCCeEEEEcCCcCCH-HHHHH-HhCCcc-cCCCCCCCc---ceEEEEeCCeeeccccchh
Confidence            99998889999999998887789999999999863 33443 443221 111111111   11111      1111    


Q ss_pred             -cchHHHHHHHHHHhhhcCCcEEEEecCHHHHHHHHHHHHHC---------------------------------CCCce
Q 002040          697 -ESDRFLRLLELLGEWYEKGKILIFVHSQEKCDALFRDLLKH---------------------------------GYPCL  742 (976)
Q Consensus       697 -~~~k~~~l~~~l~~~~~~~kvLIF~~s~~~~~~l~~~L~~~---------------------------------~~~~~  742 (976)
                       .......+...+.   .++++||||+++..|+.++..|...                                 ...+.
T Consensus       222 ~~~~~~~~~~~~~~---~~~~~LVF~~sr~~~~~~a~~L~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~l~~~~~~~v~  298 (720)
T 2zj8_A          222 RFSSWEELVYDAIR---KKKGALIFVNMRRKAERVALELSKKVKSLLTKPEIRALNELADSLEENPTNEKLAKAIRGGVA  298 (720)
T ss_dssp             ECSSTTHHHHHHHH---TTCCEEEECSCHHHHHHHHHHHHHHHGGGSCHHHHHHHHHHHHTSCSCHHHHHHHHHHTTTEE
T ss_pred             hhhHHHHHHHHHHh---CCCCEEEEecCHHHHHHHHHHHHHHHHHhcChhhHHHHHHHHHHHhcccchHHHHHHHhcCee
Confidence             1233344444432   4689999999999999999998753                                 13588


Q ss_pred             eccCCCCHHHHHHHHHHhccCCccEEEecCcccccCCCCCCcEEEE----eC----CCCCHHHHHHHhcccCCCC--Ccc
Q 002040          743 SLHGAKDQTDRESTISDFKSNVCNLLIATSVAARGLDVKELELVIN----FD----APNHYEDYVHRVGRTGRAG--RKG  812 (976)
Q Consensus       743 ~lhg~~~~~~R~~~~~~F~~g~~~vLVaT~v~~~GlDi~~v~~VI~----~d----~p~s~~~y~Qr~GR~gR~g--~~g  812 (976)
                      .+||+|++.+|..+++.|.+|.++|||||+++++|||+|++.+||+    ||    .|.++..|+||+|||||.|  ..|
T Consensus       299 ~~h~~l~~~~R~~v~~~f~~g~~~vlvaT~~l~~Gvdip~~~~VI~~~~~yd~~g~~~~s~~~~~Qr~GRaGR~g~~~~G  378 (720)
T 2zj8_A          299 FHHAGLGRDERVLVEENFRKGIIKAVVATPTLSAGINTPAFRVIIRDIWRYSDFGMERIPIIEVHQMLGRAGRPKYDEVG  378 (720)
T ss_dssp             EECTTSCHHHHHHHHHHHHTTSSCEEEECSTTGGGCCCCBSEEEECCSEECCSSSCEECCHHHHHHHHTTBCCTTTCSEE
T ss_pred             eecCCCCHHHHHHHHHHHHCCCCeEEEECcHhhccCCCCceEEEEcCCeeecCCCCccCCHHHHHHHHhhcCCCCCCCCc
Confidence            9999999999999999999999999999999999999999999998    77    5899999999999999988  579


Q ss_pred             EEEEEecCCC
Q 002040          813 CAITFISEED  822 (976)
Q Consensus       813 ~~~~~~~~~d  822 (976)
                      .||+|+++.+
T Consensus       379 ~~~~l~~~~~  388 (720)
T 2zj8_A          379 EGIIVSTSDD  388 (720)
T ss_dssp             EEEEECSSSC
T ss_pred             eEEEEecCcc
Confidence            9999998766

>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=100.00  E-value=5.5e-42  Score=428.01  Aligned_cols=331  Identities=19%  Similarity=0.258  Sum_probs=212.7

Q ss_pred             cCCCCCcHHHHHHHHHHhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHHHH
Q 002040          485 LNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFA  564 (976)
Q Consensus       485 ~~~~~p~~~Q~~~i~~il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~~~  564 (976)
                      +|+..|+|+|.++|+.++.|+++|++++||||||++|++|++.++...+   .+.++++||||||++|+.||+..|..++
T Consensus       244 ~g~~~l~~~Q~~~i~~~l~~~~~ll~~~TGsGKTl~~~~~i~~~l~~~~---~~~~~~~Lvl~Pt~~L~~Q~~~~~~~~~  320 (797)
T 4a2q_A          244 YETKKARSYQIELAQPAINGKNALICAPTGSGKTFVSILICEHHFQNMP---AGRKAKVVFLATKVPVYEQQKNVFKHHF  320 (797)
T ss_dssp             ----CCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHHTCC---SSCCCCEEEECSSHHHHHHHHHHHHHHH
T ss_pred             cCCCCCCHHHHHHHHHHHhCCCEEEEeCCCChHHHHHHHHHHHHHHhcc---ccCCCeEEEEeCCHHHHHHHHHHHHHhc
Confidence            5788999999999999999999999999999999999999999988653   2346789999999999999999999999


Q ss_pred             hhcCcEEEEeeCCCChHHHHHHHhcCCeEEEeCchhHHHHHHhcCCcccccCCceEEEecCcccccccCCchHHH-HHHH
Q 002040          565 KVMGVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMGFEPQIT-RIVQ  643 (976)
Q Consensus       565 ~~~~~~~~~~~gg~~~~~~~~~l~~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDEah~~~~~~f~~~i~-~il~  643 (976)
                      ...++.+..++|+.....+...+..+++|+||||++|.+.+...  ....+..+++|||||||++.+.+....+. .++.
T Consensus       321 ~~~~~~v~~~~g~~~~~~~~~~~~~~~~Ivv~Tp~~l~~~l~~~--~~~~~~~~~~iViDEaH~~~~~~~~~~i~~~~~~  398 (797)
T 4a2q_A          321 ERQGYSVQGISGENFSNVSVEKVIEDSDIIVVTPQILVNSFEDG--TLTSLSIFTLMIFDECHNTTGNHPYNVLMTRYLE  398 (797)
T ss_dssp             GGGTCCEEEECCC-----CHHHHHHTCSEEEECHHHHHHHHHSS--SCCCGGGCSEEEETTGGGCSTTSHHHHHHHHHHH
T ss_pred             ccCCceEEEEeCCcchhhhHHHhhCCCCEEEEchHHHHHHHHhc--cccccccCCEEEEECccccCCCccHHHHHHHHHH
Confidence            98899999999999877777777778999999999999988653  22367889999999999988765332222 2222


Q ss_pred             hc----CCCCcEEEEeccCcH-----------HHHHHHHH------------------HcCCCeEEEeCCcccccCC---
Q 002040          644 NI----RPDRQTVLFSATFPR-----------QVEILARK------------------VLNKPVEIQVGGRSVVNKD---  687 (976)
Q Consensus       644 ~~----~~~~q~i~~SAT~~~-----------~~~~l~~~------------------~l~~~~~i~~~~~~~~~~~---  687 (976)
                      ..    .+..++|+||||++.           .+..+...                  ++..|....+.........   
T Consensus       399 ~~~~~~~~~~~~l~lSATp~~~~~~~~~~~~~~i~~l~~~L~~~~i~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~  478 (797)
T 4a2q_A          399 QKFNSASQLPQILGLTASVGVGNAKNIEETIEHICSLCSYLDIQAISTVRENIQELQRFMNKPEIDVRLVKRRIHNPFAA  478 (797)
T ss_dssp             HHHTTCCCCCEEEEEESCCCCTTCCSHHHHHHHHHHHHHHHTCSEEECCCTTHHHHHHHSCCCCCEEEECCCCSCCHHHH
T ss_pred             HhhccCCCCCeEEEEcCCccccccccHHHHHHHHHHHHHhcCCcEEecccccHHHHHHhcCCCceEEEecCCCCCcHHHH
Confidence            21    566899999999852           22222211                  1122211110000000000   


Q ss_pred             ---------------------c--eEEEE---------------------------------------------------
Q 002040          688 ---------------------I--TQLVE---------------------------------------------------  693 (976)
Q Consensus       688 ---------------------i--~q~~~---------------------------------------------------  693 (976)
                                           +  .+...                                                   
T Consensus       479 ~~~~l~~~i~~~~~~~~~l~~l~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~l~~~~~~~~~  558 (797)
T 4a2q_A          479 IISNLMSETEALMRTIYSVDTLSQNSKKDFGTQNYEHWIVVTQRKCRLLQLEDKEEESRICRALFICTEHLRKYNDALII  558 (797)
T ss_dssp             HHHHHHHHHHHHHHHC------------CCSSHHHHHHHHHHHHHHHHCCCSSHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHhhHHhhhhccccccchhHHHHHHHHHHHHHHhcccccchhhHHHHHHHHHHHHHHHHHHHHhh
Confidence                                 0  00000                                                   


Q ss_pred             -------------------------------------------------ecCcchHHHHHHHHHHhh---hcCCcEEEEe
Q 002040          694 -------------------------------------------------VRPESDRFLRLLELLGEW---YEKGKILIFV  721 (976)
Q Consensus       694 -------------------------------------------------~~~~~~k~~~l~~~l~~~---~~~~kvLIF~  721 (976)
                                                                       ......|+..|..+|...   ....++||||
T Consensus       559 ~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~l~~~~~~~~~~~~K~~~L~~lL~~~~~~~~~~kvLIF~  638 (797)
T 4a2q_A          559 SEDARIIDALSYLTEFFTNVKNGPYTELEQHLTAKFQEKEPELIALSKDETNENPKLEELVCILDDAYRYNPQTRTLLFA  638 (797)
T ss_dssp             HHHSCHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHTTHHHHHHHHHCTTCCCHHHHHHHHHHHHHHHHCSSCCEEEEE
T ss_pred             hccccHHHHHHHHHHHHHHHhccCccHHHHHHHHHHHHHHHHHHHhhcCCCCCChHHHHHHHHHHHHhccCCCCeEEEEE
Confidence                                                             000244666677777653   2457999999


Q ss_pred             cCHHHHHHHHHHHHHC------------CCCceeccCCCCHHHHHHHHHHhcc-CCccEEEecCcccccCCCCCCcEEEE
Q 002040          722 HSQEKCDALFRDLLKH------------GYPCLSLHGAKDQTDRESTISDFKS-NVCNLLIATSVAARGLDVKELELVIN  788 (976)
Q Consensus       722 ~s~~~~~~l~~~L~~~------------~~~~~~lhg~~~~~~R~~~~~~F~~-g~~~vLVaT~v~~~GlDi~~v~~VI~  788 (976)
                      +++..++.|+.+|...            |..+..+||+|++.+|..++..|++ |.++|||||+++++|||+|+|++||+
T Consensus       639 ~~~~~~~~L~~~L~~~~~~~~~~~~~l~G~~~~~~hg~~~~~eR~~~l~~F~~~g~~~vLVaT~~~~~GIDlp~v~~VI~  718 (797)
T 4a2q_A          639 KTRALVSALKKCMEENPILNYIKPGVLMGRGRRDQTTGMTLPSQKGVLDAFKTSKDNRLLIATSVADEGIDIVQCNLVVL  718 (797)
T ss_dssp             SSHHHHHHHHHHHHTCSTTCSCCCEEC----------------------------CCSEEEEECC-------CCCSEEEE
T ss_pred             CcHHHHHHHHHHHHhCcccccccceEEEecCCcccCCCCCHHHHHHHHHHhhccCCceEEEEcCchhcCCCchhCCEEEE
Confidence            9999999999999873            5667778999999999999999999 99999999999999999999999999


Q ss_pred             eCCCCCHHHHHHHhcccCCCCCccEEEEEecCCC
Q 002040          789 FDAPNHYEDYVHRVGRTGRAGRKGCAITFISEED  822 (976)
Q Consensus       789 ~d~p~s~~~y~Qr~GR~gR~g~~g~~~~~~~~~d  822 (976)
                      ||+|+|+..|+||+|| ||. ..|.||+|++..+
T Consensus       719 yd~p~s~~~~iQr~GR-GR~-~~g~~i~l~~~~~  750 (797)
T 4a2q_A          719 YEYSGNVTKMIQVRGR-GRA-AGSKCILVTSKTE  750 (797)
T ss_dssp             ESCCSCHHHHHTC---------CCCEEEEECCHH
T ss_pred             eCCCCCHHHHHHhcCC-CCC-CCceEEEEEeCCc
Confidence            9999999999999999 999 7999999998754

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

Probab=100.00  E-value=5.4e-42  Score=435.04  Aligned_cols=373  Identities=24%  Similarity=0.306  Sum_probs=285.2

Q ss_pred             HcCCCCCcHHHHHHHHHHhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHHH
Q 002040          484 KLNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKF  563 (976)
Q Consensus       484 ~~~~~~p~~~Q~~~i~~il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~~  563 (976)
                      .+|| .|+|+|.++|+.++.|+|+|++|+||||||++|+++++..+.        .++++|||+||++||.|++..+..|
T Consensus        74 ~~gf-~pt~iQ~~ai~~il~g~dvlv~ApTGSGKTl~~l~~il~~~~--------~~~~~Lil~PtreLa~Q~~~~l~~l  144 (1104)
T 4ddu_A           74 KFGK-DLTGYQRLWAKRIVQGKSFTMVAPTGVGKTTFGMMTALWLAR--------KGKKSALVFPTVTLVKQTLERLQKL  144 (1104)
T ss_dssp             HSSS-CCCHHHHHHHHHHTTTCCEEECCSTTCCHHHHHHHHHHHHHT--------TTCCEEEEESSHHHHHHHHHHHHTT
T ss_pred             hcCC-CCCHHHHHHHHHHHcCCCEEEEeCCCCcHHHHHHHHHHHHHh--------cCCeEEEEechHHHHHHHHHHHHHh
Confidence            4677 599999999999999999999999999999988888877652        3678999999999999999999998


Q ss_pred             HhhcCcEEEEeeCCCCh---HHHHHHHhcC-CeEEEeCchhHHHHHHhcCCcccccCCceEEEecCcccc----------
Q 002040          564 AKVMGVRCVPVYGGSGV---AQQISELKRG-TEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRM----------  629 (976)
Q Consensus       564 ~~~~~~~~~~~~gg~~~---~~~~~~l~~~-~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDEah~~----------  629 (976)
                      + ..++.+.+++||.+.   ..++..+..+ ++|+||||++|.+++..     ..+.++++|||||||++          
T Consensus       145 ~-~~~i~v~~l~Gg~~~~er~~~~~~l~~g~~~IlV~Tp~rL~~~l~~-----l~~~~l~~lViDEaH~l~~~~r~~Dr~  218 (1104)
T 4ddu_A          145 A-DEKVKIFGFYSSMKKEEKEKFEKSFEEDDYHILVFSTQFVSKNREK-----LSQKRFDFVFVDDVDAVLKASRNIDTL  218 (1104)
T ss_dssp             S-CTTSCEEEECTTCCTTHHHHHHHHHHTSCCSEEEEEHHHHHHSHHH-----HHTSCCSEEEESCHHHHTTSSHHHHHH
T ss_pred             h-CCCCeEEEEeCCCCHHHHHHHHHHHhCCCCCEEEECHHHHHHHHHh-----hcccCcCEEEEeCCCccccccccchhh
Confidence            7 778999999999988   6677778776 89999999999888753     46778999999999754          


Q ss_pred             cc-cCCchH-HHHHHHhcC-----------CCCcEEEEecc-CcHHHH-HHHHHHcCCCeEEEeCCcccccCCceEEEEe
Q 002040          630 FD-MGFEPQ-ITRIVQNIR-----------PDRQTVLFSAT-FPRQVE-ILARKVLNKPVEIQVGGRSVVNKDITQLVEV  694 (976)
Q Consensus       630 ~~-~~f~~~-i~~il~~~~-----------~~~q~i~~SAT-~~~~~~-~l~~~~l~~~~~i~~~~~~~~~~~i~q~~~~  694 (976)
                      ++ +||... +..++..++           +..|+|+|||| +|..+. .+...++.    +.+.........+.+.+..
T Consensus       219 L~~~gf~~~~i~~il~~l~~~~~~~~~~~~~~~q~ll~SAT~~p~~~~~~~~~~~l~----i~v~~~~~~~~~i~~~~~~  294 (1104)
T 4ddu_A          219 LMMVGIPEEIIRKAFSTIKQGKIYERPKNLKPGILVVSSATAKPRGIRPLLFRDLLN----FTVGRLVSVARNITHVRIS  294 (1104)
T ss_dssp             HHTSSCCHHHHHHHHHHHHHTSCCCCCSSCCCCEEEEECBSSCCCSSTTHHHHHHTC----CCCCBCCCCCCCEEEEEES
T ss_pred             hHhcCCCHHHHHHHHHhcccchhhhhhccCCCceEEEEcCCCCcHHHHHHHhhccee----EEeccCCCCcCCceeEEEe
Confidence            45 899998 888988877           88999999999 555443 23333333    3333344455667776665


Q ss_pred             cCcchHHHHHHHHHHhhhcCCcEEEEecCHHHHHHHHHHHHHCCCCce-eccCCCCHHHHHHHHHHhccCCccEEEe---
Q 002040          695 RPESDRFLRLLELLGEWYEKGKILIFVHSQEKCDALFRDLLKHGYPCL-SLHGAKDQTDRESTISDFKSNVCNLLIA---  770 (976)
Q Consensus       695 ~~~~~k~~~l~~~l~~~~~~~kvLIF~~s~~~~~~l~~~L~~~~~~~~-~lhg~~~~~~R~~~~~~F~~g~~~vLVa---  770 (976)
                      .   .+...|..+|...  ++++||||+++..++.|+..|...|+.+. .+||     +|.. ++.|++|.++||||   
T Consensus       295 ~---~k~~~L~~ll~~~--~~~~LVF~~s~~~a~~l~~~L~~~g~~~~~~lhg-----~rr~-l~~F~~G~~~VLVatas  363 (1104)
T 4ddu_A          295 S---RSKEKLVELLEIF--RDGILIFAQTEEEGKELYEYLKRFKFNVGETWSE-----FEKN-FEDFKVGKINILIGVQA  363 (1104)
T ss_dssp             C---CCHHHHHHHHHHH--CSSEEEEESSSHHHHHHHHHHHHTTCCEEESSSS-----HHHH-HHHHHHTSCSEEEEETT
T ss_pred             c---CHHHHHHHHHHhc--CCCEEEEECcHHHHHHHHHHHHhCCCCeeeEecC-----cHHH-HHHHHCCCCCEEEEecC
Confidence            5   4556667777663  58999999999999999999999999998 9999     2555 99999999999999   


Q ss_pred             -cCcccccCCCCC-CcEEEEeCCCC-------------------------------------------------------
Q 002040          771 -TSVAARGLDVKE-LELVINFDAPN-------------------------------------------------------  793 (976)
Q Consensus       771 -T~v~~~GlDi~~-v~~VI~~d~p~-------------------------------------------------------  793 (976)
                       |+++++|||||+ |++|||||+|.                                                       
T Consensus       364 ~TdvlarGIDip~~V~~VI~~d~P~~~~Sle~~~~~~~~~~~l~~l~~~~~~~~~~~~~~~~e~~~~~l~~~~~~~~i~~  443 (1104)
T 4ddu_A          364 YYGKLTRGVDLPERIKYVIFWGTPSMRFSLELDKAPRFVLARVLKEMGLIKAQENPDVEELRKIAKEHLTQKEFVEKVKE  443 (1104)
T ss_dssp             THHHHCCSCCCTTTCCEEEEESCCEEEEECSSSSCCHHHHHHHHHHHSSCSSCCCCHHHHHHHHHHHCCCHHHHHHHHHH
T ss_pred             CCCeeEecCcCCCCCCEEEEECCCCCCCCcccccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccHHHHHHHhh
Confidence             999999999999 99999999998                                                       


Q ss_pred             -----------------CHHHHHHHhcccCCCCC----ccEEEEEecCCCcCchHHHHHHHhhc--cCC--CC-hHHHHH
Q 002040          794 -----------------HYEDYVHRVGRTGRAGR----KGCAITFISEEDAKYSPDLVKALELS--EQV--VP-DDLKAL  847 (976)
Q Consensus       794 -----------------s~~~y~Qr~GR~gR~g~----~g~~~~~~~~~d~~~~~~i~~~l~~~--~~~--vp-~~l~~l  847 (976)
                                       ++.+|+||+|||||.|.    .|.+++|+  +|...+..|.+.+...  ...  ++ .+|..+
T Consensus       444 ~~~~l~~~~~~~~~~~pd~~tYihr~GRtgR~~~gg~~~Glsi~~~--~d~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~  521 (1104)
T 4ddu_A          444 MFRGVVVKDEDLELIIPDVYTYIQASGRSSRILNGVLVKGVSVIFE--EDEEIFESLKTRLLLIAEEEIIEEAEANWKEL  521 (1104)
T ss_dssp             HCCSSEEETTTTEEEEECHHHHHHHHHTTCCEETTEECCEEEEEEC--CCHHHHHHHHHHHHHHTCCCEEEGGGCCHHHH
T ss_pred             ccceEEecCCeeEEEecChhhhhcccCchhcccCCCcccceEEEEE--ecHHHHHHHHHHHhhhcccccccccccCHHHH
Confidence                             77899999999999653    34555555  7788888888887632  111  11 234444


Q ss_pred             HHHHHHHHhhhhhhccCCCCCCCCcccchhHHHHHHHHHHHHH
Q 002040          848 ADSFMAKVNQGLEQAHGTGYGGSGFKFNEEEDEKRKAAKKAQA  890 (976)
Q Consensus       848 ~~~~~~~~~~~~~~~~~~~~~g~g~~~~~~~~~~~~~~~~~~~  890 (976)
                      ...+-..... +.... ..+-...+-+++.....+...+.++.
T Consensus       522 ~~~i~~~r~~-~~~~~-~~~m~~~LvIaEkPs~Ak~ia~~Lg~  562 (1104)
T 4ddu_A          522 VHEVEESRRR-SEREL-TDTSRSLLIIVESPTKAETLSRFLGR  562 (1104)
T ss_dssp             HHHHHHHHHH-HHSCC-CCCCBCEEEEESCHHHHHHHHHHHTC
T ss_pred             HHHHhHHHHH-hhhhh-hHhcCCeEEEEECHHHHHHHHHHhCC
Confidence            4333222111 11000 11223445666666666666665554

>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=100.00  E-value=1.1e-42  Score=428.85  Aligned_cols=331  Identities=21%  Similarity=0.277  Sum_probs=262.3

Q ss_pred             ccccCC--CCHHHHHHHHHcCCCCCcHHHHHHHHHHhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEE
Q 002040          468 TWHQTG--LTSKIMETIRKLNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLI  545 (976)
Q Consensus       468 ~~~~~~--l~~~l~~~l~~~~~~~p~~~Q~~~i~~il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLI  545 (976)
                      +|.+++  |++.+...|..+||..|+|+|.++++.+++++++|++||||||||++|.+|++..+..        ++++||
T Consensus         2 ~f~~l~~~l~~~~~~~l~~~g~~~l~~~Q~~~i~~i~~~~~~lv~apTGsGKT~~~~l~il~~~~~--------~~~~l~   73 (702)
T 2p6r_A            2 KVEELAESISSYAVGILKEEGIEELFPPQAEAVEKVFSGKNLLLAMPTAAGKTLLAEMAMVREAIK--------GGKSLY   73 (702)
T ss_dssp             CSHHHHHHHHHHHHHHHHCC---CCCCCCHHHHHHHTTCSCEEEECSSHHHHHHHHHHHHHHHHHT--------TCCEEE
T ss_pred             chhhhhhccCHHHHHHHHhCCCCCCCHHHHHHHHHHhCCCcEEEEcCCccHHHHHHHHHHHHHHHh--------CCcEEE
Confidence            477777  8999999999999999999999999999999999999999999999999999988763        468999


Q ss_pred             EccCHHHHHHHHHHHHHHHhhcCcEEEEeeCCCChHHHHHHHhcCCeEEEeCchhHHHHHHhcCCcccccCCceEEEecC
Q 002040          546 MAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDE  625 (976)
Q Consensus       546 l~Ptr~La~Q~~~~~~~~~~~~~~~~~~~~gg~~~~~~~~~l~~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDE  625 (976)
                      ++|+++||.|++..++.+. .+|+.+..++|+......   ...+++|+||||++|..++....   ..+..+++|||||
T Consensus        74 i~P~r~La~q~~~~~~~~~-~~g~~v~~~~G~~~~~~~---~~~~~~Iiv~Tpe~l~~~l~~~~---~~l~~~~~vIiDE  146 (702)
T 2p6r_A           74 VVPLRALAGEKYESFKKWE-KIGLRIGISTGDYESRDE---HLGDCDIIVTTSEKADSLIRNRA---SWIKAVSCLVVDE  146 (702)
T ss_dssp             EESSHHHHHHHHHHHTTTT-TTTCCEEEECSSCBCCSS---CSTTCSEEEEEHHHHHHHHHTTC---SGGGGCCEEEETT
T ss_pred             EeCcHHHHHHHHHHHHHHH-hcCCEEEEEeCCCCcchh---hccCCCEEEECHHHHHHHHHcCh---hHHhhcCEEEEee
Confidence            9999999999999996543 468999999998765432   11368999999999988886632   3478899999999


Q ss_pred             cccccccCCchHHHHHHHhc---CCCCcEEEEeccCcHHHHHHHHHHcCCCeEEEeCCcccccCCceEEEE------ecC
Q 002040          626 ADRMFDMGFEPQITRIVQNI---RPDRQTVLFSATFPRQVEILARKVLNKPVEIQVGGRSVVNKDITQLVE------VRP  696 (976)
Q Consensus       626 ah~~~~~~f~~~i~~il~~~---~~~~q~i~~SAT~~~~~~~l~~~~l~~~~~i~~~~~~~~~~~i~q~~~------~~~  696 (976)
                      ||.+.++++...+..++..+   .++.|+|+||||+++ ...++. ++..++ +.....+.+   +...+.      +..
T Consensus       147 ~H~l~~~~r~~~~~~ll~~l~~~~~~~~ii~lSATl~n-~~~~~~-~l~~~~-~~~~~r~~~---l~~~~~~~~~~~~~~  220 (702)
T 2p6r_A          147 IHLLDSEKRGATLEILVTKMRRMNKALRVIGLSATAPN-VTEIAE-WLDADY-YVSDWRPVP---LVEGVLCEGTLELFD  220 (702)
T ss_dssp             GGGGGCTTTHHHHHHHHHHHHHHCTTCEEEEEECCCTT-HHHHHH-HTTCEE-EECCCCSSC---EEEEEECSSEEEEEE
T ss_pred             eeecCCCCcccHHHHHHHHHHhcCcCceEEEECCCcCC-HHHHHH-HhCCCc-ccCCCCCcc---ceEEEeeCCeeeccC
Confidence            99999888888777776555   678999999999986 344444 444332 222222211   111111      111


Q ss_pred             cc-------hHHHHHHHHHHhhhcCCcEEEEecCHHHHHHHHHHHHHC------------------------------CC
Q 002040          697 ES-------DRFLRLLELLGEWYEKGKILIFVHSQEKCDALFRDLLKH------------------------------GY  739 (976)
Q Consensus       697 ~~-------~k~~~l~~~l~~~~~~~kvLIF~~s~~~~~~l~~~L~~~------------------------------~~  739 (976)
                      ..       .....+...+   ...+++||||+++..++.++..|...                              ++
T Consensus       221 ~~~~~~~~~~~~~~~~~~~---~~~~~~LVF~~s~~~~~~~a~~L~~~~~~~~~~~~~~~~i~~~~~~~~~~~l~~~~~~  297 (702)
T 2p6r_A          221 GAFSTSRRVKFEELVEECV---AENGGVLVFESTRRGAEKTAVKLSAITAKYVENEGLEKAILEENEGEMSRKLAECVRK  297 (702)
T ss_dssp             TTEEEEEECCHHHHHHHHH---HTTCCEEEECSSHHHHHHHHHHHHHHHHTTCCCSSHHHHHHTTCCSHHHHHHHHHHHT
T ss_pred             cchhhhhhhhHHHHHHHHH---hcCCCEEEEcCCHHHHHHHHHHHHHHHHhhcChHHHHHHHHhhccccccHHHHHHHhc
Confidence            00       1334444443   24689999999999999999988753                              24


Q ss_pred             CceeccCCCCHHHHHHHHHHhccCCccEEEecCcccccCCCCCCcEEEE----eC---CCCCHHHHHHHhcccCCCC--C
Q 002040          740 PCLSLHGAKDQTDRESTISDFKSNVCNLLIATSVAARGLDVKELELVIN----FD---APNHYEDYVHRVGRTGRAG--R  810 (976)
Q Consensus       740 ~~~~lhg~~~~~~R~~~~~~F~~g~~~vLVaT~v~~~GlDi~~v~~VI~----~d---~p~s~~~y~Qr~GR~gR~g--~  810 (976)
                      .+..+||+|++.+|..+++.|.+|.++|||||+++++|||+|++.+||+    ||   .|.+..+|+||+|||||.|  .
T Consensus       298 ~v~~~h~~l~~~~R~~v~~~f~~g~~~vlvaT~~l~~Gidip~~~~VI~~~~~yd~~~~~~s~~~~~Qr~GRaGR~g~~~  377 (702)
T 2p6r_A          298 GAAFHHAGLLNGQRRVVEDAFRRGNIKVVVATPTLAAGVNLPARRVIVRSLYRFDGYSKRIKVSEYKQMAGRAGRPGMDE  377 (702)
T ss_dssp             TCCEECTTSCHHHHHHHHHHHHTTSCCEEEECSTTTSSSCCCBSEEEECCSEEESSSEEECCHHHHHHHHTTBSCTTTCS
T ss_pred             CeEEecCCCCHHHHHHHHHHHHCCCCeEEEECcHHhccCCCCceEEEEcCceeeCCCCCcCCHHHHHHHhhhcCCCCCCC
Confidence            6888999999999999999999999999999999999999999999998    76   7899999999999999998  4


Q ss_pred             ccEEEEEecCCC
Q 002040          811 KGCAITFISEED  822 (976)
Q Consensus       811 ~g~~~~~~~~~d  822 (976)
                      .|.||+|++..+
T Consensus       378 ~G~~~~l~~~~~  389 (702)
T 2p6r_A          378 RGEAIIIVGKRD  389 (702)
T ss_dssp             CEEEEEECCGGG
T ss_pred             CceEEEEecCcc
Confidence            799999998765

>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=100.00  E-value=5.2e-41  Score=428.82  Aligned_cols=370  Identities=18%  Similarity=0.211  Sum_probs=281.3

Q ss_pred             CCCCHHHHHHH-HHcCCCCCcHHHHHHHHHHhc----CC--CEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEE
Q 002040          472 TGLTSKIMETI-RKLNYEKPMPIQAQALPVIMS----GR--DCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGL  544 (976)
Q Consensus       472 ~~l~~~l~~~l-~~~~~~~p~~~Q~~~i~~il~----g~--d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vL  544 (976)
                      ++++..+...+ ..++|. |||+|.++|+.++.    ++  ++|++++||+|||++|+++++..+.        .++++|
T Consensus       586 ~~~~~~~~~~~~~~f~~~-~t~~Q~~ai~~il~~~~~g~p~d~ll~~~TGsGKT~val~aa~~~~~--------~g~~vl  656 (1151)
T 2eyq_A          586 FKHDREQYQLFCDSFPFE-TTPDQAQAINAVLSDMCQPLAMDRLVCGDVGFGKTEVAMRAAFLAVD--------NHKQVA  656 (1151)
T ss_dssp             CCCCHHHHHHHHHTCCSC-CCHHHHHHHHHHHHHHHSSSCCEEEEECCCCTTTHHHHHHHHHHHHT--------TTCEEE
T ss_pred             CCCCHHHHHHHHHhCCCC-CCHHHHHHHHHHHHHHhcCCcCcEEEECCCCCCHHHHHHHHHHHHHH--------hCCeEE
Confidence            34455555555 457876 79999999999986    65  8999999999999999999887654        367899


Q ss_pred             EEccCHHHHHHHHHHHHHHHhhcCcEEEEeeCCCChHHH---HHHHhcC-CeEEEeCchhHHHHHHhcCCcccccCCceE
Q 002040          545 IMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQ---ISELKRG-TEIVVCTPGRMIDILCTSGGKITNLRRVTY  620 (976)
Q Consensus       545 Il~Ptr~La~Q~~~~~~~~~~~~~~~~~~~~gg~~~~~~---~~~l~~~-~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~  620 (976)
                      |||||++||.||+..|..++..+++.+..++|+.+....   +..+..+ ++|+||||+.|.    .    ...+.++++
T Consensus       657 vlvPt~~La~Q~~~~~~~~~~~~~i~v~~l~~~~~~~~~~~~~~~l~~g~~dIvV~T~~ll~----~----~~~~~~l~l  728 (1151)
T 2eyq_A          657 VLVPTTLLAQQHYDNFRDRFANWPVRIEMISRFRSAKEQTQILAEVAEGKIDILIGTHKLLQ----S----DVKFKDLGL  728 (1151)
T ss_dssp             EECSSHHHHHHHHHHHHHHSTTTTCCEEEESTTSCHHHHHHHHHHHHTTCCSEEEECTHHHH----S----CCCCSSEEE
T ss_pred             EEechHHHHHHHHHHHHHHhhcCCCeEEEEeCCCCHHHHHHHHHHHhcCCCCEEEECHHHHh----C----Cccccccce
Confidence            999999999999999999888888999998887765544   3445554 899999997652    1    146788999


Q ss_pred             EEecCcccccccCCchHHHHHHHhcCCCCcEEEEeccCcHHHHHHHHHHcCCCeEEEeCCcccccCCceEEEEecCcchH
Q 002040          621 LVMDEADRMFDMGFEPQITRIVQNIRPDRQTVLFSATFPRQVEILARKVLNKPVEIQVGGRSVVNKDITQLVEVRPESDR  700 (976)
Q Consensus       621 vVlDEah~~~~~~f~~~i~~il~~~~~~~q~i~~SAT~~~~~~~l~~~~l~~~~~i~~~~~~~~~~~i~q~~~~~~~~~k  700 (976)
                      |||||||++     ......++..++...++|+||||+++....++...+.++..+.  ........+...+.....   
T Consensus       729 vIiDEaH~~-----g~~~~~~l~~l~~~~~vl~lSATp~p~~l~~~~~~~~~~~~i~--~~~~~r~~i~~~~~~~~~---  798 (1151)
T 2eyq_A          729 LIVDEEHRF-----GVRHKERIKAMRANVDILTLTATPIPRTLNMAMSGMRDLSIIA--TPPARRLAVKTFVREYDS---  798 (1151)
T ss_dssp             EEEESGGGS-----CHHHHHHHHHHHTTSEEEEEESSCCCHHHHHHHTTTSEEEECC--CCCCBCBCEEEEEEECCH---
T ss_pred             EEEechHhc-----ChHHHHHHHHhcCCCCEEEEcCCCChhhHHHHHhcCCCceEEe--cCCCCccccEEEEecCCH---
Confidence            999999983     4566777888888899999999998776655555444433222  122222234433333222   


Q ss_pred             HHHHHHHHHhhhcCCcEEEEecCHHHHHHHHHHHHHC--CCCceeccCCCCHHHHHHHHHHhccCCccEEEecCcccccC
Q 002040          701 FLRLLELLGEWYEKGKILIFVHSQEKCDALFRDLLKH--GYPCLSLHGAKDQTDRESTISDFKSNVCNLLIATSVAARGL  778 (976)
Q Consensus       701 ~~~l~~~l~~~~~~~kvLIF~~s~~~~~~l~~~L~~~--~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLVaT~v~~~Gl  778 (976)
                      ......++.....++++||||+++..++.++..|...  ++.+..+||+|++.+|..++..|.+|.++|||||+++++||
T Consensus       799 ~~i~~~il~~l~~g~qvlvf~~~v~~~~~l~~~L~~~~p~~~v~~lhg~~~~~eR~~il~~F~~g~~~VLVaT~v~e~Gi  878 (1151)
T 2eyq_A          799 MVVREAILREILRGGQVYYLYNDVENIQKAAERLAELVPEARIAIGHGQMRERELERVMNDFHHQRFNVLVCTTIIETGI  878 (1151)
T ss_dssp             HHHHHHHHHHHTTTCEEEEECCCSSCHHHHHHHHHHHCTTSCEEECCSSCCHHHHHHHHHHHHTTSCCEEEESSTTGGGS
T ss_pred             HHHHHHHHHHHhcCCeEEEEECCHHHHHHHHHHHHHhCCCCeEEEEeCCCCHHHHHHHHHHHHcCCCcEEEECCcceeee
Confidence            2222333444445789999999999999999999987  88999999999999999999999999999999999999999


Q ss_pred             CCCCCcEEEEeCC-CCCHHHHHHHhcccCCCCCccEEEEEecCCCcCchHHHHHHHhhccCCCChHHHHHHHHHHHHHhh
Q 002040          779 DVKELELVINFDA-PNHYEDYVHRVGRTGRAGRKGCAITFISEEDAKYSPDLVKALELSEQVVPDDLKALADSFMAKVNQ  857 (976)
Q Consensus       779 Di~~v~~VI~~d~-p~s~~~y~Qr~GR~gR~g~~g~~~~~~~~~d~~~~~~i~~~l~~~~~~vp~~l~~l~~~~~~~~~~  857 (976)
                      |||++++||++++ ++++..|+|++||+||.|+.|+||+|+++.+.. .....+.+                   ..   
T Consensus       879 Dip~v~~VIi~~~~~~~l~~l~Qr~GRvgR~g~~g~~~ll~~~~~~l-~~~~~~rl-------------------~~---  935 (1151)
T 2eyq_A          879 DIPTANTIIIERADHFGLAQLHQLRGRVGRSHHQAYAWLLTPHPKAM-TTDAQKRL-------------------EA---  935 (1151)
T ss_dssp             CCTTEEEEEETTTTSSCHHHHHHHHTTCCBTTBCEEEEEEECCGGGS-CHHHHHHH-------------------HH---
T ss_pred             cccCCcEEEEeCCCCCCHHHHHHHHhccCcCCCceEEEEEECCcccc-CHHHHHHH-------------------HH---
Confidence            9999999999998 578999999999999999999999998754321 11111111                   11   


Q ss_pred             hhhhccCCCCCCCCcccchhHHHHHHHHHHHHHHHcCC
Q 002040          858 GLEQAHGTGYGGSGFKFNEEEDEKRKAAKKAQAKEYGF  895 (976)
Q Consensus       858 ~~~~~~~~~~~g~g~~~~~~~~~~~~~~~~~~~~~~g~  895 (976)
                       +..   ....|+||.++..++++|+++..++..|+|+
T Consensus       936 -i~~---~~~lg~gf~ia~~dl~irg~g~~lg~~q~g~  969 (1151)
T 2eyq_A          936 -IAS---LEDLGAGFALATHDLEIRGAGELLGEEQSGS  969 (1151)
T ss_dssp             -HTT---CCSBSHHHHHHHHHHHHHHHHHHHCHHHHHH
T ss_pred             -HHH---hhccCCcchHHHHHhccCCCcccCCccccCC
Confidence             111   1123568888888888888888777777664

>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=100.00  E-value=6.9e-41  Score=398.06  Aligned_cols=326  Identities=20%  Similarity=0.264  Sum_probs=260.4

Q ss_pred             HcCCCCCcHHHHHHHHHHhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHHH
Q 002040          484 KLNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKF  563 (976)
Q Consensus       484 ~~~~~~p~~~Q~~~i~~il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~~  563 (976)
                      .+|+ .|+|+|..++|.+++|+  |+.++||+|||++|++|++...+.        |+.|+||+||++||.|++.++..+
T Consensus       107 ~lG~-rP~~VQ~~~ip~Ll~G~--Iaem~TGeGKTLa~~LP~~l~aL~--------g~~v~VvTpTreLA~Qdae~m~~l  175 (922)
T 1nkt_A          107 VLDQ-RPFDVQVMGAAALHLGN--VAEMKTGEGKTLTCVLPAYLNALA--------GNGVHIVTVNDYLAKRDSEWMGRV  175 (922)
T ss_dssp             HHSC-CCCHHHHHHHHHHHTTE--EEECCTTSCHHHHTHHHHHHHHTT--------TSCEEEEESSHHHHHHHHHHHHHH
T ss_pred             HcCC-CCCHHHHHHHHhHhcCC--EEEecCCCccHHHHHHHHHHHHHh--------CCCeEEEeCCHHHHHHHHHHHHHH
Confidence            4788 89999999999999998  999999999999999999755442        457999999999999999999999


Q ss_pred             HhhcCcEEEEeeCCCChHHHHHHHhcCCeEEEeCchhH-HHHHHhcCC---cccccCCceEEEecCccccc-cc------
Q 002040          564 AKVMGVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRM-IDILCTSGG---KITNLRRVTYLVMDEADRMF-DM------  632 (976)
Q Consensus       564 ~~~~~~~~~~~~gg~~~~~~~~~l~~~~~Iiv~Tp~~L-~~~l~~~~~---~~~~l~~~~~vVlDEah~~~-~~------  632 (976)
                      +..+|+.+.+++||.+.....  +..+++|+|+||++| +++|..+-.   ....+..+.++||||||+|+ +.      
T Consensus       176 ~~~lGLsv~~i~gg~~~~~r~--~~y~~DIvygTpgrlgfDyLrD~m~~~~~~l~lr~l~~lIVDEaDsmLiDeartPLi  253 (922)
T 1nkt_A          176 HRFLGLQVGVILATMTPDERR--VAYNADITYGTNNEFGFDYLRDNMAHSLDDLVQRGHHYAIVDEVDSILIDEARTPLI  253 (922)
T ss_dssp             HHHTTCCEEECCTTCCHHHHH--HHHHSSEEEEEHHHHHHHHHHHTTCSSGGGCCCCCCCEEEETTHHHHHTTGGGSCEE
T ss_pred             HhhcCCeEEEEeCCCCHHHHH--HhcCCCEEEECchHhhHHHHHhhhhccHhhhccCCCCEEEEeChHHHHHhcCcccee
Confidence            999999999999999865443  334699999999999 788876421   23457889999999999998 43      


Q ss_pred             ---------CCchHHHHHHHhcC---------CCCcEE-----------------EEeccCcHHHHHH-----HHHHcC-
Q 002040          633 ---------GFEPQITRIVQNIR---------PDRQTV-----------------LFSATFPRQVEIL-----ARKVLN-  671 (976)
Q Consensus       633 ---------~f~~~i~~il~~~~---------~~~q~i-----------------~~SAT~~~~~~~l-----~~~~l~-  671 (976)
                               +|...+..|+..++         ..+|++                 +||||++..+..+     +..++. 
T Consensus       254 iSg~~~~~~~~y~~i~~iv~~L~~~~dy~vDek~rqv~Lte~G~~~~e~~l~i~~Lfsat~~~l~~~i~~aL~A~~l~~~  333 (922)
T 1nkt_A          254 ISGPADGASNWYTEFARLAPLMEKDVHYEVDLRKRTVGVHEKGVEFVEDQLGIDNLYEAANSPLVSYLNNALKAKELFSR  333 (922)
T ss_dssp             EEEECCCCHHHHHHHHHHHHHSCBTTTEEEETTTTEEEECHHHHHHHHHHHTCSSTTCSTTCCHHHHHHHHHHHHHHCCB
T ss_pred             ecCCCCcchhHHHHHHHHHHhCcccccceeccCcceEEecHhHHHHHHHHhCCccccCCcchhHHHHHHHHHHHHHHhhc
Confidence                     47788999999997         678888                 8999987533222     222332 


Q ss_pred             CC-------eEEEeCC---c--------------------------ccccCCce--------------------------
Q 002040          672 KP-------VEIQVGG---R--------------------------SVVNKDIT--------------------------  689 (976)
Q Consensus       672 ~~-------~~i~~~~---~--------------------------~~~~~~i~--------------------------  689 (976)
                      +.       ..+.+..   .                          ......|.                          
T Consensus       334 d~dYiV~dg~vviVDe~TGR~m~grr~sdGLHQaieaKe~V~I~~e~~TlatIt~Qnyfr~Y~kL~GMTGTa~te~~Ef~  413 (922)
T 1nkt_A          334 DKDYIVRDGEVLIVDEFTGRVLIGRRYNEGMHQAIEAKEHVEIKAENQTLATITLQNYFRLYDKLAGMTGTAQTEAAELH  413 (922)
T ss_dssp             TTTEEECSSCEEEBCSSSCCBCTTCCCSTTHHHHHHHHTTCCCCCCEEEEEEECHHHHHTTSSEEEEEESCCGGGHHHHH
T ss_pred             ccceeeecCceEEEecccCcccCCccccchhhHHHhccccccccccccccceeehHHHHHhhhhhhccccCchhHHHHHH
Confidence            11       1111110   0                          00000000                          


Q ss_pred             ---------------------EEEEecCcchHHHHHHHHHHhhhc-CCcEEEEecCHHHHHHHHHHHHHCCCCceeccCC
Q 002040          690 ---------------------QLVEVRPESDRFLRLLELLGEWYE-KGKILIFVHSQEKCDALFRDLLKHGYPCLSLHGA  747 (976)
Q Consensus       690 ---------------------q~~~~~~~~~k~~~l~~~l~~~~~-~~kvLIF~~s~~~~~~l~~~L~~~~~~~~~lhg~  747 (976)
                                           +.+.+.....|+..++..|..... +.++||||+|+..++.|+..|...|+++..|||.
T Consensus       414 ~iY~l~vv~IPtn~p~~R~d~~d~v~~t~~~K~~al~~~i~~~~~~gqpvLVft~Sie~sE~Ls~~L~~~Gi~~~vLnak  493 (922)
T 1nkt_A          414 EIYKLGVVSIPTNMPMIREDQSDLIYKTEEAKYIAVVDDVAERYAKGQPVLIGTTSVERSEYLSRQFTKRRIPHNVLNAK  493 (922)
T ss_dssp             HHHCCEEEECCCSSCCCCEECCCEEESCHHHHHHHHHHHHHHHHHTTCCEEEEESCHHHHHHHHHHHHHTTCCCEEECSS
T ss_pred             HHhCCCeEEeCCCCCcccccCCcEEEeCHHHHHHHHHHHHHHHHhcCCcEEEEECCHHHHHHHHHHHHHCCCCEEEecCC
Confidence                                 012334556788888888876544 4589999999999999999999999999999999


Q ss_pred             CCHHHHHHHHHHhccCCccEEEecCcccccCCCCCC--------------------------------------------
Q 002040          748 KDQTDRESTISDFKSNVCNLLIATSVAARGLDVKEL--------------------------------------------  783 (976)
Q Consensus       748 ~~~~~R~~~~~~F~~g~~~vLVaT~v~~~GlDi~~v--------------------------------------------  783 (976)
                      +.+.++..+.+.|+.|  .|+|||++|+||+||+.+                                            
T Consensus       494 ~~~rEa~iia~agr~G--~VtIATnmAgRGtDI~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  571 (922)
T 1nkt_A          494 YHEQEATIIAVAGRRG--GVTVATNMAGRGTDIVLGGNVDFLTDQRLRERGLDPVETPEEYEAAWHSELPIVKEEASKEA  571 (922)
T ss_dssp             CHHHHHHHHHTTTSTT--CEEEEETTCSTTCCCCTTCCHHHHHHHHHHHTTCCTTTSHHHHHHHHHHHHHHHHHHTTHHH
T ss_pred             hhHHHHHHHHhcCCCC--eEEEecchhhcCccccCCCCHHHHHHHHHhhccccccccchhhHHHHHHHHHHHHHHHHHhh
Confidence            9888888788888887  699999999999999975                                            


Q ss_pred             --------cEEEEeCCCCCHHHHHHHhcccCCCCCccEEEEEecCCCcC
Q 002040          784 --------ELVINFDAPNHYEDYVHRVGRTGRAGRKGCAITFISEEDAK  824 (976)
Q Consensus       784 --------~~VI~~d~p~s~~~y~Qr~GR~gR~g~~g~~~~~~~~~d~~  824 (976)
                              .+||+|+.|.+...|+|++||+||.|.+|.+++|++..|..
T Consensus       572 ~~V~~~GGlhVI~te~pes~riy~qr~GRTGRqGdpG~s~fflSleD~l  620 (922)
T 1nkt_A          572 KEVIEAGGLYVLGTERHESRRIDNQLRGRSGRQGDPGESRFYLSLGDEL  620 (922)
T ss_dssp             HHHHHTTSEEEEECSCCSSHHHHHHHHHTSSGGGCCEEEEEEEETTSHH
T ss_pred             hHHHhcCCcEEEeccCCCCHHHHHHHhcccccCCCCeeEEEEechhHHH
Confidence                    59999999999999999999999999999999999987753

>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=100.00  E-value=8.3e-41  Score=394.05  Aligned_cols=321  Identities=22%  Similarity=0.305  Sum_probs=250.7

Q ss_pred             CCcHHHHHHHHHHhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHHHHhhcC
Q 002040          489 KPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVMG  568 (976)
Q Consensus       489 ~p~~~Q~~~i~~il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~~~~~~~  568 (976)
                      .|+|+|.++++.++.+ ++|++++||+|||++++++++..+..       .++++||||||++|+.||+.++.+++...+
T Consensus         9 ~l~~~Q~~~i~~~~~~-~~ll~~~tG~GKT~~~~~~~~~~~~~-------~~~~~liv~P~~~L~~q~~~~~~~~~~~~~   80 (494)
T 1wp9_A            9 QPRIYQEVIYAKCKET-NCLIVLPTGLGKTLIAMMIAEYRLTK-------YGGKVLMLAPTKPLVLQHAESFRRLFNLPP   80 (494)
T ss_dssp             CCCHHHHHHHHHGGGS-CEEEECCTTSCHHHHHHHHHHHHHHH-------SCSCEEEECSSHHHHHHHHHHHHHHBCSCG
T ss_pred             CccHHHHHHHHHHhhC-CEEEEcCCCCCHHHHHHHHHHHHHhc-------CCCeEEEEECCHHHHHHHHHHHHHHhCcch
Confidence            5899999999999999 99999999999999999999888762       356899999999999999999999864344


Q ss_pred             cEEEEeeCCCChHHHHHHHhcCCeEEEeCchhHHHHHHhcCCcccccCCceEEEecCcccccccCCchHHHHHHHhcCCC
Q 002040          569 VRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMGFEPQITRIVQNIRPD  648 (976)
Q Consensus       569 ~~~~~~~gg~~~~~~~~~l~~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDEah~~~~~~f~~~i~~il~~~~~~  648 (976)
                      ..+..++|+........ +..+++|+|+||+.|...+....   ..+..+++|||||||++.+......+...+....+.
T Consensus        81 ~~v~~~~g~~~~~~~~~-~~~~~~ivv~T~~~l~~~~~~~~---~~~~~~~~vIiDEaH~~~~~~~~~~~~~~~~~~~~~  156 (494)
T 1wp9_A           81 EKIVALTGEKSPEERSK-AWARAKVIVATPQTIENDLLAGR---ISLEDVSLIVFDEAHRAVGNYAYVFIAREYKRQAKN  156 (494)
T ss_dssp             GGEEEECSCSCHHHHHH-HHHHCSEEEECHHHHHHHHHTTS---CCTTSCSEEEEETGGGCSTTCHHHHHHHHHHHHCSS
T ss_pred             hheEEeeCCcchhhhhh-hccCCCEEEecHHHHHHHHhcCC---cchhhceEEEEECCcccCCCCcHHHHHHHHHhcCCC
Confidence            58888888887665433 33458999999999998876532   467789999999999988665555566666666788


Q ss_pred             CcEEEEeccCcHH---HHHHHHHHcCCCeEEEeCCccc----ccCCceEEEE----------------------------
Q 002040          649 RQTVLFSATFPRQ---VEILARKVLNKPVEIQVGGRSV----VNKDITQLVE----------------------------  693 (976)
Q Consensus       649 ~q~i~~SAT~~~~---~~~l~~~~l~~~~~i~~~~~~~----~~~~i~q~~~----------------------------  693 (976)
                      .++|+||||++..   +..+...+....+.+.......    ........+.                            
T Consensus       157 ~~~l~lTaTp~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  236 (494)
T 1wp9_A          157 PLVIGLTASPGSTPEKIMEVINNLGIEHIEYRSENSPDVRPYVKGIRFEWVRVDLPEIYKEVRKLLREMLRDALKPLAET  236 (494)
T ss_dssp             CCEEEEESCSCSSHHHHHHHHHHTTCCEEEECCTTSTTTGGGCCCCCEEEEEECCCHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CeEEEEecCCCCCcHHHHHHHHhcChheeeccCCCcHHHHHhcCCCceeEEecCCcHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            8999999999743   3333333222211111000000    0000000000                            


Q ss_pred             --------------------------------------------------------------------------------
Q 002040          694 --------------------------------------------------------------------------------  693 (976)
Q Consensus       694 --------------------------------------------------------------------------------  693 (976)
                                                                                                      
T Consensus       237 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~  316 (494)
T 1wp9_A          237 GLLESSSPDIPKKEVLRAGQIINEEMAKGNHDLRGLLLYHAMALKLHHAIELLETQGLSALRAYIKKLYEEAKAGSTKAS  316 (494)
T ss_dssp             TSSSCCCTTSCHHHHHHHHHHHHHHHTTTCCSTTTHHHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHTTCCHHH
T ss_pred             ccccccCCCcchhHHHHHHHHHHHHhhccccchhhHHHHHHHHHHHHHHHHHHHhhcHHHHHHHHHHHHHhhccccchhh
Confidence                                                                                            


Q ss_pred             ---------------------ecCcchHHHHHHHHHHhhh---cCCcEEEEecCHHHHHHHHHHHHHCCCCceeccC---
Q 002040          694 ---------------------VRPESDRFLRLLELLGEWY---EKGKILIFVHSQEKCDALFRDLLKHGYPCLSLHG---  746 (976)
Q Consensus       694 ---------------------~~~~~~k~~~l~~~l~~~~---~~~kvLIF~~s~~~~~~l~~~L~~~~~~~~~lhg---  746 (976)
                                           ......|+..|..+|....   ..+++||||++...++.++..|...|+.+..+||   
T Consensus       317 ~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~l~~~l~~~~~~~~~~k~lVF~~~~~~~~~l~~~L~~~~~~~~~~~g~~~  396 (494)
T 1wp9_A          317 KEIFSDKRMKKAISLLVQAKEIGLDHPKMDKLKEIIREQLQRKQNSKIIVFTNYRETAKKIVNELVKDGIKAKRFVGQAS  396 (494)
T ss_dssp             HHHHTSHHHHHHHHHHHHHHHHTCSCHHHHHHHHHHHHHHHHCTTCCEEEECSCHHHHHHHHHHHHHTTCCEEEECCSSC
T ss_pred             hhhhhhHHHHHHHHHHHHHHhcCCCChHHHHHHHHHHHHhccCCCCeEEEEEccHHHHHHHHHHHHHcCCCcEEEecccc
Confidence                                 0033456677777777653   5779999999999999999999999999999999   


Q ss_pred             -----CCCHHHHHHHHHHhccCCccEEEecCcccccCCCCCCcEEEEeCCCCCHHHHHHHhcccCCCCCccEEEEEecCC
Q 002040          747 -----AKDQTDRESTISDFKSNVCNLLIATSVAARGLDVKELELVINFDAPNHYEDYVHRVGRTGRAGRKGCAITFISEE  821 (976)
Q Consensus       747 -----~~~~~~R~~~~~~F~~g~~~vLVaT~v~~~GlDi~~v~~VI~~d~p~s~~~y~Qr~GR~gR~g~~g~~~~~~~~~  821 (976)
                           +|+..+|..+++.|++|.++|||||+++++|||+|++++||+|++||++..|+||+||+||.|+ |.+|+|+++.
T Consensus       397 ~~~~~~~~~~~r~~~~~~F~~~~~~vLv~T~~~~~Gldl~~~~~Vi~~d~~~~~~~~~Qr~GR~~R~g~-g~~~~l~~~~  475 (494)
T 1wp9_A          397 KENDRGLSQREQKLILDEFARGEFNVLVATSVGEEGLDVPEVDLVVFYEPVPSAIRSIQRRGRTGRHMP-GRVIILMAKG  475 (494)
T ss_dssp             C-------CCHHHHHHHHHHHTSCSEEEECGGGGGGGGSTTCCEEEESSCCHHHHHHHHHHTTSCSCCC-SEEEEEEETT
T ss_pred             ccccccCCHHHHHHHHHHHhcCCceEEEECCccccCCCchhCCEEEEeCCCCCHHHHHHHHhhccCCCC-ceEEEEEecC
Confidence                 9999999999999999999999999999999999999999999999999999999999999997 9999999876


Q ss_pred             C
Q 002040          822 D  822 (976)
Q Consensus       822 d  822 (976)
                      +
T Consensus       476 t  476 (494)
T 1wp9_A          476 T  476 (494)
T ss_dssp             S
T ss_pred             C
Confidence            4

>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=100.00  E-value=2.7e-42  Score=438.33  Aligned_cols=320  Identities=19%  Similarity=0.296  Sum_probs=262.4

Q ss_pred             HcCCCCCcHHHHHHHHHHhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHHH
Q 002040          484 KLNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKF  563 (976)
Q Consensus       484 ~~~~~~p~~~Q~~~i~~il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~~  563 (976)
                      .+||. | |+|.++|+.++.|+|+|++|+||||||+ |++|++..+..       .++++|||+||++||.|++..+..+
T Consensus        53 ~~g~~-p-~iQ~~ai~~il~g~dvlv~apTGSGKTl-~~lp~l~~~~~-------~~~~~lil~PtreLa~Q~~~~l~~l  122 (1054)
T 1gku_B           53 CVGEP-R-AIQKMWAKRILRKESFAATAPTGVGKTS-FGLAMSLFLAL-------KGKRCYVIFPTSLLVIQAAETIRKY  122 (1054)
T ss_dssp             TTCSC-C-HHHHHHHHHHHTTCCEECCCCBTSCSHH-HHHHHHHHHHT-------TSCCEEEEESCHHHHHHHHHHHHHH
T ss_pred             hcCCC-H-HHHHHHHHHHHhCCCEEEEcCCCCCHHH-HHHHHHHHHhh-------cCCeEEEEeccHHHHHHHHHHHHHH
Confidence            48999 9 9999999999999999999999999998 88998888764       3678999999999999999999999


Q ss_pred             HhhcCc----EEEEeeCCCChHHH---HHHHhcCCeEEEeCchhHHHHHHhcCCcccccCCceEEEecCcccccccCCch
Q 002040          564 AKVMGV----RCVPVYGGSGVAQQ---ISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMGFEP  636 (976)
Q Consensus       564 ~~~~~~----~~~~~~gg~~~~~~---~~~l~~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDEah~~~~~~f~~  636 (976)
                      +..+++    .+.+++||.+...+   ...+.. ++|+||||++|.+++..       |..+++|||||||+|++  |..
T Consensus       123 ~~~~~i~~~~~v~~~~Gg~~~~~~~~~~~~l~~-~~IlV~TP~~L~~~l~~-------L~~l~~lViDEah~~l~--~~~  192 (1054)
T 1gku_B          123 AEKAGVGTENLIGYYHGRIPKREKENFMQNLRN-FKIVITTTQFLSKHYRE-------LGHFDFIFVDDVDAILK--ASK  192 (1054)
T ss_dssp             HTTTCCSGGGSEEECCSSCCSHHHHHHHHSGGG-CSEEEEEHHHHHHCSTT-------SCCCSEEEESCHHHHHT--STH
T ss_pred             HhhcCCCccceEEEEeCCCChhhHHHHHhhccC-CCEEEEcHHHHHHHHHH-------hccCCEEEEeChhhhhh--ccc
Confidence            988888    89999999988764   444555 99999999999887632       66899999999999987  567


Q ss_pred             HHHHHHHhc-----------CCCCcEEEEeccCcHHHHHHHHHHcCCCeEEEeCCcccccCCceEEEEecCcchHHHHHH
Q 002040          637 QITRIVQNI-----------RPDRQTVLFSATFPRQVEILARKVLNKPVEIQVGGRSVVNKDITQLVEVRPESDRFLRLL  705 (976)
Q Consensus       637 ~i~~il~~~-----------~~~~q~i~~SAT~~~~~~~l~~~~l~~~~~i~~~~~~~~~~~i~q~~~~~~~~~k~~~l~  705 (976)
                      .+..++..+           +...|+++||||+++. ..++..++..+..+.+.........+.+.+.   ...+...|.
T Consensus       193 ~~~~i~~~lgf~~~~~~~~~~~~~q~~l~SAT~t~~-~~~~~~~~~~~~~i~v~~~~~~~~~i~~~~~---~~~k~~~L~  268 (1054)
T 1gku_B          193 NVDKLLHLLGFHYDLKTKSWVGEARGCLMVSTATAK-KGKKAELFRQLLNFDIGSSRITVRNVEDVAV---NDESISTLS  268 (1054)
T ss_dssp             HHHHHHHHTTEEEETTTTEEEECCSSEEEECCCCSC-CCTTHHHHHHHHCCCCSCCEECCCCEEEEEE---SCCCTTTTH
T ss_pred             cHHHHHHHhCcchhhhhhhcccCCceEEEEecCCCc-hhHHHHHhhcceEEEccCcccCcCCceEEEe---chhHHHHHH
Confidence            777777665           3568899999999886 4344444444444444444445556666555   345556666


Q ss_pred             HHHHhhhcCCcEEEEecCHHHHHHHHHHHHHCCCCceeccCCCCHHHHHHHHHHhccCCccEEEe----cCcccccCCCC
Q 002040          706 ELLGEWYEKGKILIFVHSQEKCDALFRDLLKHGYPCLSLHGAKDQTDRESTISDFKSNVCNLLIA----TSVAARGLDVK  781 (976)
Q Consensus       706 ~~l~~~~~~~kvLIF~~s~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLVa----T~v~~~GlDi~  781 (976)
                      .+|...  ++++||||+++..|+.++..|... +.+..+||++.     .+++.|++|.++||||    |+++++|||||
T Consensus       269 ~ll~~~--~~~~LVF~~t~~~a~~l~~~L~~~-~~v~~lhg~~~-----~~l~~F~~G~~~VLVaTas~Tdv~~rGIDip  340 (1054)
T 1gku_B          269 SILEKL--GTGGIIYARTGEEAEEIYESLKNK-FRIGIVTATKK-----GDYEKFVEGEIDHLIGTAHYYGTLVRGLDLP  340 (1054)
T ss_dssp             HHHTTS--CSCEEEEESSHHHHHHHHHTTTTS-SCEEECTTSSS-----HHHHHHHHTSCSEEEEECC------CCSCCT
T ss_pred             HHHhhc--CCCEEEEEcCHHHHHHHHHHHhhc-cCeeEEeccHH-----HHHHHHHcCCCcEEEEecCCCCeeEeccccC
Confidence            666654  578999999999999999999988 99999999984     7889999999999999    99999999999


Q ss_pred             CC-cEEEEeCCC--------------------------------------------------------------------
Q 002040          782 EL-ELVINFDAP--------------------------------------------------------------------  792 (976)
Q Consensus       782 ~v-~~VI~~d~p--------------------------------------------------------------------  792 (976)
                      +| ++||+|++|                                                                    
T Consensus       341 ~VI~~VI~~~~P~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~  420 (1054)
T 1gku_B          341 ERIRFAVFVGCPSFRVTIEDIDSLSPQMVKLLAYLYRNVDEIERLLPAVERHIDEVREILKKVMGKERPQAKDVVVREGE  420 (1054)
T ss_dssp             TTCCEEEEESCCEEEEECSCGGGSCHHHHHHHHTTTSCHHHHHTTCTTTSSCHHHHHHHHHHHHTTSCCSCSSSEEETTE
T ss_pred             CcccEEEEeCCCcccccccccccChHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHHhccccccccceeEeecc
Confidence            95 999999999                                                                    


Q ss_pred             ---CCHHHHHHHhcccCCCCCcc--EEEEEecCCCcCchHHHHHHHhh
Q 002040          793 ---NHYEDYVHRVGRTGRAGRKG--CAITFISEEDAKYSPDLVKALEL  835 (976)
Q Consensus       793 ---~s~~~y~Qr~GR~gR~g~~g--~~~~~~~~~d~~~~~~i~~~l~~  835 (976)
                         .+...|+||+|||||.|..|  .+++|+...+...+..|.+.+..
T Consensus       421 ~~~~~~~~yiQr~GRagR~g~~g~~~g~~~~~~~d~~~~~~l~~~l~~  468 (1054)
T 1gku_B          421 VIFPDLRTYIQGSGRTSRLFAGGLTKGASFLLEDDSELLSAFIERAKL  468 (1054)
T ss_dssp             EEEECHHHHHHHHHTTCCEETTEECCEEEEEECSCHHHHHHHHHHHHT
T ss_pred             eecCcHHHHhhhhchhhhccCCCCceEEEEEEecCHHHHHHHHHHHhh
Confidence               78999999999999987765  48888888888888888888875

>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=100.00  E-value=2.7e-42  Score=421.12  Aligned_cols=318  Identities=18%  Similarity=0.237  Sum_probs=244.5

Q ss_pred             HHHHHHHHHcCCCCCcHHHHHHHHHHhcC------CCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccC
Q 002040          476 SKIMETIRKLNYEKPMPIQAQALPVIMSG------RDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPT  549 (976)
Q Consensus       476 ~~l~~~l~~~~~~~p~~~Q~~~i~~il~g------~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Pt  549 (976)
                      ..+...+..++| .||++|.++|+.|+.+      .++|++|+||||||++|++|++..+..        ++++|||+||
T Consensus       356 ~~~~~~~~~lpf-~lt~~Q~~ai~~I~~~l~~~~~~~~Ll~a~TGSGKTlvall~il~~l~~--------g~qvlvlaPt  426 (780)
T 1gm5_A          356 KLAEEFIKSLPF-KLTNAQKRAHQEIRNDMISEKPMNRLLQGDVGSGKTVVAQLAILDNYEA--------GFQTAFMVPT  426 (780)
T ss_dssp             HHHHHHHHHSSS-CCCHHHHHHHHHHHHHHHSSSCCCCEEECCSSSSHHHHHHHHHHHHHHH--------TSCEEEECSC
T ss_pred             HHHHHHHHhCCC-CCCHHHHHHHHHHHhhccccCCCcEEEEcCCCCCHHHHHHHHHHHHHHc--------CCeEEEEeCc
Confidence            344555678999 8999999999999875      599999999999999999999988753        5789999999


Q ss_pred             HHHHHHHHHHHHHHHhhcCcEEEEeeCCCChHHH---HHHHhcC-CeEEEeCchhHHHHHHhcCCcccccCCceEEEecC
Q 002040          550 RELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQ---ISELKRG-TEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDE  625 (976)
Q Consensus       550 r~La~Q~~~~~~~~~~~~~~~~~~~~gg~~~~~~---~~~l~~~-~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDE  625 (976)
                      ++||.|++..+..++..+++.+.+++|+......   +..+..+ ++|+||||+.|.+.        ..+.++++|||||
T Consensus       427 r~La~Q~~~~l~~~~~~~gi~v~~l~G~~~~~~r~~~~~~l~~g~~~IvVgT~~ll~~~--------~~~~~l~lVVIDE  498 (780)
T 1gm5_A          427 SILAIQHYRRTVESFSKFNIHVALLIGATTPSEKEKIKSGLRNGQIDVVIGTHALIQED--------VHFKNLGLVIIDE  498 (780)
T ss_dssp             HHHHHHHHHHHHHHHTCSSCCEEECCSSSCHHHHHHHHHHHHSSCCCEEEECTTHHHHC--------CCCSCCCEEEEES
T ss_pred             HHHHHHHHHHHHHHhhhcCceEEEEeCCCCHHHHHHHHHHHhcCCCCEEEECHHHHhhh--------hhccCCceEEecc
Confidence            9999999999999998889999999999887654   3445554 89999999877432        4678899999999


Q ss_pred             cccccccCCchHHHHHHHhcCCCCcEEEEeccCcHHHHHHHHHHcCCCeEEEeCCcccccCCceEEEEecCcchHHHHHH
Q 002040          626 ADRMFDMGFEPQITRIVQNIRPDRQTVLFSATFPRQVEILARKVLNKPVEIQVGGRSVVNKDITQLVEVRPESDRFLRLL  705 (976)
Q Consensus       626 ah~~~~~~f~~~i~~il~~~~~~~q~i~~SAT~~~~~~~l~~~~l~~~~~i~~~~~~~~~~~i~q~~~~~~~~~k~~~l~  705 (976)
                      ||++....     ...+.......++|+||||+++....+  .++.......+.........+...   .....+...++
T Consensus       499 aHr~g~~q-----r~~l~~~~~~~~vL~mSATp~p~tl~~--~~~g~~~~s~i~~~p~~r~~i~~~---~~~~~~~~~l~  568 (780)
T 1gm5_A          499 QHRFGVKQ-----REALMNKGKMVDTLVMSATPIPRSMAL--AFYGDLDVTVIDEMPPGRKEVQTM---LVPMDRVNEVY  568 (780)
T ss_dssp             CCCC----------CCCCSSSSCCCEEEEESSCCCHHHHH--HHTCCSSCEEECCCCSSCCCCEEC---CCCSSTHHHHH
T ss_pred             cchhhHHH-----HHHHHHhCCCCCEEEEeCCCCHHHHHH--HHhCCcceeeeeccCCCCcceEEE---EeccchHHHHH
Confidence            99863221     122233345689999999987764333  333333222222211111223221   22233445555


Q ss_pred             HHHHhhh-cCCcEEEEecCH--------HHHHHHHHHHHH---CCCCceeccCCCCHHHHHHHHHHhccCCccEEEecCc
Q 002040          706 ELLGEWY-EKGKILIFVHSQ--------EKCDALFRDLLK---HGYPCLSLHGAKDQTDRESTISDFKSNVCNLLIATSV  773 (976)
Q Consensus       706 ~~l~~~~-~~~kvLIF~~s~--------~~~~~l~~~L~~---~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLVaT~v  773 (976)
                      ..+.... .+++++|||++.        ..+..++..|..   .++.+..+||+|++.+|..++..|++|.++|||||++
T Consensus       569 ~~i~~~l~~g~qvlVf~~~ie~se~l~~~~a~~l~~~L~~~~~~~~~v~~lHG~m~~~eR~~v~~~F~~G~~~ILVaT~v  648 (780)
T 1gm5_A          569 EFVRQEVMRGGQAFIVYPLIEESDKLNVKSAVEMYEYLSKEVFPEFKLGLMHGRLSQEEKDRVMLEFAEGRYDILVSTTV  648 (780)
T ss_dssp             HHHHHHTTTSCCBCCBCCCC--------CHHHHHHHSGGGSCC---CBCCCCSSSCCSCSHHHHHHHTTTSSSBCCCSSC
T ss_pred             HHHHHHHhcCCcEEEEecchhhhhhhhHHHHHHHHHHHHhhhcCCCcEEEEeCCCCHHHHHHHHHHHHCCCCeEEEECCC
Confidence            6555443 456899999965        356788888877   4789999999999999999999999999999999999


Q ss_pred             ccccCCCCCCcEEEEeCCCC-CHHHHHHHhcccCCCCCccEEEEEecC
Q 002040          774 AARGLDVKELELVINFDAPN-HYEDYVHRVGRTGRAGRKGCAITFISE  820 (976)
Q Consensus       774 ~~~GlDi~~v~~VI~~d~p~-s~~~y~Qr~GR~gR~g~~g~~~~~~~~  820 (976)
                      +++|||+|++++||++++|. +...|.|++||+||.|.+|.|++|+++
T Consensus       649 ie~GIDiP~v~~VIi~d~~r~~l~~l~Qr~GRaGR~g~~g~~ill~~~  696 (780)
T 1gm5_A          649 IEVGIDVPRANVMVIENPERFGLAQLHQLRGRVGRGGQEAYCFLVVGD  696 (780)
T ss_dssp             CCSCSCCTTCCEEEBCSCSSSCTTHHHHHHHTSCCSSTTCEEECCCCS
T ss_pred             CCccccCCCCCEEEEeCCCCCCHHHHHHHhcccCcCCCCCEEEEEECC
Confidence            99999999999999999996 688999999999999999999999874

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

Probab=100.00  E-value=3.1e-40  Score=415.52  Aligned_cols=312  Identities=19%  Similarity=0.259  Sum_probs=250.4

Q ss_pred             HcCCCCCcHHHHHHHHHHhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHHH
Q 002040          484 KLNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKF  563 (976)
Q Consensus       484 ~~~~~~p~~~Q~~~i~~il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~~  563 (976)
                      .++|. |+|+|.++|+.++.|+++|+++|||||||++|.++++..+..        ++++||++||++|+.|++..|..+
T Consensus        82 ~~~f~-L~~~Q~eai~~l~~g~~vLV~apTGSGKTlva~lai~~~l~~--------g~rvL~l~PtkaLa~Q~~~~l~~~  152 (1010)
T 2xgj_A           82 TYPFT-LDPFQDTAISCIDRGESVLVSAHTSAGKTVVAEYAIAQSLKN--------KQRVIYTSPIKALSNQKYRELLAE  152 (1010)
T ss_dssp             CCSSC-CCHHHHHHHHHHHHTCEEEEECCTTSCHHHHHHHHHHHHHHT--------TCEEEEEESSHHHHHHHHHHHHHH
T ss_pred             hCCCC-CCHHHHHHHHHHHcCCCEEEECCCCCChHHHHHHHHHHHhcc--------CCeEEEECChHHHHHHHHHHHHHH
Confidence            35665 999999999999999999999999999999999999887642        578999999999999999999987


Q ss_pred             HhhcCcEEEEeeCCCChHHHHHHHhcCCeEEEeCchhHHHHHHhcCCcccccCCceEEEecCcccccccCCchHHHHHHH
Q 002040          564 AKVMGVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMGFEPQITRIVQ  643 (976)
Q Consensus       564 ~~~~~~~~~~~~gg~~~~~~~~~l~~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDEah~~~~~~f~~~i~~il~  643 (976)
                      +.    .+..++|+....       .+++|+||||++|.+++....   ..+..+++|||||||+|.++++...+..++.
T Consensus       153 ~~----~vglltGd~~~~-------~~~~IvV~Tpe~L~~~L~~~~---~~l~~l~lVViDEaH~l~d~~rg~~~e~il~  218 (1010)
T 2xgj_A          153 FG----DVGLMTGDITIN-------PDAGCLVMTTEILRSMLYRGS---EVMREVAWVIFDEVHYMRDKERGVVWEETII  218 (1010)
T ss_dssp             HS----CEEEECSSCEEC-------TTCSEEEEEHHHHHHHHHHTC---TTGGGEEEEEEETGGGGGCTTTHHHHHHHHH
T ss_pred             hC----CEEEEeCCCccC-------CCCCEEEEcHHHHHHHHHcCc---chhhcCCEEEEechhhhcccchhHHHHHHHH
Confidence            64    577788887543       358999999999998887642   4578899999999999999999999999999


Q ss_pred             hcCCCCcEEEEeccCcHHHH--HHHHHHcCCCeEEEeCCcccccCCceEEEEecC---------c---------------
Q 002040          644 NIRPDRQTVLFSATFPRQVE--ILARKVLNKPVEIQVGGRSVVNKDITQLVEVRP---------E---------------  697 (976)
Q Consensus       644 ~~~~~~q~i~~SAT~~~~~~--~l~~~~l~~~~~i~~~~~~~~~~~i~q~~~~~~---------~---------------  697 (976)
                      .+++..|+|+||||+|+...  .+.......+..+......  +..+.+.+....         .               
T Consensus       219 ~l~~~~~il~LSATi~n~~e~a~~l~~~~~~~~~vi~~~~r--p~pl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  296 (1010)
T 2xgj_A          219 LLPDKVRYVFLSATIPNAMEFAEWICKIHSQPCHIVYTNFR--PTPLQHYLFPAHGDGIYLVVDEKSTFREENFQKAMAS  296 (1010)
T ss_dssp             HSCTTCEEEEEECCCTTHHHHHHHHHHHHTSCEEEEEECCC--SSCEEEEEEETTSSCCEEEECTTCCBCHHHHHHHHHT
T ss_pred             hcCCCCeEEEEcCCCCCHHHHHHHHHhhcCCCeEEEecCCC--cccceEEEEecCCcceeeeeccccccchHHHHHHHHH
Confidence            99999999999999987543  2333334555444332211  112222222100         0               


Q ss_pred             -------------------------------chHHHHHHHHHHhhhcCCcEEEEecCHHHHHHHHHHHHHCCCC------
Q 002040          698 -------------------------------SDRFLRLLELLGEWYEKGKILIFVHSQEKCDALFRDLLKHGYP------  740 (976)
Q Consensus       698 -------------------------------~~k~~~l~~~l~~~~~~~kvLIF~~s~~~~~~l~~~L~~~~~~------  740 (976)
                                                     ...+..++..+... ..+++||||+++..|+.++..|...++.      
T Consensus       297 l~~~~~~~~~~~~~~g~~~~~~k~~~~~~~~~~~l~~l~~~l~~~-~~~~~IVF~~sr~~~e~la~~L~~~~~~~~~e~~  375 (1010)
T 2xgj_A          297 ISNQIGDDPNSTDSRGKKGQTYKGGSAKGDAKGDIYKIVKMIWKK-KYNPVIVFSFSKRDCEELALKMSKLDFNSDDEKE  375 (1010)
T ss_dssp             CC------------------------------CHHHHHHHHHHHH-TCCSEEEEESSHHHHHHHHHTTTTSCCCCHHHHH
T ss_pred             HhhhhcccccccccccccccccccccccccchHHHHHHHHHHHhc-CCCCEEEEECCHHHHHHHHHHHHhCCCCChHHHH
Confidence                                           11122333333321 3458999999999999999998765543      


Q ss_pred             ---------------------------------ceeccCCCCHHHHHHHHHHhccCCccEEEecCcccccCCCCCCcEEE
Q 002040          741 ---------------------------------CLSLHGAKDQTDRESTISDFKSNVCNLLIATSVAARGLDVKELELVI  787 (976)
Q Consensus       741 ---------------------------------~~~lhg~~~~~~R~~~~~~F~~g~~~vLVaT~v~~~GlDi~~v~~VI  787 (976)
                                                       +..+||+|++.+|..++..|++|.++|||||+++++|||+|++++||
T Consensus       376 ~i~~~~~~~~~~l~~~d~~l~~~~~l~~~l~~gI~~~Hggl~~~eR~~ve~~F~~G~ikVLVAT~~la~GIDiP~~~vVI  455 (1010)
T 2xgj_A          376 ALTKIFNNAIALLPETDRELPQIKHILPLLRRGIGIHHSGLLPILKEVIEILFQEGFLKVLFATETFSIGLNMPAKTVVF  455 (1010)
T ss_dssp             HHHHHHHHHHTTSCGGGTTCHHHHHHHHHHHHTEEEESTTSCHHHHHHHHHHHHTTCCSEEEEEGGGGGSTTCCBSEEEE
T ss_pred             HHHHHHHHHHHhcchhhhcchhHHHHHHHHhCCeeEECCCCCHHHHHHHHHHHhcCCCcEEEEehHhhccCCCCCceEEE
Confidence                                             67899999999999999999999999999999999999999999999


Q ss_pred             E----eCC----CCCHHHHHHHhcccCCCCC--ccEEEEEecCC
Q 002040          788 N----FDA----PNHYEDYVHRVGRTGRAGR--KGCAITFISEE  821 (976)
Q Consensus       788 ~----~d~----p~s~~~y~Qr~GR~gR~g~--~g~~~~~~~~~  821 (976)
                      +    ||.    |+++..|+||+|||||.|.  .|.||+|+++.
T Consensus       456 ~~~~kfd~~~~rp~s~~~y~Qr~GRAGR~G~d~~G~vi~l~~~~  499 (1010)
T 2xgj_A          456 TSVRKWDGQQFRWVSGGEYIQMSGRAGRRGLDDRGIVIMMIDEK  499 (1010)
T ss_dssp             SCSEEECSSCEEECCHHHHHHHHTTBCCTTTCSSEEEEEEECSC
T ss_pred             eCCcccCCcCCccCCHHHHhHhhhhcccCCCCCceEEEEEECCC
Confidence            9    999    9999999999999999996  59999999864

>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=100.00  E-value=8.7e-41  Score=421.35  Aligned_cols=331  Identities=20%  Similarity=0.277  Sum_probs=211.5

Q ss_pred             cCCCCCcHHHHHHHHHHhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHHHH
Q 002040          485 LNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFA  564 (976)
Q Consensus       485 ~~~~~p~~~Q~~~i~~il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~~~  564 (976)
                      .++..|+|+|.++|+.++.|+++|++++||+|||++|++|++.++...+   .+.++++|||+||++|+.||+..|..++
T Consensus       244 ~~~~~~r~~Q~~ai~~il~g~~~ll~a~TGsGKTl~~~~~i~~~l~~~~---~~~~~~vLvl~Pt~~L~~Q~~~~~~~~~  320 (936)
T 4a2w_A          244 YETKKARSYQIELAQPAINGKNALICAPTGSGKTFVSILICEHHFQNMP---AGRKAKVVFLATKVPVYEQQKNVFKHHF  320 (936)
T ss_dssp             ----CCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHTTTTTCC---SSCCCCEEEECSSHHHHHHHHHHHHHHH
T ss_pred             cCCCCCCHHHHHHHHHHHcCCCEEEEeCCCchHHHHHHHHHHHHHHhcc---ccCCCeEEEEeCCHHHHHHHHHHHHHHh
Confidence            4677899999999999999999999999999999999999998876542   2336789999999999999999999999


Q ss_pred             hhcCcEEEEeeCCCChHHHHHHHhcCCeEEEeCchhHHHHHHhcCCcccccCCceEEEecCcccccccCCchHHH-HHHH
Q 002040          565 KVMGVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMGFEPQIT-RIVQ  643 (976)
Q Consensus       565 ~~~~~~~~~~~gg~~~~~~~~~l~~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDEah~~~~~~f~~~i~-~il~  643 (976)
                      ...++.+..++|+.....+...+..+++|+|+||++|.+++...  ....+..+++|||||||++.+.+....+. .++.
T Consensus       321 ~~~~~~v~~~~G~~~~~~~~~~~~~~~~IvI~Tp~~L~~~l~~~--~~~~l~~~~liViDEaH~~~~~~~~~~i~~~~~~  398 (936)
T 4a2w_A          321 ERQGYSVQGISGENFSNVSVEKVIEDSDIIVVTPQILVNSFEDG--TLTSLSIFTLMIFDECHNTTGNHPYNVLMTRYLE  398 (936)
T ss_dssp             HTTTCCEEEECCC-----CCHHHHHHCSEEEECHHHHHHHHHSS--SCCCGGGCSEEEEETGGGCSTTCHHHHHHHHHHH
T ss_pred             cccCceEEEEECCcchhhHHHHhccCCCEEEecHHHHHHHHHcC--ccccccCCCEEEEECccccCCCccHHHHHHHHHH
Confidence            88899999999999777666666667999999999999988653  22357789999999999988765322222 2222


Q ss_pred             h----cCCCCcEEEEeccCcH-----------HHHHHHH------------------HHcCCCeEEEeCCcccccC----
Q 002040          644 N----IRPDRQTVLFSATFPR-----------QVEILAR------------------KVLNKPVEIQVGGRSVVNK----  686 (976)
Q Consensus       644 ~----~~~~~q~i~~SAT~~~-----------~~~~l~~------------------~~l~~~~~i~~~~~~~~~~----  686 (976)
                      .    ..+..++|+||||++.           .+..+..                  .++..|.............    
T Consensus       399 ~~~~~~~~~~~~l~LSATp~~~~~~~l~~~~~~i~~L~~~L~~~~i~~~~~~~~~l~~~~~~p~~~~~~~~~~~~~~~~~  478 (936)
T 4a2w_A          399 QKFNSASQLPQILGLTASVGVGNAKNIEETIEHICSLCSYLDIQAISTVRENIQELQRFMNKPEIDVRLVKRRIHNPFAA  478 (936)
T ss_dssp             HHHTTCSCCCEEEEEESCCCCTTCCSHHHHHHHHHHHHHHHTCSEEECCCSSHHHHHHHSCCCCEEEEECCCCSCCHHHH
T ss_pred             HhhccCCCcCeEEEecCCcccccchhHHHHHHHHHHHHHhcCCceeecccccHHHHHHhccCCcceEEecccccCcHHHH
Confidence            2    1566899999999852           2222211                  1222222111100000000    


Q ss_pred             --------------------CceEE--EE---------------------------------------------------
Q 002040          687 --------------------DITQL--VE---------------------------------------------------  693 (976)
Q Consensus       687 --------------------~i~q~--~~---------------------------------------------------  693 (976)
                                          .+.+.  ..                                                   
T Consensus       479 ~l~~l~~~i~~~~~~~l~~~~l~~~~~~~~g~~~y~~~l~~l~k~~~~~~l~~~~~~~~~~~~l~~~~~~l~~~~~al~i  558 (936)
T 4a2w_A          479 IISNLMSETEALMRTIAYVDTLSQNSKKDFGTQNYEHWIVVTQRKCRLLQLEDKEEESRICRALFICTEHLRKYNDALII  558 (936)
T ss_dssp             HHHHHHHHHHHHHHHC------------CCSSHHHHHHHHHHHHHHHHCCCSCHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHhhhhhhhccccccchHHHHHHHHHHHHHHHHhcccccchhhHHHHHHHHHHHHHHHHHHHHhh
Confidence                                00000  00                                                   


Q ss_pred             -------------------------------------------------ecCcchHHHHHHHHHHhhh---cCCcEEEEe
Q 002040          694 -------------------------------------------------VRPESDRFLRLLELLGEWY---EKGKILIFV  721 (976)
Q Consensus       694 -------------------------------------------------~~~~~~k~~~l~~~l~~~~---~~~kvLIF~  721 (976)
                                                                       ......|+..|..+|....   ...++||||
T Consensus       559 ~~~~~~~~~~~~l~~~~~~~~~~~~~~~e~~l~~~~~~~~~~l~~~~~~~~~~~~K~~~L~~lL~~~~~~~~~~rvLIF~  638 (936)
T 4a2w_A          559 SEDARIIDALSYLTEFFTNVKNGPYTELEQHLTAKFQEKEPELIALSKDETNENPKLEELVCILDDAYRYNPQTRTLLFA  638 (936)
T ss_dssp             HHHSCHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHHTSTTCCCHHHHHHHHHHHHTTTSCTTCCEEEEE
T ss_pred             hcchhHHHHHHHHHHHHHHHhhccCCHHHHHHHHHHHHHHHHHHHhhhccCCCCHHHHHHHHHHHHHhccCCCCeEEEEe
Confidence                                                             0002445666666776542   457999999


Q ss_pred             cCHHHHHHHHHHHHHC------------CCCceeccCCCCHHHHHHHHHHhcc-CCccEEEecCcccccCCCCCCcEEEE
Q 002040          722 HSQEKCDALFRDLLKH------------GYPCLSLHGAKDQTDRESTISDFKS-NVCNLLIATSVAARGLDVKELELVIN  788 (976)
Q Consensus       722 ~s~~~~~~l~~~L~~~------------~~~~~~lhg~~~~~~R~~~~~~F~~-g~~~vLVaT~v~~~GlDi~~v~~VI~  788 (976)
                      +++.+++.|+.+|...            |..+..+||+|++.+|..++..|++ |.++|||||+++++|||||+|++||+
T Consensus       639 ~t~~~ae~L~~~L~~~~~l~~ik~~~l~G~~~~~~hg~m~~~eR~~il~~Fr~~g~~~VLVaT~~~~eGIDlp~v~~VI~  718 (936)
T 4a2w_A          639 KTRALVSALKKCMEENPILNYIKPGVLMGRGRRDQTTGMTLPSQKGVLDAFKTSKDNRLLIATSVADEGIDIVQCNLVVL  718 (936)
T ss_dssp             SSHHHHHHHHHHHHHCSTTSSCCCEEC----------------------------CCSEEEEECC------CCCCSEEEE
T ss_pred             CCHHHHHHHHHHHhhCccccccceeEEecCCCcccCCCCCHHHHHHHHHHhhccCCeeEEEEeCchhcCCcchhCCEEEE
Confidence            9999999999999986            5566677899999999999999998 99999999999999999999999999


Q ss_pred             eCCCCCHHHHHHHhcccCCCCCccEEEEEecCCC
Q 002040          789 FDAPNHYEDYVHRVGRTGRAGRKGCAITFISEED  822 (976)
Q Consensus       789 ~d~p~s~~~y~Qr~GR~gR~g~~g~~~~~~~~~d  822 (976)
                      ||+|+|+..|+||+|| ||. ..|.||+|++..+
T Consensus       719 yD~p~s~~~~iQr~GR-GR~-~~g~vi~Li~~~t  750 (936)
T 4a2w_A          719 YEYSGNVTKMIQVRGR-GRA-AGSKCILVTSKTE  750 (936)
T ss_dssp             ESCCSCSHHHHCC---------CCCEEEEESCHH
T ss_pred             eCCCCCHHHHHHhcCC-CCC-CCCEEEEEEeCCC
Confidence            9999999999999999 999 6899999998754

>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=100.00  E-value=5e-41  Score=415.27  Aligned_cols=327  Identities=21%  Similarity=0.290  Sum_probs=228.5

Q ss_pred             CCCcHHHHHHHHHHhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHH-HHHHHHHHhh
Q 002040          488 EKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQI-HSDIRKFAKV  566 (976)
Q Consensus       488 ~~p~~~Q~~~i~~il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~-~~~~~~~~~~  566 (976)
                      ..|+|+|.++|+.++.|+++|++++||+|||++|++|++.++...+.  .+.++++|||+||++|+.|| +..+..++..
T Consensus         6 ~~l~~~Q~~~i~~il~g~~~ll~~~TGsGKTl~~~~~i~~~l~~~~~--~~~~~~vlvl~P~~~L~~Q~~~~~l~~~~~~   83 (699)
T 4gl2_A            6 LQLRPYQMEVAQPALEGKNIIICLPTGCGKTRVAVYIAKDHLDKKKK--ASEPGKVIVLVNKVLLVEQLFRKEFQPFLKK   83 (699)
T ss_dssp             -CCCHHHHHHHHHHHSSCCEEECCCTTSCHHHHHHHHHHHHHHHHHH--HTCCCCBCCEESCSHHHHHHHHHTHHHHHTT
T ss_pred             CCccHHHHHHHHHHHhCCCEEEEcCCCCcHHHHHHHHHHHHHHhccc--cCCCCeEEEEECCHHHHHHHHHHHHHHHcCc
Confidence            36999999999999999999999999999999999999988765321  12346799999999999999 9999998765


Q ss_pred             cCcEEEEeeCCCChHHHHHHHhcCCeEEEeCchhHHHHHHhcC---CcccccCCceEEEecCcccccccCCchHHHH-HH
Q 002040          567 MGVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSG---GKITNLRRVTYLVMDEADRMFDMGFEPQITR-IV  642 (976)
Q Consensus       567 ~~~~~~~~~gg~~~~~~~~~l~~~~~Iiv~Tp~~L~~~l~~~~---~~~~~l~~~~~vVlDEah~~~~~~f~~~i~~-il  642 (976)
                       ++.+..++|+.........+..+++|+|+||++|...+....   .....+..+++|||||||++...++...+.. ++
T Consensus        84 -~~~v~~~~g~~~~~~~~~~~~~~~~Ilv~Tp~~L~~~l~~~~~~~~~~~~~~~~~lvViDEaH~~~~~~~~~~i~~~~l  162 (699)
T 4gl2_A           84 -WYRVIGLSGDTQLKISFPEVVKSCDIIISTAQILENSLLNLENGEDAGVQLSDFSLIIIDECHHTNKEAVYNNIMRHYL  162 (699)
T ss_dssp             -TSCEEEEC----CCCCHHHHHHSCSEEEEEHHHHHHHTC--------CCCGGGCSEEEEESGGGCBTTBSSCSHHHHHH
T ss_pred             -CceEEEEeCCcchhhHHHhhhcCCCEEEECHHHHHHHHhccccccccceecccCcEEEEECccccCccchHHHHHHHHH
Confidence             588999999987666656666789999999999998773321   1224678899999999998866544433333 22


Q ss_pred             Hh----cC---------CCCcEEEEeccCcHH-----------HHHHHHHHcCCCeEEEeCC----cccccCCceEEEEe
Q 002040          643 QN----IR---------PDRQTVLFSATFPRQ-----------VEILARKVLNKPVEIQVGG----RSVVNKDITQLVEV  694 (976)
Q Consensus       643 ~~----~~---------~~~q~i~~SAT~~~~-----------~~~l~~~~l~~~~~i~~~~----~~~~~~~i~q~~~~  694 (976)
                      ..    ..         +..++|+||||++..           +..+...+....+......    .............+
T Consensus       163 ~~~~~~~~~~~~~~~~~~~~~il~lTATp~~~~~~~~~~~~~~i~~l~~~l~~~~i~~~~~~~~~l~~~~~~p~~~~~~~  242 (699)
T 4gl2_A          163 MQKLKNNRLKKENKPVIPLPQILGLTASPGVGGATKQAKAEEHILKLCANLDAFTIKTVKENLDQLKNQIQEPCKKFAIA  242 (699)
T ss_dssp             HHHHHHHHHHC----CCCCCEEEEECSCCCCCSCCSHHHHHHHHHHHHHHHTCSCCCCCCTTHHHHHHHSCCCEEEEEEE
T ss_pred             HhhhcccccccccccCCCCCEEEEecccccccccccHHHHHHHHHHHHhhcCCCEEEeecCchHHHhhhcCCCceEEEEc
Confidence            22    11         678999999999862           2222222211011000000    00000000000000


Q ss_pred             cC------------------------------------------------------------------------------
Q 002040          695 RP------------------------------------------------------------------------------  696 (976)
Q Consensus       695 ~~------------------------------------------------------------------------------  696 (976)
                      ..                                                                              
T Consensus       243 ~~~~~~~~~~~l~~l~~~i~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~  322 (699)
T 4gl2_A          243 DATREDPFKEKLLEIMTRIQTYCQMSPMSDFGTQPYEQWAIQMEKKAAKEGNRKERVCAEHLRKYNEALQINDTIRMIDA  322 (699)
T ss_dssp             C-----CHHHHHHHHHHHHHHHHTCCCCSCSSSHHHHHHHHHHHHHHHHHTCTTTHHHHHHHHHHHHHHHHHHHSCHHHH
T ss_pred             ccccCChHHHHHHHHHHHHHHHhccCcchhccchHHHHHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            00                                                                              


Q ss_pred             --------------------------------------------------------cchHHHHHHHHHHhhh---c-CCc
Q 002040          697 --------------------------------------------------------ESDRFLRLLELLGEWY---E-KGK  716 (976)
Q Consensus       697 --------------------------------------------------------~~~k~~~l~~~l~~~~---~-~~k  716 (976)
                                                                              ...|+..|+.+|....   . .++
T Consensus       323 ~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~l~~~~~~~~~~~~k~~~L~~~L~~~~~~~~~~~~  402 (699)
T 4gl2_A          323 YTHLETFYNEEKDKKFAVIEDDLKKPLKLDETDRFLMTLFFENNKMLKRLAENPEYENEKLTKLRNTIMEQYTRTEESAR  402 (699)
T ss_dssp             HHHHHHHHHHHHHHHC------------CCHHHHHHHHHHHHHHHHHHHHHTCCC----CSSCSHHHHHHHHHHSSSCCC
T ss_pred             HHHHHHHHHHHHhhhccccccccccccccchhHHHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHHHhcCCCCCc
Confidence                                                                    1122223334444322   2 679


Q ss_pred             EEEEecCHHHHHHHHHHHHHC------CCCceeccCC--------CCHHHHHHHHHHhccCCccEEEecCcccccCCCCC
Q 002040          717 ILIFVHSQEKCDALFRDLLKH------GYPCLSLHGA--------KDQTDRESTISDFKSNVCNLLIATSVAARGLDVKE  782 (976)
Q Consensus       717 vLIF~~s~~~~~~l~~~L~~~------~~~~~~lhg~--------~~~~~R~~~~~~F~~g~~~vLVaT~v~~~GlDi~~  782 (976)
                      +||||+++..++.|+..|...      |+.+..+||+        |++.+|..++..|++|.++|||||+++++|||+|+
T Consensus       403 ~IVF~~s~~~~~~l~~~L~~~~~l~~~g~~~~~lhg~~~~~~~~~~~~~eR~~~~~~F~~g~~~VLVaT~~~~~GIDip~  482 (699)
T 4gl2_A          403 GIIFTKTRQSAYALSQWITENEKFAEVGVKAHHLIGAGHSSEFKPMTQNEQKEVISKFRTGKINLLIATTVAEEGLDIKE  482 (699)
T ss_dssp             EEEECSCHHHHHHHHHHHHSSCSCC-----CEECCCSCCCTTCCCCCHHHHHHHHHHHCC---CCSEEECSCCTTSCCCS
T ss_pred             EEEEECcHHHHHHHHHHHHhCccccccCcceEEEECCCCccCCCCCCHHHHHHHHHHHhcCCCcEEEEccccccCCcccc
Confidence            999999999999999999987      8999999999        99999999999999999999999999999999999


Q ss_pred             CcEEEEeCCCCCHHHHHHHhcccCCCCCccEEEEEecC
Q 002040          783 LELVINFDAPNHYEDYVHRVGRTGRAGRKGCAITFISE  820 (976)
Q Consensus       783 v~~VI~~d~p~s~~~y~Qr~GR~gR~g~~g~~~~~~~~  820 (976)
                      +++||+||+|+|+..|+||+||+||.|   .+++|+..
T Consensus       483 v~~VI~~d~p~s~~~~~Qr~GRArr~g---~~~~l~~~  517 (699)
T 4gl2_A          483 CNIVIRYGLVTNEIAMVQARGRARADE---STYVLVAH  517 (699)
T ss_dssp             CCCCEEESCCCCHHHHHHHHTTSCSSS---CEEEEEEE
T ss_pred             CCEEEEeCCCCCHHHHHHHcCCCCCCC---ceEEEEEe
Confidence            999999999999999999999976654   44444443

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

Probab=100.00  E-value=4.7e-39  Score=404.97  Aligned_cols=308  Identities=19%  Similarity=0.254  Sum_probs=242.5

Q ss_pred             cCCCCCcHHHHHHHHHHhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHHHH
Q 002040          485 LNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFA  564 (976)
Q Consensus       485 ~~~~~p~~~Q~~~i~~il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~~~  564 (976)
                      ++|. |+|+|.++|+.++.|+++|++||||||||++|+++++..+.        .++++||++||++|+.|++..+..++
T Consensus        36 ~~f~-l~~~Q~~aI~~il~g~~vlv~apTGsGKTlv~~~~i~~~~~--------~g~~vlvl~PtraLa~Q~~~~l~~~~  106 (997)
T 4a4z_A           36 WPFE-LDTFQKEAVYHLEQGDSVFVAAHTSAGKTVVAEYAIAMAHR--------NMTKTIYTSPIKALSNQKFRDFKETF  106 (997)
T ss_dssp             CSSC-CCHHHHHHHHHHHTTCEEEEECCTTSCSHHHHHHHHHHHHH--------TTCEEEEEESCGGGHHHHHHHHHTTC
T ss_pred             CCCC-CCHHHHHHHHHHHcCCCEEEEECCCCcHHHHHHHHHHHHHh--------cCCeEEEEeCCHHHHHHHHHHHHHHc
Confidence            4554 89999999999999999999999999999999999887654        26789999999999999999998865


Q ss_pred             hhcCcEEEEeeCCCChHHHHHHHhcCCeEEEeCchhHHHHHHhcCCcccccCCceEEEecCcccccccCCchHHHHHHHh
Q 002040          565 KVMGVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMGFEPQITRIVQN  644 (976)
Q Consensus       565 ~~~~~~~~~~~gg~~~~~~~~~l~~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDEah~~~~~~f~~~i~~il~~  644 (976)
                      .  ++.+..++|+....       ..++|+|+||++|.+++....   ..+..+++|||||||++.+++|...+..++..
T Consensus       107 ~--~~~v~~l~G~~~~~-------~~~~IlV~Tpe~L~~~l~~~~---~~l~~l~lvViDEaH~l~d~~~g~~~e~ii~~  174 (997)
T 4a4z_A          107 D--DVNIGLITGDVQIN-------PDANCLIMTTEILRSMLYRGA---DLIRDVEFVIFDEVHYVNDQDRGVVWEEVIIM  174 (997)
T ss_dssp             ----CCEEEECSSCEEC-------TTSSEEEEEHHHHHHHHHHTC---SGGGGEEEEEECCTTCCCTTCTTCCHHHHHHH
T ss_pred             C--CCeEEEEeCCCccC-------CCCCEEEECHHHHHHHHHhCc---hhhcCCCEEEEECcccccccchHHHHHHHHHh
Confidence            3  67888899987532       458999999999998886643   45778999999999999999999999999999


Q ss_pred             cCCCCcEEEEeccCcHHHHHHHHHHc---CCCeEEE-eCCcccccCCceEEE----------------------------
Q 002040          645 IRPDRQTVLFSATFPRQVEILARKVL---NKPVEIQ-VGGRSVVNKDITQLV----------------------------  692 (976)
Q Consensus       645 ~~~~~q~i~~SAT~~~~~~~l~~~~l---~~~~~i~-~~~~~~~~~~i~q~~----------------------------  692 (976)
                      +++..|+|+||||+++... ++..+.   ..++.+. ......   .+.+.+                            
T Consensus       175 l~~~v~iIlLSAT~~n~~e-f~~~l~~~~~~~~~vi~~~~r~~---pl~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~l  250 (997)
T 4a4z_A          175 LPQHVKFILLSATVPNTYE-FANWIGRTKQKNIYVISTPKRPV---PLEINIWAKKELIPVINQNSEFLEANFRKHKEIL  250 (997)
T ss_dssp             SCTTCEEEEEECCCTTHHH-HHHHHHHHHTCCEEEEECSSCSS---CEEEEEEETTEEEEEECTTCCBCHHHHHHHHHHH
T ss_pred             cccCCCEEEEcCCCCChHH-HHHHHhcccCCceEEEecCCCCc---cceEEEecCCcchhcccchhhhhHHHHHHHHHHh
Confidence            9999999999999987653 333322   1222211 111111   111111                            


Q ss_pred             -----------------------------------------------------------------EecCcchHHHHHHHH
Q 002040          693 -----------------------------------------------------------------EVRPESDRFLRLLEL  707 (976)
Q Consensus       693 -----------------------------------------------------------------~~~~~~~k~~~l~~~  707 (976)
                                                                                       .......++..++..
T Consensus       251 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~rg~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~li~~  330 (997)
T 4a4z_A          251 NGESAKGAPSKTDNGRGGSTARGGRGGSNTRDGRGGRGNSTRGGANRGGSRGAGAIGSNKRKFFTQDGPSKKTWPEIVNY  330 (997)
T ss_dssp             C-----------------------------------------------------------------CCCCTTHHHHHHHH
T ss_pred             hccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccchhHHHHHHHH
Confidence                                                                             001122345556666


Q ss_pred             HHhhhcCCcEEEEecCHHHHHHHHHHHHHCCC---------------------------------------CceeccCCC
Q 002040          708 LGEWYEKGKILIFVHSQEKCDALFRDLLKHGY---------------------------------------PCLSLHGAK  748 (976)
Q Consensus       708 l~~~~~~~kvLIF~~s~~~~~~l~~~L~~~~~---------------------------------------~~~~lhg~~  748 (976)
                      |... ..+++||||+++..|+.++..|...++                                       .+..+||+|
T Consensus       331 l~~~-~~~~~IVF~~sr~~~e~la~~L~~~~~~~~~e~~~i~~~~~~~~~~l~~~d~~l~~~~~l~~~l~~gi~~~H~gl  409 (997)
T 4a4z_A          331 LRKR-ELLPMVVFVFSKKRCEEYADWLEGINFCNNKEKSQIHMFIEKSITRLKKEDRDLPQILKTRSLLERGIAVHHGGL  409 (997)
T ss_dssp             HHHT-TCCSEEEECSCHHHHHHHHHTTTTCCCCCHHHHHHHHHHHHHHHTTSCHHHHTCHHHHHHHHHHTTTEEEECTTS
T ss_pred             HHhC-CCCCEEEEECCHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHhcchhhhcchhHHHHHHHhhcCeeeecCCC
Confidence            6543 456999999999999999999977665                                       478999999


Q ss_pred             CHHHHHHHHHHhccCCccEEEecCcccccCCCCCCcEEEEeCCCC---------CHHHHHHHhcccCCCC--CccEEEEE
Q 002040          749 DQTDRESTISDFKSNVCNLLIATSVAARGLDVKELELVINFDAPN---------HYEDYVHRVGRTGRAG--RKGCAITF  817 (976)
Q Consensus       749 ~~~~R~~~~~~F~~g~~~vLVaT~v~~~GlDi~~v~~VI~~d~p~---------s~~~y~Qr~GR~gR~g--~~g~~~~~  817 (976)
                      ++.+|..++..|.+|.++|||||+++++|||+|+ .+||+++.|.         ++..|+|++|||||.|  ..|.|+++
T Consensus       410 ~~~~R~~v~~~F~~G~~kVLvAT~~~a~GIDiP~-~~VVi~~~~k~dg~~~~~~s~~~y~Qr~GRAGR~G~~~~G~vi~l  488 (997)
T 4a4z_A          410 LPIVKELIEILFSKGFIKVLFATETFAMGLNLPT-RTVIFSSIRKHDGNGLRELTPGEFTQMAGRAGRRGLDSTGTVIVM  488 (997)
T ss_dssp             CHHHHHHHHHHHHTTCCSEEEECTHHHHSCCCCC-SEEEESCSEEEETTEEEECCHHHHHHHHGGGCCTTTCSSEEEEEE
T ss_pred             CHHHHHHHHHHHHCCCCcEEEEchHhhCCCCCCC-ceEEEeccccccCccCCCCCHHHHhHHhcccccCCCCcceEEEEe
Confidence            9999999999999999999999999999999999 5555555544         9999999999999998  56778877


Q ss_pred             ec
Q 002040          818 IS  819 (976)
Q Consensus       818 ~~  819 (976)
                      +.
T Consensus       489 ~~  490 (997)
T 4a4z_A          489 AY  490 (997)
T ss_dssp             CC
T ss_pred             cC
Confidence            74

>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=100.00  E-value=3.1e-40  Score=396.23  Aligned_cols=309  Identities=17%  Similarity=0.182  Sum_probs=240.3

Q ss_pred             CCCCcHHHHHHHHHHhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHHHHhh
Q 002040          487 YEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKV  566 (976)
Q Consensus       487 ~~~p~~~Q~~~i~~il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~~~~~  566 (976)
                      ...|+|+|+.+++.++.++++|++|+||||||++|++|++..+..       .++++|||+||++||.|++..+.     
T Consensus       169 ~~~~lpiq~~~i~~l~~g~dvlv~a~TGSGKT~~~~lpil~~l~~-------~~~~vLvl~PtreLa~Qi~~~l~-----  236 (618)
T 2whx_A          169 ERIGEPDYEVDEDIFRKKRLTIMDLHPGAGKTKRILPSIVREALK-------RRLRTLILAPTRVVAAEMEEALR-----  236 (618)
T ss_dssp             CCCCCCCCCCCGGGGSTTCEEEECCCTTSSTTTTHHHHHHHHHHH-------TTCCEEEEESSHHHHHHHHHHTT-----
T ss_pred             cccCCCccccCHHHHhcCCeEEEEcCCCCCHHHHHHHHHHHHHHh-------CCCeEEEEcChHHHHHHHHHHhc-----
Confidence            467889988899999999999999999999999999999988765       36789999999999999998775     


Q ss_pred             cCcEEEEeeCCCChHHHHHHHhcCCeEEEeCchhHHHHHHhcCCcccccCCceEEEecCcccccccCCchHHHHHHHhcC
Q 002040          567 MGVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMGFEPQITRIVQNIR  646 (976)
Q Consensus       567 ~~~~~~~~~gg~~~~~~~~~l~~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDEah~~~~~~f~~~i~~il~~~~  646 (976)
                       +..+.. .+....    .....+..|.++|.+.|...+...    ..+.++++|||||||+| +++|...+..++..+.
T Consensus       237 -~~~v~~-~~~~l~----~~~tp~~~i~~~t~~~l~~~l~~~----~~l~~~~~iViDEah~~-~~~~~~~~~~i~~~l~  305 (618)
T 2whx_A          237 -GLPIRY-QTPAVK----SDHTGREIVDLMCHATFTTRLLSS----TRVPNYNLIVMDEAHFT-DPCSVAARGYISTRVE  305 (618)
T ss_dssp             -TSCEEE-CCTTSS----CCCCSSSCEEEEEHHHHHHHHHHC----SSCCCCSEEEEESTTCC-SHHHHHHHHHHHHHHH
T ss_pred             -CCceeE-ecccce----eccCCCceEEEEChHHHHHHHhcc----ccccCCeEEEEECCCCC-CccHHHHHHHHHHHhc
Confidence             233332 121100    011124577788888887766543    35788999999999998 6778878888877764


Q ss_pred             -CCCcEEEEeccCcHHHHHHHHHHcCCCeEEEeCCcccccCCceEEEEecCcchHHHHHHHHHHhhhcCCcEEEEecCHH
Q 002040          647 -PDRQTVLFSATFPRQVEILARKVLNKPVEIQVGGRSVVNKDITQLVEVRPESDRFLRLLELLGEWYEKGKILIFVHSQE  725 (976)
Q Consensus       647 -~~~q~i~~SAT~~~~~~~l~~~~l~~~~~i~~~~~~~~~~~i~q~~~~~~~~~k~~~l~~~l~~~~~~~kvLIF~~s~~  725 (976)
                       ++.|+|+||||++..+..++.   .++..+.+... .             ....+..++..|..  ..+++||||+++.
T Consensus       306 ~~~~q~il~SAT~~~~~~~~~~---~~~~~~~v~~~-~-------------~~~~~~~ll~~l~~--~~~~~LVF~~s~~  366 (618)
T 2whx_A          306 MGEAAAIFMTATPPGSTDPFPQ---SNSPIEDIERE-I-------------PERSWNTGFDWITD--YQGKTVWFVPSIK  366 (618)
T ss_dssp             HTSCEEEEECSSCTTCCCSSCC---CSSCEEEEECC-C-------------CSSCCSSSCHHHHH--CCSCEEEECSSHH
T ss_pred             ccCccEEEEECCCchhhhhhhc---cCCceeeeccc-C-------------CHHHHHHHHHHHHh--CCCCEEEEECChh
Confidence             789999999999876432221   12322222211 0             01111223333333  3679999999999


Q ss_pred             HHHHHHHHHHHCCCCceeccCCCCHHHHHHHHHHhccCCccEEEecCcccccCCCCCCcEE-------------------
Q 002040          726 KCDALFRDLLKHGYPCLSLHGAKDQTDRESTISDFKSNVCNLLIATSVAARGLDVKELELV-------------------  786 (976)
Q Consensus       726 ~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLVaT~v~~~GlDi~~v~~V-------------------  786 (976)
                      .|+.++..|...++.+..+||.    +|..+++.|++|.++|||||+++++||||| +++|                   
T Consensus       367 ~a~~l~~~L~~~g~~v~~lhg~----~R~~~l~~F~~g~~~VLVaTdv~~rGiDi~-v~~VId~g~~~~P~~~~~~~~~~  441 (618)
T 2whx_A          367 AGNDIANCLRKSGKRVIQLSRK----TFDTEYPKTKLTDWDFVVTTDISEMGANFR-AGRVIDPRRCLKPVILTDGPERV  441 (618)
T ss_dssp             HHHHHHHHHHHTTCCEEEECTT----THHHHTTHHHHSCCSEEEECGGGGTTCCCC-CSEEEECCEEEEEEEECSSSCEE
T ss_pred             HHHHHHHHHHHcCCcEEEEChH----HHHHHHHhhcCCCcEEEEECcHHHcCcccC-ceEEEECcceecceecccCCCce
Confidence            9999999999999999999984    688899999999999999999999999997 8888                   


Q ss_pred             -EEeCCCCCHHHHHHHhcccCCCCC-ccEEEEEec---CCCcCchHHHHHHHhhccCCCCh
Q 002040          787 -INFDAPNHYEDYVHRVGRTGRAGR-KGCAITFIS---EEDAKYSPDLVKALELSEQVVPD  842 (976)
Q Consensus       787 -I~~d~p~s~~~y~Qr~GR~gR~g~-~g~~~~~~~---~~d~~~~~~i~~~l~~~~~~vp~  842 (976)
                       |+|++|.+..+|+||+||+||.|. .|.||+|++   +.+...+..|...+......+|.
T Consensus       442 ~i~~d~P~s~~~yiQR~GRaGR~g~~~G~ai~l~~~~~~~d~~~l~~le~~i~l~~~~~~~  502 (618)
T 2whx_A          442 ILAGPIPVTPASAAQRRGRIGRNPAQEDDQYVFSGDPLKNDEDHAHWTEAKMLLDNIYTPE  502 (618)
T ss_dssp             EEEEEEECCHHHHHHHHTTSSCCTTCCCEEEEECSCCCCCCTTCHHHHHHHHHHTTCCCTT
T ss_pred             EEcccccCCHHHHHHhccccCCCCCCCCeEEEEccCCchhhHHHHHHHHhHhccccccCCc
Confidence             778889999999999999999965 899999998   78888888998888776666654

>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=100.00  E-value=1.5e-37  Score=332.22  Aligned_cols=238  Identities=47%  Similarity=0.838  Sum_probs=219.9

Q ss_pred             CCHHHHHHHHhhcCceeccCCCCCcccccccCCCCHHHHHHHHHcCCCCCcHHHHHHHHHHhcCCCEEEEcCCCCchHHH
Q 002040          441 MTPEEVSAYRKQLELKIHGKDVPKPIKTWHQTGLTSKIMETIRKLNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLA  520 (976)
Q Consensus       441 ~~~~~~~~~~~~~~i~~~g~~~p~pi~~~~~~~l~~~l~~~l~~~~~~~p~~~Q~~~i~~il~g~d~i~~a~TGsGKT~~  520 (976)
                      ++.+++..++..+.+.+.|..+|.|+.+|.++++++.+...|..+||..|+|+|.++|+.++.|+++|+++|||||||++
T Consensus         3 ~~~~~~~~~~~~~~i~~~~~~~p~~~~~f~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~g~~~l~~apTGsGKT~~   82 (242)
T 3fe2_A            3 RTAQEVETYRRSKEITVRGHNCPKPVLNFYEANFPANVMDVIARQNFTEPTAIQAQGWPVALSGLDMVGVAQTGSGKTLS   82 (242)
T ss_dssp             ---CHHHHHHHHHTEEEESSCCCCCCSSTTTTTCCHHHHHHHHTTTCCSCCHHHHHHHHHHHHTCCEEEEECTTSCHHHH
T ss_pred             CCHHHHHHHHhcCceEEeCCCCCCccCCHhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCcCHHHHH
Confidence            46678899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHHHHhhcCcEEEEeeCCCChHHHHHHHhcCCeEEEeCchh
Q 002040          521 FVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQISELKRGTEIVVCTPGR  600 (976)
Q Consensus       521 ~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~~~~~~~~~~~~~~gg~~~~~~~~~l~~~~~Iiv~Tp~~  600 (976)
                      |++|++.++...+......++++|||+||++||.|++..+..++...++.+.+++||.....+...+..+++|+|+||++
T Consensus        83 ~~l~~l~~l~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~I~v~Tp~~  162 (242)
T 3fe2_A           83 YLLPAIVHINHQPFLERGDGPICLVLAPTRELAQQVQQVAAEYCRACRLKSTCIYGGAPKGPQIRDLERGVEICIATPGR  162 (242)
T ss_dssp             HHHHHHHHHHTSCCCCTTCCCSEEEECSSHHHHHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHCCSEEEECHHH
T ss_pred             HHHHHHHHHHhccccccCCCCEEEEEeCcHHHHHHHHHHHHHHHhhcCceEEEEECCCChHHHHHHhcCCCCEEEECHHH
Confidence            99999999987655555678899999999999999999999999999999999999999999888888899999999999


Q ss_pred             HHHHHHhcCCcccccCCceEEEecCcccccccCCchHHHHHHHhcCCCCcEEEEeccCcHHHHHHHHHHcCCCeEEEeCC
Q 002040          601 MIDILCTSGGKITNLRRVTYLVMDEADRMFDMGFEPQITRIVQNIRPDRQTVLFSATFPRQVEILARKVLNKPVEIQVGG  680 (976)
Q Consensus       601 L~~~l~~~~~~~~~l~~~~~vVlDEah~~~~~~f~~~i~~il~~~~~~~q~i~~SAT~~~~~~~l~~~~l~~~~~i~~~~  680 (976)
                      |.+++....   ..+.++.+|||||||+|++++|...+..++..+++..|+|+||||+|+.+..++..++.+|+.+.++.
T Consensus       163 l~~~l~~~~---~~~~~~~~lViDEah~l~~~~~~~~~~~i~~~~~~~~q~~~~SAT~~~~~~~~~~~~l~~~~~i~~~~  239 (242)
T 3fe2_A          163 LIDFLECGK---TNLRRTTYLVLDEADRMLDMGFEPQIRKIVDQIRPDRQTLMWSATWPKEVRQLAEDFLKDYIHINIGA  239 (242)
T ss_dssp             HHHHHHHTS---CCCTTCCEEEETTHHHHHHTTCHHHHHHHHTTSCSSCEEEEEESCCCHHHHHHHHHHCSSCEEEEECC
T ss_pred             HHHHHHcCC---CCcccccEEEEeCHHHHhhhCcHHHHHHHHHhCCccceEEEEEeecCHHHHHHHHHHCCCCEEEEecC
Confidence            999987643   46788999999999999999999999999999999999999999999999999999999999988764


Q ss_pred             c
Q 002040          681 R  681 (976)
Q Consensus       681 ~  681 (976)
                      .
T Consensus       240 ~  240 (242)
T 3fe2_A          240 L  240 (242)
T ss_dssp             -
T ss_pred             C
Confidence            3

>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=100.00  E-value=1.8e-37  Score=406.56  Aligned_cols=341  Identities=17%  Similarity=0.208  Sum_probs=257.7

Q ss_pred             CCHHHHHHHHHcCCCCCcHHHHHHHHHHhc-CCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHH
Q 002040          474 LTSKIMETIRKLNYEKPMPIQAQALPVIMS-GRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTREL  552 (976)
Q Consensus       474 l~~~l~~~l~~~~~~~p~~~Q~~~i~~il~-g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~L  552 (976)
                      |.....+.|...+|..++|+|.++++.++. +.+++++||||||||++|.+||+.++...      .+.++|||+||++|
T Consensus       911 L~~~~~e~l~~~~f~~fnpiQ~q~~~~l~~~~~nvlv~APTGSGKTliaelail~~l~~~------~~~kavyi~P~raL  984 (1724)
T 4f92_B          911 LRNSAFESLYQDKFPFFNPIQTQVFNTVYNSDDNVFVGAPTGSGKTICAEFAILRMLLQS------SEGRCVYITPMEAL  984 (1724)
T ss_dssp             SCCHHHHTTTTTTCSBCCHHHHHHHHHHHSCCSCEEEECCTTSCCHHHHHHHHHHHHHHC------TTCCEEEECSCHHH
T ss_pred             ccCHHHHHHHHhcCCCCCHHHHHHHHHHhcCCCcEEEEeCCCCCchHHHHHHHHHHHHhC------CCCEEEEEcChHHH
Confidence            445666777778899999999999999985 56899999999999999999999998764      35689999999999


Q ss_pred             HHHHHHHHHH-HHhhcCcEEEEeeCCCChHHHHHHHhcCCeEEEeCchhHHHHHHhcCCcccccCCceEEEecCcccccc
Q 002040          553 VQQIHSDIRK-FAKVMGVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFD  631 (976)
Q Consensus       553 a~Q~~~~~~~-~~~~~~~~~~~~~gg~~~~~~~~~l~~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDEah~~~~  631 (976)
                      |.|++..|.. |...+|+.|+.++|+......   ...+++|+||||++|..++.. +.....++++++|||||+|.|.+
T Consensus       985 a~q~~~~~~~~f~~~~g~~V~~ltGd~~~~~~---~~~~~~IiV~TPEkld~llr~-~~~~~~l~~v~lvViDE~H~l~d 1060 (1724)
T 4f92_B          985 AEQVYMDWYEKFQDRLNKKVVLLTGETSTDLK---LLGKGNIIISTPEKWDILSRR-WKQRKNVQNINLFVVDEVHLIGG 1060 (1724)
T ss_dssp             HHHHHHHHHHHHTTTSCCCEEECCSCHHHHHH---HHHHCSEEEECHHHHHHHHTT-TTTCHHHHSCSEEEECCGGGGGS
T ss_pred             HHHHHHHHHHHhchhcCCEEEEEECCCCcchh---hcCCCCEEEECHHHHHHHHhC-cccccccceeeEEEeechhhcCC
Confidence            9999999976 556689999999998654332   223589999999998665543 32334578999999999998876


Q ss_pred             cCCchHHHHHH-------HhcCCCCcEEEEeccCcHHHHHHHHHHcCCCeEEEeCCcccccCCceEEEEecCcch---HH
Q 002040          632 MGFEPQITRIV-------QNIRPDRQTVLFSATFPRQVEILARKVLNKPVEIQVGGRSVVNKDITQLVEVRPESD---RF  701 (976)
Q Consensus       632 ~~f~~~i~~il-------~~~~~~~q~i~~SAT~~~~~~~l~~~~l~~~~~i~~~~~~~~~~~i~q~~~~~~~~~---k~  701 (976)
                      . .+..+..++       ..+.+..|+|+||||+++. ..++..+...+..+........+..+...+.......   ++
T Consensus      1061 ~-rg~~le~il~rl~~i~~~~~~~~riI~lSATl~N~-~dla~WL~~~~~~~~~~~~~~RPvpL~~~i~~~~~~~~~~~~ 1138 (1724)
T 4f92_B         1061 E-NGPVLEVICSRMRYISSQIERPIRIVALSSSLSNA-KDVAHWLGCSATSTFNFHPNVRPVPLELHIQGFNISHTQTRL 1138 (1724)
T ss_dssp             T-THHHHHHHHHHHHHHHHTTSSCCEEEEEESCBTTH-HHHHHHHTCCSTTEEECCGGGCSSCEEEEEEEECCCSHHHHH
T ss_pred             C-CCccHHHHHHHHHHHHhhcCCCceEEEEeCCCCCH-HHHHHHhCCCCCCeEEeCCCCCCCCeEEEEEeccCCCchhhh
Confidence            3 455544443       3456789999999999864 4455554443322222223333333444433322221   11


Q ss_pred             ----HHHHHHHHhhhcCCcEEEEecCHHHHHHHHHHHHHC----------------------------------CCCcee
Q 002040          702 ----LRLLELLGEWYEKGKILIFVHSQEKCDALFRDLLKH----------------------------------GYPCLS  743 (976)
Q Consensus       702 ----~~l~~~l~~~~~~~kvLIF~~s~~~~~~l~~~L~~~----------------------------------~~~~~~  743 (976)
                          ..+...+......+++||||+++..|..++..|...                                  ...++.
T Consensus      1139 ~~~~~~~~~~i~~~~~~~~~lVF~~sR~~~~~~A~~L~~~~~~~~~~~~~~~~~~~~l~~~l~~~~d~~L~~~l~~GIa~ 1218 (1724)
T 4f92_B         1139 LSMAKPVYHAITKHSPKKPVIVFVPSRKQTRLTAIDILTTCAADIQRQRFLHCTEKDLIPYLEKLSDSTLKETLLNGVGY 1218 (1724)
T ss_dssp             HTTHHHHHHHHHHHCSSSCEEEEESSHHHHHHHHHHHHHHHHHTTCTTTTBCSCHHHHHHHHTTCCCHHHHHHHHTTEEE
T ss_pred             hhhcchHHHHHHHhcCCCCeeeeCCCHHHHHHHHHHHHHHHhhccchhhhhcccHHHHHHHHhhcccHHHHHHHhCCEEE
Confidence                223445555666789999999999999888776431                                  235788


Q ss_pred             ccCCCCHHHHHHHHHHhccCCccEEEecCcccccCCCCCCcEEEE----eC------CCCCHHHHHHHhcccCCCCC--c
Q 002040          744 LHGAKDQTDRESTISDFKSNVCNLLIATSVAARGLDVKELELVIN----FD------APNHYEDYVHRVGRTGRAGR--K  811 (976)
Q Consensus       744 lhg~~~~~~R~~~~~~F~~g~~~vLVaT~v~~~GlDi~~v~~VI~----~d------~p~s~~~y~Qr~GR~gR~g~--~  811 (976)
                      +||+|++.+|..+...|.+|.++|||||+++++|||+|...+||.    |+      .|.++.+|+||+|||||.|.  .
T Consensus      1219 hHagL~~~~R~~VE~lF~~G~i~VLvaT~tlA~GVnlPa~~VVI~~~~~~dg~~~~~~~~s~~~~~Qm~GRAGR~g~d~~ 1298 (1724)
T 4f92_B         1219 LHEGLSPMERRLVEQLFSSGAIQVVVASRSLCWGMNVAAHLVIIMDTQYYNGKIHAYVDYPIYDVLQMVGHANRPLQDDE 1298 (1724)
T ss_dssp             ECTTSCHHHHHHHHHHHHHTSBCEEEEEGGGSSSCCCCBSEEEEECSEEEETTTTEEEECCHHHHHHHHTTBCCTTTCSC
T ss_pred             ECCCCCHHHHHHHHHHHHCCCCeEEEEChHHHcCCCCCccEEEEecCccccCcccccCCCCHHHHHHhhccccCCCCCCc
Confidence            999999999999999999999999999999999999999998883    33      36789999999999999986  6


Q ss_pred             cEEEEEecCCCcCch
Q 002040          812 GCAITFISEEDAKYS  826 (976)
Q Consensus       812 g~~~~~~~~~d~~~~  826 (976)
                      |.|++|+.+.+..++
T Consensus      1299 G~avll~~~~~~~~~ 1313 (1724)
T 4f92_B         1299 GRCVIMCQGSKKDFF 1313 (1724)
T ss_dssp             EEEEEEEEGGGHHHH
T ss_pred             eEEEEEecchHHHHH
Confidence            999999887654443

>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=100.00  E-value=9.6e-39  Score=392.72  Aligned_cols=338  Identities=19%  Similarity=0.259  Sum_probs=254.6

Q ss_pred             CCcccccccCCCCHHHHHHHHHcCCCCCcHHHHHHHHHHhc-CCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCC
Q 002040          463 PKPIKTWHQTGLTSKIMETIRKLNYEKPMPIQAQALPVIMS-GRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGP  541 (976)
Q Consensus       463 p~pi~~~~~~~l~~~l~~~l~~~~~~~p~~~Q~~~i~~il~-g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~  541 (976)
                      +.++..|..+++++.+.+.+...+ ..|+++|.++|+.++. +++++++|+||||||+  ++|++......   ..+.++
T Consensus        68 ~~~~~~f~~~~l~~~~~~~l~~r~-~lP~~~q~~~i~~~l~~~~~vii~gpTGSGKTt--llp~ll~~~~~---~~~~g~  141 (773)
T 2xau_A           68 DGKINPFTGREFTPKYVDILKIRR-ELPVHAQRDEFLKLYQNNQIMVFVGETGSGKTT--QIPQFVLFDEM---PHLENT  141 (773)
T ss_dssp             HSSBCTTTCSBCCHHHHHHHHHHT-TSGGGGGHHHHHHHHHHCSEEEEECCTTSSHHH--HHHHHHHHHHC---GGGGTC
T ss_pred             cCCCCCccccCCCHHHHHHHHHhh-cCChHHHHHHHHHHHhCCCeEEEECCCCCCHHH--HHHHHHHHhcc---ccCCCc
Confidence            456788999999999999999888 7899999999998875 4679999999999999  45544222111   112367


Q ss_pred             eEEEEccCHHHHHHHHHHHHHHHhhcCcEEEEeeCCCChHHHHHHHhcCCeEEEeCchhHHHHHHhcCCcccccCCceEE
Q 002040          542 VGLIMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYL  621 (976)
Q Consensus       542 ~vLIl~Ptr~La~Q~~~~~~~~~~~~~~~~~~~~gg~~~~~~~~~l~~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~v  621 (976)
                      .++|++|+++||.|++..+...   +++.+...+|+......  ....+++|+|+|||+|...+...    ..+..+++|
T Consensus       142 ~ilvl~P~r~La~q~~~~l~~~---~~~~v~~~vG~~i~~~~--~~~~~~~I~v~T~G~l~r~l~~~----~~l~~~~~l  212 (773)
T 2xau_A          142 QVACTQPRRVAAMSVAQRVAEE---MDVKLGEEVGYSIRFEN--KTSNKTILKYMTDGMLLREAMED----HDLSRYSCI  212 (773)
T ss_dssp             EEEEEESCHHHHHHHHHHHHHH---TTCCBTTTEEEEETTEE--ECCTTCSEEEEEHHHHHHHHHHS----TTCTTEEEE
T ss_pred             eEEecCchHHHHHHHHHHHHHH---hCCchhheecceecccc--ccCCCCCEEEECHHHHHHHHhhC----ccccCCCEE
Confidence            8999999999999998766543   34443333332211100  11235799999999999887653    458899999


Q ss_pred             EecCcc-cccccCCchHHHHHHHhcCCCCcEEEEeccCcHHHHHHHHHHcCCCeEEEeCCcccccCCceEEEEecCcchH
Q 002040          622 VMDEAD-RMFDMGFEPQITRIVQNIRPDRQTVLFSATFPRQVEILARKVLNKPVEIQVGGRSVVNKDITQLVEVRPESDR  700 (976)
Q Consensus       622 VlDEah-~~~~~~f~~~i~~il~~~~~~~q~i~~SAT~~~~~~~l~~~~l~~~~~i~~~~~~~~~~~i~q~~~~~~~~~k  700 (976)
                      |||||| ++++..+...+...+....++.|+|+||||++..  .+ ..++..+..+.+.+...   .+.+.+.......+
T Consensus       213 IlDEah~R~ld~d~~~~~l~~l~~~~~~~~iIl~SAT~~~~--~l-~~~~~~~~vi~v~gr~~---pv~~~~~~~~~~~~  286 (773)
T 2xau_A          213 ILDEAHERTLATDILMGLLKQVVKRRPDLKIIIMSATLDAE--KF-QRYFNDAPLLAVPGRTY---PVELYYTPEFQRDY  286 (773)
T ss_dssp             EECSGGGCCHHHHHHHHHHHHHHHHCTTCEEEEEESCSCCH--HH-HHHTTSCCEEECCCCCC---CEEEECCSSCCSCH
T ss_pred             EecCccccccchHHHHHHHHHHHHhCCCceEEEEeccccHH--HH-HHHhcCCCcccccCccc---ceEEEEecCCchhH
Confidence            999999 4776554444444444556789999999999753  33 44556555555554433   34444443444444


Q ss_pred             HHHHHHHHHhh---hcCCcEEEEecCHHHHHHHHHHHHH-----------CCCCceeccCCCCHHHHHHHHHHhc-----
Q 002040          701 FLRLLELLGEW---YEKGKILIFVHSQEKCDALFRDLLK-----------HGYPCLSLHGAKDQTDRESTISDFK-----  761 (976)
Q Consensus       701 ~~~l~~~l~~~---~~~~kvLIF~~s~~~~~~l~~~L~~-----------~~~~~~~lhg~~~~~~R~~~~~~F~-----  761 (976)
                      ...++..+...   ...+++||||+++..++.++..|..           .++.+..+||+|++.+|..+++.|.     
T Consensus       287 ~~~~l~~l~~~~~~~~~g~iLVF~~~~~~i~~l~~~L~~~~~~l~~~~~~~~~~v~~lhg~l~~~eR~~v~~~f~~~~~~  366 (773)
T 2xau_A          287 LDSAIRTVLQIHATEEAGDILLFLTGEDEIEDAVRKISLEGDQLVREEGCGPLSVYPLYGSLPPHQQQRIFEPAPESHNG  366 (773)
T ss_dssp             HHHHHHHHHHHHHHSCSCEEEEECSCHHHHHHHHHHHHHHHHHHHHHHCCCCEEEEEECTTCCHHHHGGGGSCCCCCSSS
T ss_pred             HHHHHHHHHHHHHhcCCCCEEEECCCHHHHHHHHHHHHHHHHhhcccccCCCeEEEEeCCCCCHHHHHHHHhhcccccCC
Confidence            44444433332   2478999999999999999999975           5788999999999999999999999     


Q ss_pred             cCCccEEEecCcccccCCCCCCcEEEEeCC------------------CCCHHHHHHHhcccCCCCCccEEEEEecCCC
Q 002040          762 SNVCNLLIATSVAARGLDVKELELVINFDA------------------PNHYEDYVHRVGRTGRAGRKGCAITFISEED  822 (976)
Q Consensus       762 ~g~~~vLVaT~v~~~GlDi~~v~~VI~~d~------------------p~s~~~y~Qr~GR~gR~g~~g~~~~~~~~~d  822 (976)
                      +|.++|||||+++++|||||++.+||++++                  |.+...|+||+|||||. .+|.||+|+++.+
T Consensus       367 ~g~~kVlVAT~iae~GidIp~v~~VId~g~~k~~~yd~~~g~~~L~~~p~S~~s~~QR~GRaGR~-~~G~~~~l~~~~~  444 (773)
T 2xau_A          367 RPGRKVVISTNIAETSLTIDGIVYVVDPGFSKQKVYNPRIRVESLLVSPISKASAQQRAGRAGRT-RPGKCFRLYTEEA  444 (773)
T ss_dssp             SCCEEEEEECTHHHHTCCCTTEEEEEECSEEEEEEEETTTTEEEEEEEECCHHHHHHHHHGGGSS-SSEEEEESSCHHH
T ss_pred             CCceEEEEeCcHHHhCcCcCCeEEEEeCCCccceeeccccCccccccccCCHHHHHhhccccCCC-CCCEEEEEecHHH
Confidence            999999999999999999999999999887                  89999999999999999 7999999997643

>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=100.00  E-value=3.8e-39  Score=375.74  Aligned_cols=309  Identities=17%  Similarity=0.162  Sum_probs=225.2

Q ss_pred             CCCCCcHHHHHHHHHHhcCCCE-EEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHHHH
Q 002040          486 NYEKPMPIQAQALPVIMSGRDC-IGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFA  564 (976)
Q Consensus       486 ~~~~p~~~Q~~~i~~il~g~d~-i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~~~  564 (976)
                      |+.+|+|+|. +||.++.++++ |++|+||||||++|++|++.++..       .++++|||+||++||.|++..+.   
T Consensus         1 G~~q~~~iq~-~i~~~l~~~~~~lv~a~TGsGKT~~~~~~~l~~~~~-------~~~~~lvl~Ptr~La~Q~~~~l~---   69 (451)
T 2jlq_A            1 GSAMGEPDYE-VDEDIFRKKRLTIMDLHPGAGKTKRILPSIVREALL-------RRLRTLILAPTRVVAAEMEEALR---   69 (451)
T ss_dssp             CCCCCSCCCC-CCGGGGSTTCEEEECCCTTSSCCTTHHHHHHHHHHH-------TTCCEEEEESSHHHHHHHHHHTT---
T ss_pred             CCCCCCCcHH-HHHHHHhcCCeEEEECCCCCCHhhHHHHHHHHHHHh-------cCCcEEEECCCHHHHHHHHHHhc---
Confidence            6788999985 79999999887 888999999999999999987664       35789999999999999998774   


Q ss_pred             hhcCcEEEEeeCCCChHHHHHHHhcCCeEEEeCchhHHHHHHhcCCcccccCCceEEEecCcccccccCCchHHHHHHH-
Q 002040          565 KVMGVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMGFEPQITRIVQ-  643 (976)
Q Consensus       565 ~~~~~~~~~~~gg~~~~~~~~~l~~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDEah~~~~~~f~~~i~~il~-  643 (976)
                         |+.+....+....     ....+..|.|+|++.|...+...    ..+.++++|||||||++ +.++...+..+.. 
T Consensus        70 ---g~~v~~~~~~~~~-----~~~~~~~i~~~t~~~l~~~l~~~----~~l~~~~~iViDEah~~-~~~~~~~~~~~~~~  136 (451)
T 2jlq_A           70 ---GLPIRYQTPAVKS-----DHTGREIVDLMCHATFTTRLLSS----TRVPNYNLIVMDEAHFT-DPCSVAARGYISTR  136 (451)
T ss_dssp             ---TSCEEECCTTCSC-----CCCSSCCEEEEEHHHHHHHHHHC----SCCCCCSEEEEETTTCC-SHHHHHHHHHHHHH
T ss_pred             ---Cceeeeeeccccc-----cCCCCceEEEEChHHHHHHhhCc----ccccCCCEEEEeCCccC-CcchHHHHHHHHHh
Confidence               3333322221111     11234679999999998877643    45788999999999976 3333333333322 


Q ss_pred             hcCCCCcEEEEeccCcHHHHHHHHHHcCCCeEEEeCCcccccCCceEEEEecCcchHHHHHHHHHHhhhcCCcEEEEecC
Q 002040          644 NIRPDRQTVLFSATFPRQVEILARKVLNKPVEIQVGGRSVVNKDITQLVEVRPESDRFLRLLELLGEWYEKGKILIFVHS  723 (976)
Q Consensus       644 ~~~~~~q~i~~SAT~~~~~~~l~~~~l~~~~~i~~~~~~~~~~~i~q~~~~~~~~~k~~~l~~~l~~~~~~~kvLIF~~s  723 (976)
                      ...++.|+|+||||+|..+..   .+..++..+.+. ...+..             .+..+...+..  ..+++||||++
T Consensus       137 ~~~~~~~~i~~SAT~~~~~~~---~~~~~~~~~~~~-~~~p~~-------------~~~~~~~~l~~--~~~~~lVF~~s  197 (451)
T 2jlq_A          137 VEMGEAAAIFMTATPPGSTDP---FPQSNSPIEDIE-REIPER-------------SWNTGFDWITD--YQGKTVWFVPS  197 (451)
T ss_dssp             HHTTSCEEEEECSSCTTCCCS---SCCCSSCEEEEE-CCCCSS-------------CCSSSCHHHHH--CCSCEEEECSS
T ss_pred             hcCCCceEEEEccCCCccchh---hhcCCCceEecC-ccCCch-------------hhHHHHHHHHh--CCCCEEEEcCC
Confidence            345689999999999875322   122333333322 111100             00111223333  36799999999


Q ss_pred             HHHHHHHHHHHHHCCCCceeccCCCCHHHHHHHHHHhccCCccEEEecCcccccCCCCCCcEEEEeC-------------
Q 002040          724 QEKCDALFRDLLKHGYPCLSLHGAKDQTDRESTISDFKSNVCNLLIATSVAARGLDVKELELVINFD-------------  790 (976)
Q Consensus       724 ~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLVaT~v~~~GlDi~~v~~VI~~d-------------  790 (976)
                      +..++.++..|...|+.+..+||.+.    ..++..|++|.++|||||+++++|||||+ ++||+|+             
T Consensus       198 ~~~a~~l~~~L~~~g~~~~~lh~~~~----~~~~~~f~~g~~~vLVaT~v~~~GiDip~-~~VI~~~~~~~~~~d~~~~~  272 (451)
T 2jlq_A          198 IKAGNDIANCLRKSGKRVIQLSRKTF----DTEYPKTKLTDWDFVVTTDISEMGANFRA-GRVIDPRRCLKPVILTDGPE  272 (451)
T ss_dssp             HHHHHHHHHHHHTTTCCEEEECTTTH----HHHGGGGGSSCCSEEEECGGGGSSCCCCC-SEEEECCEEEEEEEECSSSC
T ss_pred             HHHHHHHHHHHHHcCCeEEECCHHHH----HHHHHhhccCCceEEEECCHHHhCcCCCC-CEEEECCCcccccccccccc
Confidence            99999999999999999999999765    57899999999999999999999999999 9999999             


Q ss_pred             -------CCCCHHHHHHHhcccCCCCC-ccEEEEEecCCCc---CchHHHHHHHhhccCCCCh
Q 002040          791 -------APNHYEDYVHRVGRTGRAGR-KGCAITFISEEDA---KYSPDLVKALELSEQVVPD  842 (976)
Q Consensus       791 -------~p~s~~~y~Qr~GR~gR~g~-~g~~~~~~~~~d~---~~~~~i~~~l~~~~~~vp~  842 (976)
                             .|.+...|+||+|||||.|. .|.|++|+...+.   .....+...+...+..+|.
T Consensus       273 ~l~~~~~~p~s~~~y~Qr~GRaGR~g~~~g~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~  335 (451)
T 2jlq_A          273 RVILAGPIPVTPASAAQRRGRIGRNPAQEDDQYVFSGDPLKNDEDHAHWTEAKMLLDNIYTPE  335 (451)
T ss_dssp             EEEEEEEEECCHHHHHHHHTTSSCCTTCCCEEEEECSCCCCCCTTCHHHHHHHHHHTTCCCTT
T ss_pred             eeeecccccCCHHHHHHhccccCCCCCCCccEEEEeCCchhhcchhHHHHHHHHHHhcCCChh
Confidence                   99999999999999999998 8999888754322   2222223334445555554

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

Probab=100.00  E-value=6.7e-39  Score=381.30  Aligned_cols=311  Identities=17%  Similarity=0.132  Sum_probs=236.5

Q ss_pred             CCCcHHHHHHHHHHhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHHHHhhc
Q 002040          488 EKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVM  567 (976)
Q Consensus       488 ~~p~~~Q~~~i~~il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~~~~~~  567 (976)
                      ..|+|+|.++++.++.++++|++++||+|||++|+++++..+...       ++++||||||++|+.||+..|.++....
T Consensus       112 ~~l~~~Q~~ai~~~~~~~~~ll~~~tGsGKT~~~~~~~~~~~~~~-------~~~vlvl~P~~~L~~Q~~~~~~~~~~~~  184 (510)
T 2oca_A          112 IEPHWYQKDAVFEGLVNRRRILNLPTSAGRSLIQALLARYYLENY-------EGKILIIVPTTALTTQMADDFVDYRLFS  184 (510)
T ss_dssp             ECCCHHHHHHHHHHHHHSEEEEECCSTTTHHHHHHHHHHHHHHHC-------SSEEEEEESSHHHHHHHHHHHHHTTSSC
T ss_pred             CCCCHHHHHHHHHHHhcCCcEEEeCCCCCHHHHHHHHHHHHHhCC-------CCeEEEEECcHHHHHHHHHHHHHhhcCC
Confidence            479999999999999999999999999999999999998877542       3489999999999999999999886656


Q ss_pred             CcEEEEeeCCCChHHHHHHHhcCCeEEEeCchhHHHHHHhcCCcccccCCceEEEecCcccccccCCchHHHHHHHhcCC
Q 002040          568 GVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMGFEPQITRIVQNIRP  647 (976)
Q Consensus       568 ~~~~~~~~gg~~~~~~~~~l~~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDEah~~~~~~f~~~i~~il~~~~~  647 (976)
                      ++.+..++|+.....+   +..+++|+|+||+.|...      ....+.++++|||||||++..    ..+..++..+.+
T Consensus       185 ~~~v~~~~~~~~~~~~---~~~~~~I~i~T~~~l~~~------~~~~~~~~~liIiDE~H~~~~----~~~~~il~~~~~  251 (510)
T 2oca_A          185 HAMIKKIGGGASKDDK---YKNDAPVVVGTWQTVVKQ------PKEWFSQFGMMMNDECHLATG----KSISSIISGLNN  251 (510)
T ss_dssp             GGGEEECGGGCCTTGG---GCTTCSEEEEEHHHHTTS------CGGGGGGEEEEEEETGGGCCH----HHHHHHGGGCTT
T ss_pred             ccceEEEecCCccccc---cccCCcEEEEeHHHHhhc------hhhhhhcCCEEEEECCcCCCc----ccHHHHHHhccc
Confidence            6788889998766554   345689999999976432      124567899999999999764    567778888888


Q ss_pred             CCcEEEEeccCcHHHHHH-HHHHcCCCeEEEeCCcc------cccCCceEEEEecC---------------------cch
Q 002040          648 DRQTVLFSATFPRQVEIL-ARKVLNKPVEIQVGGRS------VVNKDITQLVEVRP---------------------ESD  699 (976)
Q Consensus       648 ~~q~i~~SAT~~~~~~~l-~~~~l~~~~~i~~~~~~------~~~~~i~q~~~~~~---------------------~~~  699 (976)
                      ..++|+||||++.....+ ....+..+..+.+....      .....+.......+                     ...
T Consensus       252 ~~~~l~lSATp~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  331 (510)
T 2oca_A          252 CMFKFGLSGSLRDGKANIMQYVGMFGEIFKPVTTSKLMEDGQVTELKINSIFLRYPDEFTTKLKGKTYQEEIKIITGLSK  331 (510)
T ss_dssp             CCEEEEEESCGGGCSSCHHHHHHHHCSEECCCCCC---------CCEEEEEEEECCHHHHHHHTTCCHHHHHHHHHTCHH
T ss_pred             CcEEEEEEeCCCCCcccHHHhHHhhCCeEEeeCHHHHhhCCcCCCceEEEEeecCChHHhccccccchHHHHHHHhccHH
Confidence            899999999997654221 11112223222221110      11111111111111                     112


Q ss_pred             HHHHHHHHHHhhhc-CC-cEEEEecCHHHHHHHHHHHHHCCCCceeccCCCCHHHHHHHHHHhccCCccEEEec-Ccccc
Q 002040          700 RFLRLLELLGEWYE-KG-KILIFVHSQEKCDALFRDLLKHGYPCLSLHGAKDQTDRESTISDFKSNVCNLLIAT-SVAAR  776 (976)
Q Consensus       700 k~~~l~~~l~~~~~-~~-kvLIF~~s~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLVaT-~v~~~  776 (976)
                      +...+..++..... ++ ++||||+ ...+..|+..|...+..+..+||+|++.+|..++..|.+|.++||||| +++++
T Consensus       332 ~~~~l~~~l~~~~~~~~~~~ivf~~-~~~~~~l~~~L~~~~~~v~~~~g~~~~~~r~~i~~~f~~g~~~vLv~T~~~~~~  410 (510)
T 2oca_A          332 RNKWIAKLAIKLAQKDENAFVMFKH-VSHGKAIFDLIKNEYDKVYYVSGEVDTETRNIMKTLAENGKGIIIVASYGVFST  410 (510)
T ss_dssp             HHHHHHHHHHHHHTTTCEEEEEESS-HHHHHHHHHHHHTTCSSEEEESSSTTHHHHHHHHHHHHHCCSCEEEEEHHHHHH
T ss_pred             HHHHHHHHHHHHHhcCCCeEEEEec-HHHHHHHHHHHHHcCCCeEEEECCCCHHHHHHHHHHHhCCCCCEEEEEcChhhc
Confidence            23334455544432 33 4555555 899999999999988899999999999999999999999999999999 99999


Q ss_pred             cCCCCCCcEEEEeCCCCCHHHHHHHhcccCCCCCccEEEEEec
Q 002040          777 GLDVKELELVINFDAPNHYEDYVHRVGRTGRAGRKGCAITFIS  819 (976)
Q Consensus       777 GlDi~~v~~VI~~d~p~s~~~y~Qr~GR~gR~g~~g~~~~~~~  819 (976)
                      |||+|++++||++++|+++..|+|++||+||.|+.|.++++++
T Consensus       411 GiDip~v~~vi~~~~~~s~~~~~Q~~GR~gR~g~~~~~v~i~~  453 (510)
T 2oca_A          411 GISVKNLHHVVLAHGVKSKIIVLQTIGRVLRKHGSKTIATVWD  453 (510)
T ss_dssp             SCCCCSEEEEEESSCCCSCCHHHHHHHHHHTTTCCCCCCEEEE
T ss_pred             ccccccCcEEEEeCCCCCHHHHHHHHhcccccCCCCceEEEEE
Confidence            9999999999999999999999999999999998774555544

>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=100.00  E-value=5.2e-37  Score=402.29  Aligned_cols=339  Identities=24%  Similarity=0.322  Sum_probs=254.4

Q ss_pred             CCCCCcHHHHHHHHHHh-cCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCC---CCCCCCeEEEEccCHHHHHHHHHHHH
Q 002040          486 NYEKPMPIQAQALPVIM-SGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPV---AAGDGPVGLIMAPTRELVQQIHSDIR  561 (976)
Q Consensus       486 ~~~~p~~~Q~~~i~~il-~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~---~~~~~~~vLIl~Ptr~La~Q~~~~~~  561 (976)
                      ||..|+++|.+++|.++ +++|+|++||||||||++|.++|+..+......   ....+.++|||+|+++||.|++..|.
T Consensus        76 g~~~ln~iQs~~~~~al~~~~N~lv~APTGsGKTlva~l~il~~l~~~~~~~~~~~~~~~k~lyiaP~kALa~e~~~~l~  155 (1724)
T 4f92_B           76 GFKTLNRIQSKLYRAALETDENLLLCAPTGAGKTNVALMCMLREIGKHINMDGTINVDDFKIIYIAPMRSLVQEMVGSFG  155 (1724)
T ss_dssp             TCSBCCHHHHHTHHHHHTCCCCEEEECCTTSCCHHHHHHHHHHHHGGGCCTTSSCCTTSCEEEEECSSHHHHHHHHHHHH
T ss_pred             CCCCCCHHHHHHHHHHHcCCCcEEEEeCCcchHHHHHHHHHHHHHHhhccccccccCCCCEEEEECCHHHHHHHHHHHHH
Confidence            78999999999999987 578999999999999999999999998764321   12357789999999999999999999


Q ss_pred             HHHhhcCcEEEEeeCCCChHHHHHHHhcCCeEEEeCchhHHHHHHhcCCcccccCCceEEEecCcccccccCCchHHHHH
Q 002040          562 KFAKVMGVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMGFEPQITRI  641 (976)
Q Consensus       562 ~~~~~~~~~~~~~~gg~~~~~~~~~l~~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDEah~~~~~~f~~~i~~i  641 (976)
                      +.+..+|+.|..++|+......   ...+++|+||||+++- .+.+.+.....+..+++|||||+|.+.+ ..+..+..+
T Consensus       156 ~~~~~~gi~V~~~tGd~~~~~~---~~~~~~IlVtTpEkld-~llr~~~~~~~l~~v~~vIiDEvH~l~d-~RG~~lE~~  230 (1724)
T 4f92_B          156 KRLATYGITVAELTGDHQLCKE---EISATQIIVCTPEKWD-IITRKGGERTYTQLVRLIILDEIHLLHD-DRGPVLEAL  230 (1724)
T ss_dssp             HHHTTTTCCEEECCSSCSSCCT---TGGGCSEEEECHHHHH-HHTTSSTTHHHHTTEEEEEETTGGGGGS-TTHHHHHHH
T ss_pred             HHHhhCCCEEEEEECCCCCCcc---ccCCCCEEEECHHHHH-HHHcCCccchhhcCcCEEEEecchhcCC-ccHHHHHHH
Confidence            9999999999999998765332   1245899999999984 4443332234578899999999996654 555555544


Q ss_pred             H-------HhcCCCCcEEEEeccCcHHHHHHHHHHcCCC-eEEEeCCcccccCCceEEEEecCcch---HHH----HHHH
Q 002040          642 V-------QNIRPDRQTVLFSATFPRQVEILARKVLNKP-VEIQVGGRSVVNKDITQLVEVRPESD---RFL----RLLE  706 (976)
Q Consensus       642 l-------~~~~~~~q~i~~SAT~~~~~~~l~~~~l~~~-~~i~~~~~~~~~~~i~q~~~~~~~~~---k~~----~l~~  706 (976)
                      +       ..+++..|+|+||||+|+. ..++..+...+ ..+.+......+..+.+.+.......   .+.    .+..
T Consensus       231 l~rl~~~~~~~~~~~riI~LSATl~N~-~dvA~wL~~~~~~~~~~~~~~~RPvpL~~~~~~~~~~~~~~~~~~~~~~~~~  309 (1724)
T 4f92_B          231 VARAIRNIEMTQEDVRLIGLSATLPNY-EDVATFLRVDPAKGLFYFDNSFRPVPLEQTYVGITEKKAIKRFQIMNEIVYE  309 (1724)
T ss_dssp             HHHHHHHHHHHTCCCEEEEEECSCTTH-HHHHHHTTCCHHHHEEECCGGGCSSCEEEECCEECCCCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhCCCCCcEEEEecccCCH-HHHHHHhCCCCCCCeEEECCCCccCccEEEEeccCCcchhhhhHHHHHHHHH
Confidence            3       3457889999999999864 44554433322 11122222333334444443222221   122    2233


Q ss_pred             HHHhhhcCCcEEEEecCHHHHHHHHHHHHHC-------------------------------------CCCceeccCCCC
Q 002040          707 LLGEWYEKGKILIFVHSQEKCDALFRDLLKH-------------------------------------GYPCLSLHGAKD  749 (976)
Q Consensus       707 ~l~~~~~~~kvLIF~~s~~~~~~l~~~L~~~-------------------------------------~~~~~~lhg~~~  749 (976)
                      .+......+++||||+++..|+.++..|...                                     ...++.+||+|+
T Consensus       310 ~v~~~~~~~~~LVF~~sR~~~~~~A~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~Gva~HHagL~  389 (1724)
T 4f92_B          310 KIMEHAGKNQVLVFVHSRKETGKTARAIRDMCLEKDTLGLFLREGSASTEVLRTEAEQCKNLELKDLLPYGFAIHHAGMT  389 (1724)
T ss_dssp             HHTTCCSSCCEEEECSSTTTTHHHHHHHHHHHHHTTSTTCCSSCCTTCSSHHHHTTSCCSTHHHHHHTTTTEEEECSSSC
T ss_pred             HHHHHhcCCcEEEECCCHHHHHHHHHHHHHHHhhccchhhhcccchhHHHHHHhhhcccccHHHHHHhhcCEEEEcCCCC
Confidence            3444445679999999999998888877542                                     234788999999


Q ss_pred             HHHHHHHHHHhccCCccEEEecCcccccCCCCCCcEEEE----eCC------CCCHHHHHHHhcccCCCCC--ccEEEEE
Q 002040          750 QTDRESTISDFKSNVCNLLIATSVAARGLDVKELELVIN----FDA------PNHYEDYVHRVGRTGRAGR--KGCAITF  817 (976)
Q Consensus       750 ~~~R~~~~~~F~~g~~~vLVaT~v~~~GlDi~~v~~VI~----~d~------p~s~~~y~Qr~GR~gR~g~--~g~~~~~  817 (976)
                      +.+|..+...|++|.++|||||++++.|||+|...+||.    |++      |.++.+|+||+|||||.|.  .|.++++
T Consensus       390 ~~~R~~vE~~F~~G~i~vlvaTsTLa~GVNlPa~~vVI~~~~~~~~~~~~~~~ls~~~~~Qm~GRAGR~g~d~~G~~ii~  469 (1724)
T 4f92_B          390 RVDRTLVEDLFADKHIQVLVSTATLAWGVNLPAHTVIIKGTQVYSPEKGRWTELGALDILQMLGRAGRPQYDTKGEGILI  469 (1724)
T ss_dssp             THHHHHHHHHHHTTCCCEEEECHHHHHHSCCCBSEEEEECCEEEETTTTEEEECCHHHHHHHHTTBSCTTTCSCEEEEEE
T ss_pred             HHHHHHHHHHHHCCCCeEEEEcchhHhhCCCCCceEEEeCCEEecCcCCCcccCCHHHHHHhhhhccCCCCCCccEEEEE
Confidence            999999999999999999999999999999999999985    554      5689999999999999874  6999999


Q ss_pred             ecCCCcCchHHHH
Q 002040          818 ISEEDAKYSPDLV  830 (976)
Q Consensus       818 ~~~~d~~~~~~i~  830 (976)
                      ++..+..+...++
T Consensus       470 ~~~~~~~~~~~ll  482 (1724)
T 4f92_B          470 TSHGELQYYLSLL  482 (1724)
T ss_dssp             EESTTCCHHHHHT
T ss_pred             ecchhHHHHHHHH
Confidence            8887766555444

>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=100.00  E-value=5.1e-38  Score=364.57  Aligned_cols=291  Identities=20%  Similarity=0.223  Sum_probs=204.2

Q ss_pred             HHhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHHHHhhcCcEEEEeeCCCC
Q 002040          500 VIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSG  579 (976)
Q Consensus       500 ~il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~~~~~~~~~~~~~~gg~~  579 (976)
                      ++++|+++|++|+||||||++|++|++..+..       .++++|||+||++||.|++..+..+    +  +....+.. 
T Consensus         4 ~l~~g~~vlv~a~TGSGKT~~~l~~~l~~~~~-------~~~~~lil~Ptr~La~Q~~~~l~~~----~--v~~~~~~~-   69 (440)
T 1yks_A            4 MLKKGMTTVLDFHPGAGKTRRFLPQILAECAR-------RRLRTLVLAPTRVVLSEMKEAFHGL----D--VKFHTQAF-   69 (440)
T ss_dssp             TTSTTCEEEECCCTTSSTTTTHHHHHHHHHHH-------TTCCEEEEESSHHHHHHHHHHTTTS----C--EEEESSCC-
T ss_pred             HhhCCCCEEEEcCCCCCHHHHHHHHHHHHHHh-------cCCeEEEEcchHHHHHHHHHHHhcC----C--eEEecccc-
Confidence            35789999999999999999999999988765       2678999999999999999887642    2  22211111 


Q ss_pred             hHHHHHHHhcCCeEEEeCchhHHHHHHhc-----CCcccccCCceEEEecCcccccccCCchHHHHHHHhc-CCCCcEEE
Q 002040          580 VAQQISELKRGTEIVVCTPGRMIDILCTS-----GGKITNLRRVTYLVMDEADRMFDMGFEPQITRIVQNI-RPDRQTVL  653 (976)
Q Consensus       580 ~~~~~~~l~~~~~Iiv~Tp~~L~~~l~~~-----~~~~~~l~~~~~vVlDEah~~~~~~f~~~i~~il~~~-~~~~q~i~  653 (976)
                                   -+|+||+++++++...     ......+.++++|||||||++ +.+|...+..+...+ ++..|+|+
T Consensus        70 -------------~~v~Tp~~l~~~l~~~~l~~~~~~~~~~~~l~~vViDEah~~-~~~~~~~~~~~~~~~~~~~~~~l~  135 (440)
T 1yks_A           70 -------------SAHGSGREVIDAMCHATLTYRMLEPTRVVNWEVIIMDEAHFL-DPASIAARGWAAHRARANESATIL  135 (440)
T ss_dssp             -------------CCCCCSSCCEEEEEHHHHHHHHTSSSCCCCCSEEEETTTTCC-SHHHHHHHHHHHHHHHTTSCEEEE
T ss_pred             -------------eeccCCccceeeecccchhHhhhCcccccCccEEEEECcccc-CcchHHHHHHHHHHhccCCceEEE
Confidence                         0366666554322111     011134788999999999997 333333333332222 46799999


Q ss_pred             EeccCcHHHHHHHHHHcCCCeEEEeCCcccccCCceEEEEecCcchHHHHHHHHHHhhhcCCcEEEEecCHHHHHHHHHH
Q 002040          654 FSATFPRQVEILARKVLNKPVEIQVGGRSVVNKDITQLVEVRPESDRFLRLLELLGEWYEKGKILIFVHSQEKCDALFRD  733 (976)
Q Consensus       654 ~SAT~~~~~~~l~~~~l~~~~~i~~~~~~~~~~~i~q~~~~~~~~~k~~~l~~~l~~~~~~~kvLIF~~s~~~~~~l~~~  733 (976)
                      ||||+++.+..++..  ..++.              ......+. .....++..|..  ..+++||||+++..++.++..
T Consensus       136 ~SAT~~~~~~~~~~~--~~~~~--------------~~~~~~~~-~~~~~~~~~l~~--~~~~~lVF~~s~~~a~~l~~~  196 (440)
T 1yks_A          136 MTATPPGTSDEFPHS--NGEIE--------------DVQTDIPS-EPWNTGHDWILA--DKRPTAWFLPSIRAANVMAAS  196 (440)
T ss_dssp             ECSSCTTCCCSSCCC--SSCEE--------------EEECCCCS-SCCSSSCHHHHH--CCSCEEEECSCHHHHHHHHHH
T ss_pred             EeCCCCchhhhhhhc--CCCee--------------EeeeccCh-HHHHHHHHHHHh--cCCCEEEEeCCHHHHHHHHHH
Confidence            999998764322111  11111              11011111 111112233333  267999999999999999999


Q ss_pred             HHHCCCCceeccCCCCHHHHHHHHHHhccCCccEEEecCcccccCCCCCCcEEEE-------------------eCCCCC
Q 002040          734 LLKHGYPCLSLHGAKDQTDRESTISDFKSNVCNLLIATSVAARGLDVKELELVIN-------------------FDAPNH  794 (976)
Q Consensus       734 L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLVaT~v~~~GlDi~~v~~VI~-------------------~d~p~s  794 (976)
                      |...++.+..+||    .+|..++..|++|.++|||||+++++||||| +++||+                   |+.|.+
T Consensus       197 L~~~~~~v~~lhg----~~R~~~~~~F~~g~~~vLVaT~v~e~GiDip-v~~VI~~g~~~~pv~~~~~~~~vi~~~~p~~  271 (440)
T 1yks_A          197 LRKAGKSVVVLNR----KTFEREYPTIKQKKPDFILATDIAEMGANLC-VERVLDCRTAFKPVLVDEGRKVAIKGPLRIS  271 (440)
T ss_dssp             HHHTTCCEEECCS----SSCC--------CCCSEEEESSSTTCCTTCC-CSEEEECCEEEEEEEETTTTEEEEEEEEECC
T ss_pred             HHHcCCCEEEecc----hhHHHHHhhhcCCCceEEEECChhheeeccC-ceEEEeCCccceeeecccccceeeccccccC
Confidence            9999999999999    4688999999999999999999999999999 999986                   899999


Q ss_pred             HHHHHHHhcccCCC-CCccEEEEEe---cCCCcCchHHHHHHHhhccCCCCh
Q 002040          795 YEDYVHRVGRTGRA-GRKGCAITFI---SEEDAKYSPDLVKALELSEQVVPD  842 (976)
Q Consensus       795 ~~~y~Qr~GR~gR~-g~~g~~~~~~---~~~d~~~~~~i~~~l~~~~~~vp~  842 (976)
                      ..+|+||+||+||. |.+|.|++|+   ++.+...+..+...+......+|.
T Consensus       272 ~~~~~Qr~GR~GR~g~~~g~~~~l~~~~~~~~~~~l~~l~~~~~~~~~~l~~  323 (440)
T 1yks_A          272 ASSAAQRRGRIGRNPNRDGDSYYYSEPTSENNAHHVCWLEASMLLDNMEVRG  323 (440)
T ss_dssp             HHHHHHHHTTSSCCTTCCCEEEEECSCCCCCCTTBHHHHHHHHHHTTSCCGG
T ss_pred             HHHHHHhccccCCCCCCCceEEEEeccCChhhhhhhhhhhHHhccccccccc
Confidence            99999999999997 6899999997   677888888888887777666654

>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=100.00  E-value=2e-37  Score=364.91  Aligned_cols=293  Identities=22%  Similarity=0.233  Sum_probs=222.3

Q ss_pred             CCCcHHHHHHHHHHhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHHHHhhc
Q 002040          488 EKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVM  567 (976)
Q Consensus       488 ~~p~~~Q~~~i~~il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~~~~~~  567 (976)
                      ..|+|+|.++++.++.+.++|++++||+|||++|++++...           +.++||||||++|+.||+..|..|    
T Consensus        92 ~~l~~~Q~~ai~~i~~~~~~ll~~~TGsGKT~~~l~~i~~~-----------~~~~Lvl~P~~~L~~Q~~~~~~~~----  156 (472)
T 2fwr_A           92 ISLRDYQEKALERWLVDKRGCIVLPTGSGKTHVAMAAINEL-----------STPTLIVVPTLALAEQWKERLGIF----  156 (472)
T ss_dssp             CCBCHHHHHHHHHHTTTTEEEEECCTTSCHHHHHHHHHHHH-----------CSCEEEEESSHHHHHHHHHHGGGG----
T ss_pred             CCcCHHHHHHHHHHHhcCCEEEEeCCCCCHHHHHHHHHHHc-----------CCCEEEEECCHHHHHHHHHHHHhC----
Confidence            36999999999999999999999999999999999988754           457999999999999999988873    


Q ss_pred             CcE-EEEeeCCCChHHHHHHHhcCCeEEEeCchhHHHHHHhcCCcccccCCceEEEecCcccccccCCchHHHHHHHhcC
Q 002040          568 GVR-CVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMGFEPQITRIVQNIR  646 (976)
Q Consensus       568 ~~~-~~~~~gg~~~~~~~~~l~~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDEah~~~~~~f~~~i~~il~~~~  646 (976)
                      ++. +..++|+...         ..+|+|+||+.|...+..      ....+++|||||||++.+.+|..    ++..+ 
T Consensus       157 ~~~~v~~~~g~~~~---------~~~Ivv~T~~~l~~~~~~------~~~~~~liIvDEaH~~~~~~~~~----~~~~~-  216 (472)
T 2fwr_A          157 GEEYVGEFSGRIKE---------LKPLTVSTYDSAYVNAEK------LGNRFMLLIFDEVHHLPAESYVQ----IAQMS-  216 (472)
T ss_dssp             CGGGEEEBSSSCBC---------CCSEEEEEHHHHHHTHHH------HTTTCSEEEEETGGGTTSTTTHH----HHHTC-
T ss_pred             CCcceEEECCCcCC---------cCCEEEEEcHHHHHHHHH------hcCCCCEEEEECCcCCCChHHHH----HHHhc-
Confidence            778 8777777642         479999999998766532      12458999999999998776643    44444 


Q ss_pred             CCCcEEEEeccCcHH-------------------HHHHHHHHcCCCeE--EEeCCccc----------------------
Q 002040          647 PDRQTVLFSATFPRQ-------------------VEILARKVLNKPVE--IQVGGRSV----------------------  683 (976)
Q Consensus       647 ~~~q~i~~SAT~~~~-------------------~~~l~~~~l~~~~~--i~~~~~~~----------------------  683 (976)
                      +..++|+||||++..                   +..+...++..+..  +.+.....                      
T Consensus       217 ~~~~~l~lSATp~~~~~~~~~l~~~~~~~~~~~~~~~l~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~  296 (472)
T 2fwr_A          217 IAPFRLGLTATFEREDGRHEILKEVVGGKVFELFPDSLAGKHLAKYTIKRIFVPLAEDERVEYEKREKVYKQFLRARGIT  296 (472)
T ss_dssp             CCSEEEEEESCCCCTTSGGGSHHHHTCCEEEECCHHHHTSCCCCSEEECCEEECCCHHHHHHTTTTTHHHHSCSSSCCCT
T ss_pred             CCCeEEEEecCccCCCCHHHHHHHHhCCeEeecCHHHHhcCcCCCeEEEEEEcCCCHHHHHHHHHHHHHHHHHHHhcCcc
Confidence            567899999999731                   12221122222211  11100000                      


Q ss_pred             --ccCCceEEE---------------------EecCcchHHHHHHHHHHhhhcCCcEEEEecCHHHHHHHHHHHHHCCCC
Q 002040          684 --VNKDITQLV---------------------EVRPESDRFLRLLELLGEWYEKGKILIFVHSQEKCDALFRDLLKHGYP  740 (976)
Q Consensus       684 --~~~~i~q~~---------------------~~~~~~~k~~~l~~~l~~~~~~~kvLIF~~s~~~~~~l~~~L~~~~~~  740 (976)
                        ....+.+.+                     .......|+..|..+|.. ..++++||||++...++.++..|     .
T Consensus       297 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~l~~~l~~-~~~~k~lvF~~~~~~~~~l~~~l-----~  370 (472)
T 2fwr_A          297 LRRAEDFNKIVMASGYDERAYEALRAWEEARRIAFNSKNKIRKLREILER-HRKDKIIIFTRHNELVYRISKVF-----L  370 (472)
T ss_dssp             TTCCSSSTTTTTTTCCSSSSSTTTHHHHHHHHHHHSCSHHHHHHHHHHHH-TSSSCBCCBCSCHHHHHHHHHHT-----T
T ss_pred             ccchhhHHHHHHHhccCHHHHHHHHHHHHHHHHhhcChHHHHHHHHHHHh-CCCCcEEEEECCHHHHHHHHHHh-----C
Confidence              000000000                     001234566777777766 45789999999999999999987     3


Q ss_pred             ceeccCCCCHHHHHHHHHHhccCCccEEEecCcccccCCCCCCcEEEEeCCCCCHHHHHHHhcccCCCCCc-c--EEEEE
Q 002040          741 CLSLHGAKDQTDRESTISDFKSNVCNLLIATSVAARGLDVKELELVINFDAPNHYEDYVHRVGRTGRAGRK-G--CAITF  817 (976)
Q Consensus       741 ~~~lhg~~~~~~R~~~~~~F~~g~~~vLVaT~v~~~GlDi~~v~~VI~~d~p~s~~~y~Qr~GR~gR~g~~-g--~~~~~  817 (976)
                      +..+||+++..+|..++..|++|.++|||||+++++|||+|++++||+|++|+++..|+|++||+||.|+. +  .+|.|
T Consensus       371 ~~~~~g~~~~~~R~~~~~~F~~g~~~vLv~T~~~~~Gldlp~~~~Vi~~~~~~s~~~~~Q~~GR~~R~g~~k~~~~i~~l  450 (472)
T 2fwr_A          371 IPAITHRTSREEREEILEGFRTGRFRAIVSSQVLDEGIDVPDANVGVIMSGSGSAREYIQRLGRILRPSKGKKEAVLYEL  450 (472)
T ss_dssp             CCBCCSSSCSHHHHTHHHHHHHSSCSBCBCSSCCCSSSCSCCBSEEEEECCSSCCHHHHHHHHHSBCCCTTTCCEEEEEE
T ss_pred             cceeeCCCCHHHHHHHHHHHhCCCCCEEEEcCchhcCcccccCcEEEEECCCCCHHHHHHHHhhccCCCCCCceEEEEEE
Confidence            67899999999999999999999999999999999999999999999999999999999999999999854 3  44556


Q ss_pred             ecCC
Q 002040          818 ISEE  821 (976)
Q Consensus       818 ~~~~  821 (976)
                      ++..
T Consensus       451 v~~~  454 (472)
T 2fwr_A          451 ISRG  454 (472)
T ss_dssp             EECS
T ss_pred             EeCC
Confidence            6643

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

Probab=100.00  E-value=1.8e-37  Score=374.46  Aligned_cols=310  Identities=18%  Similarity=0.212  Sum_probs=219.3

Q ss_pred             HHcCCC-----CCcHHHH-----HHHHHHh------cCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEE
Q 002040          483 RKLNYE-----KPMPIQA-----QALPVIM------SGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIM  546 (976)
Q Consensus       483 ~~~~~~-----~p~~~Q~-----~~i~~il------~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl  546 (976)
                      ..+||.     .|+|+|.     ++||.++      .++++|++|+||||||++|++|++..+..       .++++|||
T Consensus       204 ~~~Gf~~~~~~~pt~IQ~~~r~~~aIp~~l~~~~l~~g~dvlv~apTGSGKTl~~ll~il~~l~~-------~~~~~lil  276 (673)
T 2wv9_A          204 YGNGVILGNGAYVSAIVQGERVEEPVPEAYNPEMLKKRQLTVLDLHPGAGKTRRILPQIIKDAIQ-------KRLRTAVL  276 (673)
T ss_dssp             EEEEEECSSSCEEEEEECC-------CCCCCGGGGSTTCEEEECCCTTTTTTTTHHHHHHHHHHH-------TTCCEEEE
T ss_pred             eeccccccCCCccCceeeccccccchHHHhhHHHHhcCCeEEEEeCCCCCHHHHHHHHHHHHHHh-------CCCcEEEE
Confidence            345555     8999999     9999988      89999999999999999999999988765       35789999


Q ss_pred             ccCHHHHHHHHHHHHHHHhhcCcEEEEeeCCCChHHHHHHHhcCCeEEEeCchhHHHHHHhcCCcccccCCceEEEecCc
Q 002040          547 APTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEA  626 (976)
Q Consensus       547 ~Ptr~La~Q~~~~~~~~~~~~~~~~~~~~gg~~~~~~~~~l~~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDEa  626 (976)
                      +||++||.|++..+..+    ++.  ...+....     ....+.-+.+++.+.+...+...    ..+.++++||||||
T Consensus       277 aPTr~La~Q~~~~l~~~----~i~--~~~~~l~~-----v~tp~~ll~~l~~~~l~~~l~~~----~~l~~l~lvViDEa  341 (673)
T 2wv9_A          277 APTRVVAAEMAEALRGL----PVR--YLTPAVQR-----EHSGNEIVDVMCHATLTHRLMSP----LRVPNYNLFVMDEA  341 (673)
T ss_dssp             ESSHHHHHHHHHHTTTS----CCE--ECCC---C-----CCCSCCCEEEEEHHHHHHHHHSS----SCCCCCSEEEEEST
T ss_pred             ccHHHHHHHHHHHHhcC----Cee--eecccccc-----cCCHHHHHHHHHhhhhHHHHhcc----cccccceEEEEeCC
Confidence            99999999999887643    322  11111000     00112234445555554444321    35788999999999


Q ss_pred             ccccccCCchHHHHHHHhc-CCCCcEEEEeccCcHHHHHHHHHHcCCCeEEEeCCcccccCCceEEEEecCcchHHHHHH
Q 002040          627 DRMFDMGFEPQITRIVQNI-RPDRQTVLFSATFPRQVEILARKVLNKPVEIQVGGRSVVNKDITQLVEVRPESDRFLRLL  705 (976)
Q Consensus       627 h~~~~~~f~~~i~~il~~~-~~~~q~i~~SAT~~~~~~~l~~~~l~~~~~i~~~~~~~~~~~i~q~~~~~~~~~k~~~l~  705 (976)
                      |++ +..+...+..+...+ +...|+|+||||+++.+..+...  ..++              .......+. ..+..++
T Consensus       342 H~~-~~~~~~~~~~l~~~~~~~~~~vl~~SAT~~~~i~~~~~~--~~~i--------------~~v~~~~~~-~~~~~~l  403 (673)
T 2wv9_A          342 HFT-DPASIAARGYIATRVEAGEAAAIFMTATPPGTSDPFPDT--NSPV--------------HDVSSEIPD-RAWSSGF  403 (673)
T ss_dssp             TCC-CHHHHHHHHHHHHHHHTTSCEEEEECSSCTTCCCSSCCC--SSCE--------------EEEECCCCS-SCCSSCC
T ss_pred             ccc-CccHHHHHHHHHHhccccCCcEEEEcCCCChhhhhhccc--CCce--------------EEEeeecCH-HHHHHHH
Confidence            987 222222333333333 36789999999998653221110  1111              111000111 1111222


Q ss_pred             HHHHhhhcCCcEEEEecCHHHHHHHHHHHHHCCCCceeccCCCCHHHHHHHHHHhccCCccEEEecCcccccCCCCCCcE
Q 002040          706 ELLGEWYEKGKILIFVHSQEKCDALFRDLLKHGYPCLSLHGAKDQTDRESTISDFKSNVCNLLIATSVAARGLDVKELEL  785 (976)
Q Consensus       706 ~~l~~~~~~~kvLIF~~s~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLVaT~v~~~GlDi~~v~~  785 (976)
                      ..|..  ..+++||||+++..++.++..|...++.+..+||.    +|..++..|++|.++|||||+++++||||| +.+
T Consensus       404 ~~l~~--~~~~~lVF~~s~~~~e~la~~L~~~g~~v~~lHg~----eR~~v~~~F~~g~~~VLVaTdv~e~GIDip-v~~  476 (673)
T 2wv9_A          404 EWITD--YAGKTVWFVASVKMSNEIAQCLQRAGKRVIQLNRK----SYDTEYPKCKNGDWDFVITTDISEMGANFG-ASR  476 (673)
T ss_dssp             HHHHS--CCSCEEEECSSHHHHHHHHHHHHTTTCCEEEECSS----SHHHHGGGGGTCCCSEEEECGGGGTTCCCC-CSE
T ss_pred             HHHHh--CCCCEEEEECCHHHHHHHHHHHHhCCCeEEEeChH----HHHHHHHHHHCCCceEEEECchhhcceeeC-CcE
Confidence            33333  46799999999999999999999999999999993    789999999999999999999999999999 999


Q ss_pred             EEE--------------------eCCCCCHHHHHHHhcccCCC-CCccEEEEEe---cCCCcCchHHHHHHHhhccCC
Q 002040          786 VIN--------------------FDAPNHYEDYVHRVGRTGRA-GRKGCAITFI---SEEDAKYSPDLVKALELSEQV  839 (976)
Q Consensus       786 VI~--------------------~d~p~s~~~y~Qr~GR~gR~-g~~g~~~~~~---~~~d~~~~~~i~~~l~~~~~~  839 (976)
                      ||+                    |++|.++++|+||+||+||. |+.|.||+|+   ++.+..++..+...+.+....
T Consensus       477 VI~~g~~~~p~vi~da~~r~~ll~d~P~s~~~y~Qr~GRaGR~~g~~G~ai~l~~~~~~~d~~~l~~ie~~~~l~~~~  554 (673)
T 2wv9_A          477 VIDCRKSVKPTILDEGEGRVILSVPSAITSASAAQRRGRVGRNPSQIGDEYHYGGGTSEDDTMLAHWTEAKILLDNIH  554 (673)
T ss_dssp             EEECCEECCEEEECSTTCEEEECCSEECCHHHHHHHHTTSSCCSSCCCEEEEECSCCCCCCTTBHHHHHHHHHHHTSC
T ss_pred             EEECCCcccceeeecccccceecccCCCCHHHHHHHhhccCCCCCCCCEEEEEEecCChhHHHHHHHHHHHHhhhhcc
Confidence            998                    67899999999999999999 7899999996   567777777777665444333

>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=100.00  E-value=7.5e-37  Score=362.95  Aligned_cols=288  Identities=22%  Similarity=0.238  Sum_probs=219.7

Q ss_pred             CcHHHHHHHHHHhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHHHHhhcCc
Q 002040          490 PMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVMGV  569 (976)
Q Consensus       490 p~~~Q~~~i~~il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~~~~~~~~  569 (976)
                      ++++|..+++.+..++++|++|+||||||++|.+|++.           .+.++||++||++||.|++..+..   .++.
T Consensus       218 ~~~~q~~i~~~L~~~~~vlv~ApTGSGKT~a~~l~ll~-----------~g~~vLVl~PTReLA~Qia~~l~~---~~g~  283 (666)
T 3o8b_A          218 VFTDNSSPPAVPQSFQVAHLHAPTGSGKSTKVPAAYAA-----------QGYKVLVLNPSVAATLGFGAYMSK---AHGI  283 (666)
T ss_dssp             SCCCCCSCCCCCSSCEEEEEECCTTSCTTTHHHHHHHH-----------TTCCEEEEESCHHHHHHHHHHHHH---HHSC
T ss_pred             cHHHHHHHHHHHHcCCeEEEEeCCchhHHHHHHHHHHH-----------CCCeEEEEcchHHHHHHHHHHHHH---HhCC
Confidence            44566666667778899999999999999999998875           255899999999999999886654   4567


Q ss_pred             EEEEeeCCCChHHHHHHHhcCCeEEEeCchhHHHHHHhcCCcccccCCceEEEecCcccccccCCchHHHHHHHhcCCCC
Q 002040          570 RCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMGFEPQITRIVQNIRPDR  649 (976)
Q Consensus       570 ~~~~~~gg~~~~~~~~~l~~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDEah~~~~~~f~~~i~~il~~~~~~~  649 (976)
                      .+...+|+..       +..+++|+|+||++|+   ..   ....+.++++||||||| +++++|...+..++..++...
T Consensus       284 ~vg~~vG~~~-------~~~~~~IlV~TPGrLl---~~---~~l~l~~l~~lVlDEAH-~l~~~~~~~l~~Il~~l~~~~  349 (666)
T 3o8b_A          284 DPNIRTGVRT-------ITTGAPVTYSTYGKFL---AD---GGCSGGAYDIIICDECH-STDSTTILGIGTVLDQAETAG  349 (666)
T ss_dssp             CCEEECSSCE-------ECCCCSEEEEEHHHHH---HT---TSCCTTSCSEEEETTTT-CCSHHHHHHHHHHHHHTTTTT
T ss_pred             CeeEEECcEe-------ccCCCCEEEECcHHHH---hC---CCcccCcccEEEEccch-hcCccHHHHHHHHHHhhhhcC
Confidence            7777888864       3567899999999973   22   22567789999999996 567788888999999888777


Q ss_pred             c--EEEEeccCcHHHHHHHHHHcCCCeEEEeCCcccccCCceEEEEecCcchHHHHHHHHHHhhhcCCcEEEEecCHHHH
Q 002040          650 Q--TVLFSATFPRQVEILARKVLNKPVEIQVGGRSVVNKDITQLVEVRPESDRFLRLLELLGEWYEKGKILIFVHSQEKC  727 (976)
Q Consensus       650 q--~i~~SAT~~~~~~~l~~~~l~~~~~i~~~~~~~~~~~i~q~~~~~~~~~k~~~l~~~l~~~~~~~kvLIF~~s~~~~  727 (976)
                      |  +|+||||++..+.      ...+....+...   ....   +........       + .....+++||||+++..+
T Consensus       350 ~~llil~SAT~~~~i~------~~~p~i~~v~~~---~~~~---i~~~~~~~~-------l-~~~~~~~vLVFv~Tr~~a  409 (666)
T 3o8b_A          350 ARLVVLATATPPGSVT------VPHPNIEEVALS---NTGE---IPFYGKAIP-------I-EAIRGGRHLIFCHSKKKC  409 (666)
T ss_dssp             CSEEEEEESSCTTCCC------CCCTTEEEEECB---SCSS---EEETTEEEC-------G-GGSSSSEEEEECSCHHHH
T ss_pred             CceEEEECCCCCcccc------cCCcceEEEeec---ccch---hHHHHhhhh-------h-hhccCCcEEEEeCCHHHH
Confidence            7  6788999987311      111111111000   0000   011100000       1 122578999999999999


Q ss_pred             HHHHHHHHHCCCCceeccCCCCHHHHHHHHHHhccCCccEEEecCcccccCCCCCCcEEE----------EeC-------
Q 002040          728 DALFRDLLKHGYPCLSLHGAKDQTDRESTISDFKSNVCNLLIATSVAARGLDVKELELVI----------NFD-------  790 (976)
Q Consensus       728 ~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLVaT~v~~~GlDi~~v~~VI----------~~d-------  790 (976)
                      +.++..|...++.+..+||+|++.+       |.++..+|||||+++++||||+ +++||          |||       
T Consensus       410 e~la~~L~~~g~~v~~lHG~l~q~e-------r~~~~~~VLVATdVaerGIDId-V~~VI~~Gl~~~~ViNyDydP~~gl  481 (666)
T 3o8b_A          410 DELAAKLSGLGINAVAYYRGLDVSV-------IPTIGDVVVVATDALMTGYTGD-FDSVIDCNTCVTQTVDFSLDPTFTI  481 (666)
T ss_dssp             HHHHHHHHTTTCCEEEECTTSCGGG-------SCSSSCEEEEECTTHHHHCCCC-BSEEEECCEEEEEEEECCCSSSCEE
T ss_pred             HHHHHHHHhCCCcEEEecCCCCHHH-------HHhCCCcEEEECChHHccCCCC-CcEEEecCccccccccccccccccc
Confidence            9999999999999999999999874       5667779999999999999997 99988          677       


Q ss_pred             ----CCCCHHHHHHHhcccCCCCCccEEEEEecCCCcCc--h--HHHHHHHhh
Q 002040          791 ----APNHYEDYVHRVGRTGRAGRKGCAITFISEEDAKY--S--PDLVKALEL  835 (976)
Q Consensus       791 ----~p~s~~~y~Qr~GR~gR~g~~g~~~~~~~~~d~~~--~--~~i~~~l~~  835 (976)
                          .|.+.+.|+||+||+|| |.+|. |+|+++.+...  +  ..|.+.+..
T Consensus       482 ~~~~~P~s~~syiQRiGRtGR-g~~G~-i~lvt~~e~~~~~l~~~~i~~~~~~  532 (666)
T 3o8b_A          482 ETTTVPQDAVSRSQRRGRTGR-GRRGI-YRFVTPGERPSGMFDSSVLCECYDA  532 (666)
T ss_dssp             EEEEEECBHHHHHHHHTTBCS-SSCEE-EEESCCCCBCSSBCCHHHHHHHHHH
T ss_pred             ccccCcCCHHHHHHHhccCCC-CCCCE-EEEEecchhhcccccHHHHHHHhcC
Confidence                89999999999999999 89999 99999877665  4  666666543

>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=100.00  E-value=5.8e-37  Score=357.90  Aligned_cols=283  Identities=17%  Similarity=0.215  Sum_probs=203.5

Q ss_pred             HHHHHHhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHHHHhhcCcEEEEee
Q 002040          496 QALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVMGVRCVPVY  575 (976)
Q Consensus       496 ~~i~~il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~~~~~~~~~~~~~~  575 (976)
                      +...++..++++|++|+||||||++|++|++..+..       .++++|||+||++||.|++..+.      |+.+....
T Consensus        13 ~~~~~l~~~~~vlv~a~TGsGKT~~~~l~il~~~~~-------~~~~~lvl~Ptr~La~Q~~~~l~------g~~v~~~~   79 (459)
T 2z83_A           13 GSPNMLRKRQMTVLDLHPGSGKTRKILPQIIKDAIQ-------QRLRTAVLAPTRVVAAEMAEALR------GLPVRYQT   79 (459)
T ss_dssp             --CGGGSTTCEEEECCCTTSCTTTTHHHHHHHHHHH-------TTCCEEEEECSHHHHHHHHHHTT------TSCEEECC
T ss_pred             HHHHHHhcCCcEEEECCCCCCHHHHHHHHHHHHHHh-------CCCcEEEECchHHHHHHHHHHhc------CceEeEEe
Confidence            334456678999999999999999999999988764       25789999999999999998876      33333222


Q ss_pred             CCCChHHHHHHHhcCCeEEEeCchhHHHHHHhcCCcccccCCceEEEecCccc-----ccccCCchHHHHHHHhcCCCCc
Q 002040          576 GGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADR-----MFDMGFEPQITRIVQNIRPDRQ  650 (976)
Q Consensus       576 gg~~~~~~~~~l~~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDEah~-----~~~~~f~~~i~~il~~~~~~~q  650 (976)
                      +....     .-..+..|.++|.+.+...+...    ..+.++++|||||||+     ++.++|...+.     ..+..|
T Consensus        80 ~~~~~-----~~t~~~~i~~~~~~~l~~~l~~~----~~l~~~~~iViDEaH~~~~~~~~~~~~~~~~~-----~~~~~~  145 (459)
T 2z83_A           80 SAVQR-----EHQGNEIVDVMCHATLTHRLMSP----NRVPNYNLFVMDEAHFTDPASIAARGYIATKV-----ELGEAA  145 (459)
T ss_dssp             -------------CCCSEEEEEHHHHHHHHHSC----C-CCCCSEEEESSTTCCSHHHHHHHHHHHHHH-----HTTSCE
T ss_pred             ccccc-----CCCCCcEEEEEchHHHHHHhhcc----ccccCCcEEEEECCccCCchhhHHHHHHHHHh-----ccCCcc
Confidence            21111     11234568889999887766543    4578899999999997     44444322221     236889


Q ss_pred             EEEEeccCcHHHHHHHHHHcCCCeEEEeCCcccccCCceEEEEecCcchHHHHHHHHHHhhhcCCcEEEEecCHHHHHHH
Q 002040          651 TVLFSATFPRQVEILARKVLNKPVEIQVGGRSVVNKDITQLVEVRPESDRFLRLLELLGEWYEKGKILIFVHSQEKCDAL  730 (976)
Q Consensus       651 ~i~~SAT~~~~~~~l~~~~l~~~~~i~~~~~~~~~~~i~q~~~~~~~~~k~~~l~~~l~~~~~~~kvLIF~~s~~~~~~l  730 (976)
                      +|+||||++..+..+...  ..|+.....  .            . ....+..++..|..  ..+++||||+++..++.+
T Consensus       146 ~il~SAT~~~~~~~~~~~--~~pi~~~~~--~------------~-~~~~~~~~~~~l~~--~~~~~LVF~~s~~~~~~l  206 (459)
T 2z83_A          146 AIFMTATPPGTTDPFPDS--NAPIHDLQD--E------------I-PDRAWSSGYEWITE--YAGKTVWFVASVKMGNEI  206 (459)
T ss_dssp             EEEECSSCTTCCCSSCCC--SSCEEEEEC--C------------C-CSSCCSSCCHHHHH--CCSCEEEECSCHHHHHHH
T ss_pred             EEEEEcCCCcchhhhccC--CCCeEEecc--c------------C-CcchhHHHHHHHHh--cCCCEEEEeCChHHHHHH
Confidence            999999998653222110  222221110  0            0 01111112233333  267999999999999999


Q ss_pred             HHHHHHCCCCceeccCCCCHHHHHHHHHHhccCCccEEEecCcccccCCCCCCcEEEE--------------------eC
Q 002040          731 FRDLLKHGYPCLSLHGAKDQTDRESTISDFKSNVCNLLIATSVAARGLDVKELELVIN--------------------FD  790 (976)
Q Consensus       731 ~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLVaT~v~~~GlDi~~v~~VI~--------------------~d  790 (976)
                      +..|...++.+..+||.    +|..++..|++|.++|||||+++++|||||+ .+||+                    |+
T Consensus       207 ~~~L~~~g~~v~~lh~~----~R~~~~~~f~~g~~~iLVaT~v~~~GiDip~-~~VI~~G~~~~~~~~~~~~~~~~~~~d  281 (459)
T 2z83_A          207 AMCLQRAGKKVIQLNRK----SYDTEYPKCKNGDWDFVITTDISEMGANFGA-SRVIDCRKSVKPTILEEGEGRVILGNP  281 (459)
T ss_dssp             HHHHHHTTCCEEEESTT----CCCCCGGGSSSCCCSEEEESSCC---CCCSC-SEEEECCEECCEEEECSSSCEEEECSC
T ss_pred             HHHHHhcCCcEEecCHH----HHHHHHhhccCCCceEEEECChHHhCeecCC-CEEEECCcccccccccccccccccccC
Confidence            99999999999999995    6778999999999999999999999999999 99999                    77


Q ss_pred             CCCCHHHHHHHhcccCCCCC-ccEEEEEecCC--CcCchHHH
Q 002040          791 APNHYEDYVHRVGRTGRAGR-KGCAITFISEE--DAKYSPDL  829 (976)
Q Consensus       791 ~p~s~~~y~Qr~GR~gR~g~-~g~~~~~~~~~--d~~~~~~i  829 (976)
                      +|.++..|+||+|||||.|. +|.|++|++..  +...+..+
T Consensus       282 ~p~s~~~~~QR~GRaGR~g~~~G~~~~~~~~~~~~~~~~~~~  323 (459)
T 2z83_A          282 SPITSASAAQRRGRVGRNPNQVGDEYHYGGATSEDDSNLAHW  323 (459)
T ss_dssp             EECCHHHHHHHHTTSSCCTTCCCEEEEECSCCCCCCTTBHHH
T ss_pred             CCCCHHHHHHhccccCCCCCCCCeEEEEEcccccchhhhhhh
Confidence            99999999999999999997 99999999876  54444444

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

Probab=100.00  E-value=7.1e-35  Score=337.52  Aligned_cols=269  Identities=21%  Similarity=0.210  Sum_probs=193.9

Q ss_pred             cCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHHHHhhcCcEEEEeeCCCChHH
Q 002040          503 SGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQ  582 (976)
Q Consensus       503 ~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~~~~~~~~~~~~~~gg~~~~~  582 (976)
                      .|+++|++++||||||++|++|++..+..       .++++|||+||++||.|++..+.      ++.+..+.|+...  
T Consensus         1 kg~~~lv~a~TGsGKT~~~l~~~l~~~~~-------~g~~~lvl~Pt~~La~Q~~~~~~------~~~v~~~~~~~~~--   65 (431)
T 2v6i_A            1 KRELTVLDLHPGAGKTRRVLPQLVREAVK-------KRLRTVILAPTRVVASEMYEALR------GEPIRYMTPAVQS--   65 (431)
T ss_dssp             -CCEEEEECCTTSCTTTTHHHHHHHHHHH-------TTCCEEEEESSHHHHHHHHHHTT------TSCEEEC--------
T ss_pred             CCCEEEEEcCCCCCHHHHHHHHHHHHHHh-------CCCCEEEECcHHHHHHHHHHHhC------CCeEEEEecCccc--
Confidence            37899999999999999999999976654       36789999999999999987765      4455544443211  


Q ss_pred             HHHHHhcCCeEEEeCchhHHHHHHhcCCcccccCCceEEEecCcccccccCCchHHHHHHHh-cCCCCcEEEEeccCcHH
Q 002040          583 QISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMGFEPQITRIVQN-IRPDRQTVLFSATFPRQ  661 (976)
Q Consensus       583 ~~~~l~~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDEah~~~~~~f~~~i~~il~~-~~~~~q~i~~SAT~~~~  661 (976)
                         .-..+..+.++|.+.+...+...    ..+.++++|||||||++ +.++..+...+... .++..|+|+||||+++.
T Consensus        66 ---~~~~~~~~~~~~~~~l~~~l~~~----~~~~~l~~vViDEaH~~-~~~~~~~~~~l~~~~~~~~~~~l~~SAT~~~~  137 (431)
T 2v6i_A           66 ---ERTGNEIVDFMCHSTFTMKLLQG----VRVPNYNLYIMDEAHFL-DPASVAARGYIETRVSMGDAGAIFMTATPPGT  137 (431)
T ss_dssp             ------CCCSEEEEEHHHHHHHHHHT----CCCCCCSEEEEESTTCC-SHHHHHHHHHHHHHHHTTSCEEEEEESSCTTC
T ss_pred             ---cCCCCceEEEEchHHHHHHHhcC----ccccCCCEEEEeCCccC-CccHHHHHHHHHHHhhCCCCcEEEEeCCCCcc
Confidence               11234677788999887666542    35788999999999986 33333343333333 25689999999999874


Q ss_pred             HHHHHHHHcCCCeEEEeCCcccccCCceEEEEecCcchHHHHHHHHHHhhhcCCcEEEEecCHHHHHHHHHHHHHCCCCc
Q 002040          662 VEILARKVLNKPVEIQVGGRSVVNKDITQLVEVRPESDRFLRLLELLGEWYEKGKILIFVHSQEKCDALFRDLLKHGYPC  741 (976)
Q Consensus       662 ~~~l~~~~l~~~~~i~~~~~~~~~~~i~q~~~~~~~~~k~~~l~~~l~~~~~~~kvLIF~~s~~~~~~l~~~L~~~~~~~  741 (976)
                      +..+...  ..|              +.. +........+..++..|..  ..+++||||+++..++.++..|...++.+
T Consensus       138 ~~~~~~~--~~~--------------i~~-~~~~~~~~~~~~~~~~l~~--~~~~~lVF~~~~~~~~~l~~~L~~~~~~v  198 (431)
T 2v6i_A          138 TEAFPPS--NSP--------------IID-EETRIPDKAWNSGYEWITE--FDGRTVWFVHSIKQGAEIGTCLQKAGKKV  198 (431)
T ss_dssp             CCSSCCC--SSC--------------CEE-EECCCCSSCCSSCCHHHHS--CSSCEEEECSSHHHHHHHHHHHHHTTCCE
T ss_pred             hhhhcCC--CCc--------------eee-ccccCCHHHHHHHHHHHHc--CCCCEEEEeCCHHHHHHHHHHHHHcCCeE
Confidence            2211100  011              111 0000111112223344443  26799999999999999999999999999


Q ss_pred             eeccCCCCHHHHHHHHHHhccCCccEEEecCcccccCCCCCCcE-----------------EEEeCCCCCHHHHHHHhcc
Q 002040          742 LSLHGAKDQTDRESTISDFKSNVCNLLIATSVAARGLDVKELEL-----------------VINFDAPNHYEDYVHRVGR  804 (976)
Q Consensus       742 ~~lhg~~~~~~R~~~~~~F~~g~~~vLVaT~v~~~GlDi~~v~~-----------------VI~~d~p~s~~~y~Qr~GR  804 (976)
                      ..+||.    +|..++..|++|.++|||||+++++||||| +.+                 ||+++.|.+..+|+||+||
T Consensus       199 ~~lhg~----~r~~~~~~f~~g~~~vLVaT~v~e~GiDip-~~~VI~~g~~~~~v~d~~~~vi~~~~p~~~~~~~Qr~GR  273 (431)
T 2v6i_A          199 LYLNRK----TFESEYPKCKSEKWDFVITTDISEMGANFK-ADRVIDPRKTIKPILLDGRVSMQGPIAITPASAAQRRGR  273 (431)
T ss_dssp             EEESTT----THHHHTTHHHHSCCSEEEECGGGGTSCCCC-CSEEEECCEEEEEEEETTEEEEEEEEECCHHHHHHHHTT
T ss_pred             EEeCCc----cHHHHHHhhcCCCCeEEEECchHHcCcccC-CcEEEecCccccceecccceeecccccCCHHHHHHhhhc
Confidence            999997    578899999999999999999999999999 544                 6788999999999999999


Q ss_pred             cCCCCC-ccEEEEEe
Q 002040          805 TGRAGR-KGCAITFI  818 (976)
Q Consensus       805 ~gR~g~-~g~~~~~~  818 (976)
                      +||.|. .|.+++|.
T Consensus       274 ~GR~g~~~~~~~~~~  288 (431)
T 2v6i_A          274 IGRNPEKLGDIYAYS  288 (431)
T ss_dssp             SSCCTTCCCCEEEEC
T ss_pred             cCCCCCCCCeEEEEc
Confidence            999985 45556555

>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=100.00  E-value=3e-34  Score=308.84  Aligned_cols=237  Identities=38%  Similarity=0.640  Sum_probs=200.4

Q ss_pred             hcCceeccCCCCC--cccccccCCCCHHHHHHHHHcCCCCCcHHHHHHHHHHhcCCCEEEEcCCCCchHHHHHHHHHHHH
Q 002040          452 QLELKIHGKDVPK--PIKTWHQTGLTSKIMETIRKLNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHI  529 (976)
Q Consensus       452 ~~~i~~~g~~~p~--pi~~~~~~~l~~~l~~~l~~~~~~~p~~~Q~~~i~~il~g~d~i~~a~TGsGKT~~~~l~il~~l  529 (976)
                      .+.+.++|...|.  ++.+|.+++|++.+.+.|..+||..|+|+|.++|+.++.++++|++++||||||++|++|++.++
T Consensus         6 ~~~~~~~~~~~~~~~~~~~f~~l~l~~~l~~~l~~~g~~~~~~~Q~~~i~~i~~~~~~l~~a~TGsGKT~~~~~~~l~~l   85 (253)
T 1wrb_A            6 SIPVSVTGPDYSATNVIENFDELKLDPTIRNNILLASYQRPTPIQKNAIPAILEHRDIMACAQTGSGKTAAFLIPIINHL   85 (253)
T ss_dssp             CCCCCEECCSSSCCSCCCSSGGGSCCCSTTTTTTTTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHHH
T ss_pred             hCceeeeCCCCCCCCccCCHhhCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHH
Confidence            3446678888887  99999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             hcCCCC----CCCCCCeEEEEccCHHHHHHHHHHHHHHHhhcCcEEEEeeCCCChHHHHHHHhcCCeEEEeCchhHHHHH
Q 002040          530 KDQPPV----AAGDGPVGLIMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDIL  605 (976)
Q Consensus       530 ~~~~~~----~~~~~~~vLIl~Ptr~La~Q~~~~~~~~~~~~~~~~~~~~gg~~~~~~~~~l~~~~~Iiv~Tp~~L~~~l  605 (976)
                      ......    ....++++|||+||++||.|++..+..++...++.+.+++||.....+...+..+++|+|+||++|.+++
T Consensus        86 ~~~~~~~~~~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~Ivv~Tp~~l~~~l  165 (253)
T 1wrb_A           86 VCQDLNQQRYSKTAYPKCLILAPTRELAIQILSESQKFSLNTPLRSCVVYGGADTHSQIREVQMGCHLLVATPGRLVDFI  165 (253)
T ss_dssp             HTTCC------CCBCCSEEEECSSHHHHHHHHHHHHHHHTTSSCCEEEECSSSCSHHHHHHHSSCCSEEEECHHHHHHHH
T ss_pred             HhhccccccccccCCceEEEEECCHHHHHHHHHHHHHHhccCCceEEEEECCCCHHHHHHHhCCCCCEEEECHHHHHHHH
Confidence            754311    1234679999999999999999999999988899999999999988888888888999999999999988


Q ss_pred             HhcCCcccccCCceEEEecCcccccccCCchHHHHHHHhc--CC--CCcEEEEeccCcHHHHHHHHHHcCCCeEEEeCCc
Q 002040          606 CTSGGKITNLRRVTYLVMDEADRMFDMGFEPQITRIVQNI--RP--DRQTVLFSATFPRQVEILARKVLNKPVEIQVGGR  681 (976)
Q Consensus       606 ~~~~~~~~~l~~~~~vVlDEah~~~~~~f~~~i~~il~~~--~~--~~q~i~~SAT~~~~~~~l~~~~l~~~~~i~~~~~  681 (976)
                      ....   ..+..+.+|||||||+|++++|...+..++..+  +.  ..|+|+||||+++.+..++..++.+|+.+.++..
T Consensus       166 ~~~~---~~~~~~~~lViDEah~~~~~~~~~~~~~i~~~~~~~~~~~~q~l~~SAT~~~~~~~~~~~~l~~~~~i~~~~~  242 (253)
T 1wrb_A          166 EKNK---ISLEFCKYIVLDEADRMLDMGFEPQIRKIIEESNMPSGINRQTLMFSATFPKEIQKLAADFLYNYIFMTVGRV  242 (253)
T ss_dssp             HTTS---BCCTTCCEEEEETHHHHHHTTCHHHHHHHHHSSCCCCGGGCEEEEEESSCCHHHHHHHHHHCSSCEEEEEC--
T ss_pred             HcCC---CChhhCCEEEEeCHHHHHhCchHHHHHHHHhhccCCCCCCcEEEEEEEeCCHHHHHHHHHHcCCCEEEEECCC
Confidence            6542   467889999999999999999999999999854  33  6899999999999999999999999999988776


Q ss_pred             ccccCCceEE
Q 002040          682 SVVNKDITQL  691 (976)
Q Consensus       682 ~~~~~~i~q~  691 (976)
                      ......|.|.
T Consensus       243 ~~~~~~i~q~  252 (253)
T 1wrb_A          243 GSTSDSIKQE  252 (253)
T ss_dssp             ----------
T ss_pred             CCCcCCceec
Confidence            6665566553

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

Probab=100.00  E-value=2.8e-34  Score=347.36  Aligned_cols=308  Identities=16%  Similarity=0.152  Sum_probs=192.6

Q ss_pred             CCCcHHHHHHHHHHhc----C-CCEEEEcCCCCchHHHHHHHHHHHHhcC-CCCCCCCCCeEEEEccCHHHHHHHH-HHH
Q 002040          488 EKPMPIQAQALPVIMS----G-RDCIGVAKTGSGKTLAFVLPMLRHIKDQ-PPVAAGDGPVGLIMAPTRELVQQIH-SDI  560 (976)
Q Consensus       488 ~~p~~~Q~~~i~~il~----g-~d~i~~a~TGsGKT~~~~l~il~~l~~~-~~~~~~~~~~vLIl~Ptr~La~Q~~-~~~  560 (976)
                      ..|+|+|.++|+.++.    + +++|++++||||||++++..+...+... .......++++||||||++|+.||+ +.+
T Consensus       177 ~~lr~~Q~~ai~~~~~~~~~~~~~~ll~~~TGsGKT~~~~~~~~~l~~~~~~~~~~~~~~~vlil~P~~~L~~Q~~~~~~  256 (590)
T 3h1t_A          177 YSPRYYQQIAINRAVQSVLQGKKRSLITMATGTGKTVVAFQISWKLWSARWNRTGDYRKPRILFLADRNVLVDDPKDKTF  256 (590)
T ss_dssp             --CCHHHHHHHHHHHHHHHTTCSEEEEEECTTSCHHHHHHHHHHHHHHTTCCSSCSSSCCCEEEEEC-----------CC
T ss_pred             CCchHHHHHHHHHHHHHHhcCCCceEEEecCCCChHHHHHHHHHHHHhcccccccccCCCeEEEEeCCHHHHHHHHHHHH
Confidence            3699999999999875    4 5689999999999999665555444321 0111124688999999999999998 666


Q ss_pred             HHHHhhcCcEEEEeeCCCChHHHHHHHhcCCeEEEeCchhHHHHHHhcC-CcccccCCceEEEecCcccccccCCchHHH
Q 002040          561 RKFAKVMGVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSG-GKITNLRRVTYLVMDEADRMFDMGFEPQIT  639 (976)
Q Consensus       561 ~~~~~~~~~~~~~~~gg~~~~~~~~~l~~~~~Iiv~Tp~~L~~~l~~~~-~~~~~l~~~~~vVlDEah~~~~~~f~~~i~  639 (976)
                      ..|    +..+..+.++.        +..+.+|+|+||+.|...+.... .....+..+++|||||||++...+ ...+.
T Consensus       257 ~~~----~~~~~~~~~~~--------~~~~~~I~v~T~~~l~~~~~~~~~~~~~~~~~~~lvIiDEaH~~~~~~-~~~~~  323 (590)
T 3h1t_A          257 TPF----GDARHKIEGGK--------VVKSREIYFAIYQSIASDERRPGLYKEFPQDFFDLIIIDECHRGSARD-NSNWR  323 (590)
T ss_dssp             TTT----CSSEEECCC----------CCSSCSEEEEEGGGC------CCGGGGSCTTSCSEEEESCCC----------CH
T ss_pred             Hhc----chhhhhhhccC--------CCCCCcEEEEEhhhhccccccccccccCCCCccCEEEEECCccccccc-hHHHH
Confidence            654    44444444432        23468999999999987653211 112345678999999999987543 24556


Q ss_pred             HHHHhcCCCCcEEEEeccCcHHHHHHHHHHcCCCeEEEeCCcc----cccCCceEEEEe---------------------
Q 002040          640 RIVQNIRPDRQTVLFSATFPRQVEILARKVLNKPVEIQVGGRS----VVNKDITQLVEV---------------------  694 (976)
Q Consensus       640 ~il~~~~~~~q~i~~SAT~~~~~~~l~~~~l~~~~~i~~~~~~----~~~~~i~q~~~~---------------------  694 (976)
                      .++..++ ..++|+||||+..........+++.++........    .........+..                     
T Consensus       324 ~il~~~~-~~~~l~lTATP~~~~~~~~~~~f~~~~~~~~~~~~i~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  402 (590)
T 3h1t_A          324 EILEYFE-PAFQIGMTATPLREDNRDTYRYFGNPIYTYSLRQGIDDGFLAPYRVHRVISEVDAAGWRPSKGDVDRFGREI  402 (590)
T ss_dssp             HHHHHST-TSEEEEEESSCSCTTTHHHHHHSCSCSEEECHHHHHHHTSSCCEEEEEEEETTCC-----------------
T ss_pred             HHHHhCC-cceEEEeccccccccchhHHHHcCCceEecCHHHHhhCCccCCcEEEEeeeeeecccccccccccccccccc
Confidence            6677664 47899999998754333334444444322110000    000000000000                     


Q ss_pred             ------cCc-------chHHHHHH----HHHHhhhcCCcEEEEecCHHHHHHHHHHHHHCCC--------CceeccCCCC
Q 002040          695 ------RPE-------SDRFLRLL----ELLGEWYEKGKILIFVHSQEKCDALFRDLLKHGY--------PCLSLHGAKD  749 (976)
Q Consensus       695 ------~~~-------~~k~~~l~----~~l~~~~~~~kvLIF~~s~~~~~~l~~~L~~~~~--------~~~~lhg~~~  749 (976)
                            ...       ..+...++    ..+......+++||||+++..|+.++..|...+.        .+..+||.++
T Consensus       403 ~~~~~~~~~~~~~~~~~~r~~~i~~~l~~~l~~~~~~~k~lVF~~~~~~a~~l~~~L~~~~~~~~~~~~~~~~~i~g~~~  482 (590)
T 3h1t_A          403 PDGEYQTKDFERVIALKARTDAFAKHLTDFMKRTDRFAKTIVFCVDQEHADEMRRALNNLNSDLSRKHPDYVARVTSEEG  482 (590)
T ss_dssp             ------CCSHHHHHHHHHTHHHHHHHHHHHHHHHCTTSEEEEEESSHHHHHHHHHHHHHHTHHHHTTCTTSEEECSSTTH
T ss_pred             ccccCCHHHhhhHhcChHHHHHHHHHHHHHHHhcCCCccEEEEECCHHHHHHHHHHHHHhhhhhhccCCCeEEEEeCCCh
Confidence                  000       01122222    2333333457999999999999999999987543        2778999986


Q ss_pred             HHHHHHHHHHhccCCcc---EEEecCcccccCCCCCCcEEEEeCCCCCHHHHHHHhcccCCCCC
Q 002040          750 QTDRESTISDFKSNVCN---LLIATSVAARGLDVKELELVINFDAPNHYEDYVHRVGRTGRAGR  810 (976)
Q Consensus       750 ~~~R~~~~~~F~~g~~~---vLVaT~v~~~GlDi~~v~~VI~~d~p~s~~~y~Qr~GR~gR~g~  810 (976)
                      . .|..++..|++|...   |||||+++++|||+|++++||++++|+++..|+|++||+||.|.
T Consensus       483 ~-~r~~~l~~F~~~~~~~~~ilvtt~~l~~GiDip~v~~Vi~~~~~~s~~~~~Q~iGR~~R~~~  545 (590)
T 3h1t_A          483 K-IGKGHLSRFQELETSTPVILTTSQLLTTGVDAPTCKNVVLARVVNSMSEFKQIVGRGTRLRE  545 (590)
T ss_dssp             H-HHHHHHHHHHCTTCCCCCEEEESSTTTTTCCCTTEEEEEEESCCCCHHHHHHHHTTSCCCBG
T ss_pred             H-HHHHHHHHHhCCCCCCCEEEEECChhhcCccchheeEEEEEecCCChHHHHHHHhhhcccCc
Confidence            4 799999999998766   88999999999999999999999999999999999999999874

>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=100.00  E-value=4e-34  Score=361.05  Aligned_cols=332  Identities=15%  Similarity=0.137  Sum_probs=232.1

Q ss_pred             CCCcHHHHHHHHHHhcC--CCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHHHHh
Q 002040          488 EKPMPIQAQALPVIMSG--RDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAK  565 (976)
Q Consensus       488 ~~p~~~Q~~~i~~il~g--~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~~~~  565 (976)
                      ..|+|+|.+++..++..  .++|++++||+|||++++..+...+...      ...++|||||+ .|+.||..+|.+++ 
T Consensus       152 ~~LrpyQ~eav~~~l~~~~~~~LLad~tGlGKTi~Ai~~i~~l~~~g------~~~rvLIVvP~-sLl~Qw~~E~~~~f-  223 (968)
T 3dmq_A          152 TSLIPHQLNIAHDVGRRHAPRVLLADEVGLGKTIEAGMILHQQLLSG------AAERVLIIVPE-TLQHQWLVEMLRRF-  223 (968)
T ss_dssp             SCCCHHHHHHHHHHHHSSSCEEEECCCTTSCHHHHHHHHHHHHHHTS------SCCCEEEECCT-TTHHHHHHHHHHHS-
T ss_pred             CCCcHHHHHHHHHHHHhcCCCEEEECCCCCcHHHHHHHHHHHHHHhC------CCCeEEEEeCH-HHHHHHHHHHHHHh-
Confidence            46899999999998864  4789999999999999888777666532      23479999999 99999999997654 


Q ss_pred             hcCcEEEEeeCCCChHHHHHH---HhcCCeEEEeCchhHHHHHHhcCCcccccCCceEEEecCcccccccCCch-HHHHH
Q 002040          566 VMGVRCVPVYGGSGVAQQISE---LKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMGFEP-QITRI  641 (976)
Q Consensus       566 ~~~~~~~~~~gg~~~~~~~~~---l~~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDEah~~~~~~f~~-~i~~i  641 (976)
                        ++.+.++.|+. .......   .....+|+|+|++.|......  ........+++|||||||++.+.+... ....+
T Consensus       224 --~l~v~v~~~~~-~~~~~~~~~~~~~~~dIvI~T~~~L~~~~~~--~~~l~~~~~dlVIvDEAH~~kn~~~~~s~~~~~  298 (968)
T 3dmq_A          224 --NLRFALFDDER-YAEAQHDAYNPFDTEQLVICSLDFARRSKQR--LEHLCEAEWDLLVVDEAHHLVWSEDAPSREYQA  298 (968)
T ss_dssp             --CCCCEECCHHH-HHHHHHTTCSSSTTCSEEEECHHHHHTSTTT--THHHHTSCCCEEEECCSSCCCCBTTBCCHHHHH
T ss_pred             --CCCEEEEccch-hhhhhhhcccccccCCEEEEcHHHHhhCHHH--HHHhhhcCCCEEEehhhHhhcCCCCcchHHHHH
Confidence              66666554432 2111111   112469999999987432100  011234578999999999987655332 22233


Q ss_pred             HHhc-CCCCcEEEEeccCcHH----HHHHHHHHcCC--------------------------------------------
Q 002040          642 VQNI-RPDRQTVLFSATFPRQ----VEILARKVLNK--------------------------------------------  672 (976)
Q Consensus       642 l~~~-~~~~q~i~~SAT~~~~----~~~l~~~~l~~--------------------------------------------  672 (976)
                      +..+ ....++|++||||...    +..+...+...                                            
T Consensus       299 l~~L~~~~~~~L~LTATPi~n~~~el~sll~~L~p~~~~~~~~f~~~~~~~~~i~~~~~~l~~~~~~~~~~~~~L~~~l~  378 (968)
T 3dmq_A          299 IEQLAEHVPGVLLLTATPEQLGMESHFARLRLLDPNRFHDFAQFVEEQKNYCPVADAVAMLLAGNKLSNDELNMLGEMIG  378 (968)
T ss_dssp             HHHHHTTCSSEEESCSSCSSSCSSCTHHHHHHHCTTTCSSTHHHHHHHHHHHHHHHHHHTTTTSCCCCGGGTTSSTTTTC
T ss_pred             HHHHhhcCCcEEEEEcCCccCCHHHHHHHHHhcCccccCCHHHHHHHHHhHHHHHHHHHHHhccCCCCHHHHHHHHHHhc
Confidence            3333 3456799999998431    01111000000                                            


Q ss_pred             ------------------------------------CeEEEeCC---cccccCCceEEE---------------------
Q 002040          673 ------------------------------------PVEIQVGG---RSVVNKDITQLV---------------------  692 (976)
Q Consensus       673 ------------------------------------~~~i~~~~---~~~~~~~i~q~~---------------------  692 (976)
                                                          .+.+....   ..++...+....                     
T Consensus       379 ~~~~~~l~~~~~~~~~~~~~~~~~~i~~lld~~g~~~~l~r~~r~~i~~~p~r~~~~~~l~~~~~~~~~~~~~~~~~~~~  458 (968)
T 3dmq_A          379 EQDIEPLLQAANSDSEDAQSARQELVSMLMDRHGTSRVLFRNTRNGVKGFPKRELHTIKLPLPTQYQTAIKVSGIMGARK  458 (968)
T ss_dssp             TTCSSTTGGGTCCCSSCSTTTHHHHHHHHGGGCTTTTTEECCCTTTCCCCCCCCCCEEEECCCHHHHHHHHHHHHTTCCS
T ss_pred             chhhHHHHhcccchhhhhHHHHHHHHHHHHHhhCcchhhhhhhhhhhcccChhheEeeecCCCHHHHHHHHHHhhhhhhh
Confidence                                                00000000   000000000000                     


Q ss_pred             ------------------------EecCcchHHHHHHHHHHhhhcCCcEEEEecCHHHHHHHHHHHHH-CCCCceeccCC
Q 002040          693 ------------------------EVRPESDRFLRLLELLGEWYEKGKILIFVHSQEKCDALFRDLLK-HGYPCLSLHGA  747 (976)
Q Consensus       693 ------------------------~~~~~~~k~~~l~~~l~~~~~~~kvLIF~~s~~~~~~l~~~L~~-~~~~~~~lhg~  747 (976)
                                              .......|+..|..+|.. ...+++||||+++..++.|+..|.. .|+.+..+||+
T Consensus       459 ~~~~~~~~~l~pe~~~~~l~~~~~~~~~~~~K~~~L~~ll~~-~~~~k~iVF~~~~~~~~~l~~~L~~~~g~~~~~lhG~  537 (968)
T 3dmq_A          459 SAEDRARDMLYPERIYQEFEGDNATWWNFDPRVEWLMGYLTS-HRSQKVLVICAKAATALQLEQVLREREGIRAAVFHEG  537 (968)
T ss_dssp             SGGGGTHHHHCSGGGTTTTTSSSCCTTTTSHHHHHHHHHHHH-TSSSCCCEECSSTHHHHHHHHHHHTTTCCCEEEECTT
T ss_pred             hhHHHHhhhcChHHHHHHhhhhhhcccCccHHHHHHHHHHHh-CCCCCEEEEeCcHHHHHHHHHHHHHHcCCcEEEEeCC
Confidence                                    122334577888888876 4578999999999999999999995 69999999999


Q ss_pred             CCHHHHHHHHHHhccCC--ccEEEecCcccccCCCCCCcEEEEeCCCCCHHHHHHHhcccCCCCCccEEEEEecCCCcCc
Q 002040          748 KDQTDRESTISDFKSNV--CNLLIATSVAARGLDVKELELVINFDAPNHYEDYVHRVGRTGRAGRKGCAITFISEEDAKY  825 (976)
Q Consensus       748 ~~~~~R~~~~~~F~~g~--~~vLVaT~v~~~GlDi~~v~~VI~~d~p~s~~~y~Qr~GR~gR~g~~g~~~~~~~~~d~~~  825 (976)
                      |++.+|..++..|++|.  ++|||||+++++|||+|++++||+|++|+++..|+|++||+||.|+.|.|++|+.......
T Consensus       538 ~~~~~R~~~l~~F~~g~~~~~vLvaT~v~~~GlDl~~~~~VI~~d~p~~~~~~~Q~~GR~~R~Gq~~~v~v~~~~~~~t~  617 (968)
T 3dmq_A          538 MSIIERDRAAAWFAEEDTGAQVLLCSEIGSEGRNFQFASHMVMFDLPFNPDLLEQRIGRLDRIGQAHDIQIHVPYLEKTA  617 (968)
T ss_dssp             SCTTHHHHHHHHHHSTTSSCEEEECSCCTTCSSCCTTCCEEECSSCCSSHHHHHHHHHTTSCSSSCSCCEEEEEEETTSH
T ss_pred             CCHHHHHHHHHHHhCCCCcccEEEecchhhcCCCcccCcEEEEecCCCCHHHHHHHhhccccCCCCceEEEEEecCCChH
Confidence            99999999999999998  9999999999999999999999999999999999999999999999997777665544555


Q ss_pred             hHHHHHHH
Q 002040          826 SPDLVKAL  833 (976)
Q Consensus       826 ~~~i~~~l  833 (976)
                      ...|.+.+
T Consensus       618 ee~i~~~~  625 (968)
T 3dmq_A          618 QSVLVRWY  625 (968)
T ss_dssp             HHHHHHHH
T ss_pred             HHHHHHHH
Confidence            55566655

>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=100.00  E-value=1.1e-33  Score=299.36  Aligned_cols=217  Identities=40%  Similarity=0.726  Sum_probs=187.2

Q ss_pred             ccCCCCCccccccc-CCCCHHHHHHHHHcCCCCCcHHHHHHHHHHhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCC-
Q 002040          458 HGKDVPKPIKTWHQ-TGLTSKIMETIRKLNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPV-  535 (976)
Q Consensus       458 ~g~~~p~pi~~~~~-~~l~~~l~~~l~~~~~~~p~~~Q~~~i~~il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~-  535 (976)
                      .+..+|.|+.+|.+ +++++.+++.|..+||..|+|+|.++|+.+++|+++|+++|||||||++|++|++.++...... 
T Consensus        10 ~~~~~p~p~~~f~~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~l~~apTGsGKT~~~~l~~~~~l~~~~~~~   89 (228)
T 3iuy_A           10 EKRLIPKPTCRFKDAFQQYPDLLKSIIRVGILKPTPIQSQAWPIILQGIDLIVVAQTGTGKTLSYLMPGFIHLDSQPISR   89 (228)
T ss_dssp             SCCCCCCCCCSHHHHHTTCHHHHHHHHHHTCCSCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHC------
T ss_pred             ccCcCCCChhhHhhhhccCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHHHhccchh
Confidence            34567999999999 8999999999999999999999999999999999999999999999999999999888653211 


Q ss_pred             CCCCCCeEEEEccCHHHHHHHHHHHHHHHhhcCcEEEEeeCCCChHHHHHHHhcCCeEEEeCchhHHHHHHhcCCccccc
Q 002040          536 AAGDGPVGLIMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGGKITNL  615 (976)
Q Consensus       536 ~~~~~~~vLIl~Ptr~La~Q~~~~~~~~~~~~~~~~~~~~gg~~~~~~~~~l~~~~~Iiv~Tp~~L~~~l~~~~~~~~~l  615 (976)
                      ....++++|||+||++||.|++..+..+. ..++.+.+++||.....+...+..+++|+|+||++|.+++....   ..+
T Consensus        90 ~~~~~~~~lil~Pt~~L~~q~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~iiv~Tp~~l~~~~~~~~---~~~  165 (228)
T 3iuy_A           90 EQRNGPGMLVLTPTRELALHVEAECSKYS-YKGLKSICIYGGRNRNGQIEDISKGVDIIIATPGRLNDLQMNNS---VNL  165 (228)
T ss_dssp             ---CCCSEEEECSSHHHHHHHHHHHHHHC-CTTCCEEEECC------CHHHHHSCCSEEEECHHHHHHHHHTTC---CCC
T ss_pred             hccCCCcEEEEeCCHHHHHHHHHHHHHhc-ccCceEEEEECCCChHHHHHHhcCCCCEEEECHHHHHHHHHcCC---cCc
Confidence            12357899999999999999999999986 45889999999998888888888899999999999999876543   467


Q ss_pred             CCceEEEecCcccccccCCchHHHHHHHhcCCCCcEEEEeccCcHHHHHHHHHHcCCCeEEEe
Q 002040          616 RRVTYLVMDEADRMFDMGFEPQITRIVQNIRPDRQTVLFSATFPRQVEILARKVLNKPVEIQV  678 (976)
Q Consensus       616 ~~~~~vVlDEah~~~~~~f~~~i~~il~~~~~~~q~i~~SAT~~~~~~~l~~~~l~~~~~i~~  678 (976)
                      .++++|||||||++++++|...+..++..++++.|+|+||||+|+.+..++..++.+|+.+.+
T Consensus       166 ~~~~~lViDEah~~~~~~~~~~~~~i~~~~~~~~~~l~~SAT~~~~~~~~~~~~l~~p~~i~v  228 (228)
T 3iuy_A          166 RSITYLVIDEADKMLDMEFEPQIRKILLDVRPDRQTVMTSATWPDTVRQLALSYLKDPMIVYV  228 (228)
T ss_dssp             TTCCEEEECCHHHHHHTTCHHHHHHHHHHSCSSCEEEEEESCCCHHHHHHHHTTCSSCEEEEC
T ss_pred             ccceEEEEECHHHHhccchHHHHHHHHHhCCcCCeEEEEEeeCCHHHHHHHHHHCCCCEEEeC
Confidence            889999999999999999999999999999999999999999999999999999999987753

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

Probab=100.00  E-value=7.7e-34  Score=341.55  Aligned_cols=280  Identities=20%  Similarity=0.215  Sum_probs=207.7

Q ss_pred             HHHHHHHHhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHHHHhhcCcEEEE
Q 002040          494 QAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVMGVRCVP  573 (976)
Q Consensus       494 Q~~~i~~il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~~~~~~~~~~~~  573 (976)
                      |.......+.++++|++||||||||+.++..    +...        +.++|++||++||.|++..+..    .|+.+..
T Consensus       145 ~~~p~ar~l~rk~vlv~apTGSGKT~~al~~----l~~~--------~~gl~l~PtR~LA~Qi~~~l~~----~g~~v~l  208 (677)
T 3rc3_A          145 NWYPDARAMQRKIIFHSGPTNSGKTYHAIQK----YFSA--------KSGVYCGPLKLLAHEIFEKSNA----AGVPCDL  208 (677)
T ss_dssp             GGCHHHHTSCCEEEEEECCTTSSHHHHHHHH----HHHS--------SSEEEEESSHHHHHHHHHHHHH----TTCCEEE
T ss_pred             hhCHHHHhcCCCEEEEEcCCCCCHHHHHHHH----HHhc--------CCeEEEeCHHHHHHHHHHHHHh----cCCcEEE
Confidence            3334445678999999999999999843333    3321        2359999999999999999877    4788999


Q ss_pred             eeCCCChHHHHHHHhcCCeEEEeCchhHHHHHHhcCCcccccCCceEEEecCcccccccCCchHHHHHHHhcC-CCCcEE
Q 002040          574 VYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMGFEPQITRIVQNIR-PDRQTV  652 (976)
Q Consensus       574 ~~gg~~~~~~~~~l~~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDEah~~~~~~f~~~i~~il~~~~-~~~q~i  652 (976)
                      ++|+.....  ..-....+++++|++.+           ..+..+++|||||||++++.+|...+..++..++ ...+++
T Consensus       209 ltG~~~~iv--~TpGr~~~il~~T~e~~-----------~l~~~v~lvVIDEaH~l~d~~~g~~~~~~l~~l~~~~i~il  275 (677)
T 3rc3_A          209 VTGEERVTV--QPNGKQASHVSCTVEMC-----------SVTTPYEVAVIDEIQMIRDPARGWAWTRALLGLCAEEVHLC  275 (677)
T ss_dssp             ECSSCEECC--STTCCCCSEEEEEGGGC-----------CSSSCEEEEEECSGGGGGCTTTHHHHHHHHHHCCEEEEEEE
T ss_pred             EECCeeEEe--cCCCcccceeEecHhHh-----------hhcccCCEEEEecceecCCccchHHHHHHHHccCccceEEE
Confidence            999864400  00001256777776543           2346789999999999999999999999998887 678999


Q ss_pred             EEeccCcHHHHHHHHHHcCCCeEEEeCCcccccCCceEEEEecCcchHHHHHHHHHHhhhcCCcEEEEecCHHHHHHHHH
Q 002040          653 LFSATFPRQVEILARKVLNKPVEIQVGGRSVVNKDITQLVEVRPESDRFLRLLELLGEWYEKGKILIFVHSQEKCDALFR  732 (976)
Q Consensus       653 ~~SAT~~~~~~~l~~~~l~~~~~i~~~~~~~~~~~i~q~~~~~~~~~k~~~l~~~l~~~~~~~kvLIF~~s~~~~~~l~~  732 (976)
                      ++|||.+ .+..++... ...+.+........   +    .+....      +..+...  ....||||+++..++.++.
T Consensus       276 ~~SAT~~-~i~~l~~~~-~~~~~v~~~~r~~~---l----~~~~~~------l~~l~~~--~~g~iIf~~s~~~ie~la~  338 (677)
T 3rc3_A          276 GEPAAID-LVMELMYTT-GEEVEVRDYKRLTP---I----SVLDHA------LESLDNL--RPGDCIVCFSKNDIYSVSR  338 (677)
T ss_dssp             ECGGGHH-HHHHHHHHH-TCCEEEEECCCSSC---E----EECSSC------CCSGGGC--CTTEEEECSSHHHHHHHHH
T ss_pred             eccchHH-HHHHHHHhc-CCceEEEEeeecch---H----HHHHHH------HHHHHhc--CCCCEEEEcCHHHHHHHHH
Confidence            9999953 344444333 34443322111100   0    000000      0111111  3455889999999999999


Q ss_pred             HHHHCCCCceeccCCCCHHHHHHHHHHhcc--CCccEEEecCcccccCCCCCCcEEEEeCC--------------CCCHH
Q 002040          733 DLLKHGYPCLSLHGAKDQTDRESTISDFKS--NVCNLLIATSVAARGLDVKELELVINFDA--------------PNHYE  796 (976)
Q Consensus       733 ~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~--g~~~vLVaT~v~~~GlDi~~v~~VI~~d~--------------p~s~~  796 (976)
                      .|...++.+..+||+|++.+|..++..|++  |.++|||||+++++|||| ++++||+++.              |.+..
T Consensus       339 ~L~~~g~~v~~lHG~L~~~~R~~~~~~F~~~~g~~~VLVATdi~e~GlDi-~v~~VI~~~~~k~~~~~~G~~~~~p~s~~  417 (677)
T 3rc3_A          339 QIEIRGLESAVIYGSLPPGTKLAQAKKFNDPNDPCKILVATDAIGMGLNL-SIRRIIFYSLIKPSINEKGERELEPITTS  417 (677)
T ss_dssp             HHHHTTCCCEEECTTSCHHHHHHHHHHHHCTTSSCCEEEECGGGGSSCCC-CBSEEEESCSBC-----------CBCCHH
T ss_pred             HHHhcCCCeeeeeccCCHHHHHHHHHHHHccCCCeEEEEeCcHHHCCcCc-CccEEEECCccccccccCCccccccCCHH
Confidence            999999999999999999999999999999  899999999999999999 9999999999              88999


Q ss_pred             HHHHHhcccCCCCCc---cEEEEEecC
Q 002040          797 DYVHRVGRTGRAGRK---GCAITFISE  820 (976)
Q Consensus       797 ~y~Qr~GR~gR~g~~---g~~~~~~~~  820 (976)
                      .|+||+|||||.|..   |.|++++..
T Consensus       418 ~~~QR~GRAGR~g~~g~~G~v~~l~~~  444 (677)
T 3rc3_A          418 QALQIAGRAGRFSSRFKEGEVTTMNHE  444 (677)
T ss_dssp             HHHHHHTTBTCTTSSCSSEEEEESSTT
T ss_pred             HHHHHhcCCCCCCCCCCCEEEEEEecc
Confidence            999999999999964   777666543

>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=100.00  E-value=8.4e-33  Score=296.44  Aligned_cols=210  Identities=40%  Similarity=0.665  Sum_probs=192.7

Q ss_pred             CCcccccccCCCCHHHHHHHHHcCCCCCcHHHHHHHHHHhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCe
Q 002040          463 PKPIKTWHQTGLTSKIMETIRKLNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPV  542 (976)
Q Consensus       463 p~pi~~~~~~~l~~~l~~~l~~~~~~~p~~~Q~~~i~~il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~  542 (976)
                      +.++.+|.++++++.+...|..+||..|+++|.++|+.++.|+++|++++||||||++|++|++..+...+     .+++
T Consensus        39 ~~~~~~f~~l~l~~~l~~~l~~~g~~~~~~~Q~~~i~~i~~~~~~lv~a~TGsGKT~~~~~~il~~l~~~~-----~~~~  113 (249)
T 3ber_A           39 EEETKTFKDLGVTDVLCEACDQLGWTKPTKIQIEAIPLALQGRDIIGLAETGSGKTGAFALPILNALLETP-----QRLF  113 (249)
T ss_dssp             HHHHCCTGGGTCCHHHHHHHHHTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHHHSC-----CSSC
T ss_pred             ccccCCHHHcCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCEEEEcCCCCCchhHhHHHHHHHHhcCC-----CCce
Confidence            45678899999999999999999999999999999999999999999999999999999999999887642     3678


Q ss_pred             EEEEccCHHHHHHHHHHHHHHHhhcCcEEEEeeCCCChHHHHHHHhcCCeEEEeCchhHHHHHHhcCCcccccCCceEEE
Q 002040          543 GLIMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLV  622 (976)
Q Consensus       543 vLIl~Ptr~La~Q~~~~~~~~~~~~~~~~~~~~gg~~~~~~~~~l~~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vV  622 (976)
                      +|||+||++|+.|+++.+..++..+++.+.+++||.....+...+..+++|+|+||++|.+++....  ...+..+++||
T Consensus       114 ~lil~Ptr~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~I~v~Tp~~l~~~l~~~~--~~~l~~~~~lV  191 (249)
T 3ber_A          114 ALVLTPTRELAFQISEQFEALGSSIGVQSAVIVGGIDSMSQSLALAKKPHIIIATPGRLIDHLENTK--GFNLRALKYLV  191 (249)
T ss_dssp             EEEECSSHHHHHHHHHHHHHHHGGGTCCEEEECTTSCHHHHHHHHHTCCSEEEECHHHHHHHHHHST--TCCCTTCCEEE
T ss_pred             EEEEeCCHHHHHHHHHHHHHHhccCCeeEEEEECCCChHHHHHHhcCCCCEEEECHHHHHHHHHcCC--CcCccccCEEE
Confidence            9999999999999999999999989999999999999888888888899999999999999887532  24578899999


Q ss_pred             ecCcccccccCCchHHHHHHHhcCCCCcEEEEeccCcHHHHHHHHHHcCCCeEEEeC
Q 002040          623 MDEADRMFDMGFEPQITRIVQNIRPDRQTVLFSATFPRQVEILARKVLNKPVEIQVG  679 (976)
Q Consensus       623 lDEah~~~~~~f~~~i~~il~~~~~~~q~i~~SAT~~~~~~~l~~~~l~~~~~i~~~  679 (976)
                      |||||++++++|...+..++..+++..|+|+||||+++.+..++..++.+|+.+.++
T Consensus       192 iDEah~l~~~~~~~~l~~i~~~~~~~~~~l~~SAT~~~~v~~~~~~~l~~p~~i~v~  248 (249)
T 3ber_A          192 MDEADRILNMDFETEVDKILKVIPRDRKTFLFSATMTKKVQKLQRAALKNPVKCAVS  248 (249)
T ss_dssp             ECSHHHHHHTTCHHHHHHHHHSSCSSSEEEEEESSCCHHHHHHHHHHCSSCEEEECC
T ss_pred             EcChhhhhccChHHHHHHHHHhCCCCCeEEEEeccCCHHHHHHHHHHCCCCEEEEec
Confidence            999999999999999999999999999999999999999999999999999887653

>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=100.00  E-value=1.1e-32  Score=326.78  Aligned_cols=309  Identities=18%  Similarity=0.226  Sum_probs=218.1

Q ss_pred             CCCcHHHHHHHHHHh----cCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHHH
Q 002040          488 EKPMPIQAQALPVIM----SGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKF  563 (976)
Q Consensus       488 ~~p~~~Q~~~i~~il----~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~~  563 (976)
                      ..|+|+|.+++.++.    .+.++|++++||+|||++++..+......      +....+|||||+ .|+.||..+|.+|
T Consensus        36 ~~L~~~Q~~~v~~l~~~~~~~~~~ilad~~GlGKT~~ai~~i~~~~~~------~~~~~~LIv~P~-~l~~qw~~e~~~~  108 (500)
T 1z63_A           36 ANLRPYQIKGFSWMRFMNKLGFGICLADDMGLGKTLQTIAVFSDAKKE------NELTPSLVICPL-SVLKNWEEELSKF  108 (500)
T ss_dssp             SCCCHHHHHHHHHHHHHHHTTCCEEECCCTTSCHHHHHHHHHHHHHHT------TCCSSEEEEECS-TTHHHHHHHHHHH
T ss_pred             ccchHHHHHHHHHHHHHhhCCCCEEEEeCCCCcHHHHHHHHHHHHHhc------CCCCCEEEEccH-HHHHHHHHHHHHH
Confidence            368999999999874    57899999999999999976555444322      224579999995 5889999999998


Q ss_pred             HhhcCcEEEEeeCCCChHHHHHHHhcCCeEEEeCchhHHHHHHhcCCcccccCCceEEEecCcccccccCCchHHHHHHH
Q 002040          564 AKVMGVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMGFEPQITRIVQ  643 (976)
Q Consensus       564 ~~~~~~~~~~~~gg~~~~~~~~~l~~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDEah~~~~~~f~~~i~~il~  643 (976)
                      +.  ++.+.+++|+...     ......+|+|+||+.|.....      .....+++|||||||++.+.+  ......+.
T Consensus       109 ~~--~~~v~~~~g~~~~-----~~~~~~~ivi~t~~~l~~~~~------l~~~~~~~vIvDEaH~~kn~~--~~~~~~l~  173 (500)
T 1z63_A          109 AP--HLRFAVFHEDRSK-----IKLEDYDIILTTYAVLLRDTR------LKEVEWKYIVIDEAQNIKNPQ--TKIFKAVK  173 (500)
T ss_dssp             CT--TSCEEECSSSTTS-----CCGGGSSEEEEEHHHHTTCHH------HHTCCEEEEEEETGGGGSCTT--SHHHHHHH
T ss_pred             CC--CceEEEEecCchh-----ccccCCcEEEeeHHHHhccch------hcCCCcCEEEEeCccccCCHh--HHHHHHHH
Confidence            75  4556666665422     112357999999998865432      233468999999999987654  34555666


Q ss_pred             hcCCCCcEEEEeccCcHH----HHHHHH---------------------------------HHcCCCeEEEeCCc-----
Q 002040          644 NIRPDRQTVLFSATFPRQ----VEILAR---------------------------------KVLNKPVEIQVGGR-----  681 (976)
Q Consensus       644 ~~~~~~q~i~~SAT~~~~----~~~l~~---------------------------------~~l~~~~~i~~~~~-----  681 (976)
                      .++ ..+.+++||||..+    +..+..                                 .++ .|+.+.....     
T Consensus       174 ~l~-~~~~l~LTaTP~~n~~~el~~ll~~l~p~~~~~~~~f~~~~~~~~~~~~~~~~~~l~~~l-~~~~lrr~k~~~~~~  251 (500)
T 1z63_A          174 ELK-SKYRIALTGTPIENKVDDLWSIMTFLNPGLLGSYSEFKSKFATPIKKGDNMAKEELKAII-SPFILRRTKYDKAII  251 (500)
T ss_dssp             TSC-EEEEEEECSSCSTTCHHHHHHHHHHHSTTTTCCHHHHHTTTHHHHHTTCHHHHHHHHHHH-TTTEECCCTTCHHHH
T ss_pred             hhc-cCcEEEEecCCCCCCHHHHHHHHHHhCCCcCCCHHHHHHHhccccccccHHHHHHHHHHH-hhHeeeecccccchh
Confidence            663 45789999998432    111111                                 111 1222211100     


Q ss_pred             ccccCCceEEEEec--------------------------------------------------------CcchHHHHHH
Q 002040          682 SVVNKDITQLVEVR--------------------------------------------------------PESDRFLRLL  705 (976)
Q Consensus       682 ~~~~~~i~q~~~~~--------------------------------------------------------~~~~k~~~l~  705 (976)
                      ...+......+.+.                                                        ..+.|+..+.
T Consensus       252 ~~lp~~~~~~v~~~l~~~~~~~y~~~~~~~~~~~~~~~~~~~~~~~~~~l~~lr~~~~~p~l~~~~~~~~~~s~K~~~l~  331 (500)
T 1z63_A          252 NDLPDKIETNVYCNLTPEQAAMYKAEVENLFNNIDSVTGIKRKGMILSTLLKLKQIVDHPALLKGGEQSVRRSGKMIRTM  331 (500)
T ss_dssp             TTSCSEEEEEEEECCCHHHHHHHHHHHHHHTTTTTTCCTHHHHHHHHHHHHHHHHHTTCTHHHHCSCCCSTTCHHHHHHH
T ss_pred             hcCCCCeEEEEEcCCCHHHHHHHHHHHHHHHHHHHhhhcccchHHHHHHHHHHHHHhCCHHHhcCccchhhcchhHHHHH
Confidence            00111111111111                                                        1235566666


Q ss_pred             HHHHhhh-cCCcEEEEecCHHHHHHHHHHHHHC-CCCceeccCCCCHHHHHHHHHHhccC-Ccc-EEEecCcccccCCCC
Q 002040          706 ELLGEWY-EKGKILIFVHSQEKCDALFRDLLKH-GYPCLSLHGAKDQTDRESTISDFKSN-VCN-LLIATSVAARGLDVK  781 (976)
Q Consensus       706 ~~l~~~~-~~~kvLIF~~s~~~~~~l~~~L~~~-~~~~~~lhg~~~~~~R~~~~~~F~~g-~~~-vLVaT~v~~~GlDi~  781 (976)
                      .+|.... .+.++||||++...++.++..|... |+.+..+||++++.+|..++..|++| .+. |||||+++++|||++
T Consensus       332 ~~l~~~~~~~~k~lvF~~~~~~~~~l~~~l~~~~~~~~~~~~g~~~~~~R~~~~~~F~~~~~~~vil~st~~~~~Glnl~  411 (500)
T 1z63_A          332 EIIEEALDEGDKIAIFTQFVDMGKIIRNIIEKELNTEVPFLYGELSKKERDDIISKFQNNPSVKFIVLSVKAGGFGINLT  411 (500)
T ss_dssp             HHHHHHHTTTCCEEEECSCHHHHHHHHHHHHHHHTCCCCEEETTSCHHHHHHHHHHHHHCTTCCCCEEECCCC-CCCCCT
T ss_pred             HHHHHHHccCCcEEEEEehHHHHHHHHHHHHHhhCCCeEEEECCCCHHHHHHHHHHhcCCCCCCEEEEecccccCCCchh
Confidence            6676654 3569999999999999999999885 99999999999999999999999988 454 899999999999999


Q ss_pred             CCcEEEEeCCCCCHHHHHHHhcccCCCCCccEE--EEEecC
Q 002040          782 ELELVINFDAPNHYEDYVHRVGRTGRAGRKGCA--ITFISE  820 (976)
Q Consensus       782 ~v~~VI~~d~p~s~~~y~Qr~GR~gR~g~~g~~--~~~~~~  820 (976)
                      ++++||+|++|||+..|+|++||++|.|+.+.|  |.|++.
T Consensus       412 ~~~~vi~~d~~~~~~~~~Q~~gR~~R~Gq~~~v~v~~lv~~  452 (500)
T 1z63_A          412 SANRVIHFDRWWNPAVEDQATDRVYRIGQTRNVIVHKLISV  452 (500)
T ss_dssp             TCSEEEESSCCSCC---CHHHHTTTTTTTTSCEEEEEEEET
T ss_pred             hCCEEEEeCCCCCcchHHHHHHHHHHcCCCCeeEEEEEEeC
Confidence            999999999999999999999999999987765  445554

>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=100.00  E-value=3.8e-33  Score=298.72  Aligned_cols=232  Identities=34%  Similarity=0.600  Sum_probs=199.1

Q ss_pred             HHHHHHhhcCceeccCCCCCcccccccC----CCCHHHHHHHHHcCCCCCcHHHHHHHHHHhcCCCEEEEcCCCCchHHH
Q 002040          445 EVSAYRKQLELKIHGKDVPKPIKTWHQT----GLTSKIMETIRKLNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLA  520 (976)
Q Consensus       445 ~~~~~~~~~~i~~~g~~~p~pi~~~~~~----~l~~~l~~~l~~~~~~~p~~~Q~~~i~~il~g~d~i~~a~TGsGKT~~  520 (976)
                      ++..+++.+.+.+.|..+|.|+.+|.++    ++++.+++.|..+||..|+|+|.++|+.++.|+++|+++|||||||++
T Consensus         3 ~~~~~~~~~~i~~~~~~~p~~~~~f~~l~~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~l~~a~TGsGKT~~   82 (245)
T 3dkp_A            3 KINFLRNKHKIHVQGTDLPDPIATFQQLDQEYKINSRLLQNILDAGFQMPTPIQMQAIPVMLHGRELLASAPTGSGKTLA   82 (245)
T ss_dssp             HHHHHHHHTTEEEESSSCCCCCSSHHHHHHHHCCCHHHHHHHHHTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSCHHHH
T ss_pred             hHHHHHHhCceEecCCCCCCcccCHHHhhhccCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCCcHHHH
Confidence            4677888899999999999999999987    899999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHHHHhhcCcEEEEeeCCCChHHHH-HHHhcCCeEEEeCch
Q 002040          521 FVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQI-SELKRGTEIVVCTPG  599 (976)
Q Consensus       521 ~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~~~~~~~~~~~~~~gg~~~~~~~-~~l~~~~~Iiv~Tp~  599 (976)
                      |++|++..+...    ...++++|||+||++||.|++..+..++...++.+.+++|+....... .....+++|+|+||+
T Consensus        83 ~~l~~l~~l~~~----~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~I~v~Tp~  158 (245)
T 3dkp_A           83 FSIPILMQLKQP----ANKGFRALIISPTRELASQIHRELIKISEGTGFRIHMIHKAAVAAKKFGPKSSKKFDILVTTPN  158 (245)
T ss_dssp             HHHHHHHHHCSC----CSSSCCEEEECSSHHHHHHHHHHHHHHTTTSCCCEECCCHHHHHHTTTSTTSCCCCCEEEECHH
T ss_pred             HHHHHHHHHhhc----ccCCceEEEEeCCHHHHHHHHHHHHHHhcccCceEEEEecCccHHHHhhhhhcCCCCEEEECHH
Confidence            999999988642    235778999999999999999999999988898888887765333221 112346799999999


Q ss_pred             hHHHHHHhcCCcccccCCceEEEecCcccccc---cCCchHHHHHHHhcC-CCCcEEEEeccCcHHHHHHHHHHcCCCeE
Q 002040          600 RMIDILCTSGGKITNLRRVTYLVMDEADRMFD---MGFEPQITRIVQNIR-PDRQTVLFSATFPRQVEILARKVLNKPVE  675 (976)
Q Consensus       600 ~L~~~l~~~~~~~~~l~~~~~vVlDEah~~~~---~~f~~~i~~il~~~~-~~~q~i~~SAT~~~~~~~l~~~~l~~~~~  675 (976)
                      +|.+++.... ....+.++.+|||||||++++   .+|...+..++..+. +..|+|+||||+|+.+..++..++.+|+.
T Consensus       159 ~l~~~l~~~~-~~~~~~~~~~lViDEah~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~SAT~~~~v~~~~~~~l~~p~~  237 (245)
T 3dkp_A          159 RLIYLLKQDP-PGIDLASVEWLVVDESDKLFEDGKTGFRDQLASIFLACTSHKVRRAMFSATFAYDVEQWCKLNLDNVIS  237 (245)
T ss_dssp             HHHHHHHSSS-CSCCCTTCCEEEESSHHHHHHHC--CHHHHHHHHHHHCCCTTCEEEEEESSCCHHHHHHHHHHSSSCEE
T ss_pred             HHHHHHHhCC-CCcccccCcEEEEeChHHhcccccccHHHHHHHHHHhcCCCCcEEEEEeccCCHHHHHHHHHhCCCCEE
Confidence            9999886642 234688899999999999988   468888888887764 57899999999999999999999999999


Q ss_pred             EEeCCc
Q 002040          676 IQVGGR  681 (976)
Q Consensus       676 i~~~~~  681 (976)
                      +.++..
T Consensus       238 i~~~~~  243 (245)
T 3dkp_A          238 VSIGAR  243 (245)
T ss_dssp             EEECC-
T ss_pred             EEeCCC
Confidence            988754

>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=100.00  E-value=5.9e-33  Score=295.61  Aligned_cols=213  Identities=32%  Similarity=0.539  Sum_probs=178.8

Q ss_pred             cCCCCCcccccccCCCCHHHHHHHHHcCCCCCcHHHHHHHHHHhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCC
Q 002040          459 GKDVPKPIKTWHQTGLTSKIMETIRKLNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAG  538 (976)
Q Consensus       459 g~~~p~pi~~~~~~~l~~~l~~~l~~~~~~~p~~~Q~~~i~~il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~  538 (976)
                      ..+.|.++.+|.+++|++.++..|..+||..|+|+|.++|+.++.++++|++++||||||++|++|++..+...     .
T Consensus        22 ~~~~~~~~~~f~~l~l~~~l~~~l~~~g~~~~~~~Q~~ai~~i~~~~~~li~apTGsGKT~~~~l~~l~~l~~~-----~   96 (237)
T 3bor_A           22 ESNWNEIVDNFDDMNLKESLLRGIYAYGFEKPSAIQQRAIIPCIKGYDVIAQAQSGTGKTATFAISILQQLEIE-----F   96 (237)
T ss_dssp             -----CCCCSGGGSCCCHHHHHHHHHHTCCSCCHHHHHHHHHHHTTCCEEECCCSSHHHHHHHHHHHHHHCCTT-----S
T ss_pred             cCCCCCccCChhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCCcHHHHHHHHHHHHHHhc-----C
Confidence            34567889999999999999999999999999999999999999999999999999999999999999887542     2


Q ss_pred             CCCeEEEEccCHHHHHHHHHHHHHHHhhcCcEEEEeeCCCChHHHHHHHhcC-CeEEEeCchhHHHHHHhcCCcccccCC
Q 002040          539 DGPVGLIMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQISELKRG-TEIVVCTPGRMIDILCTSGGKITNLRR  617 (976)
Q Consensus       539 ~~~~vLIl~Ptr~La~Q~~~~~~~~~~~~~~~~~~~~gg~~~~~~~~~l~~~-~~Iiv~Tp~~L~~~l~~~~~~~~~l~~  617 (976)
                      .++++|||+||++|+.|++..+..++...++.+..++||.....+...+..+ ++|+|+||++|.+++....   ..+..
T Consensus        97 ~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~Ilv~Tp~~l~~~l~~~~---~~~~~  173 (237)
T 3bor_A           97 KETQALVLAPTRELAQQIQKVILALGDYMGATCHACIGGTNVRNEMQKLQAEAPHIVVGTPGRVFDMLNRRY---LSPKW  173 (237)
T ss_dssp             CSCCEEEECSSHHHHHHHHHHHHHHTTTTTCCEEEECC-------------CCCSEEEECHHHHHHHHHTTS---SCSTT
T ss_pred             CCceEEEEECcHHHHHHHHHHHHHHhhhcCceEEEEECCCchHHHHHHHhcCCCCEEEECHHHHHHHHHhCC---cCccc
Confidence            4678999999999999999999999988899999999998877777667665 8999999999999886532   45778


Q ss_pred             ceEEEecCcccccccCCchHHHHHHHhcCCCCcEEEEeccCcHHHHHHHHHHcCCCeEEEeC
Q 002040          618 VTYLVMDEADRMFDMGFEPQITRIVQNIRPDRQTVLFSATFPRQVEILARKVLNKPVEIQVG  679 (976)
Q Consensus       618 ~~~vVlDEah~~~~~~f~~~i~~il~~~~~~~q~i~~SAT~~~~~~~l~~~~l~~~~~i~~~  679 (976)
                      +.+|||||||++++++|...+..++..+++..|+|+||||+|+.+..++..++.+|+.+.+.
T Consensus       174 ~~~lViDEah~~~~~~~~~~l~~i~~~~~~~~~~i~~SAT~~~~~~~~~~~~l~~p~~i~v~  235 (237)
T 3bor_A          174 IKMFVLDEADEMLSRGFKDQIYEIFQKLNTSIQVVLLSATMPTDVLEVTKKFMRDPIRILVK  235 (237)
T ss_dssp             CCEEEEESHHHHHHTTCHHHHHHHHHHSCTTCEEEEECSSCCHHHHHHHHHHCSSCEEEC--
T ss_pred             CcEEEECCchHhhccCcHHHHHHHHHhCCCCCeEEEEEEecCHHHHHHHHHHCCCCEEEEec
Confidence            99999999999999999999999999999999999999999999999999999999887653

>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=100.00  E-value=5.6e-33  Score=305.81  Aligned_cols=215  Identities=28%  Similarity=0.474  Sum_probs=186.7

Q ss_pred             ceeccCCCCC---cccccccCCCCHHHHHHHHHcCCCCCcHHHHHHHHHHhcC--CCEEEEcCCCCchHHHHHHHHHHHH
Q 002040          455 LKIHGKDVPK---PIKTWHQTGLTSKIMETIRKLNYEKPMPIQAQALPVIMSG--RDCIGVAKTGSGKTLAFVLPMLRHI  529 (976)
Q Consensus       455 i~~~g~~~p~---pi~~~~~~~l~~~l~~~l~~~~~~~p~~~Q~~~i~~il~g--~d~i~~a~TGsGKT~~~~l~il~~l  529 (976)
                      +.+.+.+++.   ++.+|.+++|++.++..|..+||..|+|+|.++||.++.|  +++|++|+||||||++|++|++.++
T Consensus        77 v~v~~~~~~~p~~~~~~f~~l~l~~~l~~~l~~~g~~~pt~iQ~~ai~~il~~~~~~~l~~a~TGsGKT~a~~lp~l~~l  156 (300)
T 3fmo_B           77 VEVLQRDPNSPLYSVKSFEELRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLAMLSQV  156 (300)
T ss_dssp             EEEECSSTTCCCCCCCCSGGGTCCHHHHHHHHHTTCCSCCHHHHHHHHHHTSSSCCCEEEECCTTSSHHHHHHHHHHHHC
T ss_pred             ceeccCCCCCCcCCcCCHhhcCCCHHHHHHHHHcCCCCCCHHHHHHHHHHHcCCCCeEEEECCCCCCccHHHHHHHHHhh
Confidence            3444444443   4678999999999999999999999999999999999997  9999999999999999999999987


Q ss_pred             hcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHHHHhhc-CcEEEEeeCCCChHHHHHHHhcCCeEEEeCchhHHHHHHhc
Q 002040          530 KDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVM-GVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTS  608 (976)
Q Consensus       530 ~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~~~~~~-~~~~~~~~gg~~~~~~~~~l~~~~~Iiv~Tp~~L~~~l~~~  608 (976)
                      ...     ..++++|||+||++||.|++..+..++..+ ++.+.+++||.......   ..+++|+||||++|.+++...
T Consensus       157 ~~~-----~~~~~~lil~PtreLa~Q~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~---~~~~~IlV~TP~~l~~~l~~~  228 (300)
T 3fmo_B          157 EPA-----NKYPQCLCLSPTYELALQTGKVIEQMGKFYPELKLAYAVRGNKLERGQ---KISEQIVIGTPGTVLDWCSKL  228 (300)
T ss_dssp             CTT-----SCSCCEEEECSSHHHHHHHHHHHHHHTTTSTTCCEEEESTTCCCCTTC---CCCCSEEEECHHHHHHHHTTT
T ss_pred             hcc-----CCCceEEEEcCcHHHHHHHHHHHHHHHhhCCCcEEEEEeCCccHhhhh---cCCCCEEEECHHHHHHHHHhc
Confidence            643     357899999999999999999999998765 68888888887653321   456799999999999998543


Q ss_pred             CCcccccCCceEEEecCcccccc-cCCchHHHHHHHhcCCCCcEEEEeccCcHHHHHHHHHHcCCCeEEEeC
Q 002040          609 GGKITNLRRVTYLVMDEADRMFD-MGFEPQITRIVQNIRPDRQTVLFSATFPRQVEILARKVLNKPVEIQVG  679 (976)
Q Consensus       609 ~~~~~~l~~~~~vVlDEah~~~~-~~f~~~i~~il~~~~~~~q~i~~SAT~~~~~~~l~~~~l~~~~~i~~~  679 (976)
                        ....+.++.+|||||||+|++ .+|...+..|+..+++.+|+|+||||++..+..++..++.+|+.|.+.
T Consensus       229 --~~~~l~~l~~lVlDEad~l~~~~~~~~~~~~i~~~~~~~~q~i~~SAT~~~~v~~~a~~~l~~p~~i~~~  298 (300)
T 3fmo_B          229 --KFIDPKKIKVFVLDEADVMIATQGHQDQSIRIQRMLPRNCQMLLFSATFEDSVWKFAQKVVPDPNVIKLK  298 (300)
T ss_dssp             --CCCCGGGCSEEEETTHHHHHHSTTHHHHHHHHHTTSCTTCEEEEEESCCCHHHHHHHHHHSSSCEEEEEC
T ss_pred             --CCCChhhceEEEEeCHHHHhhccCcHHHHHHHHHhCCCCCEEEEEeccCCHHHHHHHHHHCCCCeEEEec
Confidence              235678999999999999998 689999999999999999999999999999999999999999988764

>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=100.00  E-value=1.2e-31  Score=311.88  Aligned_cols=321  Identities=20%  Similarity=0.221  Sum_probs=239.5

Q ss_pred             cCCCCCcHHHHHHHHHHhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHHHH
Q 002040          485 LNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFA  564 (976)
Q Consensus       485 ~~~~~p~~~Q~~~i~~il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~~~  564 (976)
                      +|+ .|++.|..+...+..|+  |..+.||+|||+++++|++...+.        |..|.||+||..||.|-+.++..++
T Consensus        72 lg~-r~~dvQligg~~L~~G~--iaEM~TGEGKTLva~lp~~lnAL~--------G~~vhVvT~ndyLA~rdae~m~~l~  140 (822)
T 3jux_A           72 LGM-RPFDVQVMGGIALHEGK--VAEMKTGEGKTLAATMPIYLNALI--------GKGVHLVTVNDYLARRDALWMGPVY  140 (822)
T ss_dssp             TSC-CCCHHHHHHHHHHHTTC--EEECCTTSCHHHHTHHHHHHHHTT--------SSCEEEEESSHHHHHHHHHHHHHHH
T ss_pred             hCC-CCcHHHHHHHHHHhCCC--hhhccCCCCccHHHHHHHHHHHhc--------CCceEEEeccHHHHHhHHHHHHHHH
Confidence            565 48999999999888877  899999999999999999855443        5679999999999999999999999


Q ss_pred             hhcCcEEEEeeCC--------------------------------------------------CChHHHHHHHhcCCeEE
Q 002040          565 KVMGVRCVPVYGG--------------------------------------------------SGVAQQISELKRGTEIV  594 (976)
Q Consensus       565 ~~~~~~~~~~~gg--------------------------------------------------~~~~~~~~~l~~~~~Ii  594 (976)
                      ..+|+.|.+++..                                                  .+..+.....  .|+|+
T Consensus       141 ~~Lglsvg~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~err~aY--~~DIt  218 (822)
T 3jux_A          141 LFLGLRVGVINSLGKSYEVVWKNPDLARKAIEENWSVWPDGFNGEVLKEESMNKEAVEAFQVELKEITRKEAY--LCDVT  218 (822)
T ss_dssp             HHTTCCEEEEETTTEEEEEEESSHHHHHHHHHTTCCSSCTTCCSSSCCGGGSCHHHHTTTCEECCBCCHHHHH--HSSEE
T ss_pred             HHhCCEEEEEcCCCcccccccccchhhhhhhcccccccccccccccccccccccccchhccccCCHHHHHHHh--cCCCE
Confidence            9999999999882                                                  1111222222  38999


Q ss_pred             EeCchhH-HHHHHhcC---CcccccCCceEEEecCccccc-cc--------------------------------CCc--
Q 002040          595 VCTPGRM-IDILCTSG---GKITNLRRVTYLVMDEADRMF-DM--------------------------------GFE--  635 (976)
Q Consensus       595 v~Tp~~L-~~~l~~~~---~~~~~l~~~~~vVlDEah~~~-~~--------------------------------~f~--  635 (976)
                      ++|..-| .++|..+-   ....-...+.|.||||+|.++ +.                                .|.  
T Consensus       219 YgTn~EfgFDYLRDnm~~~~~~~vqR~~~~aIVDEvDSiLIDeArtPLiISg~~~~~~~~y~~~~~~v~~l~~~~dy~vd  298 (822)
T 3jux_A          219 YGTNNEFGFDYLRDNLVLDYNDKVQRGHFYAIVDEADSVLIDEARTPLIISGPSKESPSVYRRFAQIAKKFVKDKDFTVD  298 (822)
T ss_dssp             EEEHHHHHHHHHHHTSCSSTTSCCCCCCCEEEEETHHHHHTTGGGSCEEEECCCCSCHHHHHHHHHHTTSSCBTTTEEEC
T ss_pred             EccCcchhhHhHHhhccCCHHHhccCCCCeEEEecccceeecCCCCCceeeCCCCCccHHHHHHHHHHHhcCcCCcEEEE
Confidence            9999887 45555431   111224678899999999752 10                                000  


Q ss_pred             -------------------------------hHHHHHHHh------cCCC------------------------------
Q 002040          636 -------------------------------PQITRIVQN------IRPD------------------------------  648 (976)
Q Consensus       636 -------------------------------~~i~~il~~------~~~~------------------------------  648 (976)
                                                     ..+..+...      +..+                              
T Consensus       299 ek~~~v~lTe~G~~~~E~~l~i~nly~~~n~~l~~~i~~AL~A~~l~~~d~dYiV~dg~V~iVDe~TGR~m~grr~s~GL  378 (822)
T 3jux_A          299 EKARTIILTEEGVAKAEKIIGVENLYDPGNVSLLYHLINALKALHLFKKDVDYVVMNGEVIIVDEFTGRLLPGRRYSGGL  378 (822)
T ss_dssp             CSSSCEEECHHHHHHHHHHHTCSCTTSGGGHHHHHHHHHHHHHHHHSTTTSSEEEETTEEEECSSSSCSCCCSCCCGGGH
T ss_pred             cccCeEEECHHHHHHHHHHhCCccccchhhhHHHHHHHHHHHHHHHHcCCCcEEEECCEEEEEECCCCcCCCCCcCchHH
Confidence                                           000001000      0000                              


Q ss_pred             -------------------------------CcEEEEeccCcHHHHHHHHHHcCCCeEEEeCCcccccCCceE-EEEecC
Q 002040          649 -------------------------------RQTVLFSATFPRQVEILARKVLNKPVEIQVGGRSVVNKDITQ-LVEVRP  696 (976)
Q Consensus       649 -------------------------------~q~i~~SAT~~~~~~~l~~~~l~~~~~i~~~~~~~~~~~i~q-~~~~~~  696 (976)
                                                     .++.+||||.......+...|.. .+. .++ ...+...+.+ .+.+..
T Consensus       379 HQaiEaKEgv~i~~e~~tla~IT~Qn~Fr~Y~kL~GMTGTa~te~~Ef~~iY~l-~vv-~IP-tnkp~~R~d~~d~vy~t  455 (822)
T 3jux_A          379 HQAIEAKEGVPIKEESITYATITFQNYFRMYEKLAGMTGTAKTEESEFVQVYGM-EVV-VIP-THKPMIRKDHDDLVFRT  455 (822)
T ss_dssp             HHHHHHHHSSCCCCCCCEEEEECHHHHHTTSSEEEEEESSCGGGHHHHHHHSCC-CEE-ECC-CSSCCCCEECCCEEESS
T ss_pred             HHHHHHHcCCCCCCCcchhHHHHHHHHHHHhhHHeEECCCCchHHHHHHHHhCC-eEE-EEC-CCCCcceeecCcEEEec
Confidence                                           34889999998877766555533 332 222 1222222222 245567


Q ss_pred             cchHHHHHHHHHHhhh-cCCcEEEEecCHHHHHHHHHHHHHCCCCceeccCCCCHHHHHHHHHHhccCCccEEEecCccc
Q 002040          697 ESDRFLRLLELLGEWY-EKGKILIFVHSQEKCDALFRDLLKHGYPCLSLHGAKDQTDRESTISDFKSNVCNLLIATSVAA  775 (976)
Q Consensus       697 ~~~k~~~l~~~l~~~~-~~~kvLIF~~s~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLVaT~v~~  775 (976)
                      ...|+..++..|.... .+.++||||+|+..++.|+..|...|+++..+||++.+.++..+...|..|  .|||||++|+
T Consensus       456 ~~eK~~al~~~I~~~~~~gqpVLVFt~S~e~sE~Ls~~L~~~Gi~~~vLhgkq~~rE~~ii~~ag~~g--~VtVATdmAg  533 (822)
T 3jux_A          456 QKEKYEKIVEEIEKRYKKGQPVLVGTTSIEKSELLSSMLKKKGIPHQVLNAKYHEKEAEIVAKAGQKG--MVTIATNMAG  533 (822)
T ss_dssp             HHHHHHHHHHHHHHHHHHTCCEEEEESSHHHHHHHHHHHHTTTCCCEEECSCHHHHHHHHHHHHHSTT--CEEEEETTTT
T ss_pred             HHHHHHHHHHHHHHHhhCCCCEEEEECCHHHHHHHHHHHHHCCCCEEEeeCCchHHHHHHHHhCCCCC--eEEEEcchhh
Confidence            7889999999888754 467999999999999999999999999999999996666665555666665  5999999999


Q ss_pred             ccCCCC--------CCcEEEEeCCCCCHHHHHHHhcccCCCCCccEEEEEecCCCc
Q 002040          776 RGLDVK--------ELELVINFDAPNHYEDYVHRVGRTGRAGRKGCAITFISEEDA  823 (976)
Q Consensus       776 ~GlDi~--------~v~~VI~~d~p~s~~~y~Qr~GR~gR~g~~g~~~~~~~~~d~  823 (976)
                      ||+||+        +..+||+|+.|.+...|+|++||+||+|.+|.+++|++..|.
T Consensus       534 RGtDI~lg~~V~~~GglhVInte~Pes~r~y~qriGRTGRqG~~G~a~~fvsleD~  589 (822)
T 3jux_A          534 RGTDIKLGPGVAELGGLCIIGTERHESRRIDNQLRGRAGRQGDPGESIFFLSLEDD  589 (822)
T ss_dssp             TTCCCCCCTTTTTTTSCEEEESSCCSSHHHHHHHHTTSSCSSCCCEEEEEEETTSH
T ss_pred             CCcCccCCcchhhcCCCEEEecCCCCCHHHHHHhhCccccCCCCeeEEEEechhHH
Confidence            999998        677999999999999999999999999999999999998874

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

Probab=100.00  E-value=2.6e-32  Score=290.48  Aligned_cols=229  Identities=33%  Similarity=0.502  Sum_probs=197.0

Q ss_pred             HHHHHHHHhhcCceeccCCCCCcccccccCCCCHHHHHHHHHcCCCCCcHHHHHHHHHHhcCCCEEEEcCCCCchHHHHH
Q 002040          443 PEEVSAYRKQLELKIHGKDVPKPIKTWHQTGLTSKIMETIRKLNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFV  522 (976)
Q Consensus       443 ~~~~~~~~~~~~i~~~g~~~p~pi~~~~~~~l~~~l~~~l~~~~~~~p~~~Q~~~i~~il~g~d~i~~a~TGsGKT~~~~  522 (976)
                      .+++..+++.+..     ..+.++.+|.++++++.+...|..+||..|+|+|.++++.++.|+++|++++||||||++|+
T Consensus         6 ~~~~~~~~~~~~~-----~~~~~~~~f~~~~l~~~l~~~l~~~~~~~~~~~Q~~~i~~~~~~~~~li~a~TGsGKT~~~~   80 (236)
T 2pl3_A            6 RESISRLMQNYEK-----INVNEITRFSDFPLSKKTLKGLQEAQYRLVTEIQKQTIGLALQGKDVLGAAKTGSGKTLAFL   80 (236)
T ss_dssp             HHHHHHHHHTTTT-----CCGGGCSBGGGSCCCHHHHHHHHHTTCCBCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHH
T ss_pred             HhHHHHHHhcccc-----CCCcccCCHhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEEeCCCCcHHHHHH
Confidence            4455666655542     12567889999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHHHHhhcCcEEEEeeCCCChHHHHHHHhcCCeEEEeCchhHH
Q 002040          523 LPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMI  602 (976)
Q Consensus       523 l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~~~~~~~~~~~~~~gg~~~~~~~~~l~~~~~Iiv~Tp~~L~  602 (976)
                      +|++..+..... ....++++||++||++|+.|++..+..++...++.+.+++||.....+...+ .+++|+|+||++|.
T Consensus        81 ~~~l~~l~~~~~-~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~-~~~~iiv~Tp~~l~  158 (236)
T 2pl3_A           81 VPVLEALYRLQW-TSTDGLGVLIISPTRELAYQTFEVLRKVGKNHDFSAGLIIGGKDLKHEAERI-NNINILVCTPGRLL  158 (236)
T ss_dssp             HHHHHHHHHTTC-CGGGCCCEEEECSSHHHHHHHHHHHHHHTTTSSCCEEEECCC--CHHHHHHH-TTCSEEEECHHHHH
T ss_pred             HHHHHHHHhhcc-cccCCceEEEEeCCHHHHHHHHHHHHHHhCCCCeeEEEEECCCCHHHHHHhC-CCCCEEEECHHHHH
Confidence            999998875321 1234788999999999999999999999888889999999998877766555 46899999999999


Q ss_pred             HHHHhcCCcccccCCceEEEecCcccccccCCchHHHHHHHhcCCCCcEEEEeccCcHHHHHHHHHHcCCCeEEEeCC
Q 002040          603 DILCTSGGKITNLRRVTYLVMDEADRMFDMGFEPQITRIVQNIRPDRQTVLFSATFPRQVEILARKVLNKPVEIQVGG  680 (976)
Q Consensus       603 ~~l~~~~~~~~~l~~~~~vVlDEah~~~~~~f~~~i~~il~~~~~~~q~i~~SAT~~~~~~~l~~~~l~~~~~i~~~~  680 (976)
                      .++....  ...+..+.+|||||||++++++|...+..++..+++..|+|+||||+++.+..++..++.+|..+.+..
T Consensus       159 ~~l~~~~--~~~~~~~~~lViDEah~~~~~~~~~~~~~i~~~~~~~~~~l~~SAT~~~~~~~~~~~~~~~p~~i~~~~  234 (236)
T 2pl3_A          159 QHMDETV--SFHATDLQMLVLDEADRILDMGFADTMNAVIENLPKKRQTLLFSATQTKSVKDLARLSLKNPEYVWVHE  234 (236)
T ss_dssp             HHHHHCS--SCCCTTCCEEEETTHHHHHHTTTHHHHHHHHHTSCTTSEEEEEESSCCHHHHHHHHHSCSSCEEEECCC
T ss_pred             HHHHhcC--CcccccccEEEEeChHHHhcCCcHHHHHHHHHhCCCCCeEEEEEeeCCHHHHHHHHHhCCCCEEEEeCC
Confidence            8886542  245778999999999999999999999999999999999999999999999999999999999887653

>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=100.00  E-value=2.3e-32  Score=289.62  Aligned_cols=211  Identities=29%  Similarity=0.470  Sum_probs=183.0

Q ss_pred             cCCCCCcccccccCCCCHHHHHHHHHcCCCCCcHHHHHHHHHHhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCC
Q 002040          459 GKDVPKPIKTWHQTGLTSKIMETIRKLNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAG  538 (976)
Q Consensus       459 g~~~p~pi~~~~~~~l~~~l~~~l~~~~~~~p~~~Q~~~i~~il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~  538 (976)
                      +...|.+..+|.++++++.+...|..+||..|+|+|.++|+.++.|+++|++++||+|||++|++|++..+...     .
T Consensus        16 ~~~~~~~~~~f~~l~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~l~~a~TGsGKT~~~~l~~l~~l~~~-----~   90 (230)
T 2oxc_A           16 GDVLLAEPADFESLLLSRPVLEGLRAAGFERPSPVQLKAIPLGRCGLDLIVQAKSGTGKTCVFSTIALDSLVLE-----N   90 (230)
T ss_dssp             --------CCGGGGTCCHHHHHHHHHTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHHCCTT-----S
T ss_pred             CCCCCCCCCCHhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCCcHHHHHHHHHHHHHHhc-----C
Confidence            45567888999999999999999999999999999999999999999999999999999999999999887542     2


Q ss_pred             CCCeEEEEccCHHHHHHHHHHHHHHHhhc-CcEEEEeeCCCChHHHHHHHhcCCeEEEeCchhHHHHHHhcCCcccccCC
Q 002040          539 DGPVGLIMAPTRELVQQIHSDIRKFAKVM-GVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRR  617 (976)
Q Consensus       539 ~~~~vLIl~Ptr~La~Q~~~~~~~~~~~~-~~~~~~~~gg~~~~~~~~~l~~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~  617 (976)
                      .++++|||+||++|+.|+++.+..++... ++.+.+++||.....+...+ .+++|+|+||++|.+++....   ..+.+
T Consensus        91 ~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~-~~~~Iiv~Tp~~l~~~~~~~~---~~~~~  166 (230)
T 2oxc_A           91 LSTQILILAPTREIAVQIHSVITAIGIKMEGLECHVFIGGTPLSQDKTRL-KKCHIAVGSPGRIKQLIELDY---LNPGS  166 (230)
T ss_dssp             CSCCEEEECSSHHHHHHHHHHHHHHTTTSTTCCEEEECTTSCHHHHHHHT-TSCSEEEECHHHHHHHHHTTS---SCGGG
T ss_pred             CCceEEEEeCCHHHHHHHHHHHHHHhcccCCceEEEEeCCCCHHHHHHhc-cCCCEEEECHHHHHHHHhcCC---ccccc
Confidence            46789999999999999999999988765 88999999999887765555 468999999999999886532   45778


Q ss_pred             ceEEEecCcccccccC-CchHHHHHHHhcCCCCcEEEEeccCcHHHHHHHHHHcCCCeEEEe
Q 002040          618 VTYLVMDEADRMFDMG-FEPQITRIVQNIRPDRQTVLFSATFPRQVEILARKVLNKPVEIQV  678 (976)
Q Consensus       618 ~~~vVlDEah~~~~~~-f~~~i~~il~~~~~~~q~i~~SAT~~~~~~~l~~~~l~~~~~i~~  678 (976)
                      +.+|||||||++++++ |...+..++..++...|+|+||||+|+.+..++..++.+|+.+.+
T Consensus       167 ~~~lViDEah~~~~~~~~~~~~~~i~~~~~~~~~~l~lSAT~~~~~~~~~~~~~~~p~~i~~  228 (230)
T 2oxc_A          167 IRLFILDEADKLLEEGSFQEQINWIYSSLPASKQMLAVSATYPEFLANALTKYMRDPTFVRL  228 (230)
T ss_dssp             CCEEEESSHHHHHSTTSSHHHHHHHHHHSCSSCEEEEEESCCCHHHHHHHTTTCSSCEEECC
T ss_pred             CCEEEeCCchHhhcCcchHHHHHHHHHhCCCCCeEEEEEeccCHHHHHHHHHHcCCCeEEEc
Confidence            9999999999999997 999999999999989999999999999999999999999987654

>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=100.00  E-value=3.5e-32  Score=287.04  Aligned_cols=213  Identities=31%  Similarity=0.510  Sum_probs=182.4

Q ss_pred             CCCCCcccccccCCCCHHHHHHHHHcCCCCCcHHHHHHHHHHhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCC
Q 002040          460 KDVPKPIKTWHQTGLTSKIMETIRKLNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGD  539 (976)
Q Consensus       460 ~~~p~pi~~~~~~~l~~~l~~~l~~~~~~~p~~~Q~~~i~~il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~  539 (976)
                      ...|+++.+|.++++++.++..|..+||..|+|+|.++++.++.++++|+++|||+|||++|++|++..+...     ..
T Consensus         7 ~~~~~~~~~f~~l~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~lv~~pTGsGKT~~~~~~~l~~l~~~-----~~   81 (224)
T 1qde_A            7 TNYDKVVYKFDDMELDENLLRGVFGYGFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFSIAALQRIDTS-----VK   81 (224)
T ss_dssp             BSCCCCCCCGGGGTCCHHHHHHHHHHTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHHCCTT-----CC
T ss_pred             cccCcccCChhhcCCCHHHHHHHHHCCCCCCcHHHHHHHHHHhcCCCEEEECCCCCcHHHHHHHHHHHHHhcc-----CC
Confidence            3467888999999999999999999999999999999999999999999999999999999999999887542     34


Q ss_pred             CCeEEEEccCHHHHHHHHHHHHHHHhhcCcEEEEeeCCCChHHHHHHHhcCCeEEEeCchhHHHHHHhcCCcccccCCce
Q 002040          540 GPVGLIMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVT  619 (976)
Q Consensus       540 ~~~vLIl~Ptr~La~Q~~~~~~~~~~~~~~~~~~~~gg~~~~~~~~~l~~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~  619 (976)
                      ++++||++||++|+.|++..+..++...++.+..++||.....+...+.. ++|+|+||++|..++....   ..+..+.
T Consensus        82 ~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~-~~iiv~Tp~~l~~~~~~~~---~~~~~~~  157 (224)
T 1qde_A           82 APQALMLAPTRELALQIQKVVMALAFHMDIKVHACIGGTSFVEDAEGLRD-AQIVVGTPGRVFDNIQRRR---FRTDKIK  157 (224)
T ss_dssp             SCCEEEECSSHHHHHHHHHHHHHHTTTSCCCEEEECC----------CTT-CSEEEECHHHHHHHHHTTS---SCCTTCC
T ss_pred             CceEEEEECCHHHHHHHHHHHHHHhcccCceEEEEeCCcchHHHHhcCCC-CCEEEECHHHHHHHHHhCC---cchhhCc
Confidence            67899999999999999999999998889999999999877766555544 8999999999998886542   4578899


Q ss_pred             EEEecCcccccccCCchHHHHHHHhcCCCCcEEEEeccCcHHHHHHHHHHcCCCeEEEeCCc
Q 002040          620 YLVMDEADRMFDMGFEPQITRIVQNIRPDRQTVLFSATFPRQVEILARKVLNKPVEIQVGGR  681 (976)
Q Consensus       620 ~vVlDEah~~~~~~f~~~i~~il~~~~~~~q~i~~SAT~~~~~~~l~~~~l~~~~~i~~~~~  681 (976)
                      +|||||||++++++|...+..++..+++..|+|+||||+++.+..++..++.+|+.+.+...
T Consensus       158 ~iViDEah~~~~~~~~~~l~~i~~~~~~~~~~i~lSAT~~~~~~~~~~~~~~~p~~i~~~~~  219 (224)
T 1qde_A          158 MFILDEADEMLSSGFKEQIYQIFTLLPPTTQVVLLSATMPNDVLEVTTKFMRNPVRILVKKD  219 (224)
T ss_dssp             EEEEETHHHHHHTTCHHHHHHHHHHSCTTCEEEEEESSCCHHHHHHHHHHCSSCEEEC----
T ss_pred             EEEEcChhHHhhhhhHHHHHHHHHhCCccCeEEEEEeecCHHHHHHHHHHCCCCEEEEecCC
Confidence            99999999999999999999999999999999999999999999999999999988876543

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

Probab=100.00  E-value=1.6e-32  Score=288.56  Aligned_cols=207  Identities=31%  Similarity=0.518  Sum_probs=184.6

Q ss_pred             cccccccCCCCHHHHHHHHHcCCCCCcHHHHHHHHHHhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEE
Q 002040          465 PIKTWHQTGLTSKIMETIRKLNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGL  544 (976)
Q Consensus       465 pi~~~~~~~l~~~l~~~l~~~~~~~p~~~Q~~~i~~il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vL  544 (976)
                      |+.+|.++++++.+.+.|..+||..|+|+|.++|+.+++|+++|++++||||||++|++|++..+...     ..++++|
T Consensus         2 ~~~~f~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~lv~a~TGsGKT~~~~~~~l~~l~~~-----~~~~~~l   76 (219)
T 1q0u_A            2 AETQFTRFPFQPFIIEAIKTLRFYKPTEIQERIIPGALRGESMVGQSQTGTGKTHAYLLPIMEKIKPE-----RAEVQAV   76 (219)
T ss_dssp             --CCGGGSCCCHHHHHHHHHTTCCSCCHHHHHHHHHHHHTCCEEEECCSSHHHHHHHHHHHHHHCCTT-----SCSCCEE
T ss_pred             CCCCHhhCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHHHhC-----cCCceEE
Confidence            45689999999999999999999999999999999999999999999999999999999999887642     2467899


Q ss_pred             EEccCHHHHHHHHHHHHHHHhhc----CcEEEEeeCCCChHHHHHHHhcCCeEEEeCchhHHHHHHhcCCcccccCCceE
Q 002040          545 IMAPTRELVQQIHSDIRKFAKVM----GVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTY  620 (976)
Q Consensus       545 Il~Ptr~La~Q~~~~~~~~~~~~----~~~~~~~~gg~~~~~~~~~l~~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~  620 (976)
                      ||+||++|+.|+++.+..++...    ++.+.+++||.........+..+++|+|+||++|.+++....   ..+..+.+
T Consensus        77 il~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~Iiv~Tp~~l~~~l~~~~---~~~~~~~~  153 (219)
T 1q0u_A           77 ITAPTRELATQIYHETLKITKFCPKDRMIVARCLIGGTDKQKALEKLNVQPHIVIGTPGRINDFIREQA---LDVHTAHI  153 (219)
T ss_dssp             EECSSHHHHHHHHHHHHHHHTTSCGGGCCCEEEECCCSHHHHTTCCCSSCCSEEEECHHHHHHHHHTTC---CCGGGCCE
T ss_pred             EEcCcHHHHHHHHHHHHHHhhhcccccceEEEEEeCCCCHHHHHHHcCCCCCEEEeCHHHHHHHHHcCC---CCcCcceE
Confidence            99999999999999999998776    788999999987766555555678999999999998886532   45778999


Q ss_pred             EEecCcccccccCCchHHHHHHHhcCCCCcEEEEeccCcHHHHHHHHHHcCCCeEEEeC
Q 002040          621 LVMDEADRMFDMGFEPQITRIVQNIRPDRQTVLFSATFPRQVEILARKVLNKPVEIQVG  679 (976)
Q Consensus       621 vVlDEah~~~~~~f~~~i~~il~~~~~~~q~i~~SAT~~~~~~~l~~~~l~~~~~i~~~  679 (976)
                      |||||||++++++|...+..++..+++..|+|+||||+|..+..++..++.+|..+.+.
T Consensus       154 lViDEah~~~~~~~~~~l~~i~~~~~~~~~~l~~SAT~~~~~~~~~~~~~~~p~~~~~~  212 (219)
T 1q0u_A          154 LVVDEADLMLDMGFITDVDQIAARMPKDLQMLVFSATIPEKLKPFLKKYMENPTFVHVL  212 (219)
T ss_dssp             EEECSHHHHHHTTCHHHHHHHHHTSCTTCEEEEEESCCCGGGHHHHHHHCSSCEEEECC
T ss_pred             EEEcCchHHhhhChHHHHHHHHHhCCcccEEEEEecCCCHHHHHHHHHHcCCCeEEEee
Confidence            99999999999999999999999999899999999999999999999999999887654

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

Probab=100.00  E-value=1.5e-31  Score=332.90  Aligned_cols=373  Identities=16%  Similarity=0.246  Sum_probs=250.3

Q ss_pred             ccccccccchhhhcCCHHHHHHHHhhcCce---eccCCCCCcccccccCCCCHHHHHHHHHcCCCCCcHHHHHHHHHHh-
Q 002040          427 FRKNFYIEVKEIARMTPEEVSAYRKQLELK---IHGKDVPKPIKTWHQTGLTSKIMETIRKLNYEKPMPIQAQALPVIM-  502 (976)
Q Consensus       427 f~~~~~~~~~~~~~~~~~~~~~~~~~~~i~---~~g~~~p~pi~~~~~~~l~~~l~~~l~~~~~~~p~~~Q~~~i~~il-  502 (976)
                      +....|.....+..+.++.+..|.......   ......+.....|..+...+...      .-..|+|+|.+++.+++ 
T Consensus       177 y~~~tWe~~~~~~~~~~~~i~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~------~~~~Lr~yQ~egv~~l~~  250 (800)
T 3mwy_W          177 YDEATWENATDIVKLAPEQVKHFQNRENSKILPQYSSNYTSQRPRFEKLSVQPPFI------KGGELRDFQLTGINWMAF  250 (800)
T ss_dssp             STTCBCCBHHHHTTTCHHHHHHHHHTTTCTTCSTTCCCCCSCCCCCCCCSSCCTTC------CSSCCCTHHHHHHHHHHH
T ss_pred             cccccccchhhhhhhhHHHHHHHHHhhhcccCCcchhcccccCCcccccccCCCcc------CCCCcCHHHHHHHHHHHH
Confidence            344455555556666777787776644321   11111122222344333222211      12468999999999887 


Q ss_pred             ---cCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHHHHhhcCcEEEEeeCCCC
Q 002040          503 ---SGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSG  579 (976)
Q Consensus       503 ---~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~~~~~~~~~~~~~~gg~~  579 (976)
                         .+.++|++++||+|||++++..+...+...     .....+||||| ..|+.||..+|.+++.  ++.+++++|+..
T Consensus       251 ~~~~~~~~ILademGlGKT~~ai~~i~~l~~~~-----~~~~~~LIV~P-~sll~qW~~E~~~~~p--~~~v~~~~g~~~  322 (800)
T 3mwy_W          251 LWSKGDNGILADEMGLGKTVQTVAFISWLIFAR-----RQNGPHIIVVP-LSTMPAWLDTFEKWAP--DLNCICYMGNQK  322 (800)
T ss_dssp             HHTTTCCEEECCCTTSSTTHHHHHHHHHHHHHH-----SCCSCEEEECC-TTTHHHHHHHHHHHST--TCCEEECCCSSH
T ss_pred             HhhcCCCEEEEeCCCcchHHHHHHHHHHHHHhc-----CCCCCEEEEEC-chHHHHHHHHHHHHCC--CceEEEEeCCHH
Confidence               788999999999999999776665554332     12345799999 5678999999999874  466666666655


Q ss_pred             hHHHHHHHh------------cCCeEEEeCchhHHHHHHhcCCcccccCCceEEEecCcccccccCCchHHHHHHHhcCC
Q 002040          580 VAQQISELK------------RGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMGFEPQITRIVQNIRP  647 (976)
Q Consensus       580 ~~~~~~~l~------------~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDEah~~~~~~f~~~i~~il~~~~~  647 (976)
                      ....+....            ..++|+|+|++.|......     .....+.+|||||||++-+.  ...+...+..+. 
T Consensus       323 ~r~~~~~~~~~~~~~~~~~~~~~~dvvitTy~~l~~~~~~-----l~~~~w~~vIvDEaH~lkn~--~s~~~~~l~~l~-  394 (800)
T 3mwy_W          323 SRDTIREYEFYTNPRAKGKKTMKFNVLLTTYEYILKDRAE-----LGSIKWQFMAVDEAHRLKNA--ESSLYESLNSFK-  394 (800)
T ss_dssp             HHHHHHHHHSCSCC-----CCCCCSEEEECTTHHHHTHHH-----HHTSEEEEEEETTGGGGCCS--SSHHHHHHTTSE-
T ss_pred             HHHHHHHHHhhccccccccccccCCEEEecHHHHHhhHHH-----HhcCCcceeehhhhhhhcCc--hhHHHHHHHHhh-
Confidence            444433321            2468999999998764422     12235889999999998653  345555666653 


Q ss_pred             CCcEEEEeccCc----HHHHHHHHHHcCCC-----------------------------eEEEeCCccc---ccCCceEE
Q 002040          648 DRQTVLFSATFP----RQVEILARKVLNKP-----------------------------VEIQVGGRSV---VNKDITQL  691 (976)
Q Consensus       648 ~~q~i~~SAT~~----~~~~~l~~~~l~~~-----------------------------~~i~~~~~~~---~~~~i~q~  691 (976)
                      ....|++||||.    ..+..++..+....                             +.+.-....+   .+......
T Consensus       395 ~~~rl~LTgTPiqN~l~el~~ll~fL~p~~~~~~~~~~~~~~~~~~~~~~~~L~~~l~p~~lRR~k~dv~~~LP~k~~~~  474 (800)
T 3mwy_W          395 VANRMLITGTPLQNNIKELAALVNFLMPGRFTIDQEIDFENQDEEQEEYIHDLHRRIQPFILRRLKKDVEKSLPSKTERI  474 (800)
T ss_dssp             EEEEEEECSCCCSSCSHHHHHHHHHHCSCCC---------CCTTHHHHHHHHHHHTTGGGEEECCGGGGTTTSCCEEEEE
T ss_pred             hccEEEeeCCcCCCCHHHHHHHHHHhCccccCchhhhcccccchhHHHHHHHHHHHHhHHHhhhhHHhhhhccCCcEEEE
Confidence            345789999983    22222222221111                             1110000000   00000011


Q ss_pred             EEe--------------------------------------------------------------------------cCc
Q 002040          692 VEV--------------------------------------------------------------------------RPE  697 (976)
Q Consensus       692 ~~~--------------------------------------------------------------------------~~~  697 (976)
                      +.+                                                                          ...
T Consensus       475 v~v~ls~~q~~~Y~~i~~~~~~~l~~~~~~~~~~~l~~l~~Lrk~~~hp~l~~~~~~~~~~~~~~~~~~~~~~~~~l~~~  554 (800)
T 3mwy_W          475 LRVELSDVQTEYYKNILTKNYSALTAGAKGGHFSLLNIMNELKKASNHPYLFDNAEERVLQKFGDGKMTRENVLRGLIMS  554 (800)
T ss_dssp             EEECCCHHHHHHHHHHHHHCCC----------CTHHHHHHHHHHHHHCGGGSSSHHHHHCCCC----CCSHHHHHHHHHT
T ss_pred             EEeCCCHHHHHHHHHHHHHHHHHHhhccccchhhHHHHHHHHHHHhcChhhhcchHHHHHHhcccccccHHHHHHHhhhc
Confidence            110                                                                          012


Q ss_pred             chHHHHHHHHHHhhhc-CCcEEEEecCHHHHHHHHHHHHHCCCCceeccCCCCHHHHHHHHHHhccCCc---cEEEecCc
Q 002040          698 SDRFLRLLELLGEWYE-KGKILIFVHSQEKCDALFRDLLKHGYPCLSLHGAKDQTDRESTISDFKSNVC---NLLIATSV  773 (976)
Q Consensus       698 ~~k~~~l~~~l~~~~~-~~kvLIF~~s~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~---~vLVaT~v  773 (976)
                      +.|+..|..+|..+.. +.++||||++...++.|..+|...|+.+..|||+++..+|..++..|+++..   .|||+|.+
T Consensus       555 s~K~~~L~~lL~~~~~~g~kvLIFsq~~~~ld~L~~~L~~~g~~~~~i~G~~~~~eR~~~i~~F~~~~~~~~v~LlSt~a  634 (800)
T 3mwy_W          555 SGKMVLLDQLLTRLKKDGHRVLIFSQMVRMLDILGDYLSIKGINFQRLDGTVPSAQRRISIDHFNSPDSNDFVFLLSTRA  634 (800)
T ss_dssp             CHHHHHHHHHHHHHTTTTCCEEEEESCHHHHHHHHHHHHHHTCCCEEESTTSCHHHHHHHHHTTSSTTCSCCCEEEEHHH
T ss_pred             ChHHHHHHHHHHHHhhCCCeEEEEechHHHHHHHHHHHHhCCCCEEEEeCCCCHHHHHHHHHHhhCCCCCceEEEEeccc
Confidence            4466667777776654 4599999999999999999999999999999999999999999999998654   59999999


Q ss_pred             ccccCCCCCCcEEEEeCCCCCHHHHHHHhcccCCCCCccEE--EEEecCC
Q 002040          774 AARGLDVKELELVINFDAPNHYEDYVHRVGRTGRAGRKGCA--ITFISEE  821 (976)
Q Consensus       774 ~~~GlDi~~v~~VI~~d~p~s~~~y~Qr~GR~gR~g~~g~~--~~~~~~~  821 (976)
                      ++.|||++.+++||+||+|||+..++|++||++|.|++..|  |.|++..
T Consensus       635 gg~GlNL~~a~~VI~~D~~wnp~~~~Qa~gR~~RiGQ~k~V~Vyrlv~~~  684 (800)
T 3mwy_W          635 GGLGINLMTADTVVIFDSDWNPQADLQAMARAHRIGQKNHVMVYRLVSKD  684 (800)
T ss_dssp             HTTTCCCTTCCEEEESSCCSCSHHHHHHHTTTSCSSCCSCEEEEEEEETT
T ss_pred             ccCCCCccccceEEEecCCCChhhHHHHHHHHHhcCCCceEEEEEEecCC
Confidence            99999999999999999999999999999999999987554  4456654

>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=100.00  E-value=9.5e-32  Score=279.74  Aligned_cols=202  Identities=31%  Similarity=0.593  Sum_probs=184.5

Q ss_pred             cccccCCCCHHHHHHHHHcCCCCCcHHHHHHHHHHhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEE
Q 002040          467 KTWHQTGLTSKIMETIRKLNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIM  546 (976)
Q Consensus       467 ~~~~~~~l~~~l~~~l~~~~~~~p~~~Q~~~i~~il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl  546 (976)
                      .+|.+++|++.+++.|..+||..|+|+|.++++.++.++++++++|||+|||++|++|++..+...     ..++++||+
T Consensus         3 ~~f~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~lv~apTGsGKT~~~~~~~~~~~~~~-----~~~~~~lil   77 (206)
T 1vec_A            3 NEFEDYCLKRELLMGIFEMGWEKPSPIQEESIPIALSGRDILARAKNGTGKSGAYLIPLLERLDLK-----KDNIQAMVI   77 (206)
T ss_dssp             SSGGGSCCCHHHHHHHHTTTCCSCCHHHHHHHHHHHTTCCEEEECCSSSTTHHHHHHHHHHHCCTT-----SCSCCEEEE
T ss_pred             CChhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHccCCCEEEECCCCCchHHHHHHHHHHHhccc-----CCCeeEEEE
Confidence            469999999999999999999999999999999999999999999999999999999999887542     246789999


Q ss_pred             ccCHHHHHHHHHHHHHHHhhc-CcEEEEeeCCCChHHHHHHHhcCCeEEEeCchhHHHHHHhcCCcccccCCceEEEecC
Q 002040          547 APTRELVQQIHSDIRKFAKVM-GVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDE  625 (976)
Q Consensus       547 ~Ptr~La~Q~~~~~~~~~~~~-~~~~~~~~gg~~~~~~~~~l~~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDE  625 (976)
                      +||++|+.|+++.+..++... ++.+.+++||.....+...+..+++|+|+||++|...+....   ..+..+.+|||||
T Consensus        78 ~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~i~v~T~~~l~~~~~~~~---~~~~~~~~lViDE  154 (206)
T 1vec_A           78 VPTRELALQVSQICIQVSKHMGGAKVMATTGGTNLRDDIMRLDDTVHVVIATPGRILDLIKKGV---AKVDHVQMIVLDE  154 (206)
T ss_dssp             CSCHHHHHHHHHHHHHHTTTSSSCCEEEECSSSCHHHHHHHTTSCCSEEEECHHHHHHHHHTTC---SCCTTCCEEEEET
T ss_pred             eCcHHHHHHHHHHHHHHHhhcCCceEEEEeCCccHHHHHHhcCCCCCEEEeCHHHHHHHHHcCC---cCcccCCEEEEEC
Confidence            999999999999999998877 789999999999888877777889999999999988886532   4678899999999


Q ss_pred             cccccccCCchHHHHHHHhcCCCCcEEEEeccCcHHHHHHHHHHcCCCeEE
Q 002040          626 ADRMFDMGFEPQITRIVQNIRPDRQTVLFSATFPRQVEILARKVLNKPVEI  676 (976)
Q Consensus       626 ah~~~~~~f~~~i~~il~~~~~~~q~i~~SAT~~~~~~~l~~~~l~~~~~i  676 (976)
                      ||++++.+|...+..++..+++..|+|+||||+|+.+..++..++.+|+.+
T Consensus       155 ah~~~~~~~~~~l~~i~~~~~~~~~~l~~SAT~~~~~~~~~~~~l~~p~~i  205 (206)
T 1vec_A          155 ADKLLSQDFVQIMEDIILTLPKNRQILLYSATFPLSVQKFMNSHLEKPYEI  205 (206)
T ss_dssp             HHHHTSTTTHHHHHHHHHHSCTTCEEEEEESCCCHHHHHHHHHHCSSCEEE
T ss_pred             hHHhHhhCcHHHHHHHHHhCCccceEEEEEeeCCHHHHHHHHHHcCCCeEe
Confidence            999999999999999999999899999999999999999999999999765

>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=99.98  E-value=1.6e-30  Score=315.80  Aligned_cols=322  Identities=17%  Similarity=0.214  Sum_probs=223.5

Q ss_pred             CCcHHHHHHHHHHh---------cCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHH
Q 002040          489 KPMPIQAQALPVIM---------SGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSD  559 (976)
Q Consensus       489 ~p~~~Q~~~i~~il---------~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~  559 (976)
                      .|+|+|.+++.++.         .+..+|++++||+|||++++..+...+...+. .......+|||||+ .|+.||..+
T Consensus        55 ~LrpyQ~~gv~~l~~~~~~~~~~~~~g~ILad~mGlGKT~~~i~~i~~l~~~~~~-~~p~~~~~LiV~P~-sll~qW~~E  132 (644)
T 1z3i_X           55 VLRPHQREGVKFLWDCVTGRRIENSYGCIMADEMGLGKTLQCITLIWTLLKQSPD-CKPEIDKVIVVSPS-SLVRNWYNE  132 (644)
T ss_dssp             TCCHHHHHHHHHHHHHHTTSSSTTCCEEEECCCTTSCHHHHHHHHHHHHHHCCTT-SSCSCSCEEEEECH-HHHHHHHHH
T ss_pred             cccHHHHHHHHHHHHhhhcccccCCCCeEeeeCCCchHHHHHHHHHHHHHHhCcc-ccCCCCcEEEEecH-HHHHHHHHH
Confidence            58899999999985         34678999999999999987777665554322 11223468999997 788999999


Q ss_pred             HHHHHhhcCcEEEEeeCCCChHH--HHHHHhc------CCeEEEeCchhHHHHHHhcCCcccccCCceEEEecCcccccc
Q 002040          560 IRKFAKVMGVRCVPVYGGSGVAQ--QISELKR------GTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFD  631 (976)
Q Consensus       560 ~~~~~~~~~~~~~~~~gg~~~~~--~~~~l~~------~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDEah~~~~  631 (976)
                      |.+|+.. .+.++.++||.....  .+..+..      .++|+|+|++.|.....     ......+++|||||||++-+
T Consensus       133 ~~~~~~~-~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~vvi~ty~~l~~~~~-----~l~~~~~~~vI~DEaH~ikn  206 (644)
T 1z3i_X          133 VGKWLGG-RVQPVAIDGGSKDEIDSKLVNFISQQGMRIPTPILIISYETFRLHAE-----VLHKGKVGLVICDEGHRLKN  206 (644)
T ss_dssp             HHHHHGG-GCCEEEECSSCHHHHHHHHHHHHCCCSSCCSCCEEEEEHHHHHHHTT-----TTTTSCCCEEEETTGGGCCT
T ss_pred             HHHHcCC-CeeEEEEeCCCHHHHHHHHHHHHHhcCCCCCCcEEEeeHHHHHhhHH-----HhhcCCccEEEEECceecCC
Confidence            9999865 566777777764322  1222211      36899999998865432     12335689999999999865


Q ss_pred             cCCchHHHHHHHhcCCCCcEEEEeccCcHHH----H---------------HHHHHHc----------------------
Q 002040          632 MGFEPQITRIVQNIRPDRQTVLFSATFPRQV----E---------------ILARKVL----------------------  670 (976)
Q Consensus       632 ~~f~~~i~~il~~~~~~~q~i~~SAT~~~~~----~---------------~l~~~~l----------------------  670 (976)
                      ..  ......+..+. ....|++||||-.+-    .               .+...|.                      
T Consensus       207 ~~--~~~~~al~~l~-~~~rl~LTgTPiqN~l~El~sll~fl~p~~l~~~~~F~~~f~~pi~~~~~~~~~~~~~~~~~~~  283 (644)
T 1z3i_X          207 SD--NQTYLALNSMN-AQRRVLISGTPIQNDLLEYFSLVHFVNSGILGTAQEFKKRFEIPILKGRDADASDKDRAAGEQK  283 (644)
T ss_dssp             TC--HHHHHHHHHHC-CSEEEEECSSCSGGGGGGCHHHHHHHHHHHHCCHHHHHHHTHHHHHHHHSTTCCSHHHHHHHHH
T ss_pred             hh--hHHHHHHHhcc-cCcEEEEecCcccCCHHHHHHHHHhhCCCcCCCHHHHHHhhcchhhhcCCcCCCHHHHHHHHHH
Confidence            43  34445555554 456899999973220    0               0000000                      


Q ss_pred             -------CCCeEEEeCCcc---cccCCceEEEEec---------------------------------------------
Q 002040          671 -------NKPVEIQVGGRS---VVNKDITQLVEVR---------------------------------------------  695 (976)
Q Consensus       671 -------~~~~~i~~~~~~---~~~~~i~q~~~~~---------------------------------------------  695 (976)
                             -.|+.+.-....   ..+..+.+.+.+.                                             
T Consensus       284 ~~~L~~~l~~~~lRR~k~~v~~~LP~k~~~~v~~~ls~~q~~lY~~~~~~~~~~~~~~~g~~~~~~l~~l~~Lrk~c~hp  363 (644)
T 1z3i_X          284 LQELISIVNRCLIRRTSDILSKYLPVKIEQVVCCNLTPLQKELYKLFLKQAKPVESLQTGKISVSSLSSITSLKKLCNHP  363 (644)
T ss_dssp             HHHHHHHHHHHEECCCGGGGGGTSCCEEEEEEEECCCHHHHHHHHHHHHHHCGGGSSCTTCCCHHHHHHHHHHHHHHHCT
T ss_pred             HHHHHHHHHHHHHHhhHHhHhhhCCCceEEEEEeCCCHHHHHHHHHHHHHHHHHHHHhcCccchhHHHHHHHHHHHhCCH
Confidence                   000000000000   0000011111100                                             


Q ss_pred             --------------------------------CcchHHHHHHHHHHhhh--cCCcEEEEecCHHHHHHHHHHHHHCCCCc
Q 002040          696 --------------------------------PESDRFLRLLELLGEWY--EKGKILIFVHSQEKCDALFRDLLKHGYPC  741 (976)
Q Consensus       696 --------------------------------~~~~k~~~l~~~l~~~~--~~~kvLIF~~s~~~~~~l~~~L~~~~~~~  741 (976)
                                                      ..+.|+..|..++..+.  .+.++||||++...++.|...|...|+.+
T Consensus       364 ~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~K~~~l~~ll~~~~~~~~~k~lIFs~~~~~~~~l~~~l~~~g~~~  443 (644)
T 1z3i_X          364 ALIYEKCLTGEEGFDGALDLFPQNYSTKAVEPQLSGKMLVLDYILAMTRTTTSDKVVLVSNYTQTLDLFEKLCRNRRYLY  443 (644)
T ss_dssp             HHHHHHHHHTCTTCTTGGGTSCSSCCSSSCCGGGSHHHHHHHHHHHHHHHHCCCEEEEEESCHHHHHHHHHHHHHHTCCE
T ss_pred             HHHHHHHhcccchhhhHHhhccccccccccCcccChHHHHHHHHHHHHhhcCCCEEEEEEccHHHHHHHHHHHHHCCCCE
Confidence                                            11334444444544432  35799999999999999999999999999


Q ss_pred             eeccCCCCHHHHHHHHHHhccCCc---cEEEecCcccccCCCCCCcEEEEeCCCCCHHHHHHHhcccCCCCCccE--EEE
Q 002040          742 LSLHGAKDQTDRESTISDFKSNVC---NLLIATSVAARGLDVKELELVINFDAPNHYEDYVHRVGRTGRAGRKGC--AIT  816 (976)
Q Consensus       742 ~~lhg~~~~~~R~~~~~~F~~g~~---~vLVaT~v~~~GlDi~~v~~VI~~d~p~s~~~y~Qr~GR~gR~g~~g~--~~~  816 (976)
                      ..+||++++.+|..++..|++|..   .|||+|.++++|||++++++||+||+|||+..|.|++||++|.|+...  +|.
T Consensus       444 ~~l~G~~~~~~R~~~i~~F~~~~~~~~v~L~st~a~g~Glnl~~a~~Vi~~d~~wnp~~~~Qa~gR~~R~Gq~~~v~v~~  523 (644)
T 1z3i_X          444 VRLDGTMSIKKRAKIVERFNNPSSPEFIFMLSSKAGGCGLNLIGANRLVMFDPDWNPANDEQAMARVWRDGQKKTCYIYR  523 (644)
T ss_dssp             EEECSSCCHHHHHHHHHHHHSTTCCCCEEEEEGGGSCTTCCCTTEEEEEECSCCSSHHHHHHHHTTSSSTTCCSCEEEEE
T ss_pred             EEEeCCCCHHHHHHHHHHhcCCCCCcEEEEEecccccCCcccccCCEEEEECCCCCccHHHHHHHhhhhcCCCCceEEEE
Confidence            999999999999999999999865   489999999999999999999999999999999999999999998764  445


Q ss_pred             EecCC
Q 002040          817 FISEE  821 (976)
Q Consensus       817 ~~~~~  821 (976)
                      |++..
T Consensus       524 lv~~~  528 (644)
T 1z3i_X          524 LLSTG  528 (644)
T ss_dssp             EEETT
T ss_pred             EEECC
Confidence            56654

>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=99.98  E-value=2.6e-31  Score=276.55  Aligned_cols=204  Identities=41%  Similarity=0.693  Sum_probs=184.3

Q ss_pred             ccccCCCCHHHHHHHHHcCCCCCcHHHHHHHHHHhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEc
Q 002040          468 TWHQTGLTSKIMETIRKLNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMA  547 (976)
Q Consensus       468 ~~~~~~l~~~l~~~l~~~~~~~p~~~Q~~~i~~il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~  547 (976)
                      +|.++++++.+...|..+||..|+|+|.++++.+++++++++++|||+|||++|++|++..+.....  ...++++||++
T Consensus         2 ~f~~~~l~~~l~~~l~~~~~~~~~~~Q~~~i~~~~~~~~~li~~~TGsGKT~~~~~~~~~~l~~~~~--~~~~~~~lil~   79 (207)
T 2gxq_A            2 EFKDFPLKPEILEALHGRGLTTPTPIQAAALPLALEGKDLIGQARTGTGKTLAFALPIAERLAPSQE--RGRKPRALVLT   79 (207)
T ss_dssp             CGGGSCCCHHHHHHHHHTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHCCCCCC--TTCCCSEEEEC
T ss_pred             ChhhcCCCHHHHHHHHHcCCCCCCHHHHHHHHHHcCCCCEEEECCCCChHHHHHHHHHHHHHhhccc--cCCCCcEEEEE
Confidence            6899999999999999999999999999999999999999999999999999999999998865321  23578999999


Q ss_pred             cCHHHHHHHHHHHHHHHhhcCcEEEEeeCCCChHHHHHHHhcCCeEEEeCchhHHHHHHhcCCcccccCCceEEEecCcc
Q 002040          548 PTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEAD  627 (976)
Q Consensus       548 Ptr~La~Q~~~~~~~~~~~~~~~~~~~~gg~~~~~~~~~l~~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDEah  627 (976)
                      ||++|+.|+++.+..++..  +.+..++||.....+...+..+++|+|+||++|..++....   ..+..+++|||||||
T Consensus        80 P~~~L~~q~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~i~v~T~~~l~~~~~~~~---~~~~~~~~iViDEah  154 (207)
T 2gxq_A           80 PTRELALQVASELTAVAPH--LKVVAVYGGTGYGKQKEALLRGADAVVATPGRALDYLRQGV---LDLSRVEVAVLDEAD  154 (207)
T ss_dssp             SSHHHHHHHHHHHHHHCTT--SCEEEECSSSCSHHHHHHHHHCCSEEEECHHHHHHHHHHTS---SCCTTCSEEEEESHH
T ss_pred             CCHHHHHHHHHHHHHHhhc--ceEEEEECCCChHHHHHHhhCCCCEEEECHHHHHHHHHcCC---cchhhceEEEEEChh
Confidence            9999999999999998754  67888999998887777777889999999999999887632   467889999999999


Q ss_pred             cccccCCchHHHHHHHhcCCCCcEEEEeccCcHHHHHHHHHHcCCCeEEEe
Q 002040          628 RMFDMGFEPQITRIVQNIRPDRQTVLFSATFPRQVEILARKVLNKPVEIQV  678 (976)
Q Consensus       628 ~~~~~~f~~~i~~il~~~~~~~q~i~~SAT~~~~~~~l~~~~l~~~~~i~~  678 (976)
                      ++++++|...+..++..+++..|+|+||||+++.+..++..++.+|+.+.+
T Consensus       155 ~~~~~~~~~~~~~i~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~p~~i~~  205 (207)
T 2gxq_A          155 EMLSMGFEEEVEALLSATPPSRQTLLFSATLPSWAKRLAERYMKNPVLINV  205 (207)
T ss_dssp             HHHHTTCHHHHHHHHHTSCTTSEEEEECSSCCHHHHHHHHHHCSSCEEEEC
T ss_pred             HhhccchHHHHHHHHHhCCccCeEEEEEEecCHHHHHHHHHHcCCCeEEEc
Confidence            999999999999999999999999999999999999999999999987764

>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=99.98  E-value=1.8e-31  Score=288.32  Aligned_cols=205  Identities=33%  Similarity=0.525  Sum_probs=182.2

Q ss_pred             cccccCC--CCHHHHHHHHHcCCCCCcHHHHHHHHHHhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEE
Q 002040          467 KTWHQTG--LTSKIMETIRKLNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGL  544 (976)
Q Consensus       467 ~~~~~~~--l~~~l~~~l~~~~~~~p~~~Q~~~i~~il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vL  544 (976)
                      .+|..++  +++.++..|..+||..|+|+|.++|+.++.++++|++|+||||||++|++|++..+...... ...++++|
T Consensus        52 ~~f~~l~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~lv~a~TGsGKT~~~~l~~l~~l~~~~~~-~~~~~~~l  130 (262)
T 3ly5_A           52 TSFASLCNLVNENTLKAIKEMGFTNMTEIQHKSIRPLLEGRDLLAAAKTGSGKTLAFLIPAVELIVKLRFM-PRNGTGVL  130 (262)
T ss_dssp             GCC-----CCCHHHHHHHHHTTCCBCCHHHHHHHHHHHHTCCCEECCCTTSCHHHHHHHHHHHHHHHTTCC-GGGCCCEE
T ss_pred             CChhHhccccCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCcEEEEccCCCCchHHHHHHHHHHHHhcccc-ccCCceEE
Confidence            4566666  99999999999999999999999999999999999999999999999999999988764321 23478899


Q ss_pred             EEccCHHHHHHHHHHHHHHHhhcCcEEEEeeCCCChHHHHHHHhcCCeEEEeCchhHHHHHHhcCCcccccCCceEEEec
Q 002040          545 IMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMD  624 (976)
Q Consensus       545 Il~Ptr~La~Q~~~~~~~~~~~~~~~~~~~~gg~~~~~~~~~l~~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlD  624 (976)
                      ||+||++||.|++..+..++...++.+.+++||.....+...+..+++|+||||++|.+++....  ...+.++.+||||
T Consensus       131 il~Pt~~La~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~Iiv~Tp~~l~~~~~~~~--~~~~~~l~~lViD  208 (262)
T 3ly5_A          131 ILSPTRELAMQTFGVLKELMTHHVHTYGLIMGGSNRSAEAQKLGNGINIIVATPGRLLDHMQNTP--GFMYKNLQCLVID  208 (262)
T ss_dssp             EECSSHHHHHHHHHHHHHHTTTCCSCEEEECSSSCHHHHHHHHHHCCSEEEECHHHHHHHHHHCT--TCCCTTCCEEEEC
T ss_pred             EEeCCHHHHHHHHHHHHHHHhhcCceEEEEECCCCHHHHHHHhcCCCCEEEEcHHHHHHHHHccC--CcccccCCEEEEc
Confidence            99999999999999999999989999999999999988888888889999999999998887642  2357889999999


Q ss_pred             CcccccccCCchHHHHHHHhcCCCCcEEEEeccCcHHHHHHHHHHcCCCe
Q 002040          625 EADRMFDMGFEPQITRIVQNIRPDRQTVLFSATFPRQVEILARKVLNKPV  674 (976)
Q Consensus       625 Eah~~~~~~f~~~i~~il~~~~~~~q~i~~SAT~~~~~~~l~~~~l~~~~  674 (976)
                      |||+|++++|...+..++..+++.+|+|+||||+|+.+..++..++..+.
T Consensus       209 Eah~l~~~~~~~~l~~i~~~~~~~~q~l~~SAT~~~~v~~~~~~~l~~~~  258 (262)
T 3ly5_A          209 EADRILDVGFEEELKQIIKLLPTRRQTMLFSATQTRKVEDLARISLKKEP  258 (262)
T ss_dssp             SHHHHHHTTCHHHHHHHHHHSCSSSEEEEECSSCCHHHHHHHHHHCSSCC
T ss_pred             ChHHHhhhhHHHHHHHHHHhCCCCCeEEEEEecCCHHHHHHHHHHcCCCC
Confidence            99999999999999999999999999999999999999999999987654

>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=99.97  E-value=3.6e-31  Score=278.50  Aligned_cols=207  Identities=28%  Similarity=0.509  Sum_probs=181.6

Q ss_pred             CCcccccccCCCCHHHHHHHHHcCCCCCcHHHHHHHHHHhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCe
Q 002040          463 PKPIKTWHQTGLTSKIMETIRKLNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPV  542 (976)
Q Consensus       463 p~pi~~~~~~~l~~~l~~~l~~~~~~~p~~~Q~~~i~~il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~  542 (976)
                      +....+|.+++|++.+.+.|..+||..|+|+|.++++.+++++++|++++||+|||++|++|++..+...     ..+++
T Consensus        10 ~~~~~~f~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~li~~~TGsGKT~~~~~~~~~~~~~~-----~~~~~   84 (220)
T 1t6n_A           10 SIHSSGFRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQLEPV-----TGQVS   84 (220)
T ss_dssp             ----CCSTTSCCCHHHHHHHHHTTCCCCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHCCCC-----TTCCC
T ss_pred             cccCCCHhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCCchhhhhhHHHHHhhhcc-----CCCEE
Confidence            4455679999999999999999999999999999999999999999999999999999999999887542     23568


Q ss_pred             EEEEccCHHHHHHHHHHHHHHHhhc-CcEEEEeeCCCChHHHHHHHhc-CCeEEEeCchhHHHHHHhcCCcccccCCceE
Q 002040          543 GLIMAPTRELVQQIHSDIRKFAKVM-GVRCVPVYGGSGVAQQISELKR-GTEIVVCTPGRMIDILCTSGGKITNLRRVTY  620 (976)
Q Consensus       543 vLIl~Ptr~La~Q~~~~~~~~~~~~-~~~~~~~~gg~~~~~~~~~l~~-~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~  620 (976)
                      +||||||++|+.||+..+..++... ++.+.+++||.....+...+.. .++|+|+||++|..++....   ..+..+++
T Consensus        85 ~lil~Pt~~L~~q~~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~~~~~~~~i~v~T~~~l~~~~~~~~---~~~~~~~~  161 (220)
T 1t6n_A           85 VLVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLKKNCPHIVVGTPGRILALARNKS---LNLKHIKH  161 (220)
T ss_dssp             EEEECSCHHHHHHHHHHHHHHTTTSTTCCEEEESCCSCHHHHHHHHHHSCCSEEEECHHHHHHHHHTTS---SCCTTCCE
T ss_pred             EEEEeCCHHHHHHHHHHHHHHHhhCCCceEEEEeCCCChHHHHHHHhcCCCCEEEeCHHHHHHHHHhCC---CCcccCCE
Confidence            9999999999999999999998776 7899999999988777766665 46999999999998886532   46788999


Q ss_pred             EEecCcccccc-cCCchHHHHHHHhcCCCCcEEEEeccCcHHHHHHHHHHcCCCeEEE
Q 002040          621 LVMDEADRMFD-MGFEPQITRIVQNIRPDRQTVLFSATFPRQVEILARKVLNKPVEIQ  677 (976)
Q Consensus       621 vVlDEah~~~~-~~f~~~i~~il~~~~~~~q~i~~SAT~~~~~~~l~~~~l~~~~~i~  677 (976)
                      |||||||++++ .+|...+..++..+++..|+|+||||+++.+..++..++.+|+.+.
T Consensus       162 lViDEah~~~~~~~~~~~~~~i~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~p~~i~  219 (220)
T 1t6n_A          162 FILDECDKMLEQLDMRRDVQEIFRMTPHEKQVMMFSATLSKEIRPVCRKFMQDPMEIF  219 (220)
T ss_dssp             EEEESHHHHHSSHHHHHHHHHHHHTSCSSSEEEEEESCCCTTTHHHHHTTCSSCEEEE
T ss_pred             EEEcCHHHHhcccCcHHHHHHHHHhCCCcCeEEEEEeecCHHHHHHHHHHcCCCeEEe
Confidence            99999999986 5788889999999988999999999999999999999999998764

>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=99.97  E-value=1.9e-30  Score=324.44  Aligned_cols=313  Identities=16%  Similarity=0.133  Sum_probs=216.1

Q ss_pred             CCCcHHHHHHHHHHhc--------------CCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHH
Q 002040          488 EKPMPIQAQALPVIMS--------------GRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELV  553 (976)
Q Consensus       488 ~~p~~~Q~~~i~~il~--------------g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La  553 (976)
                      ..|+|+|..|++.++.              ++++|++++||||||+++ ++++..+...     +..+++|||||+++|+
T Consensus       270 ~~~R~~Q~~AI~~il~~i~~~~~~~~~~~~~~~gli~~~TGSGKT~t~-~~l~~ll~~~-----~~~~rvLvlvpr~eL~  343 (1038)
T 2w00_A          270 LVMRPYQIAATERILWKIKSSFTAKNWSKPESGGYIWHTTGSGKTLTS-FKAARLATEL-----DFIDKVFFVVDRKDLD  343 (1038)
T ss_dssp             EECCHHHHHHHHHHHHHHHHHHHHTCCSSGGGSEEEEECTTSSHHHHH-HHHHHHHTTC-----TTCCEEEEEECGGGCC
T ss_pred             ccCCHHHHHHHHHHHHHHHhcccccccccCCCCEEEEecCCCCHHHHH-HHHHHHHHhc-----CCCceEEEEeCcHHHH
Confidence            3599999999999875              368999999999999997 5666554431     2346899999999999


Q ss_pred             HHHHHHHHHHHhhcCcEEEEeeCCCChHHHHHHHh-cCCeEEEeCchhHHHHHHhcCCcccccCCceEEEecCccccccc
Q 002040          554 QQIHSDIRKFAKVMGVRCVPVYGGSGVAQQISELK-RGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDM  632 (976)
Q Consensus       554 ~Q~~~~~~~~~~~~~~~~~~~~gg~~~~~~~~~l~-~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDEah~~~~~  632 (976)
                      .||...|..|+..      .++++.+.......+. .+.+|+|+||++|..++.... ....+..+.+|||||||++.. 
T Consensus       344 ~Q~~~~f~~f~~~------~v~~~~s~~~l~~~L~~~~~~IiVtTiqkl~~~l~~~~-~~~~~~~~~lvIiDEAHrs~~-  415 (1038)
T 2w00_A          344 YQTMKEYQRFSPD------SVNGSENTAGLKRNLDKDDNKIIVTTIQKLNNLMKAES-DLPVYNQQVVFIFDECHRSQF-  415 (1038)
T ss_dssp             HHHHHHHHTTSTT------CSSSSCCCHHHHHHHHCSSCCEEEEEHHHHHHHHHHCC-CCGGGGSCEEEEEESCCTTHH-
T ss_pred             HHHHHHHHHhccc------ccccccCHHHHHHHhcCCCCCEEEEEHHHHHHHHhccc-chhccccccEEEEEccchhcc-
Confidence            9999999887642      2355666666656664 468999999999998876432 112456789999999999763 


Q ss_pred             CCchHHHHHHHhcCCCCcEEEEeccCcHHHH----HHHHHHcCCCeEEEeCCc----ccccCCceEEEE-----------
Q 002040          633 GFEPQITRIVQNIRPDRQTVLFSATFPRQVE----ILARKVLNKPVEIQVGGR----SVVNKDITQLVE-----------  693 (976)
Q Consensus       633 ~f~~~i~~il~~~~~~~q~i~~SAT~~~~~~----~l~~~~l~~~~~i~~~~~----~~~~~~i~q~~~-----------  693 (976)
                        ...+..|+..+ ++.++|+|||||.....    .....+++.++.......    +... .+...+.           
T Consensus       416 --~~~~~~I~~~~-p~a~~lgfTATP~~~~~~~~~~~t~~~FG~~i~~Y~l~~AI~dg~l~-p~~v~y~~v~~~~~~~~~  491 (1038)
T 2w00_A          416 --GEAQKNLKKKF-KRYYQFGFTGTPIFPENALGSETTASVFGRELHSYVITDAIRDEKVL-KFKVDYNDVRPQFKSLET  491 (1038)
T ss_dssp             --HHHHHHHHHHC-SSEEEEEEESSCCCSTTCTTSCCHHHHHCSEEEEECHHHHHHHTSSC-CEEEEECCCCGGGHHHHT
T ss_pred             --hHHHHHHHHhC-CcccEEEEeCCccccccchhhhHHHHHhCCeeEeecHHHHHhCCCcC-CeEEEEEeccchhhhccc
Confidence              23345555666 45799999999874321    112223333322110000    0000 0000000           


Q ss_pred             --------------ecCcchHHHHHHHHHHhhh-----------cCCcEEEEecCHHHHHHHHHHHHHCC----------
Q 002040          694 --------------VRPESDRFLRLLELLGEWY-----------EKGKILIFVHSQEKCDALFRDLLKHG----------  738 (976)
Q Consensus       694 --------------~~~~~~k~~~l~~~l~~~~-----------~~~kvLIF~~s~~~~~~l~~~L~~~~----------  738 (976)
                                    ......++..++..|...+           .+.++||||+++..|..++..|...+          
T Consensus       492 e~d~~~~~~i~~~~~l~~~~ri~~I~~~Il~~~~~~~~~~~~~~~g~kamVf~~S~~~A~~~~~~l~~~~~~~~~~~~~~  571 (1038)
T 2w00_A          492 ETDEKKLSAAENQQAFLHPMRIQEITQYILNNFRQKTHRTFPGSKGFNAMLAVSSVDAAKAYYATFKRLQEEAANKSATY  571 (1038)
T ss_dssp             CCCHHHHHHTCSTTTTTCHHHHHHHHHHHHHHHHHHTTCSSSSCCCCEEEEEESSHHHHHHHHHHHHHHHHHHTTTSSSC
T ss_pred             cccHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHhhhhhcccCCCCcEEEEECCHHHHHHHHHHHHhhhhhhccccccc
Confidence                          0012223334444332211           23589999999999999999997754          


Q ss_pred             --CCc-eeccCC----------C----------CHH-----------------------------HHHHHHHHhccCCcc
Q 002040          739 --YPC-LSLHGA----------K----------DQT-----------------------------DRESTISDFKSNVCN  766 (976)
Q Consensus       739 --~~~-~~lhg~----------~----------~~~-----------------------------~R~~~~~~F~~g~~~  766 (976)
                        +.+ +++||.          +          ++.                             .|..++..|++|.++
T Consensus       572 ~~~k~avv~s~~~~~~~~~~G~~~~e~~~~~~~~~~~r~~l~~~I~dyn~~f~~~~~~~~~~~~~~R~~i~~~Fk~g~i~  651 (1038)
T 2w00_A          572 KPLRIATIFSFAANEEQNAIGEISDETFDTSAMDSSAKEFLDAAIREYNSHFKTNFSTDSNGFQNYYRDLAQRVKNQDID  651 (1038)
T ss_dssp             CCCCEEEECCCCC------CCCCCCCCSCGGGSCHHHHHHHHHHHHHHHHHHTCCCCSSHHHHHHHHHHHHHHHHTTSSS
T ss_pred             ccCcEEEEEeCCCccccccccccccccccccccchhHHHHHHHHHHHHHHHhcccccccchhhhHHHHHHHHHHHcCCCe
Confidence              455 455643          2          221                             478899999999999


Q ss_pred             EEEecCcccccCCCCCCcEEEEeCCCCCHHHHHHHhcccCCCCCc----cEEEEEec
Q 002040          767 LLIATSVAARGLDVKELELVINFDAPNHYEDYVHRVGRTGRAGRK----GCAITFIS  819 (976)
Q Consensus       767 vLVaT~v~~~GlDi~~v~~VI~~d~p~s~~~y~Qr~GR~gR~g~~----g~~~~~~~  819 (976)
                      |||+|+++.+|+|+|.+ .|+++|.|.+...|+|++||++|.+..    |.++.|+.
T Consensus       652 ILIvvd~lltGfDiP~l-~tlylDkpl~~~~liQaIGRtnR~~~~~K~~G~IVdf~~  707 (1038)
T 2w00_A          652 LLIVVGMFLTGFDAPTL-NTLFVDKNLRYHGLMQAFSRTNRIYDATKTFGNIVTFRD  707 (1038)
T ss_dssp             EEEESSTTSSSCCCTTE-EEEEEESCCCHHHHHHHHHTTCCCCCTTCCSEEEEESSC
T ss_pred             EEEEcchHHhCcCcccc-cEEEEccCCCccceeehhhccCcCCCCCCCcEEEEEccc
Confidence            99999999999999999 677899999999999999999998753    77777765

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

Probab=99.96  E-value=1e-27  Score=283.92  Aligned_cols=322  Identities=22%  Similarity=0.273  Sum_probs=236.9

Q ss_pred             HcCCCCCcHHHHHHHHHHhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHHH
Q 002040          484 KLNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKF  563 (976)
Q Consensus       484 ~~~~~~p~~~Q~~~i~~il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~~  563 (976)
                      .+|+ .||++|..++|.+++|+  |+.+.||+|||++|++|++.....        |..|+||+||++||.|++.++..+
T Consensus        75 ~lG~-~Pt~VQ~~~ip~LlqG~--IaeakTGeGKTLvf~Lp~~L~aL~--------G~qv~VvTPTreLA~Qdae~m~~l  143 (997)
T 2ipc_A           75 YLGM-RHFDVQLIGGAVLHEGK--IAEMKTGEGKTLVATLAVALNALT--------GKGVHVVTVNDYLARRDAEWMGPV  143 (997)
T ss_dssp             HTCC-CCCHHHHHHHHHHHTTS--EEECCSTHHHHHHHHHHHHHHHTT--------CSCCEEEESSHHHHHHHHHHHHHH
T ss_pred             HhCC-CCcHHHHhhcccccCCc--eeeccCCCchHHHHHHHHHHHHHh--------CCCEEEEeCCHHHHHHHHHHHHHH
Confidence            3798 89999999999999998  999999999999999999755432        457999999999999999999999


Q ss_pred             HhhcCcEEEEeeCCCChHHHHHHHhcCCeEEEeCchhH-HHHHHhcC---CcccccC---CceEEEecCccccc-ccCCc
Q 002040          564 AKVMGVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRM-IDILCTSG---GKITNLR---RVTYLVMDEADRMF-DMGFE  635 (976)
Q Consensus       564 ~~~~~~~~~~~~gg~~~~~~~~~l~~~~~Iiv~Tp~~L-~~~l~~~~---~~~~~l~---~~~~vVlDEah~~~-~~~f~  635 (976)
                      +..+|+.+.+++||.+....  .+..+++|+|+||+.| +++|..+.   .....+.   .+.++||||||.|+ +.+..
T Consensus       144 ~~~lGLsv~~i~Gg~~~~~r--~~ay~~DIvyGTpgrlgfDyLrd~m~~~~~~l~~r~d~~l~~lIIDEaDsmLiDeart  221 (997)
T 2ipc_A          144 YRGLGLSVGVIQHASTPAER--RKAYLADVTYVTNSELGFDYLRDNMAISPDQLVLRHDHPLHYAIIDEVDSILIDEART  221 (997)
T ss_dssp             HHTTTCCEEECCTTCCHHHH--HHHHTSSEEEEEHHHHHHHHHHHTSCSSTTTCCSCSSSSSCEEEETTHHHHTTSSTTS
T ss_pred             HHhcCCeEEEEeCCCCHHHH--HHHcCCCEEEECchhhhhHHHHHhhhcchhhcccccCCCcceEEEechHHHHHhCCCC
Confidence            99999999999999885443  3344699999999999 88887652   1123466   89999999999876 22211


Q ss_pred             h---------------HHHHHHHhcCC-----------------------------------------------------
Q 002040          636 P---------------QITRIVQNIRP-----------------------------------------------------  647 (976)
Q Consensus       636 ~---------------~i~~il~~~~~-----------------------------------------------------  647 (976)
                      +               .+..++..+..                                                     
T Consensus       222 PLIISgp~~~~~~lY~~~~~~i~~L~~~~~~~~~~~~~~~~dy~vdek~r~v~LTe~G~~~~E~~l~i~~Ly~~~n~~l~  301 (997)
T 2ipc_A          222 PLIISGPAEKATDLYYKMAEIAKKLERGLPAEPGVRKEPTGDYTVEEKNRSVHLTLQGIAKAEKLLGIEGLFSPENMELA  301 (997)
T ss_dssp             CEEEEESCSSCHHHHHHHHHHHHHSCCCCCCCSSSCCCSSCCCCCTTSCCCCCCCHHHHHHHHHHHSCHHHHTTTCHHHH
T ss_pred             CeeeeCCCccchHHHHHHHHHHHHhhhccccccccccCCCCCeEEecCcceEEEchHHHHHHHHHcCCccccCchhHHHH
Confidence            0               11111111110                                                     


Q ss_pred             ----------------------------------------------------------------------------CCcE
Q 002040          648 ----------------------------------------------------------------------------DRQT  651 (976)
Q Consensus       648 ----------------------------------------------------------------------------~~q~  651 (976)
                                                                                                  -..+
T Consensus       302 ~~i~~ALrA~~lf~rd~dYiV~dgeV~IVDe~TGR~m~grrwsdGLHQAiEAKEgv~I~~e~~TlAsIT~QnyFr~Y~kL  381 (997)
T 2ipc_A          302 HMLIQAIRAKELYHRDRDYIVQDGQVIIVDEFTGRLMPGRRYGEGLHQAIEAKEGVRIERENQTLATITYQNFFRLYEKR  381 (997)
T ss_dssp             HHHHHHHHHHHSSCHHHHEEECSSCEEEEETTTTEECTTCCCGGGHHHHHHHHTTCCCCCSCEEEEEECHHHHHTTSSEE
T ss_pred             HHHHHHHHHHHHHhcCCCeEEECCEEEEEECCCCeeCCCCcccHHHHHHHHHHhCCCCCCCceeeeeeeHHHHHHhChHh
Confidence                                                                                        0236


Q ss_pred             EEEeccCcHHHHHHHHHHcCCCeEEEeCCcccccCCceEEEEecCcchHHHHHHHHHHhhhc-CCcEEEEecCHHHHHHH
Q 002040          652 VLFSATFPRQVEILARKVLNKPVEIQVGGRSVVNKDITQLVEVRPESDRFLRLLELLGEWYE-KGKILIFVHSQEKCDAL  730 (976)
Q Consensus       652 i~~SAT~~~~~~~l~~~~l~~~~~i~~~~~~~~~~~i~q~~~~~~~~~k~~~l~~~l~~~~~-~~kvLIF~~s~~~~~~l  730 (976)
                      .+||+|.......+...|-.+ +.+.+...+...... ....+.....|+..++..+...+. +.||||+|.|++..+.|
T Consensus       382 sGMTGTA~tE~~Ef~~iY~l~-Vv~IPTn~p~~R~D~-~d~vy~t~~~K~~AIv~eI~~~~~~GqPVLVgT~SIe~SE~L  459 (997)
T 2ipc_A          382 AGMTGTAKTEEKEFQEIYGMD-VVVVPTNRPVIRKDF-PDVVYRTEKGKFYAVVEEIAEKYERGQPVLVGTISIEKSERL  459 (997)
T ss_dssp             EEEESSCGGGHHHHHHHHCCC-EEECCCSSCCCCEEE-EEEEESSHHHHHHHHHHHHHHHHHHTCCEEEECSSHHHHHHH
T ss_pred             eecCCCchHHHHHHHHHhCCC-EEEcCCCCCcccccC-CCeEEcCHHHHHHHHHHHHHHHHHCCCCEEEEeCCHHHHHHH
Confidence            788888876666555544433 333222222222222 233456778899998887776654 56999999999999999


Q ss_pred             HHHHH---------------------------------------------------------------------------
Q 002040          731 FRDLL---------------------------------------------------------------------------  735 (976)
Q Consensus       731 ~~~L~---------------------------------------------------------------------------  735 (976)
                      +..|.                                                                           
T Consensus       460 S~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~  539 (997)
T 2ipc_A          460 SQMLKEPRLYLPRLEMRLELFKKASQKQQGPEWERLRKLLERPAQLKDEDLAPFEGLIPPKGNLRTAWEGLKRAVHTLAV  539 (997)
T ss_dssp             HHHHHCGGGGHHHHHHHHHHHHHHHTTCCSHHHHHHHHHTSSSTTCSHHHHSGGGGGCCSSHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHhhccccchhhhhhhhhhhhhhhhccccchhhhhhhhhccccccccccccccccccccccccccccccchhhhhhHH
Confidence            99998                                                                           


Q ss_pred             -HCCCCceeccCCCCHHHHHHHHHHhccCC-ccEEEecCcccccCCCCCC-------------------c----------
Q 002040          736 -KHGYPCLSLHGAKDQTDRESTISDFKSNV-CNLLIATSVAARGLDVKEL-------------------E----------  784 (976)
Q Consensus       736 -~~~~~~~~lhg~~~~~~R~~~~~~F~~g~-~~vLVaT~v~~~GlDi~~v-------------------~----------  784 (976)
                       ..|+++.++++.....+- .|+.  +.|. -.|-|||++|+||.||.--                   .          
T Consensus       540 ~~~gI~H~VLNAK~he~EA-eIIA--qAG~~GaVTIATNMAGRGTDIkLggn~e~~~~~~~~~~~~~~~~~~~~~~~~~~  616 (997)
T 2ipc_A          540 LRQGIPHQVLNAKHHAREA-EIVA--QAGRSKTVTIATNMAGRGTDIKLGGNPEYLAAALLEKEGFDRYEWKVELFIKKM  616 (997)
T ss_dssp             HHHCCCCCEECSSSHHHHH-HHHH--TTTSTTCEEEECSSTTTTSCCCSSCCHHHHHHHTTSSSCSSTTHHHHHHHHHHH
T ss_pred             HHcCCCeeeccccchHHHH-HHHH--hcCCCCeEEEEecccCCCcCeecCCCHHHHHHHHHHhhcccccccccccccccc
Confidence             456777777766443332 2222  2343 3599999999999998543                   1          


Q ss_pred             ---------------------------------------------EEEEeCCCCCHHHHHHHhcccCCCCCccEEEEEec
Q 002040          785 ---------------------------------------------LVINFDAPNHYEDYVHRVGRTGRAGRKGCAITFIS  819 (976)
Q Consensus       785 ---------------------------------------------~VI~~d~p~s~~~y~Qr~GR~gR~g~~g~~~~~~~  819 (976)
                                                                   +||--..+.|.---.|..||+||.|.+|.+..|++
T Consensus       617 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~V~e~GGLhVIGTeRhESrRIDnQLRGRaGRQGDPGsSrF~LS  696 (997)
T 2ipc_A          617 VAGKEEEARALAQELGIREELLERIREIREECKQDEERVRALGGLFIIGTERHESRRIDNQLRGRAGRQGDPGGSRFYVS  696 (997)
T ss_dssp             HHTCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHHTTTCCCCEEESSCCSSHHHHHHHHHTSSCSSCCCEEEEEEE
T ss_pred             cccchhhccccchhhhhhhhHHHHHHHhhhhhhhhhhHHHhcCCeEEEeccCCchHHHHHHHhcccccCCCCCCeEEEEE
Confidence                                                         78888888888889999999999999999999988


Q ss_pred             CCCc
Q 002040          820 EEDA  823 (976)
Q Consensus       820 ~~d~  823 (976)
                      -+|.
T Consensus       697 LeDd  700 (997)
T 2ipc_A          697 FDDD  700 (997)
T ss_dssp             SSSH
T ss_pred             CChH
Confidence            7653

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

Probab=99.95  E-value=6e-27  Score=283.98  Aligned_cols=176  Identities=23%  Similarity=0.304  Sum_probs=137.4

Q ss_pred             CCCcEEEEeccCcHHHHHHHHHHcCCCeEEEeCCcccccCCceEEEEecCcchHHHHHHHHHHhhh-cCCcEEEEecCHH
Q 002040          647 PDRQTVLFSATFPRQVEILARKVLNKPVEIQVGGRSVVNKDITQLVEVRPESDRFLRLLELLGEWY-EKGKILIFVHSQE  725 (976)
Q Consensus       647 ~~~q~i~~SAT~~~~~~~l~~~~l~~~~~i~~~~~~~~~~~i~q~~~~~~~~~k~~~l~~~l~~~~-~~~kvLIF~~s~~  725 (976)
                      ...|+|+||||+++.....    ....+...+.......+    .+.+.+...++..|+..|..+. .+.++||||+++.
T Consensus       379 ~~~q~i~~SAT~~~~~~~~----~~~~~~~~~r~~~l~~p----~i~v~~~~~~~~~Ll~~l~~~~~~~~~vlVf~~t~~  450 (664)
T 1c4o_A          379 RVSQVVFVSATPGPFELAH----SGRVVEQIIRPTGLLDP----LVRVKPTENQILDLMEGIRERAARGERTLVTVLTVR  450 (664)
T ss_dssp             TCSEEEEEESSCCHHHHHH----CSEEEEECSCTTCCCCC----EEEEECSTTHHHHHHHHHHHHHHTTCEEEEECSSHH
T ss_pred             hcCCEEEEecCCCHHHHHh----hhCeeeeeeccCCCCCC----eEEEecccchHHHHHHHHHHHHhcCCEEEEEECCHH
Confidence            3578999999998753211    11111111111111111    1233444566677777776654 4669999999999


Q ss_pred             HHHHHHHHHHHCCCCceeccCCCCHHHHHHHHHHhccCCccEEEecCcccccCCCCCCcEEEEeCC-----CCCHHHHHH
Q 002040          726 KCDALFRDLLKHGYPCLSLHGAKDQTDRESTISDFKSNVCNLLIATSVAARGLDVKELELVINFDA-----PNHYEDYVH  800 (976)
Q Consensus       726 ~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLVaT~v~~~GlDi~~v~~VI~~d~-----p~s~~~y~Q  800 (976)
                      .++.|+..|...|+.+..+||++++.+|..++..|+.|.+.|||||+++++|||+|++++||+++.     |.+...|+|
T Consensus       451 ~ae~L~~~L~~~gi~~~~lh~~~~~~~R~~~~~~f~~g~~~VLvaT~~l~~GlDip~v~lVI~~d~d~~G~p~s~~~~iQ  530 (664)
T 1c4o_A          451 MAEELTSFLVEHGIRARYLHHELDAFKRQALIRDLRLGHYDCLVGINLLREGLDIPEVSLVAILDADKEGFLRSERSLIQ  530 (664)
T ss_dssp             HHHHHHHHHHHTTCCEEEECTTCCHHHHHHHHHHHHTTSCSEEEESCCCCTTCCCTTEEEEEETTTTSCSGGGSHHHHHH
T ss_pred             HHHHHHHHHHhcCCCceeecCCCCHHHHHHHHHHhhcCCceEEEccChhhcCccCCCCCEEEEeCCcccCCCCCHHHHHH
Confidence            999999999999999999999999999999999999999999999999999999999999999997     899999999


Q ss_pred             HhcccCCCCCccEEEEEecCCCcCchHHHHH
Q 002040          801 RVGRTGRAGRKGCAITFISEEDAKYSPDLVK  831 (976)
Q Consensus       801 r~GR~gR~g~~g~~~~~~~~~d~~~~~~i~~  831 (976)
                      |+|||||.| .|.|++|+++.+..+...|.+
T Consensus       531 r~GRagR~~-~G~~i~~~~~~~~~~~~~i~~  560 (664)
T 1c4o_A          531 TIGRAARNA-RGEVWLYADRVSEAMQRAIEE  560 (664)
T ss_dssp             HHGGGTTST-TCEEEEECSSCCHHHHHHHHH
T ss_pred             HHCccCcCC-CCEEEEEEcCCCHHHHHHHHH
Confidence            999999995 899999998876655444443

>2p6n_A ATP-dependent RNA helicase DDX41; DEAD, structural genomics, structural genomic consortium, SGC, hydrolase; 2.60A {Homo sapiens}

Probab=99.95  E-value=1.5e-27  Score=244.31  Aligned_cols=181  Identities=35%  Similarity=0.517  Sum_probs=148.4

Q ss_pred             HHHHcCCCeEEEeCCcccccCCceEEEEecCcchHHHHHHHHHHhhhcCCcEEEEecCHHHHHHHHHHHHHCCCCceecc
Q 002040          666 ARKVLNKPVEIQVGGRSVVNKDITQLVEVRPESDRFLRLLELLGEWYEKGKILIFVHSQEKCDALFRDLLKHGYPCLSLH  745 (976)
Q Consensus       666 ~~~~l~~~~~i~~~~~~~~~~~i~q~~~~~~~~~k~~~l~~~l~~~~~~~kvLIF~~s~~~~~~l~~~L~~~~~~~~~lh  745 (976)
                      .+.++.+|..+.++........|.|.+.......|+..|+.+|...  .+++||||++...++.++..|...|+.+..+|
T Consensus         8 ~~~~~~~p~~i~v~~~~~~~~~i~q~~~~~~~~~K~~~L~~~l~~~--~~~~lVF~~~~~~~~~l~~~L~~~g~~~~~lh   85 (191)
T 2p6n_A            8 SSGVDLGTENLYFQSMGAASLDVIQEVEYVKEEAKMVYLLECLQKT--PPPVLIFAEKKADVDAIHEYLLLKGVEAVAIH   85 (191)
T ss_dssp             --------------------CCSEEEEEECCGGGHHHHHHHHHTTS--CSCEEEECSCHHHHHHHHHHHHHHTCCEEEEC
T ss_pred             cccccCCCEEEEECCCCCCCcCceEEEEEcChHHHHHHHHHHHHhC--CCCEEEEECCHHHHHHHHHHHHHcCCcEEEEe
Confidence            4578888988888877778889999999999999999999988763  56899999999999999999999999999999


Q ss_pred             CCCCHHHHHHHHHHhccCCccEEEecCcccccCCCCCCcEEEEeCCCCCHHHHHHHhcccCCCCCccEEEEEecCC-CcC
Q 002040          746 GAKDQTDRESTISDFKSNVCNLLIATSVAARGLDVKELELVINFDAPNHYEDYVHRVGRTGRAGRKGCAITFISEE-DAK  824 (976)
Q Consensus       746 g~~~~~~R~~~~~~F~~g~~~vLVaT~v~~~GlDi~~v~~VI~~d~p~s~~~y~Qr~GR~gR~g~~g~~~~~~~~~-d~~  824 (976)
                      |+|++.+|..++..|++|.+.|||||+++++|||+|++++||+|++|+++..|+||+||+||.|+.|.|++|+++. +..
T Consensus        86 g~~~~~~R~~~l~~F~~g~~~vLvaT~~~~~Gldi~~v~~VI~~d~p~~~~~~~qr~GR~gR~g~~g~~i~l~~~~~~~~  165 (191)
T 2p6n_A           86 GGKDQEERTKAIEAFREGKKDVLVATDVASKGLDFPAIQHVINYDMPEEIENYVHRIGRTGCSGNTGIATTFINKACDES  165 (191)
T ss_dssp             TTSCHHHHHHHHHHHHHTSCSEEEECHHHHTTCCCCCCSEEEESSCCSSHHHHHHHHTTSCC---CCEEEEEECTTSCHH
T ss_pred             CCCCHHHHHHHHHHHhcCCCEEEEEcCchhcCCCcccCCEEEEeCCCCCHHHHHHHhCccccCCCCcEEEEEEcCchhHH
Confidence            9999999999999999999999999999999999999999999999999999999999999999999999999976 677


Q ss_pred             chHHHHHHHhhccCCCChHHHHHH
Q 002040          825 YSPDLVKALELSEQVVPDDLKALA  848 (976)
Q Consensus       825 ~~~~i~~~l~~~~~~vp~~l~~l~  848 (976)
                      ++..|.+.+....+.+|+.|..+.
T Consensus       166 ~~~~l~~~l~~~~~~~p~~l~~~~  189 (191)
T 2p6n_A          166 VLMDLKALLLEAKQKVPPVLQVLH  189 (191)
T ss_dssp             HHHHHHHHHHHTTCCCCHHHHSTT
T ss_pred             HHHHHHHHHHHccCcCCHHHHhhc
Confidence            888999999999999999876543

>2jgn_A DBX, DDX3, ATP-dependent RNA helicase DDX3X; phosphorylation, nucleotide-binding, hydrolase, RNA-binding, ATP-binding, DNA-binding, nuclear protein; 1.91A {Homo sapiens}

Probab=99.94  E-value=1.4e-26  Score=235.97  Aligned_cols=168  Identities=40%  Similarity=0.626  Sum_probs=143.6

Q ss_pred             ccccCCceEEEEecCcchHHHHHHHHHHhhhcCCcEEEEecCHHHHHHHHHHHHHCCCCceeccCCCCHHHHHHHHHHhc
Q 002040          682 SVVNKDITQLVEVRPESDRFLRLLELLGEWYEKGKILIFVHSQEKCDALFRDLLKHGYPCLSLHGAKDQTDRESTISDFK  761 (976)
Q Consensus       682 ~~~~~~i~q~~~~~~~~~k~~~l~~~l~~~~~~~kvLIF~~s~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~  761 (976)
                      ...+.+|.|.+..+....|+..|..+|......+++||||++...++.|+..|...|+.+..+||+|++.+|..++..|+
T Consensus        14 ~~~~~~i~q~~~~v~~~~K~~~L~~ll~~~~~~~k~lVF~~~~~~~~~l~~~L~~~g~~~~~lhg~~~~~~r~~~~~~f~   93 (185)
T 2jgn_A           14 GSTSENITQKVVWVEESDKRSFLLDLLNATGKDSLTLVFVETKKGADSLEDFLYHEGYACTSIHGDRSQRDREEALHQFR   93 (185)
T ss_dssp             --CCTTEEEEEEECCGGGHHHHHHHHHHHC-CCSCEEEEESCHHHHHHHHHHHHHTTCCEEEEC--------CHHHHHHH
T ss_pred             CCCCCCceEEEEEeCcHHHHHHHHHHHHhcCCCCeEEEEECCHHHHHHHHHHHHHcCCceEEEeCCCCHHHHHHHHHHHH
Confidence            34567899999999999999999999988656789999999999999999999999999999999999999999999999


Q ss_pred             cCCccEEEecCcccccCCCCCCcEEEEeCCCCCHHHHHHHhcccCCCCCccEEEEEecCCCcCchHHHHHHHhhccCCCC
Q 002040          762 SNVCNLLIATSVAARGLDVKELELVINFDAPNHYEDYVHRVGRTGRAGRKGCAITFISEEDAKYSPDLVKALELSEQVVP  841 (976)
Q Consensus       762 ~g~~~vLVaT~v~~~GlDi~~v~~VI~~d~p~s~~~y~Qr~GR~gR~g~~g~~~~~~~~~d~~~~~~i~~~l~~~~~~vp  841 (976)
                      +|.+.|||||+++++|||+|++++||+|++|+++..|+||+||+||.|+.|.|++|+++.+...+..|.+.+....+.+|
T Consensus        94 ~g~~~vLvaT~~~~~Gldi~~~~~VI~~d~p~s~~~~~Qr~GR~~R~g~~g~~~~~~~~~~~~~~~~l~~~l~~~~~~~~  173 (185)
T 2jgn_A           94 SGKSPILVATAVAARGLDISNVKHVINFDLPSDIEEYVHRIGRTGRVGNLGLATSFFNERNINITKDLLDLLVEAKQEVP  173 (185)
T ss_dssp             HTSSSEEEEEC------CCCSBSEEEESSCCSSHHHHHHHHTTBCCTTSCEEEEEEECGGGGGGHHHHHHHHHHTTCCCC
T ss_pred             cCCCeEEEEcChhhcCCCcccCCEEEEeCCCCCHHHHHHHccccCCCCCCcEEEEEEchhhHHHHHHHHHHHHhccCCCC
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hHHHHHHH
Q 002040          842 DDLKALAD  849 (976)
Q Consensus       842 ~~l~~l~~  849 (976)
                      .+|..++.
T Consensus       174 ~~l~~~a~  181 (185)
T 2jgn_A          174 SWLENMAY  181 (185)
T ss_dssp             HHHHHHHC
T ss_pred             HHHHHHHH
Confidence            99887764

>2d7d_A Uvrabc system protein B; helicase, protein-DNA-ADP ternary complex, hydrolase/DNA complex; HET: ADP; 2.10A {Bacillus subtilis} PDB: 2nmv_A* 2fdc_A* 1t5l_A 3uwx_B 1d9z_A* 1d9x_A 2d7d_B* 2nmv_B*

Probab=99.94  E-value=1e-25  Score=272.96  Aligned_cols=175  Identities=19%  Similarity=0.261  Sum_probs=137.8

Q ss_pred             CCCcEEEEeccCcHHHHHHHHHHcCCCeEEEeCCcccccCCceEEEEecCcchHHHHHHHHHHhhh-cCCcEEEEecCHH
Q 002040          647 PDRQTVLFSATFPRQVEILARKVLNKPVEIQVGGRSVVNKDITQLVEVRPESDRFLRLLELLGEWY-EKGKILIFVHSQE  725 (976)
Q Consensus       647 ~~~q~i~~SAT~~~~~~~l~~~~l~~~~~i~~~~~~~~~~~i~q~~~~~~~~~k~~~l~~~l~~~~-~~~kvLIF~~s~~  725 (976)
                      ...|+++||||+++.....    ....+...+.......+    .+.+.....++..|+..|..+. .+.++||||+++.
T Consensus       385 ~~~q~i~~SAT~~~~~~~~----~~~~~~~~~r~~~l~~p----~i~v~~~~~~~~~Ll~~l~~~~~~~~~vlVf~~t~~  456 (661)
T 2d7d_A          385 HMHNIVYVSATPGPYEIEH----TDEMVEQIIRPTGLLDP----LIDVRPIEGQIDDLIGEIQARIERNERVLVTTLTKK  456 (661)
T ss_dssp             TCSEEEEECSSCCHHHHHH----CSSCEEECCCTTCCCCC----EEEEECSTTHHHHHHHHHHHHHTTTCEEEEECSSHH
T ss_pred             cCCCEEEEecCCChhHHHh----hhCeeeeeecccCCCCC----eEEEecccchHHHHHHHHHHHHhcCCeEEEEECCHH
Confidence            4679999999998654221    12222221111111111    1233444556677777776655 4569999999999


Q ss_pred             HHHHHHHHHHHCCCCceeccCCCCHHHHHHHHHHhccCCccEEEecCcccccCCCCCCcEEEEeCC-----CCCHHHHHH
Q 002040          726 KCDALFRDLLKHGYPCLSLHGAKDQTDRESTISDFKSNVCNLLIATSVAARGLDVKELELVINFDA-----PNHYEDYVH  800 (976)
Q Consensus       726 ~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLVaT~v~~~GlDi~~v~~VI~~d~-----p~s~~~y~Q  800 (976)
                      .++.|+..|...|+.+..+||++++.+|..++..|++|.+.|||||+++++|||+|++++||+++.     |.+...|+|
T Consensus       457 ~ae~L~~~L~~~gi~~~~lh~~~~~~~R~~~l~~f~~g~~~VLVaT~~l~~GlDip~v~lVi~~d~d~~G~p~s~~~~iQ  536 (661)
T 2d7d_A          457 MSEDLTDYLKEIGIKVNYLHSEIKTLERIEIIRDLRLGKYDVLVGINLLREGLDIPEVSLVAILDADKEGFLRSERSLIQ  536 (661)
T ss_dssp             HHHHHHHHHHHTTCCEEEECTTCCHHHHHHHHHHHHHTSCSEEEESCCCSTTCCCTTEEEEEETTTTCCTTTTSHHHHHH
T ss_pred             HHHHHHHHHHhcCCCeEEEeCCCCHHHHHHHHHHHhcCCeEEEEecchhhCCcccCCCCEEEEeCcccccCCCCHHHHHH
Confidence            999999999999999999999999999999999999999999999999999999999999999997     999999999


Q ss_pred             HhcccCCCCCccEEEEEecCCCcCchHHHH
Q 002040          801 RVGRTGRAGRKGCAITFISEEDAKYSPDLV  830 (976)
Q Consensus       801 r~GR~gR~g~~g~~~~~~~~~d~~~~~~i~  830 (976)
                      |+|||||. ..|.|++|+++.+..+...|.
T Consensus       537 r~GRagR~-~~G~~i~~~~~~~~~~~~~i~  565 (661)
T 2d7d_A          537 TIGRAARN-AEGRVIMYADKITKSMEIAIN  565 (661)
T ss_dssp             HHHTTTTS-TTCEEEEECSSCCHHHHHHHH
T ss_pred             HhCcccCC-CCCEEEEEEeCCCHHHHHHHH
Confidence            99999998 689999999987655444443

>2hjv_A ATP-dependent RNA helicase DBPA; parallel alpha-beta, hydrolase; 1.95A {Bacillus subtilis}

Probab=99.93  E-value=6.5e-25  Score=219.08  Aligned_cols=153  Identities=36%  Similarity=0.621  Sum_probs=141.4

Q ss_pred             cccCCceEEEEecCcchHHHHHHHHHHhhhcCCcEEEEecCHHHHHHHHHHHHHCCCCceeccCCCCHHHHHHHHHHhcc
Q 002040          683 VVNKDITQLVEVRPESDRFLRLLELLGEWYEKGKILIFVHSQEKCDALFRDLLKHGYPCLSLHGAKDQTDRESTISDFKS  762 (976)
Q Consensus       683 ~~~~~i~q~~~~~~~~~k~~~l~~~l~~~~~~~kvLIF~~s~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~  762 (976)
                      ....++.|.+.......|+..|..+|... ..+++||||++...++.++..|...|+.+..+||+|++.+|..++..|++
T Consensus         5 ~~~~~i~~~~~~~~~~~K~~~L~~ll~~~-~~~~~lVF~~~~~~~~~l~~~L~~~~~~~~~~hg~~~~~~r~~~~~~f~~   83 (163)
T 2hjv_A            5 LTTRNIEHAVIQVREENKFSLLKDVLMTE-NPDSCIIFCRTKEHVNQLTDELDDLGYPCDKIHGGMIQEDRFDVMNEFKR   83 (163)
T ss_dssp             -CCCCEEEEEEECCGGGHHHHHHHHHHHH-CCSSEEEECSSHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHT
T ss_pred             cCcccceEEEEECChHHHHHHHHHHHHhc-CCCcEEEEECCHHHHHHHHHHHHHcCCcEEEEeCCCCHHHHHHHHHHHHc
Confidence            34556889999999999999999988764 56799999999999999999999999999999999999999999999999


Q ss_pred             CCccEEEecCcccccCCCCCCcEEEEeCCCCCHHHHHHHhcccCCCCCccEEEEEecCCCcCchHHHHHHHhhc
Q 002040          763 NVCNLLIATSVAARGLDVKELELVINFDAPNHYEDYVHRVGRTGRAGRKGCAITFISEEDAKYSPDLVKALELS  836 (976)
Q Consensus       763 g~~~vLVaT~v~~~GlDi~~v~~VI~~d~p~s~~~y~Qr~GR~gR~g~~g~~~~~~~~~d~~~~~~i~~~l~~~  836 (976)
                      |.+.|||||+++++|||+|++++||+|++|+++..|+||+||+||.|+.|.|++|+++.+..++..|.+.+...
T Consensus        84 g~~~vlv~T~~~~~Gld~~~~~~Vi~~~~p~~~~~~~qr~GR~~R~g~~g~~~~~~~~~~~~~~~~i~~~~~~~  157 (163)
T 2hjv_A           84 GEYRYLVATDVAARGIDIENISLVINYDLPLEKESYVHRTGRTGRAGNKGKAISFVTAFEKRFLADIEEYIGFE  157 (163)
T ss_dssp             TSCSEEEECGGGTTTCCCSCCSEEEESSCCSSHHHHHHHTTTSSCTTCCEEEEEEECGGGHHHHHHHHHHHTSC
T ss_pred             CCCeEEEECChhhcCCchhcCCEEEEeCCCCCHHHHHHhccccCcCCCCceEEEEecHHHHHHHHHHHHHHCCC
Confidence            99999999999999999999999999999999999999999999999999999999998888888887776543

>1t5i_A C_terminal domain of A probable ATP-dependent RNA helicase; RECA-like fold, PRE-mRNA processing protein; 1.90A {Homo sapiens} SCOP: c.37.1.19

Probab=99.92  E-value=6e-25  Score=221.23  Aligned_cols=158  Identities=33%  Similarity=0.603  Sum_probs=142.6

Q ss_pred             CCceEEEEecCcchHHHHHHHHHHhhhcCCcEEEEecCHHHHHHHHHHHHHCCCCceeccCCCCHHHHHHHHHHhccCCc
Q 002040          686 KDITQLVEVRPESDRFLRLLELLGEWYEKGKILIFVHSQEKCDALFRDLLKHGYPCLSLHGAKDQTDRESTISDFKSNVC  765 (976)
Q Consensus       686 ~~i~q~~~~~~~~~k~~~l~~~l~~~~~~~kvLIF~~s~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~  765 (976)
                      ..+.|.+.......|+..|..+|... ..+++||||++...++.++..|...|+.+..+||+|++.+|..++..|++|.+
T Consensus         4 ~~i~q~~~~~~~~~K~~~L~~ll~~~-~~~~~lVF~~~~~~~~~l~~~L~~~~~~~~~~hg~~~~~~r~~~~~~f~~g~~   82 (172)
T 1t5i_A            4 HGLQQYYVKLKDNEKNRKLFDLLDVL-EFNQVVIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQEERLSRYQQFKDFQR   82 (172)
T ss_dssp             -CCEEEEEECCGGGHHHHHHHHHHHS-CCSSEEEECSSHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHTTSC
T ss_pred             CCeEEEEEECChHHHHHHHHHHHHhC-CCCcEEEEECCHHHHHHHHHHHHhcCCCEEEEECCCCHHHHHHHHHHHHCCCC
Confidence            46788898899999999999988764 56799999999999999999999999999999999999999999999999999


Q ss_pred             cEEEecCcccccCCCCCCcEEEEeCCCCCHHHHHHHhcccCCCCCccEEEEEecCC-CcCchHHHHHHHhhccCCCChHH
Q 002040          766 NLLIATSVAARGLDVKELELVINFDAPNHYEDYVHRVGRTGRAGRKGCAITFISEE-DAKYSPDLVKALELSEQVVPDDL  844 (976)
Q Consensus       766 ~vLVaT~v~~~GlDi~~v~~VI~~d~p~s~~~y~Qr~GR~gR~g~~g~~~~~~~~~-d~~~~~~i~~~l~~~~~~vp~~l  844 (976)
                      .|||||+++++|||+|++++||+|++|+++..|+||+||+||.|+.|.|++|+++. +..++..|.+.+......+|..+
T Consensus        83 ~vLvaT~~~~~Gldi~~~~~Vi~~d~p~~~~~~~qr~GR~~R~g~~g~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~  162 (172)
T 1t5i_A           83 RILVATNLFGRGMDIERVNIAFNYDMPEDSDTYLHRVARAGRFGTKGLAITFVSDENDAKILNDVQDRFEVNISELPDEI  162 (172)
T ss_dssp             SEEEESSCCSTTCCGGGCSEEEESSCCSSHHHHHHHHHHHTGGGCCCEEEEEECSHHHHHHHHHHHHHHCCCEEECC---
T ss_pred             cEEEECCchhcCcchhhCCEEEEECCCCCHHHHHHHhcccccCCCCcEEEEEEcChhHHHHHHHHHHHHhcchhhCChhh
Confidence            99999999999999999999999999999999999999999999999999999875 45677788888777766777653

>1fuk_A Eukaryotic initiation factor 4A; helicase, DEAD-box protein, translation; 1.75A {Saccharomyces cerevisiae} SCOP: c.37.1.19

Probab=99.92  E-value=5.8e-25  Score=219.96  Aligned_cols=156  Identities=31%  Similarity=0.560  Sum_probs=137.3

Q ss_pred             CceEEEEecCcch-HHHHHHHHHHhhhcCCcEEEEecCHHHHHHHHHHHHHCCCCceeccCCCCHHHHHHHHHHhccCCc
Q 002040          687 DITQLVEVRPESD-RFLRLLELLGEWYEKGKILIFVHSQEKCDALFRDLLKHGYPCLSLHGAKDQTDRESTISDFKSNVC  765 (976)
Q Consensus       687 ~i~q~~~~~~~~~-k~~~l~~~l~~~~~~~kvLIF~~s~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~  765 (976)
                      .|.|.+....... |+..|..++... ..+++||||++...++.++..|...++.+..+||+|++.+|..++..|++|.+
T Consensus         3 ~i~~~~~~~~~~~~K~~~l~~ll~~~-~~~~~lVF~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~   81 (165)
T 1fuk_A            3 GIKQFYVNVEEEEYKYECLTDLYDSI-SVTQAVIFCNTRRKVEELTTKLRNDKFTVSAIYSDLPQQERDTIMKEFRSGSS   81 (165)
T ss_dssp             -CEEEEEEEESGGGHHHHHHHHHHHT-TCSCEEEEESSHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHTTSC
T ss_pred             CcEEEEEECCcchhHHHHHHHHHHhC-CCCCEEEEECCHHHHHHHHHHHHHcCCCEEEEECCCCHHHHHHHHHHHHcCCC
Confidence            4677777777666 999998888764 56899999999999999999999999999999999999999999999999999


Q ss_pred             cEEEecCcccccCCCCCCcEEEEeCCCCCHHHHHHHhcccCCCCCccEEEEEecCCCcCchHHHHHHHhhccCCCChH
Q 002040          766 NLLIATSVAARGLDVKELELVINFDAPNHYEDYVHRVGRTGRAGRKGCAITFISEEDAKYSPDLVKALELSEQVVPDD  843 (976)
Q Consensus       766 ~vLVaT~v~~~GlDi~~v~~VI~~d~p~s~~~y~Qr~GR~gR~g~~g~~~~~~~~~d~~~~~~i~~~l~~~~~~vp~~  843 (976)
                      +|||||+++++|+|+|++++||+|++|+++..|+||+||+||.|+.|.|++|+++.+...+..+.+.+....+.+|..
T Consensus        82 ~vlv~T~~~~~G~d~~~~~~Vi~~~~p~~~~~~~qr~GR~gR~g~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  159 (165)
T 1fuk_A           82 RILISTDLLARGIDVQQVSLVINYDLPANKENYIHRIGRGGRFGRKGVAINFVTNEDVGAMRELEKFYSTQIEELPSD  159 (165)
T ss_dssp             SEEEEEGGGTTTCCCCSCSEEEESSCCSSGGGGGGSSCSCC-----CEEEEEEETTTHHHHHHHHHHSSCCCEECCSC
T ss_pred             EEEEEcChhhcCCCcccCCEEEEeCCCCCHHHHHHHhcccccCCCCceEEEEEcchHHHHHHHHHHHHccCccccCcc
Confidence            999999999999999999999999999999999999999999999999999999998888888888877766666654

>2rb4_A ATP-dependent RNA helicase DDX25; rossmann fold, structural genomics, structural consortium, SGC, alternative initiation, ATP-binding, devel protein; 2.80A {Homo sapiens}

Probab=99.91  E-value=2.4e-24  Score=217.69  Aligned_cols=154  Identities=30%  Similarity=0.519  Sum_probs=135.1

Q ss_pred             ccCCceEEEEecCcch-HHHHHHHHHHhhhcCCcEEEEecCHHHHHHHHHHHHHCCCCceeccCCCCHHHHHHHHHHhcc
Q 002040          684 VNKDITQLVEVRPESD-RFLRLLELLGEWYEKGKILIFVHSQEKCDALFRDLLKHGYPCLSLHGAKDQTDRESTISDFKS  762 (976)
Q Consensus       684 ~~~~i~q~~~~~~~~~-k~~~l~~~l~~~~~~~kvLIF~~s~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~  762 (976)
                      ....|.|.+..++... |+..|..++... ..+++||||++...+..++..|...|+.+..+||+|++.+|..++..|++
T Consensus         4 ~~~~i~q~~~~~~~~~~K~~~L~~ll~~~-~~~~~lVF~~~~~~~~~l~~~L~~~~~~~~~~~g~~~~~~R~~~~~~f~~   82 (175)
T 2rb4_A            4 TLNNIRQYYVLCEHRKDKYQALCNIYGSI-TIGQAIIFCQTRRNAKWLTVEMIQDGHQVSLLSGELTVEQRASIIQRFRD   82 (175)
T ss_dssp             CBCCEEEEEEECSSHHHHHHHHHHHHTTS-CCSEEEEECSCHHHHHHHHHHHHTTTCCEEEECSSCCHHHHHHHHHHHHT
T ss_pred             ccCCceEEEEEcCChHhHHHHHHHHHHhC-CCCCEEEEECCHHHHHHHHHHHHHcCCcEEEEeCCCCHHHHHHHHHHHHc
Confidence            3457888888877655 999888888764 56799999999999999999999999999999999999999999999999


Q ss_pred             CCccEEEecCcccccCCCCCCcEEEEeCCC------CCHHHHHHHhcccCCCCCccEEEEEecCCCcCchHHHHHHHhhc
Q 002040          763 NVCNLLIATSVAARGLDVKELELVINFDAP------NHYEDYVHRVGRTGRAGRKGCAITFISEEDAKYSPDLVKALELS  836 (976)
Q Consensus       763 g~~~vLVaT~v~~~GlDi~~v~~VI~~d~p------~s~~~y~Qr~GR~gR~g~~g~~~~~~~~~d~~~~~~i~~~l~~~  836 (976)
                      |.++|||||+++++|||+|++++||+|++|      .++..|+||+||+||.|+.|.|++|+++.+...+..|.+.+...
T Consensus        83 g~~~vLvaT~~~~~Gid~~~~~~Vi~~d~p~~~~~~~~~~~~~qr~GR~gR~g~~g~~~~~~~~~~~~~~~~i~~~~~~~  162 (175)
T 2rb4_A           83 GKEKVLITTNVCARGIDVKQVTIVVNFDLPVKQGEEPDYETYLHRIGRTGRFGKKGLAFNMIEVDELPSLMKIQDHFNSS  162 (175)
T ss_dssp             TSCSEEEECCSCCTTTCCTTEEEEEESSCCC--CCSCCHHHHHHHHCBC----CCEEEEEEECGGGHHHHHHHHHHHTCC
T ss_pred             CCCeEEEEecchhcCCCcccCCEEEEeCCCCCccccCCHHHHHHHhcccccCCCCceEEEEEccchHHHHHHHHHHhcCc
Confidence            999999999999999999999999999999      88999999999999999999999999988877777777776554


Q ss_pred             cC
Q 002040          837 EQ  838 (976)
Q Consensus       837 ~~  838 (976)
                      ..
T Consensus       163 ~~  164 (175)
T 2rb4_A          163 IK  164 (175)
T ss_dssp             CE
T ss_pred             cc
Confidence            33

>3eaq_A Heat resistant RNA dependent ATPase; DEAD box RNA helicase, dimer, ATP-binding, helicase, hydrolase, nucleotide-binding; 2.30A {Thermus thermophilus} PDB: 3ear_A 3eas_A

Probab=99.91  E-value=1.1e-23  Score=219.42  Aligned_cols=148  Identities=30%  Similarity=0.519  Sum_probs=134.4

Q ss_pred             eEEEEecCcchHHHHHHHHHHhhhcCCcEEEEecCHHHHHHHHHHHHHCCCCceeccCCCCHHHHHHHHHHhccCCccEE
Q 002040          689 TQLVEVRPESDRFLRLLELLGEWYEKGKILIFVHSQEKCDALFRDLLKHGYPCLSLHGAKDQTDRESTISDFKSNVCNLL  768 (976)
Q Consensus       689 ~q~~~~~~~~~k~~~l~~~l~~~~~~~kvLIF~~s~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vL  768 (976)
                      .+.....+...|+..|..++... ..+++||||+++..++.++..|...|+.+..+||+|++.+|..++..|++|.++||
T Consensus         7 ~~~~~~~~~~~k~~~l~~ll~~~-~~~~~lVF~~~~~~~~~l~~~L~~~~~~~~~lhg~~~~~~r~~~~~~f~~g~~~vl   85 (212)
T 3eaq_A            7 EEEAVPAPVRGRLEVLSDLLYVA-SPDRAMVFTRTKAETEEIAQGLLRLGHPAQALHGDLSQGERERVLGAFRQGEVRVL   85 (212)
T ss_dssp             CCEEEECCTTSHHHHHHHHHHHH-CCSCEEEECSSHHHHHHHHHHHHHHTCCEEEECSSSCHHHHHHHHHHHHSSSCCEE
T ss_pred             eeeEEeCCHHHHHHHHHHHHHhC-CCCeEEEEeCCHHHHHHHHHHHHHcCCCEEEEECCCCHHHHHHHHHHHHCCCCeEE
Confidence            34455667788999999988754 57899999999999999999999999999999999999999999999999999999


Q ss_pred             EecCcccccCCCCCCcEEEEeCCCCCHHHHHHHhcccCCCCCccEEEEEecCCCcCchHHHHHHHhhcc
Q 002040          769 IATSVAARGLDVKELELVINFDAPNHYEDYVHRVGRTGRAGRKGCAITFISEEDAKYSPDLVKALELSE  837 (976)
Q Consensus       769 VaT~v~~~GlDi~~v~~VI~~d~p~s~~~y~Qr~GR~gR~g~~g~~~~~~~~~d~~~~~~i~~~l~~~~  837 (976)
                      |||+++++|||||++++||+|++|+++..|+||+||+||.|+.|.|++|+++.+...+..|.+.+....
T Consensus        86 vaT~~~~~Gidi~~v~~Vi~~~~p~~~~~~~qr~GR~gR~g~~g~~~~l~~~~~~~~~~~i~~~~~~~~  154 (212)
T 3eaq_A           86 VATDVAARGLDIPQVDLVVHYRLPDRAEAYQHRSGRTGRAGRGGRVVLLYGPRERRDVEALERAVGRRF  154 (212)
T ss_dssp             EECTTTTCSSSCCCBSEEEESSCCSSHHHHHHHHTTBCCCC--BEEEEEECGGGHHHHHHHHHHHSSCC
T ss_pred             EecChhhcCCCCccCcEEEECCCCcCHHHHHHHhcccCCCCCCCeEEEEEchhHHHHHHHHHHHhcCcC
Confidence            999999999999999999999999999999999999999999999999999998888888888876543

>3i32_A Heat resistant RNA dependent ATPase; RNA helicase, dimer, RNA recognition motif, ATP-BIND helicase, nucleotide-binding; 2.80A {Thermus thermophilus}

Probab=99.90  E-value=3.5e-23  Score=225.96  Aligned_cols=150  Identities=30%  Similarity=0.508  Sum_probs=134.9

Q ss_pred             CceEEEEecCcchHHHHHHHHHHhhhcCCcEEEEecCHHHHHHHHHHHHHCCCCceeccCCCCHHHHHHHHHHhccCCcc
Q 002040          687 DITQLVEVRPESDRFLRLLELLGEWYEKGKILIFVHSQEKCDALFRDLLKHGYPCLSLHGAKDQTDRESTISDFKSNVCN  766 (976)
Q Consensus       687 ~i~q~~~~~~~~~k~~~l~~~l~~~~~~~kvLIF~~s~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~  766 (976)
                      .+.+.+.......|+..|..++.... .+++||||+++..++.|+..|...|+.+..+||+|++.+|..++..|++|.++
T Consensus         2 ~v~~~~i~~~~~~K~~~L~~ll~~~~-~~~~LVF~~t~~~~~~l~~~L~~~g~~~~~lhg~l~~~~r~~~~~~f~~g~~~   80 (300)
T 3i32_A            2 TYEEEAVPAPVRGRLEVLSDLLYVAS-PDRAMVFTRTKAETEEIAQGLLRLGHPAQALHGDMSQGERERVMGAFRQGEVR   80 (300)
T ss_dssp             CSEEEEEECCSSSHHHHHHHHHHHHC-CSSEEEECSSHHHHHHHHHHHHTTTCCEEEECSCCCTHHHHHHHHHHHHTSCC
T ss_pred             ceEEEEEECCHHHHHHHHHHHHHhcC-CCCEEEEECCHHHHHHHHHHHHhCCCCEEEEeCCCCHHHHHHHHHHhhcCCce
Confidence            35677778888999999999887654 78999999999999999999999999999999999999999999999999999


Q ss_pred             EEEecCcccccCCCCCCcEEEEeCCCCCHHHHHHHhcccCCCCCccEEEEEecCCCcCchHHHHHHHhhcc
Q 002040          767 LLIATSVAARGLDVKELELVINFDAPNHYEDYVHRVGRTGRAGRKGCAITFISEEDAKYSPDLVKALELSE  837 (976)
Q Consensus       767 vLVaT~v~~~GlDi~~v~~VI~~d~p~s~~~y~Qr~GR~gR~g~~g~~~~~~~~~d~~~~~~i~~~l~~~~  837 (976)
                      |||||+++++|||||++++||+|++|+++..|+||+||+||.|+.|.|++|+++.+..++..|.+.+....
T Consensus        81 vLVaT~va~~Gidi~~v~~VI~~d~p~s~~~y~Qr~GRagR~g~~G~~i~l~~~~e~~~~~~ie~~~~~~~  151 (300)
T 3i32_A           81 VLVATDVAARGLDIPQVDLVVHYRMPDRAEAYQHRSGRTGRAGRGGRVVLLYGPRERRDVEALERAVGRRF  151 (300)
T ss_dssp             EEEECSTTTCSTTCCCCSEEEESSCCSSTTHHHHHHTCCC-----CEEEEEECSSTHHHHHHHHHHHTCCC
T ss_pred             EEEEechhhcCccccceeEEEEcCCCCCHHHHHHHccCcCcCCCCceEEEEeChHHHHHHHHHHHHhCCcc
Confidence            99999999999999999999999999999999999999999999999999999999888888888876543

>2yjt_D ATP-dependent RNA helicase SRMB, regulator of ribonuclease activity A; hydrolase inhibitor-hydrolase complex, DEAD box RNA helicase; 2.90A {Escherichia coli}

Probab=99.79  E-value=4.2e-24  Score=214.81  Aligned_cols=148  Identities=32%  Similarity=0.483  Sum_probs=133.7

Q ss_pred             CceEEEEecCc-chHHHHHHHHHHhhhcCCcEEEEecCHHHHHHHHHHHHHCCCCceeccCCCCHHHHHHHHHHhccCCc
Q 002040          687 DITQLVEVRPE-SDRFLRLLELLGEWYEKGKILIFVHSQEKCDALFRDLLKHGYPCLSLHGAKDQTDRESTISDFKSNVC  765 (976)
Q Consensus       687 ~i~q~~~~~~~-~~k~~~l~~~l~~~~~~~kvLIF~~s~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~  765 (976)
                      +|.|.+...+. ..|+..|..++.. ...+++||||++...++.++..|...++.+..+||+|++.+|..++..|++|.+
T Consensus         3 ~i~~~~~~~~~~~~k~~~l~~ll~~-~~~~~~iVF~~~~~~~~~l~~~L~~~~~~~~~~~g~~~~~~r~~~~~~f~~g~~   81 (170)
T 2yjt_D            3 KIHQWYYRADDLEHKTALLVHLLKQ-PEATRSIVFVRKRERVHELANWLREAGINNCYLEGEMVQGKRNEAIKRLTEGRV   81 (170)
Confidence            45566666666 7788888888765 345799999999999999999999999999999999999999999999999999


Q ss_pred             cEEEecCcccccCCCCCCcEEEEeCCCCCHHHHHHHhcccCCCCCccEEEEEecCCCcCchHHHHHHHhh
Q 002040          766 NLLIATSVAARGLDVKELELVINFDAPNHYEDYVHRVGRTGRAGRKGCAITFISEEDAKYSPDLVKALEL  835 (976)
Q Consensus       766 ~vLVaT~v~~~GlDi~~v~~VI~~d~p~s~~~y~Qr~GR~gR~g~~g~~~~~~~~~d~~~~~~i~~~l~~  835 (976)
                      +|||||+++++|||+|++++||+|++|+++..|+||+||+||.|+.|.|++|+++.+..++..+.+.+..
T Consensus        82 ~vLvaT~~~~~Gid~~~~~~Vi~~~~p~~~~~~~qr~GR~~R~g~~g~~~~~~~~~~~~~~~~~~~~~~~  151 (170)
T 2yjt_D           82 NVLVATDVAARGIDIPDVSHVFNFDMPRSGDTYLHRIGRTARAGRKGTAISLVEAHDHLLLGKVGRYIEE  151 (170)
Confidence            9999999999999999999999999999999999999999999999999999999888887777776543

>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=99.87  E-value=1.9e-22  Score=210.75  Aligned_cols=170  Identities=19%  Similarity=0.209  Sum_probs=122.7

Q ss_pred             cCCCCCcHHHHHHHHHHhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHH-HHHHHHHH
Q 002040          485 LNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQ-IHSDIRKF  563 (976)
Q Consensus       485 ~~~~~p~~~Q~~~i~~il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q-~~~~~~~~  563 (976)
                      .....|+|+|.++++.++.++++|++++||+|||++|+++++..+.....  ...++++||+|||++|+.| |...+..+
T Consensus        29 ~~~~~l~~~Q~~~i~~~~~~~~~li~~~tGsGKT~~~~~~~~~~~~~~~~--~~~~~~~lil~p~~~L~~q~~~~~~~~~  106 (216)
T 3b6e_A           29 EPELQLRPYQMEVAQPALEGKNIIICLPTGSGKTRVAVYIAKDHLDKKKK--ASEPGKVIVLVNKVLLVEQLFRKEFQPF  106 (216)
T ss_dssp             SCCCCCCHHHHHHHHHHHTTCCEEEECSCHHHHHHHHHHHHHHHHHHHHH--TTCCCCEEEEESSHHHHHHHHHHTHHHH
T ss_pred             cCCCCchHHHHHHHHHHhcCCCEEEEcCCCCCHHHHHHHHHHHHHhhccc--ccCCCcEEEEECHHHHHHHHHHHHHHHH
Confidence            34457999999999999999999999999999999999999887754211  1235689999999999999 77888887


Q ss_pred             HhhcCcEEEEeeCCCChHHHHHHHhcCCeEEEeCchhHHHHHHhcCC---cccccCCceEEEecCcccccccCCchHHHH
Q 002040          564 AKVMGVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGG---KITNLRRVTYLVMDEADRMFDMGFEPQITR  640 (976)
Q Consensus       564 ~~~~~~~~~~~~gg~~~~~~~~~l~~~~~Iiv~Tp~~L~~~l~~~~~---~~~~l~~~~~vVlDEah~~~~~~f~~~i~~  640 (976)
                      ... ++.+..++|+.........+..+++|+|+||+.|...+.....   ....+..+.+|||||||++...++...+..
T Consensus       107 ~~~-~~~v~~~~g~~~~~~~~~~~~~~~~i~v~T~~~l~~~~~~~~~~~~~~~~~~~~~~iIiDEah~~~~~~~~~~~~~  185 (216)
T 3b6e_A          107 LKK-WYRVIGLSGDTQLKISFPEVVKSCDIIISTAQILENSLLNLENGEDAGVQLSDFSLIIIDECHHTNKEAVYNNIMR  185 (216)
T ss_dssp             HTT-TSCEEECCC---CCCCHHHHHHHCSEEEEEHHHHHHHHHC-------CCCGGGCSEEEETTC-------CHHHHHH
T ss_pred             hcc-CceEEEEeCCcccchhHHhhccCCCEEEECHHHHHHHHhccCcccccccchhcccEEEEECchhhccCCcHHHHHH
Confidence            654 7888888888765544444445689999999999988865321   113467899999999999987766666543


Q ss_pred             HHHhc--------------CCCCcEEEEecc
Q 002040          641 IVQNI--------------RPDRQTVLFSAT  657 (976)
Q Consensus       641 il~~~--------------~~~~q~i~~SAT  657 (976)
                      .+...              .+..++|+||||
T Consensus       186 ~~~~~~~~~~~~~~~~~~~~~~~~~l~lSAT  216 (216)
T 3b6e_A          186 HYLMQKLKNNRLKKENKPVIPLPQILGLTAS  216 (216)
T ss_dssp             HHHHHHHHHHHHHHTTCCCCCCCEEEEEECC
T ss_pred             HHHHHhcccccccccccCCCCcceEEEeecC
Confidence            32211              167899999998

>2vl7_A XPD; helicase, unknown function; 2.25A {Sulfolobus tokodaii}

Probab=99.86  E-value=5.3e-21  Score=227.31  Aligned_cols=303  Identities=19%  Similarity=0.221  Sum_probs=168.8

Q ss_pred             cCCCCCcHHHHHHHHH----HhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHH
Q 002040          485 LNYEKPMPIQAQALPV----IMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDI  560 (976)
Q Consensus       485 ~~~~~p~~~Q~~~i~~----il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~  560 (976)
                      .|| .|+|+|.+++..    +..++++|+.+|||+|||++|++|++..           ++++||++||++|+.|+..++
T Consensus         4 ~~~-~~r~~Q~~~~~~v~~~~~~~~~~~~~a~TGtGKT~~~l~~~~~~-----------~~~~~~~~~t~~l~~q~~~~~   71 (540)
T 2vl7_A            4 LKL-QLRQWQAEKLGEAINALKHGKTLLLNAKPGLGKTVFVEVLGMQL-----------KKKVLIFTRTHSQLDSIYKNA   71 (540)
T ss_dssp             ------CCHHHHHHHHHHHHHHTTCEEEEECCTTSCHHHHHHHHHHHH-----------TCEEEEEESCHHHHHHHHHHH
T ss_pred             CCC-CCCHHHHHHHHHHHHHHHcCCCEEEEcCCCCcHHHHHHHHHHhC-----------CCcEEEEcCCHHHHHHHHHHH
Confidence            456 799999998654    5688999999999999999999998754           568999999999999999887


Q ss_pred             HHHHhhcCcEEEEeeCCCCh--------H------------------------HHHH---------------HHhcCCeE
Q 002040          561 RKFAKVMGVRCVPVYGGSGV--------A------------------------QQIS---------------ELKRGTEI  593 (976)
Q Consensus       561 ~~~~~~~~~~~~~~~gg~~~--------~------------------------~~~~---------------~l~~~~~I  593 (976)
                      ..    ++++++.+.|....        .                        ..+.               ....+++|
T Consensus        72 ~~----l~~~~~~l~gr~~lC~~~~~~~~~~~~~c~~c~~~~~~~~~gd~~~~~~~~~~~~~~~~Cpy~~~r~~~~~adi  147 (540)
T 2vl7_A           72 KL----LGLKTGFLIGKSASCIYAQGDEEPDEINCSKCRLKDKIKTIEDKEPSKLIEEFKDAVDYCPYYSLRANLKDKDV  147 (540)
T ss_dssp             GG----GTCCEEEC---------------------------------------------------------CTTGGGCSE
T ss_pred             Hh----cCCcEEEecCCccccCCchhcccccccCCCCCCchhcccccccCCcHHHHHHHhhhcCCChHHHHHHHhhcCCE
Confidence            66    35555555443210        0                        0000               11235799


Q ss_pred             EEeCchhHHHHHHhcCCc----ccccCCceEEEecCcccccccC--Cc-----h--------------------------
Q 002040          594 VVCTPGRMIDILCTSGGK----ITNLRRVTYLVMDEADRMFDMG--FE-----P--------------------------  636 (976)
Q Consensus       594 iv~Tp~~L~~~l~~~~~~----~~~l~~~~~vVlDEah~~~~~~--f~-----~--------------------------  636 (976)
                      |||||..|++.+......    ...+....+|||||||+|.+..  |.     .                          
T Consensus       148 VV~n~~~l~~~~~~~~~~~~~~~~~~~~~~~vIiDEAHnl~~a~~~~s~~ls~~~l~~~~~~l~~~~~~~~~~~~~l~~~  227 (540)
T 2vl7_A          148 IAMTYPYLFQKPIRNSVFCNKDDCLKLEDYLIVIDEAHNLLEADKWFTRKISRKMLERALKEIEIVERLNRIDAKKVKDY  227 (540)
T ss_dssp             EEEETHHHHSHHHHHHHSCSSTTSCCGGGEEEEETTGGGGGGGGGGGCEEECHHHHHHHHHHHHHHHHTTCCCCHHHHHH
T ss_pred             EEEChHHhcCHHHHHhhCcccccccCcCCCEEEEEccccHHHHHHHhccccCHHHHHHHHHHHHHHHhcchhhHHHHHHH
Confidence            999999998755432100    0124567899999999883310  00     0                          


Q ss_pred             --------------------------------HHHHHHHh-----------------------------------cCC--
Q 002040          637 --------------------------------QITRIVQN-----------------------------------IRP--  647 (976)
Q Consensus       637 --------------------------------~i~~il~~-----------------------------------~~~--  647 (976)
                                                      .+..++..                                   +.|  
T Consensus       228 ~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~l~~l~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~l~~~P~~  307 (540)
T 2vl7_A          228 INLLIDYMSKLIKDGRCHELSLMPLPDRETNGELIVVTRAYLNIDEGPVKKSSLKSLLKFVEMKGDLYNCNGSLVKVPSD  307 (540)
T ss_dssp             HHHHHHHHHTSCCSSSEEEESCCCCCCHHHHHHHHHHHHHHHTTCCSSSCCCHHHHHHHHHHSCCEEEEETTEEEEECSC
T ss_pred             HHHHHHHHHHhhccccccchhhcccccHHHHHHHHHHHHHHHHhhccCccHHHHHHHHHHHHhCCCEEEECCeEEEehHH
Confidence                                            00000000                                   000  


Q ss_pred             -----------CCcEEEEeccCcHHHHHHHHHHcCCCeEEEeCCcccccCCceEEEE---ecCc-ch---HHHHHHHHHH
Q 002040          648 -----------DRQTVLFSATFPRQVEILARKVLNKPVEIQVGGRSVVNKDITQLVE---VRPE-SD---RFLRLLELLG  709 (976)
Q Consensus       648 -----------~~q~i~~SAT~~~~~~~l~~~~l~~~~~i~~~~~~~~~~~i~q~~~---~~~~-~~---k~~~l~~~l~  709 (976)
                                 ...+|++|||+++.+. +...|     ...+. ...   ...+.+.   +... ..   -+..+...|.
T Consensus       308 ~~~~l~~~~~~~~~~IltSATL~p~~~-~~~~f-----~~~~~-~~~---g~~~~~~~~~l~s~f~~r~~~~~~~~~~l~  377 (540)
T 2vl7_A          308 VNQLIEDALNVKTFKVLMSGTLPESLT-LTNSY-----KIVVN-ESY---GRGEYYYCPNVTSELRKRNSNIPIYSILLK  377 (540)
T ss_dssp             HHHHHHHHTCCSSCEEEEESSCCTTCC-CTTEE-----EEECC-CC----CCCEEEECTTCCCCGGGHHHHHHHHHHHHH
T ss_pred             HHHHHHHhcCccCCeEEEcccCCCCcc-cchhc-----CCchh-hee---cCCcceeccccCCCcccccCHHHHHHHHHH
Confidence                       0113777777765100 00000     00000 000   0011111   0111 11   1133444444


Q ss_pred             hhh--cCCcEEEEecCHHHHHHHHHHHHHCCCCceeccCCCCHHHHHHHHHHhccCCccEEE--ecCcccccCCCCC---
Q 002040          710 EWY--EKGKILIFVHSQEKCDALFRDLLKHGYPCLSLHGAKDQTDRESTISDFKSNVCNLLI--ATSVAARGLDVKE---  782 (976)
Q Consensus       710 ~~~--~~~kvLIF~~s~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLV--aT~v~~~GlDi~~---  782 (976)
                      ...  .++.+||||+|...++.++..|..  +. +.++|..  ..+..+++.|+.|. .||+  +|..+++|||+|+   
T Consensus       378 ~~~~~~~g~~lvff~S~~~~~~v~~~l~~--~~-~~~q~~~--~~~~~~l~~f~~~~-~il~~V~~~~~~EGiD~~~~~~  451 (540)
T 2vl7_A          378 RIYENSSKSVLVFFPSYEMLESVRIHLSG--IP-VIEENKK--TRHEEVLELMKTGK-YLVMLVMRAKESEGVEFREKEN  451 (540)
T ss_dssp             HHHHTCSSEEEEEESCHHHHHHHHTTCTT--SC-EEESTTT--CCHHHHHHHHHTSC-CEEEEEC---------------
T ss_pred             HHHHhCCCCEEEEeCCHHHHHHHHHHhcc--Cc-eEecCCC--CcHHHHHHHHhcCC-eEEEEEecCceecceecCCCcc
Confidence            332  367899999999999999988854  33 4556654  46888999998864 5666  8899999999998   


Q ss_pred             -CcEEEEeCCCCCH------------------------------HHHHHHhcccCCCCCccEEEEEec
Q 002040          783 -LELVINFDAPNHY------------------------------EDYVHRVGRTGRAGRKGCAITFIS  819 (976)
Q Consensus       783 -v~~VI~~d~p~s~------------------------------~~y~Qr~GR~gR~g~~g~~~~~~~  819 (976)
                       +.+||+++.|...                              ..+.|.+||+-|....-.+++++.
T Consensus       452 ~~~~Vii~~lPf~~~~d~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~Q~~GR~iR~~~D~g~v~llD  519 (540)
T 2vl7_A          452 LFESLVLAGLPYPNVSDDMVRKRIERLSKLTGKDEDSIIHDLTAIVIKQTIGRAFRDPNDYVKIYLCD  519 (540)
T ss_dssp             CEEEEEEESCCCCCTTSHHHHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHHCCSTTCCCEEEEES
T ss_pred             cccEEEEECCCCCCCCCHHHHHHHHHHHHhhCCChhHHHHHHHHHHHHHHhCCcccCCCccEEEEEEc
Confidence             8999999988521                              123599999999754433455554

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

Probab=99.85  E-value=2e-19  Score=214.48  Aligned_cols=309  Identities=17%  Similarity=0.141  Sum_probs=198.6

Q ss_pred             CCcHHHHHHHHH----HhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHHHH
Q 002040          489 KPMPIQAQALPV----IMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFA  564 (976)
Q Consensus       489 ~p~~~Q~~~i~~----il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~~~  564 (976)
                      .|+|+|.+++..    +..|+++|+.+|||+|||++|++|++..           ++++||++||++|+.|+..++..+.
T Consensus         3 ~~r~~Q~~~~~~v~~~l~~~~~~~~~a~TGtGKT~~~l~p~l~~-----------~~~v~i~~pt~~l~~q~~~~~~~l~   71 (551)
T 3crv_A            3 KLRDWQEKLKDKVIEGLRNNFLVALNAPTGSGKTLFSLLVSLEV-----------KPKVLFVVRTHNEFYPIYRDLTKIR   71 (551)
T ss_dssp             SCCHHHHHHHHHHHHHHHTTCEEEEECCTTSSHHHHHHHHHHHH-----------CSEEEEEESSGGGHHHHHHHHTTCC
T ss_pred             CCCHHHHHHHHHHHHHHHcCCcEEEECCCCccHHHHHHHHHHhC-----------CCeEEEEcCCHHHHHHHHHHHHHHh
Confidence            589999997764    4578999999999999999999999962           5789999999999999999999887


Q ss_pred             hhcCcEEEEeeCCCCh---------------------------------HHHH------------------HHHhcCCeE
Q 002040          565 KVMGVRCVPVYGGSGV---------------------------------AQQI------------------SELKRGTEI  593 (976)
Q Consensus       565 ~~~~~~~~~~~gg~~~---------------------------------~~~~------------------~~l~~~~~I  593 (976)
                      ...+++++++.|+...                                 ...+                  .....+++|
T Consensus        72 ~~~~~~~~~l~gr~~~c~~~~~~~~~~~~~c~~c~~~~~~~~~g~~~~~~~~~~~~~~~G~~~~~Cpy~~ar~~~~~adI  151 (551)
T 3crv_A           72 EKRNITFSFLVGKPSSCLYAEKGAESEDIPCKYCELKGSIVEVKTDDSPLSLVKKLKKDGLQDKFCPYYSLLNSLYKADV  151 (551)
T ss_dssp             CSSCCCEEECCCHHHHCTTBCTTCCGGGCCGGGCTTTTCCCCCCCCSCHHHHHHHHHHHHHHHTCCHHHHHHHHGGGCSE
T ss_pred             hhcCccEEEEccccccCcCchhcCCCcccccCCCCCccccccccccCCHHHHHHHHHHcCCcCCcCccHHHHhhhhcCCE
Confidence            7778888888774321                                 1221                  122346899


Q ss_pred             EEeCchhHHHHHHhcCCcccccCCceEEEecCcccccccC----------------------------------------
Q 002040          594 VVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMG----------------------------------------  633 (976)
Q Consensus       594 iv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDEah~~~~~~----------------------------------------  633 (976)
                      |||||+.|++.+....  ...+....+|||||||+|.+ .                                        
T Consensus       152 VV~~~~~l~~~~~~~~--~~~~~~~~~vIiDEAHnl~d-~~~~~s~~ls~~~l~~~~~~l~~~~~~~~l~~l~~~l~~~~  228 (551)
T 3crv_A          152 IALTYPYFFIDRYREF--IDIDLREYMIVIDEAHNLDK-VNELEERSLSEITIQMAIKQSKSEESRRILSKLLNQLREVV  228 (551)
T ss_dssp             EEEETHHHHCHHHHTT--SCCCSTTEEEEETTGGGGGG-GGGGGCEEEEHHHHHHHHHHCSCHHHHHHHHHHHHHHTTSC
T ss_pred             EEeCchHhcCHHHHHh--cCCCcCCeEEEEecccchHH-HHHhhceecCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            9999999998765432  11224678999999998755 1                                        


Q ss_pred             ---------------CchHHHHH----------------------------H----------------------------
Q 002040          634 ---------------FEPQITRI----------------------------V----------------------------  642 (976)
Q Consensus       634 ---------------f~~~i~~i----------------------------l----------------------------  642 (976)
                                     +...+..+                            +                            
T Consensus       229 ~~~~~~~~~~~~~~~~~~~l~~l~~~l~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~~~~~~l~~~pl~~~~~l  308 (551)
T 3crv_A          229 LPDEKYIKVENVPKLSKEELEILADDYEDIRKDSLKQGKVNKIHIGSILRFFSLLSIGSFIPFSYSKRLVIKNPEISYYL  308 (551)
T ss_dssp             CSCSSCEECSCCCCCCHHHHHHHHHHHHHHHHHHHHTTCBCCCHHHHHHHHHHHHHHSSCEEEEETTEEEEECCCTHHHH
T ss_pred             hccccccccccChHHHHHHHHHHHHHHHHHHHhhhhcCCcccchHHHHHHHHHHHhccCCeEeccCCEEEEEECCHHHHH
Confidence                           00000000                            0                            


Q ss_pred             HhcCCC-CcEEEEeccCcHHHHHHHHHHcCC-CeEE---Ee-CCcccccCCceEEEEec--Cc------chHHHHHHHHH
Q 002040          643 QNIRPD-RQTVLFSATFPRQVEILARKVLNK-PVEI---QV-GGRSVVNKDITQLVEVR--PE------SDRFLRLLELL  708 (976)
Q Consensus       643 ~~~~~~-~q~i~~SAT~~~~~~~l~~~~l~~-~~~i---~~-~~~~~~~~~i~q~~~~~--~~------~~k~~~l~~~l  708 (976)
                      ..+... ..+|++|||+.+ ...+...+... +...   .+ ...++ .... ..+...  +.      ......+...|
T Consensus       309 ~~~~~~~~svIltSaTL~~-~~~~~~~lGl~~~~~~~~~~~~~~spf-~~~~-~l~v~~~~~~~~~~r~~~~~~~l~~~i  385 (551)
T 3crv_A          309 NLLNDNELSIILMSGTLPP-REYMEKVWGIKRNMLYLDVEREIQKRV-SGSY-ECYIGVDVTSKYDMRSDNMWKRYADYL  385 (551)
T ss_dssp             GGGGCTTCEEEEEESSCCC-HHHHHHTSCCCSCEEEEEHHHHTTSCC-SCEE-EEEEECSCCCCTTTCCHHHHHHHHHHH
T ss_pred             HHHhccCceEEEEeeCCCc-HHHHHHHhCCCCccccccceeecCCcC-CCce-EEEEeCCCCCccccCCHHHHHHHHHHH
Confidence            001122 578999999987 34344433222 2211   00 11112 1111 112111  10      11234455555


Q ss_pred             Hhhh--cCCcEEEEecCHHHHHHHHHHHHHCCCCceeccCCCCHHHHHHHHHHhccCCccEEEec--CcccccCCCC---
Q 002040          709 GEWY--EKGKILIFVHSQEKCDALFRDLLKHGYPCLSLHGAKDQTDRESTISDFKSNVCNLLIAT--SVAARGLDVK---  781 (976)
Q Consensus       709 ~~~~--~~~kvLIF~~s~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLVaT--~v~~~GlDi~---  781 (976)
                      ....  .+|.+|||++|...+..++..   .++.+..=..+++   ...+++.|+.+...||+||  ..+..|||+|   
T Consensus       386 ~~l~~~~~g~~lvlF~Sy~~l~~v~~~---~~~~v~~q~~~~~---~~~~~~~~~~~~~~vl~~v~gg~~~EGiD~~d~~  459 (551)
T 3crv_A          386 LKIYFQAKANVLVVFPSYEIMDRVMSR---ISLPKYVESEDSS---VEDLYSAISANNKVLIGSVGKGKLAEGIELRNND  459 (551)
T ss_dssp             HHHHHHCSSEEEEEESCHHHHHHHHTT---CCSSEEECCSSCC---HHHHHHHTTSSSSCEEEEESSCCSCCSSCCEETT
T ss_pred             HHHHHhCCCCEEEEecCHHHHHHHHHh---cCCcEEEcCCCCC---HHHHHHHHHhcCCeEEEEEecceecccccccccC
Confidence            4433  367999999999999998873   3444433223445   3557778854344799998  6999999999   


Q ss_pred             C--CcEEEEeCCCCC---H----------------H-----------HHHHHhcccCCCCCccEEEEEecC
Q 002040          782 E--LELVINFDAPNH---Y----------------E-----------DYVHRVGRTGRAGRKGCAITFISE  820 (976)
Q Consensus       782 ~--v~~VI~~d~p~s---~----------------~-----------~y~Qr~GR~gR~g~~g~~~~~~~~  820 (976)
                      +  +.+||+...|..   +                .           ...|.+||+-|....-.++++++.
T Consensus       460 g~~l~~viI~~lPfp~~dp~~~ar~~~~~~~~g~~~~~~~y~~pa~~~l~Qa~GRlIR~~~D~G~v~llD~  530 (551)
T 3crv_A          460 RSLISDVVIVGIPYPPPDDYLKILAQRVSLKMNRENEEFLFKIPALVTIKQAIGRAIRDVNDKCNVWLLDK  530 (551)
T ss_dssp             EESEEEEEEESCCCCCCSHHHHHHHHHTTCCSSTTTHHHHTHHHHHHHHHHHHHTTCCSTTCEEEEEEESG
T ss_pred             CcceeEEEEEcCCCCCCCHHHHHHHHHHHHhhCCchhHHHHHHHHHHHHHHHhccCccCCCccEEEEEeeh
Confidence            4  788998776541   1                1           124999999998655445555543

>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=99.85  E-value=5.5e-21  Score=202.68  Aligned_cols=177  Identities=18%  Similarity=0.211  Sum_probs=129.2

Q ss_pred             HHHcCCCCCcHHHHHHHHHHhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHH
Q 002040          482 IRKLNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIR  561 (976)
Q Consensus       482 l~~~~~~~p~~~Q~~~i~~il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~  561 (976)
                      +.......++++|.++++.+..|++++++|+||||||+++.++++..+.....   ..++.+||++|+++|+.|++..+.
T Consensus        54 ~~~~~~~p~~~~q~~~i~~i~~g~~~~i~g~TGsGKTt~~~~~~~~~~~~~~~---~~~~~~l~~~p~~~la~q~~~~~~  130 (235)
T 3llm_A           54 LQERELLPVKKFESEILEAISQNSVVIIRGATGCGKTTQVPQFILDDFIQNDR---AAECNIVVTQPRRISAVSVAERVA  130 (235)
T ss_dssp             HHHHHTSGGGGGHHHHHHHHHHCSEEEEECCTTSSHHHHHHHHHHHHHHHTTC---GGGCEEEEEESSHHHHHHHHHHHH
T ss_pred             HHHHhcCChHHHHHHHHHHHhcCCEEEEEeCCCCCcHHhHHHHHhcchhhcCC---CCceEEEEeccchHHHHHHHHHHH
Confidence            33334445789999999999999999999999999999999999887765321   235689999999999999988877


Q ss_pred             HHHh-hcCcEEEEeeCCCChHHHHHHHhcCCeEEEeCchhHHHHHHhcCCcccccCCceEEEecCcccc-cccCCchHHH
Q 002040          562 KFAK-VMGVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRM-FDMGFEPQIT  639 (976)
Q Consensus       562 ~~~~-~~~~~~~~~~gg~~~~~~~~~l~~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDEah~~-~~~~f~~~i~  639 (976)
                      .... ..+..+.........     ....+++|+||||++|.+++..      .+.++++|||||||.+ ++++|...+.
T Consensus       131 ~~~~~~~~~~~g~~~~~~~~-----~~~~~~~Ivv~Tpg~l~~~l~~------~l~~~~~lVlDEah~~~~~~~~~~~~l  199 (235)
T 3llm_A          131 FERGEEPGKSCGYSVRFESI-----LPRPHASIMFCTVGVLLRKLEA------GIRGISHVIVDEIHERDINTDFLLVVL  199 (235)
T ss_dssp             HTTTCCTTSSEEEEETTEEE-----CCCSSSEEEEEEHHHHHHHHHH------CCTTCCEEEECCTTSCCHHHHHHHHHH
T ss_pred             HHhccccCceEEEeechhhc-----cCCCCCeEEEECHHHHHHHHHh------hhcCCcEEEEECCccCCcchHHHHHHH
Confidence            6543 223333322221100     0113578999999999999864      4788999999999986 7777775444


Q ss_pred             HHHHhcCCCCcEEEEeccCcHHHHHHHHHHcCCCe
Q 002040          640 RIVQNIRPDRQTVLFSATFPRQVEILARKVLNKPV  674 (976)
Q Consensus       640 ~il~~~~~~~q~i~~SAT~~~~~~~l~~~~l~~~~  674 (976)
                      ..+....++.|+|+||||++...  ++..+...|+
T Consensus       200 ~~i~~~~~~~~~il~SAT~~~~~--~~~~~~~~pv  232 (235)
T 3llm_A          200 RDVVQAYPEVRIVLMSATIDTSM--FCEYFFNCPI  232 (235)
T ss_dssp             HHHHHHCTTSEEEEEECSSCCHH--HHHHTTSCCC
T ss_pred             HHHHhhCCCCeEEEEecCCCHHH--HHHHcCCCCE
Confidence            44444457899999999999876  5554444443

>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=99.83  E-value=4.9e-21  Score=209.03  Aligned_cols=155  Identities=17%  Similarity=0.139  Sum_probs=126.5

Q ss_pred             CCCcHHHHHHHHHHhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHHHHhhc
Q 002040          488 EKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVM  567 (976)
Q Consensus       488 ~~p~~~Q~~~i~~il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~~~~~~  567 (976)
                      ..|+|+|.++++.++.+.++|++++||+|||+++++++...+...       ..++||||||++|+.||++.+.+++...
T Consensus       112 ~~l~~~Q~~ai~~~l~~~~~ll~~~tGsGKT~~~~~~~~~~~~~~-------~~~~lil~Pt~~L~~q~~~~l~~~~~~~  184 (282)
T 1rif_A          112 IEPHWYQKDAVFEGLVNRRRILNLPTSAGRSLIQALLARYYLENY-------EGKILIIVPTTALTTQMADDFVDYRLFS  184 (282)
T ss_dssp             CCCCHHHHHHHHHHHHHSEEEECCCTTSCHHHHHHHHHHHHHHHC-------SSEEEEECSSHHHHHHHHHHHHHHTSCC
T ss_pred             cCccHHHHHHHHHHHhcCCeEEEcCCCCCcHHHHHHHHHHHHHcC-------CCeEEEEECCHHHHHHHHHHHHHhcccc
Confidence            379999999999999888999999999999999988888776532       3379999999999999999999987666


Q ss_pred             CcEEEEeeCCCChHHHHHHHhcCCeEEEeCchhHHHHHHhcCCcccccCCceEEEecCcccccccCCchHHHHHHHhcCC
Q 002040          568 GVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMGFEPQITRIVQNIRP  647 (976)
Q Consensus       568 ~~~~~~~~gg~~~~~~~~~l~~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDEah~~~~~~f~~~i~~il~~~~~  647 (976)
                      +..+..+++|.....   ....+++|+|+||+.|....      ...+..+++|||||||++.+    ..+..++..+..
T Consensus       185 ~~~~~~~~~~~~~~~---~~~~~~~I~v~T~~~l~~~~------~~~~~~~~~vIiDEaH~~~~----~~~~~il~~~~~  251 (282)
T 1rif_A          185 HAMIKKIGGGASKDD---KYKNDAPVVVGTWQTVVKQP------KEWFSQFGMMMNDECHLATG----KSISSIISGLNN  251 (282)
T ss_dssp             GGGEEECSTTCSSTT---CCCTTCSEEEECHHHHTTSC------GGGGGGEEEEEEETGGGCCH----HHHHHHTTTCTT
T ss_pred             cceEEEEeCCCcchh---hhccCCcEEEEchHHHHhhH------HHHHhhCCEEEEECCccCCc----ccHHHHHHHhhc
Confidence            678888888875432   12245899999999774331      13467899999999999863    477888888888


Q ss_pred             CCcEEEEeccCcHHH
Q 002040          648 DRQTVLFSATFPRQV  662 (976)
Q Consensus       648 ~~q~i~~SAT~~~~~  662 (976)
                      ..++|+||||+++..
T Consensus       252 ~~~~l~lSATp~~~~  266 (282)
T 1rif_A          252 CMFKFGLSGSLRDGK  266 (282)
T ss_dssp             CCEEEEECSSCCTTS
T ss_pred             CCeEEEEeCCCCCcc
Confidence            899999999998653

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

Probab=99.77  E-value=4e-17  Score=196.16  Aligned_cols=317  Identities=15%  Similarity=0.155  Sum_probs=193.3

Q ss_pred             CCcHHHHHHHH----HHhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHHHH
Q 002040          489 KPMPIQAQALP----VIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFA  564 (976)
Q Consensus       489 ~p~~~Q~~~i~----~il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~~~  564 (976)
                      .|+|.|.+.+.    .+..|+++|+.||||+|||++|++|++.++..       .+++++|++||++|+.|+.+++..+.
T Consensus         3 ~~R~~Q~~~~~~v~~~l~~~~~~~~~apTGtGKT~a~l~p~l~~~~~-------~~~kvli~t~T~~l~~Qi~~el~~l~   75 (620)
T 4a15_A            3 ENRQYQVEAIDFLRSSLQKSYGVALESPTGSGKTIMALKSALQYSSE-------RKLKVLYLVRTNSQEEQVIKELRSLS   75 (620)
T ss_dssp             --CHHHHHHHHHHHHHHHHSSEEEEECCTTSCHHHHHHHHHHHHHHH-------HTCEEEEEESSHHHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHHHHcCCCEEEECCCCCCHHHHHHHHHHHhhhh-------cCCeEEEECCCHHHHHHHHHHHHHHh
Confidence            58899998885    45689999999999999999999999998764       25789999999999999999999988


Q ss_pred             hhcCcEEEEeeCCCC----hHH--------------HHH-----------------------------------------
Q 002040          565 KVMGVRCVPVYGGSG----VAQ--------------QIS-----------------------------------------  585 (976)
Q Consensus       565 ~~~~~~~~~~~gg~~----~~~--------------~~~-----------------------------------------  585 (976)
                      ...+++++.++|+.+    ...              .+.                                         
T Consensus        76 ~~~~~~~~~l~gr~~lC~~~~~~~~~~~~~~~~~~~~C~~l~~~~~~~~~~~C~~~~~~~~~gd~~~~l~~~~~die~l~  155 (620)
T 4a15_A           76 STMKIRAIPMQGRVNMCILYRMVDDLHEINAESLAKFCNMKKREVMAGNEAACPYFNFKIRSDETKRFLFDELPTAEEFY  155 (620)
T ss_dssp             HHSCCCEEECCCHHHHCSSHHHHCCCSSCCHHHHHHHHHHHHHHHHTTCTTSSTTCSGGGGCHHHHHHHHHHCCCHHHHH
T ss_pred             hccCeEEEEEECCCcccccChhhhhcccchhhhHHHHHHHHHhccccCCCCCCCcccccCcccchhHHhccCCCCHHHHH
Confidence            777788877666431    000              000                                         


Q ss_pred             ---------------HHhcCCeEEEeCchhHHHHHHhcCC--cccccCCceEEEecCccccccc----------------
Q 002040          586 ---------------ELKRGTEIVVCTPGRMIDILCTSGG--KITNLRRVTYLVMDEADRMFDM----------------  632 (976)
Q Consensus       586 ---------------~l~~~~~Iiv~Tp~~L~~~l~~~~~--~~~~l~~~~~vVlDEah~~~~~----------------  632 (976)
                                     .....++|||+++..|++.......  .......-.+|||||||.+.+.                
T Consensus       156 ~~~~~~~~CPy~~aR~~~~~ADvVV~ny~ylld~~~r~~~~~~~~i~p~~~ivI~DEAHNL~d~a~~~~S~~ls~~~l~~  235 (620)
T 4a15_A          156 DYGERNNVCPYESMKAALPDADIVIAPYAYFLNRSVAEKFLSHWGVSRNQIVIILDEAHNLPDIGRSIGSFRISVESLNR  235 (620)
T ss_dssp             HHHHHTTCCHHHHHHHHGGGCSEEEEEHHHHTCHHHHHHHHHHHTCCGGGEEEEETTGGGHHHHHHHHHCEEEEHHHHHH
T ss_pred             HHhhhcCCCccHHHHHHhhcCCEEEeCchhhcCHHHHHHHHHhhccCcCCeEEEEECCCchHHHHHHhhcceeCHHHHHH
Confidence                           0011578999999877665432110  0001234579999999987210                


Q ss_pred             ----------CC------chH--------HH-----------------------------------H-------HHH---
Q 002040          633 ----------GF------EPQ--------IT-----------------------------------R-------IVQ---  643 (976)
Q Consensus       633 ----------~f------~~~--------i~-----------------------------------~-------il~---  643 (976)
                                .+      ...        +.                                   .       +..   
T Consensus       236 ~~~~l~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~l~~~~~~l~~~~~~~~  315 (620)
T 4a15_A          236 ADREAQAYGDPELSQKIHVSDLIEMIRSALQSMVSERCGKGDVRIRFQEFMEYMRIMNKRSEREIRSLLNYLYLFGEYVE  315 (620)
T ss_dssp             HHHHHHHTTCCEEETTEEHHHHHHHHHHHHHHHHHHHCSSSCEEECTHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhhhhhhhHHHHHHHHHHHHHHHHHHHHhhcccccCCChHHHHHHHHHhhcccHHHHHHHHHHHHHHHHHHH
Confidence                      00      000        00                                   0       000   


Q ss_pred             ----------------------h---cCC------------------------------CCcEEEEeccCcHHHHHHHHH
Q 002040          644 ----------------------N---IRP------------------------------DRQTVLFSATFPRQVEILARK  668 (976)
Q Consensus       644 ----------------------~---~~~------------------------------~~q~i~~SAT~~~~~~~l~~~  668 (976)
                                            .   ...                              ...+|++|||+.+ +..+...
T Consensus       316 ~~~~~~~~~~~~~~~~~~~fl~~~~~~~~~~~~~~~~~~~~~~l~~~~l~~~~~l~~~~~~~~il~SaTL~p-~~~~~~~  394 (620)
T 4a15_A          316 NEKEKVGKVPFSYCSSVASRIIAFSDQDEEKYAAILSPEDGGYMQAACLDPSGILEVLKESKTIHMSGTLDP-FDFYSDI  394 (620)
T ss_dssp             HHHHHTTSCCCCHHHHHHHHHHHHHTSCTTTEEEEEECGGGCEEEEEECCTHHHHGGGGGSEEEEEESSCCS-HHHHHHH
T ss_pred             hhccccccccccHHHHHHHHHHHHhhcCCCCEEEEEEeCCCcEEEEEECCHHHHHHHHhCCeEEEEccCCCc-HHHHHHH
Confidence                                  0   000                              1235899999986 4444444


Q ss_pred             HcCCCeEEEeCCcccccCCceEEEEecC--------cchHHHHHHHHHHhhh--cCCcEEEEecCHHHHHHHHHHHHHCC
Q 002040          669 VLNKPVEIQVGGRSVVNKDITQLVEVRP--------ESDRFLRLLELLGEWY--EKGKILIFVHSQEKCDALFRDLLKHG  738 (976)
Q Consensus       669 ~l~~~~~i~~~~~~~~~~~i~q~~~~~~--------~~~k~~~l~~~l~~~~--~~~kvLIF~~s~~~~~~l~~~L~~~~  738 (976)
                      +...+..+.++ .++...+.. .+....        .......+...|....  .+|.+|||++|...++.++..|.  .
T Consensus       395 lGl~~~~~~~~-spf~~~~~~-~~~~~~~~~~~~~r~~~~~~~~~~~i~~l~~~~~g~~lvlF~Sy~~l~~v~~~l~--~  470 (620)
T 4a15_A          395 TGFEIPFKKIG-EIFPPENRY-IAYYDGVSSKYDTLDEKELDRMATVIEDIILKVKKNTIVYFPSYSLMDRVENRVS--F  470 (620)
T ss_dssp             HCCCCCEEECC-CCSCGGGEE-EEEECCC-------CHHHHHHHHHHHHHHHHHHCSCEEEEESCHHHHHHHTSSCC--S
T ss_pred             hCCCceeeecC-CCCCHHHeE-EEEeCCCCCcCCCCCHHHHHHHHHHHHHHHHhCCCCEEEEeCCHHHHHHHHHHHH--h
Confidence            33223333332 222222222 111111        1111233444443332  36889999999999999988876  2


Q ss_pred             CCceeccCCCCHHHHHHHHHHhccCCccEEEecC--cccccCCCCC--CcEEEEeCCCCCH-------------------
Q 002040          739 YPCLSLHGAKDQTDRESTISDFKSNVCNLLIATS--VAARGLDVKE--LELVINFDAPNHY-------------------  795 (976)
Q Consensus       739 ~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLVaT~--v~~~GlDi~~--v~~VI~~d~p~s~-------------------  795 (976)
                      +... ...+++...+..+++.|. +...||+||.  .++.|||+++  +.+||+...|...                   
T Consensus       471 ~~~~-~~q~~~~~~~~~ll~~f~-~~~~vL~~v~~gsf~EGiD~~g~~l~~viI~~lPfp~~~p~~~ar~~~~~~~~g~~  548 (620)
T 4a15_A          471 EHMK-EYRGIDQKELYSMLKKFR-RDHGTIFAVSGGRLSEGINFPGNELEMIILAGLPFPRPDAINRSLFDYYERKYGKG  548 (620)
T ss_dssp             CCEE-CCTTCCSHHHHHHHHHHT-TSCCEEEEETTSCC--------CCCCEEEESSCCCCCCCHHHHHHHHHHHHHHSCH
T ss_pred             cchh-ccCCCChhHHHHHHHHhc-cCCcEEEEEecCceeccccCCCCceEEEEEEcCCCCCCCHHHHHHHHHHHHhhCCC
Confidence            2222 445566678999999999 8889999974  9999999998  7899998877421                   


Q ss_pred             H----------HHHHHhcccCCCCCccEEEEEec
Q 002040          796 E----------DYVHRVGRTGRAGRKGCAITFIS  819 (976)
Q Consensus       796 ~----------~y~Qr~GR~gR~g~~g~~~~~~~  819 (976)
                      -          ...|.+||+-|.-..--++++++
T Consensus       549 ~~~~y~~pa~~~l~Qa~GRlIR~~~D~G~v~llD  582 (620)
T 4a15_A          549 WEYSVVYPTAIKIRQEIGRLIRSAEDTGACVILD  582 (620)
T ss_dssp             HHHHTHHHHHHHHHHHHHTTCCSTTCCEEEEEEC
T ss_pred             chHHhHHHHHHHHHHHhCccccCCCceEEEEEEc
Confidence            1          12599999999765544555554

>1z5z_A Helicase of the SNF2/RAD54 family; hydrolase, recombination, hydrolase-recombination complex; 2.00A {Sulfolobus solfataricus} SCOP: c.37.1.19

Probab=99.75  E-value=3.4e-18  Score=184.29  Aligned_cols=127  Identities=21%  Similarity=0.265  Sum_probs=101.0

Q ss_pred             cCcchHHHHHHHHHHhhh-cCCcEEEEecCHHHHHHHHHHHHHC-CCCceeccCCCCHHHHHHHHHHhccC-Ccc-EEEe
Q 002040          695 RPESDRFLRLLELLGEWY-EKGKILIFVHSQEKCDALFRDLLKH-GYPCLSLHGAKDQTDRESTISDFKSN-VCN-LLIA  770 (976)
Q Consensus       695 ~~~~~k~~~l~~~l~~~~-~~~kvLIF~~s~~~~~~l~~~L~~~-~~~~~~lhg~~~~~~R~~~~~~F~~g-~~~-vLVa  770 (976)
                      ...+.|+..|..+|..+. .+.++||||++...++.|...|... |+.+..+||++++.+|..++..|++| .+. |||+
T Consensus        92 ~~~s~K~~~L~~ll~~~~~~~~kvlIFs~~~~~~~~l~~~L~~~~g~~~~~l~G~~~~~~R~~~i~~F~~~~~~~v~L~s  171 (271)
T 1z5z_A           92 VRRSGKMIRTMEIIEEALDEGDKIAIFTQFVDMGKIIRNIIEKELNTEVPFLYGELSKKERDDIISKFQNNPSVKFIVLS  171 (271)
T ss_dssp             STTCHHHHHHHHHHHHHHHTTCCEEEEESCHHHHHHHHHHHHHHHCSCCCEECTTSCHHHHHHHHHHHHHCTTCCEEEEE
T ss_pred             cccCHHHHHHHHHHHHHHhCCCeEEEEeccHHHHHHHHHHHHHhcCCcEEEEECCCCHHHHHHHHHHhcCCCCCCEEEEe
Confidence            456789999999998765 4569999999999999999999885 99999999999999999999999998 676 7899


Q ss_pred             cCcccccCCCCCCcEEEEeCCCCCHHHHHHHhcccCCCCCccEE--EEEecCC
Q 002040          771 TSVAARGLDVKELELVINFDAPNHYEDYVHRVGRTGRAGRKGCA--ITFISEE  821 (976)
Q Consensus       771 T~v~~~GlDi~~v~~VI~~d~p~s~~~y~Qr~GR~gR~g~~g~~--~~~~~~~  821 (976)
                      |+++++|||++++++||+||+|||+..|+|++||++|.|+.+.|  |.|++..
T Consensus       172 t~~~g~Glnl~~a~~VI~~d~~wnp~~~~Q~~gR~~R~Gq~~~v~v~~li~~~  224 (271)
T 1z5z_A          172 VKAGGFGINLTSANRVIHFDRWWNPAVEDQATDRVYRIGQTRNVIVHKLISVG  224 (271)
T ss_dssp             CCTTCCCCCCTTCSEEEECSCCSCTTTC--------------CCEEEEEEETT
T ss_pred             hhhhcCCcCcccCCEEEEECCCCChhHHHHHHHhccccCCCCceEEEEEeeCC
Confidence            99999999999999999999999999999999999999988765  5566653

>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=99.74  E-value=1e-17  Score=177.49  Aligned_cols=139  Identities=22%  Similarity=0.143  Sum_probs=110.1

Q ss_pred             CCCcHHHHHHHHHHhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHHHHhhc
Q 002040          488 EKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVM  567 (976)
Q Consensus       488 ~~p~~~Q~~~i~~il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~~~~~~  567 (976)
                      ..|+++|.+++..++.+.++|++++||+|||++++.++...           +..+||+||+++|+.||+..+..    +
T Consensus        92 ~~l~~~Q~~ai~~~~~~~~~ll~~~tG~GKT~~a~~~~~~~-----------~~~~liv~P~~~L~~q~~~~~~~----~  156 (237)
T 2fz4_A           92 ISLRDYQEKALERWLVDKRGCIVLPTGSGKTHVAMAAINEL-----------STPTLIVVPTLALAEQWKERLGI----F  156 (237)
T ss_dssp             CCCCHHHHHHHHHHTTTSEEEEEESSSTTHHHHHHHHHHHS-----------CSCEEEEESSHHHHHHHHHHHGG----G
T ss_pred             CCcCHHHHHHHHHHHhCCCEEEEeCCCCCHHHHHHHHHHHc-----------CCCEEEEeCCHHHHHHHHHHHHh----C
Confidence            47999999999999999999999999999999988776642           45689999999999999998877    3


Q ss_pred             CcE-EEEeeCCCChHHHHHHHhcCCeEEEeCchhHHHHHHhcCCcccccCCceEEEecCcccccccCCchHHHHHHHhcC
Q 002040          568 GVR-CVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMGFEPQITRIVQNIR  646 (976)
Q Consensus       568 ~~~-~~~~~gg~~~~~~~~~l~~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDEah~~~~~~f~~~i~~il~~~~  646 (976)
                      ++. +..+.|+..         ...+|+|+||+.+...+..      ....+.+|||||||++.+..    +..++..+ 
T Consensus       157 ~~~~v~~~~g~~~---------~~~~i~v~T~~~l~~~~~~------~~~~~~llIiDEaH~l~~~~----~~~i~~~~-  216 (237)
T 2fz4_A          157 GEEYVGEFSGRIK---------ELKPLTVSTYDSAYVNAEK------LGNRFMLLIFDEVHHLPAES----YVQIAQMS-  216 (237)
T ss_dssp             CGGGEEEESSSCB---------CCCSEEEEEHHHHHHTHHH------HTTTCSEEEEECSSCCCTTT----HHHHHHTC-
T ss_pred             CCCeEEEEeCCCC---------CcCCEEEEeHHHHHhhHHH------hcccCCEEEEECCccCCChH----HHHHHHhc-
Confidence            677 777777653         2579999999998765532      12458999999999987654    34455555 


Q ss_pred             CCCcEEEEeccCcHH
Q 002040          647 PDRQTVLFSATFPRQ  661 (976)
Q Consensus       647 ~~~q~i~~SAT~~~~  661 (976)
                      +..++|+||||+++.
T Consensus       217 ~~~~~l~LSATp~r~  231 (237)
T 2fz4_A          217 IAPFRLGLTATFERE  231 (237)
T ss_dssp             CCSEEEEEEESCC--
T ss_pred             cCCEEEEEecCCCCC
Confidence            467899999999764

>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=98.72  E-value=2.3e-08  Score=120.02  Aligned_cols=146  Identities=22%  Similarity=0.289  Sum_probs=93.4

Q ss_pred             cHHHHHHHHHHhcCCCEEEEcCCCCchH--HHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHHHHhhcC
Q 002040          491 MPIQAQALPVIMSGRDCIGVAKTGSGKT--LAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVMG  568 (976)
Q Consensus       491 ~~~Q~~~i~~il~g~d~i~~a~TGsGKT--~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~~~~~~~  568 (976)
                      ++.|..+++.++.++.+++.|++|+|||  +.++++++..+..      ..++.+++++||..+|.++.+.+..++..++
T Consensus       151 ~~~Q~~Ai~~~l~~~~~vi~G~pGTGKTt~l~~ll~~l~~~~~------~~~~~vll~APTg~AA~~L~e~~~~~~~~l~  224 (608)
T 1w36_D          151 INWQKVAAAVALTRRISVISGGPGTGKTTTVAKLLAALIQMAD------GERCRIRLAAPTGKAAARLTESLGKALRQLP  224 (608)
T ss_dssp             CCHHHHHHHHHHTBSEEEEECCTTSTHHHHHHHHHHHHHHTCS------SCCCCEEEEBSSHHHHHHHHHHHTHHHHHSS
T ss_pred             CHHHHHHHHHHhcCCCEEEEeCCCCCHHHHHHHHHHHHHHhhh------cCCCeEEEEeCChhHHHHHHHHHHHHHhcCC
Confidence            7899999999999999999999999999  4456666654321      2356899999999999999988887766655


Q ss_pred             cEEEEeeCCCChHHHHHHHhcCCeEEEeCchhHHHHHHhcCCcccccCCceEEEecCcccccccCCchHHHHHHHhcCCC
Q 002040          569 VRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMGFEPQITRIVQNIRPD  648 (976)
Q Consensus       569 ~~~~~~~gg~~~~~~~~~l~~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDEah~~~~~~f~~~i~~il~~~~~~  648 (976)
                      +...... +...  ....+   ..++-.+|+..  .+....   .....+++||||||+ |++   ...+..++..++..
T Consensus       225 l~~~~~~-~~~~--~~~Ti---h~ll~~~~~~~--~~~~~~---~~~l~~d~lIIDEAs-ml~---~~~~~~Ll~~l~~~  289 (608)
T 1w36_D          225 LTDEQKK-RIPE--DASTL---HRLLGAQPGSQ--RLRHHA---GNPLHLDVLVVDEAS-MID---LPMMSRLIDALPDH  289 (608)
T ss_dssp             CCSCCCC-SCSC--CCBTT---TSCC-------------CT---TSCCSCSEEEECSGG-GCB---HHHHHHHHHTCCTT
T ss_pred             CCHHHHh-ccch--hhhhh---HhhhccCCCch--HHHhcc---CCCCCCCEEEEechh-hCC---HHHHHHHHHhCCCC
Confidence            4321110 0000  00000   01121222211  011111   122368999999999 554   55778889999888


Q ss_pred             CcEEEEecc
Q 002040          649 RQTVLFSAT  657 (976)
Q Consensus       649 ~q~i~~SAT  657 (976)
                      .|+|++.-+
T Consensus       290 ~~liLvGD~  298 (608)
T 1w36_D          290 ARVIFLGDR  298 (608)
T ss_dssp             CEEEEEECT
T ss_pred             CEEEEEcch
Confidence            999998755

>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=98.32  E-value=1.3e-05  Score=96.43  Aligned_cols=69  Identities=20%  Similarity=0.247  Sum_probs=54.8

Q ss_pred             CCCCcHHHHHHHHHHhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHH
Q 002040          487 YEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRK  562 (976)
Q Consensus       487 ~~~p~~~Q~~~i~~il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~  562 (976)
                      +..+++.|..|+..++.+.-++|.||+|+|||.+. ..++.++...      .+..+||++||...+.++...+..
T Consensus       178 ~~~ln~~Q~~av~~~l~~~~~li~GppGTGKT~~~-~~~i~~l~~~------~~~~ilv~a~tn~A~~~l~~~l~~  246 (624)
T 2gk6_A          178 LPDLNHSQVYAVKTVLQRPLSLIQGPPGTGKTVTS-ATIVYHLARQ------GNGPVLVCAPSNIAVDQLTEKIHQ  246 (624)
T ss_dssp             SCCCCHHHHHHHHHHHTCSEEEEECCTTSCHHHHH-HHHHHHHHTS------SSCCEEEEESSHHHHHHHHHHHHT
T ss_pred             cCCCCHHHHHHHHHHhcCCCeEEECCCCCCHHHHH-HHHHHHHHHc------CCCeEEEEeCcHHHHHHHHHHHHh
Confidence            35688999999999998878899999999999874 4444554432      356799999999999988877754

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

Probab=98.26  E-value=3.7e-05  Score=93.06  Aligned_cols=66  Identities=23%  Similarity=0.232  Sum_probs=52.0

Q ss_pred             CCcHHHHHHHHHHhcCCC-EEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHH
Q 002040          489 KPMPIQAQALPVIMSGRD-CIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRK  562 (976)
Q Consensus       489 ~p~~~Q~~~i~~il~g~d-~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~  562 (976)
                      .+.+-|.+|+..++..++ .||+||+|||||.+.+ .++.++...       +.++||++||...+.++...+..
T Consensus       189 ~LN~~Q~~AV~~al~~~~~~lI~GPPGTGKT~ti~-~~I~~l~~~-------~~~ILv~a~TN~AvD~i~erL~~  255 (646)
T 4b3f_X          189 CLDTSQKEAVLFALSQKELAIIHGPPGTGKTTTVV-EIILQAVKQ-------GLKVLCCAPSNIAVDNLVERLAL  255 (646)
T ss_dssp             TCCHHHHHHHHHHHHCSSEEEEECCTTSCHHHHHH-HHHHHHHHT-------TCCEEEEESSHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHhcCCCceEEECCCCCCHHHHHH-HHHHHHHhC-------CCeEEEEcCchHHHHHHHHHHHh
Confidence            578999999999987665 6888999999998744 444444432       56899999999999988777654

>3hgt_A HDA1 complex subunit 3; RECA-like domain, SWI2/SNF2 helical domain, chromatin regulator, coiled coil, nucleus, repressor, transcription; 2.20A {Saccharomyces cerevisiae} PDB: 3hgq_A

Probab=98.26  E-value=5.3e-06  Score=89.39  Aligned_cols=121  Identities=14%  Similarity=0.131  Sum_probs=90.7

Q ss_pred             cchHHHHHHHHHHhhhcCC-cEEEEecCHHHHHHHHHHHHHCCCCceeccCCCCHHHHHHHHHHhccCCccEEEecCccc
Q 002040          697 ESDRFLRLLELLGEWYEKG-KILIFVHSQEKCDALFRDLLKHGYPCLSLHGAKDQTDRESTISDFKSNVCNLLIATSVAA  775 (976)
Q Consensus       697 ~~~k~~~l~~~l~~~~~~~-kvLIF~~s~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLVaT~v~~  775 (976)
                      .+.|+..|-.+|..+...+ +||||+++..+.+.|..+|...++.+..+.|......+.     -.++.+.|.+.|..++
T Consensus       107 ~SGKf~~L~~LL~~l~~~~~kVLIfsq~t~~LDilE~~l~~~~~~y~RlDG~~~~~~~k-----~~~~~~~i~Lltsag~  181 (328)
T 3hgt_A          107 NSGKFSVLRDLINLVQEYETETAIVCRPGRTMDLLEALLLGNKVHIKRYDGHSIKSAAA-----ANDFSCTVHLFSSEGI  181 (328)
T ss_dssp             TCHHHHHHHHHHHHHTTSCEEEEEEECSTHHHHHHHHHHTTSSCEEEESSSCCC------------CCSEEEEEEESSCC
T ss_pred             cCccHHHHHHHHHHHHhCCCEEEEEECChhHHHHHHHHHhcCCCceEeCCCCchhhhhh-----cccCCceEEEEECCCC
Confidence            5789988888888776544 999999999999999999999999999999986543221     1244555555577777


Q ss_pred             ccCC-----CCCCcEEEEeCCCCCHHHH-HHHhcccCCCC----CccEEEEEecCCC
Q 002040          776 RGLD-----VKELELVINFDAPNHYEDY-VHRVGRTGRAG----RKGCAITFISEED  822 (976)
Q Consensus       776 ~GlD-----i~~v~~VI~~d~p~s~~~y-~Qr~GR~gR~g----~~g~~~~~~~~~d  822 (976)
                      -|+|     +..+++||.||+.||+..- +|.+-|++|.|    ++-.+|.|++...
T Consensus       182 ~gin~~~~nl~~aD~VI~~DsdwNp~~d~iQa~~r~~R~~~gq~k~v~V~RLvt~~T  238 (328)
T 3hgt_A          182 NFTKYPIKSKARFDMLICLDTTVDTSQKDIQYLLQYKRERKGLERYAPIVRLVAINS  238 (328)
T ss_dssp             CTTTSCCCCCSCCSEEEECSTTCCTTSHHHHHHHCCC---------CCEEEEEETTS
T ss_pred             CCcCcccccCCCCCEEEEECCCCCCCChHHHHHHHHhhhccCCCCcceEEEEeCCCC
Confidence            7776     6889999999999999885 99999999973    2456777887653

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

Probab=98.21  E-value=5.7e-05  Score=91.69  Aligned_cols=72  Identities=15%  Similarity=0.125  Sum_probs=54.3

Q ss_pred             CCCcHHHHHHHHHHhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHHHHh
Q 002040          488 EKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAK  565 (976)
Q Consensus       488 ~~p~~~Q~~~i~~il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~~~~  565 (976)
                      ..+++-|.+++.  .....++|.|+.|||||.+.+--+...+....    .....+|+|++|..+|.++...+..+..
T Consensus         8 ~~Ln~~Q~~av~--~~~~~~lV~a~aGsGKT~~l~~ri~~l~~~~~----~~~~~iL~ltft~~aa~e~~~rl~~~~~   79 (647)
T 3lfu_A            8 DSLNDKQREAVA--APRSNLLVLAGAGSGKTRVLVHRIAWLMSVEN----CSPYSIMAVTFTNKAAAEMRHRIGQLMG   79 (647)
T ss_dssp             TTCCHHHHHHHT--CCSSCEEEEECTTSCHHHHHHHHHHHHHHTSC----CCGGGEEEEESSHHHHHHHHHHHHHHHC
T ss_pred             hcCCHHHHHHHh--CCCCCEEEEECCCCCHHHHHHHHHHHHHHhCC----CChhhEEEEeccHHHHHHHHHHHHHHhc
Confidence            357899999997  34678999999999999885555554444321    1234799999999999999998887653

>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=98.19  E-value=3.9e-05  Score=88.91  Aligned_cols=70  Identities=13%  Similarity=0.172  Sum_probs=50.6

Q ss_pred             HHcCCCCCcHHHHHHHHHHhcC----C-CEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHH
Q 002040          483 RKLNYEKPMPIQAQALPVIMSG----R-DCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIH  557 (976)
Q Consensus       483 ~~~~~~~p~~~Q~~~i~~il~g----~-d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~  557 (976)
                      ..+.|..|++-|.+++..++..    . .++|.|+.|||||.+ +..++.++....      ...+++++||...|..+.
T Consensus        19 ~p~~~~~Ln~~Q~~av~~~~~~i~~~~~~~li~G~aGTGKT~l-l~~~~~~l~~~~------~~~il~~a~T~~Aa~~l~   91 (459)
T 3upu_A           19 SHMTFDDLTEGQKNAFNIVMKAIKEKKHHVTINGPAGTGATTL-TKFIIEALISTG------ETGIILAAPTHAAKKILS   91 (459)
T ss_dssp             --CCSSCCCHHHHHHHHHHHHHHHSSSCEEEEECCTTSCHHHH-HHHHHHHHHHTT------CCCEEEEESSHHHHHHHH
T ss_pred             CCCccccCCHHHHHHHHHHHHHHhcCCCEEEEEeCCCCCHHHH-HHHHHHHHHhcC------CceEEEecCcHHHHHHHH
Confidence            3466788999999999977532    3 899999999999976 455555555431      136899999988876654


Q ss_pred             HH
Q 002040          558 SD  559 (976)
Q Consensus       558 ~~  559 (976)
                      ..
T Consensus        92 ~~   93 (459)
T 3upu_A           92 KL   93 (459)
T ss_dssp             HH
T ss_pred             hh
Confidence            43

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

Probab=98.19  E-value=5.8e-05  Score=92.90  Aligned_cols=70  Identities=17%  Similarity=0.293  Sum_probs=54.8

Q ss_pred             CCCCcHHHHHHHHHHhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHHH
Q 002040          487 YEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKF  563 (976)
Q Consensus       487 ~~~p~~~Q~~~i~~il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~~  563 (976)
                      +..+++.|.+|+..++.+.-++|.||.|+|||.+.. .++.++...      .+.++||++||...|.++...+...
T Consensus       358 ~~~Ln~~Q~~Av~~~l~~~~~lI~GppGTGKT~~i~-~~i~~l~~~------~~~~ILv~a~tn~A~d~l~~rL~~~  427 (802)
T 2xzl_A          358 FAQLNSSQSNAVSHVLQRPLSLIQGPPGTGKTVTSA-TIVYHLSKI------HKDRILVCAPSNVAVDHLAAKLRDL  427 (802)
T ss_dssp             SCCCCHHHHHHHHHHTTCSEEEEECSTTSSHHHHHH-HHHHHHHHH------HCCCEEEEESSHHHHHHHHHHHHHT
T ss_pred             cccCCHHHHHHHHHHhcCCCEEEECCCCCCHHHHHH-HHHHHHHhC------CCCeEEEEcCcHHHHHHHHHHHHhh
Confidence            456889999999999987778999999999998743 344444321      2457999999999999988887663

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

Probab=98.15  E-value=0.00014  Score=89.44  Aligned_cols=69  Identities=20%  Similarity=0.256  Sum_probs=54.9

Q ss_pred             CCCCcHHHHHHHHHHhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHH
Q 002040          487 YEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRK  562 (976)
Q Consensus       487 ~~~p~~~Q~~~i~~il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~  562 (976)
                      ...+++.|..|+..++.+.-++|.|++|+|||.+ +..++.++...      .+..+|+++||...|.++...+..
T Consensus       354 ~~~Ln~~Q~~Av~~~l~~~~~lI~GppGTGKT~t-i~~~i~~l~~~------~~~~ilv~a~tn~A~~~l~~~l~~  422 (800)
T 2wjy_A          354 LPDLNHSQVYAVKTVLQRPLSLIQGPPGTGKTVT-SATIVYHLARQ------GNGPVLVCAPSNIAVDQLTEKIHQ  422 (800)
T ss_dssp             SCCCCHHHHHHHHHHHTSSEEEEECCTTSCHHHH-HHHHHHHHHTT------CSSCEEEEESSHHHHHHHHHHHHT
T ss_pred             ccCCCHHHHHHHHHhccCCeEEEEcCCCCCHHHH-HHHHHHHHHHc------CCCcEEEEcCcHHHHHHHHHHHHH
Confidence            3568899999999999887889999999999987 44455555432      256799999999999888777654

>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=98.03  E-value=1.1e-05  Score=95.82  Aligned_cols=127  Identities=17%  Similarity=0.142  Sum_probs=81.0

Q ss_pred             CCcHHHHHHHHHHhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHHHHhhcC
Q 002040          489 KPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVMG  568 (976)
Q Consensus       489 ~p~~~Q~~~i~~il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~~~~~~~  568 (976)
                      .+++.|..++..++.+..+++.|+.|+|||++ +..++..+..       .+..+++++||...|..+...+       +
T Consensus       189 ~L~~~Q~~Av~~~~~~~~~~I~G~pGTGKTt~-i~~l~~~l~~-------~g~~Vl~~ApT~~Aa~~L~e~~-------~  253 (574)
T 3e1s_A          189 GLSEEQASVLDQLAGHRLVVLTGGPGTGKSTT-TKAVADLAES-------LGLEVGLCAPTGKAARRLGEVT-------G  253 (574)
T ss_dssp             TCCHHHHHHHHHHTTCSEEEEECCTTSCHHHH-HHHHHHHHHH-------TTCCEEEEESSHHHHHHHHHHH-------T
T ss_pred             CCCHHHHHHHHHHHhCCEEEEEcCCCCCHHHH-HHHHHHHHHh-------cCCeEEEecCcHHHHHHhHhhh-------c
Confidence            57899999999999999999999999999976 3444444443       2567899999998887664432       2


Q ss_pred             cEEEEeeCCCChHHHHHHHhcCCeEEEeCchhHHHHHHhcCCcccccCCceEEEecCcccccccCCchHHHHHHHhcCCC
Q 002040          569 VRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMGFEPQITRIVQNIRPD  648 (976)
Q Consensus       569 ~~~~~~~gg~~~~~~~~~l~~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDEah~~~~~~f~~~i~~il~~~~~~  648 (976)
                      .....+.          .+..   +.. +  .+    ..   .......+++||||||+.+.    ...+..++..++..
T Consensus       254 ~~a~Tih----------~ll~---~~~-~--~~----~~---~~~~~~~~dvlIIDEasml~----~~~~~~Ll~~~~~~  306 (574)
T 3e1s_A          254 RTASTVH----------RLLG---YGP-Q--GF----RH---NHLEPAPYDLLIVDEVSMMG----DALMLSLLAAVPPG  306 (574)
T ss_dssp             SCEEEHH----------HHTT---EET-T--EE----SC---SSSSCCSCSEEEECCGGGCC----HHHHHHHHTTSCTT
T ss_pred             ccHHHHH----------HHHc---CCc-c--hh----hh---hhcccccCCEEEEcCccCCC----HHHHHHHHHhCcCC
Confidence            2111110          1100   000 0  00    00   01233467899999999643    34666777777777


Q ss_pred             CcEEEEecc
Q 002040          649 RQTVLFSAT  657 (976)
Q Consensus       649 ~q~i~~SAT  657 (976)
                      .++|++.-+
T Consensus       307 ~~lilvGD~  315 (574)
T 3e1s_A          307 ARVLLVGDT  315 (574)
T ss_dssp             CEEEEEECT
T ss_pred             CEEEEEecc
Confidence            777776543

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

Probab=97.45  E-value=0.00088  Score=81.49  Aligned_cols=71  Identities=18%  Similarity=0.166  Sum_probs=53.8

Q ss_pred             CCcHHHHHHHHHHhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHHHHh
Q 002040          489 KPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAK  565 (976)
Q Consensus       489 ~p~~~Q~~~i~~il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~~~~  565 (976)
                      .+++-|.+++..  .+..++|.|..|||||.+.+--+...+....    .....+|+|+.|+.+|.++...+.....
T Consensus         2 ~L~~~Q~~av~~--~~~~~lV~AgaGSGKT~~l~~ri~~ll~~~~----~~~~~IL~lTfT~~Aa~em~~Rl~~~l~   72 (673)
T 1uaa_A            2 RLNPGQQQAVEF--VTGPCLVLAGAGSGKTRVITNKIAHLIRGCG----YQARHIAAVTFTNKAAREMKERVGQTLG   72 (673)
T ss_dssp             CCCHHHHHHHHC--CSSEEEECCCTTSCHHHHHHHHHHHHHHHHC----CCGGGEEEEESSHHHHHHHHHHHHHHSC
T ss_pred             CCCHHHHHHHhC--CCCCEEEEeCCCCChHHHHHHHHHHHHHhcC----CCHHHeEEEeccHHHHHHHHHHHHHHcC
Confidence            478999999875  3678899999999999886555555554311    1234799999999999999988887643

>1pjr_A PCRA; DNA repair, DNA replication, SOS response, helicase, ATP- binding, DNA-binding; 2.50A {Geobacillus stearothermophilus} SCOP: c.37.1.19 c.37.1.19 PDB: 1qhg_A* 3pjr_A* 2pjr_A* 1qhh_B* 1qhh_D* 1qhh_A* 1qhh_C* 2pjr_B*

Probab=97.34  E-value=0.0058  Score=74.73  Aligned_cols=80  Identities=14%  Similarity=0.062  Sum_probs=58.1

Q ss_pred             CCCcHHHHHHHHHHhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHHHHhh-
Q 002040          488 EKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKV-  566 (976)
Q Consensus       488 ~~p~~~Q~~~i~~il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~~~~~-  566 (976)
                      ..+++-|.+|+..  ....++|.|..|||||.+.+--+...+....    .....+|+|+.|+.+|.++.+.+..+... 
T Consensus        10 ~~Ln~~Q~~av~~--~~g~~lV~AgAGSGKT~vL~~ri~~ll~~~~----~~p~~IL~vTFTnkAA~Em~~Rl~~~l~~~   83 (724)
T 1pjr_A           10 AHLNKEQQEAVRT--TEGPLLIMAGAGSGKTRVLTHRIAYLMAEKH----VAPWNILAITFTNKAAREMRERVQSLLGGA   83 (724)
T ss_dssp             TTSCHHHHHHHHC--CSSCEEEEECTTSCHHHHHHHHHHHHHHTTC----CCGGGEEEEESSHHHHHHHHHHHHHHHGGG
T ss_pred             hhCCHHHHHHHhC--CCCCEEEEEcCCCCHHHHHHHHHHHHHHhcC----CCHHHeEEEeccHHHHHHHHHHHHHHhccc
Confidence            3588999999875  3568999999999999986555555554321    12347999999999999999888876532 


Q ss_pred             -cCcEEEE
Q 002040          567 -MGVRCVP  573 (976)
Q Consensus       567 -~~~~~~~  573 (976)
                       .++.+..
T Consensus        84 ~~~~~v~T   91 (724)
T 1pjr_A           84 AEDVWIST   91 (724)
T ss_dssp             GTTSEEEE
T ss_pred             ccCcEEee
Confidence             2445544

>2o0j_A Terminase, DNA packaging protein GP17; nucleotide-binding fold, hydrolase; HET: DNA ADP; 1.80A {Enterobacteria phage T4} PDB: 2o0h_A* 2o0k_A*

Probab=97.32  E-value=0.0018  Score=72.23  Aligned_cols=74  Identities=12%  Similarity=0.096  Sum_probs=58.3

Q ss_pred             CCcHHHHHHHHHHhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHHHHhhcC
Q 002040          489 KPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVMG  568 (976)
Q Consensus       489 ~p~~~Q~~~i~~il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~~~~~~~  568 (976)
                      .|+|+|...+..+...+-+++..+-+.|||.+++..++..+...      .+..+++++||...|..++..+..+....+
T Consensus       163 ~L~p~Qk~il~~l~~~R~~vi~~sRq~GKT~l~a~~~l~~a~~~------~g~~v~~vA~t~~qA~~vf~~i~~mi~~~P  236 (385)
T 2o0j_A          163 QLRDYQRDMLKIMSSKRMTVCNLSRQLGKTTVVAIFLAHFVCFN------KDKAVGILAHKGSMSAEVLDRTKQAIELLP  236 (385)
T ss_dssp             CCCHHHHHHHHHHHHSSEEEEEECSSSCHHHHHHHHHHHHHHSS------SSCEEEEEESSHHHHHHHHHHHHHHHHHSC
T ss_pred             CCCHHHHHHHHhhccCcEEEEEEcCcCChhHHHHHHHHHHHHhC------CCCeEEEEeCCHHHHHHHHHHHHHHHHhCh
Confidence            58899999998776556688899999999998776666544432      356799999999999988888888776543

>3cpe_A Terminase, DNA packaging protein GP17; large terminase, alternative initiation, ATP-binding, DNA- binding, hydrolase, nuclease; HET: DNA; 2.80A {Bacteriophage T4} PDB: 3ezk_A*

Probab=96.69  E-value=0.013  Score=69.70  Aligned_cols=74  Identities=12%  Similarity=0.096  Sum_probs=58.9

Q ss_pred             CCcHHHHHHHHHHhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHHHHhhcC
Q 002040          489 KPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVMG  568 (976)
Q Consensus       489 ~p~~~Q~~~i~~il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~~~~~~~  568 (976)
                      .|+|+|...+..+...+-+++.++-|+|||.+++..++..+...      .+..+++++|+...|..++..++.++..++
T Consensus       163 ~l~p~Q~~i~~~l~~~r~~~i~~~Rq~GKS~~~a~~~l~~~~~~------~~~~i~~va~t~~qA~~~~~~i~~~i~~~p  236 (592)
T 3cpe_A          163 QLRDYQRDMLKIMSSKRMTVCNLSRQLGKTTVVAIFLAHFVCFN------KDKAVGILAHKGSMSAEVLDRTKQAIELLP  236 (592)
T ss_dssp             CCCHHHHHHHHHHHHCSEEEEEECSSSCHHHHHHHHHHHHHHTS------SSCEEEEEESSHHHHHHHHHHHHHHHTTSC
T ss_pred             cCCHHHHHHHHhhccccEEEEEEcCccChHHHHHHHHHHHHHhC------CCCeEEEEECCHHHHHHHHHHHHHHHHhCh
Confidence            58899999998775567789999999999998766665555432      255799999999999999988888776554

>2orw_A Thymidine kinase; TMTK, TP4A, transferase; HET: 4TA; 1.50A {Thermotoga maritima} PDB: 2qpo_A 2qq0_A* 2qqe_A*

Probab=96.64  E-value=0.0068  Score=60.51  Aligned_cols=39  Identities=18%  Similarity=0.055  Sum_probs=27.7

Q ss_pred             cCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccC
Q 002040          503 SGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPT  549 (976)
Q Consensus       503 ~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Pt  549 (976)
                      .|.-.++.|++|+|||+.++-.+..+..        .+.+++++.|.
T Consensus         2 ~g~i~vi~G~~gsGKTT~ll~~~~~~~~--------~g~~v~~~~~~   40 (184)
T 2orw_A            2 SGKLTVITGPMYSGKTTELLSFVEIYKL--------GKKKVAVFKPK   40 (184)
T ss_dssp             CCCEEEEEESTTSSHHHHHHHHHHHHHH--------TTCEEEEEEEC
T ss_pred             ccEEEEEECCCCCCHHHHHHHHHHHHHH--------CCCeEEEEeec
Confidence            4566789999999999875544444432        24578888887

>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=96.63  E-value=0.0061  Score=60.42  Aligned_cols=31  Identities=32%  Similarity=0.253  Sum_probs=22.6

Q ss_pred             cHHHHHHHHHHh---------cCCCEEEEcCCCCchHHHH
Q 002040          491 MPIQAQALPVIM---------SGRDCIGVAKTGSGKTLAF  521 (976)
Q Consensus       491 ~~~Q~~~i~~il---------~g~d~i~~a~TGsGKT~~~  521 (976)
                      .+.|..++..+.         .|..++++||+|+|||+.+
T Consensus        16 ~~~~~~~~~~~~~~~~~~~~~~g~~~~l~G~~G~GKTtL~   55 (180)
T 3ec2_A           16 NVSQNRALLTIRVFVHNFNPEEGKGLTFVGSPGVGKTHLA   55 (180)
T ss_dssp             SHHHHHHHHHHHHHHHSCCGGGCCEEEECCSSSSSHHHHH
T ss_pred             CHHHHHHHHHHHHHHHhccccCCCEEEEECCCCCCHHHHH
Confidence            355666655543         4678999999999999763

>1xx6_A Thymidine kinase; NESG, northeast structural genomics consortium, protein STRU initiative, PSI, structural genomics, DNA synthesis; HET: ADP; 2.00A {Clostridium acetobutylicum} SCOP: c.37.1.24 g.39.1.14

Probab=96.53  E-value=0.0055  Score=61.48  Aligned_cols=38  Identities=18%  Similarity=0.103  Sum_probs=27.8

Q ss_pred             CCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccC
Q 002040          504 GRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPT  549 (976)
Q Consensus       504 g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Pt  549 (976)
                      |+-.++.|++|||||+.++-.+.++..        .+.+|+|+.|.
T Consensus         8 g~i~v~~G~mgsGKTT~ll~~a~r~~~--------~g~kV~v~k~~   45 (191)
T 1xx6_A            8 GWVEVIVGPMYSGKSEELIRRIRRAKI--------AKQKIQVFKPE   45 (191)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHHHHHH--------TTCCEEEEEEC
T ss_pred             CEEEEEECCCCCcHHHHHHHHHHHHHH--------CCCEEEEEEec
Confidence            455788899999999876655554432        35678999987

>3kl4_A SRP54, signal recognition 54 kDa protein; signal recognition particle, SRP, SRP54, FFH, signal sequenc peptide; 3.50A {Sulfolobus solfataricus} PDB: 1qzx_A 1qzw_A

Probab=96.15  E-value=0.022  Score=64.47  Aligned_cols=130  Identities=16%  Similarity=0.151  Sum_probs=71.6

Q ss_pred             CCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEc-c-CHHHHHHHHHHHHHHHhhcCcEEEEeeCCCChHH
Q 002040          505 RDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMA-P-TRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQ  582 (976)
Q Consensus       505 ~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~-P-tr~La~Q~~~~~~~~~~~~~~~~~~~~gg~~~~~  582 (976)
                      .-++++|++|+|||+++...+ .++..       .|.+|++++ + .+.-+   +..+..++...++.+.....+..   
T Consensus        98 ~vI~lvG~~GsGKTTt~~kLA-~~l~~-------~G~kVllv~~D~~r~~a---~eqL~~~~~~~gv~~~~~~~~~d---  163 (433)
T 3kl4_A           98 FIIMLVGVQGSGKTTTAGKLA-YFYKK-------RGYKVGLVAADVYRPAA---YDQLLQLGNQIGVQVYGEPNNQN---  163 (433)
T ss_dssp             EEEEECCCTTSCHHHHHHHHH-HHHHH-------TTCCEEEEEECCSCHHH---HHHHHHHHHTTTCCEECCTTCSC---
T ss_pred             eEEEEECCCCCCHHHHHHHHH-HHHHH-------cCCeEEEEecCccchhH---HHHHHHHHHhcCCceeeccccCC---
Confidence            347777999999998744333 33332       244555544 3 33333   24455555556665543322221   


Q ss_pred             HHHHHhcCCeEEEeCchhHH-HHHHhcCCcccccCCceEEEecCccccc---ccCCchHHHHHHHhcCCCCcEEEEeccC
Q 002040          583 QISELKRGTEIVVCTPGRMI-DILCTSGGKITNLRRVTYLVMDEADRMF---DMGFEPQITRIVQNIRPDRQTVLFSATF  658 (976)
Q Consensus       583 ~~~~l~~~~~Iiv~Tp~~L~-~~l~~~~~~~~~l~~~~~vVlDEah~~~---~~~f~~~i~~il~~~~~~~q~i~~SAT~  658 (976)
                                     |..+. ..+..     .....+++||||.+-++.   +..+...+..++..+.++.-+++++|+.
T Consensus       164 ---------------p~~i~~~al~~-----a~~~~~DvvIIDTaGr~~~~~d~~lm~el~~i~~~~~pd~vlLVlDa~~  223 (433)
T 3kl4_A          164 ---------------PIEIAKKGVDI-----FVKNKMDIIIVDTAGRHGYGEETKLLEEMKEMYDVLKPDDVILVIDASI  223 (433)
T ss_dssp             ---------------HHHHHHHHHHH-----TTTTTCSEEEEEECCCSSSCCTTHHHHHHHHHHHHHCCSEEEEEEEGGG
T ss_pred             ---------------HHHHHHHHHHH-----HHhcCCCEEEEECCCCccccCCHHHHHHHHHHHHhhCCcceEEEEeCcc
Confidence                           11111 12211     123468999999998643   2334556666777777777778888886


Q ss_pred             cHHHHHHHHH
Q 002040          659 PRQVEILARK  668 (976)
Q Consensus       659 ~~~~~~l~~~  668 (976)
                      .......+..
T Consensus       224 gq~a~~~a~~  233 (433)
T 3kl4_A          224 GQKAYDLASR  233 (433)
T ss_dssp             GGGGHHHHHH
T ss_pred             chHHHHHHHH
Confidence            5444444433

>2j9r_A Thymidine kinase; TK1, DNK, lasso, transferase, ATP-binding, deoxyribonucleoside kinase, DNA synthesis, phosphate accept nucleotide-binding; HET: THM; 2.7A {Bacillus anthracis} PDB: 2ja1_A*

Probab=96.04  E-value=0.0098  Score=60.30  Aligned_cols=39  Identities=15%  Similarity=0.101  Sum_probs=28.3

Q ss_pred             CCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCH
Q 002040          504 GRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTR  550 (976)
Q Consensus       504 g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr  550 (976)
                      |+-.++.|++|+|||+.++-.+.++..        .+.+|+|+.|..
T Consensus        28 G~l~vitG~MgsGKTT~lL~~a~r~~~--------~g~kVli~k~~~   66 (214)
T 2j9r_A           28 GWIEVICGSMFSGKSEELIRRVRRTQF--------AKQHAIVFKPCI   66 (214)
T ss_dssp             CEEEEEECSTTSCHHHHHHHHHHHHHH--------TTCCEEEEECC-
T ss_pred             CEEEEEECCCCCcHHHHHHHHHHHHHH--------CCCEEEEEEecc
Confidence            344568899999999886666665543        356799999874

>2b8t_A Thymidine kinase; deoxyribonucleoside kinase, zinc-binding domain, TK1, UU-TK, transferase; HET: THM; 2.00A {Ureaplasma parvum} SCOP: c.37.1.24 g.39.1.14 PDB: 2uz3_A*

Probab=96.00  E-value=0.018  Score=59.15  Aligned_cols=40  Identities=18%  Similarity=0.052  Sum_probs=27.8

Q ss_pred             cCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCH
Q 002040          503 SGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTR  550 (976)
Q Consensus       503 ~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr  550 (976)
                      .|.-+++.|++|+|||++++-.+.....        .+.+|+|+.|..
T Consensus        11 ~G~i~litG~mGsGKTT~ll~~~~r~~~--------~g~kVli~~~~~   50 (223)
T 2b8t_A           11 IGWIEFITGPMFAGKTAELIRRLHRLEY--------ADVKYLVFKPKI   50 (223)
T ss_dssp             CCEEEEEECSTTSCHHHHHHHHHHHHHH--------TTCCEEEEEECC
T ss_pred             CcEEEEEECCCCCcHHHHHHHHHHHHHh--------cCCEEEEEEecc
Confidence            3456788899999999876555554432        255788887753

>3vkw_A Replicase large subunit; alpha/beta domain, helicase, transferase; 1.90A {Tomato mosaic virus}

Probab=95.74  E-value=0.0089  Score=67.49  Aligned_cols=107  Identities=21%  Similarity=0.215  Sum_probs=60.1

Q ss_pred             CEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHHHHhhcCcEEEEeeCCCChHHHHH
Q 002040          506 DCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQIS  585 (976)
Q Consensus       506 d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~~~~~~~~~~~~~~gg~~~~~~~~  585 (976)
                      -.++.|+.|+|||..+. .++    .        ....+|++||++++..|.+.+...    +.                
T Consensus       163 v~~I~G~aGsGKTt~I~-~~~----~--------~~~~lVlTpT~~aa~~l~~kl~~~----~~----------------  209 (446)
T 3vkw_A          163 VVLVDGVPGCGKTKEIL-SRV----N--------FEEDLILVPGRQAAEMIRRRANAS----GI----------------  209 (446)
T ss_dssp             EEEEEECTTSCHHHHHH-HHC----C--------TTTCEEEESCHHHHHHHHHHHTTT----SC----------------
T ss_pred             EEEEEcCCCCCHHHHHH-HHh----c--------cCCeEEEeCCHHHHHHHHHHhhhc----Cc----------------
Confidence            36788999999998632 221    1        024599999999998776665321    10                


Q ss_pred             HHhcCCeEEEeCchhHHHHHHhcCCcccccCCceEEEecCcccccccCCchHHHHHHHhcCCCCcEEEEecc
Q 002040          586 ELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMGFEPQITRIVQNIRPDRQTVLFSAT  657 (976)
Q Consensus       586 ~l~~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDEah~~~~~~f~~~i~~il~~~~~~~q~i~~SAT  657 (976)
                        .....+-|.|...++.   +.. . .....+++||||||- |++.+   .+..++..+++ .++|++.-+
T Consensus       210 --~~~~~~~V~T~dsfL~---~~~-~-~~~~~~d~liiDE~s-m~~~~---~l~~l~~~~~~-~~vilvGD~  269 (446)
T 3vkw_A          210 --IVATKDNVRTVDSFLM---NYG-K-GARCQFKRLFIDEGL-MLHTG---CVNFLVEMSLC-DIAYVYGDT  269 (446)
T ss_dssp             --CCCCTTTEEEHHHHHH---TTT-S-SCCCCCSEEEEETGG-GSCHH---HHHHHHHHTTC-SEEEEEECT
T ss_pred             --cccccceEEEeHHhhc---CCC-C-CCCCcCCEEEEeCcc-cCCHH---HHHHHHHhCCC-CEEEEecCc
Confidence              0112334677665432   111 1 111247899999998 44333   33334444433 555555544

>3e2i_A Thymidine kinase; Zn-binding, ATP-binding, DNA synthesis, nucleotide-B transferase; HET: MSE; 2.01A {Staphylococcus aureus}

Probab=95.73  E-value=0.012  Score=59.66  Aligned_cols=40  Identities=20%  Similarity=0.114  Sum_probs=27.8

Q ss_pred             cCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCH
Q 002040          503 SGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTR  550 (976)
Q Consensus       503 ~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr  550 (976)
                      .|.-.++.|++|+|||+.++-.+.+...        .+.+++|+.|..
T Consensus        27 ~G~I~vitG~M~sGKTT~Llr~~~r~~~--------~g~kvli~kp~~   66 (219)
T 3e2i_A           27 SGWIECITGSMFSGKSEELIRRLRRGIY--------AKQKVVVFKPAI   66 (219)
T ss_dssp             CCEEEEEEECTTSCHHHHHHHHHHHHHH--------TTCCEEEEEEC-
T ss_pred             CceEEEEECCCCCCHHHHHHHHHHHHHH--------cCCceEEEEecc
Confidence            3556788899999999875555544432        256789999964

>3dm5_A SRP54, signal recognition 54 kDa protein; protein-RNA, signal recognition particle, SRP-GTPase, protein targeting, cytoplasm, GTP-binding; HET: GDP; 2.51A {Pyrococcus furiosus}

Probab=95.66  E-value=0.056  Score=61.15  Aligned_cols=129  Identities=16%  Similarity=0.121  Sum_probs=68.6

Q ss_pred             CEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEc--cCHHHHHHHHHHHHHHHhhcCcEEEEeeCCCChHHH
Q 002040          506 DCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMA--PTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQ  583 (976)
Q Consensus       506 d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~--Ptr~La~Q~~~~~~~~~~~~~~~~~~~~gg~~~~~~  583 (976)
                      -++++|++|+|||+++.- +..++..       .|.+|++++  |.+.-+   +..+..++...++.+.....+......
T Consensus       102 vIlivG~~G~GKTTt~~k-LA~~l~~-------~G~kVllv~~D~~R~aa---~eqL~~~~~~~gvpv~~~~~~~dp~~i  170 (443)
T 3dm5_A          102 ILLMVGIQGSGKTTTVAK-LARYFQK-------RGYKVGVVCSDTWRPGA---YHQLRQLLDRYHIEVFGNPQEKDAIKL  170 (443)
T ss_dssp             EEEEECCTTSSHHHHHHH-HHHHHHT-------TTCCEEEEECCCSSTHH---HHHHHHHHGGGTCEEECCTTCCCHHHH
T ss_pred             EEEEECcCCCCHHHHHHH-HHHHHHH-------CCCeEEEEeCCCcchhH---HHHHHHHHHhcCCcEEecCCCCCHHHH
Confidence            478889999999987443 3333333       244566555  444443   345556666677766544333221111


Q ss_pred             HHHHhcCCeEEEeCchhHHHHHHhcCCcccccCCceEEEecCccccccc-CCchHHHHHHHhcCCCCcEEEEeccCcHHH
Q 002040          584 ISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDM-GFEPQITRIVQNIRPDRQTVLFSATFPRQV  662 (976)
Q Consensus       584 ~~~l~~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDEah~~~~~-~f~~~i~~il~~~~~~~q~i~~SAT~~~~~  662 (976)
                                       +...+..     .....+++||||.+=++... .....+..+.....++.-++++.||.....
T Consensus       171 -----------------~~~al~~-----a~~~~~DvVIIDTaGrl~~d~~lm~el~~i~~~~~pd~vlLVvDA~~gq~a  228 (443)
T 3dm5_A          171 -----------------AKEGVDY-----FKSKGVDIIIVDTAGRHKEDKALIEEMKQISNVIHPHEVILVIDGTIGQQA  228 (443)
T ss_dssp             -----------------HHHHHHH-----HHHTTCSEEEEECCCCSSCCHHHHHHHHHHHHHHCCSEEEEEEEGGGGGGH
T ss_pred             -----------------HHHHHHH-----HHhCCCCEEEEECCCcccchHHHHHHHHHHHHhhcCceEEEEEeCCCchhH
Confidence                             0111111     11124788999988643211 122334455556667766777888865444


Q ss_pred             HHHHH
Q 002040          663 EILAR  667 (976)
Q Consensus       663 ~~l~~  667 (976)
                      ...+.
T Consensus       229 ~~~a~  233 (443)
T 3dm5_A          229 YNQAL  233 (443)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            33333

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

Probab=95.64  E-value=0.061  Score=58.31  Aligned_cols=27  Identities=11%  Similarity=-0.038  Sum_probs=20.0

Q ss_pred             CCCEEEEcCCCCchHHHHHHHHHHHHhc
Q 002040          504 GRDCIGVAKTGSGKTLAFVLPMLRHIKD  531 (976)
Q Consensus       504 g~d~i~~a~TGsGKT~~~~l~il~~l~~  531 (976)
                      +.++++.|++|+|||++ +-.++..+..
T Consensus        45 ~~~lli~GpPGTGKT~~-v~~v~~~L~~   71 (318)
T 3te6_A           45 NKLFYITNADDSTKFQL-VNDVMDELIT   71 (318)
T ss_dssp             CCEEEEECCCSHHHHHH-HHHHHHHHHH
T ss_pred             CCeEEEECCCCCCHHHH-HHHHHHHHHH
Confidence            45799999999999976 4455555543

>1w4r_A Thymidine kinase; type II, human, cytosolic, phosphorylation, transferase; HET: TTP; 1.83A {Homo sapiens} PDB: 1xbt_A* 2wvj_A* 2j87_A*

Probab=95.61  E-value=0.021  Score=56.99  Aligned_cols=39  Identities=15%  Similarity=0.066  Sum_probs=28.3

Q ss_pred             cCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccC
Q 002040          503 SGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPT  549 (976)
Q Consensus       503 ~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Pt  549 (976)
                      .++=.++.|++|||||+..+-.+-++...        +.+++|+.|.
T Consensus        19 ~g~l~fiyG~MgsGKTt~Ll~~i~n~~~~--------~~kvl~~kp~   57 (195)
T 1w4r_A           19 RGQIQVILGPMFSGKSTELMRRVRRFQIA--------QYKCLVIKYA   57 (195)
T ss_dssp             CCEEEEEEECTTSCHHHHHHHHHHHHHHT--------TCCEEEEEET
T ss_pred             ceEEEEEECCCCCcHHHHHHHHHHHHHHc--------CCeEEEEccc
Confidence            35667888999999997655555555443        4578999886

>2kjq_A DNAA-related protein; solution structure, NESG, structural genomics, PSI-2, protei structure initiative; NMR {Neisseria meningitidis serogroup B}

Probab=95.60  E-value=0.0081  Score=57.68  Aligned_cols=18  Identities=22%  Similarity=0.246  Sum_probs=16.1

Q ss_pred             cCCCEEEEcCCCCchHHH
Q 002040          503 SGRDCIGVAKTGSGKTLA  520 (976)
Q Consensus       503 ~g~d~i~~a~TGsGKT~~  520 (976)
                      .+..++++|++|+|||..
T Consensus        35 ~g~~~~l~G~~G~GKTtL   52 (149)
T 2kjq_A           35 HGQFIYVWGEEGAGKSHL   52 (149)
T ss_dssp             CCSEEEEESSSTTTTCHH
T ss_pred             CCCEEEEECCCCCCHHHH
Confidence            578899999999999975

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

Probab=95.53  E-value=0.084  Score=53.01  Aligned_cols=25  Identities=16%  Similarity=0.199  Sum_probs=18.5

Q ss_pred             CCEEEEcCCCCchHHHHHHHHHHHHh
Q 002040          505 RDCIGVAKTGSGKTLAFVLPMLRHIK  530 (976)
Q Consensus       505 ~d~i~~a~TGsGKT~~~~l~il~~l~  530 (976)
                      ..++++|++|+|||..+ ..+...+.
T Consensus        55 ~~~~l~G~~GtGKT~la-~~i~~~~~   79 (202)
T 2w58_A           55 KGLYLHGSFGVGKTYLL-AAIANELA   79 (202)
T ss_dssp             CEEEEECSTTSSHHHHH-HHHHHHHH
T ss_pred             CeEEEECCCCCCHHHHH-HHHHHHHH
Confidence            68999999999999863 34444443

>2qgz_A Helicase loader, putative primosome component; structural genomics, PSI-2, protein structure initiative; 2.40A {Streptococcus pyogenes serotype M3}

Probab=95.52  E-value=0.045  Score=59.33  Aligned_cols=19  Identities=16%  Similarity=0.204  Sum_probs=16.3

Q ss_pred             CCCEEEEcCCCCchHHHHH
Q 002040          504 GRDCIGVAKTGSGKTLAFV  522 (976)
Q Consensus       504 g~d~i~~a~TGsGKT~~~~  522 (976)
                      +.+++++|++|+|||..+.
T Consensus       152 ~~~lll~G~~GtGKT~La~  170 (308)
T 2qgz_A          152 QKGLYLYGDMGIGKSYLLA  170 (308)
T ss_dssp             CCEEEEECSTTSSHHHHHH
T ss_pred             CceEEEECCCCCCHHHHHH
Confidence            5789999999999997644

>2orv_A Thymidine kinase; TP4A (P1-(5'-adenosyl)P4-(5'- (2'deoxythymidil))tetraphosphate, transferase; HET: 4TA; 2.30A {Homo sapiens} SCOP: c.37.1.24 g.39.1.14

Probab=95.51  E-value=0.046  Score=55.91  Aligned_cols=40  Identities=15%  Similarity=0.087  Sum_probs=30.0

Q ss_pred             cCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCH
Q 002040          503 SGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTR  550 (976)
Q Consensus       503 ~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr  550 (976)
                      .|+-.++.|++|+|||+.++-.+.++..        .|.+++|+.|..
T Consensus        18 ~g~l~v~~G~MgsGKTT~lL~~~~r~~~--------~g~kvli~kp~~   57 (234)
T 2orv_A           18 RGQIQVILGPMFSGKSTELMRRVRRFQI--------AQYKCLVIKYAK   57 (234)
T ss_dssp             CCEEEEEECCTTSCHHHHHHHHHHHHHT--------TTCCEEEEEETT
T ss_pred             ceEEEEEECCCCCcHHHHHHHHHHHHHH--------CCCeEEEEeecC
Confidence            4566788899999999886666665533        366789998864

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

Probab=95.49  E-value=0.024  Score=55.76  Aligned_cols=25  Identities=24%  Similarity=0.230  Sum_probs=18.0

Q ss_pred             CCCEEEEcCCCCchHHHHHHHHHHHH
Q 002040          504 GRDCIGVAKTGSGKTLAFVLPMLRHI  529 (976)
Q Consensus       504 g~d~i~~a~TGsGKT~~~~l~il~~l  529 (976)
                      ...++++|++|+|||..+. .+...+
T Consensus        43 ~~~vll~G~~G~GKT~la~-~~~~~~   67 (187)
T 2p65_A           43 KNNPILLGDPGVGKTAIVE-GLAIKI   67 (187)
T ss_dssp             SCEEEEESCGGGCHHHHHH-HHHHHH
T ss_pred             CCceEEECCCCCCHHHHHH-HHHHHH
Confidence            4579999999999997633 334443

>1l8q_A Chromosomal replication initiator protein DNAA; AAA+, helix-turn-helix, nucleotide-binding, DNA binding, REP initiation, DNA binding protein; HET: ADP; 2.70A {Aquifex aeolicus} SCOP: a.4.12.2 c.37.1.20 PDB: 3r8f_A* 2hcb_A*

Probab=95.45  E-value=0.047  Score=59.58  Aligned_cols=25  Identities=16%  Similarity=0.046  Sum_probs=18.2

Q ss_pred             CCCEEEEcCCCCchHHHHHHHHHHHH
Q 002040          504 GRDCIGVAKTGSGKTLAFVLPMLRHI  529 (976)
Q Consensus       504 g~d~i~~a~TGsGKT~~~~l~il~~l  529 (976)
                      +..++++||+|+|||..+ -.+...+
T Consensus        37 ~~~lll~G~~GtGKT~la-~~i~~~~   61 (324)
T 1l8q_A           37 YNPIFIYGSVGTGKTHLL-QAAGNEA   61 (324)
T ss_dssp             CSSEEEECSSSSSHHHHH-HHHHHHH
T ss_pred             CCeEEEECCCCCcHHHHH-HHHHHHH
Confidence            468999999999999753 3344444

>2zpa_A Uncharacterized protein YPFI; RNA modification enzyme, RNA helicase, acetyltransferase, GCN5 acetyltransferase; HET: ACO ADP; 2.35A {Escherichia coli K12}

Probab=95.36  E-value=0.023  Score=67.39  Aligned_cols=113  Identities=22%  Similarity=0.336  Sum_probs=74.3

Q ss_pred             CCcHHHHHHHHHHhc--CCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHHHHhh
Q 002040          489 KPMPIQAQALPVIMS--GRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKV  566 (976)
Q Consensus       489 ~p~~~Q~~~i~~il~--g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~~~~~  566 (976)
                      .+|..|.+++..++.  ....++.|+-|.|||.+..+.+. .+..          .++|.+|+..-+..+.    .|+..
T Consensus       175 ~~T~dQ~~al~~~~~~~~~~~vlta~RGRGKSa~lG~~~a-~~~~----------~~~vtAP~~~a~~~l~----~~~~~  239 (671)
T 2zpa_A          175 APQPEQQQLLKQLMTMPPGVAAVTAARGRGKSALAGQLIS-RIAG----------RAIVTAPAKASTDVLA----QFAGE  239 (671)
T ss_dssp             SCCHHHHHHHHHHTTCCSEEEEEEECTTSSHHHHHHHHHH-HSSS----------CEEEECSSCCSCHHHH----HHHGG
T ss_pred             CCCHHHHHHHHHHHHhhhCeEEEecCCCCCHHHHHHHHHH-HHHh----------CcEEECCCHHHHHHHH----HHhhC
Confidence            689999999998886  33478889999999976554443 2221          3699999987665332    22211


Q ss_pred             cCcEEEEeeCCCChHHHHHHHhcCCeEEEeCchhHHHHHHhcCCcccccCCceEEEecCcccccccCCchHHHHHHHhcC
Q 002040          567 MGVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMGFEPQITRIVQNIR  646 (976)
Q Consensus       567 ~~~~~~~~~gg~~~~~~~~~l~~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDEah~~~~~~f~~~i~~il~~~~  646 (976)
                                               .|-+..|..+..          .+..+++||||||=.+.    .+.+..++... 
T Consensus       240 -------------------------~i~~~~Pd~~~~----------~~~~~dlliVDEAAaIp----~pll~~ll~~~-  279 (671)
T 2zpa_A          240 -------------------------KFRFIAPDALLA----------SDEQADWLVVDEAAAIP----APLLHQLVSRF-  279 (671)
T ss_dssp             -------------------------GCCBCCHHHHHH----------SCCCCSEEEEETGGGSC----HHHHHHHHTTS-
T ss_pred             -------------------------CeEEeCchhhhh----------CcccCCEEEEEchhcCC----HHHHHHHHhhC-
Confidence                                     144556654321          23458999999998653    55666666533 


Q ss_pred             CCCcEEEEeccCc
Q 002040          647 PDRQTVLFSATFP  659 (976)
Q Consensus       647 ~~~q~i~~SAT~~  659 (976)
                         ..|+||.|+.
T Consensus       280 ---~~v~~~tTv~  289 (671)
T 2zpa_A          280 ---PRTLLTTTVQ  289 (671)
T ss_dssp             ---SEEEEEEEBS
T ss_pred             ---CeEEEEecCC
Confidence               3588888864

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

Probab=95.21  E-value=0.22  Score=48.75  Aligned_cols=25  Identities=20%  Similarity=0.284  Sum_probs=18.0

Q ss_pred             CCCEEEEcCCCCchHHHHHHHHHHHH
Q 002040          504 GRDCIGVAKTGSGKTLAFVLPMLRHI  529 (976)
Q Consensus       504 g~d~i~~a~TGsGKT~~~~l~il~~l  529 (976)
                      ...++++|++|+|||..+ ..+...+
T Consensus        43 ~~~~ll~G~~G~GKT~l~-~~~~~~~   67 (195)
T 1jbk_A           43 KNNPVLIGEPGVGKTAIV-EGLAQRI   67 (195)
T ss_dssp             SCEEEEECCTTSCHHHHH-HHHHHHH
T ss_pred             CCceEEECCCCCCHHHHH-HHHHHHH
Confidence            357999999999999763 3344444

>3u4q_A ATP-dependent helicase/nuclease subunit A; helicase, nuclease, double strand DNA repair, protein-DNA CO hydrolase-DNA complex; HET: DNA; 2.80A {Bacillus subtilis} PDB: 3u44_A*

Probab=95.19  E-value=0.035  Score=71.98  Aligned_cols=128  Identities=18%  Similarity=0.112  Sum_probs=79.8

Q ss_pred             CCcHHHHHHHHHHhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHHHHhhcC
Q 002040          489 KPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVMG  568 (976)
Q Consensus       489 ~p~~~Q~~~i~~il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~~~~~~~  568 (976)
                      .+|+-|.++|...  +.+++|.|..|||||.+.+--++..+.....  ......+|+|++|...|..+.+.+...+....
T Consensus        10 ~~t~eQ~~~i~~~--~~~~~v~a~AGSGKT~vl~~ri~~ll~~~~~--~~~~~~il~~Tft~~aa~e~~~ri~~~l~~~~   85 (1232)
T 3u4q_A           10 TWTDDQWNAIVST--GQDILVAAAAGSGKTAVLVERMIRKITAEEN--PIDVDRLLVVTFTNASAAEMKHRIAEALEKEL   85 (1232)
T ss_dssp             CCCHHHHHHHHCC--SSCEEEEECTTCCHHHHHHHHHHHHHSCSSS--CCCGGGEEEECSSHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHhCC--CCCEEEEecCCCcHHHHHHHHHHHHHhcCCC--CCCccceEEEeccHHHHHHHHHHHHHHHHHHh
Confidence            5789999998753  7899999999999999877667776665311  11234799999999999999988877543210


Q ss_pred             cEEEEeeCCCChHHHHHHHhcCCeEEEeCchhHHHHHHhcCCcccccCCceEEEecCcc
Q 002040          569 VRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEAD  627 (976)
Q Consensus       569 ~~~~~~~gg~~~~~~~~~l~~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDEah  627 (976)
                      ..     .... ......+..-..+-|+|...|...+.........+. -.+-|+|+..
T Consensus        86 ~~-----~~~~-~~~~~~~~~~~~~~i~T~hsf~~~~l~~~~~~~~~~-~~f~~~d~~~  137 (1232)
T 3u4q_A           86 VQ-----RPGS-LHIRRQLSLLNRASISTLHSFCLQVLKKYYYLIDLD-PGFRIADQTE  137 (1232)
T ss_dssp             HH-----STTC-HHHHHHHHHTTTSEEECHHHHHHHHHHHHGGGTTCC-TTCEECCHHH
T ss_pred             hc-----Ccch-HHHHHHHhccCCCeEEeHHHHHHHHHHhhHHhcCCC-CCCeeCCHHH
Confidence            00     0111 111111222245688998888665554322222222 1233778765

>1d2n_A N-ethylmaleimide-sensitive fusion protein; hexamerization domain, ATPase, transport; HET: ANP; 1.75A {Cricetulus griseus} SCOP: c.37.1.20 PDB: 1nsf_A*

Probab=94.90  E-value=0.19  Score=53.16  Aligned_cols=18  Identities=22%  Similarity=0.067  Sum_probs=15.1

Q ss_pred             CCEEEEcCCCCchHHHHH
Q 002040          505 RDCIGVAKTGSGKTLAFV  522 (976)
Q Consensus       505 ~d~i~~a~TGsGKT~~~~  522 (976)
                      ..++++||+|+|||..+.
T Consensus        65 ~~vLl~G~~GtGKT~la~   82 (272)
T 1d2n_A           65 VSVLLEGPPHSGKTALAA   82 (272)
T ss_dssp             EEEEEECSTTSSHHHHHH
T ss_pred             eEEEEECCCCCcHHHHHH
Confidence            469999999999998643

>4b4t_M 26S protease regulatory subunit 6A; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=94.86  E-value=0.018  Score=65.08  Aligned_cols=55  Identities=22%  Similarity=0.366  Sum_probs=35.8

Q ss_pred             CCcccccccCCCCHHHHHHHHH---cCCCCCcHHHHHHHHHHhcCCCEEEEcCCCCchHHH
Q 002040          463 PKPIKTWHQTGLTSKIMETIRK---LNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLA  520 (976)
Q Consensus       463 p~pi~~~~~~~l~~~l~~~l~~---~~~~~p~~~Q~~~i~~il~g~d~i~~a~TGsGKT~~  520 (976)
                      ..|-.+|.+.+-...+.+.|..   +.+..|.-++...++   -.+.+|+.||+|+|||+.
T Consensus       174 ~~p~~t~~digGl~~~k~~l~e~v~~pl~~pe~f~~~g~~---~prGvLLyGPPGTGKTll  231 (434)
T 4b4t_M          174 EKPTETYSDVGGLDKQIEELVEAIVLPMKRADKFKDMGIR---APKGALMYGPPGTGKTLL  231 (434)
T ss_dssp             SSCSCCGGGSCSCHHHHHHHHHHTHHHHHCSHHHHHHCCC---CCCEEEEESCTTSSHHHH
T ss_pred             CCCCCChHhcCcHHHHHHHHHHHHHHHHhCHHHHHhCCCC---CCCeeEEECcCCCCHHHH
Confidence            4567889999888777776653   222233333222211   246899999999999975

>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=94.77  E-value=0.059  Score=59.17  Aligned_cols=39  Identities=18%  Similarity=0.249  Sum_probs=25.8

Q ss_pred             cHHHHHHHHHHh----cCC---CEEEEcCCCCchHHHHHHHHHHHHh
Q 002040          491 MPIQAQALPVIM----SGR---DCIGVAKTGSGKTLAFVLPMLRHIK  530 (976)
Q Consensus       491 ~~~Q~~~i~~il----~g~---d~i~~a~TGsGKT~~~~l~il~~l~  530 (976)
                      +|+|..++..+.    +|+   .+|+.||.|+|||..+. .+...+.
T Consensus         4 ~pw~~~~~~~l~~~i~~~~~~~a~L~~G~~G~GKt~~a~-~la~~l~   49 (334)
T 1a5t_A            4 YPWLRPDFEKLVASYQAGRGHHALLIQALPGMGDDALIY-ALSRYLL   49 (334)
T ss_dssp             CGGGHHHHHHHHHHHHTTCCCSEEEEECCTTSCHHHHHH-HHHHHHT
T ss_pred             CCchHHHHHHHHHHHHcCCcceeEEEECCCCchHHHHHH-HHHHHHh
Confidence            467776665543    443   38999999999997644 4444443

>3h4m_A Proteasome-activating nucleotidase; ATPase, PAN, ATP-binding, nucleotide-binding, HY; HET: ADP; 3.11A {Methanocaldococcus jannaschii}

Probab=94.76  E-value=0.021  Score=61.00  Aligned_cols=55  Identities=22%  Similarity=0.369  Sum_probs=31.2

Q ss_pred             CcccccccCCCCHHHHHHHHHcCCCCCcHHH-HHHHHHH--hcCCCEEEEcCCCCchHHHH
Q 002040          464 KPIKTWHQTGLTSKIMETIRKLNYEKPMPIQ-AQALPVI--MSGRDCIGVAKTGSGKTLAF  521 (976)
Q Consensus       464 ~pi~~~~~~~l~~~l~~~l~~~~~~~p~~~Q-~~~i~~i--l~g~d~i~~a~TGsGKT~~~  521 (976)
                      .|-.+|.++.-....+..|...-.   .+.+ .+.+..+  .....+++.||+|+|||+.+
T Consensus        11 ~~~~~~~~i~G~~~~~~~l~~~~~---~~~~~~~~~~~~~~~~~~~~ll~G~~GtGKT~la   68 (285)
T 3h4m_A           11 RPNVRYEDIGGLEKQMQEIREVVE---LPLKHPELFEKVGIEPPKGILLYGPPGTGKTLLA   68 (285)
T ss_dssp             SCCCCGGGSCSCHHHHHHHHHHTH---HHHHCHHHHHHHCCCCCSEEEEESSSSSSHHHHH
T ss_pred             CCCCCHHHhcCHHHHHHHHHHHHH---HHhhCHHHHHhcCCCCCCeEEEECCCCCcHHHHH
Confidence            344568887766666665543210   0110 1111111  24567999999999999753

>2z4s_A Chromosomal replication initiator protein DNAA; AAA+ ATPase, domain III (ATPase domain), ATP-binding, cytoplasm, DNA replication; HET: ADP; 3.00A {Thermotoga maritima} PDB: 2z4r_A*

Probab=94.73  E-value=0.099  Score=59.69  Aligned_cols=18  Identities=22%  Similarity=0.087  Sum_probs=15.5

Q ss_pred             CCCEEEEcCCCCchHHHH
Q 002040          504 GRDCIGVAKTGSGKTLAF  521 (976)
Q Consensus       504 g~d~i~~a~TGsGKT~~~  521 (976)
                      +..+++.|++|+|||..+
T Consensus       130 ~~~lll~Gp~G~GKTtLa  147 (440)
T 2z4s_A          130 YNPLFIYGGVGLGKTHLL  147 (440)
T ss_dssp             SCCEEEECSSSSSHHHHH
T ss_pred             CCeEEEECCCCCCHHHHH
Confidence            467999999999999763

>4b4t_J 26S protease regulatory subunit 8 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=94.63  E-value=0.027  Score=62.77  Aligned_cols=53  Identities=23%  Similarity=0.365  Sum_probs=31.8

Q ss_pred             cccccccCCCCHHHHHHHHHc---CCCCCcHHHHHHHHHHhcCCCEEEEcCCCCchHHH
Q 002040          465 PIKTWHQTGLTSKIMETIRKL---NYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLA  520 (976)
Q Consensus       465 pi~~~~~~~l~~~l~~~l~~~---~~~~p~~~Q~~~i~~il~g~d~i~~a~TGsGKT~~  520 (976)
                      |-.+|.+.|--....+.|...   .+..|--++.-.+   .-.+.+|+.||+|+|||+.
T Consensus       143 p~v~~~dIgGl~~~k~~l~e~v~~Pl~~pe~f~~~gi---~~prGvLL~GPPGTGKTll  198 (405)
T 4b4t_J          143 PDSTYDMVGGLTKQIKEIKEVIELPVKHPELFESLGI---AQPKGVILYGPPGTGKTLL  198 (405)
T ss_dssp             CSCCGGGSCSCHHHHHHHHHHTHHHHHCHHHHHHHTC---CCCCCEEEESCSSSSHHHH
T ss_pred             CCCCHHHhCCHHHHHHHHHHHHHHHHhCHHHHHhCCC---CCCCceEEeCCCCCCHHHH
Confidence            457888887666666655531   1222222221111   1247899999999999975

>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=94.54  E-value=0.098  Score=63.92  Aligned_cols=94  Identities=18%  Similarity=0.230  Sum_probs=72.2

Q ss_pred             chHHH-HHHHHHHhhhcCCcEEEEecCHHHHHHHHHHHHHC----CCCceeccCCCCHHHHHHHHHHhccCCccEEEecC
Q 002040          698 SDRFL-RLLELLGEWYEKGKILIFVHSQEKCDALFRDLLKH----GYPCLSLHGAKDQTDRESTISDFKSNVCNLLIATS  772 (976)
Q Consensus       698 ~~k~~-~l~~~l~~~~~~~kvLIF~~s~~~~~~l~~~L~~~----~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLVaT~  772 (976)
                      +.|-. .++-++.....+.++||.+|+..-+..++..|...    ++.+..+||+++..++..++..+.+|.++|||+|.
T Consensus       400 SGKTlvall~il~~l~~g~qvlvlaPtr~La~Q~~~~l~~~~~~~gi~v~~l~G~~~~~~r~~~~~~l~~g~~~IvVgT~  479 (780)
T 1gm5_A          400 SGKTVVAQLAILDNYEAGFQTAFMVPTSILAIQHYRRTVESFSKFNIHVALLIGATTPSEKEKIKSGLRNGQIDVVIGTH  479 (780)
T ss_dssp             SSHHHHHHHHHHHHHHHTSCEEEECSCHHHHHHHHHHHHHHHTCSSCCEEECCSSSCHHHHHHHHHHHHSSCCCEEEECT
T ss_pred             CCHHHHHHHHHHHHHHcCCeEEEEeCcHHHHHHHHHHHHHHhhhcCceEEEEeCCCCHHHHHHHHHHHhcCCCCEEEECH
Confidence            44433 33333333335679999999999888887777653    79999999999999999999999999999999997


Q ss_pred             c-ccccCCCCCCcEEEEeCC
Q 002040          773 V-AARGLDVKELELVINFDA  791 (976)
Q Consensus       773 v-~~~GlDi~~v~~VI~~d~  791 (976)
                      . +...+.+.++.+||.=..
T Consensus       480 ~ll~~~~~~~~l~lVVIDEa  499 (780)
T 1gm5_A          480 ALIQEDVHFKNLGLVIIDEQ  499 (780)
T ss_dssp             THHHHCCCCSCCCEEEEESC
T ss_pred             HHHhhhhhccCCceEEeccc
Confidence            3 345678888988885333

>1g5t_A COB(I)alamin adenosyltransferase; P-loop protein, cobalamin biosynthesis, RECA fold; HET: ATP; 1.80A {Salmonella typhimurium} SCOP: c.37.1.11 PDB: 1g5r_A* 1g64_A*

Probab=94.50  E-value=0.26  Score=49.08  Aligned_cols=137  Identities=13%  Similarity=0.057  Sum_probs=71.9

Q ss_pred             CCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHHHHhhcCcEEEEeeCCCC----
Q 002040          504 GRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSG----  579 (976)
Q Consensus       504 g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~~~~~~~~~~~~~~gg~~----  579 (976)
                      ...+++...+|.|||.+++-.++..+-        .|.+|+|+.-...-  .-+.+. .++..+++.+..+--|-.    
T Consensus        28 ~g~i~v~tG~GkGKTTaA~GlalRA~g--------~G~rV~~vQF~Kg~--~~~gE~-~~l~~L~v~~~~~g~gf~~~~~   96 (196)
T 1g5t_A           28 RGIIIVFTGNGKGKTTAAFGTAARAVG--------HGKNVGVVQFIKGT--WPNGER-NLLEPHGVEFQVMATGFTWETQ   96 (196)
T ss_dssp             CCCEEEEESSSSCHHHHHHHHHHHHHH--------TTCCEEEEESSCCS--SCCHHH-HHHGGGTCEEEECCTTCCCCGG
T ss_pred             CceEEEECCCCCCHHHHHHHHHHHHHH--------CCCeEEEEEeeCCC--CCccHH-HHHHhCCcEEEEcccccccCCC
Confidence            347888899999999998777776654        36778888322110  000011 111222333332211110    


Q ss_pred             -hHHHHHHHhcCCeEEEeCchhHHHHHHhcCCcccccCCceEEEecCcccccccCCc--hHHHHHHHhcCCCCcEEEEec
Q 002040          580 -VAQQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMGFE--PQITRIVQNIRPDRQTVLFSA  656 (976)
Q Consensus       580 -~~~~~~~l~~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDEah~~~~~~f~--~~i~~il~~~~~~~q~i~~SA  656 (976)
                       ........          -..| ..+..    ...-..+++|||||+-..+..++.  +.+..++...+....+|+++-
T Consensus        97 ~~~~~~~~a----------~~~l-~~a~~----~l~~~~yDlvILDEi~~al~~g~l~~~ev~~~l~~Rp~~~~vIlTGr  161 (196)
T 1g5t_A           97 NREADTAAC----------MAVW-QHGKR----MLADPLLDMVVLDELTYMVAYDYLPLEEVISALNARPGHQTVIITGR  161 (196)
T ss_dssp             GHHHHHHHH----------HHHH-HHHHH----HTTCTTCSEEEEETHHHHHHTTSSCHHHHHHHHHTSCTTCEEEEECS
T ss_pred             CcHHHHHHH----------HHHH-HHHHH----HHhcCCCCEEEEeCCCccccCCCCCHHHHHHHHHhCcCCCEEEEECC
Confidence             00000000          0111 11111    011256899999999866666644  446667776666666777777


Q ss_pred             cCcHHHHHHH
Q 002040          657 TFPRQVEILA  666 (976)
Q Consensus       657 T~~~~~~~l~  666 (976)
                      .+|+.+..++
T Consensus       162 ~ap~~l~e~A  171 (196)
T 1g5t_A          162 GCHRDILDLA  171 (196)
T ss_dssp             SCCHHHHHHC
T ss_pred             CCcHHHHHhC
Confidence            7777765554

>3cf0_A Transitional endoplasmic reticulum ATPase; AAA, P97/VCP, ERAD, CDC48, ATP-binding, lipid-binding, nucle binding, nucleus, phosphoprotein, transport; HET: ADP; 3.00A {Mus musculus}

Probab=94.36  E-value=0.057  Score=58.28  Aligned_cols=54  Identities=20%  Similarity=0.384  Sum_probs=30.3

Q ss_pred             cccccccCCCCHHHHHHHHHcCCCCCcHHHH-HHHHH--HhcCCCEEEEcCCCCchHHHH
Q 002040          465 PIKTWHQTGLTSKIMETIRKLNYEKPMPIQA-QALPV--IMSGRDCIGVAKTGSGKTLAF  521 (976)
Q Consensus       465 pi~~~~~~~l~~~l~~~l~~~~~~~p~~~Q~-~~i~~--il~g~d~i~~a~TGsGKT~~~  521 (976)
                      |-.+|.+++-...+...|...-.   .|+.. +.+..  +..++.+++.||+|+|||+.+
T Consensus        10 ~~~~~~di~G~~~~~~~l~~~v~---~~~~~~~~~~~~~~~~~~~vLL~Gp~GtGKT~la   66 (301)
T 3cf0_A           10 PQVTWEDIGGLEDVKRELQELVQ---YPVEHPDKFLKFGMTPSKGVLFYGPPGCGKTLLA   66 (301)
T ss_dssp             CCCCGGGSCSCHHHHHHHHHHHH---HHHHCHHHHHHHCCCCCSEEEEECSSSSSHHHHH
T ss_pred             CCCCHHHhCCHHHHHHHHHHHHH---HHhhCHHHHHHcCCCCCceEEEECCCCcCHHHHH
Confidence            44678888766666655543100   00000 00011  123567999999999999753

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

Probab=94.22  E-value=0.11  Score=49.35  Aligned_cols=20  Identities=10%  Similarity=0.061  Sum_probs=17.1

Q ss_pred             hcCCCEEEEcCCCCchHHHH
Q 002040          502 MSGRDCIGVAKTGSGKTLAF  521 (976)
Q Consensus       502 l~g~d~i~~a~TGsGKT~~~  521 (976)
                      ..+.++++.|++|+|||+.+
T Consensus        22 ~~~~~vll~G~~GtGKt~lA   41 (145)
T 3n70_A           22 ETDIAVWLYGAPGTGRMTGA   41 (145)
T ss_dssp             TCCSCEEEESSTTSSHHHHH
T ss_pred             CCCCCEEEECCCCCCHHHHH
Confidence            46678999999999999754

>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=93.89  E-value=0.33  Score=48.78  Aligned_cols=40  Identities=15%  Similarity=0.196  Sum_probs=24.1

Q ss_pred             CCceEEEecCcccccccCCchHHHHHHHhcCCCCcEEEEec
Q 002040          616 RRVTYLVMDEADRMFDMGFEPQITRIVQNIRPDRQTVLFSA  656 (976)
Q Consensus       616 ~~~~~vVlDEah~~~~~~f~~~i~~il~~~~~~~q~i~~SA  656 (976)
                      ....+|||||+|.+... ....+..++........+|++|.
T Consensus       101 ~~~~vliiDe~~~l~~~-~~~~l~~~l~~~~~~~~~i~~~~  140 (226)
T 2chg_A          101 APFKIIFLDEADALTAD-AQAALRRTMEMYSKSCRFILSCN  140 (226)
T ss_dssp             CSCEEEEEETGGGSCHH-HHHHHHHHHHHTTTTEEEEEEES
T ss_pred             cCceEEEEeChhhcCHH-HHHHHHHHHHhcCCCCeEEEEeC
Confidence            34679999999986432 23345555555555555555443

>4b4t_L 26S protease subunit RPT4; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=93.86  E-value=0.043  Score=62.10  Aligned_cols=54  Identities=20%  Similarity=0.291  Sum_probs=30.7

Q ss_pred             CcccccccCCCCHHHHHHHHH---cCCCCCcHHHHHHHHHHhcCCCEEEEcCCCCchHHH
Q 002040          464 KPIKTWHQTGLTSKIMETIRK---LNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLA  520 (976)
Q Consensus       464 ~pi~~~~~~~l~~~l~~~l~~---~~~~~p~~~Q~~~i~~il~g~d~i~~a~TGsGKT~~  520 (976)
                      .|-.+|.+.+-.....+.|..   +.+..|--++.-.+   .-.+.+|+.||+|+|||+.
T Consensus       175 ~p~v~~~digGl~~~k~~l~e~v~~pl~~p~~f~~~g~---~~prGvLL~GPPGtGKTll  231 (437)
T 4b4t_L          175 QGEITFDGIGGLTEQIRELREVIELPLKNPEIFQRVGI---KPPKGVLLYGPPGTGKTLL  231 (437)
T ss_dssp             SCSSCSGGGCSCHHHHHHHHHHHHHHHHCHHHHHHHCC---CCCCEEEEESCTTSSHHHH
T ss_pred             CCCCChhHhCChHHHHHHHHHHHHHHHhCHHHHHhCCC---CCCCeEEEECCCCCcHHHH
Confidence            455678888766665555442   11111111111111   1236899999999999975

>2qby_B CDC6 homolog 3, cell division control protein 6 homolog 3; winged-helix domain, helix-turn-helix, AAA+ ATPase domain, protein-DNA complex; HET: DNA SPD ADP; 3.35A {Sulfolobus solfataricus}

Probab=93.84  E-value=0.16  Score=56.51  Aligned_cols=24  Identities=25%  Similarity=0.272  Sum_probs=17.4

Q ss_pred             CCEEEEcCCCCchHHHHHHHHHHHH
Q 002040          505 RDCIGVAKTGSGKTLAFVLPMLRHI  529 (976)
Q Consensus       505 ~d~i~~a~TGsGKT~~~~l~il~~l  529 (976)
                      ..+++.|++|+|||..+ ..+...+
T Consensus        46 ~~vll~G~~G~GKT~la-~~l~~~~   69 (384)
T 2qby_B           46 FSNLFLGLTGTGKTFVS-KYIFNEI   69 (384)
T ss_dssp             CEEEEEECTTSSHHHHH-HHHHHHH
T ss_pred             CcEEEECCCCCCHHHHH-HHHHHHH
Confidence            46999999999999763 3344443

>2v1u_A Cell division control protein 6 homolog; DNA replication, nucleotide-binding, replication, archaea; HET: ADP; 3.10A {Aeropyrum pernix}

Probab=93.83  E-value=0.16  Score=56.47  Aligned_cols=18  Identities=28%  Similarity=0.300  Sum_probs=15.4

Q ss_pred             CCCEEEEcCCCCchHHHH
Q 002040          504 GRDCIGVAKTGSGKTLAF  521 (976)
Q Consensus       504 g~d~i~~a~TGsGKT~~~  521 (976)
                      +..++++||+|+|||..+
T Consensus        44 ~~~vll~G~~G~GKT~l~   61 (387)
T 2v1u_A           44 PSNALLYGLTGTGKTAVA   61 (387)
T ss_dssp             CCCEEECBCTTSSHHHHH
T ss_pred             CCcEEEECCCCCCHHHHH
Confidence            467999999999999763

>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=93.78  E-value=0.089  Score=54.12  Aligned_cols=19  Identities=16%  Similarity=0.006  Sum_probs=16.1

Q ss_pred             cCCCEEEEcCCCCchHHHH
Q 002040          503 SGRDCIGVAKTGSGKTLAF  521 (976)
Q Consensus       503 ~g~d~i~~a~TGsGKT~~~  521 (976)
                      .+..++++|++|+|||..+
T Consensus        51 ~~~~~ll~G~~G~GKT~la   69 (242)
T 3bos_A           51 GVQAIYLWGPVKSGRTHLI   69 (242)
T ss_dssp             SCSEEEEECSTTSSHHHHH
T ss_pred             CCCeEEEECCCCCCHHHHH
Confidence            3678999999999999753

>3eie_A Vacuolar protein sorting-associated protein 4; AAA ATPase, ATP-binding cassette, ATP-binding, endosome, MEM nucleotide-binding; 2.70A {Saccharomyces cerevisiae} PDB: 3eih_A* 2rko_A 3mhv_C

Probab=93.78  E-value=0.21  Score=54.27  Aligned_cols=51  Identities=16%  Similarity=0.352  Sum_probs=30.1

Q ss_pred             cccccccCCCCHHHHHHHHHcCCCCCcHHHHHHHHHHh-----cCCCEEEEcCCCCchHHHH
Q 002040          465 PIKTWHQTGLTSKIMETIRKLNYEKPMPIQAQALPVIM-----SGRDCIGVAKTGSGKTLAF  521 (976)
Q Consensus       465 pi~~~~~~~l~~~l~~~l~~~~~~~p~~~Q~~~i~~il-----~g~d~i~~a~TGsGKT~~~  521 (976)
                      |-.+|.++.-...+.+.|...=.   .|.   ..|.++     ..+.+|+.||+|+|||+.+
T Consensus        13 ~~~~~~di~G~~~~~~~l~~~i~---~~~---~~~~~~~~~~~~~~~vLl~GppGtGKT~la   68 (322)
T 3eie_A           13 PNVKWEDVAGLEGAKEALKEAVI---LPV---KFPHLFKGNRKPTSGILLYGPPGTGKSYLA   68 (322)
T ss_dssp             CCCCGGGSCSCHHHHHHHHHHTH---HHH---HCGGGCCTTCCCCCEEEEECSSSSCHHHHH
T ss_pred             CCCCHHHhcChHHHHHHHHHHHH---HHH---hCHHHHhcCCCCCCeEEEECCCCCcHHHHH
Confidence            44568888777777666543210   000   011111     1356999999999999763

>4b4t_I 26S protease regulatory subunit 4 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=93.64  E-value=0.065  Score=60.01  Aligned_cols=54  Identities=20%  Similarity=0.362  Sum_probs=32.0

Q ss_pred             CcccccccCCCCHHHHHHHHH---cCCCCCcHHHHHHHHHHhcCCCEEEEcCCCCchHHH
Q 002040          464 KPIKTWHQTGLTSKIMETIRK---LNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLA  520 (976)
Q Consensus       464 ~pi~~~~~~~l~~~l~~~l~~---~~~~~p~~~Q~~~i~~il~g~d~i~~a~TGsGKT~~  520 (976)
                      .|-.+|.+.|=-..+.+.|..   +.+..|--++...++   -.+.+|+.||+|+|||+.
T Consensus       176 ~p~v~~~DIgGld~~k~~L~e~v~~Pl~~pe~f~~~Gi~---~prGvLLyGPPGTGKTlL  232 (437)
T 4b4t_I          176 SPTESYSDIGGLESQIQEIKESVELPLTHPELYEEMGIK---PPKGVILYGAPGTGKTLL  232 (437)
T ss_dssp             SCCCCGGGTCSCHHHHHHHHHHHHHHHHCCHHHHHHTCC---CCSEEEEESSTTTTHHHH
T ss_pred             CCCCcceecCcHHHHHHHHHHHHHHHHhCHHHHHhCCCC---CCCCCceECCCCchHHHH
Confidence            455688888766655555443   222223222222111   236799999999999975

>4b4t_K 26S protease regulatory subunit 6B homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=93.62  E-value=0.055  Score=61.13  Aligned_cols=54  Identities=22%  Similarity=0.249  Sum_probs=31.0

Q ss_pred             CcccccccCCCCHHHHHHHHH---cCCCCCcHHHHHHHHHHhcCCCEEEEcCCCCchHHH
Q 002040          464 KPIKTWHQTGLTSKIMETIRK---LNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLA  520 (976)
Q Consensus       464 ~pi~~~~~~~l~~~l~~~l~~---~~~~~p~~~Q~~~i~~il~g~d~i~~a~TGsGKT~~  520 (976)
                      .|-.+|.+.|--..+.+.|..   +.+..|--++...+   .-.+.+|+.||+|+|||+.
T Consensus       166 ~p~v~~~digGl~~~k~~l~e~v~~pl~~p~~~~~~g~---~~prGiLL~GPPGtGKT~l  222 (428)
T 4b4t_K          166 KPDVTYADVGGLDMQKQEIREAVELPLVQADLYEQIGI---DPPRGVLLYGPPGTGKTML  222 (428)
T ss_dssp             SCSCCGGGSCSCHHHHHHHHHHHHHHHHCHHHHHHHCC---CCCCEEEEESCTTTTHHHH
T ss_pred             CCCCCHHHhccHHHHHHHHHHHHHHHHhCHHHHHhCCC---CCCceEEEECCCCCCHHHH
Confidence            455788888766666655443   11111111111111   1236799999999999975

>3syl_A Protein CBBX; photosynthesis, rubisco activase, AAA+ protein, calvin cycle chaperone; 3.00A {Rhodobacter sphaeroides} PDB: 3syk_A 3zuh_A*

Probab=93.59  E-value=0.058  Score=58.25  Aligned_cols=17  Identities=24%  Similarity=0.171  Sum_probs=14.8

Q ss_pred             CCEEEEcCCCCchHHHH
Q 002040          505 RDCIGVAKTGSGKTLAF  521 (976)
Q Consensus       505 ~d~i~~a~TGsGKT~~~  521 (976)
                      .++++.||+|+|||..+
T Consensus        68 ~~vll~G~~GtGKT~la   84 (309)
T 3syl_A           68 LHMSFTGNPGTGKTTVA   84 (309)
T ss_dssp             CEEEEEECTTSSHHHHH
T ss_pred             ceEEEECCCCCCHHHHH
Confidence            46999999999999764

>3u61_B DNA polymerase accessory protein 44; AAA+, ATP hydrolase, clamp loader, sliding clamp, primer-TEM DNA, DNA binding protein-DNA complex; HET: DNA ADP 08T; 3.20A {Enterobacteria phage T4} PDB: 3u5z_B* 3u60_B*

Probab=93.30  E-value=0.092  Score=57.17  Aligned_cols=40  Identities=15%  Similarity=0.197  Sum_probs=24.4

Q ss_pred             CceEEEecCcccccccCCchHHHHHHHhcCCCCcEEEEec
Q 002040          617 RVTYLVMDEADRMFDMGFEPQITRIVQNIRPDRQTVLFSA  656 (976)
Q Consensus       617 ~~~~vVlDEah~~~~~~f~~~i~~il~~~~~~~q~i~~SA  656 (976)
                      ...+|||||+|.+........+..++........+|+.|.
T Consensus       105 ~~~vliiDEi~~l~~~~~~~~L~~~le~~~~~~~iI~~~n  144 (324)
T 3u61_B          105 RQKVIVIDEFDRSGLAESQRHLRSFMEAYSSNCSIIITAN  144 (324)
T ss_dssp             CEEEEEEESCCCGGGHHHHHHHHHHHHHHGGGCEEEEEES
T ss_pred             CCeEEEEECCcccCcHHHHHHHHHHHHhCCCCcEEEEEeC
Confidence            5789999999987512223345555555555555555443

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

Probab=93.15  E-value=0.26  Score=55.59  Aligned_cols=77  Identities=12%  Similarity=0.173  Sum_probs=64.5

Q ss_pred             hcCCcEEEEecCHHHHHHHHHHHHH---CCCCceeccCCCCHHHHHHHHHHhccCCccEEEecCccc----ccCCCCCCc
Q 002040          712 YEKGKILIFVHSQEKCDALFRDLLK---HGYPCLSLHGAKDQTDRESTISDFKSNVCNLLIATSVAA----RGLDVKELE  784 (976)
Q Consensus       712 ~~~~kvLIF~~s~~~~~~l~~~L~~---~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLVaT~v~~----~GlDi~~v~  784 (976)
                      ..++++||.+|++.-+..++..|..   .++.+..+||+.+..++...+..+..|...|||+|+-.-    .-+....+.
T Consensus        62 ~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~~~~l~~~~~~Iiv~Tp~~l~~~l~~~~~~~~~  141 (414)
T 3oiy_A           62 RKGKKSALVFPTVTLVKQTLERLQKLADEKVKIFGFYSSMKKEEKEKFEKSFEEDDYHILVFSTQFVSKNREKLSQKRFD  141 (414)
T ss_dssp             TTTCCEEEEESSHHHHHHHHHHHHHHCCSSCCEEECCTTSCHHHHHHHHHHHHHTCCSEEEEEHHHHHHCHHHHTTCCCS
T ss_pred             cCCCEEEEEECCHHHHHHHHHHHHHHccCCceEEEEECCCChhhHHHHHHHhhcCCCCEEEECHHHHHHHHHHhcccccc
Confidence            3567899999999999999999988   588999999999999988889999999999999996211    125566788


Q ss_pred             EEEE
Q 002040          785 LVIN  788 (976)
Q Consensus       785 ~VI~  788 (976)
                      +||.
T Consensus       142 ~iVi  145 (414)
T 3oiy_A          142 FVFV  145 (414)
T ss_dssp             EEEE
T ss_pred             EEEE
Confidence            8885

>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=93.14  E-value=1  Score=45.75  Aligned_cols=23  Identities=17%  Similarity=0.148  Sum_probs=16.6

Q ss_pred             CEEEEcCCCCchHHHHHHHHHHHH
Q 002040          506 DCIGVAKTGSGKTLAFVLPMLRHI  529 (976)
Q Consensus       506 d~i~~a~TGsGKT~~~~l~il~~l  529 (976)
                      .+++.|++|+|||..+ ..+...+
T Consensus        47 ~~ll~G~~G~GKT~l~-~~~~~~~   69 (250)
T 1njg_A           47 AYLFSGTRGVGKTSIA-RLLAKGL   69 (250)
T ss_dssp             EEEEECSTTSCHHHHH-HHHHHHH
T ss_pred             EEEEECCCCCCHHHHH-HHHHHHh
Confidence            5899999999999753 3334443

>3vfd_A Spastin; ATPase, microtubule severing, hydrolase; 3.30A {Homo sapiens}

Probab=93.09  E-value=0.28  Score=54.85  Aligned_cols=18  Identities=28%  Similarity=0.397  Sum_probs=15.6

Q ss_pred             CCCEEEEcCCCCchHHHH
Q 002040          504 GRDCIGVAKTGSGKTLAF  521 (976)
Q Consensus       504 g~d~i~~a~TGsGKT~~~  521 (976)
                      .+.+|+.|++|+|||+++
T Consensus       148 ~~~vLL~GppGtGKT~la  165 (389)
T 3vfd_A          148 ARGLLLFGPPGNGKTMLA  165 (389)
T ss_dssp             CSEEEEESSTTSCHHHHH
T ss_pred             CceEEEECCCCCCHHHHH
Confidence            468999999999999753

>1fnn_A CDC6P, cell division control protein 6; ORC1, AAA protein, DNA replication initation factor, cell cycle control factor; HET: ADP; 2.00A {Pyrobaculum aerophilum} SCOP: a.4.5.11 c.37.1.20

Probab=92.96  E-value=0.13  Score=57.34  Aligned_cols=23  Identities=17%  Similarity=0.323  Sum_probs=17.0

Q ss_pred             CEEEEcCCCCchHHHHHHHHHHHH
Q 002040          506 DCIGVAKTGSGKTLAFVLPMLRHI  529 (976)
Q Consensus       506 d~i~~a~TGsGKT~~~~l~il~~l  529 (976)
                      .+++.|++|+|||..+ ..++..+
T Consensus        46 ~~li~G~~G~GKTtl~-~~l~~~~   68 (389)
T 1fnn_A           46 RATLLGRPGTGKTVTL-RKLWELY   68 (389)
T ss_dssp             EEEEECCTTSSHHHHH-HHHHHHH
T ss_pred             eEEEECCCCCCHHHHH-HHHHHHH
Confidence            6999999999999763 3344443

>1sxj_E Activator 1 40 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=92.96  E-value=0.17  Score=55.79  Aligned_cols=42  Identities=10%  Similarity=0.317  Sum_probs=27.2

Q ss_pred             CCceEEEecCcccccccCCchHHHHHHHhcCCCCcEEEEeccC
Q 002040          616 RRVTYLVMDEADRMFDMGFEPQITRIVQNIRPDRQTVLFSATF  658 (976)
Q Consensus       616 ~~~~~vVlDEah~~~~~~f~~~i~~il~~~~~~~q~i~~SAT~  658 (976)
                      ....+|||||+|. ++......+..++........+|+.|..+
T Consensus       133 ~~~~vlilDE~~~-L~~~~~~~L~~~le~~~~~~~~Il~t~~~  174 (354)
T 1sxj_E          133 HRYKCVIINEANS-LTKDAQAALRRTMEKYSKNIRLIMVCDSM  174 (354)
T ss_dssp             -CCEEEEEECTTS-SCHHHHHHHHHHHHHSTTTEEEEEEESCS
T ss_pred             CCCeEEEEeCccc-cCHHHHHHHHHHHHhhcCCCEEEEEeCCH
Confidence            4578999999998 44444455666677666655555555544

>3pfi_A Holliday junction ATP-dependent DNA helicase RUVB; probable holliday junction DNA helicase; HET: ADP; 2.69A {Campylobacter jejuni subsp}

Probab=92.68  E-value=0.23  Score=54.27  Aligned_cols=17  Identities=24%  Similarity=0.161  Sum_probs=14.9

Q ss_pred             CCEEEEcCCCCchHHHH
Q 002040          505 RDCIGVAKTGSGKTLAF  521 (976)
Q Consensus       505 ~d~i~~a~TGsGKT~~~  521 (976)
                      ..+++.|++|+|||+.+
T Consensus        56 ~~vll~G~~GtGKT~la   72 (338)
T 3pfi_A           56 DHILFSGPAGLGKTTLA   72 (338)
T ss_dssp             CCEEEECSTTSSHHHHH
T ss_pred             CeEEEECcCCCCHHHHH
Confidence            57999999999999753

>4b4t_H 26S protease regulatory subunit 7 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=92.56  E-value=0.1  Score=59.07  Aligned_cols=54  Identities=24%  Similarity=0.340  Sum_probs=33.3

Q ss_pred             CcccccccCCCCHHHHHHHHHc---CCCCCcHHHHHHHHHHhcCCCEEEEcCCCCchHHH
Q 002040          464 KPIKTWHQTGLTSKIMETIRKL---NYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLA  520 (976)
Q Consensus       464 ~pi~~~~~~~l~~~l~~~l~~~---~~~~p~~~Q~~~i~~il~g~d~i~~a~TGsGKT~~  520 (976)
                      .|-.+|.+.+-...+.+.|...   .+..|--++.-.   +.-.+.+|+.||+|+|||+.
T Consensus       203 ~P~vt~~DIgGl~~~k~~L~e~V~~pl~~pe~f~~~G---i~pprGILLyGPPGTGKTlL  259 (467)
T 4b4t_H          203 KPDVTYSDVGGCKDQIEKLREVVELPLLSPERFATLG---IDPPKGILLYGPPGTGKTLC  259 (467)
T ss_dssp             SCSCCCSSCTTCHHHHHHHHHHTHHHHHCHHHHHHHT---CCCCSEEEECSCTTSSHHHH
T ss_pred             CCCCCHHHhccHHHHHHHHHHHHHHHhcCHHHHHHCC---CCCCCceEeeCCCCCcHHHH
Confidence            4567899988777777766542   111111111111   11246899999999999975

>3b9p_A CG5977-PA, isoform A; AAA ATPase, ATP-binding, nucleotide-binding, hydrolase; 2.70A {Drosophila melanogaster}

Probab=92.50  E-value=0.68  Score=49.37  Aligned_cols=18  Identities=28%  Similarity=0.383  Sum_probs=15.6

Q ss_pred             CCCEEEEcCCCCchHHHH
Q 002040          504 GRDCIGVAKTGSGKTLAF  521 (976)
Q Consensus       504 g~d~i~~a~TGsGKT~~~  521 (976)
                      ...+++.||+|+|||+.+
T Consensus        54 ~~~vll~Gp~GtGKT~la   71 (297)
T 3b9p_A           54 AKGLLLFGPPGNGKTLLA   71 (297)
T ss_dssp             CSEEEEESSSSSCHHHHH
T ss_pred             CCeEEEECcCCCCHHHHH
Confidence            568999999999999753

>1xwi_A SKD1 protein; VPS4B, AAA ATPase, protein transport; 2.80A {Homo sapiens}

Probab=92.48  E-value=0.94  Score=49.14  Aligned_cols=51  Identities=20%  Similarity=0.387  Sum_probs=29.9

Q ss_pred             cccccccCCCCHHHHHHHHHcCCCCCcHHHHHHHHHHh-----cCCCEEEEcCCCCchHHHH
Q 002040          465 PIKTWHQTGLTSKIMETIRKLNYEKPMPIQAQALPVIM-----SGRDCIGVAKTGSGKTLAF  521 (976)
Q Consensus       465 pi~~~~~~~l~~~l~~~l~~~~~~~p~~~Q~~~i~~il-----~g~d~i~~a~TGsGKT~~~  521 (976)
                      |-.+|.+++-...+.+.|...-.   .|.+   .|.++     ..+.+|+.||+|+|||+.+
T Consensus         7 ~~~~~~di~G~~~~k~~l~~~v~---~p~~---~~~~~~~~~~~~~~iLL~GppGtGKT~la   62 (322)
T 1xwi_A            7 PNVKWSDVAGLEGAKEALKEAVI---LPIK---FPHLFTGKRTPWRGILLFGPPGTGKSYLA   62 (322)
T ss_dssp             CCCCGGGSCSCHHHHHHHHHHHH---HHHH---CGGGSCTTCCCCSEEEEESSSSSCHHHHH
T ss_pred             CCCCHHHhcCHHHHHHHHHHHHH---HHHh---CHHHHhCCCCCCceEEEECCCCccHHHHH
Confidence            44678888777766665542100   0000   01111     1257999999999999753

>2qby_A CDC6 homolog 1, cell division control protein 6 homolog 1; winged-helix domain, helix-turn-helix, AAA+ ATPase domain, protein-DNA complex; HET: DNA SPD ADP; 3.35A {Sulfolobus solfataricus}

Probab=92.27  E-value=0.21  Score=55.45  Aligned_cols=25  Identities=24%  Similarity=0.247  Sum_probs=18.2

Q ss_pred             CCCEEEEcCCCCchHHHHHHHHHHHH
Q 002040          504 GRDCIGVAKTGSGKTLAFVLPMLRHI  529 (976)
Q Consensus       504 g~d~i~~a~TGsGKT~~~~l~il~~l  529 (976)
                      +..+++.|++|+|||..+ ..++..+
T Consensus        45 ~~~vli~G~~G~GKTtl~-~~l~~~~   69 (386)
T 2qby_A           45 PNNIFIYGLTGTGKTAVV-KFVLSKL   69 (386)
T ss_dssp             CCCEEEEECTTSSHHHHH-HHHHHHH
T ss_pred             CCeEEEECCCCCCHHHHH-HHHHHHH
Confidence            467999999999999753 3344443

>2qp9_X Vacuolar protein sorting-associated protein 4; ATPase domain, beta domain, C-terminal helix, ATP-binding, E nucleotide-binding; 2.90A {Saccharomyces cerevisiae} PDB: 2qpa_A*

Probab=92.11  E-value=0.19  Score=55.63  Aligned_cols=18  Identities=17%  Similarity=0.204  Sum_probs=15.3

Q ss_pred             CCCEEEEcCCCCchHHHH
Q 002040          504 GRDCIGVAKTGSGKTLAF  521 (976)
Q Consensus       504 g~d~i~~a~TGsGKT~~~  521 (976)
                      .+.+|+.||+|+|||+.+
T Consensus        84 ~~~iLL~GppGtGKT~la  101 (355)
T 2qp9_X           84 TSGILLYGPPGTGKSYLA  101 (355)
T ss_dssp             CCCEEEECSTTSCHHHHH
T ss_pred             CceEEEECCCCCcHHHHH
Confidence            357999999999999863

>1lv7_A FTSH; alpha/beta domain, four helix bundle, hydrolase; 1.50A {Escherichia coli} SCOP: c.37.1.20

Probab=91.54  E-value=1.4  Score=45.68  Aligned_cols=18  Identities=33%  Similarity=0.460  Sum_probs=15.0

Q ss_pred             CCCEEEEcCCCCchHHHH
Q 002040          504 GRDCIGVAKTGSGKTLAF  521 (976)
Q Consensus       504 g~d~i~~a~TGsGKT~~~  521 (976)
                      .+.+++.||+|+|||+.+
T Consensus        45 ~~~vll~G~~GtGKT~la   62 (257)
T 1lv7_A           45 PKGVLMVGPPGTGKTLLA   62 (257)
T ss_dssp             CCEEEEECCTTSCHHHHH
T ss_pred             CCeEEEECcCCCCHHHHH
Confidence            356999999999999753

>1ls1_A Signal recognition particle protein; FFH, SRP54, SRP, GTPase, ultrahigh resolution, protein transport; 1.10A {Thermus aquaticus} SCOP: a.24.13.1 c.37.1.10 PDB: 1jpn_B* 1jpj_A* 1ry1_U* 2j45_A* 1o87_A* 2c04_A* 2j46_A* 1rj9_B* 2c03_A* 2j7p_A* 1okk_A* 2cnw_A* 1ng1_A* 2xkv_A 3ng1_A 1ffh_A 2ng1_A*

Probab=91.54  E-value=1.1  Score=47.91  Aligned_cols=46  Identities=17%  Similarity=0.327  Sum_probs=26.0

Q ss_pred             CCceEEEecCccccc-ccCCchHHHHHHHhcCCCCcEEEEeccCcHH
Q 002040          616 RRVTYLVMDEADRMF-DMGFEPQITRIVQNIRPDRQTVLFSATFPRQ  661 (976)
Q Consensus       616 ~~~~~vVlDEah~~~-~~~f~~~i~~il~~~~~~~q~i~~SAT~~~~  661 (976)
                      ..+++||||++-.+. +......+..+...+.++.-++++.++....
T Consensus       179 ~~~D~viiDtpp~~~~d~~~~~~l~~~~~~~~~~~~~lv~~~~~~~~  225 (295)
T 1ls1_A          179 EARDLILVDTAGRLQIDEPLMGELARLKEVLGPDEVLLVLDAMTGQE  225 (295)
T ss_dssp             HTCCEEEEECCCCSSCCHHHHHHHHHHHHHHCCSEEEEEEEGGGTHH
T ss_pred             CCCCEEEEeCCCCccccHHHHHHHHHHhhhcCCCEEEEEEeCCCcHH
Confidence            468999999995432 1112233444445555655556677765433

>2r6a_A DNAB helicase, replicative helicase; replication, DNAB; 2.90A {Geobacillus stearothermophilus} PDB: 2r6c_A 2r6d_A 2r6e_A 2vyf_A 2vye_A

Probab=91.52  E-value=0.62  Score=53.29  Aligned_cols=39  Identities=15%  Similarity=-0.029  Sum_probs=24.3

Q ss_pred             cCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEcc
Q 002040          503 SGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAP  548 (976)
Q Consensus       503 ~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~P  548 (976)
                      .|.-++|.|++|+|||+.++..+.......       |..|+|+..
T Consensus       202 ~G~liiI~G~pG~GKTtl~l~ia~~~~~~~-------g~~Vl~~s~  240 (454)
T 2r6a_A          202 RSDLIIVAARPSVGKTAFALNIAQNVATKT-------NENVAIFSL  240 (454)
T ss_dssp             TTCEEEEECCTTSCHHHHHHHHHHHHHHHS-------SCCEEEEES
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHHHHHHhC-------CCcEEEEEC
Confidence            345688889999999976444444333221       335677653

>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=91.26  E-value=0.47  Score=51.23  Aligned_cols=39  Identities=15%  Similarity=0.255  Sum_probs=23.4

Q ss_pred             CCceEEEecCcccccccCCchHHHHHHHhcCCCCcEEEEe
Q 002040          616 RRVTYLVMDEADRMFDMGFEPQITRIVQNIRPDRQTVLFS  655 (976)
Q Consensus       616 ~~~~~vVlDEah~~~~~~f~~~i~~il~~~~~~~q~i~~S  655 (976)
                      ....+|||||+|.+... ....+..++...+....+|+++
T Consensus       109 ~~~~vliiDe~~~l~~~-~~~~L~~~le~~~~~~~~i~~~  147 (327)
T 1iqp_A          109 ASFKIIFLDEADALTQD-AQQALRRTMEMFSSNVRFILSC  147 (327)
T ss_dssp             CSCEEEEEETGGGSCHH-HHHHHHHHHHHTTTTEEEEEEE
T ss_pred             CCCeEEEEeCCCcCCHH-HHHHHHHHHHhcCCCCeEEEEe
Confidence            35689999999987432 2334455555554555455443

>3pvs_A Replication-associated recombination protein A; maintenance of genome stability Pro recombination; 2.50A {Escherichia coli}

Probab=91.06  E-value=0.45  Score=54.24  Aligned_cols=17  Identities=29%  Similarity=0.253  Sum_probs=14.5

Q ss_pred             CCEEEEcCCCCchHHHH
Q 002040          505 RDCIGVAKTGSGKTLAF  521 (976)
Q Consensus       505 ~d~i~~a~TGsGKT~~~  521 (976)
                      ..+|++||+|+|||+.+
T Consensus        51 ~~vLL~GppGtGKTtlA   67 (447)
T 3pvs_A           51 HSMILWGPPGTGKTTLA   67 (447)
T ss_dssp             CEEEEECSTTSSHHHHH
T ss_pred             cEEEEECCCCCcHHHHH
Confidence            36999999999999753

>3uk6_A RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding, hydrolase; HET: ADP; 2.95A {Homo sapiens} PDB: 2xsz_D*

Probab=91.06  E-value=1.5  Score=48.26  Aligned_cols=24  Identities=25%  Similarity=0.401  Sum_probs=17.6

Q ss_pred             CCEEEEcCCCCchHHHHHHHHHHHH
Q 002040          505 RDCIGVAKTGSGKTLAFVLPMLRHI  529 (976)
Q Consensus       505 ~d~i~~a~TGsGKT~~~~l~il~~l  529 (976)
                      +.+|+.||+|+|||..+ ..+...+
T Consensus        71 ~~vLl~GppGtGKT~la-~~la~~l   94 (368)
T 3uk6_A           71 RAVLIAGQPGTGKTAIA-MGMAQAL   94 (368)
T ss_dssp             CEEEEEESTTSSHHHHH-HHHHHHH
T ss_pred             CEEEEECCCCCCHHHHH-HHHHHHh
Confidence            57999999999999863 3344443

>1jr3_A DNA polymerase III subunit gamma; processivity, processivity clamp, clamp loader, AAA+ ATPase, transferase; HET: DNA; 2.70A {Escherichia coli} SCOP: a.80.1.1 c.37.1.20 PDB: 1xxh_B* 3glh_B* 3glf_B* 3gli_B* 3glg_B* 1xxi_B*

Probab=90.90  E-value=1.4  Score=48.51  Aligned_cols=23  Identities=17%  Similarity=0.148  Sum_probs=16.4

Q ss_pred             CEEEEcCCCCchHHHHHHHHHHHH
Q 002040          506 DCIGVAKTGSGKTLAFVLPMLRHI  529 (976)
Q Consensus       506 d~i~~a~TGsGKT~~~~l~il~~l  529 (976)
                      .+++.|+.|+|||..+ ..+...+
T Consensus        40 ~~ll~G~~G~GKT~la-~~la~~l   62 (373)
T 1jr3_A           40 AYLFSGTRGVGKTSIA-RLLAKGL   62 (373)
T ss_dssp             EEEEESCTTSSHHHHH-HHHHHHH
T ss_pred             EEEEECCCCCCHHHHH-HHHHHHh
Confidence            3789999999999764 3333443

>2p6n_A ATP-dependent RNA helicase DDX41; DEAD, structural genomics, structural genomic consortium, SGC, hydrolase; 2.60A {Homo sapiens}

Probab=90.61  E-value=1.6  Score=43.30  Aligned_cols=71  Identities=21%  Similarity=0.378  Sum_probs=51.4

Q ss_pred             CCeEEEEccCHHHHHHHHHHHHHHHhhcCcEEEEeeCCCChHHHH---HHHhc-CCeEEEeCchhHHHHHHhcCCccccc
Q 002040          540 GPVGLIMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQI---SELKR-GTEIVVCTPGRMIDILCTSGGKITNL  615 (976)
Q Consensus       540 ~~~vLIl~Ptr~La~Q~~~~~~~~~~~~~~~~~~~~gg~~~~~~~---~~l~~-~~~Iiv~Tp~~L~~~l~~~~~~~~~l  615 (976)
                      ++++||.|+++..+..++..+..    .|+.+..++|+.+..+..   ..+.. ...|+|+|     +.+...    .++
T Consensus        54 ~~~~lVF~~~~~~~~~l~~~L~~----~g~~~~~lhg~~~~~~R~~~l~~F~~g~~~vLvaT-----~~~~~G----ldi  120 (191)
T 2p6n_A           54 PPPVLIFAEKKADVDAIHEYLLL----KGVEAVAIHGGKDQEERTKAIEAFREGKKDVLVAT-----DVASKG----LDF  120 (191)
T ss_dssp             CSCEEEECSCHHHHHHHHHHHHH----HTCCEEEECTTSCHHHHHHHHHHHHHTSCSEEEEC-----HHHHTT----CCC
T ss_pred             CCCEEEEECCHHHHHHHHHHHHH----cCCcEEEEeCCCCHHHHHHHHHHHhcCCCEEEEEc-----CchhcC----CCc
Confidence            45799999999999888777765    478899999998765543   33333 46899999     233332    577


Q ss_pred             CCceEEEe
Q 002040          616 RRVTYLVM  623 (976)
Q Consensus       616 ~~~~~vVl  623 (976)
                      ..+.+||.
T Consensus       121 ~~v~~VI~  128 (191)
T 2p6n_A          121 PAIQHVIN  128 (191)
T ss_dssp             CCCSEEEE
T ss_pred             ccCCEEEE
Confidence            77888776

>2qz4_A Paraplegin; AAA+, SPG7, protease, ADP, structural genomics, structural G consortium, SGC, ATP-binding, nucleotide-binding, hydrolase; HET: ADP; 2.22A {Homo sapiens}

Probab=90.34  E-value=1.1  Score=46.54  Aligned_cols=18  Identities=28%  Similarity=0.397  Sum_probs=15.2

Q ss_pred             CCCEEEEcCCCCchHHHH
Q 002040          504 GRDCIGVAKTGSGKTLAF  521 (976)
Q Consensus       504 g~d~i~~a~TGsGKT~~~  521 (976)
                      ...+++.||+|+|||+.+
T Consensus        39 ~~~vll~G~~GtGKT~la   56 (262)
T 2qz4_A           39 PKGALLLGPPGCGKTLLA   56 (262)
T ss_dssp             CCEEEEESCTTSSHHHHH
T ss_pred             CceEEEECCCCCCHHHHH
Confidence            457899999999999753

>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=90.33  E-value=1.1  Score=47.91  Aligned_cols=19  Identities=26%  Similarity=0.361  Sum_probs=16.1

Q ss_pred             cCCCEEEEcCCCCchHHHH
Q 002040          503 SGRDCIGVAKTGSGKTLAF  521 (976)
Q Consensus       503 ~g~d~i~~a~TGsGKT~~~  521 (976)
                      ....+++.||+|+|||..+
T Consensus        49 ~~~~vll~G~~GtGKT~la   67 (310)
T 1ofh_A           49 TPKNILMIGPTGVGKTEIA   67 (310)
T ss_dssp             CCCCEEEECCTTSSHHHHH
T ss_pred             CCceEEEECCCCCCHHHHH
Confidence            3578999999999999753

>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=90.03  E-value=0.5  Score=51.71  Aligned_cols=40  Identities=18%  Similarity=0.233  Sum_probs=24.3

Q ss_pred             CCceEEEecCcccccccCCchHHHHHHHhcCCCCcEEEEec
Q 002040          616 RRVTYLVMDEADRMFDMGFEPQITRIVQNIRPDRQTVLFSA  656 (976)
Q Consensus       616 ~~~~~vVlDEah~~~~~~f~~~i~~il~~~~~~~q~i~~SA  656 (976)
                      ....+|||||+|.+... ....+..++........+|+++.
T Consensus       132 ~~~~vliiDE~~~l~~~-~~~~Ll~~le~~~~~~~~il~~~  171 (353)
T 1sxj_D          132 PPYKIIILDEADSMTAD-AQSALRRTMETYSGVTRFCLICN  171 (353)
T ss_dssp             CSCEEEEETTGGGSCHH-HHHHHHHHHHHTTTTEEEEEEES
T ss_pred             CCceEEEEECCCccCHH-HHHHHHHHHHhcCCCceEEEEeC
Confidence            35689999999987532 22345555665555555555443

>2w0m_A SSO2452; RECA, SSPF, unknown FUN; 2.0A {Sulfolobus solfataricus P2}

Probab=89.88  E-value=0.75  Score=46.75  Aligned_cols=22  Identities=23%  Similarity=0.135  Sum_probs=16.8

Q ss_pred             cCCCEEEEcCCCCchHHHHHHH
Q 002040          503 SGRDCIGVAKTGSGKTLAFVLP  524 (976)
Q Consensus       503 ~g~d~i~~a~TGsGKT~~~~l~  524 (976)
                      .|.-+++.|++|+|||+.+...
T Consensus        22 ~G~~~~i~G~~GsGKTtl~~~l   43 (235)
T 2w0m_A           22 QGFFIALTGEPGTGKTIFSLHF   43 (235)
T ss_dssp             TTCEEEEECSTTSSHHHHHHHH
T ss_pred             CCCEEEEEcCCCCCHHHHHHHH
Confidence            4567888999999999764433

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

Probab=89.73  E-value=0.57  Score=59.61  Aligned_cols=77  Identities=12%  Similarity=0.173  Sum_probs=64.4

Q ss_pred             hcCCcEEEEecCHHHHHHHHHHHHH---CCCCceeccCCCCHHHHHHHHHHhccCCccEEEecCccc----ccCCCCCCc
Q 002040          712 YEKGKILIFVHSQEKCDALFRDLLK---HGYPCLSLHGAKDQTDRESTISDFKSNVCNLLIATSVAA----RGLDVKELE  784 (976)
Q Consensus       712 ~~~~kvLIF~~s~~~~~~l~~~L~~---~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLVaT~v~~----~GlDi~~v~  784 (976)
                      ..+.++||.+|++.-+.+++..|..   .++.+..+||+++..++...+..+..|..+|||+|+-.-    .-+++.++.
T Consensus       119 ~~~~~~Lil~PtreLa~Q~~~~l~~l~~~~i~v~~l~Gg~~~~er~~~~~~l~~g~~~IlV~Tp~rL~~~l~~l~~~~l~  198 (1104)
T 4ddu_A          119 RKGKKSALVFPTVTLVKQTLERLQKLADEKVKIFGFYSSMKKEEKEKFEKSFEEDDYHILVFSTQFVSKNREKLSQKRFD  198 (1104)
T ss_dssp             TTTCCEEEEESSHHHHHHHHHHHHTTSCTTSCEEEECTTCCTTHHHHHHHHHHTSCCSEEEEEHHHHHHSHHHHHTSCCS
T ss_pred             hcCCeEEEEechHHHHHHHHHHHHHhhCCCCeEEEEeCCCCHHHHHHHHHHHhCCCCCEEEECHHHHHHHHHhhcccCcC
Confidence            3466899999999999999999988   467899999999998888899999999999999996211    125667888


Q ss_pred             EEEE
Q 002040          785 LVIN  788 (976)
Q Consensus       785 ~VI~  788 (976)
                      +||.
T Consensus       199 ~lVi  202 (1104)
T 4ddu_A          199 FVFV  202 (1104)
T ss_dssp             EEEE
T ss_pred             EEEE
Confidence            8885

>1hqc_A RUVB; extended AAA-ATPase domain, complex with nucleotide, hydrolase; HET: ADE; 3.20A {Thermus thermophilus} SCOP: a.4.5.11 c.37.1.20 PDB: 1ixs_B* 1ixr_C*

Probab=89.71  E-value=0.67  Score=50.04  Aligned_cols=18  Identities=22%  Similarity=0.102  Sum_probs=15.4

Q ss_pred             CCCEEEEcCCCCchHHHH
Q 002040          504 GRDCIGVAKTGSGKTLAF  521 (976)
Q Consensus       504 g~d~i~~a~TGsGKT~~~  521 (976)
                      ...+++.|++|+|||+.+
T Consensus        38 ~~~vll~G~~GtGKT~la   55 (324)
T 1hqc_A           38 LEHLLLFGPPGLGKTTLA   55 (324)
T ss_dssp             CCCCEEECCTTCCCHHHH
T ss_pred             CCcEEEECCCCCCHHHHH
Confidence            368999999999999753

>1vma_A Cell division protein FTSY; TM0570, structural genomics, JCS protein structure initiative, PSI, joint center for structu genomics; HET: CIT; 1.60A {Thermotoga maritima} SCOP: a.24.13.1 c.37.1.10

Probab=89.70  E-value=3  Score=44.74  Aligned_cols=19  Identities=26%  Similarity=0.155  Sum_probs=14.7

Q ss_pred             CCEEEEcCCCCchHHHHHH
Q 002040          505 RDCIGVAKTGSGKTLAFVL  523 (976)
Q Consensus       505 ~d~i~~a~TGsGKT~~~~l  523 (976)
                      .-++++|++|+|||+.+..
T Consensus       105 ~vi~ivG~~GsGKTTl~~~  123 (306)
T 1vma_A          105 FVIMVVGVNGTGKTTSCGK  123 (306)
T ss_dssp             EEEEEECCTTSSHHHHHHH
T ss_pred             eEEEEEcCCCChHHHHHHH
Confidence            4577889999999986443

>3e70_C DPA, signal recognition particle receptor; FTSY, SRP-GTPase, protein-targeting, transport protein; HET: GDP; 1.97A {Pyrococcus furiosus} PDB: 3dmd_B 3dm9_B*

Probab=89.64  E-value=2.1  Score=46.51  Aligned_cols=52  Identities=15%  Similarity=0.213  Sum_probs=31.4

Q ss_pred             ceEEEecCccccc-ccCCchHHHHHHHhcCCCCcEEEEeccCcHHHHHHHHHH
Q 002040          618 VTYLVMDEADRMF-DMGFEPQITRIVQNIRPDRQTVLFSATFPRQVEILARKV  669 (976)
Q Consensus       618 ~~~vVlDEah~~~-~~~f~~~i~~il~~~~~~~q~i~~SAT~~~~~~~l~~~~  669 (976)
                      +.++++|-+-++. ...+...+..+...+.++..++++.+|....+...+..+
T Consensus       212 ~d~vliDtaG~~~~~~~l~~eL~~i~ral~~de~llvLDa~t~~~~~~~~~~~  264 (328)
T 3e70_C          212 IDVVLIDTAGRSETNRNLMDEMKKIARVTKPNLVIFVGDALAGNAIVEQARQF  264 (328)
T ss_dssp             CSEEEEEECCSCCTTTCHHHHHHHHHHHHCCSEEEEEEEGGGTTHHHHHHHHH
T ss_pred             chhhHHhhccchhHHHHHHHHHHHHHHHhcCCCCEEEEecHHHHHHHHHHHHH
Confidence            5677788776532 122334455556666777778888887766555555444

>2q6t_A DNAB replication FORK helicase; hydrolase; 2.90A {Thermus aquaticus}

Probab=89.55  E-value=0.48  Score=54.04  Aligned_cols=38  Identities=21%  Similarity=0.027  Sum_probs=23.7

Q ss_pred             CCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEcc
Q 002040          504 GRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAP  548 (976)
Q Consensus       504 g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~P  548 (976)
                      |.-++|+|++|+|||..++..+...+..       .+..|+++..
T Consensus       200 G~l~ii~G~pg~GKT~lal~ia~~~a~~-------~g~~vl~~sl  237 (444)
T 2q6t_A          200 GSLNIIAARPAMGKTAFALTIAQNAALK-------EGVGVGIYSL  237 (444)
T ss_dssp             TCEEEEEECTTSCHHHHHHHHHHHHHHT-------TCCCEEEEES
T ss_pred             CcEEEEEeCCCCCHHHHHHHHHHHHHHh-------CCCeEEEEEC
Confidence            4457888999999997544444443332       1345677654

>2dr3_A UPF0273 protein PH0284; RECA superfamily ATPase, hexamer, structural genomics; HET: ADP; 2.00A {Pyrococcus horikoshii}

Probab=89.53  E-value=1.4  Score=45.20  Aligned_cols=26  Identities=15%  Similarity=0.075  Sum_probs=18.8

Q ss_pred             cCCCEEEEcCCCCchHHHHHHHHHHH
Q 002040          503 SGRDCIGVAKTGSGKTLAFVLPMLRH  528 (976)
Q Consensus       503 ~g~d~i~~a~TGsGKT~~~~l~il~~  528 (976)
                      .|.-+++.|++|+|||+.++..+...
T Consensus        22 ~G~~~~i~G~~GsGKTtl~~~~~~~~   47 (247)
T 2dr3_A           22 ERNVVLLSGGPGTGKTIFSQQFLWNG   47 (247)
T ss_dssp             TTCEEEEEECTTSSHHHHHHHHHHHH
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHH
Confidence            45678999999999998644444433

>2zan_A Vacuolar protein sorting-associating protein 4B; SKD1, VPS4B, AAA ATPase, ATP-binding, coiled coil, membrane, nucleotide-binding, phosphorylation; HET: ATP; 3.00A {Mus musculus} PDB: 2zam_A* 2zao_A* 2jqh_A 2jqk_A 1wr0_A 2jq9_A 2k3w_A 1yxr_A

Probab=89.36  E-value=0.89  Score=51.77  Aligned_cols=18  Identities=22%  Similarity=0.263  Sum_probs=15.3

Q ss_pred             CCCEEEEcCCCCchHHHH
Q 002040          504 GRDCIGVAKTGSGKTLAF  521 (976)
Q Consensus       504 g~d~i~~a~TGsGKT~~~  521 (976)
                      .+.+|+.||+|+|||+.+
T Consensus       167 ~~~vLL~GppGtGKT~lA  184 (444)
T 2zan_A          167 WRGILLFGPPGTGKSYLA  184 (444)
T ss_dssp             CSEEEEECSTTSSHHHHH
T ss_pred             CceEEEECCCCCCHHHHH
Confidence            367999999999999753

>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=89.31  E-value=0.96  Score=57.91  Aligned_cols=94  Identities=9%  Similarity=0.123  Sum_probs=71.6

Q ss_pred             cCcchHHHHHH-HHHHhhhcCCcEEEEecCHHHHHHHHHHHHHC----CCCceeccCCCCHHHHHHHHHHhccCCccEEE
Q 002040          695 RPESDRFLRLL-ELLGEWYEKGKILIFVHSQEKCDALFRDLLKH----GYPCLSLHGAKDQTDRESTISDFKSNVCNLLI  769 (976)
Q Consensus       695 ~~~~~k~~~l~-~~l~~~~~~~kvLIF~~s~~~~~~l~~~L~~~----~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLV  769 (976)
                      .....|-...+ .++.....+.++||.||+..-+.+.+..|...    ++.+..++|..+..++..++..+..|.++|+|
T Consensus       632 ~TGsGKT~val~aa~~~~~~g~~vlvlvPt~~La~Q~~~~~~~~~~~~~i~v~~l~~~~~~~~~~~~~~~l~~g~~dIvV  711 (1151)
T 2eyq_A          632 DVGFGKTEVAMRAAFLAVDNHKQVAVLVPTTLLAQQHYDNFRDRFANWPVRIEMISRFRSAKEQTQILAEVAEGKIDILI  711 (1151)
T ss_dssp             CCCTTTHHHHHHHHHHHHTTTCEEEEECSSHHHHHHHHHHHHHHSTTTTCCEEEESTTSCHHHHHHHHHHHHTTCCSEEE
T ss_pred             CCCCCHHHHHHHHHHHHHHhCCeEEEEechHHHHHHHHHHHHHHhhcCCCeEEEEeCCCCHHHHHHHHHHHhcCCCCEEE
Confidence            33445543332 23333334569999999999998888887643    67889999999999999999999999999999


Q ss_pred             ecC-cccccCCCCCCcEEEE
Q 002040          770 ATS-VAARGLDVKELELVIN  788 (976)
Q Consensus       770 aT~-v~~~GlDi~~v~~VI~  788 (976)
                      +|. .+...+.+.++.+||.
T Consensus       712 ~T~~ll~~~~~~~~l~lvIi  731 (1151)
T 2eyq_A          712 GTHKLLQSDVKFKDLGLLIV  731 (1151)
T ss_dssp             ECTHHHHSCCCCSSEEEEEE
T ss_pred             ECHHHHhCCccccccceEEE
Confidence            996 4455678888888885

>1sxj_A Activator 1 95 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=89.19  E-value=0.72  Score=53.69  Aligned_cols=41  Identities=17%  Similarity=0.186  Sum_probs=25.1

Q ss_pred             CCceEEEecCcccccccC--CchHHHHHHHhcCCCCcEEEEeccC
Q 002040          616 RRVTYLVMDEADRMFDMG--FEPQITRIVQNIRPDRQTVLFSATF  658 (976)
Q Consensus       616 ~~~~~vVlDEah~~~~~~--f~~~i~~il~~~~~~~q~i~~SAT~  658 (976)
                      ....+|||||+|.|....  +...+..++..  ....+|+++++.
T Consensus       147 ~~~~vliIDEid~l~~~~~~~l~~L~~~l~~--~~~~iIli~~~~  189 (516)
T 1sxj_A          147 GKHFVIIMDEVDGMSGGDRGGVGQLAQFCRK--TSTPLILICNER  189 (516)
T ss_dssp             TTSEEEEECSGGGCCTTSTTHHHHHHHHHHH--CSSCEEEEESCT
T ss_pred             CCCeEEEEECCCccchhhHHHHHHHHHHHHh--cCCCEEEEEcCC
Confidence            345799999999876432  22344444443  344577777764

>2gno_A DNA polymerase III, gamma subunit-related protein; structural genomics, joint center for structural genomics, J protein structure initiative; HET: DNA; 2.00A {Thermotoga maritima} SCOP: a.80.1.1 c.37.1.20

Probab=88.91  E-value=1.5  Score=47.18  Aligned_cols=40  Identities=15%  Similarity=0.244  Sum_probs=22.9

Q ss_pred             cCCceEEEecCcccccccCCchHHHHHHHhcCCCCcEEEEe
Q 002040          615 LRRVTYLVMDEADRMFDMGFEPQITRIVQNIRPDRQTVLFS  655 (976)
Q Consensus       615 l~~~~~vVlDEah~~~~~~f~~~i~~il~~~~~~~q~i~~S  655 (976)
                      ...+.+|||||||.|.... ...+..++..-++...+|+++
T Consensus        80 ~~~~kvviIdead~lt~~a-~naLLk~LEep~~~t~fIl~t  119 (305)
T 2gno_A           80 LYTRKYVIVHDCERMTQQA-ANAFLKALEEPPEYAVIVLNT  119 (305)
T ss_dssp             SSSSEEEEETTGGGBCHHH-HHHTHHHHHSCCTTEEEEEEE
T ss_pred             cCCceEEEeccHHHhCHHH-HHHHHHHHhCCCCCeEEEEEE
Confidence            3467899999999875332 223444555443344344433

>2hjv_A ATP-dependent RNA helicase DBPA; parallel alpha-beta, hydrolase; 1.95A {Bacillus subtilis}

Probab=88.91  E-value=1.1  Score=43.10  Aligned_cols=72  Identities=19%  Similarity=0.380  Sum_probs=51.2

Q ss_pred             CCeEEEEccCHHHHHHHHHHHHHHHhhcCcEEEEeeCCCChHHHH---HHHhc-CCeEEEeCchhHHHHHHhcCCccccc
Q 002040          540 GPVGLIMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQI---SELKR-GTEIVVCTPGRMIDILCTSGGKITNL  615 (976)
Q Consensus       540 ~~~vLIl~Ptr~La~Q~~~~~~~~~~~~~~~~~~~~gg~~~~~~~---~~l~~-~~~Iiv~Tp~~L~~~l~~~~~~~~~l  615 (976)
                      +.++||.|+++..+..++..+..    .|+.+..++|+.+..+..   ..+.. ...|+|+|.     .+..+    .++
T Consensus        35 ~~~~lVF~~~~~~~~~l~~~L~~----~~~~~~~~hg~~~~~~r~~~~~~f~~g~~~vlv~T~-----~~~~G----ld~  101 (163)
T 2hjv_A           35 PDSCIIFCRTKEHVNQLTDELDD----LGYPCDKIHGGMIQEDRFDVMNEFKRGEYRYLVATD-----VAARG----IDI  101 (163)
T ss_dssp             CSSEEEECSSHHHHHHHHHHHHH----TTCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEECG-----GGTTT----CCC
T ss_pred             CCcEEEEECCHHHHHHHHHHHHH----cCCcEEEEeCCCCHHHHHHHHHHHHcCCCeEEEECC-----hhhcC----Cch
Confidence            45789999999998888777765    578899999998766543   33333 468999993     22221    567


Q ss_pred             CCceEEEec
Q 002040          616 RRVTYLVMD  624 (976)
Q Consensus       616 ~~~~~vVlD  624 (976)
                      ..+.+||.-
T Consensus       102 ~~~~~Vi~~  110 (163)
T 2hjv_A          102 ENISLVINY  110 (163)
T ss_dssp             SCCSEEEES
T ss_pred             hcCCEEEEe
Confidence            778888763

>3lda_A DNA repair protein RAD51; DNA binding protein, ATP-binding, DNA damage, DNA recombinat repair, nucleotide-binding; HET: DNA; 2.50A {Saccharomyces cerevisiae} PDB: 1szp_A*

Probab=88.75  E-value=2.1  Score=47.81  Aligned_cols=19  Identities=16%  Similarity=0.017  Sum_probs=15.4

Q ss_pred             CCCEEEEcCCCCchHHHHH
Q 002040          504 GRDCIGVAKTGSGKTLAFV  522 (976)
Q Consensus       504 g~d~i~~a~TGsGKT~~~~  522 (976)
                      |.-++|+|++|+|||+.+.
T Consensus       178 Gei~~I~G~sGsGKTTLl~  196 (400)
T 3lda_A          178 GSITELFGEFRTGKSQLCH  196 (400)
T ss_dssp             TSEEEEEESTTSSHHHHHH
T ss_pred             CcEEEEEcCCCCChHHHHH
Confidence            3568899999999997644

>2ffh_A Protein (FFH); SRP54, signal recognition particle, GTPase, M domain, RNA-binding, signal sequence-binding, helix-turn-helix, protein targeting; 3.20A {Thermus aquaticus} SCOP: a.24.13.1 a.36.1.1 c.37.1.10 PDB: 2iy3_A

Probab=88.74  E-value=2.5  Score=47.58  Aligned_cols=20  Identities=30%  Similarity=0.149  Sum_probs=15.1

Q ss_pred             CCCEEEEcCCCCchHHHHHH
Q 002040          504 GRDCIGVAKTGSGKTLAFVL  523 (976)
Q Consensus       504 g~d~i~~a~TGsGKT~~~~l  523 (976)
                      +.-+++++++|+|||+.+..
T Consensus        98 ~~vi~i~G~~GsGKTT~~~~  117 (425)
T 2ffh_A           98 RNLWFLVGLQGSGKTTTAAK  117 (425)
T ss_dssp             SEEEEEECCTTSSHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHH
Confidence            44577789999999986443

>3d8b_A Fidgetin-like protein 1; AAA+, ATPase, ADP, SGC, structural genomics consortium, ATP- hydrolase, magnesium, metal-binding, nucleotide-binding; HET: ADP; 2.00A {Homo sapiens}

Probab=88.61  E-value=0.36  Score=53.32  Aligned_cols=18  Identities=28%  Similarity=0.316  Sum_probs=15.5

Q ss_pred             CCCEEEEcCCCCchHHHH
Q 002040          504 GRDCIGVAKTGSGKTLAF  521 (976)
Q Consensus       504 g~d~i~~a~TGsGKT~~~  521 (976)
                      .+.+|++|++|+|||+.+
T Consensus       117 ~~~vLl~GppGtGKT~la  134 (357)
T 3d8b_A          117 PKGILLFGPPGTGKTLIG  134 (357)
T ss_dssp             CSEEEEESSTTSSHHHHH
T ss_pred             CceEEEECCCCCCHHHHH
Confidence            467999999999999763

>1nlf_A Regulatory protein REPA; replicative DNA helicase structural changes, replication; 1.95A {Escherichia coli} SCOP: c.37.1.11 PDB: 1g8y_A 1olo_A

Probab=88.48  E-value=1.5  Score=46.31  Aligned_cols=26  Identities=19%  Similarity=0.240  Sum_probs=19.5

Q ss_pred             HhcCCCEEEEcCCCCchHHHHHHHHH
Q 002040          501 IMSGRDCIGVAKTGSGKTLAFVLPML  526 (976)
Q Consensus       501 il~g~d~i~~a~TGsGKT~~~~l~il  526 (976)
                      +..|.-++|+|++|+|||+.+...+.
T Consensus        27 l~~G~i~~i~G~~GsGKTtl~~~l~~   52 (279)
T 1nlf_A           27 MVAGTVGALVSPGGAGKSMLALQLAA   52 (279)
T ss_dssp             EETTSEEEEEESTTSSHHHHHHHHHH
T ss_pred             ccCCCEEEEEcCCCCCHHHHHHHHHH
Confidence            34677889999999999986544443

>3hu3_A Transitional endoplasmic reticulum ATPase; VCP, transport protein; HET: AGS; 2.20A {Homo sapiens} PDB: 3hu2_A* 3hu1_A* 1e32_A* 1s3s_A*

Probab=88.41  E-value=0.5  Score=54.50  Aligned_cols=43  Identities=14%  Similarity=0.267  Sum_probs=27.5

Q ss_pred             ceEEEecCcccccccC----------CchHHHHHHHhcCCCCcEEEEeccCcH
Q 002040          618 VTYLVMDEADRMFDMG----------FEPQITRIVQNIRPDRQTVLFSATFPR  660 (976)
Q Consensus       618 ~~~vVlDEah~~~~~~----------f~~~i~~il~~~~~~~q~i~~SAT~~~  660 (976)
                      .++|+|||+|.+....          ....+..++..+.....++++.||-.+
T Consensus       298 p~iLfLDEId~l~~~~~~~~~~~~~~~~~~LL~~ld~~~~~~~v~vIaaTn~~  350 (489)
T 3hu3_A          298 PAIIFIDELDAIAPKREKTHGEVERRIVSQLLTLMDGLKQRAHVIVMAATNRP  350 (489)
T ss_dssp             SEEEEEESHHHHCBCTTSCCCHHHHHHHHHHHHHHHHSCTTSCEEEEEEESCG
T ss_pred             CcEEEecchhhhccccccccchHHHHHHHHHHHHhhccccCCceEEEEecCCc
Confidence            4689999999876431          112344555555566677887777544

>1sxj_B Activator 1 37 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=88.25  E-value=0.81  Score=49.20  Aligned_cols=38  Identities=16%  Similarity=0.245  Sum_probs=23.0

Q ss_pred             CceEEEecCcccccccCCchHHHHHHHhcCCCCcEEEEe
Q 002040          617 RVTYLVMDEADRMFDMGFEPQITRIVQNIRPDRQTVLFS  655 (976)
Q Consensus       617 ~~~~vVlDEah~~~~~~f~~~i~~il~~~~~~~q~i~~S  655 (976)
                      ...+|||||+|.+.... ...+..++...+....+|++|
T Consensus       107 ~~~viiiDe~~~l~~~~-~~~L~~~le~~~~~~~~il~~  144 (323)
T 1sxj_B          107 KHKIVILDEADSMTAGA-QQALRRTMELYSNSTRFAFAC  144 (323)
T ss_dssp             CCEEEEEESGGGSCHHH-HHTTHHHHHHTTTTEEEEEEE
T ss_pred             CceEEEEECcccCCHHH-HHHHHHHHhccCCCceEEEEe
Confidence            36799999999875322 233445555554555555544

>3t15_A Ribulose bisphosphate carboxylase/oxygenase activ chloroplastic; photosynthesis, rubisco activase, AAA+ protein; 2.95A {Nicotiana tabacum} PDB: 3zw6_A

Probab=88.24  E-value=0.36  Score=51.68  Aligned_cols=16  Identities=19%  Similarity=0.009  Sum_probs=13.8

Q ss_pred             CCEEEEcCCCCchHHH
Q 002040          505 RDCIGVAKTGSGKTLA  520 (976)
Q Consensus       505 ~d~i~~a~TGsGKT~~  520 (976)
                      ..+++.||+|+|||..
T Consensus        37 ~~lLl~GppGtGKT~l   52 (293)
T 3t15_A           37 LILGIWGGKGQGKSFQ   52 (293)
T ss_dssp             SEEEEEECTTSCHHHH
T ss_pred             eEEEEECCCCCCHHHH
Confidence            4588889999999975

>4a1f_A DNAB helicase, replicative DNA helicase; hydrolase, DNA replication, ATPase; HET: FLC; 2.50A {Helicobacter pylori}

Probab=88.05  E-value=0.42  Score=52.18  Aligned_cols=38  Identities=21%  Similarity=0.125  Sum_probs=24.4

Q ss_pred             cCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEcc
Q 002040          503 SGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAP  548 (976)
Q Consensus       503 ~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~P  548 (976)
                      .|.-+|+.|++|+|||..++..+. ++..       .+..|+|+..
T Consensus        45 ~G~LiiIaG~pG~GKTt~al~ia~-~~a~-------~g~~Vl~fSl   82 (338)
T 4a1f_A           45 KGSLVIIGARPSMGKTSLMMNMVL-SALN-------DDRGVAVFSL   82 (338)
T ss_dssp             TTCEEEEEECTTSCHHHHHHHHHH-HHHH-------TTCEEEEEES
T ss_pred             CCcEEEEEeCCCCCHHHHHHHHHH-HHHH-------cCCeEEEEeC
Confidence            345578889999999975444444 3332       2456777764

>1qvr_A CLPB protein; coiled coil, AAA ATPase, chaperone; HET: ANP; 3.00A {Thermus thermophilus} SCOP: a.174.1.1 c.37.1.20 c.37.1.20

Probab=87.95  E-value=0.92  Score=56.32  Aligned_cols=18  Identities=22%  Similarity=0.333  Sum_probs=15.2

Q ss_pred             CCCEEEEcCCCCchHHHH
Q 002040          504 GRDCIGVAKTGSGKTLAF  521 (976)
Q Consensus       504 g~d~i~~a~TGsGKT~~~  521 (976)
                      ..+++++|++|+|||..+
T Consensus       191 ~~~vlL~G~pG~GKT~la  208 (854)
T 1qvr_A          191 KNNPVLIGEPGVGKTAIV  208 (854)
T ss_dssp             CCCCEEEECTTSCHHHHH
T ss_pred             CCceEEEcCCCCCHHHHH
Confidence            357999999999999753

>2ce7_A Cell division protein FTSH; metalloprotease; HET: ADP; 2.44A {Thermotoga maritima} SCOP: a.269.1.1 c.37.1.20 PDB: 2cea_A* 3kds_E*

Probab=87.72  E-value=0.43  Score=54.66  Aligned_cols=17  Identities=35%  Similarity=0.479  Sum_probs=14.7

Q ss_pred             CCEEEEcCCCCchHHHH
Q 002040          505 RDCIGVAKTGSGKTLAF  521 (976)
Q Consensus       505 ~d~i~~a~TGsGKT~~~  521 (976)
                      +.++++||+|+|||+.+
T Consensus        50 ~gvLL~GppGtGKT~La   66 (476)
T 2ce7_A           50 KGILLVGPPGTGKTLLA   66 (476)
T ss_dssp             SEEEEECCTTSSHHHHH
T ss_pred             CeEEEECCCCCCHHHHH
Confidence            46999999999999853

>1cr0_A DNA primase/helicase; RECA-type protein fold, transferase; HET: DNA; 2.30A {Enterobacteria phage T7} SCOP: c.37.1.11 PDB: 1cr1_A* 1cr2_A* 1cr4_A* 1e0j_A* 1e0k_A*

Probab=87.71  E-value=0.64  Score=49.68  Aligned_cols=22  Identities=18%  Similarity=0.204  Sum_probs=17.2

Q ss_pred             cCCCEEEEcCCCCchHHHHHHH
Q 002040          503 SGRDCIGVAKTGSGKTLAFVLP  524 (976)
Q Consensus       503 ~g~d~i~~a~TGsGKT~~~~l~  524 (976)
                      .|.-++|+|++|+|||+.+...
T Consensus        34 ~G~~~~i~G~~G~GKTTl~~~i   55 (296)
T 1cr0_A           34 GGEVIMVTSGSGMGKSTFVRQQ   55 (296)
T ss_dssp             TTCEEEEEESTTSSHHHHHHHH
T ss_pred             CCeEEEEEeCCCCCHHHHHHHH
Confidence            4667889999999999764433

>2rb4_A ATP-dependent RNA helicase DDX25; rossmann fold, structural genomics, structural consortium, SGC, alternative initiation, ATP-binding, devel protein; 2.80A {Homo sapiens}

Probab=87.63  E-value=1.5  Score=42.72  Aligned_cols=71  Identities=15%  Similarity=0.207  Sum_probs=51.3

Q ss_pred             CCeEEEEccCHHHHHHHHHHHHHHHhhcCcEEEEeeCCCChHHHH---HHHhc-CCeEEEeCchhHHHHHHhcCCccccc
Q 002040          540 GPVGLIMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQI---SELKR-GTEIVVCTPGRMIDILCTSGGKITNL  615 (976)
Q Consensus       540 ~~~vLIl~Ptr~La~Q~~~~~~~~~~~~~~~~~~~~gg~~~~~~~---~~l~~-~~~Iiv~Tp~~L~~~l~~~~~~~~~l  615 (976)
                      +.++||.|+++..|..++..+..    .|+.+..++|+.+.....   ..+.. ...|+|||.-     +.    .-.++
T Consensus        34 ~~~~lVF~~~~~~~~~l~~~L~~----~~~~~~~~~g~~~~~~R~~~~~~f~~g~~~vLvaT~~-----~~----~Gid~  100 (175)
T 2rb4_A           34 IGQAIIFCQTRRNAKWLTVEMIQ----DGHQVSLLSGELTVEQRASIIQRFRDGKEKVLITTNV-----CA----RGIDV  100 (175)
T ss_dssp             CSEEEEECSCHHHHHHHHHHHHT----TTCCEEEECSSCCHHHHHHHHHHHHTTSCSEEEECCS-----CC----TTTCC
T ss_pred             CCCEEEEECCHHHHHHHHHHHHH----cCCcEEEEeCCCCHHHHHHHHHHHHcCCCeEEEEecc-----hh----cCCCc
Confidence            45899999999998887776655    578899999998766553   33333 4689999932     21    12577


Q ss_pred             CCceEEEe
Q 002040          616 RRVTYLVM  623 (976)
Q Consensus       616 ~~~~~vVl  623 (976)
                      ..+.+||.
T Consensus       101 ~~~~~Vi~  108 (175)
T 2rb4_A          101 KQVTIVVN  108 (175)
T ss_dssp             TTEEEEEE
T ss_pred             ccCCEEEE
Confidence            78888885

>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=87.56  E-value=3  Score=41.91  Aligned_cols=71  Identities=17%  Similarity=0.275  Sum_probs=54.0

Q ss_pred             CcEEEEecCHHHHHHHHHHHHHC-----CCCceeccCCCCHHHHHHHHHHhccCCccEEEecCc-----c-cccCCCCCC
Q 002040          715 GKILIFVHSQEKCDALFRDLLKH-----GYPCLSLHGAKDQTDRESTISDFKSNVCNLLIATSV-----A-ARGLDVKEL  783 (976)
Q Consensus       715 ~kvLIF~~s~~~~~~l~~~L~~~-----~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLVaT~v-----~-~~GlDi~~v  783 (976)
                      .++||.|++..-+..++..+...     ++.+..++|+.+......   .+..+...|+|+|.-     + ...+++..+
T Consensus        83 ~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~---~~~~~~~~i~v~T~~~l~~~~~~~~~~~~~~  159 (220)
T 1t6n_A           83 VSVLVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEE---VLKKNCPHIVVGTPGRILALARNKSLNLKHI  159 (220)
T ss_dssp             CCEEEECSCHHHHHHHHHHHHHHTTTSTTCCEEEESCCSCHHHHHH---HHHHSCCSEEEECHHHHHHHHHTTSSCCTTC
T ss_pred             EEEEEEeCCHHHHHHHHHHHHHHHhhCCCceEEEEeCCCChHHHHH---HHhcCCCCEEEeCHHHHHHHHHhCCCCcccC
Confidence            48999999999999988887764     688999999998765543   344567799999951     1 234677788


Q ss_pred             cEEEE
Q 002040          784 ELVIN  788 (976)
Q Consensus       784 ~~VI~  788 (976)
                      .+||.
T Consensus       160 ~~lVi  164 (220)
T 1t6n_A          160 KHFIL  164 (220)
T ss_dssp             CEEEE
T ss_pred             CEEEE
Confidence            88885

>1fuk_A Eukaryotic initiation factor 4A; helicase, DEAD-box protein, translation; 1.75A {Saccharomyces cerevisiae} SCOP: c.37.1.19

Probab=87.05  E-value=1.5  Score=42.23  Aligned_cols=72  Identities=15%  Similarity=0.318  Sum_probs=51.0

Q ss_pred             CCeEEEEccCHHHHHHHHHHHHHHHhhcCcEEEEeeCCCChHHHH---HHHhc-CCeEEEeCchhHHHHHHhcCCccccc
Q 002040          540 GPVGLIMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQI---SELKR-GTEIVVCTPGRMIDILCTSGGKITNL  615 (976)
Q Consensus       540 ~~~vLIl~Ptr~La~Q~~~~~~~~~~~~~~~~~~~~gg~~~~~~~---~~l~~-~~~Iiv~Tp~~L~~~l~~~~~~~~~l  615 (976)
                      +.++||.|+++..+..++..+..    .++.+..++|+.+..+..   ..+.. ...|+|||.     .+..+    .++
T Consensus        30 ~~~~lVF~~~~~~~~~l~~~L~~----~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~-----~~~~G----~d~   96 (165)
T 1fuk_A           30 VTQAVIFCNTRRKVEELTTKLRN----DKFTVSAIYSDLPQQERDTIMKEFRSGSSRILISTD-----LLARG----IDV   96 (165)
T ss_dssp             CSCEEEEESSHHHHHHHHHHHHH----TTCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEEEG-----GGTTT----CCC
T ss_pred             CCCEEEEECCHHHHHHHHHHHHH----cCCCEEEEECCCCHHHHHHHHHHHHcCCCEEEEEcC-----hhhcC----CCc
Confidence            45799999999998887777665    578899999998766543   33333 468999993     22221    567


Q ss_pred             CCceEEEec
Q 002040          616 RRVTYLVMD  624 (976)
Q Consensus       616 ~~~~~vVlD  624 (976)
                      ..+.+||.=
T Consensus        97 ~~~~~Vi~~  105 (165)
T 1fuk_A           97 QQVSLVINY  105 (165)
T ss_dssp             CSCSEEEES
T ss_pred             ccCCEEEEe
Confidence            778887763

>2cvh_A DNA repair and recombination protein RADB; filament formation, homologous recombination, ATPase domain, hyperthermophIle; HET: DNA; 2.20A {Thermococcus kodakarensis} PDB: 2cvf_A*

Probab=87.00  E-value=1.2  Score=44.69  Aligned_cols=22  Identities=23%  Similarity=-0.016  Sum_probs=16.8

Q ss_pred             CCCEEEEcCCCCchHHHHHHHH
Q 002040          504 GRDCIGVAKTGSGKTLAFVLPM  525 (976)
Q Consensus       504 g~d~i~~a~TGsGKT~~~~l~i  525 (976)
                      |.-+++.|++|+|||+.+...+
T Consensus        20 G~~~~i~G~~GsGKTtl~~~l~   41 (220)
T 2cvh_A           20 GVLTQVYGPYASGKTTLALQTG   41 (220)
T ss_dssp             TSEEEEECSTTSSHHHHHHHHH
T ss_pred             CEEEEEECCCCCCHHHHHHHHH
Confidence            4568899999999997644433

>3k1j_A LON protease, ATP-dependent protease LON; ATP-binding, nucleotide-binding, Pro hydrolase; HET: ADP PE8; 2.00A {Thermococcus onnurineus}

Probab=86.58  E-value=4.1  Score=48.26  Aligned_cols=24  Identities=17%  Similarity=0.257  Sum_probs=19.6

Q ss_pred             HHHHhcCCCEEEEcCCCCchHHHH
Q 002040          498 LPVIMSGRDCIGVAKTGSGKTLAF  521 (976)
Q Consensus       498 i~~il~g~d~i~~a~TGsGKT~~~  521 (976)
                      ...+..+..++++||+|+|||+.+
T Consensus        54 ~~~i~~g~~vll~Gp~GtGKTtla   77 (604)
T 3k1j_A           54 KTAANQKRHVLLIGEPGTGKSMLG   77 (604)
T ss_dssp             HHHHHTTCCEEEECCTTSSHHHHH
T ss_pred             cccccCCCEEEEEeCCCCCHHHHH
Confidence            344567889999999999999753

>3eaq_A Heat resistant RNA dependent ATPase; DEAD box RNA helicase, dimer, ATP-binding, helicase, hydrolase, nucleotide-binding; 2.30A {Thermus thermophilus} PDB: 3ear_A 3eas_A

Probab=86.41  E-value=3.8  Score=41.18  Aligned_cols=71  Identities=11%  Similarity=0.243  Sum_probs=51.2

Q ss_pred             CCeEEEEccCHHHHHHHHHHHHHHHhhcCcEEEEeeCCCChHHHHH---HHhc-CCeEEEeCchhHHHHHHhcCCccccc
Q 002040          540 GPVGLIMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQIS---ELKR-GTEIVVCTPGRMIDILCTSGGKITNL  615 (976)
Q Consensus       540 ~~~vLIl~Ptr~La~Q~~~~~~~~~~~~~~~~~~~~gg~~~~~~~~---~l~~-~~~Iiv~Tp~~L~~~l~~~~~~~~~l  615 (976)
                      +..+||.|+|+.-+..++..+..    .++.+..++|+.+..++..   .+.. ...|+|||.     .+..    -.++
T Consensus        31 ~~~~lVF~~~~~~~~~l~~~L~~----~~~~~~~lhg~~~~~~r~~~~~~f~~g~~~vlvaT~-----~~~~----Gidi   97 (212)
T 3eaq_A           31 PDRAMVFTRTKAETEEIAQGLLR----LGHPAQALHGDLSQGERERVLGAFRQGEVRVLVATD-----VAAR----GLDI   97 (212)
T ss_dssp             CSCEEEECSSHHHHHHHHHHHHH----HTCCEEEECSSSCHHHHHHHHHHHHSSSCCEEEECT-----TTTC----SSSC
T ss_pred             CCeEEEEeCCHHHHHHHHHHHHH----cCCCEEEEECCCCHHHHHHHHHHHHCCCCeEEEecC-----hhhc----CCCC
Confidence            45789999999988887776665    4788999999988766543   3333 468999993     2222    2577


Q ss_pred             CCceEEEe
Q 002040          616 RRVTYLVM  623 (976)
Q Consensus       616 ~~~~~vVl  623 (976)
                      ..+.+||.
T Consensus        98 ~~v~~Vi~  105 (212)
T 3eaq_A           98 PQVDLVVH  105 (212)
T ss_dssp             CCBSEEEE
T ss_pred             ccCcEEEE
Confidence            78888874

>2yhs_A FTSY, cell division protein FTSY; cell cycle, protein targeting, simibi class GTPase, GTP-BIND membrane, nucleotide-binding; 1.60A {Escherichia coli} PDB: 2qy9_A 2xxa_B* 1fts_A

Probab=86.39  E-value=1.3  Score=50.51  Aligned_cols=17  Identities=29%  Similarity=0.257  Sum_probs=13.9

Q ss_pred             CCEEEEcCCCCchHHHH
Q 002040          505 RDCIGVAKTGSGKTLAF  521 (976)
Q Consensus       505 ~d~i~~a~TGsGKT~~~  521 (976)
                      .-+.++|++|+|||+.+
T Consensus       294 eVI~LVGpNGSGKTTLl  310 (503)
T 2yhs_A          294 FVILMVGVNGVGKTTTI  310 (503)
T ss_dssp             EEEEEECCTTSSHHHHH
T ss_pred             eEEEEECCCcccHHHHH
Confidence            35778899999999853

>3hjh_A Transcription-repair-coupling factor; MFD, mutation frequency decline, ATP-binding, DNA DAMA repair, DNA-binding, helicase, hydrolase; 1.95A {Escherichia coli} PDB: 2b2n_A* 4dfc_A

Probab=86.27  E-value=1.5  Score=50.22  Aligned_cols=52  Identities=15%  Similarity=0.253  Sum_probs=38.7

Q ss_pred             cCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHHHHh
Q 002040          503 SGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAK  565 (976)
Q Consensus       503 ~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~~~~  565 (976)
                      .+....+.|-||||||+++.. ++..          .+..+|||||+..+|.|++..+..|+.
T Consensus        13 ~~~~~~l~g~~gs~ka~~~a~-l~~~----------~~~p~lvv~~~~~~A~~l~~~l~~~~~   64 (483)
T 3hjh_A           13 AGEQRLLGELTGAACATLVAE-IAER----------HAGPVVLIAPDMQNALRLHDEISQFTD   64 (483)
T ss_dssp             TTCEEEEECCCTTHHHHHHHH-HHHH----------SSSCEEEEESSHHHHHHHHHHHHHTCS
T ss_pred             CCCeEEEeCCCchHHHHHHHH-HHHH----------hCCCEEEEeCCHHHHHHHHHHHHhhCC
Confidence            355688899999999975322 2222          122479999999999999999998754

>2xxa_A Signal recognition particle protein; protein transport, RNA/RNA binding protein, hydrolase, gtpas; HET: GCP; 3.94A {Escherichia coli} PDB: 2j28_9

Probab=86.26  E-value=2.9  Score=47.21  Aligned_cols=57  Identities=16%  Similarity=0.176  Sum_probs=30.4

Q ss_pred             CEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEc--cCHHHHHHHHHHHHHHHhhcCcEEE
Q 002040          506 DCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMA--PTRELVQQIHSDIRKFAKVMGVRCV  572 (976)
Q Consensus       506 d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~--Ptr~La~Q~~~~~~~~~~~~~~~~~  572 (976)
                      .++++|++|+|||++.+-.+. ++...      .|.+|+++.  |.+..+...   +..+....++.+.
T Consensus       102 vI~ivG~~GvGKTT~a~~LA~-~l~~~------~G~kVllvd~D~~r~~a~~q---l~~~~~~~~l~v~  160 (433)
T 2xxa_A          102 VVLMAGLQGAGKTTSVGKLGK-FLREK------HKKKVLVVSADVYRPAAIKQ---LETLAEQVGVDFF  160 (433)
T ss_dssp             EEEEECSTTSSHHHHHHHHHH-HHHHT------SCCCEEEEECCCSSTTHHHH---HHHHHHHHTCEEC
T ss_pred             EEEEECCCCCCHHHHHHHHHH-HHHHh------cCCeEEEEecCCCCccHHHH---HHhhcccCCeeEE
Confidence            567779999999987544333 33321      144566655  444444322   2333344455543

>2jgn_A DBX, DDX3, ATP-dependent RNA helicase DDX3X; phosphorylation, nucleotide-binding, hydrolase, RNA-binding, ATP-binding, DNA-binding, nuclear protein; 1.91A {Homo sapiens}

Probab=85.96  E-value=1.8  Score=42.54  Aligned_cols=71  Identities=13%  Similarity=0.321  Sum_probs=43.3

Q ss_pred             CCeEEEEccCHHHHHHHHHHHHHHHhhcCcEEEEeeCCCChHHH---HHHHhc-CCeEEEeCchhHHHHHHhcCCccccc
Q 002040          540 GPVGLIMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQ---ISELKR-GTEIVVCTPGRMIDILCTSGGKITNL  615 (976)
Q Consensus       540 ~~~vLIl~Ptr~La~Q~~~~~~~~~~~~~~~~~~~~gg~~~~~~---~~~l~~-~~~Iiv~Tp~~L~~~l~~~~~~~~~l  615 (976)
                      +.++||.|+++..|..++..+..    .|+.+..++|+.+....   +..+.. ...|+|||.     .+..+    .++
T Consensus        46 ~~k~lVF~~~~~~~~~l~~~L~~----~g~~~~~lhg~~~~~~r~~~~~~f~~g~~~vLvaT~-----~~~~G----ldi  112 (185)
T 2jgn_A           46 DSLTLVFVETKKGADSLEDFLYH----EGYACTSIHGDRSQRDREEALHQFRSGKSPILVATA-----VAARG----LDI  112 (185)
T ss_dssp             CSCEEEEESCHHHHHHHHHHHHH----TTCCEEEEC--------CHHHHHHHHTSSSEEEEEC---------------CC
T ss_pred             CCeEEEEECCHHHHHHHHHHHHH----cCCceEEEeCCCCHHHHHHHHHHHHcCCCeEEEEcC-----hhhcC----CCc
Confidence            56799999999998887777665    57889999998765443   233333 568999993     22221    467


Q ss_pred             CCceEEEe
Q 002040          616 RRVTYLVM  623 (976)
Q Consensus       616 ~~~~~vVl  623 (976)
                      ..+.+||.
T Consensus       113 ~~~~~VI~  120 (185)
T 2jgn_A          113 SNVKHVIN  120 (185)
T ss_dssp             CSBSEEEE
T ss_pred             ccCCEEEE
Confidence            77888775

>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=85.66  E-value=1.8  Score=51.14  Aligned_cols=60  Identities=13%  Similarity=0.153  Sum_probs=55.1

Q ss_pred             cCCcEEEEecCHHHHHHHHHHHHHCCCCceeccCCCCHHHHHHHHHHh--ccCCccEEEecC
Q 002040          713 EKGKILIFVHSQEKCDALFRDLLKHGYPCLSLHGAKDQTDRESTISDF--KSNVCNLLIATS  772 (976)
Q Consensus       713 ~~~kvLIF~~s~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F--~~g~~~vLVaT~  772 (976)
                      ..+.+||++|++.-+......|...|+.+..++|+++..++..++..+  ..+..+|||+|+
T Consensus        83 ~~g~~lVisP~~~L~~q~~~~l~~~gi~~~~l~~~~~~~~~~~~~~~l~~~~~~~~Ilv~Tp  144 (591)
T 2v1x_A           83 SDGFTLVICPLISLMEDQLMVLKQLGISATMLNASSSKEHVKWVHAEMVNKNSELKLIYVTP  144 (591)
T ss_dssp             SSSEEEEECSCHHHHHHHHHHHHHHTCCEEECCSSCCHHHHHHHHHHHHCTTCCCCEEEECH
T ss_pred             cCCcEEEEeCHHHHHHHHHHHHHhcCCcEEEEeCCCCHHHHHHHHHHhhcccCCCCEEEECh
Confidence            467999999999999999999999999999999999999998888888  578899999997

>3cmu_A Protein RECA, recombinase A; homologous recombination, recombination/DNA complex; HET: DNA ADP; 4.20A {Escherichia coli}

Probab=85.45  E-value=1  Score=59.85  Aligned_cols=44  Identities=18%  Similarity=0.199  Sum_probs=31.2

Q ss_pred             HHHHhc------CCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccC
Q 002040          498 LPVIMS------GRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPT  549 (976)
Q Consensus       498 i~~il~------g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Pt  549 (976)
                      +..++.      +..++++||+|+|||..++..+.....        .|..|+++..-
T Consensus      1415 LD~lLG~GGi~~g~~vll~GppGtGKT~LA~ala~ea~~--------~G~~v~Fi~~e 1464 (2050)
T 3cmu_A         1415 LDIALGAGGLPMGRIVEIYGPESSGKTTLTLQVIAAAQR--------EGKTCAFIDAE 1464 (2050)
T ss_dssp             HHHHHSSSSEETTSEEEEECCTTSSHHHHHHHHHHHHHT--------TTCCEEEECTT
T ss_pred             HHHhcCCCCccCCeEEEEECCCCCCHHHHHHHHHHHHHH--------cCCcEEEEEcc
Confidence            555665      678999999999999876555554432        35667777754

>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=85.31  E-value=2.9  Score=43.22  Aligned_cols=71  Identities=14%  Similarity=0.246  Sum_probs=52.8

Q ss_pred             CCcEEEEecCHHHHHHHHHHHHHC----CCCceeccCCCCHHHHHHHHHHhccCCccEEEecCc-----cc--ccCCCCC
Q 002040          714 KGKILIFVHSQEKCDALFRDLLKH----GYPCLSLHGAKDQTDRESTISDFKSNVCNLLIATSV-----AA--RGLDVKE  782 (976)
Q Consensus       714 ~~kvLIF~~s~~~~~~l~~~L~~~----~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLVaT~v-----~~--~GlDi~~  782 (976)
                      ..++||.|+++.-+..++..|...    ++.+..++|+.+.......+    .+...|||+|.-     +.  .++++..
T Consensus       111 ~~~~lil~Ptr~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~----~~~~~I~v~Tp~~l~~~l~~~~~~~l~~  186 (249)
T 3ber_A          111 RLFALVLTPTRELAFQISEQFEALGSSIGVQSAVIVGGIDSMSQSLAL----AKKPHIIIATPGRLIDHLENTKGFNLRA  186 (249)
T ss_dssp             SSCEEEECSSHHHHHHHHHHHHHHHGGGTCCEEEECTTSCHHHHHHHH----HTCCSEEEECHHHHHHHHHHSTTCCCTT
T ss_pred             CceEEEEeCCHHHHHHHHHHHHHHhccCCeeEEEEECCCChHHHHHHh----cCCCCEEEECHHHHHHHHHcCCCcCccc
Confidence            347999999999998888777654    78899999998876554333    246889999951     11  3567778


Q ss_pred             CcEEEE
Q 002040          783 LELVIN  788 (976)
Q Consensus       783 v~~VI~  788 (976)
                      +.+||.
T Consensus       187 ~~~lVi  192 (249)
T 3ber_A          187 LKYLVM  192 (249)
T ss_dssp             CCEEEE
T ss_pred             cCEEEE
Confidence            888774

>1w5s_A Origin recognition complex subunit 2 ORC2; replication, CDC6, DNA replication initiation, DNA BIND protein, AAA+ ATPase; HET: ADP; 2.4A {Aeropyrum pernix} SCOP: a.4.5.11 c.37.1.20 PDB: 1w5t_A*

Probab=85.17  E-value=1.7  Score=48.55  Aligned_cols=17  Identities=29%  Similarity=0.352  Sum_probs=13.7

Q ss_pred             CCEEE--EcCCCCchHHHH
Q 002040          505 RDCIG--VAKTGSGKTLAF  521 (976)
Q Consensus       505 ~d~i~--~a~TGsGKT~~~  521 (976)
                      ..++|  .|+.|+|||..+
T Consensus        51 ~~~li~i~G~~G~GKT~L~   69 (412)
T 1w5s_A           51 VNMIYGSIGRVGIGKTTLA   69 (412)
T ss_dssp             EEEEEECTTCCSSSHHHHH
T ss_pred             CEEEEeCcCcCCCCHHHHH
Confidence            35777  799999999763

>2v3c_C SRP54, signal recognition 54 kDa protein; nucleotide-binding, signal recognition particle, GTP-binding, RNA-binding; 2.50A {Methanocaldococcus jannaschii} PDB: 3ndb_B

Probab=85.02  E-value=0.92  Score=51.32  Aligned_cols=21  Identities=29%  Similarity=0.154  Sum_probs=16.1

Q ss_pred             CCEEEEcCCCCchHHHHHHHH
Q 002040          505 RDCIGVAKTGSGKTLAFVLPM  525 (976)
Q Consensus       505 ~d~i~~a~TGsGKT~~~~l~i  525 (976)
                      ..++++|++|+|||+.+...+
T Consensus       100 ~vI~ivG~~GvGKTTla~~La  120 (432)
T 2v3c_C          100 NVILLVGIQGSGKTTTAAKLA  120 (432)
T ss_dssp             CCEEEECCSSSSTTHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHH
Confidence            468899999999998644433

>1t5i_A C_terminal domain of A probable ATP-dependent RNA helicase; RECA-like fold, PRE-mRNA processing protein; 1.90A {Homo sapiens} SCOP: c.37.1.19

Probab=84.66  E-value=1.6  Score=42.41  Aligned_cols=71  Identities=11%  Similarity=0.115  Sum_probs=50.8

Q ss_pred             CCeEEEEccCHHHHHHHHHHHHHHHhhcCcEEEEeeCCCChHHHH---HHHhc-CCeEEEeCchhHHHHHHhcCCccccc
Q 002040          540 GPVGLIMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQI---SELKR-GTEIVVCTPGRMIDILCTSGGKITNL  615 (976)
Q Consensus       540 ~~~vLIl~Ptr~La~Q~~~~~~~~~~~~~~~~~~~~gg~~~~~~~---~~l~~-~~~Iiv~Tp~~L~~~l~~~~~~~~~l  615 (976)
                      +.++||.|+++..+..++..+..    .++.+..++|+.+..+..   ..+.. ...|+|||.-     +.    .-.++
T Consensus        31 ~~~~lVF~~~~~~~~~l~~~L~~----~~~~~~~~hg~~~~~~r~~~~~~f~~g~~~vLvaT~~-----~~----~Gldi   97 (172)
T 1t5i_A           31 FNQVVIFVKSVQRCIALAQLLVE----QNFPAIAIHRGMPQEERLSRYQQFKDFQRRILVATNL-----FG----RGMDI   97 (172)
T ss_dssp             CSSEEEECSSHHHHHHHHHHHHH----TTCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEESSC-----CS----TTCCG
T ss_pred             CCcEEEEECCHHHHHHHHHHHHh----cCCCEEEEECCCCHHHHHHHHHHHHCCCCcEEEECCc-----hh----cCcch
Confidence            45799999999999888777765    478899999998766553   33333 4689999942     11    12567


Q ss_pred             CCceEEEe
Q 002040          616 RRVTYLVM  623 (976)
Q Consensus       616 ~~~~~vVl  623 (976)
                      ..+.+||.
T Consensus        98 ~~~~~Vi~  105 (172)
T 1t5i_A           98 ERVNIAFN  105 (172)
T ss_dssp             GGCSEEEE
T ss_pred             hhCCEEEE
Confidence            77888775

>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=84.60  E-value=3.3  Score=48.12  Aligned_cols=76  Identities=11%  Similarity=0.090  Sum_probs=62.9

Q ss_pred             cCCcEEEEecCHHHHHHHHHHHHHCCCCceeccCCCCHHHHHHHHHHhccCCccEEEecCc-c-----cccCCCCCCcEE
Q 002040          713 EKGKILIFVHSQEKCDALFRDLLKHGYPCLSLHGAKDQTDRESTISDFKSNVCNLLIATSV-A-----ARGLDVKELELV  786 (976)
Q Consensus       713 ~~~kvLIF~~s~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLVaT~v-~-----~~GlDi~~v~~V  786 (976)
                      ..+.+||++|++.-+......|...|+.+..+||+.+..++..++..+..|..+|||+|+- +     ...+....+.+|
T Consensus        64 ~~g~~lvi~P~~aL~~q~~~~l~~~gi~~~~l~~~~~~~~~~~~~~~~~~~~~~ilv~Tpe~l~~~~~~~~l~~~~~~~v  143 (523)
T 1oyw_A           64 LNGLTVVVSPLISLMKDQVDQLQANGVAAACLNSTQTREQQLEVMTGCRTGQIRLLYIAPERLMLDNFLEHLAHWNPVLL  143 (523)
T ss_dssp             SSSEEEEECSCHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHHTCCSEEEECHHHHTSTTHHHHHTTSCEEEE
T ss_pred             hCCCEEEECChHHHHHHHHHHHHHcCCcEEEEeCCCCHHHHHHHHHHHhcCCCCEEEECHHHHhChHHHHHHhhCCCCEE
Confidence            4689999999999999999999999999999999999999999999999999999999952 1     122334556666


Q ss_pred             EE
Q 002040          787 IN  788 (976)
Q Consensus       787 I~  788 (976)
                      |.
T Consensus       144 Vi  145 (523)
T 1oyw_A          144 AV  145 (523)
T ss_dssp             EE
T ss_pred             EE
Confidence            64

>1j8m_F SRP54, signal recognition 54 kDa protein; signaling protein; 2.00A {Acidianus ambivalens} SCOP: a.24.13.1 c.37.1.10 PDB: 1j8y_F

Probab=84.50  E-value=4  Score=43.55  Aligned_cols=20  Identities=25%  Similarity=0.084  Sum_probs=15.0

Q ss_pred             CCCEEEEcCCCCchHHHHHH
Q 002040          504 GRDCIGVAKTGSGKTLAFVL  523 (976)
Q Consensus       504 g~d~i~~a~TGsGKT~~~~l  523 (976)
                      +.-++++|++|+|||+.+..
T Consensus        98 ~~vi~i~G~~G~GKTT~~~~  117 (297)
T 1j8m_F           98 PYVIMLVGVQGTGKTTTAGK  117 (297)
T ss_dssp             SEEEEEECSSCSSTTHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHH
Confidence            34567789999999986443

>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=84.47  E-value=5.2  Score=40.93  Aligned_cols=71  Identities=8%  Similarity=0.093  Sum_probs=52.9

Q ss_pred             CCcEEEEecCHHHHHHHHHHHHH----CCCCceeccCCCCHHHHHHHHHHhccCCccEEEecC-----ccc-ccCCCCCC
Q 002040          714 KGKILIFVHSQEKCDALFRDLLK----HGYPCLSLHGAKDQTDRESTISDFKSNVCNLLIATS-----VAA-RGLDVKEL  783 (976)
Q Consensus       714 ~~kvLIF~~s~~~~~~l~~~L~~----~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLVaT~-----v~~-~GlDi~~v  783 (976)
                      ...+||.|+++.-+..++..+..    .++.+..++|+.+.......+..    ...|||+|.     .+. ..+++..+
T Consensus       102 ~~~~lil~Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~----~~~I~v~Tp~~l~~~l~~~~~~~~~~  177 (242)
T 3fe2_A          102 GPICLVLAPTRELAQQVQQVAAEYCRACRLKSTCIYGGAPKGPQIRDLER----GVEICIATPGRLIDFLECGKTNLRRT  177 (242)
T ss_dssp             CCSEEEECSSHHHHHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHH----CCSEEEECHHHHHHHHHHTSCCCTTC
T ss_pred             CCEEEEEeCcHHHHHHHHHHHHHHHhhcCceEEEEECCCChHHHHHHhcC----CCCEEEECHHHHHHHHHcCCCCcccc
Confidence            45799999999988888776654    48899999999987766554432    478999995     222 34577788


Q ss_pred             cEEEE
Q 002040          784 ELVIN  788 (976)
Q Consensus       784 ~~VI~  788 (976)
                      .+||.
T Consensus       178 ~~lVi  182 (242)
T 3fe2_A          178 TYLVL  182 (242)
T ss_dssp             CEEEE
T ss_pred             cEEEE
Confidence            88874

>2zts_A Putative uncharacterized protein PH0186; KAIC like protein, ATP-binding, nucleotide-binding, ATP- binding protein; HET: ADP; 2.07A {Pyrococcus horikoshii}

Probab=84.37  E-value=0.69  Score=47.65  Aligned_cols=50  Identities=18%  Similarity=0.310  Sum_probs=28.6

Q ss_pred             CCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHH
Q 002040          504 GRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIR  561 (976)
Q Consensus       504 g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~  561 (976)
                      |.-+++.|++|+|||..++-.+++.+...       +..+++++-. .-..++...+.
T Consensus        30 G~l~~i~G~pG~GKT~l~l~~~~~~~~~~-------~~~v~~~s~E-~~~~~~~~~~~   79 (251)
T 2zts_A           30 GTTVLLTGGTGTGKTTFAAQFIYKGAEEY-------GEPGVFVTLE-ERARDLRREMA   79 (251)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHHHHHHHHH-------CCCEEEEESS-SCHHHHHHHHH
T ss_pred             CeEEEEEeCCCCCHHHHHHHHHHHHHHhc-------CCCceeeccc-CCHHHHHHHHH
Confidence            56689999999999976444444433321       3345666532 22344444443

>1um8_A ATP-dependent CLP protease ATP-binding subunit CL; CLPP binding loop, chaperone; HET: ADP; 2.60A {Helicobacter pylori} SCOP: c.37.1.20

Probab=84.36  E-value=1.1  Score=49.55  Aligned_cols=19  Identities=42%  Similarity=0.492  Sum_probs=15.9

Q ss_pred             cCCCEEEEcCCCCchHHHH
Q 002040          503 SGRDCIGVAKTGSGKTLAF  521 (976)
Q Consensus       503 ~g~d~i~~a~TGsGKT~~~  521 (976)
                      ....++++||+|+|||..+
T Consensus        71 ~~~~ill~Gp~GtGKT~la   89 (376)
T 1um8_A           71 SKSNILLIGPTGSGKTLMA   89 (376)
T ss_dssp             CCCCEEEECCTTSSHHHHH
T ss_pred             CCCCEEEECCCCCCHHHHH
Confidence            3568999999999999753

>2j37_W Signal recognition particle 54 kDa protein (SRP54); ribosome, SRP, translation/RNA; 8.00A {Canis SP} PDB: 1wgw_A

Probab=83.93  E-value=6.2  Score=45.36  Aligned_cols=57  Identities=16%  Similarity=0.006  Sum_probs=30.6

Q ss_pred             CEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEcc--CHHHHHHHHHHHHHHHhhcCcEEEE
Q 002040          506 DCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAP--TRELVQQIHSDIRKFAKVMGVRCVP  573 (976)
Q Consensus       506 d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~P--tr~La~Q~~~~~~~~~~~~~~~~~~  573 (976)
                      .++++|.+|+|||+.+.-.+ .++..       .|.+++++..  .+..+..+.   ..+....++.+..
T Consensus       103 vI~ivG~~GvGKTTl~~kLA-~~l~~-------~G~kVllVd~D~~r~aa~~qL---~~~~~~~~i~v~~  161 (504)
T 2j37_W          103 VIMFVGLQGSGKTTTCSKLA-YYYQR-------KGWKTCLICADTFRAGAFDQL---KQNATKARIPFYG  161 (504)
T ss_dssp             EEEEECSTTSSHHHHHHHHH-HHHHH-------TTCCEEEEEECCSSSHHHHHH---HHHHHHHTCCEEE
T ss_pred             EEEEECCCCCCHHHHHHHHH-HHHHh-------CCCeEEEEeccccchhHHHHH---HHHhhccCceEEc
Confidence            47788999999998744333 33332       1445666654  344443332   2233334555444

>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=83.93  E-value=5.5  Score=46.54  Aligned_cols=96  Identities=19%  Similarity=0.253  Sum_probs=63.1

Q ss_pred             CchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHHHHhhcCcEEEEeeCCCChHHHHH---HHhc-C
Q 002040          515 SGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQIS---ELKR-G  590 (976)
Q Consensus       515 sGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~~~~~~~~~~~~~~gg~~~~~~~~---~l~~-~  590 (976)
                      ..+....+..+...+...     ..+.++||.|+|+.-|..++..+...+. .++.+..++|+.+......   .+.. .
T Consensus       319 ~~~~~~~~~~l~~~~~~~-----~~~~~~iVF~~s~~~~~~l~~~L~~~~~-~~~~v~~~h~~~~~~~R~~~~~~f~~g~  392 (563)
T 3i5x_A          319 ANSIFAAVEHIKKQIKER-----DSNYKAIIFAPTVKFTSFLCSILKNEFK-KDLPILEFHGKITQNKRTSLVKRFKKDE  392 (563)
T ss_dssp             THHHHHHHHHHHHHHHHT-----TTCCEEEEECSCHHHHHHHHHHHHHHHT-TTSCEEEESTTSCHHHHHHHHHHHHHCS
T ss_pred             HhhHHHHHHHHHHHHhhc-----CCCCcEEEEcCcHHHHHHHHHHHHHhcc-CCceEEEecCCCCHHHHHHHHHHHhcCC
Confidence            344444444444444432     2356899999999999999888877543 3778888999987665533   3333 5


Q ss_pred             CeEEEeCchhHHHHHHhcCCcccccCCceEEEecC
Q 002040          591 TEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDE  625 (976)
Q Consensus       591 ~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDE  625 (976)
                      ..|+|||.     .+...    .++..+.+||.-.
T Consensus       393 ~~vLvaT~-----~~~~G----iDip~v~~VI~~~  418 (563)
T 3i5x_A          393 SGILVCTD-----VGARG----MDFPNVHEVLQIG  418 (563)
T ss_dssp             SEEEEECG-----GGTSS----CCCTTCCEEEEES
T ss_pred             CCEEEEcc-----hhhcC----CCcccCCEEEEEC
Confidence            79999994     23222    5778888887533

>1xp8_A RECA protein, recombinase A; recombination, radioresistance, DNA-repair, ATPase, DNA-BIND protein, DNA binding protein; HET: AGS; 2.50A {Deinococcus radiodurans} SCOP: c.37.1.11 d.48.1.1

Probab=83.46  E-value=2.2  Score=47.06  Aligned_cols=38  Identities=18%  Similarity=0.218  Sum_probs=24.2

Q ss_pred             CCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccC
Q 002040          504 GRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPT  549 (976)
Q Consensus       504 g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Pt  549 (976)
                      |.-++|.|++|+|||.. ++.++..+...       +..|+|+..-
T Consensus        74 G~li~I~G~pGsGKTtl-al~la~~~~~~-------g~~vlyi~~E  111 (366)
T 1xp8_A           74 GRITEIYGPESGGKTTL-ALAIVAQAQKA-------GGTCAFIDAE  111 (366)
T ss_dssp             TSEEEEEESTTSSHHHH-HHHHHHHHHHT-------TCCEEEEESS
T ss_pred             CcEEEEEcCCCCChHHH-HHHHHHHHHHC-------CCeEEEEECC
Confidence            45688889999999975 44444444332       3356666543

>3cf2_A TER ATPase, transitional endoplasmic reticulum ATPase, valosi; AAA, CDC48, ERAD, transport protein; HET: ADP ANP; 3.50A {Mus musculus} PDB: 3cf1_A* 3cf3_A* 1r7r_A*

Probab=83.40  E-value=1.3  Score=54.04  Aligned_cols=55  Identities=22%  Similarity=0.360  Sum_probs=33.7

Q ss_pred             CCcccccccCCCCHHHHHHHHHc---CCCCCcHHHHHHHHHHhcCCCEEEEcCCCCchHHH
Q 002040          463 PKPIKTWHQTGLTSKIMETIRKL---NYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLA  520 (976)
Q Consensus       463 p~pi~~~~~~~l~~~l~~~l~~~---~~~~p~~~Q~~~i~~il~g~d~i~~a~TGsGKT~~  520 (976)
                      ..|-.+|.+.+....+.+.|...   .+..|.-++.-.   +...+.+|+.||+|+|||+.
T Consensus       470 ~~p~v~w~diggl~~~k~~l~e~v~~p~~~p~~f~~~g---~~~~~gvLl~GPPGtGKT~l  527 (806)
T 3cf2_A          470 EVPQVTWEDIGGLEDVKRELQELVQYPVEHPDKFLKFG---MTPSKGVLFYGPPGCGKTLL  527 (806)
T ss_dssp             BCCCCCSTTCCSCHHHHHHHTTTTTTTTTCSGGGSSSC---CCCCSCCEEESSTTSSHHHH
T ss_pred             cCCCCCHHHhCCHHHHHHHHHHHHHhhhhCHHHHHhcC---CCCCceEEEecCCCCCchHH
Confidence            34567899998888887776642   222221111100   01235799999999999975

>2fna_A Conserved hypothetical protein; structural genomics, joint center for structural genomics, J protein structure initiative, PSI-2; HET: MSE ADP; 2.00A {Sulfolobus solfataricus} SCOP: a.4.5.11 c.37.1.20

Probab=83.02  E-value=17  Score=38.96  Aligned_cols=16  Identities=13%  Similarity=0.069  Sum_probs=14.1

Q ss_pred             CCEEEEcCCCCchHHH
Q 002040          505 RDCIGVAKTGSGKTLA  520 (976)
Q Consensus       505 ~d~i~~a~TGsGKT~~  520 (976)
                      ..++|.|+.|+|||..
T Consensus        31 ~~v~i~G~~G~GKT~L   46 (357)
T 2fna_A           31 PITLVLGLRRTGKSSI   46 (357)
T ss_dssp             SEEEEEESTTSSHHHH
T ss_pred             CcEEEECCCCCCHHHH
Confidence            5788999999999975

>1r6b_X CLPA protein; AAA+, N-terminal domain, CLPS, crystal, binding mechanism, hydrolase; HET: ADP; 2.25A {Escherichia coli} SCOP: a.174.1.1 c.37.1.20 c.37.1.20 PDB: 1ksf_X*

Probab=82.93  E-value=2.6  Score=51.48  Aligned_cols=19  Identities=26%  Similarity=0.295  Sum_probs=15.9

Q ss_pred             cCCCEEEEcCCCCchHHHH
Q 002040          503 SGRDCIGVAKTGSGKTLAF  521 (976)
Q Consensus       503 ~g~d~i~~a~TGsGKT~~~  521 (976)
                      .+.++|++|++|+|||..+
T Consensus       206 ~~~~vlL~G~~GtGKT~la  224 (758)
T 1r6b_X          206 RKNNPLLVGESGVGKTAIA  224 (758)
T ss_dssp             SSCEEEEECCTTSSHHHHH
T ss_pred             CCCCeEEEcCCCCCHHHHH
Confidence            3567999999999999763

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

Probab=82.43  E-value=4.7  Score=40.97  Aligned_cols=70  Identities=21%  Similarity=0.287  Sum_probs=49.1

Q ss_pred             CCcEEEEecCHHHHHHHHHHHHHC----CCCceeccCCCCHHHHHHHHHHhccCCccEEEecCc-----ccc--cCCCCC
Q 002040          714 KGKILIFVHSQEKCDALFRDLLKH----GYPCLSLHGAKDQTDRESTISDFKSNVCNLLIATSV-----AAR--GLDVKE  782 (976)
Q Consensus       714 ~~kvLIF~~s~~~~~~l~~~L~~~----~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLVaT~v-----~~~--GlDi~~  782 (976)
                      ..++||.|++..-+..++..+...    ++.+..++|+.+.......+     +..+|+|+|.-     +..  .+++..
T Consensus        97 ~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~-----~~~~iiv~Tp~~l~~~l~~~~~~~~~~  171 (236)
T 2pl3_A           97 GLGVLIISPTRELAYQTFEVLRKVGKNHDFSAGLIIGGKDLKHEAERI-----NNINILVCTPGRLLQHMDETVSFHATD  171 (236)
T ss_dssp             CCCEEEECSSHHHHHHHHHHHHHHTTTSSCCEEEECCC--CHHHHHHH-----TTCSEEEECHHHHHHHHHHCSSCCCTT
T ss_pred             CceEEEEeCCHHHHHHHHHHHHHHhCCCCeeEEEEECCCCHHHHHHhC-----CCCCEEEECHHHHHHHHHhcCCccccc
Confidence            558999999999999988888765    47888999988755443333     46789999951     112  356667


Q ss_pred             CcEEEE
Q 002040          783 LELVIN  788 (976)
Q Consensus       783 v~~VI~  788 (976)
                      +.+||.
T Consensus       172 ~~~lVi  177 (236)
T 2pl3_A          172 LQMLVL  177 (236)
T ss_dssp             CCEEEE
T ss_pred             ccEEEE
Confidence            777774

>3bh0_A DNAB-like replicative helicase; ATPase, replication; 2.35A {Bacillus phage SPP1}

Probab=82.34  E-value=1  Score=48.60  Aligned_cols=50  Identities=12%  Similarity=-0.051  Sum_probs=29.1

Q ss_pred             cCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHH
Q 002040          503 SGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIR  561 (976)
Q Consensus       503 ~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~  561 (976)
                      .|.-++|+|++|+|||..++..+... ..+       +..|++++.- .-..|+...+.
T Consensus        67 ~G~l~li~G~pG~GKTtl~l~ia~~~-a~~-------g~~vl~~slE-~s~~~l~~R~~  116 (315)
T 3bh0_A           67 RRNFVLIAARPSMGKTAFALKQAKNM-SDN-------DDVVNLHSLE-MGKKENIKRLI  116 (315)
T ss_dssp             TTCEEEEECCTTSSHHHHHHHHHHHH-HTT-------TCEEEEEESS-SCHHHHHHHHH
T ss_pred             CCcEEEEEeCCCCCHHHHHHHHHHHH-HHc-------CCeEEEEECC-CCHHHHHHHHH
Confidence            35668899999999997544444433 321       3457777633 22344444443

>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=82.32  E-value=2.7  Score=42.75  Aligned_cols=70  Identities=16%  Similarity=0.296  Sum_probs=51.8

Q ss_pred             CCcEEEEecCHHHHHHHHHHHHHC-----CCCceeccCCCCHHHHHHHHHHhccCCccEEEecCc-c-----cccCCCCC
Q 002040          714 KGKILIFVHSQEKCDALFRDLLKH-----GYPCLSLHGAKDQTDRESTISDFKSNVCNLLIATSV-A-----ARGLDVKE  782 (976)
Q Consensus       714 ~~kvLIF~~s~~~~~~l~~~L~~~-----~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLVaT~v-~-----~~GlDi~~  782 (976)
                      ..++||.|+++.-+..++..+...     ++.+..++|+.+.......+     ....|+|+|.- +     ...+++..
T Consensus        92 ~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~-----~~~~Iiv~Tp~~l~~~~~~~~~~~~~  166 (230)
T 2oxc_A           92 STQILILAPTREIAVQIHSVITAIGIKMEGLECHVFIGGTPLSQDKTRL-----KKCHIAVGSPGRIKQLIELDYLNPGS  166 (230)
T ss_dssp             SCCEEEECSSHHHHHHHHHHHHHHTTTSTTCCEEEECTTSCHHHHHHHT-----TSCSEEEECHHHHHHHHHTTSSCGGG
T ss_pred             CceEEEEeCCHHHHHHHHHHHHHHhcccCCceEEEEeCCCCHHHHHHhc-----cCCCEEEECHHHHHHHHhcCCccccc
Confidence            458999999999999998888764     67889999999876654433     25789999962 1     13456667


Q ss_pred             CcEEEE
Q 002040          783 LELVIN  788 (976)
Q Consensus       783 v~~VI~  788 (976)
                      +.+||.
T Consensus       167 ~~~lVi  172 (230)
T 2oxc_A          167 IRLFIL  172 (230)
T ss_dssp             CCEEEE
T ss_pred             CCEEEe
Confidence            777764

>1n0w_A DNA repair protein RAD51 homolog 1; DNA repair, homologous recombination, breast cancer susceptibility, RECA-like ATPase, protein complex; HET: DNA MSE; 1.70A {Homo sapiens} SCOP: c.37.1.11

Probab=82.31  E-value=1.9  Score=44.12  Aligned_cols=24  Identities=17%  Similarity=0.032  Sum_probs=17.9

Q ss_pred             cCCCEEEEcCCCCchHHHHHHHHH
Q 002040          503 SGRDCIGVAKTGSGKTLAFVLPML  526 (976)
Q Consensus       503 ~g~d~i~~a~TGsGKT~~~~l~il  526 (976)
                      .|.-++++|++|+|||+.+...+.
T Consensus        23 ~G~~~~i~G~~GsGKTtl~~~l~~   46 (243)
T 1n0w_A           23 TGSITEMFGEFRTGKTQICHTLAV   46 (243)
T ss_dssp             TTSEEEEECCTTSSHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCcHHHHHHHHHH
Confidence            356788999999999986544333

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

Probab=82.21  E-value=4.6  Score=44.87  Aligned_cols=72  Identities=13%  Similarity=0.295  Sum_probs=53.2

Q ss_pred             CCCeEEEEccCHHHHHHHHHHHHHHHhhcCcEEEEeeCCCChHHHHH---HHhc-CCeEEEeCchhHHHHHHhcCCcccc
Q 002040          539 DGPVGLIMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQIS---ELKR-GTEIVVCTPGRMIDILCTSGGKITN  614 (976)
Q Consensus       539 ~~~~vLIl~Ptr~La~Q~~~~~~~~~~~~~~~~~~~~gg~~~~~~~~---~l~~-~~~Iiv~Tp~~L~~~l~~~~~~~~~  614 (976)
                      .+.++||+|+++..+..++..+..    .++.+..++|+.+..+...   .+.. ...|+|||.     .+..+    .+
T Consensus       275 ~~~~~lVf~~~~~~~~~l~~~L~~----~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlvaT~-----~~~~G----id  341 (417)
T 2i4i_A          275 KDSLTLVFVETKKGADSLEDFLYH----EGYACTSIHGDRSQRDREEALHQFRSGKSPILVATA-----VAARG----LD  341 (417)
T ss_dssp             TTCEEEEECSSHHHHHHHHHHHHH----TTCCEEEECTTSCHHHHHHHHHHHHHTSSCEEEECH-----HHHTT----SC
T ss_pred             CCCeEEEEECCHHHHHHHHHHHHH----CCCCeeEecCCCCHHHHHHHHHHHHcCCCCEEEECC-----hhhcC----CC
Confidence            467899999999999888777765    5788999999988665533   3333 468999994     44433    57


Q ss_pred             cCCceEEEe
Q 002040          615 LRRVTYLVM  623 (976)
Q Consensus       615 l~~~~~vVl  623 (976)
                      +..+.+||.
T Consensus       342 ip~v~~Vi~  350 (417)
T 2i4i_A          342 ISNVKHVIN  350 (417)
T ss_dssp             CCCEEEEEE
T ss_pred             cccCCEEEE
Confidence            778888875

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

Probab=82.00  E-value=7.3  Score=45.75  Aligned_cols=78  Identities=17%  Similarity=0.224  Sum_probs=55.8

Q ss_pred             CCCeEEEEccCHHHHHHHHHHHHHHHhhcCcEEEEeeCCCChHHHH---HHHhc-CCeEEEeCchhHHHHHHhcCCcccc
Q 002040          539 DGPVGLIMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQI---SELKR-GTEIVVCTPGRMIDILCTSGGKITN  614 (976)
Q Consensus       539 ~~~~vLIl~Ptr~La~Q~~~~~~~~~~~~~~~~~~~~gg~~~~~~~---~~l~~-~~~Iiv~Tp~~L~~~l~~~~~~~~~  614 (976)
                      .+.++||.|+|+..|..++..+...+. .++.+..++|+.+.....   ..+.. ...|+|||.     .+..+    .+
T Consensus       287 ~~~~~iVF~~t~~~~~~l~~~L~~~~~-~~~~v~~~hg~~~~~~R~~~~~~F~~g~~~vLVaT~-----~~~~G----iD  356 (579)
T 3sqw_A          287 SNYKAIIFAPTVKFTSFLCSILKNEFK-KDLPILEFHGKITQNKRTSLVKRFKKDESGILVCTD-----VGARG----MD  356 (579)
T ss_dssp             TCCEEEEECSSHHHHHHHHHHHHHHHT-TTSCEEEESTTSCHHHHHHHHHHHHHCSSEEEEECG-----GGTSS----CC
T ss_pred             CCCcEEEECCcHHHHHHHHHHHHHhhc-CCCcEEEecCCCCHHHHHHHHHHhhcCCCeEEEEcc-----hhhcC----CC
Confidence            356899999999999999888877543 377888899998766543   33333 579999994     23222    57


Q ss_pred             cCCceEEEecCc
Q 002040          615 LRRVTYLVMDEA  626 (976)
Q Consensus       615 l~~~~~vVlDEa  626 (976)
                      +..+.+||.-..
T Consensus       357 ip~v~~VI~~~~  368 (579)
T 3sqw_A          357 FPNVHEVLQIGV  368 (579)
T ss_dssp             CTTCCEEEEESC
T ss_pred             cccCCEEEEcCC
Confidence            788888885443

>3i32_A Heat resistant RNA dependent ATPase; RNA helicase, dimer, RNA recognition motif, ATP-BIND helicase, nucleotide-binding; 2.80A {Thermus thermophilus}

Probab=81.51  E-value=5.3  Score=42.61  Aligned_cols=71  Identities=11%  Similarity=0.246  Sum_probs=50.8

Q ss_pred             CCeEEEEccCHHHHHHHHHHHHHHHhhcCcEEEEeeCCCChHHHHH---HHhc-CCeEEEeCchhHHHHHHhcCCccccc
Q 002040          540 GPVGLIMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQIS---ELKR-GTEIVVCTPGRMIDILCTSGGKITNL  615 (976)
Q Consensus       540 ~~~vLIl~Ptr~La~Q~~~~~~~~~~~~~~~~~~~~gg~~~~~~~~---~l~~-~~~Iiv~Tp~~L~~~l~~~~~~~~~l  615 (976)
                      +..+||.|+|+.-+..++..+..    .++.+..++|+.+..++..   .+.. ...|+|||.     .+..    -.++
T Consensus        28 ~~~~LVF~~t~~~~~~l~~~L~~----~g~~~~~lhg~l~~~~r~~~~~~f~~g~~~vLVaT~-----va~~----Gidi   94 (300)
T 3i32_A           28 PDRAMVFTRTKAETEEIAQGLLR----LGHPAQALHGDMSQGERERVMGAFRQGEVRVLVATD-----VAAR----GLDI   94 (300)
T ss_dssp             CSSEEEECSSHHHHHHHHHHHHT----TTCCEEEECSCCCTHHHHHHHHHHHHTSCCEEEECS-----TTTC----STTC
T ss_pred             CCCEEEEECCHHHHHHHHHHHHh----CCCCEEEEeCCCCHHHHHHHHHHhhcCCceEEEEec-----hhhc----Cccc
Confidence            45789999999988777666554    5889999999987666543   3333 468999993     2222    2577


Q ss_pred             CCceEEEe
Q 002040          616 RRVTYLVM  623 (976)
Q Consensus       616 ~~~~~vVl  623 (976)
                      ..+.+||.
T Consensus        95 ~~v~~VI~  102 (300)
T 3i32_A           95 PQVDLVVH  102 (300)
T ss_dssp             CCCSEEEE
T ss_pred             cceeEEEE
Confidence            78888884

>3cf2_A TER ATPase, transitional endoplasmic reticulum ATPase, valosi; AAA, CDC48, ERAD, transport protein; HET: ADP ANP; 3.50A {Mus musculus} PDB: 3cf1_A* 3cf3_A* 1r7r_A*

Probab=81.43  E-value=1  Score=54.85  Aligned_cols=16  Identities=38%  Similarity=0.513  Sum_probs=14.4

Q ss_pred             CCEEEEcCCCCchHHH
Q 002040          505 RDCIGVAKTGSGKTLA  520 (976)
Q Consensus       505 ~d~i~~a~TGsGKT~~  520 (976)
                      +.+|+.||+|+|||+.
T Consensus       239 ~GILL~GPPGTGKT~L  254 (806)
T 3cf2_A          239 RGILLYGPPGTGKTLI  254 (806)
T ss_dssp             CEEEEECCTTSCHHHH
T ss_pred             CeEEEECCCCCCHHHH
Confidence            5799999999999975

>2px0_A Flagellar biosynthesis protein FLHF; SRP GTPase, flagellum, protein transport, biosynthetic protein; HET: GNP; 3.00A {Bacillus subtilis} PDB: 2px3_A* 3syn_A*

Probab=81.39  E-value=1.5  Score=46.81  Aligned_cols=23  Identities=22%  Similarity=0.251  Sum_probs=17.3

Q ss_pred             cCCCEEEEcCCCCchHHHHHHHH
Q 002040          503 SGRDCIGVAKTGSGKTLAFVLPM  525 (976)
Q Consensus       503 ~g~d~i~~a~TGsGKT~~~~l~i  525 (976)
                      .+..++++|++|+|||+.+...+
T Consensus       104 ~g~vi~lvG~~GsGKTTl~~~LA  126 (296)
T 2px0_A          104 HSKYIVLFGSTGAGKTTTLAKLA  126 (296)
T ss_dssp             CSSEEEEEESTTSSHHHHHHHHH
T ss_pred             CCcEEEEECCCCCCHHHHHHHHH
Confidence            35678889999999998644433

>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=81.36  E-value=11  Score=38.49  Aligned_cols=70  Identities=17%  Similarity=0.235  Sum_probs=50.1

Q ss_pred             CcEEEEecCHHHHHHHHHHHHHC----CCCceeccCCCCHHHHHHHHHHhccCCccEEEecCc-----c-cccCCCCCCc
Q 002040          715 GKILIFVHSQEKCDALFRDLLKH----GYPCLSLHGAKDQTDRESTISDFKSNVCNLLIATSV-----A-ARGLDVKELE  784 (976)
Q Consensus       715 ~kvLIF~~s~~~~~~l~~~L~~~----~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLVaT~v-----~-~~GlDi~~v~  784 (976)
                      .++||.|+++.-+..++..+...    ++.+..++|+.+.......+    .....|||+|.-     + ...+++..+.
T Consensus       101 ~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~----~~~~~Ivv~Tp~~l~~~l~~~~~~~~~~~  176 (253)
T 1wrb_A          101 PKCLILAPTRELAIQILSESQKFSLNTPLRSCVVYGGADTHSQIREV----QMGCHLLVATPGRLVDFIEKNKISLEFCK  176 (253)
T ss_dssp             CSEEEECSSHHHHHHHHHHHHHHHTTSSCCEEEECSSSCSHHHHHHH----SSCCSEEEECHHHHHHHHHTTSBCCTTCC
T ss_pred             ceEEEEECCHHHHHHHHHHHHHHhccCCceEEEEECCCCHHHHHHHh----CCCCCEEEECHHHHHHHHHcCCCChhhCC
Confidence            48999999999999888877654    57788899988765443322    345789999961     1 1235677788


Q ss_pred             EEEE
Q 002040          785 LVIN  788 (976)
Q Consensus       785 ~VI~  788 (976)
                      +||.
T Consensus       177 ~lVi  180 (253)
T 1wrb_A          177 YIVL  180 (253)
T ss_dssp             EEEE
T ss_pred             EEEE
Confidence            8774

>2z43_A DNA repair and recombination protein RADA; archaea, filament, DNA binding, molecular SWI RECA, DMC1; HET: DNA; 1.93A {Sulfolobus solfataricus} PDB: 2bke_A* 2dfl_A* 2zub_A* 2zuc_A* 2zud_A*

Probab=81.36  E-value=3.1  Score=45.05  Aligned_cols=45  Identities=16%  Similarity=0.097  Sum_probs=25.4

Q ss_pred             cCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccC
Q 002040          503 SGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPT  549 (976)
Q Consensus       503 ~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Pt  549 (976)
                      .|.-+++.|++|+|||..++..+. .+..... ..+.+..|+++.-.
T Consensus       106 ~G~i~~i~G~~GsGKT~la~~la~-~~~~~~~-~gg~~~~vlyi~~e  150 (324)
T 2z43_A          106 TRTMTEFFGEFGSGKTQLCHQLSV-NVQLPPE-KGGLSGKAVYIDTE  150 (324)
T ss_dssp             TTSEEEEEESTTSSHHHHHHHHHH-HTTSCGG-GTCCSCEEEEEESS
T ss_pred             CCcEEEEECCCCCCHhHHHHHHHH-HHhcccc-cCCCCCeEEEEECC
Confidence            356789999999999976444333 3221100 01124467777643

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

Probab=81.29  E-value=1.1  Score=42.15  Aligned_cols=21  Identities=10%  Similarity=-0.042  Sum_probs=17.6

Q ss_pred             HHhcCCCEEEEcCCCCchHHH
Q 002040          500 VIMSGRDCIGVAKTGSGKTLA  520 (976)
Q Consensus       500 ~il~g~d~i~~a~TGsGKT~~  520 (976)
                      ....+.+++++|++|+|||..
T Consensus        23 ~~~~~~~vll~G~~GtGKt~l   43 (143)
T 3co5_A           23 AAKRTSPVFLTGEAGSPFETV   43 (143)
T ss_dssp             HHTCSSCEEEEEETTCCHHHH
T ss_pred             HhCCCCcEEEECCCCccHHHH
Confidence            345678899999999999975

>3bgw_A DNAB-like replicative helicase; ATPase, replication; 3.91A {Bacillus phage SPP1}

Probab=81.15  E-value=1.6  Score=49.55  Aligned_cols=37  Identities=14%  Similarity=-0.022  Sum_probs=24.1

Q ss_pred             CCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEcc
Q 002040          504 GRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAP  548 (976)
Q Consensus       504 g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~P  548 (976)
                      |.-+||.|++|+|||+.++-.+.+.+..        |..|+|++.
T Consensus       197 G~liiIaG~pG~GKTtlal~ia~~~a~~--------g~~vl~fSl  233 (444)
T 3bgw_A          197 RNFVLIAARPSMGKTAFALKQAKNMSDN--------DDVVNLHSL  233 (444)
T ss_dssp             SCEEEEEECSSSSHHHHHHHHHHHHHHT--------TCEEEEECS
T ss_pred             CcEEEEEeCCCCChHHHHHHHHHHHHHc--------CCEEEEEEC
Confidence            4458888999999997644444443332        446777763

>3hr8_A Protein RECA; alpha and beta proteins (A/B, A+B), ATP-binding, cytoplasm, damage, DNA recombination, DNA repair, DNA-binding; 1.95A {Thermotoga maritima}

Probab=80.46  E-value=1.3  Score=48.53  Aligned_cols=39  Identities=23%  Similarity=0.254  Sum_probs=25.1

Q ss_pred             CCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCH
Q 002040          504 GRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTR  550 (976)
Q Consensus       504 g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr  550 (976)
                      |.-++|.|++|+|||+. ++.++..+..       .+..|+++..-.
T Consensus        61 G~i~~I~GppGsGKSTL-al~la~~~~~-------~gg~VlyId~E~   99 (356)
T 3hr8_A           61 GRIVEIFGQESSGKTTL-ALHAIAEAQK-------MGGVAAFIDAEH   99 (356)
T ss_dssp             TEEEEEEESTTSSHHHH-HHHHHHHHHH-------TTCCEEEEESSC
T ss_pred             CcEEEEECCCCCCHHHH-HHHHHHHHHh-------cCCeEEEEeccc
Confidence            45688899999999975 4444444433       134567776543

>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=80.14  E-value=2.8  Score=42.93  Aligned_cols=72  Identities=14%  Similarity=0.315  Sum_probs=45.2

Q ss_pred             CCcEEEEecCHHHHHHHHHHHHHC----CCCceeccCCCCHHHHHHHHHHhccCCccEEEecC-----cccc-cCCCCCC
Q 002040          714 KGKILIFVHSQEKCDALFRDLLKH----GYPCLSLHGAKDQTDRESTISDFKSNVCNLLIATS-----VAAR-GLDVKEL  783 (976)
Q Consensus       714 ~~kvLIF~~s~~~~~~l~~~L~~~----~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLVaT~-----v~~~-GlDi~~v  783 (976)
                      ..++||.|+++.-+..++..+...    ++.+..++|+.....   .+..+..+...|||+|.     .+.. .+++..+
T Consensus        98 ~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~---~~~~l~~~~~~Ilv~Tp~~l~~~l~~~~~~~~~~  174 (237)
T 3bor_A           98 ETQALVLAPTRELAQQIQKVILALGDYMGATCHACIGGTNVRN---EMQKLQAEAPHIVVGTPGRVFDMLNRRYLSPKWI  174 (237)
T ss_dssp             SCCEEEECSSHHHHHHHHHHHHHHTTTTTCCEEEECC----------------CCCSEEEECHHHHHHHHHTTSSCSTTC
T ss_pred             CceEEEEECcHHHHHHHHHHHHHHhhhcCceEEEEECCCchHH---HHHHHhcCCCCEEEECHHHHHHHHHhCCcCcccC
Confidence            458999999999999998888764    567778888765432   23445567789999994     2222 3566777


Q ss_pred             cEEEE
Q 002040          784 ELVIN  788 (976)
Q Consensus       784 ~~VI~  788 (976)
                      .+||.
T Consensus       175 ~~lVi  179 (237)
T 3bor_A          175 KMFVL  179 (237)
T ss_dssp             CEEEE
T ss_pred             cEEEE
Confidence            77774

>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=80.02  E-value=3.3  Score=41.88  Aligned_cols=72  Identities=13%  Similarity=0.272  Sum_probs=48.3

Q ss_pred             cCCcEEEEecCHHHHHHHHHHHHHC---CCCceeccCCCCHHHHHHHHHHhccCCccEEEecC------cccccCCCCCC
Q 002040          713 EKGKILIFVHSQEKCDALFRDLLKH---GYPCLSLHGAKDQTDRESTISDFKSNVCNLLIATS------VAARGLDVKEL  783 (976)
Q Consensus       713 ~~~kvLIF~~s~~~~~~l~~~L~~~---~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLVaT~------v~~~GlDi~~v  783 (976)
                      ...++||.++++.-+..++..+...   ++.+..++|+.+.......+   . ...+|||+|.      .....+++..+
T Consensus        93 ~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~-~~~~iiv~Tp~~l~~~~~~~~~~~~~~  168 (228)
T 3iuy_A           93 NGPGMLVLTPTRELALHVEAECSKYSYKGLKSICIYGGRNRNGQIEDI---S-KGVDIIIATPGRLNDLQMNNSVNLRSI  168 (228)
T ss_dssp             CCCSEEEECSSHHHHHHHHHHHHHHCCTTCCEEEECC------CHHHH---H-SCCSEEEECHHHHHHHHHTTCCCCTTC
T ss_pred             CCCcEEEEeCCHHHHHHHHHHHHHhcccCceEEEEECCCChHHHHHHh---c-CCCCEEEECHHHHHHHHHcCCcCcccc
Confidence            3457999999999999999888874   67888899987755443332   2 3478999995      11235667778


Q ss_pred             cEEEE
Q 002040          784 ELVIN  788 (976)
Q Consensus       784 ~~VI~  788 (976)
                      .+||.
T Consensus       169 ~~lVi  173 (228)
T 3iuy_A          169 TYLVI  173 (228)
T ss_dssp             CEEEE
T ss_pred             eEEEE
Confidence            88774

---

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	976
d1hv8a1	208	c.37.1.19 (A:3-210) Putative DEAD box RNA helicase	2e-51
d1wrba1	238	c.37.1.19 (A:164-401) putative ATP-dependent RNA h	3e-51
d2j0sa1	222	c.37.1.19 (A:22-243) Probable ATP-dependent RNA he	8e-51
d2g9na1	218	c.37.1.19 (A:21-238) Initiation factor 4a {Human (	9e-51
d1qdea_	212	c.37.1.19 (A:) Initiation factor 4a {Baker's yeast	3e-50
d1t6na_	207	c.37.1.19 (A:) Spliceosome RNA helicase BAT1 (UAP5	3e-45
d1s2ma1	206	c.37.1.19 (A:46-251) Putative ATP-dependent RNA he	1e-43
d1veca_	206	c.37.1.19 (A:) DEAD box RNA helicase rck/p54 {Huma	1e-42
d2bmfa2	305	c.37.1.14 (A:178-482) Dengue virus helicase {Dengu	1e-40
d1q0ua_	209	c.37.1.19 (A:) Probable DEAD box RNA helicase YqfR	3e-37
d1gkub1	237	c.37.1.16 (B:1-250) Helicase-like "domain" of reve	9e-36
d1oywa2	206	c.37.1.19 (A:1-206) RecQ helicase domain {Escheric	7e-31
d1a1va2	299	c.37.1.14 (A:326-624) HCV helicase domain {Human h	5e-30
d2p6ra3	202	c.37.1.19 (A:1-202) Hel308 helicase {Archaeoglobus	7e-28
d1fuka_	162	c.37.1.19 (A:) Initiation factor 4a {Baker's yeast	9e-26
d1hv8a2	155	c.37.1.19 (A:211-365) Putative DEAD box RNA helica	6e-21
d1wp9a2	286	c.37.1.19 (A:201-486) putative ATP-dependent RNA h	2e-20
d2j0sa2	168	c.37.1.19 (A:244-411) Probable ATP-dependent RNA h	2e-18
d1jr6a_	138	c.37.1.14 (A:) HCV helicase domain {Human hepatiti	2e-17
d1wp9a1	200	c.37.1.19 (A:1-200) putative ATP-dependent RNA hel	7e-17
d1gkub2	248	c.37.1.16 (B:251-498) Helicase-like "domain" of re	9e-16
d1t5la2	181	c.37.1.19 (A:415-595) Nucleotide excision repair e	2e-15
d1s2ma2	171	c.37.1.19 (A:252-422) Putative ATP-dependent RNA h	6e-15
d2rb4a1	168	c.37.1.19 (A:307-474) ATP-dependent RNA helicase D	3e-14
d1t5ia_	168	c.37.1.19 (A:) Spliceosome RNA helicase BAT1 (UAP5	9e-14
d1c4oa2	174	c.37.1.19 (A:410-583) Nucleotide excision repair e	2e-13
d2fwra1	200	c.37.1.19 (A:257-456) DNA repair protein RAD25 {Ar	3e-12
d2p6ra4	201	c.37.1.19 (A:203-403) Hel308 helicase {Archaeoglob	5e-08
d1tf5a4	175	c.37.1.19 (A:396-570) Translocation ATPase SecA, n	5e-07
d1a1va1	136	c.37.1.14 (A:190-325) HCV helicase domain {Human h	6e-07
d2es4d1	280	a.137.15.1 (D:53-332) Lipase chaperone LifO (LipB)	2e-06
d2es4d1	280	a.137.15.1 (D:53-332) Lipase chaperone LifO (LipB)	5e-06
d2es4d1	280	a.137.15.1 (D:53-332) Lipase chaperone LifO (LipB)	9e-06
d2es4d1	280	a.137.15.1 (D:53-332) Lipase chaperone LifO (LipB)	4e-05
d2es4d1	280	a.137.15.1 (D:53-332) Lipase chaperone LifO (LipB)	6e-05
d2es4d1	280	a.137.15.1 (D:53-332) Lipase chaperone LifO (LipB)	9e-05
d2es4d1	280	a.137.15.1 (D:53-332) Lipase chaperone LifO (LipB)	7e-04
d2es4d1	280	a.137.15.1 (D:53-332) Lipase chaperone LifO (LipB)	0.001
d1f5na1	300	a.114.1.1 (A:284-583) Interferon-induced guanylate	7e-06
d1f5na1	300	a.114.1.1 (A:284-583) Interferon-induced guanylate	1e-05
d1f5na1	300	a.114.1.1 (A:284-583) Interferon-induced guanylate	9e-05
d1f5na1	300	a.114.1.1 (A:284-583) Interferon-induced guanylate	3e-04
d1f5na1	300	a.114.1.1 (A:284-583) Interferon-induced guanylate	4e-04
d1f5na1	300	a.114.1.1 (A:284-583) Interferon-induced guanylate	8e-04
d1yksa1	140	c.37.1.14 (A:185-324) YFV helicase domain {Yellow	6e-04
d1yksa2	299	c.37.1.14 (A:325-623) YFV helicase domain {Yellow	8e-04
d1sa0e_	138	a.137.10.1 (E:) Stathmin 4 {Rat (Rattus norvegicus	0.001
d1sa0e_	138	a.137.10.1 (E:) Stathmin 4 {Rat (Rattus norvegicus	0.002
d1sa0e_	138	a.137.10.1 (E:) Stathmin 4 {Rat (Rattus norvegicus	0.004

>d1hv8a1 c.37.1.19 (A:3-210) Putative DEAD box RNA helicase {Archaeon Methanococcus jannaschii [TaxId: 2190]} Length = 208

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]

 Score =  177 bits (450), Expect = 2e-51
 Identities = 68/212 (32%), Positives = 114/212 (53%), Gaps = 11/212 (5%)

Query: 468 TWHQTGLTSKIMETIRKLNYEKPMPIQAQALPVIMSGR-DCIGVAKTGSGKTLAFVLPML 526
            +++  L+  I+  IR   +EKP  IQ + +P+ ++   + +  A+TGSGKT +F +P++
Sbjct: 5   NFNELNLSDNILNAIRNKGFEKPTDIQMKVIPLFLNDEYNIVAQARTGSGKTASFAIPLI 64

Query: 527 RHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQISE 586
             + +        G   +I+ PTREL  Q+  +I        ++   +YGG  +  QI  
Sbjct: 65  ELVNENN------GIEAIILTPTRELAIQVADEIESLKGNKNLKIAKIYGGKAIYPQIKA 118

Query: 587 LKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMGFEPQITRIVQNIR 646
           LK    IVV TPGR++D +        NL+ V Y ++DEAD M +MGF   + +I+    
Sbjct: 119 LK-NANIVVGTPGRILDHINR---GTLNLKNVKYFILDEADEMLNMGFIKDVEKILNACN 174

Query: 647 PDRQTVLFSATFPRQVEILARKVLNKPVEIQV 678
            D++ +LFSAT PR++  LA+K +     I+ 
Sbjct: 175 KDKRILLFSATMPREILNLAKKYMGDYSFIKA 206

>d1wrba1 c.37.1.19 (A:164-401) putative ATP-dependent RNA helicase VlgB {Flatworm (Dugesia japonica) [TaxId: 6161]} Length = 238

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]

 Score =  178 bits (451), Expect = 3e-51
 Identities = 89/237 (37%), Positives = 136/237 (57%), Gaps = 13/237 (5%)

Query: 453 LELKIHGKDV--PKPIKTWHQTGLTSKIMETIRKLNYEKPMPIQAQALPVIMSGRDCIGV 510
           + + + G D      I+ + +  L   I   I   +Y++P PIQ  A+P I+  RD +  
Sbjct: 5   IPVSVTGPDYSATNVIENFDELKLDPTIRNNILLASYQRPTPIQKNAIPAILEHRDIMAC 64

Query: 511 AKTGSGKTLAFVLPMLRHIKDQPPV----AAGDGPVGLIMAPTRELVQQIHSDIRKFAKV 566
           A+TGSGKT AF++P++ H+  Q       +    P  LI+APTREL  QI S+ +KF+  
Sbjct: 65  AQTGSGKTAAFLIPIINHLVCQDLNQQRYSKTAYPKCLILAPTRELAIQILSESQKFSLN 124

Query: 567 MGVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEA 626
             +R   VYGG+    QI E++ G  ++V TPGR++D +        +L    Y+V+DEA
Sbjct: 125 TPLRSCVVYGGADTHSQIREVQMGCHLLVATPGRLVDFIEK---NKISLEFCKYIVLDEA 181

Query: 627 DRMFDMGFEPQITRIVQNIR----PDRQTVLFSATFPRQVEILARKVLNKPVEIQVG 679
           DRM DMGFEPQI +I++        +RQT++FSATFP++++ LA   L   + + VG
Sbjct: 182 DRMLDMGFEPQIRKIIEESNMPSGINRQTLMFSATFPKEIQKLAADFLYNYIFMTVG 238

>d2j0sa1 c.37.1.19 (A:22-243) Probable ATP-dependent RNA helicase DDX48 {Human (Homo sapiens) [TaxId: 9606]} Length = 222

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]

 Score =  176 bits (446), Expect = 8e-51
 Identities = 71/226 (31%), Positives = 113/226 (50%), Gaps = 8/226 (3%)

Query: 454 ELKIHGKDVPKPIKTWHQTGLTSKIMETIRKLNYEKPMPIQAQALPVIMSGRDCIGVAKT 513
           +++    +      T+   GL   ++  I    +EKP  IQ +A+  I+ GRD I  +++
Sbjct: 4   KVEFETSEEVDVTPTFDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQS 63

Query: 514 GSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVMGVRCVP 573
           G+GKT  F + +L+ +  Q           LI+APTREL  QI   +      M V+C  
Sbjct: 64  GTGKTATFSISVLQCLDIQVR-----ETQALILAPTRELAVQIQKGLLALGDYMNVQCHA 118

Query: 574 VYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMG 633
             GG+ V + I +L  G  +V  TPGR+ D++     +    R +  LV+DEAD M + G
Sbjct: 119 CIGGTNVGEDIRKLDYGQHVVAGTPGRVFDMIRR---RSLRTRAIKMLVLDEADEMLNKG 175

Query: 634 FEPQITRIVQNIRPDRQTVLFSATFPRQVEILARKVLNKPVEIQVG 679
           F+ QI  + + + P  Q VL SAT P ++  +  K +  P+ I V 
Sbjct: 176 FKEQIYDVYRYLPPATQVVLISATLPHEILEMTNKFMTDPIRILVK 221

>d2g9na1 c.37.1.19 (A:21-238) Initiation factor 4a {Human (Homo sapiens) [TaxId: 9606]} Length = 218

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]

 Score =  176 bits (446), Expect = 9e-51
 Identities = 68/220 (30%), Positives = 110/220 (50%), Gaps = 9/220 (4%)

Query: 461 DVPKPIKTWHQTGLTSKIMETIRKLNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLA 520
           +  + + ++    L+  ++  I    +EKP  IQ +A+   + G D I  A++G+GKT  
Sbjct: 6   NWNEIVDSFDDMNLSESLLRGIYAYGFEKPSAIQQRAILPCIKGYDVIAQAQSGTGKTAT 65

Query: 521 FVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGV 580
           F + +L+ I+             L++APTREL QQI   +      MG  C    GG+ V
Sbjct: 66  FAISILQQIELDLK-----ATQALVLAPTRELAQQIQKVVMALGDYMGASCHACIGGTNV 120

Query: 581 AQQISELKRGT-EIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMGFEPQIT 639
             ++ +L+     I+V TPGR+ D+L     +  + + +   V+DEAD M   GF+ QI 
Sbjct: 121 RAEVQKLQMEAPHIIVGTPGRVFDMLNR---RYLSPKYIKMFVLDEADEMLSRGFKDQIY 177

Query: 640 RIVQNIRPDRQTVLFSATFPRQVEILARKVLNKPVEIQVG 679
            I Q +  + Q VL SAT P  V  + +K +  P+ I V 
Sbjct: 178 DIFQKLNSNTQVVLLSATMPSDVLEVTKKFMRDPIRILVK 217

>d1qdea_ c.37.1.19 (A:) Initiation factor 4a {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 212

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]

 Score =  174 bits (441), Expect = 3e-50
 Identities = 66/217 (30%), Positives = 102/217 (47%), Gaps = 9/217 (4%)

Query: 462 VPKPIKTWHQTGLTSKIMETIRKLNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAF 521
             K +  +    L   ++  +    +E+P  IQ +A+  I+ G D +  A++G+GKT  F
Sbjct: 5   YDKVVYKFDDMELDENLLRGVFGYGFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTF 64

Query: 522 VLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVA 581
            +  L+ I           P  L++APTREL  QI   +   A  M ++     GG+   
Sbjct: 65  SIAALQRIDTSVK-----APQALMLAPTRELALQIQKVVMALAFHMDIKVHACIGGTSFV 119

Query: 582 QQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMGFEPQITRI 641
           +    L R  +IVV TPGR+ D +     +     ++   ++DEAD M   GF+ QI +I
Sbjct: 120 EDAEGL-RDAQIVVGTPGRVFDNIQR---RRFRTDKIKMFILDEADEMLSSGFKEQIYQI 175

Query: 642 VQNIRPDRQTVLFSATFPRQVEILARKVLNKPVEIQV 678
              + P  Q VL SAT P  V  +  K +  PV I V
Sbjct: 176 FTLLPPTTQVVLLSATMPNDVLEVTTKFMRNPVRILV 212

>d1t6na_ c.37.1.19 (A:) Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo sapiens) [TaxId: 9606]} Length = 207

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]

 Score =  159 bits (403), Expect = 3e-45
 Identities = 61/214 (28%), Positives = 105/214 (49%), Gaps = 11/214 (5%)

Query: 468 TWHQTGLTSKIMETIRKLNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLR 527
            +    L  +++  I    +E P  +Q + +P  + G D +  AK+G GKT  FVL  L+
Sbjct: 2   GFRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQ 61

Query: 528 HIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVMGV-RCVPVYGGSGVAQQISE 586
            ++             L+M  TREL  QI  +  +F+K M   +    +GG  + +    
Sbjct: 62  QLEPVTG-----QVSVLVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEV 116

Query: 587 LKR-GTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFD-MGFEPQITRIVQN 644
           LK+    IVV TPGR   IL  +  K  NL+ + + ++DE D+M + +     +  I + 
Sbjct: 117 LKKNCPHIVVGTPGR---ILALARNKSLNLKHIKHFILDECDKMLEQLDMRRDVQEIFRM 173

Query: 645 IRPDRQTVLFSATFPRQVEILARKVLNKPVEIQV 678
              ++Q ++FSAT  +++  + RK +  P+EI V
Sbjct: 174 TPHEKQVMMFSATLSKEIRPVCRKFMQDPMEIFV 207

>d1s2ma1 c.37.1.19 (A:46-251) Putative ATP-dependent RNA helicase DHH1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 206

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]

 Score =  155 bits (391), Expect = 1e-43
 Identities = 78/212 (36%), Positives = 116/212 (54%), Gaps = 8/212 (3%)

Query: 468 TWHQTGLTSKIMETIRKLNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLR 527
           T+    L  +++  I +  +EKP PIQ +A+PV ++GRD +  AK G+GKT AFV+P L 
Sbjct: 2   TFEDFYLKRELLMGIFEAGFEKPSPIQEEAIPVAITGRDILARAKNGTGKTAAFVIPTLE 61

Query: 528 HIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQISEL 587
            +K +           LIM PTREL  Q    +R   K  G+ C+   GG+ +   I  L
Sbjct: 62  KVKPKLN-----KIQALIMVPTRELALQTSQVVRTLGKHCGISCMVTTGGTNLRDDILRL 116

Query: 588 KRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMGFEPQITRIVQNIRP 647
                I+V TPGR++D+      K+ +L   +  +MDEAD+M    F+  I +I+  + P
Sbjct: 117 NETVHILVGTPGRVLDLASR---KVADLSDCSLFIMDEADKMLSRDFKTIIEQILSFLPP 173

Query: 648 DRQTVLFSATFPRQVEILARKVLNKPVEIQVG 679
             Q++LFSATFP  V+    K L+KP EI + 
Sbjct: 174 THQSLLFSATFPLTVKEFMVKHLHKPYEINLM 205

>d1veca_ c.37.1.19 (A:) DEAD box RNA helicase rck/p54 {Human (Homo sapiens) [TaxId: 9606]} Length = 206

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]

 Score =  152 bits (383), Expect = 1e-42
 Identities = 62/211 (29%), Positives = 112/211 (53%), Gaps = 9/211 (4%)

Query: 467 KTWHQTGLTSKIMETIRKLNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPML 526
             +    L  +++  I ++ +EKP PIQ +++P+ +SGRD +  AK G+GK+ A+++P+L
Sbjct: 3   NEFEDYCLKRELLMGIFEMGWEKPSPIQEESIPIALSGRDILARAKNGTGKSGAYLIPLL 62

Query: 527 RHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVM-GVRCVPVYGGSGVAQQIS 585
             +  +           +++ PTREL  Q+     + +K M G + +   GG+ +   I 
Sbjct: 63  ERLDLKKD-----NIQAMVIVPTRELALQVSQICIQVSKHMGGAKVMATTGGTNLRDDIM 117

Query: 586 ELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMGFEPQITRIVQNI 645
            L     +V+ TPGR++D++      +  +  V  +V+DEAD++    F   +  I+  +
Sbjct: 118 RLDDTVHVVIATPGRILDLIKK---GVAKVDHVQMIVLDEADKLLSQDFVQIMEDIILTL 174

Query: 646 RPDRQTVLFSATFPRQVEILARKVLNKPVEI 676
             +RQ +L+SATFP  V+      L KP EI
Sbjct: 175 PKNRQILLYSATFPLSVQKFMNSHLEKPYEI 205

>d2bmfa2 c.37.1.14 (A:178-482) Dengue virus helicase {Dengue virus type 2 [TaxId: 11060]} Length = 305

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]

 Score =  150 bits (379), Expect = 1e-40
 Identities = 52/342 (15%), Positives = 99/342 (28%), Gaps = 64/342 (18%)

Query: 500 VIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSD 559
           +    R  I     G+GKT  ++  ++R        A   G   LI+APTR +  ++   
Sbjct: 5   IFRKKRLTIMDLHPGAGKTKRYLPAIVRE-------AIKRGLRTLILAPTRVVAAEMEEA 57

Query: 560 IRKFAKVMGVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVT 619
           +R          +            +E      + +         L +       +    
Sbjct: 58  LRGLPIRYQTPAI-----------RAEHTGREIVDLMCHATFTMRLLSP----IRVPNYN 102

Query: 620 YLVMDEADRMFDMGFEPQITRIVQNIRPDRQTVLFSATFPRQVEILARKVLNKPVEIQVG 679
            ++MDEA          +     +    +   +  +AT P   +   +            
Sbjct: 103 LIIMDEAHFTDPASIAARGYISTRVEMGEAAGIFMTATPPGSRDPFPQS----------- 151

Query: 680 GRSVVNKDITQLVEVRPESDRFLRLLELLGEWYEKGKILIFVHSQEKCDALFRDLLKHGY 739
                N  I       PE         +      KGK + FV S +  + +   L K+G 
Sbjct: 152 -----NAPIMDEEREIPERSWNSGHEWVT---DFKGKTVWFVPSIKAGNDIAACLRKNGK 203

Query: 740 PCLSLHGAKDQTDRESTISDFKSNVCNLLIATSVAARGLDVK---------ELELVINFD 790
             + L      ++        ++N  + ++ T ++  G + K          ++ VI  D
Sbjct: 204 KVIQLSRKTFDSEYI----KTRTNDWDFVVTTDISEMGANFKAERVIDPRRCMKPVILTD 259

Query: 791 APNH----------YEDYVHRVGRTGRAGRKGCAITFISEED 822
                         +     R GR GR  +          E 
Sbjct: 260 GEERVILAGPMPVTHSSAAQRRGRVGRNPKNENDQYIYMGEP 301

>d1q0ua_ c.37.1.19 (A:) Probable DEAD box RNA helicase YqfR {Bacillus stearothermophilus [TaxId: 1422]} Length = 209

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]

 Score =  136 bits (343), Expect = 3e-37
 Identities = 52/211 (24%), Positives = 95/211 (45%), Gaps = 4/211 (1%)

Query: 468 TWHQTGLTSKIMETIRKLNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLR 527
            + +      I+E I+ L + KP  IQ + +P  + G   +G ++TG+GKT A++LP+  
Sbjct: 2   QFTRFPFQPFIIEAIKTLRFYKPTEIQERIIPGALRGESMVGQSQTGTGKTHAYLLPI-M 60

Query: 528 HIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQISEL 587
                                  ++  +     +   K   +    + GG+   + + +L
Sbjct: 61  EKIKPERAEVQAVITAPTRELATQIYHETLKITKFCPKDRMIVARCLIGGTDKQKALEKL 120

Query: 588 KRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMGFEPQITRIVQNIRP 647
                IV+ TPGR+ D +     +  ++     LV+DEAD M DMGF   + +I   +  
Sbjct: 121 NVQPHIVIGTPGRINDFIRE---QALDVHTAHILVVDEADLMLDMGFITDVDQIAARMPK 177

Query: 648 DRQTVLFSATFPRQVEILARKVLNKPVEIQV 678
           D Q ++FSAT P +++   +K +  P  + V
Sbjct: 178 DLQMLVFSATIPEKLKPFLKKYMENPTFVHV 208

>d1gkub1 c.37.1.16 (B:1-250) Helicase-like "domain" of reverse gyrase {Archaeon Archaeoglobus fulgidus [TaxId: 2234]} Length = 237

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]

 Score =  133 bits (336), Expect = 9e-36
 Identities = 39/225 (17%), Positives = 69/225 (30%), Gaps = 33/225 (14%)

Query: 463 PKPIKTWHQTGLTSKIMETIRKLNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFV 522
              +  + +  L  + +E  RK    +P  IQ      I+        A TG GKT   +
Sbjct: 18  AASLCLFPEDFLLKEFVEFFRK-CVGEPRAIQKMWAKRILRKESFAATAPTGVGKTSFGL 76

Query: 523 LPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQ 582
              L                  ++ PT  LV Q    IRK+A+  GV    + G      
Sbjct: 77  AMSLFLALKGKRC--------YVIFPTSLLVIQAAETIRKYAEKAGVGTENLIGYYHGRI 128

Query: 583 ------QISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFD----- 631
                    +  R  +IV+ T   +             L    ++ +D+ D +       
Sbjct: 129 PKREKENFMQNLRNFKIVITTTQFLSKHYR-------ELGHFDFIFVDDVDAILKASKNV 181

Query: 632 ------MGFEPQITRIVQNIRPDRQTVLFSATFPRQVEILARKVL 670
                 +GF   +             ++ +AT  +  +    + L
Sbjct: 182 DKLLHLLGFHYDLKTKSWVGEARGCLMVSTATAKKGKKAELFRQL 226

>d1oywa2 c.37.1.19 (A:1-206) RecQ helicase domain {Escherichia coli [TaxId: 562]} Length = 206

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]

 Score =  118 bits (296), Expect = 7e-31
 Identities = 36/213 (16%), Positives = 77/213 (36%), Gaps = 22/213 (10%)

Query: 473 GLTSKIMETIRKL-NYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKD 531
            L S   + +++   Y++  P Q + +  ++SGRDC+ V  TG GK+L + +P L     
Sbjct: 8   NLESGAKQVLQETFGYQQFRPGQEEIIDTVLSGRDCLVVMPTGGGKSLCYQIPALLLN-- 65

Query: 532 QPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQISELKRGT 591
                     + ++++P   L++     ++                  +           
Sbjct: 66  ---------GLTVVVSPLISLMKDQVDQLQANGVAAACLNSTQTREQQLEVMTGCRTGQI 116

Query: 592 EIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMGFEPQ----ITRIVQNIRP 647
            ++   P R++        +         L +DEA  +   G + +        ++   P
Sbjct: 117 RLLYIAPERLMLDNFL---EHLAHWNPVLLAVDEAHCISQWGHDFRPEYAALGQLRQRFP 173

Query: 648 DRQTVLFSATFPRQV--EILARKVLNKPVEIQV 678
               +  +AT       +I+    LN P+ IQ+
Sbjct: 174 TLPFMALTATADDTTRQDIVRLLGLNDPL-IQI 205

>d1a1va2 c.37.1.14 (A:326-624) HCV helicase domain {Human hepatitis C virus (HCV), different isolates [TaxId: 11103]} Length = 299

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]

 Score =  118 bits (298), Expect = 5e-30
 Identities = 32/173 (18%), Positives = 57/173 (32%), Gaps = 20/173 (11%)

Query: 679 GGRSVVNKDITQLVEVRPESDRFLRLLELLGEWYEKGKILIFVHSQEKCDALFRDLLKHG 738
           G  +V + +I ++         F      L E  + G+ LIF HS++KCD L   L+  G
Sbjct: 2   GSVTVPHPNIEEVALSTTGEIPFYGKAIPL-EVIKGGRHLIFCHSKKKCDELAAKLVALG 60

Query: 739 YPCLSLHGAKDQTDR----------ESTISDFKSNVCNLLIATSVAARG---LDVKELEL 785
              ++ +   D +               +    +   + +I  +          +     
Sbjct: 61  INAVAYYRGLDVSVIPTSGDVVVVATDALMTGFTGDFDSVIDCNTCVTQTVDFSLDPTFT 120

Query: 786 VINFDAPNHYEDYVHRVGRTGRAGRKGCA-ITFISEEDAKYSPDLVKALELSE 837
           +     P        R GRTGR G+ G        E  +     +  +  L E
Sbjct: 121 IETTTLPQDAVSRTQRRGRTGR-GKPGIYRFVAPGERPS----GMFDSSVLCE 168

>d2p6ra3 c.37.1.19 (A:1-202) Hel308 helicase {Archaeoglobus fulgidus [TaxId: 2234]} Length = 202

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]

 Score =  110 bits (274), Expect = 7e-28
 Identities = 37/198 (18%), Positives = 79/198 (39%), Gaps = 19/198 (9%)

Query: 473 GLTSKIMETIRKLNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQ 532
            ++S  +  +++   E+  P QA+A+  + SG++ +    T +GKTL   + M+R     
Sbjct: 9   SISSYAVGILKEEGIEELFPPQAEAVEKVFSGKNLLLAMPTAAGKTLLAEMAMVREAIKG 68

Query: 533 PPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQISELKRGTE 592
                        + P R L  + +   +K+ K+     +         +   E     +
Sbjct: 69  GKSL--------YVVPLRALAGEKYESFKKWEKIGLRIGISTGDY----ESRDEHLGDCD 116

Query: 593 IVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMGFEPQITRIVQNIR---PDR 649
           I+V T  +   ++     + + ++ V+ LV+DE   +        +  +V  +R      
Sbjct: 117 IIVTTSEKADSLIRN---RASWIKAVSCLVVDEIHLLDSEKRGATLEILVTKMRRMNKAL 173

Query: 650 QTVLFSATFPRQVEILAR 667
           + +  SAT P  V  +A 
Sbjct: 174 RVIGLSATAPN-VTEIAE 190

>d1fuka_ c.37.1.19 (A:) Initiation factor 4a {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 162

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]

 Score =  102 bits (254), Expect = 9e-26
 Identities = 52/163 (31%), Positives = 90/163 (55%), Gaps = 2/163 (1%)

Query: 688 ITQ-LVEVRPESDRFLRLLELLGEWYEKGKILIFVHSQEKCDALFRDLLKHGYPCLSLHG 746
           I Q  V V  E  ++  L +L        + +IF +++ K + L   L    +   +++ 
Sbjct: 1   IKQFYVNVEEEEYKYECLTDLYDS-ISVTQAVIFCNTRRKVEELTTKLRNDKFTVSAIYS 59

Query: 747 AKDQTDRESTISDFKSNVCNLLIATSVAARGLDVKELELVINFDAPNHYEDYVHRVGRTG 806
              Q +R++ + +F+S    +LI+T + ARG+DV+++ LVIN+D P + E+Y+HR+GR G
Sbjct: 60  DLPQQERDTIMKEFRSGSSRILISTDLLARGIDVQQVSLVINYDLPANKENYIHRIGRGG 119

Query: 807 RAGRKGCAITFISEEDAKYSPDLVKALELSEQVVPDDLKALAD 849
           R GRKG AI F++ ED     +L K      + +P D+  L +
Sbjct: 120 RFGRKGVAINFVTNEDVGAMRELEKFYSTQIEELPSDIATLLN 162

>d1hv8a2 c.37.1.19 (A:211-365) Putative DEAD box RNA helicase {Archaeon Methanococcus jannaschii [TaxId: 2190]} Length = 155

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]

 Score = 88.1 bits (217), Expect = 6e-21
 Identities = 55/152 (36%), Positives = 83/152 (54%), Gaps = 2/152 (1%)

Query: 685 NKDITQLVEVRPESDRFLRLLELLGEWYEKGKILIFVHSQEKCDALFRDLLKHGYPCLSL 744
           N +I Q      E++RF  L  LL    ++   L+F  ++     L   L   G+   ++
Sbjct: 1   NANIEQSYVEVNENERFEALCRLLKN--KEFYGLVFCKTKRDTKELASMLRDIGFKAGAI 58

Query: 745 HGAKDQTDRESTISDFKSNVCNLLIATSVAARGLDVKELELVINFDAPNHYEDYVHRVGR 804
           HG   Q+ RE  I  FK     +LIAT V +RG+DV +L  VIN+  P + E Y+HR+GR
Sbjct: 59  HGDLSQSQREKVIRLFKQKKIRILIATDVMSRGIDVNDLNCVINYHLPQNPESYMHRIGR 118

Query: 805 TGRAGRKGCAITFISEEDAKYSPDLVKALELS 836
           TGRAG+KG AI+ I+  + K    + +A++L 
Sbjct: 119 TGRAGKKGKAISIINRREYKKLRYIERAMKLK 150

>d1wp9a2 c.37.1.19 (A:201-486) putative ATP-dependent RNA helicase PF2015 {Pyrococcus furiosus [TaxId: 2261]} Length = 286

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]

 Score = 90.3 bits (223), Expect = 2e-20
 Identities = 39/210 (18%), Positives = 84/210 (40%), Gaps = 21/210 (10%)

Query: 621 LVMDEADRMFDMGFEPQITRIVQNIRPDRQTVLFSATFPRQVEILARKVLNKPVEIQVGG 680
           L +  A  + +      +   ++ +  + +     A+     EI + K + K + +    
Sbjct: 80  LKLHHAIELLETQGLSALRAYIKKLYEEAKAGSTKAS----KEIFSDKRMKKAISLL--- 132

Query: 681 RSVVNKDITQLVEVRPESDRFLRLLELLGEWYEKGKILIFVHSQEKCDALFRDLLKHGYP 740
                    ++    P+ D+   ++    +  +  KI++F + +E    +  +L+K G  
Sbjct: 133 -----VQAKEIGLDHPKMDKLKEIIREQLQRKQNSKIIVFTNYRETAKKIVNELVKDGIK 187

Query: 741 CLSLHGAKDQTDR--------ESTISDFKSNVCNLLIATSVAARGLDVKELELVINFDAP 792
                G   + +         +  + +F     N+L+ATSV   GLDV E++LV+ ++  
Sbjct: 188 AKRFVGQASKENDRGLSQREQKLILDEFARGEFNVLVATSVGEEGLDVPEVDLVVFYEPV 247

Query: 793 NHYEDYVHRVGRTGRAGRKGCAITFISEED 822
                 + R GRTGR    G  I  +++  
Sbjct: 248 PSAIRSIQRRGRTGRHM-PGRVIILMAKGT 276

>d2j0sa2 c.37.1.19 (A:244-411) Probable ATP-dependent RNA helicase DDX48 {Human (Homo sapiens) [TaxId: 9606]} Length = 168

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]

 Score = 81.5 bits (200), Expect = 2e-18
 Identities = 56/160 (35%), Positives = 90/160 (56%), Gaps = 2/160 (1%)

Query: 686 KDITQ-LVEVRPESDRFLRLLELLGEWYEKGKILIFVHSQEKCDALFRDLLKHGYPCLSL 744
           + I Q  V V  E  +F  L +L        + +IF +++ K D L   + +  +   S+
Sbjct: 6   EGIKQFFVAVEREEWKFDTLCDLYDT-LTITQAVIFCNTKRKVDWLTEKMREANFTVSSM 64

Query: 745 HGAKDQTDRESTISDFKSNVCNLLIATSVAARGLDVKELELVINFDAPNHYEDYVHRVGR 804
           HG   Q +RES + +F+S    +LI+T V ARGLDV ++ L+IN+D PN+ E Y+HR+GR
Sbjct: 65  HGDMPQKERESIMKEFRSGASRVLISTDVWARGLDVPQVSLIINYDLPNNRELYIHRIGR 124

Query: 805 TGRAGRKGCAITFISEEDAKYSPDLVKALELSEQVVPDDL 844
           +GR GRKG AI F+  +D +   D+ +        +P ++
Sbjct: 125 SGRYGRKGVAINFVKNDDIRILRDIEQYYSTQIDEMPMNV 164

>d1jr6a_ c.37.1.14 (A:) HCV helicase domain {Human hepatitis C virus (HCV), different isolates [TaxId: 11103]} Length = 138

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]

 Score = 77.4 bits (190), Expect = 2e-17
 Identities = 34/147 (23%), Positives = 59/147 (40%), Gaps = 13/147 (8%)

Query: 679 GGRSVVNKDITQLVEVRPESDRFLRLLELLGEWYEKGKILIFVHSQEKCDALFRDLLKHG 738
           G  +V + +I ++         F      L E  + G+ LIF HS++KCD L   L+  G
Sbjct: 1   GSVTVPHPNIEEVALSTTGEIPFYGKAIPL-EVIKGGRHLIFCHSKKKCDELAAKLVALG 59

Query: 739 YPCLSLHGAKDQTDRESTISDFKSNVCNLLIATSVAARGLDVKE---LELVINFDAPNHY 795
              ++ +       R   +S   +N   +++AT     G        ++   +   P   
Sbjct: 60  INAVAYY-------RGLDVSVIPTNGDVVVVATDALMTGFTGDFDSVIDCNTSDGKPQDA 112

Query: 796 EDYVHRVGRTGRAGRKGCAITFISEED 822
                R GRTGR G+ G    F++  +
Sbjct: 113 VSRTQRRGRTGR-GKPG-IYRFVAPGE 137

>d1wp9a1 c.37.1.19 (A:1-200) putative ATP-dependent RNA helicase PF2015 {Pyrococcus furiosus [TaxId: 2261]} Length = 200

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]

 Score = 77.9 bits (190), Expect = 7e-17
 Identities = 41/211 (19%), Positives = 74/211 (35%), Gaps = 13/211 (6%)

Query: 482 IRKLNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGP 541
           + + +  +P   Q           +C+ V  TG GKTL  ++     +            
Sbjct: 2   VLRRDLIQPRIYQEVIYAKCK-ETNCLIVLPTGLGKTLIAMMIAEYRLTKYGGKVL---- 56

Query: 542 VGLIMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRM 601
              ++APT+ LV Q     R+   +   + V + G     ++     R   IV       
Sbjct: 57  ---MLAPTKPLVLQHAESFRRLFNLPPEKIVALTGEKSPEERSKAWARAKVIVATPQTIE 113

Query: 602 IDILCTSGGKITNLRRVTYLVMDEADRMFDMGFEPQITRIVQNIRPDRQTVLFSATFPRQ 661
            D+L        +L  V+ +V DEA R         I R  +    +   +  +A+    
Sbjct: 114 NDLLA----GRISLEDVSLIVFDEAHRAVGNYAYVFIAREYKRQAKNPLVIGLTASPGST 169

Query: 662 VEILARKVLNKPVEIQVGGRSVVNKDITQLV 692
            E +  +V+N      +  RS  + D+   V
Sbjct: 170 PEKIM-EVINNLGIEHIEYRSENSPDVRPYV 199

>d1gkub2 c.37.1.16 (B:251-498) Helicase-like "domain" of reverse gyrase {Archaeon Archaeoglobus fulgidus [TaxId: 2234]} Length = 248

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]

 Score = 76.0 bits (186), Expect = 9e-16
 Identities = 27/220 (12%), Positives = 62/220 (28%), Gaps = 17/220 (7%)

Query: 688 ITQLVEVRPESDRFLRLLELLGEWYEKGKILIFVHSQEKCDALFRDLLKHGYPCLSLHGA 747
           +  + +V    +    L  +L +       +I+  + E+ + ++  L             
Sbjct: 1   VRNVEDVAVNDESISTLSSILEK--LGTGGIIYARTGEEAEEIYESLKNK------FRIG 52

Query: 748 KDQTDRESTISDFKSNVCNLLIATS----VAARGLDVKE-LELVINFDAPNHYEDYVHRV 802
                ++     F     + LI T+       RGLD+ E +   +    P+    +   +
Sbjct: 53  IVTATKKGDYEKFVEGEIDHLIGTAHYYGTLVRGLDLPERIRFAVFVGCPS----FRVTI 108

Query: 803 GRTGRAGRKGCAITFISEEDAKYSPDLVKALELSEQVVPDDLKALADSFMAKVNQGLEQA 862
                   +   +      +      L+ A+E     V + LK +      +    + + 
Sbjct: 109 EDIDSLSPQMVKLLAYLYRNVDEIERLLPAVERHIDEVREILKKVMGKERPQAKDVVVRE 168

Query: 863 HGTGYGGSGFKFNEEEDEKRKAAKKAQAKEYGFEEDKSDS 902
               +              R  A           ED S+ 
Sbjct: 169 GEVIFPDLRTYIQGSGRTSRLFAGGLTKGASFLLEDDSEL 208

>d1t5la2 c.37.1.19 (A:415-595) Nucleotide excision repair enzyme UvrB {Bacillus caldotenax [TaxId: 1395]} Length = 181

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: Nucleotide excision repair enzyme UvrB
species: Bacillus caldotenax [TaxId: 1395]

 Score = 72.9 bits (178), Expect = 2e-15
 Identities = 27/148 (18%), Positives = 57/148 (38%), Gaps = 1/148 (0%)

Query: 692 VEVRPESDRFLRLLELLGEWYEKG-KILIFVHSQEKCDALFRDLLKHGYPCLSLHGAKDQ 750
           ++VRP   +   L+  + E  E+  + L+   +++  + L   L + G     LH     
Sbjct: 8   IDVRPTKGQIDDLIGEIRERVERNERTLVTTLTKKMAEDLTDYLKEAGIKVAYLHSEIKT 67

Query: 751 TDRESTISDFKSNVCNLLIATSVAARGLDVKELELVINFDAPNHYEDYVHRVGRTGRAGR 810
            +R   I D +    ++L+  ++   GLD+ E+ LV   DA         R         
Sbjct: 68  LERIEIIRDLRLGKYDVLVGINLLREGLDIPEVSLVAILDADKEGFLRSERSLIQTIGRA 127

Query: 811 KGCAITFISEEDAKYSPDLVKALELSEQ 838
              A   +       +  +  A++ +++
Sbjct: 128 ARNANGHVIMYADTITKSMEIAIQETKR 155

>d1s2ma2 c.37.1.19 (A:252-422) Putative ATP-dependent RNA helicase DHH1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 171

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]

 Score = 71.6 bits (174), Expect = 6e-15
 Identities = 44/160 (27%), Positives = 73/160 (45%), Gaps = 1/160 (0%)

Query: 686 KDITQLVEVRPESDRFLRLLELLGEWYEKGKILIFVHSQEKCDALFRDLLKHGYPCLSLH 745
           K ITQ      E  +   L  L  +  +  + +IF +S  + + L + +   GY C   H
Sbjct: 5   KGITQYYAFVEERQKLHCLNTLFSK-LQINQAIIFCNSTNRVELLAKKITDLGYSCYYSH 63

Query: 746 GAKDQTDRESTISDFKSNVCNLLIATSVAARGLDVKELELVINFDAPNHYEDYVHRVGRT 805
               Q +R     +F+      L+ + +  RG+D++ + +VINFD P   E Y+HR+GR+
Sbjct: 64  ARMKQQERNKVFHEFRQGKVRTLVCSDLLTRGIDIQAVNVVINFDFPKTAETYLHRIGRS 123

Query: 806 GRAGRKGCAITFISEEDAKYSPDLVKALELSEQVVPDDLK 845
           GR G  G AI  I+  D      + + L      +P  + 
Sbjct: 124 GRFGHLGLAINLINWNDRFNLYKIEQELGTEIAAIPATID 163

>d1t5ia_ c.37.1.19 (A:) Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo sapiens) [TaxId: 9606]} Length = 168

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]

 Score = 68.2 bits (165), Expect = 9e-14
 Identities = 52/158 (32%), Positives = 91/158 (57%), Gaps = 2/158 (1%)

Query: 688 ITQLVEVRPESDRFLRLLELLGEWYEKGKILIFVHSQEKCDALFRDLLKHGYPCLSLHGA 747
           + Q      ++++  +L +LL    E  +++IFV S ++C AL + L++  +P +++H  
Sbjct: 2   LQQYYVKLKDNEKNRKLFDLLDV-LEFNQVVIFVKSVQRCIALAQLLVEQNFPAIAIHRG 60

Query: 748 KDQTDRESTISDFKSNVCNLLIATSVAARGLDVKELELVINFDAPNHYEDYVHRVGRTGR 807
             Q +R S    FK     +L+AT++  RG+D++ + +  N+D P   + Y+HRV R GR
Sbjct: 61  MPQEERLSRYQQFKDFQRRILVATNLFGRGMDIERVNIAFNYDMPEDSDTYLHRVARAGR 120

Query: 808 AGRKGCAITFIS-EEDAKYSPDLVKALELSEQVVPDDL 844
            G KG AITF+S E DAK   D+    E++   +PD++
Sbjct: 121 FGTKGLAITFVSDENDAKILNDVQDRFEVNISELPDEI 158

>d1c4oa2 c.37.1.19 (A:410-583) Nucleotide excision repair enzyme UvrB {Thermus thermophilus [TaxId: 274]} Length = 174

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: Nucleotide excision repair enzyme UvrB
species: Thermus thermophilus [TaxId: 274]

 Score = 67.4 bits (164), Expect = 2e-13
 Identities = 37/146 (25%), Positives = 66/146 (45%), Gaps = 5/146 (3%)

Query: 692 VEVRPESDRFLRLLELLGEWYEKG-KILIFVHSQEKCDALFRDLLKHGYPCLSLHGAKDQ 750
           V V+P  ++ L L+E + E   +G + L+ V +    + L   L++HG     LH   D 
Sbjct: 8   VRVKPTENQILDLMEGIRERAARGERTLVTVLTVRMAEELTSFLVEHGIRARYLHHELDA 67

Query: 751 TDRESTISDFKSNVCNLLIATSVAARGLDVKELELVINFDAPNHYEDYVHR--VGRTGRA 808
             R++ I D +    + L+  ++   GLD+ E+ LV   DA         R  +   GRA
Sbjct: 68  FKRQALIRDLRLGHYDCLVGINLLREGLDIPEVSLVAILDADKEGFLRSERSLIQTIGRA 127

Query: 809 GRKGCAITFISEEDAKYSPDLVKALE 834
            R      ++  +  + S  + +A+E
Sbjct: 128 ARNARGEVWLYAD--RVSEAMQRAIE 151

>d2fwra1 c.37.1.19 (A:257-456) DNA repair protein RAD25 {Archaeoglobus fulgidus [TaxId: 2234]} Length = 200

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]

 Score = 64.5 bits (156), Expect = 3e-12
 Identities = 22/122 (18%), Positives = 50/122 (40%), Gaps = 6/122 (4%)

Query: 698 SDRFLRLLELLGEWYEKGKILIFVHSQEKCDALFRDLLKHGYPCLSLHGAKDQTDRESTI 757
            ++  +L E+L E + K KI+IF    E    + +      +   ++     + +RE  +
Sbjct: 78  KNKIRKLREIL-ERHRKDKIIIFTRHNELVYRISKV-----FLIPAITHRTSREEREEIL 131

Query: 758 SDFKSNVCNLLIATSVAARGLDVKELELVINFDAPNHYEDYVHRVGRTGRAGRKGCAITF 817
             F++     ++++ V   G+DV +  + +         +Y+ R+GR  R  +       
Sbjct: 132 EGFRTGRFRAIVSSQVLDEGIDVPDANVGVIMSGSGSAREYIQRLGRILRPSKGKKEAVL 191

Query: 818 IS 819
             
Sbjct: 192 YE 193

>d2p6ra4 c.37.1.19 (A:203-403) Hel308 helicase {Archaeoglobus fulgidus [TaxId: 2234]} Length = 201

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]

 Score = 52.2 bits (124), Expect = 5e-08
 Identities = 29/193 (15%), Positives = 61/193 (31%), Gaps = 43/193 (22%)

Query: 673 PVEIQVGGRSVVNKDITQLVEVRPESDRFLRLLELLGEWYEKGK-ILIFVHSQEKCDALF 731
           PV +  G   V+ +   +L +    + R ++  EL+ E   +   +L+F  ++   +   
Sbjct: 1   PVPLVEG---VLCEGTLELFDGAFSTSRRVKFEELVEECVAENGGVLVFESTRRGAEKTA 57

Query: 732 RDLLKHGYPCLS------------------------------LHGAKDQTDRESTISDFK 761
             L       +                                H       R      F+
Sbjct: 58  VKLSAITAKYVENEGLEKAILEENEGEMSRKLAECVRKGAAFHHAGLLNGQRRVVEDAFR 117

Query: 762 SNVCNLLIATSVAARGLDVKELELVI-------NFDAPNHYEDYVHRVGRTGRAGR--KG 812
                +++AT   A G+++    +++        +       +Y    GR GR G   +G
Sbjct: 118 RGNIKVVVATPTLAAGVNLPARRVIVRSLYRFDGYSKRIKVSEYKQMAGRAGRPGMDERG 177

Query: 813 CAITFISEEDAKY 825
            AI  + + D + 
Sbjct: 178 EAIIIVGKRDREI 190

>d1tf5a4 c.37.1.19 (A:396-570) Translocation ATPase SecA, nucleotide-binding domains {Bacillus subtilis [TaxId: 1423]} Length = 175

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: Translocation ATPase SecA, nucleotide-binding domains
species: Bacillus subtilis [TaxId: 1423]

 Score = 48.7 bits (116), Expect = 5e-07
 Identities = 40/189 (21%), Positives = 69/189 (36%), Gaps = 23/189 (12%)

Query: 681 RSVVNKDITQLVEVRPESDRFLRLLELLGEWYEKG-KILIFVHSQEKCDALFRDLLKHGY 739
           R VV  D   L+  R    +F  + E + + Y  G  +L+   + E  + + + L   G 
Sbjct: 1   RPVVRDDRPDLI-YRTMEGKFKAVAEDVAQRYMTGQPVLVGTVAVETSELISKLLKNKGI 59

Query: 740 PCLSLHGAKDQTDRESTISDFKSNVCNLLIATSVAARGLDVKELELVINFDA-------- 791
           P   L+    + + +      +     + IAT++A RG D+K  E V             
Sbjct: 60  PHQVLNAKNHEREAQIIEEAGQKGA--VTIATNMAGRGTDIKLGEGVKELGGLAVVGTER 117

Query: 792 PNHYEDYVHRVGRTGRAGRKGCAITFISEEDAKYSPDLVKALELSEQVVPDDLKALADSF 851
                      GR+GR G  G    ++S ED           EL  +   +   A+ D F
Sbjct: 118 HESRRIDNQLRGRSGRQGDPGITQFYLSMED-----------ELMRRFGAERTMAMLDRF 166

Query: 852 MAKVNQGLE 860
               +  ++
Sbjct: 167 GMDDSTPIQ 175

>d1a1va1 c.37.1.14 (A:190-325) HCV helicase domain {Human hepatitis C virus (HCV), different isolates [TaxId: 11103]} Length = 136

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]

 Score = 47.5 bits (112), Expect = 6e-07
 Identities = 23/151 (15%), Positives = 35/151 (23%), Gaps = 32/151 (21%)

Query: 510 VAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVMGV 569
            A TGSGK+                     G   L++ P+        + + K   V   
Sbjct: 14  HAPTGSGKSTKVPAAYAAQ-----------GYKVLVLNPSVAATLGFGAYMSKAHGVDPN 62

Query: 570 RCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEA--- 626
               V                  I   +P               +      ++ DE    
Sbjct: 63  IRTGVR----------------TITTGSPITYSTYGKFLADGGCSGGAYDIIICDECHST 106

Query: 627 DRMFDMGFEPQITRIVQNIRPDRQTVLFSAT 657
           D    +G               R  VL +AT
Sbjct: 107 DATSILGI--GTVLDQAETAGARLVVLATAT 135

>d1f5na1 a.114.1.1 (A:284-583) Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain {Human (Homo sapiens) [TaxId: 9606]} Length = 300

class: All alpha proteins
fold: Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain
superfamily: Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain
family: Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain
domain: Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 46.7 bits (110), Expect = 7e-06
 Identities = 23/127 (18%), Positives = 54/127 (42%)

Query: 6   RDRDREKEKEKHREKSRRSEREQSTDSDEDKHDKEKEKDKHRDRDRRRDRDRDRDREKER 65
           R   + +E  +   KS+ S  +    +D+   +KEKE +  R +            E +R
Sbjct: 169 RKGIQAEEILQTYLKSKESMTDAILQTDQTLTEKEKEIEVERVKAESAQASAKMLHEMQR 228

Query: 66  EEKRERAREKEREREKRDREREDRERERERERERRERDREREKRERERDRDKEKDRERKS 125
           + ++   +++   +E   +  E  E +R +  + +ER    + +E+E+   +   +E + 
Sbjct: 229 KNEQMMEQKERSYQEHLKQLTEKMENDRVQLLKEQERTLALKLQEQEQLLKEGFQKESRI 288

Query: 126 RDREKRR 132
              E + 
Sbjct: 289 MKNEIQD 295

>d1f5na1 a.114.1.1 (A:284-583) Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain {Human (Homo sapiens) [TaxId: 9606]} Length = 300

class: All alpha proteins
fold: Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain
superfamily: Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain
family: Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain
domain: Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 45.9 bits (108), Expect = 1e-05
 Identities = 12/139 (8%), Positives = 51/139 (36%)

Query: 11  EKEKEKHREKSRRSEREQSTDSDEDKHDKEKEKDKHRDRDRRRDRDRDRDREKEREEKRE 70
           +K+  +   K  ++E    T     +   +      +    +         + E  +   
Sbjct: 161 KKKYYEEPRKGIQAEEILQTYLKSKESMTDAILQTDQTLTEKEKEIEVERVKAESAQASA 220

Query: 71  RAREKEREREKRDREREDRERERERERERRERDREREKRERERDRDKEKDRERKSRDREK 130
           +   + + + ++  E+++R  +   ++   + + +R +  +E++R      + + +  ++
Sbjct: 221 KMLHEMQRKNEQMMEQKERSYQEHLKQLTEKMENDRVQLLKEQERTLALKLQEQEQLLKE 280

Query: 131 RRKVESDDSDEDKDRDRKR 149
             + ES     +    + +
Sbjct: 281 GFQKESRIMKNEIQDLQTK 299

>d1f5na1 a.114.1.1 (A:284-583) Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain {Human (Homo sapiens) [TaxId: 9606]} Length = 300

class: All alpha proteins
fold: Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain
superfamily: Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain
family: Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain
domain: Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 43.2 bits (101), Expect = 9e-05
 Identities = 23/228 (10%), Positives = 68/228 (29%), Gaps = 3/228 (1%)

Query: 11  EKEKEKHREKSRRSEREQSTDSDEDKHDKEKEKDKHRDRDRRRDRDRDRDREKEREEKRE 70
                    ++       S    +    KE      + RD    ++++   ++     + 
Sbjct: 71  LDLHRDSEREAIEVFIRSSFKDVDHLFQKELAAQLEKKRDDFCKQNQEASSDRCSGLLQV 130

Query: 71  RAREKEREREKRDREREDRERERERERERRERDREREKRERERDRDKEKDRERKSRDREK 130
                E E +     +    R   ++ +  ++    E R+  +  +  +   +       
Sbjct: 131 IFSPLEEEVKAGIYSKPGGYRLFVQKLQDLKKKYYEEPRKGIQAEEILQTYLKSKESMTD 190

Query: 131 RRKVESDDSDEDKDRDRKRRRRHDDDHKERVRERSLSRSNRHRDENDESPREKLVEDDSD 190
                     E +      R + +           + R N    E  E   ++ ++  ++
Sbjct: 191 AILQTDQTLTEKEKEIEVERVKAESAQASAKMLHEMQRKNEQMMEQKERSYQEHLKQLTE 250

Query: 191 K--KEKKTREEELE-DEQRKLDEEMEKRRRRVQEWQELKRKKEESERE 235
           K   ++    +E E     KL E+ +  +   Q+   + + + +  + 
Sbjct: 251 KMENDRVQLLKEQERTLALKLQEQEQLLKEGFQKESRIMKNEIQDLQT 298

>d1f5na1 a.114.1.1 (A:284-583) Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain {Human (Homo sapiens) [TaxId: 9606]} Length = 300

class: All alpha proteins
fold: Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain
superfamily: Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain
family: Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain
domain: Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 41.7 bits (97), Expect = 3e-04
 Identities = 21/232 (9%), Positives = 71/232 (30%), Gaps = 3/232 (1%)

Query: 9   DREKEKEKHREKSRRSEREQSTDSDEDKHDKEKEKDKHRDRDRRRDRDRDRDREKEREEK 68
            +     + +   +     +S     D H   + +                 +++   + 
Sbjct: 46  QKAIAHYEQQMGQKVQLPTESLQELLDLHRDSEREAIEVFIRSSFKDVDHLFQKELAAQL 105

Query: 69  RERAREKEREREKRDREREDRERERERERERRERDREREKRERERD---RDKEKDRERKS 125
            ++  +  ++ ++   +R     +        E       +        +  +  +++  
Sbjct: 106 EKKRDDFCKQNQEASSDRCSGLLQVIFSPLEEEVKAGIYSKPGGYRLFVQKLQDLKKKYY 165

Query: 126 RDREKRRKVESDDSDEDKDRDRKRRRRHDDDHKERVRERSLSRSNRHRDENDESPREKLV 185
            +  K  + E       K ++         D     +E+ +       +    S +    
Sbjct: 166 EEPRKGIQAEEILQTYLKSKESMTDAILQTDQTLTEKEKEIEVERVKAESAQASAKMLHE 225

Query: 186 EDDSDKKEKKTREEELEDEQRKLDEEMEKRRRRVQEWQELKRKKEESERENR 237
               +++  + +E   ++  ++L E+ME  R ++ + QE     +  E+E  
Sbjct: 226 MQRKNEQMMEQKERSYQEHLKQLTEKMENDRVQLLKEQERTLALKLQEQEQL 277

>d1f5na1 a.114.1.1 (A:284-583) Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain {Human (Homo sapiens) [TaxId: 9606]} Length = 300

class: All alpha proteins
fold: Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain
superfamily: Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain
family: Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain
domain: Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 41.3 bits (96), Expect = 4e-04
 Identities = 28/215 (13%), Positives = 77/215 (35%), Gaps = 2/215 (0%)

Query: 10  REKEKEKHREKSRRSEREQSTDSDEDKHDKEKEKDKHRDRDRRRDRDRDRDREKEREEKR 69
                +      ++    Q     +D   + +E    R     +      + E +     
Sbjct: 86  IRSSFKDVDHLFQKELAAQLEKKRDDFCKQNQEASSDRCSGLLQVIFSPLEEEVKAGIYS 145

Query: 70  ERAREKEREREKRDREREDRERERERERERRERDREREKRERERDRDKEKDRERKSRDRE 129
           +    +   ++ +D +++  E  R+  +         + +E   D   + D+    +++E
Sbjct: 146 KPGGYRLFVQKLQDLKKKYYEEPRKGIQAEEILQTYLKSKESMTDAILQTDQTLTEKEKE 205

Query: 130 KRRKVESDDSDEDKDRDRKRRRRHDDDHKERVRERSLSRSNRHRDENDESPREKLVEDDS 189
              +    +S +   +     +R ++   E+ +ERS     +   E  E+ R +L+++  
Sbjct: 206 IEVERVKAESAQASAKMLHEMQRKNEQMMEQ-KERSYQEHLKQLTEKMENDRVQLLKEQE 264

Query: 190 DKKEKKTREEELEDEQRKLDEEMEKRRRRVQEWQE 224
                K +E+E +  +    +E    +  +Q+ Q 
Sbjct: 265 RTLALKLQEQE-QLLKEGFQKESRIMKNEIQDLQT 298

>d1f5na1 a.114.1.1 (A:284-583) Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain {Human (Homo sapiens) [TaxId: 9606]} Length = 300

class: All alpha proteins
fold: Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain
superfamily: Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain
family: Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain
domain: Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 40.1 bits (93), Expect = 8e-04
 Identities = 8/122 (6%), Positives = 48/122 (39%)

Query: 1   MAHSHRDRDREKEKEKHREKSRRSEREQSTDSDEDKHDKEKEKDKHRDRDRRRDRDRDRD 60
           +    + ++   +     +++   + ++           +       +  R+ ++  ++ 
Sbjct: 178 LQTYLKSKESMTDAILQTDQTLTEKEKEIEVERVKAESAQASAKMLHEMQRKNEQMMEQK 237

Query: 61  REKEREEKRERAREKEREREKRDREREDRERERERERERRERDREREKRERERDRDKEKD 120
               +E  ++   + E +R +  +E+E     + +E+E+  ++  +++    ++  ++  
Sbjct: 238 ERSYQEHLKQLTEKMENDRVQLLKEQERTLALKLQEQEQLLKEGFQKESRIMKNEIQDLQ 297

Query: 121 RE 122
            +
Sbjct: 298 TK 299

>d1yksa1 c.37.1.14 (A:185-324) YFV helicase domain {Yellow fever virus [TaxId: 11089]} Length = 140

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]

 Score = 38.9 bits (89), Expect = 6e-04
 Identities = 24/160 (15%), Positives = 50/160 (31%), Gaps = 22/160 (13%)

Query: 500 VIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSD 559
           ++  G   +     G+GKT  F+  +L     +           L++APTR ++ ++   
Sbjct: 3   MLKKGMTTVLDFHPGAGKTRRFLPQILAECARR-------RLRTLVLAPTRVVLSEMKEA 55

Query: 560 IRKFAKVMGVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVT 619
                     +    +G                I       +   +       T +    
Sbjct: 56  FHGLDVKFHTQAFSAHG-----------SGREVIDAMCHATLTYRMLEP----TRVVNWE 100

Query: 620 YLVMDEADRMFDMGFEPQITRIVQNIRPDRQTVLFSATFP 659
            ++MDEA  +       +     +    +  T+L +AT P
Sbjct: 101 VIIMDEAHFLDPASIAARGWAAHRARANESATILMTATPP 140

>d1yksa2 c.37.1.14 (A:325-623) YFV helicase domain {Yellow fever virus [TaxId: 11089]} Length = 299

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]

 Score = 40.3 bits (94), Expect = 8e-04
 Identities = 26/163 (15%), Positives = 48/163 (29%), Gaps = 28/163 (17%)

Query: 685 NKDITQLVEVRPESDRFLRLLELLGEWYEKGKILIFVHSQEKCDALFRDLLKHGYPCLSL 744
           N +I  +    P         + +    +K     F+ S    + +   L K G   + L
Sbjct: 10  NGEIEDVQTDIPSEPW-NTGHDWILA--DKRPTAWFLPSIRAANVMAASLRKAGKSVVVL 66

Query: 745 HGAKDQTDRESTISDFKSNVCNLLIATSVAARGLDVKELELVIN---------FDAPNHY 795
           +        E      K    + ++AT +A  G ++  +E V++          D     
Sbjct: 67  NRKT----FEREYPTIKQKKPDFILATDIAEMGANL-CVERVLDCRTAFKPVLVDEGRKV 121

Query: 796 EDYV----------HRVGRTGR-AGRKGCAITFISEEDAKYSP 827
                          R GR GR   R G +  +        + 
Sbjct: 122 AIKGPLRISASSAAQRRGRIGRNPNRDGDSYYYSEPTSENNAH 164

>d1sa0e_ a.137.10.1 (E:) Stathmin 4 {Rat (Rattus norvegicus) [TaxId: 10116]} Length = 138

class: All alpha proteins
fold: Non-globular all-alpha subunits of globular proteins
superfamily: Stathmin
family: Stathmin
domain: Stathmin 4
species: Rat (Rattus norvegicus) [TaxId: 10116]

 Score = 37.9 bits (88), Expect = 0.001
 Identities = 14/92 (15%), Positives = 35/92 (38%)

Query: 44  DKHRDRDRRRDRDRDRDREKEREEKRERAREKEREREKRDREREDRERERERERERRERD 103
            + RD      + +    E+ R+ +     +   E+ + +RE   +  E      +  ++
Sbjct: 37  PRRRDPSLEEIQKKLEAAEERRKYQEAELLKHLAEKREHEREVIQKAIEENNNFIKMAKE 96

Query: 104 REREKRERERDRDKEKDRERKSRDREKRRKVE 135
           +  +K E  ++  +        R +EK +  E
Sbjct: 97  KLAQKMESNKENREAHLAAMLERLQEKDKHAE 128

>d1sa0e_ a.137.10.1 (E:) Stathmin 4 {Rat (Rattus norvegicus) [TaxId: 10116]} Length = 138

class: All alpha proteins
fold: Non-globular all-alpha subunits of globular proteins
superfamily: Stathmin
family: Stathmin
domain: Stathmin 4
species: Rat (Rattus norvegicus) [TaxId: 10116]

 Score = 37.2 bits (86), Expect = 0.002
 Identities = 18/88 (20%), Positives = 37/88 (42%)

Query: 51  RRRDRDRDRDREKEREEKRERAREKEREREKRDREREDRERERERERERRERDREREKRE 110
                +R + +E E  +     RE ERE  ++  E  +   +  +E+  ++ +  +E RE
Sbjct: 51  LEAAEERRKYQEAELLKHLAEKREHEREVIQKAIEENNNFIKMAKEKLAQKMESNKENRE 110

Query: 111 RERDRDKEKDRERKSRDREKRRKVESDD 138
                  E+ +E+     E R+  E  +
Sbjct: 111 AHLAAMLERLQEKDKHAEEVRKNKELKE 138

>d1sa0e_ a.137.10.1 (E:) Stathmin 4 {Rat (Rattus norvegicus) [TaxId: 10116]} Length = 138

class: All alpha proteins
fold: Non-globular all-alpha subunits of globular proteins
superfamily: Stathmin
family: Stathmin
domain: Stathmin 4
species: Rat (Rattus norvegicus) [TaxId: 10116]

 Score = 36.4 bits (84), Expect = 0.004
 Identities = 16/90 (17%), Positives = 38/90 (42%)

Query: 63  KEREEKRERAREKEREREKRDREREDRERERERERERRERDREREKRERERDRDKEKDRE 122
           +E ++K E A E+ + +E    +    +RE ERE  ++  +      +  +++  +K   
Sbjct: 45  EEIQKKLEAAEERRKYQEAELLKHLAEKREHEREVIQKAIEENNNFIKMAKEKLAQKMES 104

Query: 123 RKSRDREKRRKVESDDSDEDKDRDRKRRRR 152
            K         +     ++DK  +  R+ +
Sbjct: 105 NKENREAHLAAMLERLQEKDKHAEEVRKNK 134

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	976
d2j0sa1	222	Probable ATP-dependent RNA helicase DDX48 {Human (	100.0
d1veca_	206	DEAD box RNA helicase rck/p54 {Human (Homo sapiens	100.0
d1qdea_	212	Initiation factor 4a {Baker's yeast (Saccharomyces	100.0
d2g9na1	218	Initiation factor 4a {Human (Homo sapiens) [TaxId:	100.0
d1wrba1	238	putative ATP-dependent RNA helicase VlgB {Flatworm	100.0
d1t6na_	207	Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo	100.0
d1hv8a1	208	Putative DEAD box RNA helicase {Archaeon Methanoco	100.0
d1s2ma1	206	Putative ATP-dependent RNA helicase DHH1 {Baker's	100.0
d2bmfa2	305	Dengue virus helicase {Dengue virus type 2 [TaxId:	100.0
d1q0ua_	209	Probable DEAD box RNA helicase YqfR {Bacillus stea	99.98
d1s2ma2	171	Putative ATP-dependent RNA helicase DHH1 {Baker's	99.95
d1fuka_	162	Initiation factor 4a {Baker's yeast (Saccharomyces	99.95
d2j0sa2	168	Probable ATP-dependent RNA helicase DDX48 {Human (	99.95
d1hv8a2	155	Putative DEAD box RNA helicase {Archaeon Methanoco	99.94
d1t5ia_	168	Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo	99.94
d2rb4a1	168	ATP-dependent RNA helicase DDX25 {Human (Homo sapi	99.93
d1oywa3	200	RecQ helicase domain {Escherichia coli [TaxId: 562	99.92
d1gkub1	237	Helicase-like "domain" of reverse gyrase {Archaeon	99.91
d1oywa2	206	RecQ helicase domain {Escherichia coli [TaxId: 562	99.9
d2p6ra3	202	Hel308 helicase {Archaeoglobus fulgidus [TaxId: 22	99.9
d1c4oa2	174	Nucleotide excision repair enzyme UvrB {Thermus th	99.89
d1t5la2	181	Nucleotide excision repair enzyme UvrB {Bacillus c	99.88
d1wp9a1	200	putative ATP-dependent RNA helicase PF2015 {Pyroco	99.86
d2eyqa5	211	Transcription-repair coupling factor, TRCF {Escher	99.85
d1gm5a4	206	RecG helicase domain {Thermotoga maritima [TaxId:	99.84
d1jr6a_	138	HCV helicase domain {Human hepatitis C virus (HCV)	99.82
d1gm5a3	264	RecG helicase domain {Thermotoga maritima [TaxId:	99.79
d2eyqa3	233	Transcription-repair coupling factor, TRCF {Escher	99.79
d1wp9a2	286	putative ATP-dependent RNA helicase PF2015 {Pyroco	99.78
d2p6ra4	201	Hel308 helicase {Archaeoglobus fulgidus [TaxId: 22	99.69
d2fwra1	200	DNA repair protein RAD25 {Archaeoglobus fulgidus [	99.69
d1rifa_	282	DNA helicase UvsW {Bacteriophage T4 [TaxId: 10665]	99.68
d2fz4a1	206	DNA repair protein RAD25 {Archaeoglobus fulgidus [	99.67
d1gkub2	248	Helicase-like "domain" of reverse gyrase {Archaeon	99.66
d1a1va2	299	HCV helicase domain {Human hepatitis C virus (HCV)	99.66
d1yksa1	140	YFV helicase domain {Yellow fever virus [TaxId: 11	99.64
d1a1va1	136	HCV helicase domain {Human hepatitis C virus (HCV)	99.57
d1z3ix1	346	Rad54-like, Rad54L {Zebra fish (Danio rerio) [TaxI	99.55
d1z5za1	244	Helicase of the SNF2/Rad54 hamily {Sulfolobus solf	99.5
d1z3ix2	298	Rad54-like, Rad54L {Zebra fish (Danio rerio) [TaxI	99.44
d1yksa2	299	YFV helicase domain {Yellow fever virus [TaxId: 11	99.4
d1tf5a4	175	Translocation ATPase SecA, nucleotide-binding doma	99.26
d1z63a1	230	Helicase of the SNF2/Rad54 hamily {Sulfolobus solf	99.18
d1tf5a3	273	Translocation ATPase SecA, nucleotide-binding doma	98.92
d1nkta3	288	Translocation ATPase SecA, nucleotide-binding doma	98.79
d1nkta4	219	Translocation ATPase SecA, nucleotide-binding doma	98.75
d1w36d1	359	Exodeoxyribonuclease V alpha chain (RecD) {Escheri	98.04
d1uaaa1	306	DEXX box DNA helicase {Escherichia coli, RepD [Tax	97.03
d1ls1a2	207	GTPase domain of the signal sequence recognition p	97.0
d2qy9a2	211	GTPase domain of the signal recognition particle r	96.66
d1pjra1	318	DEXX box DNA helicase {Bacillus stearothermophilus	96.61
d1okkd2	207	GTPase domain of the signal recognition particle r	96.59
d1gm5a3	264	RecG helicase domain {Thermotoga maritima [TaxId:	96.56
d1vmaa2	213	GTPase domain of the signal recognition particle r	96.51
d1a5ta2	207	delta prime subunit of DNA polymerase III, N-domai	96.31
d1t5la1	413	Nucleotide excision repair enzyme UvrB {Bacillus c	96.28
d1j8yf2	211	GTPase domain of the signal sequence recognition p	96.21
d2eyqa3	233	Transcription-repair coupling factor, TRCF {Escher	96.02
g1qhh.1	623	DEXX box DNA helicase {Bacillus stearothermophilus	95.73
d1l8qa2	213	Chromosomal replication initiation factor DnaA {Aq	95.58
d1xbta1	133	Thymidine kinase, TK1, N-terminal domain {Human (H	95.29
d2b8ta1	139	Thymidine kinase, TK1, N-terminal domain {Ureaplas	95.26
d1xx6a1	141	Thymidine kinase, TK1, N-terminal domain {Clostrid	95.13
d2gnoa2	198	gamma subunit of DNA polymerase III, N-domain {The	94.89
d1sxje2	252	Replication factor C5 {Baker's yeast (Saccharomyce	94.73
d1ixza_	247	AAA domain of cell division protein FtsH {Thermus	94.53
d1lv7a_	256	AAA domain of cell division protein FtsH {Escheric	94.34
d1njfa_	239	delta prime subunit of DNA polymerase III, N-domai	94.3
d2eyqa5	211	Transcription-repair coupling factor, TRCF {Escher	93.68
d1c4oa2	174	Nucleotide excision repair enzyme UvrB {Thermus th	93.53
d1c4oa1	408	Nucleotide excision repair enzyme UvrB {Thermus th	93.36
d1sxjc2	227	Replication factor C3 {Baker's yeast (Saccharomyce	92.8
d1sxjd2	237	Replication factor C2 {Baker's yeast (Saccharomyce	92.48
d1sxjb2	224	Replication factor C4 {Baker's yeast (Saccharomyce	92.39
d1t5la2	181	Nucleotide excision repair enzyme UvrB {Bacillus c	92.19
d1d2na_	246	Hexamerization domain of N-ethylmalemide-sensitive	91.91
d1ye8a1	178	Hypothetical kinase-like protein Aq_1292 {Aquifex	91.82
d1qvra2	387	ClpB, AAA+ modules {Thermus thermophilus [TaxId: 2	91.38
d1hv8a2	155	Putative DEAD box RNA helicase {Archaeon Methanoco	91.15
d1r6bx2	268	ClpA, an Hsp100 chaperone, AAA+ modules {Escherich	90.69
d1sxja2	253	Replication factor C1 {Baker's yeast (Saccharomyce	90.39
d1g6oa_	323	Hexameric traffic ATPase, HP0525 {Helicobacter pyl	90.31
d1g5ta_	157	ATP:corrinoid adenosyltransferase CobA {Salmonella	90.21
d1fuka_	162	Initiation factor 4a {Baker's yeast (Saccharomyces	90.1
d1iqpa2	231	Replication factor C {Archaeon Pyrococcus furiosus	90.04
d1e32a2	258	Membrane fusion ATPase VCP/p97 {Mouse (Mus musculu	89.87
d1jbka_	195	ClpB, AAA+ modules {Escherichia coli [TaxId: 562]}	89.77
d1p9ra_	401	Extracellular secretion NTPase EpsE {Vibrio choler	89.72
d1tf7a2	242	Circadian clock protein KaiC {Synechococcus sp. st	89.14
d1oywa3	200	RecQ helicase domain {Escherichia coli [TaxId: 562	88.75
d1t5ia_	168	Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo	87.57
d2j0sa2	168	Probable ATP-dependent RNA helicase DDX48 {Human (	87.43
d1s2ma2	171	Putative ATP-dependent RNA helicase DHH1 {Baker's	86.17
d2i3ba1	189	Cancer-related NTPase, C1orf57 {Human (Homo sapien	85.39
d2rb4a1	168	ATP-dependent RNA helicase DDX25 {Human (Homo sapi	84.55
d1um8a_	364	ClpX {Helicobacter pylori [TaxId: 210]}	83.86
d1w36b1	485	Exodeoxyribonuclease V beta chain (RecB), N-termin	83.75
d1g41a_	443	HslU {Haemophilus influenzae [TaxId: 727]}	82.71
d2j0sa1	222	Probable ATP-dependent RNA helicase DDX48 {Human (	82.21
d1w44a_	321	NTPase P4 {Bacteriophage phi-12 [TaxId: 161736]}	82.17
d1hv8a1	208	Putative DEAD box RNA helicase {Archaeon Methanoco	82.06
d1yksa2	299	YFV helicase domain {Yellow fever virus [TaxId: 11	81.92
d1e9ra_	433	Bacterial conjugative coupling protein TrwB {Esche	81.69
d2eyqa2	117	Transcription-repair coupling factor, TRCF {Escher	80.7
d1kaga_	169	Shikimate kinase (AroK) {Escherichia coli [TaxId:	80.68
d1ofha_	309	HslU {Haemophilus influenzae [TaxId: 727]}	80.26

>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=100.00  E-value=7.9e-39  Score=331.96  Aligned_cols=209  Identities=34%  Similarity=0.588  Sum_probs=195.3

Q ss_pred             CCcccccccCCCCHHHHHHHHHcCCCCCcHHHHHHHHHHhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCe
Q 002040          463 PKPIKTWHQTGLTSKIMETIRKLNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPV  542 (976)
Q Consensus       463 p~pi~~~~~~~l~~~l~~~l~~~~~~~p~~~Q~~~i~~il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~  542 (976)
                      .....+|.+++|++.++++|..+||..|||+|.++||.++.|+|++++|+||||||++|++|+++++...     ...++
T Consensus        13 ~~~~~sF~~l~L~~~l~~~L~~~g~~~pt~IQ~~aIp~il~g~dvi~~a~TGSGKTlayllPil~~l~~~-----~~~~~   87 (222)
T d2j0sa1          13 VDVTPTFDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSISVLQCLDIQ-----VRETQ   87 (222)
T ss_dssp             CCCCCSGGGGCCCHHHHHHHHHHTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHTCCTT-----SCSCC
T ss_pred             CCCCCCHHHCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHCCCCeEEEcCcchhhhhhhccccccccccc-----ccCce
Confidence            4556689999999999999999999999999999999999999999999999999999999999988653     35789


Q ss_pred             EEEEccCHHHHHHHHHHHHHHHhhcCcEEEEeeCCCChHHHHHHHhcCCeEEEeCchhHHHHHHhcCCcccccCCceEEE
Q 002040          543 GLIMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLV  622 (976)
Q Consensus       543 vLIl~Ptr~La~Q~~~~~~~~~~~~~~~~~~~~gg~~~~~~~~~l~~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vV  622 (976)
                      +||++||++||.|+++.+..++...++++.+++||.....+...+..+++|||+|||+|.+++....   ..++++.+||
T Consensus        88 ~lil~PtreLa~Qi~~~~~~l~~~~~i~~~~~~g~~~~~~~~~~l~~~~~Ilv~TPgrl~~~~~~~~---~~~~~l~~lV  164 (222)
T d2j0sa1          88 ALILAPTRELAVQIQKGLLALGDYMNVQCHACIGGTNVGEDIRKLDYGQHVVAGTPGRVFDMIRRRS---LRTRAIKMLV  164 (222)
T ss_dssp             EEEECSSHHHHHHHHHHHHHHTTTTTCCEEEECTTSCHHHHHHHHHHCCSEEEECHHHHHHHHHTTS---SCCTTCCEEE
T ss_pred             eEEecchHHHHHHHHHHHHHHhCccceeEEEEeecccchhhHHHhccCCeEEeCCCCcHHhcccccc---cccccceeee
Confidence            9999999999999999999999999999999999999999999999999999999999999886643   5788999999


Q ss_pred             ecCcccccccCCchHHHHHHHhcCCCCcEEEEeccCcHHHHHHHHHHcCCCeEEEeC
Q 002040          623 MDEADRMFDMGFEPQITRIVQNIRPDRQTVLFSATFPRQVEILARKVLNKPVEIQVG  679 (976)
Q Consensus       623 lDEah~~~~~~f~~~i~~il~~~~~~~q~i~~SAT~~~~~~~l~~~~l~~~~~i~~~  679 (976)
                      |||||+|++.+|...+..|+..++..+|+++||||+|..+..++..++.+|+.|.++
T Consensus       165 lDEaD~ll~~~f~~~i~~I~~~l~~~~Q~ilfSAT~~~~v~~l~~~~l~~Pv~I~V~  221 (222)
T d2j0sa1         165 LDEADEMLNKGFKEQIYDVYRYLPPATQVVLISATLPHEILEMTNKFMTDPIRILVK  221 (222)
T ss_dssp             EETHHHHTSTTTHHHHHHHHTTSCTTCEEEEEESCCCHHHHTTGGGTCSSCEEECCC
T ss_pred             ecchhHhhhcCcHHHHHHHHHhCCCCCEEEEEEEeCCHHHHHHHHHHCCCCEEEEEe
Confidence            999999999999999999999999999999999999999999999999999988764

>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=100.00  E-value=9.4e-37  Score=313.90  Aligned_cols=202  Identities=31%  Similarity=0.593  Sum_probs=186.8

Q ss_pred             cccccCCCCHHHHHHHHHcCCCCCcHHHHHHHHHHhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEE
Q 002040          467 KTWHQTGLTSKIMETIRKLNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIM  546 (976)
Q Consensus       467 ~~~~~~~l~~~l~~~l~~~~~~~p~~~Q~~~i~~il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl  546 (976)
                      ++|++++|++.++++|..+||..|||+|.++||.+++|+|+|++|+||||||++|++|++.++...     ..++.+||+
T Consensus         3 ~~F~~l~L~~~l~~~l~~~g~~~pt~iQ~~aip~il~g~dvl~~a~TGsGKTlayllP~l~~~~~~-----~~~~~~lil   77 (206)
T d1veca_           3 NEFEDYCLKRELLMGIFEMGWEKPSPIQEESIPIALSGRDILARAKNGTGKSGAYLIPLLERLDLK-----KDNIQAMVI   77 (206)
T ss_dssp             SSGGGSCCCHHHHHHHHTTTCCSCCHHHHHHHHHHHTTCCEEEECCSSSTTHHHHHHHHHHHCCTT-----SCSCCEEEE
T ss_pred             CChhccCcCHHHHHHHHHCCCCCCCHHHHHHHHHHHcCCCEEeeccCccccccccccchhhccccc-----ccCcceEEE
Confidence            689999999999999999999999999999999999999999999999999999999999987653     457899999


Q ss_pred             ccCHHHHHHHHHHHHHHHhhc-CcEEEEeeCCCChHHHHHHHhcCCeEEEeCchhHHHHHHhcCCcccccCCceEEEecC
Q 002040          547 APTRELVQQIHSDIRKFAKVM-GVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDE  625 (976)
Q Consensus       547 ~Ptr~La~Q~~~~~~~~~~~~-~~~~~~~~gg~~~~~~~~~l~~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDE  625 (976)
                      +||++||.|++..+..+.... ++.+..++|+.....+...+..+++|||+||++|.+++....   ..+.++.+|||||
T Consensus        78 ~pt~el~~q~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~ivv~TPgrl~~~~~~~~---~~~~~l~~lVlDE  154 (206)
T d1veca_          78 VPTRELALQVSQICIQVSKHMGGAKVMATTGGTNLRDDIMRLDDTVHVVIATPGRILDLIKKGV---AKVDHVQMIVLDE  154 (206)
T ss_dssp             CSCHHHHHHHHHHHHHHTTTSSSCCEEEECSSSCHHHHHHHTTSCCSEEEECHHHHHHHHHTTC---SCCTTCCEEEEET
T ss_pred             eecchhhHHHHHHHHHHhhcccCcccccccCCccHHHHHHHHHhccCeEEeCCccccccccchh---ccccccceEEEec
Confidence            999999999999999887654 577788888988888888888899999999999999887643   5688999999999


Q ss_pred             cccccccCCchHHHHHHHhcCCCCcEEEEeccCcHHHHHHHHHHcCCCeEE
Q 002040          626 ADRMFDMGFEPQITRIVQNIRPDRQTVLFSATFPRQVEILARKVLNKPVEI  676 (976)
Q Consensus       626 ah~~~~~~f~~~i~~il~~~~~~~q~i~~SAT~~~~~~~l~~~~l~~~~~i  676 (976)
                      ||.|++.+|...+..|+..+++++|+++||||+|..+..++..++.+|+.|
T Consensus       155 aD~ll~~~f~~~i~~I~~~~~~~~Q~~l~SAT~~~~v~~l~~~~l~~P~~I  205 (206)
T d1veca_         155 ADKLLSQDFVQIMEDIILTLPKNRQILLYSATFPLSVQKFMNSHLEKPYEI  205 (206)
T ss_dssp             HHHHTSTTTHHHHHHHHHHSCTTCEEEEEESCCCHHHHHHHHHHCSSCEEE
T ss_pred             cccccccchHHHHHHHHHhCCCCCEEEEEEecCCHHHHHHHHHHCCCCEEE
Confidence            999999999999999999999999999999999999999999999999865

>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=100.00  E-value=1.2e-36  Score=314.00  Aligned_cols=211  Identities=31%  Similarity=0.518  Sum_probs=186.6

Q ss_pred             cCCCCCcccccccCCCCHHHHHHHHHcCCCCCcHHHHHHHHHHhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCC
Q 002040          459 GKDVPKPIKTWHQTGLTSKIMETIRKLNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAG  538 (976)
Q Consensus       459 g~~~p~pi~~~~~~~l~~~l~~~l~~~~~~~p~~~Q~~~i~~il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~  538 (976)
                      |.+.|.++.+|.+++|++.++++|.++||..|||+|..+||.++.|+|+|++++||||||++|++|++.++...     .
T Consensus         2 ~~~~~~~~~sF~~l~l~~~l~~~L~~~g~~~pt~iQ~~aip~il~g~dvl~~a~TGsGKT~a~~lp~i~~l~~~-----~   76 (212)
T d1qdea_           2 QTNYDKVVYKFDDMELDENLLRGVFGYGFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFSIAALQRIDTS-----V   76 (212)
T ss_dssp             CBSCCCCCCCGGGGTCCHHHHHHHHHHTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHHCCTT-----C
T ss_pred             CCCCcccccChhhCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHcCCCEEeecccccchhhhhHhhhHhhhhcc-----C
Confidence            45678999999999999999999999999999999999999999999999999999999999999999998643     4


Q ss_pred             CCCeEEEEccCHHHHHHHHHHHHHHHhhcCcEEEEeeCCCChHHHHHHHhcCCeEEEeCchhHHHHHHhcCCcccccCCc
Q 002040          539 DGPVGLIMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRV  618 (976)
Q Consensus       539 ~~~~vLIl~Ptr~La~Q~~~~~~~~~~~~~~~~~~~~gg~~~~~~~~~l~~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~  618 (976)
                      .+|.+||++||++||.|++..+..+.....+.+..++++.....+...++ +++|+|+||++|..++....   ..|.++
T Consensus        77 ~~~~~lil~pt~el~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~IvI~TP~~l~~~~~~~~---~~l~~l  152 (212)
T d1qdea_          77 KAPQALMLAPTRELALQIQKVVMALAFHMDIKVHACIGGTSFVEDAEGLR-DAQIVVGTPGRVFDNIQRRR---FRTDKI  152 (212)
T ss_dssp             CSCCEEEECSSHHHHHHHHHHHHHHTTTSCCCEEEECC----------CT-TCSEEEECHHHHHHHHHTTS---SCCTTC
T ss_pred             CCcceEEEcccHHHhhhhhhhhcccccccccceeeEeeccchhHHHHHhc-CCcEEEECCCccccccccCc---eecCcc
Confidence            68999999999999999999999999888999999999888877765554 68999999999999887643   578899


Q ss_pred             eEEEecCcccccccCCchHHHHHHHhcCCCCcEEEEeccCcHHHHHHHHHHcCCCeEEEe
Q 002040          619 TYLVMDEADRMFDMGFEPQITRIVQNIRPDRQTVLFSATFPRQVEILARKVLNKPVEIQV  678 (976)
Q Consensus       619 ~~vVlDEah~~~~~~f~~~i~~il~~~~~~~q~i~~SAT~~~~~~~l~~~~l~~~~~i~~  678 (976)
                      .+|||||||.|++++|...+..|+..+++.+|+++||||+|+.+..+++.++.+|+.|.+
T Consensus       153 ~~lVlDEad~lld~~f~~~v~~I~~~~~~~~Q~vl~SAT~~~~v~~l~~~~l~~Pv~i~v  212 (212)
T d1qdea_         153 KMFILDEADEMLSSGFKEQIYQIFTLLPPTTQVVLLSATMPNDVLEVTTKFMRNPVRILV  212 (212)
T ss_dssp             CEEEEETHHHHHHTTCHHHHHHHHHHSCTTCEEEEEESSCCHHHHHHHHHHCSSCEEEC-
T ss_pred             eEEeehhhhhhcccchHHHHHHHHHhCCCCCeEEEEEeeCCHHHHHHHHHHCCCCEEEeC
Confidence            999999999999999999999999999999999999999999999999999999987753

>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=100.00  E-value=7.5e-37  Score=316.87  Aligned_cols=211  Identities=32%  Similarity=0.556  Sum_probs=190.2

Q ss_pred             CCCCcccccccCCCCHHHHHHHHHcCCCCCcHHHHHHHHHHhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCC
Q 002040          461 DVPKPIKTWHQTGLTSKIMETIRKLNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDG  540 (976)
Q Consensus       461 ~~p~pi~~~~~~~l~~~l~~~l~~~~~~~p~~~Q~~~i~~il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~  540 (976)
                      +.|.|+.+|.+++|++.++++|.++||..|||+|.++||.++.|+|++++|+||||||++|++|++.++...     ..+
T Consensus         6 ~~~e~i~sF~~l~L~~~l~~~L~~~g~~~pt~iQ~~aip~il~g~dvl~~a~TGsGKTlayllp~l~~i~~~-----~~~   80 (218)
T d2g9na1           6 NWNEIVDSFDDMNLSESLLRGIYAYGFEKPSAIQQRAILPCIKGYDVIAQAQSGTGKTATFAISILQQIELD-----LKA   80 (218)
T ss_dssp             CCCCCCCCGGGSCCCHHHHHHHHHHTCCSCCHHHHHHHHHHHHTCCEEEECCTTSSHHHHHHHHHHHHCCTT-----CCS
T ss_pred             CCCCccCCHHHCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHcCCCEEEEcccchhhhhhhhhhhhheeccc-----ccC
Confidence            357899999999999999999999999999999999999999999999999999999999999999998643     368


Q ss_pred             CeEEEEccCHHHHHHHHHHHHHHHhhcCcEEEEeeCCCChHHHHHHH-hcCCeEEEeCchhHHHHHHhcCCcccccCCce
Q 002040          541 PVGLIMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQISEL-KRGTEIVVCTPGRMIDILCTSGGKITNLRRVT  619 (976)
Q Consensus       541 ~~vLIl~Ptr~La~Q~~~~~~~~~~~~~~~~~~~~gg~~~~~~~~~l-~~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~  619 (976)
                      +++||++||++||.|++..+..++...++.+.+++++.....+.... ..+++|||+||++|.+++....   ..+..+.
T Consensus        81 ~~alil~Pt~eL~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~IvV~TP~rl~~~l~~~~---~~~~~l~  157 (218)
T d2g9na1          81 TQALVLAPTRELAQQIQKVVMALGDYMGASCHACIGGTNVRAEVQKLQMEAPHIIVGTPGRVFDMLNRRY---LSPKYIK  157 (218)
T ss_dssp             CCEEEECSSHHHHHHHHHHHHHHHTTTTCCEEEECC--CCCSTTTSSSSCCCSEEEECHHHHHHHHHTTS---SCSTTCC
T ss_pred             ccEEEEcccchhhhhHHHHHhhhccccceeEEeeecccchhHHHHHHhcCCCEEEEeCChhHHHHHhcCC---cccccce
Confidence            89999999999999999999999999999999988887665543332 2467999999999999997643   5778899


Q ss_pred             EEEecCcccccccCCchHHHHHHHhcCCCCcEEEEeccCcHHHHHHHHHHcCCCeEEEeC
Q 002040          620 YLVMDEADRMFDMGFEPQITRIVQNIRPDRQTVLFSATFPRQVEILARKVLNKPVEIQVG  679 (976)
Q Consensus       620 ~vVlDEah~~~~~~f~~~i~~il~~~~~~~q~i~~SAT~~~~~~~l~~~~l~~~~~i~~~  679 (976)
                      +|||||||.|++.+|...+..|+..++.++|+++||||+|..+..++..++.+|+.+.+.
T Consensus       158 ~lVlDEaD~ll~~~f~~~~~~Il~~~~~~~Q~il~SAT~~~~v~~~~~~~l~~pv~i~v~  217 (218)
T d2g9na1         158 MFVLDEADEMLSRGFKDQIYDIFQKLNSNTQVVLLSATMPSDVLEVTKKFMRDPIRILVK  217 (218)
T ss_dssp             EEEEESHHHHHHTTCHHHHHHHHHHSCTTCEEEEEESCCCHHHHHHHHHHCSSCEEEECC
T ss_pred             EEEeeecchhhcCchHHHHHHHHHhCCCCCeEEEEEecCCHHHHHHHHHHCCCCEEEEEe
Confidence            999999999999999999999999999999999999999999999999999999988764

>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=100.00  E-value=2.8e-36  Score=317.15  Aligned_cols=216  Identities=40%  Similarity=0.674  Sum_probs=196.1

Q ss_pred             CCCCcccccccCCCCHHHHHHHHHcCCCCCcHHHHHHHHHHhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCC----CC
Q 002040          461 DVPKPIKTWHQTGLTSKIMETIRKLNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPP----VA  536 (976)
Q Consensus       461 ~~p~pi~~~~~~~l~~~l~~~l~~~~~~~p~~~Q~~~i~~il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~----~~  536 (976)
                      ..|.++.+|++++|++.++++|..+||..|||+|..+||.++.|+|++++|+||||||++|++|++.++.....    ..
T Consensus        15 ~~~~~~~~F~~l~l~~~l~~~L~~~g~~~pt~iQ~~~ip~il~g~dvvi~a~TGsGKTlayllp~l~~l~~~~~~~~~~~   94 (238)
T d1wrba1          15 SATNVIENFDELKLDPTIRNNILLASYQRPTPIQKNAIPAILEHRDIMACAQTGSGKTAAFLIPIINHLVCQDLNQQRYS   94 (238)
T ss_dssp             SCCSCCCSSGGGSCCCSTTTTTTTTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHHHHTTCC------
T ss_pred             CCCCccCCHHHCCCCHHHHHHHHHCCCCCCCHHHHHHhhhhhCCCCEEEECCCCCCcceeeHHHHHHHHHhccccccccc
Confidence            45778999999999999999999999999999999999999999999999999999999999999999875432    22


Q ss_pred             CCCCCeEEEEccCHHHHHHHHHHHHHHHhhcCcEEEEeeCCCChHHHHHHHhcCCeEEEeCchhHHHHHHhcCCcccccC
Q 002040          537 AGDGPVGLIMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGGKITNLR  616 (976)
Q Consensus       537 ~~~~~~vLIl~Ptr~La~Q~~~~~~~~~~~~~~~~~~~~gg~~~~~~~~~l~~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~  616 (976)
                      ...+|++||||||++||.|++..+..++...++++..++|+.....+...+..+++||||||++|.+++....   ..|.
T Consensus        95 ~~~~~~alil~pt~el~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~ivV~TP~~l~~~~~~~~---~~l~  171 (238)
T d1wrba1          95 KTAYPKCLILAPTRELAIQILSESQKFSLNTPLRSCVVYGGADTHSQIREVQMGCHLLVATPGRLVDFIEKNK---ISLE  171 (238)
T ss_dssp             CCBCCSEEEECSSHHHHHHHHHHHHHHHTTSSCCEEEECSSSCSHHHHHHHSSCCSEEEECHHHHHHHHHTTS---BCCT
T ss_pred             CCCCceEEEeccchhhhcchheeeeecccCCCcEEEEEeccchhhHHHhhcccCCceeecCHHHHHhHHccCc---eecc
Confidence            3457999999999999999999999999999999999999999888888888899999999999999887643   5688


Q ss_pred             CceEEEecCcccccccCCchHHHHHHHhcC----CCCcEEEEeccCcHHHHHHHHHHcCCCeEEEeC
Q 002040          617 RVTYLVMDEADRMFDMGFEPQITRIVQNIR----PDRQTVLFSATFPRQVEILARKVLNKPVEIQVG  679 (976)
Q Consensus       617 ~~~~vVlDEah~~~~~~f~~~i~~il~~~~----~~~q~i~~SAT~~~~~~~l~~~~l~~~~~i~~~  679 (976)
                      ++.++||||||.|++.+|...+..|+..+.    .++|+|+||||+|..+..+++.++.+|+.+.+|
T Consensus       172 ~v~~lViDEaD~ll~~~f~~~i~~Il~~~~~~~~~~~Q~il~SAT~~~~v~~l~~~~~~~p~~i~vg  238 (238)
T d1wrba1         172 FCKYIVLDEADRMLDMGFEPQIRKIIEESNMPSGINRQTLMFSATFPKEIQKLAADFLYNYIFMTVG  238 (238)
T ss_dssp             TCCEEEEETHHHHHHTTCHHHHHHHHHSSCCCCGGGCEEEEEESSCCHHHHHHHHHHCSSCEEEEEC
T ss_pred             ccceeeeehhhhhhhhccHHHHHHHHHHhcCCCCCCCEEEEEeeeCCHHHHHHHHHHCCCCEEEEeC
Confidence            999999999999999999999999998764    257999999999999999999999999988765

>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=100.00  E-value=6.8e-36  Score=307.66  Aligned_cols=204  Identities=29%  Similarity=0.519  Sum_probs=184.6

Q ss_pred             cccccCCCCHHHHHHHHHcCCCCCcHHHHHHHHHHhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEE
Q 002040          467 KTWHQTGLTSKIMETIRKLNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIM  546 (976)
Q Consensus       467 ~~~~~~~l~~~l~~~l~~~~~~~p~~~Q~~~i~~il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl  546 (976)
                      +.|++++|++.++++|..+||..|||+|.++||.+++|+|++++|+||||||++|++|+++.+...     ..++.++|+
T Consensus         1 s~F~dl~L~~~l~~~l~~~g~~~pt~iQ~~aip~il~g~dvl~~A~TGsGKTla~~lp~l~~~~~~-----~~~~~~lil   75 (207)
T d1t6na_           1 SGFRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQLEPV-----TGQVSVLVM   75 (207)
T ss_dssp             CCSTTSCCCHHHHHHHHHTTCCCCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHCCCC-----TTCCCEEEE
T ss_pred             CCccccCcCHHHHHHHHHCCCCCCCHHHHHHHHHHHcCCCeEEEeccccccccccccceeeeeccc-----CCCceEEEE
Confidence            479999999999999999999999999999999999999999999999999999999999987543     357899999


Q ss_pred             ccCHHHHHHHHHHHHHHHhhcC-cEEEEeeCCCChHHHHHHHh-cCCeEEEeCchhHHHHHHhcCCcccccCCceEEEec
Q 002040          547 APTRELVQQIHSDIRKFAKVMG-VRCVPVYGGSGVAQQISELK-RGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMD  624 (976)
Q Consensus       547 ~Ptr~La~Q~~~~~~~~~~~~~-~~~~~~~gg~~~~~~~~~l~-~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlD  624 (976)
                      +||++||.|+++.+..++...+ +.+.+++||.....+...+. .+++|+||||++|.+++...   ..+|+++.+||||
T Consensus        76 ~PtreL~~qi~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~ilI~TP~rl~~~~~~~---~~~l~~l~~lVlD  152 (207)
T d1t6na_          76 CHTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLKKNCPHIVVGTPGRILALARNK---SLNLKHIKHFILD  152 (207)
T ss_dssp             CSCHHHHHHHHHHHHHHTTTSTTCCEEEESCCSCHHHHHHHHHHSCCSEEEECHHHHHHHHHTT---SSCCTTCCEEEEE
T ss_pred             eccchhhHHHHHHHHHHHhhCCCceeEEEeccccHHHHHHHHHhcCCCEEEeCcchhhhhccCC---ceeccccceeehh
Confidence            9999999999999999988764 67788899998888776664 46899999999999998754   2578999999999


Q ss_pred             Ccccccc-cCCchHHHHHHHhcCCCCcEEEEeccCcHHHHHHHHHHcCCCeEEEe
Q 002040          625 EADRMFD-MGFEPQITRIVQNIRPDRQTVLFSATFPRQVEILARKVLNKPVEIQV  678 (976)
Q Consensus       625 Eah~~~~-~~f~~~i~~il~~~~~~~q~i~~SAT~~~~~~~l~~~~l~~~~~i~~  678 (976)
                      |||.|++ .+|...+..|+..++..+|+++||||+|..+..+++.++.+|+.|.+
T Consensus       153 EaD~ll~~~~~~~~i~~I~~~~~~~~Q~il~SAT~~~~v~~l~~~~l~~P~~I~V  207 (207)
T d1t6na_         153 ECDKMLEQLDMRRDVQEIFRMTPHEKQVMMFSATLSKEIRPVCRKFMQDPMEIFV  207 (207)
T ss_dssp             SHHHHHSSHHHHHHHHHHHHTSCSSSEEEEEESCCCTTTHHHHHTTCSSCEEEEC
T ss_pred             hhhhhhhcCCcHHHHHHHHHhCCCCCEEEEEeeeCCHHHHHHHHHHCCCCEEEeC
Confidence            9999997 48999999999999999999999999999999999999999987753

>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=100.00  E-value=8.4e-35  Score=300.02  Aligned_cols=203  Identities=33%  Similarity=0.643  Sum_probs=187.0

Q ss_pred             ccccccCCCCHHHHHHHHHcCCCCCcHHHHHHHHHHhcCC-CEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEE
Q 002040          466 IKTWHQTGLTSKIMETIRKLNYEKPMPIQAQALPVIMSGR-DCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGL  544 (976)
Q Consensus       466 i~~~~~~~l~~~l~~~l~~~~~~~p~~~Q~~~i~~il~g~-d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vL  544 (976)
                      ..+|.+++|++.++++|.++||..|+|+|.++||.++.|+ |+|++++||+|||++|++|++.+...      ..+|++|
T Consensus         3 ~msf~~l~l~~~l~~~l~~~g~~~pt~iQ~~~ip~~l~g~~d~iv~a~TGsGKT~~~~l~~~~~~~~------~~~~~~l   76 (208)
T d1hv8a1           3 YMNFNELNLSDNILNAIRNKGFEKPTDIQMKVIPLFLNDEYNIVAQARTGSGKTASFAIPLIELVNE------NNGIEAI   76 (208)
T ss_dssp             CCCGGGSSCCHHHHHHHHHHTCCSCCHHHHHHHHHHHHTCSEEEEECCSSSSHHHHHHHHHHHHSCS------SSSCCEE
T ss_pred             ccCHHHcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHcCCCCeeeechhcccccceeeccccccccc------ccCcceE
Confidence            4589999999999999999999999999999999999885 99999999999999999999987553      4689999


Q ss_pred             EEccCHHHHHHHHHHHHHHHhhcCcEEEEeeCCCChHHHHHHHhcCCeEEEeCchhHHHHHHhcCCcccccCCceEEEec
Q 002040          545 IMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMD  624 (976)
Q Consensus       545 Il~Ptr~La~Q~~~~~~~~~~~~~~~~~~~~gg~~~~~~~~~l~~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlD  624 (976)
                      |+|||++||.|++..+..++...+..+.+++|+.....+...+. +++|+||||++|.+++....   .+++++.+||||
T Consensus        77 il~pt~~l~~q~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~l~-~~~IlV~TP~~l~~~l~~~~---~~~~~l~~lViD  152 (208)
T d1hv8a1          77 ILTPTRELAIQVADEIESLKGNKNLKIAKIYGGKAIYPQIKALK-NANIVVGTPGRILDHINRGT---LNLKNVKYFILD  152 (208)
T ss_dssp             EECSCHHHHHHHHHHHHHHHCSSCCCEEEECTTSCHHHHHHHHH-TCSEEEECHHHHHHHHHTTC---SCTTSCCEEEEE
T ss_pred             EEeeccccchhhhhhhhhhcccCCeEEEEeeCCCChHHHHHhcC-CCCEEEEChHHHHHHHHcCC---CCcccCcEEEEE
Confidence            99999999999999999999999999999999999888877664 69999999999999986643   568999999999


Q ss_pred             CcccccccCCchHHHHHHHhcCCCCcEEEEeccCcHHHHHHHHHHcCCCeEEEe
Q 002040          625 EADRMFDMGFEPQITRIVQNIRPDRQTVLFSATFPRQVEILARKVLNKPVEIQV  678 (976)
Q Consensus       625 Eah~~~~~~f~~~i~~il~~~~~~~q~i~~SAT~~~~~~~l~~~~l~~~~~i~~  678 (976)
                      |||.|++.+|...+..|+..+++++|+|+||||+|+.+..++..++.+|..|.+
T Consensus       153 Ead~l~~~~~~~~i~~I~~~~~~~~Q~i~~SAT~~~~v~~~~~~~l~~~~~I~~  206 (208)
T d1hv8a1         153 EADEMLNMGFIKDVEKILNACNKDKRILLFSATMPREILNLAKKYMGDYSFIKA  206 (208)
T ss_dssp             THHHHHTTTTHHHHHHHHHTSCSSCEEEEECSSCCHHHHHHHHHHCCSEEEEEC
T ss_pred             ChHHhhcCCChHHHHHHHHhCCCCCeEEEEEccCCHHHHHHHHHHCCCCeEEEE
Confidence            999999999999999999999999999999999999999999999999987764

>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=100.00  E-value=2.6e-34  Score=296.12  Aligned_cols=205  Identities=38%  Similarity=0.622  Sum_probs=192.0

Q ss_pred             cccccCCCCHHHHHHHHHcCCCCCcHHHHHHHHHHhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEE
Q 002040          467 KTWHQTGLTSKIMETIRKLNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIM  546 (976)
Q Consensus       467 ~~~~~~~l~~~l~~~l~~~~~~~p~~~Q~~~i~~il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl  546 (976)
                      .+|.+++|++.++++|.++||..|||+|.++||.++.|+|+|++|+||||||++|++|++.++...     ..++.++++
T Consensus         1 ~sF~~l~L~~~l~~~L~~~g~~~pt~iQ~~aip~il~g~dvi~~a~tGsGKTlay~lp~i~~~~~~-----~~~~~~~~~   75 (206)
T d1s2ma1           1 NTFEDFYLKRELLMGIFEAGFEKPSPIQEEAIPVAITGRDILARAKNGTGKTAAFVIPTLEKVKPK-----LNKIQALIM   75 (206)
T ss_dssp             CCGGGGCCCHHHHHHHHHTTCCSCCHHHHHHHHHHHHTCCEEEECCTTSCHHHHHHHHHHHHCCTT-----SCSCCEEEE
T ss_pred             CChHHcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHcCCCEEEecCCcchhhhhhccccccccccc-----cccccceee
Confidence            479999999999999999999999999999999999999999999999999999999999987653     357789999


Q ss_pred             ccCHHHHHHHHHHHHHHHhhcCcEEEEeeCCCChHHHHHHHhcCCeEEEeCchhHHHHHHhcCCcccccCCceEEEecCc
Q 002040          547 APTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEA  626 (976)
Q Consensus       547 ~Ptr~La~Q~~~~~~~~~~~~~~~~~~~~gg~~~~~~~~~l~~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDEa  626 (976)
                      +|+.+++.|....+..+....++++.+++|+.....+...+..+++||||||++|.+++....   ..|.++.+||||||
T Consensus        76 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~Ili~TP~~l~~~l~~~~---~~l~~l~~lV~DEa  152 (206)
T d1s2ma1          76 VPTRELALQTSQVVRTLGKHCGISCMVTTGGTNLRDDILRLNETVHILVGTPGRVLDLASRKV---ADLSDCSLFIMDEA  152 (206)
T ss_dssp             CSSHHHHHHHHHHHHHHTTTTTCCEEEECSSSCHHHHHHHTTSCCSEEEECHHHHHHHHHTTC---SCCTTCCEEEEESH
T ss_pred             ccchhhhhhhhhhhhhcccccCeeEEeecCccchhhHHHHhcccceEEEECCcccccccccce---eecccceEEEeech
Confidence            999999999999999999999999999999999999988888999999999999999997643   57899999999999


Q ss_pred             ccccccCCchHHHHHHHhcCCCCcEEEEeccCcHHHHHHHHHHcCCCeEEEeC
Q 002040          627 DRMFDMGFEPQITRIVQNIRPDRQTVLFSATFPRQVEILARKVLNKPVEIQVG  679 (976)
Q Consensus       627 h~~~~~~f~~~i~~il~~~~~~~q~i~~SAT~~~~~~~l~~~~l~~~~~i~~~  679 (976)
                      |.|++.+|...+..|+..++..+|+|+||||+|+.+..++..++.+|+.+.++
T Consensus       153 D~l~~~~f~~~v~~I~~~l~~~~Q~il~SATl~~~v~~~~~~~l~~P~~I~~~  205 (206)
T d1s2ma1         153 DKMLSRDFKTIIEQILSFLPPTHQSLLFSATFPLTVKEFMVKHLHKPYEINLM  205 (206)
T ss_dssp             HHHSSHHHHHHHHHHHTTSCSSCEEEEEESCCCHHHHHHHHHHCSSCEEESCC
T ss_pred             hhhhhhhhHHHHHHHHHhCCCCCEEEEEEEeCCHHHHHHHHHHCCCCEEEEee
Confidence            99999999999999999999999999999999999999999999999887654

>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=100.00  E-value=2.5e-33  Score=307.63  Aligned_cols=273  Identities=20%  Similarity=0.205  Sum_probs=188.8

Q ss_pred             HhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHHHHhhcCcEEEEeeCCCCh
Q 002040          501 IMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGV  580 (976)
Q Consensus       501 il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~~~~~~~~~~~~~~gg~~~  580 (976)
                      +.+++++|+.||||||||++|+++++......       ++++||++||++||.|+++.|..+    ++.+.....+   
T Consensus         6 ~~~~~~~lv~~~TGsGKT~~~l~~~~~~~~~~-------~~~~lvi~Ptr~La~q~~~~l~~~----~~~~~~~~~~---   71 (305)
T d2bmfa2           6 FRKKRLTIMDLHPGAGKTKRYLPAIVREAIKR-------GLRTLILAPTRVVAAEMEEALRGL----PIRYQTPAIR---   71 (305)
T ss_dssp             SSTTCEEEECCCTTSSTTTTHHHHHHHHHHHH-------TCCEEEEESSHHHHHHHHHHTTTS----CCBCCC-------
T ss_pred             hhcCCcEEEEECCCCCHHHHHHHHHHHHHHhc-------CCEEEEEccHHHHHHHHHHHHhcC----CcceeeeEEe---
Confidence            45789999999999999999988888776542       568999999999999998877653    2222111111   


Q ss_pred             HHHHHHHhcCCeEEEeCchhHHHHHHhcCCcccccCCceEEEecCcccccccCCchHHHHHHHh--cCCCCcEEEEeccC
Q 002040          581 AQQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMGFEPQITRIVQN--IRPDRQTVLFSATF  658 (976)
Q Consensus       581 ~~~~~~l~~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDEah~~~~~~f~~~i~~il~~--~~~~~q~i~~SAT~  658 (976)
                          ........|+++|++.|..++...    ..+.++++|||||||.+..+++.  +..++..  .++..+++++|||+
T Consensus        72 ----~~~~~~~~i~~~t~~~l~~~~~~~----~~~~~~~~vViDE~H~~~~~~~~--~~~~l~~~~~~~~~~~v~~SAT~  141 (305)
T d2bmfa2          72 ----AEHTGREIVDLMCHATFTMRLLSP----IRVPNYNLIIMDEAHFTDPASIA--ARGYISTRVEMGEAAGIFMTATP  141 (305)
T ss_dssp             --------CCCSEEEEEHHHHHHHHTSS----SCCCCCSEEEEESTTCCSHHHHH--HHHHHHHHHHHTSCEEEEECSSC
T ss_pred             ----ecccCccccccCCcHHHHHHHhcC----ccccceeEEEeeeeeecchhhHH--HHHHHHHhhccccceEEEeecCC
Confidence                122345789999999887766432    45678999999999988765432  2222222  24678999999998


Q ss_pred             cHHHHHHHHHHcCCCeEEEeCCcccccCCceEEEEecCcchHHHHHHHHHHhhhcCCcEEEEecCHHHHHHHHHHHHHCC
Q 002040          659 PRQVEILARKVLNKPVEIQVGGRSVVNKDITQLVEVRPESDRFLRLLELLGEWYEKGKILIFVHSQEKCDALFRDLLKHG  738 (976)
Q Consensus       659 ~~~~~~l~~~~l~~~~~i~~~~~~~~~~~i~q~~~~~~~~~k~~~l~~~l~~~~~~~kvLIF~~s~~~~~~l~~~L~~~~  738 (976)
                      +.....    +....            ..+...........+... ...+.  ...+++||||+++..++.++..|...+
T Consensus       142 ~~~~~~----~~~~~------------~~~~~~~~~~~~~~~~~~-~~~~~--~~~~~~lvf~~~~~~~~~l~~~L~~~~  202 (305)
T d2bmfa2         142 PGSRDP----FPQSN------------APIMDEEREIPERSWNSG-HEWVT--DFKGKTVWFVPSIKAGNDIAACLRKNG  202 (305)
T ss_dssp             TTCCCS----SCCCS------------SCEEEEECCCCCSCCSSC-CHHHH--SSCSCEEEECSCHHHHHHHHHHHHHHT
T ss_pred             Ccceee----ecccC------------CcceEEEEeccHHHHHHH-HHHHH--hhCCCEEEEeccHHHHHHHHHHHHhCC
Confidence            753210    00000            001111111111111111 11121  236799999999999999999999999


Q ss_pred             CCceeccCCCCHHHHHHHHHHhccCCccEEEecCcccccCCCCCCcEEE----------EeCC----------CCCHHHH
Q 002040          739 YPCLSLHGAKDQTDRESTISDFKSNVCNLLIATSVAARGLDVKELELVI----------NFDA----------PNHYEDY  798 (976)
Q Consensus       739 ~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLVaT~v~~~GlDi~~v~~VI----------~~d~----------p~s~~~y  798 (976)
                      +.+..+||++.+.    ....|.+|..++||||+++++|+|++ +.+||          +|++          |.|...|
T Consensus       203 ~~~~~l~~~~~~~----~~~~~~~~~~~~lvaT~~~~~G~~~~-~~~Vi~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~  277 (305)
T d2bmfa2         203 KKVIQLSRKTFDS----EYIKTRTNDWDFVVTTDISEMGANFK-AERVIDPRRCMKPVILTDGEERVILAGPMPVTHSSA  277 (305)
T ss_dssp             CCCEECCTTCHHH----HGGGGGTSCCSEEEECGGGGTTCCCC-CSEEEECCEEEEEEEECSSSCEEEEEEEEECCHHHH
T ss_pred             CCEEEeCCcChHH----HHhhhhccchhhhhhhHHHHhcCCCC-ccEEEEcCCceeeeEecCCCCceEEeccccCCHHHH
Confidence            9999999998654    44578999999999999999999994 55554          3443          5678999


Q ss_pred             HHHhcccCCCCCccEEEEEecCC
Q 002040          799 VHRVGRTGRAGRKGCAITFISEE  821 (976)
Q Consensus       799 ~Qr~GR~gR~g~~g~~~~~~~~~  821 (976)
                      +||+||+||.|+.+..+++|...
T Consensus       278 ~Qr~GR~GR~~~~~~~~~~~~~~  300 (305)
T d2bmfa2         278 AQRRGRVGRNPKNENDQYIYMGE  300 (305)
T ss_dssp             HHHHTTSSCSSSCCCEEEEECSC
T ss_pred             hhhhcCcCcCCCCceEEEEECCC
Confidence            99999999999888777776543

>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=99.98  E-value=2.5e-32  Score=282.31  Aligned_cols=204  Identities=31%  Similarity=0.537  Sum_probs=181.9

Q ss_pred             cccccCCCCHHHHHHHHHcCCCCCcHHHHHHHHHHhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEE
Q 002040          467 KTWHQTGLTSKIMETIRKLNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIM  546 (976)
Q Consensus       467 ~~~~~~~l~~~l~~~l~~~~~~~p~~~Q~~~i~~il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl  546 (976)
                      +.|.+++|++.++++|+++||..|||+|.+|||.+++|+|+|++||||||||++|++|++..+...     ...+.++++
T Consensus         1 t~F~~l~L~~~l~~~l~~~g~~~pt~iQ~~aip~~l~G~dvii~a~TGSGKTlayllp~l~~~~~~-----~~~~~~~~~   75 (209)
T d1q0ua_           1 TQFTRFPFQPFIIEAIKTLRFYKPTEIQERIIPGALRGESMVGQSQTGTGKTHAYLLPIMEKIKPE-----RAEVQAVIT   75 (209)
T ss_dssp             CCGGGSCCCHHHHHHHHHTTCCSCCHHHHHHHHHHHHTCCEEEECCSSHHHHHHHHHHHHHHCCTT-----SCSCCEEEE
T ss_pred             CccccCCcCHHHHHHHHHCCCCCCCHHHHHHHHHHHCCCCeEeecccccccceeeeeeeccccccc-----ccccccccc
Confidence            479999999999999999999999999999999999999999999999999999999999887653     346788999


Q ss_pred             ccCHHHHHHHHHHHHHHHhhc----CcEEEEeeCCCChHHHHHHHhcCCeEEEeCchhHHHHHHhcCCcccccCCceEEE
Q 002040          547 APTRELVQQIHSDIRKFAKVM----GVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLV  622 (976)
Q Consensus       547 ~Ptr~La~Q~~~~~~~~~~~~----~~~~~~~~gg~~~~~~~~~l~~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vV  622 (976)
                      +|+..++.+.+..+..+....    ...+.++.++.....+...+..+++|+|+||++|..++....   ..+.++.++|
T Consensus        76 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~TP~~l~~~~~~~~---~~~~~l~~lV  152 (209)
T d1q0ua_          76 APTRELATQIYHETLKITKFCPKDRMIVARCLIGGTDKQKALEKLNVQPHIVIGTPGRINDFIREQA---LDVHTAHILV  152 (209)
T ss_dssp             CSSHHHHHHHHHHHHHHHTTSCGGGCCCEEEECCCSHHHHTTCCCSSCCSEEEECHHHHHHHHHTTC---CCGGGCCEEE
T ss_pred             ccccchhHHHHHHHHhhhccccccccccccccccchhhHHHHHHhccCceEEEecCchhhhhhhhhc---cccccceEEE
Confidence            999999999998888765543    456777788877776666666789999999999999887643   4678899999


Q ss_pred             ecCcccccccCCchHHHHHHHhcCCCCcEEEEeccCcHHHHHHHHHHcCCCeEEEe
Q 002040          623 MDEADRMFDMGFEPQITRIVQNIRPDRQTVLFSATFPRQVEILARKVLNKPVEIQV  678 (976)
Q Consensus       623 lDEah~~~~~~f~~~i~~il~~~~~~~q~i~~SAT~~~~~~~l~~~~l~~~~~i~~  678 (976)
                      |||||.|++++|...+..|+..++++.|+++||||+|..+..++..++.+|+.+.+
T Consensus       153 iDEad~ll~~~f~~~v~~I~~~~~~~~Q~il~SATl~~~v~~l~~~~l~~p~~i~V  208 (209)
T d1q0ua_         153 VDEADLMLDMGFITDVDQIAARMPKDLQMLVFSATIPEKLKPFLKKYMENPTFVHV  208 (209)
T ss_dssp             ECSHHHHHHTTCHHHHHHHHHTSCTTCEEEEEESCCCGGGHHHHHHHCSSCEEEEC
T ss_pred             EeecccccccccHHHHHHHHHHCCCCCEEEEEEccCCHHHHHHHHHHCCCCEEEEe
Confidence            99999999999999999999999999999999999999999999999999988764

>d1s2ma2 c.37.1.19 (A:252-422) 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=99.95  E-value=1.2e-27  Score=237.73  Aligned_cols=160  Identities=28%  Similarity=0.502  Sum_probs=149.6

Q ss_pred             ccCCceEEEEecCcchHHHHHHHHHHhhhcCCcEEEEecCHHHHHHHHHHHHHCCCCceeccCCCCHHHHHHHHHHhccC
Q 002040          684 VNKDITQLVEVRPESDRFLRLLELLGEWYEKGKILIFVHSQEKCDALFRDLLKHGYPCLSLHGAKDQTDRESTISDFKSN  763 (976)
Q Consensus       684 ~~~~i~q~~~~~~~~~k~~~l~~~l~~~~~~~kvLIF~~s~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g  763 (976)
                      ....|.|.+.++....|+..|..+|... ..+++||||+++..++.|+..|...|+.+..+||+|++.+|..++..|++|
T Consensus         3 tl~~i~q~yi~v~~~~K~~~L~~ll~~~-~~~k~iVF~~~~~~~~~l~~~L~~~g~~~~~~h~~~~~~~r~~~~~~f~~~   81 (171)
T d1s2ma2           3 TLKGITQYYAFVEERQKLHCLNTLFSKL-QINQAIIFCNSTNRVELLAKKITDLGYSCYYSHARMKQQERNKVFHEFRQG   81 (171)
T ss_dssp             BCTTEEEEEEECCGGGHHHHHHHHHHHS-CCSEEEEECSSHHHHHHHHHHHHHHTCCEEEECTTSCHHHHHHHHHHHHTT
T ss_pred             CccceEEEEEEcCHHHHHHHHHHHHHhC-CCCceEEEEeeeehhhHhHHhhhcccccccccccccchhhhhhhhhhcccC
Confidence            3457889999999999999999999764 567999999999999999999999999999999999999999999999999


Q ss_pred             CccEEEecCcccccCCCCCCcEEEEeCCCCCHHHHHHHhcccCCCCCccEEEEEecCCCcCchHHHHHHHhhccCCCChH
Q 002040          764 VCNLLIATSVAARGLDVKELELVINFDAPNHYEDYVHRVGRTGRAGRKGCAITFISEEDAKYSPDLVKALELSEQVVPDD  843 (976)
Q Consensus       764 ~~~vLVaT~v~~~GlDi~~v~~VI~~d~p~s~~~y~Qr~GR~gR~g~~g~~~~~~~~~d~~~~~~i~~~l~~~~~~vp~~  843 (976)
                      ...|||||+++++|||+|++++|||||+|+++..|+||+||+||.|+.|.|++|+++.+...+..|.+.+......+|..
T Consensus        82 ~~~ilv~Td~~~~Gid~~~v~~VI~~d~p~~~~~y~qr~GR~gR~g~~g~~i~~v~~~e~~~~~~i~~~l~~~~~~~p~~  161 (171)
T d1s2ma2          82 KVRTLVCSDLLTRGIDIQAVNVVINFDFPKTAETYLHRIGRSGRFGHLGLAINLINWNDRFNLYKIEQELGTEIAAIPAT  161 (171)
T ss_dssp             SSSEEEESSCSSSSCCCTTEEEEEESSCCSSHHHHHHHHCBSSCTTCCEEEEEEECGGGHHHHHHHHHHHTCCCEECCSS
T ss_pred             ccccccchhHhhhccccceeEEEEecCCcchHHHHHHHhhhcccCCCccEEEEEeCHHHHHHHHHHHHHHCCCCCCCCcc
Confidence            99999999999999999999999999999999999999999999999999999999999999999998888877777764


Q ss_pred             H
Q 002040          844 L  844 (976)
Q Consensus       844 l  844 (976)
                      +
T Consensus       162 ~  162 (171)
T d1s2ma2         162 I  162 (171)
T ss_dssp             C
T ss_pred             c
Confidence            4

>d1fuka_ 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=99.95  E-value=3.9e-28  Score=238.53  Aligned_cols=159  Identities=31%  Similarity=0.554  Sum_probs=140.2

Q ss_pred             ceEEEEec-CcchHHHHHHHHHHhhhcCCcEEEEecCHHHHHHHHHHHHHCCCCceeccCCCCHHHHHHHHHHhccCCcc
Q 002040          688 ITQLVEVR-PESDRFLRLLELLGEWYEKGKILIFVHSQEKCDALFRDLLKHGYPCLSLHGAKDQTDRESTISDFKSNVCN  766 (976)
Q Consensus       688 i~q~~~~~-~~~~k~~~l~~~l~~~~~~~kvLIF~~s~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~  766 (976)
                      |.|.+..+ ....|+..|..++.. .+..++||||+++..++.|+..|...++.+..+||+|++.+|..+++.|+.|..+
T Consensus         1 I~q~~~~v~~~e~K~~~L~~ll~~-~~~~k~iIF~~s~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~l~~f~~~~~~   79 (162)
T d1fuka_           1 IKQFYVNVEEEEYKYECLTDLYDS-ISVTQAVIFCNTRRKVEELTTKLRNDKFTVSAIYSDLPQQERDTIMKEFRSGSSR   79 (162)
T ss_dssp             CEEEEEEEESGGGHHHHHHHHHHH-TTCSCEEEEESSHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHTTSCS
T ss_pred             CEEEEEEeCCcHHHHHHHHHHHHh-CCCCcEEEEEEEEchHHHHHHHHhhcCceEEEeccCCchhhHHHHHHHHhhcccc
Confidence            45666655 456688888888865 4567999999999999999999999999999999999999999999999999999


Q ss_pred             EEEecCcccccCCCCCCcEEEEeCCCCCHHHHHHHhcccCCCCCccEEEEEecCCCcCchHHHHHHHhhccCCCChHHHH
Q 002040          767 LLIATSVAARGLDVKELELVINFDAPNHYEDYVHRVGRTGRAGRKGCAITFISEEDAKYSPDLVKALELSEQVVPDDLKA  846 (976)
Q Consensus       767 vLVaT~v~~~GlDi~~v~~VI~~d~p~s~~~y~Qr~GR~gR~g~~g~~~~~~~~~d~~~~~~i~~~l~~~~~~vp~~l~~  846 (976)
                      |||||+++++|||+|++++|||||+|+++..|+||+||+||.|+.|.|++|+++.+...+..|.+.+......+|.++..
T Consensus        80 iLv~Tdv~~rGiDi~~v~~VI~~d~P~~~~~yihR~GR~gR~g~~g~~i~~~~~~d~~~~~~i~~~~~~~~~~ip~~~~~  159 (162)
T d1fuka_          80 ILISTDLLARGIDVQQVSLVINYDLPANKENYIHRIGRGGRFGRKGVAINFVTNEDVGAMRELEKFYSTQIEELPSDIAT  159 (162)
T ss_dssp             EEEEEGGGTTTCCCCSCSEEEESSCCSSGGGGGGSSCSCC-----CEEEEEEETTTHHHHHHHHHHSSCCCEECCSCCTT
T ss_pred             eeeccccccccccCCCceEEEEeccchhHHHHHhhccccccCCCccEEEEEcCHHHHHHHHHHHHHHcCcCCCCChHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999998888888876644


Q ss_pred             H
Q 002040          847 L  847 (976)
Q Consensus       847 l  847 (976)
                      +
T Consensus       160 l  160 (162)
T d1fuka_         160 L  160 (162)
T ss_dssp             T
T ss_pred             h
Confidence            3

>d2j0sa2 c.37.1.19 (A:244-411) 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=99.95  E-value=1e-27  Score=236.79  Aligned_cols=159  Identities=33%  Similarity=0.554  Sum_probs=144.8

Q ss_pred             ccCCceEEEEecCc-chHHHHHHHHHHhhhcCCcEEEEecCHHHHHHHHHHHHHCCCCceeccCCCCHHHHHHHHHHhcc
Q 002040          684 VNKDITQLVEVRPE-SDRFLRLLELLGEWYEKGKILIFVHSQEKCDALFRDLLKHGYPCLSLHGAKDQTDRESTISDFKS  762 (976)
Q Consensus       684 ~~~~i~q~~~~~~~-~~k~~~l~~~l~~~~~~~kvLIF~~s~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~  762 (976)
                      ...+|.|.+..+.. ..|+..|..+|... ...++||||+++..|+.++..|...|+.+..+||++++.+|..+++.|++
T Consensus         4 tl~~i~q~~v~v~~~~~K~~~L~~ll~~~-~~~k~iiF~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~r~~~~~~fk~   82 (168)
T d2j0sa2           4 TLEGIKQFFVAVEREEWKFDTLCDLYDTL-TITQAVIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRS   82 (168)
T ss_dssp             SCTTEEEEEEEESSTTHHHHHHHHHHHHH-TSSEEEEECSSHHHHHHHHHHHHHTTCCCEEECTTSCHHHHHHHHHHHHH
T ss_pred             CCCCcEEEEEEecChHHHHHHHHHHHHhC-CCCceEEEeeeHHHHHHHHHHhhhcccchhhhhhhhhHHHHHHHHHHHhc
Confidence            34678888766655 56999999988764 56799999999999999999999999999999999999999999999999


Q ss_pred             CCccEEEecCcccccCCCCCCcEEEEeCCCCCHHHHHHHhcccCCCCCccEEEEEecCCCcCchHHHHHHHhhccCCCCh
Q 002040          763 NVCNLLIATSVAARGLDVKELELVINFDAPNHYEDYVHRVGRTGRAGRKGCAITFISEEDAKYSPDLVKALELSEQVVPD  842 (976)
Q Consensus       763 g~~~vLVaT~v~~~GlDi~~v~~VI~~d~p~s~~~y~Qr~GR~gR~g~~g~~~~~~~~~d~~~~~~i~~~l~~~~~~vp~  842 (976)
                      |.++|||||+++++|||+|++++|||||+|+++..|+||+||+||.|+.|.|++|+++.+...+..|.+.+....+.+|.
T Consensus        83 g~~~iLv~Td~~~rGiDi~~v~~VIn~d~P~~~~~yihR~GR~gR~g~~G~~i~~~~~~d~~~~~~i~~~~~~~i~e~p~  162 (168)
T d2j0sa2          83 GASRVLISTDVWARGLDVPQVSLIINYDLPNNRELYIHRIGRSGRYGRKGVAINFVKNDDIRILRDIEQYYSTQIDEMPM  162 (168)
T ss_dssp             TSSCEEEECGGGSSSCCCTTEEEEEESSCCSSHHHHHHHHTTSSGGGCCEEEEEEEEGGGHHHHHHHHHHTTCCCEECCS
T ss_pred             CCccEEeccchhcccccccCcceEEEecCCcCHHHHHhhhccccccCCCcEEEEEECHHHHHHHHHHHHHHcCcCCCCCc
Confidence            99999999999999999999999999999999999999999999999999999999999988888888888766666665


Q ss_pred             H
Q 002040          843 D  843 (976)
Q Consensus       843 ~  843 (976)
                      .
T Consensus       163 ~  163 (168)
T d2j0sa2         163 N  163 (168)
T ss_dssp             C
T ss_pred             C
Confidence            3

>d1hv8a2 c.37.1.19 (A:211-365) 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=99.94  E-value=8.1e-27  Score=227.98  Aligned_cols=149  Identities=37%  Similarity=0.552  Sum_probs=139.1

Q ss_pred             cCCceEEEEecCcchHHHHHHHHHHhhhcCCcEEEEecCHHHHHHHHHHHHHCCCCceeccCCCCHHHHHHHHHHhccCC
Q 002040          685 NKDITQLVEVRPESDRFLRLLELLGEWYEKGKILIFVHSQEKCDALFRDLLKHGYPCLSLHGAKDQTDRESTISDFKSNV  764 (976)
Q Consensus       685 ~~~i~q~~~~~~~~~k~~~l~~~l~~~~~~~kvLIF~~s~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~  764 (976)
                      +.+|.|.+..+....|+..|..+|..  .++++||||+++..|+.|+..|...|+.+..+||++++.+|..++..|++|.
T Consensus         1 n~nI~~~~i~v~~~~K~~~L~~ll~~--~~~k~IIF~~s~~~~~~l~~~L~~~g~~~~~~~~~~~~~~r~~~~~~f~~~~   78 (155)
T d1hv8a2           1 NANIEQSYVEVNENERFEALCRLLKN--KEFYGLVFCKTKRDTKELASMLRDIGFKAGAIHGDLSQSQREKVIRLFKQKK   78 (155)
T ss_dssp             SSSSEEEEEECCGGGHHHHHHHHHCS--TTCCEEEECSSHHHHHHHHHHHHHTTCCEEEECSSSCHHHHHHHHHHHHTTS
T ss_pred             CCCeEEEEEEeChHHHHHHHHHHHcc--CCCCEEEEECchHHHHHHHhhhcccccccccccccchhhhhhhhhhhhhccc
Confidence            35788999989999999999999875  3568999999999999999999999999999999999999999999999999


Q ss_pred             ccEEEecCcccccCCCCCCcEEEEeCCCCCHHHHHHHhcccCCCCCccEEEEEecCCCcCchHHHHHHHhh
Q 002040          765 CNLLIATSVAARGLDVKELELVINFDAPNHYEDYVHRVGRTGRAGRKGCAITFISEEDAKYSPDLVKALEL  835 (976)
Q Consensus       765 ~~vLVaT~v~~~GlDi~~v~~VI~~d~p~s~~~y~Qr~GR~gR~g~~g~~~~~~~~~d~~~~~~i~~~l~~  835 (976)
                      .+|||||+++++|||+|++++||+||+|+++..|+||+||+||.|+.|.|++|+++.+...+..|.+.+..
T Consensus        79 ~~ilv~T~~~~~Gid~~~v~~Vi~~d~p~~~~~y~qr~GR~gR~g~~g~~i~~~~~~d~~~~~~i~~~~~~  149 (155)
T d1hv8a2          79 IRILIATDVMSRGIDVNDLNCVINYHLPQNPESYMHRIGRTGRAGKKGKAISIINRREYKKLRYIERAMKL  149 (155)
T ss_dssp             SSEEEECTTHHHHCCCSCCSEEEESSCCSCHHHHHHHSTTTCCSSSCCEEEEEECTTSHHHHHHHHHHHTC
T ss_pred             ceeeeehhHHhhhhhhccCcEEEEecCCCCHHHHHHHHHhcCcCCCCceEEEEEchHHHHHHHHHHHHHCC
Confidence            99999999999999999999999999999999999999999999999999999999888877777776654

>d1t5ia_ 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=99.94  E-value=1.5e-26  Score=228.67  Aligned_cols=156  Identities=33%  Similarity=0.609  Sum_probs=141.7

Q ss_pred             ceEEEEecCcchHHHHHHHHHHhhhcCCcEEEEecCHHHHHHHHHHHHHCCCCceeccCCCCHHHHHHHHHHhccCCccE
Q 002040          688 ITQLVEVRPESDRFLRLLELLGEWYEKGKILIFVHSQEKCDALFRDLLKHGYPCLSLHGAKDQTDRESTISDFKSNVCNL  767 (976)
Q Consensus       688 i~q~~~~~~~~~k~~~l~~~l~~~~~~~kvLIF~~s~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~v  767 (976)
                      +.|.+.....+.|+..|..+|... ..+++||||+++..++.|+..|...|+.|..+||+|++.+|..+++.|++|.++|
T Consensus         2 l~q~~v~~~~~~K~~~L~~ll~~~-~~~k~iIF~~~~~~~~~l~~~L~~~~~~~~~ihg~~~~~~r~~~l~~F~~g~~~i   80 (168)
T d1t5ia_           2 LQQYYVKLKDNEKNRKLFDLLDVL-EFNQVVIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQEERLSRYQQFKDFQRRI   80 (168)
T ss_dssp             CEEEEEECCGGGHHHHHHHHHHHS-CCSSEEEECSSHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHTTSCSE
T ss_pred             cEEEEEEeChHHHHHHHHHHHHhC-CCCeEEEEEeeeecchhhhhhhccccccccccccccchhhhhhhhhhhcccccee
Confidence            678888889999999999998765 5679999999999999999999999999999999999999999999999999999


Q ss_pred             EEecCcccccCCCCCCcEEEEeCCCCCHHHHHHHhcccCCCCCccEEEEEecCC-CcCchHHHHHHHhhccCCCChHH
Q 002040          768 LIATSVAARGLDVKELELVINFDAPNHYEDYVHRVGRTGRAGRKGCAITFISEE-DAKYSPDLVKALELSEQVVPDDL  844 (976)
Q Consensus       768 LVaT~v~~~GlDi~~v~~VI~~d~p~s~~~y~Qr~GR~gR~g~~g~~~~~~~~~-d~~~~~~i~~~l~~~~~~vp~~l  844 (976)
                      ||||+++++|+|+|.+++||+|++|+++..|+||+||+||.|+.|.|++|+++. +...+..+.+.+......+|+.+
T Consensus        81 Lv~T~~~~~Gid~~~~~~vi~~~~p~~~~~yiqr~GR~gR~g~~g~~i~l~~~~~~~~~~~~i~~~~~~~~~elp~~~  158 (168)
T d1t5ia_          81 LVATNLFGRGMDIERVNIAFNYDMPEDSDTYLHRVARAGRFGTKGLAITFVSDENDAKILNDVQDRFEVNISELPDEI  158 (168)
T ss_dssp             EEESSCCSTTCCGGGCSEEEESSCCSSHHHHHHHHHHHTGGGCCCEEEEEECSHHHHHHHHHHHHHHCCCEEECC---
T ss_pred             eeccccccchhhcccchhhhhhhcccchhhHhhhhhhcccCCCccEEEEEECchHHHHHHHHHHHHHcCCcccCCchh
Confidence            999999999999999999999999999999999999999999999999999875 45666777777777777788765

>d1oywa3 c.37.1.19 (A:207-406) 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=99.92  E-value=6.7e-25  Score=222.36  Aligned_cols=142  Identities=20%  Similarity=0.347  Sum_probs=126.7

Q ss_pred             CCceEEEEecCcchHHHHHHHHHHhhhcCCcEEEEecCHHHHHHHHHHHHHCCCCceeccCCCCHHHHHHHHHHhccCCc
Q 002040          686 KDITQLVEVRPESDRFLRLLELLGEWYEKGKILIFVHSQEKCDALFRDLLKHGYPCLSLHGAKDQTDRESTISDFKSNVC  765 (976)
Q Consensus       686 ~~i~q~~~~~~~~~k~~~l~~~l~~~~~~~kvLIF~~s~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~  765 (976)
                      ++|.  +.+.....|+..|+.+|... ...++||||+|+..++.|+..|...|+.+..+||++++.+|..+++.|++|.+
T Consensus         5 pNi~--y~v~~~~~k~~~L~~~l~~~-~~~~~IIF~~t~~~~~~l~~~l~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~   81 (200)
T d1oywa3           5 PNIR--YMLMEKFKPLDQLMRYVQEQ-RGKSGIIYCNSRAKVEDTAARLQSKGISAAAYHAGLENNVRADVQEKFQRDDL   81 (200)
T ss_dssp             TTEE--EEEEECSSHHHHHHHHHHHT-TTCCEEEECSSHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHTTSC
T ss_pred             CCcE--EEEEcCCcHHHHHHHHHHhc-CCCCEEEEEeeehhhHHhhhhhccCCceeEEecCCCcHHHHHHHHHHHhcccc
Confidence            4454  33344567888888888764 45689999999999999999999999999999999999999999999999999


Q ss_pred             cEEEecCcccccCCCCCCcEEEEeCCCCCHHHHHHHhcccCCCCCccEEEEEecCCCcCchHHHH
Q 002040          766 NLLIATSVAARGLDVKELELVINFDAPNHYEDYVHRVGRTGRAGRKGCAITFISEEDAKYSPDLV  830 (976)
Q Consensus       766 ~vLVaT~v~~~GlDi~~v~~VI~~d~p~s~~~y~Qr~GR~gR~g~~g~~~~~~~~~d~~~~~~i~  830 (976)
                      +|||||+++++|||+|+|++||||++|+++..|+||+||+||.|++|.|++|+++.+..++..++
T Consensus        82 ~ilvaTd~~~~GiD~p~v~~VI~~~~P~~~~~y~qr~GR~gR~g~~g~ai~~~~~~d~~~l~~~i  146 (200)
T d1oywa3          82 QIVVATVAFGMGINKPNVRFVVHFDIPRNIESYYQETGRAGRDGLPAEAMLFYDPADMAWLRRCL  146 (200)
T ss_dssp             SEEEECTTSCTTTCCTTCCEEEESSCCSSHHHHHHHHTTSCTTSSCEEEEEEECHHHHHHHHHHH
T ss_pred             eEEEecchhhhccCCCCCCEEEECCCccchHHHHHHhhhhhcCCCCceEEEecCHHHHHHHHhhh
Confidence            99999999999999999999999999999999999999999999999999999987665554443

>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=99.91  E-value=3.7e-25  Score=232.72  Aligned_cols=177  Identities=21%  Similarity=0.175  Sum_probs=130.2

Q ss_pred             HHHHHcCCCCCcHHHHHHHHHHhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHH
Q 002040          480 ETIRKLNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSD  559 (976)
Q Consensus       480 ~~l~~~~~~~p~~~Q~~~i~~il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~  559 (976)
                      ..+...++.+|+++|..+|+.++.|++++++||||+|||++++++++..+..        ++++|||+||++|+.|++++
T Consensus        34 ~~~~~~~~~~p~~~Q~~~i~~~l~g~~~~i~apTGsGKT~~~~~~~~~~~~~--------~~rvliv~Pt~~La~Q~~~~  105 (237)
T d1gkub1          34 VEFFRKCVGEPRAIQKMWAKRILRKESFAATAPTGVGKTSFGLAMSLFLALK--------GKRCYVIFPTSLLVIQAAET  105 (237)
T ss_dssp             HHHHHTTTCSCCHHHHHHHHHHHTTCCEECCCCBTSCSHHHHHHHHHHHHTT--------SCCEEEEESCHHHHHHHHHH
T ss_pred             HHHHHhccCCCCHHHHHHHHHHHCCCCEEEEecCCChHHHHHHHHHHHHHHh--------cCeEEEEeccHHHHHHHHHH
Confidence            3344567889999999999999999999999999999999999998876543        56899999999999999999


Q ss_pred             HHHHHhhcCcEE----EEeeCCCChHHHHHHHh--cCCeEEEeCchhHHHHHHhcCCcccccCCceEEEecCcccccccC
Q 002040          560 IRKFAKVMGVRC----VPVYGGSGVAQQISELK--RGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMG  633 (976)
Q Consensus       560 ~~~~~~~~~~~~----~~~~gg~~~~~~~~~l~--~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDEah~~~~~~  633 (976)
                      +.+++..+++.+    ....++.........+.  .+++|+|+||+.|.+.+       ..+.++++|||||||.|++.+
T Consensus       106 l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~Ilv~Tp~~l~~~~-------~~~~~~~~vVvDE~d~~l~~~  178 (237)
T d1gkub1         106 IRKYAEKAGVGTENLIGYYHGRIPKREKENFMQNLRNFKIVITTTQFLSKHY-------RELGHFDFIFVDDVDAILKAS  178 (237)
T ss_dssp             HHHHHTTTCCSGGGSEEECCSSCCSHHHHHHHHSGGGCSEEEEEHHHHHHCS-------TTSCCCSEEEESCHHHHHTST
T ss_pred             HHHHHHHcCCceEEEEeeeecccchhhhhhhhccccccceeccChHHHHHhh-------hhcCCCCEEEEEChhhhhhcc
Confidence            999988776543    33444444444333332  35799999999875533       356789999999999987643


Q ss_pred             C-----------chHHHHHHHhcCCCCcEEEEeccCcHHHHH-HHHHHcC
Q 002040          634 F-----------EPQITRIVQNIRPDRQTVLFSATFPRQVEI-LARKVLN  671 (976)
Q Consensus       634 f-----------~~~i~~il~~~~~~~q~i~~SAT~~~~~~~-l~~~~l~  671 (976)
                      .           ...+..+........|+|++|||+++.+.. +.+.+++
T Consensus       179 ~~~~~~~~~~g~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~l~r~ll~  228 (237)
T d1gkub1         179 KNVDKLLHLLGFHYDLKTKSWVGEARGCLMVSTATAKKGKKAELFRQLLN  228 (237)
T ss_dssp             HHHHHHHHHTTEEEETTTTEEEECCSSEEEECCCCSCCCTTHHHHHHHHC
T ss_pred             cchhHHHHhcCChHHHHHHHhhCCCCCeEEEEeCCCCcccHHHHHHHHhC
Confidence            2           111222222334567899999999865433 3444444

>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=99.90  E-value=2.4e-24  Score=221.35  Aligned_cols=189  Identities=20%  Similarity=0.273  Sum_probs=139.4

Q ss_pred             ccccCCCCHHHHHHHHH-cCCCCCcHHHHHHHHHHhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEE
Q 002040          468 TWHQTGLTSKIMETIRK-LNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIM  546 (976)
Q Consensus       468 ~~~~~~l~~~l~~~l~~-~~~~~p~~~Q~~~i~~il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl  546 (976)
                      ..+.++|.+.+.+.|+. +||..++|+|.+||+.+++|+|+|+++|||||||++|.+|++..           ...++|+
T Consensus         3 ~~e~~~l~~~~~~~l~~~fg~~~~rp~Q~~ai~~~l~g~~vlv~apTGsGKT~~~~~~~~~~-----------~~~~~~v   71 (206)
T d1oywa2           3 QAEVLNLESGAKQVLQETFGYQQFRPGQEEIIDTVLSGRDCLVVMPTGGGKSLCYQIPALLL-----------NGLTVVV   71 (206)
T ss_dssp             CCCCSSHHHHHHHHHHHTTCCSSCCTTHHHHHHHHHTTCCEEEECSCHHHHHHHHHHHHHHS-----------SSEEEEE
T ss_pred             chhhCCCCHHHHHHHHHhcCCCCCCHHHHHHHHHHHcCCCEEEEcCCCCCCcchhhhhhhhc-----------cCceEEe
Confidence            34567788888888886 49999999999999999999999999999999999999998743           4578999


Q ss_pred             ccCHHHHHHHHHHHHHHHhhcCcEEEEeeCCCChHHH----HHHHhcCCeEEEeCchhHHHHHHhcCCcccccCCceEEE
Q 002040          547 APTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQ----ISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLV  622 (976)
Q Consensus       547 ~Ptr~La~Q~~~~~~~~~~~~~~~~~~~~gg~~~~~~----~~~l~~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vV  622 (976)
                      +|+++|+.|+...+..+.    .......+.......    .........|+++||..+.......   ......+.+||
T Consensus        72 ~P~~~L~~q~~~~l~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~t~~~~~~~~~~~---~~~~~~v~~lv  144 (206)
T d1oywa2          72 SPLISLMKDQVDQLQANG----VAAACLNSTQTREQQLEVMTGCRTGQIRLLYIAPERLMLDNFLE---HLAHWNPVLLA  144 (206)
T ss_dssp             CSCHHHHHHHHHHHHHTT----CCEEEECTTSCHHHHHHHHHHHHHTCCSEEEECHHHHTSTTHHH---HHTTSCEEEEE
T ss_pred             ccchhhhhhHHHHHHhhc----ccccccccccccccchhHHHHHhcCCceEEEEechhhhchhhcc---cchhheeeeee
Confidence            999999999999888753    334444433332222    1223346799999998875433221   13466799999


Q ss_pred             ecCcccccccCCchHHH----HHHHhcCCCCcEEEEeccCcHHHHH-HHHHH-cCCCe
Q 002040          623 MDEADRMFDMGFEPQIT----RIVQNIRPDRQTVLFSATFPRQVEI-LARKV-LNKPV  674 (976)
Q Consensus       623 lDEah~~~~~~f~~~i~----~il~~~~~~~q~i~~SAT~~~~~~~-l~~~~-l~~~~  674 (976)
                      +||||.+.++++.....    ..+....+..|+|+||||+++.+.. +...+ +.+|+
T Consensus       145 iDEaH~~~~~~~~~~~~~~~~~~l~~~~~~~~ii~lSATl~~~v~~di~~~L~l~~p~  202 (206)
T d1oywa2         145 VDEAHCISQWGHDFRPEYAALGQLRQRFPTLPFMALTATADDTTRQDIVRLLGLNDPL  202 (206)
T ss_dssp             ESSGGGGCTTSSCCCHHHHGGGGHHHHCTTSCEEEEESCCCHHHHHHHHHHHTCCSCE
T ss_pred             eeeeeeeeccccchHHHHHHHHHHHHhCCCCceEEEEeCCCHHHHHHHHHHcCCCCCc
Confidence            99999998876443221    2223334678999999999998754 44443 77885

>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=99.90  E-value=4.6e-24  Score=218.50  Aligned_cols=186  Identities=22%  Similarity=0.288  Sum_probs=141.7

Q ss_pred             CCHHHHHHHHHcCCCCCcHHHHHHHHHHhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHH
Q 002040          474 LTSKIMETIRKLNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELV  553 (976)
Q Consensus       474 l~~~l~~~l~~~~~~~p~~~Q~~~i~~il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La  553 (976)
                      ++..+...|...||..|+|+|.++++.+++|+++|+++|||||||++++++++..+..        ++++|||+||++|+
T Consensus        10 ~~~~~~~~l~~~g~~~l~~~Q~~ai~~l~~~~~~il~apTGsGKT~~a~l~i~~~~~~--------~~~vl~l~P~~~L~   81 (202)
T d2p6ra3          10 ISSYAVGILKEEGIEELFPPQAEAVEKVFSGKNLLLAMPTAAGKTLLAEMAMVREAIK--------GGKSLYVVPLRALA   81 (202)
T ss_dssp             HHHHHHHHHHCC---CCCCCCHHHHHHHTTCSCEEEECSSHHHHHHHHHHHHHHHHHT--------TCCEEEEESSHHHH
T ss_pred             hhHHHHHHHHHcCCCCCCHHHHHHHHHHHcCCCEEEEcCCCCchhHHHHHHHHHHhhc--------cCcceeecccHHHH
Confidence            4567788899999999999999999999999999999999999999999999887754        45799999999999


Q ss_pred             HHHHHHHHHHHhhcCcEEEEeeCCCChHHHHHHHhcCCeEEEeCchhHHHHHHhcCCcccccCCceEEEecCcccccccC
Q 002040          554 QQIHSDIRKFAKVMGVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMG  633 (976)
Q Consensus       554 ~Q~~~~~~~~~~~~~~~~~~~~gg~~~~~~~~~l~~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDEah~~~~~~  633 (976)
                      .|++..+.+++... ..+...+|+.....   .....+.|+++||..+..++....   ..+..+++||+||||.+.+..
T Consensus        82 ~q~~~~~~~~~~~~-~~v~~~~~~~~~~~---~~~~~~~ii~~~~~~~~~~~~~~~---~~~~~~~~ii~DE~h~~~~~~  154 (202)
T d2p6ra3          82 GEKYESFKKWEKIG-LRIGISTGDYESRD---EHLGDCDIIVTTSEKADSLIRNRA---SWIKAVSCLVVDEIHLLDSEK  154 (202)
T ss_dssp             HHHHHHHTTTTTTT-CCEEEECSSCBCCS---SCSTTCSEEEEEHHHHHHHHHTTC---SGGGGCCEEEETTGGGGGCTT
T ss_pred             HHHHHHHHHHhhcc-ccceeeccCccccc---ccccccceeeeccHHHHHHHhccc---hhhhhhhhccccHHHHhcccc
Confidence            99999998876543 45555555443321   112357899999999987776543   457789999999999998777


Q ss_pred             CchHHHHH---HHhcCCCCcEEEEeccCcHHHHHHHHHHcCCCeEE
Q 002040          634 FEPQITRI---VQNIRPDRQTVLFSATFPRQVEILARKVLNKPVEI  676 (976)
Q Consensus       634 f~~~i~~i---l~~~~~~~q~i~~SAT~~~~~~~l~~~~l~~~~~i  676 (976)
                      +...+..+   +..+++..|+|+||||+|+ ...++ .++..+.++
T Consensus       155 r~~~~~~~l~~i~~~~~~~~~l~lSATl~n-~~~~~-~~l~~~~~~  198 (202)
T d2p6ra3         155 RGATLEILVTKMRRMNKALRVIGLSATAPN-VTEIA-EWLDADYYV  198 (202)
T ss_dssp             THHHHHHHHHHHHHHCTTCEEEEEECCCTT-HHHHH-HHTTCEEEE
T ss_pred             cchHHHHHHHHHHhcCCCCcEEEEcCCCCc-HHHHH-HHcCCCeee
Confidence            65554443   4556788999999999976 35454 555554443

>d1c4oa2 c.37.1.19 (A:410-583) Nucleotide excision repair enzyme UvrB {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: Tandem AAA-ATPase domain
domain: Nucleotide excision repair enzyme UvrB
species: Thermus thermophilus [TaxId: 274]

Probab=99.89  E-value=1e-22  Score=198.50  Aligned_cols=125  Identities=24%  Similarity=0.396  Sum_probs=109.4

Q ss_pred             cCcchHHHHHHHHHHhh-hcCCcEEEEecCHHHHHHHHHHHHHCCCCceeccCCCCHHHHHHHHHHhccCCccEEEecCc
Q 002040          695 RPESDRFLRLLELLGEW-YEKGKILIFVHSQEKCDALFRDLLKHGYPCLSLHGAKDQTDRESTISDFKSNVCNLLIATSV  773 (976)
Q Consensus       695 ~~~~~k~~~l~~~l~~~-~~~~kvLIF~~s~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLVaT~v  773 (976)
                      .+....+..|+..|.+. ..+.++||||+++.+|+.|+.+|...|+.+..+||+|++.+|..+++.|++|++.|||||++
T Consensus        11 ~p~~~qv~dll~~i~~~~~~g~r~lvfc~t~~~~~~l~~~L~~~Gi~a~~~Hg~~~~~eR~~~l~~F~~G~~~vLVaT~v   90 (174)
T d1c4oa2          11 KPTENQILDLMEGIRERAARGERTLVTVLTVRMAEELTSFLVEHGIRARYLHHELDAFKRQALIRDLRLGHYDCLVGINL   90 (174)
T ss_dssp             ECSTTHHHHHHHHHHHHHHTTCEEEEECSSHHHHHHHHHHHHHTTCCEEEECTTCCHHHHHHHHHHHHTTSCSEEEESCC
T ss_pred             EeCCCCHHHHHHHHHHHHhcCCcEEEEEcchhHHHHHHHHHHhcCCceEEEecccchHHHHHHHHHHHCCCeEEEEeeee
Confidence            34445566666666554 34569999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccccCCCCCCcEEEEeCCCC-----CHHHHHHHhcccCCCCCccEEEEEecC
Q 002040          774 AARGLDVKELELVINFDAPN-----HYEDYVHRVGRTGRAGRKGCAITFISE  820 (976)
Q Consensus       774 ~~~GlDi~~v~~VI~~d~p~-----s~~~y~Qr~GR~gR~g~~g~~~~~~~~  820 (976)
                      +++|||+|+|++||+|++|.     +...|+|++||+||.| .|.+++|+..
T Consensus        91 ~~~GiDip~V~~Vi~~~~~~~~~~~~~~~~iq~~GR~gR~~-~g~~~~~~~~  141 (174)
T d1c4oa2          91 LREGLDIPEVSLVAILDADKEGFLRSERSLIQTIGRAARNA-RGEVWLYADR  141 (174)
T ss_dssp             CCTTCCCTTEEEEEETTTTSCSGGGSHHHHHHHHGGGTTST-TCEEEEECSS
T ss_pred             eeeeccCCCCcEEEEeccccccccchhHHHHHHhhhhhhcC-CCeeEEeecC
Confidence            99999999999999999776     4588999999999987 5777776654

>d1t5la2 c.37.1.19 (A:415-595) Nucleotide excision repair enzyme UvrB {Bacillus caldotenax [TaxId: 1395]}

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: Nucleotide excision repair enzyme UvrB
species: Bacillus caldotenax [TaxId: 1395]

Probab=99.88  E-value=1.4e-22  Score=200.86  Aligned_cols=125  Identities=22%  Similarity=0.367  Sum_probs=108.7

Q ss_pred             cCcchHHHHHHHHHHhhh-cCCcEEEEecCHHHHHHHHHHHHHCCCCceeccCCCCHHHHHHHHHHhccCCccEEEecCc
Q 002040          695 RPESDRFLRLLELLGEWY-EKGKILIFVHSQEKCDALFRDLLKHGYPCLSLHGAKDQTDRESTISDFKSNVCNLLIATSV  773 (976)
Q Consensus       695 ~~~~~k~~~l~~~l~~~~-~~~kvLIF~~s~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLVaT~v  773 (976)
                      .+....+..|+..+.... .+.++||||+++..++.++..|...|+.+..+||+|++.+|..+++.|++|+++|||||++
T Consensus        11 rp~~~qvd~ll~~i~~~~~~~~~~iif~~~~~~~~~~~~~l~~~g~~~~~~hg~~~~~eR~~~l~~Fr~g~~~vLVaTdv   90 (181)
T d1t5la2          11 RPTKGQIDDLIGEIRERVERNERTLVTTLTKKMAEDLTDYLKEAGIKVAYLHSEIKTLERIEIIRDLRLGKYDVLVGINL   90 (181)
T ss_dssp             ECSTTHHHHHHHHHHHHHHTTCEEEEECSSHHHHHHHHHHHHTTTCCEEEECSSCCHHHHHHHHHHHHHTSCSEEEESCC
T ss_pred             EECCCcHHHHHHHHHHHHhcCCeEEEEeehhhhhHHHHHHHHhCCcceeEecCCccHHHHHHHHHHHHCCCCCEEEehhH
Confidence            344555666666666543 4569999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccccCCCCCCcEEEEeCCCC-----CHHHHHHHhcccCCCCCccEEEEEecC
Q 002040          774 AARGLDVKELELVINFDAPN-----HYEDYVHRVGRTGRAGRKGCAITFISE  820 (976)
Q Consensus       774 ~~~GlDi~~v~~VI~~d~p~-----s~~~y~Qr~GR~gR~g~~g~~~~~~~~  820 (976)
                      +++|||+|+|++|||||+|.     ++..|+||+||+||.|. |.+++++..
T Consensus        91 ~~rGiDip~v~~VI~~d~p~~~~~~s~~~yi~R~GRagR~g~-~~~~~~~~~  141 (181)
T d1t5la2          91 LREGLDIPEVSLVAILDADKEGFLRSERSLIQTIGRAARNAN-GHVIMYADT  141 (181)
T ss_dssp             CSSSCCCTTEEEEEETTTTSCSGGGSHHHHHHHHGGGTTSTT-CEEEEECSS
T ss_pred             HHccCCCCCCCEEEEecCCcccccccHHHHHHHHHhhccccC-ceeEeecch
Confidence            99999999999999999995     68899999999999984 444444443

>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=99.86  E-value=2e-21  Score=198.24  Aligned_cols=166  Identities=22%  Similarity=0.240  Sum_probs=130.7

Q ss_pred             CCCcHHHHHHHHHHhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHHHHhhc
Q 002040          488 EKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVM  567 (976)
Q Consensus       488 ~~p~~~Q~~~i~~il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~~~~~~  567 (976)
                      .+|+++|.+++..+. ++++|+++|||+|||+++++++...+...       +.++||++|+++|+.|+++.+.+++...
T Consensus         8 ~~pr~~Q~~~~~~~~-~~n~lv~~pTGsGKT~i~~~~~~~~~~~~-------~~~il~i~P~~~L~~q~~~~~~~~~~~~   79 (200)
T d1wp9a1           8 IQPRIYQEVIYAKCK-ETNCLIVLPTGLGKTLIAMMIAEYRLTKY-------GGKVLMLAPTKPLVLQHAESFRRLFNLP   79 (200)
T ss_dssp             HCCCHHHHHHHHHGG-GSCEEEECCTTSCHHHHHHHHHHHHHHHS-------CSCEEEECSSHHHHHHHHHHHHHHBCSC
T ss_pred             CCCCHHHHHHHHHHh-cCCeEEEeCCCCcHHHHHHHHHHHHHHhc-------CCcEEEEcCchHHHHHHHHHHHHhhccc
Confidence            369999999999876 56799999999999999998887776542       4578999999999999999999998877


Q ss_pred             CcEEEEeeCCCChHHHHHHHhcCCeEEEeCchhHHHHHHhcCCcccccCCceEEEecCcccccccCCchHHHHHHHhcCC
Q 002040          568 GVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMGFEPQITRIVQNIRP  647 (976)
Q Consensus       568 ~~~~~~~~gg~~~~~~~~~l~~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDEah~~~~~~f~~~i~~il~~~~~  647 (976)
                      +..+..+.++.........+ ....|+|+||..+...+....   ..+..+++||+||||.+........+...+.....
T Consensus        80 ~~~v~~~~~~~~~~~~~~~~-~~~~i~i~t~~~~~~~~~~~~---~~~~~~~~vIiDE~H~~~~~~~~~~~~~~~~~~~~  155 (200)
T d1wp9a1          80 PEKIVALTGEKSPEERSKAW-ARAKVIVATPQTIENDLLAGR---ISLEDVSLIVFDEAHRAVGNYAYVFIAREYKRQAK  155 (200)
T ss_dssp             GGGEEEECSCSCHHHHHHHH-HHCSEEEECHHHHHHHHHTTS---CCTTSCSEEEEETGGGCSTTCHHHHHHHHHHHHCS
T ss_pred             ccceeeeecccchhHHHHhh-hcccccccccchhHHHHhhhh---hhccccceEEEEehhhhhcchhHHHHHHHHHhcCC
Confidence            88888877777766554433 346899999999988876542   46778999999999987655433444445555567


Q ss_pred             CCcEEEEeccCcHHHHHH
Q 002040          648 DRQTVLFSATFPRQVEIL  665 (976)
Q Consensus       648 ~~q~i~~SAT~~~~~~~l  665 (976)
                      ..++++||||++.....+
T Consensus       156 ~~~~l~~SATp~~~~~~~  173 (200)
T d1wp9a1         156 NPLVIGLTASPGSTPEKI  173 (200)
T ss_dssp             SCCEEEEESCSCSSHHHH
T ss_pred             CCcEEEEEecCCCcHHHH
Confidence            789999999986544433

>d2eyqa5 c.37.1.19 (A:779-989) 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=99.85  E-value=1.3e-21  Score=194.49  Aligned_cols=162  Identities=19%  Similarity=0.250  Sum_probs=133.0

Q ss_pred             HHHhhhcCCcEEEEecCHHHHHHHHHHHHHC--CCCceeccCCCCHHHHHHHHHHhccCCccEEEecCcccccCCCCCCc
Q 002040          707 LLGEWYEKGKILIFVHSQEKCDALFRDLLKH--GYPCLSLHGAKDQTDRESTISDFKSNVCNLLIATSVAARGLDVKELE  784 (976)
Q Consensus       707 ~l~~~~~~~kvLIF~~s~~~~~~l~~~L~~~--~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLVaT~v~~~GlDi~~v~  784 (976)
                      +..+...++++.|+||..+.++.++..|.+.  ++.+..+||.|++.+++.+|..|.+|+++|||||.+++.|||||+++
T Consensus        24 I~~El~rGgQvy~V~p~I~~~e~~~~~l~~~~p~~~i~~lHGkm~~~eke~im~~F~~g~~~ILv~TtvIEvGiDvpnA~  103 (211)
T d2eyqa5          24 ILREILRGGQVYYLYNDVENIQKAAERLAELVPEARIAIGHGQMRERELERVMNDFHHQRFNVLVCTTIIETGIDIPTAN  103 (211)
T ss_dssp             HHHHHTTTCEEEEECCCSSCHHHHHHHHHHHCTTSCEEECCSSCCHHHHHHHHHHHHTTSCCEEEESSTTGGGSCCTTEE
T ss_pred             HHHHHHcCCeEEEEEcCccchhhHHHHHHHhCCceEEEEEEeccCHHHHHHHHHHHHcCCcceEEEehhhhhccCCCCCc
Confidence            3334455789999999999999999988874  78899999999999999999999999999999999999999999999


Q ss_pred             EEEEeCCCC-CHHHHHHHhcccCCCCCccEEEEEecCCCcCchHHHHHHHhhccCCCChHHHHHHHHHHHHHhhhhhhcc
Q 002040          785 LVINFDAPN-HYEDYVHRVGRTGRAGRKGCAITFISEEDAKYSPDLVKALELSEQVVPDDLKALADSFMAKVNQGLEQAH  863 (976)
Q Consensus       785 ~VI~~d~p~-s~~~y~Qr~GR~gR~g~~g~~~~~~~~~d~~~~~~i~~~l~~~~~~vp~~l~~l~~~~~~~~~~~~~~~~  863 (976)
                      +||+++.+. -.+++.|..||+||.+..|+||+++......                    ...+..-+..+       .
T Consensus       104 ~iiI~~a~rfGLaQLhQLRGRVGR~~~~s~c~l~~~~~~~~--------------------~~~a~~RL~~l-------~  156 (211)
T d2eyqa5         104 TIIIERADHFGLAQLHQLRGRVGRSHHQAYAWLLTPHPKAM--------------------TTDAQKRLEAI-------A  156 (211)
T ss_dssp             EEEETTTTSSCHHHHHHHHTTCCBTTBCEEEEEEECCGGGS--------------------CHHHHHHHHHH-------T
T ss_pred             EEEEecchhccccccccccceeeecCccceEEEEecCCcCC--------------------CchHHHHHHHH-------H
Confidence            999999987 4777778889999999999999998653211                    11111111111       1


Q ss_pred             CCCCCCCCcccchhHHHHHHHHHHHHHHHcCC
Q 002040          864 GTGYGGSGFKFNEEEDEKRKAAKKAQAKEYGF  895 (976)
Q Consensus       864 ~~~~~g~g~~~~~~~~~~~~~~~~~~~~~~g~  895 (976)
                      .+.-.|+||.+++.|+++|+++..++..|+|+
T Consensus       157 ~~~dlg~GF~iA~~DL~iRG~G~llG~~QsG~  188 (211)
T d2eyqa5         157 SLEDLGAGFALATHDLEIRGAGELLGEEQSGS  188 (211)
T ss_dssp             TCCSBSHHHHHHHHHHHHHHHHHHHCHHHHHH
T ss_pred             hcccCCcceeeeHhHHhhcCCccccccccCCc
Confidence            22234889999999999999999999999993

>d1gm5a4 c.37.1.19 (A:550-755) 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=99.84  E-value=1.1e-22  Score=204.94  Aligned_cols=167  Identities=19%  Similarity=0.330  Sum_probs=123.0

Q ss_pred             chHHHHHHHHHHhhh-cCCcEEEEecCHHHHHH--------HHHHHHHC---CCCceeccCCCCHHHHHHHHHHhccCCc
Q 002040          698 SDRFLRLLELLGEWY-EKGKILIFVHSQEKCDA--------LFRDLLKH---GYPCLSLHGAKDQTDRESTISDFKSNVC  765 (976)
Q Consensus       698 ~~k~~~l~~~l~~~~-~~~kvLIF~~s~~~~~~--------l~~~L~~~---~~~~~~lhg~~~~~~R~~~~~~F~~g~~  765 (976)
                      .++...++..|.... .++++.|+||.++..+.        .+..|.+.   ++.+..+||.|++.+++.+|..|.+|++
T Consensus        12 ~~~~~~v~~~I~~el~~g~QvyvVcP~Ieese~~~~~~~~e~~~~l~~~~~p~~~v~~lHG~m~~~eke~~m~~F~~g~~   91 (206)
T d1gm5a4          12 MDRVNEVYEFVRQEVMRGGQAFIVYPLIEESDKLNVKSAVEMYEYLSKEVFPEFKLGLMHGRLSQEEKDRVMLEFAEGRY   91 (206)
T ss_dssp             SSTHHHHHHHHHHHTTTSCCBCCBCCCC--------CHHHHHHHSGGGSCC---CBCCCCSSSCCSCSHHHHHHHTTTSS
T ss_pred             cccHHHHHHHHHHHHHcCCCEEEEEeeecccccccchhhHHHHHHHHHhcCCCCeEEEEeecccHHHHHHHHHHHHCCCE
Confidence            345666777766554 45689999987655443        23333332   6788999999999999999999999999


Q ss_pred             cEEEecCcccccCCCCCCcEEEEeCCCCC-HHHHHHHhcccCCCCCccEEEEEecCCCcCchHHHHHHHhhccCCCChHH
Q 002040          766 NLLIATSVAARGLDVKELELVINFDAPNH-YEDYVHRVGRTGRAGRKGCAITFISEEDAKYSPDLVKALELSEQVVPDDL  844 (976)
Q Consensus       766 ~vLVaT~v~~~GlDi~~v~~VI~~d~p~s-~~~y~Qr~GR~gR~g~~g~~~~~~~~~d~~~~~~i~~~l~~~~~~vp~~l  844 (976)
                      +|||||+++++|||||++++||++++|.. .+.|.|..||+||.|.+|+||+|+++.+......+               
T Consensus        92 ~iLVaTtViE~GIDip~a~~iii~~a~~fglsqlhQlrGRvGR~~~~~~~~l~~~~~~~~~~~rl---------------  156 (206)
T d1gm5a4          92 DILVSTTVIEVGIDVPRANVMVIENPERFGLAQLHQLRGRVGRGGQEAYCFLVVGDVGEEAMERL---------------  156 (206)
T ss_dssp             SBCCCSSCCCSCSCCTTCCEEEBCSCSSSCTTHHHHHHHTSCCSSTTCEEECCCCSCCHHHHHHH---------------
T ss_pred             EEEEEehhhhccccccCCcEEEEEccCCccHHHHHhhhhheeeccccceeEeeeccccccchhhh---------------
Confidence            99999999999999999999999999985 66666778999999999999999875332111110               


Q ss_pred             HHHHHHHHHHHhhhhhhccCCCCCCCCcccchhHHHHHHHHHHHHHHHcCCCC
Q 002040          845 KALADSFMAKVNQGLEQAHGTGYGGSGFKFNEEEDEKRKAAKKAQAKEYGFEE  897 (976)
Q Consensus       845 ~~l~~~~~~~~~~~~~~~~~~~~~g~g~~~~~~~~~~~~~~~~~~~~~~g~~~  897 (976)
                      ..            +.      ..++||.+++.|+++|+++..++..|+|+..
T Consensus       157 ~~------------~~------~~~dGf~ia~~Dl~lRG~G~~lG~~QsG~~~  191 (206)
T d1gm5a4         157 RF------------FT------LNTDGFKIAEYDLKTRGPGEFFGVKQHGLSG  191 (206)
T ss_dssp             HH------------HH------TCCCSHHHHHHHHHSSCCCC----CCCSSCC
T ss_pred             hh------------cc------ccCCCchHHHHHHhccCCccccccccCCCCc
Confidence            00            00      1357999999999999999999999999754

>d1jr6a_ c.37.1.14 (A:) 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=99.82  E-value=1.9e-21  Score=183.87  Aligned_cols=101  Identities=30%  Similarity=0.501  Sum_probs=92.4

Q ss_pred             hcCCcEEEEecCHHHHHHHHHHHHHCCCCceeccCCCCHHHHHHHHHHhccCCccEEEecCcccccCCCCCCcEEEEeC-
Q 002040          712 YEKGKILIFVHSQEKCDALFRDLLKHGYPCLSLHGAKDQTDRESTISDFKSNVCNLLIATSVAARGLDVKELELVINFD-  790 (976)
Q Consensus       712 ~~~~kvLIF~~s~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLVaT~v~~~GlDi~~v~~VI~~d-  790 (976)
                      ...+++||||+|+..|+.|+..|...|+.+..+||+|++       +.|++|...|||||+++++||| +++.+||+|+ 
T Consensus        33 ~~~~k~IVFc~t~~~ae~la~~L~~~G~~~~~~H~~~~~-------~~~~~~~~~vlvaTd~~~~GiD-~~v~~Vi~~~~  104 (138)
T d1jr6a_          33 IKGGRHLIFCHSKKKCDELAAKLVALGINAVAYYRGLDV-------SVIPTNGDVVVVATDALMTGFT-GDFDSVIDCNT  104 (138)
T ss_dssp             HTTSCEEEECSCHHHHHHHHHHHHHHTCEEEEECTTCCS-------CCCTTSSCEEEEESSSSCSSSC-CCBSEEEECSE
T ss_pred             cCCCCEEEEeCcHHHHHHHHHHHhccccchhhhhccchh-------hhhhhhhcceeehhHHHHhccc-cccceEEEEEe
Confidence            457899999999999999999999999999999999984       4588999999999999999999 9999999854 


Q ss_pred             ---CCCCHHHHHHHhcccCCCCCccEEEEEecCCC
Q 002040          791 ---APNHYEDYVHRVGRTGRAGRKGCAITFISEED  822 (976)
Q Consensus       791 ---~p~s~~~y~Qr~GR~gR~g~~g~~~~~~~~~d  822 (976)
                         +|.++..|+||+||+|| |++|. |+|+++.+
T Consensus       105 ~~~~P~~~~~y~qr~GR~gR-g~~G~-~~~i~~~e  137 (138)
T d1jr6a_         105 SDGKPQDAVSRTQRRGRTGR-GKPGI-YRFVAPGE  137 (138)
T ss_dssp             ETTEECCHHHHHHHHTTBCS-SSCEE-EEECCSSC
T ss_pred             cCCCCCCHHHHHhHhccccC-CCCcE-EEEEcCCC
Confidence               69999999999999999 99995 77988765

>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=99.79  E-value=3.6e-19  Score=185.70  Aligned_cols=167  Identities=20%  Similarity=0.203  Sum_probs=128.6

Q ss_pred             HHHHHHHcCCCCCcHHHHHHHHHHhc----C--CCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHH
Q 002040          478 IMETIRKLNYEKPMPIQAQALPVIMS----G--RDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRE  551 (976)
Q Consensus       478 l~~~l~~~~~~~p~~~Q~~~i~~il~----g--~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~  551 (976)
                      +...+..+.|. +|+-|..|+..|..    +  .+.|++|.||||||.+|+.+++..+..        |.+|+||+||..
T Consensus        73 ~~~f~~~LPFe-LT~~Q~~ai~ei~~d~~~~~~m~rLL~GdvGSGKT~Va~~a~~~~~~~--------g~q~~~m~Pt~~  143 (264)
T d1gm5a3          73 AEEFIKSLPFK-LTNAQKRAHQEIRNDMISEKPMNRLLQGDVGSGKTVVAQLAILDNYEA--------GFQTAFMVPTSI  143 (264)
T ss_dssp             HHHHHHHSSSC-CCHHHHHHHHHHHHHHHSSSCCCCEEECCSSSSHHHHHHHHHHHHHHH--------TSCEEEECSCHH
T ss_pred             HHHHHhhcccc-CCchHHHHHHHHHHHhhccCcceeeeeccccccccHHHHHHHHHHHhc--------ccceeEEeehHh
Confidence            34455677774 99999999999863    2  478999999999999999999887764        678999999999


Q ss_pred             HHHHHHHHHHHHHhhcCcEEEEeeCCCChHHH---HHHHhc-CCeEEEeCchhHHHHHHhcCCcccccCCceEEEecCcc
Q 002040          552 LVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQ---ISELKR-GTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEAD  627 (976)
Q Consensus       552 La~Q~~~~~~~~~~~~~~~~~~~~gg~~~~~~---~~~l~~-~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDEah  627 (976)
                      ||.|++..+.+++..+|+.+..++|+....+.   +..+.. .++|||||...|..-        ..+.++++|||||-|
T Consensus       144 La~Qh~~~~~~~f~~~~~~v~~l~~~~~~~~r~~~~~~~~~g~~~iiIGThsl~~~~--------~~f~~LglviiDEqH  215 (264)
T d1gm5a3         144 LAIQHYRRTVESFSKFNIHVALLIGATTPSEKEKIKSGLRNGQIDVVIGTHALIQED--------VHFKNLGLVIIDEQH  215 (264)
T ss_dssp             HHHHHHHHHHHHHTCSSCCEEECCSSSCHHHHHHHHHHHHSSCCCEEEECTTHHHHC--------CCCSCCCEEEEESCC
T ss_pred             hhHHHHHHHHHhhhhccccceeeccccchHHHHHHHHHHHCCCCCEEEeehHHhcCC--------CCccccceeeecccc
Confidence            99999999999999999999999999887654   334444 479999998765432        356789999999999


Q ss_pred             cccccCCchHHHHHHHhcCCCCcEEEEeccCcHHHHHHH
Q 002040          628 RMFDMGFEPQITRIVQNIRPDRQTVLFSATFPRQVEILA  666 (976)
Q Consensus       628 ~~~~~~f~~~i~~il~~~~~~~q~i~~SAT~~~~~~~l~  666 (976)
                      ++.-.+     ...+.....+.++|+|||||.+....++
T Consensus       216 ~fgv~Q-----r~~l~~~~~~~~~l~~SATPiprtl~~~  249 (264)
T d1gm5a3         216 RFGVKQ-----REALMNKGKMVDTLVMSATPIPRSMALA  249 (264)
T ss_dssp             CC----------CCCCSSSSCCCEEEEESSCCCHHHHHH
T ss_pred             ccchhh-----HHHHHHhCcCCCEEEEECCCCHHHHHHH
Confidence            854322     2222333456789999999877754333

>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=99.79  E-value=1.2e-18  Score=178.41  Aligned_cols=169  Identities=19%  Similarity=0.227  Sum_probs=132.2

Q ss_pred             HHHHHHHH-HcCCCCCcHHHHHHHHHHhc----C--CCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEcc
Q 002040          476 SKIMETIR-KLNYEKPMPIQAQALPVIMS----G--RDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAP  548 (976)
Q Consensus       476 ~~l~~~l~-~~~~~~p~~~Q~~~i~~il~----g--~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~P  548 (976)
                      ......+. .+.| .+|+-|..++..|..    +  .+.|++|.||||||.+|+.+++..+.        +|.+|+||+|
T Consensus        42 ~~~~~~~~~~lP~-~lt~~Q~~~~~~i~~~~~~~~~~~~LL~GdvGsGKT~V~~~a~~~~~~--------~g~qv~~l~P  112 (233)
T d2eyqa3          42 REQYQLFCDSFPF-ETTPDQAQAINAVLSDMCQPLAMDRLVCGDVGFGKTEVAMRAAFLAVD--------NHKQVAVLVP  112 (233)
T ss_dssp             HHHHHHHHHTCCS-CCCHHHHHHHHHHHHHHHSSSCCEEEEECCCCTTTHHHHHHHHHHHHT--------TTCEEEEECS
T ss_pred             HHHHHhhhhcccc-ccchhHHHHHHHHHHHHhccCccCeEEEcCCCCCcHHHHHHHHHHHHH--------cCCceEEEcc
Confidence            34444444 4554 599999999988763    3  37899999999999999999988765        3789999999


Q ss_pred             CHHHHHHHHHHHHHHHhhcCcEEEEeeCCCChHHH---HHHHhcC-CeEEEeCchhHHHHHHhcCCcccccCCceEEEec
Q 002040          549 TRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQ---ISELKRG-TEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMD  624 (976)
Q Consensus       549 tr~La~Q~~~~~~~~~~~~~~~~~~~~gg~~~~~~---~~~l~~~-~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlD  624 (976)
                      |..|+.|++..|+.++..+++.+..++|+....+.   +..+..| .+|||+|...|...        ..+.++++||||
T Consensus       113 t~~La~Q~~~~~~~~~~~~~~~v~~l~~~~~~~~~~~~~~~~~~g~~~iviGths~l~~~--------~~f~~LgLiIiD  184 (233)
T d2eyqa3         113 TTLLAQQHYDNFRDRFANWPVRIEMISRFRSAKEQTQILAEVAEGKIDILIGTHKLLQSD--------VKFKDLGLLIVD  184 (233)
T ss_dssp             SHHHHHHHHHHHHHHSTTTTCCEEEESTTSCHHHHHHHHHHHHTTCCSEEEECTHHHHSC--------CCCSSEEEEEEE
T ss_pred             HHHhHHHHHHHHHHHHhhCCCEEEeccCcccchhHHHHHHHHhCCCCCEEEeehhhhccC--------Cccccccceeee
Confidence            99999999999999999999999999999886654   3444444 69999998765322        467889999999


Q ss_pred             CcccccccCCchHHHHHHHhcCCCCcEEEEeccCcHHHHHHH
Q 002040          625 EADRMFDMGFEPQITRIVQNIRPDRQTVLFSATFPRQVEILA  666 (976)
Q Consensus       625 Eah~~~~~~f~~~i~~il~~~~~~~q~i~~SAT~~~~~~~l~  666 (976)
                      |-|++     .......+.....+..+|++||||.+....++
T Consensus       185 EeH~f-----g~kQ~~~l~~~~~~~~~l~~SATPiprtl~~~  221 (233)
T d2eyqa3         185 EEHRF-----GVRHKERIKAMRANVDILTLTATPIPRTLNMA  221 (233)
T ss_dssp             SGGGS-----CHHHHHHHHHHHTTSEEEEEESSCCCHHHHHH
T ss_pred             chhhh-----hhHHHHHHHhhCCCCCEEEEecchhHHHHHHH
Confidence            99983     33344555555677899999999988764443

>d1wp9a2 c.37.1.19 (A:201-486) 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=99.78  E-value=1.7e-19  Score=194.52  Aligned_cols=124  Identities=27%  Similarity=0.473  Sum_probs=108.9

Q ss_pred             chHHHHHHHHHHhh---hcCCcEEEEecCHHHHHHHHHHHHHCCCCceeccC--------CCCHHHHHHHHHHhccCCcc
Q 002040          698 SDRFLRLLELLGEW---YEKGKILIFVHSQEKCDALFRDLLKHGYPCLSLHG--------AKDQTDRESTISDFKSNVCN  766 (976)
Q Consensus       698 ~~k~~~l~~~l~~~---~~~~kvLIF~~s~~~~~~l~~~L~~~~~~~~~lhg--------~~~~~~R~~~~~~F~~g~~~  766 (976)
                      ..|+..|.++|...   ....++||||++...++.++..|...++++..+||        ++++.+|..+++.|++|.++
T Consensus       142 ~pK~~~l~~~l~~~~~~~~~~k~iiF~~~~~~~~~~~~~L~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~F~~g~~~  221 (286)
T d1wp9a2         142 HPKMDKLKEIIREQLQRKQNSKIIVFTNYRETAKKIVNELVKDGIKAKRFVGQASKENDRGLSQREQKLILDEFARGEFN  221 (286)
T ss_dssp             CHHHHHHHHHHHHHHHHCTTCCEEEECSCHHHHHHHHHHHHHTTCCEEEECCSSCC-------CCHHHHHHHHHHHTSCS
T ss_pred             CcHHHHHHHHHHHHHHhCCCCcEEEEeCcHHhHHHHHHHHHHcCCceEEeeccccccccchhchHHHHHHHHHHHcCCCc
Confidence            45777777777654   34669999999999999999999999999988876        46667899999999999999


Q ss_pred             EEEecCcccccCCCCCCcEEEEeCCCCCHHHHHHHhcccCCCCCccEEEEEecCCC
Q 002040          767 LLIATSVAARGLDVKELELVINFDAPNHYEDYVHRVGRTGRAGRKGCAITFISEED  822 (976)
Q Consensus       767 vLVaT~v~~~GlDi~~v~~VI~~d~p~s~~~y~Qr~GR~gR~g~~g~~~~~~~~~d  822 (976)
                      |||||+++++|||+|+|++||+||+||++..|+||+||+||.+ .|.+++|+++..
T Consensus       222 vLv~T~~~~~Gld~~~~~~Vi~~d~~~~~~~~~Qr~GR~gR~~-~~~~~~l~~~~~  276 (286)
T d1wp9a2         222 VLVATSVGEEGLDVPEVDLVVFYEPVPSAIRSIQRRGRTGRHM-PGRVIILMAKGT  276 (286)
T ss_dssp             EEEECGGGGGGGGSTTCCEEEESSCCHHHHHHHHHHTTSCSCC-CSEEEEEEETTS
T ss_pred             EEEEccceeccccCCCCCEEEEeCCCCCHHHHHHHHHhCCCCC-CCEEEEEEeCCC
Confidence            9999999999999999999999999999999999999999975 799999998753

>d2p6ra4 c.37.1.19 (A:203-403) 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=99.69  E-value=2.3e-17  Score=166.84  Aligned_cols=110  Identities=20%  Similarity=0.354  Sum_probs=96.5

Q ss_pred             cCCcEEEEecCHHHHHHHHHHHHHC------------------------------CCCceeccCCCCHHHHHHHHHHhcc
Q 002040          713 EKGKILIFVHSQEKCDALFRDLLKH------------------------------GYPCLSLHGAKDQTDRESTISDFKS  762 (976)
Q Consensus       713 ~~~kvLIF~~s~~~~~~l~~~L~~~------------------------------~~~~~~lhg~~~~~~R~~~~~~F~~  762 (976)
                      .++++||||+|+..|+.++..|...                              ...++++||+|++.+|..+...|++
T Consensus        39 ~~~~~LVF~~sRk~~~~~A~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~~l~~GIa~hh~~l~~~~r~~ie~~f~~  118 (201)
T d2p6ra4          39 ENGGVLVFESTRRGAEKTAVKLSAITAKYVENEGLEKAILEENEGEMSRKLAECVRKGAAFHHAGLLNGQRRVVEDAFRR  118 (201)
T ss_dssp             TTCCEEEECSSHHHHHHHHHHHHHHHHTTCCCSSHHHHHHTTCCSHHHHHHHHHHHTTCCEECTTSCHHHHHHHHHHHHT
T ss_pred             cCCcEEEEeCCHHHHHHHHHHHHHHHHhhhchhHHHHHHHHhhhhhhhHHHHHHHhccHHHHHHHhhhhhHHHHHHHHhC
Confidence            3679999999999999888887652                              1237889999999999999999999


Q ss_pred             CCccEEEecCcccccCCCCCCcEEEE-------eCCCCCHHHHHHHhcccCCCCC--ccEEEEEecCCC
Q 002040          763 NVCNLLIATSVAARGLDVKELELVIN-------FDAPNHYEDYVHRVGRTGRAGR--KGCAITFISEED  822 (976)
Q Consensus       763 g~~~vLVaT~v~~~GlDi~~v~~VI~-------~d~p~s~~~y~Qr~GR~gR~g~--~g~~~~~~~~~d  822 (976)
                      |.++|||||+++++|||+|..++||.       ++.|.++..|+|++|||||.|.  .|.|++++.+.+
T Consensus       119 g~i~vlvaT~~l~~Gin~p~~~vvi~~~~~~d~~~~~~~~~~~~q~~GRAGR~g~~~~G~~~l~~~~~~  187 (201)
T d2p6ra4         119 GNIKVVVATPTLAAGVNLPARRVIVRSLYRFDGYSKRIKVSEYKQMAGRAGRPGMDERGEAIIIVGKRD  187 (201)
T ss_dssp             TSCCEEEECSTTTSSSCCCBSEEEECCSEEESSSEEECCHHHHHHHHTTBSCTTTCSCEEEEEECCGGG
T ss_pred             CCceEEEechHHHhhcCCCCceEEEecceeccCCcCCCCHHHHHHHhcccCCCCCCCeeEEEEEeCCCC
Confidence            99999999999999999999999986       6678899999999999999884  788888876543

>d2fwra1 c.37.1.19 (A:257-456) 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=99.69  E-value=1.6e-17  Score=168.83  Aligned_cols=117  Identities=20%  Similarity=0.386  Sum_probs=103.7

Q ss_pred             chHHHHHHHHHHhhhcCCcEEEEecCHHHHHHHHHHHHHCCCCceeccCCCCHHHHHHHHHHhccCCccEEEecCccccc
Q 002040          698 SDRFLRLLELLGEWYEKGKILIFVHSQEKCDALFRDLLKHGYPCLSLHGAKDQTDRESTISDFKSNVCNLLIATSVAARG  777 (976)
Q Consensus       698 ~~k~~~l~~~l~~~~~~~kvLIF~~s~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLVaT~v~~~G  777 (976)
                      ..|+..|..+|... ...++||||++...+..|+..|     .+..+||.+++.+|..+++.|++|.++|||||+++++|
T Consensus        78 ~~K~~~l~~ll~~~-~~~k~lvf~~~~~~~~~l~~~l-----~~~~i~g~~~~~~R~~~l~~F~~~~~~vLv~~~~~~~G  151 (200)
T d2fwra1          78 KNKIRKLREILERH-RKDKIIIFTRHNELVYRISKVF-----LIPAITHRTSREEREEILEGFRTGRFRAIVSSQVLDEG  151 (200)
T ss_dssp             SHHHHHHHHHHHHT-SSSCBCCBCSCHHHHHHHHHHT-----TCCBCCSSSCSHHHHTHHHHHHHSSCSBCBCSSCCCSS
T ss_pred             HHHHHHHHHHHHhC-CCCcEEEEeCcHHHHHHHHhhc-----CcceeeCCCCHHHHHHHHHHhhcCCeeeeeecchhhcc
Confidence            56888888888764 5679999999999999998776     45678999999999999999999999999999999999


Q ss_pred             CCCCCCcEEEEeCCCCCHHHHHHHhcccCCCCCc---cEEEEEecC
Q 002040          778 LDVKELELVINFDAPNHYEDYVHRVGRTGRAGRK---GCAITFISE  820 (976)
Q Consensus       778 lDi~~v~~VI~~d~p~s~~~y~Qr~GR~gR~g~~---g~~~~~~~~  820 (976)
                      ||+|.+++||+|++|||+..|+|++||++|.|+.   ..+|.|++.
T Consensus       152 idl~~~~~vi~~~~~~s~~~~~Q~iGR~~R~~~~k~~~~i~~~v~~  197 (200)
T d2fwra1         152 IDVPDANVGVIMSGSGSAREYIQRLGRILRPSKGKKEAVLYELISR  197 (200)
T ss_dssp             SCSCCBSEEEEECCSSCCHHHHHHHHHSBCCCTTTCCEEEEEEEEC
T ss_pred             cCCCCCCEEEEeCCCCCHHHHHHHHHhcCCCCCCCcEEEEEEEecC
Confidence            9999999999999999999999999999999863   355556664

>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=99.68  E-value=2.1e-17  Score=176.49  Aligned_cols=154  Identities=18%  Similarity=0.142  Sum_probs=115.3

Q ss_pred             CCCcHHHHHHHHHHhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHHHHhhc
Q 002040          488 EKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVM  567 (976)
Q Consensus       488 ~~p~~~Q~~~i~~il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~~~~~~  567 (976)
                      ..|+++|.+|+..++.++..|+++|||+|||+++++.+...+...       +.++|||||+++|+.||++.|..++...
T Consensus       112 ~~~rdyQ~~av~~~l~~~~~il~~pTGsGKT~i~~~i~~~~~~~~-------~~k~Liivp~~~Lv~Q~~~~f~~~~~~~  184 (282)
T d1rifa_         112 IEPHWYQKDAVFEGLVNRRRILNLPTSAGRSLIQALLARYYLENY-------EGKILIIVPTTALTTQMADDFVDYRLFS  184 (282)
T ss_dssp             CCCCHHHHHHHHHHHHHSEEEECCCTTSCHHHHHHHHHHHHHHHC-------SSEEEEECSSHHHHHHHHHHHHHHTSCC
T ss_pred             cccchHHHHHHHHHHhcCCceeEEEcccCccHHHHHHHHHhhhcc-------cceEEEEEcCchhHHHHHHHHHHhhccc
Confidence            369999999999999999999999999999998665443333321       3479999999999999999999986555


Q ss_pred             CcEEEEeeCCCChHHHHHHHhcCCeEEEeCchhHHHHHHhcCCcccccCCceEEEecCcccccccCCchHHHHHHHhcCC
Q 002040          568 GVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMGFEPQITRIVQNIRP  647 (976)
Q Consensus       568 ~~~~~~~~gg~~~~~~~~~l~~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDEah~~~~~~f~~~i~~il~~~~~  647 (976)
                      ...+..+++|......   ......|+|+|+..+....      ...+.++++||+||||++.    ...+..++..+.+
T Consensus       185 ~~~~~~~~~g~~~~~~---~~~~~~i~i~t~qs~~~~~------~~~~~~f~~VIvDEaH~~~----a~~~~~il~~~~~  251 (282)
T d1rifa_         185 HAMIKKIGGGASKDDK---YKNDAPVVVGTWQTVVKQP------KEWFSQFGMMMNDECHLAT----GKSISSIISGLNN  251 (282)
T ss_dssp             GGGEEECSTTCSSTTC---CCTTCSEEEECHHHHTTSC------GGGGGGEEEEEEETGGGCC----HHHHHHHTTTCTT
T ss_pred             cccceeecceeccccc---ccccceEEEEeeehhhhhc------ccccCCCCEEEEECCCCCC----chhHHHHHHhccC
Confidence            5556667776543211   1234689999988764332      1246689999999999864    4566777777766


Q ss_pred             CCcEEEEeccCcHH
Q 002040          648 DRQTVLFSATFPRQ  661 (976)
Q Consensus       648 ~~q~i~~SAT~~~~  661 (976)
                      ....++||||++..
T Consensus       252 ~~~rlGlTaT~~~~  265 (282)
T d1rifa_         252 CMFKFGLSGSLRDG  265 (282)
T ss_dssp             CCEEEEECSSCCTT
T ss_pred             CCeEEEEEeecCCC
Confidence            55679999998653

>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=99.67  E-value=1.5e-16  Score=162.14  Aligned_cols=136  Identities=22%  Similarity=0.160  Sum_probs=101.3

Q ss_pred             CCcHHHHHHHHHHhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHHHHhhcC
Q 002040          489 KPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVMG  568 (976)
Q Consensus       489 ~p~~~Q~~~i~~il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~~~~~~~  568 (976)
                      +|+++|.+++..++.+..+|+++|||+|||++++..+. .+          +.++|||||++.|+.||.+.+..+...  
T Consensus        70 ~Lr~yQ~eav~~~~~~~~~ll~~~tG~GKT~~a~~~~~-~~----------~~~~Liv~p~~~L~~q~~~~~~~~~~~--  136 (206)
T d2fz4a1          70 SLRDYQEKALERWLVDKRGCIVLPTGSGKTHVAMAAIN-EL----------STPTLIVVPTLALAEQWKERLGIFGEE--  136 (206)
T ss_dssp             CCCHHHHHHHHHHTTTSEEEEEESSSTTHHHHHHHHHH-HS----------CSCEEEEESSHHHHHHHHHHHGGGCGG--
T ss_pred             CcCHHHHHHHHHHHhCCCcEEEeCCCCCceehHHhHHH-Hh----------cCceeEEEcccchHHHHHHHHHhhccc--
Confidence            58999999999999999999999999999998654432 21          346899999999999999999876432  


Q ss_pred             cEEEEeeCCCChHHHHHHHhcCCeEEEeCchhHHHHHHhcCCcccccCCceEEEecCcccccccCCchHHHHHHHhcCCC
Q 002040          569 VRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMGFEPQITRIVQNIRPD  648 (976)
Q Consensus       569 ~~~~~~~gg~~~~~~~~~l~~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDEah~~~~~~f~~~i~~il~~~~~~  648 (976)
                       .+....|+.         .....|+|+|+..+......      ....+++||+||||++..    ..+..++..+. .
T Consensus       137 -~~~~~~~~~---------~~~~~i~i~t~~~~~~~~~~------~~~~~~lvIiDEaH~~~a----~~~~~i~~~~~-~  195 (206)
T d2fz4a1         137 -YVGEFSGRI---------KELKPLTVSTYDSAYVNAEK------LGNRFMLLIFDEVHHLPA----ESYVQIAQMSI-A  195 (206)
T ss_dssp             -GEEEESSSC---------BCCCSEEEEEHHHHHHTHHH------HTTTCSEEEEECSSCCCT----TTHHHHHHTCC-C
T ss_pred             -chhhccccc---------ccccccccceehhhhhhhHh------hCCcCCEEEEECCeeCCc----HHHHHHHhccC-C
Confidence             233333332         23468999999887655432      235689999999998753    34556666553 4


Q ss_pred             CcEEEEeccC
Q 002040          649 RQTVLFSATF  658 (976)
Q Consensus       649 ~q~i~~SAT~  658 (976)
                      ...|+||||+
T Consensus       196 ~~~lgLTATl  205 (206)
T d2fz4a1         196 PFRLGLTATF  205 (206)
T ss_dssp             SEEEEEEESC
T ss_pred             CcEEEEecCC
Confidence            5678999997

>d1gkub2 c.37.1.16 (B:251-498) 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=99.66  E-value=2.2e-19  Score=189.23  Aligned_cols=117  Identities=13%  Similarity=0.229  Sum_probs=100.7

Q ss_pred             cchHHHHHHHHHHhhhcCCcEEEEecCHHHHHHHHHHHHHCCCCceeccCCCCHHHHHHHHHHhccCCccEEEec----C
Q 002040          697 ESDRFLRLLELLGEWYEKGKILIFVHSQEKCDALFRDLLKHGYPCLSLHGAKDQTDRESTISDFKSNVCNLLIAT----S  772 (976)
Q Consensus       697 ~~~k~~~l~~~l~~~~~~~kvLIF~~s~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLVaT----~  772 (976)
                      ...++..|..+|...  +.++||||+++..++.|+.+|..      .+||++++.+|..+++.|++|.++|||||    +
T Consensus        10 ~~~~~~~l~~~l~~~--~~~~iif~~~~~~~~~l~~~l~~------~~hg~~~~~~R~~~~~~f~~g~~~vLVaT~a~~~   81 (248)
T d1gkub2          10 NDESISTLSSILEKL--GTGGIIYARTGEEAEEIYESLKN------KFRIGIVTATKKGDYEKFVEGEIDHLIGTAHYYG   81 (248)
T ss_dssp             SCCCTTTTHHHHTTS--CSCEEEEESSHHHHHHHHHTTTT------SSCEEECTTSSSHHHHHHHHTSCSEEEEECC---
T ss_pred             CchHHHHHHHHHHHh--CCCEEEEECCHHHHHHHHHHHHH------hccCCCCHHHHHHHHHHHHhCCCeEEEEeccccc
Confidence            566788888888754  46799999999999999999965      38999999999999999999999999999    7


Q ss_pred             cccccCCCCC-CcEEEEeCCCCCHHHHHHHhcccCCCCCccEEEEEecCCCcCc
Q 002040          773 VAARGLDVKE-LELVINFDAPNHYEDYVHRVGRTGRAGRKGCAITFISEEDAKY  825 (976)
Q Consensus       773 v~~~GlDi~~-v~~VI~~d~p~s~~~y~Qr~GR~gR~g~~g~~~~~~~~~d~~~  825 (976)
                      ++++|||+|. |++|||||+|+    |.|++||+||+|+.|.+++++...+...
T Consensus        82 v~~rGlDip~~v~~VI~~d~P~----~~~r~gR~~R~g~~~~~~~~~~~~~~~~  131 (248)
T d1gkub2          82 TLVRGLDLPERIRFAVFVGCPS----FRVTIEDIDSLSPQMVKLLAYLYRNVDE  131 (248)
T ss_dssp             ---CCSCCTTTCCEEEEESCCE----EEEECSCGGGSCHHHHHHHHTTTSCHHH
T ss_pred             hhhhccCccccccEEEEeCCCc----chhhhhhhhccCcceEeeeeccHhhHHH
Confidence            8999999996 99999999996    8899999999999999998887765443

>d1a1va2 c.37.1.14 (A:326-624) 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=99.66  E-value=3.1e-17  Score=169.86  Aligned_cols=107  Identities=21%  Similarity=0.292  Sum_probs=94.9

Q ss_pred             cCCcEEEEecCHHHHHHHHHHHHHCCCCceeccCCCCHHHH----------HHHHHHhccCCccEEEecCcccc---cCC
Q 002040          713 EKGKILIFVHSQEKCDALFRDLLKHGYPCLSLHGAKDQTDR----------ESTISDFKSNVCNLLIATSVAAR---GLD  779 (976)
Q Consensus       713 ~~~kvLIF~~s~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R----------~~~~~~F~~g~~~vLVaT~v~~~---GlD  779 (976)
                      ..+++||||+++..|+.|+..|...|+.+..+||++++..|          ..++..|.+|.+++||+|+++.+   |+|
T Consensus        35 kggk~LVFcnSR~~aE~La~~L~~~Gi~a~~~Hgglsq~~R~~~gd~~i~~~~aLe~f~~G~~dvVVaT~~~a~g~~giD  114 (299)
T d1a1va2          35 KGGRHLIFCHSKKKCDELAAKLVALGINAVAYYRGLDVSVIPTSGDVVVVATDALMTGFTGDFDSVIDCNTCVTQTVDFS  114 (299)
T ss_dssp             HSSEEEEECSSHHHHHHHHHHHHHTTCCEEEECTTSCGGGSCSSSSEEEEECTTC---CCCCBSEEEECCEEEEEEEECC
T ss_pred             cCCCEEEECCcHHHHHHHHHHHHHCCCCEEEEeCCchHHHHHhccchHHHHHHHHHHHhcCCCcEEEEEeehhccCCCCC
Confidence            47899999999999999999999999999999999999876          45788999999999999999888   678


Q ss_pred             CCCCcEEEEeCCCCCHHHHHHHhcccCCCCCccEEEEEecC
Q 002040          780 VKELELVINFDAPNHYEDYVHRVGRTGRAGRKGCAITFISE  820 (976)
Q Consensus       780 i~~v~~VI~~d~p~s~~~y~Qr~GR~gR~g~~g~~~~~~~~  820 (976)
                      ++.+.+||+|++|.|.+.|+||+||+|| |++|..++++..
T Consensus       115 id~V~~VI~~d~P~SvesyIQRiGRTGR-Gr~G~~~~l~~~  154 (299)
T d1a1va2         115 LDPTFTIETTTLPQDAVSRTQRRGRTGR-GKPGIYRFVAPG  154 (299)
T ss_dssp             CSSSCEEEEEEEECBHHHHHHHHTTBCS-SSCEEEEESCSC
T ss_pred             CCcceEEEeCCCCCCHHHHHhhccccCC-CCCceEEEEecC
Confidence            8888999999999999999999999999 889987765543

>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=99.64  E-value=7.1e-17  Score=153.42  Aligned_cols=135  Identities=18%  Similarity=0.176  Sum_probs=91.0

Q ss_pred             hcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHHHHhhcCcEEEEeeCCCChH
Q 002040          502 MSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVA  581 (976)
Q Consensus       502 l~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~~~~~~~~~~~~~~gg~~~~  581 (976)
                      ..|+++|++++||||||++++.+++..+...       +.++||++|++.|+.|+++.+..    .+..+....+.... 
T Consensus         5 ~~~~~~il~~~tGsGKT~~~~~~~~~~~~~~-------~~~vli~~p~~~l~~q~~~~~~~----~~~~~~~~~~~~~~-   72 (140)
T d1yksa1           5 KKGMTTVLDFHPGAGKTRRFLPQILAECARR-------RLRTLVLAPTRVVLSEMKEAFHG----LDVKFHTQAFSAHG-   72 (140)
T ss_dssp             STTCEEEECCCTTSSTTTTHHHHHHHHHHHT-------TCCEEEEESSHHHHHHHHHHTTT----SCEEEESSCCCCCC-
T ss_pred             HcCCcEEEEcCCCCChhHHHHHHHHHHhhhc-------CceeeeeecchhHHHHHHHHhhh----hhhhhccccccccc-
Confidence            4688999999999999998877777666543       56899999999999998776543    33333222221111 


Q ss_pred             HHHHHHhcCCeEEEeCchhHHHHHHhcCCcccccCCceEEEecCcccccccCCch-HHHHHHHhcCCCCcEEEEeccCc
Q 002040          582 QQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMGFEP-QITRIVQNIRPDRQTVLFSATFP  659 (976)
Q Consensus       582 ~~~~~l~~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDEah~~~~~~f~~-~i~~il~~~~~~~q~i~~SAT~~  659 (976)
                            .....++++|...+......    ...+.++++|||||||.+....+.. .+...+.. .+..++|+||||||
T Consensus        73 ------~~~~~~~~~~~~~l~~~~~~----~~~~~~~~lvIiDEaH~~~~~~~~~~~~~~~~~~-~~~~~~l~lTATPp  140 (140)
T d1yksa1          73 ------SGREVIDAMCHATLTYRMLE----PTRVVNWEVIIMDEAHFLDPASIAARGWAAHRAR-ANESATILMTATPP  140 (140)
T ss_dssp             ------CSSCCEEEEEHHHHHHHHTS----SSCCCCCSEEEETTTTCCSHHHHHHHHHHHHHHH-TTSCEEEEECSSCT
T ss_pred             ------ccccchhhhhHHHHHHHHhc----cccccceeEEEEccccccChhhHHHHHHHHHHhh-CCCCCEEEEEcCCC
Confidence                  12356788888777655433    2567889999999999764332221 11122222 46789999999997

>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=99.57  E-value=1.7e-15  Score=143.42  Aligned_cols=127  Identities=20%  Similarity=0.103  Sum_probs=87.6

Q ss_pred             CCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHHHHhhcCcEEEEeeCCCChHHH
Q 002040          504 GRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQ  583 (976)
Q Consensus       504 g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~~~~~~~~~~~~~~gg~~~~~~  583 (976)
                      ++..|+.+|||||||+++...++    .       .+.++||++|++.|+.||...+..++   +......++|...   
T Consensus         8 ~~~~ll~apTGsGKT~~~~~~~~----~-------~~~~vli~~P~~~l~~q~~~~~~~~~---~~~~~~~~~~~~~---   70 (136)
T d1a1va1           8 FQVAHLHAPTGSGKSTKVPAAYA----A-------QGYKVLVLNPSVAATLGFGAYMSKAH---GVDPNIRTGVRTI---   70 (136)
T ss_dssp             CEEEEEECCTTSCTTTHHHHHHH----T-------TTCCEEEEESCHHHHHHHHHHHHHHH---SCCCEEECSSCEE---
T ss_pred             CCEEEEEeCCCCCHHHHHHHHHH----H-------cCCcEEEEcChHHHHHHHHHHHHHHh---hcccccccccccc---
Confidence            45689999999999986543332    1       25679999999999999999988764   3334444554422   


Q ss_pred             HHHHhcCCeEEEeCchhHHHHHHhcCCcccccCCceEEEecCcccccccCCchHHHHHHHhc--CCCCcEEEEeccC
Q 002040          584 ISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMGFEPQITRIVQNI--RPDRQTVLFSATF  658 (976)
Q Consensus       584 ~~~l~~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDEah~~~~~~f~~~i~~il~~~--~~~~q~i~~SAT~  658 (976)
                          .....++++|++.+....      ...+..+++|||||||.+... ....+..++..+  .+...+|+|||||
T Consensus        71 ----~~~~~~~~~~~~~~~~~~------~~~~~~~~~vIiDE~H~~~~~-~~~~~~~~l~~~~~~~~~~~l~~TATP  136 (136)
T d1a1va1          71 ----TTGSPITYSTYGKFLADG------GCSGGAYDIIICDECHSTDAT-SILGIGTVLDQAETAGARLVVLATATP  136 (136)
T ss_dssp             ----CCCCSEEEEEHHHHHHTT------GGGGCCCSEEEEETTTCCSHH-HHHHHHHHHHHTTTTTCSEEEEEESSC
T ss_pred             ----ccccceEEEeeeeecccc------chhhhcCCEEEEecccccCHH-HHHHHHHHHHHHHHCCCCcEEEEeCCC
Confidence                123578999988764332      145788999999999975321 122344555544  3566889999996

>d1z3ix1 c.37.1.19 (X:390-735) Rad54-like, Rad54L {Zebra fish (Danio rerio) [TaxId: 7955]}

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: Rad54-like, Rad54L
species: Zebra fish (Danio rerio) [TaxId: 7955]

Probab=99.55  E-value=1.6e-14  Score=157.80  Aligned_cols=121  Identities=16%  Similarity=0.231  Sum_probs=108.3

Q ss_pred             cchHHHHHHHHHHhhh--cCCcEEEEecCHHHHHHHHHHHHHCCCCceeccCCCCHHHHHHHHHHhccCCc---cEEEec
Q 002040          697 ESDRFLRLLELLGEWY--EKGKILIFVHSQEKCDALFRDLLKHGYPCLSLHGAKDQTDRESTISDFKSNVC---NLLIAT  771 (976)
Q Consensus       697 ~~~k~~~l~~~l~~~~--~~~kvLIF~~s~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~---~vLVaT  771 (976)
                      .+.|+..|..+|....  .+.++|||+++...++.|..+|...|+.+..+||.++..+|..++..|+++..   -+|++|
T Consensus        99 ~S~Kl~~L~~ll~~~~~~~g~KvlIFs~~~~~ld~l~~~l~~~g~~~~~l~G~~~~~~R~~~i~~F~~~~~~~~vlLls~  178 (346)
T d1z3ix1          99 LSGKMLVLDYILAMTRTTTSDKVVLVSNYTQTLDLFEKLCRNRRYLYVRLDGTMSIKKRAKIVERFNNPSSPEFIFMLSS  178 (346)
T ss_dssp             GSHHHHHHHHHHHHHHHHCCCEEEEEESCHHHHHHHHHHHHHHTCCEEEECSSCCHHHHHHHHHHHHSTTCCCCEEEEEG
T ss_pred             cCHHHHHHHHHHHHHHHhcCCceeEEeehhhhhHHHHHHHhhhhccccccccchhHHHHHHHHHhhhcccccceeeeecc
Confidence            4678888888886643  45699999999999999999999999999999999999999999999997754   378889


Q ss_pred             CcccccCCCCCCcEEEEeCCCCCHHHHHHHhcccCCCCCccEEEEE
Q 002040          772 SVAARGLDVKELELVINFDAPNHYEDYVHRVGRTGRAGRKGCAITF  817 (976)
Q Consensus       772 ~v~~~GlDi~~v~~VI~~d~p~s~~~y~Qr~GR~gR~g~~g~~~~~  817 (976)
                      .+++.|||++++++||+||++||+..+.|++||++|.|++..|+++
T Consensus       179 ~agg~GlnL~~a~~vi~~d~~wnp~~~~Qa~~R~~R~GQ~~~V~v~  224 (346)
T d1z3ix1         179 KAGGCGLNLIGANRLVMFDPDWNPANDEQAMARVWRDGQKKTCYIY  224 (346)
T ss_dssp             GGSCTTCCCTTEEEEEECSCCSSHHHHHHHHTTSSSTTCCSCEEEE
T ss_pred             hhhhhccccccceEEEEecCCCccchHhHhhhcccccCCCCceEEE
Confidence            9999999999999999999999999999999999999998766554

>d1z5za1 c.37.1.19 (A:663-906) 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=99.50  E-value=3.7e-14  Score=148.27  Aligned_cols=126  Identities=21%  Similarity=0.269  Sum_probs=94.6

Q ss_pred             CcchHHHHHHHHHHhhhc-CCcEEEEecCHHHHHHHHHHHHHC-CCCceeccCCCCHHHHHHHHHHhccCC-ccEEE-ec
Q 002040          696 PESDRFLRLLELLGEWYE-KGKILIFVHSQEKCDALFRDLLKH-GYPCLSLHGAKDQTDRESTISDFKSNV-CNLLI-AT  771 (976)
Q Consensus       696 ~~~~k~~~l~~~l~~~~~-~~kvLIF~~s~~~~~~l~~~L~~~-~~~~~~lhg~~~~~~R~~~~~~F~~g~-~~vLV-aT  771 (976)
                      ..+.|+..|..+|..... +.++||||+....++.+...|... ++.+..+||+++..+|..++..|+++. +.||| +|
T Consensus        66 ~~S~K~~~l~~~l~~~~~~g~kviIFs~~~~~~~~l~~~l~~~~~~~~~~i~G~~~~~~R~~~i~~F~~~~~~~vll~~~  145 (244)
T d1z5za1          66 RRSGKMIRTMEIIEEALDEGDKIAIFTQFVDMGKIIRNIIEKELNTEVPFLYGELSKKERDDIISKFQNNPSVKFIVLSV  145 (244)
T ss_dssp             TTCHHHHHHHHHHHHHHHTTCCEEEEESCHHHHHHHHHHHHHHHCSCCCEECTTSCHHHHHHHHHHHHHCTTCCEEEEEC
T ss_pred             hhhhHHHHHHHHHHhhcccccceEEEeeceehHHHHHHHHHhhccceEEEEecccchhccchhhhhhhccccchhccccc
Confidence            346799999999987654 458999999999999999988754 899999999999999999999998764 56654 56


Q ss_pred             CcccccCCCCCCcEEEEeCCCCCHHHHHHHhcccCCCCCccEE--EEEecCC
Q 002040          772 SVAARGLDVKELELVINFDAPNHYEDYVHRVGRTGRAGRKGCA--ITFISEE  821 (976)
Q Consensus       772 ~v~~~GlDi~~v~~VI~~d~p~s~~~y~Qr~GR~gR~g~~g~~--~~~~~~~  821 (976)
                      .+++.|||++.+++||+|++|||+..+.|++||++|.|+...|  |.|++..
T Consensus       146 ~~~g~Glnl~~a~~vi~~~~~wn~~~~~Qa~~R~~R~Gq~~~v~i~~l~~~~  197 (244)
T d1z5za1         146 KAGGFGINLTSANRVIHFDRWWNPAVEDQATDRVYRIGQTRNVIVHKLISVG  197 (244)
T ss_dssp             CTTCCCCCCTTCSEEEECSCCSCTTTC--------------CCEEEEEEETT
T ss_pred             cccccccccchhhhhhhcCchhhhHHHhhhcceeeecCCCCceEEEEEeeCC
Confidence            7999999999999999999999999999999999999986544  4455543

>d1z3ix2 c.37.1.19 (X:92-389) Rad54-like, Rad54L {Zebra fish (Danio rerio) [TaxId: 7955]}

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: Rad54-like, Rad54L
species: Zebra fish (Danio rerio) [TaxId: 7955]

Probab=99.44  E-value=6.3e-13  Score=143.15  Aligned_cols=161  Identities=19%  Similarity=0.229  Sum_probs=106.1

Q ss_pred             CCcHHHHHHHHHHh---------cCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHH
Q 002040          489 KPMPIQAQALPVIM---------SGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSD  559 (976)
Q Consensus       489 ~p~~~Q~~~i~~il---------~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~  559 (976)
                      .+.|||.+++.++.         .+..+|++.+||+|||++++..+...+... .........+|||||.. |+.||..+
T Consensus        55 ~Lr~hQ~~gv~~l~~~~~~~~~~~~~g~iLaDemGlGKT~qaia~l~~l~~~~-~~~~~~~~~~LIV~P~s-l~~qW~~E  132 (298)
T d1z3ix2          55 VLRPHQREGVKFLWDCVTGRRIENSYGCIMADEMGLGKTLQCITLIWTLLKQS-PDCKPEIDKVIVVSPSS-LVRNWYNE  132 (298)
T ss_dssp             TCCHHHHHHHHHHHHHHTTSSSTTCCEEEECCCTTSCHHHHHHHHHHHHHHCC-TTSSCSCSCEEEEECHH-HHHHHHHH
T ss_pred             cccHHHHHHHHHHHHHHHhhhhccCCceEEEeCCCCCHHHHHHHHHHHHHHhc-ccccCCCCcEEEEccch-hhHHHHHH
Confidence            57899999999874         345699999999999998655444433332 22222334689999975 88999999


Q ss_pred             HHHHHhhcCcEEEEeeCCCChHHHH--HHHh------cCCeEEEeCchhHHHHHHhcCCcccccCCceEEEecCcccccc
Q 002040          560 IRKFAKVMGVRCVPVYGGSGVAQQI--SELK------RGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFD  631 (976)
Q Consensus       560 ~~~~~~~~~~~~~~~~gg~~~~~~~--~~l~------~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDEah~~~~  631 (976)
                      |.+++.. .+.++.++|+.......  ....      ..++|+|+|+..+......     ..-..+.+|||||||++-+
T Consensus       133 i~k~~~~-~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~i~sy~~~~~~~~~-----l~~~~~~~vI~DEaH~ikn  206 (298)
T d1z3ix2         133 VGKWLGG-RVQPVAIDGGSKDEIDSKLVNFISQQGMRIPTPILIISYETFRLHAEV-----LHKGKVGLVICDEGHRLKN  206 (298)
T ss_dssp             HHHHHGG-GCCEEEECSSCHHHHHHHHHHHHCCCSSCCSCCEEEEEHHHHHHHTTT-----TTTSCCCEEEETTGGGCCT
T ss_pred             HHhhcCC-ceeEEEEeCchHHHHHHHHHHhhhccCccccceEEEEeecccccchhc-----ccccceeeeeccccccccc
Confidence            9998864 34555566665332221  1111      1357999999887654321     2223578999999999865


Q ss_pred             cCCchHHHHHHHhcCCCCcEEEEeccCcH
Q 002040          632 MGFEPQITRIVQNIRPDRQTVLFSATFPR  660 (976)
Q Consensus       632 ~~f~~~i~~il~~~~~~~q~i~~SAT~~~  660 (976)
                      ..  ......+..+. ....+++||||..
T Consensus       207 ~~--s~~~~a~~~l~-~~~rllLTGTPi~  232 (298)
T d1z3ix2         207 SD--NQTYLALNSMN-AQRRVLISGTPIQ  232 (298)
T ss_dssp             TC--HHHHHHHHHHC-CSEEEEECSSCSG
T ss_pred             cc--chhhhhhhccc-cceeeeecchHHh
Confidence            43  33344444553 3567999999843

>d1yksa2 c.37.1.14 (A:325-623) 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=99.40  E-value=3.2e-13  Score=143.02  Aligned_cols=101  Identities=20%  Similarity=0.257  Sum_probs=82.4

Q ss_pred             CCcEEEEecCHHHHHHHHHHHHHCCCCceeccCCCCHHHHHHHHHHhccCCccEEEecCcccccCCCCCCcEEEEeCC--
Q 002040          714 KGKILIFVHSQEKCDALFRDLLKHGYPCLSLHGAKDQTDRESTISDFKSNVCNLLIATSVAARGLDVKELELVINFDA--  791 (976)
Q Consensus       714 ~~kvLIF~~s~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLVaT~v~~~GlDi~~v~~VI~~d~--  791 (976)
                      .|++||||++...++.++..|...|+.|+.+||.+...++.    .|++|..+|||||+++++|||| ++.+||+++.  
T Consensus        36 ~g~~~~F~~s~~~~~~~a~~L~~~g~~V~~l~~~~~~~e~~----~~~~~~~~~~~~t~~~~~~~~~-~~~~vid~g~~~  110 (299)
T d1yksa2          36 KRPTAWFLPSIRAANVMAASLRKAGKSVVVLNRKTFEREYP----TIKQKKPDFILATDIAEMGANL-CVERVLDCRTAF  110 (299)
T ss_dssp             CSCEEEECSCHHHHHHHHHHHHHTTCCEEECCSSSCC------------CCCSEEEESSSTTCCTTC-CCSEEEECCEEE
T ss_pred             CCCEEEEeCCHHHHHHHHHHHHhcCCeEEEEcCcCcHhHHh----hhhcCCcCEEEEechhhhceec-CceEEEecCcee
Confidence            78999999999999999999999999999999999876654    5789999999999999999999 5999996543  


Q ss_pred             -----------------CCCHHHHHHHhcccCCCCCccEEEEEec
Q 002040          792 -----------------PNHYEDYVHRVGRTGRAGRKGCAITFIS  819 (976)
Q Consensus       792 -----------------p~s~~~y~Qr~GR~gR~g~~g~~~~~~~  819 (976)
                                       |.+.++..||.||+||.+....++.+|+
T Consensus       111 ~~~~~~~~~~~~~~~~~~~~~~~~~qr~gr~gr~~~~~~~~~~y~  155 (299)
T d1yksa2         111 KPVLVDEGRKVAIKGPLRISASSAAQRRGRIGRNPNRDGDSYYYS  155 (299)
T ss_dssp             EEEEETTTTEEEEEEEEECCHHHHHHHHTTSSCCTTCCCEEEEEC
T ss_pred             ceeeecCCCCeeEEeeeecCHHHHHHhcccccccCCCceEEEEeC
Confidence                             3577889999999999875555555554

>d1tf5a4 c.37.1.19 (A:396-570) Translocation ATPase SecA, nucleotide-binding domains {Bacillus subtilis [TaxId: 1423]}

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: Translocation ATPase SecA, nucleotide-binding domains
species: Bacillus subtilis [TaxId: 1423]

Probab=99.26  E-value=3.1e-11  Score=115.27  Aligned_cols=129  Identities=22%  Similarity=0.278  Sum_probs=105.8

Q ss_pred             EecCcchHHHHHHHHHHhhhc-CCcEEEEecCHHHHHHHHHHHHHCCCCceeccCCCCHHHHHHHHHHhccCCccEEEec
Q 002040          693 EVRPESDRFLRLLELLGEWYE-KGKILIFVHSQEKCDALFRDLLKHGYPCLSLHGAKDQTDRESTISDFKSNVCNLLIAT  771 (976)
Q Consensus       693 ~~~~~~~k~~~l~~~l~~~~~-~~kvLIF~~s~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLVaT  771 (976)
                      .+.....|+..++..+...+. +.+|||||.|.+.++.|+..|.+.++++.+++......+-.  +-...-....|.|||
T Consensus        12 vf~T~~eK~~AIi~eV~~~~~~grPVLIgT~SIe~SE~ls~~L~~~gi~h~vLnAk~~~~Ea~--II~~Ag~~g~VtIAT   89 (175)
T d1tf5a4          12 IYRTMEGKFKAVAEDVAQRYMTGQPVLVGTVAVETSELISKLLKNKGIPHQVLNAKNHEREAQ--IIEEAGQKGAVTIAT   89 (175)
T ss_dssp             EESSHHHHHHHHHHHHHHHHHHTCCEEEEESCHHHHHHHHHHHHTTTCCCEEECSSCHHHHHH--HHTTTTSTTCEEEEE
T ss_pred             EEcCHHHHHHHHHHHHHHHHhcCCCEEEEeCcHHHHHHHHHHHHHcCCCceeehhhhHHHHHH--HHHhccCCCceeehh
Confidence            445677899999888876554 56999999999999999999999999999999876544433  322222234699999


Q ss_pred             CcccccCCCCC--------CcEEEEeCCCCCHHHHHHHhcccCCCCCccEEEEEecCCCc
Q 002040          772 SVAARGLDVKE--------LELVINFDAPNHYEDYVHRVGRTGRAGRKGCAITFISEEDA  823 (976)
Q Consensus       772 ~v~~~GlDi~~--------v~~VI~~d~p~s~~~y~Qr~GR~gR~g~~g~~~~~~~~~d~  823 (976)
                      ++++||.||+-        --+||....|.+.....|..||+||.|.+|.+..|++-+|.
T Consensus        90 NmAGRGtDikl~~~v~~~GGLhVI~t~~~~s~Rid~Ql~GR~gRQGdpGs~~~~~sleD~  149 (175)
T d1tf5a4          90 NMAGRGTDIKLGEGVKELGGLAVVGTERHESRRIDNQLRGRSGRQGDPGITQFYLSMEDE  149 (175)
T ss_dssp             TTSSTTCCCCCCTTSGGGTSEEEEESSCCSSHHHHHHHHTTSSGGGCCEEEEEEEETTSS
T ss_pred             hHHHcCCCccchHHHHhCCCcEEEEeccCcchhHHHHHhcchhhhCCCcccEEEEEcCHH
Confidence            99999999853        34799999999999999999999999999999999987664

>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=99.18  E-value=2.8e-11  Score=124.75  Aligned_cols=149  Identities=17%  Similarity=0.227  Sum_probs=97.5

Q ss_pred             CCcHHHHHHHHHHh----cCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHHHH
Q 002040          489 KPMPIQAQALPVIM----SGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFA  564 (976)
Q Consensus       489 ~p~~~Q~~~i~~il----~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~~~  564 (976)
                      .+.|+|.+++.++.    .+..+|++.+||+|||++++..+ .++....     ....+|||||. .++.||..++.+++
T Consensus        12 ~L~~yQ~~~v~~~~~~~~~~~g~iLaDe~GlGKT~~~i~~~-~~~~~~~-----~~~~~LIv~p~-~l~~~W~~e~~~~~   84 (230)
T d1z63a1          12 NLRPYQIKGFSWMRFMNKLGFGICLADDMGLGKTLQTIAVF-SDAKKEN-----ELTPSLVICPL-SVLKNWEEELSKFA   84 (230)
T ss_dssp             CCCHHHHHHHHHHHHHHHTTCCEEECCCTTSCHHHHHHHHH-HHHHHTT-----CCSSEEEEECS-TTHHHHHHHHHHHC
T ss_pred             chhHHHHHHHHHHHHhhhcCCCEEEEeCCCCChHHHHHHhh-hhhhhcc-----cccccceecch-hhhhHHHHHHHhhc
Confidence            57899999998764    45679999999999999865544 4443321     23468999995 57789999999886


Q ss_pred             hhcCcEEEEeeCCCChHHHHHHHhcCCeEEEeCchhHHHHHHhcCCcccccCCceEEEecCcccccccCCchHHHHHHHh
Q 002040          565 KVMGVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMGFEPQITRIVQN  644 (976)
Q Consensus       565 ~~~~~~~~~~~gg~~~~~~~~~l~~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDEah~~~~~~f~~~i~~il~~  644 (976)
                      ...  .+....+.....     ...+.+|+|+|+..+.....      ..--.+.+||+||||.+.+..  ......+..
T Consensus        85 ~~~--~~~~~~~~~~~~-----~~~~~~vvi~~~~~~~~~~~------l~~~~~~~vI~DEah~~k~~~--s~~~~~~~~  149 (230)
T d1z63a1          85 PHL--RFAVFHEDRSKI-----KLEDYDIILTTYAVLLRDTR------LKEVEWKYIVIDEAQNIKNPQ--TKIFKAVKE  149 (230)
T ss_dssp             TTS--CEEECSSSTTSC-----CGGGSSEEEEEHHHHTTCHH------HHTCCEEEEEEETGGGGSCTT--SHHHHHHHT
T ss_pred             ccc--cceeeccccchh-----hccCcCEEEeeHHHHHhHHH------HhcccceEEEEEhhhcccccc--hhhhhhhhh
Confidence            533  333332222111     01247899999987743321      112247899999999886643  233344444


Q ss_pred             cCCCCcEEEEeccCcH
Q 002040          645 IRPDRQTVLFSATFPR  660 (976)
Q Consensus       645 ~~~~~q~i~~SAT~~~  660 (976)
                      +. ....+++||||-.
T Consensus       150 l~-a~~r~~LTgTPi~  164 (230)
T d1z63a1         150 LK-SKYRIALTGTPIE  164 (230)
T ss_dssp             SC-EEEEEEECSSCST
T ss_pred             hc-cceEEEEecchHH
Confidence            43 3457899999853

>d1tf5a3 c.37.1.19 (A:1-226,A:349-395) Translocation ATPase SecA, nucleotide-binding domains {Bacillus subtilis [TaxId: 1423]}

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: Translocation ATPase SecA, nucleotide-binding domains
species: Bacillus subtilis [TaxId: 1423]

Probab=98.92  E-value=1.2e-08  Score=103.25  Aligned_cols=170  Identities=18%  Similarity=0.192  Sum_probs=125.2

Q ss_pred             cCCCCCcHHHHHHHHHHhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHHHH
Q 002040          485 LNYEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFA  564 (976)
Q Consensus       485 ~~~~~p~~~Q~~~i~~il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~~~  564 (976)
                      +|. .|++.|..+--.+..|  -|..+.||-|||+++.+|++...+.        |..|-||+..--||..=..++..++
T Consensus        77 lG~-RhyDVQLiGgi~L~~G--~iaem~TGEGKTL~a~l~a~l~al~--------g~~vhvvTvNdyLA~RDae~m~~iy  145 (273)
T d1tf5a3          77 TGM-FPFKVQLMGGVALHDG--NIAEMKTGEGKTLTSTLPVYLNALT--------GKGVHVVTVNEYLASRDAEQMGKIF  145 (273)
T ss_dssp             HSC-CCCHHHHHHHHHHHTT--SEEECCTTSCHHHHHHHHHHHHHTT--------SSCEEEEESSHHHHHHHHHHHHHHH
T ss_pred             hce-EEehhHHHHHHHHHhh--hheeecCCCcchhHHHHHHHHHHhc--------CCCceEEecCccccchhhhHHhHHH
Confidence            564 4778888777777766  5899999999999999998776554        4457788888999999999999999


Q ss_pred             hhcCcEEEEeeCCCChHHHHHHHhcCCeEEEeCchhH-HHHHHhcCC---cccccCCceEEEecCccccc-ccCCchH--
Q 002040          565 KVMGVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRM-IDILCTSGG---KITNLRRVTYLVMDEADRMF-DMGFEPQ--  637 (976)
Q Consensus       565 ~~~~~~~~~~~gg~~~~~~~~~l~~~~~Iiv~Tp~~L-~~~l~~~~~---~~~~l~~~~~vVlDEah~~~-~~~f~~~--  637 (976)
                      ..+|+.|.++..+....+......  ++|+++|..-| .++|..+-.   .......+.+.||||+|.|+ |....|.  
T Consensus       146 ~~lGlsvg~~~~~~~~~~r~~~Y~--~di~Ygt~~e~~fDyLrd~~~~~~~~~~~r~~~~aIvDEvDsiliDeartplii  223 (273)
T d1tf5a3         146 EFLGLTVGLNLNSMSKDEKREAYA--ADITYSTNNELGFDYLRDNMVLYKEQMVQRPLHFAVIDEVDSILIDEARTPLII  223 (273)
T ss_dssp             HHTTCCEEECCTTSCHHHHHHHHH--SSEEEEEHHHHHHHHHHHTTCSSGGGCCCCCCCEEEEETHHHHHTTTTTCEEEE
T ss_pred             HHcCCCccccccccCHHHHHHHhh--CCceecchhhhhhhhcchhhhcChhhhccCCCCEEEEEcchhhhhhccCCceEe
Confidence            999999999998887777665554  89999999887 455554321   11234678899999999653 3322111  


Q ss_pred             -----------HHHHHHhcCCCCcEEEEeccCcHHHHHHHHHHc
Q 002040          638 -----------ITRIVQNIRPDRQTVLFSATFPRQVEILARKVL  670 (976)
Q Consensus       638 -----------i~~il~~~~~~~q~i~~SAT~~~~~~~l~~~~l  670 (976)
                                 +..+   ++--.++.+||+|.......+..-|-
T Consensus       224 sg~~~~~a~it~q~~---f~~y~~l~gmtgta~~~~~e~~~iy~  264 (273)
T d1tf5a3         224 SGQSMTLATITFQNY---FRMYEKLAGMTGTAKTEEEEFRNIYN  264 (273)
T ss_dssp             EEEEEEEEEEEHHHH---HTTSSEEEEEESCCGGGHHHHHHHHC
T ss_pred             ccCccchhhhhHHHH---HHHHHHHhCCccccHHHHHHHHhccC
Confidence                       2333   33445789999998776666655553

>d1nkta4 c.37.1.19 (A:397-615) Translocation ATPase SecA, nucleotide-binding domains {Mycobacterium tuberculosis [TaxId: 1773]}

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: Translocation ATPase SecA, nucleotide-binding domains
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=98.75  E-value=5.6e-08  Score=93.81  Aligned_cols=129  Identities=23%  Similarity=0.315  Sum_probs=104.4

Q ss_pred             EEecCcchHHHHHHHHHHhhhcCC-cEEEEecCHHHHHHHHHHHHHCCCCceeccCCCCHHHHHHHHHHhccCC-ccEEE
Q 002040          692 VEVRPESDRFLRLLELLGEWYEKG-KILIFVHSQEKCDALFRDLLKHGYPCLSLHGAKDQTDRESTISDFKSNV-CNLLI  769 (976)
Q Consensus       692 ~~~~~~~~k~~~l~~~l~~~~~~~-kvLIF~~s~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~-~~vLV  769 (976)
                      ..+.....|+..++..+...+..| ||||.+.|++..+.|+..|.+.++++.+|+......+-. |+  -+.|. -.|-|
T Consensus        11 ~Vy~T~~~K~~Avv~ei~~~h~~GqPVLVGT~SVe~SE~lS~lL~~~gi~h~vLNAK~herEAe-II--AqAG~~GaVTI   87 (219)
T d1nkta4          11 LIYKTEEAKYIAVVDDVAERYAKGQPVLIGTTSVERSEYLSRQFTKRRIPHNVLNAKYHEQEAT-II--AVAGRRGGVTV   87 (219)
T ss_dssp             EEESCHHHHHHHHHHHHHHHHHTTCCEEEEESCHHHHHHHHHHHHHTTCCCEEECSSCHHHHHH-HH--HTTTSTTCEEE
T ss_pred             eEEcCHHHHHHHHHHHHHHHHhcCCCEEEeeCcHHHHHHHHHHHHHhccchhccchhhHHHHHH-HH--HhcccCCcEEe
Confidence            345677889999999888877654 999999999999999999999999999999975433322 22  23454 36999


Q ss_pred             ecCcccccCCCCC----------------------------------------------------CcEEEEeCCCCCHHH
Q 002040          770 ATSVAARGLDVKE----------------------------------------------------LELVINFDAPNHYED  797 (976)
Q Consensus       770 aT~v~~~GlDi~~----------------------------------------------------v~~VI~~d~p~s~~~  797 (976)
                      ||++|+||.||.=                                                    =-+||-.....|---
T Consensus        88 ATNMAGRGTDI~LGgn~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~V~~~GGL~VIGTErHeSrRI  167 (219)
T d1nkta4          88 ATNMAGRGTDIVLGGNVDFLTDQRLRERGLDPVETPEEYEAAWHSELPIVKEEASKEAKEVIEAGGLYVLGTERHESRRI  167 (219)
T ss_dssp             EETTCSTTCCCCTTCCHHHHHHHHHHHTTCCTTTSHHHHHHHHHHHHHHHHHHTTHHHHHHHHTTSEEEEECSCCSSHHH
T ss_pred             eccccCCCCceeecCchhhhhHHHhhhcccCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCcEEEeccccccccc
Confidence            9999999999932                                                    236777777888888


Q ss_pred             HHHHhcccCCCCCccEEEEEecCCCc
Q 002040          798 YVHRVGRTGRAGRKGCAITFISEEDA  823 (976)
Q Consensus       798 y~Qr~GR~gR~g~~g~~~~~~~~~d~  823 (976)
                      -.|-.||+||.|-+|.+..|++-+|.
T Consensus       168 DnQLRGRsGRQGDPGsSrFflSLeDd  193 (219)
T d1nkta4         168 DNQLRGRSGRQGDPGESRFYLSLGDE  193 (219)
T ss_dssp             HHHHHHTSSGGGCCEEEEEEEETTSH
T ss_pred             cccccccccccCCCccceeEEeccHH
Confidence            89999999999999999999987663

>d1w36d1 c.37.1.19 (D:2-360) Exodeoxyribonuclease V alpha chain (RecD) {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: Exodeoxyribonuclease V alpha chain (RecD)
species: Escherichia coli [TaxId: 562]

Probab=98.04  E-value=6.2e-06  Score=89.13  Aligned_cols=149  Identities=17%  Similarity=0.176  Sum_probs=89.7

Q ss_pred             CCCCcHHHHHHHHHHhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHHHHhh
Q 002040          487 YEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKV  566 (976)
Q Consensus       487 ~~~p~~~Q~~~i~~il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~~~~~  566 (976)
                      .......|..|+..++.++-++|.|+.|+|||++. ..++..+...   ....+..+++++||-..|..+.+.+......
T Consensus       146 ~~~~~~~Q~~A~~~al~~~~~vI~G~pGTGKTt~i-~~~l~~l~~~---~~~~~~~I~l~ApTgkAA~~L~e~~~~~~~~  221 (359)
T d1w36d1         146 VSDEINWQKVAAAVALTRRISVISGGPGTGKTTTV-AKLLAALIQM---ADGERCRIRLAAPTGKAAARLTESLGKALRQ  221 (359)
T ss_dssp             CTTSCCHHHHHHHHHHTBSEEEEECCTTSTHHHHH-HHHHHHHHHT---CSSCCCCEEEEBSSHHHHHHHHHHHTHHHHH
T ss_pred             CcccccHHHHHHHHHHcCCeEEEEcCCCCCceehH-HHHHHHHHHH---HhccCCeEEEecCcHHHHHHHHHHHHHHHhh
Confidence            34456789999999999999999999999999873 3333334332   1234678999999999998887776655443


Q ss_pred             cCcEEEEeeCCCChHHHHHHHhcCCeEEEeCchhHHHHHHhcC---CcccccCCceEEEecCcccccccCCchHHHHHHH
Q 002040          567 MGVRCVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSG---GKITNLRRVTYLVMDEADRMFDMGFEPQITRIVQ  643 (976)
Q Consensus       567 ~~~~~~~~~gg~~~~~~~~~l~~~~~Iiv~Tp~~L~~~l~~~~---~~~~~l~~~~~vVlDEah~~~~~~f~~~i~~il~  643 (976)
                      .+.........              ..-..|..+++.......   ....+...+++||||||-.+.    .+.+..++.
T Consensus       222 ~~~~~~~~~~~--------------~~~~~t~~~ll~~~~~~~~~~~~~~~~l~~d~lIIDEaSmv~----~~l~~~ll~  283 (359)
T d1w36d1         222 LPLTDEQKKRI--------------PEDASTLHRLLGAQPGSQRLRHHAGNPLHLDVLVVDEASMID----LPMMSRLID  283 (359)
T ss_dssp             SSCCSCCCCSC--------------SCCCBTTTSCC-----------CTTSCCSCSEEEECSGGGCB----HHHHHHHHH
T ss_pred             cCchhhhhhhh--------------hhhhhHHHHHHhhhhcchHHHHhhhcccccceeeehhhhccC----HHHHHHHHH
Confidence            33211100000              001112221111110000   011234468899999998542    456677888


Q ss_pred             hcCCCCcEEEEecc
Q 002040          644 NIRPDRQTVLFSAT  657 (976)
Q Consensus       644 ~~~~~~q~i~~SAT  657 (976)
                      .+++..++|++.=.
T Consensus       284 ~~~~~~~lILvGD~  297 (359)
T d1w36d1         284 ALPDHARVIFLGDR  297 (359)
T ss_dssp             TCCTTCEEEEEECT
T ss_pred             HhcCCCEEEEECCh
Confidence            88888887776644

>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=97.03  E-value=0.00035  Score=73.17  Aligned_cols=69  Identities=19%  Similarity=0.182  Sum_probs=50.2

Q ss_pred             CCcHHHHHHHHHHhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHHH
Q 002040          489 KPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKF  563 (976)
Q Consensus       489 ~p~~~Q~~~i~~il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~~  563 (976)
                      +++|-|.+|+..  ....++|.|+.|||||.+.+.-+...+....    .....+||+++|+.+|..+...+..+
T Consensus         1 ~L~~eQ~~av~~--~~~~~lI~g~aGTGKTt~l~~rv~~ll~~~~----~~~~~ILvlt~tn~a~~~i~~~~~~~   69 (306)
T d1uaaa1           1 RLNPGQQQAVEF--VTGPCLVLAGAGSGKTRVITNKIAHLIRGCG----YQARHIAAVTFTNKAAREMKERVGQT   69 (306)
T ss_dssp             CCCHHHHHHHHC--CSSEEEECCCTTSCHHHHHHHHHHHHHHHHC----CCGGGEEEEESSHHHHHHHHHHHHHH
T ss_pred             CcCHHHHHHHhC--CCCCEEEEeeCCccHHHHHHHHHHHHHHhcC----CChhHEEEEeCcHHHHHHHHHHHHHh
Confidence            478999999965  3456899999999999886554444443211    12347999999999998887777664

>d1ls1a2 c.37.1.10 (A:89-295) GTPase domain of the signal sequence recognition protein Ffh {Thermus aquaticus [TaxId: 271]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: GTPase domain of the signal sequence recognition protein Ffh
species: Thermus aquaticus [TaxId: 271]

Probab=97.00  E-value=0.001  Score=65.19  Aligned_cols=131  Identities=21%  Similarity=0.239  Sum_probs=73.0

Q ss_pred             EEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEc-c-CHHHHHHHHHHHHHHHhhcCcEEEEeeCCCChHHHH
Q 002040          507 CIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMA-P-TRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQI  584 (976)
Q Consensus       507 ~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~-P-tr~La~Q~~~~~~~~~~~~~~~~~~~~gg~~~~~~~  584 (976)
                      ++++||||+|||++..-.+. ++...       +.++++++ - .|.-|.   ++++.++..+++.+..+..........
T Consensus        13 i~lvGp~GvGKTTTiaKLA~-~~~~~-------g~kV~lit~Dt~R~gA~---eQL~~~a~~l~v~~~~~~~~~~~~~~~   81 (207)
T d1ls1a2          13 WFLVGLQGSGKTTTAAKLAL-YYKGK-------GRRPLLVAADTQRPAAR---EQLRLLGEKVGVPVLEVMDGESPESIR   81 (207)
T ss_dssp             EEEECCTTTTHHHHHHHHHH-HHHHT-------TCCEEEEECCSSCHHHH---HHHHHHHHHHTCCEEECCTTCCHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH-HHHHC-------CCcEEEEecccccchHH---HHHHHHHHhcCCccccccccchhhHHH
Confidence            56689999999987544333 33322       23444444 3 444443   567777777888777665554432211


Q ss_pred             HHHhcCCeEEEeCchhHHHHHHhcCCcccccCCceEEEecCccccccc-CCchHHHHHHHhcCCCCcEEEEeccCcHHHH
Q 002040          585 SELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDM-GFEPQITRIVQNIRPDRQTVLFSATFPRQVE  663 (976)
Q Consensus       585 ~~l~~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDEah~~~~~-~f~~~i~~il~~~~~~~q~i~~SAT~~~~~~  663 (976)
                      ...              . .+       ..+..+++|+||=|=+.... .....+..+.....+..-+++++||......
T Consensus        82 ~~~--------------~-~~-------~~~~~~d~vlIDTaGr~~~d~~~~~el~~~~~~~~~~~~llv~~a~~~~~~~  139 (207)
T d1ls1a2          82 RRV--------------E-EK-------ARLEARDLILVDTAGRLQIDEPLMGELARLKEVLGPDEVLLVLDAMTGQEAL  139 (207)
T ss_dssp             HHH--------------H-HH-------HHHHTCCEEEEECCCCSSCCHHHHHHHHHHHHHHCCSEEEEEEEGGGTHHHH
T ss_pred             HHH--------------H-HH-------HhhccCcceeecccccchhhhhhHHHHHHHHhhcCCceEEEEeccccchhHH
Confidence            100              0 00       12334566666666543211 1233455566667777778888999887665


Q ss_pred             HHHHHHc
Q 002040          664 ILARKVL  670 (976)
Q Consensus       664 ~l~~~~l  670 (976)
                      ..+..|+
T Consensus       140 ~~~~~f~  146 (207)
T d1ls1a2         140 SVARAFD  146 (207)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
Confidence            5555543

>d2qy9a2 c.37.1.10 (A:285-495) GTPase domain of the signal recognition particle receptor FtsY {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: Nitrogenase iron protein-like
domain: GTPase domain of the signal recognition particle receptor FtsY
species: Escherichia coli [TaxId: 562]

Probab=96.66  E-value=0.0055  Score=59.77  Aligned_cols=65  Identities=20%  Similarity=0.225  Sum_probs=40.1

Q ss_pred             EEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccC-HHHHHHHHHHHHHHHhhcCcEEEEeeCCCChH
Q 002040          507 CIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPT-RELVQQIHSDIRKFAKVMGVRCVPVYGGSGVA  581 (976)
Q Consensus       507 ~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Pt-r~La~Q~~~~~~~~~~~~~~~~~~~~gg~~~~  581 (976)
                      ++++||||+|||++.+=.+ .++...      +...+||.+-| |.-|   +++++.++..+++.+.....+....
T Consensus        12 i~lvGptGvGKTTTiAKLA-~~~~~~------g~kV~lit~Dt~R~gA---~eQL~~~a~~l~v~~~~~~~~~d~~   77 (211)
T d2qy9a2          12 ILMVGVNGVGKTTTIGKLA-RQFEQQ------GKSVMLAAGDTFRAAA---VEQLQVWGQRNNIPVIAQHTGADSA   77 (211)
T ss_dssp             EEEECCTTSCHHHHHHHHH-HHHHTT------TCCEEEECCCTTCHHH---HHHHHHHHHHTTCCEECCSTTCCHH
T ss_pred             EEEECCCCCCHHHHHHHHH-HHHHHC------CCcEEEEecccccccc---hhhhhhhhhhcCCcccccccCCCHH
Confidence            5678999999998744433 333332      12344555555 4333   3667777878888887666555433

>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=96.61  E-value=0.0023  Score=67.20  Aligned_cols=70  Identities=14%  Similarity=0.101  Sum_probs=51.8

Q ss_pred             CCcHHHHHHHHHHhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHHHH
Q 002040          489 KPMPIQAQALPVIMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFA  564 (976)
Q Consensus       489 ~p~~~Q~~~i~~il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~~~  564 (976)
                      .+++-|.++|..  .+..++|.|+.|||||++++--+...+....    ...-.+||+++|+.++..+...+....
T Consensus        11 ~L~~eQ~~~v~~--~~g~~lV~g~aGSGKTt~l~~ri~~ll~~~~----~~p~~il~lt~t~~aa~~~~~~~~~~~   80 (318)
T d1pjra1          11 HLNKEQQEAVRT--TEGPLLIMAGAGSGKTRVLTHRIAYLMAEKH----VAPWNILAITFTNKAAREMRERVQSLL   80 (318)
T ss_dssp             TSCHHHHHHHHC--CSSCEEEEECTTSCHHHHHHHHHHHHHHTTC----CCGGGEEEEESSHHHHHHHHHHHHHHH
T ss_pred             hCCHHHHHHHhC--CCCCEEEEecCCccHHHHHHHHHHHHHHcCC----CCHHHeEeEeccHHHHHHHHHHHHhhc
Confidence            477999999974  3557999999999999986555554444321    112379999999999998888776643

>d1okkd2 c.37.1.10 (D:97-303) GTPase domain of the signal recognition particle receptor FtsY {Thermus aquaticus [TaxId: 271]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: GTPase domain of the signal recognition particle receptor FtsY
species: Thermus aquaticus [TaxId: 271]

Probab=96.59  E-value=0.0046  Score=60.25  Aligned_cols=67  Identities=19%  Similarity=0.220  Sum_probs=39.6

Q ss_pred             CCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccC-HHHHHHHHHHHHHHHhhcCcEEEEeeCCCCh
Q 002040          504 GRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPT-RELVQQIHSDIRKFAKVMGVRCVPVYGGSGV  580 (976)
Q Consensus       504 g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Pt-r~La~Q~~~~~~~~~~~~~~~~~~~~gg~~~  580 (976)
                      ++-++++||||+|||++..=.+ .++...      ....+||.+-| |.-|.   ++++.|+..+++.+.....+...
T Consensus         6 ~~vi~lvGptGvGKTTTiaKLA-~~~~~~------g~kV~lit~Dt~R~gA~---eQL~~~a~~l~i~~~~~~~~~d~   73 (207)
T d1okkd2           6 GRVVLVVGVNGVGKTTTIAKLG-RYYQNL------GKKVMFCAGDTFRAAGG---TQLSEWGKRLSIPVIQGPEGTDP   73 (207)
T ss_dssp             SSEEEEECSTTSSHHHHHHHHH-HHHHTT------TCCEEEECCCCSSTTHH---HHHHHHHHHHTCCEECCCTTCCH
T ss_pred             CEEEEEECCCCCCHHHHHHHHH-HHHHHC------CCcEEEEEeccccccch---hhHhhcccccCceEEeccCCccH
Confidence            3457789999999998744333 333321      12334454544 55554   45666677778877665555443

>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=96.56  E-value=0.004  Score=63.04  Aligned_cols=100  Identities=17%  Similarity=0.195  Sum_probs=73.5

Q ss_pred             HHHHHHHHhhhcCCcEEEEecCHHHHHHHHHHHHH----CCCCceeccCCCCHHHHHHHHHHhccCCccEEEecCccc-c
Q 002040          702 LRLLELLGEWYEKGKILIFVHSQEKCDALFRDLLK----HGYPCLSLHGAKDQTDRESTISDFKSNVCNLLIATSVAA-R  776 (976)
Q Consensus       702 ~~l~~~l~~~~~~~kvLIF~~s~~~~~~l~~~L~~----~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLVaT~v~~-~  776 (976)
                      .++..++.....+.+++|.+++..-+.+.+..|..    .|+.+..+||+++..+|..++..+.+|.++|||+|-++- .
T Consensus       120 Va~~a~~~~~~~g~q~~~m~Pt~~La~Qh~~~~~~~f~~~~~~v~~l~~~~~~~~r~~~~~~~~~g~~~iiIGThsl~~~  199 (264)
T d1gm5a3         120 VAQLAILDNYEAGFQTAFMVPTSILAIQHYRRTVESFSKFNIHVALLIGATTPSEKEKIKSGLRNGQIDVVIGTHALIQE  199 (264)
T ss_dssp             HHHHHHHHHHHHTSCEEEECSCHHHHHHHHHHHHHHHTCSSCCEEECCSSSCHHHHHHHHHHHHSSCCCEEEECTTHHHH
T ss_pred             HHHHHHHHHHhcccceeEEeehHhhhHHHHHHHHHhhhhccccceeeccccchHHHHHHHHHHHCCCCCEEEeehHHhcC
Confidence            34444444445577999999999888777666654    478999999999999999999999999999999997554 5


Q ss_pred             cCCCCCCcEEEEeCCCCCHHHHHHHhc
Q 002040          777 GLDVKELELVINFDAPNHYEDYVHRVG  803 (976)
Q Consensus       777 GlDi~~v~~VI~~d~p~s~~~y~Qr~G  803 (976)
                      .+.+.++.+||.=.--.  ..|.||.+
T Consensus       200 ~~~f~~LglviiDEqH~--fgv~Qr~~  224 (264)
T d1gm5a3         200 DVHFKNLGLVIIDEQHR--FGVKQREA  224 (264)
T ss_dssp             CCCCSCCCEEEEESCCC--C-----CC
T ss_pred             CCCccccceeeeccccc--cchhhHHH
Confidence            68888998888544322  24667654

>d1vmaa2 c.37.1.10 (A:82-294) GTPase domain of the signal recognition particle receptor FtsY {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: Nitrogenase iron protein-like
domain: GTPase domain of the signal recognition particle receptor FtsY
species: Thermotoga maritima [TaxId: 2336]

Probab=96.51  E-value=0.0068  Score=59.22  Aligned_cols=65  Identities=18%  Similarity=0.199  Sum_probs=40.0

Q ss_pred             CEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHHHHhhcCcEEEEeeCCCC
Q 002040          506 DCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSG  579 (976)
Q Consensus       506 d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~~~~~~~~~~~~~~gg~~  579 (976)
                      -++++||||+|||++..=.+ .++...      +...+||-+.|.-.+.  .++++.|+..+++.+.....+..
T Consensus        13 vi~lvGptGvGKTTTiAKLA-a~~~~~------~~kV~lit~Dt~R~gA--~eQL~~~a~~l~i~~~~~~~~~d   77 (213)
T d1vmaa2          13 VIMVVGVNGTGKTTSCGKLA-KMFVDE------GKSVVLAAADTFRAAA--IEQLKIWGERVGATVISHSEGAD   77 (213)
T ss_dssp             EEEEECCTTSSHHHHHHHHH-HHHHHT------TCCEEEEEECTTCHHH--HHHHHHHHHHHTCEEECCSTTCC
T ss_pred             EEEEECCCCCCHHHHHHHHH-HHHHHC------CCceEEEeecccccch--hHHHHHHhhhcCccccccCCCCc
Confidence            36778999999998744333 333332      1345666666543322  25677777778888776555443

>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=96.31  E-value=0.0056  Score=59.96  Aligned_cols=40  Identities=18%  Similarity=0.167  Sum_probs=26.2

Q ss_pred             CcHHHHHHHHHH----hcCC---CEEEEcCCCCchHHHHHHHHHHHHh
Q 002040          490 PMPIQAQALPVI----MSGR---DCIGVAKTGSGKTLAFVLPMLRHIK  530 (976)
Q Consensus       490 p~~~Q~~~i~~i----l~g~---d~i~~a~TGsGKT~~~~l~il~~l~  530 (976)
                      ++|+|..++..+    .+++   .+|+.||.|+|||..+.. ++..+.
T Consensus         3 ~yPw~~~~~~~l~~~~~~~~l~h~lLl~Gp~G~GKtt~a~~-~a~~l~   49 (207)
T d1a5ta2           3 WYPWLRPDFEKLVASYQAGRGHHALLIQALPGMGDDALIYA-LSRYLL   49 (207)
T ss_dssp             CCGGGHHHHHHHHHHHHTTCCCSEEEEECCTTSCHHHHHHH-HHHHHT
T ss_pred             CCcccHHHHHHHHHHHHcCCcCeEEEEECCCCCcHHHHHHH-HHHhcc
Confidence            346776666544    3443   389999999999986443 444444

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

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: Nucleotide excision repair enzyme UvrB
species: Bacillus caldotenax [TaxId: 1395]

Probab=96.28  E-value=0.0068  Score=65.50  Aligned_cols=67  Identities=24%  Similarity=0.422  Sum_probs=49.6

Q ss_pred             CCcHHHHHHHHHHhc----C-CCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHHH
Q 002040          489 KPMPIQAQALPVIMS----G-RDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKF  563 (976)
Q Consensus       489 ~p~~~Q~~~i~~il~----g-~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~~  563 (976)
                      .|+.-|-+||..+.+    | +..++.|-||||||+++. .++...          +..+|||||+..+|.|+++.+..|
T Consensus        11 ~p~gDQP~aI~~l~~~l~~g~~~q~l~GltGS~ka~~iA-~l~~~~----------~rp~LVVt~n~~~A~qL~~dL~~~   79 (413)
T d1t5la1          11 EPQGDQPQAIAKLVDGLRRGVKHQTLLGATGTGKTFTIS-NVIAQV----------NKPTLVIAHNKTLAGQLYSELKEF   79 (413)
T ss_dssp             CCCTTHHHHHHHHHHHHHHTCSEEEEEECTTSCHHHHHH-HHHHHH----------TCCEEEECSSHHHHHHHHHHHHHH
T ss_pred             CCCCCCHHHHHHHHHHHhcCCCcEEEeCCCCcHHHHHHH-HHHHHh----------CCCEEEEeCCHHHHHHHHHHHHHH
Confidence            466777777776654    3 568889999999997532 333332          224799999999999999999998


Q ss_pred             Hhh
Q 002040          564 AKV  566 (976)
Q Consensus       564 ~~~  566 (976)
                      +..
T Consensus        80 l~~   82 (413)
T d1t5la1          80 FPH   82 (413)
T ss_dssp             CTT
T ss_pred             cCC
Confidence            643

>d1j8yf2 c.37.1.10 (F:87-297) GTPase domain of the signal sequence recognition protein Ffh {Archaeon Acidianus ambivalens [TaxId: 2283]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: GTPase domain of the signal sequence recognition protein Ffh
species: Archaeon Acidianus ambivalens [TaxId: 2283]

Probab=96.21  E-value=0.012  Score=57.25  Aligned_cols=171  Identities=16%  Similarity=0.130  Sum_probs=84.0

Q ss_pred             EEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHHHHhhcCcEEEEeeCCCChHHHHHH
Q 002040          507 CIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQISE  586 (976)
Q Consensus       507 ~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~~~~~~~~~~~~~~gg~~~~~~~~~  586 (976)
                      ++++||||+|||++..=.+ .++...      ....+||.+-|.-.+.  .++++.|+..+++.+............+..
T Consensus        15 i~lvGptGvGKTTTiAKLA-~~~~~~------g~kV~lit~Dt~R~ga--~eQL~~~a~~l~v~~~~~~~~~~~~~~~~~   85 (211)
T d1j8yf2          15 IMLVGVQGTGKATTAGKLA-YFYKKK------GFKVGLVGADVYRPAA--LEQLQQLGQQIGVPVYGEPGEKDVVGIAKR   85 (211)
T ss_dssp             EEEECSCCC----HHHHHH-HHHHHT------TCCEEEEECCCSSHHH--HHHHHHHHHHHTCCEECCTTCCCHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHH-HHHHHC------CCceEEEEeeccccch--hHHHHHhccccCcceeecccchhhhHHHHH
Confidence            5668999999998744333 333332      1234566665433222  266777777788877655544433221111


Q ss_pred             HhcCCeEEEeCchhHHHHHHhcCCcccccCCceEEEecCcccccccC---CchHHHHHHHhcCCCCcEEEEeccCcHHHH
Q 002040          587 LKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMG---FEPQITRIVQNIRPDRQTVLFSATFPRQVE  663 (976)
Q Consensus       587 l~~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDEah~~~~~~---f~~~i~~il~~~~~~~q~i~~SAT~~~~~~  663 (976)
                                       .+..     .....+++|+||=+=+.....   ....+..+...+.+..-+++++||......
T Consensus        86 -----------------a~~~-----~~~~~~d~IlIDTaGr~~~~~~~~~~~el~~~~~~~~~~~~~LVl~a~~~~~~~  143 (211)
T d1j8yf2          86 -----------------GVEK-----FLSEKMEIIIVDTAGRHGYGEEAALLEEMKNIYEAIKPDEVTLVIDASIGQKAY  143 (211)
T ss_dssp             -----------------HHHH-----HHHTTCSEEEEECCCSCCTTCHHHHHHHHHHHHHHHCCSEEEEEEEGGGGGGHH
T ss_pred             -----------------HHHH-----hhccCCceEEEecCCcCccchhhHHHHHHHHHHhhcCCceEEEEEecccCcchH
Confidence                             0000     112335566666554321111   123455666667777677888999765433


Q ss_pred             HHHHHHcCCCeEEEeCCcccccCCce-EEEEecCcchHHHHHHHHHHhhhcCCcEEEEecC
Q 002040          664 ILARKVLNKPVEIQVGGRSVVNKDIT-QLVEVRPESDRFLRLLELLGEWYEKGKILIFVHS  723 (976)
Q Consensus       664 ~l~~~~l~~~~~i~~~~~~~~~~~i~-q~~~~~~~~~k~~~l~~~l~~~~~~~kvLIF~~s  723 (976)
                      ..+..++...             .+. -.+...+...++-.++.++..+  +-++..++..
T Consensus       144 ~~~~~~~~~~-------------~~~~lI~TKlDet~~~G~~l~~~~~~--~lPi~~it~G  189 (211)
T d1j8yf2         144 DLASKFNQAS-------------KIGTIIITKMDGTAKGGGALSAVAAT--GATIKFIGTG  189 (211)
T ss_dssp             HHHHHHHHHC-------------TTEEEEEECTTSCSCHHHHHHHHHTT--TCCEEEEECS
T ss_pred             HHHhhhhccc-------------CcceEEEecccCCCcccHHHHHHHHH--CcCEEEEeCC
Confidence            3333332110             111 1234455666777777776653  3355544444

>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=96.02  E-value=0.023  Score=56.10  Aligned_cols=105  Identities=9%  Similarity=0.079  Sum_probs=79.0

Q ss_pred             cchHHHHHHHHHHh-hhcCCcEEEEecCHHHHHHHHHHHHH----CCCCceeccCCCCHHHHHHHHHHhccCCccEEEec
Q 002040          697 ESDRFLRLLELLGE-WYEKGKILIFVHSQEKCDALFRDLLK----HGYPCLSLHGAKDQTDRESTISDFKSNVCNLLIAT  771 (976)
Q Consensus       697 ~~~k~~~l~~~l~~-~~~~~kvLIF~~s~~~~~~l~~~L~~----~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLVaT  771 (976)
                      .+.|-...+..+.. ...+.+++|.+|+..-+.+++..|..    .++.+..+||.++..++..++..+.+|.++|||.|
T Consensus        86 GsGKT~V~~~a~~~~~~~g~qv~~l~Pt~~La~Q~~~~~~~~~~~~~~~v~~l~~~~~~~~~~~~~~~~~~g~~~iviGt  165 (233)
T d2eyqa3          86 GFGKTEVAMRAAFLAVDNHKQVAVLVPTTLLAQQHYDNFRDRFANWPVRIEMISRFRSAKEQTQILAEVAEGKIDILIGT  165 (233)
T ss_dssp             CTTTHHHHHHHHHHHHTTTCEEEEECSSHHHHHHHHHHHHHHSTTTTCCEEEESTTSCHHHHHHHHHHHHTTCCSEEEEC
T ss_pred             CCCcHHHHHHHHHHHHHcCCceEEEccHHHhHHHHHHHHHHHHhhCCCEEEeccCcccchhHHHHHHHHhCCCCCEEEee
Confidence            34554444444433 33466999999999999998888875    47788999999999999999999999999999999


Q ss_pred             Cccc-ccCCCCCCcEEEEeCCCCCHHHHHHHhc
Q 002040          772 SVAA-RGLDVKELELVINFDAPNHYEDYVHRVG  803 (976)
Q Consensus       772 ~v~~-~GlDi~~v~~VI~~d~p~s~~~y~Qr~G  803 (976)
                      -++- ..+.++++.+||.-.-..+  .|.|+.+
T Consensus       166 hs~l~~~~~f~~LgLiIiDEeH~f--g~kQ~~~  196 (233)
T d2eyqa3         166 HKLLQSDVKFKDLGLLIVDEEHRF--GVRHKER  196 (233)
T ss_dssp             THHHHSCCCCSSEEEEEEESGGGS--CHHHHHH
T ss_pred             hhhhccCCccccccceeeechhhh--hhHHHHH
Confidence            8554 5788889888885433322  3455543

>d1l8qa2 c.37.1.20 (A:77-289) Chromosomal replication initiation factor DnaA {Aquifex aeolicus [TaxId: 63363]}

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: Chromosomal replication initiation factor DnaA
species: Aquifex aeolicus [TaxId: 63363]

Probab=95.58  E-value=0.022  Score=55.79  Aligned_cols=45  Identities=18%  Similarity=0.317  Sum_probs=27.0

Q ss_pred             CCceEEEecCcccccccC-CchHHHHHHHhcC-CCCcEEEEeccCcH
Q 002040          616 RRVTYLVMDEADRMFDMG-FEPQITRIVQNIR-PDRQTVLFSATFPR  660 (976)
Q Consensus       616 ~~~~~vVlDEah~~~~~~-f~~~i~~il~~~~-~~~q~i~~SAT~~~  660 (976)
                      ..+++||||++|.+.... ....+..++..+. ...++|+.|...|.
T Consensus        96 ~~~dll~iDDi~~i~~~~~~~~~lf~lin~~~~~~~~iiits~~~p~  142 (213)
T d1l8qa2          96 KSVDLLLLDDVQFLSGKERTQIEFFHIFNTLYLLEKQIILASDRHPQ  142 (213)
T ss_dssp             HTCSEEEEECGGGGTTCHHHHHHHHHHHHHHHHTTCEEEEEESSCGG
T ss_pred             hhccchhhhhhhhhcCchHHHHHHHHHHHHHhhccceEEEecCCcch
Confidence            357899999999875432 3334555666554 34455554444443

>d1xbta1 c.37.1.24 (A:18-150) Thymidine kinase, TK1, N-terminal domain {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: Type II thymidine kinase
domain: Thymidine kinase, TK1, N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.29  E-value=0.031  Score=50.03  Aligned_cols=36  Identities=14%  Similarity=0.074  Sum_probs=24.7

Q ss_pred             EEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCH
Q 002040          507 CIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTR  550 (976)
Q Consensus       507 ~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr  550 (976)
                      -+++|||.||||.-.+-.+..+ ..       .+.+++++-|..
T Consensus         5 ~li~GpMfsGKTt~Li~~~~~~-~~-------~g~~v~~ikp~~   40 (133)
T d1xbta1           5 QVILGPMFSGKSTELMRRVRRF-QI-------AQYKCLVIKYAK   40 (133)
T ss_dssp             EEEECCTTSCHHHHHHHHHHHH-HT-------TTCCEEEEEETT
T ss_pred             EEEEecccCHHHHHHHHHHHHH-HH-------cCCcEEEEeccc
Confidence            4788999999998644444333 22       255789998863

>d2b8ta1 c.37.1.24 (A:11-149) Thymidine kinase, TK1, N-terminal domain {Ureaplasma urealyticum [TaxId: 2130]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Type II thymidine kinase
domain: Thymidine kinase, TK1, N-terminal domain
species: Ureaplasma urealyticum [TaxId: 2130]

Probab=95.26  E-value=0.022  Score=51.46  Aligned_cols=87  Identities=11%  Similarity=0.076  Sum_probs=50.1

Q ss_pred             EEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHHHHhhcCcEEEEeeCCCChHHHHHH
Q 002040          507 CIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQISE  586 (976)
Q Consensus       507 ~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~~~~~~~~~~~~~~gg~~~~~~~~~  586 (976)
                      -+++|||.||||.-++--+.++..        .+.+++++-|...-         +.    +-.++ ...|..       
T Consensus         5 ~~i~GpMfsGKTteLi~~~~~~~~--------~~~kv~~ikp~~D~---------R~----~~~i~-s~~g~~-------   55 (139)
T d2b8ta1           5 EFITGPMFAGKTAELIRRLHRLEY--------ADVKYLVFKPKIDT---------RS----IRNIQ-SRTGTS-------   55 (139)
T ss_dssp             EEEECSTTSCHHHHHHHHHHHHHH--------TTCCEEEEEECCCG---------GG----CSSCC-CCCCCS-------
T ss_pred             EEEEccccCHHHHHHHHHHHHHHH--------CCCcEEEEEEcccc---------cc----cceEE-cccCce-------
Confidence            478899999999875554443322        25578999997431         00    11111 111211       


Q ss_pred             HhcCCeEEEeCchhHHHHHHhcCCcccccCCceEEEecCcccc
Q 002040          587 LKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRM  629 (976)
Q Consensus       587 l~~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDEah~~  629 (976)
                        . ..+.+.+...+...+...    .....+++|.||||+-+
T Consensus        56 --~-~~~~~~~~~~~~~~~~~~----~~~~~~dvI~IDE~QFf   91 (139)
T d2b8ta1          56 --L-PSVEVESAPEILNYIMSN----SFNDETKVIGIDEVQFF   91 (139)
T ss_dssp             --S-CCEEESSTHHHHHHHHST----TSCTTCCEEEECSGGGS
T ss_pred             --e-eeEEeccchhhHHHHHhh----ccccCcCEEEechhhhc
Confidence              1 235555655566665433    23457899999999953

>d1xx6a1 c.37.1.24 (A:2-142) Thymidine kinase, TK1, N-terminal domain {Clostridium acetobutylicum [TaxId: 1488]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Type II thymidine kinase
domain: Thymidine kinase, TK1, N-terminal domain
species: Clostridium acetobutylicum [TaxId: 1488]

Probab=95.13  E-value=0.035  Score=50.22  Aligned_cols=38  Identities=16%  Similarity=0.024  Sum_probs=26.0

Q ss_pred             CCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCH
Q 002040          505 RDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTR  550 (976)
Q Consensus       505 ~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr  550 (976)
                      .=-|++|||.||||+-++--+..+..        .|.+++++.|..
T Consensus         8 ~l~lI~GpMfSGKTteLi~~~~~~~~--------~g~~vl~i~~~~   45 (141)
T d1xx6a1           8 WVEVIVGPMYSGKSEELIRRIRRAKI--------AKQKIQVFKPEI   45 (141)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHHHHH--------TTCCEEEEEEC-
T ss_pred             eEEEEEeccccHHHHHHHHHHHHhhh--------cCCcEEEEEecc
Confidence            33578899999999875544443322        255789999974

>d2gnoa2 c.37.1.20 (A:11-208) gamma subunit of DNA polymerase III, N-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: Extended AAA-ATPase domain
domain: gamma subunit of DNA polymerase III, N-domain
species: Thermotoga maritima [TaxId: 2336]

Probab=94.89  E-value=0.031  Score=53.86  Aligned_cols=115  Identities=17%  Similarity=0.153  Sum_probs=63.4

Q ss_pred             HHHHHHHHhc---CCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHHHHhhcCcE
Q 002040          494 QAQALPVIMS---GRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVMGVR  570 (976)
Q Consensus       494 Q~~~i~~il~---g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~~~~~~~~~  570 (976)
                      |.+.+..+..   +..+|+.|+.|+|||..+.. +...+....    ...|-++++.|.-.                   
T Consensus         2 ~~~~l~~~i~~~~~~~~l~~G~~g~gk~~~a~~-l~~~i~~~~----~~h~D~~~i~~~~~-------------------   57 (198)
T d2gnoa2           2 QLETLKRIIEKSEGISILINGEDLSYPREVSLE-LPEYVEKFP----PKASDVLEIDPEGE-------------------   57 (198)
T ss_dssp             HHHHHHHHHHTCSSEEEEEECSSSSHHHHHHHH-HHHHHHTSC----CCTTTEEEECCSSS-------------------
T ss_pred             HHHHHHHHHhcCCCceEEEECCCCCCHHHHHHH-HHHHHhccc----cCCCCEEEEeCCcC-------------------
Confidence            5566666653   34799999999999976443 334444321    12355677777310                   


Q ss_pred             EEEeeCCCChHHHHHHHhcCCeEEEeCchhHHHHHHhcCCcccccCCceEEEecCcccccccCCchHHHHHHHhcCCCCc
Q 002040          571 CVPVYGGSGVAQQISELKRGTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEADRMFDMGFEPQITRIVQNIRPDRQ  650 (976)
Q Consensus       571 ~~~~~gg~~~~~~~~~l~~~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDEah~~~~~~f~~~i~~il~~~~~~~q  650 (976)
                             ...-+++..              +...+...    .....+.++||||||+|... -...+..++..-+++..
T Consensus        58 -------~I~Id~IR~--------------i~~~~~~~----~~~~~~KviIId~ad~l~~~-aqNaLLK~LEEPp~~t~  111 (198)
T d2gnoa2          58 -------NIGIDDIRT--------------IKDFLNYS----PELYTRKYVIVHDCERMTQQ-AANAFLKALEEPPEYAV  111 (198)
T ss_dssp             -------CBCHHHHHH--------------HHHHHTSC----CSSSSSEEEEETTGGGBCHH-HHHHTHHHHHSCCTTEE
T ss_pred             -------CCCHHHHHH--------------HHHHHhhC----cccCCCEEEEEeCccccchh-hhhHHHHHHhCCCCCce
Confidence                   000011111              11122111    22355789999999988533 23455566666566666


Q ss_pred             EEEEeccC
Q 002040          651 TVLFSATF  658 (976)
Q Consensus       651 ~i~~SAT~  658 (976)
                      +|++|..+
T Consensus       112 fiLit~~~  119 (198)
T d2gnoa2         112 IVLNTRRW  119 (198)
T ss_dssp             EEEEESCG
T ss_pred             eeeccCCh
Confidence            66666554

>d1sxje2 c.37.1.20 (E:4-255) Replication factor C5 {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 C5
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=94.73  E-value=0.026  Score=56.43  Aligned_cols=39  Identities=10%  Similarity=0.295  Sum_probs=24.1

Q ss_pred             CCceEEEecCcccccccCCchHHHHHHHhcCCCCcEEEEe
Q 002040          616 RRVTYLVMDEADRMFDMGFEPQITRIVQNIRPDRQTVLFS  655 (976)
Q Consensus       616 ~~~~~vVlDEah~~~~~~f~~~i~~il~~~~~~~q~i~~S  655 (976)
                      ..+.+|||||+|.|... ....+..++........+|+.+
T Consensus       130 ~~~~iiiide~d~l~~~-~~~~l~~~~e~~~~~~~~Il~t  168 (252)
T d1sxje2         130 HRYKCVIINEANSLTKD-AQAALRRTMEKYSKNIRLIMVC  168 (252)
T ss_dssp             -CCEEEEEECTTSSCHH-HHHHHHHHHHHSTTTEEEEEEE
T ss_pred             CCceEEEeccccccccc-cchhhhcccccccccccceeee
Confidence            44679999999987533 3344556666655555444443

>d1ixza_ c.37.1.20 (A:) AAA domain of cell division protein FtsH {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: AAA domain of cell division protein FtsH
species: Thermus thermophilus [TaxId: 274]

Probab=94.53  E-value=0.15  Score=50.61  Aligned_cols=53  Identities=15%  Similarity=0.177  Sum_probs=29.6

Q ss_pred             cccccccCCCCHHHHHHHHHcCCCCCcHHHHHHHHHH--hcCCCEEEEcCCCCchHHH
Q 002040          465 PIKTWHQTGLTSKIMETIRKLNYEKPMPIQAQALPVI--MSGRDCIGVAKTGSGKTLA  520 (976)
Q Consensus       465 pi~~~~~~~l~~~l~~~l~~~~~~~p~~~Q~~~i~~i--l~g~d~i~~a~TGsGKT~~  520 (976)
                      |-.+|++.+-...+.+.|...  ..+ ..+.+.+..+  ...+.+|+.||+|+|||+.
T Consensus         4 p~~~~~di~G~~~~k~~l~~~--i~~-l~~~~~~~~~g~~~~~giLl~GppGtGKT~l   58 (247)
T d1ixza_           4 PKVTFKDVAGAEEAKEELKEI--VEF-LKNPSRFHEMGARIPKGVLLVGPPGVGKTHL   58 (247)
T ss_dssp             CSCCGGGCCSCHHHHHHHHHH--HHH-HHCHHHHHHTTCCCCSEEEEECCTTSSHHHH
T ss_pred             CCCcHHHHccHHHHHHHHHHH--HHH-HHCHHHHHHcCCCCCceEEEecCCCCChhHH
Confidence            447899987776666655321  000 0001111111  0124699999999999975

>d1lv7a_ c.37.1.20 (A:) AAA domain of cell division protein FtsH {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: AAA domain of cell division protein FtsH
species: Escherichia coli [TaxId: 562]

Probab=94.34  E-value=0.034  Score=55.89  Aligned_cols=52  Identities=21%  Similarity=0.257  Sum_probs=28.9

Q ss_pred             ccccccCCCCHHHHHHHHHc-C-CCCCcHHHHHHHHHHhcCCCEEEEcCCCCchHHH
Q 002040          466 IKTWHQTGLTSKIMETIRKL-N-YEKPMPIQAQALPVIMSGRDCIGVAKTGSGKTLA  520 (976)
Q Consensus       466 i~~~~~~~l~~~l~~~l~~~-~-~~~p~~~Q~~~i~~il~g~d~i~~a~TGsGKT~~  520 (976)
                      -.+|.+.+-...+.+.|... . +..|..+|.-.   +-..+.+|+.||+|+|||+.
T Consensus         8 ~~t~~Di~Gl~~~k~~l~e~v~~~~~~~~~~~~g---~~~~~~iLL~GppGtGKT~l   61 (256)
T d1lv7a_           8 KTTFADVAGCDEAKEEVAELVEYLREPSRFQKLG---GKIPKGVLMVGPPGTGKTLL   61 (256)
T ss_dssp             CCCGGGSCSCHHHHHHTHHHHHHHHCGGGC--------CCCCEEEEECCTTSCHHHH
T ss_pred             CCCHHHHhchHHHHHHHHHHHHHHHCHHHHHHcC---CCCCCeEEeeCCCCCCccHH
Confidence            45788888777666654321 0 11111111110   11235699999999999986

>d1njfa_ c.37.1.20 (A:) 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=94.30  E-value=0.21  Score=49.21  Aligned_cols=49  Identities=14%  Similarity=0.163  Sum_probs=29.9

Q ss_pred             cccccCCCCHHHHHHHHHcCCCCCcHHHHHHHHHHhcCC---CEEEEcCCCCchHHHHHHHHHHHHhc
Q 002040          467 KTWHQTGLTSKIMETIRKLNYEKPMPIQAQALPVIMSGR---DCIGVAKTGSGKTLAFVLPMLRHIKD  531 (976)
Q Consensus       467 ~~~~~~~l~~~l~~~l~~~~~~~p~~~Q~~~i~~il~g~---d~i~~a~TGsGKT~~~~l~il~~l~~  531 (976)
                      .+|.++-....+.+.|.               .++.+++   .+|+.||+|+|||.++. .++..+..
T Consensus         9 ~~~~dlig~~~~~~~L~---------------~~i~~~~~~~~~Ll~Gp~G~GKtt~a~-~~~~~l~~   60 (239)
T d1njfa_           9 QTFADVVGQEHVLTALA---------------NGLSLGRIHHAYLFSGTRGVGKTSIAR-LLAKGLNC   60 (239)
T ss_dssp             SSGGGSCSCHHHHHHHH---------------HHHHTTCCCSEEEEECSTTSSHHHHHH-HHHHHHHC
T ss_pred             CCHHHccChHHHHHHHH---------------HHHHcCCCCeeEEEECCCCCcHHHHHH-HHHHHhcC
Confidence            35666655655554433               2333443   38899999999998644 44555543

>d2eyqa5 c.37.1.19 (A:779-989) 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=93.68  E-value=0.048  Score=52.42  Aligned_cols=80  Identities=15%  Similarity=0.241  Sum_probs=61.5

Q ss_pred             CCCeEEEEccCHHHHHHHHHHHHHHHhhcCcEEEEeeCCCChHHHH---HHHhc-CCeEEEeCchhHHHHHHhcCCcccc
Q 002040          539 DGPVGLIMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQI---SELKR-GTEIVVCTPGRMIDILCTSGGKITN  614 (976)
Q Consensus       539 ~~~~vLIl~Ptr~La~Q~~~~~~~~~~~~~~~~~~~~gg~~~~~~~---~~l~~-~~~Iiv~Tp~~L~~~l~~~~~~~~~  614 (976)
                      .|.+|.||||..+-+..++..+.+++.  ++++.+++|..+..+.-   ..+.. ..+|+|||.     .+...    .+
T Consensus        30 rGgQvy~V~p~I~~~e~~~~~l~~~~p--~~~i~~lHGkm~~~eke~im~~F~~g~~~ILv~Tt-----vIEvG----iD   98 (211)
T d2eyqa5          30 RGGQVYYLYNDVENIQKAAERLAELVP--EARIAIGHGQMRERELERVMNDFHHQRFNVLVCTT-----IIETG----ID   98 (211)
T ss_dssp             TTCEEEEECCCSSCHHHHHHHHHHHCT--TSCEEECCSSCCHHHHHHHHHHHHTTSCCEEEESS-----TTGGG----SC
T ss_pred             cCCeEEEEEcCccchhhHHHHHHHhCC--ceEEEEEEeccCHHHHHHHHHHHHcCCcceEEEeh-----hhhhc----cC
Confidence            478999999999888888888887754  56888888888766543   33443 479999994     34433    67


Q ss_pred             cCCceEEEecCcccc
Q 002040          615 LRRVTYLVMDEADRM  629 (976)
Q Consensus       615 l~~~~~vVlDEah~~  629 (976)
                      +.+.+++||..|+++
T Consensus        99 vpnA~~iiI~~a~rf  113 (211)
T d2eyqa5          99 IPTANTIIIERADHF  113 (211)
T ss_dssp             CTTEEEEEETTTTSS
T ss_pred             CCCCcEEEEecchhc
Confidence            889999999999985

>d1c4oa2 c.37.1.19 (A:410-583) Nucleotide excision repair enzyme UvrB {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: Tandem AAA-ATPase domain
domain: Nucleotide excision repair enzyme UvrB
species: Thermus thermophilus [TaxId: 274]

Probab=93.53  E-value=0.32  Score=45.17  Aligned_cols=112  Identities=14%  Similarity=0.172  Sum_probs=70.3

Q ss_pred             CCeEEEEccCHHHHHHHHHHHHHHHhhcCcEEEEeeCCCChHHHH---HHHhc-CCeEEEeCchhHHHHHHhcCCccccc
Q 002040          540 GPVGLIMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQI---SELKR-GTEIVVCTPGRMIDILCTSGGKITNL  615 (976)
Q Consensus       540 ~~~vLIl~Ptr~La~Q~~~~~~~~~~~~~~~~~~~~gg~~~~~~~---~~l~~-~~~Iiv~Tp~~L~~~l~~~~~~~~~l  615 (976)
                      |.++||.|+|+.-|..+...+..    .|+.+..++|+.+..+..   ..+.. ..+|+|+|.     ++..+    .++
T Consensus        31 g~r~lvfc~t~~~~~~l~~~L~~----~Gi~a~~~Hg~~~~~eR~~~l~~F~~G~~~vLVaT~-----v~~~G----iDi   97 (174)
T d1c4oa2          31 GERTLVTVLTVRMAEELTSFLVE----HGIRARYLHHELDAFKRQALIRDLRLGHYDCLVGIN-----LLREG----LDI   97 (174)
T ss_dssp             TCEEEEECSSHHHHHHHHHHHHH----TTCCEEEECTTCCHHHHHHHHHHHHTTSCSEEEESC-----CCCTT----CCC
T ss_pred             CCcEEEEEcchhHHHHHHHHHHh----cCCceEEEecccchHHHHHHHHHHHCCCeEEEEeee-----eeeee----ccC
Confidence            66899999999988777666655    699999999999876654   33444 469999994     33222    678


Q ss_pred             CCceEEEecCccccccc-CCchHHHHHHHhcCCC-CcEEEEeccCcHHHHH
Q 002040          616 RRVTYLVMDEADRMFDM-GFEPQITRIVQNIRPD-RQTVLFSATFPRQVEI  664 (976)
Q Consensus       616 ~~~~~vVlDEah~~~~~-~f~~~i~~il~~~~~~-~q~i~~SAT~~~~~~~  664 (976)
                      .++.+||+=.++..... .....+..+-...+.. ..++++.......+..
T Consensus        98 p~V~~Vi~~~~~~~~~~~~~~~~iq~~GR~gR~~~g~~~~~~~~~~~~~~~  148 (174)
T d1c4oa2          98 PEVSLVAILDADKEGFLRSERSLIQTIGRAARNARGEVWLYADRVSEAMQR  148 (174)
T ss_dssp             TTEEEEEETTTTSCSGGGSHHHHHHHHGGGTTSTTCEEEEECSSCCHHHHH
T ss_pred             CCCcEEEEeccccccccchhHHHHHHhhhhhhcCCCeeEEeecCCCHHHHH
Confidence            89999998666643211 1111233333333332 3455555545554443

>d1c4oa1 c.37.1.19 (A:2-409) Nucleotide excision repair enzyme UvrB {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: Tandem AAA-ATPase domain
domain: Nucleotide excision repair enzyme UvrB
species: Thermus thermophilus [TaxId: 274]

Probab=93.36  E-value=0.15  Score=54.70  Aligned_cols=66  Identities=24%  Similarity=0.462  Sum_probs=45.9

Q ss_pred             CCcHHHHHHHHHHh----cCCC-EEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHHH
Q 002040          489 KPMPIQAQALPVIM----SGRD-CIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKF  563 (976)
Q Consensus       489 ~p~~~Q~~~i~~il----~g~d-~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~~  563 (976)
                      .|+.-|-+||..++    .|.. +.+.|-+||+||++. ..++..+          +..+|||||+...|.++++.+..|
T Consensus         8 ~p~~dqp~aI~~l~~~L~~g~~~~~L~GlsgS~ka~~~-A~l~~~~----------~rp~LvVt~~~~~A~~l~~dL~~~   76 (408)
T d1c4oa1           8 SPKGDQPKAIAGLVEALRDGERFVTLLGATGTGKTVTM-AKVIEAL----------GRPALVLAPNKILAAQLAAEFREL   76 (408)
T ss_dssp             CCCTTHHHHHHHHHHHHHTTCSEEEEEECTTSCHHHHH-HHHHHHH----------TCCEEEEESSHHHHHHHHHHHHHH
T ss_pred             CCCCCCHHHHHHHHHHHhcCCCcEEEecCCCCHHHHHH-HHHHHHh----------CCCEEEEeCCHHHHHHHHHHHHHh
Confidence            34555655666543    4554 688899999999752 2233221          224789999999999999999988


Q ss_pred             Hh
Q 002040          564 AK  565 (976)
Q Consensus       564 ~~  565 (976)
                      +.
T Consensus        77 l~   78 (408)
T d1c4oa1          77 FP   78 (408)
T ss_dssp             CT
T ss_pred             cC
Confidence            64

>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=92.80  E-value=0.17  Score=49.28  Aligned_cols=38  Identities=16%  Similarity=0.397  Sum_probs=22.3

Q ss_pred             cCCceEEEecCcccccccCCchHHHHHHHhcCCCCcEEE
Q 002040          615 LRRVTYLVMDEADRMFDMGFEPQITRIVQNIRPDRQTVL  653 (976)
Q Consensus       615 l~~~~~vVlDEah~~~~~~f~~~i~~il~~~~~~~q~i~  653 (976)
                      .....+|||||+|.+.... ...+..++........+++
T Consensus        97 ~~~~kiiiiDe~d~~~~~~-~~~Ll~~le~~~~~~~~~~  134 (227)
T d1sxjc2          97 SKGFKLIILDEADAMTNAA-QNALRRVIERYTKNTRFCV  134 (227)
T ss_dssp             SCSCEEEEETTGGGSCHHH-HHHHHHHHHHTTTTEEEEE
T ss_pred             CCCeEEEEEeccccchhhH-HHHHHHHhhhcccceeecc
Confidence            3446799999999875432 3344555555544443333

>d1sxjd2 c.37.1.20 (D:26-262) Replication factor C2 {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 C2
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=92.48  E-value=0.07  Score=52.49  Aligned_cols=15  Identities=27%  Similarity=0.332  Sum_probs=13.6

Q ss_pred             CEEEEcCCCCchHHH
Q 002040          506 DCIGVAKTGSGKTLA  520 (976)
Q Consensus       506 d~i~~a~TGsGKT~~  520 (976)
                      ++|+.||+|+|||++
T Consensus        35 ~lll~Gp~G~GKTtl   49 (237)
T d1sxjd2          35 HMLFYGPPGTGKTST   49 (237)
T ss_dssp             CEEEECSTTSSHHHH
T ss_pred             eEEEECCCCCChHHH
Confidence            589999999999975

>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=92.39  E-value=0.12  Score=50.52  Aligned_cols=42  Identities=14%  Similarity=0.190  Sum_probs=25.4

Q ss_pred             CCceEEEecCcccccccCCchHHHHHHHhcCCCCcEEEEeccC
Q 002040          616 RRVTYLVMDEADRMFDMGFEPQITRIVQNIRPDRQTVLFSATF  658 (976)
Q Consensus       616 ~~~~~vVlDEah~~~~~~f~~~i~~il~~~~~~~q~i~~SAT~  658 (976)
                      ....+||+||+|.|.... ...+...+........+++++...
T Consensus       100 ~~~kviiiDe~d~~~~~~-~~~ll~~~e~~~~~~~~i~~~~~~  141 (224)
T d1sxjb2         100 GKHKIVILDEADSMTAGA-QQALRRTMELYSNSTRFAFACNQS  141 (224)
T ss_dssp             TCCEEEEEESGGGSCHHH-HHTTHHHHHHTTTTEEEEEEESCG
T ss_pred             cceEEEEEecccccchhH-HHHHhhhccccccceeeeeccCch
Confidence            456799999999876432 223334455555555556655554

>d1t5la2 c.37.1.19 (A:415-595) Nucleotide excision repair enzyme UvrB {Bacillus caldotenax [TaxId: 1395]}

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: Nucleotide excision repair enzyme UvrB
species: Bacillus caldotenax [TaxId: 1395]

Probab=92.19  E-value=0.33  Score=45.48  Aligned_cols=76  Identities=13%  Similarity=0.281  Sum_probs=57.3

Q ss_pred             CCeEEEEccCHHHHHHHHHHHHHHHhhcCcEEEEeeCCCChHHHHHH---Hhc-CCeEEEeCchhHHHHHHhcCCccccc
Q 002040          540 GPVGLIMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQISE---LKR-GTEIVVCTPGRMIDILCTSGGKITNL  615 (976)
Q Consensus       540 ~~~vLIl~Ptr~La~Q~~~~~~~~~~~~~~~~~~~~gg~~~~~~~~~---l~~-~~~Iiv~Tp~~L~~~l~~~~~~~~~l  615 (976)
                      +.++||.|+|+.-+..++..+..    .|+.+..++|+.+..+....   +.. ..+|+|||.     ++..+    .++
T Consensus        31 ~~~~iif~~~~~~~~~~~~~l~~----~g~~~~~~hg~~~~~eR~~~l~~Fr~g~~~vLVaTd-----v~~rG----iDi   97 (181)
T d1t5la2          31 NERTLVTTLTKKMAEDLTDYLKE----AGIKVAYLHSEIKTLERIEIIRDLRLGKYDVLVGIN-----LLREG----LDI   97 (181)
T ss_dssp             TCEEEEECSSHHHHHHHHHHHHT----TTCCEEEECSSCCHHHHHHHHHHHHHTSCSEEEESC-----CCSSS----CCC
T ss_pred             CCeEEEEeehhhhhHHHHHHHHh----CCcceeEecCCccHHHHHHHHHHHHCCCCCEEEehh-----HHHcc----CCC
Confidence            55799999999988766665554    69999999999987766443   333 579999994     33222    688


Q ss_pred             CCceEEEecCccc
Q 002040          616 RRVTYLVMDEADR  628 (976)
Q Consensus       616 ~~~~~vVlDEah~  628 (976)
                      ..+.+||.-.+..
T Consensus        98 p~v~~VI~~d~p~  110 (181)
T d1t5la2          98 PEVSLVAILDADK  110 (181)
T ss_dssp             TTEEEEEETTTTS
T ss_pred             CCCCEEEEecCCc
Confidence            8999999887775

>d1d2na_ c.37.1.20 (A:) Hexamerization domain of N-ethylmalemide-sensitive fusion (NSF) protein {Chinese hamster (Cricetulus griseus) [TaxId: 10029]}

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: Hexamerization domain of N-ethylmalemide-sensitive fusion (NSF) protein
species: Chinese hamster (Cricetulus griseus) [TaxId: 10029]

Probab=91.91  E-value=0.45  Score=47.01  Aligned_cols=15  Identities=27%  Similarity=0.173  Sum_probs=13.7

Q ss_pred             CEEEEcCCCCchHHH
Q 002040          506 DCIGVAKTGSGKTLA  520 (976)
Q Consensus       506 d~i~~a~TGsGKT~~  520 (976)
                      .+|+.||+|+|||+.
T Consensus        42 ~vLL~GppGtGKT~l   56 (246)
T d1d2na_          42 SVLLEGPPHSGKTAL   56 (246)
T ss_dssp             EEEEECSTTSSHHHH
T ss_pred             EEEEECcCCCCHHHH
Confidence            599999999999975

>d1ye8a1 c.37.1.11 (A:1-178) Hypothetical kinase-like protein Aq_1292 {Aquifex aeolicus [TaxId: 63363]}

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: Hypothetical kinase-like protein Aq 1292
species: Aquifex aeolicus [TaxId: 63363]

Probab=91.82  E-value=0.0088  Score=56.47  Aligned_cols=42  Identities=14%  Similarity=0.125  Sum_probs=24.4

Q ss_pred             cCCceEEEecCcccccccCCchHHHHHHHhcCCCCcEEEEecc
Q 002040          615 LRRVTYLVMDEADRMFDMGFEPQITRIVQNIRPDRQTVLFSAT  657 (976)
Q Consensus       615 l~~~~~vVlDEah~~~~~~f~~~i~~il~~~~~~~q~i~~SAT  657 (976)
                      .....++|+||++.....+ ...+..+...+.....+|+++..
T Consensus        97 ~~~~~vlllDE~~~~~~~~-~~~~~~l~~~l~~~~~~il~~~h  138 (178)
T d1ye8a1          97 KDRRKVIIIDEIGKMELFS-KKFRDLVRQIMHDPNVNVVATIP  138 (178)
T ss_dssp             HCTTCEEEECCCSTTGGGC-HHHHHHHHHHHTCTTSEEEEECC
T ss_pred             hcCCCceeecCCCccchhh-HHHHHHHHHHhccCCCEEEEEEc
Confidence            4567899999998544322 23344444445544556666544

>d1qvra2 c.37.1.20 (A:149-535) ClpB, AAA+ modules {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: ClpB, AAA+ modules
species: Thermus thermophilus [TaxId: 274]

Probab=91.38  E-value=0.44  Score=50.39  Aligned_cols=26  Identities=15%  Similarity=0.415  Sum_probs=18.8

Q ss_pred             HHHHHHh--cCCCEEEEcCCCCchHHHH
Q 002040          496 QALPVIM--SGRDCIGVAKTGSGKTLAF  521 (976)
Q Consensus       496 ~~i~~il--~g~d~i~~a~TGsGKT~~~  521 (976)
                      +++..+.  ...++|++|+.|.|||...
T Consensus        33 ~~~~~L~r~~k~n~llvG~~GvGKtaiv   60 (387)
T d1qvra2          33 RVIQILLRRTKNNPVLIGEPGVGKTAIV   60 (387)
T ss_dssp             HHHHHHHCSSCCCCEEEECTTSCHHHHH
T ss_pred             HHHHHHhcCCCCCCeEECCCCCCHHHHH
Confidence            4444444  3457999999999999763

>d1hv8a2 c.37.1.19 (A:211-365) 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=91.15  E-value=0.49  Score=42.99  Aligned_cols=71  Identities=15%  Similarity=0.324  Sum_probs=51.4

Q ss_pred             CCeEEEEccCHHHHHHHHHHHHHHHhhcCcEEEEeeCCCChHHHHHH---Hhc-CCeEEEeCchhHHHHHHhcCCccccc
Q 002040          540 GPVGLIMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQISE---LKR-GTEIVVCTPGRMIDILCTSGGKITNL  615 (976)
Q Consensus       540 ~~~vLIl~Ptr~La~Q~~~~~~~~~~~~~~~~~~~~gg~~~~~~~~~---l~~-~~~Iiv~Tp~~L~~~l~~~~~~~~~l  615 (976)
                      +.++||.|+|+.-|.+++..+..    .|+.+..++|+.+..+....   +.. ...|+|||.     .+..+    .++
T Consensus        28 ~~k~IIF~~s~~~~~~l~~~L~~----~g~~~~~~~~~~~~~~r~~~~~~f~~~~~~ilv~T~-----~~~~G----id~   94 (155)
T d1hv8a2          28 EFYGLVFCKTKRDTKELASMLRD----IGFKAGAIHGDLSQSQREKVIRLFKQKKIRILIATD-----VMSRG----IDV   94 (155)
T ss_dssp             TCCEEEECSSHHHHHHHHHHHHH----TTCCEEEECSSSCHHHHHHHHHHHHTTSSSEEEECT-----THHHH----CCC
T ss_pred             CCCEEEEECchHHHHHHHhhhcc----cccccccccccchhhhhhhhhhhhhcccceeeeehh-----HHhhh----hhh
Confidence            45789999999988877776665    68889999999877666433   333 469999994     23222    577


Q ss_pred             CCceEEEe
Q 002040          616 RRVTYLVM  623 (976)
Q Consensus       616 ~~~~~vVl  623 (976)
                      ..+.+||.
T Consensus        95 ~~v~~Vi~  102 (155)
T d1hv8a2          95 NDLNCVIN  102 (155)
T ss_dssp             SCCSEEEE
T ss_pred             ccCcEEEE
Confidence            77888774

>d1r6bx2 c.37.1.20 (X:169-436) ClpA, an Hsp100 chaperone, AAA+ modules {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: ClpA, an Hsp100 chaperone, AAA+ modules
species: Escherichia coli [TaxId: 562]

Probab=90.69  E-value=0.54  Score=46.91  Aligned_cols=18  Identities=28%  Similarity=0.314  Sum_probs=15.3

Q ss_pred             CCCEEEEcCCCCchHHHH
Q 002040          504 GRDCIGVAKTGSGKTLAF  521 (976)
Q Consensus       504 g~d~i~~a~TGsGKT~~~  521 (976)
                      ..++|++|+.|.|||...
T Consensus        39 k~n~lLVG~~GvGKTalv   56 (268)
T d1r6bx2          39 KNNPLLVGESGVGKTAIA   56 (268)
T ss_dssp             SCEEEEECCTTSSHHHHH
T ss_pred             cCCcEEECCCCCcHHHHH
Confidence            357999999999999753

>d1sxja2 c.37.1.20 (A:295-547) Replication factor C1 {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 C1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=90.39  E-value=0.19  Score=49.83  Aligned_cols=17  Identities=35%  Similarity=0.350  Sum_probs=14.5

Q ss_pred             CCEEEEcCCCCchHHHH
Q 002040          505 RDCIGVAKTGSGKTLAF  521 (976)
Q Consensus       505 ~d~i~~a~TGsGKT~~~  521 (976)
                      ..+|+.||+|+|||+++
T Consensus        53 ~~lll~GPpG~GKTt~a   69 (253)
T d1sxja2          53 RAAMLYGPPGIGKTTAA   69 (253)
T ss_dssp             SEEEEECSTTSSHHHHH
T ss_pred             ceEEEECCCCCCHHHHH
Confidence            46899999999999753

>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=90.31  E-value=0.14  Score=53.13  Aligned_cols=52  Identities=25%  Similarity=0.296  Sum_probs=33.8

Q ss_pred             HHHHHHHHH-HhcCCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHH
Q 002040          492 PIQAQALPV-IMSGRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTREL  552 (976)
Q Consensus       492 ~~Q~~~i~~-il~g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~L  552 (976)
                      +-+...+.. +..++++|++|+||||||+. +-+++.++        ....+++++--+.+|
T Consensus       153 ~~~~~~l~~~v~~~~nili~G~tgSGKTT~-l~al~~~i--------~~~~rivtiEd~~El  205 (323)
T d1g6oa_         153 EQAISAIKDGIAIGKNVIVCGGTGSGKTTY-IKSIMEFI--------PKEERIISIEDTEEI  205 (323)
T ss_dssp             HHHHHHHHHHHHHTCCEEEEESTTSSHHHH-HHHHGGGS--------CTTCCEEEEESSCCC
T ss_pred             HHHHHHHHHHHHhCCCEEEEeeccccchHH-HHHHhhhc--------ccccceeeccchhhh
Confidence            344444443 45678999999999999975 44444332        124466777777776

>d1g5ta_ c.37.1.11 (A:) ATP:corrinoid adenosyltransferase CobA {Salmonella typhimurium [TaxId: 90371]}

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: ATP:corrinoid adenosyltransferase CobA
species: Salmonella typhimurium [TaxId: 90371]

Probab=90.21  E-value=0.18  Score=45.97  Aligned_cols=51  Identities=16%  Similarity=0.244  Sum_probs=37.7

Q ss_pred             CCceEEEecCcccccccCCch--HHHHHHHhcCCCCcEEEEeccCcHHHHHHH
Q 002040          616 RRVTYLVMDEADRMFDMGFEP--QITRIVQNIRPDRQTVLFSATFPRQVEILA  666 (976)
Q Consensus       616 ~~~~~vVlDEah~~~~~~f~~--~i~~il~~~~~~~q~i~~SAT~~~~~~~l~  666 (976)
                      ..+++||+||+-..++.++.+  .+..++...++...+|++.-.+|+.+..++
T Consensus        93 ~~~dllILDEi~~Ai~~gli~~~~v~~ll~~rp~~~evVlTGr~~p~~L~e~A  145 (157)
T d1g5ta_          93 PLLDMVVLDELTYMVAYDYLPLEEVISALNARPGHQTVIITGRGCHRDILDLA  145 (157)
T ss_dssp             TTCSEEEEETHHHHHHTTSSCHHHHHHHHHTSCTTCEEEEECSSCCHHHHHHC
T ss_pred             CccCEEeHHHHHHHHHcCCCCHHHHHHHHHhCCCCCEEEEECCCCCHHHHHhc
Confidence            458999999999888888654  567777777666766666666887765443

>d1fuka_ 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=90.10  E-value=0.43  Score=43.82  Aligned_cols=73  Identities=14%  Similarity=0.285  Sum_probs=53.0

Q ss_pred             CCeEEEEccCHHHHHHHHHHHHHHHhhcCcEEEEeeCCCChHHHHHHH---hc-CCeEEEeCchhHHHHHHhcCCccccc
Q 002040          540 GPVGLIMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQISEL---KR-GTEIVVCTPGRMIDILCTSGGKITNL  615 (976)
Q Consensus       540 ~~~vLIl~Ptr~La~Q~~~~~~~~~~~~~~~~~~~~gg~~~~~~~~~l---~~-~~~Iiv~Tp~~L~~~l~~~~~~~~~l  615 (976)
                      ..++||.|.++..+.+++..+..    .++.+..++|+.+..+....+   .. ...|+|||.     .+..    -.++
T Consensus        27 ~~k~iIF~~s~~~~~~l~~~L~~----~~~~~~~~~~~~~~~~r~~~l~~f~~~~~~iLv~Td-----v~~r----GiDi   93 (162)
T d1fuka_          27 VTQAVIFCNTRRKVEELTTKLRN----DKFTVSAIYSDLPQQERDTIMKEFRSGSSRILISTD-----LLAR----GIDV   93 (162)
T ss_dssp             CSCEEEEESSHHHHHHHHHHHHH----TTCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEEEG-----GGTT----TCCC
T ss_pred             CCcEEEEEEEEchHHHHHHHHhh----cCceEEEeccCCchhhHHHHHHHHhhcccceeeccc-----cccc----cccC
Confidence            45699999999999888776655    588999999998877664333   33 468999995     2222    2578


Q ss_pred             CCceEEEecC
Q 002040          616 RRVTYLVMDE  625 (976)
Q Consensus       616 ~~~~~vVlDE  625 (976)
                      ..+++||.=.
T Consensus        94 ~~v~~VI~~d  103 (162)
T d1fuka_          94 QQVSLVINYD  103 (162)
T ss_dssp             CSCSEEEESS
T ss_pred             CCceEEEEec
Confidence            8888888633

>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=90.04  E-value=0.38  Score=46.75  Aligned_cols=17  Identities=29%  Similarity=0.245  Sum_probs=14.6

Q ss_pred             CCEEEEcCCCCchHHHH
Q 002040          505 RDCIGVAKTGSGKTLAF  521 (976)
Q Consensus       505 ~d~i~~a~TGsGKT~~~  521 (976)
                      .++|+.||+|+|||+++
T Consensus        46 ~~lll~Gp~G~GKTtla   62 (231)
T d1iqpa2          46 PHLLFAGPPGVGKTTAA   62 (231)
T ss_dssp             CEEEEESCTTSSHHHHH
T ss_pred             CeEEEECCCCCcHHHHH
Confidence            46999999999999763

>d1e32a2 c.37.1.20 (A:201-458) Membrane fusion ATPase VCP/p97 {Mouse (Mus musculus) [TaxId: 10090]}

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: Membrane fusion ATPase VCP/p97
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=89.87  E-value=0.2  Score=50.04  Aligned_cols=16  Identities=38%  Similarity=0.513  Sum_probs=14.4

Q ss_pred             CCEEEEcCCCCchHHH
Q 002040          505 RDCIGVAKTGSGKTLA  520 (976)
Q Consensus       505 ~d~i~~a~TGsGKT~~  520 (976)
                      +.+|+.||+|+|||+.
T Consensus        39 ~giLL~GppGtGKT~l   54 (258)
T d1e32a2          39 RGILLYGPPGTGKTLI   54 (258)
T ss_dssp             CEEEEECCTTSSHHHH
T ss_pred             ceeEEecCCCCCchHH
Confidence            5799999999999975

>d1jbka_ c.37.1.20 (A:) ClpB, AAA+ modules {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: ClpB, AAA+ modules
species: Escherichia coli [TaxId: 562]

Probab=89.77  E-value=1.3  Score=41.60  Aligned_cols=120  Identities=14%  Similarity=0.145  Sum_probs=62.2

Q ss_pred             CCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHH-----HHHHHHHHHHHhhc---CcEEEEee
Q 002040          504 GRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELV-----QQIHSDIRKFAKVM---GVRCVPVY  575 (976)
Q Consensus       504 g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La-----~Q~~~~~~~~~~~~---~~~~~~~~  575 (976)
                      ..++|++|+.|.|||...--.+...+..+-+ ..-.+..++.+-+..-+|     -+|...++.+....   .-+++.++
T Consensus        43 k~n~lLvG~pGVGKTalv~~LA~ri~~~~vp-~~L~~~~i~~ld~~~LiAg~~~rG~~E~rl~~il~e~~~~~~~iILfI  121 (195)
T d1jbka_          43 KNNPVLIGEPGVGKTAIVEGLAQRIINGEVP-EGLKGRRVLALDMGALVAGAKYRGEFEERLKGVLNDLAKQEGNVILFI  121 (195)
T ss_dssp             SCEEEEECCTTSCHHHHHHHHHHHHHHTCSC-GGGTTCEEEEECHHHHHTTTCSHHHHHHHHHHHHHHHHHSTTTEEEEE
T ss_pred             CCCeEEEecCCcccHHHHHHHHHHHHhCCCC-HHHcCceEEEeeHHHHhccCCccHHHHHHHHHHHHHHhcCCCcEEEEc
Confidence            3589999999999997643333333332211 111244544444443332     25656565554332   21233221


Q ss_pred             -------------CCCChHHHH-HHHhcCC--eEEEeCchhHHHHHHhcCCcccccCCceEEEecCcc
Q 002040          576 -------------GGSGVAQQI-SELKRGT--EIVVCTPGRMIDILCTSGGKITNLRRVTYLVMDEAD  627 (976)
Q Consensus       576 -------------gg~~~~~~~-~~l~~~~--~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVlDEah  627 (976)
                                   |+......+ ..|..|.  -|.-|||..+..++....   ...+.|..|.|+|-.
T Consensus       122 Deih~l~~~g~~~g~~d~~~~Lkp~L~rg~l~~IgatT~eey~~~~e~d~---aL~rrF~~I~V~Ep~  186 (195)
T d1jbka_         122 DELHTMVGAGKADGAMDAGNMLKPALARGELHCVGATTLDEYRQYIEKDA---ALERRFQKVFVAEPS  186 (195)
T ss_dssp             ETGGGGTT------CCCCHHHHHHHHHTTSCCEEEEECHHHHHHHTTTCH---HHHTTEEEEECCCCC
T ss_pred             chHHHHhcCCCCCCcccHHHHHHHHHhCCCceEEecCCHHHHHHHHHcCH---HHHhcCCEeecCCCC
Confidence                         122222222 2333442  455688888877765432   235678889998865

>d1p9ra_ c.37.1.11 (A:) Extracellular secretion NTPase EpsE {Vibrio cholerae [TaxId: 666]}

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: Extracellular secretion NTPase EpsE
species: Vibrio cholerae [TaxId: 666]

Probab=89.72  E-value=0.16  Score=54.46  Aligned_cols=38  Identities=16%  Similarity=0.264  Sum_probs=26.5

Q ss_pred             HHHHHHHHHHhcCCC--EEEEcCCCCchHHHHHHHHHHHHh
Q 002040          492 PIQAQALPVIMSGRD--CIGVAKTGSGKTLAFVLPMLRHIK  530 (976)
Q Consensus       492 ~~Q~~~i~~il~g~d--~i~~a~TGsGKT~~~~l~il~~l~  530 (976)
                      +.|.+.|..++....  +|+.||||||||++ +..++..+.
T Consensus       144 ~~~~~~l~~l~~~~~GliLvtGpTGSGKSTT-l~~~l~~~~  183 (401)
T d1p9ra_         144 AHNHDNFRRLIKRPHGIILVTGPTGSGKSTT-LYAGLQELN  183 (401)
T ss_dssp             HHHHHHHHHHHTSSSEEEEEECSTTSCHHHH-HHHHHHHHC
T ss_pred             HHHHHHHHHHHhhhhceEEEEcCCCCCccHH-HHHHhhhhc
Confidence            556666666665543  67789999999986 455666654

>d1tf7a2 c.37.1.11 (A:256-497) Circadian clock protein KaiC {Synechococcus sp. strain PCC 7942 (Anacystis nidulans R2) [TaxId: 1140]}

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: Circadian clock protein KaiC
species: Synechococcus sp. strain PCC 7942 (Anacystis nidulans R2) [TaxId: 1140]

Probab=89.14  E-value=0.61  Score=45.45  Aligned_cols=37  Identities=19%  Similarity=0.164  Sum_probs=24.7

Q ss_pred             CCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEcc
Q 002040          504 GRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAP  548 (976)
Q Consensus       504 g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~P  548 (976)
                      |.-+++.|++|+|||+.++-.+.+. ..       .+..+++++-
T Consensus        26 gsl~li~G~pGsGKT~l~~qia~~~-~~-------~~~~~~~is~   62 (242)
T d1tf7a2          26 DSIILATGATGTGKTLLVSRFVENA-CA-------NKERAILFAY   62 (242)
T ss_dssp             SCEEEEEECTTSSHHHHHHHHHHHH-HT-------TTCCEEEEES
T ss_pred             CeEEEEEeCCCCCHHHHHHHHHHHH-HH-------hccccceeec
Confidence            4568899999999998655444443 32       2455677664

>d1oywa3 c.37.1.19 (A:207-406) 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=88.75  E-value=0.65  Score=44.18  Aligned_cols=71  Identities=21%  Similarity=0.324  Sum_probs=50.7

Q ss_pred             CCeEEEEccCHHHHHHHHHHHHHHHhhcCcEEEEeeCCCChHHHHH---HHhc-CCeEEEeCchhHHHHHHhcCCccccc
Q 002040          540 GPVGLIMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQIS---ELKR-GTEIVVCTPGRMIDILCTSGGKITNL  615 (976)
Q Consensus       540 ~~~vLIl~Ptr~La~Q~~~~~~~~~~~~~~~~~~~~gg~~~~~~~~---~l~~-~~~Iiv~Tp~~L~~~l~~~~~~~~~l  615 (976)
                      +.++||.|+|+..+..++..+..    .++.+..++|+........   .+.. ...|+|+|..     +..    -.++
T Consensus        30 ~~~~IIF~~t~~~~~~l~~~l~~----~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~ilvaTd~-----~~~----GiD~   96 (200)
T d1oywa3          30 GKSGIIYCNSRAKVEDTAARLQS----KGISAAAYHAGLENNVRADVQEKFQRDDLQIVVATVA-----FGM----GINK   96 (200)
T ss_dssp             TCCEEEECSSHHHHHHHHHHHHH----TTCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEECTT-----SCT----TTCC
T ss_pred             CCCEEEEEeeehhhHHhhhhhcc----CCceeEEecCCCcHHHHHHHHHHHhcccceEEEecch-----hhh----ccCC
Confidence            45789999999988877665554    6889999999988766543   3333 4689999942     222    2577


Q ss_pred             CCceEEEe
Q 002040          616 RRVTYLVM  623 (976)
Q Consensus       616 ~~~~~vVl  623 (976)
                      .++.+||.
T Consensus        97 p~v~~VI~  104 (200)
T d1oywa3          97 PNVRFVVH  104 (200)
T ss_dssp             TTCCEEEE
T ss_pred             CCCCEEEE
Confidence            78888773

>d1t5ia_ 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=87.57  E-value=0.44  Score=44.00  Aligned_cols=73  Identities=12%  Similarity=0.115  Sum_probs=50.7

Q ss_pred             CCeEEEEccCHHHHHHHHHHHHHHHhhcCcEEEEeeCCCChHHHHHH---Hhc-CCeEEEeCchhHHHHHHhcCCccccc
Q 002040          540 GPVGLIMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQISE---LKR-GTEIVVCTPGRMIDILCTSGGKITNL  615 (976)
Q Consensus       540 ~~~vLIl~Ptr~La~Q~~~~~~~~~~~~~~~~~~~~gg~~~~~~~~~---l~~-~~~Iiv~Tp~~L~~~l~~~~~~~~~l  615 (976)
                      +.++||.|+++.-+..++..+..    .|+.+..++|+.+..+....   +.. ...|+|||.-     +.    .-.++
T Consensus        27 ~~k~iIF~~~~~~~~~l~~~L~~----~~~~~~~ihg~~~~~~r~~~l~~F~~g~~~iLv~T~~-----~~----~Gid~   93 (168)
T d1t5ia_          27 FNQVVIFVKSVQRCIALAQLLVE----QNFPAIAIHRGMPQEERLSRYQQFKDFQRRILVATNL-----FG----RGMDI   93 (168)
T ss_dssp             CSSEEEECSSHHHHHHHHHHHHH----TTCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEESSC-----CS----TTCCG
T ss_pred             CCeEEEEEeeeecchhhhhhhcc----ccccccccccccchhhhhhhhhhhccccceeeecccc-----cc----chhhc
Confidence            45799999999888877665554    68889999999887766433   333 4689999942     11    12566


Q ss_pred             CCceEEEecC
Q 002040          616 RRVTYLVMDE  625 (976)
Q Consensus       616 ~~~~~vVlDE  625 (976)
                      ..+.+||+=.
T Consensus        94 ~~~~~vi~~~  103 (168)
T d1t5ia_          94 ERVNIAFNYD  103 (168)
T ss_dssp             GGCSEEEESS
T ss_pred             ccchhhhhhh
Confidence            6777776543

>d2j0sa2 c.37.1.19 (A:244-411) 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=87.43  E-value=1.8  Score=39.67  Aligned_cols=90  Identities=10%  Similarity=0.165  Sum_probs=60.5

Q ss_pred             cCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHHHHHHHHHHHHHhhcCcEEEEeeCCCChHHHHHH---H
Q 002040          511 AKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQISE---L  587 (976)
Q Consensus       511 a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La~Q~~~~~~~~~~~~~~~~~~~~gg~~~~~~~~~---l  587 (976)
                      -+....|..+ +..++...         .+.++||.|+++.-|..++..+..    .++.+..++|+.+..+....   +
T Consensus        15 v~~~~~K~~~-L~~ll~~~---------~~~k~iiF~~~~~~~~~~~~~l~~----~~~~~~~~~~~~~~~~r~~~~~~f   80 (168)
T d2j0sa2          15 VEREEWKFDT-LCDLYDTL---------TITQAVIFCNTKRKVDWLTEKMRE----ANFTVSSMHGDMPQKERESIMKEF   80 (168)
T ss_dssp             ESSTTHHHHH-HHHHHHHH---------TSSEEEEECSSHHHHHHHHHHHHH----TTCCCEEECTTSCHHHHHHHHHHH
T ss_pred             ecChHHHHHH-HHHHHHhC---------CCCceEEEeeeHHHHHHHHHHhhh----cccchhhhhhhhhHHHHHHHHHHH
Confidence            3444456543 44455432         245799999999999877666654    67888999999887766433   3


Q ss_pred             hc-CCeEEEeCchhHHHHHHhcCCcccccCCceEEEe
Q 002040          588 KR-GTEIVVCTPGRMIDILCTSGGKITNLRRVTYLVM  623 (976)
Q Consensus       588 ~~-~~~Iiv~Tp~~L~~~l~~~~~~~~~l~~~~~vVl  623 (976)
                      +. ...|+|||.     .+..    -.++..+++||.
T Consensus        81 k~g~~~iLv~Td-----~~~r----GiDi~~v~~VIn  108 (168)
T d2j0sa2          81 RSGASRVLISTD-----VWAR----GLDVPQVSLIIN  108 (168)
T ss_dssp             HHTSSCEEEECG-----GGSS----SCCCTTEEEEEE
T ss_pred             hcCCccEEeccc-----hhcc----cccccCcceEEE
Confidence            33 469999994     3322    267888888774

>d1s2ma2 c.37.1.19 (A:252-422) 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=86.17  E-value=0.68  Score=42.73  Aligned_cols=74  Identities=12%  Similarity=0.202  Sum_probs=52.5

Q ss_pred             CCeEEEEccCHHHHHHHHHHHHHHHhhcCcEEEEeeCCCChHHHHHH---Hhc-CCeEEEeCchhHHHHHHhcCCccccc
Q 002040          540 GPVGLIMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQISE---LKR-GTEIVVCTPGRMIDILCTSGGKITNL  615 (976)
Q Consensus       540 ~~~vLIl~Ptr~La~Q~~~~~~~~~~~~~~~~~~~~gg~~~~~~~~~---l~~-~~~Iiv~Tp~~L~~~l~~~~~~~~~l  615 (976)
                      +.++||.|+|+.-|..++..+..    .|+.+..++|+.+..+....   +.. ...|+|||.-     +.    .-.++
T Consensus        32 ~~k~iVF~~~~~~~~~l~~~L~~----~g~~~~~~h~~~~~~~r~~~~~~f~~~~~~ilv~Td~-----~~----~Gid~   98 (171)
T d1s2ma2          32 INQAIIFCNSTNRVELLAKKITD----LGYSCYYSHARMKQQERNKVFHEFRQGKVRTLVCSDL-----LT----RGIDI   98 (171)
T ss_dssp             CSEEEEECSSHHHHHHHHHHHHH----HTCCEEEECTTSCHHHHHHHHHHHHTTSSSEEEESSC-----SS----SSCCC
T ss_pred             CCceEEEEeeeehhhHhHHhhhc----ccccccccccccchhhhhhhhhhcccCccccccchhH-----hh----hcccc
Confidence            45899999999888777666654    58899999999887655433   333 5689999953     22    22678


Q ss_pred             CCceEEEecCc
Q 002040          616 RRVTYLVMDEA  626 (976)
Q Consensus       616 ~~~~~vVlDEa  626 (976)
                      ..+.+||.=.+
T Consensus        99 ~~v~~VI~~d~  109 (171)
T d1s2ma2          99 QAVNVVINFDF  109 (171)
T ss_dssp             TTEEEEEESSC
T ss_pred             ceeEEEEecCC
Confidence            88888885433

>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=85.39  E-value=0.41  Score=44.12  Aligned_cols=26  Identities=23%  Similarity=0.256  Sum_probs=20.2

Q ss_pred             CCEEEEcCCCCchHHHHHHHHHHHHhc
Q 002040          505 RDCIGVAKTGSGKTLAFVLPMLRHIKD  531 (976)
Q Consensus       505 ~d~i~~a~TGsGKT~~~~l~il~~l~~  531 (976)
                      ++++|.|++|+|||+. +..++..+..
T Consensus         2 k~v~ItG~~GtGKTtl-~~~i~~~l~~   27 (189)
T d2i3ba1           2 RHVFLTGPPGVGKTTL-IHKASEVLKS   27 (189)
T ss_dssp             CCEEEESCCSSCHHHH-HHHHHHHHHH
T ss_pred             cEEEEECCCCCcHHHH-HHHHHHHHHH
Confidence            6799999999999985 5556666654

>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=83.86  E-value=0.45  Score=49.88  Aligned_cols=17  Identities=41%  Similarity=0.528  Sum_probs=15.1

Q ss_pred             CCEEEEcCCCCchHHHH
Q 002040          505 RDCIGVAKTGSGKTLAF  521 (976)
Q Consensus       505 ~d~i~~a~TGsGKT~~~  521 (976)
                      .++|++||||+|||..+
T Consensus        69 ~niLfiGPTGvGKTElA   85 (364)
T d1um8a_          69 SNILLIGPTGSGKTLMA   85 (364)
T ss_dssp             CCEEEECCTTSSHHHHH
T ss_pred             cceeeeCCCCccHHHHH
Confidence            57999999999999764

>d1w36b1 c.37.1.19 (B:1-485) Exodeoxyribonuclease V beta chain (RecB), N-terminal 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: Exodeoxyribonuclease V beta chain (RecB), N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=83.75  E-value=1.2  Score=48.13  Aligned_cols=61  Identities=21%  Similarity=0.177  Sum_probs=43.4

Q ss_pred             CCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCC---C-CCCeEEEEccCHHHHHHHHHHHHHHHh
Q 002040          505 RDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAA---G-DGPVGLIMAPTRELVQQIHSDIRKFAK  565 (976)
Q Consensus       505 ~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~---~-~~~~vLIl~Ptr~La~Q~~~~~~~~~~  565 (976)
                      ..+||.|.-|||||.+.+--++..|........   + ..-.+|+|+=|+..|..+.+.+...+.
T Consensus        17 g~~lv~A~AGsGKT~~l~~r~~~ll~~~~~~~~~~~~~~~~~IL~lTFT~kAA~Emk~RI~~~L~   81 (485)
T d1w36b1          17 GERLIEASAGTGKTFTIAALYLRLLLGLGGSAAFPRPLTVEELLVVTFTEAATAELRGRIRSNIH   81 (485)
T ss_dssp             SCEEEECCTTSCHHHHHHHHHHHHHTTCSSSSSCSSCCCGGGEEEEESCHHHHHHHHHHHHHHHH
T ss_pred             CCeEEEEcCchHHHHHHHHHHHHHHhhCcccccccCCCCcccEeEeccHHHHHHHHHHHHHHHHH
Confidence            468999999999999877777777665321111   1 112589999999999998887766543

>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=82.71  E-value=0.24  Score=53.50  Aligned_cols=19  Identities=26%  Similarity=0.361  Sum_probs=16.2

Q ss_pred             cCCCEEEEcCCCCchHHHH
Q 002040          503 SGRDCIGVAKTGSGKTLAF  521 (976)
Q Consensus       503 ~g~d~i~~a~TGsGKT~~~  521 (976)
                      ...|+|++||||+|||+.+
T Consensus        48 ~ksNILliGPTGvGKTlLA   66 (443)
T d1g41a_          48 TPKNILMIGPTGVGKTEIA   66 (443)
T ss_dssp             CCCCEEEECCTTSSHHHHH
T ss_pred             ccccEEEECCCCCCHHHHH
Confidence            3569999999999999853

>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=82.21  E-value=1.5  Score=42.32  Aligned_cols=71  Identities=14%  Similarity=0.274  Sum_probs=54.0

Q ss_pred             CCcEEEEecCHHHHHHHHHHHHHC----CCCceeccCCCCHHHHHHHHHHhccCCccEEEecC------cccccCCCCCC
Q 002040          714 KGKILIFVHSQEKCDALFRDLLKH----GYPCLSLHGAKDQTDRESTISDFKSNVCNLLIATS------VAARGLDVKEL  783 (976)
Q Consensus       714 ~~kvLIF~~s~~~~~~l~~~L~~~----~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLVaT~------v~~~GlDi~~v  783 (976)
                      ...+||+|++.+-+..++..+...    ++.+..++|+.+.......+.   . ...|||+|+      +....+++.++
T Consensus        85 ~~~~lil~PtreLa~Qi~~~~~~l~~~~~i~~~~~~g~~~~~~~~~~l~---~-~~~Ilv~TPgrl~~~~~~~~~~~~~l  160 (222)
T d2j0sa1          85 ETQALILAPTRELAVQIQKGLLALGDYMNVQCHACIGGTNVGEDIRKLD---Y-GQHVVAGTPGRVFDMIRRRSLRTRAI  160 (222)
T ss_dssp             SCCEEEECSSHHHHHHHHHHHHHHTTTTTCCEEEECTTSCHHHHHHHHH---H-CCSEEEECHHHHHHHHHTTSSCCTTC
T ss_pred             CceeEEecchHHHHHHHHHHHHHHhCccceeEEEEeecccchhhHHHhc---c-CCeEEeCCCCcHHhcccccccccccc
Confidence            347999999999999998887654    567888999988766555443   2 368999995      22466788889


Q ss_pred             cEEEE
Q 002040          784 ELVIN  788 (976)
Q Consensus       784 ~~VI~  788 (976)
                      .++|.
T Consensus       161 ~~lVl  165 (222)
T d2j0sa1         161 KMLVL  165 (222)
T ss_dssp             CEEEE
T ss_pred             eeeee
Confidence            99885

>d1w44a_ c.37.1.11 (A:) NTPase P4 {Bacteriophage phi-12 [TaxId: 161736]}

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: NTPase P4
species: Bacteriophage phi-12 [TaxId: 161736]

Probab=82.17  E-value=0.29  Score=50.20  Aligned_cols=16  Identities=38%  Similarity=0.248  Sum_probs=12.5

Q ss_pred             CEEEEcCCCCchHHHH
Q 002040          506 DCIGVAKTGSGKTLAF  521 (976)
Q Consensus       506 d~i~~a~TGsGKT~~~  521 (976)
                      .+|+.||+|+|||+.+
T Consensus       125 ~~l~~G~pG~GKT~la  140 (321)
T d1w44a_         125 MVIVTGKGNSGKTPLV  140 (321)
T ss_dssp             EEEEECSSSSCHHHHH
T ss_pred             eEEEECCCCccHHHHH
Confidence            3455799999999753

>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=82.06  E-value=3.9  Score=38.57  Aligned_cols=69  Identities=13%  Similarity=0.170  Sum_probs=53.1

Q ss_pred             CcEEEEecCHHHHHHHHHHHHHC----CCCceeccCCCCHHHHHHHHHHhccCCccEEEecC-----cc-cccCCCCCCc
Q 002040          715 GKILIFVHSQEKCDALFRDLLKH----GYPCLSLHGAKDQTDRESTISDFKSNVCNLLIATS-----VA-ARGLDVKELE  784 (976)
Q Consensus       715 ~kvLIF~~s~~~~~~l~~~L~~~----~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLVaT~-----v~-~~GlDi~~v~  784 (976)
                      ..+||.|++...|..+...+...    +..+..++|+.+.......+.     ..+|||+|+     .+ ...+++.++.
T Consensus        73 ~~~lil~pt~~l~~q~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~l~-----~~~IlV~TP~~l~~~l~~~~~~~~~l~  147 (208)
T d1hv8a1          73 IEAIILTPTRELAIQVADEIESLKGNKNLKIAKIYGGKAIYPQIKALK-----NANIVVGTPGRILDHINRGTLNLKNVK  147 (208)
T ss_dssp             CCEEEECSCHHHHHHHHHHHHHHHCSSCCCEEEECTTSCHHHHHHHHH-----TCSEEEECHHHHHHHHHTTCSCTTSCC
T ss_pred             cceEEEeeccccchhhhhhhhhhcccCCeEEEEeeCCCChHHHHHhcC-----CCCEEEEChHHHHHHHHcCCCCcccCc
Confidence            47999999999999988777653    678889999988776655442     368999995     22 3467888998


Q ss_pred             EEEE
Q 002040          785 LVIN  788 (976)
Q Consensus       785 ~VI~  788 (976)
                      +||.
T Consensus       148 ~lVi  151 (208)
T d1hv8a1         148 YFIL  151 (208)
T ss_dssp             EEEE
T ss_pred             EEEE
Confidence            8885

>d1yksa2 c.37.1.14 (A:325-623) 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=81.92  E-value=0.69  Score=46.87  Aligned_cols=55  Identities=11%  Similarity=0.109  Sum_probs=38.3

Q ss_pred             CCeEEEEccCHHHHHHHHHHHHHHHhhcCcEEEEeeCCCChHHHHHHHhcCCeEEEeCc
Q 002040          540 GPVGLIMAPTRELVQQIHSDIRKFAKVMGVRCVPVYGGSGVAQQISELKRGTEIVVCTP  598 (976)
Q Consensus       540 ~~~vLIl~Ptr~La~Q~~~~~~~~~~~~~~~~~~~~gg~~~~~~~~~l~~~~~Iiv~Tp  598 (976)
                      +.++||+||+..-+..++..+.+    .|..|++++|.....++-.......+|||+|.
T Consensus        36 ~g~~~~F~~s~~~~~~~a~~L~~----~g~~V~~l~~~~~~~e~~~~~~~~~~~~~~t~   90 (299)
T d1yksa2          36 KRPTAWFLPSIRAANVMAASLRK----AGKSVVVLNRKTFEREYPTIKQKKPDFILATD   90 (299)
T ss_dssp             CSCEEEECSCHHHHHHHHHHHHH----TTCCEEECCSSSCC--------CCCSEEEESS
T ss_pred             CCCEEEEeCCHHHHHHHHHHHHh----cCCeEEEEcCcCcHhHHhhhhcCCcCEEEEec
Confidence            45689999999998888777766    57889999998776665443344568999994

>d1e9ra_ c.37.1.11 (A:) Bacterial conjugative coupling protein TrwB {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: RecA protein-like (ATPase-domain)
domain: Bacterial conjugative coupling protein TrwB
species: Escherichia coli [TaxId: 562]

Probab=81.69  E-value=0.65  Score=49.79  Aligned_cols=42  Identities=19%  Similarity=0.267  Sum_probs=29.4

Q ss_pred             CCCEEEEcCCCCchHHHHHHHHHHHHhcCCCCCCCCCCeEEEEccCHHHH
Q 002040          504 GRDCIGVAKTGSGKTLAFVLPMLRHIKDQPPVAAGDGPVGLIMAPTRELV  553 (976)
Q Consensus       504 g~d~i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~~~~~vLIl~Ptr~La  553 (976)
                      .++++|+|+||||||.++ ..++..+...       +..+||+=|.-+++
T Consensus        50 ~~H~~I~G~tGsGKT~~l-~~li~~~~~~-------g~~~iiiD~kge~~   91 (433)
T d1e9ra_          50 PRHLLVNGATGTGKSVLL-RELAYTGLLR-------GDRMVIVDPNGDML   91 (433)
T ss_dssp             GGCEEEEECTTSSHHHHH-HHHHHHHHHT-------TCEEEEEEETTHHH
T ss_pred             cceEEEEeCCCCcHHHHH-HHHHHHHHhC-------CCCEEEEeCChhHH
Confidence            468999999999999764 4444444432       45678888876653

>d2eyqa2 c.37.1.19 (A:349-465) 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=80.70  E-value=0.95  Score=38.85  Aligned_cols=74  Identities=15%  Similarity=0.093  Sum_probs=55.3

Q ss_pred             HHHHHHHHHhhhcCCcEEEEecCHHHHHHHHHHHHHCCCCceeccCCCCHHHHHHHHHHhccCCccEEEecCcccccCCC
Q 002040          701 FLRLLELLGEWYEKGKILIFVHSQEKCDALFRDLLKHGYPCLSLHGAKDQTDRESTISDFKSNVCNLLIATSVAARGLDV  780 (976)
Q Consensus       701 ~~~l~~~l~~~~~~~kvLIF~~s~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLVaT~v~~~GlDi  780 (976)
                      +..|..+|..  ..++|||+|.+...++.|...|...++.+..+.+..          .|..+.  |.|+...+..|+-+
T Consensus        23 ~~~L~~~i~~--~~~~Vli~a~s~g~~erl~e~L~~~~i~~~~~~~~~----------~~~~~~--~~i~~~~l~~GF~~   88 (117)
T d2eyqa2          23 LDALRKFLET--FDGPVVFSVESEGRREALGELLARIKIAPQRIMRLD----------EASDRG--RYLMIGAAEHGFVD   88 (117)
T ss_dssp             THHHHHHHTT--CCSCCCEEESSHHHHHHHHHHHGGGTCCCEECSSGG----------GCCTTC--CEEEECCCCSCEEE
T ss_pred             HHHHHHHHHh--CCCeEEEEECCccHHHHHHHHHHHcCCCceEecChh----------hhcCce--EEEEEecCcccccc
Confidence            4555555543  246899999999999999999999999887665422          244444  45556778999999


Q ss_pred             CCCcEEEE
Q 002040          781 KELELVIN  788 (976)
Q Consensus       781 ~~v~~VI~  788 (976)
                      +...++|+
T Consensus        89 ~~~~l~vI   96 (117)
T d2eyqa2          89 TVRNLALI   96 (117)
T ss_dssp             TTTTEEEE
T ss_pred             CCCCEEEE
Confidence            99988886

>d1kaga_ c.37.1.2 (A:) Shikimate kinase (AroK) {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: Shikimate kinase (AroK)
domain: Shikimate kinase (AroK)
species: Escherichia coli [TaxId: 562]

Probab=80.68  E-value=0.43  Score=42.91  Aligned_cols=19  Identities=26%  Similarity=0.242  Sum_probs=16.0

Q ss_pred             CCCEEEEcCCCCchHHHHH
Q 002040          504 GRDCIGVAKTGSGKTLAFV  522 (976)
Q Consensus       504 g~d~i~~a~TGsGKT~~~~  522 (976)
                      .++++++|++|||||+++-
T Consensus         2 ~k~I~l~G~~GsGKSTvak   20 (169)
T d1kaga_           2 KRNIFLVGPMGAGKSTIGR   20 (169)
T ss_dssp             CCCEEEECCTTSCHHHHHH
T ss_pred             CCeEEEECCCCCCHHHHHH
Confidence            3679999999999998644

>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=80.26  E-value=0.77  Score=46.91  Aligned_cols=19  Identities=26%  Similarity=0.361  Sum_probs=16.4

Q ss_pred             cCCCEEEEcCCCCchHHHH
Q 002040          503 SGRDCIGVAKTGSGKTLAF  521 (976)
Q Consensus       503 ~g~d~i~~a~TGsGKT~~~  521 (976)
                      ..+.+|++||||+|||+.+
T Consensus        48 ~~~~iLl~GPpG~GKT~lA   66 (309)
T d1ofha_          48 TPKNILMIGPTGVGKTEIA   66 (309)
T ss_dssp             CCCCEEEECCTTSSHHHHH
T ss_pred             CCceEEEECCCCCCHHHHH
Confidence            4578999999999999864