Citrus Sinensis ID: 039716

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340-------350-------360-------370-------380-------390-------400-------410-------420-------430-------440-------450-------460-------470-------480-------490-------500-------510-------520-------530-------540-------550-------560-------570-------580-------590-------600-------610-------620-------630-------640-------650-------660-------670-------680-------690-------700-------710-------720-------730-------740-------750-------760-------770-------780-------790-------800-------810-------820-------830-------840-------850-------860-------870-------880-------890-------900-------910-------920-------930-------940-------950-------960-------970-------980-------990------1000--
Protein Sequence
MVCNMETDLIEDMDIEGLPSMWPEDIGSDKQFNVERPGGGQDMLEEVTIPEDQTIVDFKRLLELTNYTDKGSSQMAYLVKHWEYRQSNAVRLLREELDNLSRQRQESELKKLEILEEHRFEEEGYGGDKRPISIMDELSDMWKDVCPRKNDVVFQSKRVEVDAEYDTVEYWKQRALDLEKMLEASGQREQALMEKLNESVTNLEKQSSPVEELSQILKRADNFLHFVLQNAPVVMGHQDKELRYRFIYNHFPSLHEEDILGKTDVEIFSGAGVKESQDFKREVLEKGLPAKREITFETELFGSKTFLIYVEPVFSKSGETIGVNYMGMDVTDQVRKREKMAKLREEIAVQKAKETELNKTIHITEETMRAKQMLATMSHEIRSPLTGVVSMAEILSNTKLDREQRQLLGVMISSGDLVLQLINDILDLSKVESGVMKLEAAKFRPREVVKHVLQTAAASLQKILMLEGDIADDVPIEVIGDVLRIRQILTNLISNAIKFTPEGKVGIKLYVVPEPPFAKEGLKQKSKAYQSATDAVKEEKHQPKSQTASDQNGFHDKKHGEGYQDHKHDDDPGTPVSHGNSMDEDLEATVWIRCDVYDTGIGIPENALPTLFRKYMQVSADHARKYGGTGLGLAICKQLVELMGGRLTVTSKVHCGSTFTFILPYQVSPIEENSDDPDDLSDMADQDSVTDDVTAGFFQFQPRTLGSLFSSNGTSRSKKLLPNSIGFASAHKVNGFSETSYSFPSNNRQKETAPLEDACSVAEVAETLSEPESSFSHSPEPENETEVSRGKQCHVETTSWFQNPATESTSHSEANREMIQTSKTNEPQKICEMQEKPDRISQSPSSSSAEVPETKPKPKPKILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQYFP
Secondary Structure (PSIPRED)
cccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHcccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcHHHHcccccccccccHHHHHHHHHHHHccccccccccccHHccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccEEEEEEccccEEEEcccccccccHHHccccccccccccccHHHHHHHHHHHHccccccEEEEEEEEcccEEEEEEEEEEEEcccccEEEEEEEEEHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccHHHHccHHHHHHHHHHHccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccHHHHHHHHHHHHHHHHHHHHHHccccccccccHHccHHHHHHHHHHHHHHHccccccccEEEEEEEEEcccccccccccccccHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEEEEEEEccccccccccccccccccccccccccccccccccHHHHHHHHHHHcccEEEEEEEcccccEEEEEEEccccccccccccccccccccccccccccccccHHHHHHHHHHccccccccccHHccccccccHHHHcccccccccccccccccccccccccccHHHHHHHHHHccccccccccccccccHHHHHHcccccccccEEEEcccccHHHHHHHHHHHHHcccccccHHHHHcccccccccccccccccccccccccccccEEEEcccHHHHHHHHHHHHHcccEEEEEccHHHHHHHHHcccccEEEEccccccccHHHHHHHHHHcccccccHHHHHHHHcccccccccccccccccEEEEcccccHHHHHHHHHccccccccccccHHHHHHHHHHHcc
Secondary Structure Prediction (SSPRO)
ccccccccccccccEEEcccccccccccccccccccccccHHHHHEEEEcccccEEcHHHHHHHHcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccHHHccccccccccccccccHHccccccccccccccccccEcccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcHHHHHHHHHHHHHHHHHHHHHHccccEEEEEccccEEEEEcHHHccccHHHHHcccHHHHcccccHHHHHHHHHHHHHcccccEEEEEEEcccccEEEEEEEEEEEccccccEEEEEEEEEcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccHHHHHHHHHHHHcccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccEEEEEccccHHHHHHHHHHHHHHHHHcccEEEEEEccccccEEEccHHHHHHHHHHHHHccEEEccccEEEEEEEEEEcccccccccccccEcccccccccccccEEEEEEEEcccccccHHHHHHHHHHHccccccccccccccccccccccEEEEEEEEEcccccccHHHHcHccccccEccccccccccccHHHHHHHHHHHHHHccEEEEEEcccccEEEEEEEEcccccccccccccccccccccEEEEcccHHHHHHHHHHHHcccEEEEcccHHHHHHHHHHHHHHHccccccEEEEEcccccccHHHHHHHHHccccHccccHHHccccccHccccccHHcccHHHHHHHHcccHHHHcccccHHHHHHHHHHHHccccccccHHHHHccccccccccccccccccccccHHHccccEEEEEEccHHHHHHHHHHHHHccccEEEcccHHHHHHHHccccccEEEEEcccccccHHHHHHHHHHHHHHccHHHHHHccccccccccccccccccccEEEEEHHHHHHcHHHHHHccccccccccccHHHHHHHHHHHcc
Coil and Loop (DISEMBL)
mvcnmetdliedmdieglpsmwpedigsdkqfnverpgggqdmleevtipedqtIVDFKRLLELtnytdkgssQMAYLVKHWEYRQSNAVRLLREELDNLSRQRQESELKKLEILEehrfeeegyggdkrpisIMDELSDMwkdvcprkndvvfqskrvevdaeyDTVEYWKQRALDLEKMLEASGQREQALMEKLNESVtnlekqsspvEELSQILKRADNFLHFvlqnapvvmghqdkeLRYRFIYNhfpslheedilgktdveifsgagvkesQDFKREVLEKglpakreitFETELFGSKTFLIYvepvfsksgetigvnymgmdvtdQVRKREKMAKLREEIAVQKAKETELNKTIHITEETMRAKQMLATMsheirspltgVVSMAEILSNTKLDREQRQLLGVMISSGDLVLQLINDILDLSKVESGVMKleaakfrprEVVKHVLQTAAASLQKILMLEgdiaddvpieVIGDVLRIRQILTNLISNaikftpegkvgiklyvvpeppfakeglkQKSKAYQSATDAVkeekhqpksqtasdqngfhdkkhgegyqdhkhdddpgtpvshgnsmdedlEATVWIRCdvydtgigipenalPTLFRKYMQVSADHARKYGGTGLGLAICKQLVELMggrltvtskvhcgstftfilpyqvspieensddpddlsdmadqdsvtddvtagffqfqprtlgslfssngtsrskkllpnsigfasahkvngfsetsysfpsnnrqketapledacSVAEVAEtlsepessfshspepenetevsrgkqchvettswfqnpatestshsEANREMIQtsktnepqkicemqekpdrisqspssssaevpetkpkpkpkillveDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDAAAEAGieqampssgssnhfkriPIIAMTANALSESAEECFAngmdsfvskpVTFQKLKECLEQYFP
Flexible Loop (DISEMBL)
MVCNMETDLIEDMDIEGLPSMWPEDIGSDKQFNVERPGGGQDMLEEVTIPEDQTIVDFKRLLELTNYTDKGSSQMAYLVKHWEYRQSNAVRLLREELDNLsrqrqeselkkleileehrfeeegyggdkrpISIMDELSDMWKDVCPrkndvvfqskrvevdaeydtVEYWKQRALDLEKMLEASGQREQALMEKLNESVTNLEKQSSPVEELSQILKRADNFLHFVLQNAPVVMGHQDKELRYRFIYNHFPSLHEEDILGKTDVEIFSGagvkesqdfkREVLEkglpakreitfetelfgsktfLIYVEPVfsksgetigvnymgmdvtDQVRKREKMAKLREEIAvqkaketelnktihiteETMRAKQMLATMSHEIRSPLTGVVSMAEILSNTKLDREQRQLLGVMISSGDLVLQLINDILDLSKVESGVMKLEaakfrprevVKHVLQTAAASLQKILMLEGDIADDVPIEVIGDVLRIRQILTNLISNAIKFTPEGKVGIKLYVVPEPPFAKEGLKQKSKAYQSATDAVkeekhqpksqtasdqngfhDKKHGEGYQDHKHDDDPGTPVSHGNSMDEDLEATVWIRCDVYDTGIGIPENALPTLFRKYMQVSADHARKYGGTGLGLAICKQLVELMGGRLTVTSKVHCGSTFTFILPYQVSPIEENSDDPDDLSDMADQDSVTDDVTAGFFQFQPRTLGSLFSSNGTSRSKKLLPNSIGFASAHKVNGFSETSYSFPSNNRQKETAPLEDACSVAEVAETLSepessfshspepenetevsrgKQCHvettswfqnpatestshseaNREMIqtsktnepqkICEMqekpdrisqspssssaevpetkpkpkpkillveDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQYFP
Low Complexity Region (SEG)
MVCNMETDLIEDMDIEGLPSMWPEDIGSDKQFNVERPGGGQDMLEEVTIPEDQTIVDFKRLLELTNYTDKGSSQMAYLVKHWEYRQSNAVRLLREELDNLSRQRQeselkkleileehrfeeeGYGGDKRPISIMDELSDMWKDVCPRKNDVVFQSKRVEVDAEYDTVEYWKQRALDLEKMLEASGQREQALMEKLNESVTNLEKQSSPVEELSQILKRADNFLHFVLQNAPVVMGHQDKELRYRFIYNHFPSLHEEDILGKTDVEIFSGAGVKESQDFKREVLEKGLPAKREITFETELFGSKTFLIYVEPVFSKSGETIGVNYMGMDVTDQVRKREKMAKLREEIAVQKAKETELNKTIHITEETMRAKQMLATMSHEIRSPLTGVVSMAEILSNTKLDREQRQLLGVMISSGDLVLQLINDILDLSKVESGVMKLEAAKFRPREVVKHVLQTAAASLQKILMLEGDIADDVPIEVIGDVLRIRQILTNLISNAIKFTPEGKVGIKLYVVPEPPFAKEGLKQKSKAYQSATDAVKEEKHQPKSQTASDQNGFHDKKHGEGYQDHKHDDDPGTPVSHGNSMDEDLEATVWIRCDVYDTGIGIPENALPTLFRKYMQVSADHARKYGGTGLGLAICKQLVELMGGRLTVTSKVHCGSTFTFILPYQVSPIEENsddpddlsdmadqdsVTDDVTAGFFQFQPRTLGSLFSSNGTSRSKKLLPNSIGFASAHKVNGFSETSYSFPSNNRQKETAPLEDACSVAEVAETLsepessfshspepeneTEVSRGKQCHVETTSWFQNPATESTSHSEANREMIQTSKTNEPQKICEMQEKPDRIsqspssssAEVPETkpkpkpkILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQYFP
Disordered region (IsUnstruct)
**********************************************VTIPEDQTIVDFKRLLELTNYTDKGSSQMAYLVKHWEYRQSNAVRLL**************************************ISIMDELSDMWKDVCPRKNDVVFQSKRVEVDAEYDTVEYWKQRALDL************************************QILKRADNFLHFVLQNAPVVMGHQDKELRYRFIYNHFPSLHEEDILGKTDVEIFSGAGVKESQDFKREVLEKGLPAKREITFETELFGSKTFLIYVEPVFSKSGETIGVNYMGMDVTD***************************************************PLTGVVSMAEILSNTKLDREQRQLLGVMISSGDLVLQLINDILDLSKVESGVMKLEAAKFRPREVVKHVLQTAAASLQKILMLEGDIADDVPIEVIGDVLRIRQILTNLISNAIKFTPEGKVGIKLYVVP************************************************************************LEATVWIRCDVYDTGIGIPENALPTLFRKYMQVSADHARKYGGTGLGLAICKQLVELMGGRLTVTSKVHCGSTFTFILPYQV*************************VTAGFFQFQP***************************************************************************************************************************************************************ILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDAA*****************FKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECL*****
Disordered Region (DISOPRED)
*********I**MDIEGLPSMWP**************GGGQDML********QTIVDFKRLLELT**********AYLVKHWEYRQSNAVRLLREE****************EILEEHRFEEEGYGGDKRPISIMDELSDMWKDVCPRKND*VF***RVEVDAEYDTVEYWKQRALDLEKMLEASGQREQALMEKLNESVTNLEKQSSP********KRADNFLHFVLQNAPVVMGHQDKELRYRFIYNHFPSLHEEDILGKTDVEIFSGAGVKESQDFKREVLEKGLPAKREITFETELFGSKTFLIYVEPVFSKSGETIGVNYMGMDVTDQVRKREKMAKLREEIAVQKAKETELNKTIHITEETMRAKQMLATMSHEIRSPLTGVVSMAEILSNTKLDREQRQLLGVMISSGDLVLQLINDILDLSKVESGVMKLEAAKFRPREVVKHVLQTAAASLQKILMLEGDIADDVPIEVIGDVLRIRQILTNLISNAIKFTPEGKVGIKLYVVPEPPFAKEGLKQKSKAYQSATDAVKEEKHQPKSQTASDQNGFHDKKHGEGYQDHKHDDDPGTPVSHGNSMDEDLEATVWIRCDVYDTGIGIPENALPTLFRKYMQVSADHARKYGGTGLGLAICKQLVELMGGRLTVTSKVHCGSTFTFILPYQ*****************ADQDSVTDDVTAGFFQFQPRTLGSLFSSNGTSRSKKLLPNSIGFASAHKVNGFSETSYSFPSNNRQKETAPLEDACSVAEVAETLSE*E********************CHVETTSWFQNPATESTSHSEANREMIQT*KTN*******************************KPKPKILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQYFP
Disordered Region (DISEMBL)
MVCNMETDLIEDMDIEGLPSMWPEDIGSDKQFNVERPGGGQDMLEEVTIPEDQTIVDFKRLLELTNYTDKGSSQMAYLVKHWEYRQSNAVRLLREELDNLSRQRQESELKKLEILEEHRFEEEGYGGDKRPISIMDELSDMWKDVCPRKNDVVFQSKRVEVDAEYDTVEYWKQRALDLEKMLEASGQREQALMEKLNES*************LSQILKRADNFLHFVLQNAPVVMGHQDKELRYRFIYNHFPSLHEEDILGKTDVEIFSGAGVKESQDFKREVLEKGLPAKREITFETELFGSKTFLIYVEPVFSKSGETIGVNYMGMDVTDQVRKREKMAKLREEIAVQKAKETELNKTIHITEETMRAKQMLATMSHEIRSPLTGVVSMAEILSNTKLDREQRQLLGVMISSGDLVLQLINDILDLSKVESGVMKLEAAKFRPREVVKHVLQTAAASLQKILMLEGDIADDVPIEVIGDVLRIRQILTNLISNAIKFTPEGKVGIKLYVVPEPPFAKE*******************************NGFHDKKH*********************SMDEDLEATVWIRCDVYDTGIGIPENALPTLFRKYMQVSADHARKYGGTGLGLAICKQLVELMGGRLTVTSKVHCGSTFTFILPYQVSPIEENSDDPDDLSDMADQDSVTDDVTAGFFQFQPRTLGSLFSSNGTSRSKKLLPNSIGFASAHKVNGFSETSYSFPSNNRQKETAPLEDACSVAEV*****************************HVETTSWFQN*********************NEPQKICEMQ***********************PKPKILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQYFP
Disordered Region (DISPRO)
*****ETDLIEDMDIEGLPSMWPEDIGSDKQFNVERPGGGQDMLEEVTIPEDQTIVDFKRLLELTNYTDKGSSQMAYLVKHWEYRQSNAVRLLREELDNLSRQRQESELKKLEILEEHRFEEEGYGGDKRPISIMDELSDMWKDVCPRKNDVVFQSKRVEVDAEYDTVEYWKQRALDLEKMLEASGQREQALMEKLNESVTNLEKQSSPVEELSQILKRADNFLHFVLQNAPVVMGHQDKELRYRFIYNHFPSLHEEDILGKTDVEIFSGAGVKESQDFKREVLEKGLPAKREITFETELFGSKTFLIYVEPVFSKSGETIGVNYMGMDVTDQVRKREKMAKLREEIAVQKAKETELNKTIHITEETMRAKQMLATMSHEIRSPLTGVVSMAEILSNTKLDREQRQLLGVMISSGDLVLQLINDILDLSKVESGVMKLEAAKFRPREVVKHVLQTAAASLQKILMLEGDIADDVPIEVIGDVLRIRQILTNLISNAIKFTPEGKVGIKLYVVPEP**********************EEKHQPKSQTASDQNGFHDKKHGEGYQDHKHDD***************LEATVWIRCDVYDTGIGIPENALPTLFRKYMQVSADHARKYGGTGLGLAICKQLVELMGGRLTVTSKVHCGSTFTFILPYQVS*******DPDDLSDMADQDSVTDDVTAGFFQFQPRTLGSLFSSNGTSRSKKLLPNSIGFASAHKVNGFSETSYSFPSNNRQKETAPLEDACSVAEVAETLSEPESSFSHSPEPENETEVSRGKQCHVETTSWFQNPATESTSHSEANREMIQTSKTNE**************************ETKPKPKPKILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDAAAEA*************HFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQYFP
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MVCNMETDLIEDMDIEGLPSMWPEDIGSDKQFNVERPGGGQDMLEEVTIPEDQTIVDFKRLLELTNYTDKGSSQMAYLVKHWEYRQSNAxxxxxxxxxxxxxxxxxxxxxxxxxxxxHRFEEEGYGGDKRPISIMDELSDMWKDVCPRKNDVVFQSKRVEVDAEYDTVEYWKQRALDLEKMLEASxxxxxxxxxxxxxxxxxxxxxSSPVEELSQILKRADNFLHFVLQNAPVVMGHQDKELRYRFIYNHFPSLHEEDILGKTDVEIFSGAGVKESQDFKREVLEKGLPAKREITFETELFGSKTFLIYVEPVFSKSGETIGVNYMGMDVTDQVRKREKxxxxxxxxxxxxxxxxxxxxxIHITEETMRAKQMLATMSHEIRSPLTGVVSMAEILSNTKLDREQRQLLGVMISSGDLVLQLINDILDLSKVESGVMKLEAAKFRPREVVKHVLQTAAASLQKILMLEGDIADDVPIEVIGDVLRIRQILTNLISNAIKFTPEGKVGIKLYVVPEPPFAKEGLKQKSKAYQSATDAVKEEKHQPKSQTASDQNGFHDKKHGEGYQDHKHDDDPGTPVSHGNSMDEDLEATVWIRCDVYDTGIGIPENALPTLFRKYMQVSADHARKYGGTGLGLAICKQLVELMGGRLTVTSKVHCGSTFTFILPYQVSPIEENSDDPDDLSDMADQDSVTDDVTAGFFQFQPRTLGSLFSSNGTSRSKKLLPNSIGFASAHKVNGFSETSYSFPSNNRQKETAPLEDACSVAEVAETLSEPESSFSHSPEPENETEVSRGKQCHVETTSWFQNPATESTSHSEANREMIQTSKTNEPQKICEMQEKPDRISQSPSSSSAEVPETKPKPKPKILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQYFP
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	1002	2.2.26 [Sep-21-2011]
Q3S4A7	922	Histidine kinase 5 OS=Ara	yes	no	0.909	0.988	0.606	0.0
Q9C5U0	1080	Histidine kinase 4 OS=Ara	no	no	0.276	0.256	0.351	9e-39
Q9C5U1	1036	Histidine kinase 3 OS=Ara	no	no	0.278	0.269	0.353	2e-37
Q9C5U2	1176	Histidine kinase 2 OS=Ara	no	no	0.267	0.227	0.360	7e-34
Q54YZ9	2062	Hybrid signal transductio	yes	no	0.344	0.167	0.291	3e-33
Q41342	754	Ethylene receptor 1 OS=So	N/A	no	0.274	0.364	0.296	2e-31
Q9M7M1	738	Ethylene receptor OS=Prun	N/A	no	0.263	0.357	0.289	9e-31
Q86CZ2	1213	Hybrid signal transductio	no	no	0.253	0.209	0.338	2e-29
Q9XH58	740	Ethylene receptor 1 OS=Pe	N/A	no	0.285	0.386	0.282	6e-29
Q9XH57	741	Ethylene receptor 2 OS=Pe	N/A	no	0.288	0.390	0.274	7e-29

>sp|Q3S4A7|AHK5_ARATH Histidine kinase 5 OS=Arabidopsis thaliana GN=AHK5 PE=2 SV=1

 Score = 1157 bits (2992), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 613/1011 (60%), Positives = 734/1011 (72%), Gaps = 100/1011 (9%)

Query: 1    MVCNMETDLIEDMDIEGLPSMWPEDIGS--DKQFNVERPGGGQDMLEEVTIPEDQTIVDF 58
            MVC METD IE+MD+E L SMWPED+G+  DKQFNVE+P G  D L+EVTI E +TI D 
Sbjct: 1    MVCEMETDQIEEMDVEVLSSMWPEDVGTEADKQFNVEKPAGDLDTLKEVTI-ETRTIADM 59

Query: 59   KRLLELTNYTDKGSSQMAYLVKHWEYRQSNAVRLLREELDNLSRQRQESELKKLEILEEH 118
             RL  L N T +GSSQ+  LVK WEY Q NAVRLL+EEL NL RQR+E+E K+L+I+EE+
Sbjct: 60   TRLPNLLNSTHQGSSQLTNLVKQWEYMQDNAVRLLKEELKNLDRQREEAEAKELKIIEEY 119

Query: 119  RFEEEGYGGDKRPISIMDELSDMWKDVCPRKNDVVFQSKRVEVDAEYDTVEYWKQRALDL 178
            +FE      +   + ++DE SD+++    +K D +  SK++E+  E+DTV YWKQ+AL L
Sbjct: 120  KFE----SNEPENVPVLDETSDLFRRFRQKKRDALVDSKKIEIYEEFDTVAYWKQKALSL 175

Query: 179  EKMLEASGQREQALMEKLNESVTNLEKQSSPVEELSQILKRADNFLHFVLQNAPVVMGHQ 238
            EKMLEAS +RE+ LMEKL+ES+  +E QS+PV+EL+Q LKRA+ FLHF+LQNAP+VMGHQ
Sbjct: 176  EKMLEASTERERRLMEKLSESLKTMESQSAPVQELTQNLKRAEGFLHFILQNAPIVMGHQ 235

Query: 239  DKELRYRFIYNHFPSLHEEDILGKTDVEIFSGAGVKESQDFKREVLEKGLPAKREITFET 298
            DK+LRY FIYN +PSL E+DILGKTDVEIF G GVKES+DFKREVLEKG  +KREITF T
Sbjct: 236  DKDLRYLFIYNKYPSLREQDILGKTDVEIFHGGGVKESEDFKREVLEKGKASKREITFTT 295

Query: 299  ELFGSKTFLIYVEPVFSKSGETIGVNYMGMDVTDQVRKREKMAKLREEIAVQKAKETELN 358
            +LFGSKTFLIYVEPV++K+GE IG+NYMGM+VTDQV KREKMAKLRE+ AV+KA E+ELN
Sbjct: 296  DLFGSKTFLIYVEPVYNKAGEKIGINYMGMEVTDQVVKREKMAKLREDNAVRKAMESELN 355

Query: 359  KTIHITEETMRAKQMLATMSHEIRSPLTGVVSMAEILSNTKLDREQRQLLGVMISSGDLV 418
            KTIHITEETMRAKQMLATMSHEIRSPL+GVV MAEILS TKLD+EQRQLL VMISSGDLV
Sbjct: 356  KTIHITEETMRAKQMLATMSHEIRSPLSGVVGMAEILSTTKLDKEQRQLLNVMISSGDLV 415

Query: 419  LQLINDILDLSKVESGVMKLEAAKFRPREVVKHVLQTAAASLQKILMLEGDIADDVPIEV 478
            LQLINDILDLSKVESGVM+LEA KFRPREVVKHVLQTAAASL+K L LEG+IADDVPIEV
Sbjct: 416  LQLINDILDLSKVESGVMRLEATKFRPREVVKHVLQTAAASLKKSLTLEGNIADDVPIEV 475

Query: 479  IGDVLRIRQILTNLISNAIKFTPEGKVGIKLYVVPEPPFAKEGLKQKSKAYQSATDAVKE 538
            +GDVLRIRQILTNLISNAIKFT EG VGIKL V+ EP F ++          +A +A  E
Sbjct: 476  VGDVLRIRQILTNLISNAIKFTHEGNVGIKLQVISEPSFVRD----------NALNADTE 525

Query: 539  EKHQPKSQTASDQNGFHDKKHGEGYQDHKHDDDPGTPVSHGNSMDEDLEATVWIRCDVYD 598
            E          +QNG                                 E +VWI CDV+D
Sbjct: 526  EH---------EQNGL-------------------------------TETSVWICCDVWD 545

Query: 599  TGIGIPENALPTLFRKYMQVSADHARKYGGTGLGLAICKQLVELMGGRLTVTSKVHCGST 658
            TGIGIPENALP LF+KYMQ SADHARKYGGTGLGLAICKQLVELMGG+LTVTS+V  GST
Sbjct: 546  TGIGIPENALPCLFKKYMQASADHARKYGGTGLGLAICKQLVELMGGQLTVTSRVSEGST 605

Query: 659  FTFILPYQVSPIEENSDDPDDLSDMADQDSVTDDVTAGFFQFQPRTLGSLFSSNGTSRSK 718
            FTFILPY+V   ++ SDD D+ SDMADQ S  DD   G+FQF+P  LGS++S+ G   S 
Sbjct: 606  FTFILPYKVGRSDDYSDDQDEFSDMADQQSEPDDTAEGYFQFKP-LLGSIYSNGGPGISN 664

Query: 719  KLLPNSIGFASAHK-VNGFSETSYSFPSNNR-QKETAPLEDACSVAEVAETLSEPESSFS 776
              LP+ +   S  K +NGF     + PSNN  Q E   LE+   + E     S+ E+S  
Sbjct: 665  DFLPHKVMLTSPIKLINGF----VADPSNNTGQSEMLQLENGGYMDE-----SKLETSSG 715

Query: 777  HSPEPENETEVSRGKQCHVETTSWFQNPATESTSHSEANREMIQTSKTNEPQKICEMQEK 836
            H PE  ++ E   G+    E+ S   + A+      E   E+  +S   E +        
Sbjct: 716  HCPESAHQYENGNGRCFSKESESCSSSQASSEGGTLEMESELTVSSHREEEK-------- 767

Query: 837  PDRISQSPSSSSAEVPETKPKPKPKILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAV 896
                      +  EV ET    KPKILLVEDNKIN+MVAKSMMKQLGH++D+ NNGVEA+
Sbjct: 768  ----------AETEVKET---SKPKILLVEDNKINIMVAKSMMKQLGHTMDIANNGVEAI 814

Query: 897  HAVQCQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNH-- 954
             A+   +YDL+LMDVCMPV+DGLKATRLIRS+E+TGNW+AA EAG++     S S N   
Sbjct: 815  TAINSSSYDLVLMDVCMPVLDGLKATRLIRSYEETGNWNAAIEAGVD----ISTSENEQV 870

Query: 955  ----FKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQYF 1001
                  R+PIIAMTAN L+ES+EEC+ANGMDSF+SKPVT QKL+ECL+QY 
Sbjct: 871  CMRPTNRLPIIAMTANTLAESSEECYANGMDSFISKPVTLQKLRECLQQYL 921

Functions as a histidine kinase and transmits the stress signal to a downstream MAPK cascade. This protein undergoes an ATP-dependent autophosphorylation at a conserved histidine residue in the kinase core, and a phosphoryl group is then transferred to a conserved aspartate residue in the receiver domain. Negative regulator of the ETR1-dependent abscisic acid (ABA) and ethylene signaling pathway that inhibits the root elongation. Promotes stomatal closure. Regulates stomatal opening by integrating multiple signals via hydrogen peroxide H(2)O(2) homeostasis in guard cells in an ABA-independent manner. May contribute to basal defense mechanisms by closing stomata in the presence of bacterial pathogens.
Arabidopsis thaliana (taxid: 3702)
EC: 2EC: .EC: 7EC: .EC: 1EC: 3EC: .EC: 3

>sp|Q9C5U0|AHK4_ARATH Histidine kinase 4 OS=Arabidopsis thaliana GN=AHK4 PE=1 SV=1

 Score =  162 bits (411), Expect = 9e-39,   Method: Compositional matrix adjust.
 Identities = 103/293 (35%), Positives = 160/293 (54%), Gaps = 16/293 (5%)

Query: 372 QMLATMSHEIRSPLTGVVSMAEILSNTKLDREQRQLLGVMISSGDLVLQLINDILDLSKV 431
           Q LAT+SHEIR+P+ G++ M  +L +T+L   QR         G  ++ LIN++LD +K+
Sbjct: 475 QFLATVSHEIRTPMNGILGMLAMLLDTELSSTQRDYAQTAQVCGKALIALINEVLDRAKI 534

Query: 432 ESGVMKLEAAKFRPREVVKHVLQT-AAASLQKILMLEGDIADDVPIEVIGDVLRIRQILT 490
           E+G ++LE+  F  R ++  VL   +  S  K + L   ++D VP  V GD  R RQI+ 
Sbjct: 535 EAGKLELESVPFDIRSILDDVLSLFSEESRNKSIELAVFVSDKVPEIVKGDSGRFRQIII 594

Query: 491 NLISNAIKFTPEGKVGIKLYVVPEPPFAKEGLKQKSKAYQSATDAVKEEKHQPKSQTASD 550
           NL+ N++KFT +G + +K+++        E  K +S+   +    V EE      Q++ +
Sbjct: 595 NLVGNSVKFTEKGHIFVKVHLA-------EQSKDESEPKNALNGGVSEEMIVVSKQSSYN 647

Query: 551 Q-NGFHDKKHGEGYQDHKHDDDPGTPVSHGNSMDE-DLEATVWIRCDVYDTGIGIPENAL 608
             +G+        +   KH       VS   S+ E D+ + V +   + DTGIGIP  A 
Sbjct: 648 TLSGYEAADGRNSWDSFKH------LVSEEQSLSEFDISSNVRLMVSIEDTGIGIPLVAQ 701

Query: 609 PTLFRKYMQVSADHARKYGGTGLGLAICKQLVELMGGRLTVTSKVHCGSTFTF 661
             +F  +MQ  +  +R YGGTG+GL+I K LVELM G++   S+ H GSTF F
Sbjct: 702 GRVFMPFMQADSSTSRNYGGTGIGLSISKCLVELMRGQINFISRPHIGSTFWF 754

Cytokinins (CK) receptor related to bacterial two-component regulators. Functions as a histidine kinase and transmits the stress signal to a downstream MAPK cascade. This protein undergoes an ATP-dependent autophosphorylation at a conserved histidine residue in the kinase core, and a phosphoryl group is then transferred to a conserved aspartate residue in the receiver domain. In the presence of cytokinin, feed phosphate to phosphorelay-integrating histidine phosphotransfer protein (HPt) and activates subsequent cascade. In the absence of cytokinin, removes phosphate from HPt proteins, decreasing the system phosphoload. Involved in meristems establishment in seedlings. Acts as a redundant negative regulator of drought and salt stress responses, and abscisic acid (ABA) signaling in a cytokinin-dependent manner. Required to set vascular asymmetric cell divisions that establish phloem and procambium cell lines. Redundant positive regulator of cytokinin signaling that regulates many development process including seed germination, cell division, seed size, chlorophyll retention during leaf senescence, root repression and shoot promotion. Can interact with isoprenoid-type cytokinins trans-zeatin (tZ and tZR), isopentenyladenine (iP), and isopentenyladenosine (iPR), the meta hydroxylated derivative of benzyladenine m-topolin, buta-2,3-dienyladenine (HA-8), penta-2,3-dienyladenine (HA-1), 4-methyl-penta-2,3-dienyladenine (HA-10), 4-hydroxy-2-butynyladenine (RM1), 2-butynyladenine (RM6), and to a lower extent, with cis-zeatin (cZ), zeatin riboside and dihydrozeatin (DZ). Together with AHK3, involved in the cytokinin-dependent responses to Pi starvation and sucrose stresses. Required for the formation of auxin-transporting vascular tissues in the hypocotyl, and primary and lateral roots, but not in adventitious roots, thus leading to auxin basipetal transport that regulates root development and branching. Involved in alkamides (e.g. N-isobutyl decanamide) and N-acylethanolamides (NAE) signaling that control meristematic activity and differentiation processes during plant development. Prevents the uptake of sulfate by mediating cytokinin-dependent down-regulation of high-affinity sulfate transporters (e.g. SULTR1;1 and SULTR1;2) expression in roots. Together with AHK2, required for growth and reproduction promotion stimulated by the endophytic fungus Piriformospora indica in a trans-zeatin-dependent manner. Required to trigger the phytotoxic effect of the snapdragon (Antirrhinum majus) flowers volatile organic compound (VOC) methyl benzoate (MB). Plays a role in the cytokinin-mediated repression of the iron uptake pathway.

Arabidopsis thaliana (taxid: 3702)

EC: 3

EC: .

EC: 1

EC: .

EC: 3

EC: .

EC: 1

EC: 6

>sp|Q9C5U1|AHK3_ARATH Histidine kinase 3 OS=Arabidopsis thaliana GN=AHK3 PE=1 SV=1

 Score =  158 bits (399), Expect = 2e-37,   Method: Compositional matrix adjust.
 Identities = 109/308 (35%), Positives = 166/308 (53%), Gaps = 29/308 (9%)

Query: 372 QMLATMSHEIRSPLTGVVSMAEILSNTKLDREQRQLLGVMISSGDLVLQLINDILDLSKV 431
           Q LAT+SHEIR+P+ GV+ M  +L +T+LD  Q+  +    +SG  ++ LIN++LD +K+
Sbjct: 453 QFLATVSHEIRTPMNGVLGMLHMLMDTELDVTQQDYVRTAQASGKALVSLINEVLDQAKI 512

Query: 432 ESGVMKLEAAKFRPREVVKHVLQT-AAASLQKILMLEGDIADDVPIEVIGDVLRIRQILT 490
           ESG ++LE  +F  R ++  VL   ++ S QK + L   I+D VP  +IGD  R RQILT
Sbjct: 513 ESGKLELEEVRFDLRGILDDVLSLFSSKSQQKGVELAVYISDRVPDMLIGDPGRFRQILT 572

Query: 491 NLISNAIKFTPEGKVGIKLYVVPEPPFAKEGLKQKSKAYQSATDAVKEEKHQPKSQTASD 550
           NL+ N+IKFT +G + + +++V E   + +G    S     +   V + +   ++  A  
Sbjct: 573 NLMGNSIKFTEKGHIFVTVHLVDELFESIDGETASSPESTLSGLPVADRQRSWENFKAFS 632

Query: 551 QNGFHDKKHGEGYQDHKHDDDPGTPVSHGNSMDEDLEATVWIRCDVYDTGIGIPENALPT 610
            NG            H+   +P  P         D+   V     V DTG+GIP  A   
Sbjct: 633 SNG------------HR-SFEPSPP---------DINLIV----SVEDTGVGIPVEAQSR 666

Query: 611 LFRKYMQVSADHARKYGGTGLGLAICKQLVELMGGRLTVTSKVHCGSTFTF--ILPYQVS 668
           +F  +MQV    +R +GGTG+GL+I K LV LM G +  +S    GSTFTF  +    + 
Sbjct: 667 IFTPFMQVGPSISRTHGGTGIGLSISKCLVGLMKGEIGFSSTPKVGSTFTFTAVFSNGMQ 726

Query: 669 PIEENSDD 676
           P E  +D+
Sbjct: 727 PAERKNDN 734

Cytokinins (CK) receptor related to bacterial two-component regulators. Functions as a histidine kinase and transmits the stress signal to a downstream MAPK cascade. This protein undergoes an ATP-dependent autophosphorylation at a conserved histidine residue in the kinase core, and a phosphoryl group is then transferred to a conserved aspartate residue in the receiver domain. In the presence of cytokinin, feed phosphate to phosphorelay-integrating histidine phosphotransfer protein (HPt) and activates subsequent cascade. Involved in meristems establishment in seedlings. Redundant negative regulator of drought and salt stress responses and abscisic acid (ABA) signaling. Together with AHK2, plays a negative regulatory role in cold stress signaling via inhibition of ABA response, occurring independently of the cold acclimation pathway. Redundant positive regulator of cytokinin signaling that regulates many development process including seed germination, cell division, seed size, chlorophyll retention during leaf senescence, root repression and shoot promotion. Can interact with isoprenoid-type cytokinins trans-zeatin (tZ and tZR), cis-zeatin (cZ), dihydrozeatin (DZ), buta-2,3-dienyladenine (HA-8), penta-2,3-dienyladenine (HA-1), 4-methyl-penta-2,3-dienyladenine (HA-10), 4-hydroxy-2-butynyladenine (RM1), 2-propynyladenine (RM3), 2-butynyladenine (RM6), and cytokinin ribosides and ribotides. Together with AHK4, involved in the cytokinin-dependent responses to Pi starvation and sucrose stresses. Promotes cytokinin-mediated leaf longevity through a specific phosphorylation of the response regulator ARR2. Involved in alkamides (e.g. N-isobutyl decanamide) and N-acylethanolamides (NAE) signaling that control meristematic activity and differentiation processes during plant development. Contributes to vascular bundle formation and secondary growth in a cytokinin-dependent manner, probably by promoting the maintenance of mitotic activity and/or identity of procambial cells. Plays a role in the cytokinin-mediated repression of the iron uptake pathway. Required by the cytokinin-dependent flower development regulation pathway.

Arabidopsis thaliana (taxid: 3702)

EC: 2

EC: .

EC: 7

EC: .

EC: 1

EC: 3

EC: .

EC: 3

>sp|Q9C5U2|AHK2_ARATH Histidine kinase 2 OS=Arabidopsis thaliana GN=AHK2 PE=1 SV=1

 Score =  146 bits (369), Expect = 7e-34,   Method: Compositional matrix adjust.
 Identities = 106/294 (36%), Positives = 162/294 (55%), Gaps = 26/294 (8%)

Query: 372 QMLATMSHEIRSPLTGVVSMAEILSNTKLDREQRQLLGVMISSGDLVLQLINDILDLSKV 431
           Q LAT+SHEIR+P+ GV+ M ++L +T LD +Q         SG  +  LIN++LD +K+
Sbjct: 590 QFLATVSHEIRTPMNGVLGMLKMLMDTDLDAKQMDYAQTAHGSGKDLTSLINEVLDQAKI 649

Query: 432 ESGVMKLEAAKFRPREVVKHV--LQTAAASLQKILMLEGDIADDVPIEVIGDVLRIRQIL 489
           ESG ++LE   F  R ++ +V  L +  A+ +K + L   ++  VP  V+GD  R RQI+
Sbjct: 650 ESGRLELENVPFDMRFILDNVSSLLSGKAN-EKGIELAVYVSSQVPDVVVGDPSRFRQII 708

Query: 490 TNLISNAIKFTPE-GKVGIKLYVVPEPPFAKEGLKQKSKAYQSATDAV-KEEKHQPKSQT 547
           TNL+ N+IKFT E G + I +++  E    KE L        +  DAV K+      S++
Sbjct: 709 TNLVGNSIKFTQERGHIFISVHLADE---VKEPL--------TIEDAVLKQRLALGCSES 757

Query: 548 ASDQNGFHDKKHGEGYQDHKHDDDPGTPVSHGNSMDEDLEATVWIRCDVYDTGIGIPENA 607
               +GF        +++ K      T  S  +   + ++  V     V DTG+GIP +A
Sbjct: 758 GETVSGFPAVNAWGSWKNFK------TCYSTESQNSDQIKLLV----TVEDTGVGIPVDA 807

Query: 608 LPTLFRKYMQVSADHARKYGGTGLGLAICKQLVELMGGRLTVTSKVHCGSTFTF 661
              +F  +MQ  +  +R YGGTG+GL+I K+LVELM G +   S+   GSTF+F
Sbjct: 808 QGRIFTPFMQADSSTSRTYGGTGIGLSISKRLVELMQGEMGFVSEPGIGSTFSF 861

Cytokinins (CK) receptor related to bacterial two-component regulators. Functions as a histidine kinase and transmits the stress signal to a downstream MAPK cascade. This protein undergoes an ATP-dependent autophosphorylation at a conserved histidine residue in the kinase core, and a phosphoryl group is then transferred to a conserved aspartate residue in the receiver domain. In the presence of cytokinin, feed phosphate to phosphorelay-integrating histidine phosphotransfer protein (HPt) and activates subsequent cascade. Involved in meristems establishment in seedlings. Redundant negative regulator of drought and salt stress responses and abscisic acid (ABA) signaling. Together with AHK3, plays a negative regulatory role in cold stress signaling via inhibition of ABA response, occurring independently of the cold acclimation pathway. Redundant positive regulator of cytokinin signaling that regulates many development process including seed germination, cell division, seed size, chlorophyll retention during leaf senescence, root repression and shoot promotion. Involved in alkamides (e.g. N-isobutyl decanamide) and N-acylethanolamides (NAE) signaling that control meristematic activity and differentiation processes during plant development. Contributes to vascular bundle formation and secondary growth in a cytokinin-dependent manner, probably by promoting the maintenance of mitotic activity and/or identity of procambial cells. Together with AHK4, required for growth and reproduction promotion stimulated by the endophytic fungus Piriformospora indica in a trans-zeatin-dependent manner. Required by the cytokinin-dependent flower development regulation pathway.

Arabidopsis thaliana (taxid: 3702)

EC: 2

EC: .

EC: 7

EC: .

EC: 1

EC: 3

EC: .

EC: 3

>sp|Q54YZ9|DHKJ_DICDI Hybrid signal transduction histidine kinase J OS=Dictyostelium discoideum GN=dhkJ PE=3 SV=2

 Score =  144 bits (364), Expect = 3e-33,   Method: Compositional matrix adjust.
 Identities = 122/418 (29%), Positives = 183/418 (43%), Gaps = 73/418 (17%)

Query: 590  VWIRCDVYDTGIGIPENALPTLFRKYMQVSADHARKYGGTGLGLAICKQLVELMGGRLTV 649
            V ++  V DTGIGIP++ L  +F  + Q      R+YGGTGLGL I  +LVELM G+L+V
Sbjct: 1498 VVLKFSVIDTGIGIPKDKLHLIFEAFSQADGSITRRYGGTGLGLTISTRLVELMKGKLSV 1557

Query: 650  TSKVHCGSTFTFILPYQVS----PIEENSDDPDDLSDMADQDSVTDDVTAGFFQFQPRTL 705
             SK   GSTF F   +  S    P+ E  +D   L        + DD           TL
Sbjct: 1558 VSKSGKGSTFEFTAQFPTSPNQLPLTEKLNDVHTL--------IVDD--------NKSTL 1601

Query: 706  GSLFSSNGTSRSKKLLPNSIGFASAHKVNGFSETSYSFPSNNRQKETAPLEDACSVAEVA 765
              L         K++L     F    +V+  ++ +++       K T P E     A++ 
Sbjct: 1602 KVL---------KQILSE---FGITSEVSNNTQDAFNMIVK-ATKTTKPFEFIFVDAQLG 1648

Query: 766  ETLSE--PESSFSHSPEPENETEVSRGKQCHVETTSWFQNPATESTSHSEANREMIQTSK 823
             +L +   E + +H               C  +               S +N      SK
Sbjct: 1649 TSLIDMMVEKNMNH---------------CKTKIIMLISGGGQRGYPDSSSNFITGYLSK 1693

Query: 824  TNEPQKICEMQEKPDRISQSPSSSSAEVPETKPKPKPKILLVEDNKINVMVAKSMMKQLG 883
               P +I ++  +     Q P     ++  T  +    ILL EDN +N  +A  ++++ G
Sbjct: 1694 PVSPSEIFDILTRQGITRQIPKQLCKKIQLT-SEIFGDILLAEDNAVNQRLAIRLLEKFG 1752

Query: 884  HSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDAAAEAGIE 943
            H + +  NG++AV + Q + +DLILMDV MP   G +AT  IR  E         E GI 
Sbjct: 1753 HRVQLAENGLQAVASSQLRKFDLILMDVQMPHCGGFEATAQIRKREH--------EQGIH 1804

Query: 944  QAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQYF 1001
                           PIIAMTA+AL+    +C   GMD ++SKP+   +LK  +E+Y 
Sbjct: 1805 T--------------PIIAMTAHALARDRVKCLEAGMDDYISKPINPDQLKAMIEKYL 1848

Acts as a receptor histidine kinase for a signal transduction pathway. This protein undergoes an ATP-dependent autophosphorylation at a conserved histidine residue in the kinase core, and a phosphoryl group is then transferred to a conserved aspartate residue in the receiver domain.

Dictyostelium discoideum (taxid: 44689)

EC: 2

EC: .

EC: 7

EC: .

EC: 1

EC: 3

EC: .

EC: 3

>sp|Q41342|ETR1_SOLLC Ethylene receptor 1 OS=Solanum lycopersicum GN=ETR1 PE=1 SV=1

 Score =  139 bits (349), Expect = 2e-31,   Method: Compositional matrix adjust.
 Identities = 102/344 (29%), Positives = 168/344 (48%), Gaps = 69/344 (20%)

Query: 330 VTDQVRKREKMAKLREEIAVQKAKETELNKTIHI------TEETMRAKQ-MLATMSHEIR 382
           V DQV      A + EE    +A++  + + + +       E  +RA+   LA M+HE+R
Sbjct: 313 VADQVAVALSHAAILEE--SMRARDLLMEQNVALDLARREAEMAVRARNDFLAVMNHEMR 370

Query: 383 SPLTGVVSMAEILSNTKLDREQRQLLGVMISSGDLVLQLINDILDLSKVESGVMKLEAAK 442
           +P+  +++++ +L  T L  EQR ++  ++ S +L+  LIND+LDLS++E G ++L+   
Sbjct: 371 TPMHAIIALSSLLQETDLTPEQRLMVETILKSSNLLATLINDVLDLSRLEDGSLQLDIGT 430

Query: 443 FRPREVVK--HVLQTAAASLQKILMLEGDIADDVPIEVIGDVLRIRQILTNLISNAIKFT 500
           F    + +  H L    AS++K L +   ++ D+P  VIGD  R+ QIL N++ NA+KF+
Sbjct: 431 FNLHALFREVHSLIKPIASVKK-LFVTLSLSSDLPEYVIGDEKRLMQILLNVVGNAVKFS 489

Query: 501 PEGKVGIKLYVVPEPPFAKEGLKQKSKAYQSATDAVKEEKHQPKSQTASDQNGFHDKKHG 560
            EG V I                    A+ + +D++++ +  P+      +N F      
Sbjct: 490 KEGNVSI-------------------SAFVAKSDSLRDPR-APEFFAVPSENHF------ 523

Query: 561 EGYQDHKHDDDPGTPVSHGNSMDEDLEATVWIRCDVYDTGIGIPENALPTLFRKYMQVSA 620
                                         ++R  + DTGIGI    +P LF K+ Q  A
Sbjct: 524 ------------------------------YLRVQIKDTGIGITPQDIPNLFSKFTQSQA 553

Query: 621 DHARKYGGTGLGLAICKQLVELMGGRLTVTSK-VHCGSTFTFIL 663
                 GGTGLGLAICK+ V LM G + + S+ +  GST  FI+
Sbjct: 554 LATTNSGGTGLGLAICKRFVNLMEGHIWIESEGLGKGSTAIFII 597

May act early in the ethylene signal transduction pathway, possibly as an ethylene receptor, or as a regulator of the pathway.

Solanum lycopersicum (taxid: 4081)

EC: 2

EC: .

EC: 7

EC: .

EC: 1

EC: 3

EC: .

EC: 3

>sp|Q9M7M1|ETR1_PRUPE Ethylene receptor OS=Prunus persica GN=ETR1 PE=2 SV=1

 Score =  136 bits (342), Expect = 9e-31,   Method: Compositional matrix adjust.
 Identities = 96/332 (28%), Positives = 164/332 (49%), Gaps = 68/332 (20%)

Query: 330 VTDQVRKREKMAKLREEIAVQKAKETELNKTIHI------TEETMRAKQ-MLATMSHEIR 382
           V DQV      A + EE    +A++  + + I +       E  +RA+   LA M+HE+R
Sbjct: 299 VADQVAVALSHAAILEE--SMRARDLLMEQNIALDLARREAETAIRARNDFLAVMNHEMR 356

Query: 383 SPLTGVVSMAEILSNTKLDREQRQLLGVMISSGDLVLQLINDILDLSKVESGVMKLEAAK 442
           +P+  +++++ +L  T+L  EQR ++  ++ S  L+  LIND+LDLS++E G ++LE A 
Sbjct: 357 TPMHAIIALSSLLQETELTPEQRLMVETILKSSHLLATLINDVLDLSRLEDGSLQLEIAT 416

Query: 443 FRPREVVK--HVLQTAAASLQKILMLEGDIADDVPIEVIGDVLRIRQILTNLISNAIKFT 500
           F    V +  H L    AS++K L +  ++A D+P++ +GD  R+ QI+ N++ NA+KF+
Sbjct: 417 FNLHSVFREVHNLIKPVASVKK-LSVSLNLAADLPVQAVGDEKRLMQIVLNVVGNAVKFS 475

Query: 501 PEGKVGIKLYVVPEPPFAKEGLKQKSKAYQSATDAVKEEKHQPKSQTASDQNGFHDKKHG 560
            EG + I                    A+ + ++++++ +  P+   A   N F+     
Sbjct: 476 KEGSISI-------------------TAFVAKSESLRDFR-APEFFPAQSDNHFY----- 510

Query: 561 EGYQDHKHDDDPGTPVSHGNSMDEDLEATVWIRCDVYDTGIGIPENALPTLFRKYMQVSA 620
                                          +R  V D+G GI    +P LF K+ Q  +
Sbjct: 511 -------------------------------LRVQVKDSGSGINPQDIPKLFTKFAQTQS 539

Query: 621 DHARKYGGTGLGLAICKQLVELMGGRLTVTSK 652
              R  GG+GLGLAICK+ V LM G + + S+
Sbjct: 540 LATRNSGGSGLGLAICKRFVNLMEGHIWIESE 571

May act early in the ethylene signal transduction pathway, possibly as an ethylene receptor, or as a regulator of the pathway.

Prunus persica (taxid: 3760)

EC: 2

EC: .

EC: 7

EC: .

EC: 1

EC: 3

EC: .

EC: 3

>sp|Q86CZ2|DHKK_DICDI Hybrid signal transduction histidine kinase K OS=Dictyostelium discoideum GN=dhkK PE=1 SV=1

 Score =  132 bits (331), Expect = 2e-29,   Method: Compositional matrix adjust.
 Identities = 112/331 (33%), Positives = 155/331 (46%), Gaps = 77/331 (23%)

Query: 351  KAKETELNKTIHITEETMRAKQ-MLATMSHEIRSPLTGVVSMAEILSNT-KLDREQRQLL 408
            K K  +L        E  +A+Q  LATMSHEIR+PL G++ MA +L ++  L  E++ + 
Sbjct: 796  KLKNAQLTIAKDAAIEAYQARQEFLATMSHEIRTPLNGLIGMATLLRDSHNLPPEEKTMA 855

Query: 409  GVMISSGDLVLQLINDILDLSKVESGVMKLEAAKFRPREV---VKHVLQTAAASLQKILM 465
              + S GD++L+L+NDILDLSK+E+  M LE   FR RE+   + HVL   A   +K + 
Sbjct: 856  KAVKSCGDILLRLVNDILDLSKLEANQMGLEHIPFRMRELTQQICHVLSGQAN--EKNIH 913

Query: 466  LEGDIADDVPIEVIGDVLRIRQILTNLISNAIKFTPEGKVGIKLYVVPEPPFAKEGLKQK 525
            L  +++D +P  ++GD  RI QIL NL  NA+KFT  G V I +                
Sbjct: 914  LSCEVSDKIPSILLGDSGRILQILMNLTGNALKFTQSGYVKIII---------------- 957

Query: 526  SKAYQSATDAVKEEKHQPKSQTASDQNGFHDKKHGEGYQDHKHDDDPGTPVSHGNSMDED 585
                    D ++EE      +       F  K           D   G PV    S  + 
Sbjct: 958  --------DLIEEESELVSLKKGEYNISFRVK-----------DTGIGVPVE---SHQKI 995

Query: 586  LEATVWIRCDVYDTGIGIPENALPTLFRKYMQVSADHARKYGGTGLGLAICKQLVELMGG 645
             EA V                A P+  RKY           GG+GLGL +C +LV LM G
Sbjct: 996  FEAFV---------------QADPSDSRKY-----------GGSGLGLYLCAKLVRLMKG 1029

Query: 646  RLTVTSKVHC-GSTFTFILPYQVSPIEENSD 675
             + V +   C GSTF FIL     P+EE +D
Sbjct: 1030 EIGVYNNPDCDGSTFWFIL-----PLEEGTD 1055

Involved in a signal transduction pathway that regulates morphogenesis and controls entry into the culmination stage. May act via the regA pathway, being activated by a morphogenesis-stimulated ligand, reducing phosphodiesterase regA levels and allowing cAMP level to rise to promote the culmination stage. This protein probably undergoes an ATP-dependent autophosphorylation at a conserved histidine residue in the kinase core, and a phosphoryl group is then transferred to a conserved aspartate residue in the receiver domain.

Dictyostelium discoideum (taxid: 44689)

EC: 2

EC: .

EC: 7

EC: .

EC: 1

EC: 3

EC: .

EC: 3

>sp|Q9XH58|ETR1_PELHO Ethylene receptor 1 OS=Pelargonium hortorum GN=ETR1 PE=2 SV=1

 Score =  130 bits (327), Expect = 6e-29,   Method: Compositional matrix adjust.
 Identities = 101/358 (28%), Positives = 172/358 (48%), Gaps = 72/358 (20%)

Query: 330 VTDQVRKREKMAKLREEIAVQKAKETELNKTIHI------TEETMRAKQ-MLATMSHEIR 382
           V DQV      A + EE    +A++  + + + +       E  +RA+   LA M+HE+R
Sbjct: 299 VADQVAVALSHAAILEE--SMRARDLLMEQNVALDMARREAETAIRARNDFLAVMNHEMR 356

Query: 383 SPLTGVVSMAEILSNTKLDREQRQLLGVMISSGDLVLQLINDILDLSKVESGVMKLEAAK 442
           +P+  +++++ +L  T L  EQR ++  ++ S +L+  LIND+LDLS++E G ++L+ A 
Sbjct: 357 TPMHAIIALSSLLQETDLTSEQRLMVETILKSSNLLATLINDVLDLSRLEDGSLQLDIAT 416

Query: 443 FRPREVVKHV--LQTAAASLQKILMLEGDIADDVPIEVIGDVLRIRQILTNLISNAIKFT 500
           F    V + V  L    AS++K L +  +++ D+P  VIGD  R+ QI+ N++ NA+KF+
Sbjct: 417 FNLHAVFRQVFNLIKPIASVKK-LFITLNVSPDLPEYVIGDEKRLVQIMLNVVGNAVKFS 475

Query: 501 PEGKVGIKLYVVPEPPFAKEGLKQKSKAYQSATDAVKEEKHQPKSQTASDQNGFHDKKHG 560
            EG + +                    A+ + +++V++ +  P     S  N F      
Sbjct: 476 KEGIISV-------------------TAFVAKSESVRDPR-APDFFPVSSDNQF------ 509

Query: 561 EGYQDHKHDDDPGTPVSHGNSMDEDLEATVWIRCDVYDTGIGIPENALPTLFRKYMQVSA 620
                                         ++R  V D+G GI    +P LF K+ Q   
Sbjct: 510 ------------------------------YMRVQVKDSGSGINPQDMPKLFTKFAQSQP 539

Query: 621 DHARKYGGTGLGLAICKQLVELMGGRLTVTSKVHC-GSTFTFILPYQVSPIEENSDDP 677
              +  GG+GLGLAI K+ V LM G + + S+    G T TF++      I E S++P
Sbjct: 540 VATKNSGGSGLGLAISKRFVNLMDGHIWIDSEGPSKGCTVTFVVKLG---IPEGSNEP 594

May act early in the ethylene signal transduction pathway, possibly as an ethylene receptor, or as a regulator of the pathway.

Pelargonium hortorum (taxid: 4031)

EC: 2

EC: .

EC: 7

EC: .

EC: 1

EC: 3

EC: .

EC: 3

>sp|Q9XH57|ETR2_PELHO Ethylene receptor 2 OS=Pelargonium hortorum GN=ETR2 PE=2 SV=1

 Score =  130 bits (326), Expect = 7e-29,   Method: Compositional matrix adjust.
 Identities = 99/361 (27%), Positives = 174/361 (48%), Gaps = 72/361 (19%)

Query: 330 VTDQVRKREKMAKLREEIAVQKAKETELNKTIHI------TEETMRAKQ-MLATMSHEIR 382
           V DQV      A + EE    +A++  + + + +       E  +RA+   LA M+HE+R
Sbjct: 299 VADQVAVALSHAAILEE--SMRARDLLMEQNVALDMARREAETAIRARNDFLAVMNHEMR 356

Query: 383 SPLTGVVSMAEILSNTKLDREQRQLLGVMISSGDLVLQLINDILDLSKVESGVMKLEAAK 442
           +P+  +++++ +L  T+L  EQR ++  ++ S +L+  LIND+LDLS++E G ++L+   
Sbjct: 357 TPMHAIIALSSLLQETELTPEQRLMVETVLKSSNLLATLINDVLDLSRLEDGSLQLDIGT 416

Query: 443 FRPREVVK--HVLQTAAASLQKILMLEGDIADDVPIEVIGDVLRIRQILTNLISNAIKFT 500
           F    +++  H L    AS++K L +  ++A D+P   +GD  R+ QI+ N++ NA+KF+
Sbjct: 417 FNLHALLREVHNLIKPIASVKK-LCISLNVATDLPEYAVGDEKRLVQIILNVVGNAVKFS 475

Query: 501 PEGKVGIKLYVVPEPPFAKEGLKQKSKAYQSATDAVKEEKHQPKSQTASDQNGFHDKKHG 560
            EG + I                    A+ + ++++++ +  P       +N F      
Sbjct: 476 KEGNISIT-------------------AFVAKSESLRDPR-APDFFPICGENQF------ 509

Query: 561 EGYQDHKHDDDPGTPVSHGNSMDEDLEATVWIRCDVYDTGIGIPENALPTLFRKYMQVSA 620
                                         ++R  V D+G+GI    +P LF K+ Q   
Sbjct: 510 ------------------------------YLRVQVKDSGLGINPQDIPRLFTKFAQTQP 539

Query: 621 DHARKYGGTGLGLAICKQLVELMGGRLTVTSKVHC-GSTFTFILPYQVSPIEENSDDPDD 679
              +  GG+GLGLAICK+ V LM G + + S+    G T TF++      I E S +P  
Sbjct: 540 VATKNSGGSGLGLAICKRFVNLMEGHIWIDSEGPGKGCTATFVVKLG---IPERSSEPKL 596

Query: 680 L 680
           L
Sbjct: 597 L 597

May act early in the ethylene signal transduction pathway, possibly as an ethylene receptor, or as a regulator of the pathway.

Pelargonium hortorum (taxid: 4031)

EC: 2

EC: .

EC: 7

EC: .

EC: 1

EC: 3

EC: .

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	1002
359476452	1012	PREDICTED: histidine kinase 5-like [Viti	0.987	0.977	0.726	0.0
224143389	945	histidine kinase cytokinin receptor [Pop	0.920	0.975	0.704	0.0
147778679	979	hypothetical protein VITISV_033090 [Viti	0.953	0.975	0.697	0.0
356552435	937	PREDICTED: histidine kinase 5-like [Glyc	0.922	0.986	0.693	0.0
255548630	930	sensor histidine kinase, putative [Ricin	0.898	0.967	0.713	0.0
224092694	923	histidine kinase cytokinin receptor [Pop	0.907	0.984	0.693	0.0
356509864	933	PREDICTED: histidine kinase 5-like [Glyc	0.919	0.987	0.683	0.0
357437045	1077	Histidine kinase cytokinin receptor [Med	0.983	0.914	0.646	0.0
449447373	941	PREDICTED: histidine kinase 5-like [Cucu	0.917	0.976	0.649	0.0
449486822	941	PREDICTED: LOW QUALITY PROTEIN: histidin	0.917	0.976	0.648	0.0

>gi|359476452|ref|XP_002271743.2| PREDICTED: histidine kinase 5-like [Vitis vinifera]

 Score = 1448 bits (3749), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 743/1023 (72%), Positives = 846/1023 (82%), Gaps = 34/1023 (3%)

Query: 1    MVCNMETDLIEDMDIEGLPSMWPEDIGSD--KQFNVERPGGGQDMLEEVTIPEDQTIVDF 58
            MVC ME D IE+MD+E L SMWPEDIG+D   QFN++RPG  QDMLEEV I E+ +IVDF
Sbjct: 1    MVCEMENDNIEEMDVEVLHSMWPEDIGNDAGNQFNMDRPGADQDMLEEVNIVEEPSIVDF 60

Query: 59   KRLLELTNYTDKGSSQMAYLVKHWEYRQSNAVRLLREELDNLSRQRQESELKKLEILEEH 118
            KRLLELTNY++KGSSQ+AYLVK+WEY+Q+NAVRLL+EELDNLSRQRQE ELKKLEILEEH
Sbjct: 61   KRLLELTNYSEKGSSQLAYLVKNWEYKQANAVRLLKEELDNLSRQRQEVELKKLEILEEH 120

Query: 119  RFEEEGYGGDKRPISIMDELSDMWKDVCPRKNDVVFQSKRVEVDAEYDTVEYWKQRALDL 178
            RF EE YGGDKRPISI+D + D+W++V  R+N VV Q+KR+E+DAEYDTV YWKQRA+ L
Sbjct: 121  RFVEERYGGDKRPISILDGIYDIWQEVPRRRNSVVVQNKRLEIDAEYDTVIYWKQRAVHL 180

Query: 179  EKMLEASGQREQALMEKLNESVTNLEKQSSPVEELSQILKRADNFLHFVLQNAPVVMGHQ 238
            EK+LEAS QRE  LMEK+ ES+ +LE+QSSPVEELSQILKRADNFLHFVLQNAPVV+GHQ
Sbjct: 181  EKLLEASVQREHMLMEKVQESIKSLERQSSPVEELSQILKRADNFLHFVLQNAPVVIGHQ 240

Query: 239  DKELRYRFIYNHFPSLHEEDILGKTDVEIFSGAGVKESQDFKREVLEKGLPAKREITFET 298
            DKELRYRFIYNHFPSL EEDI+GKTDVEIF+GAGVKESQ+FK+EVLE+GLPAKREITFET
Sbjct: 241  DKELRYRFIYNHFPSLQEEDIIGKTDVEIFTGAGVKESQEFKKEVLERGLPAKREITFET 300

Query: 299  ELFGSKTFLIYVEPVFSKSGETIGVNYMGMDVTDQVRKREKMAKLREEIAVQKAKETELN 358
            ELFGSKTFLIYVEPVFSK+G+TIGVNYMGMDVTDQVRKREKM K+REEIAVQKAKETELN
Sbjct: 301  ELFGSKTFLIYVEPVFSKAGDTIGVNYMGMDVTDQVRKREKMMKIREEIAVQKAKETELN 360

Query: 359  KTIHITEETMRAKQMLATMSHEIRSPLTGVVSMAEILSNTKLDREQRQLLGVMISSGDLV 418
            KTIHITEETMRAKQMLATMSHEIRSPL+GVVS+AEIL+ T LDR QRQLL VM+SSGDLV
Sbjct: 361  KTIHITEETMRAKQMLATMSHEIRSPLSGVVSIAEILATTNLDRHQRQLLNVMLSSGDLV 420

Query: 419  LQLINDILDLSKVESGVMKLEAAKFRPREVVKHVLQTAAASLQKILMLEGDIADDVPIEV 478
            LQLINDILDLSKVESGVMKLEA KFRPREVVKHVLQTAAASLQKIL LEG +ADDVP+EV
Sbjct: 421  LQLINDILDLSKVESGVMKLEATKFRPREVVKHVLQTAAASLQKILTLEGHVADDVPLEV 480

Query: 479  IGDVLRIRQILTNLISNAIKFTPEGKVGIKLYVVPEPPFAK-EGLKQKSKAYQSATDA-- 535
             GDVLRIRQILTNLISNA+KFT EGKVGI LYV+PEP     EG  Q     QS   A  
Sbjct: 481  TGDVLRIRQILTNLISNAVKFTHEGKVGINLYVIPEPSSGNGEGGPQMFIDDQSTVSANI 540

Query: 536  VKEEKHQPKSQTASDQNGFHDKKHGEGYQDHKHDDDPGTPVSHGNSMDED------LEAT 589
             KEEK    SQ++    G H        Q+H  +D+P  P++H +S  ED      LE T
Sbjct: 541  PKEEKCLSPSQSSCTSKGSH-------TQNHALNDEPIDPINHDDSKQEDKENSHPLETT 593

Query: 590  VWIRCDVYDTGIGIPENALPTLFRKYMQVSADHARKYGGTGLGLAICKQLVELMGGRLTV 649
            VWIRCDVYDTGIGIPE+ALPTLF+KYMQVSADHARKYGGTGLGLAICKQLVELMGG +TV
Sbjct: 594  VWIRCDVYDTGIGIPEHALPTLFKKYMQVSADHARKYGGTGLGLAICKQLVELMGGHMTV 653

Query: 650  TSKVHCGSTFTFILPYQVSPIEENSDDPDDLSDMADQDSVTDDVTAGFFQFQPRTLGSLF 709
            +S+ H GSTFTFILPY+VS I ++SDDPD+LSDMAD D+ TDD  AGFFQF PRTLGSLF
Sbjct: 654  SSREHSGSTFTFILPYKVSLISDHSDDPDELSDMADDDASTDDKNAGFFQFHPRTLGSLF 713

Query: 710  SSNGTSRSKKLLPNSIGFASAHKVNGFSETSYSFPSNN-RQKETAPLEDACSVAEVAETL 768
            SS G+ R++KL PN+IG+ S HK+NG S+ SYSFP N    KE   LED CSV + AETL
Sbjct: 714  SSGGSGRTQKLPPNNIGYDSLHKLNGLSDDSYSFPFNKVTSKEMTSLEDTCSVVDAAETL 773

Query: 769  SEPESSFSHSPEPENETEVSRGKQCHVETTSWFQNPATESTSHSEANREMIQTSKTNEPQ 828
            SEPES   H+ EP+N+  VSRGK+C  E      N +T ST HS+ ++E+ +  KT+E  
Sbjct: 774  SEPESLLRHNAEPDNDNAVSRGKKCQDEANGQVHNHSTGSTHHSKVSKEVDEMGKTSEAP 833

Query: 829  KICEMQEKPDRISQSPSSSSAEVPETKPKPKPKILLVEDNKINVMVAKSMMKQLGHSIDV 888
            ++C   E  +R SQ  SSSS E  E K   KPKILLVED+KINVMV +SMMKQLGH+IDV
Sbjct: 834  EMCLRLEISERSSQCTSSSSPE--EPKSTLKPKILLVEDSKINVMVTQSMMKQLGHTIDV 891

Query: 889  VNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDAAAEAGIEQAMPS 948
            VNNG+EAV AVQC++YDLILMDVCMPVMDGL+ATR+IRSFE+TGNWDAA +AGIE   PS
Sbjct: 892  VNNGIEAVRAVQCRSYDLILMDVCMPVMDGLQATRIIRSFEETGNWDAAVKAGIE---PS 948

Query: 949  SGSSNHF----------KRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLE 998
            + SS+            KR+PIIAMTANALSESA+EC+ANGMDSFVSKPVTFQKL +CL+
Sbjct: 949  TCSSDSLPNGHDSMTVTKRVPIIAMTANALSESADECYANGMDSFVSKPVTFQKLTQCLQ 1008

Query: 999  QYF 1001
            QY 
Sbjct: 1009 QYL 1011

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224143389|ref|XP_002324940.1| histidine kinase cytokinin receptor [Populus trichocarpa] gi|222866374|gb|EEF03505.1| histidine kinase cytokinin receptor [Populus trichocarpa]

 Score = 1376 bits (3561), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 719/1020 (70%), Positives = 809/1020 (79%), Gaps = 98/1020 (9%)

Query: 5    METDLIEDMDIEGLPSMWPEDIGSDKQFNVERPGGGQDMLEEVTIPEDQTIVDFKRLLEL 64
            ME + +EDMDIE LPSMWPEDI S K + VE+P G QDMLEEVTI E+ TIVDF  L+EL
Sbjct: 1    MENEQMEDMDIEALPSMWPEDIDSSKPY-VEKPVGDQDMLEEVTIVEEPTIVDFHHLVEL 59

Query: 65   TNYTDKGSSQMAYLVKHWEYRQSNAVRLLREELDNLSRQRQESELKKLEILEEHRFEEEG 124
            TNYTD+GSSQ+ +LV+HWEY+ +NAVRLLREELD LS+QR+E ELKKLEILE+ RFEEE 
Sbjct: 60   TNYTDRGSSQLTHLVQHWEYKHANAVRLLREELDILSKQREEVELKKLEILEDFRFEEER 119

Query: 125  YGGDKRPISIMDELSDMWKDVCPRKNDVVFQSKRVEVDAEYDTVEYWKQRALDLEKMLEA 184
            Y GDKRPISI+DE+ D+++D+  RK D++ QSK+V +DAE++TV YWKQRA DLEK+LEA
Sbjct: 120  YSGDKRPISILDEIIDLYQDIPRRKRDIIVQSKKVNIDAEFETVAYWKQRAKDLEKLLEA 179

Query: 185  SGQREQALMEKLNESVTNLEKQSSPVEELSQILKRADNFLHFVLQNAPVVMGHQDKELRY 244
            S  REQ LMEKL ES+ NLEKQSSPVEEL+QILKRADNFLHFVLQNAPVV+GHQDK+LRY
Sbjct: 180  SVHREQLLMEKLQESLQNLEKQSSPVEELTQILKRADNFLHFVLQNAPVVIGHQDKDLRY 239

Query: 245  RFIYNHFPSLHEEDILGKTDVEIFSGAGVKESQDFKREVLEKGLPAKREITFETELFGSK 304
            RFIYN FP L EE+ILGKTDVEIFSG+GVKESQDFK+EVL+KGLPAKREITFETELFGSK
Sbjct: 240  RFIYNQFPRLQEEEILGKTDVEIFSGSGVKESQDFKKEVLDKGLPAKREITFETELFGSK 299

Query: 305  TFLIYVEPVFSKSGETIGVNYMGMDVTDQVRKREKMAKLREEIAVQKAKETELNKTIHIT 364
            TFLIYVEPVFSKSGETIG+NYMGMDVTDQVRKREKMA+LRE+IAVQKAKETELNKTIHIT
Sbjct: 300  TFLIYVEPVFSKSGETIGINYMGMDVTDQVRKREKMAQLREQIAVQKAKETELNKTIHIT 359

Query: 365  EETMRAKQMLATMSHEIRSPLTGVVSMAEILSNTKLDREQRQLLGVMISSGDLVLQLIND 424
            EETMRAKQMLATMSHEIRSPL+GVVSMAEILS T LDREQRQLL VMISSGDLVLQLIND
Sbjct: 360  EETMRAKQMLATMSHEIRSPLSGVVSMAEILSTTNLDREQRQLLNVMISSGDLVLQLIND 419

Query: 425  ILDLSKVESGVMKLEAAKFRPREVVKHVLQTAAASLQKILMLEGDIADDVPIEVIGDVLR 484
            ILDLSKVESGVMKLEA KFRPREVVKHVLQTAAASLQKIL LEG +ADDVPIEVIGDVLR
Sbjct: 420  ILDLSKVESGVMKLEATKFRPREVVKHVLQTAAASLQKILTLEGRVADDVPIEVIGDVLR 479

Query: 485  IRQILTNLISNAIKFTPEGKVGIKLYVVPEPPFAKEGLKQKSKAYQSATDAVKEEKHQPK 544
            IRQILTNLI+NAIKFT EGKVGI LYVV +P             +++      +E  +P+
Sbjct: 480  IRQILTNLITNAIKFTHEGKVGINLYVVSDP-------------FKNGNTTDGDEGEEPQ 526

Query: 545  SQTASDQNGFHDKKHGEGYQDHKHDDDPGTPVSHGNSMDEDLEATVWIRCDVYDTGIGIP 604
                                       PGT              TVW+ CDVYDTGIGIP
Sbjct: 527  V--------------------------PGT--------------TVWLCCDVYDTGIGIP 546

Query: 605  -------------------ENALPTLFRKYMQVSADHARKYGGTGLGLAICKQLVELMGG 645
                               ENALPTLFRKYMQVSADHARKYGGTGLGLAICKQLVELMGG
Sbjct: 547  GTLVSIVEALLSTFLIHATENALPTLFRKYMQVSADHARKYGGTGLGLAICKQLVELMGG 606

Query: 646  RLTVTSKVHCGSTFTFILPYQVSPIEENSDDPDDLSDMADQDSVTDDVTAGFFQFQPRTL 705
            RLTV+SKV  GSTFTF+LPY+VS   ++SDDPDDLS+MAD ++  +D TAGFFQFQPRTL
Sbjct: 607  RLTVSSKVKSGSTFTFVLPYKVSSTCDSSDDPDDLSEMADHEAPLEDETAGFFQFQPRTL 666

Query: 706  GSLFSSNGTSRSKKLLPNSIGFASAHKVNGFSETSYSFPSNN-RQKETAPLEDACSVAEV 764
            GSLFSSNG++R++KLLP+SIGF  + K+NG SE S SFPS N R KET  +EDACS+ EV
Sbjct: 667  GSLFSSNGSTRTQKLLPHSIGFTKSPKINGISEDSCSFPSGNVRLKETTCVEDACSMVEV 726

Query: 765  AETLSEPESSFSHSPEPENETEVSRGKQCHVETTSWFQNPATESTSHSEANREMIQTSKT 824
            AETLSEPESSFSHSPE + E  V R +Q   +T    +                   + T
Sbjct: 727  AETLSEPESSFSHSPERDYENVVCRSQQSQDDTNLSLR-------------------ANT 767

Query: 825  NEPQKICEMQEKPDRISQSPSSSSAEVPETKPKPKPKILLVEDNKINVMVAKSMMKQLGH 884
             EP   C+ +EK    SQ  SSS  + PE+  KPKPKILLVEDNKINVMV KSMMKQLGH
Sbjct: 768  AEPPGSCQEEEKSVINSQCTSSSIPQKPES--KPKPKILLVEDNKINVMVTKSMMKQLGH 825

Query: 885  SIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDAAAEAGIE- 943
            ++DVVNNGVEAV AVQ   YDL+LMDVCMPVM+GL+AT+LIRSFE+TGNWDAAA+AGIE 
Sbjct: 826  TMDVVNNGVEAVRAVQSCCYDLVLMDVCMPVMNGLQATQLIRSFEETGNWDAAAKAGIEP 885

Query: 944  -QAMPSSGSSNHF-KRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQYF 1001
              ++  S SS H+ KR+PIIAMTANALSESAEEC+ANGMDSFVSKPVTFQKLKECLEQY 
Sbjct: 886  SASLQDSQSSIHYDKRMPIIAMTANALSESAEECYANGMDSFVSKPVTFQKLKECLEQYL 945

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147778679|emb|CAN76109.1| hypothetical protein VITISV_033090 [Vitis vinifera]

 Score = 1366 bits (3535), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 711/1020 (69%), Positives = 813/1020 (79%), Gaps = 65/1020 (6%)

Query: 5    METDLIEDMDIEGLPSMWPEDIGSD--KQFNVERPGGGQDMLEEVTIPEDQTIVDFKRLL 62
            ME D IE+MD+E L SMWPEDIG+D   QFN++RPG  QDMLEEV I E+ +IVDFKRLL
Sbjct: 1    MENDNIEEMDVEVLHSMWPEDIGNDAGNQFNMDRPGADQDMLEEVNIVEEPSIVDFKRLL 60

Query: 63   ELTNYTDKGSSQMAYLVKHWEYRQSNAVRLLREELDNLSRQRQESELKKLEILEEHRFEE 122
            ELTNY++KGSSQ+AYLVK+WEY+Q+NAVRLL+EELDNLSRQRQE ELKKLEILEEHRF E
Sbjct: 61   ELTNYSEKGSSQLAYLVKNWEYKQANAVRLLKEELDNLSRQRQEVELKKLEILEEHRFVE 120

Query: 123  EGYGGDKRPISIMDELSDMWKDVCPRKNDVVFQSKRVEVDAEYDTVEYWKQRALDLEKML 182
            E YGGDKRPISI+D + D+W++V  R+N VV Q+KR+E+DAEYDTV YWKQRA+ LEK+L
Sbjct: 121  ERYGGDKRPISILDGIYDIWQEVPRRRNSVVVQNKRLEIDAEYDTVIYWKQRAVHLEKLL 180

Query: 183  EASGQREQALMEKLNESVTNLEKQSSPVEELSQILKRADNFLHFVLQNAPVVMGHQDKEL 242
            EAS QRE  LMEK+ ES+ +LE+QSSPVEELSQILKRADNFLHFVLQNAPVV+GHQDKEL
Sbjct: 181  EASVQREHMLMEKVQESIKSLERQSSPVEELSQILKRADNFLHFVLQNAPVVIGHQDKEL 240

Query: 243  RYRFIYNHFPSLHEEDILGKTDVEIFSGAGVKESQDFKREVLEKG-LPAKREITFETELF 301
            RYRFIYNHFPSL EEDI+GKTDVEIF+GAGVKESQ+FK+EVLE+G L AKREITFETELF
Sbjct: 241  RYRFIYNHFPSLQEEDIIGKTDVEIFTGAGVKESQEFKKEVLERGLLSAKREITFETELF 300

Query: 302  GSKTFLIYVEPVFSKSGETIGVNYMGMDVTDQVRKREKMAKLREEIAVQKAKETELNKTI 361
            GSKTFLIYVEPVFSK+G+TIGVNYMGMDVTDQVRKREKM K+REEIAVQKAKETELNKTI
Sbjct: 301  GSKTFLIYVEPVFSKAGDTIGVNYMGMDVTDQVRKREKMMKIREEIAVQKAKETELNKTI 360

Query: 362  HITEETMRAKQMLATMSHEIRSPLTGVVSMAEILSNTKLDREQRQLLGVMISSGDLVLQL 421
            HITEETMRAKQMLATMSHEIRSPL+GVVS+AEIL+ T LDR QRQLL VM+SSGDLVLQL
Sbjct: 361  HITEETMRAKQMLATMSHEIRSPLSGVVSIAEILATTNLDRHQRQLLNVMLSSGDLVLQL 420

Query: 422  INDILDLSKVESGVMKLEAAKFRPREVVKHVLQTAAASLQKILMLEGDIADDVPIEVIGD 481
            INDILDLSKVESGVMKLEA KFRPREV                               GD
Sbjct: 421  INDILDLSKVESGVMKLEATKFRPREVT------------------------------GD 450

Query: 482  VLRIRQILTNLISNAIKFTPEGKVGIKLYVVPEPPFAK-EGLKQKSKAYQSATDA--VKE 538
            VLRIRQILTNLISNA+KFT EGKVGI LYV+PEP     EG  Q     QS   A   KE
Sbjct: 451  VLRIRQILTNLISNAVKFTHEGKVGINLYVIPEPSSGNGEGCPQMFIDDQSTVSANIPKE 510

Query: 539  EKHQPKSQTASDQNGFHDKKHGEGYQDHKHDDDPGTPVSHGNSMDED------LEATVWI 592
            +K    SQ++    G H        Q+H  +D+P  P++H +S  ED      LE TVWI
Sbjct: 511  QKCLSPSQSSCTSKGSH-------TQNHALNDEPIDPINHDDSKQEDKENSHPLETTVWI 563

Query: 593  RCDVYDTGIGIPENALPTLFRKYMQVSADHARKYGGTGLGLAICKQLVELMGGRLTVTSK 652
            RCDVYDTGIGIPE+ALPTLF+KYMQVSADHARKYGGTGLGLAICKQLVELMGG +TV+S+
Sbjct: 564  RCDVYDTGIGIPEHALPTLFKKYMQVSADHARKYGGTGLGLAICKQLVELMGGHMTVSSR 623

Query: 653  VHCGSTFTFILPYQVSPIEENSDDPDDLSDMADQDSVTDDVTAGFFQFQPRTLGSLFSSN 712
             H GSTFTFILPY+VS I ++SDDPD+LSDMAD D+ TDD  AGFFQF PRTLGSLFSS 
Sbjct: 624  EHSGSTFTFILPYKVSLISDHSDDPDELSDMADDDASTDDKNAGFFQFHPRTLGSLFSSG 683

Query: 713  GTSRSKKLLPNSIGFASAHKVNGFSETSYSFPSNN-RQKETAPLEDACSVAEVAETLSEP 771
            G+ R++KL PN+IG+ S HK+NG S+ SYSFP N    KE   LEDACSV + AETLSEP
Sbjct: 684  GSGRTQKLPPNNIGYDSLHKLNGLSDDSYSFPFNKVTSKEMTSLEDACSVVDAAETLSEP 743

Query: 772  ESSFSHSPEPENETEVSRGKQCHVETTSWFQNPATESTSHSEANREMIQTSKTNEPQKIC 831
            ES   H+ EP+N+  VSRGK+C  E      N +  ST HS+ ++E+ +  KT+E  ++C
Sbjct: 744  ESLLRHNAEPDNDNAVSRGKKCQDEANGQVHNHSXGSTHHSKVSKEVDEMGKTSEAPEMC 803

Query: 832  EMQEKPDRISQSPSSSSAEVPETKPKPKPKILLVEDNKINVMVAKSMMKQLGHSIDVVNN 891
               E  +R SQ  SSSS E    K   KPKILLVED+KINVMV +SMMKQLGH+IDVVNN
Sbjct: 804  LRLEISERSSQCTSSSSPE--XPKSTLKPKILLVEDSKINVMVTQSMMKQLGHTIDVVNN 861

Query: 892  GVEAVHAVQCQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDAAAEAGIEQAMPSSGS 951
            G+EAV AVQC++YDLILMDVCMPVMDGL+ATR+IRSFE+TGNWDAA +AGIE   PS+ S
Sbjct: 862  GIEAVRAVQCRSYDLILMDVCMPVMDGLQATRIIRSFEETGNWDAAVKAGIE---PSTCS 918

Query: 952  SNHF----------KRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQYF 1001
            S+            KR+PIIAMTANALSESA+EC+ANGMDSFVSKPVTFQKL +CL+QY 
Sbjct: 919  SDSLPNGHDSMXVTKRVPIIAMTANALSESADECYANGMDSFVSKPVTFQKLTQCLQQYL 978

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356552435|ref|XP_003544573.1| PREDICTED: histidine kinase 5-like [Glycine max]

 Score = 1357 bits (3511), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 700/1009 (69%), Positives = 797/1009 (78%), Gaps = 85/1009 (8%)

Query: 5    METDLIEDMDIEGLPSMWPEDIGSD--KQFNVERPGGGQDMLEEVTIPEDQTIVDFKRLL 62
            ME+D IEDMDIE L SMWPEDIG+D  KQFN+E+PG  QDMLEEVTI E+ TI DF+RL+
Sbjct: 1    MESDCIEDMDIEVLSSMWPEDIGTDVGKQFNIEKPGRDQDMLEEVTIIEEPTIADFQRLM 60

Query: 63   ELTNYTDKGSSQMAYLVKHWEYRQSNAVRLLREELDNLSRQRQESELKKLEILEEHRFEE 122
            ELTNYTDKGSSQ+AYL+KHWEY+Q+NAVRLLREELDNLS+QR+E EL+KLEIL++ RFEE
Sbjct: 61   ELTNYTDKGSSQLAYLMKHWEYKQANAVRLLREELDNLSKQRKEVELRKLEILKDTRFEE 120

Query: 123  EGYGGDKRPISIMDELSDMWKDV-CP-RKNDVVFQSKRVEVDAEYDTVEYWKQRALDLEK 180
            E YGGDKRP+SI+DE+   W+DV  P RK+++V Q+KR+E+DAEYDTV YWKQRAL LE+
Sbjct: 121  ENYGGDKRPVSILDEVYYTWQDVPVPLRKSNIVVQTKRIEIDAEYDTVVYWKQRALQLER 180

Query: 181  MLEASGQREQALMEKLNESVTNLEKQSSPVEELSQILKRADNFLHFVLQNAPVVMGHQDK 240
             LEAS QREQ LM+KL ESV NLE+QSSPVEELSQILKRADNFLHF+LQNAPVV+GHQDK
Sbjct: 181  QLEASVQREQILMDKLEESVKNLERQSSPVEELSQILKRADNFLHFILQNAPVVIGHQDK 240

Query: 241  ELRYRFIYNHFPSLHEEDILGKTDVEIFSGAGVKESQDFKREVLEKGLPAKREITFETEL 300
            ELRYRFIYNHFPSL EEDI+GKTDVEIF+G+GVKESQDFKREV+EKGLPAK+EITFETEL
Sbjct: 241  ELRYRFIYNHFPSLQEEDIIGKTDVEIFTGSGVKESQDFKREVMEKGLPAKKEITFETEL 300

Query: 301  FGSKTFLIYVEPVFSKSGETIGVNYMGMDVTDQVRKREKMAKLREEIAVQKAKETELNKT 360
            FGSKTFLIYVEPVFSK+GETIGVNYMGM++TDQVRKRE+MAKLREEIAVQKAKETELNKT
Sbjct: 301  FGSKTFLIYVEPVFSKAGETIGVNYMGMEITDQVRKRERMAKLREEIAVQKAKETELNKT 360

Query: 361  IHITEETMRAKQMLATMSHEIRSPLTGVVSMAEILSNTKLDREQRQLLGVMISSGDLVLQ 420
            IHITEETMRAKQMLATMSHEIRSPL+GVVSMAEILS TKLDREQRQLL VMISSGDLVLQ
Sbjct: 361  IHITEETMRAKQMLATMSHEIRSPLSGVVSMAEILSTTKLDREQRQLLNVMISSGDLVLQ 420

Query: 421  LINDILDLSKVESGVMKLEAAKFRPREVVKHVLQTAAASLQKILMLEGDIADDVPIEVIG 480
            LINDILDLSKVESGVMKLEA KFRPREVVKHVLQTAAASLQK+L LEG++ADD+PIEVIG
Sbjct: 421  LINDILDLSKVESGVMKLEATKFRPREVVKHVLQTAAASLQKMLTLEGNVADDMPIEVIG 480

Query: 481  DVLRIRQILTNLISNAIKFTPEGKVGIKLYVVPEPPFAKEGLKQKSKAYQSATDAVKEEK 540
            DVLRIRQILTNL+SNA+KFT EGKVGI LYVVPEPPFAK    QK    QS+  +     
Sbjct: 481  DVLRIRQILTNLVSNAVKFTHEGKVGINLYVVPEPPFAKAEGHQKMITEQSSVKSECSMN 540

Query: 541  HQPKSQTASDQNGFHDKKHGEGYQDHKHDDDPGTPVSHGNSMDEDLEATVWIRCDVYDTG 600
               + QT S +                                     TVWIRCDVYDTG
Sbjct: 541  GDTEEQTHSTE-------------------------------------TVWIRCDVYDTG 563

Query: 601  IGIPENALPTLFRKYMQVSADHARKYGGTGLGLAICKQLVELMGGRLTVTSKVHCGSTFT 660
            IGIPE A+PTLFR+YMQVSADHARKYGGTGLGLAICKQLVELMGGRLTVTSK H GSTFT
Sbjct: 564  IGIPEKAIPTLFRRYMQVSADHARKYGGTGLGLAICKQLVELMGGRLTVTSKEHVGSTFT 623

Query: 661  FILPYQVSPIEENSDDPDDLSDMADQDSVTDDVTAGFFQFQPRTLGSLFSSNGTSRSKKL 720
            FILPY+VS   ++SDDPD+LSD+ D D  T   T GFFQFQPRTLGSLF+SNG +R + +
Sbjct: 624  FILPYKVSTACDDSDDPDELSDVDDNDDDT---TEGFFQFQPRTLGSLFTSNGPTRPQNI 680

Query: 721  LPNSIGFASAHKVNGFSETSYSF-PSNNRQKETAPLEDACSVAEVAETLSEPESSFSHSP 779
            LP   GF S+HK NG SE SYSF  +N R K  +  ED  SV                  
Sbjct: 681  LP---GFRSSHKFNGISENSYSFLTTNTRSKGISSTEDQESVINT--------------- 722

Query: 780  EPENETEVSRGKQCHVETTSWFQNPATESTSHSEANREMIQT--SKTNEPQKICEMQE-- 835
               NE +     + H       QN + +S+ H E    M+ T  + +NEPQ+ C++    
Sbjct: 723  --NNENQ----DKAHAR----LQNGSVDSSQHKEV---MVMTLGTMSNEPQQTCQLVNTD 769

Query: 836  -KPDRISQSPSSSSAEVPETKPKPKPKILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVE 894
                R+  S +++ +EV  TK    PKILLVEDNKINVMV +SMMK+LG+S+DVVNNGVE
Sbjct: 770  ITSQRVISSNNNTLSEV--TKSSLGPKILLVEDNKINVMVTQSMMKRLGYSMDVVNNGVE 827

Query: 895  AVHAVQCQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDAAAEAGIEQAMPSSG--SS 952
            AV AVQ   YD+ILMDV MPVM+GL+ T+LIRS+EDTGNW+AA +AGIEQ +P+S   S 
Sbjct: 828  AVRAVQHHTYDIILMDVYMPVMNGLQTTKLIRSYEDTGNWEAARKAGIEQCLPASNECSV 887

Query: 953  NHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQYF 1001
                RI IIAMTAN +SESAEEC+ANGMDSFVSKPVTFQKLK+CLEQY 
Sbjct: 888  PPKNRIHIIAMTANTMSESAEECYANGMDSFVSKPVTFQKLKDCLEQYL 936

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255548630|ref|XP_002515371.1| sensor histidine kinase, putative [Ricinus communis] gi|223545315|gb|EEF46820.1| sensor histidine kinase, putative [Ricinus communis]

 Score = 1351 bits (3497), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 691/968 (71%), Positives = 777/968 (80%), Gaps = 68/968 (7%)

Query: 4   NMETDLIEDMDIEGLPSMWPEDIGSDKQFNVERPGGGQDMLEEVTIPEDQTIVDFKRLLE 63
           N +T+ IEDMDIE +PSMWPEDI S+K +NVE+P G QDMLEEVTI E+ +IVDF RL+E
Sbjct: 3   NDQTEQIEDMDIEVVPSMWPEDIDSEKPYNVEKPRGDQDMLEEVTIVEEPSIVDFHRLIE 62

Query: 64  LTNYTDKGSSQMAYLVKHWEYRQSNAVRLLREELDNLSRQRQESELKKLEILEEHRFEEE 123
           LTNYTD+GSSQ+AYLVKHWEY+Q NAVRLL+EELD LS+QRQE ELKKLEILE+ RFEEE
Sbjct: 63  LTNYTDRGSSQLAYLVKHWEYQQINAVRLLKEELDILSQQRQEVELKKLEILEDFRFEEE 122

Query: 124 GYGGDKRPISIMDELSDMWKDVCPRKNDVVFQSKRVEVDAEYDTVEYWKQRALDLEKMLE 183
           GYG DKRPISI+DE+ D+++ +  RK DV  Q+KRV VDAEYDTV YWKQR +DLEK+LE
Sbjct: 123 GYGSDKRPISILDEVIDLYQVLPIRKKDVTVQNKRVVVDAEYDTVAYWKQRTMDLEKLLE 182

Query: 184 ASGQREQALMEKLNESVTNLEKQSSPVEELSQILKRADNFLHFVLQNAPVVMGHQDKELR 243
           AS QREQ L+EKL ES+ +LE+QSSPVEELSQILKRADNFLHF+LQNAPVVMGHQDKELR
Sbjct: 183 ASIQREQVLIEKLQESIKDLERQSSPVEELSQILKRADNFLHFILQNAPVVMGHQDKELR 242

Query: 244 YRFIYNHFPSLHEEDILGKTDVEIFSGAGVKESQDFKREVLEKGLPAKREITFETELFGS 303
           YRFIYNHFP L EEDILGKTD+EIFSGAGVKESQDFKREVLEKGLPAKREITFETELFGS
Sbjct: 243 YRFIYNHFPRLGEEDILGKTDMEIFSGAGVKESQDFKREVLEKGLPAKREITFETELFGS 302

Query: 304 KTFLIYVEPVFSKSGETIGVNYMGMDVTDQVRKREKMAKLREEIAVQKAKETELNKTIHI 363
           KTFLIYVEPVFSKSG TIG+NYMGMDVTDQVRKREKMAKLREEIAVQKAKETELNKTIHI
Sbjct: 303 KTFLIYVEPVFSKSGVTIGINYMGMDVTDQVRKREKMAKLREEIAVQKAKETELNKTIHI 362

Query: 364 TEETMRAKQMLATMSHEIRSPLTGVVSMAEILSNTKLDREQRQLLGVMISSGDLVLQLIN 423
           TEETMRAKQMLATMSHEIRSPL+GVVSMAEILS T LDREQRQLL VMISSGDLVLQLIN
Sbjct: 363 TEETMRAKQMLATMSHEIRSPLSGVVSMAEILSTTNLDREQRQLLNVMISSGDLVLQLIN 422

Query: 424 DILDLSKVESGVMKLEAAKFRPREVVKHVLQTAAASLQKILMLEGDIADDVPIEVIGDVL 483
           DILDLSKVESGVMKLEA KFRPREVVKHVLQTAAASL+K L+LEG +ADDVPIEVIGDVL
Sbjct: 423 DILDLSKVESGVMKLEATKFRPREVVKHVLQTAAASLKKFLILEGCVADDVPIEVIGDVL 482

Query: 484 RIRQILTNLISNAIKFTPEGKVGIKLYVVPEPPFAK-EGLKQKSKAYQSATDAVKEEKHQ 542
           RIRQILTNLISNAIKFT EGKVGI LYVV +P F K +G  QKS A           K +
Sbjct: 483 RIRQILTNLISNAIKFTHEGKVGINLYVVADPCFGKADGNHQKSSA-----------KEE 531

Query: 543 PKSQTASDQNGFHDKKHGEGYQDHKHDDDPGTPVSHGNSMDEDLEATVWIRCDVYDTGIG 602
            +SQ                                        E  VW+RCDVYDTGIG
Sbjct: 532 AQSQ----------------------------------------ETLVWLRCDVYDTGIG 551

Query: 603 IPENALPTLFRKYMQVSADHARKYGGTGLGLAICKQLVELMGGRLTVTSKVHCGSTFTFI 662
           IPENALPTLF+KYMQVSADHARKYGGTGLGLAICKQLVELMGGRLTV+S+V+CGSTFTFI
Sbjct: 552 IPENALPTLFKKYMQVSADHARKYGGTGLGLAICKQLVELMGGRLTVSSRVNCGSTFTFI 611

Query: 663 LPYQVSPIEENSDDPDDLSDMADQDSVTDDVTAGFFQFQPRTLGSLFSSNGTSRSKKLLP 722
           LPY+VS + ++SDD ++LS+MAD D+ T+D TAGFF FQP TLGS FSSNG++R++K+ P
Sbjct: 612 LPYKVSSMCDSSDDAEELSEMADHDAGTEDETAGFFSFQPLTLGSPFSSNGSTRTQKIFP 671

Query: 723 NSIGFASAHKVNGFSETSYSFPSNN-RQKETAPLEDACSVAEVAETLSEPESSFSHSPEP 781
           +     ++HK+NG S+  YSFPS+N R KETA +EDACS  EVA+TLSEPESS+SHSPEP
Sbjct: 672 H-----NSHKLNGLSDNLYSFPSSNVRLKETASVEDACSTVEVADTLSEPESSYSHSPEP 726

Query: 782 ENETEVSRGKQCHVETTSWFQNPATESTSHSEANREMIQTSKTNEPQKICEMQEKPDRIS 841
           +NE    R KQ   + +S   N    ST H E  RE+   +   EPQ  C  QEK D  S
Sbjct: 727 DNENVACRSKQFQ-DDSSQLHNCTMVSTCHVEPCREVDAQAIEREPQGSCFAQEKSDISS 785

Query: 842 QSPSSSSAEVPETKPKPKPKILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQC 901
           Q     S +VP +  K +PKILLVEDN +NVMV +SMMKQLGH+IDVVNNG+EAV AVQ 
Sbjct: 786 QPTCGRSPQVPMS--KLQPKILLVEDNNVNVMVTRSMMKQLGHTIDVVNNGIEAVRAVQG 843

Query: 902 QNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDAAAEAGIEQAMP-------SSGSSNH 954
             YDL+LMDVCMPVMDGL+ATRLIRSFE+TG+WDAA +AGIE + P       S G    
Sbjct: 844 NCYDLVLMDVCMPVMDGLQATRLIRSFEETGSWDAATKAGIELSAPFSSSLPDSPGCMPS 903

Query: 955 FKRIPIIA 962
            +R PIIA
Sbjct: 904 TRRTPIIA 911

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224092694|ref|XP_002309700.1| histidine kinase cytokinin receptor [Populus trichocarpa] gi|222855676|gb|EEE93223.1| histidine kinase cytokinin receptor [Populus trichocarpa]

 Score = 1347 bits (3487), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 702/1012 (69%), Positives = 793/1012 (78%), Gaps = 103/1012 (10%)

Query: 5    METDLIEDMDIEGLPSMWPEDIGSDKQFNVERPGGGQDMLEEVTIPEDQTIVDFKRLLEL 64
            ME D +EDMDIE L SMWPEDI S K + VE+P G QDMLEEVTI E  TIVDF  L+EL
Sbjct: 1    MENDQMEDMDIEALSSMWPEDIDSSKPY-VEKPVGDQDMLEEVTIVEGPTIVDFHHLVEL 59

Query: 65   TNYTDKGSSQMAYLVKHWEYRQSNAVRLLREELDNLSRQRQESELKKLEILEEHRFEEEG 124
            TNYTD+GSSQ+A+LV+HWEY+Q+NAVRLLREELD L++QR+E ELKKLEILE+ RFEEE 
Sbjct: 60   TNYTDRGSSQLAHLVQHWEYKQANAVRLLREELDILNKQREEVELKKLEILEDFRFEEER 119

Query: 125  YGGDKRPISIMDELSDMWKDVCPRKNDVVFQSKRVEVDAEYDTVEYWKQRALDLEKMLEA 184
            Y GDKR ISI+DE+ D+++D+  RK+D++ QSKRV++DAE+DTV YWKQR + LEK+LEA
Sbjct: 120  YSGDKRQISILDEIFDIYQDIPRRKSDIIVQSKRVDIDAEFDTVAYWKQRVVHLEKLLEA 179

Query: 185  SGQREQALMEKLNESVTNLEKQSSPVEELSQILKRADNFLHFVLQNAPVVMGHQDKELRY 244
            S  RE+ L EKL ES+ NLEKQSSPVEEL+QILKRADNFLHFVLQNAPVV+GHQDK+LRY
Sbjct: 180  SVHREELLTEKLQESIQNLEKQSSPVEELTQILKRADNFLHFVLQNAPVVIGHQDKDLRY 239

Query: 245  RFIYNHFPSLHEEDILGKTDVEIFSGAGVKESQDFKREVLEKGLPAKREITFETELFGSK 304
            RFIYNHFP L EE+I+GKTDVEIFSGAGVKESQDFK+EVL+KGLPAKREITFETELFGSK
Sbjct: 240  RFIYNHFPRLQEEEIIGKTDVEIFSGAGVKESQDFKKEVLDKGLPAKREITFETELFGSK 299

Query: 305  TFLIYVEPVFSKSGETIGVNYMGMDVTDQVRKREKMAKLREEIAVQKAKETELNKTIHIT 364
            TFLIYVEPVFSKSGETIG+NYMGMDVTDQVRKREKMA+LREEIAVQKAKETELNKTIHIT
Sbjct: 300  TFLIYVEPVFSKSGETIGINYMGMDVTDQVRKREKMARLREEIAVQKAKETELNKTIHIT 359

Query: 365  EETMRAKQMLATMSHEIRSPLTGVVSMAEILSNTKLDREQRQLLGVMISSGDLVLQLIND 424
            EETMRAKQMLATMSHEIRSPL+GVVSMAEILS T LDREQRQLL VMISSGDLVLQLIND
Sbjct: 360  EETMRAKQMLATMSHEIRSPLSGVVSMAEILSTTNLDREQRQLLNVMISSGDLVLQLIND 419

Query: 425  ILDLSKVESGVMKLEAAKFRPREVVKHVLQTAAASLQKILMLEGDIADDVPIEVIGDVLR 484
            ILDLSKVESGVMKLEA KFRPREVVKHVLQTAAASLQKIL LEG +ADDVPIEVIGDVLR
Sbjct: 420  ILDLSKVESGVMKLEATKFRPREVVKHVLQTAAASLQKILTLEGRVADDVPIEVIGDVLR 479

Query: 485  IRQILTNLISNAIKFTPEGKVGIKLYVVPEPPFAKEGLKQKSKAYQSATDAVKEEKHQPK 544
            IRQILTNLISNAIKFT EGKVGIKLYVV +P + K                  E KHQ  
Sbjct: 480  IRQILTNLISNAIKFTHEGKVGIKLYVVSDPCYGK-----------------AERKHQ-- 520

Query: 545  SQTASDQNGFHDKKHGEGYQDHKHDDDPGTPVSHGNSMDEDL-------EATVWIRCDVY 597
                                    +++P TPV +GN+MD D          TVW+ CDVY
Sbjct: 521  ------------------------NNEPQTPVKNGNTMDGDKGEEPEVPGTTVWLCCDVY 556

Query: 598  DTGIGIPENALPTLFRKYMQVSADHARKYGGTGLGLAICKQLVELMGGRLTVTSKVHCGS 657
            DTGIGIP+NALPTLF+KYMQVSADHARKYGGTGLGLAICKQLVELMGGRLTV+SKV CGS
Sbjct: 557  DTGIGIPDNALPTLFKKYMQVSADHARKYGGTGLGLAICKQLVELMGGRLTVSSKVKCGS 616

Query: 658  TFTFILPYQVSPIEENSDDPDDLSDMADQDSVTDDVTAGFFQFQPRTLGSLFSSNGTSRS 717
            TFTF+LPY+VS   ++SDDPDDLS+MAD D+  +D TAGFFQFQPRTLGSLFSSNG++R+
Sbjct: 617  TFTFVLPYKVSSTCDSSDDPDDLSEMADHDAPLEDETAGFFQFQPRTLGSLFSSNGSTRT 676

Query: 718  KKLLPNSIGFASAHKVNGFSETSYSFPSNNRQKETAPLEDACSVAEVAETLSEPESSFSH 777
            +KLLP+SIGF+++  +NGFSE S+SFPS+                               
Sbjct: 677  QKLLPHSIGFSNSPILNGFSEDSFSFPSDR------------------------------ 706

Query: 778  SPEPENETEVSRGKQCHVETTSWFQNPATESTSHSEANREMIQTSKTNEPQKICEMQEKP 837
                +NE  V R KQC  ET S   N      +H E          + +P   C+ QEK 
Sbjct: 707  ----DNENVVCRRKQCLDETKSKIPNGTKNCNNHKEV---------SGDPPGSCQEQEKS 753

Query: 838  DRISQSPSSSSAEVPETKPKPKPKILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVH 897
               SQ  SSS  + PE+  KPKPKILLVEDNKINVMV KSMMKQLGH++DVVNNGVEAV 
Sbjct: 754  ATSSQCTSSSIPQEPES--KPKPKILLVEDNKINVMVTKSMMKQLGHTMDVVNNGVEAVR 811

Query: 898  AVQCQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKR 957
            AVQ  +YDLILMDVCMPVM+GL+AT+LIRSFE+TGNWDAA +AGIE +M     ++ F  
Sbjct: 812  AVQSCSYDLILMDVCMPVMNGLQATQLIRSFEETGNWDAAIKAGIEPSMCLGFYTSRFTP 871

Query: 958  IP-------IIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQYFP 1002
             P        + MTANALSESAEEC+ANGMDSFVSKPVTFQK+KECLEQY P
Sbjct: 872  EPPKDVLFSSVRMTANALSESAEECYANGMDSFVSKPVTFQKIKECLEQYLP 923

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356509864|ref|XP_003523664.1| PREDICTED: histidine kinase 5-like [Glycine max]

 Score = 1324 bits (3427), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 690/1009 (68%), Positives = 783/1009 (77%), Gaps = 88/1009 (8%)

Query: 1    MVCNMETDLIEDMDIEGLPSMWPEDIGSD--KQFNVERPGGGQDMLEEVTIPEDQTIVDF 58
            M+  ME D I+DMDIE +PSMWPEDIG +  KQFN+E+PG  QDMLEEVTI E+ TIVDF
Sbjct: 1    MLLEMENDCIKDMDIEVVPSMWPEDIGMEVGKQFNIEKPGRDQDMLEEVTIIEEPTIVDF 60

Query: 59   KRLLELTNYTDKGSSQMAYLVKHWEYRQSNAVRLLREELDNLSRQRQESELKKLEILEEH 118
            KRL+ELTN+T+KGSSQ+AYL+K WEY+Q+N VRLLREELDNLS+QRQ+ EL+KLEILEEH
Sbjct: 61   KRLMELTNFTEKGSSQLAYLMKQWEYKQANVVRLLREELDNLSKQRQDVELRKLEILEEH 120

Query: 119  RFEEEGYGGDKRPISIMDELSD-MWKDVCPRKNDVVFQSKRVEVDAEYDTVEYWKQRALD 177
            RFEEE +G DKRP+SI+D++ D +W+D+  R++DVV ++KR E+DAEYDTV  WKQRAL 
Sbjct: 121  RFEEERHGADKRPVSILDDVYDGIWQDIPCRRSDVVVENKRSEIDAEYDTVMCWKQRALH 180

Query: 178  LEKMLEASGQREQALMEKLNESVTNLEKQSSPVEELSQILKRADNFLHFVLQNAPVVMGH 237
             EK LEAS QREQ L EKL E + N+E+QSSPVEELSQILKRADNFLHF+LQNAP+V+GH
Sbjct: 181  SEKQLEASIQREQILEEKLQERIANIERQSSPVEELSQILKRADNFLHFILQNAPIVIGH 240

Query: 238  QDKELRYRFIYNHFPSLHEEDILGKTDVEIFSGAGVKESQDFKREVLEKGLPAKREITFE 297
            QDKELRY FIYNHFPSL EEDI+GKTDVEIF+GAGVKE+Q+FKREVLEKGLPAKREITFE
Sbjct: 241  QDKELRYCFIYNHFPSLQEEDIIGKTDVEIFTGAGVKEAQEFKREVLEKGLPAKREITFE 300

Query: 298  TELFGSKTFLIYVEPVFSKSGETIGVNYMGMDVTDQVRKREKMAKLREEIAVQKAKETEL 357
            TELFGSKTFLIYVEPVFSK+GETIG+NYMGMD+TDQVRKRE+MAK+REEIAVQKAKETEL
Sbjct: 301  TELFGSKTFLIYVEPVFSKAGETIGINYMGMDITDQVRKRERMAKIREEIAVQKAKETEL 360

Query: 358  NKTIHITEETMRAKQMLATMSHEIRSPLTGVVSMAEILSNTKLDREQRQLLGVMISSGDL 417
            NKTIHITEETMRAKQMLATMSHEIRSPL+GVVSMAEILSNTKLD EQRQLL VM+SSGDL
Sbjct: 361  NKTIHITEETMRAKQMLATMSHEIRSPLSGVVSMAEILSNTKLDWEQRQLLDVMLSSGDL 420

Query: 418  VLQLINDILDLSKVESGVMKLEAAKFRPREVVKHVLQTAAASLQKILMLEGDIADDVPIE 477
            VLQLINDILDLSKVESGVMKLEA KFRPREVV+HVLQ AAASLQKIL LEG +ADDVPIE
Sbjct: 421  VLQLINDILDLSKVESGVMKLEATKFRPREVVRHVLQIAAASLQKILTLEGHVADDVPIE 480

Query: 478  VIGDVLRIRQILTNLISNAIKFTPEGKVGIKLYVVPEPPFAKEGLKQKSKAYQSATDAVK 537
            VIGDVLR+RQILTNLISNAIKFT EGKVGI LYVV EP FAK    QK  +  S      
Sbjct: 481  VIGDVLRMRQILTNLISNAIKFTHEGKVGINLYVVSEPTFAKAECIQKMTSSHSTI---- 536

Query: 538  EEKHQPKSQTASDQNGFHDKKHGEGYQDHKHDDDPGTPVSHGNSMDEDLEATVWIRCDVY 597
                QP S                                         E TVWIRCDVY
Sbjct: 537  --SEQPNSA----------------------------------------ETTVWIRCDVY 554

Query: 598  DTGIGIPENALPTLFRKYMQVSADHARKYGGTGLGLAICKQLVELMGGRLTVTSKVHCGS 657
            DTGIGIPE+A+PTLF++YMQVSADH RKYGGTGLGLAICKQLVELMGG+LTV+SK H GS
Sbjct: 555  DTGIGIPEDAIPTLFKRYMQVSADHTRKYGGTGLGLAICKQLVELMGGQLTVSSKEHYGS 614

Query: 658  TFTFILPYQVSPIEENSDDPDDLSDMADQDSVTDDVTAGFFQFQPRTLGSLFSSNGTSRS 717
            TFTFILPY+VS   ++SDD D+LSD+ + D+ +DD    FFQFQPRTLGSLFSSNG+SR+
Sbjct: 615  TFTFILPYKVSIACDHSDDLDELSDVENNDAASDDTIESFFQFQPRTLGSLFSSNGSSRT 674

Query: 718  KKLLPNSIGFASAHKVNGFSETSYSFPSNN-RQKETAPLEDACSVAEVAETLSEPESSFS 776
             KLL + IG+ S+HK+ GFSE+ YSFPSN+   K T   +DA SV EV            
Sbjct: 675  HKLLTHKIGYTSSHKLGGFSESLYSFPSNDIMSKGTCSADDASSVVEV------------ 722

Query: 777  HSPEPENETEVSRGKQCHVETTSWFQNPATESTSHSEANREMIQTSKTNEPQKICEMQEK 836
              PE       S   Q                   +++N EM +       Q  C+   K
Sbjct: 723  --PEMSESASSSGHSQ------------------KTKSNGEMSEAKSNELQQTTCQGHGK 762

Query: 837  PDRISQSPSSSS-AEVPETKPKPKPKILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEA 895
             +   Q  ++SS +EV  TK    PKILLVEDNKINVMV +SMMKQLGHSIDVVNNGVEA
Sbjct: 763  TNTTFQCVTNSSVSEV--TKSTIIPKILLVEDNKINVMVTQSMMKQLGHSIDVVNNGVEA 820

Query: 896  VHAVQCQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDAAAEAGIEQAMP---SSGSS 952
            V AVQ   YDLILMDVCMPVM+GL+AT+LIR+FE+TGNWDAA  AGIEQ++       S 
Sbjct: 821  VRAVQRHTYDLILMDVCMPVMNGLQATKLIRTFEETGNWDAARNAGIEQSVQDPDCECSV 880

Query: 953  NHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQYF 1001
               KRIPI+AMTANALSESAEECFANGMDSFVSKPV FQKLKEC+EQY 
Sbjct: 881  PSTKRIPIVAMTANALSESAEECFANGMDSFVSKPVAFQKLKECIEQYL 929

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357437045|ref|XP_003588798.1| Histidine kinase cytokinin receptor [Medicago truncatula] gi|355477846|gb|AES59049.1| Histidine kinase cytokinin receptor [Medicago truncatula]

 Score = 1323 bits (3424), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 706/1092 (64%), Positives = 827/1092 (75%), Gaps = 107/1092 (9%)

Query: 1    MVCNMETDLIEDM-DIEGLPSMWPEDIGSD--KQFNVERPGGGQDMLEEVTIPEDQTIVD 57
            MVC ME+D IEDM DIE L SMWPED+G+D  KQFN+E+PG  QDMLEEVTI E+  I D
Sbjct: 1    MVCEMESDCIEDMMDIEELSSMWPEDVGTDVGKQFNIEKPGRDQDMLEEVTILEEPAIAD 60

Query: 58   FKRLLELTNYTDKGSSQMAYLVKHWEYRQSNAVRLLREELDNLSRQRQESELKKLEILEE 117
            F+RL+ELTNYTDKGSSQ+AYL++HWEY+Q+NAVRLLREELDNLS+QR+E E +KLEIL+E
Sbjct: 61   FQRLMELTNYTDKGSSQLAYLMQHWEYKQANAVRLLREELDNLSKQRKEVEQRKLEILKE 120

Query: 118  H-RFEEE-GYGGDKRPISIMDELSDMWKDV--CPRKNDVVFQSKRVEVDAEYDTVEYWKQ 173
            + RFEEE  YGGDKRP+SI+D+    W+D+    RK+D+V Q+KR+E++AEYDTV YWKQ
Sbjct: 121  NNRFEEEISYGGDKRPVSILDDAYYTWQDLPAAIRKSDIVVQNKRIEIEAEYDTVVYWKQ 180

Query: 174  RALDLEKMLEASGQREQALMEKLNESVTNLEKQSSPVEELSQILKRADNFLHFVLQNAPV 233
            R+ D EK LEAS +RE  L EKL ES+  +E+QSSPVEELSQILKRADNFLHF+LQNAPV
Sbjct: 181  RSQDFEKQLEASIRREDILKEKLQESIETIERQSSPVEELSQILKRADNFLHFILQNAPV 240

Query: 234  VMGHQDKELRYRFIYNHFPSLHEEDILGKTDVEIFSGAGVKESQDFKREVLEKGLPAKRE 293
            V+GHQDKELRYRFIYNHFPSL EEDI+GKTDVEIF+GAGVKESQDFKREV+EKG+PAK+E
Sbjct: 241  VIGHQDKELRYRFIYNHFPSLQEEDIIGKTDVEIFTGAGVKESQDFKREVMEKGVPAKKE 300

Query: 294  ITFETELFGSKTFLIYVEPVFSKSGETIGVNYMGMDVTD--------------------- 332
            ITFETELFG KTFLIYVEPVFSK+GETIGVNYMGM++TD                     
Sbjct: 301  ITFETELFGFKTFLIYVEPVFSKAGETIGVNYMGMEITDQVNIVILVVFKVLNCSIVLVK 360

Query: 333  ---------QVRKREKMAKLREEIAVQKAKETELNKTIHITEETMRAKQMLATMSHEIRS 383
                     QVRKRE+MAKLREEIAVQKAKETELNKTIHITEETMRAKQMLATMSHEIRS
Sbjct: 361  KIFIISKKSQVRKRERMAKLREEIAVQKAKETELNKTIHITEETMRAKQMLATMSHEIRS 420

Query: 384  PLTGVVSMAEILSNTKLDREQRQLLGVMISSGDLVLQLINDILDLSKVESGVMKLEAAKF 443
            PL+GVVSMAEIL+ TKLD+EQRQLL VM+SSGDLVLQLINDILDLSKVESG MKLEA KF
Sbjct: 421  PLSGVVSMAEILTTTKLDKEQRQLLDVMLSSGDLVLQLINDILDLSKVESGAMKLEATKF 480

Query: 444  RPREVVKHVLQTAAASLQKILMLEGDIADDVPIEVIGDVLRIRQILTNLISNAIKFTPEG 503
            RPREVV+HVLQTAAA LQK+L LEG++ADD+PIEV GDVLRIRQILTNL+SNA+KFT +G
Sbjct: 481  RPREVVRHVLQTAAAPLQKMLTLEGNVADDIPIEVTGDVLRIRQILTNLVSNAVKFTHQG 540

Query: 504  KVGIKLYVVPEPPFAK-EGLKQKSKAYQSATDA--VKEEKHQPKSQTA-SDQNGFHDKKH 559
            KVGI LYVVPEP FAK E   QK    QS   A  +KE+KH P  ++   DQN   D+KH
Sbjct: 541  KVGINLYVVPEPAFAKEEESHQKVTEDQSTISANGLKEDKHTPSPRSMRCDQNLIDDRKH 600

Query: 560  GEG-YQDHKHDDDPGTPVSHGNSMDED--------LEATVWIRCDVYDTGIGIPENALPT 610
             +   Q+H   ++  + V+   SM++D        +E TVWIRCDVYDTGIGIPE A+PT
Sbjct: 601  ADHPIQNHAFSNECRSSVNSECSMNDDDTEEQTHSIETTVWIRCDVYDTGIGIPEKAIPT 660

Query: 611  LFRKYMQVSADHARKYGGTGLGLAICKQLVELMGGRLTVTSKVHCGSTFTFILPYQVSPI 670
            LFR+YMQVSADHARKYGGTGLGLAICKQLVELMGGRLTVTSK HCGSTFTFILPY+VS  
Sbjct: 661  LFRRYMQVSADHARKYGGTGLGLAICKQLVELMGGRLTVTSKEHCGSTFTFILPYKVSTA 720

Query: 671  EENSDDPDDLSDMADQDSVTDDVTAGFFQFQPRTLGSLFSSNGTSRSKKLLPNSIGFASA 730
             ENSDDPDDLSD+ + +   DD T GFFQFQPRTLGSLF+SNG++R  ++         +
Sbjct: 721  CENSDDPDDLSDVDNNE---DDTTEGFFQFQPRTLGSLFTSNGSTRPHRI---------S 768

Query: 731  HKVNGFSET-SYSFPSNN-RQKETAPLEDACSVAEVAETLSEPESSFSHSPEPENETEVS 788
            HK NGF +  SYS  S+N     T  +EDA SV   A  +SE  +SFSHS E ++E+  +
Sbjct: 769  HKFNGFPDNDSYSNHSSNIISNGTNSIEDASSVIVDASDMSESTNSFSHSLETKHESLCN 828

Query: 789  RGKQCHVETTSW--FQNPATESTSHSEANREMIQTSKTNEPQKICEMQEKPDRISQSPSS 846
              KQ H    +    QN +  S    EA+REM   +K+NEPQ+ C+ Q K D  + + +S
Sbjct: 829  GNKQNHDNNKAHDRLQNGSANSIHWKEASREMNLETKSNEPQQTCQGQGKEDSTTSNSTS 888

Query: 847  SSAEVPETKPKPKPKILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDL 906
            S      TK   KP ILLVEDNKIN+MV KSMMKQLG+S+DVVNNGVEA+ AVQ  +YD+
Sbjct: 889  SEV----TKSTLKPNILLVEDNKINIMVTKSMMKQLGYSMDVVNNGVEAIRAVQSHSYDI 944

Query: 907  ILM-----------------------------------DVCMPVMDGLKATRLIRSFEDT 931
            ILM                                   DV MPVM+GL+ T+LIRS+E+T
Sbjct: 945  ILMVISSILNCIFHFVAFSYNSHIMGFYELRFDTFTLQDVYMPVMNGLQTTKLIRSYEET 1004

Query: 932  GNWDAAAEAGIEQAMPSSG--SSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVT 989
            GNWDAA EAG+EQ++ +S   S    KRI I+AMTAN +SESAEECFANGMD+FVSKPVT
Sbjct: 1005 GNWDAAREAGVEQSLSASDECSVPPKKRIHIVAMTANTMSESAEECFANGMDAFVSKPVT 1064

Query: 990  FQKLKECLEQYF 1001
            F KLKECLE+Y 
Sbjct: 1065 FLKLKECLEKYL 1076

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449447373|ref|XP_004141443.1| PREDICTED: histidine kinase 5-like [Cucumis sativus]

 Score = 1246 bits (3225), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 660/1016 (64%), Positives = 763/1016 (75%), Gaps = 97/1016 (9%)

Query: 5    METDLIEDMDIEGLPSMWPEDIGSD--KQFNVERPGGGQDMLEEVTIPEDQTIVDFKRLL 62
            ME  +IEDMDIE +PSMWPED+G D  KQFNVERPG  QDMLEEV I E+ TIVDFKRL+
Sbjct: 1    MENGVIEDMDIEAVPSMWPEDVGPDVRKQFNVERPGADQDMLEEVNIIEEPTIVDFKRLI 60

Query: 63   ELTNYTDKGSSQMAYLVKHWEYRQSNAVRLLREELDNLSRQRQESELKKLEILEEHRFEE 122
            ELTNYT+KGSSQ+ YL K WEY+Q+NAVRLL+EELD LS+QR+E ELKKL+ILEEH FEE
Sbjct: 61   ELTNYTEKGSSQLQYLAKQWEYKQANAVRLLKEELDILSKQRKEVELKKLKILEEHLFEE 120

Query: 123  EGYGGDKRPISIMDELSDMWKDVCPRKNDVVFQSKRVEVDAEYDTVEYWKQRALDLEKML 182
            E Y GDKRPISI++E  D+W+D+  RK D VFQSKRVE+DAEYDTV YWKQRA+DLEK+L
Sbjct: 121  ERYAGDKRPISILEESCDIWQDIPRRKTDFVFQSKRVEIDAEYDTVTYWKQRAMDLEKLL 180

Query: 183  EASGQREQALMEKLNESVTNLEKQSSPVEELSQILKRADNFLHFVLQNAPVVMGHQDKEL 242
            EAS QREQ L EKL E++ N+EKQSSPVEELSQILKRADNFLHFVLQNAPVV GHQDKEL
Sbjct: 181  EASLQREQMLAEKLKENIKNIEKQSSPVEELSQILKRADNFLHFVLQNAPVVFGHQDKEL 240

Query: 243  RYRFIYNHFPSLHEEDILGKTDVEIFSGAGVKESQDFKREVLEKGLPAKREITFETELFG 302
            RYRFIYNHFPSL EEDI+G+TDVEIFSGAGVKESQDFK+EVLEKGLPAKREI F+TELFG
Sbjct: 241  RYRFIYNHFPSLQEEDIIGRTDVEIFSGAGVKESQDFKKEVLEKGLPAKREIQFDTELFG 300

Query: 303  SKTFLIYVEPVFSKSGETIGVNYMGMDVTDQVRKREKMAKLREEIAVQKAKETELNKTIH 362
             KTFLIYVEPVFSK+GETIG+NYMGMD+TDQV+KREKMAKLREEIAVQKAKE+ELNKTIH
Sbjct: 301  LKTFLIYVEPVFSKAGETIGINYMGMDITDQVKKREKMAKLREEIAVQKAKESELNKTIH 360

Query: 363  ITEETMRAKQMLATMSHEIRSPLTGVVSMAEILSNTKLDREQRQLLGVMISSGDLVLQLI 422
            ITEETMRAKQMLATMSHEIRSPL+GVVSMAEILS TKLDREQR LL VM+SSGDLVLQLI
Sbjct: 361  ITEETMRAKQMLATMSHEIRSPLSGVVSMAEILSTTKLDREQRHLLDVMLSSGDLVLQLI 420

Query: 423  NDILDLSKVESGVMKLEAAKFRPREVVKHVLQTAAASLQKILMLEGDIADDVPIEVIGDV 482
            NDILDLSKVESGVMKLEA KFRPREVVKHVLQTAAASL+K L+LEG IADDVPIEVIGDV
Sbjct: 421  NDILDLSKVESGVMKLEATKFRPREVVKHVLQTAAASLRKFLVLEGRIADDVPIEVIGDV 480

Query: 483  LRIRQILTNLISNAIKFTPEGKVGIKLYVVPEPPFAKEGLKQKSKAYQSATDAVKEEKHQ 542
            LRIRQILTNLISNAIKFT +GKVGI LYV+P PP                          
Sbjct: 481  LRIRQILTNLISNAIKFTHQGKVGINLYVLPYPPI------------------------- 515

Query: 543  PKSQTASDQNGFHDKKHGEGYQDHKHDDDPGTPVSHGNSMDEDLEATVWIRCDVYDTGIG 602
                             G G + HK         S         E TVWIRCDVYDTGIG
Sbjct: 516  -----------------GTGEECHKKSTAENKSCSP--------ETTVWIRCDVYDTGIG 550

Query: 603  IPENALPTLFRKYMQVSADHARKYGGTGLGLAICKQLVELMGGRLTVTSKVHCGSTFTFI 662
            IPENALPTLF++YMQ SADHARKYGGTGLGLAICKQLVELMGG LTV+S+ + GSTFTF+
Sbjct: 551  IPENALPTLFKRYMQASADHARKYGGTGLGLAICKQLVELMGGHLTVSSRENHGSTFTFV 610

Query: 663  LPYQVSPIEENSDDPDDLSDMADQDSVTDDVTAGFFQFQPRTLGSLFSSNGTSRSKKLLP 722
            LPY+VS    +    DD  +++D +S  D++T GFFQFQP +  +L SSNG++R    L 
Sbjct: 611  LPYKVS---SSCSPSDDSDEISDDESTNDEMTEGFFQFQPHSFSTLSSSNGSTRIPNSLL 667

Query: 723  NSIGFASAHKVNGFSE-TSYSFPSNNRQKETAPLEDACSVAEVAETLSEPESSFSHSPEP 781
            ++ G+ ++ K+NG +E   Y  P NN            + A+V  +     SS   +P  
Sbjct: 668  HTTGYPTSTKLNGLTEGVPYPIPLNN-----------IANADVVTSSKSQCSSSHVNPNL 716

Query: 782  ENETEVSRGKQCHVETTSWFQN-------PATESTSHSEANREMIQTSKTNEPQKICEMQ 834
            +N        Q   +T +  QN       P  E+T   +   +     ++N+ QK  + +
Sbjct: 717  DN--------QNQPDTNARLQNVGGVNSLPKLETTKLEDRLEK-----QSNKLQKTDQGK 763

Query: 835  EKPDRISQSPSSSSAEVPETKPKPKPKILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVE 894
            E+ +  +   +SSS   PE     +P+ILLVEDNK N+MV +SMMK+ G  IDVV NG+E
Sbjct: 764  ERSEASNHCRNSSSG--PEVTLALEPRILLVEDNKTNIMVTQSMMKKFGQKIDVVTNGIE 821

Query: 895  AVHAVQCQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDAAAEAGI--------EQAM 946
            AV AVQ ++YDLILMDV MPVMDGL+ATRLIRSFE+TG+W+AA  AGI            
Sbjct: 822  AVRAVQRRSYDLILMDVFMPVMDGLEATRLIRSFEETGSWEAAVNAGIFHHPTTTPSWTP 881

Query: 947  PSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQYFP 1002
             SS SS+   R+PIIAMTAN++SESAEEC+ NGMDSFVSKP+TFQKLKECLE+Y P
Sbjct: 882  SSSSSSSSRNRMPIIAMTANSMSESAEECYENGMDSFVSKPITFQKLKECLERYLP 937

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449486822|ref|XP_004157413.1| PREDICTED: LOW QUALITY PROTEIN: histidine kinase 5-like [Cucumis sativus]

 Score = 1246 bits (3223), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 659/1016 (64%), Positives = 763/1016 (75%), Gaps = 97/1016 (9%)

Query: 5    METDLIEDMDIEGLPSMWPEDIGSD--KQFNVERPGGGQDMLEEVTIPEDQTIVDFKRLL 62
            ME  +IEDMDIE +PSMWPED+G D  KQFNVERPG  QDMLEEV I E+ TIVDFKRL+
Sbjct: 1    MENGVIEDMDIEAVPSMWPEDVGPDVRKQFNVERPGADQDMLEEVNIIEEPTIVDFKRLI 60

Query: 63   ELTNYTDKGSSQMAYLVKHWEYRQSNAVRLLREELDNLSRQRQESELKKLEILEEHRFEE 122
            ELTNYT+KGSSQ+ YL K WEY+Q+NAVRLL+EELD LS+QR+E ELKKL+ILEEH FEE
Sbjct: 61   ELTNYTEKGSSQLQYLAKQWEYKQANAVRLLKEELDILSKQRKEVELKKLKILEEHLFEE 120

Query: 123  EGYGGDKRPISIMDELSDMWKDVCPRKNDVVFQSKRVEVDAEYDTVEYWKQRALDLEKML 182
            E Y GDKRPISI++E  D+W+D+  RK D VFQSKRVE+DAEYDTV YWKQRA+DLEK+L
Sbjct: 121  ERYAGDKRPISILEESCDIWQDIPRRKTDFVFQSKRVEIDAEYDTVTYWKQRAMDLEKLL 180

Query: 183  EASGQREQALMEKLNESVTNLEKQSSPVEELSQILKRADNFLHFVLQNAPVVMGHQDKEL 242
            EAS QREQ L EKL E++ N+EKQSSPVEELSQILKRADNFLHFVLQNAPVV GHQDKEL
Sbjct: 181  EASLQREQMLAEKLKENIKNIEKQSSPVEELSQILKRADNFLHFVLQNAPVVFGHQDKEL 240

Query: 243  RYRFIYNHFPSLHEEDILGKTDVEIFSGAGVKESQDFKREVLEKGLPAKREITFETELFG 302
            RYRFIYNHFPSL EEDI+G+TDVEIFSGAGVKESQDFK+EVLEKGLPAKREI F+TELFG
Sbjct: 241  RYRFIYNHFPSLQEEDIIGRTDVEIFSGAGVKESQDFKKEVLEKGLPAKREIQFDTELFG 300

Query: 303  SKTFLIYVEPVFSKSGETIGVNYMGMDVTDQVRKREKMAKLREEIAVQKAKETELNKTIH 362
             KTFLIYVEPVFSK+GET+G+NYMGMD+TDQV+KREKMAKLREEIAVQKAKE+ELNKTIH
Sbjct: 301  LKTFLIYVEPVFSKAGETLGINYMGMDITDQVKKREKMAKLREEIAVQKAKESELNKTIH 360

Query: 363  ITEETMRAKQMLATMSHEIRSPLTGVVSMAEILSNTKLDREQRQLLGVMISSGDLVLQLI 422
            ITEETMRAKQMLATMSHEIRSPL+GVVSMAEILS TKLDREQR LL VM+SSGDLVLQLI
Sbjct: 361  ITEETMRAKQMLATMSHEIRSPLSGVVSMAEILSTTKLDREQRHLLDVMLSSGDLVLQLI 420

Query: 423  NDILDLSKVESGVMKLEAAKFRPREVVKHVLQTAAASLQKILMLEGDIADDVPIEVIGDV 482
            NDILDLSKVESGVMKLEA KFRPREVVKHVLQTAAASL+K L+LEG IADDVPIEVIGDV
Sbjct: 421  NDILDLSKVESGVMKLEATKFRPREVVKHVLQTAAASLRKFLVLEGRIADDVPIEVIGDV 480

Query: 483  LRIRQILTNLISNAIKFTPEGKVGIKLYVVPEPPFAKEGLKQKSKAYQSATDAVKEEKHQ 542
            LRIRQILTNLISNAIKFT +GKVGI LYV+P PP                          
Sbjct: 481  LRIRQILTNLISNAIKFTHQGKVGINLYVLPYPPI------------------------- 515

Query: 543  PKSQTASDQNGFHDKKHGEGYQDHKHDDDPGTPVSHGNSMDEDLEATVWIRCDVYDTGIG 602
                             G G + HK         S         E TVWIRCDVYDTGIG
Sbjct: 516  -----------------GTGEECHKKSTAENKSCSP--------ETTVWIRCDVYDTGIG 550

Query: 603  IPENALPTLFRKYMQVSADHARKYGGTGLGLAICKQLVELMGGRLTVTSKVHCGSTFTFI 662
            IPENALPTLF++YMQ SADHARKYGGTGLGLAICKQLVELMGG LTV+S+ + GSTFTF+
Sbjct: 551  IPENALPTLFKRYMQASADHARKYGGTGLGLAICKQLVELMGGHLTVSSRENHGSTFTFV 610

Query: 663  LPYQVSPIEENSDDPDDLSDMADQDSVTDDVTAGFFQFQPRTLGSLFSSNGTSRSKKLLP 722
            LPY+VS    +    DD  +++D +S  D++T GFFQFQP +  +L SSNG++R    L 
Sbjct: 611  LPYKVS---SSCSPSDDSDEISDDESTNDEMTEGFFQFQPHSFSTLSSSNGSTRIPNSLL 667

Query: 723  NSIGFASAHKVNGFSE-TSYSFPSNNRQKETAPLEDACSVAEVAETLSEPESSFSHSPEP 781
            ++ G+ ++ K+NG +E   Y  P NN            + A+V  +     SS   +P  
Sbjct: 668  HTTGYPTSTKLNGLTEGVPYPIPLNN-----------IANADVVTSSKSQCSSSHVNPNL 716

Query: 782  ENETEVSRGKQCHVETTSWFQN-------PATESTSHSEANREMIQTSKTNEPQKICEMQ 834
            +N        Q   +T +  QN       P  E+T   +   +     ++N+ QK  + +
Sbjct: 717  DN--------QNQPDTNARLQNVGGVNSLPKLETTKLEDRLEK-----QSNKLQKTDQGK 763

Query: 835  EKPDRISQSPSSSSAEVPETKPKPKPKILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVE 894
            E+ +  +   +SSS   PE     +P+ILLVEDNK N+MV +SMMK+ G  IDVV NG+E
Sbjct: 764  ERSEASNHCRNSSSG--PEVTLALEPRILLVEDNKTNIMVTQSMMKKFGQKIDVVTNGIE 821

Query: 895  AVHAVQCQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDAAAEAGI--------EQAM 946
            AV AVQ ++YDLILMDV MPVMDGL+ATRLIRSFE+TG+W+AA  AGI            
Sbjct: 822  AVRAVQRRSYDLILMDVFMPVMDGLEATRLIRSFEETGSWEAAVNAGIFHHPTTTPSWTP 881

Query: 947  PSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQYFP 1002
             SS SS+   R+PIIAMTAN++SESAEEC+ NGMDSFVSKP+TFQKLKECLE+Y P
Sbjct: 882  SSSSSSSSRNRMPIIAMTANSMSESAEECYENGMDSFVSKPITFQKLKECLERYLP 937

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	1002
TAIR|locus:2159669	922	HK5 "histidine kinase 5" [Arab	0.513	0.558	0.701	2.1e-286
TIGR_CMR|SPO_0094	743	SPO_0094 "sensory box sensor h	0.201	0.271	0.401	2.4e-54
DICTYBASE|DDB_G0277883	2062	dhkJ "histidine kinase J" [Dic	0.162	0.079	0.425	3.7e-53
TIGR_CMR|GSU_1285	772	GSU_1285 "sensory box sensor h	0.291	0.378	0.288	2.8e-52
TIGR_CMR|GSU_2314	1025	GSU_2314 "sensory box histidin	0.176	0.172	0.346	3e-51
CGD|CAL0002691	1081	NIK1 [Candida albicans (taxid:	0.137	0.127	0.402	3.1e-50
UNIPROTKB|Q5A599	1081	NIK1 "Putative uncharacterized	0.137	0.127	0.402	3.1e-50
TIGR_CMR|GSU_1928	810	GSU_1928 "sensor histidine kin	0.173	0.214	0.366	3.7e-50
TIGR_CMR|GSU_0718	589	GSU_0718 "sensory box histidin	0.168	0.286	0.392	2.5e-49
TAIR|locus:2015964	1036	HK3 "histidine kinase 3" [Arab	0.142	0.138	0.430	9.9e-49

TAIR|locus:2159669 HK5 "histidine kinase 5" [Arabidopsis thaliana (taxid:3702)]

 Score = 1819 (645.4 bits), Expect = 2.1e-286, Sum P(3) = 2.1e-286
 Identities = 366/522 (70%), Positives = 425/522 (81%)

Query:     1 MVCNMETDLIEDMDIEGLPSMWPEDIGS--DKQFNVERPGGGQDMLEEVTIPEDQTIVDF 58
             MVC METD IE+MD+E L SMWPED+G+  DKQFNVE+P G  D L+EVTI E +TI D 
Sbjct:     1 MVCEMETDQIEEMDVEVLSSMWPEDVGTEADKQFNVEKPAGDLDTLKEVTI-ETRTIADM 59

Query:    59 KRLLELTNYTDKGSSQMAYLVKHWEYRQSNAVRLLREELDNLSRQRQXXXXXXXXXXXXX 118
              RL  L N T +GSSQ+  LVK WEY Q NAVRLL+EEL NL RQR+             
Sbjct:    60 TRLPNLLNSTHQGSSQLTNLVKQWEYMQDNAVRLLKEELKNLDRQREEAEAKELKIIEEY 119

Query:   119 XXXXXGYGGDKRPISIMDELSDMWKDVCPRKNDVVFQSKRVEVDAEYDTVEYWKQRALDL 178
                      +   + ++DE SD+++    +K D +  SK++E+  E+DTV YWKQ+AL L
Sbjct:   120 KFES----NEPENVPVLDETSDLFRRFRQKKRDALVDSKKIEIYEEFDTVAYWKQKALSL 175

Query:   179 EKMLEASGQREQALMEKLNESVTNLEKQSSPVEELSQILKRADNFLHFVLQNAPVVMGHQ 238
             EKMLEAS +RE+ LMEKL+ES+  +E QS+PV+EL+Q LKRA+ FLHF+LQNAP+VMGHQ
Sbjct:   176 EKMLEASTERERRLMEKLSESLKTMESQSAPVQELTQNLKRAEGFLHFILQNAPIVMGHQ 235

Query:   239 DKELRYRFIYNHFPSLHEEDILGKTDVEIFSGAGVKESQDFKREVLEKGLPAKREITFET 298
             DK+LRY FIYN +PSL E+DILGKTDVEIF G GVKES+DFKREVLEKG  +KREITF T
Sbjct:   236 DKDLRYLFIYNKYPSLREQDILGKTDVEIFHGGGVKESEDFKREVLEKGKASKREITFTT 295

Query:   299 ELFGSKTFLIYVEPVFSKSGETIGVNYMGMDVTDQVRKREKMAKLREEIAVQKAKETELN 358
             +LFGSKTFLIYVEPV++K+GE IG+NYMGM+VTDQV KREKMAKLRE+ AV+KA E+ELN
Sbjct:   296 DLFGSKTFLIYVEPVYNKAGEKIGINYMGMEVTDQVVKREKMAKLREDNAVRKAMESELN 355

Query:   359 KTIHITEETMRAKQMLATMSHEIRSPLTGVVSMAEILSNTKLDREQRQLLGVMISSGDLV 418
             KTIHITEETMRAKQMLATMSHEIRSPL+GVV MAEILS TKLD+EQRQLL VMISSGDLV
Sbjct:   356 KTIHITEETMRAKQMLATMSHEIRSPLSGVVGMAEILSTTKLDKEQRQLLNVMISSGDLV 415

Query:   419 LQLINDILDLSKVESGVMKLEAAKFRPREVVKHVLQTAAASLQKILMLEGDIADDVPIEV 478
             LQLINDILDLSKVESGVM+LEA KFRPREVVKHVLQTAAASL+K L LEG+IADDVPIEV
Sbjct:   416 LQLINDILDLSKVESGVMRLEATKFRPREVVKHVLQTAAASLKKSLTLEGNIADDVPIEV 475

Query:   479 IGDVLRIRQILTNLISNAIKFTPEGKVGIKLYVVPEPPFAKE 520
             +GDVLRIRQILTNLISNAIKFT EG VGIKL V+ EP F ++
Sbjct:   476 VGDVLRIRQILTNLISNAIKFTHEGNVGIKLQVISEPSFVRD 517

GO:0000155 "phosphorelay sensor kinase activity" evidence=IEA

GO:0000156 "phosphorelay response regulator activity" evidence=IEA

GO:0000160 "phosphorelay signal transduction system" evidence=IEA

GO:0004673 "protein histidine kinase activity" evidence=IEA;ISS;IDA

GO:0004871 "signal transducer activity" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0005886 "plasma membrane" evidence=ISM;IDA

GO:0006355 "regulation of transcription, DNA-dependent" evidence=IEA

GO:0007165 "signal transduction" evidence=IEA

GO:0016020 "membrane" evidence=IEA

GO:0016310 "phosphorylation" evidence=IEA

GO:0016772 "transferase activity, transferring phosphorus-containing groups" evidence=IEA

GO:0018106 "peptidyl-histidine phosphorylation" evidence=IEA

GO:0009736 "cytokinin mediated signaling pathway" evidence=TAS

GO:0005773 "vacuole" evidence=IDA

GO:0009788 "negative regulation of abscisic acid mediated signaling pathway" evidence=IMP

GO:0010105 "negative regulation of ethylene mediated signaling pathway" evidence=IMP

GO:0048364 "root development" evidence=IMP

GO:0005737 "cytoplasm" evidence=IDA

GO:0070301 "cellular response to hydrogen peroxide" evidence=IMP

GO:0071219 "cellular response to molecule of bacterial origin" evidence=IMP

GO:0071732 "cellular response to nitric oxide" evidence=IMP

GO:0090333 "regulation of stomatal closure" evidence=IMP

GO:0010048 "vernalization response" evidence=RCA

GO:0043481 "anthocyanin accumulation in tissues in response to UV light" evidence=RCA

GO:0048440 "carpel development" evidence=RCA

TIGR_CMR|SPO_0094 SPO_0094 "sensory box sensor histidine kinase/response regulator" [Ruegeria pomeroyi DSS-3 (taxid:246200)]

 Score = 325 (119.5 bits), Expect = 2.4e-54, Sum P(4) = 2.4e-54
 Identities = 82/204 (40%), Positives = 114/204 (55%)

Query:   315 SKSGETIGVNYMGMDVTDQVRKREKMAKLREEIAVQKAKETELNKTIHITEETMRAK-QM 373
             +K G  I +    + V D+  K E    +  ++   KA+  EL       EE  RAK + 
Sbjct:   309 TKDGREIWMETNLVPVLDRNGKVEVTVAIERDVTAAKAQAEELAAARVAAEEGARAKAEF 368

Query:   374 LATMSHEIRSPLTGVVSMAEILSNTKLDREQRQLLGVMISSGDLVLQLINDILDLSKVES 433
             LATMSHEIR+P+ GVV MAE+LS TKL  EQRQ +  + SS   +L +INDIL+LS++++
Sbjct:   369 LATMSHEIRTPMNGVVGMAELLSETKLSIEQRQYVDTIRSSSTALLAIINDILELSRLDA 428

Query:   434 GVMKLEAAKFRPREVVKHVLQTAAASLQ-KILMLEGDIADDVPIEVIGDVLRIRQILTNL 492
               M+L    F P   V+  ++      Q K L L  +   DVP  V GD  R+RQ+L NL
Sbjct:   429 RKMELHPVNFDPVSCVRDTMRLLKPQAQAKGLRLSLETGADVPPLVYGDDGRLRQVLINL 488

Query:   493 ISNAIKFTPEGKVGIKLYVVPEPP 516
             + NAIKFT  G V ++L    + P
Sbjct:   489 LGNAIKFTERGGVTLRLRSEAQDP 512

GO:0000155 "phosphorelay sensor kinase activity" evidence=ISS

GO:0000156 "phosphorelay response regulator activity" evidence=ISS

GO:0000160 "phosphorelay signal transduction system" evidence=ISS

GO:0004871 "signal transducer activity" evidence=ISS

DICTYBASE|DDB_G0277883 dhkJ "histidine kinase J" [Dictyostelium discoideum (taxid:44689)]

 Score = 316 (116.3 bits), Expect = 3.7e-53, Sum P(5) = 3.7e-53
 Identities = 71/167 (42%), Positives = 106/167 (63%)

Query:   349 VQKAKETELNKTI--HITEETMRAKQ-MLATMSHEIRSPLTGVVSMAEILSNTKLDREQR 405
             +   KET L  T+     E   RAK   +A MSHEIR+P+ G++ M ++  +T+L  EQR
Sbjct:  1323 IHNLKETTLKNTLAKETAEAASRAKSDFMANMSHEIRTPMNGIIGMTDLTLDTELTAEQR 1382

Query:   406 QLLGVMISSGDLVLQLINDILDLSKVESGVMKLEAAKFRPREVVKHVLQTAA-ASLQKIL 464
             + L ++ SS   +L +INDILD SK+E+G ++L+ A+F  R  +   L+T +  + QK +
Sbjct:  1383 EYLSMVQSSAGSLLTIINDILDFSKIEAGRLELDQAEFSLRAHLYDALKTLSWRAHQKCI 1442

Query:   465 MLEGDIADDVPIEVIGDVLRIRQILTNLISNAIKFTPEGKVGIKLYV 511
              L  DIA DVP  +IGD  R+RQI+ NL+ NAIKFT +G+V + + V
Sbjct:  1443 ELVCDIASDVPDSLIGDPGRLRQIVNNLVGNAIKFTSQGEVDLVVKV 1489

GO:0005615 "extracellular space" evidence=IDA

GO:0035556 "intracellular signal transduction" evidence=IEA

GO:0023014 "signal transduction by phosphorylation" evidence=IEA

GO:0016772 "transferase activity, transferring phosphorus-containing groups" evidence=IEA

GO:0016310 "phosphorylation" evidence=IEA

GO:0016021 "integral to membrane" evidence=IEA

GO:0016020 "membrane" evidence=IEA

GO:0007165 "signal transduction" evidence=IEA

GO:0006355 "regulation of transcription, DNA-dependent" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0004871 "signal transducer activity" evidence=IEA

GO:0000160 "phosphorelay signal transduction system" evidence=IEA

GO:0000156 "phosphorelay response regulator activity" evidence=IEA

GO:0000155 "phosphorelay sensor kinase activity" evidence=IEA

GO:0004673 "protein histidine kinase activity" evidence=IEA

GO:0016740 "transferase activity" evidence=IEA

GO:0016301 "kinase activity" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

TIGR_CMR|GSU_1285 GSU_1285 "sensory box sensor histidine kinase/response regulator" [Geobacter sulfurreducens PCA (taxid:243231)]

 Score = 312 (114.9 bits), Expect = 2.8e-52, Sum P(4) = 2.8e-52
 Identities = 91/315 (28%), Positives = 150/315 (47%)

Query:   200 VTNLEKQSSPVEELSQILKRADNFLHFVLQNAP--VVMGHQDKELRY-RFIYNHFPSLHE 256
             +  + +  S  + + + L+    FL  +L  AP  + +   D  LR     +     +  
Sbjct:   137 ILGIARDVSERKRMEESLRSTSEFLDTILDEAPLPIYITSVDGTLRLANNAWERETGIPR 196

Query:   257 EDILGKTDVEIFSGAGVKESQDFKREVLEKGLPAKREITFETELFGSKTFLIYVEPVFSK 316
                +G+   E+F  A   +  +  R V+E    A ++   +    G + F     P+   
Sbjct:   197 NAAVGRRLNELFPAAMCDQFSEINRRVVESNATAVQDEFLDFGA-GVRVFHTIKFPLRDA 255

Query:   317 SGETIGVNYMGMDVTDQVRKREKMAKLREEIAVQKAKETELNKTIHITEETMRAK-QMLA 375
             +G  + V  + +D+TD    R KM             E EL        ++ RAK   LA
Sbjct:   256 AGGVVDVGGISIDITD----RSKM-------------EGELRAAHAAAVDSSRAKIDFLA 298

Query:   376 TMSHEIRSPLTGVVSMAEILSNTKLDREQRQLLGVMISSGDLVLQLINDILDLSKVESGV 435
              MSHEIR+P+ GV+   E+L  T LD  QR+   +   S + +L +IN +LD SK+ES  
Sbjct:   299 NMSHEIRTPMNGVIGTLELLRETDLDPRQREYAEIARESAESMLAVINMVLDYSKIESHQ 358

Query:   436 MKLEAAKFRPREVVKHVLQT-AAASLQKILMLEGDIADDVPIEVIGDVLRIRQILTNLIS 494
             + LEA  F  RE V+  ++   A + +K +M+  D+   VP  V+GD +R  QI+ NL+ 
Sbjct:   359 LVLEAVPFAIREAVERAVKPFRAVAARKGVMVAADVPPHVPETVVGDPVRFSQIVANLVG 418

Query:   495 NAIKFTPEGKVGIKL 509
             NA+KFT +G + ++L
Sbjct:   419 NAVKFTEQGAITVQL 433

GO:0000155 "phosphorelay sensor kinase activity" evidence=ISS

GO:0000156 "phosphorelay response regulator activity" evidence=ISS

GO:0000160 "phosphorelay signal transduction system" evidence=ISS

TIGR_CMR|GSU_2314 GSU_2314 "sensory box histidine kinase/response regulator" [Geobacter sulfurreducens PCA (taxid:243231)]

 Score = 272 (100.8 bits), Expect = 3.0e-51, Sum P(4) = 3.0e-51
 Identities = 62/179 (34%), Positives = 107/179 (59%)

Query:   333 QVRKREKMAKLREEIAVQKAKETELNKTIHITEETMRAK-QMLATMSHEIRSPLTGVVSM 391
             +V+ RE +  +  ++  +K  E EL       E   RAK + LA MSHEIR+P+ GV+ M
Sbjct:   475 EVKGREYLHSIVHDVTERKRAEEELLLAKEQAESANRAKSEFLANMSHEIRTPMNGVIGM 534

Query:   392 AEILSNTKLDREQRQLLGVMISSGDLVLQLINDILDLSKVESGVMKLEAAKFRPREVVKH 451
               +L  T L  EQR+   ++ +S   +LQ+I+DILD SK+E+G +++E   F  R ++  
Sbjct:   535 TGLLLETGLADEQRRYAEIVRTSAASLLQVIDDILDFSKIEAGRLEMETIGFDLRTLLDD 594

Query:   452 VLQTAAASL-QKILMLEGDIADDVPIEVIGDVLRIRQILTNLISNAIKFTPEGKVGIKL 509
             + ++ A    +K L     +  +VP  ++GD +R++Q+L NL  NA+KFT +G++ +++
Sbjct:   595 LAESLAFKANEKGLTFTCLLRPEVPRFLMGDPVRLKQVLVNLAGNALKFTHQGEISVEV 653

GO:0000155 "phosphorelay sensor kinase activity" evidence=ISS

GO:0000156 "phosphorelay response regulator activity" evidence=ISS

GO:0000160 "phosphorelay signal transduction system" evidence=ISS

CGD|CAL0002691 NIK1 [Candida albicans (taxid:5476)]

 Score = 265 (98.3 bits), Expect = 3.1e-50, Sum P(4) = 3.1e-50
 Identities = 56/139 (40%), Positives = 88/139 (63%)

Query:   372 QMLATMSHEIRSPLTGVVSMAEILSNTKLDREQRQLLGVMISSGDLVLQLINDILDLSKV 431
             + LA MSHEIR+PL G++ M ++  +T+L + QR++L ++ +  + +L +I+DILD+SK+
Sbjct:   503 EFLANMSHEIRTPLNGIIGMTQLSLDTELTQYQREMLSIVHNLANSLLTIIDDILDISKI 562

Query:   432 ESGVMKLEAAKFRPREVVKHVLQTAAA-SLQKILMLEGDIADDVPIEVIGDVLRIRQILT 490
             E+  M +E   F  R  V   L+T A  +++K L L        P  +IGD  R+RQ++ 
Sbjct:   563 EANRMTVEQIDFSLRGTVFGALKTLAVKAIEKNLDLTYQCDSSFPDNLIGDSFRLRQVIL 622

Query:   491 NLISNAIKFTPEGKVGIKL 509
             NL  NAIKFT EGKV + +
Sbjct:   623 NLAGNAIKFTKEGKVSVSV 641

GO:0009405 "pathogenesis" evidence=IMP

GO:0004673 "protein histidine kinase activity" evidence=ISS;IDA

GO:0007234 "osmosensory signaling via phosphorelay pathway" evidence=ISS

GO:0000155 "phosphorelay sensor kinase activity" evidence=ISS

GO:0000156 "phosphorelay response regulator activity" evidence=ISS

GO:0071216 "cellular response to biotic stimulus" evidence=IMP

GO:0030447 "filamentous growth" evidence=IMP

GO:1900445 "positive regulation of filamentous growth of a population of unicellular organisms in response to biotic stimulus" evidence=IMP

GO:0036180 "filamentous growth of a population of unicellular organisms in response to biotic stimulus" evidence=IMP

GO:0036170 "filamentous growth of a population of unicellular organisms in response to starvation" evidence=IMP

GO:1900436 "positive regulation of filamentous growth of a population of unicellular organisms in response to starvation" evidence=IMP

GO:0097308 "cellular response to farnesol" evidence=IMP

UNIPROTKB|Q5A599 NIK1 "Putative uncharacterized protein NIK1" [Candida albicans SC5314 (taxid:237561)]

 Score = 265 (98.3 bits), Expect = 3.1e-50, Sum P(4) = 3.1e-50
 Identities = 56/139 (40%), Positives = 88/139 (63%)

Query:   372 QMLATMSHEIRSPLTGVVSMAEILSNTKLDREQRQLLGVMISSGDLVLQLINDILDLSKV 431
             + LA MSHEIR+PL G++ M ++  +T+L + QR++L ++ +  + +L +I+DILD+SK+
Sbjct:   503 EFLANMSHEIRTPLNGIIGMTQLSLDTELTQYQREMLSIVHNLANSLLTIIDDILDISKI 562

Query:   432 ESGVMKLEAAKFRPREVVKHVLQTAAA-SLQKILMLEGDIADDVPIEVIGDVLRIRQILT 490
             E+  M +E   F  R  V   L+T A  +++K L L        P  +IGD  R+RQ++ 
Sbjct:   563 EANRMTVEQIDFSLRGTVFGALKTLAVKAIEKNLDLTYQCDSSFPDNLIGDSFRLRQVIL 622

Query:   491 NLISNAIKFTPEGKVGIKL 509
             NL  NAIKFT EGKV + +
Sbjct:   623 NLAGNAIKFTKEGKVSVSV 641

GO:0000155 "phosphorelay sensor kinase activity" evidence=ISS

GO:0000156 "phosphorelay response regulator activity" evidence=ISS

GO:0004673 "protein histidine kinase activity" evidence=ISS;IDA

GO:0007234 "osmosensory signaling via phosphorelay pathway" evidence=ISS

GO:0009405 "pathogenesis" evidence=IMP

GO:0023014 "signal transduction by phosphorylation" evidence=ISS

GO:0030447 "filamentous growth" evidence=IMP

GO:0035556 "intracellular signal transduction" evidence=ISS

GO:0036170 "filamentous growth of a population of unicellular organisms in response to starvation" evidence=IMP

GO:0036180 "filamentous growth of a population of unicellular organisms in response to biotic stimulus" evidence=IMP

GO:0071216 "cellular response to biotic stimulus" evidence=IMP

GO:0097308 "cellular response to farnesol" evidence=IMP

GO:1900436 "positive regulation of filamentous growth of a population of unicellular organisms in response to starvation" evidence=IMP

GO:1900445 "positive regulation of filamentous growth of a population of unicellular organisms in response to biotic stimulus" evidence=IMP

TIGR_CMR|GSU_1928 GSU_1928 "sensor histidine kinase/response regulator" [Geobacter sulfurreducens PCA (taxid:243231)]

 Score = 304 (112.1 bits), Expect = 3.7e-50, Sum P(4) = 3.7e-50
 Identities = 66/180 (36%), Positives = 115/180 (63%)

Query:   329 DVTDQVRKR-EKMAKLREEIAVQKAKETELNKTIHITEETMRAK-QMLATMSHEIRSPLT 386
             D+ ++V +R E +++  EE+  ++A   +L+K     +   ++K + LA +SHEIR+P+ 
Sbjct:   263 DLGEEVARRTEDLSRTNEEL--ERAV-ADLSKAKEAADSASQSKSRFLANVSHEIRTPMN 319

Query:   387 GVVSMAEILSNTKLDREQRQLLGVMISSGDLVLQLINDILDLSKVESGVMKLEAAKFRPR 446
             GV+ M  +L  T L  +QR+   ++ SSG+L++Q+IND+LD S++ESG +K+E   F  R
Sbjct:   320 GVLGMVSLLLETDLQAKQREYAEIIRSSGELLMQVINDLLDFSRIESGKLKMEQLPFAAR 379

Query:   447 EVVKHVLQT-AAASLQKILMLEGDIADDVPIEVIGDVLRIRQILTNLISNAIKFTPEGKV 505
              V++ +       + QK + LE  +A +VP  ++GD  R+RQ+L NL+ NA+KFT +G +
Sbjct:   380 RVIEEMATIYGERARQKGVFLEYSMAGEVPDRLLGDRHRLRQVLGNLLDNAVKFTLKGTI 439

GO:0000155 "phosphorelay sensor kinase activity" evidence=ISS

GO:0000156 "phosphorelay response regulator activity" evidence=ISS

GO:0000160 "phosphorelay signal transduction system" evidence=ISS

TIGR_CMR|GSU_0718 GSU_0718 "sensory box histidine kinase/response regulator" [Geobacter sulfurreducens PCA (taxid:243231)]

 Score = 283 (104.7 bits), Expect = 2.5e-49, Sum P(4) = 2.5e-49
 Identities = 71/181 (39%), Positives = 105/181 (58%)

Query:   329 DVTDQVRKREKMAKLREEIAVQKAKETELNKTIHITEETMRAK-QMLATMSHEIRSPLTG 387
             D+T   RK  ++ + REE+    AKE          E+  RAK + LA MSHEIR+P+ G
Sbjct:   160 DITMIKRKERELNESREELCW--AKEA--------AEDASRAKSEFLANMSHEIRTPING 209

Query:   388 VVSMAEILSNTKLDREQRQLLGVMISSGDLVLQLINDILDLSKVESGVMKLEAAKFRPRE 447
             V+ M +++ +T+L  EQR  L +   S D +L+L+NDILD S++E+  M  E+  F    
Sbjct:   210 VLGMLQLVLDTELGDEQRHCLEMAKRSADALLRLVNDILDFSRIEARKMVFESRPFDLTA 269

Query:   448 VVKHVLQTAA-ASLQKILMLEGDIADDVPIEVIGDVLRIRQILTNLISNAIKFTPEGKVG 506
              V   ++  A  + +K L +   +  DVP  V+GD  R+RQ+L NLI NA+KFT  GKV 
Sbjct:   270 CVNSAVEILAFEARRKGLAVMVRMGPDVPAAVVGDEARLRQVLVNLIGNAVKFTDRGKVE 329

Query:   507 I 507
             +
Sbjct:   330 V 330

GO:0000155 "phosphorelay sensor kinase activity" evidence=ISS

GO:0000156 "phosphorelay response regulator activity" evidence=ISS

GO:0000160 "phosphorelay signal transduction system" evidence=ISS

TAIR|locus:2015964 HK3 "histidine kinase 3" [Arabidopsis thaliana (taxid:3702)]

 Score = 280 (103.6 bits), Expect = 9.9e-49, Sum P(3) = 9.9e-49
 Identities = 62/144 (43%), Positives = 96/144 (66%)

Query:   372 QMLATMSHEIRSPLTGVVSMAEILSNTKLDREQRQLLGVMISSGDLVLQLINDILDLSKV 431
             Q LAT+SHEIR+P+ GV+ M  +L +T+LD  Q+  +    +SG  ++ LIN++LD +K+
Sbjct:   453 QFLATVSHEIRTPMNGVLGMLHMLMDTELDVTQQDYVRTAQASGKALVSLINEVLDQAKI 512

Query:   432 ESGVMKLEAAKFRPREVVKHVLQT-AAASLQKILMLEGDIADDVPIEVIGDVLRIRQILT 490
             ESG ++LE  +F  R ++  VL   ++ S QK + L   I+D VP  +IGD  R RQILT
Sbjct:   513 ESGKLELEEVRFDLRGILDDVLSLFSSKSQQKGVELAVYISDRVPDMLIGDPGRFRQILT 572

Query:   491 NLISNAIKFTPEGKVGIKLYVVPE 514
             NL+ N+IKFT +G + + +++V E
Sbjct:   573 NLMGNSIKFTEKGHIFVTVHLVDE 596

GO:0000155 "phosphorelay sensor kinase activity" evidence=IEA

GO:0000156 "phosphorelay response regulator activity" evidence=IEA

GO:0000160 "phosphorelay signal transduction system" evidence=IEA

GO:0004673 "protein histidine kinase activity" evidence=IEA;ISS;IDA;IMP

GO:0004871 "signal transducer activity" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0005886 "plasma membrane" evidence=ISM;IDA

GO:0006355 "regulation of transcription, DNA-dependent" evidence=IEA

GO:0007165 "signal transduction" evidence=IEA;RCA

GO:0016310 "phosphorylation" evidence=IEA

GO:0016772 "transferase activity, transferring phosphorus-containing groups" evidence=IEA

GO:0018106 "peptidyl-histidine phosphorylation" evidence=IEA

GO:0009736 "cytokinin mediated signaling pathway" evidence=RCA;TAS

GO:0009884 "cytokinin receptor activity" evidence=TAS

GO:0016036 "cellular response to phosphate starvation" evidence=IMP

GO:0071329 "cellular response to sucrose stimulus" evidence=IMP

GO:0010029 "regulation of seed germination" evidence=RCA;IMP

GO:0010271 "regulation of chlorophyll catabolic process" evidence=IMP

GO:0048831 "regulation of shoot system development" evidence=RCA;IMP

GO:0010150 "leaf senescence" evidence=IMP

GO:0004721 "phosphoprotein phosphatase activity" evidence=IDA

GO:0005515 "protein binding" evidence=IPI

GO:0043424 "protein histidine kinase binding" evidence=IPI

GO:0005034 "osmosensor activity" evidence=IGI

GO:0006970 "response to osmotic stress" evidence=IMP

GO:0009409 "response to cold" evidence=IEP

GO:0009414 "response to water deprivation" evidence=IEP

GO:0009651 "response to salt stress" evidence=IEP

GO:0034757 "negative regulation of iron ion transport" evidence=IMP

GO:0042742 "defense response to bacterium" evidence=IMP;IDA

GO:0010087 "phloem or xylem histogenesis" evidence=IMP

GO:0080117 "secondary growth" evidence=IMP

GO:0009909 "regulation of flower development" evidence=IMP

GO:0048509 "regulation of meristem development" evidence=IMP

GO:0070417 "cellular response to cold" evidence=IMP

GO:0071215 "cellular response to abscisic acid stimulus" evidence=IMP

GO:0000303 "response to superoxide" evidence=RCA

GO:0006635 "fatty acid beta-oxidation" evidence=RCA

GO:0007623 "circadian rhythm" evidence=RCA

GO:0008219 "cell death" evidence=RCA

GO:0009755 "hormone-mediated signaling pathway" evidence=RCA

GO:0009863 "salicylic acid mediated signaling pathway" evidence=RCA

GO:0009873 "ethylene mediated signaling pathway" evidence=RCA

GO:0016558 "protein import into peroxisome matrix" evidence=RCA

GO:0031537 "regulation of anthocyanin metabolic process" evidence=RCA

---

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)
Q3S4A7	AHK5_ARATH	2, ., 7, ., 1, 3, ., 3	0.6063	0.9091	0.9880	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	2.7.13	0.976
3rd Layer	2.7.13.3	0.991

---

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	1002
TIGR02956	968	TIGR02956, TMAO_torS, TMAO reductase sytem sensor	5e-32
COG0642	336	COG0642, BaeS, Signal transduction histidine kinas	1e-29
PRK10841	924	PRK10841, PRK10841, hybrid sensory kinase in two-c	5e-28
cd00156	113	cd00156, REC, Signal receiver domain; originally t	8e-28
PRK11107	919	PRK11107, PRK11107, hybrid sensory histidine kinas	3e-27
PRK15347	921	PRK15347, PRK15347, two component system sensor ki	5e-27
PRK11466	914	PRK11466, PRK11466, hybrid sensory histidine kinas	3e-25
smart00387	111	smart00387, HATPase_c, Histidine kinase-like ATPas	1e-23
COG0784	130	COG0784, CheY, FOG: CheY-like receiver [Signal tra	3e-23
PRK11091	779	PRK11091, PRK11091, aerobic respiration control se	4e-23
pfam02518	111	pfam02518, HATPase_c, Histidine kinase-, DNA gyras	3e-22
cd00075	103	cd00075, HATPase_c, Histidine kinase-like ATPases;	5e-22
pfam00072	111	pfam00072, Response_reg, Response regulator receiv	1e-21
PRK11107	919	PRK11107, PRK11107, hybrid sensory histidine kinas	2e-21
PRK15347	921	PRK15347, PRK15347, two component system sensor ki	7e-20
PRK11091	779	PRK11091, PRK11091, aerobic respiration control se	1e-19
PRK11107	919	PRK11107, PRK11107, hybrid sensory histidine kinas	5e-19
pfam00512	66	pfam00512, HisKA, His Kinase A (phospho-acceptor)	1e-18
TIGR02956	968	TIGR02956, TMAO_torS, TMAO reductase sytem sensor	2e-18
COG0642	336	COG0642, BaeS, Signal transduction histidine kinas	2e-18
smart00388	66	smart00388, HisKA, His Kinase A (phosphoacceptor)	2e-18
PRK10841	924	PRK10841, PRK10841, hybrid sensory kinase in two-c	1e-17
PRK09959	1197	PRK09959, PRK09959, hybrid sensory histidine kinas	1e-17
COG2205	890	COG2205, KdpD, Osmosensitive K+ channel histidine	8e-17
TIGR02966	333	TIGR02966, phoR_proteo, phosphate regulon sensor k	2e-16
PRK11091	779	PRK11091, PRK11091, aerobic respiration control se	4e-16
COG5002	459	COG5002, VicK, Signal transduction histidine kinas	4e-15
TIGR02956	968	TIGR02956, TMAO_torS, TMAO reductase sytem sensor	2e-14
TIGR02966	333	TIGR02966, phoR_proteo, phosphate regulon sensor k	5e-14
COG2205	890	COG2205, KdpD, Osmosensitive K+ channel histidine	8e-14
smart00448	55	smart00448, REC, cheY-homologous receiver domain	2e-13
cd00082	65	cd00082, HisKA, Histidine Kinase A (dimerization/p	2e-13
PRK11466	914	PRK11466, PRK11466, hybrid sensory histidine kinas	6e-13
PRK09959	1197	PRK09959, PRK09959, hybrid sensory histidine kinas	6e-13
PRK09303	380	PRK09303, PRK09303, adaptive-response sensory kina	6e-13
PRK10841	924	PRK10841, PRK10841, hybrid sensory kinase in two-c	8e-13
COG0745	229	COG0745, OmpR, Response regulators consisting of a	9e-13
PRK11100	475	PRK11100, PRK11100, sensory histidine kinase CreC;	2e-12
PRK15347	921	PRK15347, PRK15347, two component system sensor ki	3e-11
PRK10490	895	PRK10490, PRK10490, sensor protein KdpD; Provision	1e-10
COG3437	360	COG3437, COG3437, Response regulator containing a	1e-10
COG3706	435	COG3706, PleD, Response regulator containing a Che	1e-10
PRK11361	457	PRK11361, PRK11361, acetoacetate metabolism regula	2e-10
PRK10618	894	PRK10618, PRK10618, phosphotransfer intermediate p	3e-10
PRK11360	607	PRK11360, PRK11360, sensory histidine kinase AtoS;	8e-10
COG4251	750	COG4251, COG4251, Bacteriophytochrome (light-regul	1e-09
PRK09959	1197	PRK09959, PRK09959, hybrid sensory histidine kinas	2e-09
PRK10365	441	PRK10365, PRK10365, transcriptional regulatory pro	2e-09
COG3290	537	COG3290, CitA, Signal transduction histidine kinas	2e-09
PRK11006	430	PRK11006, phoR, phosphate regulon sensor protein;	4e-09
PRK09835	482	PRK09835, PRK09835, sensor kinase CusS; Provisiona	4e-09
COG4251	750	COG4251, COG4251, Bacteriophytochrome (light-regul	7e-09
COG2197	211	COG2197, CitB, Response regulator containing a Che	1e-08
PRK13837	828	PRK13837, PRK13837, two-component VirA-like sensor	1e-08
COG2204	464	COG2204, AtoC, Response regulator containing CheY-	2e-08
COG4191	603	COG4191, COG4191, Signal transduction histidine ki	3e-08
TIGR01386	457	TIGR01386, cztS_silS_copS, heavy metal sensor kina	5e-08
PRK11086	542	PRK11086, PRK11086, sensory histidine kinase DcuS;	6e-08
PRK10610	129	PRK10610, PRK10610, chemotaxis regulatory protein	6e-08
PRK09303	380	PRK09303, PRK09303, adaptive-response sensory kina	9e-08
PRK10490	895	PRK10490, PRK10490, sensor protein KdpD; Provision	1e-07
PRK12555	337	PRK12555, PRK12555, chemotaxis-specific methyleste	1e-07
PRK10364	457	PRK10364, PRK10364, sensor protein ZraS; Provision	1e-07
PRK10364	457	PRK10364, PRK10364, sensor protein ZraS; Provision	2e-07
PRK11360	607	PRK11360, PRK11360, sensory histidine kinase AtoS;	4e-07
TIGR01386	457	TIGR01386, cztS_silS_copS, heavy metal sensor kina	5e-07
COG2201	350	COG2201, CheB, Chemotaxis response regulator conta	6e-07
COG5002	459	COG5002, VicK, Signal transduction histidine kinas	1e-06
PRK13837	828	PRK13837, PRK13837, two-component VirA-like sensor	1e-06
PRK11517	223	PRK11517, PRK11517, transcriptional regulatory pro	1e-06
TIGR01387	218	TIGR01387, cztR_silR_copR, heavy metal response re	2e-06
TIGR02875	262	TIGR02875, spore_0_A, sporulation transcription fa	2e-06
COG3947	361	COG3947, COG3947, Response regulator containing Ch	2e-06
PRK11100	475	PRK11100, PRK11100, sensory histidine kinase CreC;	3e-06
PRK11006	430	PRK11006, phoR, phosphate regulon sensor protein;	3e-06
PRK10604	433	PRK10604, PRK10604, sensor protein RstB; Provision	3e-06
PRK09467	435	PRK09467, envZ, osmolarity sensor protein; Provisi	3e-06
COG3852	363	COG3852, NtrB, Signal transduction histidine kinas	4e-06
COG4191	603	COG4191, COG4191, Signal transduction histidine ki	5e-06
PRK00742	354	PRK00742, PRK00742, chemotaxis-specific methyleste	8e-06
PRK15479	221	PRK15479, PRK15479, transcriptional regulatory pro	8e-06
TIGR02916	679	TIGR02916, PEP_his_kin, putative PEP-CTERM system	9e-06
PRK09835	482	PRK09835, PRK09835, sensor kinase CusS; Provisiona	1e-05
COG3852	363	COG3852, NtrB, Signal transduction histidine kinas	1e-05
PRK09836	227	PRK09836, PRK09836, DNA-binding transcriptional ac	1e-05
PRK11073	348	PRK11073, glnL, nitrogen regulation protein NR(II)	1e-05
smart00387	111	smart00387, HATPase_c, Histidine kinase-like ATPas	2e-05
PRK10766	221	PRK10766, PRK10766, DNA-binding transcriptional re	2e-05
CHL00148	240	CHL00148, orf27, Ycf27; Reviewed	2e-05
PRK10336	219	PRK10336, PRK10336, DNA-binding transcriptional re	2e-05
COG5000	712	COG5000, NtrY, Signal transduction histidine kinas	3e-05
PRK10618	894	PRK10618, PRK10618, phosphotransfer intermediate p	5e-05
TIGR02154	226	TIGR02154, PhoB, phosphate regulon transcriptional	5e-05
pfam02518	111	pfam02518, HATPase_c, Histidine kinase-, DNA gyras	1e-04
PRK13557	540	PRK13557, PRK13557, histidine kinase; Provisional	1e-04
COG4753	475	COG4753, COG4753, Response regulator containing Ch	2e-04
PRK10710	240	PRK10710, PRK10710, DNA-binding transcriptional re	3e-04
PRK09470	461	PRK09470, cpxA, two-component sensor protein; Prov	3e-04
PRK10549	466	PRK10549, PRK10549, signal transduction histidine-	3e-04
cd00075	103	cd00075, HATPase_c, Histidine kinase-like ATPases;	4e-04
TIGR03785	703	TIGR03785, marine_sort_HK, proteobacterial dedicat	4e-04
PRK10816	223	PRK10816, PRK10816, DNA-binding transcriptional re	4e-04
COG4565	224	COG4565, CitB, Response regulator of citrate/malat	5e-04
PRK10643	222	PRK10643, PRK10643, DNA-binding transcriptional re	8e-04
COG4192	673	COG4192, COG4192, Signal transduction histidine ki	0.001
PRK11083	228	PRK11083, PRK11083, DNA-binding response regulator	0.002
pfam08448	110	pfam08448, PAS_4, PAS fold	0.003
TIGR01818	463	TIGR01818, ntrC, nitrogen regulation protein NR(I)	0.004

>gnl|CDD|234070 TIGR02956, TMAO_torS, TMAO reductase sytem sensor TorS

 Score =  134 bits (339), Expect = 5e-32
 Identities = 68/206 (33%), Positives = 109/206 (52%), Gaps = 17/206 (8%)

Query: 332 DQVRKREKMAKLREEIAVQKAKET-ELNKTIH--------------ITEETMRAK-QMLA 375
           D+ +  +++ + +E +    A+ T EL +T                  EE  RAK   LA
Sbjct: 410 DERQVAQELQEHKESLEQLVAQRTQELAETNERLNAEVKNHAKARAEAEEANRAKSAFLA 469

Query: 376 TMSHEIRSPLTGVVSMAEILSNTKLDREQRQLLGVMISSGDLVLQLINDILDLSKVESGV 435
           TMSHEIR+PL G++   E+L +T L  +Q+Q L V+  SG+ +L ++NDILD SK+E+G 
Sbjct: 470 TMSHEIRTPLNGILGTLELLGDTGLTSQQQQYLQVINRSGESLLDILNDILDYSKIEAGH 529

Query: 436 MKLEAAKFRPREVVKHVLQ-TAAASLQKILMLEGDIADDVPIEVIGDVLRIRQILTNLIS 494
           + +    F    ++  V     + +  K + L  +I + +P    GD  RIRQ+L NL+ 
Sbjct: 530 LSISPRPFDLNALLDDVHHLMVSRAQLKGIQLRLNIPEQLPNWWQGDGPRIRQVLINLVG 589

Query: 495 NAIKFTPEGKVGIKLYVVPEPPFAKE 520
           NAIKFT  G V +++ +  +     E
Sbjct: 590 NAIKFTDRGSVVLRVSLNDDSSLLFE 615

This protein, TorS, is part of a regulatory system for the torCAD operon that encodes the pterin molybdenum cofactor-containing enzyme trimethylamine-N-oxide (TMAO) reductase (TorA), a cognate chaperone (TorD), and a penta-haem cytochrome (TorC). TorS works together with the inducer-binding protein TorT and the response regulator TorR. TorS contains histidine kinase ATPase (pfam02518), HAMP (pfam00672), phosphoacceptor (pfam00512), and phosphotransfer (pfam01627) domains and a response regulator receiver domain (pfam00072) [Signal transduction, Two-component systems]. Length = 968

>gnl|CDD|223715 COG0642, BaeS, Signal transduction histidine kinase [Signal transduction mechanisms]

 Score =  120 bits (302), Expect = 1e-29
 Identities = 59/189 (31%), Positives = 102/189 (53%), Gaps = 5/189 (2%)

Query: 329 DVTDQVRKREKMAKLREEIAVQKAKETELNKTIHITEETMRA--KQMLATMSHEIRSPLT 386
           D  + +        L    +   +    LN+ +   E  +R   ++ LA +SHE+R+PLT
Sbjct: 72  DAANALAAGLTRLVLASLGSELASLAHALNELLERLERLLRRAKREFLANISHELRTPLT 131

Query: 387 GVVSMAEILSNTKLDREQRQLLGVMISSGDLVLQLINDILDLSKVESGV-MKLEAAKFRP 445
            +  + E+L    LD  QR+LL ++    + +L+L+ND+LDLS++E+G  +KL       
Sbjct: 132 AIRGLLELLLEGLLD-PQRELLEIIEEEAERLLRLVNDLLDLSRLEAGTKLKLLLELVDL 190

Query: 446 REVVKHVLQTAAASLQKILMLEGDIADDVPIEVIGDVLRIRQILTNLISNAIKFTPEGKV 505
            E+++ V++  A   Q+   +E  +       V+GD  R+RQ+L NL+SNAIK+TP G++
Sbjct: 191 AELLEEVVRLLAPLAQEK-GIELAVDLPELPYVLGDPERLRQVLVNLLSNAIKYTPGGEI 249

Query: 506 GIKLYVVPE 514
            I +    E
Sbjct: 250 TISVRQDDE 258

Length = 336

>gnl|CDD|182772 PRK10841, PRK10841, hybrid sensory kinase in two-component regulatory system with RcsB and YojN; Provisional

 Score =  121 bits (306), Expect = 5e-28
 Identities = 67/182 (36%), Positives = 109/182 (59%), Gaps = 19/182 (10%)

Query: 334 VRKREKMAKLREEIAVQKAKETELNKTIHITEETMRAKQM-LATMSHEIRSPLTGVVSMA 392
           V  R KM +  +E+A                E+  ++K M LAT+SHE+R+PL G++   
Sbjct: 423 VSARVKMEESLQEMA-------------QAAEQASQSKSMFLATVSHELRTPLYGIIGNL 469

Query: 393 EILSNTKLDREQRQLLGVMISSGDLVLQLINDILDLSKVESGVMKLEAAKFRPREVVKHV 452
           ++L   +L +   +L+  M +S  L+L++I+DILD SK+ES  +K+E  +F PREV+ H+
Sbjct: 470 DLLQTKELPKGVDRLVTAMNNSSSLLLKIISDILDFSKIESEQLKIEPREFSPREVINHI 529

Query: 453 LQTA---AASLQKILMLEGDIADDVPIEVIGDVLRIRQILTNLISNAIKFTPEGKVGIKL 509
             TA      ++K L L   I  DVP+ + GD +R++Q+++NL+SNAIKFT  G + + +
Sbjct: 530 --TANYLPLVVKKRLGLYCFIEPDVPVALNGDPMRLQQVISNLLSNAIKFTDTGCIVLHV 587

Query: 510 YV 511
            V
Sbjct: 588 RV 589

Length = 924

>gnl|CDD|238088 cd00156, REC, Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; contains a phosphoacceptor site that is phosphorylated by histidine kinase homologs; usually found N-terminal to a DNA binding effector domain; forms homodimers

 Score =  108 bits (272), Expect = 8e-28
 Identities = 35/139 (25%), Positives = 63/139 (45%), Gaps = 26/139 (18%)

Query: 863  LLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKAT 922
            L+V+D+ +   + + ++++ G+ +    +G EA+  +  +  DLIL+D+ MP MDGL+  
Sbjct: 1    LIVDDDPLIRELLRRLLEKEGYEVVEAEDGEEALALLAEEKPDLILLDIMMPGMDGLELL 60

Query: 923  RLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDS 982
            R IR                               IPII +TA+   E A E    G D 
Sbjct: 61   RRIRK--------------------------RGPDIPIIFLTAHGDDEDAVEALKAGADD 94

Query: 983  FVSKPVTFQKLKECLEQYF 1001
            +++KP + ++L   +    
Sbjct: 95   YLTKPFSPEELLARIRALL 113

Length = 113

>gnl|CDD|236848 PRK11107, PRK11107, hybrid sensory histidine kinase BarA; Provisional

 Score =  119 bits (301), Expect = 3e-27
 Identities = 62/137 (45%), Positives = 81/137 (59%), Gaps = 1/137 (0%)

Query: 374 LATMSHEIRSPLTGVVSMAEILSNTKLDREQRQLLGVMISSGDLVLQLINDILDLSKVES 433
           LA MSHE+R+PL GV+        T L   QR  L  +  S + +L +INDILD SK+E+
Sbjct: 297 LANMSHELRTPLNGVIGFTRQTLKTPLTPTQRDYLQTIERSANNLLAIINDILDFSKLEA 356

Query: 434 GVMKLEAAKFRPREVVKHVLQTAAASLQ-KILMLEGDIADDVPIEVIGDVLRIRQILTNL 492
           G + LE   F  RE +  V+   A S   K L L  +I  DVP  VIGD LR++QI+TNL
Sbjct: 357 GKLVLENIPFSLRETLDEVVTLLAHSAHEKGLELTLNIDPDVPDNVIGDPLRLQQIITNL 416

Query: 493 ISNAIKFTPEGKVGIKL 509
           + NAIKFT  G + I +
Sbjct: 417 VGNAIKFTESGNIDILV 433

Length = 919

>gnl|CDD|237951 PRK15347, PRK15347, two component system sensor kinase SsrA; Provisional

 Score =  118 bits (298), Expect = 5e-27
 Identities = 60/167 (35%), Positives = 87/167 (52%), Gaps = 14/167 (8%)

Query: 346 EIAVQKAKETELNKTIHITEETMRAKQMLATMSHEIRSPLTGVVSMAEILSNTKLDREQR 405
             A Q+A++    K+ H+T           T+SHEIR+PL GV+   E+L NT L  EQ 
Sbjct: 385 AEAKQRAEQANKRKSEHLT-----------TISHEIRTPLNGVLGALELLQNTPLTAEQM 433

Query: 406 QLLGVMISSGDLVLQLINDILDLSKVESGVMKLEAAKFRPREVVKHVLQT-AAASLQKIL 464
            L          +L +IN++LD S++ESG M L   +     ++   + T    +  K L
Sbjct: 434 DLADTARQCTLSLLAIINNLLDFSRIESGQMTLSLEETALLPLLDQAMLTIQGPAQSKSL 493

Query: 465 MLEGDIADDVPIEVIGDVLRIRQILTNLISNAIKFTPEGKVGIKLYV 511
            L   +   VP+ +  D LR+RQIL NL+ NA+KFT  G  GI+L V
Sbjct: 494 TLRTFVGAHVPLYLHLDSLRLRQILVNLLGNAVKFTETG--GIRLRV 538

Length = 921

>gnl|CDD|236914 PRK11466, PRK11466, hybrid sensory histidine kinase TorS; Provisional

 Score =  113 bits (283), Expect = 3e-25
 Identities = 65/181 (35%), Positives = 106/181 (58%), Gaps = 13/181 (7%)

Query: 329 DVTDQVRKREKMAKLREEIAVQKAKETELNKTIHITEETMRAKQ-MLATMSHEIRSPLTG 387
            +  QV+ R   A+L+E +   +    E        E+  +AK   LA MSHEIR+PL G
Sbjct: 411 QLAAQVKAR--TAELQELVIEHRQARAE-------AEKASQAKSAFLAAMSHEIRTPLYG 461

Query: 388 VVSMAEILSNTKLDREQRQLLGVMISSGDLVLQLINDILDLSKVESG--VMKLEAAKFRP 445
           ++  A++L++      QR  L  +  SG+ +L ++NDILD S +E+G   + +    F P
Sbjct: 462 ILGTAQLLADNPALNAQRDDLRAITDSGESLLTILNDILDYSAIEAGGKNVSVSDEPFEP 521

Query: 446 REVVKHVLQTAAASLQ-KILMLEGDIADDVPIEVIGDVLRIRQILTNLISNAIKFTPEGK 504
           R +++  LQ  +  ++ + + L  DIADD+P  ++GD  RIRQ++TNL+SNA++FT EG 
Sbjct: 522 RPLLESTLQLMSGRVKGRPIRLATDIADDLPTALMGDPRRIRQVITNLLSNALRFTDEGS 581

Query: 505 V 505
           +
Sbjct: 582 I 582

Length = 914

>gnl|CDD|214643 smart00387, HATPase_c, Histidine kinase-like ATPases

 Score = 96.2 bits (240), Expect = 1e-23
 Identities = 33/76 (43%), Positives = 45/76 (59%), Gaps = 1/76 (1%)

Query: 591 WIRCDVYDTGIGIPENALPTLFRKYMQVSADHARKYGGTGLGLAICKQLVELMGGRLTVT 650
            +   V D G GIP   L  +F  + +     +RK GGTGLGL+I K+LVEL GG ++V 
Sbjct: 37  HVEITVEDNGPGIPPEDLEKIFEPFFRTD-KRSRKIGGTGLGLSIVKKLVELHGGEISVE 95

Query: 651 SKVHCGSTFTFILPYQ 666
           S+   G+TFT  LP +
Sbjct: 96  SEPGGGTTFTITLPLE 111

Histidine kinase-, DNA gyrase B-, phytochrome-like ATPases. Length = 111

>gnl|CDD|223855 COG0784, CheY, FOG: CheY-like receiver [Signal transduction mechanisms]

 Score = 96.1 bits (239), Expect = 3e-23
 Identities = 36/148 (24%), Positives = 65/148 (43%), Gaps = 29/148 (19%)

Query: 858  PKPKILLVEDNKINVMVAKSMMKQLGHSIDVVNNG-VEAVHAVQCQN-YDLILMDVCMPV 915
               ++L+V+D  +N  + K +++ LG+ +    +G  EA+  ++     DLIL+D+ MP 
Sbjct: 4    SGLRVLVVDDEPVNRRLLKRLLEDLGYEVVEAADGEEEALELLRELPQPDLILLDINMPG 63

Query: 916  MDGLKATRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEEC 975
            MDG++  R +R                               IP+I +TA A     E  
Sbjct: 64   MDGIELLRRLR--------------------------ARGPNIPVILLTAYADEADRERA 97

Query: 976  FANGMDSFVSKPVTF-QKLKECLEQYFP 1002
             A G D +++KP+   ++L   L +   
Sbjct: 98   LAAGADDYLTKPIFLEEELLAALRRLLA 125

Length = 130

>gnl|CDD|236842 PRK11091, PRK11091, aerobic respiration control sensor protein ArcB; Provisional

 Score =  105 bits (265), Expect = 4e-23
 Identities = 49/155 (31%), Positives = 80/155 (51%), Gaps = 24/155 (15%)

Query: 847  SSAEVPETKPKPKPKILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDL 906
              A   +  P P   ILLVED ++NV+VA+S++++LG+S+DV   G EA+       YDL
Sbjct: 513  EDAFDEDDMPLPALNILLVEDIELNVIVARSVLEKLGNSVDVAMTGKEALEMFDPDEYDL 572

Query: 907  ILMDVCMPVMDGLKATRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTAN 966
            +L+D+ +P M GL   R +R                E  +P           P++A+TAN
Sbjct: 573  VLLDIQLPDMTGLDIARELR-----------ERYPRED-LP-----------PLVALTAN 609

Query: 967  ALSESAEECFANGMDSFVSKPVTFQKLKECLEQYF 1001
             L +  +E    GMD  +SKP++   L   +++++
Sbjct: 610  VLKDK-KEYLDAGMDDVLSKPLSVPALTAMIKKFW 643

Length = 779

>gnl|CDD|217081 pfam02518, HATPase_c, Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase

 Score = 92.0 bits (229), Expect = 3e-22
 Identities = 37/76 (48%), Positives = 50/76 (65%), Gaps = 1/76 (1%)

Query: 591 WIRCDVYDTGIGIPENALPTLFRKYMQVSADHARKYGGTGLGLAICKQLVELMGGRLTVT 650
            +R  V D GIGIP   LP +F  + +  +  +RK GGTGLGL+I ++LVEL GG +TV 
Sbjct: 37  RLRITVEDNGIGIPPEDLPKIFEPFFRTDSS-SRKVGGTGLGLSIVRKLVELHGGTITVE 95

Query: 651 SKVHCGSTFTFILPYQ 666
           S+   G+TFTF LP +
Sbjct: 96  SEPGGGTTFTFTLPLE 111

This family represents the structurally related ATPase domains of histidine kinase, DNA gyrase B and HSP90. Length = 111

>gnl|CDD|238030 cd00075, HATPase_c, Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins

 Score = 91.2 bits (227), Expect = 5e-22
 Identities = 34/73 (46%), Positives = 44/73 (60%), Gaps = 2/73 (2%)

Query: 591 WIRCDVYDTGIGIPENALPTLFRKYMQVSADHARKYGGTGLGLAICKQLVELMGGRLTVT 650
            +   V D G GIPE  L  +F ++       +RK GGTGLGL+I K+LVEL GGR+ V 
Sbjct: 33  HLEIRVEDNGPGIPEEDLERIFERF--SDGSRSRKGGGTGLGLSIVKKLVELHGGRIEVE 90

Query: 651 SKVHCGSTFTFIL 663
           S+   G+TFT  L
Sbjct: 91  SEPGGGTTFTITL 103

Length = 103

>gnl|CDD|200976 pfam00072, Response_reg, Response regulator receiver domain

 Score = 90.3 bits (225), Expect = 1e-21
 Identities = 34/134 (25%), Positives = 63/134 (47%), Gaps = 26/134 (19%)

Query: 862 ILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKA 921
           +L+V+D+ +   + + ++++ G+ +   ++G EA+  ++ +  DLIL+D+ MP MDGL+ 
Sbjct: 1   VLIVDDDPLIRELLRQLLEKEGYVVAEADDGEEALELLKEKRPDLILLDIRMPGMDGLEL 60

Query: 922 TRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMD 981
            R IR                                P+I +TA+   E A E    G +
Sbjct: 61  LRRIR--------------------------RRPPTTPVIVLTAHGDEEDAVEALKAGAN 94

Query: 982 SFVSKPVTFQKLKE 995
            F+SKP   ++L  
Sbjct: 95  DFLSKPFDPEELVA 108

This domain receives the signal from the sensor partner in bacterial two-component systems. It is usually found N-terminal to a DNA binding effector domain. Length = 111

>gnl|CDD|236848 PRK11107, PRK11107, hybrid sensory histidine kinase BarA; Provisional

 Score =  100 bits (252), Expect = 2e-21
 Identities = 35/80 (43%), Positives = 50/80 (62%)

Query: 590 VWIRCDVYDTGIGIPENALPTLFRKYMQVSADHARKYGGTGLGLAICKQLVELMGGRLTV 649
           V +   + DTGIGI E     LF+ + Q  A  +R++GGTGLGL I ++LV  MGG ++ 
Sbjct: 443 VQLEVQIRDTGIGISERQQSQLFQAFRQADASISRRHGGTGLGLVITQKLVNEMGGDISF 502

Query: 650 TSKVHCGSTFTFILPYQVSP 669
            S+ + GSTF F LP  ++P
Sbjct: 503 HSQPNRGSTFWFHLPLDLNP 522

Length = 919

>gnl|CDD|237951 PRK15347, PRK15347, two component system sensor kinase SsrA; Provisional

 Score = 95.5 bits (238), Expect = 7e-20
 Identities = 45/138 (32%), Positives = 69/138 (50%), Gaps = 22/138 (15%)

Query: 861 KILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLK 920
           +ILLV+D + N  +   M+ +LG  +    +G EA+   +   +DL+LMD+ MP +DGL+
Sbjct: 692 QILLVDDVETNRDIIGMMLVELGQQVTTAASGTEALELGRQHRFDLVLMDIRMPGLDGLE 751

Query: 921 ATRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGM 980
            T+L R  +D  N D                        I+A+TANA  E    C   GM
Sbjct: 752 TTQLWR--DDPNNLDP--------------------DCMIVALTANAAPEEIHRCKKAGM 789

Query: 981 DSFVSKPVTFQKLKECLE 998
           + +++KPVT  +L   LE
Sbjct: 790 NHYLTKPVTLAQLARALE 807

Length = 921

>gnl|CDD|236842 PRK11091, PRK11091, aerobic respiration control sensor protein ArcB; Provisional

 Score = 94.2 bits (235), Expect = 1e-19
 Identities = 77/259 (29%), Positives = 129/259 (49%), Gaps = 40/259 (15%)

Query: 256 EEDILGKTDVEIFSGAGVKESQDFKREVLE---KGLPAKREITFETELF---GSKT-FLI 308
           E+ ++G T  +++S        +   +V+E   K       +T+E  L    G K  F +
Sbjct: 192 EKQLIGLTPKDVYS-------PEAAEKVIETDEKVFRHNVSLTYEQWLDYPDGRKACFEL 244

Query: 309 YVEPVFSKSGETIGVNYMGMDVTDQVRKREKMAKLREEIAVQKAKETELNKTIHITEETM 368
              P + + G+  G+   G D+T+  RKR        + A++KA     +KT  I     
Sbjct: 245 RKVPFYDRVGKRHGLMGFGRDITE--RKRY-------QDALEKASR---DKTTFI----- 287

Query: 369 RAKQMLATMSHEIRSPLTGVVSMAEILSNTKLDREQRQLLGVMISSGDLVLQLINDILDL 428
                 +T+SHE+R+PL G+V ++ IL +T+L  EQR+ L  +  S   +  + NDI+D+
Sbjct: 288 ------STISHELRTPLNGIVGLSRILLDTELTAEQRKYLKTIHVSAITLGNIFNDIIDM 341

Query: 429 SKVESGVMKLEAAKFRPREVVKHVLQTAAASL--QKILMLEGDIADDVPIEVIGDVLRIR 486
            K+E   ++L+       + +   L+  +     QK L  + +    +P +VI D  R+R
Sbjct: 342 DKMERRKLQLDNQPIDFTDFLAD-LENLSGLQAEQKGLRFDLEPLLPLPHKVITDGTRLR 400

Query: 487 QILTNLISNAIKFTPEGKV 505
           QIL NLISNA+KFT +G V
Sbjct: 401 QILWNLISNAVKFTQQGGV 419

Length = 779

>gnl|CDD|236848 PRK11107, PRK11107, hybrid sensory histidine kinase BarA; Provisional

 Score = 92.6 bits (231), Expect = 5e-19
 Identities = 43/164 (26%), Positives = 80/164 (48%), Gaps = 25/164 (15%)

Query: 840  ISQSPSSSSAEVPETKPKPKP-KILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHA 898
            +          +P T     P  ++ V+DN  N+ +  +++++    + + ++G +AV  
Sbjct: 647  LEPCHHKQPPLLPPTDESRLPLTVMAVDDNPANLKLIGALLEEQVEHVVLCDSGHQAVEQ 706

Query: 899  VQCQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRI 958
             + + +DLILMD+ MP MDG++A  LIR                          ++ +  
Sbjct: 707  AKQRPFDLILMDIQMPGMDGIRACELIRQ-----------------------LPHN-QNT 742

Query: 959  PIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQYFP 1002
            PIIA+TA+A++   E   + GMD +++KP+    LK+ L +Y P
Sbjct: 743  PIIAVTAHAMAGERERLLSAGMDDYLAKPIDEAMLKQVLLRYKP 786

Length = 919

>gnl|CDD|215963 pfam00512, HisKA, His Kinase A (phospho-acceptor) domain

 Score = 80.3 bits (199), Expect = 1e-18
 Identities = 29/64 (45%), Positives = 47/64 (73%)

Query: 371 KQMLATMSHEIRSPLTGVVSMAEILSNTKLDREQRQLLGVMISSGDLVLQLINDILDLSK 430
            + LA +SHE+R+PLT +    E+L +T+L  EQR+ L  ++ S + +L+LIND+LDLS+
Sbjct: 3   SEFLANLSHELRTPLTAIRGYLELLLDTELSEEQREYLETILRSAERLLRLINDLLDLSR 62

Query: 431 VESG 434
           +E+G
Sbjct: 63  IEAG 66

Dimerisation and phospho-acceptor domain of histidine kinases. Length = 66

>gnl|CDD|234070 TIGR02956, TMAO_torS, TMAO reductase sytem sensor TorS

 Score = 90.6 bits (225), Expect = 2e-18
 Identities = 45/112 (40%), Positives = 57/112 (50%), Gaps = 8/112 (7%)

Query: 592 IRCDVYDTGIGIPENALPTLFRKYMQVSADHARKYGGTGLGLAICKQLVELMGGRLTVTS 651
           +  +V DTG GI E    TLF  + Q  AD  R+ GGTGLGLAI ++LVE M G L V S
Sbjct: 612 LLFEVEDTGCGIAEEEQATLFDAFTQ--ADGRRRSGGTGLGLAISQRLVEAMDGELGVES 669

Query: 652 KVHCGSTFTFILPYQVSPIEENS--DDPDDLSD----MADQDSVTDDVTAGF 697
           ++  GS F F LP       E+S      DL      + + + V   V  GF
Sbjct: 670 ELGVGSCFWFTLPLTRGKPAEDSATLTVIDLPPQRVLLVEDNEVNQMVAQGF 721

This protein, TorS, is part of a regulatory system for the torCAD operon that encodes the pterin molybdenum cofactor-containing enzyme trimethylamine-N-oxide (TMAO) reductase (TorA), a cognate chaperone (TorD), and a penta-haem cytochrome (TorC). TorS works together with the inducer-binding protein TorT and the response regulator TorR. TorS contains histidine kinase ATPase (pfam02518), HAMP (pfam00672), phosphoacceptor (pfam00512), and phosphotransfer (pfam01627) domains and a response regulator receiver domain (pfam00072) [Signal transduction, Two-component systems]. Length = 968

>gnl|CDD|223715 COG0642, BaeS, Signal transduction histidine kinase [Signal transduction mechanisms]

 Score = 87.5 bits (216), Expect = 2e-18
 Identities = 32/82 (39%), Positives = 44/82 (53%), Gaps = 4/82 (4%)

Query: 591 WIRCDVYDTGIGIPENALPTLFRKYMQVSADHARKYGGTGLGLAICKQLVELMGGRLTVT 650
            +   V DTG GIPE  L  +F  + +          GTGLGLAI K++VEL GG ++V 
Sbjct: 259 QVTISVEDTGPGIPEEELERIFEPFFRTDKSR----SGTGLGLAIVKRIVELHGGTISVE 314

Query: 651 SKVHCGSTFTFILPYQVSPIEE 672
           S+   G+TFT  LP   +  + 
Sbjct: 315 SEPGKGTTFTIRLPLAPAAADA 336

Length = 336

>gnl|CDD|214644 smart00388, HisKA, His Kinase A (phosphoacceptor) domain

 Score = 79.5 bits (197), Expect = 2e-18
 Identities = 28/64 (43%), Positives = 47/64 (73%)

Query: 371 KQMLATMSHEIRSPLTGVVSMAEILSNTKLDREQRQLLGVMISSGDLVLQLINDILDLSK 430
           ++ LA +SHE+R+PLT +    E+L +T+L  EQR+ L  ++   + +L+LIND+LDLS+
Sbjct: 3   REFLANLSHELRTPLTAIRGYLELLLDTELSEEQREYLETILREAERLLRLINDLLDLSR 62

Query: 431 VESG 434
           +E+G
Sbjct: 63  IEAG 66

Dimerisation and phosphoacceptor domain of histidine kinases. Length = 66

>gnl|CDD|182772 PRK10841, PRK10841, hybrid sensory kinase in two-component regulatory system with RcsB and YojN; Provisional

 Score = 88.1 bits (219), Expect = 1e-17
 Identities = 45/140 (32%), Positives = 71/140 (50%), Gaps = 26/140 (18%)

Query: 861  KILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLK 920
             IL+V+D+ IN  +    +  LG+     N+GV+A++ +   + D++L DV MP MDG +
Sbjct: 803  MILVVDDHPINRRLLADQLGSLGYQCKTANDGVDALNVLSKNHIDIVLTDVNMPNMDGYR 862

Query: 921  ATRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGM 980
             T+ +R                +  +           +P+I +TANAL+E  + C   GM
Sbjct: 863  LTQRLR----------------QLGL----------TLPVIGVTANALAEEKQRCLEAGM 896

Query: 981  DSFVSKPVTFQKLKECLEQY 1000
            DS +SKPVT   LK+ L  Y
Sbjct: 897  DSCLSKPVTLDVLKQTLTVY 916

Length = 924

>gnl|CDD|182169 PRK09959, PRK09959, hybrid sensory histidine kinase in two-component regulatory system with EvgA; Provisional

 Score = 88.3 bits (218), Expect = 1e-17
 Identities = 59/165 (35%), Positives = 91/165 (55%), Gaps = 9/165 (5%)

Query: 352 AKETELNKTIHITEETMRAKQMLATMSHEIRSPLTGVVSMAEILSNTKLDREQR-QLLGV 410
           A E E NK I+    T+   Q LATMSHEIR+P++ ++   E+LS + L +EQR + + +
Sbjct: 697 ALEVERNKAIN---ATVAKSQFLATMSHEIRTPISSIMGFLELLSGSGLSKEQRVEAISL 753

Query: 411 MISSGDLVLQLINDILDLSKVESGVMKLEAAKFRPREVVK---HVLQTAAASLQKILMLE 467
             ++G  +L LI +ILD+ K+ESG  +L+        +V+   H     AAS    L   
Sbjct: 754 AYATGQSLLGLIGEILDVDKIESGNYQLQPQWVDIPTLVQNTCHSFGAIAASKSIALSCS 813

Query: 468 GDIADDVPIEVIGDVLRIRQILTNLISNAIKFTPEGKVGIKLYVV 512
               D   +++  D    +Q+L+NL+SNA+KFT EG V I   + 
Sbjct: 814 STFPDHYLVKI--DPQAFKQVLSNLLSNALKFTTEGAVKITTSLG 856

Length = 1197

>gnl|CDD|225115 COG2205, KdpD, Osmosensitive K+ channel histidine kinase [Signal transduction mechanisms]

 Score = 85.4 bits (212), Expect = 8e-17
 Identities = 48/168 (28%), Positives = 83/168 (49%), Gaps = 8/168 (4%)

Query: 349 VQKAKETELNKTIHITEETMRAKQMLATMSHEIRSPLTGVVSMAEILS--NTKLDREQRQ 406
           V  A+E E  +     E    A  +LA++SH++R+PLT ++  AE L      L  E R 
Sbjct: 641 VTLAEEAEQARLAAERERLRSA--LLASISHDLRTPLTAIMGAAETLLLDGEALSPEDRA 698

Query: 407 -LLGVMISSGDLVLQLINDILDLSKVESGVMKLEAAKFRPREVVKHVLQTAAASLQKILM 465
            LL  +    + + +L+ ++LD+++++SG + L+       EVV   LQ           
Sbjct: 699 ELLSSIREESERLTRLVTNLLDMTRLQSGGVNLKLDWVLVEEVVGEALQRLRKRFTG-HK 757

Query: 466 LEGDIADDVPIEVIGDVLRIRQILTNLISNAIKFTPEG-KVGIKLYVV 512
           +   +  D+P+ +  D   I Q+L NL+ NA+K+ P G ++ I   V 
Sbjct: 758 IVVSVPVDLPL-IHVDSPLIEQVLINLLENALKYAPPGSEIRINAGVE 804

Length = 890

>gnl|CDD|234074 TIGR02966, phoR_proteo, phosphate regulon sensor kinase PhoR

 Score = 81.5 bits (202), Expect = 2e-16
 Identities = 46/141 (32%), Positives = 73/141 (51%), Gaps = 4/141 (2%)

Query: 366 ETMRAKQMLATMSHEIRSPLTGVVSMAEIL-SNTKLDRE-QRQLLGVMISSGDLVLQLIN 423
           E MR +  +A +SHE+R+PLT +    E L      D E   + L +M+     +  L+ 
Sbjct: 111 EQMR-RDFVANVSHELRTPLTVLRGYLETLADGPDEDPEEWNRALEIMLEQSQRMQSLVE 169

Query: 424 DILDLSKVESGVMKLEAAKFRPREVVKHVLQTAAASLQKILMLEGDIADDVPIEVIGDVL 483
           D+L LS++ES    LE        ++ H L+  A +L +    +     D  ++V+GD  
Sbjct: 170 DLLTLSRLESAASPLEDEPVDMPALLDH-LRDEAEALSQGKNHQITFEIDGGVDVLGDED 228

Query: 484 RIRQILTNLISNAIKFTPEGK 504
            +R   +NL+SNAIK+TPEG 
Sbjct: 229 ELRSAFSNLVSNAIKYTPEGG 249

Members of this protein family are the regulatory histidine kinase PhoR associated with the phosphate ABC transporter in most Proteobacteria. Related proteins from Gram-positive organisms are not included in this model. The phoR gene usually is adjacent to the response regulator phoB gene (TIGR02154) [Signal transduction, Two-component systems]. Length = 333

>gnl|CDD|236842 PRK11091, PRK11091, aerobic respiration control sensor protein ArcB; Provisional

 Score = 83.1 bits (206), Expect = 4e-16
 Identities = 39/93 (41%), Positives = 53/93 (56%), Gaps = 3/93 (3%)

Query: 592 IRCDVYDTGIGIPENALPTLFRKYMQVSADHARKYG-GTGLGLAICKQLVELMGGRLTVT 650
           +  +V D+GIGIPE+ L  +F  Y QV   H  K   GTG+GLA+ K+L + MGG +TVT
Sbjct: 431 LTFEVEDSGIGIPEDELDKIFAMYYQVKDSHGGKPATGTGIGLAVSKRLAQAMGGDITVT 490

Query: 651 SKVHCGSTFTFILPYQVSPIEENSDDPDDLSDM 683
           S+   GS FT  +      + E  +D  D  DM
Sbjct: 491 SEEGKGSCFTLTIHAPA--VAEEVEDAFDEDDM 521

Length = 779

>gnl|CDD|227335 COG5002, VicK, Signal transduction histidine kinase [Signal transduction mechanisms]

 Score = 78.6 bits (194), Expect = 4e-15
 Identities = 33/86 (38%), Positives = 52/86 (60%)

Query: 591 WIRCDVYDTGIGIPENALPTLFRKYMQVSADHARKYGGTGLGLAICKQLVELMGGRLTVT 650
           W+   + D G+GIP+  L  +F ++ +V    +RK GGTGLGLAI K++V+  GGR+   
Sbjct: 374 WVEISISDQGLGIPKEDLEKIFDRFYRVDKARSRKMGGTGLGLAIAKEIVQAHGGRIWAE 433

Query: 651 SKVHCGSTFTFILPYQVSPIEENSDD 676
           S+   G+TF+F LPY     ++  + 
Sbjct: 434 SEEGKGTTFSFTLPYSGEAGDDWDEA 459

Length = 459

>gnl|CDD|234070 TIGR02956, TMAO_torS, TMAO reductase sytem sensor TorS

 Score = 77.9 bits (192), Expect = 2e-14
 Identities = 37/159 (23%), Positives = 69/159 (43%), Gaps = 23/159 (14%)

Query: 842  QSPSSSSAEVPETKPKPKPKILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQC 901
            +   +  +        P  ++LLVEDN++N MVA+  + +LGH + +  +G  A+     
Sbjct: 685  RGKPAEDSATLTVIDLPPQRVLLVEDNEVNQMVAQGFLTRLGHKVTLAESGQSALECFHQ 744

Query: 902  QNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPII 961
              +DL L+D+ +P  DG+   + +R+     N                        +  I
Sbjct: 745  HAFDLALLDINLPDGDGVTLLQQLRAIYGAKN-----------------------EVKFI 781

Query: 962  AMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQY 1000
            A +A+  +E   +  A G D F++KPV  ++L   +   
Sbjct: 782  AFSAHVFNEDVAQYLAAGFDGFLAKPVVEEQLTAMIAVI 820

This protein, TorS, is part of a regulatory system for the torCAD operon that encodes the pterin molybdenum cofactor-containing enzyme trimethylamine-N-oxide (TMAO) reductase (TorA), a cognate chaperone (TorD), and a penta-haem cytochrome (TorC). TorS works together with the inducer-binding protein TorT and the response regulator TorR. TorS contains histidine kinase ATPase (pfam02518), HAMP (pfam00672), phosphoacceptor (pfam00512), and phosphotransfer (pfam01627) domains and a response regulator receiver domain (pfam00072) [Signal transduction, Two-component systems]. Length = 968

>gnl|CDD|234074 TIGR02966, phoR_proteo, phosphate regulon sensor kinase PhoR

 Score = 74.2 bits (183), Expect = 5e-14
 Identities = 33/79 (41%), Positives = 43/79 (54%), Gaps = 6/79 (7%)

Query: 591 WIRCD------VYDTGIGIPENALPTLFRKYMQVSADHARKYGGTGLGLAICKQLVELMG 644
           W R        V DTGIGI    LP L  ++ +V    +R  GGTGLGLAI K ++    
Sbjct: 255 WRRDGGGAEFSVTDTGIGIAPEHLPRLTERFYRVDKSRSRDTGGTGLGLAIVKHVLSRHH 314

Query: 645 GRLTVTSKVHCGSTFTFIL 663
            RL + S++  GSTF+FI 
Sbjct: 315 ARLEIESELGKGSTFSFIF 333

Members of this protein family are the regulatory histidine kinase PhoR associated with the phosphate ABC transporter in most Proteobacteria. Related proteins from Gram-positive organisms are not included in this model. The phoR gene usually is adjacent to the response regulator phoB gene (TIGR02154) [Signal transduction, Two-component systems]. Length = 333

>gnl|CDD|225115 COG2205, KdpD, Osmosensitive K+ channel histidine kinase [Signal transduction mechanisms]

 Score = 75.8 bits (187), Expect = 8e-14
 Identities = 31/95 (32%), Positives = 45/95 (47%), Gaps = 11/95 (11%)

Query: 587 EATVWIRC---------DVYDTGIGIPENALPTLFRKYMQVSADHARKYGGTGLGLAICK 637
            + + I            V D G GIPE  L  +F K+ + + + A    G GLGLAIC+
Sbjct: 794 GSEIRINAGVERENVVFSVIDEGPGIPEGELERIFDKFYRGNKESAT--RGVGLGLAICR 851

Query: 638 QLVELMGGRLTVTSKVHCGSTFTFILPYQVSPIEE 672
            +VE  GG ++  +    G+ F F LP +  P  E
Sbjct: 852 GIVEAHGGTISAENNPGGGAIFVFTLPVEEDPPLE 886

Length = 890

>gnl|CDD|214668 smart00448, REC, cheY-homologous receiver domain

 Score = 64.9 bits (159), Expect = 2e-13
 Identities = 17/55 (30%), Positives = 37/55 (67%)

Query: 860 PKILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMP 914
            +IL+V+D+ +   + K+++++ G+ +D   +G EA+  ++ +  DLIL+D+ MP
Sbjct: 1   MRILVVDDDPLLRELLKALLEKEGYEVDEATDGEEALELLKEEKPDLILLDIMMP 55

CheY regulates the clockwise rotation of E. coli flagellar motors. This domain contains a phosphoacceptor site that is phosphorylated by histidine kinase homologues. Length = 55

>gnl|CDD|119399 cd00082, HisKA, Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via trans-autophosphorylation by the catalytic domain of the histidine kinase

 Score = 65.3 bits (160), Expect = 2e-13
 Identities = 28/65 (43%), Positives = 43/65 (66%), Gaps = 2/65 (3%)

Query: 368 MRAK-QMLATMSHEIRSPLTGVVSMAEILSNTKL-DREQRQLLGVMISSGDLVLQLINDI 425
           ++AK + LA +SHE+R+PLT +    E+L    L D EQR+ L  +    + +L+LIND+
Sbjct: 1   LQAKGEFLANVSHELRTPLTAIRGALELLEEELLDDEEQREYLERIREEAERLLRLINDL 60

Query: 426 LDLSK 430
           LDLS+
Sbjct: 61  LDLSR 65

They subsequently transfer the phosphoryl group to the Asp acceptor residue of a response regulator protein. Two-component signalling systems, consisting of a histidine protein kinase that senses a signal input and a response regulator that mediates the output, are ancient and evolutionarily conserved signaling mechanisms in prokaryotes and eukaryotes. Length = 65

>gnl|CDD|236914 PRK11466, PRK11466, hybrid sensory histidine kinase TorS; Provisional

 Score = 72.6 bits (178), Expect = 6e-13
 Identities = 33/95 (34%), Positives = 49/95 (51%), Gaps = 8/95 (8%)

Query: 591 WIRCDVYDTGIGIPENALPTLFRKYMQVSADHARKYGGTGLGLAICKQLVELMGGRLTVT 650
            +  +V D+G GI    L  +F+ ++QVS     K GGTGLGL I  +L + MGG L+ T
Sbjct: 594 LV--EVEDSGCGIDPAKLAEIFQPFVQVSG----KRGGTGLGLTISSRLAQAMGGELSAT 647

Query: 651 SKVHCGSTFTFILPYQ--VSPIEENSDDPDDLSDM 683
           S    GS F   LP +   +P+ +  +    L  +
Sbjct: 648 STPEVGSCFCLRLPLRVATAPVPKTVNQAVRLDGL 682

Length = 914

>gnl|CDD|182169 PRK09959, PRK09959, hybrid sensory histidine kinase in two-component regulatory system with EvgA; Provisional

 Score = 72.8 bits (178), Expect = 6e-13
 Identities = 49/153 (32%), Positives = 76/153 (49%), Gaps = 27/153 (17%)

Query: 847  SSAEVPETKPKPKPKILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDL 906
            + AE P T P+ K  IL+ +D+  N ++ K  +  LG+ +D   +GV+A+H V  Q+YDL
Sbjct: 947  AKAEQPITLPE-KLSILIADDHPTNRLLLKRQLNLLGYDVDEATDGVQALHKVSMQHYDL 1005

Query: 907  ILMDVCMPVMDGLKATRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTAN 966
            ++ DV MP MDG + TR +R    +                          +PI  +TAN
Sbjct: 1006 LITDVNMPNMDGFELTRKLREQNSS--------------------------LPIWGLTAN 1039

Query: 967  ALSESAEECFANGMDSFVSKPVTFQKLKECLEQ 999
            A +   E+  + GM+  + KP+T   LK  L Q
Sbjct: 1040 AQANEREKGLSCGMNLCLFKPLTLDVLKTHLSQ 1072

Length = 1197

>gnl|CDD|236462 PRK09303, PRK09303, adaptive-response sensory kinase; Validated

 Score = 71.1 bits (175), Expect = 6e-13
 Identities = 53/187 (28%), Positives = 85/187 (45%), Gaps = 25/187 (13%)

Query: 330 VTDQVRKREKMAKLREEIAVQKAKETELNKTIHITEETMRAKQMLATMSHEIRSPLTGVV 389
             D  R  +++ +L +E+ V + +   L + +   +  +    MLA   H++R+PLT   
Sbjct: 117 EIDSGRYSQELLQLSDELFVLRQENETLLEQLKFKDRVLA---MLA---HDLRTPLTAAS 170

Query: 390 SMAEIL-------SNTKLDREQRQLLGVMISSGDLVLQLINDILDLSKVESGVMKLEAAK 442
              E L                 QL        + + +LI D+L     E G  + EA +
Sbjct: 171 LALETLELGQIDEDTELKPALIEQLQDQARRQLEEIERLITDLL-----EVGRTRWEALR 225

Query: 443 FRPREVV-KHVLQTAAASLQKI-----LMLEGDIADDVPIEVIGDVLRIRQILTNLISNA 496
           F P+++    + Q     L+K      L ++ DI  D+P  V  D  RIRQ+L NL+ NA
Sbjct: 226 FNPQKLDLGSLCQEVILELEKRWLAKSLEIQTDIPSDLP-SVYADQERIRQVLLNLLDNA 284

Query: 497 IKFTPEG 503
           IK+TPEG
Sbjct: 285 IKYTPEG 291

Length = 380

>gnl|CDD|182772 PRK10841, PRK10841, hybrid sensory kinase in two-component regulatory system with RcsB and YojN; Provisional

 Score = 72.3 bits (178), Expect = 8e-13
 Identities = 33/84 (39%), Positives = 48/84 (57%), Gaps = 2/84 (2%)

Query: 595 DVYDTGIGIPENALPTLFRKYMQVSADHARKYGGTGLGLAICKQLVELMGGRLTVTSKVH 654
            V DTG+GIP   +  LF  + QV     R + GTGLGLAIC++L+ +M G ++V S+  
Sbjct: 597 RVRDTGVGIPAKEVVRLFDPFFQVGTGVQRNFQGTGLGLAICEKLINMMDGDISVDSEPG 656

Query: 655 CGSTFTFILP-YQVS-PIEENSDD 676
            GS FT  +P Y    P ++  + 
Sbjct: 657 MGSQFTIRIPLYGAQYPQKKGVEG 680

Length = 924

>gnl|CDD|223816 COG0745, OmpR, Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]

 Score = 68.5 bits (168), Expect = 9e-13
 Identities = 34/135 (25%), Positives = 65/135 (48%), Gaps = 28/135 (20%)

Query: 860 PKILLVEDNK-INVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDG 918
            +ILLVED+  +  ++ +  +++ G+ +DV  +G EA+ A + +  DL+L+D+ +P +DG
Sbjct: 1   MRILLVEDDPELAELLKE-YLEEEGYEVDVAADGEEALEAAR-EQPDLVLLDLMLPDLDG 58

Query: 919 LKATRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFAN 978
           L+  R +R+ +                             PII +TA    E        
Sbjct: 59  LELCRRLRAKKG-------------------------SGPPIIVLTARDDEEDRVLGLEA 93

Query: 979 GMDSFVSKPVTFQKL 993
           G D +++KP + ++L
Sbjct: 94  GADDYLTKPFSPREL 108

Length = 229

>gnl|CDD|236846 PRK11100, PRK11100, sensory histidine kinase CreC; Provisional

 Score = 69.9 bits (172), Expect = 2e-12
 Identities = 43/150 (28%), Positives = 68/150 (45%), Gaps = 18/150 (12%)

Query: 366 ETMRAK--------QMLATMSHEIRSPLTGVVSMAEILSNTKLDREQRQLLGVMISSGDL 417
           E+MR K        Q + T++HE++SPL  +   AE+L       E R      I +   
Sbjct: 244 ESMRVKLEGKAYVEQYVQTLTHELKSPLAAIRGAAELL-QEDPPPEDRARFTGNILTQSA 302

Query: 418 VLQ-LINDILDLSKVESGVMKLEAAKFRPREVVKHVLQTAAASLQK---ILMLEGDIADD 473
            LQ LI+ +L+L+++E               +++ +++   A        L L  D    
Sbjct: 303 RLQQLIDRLLELARLEQRQELEVLEPVALAALLEELVEAREAQAAAKGITLRLRPD---- 358

Query: 474 VPIEVIGDVLRIRQILTNLISNAIKFTPEG 503
               V+GD   +RQ L NL+ NAI F+PEG
Sbjct: 359 -DARVLGDPFLLRQALGNLLDNAIDFSPEG 387

Length = 475

>gnl|CDD|237951 PRK15347, PRK15347, two component system sensor kinase SsrA; Provisional

 Score = 67.4 bits (165), Expect = 3e-11
 Identities = 28/72 (38%), Positives = 36/72 (50%), Gaps = 4/72 (5%)

Query: 595 DVYDTGIGIPENALPTLFRKYMQVSADHARKYGGTGLGLAICKQLVELMGGRLTVTSKVH 654
            V DTG GI       +F  + Q    H+    GTGLGL I   L ++MGG LT+ S   
Sbjct: 548 TVEDTGCGIDIQQQQQIFTPFYQAD-THS---QGTGLGLTIASSLAKMMGGELTLFSTPG 603

Query: 655 CGSTFTFILPYQ 666
            GS F+ +LP  
Sbjct: 604 VGSCFSLVLPLN 615

Length = 921

>gnl|CDD|236701 PRK10490, PRK10490, sensor protein KdpD; Provisional

 Score = 65.4 bits (160), Expect = 1e-10
 Identities = 32/95 (33%), Positives = 52/95 (54%), Gaps = 6/95 (6%)

Query: 586 LEATV---WIRCDVYDTGIGIPENALPTLFRKYMQVSADHARKYGGTGLGLAICKQLVEL 642
           ++A V    ++ DV+D G GIP      +F K+ + + + A    G GLGLAIC+ +VE+
Sbjct: 802 IDAHVEGERLQLDVWDNGPGIPPGQEQLIFDKFARGNKESA--IPGVGLGLAICRAIVEV 859

Query: 643 MGGRLTVTSKVHCGSTFTFILPYQVSP-IEENSDD 676
            GG +   ++   G+ F   LP +  P +EE  +D
Sbjct: 860 HGGTIWAENRPEGGACFRVTLPLETPPELEEFHED 894

Length = 895

>gnl|CDD|225971 COG3437, COG3437, Response regulator containing a CheY-like receiver domain and an HD-GYP domain [Transcription / Signal transduction mechanisms]

 Score = 63.9 bits (156), Expect = 1e-10
 Identities = 37/130 (28%), Positives = 63/130 (48%), Gaps = 23/130 (17%)

Query: 859 KPKILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDG 918
           K  +LLV+D   N+   + +++ +G+ +    NG EA+  +Q +  DL+L+DV MP MDG
Sbjct: 14  KLTVLLVDDEPDNLEALRQLLRMIGYRVIEAENGEEALKLLQEEPPDLVLLDVRMPEMDG 73

Query: 919 LKATRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFAN 978
            +    +++                        S   +RIP+I +TA A SE  +     
Sbjct: 74  AEVLNKLKAM-----------------------SPSTRRIPVILLTAYADSEDRQRALEA 110

Query: 979 GMDSFVSKPV 988
           G D ++SKP+
Sbjct: 111 GADDYLSKPI 120

Length = 360

>gnl|CDD|226229 COG3706, PleD, Response regulator containing a CheY-like receiver domain and a GGDEF domain [Signal transduction mechanisms]

 Score = 64.3 bits (157), Expect = 1e-10
 Identities = 39/171 (22%), Positives = 70/171 (40%), Gaps = 36/171 (21%)

Query: 838 DRISQSPSS-----SSAEVPETKPKPKPKILLVEDNKINVMVAKSMMKQLGHSIDVVNNG 892
           D +     +      S  +PE  PK   KIL+V+D+       + +++  G  +    +G
Sbjct: 109 DELRLREETGGELGVSPLLPEDAPK---KILVVDDDATQRERLRRILQVEGFRVVEATDG 165

Query: 893 VEAVHAVQCQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDAAAEAGIEQAMPSSGSS 952
            EA+  +     DL+L+D  MP MDGL+    +R  E T                     
Sbjct: 166 EEALLQLAELPPDLVLLDANMPDMDGLELCTRLRQLERT--------------------- 204

Query: 953 NHFKRIPIIAMTANALSESAEECFANGMDSFVSKPV----TFQKLKECLEQ 999
              + IPII +++    E     F  G++ +++KP+       +L+  L +
Sbjct: 205 ---RDIPIILLSSKDDDELVVRAFELGVNDYITKPIEEGELRARLRRQLRR 252

Length = 435

>gnl|CDD|183099 PRK11361, PRK11361, acetoacetate metabolism regulatory protein AtoC; Provisional

 Score = 64.1 bits (156), Expect = 2e-10
 Identities = 41/139 (29%), Positives = 60/139 (43%), Gaps = 28/139 (20%)

Query: 857 KPKPKILLVEDNK-INVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPV 915
               +IL+V+D   +  M++ +   Q G      NNG  A+H     + D++LMD+ MP 
Sbjct: 2   TAINRILIVDDEDNVRRMLSTAFALQ-GFETHCANNGRTALHLFADIHPDVVLMDIRMPE 60

Query: 916 MDGLKATRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEEC 975
           MDG+KA + +RS E                           R P+I MTA A  E+A E 
Sbjct: 61  MDGIKALKEMRSHE--------------------------TRTPVILMTAYAEVETAVEA 94

Query: 976 FANGMDSFVSKPVTFQKLK 994
              G   +V KP    +L 
Sbjct: 95  LRCGAFDYVIKPFDLDELN 113

Length = 457

>gnl|CDD|236726 PRK10618, PRK10618, phosphotransfer intermediate protein in two-component regulatory system with RcsBC; Provisional

 Score = 64.2 bits (157), Expect = 3e-10
 Identities = 35/138 (25%), Positives = 67/138 (48%), Gaps = 1/138 (0%)

Query: 371 KQMLATMSHEIRSPLTGVVSMAEILSNTKLDREQRQLLGVMISSGDLVLQLINDILDLSK 430
           K  L  +  E++ PL  +  +A  L  T  + +Q+  L  +    D++++L+++I  L+ 
Sbjct: 451 KAFLQNIGDELKQPLQSLAQLAAQLRQTSDEEQQQPELDQLAEQSDVLVRLVDNIQLLNM 510

Query: 431 VESGVMKLEAAKFRPREVVKHVLQTAAASL-QKILMLEGDIADDVPIEVIGDVLRIRQIL 489
           +E+   K E   F  ++++  VL     ++ +K L L            IGD   +R+IL
Sbjct: 511 LETQDWKPEQELFSLQDLIDEVLPEVLPAIKRKGLQLLIHNHLKAEQLRIGDRDALRKIL 570

Query: 490 TNLISNAIKFTPEGKVGI 507
             L++ AI  T  GK+ +
Sbjct: 571 LLLLNYAITTTAYGKITL 588

Length = 894

>gnl|CDD|236901 PRK11360, PRK11360, sensory histidine kinase AtoS; Provisional

 Score = 62.3 bits (152), Expect = 8e-10
 Identities = 24/70 (34%), Positives = 35/70 (50%), Gaps = 6/70 (8%)

Query: 596 VYDTGIGIPENALPTLFRKYMQVSADHARKYGGTGLGLAICKQLVELMGGRLTVTSKVHC 655
           + D G GI    L  +F  +         K  GTGLGLA+ ++++   GG + V S+   
Sbjct: 538 IEDNGCGIDPELLKKIFDPFFTT------KAKGTGLGLALSQRIINAHGGDIEVESEPGV 591

Query: 656 GSTFTFILPY 665
           G+TFT  LP 
Sbjct: 592 GTTFTLYLPI 601

Length = 607

>gnl|CDD|226702 COG4251, COG4251, Bacteriophytochrome (light-regulated signal transduction histidine kinase) [Signal transduction mechanisms]

 Score = 62.1 bits (151), Expect = 1e-09
 Identities = 30/70 (42%), Positives = 39/70 (55%), Gaps = 2/70 (2%)

Query: 596 VYDTGIGIPENALPTLFRKYMQVSADHARKYGGTGLGLAICKQLVELMGGRLTVTSKVHC 655
           V D GIGI       +F  + ++ +    +Y GTGLGLAICK++ E   GR+ V S    
Sbjct: 674 VRDNGIGIDPAYFERIFVIFQRLHSRD--EYLGTGLGLAICKKIAERHQGRIWVESTPGE 731

Query: 656 GSTFTFILPY 665
           GSTF F LP 
Sbjct: 732 GSTFYFTLPV 741

Length = 750

>gnl|CDD|182169 PRK09959, PRK09959, hybrid sensory histidine kinase in two-component regulatory system with EvgA; Provisional

 Score = 61.3 bits (148), Expect = 2e-09
 Identities = 34/95 (35%), Positives = 55/95 (57%), Gaps = 6/95 (6%)

Query: 592 IRCDVYDTGIGIPENALPTLFRKYMQVSADHARKYGGTGLGLAICKQLVELMGGRLTVTS 651
           I+  + D+G G+ +     LF++Y Q SA   R+  G+GLGL ICK+L++ M G L++ S
Sbjct: 865 IKMTIMDSGSGLSQEEQQQLFKRYSQTSA--GRQQTGSGLGLMICKELIKNMQGDLSLES 922

Query: 652 KVHCGSTFTFILPY----QVSPIEENSDDPDDLSD 682
               G+TFT  +P     QV+ +E  ++ P  L +
Sbjct: 923 HPGIGTTFTITIPVEISQQVATVEAKAEQPITLPE 957

Length = 1197

>gnl|CDD|182412 PRK10365, PRK10365, transcriptional regulatory protein ZraR; Provisional

 Score = 60.8 bits (147), Expect = 2e-09
 Identities = 35/141 (24%), Positives = 68/141 (48%), Gaps = 26/141 (18%)

Query: 859 KPKILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDG 918
              IL+V+D+  +  + +++++  G+++ + N+G +A+  V+ Q +DL+L DV M  MDG
Sbjct: 5   NIDILVVDDDISHCTILQALLRGWGYNVALANSGRQALEQVREQVFDLVLCDVRMAEMDG 64

Query: 919 LKATRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFAN 978
           +   + I++                              IP++ MTA +  E+A E    
Sbjct: 65  IATLKEIKALNPA--------------------------IPVLIMTAYSSVETAVEALKT 98

Query: 979 GMDSFVSKPVTFQKLKECLEQ 999
           G   ++ KP+ F  L+  LE+
Sbjct: 99  GALDYLIKPLDFDNLQATLEK 119

Length = 441

>gnl|CDD|225827 COG3290, CitA, Signal transduction histidine kinase regulating citrate/malate metabolism [Signal transduction mechanisms]

 Score = 60.8 bits (148), Expect = 2e-09
 Identities = 26/76 (34%), Positives = 38/76 (50%), Gaps = 5/76 (6%)

Query: 591 WIRCDVYDTGIGIPENALPTLFRKYMQVSADHARKYGGTGLGLAICKQLVELMGGRLTVT 650
            +  +V DTG GIP      +F K         +  GG G+GL + KQLVE +GG + V 
Sbjct: 462 ELVIEVADTGPGIPPEVRDKIFEK-----GVSTKNTGGRGIGLYLVKQLVERLGGSIEVE 516

Query: 651 SKVHCGSTFTFILPYQ 666
           S+   G+ F+  +P  
Sbjct: 517 SEKGQGTRFSIYIPKV 532

Length = 537

>gnl|CDD|182895 PRK11006, phoR, phosphate regulon sensor protein; Provisional

 Score = 59.6 bits (145), Expect = 4e-09
 Identities = 27/69 (39%), Positives = 40/69 (57%)

Query: 596 VYDTGIGIPENALPTLFRKYMQVSADHARKYGGTGLGLAICKQLVELMGGRLTVTSKVHC 655
           V D G GI    +P L  ++ +V    +R+ GG+GLGLAI K  +     RL + S+V  
Sbjct: 354 VEDNGPGIAPEHIPRLTERFYRVDKARSRQTGGSGLGLAIVKHALSHHDSRLEIESEVGK 413

Query: 656 GSTFTFILP 664
           G+ F+F+LP
Sbjct: 414 GTRFSFVLP 422

Length = 430

>gnl|CDD|182101 PRK09835, PRK09835, sensor kinase CusS; Provisional

 Score = 59.8 bits (145), Expect = 4e-09
 Identities = 40/136 (29%), Positives = 75/136 (55%), Gaps = 15/136 (11%)

Query: 375 ATMSHEIRSPLTGVVSMAEI-LSNTKLDREQRQLLGVMISSGD---LVLQLINDILDLSK 430
           A ++HEIR+P+T +++  EI LS +   R Q++L  V+ S+ +    + ++++D+L L++
Sbjct: 267 ADIAHEIRTPITNLITQTEIALSQS---RSQKELEDVLYSNLEELTRMAKMVSDMLFLAQ 323

Query: 431 VESGVMKLEAAKFRPREVVKHVL---QTAAASLQKILMLEGDIADDVPIEVIGDVLRIRQ 487
            ++  +  E       + V  V    +  A      L   GD     P +V GD L +R+
Sbjct: 324 ADNNQLIPEKKMLDLADEVGKVFDFFEAWAEERGVELRFVGD-----PCQVAGDPLMLRR 378

Query: 488 ILTNLISNAIKFTPEG 503
            ++NL+SNA+++TP G
Sbjct: 379 AISNLLSNALRYTPAG 394

Length = 482

>gnl|CDD|226702 COG4251, COG4251, Bacteriophytochrome (light-regulated signal transduction histidine kinase) [Signal transduction mechanisms]

 Score = 59.4 bits (144), Expect = 7e-09
 Identities = 41/157 (26%), Positives = 71/157 (45%), Gaps = 9/157 (5%)

Query: 346 EIAVQKAKETELNKTIHITEETMRAKQMLATMSHEIRSPLTGVVSMAEILS---NTKLDR 402
            I ++ A+E        +       +      SH+++ PL  + + A++LS   +  LD 
Sbjct: 501 GIVLRHAEELA-QLRRELERSNAELRAFAYVASHDLQEPLRQISNYAQLLSERYSDALDE 559

Query: 403 EQRQLLGVMISSGDLVLQLINDILDLSKVESGVMKLEAAKFRPREVVKHVLQTAAASLQK 462
           E ++ +  +     L+ QLI+D+L  SK+      L  A  +P +V K V +      Q+
Sbjct: 560 EAKEFITFISRLTSLMQQLIDDLLTYSKLG-----LTEAPLQPTDVQKVVDKVLLELSQR 614

Query: 463 ILMLEGDIADDVPIEVIGDVLRIRQILTNLISNAIKF 499
           I     +I       V  D  ++ Q+  NLI+NAIKF
Sbjct: 615 IADTGAEIRIAPLPVVAADATQLGQVFQNLIANAIKF 651

Length = 750

>gnl|CDD|225107 COG2197, CitB, Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]

 Score = 56.2 bits (136), Expect = 1e-08
 Identities = 31/151 (20%), Positives = 63/151 (41%), Gaps = 36/151 (23%)

Query: 861  KILLVEDNKINVMVAKSMMKQLGHSIDVV---NNGVEAVHAVQCQNYDLILMDVCMPVMD 917
            K+L+V+D+ +     + +++     ++VV   +NG EA+   +    D++L+D+ MP MD
Sbjct: 2    KVLIVDDHPLVREGLRQLLELEP-DLEVVGEASNGEEALDLARELKPDVVLLDLSMPGMD 60

Query: 918  GLKATRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFA 977
            GL+A + +R+                              I ++ +TA+           
Sbjct: 61   GLEALKQLRA--------------------------RGPDIKVVVLTAHDDPAYVIRALR 94

Query: 978  NGMDSFVSKPVTFQKLKECL------EQYFP 1002
             G D ++ K  + ++L E +        Y P
Sbjct: 95   AGADGYLLKDASPEELVEAIRAVAAGGTYLP 125

Length = 211

>gnl|CDD|237526 PRK13837, PRK13837, two-component VirA-like sensor kinase; Provisional

 Score = 58.9 bits (143), Expect = 1e-08
 Identities = 32/100 (32%), Positives = 40/100 (40%), Gaps = 12/100 (12%)

Query: 577 SHGNSMDEDLEATVWIRCDVYDTGIGIPENALPTLFRKYMQVSADHARKYGGTGLGLAIC 636
           SHG           ++   V DTG GI E  LP +F  +    A      GGTGLGLA  
Sbjct: 598 SHGVLPPGR-----YVLLRVSDTGAGIDEAVLPHIFEPFFTTRA------GGTGLGLATV 646

Query: 637 KQLVELMGGRLTVTSKVHCGSTFTFILPYQVSPIEENSDD 676
             +V    G + V S V  G+ F   LP   S +      
Sbjct: 647 HGIVSAHAGYIDVQSTVGRGTRFDVYLPPS-SKVPVAPQA 685

Length = 828

>gnl|CDD|225114 COG2204, AtoC, Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]

 Score = 57.7 bits (140), Expect = 2e-08
 Identities = 32/141 (22%), Positives = 61/141 (43%), Gaps = 26/141 (18%)

Query: 859 KPKILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDG 918
             +IL+V+D+     + +  ++  G+ +    +  EA+ A+    +DL+L+D+ MP MDG
Sbjct: 4   MARILVVDDDPDIRELLEQALELAGYEVVTAESAEEALEALSESPFDLVLLDIRMPGMDG 63

Query: 919 LKATRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFAN 978
           L+  + I+S                              +P+I MT +   ++A E    
Sbjct: 64  LELLKEIKS--------------------------RDPDLPVIVMTGHGDIDTAVEALRL 97

Query: 979 GMDSFVSKPVTFQKLKECLEQ 999
           G   F+ KP    +L   +E+
Sbjct: 98  GAFDFLEKPFDLDRLLAIVER 118

Length = 464

>gnl|CDD|226654 COG4191, COG4191, Signal transduction histidine kinase regulating C4-dicarboxylate transport system [Signal transduction mechanisms]

 Score = 57.3 bits (139), Expect = 3e-08
 Identities = 28/92 (30%), Positives = 39/92 (42%), Gaps = 13/92 (14%)

Query: 582 MDEDLEATVWIRCD---------VYDTGIGIPENALPTLFRKYMQVSADHARKYGGTGLG 632
           M    +  + IR           V D G GI   ALP LF  +   +    +   G GLG
Sbjct: 513 MAGQEDRRLSIRAQREGGQVVLTVRDNGPGIAPEALPHLFEPF-FTTKPVGK---GLGLG 568

Query: 633 LAICKQLVELMGGRLTVTSKVHCGSTFTFILP 664
           LAI + +   +GG L V +    G++FT  L 
Sbjct: 569 LAISQNIARDLGGSLEVANHPEGGASFTIELR 600

Length = 603

>gnl|CDD|233391 TIGR01386, cztS_silS_copS, heavy metal sensor kinase

 Score = 56.2 bits (136), Expect = 5e-08
 Identities = 25/72 (34%), Positives = 35/72 (48%), Gaps = 1/72 (1%)

Query: 593 RCDVYDTGIGIPENALPTLFRKYMQVSADHARKYGGTGLGLAICKQLVELMGGRLTVTSK 652
           R  V + G GIP   L  LF ++ +V    +    GTGLGLAI + ++E  GGR +  S 
Sbjct: 387 RVSVSNPGPGIPPEHLSRLFDRFYRVDPARSNSGEGTGLGLAIVRSIMEAHGGRASAESP 446

Query: 653 VHCGSTFTFILP 664
               + F    P
Sbjct: 447 DG-KTRFILRFP 457

Members of this family contain a sensor histidine kinase domain (pfam00512) and a domain found in bacterial signal proteins (pfam00672). This group is separated phylogenetically from related proteins with similar architecture and contains a number of proteins associated with heavy metal resistance efflux systems for copper, silver, cadmium, and/or zinc. Length = 457

>gnl|CDD|236839 PRK11086, PRK11086, sensory histidine kinase DcuS; Provisional

 Score = 56.5 bits (137), Expect = 6e-08
 Identities = 25/76 (32%), Positives = 38/76 (50%), Gaps = 6/76 (7%)

Query: 591 WIRCDVYDTGIGIPENALPTLFRKYMQVSADHARKYGGTGLGLAICKQLVELMGGRLTVT 650
           W+ C+V D G GI  + +  +F K    S     K    G+GL + KQ VE +GG + V 
Sbjct: 467 WLHCEVSDDGPGIAPDEIDAIFDK--GYST----KGSNRGVGLYLVKQSVENLGGSIAVE 520

Query: 651 SKVHCGSTFTFILPYQ 666
           S+   G+ F   +P+ 
Sbjct: 521 SEPGVGTQFFVQIPWD 536

Length = 542

>gnl|CDD|170568 PRK10610, PRK10610, chemotaxis regulatory protein CheY; Provisional

 Score = 52.3 bits (125), Expect = 6e-08
 Identities = 36/142 (25%), Positives = 67/142 (47%), Gaps = 25/142 (17%)

Query: 861  KILLVEDNKINVMVAKSMMKQLG-HSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGL 919
            K L+V+D      + ++++K+LG ++++   +GV+A++ +Q   +  ++ D  MP MDGL
Sbjct: 7    KFLVVDDFSTMRRIVRNLLKELGFNNVEEAEDGVDALNKLQAGGFGFVISDWNMPNMDGL 66

Query: 920  KATRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANG 979
            +  + IR+       D A                    +P++ +TA A  E+       G
Sbjct: 67   ELLKTIRA-------DGA-----------------MSALPVLMVTAEAKKENIIAAAQAG 102

Query: 980  MDSFVSKPVTFQKLKECLEQYF 1001
               +V KP T   L+E L + F
Sbjct: 103  ASGYVVKPFTAATLEEKLNKIF 124

Length = 129

>gnl|CDD|236462 PRK09303, PRK09303, adaptive-response sensory kinase; Validated

 Score = 55.0 bits (133), Expect = 9e-08
 Identities = 25/76 (32%), Positives = 43/76 (56%), Gaps = 2/76 (2%)

Query: 589 TVWIRCDVYDTGIGIPENALPTLFRKYMQVSADHARKYGGTGLGLAICKQLVELMGGRLT 648
           T  ++  + DTG GIPE     +F   +++  D   +  G G+GL++C+++V +  G++ 
Sbjct: 303 TQKVQVSICDTGPGIPEEEQERIFEDRVRLPRDEGTE--GYGIGLSVCRRIVRVHYGQIW 360

Query: 649 VTSKVHCGSTFTFILP 664
           V S+   GS F F LP
Sbjct: 361 VDSEPGQGSCFHFTLP 376

Length = 380

>gnl|CDD|236701 PRK10490, PRK10490, sensor protein KdpD; Provisional

 Score = 55.4 bits (134), Expect = 1e-07
 Identities = 38/149 (25%), Positives = 75/149 (50%), Gaps = 13/149 (8%)

Query: 373 MLATMSHEIRSPLTGVVSMAEILS------NTKLDREQRQLLGVMISSGDLVLQLINDIL 426
           +LA +SH++R+PLT +   AEIL+       +   R+  ++   ++++  LV    N++L
Sbjct: 667 LLAALSHDLRTPLTVLFGQAEILTLDLASEGSPHARQASEIRQQVLNTTRLV----NNLL 722

Query: 427 DLSKVESGVMKLEAAKFRPREVVKHVLQTAAASLQKILMLEGDIADDVPIEVIGDVLRIR 486
           D+++++SG   L        EVV   LQ     L     +   + + + + +  D     
Sbjct: 723 DMARIQSGGFNLRKEWLTLEEVVGSALQMLEPGLSG-HPINLSLPEPLTL-IHVDGPLFE 780

Query: 487 QILTNLISNAIKFT-PEGKVGIKLYVVPE 514
           ++L NL+ NA+K+   + ++GI  +V  E
Sbjct: 781 RVLINLLENAVKYAGAQAEIGIDAHVEGE 809

Length = 895

>gnl|CDD|237135 PRK12555, PRK12555, chemotaxis-specific methylesterase; Provisional

 Score = 54.5 bits (132), Expect = 1e-07
 Identities = 24/71 (33%), Positives = 37/71 (52%), Gaps = 10/71 (14%)

Query: 861 KILLVEDNKINVMVAKSMMKQ---LGHSIDVV---NNGVEAVHAVQCQNYDLILMDVCMP 914
           +I +V D      +A   +++        +VV    +G +AV     Q  D+ILMD+ MP
Sbjct: 2   RIGIVND----SPLAVEALRRALARDPDHEVVWVATDGAQAVERCAAQPPDVILMDLEMP 57

Query: 915 VMDGLKATRLI 925
            MDG++ATR I
Sbjct: 58  RMDGVEATRRI 68

Length = 337

>gnl|CDD|236674 PRK10364, PRK10364, sensor protein ZraS; Provisional

 Score = 54.8 bits (132), Expect = 1e-07
 Identities = 28/69 (40%), Positives = 37/69 (53%), Gaps = 6/69 (8%)

Query: 596 VYDTGIGIPENALPTLFRKYMQVSADHARKYGGTGLGLAICKQLVELMGGRLTVTSKVHC 655
           V D+G GI  + L  +F  Y    A+      GTGLGLA+   +VE  GG + V S+   
Sbjct: 385 VTDSGKGIAADQLEAIFTPYFTTKAE------GTGLGLAVVHNIVEQHGGTIQVASQEGK 438

Query: 656 GSTFTFILP 664
           G+TFT  LP
Sbjct: 439 GATFTLWLP 447

Length = 457

>gnl|CDD|236674 PRK10364, PRK10364, sensor protein ZraS; Provisional

 Score = 54.4 bits (131), Expect = 2e-07
 Identities = 37/150 (24%), Positives = 69/150 (46%), Gaps = 14/150 (9%)

Query: 365 EETMRAKQMLATM-------SHEIRSPLTGVVSMAEILS-NTKLDREQRQLLGVMISSGD 416
           ++ M+ K+ L  +       +HEIR+PL+ +  +A+  +       E  QL  VM    D
Sbjct: 225 QDEMKRKEKLVALGHLAAGVAHEIRNPLSSIKGLAKYFAERAPAGGEAHQLAQVMAKEAD 284

Query: 417 LVLQLINDILDLSKVESGVMKLEAAKFRPREVVKHVLQTAAASLQ-KILMLEGDIADDVP 475
            + ++++++L+L K       L        +++ H LQ  +     + + L     D +P
Sbjct: 285 RLNRVVSELLELVKPT----HLALQAVDLNDLINHSLQLVSQDANSREIQLRFTANDTLP 340

Query: 476 IEVIGDVLRIRQILTNLISNAIKFTPEGKV 505
            E+  D  R+ Q+L NL  NAI+   +  V
Sbjct: 341 -EIQADPDRLTQVLLNLYLNAIQAIGQHGV 369

Length = 457

>gnl|CDD|236901 PRK11360, PRK11360, sensory histidine kinase AtoS; Provisional

 Score = 53.4 bits (129), Expect = 4e-07
 Identities = 57/273 (20%), Positives = 122/273 (44%), Gaps = 48/273 (17%)

Query: 253 SLHEEDILGKTDVEIFSGAGVKESQDFK---REVLEKGLPAK-REITFETELFGSKTFLI 308
            L   +++GK   E+F       +  F     + LE G      EI+F       +T  +
Sbjct: 296 GLQRHELVGKPYSELFP-----PNTPFASPLLDTLEHGTEHVDLEISFPGR---DRTIEL 347

Query: 309 YV--EPVFSKSGETIGVNYMGMDVTDQVRKREKMAKLREEIAVQKAKETELNKTIHITEE 366
            V    + +  GE IG   +  D+T++ R + ++A+  E +A        L +       
Sbjct: 348 SVSTSLLHNTHGEMIGALVIFSDLTERKRLQRRVARQ-ERLAA-------LGE------- 392

Query: 367 TMRAKQMLATMSHEIRSPLTGVVSMAEILSNTKLDREQRQLLGVMISSGDLVLQLINDIL 426
                 ++A ++HEIR+PLT +    +I      D   ++ L V++   D + ++I+ +L
Sbjct: 393 ------LVAGVAHEIRNPLTAIRGYVQIWRQQTSDPPSQEYLSVVLREVDRLNKVIDQLL 446

Query: 427 DLSKVESGVMKLEAAKFRP---REVVKHVLQTAAASLQK-ILMLEGDIADDVPIEVIGDV 482
           + S+          ++++P     +V+ VLQ    +  +  +  E ++ +++P  +  D 
Sbjct: 447 EFSRP-------RESQWQPVSLNALVEEVLQLFQTAGVQARVDFETELDNELP-PIWADP 498

Query: 483 LRIRQILTNLISNAIKFTP-EGKVGIKLYVVPE 514
             ++Q+L N++ NA++     GK+ I+ +   +
Sbjct: 499 ELLKQVLLNILINAVQAISARGKIRIRTWQYSD 531

Length = 607

>gnl|CDD|233391 TIGR01386, cztS_silS_copS, heavy metal sensor kinase

 Score = 53.2 bits (128), Expect = 5e-07
 Identities = 40/144 (27%), Positives = 76/144 (52%), Gaps = 20/144 (13%)

Query: 369 RAKQMLATMSHEIRSPLTGVVSMAEI-LSNTKLDREQRQLLGVMISSGDLVLQLINDILD 427
           R  Q  A ++HE+R+PLT ++   ++ LS  +   E R++L   +   + + ++++D+L 
Sbjct: 240 RLSQFSADLAHELRTPLTNLLGQTQVALSQPRTGEEYREVLESNLEELERLSRMVSDMLF 299

Query: 428 LSKVESGVMKLEAAKFRPREVVKHVLQTAAASLQKILMLEGDIADD--VPIEV------I 479
           L++ ++G + LE          +  L   AA L K+      +A++  V I V       
Sbjct: 300 LARADNGQLALE----------RVRLD-LAAELAKVAEYFEPLAEERGVRIRVEGEGLVR 348

Query: 480 GDVLRIRQILTNLISNAIKFTPEG 503
           GD    R+ ++NL+SNA++ TP+G
Sbjct: 349 GDPQMFRRAISNLLSNALRHTPDG 372

Members of this family contain a sensor histidine kinase domain (pfam00512) and a domain found in bacterial signal proteins (pfam00672). This group is separated phylogenetically from related proteins with similar architecture and contains a number of proteins associated with heavy metal resistance efflux systems for copper, silver, cadmium, and/or zinc. Length = 457

>gnl|CDD|225111 COG2201, CheB, Chemotaxis response regulator containing a CheY-like receiver domain and a methylesterase domain [Cell motility and secretion / Signal transduction mechanisms]

 Score = 52.3 bits (126), Expect = 6e-07
 Identities = 27/70 (38%), Positives = 41/70 (58%), Gaps = 4/70 (5%)

Query: 859 KPKILLVEDNKINVMVAKSMMKQLGHSIDVVN---NGVEAVHAVQCQNYDLILMDVCMPV 915
           K ++L+V+D+ +   V   ++      I+VV    NG EA+  V+    D+I +DV MPV
Sbjct: 1   KIRVLVVDDSALMRKVISDILNSDP-DIEVVGTARNGREAIDKVKKLKPDVITLDVEMPV 59

Query: 916 MDGLKATRLI 925
           MDGL+A R I
Sbjct: 60  MDGLEALRKI 69

Length = 350

>gnl|CDD|227335 COG5002, VicK, Signal transduction histidine kinase [Signal transduction mechanisms]

 Score = 52.0 bits (125), Expect = 1e-06
 Identities = 36/139 (25%), Positives = 74/139 (53%), Gaps = 15/139 (10%)

Query: 375 ATMSHEIRSPLTGVVSMAEILSNTKLDREQ--RQLLGVMISSGDLVLQLINDILDLSKVE 432
           A +SHE+R+PLT + S  E L     + ++   + L V ++  + +++L+ND+L LS+++
Sbjct: 230 ANVSHELRTPLTSMKSYLEALEEGAWEDKEIAPRFLRVTLNETERMIRLVNDLLQLSRMD 289

Query: 433 SGVMKLEAAKFRPREVVKHVLQTAAASLQKILMLEGDIAD----DVPIEVI---GDVLRI 485
           +   +L       +E +           +  ++L+ +       D+P + I    D  ++
Sbjct: 290 NARYQLN------KEWINFTAFLNEIINRFEMILKKETIARFVRDIPKQDIWVEIDPDKM 343

Query: 486 RQILTNLISNAIKFTPEGK 504
            Q+L N+ISNA+K++P+G 
Sbjct: 344 TQVLDNIISNALKYSPDGG 362

Length = 459

>gnl|CDD|237526 PRK13837, PRK13837, two-component VirA-like sensor kinase; Provisional

 Score = 52.0 bits (125), Expect = 1e-06
 Identities = 36/138 (26%), Positives = 59/138 (42%), Gaps = 9/138 (6%)

Query: 378 SHEIRSPLTGVVSMAEILSNTKLDREQ--RQLLGVMISSGDLVLQLINDILDLSKVESGV 435
           +H   + L  ++  AE+  N KL R     + +  +IS+G     +I+ IL   +     
Sbjct: 458 AHNFNNILGAILGYAEMALN-KLARHSRAARYIDEIISAGARARLIIDQILAFGRKGERN 516

Query: 436 MKLEAAKFRPREVVKHVLQTAAASLQKILMLEGDIADDVPIEVIGDVLRIRQILTNLISN 495
            K     F   E+V  +      SL   + L+ D   + P  V G+   ++Q+L NL SN
Sbjct: 517 TK----PFDLSELVTEIAPLLRVSLPPGVELDFDQDQE-PAVVEGNPAELQQVLMNLCSN 571

Query: 496 AIK-FTPEGKVGIKLYVV 512
           A +     G+V I L   
Sbjct: 572 AAQAMDGAGRVDISLSRA 589

Length = 828

>gnl|CDD|183172 PRK11517, PRK11517, transcriptional regulatory protein YedW; Provisional

 Score = 50.3 bits (120), Expect = 1e-06
 Identities = 31/133 (23%), Positives = 60/133 (45%), Gaps = 27/133 (20%)

Query: 861 KILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLK 920
           KILL+EDN+         + + G+ ID V++G + ++     +Y LI++D+ +P MDG +
Sbjct: 2   KILLIEDNQRTQEWVTQGLSEAGYVIDAVSDGRDGLYLALKDDYALIILDIMLPGMDGWQ 61

Query: 921 ATRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGM 980
             + +R+ + T                           P+I +TA    +       +G 
Sbjct: 62  ILQTLRTAKQT---------------------------PVICLTARDSVDDRVRGLDSGA 94

Query: 981 DSFVSKPVTFQKL 993
           + ++ KP +F +L
Sbjct: 95  NDYLVKPFSFSEL 107

Length = 223

>gnl|CDD|130454 TIGR01387, cztR_silR_copR, heavy metal response regulator

 Score = 49.8 bits (119), Expect = 2e-06
 Identities = 35/142 (24%), Positives = 60/142 (42%), Gaps = 30/142 (21%)

Query: 862 ILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKA 921
           IL+VED +      +  + + G+ +D  +NG + +H     +YDLI++DV +P MDG   
Sbjct: 1   ILVVEDEQKTAEYLQQGLSESGYVVDAASNGRDGLHLALKDDYDLIILDVMLPGMDG--- 57

Query: 922 TRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMD 981
                       W       I Q +  SG        P++ +TA        +    G D
Sbjct: 58  ------------WQ------ILQTLRRSGKQT-----PVLFLTARDSVADKVKGLDLGAD 94

Query: 982 SFVSKPVTFQKL----KECLEQ 999
            ++ KP +F +L    +  L +
Sbjct: 95  DYLVKPFSFSELLARVRTLLRR 116

Members of this family contain a response regulator receiver domain (pfam00072) and an associated transcriptional regulatory region (pfam00486). This group is separated phylogenetically from related proteins with similar architecture and contains a number of proteins associated with heavy metal resistance efflux systems for copper, silver, cadmium, and/or zinc. Most members encoded by genes adjacent to genes for encoding a member of the heavy metal sensor histidine kinase family (TIGRFAMs:TIGR01386), its partner in the two-component response regulator system. Length = 218

>gnl|CDD|131922 TIGR02875, spore_0_A, sporulation transcription factor Spo0A

 Score = 50.6 bits (121), Expect = 2e-06
 Identities = 32/146 (21%), Positives = 61/146 (41%), Gaps = 28/146 (19%)

Query: 859  KPKILLVEDNKINVMVAKSMMKQLGHSIDVV---NNGVEAVHAVQCQNYDLILMDVCMPV 915
            K +I++ +DNK    + K  +      ++VV   +NGV+A+  ++ Q  D++++D+ MP 
Sbjct: 2    KIRIVIADDNKEFCNLLKEYLAA-QPDMEVVGVAHNGVDALELIKEQQPDVVVLDIIMPH 60

Query: 916  MDGLKATRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEEC 975
            +DG+     +   E               A P            +I ++A    +  +  
Sbjct: 61   LDGIGVLEKLNEIEL-------------SARPR-----------VIMLSAFGQEKITQRA 96

Query: 976  FANGMDSFVSKPVTFQKLKECLEQYF 1001
             A G D +V KP   + L   + Q  
Sbjct: 97   VALGADYYVLKPFDLEILAARIRQLA 122

Spo0A, the stage 0 sporulation protein A, is a transcription factor critical for the initiation of sporulation. It contains a response regulator receiver domain (pfam00072). In Bacillus subtilis, it works together with response regulator Spo0F and the phosphotransferase Spo0B, both of which are missing from at least some sporulating species and thus not part of the endospore forming bacteria minimal gene set. Spo0A, however, is universal among endospore-forming species [Cellular processes, Sporulation and germination]. Length = 262

>gnl|CDD|226456 COG3947, COG3947, Response regulator containing CheY-like receiver and SARP domains [Signal transduction mechanisms]

 Score = 50.6 bits (121), Expect = 2e-06
 Identities = 33/134 (24%), Positives = 66/134 (49%), Gaps = 28/134 (20%)

Query: 860 PKILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGL 919
           P+I++V+D+   V +   ++ + GH +   ++ VEA+  ++    DLI +D+ MP M+G+
Sbjct: 1   PRIIIVDDDAAIVKLLSVILSRAGHEVRSCSHPVEALDLLEVFKPDLIFLDIVMPYMNGI 60

Query: 920 KATRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANG 979
           +    +R                          +    +PII ++++A  E A++ F   
Sbjct: 61  EFAEQVR--------------------------DIESAVPIIFISSHA--EYADDSFGMN 92

Query: 980 MDSFVSKPVTFQKL 993
           +D ++ KPVT +KL
Sbjct: 93  LDDYLPKPVTPEKL 106

Length = 361

>gnl|CDD|236846 PRK11100, PRK11100, sensory histidine kinase CreC; Provisional

 Score = 50.6 bits (122), Expect = 3e-06
 Identities = 28/70 (40%), Positives = 38/70 (54%), Gaps = 3/70 (4%)

Query: 596 VYDTGIGIPENALPTLF-RKYMQVSADHARKYGGTGLGLAICKQLVELMGGRLTVTSKVH 654
           V D G GIP+ ALP +F R Y      + RK   TGLGLA  +++  L GG +T+ ++  
Sbjct: 405 VEDQGPGIPDYALPRIFERFYSLPRPANGRK--STGLGLAFVREVARLHGGEVTLRNRPE 462

Query: 655 CGSTFTFILP 664
            G   T  LP
Sbjct: 463 GGVLATLTLP 472

Length = 475

>gnl|CDD|182895 PRK11006, phoR, phosphate regulon sensor protein; Provisional

 Score = 50.4 bits (121), Expect = 3e-06
 Identities = 41/146 (28%), Positives = 71/146 (48%), Gaps = 18/146 (12%)

Query: 366 ETMRAKQMLATMSHEIRSPLTGVVSMAEILSNTKLDREQRQ-LLGVMISSGDLVLQLIND 424
           E  R +   A +SHE+R+PLT +    E++ +  L+   R+  L  M      +  L+  
Sbjct: 201 EGAR-RNFFANVSHELRTPLTVLQGYLEMMQDQPLEGALREKALHTMREQTQRMEGLVKQ 259

Query: 425 ILDLSKVESG-VMKLEAAKFRPREVVK-----HVLQTAAASL-QKILMLEGDIADDVPIE 477
           +L LSK+E+   + L        E V       VL+  A +L Q    +  ++  D  ++
Sbjct: 260 LLTLSKIEAAPTIDLN-------EKVDVPMMLRVLEREAQTLSQGKHTITFEV--DNSLK 310

Query: 478 VIGDVLRIRQILTNLISNAIKFTPEG 503
           V G+  ++R  ++NL+ NA+  TPEG
Sbjct: 311 VFGNEDQLRSAISNLVYNAVNHTPEG 336

Length = 430

>gnl|CDD|236724 PRK10604, PRK10604, sensor protein RstB; Provisional

 Score = 50.8 bits (122), Expect = 3e-06
 Identities = 23/69 (33%), Positives = 32/69 (46%)

Query: 596 VYDTGIGIPENALPTLFRKYMQVSADHARKYGGTGLGLAICKQLVELMGGRLTVTSKVHC 655
           V D G GIP      +F  ++++     R  GG GLGLAI   +   MGG +        
Sbjct: 354 VEDDGPGIPPEERERVFEPFVRLDPSRDRATGGCGLGLAIVHSIALAMGGSVNCDESELG 413

Query: 656 GSTFTFILP 664
           G+ F+F  P
Sbjct: 414 GARFSFSWP 422

Length = 433

>gnl|CDD|236531 PRK09467, envZ, osmolarity sensor protein; Provisional

 Score = 50.7 bits (122), Expect = 3e-06
 Identities = 24/61 (39%), Positives = 34/61 (55%), Gaps = 4/61 (6%)

Query: 590 VWIRCDVYDTGIGIPENALPTLFRKYMQVSADHARKYGGTGLGLAICKQLVELMGGRLTV 649
            W +  V D G GIP   L  LF+ + +   D AR   GTGLGLAI K++V+   G++ +
Sbjct: 362 AWFQ--VEDDGPGIPPEQLKHLFQPFTR--GDSARGSSGTGLGLAIVKRIVDQHNGKVEL 417

Query: 650 T 650
            
Sbjct: 418 G 418

Length = 435

>gnl|CDD|226370 COG3852, NtrB, Signal transduction histidine kinase, nitrogen specific [Signal transduction mechanisms]

 Score = 50.1 bits (120), Expect = 4e-06
 Identities = 25/72 (34%), Positives = 37/72 (51%), Gaps = 7/72 (9%)

Query: 593 RCDVYDTGIGIPENALPTLFRKYMQVSADHARKYGGTGLGLAICKQLVELMGGRLTVTSK 652
             +V D G G+P +    LF  Y  VS     + GGTGLGLA+ + L++  GG++   S 
Sbjct: 289 PLEVIDNGPGVPPDLQDHLF--YPMVSG----REGGTGLGLALAQNLIDQHGGKIEFDSW 342

Query: 653 VHCGSTFTFILP 664
               + F  +LP
Sbjct: 343 -PGRTVFRVLLP 353

Length = 363

>gnl|CDD|226654 COG4191, COG4191, Signal transduction histidine kinase regulating C4-dicarboxylate transport system [Signal transduction mechanisms]

 Score = 50.0 bits (120), Expect = 5e-06
 Identities = 41/190 (21%), Positives = 86/190 (45%), Gaps = 37/190 (19%)

Query: 341 AKLREEIAVQKAKETELNKTIHITEETMRAK------QMLATMSHEIRSPLTGVVSMAEI 394
           A+L+ EIA ++  E  L +      E ++A       QM A ++HE+  PL  + + A+ 
Sbjct: 352 ARLQAEIAEREQAEAALRRAQD---ELVQAGKLAALGQMSAGIAHELNQPLAAIRTYAD- 407

Query: 395 LSNTK--LDREQRQLLGVMISSGDLVLQLINDILDLSKVESGVMKLEAAKFRPR------ 446
             N +  L+R + +         +L  + I+ + +  ++ +    L++   + R      
Sbjct: 408 --NARLLLERGRTEEA-----RENL--ERISALTE--RMAAITAHLKSFARKSRDAAGPV 456

Query: 447 ---EVVKHVLQTAAASL-QKILMLEGDIADDVPIEVIGDVLRIRQILTNLISN---AIKF 499
              E ++  L+     L    + LE D+  D P+ V+ + +R+ Q+L NL+ N   A+  
Sbjct: 457 SLREAIEGALELLRGRLRAAGVELELDL-PDAPLWVMANEIRLEQVLVNLLQNALDAMAG 515

Query: 500 TPEGKVGIKL 509
             + ++ I+ 
Sbjct: 516 QEDRRLSIRA 525

Length = 603

>gnl|CDD|234828 PRK00742, PRK00742, chemotaxis-specific methylesterase; Provisional

 Score = 49.0 bits (118), Expect = 8e-06
 Identities = 17/40 (42%), Positives = 24/40 (60%)

Query: 886 IDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKATRLI 925
           +    +G+EA   ++  N D+I +DV MPVMDGL A   I
Sbjct: 32  VGTAPDGLEAREKIKKLNPDVITLDVEMPVMDGLDALEKI 71

Length = 354

>gnl|CDD|185376 PRK15479, PRK15479, transcriptional regulatory protein TctD; Provisional

 Score = 47.8 bits (114), Expect = 8e-06
 Identities = 22/59 (37%), Positives = 36/59 (61%)

Query: 861 KILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGL 919
           ++LL EDN+      +  + Q G ++D V +G+ A H +Q + Y L ++D+ MP MDGL
Sbjct: 2   RLLLAEDNRELAHWLEKALVQNGFAVDCVFDGLAADHLLQSEMYALAVLDINMPGMDGL 60

Length = 221

>gnl|CDD|234058 TIGR02916, PEP_his_kin, putative PEP-CTERM system histidine kinase

 Score = 49.3 bits (118), Expect = 9e-06
 Identities = 30/94 (31%), Positives = 44/94 (46%), Gaps = 21/94 (22%)

Query: 586 LEAT-----VWIRC---------DVYDTGIGIPENAL-PTLFRKYMQVSADHARKYGGTG 630
           LEAT     V IR          ++ D+G G+    +   LF+ +         K  G G
Sbjct: 592 LEATPGEGRVAIRVERECGAARIEIEDSGCGMSPAFIRERLFKPF------DTTKGAGMG 645

Query: 631 LGLAICKQLVELMGGRLTVTSKVHCGSTFTFILP 664
           +G+  C+Q VE +GGR+ V S    G+ FT +LP
Sbjct: 646 IGVYECRQYVEEIGGRIEVESTPGQGTIFTLVLP 679

Members of this protein family have a novel N-terminal domain, a single predicted membrane-spanning helix, and a predicted cystosolic histidine kinase domain. We designate this protein PrsK, and its companion DNA-binding response regulator protein (TIGR02915) PrsR. These predicted signal-transducing proteins appear to enable enhancer-dependent transcriptional activation. The prsK gene is often associated with exopolysaccharide biosynthesis genes [Protein fate, Protein and peptide secretion and trafficking, Signal transduction, Two-component systems]. Length = 679

>gnl|CDD|182101 PRK09835, PRK09835, sensor kinase CusS; Provisional

 Score = 49.0 bits (117), Expect = 1e-05
 Identities = 26/73 (35%), Positives = 37/73 (50%), Gaps = 1/73 (1%)

Query: 592 IRCDVYDTGIGIPENALPTLFRKYMQVSADHARKYGGTGLGLAICKQLVELMGGRLTVTS 651
           ++  V + G  I    LP LF ++ +V     RK  G+G+GLAI K +V    G + VTS
Sbjct: 408 VQLVVENPGTPIAPEHLPRLFDRFYRVDPSRQRKGEGSGIGLAIVKSIVVAHKGTVAVTS 467

Query: 652 KVHCGSTFTFILP 664
               G+ F   LP
Sbjct: 468 DAR-GTRFVISLP 479

Length = 482

>gnl|CDD|226370 COG3852, NtrB, Signal transduction histidine kinase, nitrogen specific [Signal transduction mechanisms]

 Score = 48.5 bits (116), Expect = 1e-05
 Identities = 36/139 (25%), Positives = 61/139 (43%), Gaps = 10/139 (7%)

Query: 364 TEETMRAKQMLAT-----MSHEIRSPLTGVVSMAEILSNTKLDREQRQLLGVMISSGDLV 418
            E+T  A+Q         ++HEI++PL G+   A++L     D   R+L  ++I   D +
Sbjct: 121 REQTQHAQQRAVKGLVRGLAHEIKNPLGGIRGAAQLLERALPDEALRELTQLIIEEADRL 180

Query: 419 LQLINDILDLSKVESGVMKLEAAKFRPREVVKHVLQTAAASLQKILMLEGDIADDVPIEV 478
             L++ +  L     G            EV++ V     A     + L  D    +P EV
Sbjct: 181 RNLVDRLEVLGPQRPGDRVPVNI----HEVLERVRALVEAEFADNVRLIRDYDPSLP-EV 235

Query: 479 IGDVLRIRQILTNLISNAI 497
           +GD  ++ Q+  NL+ NA 
Sbjct: 236 LGDRDQLIQVFLNLVRNAA 254

Length = 363

>gnl|CDD|182102 PRK09836, PRK09836, DNA-binding transcriptional activator CusR; Provisional

 Score = 47.6 bits (113), Expect = 1e-05
 Identities = 34/133 (25%), Positives = 58/133 (43%), Gaps = 26/133 (19%)

Query: 861 KILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLK 920
           K+L+VED K         + + G  +D+ +NG+   H     +YDLI++D+ +P ++G  
Sbjct: 2   KLLIVEDEKKTGEYLTKGLTEAGFVVDLADNGLNGYHLAMTGDYDLIILDIMLPDVNGWD 61

Query: 921 ATRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGM 980
             R++RS            A               K +PI+ +TA    E   +    G 
Sbjct: 62  IVRMLRS------------AN--------------KGMPILLLTALGTIEHRVKGLELGA 95

Query: 981 DSFVSKPVTFQKL 993
           D ++ KP  F +L
Sbjct: 96  DDYLVKPFAFAEL 108

Length = 227

>gnl|CDD|182947 PRK11073, glnL, nitrogen regulation protein NR(II); Provisional

 Score = 48.2 bits (115), Expect = 1e-05
 Identities = 29/73 (39%), Positives = 40/73 (54%), Gaps = 9/73 (12%)

Query: 593 RCDVYDTGIGIPENALPTLFRKYMQVSADHARKYGGTGLGLAICKQLVELMGGRLTVTS- 651
           R D+ D G GIP +   TLF  Y  VS     + GGTGLGL+I + L++   G++  TS 
Sbjct: 282 RIDIEDNGPGIPPHLQDTLF--YPMVSG----REGGTGLGLSIARNLIDQHSGKIEFTSW 335

Query: 652 KVHCGSTFTFILP 664
             H  + F+  LP
Sbjct: 336 PGH--TEFSVYLP 346

Length = 348

>gnl|CDD|214643 smart00387, HATPase_c, Histidine kinase-like ATPases

 Score = 44.2 bits (105), Expect = 2e-05
 Identities = 17/36 (47%), Positives = 26/36 (72%), Gaps = 1/36 (2%)

Query: 480 GDVLRIRQILTNLISNAIKFTPE-GKVGIKLYVVPE 514
           GD  R+RQ+L+NL+ NAIK+TPE G++ + L    +
Sbjct: 1   GDPDRLRQVLSNLLDNAIKYTPEGGRITVTLERDGD 36

Histidine kinase-, DNA gyrase B-, phytochrome-like ATPases. Length = 111

>gnl|CDD|182711 PRK10766, PRK10766, DNA-binding transcriptional regulator TorR; Provisional

 Score = 47.0 bits (112), Expect = 2e-05
 Identities = 24/72 (33%), Positives = 38/72 (52%)

Query: 861 KILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLK 920
            IL+VED  +     +   +Q G+++    +G      +Q Q+ DLIL+D+ +P  DGL 
Sbjct: 4   HILVVEDEPVTRARLQGYFEQEGYTVSEAASGAGMREIMQNQHVDLILLDINLPGEDGLM 63

Query: 921 ATRLIRSFEDTG 932
            TR +RS    G
Sbjct: 64  LTRELRSRSTVG 75

Length = 221

>gnl|CDD|214376 CHL00148, orf27, Ycf27; Reviewed

 Score = 46.6 bits (111), Expect = 2e-05
 Identities = 34/144 (23%), Positives = 63/144 (43%), Gaps = 31/144 (21%)

Query: 854 TKPKPKPKILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCM 913
           T    K KIL+V+D      + ++ +  +G+ +   ++G EA+   + +  DL+++DV M
Sbjct: 1   TMENSKEKILVVDDEAYIRKILETRLSIIGYEVITASDGEEALKLFRKEQPDLVILDVMM 60

Query: 914 PVMDGLKATRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAE 973
           P +DG    + IR   D                           +PII +T  AL + ++
Sbjct: 61  PKLDGYGVCQEIRKESD---------------------------VPIIMLT--ALGDVSD 91

Query: 974 EC--FANGMDSFVSKPVTFQKLKE 995
                  G D +V KP + ++L+ 
Sbjct: 92  RITGLELGADDYVVKPFSPKELEA 115

Length = 240

>gnl|CDD|182387 PRK10336, PRK10336, DNA-binding transcriptional regulator QseB; Provisional

 Score = 46.4 bits (110), Expect = 2e-05
 Identities = 34/139 (24%), Positives = 64/139 (46%), Gaps = 28/139 (20%)

Query: 861 KILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLK 920
           +ILL+ED+ +     K+ + ++G S+D    G +   A+    YD +++D+ +P MDG  
Sbjct: 2   RILLIEDDMLIGDGIKTGLSKMGFSVDWFTQGRQGKEALYSAPYDAVILDLTLPGMDGRD 61

Query: 921 ATRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTA-NALSESAEECFANG 979
              ++R + + G                       +R P++ +TA +AL+E  E     G
Sbjct: 62  ---ILREWREKG-----------------------QREPVLILTARDALAERVEG-LRLG 94

Query: 980 MDSFVSKPVTFQKLKECLE 998
            D ++ KP    ++   LE
Sbjct: 95  ADDYLCKPFALIEVAARLE 113

Length = 219

>gnl|CDD|227333 COG5000, NtrY, Signal transduction histidine kinase involved in nitrogen fixation and metabolism regulation [Signal transduction mechanisms]

 Score = 47.8 bits (114), Expect = 3e-05
 Identities = 95/482 (19%), Positives = 147/482 (30%), Gaps = 126/482 (26%)

Query: 176 LDLEKMLEASGQREQALMEKLNESVTNLEKQSSPVEELSQILKRADNFLHFVLQNAPVVM 235
           LD++  +    +    L +  N+    L  Q   +E     L++   FL  VL      +
Sbjct: 324 LDVQVPVRRVDEDVGRLSKAFNKMTEQLSSQQEALERAKDALEQRRRFLEAVLSGLTAGV 383

Query: 236 GHQDKELRYRFIYNHFPSLHEEDILGKTDVEIFSGAGVKESQDFKREVLEKG----LPAK 291
              D       I    PS   E ILGK   ++  G  +        EV  +        K
Sbjct: 384 IGFD---NRGCITTVNPS--AEQILGKPFDQLL-GQSLSAIAPELEEVFAEAGAAARTDK 437

Query: 292 REITFETELFGSKTFLIYVEPVFSKSGETIGVNYMGMDVTDQVRKREKMAKLREEIAVQK 351
           R           +T  +        +G   G      D+TD V            IA + 
Sbjct: 438 RVEVKLAREGEERTLNVQATREPEDNGN--GYVVTFDDITDLV------------IAQRS 483

Query: 352 AKETELNKTIHITEETMRAKQMLATMSHEIRSPLTGVVSMAEILSNTKLDREQRQLLGVM 411
           A   ++ + I                +HEI++PLT +   AE L   KL +E  +   V 
Sbjct: 484 AAWGDVARRI----------------AHEIKNPLTPIQLSAERLLR-KLGKEIDEDREVF 526

Query: 412 ISSGDLVLQLINDILDLSKVESGVMKLEAAKFRP---REVVKHVLQTAAASLQKILMLEG 468
               D +++ + DI  +        ++ A K      R ++K V       L +I     
Sbjct: 527 DRCTDTIIRQVEDIKRMVDEFRAFARMPAPKLEKSDLRALLKEVSF-----LYEIGNDHI 581

Query: 469 DIADDV---PIEVIGDVLRIRQILTNLISNAIKFTPEGKVGIKLYVVPEPPFAKEGLKQK 525
             A +    P+  + D   + Q+      N +K   E               A E +   
Sbjct: 582 VFAAEFGGEPLIGMADATLLGQVFG----NLLKNAAE---------------AIEAV--- 619

Query: 526 SKAYQSATDAVKEEKHQPKSQTASDQNGFHDKKHGEGYQDHKHDDDPGTPVSHGNSMDED 585
                      +E +      +  D +G                                
Sbjct: 620 ---------EAEERRTALIRVSLDDADGR------------------------------- 639

Query: 586 LEATVWIRCDVYDTGIGIPENALPTLFRKYMQVSADHARKYGGTGLGLAICKQLVELMGG 645
                 I  DV D G G P          Y+           GTGLGLAI K++VE  GG
Sbjct: 640 ------IVVDVIDNGKGFPRENRHRALEPYVTTREK------GTGLGLAIVKKIVEEHGG 687

Query: 646 RL 647
           RL
Sbjct: 688 RL 689

Length = 712

>gnl|CDD|236726 PRK10618, PRK10618, phosphotransfer intermediate protein in two-component regulatory system with RcsBC; Provisional

 Score = 47.2 bits (113), Expect = 5e-05
 Identities = 24/102 (23%), Positives = 42/102 (41%), Gaps = 13/102 (12%)

Query: 595 DVYDTGIGIPENALPTLFRKYMQVSADHARKYG-GTGLGLAICKQLVELMGGRLTVTSKV 653
            + DTG G+    L  L   +  ++     +YG  +GL   +C QL   +GG LT+ S+ 
Sbjct: 603 RILDTGAGVSIKELDNL--HFPFLNQTQGDRYGKASGLTFFLCNQLCRKLGGHLTIKSRE 660

Query: 654 HCGSTFTFILPYQVSPIEENSDDPDDLSDMADQDSVTDDVTA 695
             G+ ++  L               D     +++ + D VT 
Sbjct: 661 GLGTRYSIHLKML----------AADPEVEEEEEKLLDGVTV 692

Length = 894

>gnl|CDD|131209 TIGR02154, PhoB, phosphate regulon transcriptional regulatory protein PhoB

 Score = 45.4 bits (108), Expect = 5e-05
 Identities = 34/135 (25%), Positives = 59/135 (43%), Gaps = 26/135 (19%)

Query: 860 PKILLVEDNK-INVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDG 918
            +IL+VED   I  ++A ++ K  G+ +    +G EA+  +  +  DLIL+D  +P   G
Sbjct: 3   RRILVVEDEPAIRELIAYNLEKA-GYDVVEAGDGDEALTLINERGPDLILLDWMLPGTSG 61

Query: 919 LKATRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFAN 978
           ++  R +R   +T                          IPII +TA    E        
Sbjct: 62  IELCRRLRRRPETRA------------------------IPIIMLTARGEEEDRVRGLET 97

Query: 979 GMDSFVSKPVTFQKL 993
           G D +++KP + ++L
Sbjct: 98  GADDYITKPFSPREL 112

PhoB is a DNA-binding response regulator protein acting with PhoR in a 2-component system responding to phosphate ion. PhoB acts as a positive regulator of gene expression for phosphate-related genes such as phoA, phoS, phoE and ugpAB as well as itself. It is often found proximal to genes for the high-affinity phosphate ABC transporter (pstSCAB; GenProp0190) and presumably regulates these as well [Regulatory functions, DNA interactions, Signal transduction, Two-component systems]. Length = 226

>gnl|CDD|217081 pfam02518, HATPase_c, Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase

 Score = 42.3 bits (100), Expect = 1e-04
 Identities = 15/36 (41%), Positives = 22/36 (61%), Gaps = 1/36 (2%)

Query: 480 GDVLRIRQILTNLISNAIKFTPE-GKVGIKLYVVPE 514
           GD  R+RQ+L+NL+ NAIK  P  G++ + L     
Sbjct: 1   GDEDRLRQVLSNLLDNAIKHAPAGGEIEVTLERDGG 36

This family represents the structurally related ATPase domains of histidine kinase, DNA gyrase B and HSP90. Length = 111

>gnl|CDD|237425 PRK13557, PRK13557, histidine kinase; Provisional

 Score = 45.4 bits (108), Expect = 1e-04
 Identities = 28/92 (30%), Positives = 46/92 (50%), Gaps = 9/92 (9%)

Query: 844 PSSSSAEVPETKPKPKP-------KILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAV 896
           P+S  AE PE +PK +         IL+V+D      +A+ +++  G+   V +NG EA+
Sbjct: 393 PASDQAENPEQEPKARAIDRGGTETILIVDDRPDVAELARMILEDFGYRTLVASNGREAL 452

Query: 897 HAVQCQN-YDLILMDVCMP-VMDGLKATRLIR 926
             +      DL+  D+ MP  M+G+   R  R
Sbjct: 453 EILDSHPEVDLLFTDLIMPGGMNGVMLAREAR 484

Length = 540

>gnl|CDD|227095 COG4753, COG4753, Response regulator containing CheY-like receiver domain and AraC-type DNA-binding domain [Signal transduction mechanisms]

 Score = 44.3 bits (105), Expect = 2e-04
 Identities = 35/144 (24%), Positives = 62/144 (43%), Gaps = 33/144 (22%)

Query: 861 KILLVEDNKINVMVAKSMM--KQLGHSIDVVN---NGVEAVHAVQCQNYDLILMDVCMPV 915
           K+L+V+D  +     KS++  + LG  I+VV    NG EA+  +Q    D+++ D+ MP 
Sbjct: 3   KVLIVDDEPLIREGLKSLIDWEALG--IEVVGTAANGKEALELIQETQPDIVITDINMPG 60

Query: 916 MDGLKATRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEEC 975
           MDGL   + I+                                  I ++     E A++ 
Sbjct: 61  MDGLDLIKAIKEQSPDTE--------------------------FIILSGYDEFEYAKKA 94

Query: 976 FANGMDSFVSKPVTFQKLKECLEQ 999
              G+  ++ KPV   +L+E L++
Sbjct: 95  MKLGVKDYLLKPVDKAELEEALKK 118

Length = 475

>gnl|CDD|182665 PRK10710, PRK10710, DNA-binding transcriptional regulator BaeR; Provisional

 Score = 43.1 bits (102), Expect = 3e-04
 Identities = 24/74 (32%), Positives = 41/74 (55%), Gaps = 6/74 (8%)

Query: 860 PKILLVEDNKINVMVAKSMMKQL---GHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVM 916
           P+IL+VED      + + ++  L    ++  ++++G E +  V+    DLIL+D+ +P  
Sbjct: 11  PRILIVEDEP---KLGQLLIDYLQAASYATTLLSHGDEVLPYVRQTPPDLILLDLMLPGT 67

Query: 917 DGLKATRLIRSFED 930
           DGL   R IR F D
Sbjct: 68  DGLTLCREIRRFSD 81

Length = 240

>gnl|CDD|236532 PRK09470, cpxA, two-component sensor protein; Provisional

 Score = 44.2 bits (105), Expect = 3e-04
 Identities = 19/44 (43%), Positives = 25/44 (56%)

Query: 592 IRCDVYDTGIGIPENALPTLFRKYMQVSADHARKYGGTGLGLAI 635
           +   V D G G+PE     +FR + +V     R+ GGTGLGLAI
Sbjct: 384 LTITVDDDGPGVPEEEREQIFRPFYRVDEARDRESGGTGLGLAI 427

Length = 461

>gnl|CDD|182539 PRK10549, PRK10549, signal transduction histidine-protein kinase BaeS; Provisional

 Score = 43.9 bits (104), Expect = 3e-04
 Identities = 23/72 (31%), Positives = 34/72 (47%)

Query: 598 DTGIGIPENALPTLFRKYMQVSADHARKYGGTGLGLAICKQLVELMGGRLTVTSKVHCGS 657
           D+  G+ +  L  LF ++ +      R  GG+GLGLAIC  +VE   GR+        G 
Sbjct: 391 DSAPGVSDEQLQKLFERFYRTEGSRNRASGGSGLGLAICLNIVEAHNGRIIAAHSPFGGV 450

Query: 658 TFTFILPYQVSP 669
           + T  LP +   
Sbjct: 451 SITVELPLERDL 462

Length = 466

>gnl|CDD|238030 cd00075, HATPase_c, Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins

 Score = 40.3 bits (95), Expect = 4e-04
 Identities = 15/31 (48%), Positives = 21/31 (67%)

Query: 485 IRQILTNLISNAIKFTPEGKVGIKLYVVPEP 515
           ++Q+L NL+SNAIK TPEG   I + V  + 
Sbjct: 1   LQQVLLNLLSNAIKHTPEGGGRITISVERDG 31

Length = 103

>gnl|CDD|163497 TIGR03785, marine_sort_HK, proteobacterial dedicated sortase system histidine kinase

 Score = 44.0 bits (104), Expect = 4e-04
 Identities = 40/187 (21%), Positives = 81/187 (43%), Gaps = 22/187 (11%)

Query: 328 MDVTDQVRKREKMAKLREEIA-VQKAKETELNKTIHITE--ETMRAKQMLATMSHEIRSP 384
           +D   ++      ++ R+EI  + ++    + +    T   E M ++     +SHE+R+P
Sbjct: 445 IDSQGRISGAIPASRSRDEIGDLSRSFAQMVARLRQYTHYLENMSSR-----LSHELRTP 499

Query: 385 LTGVVSMAEILSNTKLDREQRQLLGVMISSGDLVLQLI-NDILDLSKVESGVMKLEAAKF 443
           +  V S  E L    L++E+++ L      G   L +I N++ + +++E  +   E   F
Sbjct: 500 VAVVRSSLENLELQALEQEKQKYLE-RAREGTERLSMILNNMSEATRLEQAIQSAEVEDF 558

Query: 444 RPREVVKHVLQTAAASLQKI-----LMLEGDIADDVPIEVIGDVLRIRQILTNLISNAIK 498
              EV+   +Q      Q         L       + +    ++  I Q+L  L+ NA +
Sbjct: 559 DLSEVLSGCMQ----GYQMTYPPQRFELNIP-ETPLVMRGSPEL--IAQMLDKLVDNARE 611

Query: 499 FTPEGKV 505
           F+PE  +
Sbjct: 612 FSPEDGL 618

This histidine kinase protein is paired with an adjacent response regulator (TIGR03787) gene. It co-occurs with a variant sortase enzyme (TIGR03784), usually in the same gene neighborhood, in proteobacterial species most of which are marine, and with an LPXTG motif-containing sortase target conserved protein (TIGR03788). Sortases and LPXTG proteins are far more common in Gram-positive bacteria, where sortase systems mediate attachment to the cell wall or cross-linking of pilin structures. We give this predicted sensor histidine kinase the gene symbol psdS, for Proteobacterial Dedicated Sortase system Sensor histidine kinase. Length = 703

>gnl|CDD|182755 PRK10816, PRK10816, DNA-binding transcriptional regulator PhoP; Provisional

 Score = 42.8 bits (101), Expect = 4e-04
 Identities = 30/127 (23%), Positives = 53/127 (41%), Gaps = 26/127 (20%)

Query: 861 KILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLK 920
           ++L+VEDN +     K  ++  GH +D   +  EA + +     D+ ++D+ +P  DGL 
Sbjct: 2   RVLVVEDNALLRHHLKVQLQDAGHQVDAAEDAKEADYYLNEHLPDIAIVDLGLPDEDGLS 61

Query: 921 ATRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGM 980
             R  RS                          +   +PI+ +TA    +   E  + G 
Sbjct: 62  LIRRWRS--------------------------NDVSLPILVLTARESWQDKVEVLSAGA 95

Query: 981 DSFVSKP 987
           D +V+KP
Sbjct: 96  DDYVTKP 102

Length = 223

>gnl|CDD|226931 COG4565, CitB, Response regulator of citrate/malate metabolism [Transcription / Signal transduction mechanisms]

 Score = 42.2 bits (100), Expect = 5e-04
 Identities = 33/145 (22%), Positives = 63/145 (43%), Gaps = 34/145 (23%)

Query: 861  KILLVEDNKINVMVA---KSMMKQLG--HSIDVVNNGVEAVHAVQCQNYDLILMDVCMPV 915
             +L++ED+    MVA   +  +KQ+     +       EA   ++    DLIL+D+ MP 
Sbjct: 2    NVLIIEDD---PMVAEIHRRYVKQIPGFSVVGTAGTLEEAKMIIEEFKPDLILLDIYMPD 58

Query: 916  MDGLKATRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEEC 975
             +G++    +RS                              + +I +TA +  E+ +E 
Sbjct: 59   GNGIELLPELRS--------------------------QHYPVDVIVITAASDMETIKEA 92

Query: 976  FANGMDSFVSKPVTFQKLKECLEQY 1000
               G+  ++ KP TF++L++ L +Y
Sbjct: 93   LRYGVVDYLIKPFTFERLQQALTRY 117

Length = 224

>gnl|CDD|182612 PRK10643, PRK10643, DNA-binding transcriptional regulator BasR; Provisional

 Score = 41.9 bits (99), Expect = 8e-04
 Identities = 19/66 (28%), Positives = 36/66 (54%)

Query: 861 KILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLK 920
           KIL+VED+ + +      ++  G++ D  +   EA   ++  +Y L+++D+ +P  DGL 
Sbjct: 2   KILIVEDDTLLLQGLILALQTEGYACDCASTAREAEALLESGHYSLVVLDLGLPDEDGLH 61

Query: 921 ATRLIR 926
             R  R
Sbjct: 62  LLRRWR 67

Length = 222

>gnl|CDD|226655 COG4192, COG4192, Signal transduction histidine kinase regulating phosphoglycerate transport system [Signal transduction mechanisms]

 Score = 42.6 bits (100), Expect = 0.001
 Identities = 44/173 (25%), Positives = 76/173 (43%), Gaps = 22/173 (12%)

Query: 337 REKMAKLREEIAVQKAKETELNKTIHITEETMRAK-----QMLATMSHEIRSPLTGVVSM 391
           RE+  +L+ E+  ++  E  L KT    E    AK     Q + +++HEI  PL    +M
Sbjct: 415 RERNQELQAEVEERQEAEAHLKKTQG--ELIQAAKLAVVGQTMTSLAHEINQPLN---AM 469

Query: 392 AEILSNTKLDREQR---QLLGVMISSGDLVLQ---LINDILDLSKVESGVMKLEAAKFRP 445
           +  L + +L  E+    Q    +    +L  +   ++N +   ++  S    L+  +   
Sbjct: 470 SAYLFSARLALEEAPSAQAATSLDKIENLTERMGKIVNSLRQFARKNSSDESLQPVRLNS 529

Query: 446 R-EVVKHVLQTAAASLQKILMLEGDIADDVPIEVIGDVLRIRQILTNLISNAI 497
             E    +LQT     Q  L+   D      + V+GD + I Q+L NLI NA+
Sbjct: 530 VVEQAWELLQTKHKRRQIKLINPTDD-----LMVMGDAVSIEQVLVNLIVNAL 577

Length = 673

>gnl|CDD|236838 PRK11083, PRK11083, DNA-binding response regulator CreB; Provisional

 Score = 40.7 bits (96), Expect = 0.002
 Identities = 20/74 (27%), Positives = 40/74 (54%), Gaps = 6/74 (8%)

Query: 858 PKPKILLVEDNKINVMVAKS---MMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMP 914
            +P ILLVED      +A +    ++  G +++    G+ A+  ++ Q  DL+++DV +P
Sbjct: 2   QQPTILLVEDE---QAIADTLVYALQSEGFTVEWFERGLPALDKLRQQPPDLVILDVGLP 58

Query: 915 VMDGLKATRLIRSF 928
            + G +  R + +F
Sbjct: 59  DISGFELCRQLLAF 72

Length = 228

>gnl|CDD|219845 pfam08448, PAS_4, PAS fold

 Score = 38.2 bits (89), Expect = 0.003
 Identities = 24/102 (23%), Positives = 39/102 (38%), Gaps = 8/102 (7%)

Query: 239 DKELRYRFIYNHFPSL---HEEDILGKTDVEIFSGAGVKESQDFKREVLEKGLPAKREIT 295
           D + R R+       L     E++LGKT  E+         +   R  LE   P      
Sbjct: 12  DPDGRVRYANAAAAELFGLPPEELLGKTLAELLPPEDAARLERALRRALEGEEPIDFLEE 71

Query: 296 FETELFGSKT--FLIYVEPVFSKSGETIGVNYMGMDVTDQVR 335
               L   +   + + + P+    GE IGV  +  D+T++ R
Sbjct: 72  L---LLNGEERHYELRLTPLRDPDGEVIGVLVISRDITERRR 110

The PAS fold corresponds to the structural domain that has previously been defined as PAS and PAC motifs. The PAS fold appears in archaea, eubacteria and eukarya. Length = 110

>gnl|CDD|233585 TIGR01818, ntrC, nitrogen regulation protein NR(I)

 Score = 40.5 bits (95), Expect = 0.004
 Identities = 25/126 (19%), Positives = 50/126 (39%), Gaps = 26/126 (20%)

Query: 862 ILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKA 921
           + +V+D++    V +  + + G+ +    N    + A+     DL++ DV MP  DGL  
Sbjct: 1   VWVVDDDRSIRWVLEKALSRAGYEVRTFGNAASVLRALARGQPDLLITDVRMPGEDGLDL 60

Query: 922 TRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMD 981
              I+                              ++P+I MTA++  ++A   +  G  
Sbjct: 61  LPQIKKRH--------------------------PQLPVIVMTAHSDLDTAVAAYQRGAF 94

Query: 982 SFVSKP 987
            ++ KP
Sbjct: 95  EYLPKP 100

This model represents NtrC, a DNA-binding response regulator that is phosphorylated by NtrB and interacts with sigma-54. NtrC usually controls the expression of glutamine synthase, GlnA, and may be called GlnL, GlnG, etc [Central intermediary metabolism, Nitrogen metabolism, Regulatory functions, DNA interactions, Signal transduction, Two-component systems]. Length = 463

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	1002
PRK11091	779	aerobic respiration control sensor protein ArcB; P	100.0
PRK10841	924	hybrid sensory kinase in two-component regulatory	100.0
PRK09959	1197	hybrid sensory histidine kinase in two-component r	100.0
PRK11107	919	hybrid sensory histidine kinase BarA; Provisional	100.0
TIGR02956	968	TMAO_torS TMAO reductase sytem sensor TorS. This p	100.0
PRK15347	921	two component system sensor kinase SsrA; Provision	100.0
PRK11466	914	hybrid sensory histidine kinase TorS; Provisional	100.0
PRK13557	540	histidine kinase; Provisional	100.0
COG5002	459	VicK Signal transduction histidine kinase [Signal	100.0
PRK10618	894	phosphotransfer intermediate protein in two-compon	100.0
PRK13837	828	two-component VirA-like sensor kinase; Provisional	100.0
KOG0519	786	consensus Sensory transduction histidine kinase [S	100.0
COG2205	890	KdpD Osmosensitive K+ channel histidine kinase [Si	100.0
PRK11006	430	phoR phosphate regulon sensor protein; Provisional	100.0
TIGR02938	494	nifL_nitrog nitrogen fixation negative regulator N	100.0
COG3852	363	NtrB Signal transduction histidine kinase, nitroge	100.0
TIGR02966	333	phoR_proteo phosphate regulon sensor kinase PhoR.	100.0
PRK11073	348	glnL nitrogen regulation protein NR(II); Provision	100.0
PRK09303	380	adaptive-response sensory kinase; Validated	100.0
PRK11360	607	sensory histidine kinase AtoS; Provisional	100.0
PRK13560	807	hypothetical protein; Provisional	100.0
COG5000	712	NtrY Signal transduction histidine kinase involved	100.0
PRK10490	895	sensor protein KdpD; Provisional	100.0
COG4251	750	Bacteriophytochrome (light-regulated signal transd	99.97
PRK10604	433	sensor protein RstB; Provisional	99.97
PRK11086	542	sensory histidine kinase DcuS; Provisional	99.96
PRK10815	485	sensor protein PhoQ; Provisional	99.96
COG4191	603	Signal transduction histidine kinase regulating C4	99.96
PRK10364	457	sensor protein ZraS; Provisional	99.96
PRK13559	361	hypothetical protein; Provisional	99.96
PRK10549	466	signal transduction histidine-protein kinase BaeS;	99.96
PRK10755	356	sensor protein BasS/PmrB; Provisional	99.96
PRK15053	545	dpiB sensor histidine kinase DpiB; Provisional	99.95
TIGR03785	703	marine_sort_HK proteobacterial dedicated sortase s	99.95
TIGR01386	457	cztS_silS_copS heavy metal sensor kinase. Members	99.95
PRK09835	482	sensor kinase CusS; Provisional	99.95
PRK09470	461	cpxA two-component sensor protein; Provisional	99.95
PRK10337	449	sensor protein QseC; Provisional	99.95
PRK09467	435	envZ osmolarity sensor protein; Provisional	99.94
PRK11100	475	sensory histidine kinase CreC; Provisional	99.94
COG0642	336	BaeS Signal transduction histidine kinase [Signal	99.94
TIGR02916	679	PEP_his_kin putative PEP-CTERM system histidine ki	99.94
COG3290	537	CitA Signal transduction histidine kinase regulati	99.89
PRK11644	495	sensory histidine kinase UhpB; Provisional	99.88
COG4192	673	Signal transduction histidine kinase regulating ph	99.87
COG0745	229	OmpR Response regulators consisting of a CheY-like	99.83
PF02518	111	HATPase_c: Histidine kinase-, DNA gyrase B-, and H	99.81
PRK10935	565	nitrate/nitrite sensor protein NarQ; Provisional	99.8
PRK10600	569	nitrate/nitrite sensor protein NarX; Provisional	99.75
COG3437	360	Response regulator containing a CheY-like receiver	99.72
COG2204	464	AtoC Response regulator containing CheY-like recei	99.71
PF00072	112	Response_reg: Response regulator receiver domain;	99.71
COG4753	475	Response regulator containing CheY-like receiver d	99.71
COG0784	130	CheY FOG: CheY-like receiver [Signal transduction	99.7
COG4565	224	CitB Response regulator of citrate/malate metaboli	99.68
COG4566	202	TtrR Response regulator [Signal transduction mecha	99.64
COG2197	211	CitB Response regulator containing a CheY-like rec	99.62
PLN03029	222	type-a response regulator protein; Provisional	99.62
COG3706	435	PleD Response regulator containing a CheY-like rec	99.6
PRK10547	670	chemotaxis protein CheA; Provisional	99.59
PRK10046	225	dpiA two-component response regulator DpiA; Provis	99.58
COG3947	361	Response regulator containing CheY-like receiver a	99.56
PRK11173	237	two-component response regulator; Provisional	99.54
PRK10529	225	DNA-binding transcriptional activator KdpE; Provis	99.54
PRK10816	223	DNA-binding transcriptional regulator PhoP; Provis	99.53
PRK09836	227	DNA-binding transcriptional activator CusR; Provis	99.52
PRK04184	535	DNA topoisomerase VI subunit B; Validated	99.51
PRK09468	239	ompR osmolarity response regulator; Provisional	99.51
PRK10643	222	DNA-binding transcriptional regulator BasR; Provis	99.5
PRK10766	221	DNA-binding transcriptional regulator TorR; Provis	99.5
PRK10430	239	DNA-binding transcriptional activator DcuR; Provis	99.49
PRK10336	219	DNA-binding transcriptional regulator QseB; Provis	99.49
TIGR02154	226	PhoB phosphate regulon transcriptional regulatory	99.48
PRK10701	240	DNA-binding transcriptional regulator RstA; Provis	99.48
PRK10161	229	transcriptional regulator PhoB; Provisional	99.48
TIGR02875	262	spore_0_A sporulation transcription factor Spo0A.	99.47
PRK13856	241	two-component response regulator VirG; Provisional	99.47
TIGR03787	227	marine_sort_RR proteobacterial dedicated sortase s	99.46
PRK10955	232	DNA-binding transcriptional regulator CpxR; Provis	99.46
PRK11517	223	transcriptional regulatory protein YedW; Provision	99.46
smart00387	111	HATPase_c Histidine kinase-like ATPases. Histidine	99.44
PRK11083	228	DNA-binding response regulator CreB; Provisional	99.44
PRK10840	216	transcriptional regulator RcsB; Provisional	99.43
COG4567	182	Response regulator consisting of a CheY-like recei	99.43
TIGR01387	218	cztR_silR_copR heavy metal response regulator. Mem	99.43
PRK14084	246	two-component response regulator; Provisional	99.42
CHL00148	240	orf27 Ycf27; Reviewed	99.42
PRK09958	204	DNA-binding transcriptional activator EvgA; Provis	99.42
PRK10923	469	glnG nitrogen regulation protein NR(I); Provisiona	99.41
PRK15115	444	response regulator GlrR; Provisional	99.4
PRK11361	457	acetoacetate metabolism regulatory protein AtoC; P	99.39
PRK09581	457	pleD response regulator PleD; Reviewed	99.39
PRK09483	217	response regulator; Provisional	99.38
PRK10365	441	transcriptional regulatory protein ZraR; Provision	99.38
PRK10360	196	DNA-binding transcriptional activator UhpA; Provis	99.38
TIGR02915	445	PEP_resp_reg putative PEP-CTERM system response re	99.38
PRK11697	238	putative two-component response-regulatory protein	99.37
PRK09935	210	transcriptional regulator FimZ; Provisional	99.37
TIGR01818	463	ntrC nitrogen regulation protein NR(I). This model	99.36
PRK12555	337	chemotaxis-specific methylesterase; Provisional	99.36
PRK10710	240	DNA-binding transcriptional regulator BaeR; Provis	99.35
PRK15479	221	transcriptional regulatory protein TctD; Provision	99.32
COG2201	350	CheB Chemotaxis response regulator containing a Ch	99.31
PRK09390	202	fixJ response regulator FixJ; Provisional	99.3
PRK14868	795	DNA topoisomerase VI subunit B; Provisional	99.3
TIGR01052	488	top6b DNA topoisomerase VI, B subunit. This model	99.29
PF00512	68	HisKA: His Kinase A (phospho-acceptor) domain; Int	99.28
PRK00742	354	chemotaxis-specific methylesterase; Provisional	99.27
PRK09581	457	pleD response regulator PleD; Reviewed	99.26
PRK14867	659	DNA topoisomerase VI subunit B; Provisional	99.26
PRK10100	216	DNA-binding transcriptional regulator CsgD; Provis	99.25
cd00075	103	HATPase_c Histidine kinase-like ATPases; This fami	99.24
COG3707	194	AmiR Response regulator with putative antiterminat	99.24
PRK13558	665	bacterio-opsin activator; Provisional	99.24
PRK11475	207	DNA-binding transcriptional activator BglJ; Provis	99.23
PRK10610	129	chemotaxis regulatory protein CheY; Provisional	99.23
PRK13435	145	response regulator; Provisional	99.22
TIGR01925	137	spIIAB anti-sigma F factor. This model describes t	99.21
PRK15369	211	two component system sensor kinase SsrB; Provision	99.19
PRK10403	215	transcriptional regulator NarP; Provisional	99.19
PRK10651	216	transcriptional regulator NarL; Provisional	99.18
PRK15411	207	rcsA colanic acid capsular biosynthesis activation	99.16
PRK03660	146	anti-sigma F factor; Provisional	99.13
PRK09191	261	two-component response regulator; Provisional	99.12
COG0643	716	CheA Chemotaxis protein histidine kinase and relat	99.09
PRK10693	303	response regulator of RpoS; Provisional	99.07
cd00156	113	REC Signal receiver domain; originally thought to	99.04
COG3920	221	Signal transduction histidine kinase [Signal trans	98.9
COG3850	574	NarQ Signal transduction histidine kinase, nitrate	98.9
COG3851	497	UhpB Signal transduction histidine kinase, glucose	98.88
PF08448	110	PAS_4: PAS fold; InterPro: IPR013656 The PAS fold	98.87
COG3275	557	LytS Putative regulator of cell autolysis [Signal	98.83
COG4585	365	Signal transduction histidine kinase [Signal trans	98.82
PRK04069	161	serine-protein kinase RsbW; Provisional	98.81
PRK15029	755	arginine decarboxylase; Provisional	98.76
COG3279	244	LytT Response regulator of the LytR/AlgR family [T	98.74
COG2972	456	Predicted signal transduction protein with a C-ter	98.66
PF13426	104	PAS_9: PAS domain; PDB: 3ULF_B 3UE6_E 2Z6D_B 2Z6C_	98.57
TIGR01924	159	rsbW_low_gc serine-protein kinase RsbW. This model	98.57
smart00388	66	HisKA His Kinase A (phosphoacceptor) domain. Dimer	98.53
PF00989	113	PAS: PAS fold; InterPro: IPR013767 PAS domains are	98.51
COG4564	459	Signal transduction histidine kinase [Signal trans	98.5
PRK13560	807	hypothetical protein; Provisional	98.32
PF14501	100	HATPase_c_5: GHKL domain	98.29
KOG0787	414	consensus Dehydrogenase kinase [Signal transductio	98.25
PRK11107	919	hybrid sensory histidine kinase BarA; Provisional	98.19
COG3706	435	PleD Response regulator containing a CheY-like rec	98.12
PF13596	106	PAS_10: PAS domain; PDB: 3CAX_A 2QKP_D.	98.09
cd00082	65	HisKA Histidine Kinase A (dimerization/phosphoacce	98.05
TIGR00585	312	mutl DNA mismatch repair protein MutL. All protein	98.03
PRK09776	1092	putative diguanylate cyclase; Provisional	97.85
COG1389	538	DNA topoisomerase VI, subunit B [DNA replication,	97.77
PRK13558	665	bacterio-opsin activator; Provisional	97.77
PRK09776	1092	putative diguanylate cyclase; Provisional	97.73
TIGR00229	124	sensory_box PAS domain S-box. The PAS domain was p	97.67
PF13581	125	HATPase_c_2: Histidine kinase-like ATPase domain	97.62
PRK10060	663	RNase II stability modulator; Provisional	97.52
TIGR02938	494	nifL_nitrog nitrogen fixation negative regulator N	97.42
PRK11359	799	cyclic-di-GMP phosphodiesterase; Provisional	97.37
smart00448	55	REC cheY-homologous receiver domain. CheY regulate	97.16
TIGR02040	442	PpsR-CrtJ transcriptional regulator PpsR. This mod	97.08
PF06490	109	FleQ: Flagellar regulatory protein FleQ; InterPro:	96.94
COG2172	146	RsbW Anti-sigma regulatory factor (Ser/Thr protein	96.91
TIGR02040	442	PpsR-CrtJ transcriptional regulator PpsR. This mod	96.78
PRK00095	617	mutL DNA mismatch repair protein; Reviewed	96.64
cd00130	103	PAS PAS domain; PAS motifs appear in archaea, euba	96.64
PF12860	115	PAS_7: PAS fold	96.05
KOG0519	786	consensus Sensory transduction histidine kinase [S	96.04
PF13589	137	HATPase_c_3: Histidine kinase-, DNA gyrase B-, and	95.84
cd02071	122	MM_CoA_mut_B12_BD methylmalonyl CoA mutase B12 bin	95.59
PRK02261	137	methylaspartate mutase subunit S; Provisional	95.58
COG3829	560	RocR Transcriptional regulator containing PAS, AAA	95.34
PRK11359	799	cyclic-di-GMP phosphodiesterase; Provisional	95.28
PRK10820	520	DNA-binding transcriptional regulator TyrR; Provis	95.26
PRK14083	601	HSP90 family protein; Provisional	94.69
PTZ00272	701	heat shock protein 83 kDa (Hsp83); Provisional	93.96
cd02067	119	B12-binding B12 binding domain (B12-BD). This doma	93.91
TIGR00640	132	acid_CoA_mut_C methylmalonyl-CoA mutase C-terminal	93.66
PF08447	91	PAS_3: PAS fold; InterPro: IPR013655 The PAS fold	93.57
PRK05559	631	DNA topoisomerase IV subunit B; Reviewed	93.13
PRK05218	613	heat shock protein 90; Provisional	92.84
PF14598	111	PAS_11: PAS domain; PDB: 1P97_A 3F1O_A 2A24_A 3H7W	92.23
TIGR01501	134	MthylAspMutase methylaspartate mutase, S subunit.	92.22
COG2202	232	AtoS FOG: PAS/PAC domain [Signal transduction mech	90.91
TIGR01055	625	parE_Gneg DNA topoisomerase IV, B subunit, proteob	89.71
PTZ00130	814	heat shock protein 90; Provisional	89.17
COG0323	638	MutL DNA mismatch repair enzyme (predicted ATPase)	88.85
PF02310	121	B12-binding: B12 binding domain; InterPro: IPR0061	88.4
cd02070	201	corrinoid_protein_B12-BD B12 binding domain of cor	88.16
cd02072	128	Glm_B12_BD B12 binding domain of glutamate mutase	88.08
TIGR01059	654	gyrB DNA gyrase, B subunit. This model describes t	88.07
cd02069	213	methionine_synthase_B12_BD B12 binding domain of m	87.9
COG2461	409	Uncharacterized conserved protein [Function unknow	86.98
COG2185	143	Sbm Methylmalonyl-CoA mutase, C-terminal domain/su	86.1
PRK05644	638	gyrB DNA gyrase subunit B; Validated	85.81
COG5381	184	Uncharacterized protein conserved in bacteria [Fun	85.48
PF13188	64	PAS_8: PAS domain; PDB: 2JHE_D 3VOL_A.	84.4
COG4999	140	Uncharacterized domain of BarA-like signal transdu	83.19
COG0326	623	HtpG Molecular chaperone, HSP90 family [Posttransl	83.04
PF03709	115	OKR_DC_1_N: Orn/Lys/Arg decarboxylase, N-terminal	82.92
cd04728	248	ThiG Thiazole synthase (ThiG) is the tetrameric en	81.98
smart00433	594	TOP2c TopoisomeraseII. Eukaryotic DNA topoisomeras	80.99
PRK09426	714	methylmalonyl-CoA mutase; Reviewed	80.76
TIGR03815	322	CpaE_hom_Actino helicase/secretion neighborhood Cp	80.51

>PRK11091 aerobic respiration control sensor protein ArcB; Provisional

Probab=100.00  E-value=3.6e-65  Score=642.04  Aligned_cols=504  Identities=29%  Similarity=0.466  Sum_probs=422.1

Q ss_pred             HHHhhcCChHHHHHHHHHHHHHHHHHHHhccCcEEEEecccccEEEeeccC---CCCCcccccCCCchhccCccchhhhh
Q 039716          201 TNLEKQSSPVEELSQILKRADNFLHFVLQNAPVVMGHQDKELRYRFIYNHF---PSLHEEDILGKTDVEIFSGAGVKESQ  277 (1002)
Q Consensus       201 ~~l~~~~~~~~~~~~~l~~~~~~l~~il~~~p~~i~~~d~~~~~~~~~~~~---~~~~~e~iiGk~~~e~~~~~~~~~~~  277 (1002)
                      ..|.+...+.++..+.+++++.+++.+++++|.+++..|.++++.++|..+   .|+..++++|++..+++++.......
T Consensus       134 ~~L~~~i~~r~~~~~~l~~~~~~l~~il~~~~~~i~~~D~~g~i~~~N~a~~~l~G~~~~eliG~~~~~l~~~~~~~~~~  213 (779)
T PRK11091        134 EQLKNEIKEREETQIELEQQSSLLRSFLDASPDLVYYRNEDGEFSGCNRAMELLTGKSEKQLIGLTPKDVYSPEAAEKVI  213 (779)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcceEEEECCCCcEEeEcHHHHHHhCcCHHHHcCCChHHhCCHHHHHHHH
Confidence            445555555667778899999999999999999999999999999998764   67888999999999999876555555


Q ss_pred             HHHHHHHHhCCCcceeEEEEEeecCceEEEEEEeeeecCCCCEEEEEEEeechhHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 039716          278 DFKREVLEKGLPAKREITFETELFGSKTFLIYVEPVFSKSGETIGVNYMGMDVTDQVRKREKMAKLREEIAVQKAKETEL  357 (1002)
Q Consensus       278 ~~~~~vl~~g~~~~~e~~~~~~~~~~~~~~~~~~p~~~~~G~~~gi~~~~~DITe~~~~~~~~~~l~~el~~~~~~~~el  357 (1002)
                      .....++..+.+...+..+....+...++.++..|+++.+|.+.|+++++.|||++++.++++.+..             
T Consensus       214 ~~~~~~~~~~~~~~~e~~~~~~~G~~~~~~~~~~pi~~~~g~~~g~v~~~~DITe~k~~e~~l~~a~-------------  280 (779)
T PRK11091        214 ETDEKVFRHNVSLTYEQWLDYPDGRKACFELRKVPFYDRVGKRHGLMGFGRDITERKRYQDALEKAS-------------  280 (779)
T ss_pred             HHHHHHHhcCCCeEEEEEEEcCCCCEEEEEEEeeeEEcCCCCEEEEEEEEeehhHHHHHHHHHHHHH-------------
Confidence            5566777777776666666666666678888999999999999999999999999876654432211             


Q ss_pred             HHHHHHHHHHHHHHHHHHHhhhccccHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCee
Q 039716          358 NKTIHITEETMRAKQMLATMSHEIRSPLTGVVSMAEILSNTKLDREQRQLLGVMISSGDLVLQLINDILDLSKVESGVMK  437 (1002)
Q Consensus       358 ~k~~~~~e~~~~~k~fla~iSHELRTPL~~I~g~~elL~~~~l~~~~~~~l~~i~~s~~~L~~LIndlLd~skiesg~~~  437 (1002)
                                ..+.+|+++|||||||||++|.|++++|.....++++++++..+..++.++..+|++++++++++++.+.
T Consensus       281 ----------~~~~~~~a~isHelrtPL~~I~g~~~ll~~~~~~~~~~~~l~~i~~~~~~l~~li~~ll~~~~~~~~~~~  350 (779)
T PRK11091        281 ----------RDKTTFISTISHELRTPLNGIVGLSRILLDTELTAEQRKYLKTIHVSAITLGNIFNDIIDMDKMERRKLQ  350 (779)
T ss_pred             ----------HHHHHHHHHhhHhhcCcHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHhCCCcE
Confidence                      0124799999999999999999999999888888999999999999999999999999999999999999


Q ss_pred             eEeeecCHHHHHHHHHHHHHHHHh-hcceeccccCCCCCeeEEccHHHHHHHHHHHHhhhhhcCCCCeeEEEEEecCCCC
Q 039716          438 LEAAKFRPREVVKHVLQTAAASLQ-KILMLEGDIADDVPIEVIGDVLRIRQILTNLISNAIKFTPEGKVGIKLYVVPEPP  516 (1002)
Q Consensus       438 l~~~~~~l~~li~~v~~~~~~~~~-k~i~l~~~i~~~~p~~v~gD~~rL~QIL~NLlsNAIKfT~~G~I~I~v~~~~~~~  516 (1002)
                      +...++++.++++.+...+..... +++.+........|..+.+|+.+|+|||.||++||+||++.|.|.|.+....   
T Consensus       351 ~~~~~~~l~~~i~~~~~~~~~~~~~~~i~~~~~~~~~~~~~v~~d~~~l~qvl~NLl~NAik~~~~g~v~i~~~~~~---  427 (779)
T PRK11091        351 LDNQPIDFTDFLADLENLSGLQAEQKGLRFDLEPLLPLPHKVITDGTRLRQILWNLISNAVKFTQQGGVTVRVRYEE---  427 (779)
T ss_pred             EEeeccCHHHHHHHHHHHHHHHHHhcCCEEEEEeCCCCCceEEeCHHHHHHHHHHHHHHHHHhCCCCcEEEEEEEcc---
Confidence            999999999999999887766543 6677777777777777999999999999999999999999998887764310   


Q ss_pred             cccchhhhhhhhhhcchhhhhhhccCCCCCccCCCCCCCCCCCCCCccCCCCCCCCCCCccCCCCCccccccceEEEEEE
Q 039716          517 FAKEGLKQKSKAYQSATDAVKEEKHQPKSQTASDQNGFHDKKHGEGYQDHKHDDDPGTPVSHGNSMDEDLEATVWIRCDV  596 (1002)
Q Consensus       517 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~i~V  596 (1002)
                                                                                              ...+.|+|
T Consensus       428 ------------------------------------------------------------------------~~~~~i~V  435 (779)
T PRK11091        428 ------------------------------------------------------------------------GDMLTFEV  435 (779)
T ss_pred             ------------------------------------------------------------------------CCEEEEEE
Confidence                                                                                    11378999


Q ss_pred             EecCCCCCcCcHhhhhhhccCC-CccccCcCCCccccHHHHHHHHHHhCCEEEEEeecCCceEEEEEEeCCCCCCCCCCC
Q 039716          597 YDTGIGIPENALPTLFRKYMQV-SADHARKYGGTGLGLAICKQLVELMGGRLTVTSKVHCGSTFTFILPYQVSPIEENSD  675 (1002)
Q Consensus       597 ~DtGiGI~~e~l~~IF~pF~q~-~~~~~~~~~GtGLGLaI~k~Lve~~gG~I~v~S~~g~GTtF~~~LP~~~~~~~~~~~  675 (1002)
                      .|||+|||++.+++||+|||++ +...++.++||||||+|||+||+.|||+|+|+|.+|+||+|+|+||+......... 
T Consensus       436 ~D~G~Gi~~~~~~~iF~~f~~~~~~~~~~~~~GtGLGL~i~~~iv~~~gG~i~v~s~~g~Gt~f~i~lP~~~~~~~~~~-  514 (779)
T PRK11091        436 EDSGIGIPEDELDKIFAMYYQVKDSHGGKPATGTGIGLAVSKRLAQAMGGDITVTSEEGKGSCFTLTIHAPAVAEEVED-  514 (779)
T ss_pred             EecCCCCCHHHHHHHHHHhhcccCCCCCCCCCCcchHHHHHHHHHHHcCCEEEEEecCCCeEEEEEEEecccccccccc-
Confidence            9999999999999999999998 44445557899999999999999999999999999999999999997432100000 


Q ss_pred             CCCccccccccCCcccccccccccccccccccccccCCcccccccccccccccccccccCccccccCCCCCcccccccch
Q 039716          676 DPDDLSDMADQDSVTDDVTAGFFQFQPRTLGSLFSSNGTSRSKKLLPNSIGFASAHKVNGFSETSYSFPSNNRQKETAPL  755 (1002)
Q Consensus       676 ~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  755 (1002)
                                                                                                      
T Consensus       515 --------------------------------------------------------------------------------  514 (779)
T PRK11091        515 --------------------------------------------------------------------------------  514 (779)
T ss_pred             --------------------------------------------------------------------------------
Confidence                                                                                            


Q ss_pred             hhhccHHHHHhhhCCCCCCCCCCCCCCcchhhcccccccccccccccCCCCCccchhhhhHHHhhcccCCCchhhhhhcc
Q 039716          756 EDACSVAEVAETLSEPESSFSHSPEPENETEVSRGKQCHVETTSWFQNPATESTSHSEANREMIQTSKTNEPQKICEMQE  835 (1002)
Q Consensus       756 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  835 (1002)
                                            .+                                                        
T Consensus       515 ----------------------~~--------------------------------------------------------  516 (779)
T PRK11091        515 ----------------------AF--------------------------------------------------------  516 (779)
T ss_pred             ----------------------cc--------------------------------------------------------
Confidence                                  00                                                        


Q ss_pred             CCCcccCCCCCCCCCCCCCCCCCCCeEEEEecCHHHHHHHHHHHHhcCCeEEEEcCHHHHHHHHHcCCCcEEEEcCCCCC
Q 039716          836 KPDRISQSPSSSSAEVPETKPKPKPKILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPV  915 (1002)
Q Consensus       836 ~~~~~~~~~~~~~~~~~~~~~~~~~~ILiVeDn~~n~~~l~~~L~~~g~~v~~a~~G~eAl~~~~~~~~DlIlmDi~MP~  915 (1002)
                                 .    ....+..+.+||||||++.++..+..+|+..||.|..|.+|.+|++.+....||+||||+.||+
T Consensus       517 -----------~----~~~~~~~~~~ILivdD~~~~~~~l~~~L~~~g~~v~~a~~~~eal~~~~~~~~Dlvl~D~~mp~  581 (779)
T PRK11091        517 -----------D----EDDMPLPALNILLVEDIELNVIVARSVLEKLGNSVDVAMTGKEALEMFDPDEYDLVLLDIQLPD  581 (779)
T ss_pred             -----------c----cccccccccceEEEcCCHHHHHHHHHHHHHcCCEEEEECCHHHHHHHhhcCCCCEEEEcCCCCC
Confidence                       0    0000023468999999999999999999999999999999999999999999999999999999


Q ss_pred             CCHHHHHHHHhccccCCCchhhhhhhhcccCCCCCCCCCCCC-ccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHH
Q 039716          916 MDGLKATRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKR-IPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLK  994 (1002)
Q Consensus       916 mdG~e~~~~IR~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~  994 (1002)
                      |||+++++.||....                        .+. +|||++|++... ...+|+.+||++||.||++..+|.
T Consensus       582 ~~G~e~~~~ir~~~~------------------------~~~~~~ii~~ta~~~~-~~~~~~~~G~~~~l~KP~~~~~L~  636 (779)
T PRK11091        582 MTGLDIARELRERYP------------------------REDLPPLVALTANVLK-DKKEYLDAGMDDVLSKPLSVPALT  636 (779)
T ss_pred             CCHHHHHHHHHhccc------------------------cCCCCcEEEEECCchH-hHHHHHHCCCCEEEECCCCHHHHH
Confidence            999999999996321                        134 499999998765 467899999999999999999999


Q ss_pred             HHHHhhc
Q 039716          995 ECLEQYF 1001 (1002)
Q Consensus       995 ~~l~~~l 1001 (1002)
                      .+|.+++
T Consensus       637 ~~l~~~~  643 (779)
T PRK11091        637 AMIKKFW  643 (779)
T ss_pred             HHHHHHh
Confidence            9998875

>PRK10841 hybrid sensory kinase in two-component regulatory system with RcsB and YojN; Provisional

Probab=100.00  E-value=1.7e-57  Score=574.96  Aligned_cols=595  Identities=27%  Similarity=0.417  Sum_probs=381.5

Q ss_pred             ChHHHHHHHHHHHHHHHHHHHhccCcEEEEec-ccccEEEeeccCCCCCcccccCCCchhccCccchhhhhHHHHHHHHh
Q 039716          208 SPVEELSQILKRADNFLHFVLQNAPVVMGHQD-KELRYRFIYNHFPSLHEEDILGKTDVEIFSGAGVKESQDFKREVLEK  286 (1002)
Q Consensus       208 ~~~~~~~~~l~~~~~~l~~il~~~p~~i~~~d-~~~~~~~~~~~~~~~~~e~iiGk~~~e~~~~~~~~~~~~~~~~vl~~  286 (1002)
                      .++++..+.|++++.+.+.+++++|+++...+ .++++.+.|.....     +.|.     .......   . .......
T Consensus       320 ~p~~~~~~~L~e~e~~~r~iv~~~p~gi~i~~~~~g~~~~~N~~a~~-----~~~l-----~~~~~~~---~-~~~~~~~  385 (924)
T PRK10841        320 IPAESNALRLEEHEQFNRKIVASAPVGICILRTSDGTNILSNELAHN-----YLNM-----LTHEDRQ---R-LTQIICG  385 (924)
T ss_pred             chhHHHHHHHHHHHHHHHHHHHhCCccEEEEEcCCCcEEEehHHHHH-----Hhcc-----CChhHHH---H-HHHHHhc
Confidence            46667777889999999999999999998875 67877777653211     1111     1111100   1 1111111


Q ss_pred             CCCcceeEEEEEeecCceEEEEEEeeeecCCCCEEEEEEEeechhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 039716          287 GLPAKREITFETELFGSKTFLIYVEPVFSKSGETIGVNYMGMDVTDQVRKREKMAKLREEIAVQKAKETELNKTIHITEE  366 (1002)
Q Consensus       287 g~~~~~e~~~~~~~~~~~~~~~~~~p~~~~~G~~~gi~~~~~DITe~~~~~~~~~~l~~el~~~~~~~~el~k~~~~~e~  366 (1002)
                      . .... .....  .....+.+...+.... |+. ..+++..|||++++.++++++..++++                 +
T Consensus       386 ~-~~~~-~~~~~--~~~~~~~i~~~~~~~~-~~~-~~i~~~~Dit~r~~~e~~L~~~~~~~e-----------------~  442 (924)
T PRK10841        386 Q-QVNF-VDVLT--SNNTNLQISFVHSRYR-NEN-VAICVLVDVSARVKMEESLQEMAQAAE-----------------Q  442 (924)
T ss_pred             c-ccce-eeEEc--CCCcEEEEEEEeeeec-Cce-EEEEEEEEhhHHHHHHHHHHHHHHHHH-----------------H
Confidence            1 1111 11111  1222222322222222 232 345678899998877665544332211                 1


Q ss_pred             HH-HHHHHHHHhhhccccHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCeeeEeeecCH
Q 039716          367 TM-RAKQMLATMSHEIRSPLTGVVSMAEILSNTKLDREQRQLLGVMISSGDLVLQLINDILDLSKVESGVMKLEAAKFRP  445 (1002)
Q Consensus       367 ~~-~~k~fla~iSHELRTPL~~I~g~~elL~~~~l~~~~~~~l~~i~~s~~~L~~LIndlLd~skiesg~~~l~~~~~~l  445 (1002)
                      +. .+..|+++|||||||||++|+|++++|.....+++++++++.|..++.+|..+|++||+|+|++++.+.++..+|++
T Consensus       443 a~~~k~~fla~iSHELRTPL~~I~g~lelL~~~~~~~~~~~~l~~i~~~~~~L~~lI~dlLd~srie~~~~~l~~~~~~l  522 (924)
T PRK10841        443 ASQSKSMFLATVSHELRTPLYGIIGNLDLLQTKELPKGVDRLVTAMNNSSSLLLKIISDILDFSKIESEQLKIEPREFSP  522 (924)
T ss_pred             HHHHHHHHHHHhHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCceeeeEEecH
Confidence            11 12369999999999999999999999988888889999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHH-hhcceeccccCCCCCeeEEccHHHHHHHHHHHHhhhhhcCCCCeeEEEEEecCCCCcccchhhh
Q 039716          446 REVVKHVLQTAAASL-QKILMLEGDIADDVPIEVIGDVLRIRQILTNLISNAIKFTPEGKVGIKLYVVPEPPFAKEGLKQ  524 (1002)
Q Consensus       446 ~~li~~v~~~~~~~~-~k~i~l~~~i~~~~p~~v~gD~~rL~QIL~NLlsNAIKfT~~G~I~I~v~~~~~~~~~~~~~~~  524 (1002)
                      .+++++++..+...+ .+++.+...+.++.+..+.+|+.+|+|||.||++||+|||+.|.|.|.+...            
T Consensus       523 ~~li~~v~~~~~~~~~~k~i~l~~~i~~~~~~~v~~D~~~L~qvl~NLl~NAik~t~~G~I~I~v~~~------------  590 (924)
T PRK10841        523 REVINHITANYLPLVVKKRLGLYCFIEPDVPVALNGDPMRLQQVISNLLSNAIKFTDTGCIVLHVRVD------------  590 (924)
T ss_pred             HHHHHHHHHHHHHHHHHcCcEEEEEeCCCCCcEEEECHHHHHHHHHHHHHHHHhhCCCCcEEEEEEEe------------
Confidence            999999998876654 4677777777777777899999999999999999999999999888776421            


Q ss_pred             hhhhhhcchhhhhhhccCCCCCccCCCCCCCCCCCCCCccCCCCCCCCCCCccCCCCCccccccceEEEEEEEecCCCCC
Q 039716          525 KSKAYQSATDAVKEEKHQPKSQTASDQNGFHDKKHGEGYQDHKHDDDPGTPVSHGNSMDEDLEATVWIRCDVYDTGIGIP  604 (1002)
Q Consensus       525 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~i~V~DtGiGI~  604 (1002)
                                                                                      ..++.|+|.|||+||+
T Consensus       591 ----------------------------------------------------------------~~~l~i~V~DtG~GI~  606 (924)
T PRK10841        591 ----------------------------------------------------------------GDYLSFRVRDTGVGIP  606 (924)
T ss_pred             ----------------------------------------------------------------CCEEEEEEEEcCcCCC
Confidence                                                                            1158899999999999


Q ss_pred             cCcHhhhhhhccCCCccccCcCCCccccHHHHHHHHHHhCCEEEEEeecCCceEEEEEEeCCCCCCCCCCCCCCcccccc
Q 039716          605 ENALPTLFRKYMQVSADHARKYGGTGLGLAICKQLVELMGGRLTVTSKVHCGSTFTFILPYQVSPIEENSDDPDDLSDMA  684 (1002)
Q Consensus       605 ~e~l~~IF~pF~q~~~~~~~~~~GtGLGLaI~k~Lve~~gG~I~v~S~~g~GTtF~~~LP~~~~~~~~~~~~~~~l~~~~  684 (1002)
                      ++.+++||+||++.+....+..+|+||||+||++||+.|||+|+++|.+|+||+|+|.||+........... ..+....
T Consensus       607 ~e~~~~lFepF~~~~~~~~~~~~GtGLGL~I~k~lv~~~gG~I~v~S~~g~Gt~F~i~LP~~~~~~~~~~~~-~~~~g~~  685 (924)
T PRK10841        607 AKEVVRLFDPFFQVGTGVQRNFQGTGLGLAICEKLINMMDGDISVDSEPGMGSQFTIRIPLYGAQYPQKKGV-EGLQGKR  685 (924)
T ss_pred             HHHHHHHhcccccCCCCCCCCCCCeehhHHHHHHHHHHCCCEEEEEEcCCCcEEEEEEEECCcccccccccC-cccCCCE
Confidence            999999999999987766667789999999999999999999999999999999999999864322111100 0000000


Q ss_pred             ccCCcccccccccccccccccccccccCCcccccccccccccccccccccCccccccCCCCCcccccccchhhhccHHHH
Q 039716          685 DQDSVTDDVTAGFFQFQPRTLGSLFSSNGTSRSKKLLPNSIGFASAHKVNGFSETSYSFPSNNRQKETAPLEDACSVAEV  764 (1002)
Q Consensus       685 ~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  764 (1002)
                      ............+       +...+...+......  .. ........+-      .+.+...    ...   .......
T Consensus       686 i~l~~~~~~~~~~-------l~~~l~~~G~~v~~~--~~-~~~~~~d~~i------~d~~~~~----~~~---~~~~~~~  742 (924)
T PRK10841        686 CWLAVRNASLEQF-------LETLLQRSGIQVQRY--EG-QEPTPEDVLI------TDDPVQK----KWQ---GRAVITF  742 (924)
T ss_pred             EEEEcCCHHHHHH-------HHHHHHHCCCeEEEc--cc-ccCCcCcEEE------EcCcccc----ccc---hhhhhhh
Confidence            0000000000000       000000000000000  00 0000000000      0000000    000   0000000


Q ss_pred             HhhhCCCCCCCCCCCCCCcchhhcccccccccccccccCCCCCccchhhhhHHHhhcccCCCchhhhhhccCCCcccCCC
Q 039716          765 AETLSEPESSFSHSPEPENETEVSRGKQCHVETTSWFQNPATESTSHSEANREMIQTSKTNEPQKICEMQEKPDRISQSP  844 (1002)
Q Consensus       765 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  844 (1002)
                      .    .     .+...+.   .        .....+...+...    .. ......           .............
T Consensus       743 ~----~-----~~~~~~~---~--------~~~~~~~~~~~~~----~~-l~~~l~-----------~~~~~~~~~~~~~  786 (924)
T PRK10841        743 C----R-----RHIGIPL---E--------IAPGEWVHSTATP----HE-LPALLA-----------RIYRIELESDDSA  786 (924)
T ss_pred             h----h-----ccccChh---h--------cccCceeeccCCh----HH-HHHHHH-----------HHhhccccccccc
Confidence            0    0     0000000   0        0000000000000    00 000000           0000000000000


Q ss_pred             CCCCCCCCCCCCCCCCeEEEEecCHHHHHHHHHHHHhcCCeEEEEcCHHHHHHHHHcCCCcEEEEcCCCCCCCHHHHHHH
Q 039716          845 SSSSAEVPETKPKPKPKILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKATRL  924 (1002)
Q Consensus       845 ~~~~~~~~~~~~~~~~~ILiVeDn~~n~~~l~~~L~~~g~~v~~a~~G~eAl~~~~~~~~DlIlmDi~MP~mdG~e~~~~  924 (1002)
                      ................+||||||++.++.++..+|+..||.|..|.||.+|++.+....||+||||++||+|||+++++.
T Consensus       787 ~~~~~~~~~~~~~~~~~ILvVdD~~~~~~~l~~~L~~~G~~v~~a~~g~eal~~l~~~~~DlVl~D~~mP~mdG~el~~~  866 (924)
T PRK10841        787 NALPSTDKAVSDNDDMMILVVDDHPINRRLLADQLGSLGYQCKTANDGVDALNVLSKNHIDIVLTDVNMPNMDGYRLTQR  866 (924)
T ss_pred             ccccccccccccCCCCEEEEECCCHHHHHHHHHHHHHcCCEEEEECCHHHHHHHHHhCCCCEEEEcCCCCCCCHHHHHHH
Confidence            00000011111234679999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HhccccCCCchhhhhhhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHHhhc
Q 039716          925 IRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQYF 1001 (1002)
Q Consensus       925 IR~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~~l 1001 (1002)
                      ||+.                          .+.+|||++|++...+...+|+++||++||.||++..+|...|.++.
T Consensus       867 ir~~--------------------------~~~~pII~lTa~~~~~~~~~~~~aG~d~~L~KPv~~~~L~~~L~~~~  917 (924)
T PRK10841        867 LRQL--------------------------GLTLPVIGVTANALAEEKQRCLEAGMDSCLSKPVTLDVLKQTLTVYA  917 (924)
T ss_pred             HHhc--------------------------CCCCCEEEEECCCCHHHHHHHHHCCCCEEEeCCCCHHHHHHHHHHHH
Confidence            9963                          24689999999999999999999999999999999999999998763

>PRK09959 hybrid sensory histidine kinase in two-component regulatory system with EvgA; Provisional

Probab=100.00  E-value=8.9e-52  Score=543.49  Aligned_cols=502  Identities=27%  Similarity=0.349  Sum_probs=364.6

Q ss_pred             HHHHHHHHHHHHHHHHHHhccCcEEEEecccccEEEeeccCCCCCccc---ccCCCchhccCccchhhhhHHHHHHHH-h
Q 039716          211 EELSQILKRADNFLHFVLQNAPVVMGHQDKELRYRFIYNHFPSLHEED---ILGKTDVEIFSGAGVKESQDFKREVLE-K  286 (1002)
Q Consensus       211 ~~~~~~l~~~~~~l~~il~~~p~~i~~~d~~~~~~~~~~~~~~~~~e~---iiGk~~~e~~~~~~~~~~~~~~~~vl~-~  286 (1002)
                      +.++..+++.+.+++.+++++|.+|+..|.++++.++|..+..+....   ..+...... ................. .
T Consensus       565 ~~~~~~l~~~~~~~~~i~~~~~~~i~~~d~~g~i~~~N~~~~~~~g~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~  643 (1197)
T PRK09959        565 KVIQGDLENQISFRKALSDSLPNPTYVVNWQGNVISHNSAFEHYFTADYYKNAMLPLENS-DSPFKDVFSNAHEVTAETK  643 (1197)
T ss_pred             HHHHHHHHHHHHHHHHHHhhCCCcEEEEcCCCcEEEehHHHHHHhCcccccccccccccc-cCchhhhHhHHHHHHHHHh
Confidence            445667788888999999999999999999999999987654321111   001000000 00000000000000001 1


Q ss_pred             CCCcceeEEEEEeecCceE-EEEEEeeeecCCCCEEEEEEEeechhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 039716          287 GLPAKREITFETELFGSKT-FLIYVEPVFSKSGETIGVNYMGMDVTDQVRKREKMAKLREEIAVQKAKETELNKTIHITE  365 (1002)
Q Consensus       287 g~~~~~e~~~~~~~~~~~~-~~~~~~p~~~~~G~~~gi~~~~~DITe~~~~~~~~~~l~~el~~~~~~~~el~k~~~~~e  365 (1002)
                      .........+....++... +..+..+.....+...|++..+.|||+.++..+.++..+++..                +
T Consensus       644 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~dite~~~~~~~l~~~~~~~~----------------~  707 (1197)
T PRK09959        644 ENRTIYTQVFEIDNGIEKRCINHWHTLCNLPASDHAVYICGWQDITETRDLIHALEVERNKAI----------------N  707 (1197)
T ss_pred             hccccceeeEeeecCccceeeeeeeeeeccCCCCceEEEEEEEehhHHHHHHHHHHHHHHHHH----------------H
Confidence            1111111122222222222 2222223323344556777788999987766554433222110                1


Q ss_pred             HHHHHHHHHHHhhhccccHHHHHHHHHHHHhCCCCCHH-HHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCeeeEeeecC
Q 039716          366 ETMRAKQMLATMSHEIRSPLTGVVSMAEILSNTKLDRE-QRQLLGVMISSGDLVLQLINDILDLSKVESGVMKLEAAKFR  444 (1002)
Q Consensus       366 ~~~~~k~fla~iSHELRTPL~~I~g~~elL~~~~l~~~-~~~~l~~i~~s~~~L~~LIndlLd~skiesg~~~l~~~~~~  444 (1002)
                      +....++|+++|||||||||++|.|++++|.....+.+ ..+++..+..++++|..+|++++++++++++...+...+++
T Consensus       708 ~~~~~~~~~~~isHelrtPL~~i~~~~~ll~~~~~~~~~~~~~l~~~~~~~~~l~~li~~ll~~~~~~~~~~~~~~~~~~  787 (1197)
T PRK09959        708 ATVAKSQFLATMSHEIRTPISSIMGFLELLSGSGLSKEQRVEAISLAYATGQSLLGLIGEILDVDKIESGNYQLQPQWVD  787 (1197)
T ss_pred             HHHHHHHHHHhcChhhCccHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCceeeeeeeC
Confidence            11223589999999999999999999999976655554 45788999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHh-hcceeccccCCCCCeeEEccHHHHHHHHHHHHhhhhhcCCCCeeEEEEEecCCCCcccchhh
Q 039716          445 PREVVKHVLQTAAASLQ-KILMLEGDIADDVPIEVIGDVLRIRQILTNLISNAIKFTPEGKVGIKLYVVPEPPFAKEGLK  523 (1002)
Q Consensus       445 l~~li~~v~~~~~~~~~-k~i~l~~~i~~~~p~~v~gD~~rL~QIL~NLlsNAIKfT~~G~I~I~v~~~~~~~~~~~~~~  523 (1002)
                      +.+++++++..+..... +++.+........+..+.+|+.+|+|||.||++||+||++.|.+.|.+.....         
T Consensus       788 l~~~i~~~~~~~~~~~~~~~i~~~~~~~~~~~~~v~~d~~~l~qvl~NLl~NAik~~~~g~i~i~~~~~~~---------  858 (1197)
T PRK09959        788 IPTLVQNTCHSFGAIAASKSIALSCSSTFPDHYLVKIDPQAFKQVLSNLLSNALKFTTEGAVKITTSLGHI---------  858 (1197)
T ss_pred             HHHHHHHHHHHHHHHHHhcCcEEEEecCCCCceEEEECHHHHHHHHHHHHHHHHHhCCCCCEEEEEEEeee---------
Confidence            99999999988776543 55655544332333468999999999999999999999999987776532110         


Q ss_pred             hhhhhhhcchhhhhhhccCCCCCccCCCCCCCCCCCCCCccCCCCCCCCCCCccCCCCCccccccceEEEEEEEecCCCC
Q 039716          524 QKSKAYQSATDAVKEEKHQPKSQTASDQNGFHDKKHGEGYQDHKHDDDPGTPVSHGNSMDEDLEATVWIRCDVYDTGIGI  603 (1002)
Q Consensus       524 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~i~V~DtGiGI  603 (1002)
                                                                                    .....++.|+|.|||+||
T Consensus       859 --------------------------------------------------------------~~~~~~~~i~V~D~G~Gi  876 (1197)
T PRK09959        859 --------------------------------------------------------------DDNHAVIKMTIMDSGSGL  876 (1197)
T ss_pred             --------------------------------------------------------------cCCceEEEEEEEEcCCCC
Confidence                                                                          011225789999999999


Q ss_pred             CcCcHhhhhhhccCCCccccCcCCCccccHHHHHHHHHHhCCEEEEEeecCCceEEEEEEeCCCCCCCCCCCCCCccccc
Q 039716          604 PENALPTLFRKYMQVSADHARKYGGTGLGLAICKQLVELMGGRLTVTSKVHCGSTFTFILPYQVSPIEENSDDPDDLSDM  683 (1002)
Q Consensus       604 ~~e~l~~IF~pF~q~~~~~~~~~~GtGLGLaI~k~Lve~~gG~I~v~S~~g~GTtF~~~LP~~~~~~~~~~~~~~~l~~~  683 (1002)
                      |++.+++||+||++.+.  .+..+|+||||+|||+||+.|||+|+++|.+|+||+|+|+||+........          
T Consensus       877 ~~~~~~~iF~~f~~~~~--~~~~~G~GLGL~i~~~iv~~~gG~i~v~s~~~~Gt~f~i~lP~~~~~~~~~----------  944 (1197)
T PRK09959        877 SQEEQQQLFKRYSQTSA--GRQQTGSGLGLMICKELIKNMQGDLSLESHPGIGTTFTITIPVEISQQVAT----------  944 (1197)
T ss_pred             CHHHHHHhhcccccccc--CCCCCCcCchHHHHHHHHHHcCCEEEEEeCCCCcEEEEEEEEccccchhcc----------
Confidence            99999999999998754  234579999999999999999999999999999999999999742110000          


Q ss_pred             cccCCcccccccccccccccccccccccCCcccccccccccccccccccccCccccccCCCCCcccccccchhhhccHHH
Q 039716          684 ADQDSVTDDVTAGFFQFQPRTLGSLFSSNGTSRSKKLLPNSIGFASAHKVNGFSETSYSFPSNNRQKETAPLEDACSVAE  763 (1002)
Q Consensus       684 ~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  763 (1002)
                                                                                                      
T Consensus       945 --------------------------------------------------------------------------------  944 (1197)
T PRK09959        945 --------------------------------------------------------------------------------  944 (1197)
T ss_pred             --------------------------------------------------------------------------------
Confidence                                                                                            


Q ss_pred             HHhhhCCCCCCCCCCCCCCcchhhcccccccccccccccCCCCCccchhhhhHHHhhcccCCCchhhhhhccCCCcccCC
Q 039716          764 VAETLSEPESSFSHSPEPENETEVSRGKQCHVETTSWFQNPATESTSHSEANREMIQTSKTNEPQKICEMQEKPDRISQS  843 (1002)
Q Consensus       764 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  843 (1002)
                                     ....                                         ...                 
T Consensus       945 ---------------~~~~-----------------------------------------~~~-----------------  951 (1197)
T PRK09959        945 ---------------VEAK-----------------------------------------AEQ-----------------  951 (1197)
T ss_pred             ---------------cccc-----------------------------------------ccc-----------------
Confidence                           0000                                         000                 


Q ss_pred             CCCCCCCCCCCCCCCCCeEEEEecCHHHHHHHHHHHHhcCCeEEEEcCHHHHHHHHHcCCCcEEEEcCCCCCCCHHHHHH
Q 039716          844 PSSSSAEVPETKPKPKPKILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKATR  923 (1002)
Q Consensus       844 ~~~~~~~~~~~~~~~~~~ILiVeDn~~n~~~l~~~L~~~g~~v~~a~~G~eAl~~~~~~~~DlIlmDi~MP~mdG~e~~~  923 (1002)
                         +      .......+||||||++.++..+..+|+..|+.|..+.+|.+|++.+....||+||+|+.||+|+|+++++
T Consensus       952 ---~------~~~~~~~~iLivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~al~~~~~~~~dlil~D~~mp~~~g~~~~~ 1022 (1197)
T PRK09959        952 ---P------ITLPEKLSILIADDHPTNRLLLKRQLNLLGYDVDEATDGVQALHKVSMQHYDLLITDVNMPNMDGFELTR 1022 (1197)
T ss_pred             ---c------cccccCceEEEcCCCHHHHHHHHHHHHHcCCEEEEECCHHHHHHHhhcCCCCEEEEeCCCCCCCHHHHHH
Confidence               0      0001235899999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHhccccCCCchhhhhhhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHHhh
Q 039716          924 LIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQY 1000 (1002)
Q Consensus       924 ~IR~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~~ 1000 (1002)
                      .||..                          .+.+|||++|++.......+|+.+|+++||.||++..+|...|.++
T Consensus      1023 ~i~~~--------------------------~~~~pii~lt~~~~~~~~~~~~~~G~~~~l~KP~~~~~L~~~l~~~ 1073 (1197)
T PRK09959       1023 KLREQ--------------------------NSSLPIWGLTANAQANEREKGLSCGMNLCLFKPLTLDVLKTHLSQL 1073 (1197)
T ss_pred             HHHhc--------------------------CCCCCEEEEECCCCHHHHHHHHHCCCCEEEeCCCCHHHHHHHHHHH
Confidence            99962                          2568999999999999999999999999999999999999998764

>PRK11107 hybrid sensory histidine kinase BarA; Provisional

Probab=100.00  E-value=2e-52  Score=536.27  Aligned_cols=493  Identities=31%  Similarity=0.465  Sum_probs=328.5

Q ss_pred             HHHHHHH-HHHHHHhhhccccHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCeeeEeee
Q 039716          364 TEETMRA-KQMLATMSHEIRSPLTGVVSMAEILSNTKLDREQRQLLGVMISSGDLVLQLINDILDLSKVESGVMKLEAAK  442 (1002)
Q Consensus       364 ~e~~~~~-k~fla~iSHELRTPL~~I~g~~elL~~~~l~~~~~~~l~~i~~s~~~L~~LIndlLd~skiesg~~~l~~~~  442 (1002)
                      ++++.+. .+|+++|||||||||++|+|+++++.....++.++++++.|..++++|..+|+++|+|+|++.+.+.+...+
T Consensus       286 ~~~~~~~~~~~l~~isHelrtPL~~i~~~~~~l~~~~~~~~~~~~l~~i~~~~~~l~~li~~ll~~~~~~~~~~~~~~~~  365 (919)
T PRK11107        286 AQEAARIKSEFLANMSHELRTPLNGVIGFTRQTLKTPLTPTQRDYLQTIERSANNLLAIINDILDFSKLEAGKLVLENIP  365 (919)
T ss_pred             HHHHHHHHHHHHHHhhHhhcccHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCcEEEEee
Confidence            3344443 389999999999999999999999988888889999999999999999999999999999999999999999


Q ss_pred             cCHHHHHHHHHHHHHHHH-hhcceeccccCCCCCeeEEccHHHHHHHHHHHHhhhhhcCCCCeeEEEEEecCCCCcccch
Q 039716          443 FRPREVVKHVLQTAAASL-QKILMLEGDIADDVPIEVIGDVLRIRQILTNLISNAIKFTPEGKVGIKLYVVPEPPFAKEG  521 (1002)
Q Consensus       443 ~~l~~li~~v~~~~~~~~-~k~i~l~~~i~~~~p~~v~gD~~rL~QIL~NLlsNAIKfT~~G~I~I~v~~~~~~~~~~~~  521 (1002)
                      |++.+++++++..+...+ .+++.+...+.+..|..+.+|+.+|+|||.||++||+|||+.|.|.|.+......      
T Consensus       366 ~~l~~~l~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~d~~~l~~vl~NLl~NAik~~~~g~v~i~v~~~~~~------  439 (919)
T PRK11107        366 FSLRETLDEVVTLLAHSAHEKGLELTLNIDPDVPDNVIGDPLRLQQIITNLVGNAIKFTESGNIDILVELRALS------  439 (919)
T ss_pred             cCHHHHHHHHHHHHHHHHHHcCCEEEEEeCCCCCceEEeCHHHHHHHHHHHHHHHhhcCCCCcEEEEEEEEecC------
Confidence            999999999998887655 4677777777777777789999999999999999999999999888777542110      


Q ss_pred             hhhhhhhhhcchhhhhhhccCCCCCccCCCCCCCCCCCCCCccCCCCCCCCCCCccCCCCCccccccceEEEEEEEecCC
Q 039716          522 LKQKSKAYQSATDAVKEEKHQPKSQTASDQNGFHDKKHGEGYQDHKHDDDPGTPVSHGNSMDEDLEATVWIRCDVYDTGI  601 (1002)
Q Consensus       522 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~i~V~DtGi  601 (1002)
                                                                                       ....++.|+|.|||+
T Consensus       440 -----------------------------------------------------------------~~~~~~~i~V~D~G~  454 (919)
T PRK11107        440 -----------------------------------------------------------------NTKVQLEVQIRDTGI  454 (919)
T ss_pred             -----------------------------------------------------------------CCeeEEEEEEEEeCC
Confidence                                                                             112358899999999


Q ss_pred             CCCcCcHhhhhhhccCCCccccCcCCCccccHHHHHHHHHHhCCEEEEEeecCCceEEEEEEeCCCCCCCCCCCCCCccc
Q 039716          602 GIPENALPTLFRKYMQVSADHARKYGGTGLGLAICKQLVELMGGRLTVTSKVHCGSTFTFILPYQVSPIEENSDDPDDLS  681 (1002)
Q Consensus       602 GI~~e~l~~IF~pF~q~~~~~~~~~~GtGLGLaI~k~Lve~~gG~I~v~S~~g~GTtF~~~LP~~~~~~~~~~~~~~~l~  681 (1002)
                      |||++.+++||+||++.+...+++++|+||||+|||++++.|||+|+|+|.+|+||+|+|+||+...+.......+  ..
T Consensus       455 Gi~~~~~~~if~~f~~~~~~~~~~~~g~GLGL~i~~~i~~~~gG~i~v~s~~~~Gt~f~i~lp~~~~~~~~~~~~~--~~  532 (919)
T PRK11107        455 GISERQQSQLFQAFRQADASISRRHGGTGLGLVITQKLVNEMGGDISFHSQPNRGSTFWFHLPLDLNPNPIIDGLP--TD  532 (919)
T ss_pred             CcCHHHHHHHhhhhccCCCCCCCCCCCcchhHHHHHHHHHHhCCEEEEEecCCCCEEEEEEEEeccCCccccccCC--cc
Confidence            9999999999999999988777788999999999999999999999999999999999999998654321110000  00


Q ss_pred             cccccCC-cccccccccccccccccccccccCCcccccccccccccccccccccCccccccCCCCCcccccccchhhhcc
Q 039716          682 DMADQDS-VTDDVTAGFFQFQPRTLGSLFSSNGTSRSKKLLPNSIGFASAHKVNGFSETSYSFPSNNRQKETAPLEDACS  760 (1002)
Q Consensus       682 ~~~~~~~-~~~~~~~~~~~~~~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  760 (1002)
                      ....... ..++..     .....+...+...+.....           ...........++.   ......  ......
T Consensus       533 ~~~g~~ili~d~~~-----~~~~~l~~~L~~~g~~v~~-----------~~~~~~l~~~~~d~---il~~~~--~~~~~~  591 (919)
T PRK11107        533 CLAGKRLLYVEPNS-----AAAQATLDILSETPLEVTY-----------SPTLSQLPEAHYDI---LLLGLP--VTFREP  591 (919)
T ss_pred             ccCCCeEEEEeCCH-----HHHHHHHHHHHHCCCEEEE-----------cCCHHHhccCCCCE---EEeccc--CCCCCC
Confidence            0000000 000000     0000000000000000000           00000000000000   000000  000000


Q ss_pred             HHHHHhhhCCCCCC----CCCCCCCCcchhhcccccccccccccccCCCCCccchhhhhHHHhhcccCCCchhhhhhccC
Q 039716          761 VAEVAETLSEPESS----FSHSPEPENETEVSRGKQCHVETTSWFQNPATESTSHSEANREMIQTSKTNEPQKICEMQEK  836 (1002)
Q Consensus       761 ~~~~~~~~~~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  836 (1002)
                      ..............    ....+........   .........++.+|..                    ..........
T Consensus       592 ~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~---~~~~~g~~~~l~kp~~--------------------~~~l~~~l~~  648 (919)
T PRK11107        592 LTMLHERLAKAKSMTDFLILALPCHEQVLAE---QLKQDGADACLSKPLS--------------------HTRLLPALLE  648 (919)
T ss_pred             HHHHHHHHHhhhhcCCcEEEEeCCcchhhHH---HHhhCCCceEECCCCC--------------------HHHHHHHHHH
Confidence            00000000000000    0000000000000   0000000001111110                    0000000000


Q ss_pred             CCcccCCCCCCCCCCCCCCCCCCCeEEEEecCHHHHHHHHHHHHhcCCeEEEEcCHHHHHHHHHcCCCcEEEEcCCCCCC
Q 039716          837 PDRISQSPSSSSAEVPETKPKPKPKILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVM  916 (1002)
Q Consensus       837 ~~~~~~~~~~~~~~~~~~~~~~~~~ILiVeDn~~n~~~l~~~L~~~g~~v~~a~~G~eAl~~~~~~~~DlIlmDi~MP~m  916 (1002)
                      .......+    ............+||||||++.++..++.+|+..|+.|..+.+|.+|++.+....||+||||+.||+|
T Consensus       649 ~~~~~~~~----~~~~~~~~~~~~~vLivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~al~~~~~~~~dlil~D~~mp~~  724 (919)
T PRK11107        649 PCHHKQPP----LLPPTDESRLPLTVMAVDDNPANLKLIGALLEEQVEHVVLCDSGHQAVEQAKQRPFDLILMDIQMPGM  724 (919)
T ss_pred             hhcccccc----cccccccccCCCeEEEEeCCHHHHHHHHHHHHHcCCEEEEECCHHHHHHHHHhCCCCEEEEeCCCCCC
Confidence            00000000    00001111345789999999999999999999999999999999999999999999999999999999


Q ss_pred             CHHHHHHHHhccccCCCchhhhhhhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHH
Q 039716          917 DGLKATRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKEC  996 (1002)
Q Consensus       917 dG~e~~~~IR~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~  996 (1002)
                      ||+++++.||+..                        ..+.+|||++|++...+...+|+++||++||.||++..+|...
T Consensus       725 ~g~~~~~~lr~~~------------------------~~~~~pii~lt~~~~~~~~~~~~~~G~~~~l~KP~~~~~L~~~  780 (919)
T PRK11107        725 DGIRACELIRQLP------------------------HNQNTPIIAVTAHAMAGERERLLSAGMDDYLAKPIDEAMLKQV  780 (919)
T ss_pred             cHHHHHHHHHhcc------------------------cCCCCCEEEEeCCCCHHHHHHHHHcCCCeEeeCCCCHHHHHHH
Confidence            9999999999742                        2356999999999999999999999999999999999999999


Q ss_pred             HHhhc
Q 039716          997 LEQYF 1001 (1002)
Q Consensus       997 l~~~l 1001 (1002)
                      |.+++
T Consensus       781 l~~~~  785 (919)
T PRK11107        781 LLRYK  785 (919)
T ss_pred             HHHHc
Confidence            99875

>TIGR02956 TMAO_torS TMAO reductase sytem sensor TorS

Probab=100.00  E-value=1.4e-52  Score=540.45  Aligned_cols=362  Identities=37%  Similarity=0.583  Sum_probs=313.9

Q ss_pred             HHHHHH-HHHHHHhhhccccHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCeeeEeeec
Q 039716          365 EETMRA-KQMLATMSHEIRSPLTGVVSMAEILSNTKLDREQRQLLGVMISSGDLVLQLINDILDLSKVESGVMKLEAAKF  443 (1002)
Q Consensus       365 e~~~~~-k~fla~iSHELRTPL~~I~g~~elL~~~~l~~~~~~~l~~i~~s~~~L~~LIndlLd~skiesg~~~l~~~~~  443 (1002)
                      ++..++ .+|+++|||||||||++|.|++++|.+..++++++++++.|..++++|..+|+++|+|++++.+...+...+|
T Consensus       458 ~~~~~~~~~~~~~~sHelrtPL~~i~~~~~ll~~~~~~~~~~~~l~~i~~~~~~l~~~i~~ll~~~~~e~~~~~~~~~~~  537 (968)
T TIGR02956       458 EEANRAKSAFLATMSHEIRTPLNGILGTLELLGDTGLTSQQQQYLQVINRSGESLLDILNDILDYSKIEAGHLSISPRPF  537 (968)
T ss_pred             HHHHHHHHHHHHHhHHHhhhHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCeeeeccc
Confidence            333433 4899999999999999999999999988889999999999999999999999999999999999999999999


Q ss_pred             CHHHHHHHHHHHHHHHHh-hcceeccccCCCCCeeEEccHHHHHHHHHHHHhhhhhcCCCCeeEEEEEecCCCCcccchh
Q 039716          444 RPREVVKHVLQTAAASLQ-KILMLEGDIADDVPIEVIGDVLRIRQILTNLISNAIKFTPEGKVGIKLYVVPEPPFAKEGL  522 (1002)
Q Consensus       444 ~l~~li~~v~~~~~~~~~-k~i~l~~~i~~~~p~~v~gD~~rL~QIL~NLlsNAIKfT~~G~I~I~v~~~~~~~~~~~~~  522 (1002)
                      ++.+++++++..+..... +++.+...++++.|..+.+|+.+|+|||.|||+||+|||+.|.|.|.+.....        
T Consensus       538 ~l~~ll~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~d~~~l~~il~nLi~NAik~~~~g~i~i~~~~~~~--------  609 (968)
T TIGR02956       538 DLNALLDDVHHLMVSRAQLKGIQLRLNIPEQLPNWWQGDGPRIRQVLINLVGNAIKFTDRGSVVLRVSLNDD--------  609 (968)
T ss_pred             CHHHHHHHHHHHHHHHHHHcCcEEEEEeCCCCCceEeeCHHHHHHHHHHHHHHHHhhCCCCeEEEEEEEcCC--------
Confidence            999999999998877654 67888888877778789999999999999999999999999998887743210        


Q ss_pred             hhhhhhhhcchhhhhhhccCCCCCccCCCCCCCCCCCCCCccCCCCCCCCCCCccCCCCCccccccceEEEEEEEecCCC
Q 039716          523 KQKSKAYQSATDAVKEEKHQPKSQTASDQNGFHDKKHGEGYQDHKHDDDPGTPVSHGNSMDEDLEATVWIRCDVYDTGIG  602 (1002)
Q Consensus       523 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~i~V~DtGiG  602 (1002)
                                                                                        . .+.|+|.|+|+|
T Consensus       610 ------------------------------------------------------------------~-~~~i~V~D~G~G  622 (968)
T TIGR02956       610 ------------------------------------------------------------------S-SLLFEVEDTGCG  622 (968)
T ss_pred             ------------------------------------------------------------------C-eEEEEEEeCCCC
Confidence                                                                              0 178999999999


Q ss_pred             CCcCcHhhhhhhccCCCccccCcCCCccccHHHHHHHHHHhCCEEEEEeecCCceEEEEEEeCCCCCCCCCCCCCCcccc
Q 039716          603 IPENALPTLFRKYMQVSADHARKYGGTGLGLAICKQLVELMGGRLTVTSKVHCGSTFTFILPYQVSPIEENSDDPDDLSD  682 (1002)
Q Consensus       603 I~~e~l~~IF~pF~q~~~~~~~~~~GtGLGLaI~k~Lve~~gG~I~v~S~~g~GTtF~~~LP~~~~~~~~~~~~~~~l~~  682 (1002)
                      ||++.+++||+||++.+  ..+.++|+||||+|||++|+.|||+|+++|.+|+||+|+|+||+.........        
T Consensus       623 i~~~~~~~if~~f~~~~--~~~~~~g~GLGL~i~~~l~~~~gG~i~~~s~~~~Gt~f~~~lp~~~~~~~~~~--------  692 (968)
T TIGR02956       623 IAEEEQATLFDAFTQAD--GRRRSGGTGLGLAISQRLVEAMDGELGVESELGVGSCFWFTLPLTRGKPAEDS--------  692 (968)
T ss_pred             CCHHHHHHHHhhhhccC--CCCCCCCccHHHHHHHHHHHHcCCEEEEEecCCCcEEEEEEEEcCCCCccccc--------
Confidence            99999999999999987  34566899999999999999999999999999999999999997532100000        


Q ss_pred             ccccCCcccccccccccccccccccccccCCcccccccccccccccccccccCccccccCCCCCcccccccchhhhccHH
Q 039716          683 MADQDSVTDDVTAGFFQFQPRTLGSLFSSNGTSRSKKLLPNSIGFASAHKVNGFSETSYSFPSNNRQKETAPLEDACSVA  762 (1002)
Q Consensus       683 ~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  762 (1002)
                                                                                                      
T Consensus       693 --------------------------------------------------------------------------------  692 (968)
T TIGR02956       693 --------------------------------------------------------------------------------  692 (968)
T ss_pred             --------------------------------------------------------------------------------
Confidence                                                                                            


Q ss_pred             HHHhhhCCCCCCCCCCCCCCcchhhcccccccccccccccCCCCCccchhhhhHHHhhcccCCCchhhhhhccCCCcccC
Q 039716          763 EVAETLSEPESSFSHSPEPENETEVSRGKQCHVETTSWFQNPATESTSHSEANREMIQTSKTNEPQKICEMQEKPDRISQ  842 (1002)
Q Consensus       763 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  842 (1002)
                                       ..                                                             
T Consensus       693 -----------------~~-------------------------------------------------------------  694 (968)
T TIGR02956       693 -----------------AT-------------------------------------------------------------  694 (968)
T ss_pred             -----------------cc-------------------------------------------------------------
Confidence                             00                                                             


Q ss_pred             CCCCCCCCCCCCCCCCCCeEEEEecCHHHHHHHHHHHHhcCCeEEEEcCHHHHHHHHHcCCCcEEEEcCCCCCCCHHHHH
Q 039716          843 SPSSSSAEVPETKPKPKPKILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKAT  922 (1002)
Q Consensus       843 ~~~~~~~~~~~~~~~~~~~ILiVeDn~~n~~~l~~~L~~~g~~v~~a~~G~eAl~~~~~~~~DlIlmDi~MP~mdG~e~~  922 (1002)
                               .........+||||||++.++..+..+|+..||.|..+.||.+|++.+....||+||||++||+|||++++
T Consensus       695 ---------~~~~~~~~~~iLvvdd~~~~~~~l~~~L~~~g~~v~~~~~~~~a~~~l~~~~~dlvl~D~~mp~~~g~~~~  765 (968)
T TIGR02956       695 ---------LTVIDLPPQRVLLVEDNEVNQMVAQGFLTRLGHKVTLAESGQSALECFHQHAFDLALLDINLPDGDGVTLL  765 (968)
T ss_pred             ---------cccccccccceEEEcCcHHHHHHHHHHHHHcCCEEEEECCHHHHHHHHHCCCCCEEEECCCCCCCCHHHHH
Confidence                     00000123479999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHhccccCCCchhhhhhhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHHhhc
Q 039716          923 RLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQYF 1001 (1002)
Q Consensus       923 ~~IR~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~~l 1001 (1002)
                      +.||....                       ...++|||++|++...+...+|+.+||++|+.||++..+|...|.+++
T Consensus       766 ~~ir~~~~-----------------------~~~~~pii~lta~~~~~~~~~~~~~G~~~~l~KP~~~~~L~~~l~~~~  821 (968)
T TIGR02956       766 QQLRAIYG-----------------------AKNEVKFIAFSAHVFNEDVAQYLAAGFDGFLAKPVVEEQLTAMIAVIL  821 (968)
T ss_pred             HHHHhCcc-----------------------ccCCCeEEEEECCCCHHHHHHHHHCCCCEEEeCCCCHHHHHHHHHHHh
Confidence            99997431                       112389999999999999999999999999999999999999998875

This protein, TorS, is part of a regulatory system for the torCAD operon that encodes the pterin molybdenum cofactor-containing enzyme trimethylamine-N-oxide (TMAO) reductase (TorA), a cognate chaperone (TorD), and a penta-haem cytochrome (TorC). TorS works together with the inducer-binding protein TorT and the response regulator TorR. TorS contains histidine kinase ATPase (pfam02518), HAMP (pfam00672), phosphoacceptor (pfam00512), and phosphotransfer (pfam01627) domains and a response regulator receiver domain (pfam00072).

>PRK15347 two component system sensor kinase SsrA; Provisional

Probab=100.00  E-value=2.3e-51  Score=526.58  Aligned_cols=410  Identities=32%  Similarity=0.487  Sum_probs=311.9

Q ss_pred             HHHHHHhhhccccHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCeeeEeeecCHHHHHH
Q 039716          371 KQMLATMSHEIRSPLTGVVSMAEILSNTKLDREQRQLLGVMISSGDLVLQLINDILDLSKVESGVMKLEAAKFRPREVVK  450 (1002)
Q Consensus       371 k~fla~iSHELRTPL~~I~g~~elL~~~~l~~~~~~~l~~i~~s~~~L~~LIndlLd~skiesg~~~l~~~~~~l~~li~  450 (1002)
                      .+|++++||||||||++|.|++++|.....+++++++++.+..++.+|..+|+++|+++|++.+.+.+...++++.++++
T Consensus       399 ~~~~~~isHelrtPL~~i~~~~~~l~~~~~~~~~~~~~~~i~~~~~~l~~li~~ll~~~~~~~~~~~~~~~~~~l~~~~~  478 (921)
T PRK15347        399 SEHLTTISHEIRTPLNGVLGALELLQNTPLTAEQMDLADTARQCTLSLLAIINNLLDFSRIESGQMTLSLEETALLPLLD  478 (921)
T ss_pred             HHHHHHhHHHhchhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCccceecccCHHHHHH
Confidence            48999999999999999999999999888899999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHH-hhcceeccccCCCCCeeEEccHHHHHHHHHHHHhhhhhcCCCCeeEEEEEecCCCCcccchhhhhhhhh
Q 039716          451 HVLQTAAASL-QKILMLEGDIADDVPIEVIGDVLRIRQILTNLISNAIKFTPEGKVGIKLYVVPEPPFAKEGLKQKSKAY  529 (1002)
Q Consensus       451 ~v~~~~~~~~-~k~i~l~~~i~~~~p~~v~gD~~rL~QIL~NLlsNAIKfT~~G~I~I~v~~~~~~~~~~~~~~~~~~~~  529 (1002)
                      +++..+.... .+++.+...+.+..|..+.+|+.+|+|||.|||+||+|||+.|.|.|++...                 
T Consensus       479 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~l~~il~NLl~NAik~~~~g~I~i~~~~~-----------------  541 (921)
T PRK15347        479 QAMLTIQGPAQSKSLTLRTFVGAHVPLYLHLDSLRLRQILVNLLGNAVKFTETGGIRLRVKRH-----------------  541 (921)
T ss_pred             HHHHHHHHHHHHCCcEEEEEECCCCCceEEECHHHHHHHHHHHHHHHhhcCCCCCEEEEEEEc-----------------
Confidence            9988877654 4677777777778888899999999999999999999999999888876421                 


Q ss_pred             hcchhhhhhhccCCCCCccCCCCCCCCCCCCCCccCCCCCCCCCCCccCCCCCccccccceEEEEEEEecCCCCCcCcHh
Q 039716          530 QSATDAVKEEKHQPKSQTASDQNGFHDKKHGEGYQDHKHDDDPGTPVSHGNSMDEDLEATVWIRCDVYDTGIGIPENALP  609 (1002)
Q Consensus       530 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~i~V~DtGiGI~~e~l~  609 (1002)
                                                                                 ..++.|+|.|||+||+++.++
T Consensus       542 -----------------------------------------------------------~~~~~i~V~D~G~Gi~~~~~~  562 (921)
T PRK15347        542 -----------------------------------------------------------EQQLCFTVEDTGCGIDIQQQQ  562 (921)
T ss_pred             -----------------------------------------------------------CCEEEEEEEEcCCCCCHHHHH
Confidence                                                                       114889999999999999999


Q ss_pred             hhhhhccCCCccccCcCCCccccHHHHHHHHHHhCCEEEEEeecCCceEEEEEEeCCCCCCCCCCCCCCccccccccCCc
Q 039716          610 TLFRKYMQVSADHARKYGGTGLGLAICKQLVELMGGRLTVTSKVHCGSTFTFILPYQVSPIEENSDDPDDLSDMADQDSV  689 (1002)
Q Consensus       610 ~IF~pF~q~~~~~~~~~~GtGLGLaI~k~Lve~~gG~I~v~S~~g~GTtF~~~LP~~~~~~~~~~~~~~~l~~~~~~~~~  689 (1002)
                      +||+||++.+.    ..+|+||||+||+++++.|||+|+++|.+|+||+|+|.||+.......      ......   . 
T Consensus       563 ~if~~f~~~~~----~~~g~GLGL~i~~~~~~~~gG~i~i~s~~~~Gt~f~i~lp~~~~~~~~------~~~~~~---~-  628 (921)
T PRK15347        563 QIFTPFYQADT----HSQGTGLGLTIASSLAKMMGGELTLFSTPGVGSCFSLVLPLNEYAPPE------PLKGEL---S-  628 (921)
T ss_pred             HHhcCcccCCC----CCCCCchHHHHHHHHHHHcCCEEEEEecCCCceEEEEEEECCCCCCcc------cccccc---c-
Confidence            99999998753    346999999999999999999999999999999999999985421100      000000   0 


Q ss_pred             ccccccccccccccccccccccCCcccccccccccccccccccccCccccccCCCCCcccccccchhhhccHHHHHhhhC
Q 039716          690 TDDVTAGFFQFQPRTLGSLFSSNGTSRSKKLLPNSIGFASAHKVNGFSETSYSFPSNNRQKETAPLEDACSVAEVAETLS  769 (1002)
Q Consensus       690 ~~~~~~~~~~~~~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  769 (1002)
                                 .+..+.......+             .                                          
T Consensus       629 -----------~~~~~~~~~~~~~-------------~------------------------------------------  642 (921)
T PRK15347        629 -----------APLALHRQLSAWG-------------I------------------------------------------  642 (921)
T ss_pred             -----------chHHHHHHHHHcC-------------C------------------------------------------
Confidence                       0000000000000             0                                          


Q ss_pred             CCCCCCCCCCCCCcchhhcccccccccccccccCCCCCccchhhhhHHHhhcccCCCchhhhhhccCCCcccCCCCCCCC
Q 039716          770 EPESSFSHSPEPENETEVSRGKQCHVETTSWFQNPATESTSHSEANREMIQTSKTNEPQKICEMQEKPDRISQSPSSSSA  849 (1002)
Q Consensus       770 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  849 (1002)
                      .+.... ......      .      .....+  +       ... .....           ......      +.....
T Consensus       643 ~~~~~~-~~~~~~------~------~~~~~~--~-------~~~-~~~~~-----------~~~~~~------~~~~~~  682 (921)
T PRK15347        643 TCQPGH-QNPALL------D------PELAYL--P-------GRL-YDLLQ-----------QIIQGA------PNEPVI  682 (921)
T ss_pred             cccccc-cchhhc------c------hhhhhc--c-------hHH-HHHHH-----------HHhhcC------CCcccc
Confidence            000000 000000      0      000000  0       000 00000           000000      000000


Q ss_pred             CCCCCCCCCCCeEEEEecCHHHHHHHHHHHHhcCCeEEEEcCHHHHHHHHHcCCCcEEEEcCCCCCCCHHHHHHHHhccc
Q 039716          850 EVPETKPKPKPKILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKATRLIRSFE  929 (1002)
Q Consensus       850 ~~~~~~~~~~~~ILiVeDn~~n~~~l~~~L~~~g~~v~~a~~G~eAl~~~~~~~~DlIlmDi~MP~mdG~e~~~~IR~~~  929 (1002)
                      ..+  ....+.+||||||++.++..+..+|+..|+.|..|.+|.+|++.+....||+||||+.||+|||+++++.||+..
T Consensus       683 ~~~--~~~~~~~iLivdd~~~~~~~l~~~L~~~g~~v~~a~~~~~al~~~~~~~~dlil~D~~mp~~~G~~~~~~ir~~~  760 (921)
T PRK15347        683 NLP--LQPWQLQILLVDDVETNRDIIGMMLVELGQQVTTAASGTEALELGRQHRFDLVLMDIRMPGLDGLETTQLWRDDP  760 (921)
T ss_pred             cCC--CCcccCCEEEEeCCHHHHHHHHHHHHHcCCEEEEECCHHHHHHHHhcCCCCEEEEeCCCCCCCHHHHHHHHHhch
Confidence            001  112346899999999999999999999999999999999999999999999999999999999999999999743


Q ss_pred             cCCCchhhhhhhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHHhh
Q 039716          930 DTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQY 1000 (1002)
Q Consensus       930 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~~ 1000 (1002)
                      ..                      ..+++|||++|++...+...+|+++||++||.||++..+|..+|.++
T Consensus       761 ~~----------------------~~~~~pii~lt~~~~~~~~~~~~~~G~~~~l~KP~~~~~L~~~l~~~  809 (921)
T PRK15347        761 NN----------------------LDPDCMIVALTANAAPEEIHRCKKAGMNHYLTKPVTLAQLARALELA  809 (921)
T ss_pred             hh----------------------cCCCCcEEEEeCCCCHHHHHHHHHCCCCEEEECCCCHHHHHHHHHHH
Confidence            11                      23679999999999999999999999999999999999999998764

>PRK11466 hybrid sensory histidine kinase TorS; Provisional

Probab=100.00  E-value=1e-50  Score=519.94  Aligned_cols=350  Identities=32%  Similarity=0.546  Sum_probs=303.8

Q ss_pred             HHHHHHhhhccccHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCC--eeeEeeecCHHHH
Q 039716          371 KQMLATMSHEIRSPLTGVVSMAEILSNTKLDREQRQLLGVMISSGDLVLQLINDILDLSKVESGV--MKLEAAKFRPREV  448 (1002)
Q Consensus       371 k~fla~iSHELRTPL~~I~g~~elL~~~~l~~~~~~~l~~i~~s~~~L~~LIndlLd~skiesg~--~~l~~~~~~l~~l  448 (1002)
                      .+|+++|||||||||++|.|++++|.....++++++++..+..++++|..+|+++|+|++++.|.  +.+...+|++.++
T Consensus       445 ~~~l~~isHelrtPL~~i~~~~~ll~~~~~~~~~~~~l~~i~~~~~~l~~li~~ll~~s~~~~~~~~~~~~~~~~~l~~l  524 (914)
T PRK11466        445 SAFLAAMSHEIRTPLYGILGTAQLLADNPALNAQRDDLRAITDSGESLLTILNDILDYSAIEAGGKNVSVSDEPFEPRPL  524 (914)
T ss_pred             HHHHHHhHHHHhhHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCcceecccccCHHHH
Confidence            48999999999999999999999999888888999999999999999999999999999999884  5677789999999


Q ss_pred             HHHHHHHHHHHHh-hcceeccccCCCCCeeEEccHHHHHHHHHHHHhhhhhcCCCCeeEEEEEecCCCCcccchhhhhhh
Q 039716          449 VKHVLQTAAASLQ-KILMLEGDIADDVPIEVIGDVLRIRQILTNLISNAIKFTPEGKVGIKLYVVPEPPFAKEGLKQKSK  527 (1002)
Q Consensus       449 i~~v~~~~~~~~~-k~i~l~~~i~~~~p~~v~gD~~rL~QIL~NLlsNAIKfT~~G~I~I~v~~~~~~~~~~~~~~~~~~  527 (1002)
                      ++.++..+...+. +++.+...+.+..|..+.+|+.+|+|||.||++||+||++.|.|.|.+...               
T Consensus       525 l~~~~~~~~~~~~~~~i~~~~~~~~~~~~~v~~d~~~l~qil~NLl~NAik~~~~g~I~i~~~~~---------------  589 (914)
T PRK11466        525 LESTLQLMSGRVKGRPIRLATDIADDLPTALMGDPRRIRQVITNLLSNALRFTDEGSIVLRSRTD---------------  589 (914)
T ss_pred             HHHHHHHHHHHHHhCCcEEEEEeCCCCCceEEECHHHHHHHHHHHHHHHHHhCCCCeEEEEEEEc---------------
Confidence            9999988876654 667787777777777899999999999999999999999999888776421               


Q ss_pred             hhhcchhhhhhhccCCCCCccCCCCCCCCCCCCCCccCCCCCCCCCCCccCCCCCccccccceEEEEEEEecCCCCCcCc
Q 039716          528 AYQSATDAVKEEKHQPKSQTASDQNGFHDKKHGEGYQDHKHDDDPGTPVSHGNSMDEDLEATVWIRCDVYDTGIGIPENA  607 (1002)
Q Consensus       528 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~i~V~DtGiGI~~e~  607 (1002)
                                                                                   ...+.|.|.|||+|||++.
T Consensus       590 -------------------------------------------------------------~~~~~i~V~D~G~Gi~~~~  608 (914)
T PRK11466        590 -------------------------------------------------------------GEQWLVEVEDSGCGIDPAK  608 (914)
T ss_pred             -------------------------------------------------------------CCEEEEEEEECCCCCCHHH
Confidence                                                                         1147799999999999999


Q ss_pred             HhhhhhhccCCCccccCcCCCccccHHHHHHHHHHhCCEEEEEeecCCceEEEEEEeCCCCCCCCCCCCCCccccccccC
Q 039716          608 LPTLFRKYMQVSADHARKYGGTGLGLAICKQLVELMGGRLTVTSKVHCGSTFTFILPYQVSPIEENSDDPDDLSDMADQD  687 (1002)
Q Consensus       608 l~~IF~pF~q~~~~~~~~~~GtGLGLaI~k~Lve~~gG~I~v~S~~g~GTtF~~~LP~~~~~~~~~~~~~~~l~~~~~~~  687 (1002)
                      +++||+||++.+.    +.+|+||||+||+++++.|||+|+++|.+|+||+|+|.||+........              
T Consensus       609 ~~~if~~f~~~~~----~~~g~GLGL~i~~~l~~~~gG~i~v~s~~~~Gt~f~i~lP~~~~~~~~~--------------  670 (914)
T PRK11466        609 LAEIFQPFVQVSG----KRGGTGLGLTISSRLAQAMGGELSATSTPEVGSCFCLRLPLRVATAPVP--------------  670 (914)
T ss_pred             HHHHhchhhcCCC----CCCCCcccHHHHHHHHHHcCCEEEEEecCCCCeEEEEEEEccccccccc--------------
Confidence            9999999998642    4579999999999999999999999999999999999999743110000              


Q ss_pred             CcccccccccccccccccccccccCCcccccccccccccccccccccCccccccCCCCCcccccccchhhhccHHHHHhh
Q 039716          688 SVTDDVTAGFFQFQPRTLGSLFSSNGTSRSKKLLPNSIGFASAHKVNGFSETSYSFPSNNRQKETAPLEDACSVAEVAET  767 (1002)
Q Consensus       688 ~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  767 (1002)
                                                                                                      
T Consensus       671 --------------------------------------------------------------------------------  670 (914)
T PRK11466        671 --------------------------------------------------------------------------------  670 (914)
T ss_pred             --------------------------------------------------------------------------------
Confidence                                                                                            


Q ss_pred             hCCCCCCCCCCCCCCcchhhcccccccccccccccCCCCCccchhhhhHHHhhcccCCCchhhhhhccCCCcccCCCCCC
Q 039716          768 LSEPESSFSHSPEPENETEVSRGKQCHVETTSWFQNPATESTSHSEANREMIQTSKTNEPQKICEMQEKPDRISQSPSSS  847 (1002)
Q Consensus       768 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  847 (1002)
                                  ..                                                                 .
T Consensus       671 ------------~~-----------------------------------------------------------------~  673 (914)
T PRK11466        671 ------------KT-----------------------------------------------------------------V  673 (914)
T ss_pred             ------------cc-----------------------------------------------------------------c
Confidence                        00                                                                 0


Q ss_pred             CCCCCCCCCCCCCeEEEEecCHHHHHHHHHHHHhcCCeEEEEcCHHHHHHHHHc-CCCcEEEEcCCCCCCCHHHHHHHHh
Q 039716          848 SAEVPETKPKPKPKILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQC-QNYDLILMDVCMPVMDGLKATRLIR  926 (1002)
Q Consensus       848 ~~~~~~~~~~~~~~ILiVeDn~~n~~~l~~~L~~~g~~v~~a~~G~eAl~~~~~-~~~DlIlmDi~MP~mdG~e~~~~IR  926 (1002)
                          .......+.+|||||||+.++..+..+|...||.|..|.+|.+|++.+.. ..||+||||++||+|||+++++.||
T Consensus       674 ----~~~~~~~~~~vLivdD~~~~~~~l~~~L~~~g~~v~~a~~~~~al~~~~~~~~~Dlvl~D~~mp~~~G~~~~~~lr  749 (914)
T PRK11466        674 ----NQAVRLDGLRLLLIEDNPLTQRITAEMLNTSGAQVVAVGNAAQALETLQNSEPFAAALVDFDLPDYDGITLARQLA  749 (914)
T ss_pred             ----ccccccCCcceEEEeCCHHHHHHHHHHHHhcCCceEEeCCHHHHHHHHHcCCCCCEEEEeCCCCCCCHHHHHHHHH
Confidence                00000124579999999999999999999999999999999999998865 5799999999999999999999999


Q ss_pred             ccccCCCchhhhhhhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHHhhc
Q 039716          927 SFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQYF 1001 (1002)
Q Consensus       927 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~~l 1001 (1002)
                      ..                          .+.+|||++|++.......+|+.+|+++||.||++.++|...|.+++
T Consensus       750 ~~--------------------------~~~~~ii~~t~~~~~~~~~~~~~~g~~~~l~KP~~~~~L~~~i~~~~  798 (914)
T PRK11466        750 QQ--------------------------YPSLVLIGFSAHVIDETLRQRTSSLFRGIIPKPVPREVLGQLLAHYL  798 (914)
T ss_pred             hh--------------------------CCCCCEEEEeCCCchhhHHHHHhcCcCCEEeCCCCHHHHHHHHHHHh
Confidence            62                          35689999999999999999999999999999999999999998875

>PRK13557 histidine kinase; Provisional

Probab=100.00  E-value=6.6e-47  Score=455.75  Aligned_cols=493  Identities=18%  Similarity=0.245  Sum_probs=373.9

Q ss_pred             HHHHHHHHHHhccCcEEEEecc---cccEEEeecc---CCCCCcccccCCCchhccCccchhhhhHHHHHHHHhCCCcce
Q 039716          219 RADNFLHFVLQNAPVVMGHQDK---ELRYRFIYNH---FPSLHEEDILGKTDVEIFSGAGVKESQDFKREVLEKGLPAKR  292 (1002)
Q Consensus       219 ~~~~~l~~il~~~p~~i~~~d~---~~~~~~~~~~---~~~~~~e~iiGk~~~e~~~~~~~~~~~~~~~~vl~~g~~~~~  292 (1002)
                      ....+++.+++++|..|+..|.   ++++.|+|+.   +.|++.++++|++..+++++.............+..+.....
T Consensus        27 ~~~~~~~~~~~~~~~~i~v~d~~~~~g~i~~~N~a~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~  106 (540)
T PRK13557         27 HRSDIFFAAVETTRMPMIVTDPNQPDNPIVFANRAFLEMTGYAAEEIIGNNCRFLQGPETDRATVAEVRDAIAERREIAT  106 (540)
T ss_pred             hhhHHHHHHHHhCcCcEEEEcCCCCCCCEEEEcHHHHHHhCCCHHHhcCCChHhhcCCCCCHHHHHHHHHHHHcCCCceE
Confidence            4467889999999999999885   7899999876   468899999999998887665444444445556666665555


Q ss_pred             eEEEEEeecCceEEEEEEeeeecCCCCEEEEEEEeechhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 039716          293 EITFETELFGSKTFLIYVEPVFSKSGETIGVNYMGMDVTDQVRKREKMAKLREEIAVQKAKETELNKTIHITEETMRAKQ  372 (1002)
Q Consensus       293 e~~~~~~~~~~~~~~~~~~p~~~~~G~~~gi~~~~~DITe~~~~~~~~~~l~~el~~~~~~~~el~k~~~~~e~~~~~k~  372 (1002)
                      ++......+...++..+..|+++.+|.++|++.+..|||++++.++.+.+.+                     +.....+
T Consensus       107 ~~~~~~~~G~~~~~~~~~~~i~~~~g~~~~~~~~~~dit~~~~~e~~l~~~~---------------------~~~~l~~  165 (540)
T PRK13557        107 EILNYRKDGSSFWNALFVSPVYNDAGDLVYFFGSQLDVSRRRDAEDALRQAQ---------------------KMEALGQ  165 (540)
T ss_pred             EEEEEeCCCCEEEEEEEEEEeECCCCCEEEEEEEecChHHHHHHHHHHHHHH---------------------HHHHhhh
Confidence            5554444455556668889999999999999999999998765543332111                     1112346


Q ss_pred             HHHHhhhccccHHHHHHHHHHHHhCC-----CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCeeeEeeecCHHH
Q 039716          373 MLATMSHEIRSPLTGVVSMAEILSNT-----KLDREQRQLLGVMISSGDLVLQLINDILDLSKVESGVMKLEAAKFRPRE  447 (1002)
Q Consensus       373 fla~iSHELRTPL~~I~g~~elL~~~-----~l~~~~~~~l~~i~~s~~~L~~LIndlLd~skiesg~~~l~~~~~~l~~  447 (1002)
                      +++.++||+||||+.|.+++++|...     .......++++.+..++.++..++++++++++..    .+....+++..
T Consensus       166 ~~~~i~h~l~~pl~~i~~~~~~l~~~~~~~~~~~~~~~~~l~~i~~~~~~~~~li~~l~~~~~~~----~~~~~~~~l~~  241 (540)
T PRK13557        166 LTGGIAHDFNNLLQVMSGYLDVIQAALSHPDADRGRMARSVENIRAAAERAATLTQQLLAFARKQ----RLEGRVLNLNG  241 (540)
T ss_pred             hhhhhhHHhhhHHHHHHhHHHHHHHhhccCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCcC----CCCCcccCHHH
Confidence            89999999999999999999987532     1234566788999999999999999999999854    23456788899


Q ss_pred             HHHHHHHHHHHHHhhcceeccccCCCCCeeEEccHHHHHHHHHHHHhhhhhcCCCC-eeEEEEEecCCCCcccchhhhhh
Q 039716          448 VVKHVLQTAAASLQKILMLEGDIADDVPIEVIGDVLRIRQILTNLISNAIKFTPEG-KVGIKLYVVPEPPFAKEGLKQKS  526 (1002)
Q Consensus       448 li~~v~~~~~~~~~k~i~l~~~i~~~~p~~v~gD~~rL~QIL~NLlsNAIKfT~~G-~I~I~v~~~~~~~~~~~~~~~~~  526 (1002)
                      ++..+...+.....+.+.+.....+..+ .+.+|+.+|.|||.||+.||+||++.| .|.|.+........         
T Consensus       242 ~i~~~~~~~~~~~~~~~~i~~~~~~~~~-~~~~d~~~l~~vl~nll~NA~~~~~~~~~i~i~~~~~~~~~~---------  311 (540)
T PRK13557        242 LVSGMGELAERTLGDAVTIETDLAPDLW-NCRIDPTQAEVALLNVLINARDAMPEGGRVTIRTRNVEIEDE---------  311 (540)
T ss_pred             HHHHHHHHHHHhcCCCeEEEEecCCCCC-ceeeCHHHHHHHHHHHHHHHHHhcccCCeEEEEEeeeccCcc---------
Confidence            8888776655544555566555544443 478899999999999999999999764 45554422110000         


Q ss_pred             hhhhcchhhhhhhccCCCCCccCCCCCCCCCCCCCCccCCCCCCCCCCCccCCCCCccccccceEEEEEEEecCCCCCcC
Q 039716          527 KAYQSATDAVKEEKHQPKSQTASDQNGFHDKKHGEGYQDHKHDDDPGTPVSHGNSMDEDLEATVWIRCDVYDTGIGIPEN  606 (1002)
Q Consensus       527 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~i~V~DtGiGI~~e  606 (1002)
                                                                    ....      ........++.|+|.|+|+||+++
T Consensus       312 ----------------------------------------------~~~~------~~~~~~~~~~~i~v~D~G~Gi~~~  339 (540)
T PRK13557        312 ----------------------------------------------DLAM------YHGLPPGRYVSIAVTDTGSGMPPE  339 (540)
T ss_pred             ----------------------------------------------cccc------ccCCCCCCEEEEEEEcCCCCCCHH
Confidence                                                          0000      000011235789999999999999


Q ss_pred             cHhhhhhhccCCCccccCcCCCccccHHHHHHHHHHhCCEEEEEeecCCceEEEEEEeCCCCCCCCCCCCCCcccccccc
Q 039716          607 ALPTLFRKYMQVSADHARKYGGTGLGLAICKQLVELMGGRLTVTSKVHCGSTFTFILPYQVSPIEENSDDPDDLSDMADQ  686 (1002)
Q Consensus       607 ~l~~IF~pF~q~~~~~~~~~~GtGLGLaI~k~Lve~~gG~I~v~S~~g~GTtF~~~LP~~~~~~~~~~~~~~~l~~~~~~  686 (1002)
                      .+.++|+||++.+.    ..+|+||||+|||++++.|||.|+++|.+|+||+|+|+||.........   +         
T Consensus       340 ~~~~if~~~~~~~~----~~~g~GlGL~i~~~~v~~~gG~i~~~s~~~~G~~f~i~lP~~~~~~~~~---~---------  403 (540)
T PRK13557        340 ILARVMDPFFTTKE----EGKGTGLGLSMVYGFAKQSGGAVRIYSEVGEGTTVRLYFPASDQAENPE---Q---------  403 (540)
T ss_pred             HHHhccCCCcccCC----CCCCCCccHHHHHHHHHHCCCEEEEEecCCCceEEEEEeeCCCCccCCC---C---------
Confidence            99999999997643    3469999999999999999999999999999999999999742110000   0         


Q ss_pred             CCcccccccccccccccccccccccCCcccccccccccccccccccccCccccccCCCCCcccccccchhhhccHHHHHh
Q 039716          687 DSVTDDVTAGFFQFQPRTLGSLFSSNGTSRSKKLLPNSIGFASAHKVNGFSETSYSFPSNNRQKETAPLEDACSVAEVAE  766 (1002)
Q Consensus       687 ~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  766 (1002)
                                                                                                      
T Consensus       404 --------------------------------------------------------------------------------  403 (540)
T PRK13557        404 --------------------------------------------------------------------------------  403 (540)
T ss_pred             --------------------------------------------------------------------------------
Confidence                                                                                            


Q ss_pred             hhCCCCCCCCCCCCCCcchhhcccccccccccccccCCCCCccchhhhhHHHhhcccCCCchhhhhhccCCCcccCCCCC
Q 039716          767 TLSEPESSFSHSPEPENETEVSRGKQCHVETTSWFQNPATESTSHSEANREMIQTSKTNEPQKICEMQEKPDRISQSPSS  846 (1002)
Q Consensus       767 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  846 (1002)
                                 .+                                                                   
T Consensus       404 -----------~~-------------------------------------------------------------------  405 (540)
T PRK13557        404 -----------EP-------------------------------------------------------------------  405 (540)
T ss_pred             -----------CC-------------------------------------------------------------------
Confidence                       00                                                                   


Q ss_pred             CCCCCCCCCCCCCCeEEEEecCHHHHHHHHHHHHhcCCeEEEEcCHHHHHHHHHcC-CCcEEEEcCCCCC-CCHHHHHHH
Q 039716          847 SSAEVPETKPKPKPKILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQ-NYDLILMDVCMPV-MDGLKATRL  924 (1002)
Q Consensus       847 ~~~~~~~~~~~~~~~ILiVeDn~~n~~~l~~~L~~~g~~v~~a~~G~eAl~~~~~~-~~DlIlmDi~MP~-mdG~e~~~~  924 (1002)
                      . .  .......+.+||||+|++..+..+..+|+..||.+..+.++.+|+..+... .||+|++|..||. ++|+++++.
T Consensus       406 ~-~--~~~~~~~~~~iliv~~~~~~~~~l~~~l~~~~~~v~~~~~~~~~~~~~~~~~~~d~vi~d~~~~~~~~~~~~~~~  482 (540)
T PRK13557        406 K-A--RAIDRGGTETILIVDDRPDVAELARMILEDFGYRTLVASNGREALEILDSHPEVDLLFTDLIMPGGMNGVMLARE  482 (540)
T ss_pred             C-C--cccccCCCceEEEEcCcHHHHHHHHHHHHhcCCeEEEeCCHHHHHHHHhcCCCceEEEEeccCCCCCCHHHHHHH
Confidence            0 0  000002345899999999999999999999999999999999999998765 6999999999997 999999999


Q ss_pred             HhccccCCCchhhhhhhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHHhhc
Q 039716          925 IRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQYF 1001 (1002)
Q Consensus       925 IR~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~~l 1001 (1002)
                      ||..                          .+.+|||++|..........++..|+++|+.||++..+|...|++++
T Consensus       483 l~~~--------------------------~~~~~ii~~~~~~~~~~~~~~~~~g~~~~l~kp~~~~~l~~~l~~~~  533 (540)
T PRK13557        483 ARRR--------------------------QPKIKVLLTTGYAEASIERTDAGGSEFDILNKPYRRAELARRVRMVL  533 (540)
T ss_pred             HHHh--------------------------CCCCcEEEEcCCCchhhhhhhccccCCceeeCCCCHHHHHHHHHHHh
Confidence            9963                          24589999999998888888999999999999999999999998754

>COG5002 VicK Signal transduction histidine kinase [Signal transduction mechanisms]

Probab=100.00  E-value=8.7e-48  Score=406.01  Aligned_cols=345  Identities=26%  Similarity=0.432  Sum_probs=280.2

Q ss_pred             hHHHHHHHHHHHHHHHHHHHhccCcEEEEecccccEEEeecc---CCCCCcccccCCCchhccCccchhhhhHHHHHHHH
Q 039716          209 PVEELSQILKRADNFLHFVLQNAPVVMGHQDKELRYRFIYNH---FPSLHEEDILGKTDVEIFSGAGVKESQDFKREVLE  285 (1002)
Q Consensus       209 ~~~~~~~~l~~~~~~l~~il~~~p~~i~~~d~~~~~~~~~~~---~~~~~~e~iiGk~~~e~~~~~~~~~~~~~~~~vl~  285 (1002)
                      .+++++..++...+.|.+++..+..++...|+.|++..+|..   ..+...++++|++..+++.-...   .. .+.+++
T Consensus        98 ~~~~aq~n~e~Er~kL~SvlayMtDGViATdRrG~iI~iN~~A~k~L~~~~E~~~~~~i~elL~i~d~---y~-~~dL~e  173 (459)
T COG5002          98 RVQEAQANTEQERRKLDSVLAYMTDGVIATDRRGKIILINKPALKMLGVSKEDALGRSILELLKIEDT---YT-FEDLVE  173 (459)
T ss_pred             HHHHHHHhHHHHHHHHHHHHHHHcCceEeecCCCcEEEeccHHHHHhCcCHHHHhcccHHHHhCCccc---ee-HHHHHh
Confidence            455666667777889999999999999999999999999874   46778899999999998764321   11 122232


Q ss_pred             hCCCcceeEEEEEeecCc-eEEEEEEeeeecCCCCEEEEEEEeechhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 039716          286 KGLPAKREITFETELFGS-KTFLIYVEPVFSKSGETIGVNYMGMDVTDQVRKREKMAKLREEIAVQKAKETELNKTIHIT  364 (1002)
Q Consensus       286 ~g~~~~~e~~~~~~~~~~-~~~~~~~~p~~~~~G~~~gi~~~~~DITe~~~~~~~~~~l~~el~~~~~~~~el~k~~~~~  364 (1002)
                          ...++.++....+. ....+..+.+.-++|.+.|++.+..|+|++.+.+++                         
T Consensus       174 ----~~~s~lld~~~~~E~~~lrv~Fs~i~rEsGfisGlIaVlhDvTEqek~e~E-------------------------  224 (459)
T COG5002         174 ----KNDSLLLDSSDEEEGYVLRVNFSVIQRESGFISGLIAVLHDVTEQEKVERE-------------------------  224 (459)
T ss_pred             ----cCCcEEEeecCCCccEEEEEEEEEEeecccccceeEEEEecccHHHHHHHH-------------------------
Confidence                22345555553333 234466677788999999999999999987443221                         


Q ss_pred             HHHHHHHHHHHHhhhccccHHHHHHHHHHHHhCCCCCHH--HHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCeeeEeee
Q 039716          365 EETMRAKQMLATMSHEIRSPLTGVVSMAEILSNTKLDRE--QRQLLGVMISSGDLVLQLINDILDLSKVESGVMKLEAAK  442 (1002)
Q Consensus       365 e~~~~~k~fla~iSHELRTPL~~I~g~~elL~~~~l~~~--~~~~l~~i~~s~~~L~~LIndlLd~skiesg~~~l~~~~  442 (1002)
                           ...|+|++||||||||+++.+|++.|....+.+.  ...++..-....+||.+||||||.+||++....+++.+.
T Consensus       225 -----rRefvanvSHElRTPltsmksyLEALe~ga~~d~eiAp~Fl~vt~~ETeRMiRlV~DLl~lsr~d~~~~qln~e~  299 (459)
T COG5002         225 -----RREFVANVSHELRTPLTSMKSYLEALEEGAWEDKEIAPRFLRVTLNETERMIRLVNDLLQLSRMDNARYQLNKEW  299 (459)
T ss_pred             -----HHHHHHhcchhhcCchHHHHHHHHHHhcCCccChhhhhHHHHHhHHHHHHHHHHHHHHHHHccCcchhhhhhHHH
Confidence                 1369999999999999999999999988765444  567899999999999999999999999999999999999


Q ss_pred             cCHHHHHHHHHHHHHHHHhh-cce-eccccCCCCCeeEEccHHHHHHHHHHHHhhhhhcCCCC-eeEEEEEecCCCCccc
Q 039716          443 FRPREVVKHVLQTAAASLQK-ILM-LEGDIADDVPIEVIGDVLRIRQILTNLISNAIKFTPEG-KVGIKLYVVPEPPFAK  519 (1002)
Q Consensus       443 ~~l~~li~~v~~~~~~~~~k-~i~-l~~~i~~~~p~~v~gD~~rL~QIL~NLlsNAIKfT~~G-~I~I~v~~~~~~~~~~  519 (1002)
                      +++...+..++..+...+.+ ... +..++ +..+.+|..|+.++.||+-|+|+||+||+|+| .|++.+...       
T Consensus       300 inft~fl~~ii~R~e~~~~~e~~~~~vR~~-p~~~~~veiD~DK~tQVldNii~NA~KYsP~Gg~Itv~~~~~-------  371 (459)
T COG5002         300 INFTAFLNEIINRFEMILKKETIARFVRDI-PKQDIWVEIDPDKMTQVLDNIISNALKYSPDGGRITVSVKQR-------  371 (459)
T ss_pred             HHhHHHHHHHHHHHHHHHhhHHHHHHHhcC-CCCceEEEeChhHHHHHHHHHHHHHhhcCCCCCeEEEEEeee-------
Confidence            99999999988876655332 222 23333 45567899999999999999999999999985 677766321       


Q ss_pred             chhhhhhhhhhcchhhhhhhccCCCCCccCCCCCCCCCCCCCCccCCCCCCCCCCCccCCCCCccccccceEEEEEEEec
Q 039716          520 EGLKQKSKAYQSATDAVKEEKHQPKSQTASDQNGFHDKKHGEGYQDHKHDDDPGTPVSHGNSMDEDLEATVWIRCDVYDT  599 (1002)
Q Consensus       520 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~i~V~Dt  599 (1002)
                                                                                           ..|+.++|+|.
T Consensus       372 ---------------------------------------------------------------------~~~v~iSI~D~  382 (459)
T COG5002         372 ---------------------------------------------------------------------ETWVEISISDQ  382 (459)
T ss_pred             ---------------------------------------------------------------------CcEEEEEEccC
Confidence                                                                                 22799999999


Q ss_pred             CCCCCcCcHhhhhhhccCCCccccCcCCCccccHHHHHHHHHHhCCEEEEEeecCCceEEEEEEeCCCC
Q 039716          600 GIGIPENALPTLFRKYMQVSADHARKYGGTGLGLAICKQLVELMGGRLTVTSKVHCGSTFTFILPYQVS  668 (1002)
Q Consensus       600 GiGI~~e~l~~IF~pF~q~~~~~~~~~~GtGLGLaI~k~Lve~~gG~I~v~S~~g~GTtF~~~LP~~~~  668 (1002)
                      |.|||.+++++||++||+++...+++.|||||||||+|.||+.|||.||++|..|+||||+|+||+...
T Consensus       383 G~gIPk~d~~~iFdrfyRvdkARsR~~gGTGLGLaIakeiV~~hgG~iWA~s~~gkgtt~~ftLPy~~~  451 (459)
T COG5002         383 GLGIPKEDLEKIFDRFYRVDKARSRKMGGTGLGLAIAKEIVQAHGGRIWAESEEGKGTTFSFTLPYSGE  451 (459)
T ss_pred             CCCCCchhHHHHHHHHhhhhhhhhhcCCCCchhHHHHHHHHHHhCCeEEEecccCCceEEEEEecccCc
Confidence            999999999999999999999999999999999999999999999999999999999999999999653

>PRK10618 phosphotransfer intermediate protein in two-component regulatory system with RcsBC; Provisional

Probab=100.00  E-value=3.4e-46  Score=465.63  Aligned_cols=343  Identities=20%  Similarity=0.275  Sum_probs=253.7

Q ss_pred             ChHHHHHHHHHHHHHHHHHHHhccCcEEEEec-ccccEEEeeccCCCCCcccccCCCchhccCccchhhhhHHHHHHHHh
Q 039716          208 SPVEELSQILKRADNFLHFVLQNAPVVMGHQD-KELRYRFIYNHFPSLHEEDILGKTDVEIFSGAGVKESQDFKREVLEK  286 (1002)
Q Consensus       208 ~~~~~~~~~l~~~~~~l~~il~~~p~~i~~~d-~~~~~~~~~~~~~~~~~e~iiGk~~~e~~~~~~~~~~~~~~~~vl~~  286 (1002)
                      .+...+.+.++.++.+.+.+++++|+++...| .++++.++|..+.     .++|.....-+     .........++..
T Consensus       329 ~p~~~l~~~L~~~~~l~~~Ii~~lp~Gilv~D~~~~~Ii~~N~aA~-----~ll~~~~l~~i-----~~~~~~~~~~i~~  398 (894)
T PRK10618        329 RPTESMSHELRILRALNEEIVSNLPLGLLVYDFESNRTVISNKIAD-----HLLPHLNLQKI-----TTMAEQHQGVIQA  398 (894)
T ss_pred             CcchHHHHHHHHHHHHHHHHHHhCCceEEEEECCCCeEEEEhHHHH-----HHhCccchhhH-----HHHHHhcchhhhh
Confidence            35566777899999999999999999999999 5678888876532     23332111000     0000000111111


Q ss_pred             CCCcceeEEEEEeecCceEEEEEEeeeecCCCCEEEEEEEeechhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 039716          287 GLPAKREITFETELFGSKTFLIYVEPVFSKSGETIGVNYMGMDVTDQVRKREKMAKLREEIAVQKAKETELNKTIHITEE  366 (1002)
Q Consensus       287 g~~~~~e~~~~~~~~~~~~~~~~~~p~~~~~G~~~gi~~~~~DITe~~~~~~~~~~l~~el~~~~~~~~el~k~~~~~e~  366 (1002)
                      ..            .+. .+.+...   .......+.+.+..|++..+...+++.+.+++++                +.
T Consensus       399 ~i------------~~~-~~eir~~---~~~~~~~~~l~~l~d~~~~~~~~~~L~~a~~~le----------------~~  446 (894)
T PRK10618        399 TI------------NNE-LYEIRMF---RSQLAPRTQLFLLRDQDREVLVNKKLQQAQREYE----------------KN  446 (894)
T ss_pred             hc------------cCc-eeEEEEe---eccccCceEEEEEeehHHHHHHHHHHHHHHHHHH----------------HH
Confidence            00            010 0111110   1111123556778898876554443332221111                11


Q ss_pred             HHHHHHHHHHhhhccccHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCeeeEeeecCHH
Q 039716          367 TMRAKQMLATMSHEIRSPLTGVVSMAEILSNTKLDREQRQLLGVMISSGDLVLQLINDILDLSKVESGVMKLEAAKFRPR  446 (1002)
Q Consensus       367 ~~~~k~fla~iSHELRTPL~~I~g~~elL~~~~l~~~~~~~l~~i~~s~~~L~~LIndlLd~skiesg~~~l~~~~~~l~  446 (1002)
                      ...+++|+++|||||||||++|.|++++|.....++++++++..+..++++|..+|+++++++|+++|.+.+...+|++.
T Consensus       447 ~~~k~~fla~iSHELRtPL~aI~g~~elL~~~~~~~~~~~~l~~I~~~~~~L~~lI~dILdlsrle~~~~~l~~~~~~L~  526 (894)
T PRK10618        447 QQARKAFLQNIGDELKQPLQSLAQLAAQLRQTSDEEQQQPELDQLAEQSDVLVRLVDNIQLLNMLETQDWKPEQELFSLQ  526 (894)
T ss_pred             HHHHHHHHHHHHHHHhHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCcccceeECHH
Confidence            11234899999999999999999999999887778889999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHh-hcceeccccCCCCCeeEEccHHHHHHHHHHHHhhhhhcCCCCeeEEEEEecCCCCcccchhhhh
Q 039716          447 EVVKHVLQTAAASLQ-KILMLEGDIADDVPIEVIGDVLRIRQILTNLISNAIKFTPEGKVGIKLYVVPEPPFAKEGLKQK  525 (1002)
Q Consensus       447 ~li~~v~~~~~~~~~-k~i~l~~~i~~~~p~~v~gD~~rL~QIL~NLlsNAIKfT~~G~I~I~v~~~~~~~~~~~~~~~~  525 (1002)
                      +++++++..+...+. +++.+...+....+..+.+|+.+|+|||.||++||+|||+.|.|.|.+.....           
T Consensus       527 ~ll~~vl~~~~~~a~~k~i~l~~~~~~~~~~~v~~D~~~L~QVL~NLL~NAik~t~~G~I~I~v~~~~~-----------  595 (894)
T PRK10618        527 DLIDEVLPEVLPAIKRKGLQLLIHNHLKAEQLRIGDRDALRKILLLLLNYAITTTAYGKITLEVDQDES-----------  595 (894)
T ss_pred             HHHHHHHHHHHHHHHHCCCEEEEEeCCCCCcEEEecHHHHHHHHHHHHHHHHHhCCCCeEEEEEEEccC-----------
Confidence            999999988776554 66777666655556678999999999999999999999999998887743210           


Q ss_pred             hhhhhcchhhhhhhccCCCCCccCCCCCCCCCCCCCCccCCCCCCCCCCCccCCCCCccccccceEEEEEEEecCCCCCc
Q 039716          526 SKAYQSATDAVKEEKHQPKSQTASDQNGFHDKKHGEGYQDHKHDDDPGTPVSHGNSMDEDLEATVWIRCDVYDTGIGIPE  605 (1002)
Q Consensus       526 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~i~V~DtGiGI~~  605 (1002)
                                                                                    ...++.|+|.|||+|||+
T Consensus       596 --------------------------------------------------------------~~~~l~I~V~DtG~GI~~  613 (894)
T PRK10618        596 --------------------------------------------------------------SPDRLTIRILDTGAGVSI  613 (894)
T ss_pred             --------------------------------------------------------------CCcEEEEEEEECCCCCCH
Confidence                                                                          012588999999999999


Q ss_pred             CcHhhhhhhccCCCccccCcCCCccccHHHHHHHHHHhCCEEEEEeecCCceEEEEEEeCC
Q 039716          606 NALPTLFRKYMQVSADHARKYGGTGLGLAICKQLVELMGGRLTVTSKVHCGSTFTFILPYQ  666 (1002)
Q Consensus       606 e~l~~IF~pF~q~~~~~~~~~~GtGLGLaI~k~Lve~~gG~I~v~S~~g~GTtF~~~LP~~  666 (1002)
                      +.+++||+||++.+.. .+..+|+||||+|||+||+.|||+|+|+|.+|+||+|+|+||+.
T Consensus       614 e~l~~IFePF~t~~~~-~~~~~GtGLGLaI~k~Lve~~GG~I~v~S~~g~GT~F~I~LPl~  673 (894)
T PRK10618        614 KELDNLHFPFLNQTQG-DRYGKASGLTFFLCNQLCRKLGGHLTIKSREGLGTRYSIHLKML  673 (894)
T ss_pred             HHHHHhcCccccCCCC-CCCCCCcChhHHHHHHHHHHcCCEEEEEECCCCcEEEEEEEEcc
Confidence            9999999999986542 34457999999999999999999999999999999999999974

>PRK13837 two-component VirA-like sensor kinase; Provisional

Probab=100.00  E-value=1e-43  Score=448.51  Aligned_cols=365  Identities=23%  Similarity=0.311  Sum_probs=289.3

Q ss_pred             HHHHHHHHHHHHHhhhccccHHHHHHHHHHHHhCC-CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCeeeEeee
Q 039716          364 TEETMRAKQMLATMSHEIRSPLTGVVSMAEILSNT-KLDREQRQLLGVMISSGDLVLQLINDILDLSKVESGVMKLEAAK  442 (1002)
Q Consensus       364 ~e~~~~~k~fla~iSHELRTPL~~I~g~~elL~~~-~l~~~~~~~l~~i~~s~~~L~~LIndlLd~skiesg~~~l~~~~  442 (1002)
                      ++.....++|+++|||||||||++|.|+++++... ..+...+++++.|..+++++..+|++++++++...+.    ..+
T Consensus       444 ~~rl~~l~~~~~~iaHeLrtPL~~I~~~~~~l~~~~~~~~~~~~~l~~i~~~~~rl~~li~~ll~~sr~~~~~----~~~  519 (828)
T PRK13837        444 ARRLEAVGTLASGIAHNFNNILGAILGYAEMALNKLARHSRAARYIDEIISAGARARLIIDQILAFGRKGERN----TKP  519 (828)
T ss_pred             HHHHHHHHHHHHHhhHHhhhHHHHHHHHHHHHHhhccCChHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCC----CcE
Confidence            33344456899999999999999999999987643 3345778899999999999999999999999976543    457


Q ss_pred             cCHHHHHHHHHHHHHHHHhhcceeccccCCCCCeeEEccHHHHHHHHHHHHhhhhhcCCC-CeeEEEEEecCCCCcccch
Q 039716          443 FRPREVVKHVLQTAAASLQKILMLEGDIADDVPIEVIGDVLRIRQILTNLISNAIKFTPE-GKVGIKLYVVPEPPFAKEG  521 (1002)
Q Consensus       443 ~~l~~li~~v~~~~~~~~~k~i~l~~~i~~~~p~~v~gD~~rL~QIL~NLlsNAIKfT~~-G~I~I~v~~~~~~~~~~~~  521 (1002)
                      +++.+++.+++..+.....+++.+....... +..+.+|+.+|.|||.||++||+||++. |.|.|++.........   
T Consensus       520 ~~l~~ll~~~~~~~~~~~~~~i~l~~~~~~~-~~~v~~d~~~L~qvl~NLl~NAik~~~~~g~I~I~~~~~~~~~~~---  595 (828)
T PRK13837        520 FDLSELVTEIAPLLRVSLPPGVELDFDQDQE-PAVVEGNPAELQQVLMNLCSNAAQAMDGAGRVDISLSRAKLRAPK---  595 (828)
T ss_pred             EcHHHHHHHHHHHHHHHccCCcEEEEEeCCC-CceEEECHHHHHHHHHHHHHHHHHHcccCCeEEEEEEEeeccccc---
Confidence            9999999999887776555666666555443 4468999999999999999999999865 6777776542110000   


Q ss_pred             hhhhhhhhhcchhhhhhhccCCCCCccCCCCCCCCCCCCCCccCCCCCCCCCCCccCCCCCccccccceEEEEEEEecCC
Q 039716          522 LKQKSKAYQSATDAVKEEKHQPKSQTASDQNGFHDKKHGEGYQDHKHDDDPGTPVSHGNSMDEDLEATVWIRCDVYDTGI  601 (1002)
Q Consensus       522 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~i~V~DtGi  601 (1002)
                                                                           ....+     ......++.|+|.|+|+
T Consensus       596 -----------------------------------------------------~~~~~-----~~~~~~~v~i~V~D~G~  617 (828)
T PRK13837        596 -----------------------------------------------------VLSHG-----VLPPGRYVLLRVSDTGA  617 (828)
T ss_pred             -----------------------------------------------------ccccc-----cCCCCCEEEEEEEECCC
Confidence                                                                 00000     00112368899999999


Q ss_pred             CCCcCcHhhhhhhccCCCccccCcCCCccccHHHHHHHHHHhCCEEEEEeecCCceEEEEEEeCCCCCCCCCCCCCCccc
Q 039716          602 GIPENALPTLFRKYMQVSADHARKYGGTGLGLAICKQLVELMGGRLTVTSKVHCGSTFTFILPYQVSPIEENSDDPDDLS  681 (1002)
Q Consensus       602 GI~~e~l~~IF~pF~q~~~~~~~~~~GtGLGLaI~k~Lve~~gG~I~v~S~~g~GTtF~~~LP~~~~~~~~~~~~~~~l~  681 (1002)
                      ||+++.+++||+|||+.+.      +|+||||+|||++|+.|||+|+++|.+|+||+|+|+||........    +.   
T Consensus       618 GI~~e~~~~iFe~F~~~~~------~G~GLGL~i~~~iv~~~gG~i~v~s~~g~Gt~f~i~LP~~~~~~~~----~~---  684 (828)
T PRK13837        618 GIDEAVLPHIFEPFFTTRA------GGTGLGLATVHGIVSAHAGYIDVQSTVGRGTRFDVYLPPSSKVPVA----PQ---  684 (828)
T ss_pred             CCCHHHHHHhhCCcccCCC------CCCcchHHHHHHHHHHCCCEEEEEecCCCeEEEEEEEeCCCCCCCC----cc---
Confidence            9999999999999997532      7999999999999999999999999999999999999974211000    00   


Q ss_pred             cccccCCcccccccccccccccccccccccCCcccccccccccccccccccccCccccccCCCCCcccccccchhhhccH
Q 039716          682 DMADQDSVTDDVTAGFFQFQPRTLGSLFSSNGTSRSKKLLPNSIGFASAHKVNGFSETSYSFPSNNRQKETAPLEDACSV  761 (1002)
Q Consensus       682 ~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  761 (1002)
                                                                                                      
T Consensus       685 --------------------------------------------------------------------------------  684 (828)
T PRK13837        685 --------------------------------------------------------------------------------  684 (828)
T ss_pred             --------------------------------------------------------------------------------
Confidence                                                                                            


Q ss_pred             HHHHhhhCCCCCCCCCCCCCCcchhhcccccccccccccccCCCCCccchhhhhHHHhhcccCCCchhhhhhccCCCccc
Q 039716          762 AEVAETLSEPESSFSHSPEPENETEVSRGKQCHVETTSWFQNPATESTSHSEANREMIQTSKTNEPQKICEMQEKPDRIS  841 (1002)
Q Consensus       762 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  841 (1002)
                                 .  ..                                                                
T Consensus       685 -----------~--~~----------------------------------------------------------------  687 (828)
T PRK13837        685 -----------A--FF----------------------------------------------------------------  687 (828)
T ss_pred             -----------c--cC----------------------------------------------------------------
Confidence                       0  00                                                                


Q ss_pred             CCCCCCCCCCCCCCCCCCCeEEEEecCHHHHHHHHHHHHhcCCeEEEEcCHHHHHHHHHcC--CCcEEEEcCCCCCCCHH
Q 039716          842 QSPSSSSAEVPETKPKPKPKILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQ--NYDLILMDVCMPVMDGL  919 (1002)
Q Consensus       842 ~~~~~~~~~~~~~~~~~~~~ILiVeDn~~n~~~l~~~L~~~g~~v~~a~~G~eAl~~~~~~--~~DlIlmDi~MP~mdG~  919 (1002)
                           ....   .....+.+||||||++.++..+...|...||.+..+.++.+|++.+...  .||+||+  .||.|+|+
T Consensus       688 -----~~~~---~~~~~~~~ILvVddd~~~~~~l~~~L~~~G~~v~~~~s~~~al~~l~~~~~~~DlVll--~~~~~~g~  757 (828)
T PRK13837        688 -----GPGP---LPRGRGETVLLVEPDDATLERYEEKLAALGYEPVGFSTLAAAIAWISKGPERFDLVLV--DDRLLDEE  757 (828)
T ss_pred             -----CCcc---cCCCCCCEEEEEcCCHHHHHHHHHHHHHCCCEEEEeCCHHHHHHHHHhCCCCceEEEE--CCCCCCHH
Confidence                 0000   0002345899999999999999999999999999999999999998754  4899999  79999999


Q ss_pred             HHHHHHhccccCCCchhhhhhhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHHh
Q 039716          920 KATRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQ  999 (1002)
Q Consensus       920 e~~~~IR~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~  999 (1002)
                      ++++.|+..                          .+.+|||++|++........++.+| ++||.||++..+|...|.+
T Consensus       758 ~l~~~l~~~--------------------------~~~ipIIvls~~~~~~~~~~~~~~G-~d~L~KP~~~~~L~~~l~~  810 (828)
T PRK13837        758 QAAAALHAA--------------------------APTLPIILGGNSKTMALSPDLLASV-AEILAKPISSRTLAYALRT  810 (828)
T ss_pred             HHHHHHHhh--------------------------CCCCCEEEEeCCCchhhhhhHhhcc-CcEEeCCCCHHHHHHHHHH
Confidence            999999852                          3568999999999999999999999 9999999999999999987


Q ss_pred             hc
Q 039716         1000 YF 1001 (1002)
Q Consensus      1000 ~l 1001 (1002)
                      ++
T Consensus       811 ~l  812 (828)
T PRK13837        811 AL  812 (828)
T ss_pred             HH
Confidence            64

>KOG0519 consensus Sensory transduction histidine kinase [Signal transduction mechanisms]

Probab=100.00  E-value=6.9e-44  Score=439.63  Aligned_cols=534  Identities=32%  Similarity=0.430  Sum_probs=328.5

Q ss_pred             HHHHhhhccccHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCeeeEeeecCHHHHHHHH
Q 039716          373 MLATMSHEIRSPLTGVVSMAEILSNTKLDREQRQLLGVMISSGDLVLQLINDILDLSKVESGVMKLEAAKFRPREVVKHV  452 (1002)
Q Consensus       373 fla~iSHELRTPL~~I~g~~elL~~~~l~~~~~~~l~~i~~s~~~L~~LIndlLd~skiesg~~~l~~~~~~l~~li~~v  452 (1002)
                      |+++++||||+||++  |+...+..+..+.+++.++.....++..++.++++++|.+++++|.+.+...+|++..++..+
T Consensus       224 ~~~~~sHeir~p~~~--~~~~~~~~t~~~~~~~~~~~~~~~~~~~~~s~ln~i~d~~~v~~g~~~l~~~rf~l~~ll~~~  301 (786)
T KOG0519|consen  224 FLATLSHEIRTPLNG--GMLGGLSDTDLDSDQRLILNTDRVSAKSLLSLLNDILDLSKVESGKGELVAKRFDLRTLLNFV  301 (786)
T ss_pred             hcccccceeeccccc--CcceEEeccccchHHHHHHHHHhhhccccchhHHHhhcccccccccceeeeeecchHhhhhhh
Confidence            999999999999998  777777788889999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHh-hcceeccccCCCCCeeEEccHHHHHHHHHHHHhhhhhcCCCCeeEEEEEecCCCCcccchhhhhhhhhhc
Q 039716          453 LQTAAASLQ-KILMLEGDIADDVPIEVIGDVLRIRQILTNLISNAIKFTPEGKVGIKLYVVPEPPFAKEGLKQKSKAYQS  531 (1002)
Q Consensus       453 ~~~~~~~~~-k~i~l~~~i~~~~p~~v~gD~~rL~QIL~NLlsNAIKfT~~G~I~I~v~~~~~~~~~~~~~~~~~~~~~~  531 (1002)
                      ++.+..... +...+....+...|..+.+|..+++||+.|+++||||||..|.+.+++.............         
T Consensus       302 ~~~~~e~~~~~~~~l~~~~~~~~p~~v~~de~~~~qv~~n~v~naik~t~~~~i~~~~~~~~~~~~~~~~l---------  372 (786)
T KOG0519|consen  302 ISLLSELSQAKYAILVLDLSSGVPRNVRGDEARLRQVIANLVSNAIKFTHAGHLEESVIAREELSESNDVL---------  372 (786)
T ss_pred             hhhhHHHhhcCCeEEEEecCCCCcceeeccceeeeeeehhhccceecccccceEEEEEEeehhcchhhHHH---------
Confidence            988776655 5566666666667888999999999999999999999999999988887655433221110         


Q ss_pred             chhhhhhhccCCCCCccCCCCCCCCCCCCCCccCCCCCCCCCCCccCCCCCccccccceEEEEEEEecCCCCCcCcHhh-
Q 039716          532 ATDAVKEEKHQPKSQTASDQNGFHDKKHGEGYQDHKHDDDPGTPVSHGNSMDEDLEATVWIRCDVYDTGIGIPENALPT-  610 (1002)
Q Consensus       532 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~i~V~DtGiGI~~e~l~~-  610 (1002)
                        ...+.+.+...........-   ..++       ........+....       ......+.+.|+|.||+...... 
T Consensus       373 --~~~~~e~~~~~~~~~~~~~~---~~~~-------~~~~~~~~i~~~~-------~l~~~~~~~~~~~~~i~~~~~~~~  433 (786)
T KOG0519|consen  373 --LRAKEEAHMAGKARIDFLQK---MSHA-------MRAPRHNIISLLS-------LLLQDIVLSPDSGLEIQTVMRSSN  433 (786)
T ss_pred             --HhhhhhhhhccchhhhHHHH---hccc-------cccccccccccch-------hhHhheEeccCCceeEehhhhhhh
Confidence              00000000000000000000   0000       0000000000000       01123466899999999999988 


Q ss_pred             hhhhccCCCccccCcCCCccccHHHHHHHHHHhCCEEEEEeecCCceEEEEEEeCCCCCCCCCCCCCCc-cc---ccccc
Q 039716          611 LFRKYMQVSADHARKYGGTGLGLAICKQLVELMGGRLTVTSKVHCGSTFTFILPYQVSPIEENSDDPDD-LS---DMADQ  686 (1002)
Q Consensus       611 IF~pF~q~~~~~~~~~~GtGLGLaI~k~Lve~~gG~I~v~S~~g~GTtF~~~LP~~~~~~~~~~~~~~~-l~---~~~~~  686 (1002)
                      +|.+|.++..+.++.++|+|+|+.||+.++++|+|.+.+.+....|++|+|.+++..........+... ..   ++...
T Consensus       434 ~~~~~~q~~~~~~~~~~gt~~~~~i~~~l~~l~~~~~~~~~~~~~~~t~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~  513 (786)
T KOG0519|consen  434 VFTSLIQADPDITRLYGGTGLGESIVFSLVELMSGEISDISCISLGKTFSFTLDLLTNLPKSVVGDEKRLFQIILDFNGM  513 (786)
T ss_pred             HHHHHhccccccccccCCCcccchhhccHHHHHHHHhhhhhhhccCceeeEEEEeccCCCccchhhhhhhhhhhhhhcch
Confidence            999999999999999999999999999999999999999999999999999999865432222111111 00   00000


Q ss_pred             CCcccccccc---cccccccccccccccCCcccccccccccccc---cccccccCccccccCCCCCcccccccchhhhcc
Q 039716          687 DSVTDDVTAG---FFQFQPRTLGSLFSSNGTSRSKKLLPNSIGF---ASAHKVNGFSETSYSFPSNNRQKETAPLEDACS  760 (1002)
Q Consensus       687 ~~~~~~~~~~---~~~~~~~~~~s~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  760 (1002)
                      .+...+...+   .+++.+..++........ ............   ..........            .. ....+...
T Consensus       514 ~~~~~~~~~~~~~~~~~~~~~~~~~vd~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~------------~~-~~~~~~s~  579 (786)
T KOG0519|consen  514 LALLIDTKLGREQIFQVLAELLGISVDVSLS-LSLAFWFLDLSLSDLEVCKQIEDNE------------EG-SNNGDISS  579 (786)
T ss_pred             hhhhhccccCcceeEEEEecccCcccccccc-chhhhhhcccccccchheEEeeecc------------cc-ccCCCcch
Confidence            0000000000   112211111100000000 000000000000   0000000000            00 00000000


Q ss_pred             HHHHHhhhCC--------CCCCCCCCCCCCcchhhcccccccccccccccCCCCCccchhhhhHHHhhcccCCCchhhhh
Q 039716          761 VAEVAETLSE--------PESSFSHSPEPENETEVSRGKQCHVETTSWFQNPATESTSHSEANREMIQTSKTNEPQKICE  832 (1002)
Q Consensus       761 ~~~~~~~~~~--------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  832 (1002)
                      ..........        ...+...++...  ....        ...++..+...                .......+-
T Consensus       580 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~--------~~~~~~~~~~~----------------~~~~~s~~~  633 (786)
T KOG0519|consen  580 SNPLHKSLRDLTSKLSSGSGLSLALCPENS--QLME--------GNIGLVPSSDG----------------LPKSPSLCL  633 (786)
T ss_pred             hhhhhhccccchhhcccccccccccchhhH--Hhhh--------ccccccccccc----------------CCccHHHHH
Confidence            0000000000        000000000000  0000        00000000000                000000000


Q ss_pred             hccCCC---cccCCCCCCC---CCCCCCCCCCCCeEEEEecCHHHHHHHHHHHHhcCCeEEEEcCHHHHHHHHH-cCCCc
Q 039716          833 MQEKPD---RISQSPSSSS---AEVPETKPKPKPKILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQ-CQNYD  905 (1002)
Q Consensus       833 ~~~~~~---~~~~~~~~~~---~~~~~~~~~~~~~ILiVeDn~~n~~~l~~~L~~~g~~v~~a~~G~eAl~~~~-~~~~D  905 (1002)
                      ......   ......+...   ..........+++|||||||++|+++.+.||+++|+.++.+.+|.||+++++ .+.||
T Consensus       634 ~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~l~g~~iLlvddn~vn~~Va~~~l~~~g~~~~~~~sg~e~l~~~~~~~~y~  713 (786)
T KOG0519|consen  634 EACLRVELNSMGSKLSGNPEKLAEPRDSKLLTGPKILLVDDNPVNRKVATGMLKKLGAEVTEVNSGQEALDKLKPPHSYD  713 (786)
T ss_pred             HhhccccccccccccCCCcccccCccccccccCCceEEEecccchHHHHHHHHHHhCCeeEeecCcHHHHHhcCCCCccc
Confidence            000000   0000000000   0001222346789999999999999999999999999999999999999998 78899


Q ss_pred             EEEEcCCCCCCCHHHHHHHHhccccCCCchhhhhhhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEe
Q 039716          906 LILMDVCMPVMDGLKATRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVS  985 (1002)
Q Consensus       906 lIlmDi~MP~mdG~e~~~~IR~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~  985 (1002)
                      +||||++||+|||+|++++||+.+.                         .++|||||||++.++..++|++.|||+||+
T Consensus       714 ~ifmD~qMP~mDG~e~~~~irk~~~-------------------------~~~pIvAlTa~~~~~~~~~c~~~Gmd~yl~  768 (786)
T KOG0519|consen  714 VIFMDLQMPEMDGYEATREIRKKER-------------------------WHLPIVALTADADPSTEEECLEVGMDGYLS  768 (786)
T ss_pred             EEEEEcCCcccchHHHHHHHHHhhc-------------------------CCCCEEEEecCCcHHHHHHHHHhCCceEEc
Confidence            9999999999999999999998652                         579999999999999999999999999999


Q ss_pred             CCCChHHHHHHHHhhc
Q 039716          986 KPVTFQKLKECLEQYF 1001 (1002)
Q Consensus       986 KP~~~~~L~~~l~~~l 1001 (1002)
                      |||+.+.|..+|.+++
T Consensus       769 KP~~~~~l~~~l~~~~  784 (786)
T KOG0519|consen  769 KPFTLEKLVKILREFL  784 (786)
T ss_pred             ccccHHHHHHHHHHHh
Confidence            9999999999999986

>COG2205 KdpD Osmosensitive K+ channel histidine kinase [Signal transduction mechanisms]

Probab=100.00  E-value=1.3e-37  Score=362.32  Aligned_cols=218  Identities=32%  Similarity=0.520  Sum_probs=189.5

Q ss_pred             HHHHHHhhhccccHHHHHHHHHHHHhCC--CCCHH-HHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCeeeEeeecCHHH
Q 039716          371 KQMLATMSHEIRSPLTGVVSMAEILSNT--KLDRE-QRQLLGVMISSGDLVLQLINDILDLSKVESGVMKLEAAKFRPRE  447 (1002)
Q Consensus       371 k~fla~iSHELRTPL~~I~g~~elL~~~--~l~~~-~~~~l~~i~~s~~~L~~LIndlLd~skiesg~~~l~~~~~~l~~  447 (1002)
                      ..|+++|||||||||++|+|.++.|...  .++++ +.+++..|...+++|..+|++|||++|+++|.+++...+..+.+
T Consensus       661 saLL~sISHDLRTPLt~i~Gaa~tL~~~~~~l~~~~~aeLl~~I~ees~~L~rlV~NLLdmTRi~sG~~~l~~~~~~veE  740 (890)
T COG2205         661 SALLASISHDLRTPLTAIMGAAETLLLDGEALSPEDRAELLSSIREESERLTRLVTNLLDMTRLQSGGVNLKLDWVLVEE  740 (890)
T ss_pred             HHHHHHhhccccCcHHHHhhhHHHhhhcccccCcHhHHHHHHHHHHHHHHHHHHHHHHHhHHHHhcCCcccccchhhHHH
Confidence            4799999999999999999999988653  45555 67899999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHhhcceeccccCCCCCeeEEccHHHHHHHHHHHHhhhhhcCCCCe-eEEEEEecCCCCcccchhhhhh
Q 039716          448 VVKHVLQTAAASLQKILMLEGDIADDVPIEVIGDVLRIRQILTNLISNAIKFTPEGK-VGIKLYVVPEPPFAKEGLKQKS  526 (1002)
Q Consensus       448 li~~v~~~~~~~~~k~i~l~~~i~~~~p~~v~gD~~rL~QIL~NLlsNAIKfT~~G~-I~I~v~~~~~~~~~~~~~~~~~  526 (1002)
                      ++.+++..+...... ..+...++.+++ .+..|...|.|||.|||.||+||+|.|. |.|.+....             
T Consensus       741 vVg~Al~r~~k~~~~-~~i~v~~~~dl~-li~~D~~LieQVLiNLleNA~Kyap~~s~I~I~~~~~~-------------  805 (890)
T COG2205         741 VVGEALQRLRKRFTG-HKIVVSVPVDLP-LIHVDSPLIEQVLINLLENALKYAPPGSEIRINAGVER-------------  805 (890)
T ss_pred             HHHHHHHHhhhhcCC-ceEEEecCCCCc-eEecCHHHHHHHHHHHHHHHHhhCCCCCeEEEEEEEec-------------
Confidence            999988876655432 225556667766 5899999999999999999999999875 777765321             


Q ss_pred             hhhhcchhhhhhhccCCCCCccCCCCCCCCCCCCCCccCCCCCCCCCCCccCCCCCccccccceEEEEEEEecCCCCCcC
Q 039716          527 KAYQSATDAVKEEKHQPKSQTASDQNGFHDKKHGEGYQDHKHDDDPGTPVSHGNSMDEDLEATVWIRCDVYDTGIGIPEN  606 (1002)
Q Consensus       527 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~i~V~DtGiGI~~e  606 (1002)
                                                                                     ..+.|+|.|+|+|||++
T Consensus       806 ---------------------------------------------------------------~~v~~~V~DeGpGIP~~  822 (890)
T COG2205         806 ---------------------------------------------------------------ENVVFSVIDEGPGIPEG  822 (890)
T ss_pred             ---------------------------------------------------------------ceEEEEEEeCCCCCChh
Confidence                                                                           24889999999999999


Q ss_pred             cHhhhhhhccCCCccccCcCCCccccHHHHHHHHHHhCCEEEEEeecCCceEEEEEEeCCCC
Q 039716          607 ALPTLFRKYMQVSADHARKYGGTGLGLAICKQLVELMGGRLTVTSKVHCGSTFTFILPYQVS  668 (1002)
Q Consensus       607 ~l~~IF~pF~q~~~~~~~~~~GtGLGLaI~k~Lve~~gG~I~v~S~~g~GTtF~~~LP~~~~  668 (1002)
                      .+++||++||+......  ..|+|||||||+.||+.|||+|++.+.+++|++|+|+||....
T Consensus       823 ~~~~IFD~F~r~~~~~~--~~G~GLGLsIc~~iv~ahgG~I~a~~~~~gGa~f~~~LP~~~~  882 (890)
T COG2205         823 ELERIFDKFYRGNKESA--TRGVGLGLAICRGIVEAHGGTISAENNPGGGAIFVFTLPVEED  882 (890)
T ss_pred             HHHHhhhhhhcCCCCCC--CCCccccHHHHHHHHHHcCCeEEEEEcCCCceEEEEEeecCCC
Confidence            99999999999876433  6799999999999999999999999999999999999998654

>PRK11006 phoR phosphate regulon sensor protein; Provisional

Probab=100.00  E-value=2.2e-38  Score=372.17  Aligned_cols=330  Identities=23%  Similarity=0.317  Sum_probs=250.8

Q ss_pred             HHHHHHHHHHHHHHhccCcEEEEecccccEEEeeccC---CCCCcccccCCCchhccCccchhhhhHHHHHHHHhCCCcc
Q 039716          215 QILKRADNFLHFVLQNAPVVMGHQDKELRYRFIYNHF---PSLHEEDILGKTDVEIFSGAGVKESQDFKREVLEKGLPAK  291 (1002)
Q Consensus       215 ~~l~~~~~~l~~il~~~p~~i~~~d~~~~~~~~~~~~---~~~~~e~iiGk~~~e~~~~~~~~~~~~~~~~vl~~g~~~~  291 (1002)
                      +.+++...+++.+++++|.+++..|.++++.++|..+   .|+..++++|++..+++.....      . ..+.... ..
T Consensus        91 ~~l~~~~~~~~~~~~~~~~~i~~~d~~g~i~~~N~~a~~l~g~~~~~~~g~~~~~~~~~~~~------~-~~~~~~~-~~  162 (430)
T PRK11006         91 RELGNLIKRFRSGAESLPDAVVLTTEEGNIFWCNGLAQQLLGFRWPEDNGQNILNLLRYPEF------T-QYLKTRD-FS  162 (430)
T ss_pred             HHHHHHHHHHHHHHHhCCCeEEEEcCCCceeHHHHHHHHHhCCCChHhCCCcHHHHhcCHHH------H-HHHHhcc-cC
Confidence            3455556778899999999999999999999998754   5777788899988877653211      1 1122211 11


Q ss_pred             eeEEEEEeecCceEEEEEEeeeecCCCCEEEEEEEeechhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 039716          292 REITFETELFGSKTFLIYVEPVFSKSGETIGVNYMGMDVTDQVRKREKMAKLREEIAVQKAKETELNKTIHITEETMRAK  371 (1002)
Q Consensus       292 ~e~~~~~~~~~~~~~~~~~~p~~~~~G~~~gi~~~~~DITe~~~~~~~~~~l~~el~~~~~~~~el~k~~~~~e~~~~~k  371 (1002)
                      ....+.  .....++.+...|..+  +   +++.+..|||+..+.++                              ..+
T Consensus       163 ~~~~~~--~~~~~~~~~~~~~~~~--~---~~~~~~~dit~~~~~e~------------------------------~~~  205 (430)
T PRK11006        163 RPLTLV--LNNGRHLEIRVMPYTE--G---QLLMVARDVTQMHQLEG------------------------------ARR  205 (430)
T ss_pred             CCeEEE--cCCCCEEEEEEEEcCC--C---cEEEEEehhhHHHHHHH------------------------------HHH
Confidence            122222  2334455566666542  2   24567899997532211                              013


Q ss_pred             HHHHHhhhccccHHHHHHHHHHHHhCCCC-CHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCeeeEeeecCHHHHHH
Q 039716          372 QMLATMSHEIRSPLTGVVSMAEILSNTKL-DREQRQLLGVMISSGDLVLQLINDILDLSKVESGVMKLEAAKFRPREVVK  450 (1002)
Q Consensus       372 ~fla~iSHELRTPL~~I~g~~elL~~~~l-~~~~~~~l~~i~~s~~~L~~LIndlLd~skiesg~~~l~~~~~~l~~li~  450 (1002)
                      +|++++||||||||++|.|++++|..... ++....+++.|..++++|..++++++++++++.+........+++..+++
T Consensus       206 ~~~~~isHelrtPL~~i~~~~~~l~~~~~~~~~~~~~l~~i~~~~~~l~~li~~ll~~~r~~~~~~~~~~~~~~~~~~~~  285 (430)
T PRK11006        206 NFFANVSHELRTPLTVLQGYLEMMQDQPLEGALREKALHTMREQTQRMEGLVKQLLTLSKIEAAPTIDLNEKVDVPMMLR  285 (430)
T ss_pred             HHHHHhHHHhcchHHHHHHHHHHHhcCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCcccCCccCHHHHHH
Confidence            69999999999999999999999876543 45567789999999999999999999999999887766667888888888


Q ss_pred             HHHHHHHHHHhhcceeccccCCCCCeeEEccHHHHHHHHHHHHhhhhhcCCCC-eeEEEEEecCCCCcccchhhhhhhhh
Q 039716          451 HVLQTAAASLQKILMLEGDIADDVPIEVIGDVLRIRQILTNLISNAIKFTPEG-KVGIKLYVVPEPPFAKEGLKQKSKAY  529 (1002)
Q Consensus       451 ~v~~~~~~~~~k~i~l~~~i~~~~p~~v~gD~~rL~QIL~NLlsNAIKfT~~G-~I~I~v~~~~~~~~~~~~~~~~~~~~  529 (1002)
                      .+...+.....+.+.+....++.  ..+.+|+.+|.|||.||++||+||+++| .|.|.+...                 
T Consensus       286 ~l~~~~~~~~~~~~~i~~~~~~~--~~i~~d~~~l~~vl~NLl~NAik~~~~~~~I~i~~~~~-----------------  346 (430)
T PRK11006        286 VLEREAQTLSQGKHTITFEVDNS--LKVFGNEDQLRSAISNLVYNAVNHTPEGTHITVRWQRV-----------------  346 (430)
T ss_pred             HHHHHHHHHhcCCcEEEEecCCC--ceEEECHHHHHHHHHHHHHHHHhcCCCCCeEEEEEEEc-----------------
Confidence            77665554445555565555444  3588999999999999999999999865 565554311                 


Q ss_pred             hcchhhhhhhccCCCCCccCCCCCCCCCCCCCCccCCCCCCCCCCCccCCCCCccccccceEEEEEEEecCCCCCcCcHh
Q 039716          530 QSATDAVKEEKHQPKSQTASDQNGFHDKKHGEGYQDHKHDDDPGTPVSHGNSMDEDLEATVWIRCDVYDTGIGIPENALP  609 (1002)
Q Consensus       530 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~i~V~DtGiGI~~e~l~  609 (1002)
                                                                                 ...+.|+|.|+|+|||++.++
T Consensus       347 -----------------------------------------------------------~~~~~i~V~D~G~Gi~~~~~~  367 (430)
T PRK11006        347 -----------------------------------------------------------PQGAEFSVEDNGPGIAPEHIP  367 (430)
T ss_pred             -----------------------------------------------------------CCEEEEEEEEcCCCCCHHHHH
Confidence                                                                       113789999999999999999


Q ss_pred             hhhhhccCCCccccCcCCCccccHHHHHHHHHHhCCEEEEEeecCCceEEEEEEeCCC
Q 039716          610 TLFRKYMQVSADHARKYGGTGLGLAICKQLVELMGGRLTVTSKVHCGSTFTFILPYQV  667 (1002)
Q Consensus       610 ~IF~pF~q~~~~~~~~~~GtGLGLaI~k~Lve~~gG~I~v~S~~g~GTtF~~~LP~~~  667 (1002)
                      +||+|||+.+...+++.+|+||||+|||++|+.|||+|+++|.+|+||+|+|+||...
T Consensus       368 ~if~~f~~~~~~~~~~~~G~GLGL~ivk~iv~~~gG~i~i~s~~~~Gt~f~i~lP~~~  425 (430)
T PRK11006        368 RLTERFYRVDKARSRQTGGSGLGLAIVKHALSHHDSRLEIESEVGKGTRFSFVLPERL  425 (430)
T ss_pred             HhccCcccccCCCCCCCCCCchHHHHHHHHHHHCCCEEEEEecCCCceEEEEEechHh
Confidence            9999999987766667789999999999999999999999999999999999999753

>TIGR02938 nifL_nitrog nitrogen fixation negative regulator NifL

Probab=100.00  E-value=5.8e-38  Score=372.71  Aligned_cols=360  Identities=16%  Similarity=0.241  Sum_probs=249.1

Q ss_pred             HHHHHHHhccCcEEEEecccccEEEeeccC---CCCCcccccCCCchhccCccchhhhhHHHHHHHHhCCCcceeEEEEE
Q 039716          222 NFLHFVLQNAPVVMGHQDKELRYRFIYNHF---PSLHEEDILGKTDVEIFSGAGVKESQDFKREVLEKGLPAKREITFET  298 (1002)
Q Consensus       222 ~~l~~il~~~p~~i~~~d~~~~~~~~~~~~---~~~~~e~iiGk~~~e~~~~~~~~~~~~~~~~vl~~g~~~~~e~~~~~  298 (1002)
                      ..++.+++++|.+++..|.++++.++|..+   .|+++++++|++...+................+..+.+...++....
T Consensus         4 ~~~~~i~~~~~~~i~~~d~~g~~~~~N~~~~~~~G~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   83 (494)
T TIGR02938         4 EAYRQTVDQAPLAISITDLKANILYANDAFTRITGYTKEEIIGKNESVLSNHTTPPEVYQALWGSLAEQKPWAGKLLNRR   83 (494)
T ss_pred             HHHHHHHHhCCceEEEECCCCcEEEEchhheeecCCCHHHHhCCCchhhcCCCCCHHHHHHHHHHHHhCCcccceeeccC
Confidence            467889999999999999999999998765   57788999999876655443333222223334444555444443333


Q ss_pred             eecCceEEEEEEeeeecCCCCEEEEEEEeechhHHHHHHHHHHHHHHHHH------------------------------
Q 039716          299 ELFGSKTFLIYVEPVFSKSGETIGVNYMGMDVTDQVRKREKMAKLREEIA------------------------------  348 (1002)
Q Consensus       299 ~~~~~~~~~~~~~p~~~~~G~~~gi~~~~~DITe~~~~~~~~~~l~~el~------------------------------  348 (1002)
                      ..+...++.....|+++.+|.+.|+++++.|||++++.++++......++                              
T Consensus        84 ~~g~~~~~~~~~~~~~~~~g~~~~~~~~~~DIt~~k~~e~~l~~~~~~~~~~~~~~~~~i~~~d~~~~i~~~N~~~~~~~  163 (494)
T TIGR02938        84 KDGELYLAELTVAPVLNEAGETTHFLGMHRDITELHRLEQVVANQKLLIESVVDAAPVAFVLLDPTGRVILDNQEYKKLA  163 (494)
T ss_pred             CCccchhhheeeEEEECCCCCEEEEEEehhhhhHHHHHHHHHHHHHHHHHHHHhcccceEEEEcCCCCEEEechhHHHhh
Confidence            33333444577889999999999999999999998877655432211000                              


Q ss_pred             --------------------------------------------------------------------------------
Q 039716          349 --------------------------------------------------------------------------------  348 (1002)
Q Consensus       349 --------------------------------------------------------------------------------  348 (1002)
                                                                                                      
T Consensus       164 g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  243 (494)
T TIGR02938       164 TDLRVKEPAHTVLDLLREAWREALAENWPQQLAFSNREARFDRGGGRPARWLSCTGSVIGMESDCADSFFCAAEQPYLLL  243 (494)
T ss_pred             chhhhhHHHHHHHHHhhHHhhhhhhhcchhhhccccceeeeccCCCceeeEEEecCceEEeecchhhheeccCCCchhee
Confidence                                                                                            


Q ss_pred             ------HHHHHHHHHH-----HHHHHHHHHHHHHHHHHHhhhccccHHHHHHHHHHHHhCCCCC---HHHHHHHHHHHHH
Q 039716          349 ------VQKAKETELN-----KTIHITEETMRAKQMLATMSHEIRSPLTGVVSMAEILSNTKLD---REQRQLLGVMISS  414 (1002)
Q Consensus       349 ------~~~~~~~el~-----k~~~~~e~~~~~k~fla~iSHELRTPL~~I~g~~elL~~~~l~---~~~~~~l~~i~~s  414 (1002)
                            .+++.++++.     ......+...+.+++++.++|||||||++|.|++++|.....+   +.....+..+...
T Consensus       244 ~~~DITe~k~~ee~l~~~al~~~~~~~~~~~~l~~~~~~~~h~lr~pL~~i~~~~~~l~~~~~~~~~~~~~~~~~~~~~~  323 (494)
T TIGR02938       244 TIADISNLREEQERARLSALQALMAEEERLEAIRETLSAAIHRLQGPMNLISAAISVLQRRGDDAGNPASAAMLQQALSA  323 (494)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcHHHHHHHHHHHHHhccccccCHHHHHHHHHHHHH
Confidence                  0000000000     0000011122234678899999999999999999998764332   3334444444444


Q ss_pred             HHHHHHHHHHHHHHHhhhcCCeeeEeeecCHHHHHHHHHHHHHHHH-hhcceeccccCCCCCeeEEccHHHHHHHHHHHH
Q 039716          415 GDLVLQLINDILDLSKVESGVMKLEAAKFRPREVVKHVLQTAAASL-QKILMLEGDIADDVPIEVIGDVLRIRQILTNLI  493 (1002)
Q Consensus       415 ~~~L~~LIndlLd~skiesg~~~l~~~~~~l~~li~~v~~~~~~~~-~k~i~l~~~i~~~~p~~v~gD~~rL~QIL~NLl  493 (1002)
                      +..+...+.++++.      .......+|++..++++++..+...+ .+++.+.......++ .+.+|+.+|+|||.||+
T Consensus       324 ~~~~~~~l~~~~~~------~~~~~~~~~dl~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~-~v~~d~~~l~~vl~Nl~  396 (494)
T TIGR02938       324 GREHMEALRQVIPQ------SPQEIVVPVNLNQILRDVITLSTPRLLAAGIVVDWQPAATLP-AILGRELQLRSLFKALV  396 (494)
T ss_pred             HHHHHHHHHHhhcc------CcccccccccHHHHHHHHHHHhHHHHHhCCCEEEEecCCCCC-eeecCHHHHHHHHHHHH
Confidence            44444444444332      23344578999999999988776544 466777766665555 58899999999999999


Q ss_pred             hhhhhcCCCCe---eEEEEEecCCCCcccchhhhhhhhhhcchhhhhhhccCCCCCccCCCCCCCCCCCCCCccCCCCCC
Q 039716          494 SNAIKFTPEGK---VGIKLYVVPEPPFAKEGLKQKSKAYQSATDAVKEEKHQPKSQTASDQNGFHDKKHGEGYQDHKHDD  570 (1002)
Q Consensus       494 sNAIKfT~~G~---I~I~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  570 (1002)
                      +||+||++.|.   ..|.+....                                                         
T Consensus       397 ~NAik~~~~~~~~~~~i~i~~~~---------------------------------------------------------  419 (494)
T TIGR02938       397 DNAIEAMNIKGWKRRELSITTAL---------------------------------------------------------  419 (494)
T ss_pred             HHHHHHhhccCCCcceEEEEEEe---------------------------------------------------------
Confidence            99999997652   223332110                                                         


Q ss_pred             CCCCCccCCCCCccccccceEEEEEEEecCCCCCcCcHhhhhhhccCCCccccCcCCCccccHHHHHHHHHHhCCEEEEE
Q 039716          571 DPGTPVSHGNSMDEDLEATVWIRCDVYDTGIGIPENALPTLFRKYMQVSADHARKYGGTGLGLAICKQLVELMGGRLTVT  650 (1002)
Q Consensus       571 ~~~~~~~~~~~~~~~~~~~~~l~i~V~DtGiGI~~e~l~~IF~pF~q~~~~~~~~~~GtGLGLaI~k~Lve~~gG~I~v~  650 (1002)
                                       ...++.|+|.|||+|||++.+.+||+|||+++...   ++||||||+|||+||+.|||+|+|+
T Consensus       420 -----------------~~~~~~~~V~D~G~Gi~~~~~~~iF~~f~~~~~~~---~~G~GlGL~i~~~iv~~~gG~i~~~  479 (494)
T TIGR02938       420 -----------------NGDLIVVSILDSGPGIPQDLRYKVFEPFFTTKGGS---RKHIGMGLSVAQEIVADHGGIIDLD  479 (494)
T ss_pred             -----------------cCCEEEEEEEeCCCCCCHHHHHHhcCCCcccCCCC---CCCCcccHHHHHHHHHHcCCEEEEE
Confidence                             11257899999999999999999999999876432   5799999999999999999999999


Q ss_pred             eecCCceEEEEEEeC
Q 039716          651 SKVHCGSTFTFILPY  665 (1002)
Q Consensus       651 S~~g~GTtF~~~LP~  665 (1002)
                      |.+|+||+|+|+||+
T Consensus       480 s~~~~G~~f~i~lp~  494 (494)
T TIGR02938       480 DDYSEGCRIIVEFRV  494 (494)
T ss_pred             ECCCCCEEEEEEecC
Confidence            999999999999995

NifL is a modulator of the nitrogen fixation positive regulator protein NifA, and is therefore a negative regulator. It binds NifA. NifA and NifL are encoded by adjacent genes.

>COG3852 NtrB Signal transduction histidine kinase, nitrogen specific [Signal transduction mechanisms]

Probab=100.00  E-value=1.7e-35  Score=309.72  Aligned_cols=337  Identities=23%  Similarity=0.324  Sum_probs=256.3

Q ss_pred             HHHhccCcEEEEecccccEEEeecc---CCCCCcccccCCCchhccCccchhhhhHHHHHHHHhCCCc-ceeEEEEEeec
Q 039716          226 FVLQNAPVVMGHQDKELRYRFIYNH---FPSLHEEDILGKTDVEIFSGAGVKESQDFKREVLEKGLPA-KREITFETELF  301 (1002)
Q Consensus       226 ~il~~~p~~i~~~d~~~~~~~~~~~---~~~~~~e~iiGk~~~e~~~~~~~~~~~~~~~~vl~~g~~~-~~e~~~~~~~~  301 (1002)
                      .++++.+-.+...|.++++.|+|..   |++.+..-+.|.+..++++..  .....+.+++.+.+.+. .+++++. ..+
T Consensus        11 ~~Ln~~~~pVl~vd~~~~i~yaN~aAe~~~~~Sa~~L~~~~l~~l~~~g--s~ll~ll~q~~~~~~~~~~~~v~l~-~~g   87 (363)
T COG3852          11 AILNNLINPVLLVDDELAIHYANPAAEQLLAVSARRLAGTRLSELLPFG--SLLLSLLDQVLERGQPVTEYEVTLV-ILG   87 (363)
T ss_pred             hHHhccCCceEEEcCCCcEEecCHHHHHHHHHHHHHHhcCChHHHcCCC--cHHHHHHHHHHHhcCCcccceeeee-ecC
Confidence            5788888888888999999999864   445555667788777777643  23455677888888764 4566665 566


Q ss_pred             CceEEEEEEeeeecCCCCEEEEEEEeechhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcc
Q 039716          302 GSKTFLIYVEPVFSKSGETIGVNYMGMDVTDQVRKREKMAKLREEIAVQKAKETELNKTIHITEETMRAKQMLATMSHEI  381 (1002)
Q Consensus       302 ~~~~~~~~~~p~~~~~G~~~gi~~~~~DITe~~~~~~~~~~l~~el~~~~~~~~el~k~~~~~e~~~~~k~fla~iSHEL  381 (1002)
                      ....+..++.|+-...|.+.   ..+.-+....+       +..++..              ...+...+.++.++||||
T Consensus        88 ~~~~v~~~v~~v~~~~G~vl---le~~~~~~~~r-------idre~~q--------------~a~~~a~~~L~r~LAHEI  143 (363)
T COG3852          88 RSHIVDLTVAPVPEEPGSVL---LEFHPRDMQRR-------LDREQTQ--------------HAQQRAVKGLVRGLAHEI  143 (363)
T ss_pred             ccceEEEEEeeccCCCCeEE---EEechhHHHhH-------hhHHHHH--------------HHHHHHHHHHHHHHHHHh
Confidence            77788899999988777543   22222222111       1111000              011112356899999999


Q ss_pred             ccHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCeeeEeeecCHHHHHHHHHHHHHHHHh
Q 039716          382 RSPLTGVVSMAEILSNTKLDREQRQLLGVMISSGDLVLQLINDILDLSKVESGVMKLEAAKFRPREVVKHVLQTAAASLQ  461 (1002)
Q Consensus       382 RTPL~~I~g~~elL~~~~l~~~~~~~l~~i~~s~~~L~~LIndlLd~skiesg~~~l~~~~~~l~~li~~v~~~~~~~~~  461 (1002)
                      ||||.+|.|.++||...-.++..++|.+.|...++|+.+|++.+.-|+--    ......+++++++++.|.........
T Consensus       144 KNPL~GiRGAAQLLe~~lpd~~~~~lt~lIieE~DRl~~LVDRme~~~~~----rp~~r~~~NIH~VLerV~~lv~~e~~  219 (363)
T COG3852         144 KNPLGGIRGAAQLLERALPDEALRELTQLIIEEADRLRNLVDRLEVLGPQ----RPGDRVPVNIHEVLERVRALVEAEFA  219 (363)
T ss_pred             cCcccchhhHHHHHHhhCCChHHHHHHHHHHHHHHHHHHHHHHHHhcCCC----CCcccccchHHHHHHHHHHHHhcccC
Confidence            99999999999999987777779999999999999999999999766643    23345689999999999999888888


Q ss_pred             hcceeccccCCCCCeeEEccHHHHHHHHHHHHhhhhhcCC---C--CeeEEEEEecCCCCcccchhhhhhhhhhcchhhh
Q 039716          462 KILMLEGDIADDVPIEVIGDVLRIRQILTNLISNAIKFTP---E--GKVGIKLYVVPEPPFAKEGLKQKSKAYQSATDAV  536 (1002)
Q Consensus       462 k~i~l~~~i~~~~p~~v~gD~~rL~QIL~NLlsNAIKfT~---~--G~I~I~v~~~~~~~~~~~~~~~~~~~~~~~~~~~  536 (1002)
                      .++.+..++++.+| .+++|+.+|.|++.||+.||..+-.   .  |.|.++.+.  ......                 
T Consensus       220 ~~i~l~rdYDPSLP-~v~~d~DqliQv~LNlVrNAaqA~~~~~~~~g~I~LrTR~--~~q~~i-----------------  279 (363)
T COG3852         220 DNVRLIRDYDPSLP-EVLGDRDQLIQVFLNLVRNAAQALGGRADEGGEIILRTRT--GIQLTI-----------------  279 (363)
T ss_pred             CceEEeecCCCCCc-cccCCHHHHHHHHHHHHHHHHHHhcCCCCCCceEEEEecc--ceEEEc-----------------
Confidence            89999999999998 5999999999999999999999975   3  666554321  100000                 


Q ss_pred             hhhccCCCCCccCCCCCCCCCCCCCCccCCCCCCCCCCCccCCCCCccccccceEEEEEEEecCCCCCcCcHhhhhhhcc
Q 039716          537 KEEKHQPKSQTASDQNGFHDKKHGEGYQDHKHDDDPGTPVSHGNSMDEDLEATVWIRCDVYDTGIGIPENALPTLFRKYM  616 (1002)
Q Consensus       537 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~i~V~DtGiGI~~e~l~~IF~pF~  616 (1002)
                                                                     ........+.++|.|||+|||++.+++||.||.
T Consensus       280 -----------------------------------------------~g~r~rl~l~leViDNGPGVP~~L~~~lF~P~V  312 (363)
T COG3852         280 -----------------------------------------------AGTRYRLALPLEVIDNGPGVPPDLQDHLFYPMV  312 (363)
T ss_pred             -----------------------------------------------cCceeEeeeeeEEecCCCCCChHHhhhcccccc
Confidence                                                           000123347788999999999999999999998


Q ss_pred             CCCccccCcCCCccccHHHHHHHHHHhCCEEEEEeecCCceEEEEEEeCCC
Q 039716          617 QVSADHARKYGGTGLGLAICKQLVELMGGRLTVTSKVHCGSTFTFILPYQV  667 (1002)
Q Consensus       617 q~~~~~~~~~~GtGLGLaI~k~Lve~~gG~I~v~S~~g~GTtF~~~LP~~~  667 (1002)
                      ++      +.+||||||+|+++||..|||.|.++|.|| .|+|++.+|...
T Consensus       313 s~------r~~GsGLGLala~~li~qH~G~Ie~~S~Pg-~T~FrvllP~~~  356 (363)
T COG3852         313 SG------REGGTGLGLALAQNLIDQHGGKIEFDSWPG-RTVFRVLLPIRK  356 (363)
T ss_pred             cc------CCCCccccHHHHHHHHHhcCCEEEEeccCC-ceEEEEEeeccc
Confidence            64      457999999999999999999999999998 699999999754

>TIGR02966 phoR_proteo phosphate regulon sensor kinase PhoR

Probab=100.00  E-value=3e-34  Score=322.93  Aligned_cols=324  Identities=28%  Similarity=0.377  Sum_probs=255.8

Q ss_pred             HHHHHHHHHHhccCcEEEEecccccEEEeeccC---CCCCcccccCCCchhccCccchhhhhHHHHHHHHhCCCcceeEE
Q 039716          219 RADNFLHFVLQNAPVVMGHQDKELRYRFIYNHF---PSLHEEDILGKTDVEIFSGAGVKESQDFKREVLEKGLPAKREIT  295 (1002)
Q Consensus       219 ~~~~~l~~il~~~p~~i~~~d~~~~~~~~~~~~---~~~~~e~iiGk~~~e~~~~~~~~~~~~~~~~vl~~g~~~~~e~~  295 (1002)
                      +..+.++.+++++|.+++..|.++++.++|..+   .|+++++++|++..+++...       .....+..+.. ...+.
T Consensus         3 ~~~~~l~~~~~~~~~~i~~~d~~g~i~~~N~~~~~~~g~~~~~~~g~~~~~~~~~~-------~~~~~l~~~~~-~~~~~   74 (333)
T TIGR02966         3 ALLSRFRAAAQALPDAVVVLDEEGQIEWCNPAAERLLGLRWPDDLGQRITNLIRHP-------EFVEYLAAGRF-SEPLE   74 (333)
T ss_pred             hHHHHHHHHHHhCcCcEEEECCCCcEEEEcHHHHHHhCCChHHHcCCcHHHHccCH-------HHHHHHHhccc-CCCeE
Confidence            345678899999999999999999999999865   57778889999888776432       12334444333 22344


Q ss_pred             EEEeecCceEEEEEEeeeecCCCCEEEEEEEeechhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 039716          296 FETELFGSKTFLIYVEPVFSKSGETIGVNYMGMDVTDQVRKREKMAKLREEIAVQKAKETELNKTIHITEETMRAKQMLA  375 (1002)
Q Consensus       296 ~~~~~~~~~~~~~~~~p~~~~~G~~~gi~~~~~DITe~~~~~~~~~~l~~el~~~~~~~~el~k~~~~~e~~~~~k~fla  375 (1002)
                      +....+...++.+...|+.+..     ++.+..|||++++.++.                              ..+|++
T Consensus        75 ~~~~~~~~~~~~~~~~p~~~~~-----~~~~~~dit~~~~~~~~------------------------------~~~~~~  119 (333)
T TIGR02966        75 LPSPINSERVLEIRIAPYGEEQ-----KLLVARDVTRLRRLEQM------------------------------RRDFVA  119 (333)
T ss_pred             eecCCCCceEEEEEEEEcCCCc-----eEEEEeCchHHHHHHHH------------------------------HHHHHH
Confidence            4434556677778888887543     56678999975432110                              125899


Q ss_pred             HhhhccccHHHHHHHHHHHHhCC--CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCeeeEeeecCHHHHHHHHH
Q 039716          376 TMSHEIRSPLTGVVSMAEILSNT--KLDREQRQLLGVMISSGDLVLQLINDILDLSKVESGVMKLEAAKFRPREVVKHVL  453 (1002)
Q Consensus       376 ~iSHELRTPL~~I~g~~elL~~~--~l~~~~~~~l~~i~~s~~~L~~LIndlLd~skiesg~~~l~~~~~~l~~li~~v~  453 (1002)
                      .++|||||||++|.+++++|...  ..++...+++..|..+++++..++++++++++++.+.......++++.+++..++
T Consensus       120 ~l~h~l~~pL~~i~~~~~~l~~~~~~~~~~~~~~~~~i~~~~~~l~~~i~~l~~~~~~~~~~~~~~~~~~~l~~~i~~~~  199 (333)
T TIGR02966       120 NVSHELRTPLTVLRGYLETLADGPDEDPEEWNRALEIMLEQSQRMQSLVEDLLTLSRLESAASPLEDEPVDMPALLDHLR  199 (333)
T ss_pred             hhhhhhcccHHHHHHHHHHHHhcccCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCccccccccCHHHHHHHHH
Confidence            99999999999999999988654  3455677889999999999999999999999999988888889999999999998


Q ss_pred             HHHHHHHh-hcceeccccCCCCCeeEEccHHHHHHHHHHHHhhhhhcCCC-CeeEEEEEecCCCCcccchhhhhhhhhhc
Q 039716          454 QTAAASLQ-KILMLEGDIADDVPIEVIGDVLRIRQILTNLISNAIKFTPE-GKVGIKLYVVPEPPFAKEGLKQKSKAYQS  531 (1002)
Q Consensus       454 ~~~~~~~~-k~i~l~~~i~~~~p~~v~gD~~rL~QIL~NLlsNAIKfT~~-G~I~I~v~~~~~~~~~~~~~~~~~~~~~~  531 (1002)
                      ..+..... +++.+....  ..+..+.+|+..|.+||.||+.||+||++. +.|.|.+...                   
T Consensus       200 ~~~~~~~~~~~i~i~~~~--~~~~~~~~d~~~l~~vl~nll~Nai~~~~~~~~i~i~~~~~-------------------  258 (333)
T TIGR02966       200 DEAEALSQGKNHQITFEI--DGGVDVLGDEDELRSAFSNLVSNAIKYTPEGGTITVRWRRD-------------------  258 (333)
T ss_pred             HHHHHHHHHcCcEEEEcC--CCCceEEECHHHHHHHHHHHHHHhheeCCCCCeEEEEEEEc-------------------
Confidence            88776554 446666555  224468999999999999999999999875 5566654321                   


Q ss_pred             chhhhhhhccCCCCCccCCCCCCCCCCCCCCccCCCCCCCCCCCccCCCCCccccccceEEEEEEEecCCCCCcCcHhhh
Q 039716          532 ATDAVKEEKHQPKSQTASDQNGFHDKKHGEGYQDHKHDDDPGTPVSHGNSMDEDLEATVWIRCDVYDTGIGIPENALPTL  611 (1002)
Q Consensus       532 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~i~V~DtGiGI~~e~l~~I  611 (1002)
                                                                               ...+.|.|.|+|+||+++.++++
T Consensus       259 ---------------------------------------------------------~~~~~i~i~d~G~gi~~~~~~~i  281 (333)
T TIGR02966       259 ---------------------------------------------------------GGGAEFSVTDTGIGIAPEHLPRL  281 (333)
T ss_pred             ---------------------------------------------------------CCEEEEEEEecCCCCCHHHHhhh
Confidence                                                                     01377899999999999999999


Q ss_pred             hhhccCCCccccCcCCCccccHHHHHHHHHHhCCEEEEEeecCCceEEEEEE
Q 039716          612 FRKYMQVSADHARKYGGTGLGLAICKQLVELMGGRLTVTSKVHCGSTFTFIL  663 (1002)
Q Consensus       612 F~pF~q~~~~~~~~~~GtGLGLaI~k~Lve~~gG~I~v~S~~g~GTtF~~~L  663 (1002)
                      |+|||+.+...+...+|+||||+||+.+++.|||+|++.|.+++||+|+++|
T Consensus       282 f~~~~~~~~~~~~~~~g~glGL~~~~~~~~~~gG~i~~~s~~~~Gt~~~i~l  333 (333)
T TIGR02966       282 TERFYRVDKSRSRDTGGTGLGLAIVKHVLSRHHARLEIESELGKGSTFSFIF  333 (333)
T ss_pred             ccCceecCcccccCCCCCcccHHHHHHHHHHCCCEEEEEecCCCCeEEEEEC
Confidence            9999987665555667999999999999999999999999999999999975

Members of this protein family are the regulatory histidine kinase PhoR associated with the phosphate ABC transporter in most Proteobacteria. Related proteins from Gram-positive organisms are not included in this model. The phoR gene usually is adjacent to the response regulator phoB gene (TIGR02154).

>PRK11073 glnL nitrogen regulation protein NR(II); Provisional

Probab=100.00  E-value=2.2e-34  Score=328.22  Aligned_cols=335  Identities=22%  Similarity=0.284  Sum_probs=244.8

Q ss_pred             HHHHHHHhccCcEEEEecccccEEEeeccC---CCCCcccccCCCchhccCccchhhhhHHHHHHHHhCCCcc-eeEEEE
Q 039716          222 NFLHFVLQNAPVVMGHQDKELRYRFIYNHF---PSLHEEDILGKTDVEIFSGAGVKESQDFKREVLEKGLPAK-REITFE  297 (1002)
Q Consensus       222 ~~l~~il~~~p~~i~~~d~~~~~~~~~~~~---~~~~~e~iiGk~~~e~~~~~~~~~~~~~~~~vl~~g~~~~-~e~~~~  297 (1002)
                      ..++.+++++|.+++..|.++++.++|..+   .|+..++++|++..++++....  ........+..+.... .++.+.
T Consensus         7 ~~~~~il~~~~~gi~~~d~~~~i~~~N~a~~~~~g~~~~~~~g~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~   84 (348)
T PRK11073          7 PDAGQILNSLINSILLLDDDLAIHYANPAAQQLLAQSSRKLFGTPLPELLSYFSL--NIELMRESLQAGQGFTDNEVTLV   84 (348)
T ss_pred             chHHHHHhcCcCeEEEECCCCeEeeEcHHHHHHhCCCHHHHcCCCHHHHcCcchh--hHHHHHHHHHcCCcccccceEEE
Confidence            456789999999999999999999998764   5778888999999888765322  1233344555554322 233232


Q ss_pred             EeecCceEEEEEEeeeecCCCCEEEEEEEeechhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 039716          298 TELFGSKTFLIYVEPVFSKSGETIGVNYMGMDVTDQVRKREKMAKLREEIAVQKAKETELNKTIHITEETMRAKQMLATM  377 (1002)
Q Consensus       298 ~~~~~~~~~~~~~~p~~~~~G~~~gi~~~~~DITe~~~~~~~~~~l~~el~~~~~~~~el~k~~~~~e~~~~~k~fla~i  377 (1002)
                       ..+...++.+...|+.  .   .++++...|+|++.+.++++.+..                     +....++|++.+
T Consensus        85 -~~g~~~~~~~~~~~~~--~---~~~~~~~~dit~~~~~~~~~~~~~---------------------~~~~~~~~~~~i  137 (348)
T PRK11073         85 -IDGRSHILSLTAQRLP--E---GMILLEMAPMDNQRRLSQEQLQHA---------------------QQVAARDLVRGL  137 (348)
T ss_pred             -ECCceEEEEEEEEEcc--C---ceeEEEEechhHHHHHHHHHHHHH---------------------HHHHHHHHHHhh
Confidence             2344556667777876  2   345667889998765433322110                     001124799999


Q ss_pred             hhccccHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCeeeEeeecCHHHHHHHHHHHHH
Q 039716          378 SHEIRSPLTGVVSMAEILSNTKLDREQRQLLGVMISSGDLVLQLINDILDLSKVESGVMKLEAAKFRPREVVKHVLQTAA  457 (1002)
Q Consensus       378 SHELRTPL~~I~g~~elL~~~~l~~~~~~~l~~i~~s~~~L~~LIndlLd~skiesg~~~l~~~~~~l~~li~~v~~~~~  457 (1002)
                      ||||||||++|.|++++|.+...++...+++..+..+++++..++++++.+++...      ...+++..+++.+...+.
T Consensus       138 aHelr~pL~~i~~~~~~l~~~~~~~~~~~~~~~i~~~~~~l~~lv~~l~~~~~~~~------~~~~~l~~~~~~~~~~~~  211 (348)
T PRK11073        138 AHEIKNPLGGLRGAAQLLSKALPDPALTEYTKVIIEQADRLRNLVDRLLGPQRPGT------HVTESIHKVAERVVQLVS  211 (348)
T ss_pred             hHhhcChHHHHHHHHHHhhhcCCChHHHHHHHHHHHHHHHHHHHHHHHhcccCCCC------CccccHHHHHHHHHHHHh
Confidence            99999999999999999887666677888999999999999999999998766432      245688888888777666


Q ss_pred             HHHhhcceeccccCCCCCeeEEccHHHHHHHHHHHHhhhhhcC-C-CCeeEEEEEecCCCCcccchhhhhhhhhhcchhh
Q 039716          458 ASLQKILMLEGDIADDVPIEVIGDVLRIRQILTNLISNAIKFT-P-EGKVGIKLYVVPEPPFAKEGLKQKSKAYQSATDA  535 (1002)
Q Consensus       458 ~~~~k~i~l~~~i~~~~p~~v~gD~~rL~QIL~NLlsNAIKfT-~-~G~I~I~v~~~~~~~~~~~~~~~~~~~~~~~~~~  535 (1002)
                      ....+.+.+.....+..+ .+.+|+.+|.||+.||++||+||+ + .|.|.|.+.......                   
T Consensus       212 ~~~~~~i~i~~~~~~~~~-~i~~d~~~l~~vl~nLl~NA~~~~~~~~~~i~i~~~~~~~~~-------------------  271 (348)
T PRK11073        212 LELPDNVRLIRDYDPSLP-ELAHDPDQIEQVLLNIVRNALQALGPEGGTITLRTRTAFQLT-------------------  271 (348)
T ss_pred             hhccCCcEEEEecCCCCC-ceeeCHHHHHHHHHHHHHHHHHHhccCCCeEEEEEccccccc-------------------
Confidence            555555666665555544 588999999999999999999997 3 455655442110000                   


Q ss_pred             hhhhccCCCCCccCCCCCCCCCCCCCCccCCCCCCCCCCCccCCCCCccccccceEEEEEEEecCCCCCcCcHhhhhhhc
Q 039716          536 VKEEKHQPKSQTASDQNGFHDKKHGEGYQDHKHDDDPGTPVSHGNSMDEDLEATVWIRCDVYDTGIGIPENALPTLFRKY  615 (1002)
Q Consensus       536 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~i~V~DtGiGI~~e~l~~IF~pF  615 (1002)
                                                               .      ........+.+.|.|+|+||+++.++++|+||
T Consensus       272 -----------------------------------------~------~~~~~~~~~~i~v~D~G~Gi~~~~~~~iF~~~  304 (348)
T PRK11073        272 -----------------------------------------L------HGERYRLAARIDIEDNGPGIPPHLQDTLFYPM  304 (348)
T ss_pred             -----------------------------------------c------CCccCCceEEEEEEeCCCCCCHHHHhhccCCc
Confidence                                                     0      00001123678999999999999999999999


Q ss_pred             cCCCccccCcCCCccccHHHHHHHHHHhCCEEEEEeecCCceEEEEEEeC
Q 039716          616 MQVSADHARKYGGTGLGLAICKQLVELMGGRLTVTSKVHCGSTFTFILPY  665 (1002)
Q Consensus       616 ~q~~~~~~~~~~GtGLGLaI~k~Lve~~gG~I~v~S~~g~GTtF~~~LP~  665 (1002)
                      |+.+      .+|+||||+|||++|+.|||+|+++|.+| ||+|+|+||+
T Consensus       305 ~~~~------~~g~GlGL~i~~~iv~~~gG~i~~~s~~~-~~~f~i~lP~  347 (348)
T PRK11073        305 VSGR------EGGTGLGLSIARNLIDQHSGKIEFTSWPG-HTEFSVYLPI  347 (348)
T ss_pred             ccCC------CCCccCCHHHHHHHHHHcCCeEEEEecCC-ceEEEEEEec
Confidence            8642      46999999999999999999999999988 5999999996

>PRK09303 adaptive-response sensory kinase; Validated

Probab=100.00  E-value=1.2e-34  Score=334.84  Aligned_cols=220  Identities=30%  Similarity=0.492  Sum_probs=189.0

Q ss_pred             HHHHHHHHhhhccccHHHHHHHHHHHHhCCCCC-------HHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCeeeEee
Q 039716          369 RAKQMLATMSHEIRSPLTGVVSMAEILSNTKLD-------REQRQLLGVMISSGDLVLQLINDILDLSKVESGVMKLEAA  441 (1002)
Q Consensus       369 ~~k~fla~iSHELRTPL~~I~g~~elL~~~~l~-------~~~~~~l~~i~~s~~~L~~LIndlLd~skiesg~~~l~~~  441 (1002)
                      ..++|++++||||||||++|.+++++|.....+       +..+++++.+..++++|..+|++++++++.+.+...+...
T Consensus       150 ~~~~l~~~iaHeLrtPLt~i~~~~e~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~li~~ll~~~~~~~~~~~~~~~  229 (380)
T PRK09303        150 FKDRVLAMLAHDLRTPLTAASLALETLELGQIDEDTELKPALIEQLQDQARRQLEEIERLITDLLEVGRTRWEALRFNPQ  229 (380)
T ss_pred             HHHHHHHHHhHhhcchHHHHHHHHHHHhccCccccchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCceeccc
Confidence            345899999999999999999999999754322       2367788999999999999999999999999999999999


Q ss_pred             ecCHHHHHHHHHHHHHHHHh-hcceeccccCCCCCeeEEccHHHHHHHHHHHHhhhhhcCCC-CeeEEEEEecCCCCccc
Q 039716          442 KFRPREVVKHVLQTAAASLQ-KILMLEGDIADDVPIEVIGDVLRIRQILTNLISNAIKFTPE-GKVGIKLYVVPEPPFAK  519 (1002)
Q Consensus       442 ~~~l~~li~~v~~~~~~~~~-k~i~l~~~i~~~~p~~v~gD~~rL~QIL~NLlsNAIKfT~~-G~I~I~v~~~~~~~~~~  519 (1002)
                      ++++.+++.+++..+..... +.+.+..+++.+.| .+.+|+.+|.|||.|||+||+||++. |.|.|.+...       
T Consensus       230 ~~~l~~ll~~~~~~~~~~~~~~~i~l~~~~~~~~~-~v~~d~~~l~qvl~NLl~NAik~~~~~~~I~i~~~~~-------  301 (380)
T PRK09303        230 KLDLGSLCQEVILELEKRWLAKSLEIQTDIPSDLP-SVYADQERIRQVLLNLLDNAIKYTPEGGTITLSMLHR-------  301 (380)
T ss_pred             cCCHHHHHHHHHHHHHHHHHHcCCEEEEEcCCCCC-eEEeCHHHHHHHHHHHHHHHHhcCCCCceEEEEEEec-------
Confidence            99999999999988876554 56777777766655 58999999999999999999999986 4565554210       


Q ss_pred             chhhhhhhhhhcchhhhhhhccCCCCCccCCCCCCCCCCCCCCccCCCCCCCCCCCccCCCCCccccccceEEEEEEEec
Q 039716          520 EGLKQKSKAYQSATDAVKEEKHQPKSQTASDQNGFHDKKHGEGYQDHKHDDDPGTPVSHGNSMDEDLEATVWIRCDVYDT  599 (1002)
Q Consensus       520 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~i~V~Dt  599 (1002)
                                                                                          ...++.|+|.|+
T Consensus       302 --------------------------------------------------------------------~~~~v~i~V~D~  313 (380)
T PRK09303        302 --------------------------------------------------------------------TTQKVQVSICDT  313 (380)
T ss_pred             --------------------------------------------------------------------CCCEEEEEEEEc
Confidence                                                                                112588999999


Q ss_pred             CCCCCcCcHhhhhhhccCCCccccCcCCCccccHHHHHHHHHHhCCEEEEEeecCCceEEEEEEeCC
Q 039716          600 GIGIPENALPTLFRKYMQVSADHARKYGGTGLGLAICKQLVELMGGRLTVTSKVHCGSTFTFILPYQ  666 (1002)
Q Consensus       600 GiGI~~e~l~~IF~pF~q~~~~~~~~~~GtGLGLaI~k~Lve~~gG~I~v~S~~g~GTtF~~~LP~~  666 (1002)
                      |+|||++.+++||+|||+.+.  ....+|+||||+||++||+.|||+|+++|.+|+||+|+|+||..
T Consensus       314 G~GI~~~~~~~iF~pf~~~~~--~~~~~G~GLGL~i~~~iv~~~gG~i~v~s~~~~Gt~f~i~lP~~  378 (380)
T PRK09303        314 GPGIPEEEQERIFEDRVRLPR--DEGTEGYGIGLSVCRRIVRVHYGQIWVDSEPGQGSCFHFTLPVY  378 (380)
T ss_pred             CCCCCHHHHHHHccCceeCCC--CCCCCcccccHHHHHHHHHHcCCEEEEEecCCCccEEEEEEecC
Confidence            999999999999999998865  34567999999999999999999999999999999999999974

>PRK11360 sensory histidine kinase AtoS; Provisional

Probab=100.00  E-value=1.2e-32  Score=335.33  Aligned_cols=346  Identities=23%  Similarity=0.378  Sum_probs=271.3

Q ss_pred             HHHHHHHHHHHHHHHHHHhccCcEEEEecccccEEEeeccC---CCCCcccccCCCchhccCccchhhhhHHHHHHHHhC
Q 039716          211 EELSQILKRADNFLHFVLQNAPVVMGHQDKELRYRFIYNHF---PSLHEEDILGKTDVEIFSGAGVKESQDFKREVLEKG  287 (1002)
Q Consensus       211 ~~~~~~l~~~~~~l~~il~~~p~~i~~~d~~~~~~~~~~~~---~~~~~e~iiGk~~~e~~~~~~~~~~~~~~~~vl~~g  287 (1002)
                      ..+.+.++.++.+++.+++++|.+++..|.++++.++|..+   .|+.+++++|++..+++++..  .........+..+
T Consensus       251 ~~~~~~l~~~~~~~~~i~~~~~~~i~~~d~~g~i~~~N~~~~~l~g~~~~~~~g~~~~~~~~~~~--~~~~~~~~~~~~~  328 (607)
T PRK11360        251 NNLAQALRETRSLNELILESIADGVIAIDRQGKITTMNPAAEVITGLQRHELVGKPYSELFPPNT--PFASPLLDTLEHG  328 (607)
T ss_pred             HHHHHHHHHHHHHHHHHHHhccCeEEEEcCCCCEEEECHHHHHHhCCChHHhcCCcHHHHcCCch--hHHHHHHHHHhcC
Confidence            34456677778889999999999999999999999998754   577888999999988887432  1222334445544


Q ss_pred             CCcc-eeEEEEEeecCceEEEEEEeeeecCCCCEEEEEEEeechhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 039716          288 LPAK-REITFETELFGSKTFLIYVEPVFSKSGETIGVNYMGMDVTDQVRKREKMAKLREEIAVQKAKETELNKTIHITEE  366 (1002)
Q Consensus       288 ~~~~-~e~~~~~~~~~~~~~~~~~~p~~~~~G~~~gi~~~~~DITe~~~~~~~~~~l~~el~~~~~~~~el~k~~~~~e~  366 (1002)
                      .... .++.+... .+...+.+...|+++.+|.+.|+++++.|||++++.++++.+..+                     
T Consensus       329 ~~~~~~~~~~~~~-~~~~~~~~~~~~i~~~~g~~~~~i~~~~Dite~~~~e~~l~~~~~---------------------  386 (607)
T PRK11360        329 TEHVDLEISFPGR-DRTIELSVSTSLLHNTHGEMIGALVIFSDLTERKRLQRRVARQER---------------------  386 (607)
T ss_pred             CCccceEEEEEcC-CCcEEEEEEEeeEEcCCCCEEEEEEEEeechHHHHHHHHHHHHHH---------------------
Confidence            4332 23333333 344457788899999999999999999999998776555432211                     


Q ss_pred             HHHHHHHHHHhhhccccHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCeeeEeeecCHH
Q 039716          367 TMRAKQMLATMSHEIRSPLTGVVSMAEILSNTKLDREQRQLLGVMISSGDLVLQLINDILDLSKVESGVMKLEAAKFRPR  446 (1002)
Q Consensus       367 ~~~~k~fla~iSHELRTPL~~I~g~~elL~~~~l~~~~~~~l~~i~~s~~~L~~LIndlLd~skiesg~~~l~~~~~~l~  446 (1002)
                      .....+|++.++|||||||++|.|+++++.....+.+..++++.+...++++..++++++++++.....    ..++++.
T Consensus       387 ~~~l~~~~~~~~hel~~~l~~i~~~~~~~~~~~~~~~~~~~l~~i~~~~~~~~~~~~~l~~~~~~~~~~----~~~~~~~  462 (607)
T PRK11360        387 LAALGELVAGVAHEIRNPLTAIRGYVQIWRQQTSDPPSQEYLSVVLREVDRLNKVIDQLLEFSRPRESQ----WQPVSLN  462 (607)
T ss_pred             HHHHHHHHHHHHHHhhhHHHHHHHHHHHHHhcccChhHHHHHHHHHHHHHHHHHHHHHHHHhhCCCcCc----cceecHH
Confidence            111347999999999999999999999987765667788999999999999999999999999876543    3578999


Q ss_pred             HHHHHHHHHHHHH-HhhcceeccccCCCCCeeEEccHHHHHHHHHHHHhhhhhcCCC-CeeEEEEEecCCCCcccchhhh
Q 039716          447 EVVKHVLQTAAAS-LQKILMLEGDIADDVPIEVIGDVLRIRQILTNLISNAIKFTPE-GKVGIKLYVVPEPPFAKEGLKQ  524 (1002)
Q Consensus       447 ~li~~v~~~~~~~-~~k~i~l~~~i~~~~p~~v~gD~~rL~QIL~NLlsNAIKfT~~-G~I~I~v~~~~~~~~~~~~~~~  524 (1002)
                      .++..+...+... ..+.+.+....+++.+ .+.+|+..|.|++.||+.||+||+.. |.|.|++....           
T Consensus       463 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~l~~~~~nli~na~~~~~~~~~i~v~~~~~~-----------  530 (607)
T PRK11360        463 ALVEEVLQLFQTAGVQARVDFETELDNELP-PIWADPELLKQVLLNILINAVQAISARGKIRIRTWQYS-----------  530 (607)
T ss_pred             HHHHHHHHHHHHhhhccCcEEEEEcCCCCC-eEEECHHHHHHHHHHHHHHHHHHhcCCCeEEEEEEEcC-----------
Confidence            9999988877654 3455666666655544 57889999999999999999999764 56666653210           


Q ss_pred             hhhhhhcchhhhhhhccCCCCCccCCCCCCCCCCCCCCccCCCCCCCCCCCccCCCCCccccccceEEEEEEEecCCCCC
Q 039716          525 KSKAYQSATDAVKEEKHQPKSQTASDQNGFHDKKHGEGYQDHKHDDDPGTPVSHGNSMDEDLEATVWIRCDVYDTGIGIP  604 (1002)
Q Consensus       525 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~i~V~DtGiGI~  604 (1002)
                                                                                     +. .+.|+|.|+|+|||
T Consensus       531 ---------------------------------------------------------------~~-~~~i~v~D~G~G~~  546 (607)
T PRK11360        531 ---------------------------------------------------------------DG-QVAVSIEDNGCGID  546 (607)
T ss_pred             ---------------------------------------------------------------CC-EEEEEEEeCCCCCC
Confidence                                                                           00 17789999999999


Q ss_pred             cCcHhhhhhhccCCCccccCcCCCccccHHHHHHHHHHhCCEEEEEeecCCceEEEEEEeCC
Q 039716          605 ENALPTLFRKYMQVSADHARKYGGTGLGLAICKQLVELMGGRLTVTSKVHCGSTFTFILPYQ  666 (1002)
Q Consensus       605 ~e~l~~IF~pF~q~~~~~~~~~~GtGLGLaI~k~Lve~~gG~I~v~S~~g~GTtF~~~LP~~  666 (1002)
                      ++.+.++|+||++.+      ..|+||||++|+++|+.|||+|+++|.+|+||+|+|+||..
T Consensus       547 ~~~~~~~f~~~~~~~------~~g~glGL~~~~~~~~~~~G~i~~~s~~~~Gt~~~i~lp~~  602 (607)
T PRK11360        547 PELLKKIFDPFFTTK------AKGTGLGLALSQRIINAHGGDIEVESEPGVGTTFTLYLPIN  602 (607)
T ss_pred             HHHHhhhcCCceeCC------CCCCchhHHHHHHHHHHcCCEEEEEEcCCCceEEEEEecCC
Confidence            999999999999643      35899999999999999999999999999999999999984

>PRK13560 hypothetical protein; Provisional

Probab=100.00  E-value=2.3e-32  Score=345.39  Aligned_cols=355  Identities=17%  Similarity=0.218  Sum_probs=241.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHhccCcEEEEecccccEEEeecc----CCCCCcccccCCCchhccCccchhhhhHH------
Q 039716          210 VEELSQILKRADNFLHFVLQNAPVVMGHQDKELRYRFIYNH----FPSLHEEDILGKTDVEIFSGAGVKESQDF------  279 (1002)
Q Consensus       210 ~~~~~~~l~~~~~~l~~il~~~p~~i~~~d~~~~~~~~~~~----~~~~~~e~iiGk~~~e~~~~~~~~~~~~~------  279 (1002)
                      .+++++.|++++.+++.+++++|.+++..|.++++.++|+.    +.|++.++++|++..++.+......+...      
T Consensus       320 rk~~e~~L~~se~~l~~l~~~~~~~i~~~d~~g~i~~~nn~~~~~~~G~~~~e~~g~~~~~~~~~~~~~~~~~~~~~~~~  399 (807)
T PRK13560        320 RRAAERELLEKEDMLRAIIEAAPIAAIGLDADGNICFVNNNAAERMLGWSAAEVMGKPLPGMDPELNEEFWCGDFQEWYP  399 (807)
T ss_pred             HHHHHHHHHHHHHHHHHHHHhCcccEEEEcCCCCEEEecCHHHHHHhCCCHHHHcCCCccccChhhhhhhhhchhhhcCC
Confidence            44556678888899999999999999999999999988653    56888899999987665443211110000      


Q ss_pred             -----------HHHHHHhCCCc-ceeEEEEEeecCceEEEEEEeeeecCCCCEEEEEEEeechhHHHHHHHHHHHHHHHH
Q 039716          280 -----------KREVLEKGLPA-KREITFETELFGSKTFLIYVEPVFSKSGETIGVNYMGMDVTDQVRKREKMAKLREEI  347 (1002)
Q Consensus       280 -----------~~~vl~~g~~~-~~e~~~~~~~~~~~~~~~~~~p~~~~~G~~~gi~~~~~DITe~~~~~~~~~~l~~el  347 (1002)
                                 ....+..+.+. ..++.+....++..++.++..|+++.+|.+.|++++..|||++++.++++.+.+..+
T Consensus       400 ~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~g~~~~~~~~~~p~~d~~g~~~~~~~~~~DITerk~~E~~L~~~~~~~  479 (807)
T PRK13560        400 DGRPMAFDACPMAKTIKGGKIFDGQEVLIEREDDGPADCSAYAEPLHDADGNIIGAIALLVDITERKQVEEQLLLANLIV  479 (807)
T ss_pred             cCCcchhhhhhHHHHHhcCCcccCceEEEEcCCCCeEEEEEEEeeeECCCCCEEEEEEEeehhhhHHHHHHHHHHHHHHH
Confidence                       11223444332 235555555566667778889999999999999999999999999887776542111


Q ss_pred             HH---------------------------------------------------HHHHH----------------------
Q 039716          348 AV---------------------------------------------------QKAKE----------------------  354 (1002)
Q Consensus       348 ~~---------------------------------------------------~~~~~----------------------  354 (1002)
                      +.                                                   .....                      
T Consensus       480 e~~~~~i~~~~~~~~~~~~~~~~~~~~~G~~~~e~~~~~~~~~~~~~p~d~~~~~~~~~~~~~~g~~~~~~e~r~~~~dG  559 (807)
T PRK13560        480 ENSPLVLFRWKAEEGWPVELVSKNITQFGYEPDEFISGKRMFAAIIHPADLEQVAAEVAEFAAQGVDRFEQEYRILGKGG  559 (807)
T ss_pred             hcCCceEEEEecCCCceEEEecchhhhcCCCHHHhhcccchHhhhcChhhHHHHHHHHHHHHhcCCccceeEEEEEcCCC
Confidence            00                                                   00000                      


Q ss_pred             -----------------------------HHHHHHH-HHHHHHHHHHHHHHHhhhccccHHHHHHHHHHHHhCCCCCHHH
Q 039716          355 -----------------------------TELNKTI-HITEETMRAKQMLATMSHEIRSPLTGVVSMAEILSNTKLDREQ  404 (1002)
Q Consensus       355 -----------------------------~el~k~~-~~~e~~~~~k~fla~iSHELRTPL~~I~g~~elL~~~~l~~~~  404 (1002)
                                                   ++..+.- ++.+....+.+|+++|||||||||++|.|+++++.....++..
T Consensus       560 ~~~w~~~~~~~~~d~~G~~~~~~g~~~DITerK~aE~~L~~a~~~~~~~l~~isHelrnpL~~I~~~~~l~~~~~~~~~~  639 (807)
T PRK13560        560 AVCWIDDQSAAERDEEGQISHFEGIVIDISERKHAEEKIKAALTEKEVLLKEIHHRVKNNLQIISSLLDLQAEKLHDEEA  639 (807)
T ss_pred             CEEEEEecceeeeCCCCCEEEEEEEEechHHHHHHHHHHHHHHHHHHHHHHHhHHHHhChHHHHHHHHHHhhhhcCCHHH
Confidence                                         0000000 0111122344899999999999999999999998877667777


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCeeeEeeecCHHHHHHHHHHHHHHHHh-hcceeccccCCCCCeeEEccHH
Q 039716          405 RQLLGVMISSGDLVLQLINDILDLSKVESGVMKLEAAKFRPREVVKHVLQTAAASLQ-KILMLEGDIADDVPIEVIGDVL  483 (1002)
Q Consensus       405 ~~~l~~i~~s~~~L~~LIndlLd~skiesg~~~l~~~~~~l~~li~~v~~~~~~~~~-k~i~l~~~i~~~~p~~v~gD~~  483 (1002)
                      ..++..+......+..+++.++..         ....++++..+++.+...+...+. ....+...+....+.....+..
T Consensus       640 ~~~~~~~~~~~~~~~~~~~~l~~~---------~~~~~~~l~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  710 (807)
T PRK13560        640 KCAFAESQDRICAMALAHEKLYQS---------EDLADIDFLDYIESLTAHLKNSFAIDFGRIDCKIDADDGCLDIDKAI  710 (807)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhcc---------ccchhccHHHHHHHHHHHHHHHhccccCceEEEEecCcccccccccc
Confidence            777766666655665555554332         133568889999888877665443 2222333333332222345667


Q ss_pred             HHHHHHHHHHhhhhhcCCC----CeeEEEEEecCCCCcccchhhhhhhhhhcchhhhhhhccCCCCCccCCCCCCCCCCC
Q 039716          484 RIRQILTNLISNAIKFTPE----GKVGIKLYVVPEPPFAKEGLKQKSKAYQSATDAVKEEKHQPKSQTASDQNGFHDKKH  559 (1002)
Q Consensus       484 rL~QIL~NLlsNAIKfT~~----G~I~I~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  559 (1002)
                      .+.|||.||++||+||+..    |.|.|.+...                                               
T Consensus       711 ~~~~il~NLl~NAik~~~~~~~~~~i~i~~~~~-----------------------------------------------  743 (807)
T PRK13560        711 PCGLIISELLSNALKHAFPDGAAGNIKVEIREQ-----------------------------------------------  743 (807)
T ss_pred             chHHHHHHHHHHHHHhhccCCCCceEEEEEEEc-----------------------------------------------
Confidence            7899999999999999843    4555544210                                               


Q ss_pred             CCCccCCCCCCCCCCCccCCCCCccccccceEEEEEEEecCCCCCcCcHhhhhhhccCCCccccCcCCCccccHHHHHHH
Q 039716          560 GEGYQDHKHDDDPGTPVSHGNSMDEDLEATVWIRCDVYDTGIGIPENALPTLFRKYMQVSADHARKYGGTGLGLAICKQL  639 (1002)
Q Consensus       560 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~i~V~DtGiGI~~e~l~~IF~pF~q~~~~~~~~~~GtGLGLaI~k~L  639 (1002)
                                                  ...++.|+|+|||+|||++..                ...|+||||+|||+|
T Consensus       744 ----------------------------~~~~v~i~V~D~G~GI~~~~~----------------~~~~~gLGLai~~~i  779 (807)
T PRK13560        744 ----------------------------GDGMVNLCVADDGIGLPAGFD----------------FRAAETLGLQLVCAL  779 (807)
T ss_pred             ----------------------------CCCEEEEEEEeCCCcCCcccc----------------ccccCCccHHHHHHH
Confidence                                        012588999999999998731                123789999999999


Q ss_pred             HHHhCCEEEEEeecCCceEEEEEEeCC
Q 039716          640 VELMGGRLTVTSKVHCGSTFTFILPYQ  666 (1002)
Q Consensus       640 ve~~gG~I~v~S~~g~GTtF~~~LP~~  666 (1002)
                      |+.|||+|+|+|.  +||||+|+||+.
T Consensus       780 v~~~gG~I~v~S~--~Gt~F~i~lP~~  804 (807)
T PRK13560        780 VKQLDGEIALDSR--GGARFNIRFPMS  804 (807)
T ss_pred             HHHcCCEEEEEcC--CceEEEEEecCC
Confidence            9999999999994  799999999974

>COG5000 NtrY Signal transduction histidine kinase involved in nitrogen fixation and metabolism regulation [Signal transduction mechanisms]

Probab=100.00  E-value=1.3e-31  Score=302.17  Aligned_cols=350  Identities=21%  Similarity=0.272  Sum_probs=261.1

Q ss_pred             HHHHHHHHHHHHHHhhcCChHHHHHHHHHHHHHHHHHHHhccCcEEEEecccccEEEeecc---CCCCCcccccCCCchh
Q 039716          190 QALMEKLNESVTNLEKQSSPVEELSQILKRADNFLHFVLQNAPVVMGHQDKELRYRFIYNH---FPSLHEEDILGKTDVE  266 (1002)
Q Consensus       190 ~~l~~~l~~~~~~l~~~~~~~~~~~~~l~~~~~~l~~il~~~p~~i~~~d~~~~~~~~~~~---~~~~~~e~iiGk~~~e  266 (1002)
                      -.|...+|.|+.+|..|+.++++....+++++.|++.+|...+.++...|.++++.-+|..   +.+.+..+++|.+...
T Consensus       338 g~Ls~~FN~M~~eL~~qq~~l~~ak~~~e~rr~f~E~VLsgvtaGVi~~d~~g~i~t~N~~ae~~l~~~~~~~~G~~lsa  417 (712)
T COG5000         338 GRLSKAFNKMTEQLSSQQEALERAKDALEQRRRFLEAVLSGLTAGVIGFDNRGCITTVNPSAEQILGKPFDQLLGQSLSA  417 (712)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCceeEEEEcCCCeeEeecchHHHHhcCChhHhhcchhhh
Confidence            4578899999999999999999999999999999999999999999999999999988753   3344444455544333


Q ss_pred             ccCccchhhhhHHHHHHHHhC----CCcc-eeEEEEEeecCceEEEEEEeeeecCCCCEEEEEEEeechhHHHHHHHHHH
Q 039716          267 IFSGAGVKESQDFKREVLEKG----LPAK-REITFETELFGSKTFLIYVEPVFSKSGETIGVNYMGMDVTDQVRKREKMA  341 (1002)
Q Consensus       267 ~~~~~~~~~~~~~~~~vl~~g----~~~~-~e~~~~~~~~~~~~~~~~~~p~~~~~G~~~gi~~~~~DITe~~~~~~~~~  341 (1002)
                      +         .....+|+..+    .+.. .++.+ .+.+..+++.+........+|  -|+++++.|||+.+.+++.  
T Consensus       418 ~---------ap~~~~vf~~~~a~~~~~~~~ev~~-~r~g~~rtl~Vq~t~~~~d~~--~gyVvt~DDITdLV~AQRs--  483 (712)
T COG5000         418 I---------APELEEVFAEAGAAARTDKRVEVKL-AREGEERTLNVQATREPEDNG--NGYVVTFDDITDLVIAQRS--  483 (712)
T ss_pred             h---------hhHHHHHHHHhhhhcCCCccceeec-ccCCCceeeeeeeeecccccC--CceEEEecchHHHHHHHHH--
Confidence            2         22233444433    2222 23333 234566777766654443322  3788899999998765332  


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhccccHHHHHHHHHHHHhCC---CCCH---HHHHHHHHHHHHH
Q 039716          342 KLREEIAVQKAKETELNKTIHITEETMRAKQMLATMSHEIRSPLTGVVSMAEILSNT---KLDR---EQRQLLGVMISSG  415 (1002)
Q Consensus       342 ~l~~el~~~~~~~~el~k~~~~~e~~~~~k~fla~iSHELRTPL~~I~g~~elL~~~---~l~~---~~~~~l~~i~~s~  415 (1002)
                                                ..+++.+..++||||||||.|.-.++-|...   ..++   ...++.++|.+..
T Consensus       484 --------------------------~AW~dVArRIAHEIKNPLTPIQLSAERl~rk~gk~i~eDrevfd~~tdTIirQV  537 (712)
T COG5000         484 --------------------------AAWGDVARRIAHEIKNPLTPIQLSAERLLRKLGKEIDEDREVFDRCTDTIIRQV  537 (712)
T ss_pred             --------------------------HHHHHHHHHHHHHhcCCCchhhhhHHHHHHHhccccchHHHHHHHHHHHHHHHH
Confidence                                      2245677789999999999999999987642   2332   2467899999999


Q ss_pred             HHHHHHHHHHHHHHhhhcCCeeeEeeecCHHHHHHHHHHHHHHHHhhcceeccccCCCCCeeEEccHHHHHHHHHHHHhh
Q 039716          416 DLVLQLINDILDLSKVESGVMKLEAAKFRPREVVKHVLQTAAASLQKILMLEGDIADDVPIEVIGDVLRIRQILTNLISN  495 (1002)
Q Consensus       416 ~~L~~LIndlLd~skiesg~~~l~~~~~~l~~li~~v~~~~~~~~~k~i~l~~~i~~~~p~~v~gD~~rL~QIL~NLlsN  495 (1002)
                      ..+.++|+++-+|+|+-.    +..++.||++++.+++....... ..+.+......+ |....+|+..|.|+|.||+.|
T Consensus       538 ~dI~rMVdeF~afARmP~----p~~e~~dL~~ll~e~~~L~e~~~-~~i~f~~e~g~e-pl~~~~D~~~l~Qvf~NliKN  611 (712)
T COG5000         538 EDIKRMVDEFRAFARMPA----PKLEKSDLRALLKEVSFLYEIGN-DHIVFAAEFGGE-PLIGMADATLLGQVFGNLLKN  611 (712)
T ss_pred             HHHHHHHHHHHHHhcCCC----CCCCcchHHHHHHHHHHHHhccC-CCeEEEeecCCC-ceeeecCHHHHHHHHHHHHHh
Confidence            999999999999999754    44567899999999877654332 345555555555 778888999999999999999


Q ss_pred             hhhcCCC-----Ce-eEEEEEecCCCCcccchhhhhhhhhhcchhhhhhhccCCCCCccCCCCCCCCCCCCCCccCCCCC
Q 039716          496 AIKFTPE-----GK-VGIKLYVVPEPPFAKEGLKQKSKAYQSATDAVKEEKHQPKSQTASDQNGFHDKKHGEGYQDHKHD  569 (1002)
Q Consensus       496 AIKfT~~-----G~-I~I~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  569 (1002)
                      |..+-..     +. -.|++...                                                         
T Consensus       612 A~EAi~~~~~~e~~~~~i~~~~~---------------------------------------------------------  634 (712)
T COG5000         612 AAEAIEAVEAEERRTALIRVSLD---------------------------------------------------------  634 (712)
T ss_pred             HHHHhhhcccccCCcceEEEEEe---------------------------------------------------------
Confidence            9988532     10 01111110                                                         


Q ss_pred             CCCCCCccCCCCCccccccceEEEEEEEecCCCCCcCcHhhhhhhccCCCccccCcCCCccccHHHHHHHHHHhCCEEEE
Q 039716          570 DDPGTPVSHGNSMDEDLEATVWIRCDVYDTGIGIPENALPTLFRKYMQVSADHARKYGGTGLGLAICKQLVELMGGRLTV  649 (1002)
Q Consensus       570 ~~~~~~~~~~~~~~~~~~~~~~l~i~V~DtGiGI~~e~l~~IF~pF~q~~~~~~~~~~GtGLGLaI~k~Lve~~gG~I~v  649 (1002)
                                       .....+++.|.|||.|+|.+.+.++|+||.++      +.+||||||+|||+|+|-|||.|.+
T Consensus       635 -----------------~~~g~i~v~V~DNGkG~p~e~r~r~~EPYvTt------r~KGTGLGLAiVKkIvEeHGG~leL  691 (712)
T COG5000         635 -----------------DADGRIVVDVIDNGKGFPRENRHRALEPYVTT------REKGTGLGLAIVKKIVEEHGGRLEL  691 (712)
T ss_pred             -----------------cCCCeEEEEEecCCCCCChHHhhhhccCceec------ccccccccHHHHHHHHHhcCCeEEe
Confidence                             11124889999999999999999999999975      3469999999999999999999999


Q ss_pred             Eeec-CCceEEEEEEeC
Q 039716          650 TSKV-HCGSTFTFILPY  665 (1002)
Q Consensus       650 ~S~~-g~GTtF~~~LP~  665 (1002)
                      ...+ -.|..+.+.||.
T Consensus       692 ~da~d~~GA~i~i~fp~  708 (712)
T COG5000         692 HNAPDFDGAMIRIKFPL  708 (712)
T ss_pred             cCCCCCCCcEEEEEccc
Confidence            9884 349999999997

>PRK10490 sensor protein KdpD; Provisional

Probab=100.00  E-value=1.7e-30  Score=328.10  Aligned_cols=216  Identities=28%  Similarity=0.453  Sum_probs=180.6

Q ss_pred             HHHHHHhhhccccHHHHHHHHHHHHhCCC--CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCeeeEeeecCHHHH
Q 039716          371 KQMLATMSHEIRSPLTGVVSMAEILSNTK--LDREQRQLLGVMISSGDLVLQLINDILDLSKVESGVMKLEAAKFRPREV  448 (1002)
Q Consensus       371 k~fla~iSHELRTPL~~I~g~~elL~~~~--l~~~~~~~l~~i~~s~~~L~~LIndlLd~skiesg~~~l~~~~~~l~~l  448 (1002)
                      .+|++.+||||||||++|.|++++|....  ......+.+..+...+.++..+|+++|+++++++|.+.+...++++.++
T Consensus       665 ~~lla~isHELrtPLt~I~g~~~lL~~~l~~~~~~~~~~~~~i~~~~~~l~~li~~LL~~srl~~~~~~l~~~~~~L~el  744 (895)
T PRK10490        665 NALLAALSHDLRTPLTVLFGQAEILTLDLASEGSPHARQASEIRQQVLNTTRLVNNLLDMARIQSGGFNLRKEWLTLEEV  744 (895)
T ss_pred             HHHHHHhHHHHhHHHHHHHHHHHHHhhcccccCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCcccccccCHHHH
Confidence            47999999999999999999999886432  2233446788899999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHh-hcceeccccCCCCCeeEEccHHHHHHHHHHHHhhhhhcCCCC-eeEEEEEecCCCCcccchhhhhh
Q 039716          449 VKHVLQTAAASLQ-KILMLEGDIADDVPIEVIGDVLRIRQILTNLISNAIKFTPEG-KVGIKLYVVPEPPFAKEGLKQKS  526 (1002)
Q Consensus       449 i~~v~~~~~~~~~-k~i~l~~~i~~~~p~~v~gD~~rL~QIL~NLlsNAIKfT~~G-~I~I~v~~~~~~~~~~~~~~~~~  526 (1002)
                      ++.++..+..... +.+.  ..++.+.+ .+.+|+.+|.|||.|||+||+||++.| .|.|.+...              
T Consensus       745 i~~~l~~l~~~~~~~~i~--l~~~~~~~-~v~~D~~~L~qVL~NLL~NAik~s~~g~~I~I~~~~~--------------  807 (895)
T PRK10490        745 VGSALQMLEPGLSGHPIN--LSLPEPLT-LIHVDGPLFERVLINLLENAVKYAGAQAEIGIDAHVE--------------  807 (895)
T ss_pred             HHHHHHHHHHHhcCCCEE--EEcCCCCe-EEEECHHHHHHHHHHHHHHHHHhCCCCCeEEEEEEEe--------------
Confidence            9999887765543 3333  34444444 589999999999999999999999875 566655321              


Q ss_pred             hhhhcchhhhhhhccCCCCCccCCCCCCCCCCCCCCccCCCCCCCCCCCccCCCCCccccccceEEEEEEEecCCCCCcC
Q 039716          527 KAYQSATDAVKEEKHQPKSQTASDQNGFHDKKHGEGYQDHKHDDDPGTPVSHGNSMDEDLEATVWIRCDVYDTGIGIPEN  606 (1002)
Q Consensus       527 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~i~V~DtGiGI~~e  606 (1002)
                                                                                    ..++.|+|.|+|+|||++
T Consensus       808 --------------------------------------------------------------~~~v~I~V~D~G~GI~~e  825 (895)
T PRK10490        808 --------------------------------------------------------------GERLQLDVWDNGPGIPPG  825 (895)
T ss_pred             --------------------------------------------------------------CCEEEEEEEECCCCCCHH
Confidence                                                                          114789999999999999


Q ss_pred             cHhhhhhhccCCCccccCcCCCccccHHHHHHHHHHhCCEEEEEeecCCceEEEEEEeCCC
Q 039716          607 ALPTLFRKYMQVSADHARKYGGTGLGLAICKQLVELMGGRLTVTSKVHCGSTFTFILPYQV  667 (1002)
Q Consensus       607 ~l~~IF~pF~q~~~~~~~~~~GtGLGLaI~k~Lve~~gG~I~v~S~~g~GTtF~~~LP~~~  667 (1002)
                      .+++||+||++.+..  ...+|+||||+|||+|++.|||+|+++|.+|+||+|+|.||...
T Consensus       826 ~~~~IFepF~~~~~~--~~~~G~GLGL~Ivk~ive~hGG~I~v~s~~~~Gt~f~i~LPl~~  884 (895)
T PRK10490        826 QEQLIFDKFARGNKE--SAIPGVGLGLAICRAIVEVHGGTIWAENRPEGGACFRVTLPLET  884 (895)
T ss_pred             HHHHhcCCCccCCCC--CCCCCccHHHHHHHHHHHHcCCEEEEEECCCCeEEEEEEeECCC
Confidence            999999999986542  34469999999999999999999999999999999999999854

>COG4251 Bacteriophytochrome (light-regulated signal transduction histidine kinase) [Signal transduction mechanisms]

Probab=99.97  E-value=4.9e-30  Score=289.96  Aligned_cols=217  Identities=31%  Similarity=0.454  Sum_probs=178.4

Q ss_pred             HHHHHHHHhhhccccHHHHHHHHHHHHhCC---CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCeeeEeeecCH
Q 039716          369 RAKQMLATMSHEIRSPLTGVVSMAEILSNT---KLDREQRQLLGVMISSGDLVLQLINDILDLSKVESGVMKLEAAKFRP  445 (1002)
Q Consensus       369 ~~k~fla~iSHELRTPL~~I~g~~elL~~~---~l~~~~~~~l~~i~~s~~~L~~LIndlLd~skiesg~~~l~~~~~~l  445 (1002)
                      +.++|...+||+||+||+.|.+++++|...   .++.+.++++..+.+.+.+|.+||+|++.||++......+.  +.++
T Consensus       523 el~~f~yv~sHdlqePl~~I~~~a~lL~~~~~~~~d~~~~~~i~~~~~~~~~~~~lidd~l~~s~l~~~~~~l~--~td~  600 (750)
T COG4251         523 ELRAFAYVASHDLQEPLRQISNYAQLLSERYSDALDEEAKEFITFISRLTSLMQQLIDDLLTYSKLGLTEAPLQ--PTDV  600 (750)
T ss_pred             HHHHHHHHhhhhhhHHHHHHHHHHHhhhhccccccChHHHHHHHHHHHHHHHHHHHHHHHhhhhhhccccCCCC--Ccch
Confidence            345799999999999999999999999754   57889999999999999999999999999999976655554  6778


Q ss_pred             HHHHHHHHHHHHHHHh-hcceeccccCCCCCeeEEccHHHHHHHHHHHHhhhhhcCCCCeeEEEEEecCCCCcccchhhh
Q 039716          446 REVVKHVLQTAAASLQ-KILMLEGDIADDVPIEVIGDVLRIRQILTNLISNAIKFTPEGKVGIKLYVVPEPPFAKEGLKQ  524 (1002)
Q Consensus       446 ~~li~~v~~~~~~~~~-k~i~l~~~i~~~~p~~v~gD~~rL~QIL~NLlsNAIKfT~~G~I~I~v~~~~~~~~~~~~~~~  524 (1002)
                      .++++.++........ .++.+.  +.+ +| .+.+|+.++.||+.||+.|||||...+.-.|.+.....          
T Consensus       601 ~~vv~~vl~~l~~ri~dtgaei~--i~~-lp-~v~~d~~~l~qv~~NLi~Naik~~~~e~~~i~I~~~r~----------  666 (750)
T COG4251         601 QKVVDKVLLELSQRIADTGAEIR--IAP-LP-VVAADATQLGQVFQNLIANAIKFGGPENPDIEISAERQ----------  666 (750)
T ss_pred             HHHHHHHHHhcccccccccceEE--ecc-cc-eeecCHHHHHHHHHHHHhhheecCCCCCCceEEeeecc----------
Confidence            8999988877665443 333332  333 45 58899999999999999999999866533333321100          


Q ss_pred             hhhhhhcchhhhhhhccCCCCCccCCCCCCCCCCCCCCccCCCCCCCCCCCccCCCCCccccccceEEEEEEEecCCCCC
Q 039716          525 KSKAYQSATDAVKEEKHQPKSQTASDQNGFHDKKHGEGYQDHKHDDDPGTPVSHGNSMDEDLEATVWIRCDVYDTGIGIP  604 (1002)
Q Consensus       525 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~i~V~DtGiGI~  604 (1002)
                                                                                      ..-+.|.|.|+|+||+
T Consensus       667 ----------------------------------------------------------------ed~~t~sV~dng~Gi~  682 (750)
T COG4251         667 ----------------------------------------------------------------EDEWTFSVRDNGIGID  682 (750)
T ss_pred             ----------------------------------------------------------------CCceEEEecCCCCCcC
Confidence                                                                            0126789999999999


Q ss_pred             cCcHhhhhhhccCCCccccCcCCCccccHHHHHHHHHHhCCEEEEEeecCCceEEEEEEeCCC
Q 039716          605 ENALPTLFRKYMQVSADHARKYGGTGLGLAICKQLVELMGGRLTVTSKVHCGSTFTFILPYQV  667 (1002)
Q Consensus       605 ~e~l~~IF~pF~q~~~~~~~~~~GtGLGLaI~k~Lve~~gG~I~v~S~~g~GTtF~~~LP~~~  667 (1002)
                      +...++||..|.+...  ..+|.||||||+|||+|++.|+|+|||+|.+|+|+||+|+||...
T Consensus       683 ~a~~~riF~iFqRl~s--~~~y~gtG~GL~I~kkI~e~H~G~i~vEs~~gEgsTF~f~lp~~~  743 (750)
T COG4251         683 PAYFERIFVIFQRLHS--RDEYLGTGLGLAICKKIAERHQGRIWVESTPGEGSTFYFTLPVGG  743 (750)
T ss_pred             HHHHHHHHHHHHhcCc--hhhhcCCCccHHHHHHHHHHhCceEEEeecCCCceeEEEEeecCC
Confidence            9999999999998764  347889999999999999999999999999999999999999864

>PRK10604 sensor protein RstB; Provisional

Probab=99.97  E-value=3.3e-29  Score=294.60  Aligned_cols=213  Identities=23%  Similarity=0.334  Sum_probs=176.3

Q ss_pred             HHHHHHHhhhccccHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCeeeEeeecCHHHHH
Q 039716          370 AKQMLATMSHEIRSPLTGVVSMAEILSNTKLDREQRQLLGVMISSGDLVLQLINDILDLSKVESGVMKLEAAKFRPREVV  449 (1002)
Q Consensus       370 ~k~fla~iSHELRTPL~~I~g~~elL~~~~l~~~~~~~l~~i~~s~~~L~~LIndlLd~skiesg~~~l~~~~~~l~~li  449 (1002)
                      .++|++++||||||||+.|.+.++++...  ..+..   ..+.+..++|..++++++.+++++.+...+...++++.+++
T Consensus       212 ~~~l~~~vsHeLrtPL~~i~~~l~~l~~~--~~~~~---~~i~~~~~~l~~li~~ll~~~rl~~~~~~~~~~~~~l~~~l  286 (433)
T PRK10604        212 KKQLIDGIAHELRTPLVRLRYRLEMSDNL--SAAES---QALNRDIGQLEALIEELLTYARLDRPQNELHLSEPDLPAWL  286 (433)
T ss_pred             HHHHHHHhhHhhcChHHHHHHHHHHhcCC--CcHHH---HHHHHHHHHHHHHHHHHHHHHhccCCCcccCCCCCCHHHHH
Confidence            35899999999999999999999988632  22222   23677889999999999999999999888888899999999


Q ss_pred             HHHHHHHHHHHh-hcceeccccCCCCCeeEEccHHHHHHHHHHHHhhhhhcCCCCeeEEEEEecCCCCcccchhhhhhhh
Q 039716          450 KHVLQTAAASLQ-KILMLEGDIADDVPIEVIGDVLRIRQILTNLISNAIKFTPEGKVGIKLYVVPEPPFAKEGLKQKSKA  528 (1002)
Q Consensus       450 ~~v~~~~~~~~~-k~i~l~~~i~~~~p~~v~gD~~rL~QIL~NLlsNAIKfT~~G~I~I~v~~~~~~~~~~~~~~~~~~~  528 (1002)
                      .+++..+..... +.+.+...  .. +..+.+|+..+.+|+.||++||+||+. |.|.|++....               
T Consensus       287 ~~~i~~~~~~~~~~~i~~~~~--~~-~~~~~~d~~~l~~vl~NLl~NAik~~~-~~I~I~~~~~~---------------  347 (433)
T PRK10604        287 STHLADIQAVTPEKTVRLDTP--HQ-GDYGALDMRLMERVLDNLLNNALRYAH-SRVRVSLLLDG---------------  347 (433)
T ss_pred             HHHHHHHHHHhhcCcEEEEec--CC-CceEecCHHHHHHHHHHHHHHHHHhCC-CeEEEEEEEEC---------------
Confidence            998877665432 34444332  22 335678999999999999999999985 67777664211               


Q ss_pred             hhcchhhhhhhccCCCCCccCCCCCCCCCCCCCCccCCCCCCCCCCCccCCCCCccccccceEEEEEEEecCCCCCcCcH
Q 039716          529 YQSATDAVKEEKHQPKSQTASDQNGFHDKKHGEGYQDHKHDDDPGTPVSHGNSMDEDLEATVWIRCDVYDTGIGIPENAL  608 (1002)
Q Consensus       529 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~i~V~DtGiGI~~e~l  608 (1002)
                                                                                   ..+.|.|.|+|+|||++.+
T Consensus       348 -------------------------------------------------------------~~~~I~V~D~G~Gi~~e~~  366 (433)
T PRK10604        348 -------------------------------------------------------------NQACLIVEDDGPGIPPEER  366 (433)
T ss_pred             -------------------------------------------------------------CEEEEEEEEcCCCCCHHHH
Confidence                                                                         1378999999999999999


Q ss_pred             hhhhhhccCCCccccCcCCCccccHHHHHHHHHHhCCEEEEEeecCCceEEEEEEeCCC
Q 039716          609 PTLFRKYMQVSADHARKYGGTGLGLAICKQLVELMGGRLTVTSKVHCGSTFTFILPYQV  667 (1002)
Q Consensus       609 ~~IF~pF~q~~~~~~~~~~GtGLGLaI~k~Lve~~gG~I~v~S~~g~GTtF~~~LP~~~  667 (1002)
                      ++||+|||+.+....++.+|+||||+|||++++.|||+|+++|.+++||+|++.||...
T Consensus       367 ~~if~~f~r~~~~~~~~~~g~GLGL~ivk~i~~~~gG~i~v~s~~~~G~~f~i~lP~~~  425 (433)
T PRK10604        367 ERVFEPFVRLDPSRDRATGGCGLGLAIVHSIALAMGGSVNCDESELGGARFSFSWPVWH  425 (433)
T ss_pred             hhcCCCCccCCCCCCCCCCCccchHHHHHHHHHHCCCEEEEEecCCCeeEEEEEEeCCC
Confidence            99999999988766667789999999999999999999999999999999999999864

>PRK11086 sensory histidine kinase DcuS; Provisional

Probab=99.96  E-value=3.9e-28  Score=293.19  Aligned_cols=306  Identities=23%  Similarity=0.291  Sum_probs=202.3

Q ss_pred             HHHHHHHHhccCcEEEEecccccEEEeeccCCC---C---CcccccCCCchhccCccchhhhhHHHHHHHHhCCCcce-e
Q 039716          221 DNFLHFVLQNAPVVMGHQDKELRYRFIYNHFPS---L---HEEDILGKTDVEIFSGAGVKESQDFKREVLEKGLPAKR-E  293 (1002)
Q Consensus       221 ~~~l~~il~~~p~~i~~~d~~~~~~~~~~~~~~---~---~~e~iiGk~~~e~~~~~~~~~~~~~~~~vl~~g~~~~~-e  293 (1002)
                      ...++.++++++.+|...|.++++.++|..+..   +   .+.+.+|+...++++.       .....++..+.+... +
T Consensus       220 ~~~~~~il~~~~~gIi~~D~~g~I~~~N~~a~~llg~~~~~~~~~~~~~~~~~~~~-------~~~~~~~~~~~~~~~~~  292 (542)
T PRK11086        220 FEQRQAMLQSIKEGVIAVDDRGEVTLINDEAKRLFNYKKGLEDDPLGTDVESWMPV-------SRLKEVLRTGTPRRDEE  292 (542)
T ss_pred             HHHHHHHHHHhcCcEEEECCCCeEEEEhHHHHHHhCCCcCCcccccCCcHHHhCCc-------hhHHHHHhcCCCccceE
Confidence            344578999999999999999999999986432   2   2345667766665542       123456666655432 2


Q ss_pred             EEEEEeecCceEEEEEEeeeecCCCCEEEEEEEeechhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 039716          294 ITFETELFGSKTFLIYVEPVFSKSGETIGVNYMGMDVTDQVRKREKMAKLREEIAVQKAKETELNKTIHITEETMRAKQM  373 (1002)
Q Consensus       294 ~~~~~~~~~~~~~~~~~~p~~~~~G~~~gi~~~~~DITe~~~~~~~~~~l~~el~~~~~~~~el~k~~~~~e~~~~~k~f  373 (1002)
                      ..     .+...+.+...|+.+ +|.+.|++.+++|+|+..+.++++..+.                        ...++
T Consensus       293 ~~-----~~g~~~~~~~~pi~~-~g~~~g~v~~~rDite~~~l~~~l~~~~------------------------~~~~~  342 (542)
T PRK11086        293 IN-----INGRLLLTNTVPVRV-NGEIIGAIATFRDKTEVRQLAQRLDGMV------------------------NYADA  342 (542)
T ss_pred             EE-----ECCEEEEEEEEEEeE-CCEEEEEEEEEEEchHHHHHHHHHHHHH------------------------HHHHH
Confidence            21     134566777789988 8999999999999998654433322111                        11246


Q ss_pred             HHHhhhccccHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCeeeEeeecCHHHHHHHHH
Q 039716          374 LATMSHEIRSPLTGVVSMAEILSNTKLDREQRQLLGVMISSGDLVLQLINDILDLSKVESGVMKLEAAKFRPREVVKHVL  453 (1002)
Q Consensus       374 la~iSHELRTPL~~I~g~~elL~~~~l~~~~~~~l~~i~~s~~~L~~LIndlLd~skiesg~~~l~~~~~~l~~li~~v~  453 (1002)
                      ++.+||||||||++|.|++++...    .+..+++..+   +......++++++..+  .        ++ +..+   +.
T Consensus       343 l~~~sHel~npL~~I~g~~~~~~~----~~~~~~~~~~---~~~~~~~~~~~~~~~~--~--------~~-~~~~---~~  401 (542)
T PRK11086        343 LRAQSHEFMNKLHVILGLLHLKSY----DQLEDYILKT---ANNYQEEIGSLLGKIK--S--------PV-IAGF---LL  401 (542)
T ss_pred             HHhhchhhcCHHHHHHHHHHhCch----HHHHHHHHHH---HHHHHHHHHHHHHhcc--C--------HH-HHHH---HH
Confidence            778999999999999999987432    2222333222   2222223333332111  0        00 0111   11


Q ss_pred             HHHHHHHhhcceeccccCCCCCee-EEccHHHHHHHHHHHHhhhhhcCC---CCeeEEEEEecCCCCcccchhhhhhhhh
Q 039716          454 QTAAASLQKILMLEGDIADDVPIE-VIGDVLRIRQILTNLISNAIKFTP---EGKVGIKLYVVPEPPFAKEGLKQKSKAY  529 (1002)
Q Consensus       454 ~~~~~~~~k~i~l~~~i~~~~p~~-v~gD~~rL~QIL~NLlsNAIKfT~---~G~I~I~v~~~~~~~~~~~~~~~~~~~~  529 (1002)
                      ........+++.+.......++.. ...+...|.|||.||++||+||+.   .|.|.|++...                 
T Consensus       402 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~vl~nLl~NAi~~~~~~~~~~I~i~~~~~-----------------  464 (542)
T PRK11086        402 GKISRARELGITLIISEDSQLPDSGDEDQVHELITILGNLIENALEAVGGEEGGEISVSLHYR-----------------  464 (542)
T ss_pred             HHHHHHHHcCCEEEEeCCCCCCcccccccHHHHHHHHHHHHHHHHHHhhcCCCcEEEEEEEEc-----------------
Confidence            111122234555554444433321 123445899999999999999963   35666655321                 


Q ss_pred             hcchhhhhhhccCCCCCccCCCCCCCCCCCCCCccCCCCCCCCCCCccCCCCCccccccceEEEEEEEecCCCCCcCcHh
Q 039716          530 QSATDAVKEEKHQPKSQTASDQNGFHDKKHGEGYQDHKHDDDPGTPVSHGNSMDEDLEATVWIRCDVYDTGIGIPENALP  609 (1002)
Q Consensus       530 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~i~V~DtGiGI~~e~l~  609 (1002)
                                                                                 ..++.|.|.|+|+||+++.++
T Consensus       465 -----------------------------------------------------------~~~~~i~V~D~G~gi~~~~~~  485 (542)
T PRK11086        465 -----------------------------------------------------------NGWLHCEVSDDGPGIAPDEID  485 (542)
T ss_pred             -----------------------------------------------------------CCEEEEEEEECCCCCCHHHHH
Confidence                                                                       114788999999999999999


Q ss_pred             hhhhhccCCCccccCcCCCccccHHHHHHHHHHhCCEEEEEeecCCceEEEEEEeCC
Q 039716          610 TLFRKYMQVSADHARKYGGTGLGLAICKQLVELMGGRLTVTSKVHCGSTFTFILPYQ  666 (1002)
Q Consensus       610 ~IF~pF~q~~~~~~~~~~GtGLGLaI~k~Lve~~gG~I~v~S~~g~GTtF~~~LP~~  666 (1002)
                      +||+||++.      +.+|+||||+|||++|+.|||+|+++|.+|+||+|+|+||+.
T Consensus       486 ~iF~~~~~~------~~~g~GlGL~iv~~iv~~~~G~i~v~s~~~~G~~f~i~lP~~  536 (542)
T PRK11086        486 AIFDKGYST------KGSNRGVGLYLVKQSVENLGGSIAVESEPGVGTQFFVQIPWD  536 (542)
T ss_pred             HHHhCCCcc------CCCCCcCcHHHHHHHHHHcCCEEEEEeCCCCcEEEEEEEeCC
Confidence            999999864      345999999999999999999999999999999999999975

>PRK10815 sensor protein PhoQ; Provisional

Probab=99.96  E-value=2.4e-28  Score=290.62  Aligned_cols=213  Identities=22%  Similarity=0.301  Sum_probs=176.0

Q ss_pred             HHHHHHHHhhhccccHHHHHHHHHHHHhCCC-CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCeeeEeeecCHHH
Q 039716          369 RAKQMLATMSHEIRSPLTGVVSMAEILSNTK-LDREQRQLLGVMISSGDLVLQLINDILDLSKVESGVMKLEAAKFRPRE  447 (1002)
Q Consensus       369 ~~k~fla~iSHELRTPL~~I~g~~elL~~~~-l~~~~~~~l~~i~~s~~~L~~LIndlLd~skiesg~~~l~~~~~~l~~  447 (1002)
                      +.++|++++||||||||++|.++++.|.... .+.+  +....+.....++.++|++++++++.+++...+....+++..
T Consensus       265 ~~~~~l~~isHELRTPLt~I~~~l~~L~~~~~~~~~--~~~~~~~~~i~ri~~~i~~ll~~~~~~~~~~~~~~~~~~l~~  342 (485)
T PRK10815        265 KYRTTLTDLTHSLKTPLAVLQSTLRSLRSGKQMSVE--QAEPIMLEQISRISQQIGYYLHRASMRSEHNLLSRELHSVAP  342 (485)
T ss_pred             HHHHHHHHhhHHHHHHHHHHHHHHHHHhcCCCCCHH--HHHHHHHHHHHHHHHHHHHHHHHHHhhcCCcccccceecHHH
Confidence            3457999999999999999999999886643 3322  334556778899999999999999999988888888999999


Q ss_pred             HHHHHHHHHHHHHh-hcceeccccCCCCCeeEEccHHHHHHHHHHHHhhhhhcCCCCeeEEEEEecCCCCcccchhhhhh
Q 039716          448 VVKHVLQTAAASLQ-KILMLEGDIADDVPIEVIGDVLRIRQILTNLISNAIKFTPEGKVGIKLYVVPEPPFAKEGLKQKS  526 (1002)
Q Consensus       448 li~~v~~~~~~~~~-k~i~l~~~i~~~~p~~v~gD~~rL~QIL~NLlsNAIKfT~~G~I~I~v~~~~~~~~~~~~~~~~~  526 (1002)
                      +++.++..+..... +++.+...+.++  ..+.+|+..|.||+.||++||+||++++ |.|.+...              
T Consensus       343 ll~~~~~~l~~~~~~~~i~i~~~~~~~--~~v~~d~~~l~~vl~NLi~NAik~~~~~-i~I~~~~~--------------  405 (485)
T PRK10815        343 LLDNLTSALNKVYQRKGVNITLDISPE--ITFVGEKNDFMEVMGNVLDNACKYCLEF-VEISARQT--------------  405 (485)
T ss_pred             HHHHHHHHHHHHHHHCCcEEEEecCCC--cEEEeCHHHHHHHHHHHHHHHHHhcCCc-EEEEEEEe--------------
Confidence            99999888776543 566666665443  3578999999999999999999999753 44544211              


Q ss_pred             hhhhcchhhhhhhccCCCCCccCCCCCCCCCCCCCCccCCCCCCCCCCCccCCCCCccccccceEEEEEEEecCCCCCcC
Q 039716          527 KAYQSATDAVKEEKHQPKSQTASDQNGFHDKKHGEGYQDHKHDDDPGTPVSHGNSMDEDLEATVWIRCDVYDTGIGIPEN  606 (1002)
Q Consensus       527 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~i~V~DtGiGI~~e  606 (1002)
                                                                                    ...+.|.|.|+|+||+++
T Consensus       406 --------------------------------------------------------------~~~v~I~V~D~G~GI~~e  423 (485)
T PRK10815        406 --------------------------------------------------------------DEHLHIVVEDDGPGIPES  423 (485)
T ss_pred             --------------------------------------------------------------CCEEEEEEEECCCCcCHH
Confidence                                                                          114789999999999999


Q ss_pred             cHhhhhhhccCCCccccCcCCCccccHHHHHHHHHHhCCEEEEEeecCCceEEEEEEeCC
Q 039716          607 ALPTLFRKYMQVSADHARKYGGTGLGLAICKQLVELMGGRLTVTSKVHCGSTFTFILPYQ  666 (1002)
Q Consensus       607 ~l~~IF~pF~q~~~~~~~~~~GtGLGLaI~k~Lve~~gG~I~v~S~~g~GTtF~~~LP~~  666 (1002)
                      .+++||+||++.+.    ..+|+||||+||++||+.|||+|.++|.+++||+|++.||.+
T Consensus       424 ~~~~iF~~f~~~~~----~~~G~GLGL~Ivk~iv~~~gG~i~v~s~~~~Gt~f~i~lp~~  479 (485)
T PRK10815        424 KRELIFDRGQRADT----LRPGQGLGLSVAREITEQYEGKISAGDSPLGGARMEVIFGRQ  479 (485)
T ss_pred             HHHHHhCCcccCCC----CCCCcchhHHHHHHHHHHcCCEEEEEECCCCEEEEEEEEcCC
Confidence            99999999998643    235999999999999999999999999999999999999975

>COG4191 Signal transduction histidine kinase regulating C4-dicarboxylate transport system [Signal transduction mechanisms]

Probab=99.96  E-value=3.1e-28  Score=276.99  Aligned_cols=211  Identities=27%  Similarity=0.410  Sum_probs=176.7

Q ss_pred             HHHHHHHhhhccccHHHHHHHHHH---HHhCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCeeeEeeecCHH
Q 039716          370 AKQMLATMSHEIRSPLTGVVSMAE---ILSNTKLDREQRQLLGVMISSGDLVLQLINDILDLSKVESGVMKLEAAKFRPR  446 (1002)
Q Consensus       370 ~k~fla~iSHELRTPL~~I~g~~e---lL~~~~l~~~~~~~l~~i~~s~~~L~~LIndlLd~skiesg~~~l~~~~~~l~  446 (1002)
                      .++|.+++||||+.||++|.++++   +|.+....++.++.+..|..=.+||-.+...|-.|++--.+.    ..++.+.
T Consensus       384 LGQmSA~iaHElNQPLaaiRt~adna~~lLergr~e~a~~Nl~~I~~LteRma~It~~Lk~FArk~~~a----~~~v~l~  459 (603)
T COG4191         384 LGQMSAGIAHELNQPLAAIRTYADNARLLLERGRTEEARENLERISALTERMAAITAHLKSFARKSRDA----AGPVSLR  459 (603)
T ss_pred             HHHHHHHHHHHhcCcHHHHHhHHHHHHHHHHcCChHHHHhHHHHHHHHHHHHHHHHHHHHHHhccCccc----cCCccHH
Confidence            358999999999999999999987   455666677888999999999999999999999999865443    4678899


Q ss_pred             HHHHHHHHHHHHHHh-hcceeccccCCCCCeeEEccHHHHHHHHHHHHhhhhhcCC---CCeeEEEEEecCCCCcccchh
Q 039716          447 EVVKHVLQTAAASLQ-KILMLEGDIADDVPIEVIGDVLRIRQILTNLISNAIKFTP---EGKVGIKLYVVPEPPFAKEGL  522 (1002)
Q Consensus       447 ~li~~v~~~~~~~~~-k~i~l~~~i~~~~p~~v~gD~~rL~QIL~NLlsNAIKfT~---~G~I~I~v~~~~~~~~~~~~~  522 (1002)
                      ++|+.++..+...+. ....+..+.. +.++.|.+|+.||+|||.|||+||++++.   ++.|.|.+...          
T Consensus       460 ~ai~~Al~ll~~R~~~~~~~l~~~~~-~~~~~V~~~~iRLeQVLvNLl~NALDA~~~~~~~~i~i~~~~~----------  528 (603)
T COG4191         460 EAIEGALELLRGRLRAAGVELELDLP-DAPLWVMANEIRLEQVLVNLLQNALDAMAGQEDRRLSIRAQRE----------  528 (603)
T ss_pred             HHHHHHHHHHHHhhhccCceeeccCC-CCCceeecchhhHHHHHHHHHHHHHHHhcCCCCCeeEEEEEec----------
Confidence            999999988877664 3455555544 34568999999999999999999999974   46666655311          


Q ss_pred             hhhhhhhhcchhhhhhhccCCCCCccCCCCCCCCCCCCCCccCCCCCCCCCCCccCCCCCccccccceEEEEEEEecCCC
Q 039716          523 KQKSKAYQSATDAVKEEKHQPKSQTASDQNGFHDKKHGEGYQDHKHDDDPGTPVSHGNSMDEDLEATVWIRCDVYDTGIG  602 (1002)
Q Consensus       523 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~i~V~DtGiG  602 (1002)
                                                                                        ...+.|+|.|||+|
T Consensus       529 ------------------------------------------------------------------~~~v~l~VrDnGpG  542 (603)
T COG4191         529 ------------------------------------------------------------------GGQVVLTVRDNGPG  542 (603)
T ss_pred             ------------------------------------------------------------------CCeEEEEEccCCCC
Confidence                                                                              11378999999999


Q ss_pred             CCcCcHhhhhhhccCCCccccCcCCCccccHHHHHHHHHHhCCEEEEEeecCCceEEEEEEeC
Q 039716          603 IPENALPTLFRKYMQVSADHARKYGGTGLGLAICKQLVELMGGRLTVTSKVHCGSTFTFILPY  665 (1002)
Q Consensus       603 I~~e~l~~IF~pF~q~~~~~~~~~~GtGLGLaI~k~Lve~~gG~I~v~S~~g~GTtF~~~LP~  665 (1002)
                      |+++.+.++|+|||+++..    ..|.||||+||+.|++-+||+|.+.+.++.|+.|++.||.
T Consensus       543 i~~e~~~~lFePF~TtK~~----~~GLGLGLaIS~~i~~d~GGsL~v~n~~~~Ga~F~i~L~~  601 (603)
T COG4191         543 IAPEALPHLFEPFFTTKPV----GKGLGLGLAISQNIARDLGGSLEVANHPEGGASFTIELRR  601 (603)
T ss_pred             CCHHHHHhhcCCccccCcc----cCCcchhHHHHHHHHHHhCCeEEeecCCCCceEEEEEeec
Confidence            9999999999999987542    4599999999999999999999999999999999999984

>PRK10364 sensor protein ZraS; Provisional

Probab=99.96  E-value=1.4e-27  Score=282.86  Aligned_cols=216  Identities=29%  Similarity=0.467  Sum_probs=178.8

Q ss_pred             HHHHHHHHHHHHHhhhccccHHHHHHHHHHHHhCC-CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCeeeEeee
Q 039716          364 TEETMRAKQMLATMSHEIRSPLTGVVSMAEILSNT-KLDREQRQLLGVMISSGDLVLQLINDILDLSKVESGVMKLEAAK  442 (1002)
Q Consensus       364 ~e~~~~~k~fla~iSHELRTPL~~I~g~~elL~~~-~l~~~~~~~l~~i~~s~~~L~~LIndlLd~skiesg~~~l~~~~  442 (1002)
                      .++....++|++.+||||||||++|.|+++++... ....+.+++++.+...++++..++++++++++...    ....+
T Consensus       231 ~~~l~~~~~~~~~laHelrtpL~~i~~~~~~l~~~~~~~~~~~~~~~~i~~~~~~l~~~i~~ll~~~~~~~----~~~~~  306 (457)
T PRK10364        231 KEKLVALGHLAAGVAHEIRNPLSSIKGLAKYFAERAPAGGEAHQLAQVMAKEADRLNRVVSELLELVKPTH----LALQA  306 (457)
T ss_pred             HHHHHHHHHHHHHhhHHhccHHHHHHHHHHHHHhhccCchHHHHHHHHHHHHHHHHHHHHHHHHHHhCcCC----CcceE
Confidence            34444556899999999999999999999998754 33456678889999999999999999999998532    44567


Q ss_pred             cCHHHHHHHHHHHHHHHHh-hcceeccccCCCCCeeEEccHHHHHHHHHHHHhhhhhcCCC-CeeEEEEEecCCCCcccc
Q 039716          443 FRPREVVKHVLQTAAASLQ-KILMLEGDIADDVPIEVIGDVLRIRQILTNLISNAIKFTPE-GKVGIKLYVVPEPPFAKE  520 (1002)
Q Consensus       443 ~~l~~li~~v~~~~~~~~~-k~i~l~~~i~~~~p~~v~gD~~rL~QIL~NLlsNAIKfT~~-G~I~I~v~~~~~~~~~~~  520 (1002)
                      +++.++++.++..+..... +++.+........+ .+.+|+.+|.|++.||++||+||++. |.|.|.+...        
T Consensus       307 ~~l~~~l~~~~~~~~~~~~~~~i~l~~~~~~~~~-~~~~d~~~l~~il~NLl~NA~k~~~~~~~I~i~~~~~--------  377 (457)
T PRK10364        307 VDLNDLINHSLQLVSQDANSREIQLRFTANDTLP-EIQADPDRLTQVLLNLYLNAIQAIGQHGVISVTASES--------  377 (457)
T ss_pred             ecHHHHHHHHHHHHHHHHHhcCeEEEEEcCCCCc-eEEECHHHHHHHHHHHHHHHHHhcCCCCeEEEEEEEe--------
Confidence            8999999999888776543 56777766655444 57899999999999999999999865 5676665321        


Q ss_pred             hhhhhhhhhhcchhhhhhhccCCCCCccCCCCCCCCCCCCCCccCCCCCCCCCCCccCCCCCccccccceEEEEEEEecC
Q 039716          521 GLKQKSKAYQSATDAVKEEKHQPKSQTASDQNGFHDKKHGEGYQDHKHDDDPGTPVSHGNSMDEDLEATVWIRCDVYDTG  600 (1002)
Q Consensus       521 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~i~V~DtG  600 (1002)
                                                                                          ...+.|.|.|+|
T Consensus       378 --------------------------------------------------------------------~~~~~i~V~D~G  389 (457)
T PRK10364        378 --------------------------------------------------------------------GAGVKISVTDSG  389 (457)
T ss_pred             --------------------------------------------------------------------CCeEEEEEEECC
Confidence                                                                                113789999999


Q ss_pred             CCCCcCcHhhhhhhccCCCccccCcCCCccccHHHHHHHHHHhCCEEEEEeecCCceEEEEEEeCC
Q 039716          601 IGIPENALPTLFRKYMQVSADHARKYGGTGLGLAICKQLVELMGGRLTVTSKVHCGSTFTFILPYQ  666 (1002)
Q Consensus       601 iGI~~e~l~~IF~pF~q~~~~~~~~~~GtGLGLaI~k~Lve~~gG~I~v~S~~g~GTtF~~~LP~~  666 (1002)
                      +|||++.++++|++|++.+      .+|+||||+|||++++.|||+|+++|.+|+||+|+++||..
T Consensus       390 ~Gi~~~~~~~if~~~~~~k------~~g~GlGL~iv~~~v~~~gG~i~i~s~~~~Gt~f~i~lP~~  449 (457)
T PRK10364        390 KGIAADQLEAIFTPYFTTK------AEGTGLGLAVVHNIVEQHGGTIQVASQEGKGATFTLWLPVN  449 (457)
T ss_pred             CCCCHHHHHHHhCccccCC------CCCCcccHHHHHHHHHHCCCEEEEEeCCCCcEEEEEEecCC
Confidence            9999999999999998643      45999999999999999999999999999999999999975

>PRK13559 hypothetical protein; Provisional

Probab=99.96  E-value=1.9e-27  Score=272.75  Aligned_cols=308  Identities=16%  Similarity=0.161  Sum_probs=221.4

Q ss_pred             HHHHHHHHHhccCcEEEEecc---cccEEEeecc---CCCCCcccccCCCchhccCccchhhhhHHHHHHHHhCCCccee
Q 039716          220 ADNFLHFVLQNAPVVMGHQDK---ELRYRFIYNH---FPSLHEEDILGKTDVEIFSGAGVKESQDFKREVLEKGLPAKRE  293 (1002)
Q Consensus       220 ~~~~l~~il~~~p~~i~~~d~---~~~~~~~~~~---~~~~~~e~iiGk~~~e~~~~~~~~~~~~~~~~vl~~g~~~~~e  293 (1002)
                      +...++.+++++|.+++..|.   ++++.++|..   +.|++.++++|++...+..+.............+..+.+...+
T Consensus        41 ~~~~~~~~~e~~~~~i~i~D~~~~~g~i~~~N~a~~~l~G~~~~e~iG~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e  120 (361)
T PRK13559         41 SGRLFEQAMEQTRMAMCITDPHQPDLPIVLANQAFLDLTGYAAEEVVGRNCRFLQGAATDPIAVAKIRAAIAAEREIVVE  120 (361)
T ss_pred             hhhHHHHHHHhCCCcEEEecCCCCCCcEEEEchHHHHHhCCCHHHHcCCChhhhcCCCCCHHHHHHHHHHhccCCceEEE
Confidence            356677889999999999996   5678998876   4677788999999776654433333333444555555555444


Q ss_pred             EEEEEeecCceEEEEEEeeeecCCCCEEEEEEEeechhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 039716          294 ITFETELFGSKTFLIYVEPVFSKSGETIGVNYMGMDVTDQVRKREKMAKLREEIAVQKAKETELNKTIHITEETMRAKQM  373 (1002)
Q Consensus       294 ~~~~~~~~~~~~~~~~~~p~~~~~G~~~gi~~~~~DITe~~~~~~~~~~l~~el~~~~~~~~el~k~~~~~e~~~~~k~f  373 (1002)
                      +......+...++.....|+++.+|.+.|++++..|||++++.++..+                           .+++|
T Consensus       121 ~~~~~~dG~~~~~~~~~~~i~d~~G~~~~~v~~~~DITerk~~e~~~~---------------------------~~~~l  173 (361)
T PRK13559        121 LLNYRKDGEPFWNALHLGPVYGEDGRLLYFFGSQWDVTDIRAVRALEA---------------------------HERRL  173 (361)
T ss_pred             EEEEcCCCCEEEEEEEEEEEEcCCCCEEEeeeeeeehhcchhhHHHHH---------------------------HHHHH
Confidence            444444444455567788999999999999999999998765421100                           01358


Q ss_pred             HHHhhhccccHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCeeeEeeecCHHHHHHHHH
Q 039716          374 LATMSHEIRSPLTGVVSMAEILSNTKLDREQRQLLGVMISSGDLVLQLINDILDLSKVESGVMKLEAAKFRPREVVKHVL  453 (1002)
Q Consensus       374 la~iSHELRTPL~~I~g~~elL~~~~l~~~~~~~l~~i~~s~~~L~~LIndlLd~skiesg~~~l~~~~~~l~~li~~v~  453 (1002)
                      ++.++||+||||++|.|+++++...   .+..++++.+...+..|..+++++|+.++         ..++++.++++.++
T Consensus       174 ~~~l~H~~~n~L~~i~~~~~l~~~~---~~~~~~~~~i~~~~~~l~~~~~~ll~~~~---------~~~v~l~~~~~~~~  241 (361)
T PRK13559        174 AREVDHRSKNVFAVVDSIVRLTGRA---DDPSLYAAAIQERVQALARAHETLLDERG---------WETVEVEELIRAQV  241 (361)
T ss_pred             HHHHHHhhhhHHHHHHHHHHhhccC---CCHHHHHHHHHHHHHHHHHHHHHHhccCC---------cCcccHHHHHHHHH
Confidence            8899999999999999999988632   23345778888999999999999987654         24688888888887


Q ss_pred             HHHHHHHhhcceeccccCCCCCeeEEcc-HHHHHHHHHHHHhhhhhc---CC-CCeeEEEEEecCCCCcccchhhhhhhh
Q 039716          454 QTAAASLQKILMLEGDIADDVPIEVIGD-VLRIRQILTNLISNAIKF---TP-EGKVGIKLYVVPEPPFAKEGLKQKSKA  528 (1002)
Q Consensus       454 ~~~~~~~~k~i~l~~~i~~~~p~~v~gD-~~rL~QIL~NLlsNAIKf---T~-~G~I~I~v~~~~~~~~~~~~~~~~~~~  528 (1002)
                      ..+...   ...+.... +  +..+..+ ...|.|||.||++||+||   ++ .|.|.|.+....               
T Consensus       242 ~~~~~~---~~~i~~~~-~--~~~~~~~~~~~l~~vl~nLi~NA~k~~~~~~~~g~i~v~~~~~~---------------  300 (361)
T PRK13559        242 APYAPR---ATRVAFEG-P--GIRLGAASVQPLGLVLHELAVNAIKHGALSADQGRISISWKPSP---------------  300 (361)
T ss_pred             HhhcCC---CceEEEEC-C--CeeeCHHHHHHHHHHHHHHHHhHHHhccccCCCcEEEEEEEecC---------------
Confidence            655422   22222222 1  1223323 357999999999999999   43 477777652110               


Q ss_pred             hhcchhhhhhhccCCCCCccCCCCCCCCCCCCCCccCCCCCCCCCCCccCCCCCccccccceEEEEEEEecCCCCCcCcH
Q 039716          529 YQSATDAVKEEKHQPKSQTASDQNGFHDKKHGEGYQDHKHDDDPGTPVSHGNSMDEDLEATVWIRCDVYDTGIGIPENAL  608 (1002)
Q Consensus       529 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~i~V~DtGiGI~~e~l  608 (1002)
                                                                                 ....+.+.|.|+|.|++++  
T Consensus       301 -----------------------------------------------------------~~~~~~i~v~d~G~~~~~~--  319 (361)
T PRK13559        301 -----------------------------------------------------------EGAGFRIDWQEQGGPTPPK--  319 (361)
T ss_pred             -----------------------------------------------------------CCCeEEEEEECCCCCCCCC--
Confidence                                                                       0114788999999997764  


Q ss_pred             hhhhhhccCCCccccCcCCCccccHHHHHHHHHH-hCCEEEEEeecCCceEEEEEEeCC
Q 039716          609 PTLFRKYMQVSADHARKYGGTGLGLAICKQLVEL-MGGRLTVTSKVHCGSTFTFILPYQ  666 (1002)
Q Consensus       609 ~~IF~pF~q~~~~~~~~~~GtGLGLaI~k~Lve~-~gG~I~v~S~~g~GTtF~~~LP~~  666 (1002)
                                       ..|+|+||+||+++++. |||+|++++. +.||+|+|+||..
T Consensus       320 -----------------~~~~g~Gl~i~~~~v~~~~gG~i~~~~~-~~G~~~~l~~P~~  360 (361)
T PRK13559        320 -----------------LAKRGFGTVIIGAMVESQLNGQLEKTWS-DDGLLARIEIPSR  360 (361)
T ss_pred             -----------------CCCCCcHHHHHHHHHHHHcCCeEEEEEc-CCeEEEEEEEeCC
Confidence                             23889999999999997 9999999998 5699999999963

>PRK10549 signal transduction histidine-protein kinase BaeS; Provisional

Probab=99.96  E-value=1.7e-27  Score=282.49  Aligned_cols=218  Identities=23%  Similarity=0.406  Sum_probs=184.6

Q ss_pred             HHHHHHhhhccccHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCeeeEeeecCHHHHHH
Q 039716          371 KQMLATMSHEIRSPLTGVVSMAEILSNTKLDREQRQLLGVMISSGDLVLQLINDILDLSKVESGVMKLEAAKFRPREVVK  450 (1002)
Q Consensus       371 k~fla~iSHELRTPL~~I~g~~elL~~~~l~~~~~~~l~~i~~s~~~L~~LIndlLd~skiesg~~~l~~~~~~l~~li~  450 (1002)
                      .+|++.+|||+||||+.|.+.++.+.+... ....+.+..+...+.++..++++++++++.+.+...+...++++.++++
T Consensus       241 ~~~~~~~shel~~pL~~i~~~~~~l~~~~~-~~~~~~l~~~~~~~~~l~~li~~l~~l~~~~~~~~~~~~~~~~~~~~l~  319 (466)
T PRK10549        241 RDFMADISHELRTPLAVLRGELEAIQDGVR-KFTPESVASLQAEVGTLTKLVDDLHQLSLSDEGALAYRKTPVDLVPLLE  319 (466)
T ss_pred             HHHHHHHhHHhCChHHHHHHHHHHHHhccc-cCCHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCcccccCCCCHHHHHH
Confidence            479999999999999999999999876422 2234567788888999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHh-hcceeccccCCCCCeeEEccHHHHHHHHHHHHhhhhhcCCC-CeeEEEEEecCCCCcccchhhhhhhh
Q 039716          451 HVLQTAAASLQ-KILMLEGDIADDVPIEVIGDVLRIRQILTNLISNAIKFTPE-GKVGIKLYVVPEPPFAKEGLKQKSKA  528 (1002)
Q Consensus       451 ~v~~~~~~~~~-k~i~l~~~i~~~~p~~v~gD~~rL~QIL~NLlsNAIKfT~~-G~I~I~v~~~~~~~~~~~~~~~~~~~  528 (1002)
                      .++..+..... +.+.+...+++.  ..+.+|+..+.||+.|||.||+||++. |.|.|.+...                
T Consensus       320 ~~~~~~~~~~~~~~i~i~~~~~~~--~~~~~d~~~l~qvl~nll~NAi~~~~~~~~I~i~~~~~----------------  381 (466)
T PRK10549        320 VAGGAFRERFASRGLTLQLSLPDS--ATVFGDPDRLMQLFNNLLENSLRYTDSGGSLHISAEQR----------------  381 (466)
T ss_pred             HHHHHHHHHHHHCCcEEEEecCCC--cEEEeCHHHHHHHHHHHHHHHHHhCCCCCEEEEEEEEc----------------
Confidence            99888776543 556666655443  357799999999999999999999976 5676665321                


Q ss_pred             hhcchhhhhhhccCCCCCccCCCCCCCCCCCCCCccCCCCCCCCCCCccCCCCCccccccceEEEEEEEecCCCCCcCcH
Q 039716          529 YQSATDAVKEEKHQPKSQTASDQNGFHDKKHGEGYQDHKHDDDPGTPVSHGNSMDEDLEATVWIRCDVYDTGIGIPENAL  608 (1002)
Q Consensus       529 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~i~V~DtGiGI~~e~l  608 (1002)
                                                                                  ...+.|.|.|+|+|||++.+
T Consensus       382 ------------------------------------------------------------~~~~~i~V~D~G~Gi~~e~~  401 (466)
T PRK10549        382 ------------------------------------------------------------DKTLRLTFADSAPGVSDEQL  401 (466)
T ss_pred             ------------------------------------------------------------CCEEEEEEEecCCCcCHHHH
Confidence                                                                        11478999999999999999


Q ss_pred             hhhhhhccCCCccccCcCCCccccHHHHHHHHHHhCCEEEEEeecCCceEEEEEEeCCC
Q 039716          609 PTLFRKYMQVSADHARKYGGTGLGLAICKQLVELMGGRLTVTSKVHCGSTFTFILPYQV  667 (1002)
Q Consensus       609 ~~IF~pF~q~~~~~~~~~~GtGLGLaI~k~Lve~~gG~I~v~S~~g~GTtF~~~LP~~~  667 (1002)
                      ++||+|||+.+....+..+|+||||+||+++++.|||+|+++|.+++||+|+|.||+..
T Consensus       402 ~~lf~~~~~~~~~~~~~~~g~GlGL~iv~~i~~~~~G~l~~~s~~~~G~~~~i~lP~~~  460 (466)
T PRK10549        402 QKLFERFYRTEGSRNRASGGSGLGLAICLNIVEAHNGRIIAAHSPFGGVSITVELPLER  460 (466)
T ss_pred             HHhccCcccCCCCcCCCCCCCcHHHHHHHHHHHHcCCEEEEEECCCCeEEEEEEccCCC
Confidence            99999999987765566789999999999999999999999999999999999999864

>PRK10755 sensor protein BasS/PmrB; Provisional

Probab=99.96  E-value=1.9e-27  Score=272.29  Aligned_cols=210  Identities=25%  Similarity=0.393  Sum_probs=164.7

Q ss_pred             HHHHHHhhhccccHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCeeeEeeecCH-HHHH
Q 039716          371 KQMLATMSHEIRSPLTGVVSMAEILSNTKLDREQRQLLGVMISSGDLVLQLINDILDLSKVESGVMKLEAAKFRP-REVV  449 (1002)
Q Consensus       371 k~fla~iSHELRTPL~~I~g~~elL~~~~l~~~~~~~l~~i~~s~~~L~~LIndlLd~skiesg~~~l~~~~~~l-~~li  449 (1002)
                      ++|++++||||||||++|.++++++..... .    ....+....+++..++++++++++.+..........+++ .+++
T Consensus       138 ~~~~~~~sHelrtPL~~i~~~~e~l~~~~~-~----~~~~~~~~~~~l~~~i~~ll~~~r~~~~~~~~~~~~~~l~~~~i  212 (356)
T PRK10755        138 RLFTADVAHELRTPLAGIRLHLELLEKQHH-I----DVAPLIARLDQMMHTVEQLLQLARAGQSFSSGHYQTVKLLEDVI  212 (356)
T ss_pred             HHHHHHhhHhhcChHHHHHHHHHHHHhccc-h----hHHHHHHHHHHHHHHHHHHHHHHHcccccccccchhhhHHHHHH
Confidence            469999999999999999999998865322 1    233455667889999999999999876655555566776 7777


Q ss_pred             HHHHHHHHHHHh-hcceeccccCCCCCeeEEccHHHHHHHHHHHHhhhhhcCCCC-eeEEEEEecCCCCcccchhhhhhh
Q 039716          450 KHVLQTAAASLQ-KILMLEGDIADDVPIEVIGDVLRIRQILTNLISNAIKFTPEG-KVGIKLYVVPEPPFAKEGLKQKSK  527 (1002)
Q Consensus       450 ~~v~~~~~~~~~-k~i~l~~~i~~~~p~~v~gD~~rL~QIL~NLlsNAIKfT~~G-~I~I~v~~~~~~~~~~~~~~~~~~  527 (1002)
                      ..++..+..... +.+.+.... ...+..+.+|+..+++|+.||++||+||+++| .|.|.+...               
T Consensus       213 ~~~~~~~~~~~~~~~~~~~~~~-~~~~~~v~~d~~~l~~il~nLi~NA~k~~~~~~~I~I~~~~~---------------  276 (356)
T PRK10755        213 LPSQDELSEMLEQRQQTLLLPE-SAADITVQGDATLLRLLLRNLVENAHRYSPEGSTITIKLSQE---------------  276 (356)
T ss_pred             HHHHHHHHHHHHHhCCeEEecc-CCCceEEEECHHHHHHHHHHHHHHHHhhCCCCCcEEEEEEEc---------------
Confidence            776665554332 444444422 23345789999999999999999999999754 566655311               


Q ss_pred             hhhcchhhhhhhccCCCCCccCCCCCCCCCCCCCCccCCCCCCCCCCCccCCCCCccccccceEEEEEEEecCCCCCcCc
Q 039716          528 AYQSATDAVKEEKHQPKSQTASDQNGFHDKKHGEGYQDHKHDDDPGTPVSHGNSMDEDLEATVWIRCDVYDTGIGIPENA  607 (1002)
Q Consensus       528 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~i~V~DtGiGI~~e~  607 (1002)
                                                                                   ...+.|.|.|+|+||+++.
T Consensus       277 -------------------------------------------------------------~~~~~i~V~D~G~Gi~~~~  295 (356)
T PRK10755        277 -------------------------------------------------------------DGGAVLAVEDEGPGIDESK  295 (356)
T ss_pred             -------------------------------------------------------------CCEEEEEEEECCCCCCHHH
Confidence                                                                         1137899999999999999


Q ss_pred             HhhhhhhccCCCccccCcCCCccccHHHHHHHHHHhCCEEEEEeecC-CceEEEEEEeCC
Q 039716          608 LPTLFRKYMQVSADHARKYGGTGLGLAICKQLVELMGGRLTVTSKVH-CGSTFTFILPYQ  666 (1002)
Q Consensus       608 l~~IF~pF~q~~~~~~~~~~GtGLGLaI~k~Lve~~gG~I~v~S~~g-~GTtF~~~LP~~  666 (1002)
                      ++++|++|++.+.    +.+|+||||+||+++++.|||+|+++|.++ +||+|++.||..
T Consensus       296 ~~~if~~f~~~~~----~~~g~GlGL~i~~~i~~~~gg~i~i~s~~~~~Gt~~~i~~p~~  351 (356)
T PRK10755        296 CGELSKAFVRMDS----RYGGIGLGLSIVSRITQLHHGQFFLQNRQERSGTRAWVWLPKA  351 (356)
T ss_pred             HHHhCCCeEeCCC----CCCCcCHHHHHHHHHHHHCCCEEEEEECCCCCeEEEEEEecCC
Confidence            9999999997642    356999999999999999999999999998 999999999964

>PRK15053 dpiB sensor histidine kinase DpiB; Provisional

Probab=99.95  E-value=2.1e-26  Score=278.82  Aligned_cols=308  Identities=18%  Similarity=0.209  Sum_probs=210.3

Q ss_pred             HHHHHHHhccCcEEEEecccccEEEeeccCC---CCCc--ccccCCCchhccCccchhhhhHHHHHHHHhCCCcceeEEE
Q 039716          222 NFLHFVLQNAPVVMGHQDKELRYRFIYNHFP---SLHE--EDILGKTDVEIFSGAGVKESQDFKREVLEKGLPAKREITF  296 (1002)
Q Consensus       222 ~~l~~il~~~p~~i~~~d~~~~~~~~~~~~~---~~~~--e~iiGk~~~e~~~~~~~~~~~~~~~~vl~~g~~~~~e~~~  296 (1002)
                      ..++.++++.+.++...|.++++.++|..+.   ++..  ++++|++..+++++...      ....... ......+. 
T Consensus       222 ~~~~~il~~~~egii~~D~~g~I~~~N~~a~~ll~~~~~~~~~~g~~~~~~~~~~~~------~~~~~~~-~~~~~~~~-  293 (545)
T PRK15053        222 RQQEALFSSVYEGLIAVDPHGYITAINRNARKMLGLSSPGRQWLGKPIAEVVRPADF------FTEQIDE-KRQDVVAN-  293 (545)
T ss_pred             HHHHHHHHHhCceEEEECCCCeEEeecHHHHHHhCCCCcchhhcCCcHHHhCCCchh------hhhhcCC-cccceEEE-
Confidence            4467788999999999999999999987653   4432  46899998888764311      1111111 11111111 


Q ss_pred             EEeecCceEEEEEEeeeecCCCCEEEEEEEeechhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 039716          297 ETELFGSKTFLIYVEPVFSKSGETIGVNYMGMDVTDQVRKREKMAKLREEIAVQKAKETELNKTIHITEETMRAKQMLAT  376 (1002)
Q Consensus       297 ~~~~~~~~~~~~~~~p~~~~~G~~~gi~~~~~DITe~~~~~~~~~~l~~el~~~~~~~~el~k~~~~~e~~~~~k~fla~  376 (1002)
                          .+...+.....|+.. .|.++|++.++.|+|+..+.+.++.+++.                        ..+.+..
T Consensus       294 ----~~~~~~~~~~~~i~~-~~~~~G~v~~~~d~te~~~l~~~l~~~~~------------------------~~e~l~~  344 (545)
T PRK15053        294 ----FNGLSVIANREAIRS-GDDLLGAIISFRSKDEISTLNAQLTQIKQ------------------------YVESLRT  344 (545)
T ss_pred             ----ECCEEEEEEeeeEEE-CCeEEEEEEEEEchHHHHHHHHHHHHHHH------------------------HHHHHHH
Confidence                123455667778765 56778999999999987654433322211                        1134567


Q ss_pred             hhhccccHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCeeeEeeecCHHHHHHHHHHHH
Q 039716          377 MSHEIRSPLTGVVSMAEILSNTKLDREQRQLLGVMISSGDLVLQLINDILDLSKVESGVMKLEAAKFRPREVVKHVLQTA  456 (1002)
Q Consensus       377 iSHELRTPL~~I~g~~elL~~~~l~~~~~~~l~~i~~s~~~L~~LIndlLd~skiesg~~~l~~~~~~l~~li~~v~~~~  456 (1002)
                      ++||++|||++|.|++++-       +..+.++.+...+..+..+++++...-+              ...+...+....
T Consensus       345 ~~he~~n~L~~i~g~l~~~-------~~~~~~~~i~~~s~~~~~l~~~l~~~~~--------------~~~~~~~l~~~~  403 (545)
T PRK15053        345 LRHEHLNWMSTLNGLLQMK-------EYDRVLEMVQGESQAQQQLIDSLREAFA--------------DRQVAGLLFGKV  403 (545)
T ss_pred             HHHHHhhhHHHHHHHHhhc-------hhhHHHHHHHHHHHHHHHHHHHHHHhcc--------------cHHHHHHHHHHH
Confidence            8999999999999987752       2234667777888888888888776422              122222232222


Q ss_pred             HHHHhhcceeccccCCCC-CeeEEccHHHHHHHHHHHHhhhhhcC---CCC--eeEEEEEecCCCCcccchhhhhhhhhh
Q 039716          457 AASLQKILMLEGDIADDV-PIEVIGDVLRIRQILTNLISNAIKFT---PEG--KVGIKLYVVPEPPFAKEGLKQKSKAYQ  530 (1002)
Q Consensus       457 ~~~~~k~i~l~~~i~~~~-p~~v~gD~~rL~QIL~NLlsNAIKfT---~~G--~I~I~v~~~~~~~~~~~~~~~~~~~~~  530 (1002)
                      .....+.+.+........ .....+|+..|.|||.||++||+||+   +.|  .|.|.+..                   
T Consensus       404 ~~~~~~~i~~~~~~~~~~~~l~~~~~~~~l~~vl~nLl~NAi~~~~~~~~~~~~i~i~~~~-------------------  464 (545)
T PRK15053        404 QRARELGLKMVIVPGSQLSQLPPGLDSTEFAAIVGNLLDNAFEASLRSDEGNKIVELFLSD-------------------  464 (545)
T ss_pred             HHHHHhCCceEEcCCCccccccccCCHHHHHHHHHHHHHHHHHHHhhCCCCCceEEEEEEE-------------------
Confidence            333334444443332221 12346799999999999999999994   333  45444321                   


Q ss_pred             cchhhhhhhccCCCCCccCCCCCCCCCCCCCCccCCCCCCCCCCCccCCCCCccccccceEEEEEEEecCCCCCcCcHhh
Q 039716          531 SATDAVKEEKHQPKSQTASDQNGFHDKKHGEGYQDHKHDDDPGTPVSHGNSMDEDLEATVWIRCDVYDTGIGIPENALPT  610 (1002)
Q Consensus       531 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~i~V~DtGiGI~~e~l~~  610 (1002)
                                                                               ....+.|.|.|+|+|||++.+++
T Consensus       465 ---------------------------------------------------------~~~~~~i~V~D~G~Gi~~~~~~~  487 (545)
T PRK15053        465 ---------------------------------------------------------EGDDVVIEVADQGCGVPESLRDK  487 (545)
T ss_pred             ---------------------------------------------------------CCCEEEEEEEeCCCCcCHHHHHH
Confidence                                                                     01147899999999999999999


Q ss_pred             hhhhccCCCccccCcCCCccccHHHHHHHHHHhCCEEEEEeecCCceEEEEEEeCC
Q 039716          611 LFRKYMQVSADHARKYGGTGLGLAICKQLVELMGGRLTVTSKVHCGSTFTFILPYQ  666 (1002)
Q Consensus       611 IF~pF~q~~~~~~~~~~GtGLGLaI~k~Lve~~gG~I~v~S~~g~GTtF~~~LP~~  666 (1002)
                      ||+|||+++.   +..+|+||||+|||++|+.|||+|+++|.+|.||+|+|+||..
T Consensus       488 iF~~~~~tk~---~~~~g~GlGL~ivk~iv~~~~G~i~v~s~~~~Gt~f~i~lP~~  540 (545)
T PRK15053        488 IFEQGVSTRA---DEPGEHGIGLYLIASYVTRCGGVITLEDNDPCGTLFSIFIPKV  540 (545)
T ss_pred             HhCCCCCCCC---CCCCCceeCHHHHHHHHHHcCCEEEEEECCCCeEEEEEEECCC
Confidence            9999997542   3456899999999999999999999999999999999999974

>TIGR03785 marine_sort_HK proteobacterial dedicated sortase system histidine kinase

Probab=99.95  E-value=5.8e-27  Score=289.55  Aligned_cols=216  Identities=24%  Similarity=0.372  Sum_probs=182.2

Q ss_pred             HHHHHHHhhhccccHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCeeeEeeecCHHHHH
Q 039716          370 AKQMLATMSHEIRSPLTGVVSMAEILSNTKLDREQRQLLGVMISSGDLVLQLINDILDLSKVESGVMKLEAAKFRPREVV  449 (1002)
Q Consensus       370 ~k~fla~iSHELRTPL~~I~g~~elL~~~~l~~~~~~~l~~i~~s~~~L~~LIndlLd~skiesg~~~l~~~~~~l~~li  449 (1002)
                      .++|++.+|||+||||+.|.+.++.+.....+.+..++++.+..+++++..++++++++++++.+.......++++.+++
T Consensus       485 l~~~s~~lSHELrtPL~~I~~~le~L~~~~~~~~~~~~le~i~~~i~~L~~li~~l~~~arle~~~~~~~~~~~dl~~ll  564 (703)
T TIGR03785       485 LENMSSRLSHELRTPVAVVRSSLENLELQALEQEKQKYLERAREGTERLSMILNNMSEATRLEQAIQSAEVEDFDLSEVL  564 (703)
T ss_pred             HHHHHHHHHHHHhhHHHHHHHHHHHHhccCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcccccccceeecHHHHH
Confidence            45799999999999999999999999877777788889999999999999999999999999988777788899999999


Q ss_pred             HHHHHHHHHHHh-hcceeccccCCCCCeeEEccHHHHHHHHHHHHhhhhhcCCCC-eeEEEEEecCCCCcccchhhhhhh
Q 039716          450 KHVLQTAAASLQ-KILMLEGDIADDVPIEVIGDVLRIRQILTNLISNAIKFTPEG-KVGIKLYVVPEPPFAKEGLKQKSK  527 (1002)
Q Consensus       450 ~~v~~~~~~~~~-k~i~l~~~i~~~~p~~v~gD~~rL~QIL~NLlsNAIKfT~~G-~I~I~v~~~~~~~~~~~~~~~~~~  527 (1002)
                      +.++..+..... +.+.+..  ..+ +..+.+|+..|.|||.|||+||+||++.| .|.|.+...               
T Consensus       565 ~~~i~~~~~~~~~~~i~l~i--~~~-~~~i~~d~~~L~~il~NLI~NAik~s~~~~~I~I~~~~~---------------  626 (703)
T TIGR03785       565 SGCMQGYQMTYPPQRFELNI--PET-PLVMRGSPELIAQMLDKLVDNAREFSPEDGLIEVGLSQN---------------  626 (703)
T ss_pred             HHHHHHHHHHhhcCCEEEEe--cCC-CeEEEECHHHHHHHHHHHHHHHHHHCCCCCeEEEEEEEc---------------
Confidence            999887765543 3344333  222 33688999999999999999999999764 565554321               


Q ss_pred             hhhcchhhhhhhccCCCCCccCCCCCCCCCCCCCCccCCCCCCCCCCCccCCCCCccccccceEEEEEEEecCCCCCcCc
Q 039716          528 AYQSATDAVKEEKHQPKSQTASDQNGFHDKKHGEGYQDHKHDDDPGTPVSHGNSMDEDLEATVWIRCDVYDTGIGIPENA  607 (1002)
Q Consensus       528 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~i~V~DtGiGI~~e~  607 (1002)
                                                                                   ...+.|+|.|+|+||+++.
T Consensus       627 -------------------------------------------------------------~~~v~I~V~D~G~GI~~e~  645 (703)
T TIGR03785       627 -------------------------------------------------------------KSHALLTVSNEGPPLPEDM  645 (703)
T ss_pred             -------------------------------------------------------------CCEEEEEEEEcCCCCCHHH
Confidence                                                                         1147899999999999999


Q ss_pred             HhhhhhhccCCCccccCcCCCccccHHHHHHHHHHhCCEEEEEeecC-CceEEEEEEe
Q 039716          608 LPTLFRKYMQVSADHARKYGGTGLGLAICKQLVELMGGRLTVTSKVH-CGSTFTFILP  664 (1002)
Q Consensus       608 l~~IF~pF~q~~~~~~~~~~GtGLGLaI~k~Lve~~gG~I~v~S~~g-~GTtF~~~LP  664 (1002)
                      +++||+||++.+.......+|+||||+|||+||+.|||+|++.|.++ +|++|+|+||
T Consensus       646 ~~~IFe~F~t~~~~~~~~~~g~GLGL~Ivr~Iv~~~gG~I~v~s~~~g~Gt~f~I~LP  703 (703)
T TIGR03785       646 GEQLFDSMVSVRDQGAQDQPHLGLGLYIVRLIADFHQGRIQAENRQQNDGVVFRISLP  703 (703)
T ss_pred             HHHHhCCCeecCCCCCCCCCCccHHHHHHHHHHHHcCCEEEEEECCCCCeEEEEEEeC
Confidence            99999999987654444456899999999999999999999999875 8999999998

This histidine kinase protein is paired with an adjacent response regulator (TIGR03787) gene. It co-occurs with a variant sortase enzyme (TIGR03784), usually in the same gene neighborhood, in proteobacterial species most of which are marine, and with an LPXTG motif-containing sortase target conserved protein (TIGR03788). Sortases and LPXTG proteins are far more common in Gram-positive bacteria, where sortase systems mediate attachment to the cell wall or cross-linking of pilin structures. We give this predicted sensor histidine kinase the gene symbol psdS, for Proteobacterial Dedicated Sortase system Sensor histidine kinase.

>TIGR01386 cztS_silS_copS heavy metal sensor kinase

Probab=99.95  E-value=1.9e-26  Score=272.14  Aligned_cols=215  Identities=26%  Similarity=0.456  Sum_probs=180.2

Q ss_pred             HHHHHHHHhhhccccHHHHHHHHHHHHhCCC-CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCeeeEeeecCHHH
Q 039716          369 RAKQMLATMSHEIRSPLTGVVSMAEILSNTK-LDREQRQLLGVMISSGDLVLQLINDILDLSKVESGVMKLEAAKFRPRE  447 (1002)
Q Consensus       369 ~~k~fla~iSHELRTPL~~I~g~~elL~~~~-l~~~~~~~l~~i~~s~~~L~~LIndlLd~skiesg~~~l~~~~~~l~~  447 (1002)
                      +.++|.+.+||||||||+++.+.++.+.... ..++..+++..+.....++..++++++.+++++.....+...++++.+
T Consensus       240 ~~~~~~~~~~h~l~tpl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~ll~~~~~~~~~~~~~~~~~~~~~  319 (457)
T TIGR01386       240 RLSQFSADLAHELRTPLTNLLGQTQVALSQPRTGEEYREVLESNLEELERLSRMVSDMLFLARADNGQLALERVRLDLAA  319 (457)
T ss_pred             HHHHHHHhhhhhhcCcHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcccccccccccCHHH
Confidence            3457999999999999999999999875433 334556788888888999999999999999999988888888999999


Q ss_pred             HHHHHHHHHHHHH-hhcceeccccCCCCCeeEEccHHHHHHHHHHHHhhhhhcCCC-CeeEEEEEecCCCCcccchhhhh
Q 039716          448 VVKHVLQTAAASL-QKILMLEGDIADDVPIEVIGDVLRIRQILTNLISNAIKFTPE-GKVGIKLYVVPEPPFAKEGLKQK  525 (1002)
Q Consensus       448 li~~v~~~~~~~~-~k~i~l~~~i~~~~p~~v~gD~~rL~QIL~NLlsNAIKfT~~-G~I~I~v~~~~~~~~~~~~~~~~  525 (1002)
                      ++..++..+.... ++.+.+...  ..  ..+.+|+..|.+++.||+.||+||++. |.|.|.+...             
T Consensus       320 ~~~~~~~~~~~~~~~~~i~~~~~--~~--~~~~~~~~~l~~~~~nll~Nai~~~~~~~~I~i~~~~~-------------  382 (457)
T TIGR01386       320 ELAKVAEYFEPLAEERGVRIRVE--GE--GLVRGDPQMFRRAISNLLSNALRHTPDGGTITVRIERR-------------  382 (457)
T ss_pred             HHHHHHHHHHHHHHhCCeEEEec--CC--ceEEECHHHHHHHHHHHHHHHHHcCCCCceEEEEEEec-------------
Confidence            9999988776533 344444333  22  468899999999999999999999976 5677765321             


Q ss_pred             hhhhhcchhhhhhhccCCCCCccCCCCCCCCCCCCCCccCCCCCCCCCCCccCCCCCccccccceEEEEEEEecCCCCCc
Q 039716          526 SKAYQSATDAVKEEKHQPKSQTASDQNGFHDKKHGEGYQDHKHDDDPGTPVSHGNSMDEDLEATVWIRCDVYDTGIGIPE  605 (1002)
Q Consensus       526 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~i~V~DtGiGI~~  605 (1002)
                                                                                     ...+.|+|.|+|+|||+
T Consensus       383 ---------------------------------------------------------------~~~~~i~v~D~G~g~~~  399 (457)
T TIGR01386       383 ---------------------------------------------------------------SDEVRVSVSNPGPGIPP  399 (457)
T ss_pred             ---------------------------------------------------------------CCEEEEEEEeCCCCCCH
Confidence                                                                           11378999999999999


Q ss_pred             CcHhhhhhhccCCCccccCcCCCccccHHHHHHHHHHhCCEEEEEeecCCceEEEEEEe
Q 039716          606 NALPTLFRKYMQVSADHARKYGGTGLGLAICKQLVELMGGRLTVTSKVHCGSTFTFILP  664 (1002)
Q Consensus       606 e~l~~IF~pF~q~~~~~~~~~~GtGLGLaI~k~Lve~~gG~I~v~S~~g~GTtF~~~LP  664 (1002)
                      +.+.++|+|||+.+...+.+.+|+||||+||+++++.|||+|++++ +++||+|++.||
T Consensus       400 ~~~~~~~~~~~~~~~~~~~~~~g~GlGL~i~~~~~~~~~G~~~~~~-~~~G~~~~~~~P  457 (457)
T TIGR01386       400 EHLSRLFDRFYRVDPARSNSGEGTGLGLAIVRSIMEAHGGRASAES-PDGKTRFILRFP  457 (457)
T ss_pred             HHHHHhccccccCCcccCCCCCCccccHHHHHHHHHHCCCEEEEEe-CCCceEEEEecC
Confidence            9999999999998876556678999999999999999999999999 999999999998

Members of this family contain a sensor histidine kinase domain (Pfam:PF00512) and a domain found in bacterial signal proteins (Pfam:PF00672). This group is separated phylogenetically from related proteins with similar architecture and contains a number of proteins associated with heavy metal resistance efflux systems for copper, silver, cadmium, and/or zinc.

>PRK09835 sensor kinase CusS; Provisional

Probab=99.95  E-value=1.5e-26  Score=275.31  Aligned_cols=216  Identities=28%  Similarity=0.447  Sum_probs=178.3

Q ss_pred             HHHHHHHhhhccccHHHHHHHHHHHHhCCC-CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCeeeEeeecCHHHH
Q 039716          370 AKQMLATMSHEIRSPLTGVVSMAEILSNTK-LDREQRQLLGVMISSGDLVLQLINDILDLSKVESGVMKLEAAKFRPREV  448 (1002)
Q Consensus       370 ~k~fla~iSHELRTPL~~I~g~~elL~~~~-l~~~~~~~l~~i~~s~~~L~~LIndlLd~skiesg~~~l~~~~~~l~~l  448 (1002)
                      .++|++.+||||||||+.|.+.++.+.... ...+..+.+..+.....++..++++++++++.+.+.......++++.++
T Consensus       262 ~~~~~~~laheL~tpl~~i~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~i~~ll~~~~~~~~~~~~~~~~~~l~~~  341 (482)
T PRK09835        262 QSNFSADIAHEIRTPITNLITQTEIALSQSRSQKELEDVLYSNLEELTRMAKMVSDMLFLAQADNNQLIPEKKMLDLADE  341 (482)
T ss_pred             HHHHHHHHHHHhhhhHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCceeecHHHH
Confidence            347999999999999999999999765433 2345566777888888999999999999999999888777889999999


Q ss_pred             HHHHHHHHHHHH-hhcceeccccCCCCCeeEEccHHHHHHHHHHHHhhhhhcCCCC-eeEEEEEecCCCCcccchhhhhh
Q 039716          449 VKHVLQTAAASL-QKILMLEGDIADDVPIEVIGDVLRIRQILTNLISNAIKFTPEG-KVGIKLYVVPEPPFAKEGLKQKS  526 (1002)
Q Consensus       449 i~~v~~~~~~~~-~k~i~l~~~i~~~~p~~v~gD~~rL~QIL~NLlsNAIKfT~~G-~I~I~v~~~~~~~~~~~~~~~~~  526 (1002)
                      ++.+...+.... .+.+.+...  .. +..+.+|+.+|.||+.||+.||+||+++| .|.|.+...              
T Consensus       342 i~~~~~~~~~~~~~~~~~~~~~--~~-~~~v~~d~~~l~~vl~nll~Na~~~~~~~~~I~i~~~~~--------------  404 (482)
T PRK09835        342 VGKVFDFFEAWAEERGVELRFV--GD-PCQVAGDPLMLRRAISNLLSNALRYTPAGEAITVRCQEV--------------  404 (482)
T ss_pred             HHHHHHHHHHHHhhCCEEEEEe--CC-CcEEEECHHHHHHHHHHHHHHHHhcCCCCCeEEEEEEEe--------------
Confidence            999888776544 344554433  22 34688999999999999999999999765 466665321              


Q ss_pred             hhhhcchhhhhhhccCCCCCccCCCCCCCCCCCCCCccCCCCCCCCCCCccCCCCCccccccceEEEEEEEecCCCCCcC
Q 039716          527 KAYQSATDAVKEEKHQPKSQTASDQNGFHDKKHGEGYQDHKHDDDPGTPVSHGNSMDEDLEATVWIRCDVYDTGIGIPEN  606 (1002)
Q Consensus       527 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~i~V~DtGiGI~~e  606 (1002)
                                                                                    ...+.|+|.|+|+|||++
T Consensus       405 --------------------------------------------------------------~~~~~i~v~d~G~gi~~~  422 (482)
T PRK09835        405 --------------------------------------------------------------DHQVQLVVENPGTPIAPE  422 (482)
T ss_pred             --------------------------------------------------------------CCEEEEEEEECCCCcCHH
Confidence                                                                          013778999999999999


Q ss_pred             cHhhhhhhccCCCccccCcCCCccccHHHHHHHHHHhCCEEEEEeecCCceEEEEEEeC
Q 039716          607 ALPTLFRKYMQVSADHARKYGGTGLGLAICKQLVELMGGRLTVTSKVHCGSTFTFILPY  665 (1002)
Q Consensus       607 ~l~~IF~pF~q~~~~~~~~~~GtGLGLaI~k~Lve~~gG~I~v~S~~g~GTtF~~~LP~  665 (1002)
                      .++++|+|||+.+....++.+|+||||+||+++++.|||+|+++|.+ +||+|+|.||.
T Consensus       423 ~~~~if~~f~~~~~~~~~~~~g~GlGL~i~~~i~~~~~g~i~~~s~~-~g~~~~i~lP~  480 (482)
T PRK09835        423 HLPRLFDRFYRVDPSRQRKGEGSGIGLAIVKSIVVAHKGTVAVTSDA-RGTRFVISLPR  480 (482)
T ss_pred             HHHHHhCCcccCCCCCCCCCCCcchHHHHHHHHHHHCCCEEEEEECC-CcEEEEEEeeC
Confidence            99999999999876655566799999999999999999999999974 69999999995

>PRK09470 cpxA two-component sensor protein; Provisional

Probab=99.95  E-value=5.1e-26  Score=269.15  Aligned_cols=215  Identities=26%  Similarity=0.397  Sum_probs=175.1

Q ss_pred             HHHHHHHhhhccccHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCeeeEeeecCHHHHH
Q 039716          370 AKQMLATMSHEIRSPLTGVVSMAEILSNTKLDREQRQLLGVMISSGDLVLQLINDILDLSKVESGVMKLEAAKFRPREVV  449 (1002)
Q Consensus       370 ~k~fla~iSHELRTPL~~I~g~~elL~~~~l~~~~~~~l~~i~~s~~~L~~LIndlLd~skiesg~~~l~~~~~~l~~li  449 (1002)
                      .++|++++||||||||++|.+..+++.....+.   ..+..+...++++..+|++++.+++.+... .+....+++..++
T Consensus       243 ~~~~~~~~shel~tpl~~i~~~~~~~~~~~~~~---~~~~~i~~~~~~l~~~i~~l~~~~~~~~~~-~~~~~~~~l~~~~  318 (461)
T PRK09470        243 QQRLLSDISHELRTPLTRLQLATALLRRRQGES---KELERIETEAQRLDSMINDLLVLSRNQQKN-HLERETFKANSLW  318 (461)
T ss_pred             HHHHHHhhhHhhCCHHHHHHHHHHHHhhccCCh---HHHHHHHHHHHHHHHHHHHHHHHHHhhccc-ccccceecHHHHH
Confidence            357999999999999999999999886543332   245677889999999999999999987643 4566789999999


Q ss_pred             HHHHHHHHHHH-hhcceeccccCCCCCeeEEccHHHHHHHHHHHHhhhhhcCCCCeeEEEEEecCCCCcccchhhhhhhh
Q 039716          450 KHVLQTAAASL-QKILMLEGDIADDVPIEVIGDVLRIRQILTNLISNAIKFTPEGKVGIKLYVVPEPPFAKEGLKQKSKA  528 (1002)
Q Consensus       450 ~~v~~~~~~~~-~k~i~l~~~i~~~~p~~v~gD~~rL~QIL~NLlsNAIKfT~~G~I~I~v~~~~~~~~~~~~~~~~~~~  528 (1002)
                      ++++....... ...+.+.....+ .+..+.+|+..|.+++.||+.||+||++ +.|.|.+...                
T Consensus       319 ~~~~~~~~~~~~~~~~~~~i~~~~-~~~~~~~~~~~l~~~l~nli~NA~~~~~-~~i~i~~~~~----------------  380 (461)
T PRK09470        319 SEVLEDAKFEAEQMGKSLTVSAPP-GPWPINGNPNALASALENIVRNALRYSH-TKIEVAFSVD----------------  380 (461)
T ss_pred             HHHHHHHHHHHHHCCCeEEEecCC-cceEEEECHHHHHHHHHHHHHHHHHhCC-CcEEEEEEEE----------------
Confidence            98887665433 244544444222 3457899999999999999999999986 4566655321                


Q ss_pred             hhcchhhhhhhccCCCCCccCCCCCCCCCCCCCCccCCCCCCCCCCCccCCCCCccccccceEEEEEEEecCCCCCcCcH
Q 039716          529 YQSATDAVKEEKHQPKSQTASDQNGFHDKKHGEGYQDHKHDDDPGTPVSHGNSMDEDLEATVWIRCDVYDTGIGIPENAL  608 (1002)
Q Consensus       529 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~i~V~DtGiGI~~e~l  608 (1002)
                                                                                  ...+.|+|.|+|+||+++.+
T Consensus       381 ------------------------------------------------------------~~~~~i~V~D~G~Gi~~~~~  400 (461)
T PRK09470        381 ------------------------------------------------------------KDGLTITVDDDGPGVPEEER  400 (461)
T ss_pred             ------------------------------------------------------------CCEEEEEEEECCCCCCHHHH
Confidence                                                                        11478999999999999999


Q ss_pred             hhhhhhccCCCccccCcCCCccccHHHHHHHHHHhCCEEEEEeecCCceEEEEEEeCC
Q 039716          609 PTLFRKYMQVSADHARKYGGTGLGLAICKQLVELMGGRLTVTSKVHCGSTFTFILPYQ  666 (1002)
Q Consensus       609 ~~IF~pF~q~~~~~~~~~~GtGLGLaI~k~Lve~~gG~I~v~S~~g~GTtF~~~LP~~  666 (1002)
                      +++|+|||+.+....+..+|+||||+||+++|+.|||++.+.|.+++||+|++.||+.
T Consensus       401 ~~if~~~~~~~~~~~~~~~g~GlGL~iv~~~v~~~~G~l~~~s~~~~Gt~~~i~lp~~  458 (461)
T PRK09470        401 EQIFRPFYRVDEARDRESGGTGLGLAIVENAIQQHRGWVKAEDSPLGGLRLTIWLPLY  458 (461)
T ss_pred             HHhcCCCccCCcccCCCCCCcchhHHHHHHHHHHCCCEEEEEECCCCeEEEEEEeeCC
Confidence            9999999998766666678999999999999999999999999999999999999974

>PRK10337 sensor protein QseC; Provisional

Probab=99.95  E-value=2.8e-26  Score=270.89  Aligned_cols=212  Identities=21%  Similarity=0.362  Sum_probs=174.5

Q ss_pred             HHHHHHHHHhhhccccHHHHHHHHHHHHhCCCCCHH-HHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCeeeEeeecCHH
Q 039716          368 MRAKQMLATMSHEIRSPLTGVVSMAEILSNTKLDRE-QRQLLGVMISSGDLVLQLINDILDLSKVESGVMKLEAAKFRPR  446 (1002)
Q Consensus       368 ~~~k~fla~iSHELRTPL~~I~g~~elL~~~~l~~~-~~~~l~~i~~s~~~L~~LIndlLd~skiesg~~~l~~~~~~l~  446 (1002)
                      .+.++|++.+||||||||+.|.+.++.+.....+++ ...++..+...+.++..++++++.+++++.+.......++++.
T Consensus       235 ~~~~~~~~~~ahelrtpl~~i~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~l~~~ll~~~r~~~~~~~~~~~~~~l~  314 (449)
T PRK10337        235 VRERRFTSDAAHELRSPLAALKVQTEVAQLSDDDPQARKKALLQLHAGIDRATRLVDQLLTLSRLDSLDNLQDVAEIPLE  314 (449)
T ss_pred             HHHHHHHHHHHHHhcCHHHHHHHHHHHHhccCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCCCcccCHH
Confidence            344589999999999999999999988765444443 4568889999999999999999999999887666667789999


Q ss_pred             HHHHHHHHHHHHHHh-hcceeccccCCCCCeeEEccHHHHHHHHHHHHhhhhhcCCCC-eeEEEEEecCCCCcccchhhh
Q 039716          447 EVVKHVLQTAAASLQ-KILMLEGDIADDVPIEVIGDVLRIRQILTNLISNAIKFTPEG-KVGIKLYVVPEPPFAKEGLKQ  524 (1002)
Q Consensus       447 ~li~~v~~~~~~~~~-k~i~l~~~i~~~~p~~v~gD~~rL~QIL~NLlsNAIKfT~~G-~I~I~v~~~~~~~~~~~~~~~  524 (1002)
                      ++++.++..+..... +.+.+....++. +..+.+|+..|.+++.||++||+||+++| .|.|.+..             
T Consensus       315 ~~~~~~~~~~~~~~~~~~i~~~~~~~~~-~~~~~~~~~~l~~vl~Nli~NA~k~~~~~~~i~i~~~~-------------  380 (449)
T PRK10337        315 DLLQSAVMDIYHTAQQAGIDVRLTLNAH-PVIRTGQPLLLSLLVRNLLDNAIRYSPQGSVVDVTLNA-------------  380 (449)
T ss_pred             HHHHHHHHHHHHHHHHcCCEEEEecCCC-CceeecCHHHHHHHHHHHHHHHHhhCCCCCeEEEEEEe-------------
Confidence            999998877665443 566666655433 34578999999999999999999999875 55554310             


Q ss_pred             hhhhhhcchhhhhhhccCCCCCccCCCCCCCCCCCCCCccCCCCCCCCCCCccCCCCCccccccceEEEEEEEecCCCCC
Q 039716          525 KSKAYQSATDAVKEEKHQPKSQTASDQNGFHDKKHGEGYQDHKHDDDPGTPVSHGNSMDEDLEATVWIRCDVYDTGIGIP  604 (1002)
Q Consensus       525 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~i~V~DtGiGI~  604 (1002)
                                                                                         ..++|.|+|+|||
T Consensus       381 -------------------------------------------------------------------~~i~i~D~G~Gi~  393 (449)
T PRK10337        381 -------------------------------------------------------------------RNFTVRDNGPGVT  393 (449)
T ss_pred             -------------------------------------------------------------------eEEEEEECCCCCC
Confidence                                                                               2478999999999


Q ss_pred             cCcHhhhhhhccCCCccccCcCCCccccHHHHHHHHHHhCCEEEEEeecCCceEEEEEE
Q 039716          605 ENALPTLFRKYMQVSADHARKYGGTGLGLAICKQLVELMGGRLTVTSKVHCGSTFTFIL  663 (1002)
Q Consensus       605 ~e~l~~IF~pF~q~~~~~~~~~~GtGLGLaI~k~Lve~~gG~I~v~S~~g~GTtF~~~L  663 (1002)
                      ++.++++|+|||+.+.   ...+|+||||+||++++++|||+|+++|.+++|++|++.|
T Consensus       394 ~~~~~~if~~f~~~~~---~~~~g~GlGL~iv~~i~~~~gg~l~~~s~~~~G~~~~i~~  449 (449)
T PRK10337        394 PEALARIGERFYRPPG---QEATGSGLGLSIVRRIAKLHGMNVSFGNAPEGGFEAKVSW  449 (449)
T ss_pred             HHHHHHhcccccCCCC---CCCCccchHHHHHHHHHHHcCCEEEEEecCCCeEEEEEeC
Confidence            9999999999998643   2346999999999999999999999999999999999875

>PRK09467 envZ osmolarity sensor protein; Provisional

Probab=99.94  E-value=8.1e-26  Score=265.76  Aligned_cols=205  Identities=24%  Similarity=0.363  Sum_probs=164.2

Q ss_pred             HHHHHHhhhccccHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCeeeEeeecCHHHHHH
Q 039716          371 KQMLATMSHEIRSPLTGVVSMAEILSNTKLDREQRQLLGVMISSGDLVLQLINDILDLSKVESGVMKLEAAKFRPREVVK  450 (1002)
Q Consensus       371 k~fla~iSHELRTPL~~I~g~~elL~~~~l~~~~~~~l~~i~~s~~~L~~LIndlLd~skiesg~~~l~~~~~~l~~li~  450 (1002)
                      +.|++++||||||||+.|.++++++...     .....+.+....++|..++++++++.+.+.+   ....++++.+++.
T Consensus       230 ~~~~~~lsHeLrtPL~~i~~~~e~~~~~-----~~~~~~~i~~~~~~~~~~i~~~l~~~r~~~~---~~~~~~~l~~~~~  301 (435)
T PRK09467        230 TLLMAGVSHDLRTPLTRIRLATEMMSEE-----DGYLAESINKDIEECNAIIEQFIDYLRTGQE---MPMEMADLNALLG  301 (435)
T ss_pred             HHHHHHhhhhccchHHHHHHHHHhcccc-----hHHHHHHHHHHHHHHHHHHHHHHHHhcccCC---CCccccCHHHHHH
Confidence            4799999999999999999999877432     2234456778899999999999999987653   2356788999988


Q ss_pred             HHHHHHHHHHhhcceeccccCCCCCeeEEccHHHHHHHHHHHHhhhhhcCCCCeeEEEEEecCCCCcccchhhhhhhhhh
Q 039716          451 HVLQTAAASLQKILMLEGDIADDVPIEVIGDVLRIRQILTNLISNAIKFTPEGKVGIKLYVVPEPPFAKEGLKQKSKAYQ  530 (1002)
Q Consensus       451 ~v~~~~~~~~~k~i~l~~~i~~~~p~~v~gD~~rL~QIL~NLlsNAIKfT~~G~I~I~v~~~~~~~~~~~~~~~~~~~~~  530 (1002)
                      +++....   .....+...+... +..+.+|+..|.+|+.||+.||+||+ .|.|.|.+...                  
T Consensus       302 ~~~~~~~---~~~~~i~~~~~~~-~~~~~~~~~~l~~il~NLl~NA~k~~-~~~i~i~~~~~------------------  358 (435)
T PRK09467        302 EVIAAES---GYEREIETALQPG-PIEVPMNPIAIKRALANLVVNAARYG-NGWIKVSSGTE------------------  358 (435)
T ss_pred             HHHHHhh---hcCCeEEEecCCC-CceEEECHHHHHHHHHHHHHHHHHhC-CCeEEEEEEec------------------
Confidence            8876544   2223333333333 34789999999999999999999998 56676665321                  


Q ss_pred             cchhhhhhhccCCCCCccCCCCCCCCCCCCCCccCCCCCCCCCCCccCCCCCccccccceEEEEEEEecCCCCCcCcHhh
Q 039716          531 SATDAVKEEKHQPKSQTASDQNGFHDKKHGEGYQDHKHDDDPGTPVSHGNSMDEDLEATVWIRCDVYDTGIGIPENALPT  610 (1002)
Q Consensus       531 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~i~V~DtGiGI~~e~l~~  610 (1002)
                                                                                ...+.|+|.|+|+||+++.+++
T Consensus       359 ----------------------------------------------------------~~~~~i~V~D~G~Gi~~~~~~~  380 (435)
T PRK09467        359 ----------------------------------------------------------GKRAWFQVEDDGPGIPPEQLKH  380 (435)
T ss_pred             ----------------------------------------------------------CCEEEEEEEecCCCcCHHHHHH
Confidence                                                                      1137899999999999999999


Q ss_pred             hhhhccCCCccccCcCCCccccHHHHHHHHHHhCCEEEEEeecCCceEEEEEEeCC
Q 039716          611 LFRKYMQVSADHARKYGGTGLGLAICKQLVELMGGRLTVTSKVHCGSTFTFILPYQ  666 (1002)
Q Consensus       611 IF~pF~q~~~~~~~~~~GtGLGLaI~k~Lve~~gG~I~v~S~~g~GTtF~~~LP~~  666 (1002)
                      +|+||++.+..  ++.+|+||||+||+++++.|||+|.+.|.+++|++|+++||..
T Consensus       381 ~~~~f~~~~~~--~~~~g~GlGL~iv~~i~~~~~g~l~i~~~~~~G~~~~i~lp~~  434 (435)
T PRK09467        381 LFQPFTRGDSA--RGSSGTGLGLAIVKRIVDQHNGKVELGNSEEGGLSARAWLPLT  434 (435)
T ss_pred             hcCCcccCCCC--CCCCCeehhHHHHHHHHHHCCCEEEEEECCCCcEEEEEEEeCC
Confidence            99999987643  3457999999999999999999999999999999999999964

>PRK11100 sensory histidine kinase CreC; Provisional

Probab=99.94  E-value=3.6e-25  Score=262.49  Aligned_cols=217  Identities=28%  Similarity=0.467  Sum_probs=183.5

Q ss_pred             HHHHHHHhhhccccHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCeeeEeeecCHHHHH
Q 039716          370 AKQMLATMSHEIRSPLTGVVSMAEILSNTKLDREQRQLLGVMISSGDLVLQLINDILDLSKVESGVMKLEAAKFRPREVV  449 (1002)
Q Consensus       370 ~k~fla~iSHELRTPL~~I~g~~elL~~~~l~~~~~~~l~~i~~s~~~L~~LIndlLd~skiesg~~~l~~~~~~l~~li  449 (1002)
                      ..+|++.++||||||++.|.+.+++|......+...+++..+...++++..++++++.+++++.+.......++++.+++
T Consensus       256 ~~~~~~~~~h~l~~pl~~i~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~i~~l~~~~~~~~~~~~~~~~~~~~~~~~  335 (475)
T PRK11100        256 VEQYVQTLTHELKSPLAAIRGAAELLQEDPPPEDRARFTGNILTQSARLQQLIDRLLELARLEQRQELEVLEPVALAALL  335 (475)
T ss_pred             HHHHHHHhhhhhcCcHHHHHHHHHHHhccCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCCCCccceeccHHHHH
Confidence            35789999999999999999999998875445667789999999999999999999999999988777778899999999


Q ss_pred             HHHHHHHHHHH-hhcceeccccCCCCCeeEEccHHHHHHHHHHHHhhhhhcCCC-CeeEEEEEecCCCCcccchhhhhhh
Q 039716          450 KHVLQTAAASL-QKILMLEGDIADDVPIEVIGDVLRIRQILTNLISNAIKFTPE-GKVGIKLYVVPEPPFAKEGLKQKSK  527 (1002)
Q Consensus       450 ~~v~~~~~~~~-~k~i~l~~~i~~~~p~~v~gD~~rL~QIL~NLlsNAIKfT~~-G~I~I~v~~~~~~~~~~~~~~~~~~  527 (1002)
                      +.++..+.... .+.+.+....+   +..+.+|...|.+|+.||+.||+||+.+ |.|.|++...               
T Consensus       336 ~~~~~~~~~~~~~~~i~~~~~~~---~~~~~~~~~~l~~vl~nli~Na~~~~~~~~~i~i~~~~~---------------  397 (475)
T PRK11100        336 EELVEAREAQAAAKGITLRLRPD---DARVLGDPFLLRQALGNLLDNAIDFSPEGGTITLSAEVD---------------  397 (475)
T ss_pred             HHHHHHHHHHHHhCCceEEEeCC---CceEEECHHHHHHHHHHHHHHHHHhCCCCCEEEEEEEEc---------------
Confidence            99988776544 35566655543   4568899999999999999999999965 6777766421               


Q ss_pred             hhhcchhhhhhhccCCCCCccCCCCCCCCCCCCCCccCCCCCCCCCCCccCCCCCccccccceEEEEEEEecCCCCCcCc
Q 039716          528 AYQSATDAVKEEKHQPKSQTASDQNGFHDKKHGEGYQDHKHDDDPGTPVSHGNSMDEDLEATVWIRCDVYDTGIGIPENA  607 (1002)
Q Consensus       528 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~i~V~DtGiGI~~e~  607 (1002)
                                                                                   ...+.++|.|+|+|||++.
T Consensus       398 -------------------------------------------------------------~~~~~i~i~D~G~Gi~~~~  416 (475)
T PRK11100        398 -------------------------------------------------------------GEQVALSVEDQGPGIPDYA  416 (475)
T ss_pred             -------------------------------------------------------------CCEEEEEEEECCCCCCHHH
Confidence                                                                         1137889999999999999


Q ss_pred             HhhhhhhccCCCccccCcCCCccccHHHHHHHHHHhCCEEEEEeecCCceEEEEEEeCC
Q 039716          608 LPTLFRKYMQVSADHARKYGGTGLGLAICKQLVELMGGRLTVTSKVHCGSTFTFILPYQ  666 (1002)
Q Consensus       608 l~~IF~pF~q~~~~~~~~~~GtGLGLaI~k~Lve~~gG~I~v~S~~g~GTtF~~~LP~~  666 (1002)
                      ++++|++|++.... ....+|+||||+||+++++.|||+|.++|.++.||+|++.||..
T Consensus       417 ~~~i~~~~~~~~~~-~~~~~~~GlGL~i~~~~~~~~~G~i~i~s~~~~Gt~v~i~lp~~  474 (475)
T PRK11100        417 LPRIFERFYSLPRP-ANGRKSTGLGLAFVREVARLHGGEVTLRNRPEGGVLATLTLPRH  474 (475)
T ss_pred             HHHHHHHHccCCCC-CCCCCCcchhHHHHHHHHHHCCCEEEEEEcCCCeEEEEEEeeCC
Confidence            99999999976432 23457999999999999999999999999999999999999963

>COG0642 BaeS Signal transduction histidine kinase [Signal transduction mechanisms]

Probab=99.94  E-value=1.9e-25  Score=249.01  Aligned_cols=215  Identities=40%  Similarity=0.621  Sum_probs=174.7

Q ss_pred             HHHHHHHhhhccccHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCC-eeeEeeecCHHHH
Q 039716          370 AKQMLATMSHEIRSPLTGVVSMAEILSNTKLDREQRQLLGVMISSGDLVLQLINDILDLSKVESGV-MKLEAAKFRPREV  448 (1002)
Q Consensus       370 ~k~fla~iSHELRTPL~~I~g~~elL~~~~l~~~~~~~l~~i~~s~~~L~~LIndlLd~skiesg~-~~l~~~~~~l~~l  448 (1002)
                      ...|++.++||+|||++++.++++.+.....+ ...+++..+...++++..++++++++++.+.+. .......+++..+
T Consensus       115 ~~~~~~~~~hel~~pl~~i~~~~~~~~~~~~~-~~~~~~~~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~l~~~  193 (336)
T COG0642         115 KREFLANISHELRTPLTAIRGLLELLLEGLLD-PQRELLEIIEEEAERLLRLVNDLLDLSRLEAGTKLKLLLELVDLAEL  193 (336)
T ss_pred             HHHHHHhhhhhhcCcHHHHHHHHHHhccCCch-hHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccccCCCCcCHHHH
Confidence            35799999999999999999999866554222 267788888889999999999999999998863 3333566778888


Q ss_pred             HHHHHHHHHHHHh-hcceeccccCCCCCeeEEccHHHHHHHHHHHHhhhhhcCCCCeeEEEEEecCCCCcccchhhhhhh
Q 039716          449 VKHVLQTAAASLQ-KILMLEGDIADDVPIEVIGDVLRIRQILTNLISNAIKFTPEGKVGIKLYVVPEPPFAKEGLKQKSK  527 (1002)
Q Consensus       449 i~~v~~~~~~~~~-k~i~l~~~i~~~~p~~v~gD~~rL~QIL~NLlsNAIKfT~~G~I~I~v~~~~~~~~~~~~~~~~~~  527 (1002)
                      +.+++........ ..+.+.....  .+..+.+|+.++.|||.||++||+||++.|.|.|.+...               
T Consensus       194 ~~~~~~~~~~~~~~~~~~~~~~~~--~~~~v~~~~~~l~~vl~nLi~NAi~~~~~~~i~i~~~~~---------------  256 (336)
T COG0642         194 LEEVVRLLAPLAQEKGIELAVDLP--ELPYVLGDPERLRQVLVNLLSNAIKYTPGGEITISVRQD---------------  256 (336)
T ss_pred             HHHHHHHHHHHHHHcCCEEEEecC--CCceEeeCHHHHHHHHHHHHHHHhccCCCCeEEEEEEec---------------
Confidence            8888877766543 4454443332  344688999999999999999999999966777766321               


Q ss_pred             hhhcchhhhhhhccCCCCCccCCCCCCCCCCCCCCccCCCCCCCCCCCccCCCCCccccccceEEEEEEEecCCCCCcCc
Q 039716          528 AYQSATDAVKEEKHQPKSQTASDQNGFHDKKHGEGYQDHKHDDDPGTPVSHGNSMDEDLEATVWIRCDVYDTGIGIPENA  607 (1002)
Q Consensus       528 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~i~V~DtGiGI~~e~  607 (1002)
                                                                                   ..++.+.|.|+|+||+++.
T Consensus       257 -------------------------------------------------------------~~~i~i~V~D~G~Gi~~~~  275 (336)
T COG0642         257 -------------------------------------------------------------DEQVTISVEDTGPGIPEEE  275 (336)
T ss_pred             -------------------------------------------------------------CCeEEEEEEcCCCCCCHHH
Confidence                                                                         0158899999999999999


Q ss_pred             HhhhhhhccCCCccccCcCCCccccHHHHHHHHHHhCCEEEEEeecCCceEEEEEEeCCC
Q 039716          608 LPTLFRKYMQVSADHARKYGGTGLGLAICKQLVELMGGRLTVTSKVHCGSTFTFILPYQV  667 (1002)
Q Consensus       608 l~~IF~pF~q~~~~~~~~~~GtGLGLaI~k~Lve~~gG~I~v~S~~g~GTtF~~~LP~~~  667 (1002)
                      ++++|+||++.+....    |+||||+||+++++.|||.|.++|.+|.||+|+++||...
T Consensus       276 ~~~if~~~~~~~~~~~----g~GlGL~i~~~~~~~~~g~i~~~~~~~~Gt~~~i~lP~~~  331 (336)
T COG0642         276 LERIFEPFFRTDKSRS----GTGLGLAIVKRIVELHGGTISVESEPGKGTTFTIRLPLAP  331 (336)
T ss_pred             HHHhccCeeccCCCCC----CCCccHHHHHHHHHHcCCEEEEEecCCCceEEEEEEeccc
Confidence            9999999998765322    9999999999999999999999999999999999999754

>TIGR02916 PEP_his_kin putative PEP-CTERM system histidine kinase

Probab=99.94  E-value=5.3e-25  Score=272.94  Aligned_cols=261  Identities=21%  Similarity=0.322  Sum_probs=183.0

Q ss_pred             EEeeeecCCCCEEEEEEEeechhHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhccccHH
Q 039716          309 YVEPVFSKSGETIGVNYMGMDVTDQV---RKREKMAKLREEIAVQKAKETELNKTIHITEETMRAKQMLATMSHEIRSPL  385 (1002)
Q Consensus       309 ~~~p~~~~~G~~~gi~~~~~DITe~~---~~~~~~~~l~~el~~~~~~~~el~k~~~~~e~~~~~k~fla~iSHELRTPL  385 (1002)
                      .+.|+.. .|+++|++++..+.+...   .....+..+..+.+...+ ..++.+.+...++....+++.+.++||||||+
T Consensus       413 l~vPL~~-~~~~~G~l~l~~~~~~~~~~~e~~~lL~~l~~q~a~~l~-~~~~~~~l~~~~~~~~~~~~~a~i~HdLrn~l  490 (679)
T TIGR02916       413 LIVPLIS-GEELVGFVVLARPRTAGEFNWEVRDLLKTAGRQAASYLA-QMEASEALAEARQFEAFNRMSAFVVHDLKNLV  490 (679)
T ss_pred             EEEEecc-CCEEEEEEEEecCCCCCCCCHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHhccHH
Confidence            3468765 467899988876544210   011111111111111111 11111111122222333578899999999999


Q ss_pred             HHHHHHHHHHhCCCCCH-HHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCeeeEeeecCHHHHHHHHHHHHHHHHhhcc
Q 039716          386 TGVVSMAEILSNTKLDR-EQRQLLGVMISSGDLVLQLINDILDLSKVESGVMKLEAAKFRPREVVKHVLQTAAASLQKIL  464 (1002)
Q Consensus       386 ~~I~g~~elL~~~~l~~-~~~~~l~~i~~s~~~L~~LIndlLd~skiesg~~~l~~~~~~l~~li~~v~~~~~~~~~k~i  464 (1002)
                      +.+..+.+.+.....++ ...++++.+..+.++|.++++++.+..      ......++++.++++++....... ...+
T Consensus       491 ~~l~~~l~~~~~~~~~~~~~~~~l~~i~~~~~rl~~ll~~l~~~~------~~~~~~~~~l~~ll~~~~~~~~~~-~~~~  563 (679)
T TIGR02916       491 AQLSLLLRNAERHKDNPEFQDDMLETVENAVNRMKKLLAQLRSKG------LEEEKLCVDLVDLLRRAIASKRAQ-GPRP  563 (679)
T ss_pred             HHHHHHHHHHHhcccCHHHHHHHHHHHHHHHHHHHHHHHHHHhcc------cccCCccccHHHHHHHHHHHhhhh-cCCc
Confidence            99998888766544444 355688889999999999988875433      244556789999998887765432 1222


Q ss_pred             eeccccCCCCCeeEEccHHHHHHHHHHHHhhhhhcCCC-CeeEEEEEecCCCCcccchhhhhhhhhhcchhhhhhhccCC
Q 039716          465 MLEGDIADDVPIEVIGDVLRIRQILTNLISNAIKFTPE-GKVGIKLYVVPEPPFAKEGLKQKSKAYQSATDAVKEEKHQP  543 (1002)
Q Consensus       465 ~l~~~i~~~~p~~v~gD~~rL~QIL~NLlsNAIKfT~~-G~I~I~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  543 (1002)
                      .+.  +..+  ..+.+|+.+|.||+.||+.||+||++. |.|.|++...                               
T Consensus       564 ~l~--~~~~--~~v~~d~~~l~~vl~nLl~NAik~~~~~~~I~I~~~~~-------------------------------  608 (679)
T TIGR02916       564 EVS--IDTD--LSVRADRERLERVLGHLVQNALEATPGEGRVAIRVERE-------------------------------  608 (679)
T ss_pred             eEE--eCCC--ceEEECHHHHHHHHHHHHHHHHHhCCCCCcEEEEEEEc-------------------------------
Confidence            222  2222  468899999999999999999999975 6777766421                               


Q ss_pred             CCCccCCCCCCCCCCCCCCccCCCCCCCCCCCccCCCCCccccccceEEEEEEEecCCCCCcCc-HhhhhhhccCCCccc
Q 039716          544 KSQTASDQNGFHDKKHGEGYQDHKHDDDPGTPVSHGNSMDEDLEATVWIRCDVYDTGIGIPENA-LPTLFRKYMQVSADH  622 (1002)
Q Consensus       544 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~i~V~DtGiGI~~e~-l~~IF~pF~q~~~~~  622 (1002)
                                                                   ...+.|+|.|+|+|||++. .+++|+||++.+   
T Consensus       609 ---------------------------------------------~~~~~i~V~D~G~Gi~~~~i~~~lF~pf~~~~---  640 (679)
T TIGR02916       609 ---------------------------------------------CGAARIEIEDSGCGMSPAFIRERLFKPFDTTK---  640 (679)
T ss_pred             ---------------------------------------------CCEEEEEEEEcCCCcChHHHHHhcCCCCCCCC---
Confidence                                                         0147899999999999999 999999998753   


Q ss_pred             cCcCCCccccHHHHHHHHHHhCCEEEEEeecCCceEEEEEEe
Q 039716          623 ARKYGGTGLGLAICKQLVELMGGRLTVTSKVHCGSTFTFILP  664 (1002)
Q Consensus       623 ~~~~~GtGLGLaI~k~Lve~~gG~I~v~S~~g~GTtF~~~LP  664 (1002)
                         .+|+||||+|||++++.|||+|+++|.+|+||+|+++||
T Consensus       641 ---~~G~GLGL~i~~~iv~~~gG~i~v~s~~g~Gt~f~i~LP  679 (679)
T TIGR02916       641 ---GAGMGIGVYECRQYVEEIGGRIEVESTPGQGTIFTLVLP  679 (679)
T ss_pred             ---CCCcchhHHHHHHHHHHcCCEEEEEecCCCceEEEEEeC
Confidence               269999999999999999999999999999999999998

Members of this protein family have a novel N-terminal domain, a single predicted membrane-spanning helix, and a predicted cystosolic histidine kinase domain. We designate this protein PrsK, and its companion DNA-binding response regulator protein (TIGR02915) PrsR. These predicted signal-transducing proteins appear to enable enhancer-dependent transcriptional activation. The prsK gene is often associated with exopolysaccharide biosynthesis genes.

>COG3290 CitA Signal transduction histidine kinase regulating citrate/malate metabolism [Signal transduction mechanisms]

Probab=99.89  E-value=4.9e-20  Score=209.50  Aligned_cols=317  Identities=24%  Similarity=0.303  Sum_probs=210.5

Q ss_pred             hHHHHHHHHHHHHHHHHHHHhccCcEEEEecccccEEEeeccC---CCCC--cccccCCCchhccCccchhhhhHHHHHH
Q 039716          209 PVEELSQILKRADNFLHFVLQNAPVVMGHQDKELRYRFIYNHF---PSLH--EEDILGKTDVEIFSGAGVKESQDFKREV  283 (1002)
Q Consensus       209 ~~~~~~~~l~~~~~~l~~il~~~p~~i~~~d~~~~~~~~~~~~---~~~~--~e~iiGk~~~e~~~~~~~~~~~~~~~~v  283 (1002)
                      +=.|+.+.+++.++.|..    +--++...|..|.++.+|...   .++.  ..+.+|++..+++++..      ...++
T Consensus       206 EP~EIa~l~~er~A~l~s----i~EGviAvd~~G~It~~N~~A~~ll~~~~~~~~~ig~~i~~v~~p~~------~l~~v  275 (537)
T COG3290         206 EPEEIATLLEERQAMLQS----IKEGVIAVDKKGVITLINQAAQKLLGLRQPSGDPIGRSIVEVLPPDS------DLPEV  275 (537)
T ss_pred             CHHHHHHHHHHHHHHHHH----hhceEEEECCCCeEeehhHHHHHHhcccCcCcccccccceEeecccc------CcHHH
Confidence            345667777776666555    445788899999999998753   3333  35789999999988521      13456


Q ss_pred             HHhCCCcceeEEEEEeecCceEEEEEEeeeecCCCCEEEEEEEeechhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 039716          284 LEKGLPAKREITFETELFGSKTFLIYVEPVFSKSGETIGVNYMGMDVTDQVRKREKMAKLREEIAVQKAKETELNKTIHI  363 (1002)
Q Consensus       284 l~~g~~~~~e~~~~~~~~~~~~~~~~~~p~~~~~G~~~gi~~~~~DITe~~~~~~~~~~l~~el~~~~~~~~el~k~~~~  363 (1002)
                      ++.+.+...+..    ..+...+.+...|+.. .|+++|.+..++|-||-.+.-+++...++-                 
T Consensus       276 l~~~~~~~~~e~----~~ng~~~i~nr~pI~~-~~~~~GaI~tFRdktei~~L~eqLt~vr~y-----------------  333 (537)
T COG3290         276 LETGKPQHDEEI----RINGRLLVANRVPIRS-GGQIVGAIITFRDKTEIKKLTEQLTGVRQY-----------------  333 (537)
T ss_pred             HhcCCcccchhh----hcCCeEEEEEeccEEE-CCEEeEEEEEEecHHHHHHHHHHHHHHHHH-----------------
Confidence            777776533221    1245667777888875 689999999999998765443333322210                 


Q ss_pred             HHHHHHHHHHHHHhhhccccHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCeeeEeeec
Q 039716          364 TEETMRAKQMLATMSHEIRSPLTGVVSMAEILSNTKLDREQRQLLGVMISSGDLVLQLINDILDLSKVESGVMKLEAAKF  443 (1002)
Q Consensus       364 ~e~~~~~k~fla~iSHELRTPL~~I~g~~elL~~~~l~~~~~~~l~~i~~s~~~L~~LIndlLd~skiesg~~~l~~~~~  443 (1002)
                             .+-+...+||+.|=|+.|.|++++=.    -++..+|   |...+..-..+++.+..  ++            
T Consensus       334 -------a~aLRaq~HEfmNkLhtI~GLlql~~----yd~a~~~---I~~~~~~qq~~~~~l~~--~i------------  385 (537)
T COG3290         334 -------AEALRAQSHEFMNKLHTILGLLQLGE----YDDALDY---IQQESEEQQELIDSLSE--KI------------  385 (537)
T ss_pred             -------HHHHHHhhHHHHHHHHHHHHHHhhcc----HHHHHHH---HHHHHhhhhhhHHHHHH--hc------------
Confidence                   13456689999999999999888621    1223333   33333333334443321  11            


Q ss_pred             CHHHHHHHHH-HHHHHHHhhcceeccccCCCCCe-eEEccHHHHHHHHHHHHhhhhhcCC---C-CeeEEEEEecCCCCc
Q 039716          444 RPREVVKHVL-QTAAASLQKILMLEGDIADDVPI-EVIGDVLRIRQILTNLISNAIKFTP---E-GKVGIKLYVVPEPPF  517 (1002)
Q Consensus       444 ~l~~li~~v~-~~~~~~~~k~i~l~~~i~~~~p~-~v~gD~~rL~QIL~NLlsNAIKfT~---~-G~I~I~v~~~~~~~~  517 (1002)
                      . ..++..++ ......-..++.+..+....+|. .-.-++.-+--|+-||+.||+.++.   + ..|.+.+.-      
T Consensus       386 ~-~~~lAg~LlgK~~rArElgv~l~Id~~S~l~~~p~~~~~~~litIlGNLidNA~eA~~~~~~~k~I~l~i~~------  458 (537)
T COG3290         386 K-DPVLAGFLLGKISRARELGVSLIIDPNSQLPQLPSELQPHDLVTILGNLIDNALEALLAPEENKEIELSLSD------  458 (537)
T ss_pred             c-cHHHHHHHHhHHHHHHHcCceEEEcCCCcCCCCCCccChHHHHHHHHHHHHHHHHHhhccCCCcEEEEEEEe------
Confidence            0 11222222 22223333555555444333331 1335788889999999999999975   2 345444421      


Q ss_pred             ccchhhhhhhhhhcchhhhhhhccCCCCCccCCCCCCCCCCCCCCccCCCCCCCCCCCccCCCCCccccccceEEEEEEE
Q 039716          518 AKEGLKQKSKAYQSATDAVKEEKHQPKSQTASDQNGFHDKKHGEGYQDHKHDDDPGTPVSHGNSMDEDLEATVWIRCDVY  597 (1002)
Q Consensus       518 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~i~V~  597 (1002)
                                                                                            ...++.|+|.
T Consensus       459 ----------------------------------------------------------------------~~~~lvieV~  468 (537)
T COG3290         459 ----------------------------------------------------------------------RGDELVIEVA  468 (537)
T ss_pred             ----------------------------------------------------------------------cCCEEEEEEe
Confidence                                                                                  1226899999


Q ss_pred             ecCCCCCcCcHhhhhhhccCCCccccCcCCCccccHHHHHHHHHHhCCEEEEEeecCCceEEEEEEeCCC
Q 039716          598 DTGIGIPENALPTLFRKYMQVSADHARKYGGTGLGLAICKQLVELMGGRLTVTSKVHCGSTFTFILPYQV  667 (1002)
Q Consensus       598 DtGiGI~~e~l~~IF~pF~q~~~~~~~~~~GtGLGLaI~k~Lve~~gG~I~v~S~~g~GTtF~~~LP~~~  667 (1002)
                      |||+||||+..++||+.=|.++     ..+|.|.||++||++|+.+||.|+++|+.+.||+|+++||...
T Consensus       469 D~G~GI~~~~~~~iFe~G~Stk-----~~~~rGiGL~Lvkq~V~~~~G~I~~~s~~~~Gt~F~i~iP~~~  533 (537)
T COG3290         469 DTGPGIPPEVRDKIFEKGVSTK-----NTGGRGIGLYLVKQLVERLGGSIEVESEKGQGTRFSIYIPKVK  533 (537)
T ss_pred             CCCCCCChHHHHHHHhcCcccc-----CCCCCchhHHHHHHHHHHcCceEEEeeCCCCceEEEEECCCCc
Confidence            9999999999999999876543     2468999999999999999999999999999999999999853

>PRK11644 sensory histidine kinase UhpB; Provisional

Probab=99.88  E-value=7.6e-21  Score=226.55  Aligned_cols=190  Identities=15%  Similarity=0.252  Sum_probs=146.7

Q ss_pred             HHHHHHhhhccccHHHHHHHHHHHHhCCCC-CHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCeeeEeeecCHHHHH
Q 039716          371 KQMLATMSHEIRSPLTGVVSMAEILSNTKL-DREQRQLLGVMISSGDLVLQLINDILDLSKVESGVMKLEAAKFRPREVV  449 (1002)
Q Consensus       371 k~fla~iSHELRTPL~~I~g~~elL~~~~l-~~~~~~~l~~i~~s~~~L~~LIndlLd~skiesg~~~l~~~~~~l~~li  449 (1002)
                      +++.+.++||++|||++|.+.++++.+... +++..+..+.+...+.++.+.++++++..+..      ...++++.+.+
T Consensus       303 ~~ia~elhdeI~~pLtaI~~~a~ll~~~~~~~~~~~~~~~~I~~~~~~l~~~vr~LL~~lr~~------~l~~~~L~~~l  376 (495)
T PRK11644        303 RDVARELHDEIGQTITAIRTQAGIIKRLAADNASVKQSAQLIEQLSLGVYDTVRRLLGRLRPR------QLDDLTLEQAI  376 (495)
T ss_pred             HHHHHHhhhhhhhHHHHHHHHHHHHHhhccCChHHHHHHHHHHHHHHHHHHHHHHHHhccCCc------ccccCCHHHHH
Confidence            478889999999999999999999876433 34455778889999999999999998765422      23467888888


Q ss_pred             HHHHHHHHHHHh-hcceeccccCCCCCeeEEccHHHHHHHHHHHHhhhhhcCCCCeeEEEEEecCCCCcccchhhhhhhh
Q 039716          450 KHVLQTAAASLQ-KILMLEGDIADDVPIEVIGDVLRIRQILTNLISNAIKFTPEGKVGIKLYVVPEPPFAKEGLKQKSKA  528 (1002)
Q Consensus       450 ~~v~~~~~~~~~-k~i~l~~~i~~~~p~~v~gD~~rL~QIL~NLlsNAIKfT~~G~I~I~v~~~~~~~~~~~~~~~~~~~  528 (1002)
                      ++++..+..... ....+....+.  +....+|+..+.|++.|+++||+||++.|.|.|++...                
T Consensus       377 ~~l~~~l~~~~~~~~v~l~~~~~~--~~l~~~~~~~L~ril~nlL~NAiKha~~~~I~I~l~~~----------------  438 (495)
T PRK11644        377 RSLMREMELEDRGIVSHLDWRIDE--SALSETQRVTLFRVCQEGLNNIVKHADASAVTLQGWQQ----------------  438 (495)
T ss_pred             HHHHHHHHHhhcCceEEEEecCCc--ccCChhHHHHHHHHHHHHHHHHHHhCCCCEEEEEEEEc----------------
Confidence            888776653322 22333333222  22345678889999999999999999988877766421                


Q ss_pred             hhcchhhhhhhccCCCCCccCCCCCCCCCCCCCCccCCCCCCCCCCCccCCCCCccccccceEEEEEEEecCCCCCcCcH
Q 039716          529 YQSATDAVKEEKHQPKSQTASDQNGFHDKKHGEGYQDHKHDDDPGTPVSHGNSMDEDLEATVWIRCDVYDTGIGIPENAL  608 (1002)
Q Consensus       529 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~i~V~DtGiGI~~e~l  608 (1002)
                                                                                  ...+.++|+|+|+|||++. 
T Consensus       439 ------------------------------------------------------------~~~i~l~V~DnG~Gi~~~~-  457 (495)
T PRK11644        439 ------------------------------------------------------------DERLMLVIEDDGSGLPPGS-  457 (495)
T ss_pred             ------------------------------------------------------------CCEEEEEEEECCCCCCcCC-
Confidence                                                                        1147899999999999752 


Q ss_pred             hhhhhhccCCCccccCcCCCccccHHHHHHHHHHhCCEEEEEeecCCceEEEEEEeC
Q 039716          609 PTLFRKYMQVSADHARKYGGTGLGLAICKQLVELMGGRLTVTSKVHCGSTFTFILPY  665 (1002)
Q Consensus       609 ~~IF~pF~q~~~~~~~~~~GtGLGLaI~k~Lve~~gG~I~v~S~~g~GTtF~~~LP~  665 (1002)
                                        .|+|+||+|||++++.|||+|+++|  ++||+|+++||.
T Consensus       458 ------------------~~~GLGL~ivr~iv~~~GG~i~v~S--~~Gt~f~I~LP~  494 (495)
T PRK11644        458 ------------------GQQGFGLRGMRERVTALGGTLTISC--THGTRLSVSLPQ  494 (495)
T ss_pred             ------------------CCCCCcHHHHHHHHHHcCCEEEEEc--CCCEEEEEEEeC
Confidence                              3689999999999999999999999  789999999995

>COG4192 Signal transduction histidine kinase regulating phosphoglycerate transport system [Signal transduction mechanisms]

Probab=99.87  E-value=1.4e-20  Score=205.71  Aligned_cols=211  Identities=23%  Similarity=0.335  Sum_probs=166.9

Q ss_pred             HHHHHHhhhccccHHHHHHHHHHH---HhCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCeeeEeeecCHHH
Q 039716          371 KQMLATMSHEIRSPLTGVVSMAEI---LSNTKLDREQRQLLGVMISSGDLVLQLINDILDLSKVESGVMKLEAAKFRPRE  447 (1002)
Q Consensus       371 k~fla~iSHELRTPL~~I~g~~el---L~~~~l~~~~~~~l~~i~~s~~~L~~LIndlLd~skiesg~~~l~~~~~~l~~  447 (1002)
                      ++=+.++||||+.|||++..|.=-   ..+...+...+.+++.|..=.+|+-.+|+.+-.|+|-.+++-.+  .|+++.+
T Consensus       452 GqTmTslaHEinQPLnAmsaYLFsA~~A~e~~~s~qa~~~L~kie~L~eR~~~Iv~sLRqF~Rk~s~~~~l--qpV~L~~  529 (673)
T COG4192         452 GQTMTSLAHEINQPLNAMSAYLFSARLALEEAPSAQAATSLDKIENLTERMGKIVNSLRQFARKNSSDESL--QPVRLNS  529 (673)
T ss_pred             HHHHHHHHHHhcCchHHHHHHHHHHHHHHhhCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCc--ccccHHH
Confidence            467789999999999999887642   23344556678899999999999999999999999988877554  4788999


Q ss_pred             HHHHHHHHHHHHHhh-cceeccccCCCCCeeEEccHHHHHHHHHHHHhhhhhcCCCCeeEEEEEecCCCCcccchhhhhh
Q 039716          448 VVKHVLQTAAASLQK-ILMLEGDIADDVPIEVIGDVLRIRQILTNLISNAIKFTPEGKVGIKLYVVPEPPFAKEGLKQKS  526 (1002)
Q Consensus       448 li~~v~~~~~~~~~k-~i~l~~~i~~~~p~~v~gD~~rL~QIL~NLlsNAIKfT~~G~I~I~v~~~~~~~~~~~~~~~~~  526 (1002)
                      ++..+...+....+. .+.+....  + .+.|.||..+|+|||.||+-||+.++..-...|.+....             
T Consensus       530 ~v~~AweLl~~khk~rQ~~Li~pt--D-~~~V~gd~v~ieQVlvNl~~NaldA~~h~~p~i~~~~~~-------------  593 (673)
T COG4192         530 VVEQAWELLQTKHKRRQIKLINPT--D-DLMVMGDAVSIEQVLVNLIVNALDASTHFAPWIKLIALG-------------  593 (673)
T ss_pred             HHHHHHHHHHhhhhhccccccCCc--c-cceecchhhhHHHHHHHHHHHHHhhhccCCceEEEEeec-------------
Confidence            999888877765542 33333222  3 347999999999999999999999975432233332211             


Q ss_pred             hhhhcchhhhhhhccCCCCCccCCCCCCCCCCCCCCccCCCCCCCCCCCccCCCCCccccccceEEEEEEEecCCCCCcC
Q 039716          527 KAYQSATDAVKEEKHQPKSQTASDQNGFHDKKHGEGYQDHKHDDDPGTPVSHGNSMDEDLEATVWIRCDVYDTGIGIPEN  606 (1002)
Q Consensus       527 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~i~V~DtGiGI~~e  606 (1002)
                                                                                  .....+++.|.|+|.|.|-+
T Consensus       594 ------------------------------------------------------------~~~e~l~i~i~DnGqGwp~~  613 (673)
T COG4192         594 ------------------------------------------------------------TEQEMLRIAIIDNGQGWPHE  613 (673)
T ss_pred             ------------------------------------------------------------CcccceEEEEecCCCCCchh
Confidence                                                                        01124788999999999999


Q ss_pred             cHhhhhhhccCCCccccCcCCCccccHHHHHHHHHHhCCEEEEEeecCCceEEEEEEeC
Q 039716          607 ALPTLFRKYMQVSADHARKYGGTGLGLAICKQLVELMGGRLTVTSKVHCGSTFTFILPY  665 (1002)
Q Consensus       607 ~l~~IF~pF~q~~~~~~~~~~GtGLGLaI~k~Lve~~gG~I~v~S~~g~GTtF~~~LP~  665 (1002)
                      ..+++|.||.+.      |.-|.||||+||..|++.|.|.+.+.|...+|+++.+.|..
T Consensus       614 l~dkLl~PFtts------K~vgLGlGLSIsqSlmeqmqG~l~lAStLt~nA~ViL~f~v  666 (673)
T COG4192         614 LVDKLLTPFTTS------KEVGLGLGLSISQSLMEQMQGRLALASTLTKNAMVILEFQV  666 (673)
T ss_pred             HHHHhcCCcccc------cccccccchhHHHHHHHHhcCcchHhhhcccCcEEEEEEee
Confidence            999999999754      44599999999999999999999999999999999888864

>COG0745 OmpR Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]

Probab=99.83  E-value=4.1e-20  Score=197.21  Aligned_cols=116  Identities=32%  Similarity=0.460  Sum_probs=109.0

Q ss_pred             CeEEEEecCHHHHHHHHHHHHhcCCeEEEEcCHHHHHHHHHcCCCcEEEEcCCCCCCCHHHHHHHHhccccCCCchhhhh
Q 039716          860 PKILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDAAAE  939 (1002)
Q Consensus       860 ~~ILiVeDn~~n~~~l~~~L~~~g~~v~~a~~G~eAl~~~~~~~~DlIlmDi~MP~mdG~e~~~~IR~~~~~~~~~~~~~  939 (1002)
                      .+||||||++.....+...|++.||.|+.+.+|.+|++.+... ||+||+|++||+|||+++|++||+. .         
T Consensus         1 ~~ILiveDd~~i~~~l~~~L~~~g~~v~~~~~~~~a~~~~~~~-~dlviLD~~lP~~dG~~~~~~iR~~-~---------   69 (229)
T COG0745           1 MRILLVEDDPELAELLKEYLEEEGYEVDVAADGEEALEAAREQ-PDLVLLDLMLPDLDGLELCRRLRAK-K---------   69 (229)
T ss_pred             CeEEEEcCCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHHhcC-CCEEEEECCCCCCCHHHHHHHHHhh-c---------
Confidence            3799999999999999999999999999999999999999988 9999999999999999999999963 1         


Q ss_pred             hhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHHhhc
Q 039716          940 AGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQYF 1001 (1002)
Q Consensus       940 ~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~~l 1001 (1002)
                                     ...+|||++||..+.+++..++++|||||++|||++.+|...|+..+
T Consensus        70 ---------------~~~~PIi~Lta~~~~~d~v~gl~~GADDYl~KPf~~~EL~ARi~a~l  116 (229)
T COG0745          70 ---------------GSGPPIIVLTARDDEEDRVLGLEAGADDYLTKPFSPRELLARLRALL  116 (229)
T ss_pred             ---------------CCCCcEEEEECCCcHHHHHHHHhCcCCeeeeCCCCHHHHHHHHHHHH
Confidence                           24689999999999999999999999999999999999999988764

>PF02518 HATPase_c: Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase; InterPro: IPR003594 This domain is found in several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases [], heat shock protein HSP90 [, , ], phytochrome-like ATPases and DNA mismatch repair proteins

Probab=99.81  E-value=9.3e-20  Score=172.83  Aligned_cols=109  Identities=41%  Similarity=0.675  Sum_probs=97.1

Q ss_pred             ccHHHHHHHHHHHHhhhhhcCCC-CeeEEEEEecCCCCcccchhhhhhhhhhcchhhhhhhccCCCCCccCCCCCCCCCC
Q 039716          480 GDVLRIRQILTNLISNAIKFTPE-GKVGIKLYVVPEPPFAKEGLKQKSKAYQSATDAVKEEKHQPKSQTASDQNGFHDKK  558 (1002)
Q Consensus       480 gD~~rL~QIL~NLlsNAIKfT~~-G~I~I~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  558 (1002)
                      ||+.+|++||.||+.||++|++. |.|.|.+...                                              
T Consensus         1 gd~~~l~~il~~ll~Na~~~~~~~~~I~i~~~~~----------------------------------------------   34 (111)
T PF02518_consen    1 GDPDRLRQILSELLDNAIKHSPEGGKIDITIEED----------------------------------------------   34 (111)
T ss_dssp             ETHHHHHHHHHHHHHHHHHHHHHTSEEEEEEEEE----------------------------------------------
T ss_pred             CcHHHHHHHHHHHHHHHHHHhcCCCEEEEEEEEe----------------------------------------------
Confidence            79999999999999999999987 7888877532                                              


Q ss_pred             CCCCccCCCCCCCCCCCccCCCCCccccccceEEEEEEEecCCCCCcCcHhhhhhhccCCCccccCcCCCccccHHHHHH
Q 039716          559 HGEGYQDHKHDDDPGTPVSHGNSMDEDLEATVWIRCDVYDTGIGIPENALPTLFRKYMQVSADHARKYGGTGLGLAICKQ  638 (1002)
Q Consensus       559 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~i~V~DtGiGI~~e~l~~IF~pF~q~~~~~~~~~~GtGLGLaI~k~  638 (1002)
                                                    ..++.|+|.|+|.|||++.++++|.||++.+. .....+|+||||++|+.
T Consensus        35 ------------------------------~~~~~i~i~d~G~gi~~~~l~~~~~~~~~~~~-~~~~~~g~GlGL~~~~~   83 (111)
T PF02518_consen   35 ------------------------------DDHLSIEISDNGVGIPPEELEKLFEPFFTSDK-SETSISGHGLGLYIVKQ   83 (111)
T ss_dssp             ------------------------------TTEEEEEEEESSSSTTHHHHHHHCSTTSHSSS-SSGGSSSSSHHHHHHHH
T ss_pred             ------------------------------cCeEEEEEEeccccccccccccchhhcccccc-cccccCCCChHHHHHHH
Confidence                                          12588999999999999999999999998775 33456789999999999


Q ss_pred             HHHHhCCEEEEEeecCCceEEEEEEeC
Q 039716          639 LVELMGGRLTVTSKVHCGSTFTFILPY  665 (1002)
Q Consensus       639 Lve~~gG~I~v~S~~g~GTtF~~~LP~  665 (1002)
                      +++.|||+|++.|.+++||+|+|+||+
T Consensus        84 ~~~~~~g~l~~~~~~~~gt~v~~~~p~  110 (111)
T PF02518_consen   84 IAERHGGELTIESSEGGGTTVTFTLPL  110 (111)
T ss_dssp             HHHHTTEEEEEEEETTTEEEEEEEEEG
T ss_pred             HHHHCCCEEEEEEcCCCcEEEEEEEEC
Confidence            999999999999999999999999996

The fold of this domain consists of two layers, alpha/beta, which contains an 8-stranded mixed beta-sheet. More information about this protein can be found at Protein of the Month: DNA Topoisomerase [].; GO: 0005524 ATP binding; PDB: 3JZ3_A 3DGE_A 2C2A_A 2BU5_A 2BU8_A 2BU6_A 2BU7_A 2BU2_A 2BTZ_A 3K99_D ....

>PRK10935 nitrate/nitrite sensor protein NarQ; Provisional

Probab=99.80  E-value=1.4e-16  Score=193.98  Aligned_cols=193  Identities=19%  Similarity=0.260  Sum_probs=142.2

Q ss_pred             HHHHHhhhccccHHHHHHHHHHH----HhCC--CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCeeeEeeecCH
Q 039716          372 QMLATMSHEIRSPLTGVVSMAEI----LSNT--KLDREQRQLLGVMISSGDLVLQLINDILDLSKVESGVMKLEAAKFRP  445 (1002)
Q Consensus       372 ~fla~iSHELRTPL~~I~g~~el----L~~~--~l~~~~~~~l~~i~~s~~~L~~LIndlLd~skiesg~~~l~~~~~~l  445 (1002)
                      +..+.++||+++|++.+++++.+    +...  ...+...+.+..+.....++...+.+++...+.       ...++++
T Consensus       362 ~~~~~la~el~~~l~~~l~~~~~~~~~l~~~~~~~~~~~~~~l~~~~~~~~~~~~~l~~l~~~~~~-------~~~~~~l  434 (565)
T PRK10935        362 EERATIARELHDSLAQVLSYLKIQLTLLKRSLDEDNAKAQSIIAEFDQALSDAYRQLRELLTTFRL-------TIQEANL  434 (565)
T ss_pred             HHHHHHHHHhcchHHHHHHHHHHHHHHHHHhcccChHHHHHHHHHHHHHHHHHHHHHHHHHHHcCC-------CCCCCCH
Confidence            45567999999999988877653    3321  223455667777777888888888888865543       3456788


Q ss_pred             HHHHHHHHHHHHHHHhhcceeccccCCCCCeeEEccHHHHHHHHHHHHhhhhhcCCCCeeEEEEEecCCCCcccchhhhh
Q 039716          446 REVVKHVLQTAAASLQKILMLEGDIADDVPIEVIGDVLRIRQILTNLISNAIKFTPEGKVGIKLYVVPEPPFAKEGLKQK  525 (1002)
Q Consensus       446 ~~li~~v~~~~~~~~~k~i~l~~~i~~~~p~~v~gD~~rL~QIL~NLlsNAIKfT~~G~I~I~v~~~~~~~~~~~~~~~~  525 (1002)
                      .+++..++..+.......+.+....+.  .....+++.++.|++.||+.||+||++.|.|.|.+....            
T Consensus       435 ~~~l~~~~~~~~~~~~~~i~~~~~~~~--~~~~~~~~~~l~qv~~nll~NA~k~~~~~~i~i~~~~~~------------  500 (565)
T PRK10935        435 GSALEEMLDQLRNQTDAKITLDCRLPS--QALDAQQQVHLLQIIREATLNAIKHANASEIAVSCVTNP------------  500 (565)
T ss_pred             HHHHHHHHHHHHHhhCCeEEEEeeCCC--CCCCHHHHHHHHHHHHHHHHHHHhcCCCCeEEEEEEEcC------------
Confidence            899988888776544333333332221  112334566799999999999999999888777664210            


Q ss_pred             hhhhhcchhhhhhhccCCCCCccCCCCCCCCCCCCCCccCCCCCCCCCCCccCCCCCccccccceEEEEEEEecCCCCCc
Q 039716          526 SKAYQSATDAVKEEKHQPKSQTASDQNGFHDKKHGEGYQDHKHDDDPGTPVSHGNSMDEDLEATVWIRCDVYDTGIGIPE  605 (1002)
Q Consensus       526 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~i~V~DtGiGI~~  605 (1002)
                                                                                     ..++.|+|.|+|+|||+
T Consensus       501 ---------------------------------------------------------------~~~~~i~V~D~G~Gi~~  517 (565)
T PRK10935        501 ---------------------------------------------------------------DGEHTVSIRDDGIGIGE  517 (565)
T ss_pred             ---------------------------------------------------------------CCEEEEEEEECCcCcCC
Confidence                                                                           11478999999999997


Q ss_pred             CcHhhhhhhccCCCccccCcCCCccccHHHHHHHHHHhCCEEEEEeecCCceEEEEEEeCC
Q 039716          606 NALPTLFRKYMQVSADHARKYGGTGLGLAICKQLVELMGGRLTVTSKVHCGSTFTFILPYQ  666 (1002)
Q Consensus       606 e~l~~IF~pF~q~~~~~~~~~~GtGLGLaI~k~Lve~~gG~I~v~S~~g~GTtF~~~LP~~  666 (1002)
                      +.                  ..|+||||+||+++++.|||+|+++|.+|+||+|+|.||..
T Consensus       518 ~~------------------~~~~glGL~i~~~iv~~~~G~i~v~s~~~~Gt~~~i~lP~~  560 (565)
T PRK10935        518 LK------------------EPEGHYGLNIMQERAERLGGTLTISQPPGGGTTVSLTFPSQ  560 (565)
T ss_pred             CC------------------CCCCCcCHHHHHHHHHHcCCEEEEEECCCCcEEEEEEECCC
Confidence            32                  23789999999999999999999999999999999999975

>PRK10600 nitrate/nitrite sensor protein NarX; Provisional

Probab=99.75  E-value=6.8e-16  Score=188.15  Aligned_cols=183  Identities=17%  Similarity=0.215  Sum_probs=134.6

Q ss_pred             cccHHHHHHHHHHHHhC--CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCeeeEeeecCHHHHHHHHHHHHHH
Q 039716          381 IRSPLTGVVSMAEILSN--TKLDREQRQLLGVMISSGDLVLQLINDILDLSKVESGVMKLEAAKFRPREVVKHVLQTAAA  458 (1002)
Q Consensus       381 LRTPL~~I~g~~elL~~--~~l~~~~~~~l~~i~~s~~~L~~LIndlLd~skiesg~~~l~~~~~~l~~li~~v~~~~~~  458 (1002)
                      +..+|+.+...+..+..  ...+++.++.+..|....+++...+.++|...+..       ..+.++.+.+..++..+..
T Consensus       373 i~~~L~~l~~~~~~l~~~~~~~~~~~~~~l~~i~~~~~~~~~~lr~ll~~~r~~-------~~~~~l~~~l~~~~~~~~~  445 (569)
T PRK10600        373 IAQSLSCMKMQVSCLQMQGDALPESSRELLSQIRNELNASWRQLRELLTTFRLQ-------LTEPGLRPALEASCEEFSA  445 (569)
T ss_pred             HHHHHHHHHHHHHHHHhcccCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHcCcC-------cccCCHHHHHHHHHHHHHH
Confidence            33445555555554432  33456778899999999999999999999877643       2456788888888877665


Q ss_pred             HHhhcceeccccCCCCCeeEEccHHHHHHHHHHHHhhhhhcCCCCeeEEEEEecCCCCcccchhhhhhhhhhcchhhhhh
Q 039716          459 SLQKILMLEGDIADDVPIEVIGDVLRIRQILTNLISNAIKFTPEGKVGIKLYVVPEPPFAKEGLKQKSKAYQSATDAVKE  538 (1002)
Q Consensus       459 ~~~k~i~l~~~i~~~~p~~v~gD~~rL~QIL~NLlsNAIKfT~~G~I~I~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  538 (1002)
                      .....+.+....++. + ....++..|.||+.|+++||+||++.|.|.|.+...                          
T Consensus       446 ~~~~~i~~~~~~~~~-~-~~~~~~~~l~~il~ell~NA~kha~a~~i~V~~~~~--------------------------  497 (569)
T PRK10600        446 RFGFPVKLDYQLPPR-L-VPSHQAIHLLQIAREALSNALKHAQASEVVVTVAQN--------------------------  497 (569)
T ss_pred             HhCCeEEEEecCCcc-c-CCHHHHHHHHHHHHHHHHHHHHhCCCCeEEEEEEEc--------------------------
Confidence            443333333322221 1 111245569999999999999999888777766321                          


Q ss_pred             hccCCCCCccCCCCCCCCCCCCCCccCCCCCCCCCCCccCCCCCccccccceEEEEEEEecCCCCCcCcHhhhhhhccCC
Q 039716          539 EKHQPKSQTASDQNGFHDKKHGEGYQDHKHDDDPGTPVSHGNSMDEDLEATVWIRCDVYDTGIGIPENALPTLFRKYMQV  618 (1002)
Q Consensus       539 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~i~V~DtGiGI~~e~l~~IF~pF~q~  618 (1002)
                                                                        ...+.|+|.|+|+|||++.           
T Consensus       498 --------------------------------------------------~~~~~l~V~D~G~Gi~~~~-----------  516 (569)
T PRK10600        498 --------------------------------------------------QNQVKLSVQDNGCGVPENA-----------  516 (569)
T ss_pred             --------------------------------------------------CCEEEEEEEECCCCCCccc-----------
Confidence                                                              1147899999999999863           


Q ss_pred             CccccCcCCCccccHHHHHHHHHHhCCEEEEEeecCCceEEEEEEeCC
Q 039716          619 SADHARKYGGTGLGLAICKQLVELMGGRLTVTSKVHCGSTFTFILPYQ  666 (1002)
Q Consensus       619 ~~~~~~~~~GtGLGLaI~k~Lve~~gG~I~v~S~~g~GTtF~~~LP~~  666 (1002)
                             ..|+|+||+||+.+++.|||+|++.|.+|+||+|+|+||..
T Consensus       517 -------~~~~glGL~i~~~~~~~lgG~l~i~s~~~~Gt~v~i~lp~~  557 (569)
T PRK10600        517 -------ERSNHYGLIIMRDRAQSLRGDCRVRRRESGGTEVVVTFIPE  557 (569)
T ss_pred             -------cCCCCccHHHHHHHHHHcCCEEEEEECCCCCEEEEEEEecC
Confidence                   12789999999999999999999999999999999999974

>COG3437 Response regulator containing a CheY-like receiver domain and an HD-GYP domain [Transcription / Signal transduction mechanisms]

Probab=99.72  E-value=2.8e-17  Score=178.54  Aligned_cols=119  Identities=31%  Similarity=0.507  Sum_probs=111.3

Q ss_pred             CCCCeEEEEecCHHHHHHHHHHHHhcCCeEEEEcCHHHHHHHHHcCCCcEEEEcCCCCCCCHHHHHHHHhccccCCCchh
Q 039716          857 KPKPKILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDA  936 (1002)
Q Consensus       857 ~~~~~ILiVeDn~~n~~~l~~~L~~~g~~v~~a~~G~eAl~~~~~~~~DlIlmDi~MP~mdG~e~~~~IR~~~~~~~~~~  936 (1002)
                      ....+||+|||.+.++..+...|+..||.|..|.||.+|++....+.+|+||+|++||+|||+++|++|+...       
T Consensus        12 ~~~~~vl~vDD~~~~~~~~~~lL~~~~y~v~~ae~g~~a~kl~~~~~~dlvllD~~mp~mdg~ev~~~lk~~~-------   84 (360)
T COG3437          12 DEKLTVLLVDDEPDNLEALRQLLRMIGYRVIEAENGEEALKLLQEEPPDLVLLDVRMPEMDGAEVLNKLKAMS-------   84 (360)
T ss_pred             cccceEEEecCchhHHHHHHHHHHhcccceeeecCchHHHHHhcccCCceEEeeccCCCccHHHHHHHHHhcC-------
Confidence            3467899999999999999999999999999999999999999999999999999999999999999999732       


Q ss_pred             hhhhhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHH
Q 039716          937 AAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLE  998 (1002)
Q Consensus       937 ~~~~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~  998 (1002)
                                      +...++|||++||.++.+...+|+++|+++||.||+++.+|...+.
T Consensus        85 ----------------p~t~~ip~i~lT~~~d~~~~~~~~~~g~~dyl~KP~~~~~l~~rv~  130 (360)
T COG3437          85 ----------------PSTRRIPVILLTAYADSEDRQRALEAGADDYLSKPISPKELVARVS  130 (360)
T ss_pred             ----------------CcccccceEEEeecCChHHHHHHHHhhHHHHhcCCCCHHHHHHHHH
Confidence                            3567899999999999999999999999999999999999988774

>COG2204 AtoC Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]

Probab=99.71  E-value=6.9e-17  Score=184.88  Aligned_cols=116  Identities=28%  Similarity=0.434  Sum_probs=110.5

Q ss_pred             CeEEEEecCHHHHHHHHHHHHhcCCeEEEEcCHHHHHHHHHcCCCcEEEEcCCCCCCCHHHHHHHHhccccCCCchhhhh
Q 039716          860 PKILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDAAAE  939 (1002)
Q Consensus       860 ~~ILiVeDn~~n~~~l~~~L~~~g~~v~~a~~G~eAl~~~~~~~~DlIlmDi~MP~mdG~e~~~~IR~~~~~~~~~~~~~  939 (1002)
                      .+||||||++..+..+..+|+..||.|..|.|+.+|++++....||+||+|+.||+|||+++++.|++.           
T Consensus         5 ~~iLvVDDd~~ir~~l~~~L~~~G~~v~~a~~~~~al~~i~~~~~~lvl~Di~mp~~~Gl~ll~~i~~~-----------   73 (464)
T COG2204           5 ARILVVDDDPDIRELLEQALELAGYEVVTAESAEEALEALSESPFDLVLLDIRMPGMDGLELLKEIKSR-----------   73 (464)
T ss_pred             CCEEEEeCCHHHHHHHHHHHHHcCCeEEEeCCHHHHHHHHhcCCCCEEEEecCCCCCchHHHHHHHHhh-----------
Confidence            469999999999999999999999999999999999999999899999999999999999999999973           


Q ss_pred             hhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHHhhc
Q 039716          940 AGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQYF 1001 (1002)
Q Consensus       940 ~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~~l 1001 (1002)
                                     .+.+|||+||++.+.+...+|++.||.|||.|||+++.|...+++.+
T Consensus        74 ---------------~~~~pVI~~Tg~g~i~~AV~A~k~GA~Dfl~KP~~~~~L~~~v~ral  120 (464)
T COG2204          74 ---------------DPDLPVIVMTGHGDIDTAVEALRLGAFDFLEKPFDLDRLLAIVERAL  120 (464)
T ss_pred             ---------------CCCCCEEEEeCCCCHHHHHHHHhcCcceeeeCCCCHHHHHHHHHHHH
Confidence                           37799999999999999999999999999999999999999998754

>PF00072 Response_reg: Response regulator receiver domain; InterPro: IPR001789 Two-component signal transduction systems enable bacteria to sense, respond, and adapt to a wide range of environments, stressors, and growth conditions []

Probab=99.71  E-value=1.1e-16  Score=151.27  Aligned_cols=111  Identities=28%  Similarity=0.484  Sum_probs=106.0

Q ss_pred             EEEEecCHHHHHHHHHHHHhcCC-eEEEEcCHHHHHHHHHcCCCcEEEEcCCCCCCCHHHHHHHHhccccCCCchhhhhh
Q 039716          862 ILLVEDNKINVMVAKSMMKQLGH-SIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDAAAEA  940 (1002)
Q Consensus       862 ILiVeDn~~n~~~l~~~L~~~g~-~v~~a~~G~eAl~~~~~~~~DlIlmDi~MP~mdG~e~~~~IR~~~~~~~~~~~~~~  940 (1002)
                      ||||||++..+..++..|+..|+ .|..+.++.+|+..+....||+||+|+.||+++|+++++.||..            
T Consensus         1 Ilivd~~~~~~~~l~~~l~~~~~~~v~~~~~~~~~~~~~~~~~~d~iiid~~~~~~~~~~~~~~i~~~------------   68 (112)
T PF00072_consen    1 ILIVDDDPEIRELLEKLLERAGYEEVTTASSGEEALELLKKHPPDLIIIDLELPDGDGLELLEQIRQI------------   68 (112)
T ss_dssp             EEEEESSHHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHHSTESEEEEESSSSSSBHHHHHHHHHHH------------
T ss_pred             cEEEECCHHHHHHHHHHHHhCCCCEEEEECCHHHHHHHhcccCceEEEEEeeeccccccccccccccc------------
Confidence            79999999999999999999999 99999999999999999999999999999999999999999973            


Q ss_pred             hhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHH
Q 039716          941 GIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLE  998 (1002)
Q Consensus       941 ~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~  998 (1002)
                                    .+.+|||++|++.+.....+++++|+++||.||++.++|...|+
T Consensus        69 --------------~~~~~ii~~t~~~~~~~~~~~~~~g~~~~l~kp~~~~~l~~~i~  112 (112)
T PF00072_consen   69 --------------NPSIPIIVVTDEDDSDEVQEALRAGADDYLSKPFSPEELRAAIN  112 (112)
T ss_dssp             --------------TTTSEEEEEESSTSHHHHHHHHHTTESEEEESSSSHHHHHHHHH
T ss_pred             --------------cccccEEEecCCCCHHHHHHHHHCCCCEEEECCCCHHHHHHhhC
Confidence                          25799999999999999999999999999999999999998874

Some bacteria can contain up to as many as 200 two-component systems that need tight regulation to prevent unwanted cross-talk []. These pathways have been adapted to response to a wide variety of stimuli, including nutrients, cellular redox state, changes in osmolarity, quorum signals, antibiotics, and more []. Two-component systems are comprised of a sensor histidine kinase (HK) and its cognate response regulator (RR) []. The HK catalyses its own auto-phosphorylation followed by the transfer of the phosphoryl group to the receiver domain on RR; phosphorylation of the RR usually activates an attached output domain, which can then effect changes in cellular physiology, often by regulating gene expression. Some HK are bifunctional, catalysing both the phosphorylation and dephosphorylation of their cognate RR. The input stimuli can regulate either the kinase or phosphatase activity of the bifunctional HK. A variant of the two-component system is the phospho-relay system. Here a hybrid HK auto-phosphorylates and then transfers the phosphoryl group to an internal receiver domain, rather than to a separate RR protein. The phosphoryl group is then shuttled to histidine phosphotransferase (HPT) and subsequently to a terminal RR, which can evoke the desired response [, ]. Bipartite response regulator proteins are involved in a two-component signal transduction system in bacteria, and certain eukaryotes like protozoa, that functions to detect and respond to environmental changes []. These systems have been detected during host invasion, drug resistance, motility, phosphate uptake, osmoregulation, and nitrogen fixation, amongst others []. The two-component system consists of a histidine protein kinase environmental sensor that phosphorylates the receiver domain of a response regulator protein; phosphorylation induces a conformational change in the response regulator, which activates the effector domain, triggering the cellular response []. The domains of the two-component proteins are highly modular, but the core structures and activities are maintained. The response regulators act as phosphorylation-activated switches to affect a cellular response, usually by transcriptional regulation. Most of these proteins consist of two domains, an N-terminal response regulator receiver domain, and a variable C-terminal effector domain with DNA-binding activity. This entry represents the response regulator receiver domain, which belongs to the CheY family, and receives the signal from the sensor partner in the two-component system.; GO: 0000156 two-component response regulator activity, 0000160 two-component signal transduction system (phosphorelay), 0006355 regulation of transcription, DNA-dependent; PDB: 2QR3_A 2QXY_A 1I3C_A 1JLK_A 2PKX_A 2PL1_A 3H1F_A 3H1E_A 3GWG_A 3H1G_A ....

>COG4753 Response regulator containing CheY-like receiver domain and AraC-type DNA-binding domain [Signal transduction mechanisms]

Probab=99.71  E-value=3.7e-17  Score=186.57  Aligned_cols=115  Identities=28%  Similarity=0.425  Sum_probs=107.0

Q ss_pred             CeEEEEecCHHHHHHHHHHHH--hcCCe-EEEEcCHHHHHHHHHcCCCcEEEEcCCCCCCCHHHHHHHHhccccCCCchh
Q 039716          860 PKILLVEDNKINVMVAKSMMK--QLGHS-IDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDA  936 (1002)
Q Consensus       860 ~~ILiVeDn~~n~~~l~~~L~--~~g~~-v~~a~~G~eAl~~~~~~~~DlIlmDi~MP~mdG~e~~~~IR~~~~~~~~~~  936 (1002)
                      .+||||||.+..++-|+.++.  ++|+. |.+|.||+||++.++...|||||+|+.||+|||+++++.|++.        
T Consensus         2 ykVlIVDDE~lIr~GLk~lI~w~~~g~eiVgtA~NG~eAleli~e~~pDiviTDI~MP~mdGLdLI~~ike~--------   73 (475)
T COG4753           2 YKVLIVDDEPLIREGLKSLIDWEALGIEVVGTAANGKEALELIQETQPDIVITDINMPGMDGLDLIKAIKEQ--------   73 (475)
T ss_pred             eeEEEecChHHHHHHHHHhCChhhcCCeEEEecccHHHHHHHHHhcCCCEEEEecCCCCCcHHHHHHHHHHh--------
Confidence            589999999999999999986  56776 6689999999999999999999999999999999999999973        


Q ss_pred             hhhhhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHHhh
Q 039716          937 AAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQY 1000 (1002)
Q Consensus       937 ~~~~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~~ 1000 (1002)
                                        .|.+-+|++||+.+=+.+.+|+..|+.|||.||++.++|..+|.++
T Consensus        74 ------------------~p~~~~IILSGy~eFeYak~Am~lGV~dYLLKP~~k~eL~~~L~ki  119 (475)
T COG4753          74 ------------------SPDTEFIILSGYDEFEYAKKAMKLGVKDYLLKPVDKAELEEALKKI  119 (475)
T ss_pred             ------------------CCCceEEEEeccchhHHHHHHHhcCchhheeCcCCHHHHHHHHHHH
Confidence                              3567899999999999999999999999999999999999999875

>COG0784 CheY FOG: CheY-like receiver [Signal transduction mechanisms]

Probab=99.70  E-value=3.8e-16  Score=151.48  Aligned_cols=118  Identities=31%  Similarity=0.515  Sum_probs=106.3

Q ss_pred             CCCeEEEEecCHHHHHHHHHHHHhcCCeEEEEcCHH-HHHHHHHcC-CCcEEEEcCCCCCCCHHHHHHHHhccccCCCch
Q 039716          858 PKPKILLVEDNKINVMVAKSMMKQLGHSIDVVNNGV-EAVHAVQCQ-NYDLILMDVCMPVMDGLKATRLIRSFEDTGNWD  935 (1002)
Q Consensus       858 ~~~~ILiVeDn~~n~~~l~~~L~~~g~~v~~a~~G~-eAl~~~~~~-~~DlIlmDi~MP~mdG~e~~~~IR~~~~~~~~~  935 (1002)
                      ...+||+|||++.++..+..+|...|+.+..+.+|. +|++.+... .||+|++|+.||+|||+++++.+|..       
T Consensus         4 ~~~~vLivdD~~~~~~~~~~~l~~~g~~v~~a~~g~~~al~~~~~~~~~dlii~D~~mp~~~G~~~~~~l~~~-------   76 (130)
T COG0784           4 SGLRVLVVDDEPVNRRLLKRLLEDLGYEVVEAADGEEEALELLRELPQPDLILLDINMPGMDGIELLRRLRAR-------   76 (130)
T ss_pred             CCcEEEEEcCCHHHHHHHHHHHHHcCCeEEEeCChHHHHHHHHHhCCCCCEEEEeCCCCCCCHHHHHHHHHhC-------
Confidence            456899999999999999999999999999999995 999999999 59999999999999999999999963       


Q ss_pred             hhhhhhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHH-HHHHHHhhc
Q 039716          936 AAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQK-LKECLEQYF 1001 (1002)
Q Consensus       936 ~~~~~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~-L~~~l~~~l 1001 (1002)
                                         .+.+|||++|++........++.+|+++|+.||+...+ |...+.+++
T Consensus        77 -------------------~~~~pvv~~t~~~~~~~~~~~~~~g~~~~l~kP~~~~~~l~~~i~~~~  124 (130)
T COG0784          77 -------------------GPNIPVILLTAYADEADRERALAAGADDYLTKPIFLEEELLAALRRLL  124 (130)
T ss_pred             -------------------CCCCCEEEEEcCcCHHHHHHHHHcCCCeEEcCCCCcHHHHHHHHHHHH
Confidence                               24578999999999988888899999999999977766 777777654

>COG4565 CitB Response regulator of citrate/malate metabolism [Transcription / Signal transduction mechanisms]

Probab=99.68  E-value=3e-16  Score=158.77  Aligned_cols=115  Identities=28%  Similarity=0.468  Sum_probs=107.0

Q ss_pred             eEEEEecCHHHHHHHHHHHHhc-CCe-EEEEcCHHHHHHHHHcCCCcEEEEcCCCCCCCHHHHHHHHhccccCCCchhhh
Q 039716          861 KILLVEDNKINVMVAKSMMKQL-GHS-IDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDAAA  938 (1002)
Q Consensus       861 ~ILiVeDn~~n~~~l~~~L~~~-g~~-v~~a~~G~eAl~~~~~~~~DlIlmDi~MP~mdG~e~~~~IR~~~~~~~~~~~~  938 (1002)
                      +||||||++...++-+.++++. ||. |-+|.++++|..++....|||||+|+.||+.+|++++..||+.          
T Consensus         2 ~VLIiEDD~mVaeih~~yv~~~~gF~~vg~A~~~~ea~~~i~~~~pDLILLDiYmPd~~Gi~lL~~ir~~----------   71 (224)
T COG4565           2 NVLIIEDDPMVAEIHRRYVKQIPGFSVVGTAGTLEEAKMIIEEFKPDLILLDIYMPDGNGIELLPELRSQ----------   71 (224)
T ss_pred             cEEEEcCchHHHHHHHHHHHhCCCceEEEeeccHHHHHHHHHhhCCCEEEEeeccCCCccHHHHHHHHhc----------
Confidence            7999999999999999999976 675 6689999999999999999999999999999999999999963          


Q ss_pred             hhhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHHhhc
Q 039716          939 EAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQYF 1001 (1002)
Q Consensus       939 ~~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~~l 1001 (1002)
                                      ...+-||++||-.+.+...+++..|+-|||.|||.++.|.++|.+|.
T Consensus        72 ----------------~~~~DVI~iTAA~d~~tI~~alr~Gv~DYLiKPf~~eRl~~aL~~y~  118 (224)
T COG4565          72 ----------------HYPVDVIVITAASDMETIKEALRYGVVDYLIKPFTFERLQQALTRYR  118 (224)
T ss_pred             ----------------CCCCCEEEEeccchHHHHHHHHhcCchhheecceeHHHHHHHHHHHH
Confidence                            35577999999999999999999999999999999999999999884

>COG4566 TtrR Response regulator [Signal transduction mechanisms]

Probab=99.64  E-value=1.8e-15  Score=150.25  Aligned_cols=117  Identities=22%  Similarity=0.326  Sum_probs=109.2

Q ss_pred             CCeEEEEecCHHHHHHHHHHHHhcCCeEEEEcCHHHHHHHHHcCCCcEEEEcCCCCCCCHHHHHHHHhccccCCCchhhh
Q 039716          859 KPKILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDAAA  938 (1002)
Q Consensus       859 ~~~ILiVeDn~~n~~~l~~~L~~~g~~v~~a~~G~eAl~~~~~~~~DlIlmDi~MP~mdG~e~~~~IR~~~~~~~~~~~~  938 (1002)
                      .+-|-||||+...+..+..+|+..||.+.+..++.+-+.......|-++|+|+.||+|+|+++-+++...          
T Consensus         4 ~~~V~vVDDD~~vr~al~~Ll~s~G~~v~~~~s~~~fL~~~~~~~pGclllDvrMPg~sGlelq~~L~~~----------   73 (202)
T COG4566           4 EPLVHVVDDDESVRDALAFLLESAGFQVKCFASAEEFLAAAPLDRPGCLLLDVRMPGMSGLELQDRLAER----------   73 (202)
T ss_pred             CCeEEEEcCcHHHHHHHHHHHHhCCceeeeecCHHHHHhhccCCCCCeEEEecCCCCCchHHHHHHHHhc----------
Confidence            4569999999999999999999999999999999999999778899999999999999999999999863          


Q ss_pred             hhhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHHhhc
Q 039716          939 EAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQYF 1001 (1002)
Q Consensus       939 ~~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~~l 1001 (1002)
                                      ..++|||++|++.+.....+++++|+-|||.|||+.+.|..+|++-+
T Consensus        74 ----------------~~~~PVIfiTGhgDIpmaV~AmK~GAvDFLeKP~~~q~Lldav~~Al  120 (202)
T COG4566          74 ----------------GIRLPVIFLTGHGDIPMAVQAMKAGAVDFLEKPFSEQDLLDAVERAL  120 (202)
T ss_pred             ----------------CCCCCEEEEeCCCChHHHHHHHHcchhhHHhCCCchHHHHHHHHHHH
Confidence                            35799999999999999999999999999999999999999988643

>COG2197 CitB Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]

Probab=99.62  E-value=6.2e-15  Score=156.04  Aligned_cols=115  Identities=23%  Similarity=0.367  Sum_probs=106.3

Q ss_pred             eEEEEecCHHHHHHHHHHHHhcC-Ce-EEEEcCHHHHHHHHHcCCCcEEEEcCCCCCCCHHHHHHHHhccccCCCchhhh
Q 039716          861 KILLVEDNKINVMVAKSMMKQLG-HS-IDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDAAA  938 (1002)
Q Consensus       861 ~ILiVeDn~~n~~~l~~~L~~~g-~~-v~~a~~G~eAl~~~~~~~~DlIlmDi~MP~mdG~e~~~~IR~~~~~~~~~~~~  938 (1002)
                      +||||||++..+.-++.+|...+ ++ +..+.||.+|++.+....||+||||+.||+|||+++++.||+           
T Consensus         2 ~vlivDDh~l~r~gl~~~L~~~~~~~vv~~a~~~~~~l~~~~~~~pdvvl~Dl~mP~~~G~e~~~~l~~-----------   70 (211)
T COG2197           2 KVLIVDDHPLVREGLRQLLELEPDLEVVGEASNGEEALDLARELKPDVVLLDLSMPGMDGLEALKQLRA-----------   70 (211)
T ss_pred             eEEEECCcHHHHHHHHHHHhhCCCCEEEEEeCCHHHHHHHhhhcCCCEEEEcCCCCCCChHHHHHHHHH-----------
Confidence            69999999999999999999876 66 556788999999999999999999999999999999999995           


Q ss_pred             hhhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHHhhc
Q 039716          939 EAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQYF 1001 (1002)
Q Consensus       939 ~~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~~l 1001 (1002)
                                     ..++++|+++|++.+.....+++++|+++|+.|..++++|..+|+..+
T Consensus        71 ---------------~~p~~~vvvlt~~~~~~~v~~al~~Ga~Gyl~K~~~~~~l~~ai~~v~  118 (211)
T COG2197          71 ---------------RGPDIKVVVLTAHDDPAYVIRALRAGADGYLLKDASPEELVEAIRAVA  118 (211)
T ss_pred             ---------------HCCCCcEEEEeccCCHHHHHHHHHcCCCEEEeCCCCHHHHHHHHHHHH
Confidence                           246789999999999999999999999999999999999999998653

>PLN03029 type-a response regulator protein; Provisional

Probab=99.62  E-value=6.2e-15  Score=157.62  Aligned_cols=119  Identities=23%  Similarity=0.482  Sum_probs=106.4

Q ss_pred             CCCeEEEEecCHHHHHHHHHHHHhcCCeEEEEcCHHHHHHHHHcC--------------------CCcEEEEcCCCCCCC
Q 039716          858 PKPKILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQ--------------------NYDLILMDVCMPVMD  917 (1002)
Q Consensus       858 ~~~~ILiVeDn~~n~~~l~~~L~~~g~~v~~a~~G~eAl~~~~~~--------------------~~DlIlmDi~MP~md  917 (1002)
                      ...+||||||++.++..+..+|+..||.|.++.+|.+|++.+..+                    .||+||+|+.||+|+
T Consensus         7 ~~~~VLiVdd~~~~~~~l~~~L~~~g~~v~~a~sg~~al~~l~~~~~d~~~p~~~~~~~~~~~~~~~dlVllD~~mp~~~   86 (222)
T PLN03029          7 SQFHVLAVDDSLIDRKLIEKLLKTSSYQVTTVDSGSKALKFLGLHEDDRSNPDTPSVSPNSHQEVEVNLIITDYCMPGMT   86 (222)
T ss_pred             CCccEEEEeCCHHHHHHHHHHHHHcCceEEEECCHHHHHHHHHhccccccccccccccccccccccCCEEEEcCCCCCCC
Confidence            457899999999999999999999999999999999999998654                    367999999999999


Q ss_pred             HHHHHHHHhccccCCCchhhhhhhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHH
Q 039716          918 GLKATRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECL  997 (1002)
Q Consensus       918 G~e~~~~IR~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l  997 (1002)
                      |+++++.||...                        ....+|||++|+........+|+.+|+++||.||++..+|...+
T Consensus        87 G~e~l~~ir~~~------------------------~~~~ipvIils~~~~~~~~~~al~~Ga~dyl~KP~~~~~L~~l~  142 (222)
T PLN03029         87 GYDLLKKIKESS------------------------SLRNIPVVIMSSENVPSRITRCLEEGAEEFFLKPVQLSDLNRLK  142 (222)
T ss_pred             HHHHHHHHHhcc------------------------ccCCCcEEEEeCCCCHHHHHHHHHhCchheEECCCCHHHHHHHH
Confidence            999999999632                        23568999999999999999999999999999999999997776


Q ss_pred             Hhh
Q 039716          998 EQY 1000 (1002)
Q Consensus       998 ~~~ 1000 (1002)
                      ..+
T Consensus       143 ~~~  145 (222)
T PLN03029        143 PHM  145 (222)
T ss_pred             HHH
Confidence            543

>COG3706 PleD Response regulator containing a CheY-like receiver domain and a GGDEF domain [Signal transduction mechanisms]

Probab=99.60  E-value=7.3e-15  Score=167.11  Aligned_cols=119  Identities=27%  Similarity=0.446  Sum_probs=111.3

Q ss_pred             CCCeEEEEecCHHHHHHHHHHHHhcCCeEEEEcCHHHHHHHHHcCCCcEEEEcCCCCCCCHHHHHHHHhccccCCCchhh
Q 039716          858 PKPKILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDAA  937 (1002)
Q Consensus       858 ~~~~ILiVeDn~~n~~~l~~~L~~~g~~v~~a~~G~eAl~~~~~~~~DlIlmDi~MP~mdG~e~~~~IR~~~~~~~~~~~  937 (1002)
                      ...+||+|||+..++..++.+|...||.|..|.+|.+|+..+....||+||.|+.||+|||+++|+++|+...       
T Consensus       131 ~~~kILvvdD~~~~~~~l~~~L~~~g~~v~~a~~~~~Al~~~~e~~~dlil~d~~mp~~dg~el~~~lr~~~~-------  203 (435)
T COG3706         131 APKKILVVDDDATQRERLRRILQVEGFRVVEATDGEEALLQLAELPPDLVLLDANMPDMDGLELCTRLRQLER-------  203 (435)
T ss_pred             cCceEEEEcCcHHHHHHHHHHHHhccceeeeecCHHHHHHHHhcCCCcEEEEecCCCccCHHHHHHHHhcccc-------
Confidence            4568999999999999999999999999999999999999999999999999999999999999999998643       


Q ss_pred             hhhhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHHhh
Q 039716          938 AEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQY 1000 (1002)
Q Consensus       938 ~~~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~~ 1000 (1002)
                                       ...+|||++|+..+.....++++.|++|||+||+...+|...+++.
T Consensus       204 -----------------t~~ipii~~~~~~d~~~~~~Af~~G~~Dyi~kPi~~~~l~~Rl~~~  249 (435)
T COG3706         204 -----------------TRDIPIILLSSKDDDELVVRAFELGVNDYITKPIEEGELRARLRRQ  249 (435)
T ss_pred             -----------------cccccEEEEecccchHHHHHHHHcCCcceEecCCCHHHHHHHHHHH
Confidence                             3679999999999999999999999999999999999888877654

>PRK10547 chemotaxis protein CheA; Provisional

Probab=99.59  E-value=2.2e-14  Score=173.55  Aligned_cols=77  Identities=25%  Similarity=0.483  Sum_probs=65.8

Q ss_pred             EEEEEEEecCCCCCcCcHh---------------------hhhhhccCCCccccCcCCCccccHHHHHHHHHHhCCEEEE
Q 039716          591 WIRCDVYDTGIGIPENALP---------------------TLFRKYMQVSADHARKYGGTGLGLAICKQLVELMGGRLTV  649 (1002)
Q Consensus       591 ~l~i~V~DtGiGI~~e~l~---------------------~IF~pF~q~~~~~~~~~~GtGLGLaI~k~Lve~~gG~I~v  649 (1002)
                      .+.|+|.|+|.||+++.+.                     .||.|||.+... .+..+|+|+||+|||++++.|||+|++
T Consensus       429 ~v~I~V~DdG~GId~e~i~~~a~~~Gl~~~~~ls~~e~~~lIF~pgfst~~~-~~~~sGrGvGL~iVk~~ve~lgG~I~v  507 (670)
T PRK10547        429 NICIEVTDDGAGLNRERILAKAASQGLAVSENMSDEEVGMLIFAPGFSTAEQ-VTDVSGRGVGMDVVKRNIQEMGGHVEI  507 (670)
T ss_pred             EEEEEEEeCCCCCCHHHHHHHHHHcCCCccccCCHHHHHHHhhcCCcccccc-cccCCCCchhHHHHHHHHHHcCCEEEE
Confidence            4789999999999987553                     699998765432 234579999999999999999999999


Q ss_pred             EeecCCceEEEEEEeCCCC
Q 039716          650 TSKVHCGSTFTFILPYQVS  668 (1002)
Q Consensus       650 ~S~~g~GTtF~~~LP~~~~  668 (1002)
                      +|.+|+||+|++.||+..+
T Consensus       508 ~S~~g~Gt~f~i~LPltla  526 (670)
T PRK10547        508 QSKQGKGTTIRILLPLTLA  526 (670)
T ss_pred             EecCCCcEEEEEEEechhh
Confidence            9999999999999998753

>PRK10046 dpiA two-component response regulator DpiA; Provisional

Probab=99.58  E-value=3.4e-14  Score=152.34  Aligned_cols=116  Identities=21%  Similarity=0.303  Sum_probs=106.0

Q ss_pred             CCeEEEEecCHHHHHHHHHHHHhc-CCe-EEEEcCHHHHHHHHHcCCCcEEEEcCCCCCCCHHHHHHHHhccccCCCchh
Q 039716          859 KPKILLVEDNKINVMVAKSMMKQL-GHS-IDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDA  936 (1002)
Q Consensus       859 ~~~ILiVeDn~~n~~~l~~~L~~~-g~~-v~~a~~G~eAl~~~~~~~~DlIlmDi~MP~mdG~e~~~~IR~~~~~~~~~~  936 (1002)
                      ..+||||||++..+..+..+|... |+. |..+.+|.+|++.+....||+||+|+.||+++|+++++.||..        
T Consensus         4 ~~~ilivdd~~~~~~~l~~~L~~~~~~~~v~~a~~~~~al~~~~~~~pdlvllD~~mp~~~gle~~~~l~~~--------   75 (225)
T PRK10046          4 PLTLLIVEDETPLAEMHAEYIRHIPGFSQILLAGNLAQARMMIERFKPGLILLDNYLPDGRGINLLHELVQA--------   75 (225)
T ss_pred             cceEEEECCCHHHHHHHHHHHHhCCCcEEEEEECCHHHHHHHHHhcCCCEEEEeCCCCCCcHHHHHHHHHhc--------
Confidence            368999999999999999999864 774 7789999999999999999999999999999999999999962        


Q ss_pred             hhhhhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHHhh
Q 039716          937 AAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQY 1000 (1002)
Q Consensus       937 ~~~~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~~ 1000 (1002)
                                        .+.+|||++|++...+...+++++|+++|+.||++.++|...|+++
T Consensus        76 ------------------~~~~~iivls~~~~~~~~~~al~~Ga~~yl~Kp~~~~~L~~~i~~~  121 (225)
T PRK10046         76 ------------------HYPGDVVFTTAASDMETVSEAVRCGVFDYLIKPIAYERLGQTLTRF  121 (225)
T ss_pred             ------------------CCCCCEEEEEcCCCHHHHHHHHHcCccEEEECCcCHHHHHHHHHHH
Confidence                              2457899999999999999999999999999999999999999764

>COG3947 Response regulator containing CheY-like receiver and SARP domains [Signal transduction mechanisms]

Probab=99.56  E-value=9.7e-15  Score=153.01  Aligned_cols=114  Identities=29%  Similarity=0.594  Sum_probs=103.0

Q ss_pred             CeEEEEecCHHHHHHHHHHHHhcCCeEEEEcCHHHHHHHHHcCCCcEEEEcCCCCCCCHHHHHHHHhccccCCCchhhhh
Q 039716          860 PKILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDAAAE  939 (1002)
Q Consensus       860 ~~ILiVeDn~~n~~~l~~~L~~~g~~v~~a~~G~eAl~~~~~~~~DlIlmDi~MP~mdG~e~~~~IR~~~~~~~~~~~~~  939 (1002)
                      ++|+||||+......+..+|++.|+.+-.++...+|++.+....|||||+|+.||+|+|++++.++|..+          
T Consensus         1 ~~~iiVDdd~a~~~~l~~iLs~~~~~~~~~~~~~eal~~Le~~kpDLifldI~mp~~ngiefaeQvr~i~----------   70 (361)
T COG3947           1 PRIIIVDDDAAIVKLLSVILSRAGHEVRSCSHPVEALDLLEVFKPDLIFLDIVMPYMNGIEFAEQVRDIE----------   70 (361)
T ss_pred             CcEEEEcchHHHHHHHHHHHHhccchhhccCCHHHHHHHHHhcCCCEEEEEeecCCccHHHHHHHHHHhh----------
Confidence            4799999999999999999999999999999999999999999999999999999999999999999753          


Q ss_pred             hhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHHhhc
Q 039716          940 AGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQYF 1001 (1002)
Q Consensus       940 ~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~~l 1001 (1002)
                                      +.+|||++|+++.  .....+..-.+|||.|||+++.|..+|.+.+
T Consensus        71 ----------------~~v~iifIssh~e--ya~dsf~~n~~dYl~KPvt~ekLnraIdr~~  114 (361)
T COG3947          71 ----------------SAVPIIFISSHAE--YADDSFGMNLDDYLPKPVTPEKLNRAIDRRL  114 (361)
T ss_pred             ----------------ccCcEEEEecchh--hhhhhcccchHhhccCCCCHHHHHHHHHHHh
Confidence                            5699999999864  4445555566999999999999999998765

>PRK11173 two-component response regulator; Provisional

Probab=99.54  E-value=1.2e-13  Score=148.60  Aligned_cols=114  Identities=22%  Similarity=0.363  Sum_probs=106.3

Q ss_pred             CeEEEEecCHHHHHHHHHHHHhcCCeEEEEcCHHHHHHHHHcCCCcEEEEcCCCCCCCHHHHHHHHhccccCCCchhhhh
Q 039716          860 PKILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDAAAE  939 (1002)
Q Consensus       860 ~~ILiVeDn~~n~~~l~~~L~~~g~~v~~a~~G~eAl~~~~~~~~DlIlmDi~MP~mdG~e~~~~IR~~~~~~~~~~~~~  939 (1002)
                      .+||||||++..+..+...|+..|+.|..+.++.+|+..+....||+||+|+.||.++|+++++.||..           
T Consensus         4 ~~iLiv~dd~~~~~~l~~~L~~~g~~v~~~~~~~~~~~~~~~~~~dlvild~~l~~~~g~~~~~~lr~~-----------   72 (237)
T PRK11173          4 PHILIVEDELVTRNTLKSIFEAEGYDVFEATDGAEMHQILSENDINLVIMDINLPGKNGLLLARELREQ-----------   72 (237)
T ss_pred             CeEEEEeCCHHHHHHHHHHHHHcCCEEEEECCHHHHHHHHhhCCCCEEEEcCCCCCCCHHHHHHHHhcC-----------
Confidence            589999999999999999999999999999999999999999999999999999999999999999952           


Q ss_pred             hhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHHhh
Q 039716          940 AGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQY 1000 (1002)
Q Consensus       940 ~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~~ 1000 (1002)
                                      +.+|||++|+.........++++|+++|+.||++..+|...+...
T Consensus        73 ----------------~~~pii~lt~~~~~~~~~~~~~~ga~d~l~kP~~~~eL~~~i~~~  117 (237)
T PRK11173         73 ----------------ANVALMFLTGRDNEVDKILGLEIGADDYITKPFNPRELTIRARNL  117 (237)
T ss_pred             ----------------CCCCEEEEECCCCHHHHHHHHHCCCCEEEECCCCHHHHHHHHHHH
Confidence                            358999999999999999999999999999999999998777654

>PRK10529 DNA-binding transcriptional activator KdpE; Provisional

Probab=99.54  E-value=1.4e-13  Score=146.64  Aligned_cols=115  Identities=22%  Similarity=0.371  Sum_probs=106.7

Q ss_pred             CeEEEEecCHHHHHHHHHHHHhcCCeEEEEcCHHHHHHHHHcCCCcEEEEcCCCCCCCHHHHHHHHhccccCCCchhhhh
Q 039716          860 PKILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDAAAE  939 (1002)
Q Consensus       860 ~~ILiVeDn~~n~~~l~~~L~~~g~~v~~a~~G~eAl~~~~~~~~DlIlmDi~MP~mdG~e~~~~IR~~~~~~~~~~~~~  939 (1002)
                      .+||||||++..+..+...|...|+.+..+.++.+|+..+....||+||+|+.||+++|+++++.||..           
T Consensus         2 ~~iLivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~~~~~~~~~~~dlvild~~l~~~~g~~~~~~lr~~-----------   70 (225)
T PRK10529          2 TNVLIVEDEQAIRRFLRTALEGDGMRVFEAETLQRGLLEAATRKPDLIILDLGLPDGDGIEFIRDLRQW-----------   70 (225)
T ss_pred             CEEEEEeCCHHHHHHHHHHHHHCCCEEEEeCCHHHHHHHHhcCCCCEEEEeCCCCCCCHHHHHHHHHcC-----------
Confidence            379999999999999999999999999999999999999988899999999999999999999999952           


Q ss_pred             hhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHHhhc
Q 039716          940 AGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQYF 1001 (1002)
Q Consensus       940 ~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~~l 1001 (1002)
                                      +.+|||++|+....+....++.+|+++|+.||++..+|...++..+
T Consensus        71 ----------------~~~pvi~lt~~~~~~~~~~~~~~ga~~~l~kP~~~~~l~~~i~~~~  116 (225)
T PRK10529         71 ----------------SAIPVIVLSARSEESDKIAALDAGADDYLSKPFGIGELQARLRVAL  116 (225)
T ss_pred             ----------------CCCCEEEEECCCCHHHHHHHHHcCCCEEEeCCCCHHHHHHHHHHHH
Confidence                            3589999999999999999999999999999999999998887643

>PRK10816 DNA-binding transcriptional regulator PhoP; Provisional

Probab=99.53  E-value=1.5e-13  Score=146.28  Aligned_cols=115  Identities=26%  Similarity=0.407  Sum_probs=107.4

Q ss_pred             eEEEEecCHHHHHHHHHHHHhcCCeEEEEcCHHHHHHHHHcCCCcEEEEcCCCCCCCHHHHHHHHhccccCCCchhhhhh
Q 039716          861 KILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDAAAEA  940 (1002)
Q Consensus       861 ~ILiVeDn~~n~~~l~~~L~~~g~~v~~a~~G~eAl~~~~~~~~DlIlmDi~MP~mdG~e~~~~IR~~~~~~~~~~~~~~  940 (1002)
                      +||+|||++.....+...|+..|+.|..+.++.+|+..+....||+|++|+.||.++|+++++.||..            
T Consensus         2 ~iLlv~d~~~~~~~l~~~L~~~g~~v~~~~~~~~~l~~~~~~~~dlvild~~l~~~~g~~l~~~lr~~------------   69 (223)
T PRK10816          2 RVLVVEDNALLRHHLKVQLQDAGHQVDAAEDAKEADYYLNEHLPDIAIVDLGLPDEDGLSLIRRWRSN------------   69 (223)
T ss_pred             eEEEEeCCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHHhhCCCCEEEEECCCCCCCHHHHHHHHHhc------------
Confidence            79999999999999999999999999999999999999999999999999999999999999999962            


Q ss_pred             hhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHHhhc
Q 039716          941 GIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQYF 1001 (1002)
Q Consensus       941 ~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~~l 1001 (1002)
                                    .+.+|||++|+....+....++++|+++|+.||++..+|...+...+
T Consensus        70 --------------~~~~pii~ls~~~~~~~~~~~l~~Ga~d~l~kp~~~~eL~~~i~~~~  116 (223)
T PRK10816         70 --------------DVSLPILVLTARESWQDKVEVLSAGADDYVTKPFHIEEVMARMQALM  116 (223)
T ss_pred             --------------CCCCCEEEEEcCCCHHHHHHHHHcCCCeeEeCCCCHHHHHHHHHHHH
Confidence                          24689999999999999999999999999999999999998887643

>PRK09836 DNA-binding transcriptional activator CusR; Provisional

Probab=99.52  E-value=2.2e-13  Score=145.36  Aligned_cols=114  Identities=29%  Similarity=0.507  Sum_probs=106.7

Q ss_pred             eEEEEecCHHHHHHHHHHHHhcCCeEEEEcCHHHHHHHHHcCCCcEEEEcCCCCCCCHHHHHHHHhccccCCCchhhhhh
Q 039716          861 KILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDAAAEA  940 (1002)
Q Consensus       861 ~ILiVeDn~~n~~~l~~~L~~~g~~v~~a~~G~eAl~~~~~~~~DlIlmDi~MP~mdG~e~~~~IR~~~~~~~~~~~~~~  940 (1002)
                      +||||||++..+..+...|+..|+.|..+.++.+|++.+....||+||+|+.||.++|+++++.+|..            
T Consensus         2 ~iliv~d~~~~~~~l~~~L~~~g~~v~~~~~~~~~~~~~~~~~~dlvild~~~~~~~g~~~~~~lr~~------------   69 (227)
T PRK09836          2 KLLIVEDEKKTGEYLTKGLTEAGFVVDLADNGLNGYHLAMTGDYDLIILDIMLPDVNGWDIVRMLRSA------------   69 (227)
T ss_pred             eEEEEeCCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHHhhCCCCEEEEECCCCCCCHHHHHHHHHhc------------
Confidence            69999999999999999999999999999999999999988899999999999999999999999962            


Q ss_pred             hhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHHhh
Q 039716          941 GIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQY 1000 (1002)
Q Consensus       941 ~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~~ 1000 (1002)
                                    .+.+|||++|+....+....++++|+++|+.||++..+|...++..
T Consensus        70 --------------~~~~pii~ls~~~~~~~~~~~~~~Ga~~~l~kp~~~~~l~~~i~~~  115 (227)
T PRK09836         70 --------------NKGMPILLLTALGTIEHRVKGLELGADDYLVKPFAFAELLARVRTL  115 (227)
T ss_pred             --------------CCCCCEEEEEcCCCHHHHHHHHhCCCCEEEeCCCCHHHHHHHHHHH
Confidence                          2468999999999999999999999999999999999999888764

>PRK04184 DNA topoisomerase VI subunit B; Validated

Probab=99.51  E-value=5.1e-14  Score=164.65  Aligned_cols=77  Identities=26%  Similarity=0.447  Sum_probs=66.0

Q ss_pred             EEEEEEEecCCCCCcCcHhhhhhhccCCCccc--cCcCCCccccHHHHHHHHHHhCCE-EEEEeecCCce-EEEEEEeCC
Q 039716          591 WIRCDVYDTGIGIPENALPTLFRKYMQVSADH--ARKYGGTGLGLAICKQLVELMGGR-LTVTSKVHCGS-TFTFILPYQ  666 (1002)
Q Consensus       591 ~l~i~V~DtGiGI~~e~l~~IF~pF~q~~~~~--~~~~~GtGLGLaI~k~Lve~~gG~-I~v~S~~g~GT-tF~~~LP~~  666 (1002)
                      ++.|.|.|||+||+++.++++|.+|++.+...  ....+|+||||++|+.+++.|+|. |+|.|.++.|+ .|+|.||+.
T Consensus        74 ~~~I~V~DNG~GIp~e~l~~iF~~f~~~SK~~~~~~s~G~~GLGLsiv~~isq~~~G~~I~V~S~~~~g~~~~~~~l~id  153 (535)
T PRK04184         74 HYRVTVEDNGPGIPPEEIPKVFGKLLYGSKFHNLRQSRGQQGIGISAAVLYAQMTTGKPVRVISSTGGSKKAYYFELKID  153 (535)
T ss_pred             EEEEEEEcCCCCCCHHHHHHHhhhhhccccccccccCCCCCCcchHHHHHHHHHhcCCcEEEEEecCCCceEEEEEEEec
Confidence            47799999999999999999999997654322  224578999999999999999997 99999999998 899999875


Q ss_pred             C
Q 039716          667 V  667 (1002)
Q Consensus       667 ~  667 (1002)
                      .
T Consensus       154 ~  154 (535)
T PRK04184        154 T  154 (535)
T ss_pred             c
Confidence            4

>PRK09468 ompR osmolarity response regulator; Provisional

Probab=99.51  E-value=3.4e-13  Score=145.19  Aligned_cols=117  Identities=22%  Similarity=0.344  Sum_probs=108.6

Q ss_pred             CCeEEEEecCHHHHHHHHHHHHhcCCeEEEEcCHHHHHHHHHcCCCcEEEEcCCCCCCCHHHHHHHHhccccCCCchhhh
Q 039716          859 KPKILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDAAA  938 (1002)
Q Consensus       859 ~~~ILiVeDn~~n~~~l~~~L~~~g~~v~~a~~G~eAl~~~~~~~~DlIlmDi~MP~mdG~e~~~~IR~~~~~~~~~~~~  938 (1002)
                      ..+||||||++..+..+...|...|+.+..+.++.+|++.+....||+||+|+.||.++|+++++.||..          
T Consensus         5 ~~~iLiv~d~~~~~~~l~~~L~~~g~~v~~~~~~~~~~~~~~~~~~dlvild~~l~~~~g~~~~~~lr~~----------   74 (239)
T PRK09468          5 NYKILVVDDDMRLRALLERYLTEQGFQVRSAANAEQMDRLLTRESFHLMVLDLMLPGEDGLSICRRLRSQ----------   74 (239)
T ss_pred             CCeEEEEcCCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHHhcCCCCEEEEeCCCCCCCHHHHHHHHHhc----------
Confidence            4589999999999999999999999999999999999999999999999999999999999999999962          


Q ss_pred             hhhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHHhhc
Q 039716          939 EAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQYF 1001 (1002)
Q Consensus       939 ~~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~~l 1001 (1002)
                                      .+.+|||++|+....+....++.+|+++|+.||++..+|...+...+
T Consensus        75 ----------------~~~~pii~ls~~~~~~~~~~~l~~Ga~~~l~kP~~~~~L~~~i~~~~  121 (239)
T PRK09468         75 ----------------NNPTPIIMLTAKGEEVDRIVGLEIGADDYLPKPFNPRELLARIRAVL  121 (239)
T ss_pred             ----------------CCCCCEEEEECCCcHHHHHHHHhcCCCeEEECCCCHHHHHHHHHHHh
Confidence                            24689999999999999999999999999999999999998887653

>PRK10643 DNA-binding transcriptional regulator BasR; Provisional

Probab=99.50  E-value=3.6e-13  Score=142.50  Aligned_cols=114  Identities=25%  Similarity=0.392  Sum_probs=106.5

Q ss_pred             eEEEEecCHHHHHHHHHHHHhcCCeEEEEcCHHHHHHHHHcCCCcEEEEcCCCCCCCHHHHHHHHhccccCCCchhhhhh
Q 039716          861 KILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDAAAEA  940 (1002)
Q Consensus       861 ~ILiVeDn~~n~~~l~~~L~~~g~~v~~a~~G~eAl~~~~~~~~DlIlmDi~MP~mdG~e~~~~IR~~~~~~~~~~~~~~  940 (1002)
                      +||||||++..+..+..+|...|+.+..+.++.+|+..+....||+||+|+.||+++|+++++.+|..            
T Consensus         2 ~ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~~~~~~~d~illd~~~~~~~g~~~~~~l~~~------------   69 (222)
T PRK10643          2 KILIVEDDTLLLQGLILALQTEGYACDCASTAREAEALLESGHYSLVVLDLGLPDEDGLHLLRRWRQK------------   69 (222)
T ss_pred             EEEEEeCCHHHHHHHHHHHHHCCCEEEEeCCHHHHHHHHHhCCCCEEEEECCCCCCCHHHHHHHHHhc------------
Confidence            69999999999999999999999999999999999999998899999999999999999999999952            


Q ss_pred             hhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHHhh
Q 039716          941 GIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQY 1000 (1002)
Q Consensus       941 ~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~~ 1000 (1002)
                                    .+.+|||++|+..+......++.+|+++|+.||++..+|...++.+
T Consensus        70 --------------~~~~pii~ls~~~~~~~~~~~~~~ga~~~l~kp~~~~~l~~~i~~~  115 (222)
T PRK10643         70 --------------KYTLPVLILTARDTLEDRVAGLDVGADDYLVKPFALEELHARIRAL  115 (222)
T ss_pred             --------------CCCCcEEEEECCCCHHHHHHHHhcCCCeEEeCCCCHHHHHHHHHHH
Confidence                          2468999999999999999999999999999999999999888764

>PRK10766 DNA-binding transcriptional regulator TorR; Provisional

Probab=99.50  E-value=3.4e-13  Score=143.18  Aligned_cols=114  Identities=29%  Similarity=0.393  Sum_probs=106.2

Q ss_pred             CeEEEEecCHHHHHHHHHHHHhcCCeEEEEcCHHHHHHHHHcCCCcEEEEcCCCCCCCHHHHHHHHhccccCCCchhhhh
Q 039716          860 PKILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDAAAE  939 (1002)
Q Consensus       860 ~~ILiVeDn~~n~~~l~~~L~~~g~~v~~a~~G~eAl~~~~~~~~DlIlmDi~MP~mdG~e~~~~IR~~~~~~~~~~~~~  939 (1002)
                      .+||+|||++.....+...|...|+.|..+.++.+|++.+....||+|++|+.||.++|+++++.||..           
T Consensus         3 ~~iLlv~d~~~~~~~l~~~l~~~~~~v~~~~~~~~~~~~~~~~~~dlvild~~l~~~~g~~~~~~lr~~-----------   71 (221)
T PRK10766          3 YHILVVEDEPVTRARLQGYFEQEGYTVSEAASGAGMREIMQNQHVDLILLDINLPGEDGLMLTRELRSR-----------   71 (221)
T ss_pred             CEEEEEeCCHHHHHHHHHHHHHcCCEEEEECCHHHHHHHHhcCCCCEEEEeCCCCCCCHHHHHHHHHhC-----------
Confidence            479999999999999999999999999999999999999998999999999999999999999999952           


Q ss_pred             hhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHHhh
Q 039716          940 AGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQY 1000 (1002)
Q Consensus       940 ~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~~ 1000 (1002)
                                      +.+|||++|+.........++++|+++|+.||++..+|...+..+
T Consensus        72 ----------------~~~~ii~l~~~~~~~~~~~~l~~Ga~d~l~kP~~~~~L~~~i~~~  116 (221)
T PRK10766         72 ----------------STVGIILVTGRTDSIDRIVGLEMGADDYVTKPLELRELLVRVKNL  116 (221)
T ss_pred             ----------------CCCCEEEEECCCcHHHHHHHHHcCCCcEEeCCCCHHHHHHHHHHH
Confidence                            358999999999999999999999999999999999998887654

>PRK10430 DNA-binding transcriptional activator DcuR; Provisional

Probab=99.49  E-value=4.4e-13  Score=145.04  Aligned_cols=115  Identities=18%  Similarity=0.330  Sum_probs=102.9

Q ss_pred             CeEEEEecCHHHHHHHHHHHHhc-CCe-EEEEcCHHHHHHHHH--cCCCcEEEEcCCCCCCCHHHHHHHHhccccCCCch
Q 039716          860 PKILLVEDNKINVMVAKSMMKQL-GHS-IDVVNNGVEAVHAVQ--CQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWD  935 (1002)
Q Consensus       860 ~~ILiVeDn~~n~~~l~~~L~~~-g~~-v~~a~~G~eAl~~~~--~~~~DlIlmDi~MP~mdG~e~~~~IR~~~~~~~~~  935 (1002)
                      .+||||||++..+..+..+|... |+. +..+.++.+|+..+.  ...||+||+|+.||+|+|+++++.|+..       
T Consensus         2 ~~VLivdd~~~~~~~l~~~L~~~~~~~~~~~~~~~~~a~~~~~~~~~~~DlvilD~~~p~~~G~eli~~l~~~-------   74 (239)
T PRK10430          2 INVLIVDDDAMVAELNRRYVAQIPGFQCCGTASTLEQAKEIIFNSDTPIDLILLDIYMQQENGLDLLPVLHEA-------   74 (239)
T ss_pred             eeEEEEcCCHHHHHHHHHHHHhCCCceEEEEeCCHHHHHHHHHhcCCCCCEEEEecCCCCCCcHHHHHHHHhh-------
Confidence            47999999999999999999864 676 457899999999886  3679999999999999999999999962       


Q ss_pred             hhhhhhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHHhh
Q 039716          936 AAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQY 1000 (1002)
Q Consensus       936 ~~~~~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~~ 1000 (1002)
                                         .+.+|||++|+.........++.+|+++|+.||++.++|..+|.++
T Consensus        75 -------------------~~~~~vI~ls~~~~~~~~~~al~~Ga~~yl~Kp~~~~~l~~~i~~~  120 (239)
T PRK10430         75 -------------------GCKSDVIVISSAADAATIKDSLHYGVVDYLIKPFQASRFEEALTGW  120 (239)
T ss_pred             -------------------CCCCCEEEEECCCcHHHHHHHHHcCCCEEEeCCCCHHHHHHHHHHH
Confidence                               2568999999999999999999999999999999999999998753

>PRK10336 DNA-binding transcriptional regulator QseB; Provisional

Probab=99.49  E-value=5.7e-13  Score=140.82  Aligned_cols=114  Identities=27%  Similarity=0.423  Sum_probs=106.3

Q ss_pred             eEEEEecCHHHHHHHHHHHHhcCCeEEEEcCHHHHHHHHHcCCCcEEEEcCCCCCCCHHHHHHHHhccccCCCchhhhhh
Q 039716          861 KILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDAAAEA  940 (1002)
Q Consensus       861 ~ILiVeDn~~n~~~l~~~L~~~g~~v~~a~~G~eAl~~~~~~~~DlIlmDi~MP~mdG~e~~~~IR~~~~~~~~~~~~~~  940 (1002)
                      +||||||++.....+..+|+..|+.+..+.++.+|+..+....||+||+|+.||+++|+++++.||..            
T Consensus         2 ~ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~~~~~~~dlvild~~l~~~~g~~~~~~i~~~------------   69 (219)
T PRK10336          2 RILLIEDDMLIGDGIKTGLSKMGFSVDWFTQGRQGKEALYSAPYDAVILDLTLPGMDGRDILREWREK------------   69 (219)
T ss_pred             eEEEEcCCHHHHHHHHHHHHHCCCEEEEeCCHHHHHHHHhhCCCCEEEEECCCCCCCHHHHHHHHHhc------------
Confidence            79999999999999999999999999999999999999988899999999999999999999999962            


Q ss_pred             hhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHHhh
Q 039716          941 GIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQY 1000 (1002)
Q Consensus       941 ~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~~ 1000 (1002)
                                    .+.+|||++|+....+....++.+|+++|+.||++..+|...++..
T Consensus        70 --------------~~~~~ii~lt~~~~~~~~~~~~~~ga~~~i~kp~~~~~l~~~i~~~  115 (219)
T PRK10336         70 --------------GQREPVLILTARDALAERVEGLRLGADDYLCKPFALIEVAARLEAL  115 (219)
T ss_pred             --------------CCCCcEEEEECCCCHHHHHHHHhCCCCeEEECCCCHHHHHHHHHHH
Confidence                          2568999999999999999999999999999999999999888764

>TIGR02154 PhoB phosphate regulon transcriptional regulatory protein PhoB

Probab=99.48  E-value=6.9e-13  Score=140.65  Aligned_cols=117  Identities=26%  Similarity=0.392  Sum_probs=107.6

Q ss_pred             CeEEEEecCHHHHHHHHHHHHhcCCeEEEEcCHHHHHHHHHcCCCcEEEEcCCCCCCCHHHHHHHHhccccCCCchhhhh
Q 039716          860 PKILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDAAAE  939 (1002)
Q Consensus       860 ~~ILiVeDn~~n~~~l~~~L~~~g~~v~~a~~G~eAl~~~~~~~~DlIlmDi~MP~mdG~e~~~~IR~~~~~~~~~~~~~  939 (1002)
                      .+||||||++..+..+...|+..|+.+..+.++.+|+..+....||+||+|+.||+++|+++++.||...          
T Consensus         3 ~~ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~~~~~~~d~vi~d~~~~~~~g~~~~~~l~~~~----------   72 (226)
T TIGR02154         3 RRILVVEDEPAIRELIAYNLEKAGYDVVEAGDGDEALTLINERGPDLILLDWMLPGTSGIELCRRLRRRP----------   72 (226)
T ss_pred             CeEEEEeCCHHHHHHHHHHHHHCCCEEEEEcCHHHHHHHHHhcCCCEEEEECCCCCCcHHHHHHHHHccc----------
Confidence            4799999999999999999999999999999999999999999999999999999999999999998632          


Q ss_pred             hhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHHhh
Q 039716          940 AGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQY 1000 (1002)
Q Consensus       940 ~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~~ 1000 (1002)
                                    ..+.+|||++|+.........++.+|+++|+.||++..+|...+..+
T Consensus        73 --------------~~~~~~ii~ls~~~~~~~~~~~~~~Ga~~~l~kp~~~~~l~~~i~~~  119 (226)
T TIGR02154        73 --------------ETRAIPIIMLTARGEEEDRVRGLETGADDYITKPFSPRELLARIKAV  119 (226)
T ss_pred             --------------cCCCCCEEEEecCCCHHHHHHHHhcCcceEEeCCCCHHHHHHHHHHH
Confidence                          13568999999999999999999999999999999999999888765

PhoB is a DNA-binding response regulator protein acting with PhoR in a 2-component system responding to phosphate ion. PhoB acts as a positive regulator of gene expression for phosphate-related genes such as phoA, phoS, phoE and ugpAB as well as itself. It is often found proximal to genes for the high-affinity phosphate ABC transporter (pstSCAB; GenProp0190) and presumably regulates these as well.

>PRK10701 DNA-binding transcriptional regulator RstA; Provisional

Probab=99.48  E-value=6.1e-13  Score=143.41  Aligned_cols=113  Identities=21%  Similarity=0.243  Sum_probs=105.4

Q ss_pred             eEEEEecCHHHHHHHHHHHHhcCCeEEEEcCHHHHHHHHHcCCCcEEEEcCCCCCCCHHHHHHHHhccccCCCchhhhhh
Q 039716          861 KILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDAAAEA  940 (1002)
Q Consensus       861 ~ILiVeDn~~n~~~l~~~L~~~g~~v~~a~~G~eAl~~~~~~~~DlIlmDi~MP~mdG~e~~~~IR~~~~~~~~~~~~~~  940 (1002)
                      +||||||++..+..+...|+..|+.+..+.+|.+|+..+....||+|++|+.||+++|+++++.||..            
T Consensus         3 ~iLivedd~~~~~~l~~~L~~~g~~v~~~~~~~~~l~~~~~~~~dlvild~~l~~~~g~~~~~~ir~~------------   70 (240)
T PRK10701          3 KIVFVEDDAEVGSLIAAYLAKHDIDVTVEPRGDRAEATILREQPDLVLLDIMLPGKDGMTICRDLRPK------------   70 (240)
T ss_pred             eEEEEeCCHHHHHHHHHHHHHcCCEEEEeCCHHHHHHHHhhCCCCEEEEeCCCCCCCHHHHHHHHHhc------------
Confidence            79999999999999999999999999999999999999999999999999999999999999999951            


Q ss_pred             hhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHHhh
Q 039716          941 GIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQY 1000 (1002)
Q Consensus       941 ~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~~ 1000 (1002)
                                     ..+|||++|+.........++++|+++|+.||++..+|...+...
T Consensus        71 ---------------~~~pii~l~~~~~~~~~~~~~~~Ga~d~l~kP~~~~~l~~~i~~~  115 (240)
T PRK10701         71 ---------------WQGPIVLLTSLDSDMNHILALEMGACDYILKTTPPAVLLARLRLH  115 (240)
T ss_pred             ---------------CCCCEEEEECCCCHHHHHHHHHcCCCEEEECCCCHHHHHHHHHHH
Confidence                           246999999999999999999999999999999999998888754

>PRK10161 transcriptional regulator PhoB; Provisional

Probab=99.48  E-value=6.9e-13  Score=141.70  Aligned_cols=117  Identities=22%  Similarity=0.302  Sum_probs=107.6

Q ss_pred             CeEEEEecCHHHHHHHHHHHHhcCCeEEEEcCHHHHHHHHHcCCCcEEEEcCCCCCCCHHHHHHHHhccccCCCchhhhh
Q 039716          860 PKILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDAAAE  939 (1002)
Q Consensus       860 ~~ILiVeDn~~n~~~l~~~L~~~g~~v~~a~~G~eAl~~~~~~~~DlIlmDi~MP~mdG~e~~~~IR~~~~~~~~~~~~~  939 (1002)
                      .+||||||++.....+...|+..|+.+..+.++.+|++.+....||+||+|+.||.++|+++++.||...          
T Consensus         3 ~~Ilivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~~~~~~~~~~~dlvild~~l~~~~g~~~~~~l~~~~----------   72 (229)
T PRK10161          3 RRILVVEDEAPIREMVCFVLEQNGFQPVEAEDYDSAVNQLNEPWPDLILLDWMLPGGSGIQFIKHLKRES----------   72 (229)
T ss_pred             CeEEEEcCCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHHhccCCCEEEEeCCCCCCCHHHHHHHHHhcc----------
Confidence            4799999999999999999999999999999999999999989999999999999999999999999631          


Q ss_pred             hhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHHhh
Q 039716          940 AGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQY 1000 (1002)
Q Consensus       940 ~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~~ 1000 (1002)
                                    ..+.+|||++|+.........++++|+++|+.||++..+|...+..+
T Consensus        73 --------------~~~~~pvi~ls~~~~~~~~~~~~~~Ga~~~l~kp~~~~~L~~~i~~~  119 (229)
T PRK10161         73 --------------MTRDIPVVMLTARGEEEDRVRGLETGADDYITKPFSPKELVARIKAV  119 (229)
T ss_pred             --------------ccCCCCEEEEECCCCHHHHHHHHHcCCCEEEECCCCHHHHHHHHHHH
Confidence                          12568999999999999999999999999999999999998888764

>TIGR02875 spore_0_A sporulation transcription factor Spo0A

Probab=99.47  E-value=6.3e-13  Score=145.82  Aligned_cols=119  Identities=25%  Similarity=0.402  Sum_probs=105.3

Q ss_pred             CCeEEEEecCHHHHHHHHHHHHhc-CCe-EEEEcCHHHHHHHHHcCCCcEEEEcCCCCCCCHHHHHHHHhccccCCCchh
Q 039716          859 KPKILLVEDNKINVMVAKSMMKQL-GHS-IDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDA  936 (1002)
Q Consensus       859 ~~~ILiVeDn~~n~~~l~~~L~~~-g~~-v~~a~~G~eAl~~~~~~~~DlIlmDi~MP~mdG~e~~~~IR~~~~~~~~~~  936 (1002)
                      +.+||||||++..+..+..+|... ++. +..+.+|.+|++.+....||+||+|+.||+|||+++++.||...       
T Consensus         2 ~~~vLivdd~~~~~~~l~~~L~~~~~~~~~~~a~~~~eal~~l~~~~~DlvllD~~mp~~dG~~~l~~i~~~~-------   74 (262)
T TIGR02875         2 KIRIVIADDNKEFCNLLKEYLAAQPDMEVVGVAHNGVDALELIKEQQPDVVVLDIIMPHLDGIGVLEKLNEIE-------   74 (262)
T ss_pred             CcEEEEEcCCHHHHHHHHHHHhcCCCeEEEEEeCCHHHHHHHHHhcCCCEEEEeCCCCCCCHHHHHHHHHhhc-------
Confidence            358999999999999999999864 455 45789999999999999999999999999999999999999632       


Q ss_pred             hhhhhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHHhhc
Q 039716          937 AAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQYF 1001 (1002)
Q Consensus       937 ~~~~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~~l 1001 (1002)
                                       ....+|||++|+.........++++|+++|+.||++..+|...|.+++
T Consensus        75 -----------------~~~~~~iI~lt~~~~~~~~~~~~~~G~~~~l~KP~~~~~L~~~i~~~~  122 (262)
T TIGR02875        75 -----------------LSARPRVIMLSAFGQEKITQRAVALGADYYVLKPFDLEILAARIRQLA  122 (262)
T ss_pred             -----------------cccCCeEEEEeCCCCHHHHHHHHHCCCCEEEECCCCHHHHHHHHHHHH
Confidence                             123479999999999999999999999999999999999999987653

Spo0A, the stage 0 sporulation protein A, is a transcription factor critical for the initiation of sporulation. It contains a response regulator receiver domain (pfam00072). In Bacillus subtilis, it works together with response regulator Spo0F and the phosphotransferase Spo0B, both of which are missing from at least some sporulating species and thus not part of the endospore forming bacteria minimal gene set. Spo0A, however, is universal among endospore-forming species.

>PRK13856 two-component response regulator VirG; Provisional

Probab=99.47  E-value=6.7e-13  Score=143.44  Aligned_cols=113  Identities=14%  Similarity=0.287  Sum_probs=103.4

Q ss_pred             eEEEEecCHHHHHHHHHHHHhcCCeEEEEcCHHHHHHHHHcCCCcEEEEcCCCCCCCHHHHHHHHhccccCCCchhhhhh
Q 039716          861 KILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDAAAEA  940 (1002)
Q Consensus       861 ~ILiVeDn~~n~~~l~~~L~~~g~~v~~a~~G~eAl~~~~~~~~DlIlmDi~MP~mdG~e~~~~IR~~~~~~~~~~~~~~  940 (1002)
                      +||||||++..+..+...|+..|+.|..+.++.+|++.+....||+||+|+.||.++|+++++.||..            
T Consensus         3 ~ILived~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~~~~~~~dlvi~d~~l~~~~g~~l~~~i~~~------------   70 (241)
T PRK13856          3 HVLVIDDDVAMRHLIVEYLTIHAFKVTAVADSQQFNRVLASETVDVVVVDLNLGREDGLEIVRSLATK------------   70 (241)
T ss_pred             eEEEEeCCHHHHHHHHHHHHHcCCEEEEECCHHHHHHHHhhCCCCEEEEeCCCCCCCHHHHHHHHHhc------------
Confidence            79999999999999999999999999999999999999999999999999999999999999999852            


Q ss_pred             hhcccCCCCCCCCCCCCccEEEEcCCC-CHHHHHHHHHcCCCEEEeCCCChHHHHHHHHhh
Q 039716          941 GIEQAMPSSGSSNHFKRIPIIAMTANA-LSESAEECFANGMDSFVSKPVTFQKLKECLEQY 1000 (1002)
Q Consensus       941 ~~~~~~~~~~~~~~~~~ipIIalTa~~-~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~~ 1000 (1002)
                                     ..+|||++|+.. .......++++|+++|+.||++..+|...++..
T Consensus        71 ---------------~~~pii~lt~~~~~~~~~~~~l~~Ga~~yl~kP~~~~eL~~~i~~~  116 (241)
T PRK13856         71 ---------------SDVPIIIISGDRLEEADKVVALELGATDFIAKPFGTREFLARIRVA  116 (241)
T ss_pred             ---------------CCCcEEEEECCCCcHHHHHHHHhcCcCeEEeCCCCHHHHHHHHHHH
Confidence                           358999999854 667778999999999999999999998888654

>TIGR03787 marine_sort_RR proteobacterial dedicated sortase system response regulator

Probab=99.46  E-value=1e-12  Score=140.14  Aligned_cols=114  Identities=20%  Similarity=0.276  Sum_probs=105.5

Q ss_pred             eEEEEecCHHHHHHHHHHHHhcCCeEEEEcCHHHHHHHHHcCCCcEEEEcCCCCC--CCHHHHHHHHhccccCCCchhhh
Q 039716          861 KILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPV--MDGLKATRLIRSFEDTGNWDAAA  938 (1002)
Q Consensus       861 ~ILiVeDn~~n~~~l~~~L~~~g~~v~~a~~G~eAl~~~~~~~~DlIlmDi~MP~--mdG~e~~~~IR~~~~~~~~~~~~  938 (1002)
                      +||||||++..+..+...|+..|+.+..+.++.+++..+....||+|++|+.||+  ++|+++++.||..          
T Consensus         2 ~iLivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~~~~~~~dlvild~~l~~~~~~g~~~~~~i~~~----------   71 (227)
T TIGR03787         2 RIAIVEDEAAIRENYADALKRQGYQVTTYADRPSAMQAFRQRLPDLAIIDIGLGEEIDGGFMLCQDLRSL----------   71 (227)
T ss_pred             eEEEEeCCHHHHHHHHHHHHHCCcEEEEecCHHHHHHHHHhCCCCEEEEECCCCCCCCCHHHHHHHHHhc----------
Confidence            6999999999999999999999999999999999999999999999999999998  5899999999962          


Q ss_pred             hhhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHHhh
Q 039716          939 EAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQY 1000 (1002)
Q Consensus       939 ~~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~~ 1000 (1002)
                                      .+.+|||++|+....+....++.+|+++|+.||++..+|...++..
T Consensus        72 ----------------~~~~pii~ls~~~~~~~~~~~~~~Ga~~~l~kp~~~~~l~~~i~~~  117 (227)
T TIGR03787        72 ----------------SATLPIIFLTARDSDFDTVSGLRLGADDYLTKDISLPHLLARITAL  117 (227)
T ss_pred             ----------------CCCCCEEEEECCCCHHHHHHHHhcCCCEEEECCCCHHHHHHHHHHH
Confidence                            2458999999999999999999999999999999999999888754

This model describes a family of DNA-binding response regulator proteins, associated with an adjacent histidine kinase (TIGR03785) to form a two-component system. This system co-occurs with, and often is adjacent to, a proteobacterial variant form of the protein sorting transpeptidase called sortase (TIGR03784), and a single target protein for the sortase. We give this protein the gene symbol pdsR, for Proteobacterial Dedicated Sortase system Response regulator.

>PRK10955 DNA-binding transcriptional regulator CpxR; Provisional

Probab=99.46  E-value=9.3e-13  Score=140.64  Aligned_cols=112  Identities=26%  Similarity=0.448  Sum_probs=103.3

Q ss_pred             eEEEEecCHHHHHHHHHHHHhcCCeEEEEcCHHHHHHHHHcCCCcEEEEcCCCCCCCHHHHHHHHhccccCCCchhhhhh
Q 039716          861 KILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDAAAEA  940 (1002)
Q Consensus       861 ~ILiVeDn~~n~~~l~~~L~~~g~~v~~a~~G~eAl~~~~~~~~DlIlmDi~MP~mdG~e~~~~IR~~~~~~~~~~~~~~  940 (1002)
                      +||||||++..+..+..+|+..|+.+..+.++.+|+..+. ..||+||+|+.||+++|+++++.||..            
T Consensus         3 ~ilivdd~~~~~~~l~~~l~~~~~~v~~~~~~~~~~~~~~-~~~d~vl~d~~~~~~~g~~~~~~l~~~------------   69 (232)
T PRK10955          3 KILLVDDDRELTSLLKELLEMEGFNVIVAHDGEQALDLLD-DSIDLLLLDVMMPKKNGIDTLKELRQT------------   69 (232)
T ss_pred             eEEEEeCCHHHHHHHHHHHHHCCCEEEEeCCHHHHHHHhh-cCCCEEEEeCCCCCCcHHHHHHHHHhc------------
Confidence            7999999999999999999999999999999999999886 479999999999999999999999952            


Q ss_pred             hhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHHhh
Q 039716          941 GIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQY 1000 (1002)
Q Consensus       941 ~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~~ 1000 (1002)
                                    .+ +|||++|+.........++++|+++|+.||++..+|...+...
T Consensus        70 --------------~~-~~ii~lt~~~~~~~~~~~~~~ga~~~l~kp~~~~~l~~~i~~~  114 (232)
T PRK10955         70 --------------HQ-TPVIMLTARGSELDRVLGLELGADDYLPKPFNDRELVARIRAI  114 (232)
T ss_pred             --------------CC-CcEEEEECCCCHHHHHHHHHcCCCEEEcCCCCHHHHHHHHHHH
Confidence                          12 8999999999999999999999999999999999999888764

>PRK11517 transcriptional regulatory protein YedW; Provisional

Probab=99.46  E-value=1.3e-12  Score=138.53  Aligned_cols=113  Identities=27%  Similarity=0.488  Sum_probs=105.8

Q ss_pred             eEEEEecCHHHHHHHHHHHHhcCCeEEEEcCHHHHHHHHHcCCCcEEEEcCCCCCCCHHHHHHHHhccccCCCchhhhhh
Q 039716          861 KILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDAAAEA  940 (1002)
Q Consensus       861 ~ILiVeDn~~n~~~l~~~L~~~g~~v~~a~~G~eAl~~~~~~~~DlIlmDi~MP~mdG~e~~~~IR~~~~~~~~~~~~~~  940 (1002)
                      +||||||++..+..+...|...|+.+..+.++.+|+..+....||+|++|+.||+++|+++++.||..            
T Consensus         2 ~iliv~~~~~~~~~l~~~L~~~~~~v~~~~~~~~~l~~~~~~~~dlvi~d~~~~~~~g~~~~~~l~~~------------   69 (223)
T PRK11517          2 KILLIEDNQRTQEWVTQGLSEAGYVIDAVSDGRDGLYLALKDDYALIILDIMLPGMDGWQILQTLRTA------------   69 (223)
T ss_pred             EEEEEeCCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHHhcCCCCEEEEECCCCCCCHHHHHHHHHcC------------
Confidence            69999999999999999999999999999999999999999999999999999999999999999852            


Q ss_pred             hhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHHhh
Q 039716          941 GIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQY 1000 (1002)
Q Consensus       941 ~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~~ 1000 (1002)
                                     ..+|||++|+....+....++.+|+++|+.||++..+|...++..
T Consensus        70 ---------------~~~~ii~ls~~~~~~~~~~a~~~Ga~~~l~kp~~~~~l~~~i~~~  114 (223)
T PRK11517         70 ---------------KQTPVICLTARDSVDDRVRGLDSGANDYLVKPFSFSELLARVRAQ  114 (223)
T ss_pred             ---------------CCCCEEEEECCCCHHHHHHHHhcCCCEEEECCCCHHHHHHHHHHH
Confidence                           247999999999999999999999999999999999999888764

>smart00387 HATPase_c Histidine kinase-like ATPases

Probab=99.44  E-value=1.2e-12  Score=121.67  Aligned_cols=109  Identities=46%  Similarity=0.770  Sum_probs=91.9

Q ss_pred             ccHHHHHHHHHHHHhhhhhcCCC-CeeEEEEEecCCCCcccchhhhhhhhhhcchhhhhhhccCCCCCccCCCCCCCCCC
Q 039716          480 GDVLRIRQILTNLISNAIKFTPE-GKVGIKLYVVPEPPFAKEGLKQKSKAYQSATDAVKEEKHQPKSQTASDQNGFHDKK  558 (1002)
Q Consensus       480 gD~~rL~QIL~NLlsNAIKfT~~-G~I~I~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  558 (1002)
                      +|+..|.+++.|++.||+++... +.|.|.+...                                              
T Consensus         1 ~~~~~l~~~~~~l~~n~~~~~~~~~~v~i~~~~~----------------------------------------------   34 (111)
T smart00387        1 GDPDRLRQVLSNLLDNAIKYTPEGGRITVTLERD----------------------------------------------   34 (111)
T ss_pred             CCHHHHHHHHHHHHHHHHhcCCCCCeEEEEEEEc----------------------------------------------
Confidence            57889999999999999999986 6666665321                                              


Q ss_pred             CCCCccCCCCCCCCCCCccCCCCCccccccceEEEEEEEecCCCCCcCcHhhhhhhccCCCccccCcCCCccccHHHHHH
Q 039716          559 HGEGYQDHKHDDDPGTPVSHGNSMDEDLEATVWIRCDVYDTGIGIPENALPTLFRKYMQVSADHARKYGGTGLGLAICKQ  638 (1002)
Q Consensus       559 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~i~V~DtGiGI~~e~l~~IF~pF~q~~~~~~~~~~GtGLGLaI~k~  638 (1002)
                                                    ..++.|.|.|+|.||+++.+.++|.+|+.... ......+.|+||++|+.
T Consensus        35 ------------------------------~~~~~i~i~d~g~g~~~~~~~~~~~~~~~~~~-~~~~~~~~g~gl~~~~~   83 (111)
T smart00387       35 ------------------------------GDHLEITVEDNGPGIPPEDLEKIFEPFFRTDG-RSRKIGGTGLGLSIVKK   83 (111)
T ss_pred             ------------------------------CCEEEEEEEeCCCCCCHHHHHHHhcCeEECCC-CCCCCCcccccHHHHHH
Confidence                                          11478899999999999999999999986543 22334679999999999


Q ss_pred             HHHHhCCEEEEEeecCCceEEEEEEeC
Q 039716          639 LVELMGGRLTVTSKVHCGSTFTFILPY  665 (1002)
Q Consensus       639 Lve~~gG~I~v~S~~g~GTtF~~~LP~  665 (1002)
                      +++.|+|.+++.+..+.|++|+|.+|+
T Consensus        84 ~~~~~~g~~~~~~~~~~g~~~~~~~~~  110 (111)
T smart00387       84 LVELHGGEISVESEPGGGTTFTITLPL  110 (111)
T ss_pred             HHHHcCCEEEEEecCCCcEEEEEEeeC
Confidence            999999999999998999999999996

Histidine kinase-, DNA gyrase B-, phytochrome-like ATPases.

>PRK11083 DNA-binding response regulator CreB; Provisional

Probab=99.44  E-value=1.8e-12  Score=137.74  Aligned_cols=115  Identities=24%  Similarity=0.418  Sum_probs=106.6

Q ss_pred             CeEEEEecCHHHHHHHHHHHHhcCCeEEEEcCHHHHHHHHHcCCCcEEEEcCCCCCCCHHHHHHHHhccccCCCchhhhh
Q 039716          860 PKILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDAAAE  939 (1002)
Q Consensus       860 ~~ILiVeDn~~n~~~l~~~L~~~g~~v~~a~~G~eAl~~~~~~~~DlIlmDi~MP~mdG~e~~~~IR~~~~~~~~~~~~~  939 (1002)
                      .+||||||++.....+...|...|+.+..+.++.+|+..+....||+||+|+.||.++|+++++.||..           
T Consensus         4 ~~ilivdd~~~~~~~l~~~l~~~~~~v~~~~~~~~~~~~~~~~~~dlvl~d~~~~~~~g~~~~~~l~~~-----------   72 (228)
T PRK11083          4 PTILLVEDEQAIADTLVYALQSEGFTVEWFERGLPALDKLRQQPPDLVILDVGLPDISGFELCRQLLAF-----------   72 (228)
T ss_pred             CEEEEEeCCHHHHHHHHHHHHHCCCEEEEEcCHHHHHHHHhcCCCCEEEEeCCCCCCCHHHHHHHHHhh-----------
Confidence            479999999999999999999999999999999999999988899999999999999999999999962           


Q ss_pred             hhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHHhh
Q 039716          940 AGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQY 1000 (1002)
Q Consensus       940 ~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~~ 1000 (1002)
                                     .+.+|||++|+.........++.+|+++|+.||++..+|...+...
T Consensus        73 ---------------~~~~~ii~ls~~~~~~~~~~a~~~Ga~~~l~kp~~~~~l~~~i~~~  118 (228)
T PRK11083         73 ---------------HPALPVIFLTARSDEVDRLVGLEIGADDYVAKPFSPREVAARVRTI  118 (228)
T ss_pred             ---------------CCCCCEEEEEcCCcHHHHHHHhhcCCCeEEECCCCHHHHHHHHHHH
Confidence                           2568999999999998999999999999999999999998888764

>PRK10840 transcriptional regulator RcsB; Provisional

Probab=99.43  E-value=1.7e-12  Score=138.07  Aligned_cols=115  Identities=16%  Similarity=0.305  Sum_probs=104.5

Q ss_pred             CeEEEEecCHHHHHHHHHHHHhcCC-e-EEEEcCHHHHHHHHHcCCCcEEEEcCCCCC---CCHHHHHHHHhccccCCCc
Q 039716          860 PKILLVEDNKINVMVAKSMMKQLGH-S-IDVVNNGVEAVHAVQCQNYDLILMDVCMPV---MDGLKATRLIRSFEDTGNW  934 (1002)
Q Consensus       860 ~~ILiVeDn~~n~~~l~~~L~~~g~-~-v~~a~~G~eAl~~~~~~~~DlIlmDi~MP~---mdG~e~~~~IR~~~~~~~~  934 (1002)
                      .+||||||++..+..++.+|+..++ . +..+.++.++++.+....||+||+|+.||+   ++|+++++.||..      
T Consensus         4 ~~Ilivdd~~~~~~~l~~~L~~~~~~~~v~~~~~~~~~~~~~~~~~~DlvllD~~l~~~~~~~g~~~~~~l~~~------   77 (216)
T PRK10840          4 MNVIIADDHPIVLFGIRKSLEQIEWVNVVGEFEDSTALINNLPKLDAHVLITDLSMPGDKYGDGITLIKYIKRH------   77 (216)
T ss_pred             eEEEEECCcHHHHHHHHHHHhcCCCCEEEEEECCHHHHHHHHHhCCCCEEEEeCcCCCCCCCCHHHHHHHHHHH------
Confidence            5899999999999999999987765 3 678899999999999889999999999999   5999999999862      


Q ss_pred             hhhhhhhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHHhh
Q 039716          935 DAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQY 1000 (1002)
Q Consensus       935 ~~~~~~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~~ 1000 (1002)
                                          .+.+|||++|++........++++|+++|+.||++..+|..+|+..
T Consensus        78 --------------------~~~~~iIvls~~~~~~~~~~a~~~Ga~~yl~K~~~~~~l~~ai~~v  123 (216)
T PRK10840         78 --------------------FPSLSIIVLTMNNNPAILSAVLDLDIEGIVLKQGAPTDLPKALAAL  123 (216)
T ss_pred             --------------------CCCCcEEEEEecCCHHHHHHHHHCCCeEEEECCCCHHHHHHHHHHH
Confidence                                3568999999999999999999999999999999999999998764

>COG4567 Response regulator consisting of a CheY-like receiver domain and a Fis-type HTH domain [Signal transduction mechanisms / Transcription]

Probab=99.43  E-value=1.1e-12  Score=124.99  Aligned_cols=113  Identities=19%  Similarity=0.243  Sum_probs=107.2

Q ss_pred             eEEEEecCHHHHHHHHHHHHhcCCeEEEEcCHHHHHHHHHcCCCcEEEEcCCCCCCCHHHHHHHHhccccCCCchhhhhh
Q 039716          861 KILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDAAAEA  940 (1002)
Q Consensus       861 ~ILiVeDn~~n~~~l~~~L~~~g~~v~~a~~G~eAl~~~~~~~~DlIlmDi~MP~mdG~e~~~~IR~~~~~~~~~~~~~~  940 (1002)
                      ..|||||+......|...|++.||.|.+|.+..||+..++...|...++|+.|-+-+|+.+++.||+.            
T Consensus        11 ~lllvdDD~~f~~~LaRa~e~RGf~v~~a~~~~eal~~art~~PayAvvDlkL~~gsGL~~i~~lr~~------------   78 (182)
T COG4567          11 SLLLVDDDTPFLRTLARAMERRGFAVVTAESVEEALAAARTAPPAYAVVDLKLGDGSGLAVIEALRER------------   78 (182)
T ss_pred             eeEEecCChHHHHHHHHHHhccCceeEeeccHHHHHHHHhcCCCceEEEEeeecCCCchHHHHHHHhc------------
Confidence            69999999999999999999999999999999999999999999999999999999999999999973            


Q ss_pred             hhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHHh
Q 039716          941 GIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQ  999 (1002)
Q Consensus       941 ~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~  999 (1002)
                                    .+++.||++|++++.....++.+.|+++||.||-+.+.+..+|.+
T Consensus        79 --------------~~d~rivvLTGy~sIATAV~AvKlGA~~YLaKPAdaDdi~aAl~~  123 (182)
T COG4567          79 --------------RADMRIVVLTGYASIATAVEAVKLGACDYLAKPADADDILAALLR  123 (182)
T ss_pred             --------------CCcceEEEEecchHHHHHHHHHHhhhhhhcCCCCChHHHHHHHhh
Confidence                          356889999999999999999999999999999999999888765

>TIGR01387 cztR_silR_copR heavy metal response regulator

Probab=99.43  E-value=2.2e-12  Score=136.03  Aligned_cols=113  Identities=27%  Similarity=0.467  Sum_probs=105.4

Q ss_pred             EEEEecCHHHHHHHHHHHHhcCCeEEEEcCHHHHHHHHHcCCCcEEEEcCCCCCCCHHHHHHHHhccccCCCchhhhhhh
Q 039716          862 ILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDAAAEAG  941 (1002)
Q Consensus       862 ILiVeDn~~n~~~l~~~L~~~g~~v~~a~~G~eAl~~~~~~~~DlIlmDi~MP~mdG~e~~~~IR~~~~~~~~~~~~~~~  941 (1002)
                      ||||||++..+..+...|...|+.+..+.++.+|+..+....||+|++|+.||.++|+++++.||..             
T Consensus         1 iliidd~~~~~~~l~~~l~~~~~~v~~~~~~~~~~~~~~~~~~dlvl~d~~~~~~~g~~~~~~l~~~-------------   67 (218)
T TIGR01387         1 ILVVEDEQKTAEYLQQGLSESGYVVDAASNGRDGLHLALKDDYDLIILDVMLPGMDGWQILQTLRRS-------------   67 (218)
T ss_pred             CEEEECCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHHhcCCCCEEEEeCCCCCCCHHHHHHHHHcc-------------
Confidence            6899999999999999999999999999999999999999999999999999999999999999952             


Q ss_pred             hcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHHhh
Q 039716          942 IEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQY 1000 (1002)
Q Consensus       942 ~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~~ 1000 (1002)
                                   .+.+|||++|+.........++.+|+++|+.||++..+|...+...
T Consensus        68 -------------~~~~~iivls~~~~~~~~~~~~~~Ga~~~l~kp~~~~~l~~~i~~~  113 (218)
T TIGR01387        68 -------------GKQTPVLFLTARDSVADKVKGLDLGADDYLVKPFSFSELLARVRTL  113 (218)
T ss_pred             -------------CCCCcEEEEEcCCCHHHHHHHHHcCCCeEEECCCCHHHHHHHHHHH
Confidence                         2568999999999999999999999999999999999999888764

Members of this family contain a response regulator receiver domain (Pfam:PF00072) and an associated transcriptional regulatory region (Pfam:PF00486). This group is separated phylogenetically from related proteins with similar architecture and contains a number of proteins associated with heavy metal resistance efflux systems for copper, silver, cadmium, and/or zinc. Most members encoded by genes adjacent to genes for encoding a member of the heavy metal sensor histidine kinase family (TIGRFAMs:TIGR01386), its partner in the two-component response regulator system.

>PRK14084 two-component response regulator; Provisional

Probab=99.42  E-value=2.5e-12  Score=139.58  Aligned_cols=113  Identities=20%  Similarity=0.360  Sum_probs=99.8

Q ss_pred             CeEEEEecCHHHHHHHHHHHHhcC-C-eEEEEcCHHHHHHHHHcCCCcEEEEcCCCCCCCHHHHHHHHhccccCCCchhh
Q 039716          860 PKILLVEDNKINVMVAKSMMKQLG-H-SIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDAA  937 (1002)
Q Consensus       860 ~~ILiVeDn~~n~~~l~~~L~~~g-~-~v~~a~~G~eAl~~~~~~~~DlIlmDi~MP~mdG~e~~~~IR~~~~~~~~~~~  937 (1002)
                      .+||||||++..+..+..+|+..+ + .+..+.++.+|+..+....||+||+|+.||+|+|+++++.||..         
T Consensus         1 ~~ilivdd~~~~~~~l~~~l~~~~~~~~v~~~~~~~~~l~~~~~~~~dlv~lDi~m~~~~G~~~~~~i~~~---------   71 (246)
T PRK14084          1 MKALIVDDEPLARNELTYLLNEIGGFEEINEAENVKETLEALLINQYDIIFLDINLMDESGIELAAKIQKM---------   71 (246)
T ss_pred             CEEEEECCCHHHHHHHHHHHHhCCCceEEEEECCHHHHHHHHHhcCCCEEEEeCCCCCCCHHHHHHHHHhc---------
Confidence            379999999999999999999876 3 57789999999999998899999999999999999999999963         


Q ss_pred             hhhhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHHhh
Q 039716          938 AEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQY 1000 (1002)
Q Consensus       938 ~~~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~~ 1000 (1002)
                                       .+..|||++|++.  +...++++.|+++||.||++..+|..+++++
T Consensus        72 -----------------~~~~~iI~~t~~~--~~~~~~~~~~~~~yl~KP~~~~~l~~~l~~~  115 (246)
T PRK14084         72 -----------------KEPPAIIFATAHD--QFAVKAFELNATDYILKPFEQKRIEQAVNKV  115 (246)
T ss_pred             -----------------CCCCEEEEEecCh--HHHHHHHhcCCcEEEECCCCHHHHHHHHHHH
Confidence                             2346899999875  3567899999999999999999999998775

>CHL00148 orf27 Ycf27; Reviewed

Probab=99.42  E-value=4e-12  Score=136.52  Aligned_cols=115  Identities=27%  Similarity=0.414  Sum_probs=106.6

Q ss_pred             CCeEEEEecCHHHHHHHHHHHHhcCCeEEEEcCHHHHHHHHHcCCCcEEEEcCCCCCCCHHHHHHHHhccccCCCchhhh
Q 039716          859 KPKILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDAAA  938 (1002)
Q Consensus       859 ~~~ILiVeDn~~n~~~l~~~L~~~g~~v~~a~~G~eAl~~~~~~~~DlIlmDi~MP~mdG~e~~~~IR~~~~~~~~~~~~  938 (1002)
                      ..+||||||++.....+...|...|+.+..+.++.+|+..+....||+||+|+.||.++|+++++.|+..          
T Consensus         6 ~~~ilivdd~~~~~~~l~~~l~~~~~~v~~~~~~~~~l~~~~~~~~d~illd~~~~~~~g~~~~~~l~~~----------   75 (240)
T CHL00148          6 KEKILVVDDEAYIRKILETRLSIIGYEVITASDGEEALKLFRKEQPDLVILDVMMPKLDGYGVCQEIRKE----------   75 (240)
T ss_pred             CceEEEEeCCHHHHHHHHHHHHHCCCEEEEeCCHHHHHHHHHhcCCCEEEEeCCCCCCCHHHHHHHHHhc----------
Confidence            4589999999999999999999999999999999999999998999999999999999999999999852          


Q ss_pred             hhhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHHhh
Q 039716          939 EAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQY 1000 (1002)
Q Consensus       939 ~~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~~ 1000 (1002)
                                       +.+|||++|+.........++.+|+++|+.||++..+|...+...
T Consensus        76 -----------------~~~~ii~ls~~~~~~~~~~~~~~Ga~~~l~kp~~~~~L~~~i~~~  120 (240)
T CHL00148         76 -----------------SDVPIIMLTALGDVSDRITGLELGADDYVVKPFSPKELEARIRSV  120 (240)
T ss_pred             -----------------CCCcEEEEECCCCHHhHHHHHHCCCCEEEeCCCCHHHHHHHHHHH
Confidence                             358999999999999999999999999999999999999888754

>PRK09958 DNA-binding transcriptional activator EvgA; Provisional

Probab=99.42  E-value=3.1e-12  Score=133.91  Aligned_cols=114  Identities=19%  Similarity=0.329  Sum_probs=105.7

Q ss_pred             eEEEEecCHHHHHHHHHHHHhcCCeEE-EEcCHHHHHHHHHcCCCcEEEEcCCCCCCCHHHHHHHHhccccCCCchhhhh
Q 039716          861 KILLVEDNKINVMVAKSMMKQLGHSID-VVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDAAAE  939 (1002)
Q Consensus       861 ~ILiVeDn~~n~~~l~~~L~~~g~~v~-~a~~G~eAl~~~~~~~~DlIlmDi~MP~mdG~e~~~~IR~~~~~~~~~~~~~  939 (1002)
                      +||+|||++..+..+...|+..|+.+. .+.++.+++..+....||+|++|+.||.++|+++++.++..           
T Consensus         2 ~ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~~~~~~~~dlvi~d~~~~~~~g~~~~~~l~~~-----------   70 (204)
T PRK09958          2 NAIIIDDHPLAIAAIRNLLIKNDIEILAELTEGGSAVQRVETLKPDIVIIDVDIPGVNGIQVLETLRKR-----------   70 (204)
T ss_pred             cEEEECCcHHHHHHHHHHHhcCCCEEEEEeCCHHHHHHHHHccCCCEEEEeCCCCCCCHHHHHHHHHhh-----------
Confidence            699999999999999999999999987 69999999999999999999999999999999999999962           


Q ss_pred             hhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHHhh
Q 039716          940 AGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQY 1000 (1002)
Q Consensus       940 ~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~~ 1000 (1002)
                                     .+..|||++|+.........++.+|+++|+.||++..+|...++..
T Consensus        71 ---------------~~~~~ii~ls~~~~~~~~~~~~~~ga~~~i~kp~~~~~l~~~i~~~  116 (204)
T PRK09958         71 ---------------QYSGIIIIVSAKNDHFYGKHCADAGANGFVSKKEGMNNIIAAIEAA  116 (204)
T ss_pred             ---------------CCCCeEEEEeCCCCHHHHHHHHHCCCCEEEecCCCHHHHHHHHHHH
Confidence                           2457899999999999999999999999999999999999998865

>PRK10923 glnG nitrogen regulation protein NR(I); Provisional

Probab=99.41  E-value=2.5e-12  Score=153.28  Aligned_cols=115  Identities=24%  Similarity=0.388  Sum_probs=107.8

Q ss_pred             CeEEEEecCHHHHHHHHHHHHhcCCeEEEEcCHHHHHHHHHcCCCcEEEEcCCCCCCCHHHHHHHHhccccCCCchhhhh
Q 039716          860 PKILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDAAAE  939 (1002)
Q Consensus       860 ~~ILiVeDn~~n~~~l~~~L~~~g~~v~~a~~G~eAl~~~~~~~~DlIlmDi~MP~mdG~e~~~~IR~~~~~~~~~~~~~  939 (1002)
                      .+||||||++..+..+..+|...|+.|..+.++.+|+..+....||+||+|+.||++||+++++.||..           
T Consensus         4 ~~ILiVdd~~~~~~~L~~~L~~~g~~v~~~~s~~~al~~l~~~~~DlvllD~~lp~~dgl~~l~~ir~~-----------   72 (469)
T PRK10923          4 GIVWVVDDDSSIRWVLERALAGAGLTCTTFENGNEVLEALASKTPDVLLSDIRMPGMDGLALLKQIKQR-----------   72 (469)
T ss_pred             CeEEEEECCHHHHHHHHHHHHHcCCEEEEECCHHHHHHHHhcCCCCEEEECCCCCCCCHHHHHHHHHhh-----------
Confidence            489999999999999999999999999999999999999999999999999999999999999999862           


Q ss_pred             hhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHHhh
Q 039716          940 AGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQY 1000 (1002)
Q Consensus       940 ~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~~ 1000 (1002)
                                     .+.+|||++|++...+....++++|+++|+.||++..+|...+.+.
T Consensus        73 ---------------~~~~pvIvlt~~~~~~~~~~a~~~Ga~~~l~KP~~~~~L~~~i~~~  118 (469)
T PRK10923         73 ---------------HPMLPVIIMTAHSDLDAAVSAYQQGAFDYLPKPFDIDEAVALVERA  118 (469)
T ss_pred             ---------------CCCCeEEEEECCCCHHHHHHHHhcCcceEEecCCcHHHHHHHHHHH
Confidence                           2568999999999999999999999999999999999999888754

>PRK15115 response regulator GlrR; Provisional

Probab=99.40  E-value=2.5e-12  Score=152.09  Aligned_cols=116  Identities=25%  Similarity=0.368  Sum_probs=108.3

Q ss_pred             CCeEEEEecCHHHHHHHHHHHHhcCCeEEEEcCHHHHHHHHHcCCCcEEEEcCCCCCCCHHHHHHHHhccccCCCchhhh
Q 039716          859 KPKILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDAAA  938 (1002)
Q Consensus       859 ~~~ILiVeDn~~n~~~l~~~L~~~g~~v~~a~~G~eAl~~~~~~~~DlIlmDi~MP~mdG~e~~~~IR~~~~~~~~~~~~  938 (1002)
                      ..+||||||++.++..+..+|+..|+.|..+.++.+|+..+....||+||+|+.||+|+|+++++.|+..          
T Consensus         5 ~~~vLiVdd~~~~~~~l~~~L~~~g~~v~~~~~~~eal~~l~~~~~dlvilD~~lp~~~g~~ll~~l~~~----------   74 (444)
T PRK15115          5 PAHLLLVDDDPGLLKLLGMRLTSEGYSVVTAESGQEALRVLNREKVDLVISDLRMDEMDGMQLFAEIQKV----------   74 (444)
T ss_pred             CCeEEEEECCHHHHHHHHHHHHHCCCEEEEeCCHHHHHHHHhcCCCCEEEEcCCCCCCCHHHHHHHHHhc----------
Confidence            4689999999999999999999999999999999999999999999999999999999999999999852          


Q ss_pred             hhhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHHhh
Q 039716          939 EAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQY 1000 (1002)
Q Consensus       939 ~~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~~ 1000 (1002)
                                      .+.+|||++|+........+++.+|+++|+.||++..+|...|.+.
T Consensus        75 ----------------~~~~pvIvlt~~~~~~~~~~a~~~Ga~~~l~KP~~~~~L~~~l~~~  120 (444)
T PRK15115         75 ----------------QPGMPVIILTAHGSIPDAVAATQQGVFSFLTKPVDRDALYKAIDDA  120 (444)
T ss_pred             ----------------CCCCcEEEEECCCCHHHHHHHHhcChhhhccCCCCHHHHHHHHHHH
Confidence                            3568999999999999999999999999999999999999988764

>PRK11361 acetoacetate metabolism regulatory protein AtoC; Provisional

Probab=99.39  E-value=4.4e-12  Score=150.57  Aligned_cols=117  Identities=32%  Similarity=0.451  Sum_probs=108.7

Q ss_pred             CCeEEEEecCHHHHHHHHHHHHhcCCeEEEEcCHHHHHHHHHcCCCcEEEEcCCCCCCCHHHHHHHHhccccCCCchhhh
Q 039716          859 KPKILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDAAA  938 (1002)
Q Consensus       859 ~~~ILiVeDn~~n~~~l~~~L~~~g~~v~~a~~G~eAl~~~~~~~~DlIlmDi~MP~mdG~e~~~~IR~~~~~~~~~~~~  938 (1002)
                      ..+||||||++..+..+...|...||.|..+.++.+|+..+....||+||+|+.||+++|+++++.|+..          
T Consensus         4 ~~~iLivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~al~~l~~~~~dlillD~~~p~~~g~~ll~~i~~~----------   73 (457)
T PRK11361          4 INRILIVDDEDNVRRMLSTAFALQGFETHCANNGRTALHLFADIHPDVVLMDIRMPEMDGIKALKEMRSH----------   73 (457)
T ss_pred             CCeEEEEECCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHHhcCCCCEEEEeCCCCCCCHHHHHHHHHhc----------
Confidence            4589999999999999999999999999999999999999999999999999999999999999999862          


Q ss_pred             hhhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHHhhc
Q 039716          939 EAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQYF 1001 (1002)
Q Consensus       939 ~~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~~l 1001 (1002)
                                      .+.+|||++|+....+....++++|+++|+.||++..+|...+.+.+
T Consensus        74 ----------------~~~~pvI~lt~~~~~~~~~~a~~~Ga~d~l~KP~~~~~L~~~i~~~l  120 (457)
T PRK11361         74 ----------------ETRTPVILMTAYAEVETAVEALRCGAFDYVIKPFDLDELNLIVQRAL  120 (457)
T ss_pred             ----------------CCCCCEEEEeCCCCHHHHHHHHHCCccEEEecccCHHHHHHHHhhhc
Confidence                            25689999999999999999999999999999999999998887643

>PRK09581 pleD response regulator PleD; Reviewed

Probab=99.39  E-value=1.5e-12  Score=153.64  Aligned_cols=117  Identities=21%  Similarity=0.355  Sum_probs=106.3

Q ss_pred             CCCeEEEEecCHHHHHHHHHHHHhcCCeEEEEcCHHHHHHHHHcCCCcEEEEcCCCCCCCHHHHHHHHhccccCCCchhh
Q 039716          858 PKPKILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDAA  937 (1002)
Q Consensus       858 ~~~~ILiVeDn~~n~~~l~~~L~~~g~~v~~a~~G~eAl~~~~~~~~DlIlmDi~MP~mdG~e~~~~IR~~~~~~~~~~~  937 (1002)
                      ...+||||||++..+..+..+|.. ++.+..+.+|.+|+..+....||+||+|+.||+|+|+++++.||+..        
T Consensus       154 ~~~~vlivdd~~~~~~~l~~~l~~-~~~~~~~~~~~~a~~~~~~~~~d~vi~d~~~p~~~g~~l~~~i~~~~--------  224 (457)
T PRK09581        154 EDGRILLVDDDVSQAERIANILKE-EFRVVVVSDPSEALFNAAETNYDLVIVSANFENYDPLRLCSQLRSKE--------  224 (457)
T ss_pred             cCceEEEEecccchHHHHHHHHhh-cceeeeecChHHHHHhcccCCCCEEEecCCCCCchHhHHHHHHHhcc--------
Confidence            456899999999999999999975 57777899999999999999999999999999999999999999632        


Q ss_pred             hhhhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHHh
Q 039716          938 AEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQ  999 (1002)
Q Consensus       938 ~~~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~  999 (1002)
                                      ..+.+|||++|++.+.+...+|+.+|++||+.||++.++|...+..
T Consensus       225 ----------------~~~~~~ii~ls~~~~~~~~~~a~~~Ga~d~l~kp~~~~~l~~~i~~  270 (457)
T PRK09581        225 ----------------RTRYVPILLLVDEDDDPRLVKALELGVNDYLMRPIDKNELLARVRT  270 (457)
T ss_pred             ----------------ccCCCcEEEEeCCCChHHHHHHHHccchhhhhCCCcHHHHHHHHHH
Confidence                            2367999999999999999999999999999999999999888764

>PRK09483 response regulator; Provisional

Probab=99.38  E-value=6.4e-12  Score=132.84  Aligned_cols=116  Identities=23%  Similarity=0.377  Sum_probs=105.8

Q ss_pred             CeEEEEecCHHHHHHHHHHHHhc-CCeEE-EEcCHHHHHHHHHcCCCcEEEEcCCCCCCCHHHHHHHHhccccCCCchhh
Q 039716          860 PKILLVEDNKINVMVAKSMMKQL-GHSID-VVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDAA  937 (1002)
Q Consensus       860 ~~ILiVeDn~~n~~~l~~~L~~~-g~~v~-~a~~G~eAl~~~~~~~~DlIlmDi~MP~mdG~e~~~~IR~~~~~~~~~~~  937 (1002)
                      .+||||||++..+..+..+|+.. |+.+. .+.++.+|+..+....||+||+|+.||+++|+++++.|+..         
T Consensus         2 ~~ilivd~~~~~~~~l~~~L~~~~~~~~v~~~~~~~~~~~~~~~~~~dlvi~d~~~~~~~g~~~~~~l~~~---------   72 (217)
T PRK09483          2 INVLLVDDHELVRAGIRRILEDIKGIKVVGEACCGEDAVKWCRTNAVDVVLMDMNMPGIGGLEATRKILRY---------   72 (217)
T ss_pred             eEEEEECCcHHHHHHHHHHHccCCCCEEEEEeCCHHHHHHHHHhcCCCEEEEeCCCCCCCHHHHHHHHHHH---------
Confidence            47999999999999999999874 78765 78999999999999999999999999999999999999852         


Q ss_pred             hhhhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHHhhc
Q 039716          938 AEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQYF 1001 (1002)
Q Consensus       938 ~~~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~~l 1001 (1002)
                                       .+.+|||++|..........++..|+++|+.||++.++|..+++.++
T Consensus        73 -----------------~~~~~ii~ls~~~~~~~~~~~~~~g~~~~l~k~~~~~~l~~~i~~~~  119 (217)
T PRK09483         73 -----------------TPDVKIIMLTVHTENPLPAKVMQAGAAGYLSKGAAPQEVVSAIRSVH  119 (217)
T ss_pred             -----------------CCCCeEEEEeCCCCHHHHHHHHHcCCCEEEeCCCCHHHHHHHHHHHH
Confidence                             35689999999999999999999999999999999999999998753

>PRK10365 transcriptional regulatory protein ZraR; Provisional

Probab=99.38  E-value=2.8e-12  Score=151.57  Aligned_cols=116  Identities=30%  Similarity=0.528  Sum_probs=108.2

Q ss_pred             CCeEEEEecCHHHHHHHHHHHHhcCCeEEEEcCHHHHHHHHHcCCCcEEEEcCCCCCCCHHHHHHHHhccccCCCchhhh
Q 039716          859 KPKILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDAAA  938 (1002)
Q Consensus       859 ~~~ILiVeDn~~n~~~l~~~L~~~g~~v~~a~~G~eAl~~~~~~~~DlIlmDi~MP~mdG~e~~~~IR~~~~~~~~~~~~  938 (1002)
                      ..+||||||++..+..+..+|...|+.|..+.++.+|+..+....||+||+|+.||+++|+++++.||..          
T Consensus         5 ~~~Ilivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~al~~l~~~~~DlvilD~~m~~~~G~~~~~~ir~~----------   74 (441)
T PRK10365          5 NIDILVVDDDISHCTILQALLRGWGYNVALANSGRQALEQVREQVFDLVLCDVRMAEMDGIATLKEIKAL----------   74 (441)
T ss_pred             cceEEEEECCHHHHHHHHHHHHHCCCeEEEeCCHHHHHHHHhcCCCCEEEEeCCCCCCCHHHHHHHHHhh----------
Confidence            4689999999999999999999999999999999999999999999999999999999999999999963          


Q ss_pred             hhhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHHhh
Q 039716          939 EAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQY 1000 (1002)
Q Consensus       939 ~~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~~ 1000 (1002)
                                      .+.+|||++|++...+....++++|+.+|+.||++..+|...|.+.
T Consensus        75 ----------------~~~~~vi~lt~~~~~~~~~~a~~~ga~~~l~Kp~~~~~L~~~l~~~  120 (441)
T PRK10365         75 ----------------NPAIPVLIMTAYSSVETAVEALKTGALDYLIKPLDFDNLQATLEKA  120 (441)
T ss_pred             ----------------CCCCeEEEEECCCCHHHHHHHHHhhhHHHhcCCCCHHHHHHHHHHH
Confidence                            2568999999999999999999999999999999999998888754

>PRK10360 DNA-binding transcriptional activator UhpA; Provisional

Probab=99.38  E-value=7.2e-12  Score=130.23  Aligned_cols=113  Identities=16%  Similarity=0.254  Sum_probs=102.1

Q ss_pred             CeEEEEecCHHHHHHHHHHHHhc-CCe-EEEEcCHHHHHHHHHcCCCcEEEEcCCCCCCCHHHHHHHHhccccCCCchhh
Q 039716          860 PKILLVEDNKINVMVAKSMMKQL-GHS-IDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDAA  937 (1002)
Q Consensus       860 ~~ILiVeDn~~n~~~l~~~L~~~-g~~-v~~a~~G~eAl~~~~~~~~DlIlmDi~MP~mdG~e~~~~IR~~~~~~~~~~~  937 (1002)
                      .+||||||++..+..+..+|... |+. +..+.++.+|+..+....||+||+|+.||+++|+++++.++.          
T Consensus         2 ~~ilivd~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~l~~~~~~~~dlvi~d~~~~~~~g~~~~~~l~~----------   71 (196)
T PRK10360          2 ITVALIDDHLIVRSGFAQLLGLEPDLQVVAEFGSGREALAGLPGRGVQVCICDISMPDISGLELLSQLPK----------   71 (196)
T ss_pred             eEEEEECCcHHHHHHHHHHHccCCCcEEEEEECCHHHHHHHHhcCCCCEEEEeCCCCCCCHHHHHHHHcc----------
Confidence            47999999999999999999854 565 568899999999999899999999999999999999998862          


Q ss_pred             hhhhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHHhhc
Q 039716          938 AEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQYF 1001 (1002)
Q Consensus       938 ~~~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~~l 1001 (1002)
                                         .+|||++|+....+....|+.+|+++|+.||++.++|...|+.++
T Consensus        72 -------------------~~~vi~~s~~~~~~~~~~~~~~ga~~~i~kp~~~~~l~~~i~~~~  116 (196)
T PRK10360         72 -------------------GMATIMLSVHDSPALVEQALNAGARGFLSKRCSPDELIAAVHTVA  116 (196)
T ss_pred             -------------------CCCEEEEECCCCHHHHHHHHHcCCcEEEECCCCHHHHHHHHHHHH
Confidence                               368999999999999999999999999999999999999998753

>TIGR02915 PEP_resp_reg putative PEP-CTERM system response regulator

Probab=99.38  E-value=3.9e-12  Score=150.51  Aligned_cols=111  Identities=23%  Similarity=0.272  Sum_probs=102.9

Q ss_pred             EEEEecCHHHHHHHHHHHHhcCCeEEEEcCHHHHHHHHHcCCCcEEEEcCCCCC-----CCHHHHHHHHhccccCCCchh
Q 039716          862 ILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPV-----MDGLKATRLIRSFEDTGNWDA  936 (1002)
Q Consensus       862 ILiVeDn~~n~~~l~~~L~~~g~~v~~a~~G~eAl~~~~~~~~DlIlmDi~MP~-----mdG~e~~~~IR~~~~~~~~~~  936 (1002)
                      ||||||++..+..+...|  .||.|..+.++.+|++.+....||+||+|+.||+     ++|+++++.|++.        
T Consensus         1 ILivddd~~~~~~l~~~l--~~~~v~~a~~~~~al~~l~~~~~dlvllD~~mp~~~~~~~~g~~~l~~i~~~--------   70 (445)
T TIGR02915         1 LLIVEDDLGLQKQLKWSF--ADYELAVAADRESAIALVRRHEPAVVTLDLGLPPDADGASEGLAALQQILAI--------   70 (445)
T ss_pred             CEEEECCHHHHHHHHHHh--CCCeEEEeCCHHHHHHHHhhCCCCEEEEeCCCCCCcCCCCCHHHHHHHHHhh--------
Confidence            689999999999999888  7999999999999999999999999999999996     9999999999862        


Q ss_pred             hhhhhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHHhh
Q 039716          937 AAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQY 1000 (1002)
Q Consensus       937 ~~~~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~~ 1000 (1002)
                                        .+.+|||++|++.+.+...+|+++|+++||.||++.++|...|++.
T Consensus        71 ------------------~~~~piI~lt~~~~~~~~~~a~~~Ga~dyl~KP~~~~~L~~~i~~~  116 (445)
T TIGR02915        71 ------------------APDTKVIVITGNDDRENAVKAIGLGAYDFYQKPIDPDVLKLIVDRA  116 (445)
T ss_pred             ------------------CCCCCEEEEecCCCHHHHHHHHHCCccEEEeCCCCHHHHHHHHhhh
Confidence                              3568999999999999999999999999999999999999888654

Members of this protein family share full-length homology with (but do not include) the acetoacetate metabolism regulatory protein AtoC. These proteins have a Fis family DNA binding sequence (pfam02954), a response regulator receiver domain (pfam00072), and sigma-54 interaction domain (pfam00158).

>PRK11697 putative two-component response-regulatory protein YehT; Provisional

Probab=99.37  E-value=6e-12  Score=135.68  Aligned_cols=112  Identities=22%  Similarity=0.383  Sum_probs=97.7

Q ss_pred             CeEEEEecCHHHHHHHHHHHHhcCC-e-EEEEcCHHHHHHHHHcCCCcEEEEcCCCCCCCHHHHHHHHhccccCCCchhh
Q 039716          860 PKILLVEDNKINVMVAKSMMKQLGH-S-IDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDAA  937 (1002)
Q Consensus       860 ~~ILiVeDn~~n~~~l~~~L~~~g~-~-v~~a~~G~eAl~~~~~~~~DlIlmDi~MP~mdG~e~~~~IR~~~~~~~~~~~  937 (1002)
                      .+||||||++..+..+..+|+..|. . +..+.++.+|+..+....||+||+|+.||+++|+++++.++..         
T Consensus         2 ~~IlIvdd~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~dlv~lDi~~~~~~G~~~~~~l~~~---------   72 (238)
T PRK11697          2 IKVLIVDDEPLAREELRELLQEEGDIEIVGECSNAIEAIGAIHRLKPDVVFLDIQMPRISGLELVGMLDPE---------   72 (238)
T ss_pred             cEEEEECCCHHHHHHHHHHHhhCCCcEEEEEeCCHHHHHHHHHhcCCCEEEEeCCCCCCCHHHHHHHhccc---------
Confidence            4799999999999999999998883 3 4578999999999988899999999999999999999998631         


Q ss_pred             hhhhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHHhh
Q 039716          938 AEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQY 1000 (1002)
Q Consensus       938 ~~~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~~ 1000 (1002)
                                        ...+||++|++.  +...++++.|+.+||.||++.++|..++.++
T Consensus        73 ------------------~~~~ii~vt~~~--~~~~~a~~~~~~~yl~KP~~~~~l~~~l~~~  115 (238)
T PRK11697         73 ------------------HMPYIVFVTAFD--EYAIKAFEEHAFDYLLKPIDPARLAKTLARL  115 (238)
T ss_pred             ------------------CCCEEEEEeccH--HHHHHHHhcCCcEEEECCCCHHHHHHHHHHH
Confidence                              234689999875  4667899999999999999999999988765

>PRK09935 transcriptional regulator FimZ; Provisional

Probab=99.37  E-value=1.1e-11  Score=129.99  Aligned_cols=115  Identities=16%  Similarity=0.269  Sum_probs=104.3

Q ss_pred             CeEEEEecCHHHHHHHHHHHHhc-CCeEE-EEcCHHHHHHHHHcCCCcEEEEcCCCCCCCHHHHHHHHhccccCCCchhh
Q 039716          860 PKILLVEDNKINVMVAKSMMKQL-GHSID-VVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDAA  937 (1002)
Q Consensus       860 ~~ILiVeDn~~n~~~l~~~L~~~-g~~v~-~a~~G~eAl~~~~~~~~DlIlmDi~MP~mdG~e~~~~IR~~~~~~~~~~~  937 (1002)
                      .+||||||++..+..+...|... ++.+. .+.++.+++..+....||+|++|+.||+++|+++++.++..         
T Consensus         4 ~~iliv~d~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~dlvild~~l~~~~g~~~~~~l~~~---------   74 (210)
T PRK09935          4 ASVIIMDTHPIIRMSIEVLLQKNSELQIVLKTDDYRITIDYLRTRPVDLIIMDIDLPGTDGFTFLKRIKQI---------   74 (210)
T ss_pred             ceEEEECCcHHHHHHHHHHHhhCCCceEEEEeCCHHHHHHHHHhcCCCEEEEeCCCCCCCHHHHHHHHHHh---------
Confidence            47999999999999999999877 57765 68999999999998999999999999999999999999952         


Q ss_pred             hhhhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHHhh
Q 039716          938 AEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQY 1000 (1002)
Q Consensus       938 ~~~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~~ 1000 (1002)
                                       .+.+|||++|+.........++.+|+++|+.||++..+|...|+..
T Consensus        75 -----------------~~~~~ii~ls~~~~~~~~~~~~~~g~~~~l~kp~~~~~l~~~i~~~  120 (210)
T PRK09935         75 -----------------QSTVKVLFLSSKSECFYAGRAIQAGANGFVSKCNDQNDIFHAVQMI  120 (210)
T ss_pred             -----------------CCCCcEEEEECCCcHHHHHHHHHcCCCEEEeCCCCHHHHHHHHHHH
Confidence                             2458999999999999999999999999999999999999998764

>TIGR01818 ntrC nitrogen regulation protein NR(I)

Probab=99.36  E-value=5.7e-12  Score=149.90  Aligned_cols=113  Identities=23%  Similarity=0.386  Sum_probs=106.0

Q ss_pred             EEEEecCHHHHHHHHHHHHhcCCeEEEEcCHHHHHHHHHcCCCcEEEEcCCCCCCCHHHHHHHHhccccCCCchhhhhhh
Q 039716          862 ILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDAAAEAG  941 (1002)
Q Consensus       862 ILiVeDn~~n~~~l~~~L~~~g~~v~~a~~G~eAl~~~~~~~~DlIlmDi~MP~mdG~e~~~~IR~~~~~~~~~~~~~~~  941 (1002)
                      ||||||++..+..+..+|...|+.|..+.++.+|+..+....||+||+|+.||+++|+++++.|+..             
T Consensus         1 ILivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~al~~~~~~~~DlVllD~~~p~~~g~~ll~~l~~~-------------   67 (463)
T TIGR01818         1 VWVVDDDRSIRWVLEKALSRAGYEVRTFGNAASVLRALARGQPDLLITDVRMPGEDGLDLLPQIKKR-------------   67 (463)
T ss_pred             CEEEECCHHHHHHHHHHHHHcCCEEEEECCHHHHHHHHhcCCCCEEEEcCCCCCCCHHHHHHHHHHh-------------
Confidence            6899999999999999999999999999999999999999999999999999999999999999962             


Q ss_pred             hcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHHhh
Q 039716          942 IEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQY 1000 (1002)
Q Consensus       942 ~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~~ 1000 (1002)
                                   .+.+|||++|++.......+++.+|+++|+.||++.+.|...+.+.
T Consensus        68 -------------~~~~~vIvlt~~~~~~~~~~a~~~Ga~~~l~KP~~~~~L~~~i~~~  113 (463)
T TIGR01818        68 -------------HPQLPVIVMTAHSDLDTAVAAYQRGAFEYLPKPFDLDEAVTLVERA  113 (463)
T ss_pred             -------------CCCCeEEEEeCCCCHHHHHHHHHcCcceeecCCCCHHHHHHHHHHH
Confidence                         2568999999999999999999999999999999999999988764

This model represents NtrC, a DNA-binding response regulator that is phosphorylated by NtrB and interacts with sigma-54. NtrC usually controls the expression of glutamine synthase, GlnA, and may be called GlnL, GlnG, etc.

>PRK12555 chemotaxis-specific methylesterase; Provisional

Probab=99.36  E-value=7.3e-12  Score=142.67  Aligned_cols=112  Identities=29%  Similarity=0.408  Sum_probs=96.3

Q ss_pred             eEEEEecCHHHHHHHHHHHH-hcCCeEE-EEcCHHHHHHHHHcCCCcEEEEcCCCCCCCHHHHHHHHhccccCCCchhhh
Q 039716          861 KILLVEDNKINVMVAKSMMK-QLGHSID-VVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDAAA  938 (1002)
Q Consensus       861 ~ILiVeDn~~n~~~l~~~L~-~~g~~v~-~a~~G~eAl~~~~~~~~DlIlmDi~MP~mdG~e~~~~IR~~~~~~~~~~~~  938 (1002)
                      +||||||++..+..+..+|. ..|+.+. .+.+|.+|++.+....||+|++|+.||+|+|+++++.|+..          
T Consensus         2 ~VLvVdd~~~~~~~l~~~L~~~~~~~vv~~a~~~~eal~~l~~~~pDlVllD~~mp~~~G~e~l~~l~~~----------   71 (337)
T PRK12555          2 RIGIVNDSPLAVEALRRALARDPDHEVVWVATDGAQAVERCAAQPPDVILMDLEMPRMDGVEATRRIMAE----------   71 (337)
T ss_pred             EEEEEeCCHHHHHHHHHHHhhCCCCEEEEEECCHHHHHHHHhccCCCEEEEcCCCCCCCHHHHHHHHHHH----------
Confidence            79999999999999999994 6678875 78999999999999999999999999999999999999852          


Q ss_pred             hhhhcccCCCCCCCCCCCCccEEEEcCCCC--HHHHHHHHHcCCCEEEeCCC---------ChHHHHHHHHh
Q 039716          939 EAGIEQAMPSSGSSNHFKRIPIIAMTANAL--SESAEECFANGMDSFVSKPV---------TFQKLKECLEQ  999 (1002)
Q Consensus       939 ~~~~~~~~~~~~~~~~~~~ipIIalTa~~~--~~~~~~~~~aG~d~~l~KP~---------~~~~L~~~l~~  999 (1002)
                                       ..+|||++|+...  .....+|+++|+++|+.||+         ..++|...|+.
T Consensus        72 -----------------~~~pvivvs~~~~~~~~~~~~al~~Ga~d~l~KP~~~~~~~~~~~~~~l~~~i~~  126 (337)
T PRK12555         72 -----------------RPCPILIVTSLTERNASRVFEAMGAGALDAVDTPTLGIGAGLEEYAAELLAKIDQ  126 (337)
T ss_pred             -----------------CCCcEEEEeCCCCcCHHHHHHHHhcCceEEEECCCCCcchhHHHHHHHHHHHHHH
Confidence                             2489999998754  45677899999999999999         44555555554

>PRK10710 DNA-binding transcriptional regulator BaeR; Provisional

Probab=99.35  E-value=2.1e-11  Score=130.87  Aligned_cols=115  Identities=27%  Similarity=0.399  Sum_probs=106.1

Q ss_pred             CCeEEEEecCHHHHHHHHHHHHhcCCeEEEEcCHHHHHHHHHcCCCcEEEEcCCCCCCCHHHHHHHHhccccCCCchhhh
Q 039716          859 KPKILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDAAA  938 (1002)
Q Consensus       859 ~~~ILiVeDn~~n~~~l~~~L~~~g~~v~~a~~G~eAl~~~~~~~~DlIlmDi~MP~mdG~e~~~~IR~~~~~~~~~~~~  938 (1002)
                      ..+||||||++.....+..+|...|+.+..+.++.+|+..+....||+||+|+.||.++|+++++.||..          
T Consensus        10 ~~~ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~~~~~~~dlvl~d~~~~~~~g~~~~~~l~~~----------   79 (240)
T PRK10710         10 TPRILIVEDEPKLGQLLIDYLQAASYATTLLSHGDEVLPYVRQTPPDLILLDLMLPGTDGLTLCREIRRF----------   79 (240)
T ss_pred             CCeEEEEeCCHHHHHHHHHHHHHCCCEEEEeCCHHHHHHHHhhCCCCEEEEeCCCCCCCHHHHHHHHHhc----------
Confidence            3489999999999999999999999999999999999999998999999999999999999999999851          


Q ss_pred             hhhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHHhh
Q 039716          939 EAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQY 1000 (1002)
Q Consensus       939 ~~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~~ 1000 (1002)
                                       +.+|||++|+.........++.+|+++|+.||++..+|...+...
T Consensus        80 -----------------~~~pii~l~~~~~~~~~~~~~~~ga~~~l~kp~~~~~L~~~i~~~  124 (240)
T PRK10710         80 -----------------SDIPIVMVTAKIEEIDRLLGLEIGADDYICKPYSPREVVARVKTI  124 (240)
T ss_pred             -----------------CCCCEEEEEcCCCHHHHHHHHhcCCCeEEECCCCHHHHHHHHHHH
Confidence                             358999999999888899999999999999999999998887654

>PRK15479 transcriptional regulatory protein TctD; Provisional

Probab=99.32  E-value=3e-11  Score=127.76  Aligned_cols=114  Identities=28%  Similarity=0.476  Sum_probs=105.5

Q ss_pred             eEEEEecCHHHHHHHHHHHHhcCCeEEEEcCHHHHHHHHHcCCCcEEEEcCCCCCCCHHHHHHHHhccccCCCchhhhhh
Q 039716          861 KILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDAAAEA  940 (1002)
Q Consensus       861 ~ILiVeDn~~n~~~l~~~L~~~g~~v~~a~~G~eAl~~~~~~~~DlIlmDi~MP~mdG~e~~~~IR~~~~~~~~~~~~~~  940 (1002)
                      +||++||++.....+...|...|+.+..+.++.+++..+....||+|++|+.||.++|+++++.|+..            
T Consensus         2 ~ilivd~~~~~~~~l~~~l~~~~~~v~~~~~~~~~~~~~~~~~~d~vild~~~~~~~~~~~~~~i~~~------------   69 (221)
T PRK15479          2 RLLLAEDNRELAHWLEKALVQNGFAVDCVFDGLAADHLLQSEMYALAVLDINMPGMDGLEVLQRLRKR------------   69 (221)
T ss_pred             eEEEEeCCHHHHHHHHHHHHHCCCEEEEeCCHHHHHHHHhhCCCCEEEEeCCCCCCcHHHHHHHHHhc------------
Confidence            69999999999999999999999999999999999999988899999999999999999999999862            


Q ss_pred             hhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHHhh
Q 039716          941 GIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQY 1000 (1002)
Q Consensus       941 ~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~~ 1000 (1002)
                                    .+.+|||++|+........+++.+|+++|+.||++..+|...+..+
T Consensus        70 --------------~~~~~ii~lt~~~~~~~~~~~~~~g~~~~i~kp~~~~~l~~~i~~~  115 (221)
T PRK15479         70 --------------GQTLPVLLLTARSAVADRVKGLNVGADDYLPKPFELEELDARLRAL  115 (221)
T ss_pred             --------------CCCCCEEEEECCCCHHHHHHHHHcCCCeeEeCCCCHHHHHHHHHHH
Confidence                          2458999999999999999999999999999999999998888654

>COG2201 CheB Chemotaxis response regulator containing a CheY-like receiver domain and a methylesterase domain [Cell motility and secretion / Signal transduction mechanisms]

Probab=99.31  E-value=1.1e-11  Score=137.13  Aligned_cols=103  Identities=30%  Similarity=0.482  Sum_probs=92.1

Q ss_pred             CeEEEEecCHHHHHHHHHHHHhcC--CeEEEEcCHHHHHHHHHcCCCcEEEEcCCCCCCCHHHHHHHHhccccCCCchhh
Q 039716          860 PKILLVEDNKINVMVAKSMMKQLG--HSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDAA  937 (1002)
Q Consensus       860 ~~ILiVeDn~~n~~~l~~~L~~~g--~~v~~a~~G~eAl~~~~~~~~DlIlmDi~MP~mdG~e~~~~IR~~~~~~~~~~~  937 (1002)
                      .+||||||.+..+.+++.+|...|  .-|.++.||.+|++++.+..||+|.||+.||.|||+++++.|-..         
T Consensus         2 irVlvVddsal~R~~i~~~l~~~~~i~vv~~a~ng~~a~~~~~~~~PDVi~ld~emp~mdgl~~l~~im~~---------   72 (350)
T COG2201           2 IRVLVVDDSALMRKVISDILNSDPDIEVVGTARNGREAIDKVKKLKPDVITLDVEMPVMDGLEALRKIMRL---------   72 (350)
T ss_pred             cEEEEEcCcHHHHHHHHHHHhcCCCeEEEEecCCHHHHHHHHHhcCCCEEEEecccccccHHHHHHHHhcC---------
Confidence            589999999999999999999998  457789999999999999999999999999999999999999752         


Q ss_pred             hhhhhcccCCCCCCCCCCCCccEEEEcCCCC--HHHHHHHHHcCCCEEEeCCCC
Q 039716          938 AEAGIEQAMPSSGSSNHFKRIPIIAMTANAL--SESAEECFANGMDSFVSKPVT  989 (1002)
Q Consensus       938 ~~~~~~~~~~~~~~~~~~~~ipIIalTa~~~--~~~~~~~~~aG~d~~l~KP~~  989 (1002)
                                        ..+|||++|+-..  .+...+|++.|+-||+.||..
T Consensus        73 ------------------~p~pVimvsslt~~g~~~t~~al~~gAvD~i~kp~~  108 (350)
T COG2201          73 ------------------RPLPVIMVSSLTEEGAEATLEALELGAVDFIAKPSG  108 (350)
T ss_pred             ------------------CCCcEEEEeccccccHHHHHHHHhcCcceeecCCCc
Confidence                              5689999987544  455668999999999999984

>PRK09390 fixJ response regulator FixJ; Provisional

Probab=99.30  E-value=2.1e-11  Score=126.18  Aligned_cols=115  Identities=21%  Similarity=0.335  Sum_probs=106.1

Q ss_pred             CCeEEEEecCHHHHHHHHHHHHhcCCeEEEEcCHHHHHHHHHcCCCcEEEEcCCCCCCCHHHHHHHHhccccCCCchhhh
Q 039716          859 KPKILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDAAA  938 (1002)
Q Consensus       859 ~~~ILiVeDn~~n~~~l~~~L~~~g~~v~~a~~G~eAl~~~~~~~~DlIlmDi~MP~mdG~e~~~~IR~~~~~~~~~~~~  938 (1002)
                      +.+||||||++.....+...|...|+.+..+.++.+++..+....||+||+|+.||.++|+++++.|+..          
T Consensus         3 ~~~iliv~~~~~~~~~l~~~l~~~~~~v~~~~~~~~~~~~~~~~~~d~ii~d~~~~~~~~~~~~~~l~~~----------   72 (202)
T PRK09390          3 KGVVHVVDDDEAMRDSLAFLLDSAGFEVRLFESAQAFLDALPGLRFGCVVTDVRMPGIDGIELLRRLKAR----------   72 (202)
T ss_pred             CCEEEEEeCCHHHHHHHHHHHHHCCCeEEEeCCHHHHHHHhccCCCCEEEEeCCCCCCcHHHHHHHHHhc----------
Confidence            4689999999999999999999999999999999999999998999999999999999999999999852          


Q ss_pred             hhhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHHh
Q 039716          939 EAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQ  999 (1002)
Q Consensus       939 ~~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~  999 (1002)
                                      .+.+|||++|+.........++.+|+++|+.||++...|...+..
T Consensus        73 ----------------~~~~~ii~l~~~~~~~~~~~~~~~g~~~~l~~p~~~~~l~~~l~~  117 (202)
T PRK09390         73 ----------------GSPLPVIVMTGHGDVPLAVEAMKLGAVDFIEKPFEDERLIGAIER  117 (202)
T ss_pred             ----------------CCCCCEEEEECCCCHHHHHHHHHcChHHHhhCCCCHHHHHHHHHH
Confidence                            256899999999999999999999999999999999998887764

>PRK14868 DNA topoisomerase VI subunit B; Provisional

Probab=99.30  E-value=1.3e-11  Score=147.00  Aligned_cols=74  Identities=26%  Similarity=0.371  Sum_probs=54.3

Q ss_pred             EEEEEEEecCCCCCcCcHhhhhhhccCCCc----cccCcCCCccccHHHHHHHHHHhCCEEEEEeecCC-ceEEEEEEeC
Q 039716          591 WIRCDVYDTGIGIPENALPTLFRKYMQVSA----DHARKYGGTGLGLAICKQLVELMGGRLTVTSKVHC-GSTFTFILPY  665 (1002)
Q Consensus       591 ~l~i~V~DtGiGI~~e~l~~IF~pF~q~~~----~~~~~~~GtGLGLaI~k~Lve~~gG~I~v~S~~g~-GTtF~~~LP~  665 (1002)
                      ++.|.|.|||+||++++++++|++|++++.    ..++...|.||||++|...+. +||.|+|.|..+. +..+.+.|++
T Consensus        81 ~v~I~VeDNG~GIp~EdLp~IFerf~~tSKf~~~~~srG~rG~GLglai~~sqlt-~GgpI~I~S~~~~~~~g~~~~L~I  159 (795)
T PRK14868         81 YYRLVVEDNGPGITKEQIPKVFGKLLYGSRFHAREQSRGQQGIGISAAVLYSQLT-SGKPAKITSRTQGSEEAQYFELII  159 (795)
T ss_pred             EEEEEEEEcCCCCCHHHHHHHhhhhcccccccccccCCCCCceehHHHHHHHHHc-CCCcEEEEeCCCCCCceeEEEEEE
Confidence            478999999999999999999999986542    123344577777777777763 7999999999754 3344444444

>TIGR01052 top6b DNA topoisomerase VI, B subunit

Probab=99.29  E-value=1.3e-11  Score=143.12  Aligned_cols=68  Identities=28%  Similarity=0.494  Sum_probs=57.9

Q ss_pred             EEEEEEEecCCCCCcCcHhhhhhhccCCCccc--cCcCCCccccHHHHHHHHHHhCCE-EEEEeecCCceEE
Q 039716          591 WIRCDVYDTGIGIPENALPTLFRKYMQVSADH--ARKYGGTGLGLAICKQLVELMGGR-LTVTSKVHCGSTF  659 (1002)
Q Consensus       591 ~l~i~V~DtGiGI~~e~l~~IF~pF~q~~~~~--~~~~~GtGLGLaI~k~Lve~~gG~-I~v~S~~g~GTtF  659 (1002)
                      ++.|.|.|+|+||+++.++++|++|++++...  ....||.|+||++|+.+++.|+|. ++|.|..+ |+.|
T Consensus        64 ~~~I~V~DNG~GIp~edl~~iF~rf~~tsK~~~~~~s~G~~GlGLs~~~~isq~~~G~~i~V~S~~~-g~~~  134 (488)
T TIGR01052        64 HYKVTVEDNGPGIPEEYIPKVFGKMLAGSKFHRIIQSRGQQGIGISGAVLYSQMTTGKPVKVISSTG-GEIY  134 (488)
T ss_pred             eEEEEEEECCCCCCHHHHHhhhhhccccCccccccccCCCccEehhHHHHHHHHcCCceEEEEEecC-CceE
Confidence            36789999999999999999999998776432  223578999999999999999998 99999987 6666

This model describes DNA topoisomerase VI, an archaeal type II DNA topoisomerase (DNA gyrase).

>PF00512 HisKA: His Kinase A (phospho-acceptor) domain; InterPro: IPR003661 Two-component signal transduction systems enable bacteria to sense, respond, and adapt to a wide range of environments, stressors, and growth conditions []

Probab=99.28  E-value=1.4e-11  Score=106.01  Aligned_cols=64  Identities=45%  Similarity=0.731  Sum_probs=60.0

Q ss_pred             HHHHHHhhhccccHHHHHHHHHHHHhC-CCCCHHH-HHHHHHHHHHHHHHHHHHHHHHHHHhhhcC
Q 039716          371 KQMLATMSHEIRSPLTGVVSMAEILSN-TKLDREQ-RQLLGVMISSGDLVLQLINDILDLSKVESG  434 (1002)
Q Consensus       371 k~fla~iSHELRTPL~~I~g~~elL~~-~~l~~~~-~~~l~~i~~s~~~L~~LIndlLd~skiesg  434 (1002)
                      ++|++++||||||||++|.+++++|.. ...++++ ++++..+..+++++..+|+++|+|+|+++|
T Consensus         3 ~~~~~~isHelr~PL~~i~~~~~~l~~~~~~~~~~~~~~l~~i~~~~~~l~~li~~ll~~sr~~~G   68 (68)
T PF00512_consen    3 GEFLASISHELRNPLTAIRGYLELLERDSDLDPEQLREYLDRIRSAADRLNELINDLLDFSRIESG   68 (68)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHCSSCC-HHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHCTT
T ss_pred             HHHHHHHhHHHHHHHHHHHHHHHHHHHccCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccC
Confidence            479999999999999999999999998 7788887 999999999999999999999999999987

Some bacteria can contain up to as many as 200 two-component systems that need tight regulation to prevent unwanted cross-talk []. These pathways have been adapted to response to a wide variety of stimuli, including nutrients, cellular redox state, changes in osmolarity, quorum signals, antibiotics, and more []. Two-component systems are comprised of a sensor histidine kinase (HK) and its cognate response regulator (RR) []. The HK catalyses its own auto-phosphorylation followed by the transfer of the phosphoryl group to the receiver domain on RR; phosphorylation of the RR usually activates an attached output domain, which can then effect changes in cellular physiology, often by regulating gene expression. Some HK are bifunctional, catalysing both the phosphorylation and dephosphorylation of their cognate RR. The input stimuli can regulate either the kinase or phosphatase activity of the bifunctional HK. A variant of the two-component system is the phospho-relay system. Here a hybrid HK auto-phosphorylates and then transfers the phosphoryl group to an internal receiver domain, rather than to a separate RR protein. The phosphoryl group is then shuttled to histidine phosphotransferase (HPT) and subsequently to a terminal RR, which can evoke the desired response [, ]. Signal transducing histidine kinases are the key elements in two-component signal transduction systems, which control complex processes such as the initiation of development in microorganisms [, ]. Examples of histidine kinases are EnvZ, which plays a central role in osmoregulation [], and CheA, which plays a central role in the chemotaxis system []. Histidine kinases usually have an N-terminal ligand-binding domain and a C-terminal kinase domain, but other domains may also be present. The kinase domain is responsible for the autophosphorylation of the histidine with ATP, the phosphotransfer from the kinase to an aspartate of the response regulator, and (with bifunctional enzymes) the phosphotransfer from aspartyl phosphate back to ADP or to water []. The kinase core has a unique fold, distinct from that of the Ser/Thr/Tyr kinase superfamily. HKs can be roughly divided into two classes: orthodox and hybrid kinases [, ]. Most orthodox HKs, typified by the Escherichia coli EnvZ protein, function as periplasmic membrane receptors and have a signal peptide and transmembrane segment(s) that separate the protein into a periplasmic N-terminal sensing domain and a highly conserved cytoplasmic C-terminal kinase core. Members of this family, however, have an integral membrane sensor domain. Not all orthodox kinases are membrane bound, e.g., the nitrogen regulatory kinase NtrB (GlnL) is a soluble cytoplasmic HK []. Hybrid kinases contain multiple phosphodonor and phosphoacceptor sites and use multi-step phospho-relay schemes instead of promoting a single phosphoryl transfer. In addition to the sensor domain and kinase core, they contain a CheY-like receiver domain and a His-containing phosphotransfer (HPt) domain. This entry represents the dimerisation and phosphoacceptor domain found in histidine kinases. It has been found in bacterial sensor protein/histidine kinases. Signal transducing histidine kinases are the key elements in two-component signal transduction systems, which control complex processes such as the initiation of development in microorganisms []. Examples of histidine kinases are EnvZ, which plays a central role in osmoregulation [], and CheA, which plays a central role in the chemotaxis system []. Histidine kinases usually have an N-terminal ligand-binding domain and a C-terminal kinase domain, but other domains may also be present. The kinase domain is responsible for the autophosphorylation of the histidine with ATP, the phosphotransfer from the kinase to an aspartate of the response regulator, and the phosphotransfer from aspartyl phosphate back to ADP or to water []. The homodimeric domain includes the site of histidine autophosphorylation and phosphate transfer reactions. The structure of the homodimeric domain comprises a closed, four-helical bundle with a left-handed twist, formed by two identical alpha-hairpin subunits.; GO: 0000155 two-component sensor activity, 0007165 signal transduction, 0016020 membrane; PDB: 3DGE_A 2C2A_A 3A0R_A 4EW8_A 2LFS_B 2LFR_B 3JZ3_A 1JOY_B 3ZRW_C 3ZRV_A ....

>PRK00742 chemotaxis-specific methylesterase; Provisional

Probab=99.27  E-value=4.7e-11  Score=137.02  Aligned_cols=104  Identities=27%  Similarity=0.400  Sum_probs=92.1

Q ss_pred             CCeEEEEecCHHHHHHHHHHHHhc-CCeEE-EEcCHHHHHHHHHcCCCcEEEEcCCCCCCCHHHHHHHHhccccCCCchh
Q 039716          859 KPKILLVEDNKINVMVAKSMMKQL-GHSID-VVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDA  936 (1002)
Q Consensus       859 ~~~ILiVeDn~~n~~~l~~~L~~~-g~~v~-~a~~G~eAl~~~~~~~~DlIlmDi~MP~mdG~e~~~~IR~~~~~~~~~~  936 (1002)
                      ..+||||||++.++..+..+|... |+.+. .+.++.+|+..+....||+|++|+.||+|+|+++++.|++.        
T Consensus         3 ~~~ILiVdd~~~~~~~L~~~L~~~~~~~vv~~a~~~~~al~~~~~~~~DlVllD~~mp~~dgle~l~~i~~~--------   74 (354)
T PRK00742          3 KIRVLVVDDSAFMRRLISEILNSDPDIEVVGTAPDGLEAREKIKKLNPDVITLDVEMPVMDGLDALEKIMRL--------   74 (354)
T ss_pred             ccEEEEECCCHHHHHHHHHHHhhCCCCEEEEEECCHHHHHHHHhhhCCCEEEEeCCCCCCChHHHHHHHHHh--------
Confidence            358999999999999999999876 78776 89999999999999999999999999999999999999962        


Q ss_pred             hhhhhhcccCCCCCCCCCCCCccEEEEcCCCC--HHHHHHHHHcCCCEEEeCCCC
Q 039716          937 AAEAGIEQAMPSSGSSNHFKRIPIIAMTANAL--SESAEECFANGMDSFVSKPVT  989 (1002)
Q Consensus       937 ~~~~~~~~~~~~~~~~~~~~~ipIIalTa~~~--~~~~~~~~~aG~d~~l~KP~~  989 (1002)
                                        .+ +|||++|+...  .....+++++|+++|+.||+.
T Consensus        75 ------------------~~-~piIvls~~~~~~~~~~~~al~~Ga~d~l~kP~~  110 (354)
T PRK00742         75 ------------------RP-TPVVMVSSLTERGAEITLRALELGAVDFVTKPFL  110 (354)
T ss_pred             ------------------CC-CCEEEEecCCCCCHHHHHHHHhCCCcEEEeCCcc
Confidence                              13 89999998643  466778999999999999994

>PRK09581 pleD response regulator PleD; Reviewed

Probab=99.26  E-value=7e-11  Score=139.56  Aligned_cols=117  Identities=27%  Similarity=0.396  Sum_probs=107.7

Q ss_pred             CeEEEEecCHHHHHHHHHHHHhcCCeEEEEcCHHHHHHHHHcCCCcEEEEcCCCCCCCHHHHHHHHhccccCCCchhhhh
Q 039716          860 PKILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDAAAE  939 (1002)
Q Consensus       860 ~~ILiVeDn~~n~~~l~~~L~~~g~~v~~a~~G~eAl~~~~~~~~DlIlmDi~MP~mdG~e~~~~IR~~~~~~~~~~~~~  939 (1002)
                      .+||+|||++..+..+..+|...|+.+..+.++.+|+..+....||+|++|+.||+++|+++++.||...          
T Consensus         3 ~~ilii~~~~~~~~~l~~~l~~~~~~v~~~~~~~~~~~~~~~~~~dlvi~d~~~~~~~g~~l~~~i~~~~----------   72 (457)
T PRK09581          3 ARILVVDDIPANVKLLEAKLLAEYYTVLTASSGAEAIAICEREQPDIILLDVMMPGMDGFEVCRRLKSDP----------   72 (457)
T ss_pred             CeEEEEeCCHHHHHHHHHHHHhCCCEEEEeCCHHHHHHHHhhcCCCEEEEeCCCCCCCHHHHHHHHHcCc----------
Confidence            3799999999999999999998999999999999999999999999999999999999999999999631          


Q ss_pred             hhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHHhh
Q 039716          940 AGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQY 1000 (1002)
Q Consensus       940 ~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~~ 1000 (1002)
                                    ..+.+|||++|+........+++.+|+++|+.||++..+|...+.+.
T Consensus        73 --------------~~~~~~ii~~s~~~~~~~~~~~~~~ga~~~l~kp~~~~~l~~~i~~~  119 (457)
T PRK09581         73 --------------ATTHIPVVMVTALDDPEDRVRGLEAGADDFLTKPINDVALFARVKSL  119 (457)
T ss_pred             --------------ccCCCCEEEEECCCCHHHHHHHHHCCCCEEEECCCCHHHHHHHHHHH
Confidence                          23468999999999999999999999999999999999998888764

>PRK14867 DNA topoisomerase VI subunit B; Provisional

Probab=99.26  E-value=2.5e-11  Score=144.72  Aligned_cols=77  Identities=26%  Similarity=0.399  Sum_probs=65.4

Q ss_pred             EEEEEEEecCCCCCcCcHhhhhhhccCCCcccc--CcCCCccccHHHHHHHHHHh-CCEEEEEeecCCceEEEEEEeCCC
Q 039716          591 WIRCDVYDTGIGIPENALPTLFRKYMQVSADHA--RKYGGTGLGLAICKQLVELM-GGRLTVTSKVHCGSTFTFILPYQV  667 (1002)
Q Consensus       591 ~l~i~V~DtGiGI~~e~l~~IF~pF~q~~~~~~--~~~~GtGLGLaI~k~Lve~~-gG~I~v~S~~g~GTtF~~~LP~~~  667 (1002)
                      ++.|.|.|||+||+++.++++|++|+.++.-..  ...++.|+||+++..+++.+ ||.|.+.|.++.|++|++.||+..
T Consensus        72 ~~~I~V~DNG~GIp~e~l~~iFerF~atSK~~~~~qS~G~rG~GLa~a~~vsql~~G~pI~I~S~~g~G~~f~i~L~i~i  151 (659)
T PRK14867         72 HYKVAVEDNGPGIPPEFVPKVFGKMLAGSKMHRLIQSRGQQGIGAAGVLLFSQITTGKPLKITTSTGDGKIHEMEIKMSV  151 (659)
T ss_pred             EEEEEEEeeCeeCCHHHHhhhhccccccCcccceeccCCCCcccHHHHHHHHHHhcCCcEEEEEEcCCCEEEEEEEEEEe
Confidence            578999999999999999999999987543211  34568999999999999886 566999999999999999999865

>PRK10100 DNA-binding transcriptional regulator CsgD; Provisional

Probab=99.25  E-value=5.3e-11  Score=126.42  Aligned_cols=112  Identities=10%  Similarity=0.077  Sum_probs=93.2

Q ss_pred             CCCeEEEEecCHHHHHHHHHHHHhcCCe-EEEEcCHHHHHHHHHcCCCcEEEEcCCCCCCCHHHHH-HHHhccccCCCch
Q 039716          858 PKPKILLVEDNKINVMVAKSMMKQLGHS-IDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKAT-RLIRSFEDTGNWD  935 (1002)
Q Consensus       858 ~~~~ILiVeDn~~n~~~l~~~L~~~g~~-v~~a~~G~eAl~~~~~~~~DlIlmDi~MP~mdG~e~~-~~IR~~~~~~~~~  935 (1002)
                      ...++++|||+|.....++.+|+. ++. +..+.++.+|+..+.  .|||||||+.||+++|++++ +.||..       
T Consensus         9 ~~~~~~~v~~~~l~~~~l~~~L~~-~~~v~~~~~~~~~~~~~~~--~~DvvllDi~~p~~~G~~~~~~~i~~~-------   78 (216)
T PRK10100          9 HGHTLLLITKPSLQATALLQHLKQ-SLAITGKLHNIQRSLDDIS--SGSIILLDMMEADKKLIHYWQDTLSRK-------   78 (216)
T ss_pred             cCceEEEEeChHhhhHHHHHHHHH-hCCCeEEEcCHHHhhccCC--CCCEEEEECCCCCccHHHHHHHHHHHh-------
Confidence            345799999999999999999984 554 567889999998754  49999999999999999997 567752       


Q ss_pred             hhhhhhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHH--cCCCEEEeCCCChHHHHHHHHhh
Q 039716          936 AAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFA--NGMDSFVSKPVTFQKLKECLEQY 1000 (1002)
Q Consensus       936 ~~~~~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~--aG~d~~l~KP~~~~~L~~~l~~~ 1000 (1002)
                                         .+.++||++|+...  ....++.  +|+++|+.|+.+.++|.++|+..
T Consensus        79 -------------------~p~~~vvvlt~~~~--~~~~~~~~~~Ga~G~l~K~~~~~~L~~aI~~v  124 (216)
T PRK10100         79 -------------------NNNIKILLLNTPED--YPYREIENWPHINGVFYAMEDQERVVNGLQGV  124 (216)
T ss_pred             -------------------CCCCcEEEEECCch--hHHHHHHHhcCCeEEEECCCCHHHHHHHHHHH
Confidence                               35689999999876  3345555  59999999999999999999754

>cd00075 HATPase_c Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins

Probab=99.24  E-value=6.3e-11  Score=108.27  Aligned_cols=71  Identities=48%  Similarity=0.769  Sum_probs=59.5

Q ss_pred             EEEEEEEecCCCCCcCcHhhhhhhccCCCccccCcCCCccccHHHHHHHHHHhCCEEEEEeecCCceEEEEEE
Q 039716          591 WIRCDVYDTGIGIPENALPTLFRKYMQVSADHARKYGGTGLGLAICKQLVELMGGRLTVTSKVHCGSTFTFIL  663 (1002)
Q Consensus       591 ~l~i~V~DtGiGI~~e~l~~IF~pF~q~~~~~~~~~~GtGLGLaI~k~Lve~~gG~I~v~S~~g~GTtF~~~L  663 (1002)
                      .+.|.|.|+|.|+++..+.++|.+|...  .......+.|+||++|++++..|||.+++.+..+.|++|++.+
T Consensus        33 ~~~v~i~d~g~g~~~~~~~~~~~~~~~~--~~~~~~~~~g~gl~~~~~~~~~~~g~~~~~~~~~~g~~~~~~~  103 (103)
T cd00075          33 HLEIRVEDNGPGIPEEDLERIFERFSDG--SRSRKGGGTGLGLSIVKKLVELHGGRIEVESEPGGGTTFTITL  103 (103)
T ss_pred             EEEEEEEeCCCCCCHHHHHHHhhhhhcC--CCCCCCCccccCHHHHHHHHHHcCCEEEEEeCCCCcEEEEEEC
Confidence            4789999999999999999999987211  1222345899999999999999999999999988899998864

>COG3707 AmiR Response regulator with putative antiterminator output domain [Signal transduction mechanisms]

Probab=99.24  E-value=4.2e-11  Score=120.43  Aligned_cols=113  Identities=24%  Similarity=0.381  Sum_probs=98.3

Q ss_pred             CCeEEEEecCHHHHHHHHHHHHhcCCe-EEEEcCHHHHHHHHHcCCCcEEEEcCCCCCCCHHHHHHHHhccccCCCchhh
Q 039716          859 KPKILLVEDNKINVMVAKSMMKQLGHS-IDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDAA  937 (1002)
Q Consensus       859 ~~~ILiVeDn~~n~~~l~~~L~~~g~~-v~~a~~G~eAl~~~~~~~~DlIlmDi~MP~mdG~e~~~~IR~~~~~~~~~~~  937 (1002)
                      ..+||++||+++++..+...|...||. |.++.+|.++.+.....+||+||||+.||..|-.+.. .+.+          
T Consensus         5 ~lrvlv~~d~~i~~~~i~~~l~eag~~~Vg~~~~~~~~~~~~~~~~pDvVildie~p~rd~~e~~-~~~~----------   73 (194)
T COG3707           5 LLRVLVADDEALTRMDIREGLLEAGYQRVGEAADGLEAVEVCERLQPDVVILDIEMPRRDIIEAL-LLAS----------   73 (194)
T ss_pred             ccceeeccccccchhhHHHHHHHcCCeEeeeecccccchhHHHhcCCCEEEEecCCCCccHHHHH-HHhh----------
Confidence            458999999999999999999999996 6788999999999999999999999999999933332 3332          


Q ss_pred             hhhhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHH
Q 039716          938 AEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLE  998 (1002)
Q Consensus       938 ~~~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~  998 (1002)
                                      .....|||++|++.++...+.+.++|+.+||+||++...|...|.
T Consensus        74 ----------------~~~~~piv~lt~~s~p~~i~~a~~~Gv~ayivkpi~~~rl~p~L~  118 (194)
T COG3707          74 ----------------ENVARPIVALTAYSDPALIEAAIEAGVMAYIVKPLDESRLLPILD  118 (194)
T ss_pred             ----------------cCCCCCEEEEEccCChHHHHHHHHcCCeEEEecCcchhhhhHHHH
Confidence                            235678999999999999999999999999999999988877764

>PRK13558 bacterio-opsin activator; Provisional

Probab=99.24  E-value=5.5e-11  Score=148.00  Aligned_cols=114  Identities=16%  Similarity=0.154  Sum_probs=102.2

Q ss_pred             CCeEEEEecCHHHHHHHHHHHHhcCCeEEEEcCHHHHHHHHHcCCCcEEEEcCCCCCCCHHHHHHHHhccccCCCchhhh
Q 039716          859 KPKILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDAAA  938 (1002)
Q Consensus       859 ~~~ILiVeDn~~n~~~l~~~L~~~g~~v~~a~~G~eAl~~~~~~~~DlIlmDi~MP~mdG~e~~~~IR~~~~~~~~~~~~  938 (1002)
                      ..+||||||++.++..+..+|...||.|..+.++.+|+..+....||+||+|+.||+|+|+++++.||..          
T Consensus         7 ~~~ILivdd~~~~~~~l~~~l~~~~~~v~~~~~~~~al~~~~~~~~Dlvl~d~~lp~~~g~~~l~~l~~~----------   76 (665)
T PRK13558          7 TRGVLFVGDDPEAGPVDCDLDEDGRLDVTQIRDFVAARDRVEAGEIDCVVADHEPDGFDGLALLEAVRQT----------   76 (665)
T ss_pred             ceeEEEEccCcchHHHHHHHhhccCcceEeeCCHHHHHHHhhccCCCEEEEeccCCCCcHHHHHHHHHhc----------
Confidence            3589999999999999999999999999999999999999998899999999999999999999999862          


Q ss_pred             hhhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChH--HHHHHHH
Q 039716          939 EAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQ--KLKECLE  998 (1002)
Q Consensus       939 ~~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~--~L~~~l~  998 (1002)
                                      .+.+|||++|+..+.+...+++.+|+++|+.||....  .+...++
T Consensus        77 ----------------~~~~piI~lt~~~~~~~~~~al~~Ga~dyl~k~~~~~~~~l~~~i~  122 (665)
T PRK13558         77 ----------------TAVPPVVVVPTAGDEAVARRAVDADAAAYVPAVSDDATAAIAERIE  122 (665)
T ss_pred             ----------------CCCCCEEEEECCCCHHHHHHHHhcCcceEEeccchhHHHHHHHHHH
Confidence                            3568999999999999999999999999999997643  4444444

>PRK11475 DNA-binding transcriptional activator BglJ; Provisional

Probab=99.23  E-value=6.9e-11  Score=124.67  Aligned_cols=103  Identities=12%  Similarity=0.163  Sum_probs=88.1

Q ss_pred             HHHHHHHHHh---cCCeEEEEcCHHHHHHHHHcCCCcEEE---EcCCCCCCCHHHHHHHHhccccCCCchhhhhhhhccc
Q 039716          872 VMVAKSMMKQ---LGHSIDVVNNGVEAVHAVQCQNYDLIL---MDVCMPVMDGLKATRLIRSFEDTGNWDAAAEAGIEQA  945 (1002)
Q Consensus       872 ~~~l~~~L~~---~g~~v~~a~~G~eAl~~~~~~~~DlIl---mDi~MP~mdG~e~~~~IR~~~~~~~~~~~~~~~~~~~  945 (1002)
                      +..+..+|..   .|+.|..+.++.++++.+....||++|   +|+.||++||++++++|+..                 
T Consensus         3 r~gi~~lL~~~~~~~~~v~~~~~~~~~l~~~~~~~pd~vl~dl~d~~mp~~~Gl~~~~~l~~~-----------------   65 (207)
T PRK11475          3 SIGIESLFRKFPGNPYKLHTFSSQSSFQDAMSRISFSAVIFSLSAMRSERREGLSCLTELAIK-----------------   65 (207)
T ss_pred             hHHHHHHHhcCCCCeeEEEEeCCHHHHHHHhccCCCCEEEeeccccCCCCCCHHHHHHHHHHH-----------------
Confidence            4567788865   466678899999999999988999998   78899999999999999862                 


Q ss_pred             CCCCCCCCCCCCccEEEEcCCCCHHHHHHHH-HcCCCEEEeCCCChHHHHHHHHhh
Q 039716          946 MPSSGSSNHFKRIPIIAMTANALSESAEECF-ANGMDSFVSKPVTFQKLKECLEQY 1000 (1002)
Q Consensus       946 ~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~-~aG~d~~l~KP~~~~~L~~~l~~~ 1000 (1002)
                               .+.+|||++|++..+.....++ ++|+++||.||++.++|..+|+..
T Consensus        66 ---------~p~~~iIvlt~~~~~~~~~~~~~~~Ga~gyl~K~~~~~eL~~aI~~v  112 (207)
T PRK11475         66 ---------FPRMRRLVIADDDIEARLIGSLSPSPLDGVLSKASTLEILQQELFLS  112 (207)
T ss_pred             ---------CCCCCEEEEeCCCCHHHHHHHHHHcCCeEEEecCCCHHHHHHHHHHH
Confidence                     4678999999988776666655 799999999999999999999864

>PRK10610 chemotaxis regulatory protein CheY; Provisional

Probab=99.23  E-value=3.9e-10  Score=106.51  Aligned_cols=118  Identities=28%  Similarity=0.491  Sum_probs=105.9

Q ss_pred             CCeEEEEecCHHHHHHHHHHHHhcCCe-EEEEcCHHHHHHHHHcCCCcEEEEcCCCCCCCHHHHHHHHhccccCCCchhh
Q 039716          859 KPKILLVEDNKINVMVAKSMMKQLGHS-IDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDAA  937 (1002)
Q Consensus       859 ~~~ILiVeDn~~n~~~l~~~L~~~g~~-v~~a~~G~eAl~~~~~~~~DlIlmDi~MP~mdG~e~~~~IR~~~~~~~~~~~  937 (1002)
                      ..+||++++++.....+...|...|+. +..+.++.+++..+....||++++|..+|.++|+++++.++...        
T Consensus         5 ~~~il~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~di~l~d~~~~~~~~~~~~~~l~~~~--------   76 (129)
T PRK10610          5 ELKFLVVDDFSTMRRIVRNLLKELGFNNVEEAEDGVDALNKLQAGGFGFVISDWNMPNMDGLELLKTIRADG--------   76 (129)
T ss_pred             cceEEEEcCCHHHHHHHHHHHHHcCCCeEEEeCCHHHHHHHhhccCCCEEEEcCCCCCCCHHHHHHHHHhCC--------
Confidence            468999999999999999999998984 77899999999999888999999999999999999999998632        


Q ss_pred             hhhhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHHhh
Q 039716          938 AEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQY 1000 (1002)
Q Consensus       938 ~~~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~~ 1000 (1002)
                                      ..+.+|+++++..........++..|+++|+.||++..+|...++++
T Consensus        77 ----------------~~~~~~~i~~~~~~~~~~~~~~~~~g~~~~i~~p~~~~~l~~~l~~~  123 (129)
T PRK10610         77 ----------------AMSALPVLMVTAEAKKENIIAAAQAGASGYVVKPFTAATLEEKLNKI  123 (129)
T ss_pred             ----------------CcCCCcEEEEECCCCHHHHHHHHHhCCCeEEECCCCHHHHHHHHHHH
Confidence                            22457999999988888899999999999999999999999888765

>PRK13435 response regulator; Provisional

Probab=99.22  E-value=1.6e-10  Score=114.64  Aligned_cols=112  Identities=19%  Similarity=0.280  Sum_probs=98.5

Q ss_pred             CCeEEEEecCHHHHHHHHHHHHhcCCeEE-EEcCHHHHHHHHHcCCCcEEEEcCCCC-CCCHHHHHHHHhccccCCCchh
Q 039716          859 KPKILLVEDNKINVMVAKSMMKQLGHSID-VVNNGVEAVHAVQCQNYDLILMDVCMP-VMDGLKATRLIRSFEDTGNWDA  936 (1002)
Q Consensus       859 ~~~ILiVeDn~~n~~~l~~~L~~~g~~v~-~a~~G~eAl~~~~~~~~DlIlmDi~MP-~mdG~e~~~~IR~~~~~~~~~~  936 (1002)
                      ..+|||++|++.....+...|+..|+.+. .+.++.++++.+....||+|++|+.|| +++|+++.+.++..        
T Consensus         5 ~~~iliid~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~dliivd~~~~~~~~~~~~~~~l~~~--------   76 (145)
T PRK13435          5 QLKVLIVEDEALIALELEKLVEEAGHEVVGIAMSSEQAIALGRRRQPDVALVDVHLADGPTGVEVARRLSAD--------   76 (145)
T ss_pred             cceEEEEcCcHHHHHHHHHHHHhcCCeEEEeeCCHHHHHHHhhhcCCCEEEEeeecCCCCcHHHHHHHHHhC--------
Confidence            56899999999999999999999999876 789999999999888999999999998 59999999999741        


Q ss_pred             hhhhhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHHhh
Q 039716          937 AAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQY 1000 (1002)
Q Consensus       937 ~~~~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~~ 1000 (1002)
                                         +.+|||++|+...   ...++.+|+++|+.||++..+|...|+++
T Consensus        77 -------------------~~~pii~ls~~~~---~~~~~~~ga~~~l~kp~~~~~l~~~i~~~  118 (145)
T PRK13435         77 -------------------GGVEVVFMTGNPE---RVPHDFAGALGVIAKPYSPRGVARALSYL  118 (145)
T ss_pred             -------------------CCCCEEEEeCCHH---HHHHHhcCcceeEeCCCCHHHHHHHHHHH
Confidence                               3589999997643   35678899999999999999999999765

>TIGR01925 spIIAB anti-sigma F factor

Probab=99.21  E-value=1e-10  Score=115.25  Aligned_cols=63  Identities=19%  Similarity=0.287  Sum_probs=52.2

Q ss_pred             EEEEEEEecCCCCCcCcHhhhhhhccCCCccccCcCCCccccHHHHHHHHHHhCCEEEEEeecCCceEEEEEE
Q 039716          591 WIRCDVYDTGIGIPENALPTLFRKYMQVSADHARKYGGTGLGLAICKQLVELMGGRLTVTSKVHCGSTFTFIL  663 (1002)
Q Consensus       591 ~l~i~V~DtGiGI~~e~l~~IF~pF~q~~~~~~~~~~GtGLGLaI~k~Lve~~gG~I~v~S~~g~GTtF~~~L  663 (1002)
                      .+.|.|.|+|.||+  ...++|+||+....    ..+|+|+||+++++    +.|.+++++.+++||+|+++.
T Consensus        74 ~~~i~I~D~G~gi~--~~~~~~~~~~~~~~----~~~~~GlGL~lv~~----~~~~l~~~~~~~~Gt~v~i~~  136 (137)
T TIGR01925        74 EVYITVRDEGIGIE--NLEEAREPLYTSKP----ELERSGMGFTVMEN----FMDDVSVDSEKEKGTKIIMKK  136 (137)
T ss_pred             EEEEEEEEcCCCcC--chhHhhCCCcccCC----CCCCCcccHHHHHH----hCCcEEEEECCCCCeEEEEEe
Confidence            47899999999998  37789999986543    23589999999887    457999999999999999864

This model describes the SpoIIAB anti-sigma F factor. Sigma F regulates spore development in B subtilis. SpoIIAB binds to sigma F, preventing formation of the transcription complex at the promoter. SpoIIAA (anti-anti-sigma F factor) binds to SpoIIAB to inhibit association with sigma F, however SpoIIAB can phosphorylate SpoIIAA, causing disassociation of the SpoIIAA/B complex. The SpoIIE phosphatase dephosphorylates SpoIIAA.

>PRK15369 two component system sensor kinase SsrB; Provisional

Probab=99.19  E-value=3.2e-10  Score=118.01  Aligned_cols=116  Identities=25%  Similarity=0.373  Sum_probs=103.8

Q ss_pred             CCeEEEEecCHHHHHHHHHHHHhcC-Ce-EEEEcCHHHHHHHHHcCCCcEEEEcCCCCCCCHHHHHHHHhccccCCCchh
Q 039716          859 KPKILLVEDNKINVMVAKSMMKQLG-HS-IDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDA  936 (1002)
Q Consensus       859 ~~~ILiVeDn~~n~~~l~~~L~~~g-~~-v~~a~~G~eAl~~~~~~~~DlIlmDi~MP~mdG~e~~~~IR~~~~~~~~~~  936 (1002)
                      ..+||||||++..+..+...|...+ +. +..+.++.+++..+....||+|++|+.||.++|+++++.++..        
T Consensus         3 ~~~iliv~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~dlvl~d~~~~~~~~~~~~~~l~~~--------   74 (211)
T PRK15369          3 NYKILLVDDHELIINGIKNMLAPYPRYKIVGQVDNGLEVYNACRQLEPDIVILDLGLPGMNGLDVIPQLHQR--------   74 (211)
T ss_pred             ccEEEEECCcHHHHHHHHHHHccCCCcEEEEEECCHHHHHHHHHhcCCCEEEEeCCCCCCCHHHHHHHHHHH--------
Confidence            3589999999999999999998763 55 4578999999999999999999999999999999999999862        


Q ss_pred             hhhhhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHHhh
Q 039716          937 AAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQY 1000 (1002)
Q Consensus       937 ~~~~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~~ 1000 (1002)
                                        .+.+|||++|+.........++.+|+++|+.||++..+|...+...
T Consensus        75 ------------------~~~~~ii~ls~~~~~~~~~~~~~~g~~~~l~kp~~~~~l~~~i~~~  120 (211)
T PRK15369         75 ------------------WPAMNILVLTARQEEHMASRTLAAGALGYVLKKSPQQILLAAIQTV  120 (211)
T ss_pred             ------------------CCCCcEEEEeCCCCHHHHHHHHHhCCCEEEeCCCCHHHHHHHHHHH
Confidence                              2457999999999999999999999999999999999999988764

>PRK10403 transcriptional regulator NarP; Provisional

Probab=99.19  E-value=3.5e-10  Score=118.55  Aligned_cols=115  Identities=21%  Similarity=0.274  Sum_probs=103.1

Q ss_pred             CeEEEEecCHHHHHHHHHHHHh-cCCeEE-EEcCHHHHHHHHHcCCCcEEEEcCCCCCCCHHHHHHHHhccccCCCchhh
Q 039716          860 PKILLVEDNKINVMVAKSMMKQ-LGHSID-VVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDAA  937 (1002)
Q Consensus       860 ~~ILiVeDn~~n~~~l~~~L~~-~g~~v~-~a~~G~eAl~~~~~~~~DlIlmDi~MP~mdG~e~~~~IR~~~~~~~~~~~  937 (1002)
                      .+||+|||++.....+...|.. .++.+. .+.++.+++..+....||+|++|+.||.++|+++++.++..         
T Consensus         7 ~~ilii~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~dlvi~d~~~~~~~~~~~~~~l~~~---------   77 (215)
T PRK10403          7 FQVLIVDDHPLMRRGVRQLLELDPGFEVVAEAGDGASAIDLANRLDPDVILLDLNMKGMSGLDTLNALRRD---------   77 (215)
T ss_pred             EEEEEEcCCHHHHHHHHHHHhcCCCCEEEEEeCCHHHHHHHHHhcCCCEEEEecCCCCCcHHHHHHHHHHh---------
Confidence            5799999999999999999975 467764 68999999999988999999999999999999999999863         


Q ss_pred             hhhhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHHhh
Q 039716          938 AEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQY 1000 (1002)
Q Consensus       938 ~~~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~~ 1000 (1002)
                                       .+.+|++++|..........++.+|+++|+.||++..+|...++..
T Consensus        78 -----------------~~~~~ii~l~~~~~~~~~~~~~~~g~~~~i~kp~~~~~l~~~i~~~  123 (215)
T PRK10403         78 -----------------GVTAQIIILTVSDASSDVFALIDAGADGYLLKDSDPEVLLEAIRAG  123 (215)
T ss_pred             -----------------CCCCeEEEEeCCCChHHHHHHHHcCCCeEEecCCCHHHHHHHHHHH
Confidence                             2457899999999888999999999999999999999999888763

>PRK10651 transcriptional regulator NarL; Provisional

Probab=99.18  E-value=4.2e-10  Score=118.21  Aligned_cols=117  Identities=22%  Similarity=0.340  Sum_probs=104.1

Q ss_pred             CCeEEEEecCHHHHHHHHHHHHhc-CCe-EEEEcCHHHHHHHHHcCCCcEEEEcCCCCCCCHHHHHHHHhccccCCCchh
Q 039716          859 KPKILLVEDNKINVMVAKSMMKQL-GHS-IDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDA  936 (1002)
Q Consensus       859 ~~~ILiVeDn~~n~~~l~~~L~~~-g~~-v~~a~~G~eAl~~~~~~~~DlIlmDi~MP~mdG~e~~~~IR~~~~~~~~~~  936 (1002)
                      ..+||||||++..+..+...|... ++. +..+.++.+++..+....||+||+|+.||.++|+++++.++..        
T Consensus         6 ~~~iliv~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~dlvl~d~~l~~~~~~~~~~~l~~~--------   77 (216)
T PRK10651          6 PATILLIDDHPMLRTGVKQLISMAPDITVVGEASNGEQGIELAESLDPDLILLDLNMPGMNGLETLDKLREK--------   77 (216)
T ss_pred             ceEEEEECCCHHHHHHHHHHHccCCCcEEEEEeCCHHHHHHHHHhCCCCEEEEeCCCCCCcHHHHHHHHHHh--------
Confidence            458999999999999999999865 455 4568999999999999999999999999999999999999863        


Q ss_pred             hhhhhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHHhhc
Q 039716          937 AAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQYF 1001 (1002)
Q Consensus       937 ~~~~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~~l 1001 (1002)
                                        .+.+|+|++++.........++.+|+++|+.||++..+|...+.+.+
T Consensus        78 ------------------~~~~~vi~l~~~~~~~~~~~~~~~g~~~~i~k~~~~~~l~~~i~~~~  124 (216)
T PRK10651         78 ------------------SLSGRIVVFSVSNHEEDVVTALKRGADGYLLKDMEPEDLLKALQQAA  124 (216)
T ss_pred             ------------------CCCCcEEEEeCCCCHHHHHHHHHcCCCEEEeCCCCHHHHHHHHHHHH
Confidence                              24579999999999999999999999999999999999999887653

>PRK15411 rcsA colanic acid capsular biosynthesis activation protein A; Provisional

Probab=99.16  E-value=3.3e-10  Score=119.81  Aligned_cols=113  Identities=11%  Similarity=0.065  Sum_probs=95.4

Q ss_pred             eEEEEecCHHHHHHHHHHHHhcCC---eEEEEcCHHHHHHHHHcCCCcEEEEcCC--CCCCCHHHHHHHHhccccCCCch
Q 039716          861 KILLVEDNKINVMVAKSMMKQLGH---SIDVVNNGVEAVHAVQCQNYDLILMDVC--MPVMDGLKATRLIRSFEDTGNWD  935 (1002)
Q Consensus       861 ~ILiVeDn~~n~~~l~~~L~~~g~---~v~~a~~G~eAl~~~~~~~~DlIlmDi~--MP~mdG~e~~~~IR~~~~~~~~~  935 (1002)
                      .||||||++..+..++.+|...++   .+..+.++.+|+..+....||+||||+.  ||.++|.++++.|++.       
T Consensus         2 ~~lIvDD~~~~~~gl~~~L~~~~~~~~vv~~~~~~~~~~~~~~~~~pDlvLlDl~~~l~~~~g~~~i~~i~~~-------   74 (207)
T PRK15411          2 STIIMDLCSYTRLGLTGYLLSRGVKKREINDIETVDDLAIACDSLRPSVVFINEDCFIHDASNSQRIKQIINQ-------   74 (207)
T ss_pred             CEEEEcCCHHHHHHHHHHHHhCCCcceEEEecCCHHHHHHHHhccCCCEEEEeCcccCCCCChHHHHHHHHHH-------
Confidence            589999999999999999987653   3557899999999998889999999966  8989999999999862       


Q ss_pred             hhhhhhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCE-EEeCCCChHHHHHHHHhh
Q 039716          936 AAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDS-FVSKPVTFQKLKECLEQY 1000 (1002)
Q Consensus       936 ~~~~~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~-~l~KP~~~~~L~~~l~~~ 1000 (1002)
                                         .+.+|||++|+........ ++..|... |+.|+.+.++|..+|+..
T Consensus        75 -------------------~p~~~iivlt~~~~~~~~~-~~~~~~~~~~~~K~~~~~~L~~aI~~v  120 (207)
T PRK15411         75 -------------------HPNTLFIVFMAIANIHFDE-YLLVRKNLLISSKSIKPESLDDLLGDI  120 (207)
T ss_pred             -------------------CCCCeEEEEECCCchhHHH-HHHHHhhceeeeccCCHHHHHHHHHHH
Confidence                               3568999999987776543 55556555 889999999999999864

>PRK03660 anti-sigma F factor; Provisional

Probab=99.13  E-value=4.9e-10  Score=111.64  Aligned_cols=67  Identities=16%  Similarity=0.269  Sum_probs=55.1

Q ss_pred             EEEEEEEecCCCCCcCcHhhhhhhccCCCccccCcCCCccccHHHHHHHHHHhCCEEEEEeecCCceEEEEEEeCCC
Q 039716          591 WIRCDVYDTGIGIPENALPTLFRKYMQVSADHARKYGGTGLGLAICKQLVELMGGRLTVTSKVHCGSTFTFILPYQV  667 (1002)
Q Consensus       591 ~l~i~V~DtGiGI~~e~l~~IF~pF~q~~~~~~~~~~GtGLGLaI~k~Lve~~gG~I~v~S~~g~GTtF~~~LP~~~  667 (1002)
                      .+.|.|.|+|.||++  ..++|+||++...    ...++|+||+|+++    +.+.|++++.++.||+|+|++++..
T Consensus        74 ~l~i~I~D~G~g~~~--~~~~~~~~~~~~~----~~~~~GlGL~i~~~----~~~~i~~~~~~~~Gt~~~i~~~~~~  140 (146)
T PRK03660         74 ELEITVRDEGKGIED--IEEAMQPLYTTKP----ELERSGMGFTVMES----FMDEVEVESEPGKGTTVRMKKYLKK  140 (146)
T ss_pred             EEEEEEEEccCCCCh--HHHhhCCCcccCC----CCCCccccHHHHHH----hCCeEEEEecCCCcEEEEEEEEecc
Confidence            378999999999986  6789999986432    12478999999875    5678999999999999999998754

>PRK09191 two-component response regulator; Provisional

Probab=99.12  E-value=7.7e-10  Score=121.00  Aligned_cols=113  Identities=24%  Similarity=0.331  Sum_probs=98.5

Q ss_pred             CCeEEEEecCHHHHHHHHHHHHhcCCeEE-EEcCHHHHHHHHHcCCCcEEEEcCCCCC-CCHHHHHHHHhccccCCCchh
Q 039716          859 KPKILLVEDNKINVMVAKSMMKQLGHSID-VVNNGVEAVHAVQCQNYDLILMDVCMPV-MDGLKATRLIRSFEDTGNWDA  936 (1002)
Q Consensus       859 ~~~ILiVeDn~~n~~~l~~~L~~~g~~v~-~a~~G~eAl~~~~~~~~DlIlmDi~MP~-mdG~e~~~~IR~~~~~~~~~~  936 (1002)
                      ..+|||+||++..+..+..+|+..|+.+. .+.++.++++.+....||+||+|+.||+ ++|+++++.++..        
T Consensus       137 ~~~~liidd~~~~~~~l~~~L~~~~~~~~~~~~~~~~~l~~l~~~~~dlvi~d~~~~~~~~g~e~l~~l~~~--------  208 (261)
T PRK09191        137 ATRVLIIEDEPIIAMDLEQLVESLGHRVTGIARTRAEAVALAKKTRPGLILADIQLADGSSGIDAVNDILKT--------  208 (261)
T ss_pred             CCeEEEEcCcHHHHHHHHHHHhcCCCEEEEEECCHHHHHHHHhccCCCEEEEecCCCCCCCHHHHHHHHHHh--------
Confidence            45799999999999999999999999877 7899999999999899999999999995 8999999999852        


Q ss_pred             hhhhhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHHhh
Q 039716          937 AAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQY 1000 (1002)
Q Consensus       937 ~~~~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~~ 1000 (1002)
                                        . ++|||++|+......  .+...|+++|+.||++..+|...|++.
T Consensus       209 ------------------~-~~pii~ls~~~~~~~--~~~~~~~~~~l~kP~~~~~l~~~i~~~  251 (261)
T PRK09191        209 ------------------F-DVPVIFITAFPERLL--TGERPEPAFLITKPFQPDTVKAAISQA  251 (261)
T ss_pred             ------------------C-CCCEEEEeCCCcHHH--HHHhcccCceEECCCCHHHHHHHHHHH
Confidence                              2 589999999765543  344567899999999999999999875

>COG0643 CheA Chemotaxis protein histidine kinase and related kinases [Cell motility and secretion / Signal transduction mechanisms]

Probab=99.09  E-value=1e-09  Score=133.75  Aligned_cols=77  Identities=30%  Similarity=0.523  Sum_probs=64.4

Q ss_pred             EEEEEEEecCCCCCcCc------------------------HhhhhhhccCCCccccCcCCCccccHHHHHHHHHHhCCE
Q 039716          591 WIRCDVYDTGIGIPENA------------------------LPTLFRKYMQVSADHARKYGGTGLGLAICKQLVELMGGR  646 (1002)
Q Consensus       591 ~l~i~V~DtGiGI~~e~------------------------l~~IF~pF~q~~~~~~~~~~GtGLGLaI~k~Lve~~gG~  646 (1002)
                      .+.|+|.|.|.||+.+.                        ..-||.|=|.+... -..-+|-|.||=+||+-|+.+||+
T Consensus       476 ~ivIev~DDG~Gid~ekI~~KAiErGli~~~~a~~lSd~Ei~~LIF~PGFSTa~~-VtdvSGRGVGMDVVk~~I~~LgG~  554 (716)
T COG0643         476 NIVIEVSDDGAGIDREKIREKAIERGLITEEEAETLSDEEILNLIFAPGFSTAEQ-VTDVSGRGVGMDVVKTNIEQLGGS  554 (716)
T ss_pred             eEEEEEeeCCCCCCHHHHHHHHHHcCCCChHHhccCCHHHHHHHHhcCCCCcchh-hhcccCCccCHHHHHHHHHHcCCE
Confidence            48899999999999654                        34578886655432 235679999999999999999999


Q ss_pred             EEEEeecCCceEEEEEEeCCCC
Q 039716          647 LTVTSKVHCGSTFTFILPYQVS  668 (1002)
Q Consensus       647 I~v~S~~g~GTtF~~~LP~~~~  668 (1002)
                      |.|+|++|+||+|++.||+..+
T Consensus       555 I~V~S~~G~GT~Fti~LPLTLa  576 (716)
T COG0643         555 ISVSSEPGKGTTFTIRLPLTLA  576 (716)
T ss_pred             EEEEecCCCCeEEEEecCcHHH
Confidence            9999999999999999998753

>PRK10693 response regulator of RpoS; Provisional

Probab=99.07  E-value=6.5e-10  Score=124.67  Aligned_cols=87  Identities=24%  Similarity=0.433  Sum_probs=79.1

Q ss_pred             EEcCHHHHHHHHHcCCCcEEEEcCCCCCCCHHHHHHHHhccccCCCchhhhhhhhcccCCCCCCCCCCCCccEEEEcCCC
Q 039716          888 VVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANA  967 (1002)
Q Consensus       888 ~a~~G~eAl~~~~~~~~DlIlmDi~MP~mdG~e~~~~IR~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipIIalTa~~  967 (1002)
                      .+.+|.+|++.+....||+||+|+.||+|+|+++++.||+.                          .+.+|||++|+..
T Consensus         2 ~a~~g~~al~~l~~~~pDlVL~D~~mp~~~Gle~~~~ir~~--------------------------~~~ipiI~lt~~~   55 (303)
T PRK10693          2 LAANGVDALELLGGFTPDLIICDLAMPRMNGIEFVEHLRNR--------------------------GDQTPVLVISATE   55 (303)
T ss_pred             EeCCHHHHHHHHhcCCCCEEEEeCCCCCCCHHHHHHHHHhc--------------------------CCCCcEEEEECCC
Confidence            57899999999999999999999999999999999999963                          2458999999999


Q ss_pred             CHHHHHHHHHcCCCEEEeCCC-ChHHHHHHHHhh
Q 039716          968 LSESAEECFANGMDSFVSKPV-TFQKLKECLEQY 1000 (1002)
Q Consensus       968 ~~~~~~~~~~aG~d~~l~KP~-~~~~L~~~l~~~ 1000 (1002)
                      ..+...+++++|++||+.||+ +.++|...+...
T Consensus        56 ~~~~~~~al~~Ga~dyl~KP~~~~~~L~~~i~~~   89 (303)
T PRK10693         56 NMADIAKALRLGVQDVLLKPVKDLNRLREMVFAC   89 (303)
T ss_pred             CHHHHHHHHHCCCcEEEECCCCcHHHHHHHHHHH
Confidence            999999999999999999999 589888887654

>cd00156 REC Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; contains a phosphoacceptor site that is phosphorylated by histidine kinase homologs; usually found N-terminal to a DNA binding effector domain; forms homodimers

Probab=99.04  E-value=3.2e-09  Score=95.93  Aligned_cols=112  Identities=31%  Similarity=0.479  Sum_probs=101.9

Q ss_pred             EEEecCHHHHHHHHHHHHhcCCeEEEEcCHHHHHHHHHcCCCcEEEEcCCCCCCCHHHHHHHHhccccCCCchhhhhhhh
Q 039716          863 LLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDAAAEAGI  942 (1002)
Q Consensus       863 LiVeDn~~n~~~l~~~L~~~g~~v~~a~~G~eAl~~~~~~~~DlIlmDi~MP~mdG~e~~~~IR~~~~~~~~~~~~~~~~  942 (1002)
                      |++++++..+..+...|...|+.+..+.++.+++..+....||++++|..++..+|++..+.++..              
T Consensus         1 l~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~ii~~~~~~~~~~~~~~~~l~~~--------------   66 (113)
T cd00156           1 LIVDDDPLIRELLRRLLEKEGYEVVEAEDGEEALALLAEEKPDLILLDIMMPGMDGLELLRRIRKR--------------   66 (113)
T ss_pred             CeecCcHHHHHHHHHHHhhcCceEEEecCHHHHHHHHHhCCCCEEEEecCCCCCchHHHHHHHHHh--------------
Confidence            578999999999999999999999999999999999998999999999999999999999999863              


Q ss_pred             cccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHHhh
Q 039716          943 EQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQY 1000 (1002)
Q Consensus       943 ~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~~ 1000 (1002)
                                  .+.+|+++++..........++..|+++|+.||++...|...+.+.
T Consensus        67 ------------~~~~~~i~~~~~~~~~~~~~~~~~~~~~~i~~p~~~~~l~~~l~~~  112 (113)
T cd00156          67 ------------GPDIPIIFLTAHGDDEDAVEALKAGADDYLTKPFSPEELLARIRAL  112 (113)
T ss_pred             ------------CCCCCEEEEEecccHHHHHHHHHcChhhHccCCCCHHHHHHHHHhh
Confidence                        2457999999888788888999999999999999999999998765

>COG3920 Signal transduction histidine kinase [Signal transduction mechanisms]

Probab=98.90  E-value=2.2e-07  Score=98.95  Aligned_cols=190  Identities=22%  Similarity=0.296  Sum_probs=123.9

Q ss_pred             HHHHHhhhccccHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCeeeEeeecCHHHHHHH
Q 039716          372 QMLATMSHEIRSPLTGVVSMAEILSNTKLDREQRQLLGVMISSGDLVLQLINDILDLSKVESGVMKLEAAKFRPREVVKH  451 (1002)
Q Consensus       372 ~fla~iSHELRTPL~~I~g~~elL~~~~l~~~~~~~l~~i~~s~~~L~~LIndlLd~skiesg~~~l~~~~~~l~~li~~  451 (1002)
                      .++.-+.|-++|=|..|.+++.+-.....++ ..+.+.........| .++.++|--+         ....++...+++.
T Consensus        21 ~ll~Ei~HRVKNnLqiIsSll~lq~r~~~~~-~~~~~~~~~~Ri~sl-a~~He~L~~s---------~~~~~~~~~~~~~   89 (221)
T COG3920          21 LLLREIHHRVKNNLQIISSLLRLQARKFEDE-VLEALRESQNRIQSL-ALIHELLYKS---------GDDTWDFASYLEL   89 (221)
T ss_pred             HHHHHhhhhhhhHHHHHHHHHHHHHhhcCCH-HHHHHHHHHHHHHHH-HHHHHHHhcC---------CcceEcHHHHHHH
Confidence            3666799999999999999998766544443 333333333332222 2445555332         1234566777777


Q ss_pred             HHHHHHHH-HhhcceeccccCCCCCeeEEcc-HHHHHHHHHHHHhhhhhcC----CCCeeEEEEEecCCCCcccchhhhh
Q 039716          452 VLQTAAAS-LQKILMLEGDIADDVPIEVIGD-VLRIRQILTNLISNAIKFT----PEGKVGIKLYVVPEPPFAKEGLKQK  525 (1002)
Q Consensus       452 v~~~~~~~-~~k~i~l~~~i~~~~p~~v~gD-~~rL~QIL~NLlsNAIKfT----~~G~I~I~v~~~~~~~~~~~~~~~~  525 (1002)
                      +...+... ..+.+.+.....+.  ..+-.| ..-|--|+.-|++||+||.    +.|.|.|.+.....           
T Consensus        90 L~~~l~~~~~~~~~~~~~~~~~~--~~l~~d~A~~Lgliv~EL~tNa~Khaf~~~~~G~I~I~~~~~~~-----------  156 (221)
T COG3920          90 LASNLFPSYGGKDIRLILDSGPN--VFLDPDTAVPLGLIVHELVTNALKHAFLSRPGGEIRITLSREGD-----------  156 (221)
T ss_pred             HHHHHHHhcCCCCceEEEecCCc--eEECchhhHHHHHHHHHHHHHHHHhcCCCCCCCEEEEEEEEcCC-----------
Confidence            66666554 22334444333332  223223 2357889999999999995    36788777754211           


Q ss_pred             hhhhhcchhhhhhhccCCCCCccCCCCCCCCCCCCCCccCCCCCCCCCCCccCCCCCccccccceEEEEEEEecCCCCCc
Q 039716          526 SKAYQSATDAVKEEKHQPKSQTASDQNGFHDKKHGEGYQDHKHDDDPGTPVSHGNSMDEDLEATVWIRCDVYDTGIGIPE  605 (1002)
Q Consensus       526 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~i~V~DtGiGI~~  605 (1002)
                                                                                    .. +..+.|+|+|.|+|.
T Consensus       157 --------------------------------------------------------------~~-~~~l~v~deg~G~~~  173 (221)
T COG3920         157 --------------------------------------------------------------GG-RFLLTVWDEGGGPPV  173 (221)
T ss_pred             --------------------------------------------------------------CC-eEEEEEEECCCCCCC
Confidence                                                                          00 356789999999996


Q ss_pred             CcHhhhhhhccCCCccccCcCCCccccHHHHHHHH-HHhCCEEEEEeecCCceEEEEEEeCCC
Q 039716          606 NALPTLFRKYMQVSADHARKYGGTGLGLAICKQLV-ELMGGRLTVTSKVHCGSTFTFILPYQV  667 (1002)
Q Consensus       606 e~l~~IF~pF~q~~~~~~~~~~GtGLGLaI~k~Lv-e~~gG~I~v~S~~g~GTtF~~~LP~~~  667 (1002)
                      +.      ++           ...|+|+.+++.+| ++.||.+...+..  ||+|++.+|...
T Consensus       174 ~~------~~-----------~~~g~G~~Lv~~lv~~q~~g~~~~~~~~--Gt~~~i~~~~~~  217 (221)
T COG3920         174 EA------PL-----------SRGGFGLQLVERLVPEQLGGELEDERPD--GTEFRLRFPLSE  217 (221)
T ss_pred             CC------CC-----------CCCCcHHHHHHHHHHHHcCCeEEEEcCC--CEEEEEEEeccc
Confidence            53      11           25699999999999 8999999888765  999999999753

>COG3850 NarQ Signal transduction histidine kinase, nitrate/nitrite-specific [Signal transduction mechanisms]

Probab=98.90  E-value=2.9e-06  Score=97.25  Aligned_cols=187  Identities=18%  Similarity=0.318  Sum_probs=130.5

Q ss_pred             HHhhhccccHHHHHHHHHHH----HhCC---CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCeeeEeeecCHHH
Q 039716          375 ATMSHEIRSPLTGVVSMAEI----LSNT---KLDREQRQLLGVMISSGDLVLQLINDILDLSKVESGVMKLEAAKFRPRE  447 (1002)
Q Consensus       375 a~iSHELRTPL~~I~g~~el----L~~~---~l~~~~~~~l~~i~~s~~~L~~LIndlLd~skiesg~~~l~~~~~~l~~  447 (1002)
                      +.||-||---|.-.++|..+    |+..   ...++.++.+..+.....---.-+.+||.--|+       ....-++..
T Consensus       374 atIAReLHDSiAQsLS~LkiQvt~L~~~~~~~~~e~s~~~i~~~r~~Ln~~Y~QLRELLtTFRl-------tL~e~~L~~  446 (574)
T COG3850         374 ATIARELHDSIAQSLSFLKIQVTLLKTAIPEELPEKAREIIAQIRQGLNDAYRQLRELLTTFRL-------TLQEAELPP  446 (574)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHhhCCccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-------hcccCchHH
Confidence            46777777777777776653    4432   233456777888887777777777777765443       223345566


Q ss_pred             HHHHHHHHHHHHHhhcceeccccCCCCCeeEEc-cHHHHHHHHHHHHhhhhhcCCCCeeEEEEEecCCCCcccchhhhhh
Q 039716          448 VVKHVLQTAAASLQKILMLEGDIADDVPIEVIG-DVLRIRQILTNLISNAIKFTPEGKVGIKLYVVPEPPFAKEGLKQKS  526 (1002)
Q Consensus       448 li~~v~~~~~~~~~k~i~l~~~i~~~~p~~v~g-D~~rL~QIL~NLlsNAIKfT~~G~I~I~v~~~~~~~~~~~~~~~~~  526 (1002)
                      -++.++..+.....-.+.+.+..++..   +.. -...+-||+.-=++||+|++..-.|.|++....             
T Consensus       447 AL~~~~~~f~~qtg~~~~l~~qlp~~~---lpa~qqvHlLqIvREAlsNa~KHa~As~i~V~~~~~~-------------  510 (574)
T COG3850         447 ALEQMLAEFSNQTGITVTLDYQLPPRA---LPAHQQVHLLQIVREALSNAIKHAQASEIKVTVSQND-------------  510 (574)
T ss_pred             HHHHHHHHHHhccCCeEEEeccCCCCC---CCHHHHHHHHHHHHHHHHHHHHhcccCeEEEEEEecC-------------
Confidence            677777776655444444444443322   111 123577999999999999998888877764210             


Q ss_pred             hhhhcchhhhhhhccCCCCCccCCCCCCCCCCCCCCccCCCCCCCCCCCccCCCCCccccccceEEEEEEEecCCCCCcC
Q 039716          527 KAYQSATDAVKEEKHQPKSQTASDQNGFHDKKHGEGYQDHKHDDDPGTPVSHGNSMDEDLEATVWIRCDVYDTGIGIPEN  606 (1002)
Q Consensus       527 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~i~V~DtGiGI~~e  606 (1002)
                                                                                     ..+.+.|.|+|+|||+.
T Consensus       511 ---------------------------------------------------------------g~~~~~VeDnG~Gi~~~  527 (574)
T COG3850         511 ---------------------------------------------------------------GQVTLTVEDNGVGIDEA  527 (574)
T ss_pred             ---------------------------------------------------------------CeEEEEEeeCCcCCCCc
Confidence                                                                           13788999999999975


Q ss_pred             cHhhhhhhccCCCccccCcCCCccccHHHHHHHHHHhCCEEEEEeecCCceEEEEEEeC
Q 039716          607 ALPTLFRKYMQVSADHARKYGGTGLGLAICKQLVELMGGRLTVTSKVHCGSTFTFILPY  665 (1002)
Q Consensus       607 ~l~~IF~pF~q~~~~~~~~~~GtGLGLaI~k~Lve~~gG~I~v~S~~g~GTtF~~~LP~  665 (1002)
                      .                 ..+| --||.|.+.=++.+||.+.|++.+|+||.+.++||-
T Consensus       528 ~-----------------e~~g-HyGL~IM~ERA~~L~~~L~i~~~~~gGT~V~ltf~~  568 (574)
T COG3850         528 A-----------------EPSG-HYGLNIMRERAQRLGGQLRIRRREGGGTEVSLTFPP  568 (574)
T ss_pred             c-----------------CCCC-CcchHHHHHHHHHhcCeEEEeecCCCCeEEEEEecc
Confidence            2                 1224 679999999999999999999999999999999983

>COG3851 UhpB Signal transduction histidine kinase, glucose-6-phosphate specific [Signal transduction mechanisms]

Probab=98.88  E-value=5.8e-07  Score=97.55  Aligned_cols=218  Identities=19%  Similarity=0.306  Sum_probs=146.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhccccHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHHHH
Q 039716          340 MAKLREEIAVQKAKETELNKTIHITEETMRAKQMLATMSHEIRSPLTGVVSMAEILSNTKLDREQRQLLGVMISSGDLVL  419 (1002)
Q Consensus       340 ~~~l~~el~~~~~~~~el~k~~~~~e~~~~~k~fla~iSHELRTPL~~I~g~~elL~~~~l~~~~~~~l~~i~~s~~~L~  419 (1002)
                      +.++++.++.+-++...+.+.+--+||..| |+.+.-+-.||-.-+|+|.--+.++++...++..++.-+.|..=+.++.
T Consensus       274 lrelnqrL~~EL~~~raLaeqListEEsiR-k~vARELHDeIGQnITAIr~Qa~ivkR~~~~~q~kqaas~Ie~LslrI~  352 (497)
T COG3851         274 LRELNQRLQKELARNRALAEQLISTEESIR-KDVARELHDEIGQNITAIRTQAGIVKRAADNAQVKQAASLIEQLSLRIY  352 (497)
T ss_pred             HHHHHHHHHHHHHHhHHHHHHHHhhHHHHH-HHHHHHHHHHhcchHHHHHHHHHHHHhccCCHhHHhHHHHHHHHHHHHH
Confidence            334444444444444445444444555555 4677777889999999999999999886666666666666666677777


Q ss_pred             HHHHHHHHHHhhhcCCeeeEeeecCHHHHHHHHHHHHHHHHhhcceeccccCCCCCeeEEccH---HHHHHHHHHHHhhh
Q 039716          420 QLINDILDLSKVESGVMKLEAAKFRPREVVKHVLQTAAASLQKILMLEGDIADDVPIEVIGDV---LRIRQILTNLISNA  496 (1002)
Q Consensus       420 ~LIndlLd~skiesg~~~l~~~~~~l~~li~~v~~~~~~~~~k~i~l~~~i~~~~p~~v~gD~---~rL~QIL~NLlsNA  496 (1002)
                      .-+..+|.--|.      -...+.-+.+.+.++++.+.-. +.++....+...+..   .-|+   .-+.+++.-++.|-
T Consensus       353 ~svrqLL~rLRP------~~LDdL~l~qai~~l~~Em~~~-ergihcq~~~~~n~~---~ldet~rvTLyRl~QE~LNNI  422 (497)
T COG3851         353 DSVRQLLGRLRP------RQLDDLTLEQAIRSLLREMELE-ERGIHCQLDWRINET---ALDETQRVTLYRLCQELLNNI  422 (497)
T ss_pred             HHHHHHHHhcCC------cccccccHHHHHHHHHHHhhhh-hcCeEEEeccccCcc---cCCcceeEeHHHHHHHHHHHH
Confidence            767766642221      1123455677777777776543 234433333221110   1121   23678888999999


Q ss_pred             hhcCCCCeeEEEEEecCCCCcccchhhhhhhhhhcchhhhhhhccCCCCCccCCCCCCCCCCCCCCccCCCCCCCCCCCc
Q 039716          497 IKFTPEGKVGIKLYVVPEPPFAKEGLKQKSKAYQSATDAVKEEKHQPKSQTASDQNGFHDKKHGEGYQDHKHDDDPGTPV  576 (1002)
Q Consensus       497 IKfT~~G~I~I~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  576 (1002)
                      +|+.+...|+|.+...                                                                
T Consensus       423 ~KHA~AS~V~i~l~~~----------------------------------------------------------------  438 (497)
T COG3851         423 CKHADASAVTIQLWQQ----------------------------------------------------------------  438 (497)
T ss_pred             HhccccceEEEEEeeC----------------------------------------------------------------
Confidence            9999888888877431                                                                


Q ss_pred             cCCCCCccccccceEEEEEEEecCCCCCcCcHhhhhhhccCCCccccCcCCCccccHHHHHHHHHHhCCEEEEEeecCCc
Q 039716          577 SHGNSMDEDLEATVWIRCDVYDTGIGIPENALPTLFRKYMQVSADHARKYGGTGLGLAICKQLVELMGGRLTVTSKVHCG  656 (1002)
Q Consensus       577 ~~~~~~~~~~~~~~~l~i~V~DtGiGI~~e~l~~IF~pF~q~~~~~~~~~~GtGLGLaI~k~Lve~~gG~I~v~S~~g~G  656 (1002)
                                  ...+.++|+|+|+|+|+..                   +-+|.||.=.+.=|...||+++++|  -.|
T Consensus       439 ------------~e~l~Lei~DdG~Gl~~~~-------------------~v~G~Gl~GmrERVsaLGG~ltlss--q~G  485 (497)
T COG3851         439 ------------DERLMLEIEDDGSGLPPGS-------------------GVQGFGLTGMRERVSALGGTLTLSS--QHG  485 (497)
T ss_pred             ------------CcEEEEEEecCCcCCCCCC-------------------CccCcCcchHHHHHHHhCCceEEEe--ccC
Confidence                        1137789999999999642                   2478999999999999999999999  468


Q ss_pred             eEEEEEEeC
Q 039716          657 STFTFILPY  665 (1002)
Q Consensus       657 TtF~~~LP~  665 (1002)
                      |.+.+.||-
T Consensus       486 TrviVnLPq  494 (497)
T COG3851         486 TRVIVNLPQ  494 (497)
T ss_pred             cEEEEecch
Confidence            999999993

>PF08448 PAS_4: PAS fold; InterPro: IPR013656 The PAS fold corresponds to the structural domain that has previously been defined as PAS and PAC motifs []

Probab=98.87  E-value=6.1e-09  Score=97.03  Aligned_cols=107  Identities=21%  Similarity=0.284  Sum_probs=90.5

Q ss_pred             HhccCcEEEEecccccEEEeeccC---CCCCcccccCCCchhccCccchhhhhHHHHHHHHhCCCcceeEEEEEeecCce
Q 039716          228 LQNAPVVMGHQDKELRYRFIYNHF---PSLHEEDILGKTDVEIFSGAGVKESQDFKREVLEKGLPAKREITFETELFGSK  304 (1002)
Q Consensus       228 l~~~p~~i~~~d~~~~~~~~~~~~---~~~~~e~iiGk~~~e~~~~~~~~~~~~~~~~vl~~g~~~~~e~~~~~~~~~~~  304 (1002)
                      ++++|.++++.|.+++|.++|..+   .+..+++++|++..+++++...+......++++.++.+...+..... .++..
T Consensus         1 l~~~p~~i~v~D~~~~i~~~N~~~~~~~~~~~~~~~G~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~   79 (110)
T PF08448_consen    1 LDSSPDGIFVIDPDGRIVYANQAAAELFGVSPEELIGRSLFDLLPPEDREEFQAALRRALAGGEPVFFEEILLR-DGEER   79 (110)
T ss_dssp             HHHCSSEEEEEETTSBEEEE-HHHHHHHTSTHHHHTTSBHHHHSCCGCHHHHHHHHHHHHHHTSEEEEEEEECT-TSCEE
T ss_pred             CCCCCceeEEECCCCEEEEEHHHHHHHhCCCHHHHhhccchhccccchhhhhHHHHHHhhccCceEEEEEEEee-cCCcE
Confidence            578999999999999999999864   57789999999999999988777888888999998877655544433 45677


Q ss_pred             EEEEEEeeeecCCCCEEEEEEEeechhHHHH
Q 039716          305 TFLIYVEPVFSKSGETIGVNYMGMDVTDQVR  335 (1002)
Q Consensus       305 ~~~~~~~p~~~~~G~~~gi~~~~~DITe~~~  335 (1002)
                      ++.+.+.|+++.+|.+.|+++++.|||++++
T Consensus        80 ~~~~~~~Pi~~~~g~~~g~~~~~~DiT~~rr  110 (110)
T PF08448_consen   80 WFEVSISPIFDEDGEVVGVLVIIRDITERRR  110 (110)
T ss_dssp             EEEEEEEEEECTTTCEEEEEEEEEEECCHHH
T ss_pred             EEEEEEEEeEcCCCCEEEEEEEEEECchhhC
Confidence            8889999999999999999999999998764

The PAS fold appears in archaea, eubacteria and eukarya. ; PDB: 3K3D_A 3K3C_B 3KX0_X 3FC7_B 3LUQ_D 3MXQ_A 3BWL_C 3FG8_A.

>COG3275 LytS Putative regulator of cell autolysis [Signal transduction mechanisms]

Probab=98.83  E-value=7.2e-07  Score=100.47  Aligned_cols=59  Identities=34%  Similarity=0.510  Sum_probs=52.5

Q ss_pred             EEEEEEecCCCCCcCcHhhhhhhccCCCccccCcCCCccccHHHHHHHHHHhCC---EEEEEeecCCceEEEEEEeCCCC
Q 039716          592 IRCDVYDTGIGIPENALPTLFRKYMQVSADHARKYGGTGLGLAICKQLVELMGG---RLTVTSKVHCGSTFTFILPYQVS  668 (1002)
Q Consensus       592 l~i~V~DtGiGI~~e~l~~IF~pF~q~~~~~~~~~~GtGLGLaI~k~Lve~~gG---~I~v~S~~g~GTtF~~~LP~~~~  668 (1002)
                      +++.|+|||-||+|+                  ...|+|+||+.+++=++.+=|   -+.+.|.+..||+++|.||.+..
T Consensus       493 l~i~VeDng~li~p~------------------~~~g~giGL~nv~~RLk~lyG~~~gl~i~~~~q~gTri~f~lp~~~~  554 (557)
T COG3275         493 LRIEVEDNGGLIQPD------------------EEDGTGIGLANVHKRLKLLYGDDEGLHIESLEQAGTRIIFRLPLQRT  554 (557)
T ss_pred             EEEEEecCCCCcCCC------------------CCCCCChHHHHHHHHHHHhcCccccceEEeccCCCcEEEEEecCccc
Confidence            889999999999987                  124899999999999998888   79999999999999999998753

>COG4585 Signal transduction histidine kinase [Signal transduction mechanisms]

Probab=98.82  E-value=5.3e-07  Score=104.07  Aligned_cols=90  Identities=30%  Similarity=0.442  Sum_probs=76.7

Q ss_pred             cHHHHHHHHHHHHhhhhhcCCCCeeEEEEEecCCCCcccchhhhhhhhhhcchhhhhhhccCCCCCccCCCCCCCCCCCC
Q 039716          481 DVLRIRQILTNLISNAIKFTPEGKVGIKLYVVPEPPFAKEGLKQKSKAYQSATDAVKEEKHQPKSQTASDQNGFHDKKHG  560 (1002)
Q Consensus       481 D~~rL~QIL~NLlsNAIKfT~~G~I~I~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  560 (1002)
                      -..-+-+|+.-.++||+||+..-.+.|++....                                               
T Consensus       276 ~e~~l~rivQEaltN~~rHa~A~~v~V~l~~~~-----------------------------------------------  308 (365)
T COG4585         276 AEDALFRIVQEALTNAIRHAQATEVRVTLERTD-----------------------------------------------  308 (365)
T ss_pred             HHHHHHHHHHHHHHHHHhccCCceEEEEEEEcC-----------------------------------------------
Confidence            455788999999999999998888887775321                                               


Q ss_pred             CCccCCCCCCCCCCCccCCCCCccccccceEEEEEEEecCCCCCcCcHhhhhhhccCCCccccCcCCCccccHHHHHHHH
Q 039716          561 EGYQDHKHDDDPGTPVSHGNSMDEDLEATVWIRCDVYDTGIGIPENALPTLFRKYMQVSADHARKYGGTGLGLAICKQLV  640 (1002)
Q Consensus       561 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~i~V~DtGiGI~~e~l~~IF~pF~q~~~~~~~~~~GtGLGLaI~k~Lv  640 (1002)
                                                   ..+.++|.|+|.|++++..                   |.|+||.=-|+=|
T Consensus       309 -----------------------------~~l~l~V~DnG~Gf~~~~~-------------------~~~~GL~~mreRv  340 (365)
T COG4585         309 -----------------------------DELRLEVIDNGVGFDPDKE-------------------GGGFGLLGMRERV  340 (365)
T ss_pred             -----------------------------CEEEEEEEECCcCCCcccc-------------------CCCcchhhHHHHH
Confidence                                         1388999999999986531                   2689999999999


Q ss_pred             HHhCCEEEEEeecCCceEEEEEEeC
Q 039716          641 ELMGGRLTVTSKVHCGSTFTFILPY  665 (1002)
Q Consensus       641 e~~gG~I~v~S~~g~GTtF~~~LP~  665 (1002)
                      +.+||++++.|.+|+||++++++|+
T Consensus       341 ~~lgG~l~i~S~~g~Gt~i~i~lPl  365 (365)
T COG4585         341 EALGGTLTIDSAPGQGTTVTITLPL  365 (365)
T ss_pred             HHcCCEEEEEecCCCceEEEEecCC
Confidence            9999999999999999999999995

>PRK04069 serine-protein kinase RsbW; Provisional

Probab=98.81  E-value=3.6e-08  Score=100.04  Aligned_cols=69  Identities=20%  Similarity=0.238  Sum_probs=54.6

Q ss_pred             EEEEEEEecCCCCCcCcHhhhhhhccCCCccccCcCCCccccHHHHHHHHHHhCCEEEEEeecCCceEEEEEEeCCC
Q 039716          591 WIRCDVYDTGIGIPENALPTLFRKYMQVSADHARKYGGTGLGLAICKQLVELMGGRLTVTSKVHCGSTFTFILPYQV  667 (1002)
Q Consensus       591 ~l~i~V~DtGiGI~~e~l~~IF~pF~q~~~~~~~~~~GtGLGLaI~k~Lve~~gG~I~v~S~~g~GTtF~~~LP~~~  667 (1002)
                      .+.|.|.|+|+||+++.+...|.||+......  ...+.|+||+++++|++.    +.+.+  ..|++|++.-.+..
T Consensus        77 ~l~i~V~D~G~g~d~~~~~~~~~p~~~~~~~~--~~~~~G~GL~li~~l~d~----v~~~~--~~G~~v~~~k~~~~  145 (161)
T PRK04069         77 RLEIVVADNGVSFDYETLKSKLGPYDISKPIE--DLREGGLGLFLIETLMDD----VTVYK--DSGVTVSMTKYINR  145 (161)
T ss_pred             EEEEEEEECCcCCChHHhccccCCCCCCCccc--ccCCCceeHHHHHHHHHh----EEEEc--CCCcEEEEEEEcCc
Confidence            58899999999999999999999988654322  224679999999999986    66665  46899998876643

>PRK15029 arginine decarboxylase; Provisional

Probab=98.76  E-value=3.9e-08  Score=120.62  Aligned_cols=105  Identities=11%  Similarity=0.118  Sum_probs=84.7

Q ss_pred             eEEEEecCHH--------HHHHHHHHHHhcCCeEEEEcCHHHHHHHHHc-CCCcEEEEcCCCCCCCHH----HHHHHHhc
Q 039716          861 KILLVEDNKI--------NVMVAKSMMKQLGHSIDVVNNGVEAVHAVQC-QNYDLILMDVCMPVMDGL----KATRLIRS  927 (1002)
Q Consensus       861 ~ILiVeDn~~--------n~~~l~~~L~~~g~~v~~a~~G~eAl~~~~~-~~~DlIlmDi~MP~mdG~----e~~~~IR~  927 (1002)
                      +||||||+..        ....++..|+..||+|..+.++.+|+..+.. ..||+||+|++||+|+|+    ++++.||.
T Consensus         2 kILIVDDD~~~~~~~~~~i~~~L~~~Le~~G~eV~~a~s~~dAl~~l~~~~~~DlVLLD~~LPd~dG~~~~~ell~~IR~   81 (755)
T PRK15029          2 KVLIVESEFLHQDTWVGNAVERLADALSQQNVTVIKSTSFDDGFAILSSNEAIDCLMFSYQMEHPDEHQNVRQLIGKLHE   81 (755)
T ss_pred             eEEEEeCCcccccchhHHHHHHHHHHHHHCCCEEEEECCHHHHHHHHHhcCCCcEEEEECCCCCCccchhHHHHHHHHHh
Confidence            6999999995        6899999999999999999999999999987 689999999999999998    89999995


Q ss_pred             cccCCCchhhhhhhhcccCCCCCCCCCCCCccEEEEcCCCC--HHHHHHHHHcCCCEEEeCCCChHH
Q 039716          928 FEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANAL--SESAEECFANGMDSFVSKPVTFQK  992 (1002)
Q Consensus       928 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipIIalTa~~~--~~~~~~~~~aG~d~~l~KP~~~~~  992 (1002)
                      .                          .+.+|||++|+...  .......+ --++.|+-+--+..+
T Consensus        82 ~--------------------------~~~iPIIlLTar~~~~~~~~~~~~-~~~~~~~~~~~~~~~  121 (755)
T PRK15029         82 R--------------------------QQNVPVFLLGDREKALAAMDRDLL-ELVDEFAWILEDTAD  121 (755)
T ss_pred             h--------------------------CCCCCEEEEEcCCcccccCCHHHH-HhhheEEEecCCCHH
Confidence            2                          24699999999986  22222222 225667666554333

>COG3279 LytT Response regulator of the LytR/AlgR family [Transcription / Signal transduction mechanisms]

Probab=98.74  E-value=4.1e-08  Score=106.40  Aligned_cols=113  Identities=26%  Similarity=0.411  Sum_probs=96.8

Q ss_pred             CeEEEEecCHHHHHHHHHHHHhcC-Ce-EEEEcCHHHHHHHHHcCCCcEEEEcCCCCCCCHHHHHHHHhccccCCCchhh
Q 039716          860 PKILLVEDNKINVMVAKSMMKQLG-HS-IDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDAA  937 (1002)
Q Consensus       860 ~~ILiVeDn~~n~~~l~~~L~~~g-~~-v~~a~~G~eAl~~~~~~~~DlIlmDi~MP~mdG~e~~~~IR~~~~~~~~~~~  937 (1002)
                      .+|++|||++..+.-+..++.... ++ +..+.++.++++.+....+|++|+|+.||.|+|+++++.||..         
T Consensus         2 ~~i~i~dd~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~fldI~~~~~~G~ela~~i~~~---------   72 (244)
T COG3279           2 LKVLIVDDEPLAREELRRILNEIPDIEIVGEAENGEEALQLLQGLRPDLVFLDIAMPDINGIELAARIRKG---------   72 (244)
T ss_pred             CcEEEecCCHHHHHHHHHHHHhhhhcCeeeeeccchhhHHHHhccCCCeEEEeeccCccchHHHHHHhccc---------
Confidence            479999999999999999998422 33 3368999999999999999999999999999999999999963         


Q ss_pred             hhhhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHHhh
Q 039716          938 AEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQY 1000 (1002)
Q Consensus       938 ~~~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~~ 1000 (1002)
                                       .+..+|+++|++.  +....+++..+-||+.||++.+.|...+.+.
T Consensus        73 -----------------~~~~~Ivfvt~~~--~~a~~afev~a~d~i~kp~~~~~l~~~l~~~  116 (244)
T COG3279          73 -----------------DPRPAIVFVTAHD--EYAVAAFEVEALDYLLKPISEERLAKTLERL  116 (244)
T ss_pred             -----------------CCCCeEEEEEehH--HHHHHHHhHHHHhhhcCcchHHHHHHHHHHH
Confidence                             2567899999984  5666677888999999999999999998753

>COG2972 Predicted signal transduction protein with a C-terminal ATPase domain [Signal transduction mechanisms]

Probab=98.66  E-value=2e-06  Score=102.17  Aligned_cols=65  Identities=31%  Similarity=0.448  Sum_probs=55.2

Q ss_pred             EEEEEEEecCCCCCcCcHhhhhhhccCCCccccCcCCC-ccccHHHHHHHHHHhCCE--EEEEeecCCceEEEEEEeCC
Q 039716          591 WIRCDVYDTGIGIPENALPTLFRKYMQVSADHARKYGG-TGLGLAICKQLVELMGGR--LTVTSKVHCGSTFTFILPYQ  666 (1002)
Q Consensus       591 ~l~i~V~DtGiGI~~e~l~~IF~pF~q~~~~~~~~~~G-tGLGLaI~k~Lve~~gG~--I~v~S~~g~GTtF~~~LP~~  666 (1002)
                      ++.++|.|||+||+++....+...           .++ .|+||+=+++.++.+-|.  +.++|.+++||+..+.+|..
T Consensus       386 ~i~i~i~Dng~g~~~~~~~~~~~~-----------~~~r~giGL~Nv~~rl~~~~g~~~~~i~s~~~~gt~v~~~~~~~  453 (456)
T COG2972         386 VIQISISDNGPGIDEEKLEGLSTK-----------GENRSGIGLSNVKERLKLYFGEPGLSIDSQPGKGTFVQIIIPKR  453 (456)
T ss_pred             EEEEEEeeCCCCCChhHHHHHHhh-----------ccCcccccHHHHHHHHHHeeCCcceeEeecCCCcEEEEEEeehh
Confidence            588999999999999887765432           122 599999999999999887  58999999999999999964

>PF13426 PAS_9: PAS domain; PDB: 3ULF_B 3UE6_E 2Z6D_B 2Z6C_B 3P7N_B 1LL8_A 3MJQ_A 3BWL_A 4EET_B 4EEP_A

Probab=98.57  E-value=2.8e-07  Score=84.67  Aligned_cols=101  Identities=19%  Similarity=0.220  Sum_probs=83.2

Q ss_pred             CcEEEEecccccEEEeeccC---CCCCcccccCCCchhccCccchhhhhHHHHHHHHhCCCcceeEEEEEeecCceEEEE
Q 039716          232 PVVMGHQDKELRYRFIYNHF---PSLHEEDILGKTDVEIFSGAGVKESQDFKREVLEKGLPAKREITFETELFGSKTFLI  308 (1002)
Q Consensus       232 p~~i~~~d~~~~~~~~~~~~---~~~~~e~iiGk~~~e~~~~~~~~~~~~~~~~vl~~g~~~~~e~~~~~~~~~~~~~~~  308 (1002)
                      |.+++..|.++++.++|..|   .|++.++++|++..+++++...........+.+..+.....++.+....+...++.+
T Consensus         1 p~~i~i~d~~g~i~~~N~~~~~~~g~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~g~~~~~~~   80 (104)
T PF13426_consen    1 PDGIFILDPDGRILYVNPAFERLFGYSREELIGKSISDFFPEEDRPEFEEQIERALEEGGSWSGEVRLRRKDGETFWVEV   80 (104)
T ss_dssp             -SEEEEEETTSBEEEE-HHHHHHHTS-HHHHTTSBGGGGCSTTSCHHHHHHHHHHHHHTSSEEEEEEEEETTSEEEEEEE
T ss_pred             CEEEEEECCcCcEEehhHHHHHHHCcCHHHHcCCCcccccCcccchhhHHHHHHHHhcCCceeEEEEEEcCCCCEEEEEE
Confidence            78899999999999999865   588899999999999998766555666667777777777778877776666777889


Q ss_pred             EEeeeecCCCCEEEEEEEeechhH
Q 039716          309 YVEPVFSKSGETIGVNYMGMDVTD  332 (1002)
Q Consensus       309 ~~~p~~~~~G~~~gi~~~~~DITe  332 (1002)
                      +..|+.+.+|++.++++++.|||+
T Consensus        81 ~~~~i~~~~g~~~~~i~~~~DiTe  104 (104)
T PF13426_consen   81 SASPIRDEDGEITGIIGIFRDITE  104 (104)
T ss_dssp             EEEEEEETTSSEEEEEEEEEEEHH
T ss_pred             EEEEEECCCCCEEEEEEEEEECCC
Confidence            999999999999999999999996

...

>TIGR01924 rsbW_low_gc serine-protein kinase RsbW

Probab=98.57  E-value=5.6e-07  Score=91.13  Aligned_cols=69  Identities=17%  Similarity=0.205  Sum_probs=53.0

Q ss_pred             EEEEEEEecCCCCCcCcHhhhhhhccCCCccccCcCCCccccHHHHHHHHHHhCCEEEEEeecCCceEEEEEEeCCC
Q 039716          591 WIRCDVYDTGIGIPENALPTLFRKYMQVSADHARKYGGTGLGLAICKQLVELMGGRLTVTSKVHCGSTFTFILPYQV  667 (1002)
Q Consensus       591 ~l~i~V~DtGiGI~~e~l~~IF~pF~q~~~~~~~~~~GtGLGLaI~k~Lve~~gG~I~v~S~~g~GTtF~~~LP~~~  667 (1002)
                      .+.+.|.|+|.||+++.+...|.++.......  ...+.|+||+|+++|++    .+.+.+  +.|+++++...+..
T Consensus        77 ~l~i~V~D~G~gfd~~~~~~~~~~~~~~~~~~--~~~~~G~GL~Li~~L~D----~v~~~~--~~G~~l~l~k~~~~  145 (159)
T TIGR01924        77 RLEIIVSDQGDSFDMDTFKQSLGPYDGSEPID--DLREGGLGLFLIETLMD----EVEVYE--DSGVTVAMTKYLNR  145 (159)
T ss_pred             EEEEEEEEcccccCchhhccccCCCCCCCCcc--cCCCCccCHHHHHHhcc----EEEEEe--CCCEEEEEEEEEcc
Confidence            47899999999999999888888876543321  23467999999999998    677776  45788888766543

This model describes the anti-sigma B factor also known as serine-protein kinase RsbW. Sigma B controls the general stress regulon in B subtilis and is activated by cell stresses such as stationary phase and heat shock. RsbW binds to sigma B and prevents formation of the transcription complex at the promoter. RsbV (anti-anti-sigma factor) binds to RsbW to inhibit association with sigma B, however RsbW can phosphorylate RsbV, causing disassociation of the RsbV/RsbW complex. Low ATP level or environmental stress causes the dephosphorylation of RsbV.

>smart00388 HisKA His Kinase A (phosphoacceptor) domain

Probab=98.53  E-value=3.8e-07  Score=76.44  Aligned_cols=63  Identities=44%  Similarity=0.787  Sum_probs=56.5

Q ss_pred             HHHHHHhhhccccHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhc
Q 039716          371 KQMLATMSHEIRSPLTGVVSMAEILSNTKLDREQRQLLGVMISSGDLVLQLINDILDLSKVES  433 (1002)
Q Consensus       371 k~fla~iSHELRTPL~~I~g~~elL~~~~l~~~~~~~l~~i~~s~~~L~~LIndlLd~skies  433 (1002)
                      ++|++.++|||||||++|.++++.+.....+++...++..+..+++++..+++++++|++.+.
T Consensus         3 ~~~~~~i~Hel~~pl~~i~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~v~~l~~~~~~~~   65 (66)
T smart00388        3 REFLANLSHELRTPLTAIRGYLELLEDTELSEEQREYLETILRSAERLLRLINDLLDLSRIEA   65 (66)
T ss_pred             HHHHHHHHHhccCcHHHHHHHHHHHHhCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence            368999999999999999999999877666666688999999999999999999999998765

Dimerisation and phosphoacceptor domain of histidine kinases.

>PF00989 PAS: PAS fold; InterPro: IPR013767 PAS domains are involved in many signalling proteins where they are used as a signal sensor domain []

Probab=98.51  E-value=7.2e-07  Score=83.39  Aligned_cols=109  Identities=18%  Similarity=0.259  Sum_probs=85.0

Q ss_pred             HHHHHHHhccCcEEEEecccccEEEeeccC---CCCCcccccCCCchhccCccchhhhhHHHHHHHHhCCCc-ceeEEEE
Q 039716          222 NFLHFVLQNAPVVMGHQDKELRYRFIYNHF---PSLHEEDILGKTDVEIFSGAGVKESQDFKREVLEKGLPA-KREITFE  297 (1002)
Q Consensus       222 ~~l~~il~~~p~~i~~~d~~~~~~~~~~~~---~~~~~e~iiGk~~~e~~~~~~~~~~~~~~~~vl~~g~~~-~~e~~~~  297 (1002)
                      ++++.+++++|.+++..|.++++.++|.++   .|+..++++|++..+++++...........+.+..+.+. ..++.+.
T Consensus         1 e~~~~i~~~~~~~i~~~d~~g~I~~~N~a~~~l~g~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   80 (113)
T PF00989_consen    1 ERYRAILENSPDGIFVIDEDGRILYVNQAAEELLGYSREELIGKSLFDLIHPEDRRELRERLRQALSQGESGESFEVRFR   80 (113)
T ss_dssp             HHHHHHHHCSSSEEEEEETTSBEEEECHHHHHHHSS-HHHHTTSBGGGGCSGGGHHHHHHHHHHHHHHCCHECEEEEEEE
T ss_pred             CHHHHHHhcCCceEEEEeCcCeEEEECHHHHHHHccCHHHHcCCcHHHhcCchhhHHHHHHHHHHHHcCCCceeEEEEEE
Confidence            367889999999999999999999999865   688999999999999998765444555555666555433 3344444


Q ss_pred             EeecCceEEEEEEeeeecCCCCEEEEEEEeech
Q 039716          298 TELFGSKTFLIYVEPVFSKSGETIGVNYMGMDV  330 (1002)
Q Consensus       298 ~~~~~~~~~~~~~~p~~~~~G~~~gi~~~~~DI  330 (1002)
                      ...++..++.+...|+++.+|.+.|+++++.||
T Consensus        81 ~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~DI  113 (113)
T PF00989_consen   81 LRDGRPRWVEVRASPVRDEDGQIIGILVIFRDI  113 (113)
T ss_dssp             ETTSCEEEEEEEEEEEEETTEEEEEEEEEEEE-
T ss_pred             ecCCcEEEEEEEEEEEEeCCCCEEEEEEEEEeC
Confidence            435666778899999999999999999999997

PAS domains appear in archaea, bacteria and eukaryotes. Several PAS-domain proteins are known to detect their signal by way of an associated cofactor. Haeme, flavin, and a 4-hydroxycinnamyl chromophore are used in different proteins. The PAS domain was named after three proteins that it occurs in: Per- period circadian protein Arnt- Ah receptor nuclear translocator protein Sim- single-minded protein. PAS domains are often associated with PAC domains IPR001610 from INTERPRO. It appears that these domains are directly linked, and that together they form the conserved 3D PAS fold. The division between the PAS and PAC domains is caused by major differences in sequences in the region connecting these two motifs []. In human PAS kinase, this region has been shown to be very flexible, and adopts different conformations depending on the bound ligand []. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels [].; GO: 0006355 regulation of transcription, DNA-dependent; PDB: 2GJ3_A 4F3L_B 1XFN_A 1OTD_A 2PYR_A 1KOU_A 1XFQ_A 2ZOI_A 2ZOH_A 1OTA_A ....

>COG4564 Signal transduction histidine kinase [Signal transduction mechanisms]

Probab=98.50  E-value=0.00031  Score=76.00  Aligned_cols=305  Identities=17%  Similarity=0.183  Sum_probs=158.3

Q ss_pred             ccccCCCchhccCccchhhhhHHHHHHHHhCCCcceeEEEEEeecCceEEEEEEeeeecCCCCEEEEEEEeechhHHHHH
Q 039716          257 EDILGKTDVEIFSGAGVKESQDFKREVLEKGLPAKREITFETELFGSKTFLIYVEPVFSKSGETIGVNYMGMDVTDQVRK  336 (1002)
Q Consensus       257 e~iiGk~~~e~~~~~~~~~~~~~~~~vl~~g~~~~~e~~~~~~~~~~~~~~~~~~p~~~~~G~~~gi~~~~~DITe~~~~  336 (1002)
                      -+..|+++.++..+.+..-++...-...+.|.-  ..+-++.+..+...-........|+-+..+|.-....|+....++
T Consensus       113 pelvG~nlw~L~D~rGd~~Iq~Li~kAq~GGG~--~qYlWeKPSs~e~v~KLsyaa~ldkW~WMiGTGlYldDv~~~~~~  190 (459)
T COG4564         113 PELVGQNLWQLTDPRGDRVIQALIAKAQEGGGL--HQYLWEKPSSHETVDKLSYAAGLDKWEWMIGTGLYLDDVSAETAA  190 (459)
T ss_pred             ccccccchhhccCCCcChHHHHHHHHHHhCCCe--EEEeecCCCcccchhhhccccCccccceeeecceehHhHHHHHHH
Confidence            357899988887665544444444333333321  222333322222111122233346666777776667777766554


Q ss_pred             HHHHHHHH-------------------------HHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHhhhccccHHHHH
Q 039716          337 REKMAKLR-------------------------EEIAV---QKAKETELNKTIHITEETMRAKQMLATMSHEIRSPLTGV  388 (1002)
Q Consensus       337 ~~~~~~l~-------------------------~el~~---~~~~~~el~k~~~~~e~~~~~k~fla~iSHELRTPL~~I  388 (1002)
                      .+...+.+                         -.+..   .-.+.++|.+..-.+.+..++ ++..-+-.-|..-|-+.
T Consensus       191 ~~~~~~anId~tf~~Vv~iavv~vllV~~t~lalNl~ehRlAD~kLkeL~qrvv~tQedEr~-rlaRELHDGIsQ~LVs~  269 (459)
T COG4564         191 AQAAVRANIDTTFLIVVLIAVVAVLLVFATCLALNLREHRLADKKLKELAQRVVDTQEDERA-RLARELHDGISQNLVSV  269 (459)
T ss_pred             HHHHHhcCcchhHHHHHHHHHHHHHHHHHHHHHhhhHHHHhhhhHHHHHHHHHhhchhHHHH-HHHHHHhhhHHHHHHHH
Confidence            33221100                         00111   112222333222112222221 12222222233445556


Q ss_pred             HHHHHHHhCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCeeeEee---ecCHHHHHHHHHHHHHHHHhhcce
Q 039716          389 VSMAEILSNTKLDREQRQLLGVMISSGDLVLQLINDILDLSKVESGVMKLEAA---KFRPREVVKHVLQTAAASLQKILM  465 (1002)
Q Consensus       389 ~g~~elL~~~~l~~~~~~~l~~i~~s~~~L~~LIndlLd~skiesg~~~l~~~---~~~l~~li~~v~~~~~~~~~k~i~  465 (1002)
                      .-..+++...-.++.+. ....+..+++.|..-|+++-.+|--      +.+.   ..-+..-++-++..+...-.-.+.
T Consensus       270 k~~lela~~ql~~p~~~-a~~aieKaa~aL~~Ai~EVRRiSH~------LRP~~LDDLGL~aALe~L~~~f~~~tg~~it  342 (459)
T COG4564         270 KCALELAARQLNPPKGG-AHPAIEKAADALNGAIKEVRRISHD------LRPRALDDLGLTAALEALLEDFKERTGIEIT  342 (459)
T ss_pred             HHHHHHHhccCCCCCCC-CchhhhhHHHHHHHHHHHHHHhccc------cChhhhhhhhHHHHHHHHHHHhhhccCeEEE
Confidence            66667765543222221 1245667778888888887666531      1111   111222222233333221111233


Q ss_pred             eccccCCCCCeeEE-ccHHHHHHHHHHHHhhhhhcCCCCeeEEEEEecCCCCcccchhhhhhhhhhcchhhhhhhccCCC
Q 039716          466 LEGDIADDVPIEVI-GDVLRIRQILTNLISNAIKFTPEGKVGIKLYVVPEPPFAKEGLKQKSKAYQSATDAVKEEKHQPK  544 (1002)
Q Consensus       466 l~~~i~~~~p~~v~-gD~~rL~QIL~NLlsNAIKfT~~G~I~I~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  544 (1002)
                      +.++..   |..+. .-...|.+|..--++|-=+++..-.|+|.+.-                                 
T Consensus       343 le~~~~---p~~l~~e~~talyRv~QEaltNIErHa~Atrv~ill~~---------------------------------  386 (459)
T COG4564         343 LEFDTQ---PGKLKPEVATALYRVVQEALTNIERHAGATRVTILLQQ---------------------------------  386 (459)
T ss_pred             EEecCC---cccCCcHHHHHHHHHHHHHHHHHHhhcCCeEEEEEecc---------------------------------
Confidence            333222   21111 12346778888888888888755566665521                                 


Q ss_pred             CCccCCCCCCCCCCCCCCccCCCCCCCCCCCccCCCCCccccccceEEEEEEEecCCCCCcCcHhhhhhhccCCCccccC
Q 039716          545 SQTASDQNGFHDKKHGEGYQDHKHDDDPGTPVSHGNSMDEDLEATVWIRCDVYDTGIGIPENALPTLFRKYMQVSADHAR  624 (1002)
Q Consensus       545 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~i~V~DtGiGI~~e~l~~IF~pF~q~~~~~~~  624 (1002)
                                                                 ....+++.|.|+|.|++-+...               
T Consensus       387 -------------------------------------------~~d~vql~vrDnG~GF~~~~~~---------------  408 (459)
T COG4564         387 -------------------------------------------MGDMVQLMVRDNGVGFSVKEAL---------------  408 (459)
T ss_pred             -------------------------------------------CCcceEEEEecCCCCccchhhc---------------
Confidence                                                       0114789999999999865432               


Q ss_pred             cCCCccccHHHHHHHHHHhCCEEEEEeecCCceEEEEEEeCCC
Q 039716          625 KYGGTGLGLAICKQLVELMGGRLTVTSKVHCGSTFTFILPYQV  667 (1002)
Q Consensus       625 ~~~GtGLGLaI~k~Lve~~gG~I~v~S~~g~GTtF~~~LP~~~  667 (1002)
                       ..-.||||-=.+.=+...||.+.|+|.+. ||..++.||...
T Consensus       409 -~~~~GiGLRNMrERma~~GG~~~v~s~p~-GTel~v~Lp~~~  449 (459)
T COG4564         409 -QKRHGIGLRNMRERMAHFGGELEVESSPQ-GTELTVLLPLDA  449 (459)
T ss_pred             -cCccccccccHHHHHHHhCceEEEEecCC-CcEEEEEecchh
Confidence             11269999999999999999999999987 999999999753

>PRK13560 hypothetical protein; Provisional

Probab=98.32  E-value=5.5e-06  Score=105.37  Aligned_cols=134  Identities=11%  Similarity=0.092  Sum_probs=99.2

Q ss_pred             hHHHHHHHHHHHHHHHHHHHhccCcEEEEecccccEEEeeccC---CCCCcccccCCCchhccCccchhhhhHHHHHHHH
Q 039716          209 PVEELSQILKRADNFLHFVLQNAPVVMGHQDKELRYRFIYNHF---PSLHEEDILGKTDVEIFSGAGVKESQDFKREVLE  285 (1002)
Q Consensus       209 ~~~~~~~~l~~~~~~l~~il~~~p~~i~~~d~~~~~~~~~~~~---~~~~~e~iiGk~~~e~~~~~~~~~~~~~~~~vl~  285 (1002)
                      +.+++++.|++++.+++.+++++|.+++..|.++++.++|..+   .|++.++++|++..+++++.............+.
T Consensus       191 ~rk~ae~~l~~~~~~l~~l~e~~~~~i~~~d~~g~i~~~N~~~~~~~G~~~~e~~g~~~~~~~~~~~~~~~~~~~~~~~~  270 (807)
T PRK13560        191 ERKRAEERIDEALHFLQQLLDNIADPAFWKDEDAKVFGCNDAACLACGFRREEIIGMSIHDFAPAQPADDYQEADAAKFD  270 (807)
T ss_pred             hHHHHHHHHHHHHHHHHHHHhhCCCeEEEEcCCCCEEEEhHHHHHHhCCCHHHHcCCcchhcCCcchhHHHHHHHHHHhc
Confidence            4556677888999999999999999999999999999998764   6889999999999998876554444333444444


Q ss_pred             hCCCcceeEEEEEeecCceEE--EEEEeeeecCCCCEEEEEEEeechhHHHHHHHHHHH
Q 039716          286 KGLPAKREITFETELFGSKTF--LIYVEPVFSKSGETIGVNYMGMDVTDQVRKREKMAK  342 (1002)
Q Consensus       286 ~g~~~~~e~~~~~~~~~~~~~--~~~~~p~~~~~G~~~gi~~~~~DITe~~~~~~~~~~  342 (1002)
                      .+.....+..+....+...++  .+...|+.+..|.+.|+++++.|||+++++++++.+
T Consensus       271 ~~~~~~~e~~~~~~dG~~~~~~~~~~~~~~~~~~g~~~g~~~~~~DITerk~~e~~L~~  329 (807)
T PRK13560        271 ADGSQIIEAEFQNKDGRTRPVDVIFNHAEFDDKENHCAGLVGAITDISGRRAAERELLE  329 (807)
T ss_pred             cCCceEEEEEEEcCCCCEEEEEEEecceEEEcCCCCEEEEEEEEEechHHHHHHHHHHH
Confidence            444444455554444433322  334457789999999999999999998887665543

>PF14501 HATPase_c_5: GHKL domain

Probab=98.29  E-value=8.4e-06  Score=75.80  Aligned_cols=61  Identities=21%  Similarity=0.310  Sum_probs=41.4

Q ss_pred             EEEEEEEecCCCCCcCcHhhhhhhccCCCccccCcCCCccccHHHHHHHHHHhCCEEEEEeecCCceEEEEEEe
Q 039716          591 WIRCDVYDTGIGIPENALPTLFRKYMQVSADHARKYGGTGLGLAICKQLVELMGGRLTVTSKVHCGSTFTFILP  664 (1002)
Q Consensus       591 ~l~i~V~DtGiGI~~e~l~~IF~pF~q~~~~~~~~~~GtGLGLaI~k~Lve~~gG~I~v~S~~g~GTtF~~~LP  664 (1002)
                      ++.|.|..+-.+   +. +.++    .    .+.+.+|.|+||.+++++++.++|.+.++++.+ =-++++.||
T Consensus        40 ~~~i~i~N~~~~---~~-~~~~----~----~~~~~~~~G~GL~~v~~i~~~y~g~~~~~~~~~-~f~~~i~ip  100 (100)
T PF14501_consen   40 FLVIIIENSCEK---EI-EKLE----S----SSSKKKGHGIGLKNVKKILEKYNGSLSIESEDG-IFTVKIVIP  100 (100)
T ss_pred             EEEEEEEECCCC---cc-cccc----c----cccCCCCCCcCHHHHHHHHHHCCCEEEEEEECC-EEEEEEEEC
Confidence            477888888444   21 2222    1    123456899999999999999999999988754 234444444

>KOG0787 consensus Dehydrogenase kinase [Signal transduction mechanisms]

Probab=98.25  E-value=4.2e-05  Score=84.29  Aligned_cols=74  Identities=23%  Similarity=0.422  Sum_probs=62.5

Q ss_pred             EEEEEEecCCCCCcCcHhhhhhhccCCCc------cccCcCCCccccHHHHHHHHHHhCCEEEEEeecCCceEEEEEEeC
Q 039716          592 IRCDVYDTGIGIPENALPTLFRKYMQVSA------DHARKYGGTGLGLAICKQLVELMGGRLTVTSKVHCGSTFTFILPY  665 (1002)
Q Consensus       592 l~i~V~DtGiGI~~e~l~~IF~pF~q~~~------~~~~~~~GtGLGLaI~k~Lve~~gG~I~v~S~~g~GTtF~~~LP~  665 (1002)
                      +.|.|+|-|-||+.+..+++|.=-|.+..      .....-.|.|-||.|||-..+-.||.+.+.|-.|-||-..++|..
T Consensus       301 l~ikISDrGGGV~~~~~drlf~Y~ySTa~~~~~d~~~~~plaGfG~GLPisrlYa~yf~Gdl~L~SleG~GTD~yI~Lk~  380 (414)
T KOG0787|consen  301 LLIKISDRGGGVPHRDIDRLFSYMYSTAPAPSSDNNRTAPLAGFGFGLPISRLYARYFGGDLKLQSLEGIGTDVYIYLKA  380 (414)
T ss_pred             eEEEEecCCCCcChhHHHHHHhhhcccCCCCCCCCCCcCcccccccCCcHHHHHHHHhCCCeeEEeeeccccceEEEecc
Confidence            66779999999999999999985554322      112234599999999999999999999999999999999999964

>PRK11107 hybrid sensory histidine kinase BarA; Provisional

Probab=98.19  E-value=1.6e-05  Score=102.94  Aligned_cols=115  Identities=16%  Similarity=0.161  Sum_probs=97.5

Q ss_pred             CCCCeEEEEecCHHHHHHHHHHHHhcCCeEEEEcCHHHHHHHHHcCCCcEEEEcCCCCCCCHHHHHHHHhccccCCCchh
Q 039716          857 KPKPKILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDA  936 (1002)
Q Consensus       857 ~~~~~ILiVeDn~~n~~~l~~~L~~~g~~v~~a~~G~eAl~~~~~~~~DlIlmDi~MP~mdG~e~~~~IR~~~~~~~~~~  936 (1002)
                      ..+.+|||+||++.++..+..+|...|+.+..+.++.+    +....||++++|+.||.+++...+........      
T Consensus       534 ~~g~~ili~d~~~~~~~~l~~~L~~~g~~v~~~~~~~~----l~~~~~d~il~~~~~~~~~~~~~~~~~~~~~~------  603 (919)
T PRK11107        534 LAGKRLLYVEPNSAAAQATLDILSETPLEVTYSPTLSQ----LPEAHYDILLLGLPVTFREPLTMLHERLAKAK------  603 (919)
T ss_pred             cCCCeEEEEeCCHHHHHHHHHHHHHCCCEEEEcCCHHH----hccCCCCEEEecccCCCCCCHHHHHHHHHhhh------
Confidence            34679999999999999999999999999999999888    56678999999999998888776655543211      


Q ss_pred             hhhhhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHHh
Q 039716          937 AAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQ  999 (1002)
Q Consensus       937 ~~~~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~  999 (1002)
                                        ....++|++++.........+.+.|+++|+.||++..+|...+..
T Consensus       604 ------------------~~~~~~i~~~~~~~~~~~~~~~~~g~~~~l~kp~~~~~l~~~l~~  648 (919)
T PRK11107        604 ------------------SMTDFLILALPCHEQVLAEQLKQDGADACLSKPLSHTRLLPALLE  648 (919)
T ss_pred             ------------------hcCCcEEEEeCCcchhhHHHHhhCCCceEECCCCCHHHHHHHHHH
Confidence                              123568888999999999999999999999999999999888864

>COG3706 PleD Response regulator containing a CheY-like receiver domain and a GGDEF domain [Signal transduction mechanisms]

Probab=98.12  E-value=2.6e-06  Score=97.89  Aligned_cols=89  Identities=25%  Similarity=0.337  Sum_probs=79.4

Q ss_pred             CeEEEEcCHHHHHHHHHcCCCcEEEEcCCCCCCCHHHHHHHHhccccCCCchhhhhhhhcccCCCCCCCCCCCCccEEEE
Q 039716          884 HSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAM  963 (1002)
Q Consensus       884 ~~v~~a~~G~eAl~~~~~~~~DlIlmDi~MP~mdG~e~~~~IR~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipIIal  963 (1002)
                      ++|.+|..|.+|+..+..+.+|.+|+|++||+|||+++|+.+++..                            .+++++
T Consensus        13 ~~v~~a~~g~~~l~~~~~~~~~~~lld~~m~~~~~~~~~~~lk~~~----------------------------~~~v~~   64 (435)
T COG3706          13 KEVATAKKGLIALAILLDHKPDYKLLDVMMPGMDGFELCRRLKAEP----------------------------ATVVMV   64 (435)
T ss_pred             hhhhhccchHHHHHHHhcCCCCeEEeecccCCcCchhHHHHHhcCC----------------------------cceEEE
Confidence            4677799999999999999999999999999999999999999742                            228999


Q ss_pred             cCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHHhh
Q 039716          964 TANALSESAEECFANGMDSFVSKPVTFQKLKECLEQY 1000 (1002)
Q Consensus       964 Ta~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~~ 1000 (1002)
                      |+...+....+.+++|+++|++||++...+.......
T Consensus        65 t~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~r~~~l  101 (435)
T COG3706          65 TALDDSAPRVRGLKAGADDFLTKPVNDSQLFLRAKSL  101 (435)
T ss_pred             EecCCCCcchhHHhhhhhhhccCCCChHHHHHhhhhh
Confidence            9999999999999999999999999988887666543

>PF13596 PAS_10: PAS domain; PDB: 3CAX_A 2QKP_D

Probab=98.09  E-value=4.1e-05  Score=71.75  Aligned_cols=103  Identities=21%  Similarity=0.308  Sum_probs=72.3

Q ss_pred             HHHHHhccCcEEEEecccccEEEeeccCC---CCCcccccCCCchhccCccchhhhhHHHHHHHHhCCCcceeEEEEEee
Q 039716          224 LHFVLQNAPVVMGHQDKELRYRFIYNHFP---SLHEEDILGKTDVEIFSGAGVKESQDFKREVLEKGLPAKREITFETEL  300 (1002)
Q Consensus       224 l~~il~~~p~~i~~~d~~~~~~~~~~~~~---~~~~e~iiGk~~~e~~~~~~~~~~~~~~~~vl~~g~~~~~e~~~~~~~  300 (1002)
                      |..+++++|.++...|.++++++.|....   .+.+ ..+|++..++.++...+......+.+.. |.....+....   
T Consensus         1 L~~il~s~~~~i~~vD~~~~I~~~n~~a~~~f~~~~-~~iGr~l~~~~~~~~~~~l~~~i~~~~~-~~~~~~~~~~~---   75 (106)
T PF13596_consen    1 LNNILDSMPIGIIFVDRNLRIRYFNPAAARLFNLSP-SDIGRPLFDIHPPLSYPNLKKIIEQVRS-GKEEEFEIVIP---   75 (106)
T ss_dssp             HHHHHHHSSSEEEEEETTSBEEEE-SCGC-SS---G-GGTTSBCCCSS-HHHHHHHHHHHHHHHT-TSBSEEEEEEE---
T ss_pred             ChHHHhcCCCCEEEEcCCCeEEEeChhHhhhcCCCh-HHCCCCHHHcCCccchHHHHHHHHHHHc-CCCceEEEEec---
Confidence            45689999999999999999999987643   3343 4589999999877555555555555553 33332333332   


Q ss_pred             cCceEEEEEEeeeecCCCCEEEEEEEeechh
Q 039716          301 FGSKTFLIYVEPVFSKSGETIGVNYMGMDVT  331 (1002)
Q Consensus       301 ~~~~~~~~~~~p~~~~~G~~~gi~~~~~DIT  331 (1002)
                      .+.+++.+.+.|+++.+|+..|++.++.|||
T Consensus        76 ~~~~~~~~~~~P~~~~~g~~~G~v~~~~DIT  106 (106)
T PF13596_consen   76 NGGRWYLVRYRPYRDEDGEYAGAVITFQDIT  106 (106)
T ss_dssp             ETTEEEEEEEEEEE-TTS-EEEEEEEEEE-G
T ss_pred             CCCEEEEEEEEEEECCCCCEEEEEEEEEecC
Confidence            4678899999999999999999999999997

>cd00082 HisKA Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via trans-autophosphorylation by the catalytic domain of the histidine kinase

Probab=98.05  E-value=1.8e-05  Score=65.54  Aligned_cols=60  Identities=43%  Similarity=0.687  Sum_probs=52.0

Q ss_pred             HHHHHHhhhccccHHHHHHHHHHHHhCCCC-CHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 039716          371 KQMLATMSHEIRSPLTGVVSMAEILSNTKL-DREQRQLLGVMISSGDLVLQLINDILDLSK  430 (1002)
Q Consensus       371 k~fla~iSHELRTPL~~I~g~~elL~~~~l-~~~~~~~l~~i~~s~~~L~~LIndlLd~sk  430 (1002)
                      .++++.++|||||||++|.++++.+..... .+....++..+..++.++..++++++++++
T Consensus         5 ~~~~~~~~hel~~pl~~i~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~   65 (65)
T cd00082           5 GEFLANVSHELRTPLTAIRGALELLEEELLDDEEQREYLERIREEAERLLRLINDLLDLSR   65 (65)
T ss_pred             HHHHHHHhHHhcchHHHHHHHHHHHHhcccCcHHHHHHHHHHHHHHHHHHHHHHHHHHHhC
Confidence            468999999999999999999998876432 566678899999999999999999999875

They subsequently transfer the phosphoryl group to the Asp acceptor residue of a response regulator protein. Two-component signalling systems, consisting of a histidine protein kinase that senses a signal input and a response regulator that mediates the output, are ancient and evolutionarily conserved signaling mechanisms in prokaryotes and eukaryotes.

>TIGR00585 mutl DNA mismatch repair protein MutL

Probab=98.03  E-value=2.3e-05  Score=88.37  Aligned_cols=66  Identities=26%  Similarity=0.327  Sum_probs=47.1

Q ss_pred             EEEEEEecCCCCCcCcHhhhhhhccCCCcccc------CcCCCccccHHHHHHHHHHhCCEEEEEeec--CCceEEEEE
Q 039716          592 IRCDVYDTGIGIPENALPTLFRKYMQVSADHA------RKYGGTGLGLAICKQLVELMGGRLTVTSKV--HCGSTFTFI  662 (1002)
Q Consensus       592 l~i~V~DtGiGI~~e~l~~IF~pF~q~~~~~~------~~~~GtGLGLaI~k~Lve~~gG~I~v~S~~--g~GTtF~~~  662 (1002)
                      ..|.|.|+|.||++++++++|++|++.+....      ..+|--|.||+-...+     +.+.|.|..  +.+..+.+.
T Consensus        52 ~~i~V~DnG~Gi~~~~l~~~~~~~~tsk~~~~~~~~~~~~~G~rG~al~si~~~-----s~~~i~S~~~~~~~~~~~~~  125 (312)
T TIGR00585        52 KLIEVSDNGSGIDKEDLPLACERHATSKIQSFEDLERIETLGFRGEALASISSV-----SRLTITTKTSAADGLAWQAL  125 (312)
T ss_pred             EEEEEEecCCCCCHHHHHHHhhCCCcCCCCChhHhhcccccCccchHHHHHHhh-----CcEEEEEeecCCCcceEEEE
Confidence            46889999999999999999999998754321      2345568888654443     378999875  445555444

All proteins in this family for which the functions are known are involved in the process of generalized mismatch repair. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).

>PRK09776 putative diguanylate cyclase; Provisional

Probab=97.85  E-value=7.8e-05  Score=98.46  Aligned_cols=135  Identities=10%  Similarity=0.055  Sum_probs=100.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHhccCcEEEEecccccEEEeeccC---CCCCcccccCCCchhccCccchhhhhHHHHHHHHh
Q 039716          210 VEELSQILKRADNFLHFVLQNAPVVMGHQDKELRYRFIYNHF---PSLHEEDILGKTDVEIFSGAGVKESQDFKREVLEK  286 (1002)
Q Consensus       210 ~~~~~~~l~~~~~~l~~il~~~p~~i~~~d~~~~~~~~~~~~---~~~~~e~iiGk~~~e~~~~~~~~~~~~~~~~vl~~  286 (1002)
                      .+...+.+++++.+++.+++++|.+|+..|.++++.++|..+   .|++.++++|++..+++++.............+..
T Consensus       271 ~r~~~~~l~~~e~r~~~l~e~~~~~i~~~d~dG~i~~~N~~~~~l~G~~~~el~g~~~~~~~~~~d~~~~~~~~~~~~~~  350 (1092)
T PRK09776        271 FRAERKHISESETRFRNAMEYSAIGMALVGTEGQWLQVNKALCQFLGYSQEELRGLTFQQLTWPEDLNKDLQQVEKLLSG  350 (1092)
T ss_pred             HHHHHHHHHHHHHHHHHHHHhCCceEEEEcCCCcEEehhHHHHHHhCCCHHHHccCCceeccCcchhHhHHHHHHHHHcC
Confidence            334456778888999999999999999999999999998764   67888999999988887766554444444444433


Q ss_pred             CC-CcceeEEEEEeecCceEEEEEEeeeecCCCCEEEEEEEeechhHHHHHHHHHHHHH
Q 039716          287 GL-PAKREITFETELFGSKTFLIYVEPVFSKSGETIGVNYMGMDVTDQVRKREKMAKLR  344 (1002)
Q Consensus       287 g~-~~~~e~~~~~~~~~~~~~~~~~~p~~~~~G~~~gi~~~~~DITe~~~~~~~~~~l~  344 (1002)
                      +. ....+..+..+.+...++.....|+.+.+|.+.|++++..|||++++.++++++..
T Consensus       351 ~~~~~~~e~~~~~~dG~~~~~~~~~~~~~~~~g~~~~~i~~~~DITerk~~e~~l~~~~  409 (1092)
T PRK09776        351 EINSYSMEKRYYRRDGEVVWALLAVSLVRDTDGTPLYFIAQIEDINELKRTEQVNERLM  409 (1092)
T ss_pred             CccceeeeeEEEcCCCCEEEEEEEEEEEECCCCCEeeehhhHHhhHHHHHHHHHHHHHH
Confidence            22 22334444444455556677888999999999999999999999988776665443

>COG1389 DNA topoisomerase VI, subunit B [DNA replication, recombination, and repair]

Probab=97.77  E-value=0.00013  Score=82.33  Aligned_cols=77  Identities=27%  Similarity=0.460  Sum_probs=58.1

Q ss_pred             EEEEEEEecCCCCCcCcHhhhhhhccCCCccc-cC-cCCCccccHHHHHHHHHHhCCE-EEEEeecCC-ceEEEEEEeCC
Q 039716          591 WIRCDVYDTGIGIPENALPTLFRKYMQVSADH-AR-KYGGTGLGLAICKQLVELMGGR-LTVTSKVHC-GSTFTFILPYQ  666 (1002)
Q Consensus       591 ~l~i~V~DtGiGI~~e~l~~IF~pF~q~~~~~-~~-~~~GtGLGLaI~k~Lve~~gG~-I~v~S~~g~-GTtF~~~LP~~  666 (1002)
                      ++.+.|.|||+|||+++++++|-.++-.+.-+ .+ ..|--|||.+-|=-..++.-|+ +.|.|..+. ++...+.|-..
T Consensus        72 ~y~v~veDNGpGIP~e~IPkvFGk~LygSKfh~~~QsRGqqGiGis~avLysQmTtGkPv~V~s~T~~s~~~~~~~l~id  151 (538)
T COG1389          72 HYKVIVEDNGPGIPEEQIPKVFGKMLYGSKFHRNIQSRGQQGIGISAAVLYSQMTTGKPVRVISSTGDSGTAYEYELKID  151 (538)
T ss_pred             eEEEEEecCCCCCChhHhHHHHHHHhccchhhhhhhccccccccHHHHHHHHHhcCCCceEEEecCCCCcceEEEEEEec
Confidence            67889999999999999999998876543321 11 2245699999999889988775 778777654 78777777654


Q ss_pred             C
Q 039716          667 V  667 (1002)
Q Consensus       667 ~  667 (1002)
                      .
T Consensus       152 ~  152 (538)
T COG1389         152 V  152 (538)
T ss_pred             C
Confidence            4

>PRK13558 bacterio-opsin activator; Provisional

Probab=97.77  E-value=0.00032  Score=87.60  Aligned_cols=121  Identities=15%  Similarity=0.157  Sum_probs=90.4

Q ss_pred             HHHHHHHhccCcEEEEec---ccccEEEeecc---CCCCCcccccCCCchhccCccchhhhhHHHHHHHHhCCCcceeEE
Q 039716          222 NFLHFVLQNAPVVMGHQD---KELRYRFIYNH---FPSLHEEDILGKTDVEIFSGAGVKESQDFKREVLEKGLPAKREIT  295 (1002)
Q Consensus       222 ~~l~~il~~~p~~i~~~d---~~~~~~~~~~~---~~~~~~e~iiGk~~~e~~~~~~~~~~~~~~~~vl~~g~~~~~e~~  295 (1002)
                      .+++.+++++|.+++..|   .++++.++|..   +.|+++++++|++..+++++.............+..+.+...++.
T Consensus       148 r~~~~~~~~~~~gi~~~d~~~~dg~i~~~N~~~~~l~G~~~eel~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~  227 (665)
T PRK13558        148 RLKERALDEAPVGITIADATLPDEPLIYINDAFERITGYSPDEVLGRNCRFLQGEDTNEERVAELREAIDEERPTSVELR  227 (665)
T ss_pred             HHHHHHHhcCCccEEEEcCCCCCCcEEEEcHHHHHHhCcCHHHHcCCCHHHhcCCCccHHHHHHHHHHHhcCCCeEEEEE
Confidence            345678999999999887   47889998875   467888999999988777654433333334455666666656665


Q ss_pred             EEEeecCceEEEEEEeeeecCCCCEEEEEEEeechhHHHHHHHHHHH
Q 039716          296 FETELFGSKTFLIYVEPVFSKSGETIGVNYMGMDVTDQVRKREKMAK  342 (1002)
Q Consensus       296 ~~~~~~~~~~~~~~~~p~~~~~G~~~gi~~~~~DITe~~~~~~~~~~  342 (1002)
                      +....+...++.....|+++..|.+.|++++..|||++++.++++.+
T Consensus       228 ~~~~dG~~~~~~~~~~pi~d~~G~~~~~vgi~~DITerk~~E~~L~~  274 (665)
T PRK13558        228 NYRKDGSTFWNQVDIAPIRDEDGTVTHYVGFQTDVTERKEAELALQR  274 (665)
T ss_pred             EECCCCCEEEEEEEEEEEECCCCCEEEEEEEEEeCcHHHHHHHHHHH
Confidence            55555555667788889999999999999999999999887666553

>PRK09776 putative diguanylate cyclase; Provisional

Probab=97.73  E-value=0.00027  Score=93.38  Aligned_cols=127  Identities=17%  Similarity=0.201  Sum_probs=92.6

Q ss_pred             hHHHHHHHHHHHHHHHHHHHhccCcEEEEecccccEEEeeccC---CCCCcccccCCCchhccCccchh---hhhHHHHH
Q 039716          209 PVEELSQILKRADNFLHFVLQNAPVVMGHQDKELRYRFIYNHF---PSLHEEDILGKTDVEIFSGAGVK---ESQDFKRE  282 (1002)
Q Consensus       209 ~~~~~~~~l~~~~~~l~~il~~~p~~i~~~d~~~~~~~~~~~~---~~~~~e~iiGk~~~e~~~~~~~~---~~~~~~~~  282 (1002)
                      +.+++++.|++++++++.+++++|.+++..|.++++.++|..+   .|++.++++|++..+++......   .... ...
T Consensus       523 erk~~e~~L~~~~~~l~~~l~~~~~~i~~~D~~g~i~~~N~a~~~l~G~~~~e~iG~~~~~~~~~~~~~~~~~~~~-~~~  601 (1092)
T PRK09776        523 EVRQLNEALFQEKERLHITLDSIGEAVVCTDMAMKVTFMNPVAEKMTGWTQEEALGVPLLTVLHITFGDNGPLMEN-IYS  601 (1092)
T ss_pred             HHHHHHHHHHHHHHHHHHHHhccccEEEEECCCCeEEEEcHHHHHHhCCCHHHHcCCCHHHHcccccCCcchhhHH-HHH
Confidence            4566778888999999999999999999999999999998754   57888999999988776532211   1111 222


Q ss_pred             HHHhCCC--cceeEEEEEeecCceEEEEEEeeeecCCCCEEEEEEEeechhHHHHH
Q 039716          283 VLEKGLP--AKREITFETELFGSKTFLIYVEPVFSKSGETIGVNYMGMDVTDQVRK  336 (1002)
Q Consensus       283 vl~~g~~--~~~e~~~~~~~~~~~~~~~~~~p~~~~~G~~~gi~~~~~DITe~~~~  336 (1002)
                      ....+.+  ...+..+....+...++.....|+++.+|.+.|++++..|||++++.
T Consensus       602 ~~~~~~~~~~~~~~~~~~~~G~~~~~~~~~~pi~~~~g~~~g~v~~~~DITe~k~~  657 (1092)
T PRK09776        602 CLTSRSAAYLEQDVVLHCRSGGSYDVHYSITPLSTLDGENIGSVLVIQDVTESRKM  657 (1092)
T ss_pred             HHhcCCCccccceEEEEeCCCcEEEEEEEeeeeecCCCCEEEEEEEEEecchHHHH
Confidence            2222222  22344444445555566778889999999999999999999987554

>TIGR00229 sensory_box PAS domain S-box

Probab=97.67  E-value=0.00029  Score=62.85  Aligned_cols=115  Identities=17%  Similarity=0.225  Sum_probs=76.7

Q ss_pred             HHHHHHHhccCcEEEEecccccEEEeeccC---CCCCcccccCCCchhccCccchhhhhHHHHHHHHhCC-CcceeEEEE
Q 039716          222 NFLHFVLQNAPVVMGHQDKELRYRFIYNHF---PSLHEEDILGKTDVEIFSGAGVKESQDFKREVLEKGL-PAKREITFE  297 (1002)
Q Consensus       222 ~~l~~il~~~p~~i~~~d~~~~~~~~~~~~---~~~~~e~iiGk~~~e~~~~~~~~~~~~~~~~vl~~g~-~~~~e~~~~  297 (1002)
                      ..++.+++++|.++...|.++++.++|..+   .++...+++|+...+++++............++..+. ....+..+.
T Consensus         3 ~~~~~~~~~~~~~~~~~d~~~~i~~~n~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   82 (124)
T TIGR00229         3 ERYRAIFESSPDAIIVIDLEGNILYVNPAFEEIFGYSAEELIGRNVLELIPEEDREEVRERIERLLEGEREPVSEERRVR   82 (124)
T ss_pred             hHHHHHHhhCCceEEEEcCCCcEEEEchHHHHHhCCChHHhcCcchhhhcChhhhHHHHHHHHHHHcCCCCCcceEeeeE
Confidence            356778999999999999999999998754   4666778889888877665444433333344444221 122222322


Q ss_pred             EeecCceEEEEEEeeeecCCCCEEEEEEEeechhHHHHHH
Q 039716          298 TELFGSKTFLIYVEPVFSKSGETIGVNYMGMDVTDQVRKR  337 (1002)
Q Consensus       298 ~~~~~~~~~~~~~~p~~~~~G~~~gi~~~~~DITe~~~~~  337 (1002)
                      ...+...++.....|+. .+|...+++++..|||++++.+
T Consensus        83 ~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~dit~~~~~~  121 (124)
T TIGR00229        83 RKDGSEIWVEVSVSPIR-TNGGELGVVGIVRDITERKQAE  121 (124)
T ss_pred             cCCCCEEEEEEEEeehh-hCCCeeEEEEEeeehhHHHHHH
Confidence            23333445556677887 7888999999999999875543

The PAS domain was previously described. This sensory box, or S-box domain occupies the central portion of the PAS domain but is more widely distributed. It is often tandemly repeated. Known prosthetic groups bound in the S-box domain include heme in the oxygen sensor FixL, FAD in the redox potential sensor NifL, and a 4-hydroxycinnamyl chromophore in photoactive yellow protein. Proteins containing the domain often contain other regulatory domains such as response regulator or sensor histidine kinase domains. Other S-box proteins include phytochromes and the aryl hydrocarbon receptor nuclear translocator.

>PF13581 HATPase_c_2: Histidine kinase-like ATPase domain

Probab=97.62  E-value=0.00029  Score=68.09  Aligned_cols=59  Identities=24%  Similarity=0.284  Sum_probs=42.4

Q ss_pred             EEEEEEEecCCCCCcCcHhhhhhhccCCCccccCcCCCccccHHHHHHHHHHhCCEEEEEeecCCceEEEEE
Q 039716          591 WIRCDVYDTGIGIPENALPTLFRKYMQVSADHARKYGGTGLGLAICKQLVELMGGRLTVTSKVHCGSTFTFI  662 (1002)
Q Consensus       591 ~l~i~V~DtGiGI~~e~l~~IF~pF~q~~~~~~~~~~GtGLGLaI~k~Lve~~gG~I~v~S~~g~GTtF~~~  662 (1002)
                      .+.|.|.|+|.|+++.....-...=       .......|+||.|++++++..    .+ + .+.|+++++.
T Consensus        66 ~l~i~v~D~G~~~d~~~~~~~~~~~-------~~~~~~~G~Gl~li~~l~D~~----~~-~-~~~gn~v~l~  124 (125)
T PF13581_consen   66 RLRISVRDNGPGFDPEQLPQPDPWE-------PDSLREGGRGLFLIRSLMDEV----DY-R-EDGGNTVTLR  124 (125)
T ss_pred             EEEEEEEECCCCCChhhccCccccc-------CCCCCCCCcCHHHHHHHHcEE----EE-E-CCCeEEEEEE
Confidence            3889999999999987554321100       022346799999999999975    55 4 7779999875

>PRK10060 RNase II stability modulator; Provisional

Probab=97.52  E-value=0.00091  Score=83.47  Aligned_cols=122  Identities=23%  Similarity=0.270  Sum_probs=84.3

Q ss_pred             HHHHHHHHHhccCcEEEEecccccEEEeeccC---CCCCcccccCCCchhccCcc-chhhhhHHHHHHHHhCCCcceeEE
Q 039716          220 ADNFLHFVLQNAPVVMGHQDKELRYRFIYNHF---PSLHEEDILGKTDVEIFSGA-GVKESQDFKREVLEKGLPAKREIT  295 (1002)
Q Consensus       220 ~~~~l~~il~~~p~~i~~~d~~~~~~~~~~~~---~~~~~e~iiGk~~~e~~~~~-~~~~~~~~~~~vl~~g~~~~~e~~  295 (1002)
                      ...+++.++++++.+|+..|.++++.++|..+   .|++.++++|++..+++.+. ...........++..+.....+..
T Consensus       109 ~~~~~~~v~~~~~~gI~i~D~~g~I~~~N~a~~~l~Gy~~~eliG~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~e~~  188 (663)
T PRK10060        109 GLSFAEQVVSEANSVIVILDSRGNIQRFNRLCEEYTGLKEHDVIGQSVFKLFMSRREAAASRRNIRGFFRSGNAYEVERW  188 (663)
T ss_pred             HHHHHHHHHhhCCceEEEEeCCCCEEEEcHHHHHHHCcCHHHHcCCCHHHHhCChhhHHHHHHHHHHHHhcCCceEEEEE
Confidence            34567789999999999999999999998765   57888999999988876432 223333444556666666555555


Q ss_pred             EEEeecCceEEEEEEeeeecCCCC-EEEEEEEeechhHHHHHHHHHHH
Q 039716          296 FETELFGSKTFLIYVEPVFSKSGE-TIGVNYMGMDVTDQVRKREKMAK  342 (1002)
Q Consensus       296 ~~~~~~~~~~~~~~~~p~~~~~G~-~~gi~~~~~DITe~~~~~~~~~~  342 (1002)
                      +.+.. |...+.....++.+.+|. ..+++++..|||++++.++++..
T Consensus       189 ~~~~~-G~~~~~~~~~~~~~~~g~~~~~~i~~~~DITe~k~~e~~l~~  235 (663)
T PRK10060        189 IKTRK-GQRLFLFRNKFVHSGSGKNEIFLICSGTDITEERRAQERLRI  235 (663)
T ss_pred             EEeCC-CCEEEEEeeeEEEcCCCCceEEEEEEEEechHHHHHHHHHHH
Confidence            54433 444444445566665554 45677888999998776655543

>TIGR02938 nifL_nitrog nitrogen fixation negative regulator NifL

Probab=97.42  E-value=0.0029  Score=75.18  Aligned_cols=39  Identities=18%  Similarity=0.223  Sum_probs=32.7

Q ss_pred             HHHHHHHHHHHHHhccCcEEEEecccccEEEeeccCCCC
Q 039716          216 ILKRADNFLHFVLQNAPVVMGHQDKELRYRFIYNHFPSL  254 (1002)
Q Consensus       216 ~l~~~~~~l~~il~~~p~~i~~~d~~~~~~~~~~~~~~~  254 (1002)
                      .|++++.+++.+++++|.+++..|.++++.++|..|..+
T Consensus       124 ~l~~~~~~~~~~~~~~~~~i~~~d~~~~i~~~N~~~~~~  162 (494)
T TIGR02938       124 VVANQKLLIESVVDAAPVAFVLLDPTGRVILDNQEYKKL  162 (494)
T ss_pred             HHHHHHHHHHHHHhcccceEEEEcCCCCEEEechhHHHh
Confidence            455566778899999999999999999999999876544

NifL is a modulator of the nitrogen fixation positive regulator protein NifA, and is therefore a negative regulator. It binds NifA. NifA and NifL are encoded by adjacent genes.

>PRK11359 cyclic-di-GMP phosphodiesterase; Provisional

Probab=97.37  E-value=0.0014  Score=83.58  Aligned_cols=114  Identities=13%  Similarity=0.018  Sum_probs=81.9

Q ss_pred             HHHHHhccCcEEEEecccccEEEeeccC---CCCCcccccCCCchhccCcc-chhhhhHHHHHHHHhCCCcceeEEEEEe
Q 039716          224 LHFVLQNAPVVMGHQDKELRYRFIYNHF---PSLHEEDILGKTDVEIFSGA-GVKESQDFKREVLEKGLPAKREITFETE  299 (1002)
Q Consensus       224 l~~il~~~p~~i~~~d~~~~~~~~~~~~---~~~~~e~iiGk~~~e~~~~~-~~~~~~~~~~~vl~~g~~~~~e~~~~~~  299 (1002)
                      +..+++++|.+++..|.++++.++|..+   .|++.++++|++..+++... ............+..+.....+..+...
T Consensus       138 ~~~~~~~~~~~i~~~d~~g~i~~~N~~~~~l~G~~~~e~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~  217 (799)
T PRK11359        138 LIIAVDHLDRPVIVLDPERRIVQCNRAFTEMFGYCISEASGMQPDTLLNIPEFPADNRIRLQQLLWKTARDQDEFLLLTR  217 (799)
T ss_pred             HHHHHhcCCCcEEEEcCCCcEEEEChhhHhhhCCCHHHHCCCChHHhcCCCCCcHHHHHHHHHhhccCCCCcceeEEeCC
Confidence            4457899999999999999999998765   57788899999988776532 2222222333444444444445555444


Q ss_pred             ecCceEEEEEEeeeecCCCCEEEEEEEeechhHHHHHH
Q 039716          300 LFGSKTFLIYVEPVFSKSGETIGVNYMGMDVTDQVRKR  337 (1002)
Q Consensus       300 ~~~~~~~~~~~~p~~~~~G~~~gi~~~~~DITe~~~~~  337 (1002)
                      .+...++.....|+.+.+|.+.|++++..|||++++.+
T Consensus       218 dG~~~~~~~~~~~v~d~~g~~~~~~~~~~DITerk~~e  255 (799)
T PRK11359        218 TGEKIWIKASISPVYDVLAHLQNLVMTFSDITEERQIR  255 (799)
T ss_pred             CCCEEEEEeeeeeeecCCCceeEEEEEeehhhhHHHHH
Confidence            44555666778899999999999999999999976553

>smart00448 REC cheY-homologous receiver domain

Probab=97.16  E-value=0.0023  Score=48.88  Aligned_cols=54  Identities=31%  Similarity=0.581  Sum_probs=49.9

Q ss_pred             eEEEEecCHHHHHHHHHHHHhcCCeEEEEcCHHHHHHHHHcCCCcEEEEcCCCC
Q 039716          861 KILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMP  914 (1002)
Q Consensus       861 ~ILiVeDn~~n~~~l~~~L~~~g~~v~~a~~G~eAl~~~~~~~~DlIlmDi~MP  914 (1002)
                      +|++++|++.....+...+...|+.+..+.++.+++..+....||++++|+.+|
T Consensus         2 ~i~i~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~vi~~~~~~   55 (55)
T smart00448        2 RILVVDDDPLLRELLKALLEREGYEVDEATDGEEALELLKEEKPDLILLDIMMP   55 (55)
T ss_pred             eEEEEcCCHHHHHHHHHHHhhcCcEEEEeCCHHHHHHHHHhcCCCEEEEeccCC
Confidence            689999999999999999999999999999999999998888899999998765

CheY regulates the clockwise rotation of E. coli flagellar motors. This domain contains a phosphoacceptor site that is phosphorylated by histidine kinase homologues.

>TIGR02040 PpsR-CrtJ transcriptional regulator PpsR

Probab=97.08  E-value=0.0069  Score=71.84  Aligned_cols=117  Identities=16%  Similarity=0.027  Sum_probs=79.9

Q ss_pred             HHHHHHHHHHHHHHHhccCcEEEEecc-cccEEEeeccC---CCCCcccccCCCchhccCccchhhhhHHHHHHHHhCCC
Q 039716          214 SQILKRADNFLHFVLQNAPVVMGHQDK-ELRYRFIYNHF---PSLHEEDILGKTDVEIFSGAGVKESQDFKREVLEKGLP  289 (1002)
Q Consensus       214 ~~~l~~~~~~l~~il~~~p~~i~~~d~-~~~~~~~~~~~---~~~~~e~iiGk~~~e~~~~~~~~~~~~~~~~vl~~g~~  289 (1002)
                      ...|++++..++.+++++|.+++..|. ++++.++|..+   .|+.+++++|++..+++++..........+.....|..
T Consensus       125 ~~~l~~~e~r~~~l~e~~~~~i~~~d~~~g~i~~~N~a~~~l~G~~~~el~g~~~~~~~~~~~~~~~~~~l~~~~~~g~~  204 (442)
T TIGR02040       125 YWTLREMETRYRVVLEVSSDAVLLVDMSTGRIVEANSAAAALLGGVGQSLVGRAFPQEFEGRRREELMLTLRNVRATGSA  204 (442)
T ss_pred             HHHHHHHHHHHHHHHhhCCceEEEEECCCCEEEEEcHHHHHHhCcCHHHHcCCCHHHhCCHHHHHHHHHHHHHHHhcCCC
Confidence            345677788899999999999999997 79999998754   58889999999998888776555555555556666654


Q ss_pred             cceeEEEEEeecCceEEEEEEeeeecCCCCEEEEEEEeechhHHHH
Q 039716          290 AKREITFETELFGSKTFLIYVEPVFSKSGETIGVNYMGMDVTDQVR  335 (1002)
Q Consensus       290 ~~~e~~~~~~~~~~~~~~~~~~p~~~~~G~~~gi~~~~~DITe~~~  335 (1002)
                      ...++.  ...++ ..+.+...++.. .|.. ++++...|||++.+
T Consensus       205 ~~~~~~--~~~~~-~~~~~~~~~~~~-~~~~-~~l~~~~dit~~~~  245 (442)
T TIGR02040       205 APVRIL--LRRSQ-KRLLVVVSVFRQ-DGES-LFLCQLSPAGATQP  245 (442)
T ss_pred             cceEEE--EcCCC-eEEEEEEEEEEe-CCce-EEEEEEcccchhhh
Confidence            433332  23333 334445555543 3333 45667789987643

This model represents the transcriptional regulator PpsR which is strictly associated with photosynthetic proteobacteria and found in photosynthetic operons. PpsR has been reported to be a repressor. These proteins contain a Helix-Turn_Helix motif of the "fis" type (pfam02954).

>PF06490 FleQ: Flagellar regulatory protein FleQ; InterPro: IPR010518 This domain is found at the N terminus of a subset of sigma54-dependent transcriptional activators that are involved in regulation of flagellar motility e

Probab=96.94  E-value=0.0061  Score=57.60  Aligned_cols=106  Identities=13%  Similarity=0.218  Sum_probs=76.2

Q ss_pred             eEEEEecCHHHHHHHHHHHHhcCCeEEEEcCHHHHHHHHHcCCCcEE-EEcCCCCCCCHHHHHHHHhccccCCCchhhhh
Q 039716          861 KILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLI-LMDVCMPVMDGLKATRLIRSFEDTGNWDAAAE  939 (1002)
Q Consensus       861 ~ILiVeDn~~n~~~l~~~L~~~g~~v~~a~~G~eAl~~~~~~~~DlI-lmDi~MP~mdG~e~~~~IR~~~~~~~~~~~~~  939 (1002)
                      ||||||||...+.-+..+|+=.|+.+..+....- ........++.+ ++...++  ...+.++.+-+            
T Consensus         1 kILvIddd~~R~~~L~~ILeFlGe~~~~~~~~~~-~~~~~~~~~~~~~v~~g~~~--~~~~~l~~l~~------------   65 (109)
T PF06490_consen    1 KILVIDDDAERRQRLSTILEFLGEQCEAVSSSDW-SQADWSSPWEACAVILGSCS--KLAELLKELLK------------   65 (109)
T ss_pred             CEEEECCcHHHHHhhhhhhhhcCCCeEEecHHHH-HHhhhhcCCcEEEEEecCch--hHHHHHHHHHh------------
Confidence            6999999999999999999999999988886544 333344445544 4444444  44455555543            


Q ss_pred             hhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHHhh
Q 039716          940 AGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQY 1000 (1002)
Q Consensus       940 ~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~~ 1000 (1002)
                                    ..+++||+++.........     ..+-+-|.-|++..+|...|++.
T Consensus        66 --------------~~~~~Pvlllg~~~~~~~~-----~nvvg~Le~Pl~Y~qLt~~L~~c  107 (109)
T PF06490_consen   66 --------------WAPHIPVLLLGEHDSPEEL-----PNVVGELEEPLNYPQLTDALHRC  107 (109)
T ss_pred             --------------hCCCCCEEEECCCCccccc-----cCeeEecCCCCCHHHHHHHHHHh
Confidence                          3478999999987766111     11666799999999999999864

g. FleQ in Pseudomonas aeruginosa. It is clearly related to IPR001789 from INTERPRO, but lacks the conserved aspartate residue that undergoes phosphorylation in the classic two-component system response regulator (IPR001789 from INTERPRO).

>COG2172 RsbW Anti-sigma regulatory factor (Ser/Thr protein kinase) [Signal transduction mechanisms]

Probab=96.91  E-value=0.0072  Score=60.18  Aligned_cols=56  Identities=20%  Similarity=0.294  Sum_probs=37.6

Q ss_pred             EEEEEEEecCCCCCcCcHhhhhhhccCCCccccCcCCCccccHHHHHHHHHHhCCEEEEEeecCCc
Q 039716          591 WIRCDVYDTGIGIPENALPTLFRKYMQVSADHARKYGGTGLGLAICKQLVELMGGRLTVTSKVHCG  656 (1002)
Q Consensus       591 ~l~i~V~DtGiGI~~e~l~~IF~pF~q~~~~~~~~~~GtGLGLaI~k~Lve~~gG~I~v~S~~g~G  656 (1002)
                      .+.+.|+|.|+||.  ....-+.|.+....    .-..-|+||.+.++++.    ++.+++..+.+
T Consensus        76 ~~~i~i~D~G~~~~--~~~~~~~~~~~~~~----~~~~~G~Gl~l~~~~~D----~~~~~~~~~~~  131 (146)
T COG2172          76 KLEIRIWDQGPGIE--DLEESLGPGDTTAE----GLQEGGLGLFLAKRLMD----EFSYERSEDGR  131 (146)
T ss_pred             eEEEEEEeCCCCCC--CHHHhcCCCCCCCc----ccccccccHHHHhhhhe----eEEEEeccCCc
Confidence            37889999997765  45566666643221    11234899999999775    57888666654

>TIGR02040 PpsR-CrtJ transcriptional regulator PpsR

Probab=96.78  E-value=0.012  Score=69.68  Aligned_cols=110  Identities=17%  Similarity=0.046  Sum_probs=68.0

Q ss_pred             HhccCcEEEEecccccEEEeeccC---CCCCcccccCCCchhccCccchhhhhHHHHHHHHhCCCcceeEEEEEeecCce
Q 039716          228 LQNAPVVMGHQDKELRYRFIYNHF---PSLHEEDILGKTDVEIFSGAGVKESQDFKREVLEKGLPAKREITFETELFGSK  304 (1002)
Q Consensus       228 l~~~p~~i~~~d~~~~~~~~~~~~---~~~~~e~iiGk~~~e~~~~~~~~~~~~~~~~vl~~g~~~~~e~~~~~~~~~~~  304 (1002)
                      ++++|.+++..|.+|++.++|..+   .++..++++|++..+++++................+.. ..+.......+...
T Consensus         2 ~~~~~d~~~~~d~~g~i~~~n~~~~~~~g~~~~el~G~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~e~~~~~~~g~   80 (442)
T TIGR02040         2 LATAADVTLLLDAEGVVREVAANPHHPSFEQLSEWEGRRWEEIVTAESVEKFELRLSEALRTGRG-AVRVELNHIDPSSF   80 (442)
T ss_pred             CcccCcEEEEECCCCcEEEEEECCCcccccccccCCCCcHhHhhCcchHHHHHHHHHHHhccCCC-cceEeeccCCCCCC
Confidence            578899999999999999998764   57788999999999988876544444433344444432 12222222222222


Q ss_pred             EEEEEEeeeecCCCCEEEEEEEeechhHHHHHHHHH
Q 039716          305 TFLIYVEPVFSKSGETIGVNYMGMDVTDQVRKREKM  340 (1002)
Q Consensus       305 ~~~~~~~p~~~~~G~~~gi~~~~~DITe~~~~~~~~  340 (1002)
                      ++.+...++...++  .|+++++.|||+....++++
T Consensus        81 ~~~~~~~~~~~~~~--~~~~~i~rDi~~~~~~~~~l  114 (442)
T TIGR02040        81 ELPMRFILVRLGAD--RGVLALGRDLRAVAELQQQL  114 (442)
T ss_pred             ccCeEEEEEEeCCC--CeEEEEecccHHHHHHHHHH
Confidence            33333333332222  26778899999877655544

This model represents the transcriptional regulator PpsR which is strictly associated with photosynthetic proteobacteria and found in photosynthetic operons. PpsR has been reported to be a repressor. These proteins contain a Helix-Turn_Helix motif of the "fis" type (pfam02954).

>PRK00095 mutL DNA mismatch repair protein; Reviewed

Probab=96.64  E-value=0.0061  Score=75.06  Aligned_cols=48  Identities=21%  Similarity=0.226  Sum_probs=33.6

Q ss_pred             EEEEEEecCCCCCcCcHhhhhhhccCCCcccc------CcCCCccccHHHHHHH
Q 039716          592 IRCDVYDTGIGIPENALPTLFRKYMQVSADHA------RKYGGTGLGLAICKQL  639 (1002)
Q Consensus       592 l~i~V~DtGiGI~~e~l~~IF~pF~q~~~~~~------~~~~GtGLGLaI~k~L  639 (1002)
                      ..|+|.|+|.||+++.+..+|.++.+.+-...      ..+|=-|.||+-.-.+
T Consensus        52 ~~i~V~DnG~Gi~~~~~~~~~~~~~tsKi~~~~dl~~~~t~GfrGeAL~sI~~v  105 (617)
T PRK00095         52 KLIRVRDNGCGISKEDLALALARHATSKIASLDDLEAIRTLGFRGEALPSIASV  105 (617)
T ss_pred             EEEEEEEcCCCCCHHHHHHHhhccCCCCCCChhHhhccccCCcchhHHHhhhhc
Confidence            56889999999999999999999876543221      1233356677654444

>cd00130 PAS PAS domain; PAS motifs appear in archaea, eubacteria and eukarya

Probab=96.64  E-value=0.017  Score=48.36  Aligned_cols=100  Identities=18%  Similarity=0.218  Sum_probs=67.2

Q ss_pred             cCcEEEEecccccEEEeeccC---CCCCcccccCCCchhccCccchhhhhHHHHHHHHhCCCcceeEEEEEeecCceEEE
Q 039716          231 APVVMGHQDKELRYRFIYNHF---PSLHEEDILGKTDVEIFSGAGVKESQDFKREVLEKGLPAKREITFETELFGSKTFL  307 (1002)
Q Consensus       231 ~p~~i~~~d~~~~~~~~~~~~---~~~~~e~iiGk~~~e~~~~~~~~~~~~~~~~vl~~g~~~~~e~~~~~~~~~~~~~~  307 (1002)
                      +|.+++..|.++.+.++|..+   .++...+++|+...+++.+................+.....++.+....+...++.
T Consensus         1 ~~~~i~~~d~~~~~~~~n~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   80 (103)
T cd00130           1 LPDGVIVLDLDGRILYANPAAEQLLGYSPEELIGKSLLDLIHPEDREELRERLENLLSGGEPVTLEVRLRRKDGSVIWVL   80 (103)
T ss_pred             CCceEEEECCCCcEEEECHHHHHHhCCCHHHHcCccHHHhcCCccchHHHHHHHHHHhcCcCeEEEEEEEccCCCEEEEE
Confidence            366788889999999988754   56677888999888877765544443434444443333334444443334445566


Q ss_pred             EEEeeeecCCCCEEEEEEEeech
Q 039716          308 IYVEPVFSKSGETIGVNYMGMDV  330 (1002)
Q Consensus       308 ~~~~p~~~~~G~~~gi~~~~~DI  330 (1002)
                      ....|+.+..|...+++++..||
T Consensus        81 ~~~~~~~~~~~~~~~~~~~~~di  103 (103)
T cd00130          81 VSLTPIRDEGGEVIGLLGVVRDI  103 (103)
T ss_pred             EEEEEEecCCCCEEEEEEEEecC
Confidence            77788888888999988888775

Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in signal transduction.

>PF12860 PAS_7: PAS fold

Probab=96.05  E-value=0.015  Score=55.04  Aligned_cols=104  Identities=20%  Similarity=0.251  Sum_probs=65.5

Q ss_pred             HhccCcEEEEecccccEEEeeccC---CCCCcccc-cCCCchhccCcc------chhhhhHHHHHHHHhCCCcceeEEEE
Q 039716          228 LQNAPVVMGHQDKELRYRFIYNHF---PSLHEEDI-LGKTDVEIFSGA------GVKESQDFKREVLEKGLPAKREITFE  297 (1002)
Q Consensus       228 l~~~p~~i~~~d~~~~~~~~~~~~---~~~~~e~i-iGk~~~e~~~~~------~~~~~~~~~~~vl~~g~~~~~e~~~~  297 (1002)
                      |+++|.+|...|.+++..++|..|   .++.++.+ .|.+..+++...      ..........+.+..... .....++
T Consensus         1 Ld~l~~Gv~v~D~~~rl~~~N~~~~~l~~~~~~~~~~G~~~~~l~~~~~~~g~~~~~~~~~~~~~~~~~~~~-~~~~~~~   79 (115)
T PF12860_consen    1 LDSLPQGVAVFDSDGRLVFWNQRFRELFGLPPEMLRPGASFRDLLRRLAERGEFPPGDPEAWVRQRLARLRR-RQPRSFE   79 (115)
T ss_pred             CCCcCceEEEEcCCCeEEeEcHHHHHHhCCCHHHhcCCCCHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHhc-CCCceeE
Confidence            578999999999999999999875   45566665 788877665311      111222333333322211 1112233


Q ss_pred             EeecCceEEEEEEeeeecCCCCEEEEEEEeechhHHHHHH
Q 039716          298 TELFGSKTFLIYVEPVFSKSGETIGVNYMGMDVTDQVRKR  337 (1002)
Q Consensus       298 ~~~~~~~~~~~~~~p~~~~~G~~~gi~~~~~DITe~~~~~  337 (1002)
                      ....+.+++.+...|.-  +|   |++.++.|||+.++++
T Consensus        80 ~~~~dgr~l~~~~~~~~--~G---g~v~~~~DVT~~~~~E  114 (115)
T PF12860_consen   80 LRLPDGRWLEVRAQPLP--DG---GFVLTFTDVTERRRAE  114 (115)
T ss_pred             EECCCCEEEEEEeEECC--CC---CEEEEEEeCCHHHHhc
Confidence            34456677888888874  34   6778899999987654

>KOG0519 consensus Sensory transduction histidine kinase [Signal transduction mechanisms]

Probab=96.04  E-value=0.011  Score=74.63  Aligned_cols=227  Identities=19%  Similarity=0.218  Sum_probs=158.7

Q ss_pred             HHHHHhhhccccHHHHHHHHHHHH-hCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCeeeEeeecCHHHHHH
Q 039716          372 QMLATMSHEIRSPLTGVVSMAEIL-SNTKLDREQRQLLGVMISSGDLVLQLINDILDLSKVESGVMKLEAAKFRPREVVK  450 (1002)
Q Consensus       372 ~fla~iSHELRTPL~~I~g~~elL-~~~~l~~~~~~~l~~i~~s~~~L~~LIndlLd~skiesg~~~l~~~~~~l~~li~  450 (1002)
                      .+...++|..|+|.+++++...++ ....+..++.-.+.....+...+..+++.-.+.++...|........+.+..++.
T Consensus       388 ~~~~~~~~~~~~~~~~~i~~~~~l~~~~~~~~~~~~~i~~~~~~~~~~~~~~q~~~~~~~~~~gt~~~~~i~~~l~~l~~  467 (786)
T KOG0519|consen  388 DFLQKMSHAMRAPRHNIISLLSLLLQDIVLSPDSGLEIQTVMRSSNVFTSLIQADPDITRLYGGTGLGESIVFSLVELMS  467 (786)
T ss_pred             hHHHHhccccccccccccccchhhHhheEeccCCceeEehhhhhhhHHHHHhccccccccccCCCcccchhhccHHHHHH
Confidence            566777799999999999988844 4444445555566777788888999999999999877777777778889999988


Q ss_pred             HHHHHHHHHH-hhcceeccccCCCCCeeEEccHHHHHHHHHHHHhhhhh--cCCCCe-eEEEEEecCCCCcccchhhhhh
Q 039716          451 HVLQTAAASL-QKILMLEGDIADDVPIEVIGDVLRIRQILTNLISNAIK--FTPEGK-VGIKLYVVPEPPFAKEGLKQKS  526 (1002)
Q Consensus       451 ~v~~~~~~~~-~k~i~l~~~i~~~~p~~v~gD~~rL~QIL~NLlsNAIK--fT~~G~-I~I~v~~~~~~~~~~~~~~~~~  526 (1002)
                      ..+....... .+...+...+....+..+.+|..++.|++.+..+++.+  ++..|. ..+.+....-...         
T Consensus       468 ~~~~~~~~~~~~~t~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~~~~~~~~~~~~~~~~~~~~~~~~~---------  538 (786)
T KOG0519|consen  468 GEISDISCISLGKTFSFTLDLLTNLPKSVVGDEKRLFQIILDFNGMLALLIDTKLGREQIFQVLAELLGIS---------  538 (786)
T ss_pred             HHhhhhhhhccCceeeEEEEeccCCCccchhhhhhhhhhhhhhcchhhhhhccccCcceeEEEEecccCcc---------
Confidence            8776655433 45666777777777878999999999999999999999  887763 1222211100000         


Q ss_pred             hhhhcchhhhhhhccCCCCCccCCCCCCCCCCCCCCccCCCCCCCCCCCccCCCCCccccccceEEEEEEEecCCCCCcC
Q 039716          527 KAYQSATDAVKEEKHQPKSQTASDQNGFHDKKHGEGYQDHKHDDDPGTPVSHGNSMDEDLEATVWIRCDVYDTGIGIPEN  606 (1002)
Q Consensus       527 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~i~V~DtGiGI~~e  606 (1002)
                            .+..     .      .....++.                     .+     .......+.+.+.+++.|+...
T Consensus       539 ------vd~~-----~------~~~~~~~~---------------------~~-----~~~~~~~~~~~~~~~~~~~~~~  575 (786)
T KOG0519|consen  539 ------VDVS-----L------SLSLAFWF---------------------LD-----LSLSDLEVCKQIEDNEEGSNNG  575 (786)
T ss_pred             ------cccc-----c------cchhhhhh---------------------cc-----cccccchheEEeeeccccccCC
Confidence                  0000     0      00000000                     00     0001124778899999999999


Q ss_pred             cHhhhhhhccCCCccccCcCCCccccHHHHHHHHHHhCCEEEEE
Q 039716          607 ALPTLFRKYMQVSADHARKYGGTGLGLAICKQLVELMGGRLTVT  650 (1002)
Q Consensus       607 ~l~~IF~pF~q~~~~~~~~~~GtGLGLaI~k~Lve~~gG~I~v~  650 (1002)
                      .....|..|.+......+...+.+++|+.|....+.++|.+++.
T Consensus       576 ~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  619 (786)
T KOG0519|consen  576 DISSSNPLHKSLRDLTSKLSSGSGLSLALCPENSQLMEGNIGLV  619 (786)
T ss_pred             CcchhhhhhhccccchhhcccccccccccchhhHHhhhcccccc
Confidence            99999888887765555445688999999999999999998865

>PF13589 HATPase_c_3: Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase; PDB: 3IED_A 2XCM_B 2JKI_B 3OPD_A 2O1V_B 2GQP_A 2O1W_C 1YT2_A 1TC6_A 2H8M_B

Probab=95.84  E-value=0.0051  Score=60.66  Aligned_cols=67  Identities=28%  Similarity=0.392  Sum_probs=41.8

Q ss_pred             EEEEEecCCCCCcCcHhhhhhhccCCCcc--ccCcCCCcccc--HHHHHHHHHHhCCEEEEEeecC-CceEEEEEEe
Q 039716          593 RCDVYDTGIGIPENALPTLFRKYMQVSAD--HARKYGGTGLG--LAICKQLVELMGGRLTVTSKVH-CGSTFTFILP  664 (1002)
Q Consensus       593 ~i~V~DtGiGI~~e~l~~IF~pF~q~~~~--~~~~~~GtGLG--LaI~k~Lve~~gG~I~v~S~~g-~GTtF~~~LP  664 (1002)
                      .|.|.|+|.||+.+.+..+|......+..  .....|--|+|  +|+.     .++..+.|.|... ..++++|..+
T Consensus        35 ~i~I~DnG~Gm~~~~l~~~~~~g~s~k~~~~~~~~~G~~G~G~k~A~~-----~~~~~~~v~S~~~~~~~~~~~~~~  106 (137)
T PF13589_consen   35 YIVIEDNGEGMSREDLESFFRIGRSSKKSEKDRQSIGRFGIGLKLAIF-----SLGDRVEVISKTNGESFTYTIDYD  106 (137)
T ss_dssp             EEEEEESSS---HHHHHHHTTCHHTHHHHHHHGGGGGGGTSGCGGGGG-----GTEEEEEEEEESTTSSSEEEEEEE
T ss_pred             EEEEEECCcCCCHHHHHHhccccCCCCCchhhhhcCCCcceEHHHHHH-----HhcCEEEEEEEECCCCcEEEEEEe
Confidence            47799999999999999987655543321  12234556777  4443     3678899999854 3456666555

...

>cd02071 MM_CoA_mut_B12_BD methylmalonyl CoA mutase B12 binding domain

Probab=95.59  E-value=0.33  Score=46.82  Aligned_cols=111  Identities=14%  Similarity=0.132  Sum_probs=79.7

Q ss_pred             EEEE----ecCHHHHHHHHHHHHhcCCeEEEE---cCHHHHHHHHHcCCCcEEEEcCCCCCCCH--HHHHHHHhccccCC
Q 039716          862 ILLV----EDNKINVMVAKSMMKQLGHSIDVV---NNGVEAVHAVQCQNYDLILMDVCMPVMDG--LKATRLIRSFEDTG  932 (1002)
Q Consensus       862 ILiV----eDn~~n~~~l~~~L~~~g~~v~~a---~~G~eAl~~~~~~~~DlIlmDi~MP~mdG--~e~~~~IR~~~~~~  932 (1002)
                      |++.    |.+.+=..++..+|+..||+|...   ...++.++.+....+|+|.+-..|+..-.  -++++.+|+.    
T Consensus         2 vv~~~~~gd~H~lG~~~~~~~l~~~G~~vi~lG~~vp~e~~~~~a~~~~~d~V~iS~~~~~~~~~~~~~~~~L~~~----   77 (122)
T cd02071           2 ILVAKPGLDGHDRGAKVIARALRDAGFEVIYTGLRQTPEEIVEAAIQEDVDVIGLSSLSGGHMTLFPEVIELLREL----   77 (122)
T ss_pred             EEEEecCCChhHHHHHHHHHHHHHCCCEEEECCCCCCHHHHHHHHHHcCCCEEEEcccchhhHHHHHHHHHHHHhc----
Confidence            5555    666777788899999999998865   45788889999999999999887753222  2334444431    


Q ss_pred             CchhhhhhhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHH
Q 039716          933 NWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLE  998 (1002)
Q Consensus       933 ~~~~~~~~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~  998 (1002)
                                           ....+ .|++-+....++..++.++|+|.|+..=-+.++....|+
T Consensus        78 ---------------------~~~~i-~i~~GG~~~~~~~~~~~~~G~d~~~~~~~~~~~~~~~~~  121 (122)
T cd02071          78 ---------------------GAGDI-LVVGGGIIPPEDYELLKEMGVAEIFGPGTSIEEIIDKIR  121 (122)
T ss_pred             ---------------------CCCCC-EEEEECCCCHHHHHHHHHCCCCEEECCCCCHHHHHHHHh
Confidence                                 01234 455665666777888999999999998888777666553

This domain binds to B12 (adenosylcobamide), which initiates the conversion of succinyl CoA and methylmalonyl CoA by forming an adenosyl radical, which then undergoes a rearrangement exchanging a hydrogen atom with a group attached to a neighboring carbon atom. This family is present in both mammals and bacteria. Bacterial members are heterodimers and involved in the fermentation of pyruvate to propionate. Mammalian members are homodimers and responsible for the conversion of odd-chain fatty acids and branched-chain amino acids via propionyl CoA to succinyl CoA for further degradation.

>PRK02261 methylaspartate mutase subunit S; Provisional

Probab=95.58  E-value=0.48  Score=46.71  Aligned_cols=117  Identities=13%  Similarity=0.100  Sum_probs=88.5

Q ss_pred             CCeEEEE----ecCHHHHHHHHHHHHhcCCeEEEE---cCHHHHHHHHHcCCCcEEEEcCCCCCC--CHHHHHHHHhccc
Q 039716          859 KPKILLV----EDNKINVMVAKSMMKQLGHSIDVV---NNGVEAVHAVQCQNYDLILMDVCMPVM--DGLKATRLIRSFE  929 (1002)
Q Consensus       859 ~~~ILiV----eDn~~n~~~l~~~L~~~g~~v~~a---~~G~eAl~~~~~~~~DlIlmDi~MP~m--dG~e~~~~IR~~~  929 (1002)
                      +++||+.    |.+..-..++..+|+..||+|...   ...++.++.+.+..+|+|.+-..|+..  .-.++.+.+|+. 
T Consensus         3 ~~~vl~~~~~gD~H~lG~~iv~~~lr~~G~eVi~LG~~vp~e~i~~~a~~~~~d~V~lS~~~~~~~~~~~~~~~~L~~~-   81 (137)
T PRK02261          3 KKTVVLGVIGADCHAVGNKILDRALTEAGFEVINLGVMTSQEEFIDAAIETDADAILVSSLYGHGEIDCRGLREKCIEA-   81 (137)
T ss_pred             CCEEEEEeCCCChhHHHHHHHHHHHHHCCCEEEECCCCCCHHHHHHHHHHcCCCEEEEcCccccCHHHHHHHHHHHHhc-
Confidence            4678888    888888999999999999998875   467888899999999999999988743  223445555532 


Q ss_pred             cCCCchhhhhhhhcccCCCCCCCCCCCCccEEEEcCCC------CHHHHHHHHHcCCCEEEeCCCChHHHHHHHHhhc
Q 039716          930 DTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANA------LSESAEECFANGMDSFVSKPVTFQKLKECLEQYF 1001 (1002)
Q Consensus       930 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipIIalTa~~------~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~~l 1001 (1002)
                                              ..+.++|+ +-+..      ..++..++.+.|++.+....-+.++....|++.+
T Consensus        82 ------------------------~~~~~~i~-vGG~~~~~~~~~~~~~~~l~~~G~~~vf~~~~~~~~i~~~l~~~~  134 (137)
T PRK02261         82 ------------------------GLGDILLY-VGGNLVVGKHDFEEVEKKFKEMGFDRVFPPGTDPEEAIDDLKKDL  134 (137)
T ss_pred             ------------------------CCCCCeEE-EECCCCCCccChHHHHHHHHHcCCCEEECcCCCHHHHHHHHHHHh
Confidence                                    12345544 44433      4556678999999999999999999988888764

>COG3829 RocR Transcriptional regulator containing PAS, AAA-type ATPase, and DNA-binding domains [Transcription / Signal transduction mechanisms]

Probab=95.34  E-value=0.093  Score=61.73  Aligned_cols=110  Identities=25%  Similarity=0.348  Sum_probs=76.6

Q ss_pred             HHHHHHHHHHHhccCcEEEEecccccEEEeecc---CCCCCcccccCCCchhccCccchhhhhHHHHHHHHhCCCcceeE
Q 039716          218 KRADNFLHFVLQNAPVVMGHQDKELRYRFIYNH---FPSLHEEDILGKTDVEIFSGAGVKESQDFKREVLEKGLPAKREI  294 (1002)
Q Consensus       218 ~~~~~~l~~il~~~p~~i~~~d~~~~~~~~~~~---~~~~~~e~iiGk~~~e~~~~~~~~~~~~~~~~vl~~g~~~~~e~  294 (1002)
                      +....+|+.+++.+..++.+.|.+|++.++|..   ..+++.++++|++..+++ ...   ......+++.++.|....+
T Consensus       113 ~~~~~~l~~il~~~~~~l~vvD~~G~~i~~N~~~~~~~gl~~e~~~gk~~~~v~-~~~---~~s~~l~vl~~~kp~~~~~  188 (560)
T COG3829         113 RQLRQRLEAILDSIDDGLLVVDEDGIIIYYNKAYAKLLGLSPEEVLGKHLLDVV-SAG---EDSTLLEVLRTGKPIRDVV  188 (560)
T ss_pred             HHHHHHHHHHHhhccCceEEEcCCCcEEEEcHHHHHHhCCCHHHHcCCcHHHHH-hcc---CCceehhhhhcCCcceeee
Confidence            444567888999999999999999999998875   467889999999998887 111   1123456778877753322


Q ss_pred             EEEEeecCceEEEEEEeeeecCCCCEEEEEEEeechhHHHHH
Q 039716          295 TFETELFGSKTFLIYVEPVFSKSGETIGVNYMGMDVTDQVRK  336 (1002)
Q Consensus       295 ~~~~~~~~~~~~~~~~~p~~~~~G~~~gi~~~~~DITe~~~~  336 (1002)
                      .  +.. +.. ......|+ ..+|.++|++.++.|+++..+.
T Consensus       189 ~--~~~-~~~-~i~~~~pv-~~~g~l~G~v~~~~~~~~l~~l  225 (560)
T COG3829         189 Q--TYN-GNK-IIVNVAPV-YADGQLIGVVGISKDVSELERL  225 (560)
T ss_pred             e--eec-CCc-eeEeeccE-ecCCcEEEEEEeecchHHHHHH
Confidence            1  111 211 23444454 5677999999999999976544

>PRK11359 cyclic-di-GMP phosphodiesterase; Provisional

Probab=95.28  E-value=0.065  Score=68.44  Aligned_cols=116  Identities=14%  Similarity=0.086  Sum_probs=76.0

Q ss_pred             HHHHHHHHhccCcEEEEecccccEEEeeccC---CCCCcccccCCCchhccCccchhhhhHHHHHHHHhCCCc----cee
Q 039716          221 DNFLHFVLQNAPVVMGHQDKELRYRFIYNHF---PSLHEEDILGKTDVEIFSGAGVKESQDFKREVLEKGLPA----KRE  293 (1002)
Q Consensus       221 ~~~l~~il~~~p~~i~~~d~~~~~~~~~~~~---~~~~~e~iiGk~~~e~~~~~~~~~~~~~~~~vl~~g~~~----~~e  293 (1002)
                      +..+...++++|.+++..|.++++.++|..+   .|++.++++|++..+++++................+...    ..+
T Consensus        11 ~~~~~~~le~~~~~i~~~d~~g~i~~~N~~~~~l~G~s~eeliG~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e   90 (799)
T PRK11359         11 DGIFFPALEQNMMGAVLINENDEVLFFNPAAEKLWGYKREEVIGNNIDMLIPRDLRPAHPEYIRHNREGGKARVEGMSRE   90 (799)
T ss_pred             hhhHHHHHHhhcCcEEEEcCCCeEEEEcHHHHHHhCCCHHHHcCCCHHHhcCccccccchHHHhhhhccCCcccccccee
Confidence            3444567889999999999999999998754   688999999999999887754444444444444444322    224


Q ss_pred             EEEEEeecCceEEEEEEeeeecCCCCEEEEEEEeechhHHHHHHH
Q 039716          294 ITFETELFGSKTFLIYVEPVFSKSGETIGVNYMGMDVTDQVRKRE  338 (1002)
Q Consensus       294 ~~~~~~~~~~~~~~~~~~p~~~~~G~~~gi~~~~~DITe~~~~~~  338 (1002)
                      +.+....+...++.+...|+ +..|.+ +++++..|||++++.++
T Consensus        91 ~~~~~~dG~~~~v~~~~~~~-~~~g~~-~~~~~~~DiT~~~~~~~  133 (799)
T PRK11359         91 LQLEKKDGSKIWTRFALSKV-SAEGKV-YYLALVRDASVEMAQKE  133 (799)
T ss_pred             eEEecCCcCEEEEEEEeeee-ccCCce-EEEEEEeeccchhhhHH
Confidence            44444444444444555554 455665 45677899998655443

>PRK10820 DNA-binding transcriptional regulator TyrR; Provisional

Probab=95.26  E-value=0.098  Score=63.36  Aligned_cols=106  Identities=16%  Similarity=0.197  Sum_probs=76.5

Q ss_pred             HHHHHHHHHHHHhccCcEEEEecccccEEEeeccC---CCCCcccccCCCchhccCccchhhhhHHHHHHHHhCCCccee
Q 039716          217 LKRADNFLHFVLQNAPVVMGHQDKELRYRFIYNHF---PSLHEEDILGKTDVEIFSGAGVKESQDFKREVLEKGLPAKRE  293 (1002)
Q Consensus       217 l~~~~~~l~~il~~~p~~i~~~d~~~~~~~~~~~~---~~~~~e~iiGk~~~e~~~~~~~~~~~~~~~~vl~~g~~~~~e  293 (1002)
                      +++....+..+++++|.+|...|.+|++.++|..+   .++..++++|++..+++++..       ..++++.+.+....
T Consensus        75 ~e~e~~~L~aIL~sm~eGVi~vD~~G~I~~iN~aA~~Llg~~~eel~Gk~i~eli~~~~-------l~~~le~~~~~~~~  147 (520)
T PRK10820         75 SEREHRALSALLEALPEPVLSIDMKGKVELANPASCQLFGQSEEKLRNHTAAQLINGFN-------FLRWLESEPQDSHN  147 (520)
T ss_pred             HHHHHHHHHHHHHhCCCcEEEECCCCeeeHhHHHHHHHHCcCHHHHCCCcHHHHcCcch-------HHHHHHcCCCccce
Confidence            34456678999999999999999999999998754   577778899999999887532       23456666542211


Q ss_pred             EEEEEeecCceEEEEEEeeee--cCCCCE--EEEEEEeechhH
Q 039716          294 ITFETELFGSKTFLIYVEPVF--SKSGET--IGVNYMGMDVTD  332 (1002)
Q Consensus       294 ~~~~~~~~~~~~~~~~~~p~~--~~~G~~--~gi~~~~~DITe  332 (1002)
                      .  .... +...+.+...|++  +.+|..  +|++.++.|+++
T Consensus       148 ~--~v~~-~g~~~~v~~~PI~~~d~~g~~~~~GaVivlrd~~~  187 (520)
T PRK10820        148 E--HVVI-NGQDFLMEITPVYLQDENDQHVLVGAVVMLRSTAR  187 (520)
T ss_pred             E--EEEE-CCEEEEEEEEeeeecCCCCceeEEEEEEEeccHHH
Confidence            1  1122 2356778889998  566654  899999999885

>PRK14083 HSP90 family protein; Provisional

Probab=94.69  E-value=0.019  Score=69.90  Aligned_cols=48  Identities=25%  Similarity=0.366  Sum_probs=30.3

Q ss_pred             EEEEEecCCCCCcCcHhhhhhhccCCCc-------cccCcCCCccccHHHHHHHH
Q 039716          593 RCDVYDTGIGIPENALPTLFRKYMQVSA-------DHARKYGGTGLGLAICKQLV  640 (1002)
Q Consensus       593 ~i~V~DtGiGI~~e~l~~IF~pF~q~~~-------~~~~~~~GtGLGLaI~k~Lv  640 (1002)
                      .|+|.|||+||+.+.+.+.|-.......       ......|.-|+|+.-|-.++
T Consensus        64 ~l~I~DnGiGmt~eel~~~l~~ig~S~k~~~~~~~~~~~~IG~FGIGf~S~F~va  118 (601)
T PRK14083         64 TLIVEDNGIGLTEEEVHEFLATIGRSSKRDENLGFARNDFLGQFGIGLLSCFLVA  118 (601)
T ss_pred             EEEEEeCCCCCCHHHHHHHHhhhccchhhhhhhcccccccccccccceEEEEEec
Confidence            5789999999999999987632221110       01112366788887665543

>PTZ00272 heat shock protein 83 kDa (Hsp83); Provisional

Probab=93.96  E-value=0.058  Score=66.62  Aligned_cols=20  Identities=30%  Similarity=0.439  Sum_probs=16.6

Q ss_pred             EEEEEecCCCCCcCcHhhhh
Q 039716          593 RCDVYDTGIGIPENALPTLF  612 (1002)
Q Consensus       593 ~i~V~DtGiGI~~e~l~~IF  612 (1002)
                      ++.|.|||+||+++++.+-|
T Consensus        73 ~L~I~DnGiGMt~edl~~~L   92 (701)
T PTZ00272         73 TLTVEDNGIGMTKADLVNNL   92 (701)
T ss_pred             EEEEEECCCCCCHHHHHHHh
Confidence            57899999999998876544

>cd02067 B12-binding B12 binding domain (B12-BD)

Probab=93.91  E-value=0.8  Score=43.73  Aligned_cols=94  Identities=12%  Similarity=0.113  Sum_probs=68.1

Q ss_pred             ecCHHHHHHHHHHHHhcCCeEEEE---cCHHHHHHHHHcCCCcEEEEcCCCCCC--CHHHHHHHHhccccCCCchhhhhh
Q 039716          866 EDNKINVMVAKSMMKQLGHSIDVV---NNGVEAVHAVQCQNYDLILMDVCMPVM--DGLKATRLIRSFEDTGNWDAAAEA  940 (1002)
Q Consensus       866 eDn~~n~~~l~~~L~~~g~~v~~a---~~G~eAl~~~~~~~~DlIlmDi~MP~m--dG~e~~~~IR~~~~~~~~~~~~~~  940 (1002)
                      |.+.+-..++..+|+..||+|...   ...++.++.+...+||+|.+-..|...  +..++++.+|+.            
T Consensus        10 e~H~lG~~~~~~~l~~~G~~V~~lg~~~~~~~l~~~~~~~~pdvV~iS~~~~~~~~~~~~~i~~l~~~------------   77 (119)
T cd02067          10 DGHDIGKNIVARALRDAGFEVIDLGVDVPPEEIVEAAKEEDADAIGLSGLLTTHMTLMKEVIEELKEA------------   77 (119)
T ss_pred             chhhHHHHHHHHHHHHCCCEEEECCCCCCHHHHHHHHHHcCCCEEEEeccccccHHHHHHHHHHHHHc------------
Confidence            666677788999999999998653   356788888999999999998876532  345566666642            


Q ss_pred             hhcccCCCCCCCCCCC-CccEEEEcCCCCHHHHHHHHHcCCCEEEeC
Q 039716          941 GIEQAMPSSGSSNHFK-RIPIIAMTANALSESAEECFANGMDSFVSK  986 (1002)
Q Consensus       941 ~~~~~~~~~~~~~~~~-~ipIIalTa~~~~~~~~~~~~aG~d~~l~K  986 (1002)
                                    .+ .++ |++.+.........+.+.|+|.|+..
T Consensus        78 --------------~~~~~~-i~vGG~~~~~~~~~~~~~G~D~~~~~  109 (119)
T cd02067          78 --------------GLDDIP-VLVGGAIVTRDFKFLKEIGVDAYFGP  109 (119)
T ss_pred             --------------CCCCCe-EEEECCCCChhHHHHHHcCCeEEECC
Confidence                          12 444 55666666666678899999888763

This domain binds different cobalamid derivates, like B12 (adenosylcobamide) or methylcobalamin or methyl-Co(III) 5-hydroxybenzimidazolylcobamide, it is found in several enzymes, such as glutamate mutase, methionine synthase and methylmalonyl-CoA mutase. Cobalamin undergoes a conformational change on binding the protein; the dimethylbenzimidazole group, which is coordinated to the cobalt in the free cofactor, moves away from the corrin and is replaced by a histidine contributed by the protein. The sequence Asp-X-His-X-X-Gly, which contains this histidine ligand, is conserved in many cobalamin-binding proteins.

>TIGR00640 acid_CoA_mut_C methylmalonyl-CoA mutase C-terminal domain

Probab=93.66  E-value=2.4  Score=41.56  Aligned_cols=114  Identities=11%  Similarity=0.095  Sum_probs=78.3

Q ss_pred             CeEEEE----ecCHHHHHHHHHHHHhcCCeEEEE---cCHHHHHHHHHcCCCcEEEEcCCCCCC-CH-HHHHHHHhcccc
Q 039716          860 PKILLV----EDNKINVMVAKSMMKQLGHSIDVV---NNGVEAVHAVQCQNYDLILMDVCMPVM-DG-LKATRLIRSFED  930 (1002)
Q Consensus       860 ~~ILiV----eDn~~n~~~l~~~L~~~g~~v~~a---~~G~eAl~~~~~~~~DlIlmDi~MP~m-dG-~e~~~~IR~~~~  930 (1002)
                      ++|++.    |-+..-..++..+|+..||+|...   .+.++.++.+.+..+|+|.+--.|... .. -++++.+++.  
T Consensus         3 ~~v~~a~~g~D~Hd~g~~iv~~~l~~~GfeVi~lg~~~s~e~~v~aa~e~~adii~iSsl~~~~~~~~~~~~~~L~~~--   80 (132)
T TIGR00640         3 PRILVAKMGQDGHDRGAKVIATAYADLGFDVDVGPLFQTPEEIARQAVEADVHVVGVSSLAGGHLTLVPALRKELDKL--   80 (132)
T ss_pred             CEEEEEeeCCCccHHHHHHHHHHHHhCCcEEEECCCCCCHHHHHHHHHHcCCCEEEEcCchhhhHHHHHHHHHHHHhc--
Confidence            355544    445566678899999999998764   468899999999999999986655321 11 2233444431  


Q ss_pred             CCCchhhhhhhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHHh
Q 039716          931 TGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQ  999 (1002)
Q Consensus       931 ~~~~~~~~~~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~  999 (1002)
                                             ....++ |++-+....++..+..++|+|+|+..=-++.+....|.+
T Consensus        81 -----------------------g~~~i~-vivGG~~~~~~~~~l~~~Gvd~~~~~gt~~~~i~~~l~~  125 (132)
T TIGR00640        81 -----------------------GRPDIL-VVVGGVIPPQDFDELKEMGVAEIFGPGTPIPESAIFLLK  125 (132)
T ss_pred             -----------------------CCCCCE-EEEeCCCChHhHHHHHHCCCCEEECCCCCHHHHHHHHHH
Confidence                                   112344 445655667778889999999999887777777666654

Methylmalonyl-CoA mutase (EC 5.4.99.2) catalyzes a reversible isomerization between L-methylmalonyl-CoA and succinyl-CoA. The enzyme uses an adenosylcobalamin cofactor. It may be a homodimer, as in mitochondrion, or a heterodimer with partially homologous beta chain that does not bind the adenosylcobalamin cofactor, as in Propionibacterium freudenreichii. The most similar archaeal sequences are separate chains, such as AF2215 and AF2219 of Archaeoglobus fulgidus, that correspond roughly to the first 500 and last 130 residues, respectively of known methylmalonyl-CoA mutases. This model describes the C-terminal domain subfamily. In a neighbor-joining tree (methylaspartate mutase S chain as the outgroup), AF2219 branches with a coenzyme B12-dependent enzyme known not to be 5.4.99.2.

>PF08447 PAS_3: PAS fold; InterPro: IPR013655 The PAS fold corresponds to the structural domain that has previously been defined as PAS and PAC motifs []

Probab=93.57  E-value=0.18  Score=44.99  Aligned_cols=75  Identities=17%  Similarity=0.208  Sum_probs=55.4

Q ss_pred             CCCCCcccccCCC----chhccCccchhhhhHHHHH-HHHhCCCcceeEEEEEeecCceEEEEEEeeeecCCCCEEEEEE
Q 039716          251 FPSLHEEDILGKT----DVEIFSGAGVKESQDFKRE-VLEKGLPAKREITFETELFGSKTFLIYVEPVFSKSGETIGVNY  325 (1002)
Q Consensus       251 ~~~~~~e~iiGk~----~~e~~~~~~~~~~~~~~~~-vl~~g~~~~~e~~~~~~~~~~~~~~~~~~p~~~~~G~~~gi~~  325 (1002)
                      ..|++++++ |..    ....+++++.+........ ....+.+...++++..+.+...++.....++++.+|.++.+++
T Consensus        11 i~G~~~~~~-~~~~~~~~~~~ihpdD~~~~~~~~~~~~~~~~~~~~~e~R~~~~~G~~~wi~~~~~~~~d~~g~~~~~~G   89 (91)
T PF08447_consen   11 IFGYSPEEI-GKPDFEEWLERIHPDDRERVRQAIQQAALQNGEPFEIEYRIRRKDGEYRWIEVRGRPIFDENGKPIRIIG   89 (91)
T ss_dssp             HHTS-HHHH-TCBEHHHHHHHB-TTTHHHHHHHHHHHHHHTT-EEEEEEEEEGTTSTEEEEEEEEEEEETTTS-EEEEEE
T ss_pred             HhCCCHHHh-ccCCHHHHHhhcCHHHHHHHHHHHHHHhhccCcceEEEEEEECCCCCEEEEEEEEEEEECCCCCEEEEEE
Confidence            457888888 777    5566777777777776777 5666777777888877777778888999999999999998887


Q ss_pred             E
Q 039716          326 M  326 (1002)
Q Consensus       326 ~  326 (1002)
                      +
T Consensus        90 v   90 (91)
T PF08447_consen   90 V   90 (91)
T ss_dssp             E
T ss_pred             E
Confidence            6

The PAS fold appears in archaea, eubacteria and eukarya. The PAS domain contains a sensory box, or S-box domain that occupies the central portion of the PAS domain but is more widely distributed. It is often tandemly repeated. Known prosthetic groups bound in the S-box domain include haem in the oxygen sensor FixL [], FAD in the redox potential sensor NifL [], and a 4-hydroxycinnamyl chromophore in photoactive yellow protein []. Proteins containing the domain often contain other regulatory domains such as response regulator or sensor histidine kinase domains. Other S-box proteins include phytochromes and the aryl hydrocarbon receptor nuclear translocator. This domain has been found in the gene product of the madA gene of the filamentous zygomycete fungus Phycomyces blakesleeanus. It has been shown that MadA encodes a blue-light photoreceptor for phototropism and other light responses. The gene is involved in the phototropic responses associated with sporangiophore growth; they exhibit phototropism by bending toward near-UV and blue wavelengths and away from far-UV wavelengths in a manner that is physiologically similar to plant phototropic responses [].; GO: 0005515 protein binding; PDB: 3NJA_D 3H9W_A 3GDI_B 3ICY_A 3EEH_A 3MR0_B.

>PRK05559 DNA topoisomerase IV subunit B; Reviewed

Probab=93.13  E-value=0.18  Score=62.34  Aligned_cols=49  Identities=27%  Similarity=0.433  Sum_probs=33.5

Q ss_pred             EEEEEecCCCCCcCcHhh--------hhhhccCCCcc---ccCcCCC-ccccHHHHHHHHH
Q 039716          593 RCDVYDTGIGIPENALPT--------LFRKYMQVSAD---HARKYGG-TGLGLAICKQLVE  641 (1002)
Q Consensus       593 ~i~V~DtGiGI~~e~l~~--------IF~pF~q~~~~---~~~~~~G-tGLGLaI~k~Lve  641 (1002)
                      .|+|.|+|.|||.+..+.        +|..+..+..-   .....+| .|.||+.|.-+.+
T Consensus        70 ~I~V~DnGrGIP~~~~~~~~~~~~E~v~t~lhagsKf~~~~yk~SgGl~GvGls~vNalS~  130 (631)
T PRK05559         70 SVSVRDNGRGIPVGIHPEEGKSGVEVILTKLHAGGKFSNKAYKFSGGLHGVGVSVVNALSS  130 (631)
T ss_pred             cEEEEEcCCCCCcccccccCCcchheeeeeccccCccCCccccccCcccccchhhhhhhee
Confidence            377999999999999888        78764432211   1112233 6999999888854

>PRK05218 heat shock protein 90; Provisional

Probab=92.84  E-value=0.23  Score=61.19  Aligned_cols=47  Identities=15%  Similarity=0.268  Sum_probs=30.3

Q ss_pred             EEEEecCCCCCcCcHhhhhhhccCCC------------ccccCcCCCccccHHHHHHHH
Q 039716          594 CDVYDTGIGIPENALPTLFRKYMQVS------------ADHARKYGGTGLGLAICKQLV  640 (1002)
Q Consensus       594 i~V~DtGiGI~~e~l~~IF~pF~q~~------------~~~~~~~~GtGLGLaI~k~Lv  640 (1002)
                      |.|.|||+||+.+++...|...-+..            .....-.|-.|+|+.-|-.++
T Consensus        75 i~I~DnG~GMt~eel~~~l~~ia~Sg~~~f~~k~~~~~~~~~~~iG~fGiGf~S~f~va  133 (613)
T PRK05218         75 LTISDNGIGMTREEVIENLGTIAKSGTKEFLEKLKGDQKKDSQLIGQFGVGFYSAFMVA  133 (613)
T ss_pred             EEEEECCCCCCHHHHHHHHHhhccccchhHHHHhhcccccccccccccCcCchhhhhcc
Confidence            78999999999999998774433210            001122455789997555443

>PF14598 PAS_11: PAS domain; PDB: 1P97_A 3F1O_A 2A24_A 3H7W_A 3F1P_A 3H82_A 3F1N_A 4F3L_B 4DJ3_A 2KDK_A

Probab=92.23  E-value=1  Score=42.65  Aligned_cols=94  Identities=12%  Similarity=0.149  Sum_probs=64.7

Q ss_pred             EEEecccccEEEeecc----CCCCCcccccCCCchhccCccchhh-hhHHHHHHHHhCCCcceeEEEEEeecCceEEEEE
Q 039716          235 MGHQDKELRYRFIYNH----FPSLHEEDILGKTDVEIFSGAGVKE-SQDFKREVLEKGLPAKREITFETELFGSKTFLIY  309 (1002)
Q Consensus       235 i~~~d~~~~~~~~~~~----~~~~~~e~iiGk~~~e~~~~~~~~~-~~~~~~~vl~~g~~~~~e~~~~~~~~~~~~~~~~  309 (1002)
                      +..-+.++.+.++-..    +.|+.++|++|++.++++++.+... .....++++.+|.....-+++....++-.+....
T Consensus         5 ~trhs~dgki~~~d~~~v~~~lgy~~~eLvG~s~y~~~H~~D~~~~~~~~~~~~~~~g~~~~~~yR~~~k~g~~vwvqt~   84 (111)
T PF14598_consen    5 TTRHSLDGKITYVDSRAVSSLLGYLPEELVGRSIYDFVHPDDLQRVLKQHHREVLQKGQSVSPYYRFRTKNGGYVWVQTK   84 (111)
T ss_dssp             EEEEETTSBEEEEETTHHHHHHSS-HHHHTTSBGGGGBSCCTHHHHHHHHHHHHHHHSSEEEEEEEEE-TTSSEEEEEEE
T ss_pred             EEEECCCcEEEEEcCccChhhcCCCcHHHcCCchHHhCCHhhhhhHHHHHHHHHhhCCCcCcceEEEEecCCcEEEEEEE
Confidence            4456788999888655    2588999999999999999988886 7778889999998755556666655544444444


Q ss_pred             Eeeeec-CCCCEEEEEEEee
Q 039716          310 VEPVFS-KSGETIGVNYMGM  328 (1002)
Q Consensus       310 ~~p~~~-~~G~~~gi~~~~~  328 (1002)
                      ..+.++ .+++.-.++++-.
T Consensus        85 ~~~~~n~~~~~~~~Iv~~n~  104 (111)
T PF14598_consen   85 ATLFYNPWTSKPEFIVCTNT  104 (111)
T ss_dssp             EEEEEETTTTCEEEEEEEEE
T ss_pred             EEEEECCCCCCccEEEEEEE
Confidence            555554 3556555554443

...

>TIGR01501 MthylAspMutase methylaspartate mutase, S subunit

Probab=92.22  E-value=4.5  Score=39.67  Aligned_cols=108  Identities=10%  Similarity=0.065  Sum_probs=76.5

Q ss_pred             CHHHHHHHHHHHHhcCCeEEE---EcCHHHHHHHHHcCCCcEEEEcCCCCCCC--HHHHHHHHhccccCCCchhhhhhhh
Q 039716          868 NKINVMVAKSMMKQLGHSIDV---VNNGVEAVHAVQCQNYDLILMDVCMPVMD--GLKATRLIRSFEDTGNWDAAAEAGI  942 (1002)
Q Consensus       868 n~~n~~~l~~~L~~~g~~v~~---a~~G~eAl~~~~~~~~DlIlmDi~MP~md--G~e~~~~IR~~~~~~~~~~~~~~~~  942 (1002)
                      +..-..++..+|+..||+|..   ....++-++++.++.+|+|.+...|-..-  --++.+.+|+.              
T Consensus        14 HdiGk~iv~~~l~~~GfeVi~LG~~v~~e~~v~aa~~~~adiVglS~l~~~~~~~~~~~~~~l~~~--------------   79 (134)
T TIGR01501        14 HAVGNKILDHAFTNAGFNVVNLGVLSPQEEFIKAAIETKADAILVSSLYGHGEIDCKGLRQKCDEA--------------   79 (134)
T ss_pred             hhHhHHHHHHHHHHCCCEEEECCCCCCHHHHHHHHHHcCCCEEEEecccccCHHHHHHHHHHHHHC--------------
Confidence            345567889999999999875   36789999999999999999988774221  22344455541              


Q ss_pred             cccCCCCCCCCCCCCccEEEEcCCC--CHHH----HHHHHHcCCCEEEeCCCChHHHHHHHHhhc
Q 039716          943 EQAMPSSGSSNHFKRIPIIAMTANA--LSES----AEECFANGMDSFVSKPVTFQKLKECLEQYF 1001 (1002)
Q Consensus       943 ~~~~~~~~~~~~~~~ipIIalTa~~--~~~~----~~~~~~aG~d~~l~KP~~~~~L~~~l~~~l 1001 (1002)
                                 ....+ +|++-+..  ..++    ..++.+.|++......-.++++...|++.|
T Consensus        80 -----------gl~~~-~vivGG~~vi~~~d~~~~~~~l~~~Gv~~vF~pgt~~~~iv~~l~~~~  132 (134)
T TIGR01501        80 -----------GLEGI-LLYVGGNLVVGKQDFPDVEKRFKEMGFDRVFAPGTPPEVVIADLKKDL  132 (134)
T ss_pred             -----------CCCCC-EEEecCCcCcChhhhHHHHHHHHHcCCCEEECcCCCHHHHHHHHHHHh
Confidence                       11233 45566532  2222    346889999999999999999999988765

This model represents the S (sigma) subunit of methylaspartate mutase (glutamate mutase), a cobalamin-dependent enzyme that catalyzes the first step in a pathway of glutamate fermentation.

>COG2202 AtoS FOG: PAS/PAC domain [Signal transduction mechanisms]

Probab=90.91  E-value=3.5  Score=40.00  Aligned_cols=122  Identities=18%  Similarity=0.241  Sum_probs=70.4

Q ss_pred             HHHHHHHHHHHHHHHHhccCcEEEEecccccEEEeeccC---CCCCcccccCCCchhccCccchhh-hhHHHHHH-HHhC
Q 039716          213 LSQILKRADNFLHFVLQNAPVVMGHQDKELRYRFIYNHF---PSLHEEDILGKTDVEIFSGAGVKE-SQDFKREV-LEKG  287 (1002)
Q Consensus       213 ~~~~l~~~~~~l~~il~~~p~~i~~~d~~~~~~~~~~~~---~~~~~e~iiGk~~~e~~~~~~~~~-~~~~~~~v-l~~g  287 (1002)
                      ..+.++..+..++.++++.|.+++..|.++++.++|..+   .++...+.++....+......... ........ ....
T Consensus       103 ~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~n~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  182 (232)
T COG2202         103 AEEALRESEERLRALLEASPDGIWVLDEDGRILYANPAAEELLGYSPEEELGRGLSDLIHPEDEERRELELARALAEGRG  182 (232)
T ss_pred             HHHHHHHHHHHHHHHHhhCCceEEEEeCCCCEEEeCHHHHHHhCCChHHhcCCChhheEecCCCchhhHHHHHHhhccCC
Confidence            334444455558899999999999999999999998754   456655555666555543322211 11112222 2222


Q ss_pred             CCcceeEEEEEeecCc-eEEEEEEeeeecCCCCEEEEEEEeechhHHHH
Q 039716          288 LPAKREITFETELFGS-KTFLIYVEPVFSKSGETIGVNYMGMDVTDQVR  335 (1002)
Q Consensus       288 ~~~~~e~~~~~~~~~~-~~~~~~~~p~~~~~G~~~gi~~~~~DITe~~~  335 (1002)
                      .....+.......+.. ........+... .|.+.++.....|+++..+
T Consensus       183 ~~~~~~~~~~~~~g~~~~~~~~~~~~~~~-~~~~~~~~~~~~d~~~~~~  230 (232)
T COG2202         183 GPLEIEYRVRRKDGERVRWILSRISPVRD-DGEIVGVVGIARDITERKQ  230 (232)
T ss_pred             CCcceEEEEEecCCCEEEEEEeeeeEecC-CCceEEEEEEEechHHHhh
Confidence            2334444444433332 233333334333 6888888888899987643

>TIGR01055 parE_Gneg DNA topoisomerase IV, B subunit, proteobacterial

Probab=89.71  E-value=0.41  Score=59.00  Aligned_cols=49  Identities=20%  Similarity=0.426  Sum_probs=32.5

Q ss_pred             EEEEecCCCCCcCc--------Hhhhh-hhccCCCc--cccCcCCC-ccccHHHHHHHHHH
Q 039716          594 CDVYDTGIGIPENA--------LPTLF-RKYMQVSA--DHARKYGG-TGLGLAICKQLVEL  642 (1002)
Q Consensus       594 i~V~DtGiGI~~e~--------l~~IF-~pF~q~~~--~~~~~~~G-tGLGLaI~k~Lve~  642 (1002)
                      |+|.|+|.|||.+.        ++-+| .+....+-  ...+..+| .|.||+.+.-+.+.
T Consensus        64 I~V~DnGrGIp~~~h~~~g~~~~e~v~t~lhagsK~~~~~~~~SgG~~GvGls~vnalS~~  124 (625)
T TIGR01055        64 IEVFDNGRGMPVDIHPKEGVSAVEVILTTLHAGGKFSNKNYHFSGGLHGVGISVVNALSKR  124 (625)
T ss_pred             EEEEecCCccCcccccccCCcHHHHhhhcccccCCCCCCcceecCCCcchhHHHHHHhcCe
Confidence            68999999999988        77777 33221111  11112233 69999999988873

This protein is active as an alpha(2)beta(2) heterotetramer.

>PTZ00130 heat shock protein 90; Provisional

Probab=89.17  E-value=0.46  Score=59.25  Aligned_cols=48  Identities=21%  Similarity=0.339  Sum_probs=29.0

Q ss_pred             EEEEEecCCCCCcCcHhhhhh--------hccC---CCccccCcCCCccccHHHHHHHH
Q 039716          593 RCDVYDTGIGIPENALPTLFR--------KYMQ---VSADHARKYGGTGLGLAICKQLV  640 (1002)
Q Consensus       593 ~i~V~DtGiGI~~e~l~~IF~--------pF~q---~~~~~~~~~~GtGLGLaI~k~Lv  640 (1002)
                      .|+|.|||+||+.+.+..-+-        .|.+   .......-.|-.|+|++-|--++
T Consensus       136 tLtI~DnGIGMT~eEl~~nLgTIA~Sgt~~F~~~l~~~~~~~~lIGQFGVGFYSaFmVA  194 (814)
T PTZ00130        136 ILSITDTGIGMTKEDLINNLGTIAKSGTSNFLEAISKSGGDMSLIGQFGVGFYSAFLVA  194 (814)
T ss_pred             EEEEEECCCCCCHHHHHHHhhhhcccccHHHHHHhhccCCCcccccccccchhheeeec
Confidence            467999999999998764331        1211   00111223456799998775443

>COG0323 MutL DNA mismatch repair enzyme (predicted ATPase) [DNA replication, recombination, and repair]

Probab=88.85  E-value=0.45  Score=58.79  Aligned_cols=27  Identities=26%  Similarity=0.341  Sum_probs=24.4

Q ss_pred             EEEEEecCCCCCcCcHhhhhhhccCCC
Q 039716          593 RCDVYDTGIGIPENALPTLFRKYMQVS  619 (1002)
Q Consensus       593 ~i~V~DtGiGI~~e~l~~IF~pF~q~~  619 (1002)
                      .|.|.|||+||++++++-.+.++.+.+
T Consensus        54 ~I~V~DNG~Gi~~~Dl~la~~rHaTSK   80 (638)
T COG0323          54 LIRVRDNGSGIDKEDLPLALLRHATSK   80 (638)
T ss_pred             EEEEEECCCCCCHHHHHHHHhhhcccc
Confidence            478999999999999999999998764

>PF02310 B12-binding: B12 binding domain; InterPro: IPR006158 The cobalamin (vitamin B12) binding domain can bind two different forms of the cobalamin cofactor, with cobalt bonded either to a methyl group (methylcobalamin) or to 5'-deoxyadenosine (adenosylcobalamin)

Probab=88.40  E-value=3.3  Score=39.34  Aligned_cols=93  Identities=20%  Similarity=0.394  Sum_probs=63.4

Q ss_pred             CHHHHHHHHHHHHhcCCeEEEE---cCHHHHHHHHHcCCCcEEEEcC-CCCCC-CHHHHHHHHhccccCCCchhhhhhhh
Q 039716          868 NKINVMVAKSMMKQLGHSIDVV---NNGVEAVHAVQCQNYDLILMDV-CMPVM-DGLKATRLIRSFEDTGNWDAAAEAGI  942 (1002)
Q Consensus       868 n~~n~~~l~~~L~~~g~~v~~a---~~G~eAl~~~~~~~~DlIlmDi-~MP~m-dG~e~~~~IR~~~~~~~~~~~~~~~~  942 (1002)
                      .+.-...+..+|++.||+|...   .+..+..+.+...+||+|.+.. ..+.. ...++++.+|+               
T Consensus        13 ~~lGl~~la~~l~~~G~~v~~~d~~~~~~~l~~~~~~~~pd~V~iS~~~~~~~~~~~~l~~~~k~---------------   77 (121)
T PF02310_consen   13 HPLGLLYLAAYLRKAGHEVDILDANVPPEELVEALRAERPDVVGISVSMTPNLPEAKRLARAIKE---------------   77 (121)
T ss_dssp             TSHHHHHHHHHHHHTTBEEEEEESSB-HHHHHHHHHHTTCSEEEEEESSSTHHHHHHHHHHHHHT---------------
T ss_pred             hhHHHHHHHHHHHHCCCeEEEECCCCCHHHHHHHHhcCCCcEEEEEccCcCcHHHHHHHHHHHHh---------------
Confidence            3567788999999999999877   3567777888999999999998 44433 23455555554               


Q ss_pred             cccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHH--cCCCEEEeCC
Q 039716          943 EQAMPSSGSSNHFKRIPIIAMTANALSESAEECFA--NGMDSFVSKP  987 (1002)
Q Consensus       943 ~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~--aG~d~~l~KP  987 (1002)
                                 ..++++|++ -+.......+.+++  .|+|..+.-.
T Consensus        78 -----------~~p~~~iv~-GG~~~t~~~~~~l~~~~~~D~vv~Ge  112 (121)
T PF02310_consen   78 -----------RNPNIPIVV-GGPHATADPEEILREYPGIDYVVRGE  112 (121)
T ss_dssp             -----------TCTTSEEEE-EESSSGHHHHHHHHHHHTSEEEEEET
T ss_pred             -----------cCCCCEEEE-ECCchhcChHHHhccCcCcceecCCC
Confidence                       234565554 44444555566665  7988876543

Cobalamin-binding domains are mainly found in two families of enzymes present in animals and prokaryotes, which perform distinct kinds of reactions at the cobalt-carbon bond. Enzymes that require methylcobalamin carry out methyl transfer reactions. Enzymes that require adenosylcobalamin catalyse reactions in which the first step is the cleavage of adenosylcobalamin to form cob(II)alamin and the 5'-deoxyadenosyl radical, and thus act as radical generators. In both types of enzymes the B12-binding domain uses a histidine to bind the cobalt atom of cobalamin cofactors. This histidine is embedded in a DXHXXG sequence, the most conserved primary sequence motif of the domain [, , ]. Proteins containing the cobalamin-binding domain include: Animal and prokaryotic methionine synthase (2.1.1.13 from EC), which catalyse the transfer of a methyl group from methyl-cobalamin to homocysteine, yielding enzyme-bound cob(I)alamin and methionine. Animal and prokaryotic methylmalonyl-CoA mutase (5.4.99.2 from EC), which are involved in the degradation of several amino acids, odd-chain fatty acids and cholesterol via propionyl-CoA to the tricarboxylic acid cycle. Prokaryotic lysine 5,6-aminomutase (5.4.3.4 from EC). Prokaryotic glutamate mutase (5.4.99.1 from EC) []. Prokaryotic methyleneglutarate mutase (5.4.99.4 from EC). Prokaryotic isobutyryl-CoA mutase (5.4.99.13 from EC). The core structure of the cobalamin-binding domain is characterised by a five-stranded alpha/beta (Rossmann) fold, which consists of 5 parallel beta-sheets surrounded by 4-5 alpha helices in three layers (alpha/beta/alpha) []. Upon binding cobalamin, important elements of the binding site appear to become structured, including an alpha-helix that forms on one side of the cleft accommodating the nucleotide 'tail' of the cofactor. In cobalamin, the cobalt atom can be either free (dmb-off) or bound to dimethylbenzimidazole (dmb-on) according to the pH. When bound to the cobalamin-binding domain, the dimethylbenzimidazole ligand is replaced by the active histidine (His-on) of the DXHXXG motif. The replacement of dimethylbenzimidazole by histidine allows switching between the catalytic and activation cycles []. In methionine synthase the cobalamin cofactor is sandwiched between the cobalamin-binding domain and an approximately 90 residues N-terminal domain forming a helical bundle comprising two pairs of antiparallel helices []. In methionine synthase, there is a second, adjacent domain involved in cobalamin binding that forms a 4-helical bundle cap (IPR003759 from INTERPRO); in the conversion to the active conformation of this enzyme, the 4-helical cap rotates to allow the cobalamin cofactor to bind the activation domain (IPR004223 from INTERPRO) [].; GO: 0031419 cobalamin binding, 0046872 metal ion binding; PDB: 1Y80_A 3BUL_A 1K7Y_A 1BMT_A 3IV9_A 1K98_A 3IVA_A 3KP1_A 3KOW_A 3KOZ_A ....

>cd02070 corrinoid_protein_B12-BD B12 binding domain of corrinoid proteins

Probab=88.16  E-value=7.2  Score=41.03  Aligned_cols=100  Identities=14%  Similarity=0.140  Sum_probs=70.5

Q ss_pred             CCeEEEE----ecCHHHHHHHHHHHHhcCCeEEEE---cCHHHHHHHHHcCCCcEEEEcCCCCCC--CHHHHHHHHhccc
Q 039716          859 KPKILLV----EDNKINVMVAKSMMKQLGHSIDVV---NNGVEAVHAVQCQNYDLILMDVCMPVM--DGLKATRLIRSFE  929 (1002)
Q Consensus       859 ~~~ILiV----eDn~~n~~~l~~~L~~~g~~v~~a---~~G~eAl~~~~~~~~DlIlmDi~MP~m--dG~e~~~~IR~~~  929 (1002)
                      +.+||+.    |-+.+=..++..+|+..||+|...   ...++.++.+...+||+|.+-+.|+..  +..++++.+|+..
T Consensus        82 ~~~vl~~~~~gd~H~lG~~~v~~~l~~~G~~vi~lG~~~p~~~l~~~~~~~~~d~v~lS~~~~~~~~~~~~~i~~lr~~~  161 (201)
T cd02070          82 KGKVVIGTVEGDIHDIGKNLVATMLEANGFEVIDLGRDVPPEEFVEAVKEHKPDILGLSALMTTTMGGMKEVIEALKEAG  161 (201)
T ss_pred             CCeEEEEecCCccchHHHHHHHHHHHHCCCEEEECCCCCCHHHHHHHHHHcCCCEEEEeccccccHHHHHHHHHHHHHCC
Confidence            4578888    777777888999999999998753   356888889999999999999987754  2334455666421


Q ss_pred             cCCCchhhhhhhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEe
Q 039716          930 DTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVS  985 (1002)
Q Consensus       930 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~  985 (1002)
                                              ..++++|++=-+... .+  -+-..|+|.|-.
T Consensus       162 ------------------------~~~~~~i~vGG~~~~-~~--~~~~~GaD~~~~  190 (201)
T cd02070         162 ------------------------LRDKVKVMVGGAPVN-QE--FADEIGADGYAE  190 (201)
T ss_pred             ------------------------CCcCCeEEEECCcCC-HH--HHHHcCCcEEEC
Confidence                                    123566665554433 33  466679998864

A family of small methanogenic corrinoid proteins that bind methyl-Co(III) 5-hydroxybenzimidazolylcobamide as a cofactor. They play a role on the methanogenesis from trimethylamine, dimethylamine or monomethylamine, which is initiated by a series of corrinoid-dependent methyltransferases.

>cd02072 Glm_B12_BD B12 binding domain of glutamate mutase (Glm)

Probab=88.08  E-value=13  Score=36.13  Aligned_cols=105  Identities=11%  Similarity=0.043  Sum_probs=74.3

Q ss_pred             CHHHHHHHHHHHHhcCCeEEE---EcCHHHHHHHHHcCCCcEEEEcCCCCCC-C-HHHHHHHHhccccCCCchhhhhhhh
Q 039716          868 NKINVMVAKSMMKQLGHSIDV---VNNGVEAVHAVQCQNYDLILMDVCMPVM-D-GLKATRLIRSFEDTGNWDAAAEAGI  942 (1002)
Q Consensus       868 n~~n~~~l~~~L~~~g~~v~~---a~~G~eAl~~~~~~~~DlIlmDi~MP~m-d-G~e~~~~IR~~~~~~~~~~~~~~~~  942 (1002)
                      +.+-..++..+|+..||+|.-   ....++-++++.++++|+|.+...|... . .-++.+.+|+.              
T Consensus        12 HdiGkniv~~~L~~~GfeVidLG~~v~~e~~v~aa~~~~adiVglS~L~t~~~~~~~~~~~~l~~~--------------   77 (128)
T cd02072          12 HAVGNKILDHAFTEAGFNVVNLGVLSPQEEFIDAAIETDADAILVSSLYGHGEIDCKGLREKCDEA--------------   77 (128)
T ss_pred             hHHHHHHHHHHHHHCCCEEEECCCCCCHHHHHHHHHHcCCCEEEEeccccCCHHHHHHHHHHHHHC--------------
Confidence            345567889999999999875   3577889999999999999998877533 2 23455566642              


Q ss_pred             cccCCCCCCCCCCCCccEEEEcCCC--C----HHHHHHHHHcCCCEEEeCCCChHHHHHHHH
Q 039716          943 EQAMPSSGSSNHFKRIPIIAMTANA--L----SESAEECFANGMDSFVSKPVTFQKLKECLE  998 (1002)
Q Consensus       943 ~~~~~~~~~~~~~~~ipIIalTa~~--~----~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~  998 (1002)
                                 ....+||+ +-+..  .    .++..+..+.|++..+...-++.++...|+
T Consensus        78 -----------gl~~v~vi-vGG~~~i~~~d~~~~~~~L~~~Gv~~vf~pgt~~~~i~~~l~  127 (128)
T cd02072          78 -----------GLKDILLY-VGGNLVVGKQDFEDVEKRFKEMGFDRVFAPGTPPEEAIADLK  127 (128)
T ss_pred             -----------CCCCCeEE-EECCCCCChhhhHHHHHHHHHcCCCEEECcCCCHHHHHHHHh
Confidence                       11245544 44442  2    344567889999999998888888877665

Glutamate mutase catalysis the conversion of (S)-glutamate with (2S,3S)-3-methylaspartate. The rearrangement reaction is initiated by the extraction of a hydrogen from the protein-bound substrate by a 5'-desoxyadenosyl radical, which is generated by the homolytic cleavage of the organometallic bond of the cofactor B12. Glm is a heterotetrameric molecule consisting of two alpha and two epsilon polypeptide chains.

>TIGR01059 gyrB DNA gyrase, B subunit

Probab=88.07  E-value=0.76  Score=57.19  Aligned_cols=29  Identities=10%  Similarity=0.339  Sum_probs=20.4

Q ss_pred             cHHHHHHHHHHHHhhhhhcCCCC---eeEEEE
Q 039716          481 DVLRIRQILTNLISNAIKFTPEG---KVGIKL  509 (1002)
Q Consensus       481 D~~rL~QIL~NLlsNAIKfT~~G---~I~I~v  509 (1002)
                      |+.-|.+++.-||.|||+-...|   .|.|.+
T Consensus        27 ~~~gl~~vv~Elv~NaiDe~~ag~a~~I~V~i   58 (654)
T TIGR01059        27 GETGLHHLVYEVVDNSIDEAMAGYCDTINVTI   58 (654)
T ss_pred             CcchHHhhhHHhhhccccccccCCCCEEEEEE
Confidence            55678999999999999843334   444444

This model describes the common type II DNA topoisomerase (DNA gyrase). Two apparently independently arising families, one in the Proteobacteria and one in Gram-positive lineages, are both designated toposisomerase IV. Proteins scoring above the noise cutoff for this model and below the trusted cutoff for topoisomerase IV models probably should be designated GyrB.

>cd02069 methionine_synthase_B12_BD B12 binding domain of methionine synthase

Probab=87.90  E-value=5.4  Score=42.47  Aligned_cols=103  Identities=14%  Similarity=0.098  Sum_probs=71.9

Q ss_pred             CCeEEEE----ecCHHHHHHHHHHHHhcCCeEEEE---cCHHHHHHHHHcCCCcEEEEcCCCCCC--CHHHHHHHHhccc
Q 039716          859 KPKILLV----EDNKINVMVAKSMMKQLGHSIDVV---NNGVEAVHAVQCQNYDLILMDVCMPVM--DGLKATRLIRSFE  929 (1002)
Q Consensus       859 ~~~ILiV----eDn~~n~~~l~~~L~~~g~~v~~a---~~G~eAl~~~~~~~~DlIlmDi~MP~m--dG~e~~~~IR~~~  929 (1002)
                      ..+|++.    |.+.+=..++..+|+..||+|...   ...++.++.+.+.++|+|.+-..|+..  +--++++.+++. 
T Consensus        88 ~~~vvl~t~~gd~HdiG~~iv~~~l~~~G~~Vi~LG~~vp~e~~v~~~~~~~~~~V~lS~~~~~~~~~~~~~i~~L~~~-  166 (213)
T cd02069          88 KGKIVLATVKGDVHDIGKNLVGVILSNNGYEVIDLGVMVPIEKILEAAKEHKADIIGLSGLLVPSLDEMVEVAEEMNRR-  166 (213)
T ss_pred             CCeEEEEeCCCchhHHHHHHHHHHHHhCCCEEEECCCCCCHHHHHHHHHHcCCCEEEEccchhccHHHHHHHHHHHHhc-
Confidence            4578888    778888889999999999998865   357888889999999999999988732  123344555531 


Q ss_pred             cCCCchhhhhhhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHH---HHHcCCCEEEeCC
Q 039716          930 DTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEE---CFANGMDSFVSKP  987 (1002)
Q Consensus       930 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~---~~~aG~d~~l~KP  987 (1002)
                                               ..+++|++--+-...+....   |-..|+|.|-.=.
T Consensus       167 -------------------------~~~~~i~vGG~~~~~~~~~~~~~~~~~gad~y~~da  202 (213)
T cd02069         167 -------------------------GIKIPLLIGGAATSRKHTAVKIAPEYDGPVVYVKDA  202 (213)
T ss_pred             -------------------------CCCCeEEEEChhcCHHHHhhhhccccCCCceEecCH
Confidence                                     23577766555444444332   3457999886433

This domain binds methylcobalamin, which it uses as an intermediate methyl carrier from methyltetrahydrofolate (CH3H4folate) to homocysteine (Hcy).

>COG2461 Uncharacterized conserved protein [Function unknown]

Probab=86.98  E-value=2.2  Score=48.37  Aligned_cols=108  Identities=19%  Similarity=0.150  Sum_probs=74.7

Q ss_pred             HHHHHHHhccCcEEEEecccccEEEeecc--CCCCCcccccCCCchhccCccchhhhhHHHHHHHHhCCCcceeEEEEEe
Q 039716          222 NFLHFVLQNAPVVMGHQDKELRYRFIYNH--FPSLHEEDILGKTDVEIFSGAGVKESQDFKREVLEKGLPAKREITFETE  299 (1002)
Q Consensus       222 ~~l~~il~~~p~~i~~~d~~~~~~~~~~~--~~~~~~e~iiGk~~~e~~~~~~~~~~~~~~~~vl~~g~~~~~e~~~~~~  299 (1002)
                      +-+..++.+.|+=|...|.+.+++|.+..  .+..++ .++|++.....|+........ .-..+++|.....++..   
T Consensus       290 ~e~naif~~lP~Ditfvdk~diV~ffs~~~rif~rt~-sviGr~v~~chpPksv~iv~k-i~~~fksG~kd~~efw~---  364 (409)
T COG2461         290 EELNAIFKHLPVDITFVDKNDIVRFFSGGERIFPRTP-SVIGRRVQLCHPPKSVHIVEK-ILKDFKSGEKDFAEFWI---  364 (409)
T ss_pred             HHHHHHHhhCCCceEEecccceEEecCCcceecccCh-HhhCCcccCCCCCchHHHHHH-HHHHhhcCCcchHHHhc---
Confidence            45678899999989999999999886543  122233 368988777666644333322 22345566655555542   


Q ss_pred             ecCceEEEEEEeeeecCCCCEEEEEEEeechhHHH
Q 039716          300 LFGSKTFLIYVEPVFSKSGETIGVNYMGMDVTDQV  334 (1002)
Q Consensus       300 ~~~~~~~~~~~~p~~~~~G~~~gi~~~~~DITe~~  334 (1002)
                      .-+.+...+...+++|++|+-.|++-+..|||..+
T Consensus       365 ~~~~~~i~i~Y~av~de~ge~~g~le~~qdi~~i~  399 (409)
T COG2461         365 NMGDKFIHIRYFAVKDEEGEYLGTLEVVQDITRIK  399 (409)
T ss_pred             cCCCceEEEEEEEEEcCCCceeeeehhhhhhHHHH
Confidence            23556677888899999999999999999999654

>COG2185 Sbm Methylmalonyl-CoA mutase, C-terminal domain/subunit (cobalamin-binding) [Lipid metabolism]

Probab=86.10  E-value=18  Score=35.84  Aligned_cols=117  Identities=16%  Similarity=0.162  Sum_probs=84.1

Q ss_pred             CCCeEEEE----ecCHHHHHHHHHHHHhcCCeEEE---EcCHHHHHHHHHcCCCcEEEEcCCCCCCCHHHHHHHHhcccc
Q 039716          858 PKPKILLV----EDNKINVMVAKSMMKQLGHSIDV---VNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKATRLIRSFED  930 (1002)
Q Consensus       858 ~~~~ILiV----eDn~~n~~~l~~~L~~~g~~v~~---a~~G~eAl~~~~~~~~DlIlmDi~MP~mdG~e~~~~IR~~~~  930 (1002)
                      .+++||++    |-+..-..++...|+..||+|+.   ...+.|++.+..++..|+|.+-..  .-...+++..++..  
T Consensus        11 ~rprvlvak~GlDgHd~gakvia~~l~d~GfeVi~~g~~~tp~e~v~aA~~~dv~vIgvSsl--~g~h~~l~~~lve~--   86 (143)
T COG2185          11 ARPRVLVAKLGLDGHDRGAKVIARALADAGFEVINLGLFQTPEEAVRAAVEEDVDVIGVSSL--DGGHLTLVPGLVEA--   86 (143)
T ss_pred             CCceEEEeccCccccccchHHHHHHHHhCCceEEecCCcCCHHHHHHHHHhcCCCEEEEEec--cchHHHHHHHHHHH--
Confidence            45677775    77777889999999999999986   479999999998999999887542  23445666666542  


Q ss_pred             CCCchhhhhhhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHH
Q 039716          931 TGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLE  998 (1002)
Q Consensus       931 ~~~~~~~~~~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~  998 (1002)
                            .+++|.             .++. +++-+.-.+++.....+.|++.++.-=....+...-|.
T Consensus        87 ------lre~G~-------------~~i~-v~~GGvip~~d~~~l~~~G~~~if~pgt~~~~~~~~v~  134 (143)
T COG2185          87 ------LREAGV-------------EDIL-VVVGGVIPPGDYQELKEMGVDRIFGPGTPIEEALSDLL  134 (143)
T ss_pred             ------HHHhCC-------------cceE-EeecCccCchhHHHHHHhCcceeeCCCCCHHHHHHHHH
Confidence                  122222             2343 46778888888888889999999987666655544443

>PRK05644 gyrB DNA gyrase subunit B; Validated

Probab=85.81  E-value=1.4  Score=54.57  Aligned_cols=29  Identities=10%  Similarity=0.334  Sum_probs=21.1

Q ss_pred             cHHHHHHHHHHHHhhhhhcCCCC---eeEEEE
Q 039716          481 DVLRIRQILTNLISNAIKFTPEG---KVGIKL  509 (1002)
Q Consensus       481 D~~rL~QIL~NLlsNAIKfT~~G---~I~I~v  509 (1002)
                      |+.-|.+++.-||.||+.-...|   .|.|.+
T Consensus        34 ~~~gl~~~v~ElvdNaiDe~~ag~a~~I~V~i   65 (638)
T PRK05644         34 GERGLHHLVYEIVDNSIDEALAGYCDHIEVTI   65 (638)
T ss_pred             ChhhHHhhhHHhhhcccccccCCCCCEEEEEE
Confidence            56678999999999999844344   455544

>COG5381 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=85.48  E-value=2.2  Score=41.56  Aligned_cols=26  Identities=31%  Similarity=0.507  Sum_probs=21.5

Q ss_pred             HHHHHHHHhhhhhcCCCCeeEEEEEe
Q 039716          486 RQILTNLISNAIKFTPEGKVGIKLYV  511 (1002)
Q Consensus       486 ~QIL~NLlsNAIKfT~~G~I~I~v~~  511 (1002)
                      --+..-||.||+||...|.|.|.+.+
T Consensus        65 gYl~NELiENAVKfra~geIvieasl   90 (184)
T COG5381          65 GYLANELIENAVKFRATGEIVIEASL   90 (184)
T ss_pred             HHHHHHHHHhhhcccCCCcEEEEEEe
Confidence            34667899999999999998887754

>PF13188 PAS_8: PAS domain; PDB: 2JHE_D 3VOL_A

Probab=84.40  E-value=0.53  Score=39.32  Aligned_cols=48  Identities=17%  Similarity=0.189  Sum_probs=33.3

Q ss_pred             HHHHHHHhccCcEEEEecccccEEEeeccCCCCCcccccCCCchhccCc
Q 039716          222 NFLHFVLQNAPVVMGHQDKELRYRFIYNHFPSLHEEDILGKTDVEIFSG  270 (1002)
Q Consensus       222 ~~l~~il~~~p~~i~~~d~~~~~~~~~~~~~~~~~e~iiGk~~~e~~~~  270 (1002)
                      ++++.+++++|.+|+..| ++++.++|.++..+..-...|+....+++.
T Consensus         1 e~~~~l~~~~~~~i~i~d-~~~i~~~N~~~~~l~g~~~~~~~~~~~~~~   48 (64)
T PF13188_consen    1 ERYRSLFDNSPDGILIID-GGRIIYVNPAFEELFGYSLEGEDIGQLFPD   48 (64)
T ss_dssp             HHHHHHHCCSSSEEEEEE-TSBEEEE-HHHHHHHCS-HTCCCHHCTSTT
T ss_pred             CHHHHHHHcCccceEEEE-CCChHHhhHHHHHHhCCCCCCCCHHHhCcc
Confidence            367889999999999999 889999998764332222556665555443

>COG4999 Uncharacterized domain of BarA-like signal transduction histidine kinases [Signal transduction mechanisms]

Probab=83.19  E-value=4.2  Score=38.40  Aligned_cols=111  Identities=17%  Similarity=0.310  Sum_probs=80.0

Q ss_pred             CCCCeEEEEecCHHHHHHHHHHHHhcCCeEEEEcCHHHHHHHHHcCCCcEEEEcCCCCCCCHHHHHH--HHhccccCCCc
Q 039716          857 KPKPKILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKATR--LIRSFEDTGNW  934 (1002)
Q Consensus       857 ~~~~~ILiVeDn~~n~~~l~~~L~~~g~~v~~a~~G~eAl~~~~~~~~DlIlmDi~MP~mdG~e~~~--~IR~~~~~~~~  934 (1002)
                      ..+.+.+.||-|..-......+|...|.+|+.-..    +..+-...||.+|+.+-.+-..-..+-.  ..|..      
T Consensus         9 L~gk~LayiEpNstAA~~t~~iL~~tpleVtyr~t----~~~lp~~hYD~~Ll~vavtfr~n~tm~~~~l~~Al------   78 (140)
T COG4999           9 LAGKRLAYIEPNSTAAQCTLDILSETPLEVTYRPT----FSALPPAHYDMMLLGVAVTFRENLTMQHERLAKAL------   78 (140)
T ss_pred             hccceeEEecCccHHHHHHHHHHhcCCceEEeccc----ccccChhhhceeeecccccccCCchHHHHHHHHHH------
Confidence            45678999999999999999999999988876443    4445567899999999777655544322  12221      


Q ss_pred             hhhhhhhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHH
Q 039716          935 DAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECL  997 (1002)
Q Consensus       935 ~~~~~~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l  997 (1002)
                                         ...+--|+++-..+ .-..++....|+-++|.||++...|...+
T Consensus        79 -------------------~mtd~vilalPs~~-qv~AeqLkQ~g~~~CllKPls~~rLlptl  121 (140)
T COG4999          79 -------------------SMTDFVILALPSHA-QVNAEQLKQDGAGACLLKPLSSTRLLPTL  121 (140)
T ss_pred             -------------------hhhcceEEecCcHH-HHhHHHHhhcchHhHhhCcchhhhhHHHH
Confidence                               11233477776554 44567788999999999999999988733

>COG0326 HtpG Molecular chaperone, HSP90 family [Posttranslational modification, protein turnover, chaperones]

Probab=83.04  E-value=2.1  Score=51.77  Aligned_cols=49  Identities=18%  Similarity=0.416  Sum_probs=29.6

Q ss_pred             EEEEEecCCCCCcCcHhhhh--------hhccCC-Ccc--ccCcCCCccccHHHHHHHHH
Q 039716          593 RCDVYDTGIGIPENALPTLF--------RKYMQV-SAD--HARKYGGTGLGLAICKQLVE  641 (1002)
Q Consensus       593 ~i~V~DtGiGI~~e~l~~IF--------~pF~q~-~~~--~~~~~~GtGLGLaI~k~Lve  641 (1002)
                      +++|.||||||+.+++..-.        ..|... ...  .+.--|-.|+|++-|--+++
T Consensus        75 TLtI~DNGIGMT~~Ev~~~LgTIAkSgT~~F~~~l~~~~~~~~lIGQFGVGFYSaFmVAd  134 (623)
T COG0326          75 TLTISDNGIGMTKDEVIENLGTIAKSGTKEFLESLSEDQKDSDLIGQFGVGFYSAFMVAD  134 (623)
T ss_pred             EEEEEeCCCCCCHHHHHHHHHHhhhccHHHHHHHhccccccccccccccchhhheeeeee
Confidence            46799999999998875432        122221 111  11123567999998766553

>PF03709 OKR_DC_1_N: Orn/Lys/Arg decarboxylase, N-terminal domain; InterPro: IPR005308 This domain has a flavodoxin-like fold, and is termed the "wing" domain because of its position in the overall 3D structure

Probab=82.92  E-value=3.2  Score=39.59  Aligned_cols=91  Identities=11%  Similarity=0.091  Sum_probs=69.2

Q ss_pred             HHHHHHHHhcCCeEEEEcCHHHHHHHHHc-CCCcEEEEcCCCCC--CCHHHHHHHHhccccCCCchhhhhhhhcccCCCC
Q 039716          873 MVAKSMMKQLGHSIDVVNNGVEAVHAVQC-QNYDLILMDVCMPV--MDGLKATRLIRSFEDTGNWDAAAEAGIEQAMPSS  949 (1002)
Q Consensus       873 ~~l~~~L~~~g~~v~~a~~G~eAl~~~~~-~~~DlIlmDi~MP~--mdG~e~~~~IR~~~~~~~~~~~~~~~~~~~~~~~  949 (1002)
                      ..+...|++.|++|..+.+-.+|+..+.. ..++.|++|+. +.  ....++++.||..                     
T Consensus         7 ~~l~~~L~~~~~~vv~~~~~dd~~~~i~~~~~i~avvi~~d-~~~~~~~~~ll~~i~~~---------------------   64 (115)
T PF03709_consen    7 RELAEALEQRGREVVDADSTDDALAIIESFTDIAAVVISWD-GEEEDEAQELLDKIRER---------------------   64 (115)
T ss_dssp             HHHHHHHHHTTTEEEEESSHHHHHHHHHCTTTEEEEEEECH-HHHHHHHHHHHHHHHHH---------------------
T ss_pred             HHHHHHHHHCCCEEEEeCChHHHHHHHHhCCCeeEEEEEcc-cccchhHHHHHHHHHHh---------------------
Confidence            44677788889999999999999999987 57999999986 21  1235677888863                     


Q ss_pred             CCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCCh
Q 039716          950 GSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTF  990 (1002)
Q Consensus       950 ~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~  990 (1002)
                           ...+||.+++.....+..-...-.-+++|+-..-+-
T Consensus        65 -----~~~iPVFl~~~~~~~~~l~~~~l~~v~~~i~l~~~t  100 (115)
T PF03709_consen   65 -----NFGIPVFLLAERDTTEDLPAEVLGEVDGFIWLFEDT  100 (115)
T ss_dssp             -----STT-EEEEEESCCHHHCCCHHHHCCESEEEETTTTT
T ss_pred             -----CCCCCEEEEecCCCcccCCHHHHhhccEEEEecCCC
Confidence                 357999999987766666666677788898776543

Ornithine decarboxylase from Lactobacillus 30a (L30a OrnDC, P43099 from SWISSPROT) is representative of the large, pyridoxal-5'-phosphate-dependent decarboxylases that act on lysine, arginine or ornithine. The crystal structure of the L30a OrnDC has been solved to 3.0 A resolution. Six dimers related by C6 symmetry compose the enzymatically active dodecamer (approximately 106 Da). Each monomer of L30a OrnDC can be described in terms of five sequential folding domains. The amino-terminal domain, residues 1 to 107, consists of a five-stranded beta-sheet termed the "wing" domain. Two wing domains of each dimer project inward towards the centre of the dodecamer and contribute to dodecamer stabilisation [].; GO: 0016831 carboxy-lyase activity; PDB: 3Q16_C 3N75_A 1C4K_A 1ORD_A 2VYC_D.

>cd04728 ThiG Thiazole synthase (ThiG) is the tetrameric enzyme that is involved in the formation of the thiazole moiety of thiamin pyrophosphate, an essential ubiquitous cofactor that plays an important role in carbohydrate and amino acid metabolism

Probab=81.98  E-value=10  Score=40.92  Aligned_cols=87  Identities=14%  Similarity=0.176  Sum_probs=58.3

Q ss_pred             ecCHHHHHHHHHHHHhcCCeEE-EEcCHHHHHHHHHcCCCcEEEEcCCCC---------CCCHHHHHHHHhccccCCCch
Q 039716          866 EDNKINVMVAKSMMKQLGHSID-VVNNGVEAVHAVQCQNYDLILMDVCMP---------VMDGLKATRLIRSFEDTGNWD  935 (1002)
Q Consensus       866 eDn~~n~~~l~~~L~~~g~~v~-~a~~G~eAl~~~~~~~~DlIlmDi~MP---------~mdG~e~~~~IR~~~~~~~~~  935 (1002)
                      .|.....+..+.+. +.|+.|. ++.+-...-..+..-.+++|     ||         +..-.+.++.|++.       
T Consensus       107 pd~~~tv~aa~~L~-~~Gf~vlpyc~dd~~~ar~l~~~G~~~v-----mPlg~pIGsg~Gi~~~~~I~~I~e~-------  173 (248)
T cd04728         107 PDPIETLKAAEILV-KEGFTVLPYCTDDPVLAKRLEDAGCAAV-----MPLGSPIGSGQGLLNPYNLRIIIER-------  173 (248)
T ss_pred             cCHHHHHHHHHHHH-HCCCEEEEEeCCCHHHHHHHHHcCCCEe-----CCCCcCCCCCCCCCCHHHHHHHHHh-------
Confidence            34444444444444 4599877 55444444444455578877     77         22116777888752       


Q ss_pred             hhhhhhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEe
Q 039716          936 AAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVS  985 (1002)
Q Consensus       936 ~~~~~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~  985 (1002)
                                          ..+|||+=.+-..+++..+|++.|+|+++.
T Consensus       174 --------------------~~vpVI~egGI~tpeda~~AmelGAdgVlV  203 (248)
T cd04728         174 --------------------ADVPVIVDAGIGTPSDAAQAMELGADAVLL  203 (248)
T ss_pred             --------------------CCCcEEEeCCCCCHHHHHHHHHcCCCEEEE
Confidence                                358999999999999999999999999874

ThiG catalyzes the formation of thiazole from 1-deoxy-D-xylulose 5-phosphate (DXP) and dehydroglycine, with the help of the sulfur carrier protein ThiS that carries the sulfur needed for thiazole assembly on its carboxy terminus (ThiS-COSH).

>smart00433 TOP2c TopoisomeraseII

Probab=80.99  E-value=2.4  Score=52.28  Aligned_cols=48  Identities=27%  Similarity=0.408  Sum_probs=27.9

Q ss_pred             EEEEEecCCCCCcCcHh--------hhhhhccCCC---ccccC-cCCCccccHHHHHHHH
Q 039716          593 RCDVYDTGIGIPENALP--------TLFRKYMQVS---ADHAR-KYGGTGLGLAICKQLV  640 (1002)
Q Consensus       593 ~i~V~DtGiGI~~e~l~--------~IF~pF~q~~---~~~~~-~~~GtGLGLaI~k~Lv  640 (1002)
                      .|+|.|+|.|||-+..+        -+|.......   ..... ..|--|.||+.+.-+-
T Consensus        34 ~I~V~DnG~GIp~~~h~~~~~~~~e~v~~~lhag~kfd~~~~k~s~G~~G~Gls~vnalS   93 (594)
T smart00433       34 SISVEDNGRGIPVEIHPKEKKYAPEVIFTVLHAGGKFDDDAYKVSGGLHGVGASVVNALS   93 (594)
T ss_pred             eEEEEEeCCceeCCccCcCCCCcHHHhhhhhcccCCCCCCCccccCCcccchHHHHHHhc
Confidence            47899999999976543        2333332111   11111 1233699999988874

Eukaryotic DNA topoisomerase II, GyrB, ParE

>PRK09426 methylmalonyl-CoA mutase; Reviewed

Probab=80.76  E-value=19  Score=45.28  Aligned_cols=117  Identities=10%  Similarity=0.135  Sum_probs=81.4

Q ss_pred             CCeEEEE----ecCHHHHHHHHHHHHhcCCeEEEE---cCHHHHHHHHHcCCCcEEEEcCCCCCC--CHHHHHHHHhccc
Q 039716          859 KPKILLV----EDNKINVMVAKSMMKQLGHSIDVV---NNGVEAVHAVQCQNYDLILMDVCMPVM--DGLKATRLIRSFE  929 (1002)
Q Consensus       859 ~~~ILiV----eDn~~n~~~l~~~L~~~g~~v~~a---~~G~eAl~~~~~~~~DlIlmDi~MP~m--dG~e~~~~IR~~~  929 (1002)
                      .++|+|.    |.+..-..++..+|+..||+|+.-   .+.+++++.+....+|+|.+-..+...  ..-++++.+|...
T Consensus       582 rpkV~LatlG~d~H~~ra~fv~~~l~~~GfeV~~~~~~~s~e~~v~aa~~~~a~ivvlcs~d~~~~e~~~~l~~~Lk~~G  661 (714)
T PRK09426        582 RPRILVAKMGQDGHDRGAKVIATAFADLGFDVDIGPLFQTPEEAARQAVENDVHVVGVSSLAAGHKTLVPALIEALKKLG  661 (714)
T ss_pred             CceEEEEecCCcchhHhHHHHHHHHHhCCeeEecCCCCCCHHHHHHHHHHcCCCEEEEeccchhhHHHHHHHHHHHHhcC
Confidence            4566654    445556678899999999999643   457899999999999999875555432  2445667777521


Q ss_pred             cCCCchhhhhhhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHHhhc
Q 039716          930 DTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQYF 1001 (1002)
Q Consensus       930 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~~l 1001 (1002)
                                               .++++ |++.+...+++...+.++|+|+|+..=.+..+....+.+.|
T Consensus       662 -------------------------~~~v~-vl~GG~~~~~~~~~l~~aGvD~~i~~g~d~~~~L~~l~~~l  707 (714)
T PRK09426        662 -------------------------REDIM-VVVGGVIPPQDYDFLYEAGVAAIFGPGTVIADAAIDLLELL  707 (714)
T ss_pred             -------------------------CCCcE-EEEeCCCChhhHHHHHhCCCCEEECCCCCHHHHHHHHHHHH
Confidence                                     12343 34556545666677889999999998888877777666543

>TIGR03815 CpaE_hom_Actino helicase/secretion neighborhood CpaE-like protein

Probab=80.51  E-value=4.8  Score=45.63  Aligned_cols=84  Identities=20%  Similarity=0.123  Sum_probs=56.6

Q ss_pred             CCeEEEEcCHHHHHHHHHcCCCcEEEEcCCCCCCCHHHHHHHHhccccCCCchhhhhhhhcccCCCCCCCCCCCCccEE-
Q 039716          883 GHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPII-  961 (1002)
Q Consensus       883 g~~v~~a~~G~eAl~~~~~~~~DlIlmDi~MP~mdG~e~~~~IR~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipII-  961 (1002)
                      |..+..+.+..++-..+.  .-.+||+|..|       +...++...                       +  ++..+| 
T Consensus         1 ~~~~~~~~~~~~~~~~~~--~~~~v~~~~~~-------~~~~~~~~~-----------------------p--~~~~vv~   46 (322)
T TIGR03815         1 GVELDVAPDPEAARRAWA--RAPLVLVDADM-------AEACAAAGL-----------------------P--RRRRVVL   46 (322)
T ss_pred             CCceEEccCchhhhhccc--cCCeEEECchh-------hhHHHhccC-----------------------C--CCCCEEE
Confidence            566777777666544433  35789998654       112233211                       1  222345 


Q ss_pred             EEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHHhh
Q 039716          962 AMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQY 1000 (1002)
Q Consensus       962 alTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~~ 1000 (1002)
                      +++...+.+....++.+|+.+||.+|++..+|...|.+.
T Consensus        47 v~~~~~~~~~~~~a~~~Ga~~~l~~P~~~~~l~~~l~~~   85 (322)
T TIGR03815        47 VGGGEPGGALWRAAAAVGAEHVAVLPEAEGWLVELLADL   85 (322)
T ss_pred             EeCCCCCHHHHHHHHHhChhheeeCCCCHHHHHHHHHhh
Confidence            444456788899999999999999999999999988765

Members of this protein family belong to the MinD/ParA family of P-loop NTPases, and in particular show homology to the CpaE family of pilus assembly proteins (see PubMed:12370432). Nearly all members are found, not only in a gene context consistent with pilus biogenesis or a pilus-like secretion apparatus, but also near a DEAD/DEAH-box helicase, suggesting an involvement in DNA transfer activity. The model describes a clade restricted to the Actinobacteria.

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	1002
4euk_A	153	Crystal Structure Length = 153		1e-55
2ayx_A	254	Solution Structure Of The E.Coli Rcsc C-Terminus (R		2e-15
2ayz_A	133	Solution Structure Of The E.Coli Rcsc C-Terminus (R		1e-14
3c97_A	140	Crystal Structure Of The Response Regulator Receive		2e-13
2r25_B	133	Complex Of Ypd1 And Sln1-R1 With Bound Mg2+ And Bef		2e-12
1oxb_B	134	Complex Between Ypd1 And Sln1 Response Regulator Do		2e-12
3sl2_A	177	Atp Forms A Stable Complex With The Essential Histi		3e-11
2c2a_A	258	Structure Of The Entire Cytoplasmic Portion Of A Se		2e-10
3dge_A	258	Structure Of A Histidine Kinase-response Regulator		2e-10
3m6m_D	143	Crystal Structure Of Rpff Complexed With Rec Domain		1e-08
3kht_A	144	Crystal Structure Of Response Regulator From Hahell		9e-08
4ew8_A	268	Crystal Structure Of A C-Terminal Part Of Tyrosine		9e-08
1m5t_A	124	Crystal Structure Of The Response Regulator Divk Le		1e-07
3mm4_A	206	Crystal Structure Of The Receiver Domain Of The His		2e-07
1ab5_A	125	Structure Of Chey Mutant F14n, V21t Length = 125		3e-07
1ab6_A	125	Structure Of Chey Mutant F14n, V86t Length = 125		5e-07
3fgz_A	128	Crystal Structure Of Chey Triple Mutant F14e, N59m,		1e-06
1ymv_A	129	Signal Transduction Protein Chey Mutant With Phe 14		2e-06
1udr_A	129	Chey Mutant With Lys 91 Replaced By Asp, Lys 92 Rep		2e-06
3ffx_A	128	Crystal Structure Of Chey Triple Mutant F14e, N59r,		2e-06
3fft_A	128	Crystal Structure Of Chey Double Mutant F14e, E89r		2e-06
3rvj_A	132	Structure Of The Chey-Bef3 Complex With Substitutio		2e-06
1ymu_A	130	Signal Transduction Protein Chey Mutant With Met 17		2e-06
1d4z_A	128	Crystal Structure Of Chey-95iv, A Hyperactive Chey		3e-06
3ffw_A	128	Crystal Structure Of Chey Triple Mutant F14q, N59k,		3e-06
3f7n_A	128	Crystal Structure Of Chey Triple Mutant F14e, N59m,		3e-06
1djm_A	129	Solution Structure Of Bef3-Activated Chey From Esch		4e-06
1eay_A	128	Chey-Binding (P2) Domain Of Chea In Complex With Ch		4e-06
1cye_A	129	Three Dimensional Structure Of Chemotactic Che Y Pr		4e-06
1cey_A	128	Assignments, Secondary Structure, Global Fold, And		4e-06
3rvp_A	132	Structure Of The Chey-Bef3 Complex With Substitutio		4e-06
3rvl_A	132	Structure Of The Chey-Bef3 Complex With Substitutio		4e-06
1mih_A	129	A Role For Chey Glu 89 In Chez-Mediated Dephosphory		5e-06
2chy_A	128	Three-Dimensional Structure Of Chey, The Response R		5e-06
3gt7_A	154	Crystal Structure Of Signal Receiver Domain Of Sign		6e-06
3myy_A	128	Structure Of E. Coli Chey Mutant A113p Bound To Ber		6e-06
3oo0_A	129	Structure Of Apo Chey A113p Length = 129		6e-06
3rvn_A	132	Structure Of The Chey-Bef3 Complex With Substitutio		6e-06
2fka_A	129	Crystal Structure Of Mg(2+) And Bef(3)(-)-Bound Che		6e-06
2che_A	128	Structure Of The Mg2+-Bound Form Of Chey And Mechan		6e-06
5chy_A	128	Structure Of Chemotaxis Protein Chey Length = 128		6e-06
1e6k_A	130	Two-Component Signal Transduction System D12a Mutan		7e-06
3olx_A	129	Structural And Functional Effects Of Substitution A		9e-06
3olw_A	129	Structural And Functional Effects Of Substitution A		1e-05
3olv_A	129	Structural And Functional Effects Of Substitution A		1e-05
1jbe_A	128	1.08 A Structure Of Apo-Chey Reveals Meta-Active Co		1e-05
3oly_A	129	Structural And Functional Effects Of Substitution A		2e-05
1vlz_A	128	Uncoupled Phosphorylation And Activation In Bacteri		2e-05
1e6l_A	127	Two-Component Signal Transduction System D13a Mutan		2e-05
1ehc_A	128	Structure Of Signal Transduction Protein Chey Lengt		2e-05
3to5_A	134	High Resolution Structure Of Chey3 From Vibrio Chol		2e-05
1dcf_A	136	Crystal Structure Of The Receiver Domain Of The Eth		2e-05
3i42_A	127	Structure Of Response Regulator Receiver Domain (Ch		2e-05
6chy_A	128	Structure Of Chemotaxis Protein Chey Length = 128		2e-05
1zdm_A	129	Crystal Structure Of Activated Chey Bound To Xe Len		3e-05
1c4w_A	128	1.9 A Structure Of A-Thiophosphonate Modified Chey		3e-05
1hey_A	128	Investigating The Structural Determinants Of The P2		3e-05
1e6m_A	128	Two-Component Signal Transduction System D57a Mutan		3e-05
3h1g_A	129	Crystal Structure Of Chey Mutant T84a Of Helicobact		1e-04
2id7_A	128	1.75 A Structure Of T87i Phosphono-Chey Length = 12		1e-04
3dge_C	122	Structure Of A Histidine Kinase-response Regulator		1e-04
2id9_A	128	1.85 A Structure Of T87iY106W PHOSPHONO-Chey Length		2e-04
3gwg_A	129	Crystal Structure Of Chey Of Helicobacter Pylori Le		3e-04
3d36_A	244	How To Switch Off A Histidine Kinase: Crystal Struc		5e-04
1u8t_A	128	Crystal Structure Of Chey D13k Y106w Alone And In C		6e-04
3a0r_A	349	Crystal Structure Of Histidine Kinase Thka (Tm1359)		6e-04

>pdb|4EUK|A Chain A, Crystal Structure Length = 153

Iteration: 1
 Score =  215 bits (547), Expect = 1e-55,   Method: Compositional matrix adjust.
 Identities = 100/146 (68%), Positives = 121/146 (82%), Gaps = 10/146 (6%)
Query: 862  ILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKA 921
            ILLVEDNKIN+MVAKSMMKQLGH++D+ NNGVEA+ A+   +YDL+LMDVCMPV+DGLKA
Sbjct: 11   ILLVEDNKINIMVAKSMMKQLGHTMDIANNGVEAITAINSSSYDLVLMDVCMPVLDGLKA 70
Query: 922  TRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNH------FKRIPIIAMTANALSESAEEC 975
            TRLIRS+E+TGNW+AA EAG++     S S N         R+PIIAMTAN L+ES+EEC
Sbjct: 71   TRLIRSYEETGNWNAAIEAGVD----ISTSENEQVCMRPTNRLPIIAMTANTLAESSEEC 126
Query: 976  FANGMDSFVSKPVTFQKLKECLEQYF 1001
            +ANGMDSF+SKPVT QKL+ECL+QY 
Sbjct: 127  YANGMDSFISKPVTLQKLRECLQQYL 152

>pdb|2AYX|A Chain A, Solution Structure Of The E.Coli Rcsc C-Terminus (Residues 700-949) Containing Linker Region And Phosphoreceiver Domain Length = 254

Iteration: 1
 Score = 81.6 bits (200), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 46/139 (33%), Positives = 71/139 (51%), Gaps = 26/139 (18%)
Query: 862  ILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKA 921
            IL+V+D+ IN  +    +  LG+     N+GV+A++ +   + D++L DV MP MDG + 
Sbjct: 132  ILVVDDHPINRRLLADQLGSLGYQCKTANDGVDALNVLSKNHIDIVLSDVNMPNMDGYRL 191
Query: 922  TRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMD 981
            T+ IR    T                          +P+I +TANAL+E  + C  +GMD
Sbjct: 192  TQRIRQLGLT--------------------------LPVIGVTANALAEEKQRCLESGMD 225
Query: 982  SFVSKPVTFQKLKECLEQY 1000
            S +SKPVT   +K+ L  Y
Sbjct: 226  SCLSKPVTLDVIKQTLTLY 244

>pdb|2AYZ|A Chain A, Solution Structure Of The E.Coli Rcsc C-Terminus (Residues 817-949) Containing Phosphoreceiver Domain Length = 133

Iteration: 1
 Score = 79.0 bits (193), Expect = 1e-14,   Method: Composition-based stats.
 Identities = 46/139 (33%), Positives = 71/139 (51%), Gaps = 26/139 (18%)
Query: 862  ILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKA 921
            IL+V+D+ IN  +    +  LG+     N+GV+A++ +   + D++L DV MP MDG + 
Sbjct: 11   ILVVDDHPINRRLLADQLGSLGYQCKTANDGVDALNVLSKNHIDIVLSDVNMPNMDGYRL 70
Query: 922  TRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMD 981
            T+ IR    T                          +P+I +TANAL+E  + C  +GMD
Sbjct: 71   TQRIRQLGLT--------------------------LPVIGVTANALAEEKQRCLESGMD 104
Query: 982  SFVSKPVTFQKLKECLEQY 1000
            S +SKPVT   +K+ L  Y
Sbjct: 105  SCLSKPVTLDVIKQTLTLY 123

>pdb|3C97|A Chain A, Crystal Structure Of The Response Regulator Receiver Domain Of A Signal Transduction Histidine Kinase From Aspergillus Oryzae Length = 140

Iteration: 1
 Score = 75.5 bits (184), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 45/134 (33%), Positives = 73/134 (54%), Gaps = 24/134 (17%)
Query: 862 ILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKA 921
           +L+ EDN I  +VA   +++  + I VV NG++A+ A Q + +D+I+MD+ MPVMDGL+A
Sbjct: 13  VLIAEDNDICRLVAAKALEKCTNDITVVTNGLQALQAYQNRQFDVIIMDIQMPVMDGLEA 72
Query: 922 TRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMD 981
              IR++E T N                      KR  IIA+TA+ + +         +D
Sbjct: 73  VSEIRNYERTHNT---------------------KRASIIAITADTIDDDRP---GAELD 108
Query: 982 SFVSKPVTFQKLKE 995
            +VSKP+   +L++
Sbjct: 109 EYVSKPLNPNQLRD 122

>pdb|2R25|B Chain B, Complex Of Ypd1 And Sln1-R1 With Bound Mg2+ And Bef3- Length = 133

Iteration: 1
 Score = 71.6 bits (174), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 50/145 (34%), Positives = 75/145 (51%), Gaps = 31/145 (21%)
Query: 862  ILLVEDNKINVMVAKSMMKQLG-HSIDVVNNGVEAVHAVQ-----CQNYDLILMDVCMPV 915
            IL+VEDN +N  V K M+   G  +I++  +G EA   V+      +NY++I MDV MP 
Sbjct: 5    ILVVEDNHVNQEVIKRMLNLEGIENIELACDGQEAFDKVKELTSKGENYNMIFMDVQMPK 64
Query: 916  MDGLKATRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEEC 975
            +DGL +T++IR   D G                          PI+A+TA A   + +EC
Sbjct: 65   VDGLLSTKMIR--RDLGYTS-----------------------PIVALTAFADDSNIKEC 99
Query: 976  FANGMDSFVSKPVTFQKLKECLEQY 1000
              +GM+ F+SKP+   KLK  L ++
Sbjct: 100  LESGMNGFLSKPIKRPKLKTILTEF 124

>pdb|1OXB|B Chain B, Complex Between Ypd1 And Sln1 Response Regulator Domain In Space Group P2(1)2(1)2(1) Length = 134

Iteration: 1
 Score = 71.6 bits (174), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 50/145 (34%), Positives = 75/145 (51%), Gaps = 31/145 (21%)
Query: 862  ILLVEDNKINVMVAKSMMKQLG-HSIDVVNNGVEAVHAVQ-----CQNYDLILMDVCMPV 915
            IL+VEDN +N  V K M+   G  +I++  +G EA   V+      +NY++I MDV MP 
Sbjct: 4    ILVVEDNHVNQEVIKRMLNLEGIENIELACDGQEAFDKVKELTSKGENYNMIFMDVQMPK 63
Query: 916  MDGLKATRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEEC 975
            +DGL +T++IR   D G                          PI+A+TA A   + +EC
Sbjct: 64   VDGLLSTKMIR--RDLGYTS-----------------------PIVALTAFADDSNIKEC 98
Query: 976  FANGMDSFVSKPVTFQKLKECLEQY 1000
              +GM+ F+SKP+   KLK  L ++
Sbjct: 99   LESGMNGFLSKPIKRPKLKTILTEF 123

>pdb|3SL2|A Chain A, Atp Forms A Stable Complex With The Essential Histidine Kinase Walk (yycg) Domain Length = 177

Iteration: 1
 Score = 67.8 bits (164), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 32/71 (45%), Positives = 44/71 (61%)
Query: 596 VYDTGIGIPENALPTLFRKYMQVSADHARKYGGTGLGLAICKQLVELMGGRLTVTSKVHC 655
           V D GIGIP+  +  +F ++ +V     RK GGTGLGLAI K++V+  GG +   S    
Sbjct: 82  VKDEGIGIPKKDVEKVFDRFYRVDKARTRKLGGTGLGLAIAKEMVQAHGGDIWADSIEGK 141
Query: 656 GSTFTFILPYQ 666
           G+T TF LPY+
Sbjct: 142 GTTITFTLPYK 152

>pdb|2C2A|A Chain A, Structure Of The Entire Cytoplasmic Portion Of A Sensor Histidine Kinase Protein Length = 258

Iteration: 1
 Score = 65.1 bits (157), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 32/69 (46%), Positives = 45/69 (65%)
Query: 596 VYDTGIGIPENALPTLFRKYMQVSADHARKYGGTGLGLAICKQLVELMGGRLTVTSKVHC 655
           V D GIGIP++A   +F ++ +V +    +  GTGLGLAI K++VEL GGR+ V S+V  
Sbjct: 178 VEDNGIGIPDHAKDRIFEQFYRVDSSLTYEVPGTGLGLAITKEIVELHGGRIWVESEVGK 237
Query: 656 GSTFTFILP 664
           GS F   +P
Sbjct: 238 GSRFFVWIP 246

>pdb|3DGE|A Chain A, Structure Of A Histidine Kinase-response Regulator Complex Reveals Insights Into Two-component Signaling And A Novel Cis- Autophosphorylation Mechanism Length = 258

Iteration: 1
 Score = 65.1 bits (157), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 32/69 (46%), Positives = 45/69 (65%)
Query: 596 VYDTGIGIPENALPTLFRKYMQVSADHARKYGGTGLGLAICKQLVELMGGRLTVTSKVHC 655
           V D GIGIP++A   +F ++ +V +    +  GTGLGLAI K++VEL GGR+ V S+V  
Sbjct: 178 VEDNGIGIPDHAKDRIFEQFYRVDSSLTYEVPGTGLGLAITKEIVELHGGRIWVESEVGK 237
Query: 656 GSTFTFILP 664
           GS F   +P
Sbjct: 238 GSRFFVWIP 246

>pdb|3M6M|D Chain D, Crystal Structure Of Rpff Complexed With Rec Domain Of Rpfc Length = 143

Iteration: 1
 Score = 59.3 bits (142), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 32/136 (23%), Positives = 68/136 (50%), Gaps = 22/136 (16%)
Query: 862 ILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKA 921
           +L+ +D++ N MV + ++++ GH +  VN   + + A+  ++YD +++D+ MP M+GL  
Sbjct: 17  MLVADDHEANRMVLQRLLEKAGHKVLCVNGAEQVLDAMAEEDYDAVIVDLHMPGMNGLDM 76
Query: 922 TRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMD 981
            + +R  + +G                       +  P++ ++A+   E+   C   G  
Sbjct: 77  LKQLRVMQASG----------------------MRYTPVVVLSADVTPEAIRACEQAGAR 114
Query: 982 SFVSKPVTFQKLKECL 997
           +F++KPV   KL + L
Sbjct: 115 AFLAKPVVAAKLLDTL 130

>pdb|3KHT|A Chain A, Crystal Structure Of Response Regulator From Hahella Chejuensis Length = 144

Iteration: 1
 Score = 56.2 bits (134), Expect = 9e-08,   Method: Composition-based stats.
 Identities = 33/127 (25%), Positives = 63/127 (49%), Gaps = 26/127 (20%)
Query: 862 ILLVEDNKINVMVAKSMM--KQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGL 919
           +L+VEDN  ++ + + ++  K +   ++ V+NG +A++ VQ   YDLI++D+ +P+ +G 
Sbjct: 8   VLVVEDNPDDIALIRRVLDRKDIHCQLEFVDNGAKALYQVQQAKYDLIILDIGLPIANGF 67
Query: 920 KATRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANG 979
           +    +R                       G++ H    PI+ +T N   + A++C A G
Sbjct: 68  EVXSAVR---------------------KPGANQH---TPIVILTDNVSDDRAKQCXAAG 103
Query: 980 MDSFVSK 986
             S V K
Sbjct: 104 ASSVVDK 110

>pdb|4EW8|A Chain A, Crystal Structure Of A C-Terminal Part Of Tyrosine Kinase (Divl) From Caulobacter Crescentus Cb15 At 2.50 A Resolution Length = 268

Iteration: 1
 Score = 56.2 bits (134), Expect = 9e-08,   Method: Composition-based stats.
 Identities = 33/78 (42%), Positives = 44/78 (56%), Gaps = 6/78 (7%)
Query: 592 IRCDVYDTGIGIPENALPTLFRKYMQVSADHARKYGGTGLGLAICKQLVELMGGRLTVTS 651
           +R DV DTG G+P +    +F +++       R  GG GLGLA+ K LVEL GG + + S
Sbjct: 188 VRLDVSDTGRGVPFHVQAHIFDRFV------GRDRGGPGLGLALVKALVELHGGWVALES 241
Query: 652 KVHCGSTFTFILPYQVSP 669
           +   GSTFT  LP    P
Sbjct: 242 EPGNGSTFTCHLPETQQP 259

>pdb|1M5T|A Chain A, Crystal Structure Of The Response Regulator Divk Length = 124

Iteration: 1
 Score = 56.2 bits (134), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 32/140 (22%), Positives = 67/140 (47%), Gaps = 24/140 (17%)
Query: 862  ILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKA 921
            +L+VEDN++N+ +   +++  G+       G+ A+   +    DLILMD+ +P + GL+ 
Sbjct: 4    VLIVEDNELNMKLFHDLLEAQGYETLQTREGLSALSIARENKPDLILMDIQLPEISGLEV 63
Query: 922  TRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMD 981
            T+ ++  +D  +                        IP++A+TA A+    E     G +
Sbjct: 64   TKWLKEDDDLAH------------------------IPVVAVTAFAMKGDEERIREGGCE 99
Query: 982  SFVSKPVTFQKLKECLEQYF 1001
            +++SKP++     E +++  
Sbjct: 100  AYISKPISVVHFLETIKRLL 119

>pdb|3MM4|A Chain A, Crystal Structure Of The Receiver Domain Of The Histidine Kinase Cki1 From Arabidopsis Thaliana Length = 206

Iteration: 1
 Score = 55.1 bits (131), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 43/140 (30%), Positives = 65/140 (46%), Gaps = 37/140 (26%)
Query: 862 ILLVEDNKINVMVAKSMMKQLGHS-IDVVNNGVEAVH-------------AVQCQNYDLI 907
           +L+V+DN I+  VA   +K++G S ++  ++G EA+              +V    +D I
Sbjct: 64  VLVVDDNFISRKVATGKLKKMGVSEVEQCDSGKEALRLVTEGLTQREEQGSVDKLPFDYI 123
Query: 908 LMDVCMPVMDGLKATRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTA-N 966
            MD  MP MDG +ATR IR  E                       ++  R PIIA++  +
Sbjct: 124 FMDCQMPEMDGYEATREIRKVE----------------------KSYGVRTPIIAVSGHD 161
Query: 967 ALSESAEECFANGMDSFVSK 986
             SE A E    GMD+F+ K
Sbjct: 162 PGSEEARETIQAGMDAFLDK 181

>pdb|1AB5|A Chain A, Structure Of Chey Mutant F14n, V21t Length = 125

Iteration: 1
 Score = 54.3 bits (129), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 38/140 (27%), Positives = 68/140 (48%), Gaps = 25/140 (17%)
Query: 863  LLVEDNKINVMVAKSMMKQLG-HSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKA 921
            L+V+DN     + ++++K+LG ++++   +GV+A++ +Q   Y  ++ D  MP MDGL+ 
Sbjct: 5    LVVDDNSTMRRITRNLLKELGFNNVEEAEDGVDALNKLQAGGYGFVISDWNMPNMDGLEL 64
Query: 922  TRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMD 981
             + IR+       D A  A                 +P++ +TA A  E+       G  
Sbjct: 65   LKTIRA-------DGAMSA-----------------LPVLMVTAEAKKENIIAAAQAGAS 100
Query: 982  SFVSKPVTFQKLKECLEQYF 1001
             +V KP T   L+E L + F
Sbjct: 101  GYVVKPFTAATLEEKLNKIF 120

>pdb|1AB6|A Chain A, Structure Of Chey Mutant F14n, V86t Length = 125

Iteration: 1
 Score = 53.5 bits (127), Expect = 5e-07,   Method: Composition-based stats.
 Identities = 38/140 (27%), Positives = 67/140 (47%), Gaps = 25/140 (17%)
Query: 863  LLVEDNKINVMVAKSMMKQLG-HSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKA 921
            L+V+DN     + ++++K+LG ++++   +GV+A++ +Q   Y  ++ D  MP MDGL+ 
Sbjct: 5    LVVDDNSTMRRIVRNLLKELGFNNVEEAEDGVDALNKLQAGGYGFVISDWNMPNMDGLEL 64
Query: 922  TRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMD 981
             + IR+       D A  A                 +P++  TA A  E+       G  
Sbjct: 65   LKTIRA-------DGAMSA-----------------LPVLMTTAEAKKENIIAAAQAGAS 100
Query: 982  SFVSKPVTFQKLKECLEQYF 1001
             +V KP T   L+E L + F
Sbjct: 101  GYVVKPFTAATLEEKLNKIF 120

>pdb|3FGZ|A Chain A, Crystal Structure Of Chey Triple Mutant F14e, N59m, E89r Complexed With Bef3- And Mn2+ Length = 128

Iteration: 1
 Score = 52.0 bits (123), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 37/140 (26%), Positives = 67/140 (47%), Gaps = 25/140 (17%)
Query: 863  LLVEDNKINVMVAKSMMKQLG-HSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKA 921
            L+V+D      + ++++K+LG ++++   +GV+A++ +Q   Y  ++ D  MP MDGL+ 
Sbjct: 8    LVVDDESTMRRIVRNLLKELGFNNVEEAEDGVDALNKLQAGGYGFVISDWMMPNMDGLEL 67
Query: 922  TRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMD 981
             + IR+       D A  A                 +P++ +TA A  E+       G  
Sbjct: 68   LKTIRA-------DGAMSA-----------------LPVLMVTARAKKENIIAAAQAGAS 103
Query: 982  SFVSKPVTFQKLKECLEQYF 1001
             +V KP T   L+E L + F
Sbjct: 104  GYVVKPFTAATLEEKLNKIF 123

>pdb|1YMV|A Chain A, Signal Transduction Protein Chey Mutant With Phe 14 Replaced By Gly, Ser 15 Replaced By Gly, And Met 17 Replaced By Gly Length = 129

Iteration: 1
 Score = 52.0 bits (123), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 37/140 (26%), Positives = 67/140 (47%), Gaps = 25/140 (17%)
Query: 863  LLVEDNKINVMVAKSMMKQLG-HSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKA 921
            L+V+D      + ++++K+LG ++++   +GV+A++ +Q   Y  ++ D  MP MDGL+ 
Sbjct: 9    LVVDDGGTGRRIVRNLLKELGFNNVEEAEDGVDALNKLQAGGYGFVISDWNMPNMDGLEL 68
Query: 922  TRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMD 981
             + IR+       D A  A                 +P++ +TA A  E+       G  
Sbjct: 69   LKTIRA-------DGAMSA-----------------LPVLMVTAEAKKENIIAAAQAGAS 104
Query: 982  SFVSKPVTFQKLKECLEQYF 1001
             +V KP T   L+E L + F
Sbjct: 105  GYVVKPFTAATLEEKLNKIF 124

>pdb|1UDR|A Chain A, Chey Mutant With Lys 91 Replaced By Asp, Lys 92 Replaced By Ala, Ile 96 Replaced By Lys And Ala 98 Replaced By Leu (Stabilizing Mutations In Helix 4) Length = 129

Iteration: 1
 Score = 52.0 bits (123), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 37/140 (26%), Positives = 69/140 (49%), Gaps = 25/140 (17%)
Query: 863  LLVEDNKINVMVAKSMMKQLG-HSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKA 921
            L+V+D      + ++++K+LG ++++   +GV+A++ +Q   Y  ++ D  MP MDGL+ 
Sbjct: 9    LVVDDFSTMRRIVRNLLKELGFNNVEEAEDGVDALNKLQAGGYGFVISDWNMPNMDGLEL 68
Query: 922  TRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMD 981
             + IR+       D A  A                 +P++ +TA A +E+ +     G  
Sbjct: 69   LKTIRA-------DGAMSA-----------------LPVLMVTAEADAENIKALAQAGAS 104
Query: 982  SFVSKPVTFQKLKECLEQYF 1001
             +V KP T   L+E L + F
Sbjct: 105  GYVVKPFTAATLEEKLNKIF 124

>pdb|3FFX|A Chain A, Crystal Structure Of Chey Triple Mutant F14e, N59r, E89h Complexed With Bef3- And Mn2+ Length = 128

Iteration: 1
 Score = 52.0 bits (123), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 37/140 (26%), Positives = 68/140 (48%), Gaps = 25/140 (17%)
Query: 863  LLVEDNKINVMVAKSMMKQLG-HSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKA 921
            L+V+D      + ++++K+LG ++++   +GV+A++ +Q   Y  ++ D  MP MDGL+ 
Sbjct: 8    LVVDDESTMRRIVRNLLKELGFNNVEEAEDGVDALNKLQAGGYGFVISDWRMPNMDGLEL 67
Query: 922  TRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMD 981
             + IR+       D A  A                 +P++ +TA+A  E+       G  
Sbjct: 68   LKTIRA-------DGAMSA-----------------LPVLMVTAHAKKENIIAAAQAGAS 103
Query: 982  SFVSKPVTFQKLKECLEQYF 1001
             +V KP T   L+E L + F
Sbjct: 104  GYVVKPFTAATLEEKLNKIF 123

>pdb|3FFT|A Chain A, Crystal Structure Of Chey Double Mutant F14e, E89r Complexed With Bef3- And Mn2+ Length = 128

Iteration: 1
 Score = 51.6 bits (122), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 37/140 (26%), Positives = 67/140 (47%), Gaps = 25/140 (17%)
Query: 863  LLVEDNKINVMVAKSMMKQLG-HSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKA 921
            L+V+D      + ++++K+LG ++++   +GV+A++ +Q   Y  ++ D  MP MDGL+ 
Sbjct: 8    LVVDDESTMRRIVRNLLKELGFNNVEEAEDGVDALNKLQAGGYGFVISDWNMPNMDGLEL 67
Query: 922  TRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMD 981
             + IR+       D A  A                 +P++ +TA A  E+       G  
Sbjct: 68   LKTIRA-------DGAMSA-----------------LPVLMVTARAKKENIIAAAQAGAS 103
Query: 982  SFVSKPVTFQKLKECLEQYF 1001
             +V KP T   L+E L + F
Sbjct: 104  GYVVKPFTAATLEEKLNKIF 123

>pdb|3RVJ|A Chain A, Structure Of The Chey-Bef3 Complex With Substitutions At 59 And 89: N59d And E89q Length = 132

Iteration: 1
 Score = 51.6 bits (122), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 37/141 (26%), Positives = 67/141 (47%), Gaps = 25/141 (17%)
Query: 862  ILLVEDNKINVMVAKSMMKQLG-HSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLK 920
             L+V+D      + ++++K+LG ++++   +GV+A++ +Q   Y  ++ D  MP MDGL+
Sbjct: 11   FLVVDDFSTMRRIVRNLLKELGFNNVEEAEDGVDALNKLQAGGYGFVISDWDMPNMDGLE 70
Query: 921  ATRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGM 980
              + IR+       D A  A                 +P++ +TA A  E+       G 
Sbjct: 71   LLKTIRA-------DGAMSA-----------------LPVLMVTAQAKKENIIAAAQAGA 106
Query: 981  DSFVSKPVTFQKLKECLEQYF 1001
              +V KP T   L+E L + F
Sbjct: 107  SGYVVKPFTAATLEEKLNKIF 127

>pdb|1YMU|A Chain A, Signal Transduction Protein Chey Mutant With Met 17 Replaced By Gly (M17g) Length = 130

Iteration: 1
 Score = 51.6 bits (122), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 37/140 (26%), Positives = 67/140 (47%), Gaps = 25/140 (17%)
Query: 863  LLVEDNKINVMVAKSMMKQLG-HSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKA 921
            L+V+D      + ++++K+LG ++++   +GV+A++ +Q   Y  ++ D  MP MDGL+ 
Sbjct: 10   LVVDDFSTGRRIVRNLLKELGFNNVEEAEDGVDALNKLQAGGYGFVISDWNMPNMDGLEL 69
Query: 922  TRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMD 981
             + IR+       D A  A                 +P++ +TA A  E+       G  
Sbjct: 70   LKTIRA-------DGAMSA-----------------LPVLMVTAEAKKENIIAAAQAGAS 105
Query: 982  SFVSKPVTFQKLKECLEQYF 1001
             +V KP T   L+E L + F
Sbjct: 106  GYVVKPFTAATLEEKLNKIF 125

>pdb|1D4Z|A Chain A, Crystal Structure Of Chey-95iv, A Hyperactive Chey Mutant Length = 128

Iteration: 1
 Score = 51.2 bits (121), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 37/140 (26%), Positives = 67/140 (47%), Gaps = 25/140 (17%)
Query: 863  LLVEDNKINVMVAKSMMKQLG-HSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKA 921
            L+V+D      + ++++K+LG ++++   +GV+A++ +Q   Y  ++ D  MP MDGL+ 
Sbjct: 8    LVVDDFSTMRRIVRNLLKELGFNNVEEAEDGVDALNKLQAGGYGFVISDWNMPNMDGLEL 67
Query: 922  TRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMD 981
             + IR+       D A  A                 +P++ +TA A  E+       G  
Sbjct: 68   LKTIRA-------DGAMSA-----------------LPVLMVTAEAKKENVIAAAQAGAS 103
Query: 982  SFVSKPVTFQKLKECLEQYF 1001
             +V KP T   L+E L + F
Sbjct: 104  GYVVKPFTAATLEEKLNKIF 123

>pdb|3FFW|A Chain A, Crystal Structure Of Chey Triple Mutant F14q, N59k, E89y Complexed With Bef3- And Mn2+ Length = 128

Iteration: 1
 Score = 51.2 bits (121), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 37/140 (26%), Positives = 67/140 (47%), Gaps = 25/140 (17%)
Query: 863  LLVEDNKINVMVAKSMMKQLG-HSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKA 921
            L+V+D      + ++++K+LG ++++   +GV+A++ +Q   Y  ++ D  MP MDGL+ 
Sbjct: 8    LVVDDQSTMRRIVRNLLKELGFNNVEEAEDGVDALNKLQAGGYGFVISDWKMPNMDGLEL 67
Query: 922  TRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMD 981
             + IR+       D A  A                 +P++ +TA A  E+       G  
Sbjct: 68   LKTIRA-------DGAMSA-----------------LPVLMVTAYAKKENIIAAAQAGAS 103
Query: 982  SFVSKPVTFQKLKECLEQYF 1001
             +V KP T   L+E L + F
Sbjct: 104  GYVVKPFTAATLEEKLNKIF 123

>pdb|3F7N|A Chain A, Crystal Structure Of Chey Triple Mutant F14e, N59m, E89l Complexed With Bef3- And Mn2+ Length = 128

Iteration: 1
 Score = 51.2 bits (121), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 37/140 (26%), Positives = 67/140 (47%), Gaps = 25/140 (17%)
Query: 863  LLVEDNKINVMVAKSMMKQLG-HSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKA 921
            L+V+D      + ++++K+LG ++++   +GV+A++ +Q   Y  ++ D  MP MDGL+ 
Sbjct: 8    LVVDDESTMRRIVRNLLKELGFNNVEEAEDGVDALNKLQAGGYGFVISDWMMPNMDGLEL 67
Query: 922  TRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMD 981
             + IR+       D A  A                 +P++ +TA A  E+       G  
Sbjct: 68   LKTIRA-------DGAMSA-----------------LPVLMVTALAKKENIIAAAQAGAS 103
Query: 982  SFVSKPVTFQKLKECLEQYF 1001
             +V KP T   L+E L + F
Sbjct: 104  GYVVKPFTAATLEEKLNKIF 123

>pdb|1DJM|A Chain A, Solution Structure Of Bef3-Activated Chey From Escherichia Coli Length = 129

Iteration: 1
 Score = 50.8 bits (120), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 37/140 (26%), Positives = 67/140 (47%), Gaps = 25/140 (17%)
Query: 863  LLVEDNKINVMVAKSMMKQLG-HSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKA 921
            L+V+D      + ++++K+LG ++++   +GV+A++ +Q   Y  ++ D  MP MDGL+ 
Sbjct: 9    LVVDDFSTMRRIVRNLLKELGFNNVEEAEDGVDALNKLQAGGYGFVISDWNMPNMDGLEL 68
Query: 922  TRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMD 981
             + IR+       D A  A                 +P++ +TA A  E+       G  
Sbjct: 69   LKTIRA-------DGAMSA-----------------LPVLMVTAEAKKENIIAAAQAGAS 104
Query: 982  SFVSKPVTFQKLKECLEQYF 1001
             +V KP T   L+E L + F
Sbjct: 105  GYVVKPFTAATLEEKLNKIF 124

>pdb|1EAY|A Chain A, Chey-Binding (P2) Domain Of Chea In Complex With Chey From Escherichia Coli Length = 128

Iteration: 1
 Score = 50.8 bits (120), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 37/140 (26%), Positives = 67/140 (47%), Gaps = 25/140 (17%)
Query: 863  LLVEDNKINVMVAKSMMKQLG-HSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKA 921
            L+V+D      + ++++K+LG ++++   +GV+A++ +Q   Y  ++ D  MP MDGL+ 
Sbjct: 8    LVVDDFSTMRRIVRNLLKELGFNNVEEAEDGVDALNKLQAGGYGFVISDWNMPNMDGLEL 67
Query: 922  TRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMD 981
             + IR+       D A  A                 +P++ +TA A  E+       G  
Sbjct: 68   LKTIRA-------DGAMSA-----------------LPVLMVTAEAKKENIIAAAQAGAS 103
Query: 982  SFVSKPVTFQKLKECLEQYF 1001
             +V KP T   L+E L + F
Sbjct: 104  GYVVKPFTAATLEEKLNKIF 123

>pdb|1CYE|A Chain A, Three Dimensional Structure Of Chemotactic Che Y Protein In Aqueous Solution By Nuclear Magnetic Resonance Methods Length = 129

Iteration: 1
 Score = 50.8 bits (120), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 37/140 (26%), Positives = 67/140 (47%), Gaps = 25/140 (17%)
Query: 863  LLVEDNKINVMVAKSMMKQLG-HSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKA 921
            L+V+D      + ++++K+LG ++++   +GV+A++ +Q   Y  ++ D  MP MDGL+ 
Sbjct: 9    LVVDDFSTMRRIVRNLLKELGFNNVEEAEDGVDALNKLQAGGYGFVISDWNMPNMDGLEL 68
Query: 922  TRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMD 981
             + IR+       D A  A                 +P++ +TA A  E+       G  
Sbjct: 69   LKTIRA-------DGAMSA-----------------LPVLMVTAEAKKENIIAAAQAGAS 104
Query: 982  SFVSKPVTFQKLKECLEQYF 1001
             +V KP T   L+E L + F
Sbjct: 105  GYVVKPFTAATLEEKLNKIF 124

>pdb|1CEY|A Chain A, Assignments, Secondary Structure, Global Fold, And Dynamics Of Chemotaxis Y Protein Using Three-And Four-Dimensional Heteronuclear (13c,15n) Nmr Spectroscopy Length = 128

Iteration: 1
 Score = 50.8 bits (120), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 37/140 (26%), Positives = 67/140 (47%), Gaps = 25/140 (17%)
Query: 863  LLVEDNKINVMVAKSMMKQLG-HSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKA 921
            L+V+D      + ++++K+LG ++++   +GV+A++ +Q   Y  ++ D  MP MDGL+ 
Sbjct: 8    LVVDDFSTMRRIVRNLLKELGFNNVEEAEDGVDALNKLQAGGYGFVISDWNMPNMDGLEL 67
Query: 922  TRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMD 981
             + IR+       D A  A                 +P++ +TA A  E+       G  
Sbjct: 68   LKTIRA-------DGAMSA-----------------LPVLMVTAEAKKENIIAAAQAGAS 103
Query: 982  SFVSKPVTFQKLKECLEQYF 1001
             +V KP T   L+E L + F
Sbjct: 104  GYVVKPFTAATLEEKLNKIF 123

>pdb|3RVP|A Chain A, Structure Of The Chey-Bef3 Complex With Substitutions At 59 And 89: N59d And E89k Length = 132

Iteration: 1
 Score = 50.4 bits (119), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 37/140 (26%), Positives = 67/140 (47%), Gaps = 25/140 (17%)
Query: 863  LLVEDNKINVMVAKSMMKQLG-HSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKA 921
            L+V+D      + ++++K+LG ++++   +GV+A++ +Q   Y  ++ D  MP MDGL+ 
Sbjct: 12   LVVDDFSTMRRIVRNLLKELGFNNVEEAEDGVDALNKLQAGGYGFVISDWDMPNMDGLEL 71
Query: 922  TRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMD 981
             + IR+       D A  A                 +P++ +TA A  E+       G  
Sbjct: 72   LKTIRA-------DGAMSA-----------------LPVLMVTAKAKKENIIAAAQAGAS 107
Query: 982  SFVSKPVTFQKLKECLEQYF 1001
             +V KP T   L+E L + F
Sbjct: 108  GYVVKPFTAATLEEKLNKIF 127

>pdb|3RVL|A Chain A, Structure Of The Chey-Bef3 Complex With Substitutions At 59 And 89: N59d And E89r Length = 132

Iteration: 1
 Score = 50.4 bits (119), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 37/140 (26%), Positives = 67/140 (47%), Gaps = 25/140 (17%)
Query: 863  LLVEDNKINVMVAKSMMKQLG-HSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKA 921
            L+V+D      + ++++K+LG ++++   +GV+A++ +Q   Y  ++ D  MP MDGL+ 
Sbjct: 12   LVVDDFSTMRRIVRNLLKELGFNNVEEAEDGVDALNKLQAGGYGFVISDWDMPNMDGLEL 71
Query: 922  TRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMD 981
             + IR+       D A  A                 +P++ +TA A  E+       G  
Sbjct: 72   LKTIRA-------DGAMSA-----------------LPVLMVTARAKKENIIAAAQAGAS 107
Query: 982  SFVSKPVTFQKLKECLEQYF 1001
             +V KP T   L+E L + F
Sbjct: 108  GYVVKPFTAATLEEKLNKIF 127

>pdb|1MIH|A Chain A, A Role For Chey Glu 89 In Chez-Mediated Dephosphorylation Of The E. Coli Chemotaxis Response Regulator Chey Length = 129

Iteration: 1
 Score = 50.4 bits (119), Expect = 5e-06,   Method: Composition-based stats.
 Identities = 37/140 (26%), Positives = 67/140 (47%), Gaps = 25/140 (17%)
Query: 863  LLVEDNKINVMVAKSMMKQLG-HSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKA 921
            L+V+D      + ++++K+LG ++++   +GV+A++ +Q   Y  ++ D  MP MDGL+ 
Sbjct: 9    LVVDDFSTMRRIVRNLLKELGFNNVEEAEDGVDALNKLQAGGYGFVISDWRMPNMDGLEL 68
Query: 922  TRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMD 981
             + IR+       D A  A                 +P++ +TA A  E+       G  
Sbjct: 69   LKTIRA-------DGAMSA-----------------LPVLMVTAEAKKENIIAAAQAGAS 104
Query: 982  SFVSKPVTFQKLKECLEQYF 1001
             +V KP T   L+E L + F
Sbjct: 105  GYVVKPFTAATLEEKLNKIF 124

>pdb|2CHY|A Chain A, Three-Dimensional Structure Of Chey, The Response Regulator Of Bacterial Chemotaxis Length = 128

Iteration: 1
 Score = 50.4 bits (119), Expect = 5e-06,   Method: Composition-based stats.
 Identities = 37/140 (26%), Positives = 68/140 (48%), Gaps = 25/140 (17%)
Query: 863  LLVEDNKINVMVAKSMMKQLG-HSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKA 921
            L+V+D      + ++++K+LG ++++   +GV+A++ +Q   +  I+ D  MP MDGL+ 
Sbjct: 8    LVVDDFSTMRRIVRNLLKELGFNNVEEAEDGVDALNKLQAGGFGFIICDWNMPNMDGLEL 67
Query: 922  TRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMD 981
             + IR+       D+A  A                 +P++ +TA A  E+       G  
Sbjct: 68   LKTIRA-------DSAMSA-----------------LPVLMVTAEAKKENIIAAAQAGAS 103
Query: 982  SFVSKPVTFQKLKECLEQYF 1001
             +V KP T   L+E L + F
Sbjct: 104  GYVVKPFTAATLEEKLNKIF 123

>pdb|3GT7|A Chain A, Crystal Structure Of Signal Receiver Domain Of Signal Transduction Histidine Kinase From Syntrophus Aciditrophicus Length = 154

Iteration: 1
 Score = 50.1 bits (118), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 34/126 (26%), Positives = 52/126 (41%), Gaps = 24/126 (19%)
Query: 862 ILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKA 921
           IL+VED+       K ++++ G+  + V NG EAV  +     DLI+ DV MP MDG   
Sbjct: 10  ILIVEDSPTQAEHLKHILEETGYQTEHVRNGREAVRFLSLTRPDLIISDVLMPEMDGYAL 69
Query: 922 TRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMD 981
            R ++   D                         + IP+I +T  +           G D
Sbjct: 70  CRWLKGQPD------------------------LRTIPVILLTILSDPRDVVRSLECGAD 105
Query: 982 SFVSKP 987
            F++KP
Sbjct: 106 DFITKP 111

>pdb|3MYY|A Chain A, Structure Of E. Coli Chey Mutant A113p Bound To Beryllium Fluoride Length = 128

Iteration: 1
 Score = 50.1 bits (118), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 37/140 (26%), Positives = 67/140 (47%), Gaps = 25/140 (17%)
Query: 863  LLVEDNKINVMVAKSMMKQLG-HSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKA 921
            L+V+D      + ++++K+LG ++++   +GV+A++ +Q   Y  ++ D  MP MDGL+ 
Sbjct: 8    LVVDDFSTMRRIVRNLLKELGFNNVEEAEDGVDALNKLQAGGYGFVISDWNMPNMDGLEL 67
Query: 922  TRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMD 981
             + IR+       D A  A                 +P++ +TA A  E+       G  
Sbjct: 68   LKTIRA-------DGAMSA-----------------LPVLMVTAEAKKENIIAAAQAGAS 103
Query: 982  SFVSKPVTFQKLKECLEQYF 1001
             +V KP T   L+E L + F
Sbjct: 104  GYVVKPFTPATLEEKLNKIF 123

>pdb|3OO0|A Chain A, Structure Of Apo Chey A113p Length = 129

Iteration: 1
 Score = 50.1 bits (118), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 37/140 (26%), Positives = 67/140 (47%), Gaps = 25/140 (17%)
Query: 863  LLVEDNKINVMVAKSMMKQLG-HSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKA 921
            L+V+D      + ++++K+LG ++++   +GV+A++ +Q   Y  ++ D  MP MDGL+ 
Sbjct: 9    LVVDDFSTMRRIVRNLLKELGFNNVEEAEDGVDALNKLQAGGYGFVISDWNMPNMDGLEL 68
Query: 922  TRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMD 981
             + IR+       D A  A                 +P++ +TA A  E+       G  
Sbjct: 69   LKTIRA-------DGAMSA-----------------LPVLMVTAEAKKENIIAAAQAGAS 104
Query: 982  SFVSKPVTFQKLKECLEQYF 1001
             +V KP T   L+E L + F
Sbjct: 105  GYVVKPFTPATLEEKLNKIF 124

>pdb|3RVN|A Chain A, Structure Of The Chey-Bef3 Complex With Substitutions At 59 And 89: N59d And E89y Length = 132

Iteration: 1
 Score = 50.1 bits (118), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 37/140 (26%), Positives = 67/140 (47%), Gaps = 25/140 (17%)
Query: 863  LLVEDNKINVMVAKSMMKQLG-HSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKA 921
            L+V+D      + ++++K+LG ++++   +GV+A++ +Q   Y  ++ D  MP MDGL+ 
Sbjct: 12   LVVDDFSTMRRIVRNLLKELGFNNVEEAEDGVDALNKLQAGGYGFVISDWDMPNMDGLEL 71
Query: 922  TRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMD 981
             + IR+       D A  A                 +P++ +TA A  E+       G  
Sbjct: 72   LKTIRA-------DGAMSA-----------------LPVLMVTAYAKKENIIAAAQAGAS 107
Query: 982  SFVSKPVTFQKLKECLEQYF 1001
             +V KP T   L+E L + F
Sbjct: 108  GYVVKPFTAATLEEKLNKIF 127

>pdb|2FKA|A Chain A, Crystal Structure Of Mg(2+) And Bef(3)(-)-Bound Chey In Complex With Chez(200-214) Solved From A F432 Crystal Grown In Caps (Ph 10.5) Length = 129

Iteration: 1
 Score = 50.1 bits (118), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 37/140 (26%), Positives = 68/140 (48%), Gaps = 25/140 (17%)
Query: 863  LLVEDNKINVMVAKSMMKQLG-HSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKA 921
            L+V+D      + ++++K+LG ++++   +GV+A++ +Q   +  I+ D  MP MDGL+ 
Sbjct: 9    LVVDDFSTMRRIVRNLLKELGFNNVEEAEDGVDALNKLQAGGFGFIISDWNMPNMDGLEL 68
Query: 922  TRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMD 981
             + IR+       D+A  A                 +P++ +TA A  E+       G  
Sbjct: 69   LKTIRA-------DSAMSA-----------------LPVLMVTAEAKKENIIAAAQAGAS 104
Query: 982  SFVSKPVTFQKLKECLEQYF 1001
             +V KP T   L+E L + F
Sbjct: 105  GYVVKPFTAATLEEKLNKIF 124

>pdb|2CHE|A Chain A, Structure Of The Mg2+-Bound Form Of Chey And Mechanism Of Phosphoryl Transfer In Bacterial Chemotaxis Length = 128

Iteration: 1
 Score = 50.1 bits (118), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 37/140 (26%), Positives = 68/140 (48%), Gaps = 25/140 (17%)
Query: 863  LLVEDNKINVMVAKSMMKQLG-HSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKA 921
            L+V+D      + ++++K+LG ++++   +GV+A++ +Q   +  I+ D  MP MDGL+ 
Sbjct: 8    LVVDDFSTMRRIVRNLLKELGFNNVEEAEDGVDALNKLQAGGFGFIISDWNMPNMDGLEL 67
Query: 922  TRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMD 981
             + IR+       D+A  A                 +P++ +TA A  E+       G  
Sbjct: 68   LKTIRA-------DSAMSA-----------------LPVLMVTAEAKKENIIAAAQAGAS 103
Query: 982  SFVSKPVTFQKLKECLEQYF 1001
             +V KP T   L+E L + F
Sbjct: 104  GYVVKPFTAATLEEKLNKIF 123

>pdb|5CHY|A Chain A, Structure Of Chemotaxis Protein Chey Length = 128

Iteration: 1
 Score = 50.1 bits (118), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 37/140 (26%), Positives = 67/140 (47%), Gaps = 25/140 (17%)
Query: 863  LLVEDNKINVMVAKSMMKQLG-HSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKA 921
            L+V+D      + ++++K+LG ++++   +GV+A++ +Q   Y  ++ D  MP MDGL+ 
Sbjct: 8    LVVDDFSTMRRIVRNLLKELGFNNVEEAEDGVDALNKLQAGGYGFVISDWNMPNMDGLEL 67
Query: 922  TRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMD 981
             + IR+       D A  A                 +P++ +TA A  E+       G  
Sbjct: 68   LKTIRA-------DGAMSA-----------------LPVLMVTAEAKKENIIAAAQAGAS 103
Query: 982  SFVSKPVTFQKLKECLEQYF 1001
             +V KP T   L+E L + F
Sbjct: 104  GWVVKPFTAATLEEKLNKIF 123

>pdb|1E6K|A Chain A, Two-Component Signal Transduction System D12a Mutant Of Chey Length = 130

Iteration: 1
 Score = 49.7 bits (117), Expect = 7e-06,   Method: Composition-based stats.
 Identities = 37/140 (26%), Positives = 66/140 (47%), Gaps = 25/140 (17%)
Query: 863  LLVEDNKINVMVAKSMMKQLG-HSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKA 921
            L+V D      + ++++K+LG ++++   +GV+A++ +Q   Y  ++ D  MP MDGL+ 
Sbjct: 10   LVVADFSTMRRIVRNLLKELGFNNVEEAEDGVDALNKLQAGGYGFVISDWNMPNMDGLEL 69
Query: 922  TRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMD 981
             + IR+       D A  A                 +P++ +TA A  E+       G  
Sbjct: 70   LKTIRA-------DGAMSA-----------------LPVLMVTAEAKKENIIAAAQAGAS 105
Query: 982  SFVSKPVTFQKLKECLEQYF 1001
             +V KP T   L+E L + F
Sbjct: 106  GYVVKPFTAATLEEKLNKIF 125

>pdb|3OLX|A Chain A, Structural And Functional Effects Of Substitution At Position T+1 In Chey: Cheya88s-Bef3-Mn Complex Length = 129

Iteration: 1
 Score = 49.7 bits (117), Expect = 9e-06,   Method: Composition-based stats.
 Identities = 36/140 (25%), Positives = 67/140 (47%), Gaps = 25/140 (17%)
Query: 863  LLVEDNKINVMVAKSMMKQLG-HSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKA 921
            L+V+D      + ++++K+LG ++++   +GV+A++ +Q   Y  ++ D  MP MDGL+ 
Sbjct: 9    LVVDDFSTMRRIVRNLLKELGFNNVEEAEDGVDALNKLQAGGYGFVISDWNMPNMDGLEL 68
Query: 922  TRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMD 981
             + IR+       D A  A                 +P++ +T+ A  E+       G  
Sbjct: 69   LKTIRA-------DGAMSA-----------------LPVLMVTSEAKKENIIAAAQAGAS 104
Query: 982  SFVSKPVTFQKLKECLEQYF 1001
             +V KP T   L+E L + F
Sbjct: 105  GYVVKPFTAATLEEKLNKIF 124

>pdb|3OLW|A Chain A, Structural And Functional Effects Of Substitution At Position T+1 In Chey: Cheya88t-Bef3-Mn Complex Length = 129

Iteration: 1
 Score = 49.3 bits (116), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 36/140 (25%), Positives = 66/140 (47%), Gaps = 25/140 (17%)
Query: 863  LLVEDNKINVMVAKSMMKQLG-HSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKA 921
            L+V+D      + ++++K+LG ++++   +GV+A++ +Q   Y  ++ D  MP MDGL+ 
Sbjct: 9    LVVDDFSTMRRIVRNLLKELGFNNVEEAEDGVDALNKLQAGGYGFVISDWNMPNMDGLEL 68
Query: 922  TRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMD 981
             + IR+       D A  A                 +P++ +T  A  E+       G  
Sbjct: 69   LKTIRA-------DGAMSA-----------------LPVLMVTTEAKKENIIAAAQAGAS 104
Query: 982  SFVSKPVTFQKLKECLEQYF 1001
             +V KP T   L+E L + F
Sbjct: 105  GYVVKPFTAATLEEKLNKIF 124

>pdb|3OLV|A Chain A, Structural And Functional Effects Of Substitution At Position T+1 In Chey: Cheya88v-Bef3-Mg Complex Length = 129

Iteration: 1
 Score = 49.3 bits (116), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 36/140 (25%), Positives = 66/140 (47%), Gaps = 25/140 (17%)
Query: 863  LLVEDNKINVMVAKSMMKQLG-HSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKA 921
            L+V+D      + ++++K+LG ++++   +GV+A++ +Q   Y  ++ D  MP MDGL+ 
Sbjct: 9    LVVDDFSTMRRIVRNLLKELGFNNVEEAEDGVDALNKLQAGGYGFVISDWNMPNMDGLEL 68
Query: 922  TRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMD 981
             + IR+       D A  A                 +P++ +T  A  E+       G  
Sbjct: 69   LKTIRA-------DGAMSA-----------------LPVLMVTVEAKKENIIAAAQAGAS 104
Query: 982  SFVSKPVTFQKLKECLEQYF 1001
             +V KP T   L+E L + F
Sbjct: 105  GYVVKPFTAATLEEKLNKIF 124

>pdb|1JBE|A Chain A, 1.08 A Structure Of Apo-Chey Reveals Meta-Active Conformation Length = 128

Iteration: 1
 Score = 48.9 bits (115), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 36/140 (25%), Positives = 67/140 (47%), Gaps = 25/140 (17%)
Query: 863  LLVEDNKINVMVAKSMMKQLG-HSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKA 921
            L+V+D      + ++++K+LG ++++   +GV+A++ +Q   Y  ++ D  MP MDGL+ 
Sbjct: 8    LVVDDFSTMRRIVRNLLKELGFNNVEEAEDGVDALNKLQAGGYGFVISDWNMPNMDGLEL 67
Query: 922  TRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMD 981
             + IR+                 AM +         +P++ +TA A  E+       G  
Sbjct: 68   LKTIRA---------------XXAMSA---------LPVLMVTAEAKKENIIAAAQAGAS 103
Query: 982  SFVSKPVTFQKLKECLEQYF 1001
             +V KP T   L+E L + F
Sbjct: 104  GYVVKPFTAATLEEKLNKIF 123

>pdb|3OLY|A Chain A, Structural And Functional Effects Of Substitution At Position T+1 In Chey: Cheya88m-Bef3-Mn Complex Length = 129

Iteration: 1
 Score = 48.9 bits (115), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 36/140 (25%), Positives = 66/140 (47%), Gaps = 25/140 (17%)
Query: 863  LLVEDNKINVMVAKSMMKQLG-HSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKA 921
            L+V+D      + ++++K+LG ++++   +GV+A++ +Q   Y  ++ D  MP MDGL+ 
Sbjct: 9    LVVDDFSTMRRIVRNLLKELGFNNVEEAEDGVDALNKLQAGGYGFVISDWNMPNMDGLEL 68
Query: 922  TRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMD 981
             + IR+       D A  A                 +P++ +T  A  E+       G  
Sbjct: 69   LKTIRA-------DGAMSA-----------------LPVLMVTMEAKKENIIAAAQAGAS 104
Query: 982  SFVSKPVTFQKLKECLEQYF 1001
             +V KP T   L+E L + F
Sbjct: 105  GYVVKPFTAATLEEKLNKIF 124

>pdb|1VLZ|A Chain A, Uncoupled Phosphorylation And Activation In Bacterial Chemotaxis: The 2.1 Angstrom Structure Of A Threonine To Isoleucine Mutant At Position 87 Of Chey Length = 128

Iteration: 1
 Score = 48.9 bits (115), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 36/140 (25%), Positives = 66/140 (47%), Gaps = 25/140 (17%)
Query: 863  LLVEDNKINVMVAKSMMKQLG-HSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKA 921
            L+V+D      + ++++K+LG ++++   +GV+A++ +Q   Y  ++ D  MP MDGL+ 
Sbjct: 8    LVVDDFSTMRRIVRNLLKELGFNNVEEAEDGVDALNKLQAGGYGFVISDWNMPNMDGLEL 67
Query: 922  TRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMD 981
             + IR+       D A  A                 +P++ + A A  E+       G  
Sbjct: 68   LKTIRA-------DGAMSA-----------------LPVLMVIAEAKKENIIAAAQAGAS 103
Query: 982  SFVSKPVTFQKLKECLEQYF 1001
             +V KP T   L+E L + F
Sbjct: 104  GYVVKPFTAATLEEKLNKIF 123

>pdb|1E6L|A Chain A, Two-Component Signal Transduction System D13a Mutant Of Chey Length = 127

Iteration: 1
 Score = 48.5 bits (114), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 34/129 (26%), Positives = 62/129 (48%), Gaps = 25/129 (19%)
Query: 874  VAKSMMKQLG-HSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKATRLIRSFEDTG 932
            + ++++K+LG ++++   +GV+A++ +Q   Y  ++ D  MP MDGL+  + IR+     
Sbjct: 18   IVRNLLKELGFNNVEEAEDGVDALNKLQAGGYGFVISDWNMPNMDGLELLKTIRA----- 72
Query: 933  NWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQK 992
              D A  A                 +P++ +TA A  E+       G   +V KP T   
Sbjct: 73   --DGAMSA-----------------LPVLMVTAEAKKENIIAAAQAGASGYVVKPFTAAT 113
Query: 993  LKECLEQYF 1001
            L+E L + F
Sbjct: 114  LEEKLNKIF 122

>pdb|1EHC|A Chain A, Structure Of Signal Transduction Protein Chey Length = 128

Iteration: 1
 Score = 48.5 bits (114), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 34/129 (26%), Positives = 62/129 (48%), Gaps = 25/129 (19%)
Query: 874  VAKSMMKQLG-HSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKATRLIRSFEDTG 932
            + ++++K+LG ++++   +GV+A++ +Q   Y  ++ D  MP MDGL+  + IR+     
Sbjct: 19   IVRNLLKELGFNNVEEAEDGVDALNKLQAGGYGFVISDWNMPNMDGLELLKTIRA----- 73
Query: 933  NWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQK 992
              D A  A                 +P++ +TA A  E+       G   +V KP T   
Sbjct: 74   --DGAMSA-----------------LPVLMVTAEAKKENIIAAAQAGASGYVVKPFTAAT 114
Query: 993  LKECLEQYF 1001
            L+E L + F
Sbjct: 115  LEEKLNKIF 123

>pdb|3TO5|A Chain A, High Resolution Structure Of Chey3 From Vibrio Cholerae Length = 134

Iteration: 1
 Score = 48.1 bits (113), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 34/141 (24%), Positives = 67/141 (47%), Gaps = 25/141 (17%)
Query: 862  ILLVEDNKINVMVAKSMMKQLG-HSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLK 920
            IL+V+D      + K++++ LG ++    ++G+ A+  ++  ++D ++ D  MP M G+ 
Sbjct: 15   ILIVDDFSTMRRIVKNLLRDLGFNNTQEADDGLTALPMLKKGDFDFVVTDWNMPGMQGID 74
Query: 921  ATRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGM 980
              + IR+ E+                         K +P++ +TA A  E   E    G+
Sbjct: 75   LLKNIRADEE------------------------LKHLPVLMITAEAKREQIIEAAQAGV 110
Query: 981  DSFVSKPVTFQKLKECLEQYF 1001
            + ++ KP T   LKE L++ F
Sbjct: 111  NGYIVKPFTAATLKEKLDKIF 131

>pdb|1DCF|A Chain A, Crystal Structure Of The Receiver Domain Of The Ethylene Receptor Of Arabidopsis Thaliana Length = 136

Iteration: 1
 Score = 48.1 bits (113), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 30/137 (21%), Positives = 65/137 (47%), Gaps = 24/137 (17%)
Query: 862 ILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLK- 920
           +L++++N ++ MV K ++  LG  +  V++  E +  V    + ++ MDVCMP ++  + 
Sbjct: 10  VLVMDENGVSRMVTKGLLVHLGCEVTTVSSNEECLRVVS-HEHKVVFMDVCMPGVENYQI 68
Query: 921 ATRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGM 980
           A R+   F                      +    +R  ++A++ N    + E+C + G+
Sbjct: 69  ALRIHEKF----------------------TKQRHQRPLLVALSGNTDKSTKEKCMSFGL 106
Query: 981 DSFVSKPVTFQKLKECL 997
           D  + KPV+   +++ L
Sbjct: 107 DGVLLKPVSLDNIRDVL 123

>pdb|3I42|A Chain A, Structure Of Response Regulator Receiver Domain (Chey-Like) From Methylobacillus Flagellatus Length = 127

Iteration: 1
 Score = 48.1 bits (113), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 34/136 (25%), Positives = 60/136 (44%), Gaps = 25/136 (18%)
Query: 863 LLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKAT 922
           L+VED +      K +++ LG   D V +G +A+HA+  + YD + +D+ +P   GL   
Sbjct: 7   LIVEDYQAAAETFKELLEMLGFQADYVMSGTDALHAMSTRGYDAVFIDLNLPDTSGLALV 66
Query: 923 RLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDS 982
           + +R                  A+P   +S   K + +     N L + A E F    D 
Sbjct: 67  KQLR------------------ALPMEKTS---KFVAVSGFAKNDLGKEACELF----DF 101
Query: 983 FVSKPVTFQKLKECLE 998
           ++ KP+    L+  L+
Sbjct: 102 YLEKPIDIASLEPILQ 117

>pdb|6CHY|A Chain A, Structure Of Chemotaxis Protein Chey Length = 128

Iteration: 1
 Score = 48.1 bits (113), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 36/140 (25%), Positives = 66/140 (47%), Gaps = 25/140 (17%)
Query: 863  LLVEDNKINVMVAKSMMKQLG-HSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKA 921
            L+V+D      + ++++K+LG ++++   +GV+A++ +Q   Y  ++ D  MP MDGL+ 
Sbjct: 8    LVVDDFSTMRRIVRNLLKELGFNNVEEAEDGVDALNKLQAGGYGFVISDWNMPNMDGLEL 67
Query: 922  TRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMD 981
             + IR+       D A  A                 +P++ + A A  E+       G  
Sbjct: 68   LKTIRA-------DGAMSA-----------------LPVLMVIAEAKKENIIAAAQAGAS 103
Query: 982  SFVSKPVTFQKLKECLEQYF 1001
             +V KP T   L+E L + F
Sbjct: 104  GWVVKPFTAATLEEKLNKIF 123

>pdb|1ZDM|A Chain A, Crystal Structure Of Activated Chey Bound To Xe Length = 129

Iteration: 1
 Score = 48.1 bits (113), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 36/140 (25%), Positives = 66/140 (47%), Gaps = 25/140 (17%)
Query: 863  LLVEDNKINVMVAKSMMKQLG-HSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKA 921
            L+V+D      + ++++K+LG ++++   +GV+A++ +Q   Y  ++    MP MDGL+ 
Sbjct: 9    LVVDDFSTMRRIVRNLLKELGFNNVEEAEDGVDALNKLQAGGYGFVISXWNMPNMDGLEL 68
Query: 922  TRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMD 981
             + IR+       D A  A                 +P++ +TA A  E+       G  
Sbjct: 69   LKTIRA-------DGAMSA-----------------LPVLMVTAEAKKENIIAAAQAGAS 104
Query: 982  SFVSKPVTFQKLKECLEQYF 1001
             +V KP T   L+E L + F
Sbjct: 105  GYVVKPFTAATLEEKLNKIF 124

>pdb|1C4W|A Chain A, 1.9 A Structure Of A-Thiophosphonate Modified Chey D57c Length = 128

Iteration: 1
 Score = 48.1 bits (113), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 36/140 (25%), Positives = 66/140 (47%), Gaps = 25/140 (17%)
Query: 863  LLVEDNKINVMVAKSMMKQLG-HSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKA 921
            L+V+D      + ++++K+LG ++++   +GV+A++ +Q   Y  ++    MP MDGL+ 
Sbjct: 8    LVVDDFSTMRRIVRNLLKELGFNNVEEAEDGVDALNKLQAGGYGFVISXWNMPNMDGLEL 67
Query: 922  TRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMD 981
             + IR+       D A  A                 +P++ +TA A  E+       G  
Sbjct: 68   LKTIRA-------DGAMSA-----------------LPVLMVTAEAKKENIIAAAQAGAS 103
Query: 982  SFVSKPVTFQKLKECLEQYF 1001
             +V KP T   L+E L + F
Sbjct: 104  GYVVKPFTAATLEEKLNKIF 123

>pdb|1HEY|A Chain A, Investigating The Structural Determinants Of The P21-Like Triphosphate And Mg2+ Binding Site Length = 128

Iteration: 1
 Score = 48.1 bits (113), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 36/140 (25%), Positives = 65/140 (46%), Gaps = 25/140 (17%)
Query: 863  LLVEDNKINVMVAKSMMKQLG-HSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKA 921
            L+V +        ++++K+LG ++++   +GV+A++ +Q   Y  ++ D  MP MDGL+ 
Sbjct: 8    LVVGNGGTGKSTVRNLLKELGFNNVEDAEDGVDALNKLQAGGYGFVISDWNMPNMDGLEL 67
Query: 922  TRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMD 981
             + IR+       D A  A                 +P++ +TA A  E+       G  
Sbjct: 68   LKTIRA-------DGAMSA-----------------LPVLMVTAEAKKENIIAAAQAGAS 103
Query: 982  SFVSKPVTFQKLKECLEQYF 1001
             +V KP T   L+E L + F
Sbjct: 104  GYVVKPFTAATLEEKLNKIF 123

>pdb|1E6M|A Chain A, Two-Component Signal Transduction System D57a Mutant Of Chey Length = 128

Iteration: 1
 Score = 47.8 bits (112), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 36/140 (25%), Positives = 66/140 (47%), Gaps = 25/140 (17%)
Query: 863  LLVEDNKINVMVAKSMMKQLG-HSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKA 921
            L+V+D      + ++++K+LG ++++   +GV+A++ +Q   Y  ++    MP MDGL+ 
Sbjct: 8    LVVDDFSTMRRIVRNLLKELGFNNVEEAEDGVDALNKLQAGGYGFVISAWNMPNMDGLEL 67
Query: 922  TRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMD 981
             + IR+       D A  A                 +P++ +TA A  E+       G  
Sbjct: 68   LKTIRA-------DGAMSA-----------------LPVLMVTAEAKKENIIAAAQAGAS 103
Query: 982  SFVSKPVTFQKLKECLEQYF 1001
             +V KP T   L+E L + F
Sbjct: 104  GYVVKPFTAATLEEKLNKIF 123

>pdb|3H1G|A Chain A, Crystal Structure Of Chey Mutant T84a Of Helicobacter Pylori Length = 129

Iteration: 1
 Score = 46.2 bits (108), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 38/140 (27%), Positives = 64/140 (45%), Gaps = 28/140 (20%)
Query: 862 ILLVEDNKINVMVAKSMMKQLGHSIDVVN--NGVEAVHAVQCQ-NYDLILMDVCMPVMDG 918
           +L+V+D+     + K+ + +LG+  DV+   +GVEA   +    +  +++ D  MP M+G
Sbjct: 8   LLVVDDSSTMRRIIKNTLSRLGYE-DVLEAEHGVEAWEKLDANADTKVLITDWNMPEMNG 66
Query: 919 LKATRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFAN 978
           L   + +RS                         + FK IPII +TA             
Sbjct: 67  LDLVKKVRS------------------------DSRFKEIPIIMITAEGGKAEVITALKA 102
Query: 979 GMDSFVSKPVTFQKLKECLE 998
           G+++++ KP T Q LKE LE
Sbjct: 103 GVNNYIVKPFTPQVLKEKLE 122

>pdb|2ID7|A Chain A, 1.75 A Structure Of T87i Phosphono-Chey Length = 128

Iteration: 1
 Score = 46.2 bits (108), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 35/140 (25%), Positives = 65/140 (46%), Gaps = 25/140 (17%)
Query: 863  LLVEDNKINVMVAKSMMKQLG-HSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKA 921
            L+V+D      + ++++K+LG ++++   +GV+A++ +Q   Y  ++    MP MDGL+ 
Sbjct: 8    LVVDDFSTMRRIVRNLLKELGFNNVEEAEDGVDALNKLQAGGYGFVISXWNMPNMDGLEL 67
Query: 922  TRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMD 981
             + IR+       D A  A                 +P++ + A A  E+       G  
Sbjct: 68   LKTIRA-------DGAMSA-----------------LPVLMVIAEAKKENIIAAAQAGAS 103
Query: 982  SFVSKPVTFQKLKECLEQYF 1001
             +V KP T   L+E L + F
Sbjct: 104  GYVVKPFTAATLEEKLNKIF 123

>pdb|3DGE|C Chain C, Structure Of A Histidine Kinase-response Regulator Complex Reveals Insights Into Two-component Signaling And A Novel Cis- Autophosphorylation Mechanism Length = 122

Iteration: 1
 Score = 45.8 bits (107), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 31/128 (24%), Positives = 55/128 (42%), Gaps = 24/128 (18%)
Query: 862 ILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKA 921
           +LLV+D+ +   +    +K+ G+ +    NG  A+  +     DLI++D+ MPVMDG   
Sbjct: 5   VLLVDDSAVLRKIVSFNLKKEGYEVIEAENGQIALEKLSEFTPDLIVLDIMMPVMDGF-- 62
Query: 922 TRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMD 981
             +++  ++   W                     KRIP+I +TA    E      + G  
Sbjct: 63  -TVLKKLQEKEEW---------------------KRIPVIVLTAKGGEEDESLALSLGAR 100
Query: 982 SFVSKPVT 989
             + KP +
Sbjct: 101 KVMRKPFS 108

>pdb|2ID9|A Chain A, 1.85 A Structure Of T87iY106W PHOSPHONO-Chey Length = 128

Iteration: 1
 Score = 45.4 bits (106), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 35/140 (25%), Positives = 65/140 (46%), Gaps = 25/140 (17%)
Query: 863  LLVEDNKINVMVAKSMMKQLG-HSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKA 921
            L+V+D      + ++++K+LG ++++   +GV+A++ +Q   Y  ++    MP MDGL+ 
Sbjct: 8    LVVDDFSTMRRIVRNLLKELGFNNVEEAEDGVDALNKLQAGGYGFVISXWNMPNMDGLEL 67
Query: 922  TRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMD 981
             + IR+       D A  A                 +P++ + A A  E+       G  
Sbjct: 68   LKTIRA-------DGAMSA-----------------LPVLMVIAEAKKENIIAAAQAGAS 103
Query: 982  SFVSKPVTFQKLKECLEQYF 1001
             +V KP T   L+E L + F
Sbjct: 104  GWVVKPFTAATLEEKLNKIF 123

>pdb|3GWG|A Chain A, Crystal Structure Of Chey Of Helicobacter Pylori Length = 129

Iteration: 1
 Score = 44.3 bits (103), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 37/140 (26%), Positives = 63/140 (45%), Gaps = 28/140 (20%)
Query: 862 ILLVEDNKINVMVAKSMMKQLGHSIDVVN--NGVEAVHAVQCQ-NYDLILMDVCMPVMDG 918
           +L+V+D+     + K+ + +LG+  DV+   +GVEA   +    +  +++ D  MP M+G
Sbjct: 8   LLVVDDSSTMRRIIKNTLSRLGYE-DVLEAEHGVEAWEKLDANADTKVLITDWNMPEMNG 66
Query: 919 LKATRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFAN 978
           L   + +RS                         + FK IPII +T              
Sbjct: 67  LDLVKKVRS------------------------DSRFKEIPIIMITTEGGKAEVITALKA 102
Query: 979 GMDSFVSKPVTFQKLKECLE 998
           G+++++ KP T Q LKE LE
Sbjct: 103 GVNNYIVKPFTPQVLKEKLE 122

>pdb|3D36|A Chain A, How To Switch Off A Histidine Kinase: Crystal Structure Of Geobacillus Stearothermophilus Kinb With The Inhibitor Sda Length = 244

Iteration: 1
 Score = 43.9 bits (102), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 24/75 (32%), Positives = 40/75 (53%), Gaps = 7/75 (9%)
Query: 590 VWIRCDVYDTGIGIPENALPTLFRKYMQVSADHARKYGGTGLGLAICKQLVELMGGRLTV 649
           V IR  + DTG+G+ +  L  L   Y        +   GTGLG+ +  +++E M G + +
Sbjct: 156 VLIR--IADTGVGMTKEQLERLGEPYFT-----TKGVKGTGLGMMVVYRIIESMNGTIRI 208
Query: 650 TSKVHCGSTFTFILP 664
            S++H G+T +  LP
Sbjct: 209 ESEIHKGTTVSIYLP 223

>pdb|1U8T|A Chain A, Crystal Structure Of Chey D13k Y106w Alone And In Complex With A Flim Peptide Length = 128

Iteration: 1
 Score = 43.5 bits (101), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 34/140 (24%), Positives = 64/140 (45%), Gaps = 25/140 (17%)
Query: 863  LLVEDNKINVMVAKSMMKQLG-HSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKA 921
            L+V+       + ++++K+LG ++++   +GV+A++ +Q   Y  ++ D   P  DGL+ 
Sbjct: 8    LVVDKFSTXRRIVRNLLKELGFNNVEEAEDGVDALNKLQAGGYGFVISDWNXPNXDGLEL 67
Query: 922  TRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMD 981
             + IR+       D A  A                 +P++ +TA A  E+       G  
Sbjct: 68   LKTIRA-------DGAXSA-----------------LPVLXVTAEAKKENIIAAAQAGAS 103
Query: 982  SFVSKPVTFQKLKECLEQYF 1001
             +V KP T   L+E L + F
Sbjct: 104  GWVVKPFTAATLEEKLNKIF 123

>pdb|3A0R|A Chain A, Crystal Structure Of Histidine Kinase Thka (Tm1359) In Complex With Response Regulator Protein Trra (Tm1360) Length = 349

Iteration: 1
 Score = 43.5 bits (101), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 53/205 (25%), Positives = 96/205 (46%), Gaps = 26/205 (12%)
Query: 372 QMLATMSHEIRSPLTGVVSMAEILSNTKLDREQ-RQLLGVMISSGDLVLQLINDILDLSK 430
           +M A ++HEIR+P+T +      +     D E  ++ + ++ +    +  ++ +IL+ SK
Sbjct: 134 EMTARVAHEIRNPITIIGGFIMRMKKHLDDPETLKKYINIITNELSRLETIVKEILEYSK 193
Query: 431 VESGVMKLEAAKFRPREVVKHVLQTAAASLQKILMLEGDIADDVPIEVIGDVLRIRQILT 490
            E  V  LE  +F   E+++ V       ++K+ +      D+  + V  D  RI+Q+L 
Sbjct: 194 -ERQV--LEFTEFNLNELIREVYVLFEEKIRKMNIDFCFETDNEDLRVEADRTRIKQVLI 250
Query: 491 NLISNAIKFTPE-GKVGI---------KLYVVPEPPFAKEGLKQK--SKAYQSATDA--- 535
           NL+ NAI+ T E GK+ I         ++ V    P   E LK+K  S  + + T     
Sbjct: 251 NLVQNAIEATGENGKIKITSEDMYTKVRVSVWNSGPPIPEELKEKIFSPFFTTKTQGTGL 310
Query: 536 -------VKEEKHQPKSQTASDQNG 553
                  + E++H  K  T + +NG
Sbjct: 311 GLSICRKIIEDEHGGKIWTENRENG 335

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	1002
1dcf_A	136	ETR1 protein; beta-alpha five sandwich, transferas	7e-52
3m6m_D	143	Sensory/regulatory protein RPFC; RPFF, REC, enoyl-	1e-51
2ayx_A	254	Sensor kinase protein RCSC; two independent struct	3e-50
2ayx_A	254	Sensor kinase protein RCSC; two independent struct	1e-13
3c97_A	140	Signal transduction histidine kinase; structural g	4e-50
2r25_B	133	Osmosensing histidine protein kinase SLN1; alpha5-	1e-47
4ew8_A	268	Sensor protein DIVL; signal transduction, two-comp	2e-47
4ew8_A	268	Sensor protein DIVL; signal transduction, two-comp	1e-27
1mb3_A	124	Cell division response regulator DIVK; signal tran	8e-47
3kht_A	144	Response regulator; PSI-II, 11023K, structural gen	1e-45
3mm4_A	206	Histidine kinase homolog; receiver domain, CKI1, c	2e-42
2c2a_A	258	Sensor histidine kinase; phosphotransfer, PHOQ, se	4e-40
2c2a_A	258	Sensor histidine kinase; phosphotransfer, PHOQ, se	3e-29
3i42_A	127	Response regulator receiver domain protein (CHEY-	5e-40
3luf_A	259	Two-component system response regulator/ggdef doma	1e-34
3luf_A	259	Two-component system response regulator/ggdef doma	2e-18
2qvg_A	143	Two component response regulator; NYSGXRC, PSI-2,	2e-28
3a0r_A	349	Sensor protein; four helix bundle, PAS fold, kinas	4e-27
3a0r_A	349	Sensor protein; four helix bundle, PAS fold, kinas	2e-13
3ilh_A	146	Two component response regulator; NYSGXRC, PSI-II,	5e-27
3sl2_A	177	Sensor histidine kinase YYCG; ATP binding, intact	2e-26
3sl2_A	177	Sensor histidine kinase YYCG; ATP binding, intact	3e-10
3grc_A	140	Sensor protein, kinase; protein structure initiati	3e-24
1k66_A	149	Phytochrome response regulator RCPB; CHEY homologu	1e-23
3bre_A	358	Probable two-component response regulator; protein	2e-22
1w25_A	459	Stalked-cell differentiation controlling protein;	8e-22
1w25_A	459	Stalked-cell differentiation controlling protein;	4e-12
1p6q_A	129	CHEY2; chemotaxis, signal transduction, response r	3e-20
3jz3_A	222	Sensor protein QSEC; helix-turn-helix, kinase doma	6e-20
3jz3_A	222	Sensor protein QSEC; helix-turn-helix, kinase doma	6e-13
3cnb_A	143	DNA-binding response regulator, MERR family; signa	1e-19
3heb_A	152	Response regulator receiver domain protein (CHEY);	1e-19
1gkz_A	388	[3-methyl-2-oxobutanoate dehydrogenase [lipoamide]	2e-19
1gkz_A	388	[3-methyl-2-oxobutanoate dehydrogenase [lipoamide]	2e-10
3h5i_A	140	Response regulator/sensory box protein/ggdef domai	7e-19
3gt7_A	154	Sensor protein; structural genomics, signal receiv	1e-18
3eq2_A	394	Probable two-component response regulator; adaptor	2e-18
3cg0_A	140	Response regulator receiver modulated diguanylate	2e-18
1i3c_A	149	Response regulator RCP1; phytochrome, signaling pr	3e-18
1jbe_A	128	Chemotaxis protein CHEY; signaling protein; 1.08A	3e-18
2zay_A	147	Response regulator receiver protein; structural ge	6e-18
3hdg_A	137	Uncharacterized protein; two-component sensor acti	1e-17
1ysr_A	150	Sensor-type histidine kinase PRRB; ATP-binding dom	2e-17
1ysr_A	150	Sensor-type histidine kinase PRRB; ATP-binding dom	4e-07
1bxd_A	161	ENVZ(290-450), protein (osmolarity sensor protein	2e-17
3nhm_A	133	Response regulator; protein structure initiative I	3e-17
3a0y_A	152	Sensor protein; ATP-LID, kinase, phosphoprotein, t	1e-16
3a0y_A	152	Sensor protein; ATP-LID, kinase, phosphoprotein, t	3e-06
3eod_A	130	Protein HNR; response regulator, phosphoprotein, t	3e-16
3n0r_A	286	Response regulator; sigma factor, receiver, two-co	4e-16
1srr_A	124	SPO0F, sporulation response regulatory protein; as	5e-16
3c3m_A	138	Response regulator receiver protein; structural ge	7e-16
1tmy_A	120	CHEY protein, TMY; chemotaxis, phosphoryl transfer	2e-15
1k68_A	140	Phytochrome response regulator RCPA; phosphorylate	3e-15
3r0j_A	250	Possible two component system response transcript	5e-15
3n53_A	140	Response regulator receiver modulated diguanylate;	5e-15
1mu5_A	471	Type II DNA topoisomerase VI subunit B; GHKL ATPas	6e-15
3d36_A	244	Sporulation kinase B; GHKL ATPase, four helix bund	1e-14
3d36_A	244	Sporulation kinase B; GHKL ATPase, four helix bund	1e-13
1y8o_A	419	[pyruvate dehydrogenase [lipoamide]] kinase isozy;	1e-14
1y8o_A	419	[pyruvate dehydrogenase [lipoamide]] kinase isozy;	9e-08
1s8n_A	205	Putative antiterminator; RV1626, structural genomi	1e-14
3cfy_A	137	Putative LUXO repressor protein; structural genomi	2e-14
3cg4_A	142	Response regulator receiver domain protein (CHEY-;	2e-14
3snk_A	135	Response regulator CHEY-like protein; P-loop conta	3e-14
3hdv_A	136	Response regulator; PSI-II, structural genomics, P	3e-14
2zbk_B	530	Type 2 DNA topoisomerase 6 subunit B; DNA binding	3e-14
3lua_A	140	Response regulator receiver protein; two-component	3e-14
2e0a_A	394	Pyruvate dehydrogenase kinase isozyme 4; PDK4, ATP	5e-14
3h1g_A	129	Chemotaxis protein CHEY homolog; sulfate-bound CHE	8e-14
3dzd_A	368	Transcriptional regulator (NTRC family); sigma43 a	1e-13
1ys7_A	233	Transcriptional regulatory protein PRRA; response	1e-13
2qxy_A	142	Response regulator; regulation of transcription, N	1e-13
2j48_A	119	Two-component sensor kinase; pseudo-receiver, circ	1e-13
3q9s_A	249	DNA-binding response regulator; DNA binding protei	1e-13
1id0_A	152	PHOQ histidine kinase; PHOQ/PHOP, signal transduct	2e-13
1id0_A	152	PHOQ histidine kinase; PHOQ/PHOP, signal transduct	4e-04
2q8g_A	407	[pyruvate dehydrogenase [lipoamide]] kinase isozy;	2e-13
2q8g_A	407	[pyruvate dehydrogenase [lipoamide]] kinase isozy;	1e-08
3lte_A	132	Response regulator; structural genomics, PSI, prot	2e-13
3hzh_A	157	Chemotaxis response regulator (CHEY-3); phosphatas	2e-13
2pl1_A	121	Transcriptional regulatory protein PHOP; CHEY-like	2e-13
1ny5_A	387	Transcriptional regulator (NTRC family); AAA+ ATPa	2e-13
1kgs_A	225	DRRD, DNA binding response regulator D; DNA-bindin	4e-13
3k3c_A	158	Protein RV1364C/MT1410; sensor, PAS, signal transd	5e-13
3kx0_X	185	Uncharacterized protein RV1364C/MT1410; PAS domain	7e-13
2btz_A	394	Pyruvate dehydrogenase kinase isoenzyme 2; GHKL mo	7e-13
2btz_A	394	Pyruvate dehydrogenase kinase isoenzyme 2; GHKL mo	2e-11
2qzj_A	136	Two-component response regulator; 11017X, PSI-II,	7e-13
1xhf_A	123	DYE resistance, aerobic respiration control protei	1e-12
3eqz_A	135	Response regulator; structural genomics, unknown f	2e-12
2a9o_A	120	Response regulator; essential protein, YYCF/YYCG h	3e-12
3a10_A	116	Response regulator; phosphoacceptor, signaling pro	3e-12
3f6p_A	120	Transcriptional regulatory protein YYCF; unphospho	3e-12
1r62_A	160	Nitrogen regulation protein NR(II); PII, histidine	3e-12
2rjn_A	154	Response regulator receiver:metal-dependent phosph	6e-12
4dad_A	146	Putative pilus assembly-related protein; response	6e-12
3gl9_A	122	Response regulator; beta-sheet, surrounded by alph	6e-12
1dc7_A	124	NTRC, nitrogen regulation protein; receiver domain	9e-12
4e7p_A	150	Response regulator; DNA binding, cytosol, transcri	9e-12
2q2e_B	621	Type 2 DNA topoisomerase 6 subunit B; DNA-binding,	9e-12
3hv2_A	153	Response regulator/HD domain protein; PSI-2, NYSGX	1e-11
1mvo_A	136	PHOP response regulator; phosphate regulon, transc	1e-11
1zgz_A	122	Torcad operon transcriptional regulatory protein;	2e-11
3t6k_A	136	Response regulator receiver; flavodoxin-like, stru	2e-11
3rqi_A	184	Response regulator protein; structural genomics, s	2e-11
2oqr_A	230	Sensory transduction protein REGX3; response regul	3e-11
2gwr_A	238	DNA-binding response regulator MTRA; two-component	3e-11
3cu5_A	141	Two component transcriptional regulator, ARAC FAM;	4e-11
2b4a_A	138	BH3024; flavodoxin-like fold, structural genomics,	5e-11
3crn_A	132	Response regulator receiver domain protein, CHEY-;	5e-11
2gkg_A	127	Response regulator homolog; social motility, recei	6e-11
3jte_A	143	Response regulator receiver protein; structural ge	7e-11
2jba_A	127	Phosphate regulon transcriptional regulatory PROT;	1e-10
3b2n_A	133	Uncharacterized protein Q99UF4; structural genomic	1e-10
2pln_A	137	HP1043, response regulator; signaling protein; 1.8	2e-10
1dz3_A	130	Stage 0 sporulation protein A; response regulator,	3e-10
3eul_A	152	Possible nitrate/nitrite response transcriptional	8e-10
3luq_A	114	Sensor protein; PAS, histidine, kinase, PSI, MCSG,	1e-09
2hqr_A	223	Putative transcriptional regulator; phosporylation	2e-09
3f6c_A	134	Positive transcription regulator EVGA; structural	2e-09
2qr3_A	140	Two-component system response regulator; structura	3e-09
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	5e-09
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	3e-08
3cz5_A	153	Two-component response regulator, LUXR family; str	6e-09
1yio_A	208	Response regulatory protein; transcription regulat	7e-09
1zh2_A	121	KDP operon transcriptional regulatory protein KDPE	7e-09
1th8_A	145	Anti-sigma F factor; SPOIIAB, SPOIIAA, anti-ANTI-s	9e-09
1a04_A	215	Nitrate/nitrite response regulator protein NARL; s	9e-09
2rdm_A	132	Response regulator receiver protein; structural ge	2e-08
3t8y_A	164	CHEB, chemotaxis response regulator protein-glutam	3e-08
3c3w_A	225	Two component transcriptional regulatory protein;	3e-08
3klo_A	225	Transcriptional regulator VPST; REC domain, HTH do	5e-08
1a2o_A	349	CHEB methylesterase; bacterial chemotaxis, adaptat	5e-08
3sy8_A	400	ROCR; TIM barrel phosphodiesterase-A, transcriptio	6e-08
1qkk_A	155	DCTD, C4-dicarboxylate transport transcriptional r	7e-08
1p2f_A	220	Response regulator; DRRB, OMPR/PHOB, transcription	9e-08
2qv0_A	143	Protein MRKE; structural genomics, transcription,	2e-07
3kyj_B	145	CHEY6 protein, putative histidine protein kinase;	3e-07
2qsj_A	154	DNA-binding response regulator, LUXR family; struc	5e-07
3kcn_A	151	Adenylate cyclase homolog; SGX, PSI 2, structural	2e-06
4fmt_A	228	CHPT protein; A phosphotransfer protein, A two-com	2e-06
4fmt_A	228	CHPT protein; A phosphotransfer protein, A two-com	5e-05
2jk1_A	139	HUPR, hydrogenase transcriptional regulatory prote	2e-06
1dbw_A	126	Transcriptional regulatory protein FIXJ; doubly wo	9e-06
1qo0_D	196	AMIR; binding protein, gene regulator, receptor; 2	3e-05
3mxq_A	152	Sensor protein; PSI2, MCSG, structural genomics, p	7e-05
3fc7_A	125	HTR-like protein, sensor protein; APC87712.1, HTR-	2e-04
3cax_A	369	Uncharacterized protein PF0695; structural genomic	7e-04

>1dcf_A ETR1 protein; beta-alpha five sandwich, transferase; 2.50A {Arabidopsis thaliana} SCOP: c.23.1.2 Length = 136

 Score =  177 bits (451), Expect = 7e-52
 Identities = 29/142 (20%), Positives = 63/142 (44%), Gaps = 22/142 (15%)

Query: 861  KILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLK 920
            K+L++++N ++ MV K ++  LG  +  V++  E +  V    + ++ MDVCMP ++  +
Sbjct: 9    KVLVMDENGVSRMVTKGLLVHLGCEVTTVSSNEECLRVVS-HEHKVVFMDVCMPGVENYQ 67

Query: 921  ATRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGM 980
                I                         +    +R  ++A++ N    + E+C + G+
Sbjct: 68   IALRIHEKF---------------------TKQRHQRPLLVALSGNTDKSTKEKCMSFGL 106

Query: 981  DSFVSKPVTFQKLKECLEQYFP 1002
            D  + KPV+   +++ L     
Sbjct: 107  DGVLLKPVSLDNIRDVLSDLLE 128

>3m6m_D Sensory/regulatory protein RPFC; RPFF, REC, enoyl-COA hydratase, lyase-transferase COMP; 2.50A {Xanthomonas campestris PV} Length = 143

 Score =  177 bits (450), Expect = 1e-51
 Identities = 33/156 (21%), Positives = 72/156 (46%), Gaps = 22/156 (14%)

Query: 847  SSAEVPETKPKPKPKILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDL 906
            S+  +         ++L+ +D++ N MV + ++++ GH +  VN   + + A+  ++YD 
Sbjct: 2    SNPFLRHRARVRSMRMLVADDHEANRMVLQRLLEKAGHKVLCVNGAEQVLDAMAEEDYDA 61

Query: 907  ILMDVCMPVMDGLKATRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTAN 966
            +++D+ MP M+GL   + +R  + +G                       +  P++ ++A+
Sbjct: 62   VIVDLHMPGMNGLDMLKQLRVMQASGM----------------------RYTPVVVLSAD 99

Query: 967  ALSESAEECFANGMDSFVSKPVTFQKLKECLEQYFP 1002
               E+   C   G  +F++KPV   KL + L     
Sbjct: 100  VTPEAIRACEQAGARAFLAKPVVAAKLLDTLADLAV 135

>2ayx_A Sensor kinase protein RCSC; two independent structural domains, transferase; NMR {Escherichia coli} SCOP: c.23.1.1 c.23.1.6 PDB: 2ayz_A 2ayy_A Length = 254

 Score =  177 bits (450), Expect = 3e-50
 Identities = 47/163 (28%), Positives = 76/163 (46%), Gaps = 27/163 (16%)

Query: 841  SQSPSSSSAEVPETKPKPKP-KILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAV 899
            S  P+++     +         IL+V+D+ IN  +    +  LG+     N+GV+A++ +
Sbjct: 110  SDDPANALPSTDKAVSDNDDMMILVVDDHPINRRLLADQLGSLGYQCKTANDGVDALNVL 169

Query: 900  QCQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIP 959
               + D++L DV MP MDG + T+ IR                               +P
Sbjct: 170  SKNHIDIVLSDVNMPNMDGYRLTQRIRQLG--------------------------LTLP 203

Query: 960  IIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQYFP 1002
            +I +TANAL+E  + C  +GMDS +SKPVT   +K+ L  Y  
Sbjct: 204  VIGVTANALAEEKQRCLESGMDSCLSKPVTLDVIKQTLTLYAE 246

>2ayx_A Sensor kinase protein RCSC; two independent structural domains, transferase; NMR {Escherichia coli} SCOP: c.23.1.1 c.23.1.6 PDB: 2ayz_A 2ayy_A Length = 254

 Score = 70.9 bits (174), Expect = 1e-13
 Identities = 7/103 (6%), Positives = 30/103 (29%), Gaps = 7/103 (6%)

Query: 583 DEDLEATVWIRCDVYDTGIGIPENA-LPTLFRKYMQVSADHARKYGGTGLGLAICKQLVE 641
             +     ++   +  +GI +             +      ++K+ G  + +  C++ + 
Sbjct: 18  VRNASLCQFLETSLQRSGIVVTTYEGQEPTPEDVLITDEVVSKKWQGRAV-VTFCRRHIG 76

Query: 642 L-----MGGRLTVTSKVHCGSTFTFILPYQVSPIEENSDDPDD 679
           +      G  +   +  H        +       ++ ++    
Sbjct: 77  IPLEKAPGEWVHSVAAPHELPALLARIYLIEMESDDPANALPS 119

>3c97_A Signal transduction histidine kinase; structural genomics, signaling, PSI-2, protein structure initiative; 1.70A {Aspergillus oryzae RIB40} Length = 140

 Score =  172 bits (438), Expect = 4e-50
 Identities = 46/151 (30%), Positives = 75/151 (49%), Gaps = 24/151 (15%)

Query: 852  PETKPKPKPKILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDV 911
             E        +L+ EDN I  +VA   +++  + I VV NG++A+ A Q + +D+I+MD+
Sbjct: 3    LEPSQIMPLSVLIAEDNDICRLVAAKALEKCTNDITVVTNGLQALQAYQNRQFDVIIMDI 62

Query: 912  CMPVMDGLKATRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSES 971
             MPVMDGL+A   IR++E T N                      KR  IIA+TA+ + + 
Sbjct: 63   QMPVMDGLEAVSEIRNYERTHNT---------------------KRASIIAITADTIDDD 101

Query: 972  AEECFANGMDSFVSKPVTFQKLKECLEQYFP 1002
                    +D +VSKP+   +L++ +     
Sbjct: 102  RPGA---ELDEYVSKPLNPNQLRDVVLTCHS 129

>2r25_B Osmosensing histidine protein kinase SLN1; alpha5-BETA5, response regulator, four helix bundle, histidine phosphotransfer (HPT) protein; 1.70A {Saccharomyces cerevisiae} SCOP: c.23.1.1 PDB: 1oxk_B 1oxb_B Length = 133

 Score =  165 bits (419), Expect = 1e-47
 Identities = 49/148 (33%), Positives = 74/148 (50%), Gaps = 31/148 (20%)

Query: 861  KILLVEDNKINVMVAKSMMKQLG-HSIDVVNNGVEAVHAVQ-----CQNYDLILMDVCMP 914
            KIL+VEDN +N  V K M+   G  +I++  +G EA   V+      +NY++I MDV MP
Sbjct: 4    KILVVEDNHVNQEVIKRMLNLEGIENIELACDGQEAFDKVKELTSKGENYNMIFMDVQMP 63

Query: 915  VMDGLKATRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEE 974
             +DGL +T++IR                                PI+A+TA A   + +E
Sbjct: 64   KVDGLLSTKMIRRDLG-------------------------YTSPIVALTAFADDSNIKE 98

Query: 975  CFANGMDSFVSKPVTFQKLKECLEQYFP 1002
            C  +GM+ F+SKP+   KLK  L ++  
Sbjct: 99   CLESGMNGFLSKPIKRPKLKTILTEFCA 126

>4ew8_A Sensor protein DIVL; signal transduction, two-component regulatory system, hiska GHKL domain, structural genomics; 2.50A {Caulobacter crescentus} Length = 268

 Score =  169 bits (431), Expect = 2e-47
 Identities = 39/183 (21%), Positives = 81/183 (44%), Gaps = 5/183 (2%)

Query: 336 KREKMAKLREEIAVQKAKETELNKTIHITEETMRAK-QMLATMSHEIRSPLTGVVSMAEI 394
                             ++ L        E  R K   +  +S+E+R+PLT ++  +E+
Sbjct: 5   HHHHHHSSGLVPRGSHMLQSALADRSAALAEAERLKRDFVGNVSYELRTPLTTIIGYSEL 64

Query: 395 LSNTK-LDREQRQLLGVMISSGDLVLQLINDILDLSKVESGVMKLEAAKFRPREVVKHVL 453
           L     +    R  +  + ++   + + I+D+LD++++++G M LE    R  +++ +  
Sbjct: 65  LERADGISERGRNHVAAVRAAATQLARSIDDVLDMAQIDAGEMALEIEDIRVSDLLLNAQ 124

Query: 454 QTAAASLQ-KILMLEGDIADDVPIEVIGDVLRIRQILTNLISNAIKFTPE-GKVGIKLYV 511
           + A    Q   + L  +  +DV   + GD  R+ Q L +L+ NA++ TP  G+V +    
Sbjct: 125 ERALKDAQLGGVTLAVECEEDVG-LIRGDGKRLAQTLDHLVENALRQTPPGGRVTLSARR 183

Query: 512 VPE 514
              
Sbjct: 184 ALG 186

>4ew8_A Sensor protein DIVL; signal transduction, two-component regulatory system, hiska GHKL domain, structural genomics; 2.50A {Caulobacter crescentus} Length = 268

 Score =  112 bits (282), Expect = 1e-27
 Identities = 33/79 (41%), Positives = 44/79 (55%), Gaps = 6/79 (7%)

Query: 591 WIRCDVYDTGIGIPENALPTLFRKYMQVSADHARKYGGTGLGLAICKQLVELMGGRLTVT 650
            +R DV DTG G+P +    +F +++       R  GG GLGLA+ K LVEL GG + + 
Sbjct: 187 EVRLDVSDTGRGVPFHVQAHIFDRFVG------RDRGGPGLGLALVKALVELHGGWVALE 240

Query: 651 SKVHCGSTFTFILPYQVSP 669
           S+   GSTFT  LP    P
Sbjct: 241 SEPGNGSTFTCHLPETQQP 259

>1mb3_A Cell division response regulator DIVK; signal transduction protein, structural proteomics in europe, spine, structural genomics; 1.41A {Caulobacter vibrioides} SCOP: c.23.1.1 PDB: 1m5u_A 1mav_A 1mb0_A 1m5t_A Length = 124

 Score =  162 bits (412), Expect = 8e-47
 Identities = 33/142 (23%), Positives = 67/142 (47%), Gaps = 24/142 (16%)

Query: 861  KILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLK 920
            K+L+VEDN++N+ +   +++  G+       G+ A+   +    DLILMD+ +P + GL+
Sbjct: 3    KVLIVEDNELNMKLFHDLLEAQGYETLQTREGLSALSIARENKPDLILMDIQLPEISGLE 62

Query: 921  ATRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGM 980
             T+ ++  +D                           IP++A+TA A+    E     G 
Sbjct: 63   VTKWLKEDDD------------------------LAHIPVVAVTAFAMKGDEERIREGGC 98

Query: 981  DSFVSKPVTFQKLKECLEQYFP 1002
            ++++SKP++     E +++   
Sbjct: 99   EAYISKPISVVHFLETIKRLLE 120

>3kht_A Response regulator; PSI-II, 11023K, structural genomics, Pro structure initiative, NEW YORK SGX research center for STRU genomics, nysgxrc; 2.10A {Hahella chejuensis} Length = 144

 Score =  160 bits (406), Expect = 1e-45
 Identities = 30/149 (20%), Positives = 65/149 (43%), Gaps = 31/149 (20%)

Query: 861  KILLVEDNKINVMVAKSMMKQ--LGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDG 918
            ++L+VEDN  ++ + + ++ +  +   ++ V+NG +A++ VQ   YDLI++D+ +P+ +G
Sbjct: 7    RVLVVEDNPDDIALIRRVLDRKDIHCQLEFVDNGAKALYQVQQAKYDLIILDIGLPIANG 66

Query: 919  LKATRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFAN 978
             +    +R                             +  PI+ +T N   + A++C A 
Sbjct: 67   FEVMSAVRKPGA------------------------NQHTPIVILTDNVSDDRAKQCMAA 102

Query: 979  GMDSFVSKPV-----TFQKLKECLEQYFP 1002
            G  S V K        + ++      +  
Sbjct: 103  GASSVVDKSSNNVTDFYGRIYAIFSYWLT 131

>3mm4_A Histidine kinase homolog; receiver domain, CKI1, cytokinin signaling, ROS fold, CHEY-like, transferase; 2.00A {Arabidopsis thaliana} PDB: 3mmn_A Length = 206

 Score =  152 bits (386), Expect = 2e-42
 Identities = 48/183 (26%), Positives = 77/183 (42%), Gaps = 40/183 (21%)

Query: 835  EKPDRISQSPSSSSAEVPETKPKPKPKILLVEDNKINVMVAKSMMKQLGHS-IDVVNNGV 893
             KP    +    +S    +   + K ++L+V+DN I+  VA   +K++G S ++  ++G 
Sbjct: 38   RKPIGNPEDEQETSKPSDDEFLRGK-RVLVVDDNFISRKVATGKLKKMGVSEVEQCDSGK 96

Query: 894  EAVHAVQ-------------CQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDAAAEA 940
            EA+  V                 +D I MD  MP MDG +ATR IR  E +         
Sbjct: 97   EALRLVTEGLTQREEQGSVDKLPFDYIFMDCQMPEMDGYEATREIRKVEKSYG------- 149

Query: 941  GIEQAMPSSGSSNHFKRIPIIAMTANAL-SESAEECFANGMDSFVSKPVTFQKLKECLEQ 999
                            R PIIA++ +   SE A E    GMD+F+ K +   +L   + +
Sbjct: 150  ---------------VRTPIIAVSGHDPGSEEARETIQAGMDAFLDKSL--NQLANVIRE 192

Query: 1000 YFP 1002
               
Sbjct: 193  IES 195

>2c2a_A Sensor histidine kinase; phosphotransfer, PHOQ, selenomethionyl MAD, two-component systems, transferase; HET: ADP; 1.9A {Thermotoga maritima} SCOP: a.30.2.1 d.122.1.3 PDB: 3dge_A* Length = 258

 Score =  148 bits (375), Expect = 4e-40
 Identities = 39/171 (22%), Positives = 84/171 (49%), Gaps = 11/171 (6%)

Query: 345 EEIAVQKAKETELNKTIHITEETMRAKQMLATMSHEIRSPLTGVVSMAEILSNTKLDR-- 402
           E +   K +   L +      + M+  + +A +SHE+R+PLT + + AE + N+  +   
Sbjct: 2   ENVTESK-ELERLKRI-----DRMK-TEFIANISHELRTPLTAIKAYAETIYNSLGELDL 54

Query: 403 -EQRQLLGVMISSGDLVLQLINDILDLSKVESGVMKLEAAKFRPREVVKHVLQT-AAASL 460
              ++ L V+I   + +  L+N++LD S++E   +++   K    ++V+  +      + 
Sbjct: 55  STLKEFLEVIIDQSNHLENLLNELLDFSRLERKSLQINREKVDLCDLVESAVNAIKEFAS 114

Query: 461 QKILMLEGDIADDVPIEVIGDVLRIRQILTNLISNAIKFTPEGKVGIKLYV 511
              + +  +     P+E   D  RIRQ+L NL++N +K++ +      + V
Sbjct: 115 SHNVNVLFESNVPCPVEAYIDPTRIRQVLLNLLNNGVKYSKKDAPDKYVKV 165

>2c2a_A Sensor histidine kinase; phosphotransfer, PHOQ, selenomethionyl MAD, two-component systems, transferase; HET: ADP; 1.9A {Thermotoga maritima} SCOP: a.30.2.1 d.122.1.3 PDB: 3dge_A* Length = 258

 Score =  116 bits (294), Expect = 3e-29
 Identities = 33/86 (38%), Positives = 50/86 (58%)

Query: 591 WIRCDVYDTGIGIPENALPTLFRKYMQVSADHARKYGGTGLGLAICKQLVELMGGRLTVT 650
            +   V D GIGIP++A   +F ++ +V +    +  GTGLGLAI K++VEL GGR+ V 
Sbjct: 173 GVLIIVEDNGIGIPDHAKDRIFEQFYRVDSSLTYEVPGTGLGLAITKEIVELHGGRIWVE 232

Query: 651 SKVHCGSTFTFILPYQVSPIEENSDD 676
           S+V  GS F   +P   +  +   D+
Sbjct: 233 SEVGKGSRFFVWIPKDRAGEDNRQDN 258

>3i42_A Response regulator receiver domain protein (CHEY- like); structural genomics, PSI-2, protein structure initiative; 2.15A {Methylobacillus flagellatus KT} Length = 127

 Score =  143 bits (362), Expect = 5e-40
 Identities = 28/142 (19%), Positives = 57/142 (40%), Gaps = 25/142 (17%)

Query: 859  KPKILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDG 918
              + L+VED +      K +++ LG   D V +G +A+HA+  + YD + +D+ +P   G
Sbjct: 3    LQQALIVEDYQAAAETFKELLEMLGFQADYVMSGTDALHAMSTRGYDAVFIDLNLPDTSG 62

Query: 919  LKATRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFAN 978
            L   + +R+                            K    +A++  A ++   +    
Sbjct: 63   LALVKQLRALPME------------------------KTSKFVAVSGFAKND-LGKEACE 97

Query: 979  GMDSFVSKPVTFQKLKECLEQY 1000
              D ++ KP+    L+  L+  
Sbjct: 98   LFDFYLEKPIDIASLEPILQSI 119

>3luf_A Two-component system response regulator/ggdef domain protein; structural genomics, ASA_2441, PSI-2, protein structure initiative; HET: MSE; 1.76A {Aeromonas salmonicida} PDB: 3mf4_A* Length = 259

 Score =  132 bits (334), Expect = 1e-34
 Identities = 21/141 (14%), Positives = 58/141 (41%), Gaps = 25/141 (17%)

Query: 861  KILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAV-QCQNYDLILMDVCMPVMDGL 919
            ++L+V+D++ +     + +++    +   ++  EA+  + Q     L+L+D  MP +DG+
Sbjct: 126  EVLVVDDSRTSRHRTMAQLRKQLLQVHEASHAREALATLEQHPAIRLVLVDYYMPEIDGI 185

Query: 920  KATRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANG 979
               R++R                             +++ II ++ +     +      G
Sbjct: 186  SLVRMLRERYS------------------------KQQLAIIGISVSDKRGLSARYLKQG 221

Query: 980  MDSFVSKPVTFQKLKECLEQY 1000
             + F+++P   ++L+  +   
Sbjct: 222  ANDFLNQPFEPEELQCRVSHN 242

>3luf_A Two-component system response regulator/ggdef domain protein; structural genomics, ASA_2441, PSI-2, protein structure initiative; HET: MSE; 1.76A {Aeromonas salmonicida} PDB: 3mf4_A* Length = 259

 Score = 85.4 bits (212), Expect = 2e-18
 Identities = 22/131 (16%), Positives = 45/131 (34%), Gaps = 28/131 (21%)

Query: 859 KPKILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDG 918
           K KIL+VED+     +    + Q         + +E     Q   Y + L+D+ +P    
Sbjct: 4   KQKILIVEDSMTIRRMLIQAIAQQTGLEIDAFDTLEGARHCQGDEYVVALVDLTLPDAPS 63

Query: 919 LKATRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFAN 978
            +A +++                              + +P++ +TA+   +  E     
Sbjct: 64  GEAVKVLLE----------------------------RGLPVVILTADISEDKREAWLEA 95

Query: 979 GMDSFVSKPVT 989
           G+  +V K   
Sbjct: 96  GVLDYVMKDSR 106

>2qvg_A Two component response regulator; NYSGXRC, PSI-2, structural genomics, protein structure initiative; 1.50A {Legionella pneumophila subsp} Length = 143

 Score =  110 bits (277), Expect = 2e-28
 Identities = 24/150 (16%), Positives = 61/150 (40%), Gaps = 32/150 (21%)

Query: 854 TKPKPKPKILLVEDNKINVMVAKSMMKQLG--HSIDVVNNGVEAVHAVQCQNY------D 905
           +    K  IL +ED+++++   + +  ++     I++  +G +A+  +  +N        
Sbjct: 2   SLAADKVDILYLEDDEVDIQSVERVFHKISSLIKIEIAKSGNQALDMLYGRNKENKIHPK 61

Query: 906 LILMDVCMPVMDGLKATRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTA 965
           LIL+D+ +P M+G++  + +R                          + F  I +  +TA
Sbjct: 62  LILLDINIPKMNGIEFLKELRD------------------------DSSFTDIEVFVLTA 97

Query: 966 NALSESAEECFANGMDSFVSKPVTFQKLKE 995
              S+      +  +   + KP+ + +  +
Sbjct: 98  AYTSKDKLAFESLNIRGHLIKPLDYGEAIK 127

>3a0r_A Sensor protein; four helix bundle, PAS fold, kinase, phosphoprotein, transfe two-component regulatory system; 3.80A {Thermotoga maritima} Length = 349

 Score =  112 bits (283), Expect = 4e-27
 Identities = 63/308 (20%), Positives = 120/308 (38%), Gaps = 43/308 (13%)

Query: 216 ILKRADNFLHFVLQNAPVVMGHQDKELRYRFIYNH----FPSLHEEDILGKTDVEIFSGA 271
           +++   NF   +L++    +    K+ R     N        L +E++LG+   ++    
Sbjct: 2   LVEHLRNFSESILESLETAIITLSKDGRITEW-NKKAEQLFGLKKENVLGRRLKDLPDF- 59

Query: 272 GVKESQDFKREVLEKGLPAKREITFETELFGSKTFLIYVEPVFSKSGETI-GVNYMGMDV 330
             +E       V E     K  +      FG + F I   P  +   + + GV     DV
Sbjct: 60  --EEIGSVAESVFEN----KEPVFLNFYKFGERYFNIRFSPFRNAKTQLLEGVIITIDDV 113

Query: 331 TDQVRKREKMAKLREEIAVQKAKETELNKTIHITEETMRAKQMLATMSHEIRSPLTGVVS 390
           T+   K E+  K RE +++                      +M A ++HEIR+P+T +  
Sbjct: 114 TEL-YKYEEERKRRERLSI--------------------LGEMTARVAHEIRNPITIIGG 152

Query: 391 MAEIL-SNTKLDREQRQLLGVMISSGDLVLQLINDILDLSKVESGVMKLEAAKFRPREVV 449
               +  +       ++ + ++ +    +  ++ +IL+ SK       LE  +F   E++
Sbjct: 153 FIMRMKKHLDDPETLKKYINIITNELSRLETIVKEILEYSKERQ---VLEFTEFNLNELI 209

Query: 450 KHVLQ--TAAASLQKILMLEGDIADDVPIEVIGDVLRIRQILTNLISNAIKFTPE-GKVG 506
           + V            I     +  ++    V  D  RI+Q+L NL+ NAI+ T E GK+ 
Sbjct: 210 REVYVLFEEKIRKMNI-DFCFETDNEDL-RVEADRTRIKQVLINLVQNAIEATGENGKIK 267

Query: 507 IKLYVVPE 514
           I    +  
Sbjct: 268 ITSEDMYT 275

>3a0r_A Sensor protein; four helix bundle, PAS fold, kinase, phosphoprotein, transfe two-component regulatory system; 3.80A {Thermotoga maritima} Length = 349

 Score = 71.9 bits (177), Expect = 2e-13
 Identities = 23/77 (29%), Positives = 40/77 (51%), Gaps = 8/77 (10%)

Query: 591 WIRCDVYDTGIGIPENALPTLFRKYMQVSADHARKYGGTGLGLAICKQLVELM-GGRLTV 649
            +R  V+++G  IPE     +F  +         K  GTGLGL+IC++++E   GG++  
Sbjct: 276 KVRVSVWNSGPPIPEELKEKIFSPF------FTTKTQGTGLGLSICRKIIEDEHGGKIWT 329

Query: 650 TSKVHCGSTFTFILPYQ 666
            ++ + G  F F +P  
Sbjct: 330 ENREN-GVVFIFEIPKT 345

>3ilh_A Two component response regulator; NYSGXRC, PSI-II, protein S initiative, structural genomics; 2.59A {Cytophaga hutchinsonii} Length = 146

 Score =  106 bits (267), Expect = 5e-27
 Identities = 22/153 (14%), Positives = 56/153 (36%), Gaps = 30/153 (19%)

Query: 857  KPKPKILLVEDNKINVMVAKSMMKQLG--HSIDVVNNGVEAVHAVQ-----CQNYDLILM 909
            +    +LL++D+ I   +  ++++       I  V +G  A++ +       +   +I +
Sbjct: 7    RKIDSVLLIDDDDIVNFLNTTIIRMTHRVEEIQSVTSGNAAINKLNELYAAGRWPSIICI 66

Query: 910  DVCMPVMDGLKATRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALS 969
            D+ MP ++G +   L +                              +  +  ++++   
Sbjct: 67   DINMPGINGWELIDLFKQHFQP----------------------MKNKSIVCLLSSSLDP 104

Query: 970  ESAEECFAN-GMDSFVSKPVTFQKLKECLEQYF 1001
                +  A+  +D +VSKP+T   L     +  
Sbjct: 105  RDQAKAEASDWVDYYVSKPLTANALNNLYNKVL 137

>3sl2_A Sensor histidine kinase YYCG; ATP binding, intact ATP, bergerat fold, TR; HET: ATP; 1.61A {Bacillus subtilis} Length = 177

 Score =  105 bits (265), Expect = 2e-26
 Identities = 32/92 (34%), Positives = 49/92 (53%)

Query: 591 WIRCDVYDTGIGIPENALPTLFRKYMQVSADHARKYGGTGLGLAICKQLVELMGGRLTVT 650
            +   V D GIGIP+  +  +F ++ +V     RK GGTGLGLAI K++V+  GG +   
Sbjct: 77  LLYISVKDEGIGIPKKDVEKVFDRFYRVDKARTRKLGGTGLGLAIAKEMVQAHGGDIWAD 136

Query: 651 SKVHCGSTFTFILPYQVSPIEENSDDPDDLSD 682
           S    G+T TF LPY+    ++  +  +    
Sbjct: 137 SIEGKGTTITFTLPYKEEQEDDWDEAENLYFQ 168

>3sl2_A Sensor histidine kinase YYCG; ATP binding, intact ATP, bergerat fold, TR; HET: ATP; 1.61A {Bacillus subtilis} Length = 177

 Score = 59.2 bits (144), Expect = 3e-10
 Identities = 18/70 (25%), Positives = 35/70 (50%), Gaps = 2/70 (2%)

Query: 446 REVVKHVLQTAAASLQKILMLEGDIADDVPIEVIGDVLRIRQILTNLISNAIKFTPE-GK 504
              +  ++     + ++ +    ++ D   + V  D  +I Q+L N+ISNA+K++PE G 
Sbjct: 6   VRFMSLIIDRFEMTKEQHVEFIRNLPDR-DLYVEIDQDKITQVLDNIISNALKYSPEGGH 64

Query: 505 VGIKLYVVPE 514
           V   + V  E
Sbjct: 65  VTFSIDVNEE 74

>3grc_A Sensor protein, kinase; protein structure initiative II(PSI II), NYSGXRC, 11025B, structural genomics; 2.21A {Polaromonas SP} Length = 140

 Score = 98.4 bits (246), Expect = 3e-24
 Identities = 27/133 (20%), Positives = 56/133 (42%), Gaps = 25/133 (18%)

Query: 856 PKPKPKILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPV 915
             P+P+IL+ ED+     +   M+++ G   D+V++  +A+  V  + Y  + +D+ +P 
Sbjct: 3   LAPRPRILICEDDPDIARLLNLMLEKGGFDSDMVHSAAQALEQVARRPYAAMTVDLNLPD 62

Query: 916 MDGLKATRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANAL-SESAEE 974
            DG+   R +R    T                        + + I+ ++ANA   E    
Sbjct: 63  QDGVSLIRALRRDSRT------------------------RDLAIVVVSANAREGELEFN 98

Query: 975 CFANGMDSFVSKP 987
                + +++ KP
Sbjct: 99  SQPLAVSTWLEKP 111

>1k66_A Phytochrome response regulator RCPB; CHEY homologue, homodimer, APO-protein, (beta/alpha)5, signaling protein; 1.75A {Tolypothrix SP} SCOP: c.23.1.1 Length = 149

 Score = 96.9 bits (242), Expect = 1e-23
 Identities = 28/156 (17%), Positives = 63/156 (40%), Gaps = 36/156 (23%)

Query: 856 PKPKPKILLVEDNKINVMVAKSMMKQLG--HSIDVVNNGVEAVHAVQCQNY--------- 904
                 +L+VED+  +    + ++++ G  + I     G +A+  +              
Sbjct: 3   GNATQPLLVVEDSDEDFSTFQRLLQREGVVNPIYRCITGDQALDFLYQTGSYCNPDIAPR 62

Query: 905 -DLILMDVCMPVMDGLKATRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAM 963
             +IL+D+ +P  DG +  + I+  E                          K+IP++ M
Sbjct: 63  PAVILLDLNLPGTDGREVLQEIKQDEVL------------------------KKIPVVIM 98

Query: 964 TANALSESAEECFANGMDSFVSKPVTFQKLKECLEQ 999
           T ++  +  E C++  + S++ KP+   +L E ++ 
Sbjct: 99  TTSSNPKDIEICYSYSISSYIVKPLEIDRLTETVQT 134

>3bre_A Probable two-component response regulator; protein-nucleotide complex, signaling protein; HET: C2E; 2.40A {Pseudomonas aeruginosa} PDB: 3i5a_A* Length = 358

 Score = 99.0 bits (247), Expect = 2e-22
 Identities = 29/154 (18%), Positives = 51/154 (33%), Gaps = 26/154 (16%)

Query: 842 QSPSSSSAEVPETKPKPKPKILLVEDNKINVMV-AKSMMKQLGHSIDVVNNGVEAVHAVQ 900
            +P  S  ++          +LLV+D  +      +S+  + G      ++  +AV    
Sbjct: 2   HNPHESKTDLGAPLDGA-VMVLLVDDQAMIGEAVRRSLASEAGIDFHFCSDPQQAVAVAN 60

Query: 901 CQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPI 960
                +IL D+ MP +DGL      R    T                        + IPI
Sbjct: 61  QIKPTVILQDLVMPGVDGLTLLAAYRGNPAT------------------------RDIPI 96

Query: 961 IAMTANALSESAEECFANGMDSFVSKPVTFQKLK 994
           I ++           FA G + ++ K     +L 
Sbjct: 97  IVLSTKEEPTVKSAAFAAGANDYLVKLPDAIELV 130

>1w25_A Stalked-cell differentiation controlling protein; two-component system, ggdef domain, cyclic dinucleotide, cyclic-digmp; HET: C2E; 2.70A {Caulobacter vibrioides} SCOP: c.23.1.1 c.23.1.1 d.58.29.2 PDB: 2v0n_A* 2wb4_A* Length = 459

 Score = 98.7 bits (246), Expect = 8e-22
 Identities = 29/140 (20%), Positives = 55/140 (39%), Gaps = 24/140 (17%)

Query: 861  KILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLK 920
            +IL+V+D + NV + ++ +    + +    +G  A+        D+IL+DV MP MDG  
Sbjct: 3    RILVVDDIEANVRLLEAKLTAEYYEVSTAMDGPTALAMAARDLPDIILLDVMMPGMDGFT 62

Query: 921  ATRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGM 980
              R ++    T                        + IP++ +TA        +   +G 
Sbjct: 63   VCRKLKDDPTT------------------------RHIPVVLITALDGRGDRIQGLESGA 98

Query: 981  DSFVSKPVTFQKLKECLEQY 1000
              F++KP+    L   +   
Sbjct: 99   SDFLTKPIDDVMLFARVRSL 118

>1w25_A Stalked-cell differentiation controlling protein; two-component system, ggdef domain, cyclic dinucleotide, cyclic-digmp; HET: C2E; 2.70A {Caulobacter vibrioides} SCOP: c.23.1.1 c.23.1.1 d.58.29.2 PDB: 2v0n_A* 2wb4_A* Length = 459

 Score = 68.7 bits (168), Expect = 4e-12
 Identities = 22/133 (16%), Positives = 48/133 (36%), Gaps = 26/133 (19%)

Query: 856 PKPKPKILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPV 915
                ++L+V+DN+       + +        V+ +  E          DL++++     
Sbjct: 149 DGLGGRVLIVDDNERQAQRVAAELGVEHRP--VIESDPEKAKISAGGPVDLVIVNAAAKN 206

Query: 916 MDGLKATRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEEC 975
            DGL+ T  +RS E T                        +++P++AM          + 
Sbjct: 207 FDGLRFTAALRSEERT------------------------RQLPVLAMVDPDDRGRMVKA 242

Query: 976 FANGMDSFVSKPV 988
              G++  +S+P+
Sbjct: 243 LEIGVNDILSRPI 255

>1p6q_A CHEY2; chemotaxis, signal transduction, response regulator, structural proteomics in europe, spine, structural genomics; NMR {Sinorhizobium meliloti} SCOP: c.23.1.1 PDB: 1p6u_A Length = 129

 Score = 86.4 bits (215), Expect = 3e-20
 Identities = 32/143 (22%), Positives = 61/143 (42%), Gaps = 25/143 (17%)

Query: 857 KPKPKILLVEDNKINVMVAKSMMKQLGHS-IDVVNNGVEAVHAVQCQNYDLILMDVCMPV 915
             K K+L+V+D   + ++    ++QLG   I    +G + +  +    + L++ D  MP 
Sbjct: 4   AEKIKVLIVDDQVTSRLLLGDALQQLGFKQITAAGDGEQGMKIMAQNPHHLVISDFNMPK 63

Query: 916 MDGLKATRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEEC 975
           MDGL   + +R+   T                        K+   I +TA       ++ 
Sbjct: 64  MDGLGLLQAVRANPAT------------------------KKAAFIILTAQGDRALVQKA 99

Query: 976 FANGMDSFVSKPVTFQKLKECLE 998
            A G ++ ++KP T +K+K  +E
Sbjct: 100 AALGANNVLAKPFTIEKMKAAIE 122

>3jz3_A Sensor protein QSEC; helix-turn-helix, kinase domain, ATP-binding, cell inner MEM cell membrane, kinase, membrane, nucleotide-binding; 2.50A {Escherichia coli} Length = 222

 Score = 88.8 bits (221), Expect = 6e-20
 Identities = 29/128 (22%), Positives = 65/128 (50%), Gaps = 3/128 (2%)

Query: 378 SHEIRSPLTGVVSMAEILSNTKLDREQR-QLLGVMISSGDLVLQLINDILDLSKVESGVM 436
           +HE+RSPLT +    E+   +  D + R + L  + S  D   +L++ +L LS+++S   
Sbjct: 10  AHELRSPLTALKVQTEVAQLSDDDPQARKKALLQLHSGIDRATRLVDQLLTLSRLDSLDN 69

Query: 437 KLEAAKFRPREVVKHVLQTAA-ASLQKILMLEGDIADDVPIEVIGDVLRIRQILTNLISN 495
             + A+    ++++  +      + Q  + +     +   I+  G  L +  ++ NL+ N
Sbjct: 70  LQDVAEIPLEDLLQSSVMDIYHTAQQAKIDVRLT-LNAHSIKRTGQPLLLSLLVRNLLDN 128

Query: 496 AIKFTPEG 503
           A++++P+G
Sbjct: 129 AVRYSPQG 136

>3jz3_A Sensor protein QSEC; helix-turn-helix, kinase domain, ATP-binding, cell inner MEM cell membrane, kinase, membrane, nucleotide-binding; 2.50A {Escherichia coli} Length = 222

 Score = 68.3 bits (168), Expect = 6e-13
 Identities = 17/86 (19%), Positives = 30/86 (34%), Gaps = 16/86 (18%)

Query: 588 ATVWIRCD-----VYDTGIGIPENALPTLF----RKYMQVSADHARKYGGTGLGLAICKQ 638
           + V +  +     V D G G+   AL  +     R              G+GLGL+I ++
Sbjct: 137 SVVDVTLNADNFIVRDNGPGVTPEALARIGERFYR------PPGQTA-TGSGLGLSIVQR 189

Query: 639 LVELMGGRLTVTSKVHCGSTFTFILP 664
           + +L G  +   +    G        
Sbjct: 190 IAKLHGMNVEFGNAEQGGFEAKVSWL 215

>3cnb_A DNA-binding response regulator, MERR family; signal receiver domain, DNA binding protein, protein structu initiative, PSI-2; 2.00A {Colwellia psychrerythraea} Length = 143

 Score = 85.3 bits (212), Expect = 1e-19
 Identities = 29/142 (20%), Positives = 51/142 (35%), Gaps = 26/142 (18%)

Query: 855 KPKPKPKILLVEDNKINVMVAKSMMKQLGHSIDVV--NNGVEAVHAVQCQNYDLILMDVC 912
             K    IL++ED+K    +    ++ L     +    N  +A   +     D++++D+ 
Sbjct: 4   NVKNDFSILIIEDDKEFADMLTQFLENLFPYAKIKIAYNPFDAGDLLHTVKPDVVMLDLM 63

Query: 913 MPVMDGLKATRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESA 972
           M  MDG      I+S   T                          I +IAMT     ++ 
Sbjct: 64  MVGMDGFSICHRIKSTPAT------------------------ANIIVIAMTGALTDDNV 99

Query: 973 EECFANGMDSFVSKPVTFQKLK 994
               A G ++   KP+ F  L+
Sbjct: 100 SRIVALGAETCFGKPLNFTLLE 121

>3heb_A Response regulator receiver domain protein (CHEY); NYSGXRC, PSI-II, respose regulator, structure initiative, structural genomics; 2.40A {Rhodospirillum rubrum} Length = 152

 Score = 85.4 bits (212), Expect = 1e-19
 Identities = 25/157 (15%), Positives = 62/157 (39%), Gaps = 38/157 (24%)

Query: 859  KPKILLVEDNKINVMVAKSMMKQLG--HSIDVVNNGVEAVHAVQCQNY---------DLI 907
               I+++ED+  +  + +  +++ G  + I    +G  A++ +   +           L+
Sbjct: 4    SVTIVMIEDDLGHARLIEKNIRRAGVNNEIIAFTDGTSALNYLFGDDKSGRVSAGRAQLV 63

Query: 908  LMDVCMPVMDGLKATRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANA 967
            L+D+ +P M G+   +L++    T                        +R P++ +T   
Sbjct: 64   LLDLNLPDMTGIDILKLVKENPHT------------------------RRSPVVILTTTD 99

Query: 968  LSESAEECFANGMDSFVSKPVTFQKLKE---CLEQYF 1001
                 + C+  G + +++KPV ++        L  +F
Sbjct: 100  DQREIQRCYDLGANVYITKPVNYENFANAIRQLGLFF 136

>1gkz_A [3-methyl-2-oxobutanoate dehydrogenase [lipoamide]] kinase; transferase, mitochondrial protein kinase, potassium; HET: ADP; 2.2A {Rattus norvegicus} SCOP: a.29.5.1 d.122.1.4 PDB: 1gjv_A 1gkx_A* Length = 388

 Score = 90.9 bits (225), Expect = 2e-19
 Identities = 22/148 (14%), Positives = 50/148 (33%), Gaps = 6/148 (4%)

Query: 372 QMLATMSHEIRSPLTGVVSMA----EILSNTKLDREQRQLLGVMISSGDLVLQLINDILD 427
           Q    +   +      V  +A    E   + + ++  R  L   ++S   +  L    L 
Sbjct: 120 QYCQLVRQLLDDHKDVVTLLAEGLRESRKHIEDEKLVRYFLDKTLTSRLGIRMLATHHLA 179

Query: 428 LSKVESGVMKLEAAKFRPREVVKHVLQTAAASLQ--KILMLEGDIADDVPIEVIGDVLRI 485
           L + +   + +   +  P+++++  +  A    +          I   V        + +
Sbjct: 180 LHEDKPDFVGIICTRLSPKKIIEKWVDFARRLCEHKYGNAPRVRINGHVAARFPFIPMPL 239

Query: 486 RQILTNLISNAIKFTPEGKVGIKLYVVP 513
             IL  L+ NA++ T E  +     V  
Sbjct: 240 DYILPELLKNAMRATMESHLDTPYNVPD 267

>1gkz_A [3-methyl-2-oxobutanoate dehydrogenase [lipoamide]] kinase; transferase, mitochondrial protein kinase, potassium; HET: ADP; 2.2A {Rattus norvegicus} SCOP: a.29.5.1 d.122.1.4 PDB: 1gjv_A 1gkx_A* Length = 388

 Score = 63.1 bits (153), Expect = 2e-10
 Identities = 18/102 (17%), Positives = 28/102 (27%), Gaps = 20/102 (19%)

Query: 591 WIRCDVYDTGIGIPENALPTLFRKY--------------------MQVSADHARKYGGTG 630
            +   + D G GI    L  +   +                       S   +    G G
Sbjct: 278 DLIIRISDRGGGIAHKDLDRVMDYHFTTAEASTQDPRISPLFGHLDMHSGGQSGPMHGFG 337

Query: 631 LGLAICKQLVELMGGRLTVTSKVHCGSTFTFILPYQVSPIEE 672
            GL   +   E +GG L + S    G+     L +     E 
Sbjct: 338 FGLPTSRAYAEYLGGSLQLQSLQGIGTDVYLRLRHIDGREES 379

>3h5i_A Response regulator/sensory box protein/ggdef domain protein; structural genomics, transcription, PSI-2; 1.90A {Carboxydothermus hydrogenoformans z-2901} Length = 140

 Score = 83.0 bits (206), Expect = 7e-19
 Identities = 29/133 (21%), Positives = 54/133 (40%), Gaps = 29/133 (21%)

Query: 858 PKPKILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNY-DLILMDVCMP-V 915
              KIL+VED+K       +++ + G+++++   G  AV  V    Y DLILMD+ +   
Sbjct: 4   KDKKILIVEDSKFQAKTIANILNKYGYTVEIALTGEAAVEKVSGGWYPDLILMDIELGEG 63

Query: 916 MDGLKATRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEEC 975
           MDG++    I+   +                           +P++ +TA+      E+ 
Sbjct: 64  MDGVQTALAIQQISE---------------------------LPVVFLTAHTEPAVVEKI 96

Query: 976 FANGMDSFVSKPV 988
            +     +V K  
Sbjct: 97  RSVTAYGYVMKSA 109

>3gt7_A Sensor protein; structural genomics, signal receiver domain, kinase, PSI-2, protein structure initiative; 2.30A {Syntrophus aciditrophicus SB} Length = 154

 Score = 83.1 bits (206), Expect = 1e-18
 Identities = 37/139 (26%), Positives = 57/139 (41%), Gaps = 28/139 (20%)

Query: 857 KPKPKILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVM 916
               +IL+VED+       K ++++ G+  + V NG EAV  +     DLI+ DV MP M
Sbjct: 5   NRAGEILIVEDSPTQAEHLKHILEETGYQTEHVRNGREAVRFLSLTRPDLIISDVLMPEM 64

Query: 917 DGLKATRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEEC- 975
           DG    R ++   D                         + IP+I +T   LS+  +   
Sbjct: 65  DGYALCRWLKGQPDL------------------------RTIPVILLT--ILSDPRDVVR 98

Query: 976 -FANGMDSFVSKPVTFQKL 993
               G D F++KP     L
Sbjct: 99  SLECGADDFITKPCKDVVL 117

>3eq2_A Probable two-component response regulator; adaptor sigmas, signaling protein; 3.40A {Pseudomonas aeruginosa} PDB: 3f7a_A Length = 394

 Score = 87.6 bits (217), Expect = 2e-18
 Identities = 25/140 (17%), Positives = 53/140 (37%), Gaps = 26/140 (18%)

Query: 857 KPKPKILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVM 916
           K    +L+++D+++      + ++     +    NG++ +   + +  DL++ D+ MP +
Sbjct: 3   KVSATLLIIDDDEVVRESLAAYLEDSNFKVLQALNGLQGLQIFESEQPDLVICDLRMPQI 62

Query: 917 DGLKATRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECF 976
           DGL+  R IR                                PII ++   +   A E  
Sbjct: 63  DGLELIRRIRQTA--------------------------SETPIIVLSGAGVMSDAVEAL 96

Query: 977 ANGMDSFVSKPVTFQKLKEC 996
             G   ++ KP+    + E 
Sbjct: 97  RLGAADYLIKPLEDLAVLEH 116

>3cg0_A Response regulator receiver modulated diguanylate with PAS/PAC sensor; signal receiver domain, diguanylate cyclase; 2.15A {Desulfovibrio desulfuricans subsp} Length = 140

 Score = 81.8 bits (203), Expect = 2e-18
 Identities = 29/147 (19%), Positives = 59/147 (40%), Gaps = 29/147 (19%)

Query: 854 TKPKPKPKILLVEDNKINVMVAKSMMKQLGHSI-DVVNNGVEAVHAVQCQNYDLILMDVC 912
           T     P +L+VED ++     +  ++ LG+ +  V +NG EAV        D+ L+D+ 
Sbjct: 4   TASDDLPGVLIVEDGRLAAATLRIQLESLGYDVLGVFDNGEEAVRCAPDLRPDIALVDIM 63

Query: 913 M-PVMDGLKATRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSES 971
           +   +DG++    + +  +                           +PII +T++   E+
Sbjct: 64  LCGALDGVETAARLAAGCN---------------------------LPIIFITSSQDVET 96

Query: 972 AEECFANGMDSFVSKPVTFQKLKECLE 998
            +         +++KPV    L   +E
Sbjct: 97  FQRAKRVNPFGYLAKPVAADTLHRSIE 123

>1i3c_A Response regulator RCP1; phytochrome, signaling protein; 1.90A {Synechocystis SP} SCOP: c.23.1.1 PDB: 1jlk_A Length = 149

 Score = 81.6 bits (202), Expect = 3e-18
 Identities = 30/150 (20%), Positives = 63/150 (42%), Gaps = 33/150 (22%)

Query: 855 KPKPKPKILLVEDNKINVMVAKSMMKQLG--HSIDVVNNGVEAVHAVQCQNY-------D 905
           +  P   ILLVED+K +  + + ++K     H + ++ +G+ A+  +Q Q         +
Sbjct: 4   ESNPPKVILLVEDSKADSRLVQEVLKTSTIDHELIILRDGLAAMAFLQQQGEYENSPRPN 63

Query: 906 LILMDVCMPVMDGLKATRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTA 965
           LIL+D+ +P  DG +    I+   D                         KRIP++ +T 
Sbjct: 64  LILLDLNLPKKDGREVLAEIKQNPDL------------------------KRIPVVVLTT 99

Query: 966 NALSESAEECFANGMDSFVSKPVTFQKLKE 995
           +   +     +   ++ +++K    + L +
Sbjct: 100 SHNEDDVIASYELHVNCYLTKSRNLKDLFK 129

>1jbe_A Chemotaxis protein CHEY; signaling protein; 1.08A {Escherichia coli} SCOP: c.23.1.1 PDB: 3chy_A 1a0o_A 1cey_A 1bdj_A 1eay_A 1f4v_A 1ffg_A 1ffs_A 1ffw_A 1fqw_A 2b1j_A 1chn_A 1djm_A 1kmi_Y* 1d4z_A 3olx_A 3olw_A 1cye_A 2che_A 2chf_A ... Length = 128

 Score = 81.1 bits (201), Expect = 3e-18
 Identities = 34/143 (23%), Positives = 65/143 (45%), Gaps = 25/143 (17%)

Query: 858 PKPKILLVEDNKINVMVAKSMMKQLG-HSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVM 916
            + K L+V+D      + ++++K+LG ++++   +GV+A++ +Q   Y  ++ D  MP M
Sbjct: 3   KELKFLVVDDFSTMRRIVRNLLKELGFNNVEEAEDGVDALNKLQAGGYGFVISDWNMPNM 62

Query: 917 DGLKATRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECF 976
           DGL+  + IR+                              +P++ +TA A  E+     
Sbjct: 63  DGLELLKTIRAXXA------------------------MSALPVLMVTAEAKKENIIAAA 98

Query: 977 ANGMDSFVSKPVTFQKLKECLEQ 999
             G   +V KP T   L+E L +
Sbjct: 99  QAGASGYVVKPFTAATLEEKLNK 121

>2zay_A Response regulator receiver protein; structural genomics, NYSGXRC, target 11006U, protein structure initiative; 2.00A {Desulfuromonas acetoxidans} Length = 147

 Score = 80.7 bits (200), Expect = 6e-18
 Identities = 28/134 (20%), Positives = 49/134 (36%), Gaps = 28/134 (20%)

Query: 857 KPKPKILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVM 916
               +I+LV+     +  + S + Q G  I    N +EAV      +  LI+ +  MP +
Sbjct: 6   GKWWRIMLVDTQLPALAASISALSQEGFDIIQCGNAIEAVPVAVKTHPHLIITEANMPKI 65

Query: 917 DGLKATRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEEC- 975
            G+     ++    T                          IP+IA++    + + EE  
Sbjct: 66  SGMDLFNSLKKNPQT------------------------ASIPVIALS--GRATAKEEAQ 99

Query: 976 -FANGMDSFVSKPV 988
               G   F++KPV
Sbjct: 100 LLDMGFIDFIAKPV 113

>3hdg_A Uncharacterized protein; two-component sensor activity, response regulator, PSI-II, 11227F, NYSGXRC, structural genomics; 2.27A {Wolinella succinogenes} Length = 137

 Score = 79.1 bits (196), Expect = 1e-17
 Identities = 26/143 (18%), Positives = 52/143 (36%), Gaps = 26/143 (18%)

Query: 857 KPKPKILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVM 916
           +   KIL+VED+        +++      +    +G E          D+I+ D+ MP +
Sbjct: 5   EVALKILIVEDDTDAREWLSTIISNHFPEVWSAGDGEEGERLFGLHAPDVIITDIRMPKL 64

Query: 917 DGLKATRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECF 976
            GL+    I++                             +  +I ++A +  +   +  
Sbjct: 65  GGLEMLDRIKA--------------------------GGAKPYVIVISAFSEMKYFIKAI 98

Query: 977 ANGMDSFVSKPVTFQKLKECLEQ 999
             G+  F+ KP+   +L E LE 
Sbjct: 99  ELGVHLFLPKPIEPGRLMETLED 121

>1ysr_A Sensor-type histidine kinase PRRB; ATP-binding domain, structural genomics, mycobacterium tuberculosis structural proteomics project; 1.78A {Mycobacterium tuberculosis} SCOP: d.122.1.3 PDB: 1ys3_A Length = 150

 Score = 79.6 bits (197), Expect = 2e-17
 Identities = 22/93 (23%), Positives = 36/93 (38%), Gaps = 8/93 (8%)

Query: 572 PGTPVSHGNSMDEDLEATVWIRCDVYDTGIGIPENALPTLFRKYMQVSADHARKYGGTGL 631
             T V               +   + D G G+PE     +F ++       A  + G+GL
Sbjct: 63  GATLVQLSAVSSRA-----GVEIAIDDNGSGVPEGERQVVFERF--SRGSTAS-HSGSGL 114

Query: 632 GLAICKQLVELMGGRLTVTSKVHCGSTFTFILP 664
           GLA+  Q  +L GG  ++ +    G+     LP
Sbjct: 115 GLALVAQQAQLHGGTASLENSPLGGARLVLRLP 147

>1ysr_A Sensor-type histidine kinase PRRB; ATP-binding domain, structural genomics, mycobacterium tuberculosis structural proteomics project; 1.78A {Mycobacterium tuberculosis} SCOP: d.122.1.3 PDB: 1ys3_A Length = 150

 Score = 49.5 bits (119), Expect = 4e-07
 Identities = 10/64 (15%), Positives = 23/64 (35%), Gaps = 3/64 (4%)

Query: 446 REVVKHVLQTAAASLQKILMLEGDIADDVPIEVIGDVLRIRQILTNLISNAIKFTPEGKV 505
            +++      AA     +   +  +       ++G    +R  + N I+NA+K      V
Sbjct: 11  TDLLDRAAHDAARIYPDL---DVSLVPSPTCIIVGLPAGLRLAVDNAIANAVKHGGATLV 67

Query: 506 GIKL 509
            +  
Sbjct: 68  QLSA 71

>1bxd_A ENVZ(290-450), protein (osmolarity sensor protein (ENVZ)); histidine kinase, osmosensor, His-Asp phosphorelay system, signal transduction; HET: ANP; NMR {Escherichia coli BL21} SCOP: d.122.1.3 Length = 161

 Score = 79.6 bits (197), Expect = 2e-17
 Identities = 25/86 (29%), Positives = 40/86 (46%), Gaps = 2/86 (2%)

Query: 591 WIRCDVYDTGIGIPENALPTLFRKYMQVSADHARKYGGTGLGLAICKQLVELMGGRLTVT 650
                V D G GI       LF+ +++   D AR   GTGLGLAI +++V+   G L + 
Sbjct: 77  RAWFQVEDDGPGIAPEQRKHLFQPFVRG--DSARTISGTGLGLAIVQRIVDNHNGMLELG 134

Query: 651 SKVHCGSTFTFILPYQVSPIEENSDD 676
           +    G +    LP  V+  +  + +
Sbjct: 135 TSERGGLSIRAWLPVPVTRAQGTTKE 160

>3nhm_A Response regulator; protein structure initiative II(PSI II), NYSGXRC, structural genomics; 2.19A {Myxococcus xanthus} Length = 133

 Score = 78.0 bits (193), Expect = 3e-17
 Identities = 26/136 (19%), Positives = 45/136 (33%), Gaps = 26/136 (19%)

Query: 859 KPKILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDG 918
           KPK+L+VE++       + ++           +G   +        D+++ DV M  MDG
Sbjct: 4   KPKVLIVENSWTMRETLRLLLSG-EFDCTTAADGASGLQQALAHPPDVLISDVNMDGMDG 62

Query: 919 LKATRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFAN 978
                  RS                            K IP+I ++  A   +       
Sbjct: 63  YALCGHFRSEPTL------------------------KHIPVIFVSGYA-PRTEGPADQP 97

Query: 979 GMDSFVSKPVTFQKLK 994
             D+++ KPV    L 
Sbjct: 98  VPDAYLVKPVKPPVLI 113

>3a0y_A Sensor protein; ATP-LID, kinase, phosphoprotein, transferase, two-component regulatory system; 1.57A {Thermotoga maritima} PDB: 3a0t_A* 3a0x_A 3a0w_A 3a0z_A Length = 152

 Score = 77.2 bits (191), Expect = 1e-16
 Identities = 23/75 (30%), Positives = 40/75 (53%), Gaps = 8/75 (10%)

Query: 591 WIRCDVYDTGIGIPENALPTLFRKYMQVSADHARKYGGTGLGLAICKQLVELM-GGRLTV 649
            +R  V+++G  IPE     +F  +         K  GTGLGL+IC++++E   GG++  
Sbjct: 79  KVRVSVWNSGPPIPEELKEKIFSPFFT------TKTQGTGLGLSICRKIIEDEHGGKIWT 132

Query: 650 TSKVHCGSTFTFILP 664
            ++ + G  F F +P
Sbjct: 133 ENREN-GVVFIFEIP 146

>3a0y_A Sensor protein; ATP-LID, kinase, phosphoprotein, transferase, two-component regulatory system; 1.57A {Thermotoga maritima} PDB: 3a0t_A* 3a0x_A 3a0w_A 3a0z_A Length = 152

 Score = 47.2 bits (113), Expect = 3e-06
 Identities = 20/79 (25%), Positives = 37/79 (46%), Gaps = 3/79 (3%)

Query: 438 LEAAKFRPREVVKHVLQTAAASL-QKILMLEGDIADDVPIEVIGDVLRIRQILTNLISNA 496
           +E  +F   E+++ V       + +  +    +  ++    V  D  RI+Q+L NL+ NA
Sbjct: 1   MEFTEFNLNELIREVYVLFEEKIRKMNIDFCFETDNEDL-RVEADRTRIKQVLINLVQNA 59

Query: 497 IKFTPE-GKVGIKLYVVPE 514
           I+ T E GK+ I    +  
Sbjct: 60  IEATGENGKIKITSEDMYT 78

>3eod_A Protein HNR; response regulator, phosphoprotein, two-component regulatory system, signaling protein; 1.75A {Escherichia coli K12} Length = 130

 Score = 75.3 bits (186), Expect = 3e-16
 Identities = 30/142 (21%), Positives = 57/142 (40%), Gaps = 28/142 (19%)

Query: 854 TKPKPKPKILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCM 913
           T+P    +IL+VED ++   +  S    LG +  +  +GV+A+  +     DL++ D+ M
Sbjct: 2   TQPLVGKQILIVEDEQVFRSLLDSWFSSLGATTVLAADGVDALELLGGFTPDLMICDIAM 61

Query: 914 PVMDGLKATRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAE 973
           P M+GLK    IR+                             + P++ ++A        
Sbjct: 62  PRMNGLKLLEHIRN--------------------------RGDQTPVLVISATENMADIA 95

Query: 974 ECFANGMDSFVSKPVTFQKLKE 995
           +    G++  + KP   + L  
Sbjct: 96  KALRLGVEDVLLKP--VKDLNR 115

>3n0r_A Response regulator; sigma factor, receiver, two-component SI transduction, signaling protein; HET: MSE GOL; 1.25A {Caulobacter vibrioides} PDB: 3t0y_A Length = 286

 Score = 79.1 bits (195), Expect = 4e-16
 Identities = 32/211 (15%), Positives = 72/211 (34%), Gaps = 41/211 (19%)

Query: 796 ETTSWFQNPATESTSHSEANREM-----IQTSKTNEPQKICEMQEKPDRISQSPSSSSAE 850
           +      + A      +  +R+      ++     E  +I +            + +   
Sbjct: 97  QGLHAGDDAAQRLMRIAPRSRQAFLLTALEGFTPTEAAQILDCDFGEVERLIGDAQA--- 153

Query: 851 VPETKPKPKPKILLVEDNKINVMVAKSMMKQLGHSI-DVVNNGVEAVHAVQCQNYDLILM 909
             E   +   ++L++ED  +     ++++++LGH + D+     EA+ AV  +   L+L 
Sbjct: 154 --EIDAELATEVLIIEDEPVIAADIEALVRELGHDVTDIAATRGEALEAVTRRTPGLVLA 211

Query: 910 DVCMP-VMDGLKATRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANAL 968
           D+ +     G+ A + I    D                           +P+I +TA   
Sbjct: 212 DIQLADGSSGIDAVKDILGRMD---------------------------VPVIFITAF-- 242

Query: 969 SESAEECFANGMDSFVSKPVTFQKLKECLEQ 999
            E             ++KP   + +K  + Q
Sbjct: 243 PERLLTGERPEPTFLITKPFQPETVKAAIGQ 273

>1srr_A SPO0F, sporulation response regulatory protein; aspartate pocket, two component system; 1.90A {Bacillus subtilis} SCOP: c.23.1.1 PDB: 1pey_A 3q15_C 2ftk_E* 1fsp_A 1nat_A 1pux_A 2fsp_A 2jvj_A 2jvk_A 2jvi_A 1f51_E Length = 124

 Score = 74.4 bits (184), Expect = 5e-16
 Identities = 27/141 (19%), Positives = 60/141 (42%), Gaps = 26/141 (18%)

Query: 859 KPKILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDG 918
             KIL+V+D     ++   +  + G+      NG++A+  V  +  DL+L+D+ +P MDG
Sbjct: 3   NEKILIVDDQSGIRILLNEVFNKEGYQTFQAANGLQALDIVTKERPDLVLLDMKIPGMDG 62

Query: 919 LKATRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFAN 978
           ++  + ++                             + I +I MTA    +  +E    
Sbjct: 63  IEILKRMKV--------------------------IDENIRVIIMTAYGELDMIQESKEL 96

Query: 979 GMDSFVSKPVTFQKLKECLEQ 999
           G  +  +KP    ++++ +++
Sbjct: 97  GALTHFAKPFDIDEIRDAVKK 117

>3c3m_A Response regulator receiver protein; structural genomics, unknown function, PSI-2, protein struct initiative; HET: MSE; 1.70A {Methanoculleus marisnigri JR1} Length = 138

 Score = 74.5 bits (184), Expect = 7e-16
 Identities = 29/132 (21%), Positives = 58/132 (43%), Gaps = 28/132 (21%)

Query: 858 PKPKILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMD 917
               IL+V+D+ + V V  +M+++ G+      +G E + A+     DL+L+D+ M  MD
Sbjct: 2   SLYTILVVDDSPMIVDVFVTMLERGGYRPITAFSGEECLEALNATPPDLVLLDIMMEPMD 61

Query: 918 GLKATRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEEC-- 975
           G +    I++   T                        + IP++ +T  A   + EE   
Sbjct: 62  GWETLERIKTDPAT------------------------RDIPVLMLT--AKPLTPEEANE 95

Query: 976 FANGMDSFVSKP 987
           + + ++ ++ KP
Sbjct: 96  YGSYIEDYILKP 107

>1tmy_A CHEY protein, TMY; chemotaxis, phosphoryl transfer, signal transduction; 1.90A {Thermotoga maritima} SCOP: c.23.1.1 PDB: 2tmy_A 3tmy_A 4tmy_A 1u0s_Y Length = 120

 Score = 72.5 bits (179), Expect = 2e-15
 Identities = 31/142 (21%), Positives = 52/142 (36%), Gaps = 31/142 (21%)

Query: 861 KILLVEDNKINVMVAKSMMKQLGHSIDVV---NNGVEAVHAVQCQNYDLILMDVCMPVMD 917
           ++L+V+D     M+ K ++ + G   +V     NG EAV   +    D++ MD+ MP M+
Sbjct: 4   RVLIVDDAAFMRMMLKDIITKAG--YEVAGEATNGREAVEKYKELKPDIVTMDITMPEMN 61

Query: 918 GLKATRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFA 977
           G+ A + I                                  II  +A        E   
Sbjct: 62  GIDAIKEIMK--------------------------IDPNAKIIVCSAMGQQAMVIEAIK 95

Query: 978 NGMDSFVSKPVTFQKLKECLEQ 999
            G   F+ KP    ++ E L +
Sbjct: 96  AGAKDFIVKPFQPSRVVEALNK 117

>1k68_A Phytochrome response regulator RCPA; phosphorylated aspartate, CHEY homologue, homodimer, (beta/alpha)5, signaling protein; HET: PHD; 1.90A {Tolypothrix SP} SCOP: c.23.1.1 Length = 140

 Score = 72.6 bits (178), Expect = 3e-15
 Identities = 28/146 (19%), Positives = 59/146 (40%), Gaps = 33/146 (22%)

Query: 859 KPKILLVEDNKINVMVAKSMMKQLG--HSIDVVNNGVEAVHAVQCQNY-------DLILM 909
             KI LVEDNK ++ + +  +      H +  V +G+EA+  ++ +         DLIL+
Sbjct: 2   HKKIFLVEDNKADIRLIQEALANSTVPHEVVTVRDGMEAMAYLRQEGEYANASRPDLILL 61

Query: 910 DVCMPVMDGLKATRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALS 969
            + +P  DG +    I+S                            KRIP++ ++ +   
Sbjct: 62  XLNLPKKDGREVLAEIKSDPTL------------------------KRIPVVVLSTSINE 97

Query: 970 ESAEECFANGMDSFVSKPVTFQKLKE 995
           +     +   ++ +++K     +L +
Sbjct: 98  DDIFHSYDLHVNCYITKSANLSQLFQ 123

>3r0j_A Possible two component system response transcript positive regulator PHOP; beta-alpha fold, winged helix-turn-helix; 2.50A {Mycobacterium tuberculosis} Length = 250

 Score = 75.1 bits (184), Expect = 5e-15
 Identities = 31/148 (20%), Positives = 59/148 (39%), Gaps = 28/148 (18%)

Query: 847 SSAEVPETKPKPKPKILLVED-NKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYD 905
            +A  P     P+ ++L+V+D   I  +++ S+  Q G  +    NG +A+   +    D
Sbjct: 11  VTAGTPGENTTPEARVLVVDDEANIVELLSVSLKFQ-GFEVYTATNGAQALDRARETRPD 69

Query: 906 LILMDVCMPVMDGLKATRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTA 965
            +++DV MP MDG    R +R+                               P + +TA
Sbjct: 70  AVILDVXMPGMDGFGVLRRLRADGID--------------------------APALFLTA 103

Query: 966 NALSESAEECFANGMDSFVSKPVTFQKL 993
               +        G D +V+KP + +++
Sbjct: 104 RDSLQDKIAGLTLGGDDYVTKPFSLEEV 131

>3n53_A Response regulator receiver modulated diguanylate; diguanylate cyclase, protein structure I II(PSI II), NYSGXRC, structural genomics; 2.20A {Pelobacter carbinolicus} Length = 140

 Score = 71.8 bits (177), Expect = 5e-15
 Identities = 18/130 (13%), Positives = 49/130 (37%), Gaps = 25/130 (19%)

Query: 858 PKPKILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMD 917
              KIL+++    + +  K+ +    + +    N  EA+  +   + DL+++D+ +   +
Sbjct: 2   SLKKILIIDQQDFSRIELKNFLDS-EYLVIESKNEKEALEQIDHHHPDLVILDMDIIGEN 60

Query: 918 GLKATRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFA 977
                  ++  +   N                        +P+I + ++   E+      
Sbjct: 61  SPNLCLKLKRSKGLKN------------------------VPLILLFSSEHKEAIVNGLH 96

Query: 978 NGMDSFVSKP 987
           +G D +++KP
Sbjct: 97  SGADDYLTKP 106

>1mu5_A Type II DNA topoisomerase VI subunit B; GHKL ATPase, helix two-turns helix; 2.00A {Sulfolobus shibatae} SCOP: a.156.1.3 d.14.1.3 d.122.1.2 PDB: 1mx0_A* 1z5b_A* 1z5a_A* 1z59_A* 1z5c_A* 2hkj_A* Length = 471

 Score = 77.5 bits (190), Expect = 6e-15
 Identities = 18/84 (21%), Positives = 32/84 (38%), Gaps = 2/84 (2%)

Query: 591 WIRCDVYDTGIGIPENALPTLFRKYMQVSADHARKY-GGTGLGLAICKQLVELMGGRLTV 649
             + +V D GIGIP   +P  F + +  S    R+  G  GLG+       ++   +   
Sbjct: 70  IYKVNVVDNGIGIPPQEVPNAFGRVLYSSKYVNRQTRGMYGLGVKAAVLYSQMHQDKPIE 129

Query: 650 TSKVHCGSTFTFILPYQVSPIEEN 673
                  S   +    ++  I +N
Sbjct: 130 IETSPVNSKRIYTFKLKI-DINKN 152

>3d36_A Sporulation kinase B; GHKL ATPase, four helix bundle, class I two-component histidine kinase, phosphoprotein; HET: ADP; 2.03A {Geobacillus stearothermophilus} Length = 244

 Score = 74.1 bits (183), Expect = 1e-14
 Identities = 24/93 (25%), Positives = 41/93 (44%), Gaps = 15/93 (16%)

Query: 591 WIRCDVYDTGIGIPENALPTLF-----RKYMQVSADHARKYGGTGLGLAICKQLVELMGG 645
            +   + DTG+G+ +  L  L       K             GTGLG+ +  +++E M G
Sbjct: 155 RVLIRIADTGVGMTKEQLERLGEPYFTTK----------GVKGTGLGMMVVYRIIESMNG 204

Query: 646 RLTVTSKVHCGSTFTFILPYQVSPIEENSDDPD 678
            + + S++H G+T +  LP   SP      D +
Sbjct: 205 TIRIESEIHKGTTVSIYLPLASSPSSSTISDKE 237

>3d36_A Sporulation kinase B; GHKL ATPase, four helix bundle, class I two-component histidine kinase, phosphoprotein; HET: ADP; 2.03A {Geobacillus stearothermophilus} Length = 244

 Score = 71.0 bits (175), Expect = 1e-13
 Identities = 34/144 (23%), Positives = 64/144 (44%), Gaps = 12/144 (8%)

Query: 372 QMLATMSHEIRSPLTGVVSMAEIL-SNTKLDREQRQLLGVMISSGDLVLQLINDILDLSK 430
            + A++SHEIR+PLT      +++        ++RQ   + I   D    +I D L  +K
Sbjct: 16  HLAASISHEIRNPLTAARGFIQLIEEQPLAADKRRQYARIAIEELDRAEAIITDYLTFAK 75

Query: 431 VESGVMKLEAAKFRPREVVKHVLQ--TAAASLQKILMLEGDIADDVPIEVIGDVLRIRQI 488
                 +    K   +  ++ V+      A++  + +     A   P  VIG+  + RQ 
Sbjct: 76  PAPETPE----KLNVKLEIERVIDILRPLANMSCVDI----QATLAPFSVIGEREKFRQC 127

Query: 489 LTNLISNAIKFTPE-GKVGIKLYV 511
           L N++ NAI+  P  G + + + +
Sbjct: 128 LLNVMKNAIEAMPNGGTLQVYVSI 151

>1y8o_A [pyruvate dehydrogenase [lipoamide]] kinase isozy; pyruvate dehydrogenase kinase 3, lipoyl-bearing domain; HET: RED ADP; 2.48A {Homo sapiens} SCOP: a.29.5.1 d.122.1.4 PDB: 1y8n_A* 1y8p_A* 2pnr_A* 2q8i_A* Length = 419

 Score = 76.4 bits (187), Expect = 1e-14
 Identities = 18/107 (16%), Positives = 34/107 (31%), Gaps = 11/107 (10%)

Query: 564 QDHKHDDDPGTPVSHGNSMDEDLEATVWIRCDVYDTGIGIPENALPTLFRKYMQ------ 617
           + ++   +    V    ++ ++      +   + D G G+P   +  LF           
Sbjct: 271 ELYEDRKEGYPAVKTLVTLGKE-----DLSIKISDLGGGVPLRKIDRLFNYMYSTAPRPS 325

Query: 618 VSADHARKYGGTGLGLAICKQLVELMGGRLTVTSKVHCGSTFTFILP 664
           +    A    G G GL I +       G L + S    G+     L 
Sbjct: 326 LEPTRAAPLAGFGYGLPISRLYARYFQGDLKLYSMEGVGTDAVIYLK 372

>1y8o_A [pyruvate dehydrogenase [lipoamide]] kinase isozy; pyruvate dehydrogenase kinase 3, lipoyl-bearing domain; HET: RED ADP; 2.48A {Homo sapiens} SCOP: a.29.5.1 d.122.1.4 PDB: 1y8n_A* 1y8p_A* 2pnr_A* 2q8i_A* Length = 419

 Score = 54.8 bits (131), Expect = 9e-08
 Identities = 27/181 (14%), Positives = 50/181 (27%), Gaps = 21/181 (11%)

Query: 354 ETELNKTIHITEETMRAKQMLATMSHEIRSPLTGVVSMAE--------ILSNTKLDREQR 405
              L       E+       L  +          V +MA+           +  +    +
Sbjct: 102 LELLEYENKSPEDPQVLDNFLQVLIKVRNRHNDVVPTMAQGVIEYKEKFGFDPFISTNIQ 161

Query: 406 QLLGVMISSGDLVLQLINDILDLSKVESGVMK-----LEAAKFRPREVVKHVLQTAAASL 460
             L    ++      LIN    L   ++  +               +VVK   +TA    
Sbjct: 162 YFLDRFYTNRISFRMLINQHTLLFGGDTNPVHPKHIGSIDPTCNVADVVKDAYETAKMLC 221

Query: 461 Q--------KILMLEGDIADDVPIEVIGDVLRIRQILTNLISNAIKFTPEGKVGIKLYVV 512
           +          +      A D PI+V+     +  +L  L  N+++ T E     K    
Sbjct: 222 EQYYLVAPELEVEEFNAKAPDKPIQVVYVPSHLFHMLFELFKNSMRATVELYEDRKEGYP 281

Query: 513 P 513
            
Sbjct: 282 A 282

>1s8n_A Putative antiterminator; RV1626, structural genomics, transcriptional antiterminator, component system, PSI; 1.48A {Mycobacterium tuberculosis} SCOP: c.23.1.1 PDB: 1sd5_A Length = 205

 Score = 72.8 bits (179), Expect = 1e-14
 Identities = 32/152 (21%), Positives = 57/152 (37%), Gaps = 28/152 (18%)

Query: 848 SAEVPETKPKPKPKILLVEDNKINVMVAKSMMKQLGHS-IDVVNNGVEAVHAVQCQNYDL 906
           +    +       ++L+ ED  +  M    M+++ G+  +    +G EAV   +    DL
Sbjct: 2   TGPTTDADAAVPRRVLIAEDEALIRMDLAEMLREEGYEIVGEAGDGQEAVELAELHKPDL 61

Query: 907 ILMDVCMPVMDGLKATRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTAN 966
           ++MDV MP  DG+ A   I S                               PI+ +TA 
Sbjct: 62  VIMDVKMPRRDGIDAASEIASKRI---------------------------APIVVLTAF 94

Query: 967 ALSESAEECFANGMDSFVSKPVTFQKLKECLE 998
           +  +  E     G  +++ KP +   L   +E
Sbjct: 95  SQRDLVERARDAGAMAYLVKPFSISDLIPAIE 126

>3cfy_A Putative LUXO repressor protein; structural genomics, unknown function, uncharacterized protein, signal receiver domain; 2.50A {Vibrio parahaemolyticus rimd 2210633} Length = 137

 Score = 70.3 bits (173), Expect = 2e-14
 Identities = 29/136 (21%), Positives = 53/136 (38%), Gaps = 26/136 (19%)

Query: 859 KPKILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDG 918
           +P++LLVED+    ++ K  +K   + I  V  G +A+  ++     LI++D+ +P M G
Sbjct: 4   RPRVLLVEDSTSLAILYKQYVKDEPYDIFHVETGRDAIQFIERSKPQLIILDLKLPDMSG 63

Query: 919 LKATRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFAN 978
                 I                            +     +I  TA+   + A      
Sbjct: 64  EDVLDWINQ--------------------------NDIPTSVIIATAHGSVDLAVNLIQK 97

Query: 979 GMDSFVSKPVTFQKLK 994
           G + F+ KP+   +LK
Sbjct: 98  GAEDFLEKPINADRLK 113

>3cg4_A Response regulator receiver domain protein (CHEY-; structural genomics, unknown function; HET: MSE; 1.61A {Methanospirillum hungatei jf-1} Length = 142

 Score = 70.3 bits (173), Expect = 2e-14
 Identities = 20/109 (18%), Positives = 42/109 (38%), Gaps = 24/109 (22%)

Query: 857 KPKPKILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVM 916
           + K  +++V+D+    +  K+++   G  I   ++G + +  ++     ++L+D+ MP M
Sbjct: 5   EHKGDVMIVDDDAHVRIAVKTILSDAGFHIISADSGGQCIDLLKKGFSGVVLLDIMMPGM 64

Query: 917 DGLKATRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTA 965
           DG    R I                                I I+ +TA
Sbjct: 65  DGWDTIRAILDNSLEQG------------------------IAIVMLTA 89

>3snk_A Response regulator CHEY-like protein; P-loop containing nucleoside triphosphate hydrolases, struct genomics; 2.02A {Mesorhizobium loti} Length = 135

 Score = 70.0 bits (172), Expect = 3e-14
 Identities = 17/139 (12%), Positives = 40/139 (28%), Gaps = 27/139 (19%)

Query: 856 PKPKPKILLVEDNK-INVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMP 914
           P  + ++ L   +      VA  +     + + V                 ++++D+   
Sbjct: 11  PTKRKQVALFSSDPNFKRDVATRLDALAIYDVRVSETDDFLKGPPADTRPGIVILDLGGG 70

Query: 915 VMDGLKATRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEE 974
            + G       R+   T                          +P+IA++    SE    
Sbjct: 71  DLLGKPGIVEARALWAT--------------------------VPLIAVSDELTSEQTRV 104

Query: 975 CFANGMDSFVSKPVTFQKL 993
                   ++ KP+  ++L
Sbjct: 105 LVRMNASDWLHKPLDGKEL 123

>3hdv_A Response regulator; PSI-II, structural genomics, Pro structure initiative, NEW YORK SGX research center for STRU genomics, nysgxrc; 2.09A {Pseudomonas putida} Length = 136

 Score = 69.9 bits (172), Expect = 3e-14
 Identities = 31/147 (21%), Positives = 54/147 (36%), Gaps = 26/147 (17%)

Query: 854 TKPKPKPKILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQN-YDLILMDVC 912
           +    +P +L+V+DN +N       +K  G      +   EA   +  Q    L++ D+ 
Sbjct: 2   SLVAARPLVLVVDDNAVNREALILYLKSRGIDAVGADGAEEARLYLHYQKRIGLMITDLR 61

Query: 913 MPVMDGLKATRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESA 972
           M    GL   R IR                         ++    + II ++ +   E A
Sbjct: 62  MQPESGLDLIRTIR-------------------------ASERAALSIIVVSGDTDVEEA 96

Query: 973 EECFANGMDSFVSKPVTFQKLKECLEQ 999
            +    G+  F+ KPV   KL E + +
Sbjct: 97  VDVMHLGVVDFLLKPVDLGKLLELVNK 123

>2zbk_B Type 2 DNA topoisomerase 6 subunit B; DNA binding protein, decatenation, ATPase, drug design, DNA-binding, magnesium, metal-binding; HET: RDC; 3.56A {Sulfolobus shibatae} Length = 530

 Score = 75.6 bits (185), Expect = 3e-14
 Identities = 18/87 (20%), Positives = 32/87 (36%), Gaps = 2/87 (2%)

Query: 591 WIRCDVYDTGIGIPENALPTLFRKYMQVSADHARKYGGT-GLGLAICKQLVELMGGRLTV 649
             + +V D GIGIP   +P  F + +  S    R+  G  GLG+       ++   +   
Sbjct: 69  IYKVNVVDNGIGIPPQEVPNAFGRVLYSSKYVNRQTRGMYGLGVKAAVLYSQMHQDKPIE 128

Query: 650 TSKVHCGSTFTFILPYQVSPIEENSDD 676
                  S   +    ++  I +N   
Sbjct: 129 IETSPVNSKRIYTFKLKI-DINKNEPI 154

>3lua_A Response regulator receiver protein; two-component signal transduction system, histidine kinase, phosphorelay, receiver domain, nysgxrc; 2.40A {Clostridium thermocellum} Length = 140

 Score = 69.6 bits (171), Expect = 3e-14
 Identities = 23/132 (17%), Positives = 41/132 (31%), Gaps = 27/132 (20%)

Query: 859 KPKILLVEDNKINVMVAKSMMKQLGH-SIDVVNNGVEAVHAV-QCQNYDLILMDVCMPV- 915
              +LL++  +      K +   +G      V N  +         +  LI+MD+  PV 
Sbjct: 4   DGTVLLIDYFEYEREKTKIIFDNIGEYDFIEVENLKKFYSIFKDLDSITLIIMDIAFPVE 63

Query: 916 MDGLKATRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEEC 975
            +GL+    IR+   T N                         P+I  T +         
Sbjct: 64  KEGLEVLSAIRNNSRTAN------------------------TPVIIATKSDNPGYRHAA 99

Query: 976 FANGMDSFVSKP 987
               +  ++ KP
Sbjct: 100 LKFKVSDYILKP 111

>2e0a_A Pyruvate dehydrogenase kinase isozyme 4; PDK4, ATP-binding, structural genomics, NPPSFA, NATI project on protein structural and functional analyses; HET: ANP; 1.86A {Homo sapiens} PDB: 2zdx_A* 2zdy_A* 2zkj_A* 3d2r_A* Length = 394

 Score = 74.1 bits (181), Expect = 5e-14
 Identities = 44/318 (13%), Positives = 90/318 (28%), Gaps = 59/318 (18%)

Query: 356 ELNKTIHITEETMRAKQM-LATMSHEIRSPLTGVVSMAEILSNTKLDREQRQLLGVMISS 414
           +L +    + +  +A    + T+          V +MA+ +       E +       + 
Sbjct: 81  DLVEFHEKSPDDQKALSDFVDTLIKVRNRHHNVVPTMAQGI------IEYKDAC----TV 130

Query: 415 GDLVLQLINDILDLSKVESGVMKLEAAKFRPREVVKHVLQTAAASLQKILMLEGDIADDV 474
             +  Q +   LD   +              R ++   +   + S        G I  + 
Sbjct: 131 DPVTNQNLQYFLDRFYMNRIST---------RMLMNQHILIFSDSQTGNPSHIGSIDPNC 181

Query: 475 -PIEVIGDVLRIRQILTNLISNAIKFTPEGKVGIKLYVVPEPPFAKEGLKQKSKAYQSAT 533
             + V+ D     ++L +    +    PE K+       P+ P     +   S  +    
Sbjct: 182 DVVAVVQDAFECSRMLCDQYYLSS---PELKLTQVNGKFPDQPIHIVYVP--SHLHHMLF 236

Query: 534 DAVKEEKHQPKSQTASDQNGFHDKKHGEGYQDHKHDDDP-GTPVSHGNSMDEDLEATVWI 592
           +  K              N                ++ P  TP+     + ++      +
Sbjct: 237 ELFK--------------NAMR-------ATVEHQENQPSLTPIEVIVVLGKE-----DL 270

Query: 593 RCDVYDTGIGIPENALPTLFRKYMQ------VSADHARKYGGTGLGLAICKQLVELMGGR 646
              + D G G+P   +  LF           +         G G GL I +   +   G 
Sbjct: 271 TIKISDRGGGVPLRIIDRLFSYTYSTAPTPVMDNSRNAPLAGFGYGLPISRLYAKYFQGD 330

Query: 647 LTVTSKVHCGSTFTFILP 664
           L + S    G+     L 
Sbjct: 331 LNLYSLSGYGTDAIIYLK 348

>3h1g_A Chemotaxis protein CHEY homolog; sulfate-bound CHEY, cytoplasm, flagellar rotatio magnesium, metal-binding, phosphoprotein; 1.70A {Helicobacter pylori} PDB: 3gwg_A 3h1e_A 3h1f_A Length = 129

 Score = 68.3 bits (168), Expect = 8e-14
 Identities = 35/142 (24%), Positives = 60/142 (42%), Gaps = 26/142 (18%)

Query: 856 PKPKPKILLVEDNKINVMVAKSMMKQLGH-SIDVVNNGVEAVHAVQCQ-NYDLILMDVCM 913
           P    K+L+V+D+     + K+ + +LG+  +    +GVEA   +    +  +++ D  M
Sbjct: 2   PLGSMKLLVVDDSSTMRRIIKNTLSRLGYEDVLEAEHGVEAWEKLDANADTKVLITDWNM 61

Query: 914 PVMDGLKATRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAE 973
           P M+GL   + +RS                            K IPII +TA        
Sbjct: 62  PEMNGLDLVKKVRSDSRF------------------------KEIPIIMITAEGGKAEVI 97

Query: 974 ECFANGMDSFVSKPVTFQKLKE 995
                G+++++ KP T Q LKE
Sbjct: 98  TALKAGVNNYIVKPFTPQVLKE 119

>3dzd_A Transcriptional regulator (NTRC family); sigma43 activator, AAA+ ATPase, response regulator, transcriptional activator, ATP-binding; HET: ADP; 2.40A {Aquifex aeolicus} PDB: 1zit_A 2jrl_A Length = 368

 Score = 72.9 bits (180), Expect = 1e-13
 Identities = 22/139 (15%), Positives = 54/139 (38%), Gaps = 26/139 (18%)

Query: 861 KILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLK 920
           ++L+V+D +       +++++ G+  D      EA   ++   + +I++DV MP  DG+ 
Sbjct: 2   RVLVVDDEESITSSLSAILEEEGYHPDTAKTLREAEKKIKELFFPVIVLDVWMPDGDGVN 61

Query: 921 ATRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGM 980
               I+                           +     +I +T +   ++A +    G 
Sbjct: 62  FIDFIKE--------------------------NSPDSVVIVITGHGSVDTAVKAIKKGA 95

Query: 981 DSFVSKPVTFQKLKECLEQ 999
             F+ KP + ++    ++ 
Sbjct: 96  YEFLEKPFSVERFLLTIKH 114

>1ys7_A Transcriptional regulatory protein PRRA; response regulator, DNA binding domain, phosphorylation; 1.58A {Mycobacterium tuberculosis} SCOP: a.4.6.1 c.23.1.1 PDB: 1ys6_A Length = 233

 Score = 70.6 bits (174), Expect = 1e-13
 Identities = 17/75 (22%), Positives = 37/75 (49%), Gaps = 2/75 (2%)

Query: 854 TKPKPKPKILLVED-NKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVC 912
                 P++L+V+D + +   + + +    G  +    +G EA+ +      D I++D+ 
Sbjct: 2   DTGVTSPRVLVVDDDSDVLASLERGLRLS-GFEVATAVDGAEALRSATENRPDAIVLDIN 60

Query: 913 MPVMDGLKATRLIRS 927
           MPV+DG+     +R+
Sbjct: 61  MPVLDGVSVVTALRA 75

>2qxy_A Response regulator; regulation of transcription, NYSGXRC, protein structure initiative II (PSI II), structural genomics; 1.95A {Thermotoga maritima} Length = 142

 Score = 68.0 bits (167), Expect = 1e-13
 Identities = 22/136 (16%), Positives = 48/136 (35%), Gaps = 27/136 (19%)

Query: 859 KPKILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDG 918
            P +++V++++I  +  K+ +++ G ++    N  EA   ++ +  DL+ +DV     + 
Sbjct: 4   TPTVMVVDESRITFLAVKNALEKDGFNVIWAKNEQEAFTFLRREKIDLVFVDV-FEGEES 62

Query: 919 LKATRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFAN 978
           L   R IR                            F    +  ++A    +        
Sbjct: 63  LNLIRRIRE--------------------------EFPDTKVAVLSAYVDKDLIINSVKA 96

Query: 979 GMDSFVSKPVTFQKLK 994
           G   ++ KP     L 
Sbjct: 97  GAVDYILKPFRLDYLL 112

>2j48_A Two-component sensor kinase; pseudo-receiver, circadian clock, transferase, response regulator, histidine protein kinase; NMR {Synechococcus elongatus} Length = 119

 Score = 67.1 bits (165), Expect = 1e-13
 Identities = 20/128 (15%), Positives = 37/128 (28%), Gaps = 29/128 (22%)

Query: 861 KILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLK 920
            ILL+E+      V   M+   G  +  + +G  A+  +      +ILM    P    L 
Sbjct: 3   HILLLEEEDEAATVVCEMLTAAGFKVIWLVDGSTALDQLDLLQPIVILMAWPPPDQSCLL 62

Query: 921 ATRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEE-CFANG 979
             + +R  +                             P++        E   +      
Sbjct: 63  LLQHLREHQAD------------------------PHPPLVLFLG----EPPVDPLLTAQ 94

Query: 980 MDSFVSKP 987
             + +SKP
Sbjct: 95  ASAILSKP 102

>3q9s_A DNA-binding response regulator; DNA binding protein; 2.40A {Deinococcus radiodurans} Length = 249

 Score = 70.7 bits (174), Expect = 1e-13
 Identities = 18/96 (18%), Positives = 41/96 (42%), Gaps = 2/96 (2%)

Query: 837 PDRISQSPSSSSAEVPETKPKPKPKILLVEDN-KINVMVAKSMMKQLGHSIDVVNNGVEA 895
                 S  +S     +     + +IL++ED+  I  ++   +    G+ +D  ++ +  
Sbjct: 15  NLYFEGSHMASMTGGQQMGRMNEQRILVIEDDHDIANVLRMDLTDA-GYVVDHADSAMNG 73

Query: 896 VHAVQCQNYDLILMDVCMPVMDGLKATRLIRSFEDT 931
           +   +  + DLIL+D+ +P  DG    + +R     
Sbjct: 74  LIKAREDHPDLILLDLGLPDFDGGDVVQRLRKNSAL 109

>1id0_A PHOQ histidine kinase; PHOQ/PHOP, signal transduction, transferase; HET: ANP; 1.60A {Escherichia coli} SCOP: d.122.1.3 PDB: 3cgz_A 3cgy_A Length = 152

 Score = 68.0 bits (167), Expect = 2e-13
 Identities = 20/82 (24%), Positives = 35/82 (42%), Gaps = 4/82 (4%)

Query: 591 WIRCDVYDTGIGIPENALPTLFRKYMQVSADHARKYGGTGLGLAICKQLVELMGGRLTVT 650
            +   V D G GIP +    +F +      D  R   G G+GLA+ +++ E   G++   
Sbjct: 74  HLYIVVEDDGPGIPLSKREVIFDRG--QRVDTLR--PGQGVGLAVAREITEQYEGKIVAG 129

Query: 651 SKVHCGSTFTFILPYQVSPIEE 672
             +  G+    I   Q S  ++
Sbjct: 130 ESMLGGARMEVIFGRQHSAPKD 151

>1id0_A PHOQ histidine kinase; PHOQ/PHOP, signal transduction, transferase; HET: ANP; 1.60A {Escherichia coli} SCOP: d.122.1.3 PDB: 3cgz_A 3cgy_A Length = 152

 Score = 41.1 bits (97), Expect = 4e-04
 Identities = 14/64 (21%), Positives = 31/64 (48%), Gaps = 9/64 (14%)

Query: 446 REV--VKHVLQTAAASLQKI-----LMLEGDIADDVPIEVIGDVLRIRQILTNLISNAIK 498
           RE+  V  +L    ++L K+     + +  DI+ ++     G+     +++ N++ NA K
Sbjct: 1   RELHPVAPLLDNLTSALNKVYQRKGVNISLDISPEISFV--GEQNDFVEVMGNVLDNACK 58

Query: 499 FTPE 502
           +  E
Sbjct: 59  YCLE 62

>2q8g_A [pyruvate dehydrogenase [lipoamide]] kinase isozy; GHKL ATPase/kinase family, pyruvate dehydrogenase complex, mitochondrial kinase; HET: AZX; 1.90A {Homo sapiens} PDB: 2q8f_A* 2q8h_A Length = 407

 Score = 72.5 bits (177), Expect = 2e-13
 Identities = 18/89 (20%), Positives = 29/89 (32%), Gaps = 6/89 (6%)

Query: 591 WIRCDVYDTGIGIPENALPTLF------RKYMQVSADHARKYGGTGLGLAICKQLVELMG 644
            +   + D G G+P   +  LF          +V    A    G G GL I +   +   
Sbjct: 282 DLTVKMSDRGGGVPLRKIDRLFNYMYSTAPRPRVETSRAVPLAGFGYGLPISRLYAQYFQ 341

Query: 645 GRLTVTSKVHCGSTFTFILPYQVSPIEEN 673
           G L + S    G+     +    +   E 
Sbjct: 342 GDLKLYSLEGYGTDAVIYIKALSTDSIER 370

>2q8g_A [pyruvate dehydrogenase [lipoamide]] kinase isozy; GHKL ATPase/kinase family, pyruvate dehydrogenase complex, mitochondrial kinase; HET: AZX; 1.90A {Homo sapiens} PDB: 2q8f_A* 2q8h_A Length = 407

 Score = 57.5 bits (138), Expect = 1e-08
 Identities = 25/175 (14%), Positives = 50/175 (28%), Gaps = 20/175 (11%)

Query: 358 NKTIHITEETMRAKQMLATMSHEIRSPLT----GVVSMAEILSNTKLDREQRQ-LLGVMI 412
           +K+    +        +  + +     +     GV+   E      +  +  Q  L    
Sbjct: 97  DKSAEDAKAIYDFTDTVIRIRNRHNDVIPTMAQGVIEYKESFGVDPVTSQNVQYFLDRFY 156

Query: 413 SSGDLVLQLINDILDLSKVESGVMKLEAAKF-------RPREVVKHVLQTA--------A 457
            S   +  L+N    L   +                     EV+K   + A         
Sbjct: 157 MSRISIRMLLNQHSLLFGGKGKGSPSHRKHIGSINPNCNVLEVIKDGYENARRLCDLYYI 216

Query: 458 ASLQKILMLEGDIADDVPIEVIGDVLRIRQILTNLISNAIKFTPEGKVGIKLYVV 512
            S +  L      +   PI+V+     +  ++  L  NA++ T E      +Y  
Sbjct: 217 NSPELELEELNAKSPGQPIQVVYVPSHLYHMVFELFKNAMRATMEHHANRGVYPP 271

>3lte_A Response regulator; structural genomics, PSI, protein structure initiative, NYSG YORK structural genomix research consortium, nysgxrc; 2.00A {Bermanella marisrubri} Length = 132

 Score = 67.2 bits (165), Expect = 2e-13
 Identities = 19/107 (17%), Positives = 42/107 (39%), Gaps = 25/107 (23%)

Query: 859 KPKILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDG 918
             +IL+V+D++      + ++K+    +++ +NG +A   +      ++ +D+ MP +DG
Sbjct: 6   SKRILVVDDDQAMAAAIERVLKRDHWQVEIAHNGFDAGIKLSTFEPAIMTLDLSMPKLDG 65

Query: 919 LKATRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTA 965
           L   R +R                          N     P I + +
Sbjct: 66  LDVIRSLR-------------------------QNKVANQPKILVVS 87

>3hzh_A Chemotaxis response regulator (CHEY-3); phosphatase, complex, response regulator, receiver domain, two-component signal transduction; HET: BFD; 1.96A {Borrelia burgdorferi} Length = 157

 Score = 68.0 bits (166), Expect = 2e-13
 Identities = 32/155 (20%), Positives = 57/155 (36%), Gaps = 29/155 (18%)

Query: 844 PSSSSAEVPETKPKPKPKILLVEDNKINVMVAKSMMKQLGHS-IDVVNNGVEAVHAVQCQ 902
            SSS              +L+V+D+   V     +    G + ID   +G EAV   +  
Sbjct: 21  DSSSKPRGINYDTGIPFNVLIVDDSVFTVKQLTQIFTSEGFNIIDTAADGEEAVIKYKNH 80

Query: 903 --NYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPI 960
             N D++ + + MP MDG+     I  F+                          K   +
Sbjct: 81  YPNIDIVTLXITMPKMDGITCLSNIMEFD--------------------------KNARV 114

Query: 961 IAMTANALSESAEECFANGMDSFVSKPVTFQKLKE 995
           I ++A    +  ++C   G  +F+ KP+   K+ +
Sbjct: 115 IMISALGKEQLVKDCLIKGAKTFIVKPLDRAKVLQ 149

>2pl1_A Transcriptional regulatory protein PHOP; CHEY-like fold, response regulator, beryllium fluoride, transcription factor, activated, virulence; 1.90A {Escherichia coli} SCOP: c.23.1.1 PDB: 2pkx_A Length = 121

 Score = 66.7 bits (164), Expect = 2e-13
 Identities = 20/70 (28%), Positives = 36/70 (51%), Gaps = 6/70 (8%)

Query: 861 KILLVEDNKINVMVAKSMMKQL---GHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMD 917
           ++L+VEDN    ++   +  Q+   GH +D   +  EA + +     D+ ++D+ +P  D
Sbjct: 2   RVLVVEDNA---LLRHHLKVQIQDAGHQVDDAEDAKEADYYLNEHIPDIAIVDLGLPDED 58

Query: 918 GLKATRLIRS 927
           GL   R  RS
Sbjct: 59  GLSLIRRWRS 68

>1ny5_A Transcriptional regulator (NTRC family); AAA+ ATPase, sigma54 activator, bacterial transcription, DIM transcription; HET: ADP; 2.40A {Aquifex aeolicus} SCOP: c.23.1.1 c.37.1.20 PDB: 1ny6_A* 3m0e_A* 1zy2_A* Length = 387

 Score = 72.1 bits (178), Expect = 2e-13
 Identities = 22/138 (15%), Positives = 59/138 (42%), Gaps = 26/138 (18%)

Query: 861 KILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLK 920
            +L++ED+K+   + +  +   G  ++    G EA   +  ++++++L+D+ +P ++GL+
Sbjct: 2   NVLVIEDDKVFRGLLEEYLSMKGIKVESAERGKEAYKLLSEKHFNVVLLDLLLPDVNGLE 61

Query: 921 ATRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGM 980
             + I+                                 +I +T +   ++A E    G 
Sbjct: 62  ILKWIKE--------------------------RSPETEVIVITGHGTIKTAVEAMKMGA 95

Query: 981 DSFVSKPVTFQKLKECLE 998
             F++KP   ++++  + 
Sbjct: 96  YDFLTKPCMLEEIELTIN 113

>1kgs_A DRRD, DNA binding response regulator D; DNA-binding protein, ALPH-beta sandwich, winged-helix, helix helix, DNA binding protein; HET: DNA MSE; 1.50A {Thermotoga maritima} SCOP: a.4.6.1 c.23.1.1 PDB: 3nnn_A* Length = 225

 Score = 69.0 bits (170), Expect = 4e-13
 Identities = 16/68 (23%), Positives = 42/68 (61%), Gaps = 2/68 (2%)

Query: 861 KILLVEDN-KINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGL 919
           ++L+VED   +  ++ +++ K+   ++DV  +G E ++    + +D++++D+ +PV DG 
Sbjct: 4   RVLVVEDERDLADLITEALKKE-MFTVDVCYDGEEGMYMALNEPFDVVILDIMLPVHDGW 62

Query: 920 KATRLIRS 927
           +  + +R 
Sbjct: 63  EILKSMRE 70

>3k3c_A Protein RV1364C/MT1410; sensor, PAS, signal transduction, fatty-acid binding, sigma regulator, signaling protein; HET: PLM; 1.62A {Mycobacterium tuberculosis} PDB: 3k3d_A Length = 158

 Score = 66.9 bits (164), Expect = 5e-13
 Identities = 28/138 (20%), Positives = 51/138 (36%), Gaps = 9/138 (6%)

Query: 217 LKRADNFLHFVLQNAPVVMGH-QDKELRYRFIYNH--FPSLHEEDILGKTDVEIFSGAGV 273
              A   +  + ++ P ++   +  + R+    N          D +G+   E++     
Sbjct: 12  TVGAAEDVRRIFEHIPAILVGLEGPDHRFVA-VNAAYRGFSPLLDTVGQPAREVYPELEG 70

Query: 274 KESQDFKREVLEKGLP-AKREITFETELFGSKT----FLIYVEPVFSKSGETIGVNYMGM 328
           ++  +    V + G P +  E   +T+  GS      F   V P     G   GV  +  
Sbjct: 71  QQIYEMLDRVYQTGEPQSGSEWRLQTDYDGSGVEERYFDFVVTPRRRADGSIEGVQLIVD 130

Query: 329 DVTDQVRKREKMAKLREE 346
           DVT +VR R+      EE
Sbjct: 131 DVTSRVRARQAAEARVEE 148

>3kx0_X Uncharacterized protein RV1364C/MT1410; PAS domain, sensory domain, mycobacteium tuberculos molecule binding domain; 2.30A {Mycobacterium tuberculosis} Length = 185

 Score = 67.4 bits (165), Expect = 7e-13
 Identities = 27/131 (20%), Positives = 50/131 (38%), Gaps = 9/131 (6%)

Query: 224 LHFVLQNAPVVMGH-QDKELRYRFIYNH--FPSLHEEDILGKTDVEIFSGAGVKESQDFK 280
           +  + ++ P ++   +  + R+    N          D +G+   E++     ++  +  
Sbjct: 39  VRRIFEHIPAILVGLEGPDHRFVA-VNAAYRGFSPLLDTVGQPAREVYPELEGQQIYEML 97

Query: 281 REVLEKGLP-AKREITFETELFGSKT----FLIYVEPVFSKSGETIGVNYMGMDVTDQVR 335
             V + G P +  E   +T+  GS      F   V P     G   GV  +  DVT +VR
Sbjct: 98  DRVYQTGEPQSGSEWRLQTDYDGSGVEERYFDFVVTPRRRADGSIEGVQLIVDDVTSRVR 157

Query: 336 KREKMAKLREE 346
            R+      EE
Sbjct: 158 ARQAAEARVEE 168

>2btz_A Pyruvate dehydrogenase kinase isoenzyme 2; GHKL motif regulation, transferase; 2.2A {Homo sapiens} PDB: 2bu2_A* 2bu5_A* 2bu6_A* 2bu7_A* 2bu8_A* 3crk_A* 1jm6_A* 3crl_A* Length = 394

 Score = 70.6 bits (172), Expect = 7e-13
 Identities = 18/87 (20%), Positives = 28/87 (32%), Gaps = 5/87 (5%)

Query: 591 WIRCDVYDTGIGIPENALPTLFRKYMQVSADHARKYG-----GTGLGLAICKQLVELMGG 645
            +   + D G G+P   +  LF      +       G     G G GL I +   +   G
Sbjct: 270 DLSIKMSDRGGGVPLRKIERLFSYMYSTAPTPQPGTGGTPLAGFGYGLPISRLYAKYFQG 329

Query: 646 RLTVTSKVHCGSTFTFILPYQVSPIEE 672
            L + S    G+     L    +   E
Sbjct: 330 DLQLFSMEGFGTDAVIYLKALSTDSVE 356

>2btz_A Pyruvate dehydrogenase kinase isoenzyme 2; GHKL motif regulation, transferase; 2.2A {Homo sapiens} PDB: 2bu2_A* 2bu5_A* 2bu6_A* 2bu7_A* 2bu8_A* 3crk_A* 1jm6_A* 3crl_A* Length = 394

 Score = 66.0 bits (160), Expect = 2e-11
 Identities = 16/150 (10%), Positives = 48/150 (32%), Gaps = 20/150 (13%)

Query: 356 ELNKTIHITEETMRAKQMLATMSHEIRSPLTGVVSMAEILSNTKLDREQRQLLGVMISSG 415
           E   T      + +  Q      +  R  +  +++   ++ +   +    + +G +  + 
Sbjct: 123 EYKDTYGDDPVSNQNIQYFLDRFYLSRISIRMLINQHTLIFDGSTNPAHPKHIGSIDPNC 182

Query: 416 DLVLQLINDILDLSKVESGVMKLEAAKFRPREVVKHVLQTAAASLQKILMLEGDIADDVP 475
           ++  +++ D  D++K+      + +                       +          P
Sbjct: 183 NVS-EVVKDAYDMAKLLCDKYYMASP-------------------DLEIQEINAANSKQP 222

Query: 476 IEVIGDVLRIRQILTNLISNAIKFTPEGKV 505
           I ++     +  +L  L  NA++ T E   
Sbjct: 223 IHMVYVPSHLYHMLFELFKNAMRATVESHE 252

>2qzj_A Two-component response regulator; 11017X, PSI-II, structural genomics; 2.89A {Clostridium difficile} Length = 136

 Score = 65.6 bits (161), Expect = 7e-13
 Identities = 21/73 (28%), Positives = 38/73 (52%)

Query: 859 KPKILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDG 918
           + KIL+++ +K N    K  +++ G SID+  N  EA+  +    YDLI +++ +   DG
Sbjct: 4   QTKILIIDGDKDNCQKLKGFLEEKGISIDLAYNCEEAIGKIFSNKYDLIFLEIILSDGDG 63

Query: 919 LKATRLIRSFEDT 931
               + IR+    
Sbjct: 64  WTLCKKIRNVTTC 76

>1xhf_A DYE resistance, aerobic respiration control protein ARCA; two-component system, gene regulation, transcription factor, anoxic redox control; 2.15A {Escherichia coli} SCOP: c.23.1.1 PDB: 1xhe_A Length = 123

 Score = 64.8 bits (159), Expect = 1e-12
 Identities = 19/73 (26%), Positives = 36/73 (49%)

Query: 859 KPKILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDG 918
            P IL+VED  +     KS+ +  G+ +    +G E    +   + +L++MD+ +P  +G
Sbjct: 3   TPHILIVEDELVTRNTLKSIFEAEGYDVFEATDGAEMHQILSEYDINLVIMDINLPGKNG 62

Query: 919 LKATRLIRSFEDT 931
           L   R +R   + 
Sbjct: 63  LLLARELREQANV 75

>3eqz_A Response regulator; structural genomics, unknown function, PSI-2, protein struct initiative; 2.15A {Colwellia psychrerythraea} Length = 135

 Score = 64.2 bits (157), Expect = 2e-12
 Identities = 13/73 (17%), Positives = 37/73 (50%), Gaps = 1/73 (1%)

Query: 859 KPKILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDG 918
             ++ +V+D+ +   + K++++ +  +++       A   +     D+I++D+ MP MDG
Sbjct: 3   LNRVFIVDDDTLTCNLLKTIVEPIFGNVEAFQ-HPRAFLTLSLNKQDIIILDLMMPDMDG 61

Query: 919 LKATRLIRSFEDT 931
           ++  R +   +  
Sbjct: 62  IEVIRHLAEHKSP 74

>2a9o_A Response regulator; essential protein, YYCF/YYCG homolog, signaling protein; 1.65A {Streptococcus pneumoniae} SCOP: c.23.1.1 PDB: 1nxo_A 1nxs_A 1nxv_A 1nxw_A 1nxx_A 1nxp_A 2a9p_A 2a9q_A 1nxt_A* 2a9r_A* Length = 120

 Score = 63.6 bits (156), Expect = 3e-12
 Identities = 22/71 (30%), Positives = 39/71 (54%)

Query: 861 KILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLK 920
           KIL+V+D K    + K  M + G+ +    NG EA+   + +  D+I++D+ +P +DGL+
Sbjct: 3   KILIVDDEKPISDIIKFNMTKEGYEVVTAFNGREALEQFEAEQPDIIILDLMLPEIDGLE 62

Query: 921 ATRLIRSFEDT 931
             + IR     
Sbjct: 63  VAKTIRKTSSV 73

>3a10_A Response regulator; phosphoacceptor, signaling protein; HET: MSE PG4; 1.63A {Thermotoga maritima} PDB: 3a0r_B* 3a0u_A* Length = 116

 Score = 63.2 bits (155), Expect = 3e-12
 Identities = 23/66 (34%), Positives = 38/66 (57%)

Query: 861 KILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLK 920
           +IL+V+D      + K  +++ G+ ID   NG EA+      NYDL+++D+ MP + GL+
Sbjct: 3   RILVVDDEPNIRELLKEELQEEGYEIDTAENGEEALKKFFSGNYDLVILDIEMPGISGLE 62

Query: 921 ATRLIR 926
               IR
Sbjct: 63  VAGEIR 68

>3f6p_A Transcriptional regulatory protein YYCF; unphosphorelated, receiver domain, cytoplasm, DNA-binding, phosphoprotein, transcription regulation; 1.95A {Bacillus subtilis} PDB: 2zwm_A Length = 120

 Score = 63.2 bits (155), Expect = 3e-12
 Identities = 23/73 (31%), Positives = 41/73 (56%)

Query: 859 KPKILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDG 918
             KIL+V+D K    + +  +++ G+ +   ++G EAV  V+    DLIL+D+ +P  DG
Sbjct: 2   DKKILVVDDEKPIADILEFNLRKEGYEVHCAHDGNEAVEMVEELQPDLILLDIMLPNKDG 61

Query: 919 LKATRLIRSFEDT 931
           ++  R +R   D 
Sbjct: 62  VEVCREVRKKYDM 74

>1r62_A Nitrogen regulation protein NR(II); PII, histidine kinase, two component system, transfera; 1.60A {Escherichia coli} SCOP: d.122.1.3 Length = 160

 Score = 64.5 bits (158), Expect = 3e-12
 Identities = 29/74 (39%), Positives = 39/74 (52%), Gaps = 7/74 (9%)

Query: 591 WIRCDVYDTGIGIPENALPTLFRKYMQVSADHARKYGGTGLGLAICKQLVELMGGRLTVT 650
             R DV D G GIP +   TLF  Y  VS     + GGTGLGL+I + L++   G++  T
Sbjct: 91  AARIDVEDNGPGIPPHLQDTLF--YPMVSG----REGGTGLGLSIARNLIDQHSGKIEFT 144

Query: 651 SKVHCGSTFTFILP 664
           S     + F+  LP
Sbjct: 145 SWPG-HTEFSVYLP 157

>2rjn_A Response regulator receiver:metal-dependent phosphohydrolase, HD subdomain; structural genomics, oceanospirillum SP. MED92; 2.10A {Neptuniibacter caesariensis} Length = 154

 Score = 63.8 bits (156), Expect = 6e-12
 Identities = 23/144 (15%), Positives = 58/144 (40%), Gaps = 27/144 (18%)

Query: 857 KPKPKILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVM 916
                ++LV+D +  +   K ++K+LG +I    + ++A+ A++  +  L++ D+ MP M
Sbjct: 5   YKNYTVMLVDDEQPILNSLKRLIKRLGCNIITFTSPLDALEALKGTSVQLVISDMRMPEM 64

Query: 917 DGLKATRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECF 976
            G      +                             +  I  + ++  A +++  +  
Sbjct: 65  GGEVFLEQVAK--------------------------SYPDIERVVISGYADAQATIDAV 98

Query: 977 ANG-MDSFVSKPVTFQKLKECLEQ 999
             G +  F+ KP   + + + +E+
Sbjct: 99  NRGKISRFLLKPWEDEDVFKVVEK 122

>4dad_A Putative pilus assembly-related protein; response regulator receiver domain, CHEY-related protein, ST genomics; 2.50A {Burkholderia pseudomallei} PDB: 4dn6_A Length = 146

 Score = 63.2 bits (154), Expect = 6e-12
 Identities = 16/143 (11%), Positives = 42/143 (29%), Gaps = 29/143 (20%)

Query: 861  KILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEA---VHAVQCQNYDLILMDVCMPVMD 917
             IL+  ++   +     ++   G        G  A           +D++++D       
Sbjct: 22   NILVASEDASRLAHLARLVGDAGRYRVTRTVGRAAQIVQRTDGLDAFDILMIDGAALDTA 81

Query: 918  GLKATRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFA 977
             L A   +                                +  + +T +A S++  +   
Sbjct: 82   ELAAIEKLSR--------------------------LHPGLTCLLVTTDASSQTLLDAMR 115

Query: 978  NGMDSFVSKPVTFQKLKECLEQY 1000
             G+   +  P+  + L + L++ 
Sbjct: 116  AGVRDVLRWPLEPRALDDALKRA 138

>3gl9_A Response regulator; beta-sheet, surrounded by alpha helices, BOTH sides, signaling protein; HET: BFD; 1.80A {Thermotoga maritima} PDB: 3dgf_C 3dge_C Length = 122

 Score = 62.5 bits (152), Expect = 6e-12
 Identities = 31/135 (22%), Positives = 55/135 (40%), Gaps = 24/135 (17%)

Query: 859 KPKILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDG 918
             K+LLV+D+ +   +    +K+ G+ +    NG  A+  +     DLI++ + MPVMDG
Sbjct: 2   SKKVLLVDDSAVLRKIVSFNLKKEGYEVIEAENGQIALEKLSEFTPDLIVLXIMMPVMDG 61

Query: 919 LKATRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFAN 978
               + ++  E+                         KRIP+I +TA    E      + 
Sbjct: 62  FTVLKKLQEKEEW------------------------KRIPVIVLTAKGGEEDESLALSL 97

Query: 979 GMDSFVSKPVTFQKL 993
           G    + KP +  + 
Sbjct: 98  GARKVMRKPFSPSQF 112

>1dc7_A NTRC, nitrogen regulation protein; receiver domain, phosphorylation, signal transduction, conformational rearrangement; NMR {Salmonella typhimurium} SCOP: c.23.1.1 PDB: 1j56_A 1krw_A 1krx_A 1ntr_A 1dc8_A* Length = 124

 Score = 62.1 bits (152), Expect = 9e-12
 Identities = 28/142 (19%), Positives = 56/142 (39%), Gaps = 26/142 (18%)

Query: 858 PKPKILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMD 917
            +  + +V+D+     V +  +   G +     NG E + A+  +  D++L D+ MP MD
Sbjct: 2   QRGIVWVVDDDSSIRWVLERALAGAGLTCTTFENGNEVLAALASKTPDVLLSDIRMPGMD 61

Query: 918 GLKATRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFA 977
           GL   + I+                               +P+I MTA++  ++A   + 
Sbjct: 62  GLALLKQIK--------------------------QRHPMLPVIIMTAHSDLDAAVSAYQ 95

Query: 978 NGMDSFVSKPVTFQKLKECLEQ 999
            G   ++ KP    +    +E+
Sbjct: 96  QGAFDYLPKPFDIDEAVALVER 117

>4e7p_A Response regulator; DNA binding, cytosol, transcription regulator; 1.89A {Streptococcus pneumoniae} PDB: 4e7o_A Length = 150

 Score = 63.0 bits (154), Expect = 9e-12
 Identities = 23/88 (26%), Positives = 40/88 (45%), Gaps = 5/88 (5%)

Query: 843 SPSSSSAEVPETKPKPKP-KILLVEDNKINVMVAKSMMKQLGHSIDVV---NNGVEAVHA 898
           S            P+    K+L+ ED  + +  A   +  L   ++ V    NG EA+  
Sbjct: 3   SSHHHHHHSSGLVPRGSHMKVLVAEDQSM-LRDAMCQLLTLQPDVESVLQAKNGQEAIQL 61

Query: 899 VQCQNYDLILMDVCMPVMDGLKATRLIR 926
           ++ ++ D+ ++DV MPV  GL+    IR
Sbjct: 62  LEKESVDIAILDVEMPVKTGLEVLEWIR 89

>2q2e_B Type 2 DNA topoisomerase 6 subunit B; DNA-binding, SPO11, ATPase; 4.00A {Methanosarcina mazei} Length = 621

 Score = 67.9 bits (165), Expect = 9e-12
 Identities = 17/81 (20%), Positives = 31/81 (38%), Gaps = 2/81 (2%)

Query: 591 WIRCDVYDTGIGIPENALPTLFRKYMQVSADHARK--YGGTGLGLAICKQLVELMGGRLT 648
           ++   + D G GI    +P +F K +  S  HA K   G  G+G++      ++  GR T
Sbjct: 73  YVTVIIEDNGPGIVREQIPKVFAKLLYGSRFHALKQSRGQQGIGISAAVLYAQMTAGRHT 132

Query: 649 VTSKVHCGSTFTFILPYQVSP 669
                   +         ++ 
Sbjct: 133 KILSKTSPTAPAHYYELMINT 153

>3hv2_A Response regulator/HD domain protein; PSI-2, NYSGXRC, structural genomics, protein structure initiative; 1.50A {Pseudomonas fluorescens pf-5} Length = 153

 Score = 62.6 bits (153), Expect = 1e-11
 Identities = 26/154 (16%), Positives = 56/154 (36%), Gaps = 27/154 (17%)

Query: 847 SSAEVPETKPKPKPKILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDL 906
           S  E+       +P+ILLV+  ++ +   + ++  L +++    +  +A+  +  +  DL
Sbjct: 2   SLGELNVATVTRRPEILLVDSQEVILQRLQQLLSPLPYTLHFARDATQALQLLASREVDL 61

Query: 907 ILMDVCMPVMDGLKATRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTAN 966
           ++    +P MDG      I                             +     I +T +
Sbjct: 62  VISAAHLPQMDGPTLLARIHQ--------------------------QYPSTTRILLTGD 95

Query: 967 ALSESAEECFANG-MDSFVSKPVTFQKLKECLEQ 999
              +   +    G +  ++SKP   Q+L   L Q
Sbjct: 96  PDLKLIAKAINEGEIYRYLSKPWDDQELLLALRQ 129

>1mvo_A PHOP response regulator; phosphate regulon, transcriptional regulatory protein, alpha/beta doubly wound fold, phosphorylation; 1.60A {Bacillus subtilis} SCOP: c.23.1.1 Length = 136

 Score = 62.2 bits (152), Expect = 1e-11
 Identities = 19/73 (26%), Positives = 43/73 (58%)

Query: 859 KPKILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDG 918
             KIL+V+D +  V + +  +++ G+ +   ++G EA+   + +  DLI++DV +P +DG
Sbjct: 3   NKKILVVDDEESIVTLLQYNLERSGYDVITASDGEEALKKAETEKPDLIVLDVMLPKLDG 62

Query: 919 LKATRLIRSFEDT 931
           ++  + +R  +  
Sbjct: 63  IEVCKQLRQQKLM 75

>1zgz_A Torcad operon transcriptional regulatory protein; two-component system, gene regulation, transcription factor, respiratory system; 1.80A {Escherichia coli} SCOP: c.23.1.1 Length = 122

 Score = 61.3 bits (150), Expect = 2e-11
 Identities = 20/74 (27%), Positives = 36/74 (48%), Gaps = 2/74 (2%)

Query: 859 KPKILLVED-NKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMD 917
              I++VED       +     ++ G+++ V  +G      +Q Q+ DLIL+D+ +P  +
Sbjct: 2   PHHIVIVEDEPVTQARLQSYFTQE-GYTVSVTASGAGLREIMQNQSVDLILLDINLPDEN 60

Query: 918 GLKATRLIRSFEDT 931
           GL  TR +R     
Sbjct: 61  GLMLTRALRERSTV 74

>3t6k_A Response regulator receiver; flavodoxin-like, structural genomics, joint center for struc genomics, JCSG, protein structure initiative; HET: MSE; 1.86A {Chloroflexus aurantiacus} Length = 136

 Score = 61.4 bits (150), Expect = 2e-11
 Identities = 21/109 (19%), Positives = 42/109 (38%), Gaps = 26/109 (23%)

Query: 858 PKPKILLVEDNK-INVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVM 916
               +L+V+D+  +  M+   +    G+ +    +G EA+  +     D ++ DV +P +
Sbjct: 3   KPHTLLIVDDDDTVAEMLELVLRGA-GYEVRRAASGEEALQQIYKNLPDALICDVLLPGI 61

Query: 917 DGLKATRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTA 965
           DG    + +R    T                        K +PI+ +TA
Sbjct: 62  DGYTLCKRVRQHPLT------------------------KTLPILMLTA 86

>3rqi_A Response regulator protein; structural genomics, seattle structural genomics center for infectious disease, ssgcid; HET: PHD CIT; 1.70A {Burkholderia pseudomallei} Length = 184

 Score = 62.7 bits (153), Expect = 2e-11
 Identities = 18/136 (13%), Positives = 49/136 (36%), Gaps = 28/136 (20%)

Query: 859 KPKILLVED-NKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMD 917
               L+++D       +A+ + ++ G+++   +N  EA+     + ++ I + + +    
Sbjct: 7   DKNFLVIDDNEVFAGTLARGLERR-GYAVRQAHNKDEALKLAGAEKFEFITVXLHLGNDS 65

Query: 918 GLKATRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFA 977
           GL     +                                  I+ +T  A   +A +   
Sbjct: 66  GLSLIAPLCD--------------------------LQPDARILVLTGYASIATAVQAVK 99

Query: 978 NGMDSFVSKPVTFQKL 993
           +G D++++KP   + +
Sbjct: 100 DGADNYLAKPANVESI 115

>2oqr_A Sensory transduction protein REGX3; response regulator, winged-helix-turn-helix, DNA-binding, 3D swapping, two component system; 2.03A {Mycobacterium tuberculosis H37RV} Length = 230

 Score = 63.3 bits (155), Expect = 3e-11
 Identities = 16/73 (21%), Positives = 33/73 (45%)

Query: 859 KPKILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDG 918
              +L+VED +        ++++ G    VV +G  A+        D++L+D+ +P M G
Sbjct: 4   ATSVLIVEDEESLADPLAFLLRKEGFEATVVTDGPAALAEFDRAGADIVLLDLMLPGMSG 63

Query: 919 LKATRLIRSFEDT 931
               + +R+    
Sbjct: 64  TDVCKQLRARSSV 76

>2gwr_A DNA-binding response regulator MTRA; two-component regulatory system, transcription regulation, phosphorylation, OMPR family; 2.10A {Mycobacterium tuberculosis} PDB: 3nhz_A Length = 238

 Score = 63.3 bits (155), Expect = 3e-11
 Identities = 19/73 (26%), Positives = 42/73 (57%)

Query: 859 KPKILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDG 918
           + +IL+V+D+     +   +++  G    V+ +G +A+ AV+    DL+L+D+ +P M+G
Sbjct: 5   RQRILVVDDDASLAEMLTIVLRGEGFDTAVIGDGTQALTAVRELRPDLVLLDLMLPGMNG 64

Query: 919 LKATRLIRSFEDT 931
           +   R++R+    
Sbjct: 65  IDVCRVLRADSGV 77

>3cu5_A Two component transcriptional regulator, ARAC FAM; structural genomics, protein structure initiative; 2.60A {Clostridium phytofermentans isdg} Length = 141

 Score = 60.6 bits (148), Expect = 4e-11
 Identities = 26/142 (18%), Positives = 53/142 (37%), Gaps = 29/142 (20%)

Query: 861 KILLVEDNKINVMVAKSMMKQLGHSIDVV---NNGVEAVHAVQCQNYDLILMDVCMPVMD 917
           +IL+V+D K+      + +     S D +   ++G+ A+        +++L DV MP MD
Sbjct: 4   RILIVDDEKLTRDGLIANINWKALSFDQIDQADDGINAIQIALKHPPNVLLTDVRMPRMD 63

Query: 918 GLKATRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFA 977
           G++    I                             +    +I M+  +  E  +    
Sbjct: 64  GIELVDNILK--------------------------LYPDCSVIFMSGYSDKEYLKAAIK 97

Query: 978 NGMDSFVSKPVTFQKLKECLEQ 999
                +V KP+   ++ + L+Q
Sbjct: 98  FRAIRYVEKPIDPSEIMDALKQ 119

>2b4a_A BH3024; flavodoxin-like fold, structural genomics, joint center for structural genomics, JCSG, protein structure initiative; 2.42A {Bacillus halodurans} SCOP: c.23.1.1 Length = 138

 Score = 60.7 bits (148), Expect = 5e-11
 Identities = 13/70 (18%), Positives = 29/70 (41%), Gaps = 1/70 (1%)

Query: 859 KPKILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAV-HAVQCQNYDLILMDVCMPVMD 917
             ++ LVED   +  + +  + QLG  + V  +G     H  Q    DL+++   +  + 
Sbjct: 15  PFRVTLVEDEPSHATLIQYHLNQLGAEVTVHPSGSAFFQHRSQLSTCDLLIVSDQLVDLS 74

Query: 918 GLKATRLIRS 927
                 +++ 
Sbjct: 75  IFSLLDIVKE 84

>3crn_A Response regulator receiver domain protein, CHEY-; structural genomics, signal regulator receiver domain; HET: PHD; 1.58A {Methanospirillum hungatei jf-1} Length = 132

 Score = 60.2 bits (146), Expect = 5e-11
 Identities = 22/136 (16%), Positives = 52/136 (38%), Gaps = 26/136 (19%)

Query: 859 KPKILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDG 918
             +IL+V+D+   +   K +++  G+ +++     E +  ++ + ++L L  + +P M+G
Sbjct: 3   LKRILIVDDDTAILDSTKQILEFEGYEVEIAATAGEGLAKIENEFFNLALFXIKLPDMEG 62

Query: 919 LKATRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFAN 978
            +                                     +  I +T  A  E++      
Sbjct: 63  TELLEKAHKLRPG--------------------------MKKIMVTGYASLENSVFSLNA 96

Query: 979 GMDSFVSKPVTFQKLK 994
           G D+++ KPV  + L 
Sbjct: 97  GADAYIMKPVNPRDLL 112

>2gkg_A Response regulator homolog; social motility, receiver domain, signalling, high resolutio signaling protein; 1.00A {Myxococcus xanthus} PDB: 2i6f_A 2nt4_A 2nt3_A Length = 127

 Score = 59.8 bits (146), Expect = 6e-11
 Identities = 18/108 (16%), Positives = 40/108 (37%), Gaps = 25/108 (23%)

Query: 859 KPKILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCM-PVMD 917
             KIL+VE +       +S ++  G ++D   +G  +V  ++    DL+++ V +    +
Sbjct: 5   SKKILIVESDTALSATLRSALEGRGFTVDETTDGKGSVEQIRRDRPDLVVLAVDLSAGQN 64

Query: 918 GLKATRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTA 965
           G      ++  +D                         K +PI+ +  
Sbjct: 65  GYLICGKLKKDDDL------------------------KNVPIVIIGN 88

>3jte_A Response regulator receiver protein; structural genomics, nysgrc, response regulator receiver domain, target 11226E, PSI-2; 1.90A {Clostridium thermocellum atcc 27405} Length = 143

 Score = 60.2 bits (147), Expect = 7e-11
 Identities = 25/142 (17%), Positives = 54/142 (38%), Gaps = 28/142 (19%)

Query: 859 KPKILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAV--QCQNYDLILMDVCMPVM 916
             KIL+++D    +   K +++  G+ +   ++  E +      C + D+++ D+ MP +
Sbjct: 3   LAKILVIDDESTILQNIKFLLEIDGNEVLTASSSTEGLRIFTENCNSIDVVITDMKMPKL 62

Query: 917 DGLKATRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECF 976
            G+   R I+                               + +I +T +   ++A    
Sbjct: 63  SGMDILREIKK--------------------------ITPHMAVIILTGHGDLDNAILAM 96

Query: 977 ANGMDSFVSKPVTFQKLKECLE 998
             G   ++ KPVT Q L   + 
Sbjct: 97  KEGAFEYLRKPVTAQDLSIAIN 118

>2jba_A Phosphate regulon transcriptional regulatory PROT; transcription factor, sensory transduction, phosphate regula transcription regulation; 1.45A {Escherichia coli} PDB: 2jba_B 1b00_A 2iyn_A 2jb9_A 1zes_A Length = 127

 Score = 59.4 bits (145), Expect = 1e-10
 Identities = 23/108 (21%), Positives = 40/108 (37%), Gaps = 26/108 (24%)

Query: 859 KPKILLVED-NKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMD 917
             +IL+VED   I  MV   + +  G       +   AV+ +     DLIL+   +P   
Sbjct: 2   ARRILVVEDEAPIREMVCFVLEQN-GFQPVEAEDYDSAVNQLNEPWPDLILLAWMLPGGS 60

Query: 918 GLKATRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTA 965
           G++  + +R    T +                        IP++ +TA
Sbjct: 61  GIQFIKHLRRESMTRD------------------------IPVVMLTA 84

>3b2n_A Uncharacterized protein Q99UF4; structural genomics, PSI-2, protein structure initiative, NE SGX research center for structural genomics; 2.04A {Staphylococcus aureus} Length = 133

 Score = 59.4 bits (145), Expect = 1e-10
 Identities = 16/69 (23%), Positives = 39/69 (56%), Gaps = 4/69 (5%)

Query: 861 KILLVEDNKINVMVAKSMMKQLGHSIDVV---NNGVEAVHAVQCQNYDLILMDVCMPVMD 917
            +++ ED  + +  A   + +L    +++   +NG++A+  ++  N +++++D+ MP M 
Sbjct: 5   SLIIAEDQNM-LRQAMVQLIKLHGDFEILADTDNGLDAMKLIEEYNPNVVILDIEMPGMT 63

Query: 918 GLKATRLIR 926
           GL+    IR
Sbjct: 64  GLEVLAEIR 72

>2pln_A HP1043, response regulator; signaling protein; 1.80A {Helicobacter pylori} PDB: 2hqo_A Length = 137

 Score = 58.7 bits (143), Expect = 2e-10
 Identities = 15/70 (21%), Positives = 31/70 (44%), Gaps = 10/70 (14%)

Query: 861 KILLVEDNKINVMVAKSMMKQL---GHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMD 917
           ++LL+E N    ++   + K L   G   DV  +  +  + +  +NYDL++    +   +
Sbjct: 20  RVLLIEKNS---VLGGEIEKGLNVKGFMADVTESLEDGEYLMDIRNYDLVM----VSDKN 72

Query: 918 GLKATRLIRS 927
            L     I+ 
Sbjct: 73  ALSFVSRIKE 82

>1dz3_A Stage 0 sporulation protein A; response regulator, domain swapping; 1.65A {Bacillus stearothermophilus} SCOP: c.23.1.1 PDB: 1qmp_A* Length = 130

 Score = 57.9 bits (141), Expect = 3e-10
 Identities = 16/70 (22%), Positives = 36/70 (51%), Gaps = 4/70 (5%)

Query: 861 KILLVEDNKINVMVAKSMMKQLGHSIDVV---NNGVEAVHAVQCQNYDLILMDVCMPVMD 917
           K+ + +DN+  ++            ++V+    NG + +  ++ +  D++L+D+ MP +D
Sbjct: 4   KVCIADDNRE-LVSLLDEYISSQPDMEVIGTAYNGQDCLQMLEEKRPDILLLDIIMPHLD 62

Query: 918 GLKATRLIRS 927
           GL     IR+
Sbjct: 63  GLAVLERIRA 72

>3eul_A Possible nitrate/nitrite response transcriptional regulatory protein NARL (DNA-binding...; central beta strand flanked by alpha helices; 1.90A {Mycobacterium tuberculosis} Length = 152

 Score = 57.5 bits (140), Expect = 8e-10
 Identities = 19/78 (24%), Positives = 40/78 (51%), Gaps = 5/78 (6%)

Query: 854 TKPKPKP-KILLVEDNKINVMVAKSMMKQLGHSIDVV---NNGVEAVHAVQCQNYDLILM 909
           + P+P+  ++++ +D+ +           L  S++VV   ++G  A+  ++    D+ L+
Sbjct: 9   SNPQPEKVRVVVGDDHPL-FREGVVRALSLSGSVNVVGEADDGAAALELIKAHLPDVALL 67

Query: 910 DVCMPVMDGLKATRLIRS 927
           D  MP MDG +    +RS
Sbjct: 68  DYRMPGMDGAQVAAAVRS 85

>3luq_A Sensor protein; PAS, histidine, kinase, PSI, MCSG, structural genomics, midwest center for structural genomics; HET: PGE; 2.49A {Geobacter sulfurreducens} Length = 114

 Score = 56.1 bits (136), Expect = 1e-09
 Identities = 26/113 (23%), Positives = 43/113 (38%), Gaps = 4/113 (3%)

Query: 222 NFLHFVLQNAPVVMGHQDKELRYRFI---YNHFPSLHEEDILGKTDVEIFSGAGVKESQD 278
             L    ++AP  +   D+E+RY  +   +     L + DILG +  +IF     +E + 
Sbjct: 3   ERLRLFTEHAPAALAMFDREMRYLAVSRRWREDYGLGDGDILGMSHYDIF-PEIGEEWKS 61

Query: 279 FKREVLEKGLPAKREITFETELFGSKTFLIYVEPVFSKSGETIGVNYMGMDVT 331
             R  L   +    E  F      ++     V P +   G   GV     D+T
Sbjct: 62  VHRRGLAGEVIRVEEDCFVRADGRTQWLRWEVRPWYEGEGRVGGVVIFTEDIT 114

>2hqr_A Putative transcriptional regulator; phosporylation-independent response regulator, H. pylori, SY dimer, signaling protein; NMR {Helicobacter pylori} Length = 223

 Score = 57.9 bits (141), Expect = 2e-09
 Identities = 14/68 (20%), Positives = 31/68 (45%), Gaps = 6/68 (8%)

Query: 861 KILLVEDN-KINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGL 919
           ++LL+E N  +   + K +  + G   DV  +  +  + +  +NYDL++    +   + L
Sbjct: 2   RVLLIEKNSVLGGEIEKGLNVK-GFMADVTESLEDGEYLMDIRNYDLVM----VSDKNAL 56

Query: 920 KATRLIRS 927
                I+ 
Sbjct: 57  SFVSRIKE 64

>3f6c_A Positive transcription regulator EVGA; structural genomics, PSI-2, protein structure initiative, PO transcription regulator EVGA; 1.45A {Escherichia coli k-12} Length = 134

 Score = 55.6 bits (135), Expect = 2e-09
 Identities = 11/44 (25%), Positives = 25/44 (56%), Gaps = 3/44 (6%)

Query: 886 IDVV---NNGVEAVHAVQCQNYDLILMDVCMPVMDGLKATRLIR 926
           I+++     G  AV  V+    D++++DV +P ++G++    +R
Sbjct: 26  IEILAELTEGGSAVQRVETLKPDIVIIDVDIPGVNGIQVLETLR 69

>2qr3_A Two-component system response regulator; structural genomics, signal receiver, PSI-2, protein structu initiative; 1.80A {Bacteroides fragilis} Length = 140

 Score = 55.7 bits (135), Expect = 3e-09
 Identities = 28/146 (19%), Positives = 55/146 (37%), Gaps = 31/146 (21%)

Query: 859 KPKILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPV--- 915
              I++V+DNK  +   + ++K     +  +++ V     ++ +N +++L+D+       
Sbjct: 3   LGTIIIVDDNKGVLTAVQLLLKNHFSKVITLSSPVSLSTVLREENPEVVLLDMNFTSGIN 62

Query: 916 --MDGLKATRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAE 973
              +GL     I+                            ++ +P++  TA A  + A 
Sbjct: 63  NGNEGLFWLHEIKR--------------------------QYRDLPVVLFTAYADIDLAV 96

Query: 974 ECFANGMDSFVSKPVTFQKLKECLEQ 999
                G   FV KP   QKL E L  
Sbjct: 97  RGIKEGASDFVVKPWDNQKLLETLLN 122

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

 Score = 59.5 bits (143), Expect = 5e-09
 Identities = 85/624 (13%), Positives = 170/624 (27%), Gaps = 227/624 (36%)

Query: 6   ETDLIEDMDIEGLPSMWPEDIGSDKQFNVERPGGGQDMLEEVTIPEDQTIVDFKRLLELT 65
           E   +++ D + +  M P+ I S ++ +         ++         T     RL    
Sbjct: 26  EDAFVDNFDCKDVQDM-PKSILSKEEID--------HIIMSKD-AVSGT----LRLFWT- 70

Query: 66  NYTDKGSSQMAYLVKH-------W-------EYRQSNAVRLL----REEL---------D 98
               K    +   V+        +       E RQ + +  +    R+ L          
Sbjct: 71  -LLSKQEEMVQKFVEEVLRINYKFLMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFAKY 129

Query: 99  NLSRQRQESELKK-------------------------LEILEEHRFEEEGYGG------ 127
           N+SR +   +L++                         L++   ++ + +          
Sbjct: 130 NVSRLQPYLKLRQALLELRPAKNVLIDGVLGSGKTWVALDVCLSYKVQCKMDFKIFWLNL 189

Query: 128 --DKRPISIMDELSDMWKDVCP--------------RKNDVVFQSKRVEVDAEY------ 165
                P ++++ L  +   + P              R + +  + +R+     Y      
Sbjct: 190 KNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLV 249

Query: 166 -DTVEYWKQ-RALDLE-KML-----------EASGQREQALMEKLNESVT---------- 201
              V+  K   A +L  K+L            ++       ++  + ++T          
Sbjct: 250 LLNVQNAKAWNAFNLSCKILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLK 309

Query: 202 --NLEKQSSPVEE-------LSQI-------LKRADNFLHFVLQNAPVVMG----HQD-K 240
             +   Q  P E        LS I       L   DN+ H        ++       +  
Sbjct: 310 YLDCRPQDLPREVLTTNPRRLSIIAESIRDGLATWDNWKHVNCDKLTTIIESSLNVLEPA 369

Query: 241 ELRYRF----IYNHFPSLHEEDILGKTDV-EIFSGAGVK-ESQDFKREVLEKGLPAKREI 294
           E R  F    +   FP          T +  +     +K +      ++ +  L  K+  
Sbjct: 370 EYRKMFDRLSV---FP----PSAHIPTILLSLIWFDVIKSDVMVVVNKLHKYSLVEKQ-- 420

Query: 295 TFETELFGSKTFLIYVEPVFSKSGETIGVNYMGMDVTDQVR-KREKMAKLREEI--AVQK 351
                    K   I +                   +  +++ K E    L   I      
Sbjct: 421 --------PKESTISI-----------------PSIYLELKVKLENEYALHRSIVDHYNI 455

Query: 352 AKETELNKTI----------HI------TEETMRAKQM------LATMSHEIR---SPLT 386
            K  + +  I          HI       E   R             +  +IR   +   
Sbjct: 456 PKTFDSDDLIPPYLDQYFYSHIGHHLKNIEHPERMTLFRMVFLDFRFLEQKIRHDSTAWN 515

Query: 387 GVVSMAEILSNTKLDREQRQLLGVMISSGDLVL-QLINDILD-LSKVESGVMK------L 438
              S+   L   K  +         I   D    +L+N ILD L K+E  ++       L
Sbjct: 516 ASGSILNTLQQLKFYKPY-------ICDNDPKYERLVNAILDFLPKIEENLICSKYTDLL 568

Query: 439 EAAKFRPREVVKHVLQTAAASLQK 462
             A     E    + + A   +Q+
Sbjct: 569 RIALMAEDEA---IFEEAHKQVQR 589

>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 = 57.2 bits (137), Expect = 3e-08
 Identities = 69/438 (15%), Positives = 136/438 (31%), Gaps = 128/438 (29%)

Query: 237 HQDKE-----LRYRFIYNHFPSLHEEDILGKTDVEIFSGAGVKESQDFKREVLEKGLPAK 291
           H D E      +Y+ I + F    E+  +   D         K+ QD  + +L     +K
Sbjct: 6   HMDFETGEHQYQYKDILSVF----EDAFVDNFDC--------KDVQDMPKSIL-----SK 48

Query: 292 REITFETELFGSKT------FLIYVEPVFSKSGETIGVNYMGMDVTDQVRKREK--MAKL 343
            EI     +  SK        L +         E +   ++     + +R   K  M+ +
Sbjct: 49  EEID---HIIMSKDAVSGTLRLFWT---LLSKQEEMVQKFVE----EVLRINYKFLMSPI 98

Query: 344 REEIAVQKAKETELNKTIHIT--EETMRAKQMLATMS-------HEIRSPLTGVVSMAEI 394
           + E      ++  +   ++I   +      Q+ A  +        ++R  L         
Sbjct: 99  KTE-----QRQPSMMTRMYIEQRDRLYNDNQVFAKYNVSRLQPYLKLRQALL-------- 145

Query: 395 LSNTKLDREQRQLL-GVMISSGD--LVLQLINDILDLSKVESGV--MKLEAAKFRPREVV 449
               +L   +  L+ G ++ SG   + L +        K++  +  + L      P  V+
Sbjct: 146 ----ELRPAKNVLIDG-VLGSGKTWVALDVCLSYKVQCKMDFKIFWLNL-KNCNSPETVL 199

Query: 450 KHVLQTAAASLQKILMLEGDIADDVPIEVIGDVLRIRQILTN-------LI------SNA 496
           +  LQ     +        D + ++ + +      +R++L +       L+      + A
Sbjct: 200 EM-LQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVLLNVQNAKA 258

Query: 497 IK-FTPEGKVGIKLYVVPEPPFAKEGLKQKSKAYQSATDAVKEEKHQPKSQTASDQNGFH 555
              F     +  K+ +                 ++  TD +        S          
Sbjct: 259 WNAF----NLSCKILLT--------------TRFKQVTDFLSAATTTHISLD-HHSMTLT 299

Query: 556 DKKHGEG----YQDHKHDDDP-----GTPVSH---GNSMDEDLEATVW-----IRCDVYD 598
             +  +     Y D +  D P       P        S+ + L AT W     + CD   
Sbjct: 300 PDE-VKSLLLKYLDCRPQDLPREVLTTNPRRLSIIAESIRDGL-AT-WDNWKHVNCDKLT 356

Query: 599 TGIGIPENAL-PTLFRKY 615
           T I    N L P  +RK 
Sbjct: 357 TIIESSLNVLEPAEYRKM 374

>3cz5_A Two-component response regulator, LUXR family; structural genomics, protein structure initiative; 2.70A {Aurantimonas SP} Length = 153

 Score = 54.9 bits (133), Expect = 6e-09
 Identities = 20/69 (28%), Positives = 35/69 (50%), Gaps = 4/69 (5%)

Query: 861 KILLVEDNKINVMVAKSMMKQLGHSIDVV---NNGVEAVHAVQCQNYDLILMDVCMPVMD 917
           +I+LV+D+ I V      + +      VV    +  EA    +    D+++MD+ +P   
Sbjct: 7   RIMLVDDHPI-VREGYRRLIERRPGYAVVAEAADAGEAYRLYRETTPDIVVMDLTLPGPG 65

Query: 918 GLKATRLIR 926
           G++ATR IR
Sbjct: 66  GIEATRHIR 74

>1yio_A Response regulatory protein; transcription regulation, DNA binding protein; 2.20A {Pseudomonas fluorescens} SCOP: a.4.6.2 c.23.1.1 PDB: 1zn2_A Length = 208

 Score = 56.1 bits (136), Expect = 7e-09
 Identities = 23/141 (16%), Positives = 53/141 (37%), Gaps = 26/141 (18%)

Query: 859 KPKILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDG 918
           KP + +V+D+       +++++  G  ++  +     +   + + +  +++D+ MP M G
Sbjct: 4   KPTVFVVDDDMSVREGLRNLLRSAGFEVETFDCASTFLEHRRPEQHGCLVLDMRMPGMSG 63

Query: 919 LKATRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFAN 978
           ++    + +                              IPI+ +TA+            
Sbjct: 64  IELQEQLTA--------------------------ISDGIPIVFITAHGDIPMTVRAMKA 97

Query: 979 GMDSFVSKPVTFQKLKECLEQ 999
           G   F+ KP   Q L + +EQ
Sbjct: 98  GAIEFLPKPFEEQALLDAIEQ 118

>1zh2_A KDP operon transcriptional regulatory protein KDPE; two-component system, gene regulation, transcription factor, KDP potassium transport system; 2.00A {Escherichia coli} SCOP: c.23.1.1 PDB: 1zh4_A Length = 121

 Score = 53.6 bits (130), Expect = 7e-09
 Identities = 15/73 (20%), Positives = 32/73 (43%), Gaps = 2/73 (2%)

Query: 860 PKILLVEDNK-INVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDG 918
             +L+VED + I   +  ++    G  +         +     +  DLI++D+ +P  DG
Sbjct: 2   TNVLIVEDEQAIRRFLRTALEGD-GMRVFEAETLQRGLLEAATRKPDLIILDLGLPDGDG 60

Query: 919 LKATRLIRSFEDT 931
           ++  R +R +   
Sbjct: 61  IEFIRDLRQWSAV 73

>1th8_A Anti-sigma F factor; SPOIIAB, SPOIIAA, anti-ANTI-sigma, sporulation, serine kinase, transcription; HET: ADP; 2.40A {Geobacillus stearothermophilus} SCOP: d.122.1.3 PDB: 1thn_A* 1til_A* 1l0o_A* 1tid_A* Length = 145

 Score = 54.2 bits (131), Expect = 9e-09
 Identities = 21/100 (21%), Positives = 40/100 (40%), Gaps = 15/100 (15%)

Query: 565 DHKHDDDPGTPVSHGNSMDEDLEATVWIRCDVYDTGIGIPENALPTLFRKYMQVSADHAR 624
            H +++DP   VS    +++     V +   V D G+GIP+        +  Q       
Sbjct: 53  IHGYNNDPNGIVSISVIIEDG---VVHLT--VRDEGVGIPD------IEEARQPLFTTKP 101

Query: 625 KYGGTGLGLAICKQLVELMGGRLTVTSKVHCGSTFTFILP 664
           +   +G+G  I +  +      + V S+V+ G+T      
Sbjct: 102 ELERSGMGFTIMENFM----DEVIVESEVNKGTTVYLKKH 137

>1a04_A Nitrate/nitrite response regulator protein NARL; signal transduction protein, response regulators, two- component systems; 2.20A {Escherichia coli} SCOP: a.4.6.2 c.23.1.1 PDB: 1rnl_A Length = 215

 Score = 55.9 bits (136), Expect = 9e-09
 Identities = 16/45 (35%), Positives = 26/45 (57%), Gaps = 3/45 (6%)

Query: 886 IDVV---NNGVEAVHAVQCQNYDLILMDVCMPVMDGLKATRLIRS 927
           I VV   +NG + +   +  + DLIL+D+ MP M+GL+    +R 
Sbjct: 31  ITVVGEASNGEQGIELAESLDPDLILLDLNMPGMNGLETLDKLRE 75

>2rdm_A Response regulator receiver protein; structural genomics, unknown function, PSI-2, protein struct initiative; HET: MSE; 1.76A {Sinorhizobium medicae} Length = 132

 Score = 53.0 bits (128), Expect = 2e-08
 Identities = 27/143 (18%), Positives = 54/143 (37%), Gaps = 30/143 (20%)

Query: 859 KPKILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQ-CQNYDLILMDVCMPV-M 916
              ILL +D  I ++  +S +   G  +  V++G +A+  ++     D ++ D+      
Sbjct: 5   AVTILLADDEAILLLDFESTLTDAGFLVTAVSSGAKAIEMLKSGAAIDGVVTDIRFCQPP 64

Query: 917 DGLKATRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECF 976
           DG +  R+ R                 +  P          +PI+ ++ +A  E A    
Sbjct: 65  DGWQVARVAR-----------------EIDP---------NMPIVYISGHAALEWASNGV 98

Query: 977 ANGMDSFVSKPVTFQKLKECLEQ 999
            +     + KP T  +L   + Q
Sbjct: 99  PDS--IILEKPFTSAQLITAVSQ 119

>3t8y_A CHEB, chemotaxis response regulator protein-glutamate methylesterase; CHEA, hydrolase; 1.90A {Thermotoga maritima} Length = 164

 Score = 53.1 bits (128), Expect = 3e-08
 Identities = 27/91 (29%), Positives = 42/91 (46%), Gaps = 6/91 (6%)

Query: 842 QSPSSSSAEVPETKPKPKPKI--LLVEDNKINVMVAKSMMKQLGHSIDVV---NNGVEAV 896
                SS  VP         I  L+V+D+    MV K ++      + VV    +G+EAV
Sbjct: 6   HHHHHSSGLVPRGSHMTDRVIRVLVVDDSAFMRMVLKDIIDSQP-DMKVVGFAKDGLEAV 64

Query: 897 HAVQCQNYDLILMDVCMPVMDGLKATRLIRS 927
                   D+I MD+ MP ++G++A +LI  
Sbjct: 65  EKAIELKPDVITMDIEMPNLNGIEALKLIMK 95

>3c3w_A Two component transcriptional regulatory protein; response regulator, two-component regulatory system, DNA-BIN protein; 2.20A {Mycobacterium tuberculosis} Length = 225

 Score = 54.4 bits (132), Expect = 3e-08
 Identities = 13/45 (28%), Positives = 24/45 (53%), Gaps = 3/45 (6%)

Query: 886 IDVV---NNGVEAVHAVQCQNYDLILMDVCMPVMDGLKATRLIRS 927
           +DVV    +  EA+  V     D+ ++DV +P  +G++  R + S
Sbjct: 27  LDVVGEAGSVAEAMARVPAARPDVAVLDVRLPDGNGIELCRDLLS 71

>3klo_A Transcriptional regulator VPST; REC domain, HTH domain, DNA-binding, transcription regulation; HET: C2E TAR; 2.80A {Vibrio cholerae} PDB: 3kln_A* Length = 225

 Score = 53.8 bits (130), Expect = 5e-08
 Identities = 9/75 (12%), Positives = 28/75 (37%), Gaps = 13/75 (17%)

Query: 866 EDNKINVMVA--KSMM---------KQLGHSIDVV--NNGVEAVHAVQCQNYDLILMDVC 912
           ++NK+NV +     M           +L  ++++   +      +  + ++  ++++D  
Sbjct: 4   DENKLNVRMLSDVCMQSRLLKEALESKLPLALEITPFSELWLEENKPESRSIQMLVIDYS 63

Query: 913 MPVMDGLKATRLIRS 927
               D L      + 
Sbjct: 64  RISDDVLTDYSSFKH 78

>1a2o_A CHEB methylesterase; bacterial chemotaxis, adaptation, serine hydrolase; 2.40A {Salmonella typhimurium} SCOP: c.23.1.1 c.40.1.1 Length = 349

 Score = 54.8 bits (133), Expect = 5e-08
 Identities = 16/72 (22%), Positives = 31/72 (43%), Gaps = 12/72 (16%)

Query: 868 NKINVMVA---KSMMKQLGH------SIDVV---NNGVEAVHAVQCQNYDLILMDVCMPV 915
           +KI V+       M + +         +++V    + + A   ++  N D++ +DV MP 
Sbjct: 2   SKIRVLSVDDSALMRQIMTEIINSHSDMEMVATAPDPLVARDLIKKFNPDVLTLDVEMPR 61

Query: 916 MDGLKATRLIRS 927
           MDGL     +  
Sbjct: 62  MDGLDFLEKLMR 73

>3sy8_A ROCR; TIM barrel phosphodiesterase-A, transcription regulator; HET: EPE; 2.50A {Pseudomonas aeruginosa} Length = 400

 Score = 55.0 bits (133), Expect = 6e-08
 Identities = 25/140 (17%), Positives = 52/140 (37%), Gaps = 6/140 (4%)

Query: 859 KPKILLVEDNKINVMVAKSMMKQLGHSIDVVN--NGVEAV-HAVQCQNYDLILMDVCMPV 915
              +L++ED     +VA + +K++     ++   +G EAV     C + D+ + D+ M  
Sbjct: 3   DLNVLVLEDEPFQRLVAVTALKKVVPG-SILEAADGKEAVAILESCGHVDIAICDLQMSG 61

Query: 916 MDGLKATRLIRSFEDTGNW--DAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAE 973
           MDGL   R         +    +  +  + QA  S         +  +    +    +A 
Sbjct: 62  MDGLAFLRHASLSGKVHSVILSSEVDPILRQATISMIECLGLNFLGDLGKPFSLERITAL 121

Query: 974 ECFANGMDSFVSKPVTFQKL 993
               N     + + +   +L
Sbjct: 122 LTRYNARRQDLPRQIEVAEL 141

>1qkk_A DCTD, C4-dicarboxylate transport transcriptional regulatory protein; receiver domain, 2-component signal transduction; 1.7A {Sinorhizobium meliloti} SCOP: c.23.1.1 PDB: 1l5z_A 1l5y_A Length = 155

 Score = 51.8 bits (125), Expect = 7e-08
 Identities = 24/141 (17%), Positives = 52/141 (36%), Gaps = 26/141 (18%)

Query: 858 PKPKILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMD 917
             P + L++D++      +  ++  G ++    +  EA+  +      +++ D+ MP MD
Sbjct: 2   AAPSVFLIDDDRDLRKAMQQTLELAGFTVSSFASATEALAGLSADFAGIVISDIRMPGMD 61

Query: 918 GLKATRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFA 977
           GL   R I +                              +P+I +T +     A +   
Sbjct: 62  GLALFRKILA--------------------------LDPDLPMILVTGHGDIPMAVQAIQ 95

Query: 978 NGMDSFVSKPVTFQKLKECLE 998
           +G   F++KP    +L +   
Sbjct: 96  DGAYDFIAKPFAADRLVQSAR 116

>1p2f_A Response regulator; DRRB, OMPR/PHOB, transcription; HET: MSE; 1.80A {Thermotoga maritima} SCOP: a.4.6.1 c.23.1.1 PDB: 3nns_A* Length = 220

 Score = 52.8 bits (128), Expect = 9e-08
 Identities = 15/68 (22%), Positives = 35/68 (51%), Gaps = 3/68 (4%)

Query: 859 KPKILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDG 918
             KI +V+D+K  +      ++QLG  +     G + ++  +   + ++++DV +P   G
Sbjct: 2   MWKIAVVDDDKNILKKVSEKLQQLGR-VKTFLTGEDFLNDEE--AFHVVVLDVMLPDYSG 58

Query: 919 LKATRLIR 926
            +  R+I+
Sbjct: 59  YEICRMIK 66

>2qv0_A Protein MRKE; structural genomics, transcription, PSI-2, protein structure initiative; 2.40A {Klebsiella pneumoniae} Length = 143

 Score = 50.7 bits (122), Expect = 2e-07
 Identities = 16/82 (19%), Positives = 38/82 (46%), Gaps = 4/82 (4%)

Query: 851 VPETKPKPKPKILLVEDNKINVMVAKSMMKQLGHSIDVV---NNGVEAVHAVQCQNYDLI 907
           +       K K+++VED  +       ++      +++V   ++G++ +  +Q    D I
Sbjct: 1   MSLVMSGEKMKVIIVEDEFLAQQELSWLINTHSQ-MEIVGSFDDGLDVLKFLQHNKVDAI 59

Query: 908 LMDVCMPVMDGLKATRLIRSFE 929
            +D+ +P +DG+   + I  F 
Sbjct: 60  FLDINIPSLDGVLLAQNISQFA 81

>3kyj_B CHEY6 protein, putative histidine protein kinase; protein-protein interaction, histidine kinase, response regulator, phosphorylation; 1.40A {Rhodobacter sphaeroides} PDB: 3kyi_B* Length = 145

 Score = 49.5 bits (119), Expect = 3e-07
 Identities = 25/84 (29%), Positives = 39/84 (46%), Gaps = 5/84 (5%)

Query: 848 SAEVPETKPKPKPKILLVEDNKINVMVAKSMMKQLGHSIDVV---NNGVEAVHAVQCQ-N 903
                         +++V+D  +  +   S +K L     VV    NG EA+  +  Q N
Sbjct: 2   RGSHHHHHHGSPYNVMIVDDAAMMRLYIASFIKTLP-DFKVVAQAANGQEALDKLAAQPN 60

Query: 904 YDLILMDVCMPVMDGLKATRLIRS 927
            DLIL+D+ MPVMDG++  R  + 
Sbjct: 61  VDLILLDIEMPVMDGMEFLRHAKL 84

>2qsj_A DNA-binding response regulator, LUXR family; structural genomics, PSI-2, protein structure initiative; 2.10A {Silicibacter pomeroyi dss-3} Length = 154

 Score = 49.5 bits (119), Expect = 5e-07
 Identities = 14/70 (20%), Positives = 32/70 (45%), Gaps = 5/70 (7%)

Query: 861 KILLVEDNKINVMVAKSMMKQLGHSIDVV---NNGVEAVHAVQCQNY-DLILMDVCMPVM 916
            +L+V+D+ + +      + +   S   V       +A+  ++  N  DLIL+DV +P  
Sbjct: 5   VVLIVDDHHL-IRAGAKNLLEGAFSGMRVEGAETVSDALAFLEADNTVDLILLDVNLPDA 63

Query: 917 DGLKATRLIR 926
           + +     ++
Sbjct: 64  EAIDGLVRLK 73

>3kcn_A Adenylate cyclase homolog; SGX, PSI 2, structural genomics, protein structure initiative; 2.45A {Rhodopirellula baltica} Length = 151

 Score = 47.6 bits (114), Expect = 2e-06
 Identities = 25/143 (17%), Positives = 50/143 (34%), Gaps = 29/143 (20%)

Query: 859 KPKILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAV-QCQNYDLILMDVCMPVMD 917
             +ILLV+D+   +   K  +      +    +G EA+  + +   + +I++D+ MP M+
Sbjct: 4   NERILLVDDDYSLLNTLKRNLSF-DFEVTTCESGPEALACIKKSDPFSVIMVDMRMPGME 62

Query: 918 GLKATRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFA 977
           G +  +  R                                  + +T N    +A E   
Sbjct: 63  GTEVIQKARL--------------------------ISPNSVYLMLTGNQDLTTAMEAVN 96

Query: 978 NGM-DSFVSKPVTFQKLKECLEQ 999
            G    F++KP     +K  +  
Sbjct: 97  EGQVFRFLNKPCQMSDIKAAINA 119

>4fmt_A CHPT protein; A phosphotransfer protein, A two-component signaling pathway structural genomics, joint center for structural genomics; 2.30A {Caulobacter crescentus} Length = 228

 Score = 48.9 bits (116), Expect = 2e-06
 Identities = 14/81 (17%), Positives = 24/81 (29%), Gaps = 7/81 (8%)

Query: 584 EDLEATVWIRCDVYDTGIGIPENALPTLFRKYMQVSADHARKYGGTGLGLAICKQLVELM 643
              +    I  D       +    L  L  + +      A   GG  +  A    LV   
Sbjct: 154 VAADGRFSIIADAKGPRARLRPEVLAGLKGEPL------AEGLGGPWVQAAYLNALVRAA 207

Query: 644 GGRLTVTSKVHCGSTFTFILP 664
           GG++ V       ++    +P
Sbjct: 208 GGQIAVEIGED-RASIAAWVP 227

>4fmt_A CHPT protein; A phosphotransfer protein, A two-component signaling pathway structural genomics, joint center for structural genomics; 2.30A {Caulobacter crescentus} Length = 228

 Score = 44.7 bits (105), Expect = 5e-05
 Identities = 23/153 (15%), Positives = 45/153 (29%), Gaps = 15/153 (9%)

Query: 352 AKETELNKTIHITEETMRAKQMLAT-MSHEIRSPLTGVVSMAEILSNTKLDREQRQLLGV 410
             ET    +     +      MLA  + H+  SP + +VS  ++L +      +   + +
Sbjct: 8   VTETTAPASPEADVQGPDFAAMLAARLCHDFISPASAIVSGLDLLEDPSAQDMRDDAMNL 67

Query: 411 MISSGDLVLQLINDILDLSKVESGVMKLEAAKFRPREVVKHVLQTAAASLQKILMLEGDI 470
           + SS   +  L+                    F      ++        L + +      
Sbjct: 68  IASSARKLADLLQFTR--------------VAFGASASAENFDSRELEKLAQGVFAHVRP 113

Query: 471 ADDVPIEVIGDVLRIRQILTNLISNAIKFTPEG 503
             D  IE         + + N+   A    P G
Sbjct: 114 TLDWQIEPQAMNKPSSRAVLNIAQIAASALPAG 146

>2jk1_A HUPR, hydrogenase transcriptional regulatory protein HU; nucleotide-binding, transcription regulation; 2.10A {Rhodobacter capsulatus} PDB: 2vui_B 2vuh_B Length = 139

 Score = 47.1 bits (113), Expect = 2e-06
 Identities = 23/141 (16%), Positives = 44/141 (31%), Gaps = 28/141 (19%)

Query: 860 PKILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGL 919
           P ILLV+D   ++   K  ++     +        A+  ++ +   +I+ D  MP   G+
Sbjct: 2   PAILLVDDEPHSLAAMKLALED-DFDVLTAQGAEAAIAILEEEWVQVIICDQRMPGRTGV 60

Query: 920 KATRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECF-AN 978
                +R                            +     I +T    S S        
Sbjct: 61  DFLTEVRE--------------------------RWPETVRIIITGYTDSASMMAAINDA 94

Query: 979 GMDSFVSKPVTFQKLKECLEQ 999
           G+  F++KP   ++L      
Sbjct: 95  GIHQFLTKPWHPEQLLSSARN 115

>1dbw_A Transcriptional regulatory protein FIXJ; doubly wound five-stranded beta/alpha fold, nitrogen fixatio regulation; HET: 15P; 1.60A {Sinorhizobium meliloti} SCOP: c.23.1.1 PDB: 1dck_A* 1dcm_A 1d5w_A* Length = 126

 Score = 45.2 bits (108), Expect = 9e-06
 Identities = 23/141 (16%), Positives = 47/141 (33%), Gaps = 26/141 (18%)

Query: 859 KPKILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDG 918
              + +V+D +        M+   G ++ +  +    +         +++ D+ MP M G
Sbjct: 3   DYTVHIVDDEEPVRKSLAFMLTMNGFAVKMHQSAEAFLAFAPDVRNGVLVTDLRMPDMSG 62

Query: 919 LKATRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFAN 978
           ++  R +             +  I               IP I +T +     A E    
Sbjct: 63  VELLRNLG------------DLKIN--------------IPSIVITGHGDVPMAVEAMKA 96

Query: 979 GMDSFVSKPVTFQKLKECLEQ 999
           G   F+ KP     + E +E+
Sbjct: 97  GAVDFIEKPFEDTVIIEAIER 117

>1qo0_D AMIR; binding protein, gene regulator, receptor; 2.25A {Pseudomonas aeruginosa} SCOP: c.23.1.3 Length = 196

 Score = 45.1 bits (106), Expect = 3e-05
 Identities = 11/133 (8%), Positives = 32/133 (24%), Gaps = 31/133 (23%)

Query: 861 KILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLK 920
           ++L++             + ++G S+       EA         D++   +         
Sbjct: 14  QVLVLNPPGEVSDALVLQLIRIGCSVRQCWPPPEA----FDVPVDVVFTSIFQNRHHDEI 69

Query: 921 ATRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGM 980
           A  L                                R  ++A+          +      
Sbjct: 70  AALLAAGT---------------------------PRTTLVALVEYESPAVLSQIIELEC 102

Query: 981 DSFVSKPVTFQKL 993
              +++P+   ++
Sbjct: 103 HGVITQPLDAHRV 115

>3mxq_A Sensor protein; PSI2, MCSG, structural genomics, protein structure initiativ midwest center for structural genomics; 2.78A {Vibrio cholerae o1 biovar el tor} Length = 152

 Score = 43.1 bits (101), Expect = 7e-05
 Identities = 21/145 (14%), Positives = 43/145 (29%), Gaps = 18/145 (12%)

Query: 210 VEELSQILKRADNFLHFVLQNAPVVMGHQDKELRYRFIYNHFPSLH----EEDILGKTDV 265
           +   S  + ++   L  +L      +     +       N +         E + GK  +
Sbjct: 10  LYFQSNAMAKSRLLLSELLDQLSFALCIVRNDYVIVK-VNEYFESRVIFDGETMQGKNIL 68

Query: 266 EIFSGAGVKESQDFKREVLEKGLPAKREITFETELFGSKTFL------------IYVEPV 313
           E+F  +     +      L     +      +  L   K+              + V P+
Sbjct: 69  ELFPESA-DYLKRKIDTALVIESSSFSSWEQKPHLLPFKSSRPVSGEEEQMYQNLEVIPI 127

Query: 314 FSKSGETIGVNYMGMDVTDQVRKRE 338
            S+ G    V     DVT Q  +++
Sbjct: 128 HSEDGTIEHVCLCVYDVTIQASQQQ 152

>3fc7_A HTR-like protein, sensor protein; APC87712.1, HTR-like protein,haloarcula marismortui ATCC 430 structural genomics, PSI-2; 2.65A {Haloarcula marismortui} Length = 125

 Score = 41.5 bits (98), Expect = 2e-04
 Identities = 13/118 (11%), Positives = 36/118 (30%), Gaps = 9/118 (7%)

Query: 217 LKRADNFLHFVLQNAPVVMGHQDKELRYRFIYNHFPSLH---EEDILGKTDVEIFSGAGV 273
            +R       ++ ++P  + H         +            + ++G+    +      
Sbjct: 14  QERTRKKFESLVSDSPDGIVHLTTNGTILSVNPSMAGRLGADPDTLVGQQLSAVMDSEAA 73

Query: 274 KESQDFKREVLEKGLPAKREITFETELFGSKTFLIYVEPVFSKSGETIGVNYMGMDVT 331
            +  +  +  +E G         E  + G + +     PV S   ++     +  D+T
Sbjct: 74  NQRLEAGKSAVENGTA----TRSEDAVGG-RHYHNQYIPVDS-HRKSDTFQLVSRDIT 125

>3cax_A Uncharacterized protein PF0695; structural genomics, unknown function, PSI-2, protein struct initiative; 2.43A {Pyrococcus furiosus dsm 3638} Length = 369

 Score = 42.0 bits (98), Expect = 7e-04
 Identities = 44/263 (16%), Positives = 85/263 (32%), Gaps = 26/263 (9%)

Query: 88  NAVRLLREELDNLSRQRQESELKKL--------EILEEHRFEEEGYGGDKRPISIMDELS 139
             ++ L E L        E  ++K           L +  F E        P        
Sbjct: 98  AMIKQLAELLRKREEMPWEEFVEKFKAKAGEVAFALSDMVFRENNIF---YPTLKALLSE 154

Query: 140 DMWKDVCPRKNDVVFQSKRVEVDAEYDTVEYWKQRALDLEKMLEASGQREQALMEKLNES 199
             WK +  +++++ +   +       + V+      ++ E  +E      + + + L   
Sbjct: 155 GEWKAIKMQEDEIGYYKVKPPEWDPGEDVKPLHPWEINPELNVEQLLTLPKEVQQALRGQ 214

Query: 200 VTNLEKQSSPVEELSQI--LKRADNFLHFVLQNAPVVMGHQDKELRYRFIYNH----FPS 253
               +K     EE   +         L  + +  PV +   DK+ R RF ++     F  
Sbjct: 215 PLEFDKTQLKREEDIDLGTGYLNIEELKAIFEALPVDVTFIDKDDRVRF-FSPGERIFT- 272

Query: 254 LHEEDILGKTDVEIFSGAGVKESQDFKREVLEKGLPAKREITFETEL-FGSKTFLIYVEP 312
                +LG+            +S     ++L+      R+      L    K   I   P
Sbjct: 273 -RTPSVLGRPVQLCHP----PKSVYVVNKILKA-FKEGRKKEATFWLRLREKYVYIKYVP 326

Query: 313 VFSKSGETIGVNYMGMDVTDQVR 335
           +F++ GE IG   M MD+    +
Sbjct: 327 LFNEKGEYIGTLEMTMDIAPYKK 349

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	1002
3a0r_A	349	Sensor protein; four helix bundle, PAS fold, kinas	100.0
2c2a_A	258	Sensor histidine kinase; phosphotransfer, PHOQ, se	100.0
4ew8_A	268	Sensor protein DIVL; signal transduction, two-comp	100.0
3jz3_A	222	Sensor protein QSEC; helix-turn-helix, kinase doma	100.0
1gkz_A	388	[3-methyl-2-oxobutanoate dehydrogenase [lipoamide]	100.0
2btz_A	394	Pyruvate dehydrogenase kinase isoenzyme 2; GHKL mo	100.0
2e0a_A	394	Pyruvate dehydrogenase kinase isozyme 4; PDK4, ATP	100.0
2q8g_A	407	[pyruvate dehydrogenase [lipoamide]] kinase isozy;	99.98
4fpp_A	247	Phosphotransferase; four helix bundle, bergerat fo	99.97
3d36_A	244	Sporulation kinase B; GHKL ATPase, four helix bund	99.97
1y8o_A	419	[pyruvate dehydrogenase [lipoamide]] kinase isozy;	99.97
3to5_A	134	CHEY homolog; alpha(5)beta(5), chemotaxis, FLIM, p	99.93
1b3q_A	379	Protein (chemotaxis protein CHEA); histine kinase,	99.93
3ehh_A	218	Sensor kinase (YOCF protein); four-helix bundle, G	99.91
3mm4_A	206	Histidine kinase homolog; receiver domain, CKI1, c	99.91
1ysr_A	150	Sensor-type histidine kinase PRRB; ATP-binding dom	99.9
1id0_A	152	PHOQ histidine kinase; PHOQ/PHOP, signal transduct	99.89
1bxd_A	161	ENVZ(290-450), protein (osmolarity sensor protein	99.89
3sl2_A	177	Sensor histidine kinase YYCG; ATP binding, intact	99.88
1r62_A	160	Nitrogen regulation protein NR(II); PII, histidine	99.87
3a0y_A	152	Sensor protein; ATP-LID, kinase, phosphoprotein, t	99.87
2lpm_A	123	Two-component response regulator; transcription re	99.87
1i58_A	189	Chemotaxis protein CHEA; beta-alpha sandwich, sign	99.85
3gl9_A	122	Response regulator; beta-sheet, surrounded by alph	99.84
2r25_B	133	Osmosensing histidine protein kinase SLN1; alpha5-	99.82
3t6k_A	136	Response regulator receiver; flavodoxin-like, stru	99.82
3f6p_A	120	Transcriptional regulatory protein YYCF; unphospho	99.81
3h1g_A	129	Chemotaxis protein CHEY homolog; sulfate-bound CHE	99.81
3n0r_A	286	Response regulator; sigma factor, receiver, two-co	99.8
3m6m_D	143	Sensory/regulatory protein RPFC; RPFF, REC, enoyl-	99.8
3rqi_A	184	Response regulator protein; structural genomics, s	99.79
3ehg_A	128	Sensor kinase (YOCF protein); GHL ATPase domain, t	99.78
2ayx_A	254	Sensor kinase protein RCSC; two independent struct	99.78
1dbw_A	126	Transcriptional regulatory protein FIXJ; doubly wo	99.78
1srr_A	124	SPO0F, sporulation response regulatory protein; as	99.77
2pl1_A	121	Transcriptional regulatory protein PHOP; CHEY-like	99.77
3gt7_A	154	Sensor protein; structural genomics, signal receiv	99.77
3crn_A	132	Response regulator receiver domain protein, CHEY-;	99.77
3zxo_A	129	Redox sensor histidine kinase response regulator;	99.77
3luf_A	259	Two-component system response regulator/ggdef doma	99.77
3eod_A	130	Protein HNR; response regulator, phosphoprotein, t	99.76
1mb3_A	124	Cell division response regulator DIVK; signal tran	99.76
1tmy_A	120	CHEY protein, TMY; chemotaxis, phosphoryl transfer	99.76
1jbe_A	128	Chemotaxis protein CHEY; signaling protein; 1.08A	99.76
3hv2_A	153	Response regulator/HD domain protein; PSI-2, NYSGX	99.76
3r0j_A	250	Possible two component system response transcript	99.76
4e7p_A	150	Response regulator; DNA binding, cytosol, transcri	99.76
1zgz_A	122	Torcad operon transcriptional regulatory protein;	99.75
3i42_A	127	Response regulator receiver domain protein (CHEY-	99.75
3hdv_A	136	Response regulator; PSI-II, structural genomics, P	99.75
1xhf_A	123	DYE resistance, aerobic respiration control protei	99.75
1p6q_A	129	CHEY2; chemotaxis, signal transduction, response r	99.75
3lua_A	140	Response regulator receiver protein; two-component	99.75
3hzh_A	157	Chemotaxis response regulator (CHEY-3); phosphatas	99.75
3heb_A	152	Response regulator receiver domain protein (CHEY);	99.75
2a9o_A	120	Response regulator; essential protein, YYCF/YYCG h	99.75
3kto_A	136	Response regulator receiver protein; PSI-II,struct	99.75
1i3c_A	149	Response regulator RCP1; phytochrome, signaling pr	99.75
3grc_A	140	Sensor protein, kinase; protein structure initiati	99.74
3b2n_A	133	Uncharacterized protein Q99UF4; structural genomic	99.74
4dad_A	146	Putative pilus assembly-related protein; response	99.74
3cfy_A	137	Putative LUXO repressor protein; structural genomi	99.74
3hdg_A	137	Uncharacterized protein; two-component sensor acti	99.74
2qzj_A	136	Two-component response regulator; 11017X, PSI-II,	99.74
3ilh_A	146	Two component response regulator; NYSGXRC, PSI-II,	99.74
3snk_A	135	Response regulator CHEY-like protein; P-loop conta	99.74
3kht_A	144	Response regulator; PSI-II, 11023K, structural gen	99.74
3jte_A	143	Response regulator receiver protein; structural ge	99.74
3dzd_A	368	Transcriptional regulator (NTRC family); sigma43 a	99.73
1k68_A	140	Phytochrome response regulator RCPA; phosphorylate	99.73
3nhm_A	133	Response regulator; protein structure initiative I	99.73
3eul_A	152	Possible nitrate/nitrite response transcriptional	99.73
3c3m_A	138	Response regulator receiver protein; structural ge	99.73
3f6c_A	134	Positive transcription regulator EVGA; structural	99.73
1mvo_A	136	PHOP response regulator; phosphate regulon, transc	99.73
3zxq_A	124	Hypoxia sensor histidine kinase response regulato;	99.72
1k66_A	149	Phytochrome response regulator RCPB; CHEY homologu	99.72
3lte_A	132	Response regulator; structural genomics, PSI, prot	99.72
1dcf_A	136	ETR1 protein; beta-alpha five sandwich, transferas	99.72
3a10_A	116	Response regulator; phosphoacceptor, signaling pro	99.72
1zh2_A	121	KDP operon transcriptional regulatory protein KDPE	99.72
1dz3_A	130	Stage 0 sporulation protein A; response regulator,	99.72
3h5i_A	140	Response regulator/sensory box protein/ggdef domai	99.72
3cnb_A	143	DNA-binding response regulator, MERR family; signa	99.72
1yio_A	208	Response regulatory protein; transcription regulat	99.72
2jba_A	127	Phosphate regulon transcriptional regulatory PROT;	99.71
3q9s_A	249	DNA-binding response regulator; DNA binding protei	99.71
1a04_A	215	Nitrate/nitrite response regulator protein NARL; s	99.71
2zay_A	147	Response regulator receiver protein; structural ge	99.71
2qxy_A	142	Response regulator; regulation of transcription, N	99.7
2rjn_A	154	Response regulator receiver:metal-dependent phosph	99.7
3cu5_A	141	Two component transcriptional regulator, ARAC FAM;	99.7
3eq2_A	394	Probable two-component response regulator; adaptor	99.7
2jk1_A	139	HUPR, hydrogenase transcriptional regulatory prote	99.69
3n53_A	140	Response regulator receiver modulated diguanylate;	99.69
1kgs_A	225	DRRD, DNA binding response regulator D; DNA-bindin	99.69
3kcn_A	151	Adenylate cyclase homolog; SGX, PSI 2, structural	99.69
1s8n_A	205	Putative antiterminator; RV1626, structural genomi	99.69
3cg0_A	140	Response regulator receiver modulated diguanylate	99.69
3cg4_A	142	Response regulator receiver domain protein (CHEY-;	99.69
1qkk_A	155	DCTD, C4-dicarboxylate transport transcriptional r	99.69
2qr3_A	140	Two-component system response regulator; structura	99.69
2qvg_A	143	Two component response regulator; NYSGXRC, PSI-2,	99.69
1w25_A	459	Stalked-cell differentiation controlling protein;	99.68
3cz5_A	153	Two-component response regulator, LUXR family; str	99.68
1ny5_A	387	Transcriptional regulator (NTRC family); AAA+ ATPa	99.68
3eqz_A	135	Response regulator; structural genomics, unknown f	99.68
2pln_A	137	HP1043, response regulator; signaling protein; 1.8	99.67
1ys7_A	233	Transcriptional regulatory protein PRRA; response	99.67
1mu5_A	471	Type II DNA topoisomerase VI subunit B; GHKL ATPas	99.67
2zbk_B	530	Type 2 DNA topoisomerase 6 subunit B; DNA binding	99.67
3kyj_B	145	CHEY6 protein, putative histidine protein kinase;	99.67
2gkg_A	127	Response regulator homolog; social motility, recei	99.67
1th8_A	145	Anti-sigma F factor; SPOIIAB, SPOIIAA, anti-ANTI-s	99.66
2gwr_A	238	DNA-binding response regulator MTRA; two-component	99.65
2qv0_A	143	Protein MRKE; structural genomics, transcription,	99.65
2j48_A	119	Two-component sensor kinase; pseudo-receiver, circ	99.65
3c97_A	140	Signal transduction histidine kinase; structural g	99.65
3bre_A	358	Probable two-component response regulator; protein	99.64
2oqr_A	230	Sensory transduction protein REGX3; response regul	99.64
3t8y_A	164	CHEB, chemotaxis response regulator protein-glutam	99.64
2rdm_A	132	Response regulator receiver protein; structural ge	99.64
2qsj_A	154	DNA-binding response regulator, LUXR family; struc	99.64
2b4a_A	138	BH3024; flavodoxin-like fold, structural genomics,	99.64
1p2f_A	220	Response regulator; DRRB, OMPR/PHOB, transcription	99.62
3c3w_A	225	Two component transcriptional regulatory protein;	99.62
3sy8_A	400	ROCR; TIM barrel phosphodiesterase-A, transcriptio	99.62
3klo_A	225	Transcriptional regulator VPST; REC domain, HTH do	99.62
1qo0_D	196	AMIR; binding protein, gene regulator, receptor; 2	99.6
1dc7_A	124	NTRC, nitrogen regulation protein; receiver domain	99.6
2hqr_A	223	Putative transcriptional regulator; phosporylation	99.59
3luf_A	259	Two-component system response regulator/ggdef doma	99.57
1a2o_A	349	CHEB methylesterase; bacterial chemotaxis, adaptat	99.53
2vyc_A	755	Biodegradative arginine decarboxylase; pyridoxal p	99.45
2q2e_B	621	Type 2 DNA topoisomerase 6 subunit B; DNA-binding,	99.42
3p7n_A	258	Sensor histidine kinase; LOV domain, light-activat	99.1
1w25_A	459	Stalked-cell differentiation controlling protein;	99.05
3k3c_A	158	Protein RV1364C/MT1410; sensor, PAS, signal transd	98.99
3mxq_A	152	Sensor protein; PSI2, MCSG, structural genomics, p	98.93
3cwo_X	237	Beta/alpha-barrel protein based on 1THF and 1TMY;	98.9
3mr0_A	142	Sensory box histidine kinase/response regulator; P	98.88
2gj3_A	120	Nitrogen fixation regulatory protein; PAS domain,	98.81
3ue6_A	166	Aureochrome1; PAS/LOV domain, FMN-binding blue-lig	98.8
4hia_A	176	LOV protein; PAS, HTH, signaling protein; HET: FMN	98.8
2pr5_A	132	Blue-light photoreceptor; light-oxygen-voltage, LO	98.77
3sw1_A	162	Sensory box protein; light-oxygen-voltage, LOV, PA	98.76
3kx0_X	185	Uncharacterized protein RV1364C/MT1410; PAS domain	98.74
3nja_A	125	Probable ggdef family protein; structural genomics	98.71
3f1p_B	121	ARYL hydrocarbon receptor nuclear translocator; PA	98.68
3luq_A	114	Sensor protein; PAS, histidine, kinase, PSI, MCSG,	98.67
3t50_A	128	Blue-light-activated histidine kinase; PAS superfa	98.64
3lyx_A	124	Sensory BOX/ggdef domain protein; structural genom	98.59
3vol_A	233	Aerotaxis transducer AER2; heme, oxygen sensor pro	98.56
2z6d_A	130	Phototropin-2; PAS-fold, LOV-fold, alternative spl	98.52
3eeh_A	125	Putative light and redox sensing histidine kinase;	98.47
4eet_B	115	Phototropin-2; LOV, blue light photoreceptor, sign	98.47
1d06_A	130	Nitrogen fixation regulatory protein FIXL; oxygen	98.46
2v0u_A	146	NPH1-1, LOV2; kinase, transferase, ATP-binding, se	98.46
3f1p_A	117	Endothelial PAS domain-containing protein 1; PAS d	98.46
3icy_A	118	Sensor protein; sensory box histidine kinase/respo	98.45
1v9y_A	167	Heme PAS sensor protein; signaling protein; HET: H	98.38
1b63_A	333	MUTL; DNA mismatch repair, ATPase; HET: ANP; 1.90A	98.36
2qkp_A	151	Uncharacterized protein; structural genomics, unkn	98.35
1kij_A	390	DNA gyrase subunit B; topoisomerase, gyrase B-coum	98.34
3mqq_A	120	Transcriptional regulator, LUXR family; PAS domain	98.31
2wkq_A	332	NPH1-1, RAS-related C3 botulinum toxin substrate 1	98.28
3ewk_A	227	Sensor protein; PAS domain, alpha/beta fold, kinas	98.27
1h7s_A	365	PMS1 protein homolog 2; DNA repair, GHL ATPase, mi	98.27
1n9l_A	109	PHOT-LOV1, putative blue light receptor; phototrop	98.26
4hi4_A	121	Aerotaxis transducer AER2; PAS domain, diatomic GA	98.26
3na3_A	348	DNA mismatch repair protein MLH1; MUTL protein hom	98.21
3fc7_A	125	HTR-like protein, sensor protein; APC87712.1, HTR-	98.21
3ke6_A	399	Protein RV1364C/MT1410; anti-sigma factor, anti-si	98.21
2vv6_A	119	FIXL, sensor protein FIXL; signaling protein, tran	98.18
2r78_A	117	Sensor protein; sensory box sensor histidine kinas	98.17
3mjq_A	126	Uncharacterized protein; NESG, structural genomics	98.16
3h9w_A	115	Diguanylate cyclase with PAS/PAC sensor; alpha-bet	98.11
3ewk_A	227	Sensor protein; PAS domain, alpha/beta fold, kinas	98.05
3olo_A	118	Two-component sensor histidine kinase; structural	98.03
3fg8_A	118	Uncharacterized protein RHA05790; PAS domain, stru	97.97
3bwl_A	126	Sensor protein; structural genomics, APC87707.1, P	97.95
2kdk_A	121	ARYL hydrocarbon receptor nuclear translocator-LI	97.95
4eho_A	635	Bacteriophytochrome, PAS/PAC sensor; photoreceptor	97.9
2l0w_A	138	Potassium voltage-gated channel, subfamily H (EAG	97.89
3cax_A	369	Uncharacterized protein PF0695; structural genomic	97.88
3zcc_A	114	HAMP, osmolarity sensor protein ENVZ; signaling pr	97.87
3h4l_A	367	DNA mismatch repair protein PMS1; ATP binding, DNA	97.87
3b33_A	115	Sensor protein; structural genomics, PAS domain, n	97.64
2wer_A	220	ATP-dependent molecular chaperone HSP82; ATPase, A	97.59
1byw_A	110	Protein (human ERG potassium channel); PAS domain,	97.57
4f3l_A	361	Mclock, circadian locomoter output cycles protein	97.55
2w0n_A	118	Sensor protein DCUS; signal transduction, two-comp	97.5
3d72_A	149	Vivid PAS protein VVD; circadian, photoreceptor, b	97.47
1qy5_A	269	Endoplasmin; GRP94, NECA, HSP90, chaperone; HET: N	97.39
1ixm_A	192	SPO0B, protein (sporulation response regulatory pr	97.38
2ior_A	235	Chaperone protein HTPG; heat shock protein, HSP90;	97.27
1yc1_A	264	HSP 86, heat shock protein HSP 90-alpha; cell-cycl	97.25
3mfx_A	129	Sensory BOX/ggdef family protein; alpha-beta prote	97.16
2jhe_A	190	Transcription regulator TYRR; aromatic hydrocarbon	97.12
4f3l_B	387	BMAL1B; BHLH, PAS, circadian rhythm proteins, tran	97.1
3zrx_A	115	AF1503 protein, osmolarity sensor protein ENVZ; si	96.9
2ayx_A	254	Sensor kinase protein RCSC; two independent struct	96.88
1nwz_A	125	PYP, photoactive yellow protein; PAS, LOV, GAF, do	96.77
3a0s_A	96	Sensor protein; PAS-fold, kinase, phosphoprotein,	96.72
1mzu_A	129	PPR; photoactive yellow protein, PAS, PYP, signali	96.68
2vlg_A	111	Sporulation kinase A; histidine kinase, two-compon	96.67
1s16_A	390	Topoisomerase IV subunit B; two-domain protein com	96.47
3cwo_X	237	Beta/alpha-barrel protein based on 1THF and 1TMY;	96.28
2ykf_A	305	Pdtas, probable sensor histidine kinase pdtas; tra	95.13
3t0h_A	228	Heat shock protein HSP 90-alpha; chaperone, ATPase	96.12
1ll8_A	114	PAS kinase; PAS domain, ligand binding, ligand scr	95.92
3peh_A	281	Endoplasmin homolog; structural genomics, structur	95.73
3o0i_A	256	HSP90AA1 protein; HSP90 heat-shock proteins, chape	95.52
2gqp_A	236	Endoplasmin; GRP94, HSP82, HSP90, HTPG, chaperone,	95.5
1y4s_A	559	Chaperone protein HTPG; HSP90, molecular chaperone	95.39
3n75_A	715	LDC, lysine decarboxylase, inducible; pyridoxal-5'	95.27
3rty_A	339	Period circadian protein; PAS domain, signalling,	95.18
2cg9_A	677	ATP-dependent molecular chaperone HSP82; chaperone	94.71
3nmq_A	239	Heat shock protein HSP 90-beta; ATPase, chaperone-	94.63
2ioq_A	624	Chaperone protein HTPG; heat shock protein, HSP90;	94.58
1ei1_A	391	DNA gyrase B, GYRB; ATPase domain, dimer, isomeras	94.54
2o1u_A	666	Endoplasmin; GRP94, HSP82, HSP90, HTPG, chaperone,	94.24
2yxb_A	161	Coenzyme B12-dependent mutase; alpha/beta, structu	93.68
3fv5_A	201	DNA topoisomerase 4 subunit B; topoisomerase IV B	93.62
3cwv_A	369	DNA gyrase, B subunit, truncated; structural genom	92.69
4dj3_A	317	Period circadian protein homolog 3; PAS domain, ci	92.63
3gdi_A	309	Period circadian protein homolog 2; tandem PAS dom	91.73
3q7r_A	121	Transcriptional regulatory protein; CHXR, receiver	91.63
4dj2_A	320	Period circadian protein homolog 1; PAS domains, c	91.47
4duh_A	220	DNA gyrase subunit B; structure-based drug design,	90.08
1ccw_A	137	Protein (glutamate mutase); coenzyme B12, radical	89.58
1wv2_A	265	Thiazole moeity, thiazole biosynthesis protein THI	87.43
4emv_A	226	DNA topoisomerase IV, B subunit; protein-inhibitor	87.34
1zxm_A	400	TOPO IIA ATPase, DNA topoisomerase II, alpha isozy	87.08
3ied_A	272	Heat shock protein; HSP90, chaperone, structural g	85.77
3ttz_A	198	DNA gyrase subunit B; protein-inhibitor complex, A	83.73
4f3l_A	361	Mclock, circadian locomoter output cycles protein	83.19
1oj5_A	132	Steroid receptor coactivator 1A; transcriptional c	81.06
2i2x_B	258	MTAC, methyltransferase 1; TIM barrel and helix bu	80.67

>3a0r_A Sensor protein; four helix bundle, PAS fold, kinase, phosphoprotein, transfe two-component regulatory system; 3.80A {Thermotoga maritima}

Probab=100.00  E-value=2.6e-40  Score=374.05  Aligned_cols=335  Identities=24%  Similarity=0.351  Sum_probs=255.6

Q ss_pred             HHHHHHHHHHHHhccCcEEEEecccccEEEeeccC---CCCCcccccCCCchhccCccchhhhhHHHHHHHHhCCCccee
Q 039716          217 LKRADNFLHFVLQNAPVVMGHQDKELRYRFIYNHF---PSLHEEDILGKTDVEIFSGAGVKESQDFKREVLEKGLPAKRE  293 (1002)
Q Consensus       217 l~~~~~~l~~il~~~p~~i~~~d~~~~~~~~~~~~---~~~~~e~iiGk~~~e~~~~~~~~~~~~~~~~vl~~g~~~~~e  293 (1002)
                      +++++.+++.+++++|.+|+..|.++++.++|..+   .|+..++++|++..++...   .........++..+.+..  
T Consensus         3 l~~~~~~~~~i~~~~~~~i~~~d~~g~i~~~N~a~~~l~G~~~~e~~G~~~~~~~~~---~~~~~~~~~~~~~~~~~~--   77 (349)
T 3a0r_A            3 VEHLRNFSESILESLETAIITLSKDGRITEWNKKAEQLFGLKKENVLGRRLKDLPDF---EEIGSVAESVFENKEPVF--   77 (349)
T ss_dssp             ------CCCSSGGGSSSEEEEEESSSBCSCBCHHHHHHHSCCSTTTTTCBSTTSTTT---THHHHHHHHHHHHCCCCE--
T ss_pred             hHHHHHHHHHHHhhhcCeEEEECCCCCEEeeHHHHHHHhCCCHHHHcCcCHHHCcCh---hHHHHHHHHHHhcCCcee--
Confidence            44556778889999999999999999999998764   6888999999998887332   223334455666655432  


Q ss_pred             EEEEEeecCceEEEEEEeeeecCCCCE-EEEEEEeechhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 039716          294 ITFETELFGSKTFLIYVEPVFSKSGET-IGVNYMGMDVTDQVRKREKMAKLREEIAVQKAKETELNKTIHITEETMRAKQ  372 (1002)
Q Consensus       294 ~~~~~~~~~~~~~~~~~~p~~~~~G~~-~gi~~~~~DITe~~~~~~~~~~l~~el~~~~~~~~el~k~~~~~e~~~~~k~  372 (1002)
                        ......+..++.+...|+.+..|.. .|+++++.|||++++.++++.+.                     +.....++
T Consensus        78 --~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~DiTe~~~~e~~~~~~---------------------~~~~~~~~  134 (349)
T 3a0r_A           78 --LNFYKFGERYFNIRFSPFRNAKTQLLEGVIITIDDVTELYKYEEERKRR---------------------ERLSILGE  134 (349)
T ss_dssp             --EECCCBTTBCCEEEEEEECCTTTTSSCEEEEEEECCSTTTTTTTTTTHH---------------------HHHHHHHH
T ss_pred             --ecccccCceEEEEEEEEEEcCCCceeeEEEEEEEechHHHHHHHHHHHH---------------------HHHHHHHH
Confidence              2222346677888899999988775 58999999999987654433211                     11112357


Q ss_pred             HHHHhhhccccHHHHHHHHHHHHhCCCCC-HHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCeeeEeeecCHHHHHHH
Q 039716          373 MLATMSHEIRSPLTGVVSMAEILSNTKLD-REQRQLLGVMISSGDLVLQLINDILDLSKVESGVMKLEAAKFRPREVVKH  451 (1002)
Q Consensus       373 fla~iSHELRTPL~~I~g~~elL~~~~l~-~~~~~~l~~i~~s~~~L~~LIndlLd~skiesg~~~l~~~~~~l~~li~~  451 (1002)
                      |++.+||||||||++|.+++++|.....+ +..+++++.+..++.++..++++++++++..   ..+...++++.++++.
T Consensus       135 ~~~~i~Helr~pL~~i~~~~~~l~~~~~~~~~~~~~l~~i~~~~~~l~~li~~ll~~~~~~---~~~~~~~~~l~~~~~~  211 (349)
T 3a0r_A          135 MTARVAHEIRNPITIIGGFIMRMKKHLDDPETLKKYINIITNELSRLETIVKEILEYSKER---QVLEFTEFNLNELIRE  211 (349)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHTTSCSCSSCTTHHHHHHHHHHHHHHHHHHHHHHHHHCC----CEEEEEEEHHHHHHH
T ss_pred             HHHHHHHHhcchHHHHHHHHHHHHhhccCcHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCc---cccCCcccCHHHHHHH
Confidence            99999999999999999999999765333 3457889999999999999999999999943   3466788999999999


Q ss_pred             HHHHHHHHHh-hcceeccccCCCCCeeEEccHHHHHHHHHHHHhhhhhcCC-CCeeEEEEEecCCCCcccchhhhhhhhh
Q 039716          452 VLQTAAASLQ-KILMLEGDIADDVPIEVIGDVLRIRQILTNLISNAIKFTP-EGKVGIKLYVVPEPPFAKEGLKQKSKAY  529 (1002)
Q Consensus       452 v~~~~~~~~~-k~i~l~~~i~~~~p~~v~gD~~rL~QIL~NLlsNAIKfT~-~G~I~I~v~~~~~~~~~~~~~~~~~~~~  529 (1002)
                      ++..+...+. +.+.+....... +..+.+|+.+|.|||.||++||+||++ .|.|.|.+...                 
T Consensus       212 ~~~~~~~~~~~~~i~~~~~~~~~-~~~~~~d~~~l~~vl~nLl~NA~k~~~~~~~i~i~~~~~-----------------  273 (349)
T 3a0r_A          212 VYVLFEEKIRKMNIDFCFETDNE-DLRVEADRTRIKQVLINLVQNAIEATGENGKIKITSEDM-----------------  273 (349)
T ss_dssp             HHHHHHHHHTTTTCCCEEEESCS-CCEEEECHHHHHHHHHHHHTHHHHTTCTTCCEEEEEEEE-----------------
T ss_pred             HHHHHHHHHHHcCcEEEEecCCC-CceEEeCHHHHHHHHHHHHHHHHHhccCCCEEEEEEEec-----------------
Confidence            9988876654 456666555544 346889999999999999999999995 57777766421                 


Q ss_pred             hcchhhhhhhccCCCCCccCCCCCCCCCCCCCCccCCCCCCCCCCCccCCCCCccccccceEEEEEEEecCCCCCcCcHh
Q 039716          530 QSATDAVKEEKHQPKSQTASDQNGFHDKKHGEGYQDHKHDDDPGTPVSHGNSMDEDLEATVWIRCDVYDTGIGIPENALP  609 (1002)
Q Consensus       530 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~i~V~DtGiGI~~e~l~  609 (1002)
                                                                                 ..++.|+|.|+|+|||++.++
T Consensus       274 -----------------------------------------------------------~~~~~i~v~D~G~Gi~~~~~~  294 (349)
T 3a0r_A          274 -----------------------------------------------------------YTKVRVSVWNSGPPIPEELKE  294 (349)
T ss_dssp             -----------------------------------------------------------TTEEEEEEEEESCCCCGGGGT
T ss_pred             -----------------------------------------------------------CCEEEEEEEECCCCCChHHHh
Confidence                                                                       114889999999999999999


Q ss_pred             hhhhhccCCCccccCcCCCccccHHHHHHHHH-HhCCEEEEEeecCCceEEEEEEeCC
Q 039716          610 TLFRKYMQVSADHARKYGGTGLGLAICKQLVE-LMGGRLTVTSKVHCGSTFTFILPYQ  666 (1002)
Q Consensus       610 ~IF~pF~q~~~~~~~~~~GtGLGLaI~k~Lve-~~gG~I~v~S~~g~GTtF~~~LP~~  666 (1002)
                      +||+||++.+      .+|+||||+|||++|+ .|||.|+++|.++ ||+|+|+||..
T Consensus       295 ~if~~f~~~~------~~g~GlGL~i~~~~v~~~~gg~i~~~~~~~-Gt~f~i~lP~~  345 (349)
T 3a0r_A          295 KIFSPFFTTK------TQGTGLGLSICRKIIEDEHGGKIWTENREN-GVVFIFEIPKT  345 (349)
T ss_dssp             TTSSSCCCC------------CCCTHHHHHHHHTTCSBCCEEECSS-EEEEEEEEESC
T ss_pred             hcCCCCccCC------CCCccchHHHHHHHHHHhCCCEEEEEeCCC-cEEEEEEecCC
Confidence            9999999753      4599999999999999 8999999999865 99999999975

>2c2a_A Sensor histidine kinase; phosphotransfer, PHOQ, selenomethionyl MAD, two-component systems, transferase; HET: ADP; 1.9A {Thermotoga maritima} SCOP: a.30.2.1 d.122.1.3 PDB: 3dge_A*

Probab=100.00  E-value=1.5e-37  Score=337.42  Aligned_cols=221  Identities=31%  Similarity=0.470  Sum_probs=180.8

Q ss_pred             HHHHHHhhhccccHHHHHHHHHHHHhCC--C-CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCeeeEeeecCHHH
Q 039716          371 KQMLATMSHEIRSPLTGVVSMAEILSNT--K-LDREQRQLLGVMISSGDLVLQLINDILDLSKVESGVMKLEAAKFRPRE  447 (1002)
Q Consensus       371 k~fla~iSHELRTPL~~I~g~~elL~~~--~-l~~~~~~~l~~i~~s~~~L~~LIndlLd~skiesg~~~l~~~~~~l~~  447 (1002)
                      ++|++++||||||||++|.|++++|...  . .....+++++.|..++.+|..+|++++++++++.+...+...++++.+
T Consensus        21 ~~~~~~isHelrtPL~~i~~~~~~l~~~~~~~~~~~~~~~l~~i~~~~~~l~~li~~ll~~~~~~~~~~~~~~~~~~l~~  100 (258)
T 2c2a_A           21 TEFIANISHELRTPLTAIKAYAETIYNSLGELDLSTLKEFLEVIIDQSNHLENLLNELLDFSRLERKSLQINREKVDLCD  100 (258)
T ss_dssp             HHHHHHHHHHTHHHHHHHHHHHHHHHHTGGGCCTTTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCCCCCCEEEEHHH
T ss_pred             HHHHHHhhhhhcCCHHHHHHHHHHHHhhccCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCccCccceecHHH
Confidence            4799999999999999999999988643  1 234567899999999999999999999999999999888889999999


Q ss_pred             HHHHHHHHHHHHHh-hcceeccccCCCCCeeEEccHHHHHHHHHHHHhhhhhcCCCC----eeEEEEEecCCCCcccchh
Q 039716          448 VVKHVLQTAAASLQ-KILMLEGDIADDVPIEVIGDVLRIRQILTNLISNAIKFTPEG----KVGIKLYVVPEPPFAKEGL  522 (1002)
Q Consensus       448 li~~v~~~~~~~~~-k~i~l~~~i~~~~p~~v~gD~~rL~QIL~NLlsNAIKfT~~G----~I~I~v~~~~~~~~~~~~~  522 (1002)
                      ++++++..+...+. +.+.+........+..+.+|+.+|.|||.|||.||+||++.|    .|.|.+...          
T Consensus       101 ~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~d~~~l~~il~NLl~NAik~~~~~~~~~~i~i~~~~~----------  170 (258)
T 2c2a_A          101 LVESAVNAIKEFASSHNVNVLFESNVPCPVEAYIDPTRIRQVLLNLLNNGVKYSKKDAPDKYVKVILDEK----------  170 (258)
T ss_dssp             HHHHHHHHHHHHHHHTTCEEEEEESSCSCCEEEECHHHHHHHHHHHHHHHHHTCCTTCTTCEEEEEEEEE----------
T ss_pred             HHHHHHHHHHHHHHHcCcEEEeecCCCCCceEEeCHHHHHHHHHHHHHHHHhcCcCCCCceeEEEEEecC----------
Confidence            99999988776543 556655554444456788999999999999999999999754    355444211          


Q ss_pred             hhhhhhhhcchhhhhhhccCCCCCccCCCCCCCCCCCCCCccCCCCCCCCCCCccCCCCCccccccceEEEEEEEecCCC
Q 039716          523 KQKSKAYQSATDAVKEEKHQPKSQTASDQNGFHDKKHGEGYQDHKHDDDPGTPVSHGNSMDEDLEATVWIRCDVYDTGIG  602 (1002)
Q Consensus       523 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~i~V~DtGiG  602 (1002)
                                                                                        ...+.|.|.|+|+|
T Consensus       171 ------------------------------------------------------------------~~~~~i~V~D~G~G  184 (258)
T 2c2a_A          171 ------------------------------------------------------------------DGGVLIIVEDNGIG  184 (258)
T ss_dssp             ------------------------------------------------------------------TTEEEEEEEECSSC
T ss_pred             ------------------------------------------------------------------CCeEEEEEEecCCC
Confidence                                                                              11478999999999


Q ss_pred             CCcCcHhhhhhhccCCCccccCcCCCccccHHHHHHHHHHhCCEEEEEeecCCceEEEEEEeCCC
Q 039716          603 IPENALPTLFRKYMQVSADHARKYGGTGLGLAICKQLVELMGGRLTVTSKVHCGSTFTFILPYQV  667 (1002)
Q Consensus       603 I~~e~l~~IF~pF~q~~~~~~~~~~GtGLGLaI~k~Lve~~gG~I~v~S~~g~GTtF~~~LP~~~  667 (1002)
                      |+++.+++||+|||+.+...+...+|+||||+|||++|+.|||+|+++|.+|+||+|+|+||...
T Consensus       185 i~~~~~~~if~~f~~~~~~~~~~~~G~GLGL~i~~~iv~~~gG~i~v~s~~~~Gt~f~i~lP~~~  249 (258)
T 2c2a_A          185 IPDHAKDRIFEQFYRVDSSLTYEVPGTGLGLAITKEIVELHGGRIWVESEVGKGSRFFVWIPKDR  249 (258)
T ss_dssp             CCGGGTTGGGSTTCCCC---------CCCTHHHHHHHHHHTTCEEEEEEETTTEEEEEEEEECCC
T ss_pred             CCHHHHHhhccccccCCCCCCCCCCCcchHHHHHHHHHHHcCCEEEEEecCCCCcEEEEEeeCCC
Confidence            99999999999999987655555679999999999999999999999999999999999999753

>4ew8_A Sensor protein DIVL; signal transduction, two-component regulatory system, hiska GHKL domain, structural genomics; 2.50A {Caulobacter crescentus}

Probab=100.00  E-value=1.8e-32  Score=298.65  Aligned_cols=215  Identities=31%  Similarity=0.504  Sum_probs=188.1

Q ss_pred             HHHHHHhhhccccHHHHHHHHHHHHhCC-CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCeeeEeeecCHHHHH
Q 039716          371 KQMLATMSHEIRSPLTGVVSMAEILSNT-KLDREQRQLLGVMISSGDLVLQLINDILDLSKVESGVMKLEAAKFRPREVV  449 (1002)
Q Consensus       371 k~fla~iSHELRTPL~~I~g~~elL~~~-~l~~~~~~~l~~i~~s~~~L~~LIndlLd~skiesg~~~l~~~~~~l~~li  449 (1002)
                      ++|++.++|||||||++|.+++++|... ..+++.++++..+..++.++..++++++++++++.+...+...++++.+++
T Consensus        41 ~~~~~~l~Helr~pL~~i~~~~~~l~~~~~~~~~~~~~l~~i~~~~~~l~~~i~~l~~~~~~~~~~~~~~~~~~~l~~~l  120 (268)
T 4ew8_A           41 RDFVGNVSYELRTPLTTIIGYSELLERADGISERGRNHVAAVRAAATQLARSIDDVLDMAQIDAGEMALEIEDIRVSDLL  120 (268)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHTCSSCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCCCCCCEEEEHHHHH
T ss_pred             HHHHHHHHHHHhhHHHHHHHHHHHHhhccCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCcceeeeeccHHHHH
Confidence            4799999999999999999999999764 357788999999999999999999999999999999988888999999999


Q ss_pred             HHHHHHHHHHHh-hcceeccccCCCCCeeEEccHHHHHHHHHHHHhhhhhcCCC-CeeEEEEEecCCCCcccchhhhhhh
Q 039716          450 KHVLQTAAASLQ-KILMLEGDIADDVPIEVIGDVLRIRQILTNLISNAIKFTPE-GKVGIKLYVVPEPPFAKEGLKQKSK  527 (1002)
Q Consensus       450 ~~v~~~~~~~~~-k~i~l~~~i~~~~p~~v~gD~~rL~QIL~NLlsNAIKfT~~-G~I~I~v~~~~~~~~~~~~~~~~~~  527 (1002)
                      ..++..+..... +.+.+...+....+ .+.+|+..|.|||.|||.||+||++. |.|.|.+...               
T Consensus       121 ~~~~~~~~~~~~~~~i~i~~~~~~~~~-~v~~d~~~l~~il~nLl~NA~~~~~~~~~I~i~~~~~---------------  184 (268)
T 4ew8_A          121 LNAQERALKDAQLGGVTLAVECEEDVG-LIRGDGKRLAQTLDHLVENALRQTPPGGRVTLSARRA---------------  184 (268)
T ss_dssp             HHHHHHHHHHHHHTTCEEEEECCTTSC-EEEECHHHHHHHHHHHHHHHHHHSCTTCEEEEEEEEC---------------
T ss_pred             HHHHHHHHhhhhccCceEEEEcCCCCc-eEecCHHHHHHHHHHHHHHHHHhCCCCCEEEEEEEec---------------
Confidence            999988776544 56777777766554 58899999999999999999999986 6777766421               


Q ss_pred             hhhcchhhhhhhccCCCCCccCCCCCCCCCCCCCCccCCCCCCCCCCCccCCCCCccccccceEEEEEEEecCCCCCcCc
Q 039716          528 AYQSATDAVKEEKHQPKSQTASDQNGFHDKKHGEGYQDHKHDDDPGTPVSHGNSMDEDLEATVWIRCDVYDTGIGIPENA  607 (1002)
Q Consensus       528 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~i~V~DtGiGI~~e~  607 (1002)
                                                                                   ..++.|.|.|+|+||+++.
T Consensus       185 -------------------------------------------------------------~~~~~i~V~D~G~Gi~~~~  203 (268)
T 4ew8_A          185 -------------------------------------------------------------LGEVRLDVSDTGRGVPFHV  203 (268)
T ss_dssp             -------------------------------------------------------------SSEEEEEEEESSCCCCHHH
T ss_pred             -------------------------------------------------------------CCEEEEEEEcCCCCCCHHH
Confidence                                                                         1148899999999999999


Q ss_pred             HhhhhhhccCCCccccCcCCCccccHHHHHHHHHHhCCEEEEEeecCCceEEEEEEeCCCC
Q 039716          608 LPTLFRKYMQVSADHARKYGGTGLGLAICKQLVELMGGRLTVTSKVHCGSTFTFILPYQVS  668 (1002)
Q Consensus       608 l~~IF~pF~q~~~~~~~~~~GtGLGLaI~k~Lve~~gG~I~v~S~~g~GTtF~~~LP~~~~  668 (1002)
                      ++++|+||++.      +.+|+||||+||+++++.|||+|++.|.+|+||+|+|.||....
T Consensus       204 ~~~if~~~~~~------~~~g~GlGL~i~~~~~~~~gG~i~i~s~~~~Gt~~~i~lP~~~~  258 (268)
T 4ew8_A          204 QAHIFDRFVGR------DRGGPGLGLALVKALVELHGGWVALESEPGNGSTFTCHLPETQQ  258 (268)
T ss_dssp             HTTTTSTTCCC------SSCCCTTHHHHHHHHHHHTTCEEEEEECTTSCEEEEEEEECCC-
T ss_pred             HHHHHHHHhcC------CCCCCcccHHHHHHHHHHcCCEEEEEecCCCCEEEEEEecCCCC
Confidence            99999999953      33699999999999999999999999999999999999998643

>3jz3_A Sensor protein QSEC; helix-turn-helix, kinase domain, ATP-binding, cell inner MEM cell membrane, kinase, membrane, nucleotide-binding; 2.50A {Escherichia coli}

Probab=100.00  E-value=4e-34  Score=301.96  Aligned_cols=213  Identities=21%  Similarity=0.336  Sum_probs=127.7

Q ss_pred             HHHHHHhhhccccHHHHHHHHHHHHhCCCCC-HHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCeeeEeeecCHHHHH
Q 039716          371 KQMLATMSHEIRSPLTGVVSMAEILSNTKLD-REQRQLLGVMISSGDLVLQLINDILDLSKVESGVMKLEAAKFRPREVV  449 (1002)
Q Consensus       371 k~fla~iSHELRTPL~~I~g~~elL~~~~l~-~~~~~~l~~i~~s~~~L~~LIndlLd~skiesg~~~l~~~~~~l~~li  449 (1002)
                      ++|++.+||||||||++|.++++++.....+ +..++++..+..+++++..++++++++++++.+.......++++.+++
T Consensus         3 ~~~~~~~~Helr~pL~~i~~~~~~l~~~~~~~~~~~~~l~~i~~~~~~l~~~i~~l~~~~~~~~~~~~~~~~~~~l~~~~   82 (222)
T 3jz3_A            3 RRFTSDAAHELRSPLTALKVQTEVAQLSDDDPQARKKALLQLHSGIDRATRLVDQLLTLSRLDSLDNLQDVAEIPLEDLL   82 (222)
T ss_dssp             -------------------------------------CEECCC-CHHHHHHHHHHHHHHHTCCCSTTSTTCEEEEHHHHH
T ss_pred             HHHHHHHhHHhcCcHHHHHHHHHHHhhccCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCccCcccCCHHHHH
Confidence            4799999999999999999999998755433 344677888999999999999999999999998888888899999999


Q ss_pred             HHHHHHHHHHH-hhcceeccccCCCCCeeEEccHHHHHHHHHHHHhhhhhcCCCC-eeEEEEEecCCCCcccchhhhhhh
Q 039716          450 KHVLQTAAASL-QKILMLEGDIADDVPIEVIGDVLRIRQILTNLISNAIKFTPEG-KVGIKLYVVPEPPFAKEGLKQKSK  527 (1002)
Q Consensus       450 ~~v~~~~~~~~-~k~i~l~~~i~~~~p~~v~gD~~rL~QIL~NLlsNAIKfT~~G-~I~I~v~~~~~~~~~~~~~~~~~~  527 (1002)
                      ++++..+.... .+.+.+...+... +..+.+|+.+|.|||.|||.||+||++.| .|.|.+..                
T Consensus        83 ~~~~~~~~~~~~~~~i~~~~~~~~~-~~~~~~d~~~l~~il~nLl~NAi~~~~~~~~i~i~~~~----------------  145 (222)
T 3jz3_A           83 QSSVMDIYHTAQQAKIDVRLTLNAH-SIKRTGQPLLLSLLVRNLLDNAVRYSPQGSVVDVTLNA----------------  145 (222)
T ss_dssp             HHHHHHHHHHHHHTTCEEEEEESSC-SCEEEECHHHHHHHHHHHHHHHHHTCCTTCEEEEEECS----------------
T ss_pred             HHHHHHHHHHHHHhCCeEEEeeCCc-ceEEecCHHHHHHHHHHHHHHHHHcCCCCCeEEEEEcc----------------
Confidence            99988876654 3567777666555 34688999999999999999999999765 45554310                


Q ss_pred             hhhcchhhhhhhccCCCCCccCCCCCCCCCCCCCCccCCCCCCCCCCCccCCCCCccccccceEEEEEEEecCCCCCcCc
Q 039716          528 AYQSATDAVKEEKHQPKSQTASDQNGFHDKKHGEGYQDHKHDDDPGTPVSHGNSMDEDLEATVWIRCDVYDTGIGIPENA  607 (1002)
Q Consensus       528 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~i~V~DtGiGI~~e~  607 (1002)
                                                                                  .    .|.|.|+|+||+++.
T Consensus       146 ------------------------------------------------------------~----~i~V~D~G~Gi~~~~  161 (222)
T 3jz3_A          146 ------------------------------------------------------------D----NFIVRDNGPGVTPEA  161 (222)
T ss_dssp             ------------------------------------------------------------S----EEEEECSCC------
T ss_pred             ------------------------------------------------------------C----eEEEEECCCCCCHHH
Confidence                                                                        0    167999999999999


Q ss_pred             HhhhhhhccCCCccccCcCCCccccHHHHHHHHHHhCCEEEEEeecCCceEEEEEEeCCC
Q 039716          608 LPTLFRKYMQVSADHARKYGGTGLGLAICKQLVELMGGRLTVTSKVHCGSTFTFILPYQV  667 (1002)
Q Consensus       608 l~~IF~pF~q~~~~~~~~~~GtGLGLaI~k~Lve~~gG~I~v~S~~g~GTtF~~~LP~~~  667 (1002)
                      +++||+||++.+.   .+.+|+||||+|||++++.|||+|+++|.+|+||+|+|+||...
T Consensus       162 ~~~if~~f~~~~~---~~~~g~GlGL~i~~~i~~~~gG~i~i~s~~~~Gt~v~~~~P~~~  218 (222)
T 3jz3_A          162 LARIGERFYRPPG---QTATGSGLGLSIVQRIAKLHGMNVEFGNAEQGGFEAKVSWLEHH  218 (222)
T ss_dssp             -----------------------CTHHHHHHHHHHTTCEEECCBCTTSSBEEEEECCCC-
T ss_pred             HHHHHhhhccCCC---CCCCcccccHHHHHHHHHHcCCEEEEEcCCCCcEEEEEeecCCC
Confidence            9999999998543   24469999999999999999999999999999999999999754

>1gkz_A [3-methyl-2-oxobutanoate dehydrogenase [lipoamide]] kinase; transferase, mitochondrial protein kinase, potassium; HET: ADP; 2.2A {Rattus norvegicus} SCOP: a.29.5.1 d.122.1.4 PDB: 1gjv_A 1gkx_A*

Probab=100.00  E-value=1e-32  Score=318.11  Aligned_cols=219  Identities=18%  Similarity=0.227  Sum_probs=183.2

Q ss_pred             HHHHHHHHhhhccccHHHHHH-HHHHHHhCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCeeeEeeecCHHH
Q 039716          369 RAKQMLATMSHEIRSPLTGVV-SMAEILSNTKLDREQRQLLGVMISSGDLVLQLINDILDLSKVESGVMKLEAAKFRPRE  447 (1002)
Q Consensus       369 ~~k~fla~iSHELRTPL~~I~-g~~elL~~~~l~~~~~~~l~~i~~s~~~L~~LIndlLd~skiesg~~~l~~~~~~l~~  447 (1002)
                      +..+|+++++||+||||++|. |+.+++.....+++.+++++.+..++.+|..+|+++|++++++.+.+.+...++++.+
T Consensus       120 ~~~~~l~~i~helrtpL~~i~~g~~~l~~~~~~~~~~~~~l~~i~~~~~~l~~li~~ll~l~~~~~~~~~~~~~~~~l~~  199 (388)
T 1gkz_A          120 QYCQLVRQLLDDHKDVVTLLAEGLRESRKHIEDEKLVRYFLDKTLTSRLGIRMLATHHLALHEDKPDFVGIICTRLSPKK  199 (388)
T ss_dssp             HHHHHHHHHHHHTTTHHHHHHHHHHHSSSSCCSTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSCCTTEETTEEEEECHHH
T ss_pred             HHHHHHHHHHHHhccHHHHHHHHHHHHHhhccCcHHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCccceecCCCCHHH
Confidence            445899999999999999999 7777766544467788999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHh-h-----cceeccccCCCCCeeEEccHHHHHHHHHHHHhhhhhcCCCC---------eeEEEEEec
Q 039716          448 VVKHVLQTAAASLQ-K-----ILMLEGDIADDVPIEVIGDVLRIRQILTNLISNAIKFTPEG---------KVGIKLYVV  512 (1002)
Q Consensus       448 li~~v~~~~~~~~~-k-----~i~l~~~i~~~~p~~v~gD~~rL~QIL~NLlsNAIKfT~~G---------~I~I~v~~~  512 (1002)
                      ++++++..+..... +     .+.+..    +.+..+.+|+.+|.|||.|||.||+||+.+|         .|.|.+...
T Consensus       200 li~~~~~~~~~~~~~~~g~~~~i~i~~----~~~~~~~~~~~~L~~il~NLl~NAik~~~~~~~~~~~~~~~I~I~~~~~  275 (388)
T 1gkz_A          200 IIEKWVDFARRLCEHKYGNAPRVRING----HVAARFPFIPMPLDYILPELLKNAMRATMESHLDTPYNVPDVVITIANN  275 (388)
T ss_dssp             HHHHHHHHHHHHHHHHHSCCCCEEEEE----STTCCEEECCHHHHHHHHHHHHHHHHHHHHTCTTCTTSCCCEEEEEEEC
T ss_pred             HHHHHHHHHHHHHHHhcCCCCcEEEEc----cCCCceeecHHHHHHHHHHHHHHHHHHhhccccCCCCCCCCEEEEEEeC
Confidence            99999988876554 3     233332    2234578899999999999999999999765         566665321


Q ss_pred             CCCCcccchhhhhhhhhhcchhhhhhhccCCCCCccCCCCCCCCCCCCCCccCCCCCCCCCCCccCCCCCccccccceEE
Q 039716          513 PEPPFAKEGLKQKSKAYQSATDAVKEEKHQPKSQTASDQNGFHDKKHGEGYQDHKHDDDPGTPVSHGNSMDEDLEATVWI  592 (1002)
Q Consensus       513 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l  592 (1002)
                                                                                                  ..++
T Consensus       276 ----------------------------------------------------------------------------~~~v  279 (388)
T 1gkz_A          276 ----------------------------------------------------------------------------DVDL  279 (388)
T ss_dssp             ----------------------------------------------------------------------------SSEE
T ss_pred             ----------------------------------------------------------------------------CCEE
Confidence                                                                                        1258


Q ss_pred             EEEEEecCCCCCcCcHhhhhhhccCCCccc--------------------cCcCCCccccHHHHHHHHHHhCCEEEEEee
Q 039716          593 RCDVYDTGIGIPENALPTLFRKYMQVSADH--------------------ARKYGGTGLGLAICKQLVELMGGRLTVTSK  652 (1002)
Q Consensus       593 ~i~V~DtGiGI~~e~l~~IF~pF~q~~~~~--------------------~~~~~GtGLGLaI~k~Lve~~gG~I~v~S~  652 (1002)
                      .|.|.|+|+||+++.+++||+|||+++...                    ++..+|+||||+|||.+|+.|||+|++.|.
T Consensus       280 ~i~V~D~G~GI~~~~~~~iF~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~GLGL~i~r~i~~~~gG~i~v~s~  359 (388)
T 1gkz_A          280 IIRISDRGGGIAHKDLDRVMDYHFTTAEASTQDPRISPLFGHLDMHSGGQSGPMHGFGFGLPTSRAYAEYLGGSLQLQSL  359 (388)
T ss_dssp             EEEEECCSCCCCTTTTTTTTSTTCCCC-------------------------CCSCSSCHHHHHHHHHHHTTCEEEEEEE
T ss_pred             EEEEEEeCCCcCHHHHHHhcCcccccCCCcccccccccchhhcccccccCCCCcCCccCCHHHHHHHHHHhCCEEEEEec
Confidence            899999999999999999999999987532                    223479999999999999999999999999


Q ss_pred             cCCceEEEEEEeCCC
Q 039716          653 VHCGSTFTFILPYQV  667 (1002)
Q Consensus       653 ~g~GTtF~~~LP~~~  667 (1002)
                      +|.||+|+|+||...
T Consensus       360 ~g~Gt~f~i~LP~~~  374 (388)
T 1gkz_A          360 QGIGTDVYLRLRHID  374 (388)
T ss_dssp             TTTEEEEEEEEECSS
T ss_pred             CCCcEEEEEEecCCC
Confidence            999999999999754

>2btz_A Pyruvate dehydrogenase kinase isoenzyme 2; GHKL motif regulation, transferase; 2.2A {Homo sapiens} PDB: 2bu2_A* 2bu5_A* 2bu6_A* 2bu7_A* 2bu8_A* 3crk_A* 1jm6_A* 3crl_A*

Probab=100.00  E-value=1.5e-32  Score=317.32  Aligned_cols=218  Identities=18%  Similarity=0.156  Sum_probs=169.1

Q ss_pred             HHHHHhhhcccc-----HHHHHHHHHHHHhCCCCCHH----HHHHHH--HHHHHHHHHHHHHHHHHHHHhhhc-CCeeeE
Q 039716          372 QMLATMSHEIRS-----PLTGVVSMAEILSNTKLDRE----QRQLLG--VMISSGDLVLQLINDILDLSKVES-GVMKLE  439 (1002)
Q Consensus       372 ~fla~iSHELRT-----PL~~I~g~~elL~~~~l~~~----~~~~l~--~i~~s~~~L~~LIndlLd~skies-g~~~l~  439 (1002)
                      +|++++||||||     ||+.|.|+++++.....++.    ..++++  .+...+.+|  +|+++|++++.+. +...+.
T Consensus        97 ~~~~~~~HeLrtpl~~vPlt~i~g~~ell~~~~~~~~~~~~~~~~l~~~~i~~~~~rl--li~~ll~l~~~~~~~~~~~~  174 (394)
T 2btz_A           97 SQFTDALVTIRNRHNDVVPTMAQGVLEYKDTYGDDPVSNQNIQYFLDRFYLSRISIRM--LINQHTLIFDGSTNPAHPKH  174 (394)
T ss_dssp             HHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHH--HHHHHHHHCC--------CC
T ss_pred             HHHHHHHHHHHhhcchhHHHHHHHHHHHHHhhcCCcccHHHHHHHHHHHHHhhhHHHH--HHHHHHHHhcccccCCCCcc
Confidence            488899999999     99999999999876544433    334777  478888999  9999999999987 566666


Q ss_pred             e----eecCHHHHHHHHHHHHHHHHh------hcceecccc--CCCCCeeEEccHHHHHHHHHHHHhhhhhcCCCCe---
Q 039716          440 A----AKFRPREVVKHVLQTAAASLQ------KILMLEGDI--ADDVPIEVIGDVLRIRQILTNLISNAIKFTPEGK---  504 (1002)
Q Consensus       440 ~----~~~~l~~li~~v~~~~~~~~~------k~i~l~~~i--~~~~p~~v~gD~~rL~QIL~NLlsNAIKfT~~G~---  504 (1002)
                      .    .++++.+++++++..+...+.      +.+.+....  .+..+..+.+|+.+|.|||.|||.||+||+++|.   
T Consensus       175 ~g~i~~~~~l~~li~~~~~~~~~~~~~~~~~~~~i~l~~~~~~~~~~~~~v~~d~~~L~~il~NLl~NAik~~~~~~~~~  254 (394)
T 2btz_A          175 IGSIDPNCNVSEVVKDAYDMAKLLCDKYYMASPDLEIQEINAANSKQPIHMVYVPSHLYHMLFELFKNAMRATVESHESS  254 (394)
T ss_dssp             BTTBEEEEEHHHHHHHHHHHHHHHHHHHHSCCCCEEEEEEETTSTTSCCEEEECHHHHHHHHHHHHHHHHHHHHHTTTTC
T ss_pred             cceecCCCCHHHHHHHHHHHHHHHHHHhhCCCCCeEEEEeccCCCCCCeEEEecHHHHHHHHHHHHHHHHHHhhhccccC
Confidence            6    889999999999988876654      556665422  1233457899999999999999999999998764   


Q ss_pred             -----eEEEEEecCCCCcccchhhhhhhhhhcchhhhhhhccCCCCCccCCCCCCCCCCCCCCccCCCCCCCCCCCccCC
Q 039716          505 -----VGIKLYVVPEPPFAKEGLKQKSKAYQSATDAVKEEKHQPKSQTASDQNGFHDKKHGEGYQDHKHDDDPGTPVSHG  579 (1002)
Q Consensus       505 -----I~I~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  579 (1002)
                           |.|.+...                                                                   
T Consensus       255 ~~~~~I~I~~~~~-------------------------------------------------------------------  267 (394)
T 2btz_A          255 LILPPIKVMVALG-------------------------------------------------------------------  267 (394)
T ss_dssp             SCCCCEEEEEEEC-------------------------------------------------------------------
T ss_pred             CCCCCEEEEEEeC-------------------------------------------------------------------
Confidence                 77665321                                                                   


Q ss_pred             CCCccccccceEEEEEEEecCCCCCcCcHhhhhhhccCCCcc-----ccCcCCCccccHHHHHHHHHHhCCEEEEEeecC
Q 039716          580 NSMDEDLEATVWIRCDVYDTGIGIPENALPTLFRKYMQVSAD-----HARKYGGTGLGLAICKQLVELMGGRLTVTSKVH  654 (1002)
Q Consensus       580 ~~~~~~~~~~~~l~i~V~DtGiGI~~e~l~~IF~pF~q~~~~-----~~~~~~GtGLGLaI~k~Lve~~gG~I~v~S~~g  654 (1002)
                               ..++.|.|.|+|+||+++.+++||+|||+++..     ..+..+|+||||+|||.+|+.|||+|++.|.+|
T Consensus       268 ---------~~~v~i~V~D~G~GI~~~~~~~iF~~f~~~~~~~~~~~~~~~~~G~GLGL~i~~~i~~~~gG~i~v~s~~g  338 (394)
T 2btz_A          268 ---------EEDLSIKMSDRGGGVPLRKIERLFSYMYSTAPTPQPGTGGTPLAGFGYGLPISRLYAKYFQGDLQLFSMEG  338 (394)
T ss_dssp             ---------SSEEEEEEEECSCCCCHHHHHHHTCTTTTCCC--------------CCHHHHHHHHHHHTTCEEEEEEETT
T ss_pred             ---------CCEEEEEEEeCCCCCCHHHHHHHhcccccCCCCCCcccCCCCCCCccCCHHHHHHHHHHhCCEEEEEecCC
Confidence                     125889999999999999999999999998764     344567999999999999999999999999999


Q ss_pred             CceEEEEEEeCCC
Q 039716          655 CGSTFTFILPYQV  667 (1002)
Q Consensus       655 ~GTtF~~~LP~~~  667 (1002)
                      +||+|+|+||...
T Consensus       339 ~Gt~f~i~lP~~~  351 (394)
T 2btz_A          339 FGTDAVIYLKALS  351 (394)
T ss_dssp             TEEEEEEEEESST
T ss_pred             CceEEEEEecCCC
Confidence            9999999999754

>2e0a_A Pyruvate dehydrogenase kinase isozyme 4; PDK4, ATP-binding, structural genomics, NPPSFA, NATI project on protein structural and functional analyses; HET: ANP; 1.86A {Homo sapiens} PDB: 2zdx_A* 2zdy_A* 2zkj_A* 3d2r_A*

Probab=100.00  E-value=4.1e-32  Score=313.71  Aligned_cols=217  Identities=17%  Similarity=0.179  Sum_probs=178.3

Q ss_pred             HHHHHhhhcccc-----HHHHHHHHHHHHhCCC----CCHHHHHHHH--HHHHHHHHHHHHHHHHHH-HHhhhcCCeeeE
Q 039716          372 QMLATMSHEIRS-----PLTGVVSMAEILSNTK----LDREQRQLLG--VMISSGDLVLQLINDILD-LSKVESGVMKLE  439 (1002)
Q Consensus       372 ~fla~iSHELRT-----PL~~I~g~~elL~~~~----l~~~~~~~l~--~i~~s~~~L~~LIndlLd-~skiesg~~~l~  439 (1002)
                      +|+++++|||||     ||+.|.|+++++....    ..++.+++++  .+.+.+.+|  +|+++|+ +++. ++...+.
T Consensus        97 ~~~~~~~HeLrtpl~~vPlt~i~g~~el~~~~~~~~~~~~~~~~~l~~~~i~~~~~rl--li~~lL~l~~~~-~~~~~~~  173 (394)
T 2e0a_A           97 SDFVDTLIKVRNRHHNVVPTMAQGIIEYKDACTVDPVTNQNLQYFLDRFYMNRISTRM--LMNQHILIFSDS-QTGNPSH  173 (394)
T ss_dssp             HHHHHHHHHHHHHHTTHHHHHHHHHHHHHTTSCCCTTTCHHHHHHHHHHHHHHHHHHH--HHHHHHHHHCSS-CCCCTTS
T ss_pred             HHHHHHHHHHHhhhhhhHHHHHHHHHHHHhhhccCcccHHHHHHHHHHHHHHHHHHHH--HHHHHHHHhhcc-cCCCCCc
Confidence            478889999999     8999999999876542    3455678888  688999999  9999999 7776 6666665


Q ss_pred             e----eecCHHHHHHHHHHHHHHHHh-h-----cceecccc--CCCCCeeEEccHHHHHHHHHHHHhhhhhcCCCCe---
Q 039716          440 A----AKFRPREVVKHVLQTAAASLQ-K-----ILMLEGDI--ADDVPIEVIGDVLRIRQILTNLISNAIKFTPEGK---  504 (1002)
Q Consensus       440 ~----~~~~l~~li~~v~~~~~~~~~-k-----~i~l~~~i--~~~~p~~v~gD~~rL~QIL~NLlsNAIKfT~~G~---  504 (1002)
                      .    .++++.+++++++..+...+. +     .+.+...+  .+..+..+.+|+.+|.|||.|||.||+||+++|.   
T Consensus       174 ~g~i~~~~~l~~ll~~~~~~~~~~~~~~~~~~~~i~l~~~~~~~~~~~~~v~~d~~~L~~il~NLl~NAik~~~~~~~~~  253 (394)
T 2e0a_A          174 IGSIDPNCDVVAVVQDAFECSRMLCDQYYLSSPELKLTQVNGKFPDQPIHIVYVPSHLHHMLFELFKNAMRATVEHQENQ  253 (394)
T ss_dssp             BTTBEEEEEHHHHHHHHHHHHHHHHHHHHSCCCCEEEEEEESSSTTSCCEEEECHHHHHHHHHHHHHHHHHHHHHHTTTS
T ss_pred             cccccCCCCHHHHHHHHHHHHHHHHHHhcCCCCceEEEEeccCCCCCCeEEEEcHHHHHHHHHHHHHHHHHHHHhccccc
Confidence            5    789999999999988776553 4     56666532  2234457899999999999999999999997654   


Q ss_pred             -----eEEEEEecCCCCcccchhhhhhhhhhcchhhhhhhccCCCCCccCCCCCCCCCCCCCCccCCCCCCCCCCCccCC
Q 039716          505 -----VGIKLYVVPEPPFAKEGLKQKSKAYQSATDAVKEEKHQPKSQTASDQNGFHDKKHGEGYQDHKHDDDPGTPVSHG  579 (1002)
Q Consensus       505 -----I~I~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  579 (1002)
                           |.|.+...                                                                   
T Consensus       254 ~~~~~I~I~~~~~-------------------------------------------------------------------  266 (394)
T 2e0a_A          254 PSLTPIEVIVVLG-------------------------------------------------------------------  266 (394)
T ss_dssp             SSCCCEEEEEEEC-------------------------------------------------------------------
T ss_pred             CCCCCEEEEEEeC-------------------------------------------------------------------
Confidence                 77766321                                                                   


Q ss_pred             CCCccccccceEEEEEEEecCCCCCcCcHhhhhhhccCCCcc------ccCcCCCccccHHHHHHHHHHhCCEEEEEeec
Q 039716          580 NSMDEDLEATVWIRCDVYDTGIGIPENALPTLFRKYMQVSAD------HARKYGGTGLGLAICKQLVELMGGRLTVTSKV  653 (1002)
Q Consensus       580 ~~~~~~~~~~~~l~i~V~DtGiGI~~e~l~~IF~pF~q~~~~------~~~~~~GtGLGLaI~k~Lve~~gG~I~v~S~~  653 (1002)
                               ..++.|.|.|+|+||+++.+++||+|||+++..      ..+..+|+||||+|||.+|+.|||+|+++|.+
T Consensus       267 ---------~~~v~i~V~D~G~GI~~~~~~~if~~f~~~~~~~~~~~~~~~~~~G~GLGL~i~~~i~~~~gG~i~v~s~~  337 (394)
T 2e0a_A          267 ---------KEDLTIKISDRGGGVPLRIIDRLFSYTYSTAPTPVMDNSRNAPLAGFGYGLPISRLYAKYFQGDLNLYSLS  337 (394)
T ss_dssp             ---------SSEEEEEEEECSCCCCGGGHHHHTSTTCCSSCCC------CCCSSCSSCHHHHHHHHHHHTTCEEEEEEET
T ss_pred             ---------CCEEEEEEEeCCCCcCHHHHHHHhCcCccCCCCCCcCcCCCCCCCCcccCHHHHHHHHHHhCCEEEEEecC
Confidence                     125889999999999999999999999998765      44456799999999999999999999999999


Q ss_pred             CCceEEEEEEeCCC
Q 039716          654 HCGSTFTFILPYQV  667 (1002)
Q Consensus       654 g~GTtF~~~LP~~~  667 (1002)
                      |.||+|+|+||...
T Consensus       338 g~Gt~f~i~lP~~~  351 (394)
T 2e0a_A          338 GYGTDAIIYLKALS  351 (394)
T ss_dssp             TTEEEEEEEEESSG
T ss_pred             CccEEEEEEeCCCC
Confidence            99999999999753

>2q8g_A [pyruvate dehydrogenase [lipoamide]] kinase isozy; GHKL ATPase/kinase family, pyruvate dehydrogenase complex, mitochondrial kinase; HET: AZX; 1.90A {Homo sapiens} PDB: 2q8f_A* 2q8h_A

Probab=99.98  E-value=1.8e-31  Score=309.71  Aligned_cols=217  Identities=19%  Similarity=0.172  Sum_probs=172.6

Q ss_pred             HHHHhhhcccc-----HHHHHHHHHHHHhCCCCC----HHHHHHHHH--HHHHHHHHHHHHHHHHHHHhhhc----C---
Q 039716          373 MLATMSHEIRS-----PLTGVVSMAEILSNTKLD----REQRQLLGV--MISSGDLVLQLINDILDLSKVES----G---  434 (1002)
Q Consensus       373 fla~iSHELRT-----PL~~I~g~~elL~~~~l~----~~~~~~l~~--i~~s~~~L~~LIndlLd~skies----g---  434 (1002)
                      +++.++|||||     ||+.|.|+++++.....+    ++.+++++.  +...+.+|  +|+++|++++.+.    +   
T Consensus       108 ~f~~~~HeLrt~~~~vPLt~i~g~~ell~~~~~~~~~~~~~~~~l~~~~~~~~~~rl--li~~ll~l~~~e~~~~~~~~~  185 (407)
T 2q8g_A          108 DFTDTVIRIRNRHNDVIPTMAQGVIEYKESFGVDPVTSQNVQYFLDRFYMSRISIRM--LLNQHSLLFGGKGKGSPSHRK  185 (407)
T ss_dssp             HHHHHHHHHHHHTTTHHHHHHHHHHHHHHHC--CHHHHHHHHHHHHHHHHHHHHHHH--HHHHHHHHHC----------C
T ss_pred             HHHHHHHHHHhhhccchHHHHHHHHHHHHhhccCccCHHHHHHHHHHHHHHHHHHHH--HHHHHHHHhccccccCCCCcc
Confidence            44445599999     999999999988754433    234677887  67778888  9999999999976    3   


Q ss_pred             CeeeEeeecCHHHHHHHHHHHHHHHHh-h-----cceecccc--CCCCCeeEEccHHHHHHHHHHHHhhhhhcCCCC---
Q 039716          435 VMKLEAAKFRPREVVKHVLQTAAASLQ-K-----ILMLEGDI--ADDVPIEVIGDVLRIRQILTNLISNAIKFTPEG---  503 (1002)
Q Consensus       435 ~~~l~~~~~~l~~li~~v~~~~~~~~~-k-----~i~l~~~i--~~~~p~~v~gD~~rL~QIL~NLlsNAIKfT~~G---  503 (1002)
                      .+.+...++++.+++++++..+..... +     .+.+...+  .+..+..+.+|+.+|.|||.|||.||+||+++|   
T Consensus       186 ~~~~~~~~~~l~~li~~~~~~~~~~~~~~~~~~~~i~l~~~~~~~~~~~~~v~~d~~~L~~il~NLl~NAik~t~~~~~~  265 (407)
T 2q8g_A          186 HIGSINPNCNVLEVIKDGYENARRLCDLYYINSPELELEELNAKSPGQPIQVVYVPSHLYHMVFELFKNAMRATMEHHAN  265 (407)
T ss_dssp             CBTTBEEEEEHHHHHHHHHHHHHHHHHHHHSCCCCEEEEEEESSSTTSCCEEEECHHHHHHHHHHHHHHHHHHHHHHSTT
T ss_pred             ccccccCCCCHHHHHHHHHHHHHHHHHHhcCCCCceEEEEeecCCCCCCeEEEEcHHHHHHHHHHHHHHHHHHHhhcccc
Confidence            556677889999999999988776543 3     56666544  123445789999999999999999999999765   


Q ss_pred             -----eeEEEEEecCCCCcccchhhhhhhhhhcchhhhhhhccCCCCCccCCCCCCCCCCCCCCccCCCCCCCCCCCccC
Q 039716          504 -----KVGIKLYVVPEPPFAKEGLKQKSKAYQSATDAVKEEKHQPKSQTASDQNGFHDKKHGEGYQDHKHDDDPGTPVSH  578 (1002)
Q Consensus       504 -----~I~I~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  578 (1002)
                           .|.|.+...                                                                  
T Consensus       266 ~~~~~~I~I~~~~~------------------------------------------------------------------  279 (407)
T 2q8g_A          266 RGVYPPIQVHVTLG------------------------------------------------------------------  279 (407)
T ss_dssp             TCCCCCEEEEEEEC------------------------------------------------------------------
T ss_pred             CCCCCCEEEEEEeC------------------------------------------------------------------
Confidence                 476665321                                                                  


Q ss_pred             CCCCccccccceEEEEEEEecCCCCCcCcHhhhhhhccCCCcc------ccCcCCCccccHHHHHHHHHHhCCEEEEEee
Q 039716          579 GNSMDEDLEATVWIRCDVYDTGIGIPENALPTLFRKYMQVSAD------HARKYGGTGLGLAICKQLVELMGGRLTVTSK  652 (1002)
Q Consensus       579 ~~~~~~~~~~~~~l~i~V~DtGiGI~~e~l~~IF~pF~q~~~~------~~~~~~GtGLGLaI~k~Lve~~gG~I~v~S~  652 (1002)
                                ..++.|.|.|+|+||+++.+++||+|||+++..      ..+..+|+||||+|||.+|+.|||+|++.|.
T Consensus       280 ----------~~~v~i~V~D~G~GI~~e~~~~if~~f~~~~~~~~~~~~~~~~~~G~GLGL~Ivr~i~~~~gG~i~v~s~  349 (407)
T 2q8g_A          280 ----------NEDLTVKMSDRGGGVPLRKIDRLFNYMYSTAPRPRVETSRAVPLAGFGYGLPISRLYAQYFQGDLKLYSL  349 (407)
T ss_dssp             ----------SSEEEEEEEECSCCCCHHHHGGGGCTTTTCCCCCCSSCCSCCCSSCTTCHHHHHHHHHHHTTCEEEEEEE
T ss_pred             ----------CCEEEEEEEecCCCCCHHHHHHHhCccccCCCCCCccccCCCCCCCcCCCHHHHHHHHHHhCCEEEEEEc
Confidence                      115889999999999999999999999998764      2345579999999999999999999999999


Q ss_pred             cCCceEEEEEEeCCC
Q 039716          653 VHCGSTFTFILPYQV  667 (1002)
Q Consensus       653 ~g~GTtF~~~LP~~~  667 (1002)
                      +|.||+|+|+||...
T Consensus       350 ~g~Gt~f~i~LP~~~  364 (407)
T 2q8g_A          350 EGYGTDAVIYIKALS  364 (407)
T ss_dssp             TTTEEEEEEEEESSG
T ss_pred             CCCceEEEEEECCCC
Confidence            999999999999753

>4fpp_A Phosphotransferase; four helix bundle, bergerat fold, CCKA, CTRA, CPDR, bacterial cytoplasme; 2.20A {Caulobacter crescentus} PDB: 4fmt_A

Probab=99.97  E-value=1.9e-31  Score=288.31  Aligned_cols=195  Identities=18%  Similarity=0.224  Sum_probs=144.0

Q ss_pred             HHHHhhhccccHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCeeeEeeecCHHHHHHHH
Q 039716          373 MLATMSHEIRSPLTGVVSMAEILSNTKLDREQRQLLGVMISSGDLVLQLINDILDLSKVESGVMKLEAAKFRPREVVKHV  452 (1002)
Q Consensus       373 fla~iSHELRTPL~~I~g~~elL~~~~l~~~~~~~l~~i~~s~~~L~~LIndlLd~skiesg~~~l~~~~~~l~~li~~v  452 (1002)
                      ++++|||||||||++|.|++++|.+...++...++++.|..+++++..++    +++++..+.. ....++++.++...+
T Consensus        49 las~IaHELrtPL~~I~~~~elL~~~~~~~~~~~~l~~I~~~~~~~~~ll----~~~r~~~~~~-~~~~~~~~~~l~~~~  123 (247)
T 4fpp_A           49 LAARLCHDFISPASAIVSGLDLLEDPSAQDMRDDAMNLIASSARKLADLL----QFTRVAFGAS-ASAENFDSRELEKLA  123 (247)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHCTTCGGGHHHHHHHHHHHHHHHHHHH----HHHHHHTTCC-SSCCCEEHHHHHHHH
T ss_pred             HHhccCHHHhHHHHHHHHHHHHHhccCCchHHHHHHHHHHHHHHHHHHHH----HHHHHhhccc-cccccccHHHHHHHH
Confidence            67889999999999999999999887777777788999999888876655    5555543322 223456666544322


Q ss_pred             HHHHHHHH-hhcceeccccCCCCCeeEEccHHHHHHHHHHHHhhhhhcCCCC-eeEEEEEecCCCCcccchhhhhhhhhh
Q 039716          453 LQTAAASL-QKILMLEGDIADDVPIEVIGDVLRIRQILTNLISNAIKFTPEG-KVGIKLYVVPEPPFAKEGLKQKSKAYQ  530 (1002)
Q Consensus       453 ~~~~~~~~-~k~i~l~~~i~~~~p~~v~gD~~rL~QIL~NLlsNAIKfT~~G-~I~I~v~~~~~~~~~~~~~~~~~~~~~  530 (1002)
                          .... .+.+.+....++.      ..+..+.|++.||+.||+||++.| .|.|.+...                  
T Consensus       124 ----~~~~~~~~i~l~~~~~~~------~~~~~~~qvl~NLl~NA~~a~~~gg~I~v~~~~~------------------  175 (247)
T 4fpp_A          124 ----QGVFAHVRPTLDWQIEPQ------AMNKPSSRAVLNIAQIAASALPAGGVATVKGVAA------------------  175 (247)
T ss_dssp             ----HHHHTTSSSEEEECCCSC------EECHHHHHHHHHHHHHHHTTCTTCCEEEEEEEEE------------------
T ss_pred             ----HHHHHhhhhhccccccch------hhhHHHHHHHHHHHHHHHHhcCCCCeEEEEEEEE------------------
Confidence                2222 2445555444322      135678999999999999999875 666665421                  


Q ss_pred             cchhhhhhhccCCCCCccCCCCCCCCCCCCCCccCCCCCCCCCCCccCCCCCccccccceEEEEEEEecCCC--CCcCcH
Q 039716          531 SATDAVKEEKHQPKSQTASDQNGFHDKKHGEGYQDHKHDDDPGTPVSHGNSMDEDLEATVWIRCDVYDTGIG--IPENAL  608 (1002)
Q Consensus       531 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~i~V~DtGiG--I~~e~l  608 (1002)
                                                                                ...+.|.|.|+|+|  |+++..
T Consensus       176 ----------------------------------------------------------~~~~~i~V~D~G~Gi~i~~~~~  197 (247)
T 4fpp_A          176 ----------------------------------------------------------DGRFSIIADAKGPRARLRPEVL  197 (247)
T ss_dssp             ----------------------------------------------------------TTEEEEEEEEESTTCCCCHHHH
T ss_pred             ----------------------------------------------------------CCEEEEEEEEcCCCCCCCHHHH
Confidence                                                                      11467788888876  677777


Q ss_pred             hhhhhhccCCCccccCcCCCccccHHHHHHHHHHhCCEEEEEeecCCceEEEEEEeC
Q 039716          609 PTLFRKYMQVSADHARKYGGTGLGLAICKQLVELMGGRLTVTSKVHCGSTFTFILPY  665 (1002)
Q Consensus       609 ~~IF~pF~q~~~~~~~~~~GtGLGLaI~k~Lve~~gG~I~v~S~~g~GTtF~~~LP~  665 (1002)
                      +++|++|++.      +.+|+||||+|||+||+.|||+|+|+|.+| ||+|+|+||.
T Consensus       198 ~~~f~~~~~~------~~~G~GLGLai~~~iv~~hGG~i~v~s~~~-G~~f~v~LPA  247 (247)
T 4fpp_A          198 AGLKGEPLAE------GLGGPWVQAAYLNALVRAAGGQIAVEIGED-RASIAAWVPA  247 (247)
T ss_dssp             HHHTTCCCCS------SCHHHHHHHHHHHHHHHHTTCEEEEEEETT-EEEEEEEEEC
T ss_pred             HHhcCCCCCC------CCCCccHHHHHHHHHHHHcCCEEEEEEcCC-EEEEEEEecC
Confidence            7888887643      446999999999999999999999999876 9999999993

>3d36_A Sporulation kinase B; GHKL ATPase, four helix bundle, class I two-component histidine kinase, phosphoprotein; HET: ADP; 2.03A {Geobacillus stearothermophilus}

Probab=99.97  E-value=3.9e-31  Score=283.26  Aligned_cols=211  Identities=26%  Similarity=0.446  Sum_probs=176.4

Q ss_pred             HHHHHHHhhhccccHHHHHHHHHHHHhCCCCC-HHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCeeeEeeecCHHHH
Q 039716          370 AKQMLATMSHEIRSPLTGVVSMAEILSNTKLD-REQRQLLGVMISSGDLVLQLINDILDLSKVESGVMKLEAAKFRPREV  448 (1002)
Q Consensus       370 ~k~fla~iSHELRTPL~~I~g~~elL~~~~l~-~~~~~~l~~i~~s~~~L~~LIndlLd~skiesg~~~l~~~~~~l~~l  448 (1002)
                      .++|++.++|||||||++|.+++++|.....+ ++.+++++.+..++.++..++++++++++.+.+    ...++++..+
T Consensus        14 ~~~~~~~l~Helr~pL~~i~~~~~~l~~~~~~~~~~~~~~~~i~~~~~~l~~~i~~l~~~~~~~~~----~~~~~~l~~~   89 (244)
T 3d36_A           14 VTHLAASISHEIRNPLTAARGFIQLIEEQPLAADKRRQYARIAIEELDRAEAIITDYLTFAKPAPE----TPEKLNVKLE   89 (244)
T ss_dssp             ---CCCCHHHHHHHHHHHHHHHHHHGGGCTTCHHHHHHHHHHHHHHHHHHHHHHHHHHSSCCSSCC----CCEEEEHHHH
T ss_pred             HHHHHHHhhHHhccHHHHHHHHHHHHHhcccChhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccC----CcchhhHHHH
Confidence            35799999999999999999999999876554 456789999999999999999999999998765    3467889999


Q ss_pred             HHHHHHHHHHHHh-hcceeccccCCCCCeeEEccHHHHHHHHHHHHhhhhhcCC-CCeeEEEEEecCCCCcccchhhhhh
Q 039716          449 VKHVLQTAAASLQ-KILMLEGDIADDVPIEVIGDVLRIRQILTNLISNAIKFTP-EGKVGIKLYVVPEPPFAKEGLKQKS  526 (1002)
Q Consensus       449 i~~v~~~~~~~~~-k~i~l~~~i~~~~p~~v~gD~~rL~QIL~NLlsNAIKfT~-~G~I~I~v~~~~~~~~~~~~~~~~~  526 (1002)
                      +..++..+..... +.+.+.....+   ..+.+|+..|.|||.||+.||+||++ .|.|.|.+...              
T Consensus        90 l~~~~~~~~~~~~~~~i~~~~~~~~---~~~~~d~~~l~~il~nLl~NA~~~~~~~~~i~i~~~~~--------------  152 (244)
T 3d36_A           90 IERVIDILRPLANMSCVDIQATLAP---FSVIGEREKFRQCLLNVMKNAIEAMPNGGTLQVYVSID--------------  152 (244)
T ss_dssp             HHHHHHHHHHHHTTTTEEEEEECCC---CEEEECHHHHHHHHHHHHHHHHHTCTTCEEEEEEEEEE--------------
T ss_pred             HHHHHHHHHHHHHhcCeEEeccCCC---ceEEeCHHHHHHHHHHHHHHHHHhccCCCeEEEEEEEe--------------
Confidence            9999888776554 45666555433   46889999999999999999999995 46677766421              


Q ss_pred             hhhhcchhhhhhhccCCCCCccCCCCCCCCCCCCCCccCCCCCCCCCCCccCCCCCccccccceEEEEEEEecCCCCCcC
Q 039716          527 KAYQSATDAVKEEKHQPKSQTASDQNGFHDKKHGEGYQDHKHDDDPGTPVSHGNSMDEDLEATVWIRCDVYDTGIGIPEN  606 (1002)
Q Consensus       527 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~i~V~DtGiGI~~e  606 (1002)
                                                                                    ..++.|.|.|+|+||+++
T Consensus       153 --------------------------------------------------------------~~~~~i~i~D~G~gi~~~  170 (244)
T 3d36_A          153 --------------------------------------------------------------NGRVLIRIADTGVGMTKE  170 (244)
T ss_dssp             --------------------------------------------------------------TTEEEEEEEECSSCCCHH
T ss_pred             --------------------------------------------------------------CCEEEEEEEecCCCCCHH
Confidence                                                                          114789999999999999


Q ss_pred             cHhhhhhhccCCCccccCcCCCccccHHHHHHHHHHhCCEEEEEeecCCceEEEEEEeCCCC
Q 039716          607 ALPTLFRKYMQVSADHARKYGGTGLGLAICKQLVELMGGRLTVTSKVHCGSTFTFILPYQVS  668 (1002)
Q Consensus       607 ~l~~IF~pF~q~~~~~~~~~~GtGLGLaI~k~Lve~~gG~I~v~S~~g~GTtF~~~LP~~~~  668 (1002)
                      .++++|+||++.+     ..+|+||||+||+++++.|||+|+++|.+++||+|+|+||+...
T Consensus       171 ~~~~if~~~~~~~-----~~~g~GlGL~i~~~i~~~~gG~i~~~~~~~~G~~~~i~lP~~~~  227 (244)
T 3d36_A          171 QLERLGEPYFTTK-----GVKGTGLGMMVVYRIIESMNGTIRIESEIHKGTTVSIYLPLASS  227 (244)
T ss_dssp             HHHHTTSTTCCSS-----GGGCCSCHHHHHHHHHHHTTCEEEEEEETTTEEEEEEEEECCC-
T ss_pred             HHHHHhcccccCC-----CCCCcchhHHHHHHHHHHcCCEEEEEecCCCcEEEEEEecCCCC
Confidence            9999999999754     23589999999999999999999999999999999999998654

>1y8o_A [pyruvate dehydrogenase [lipoamide]] kinase isozy; pyruvate dehydrogenase kinase 3, lipoyl-bearing domain; HET: RED ADP; 2.48A {Homo sapiens} SCOP: a.29.5.1 d.122.1.4 PDB: 1y8n_A* 1y8p_A* 2pnr_A* 2q8i_A*

Probab=99.97  E-value=4.3e-31  Score=307.51  Aligned_cols=217  Identities=21%  Similarity=0.192  Sum_probs=163.2

Q ss_pred             HHHHHhhhccccHHH-----HHHHHHHHHhCCCCC----HHHHHHHHHHHHH--HHHHHHHHHHHHHHHhh-hcCCee--
Q 039716          372 QMLATMSHEIRSPLT-----GVVSMAEILSNTKLD----REQRQLLGVMISS--GDLVLQLINDILDLSKV-ESGVMK--  437 (1002)
Q Consensus       372 ~fla~iSHELRTPL~-----~I~g~~elL~~~~l~----~~~~~~l~~i~~s--~~~L~~LIndlLd~ski-esg~~~--  437 (1002)
                      +|+ +++|||||||+     .|.|+++++.....+    ++..++++.+..+  +.+|  +|+++|.+++. +.+...  
T Consensus       120 ~f~-~~~HeLrtPL~~vi~~~i~g~~ell~~~~~~~~~~~~~~~~l~~i~~~~~~~rl--li~~lL~l~~~~~~~~~~~~  196 (419)
T 1y8o_A          120 NFL-QVLIKVRNRHNDVVPTMAQGVIEYKEKFGFDPFISTNIQYFLDRFYTNRISFRM--LINQHTLLFGGDTNPVHPKH  196 (419)
T ss_dssp             HHH-HHHHHHHHHGGGHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHH--HHHHHHHHHSCCSSCSSTTS
T ss_pred             HHH-HHHHHHhcchhhhHHHHHHHHHHHHHHhccCcccHHHHHHHHHHHHHHHHHHHH--HHHHHHHHhcccccCCCCCc
Confidence            465 56699999999     889999987653222    3456678886665  7788  99999776654 333322  


Q ss_pred             --eEeeecCHHHHHHHHHHHHHHHHh------hcceecccc--CCCCCeeEEccHHHHHHHHHHHHhhhhhcCCCC----
Q 039716          438 --LEAAKFRPREVVKHVLQTAAASLQ------KILMLEGDI--ADDVPIEVIGDVLRIRQILTNLISNAIKFTPEG----  503 (1002)
Q Consensus       438 --l~~~~~~l~~li~~v~~~~~~~~~------k~i~l~~~i--~~~~p~~v~gD~~rL~QIL~NLlsNAIKfT~~G----  503 (1002)
                        ....++++.+++++++..+.....      +.+.+....  .+..+..+.+|+.+|.|||.|||.||+||+++|    
T Consensus       197 ~~~~~~~~~l~~li~~~~~~~~~~~~~~~~~~~~i~i~~~~~~~~~~~~~v~~d~~~L~~vl~NLl~NAik~~~~~~~~~  276 (419)
T 1y8o_A          197 IGSIDPTCNVADVVKDAYETAKMLCEQYYLVAPELEVEEFNAKAPDKPIQVVYVPSHLFHMLFELFKNSMRATVELYEDR  276 (419)
T ss_dssp             BTTBEEEEEHHHHHHHHHHHHHHHHHHHHSCCCCEEEEEEETTSTTSCCEEEECHHHHHHHHHHHHHHHHHHHHHHHTTC
T ss_pred             cccccCcCCHHHHHHHHHHHHHHHHHHhcCCCCcEEEEeeecCCCCCCeEEEEcHHHHHHHHHHHHHHHHHHHHhhcccc
Confidence              234789999999999988766543      345554422  123455789999999999999999999999765    


Q ss_pred             -----eeEEEEEecCCCCcccchhhhhhhhhhcchhhhhhhccCCCCCccCCCCCCCCCCCCCCccCCCCCCCCCCCccC
Q 039716          504 -----KVGIKLYVVPEPPFAKEGLKQKSKAYQSATDAVKEEKHQPKSQTASDQNGFHDKKHGEGYQDHKHDDDPGTPVSH  578 (1002)
Q Consensus       504 -----~I~I~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  578 (1002)
                           .|.|.+...                                                                  
T Consensus       277 ~~~~~~I~I~~~~~------------------------------------------------------------------  290 (419)
T 1y8o_A          277 KEGYPAVKTLVTLG------------------------------------------------------------------  290 (419)
T ss_dssp             SSCCCCEEEEEEEC------------------------------------------------------------------
T ss_pred             CCCCCCEEEEEEeC------------------------------------------------------------------
Confidence                 466655321                                                                  


Q ss_pred             CCCCccccccceEEEEEEEecCCCCCcCcHhhhhhhccCCCcc------ccCcCCCccccHHHHHHHHHHhCCEEEEEee
Q 039716          579 GNSMDEDLEATVWIRCDVYDTGIGIPENALPTLFRKYMQVSAD------HARKYGGTGLGLAICKQLVELMGGRLTVTSK  652 (1002)
Q Consensus       579 ~~~~~~~~~~~~~l~i~V~DtGiGI~~e~l~~IF~pF~q~~~~------~~~~~~GtGLGLaI~k~Lve~~gG~I~v~S~  652 (1002)
                                ..++.|.|.|+|+|||++.+++||+|||+++..      ..+..+|+||||+|||+||+.|||+|+++|.
T Consensus       291 ----------~~~v~I~V~D~G~GI~~e~l~~iF~~f~~~~~~~~~~~~~~~~~~G~GLGL~I~k~iv~~~gG~I~v~s~  360 (419)
T 1y8o_A          291 ----------KEDLSIKISDLGGGVPLRKIDRLFNYMYSTAPRPSLEPTRAAPLAGFGYGLPISRLYARYFQGDLKLYSM  360 (419)
T ss_dssp             ----------SSEEEEEEEECSCCCCHHHHGGGGCTTTC-------------CC--CTTHHHHHHHHHHHTTCEEEEEEE
T ss_pred             ----------CCEEEEEEEECCCCCCHHHHHHHhCcccccCCCCCccccCCCCcCCeecCHHHHHHHHHHhCCEEEEEec
Confidence                      115889999999999999999999999998764      3445679999999999999999999999999


Q ss_pred             cCCceEEEEEEeCCC
Q 039716          653 VHCGSTFTFILPYQV  667 (1002)
Q Consensus       653 ~g~GTtF~~~LP~~~  667 (1002)
                      +|.||+|+|+||...
T Consensus       361 ~g~Gt~f~i~LP~~~  375 (419)
T 1y8o_A          361 EGVGTDAVIYLKALS  375 (419)
T ss_dssp             TTTEEEEEEEEESCG
T ss_pred             CCCCEEEEEEecCCC
Confidence            999999999999754

>3to5_A CHEY homolog; alpha(5)beta(5), chemotaxis, FLIM, phosphorylation, motor AC signaling protein; 1.65A {Vibrio cholerae}

Probab=99.93  E-value=1e-25  Score=219.51  Aligned_cols=120  Identities=29%  Similarity=0.517  Sum_probs=112.8

Q ss_pred             CCCeEEEEecCHHHHHHHHHHHHhcCCe-EEEEcCHHHHHHHHHcCCCcEEEEcCCCCCCCHHHHHHHHhccccCCCchh
Q 039716          858 PKPKILLVEDNKINVMVAKSMMKQLGHS-IDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDA  936 (1002)
Q Consensus       858 ~~~~ILiVeDn~~n~~~l~~~L~~~g~~-v~~a~~G~eAl~~~~~~~~DlIlmDi~MP~mdG~e~~~~IR~~~~~~~~~~  936 (1002)
                      .+.|||||||++.++.+++.+|+..||. |..|.||.+|++.++...|||||+|++||+|||+++++.||+.+       
T Consensus        11 k~~rILiVDD~~~~r~~l~~~L~~~G~~~v~~a~~g~~al~~~~~~~~DlillD~~MP~mdG~el~~~ir~~~-------   83 (134)
T 3to5_A           11 KNMKILIVDDFSTMRRIVKNLLRDLGFNNTQEADDGLTALPMLKKGDFDFVVTDWNMPGMQGIDLLKNIRADE-------   83 (134)
T ss_dssp             TTCCEEEECSCHHHHHHHHHHHHHTTCCCEEEESSHHHHHHHHHHHCCSEEEEESCCSSSCHHHHHHHHHHST-------
T ss_pred             CCCEEEEEeCCHHHHHHHHHHHHHcCCcEEEEECCHHHHHHHHHhCCCCEEEEcCCCCCCCHHHHHHHHHhCC-------
Confidence            4568999999999999999999999986 78899999999999999999999999999999999999999743       


Q ss_pred             hhhhhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHHhhc
Q 039716          937 AAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQYF 1001 (1002)
Q Consensus       937 ~~~~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~~l 1001 (1002)
                                       ..+++|||++||+...+...+|+++|+++||+|||+.++|...|++++
T Consensus        84 -----------------~~~~ipvI~lTa~~~~~~~~~~~~~Ga~~yl~KP~~~~~L~~~i~~~l  131 (134)
T 3to5_A           84 -----------------ELKHLPVLMITAEAKREQIIEAAQAGVNGYIVKPFTAATLKEKLDKIF  131 (134)
T ss_dssp             -----------------TTTTCCEEEEESSCCHHHHHHHHHTTCCEEEESSCCHHHHHHHHHHHC
T ss_pred             -----------------CCCCCeEEEEECCCCHHHHHHHHHCCCCEEEECCCCHHHHHHHHHHHH
Confidence                             346799999999999999999999999999999999999999999876

>1b3q_A Protein (chemotaxis protein CHEA); histine kinase, signal transduction, multi-domai protein, transferase; 2.60A {Thermotoga maritima} SCOP: a.30.2.1 b.40.7.1 d.122.1.3 PDB: 2ch4_A* 3ur1_A

Probab=99.93  E-value=7.4e-26  Score=259.65  Aligned_cols=197  Identities=17%  Similarity=0.177  Sum_probs=145.0

Q ss_pred             HHHHHhhhccccHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCeeeEeeecCHHHHHHH
Q 039716          372 QMLATMSHEIRSPLTGVVSMAEILSNTKLDREQRQLLGVMISSGDLVLQLINDILDLSKVESGVMKLEAAKFRPREVVKH  451 (1002)
Q Consensus       372 ~fla~iSHELRTPL~~I~g~~elL~~~~l~~~~~~~l~~i~~s~~~L~~LIndlLd~skiesg~~~l~~~~~~l~~li~~  451 (1002)
                      +|+++++||||||++.|.++++.+..           +.+..++++|..+++++++++.-      +  ..+++..++..
T Consensus        12 d~l~~~~~el~~~~~~l~~~~~~~~~-----------~~i~~~~~~l~~l~~~l~~~~~~------~--~~~~~~~~~~~   72 (379)
T 1b3q_A           12 DNLMDLMGELVIARSRILETLKKYNI-----------KELDESLSHLSRITLDLQNVVMK------I--RMVPISFVFNR   72 (379)
T ss_dssp             HHHHHHHHHHHHHHHHHHHTTSSCCC-----------HHHHHHHHHHHHHHHHHHHHHHH------H--HEEETHHHHTT
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhhhH-----------HHHHHHHHHHHHHHHHHHHHHHH------c--ceecHHHHHHH
Confidence            79999999999999999998776543           46788899999999999999742      1  23445677766


Q ss_pred             HHHHHHHHHh-hcceeccccCCCCCeeEEccHH---HHHHHHHHHHhhhhhcC-------------CCCeeEEEEEecCC
Q 039716          452 VLQTAAASLQ-KILMLEGDIADDVPIEVIGDVL---RIRQILTNLISNAIKFT-------------PEGKVGIKLYVVPE  514 (1002)
Q Consensus       452 v~~~~~~~~~-k~i~l~~~i~~~~p~~v~gD~~---rL~QIL~NLlsNAIKfT-------------~~G~I~I~v~~~~~  514 (1002)
                      +...+..... .+..+...+....   +..|+.   ++.|+|.||+.||+||+             +.|.|.|+++..  
T Consensus        73 ~~~~~~~~~~~~~~~v~l~~~~~~---~~~d~~~~~~l~~~l~nLl~NAi~h~~e~~~~r~~~gk~~~g~I~i~~~~~--  147 (379)
T 1b3q_A           73 FPRMVRDLAKKMNKEVNFIMRGED---TELDRTFVEEIGEPLLHLLRNAIDHGIEPKEERIAKGKPPIGTLILSARHE--  147 (379)
T ss_dssp             HHHHHHHHHHHTTCCEEEEEECTT---CEEEHHHHHHHHHHHHHHHHHHHHHTSCCHHHHHHTTCCSSEEEEEEEEEE--
T ss_pred             HHHHHHHHHHHhCCeEEEEEcCCC---eeecHHHHHHHHHHHHHHHHHHHHhcCCCHHHHHhcCCCCCcEEEEEEEEe--
Confidence            6665554432 2333333333221   345774   56666999999999996             457777766421  


Q ss_pred             CCcccchhhhhhhhhhcchhhhhhhccCCCCCccCCCCCCCCCCCCCCccCCCCCCCCCCCccCCCCCccccccceEEEE
Q 039716          515 PPFAKEGLKQKSKAYQSATDAVKEEKHQPKSQTASDQNGFHDKKHGEGYQDHKHDDDPGTPVSHGNSMDEDLEATVWIRC  594 (1002)
Q Consensus       515 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~i  594 (1002)
                                                                                                ..++.|
T Consensus       148 --------------------------------------------------------------------------~~~v~i  153 (379)
T 1b3q_A          148 --------------------------------------------------------------------------GNNVVI  153 (379)
T ss_dssp             --------------------------------------------------------------------------TTEEEE
T ss_pred             --------------------------------------------------------------------------CCEEEE
Confidence                                                                                      115889


Q ss_pred             EEEecCCCCCcCcH------------------------hhhhhhccCCCccccCcCCCccccHHHHHHHHHHhCCEEEEE
Q 039716          595 DVYDTGIGIPENAL------------------------PTLFRKYMQVSADHARKYGGTGLGLAICKQLVELMGGRLTVT  650 (1002)
Q Consensus       595 ~V~DtGiGI~~e~l------------------------~~IF~pF~q~~~~~~~~~~GtGLGLaI~k~Lve~~gG~I~v~  650 (1002)
                      +|.|+|+||+++.+                        ++||+|||++... .+..+|+||||+|||++++.|||+|+++
T Consensus       154 ~V~D~G~Gi~~~~~~~~a~~~gl~~~~~~~~~~~~~~~~~iF~p~fst~~~-~~~~~G~GlGL~iv~~~v~~~gG~i~v~  232 (379)
T 1b3q_A          154 EVEDDGRGIDKEKIIRKAIEKGLIDESKAATLSDQEILNFLFVPGFSTKEK-VSEVSGRGVGMDVVKNVVESLNGSMGIE  232 (379)
T ss_dssp             EEEECSCCCCHHHHHHHHHHSSSCCSTTTTTSCTHHHHSGGGSTTCC------------CCCSHHHHHHHHHTTCEEEEE
T ss_pred             EEEECCCCCCHHHHHHHHHHcCCCChhhhhcCCHHHHHHHhcCCCCccCCc-cCCCCCccccHHHHHHHHHHCCCEEEEE
Confidence            99999999999987                        8899999987643 3356799999999999999999999999


Q ss_pred             eecCCceEEEEEEeCCC
Q 039716          651 SKVHCGSTFTFILPYQV  667 (1002)
Q Consensus       651 S~~g~GTtF~~~LP~~~  667 (1002)
                      |.+|+||+|+|+||+..
T Consensus       233 s~~g~Gt~f~i~lPl~~  249 (379)
T 1b3q_A          233 SEKDKGTKVTIRLPLTL  249 (379)
T ss_dssp             EETTTEEEEEEEEESSC
T ss_pred             EcCCCCeEEEeccCCcc
Confidence            99999999999999864

>3ehh_A Sensor kinase (YOCF protein); four-helix bundle, GHL ATPase domain, transferase; HET: MSE ADP; 2.10A {Bacillus subtilis} PDB: 3ehj_A* 3gie_A* 3gif_A* 3gig_A* 3ehf_A*

Probab=99.91  E-value=1.6e-23  Score=220.61  Aligned_cols=186  Identities=13%  Similarity=0.133  Sum_probs=138.8

Q ss_pred             HHHHHHhhhccccHHHHHHHHHHHHhCC--CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCeeeEeeecCHHHH
Q 039716          371 KQMLATMSHEIRSPLTGVVSMAEILSNT--KLDREQRQLLGVMISSGDLVLQLINDILDLSKVESGVMKLEAAKFRPREV  448 (1002)
Q Consensus       371 k~fla~iSHELRTPL~~I~g~~elL~~~--~l~~~~~~~l~~i~~s~~~L~~LIndlLd~skiesg~~~l~~~~~~l~~l  448 (1002)
                      .++++.+.|++++||++|.++++++...  ..++..++.+..+...+.+++..+.+++...           .+.++.++
T Consensus        29 ~~la~~l~~~l~~~L~~i~~~~~~~~~~~~~~~~~~~~~l~~i~~~~~~~~~~~r~~~~~~-----------~~~~l~~~   97 (218)
T 3ehh_A           29 QRMARDLVDTLGQKLSLMGLKSDLARKLIYKDPEQAARELKSVQQTARTSLNEVRKIVSSM-----------KGIRLKDE   97 (218)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHHHHHHHHHTTT-----------CCCCHHHH
T ss_pred             HHHHHHhhhhHHHHHHHHHHHHHHHHHhhcCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHc-----------CCcCHHHH
Confidence            4688899999999999999999987542  2334466788888888888888888776432           24567777


Q ss_pred             HHHHHHHHHHHHhhcceeccccCCCCCeeEEccHHHHHHHHHHHHhhhhhcCCCCeeEEEEEecCCCCcccchhhhhhhh
Q 039716          449 VKHVLQTAAASLQKILMLEGDIADDVPIEVIGDVLRIRQILTNLISNAIKFTPEGKVGIKLYVVPEPPFAKEGLKQKSKA  528 (1002)
Q Consensus       449 i~~v~~~~~~~~~k~i~l~~~i~~~~p~~v~gD~~rL~QIL~NLlsNAIKfT~~G~I~I~v~~~~~~~~~~~~~~~~~~~  528 (1002)
                      +..+...+.   ..++.+........+.....+...|.+|+.||++||+||++.|.|.|.+...                
T Consensus        98 l~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~l~~il~nll~Na~k~~~~~~i~i~~~~~----------------  158 (218)
T 3ehh_A           98 LINIKQILE---AADIMFIYEEEKWPENISLLNENILSMCLKEAVTNVVKHSQAKTCRVDIQQL----------------  158 (218)
T ss_dssp             HHHHHHHHH---HTTCEEECCCCCCCSCCCHHHHHHHHHHHHHHHHHHHHHTCCSEEEEEEEEE----------------
T ss_pred             HHHHHHHHH---hcCCEEEEeCCCCCCCCCHHHHHHHHHHHHHHHHHHHHhCCCCEEEEEEEEe----------------
Confidence            776655543   2455555555544333345688899999999999999999888887776431                


Q ss_pred             hhcchhhhhhhccCCCCCccCCCCCCCCCCCCCCccCCCCCCCCCCCccCCCCCccccccceEEEEEEEecCCCCCcCcH
Q 039716          529 YQSATDAVKEEKHQPKSQTASDQNGFHDKKHGEGYQDHKHDDDPGTPVSHGNSMDEDLEATVWIRCDVYDTGIGIPENAL  608 (1002)
Q Consensus       529 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~i~V~DtGiGI~~e~l  608 (1002)
                                                                                  ..++.|+|.|+|+||+++..
T Consensus       159 ------------------------------------------------------------~~~~~i~V~D~G~Gi~~~~~  178 (218)
T 3ehh_A          159 ------------------------------------------------------------WKEVVITVSDDGTFKGEENS  178 (218)
T ss_dssp             ------------------------------------------------------------TTEEEEEEEESSCCCC----
T ss_pred             ------------------------------------------------------------CCEEEEEEEECCcCCCCCCC
Confidence                                                                        11488999999999999865


Q ss_pred             hhhhhhccCCCccccCcCCCccccHHHHHHHHHHhCCEEEEEeecCCceEEEEEEeCC
Q 039716          609 PTLFRKYMQVSADHARKYGGTGLGLAICKQLVELMGGRLTVTSKVHCGSTFTFILPYQ  666 (1002)
Q Consensus       609 ~~IF~pF~q~~~~~~~~~~GtGLGLaI~k~Lve~~gG~I~v~S~~g~GTtF~~~LP~~  666 (1002)
                                        +|+||||+||+++|+.|||+|++.|.+  ||+|+|+||+.
T Consensus       179 ------------------~g~GlGL~~~~~~v~~~gG~i~~~s~~--Gt~~~i~lP~~  216 (218)
T 3ehh_A          179 ------------------FSKGHGLLGMRERLEFANGSLHIDTEN--GTKLTMAIPNN  216 (218)
T ss_dssp             ----------------------CHHHHHHHHHHHTTCEEEEECSS--SEEEEEEEEC-
T ss_pred             ------------------CCCCCCHHHHHHHHHHcCCEEEEeCCC--CeEEEEEEecC
Confidence                              489999999999999999999999998  99999999974

>3mm4_A Histidine kinase homolog; receiver domain, CKI1, cytokinin signaling, ROS fold, CHEY-like, transferase; 2.00A {Arabidopsis thaliana} PDB: 3mmn_A

Probab=99.91  E-value=3.5e-24  Score=224.73  Aligned_cols=120  Identities=36%  Similarity=0.540  Sum_probs=108.0

Q ss_pred             CCCeEEEEecCHHHHHHHHHHHHhcCC-eEEEEcCHHHHHHHHHcC-------------CCcEEEEcCCCCCCCHHHHHH
Q 039716          858 PKPKILLVEDNKINVMVAKSMMKQLGH-SIDVVNNGVEAVHAVQCQ-------------NYDLILMDVCMPVMDGLKATR  923 (1002)
Q Consensus       858 ~~~~ILiVeDn~~n~~~l~~~L~~~g~-~v~~a~~G~eAl~~~~~~-------------~~DlIlmDi~MP~mdG~e~~~  923 (1002)
                      .+.+||||||++.++..++.+|+..|| .|..|.++.+|++.+...             .|||||+|+.||+|||+++++
T Consensus        60 ~~~~ILiVdDd~~~~~~l~~~L~~~g~~~v~~a~~~~eal~~l~~~~~~~~~~~~~~~~~~dlillD~~lp~~~G~el~~  139 (206)
T 3mm4_A           60 RGKRVLVVDDNFISRKVATGKLKKMGVSEVEQCDSGKEALRLVTEGLTQREEQGSVDKLPFDYIFMDCQMPEMDGYEATR  139 (206)
T ss_dssp             TTCEEEEECSCHHHHHHHHHHHHHTTCSEEEEESSHHHHHHHHHHHHHHHHHHTCSSCCSCSEEEEESCCSSSCHHHHHH
T ss_pred             CCCEEEEEeCCHHHHHHHHHHHHHcCCCeeeeeCCHHHHHHHHHhhcccccccccccCCCCCEEEEcCCCCCCCHHHHHH
Confidence            356899999999999999999999998 899999999999999875             899999999999999999999


Q ss_pred             HHhccccCCCchhhhhhhhcccCCCCCCCCCCCCccEEEEcCCC-CHHHHHHHHHcCCCEEEeCCCChHHHHHHHHhhc
Q 039716          924 LIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANA-LSESAEECFANGMDSFVSKPVTFQKLKECLEQYF 1001 (1002)
Q Consensus       924 ~IR~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipIIalTa~~-~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~~l 1001 (1002)
                      .||+....                      ..+.+|||++|++. ..+...+|+++|+++||.||++  +|...|++++
T Consensus       140 ~lr~~~~~----------------------~~~~~piI~ls~~~~~~~~~~~~~~~Ga~~~l~KP~~--~L~~~i~~~l  194 (206)
T 3mm4_A          140 EIRKVEKS----------------------YGVRTPIIAVSGHDPGSEEARETIQAGMDAFLDKSLN--QLANVIREIE  194 (206)
T ss_dssp             HHHHHHHT----------------------TTCCCCEEEEESSCCCHHHHHHHHHHTCSEEEETTCT--THHHHHHHHC
T ss_pred             HHHhhhhh----------------------cCCCCcEEEEECCCCcHHHHHHHHhCCCCEEEcCcHH--HHHHHHHHHH
Confidence            99975321                      13679999999998 7888999999999999999999  8998888765

>1ysr_A Sensor-type histidine kinase PRRB; ATP-binding domain, structural genomics, mycobacterium tuberculosis structural proteomics project; 1.78A {Mycobacterium tuberculosis} SCOP: d.122.1.3 PDB: 1ys3_A

Probab=99.90  E-value=2.2e-23  Score=206.58  Aligned_cols=146  Identities=21%  Similarity=0.293  Sum_probs=113.5

Q ss_pred             EeeecCHHHHHHHHHHHHHHHHhhcceeccccCCCCCeeEEccHHHHHHHHHHHHhhhhhcCCCCeeEEEEEecCCCCcc
Q 039716          439 EAAKFRPREVVKHVLQTAAASLQKILMLEGDIADDVPIEVIGDVLRIRQILTNLISNAIKFTPEGKVGIKLYVVPEPPFA  518 (1002)
Q Consensus       439 ~~~~~~l~~li~~v~~~~~~~~~k~i~l~~~i~~~~p~~v~gD~~rL~QIL~NLlsNAIKfT~~G~I~I~v~~~~~~~~~  518 (1002)
                      +..++++.+++++++..+.... +.+.+.....  .+..+.+|+.+|.|||.|||.||+||++.|.|.|.+...      
T Consensus         4 ~~~~~~l~~~~~~~~~~~~~~~-~~~~i~~~~~--~~~~~~~d~~~l~~il~nLl~NA~~~~~~~~I~i~~~~~------   74 (150)
T 1ysr_A            4 DHVPVDITDLLDRAAHDAARIY-PDLDVSLVPS--PTCIIVGLPAGLRLAVDNAIANAVKHGGATLVQLSAVSS------   74 (150)
T ss_dssp             CCEEEEHHHHHHHHHHHHHHHS-TTCEEEECSC--CCCEEEECHHHHHHHHHHHHHHHHHTTCCSEEEEEEEEE------
T ss_pred             cccccCHHHHHHHHHHHHHHhc-cCCceEEccC--CCceEecCHHHHHHHHHHHHHHHHhcCCCcEEEEEEEec------
Confidence            3467899999999998876544 3344444433  345789999999999999999999999999777766421      


Q ss_pred             cchhhhhhhhhhcchhhhhhhccCCCCCccCCCCCCCCCCCCCCccCCCCCCCCCCCccCCCCCccccccceEEEEEEEe
Q 039716          519 KEGLKQKSKAYQSATDAVKEEKHQPKSQTASDQNGFHDKKHGEGYQDHKHDDDPGTPVSHGNSMDEDLEATVWIRCDVYD  598 (1002)
Q Consensus       519 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~i~V~D  598 (1002)
                                                                                            ...+.|.|.|
T Consensus        75 ----------------------------------------------------------------------~~~~~i~v~D   84 (150)
T 1ysr_A           75 ----------------------------------------------------------------------RAGVEIAIDD   84 (150)
T ss_dssp             ----------------------------------------------------------------------TTEEEEEEEE
T ss_pred             ----------------------------------------------------------------------CCEEEEEEEE
Confidence                                                                                  1147899999


Q ss_pred             cCCCCCcCcHhhhhhhccCCCccccCcCCCccccHHHHHHHHHHhCCEEEEEeecCCceEEEEEEeCC
Q 039716          599 TGIGIPENALPTLFRKYMQVSADHARKYGGTGLGLAICKQLVELMGGRLTVTSKVHCGSTFTFILPYQ  666 (1002)
Q Consensus       599 tGiGI~~e~l~~IF~pF~q~~~~~~~~~~GtGLGLaI~k~Lve~~gG~I~v~S~~g~GTtF~~~LP~~  666 (1002)
                      +|+||+++.++++|+||++.+..   +.+|+||||+||+++++.|||+|+++|.+++||+|+|.||..
T Consensus        85 ~G~gi~~~~~~~if~~f~~~~~~---~~~g~GlGL~i~~~~~~~~gG~i~~~~~~~~G~~~~i~lP~~  149 (150)
T 1ysr_A           85 NGSGVPEGERQVVFERFSRGSTA---SHSGSGLGLALVAQQAQLHGGTASLENSPLGGARLVLRLPGP  149 (150)
T ss_dssp             SSSCCCGGGHHHHHTSCC--------------CCCHHHHHHHHHTTCEEEEEECTTSSEEEEEEEECC
T ss_pred             CCCCCCHHHHHHHhcccccCCCC---CCCCCCcCHHHHHHHHHHcCCEEEEeecCCCCEEEEEEEeCC
Confidence            99999999999999999986432   346999999999999999999999999999999999999963

>1id0_A PHOQ histidine kinase; PHOQ/PHOP, signal transduction, transferase; HET: ANP; 1.60A {Escherichia coli} SCOP: d.122.1.3 PDB: 3cgz_A 3cgy_A

Probab=99.89  E-value=1.7e-22  Score=200.25  Aligned_cols=144  Identities=21%  Similarity=0.306  Sum_probs=121.2

Q ss_pred             eecCHHHHHHHHHHHHHHHHh-hcceeccccCCCCCeeEEccHHHHHHHHHHHHhhhhhcCCCCeeEEEEEecCCCCccc
Q 039716          441 AKFRPREVVKHVLQTAAASLQ-KILMLEGDIADDVPIEVIGDVLRIRQILTNLISNAIKFTPEGKVGIKLYVVPEPPFAK  519 (1002)
Q Consensus       441 ~~~~l~~li~~v~~~~~~~~~-k~i~l~~~i~~~~p~~v~gD~~rL~QIL~NLlsNAIKfT~~G~I~I~v~~~~~~~~~~  519 (1002)
                      +++++.+++++++..+...+. +.+.+...++...  .+.+|+..|.|||.|||.||+||++. .|.|.+...       
T Consensus         2 e~~~l~~~l~~~~~~~~~~~~~~~i~~~~~~~~~~--~~~~d~~~l~~il~nLl~NAi~~~~~-~i~i~~~~~-------   71 (152)
T 1id0_A            2 ELHPVAPLLDNLTSALNKVYQRKGVNISLDISPEI--SFVGEQNDFVEVMGNVLDNACKYCLE-FVEISARQT-------   71 (152)
T ss_dssp             CEEEHHHHHHHHHHHHHHHTTTTTCEEEEECCTTC--EEESCHHHHHHHHHHHHHHHHHHCSS-EEEEEEEEC-------
T ss_pred             CcccHHHHHHHHHHHHHHHHHhCCcEEEEEcCCCc--eEeeCHHHHHHHHHHHHHHHHHhCcC-eEEEEEEec-------
Confidence            468899999999998877664 5677777665543  58899999999999999999999976 666655321       


Q ss_pred             chhhhhhhhhhcchhhhhhhccCCCCCccCCCCCCCCCCCCCCccCCCCCCCCCCCccCCCCCccccccceEEEEEEEec
Q 039716          520 EGLKQKSKAYQSATDAVKEEKHQPKSQTASDQNGFHDKKHGEGYQDHKHDDDPGTPVSHGNSMDEDLEATVWIRCDVYDT  599 (1002)
Q Consensus       520 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~i~V~Dt  599 (1002)
                                                                                           ..++.|.|.|+
T Consensus        72 ---------------------------------------------------------------------~~~~~i~i~D~   82 (152)
T 1id0_A           72 ---------------------------------------------------------------------DEHLYIVVEDD   82 (152)
T ss_dssp             ---------------------------------------------------------------------SSCEEEEEEES
T ss_pred             ---------------------------------------------------------------------CCEEEEEEEeC
Confidence                                                                                 11378999999


Q ss_pred             CCCCCcCcHhhhhhhccCCCccccCcCCCccccHHHHHHHHHHhCCEEEEEeecCCceEEEEEEeCCC
Q 039716          600 GIGIPENALPTLFRKYMQVSADHARKYGGTGLGLAICKQLVELMGGRLTVTSKVHCGSTFTFILPYQV  667 (1002)
Q Consensus       600 GiGI~~e~l~~IF~pF~q~~~~~~~~~~GtGLGLaI~k~Lve~~gG~I~v~S~~g~GTtF~~~LP~~~  667 (1002)
                      |+||+++.++++|+||++.+..    .+|+||||+||+++++.|||+|+++|.++.||+|+|+||...
T Consensus        83 G~gi~~~~~~~~f~~~~~~~~~----~~g~GlGL~i~~~~~~~~gG~i~~~~~~~~G~~~~i~lP~~~  146 (152)
T 1id0_A           83 GPGIPLSKREVIFDRGQRVDTL----RPGQGVGLAVAREITEQYEGKIVAGESMLGGARMEVIFGRQH  146 (152)
T ss_dssp             SSCCCGGGTTGGGSCCCCTTCC----CTTCCSCHHHHHHHHHHTTCEEEEEECTTSSEEEEEEECCCC
T ss_pred             CCCcCHHHHHHHhccceeccCC----CCCcccCHHHHHHHHHHcCCEEEEEeCCCCcEEEEEEEeccc
Confidence            9999999999999999986542    369999999999999999999999999999999999999864

>1bxd_A ENVZ(290-450), protein (osmolarity sensor protein (ENVZ)); histidine kinase, osmosensor, His-Asp phosphorelay system, signal transduction; HET: ANP; NMR {Escherichia coli BL21} SCOP: d.122.1.3

Probab=99.89  E-value=9.1e-23  Score=204.73  Aligned_cols=148  Identities=24%  Similarity=0.329  Sum_probs=120.4

Q ss_pred             eEeeecCHHHHHHHHHHHHHHHHhhcceeccccCCCCCeeEEccHHHHHHHHHHHHhhhhhcCCCCeeEEEEEecCCCCc
Q 039716          438 LEAAKFRPREVVKHVLQTAAASLQKILMLEGDIADDVPIEVIGDVLRIRQILTNLISNAIKFTPEGKVGIKLYVVPEPPF  517 (1002)
Q Consensus       438 l~~~~~~l~~li~~v~~~~~~~~~k~i~l~~~i~~~~p~~v~gD~~rL~QIL~NLlsNAIKfT~~G~I~I~v~~~~~~~~  517 (1002)
                      +...++++.+++++++..+..   ....+...+.. .+..+.+|+.+|.|||.|||.||+||+ .|.|.|.+...     
T Consensus         5 ~~~~~~~l~~~~~~~~~~~~~---~~~~i~~~~~~-~~~~v~~d~~~l~~il~nll~NAik~~-~~~I~i~~~~~-----   74 (161)
T 1bxd_A            5 MPMEMADLNAVLGEVIAAESG---YEREIETALYP-GSIEVKMHPLSIKRAVANMVVNAARYG-NGWIKVSSGTE-----   74 (161)
T ss_dssp             CCSEEECHHHHHHHHHHHHCS---SSCCEEEECCS-SCCCEEECHHHHHHHHHHHHHHHHTTC-CSCEEEEEEEE-----
T ss_pred             ccccccCHHHHHHHHHHHhhh---hcceEEEEecC-CCceEEECHHHHHHHHHHHHHHHHhhc-CCeEEEEEEEc-----
Confidence            455789999999998877432   23333333322 234688999999999999999999999 78888776421     


Q ss_pred             ccchhhhhhhhhhcchhhhhhhccCCCCCccCCCCCCCCCCCCCCccCCCCCCCCCCCccCCCCCccccccceEEEEEEE
Q 039716          518 AKEGLKQKSKAYQSATDAVKEEKHQPKSQTASDQNGFHDKKHGEGYQDHKHDDDPGTPVSHGNSMDEDLEATVWIRCDVY  597 (1002)
Q Consensus       518 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~i~V~  597 (1002)
                                                                                             ..++.|.|.
T Consensus        75 -----------------------------------------------------------------------~~~~~i~i~   83 (161)
T 1bxd_A           75 -----------------------------------------------------------------------PNRAWFQVE   83 (161)
T ss_dssp             -----------------------------------------------------------------------TTEEEEEEE
T ss_pred             -----------------------------------------------------------------------CCEEEEEEE
Confidence                                                                                   114789999


Q ss_pred             ecCCCCCcCcHhhhhhhccCCCccccCcCCCccccHHHHHHHHHHhCCEEEEEeecCCceEEEEEEeCCCC
Q 039716          598 DTGIGIPENALPTLFRKYMQVSADHARKYGGTGLGLAICKQLVELMGGRLTVTSKVHCGSTFTFILPYQVS  668 (1002)
Q Consensus       598 DtGiGI~~e~l~~IF~pF~q~~~~~~~~~~GtGLGLaI~k~Lve~~gG~I~v~S~~g~GTtF~~~LP~~~~  668 (1002)
                      |+|+||+++.++++|+||++.+..  +..+|+||||+||+++++.|||+|+++|.++.||+|+|.||+...
T Consensus        84 D~G~gi~~~~~~~~f~~f~~~~~~--~~~~g~GlGL~i~~~~~~~~gG~i~~~~~~~~G~~~~i~lP~~~~  152 (161)
T 1bxd_A           84 DDGPGIAPEQRKHLFQPFVRGDSA--RTISGTGLGLAIVQRIVDNHNGMLELGTSERGGLSIRAWLPVPVT  152 (161)
T ss_dssp             EESSCSCTTGGGCSSCCCCCCSCC--CCCCCCSCCCCTTHHHHHHHTSEEEEEEETTTEEEEEEEECCCSC
T ss_pred             eCCCCCCHHHHHHhCCCceeCCCC--CCCCCcccCHHHHHHHHHHcCCEEEEEECCCCeEEEEEEEeCCcc
Confidence            999999999999999999987653  334699999999999999999999999999999999999998643

>3sl2_A Sensor histidine kinase YYCG; ATP binding, intact ATP, bergerat fold, TR; HET: ATP; 1.61A {Bacillus subtilis}

Probab=99.88  E-value=1.6e-22  Score=206.43  Aligned_cols=152  Identities=33%  Similarity=0.529  Sum_probs=121.0

Q ss_pred             ecCHHHHHHHHHHHHHHHHhhcceeccccCCCCCeeEEccHHHHHHHHHHHHhhhhhcCCC-CeeEEEEEecCCCCcccc
Q 039716          442 KFRPREVVKHVLQTAAASLQKILMLEGDIADDVPIEVIGDVLRIRQILTNLISNAIKFTPE-GKVGIKLYVVPEPPFAKE  520 (1002)
Q Consensus       442 ~~~l~~li~~v~~~~~~~~~k~i~l~~~i~~~~p~~v~gD~~rL~QIL~NLlsNAIKfT~~-G~I~I~v~~~~~~~~~~~  520 (1002)
                      +|++.++++.++..+.....+.+.+...+... +..+.+|+..|.+||.|||.||+||++. |.|.|.+.....      
T Consensus         2 ~v~l~~~l~~~~~~~~~~~~~~i~~~~~~~~~-~~~~~~d~~~l~~il~nLl~NAi~~~~~~~~i~I~i~~~~~------   74 (177)
T 3sl2_A            2 WIQIVRFMSLIIDRFEMTKEQHVEFIRNLPDR-DLYVEIDQDKITQVLDNIISNALKYSPEGGHVTFSIDVNEE------   74 (177)
T ss_dssp             EEEHHHHHHHHHHHHHTSSCC--CEEEECCSS-CCEEESCHHHHHHHHHHHHHHHHHTCCTTCCEEEEEEEETT------
T ss_pred             eeeHHHHHHHHHHHHHHHHhcCcEEEEecCCC-CcEEEeCHHHHHHHHHHHHHHHHHhCCCCCeEEEEEEEccC------
Confidence            57889999999888776644566666666543 4568999999999999999999999965 666666643211      


Q ss_pred             hhhhhhhhhhcchhhhhhhccCCCCCccCCCCCCCCCCCCCCccCCCCCCCCCCCccCCCCCccccccceEEEEEEEecC
Q 039716          521 GLKQKSKAYQSATDAVKEEKHQPKSQTASDQNGFHDKKHGEGYQDHKHDDDPGTPVSHGNSMDEDLEATVWIRCDVYDTG  600 (1002)
Q Consensus       521 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~i~V~DtG  600 (1002)
                                                                                          ..++.|.|.|+|
T Consensus        75 --------------------------------------------------------------------~~~~~i~V~D~G   86 (177)
T 3sl2_A           75 --------------------------------------------------------------------EELLYISVKDEG   86 (177)
T ss_dssp             --------------------------------------------------------------------TTEEEEEEECCS
T ss_pred             --------------------------------------------------------------------CCEEEEEEEECC
Confidence                                                                                114889999999


Q ss_pred             CCCCcCcHhhhhhhccCCCccccCcCCCccccHHHHHHHHHHhCCEEEEEeecCCceEEEEEEeCCCC
Q 039716          601 IGIPENALPTLFRKYMQVSADHARKYGGTGLGLAICKQLVELMGGRLTVTSKVHCGSTFTFILPYQVS  668 (1002)
Q Consensus       601 iGI~~e~l~~IF~pF~q~~~~~~~~~~GtGLGLaI~k~Lve~~gG~I~v~S~~g~GTtF~~~LP~~~~  668 (1002)
                      +||+++.+.++|++|++.+...+.+.+|+||||+||+++++.|||+|++.|.++.||+|+|.||+...
T Consensus        87 ~gi~~~~~~~lf~~~~~~~~~~~~~~~g~GlGL~iv~~~~~~~~G~i~i~~~~~~Gt~~~i~lP~~~~  154 (177)
T 3sl2_A           87 IGIPKKDVEKVFDRFYRVDKARTRKLGGTGLGLAIAKEMVQAHGGDIWADSIEGKGTTITFTLPYKEE  154 (177)
T ss_dssp             SCCCTTTTTTTTSTTCCCC------CCCCCCHHHHHHHHHHHTTCCEEEEEETTTEEEEEEEEEEEC-
T ss_pred             CCCCHHHHHHHHhhhccCCCCCCCCCCCCCcCHHHHHHHHHHcCCEEEEEecCCCCeEEEEEEeCCCC
Confidence            99999999999999999876656667799999999999999999999999999999999999998653

>1r62_A Nitrogen regulation protein NR(II); PII, histidine kinase, two component system, transfera; 1.60A {Escherichia coli} SCOP: d.122.1.3

Probab=99.87  E-value=2.4e-22  Score=200.46  Aligned_cols=156  Identities=26%  Similarity=0.348  Sum_probs=105.8

Q ss_pred             eeEeeecCHHHHHHHHHHHHHHHHhhcceeccccCCCCCeeEEccHHHHHHHHHHHHhhhhhcCC--CCeeEEEEEecCC
Q 039716          437 KLEAAKFRPREVVKHVLQTAAASLQKILMLEGDIADDVPIEVIGDVLRIRQILTNLISNAIKFTP--EGKVGIKLYVVPE  514 (1002)
Q Consensus       437 ~l~~~~~~l~~li~~v~~~~~~~~~k~i~l~~~i~~~~p~~v~gD~~rL~QIL~NLlsNAIKfT~--~G~I~I~v~~~~~  514 (1002)
                      .++..++++.++++.++..+.....+.+.+...+....+ .+.+|+.+|.|||.||+.||+||++  .|.|.|.+.....
T Consensus         2 ~~~~~~~~l~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~-~i~~d~~~l~~il~nLl~NAik~~~~~~~~I~i~~~~~~~   80 (160)
T 1r62_A            2 PGTRVTESIHKVAERVVTLVSMELPDNVRLIRDYDPSLP-ELAHDPDQIEQVLLNIVRNALQALGPEGGEIILRTRTAFQ   80 (160)
T ss_dssp             ---CEEECHHHHHHHHHHHHTTTCCTTEEEEEECCTTCC-CEEECHHHHHHHHHHHHHHHHHHHGGGCEEEEEEEEEEEE
T ss_pred             CCccccCCHHHHHHHHHHHHHhhcccCcEEEEEcCCCCC-eeeeCHHHHHHHHHHHHHHHHHHhhccCCeEEEEEecccc
Confidence            356678999999999998877654456777777665554 4889999999999999999999997  6777777643211


Q ss_pred             CCcccchhhhhhhhhhcchhhhhhhccCCCCCccCCCCCCCCCCCCCCccCCCCCCCCCCCccCCCCCccccccceEEEE
Q 039716          515 PPFAKEGLKQKSKAYQSATDAVKEEKHQPKSQTASDQNGFHDKKHGEGYQDHKHDDDPGTPVSHGNSMDEDLEATVWIRC  594 (1002)
Q Consensus       515 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~i  594 (1002)
                      ..                                                                  ........++.|
T Consensus        81 ~~------------------------------------------------------------------~~~~~~~~~~~i   94 (160)
T 1r62_A           81 LT------------------------------------------------------------------LHGERYRLAARI   94 (160)
T ss_dssp             EE------------------------------------------------------------------ETTEEEEEEEEE
T ss_pred             cc------------------------------------------------------------------ccccccccEEEE
Confidence            00                                                                  000012236889


Q ss_pred             EEEecCCCCCcCcHhhhhhhccCCCccccCcCCCccccHHHHHHHHHHhCCEEEEEeecCCceEEEEEEeCC
Q 039716          595 DVYDTGIGIPENALPTLFRKYMQVSADHARKYGGTGLGLAICKQLVELMGGRLTVTSKVHCGSTFTFILPYQ  666 (1002)
Q Consensus       595 ~V~DtGiGI~~e~l~~IF~pF~q~~~~~~~~~~GtGLGLaI~k~Lve~~gG~I~v~S~~g~GTtF~~~LP~~  666 (1002)
                      .|.|+|+||+++.++++|+||++.+      .+|+||||+||+++++.|||+|+++|.+++ |+|+|.||+.
T Consensus        95 ~v~D~G~gi~~~~~~~lf~~~~~~~------~~g~GlGL~i~~~~~~~~gG~l~i~s~~~~-~~~~i~lP~~  159 (160)
T 1r62_A           95 DVEDNGPGIPPHLQDTLFYPMVSGR------EGGTGLGLSIARNLIDQHSGKIEFTSWPGH-TEFSVYLPIR  159 (160)
T ss_dssp             EEEEECTTC--------------------------CHHHHHHHHHHHHTTCEEEEEEETTE-EEEEEEEEEE
T ss_pred             EEEeCCCCCCHHHHHHhhCccccCC------CCCCccCHHHHHHHHHHCCCeEEEEeCCCC-EEEEEEEecc
Confidence            9999999999999999999999753      358999999999999999999999999886 9999999974

>3a0y_A Sensor protein; ATP-LID, kinase, phosphoprotein, transferase, two-component regulatory system; 1.57A {Thermotoga maritima} PDB: 3a0t_A* 3a0x_A 3a0w_A 3a0z_A

Probab=99.87  E-value=1.4e-21  Score=193.42  Aligned_cols=144  Identities=28%  Similarity=0.504  Sum_probs=118.9

Q ss_pred             EeeecCHHHHHHHHHHHHHHHHh-hcceeccccCCCCCeeEEccHHHHHHHHHHHHhhhhhcCC-CCeeEEEEEecCCCC
Q 039716          439 EAAKFRPREVVKHVLQTAAASLQ-KILMLEGDIADDVPIEVIGDVLRIRQILTNLISNAIKFTP-EGKVGIKLYVVPEPP  516 (1002)
Q Consensus       439 ~~~~~~l~~li~~v~~~~~~~~~-k~i~l~~~i~~~~p~~v~gD~~rL~QIL~NLlsNAIKfT~-~G~I~I~v~~~~~~~  516 (1002)
                      +..++++.+++++++..+...+. +.+.+...+... +..+.+|+..|.|||.||+.||+||++ .|.|.|.+...    
T Consensus         2 ~~~~~~l~~~~~~~~~~~~~~~~~~~i~~~~~~~~~-~~~i~~d~~~l~~il~nll~NAi~~~~~~~~I~i~~~~~----   76 (152)
T 3a0y_A            2 EFTEFNLNELIREVYVLFEEKIRKMNIDFCFETDNE-DLRVEADRTRIKQVLINLVQNAIEATGENGKIKITSEDM----   76 (152)
T ss_dssp             CCEEEEHHHHHHHHHHHHHHHHHHTTCEEEEEESCS-SCEEEECHHHHHHHHHHHHHHHHHHHCTTCEEEEEEEEC----
T ss_pred             ccEEecHHHHHHHHHHHHHHHHHHcCcEEEEecCCC-CcEEEECHHHHHHHHHHHHHHHHHhcCCCCEEEEEEEec----
Confidence            35678999999999988876554 567777666543 446899999999999999999999995 56777765321    


Q ss_pred             cccchhhhhhhhhhcchhhhhhhccCCCCCccCCCCCCCCCCCCCCccCCCCCCCCCCCccCCCCCccccccceEEEEEE
Q 039716          517 FAKEGLKQKSKAYQSATDAVKEEKHQPKSQTASDQNGFHDKKHGEGYQDHKHDDDPGTPVSHGNSMDEDLEATVWIRCDV  596 (1002)
Q Consensus       517 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~i~V  596 (1002)
                                                                                              ..++.|.|
T Consensus        77 ------------------------------------------------------------------------~~~~~i~i   84 (152)
T 3a0y_A           77 ------------------------------------------------------------------------YTKVRVSV   84 (152)
T ss_dssp             ------------------------------------------------------------------------SSEEEEEE
T ss_pred             ------------------------------------------------------------------------CCEEEEEE
Confidence                                                                                    11488999


Q ss_pred             EecCCCCCcCcHhhhhhhccCCCccccCcCCCccccHHHHHHHHH-HhCCEEEEEeecCCceEEEEEEeCC
Q 039716          597 YDTGIGIPENALPTLFRKYMQVSADHARKYGGTGLGLAICKQLVE-LMGGRLTVTSKVHCGSTFTFILPYQ  666 (1002)
Q Consensus       597 ~DtGiGI~~e~l~~IF~pF~q~~~~~~~~~~GtGLGLaI~k~Lve-~~gG~I~v~S~~g~GTtF~~~LP~~  666 (1002)
                      .|+|+||+++.++++|+||++.+      .+|+||||+||+++++ .|||.+.+++.++ ||+|+|.||..
T Consensus        85 ~D~G~g~~~~~~~~~f~~~~~~~------~~g~GlGL~i~~~~~~~~~gg~~~~~~~~~-g~~~~i~lP~~  148 (152)
T 3a0y_A           85 WNSGPPIPEELKEKIFSPFFTTK------TQGTGLGLSICRKIIEDEHGGKIWTENREN-GVVFIFEIPKT  148 (152)
T ss_dssp             EEESCCCCGGGTTGGGSTTCCCC--------CCCCSHHHHHHHHHTTTSCEEEEEEETT-EEEEEEEEESC
T ss_pred             EeCCCCcCHHHHHhHhhhhccCC------CCCCCcCHHHHHHHHHHhCCcEEEEecCCC-CEEEEEEeCCC
Confidence            99999999999999999999743      3589999999999999 9999999999865 99999999975

>2lpm_A Two-component response regulator; transcription regulator; NMR {Sinorhizobium meliloti}

Probab=99.87  E-value=2.7e-23  Score=199.06  Aligned_cols=113  Identities=19%  Similarity=0.288  Sum_probs=103.0

Q ss_pred             CCCeEEEEecCHHHHHHHHHHHHhcCCeEE-EEcCHHHHHHHHHcCCCcEEEEcCCCCCCCHHHHHHHHhccccCCCchh
Q 039716          858 PKPKILLVEDNKINVMVAKSMMKQLGHSID-VVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDA  936 (1002)
Q Consensus       858 ~~~~ILiVeDn~~n~~~l~~~L~~~g~~v~-~a~~G~eAl~~~~~~~~DlIlmDi~MP~mdG~e~~~~IR~~~~~~~~~~  936 (1002)
                      .+.|||||||++.++..++.+|+..||.|. +|.||.+|++.+...+||+||+|++||+|||+++++.||+         
T Consensus         7 r~~rILiVdD~~~~~~~l~~~L~~~G~~v~~~a~~g~eAl~~~~~~~~DlvllDi~mP~~~G~el~~~lr~---------   77 (123)
T 2lpm_A            7 RRLRVLVVEDESMIAMLIEDTLCELGHEVAATASRMQEALDIARKGQFDIAIIDVNLDGEPSYPVADILAE---------   77 (123)
T ss_dssp             CCCCEEEESSSTTTSHHHHHHHHHHCCCCCBCSCCHHHHHHHHHHCCSSEEEECSSSSSCCSHHHHHHHHH---------
T ss_pred             CCCEEEEEeCCHHHHHHHHHHHHHCCCEEEEEECCHHHHHHHHHhCCCCEEEEecCCCCCCHHHHHHHHHc---------
Confidence            457899999999999999999999999975 7999999999999999999999999999999999999996         


Q ss_pred             hhhhhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHHhhc
Q 039716          937 AAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQYF 1001 (1002)
Q Consensus       937 ~~~~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~~l 1001 (1002)
                                         +++|||++||+.+...   +.++|+++||+|||+.++|..+|++++
T Consensus        78 -------------------~~ipvI~lTa~~~~~~---~~~~g~~~yl~KP~~~~~L~~~l~~~~  120 (123)
T 2lpm_A           78 -------------------RNVPFIFATGYGSKGL---DTRYSNIPLLTKPFLDSELEAVLVQIS  120 (123)
T ss_dssp             -------------------TCCSSCCBCTTCTTSC---CSSSCSCSCBCSSSSHHHHHHHHSTTC
T ss_pred             -------------------CCCCEEEEecCccHHH---HHhCCCCcEEECCCCHHHHHHHHHHHH
Confidence                               2489999999986554   346799999999999999999998865

>1i58_A Chemotaxis protein CHEA; beta-alpha sandwich, signaling protein, transferase; HET: ACP ADP; 1.60A {Thermotoga maritima} SCOP: d.122.1.3 PDB: 1i59_A* 1i5a_A* 1i5b_A* 1i5c_A* 1i5d_A*

Probab=99.85  E-value=3e-21  Score=199.02  Aligned_cols=148  Identities=20%  Similarity=0.202  Sum_probs=114.0

Q ss_pred             eecCHHHHHHHHHHHHHHHHh-hcceeccccCCCCCeeEEccHHHHHHHHHHHHhhhhhcC-------------CCCeeE
Q 039716          441 AKFRPREVVKHVLQTAAASLQ-KILMLEGDIADDVPIEVIGDVLRIRQILTNLISNAIKFT-------------PEGKVG  506 (1002)
Q Consensus       441 ~~~~l~~li~~v~~~~~~~~~-k~i~l~~~i~~~~p~~v~gD~~rL~QIL~NLlsNAIKfT-------------~~G~I~  506 (1002)
                      .++++.++++.+...+...+. +.+.+...+..........+..+|.|||.|||.||+||+             +.|.|.
T Consensus         3 ~~~~l~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~l~~il~nLl~NAik~~~~~~~~~~~~~~~~~~~I~   82 (189)
T 1i58_A            3 HMVPISFVFNRFPRMVRDLAKKMNKEVNFIMRGEDTELDRTFVEEIGEPLLHLLRNAIDHGIEPKEERIAKGKPPIGTLI   82 (189)
T ss_dssp             SEEETHHHHTTHHHHHHHHHHHTTCCEEEEEECTTCEEEHHHHHHHHHHHHHHHHHHHHHTSCCHHHHHHHTSCSSEEEE
T ss_pred             eEecHHHHHHHHHHHHHHHHHHhCCcEEEEEcCCcccccHHHHHHHHHHHHHHHHHHHHhhhccccccccccCCCCCeEE
Confidence            467888999998888776554 445555544433322223445667777999999999995             456777


Q ss_pred             EEEEecCCCCcccchhhhhhhhhhcchhhhhhhccCCCCCccCCCCCCCCCCCCCCccCCCCCCCCCCCccCCCCCcccc
Q 039716          507 IKLYVVPEPPFAKEGLKQKSKAYQSATDAVKEEKHQPKSQTASDQNGFHDKKHGEGYQDHKHDDDPGTPVSHGNSMDEDL  586 (1002)
Q Consensus       507 I~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  586 (1002)
                      |.+...                                                                          
T Consensus        83 I~~~~~--------------------------------------------------------------------------   88 (189)
T 1i58_A           83 LSARHE--------------------------------------------------------------------------   88 (189)
T ss_dssp             EEEEEE--------------------------------------------------------------------------
T ss_pred             EEEEec--------------------------------------------------------------------------
Confidence            766421                                                                          


Q ss_pred             ccceEEEEEEEecCCCCCcCcH------------------------hhhhhhccCCCccccCcCCCccccHHHHHHHHHH
Q 039716          587 EATVWIRCDVYDTGIGIPENAL------------------------PTLFRKYMQVSADHARKYGGTGLGLAICKQLVEL  642 (1002)
Q Consensus       587 ~~~~~l~i~V~DtGiGI~~e~l------------------------~~IF~pF~q~~~~~~~~~~GtGLGLaI~k~Lve~  642 (1002)
                        ..++.|.|.|+|+||+++.+                        +++|+||++.... .+..+|+||||+||+++++.
T Consensus        89 --~~~~~i~V~D~G~Gi~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~if~~~~~~~~~-~~~~~g~GlGL~iv~~~~~~  165 (189)
T 1i58_A           89 --GNNVVIEVEDDGRGIDKEKIIRKAIEKGLIDESKAATLSDQEILNFLFVPGFSTKEK-VSEVSGRGVGMDVVKNVVES  165 (189)
T ss_dssp             --TTEEEEEEEECSSCCCHHHHHHHHHHTTSSCHHHHTTCCHHHHHGGGGSTTCSHHHH-HHGGGTCCCHHHHHHHHHHH
T ss_pred             --CCEEEEEEEeCCCCcCHHHHhhhhhhccchhhhhhcccchhhhHHHhcCCccccccc-CCCCCCCccCHHHHHHHHHH
Confidence              11588999999999999986                        8999999986542 22346999999999999999


Q ss_pred             hCCEEEEEeecCCceEEEEEEeC
Q 039716          643 MGGRLTVTSKVHCGSTFTFILPY  665 (1002)
Q Consensus       643 ~gG~I~v~S~~g~GTtF~~~LP~  665 (1002)
                      |||+|+++|.+++||+|+|+||+
T Consensus       166 ~~G~i~i~s~~~~Gt~~~i~lPl  188 (189)
T 1i58_A          166 LNGSISIESEKDKGTKVTIRLPL  188 (189)
T ss_dssp             TTCEEEEEEETTTEEEEEEEEEC
T ss_pred             cCCEEEEEeCCCCceEEEEEEeC
Confidence            99999999999999999999997

>3gl9_A Response regulator; beta-sheet, surrounded by alpha helices, BOTH sides, signaling protein; HET: BFD; 1.80A {Thermotoga maritima} SCOP: c.23.1.0 PDB: 3dgf_C 3dge_C

Probab=99.84  E-value=2.8e-20  Score=177.35  Aligned_cols=118  Identities=27%  Similarity=0.427  Sum_probs=110.8

Q ss_pred             CeEEEEecCHHHHHHHHHHHHhcCCeEEEEcCHHHHHHHHHcCCCcEEEEcCCCCCCCHHHHHHHHhccccCCCchhhhh
Q 039716          860 PKILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDAAAE  939 (1002)
Q Consensus       860 ~~ILiVeDn~~n~~~l~~~L~~~g~~v~~a~~G~eAl~~~~~~~~DlIlmDi~MP~mdG~e~~~~IR~~~~~~~~~~~~~  939 (1002)
                      .+||||||++..+..++.+|+..||.|..+.||.+|++.+....||+||+|+.||+|||+++++.||+..          
T Consensus         3 ~~ILivdd~~~~~~~l~~~l~~~g~~v~~~~~~~~al~~l~~~~~dlvllD~~~p~~~g~~~~~~l~~~~----------   72 (122)
T 3gl9_A            3 KKVLLVDDSAVLRKIVSFNLKKEGYEVIEAENGQIALEKLSEFTPDLIVLXIMMPVMDGFTVLKKLQEKE----------   72 (122)
T ss_dssp             CEEEEECSCHHHHHHHHHHHHHTTCEEEEESSHHHHHHHHTTBCCSEEEECSCCSSSCHHHHHHHHHTST----------
T ss_pred             ceEEEEeCCHHHHHHHHHHHHHCCcEEEEeCCHHHHHHHHHhcCCCEEEEeccCCCCcHHHHHHHHHhcc----------
Confidence            4799999999999999999999999999999999999999999999999999999999999999999632          


Q ss_pred             hhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHHhhc
Q 039716          940 AGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQYF 1001 (1002)
Q Consensus       940 ~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~~l 1001 (1002)
                                    ..+++|||++|+....+...+++++|+++||.||++.++|...|++.+
T Consensus        73 --------------~~~~~pii~~s~~~~~~~~~~~~~~Ga~~~l~KP~~~~~L~~~i~~~l  120 (122)
T 3gl9_A           73 --------------EWKRIPVIVLTAKGGEEDESLALSLGARKVMRKPFSPSQFIEEVKHLL  120 (122)
T ss_dssp             --------------TTTTSCEEEEESCCSHHHHHHHHHTTCSEEEESSCCHHHHHHHHHHHH
T ss_pred             --------------cccCCCEEEEecCCchHHHHHHHhcChhhhccCCCCHHHHHHHHHHHh
Confidence                          236799999999999999999999999999999999999999998865

>2r25_B Osmosensing histidine protein kinase SLN1; alpha5-BETA5, response regulator, four helix bundle, histidine phosphotransfer (HPT) protein; 1.70A {Saccharomyces cerevisiae} SCOP: c.23.1.1 PDB: 1oxk_B 1oxb_B

Probab=99.82  E-value=1.7e-19  Score=174.71  Aligned_cols=117  Identities=42%  Similarity=0.632  Sum_probs=107.8

Q ss_pred             CeEEEEecCHHHHHHHHHHHHhcCC-eEEEEcCHHHHHHHHHc-----CCCcEEEEcCCCCCCCHHHHHHHHhccccCCC
Q 039716          860 PKILLVEDNKINVMVAKSMMKQLGH-SIDVVNNGVEAVHAVQC-----QNYDLILMDVCMPVMDGLKATRLIRSFEDTGN  933 (1002)
Q Consensus       860 ~~ILiVeDn~~n~~~l~~~L~~~g~-~v~~a~~G~eAl~~~~~-----~~~DlIlmDi~MP~mdG~e~~~~IR~~~~~~~  933 (1002)
                      .+||||||++.++..++.+|+..|+ .|..+.+|.+|++.+..     ..||+||+|+.||+|||+++++.||+..    
T Consensus         3 ~~ILivdD~~~~~~~l~~~L~~~g~~~v~~~~~~~~al~~~~~~~~~~~~~dlvllD~~mp~~~G~~~~~~lr~~~----   78 (133)
T 2r25_B            3 VKILVVEDNHVNQEVIKRMLNLEGIENIELACDGQEAFDKVKELTSKGENYNMIFMDVQMPKVDGLLSTKMIRRDL----   78 (133)
T ss_dssp             SCEEEECSCHHHHHHHHHHHHHTTCCCEEEESSHHHHHHHHHHHHHHTCCCSEEEECSCCSSSCHHHHHHHHHHHS----
T ss_pred             ceEEEEcCCHHHHHHHHHHHHHcCCceEEEECCHHHHHHHHHHHHhcCCCCCEEEEeCCCCCCChHHHHHHHHhhc----
Confidence            5799999999999999999999997 48899999999999887     7899999999999999999999999621    


Q ss_pred             chhhhhhhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHHhhc
Q 039716          934 WDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQYF 1001 (1002)
Q Consensus       934 ~~~~~~~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~~l 1001 (1002)
                                           .+.+|||++|++...+...+|+++|+++||.||++.++|...|++++
T Consensus        79 ---------------------~~~~~ii~lt~~~~~~~~~~~~~~ga~~~l~KP~~~~~L~~~l~~~~  125 (133)
T 2r25_B           79 ---------------------GYTSPIVALTAFADDSNIKECLESGMNGFLSKPIKRPKLKTILTEFC  125 (133)
T ss_dssp             ---------------------CCCSCEEEEESCCSHHHHHHHHHTTCSEEEESSCCHHHHHHHHHHHC
T ss_pred             ---------------------CCCCCEEEEECCCCHHHHHHHHHcCCCEEEeCCCCHHHHHHHHHHHH
Confidence                                 23589999999999999999999999999999999999999998875

>3t6k_A Response regulator receiver; flavodoxin-like, structural genomics, joint center for struc genomics, JCSG, protein structure initiative; HET: MSE; 1.86A {Chloroflexus aurantiacus} SCOP: c.23.1.0

Probab=99.82  E-value=1.7e-19  Score=175.40  Aligned_cols=119  Identities=21%  Similarity=0.358  Sum_probs=110.8

Q ss_pred             CCeEEEEecCHHHHHHHHHHHHhcCCeEEEEcCHHHHHHHHHcCCCcEEEEcCCCCCCCHHHHHHHHhccccCCCchhhh
Q 039716          859 KPKILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDAAA  938 (1002)
Q Consensus       859 ~~~ILiVeDn~~n~~~l~~~L~~~g~~v~~a~~G~eAl~~~~~~~~DlIlmDi~MP~mdG~e~~~~IR~~~~~~~~~~~~  938 (1002)
                      ..+||||||++..+..++.+|+..||.|..+.+|.+|++.+....||+||+|+.||+|||+++++.||+..         
T Consensus         4 ~~~iLivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~al~~~~~~~~dlvl~D~~lp~~~g~~~~~~lr~~~---------   74 (136)
T 3t6k_A            4 PHTLLIVDDDDTVAEMLELVLRGAGYEVRRAASGEEALQQIYKNLPDALICDVLLPGIDGYTLCKRVRQHP---------   74 (136)
T ss_dssp             CCEEEEECSCHHHHHHHHHHHHHTTCEEEEESSHHHHHHHHHHSCCSEEEEESCCSSSCHHHHHHHHHHSG---------
T ss_pred             CCEEEEEeCCHHHHHHHHHHHHHCCCEEEEeCCHHHHHHHHHhCCCCEEEEeCCCCCCCHHHHHHHHHcCC---------
Confidence            45899999999999999999999999999999999999999999999999999999999999999999732         


Q ss_pred             hhhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHHhhc
Q 039716          939 EAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQYF 1001 (1002)
Q Consensus       939 ~~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~~l 1001 (1002)
                                     ..+.+|||++|+..+.+...+++++|+++||.||++.++|...|++.+
T Consensus        75 ---------------~~~~~pii~~t~~~~~~~~~~~~~~ga~~~l~KP~~~~~L~~~i~~~l  122 (136)
T 3t6k_A           75 ---------------LTKTLPILMLTAQGDISAKIAGFEAGANDYLAKPFEPQELVYRVKNIL  122 (136)
T ss_dssp             ---------------GGTTCCEEEEECTTCHHHHHHHHHHTCSEEEETTCCHHHHHHHHHHHH
T ss_pred             ---------------CcCCccEEEEecCCCHHHHHHHHhcCcceEEeCCCCHHHHHHHHHHHH
Confidence                           135789999999999999999999999999999999999999998754

>3f6p_A Transcriptional regulatory protein YYCF; unphosphorelated, receiver domain, cytoplasm, DNA-binding, phosphoprotein, transcription regulation; 1.95A {Bacillus subtilis} SCOP: c.23.1.1 PDB: 2zwm_A

Probab=99.81  E-value=2.6e-19  Score=170.01  Aligned_cols=115  Identities=29%  Similarity=0.426  Sum_probs=108.7

Q ss_pred             CeEEEEecCHHHHHHHHHHHHhcCCeEEEEcCHHHHHHHHHcCCCcEEEEcCCCCCCCHHHHHHHHhccccCCCchhhhh
Q 039716          860 PKILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDAAAE  939 (1002)
Q Consensus       860 ~~ILiVeDn~~n~~~l~~~L~~~g~~v~~a~~G~eAl~~~~~~~~DlIlmDi~MP~mdG~e~~~~IR~~~~~~~~~~~~~  939 (1002)
                      .+||||||++..+..++.+|+..||.|..+.+|.+|++.+....||+||+|+.||+++|+++++.||+.           
T Consensus         3 ~~ilivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~al~~~~~~~~dlii~D~~~p~~~g~~~~~~lr~~-----------   71 (120)
T 3f6p_A            3 KKILVVDDEKPIADILEFNLRKEGYEVHCAHDGNEAVEMVEELQPDLILLDIMLPNKDGVEVCREVRKK-----------   71 (120)
T ss_dssp             CEEEEECSCHHHHHHHHHHHHHTTCEEEEESSHHHHHHHHHTTCCSEEEEETTSTTTHHHHHHHHHHTT-----------
T ss_pred             CeEEEEECCHHHHHHHHHHHHhCCEEEEEeCCHHHHHHHHhhCCCCEEEEeCCCCCCCHHHHHHHHHhc-----------
Confidence            489999999999999999999999999999999999999999999999999999999999999999952           


Q ss_pred             hhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHHhhc
Q 039716          940 AGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQYF 1001 (1002)
Q Consensus       940 ~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~~l 1001 (1002)
                                      ..+|||++|+........+++++|+++||.||++.++|...|++.+
T Consensus        72 ----------------~~~~ii~~t~~~~~~~~~~~~~~ga~~~l~KP~~~~~l~~~i~~~l  117 (120)
T 3f6p_A           72 ----------------YDMPIIMLTAKDSEIDKVIGLEIGADDYVTKPFSTRELLARVKANL  117 (120)
T ss_dssp             ----------------CCSCEEEEEESSCHHHHHHHHHTTCCEEEEESCCHHHHHHHHHHHH
T ss_pred             ----------------CCCCEEEEECCCChHHHHHHHhCCcceeEcCCCCHHHHHHHHHHHH
Confidence                            3589999999999999999999999999999999999999998764

>3h1g_A Chemotaxis protein CHEY homolog; sulfate-bound CHEY, cytoplasm, flagellar rotatio magnesium, metal-binding, phosphoprotein; 1.70A {Helicobacter pylori} SCOP: c.23.1.1 PDB: 3gwg_A 3h1e_A 3h1f_A

Probab=99.81  E-value=4e-19  Score=170.80  Aligned_cols=120  Identities=31%  Similarity=0.466  Sum_probs=109.0

Q ss_pred             CCCeEEEEecCHHHHHHHHHHHHhcCCe-EEEEcCHHHHHHHHHcC-CCcEEEEcCCCCCCCHHHHHHHHhccccCCCch
Q 039716          858 PKPKILLVEDNKINVMVAKSMMKQLGHS-IDVVNNGVEAVHAVQCQ-NYDLILMDVCMPVMDGLKATRLIRSFEDTGNWD  935 (1002)
Q Consensus       858 ~~~~ILiVeDn~~n~~~l~~~L~~~g~~-v~~a~~G~eAl~~~~~~-~~DlIlmDi~MP~mdG~e~~~~IR~~~~~~~~~  935 (1002)
                      .+.+||||||++..+..++.+|++.||. +..+.++.+|++.+... .||+||+|+.||+|||+++++.||+..      
T Consensus         4 ~~~~iLivdd~~~~~~~l~~~L~~~g~~~v~~~~~~~~a~~~~~~~~~~dlvi~D~~~p~~~g~~~~~~lr~~~------   77 (129)
T 3h1g_A            4 GSMKLLVVDDSSTMRRIIKNTLSRLGYEDVLEAEHGVEAWEKLDANADTKVLITDWNMPEMNGLDLVKKVRSDS------   77 (129)
T ss_dssp             --CCEEEECSCHHHHHHHHHHHHHTTCCCEEEESSHHHHHHHHHHCTTCCEEEECSCCSSSCHHHHHHHHHTST------
T ss_pred             CCcEEEEEeCCHHHHHHHHHHHHHcCCcEEEEeCCHHHHHHHHHhCCCCCEEEEeCCCCCCCHHHHHHHHHhcC------
Confidence            3568999999999999999999999995 89999999999988765 799999999999999999999999632      


Q ss_pred             hhhhhhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHHhhc
Q 039716          936 AAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQYF 1001 (1002)
Q Consensus       936 ~~~~~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~~l 1001 (1002)
                                        ..+.+|||++|++.......+|+++|+++||.||++.++|...|++++
T Consensus        78 ------------------~~~~~pii~~s~~~~~~~~~~~~~~g~~~~l~KP~~~~~L~~~l~~~l  125 (129)
T 3h1g_A           78 ------------------RFKEIPIIMITAEGGKAEVITALKAGVNNYIVKPFTPQVLKEKLEVVL  125 (129)
T ss_dssp             ------------------TCTTCCEEEEESCCSHHHHHHHHHHTCCEEEESCCCHHHHHHHHHHHH
T ss_pred             ------------------CCCCCeEEEEeCCCChHHHHHHHHcCccEEEeCCCCHHHHHHHHHHHh
Confidence                              236799999999999999999999999999999999999999998875

>3n0r_A Response regulator; sigma factor, receiver, two-component SI transduction, signaling protein; HET: MSE GOL; 1.25A {Caulobacter vibrioides} PDB: 3t0y_A

Probab=99.80  E-value=2.9e-20  Score=204.95  Aligned_cols=114  Identities=22%  Similarity=0.335  Sum_probs=106.0

Q ss_pred             CCeEEEEecCHHHHHHHHHHHHhcCCeEE-EEcCHHHHHHHHHcCCCcEEEEcCCCC-CCCHHHHHHHHhccccCCCchh
Q 039716          859 KPKILLVEDNKINVMVAKSMMKQLGHSID-VVNNGVEAVHAVQCQNYDLILMDVCMP-VMDGLKATRLIRSFEDTGNWDA  936 (1002)
Q Consensus       859 ~~~ILiVeDn~~n~~~l~~~L~~~g~~v~-~a~~G~eAl~~~~~~~~DlIlmDi~MP-~mdG~e~~~~IR~~~~~~~~~~  936 (1002)
                      ..+|||||||+.++.+++.+|+..||.|. .|.||.+|++.+....|||||||++|| +|||+++++.||+.        
T Consensus       160 ~~rILvVdD~~~~~~~l~~~L~~~g~~v~~~a~~g~eAl~~~~~~~~dlvl~D~~MPd~mdG~e~~~~ir~~--------  231 (286)
T 3n0r_A          160 ATEVLIIEDEPVIAADIEALVRELGHDVTDIAATRGEALEAVTRRTPGLVLADIQLADGSSGIDAVKDILGR--------  231 (286)
T ss_dssp             CCEEEEECCSHHHHHHHHHHHHHTTCEEEEEESSHHHHHHHHHHCCCSEEEEESCCTTSCCTTTTTHHHHHH--------
T ss_pred             CCcEEEEcCCHHHHHHHHHHhhccCceEEEEeCCHHHHHHHHHhCCCCEEEEcCCCCCCCCHHHHHHHHHhc--------
Confidence            45899999999999999999999999999 999999999999999999999999999 89999999999973        


Q ss_pred             hhhhhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHHhhc
Q 039716          937 AAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQYF 1001 (1002)
Q Consensus       937 ~~~~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~~l 1001 (1002)
                                         +++|||++|++.  +...+|+++|+++||+|||++++|...|.+++
T Consensus       232 -------------------~~~piI~lT~~~--~~~~~~~~~G~~~~l~KP~~~~~L~~~i~~~l  275 (286)
T 3n0r_A          232 -------------------MDVPVIFITAFP--ERLLTGERPEPTFLITKPFQPETVKAAIGQAL  275 (286)
T ss_dssp             -------------------TTCCEEEEESCG--GGGCCSSSCCCSSEEESSCCHHHHHHHHHHHH
T ss_pred             -------------------CCCCEEEEeCCH--HHHHHHHhCCCcEEEeCCCCHHHHHHHHHHHH
Confidence                               169999999985  45778999999999999999999999998875

>3m6m_D Sensory/regulatory protein RPFC; RPFF, REC, enoyl-COA hydratase, lyase-transferase COMP; 2.50A {Xanthomonas campestris PV}

Probab=99.80  E-value=5.8e-19  Score=173.24  Aligned_cols=122  Identities=25%  Similarity=0.527  Sum_probs=109.1

Q ss_pred             CCCeEEEEecCHHHHHHHHHHHHhcCCeEEEEcCHHHHHHHHHcCCCcEEEEcCCCCCCCHHHHHHHHhccccCCCchhh
Q 039716          858 PKPKILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDAA  937 (1002)
Q Consensus       858 ~~~~ILiVeDn~~n~~~l~~~L~~~g~~v~~a~~G~eAl~~~~~~~~DlIlmDi~MP~mdG~e~~~~IR~~~~~~~~~~~  937 (1002)
                      ...+||||||++..+..++.+|+..||.|..+.++.+|++.+....||+||+|+.||+|||+++++.||.....      
T Consensus        13 ~~~~iLivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~al~~~~~~~~dlvl~D~~mp~~~g~~~~~~lr~~~~~------   86 (143)
T 3m6m_D           13 RSMRMLVADDHEANRMVLQRLLEKAGHKVLCVNGAEQVLDAMAEEDYDAVIVDLHMPGMNGLDMLKQLRVMQAS------   86 (143)
T ss_dssp             --CEEEEECSSHHHHHHHHHHHHC--CEEEEESSHHHHHHHHHHSCCSEEEEESCCSSSCHHHHHHHHHHHHHT------
T ss_pred             ccceEEEEeCCHHHHHHHHHHHHHcCCeEEEeCCHHHHHHHHhcCCCCEEEEeCCCCCCCHHHHHHHHHhchhc------
Confidence            45799999999999999999999999999999999999999999999999999999999999999999964211      


Q ss_pred             hhhhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHHhhc
Q 039716          938 AEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQYF 1001 (1002)
Q Consensus       938 ~~~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~~l 1001 (1002)
                                      ..+.+|||++|+....+...+|+++|+++||.||++.++|...|.++.
T Consensus        87 ----------------~~~~~pii~~s~~~~~~~~~~~~~~Ga~~~l~KP~~~~~L~~~l~~~~  134 (143)
T 3m6m_D           87 ----------------GMRYTPVVVLSADVTPEAIRACEQAGARAFLAKPVVAAKLLDTLADLA  134 (143)
T ss_dssp             ----------------TCCCCCEEEEESCCCHHHHHHHHHTTCSEEEESSCCHHHHHHHHHHHC
T ss_pred             ----------------cCCCCeEEEEeCCCCHHHHHHHHHcChhheeeCCCCHHHHHHHHHHHH
Confidence                            235689999999999999999999999999999999999999998764

>3rqi_A Response regulator protein; structural genomics, seattle structural genomics center for infectious disease, ssgcid; HET: PHD CIT; 1.70A {Burkholderia pseudomallei}

Probab=99.79  E-value=2.6e-19  Score=183.73  Aligned_cols=117  Identities=16%  Similarity=0.300  Sum_probs=109.8

Q ss_pred             CCCeEEEEecCHHHHHHHHHHHHhcCCeEEEEcCHHHHHHHHHcCCCcEEEEcCCCCCCCHHHHHHHHhccccCCCchhh
Q 039716          858 PKPKILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDAA  937 (1002)
Q Consensus       858 ~~~~ILiVeDn~~n~~~l~~~L~~~g~~v~~a~~G~eAl~~~~~~~~DlIlmDi~MP~mdG~e~~~~IR~~~~~~~~~~~  937 (1002)
                      .+.+||||||++..+..++.+|+..||.|..|.||.+|++.+....||+||+|+.||+|||+++++.||+.         
T Consensus         6 ~~~~iLivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~al~~~~~~~~dlvl~D~~lp~~~g~~~~~~l~~~---------   76 (184)
T 3rqi_A            6 SDKNFLVIDDNEVFAGTLARGLERRGYAVRQAHNKDEALKLAGAEKFEFITVXLHLGNDSGLSLIAPLCDL---------   76 (184)
T ss_dssp             -CCEEEEECSCHHHHHHHHHHHHHTTCEEEEECSHHHHHHHHTTSCCSEEEECSEETTEESHHHHHHHHHH---------
T ss_pred             CCCeEEEEcCCHHHHHHHHHHHHHCCCEEEEeCCHHHHHHHHhhCCCCEEEEeccCCCccHHHHHHHHHhc---------
Confidence            35689999999999999999999999999999999999999999999999999999999999999999973         


Q ss_pred             hhhhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHHhh
Q 039716          938 AEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQY 1000 (1002)
Q Consensus       938 ~~~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~~ 1000 (1002)
                                       .+.+|||++|++.+.+...+|+.+|+++||.||++.++|...|++.
T Consensus        77 -----------------~~~~~ii~lt~~~~~~~~~~a~~~Ga~~~l~KP~~~~~L~~~i~~~  122 (184)
T 3rqi_A           77 -----------------QPDARILVLTGYASIATAVQAVKDGADNYLAKPANVESILAALQTN  122 (184)
T ss_dssp             -----------------CTTCEEEEEESSCCHHHHHHHHHHTCSEEEESSCCHHHHHHHTSTT
T ss_pred             -----------------CCCCCEEEEeCCCCHHHHHHHHHhCHHHheeCCCCHHHHHHHHHHH
Confidence                             2568999999999999999999999999999999999999988764

>3ehg_A Sensor kinase (YOCF protein); GHL ATPase domain, transferase; HET: ATP; 1.74A {Bacillus subtilis}

Probab=99.78  E-value=1.4e-18  Score=167.57  Aligned_cols=125  Identities=15%  Similarity=0.154  Sum_probs=96.6

Q ss_pred             cCHHHHHHHHHHHHHHHHhhcceeccccCCCCCeeEEccHHHHHHHHHHHHhhhhhcCCCCeeEEEEEecCCCCcccchh
Q 039716          443 FRPREVVKHVLQTAAASLQKILMLEGDIADDVPIEVIGDVLRIRQILTNLISNAIKFTPEGKVGIKLYVVPEPPFAKEGL  522 (1002)
Q Consensus       443 ~~l~~li~~v~~~~~~~~~k~i~l~~~i~~~~p~~v~gD~~rL~QIL~NLlsNAIKfT~~G~I~I~v~~~~~~~~~~~~~  522 (1002)
                      +++.+++..+...+.   .+++.+........+.....+...|.+|+.||++||+||++.|.|.|.+...          
T Consensus         2 v~l~~~l~~~~~~~~---~~~i~~~~~~~~~~~~~~~~~~~~l~~il~nll~Na~k~~~~~~i~i~~~~~----------   68 (128)
T 3ehg_A            2 IRLKDELINIKQILE---AADIMFIYEEEKWPENISLLNENILSMCLKEAVTNVVKHSQAKTCRVDIQQL----------   68 (128)
T ss_dssp             CCHHHHHHHHHHHHH---HTTCEEECCCCSCCSCCCHHHHHHHHHHHHHHHHHHHHHTCCSEEEEEEEEE----------
T ss_pred             ccHHHHHHHHHHHHH---HcCCEEEEEcCccccccCHHHHHHHHHHHHHHHHHHHhcCCCcEEEEEEEEe----------
Confidence            455566655544433   2455555555443333345688999999999999999999888888776431          


Q ss_pred             hhhhhhhhcchhhhhhhccCCCCCccCCCCCCCCCCCCCCccCCCCCCCCCCCccCCCCCccccccceEEEEEEEecCCC
Q 039716          523 KQKSKAYQSATDAVKEEKHQPKSQTASDQNGFHDKKHGEGYQDHKHDDDPGTPVSHGNSMDEDLEATVWIRCDVYDTGIG  602 (1002)
Q Consensus       523 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~i~V~DtGiG  602 (1002)
                                                                                        ..++.|+|.|+|+|
T Consensus        69 ------------------------------------------------------------------~~~~~i~V~D~G~G   82 (128)
T 3ehg_A           69 ------------------------------------------------------------------WKEVVITVSDDGTF   82 (128)
T ss_dssp             ------------------------------------------------------------------TTEEEEEEEESSCC
T ss_pred             ------------------------------------------------------------------CCEEEEEEEECCcC
Confidence                                                                              11488999999999


Q ss_pred             CCcCcHhhhhhhccCCCccccCcCCCccccHHHHHHHHHHhCCEEEEEeecCCceEEEEEEeCC
Q 039716          603 IPENALPTLFRKYMQVSADHARKYGGTGLGLAICKQLVELMGGRLTVTSKVHCGSTFTFILPYQ  666 (1002)
Q Consensus       603 I~~e~l~~IF~pF~q~~~~~~~~~~GtGLGLaI~k~Lve~~gG~I~v~S~~g~GTtF~~~LP~~  666 (1002)
                      |+++.+                  +|+||||+||+++++.|||+|+++|.+  ||+|+++||+.
T Consensus        83 i~~~~~------------------~g~GlGL~~~~~~~~~~gG~i~~~s~~--Gt~~~i~lP~~  126 (128)
T 3ehg_A           83 KGEENS------------------FSKGHGLLGMRERLEFANGSLHIDTEN--GTKLTMAIPNN  126 (128)
T ss_dssp             CSCSSC------------------CCTTSHHHHHHHHHHHTTCEEEEECSS--SEEEEEEEEC-
T ss_pred             cCcccC------------------CCCCccHHHHHHHHHHcCCEEEEEeCC--CEEEEEEEecC
Confidence            998765                  489999999999999999999999998  99999999974

>2ayx_A Sensor kinase protein RCSC; two independent structural domains, transferase; NMR {Escherichia coli} SCOP: c.23.1.1 c.23.1.6 PDB: 2ayz_A 2ayy_A

Probab=99.78  E-value=1.3e-18  Score=188.32  Aligned_cols=119  Identities=38%  Similarity=0.622  Sum_probs=112.0

Q ss_pred             CCCCeEEEEecCHHHHHHHHHHHHhcCCeEEEEcCHHHHHHHHHcCCCcEEEEcCCCCCCCHHHHHHHHhccccCCCchh
Q 039716          857 KPKPKILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDA  936 (1002)
Q Consensus       857 ~~~~~ILiVeDn~~n~~~l~~~L~~~g~~v~~a~~G~eAl~~~~~~~~DlIlmDi~MP~mdG~e~~~~IR~~~~~~~~~~  936 (1002)
                      ..+.+||||||++.++..+..+|+..||.|..+.||.+|++.+....||+||||+.||+|||+++++.||+..       
T Consensus       127 ~~~~~ILivdd~~~~~~~l~~~L~~~g~~v~~a~~~~eal~~l~~~~~dlvl~D~~mp~~~G~~l~~~ir~~~-------  199 (254)
T 2ayx_A          127 NDDMMILVVDDHPINRRLLADQLGSLGYQCKTANDGVDALNVLSKNHIDIVLSDVNMPNMDGYRLTQRIRQLG-------  199 (254)
T ss_dssp             CCCCEEEEEESSHHHHHHHHHHHHHHTSEEEEECCSHHHHHHHHHSCCSEEEEEESSCSSCCHHHHHHHHHHH-------
T ss_pred             CCCCEEEEEeCCHHHHHHHHHHHHHcCCEEEEECCHHHHHHHHHhCCCCEEEEcCCCCCCCHHHHHHHHHhcC-------
Confidence            3467999999999999999999999999999999999999999999999999999999999999999999742       


Q ss_pred             hhhhhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHHhhc
Q 039716          937 AAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQYF 1001 (1002)
Q Consensus       937 ~~~~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~~l 1001 (1002)
                                         +.+|||++|++...+...+|+++|+++||.||++.++|...|++++
T Consensus       200 -------------------~~~piI~lt~~~~~~~~~~~~~~G~~~~l~KP~~~~~L~~~l~~~~  245 (254)
T 2ayx_A          200 -------------------LTLPVIGVTANALAEEKQRCLESGMDSCLSKPVTLDVIKQTLTLYA  245 (254)
T ss_dssp             -------------------CCSCEEEEESSTTSHHHHHHHHCCCEEEEESSCCHHHHHHHHHHHH
T ss_pred             -------------------CCCcEEEEECCCCHHHHHHHHHcCCceEEECCCCHHHHHHHHHHHH
Confidence                               4689999999999999999999999999999999999999998874

>1dbw_A Transcriptional regulatory protein FIXJ; doubly wound five-stranded beta/alpha fold, nitrogen fixatio regulation; HET: 15P; 1.60A {Sinorhizobium meliloti} SCOP: c.23.1.1 PDB: 1dck_A* 1dcm_A 1d5w_A*

Probab=99.78  E-value=4.9e-18  Score=162.15  Aligned_cols=117  Identities=19%  Similarity=0.239  Sum_probs=109.5

Q ss_pred             CCeEEEEecCHHHHHHHHHHHHhcCCeEEEEcCHHHHHHHHHcCCCcEEEEcCCCCCCCHHHHHHHHhccccCCCchhhh
Q 039716          859 KPKILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDAAA  938 (1002)
Q Consensus       859 ~~~ILiVeDn~~n~~~l~~~L~~~g~~v~~a~~G~eAl~~~~~~~~DlIlmDi~MP~mdG~e~~~~IR~~~~~~~~~~~~  938 (1002)
                      ..+||||||++..+..++.+|...||.+..+.++.+|++.+....||+||+|+.||+++|+++++.||+.          
T Consensus         3 ~~~ilivdd~~~~~~~l~~~l~~~~~~v~~~~~~~~~~~~~~~~~~dlvi~D~~l~~~~g~~~~~~l~~~----------   72 (126)
T 1dbw_A            3 DYTVHIVDDEEPVRKSLAFMLTMNGFAVKMHQSAEAFLAFAPDVRNGVLVTDLRMPDMSGVELLRNLGDL----------   72 (126)
T ss_dssp             CCEEEEEESSHHHHHHHHHHHHHTTCEEEEESCHHHHHHHGGGCCSEEEEEECCSTTSCHHHHHHHHHHT----------
T ss_pred             CCEEEEEcCCHHHHHHHHHHHHhCCcEEEEeCCHHHHHHHHhcCCCCEEEEECCCCCCCHHHHHHHHHhc----------
Confidence            3589999999999999999999999999999999999999999999999999999999999999999962          


Q ss_pred             hhhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHHhhc
Q 039716          939 EAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQYF 1001 (1002)
Q Consensus       939 ~~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~~l 1001 (1002)
                                      .+.+|||++|+....+...+++++|+++||.||++.++|...|++.+
T Consensus        73 ----------------~~~~~ii~~s~~~~~~~~~~~~~~ga~~~l~Kp~~~~~l~~~i~~~~  119 (126)
T 1dbw_A           73 ----------------KINIPSIVITGHGDVPMAVEAMKAGAVDFIEKPFEDTVIIEAIERAS  119 (126)
T ss_dssp             ----------------TCCCCEEEEECTTCHHHHHHHHHTTCSEEEESSCCHHHHHHHHHHHH
T ss_pred             ----------------CCCCCEEEEECCCCHHHHHHHHHhCHHHheeCCCCHHHHHHHHHHHH
Confidence                            25689999999999999999999999999999999999999998753

>1srr_A SPO0F, sporulation response regulatory protein; aspartate pocket, two component system; 1.90A {Bacillus subtilis} SCOP: c.23.1.1 PDB: 1pey_A 3q15_C 2ftk_E* 1fsp_A 1nat_A 1pux_A 2fsp_A 2jvj_A 2jvk_A 2jvi_A 1f51_E

Probab=99.77  E-value=3.7e-18  Score=162.40  Aligned_cols=116  Identities=24%  Similarity=0.405  Sum_probs=109.4

Q ss_pred             CeEEEEecCHHHHHHHHHHHHhcCCeEEEEcCHHHHHHHHHcCCCcEEEEcCCCCCCCHHHHHHHHhccccCCCchhhhh
Q 039716          860 PKILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDAAAE  939 (1002)
Q Consensus       860 ~~ILiVeDn~~n~~~l~~~L~~~g~~v~~a~~G~eAl~~~~~~~~DlIlmDi~MP~mdG~e~~~~IR~~~~~~~~~~~~~  939 (1002)
                      .+||||||++..+..++.+|+..||.+..+.++.+|+..+....||+||+|+.||+++|+++++.||+.           
T Consensus         4 ~~ilivdd~~~~~~~l~~~l~~~~~~v~~~~~~~~a~~~~~~~~~dlvl~D~~l~~~~g~~~~~~l~~~-----------   72 (124)
T 1srr_A            4 EKILIVDDQSGIRILLNEVFNKEGYQTFQAANGLQALDIVTKERPDLVLLDMKIPGMDGIEILKRMKVI-----------   72 (124)
T ss_dssp             CEEEEECSCHHHHHHHHHHHHTTTCEEEEESSHHHHHHHHHHHCCSEEEEESCCTTCCHHHHHHHHHHH-----------
T ss_pred             ceEEEEeCCHHHHHHHHHHHHHCCcEEEEeCCHHHHHHHHhccCCCEEEEecCCCCCCHHHHHHHHHHh-----------
Confidence            489999999999999999999999999999999999999998899999999999999999999999963           


Q ss_pred             hhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHHhhc
Q 039716          940 AGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQYF 1001 (1002)
Q Consensus       940 ~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~~l 1001 (1002)
                                     .+.+|||++|+....+...+++++|+++||.||++.++|...|++++
T Consensus        73 ---------------~~~~~ii~~s~~~~~~~~~~~~~~g~~~~l~KP~~~~~l~~~i~~~~  119 (124)
T 1srr_A           73 ---------------DENIRVIIMTAYGELDMIQESKELGALTHFAKPFDIDEIRDAVKKYL  119 (124)
T ss_dssp             ---------------CTTCEEEEEESSCCHHHHHHHHHHTCCCEEESSCCHHHHHHHHHHHS
T ss_pred             ---------------CCCCCEEEEEccCchHHHHHHHhcChHhhccCCCCHHHHHHHHHHHh
Confidence                           25689999999999999999999999999999999999999998865

>2pl1_A Transcriptional regulatory protein PHOP; CHEY-like fold, response regulator, beryllium fluoride, transcription factor, activated, virulence; 1.90A {Escherichia coli} SCOP: c.23.1.1 PDB: 2pkx_A

Probab=99.77  E-value=7.9e-18  Score=159.04  Aligned_cols=114  Identities=26%  Similarity=0.396  Sum_probs=107.7

Q ss_pred             eEEEEecCHHHHHHHHHHHHhcCCeEEEEcCHHHHHHHHHcCCCcEEEEcCCCCCCCHHHHHHHHhccccCCCchhhhhh
Q 039716          861 KILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDAAAEA  940 (1002)
Q Consensus       861 ~ILiVeDn~~n~~~l~~~L~~~g~~v~~a~~G~eAl~~~~~~~~DlIlmDi~MP~mdG~e~~~~IR~~~~~~~~~~~~~~  940 (1002)
                      +||||||++..+..++.+|+..||.|..+.++.+|+..+....||+||+|+.||+++|+++++.||..            
T Consensus         2 ~ilivdd~~~~~~~l~~~l~~~g~~v~~~~~~~~a~~~~~~~~~dlil~D~~l~~~~g~~~~~~l~~~------------   69 (121)
T 2pl1_A            2 RVLVVEDNALLRHHLKVQIQDAGHQVDDAEDAKEADYYLNEHIPDIAIVDLGLPDEDGLSLIRRWRSN------------   69 (121)
T ss_dssp             EEEEECSCHHHHHHHHHHHHHTTCEEEEESSHHHHHHHHHHSCCSEEEECSCCSSSCHHHHHHHHHHT------------
T ss_pred             eEEEEeCcHHHHHHHHHHHhhcCCEEEEeCCHHHHHHHHhccCCCEEEEecCCCCCCHHHHHHHHHhc------------
Confidence            79999999999999999999999999999999999999999999999999999999999999999962            


Q ss_pred             hhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHHhh
Q 039716          941 GIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQY 1000 (1002)
Q Consensus       941 ~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~~ 1000 (1002)
                                    .+.+|||++|+........+++++|+++|+.||++.++|...|++.
T Consensus        70 --------------~~~~~ii~~s~~~~~~~~~~~~~~g~~~~l~kp~~~~~l~~~i~~~  115 (121)
T 2pl1_A           70 --------------DVSLPILVLTARESWQDKVEVLSAGADDYVTKPFHIEEVMARMQAL  115 (121)
T ss_dssp             --------------TCCSCEEEEESCCCHHHHHHHHHTTCSEEEESSCCHHHHHHHHHHH
T ss_pred             --------------CCCCCEEEEecCCCHHHHHHHHHcCccceEECCCCHHHHHHHHHHH
Confidence                          2568999999999999999999999999999999999999998865

>3gt7_A Sensor protein; structural genomics, signal receiver domain, kinase, PSI-2, protein structure initiative; 2.30A {Syntrophus aciditrophicus SB}

Probab=99.77  E-value=5.2e-18  Score=168.47  Aligned_cols=120  Identities=28%  Similarity=0.432  Sum_probs=111.4

Q ss_pred             CCCeEEEEecCHHHHHHHHHHHHhcCCeEEEEcCHHHHHHHHHcCCCcEEEEcCCCCCCCHHHHHHHHhccccCCCchhh
Q 039716          858 PKPKILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDAA  937 (1002)
Q Consensus       858 ~~~~ILiVeDn~~n~~~l~~~L~~~g~~v~~a~~G~eAl~~~~~~~~DlIlmDi~MP~mdG~e~~~~IR~~~~~~~~~~~  937 (1002)
                      .+.+||||||++..+..++.+|+..||.|..+.++.+|++.+....||+||+|+.||+++|+++++.||+..        
T Consensus         6 ~~~~ILivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~al~~l~~~~~dlii~D~~l~~~~g~~~~~~lr~~~--------   77 (154)
T 3gt7_A            6 RAGEILIVEDSPTQAEHLKHILEETGYQTEHVRNGREAVRFLSLTRPDLIISDVLMPEMDGYALCRWLKGQP--------   77 (154)
T ss_dssp             -CCEEEEECSCHHHHHHHHHHHHTTTCEEEEESSHHHHHHHHTTCCCSEEEEESCCSSSCHHHHHHHHHHST--------
T ss_pred             CCCcEEEEeCCHHHHHHHHHHHHHCCCEEEEeCCHHHHHHHHHhCCCCEEEEeCCCCCCCHHHHHHHHHhCC--------
Confidence            356899999999999999999999999999999999999999999999999999999999999999999732        


Q ss_pred             hhhhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHHhhc
Q 039716          938 AEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQYF 1001 (1002)
Q Consensus       938 ~~~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~~l 1001 (1002)
                                      ..+.+|||++|+....+...+|+++|+++||.||++..+|...|++++
T Consensus        78 ----------------~~~~~pii~~s~~~~~~~~~~~~~~g~~~~l~KP~~~~~l~~~i~~~l  125 (154)
T 3gt7_A           78 ----------------DLRTIPVILLTILSDPRDVVRSLECGADDFITKPCKDVVLASHVKRLL  125 (154)
T ss_dssp             ----------------TTTTSCEEEEECCCSHHHHHHHHHHCCSEEEESSCCHHHHHHHHHHHH
T ss_pred             ----------------CcCCCCEEEEECCCChHHHHHHHHCCCCEEEeCCCCHHHHHHHHHHHH
Confidence                            236799999999999999999999999999999999999999998754

>3crn_A Response regulator receiver domain protein, CHEY-; structural genomics, signal regulator receiver domain; HET: PHD; 1.58A {Methanospirillum hungatei jf-1}

Probab=99.77  E-value=5e-18  Score=163.80  Aligned_cols=116  Identities=20%  Similarity=0.343  Sum_probs=108.8

Q ss_pred             CeEEEEecCHHHHHHHHHHHHhcCCeEEEEcCHHHHHHHHHcCCCcEEEEcCCCCCCCHHHHHHHHhccccCCCchhhhh
Q 039716          860 PKILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDAAAE  939 (1002)
Q Consensus       860 ~~ILiVeDn~~n~~~l~~~L~~~g~~v~~a~~G~eAl~~~~~~~~DlIlmDi~MP~mdG~e~~~~IR~~~~~~~~~~~~~  939 (1002)
                      .+||||||++..+..++.+|+..||.|..+.++.+|++.+....||+||+|+.||+++|+++++.||..           
T Consensus         4 ~~Ilivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~al~~~~~~~~dlvl~D~~l~~~~g~~~~~~l~~~-----------   72 (132)
T 3crn_A            4 KRILIVDDDTAILDSTKQILEFEGYEVEIAATAGEGLAKIENEFFNLALFXIKLPDMEGTELLEKAHKL-----------   72 (132)
T ss_dssp             CEEEEECSCHHHHHHHHHHHHHTTCEEEEESSHHHHHHHHHHSCCSEEEECSBCSSSBHHHHHHHHHHH-----------
T ss_pred             cEEEEEeCCHHHHHHHHHHHHHCCceEEEeCCHHHHHHHHhcCCCCEEEEecCCCCCchHHHHHHHHhh-----------
Confidence            589999999999999999999999999999999999999999999999999999999999999999963           


Q ss_pred             hhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHHhhc
Q 039716          940 AGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQYF 1001 (1002)
Q Consensus       940 ~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~~l 1001 (1002)
                                     .+.+|||++|+....+...+++++|+++||.||++.++|...|++.+
T Consensus        73 ---------------~~~~~ii~~s~~~~~~~~~~~~~~ga~~~l~KP~~~~~L~~~i~~~~  119 (132)
T 3crn_A           73 ---------------RPGMKKIMVTGYASLENSVFSLNAGADAYIMKPVNPRDLLEKIKEKL  119 (132)
T ss_dssp             ---------------CTTSEEEEEESCCCHHHHHHHHHTTCSEEEESSCCHHHHHHHHHHHH
T ss_pred             ---------------CCCCcEEEEeccccHHHHHHHHhccchhhccCCCCHHHHHHHHHHHH
Confidence                           24689999999999999999999999999999999999999987653

>3zxo_A Redox sensor histidine kinase response regulator; transferase; HET: MSE; 1.90A {Mycobacterium tuberculosis}

Probab=99.77  E-value=2.4e-18  Score=165.55  Aligned_cols=125  Identities=19%  Similarity=0.286  Sum_probs=98.5

Q ss_pred             eecCHHHHHHHHHHHHHHHHhhcceeccccCCCCCeeEEccHHHHHHHHHHHHhhhhhcCCCCeeEEEEEecCCCCcccc
Q 039716          441 AKFRPREVVKHVLQTAAASLQKILMLEGDIADDVPIEVIGDVLRIRQILTNLISNAIKFTPEGKVGIKLYVVPEPPFAKE  520 (1002)
Q Consensus       441 ~~~~l~~li~~v~~~~~~~~~k~i~l~~~i~~~~p~~v~gD~~rL~QIL~NLlsNAIKfT~~G~I~I~v~~~~~~~~~~~  520 (1002)
                      ..+++.+++..++..+   ..+.+.+...+....+.....|+..|.||+.||++||+||++.|.|.|.+..         
T Consensus         3 ~~~~l~~~l~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~l~~il~nll~NA~k~~~~~~i~i~~~~---------   70 (129)
T 3zxo_A            3 MVTRLRQRIDAAVAQF---ADSGLRTSVQFVGPLSVVDSALADQAEAVVREAVSNAVRHAAASTLTVRVKV---------   70 (129)
T ss_dssp             --CCHHHHHHHHHHHH---SCTTSEEEEEEESCGGGSCHHHHHHHHHHHHHHHHHCCCCSSCCEEEEEEEE---------
T ss_pred             ccccHHHHHHHHHHHH---hhcCceEEEEecCCcccCCHHHHHHHHHHHHHHHHHHHHhCCCceEEEEEEE---------
Confidence            4678888888887766   3344555554444433333456899999999999999999988888877642         


Q ss_pred             hhhhhhhhhhcchhhhhhhccCCCCCccCCCCCCCCCCCCCCccCCCCCCCCCCCccCCCCCccccccceEEEEEEEecC
Q 039716          521 GLKQKSKAYQSATDAVKEEKHQPKSQTASDQNGFHDKKHGEGYQDHKHDDDPGTPVSHGNSMDEDLEATVWIRCDVYDTG  600 (1002)
Q Consensus       521 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~i~V~DtG  600 (1002)
                                                                                         ... +.|.|.|+|
T Consensus        71 -------------------------------------------------------------------~~~-~~i~v~D~G   82 (129)
T 3zxo_A           71 -------------------------------------------------------------------DDD-LCIEVTDNG   82 (129)
T ss_dssp             -------------------------------------------------------------------SSE-EEEEEEECC
T ss_pred             -------------------------------------------------------------------cCC-EEEEEecCC
Confidence                                                                               112 678999999


Q ss_pred             CCCCcCcHhhhhhhccCCCccccCcCCCccccHHHHHHHHHHhCCEEEEEeecC-CceEEEEEEeCC
Q 039716          601 IGIPENALPTLFRKYMQVSADHARKYGGTGLGLAICKQLVELMGGRLTVTSKVH-CGSTFTFILPYQ  666 (1002)
Q Consensus       601 iGI~~e~l~~IF~pF~q~~~~~~~~~~GtGLGLaI~k~Lve~~gG~I~v~S~~g-~GTtF~~~LP~~  666 (1002)
                      +||+++.                     +||||+||+++++.|||+|++.|.++ +|++|+++||+.
T Consensus        83 ~gi~~~~---------------------~GlGL~i~~~~~~~~gG~i~~~~~~~~~G~~~~i~lP~~  128 (129)
T 3zxo_A           83 RGMPDEF---------------------TGSGLTNLRQRAEQAGGEFTLASMPGASGTVLRWSAPLS  128 (129)
T ss_dssp             CCCTTTT---------------------CSHHHHHHHHHHHHTTCEEEEEECTTTCCEEEEEEEESC
T ss_pred             CCCCccc---------------------CCcCHHHHHHHHHHcCCEEEEeeCCCCCcEEEEEEecCC
Confidence            9999765                     69999999999999999999999999 899999999974

>3luf_A Two-component system response regulator/ggdef domain protein; structural genomics, ASA_2441, PSI-2, protein structure initiative; HET: MSE; 1.76A {Aeromonas salmonicida} PDB: 3mf4_A*

Probab=99.77  E-value=2.9e-18  Score=186.31  Aligned_cols=119  Identities=17%  Similarity=0.344  Sum_probs=109.7

Q ss_pred             CCeEEEEecCHHHHHHHHHHHHhcCCeEEEEcCHHHHHHHHHcCC-CcEEEEcCCCCCCCHHHHHHHHhccccCCCchhh
Q 039716          859 KPKILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQN-YDLILMDVCMPVMDGLKATRLIRSFEDTGNWDAA  937 (1002)
Q Consensus       859 ~~~ILiVeDn~~n~~~l~~~L~~~g~~v~~a~~G~eAl~~~~~~~-~DlIlmDi~MP~mdG~e~~~~IR~~~~~~~~~~~  937 (1002)
                      ..+||||||++.++..+...|+..|+.|..+.||.+|++.+.... ||+||+|+.||+|||+++++.||+..        
T Consensus       124 ~~~ILivDD~~~~~~~l~~~L~~~~~~v~~a~~~~eal~~l~~~~~~dlvllD~~mP~~dG~~l~~~lr~~~--------  195 (259)
T 3luf_A          124 QIEVLVVDDSRTSRHRTMAQLRKQLLQVHEASHAREALATLEQHPAIRLVLVDYYMPEIDGISLVRMLRERY--------  195 (259)
T ss_dssp             TCEEEEECSCHHHHHHHHHHHHTTTCEEEEESSHHHHHHHHHHCTTEEEEEECSCCSSSCHHHHHHHHHHHC--------
T ss_pred             CCcEEEEeCCHHHHHHHHHHHHHcCcEEEEeCCHHHHHHHHhcCCCCCEEEEcCCCCCCCHHHHHHHHHhcc--------
Confidence            458999999999999999999999999999999999999998775 89999999999999999999999742        


Q ss_pred             hhhhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHHhhc
Q 039716          938 AEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQYF 1001 (1002)
Q Consensus       938 ~~~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~~l 1001 (1002)
                                      ....+|||++|++...+...+|+++|+++||.||++.++|...|++.+
T Consensus       196 ----------------~~~~~~ii~~s~~~~~~~~~~a~~~Ga~~yl~KP~~~~~L~~~i~~~l  243 (259)
T 3luf_A          196 ----------------SKQQLAIIGISVSDKRGLSARYLKQGANDFLNQPFEPEELQCRVSHNL  243 (259)
T ss_dssp             ----------------CTTTSEEEEEECSSSSSHHHHHHHTTCSEEEESSCCHHHHHHHHHHHH
T ss_pred             ----------------CCCCCeEEEEEccCCHHHHHHHHhcChhheEcCCCCHHHHHHHHHHHH
Confidence                            234689999999999999999999999999999999999999988754

>3eod_A Protein HNR; response regulator, phosphoprotein, two-component regulatory system, signaling protein; 1.75A {Escherichia coli K12}

Probab=99.76  E-value=5.8e-18  Score=162.41  Aligned_cols=118  Identities=25%  Similarity=0.426  Sum_probs=104.2

Q ss_pred             CCCeEEEEecCHHHHHHHHHHHHhcCCeEEEEcCHHHHHHHHHcCCCcEEEEcCCCCCCCHHHHHHHHhccccCCCchhh
Q 039716          858 PKPKILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDAA  937 (1002)
Q Consensus       858 ~~~~ILiVeDn~~n~~~l~~~L~~~g~~v~~a~~G~eAl~~~~~~~~DlIlmDi~MP~mdG~e~~~~IR~~~~~~~~~~~  937 (1002)
                      .+.+||||||++..+..++.+|+..|+.+..+.++.+|++.+....||+||+|+.||+++|+++++.||+.         
T Consensus         6 ~~~~ilivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~a~~~l~~~~~dlvi~d~~l~~~~g~~~~~~l~~~---------   76 (130)
T 3eod_A            6 VGKQILIVEDEQVFRSLLDSWFSSLGATTVLAADGVDALELLGGFTPDLMICDIAMPRMNGLKLLEHIRNR---------   76 (130)
T ss_dssp             TTCEEEEECSCHHHHHHHHHHHHHTTCEEEEESCHHHHHHHHTTCCCSEEEECCC-----CHHHHHHHHHT---------
T ss_pred             CCCeEEEEeCCHHHHHHHHHHHHhCCceEEEeCCHHHHHHHHhcCCCCEEEEecCCCCCCHHHHHHHHHhc---------
Confidence            45699999999999999999999999999999999999999999999999999999999999999999962         


Q ss_pred             hhhhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCC-ChHHHHHHHHhhc
Q 039716          938 AEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPV-TFQKLKECLEQYF 1001 (1002)
Q Consensus       938 ~~~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~-~~~~L~~~l~~~l 1001 (1002)
                                       .+.+|||++|+....+...+++.+|+++||.||+ +.+.|...|++.+
T Consensus        77 -----------------~~~~~ii~~t~~~~~~~~~~~~~~g~~~~l~KP~~~~~~l~~~i~~~l  124 (130)
T 3eod_A           77 -----------------GDQTPVLVISATENMADIAKALRLGVEDVLLKPVKDLNRLREMVFACL  124 (130)
T ss_dssp             -----------------TCCCCEEEEECCCCHHHHHHHHHHCCSEEEESCC---CHHHHHHHHHH
T ss_pred             -----------------CCCCCEEEEEcCCCHHHHHHHHHcCCCEEEeCCCCcHHHHHHHHHHHh
Confidence                             3578999999999999999999999999999999 8999999998764

>1mb3_A Cell division response regulator DIVK; signal transduction protein, structural proteomics in europe, spine, structural genomics; 1.41A {Caulobacter vibrioides} SCOP: c.23.1.1 PDB: 1m5u_A 1mav_A 1mb0_A 1m5t_A

Probab=99.76  E-value=4.6e-18  Score=161.35  Aligned_cols=118  Identities=27%  Similarity=0.522  Sum_probs=103.7

Q ss_pred             CeEEEEecCHHHHHHHHHHHHhcCCeEEEEcCHHHHHHHHHcCCCcEEEEcCCCCCCCHHHHHHHHhccccCCCchhhhh
Q 039716          860 PKILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDAAAE  939 (1002)
Q Consensus       860 ~~ILiVeDn~~n~~~l~~~L~~~g~~v~~a~~G~eAl~~~~~~~~DlIlmDi~MP~mdG~e~~~~IR~~~~~~~~~~~~~  939 (1002)
                      .+||||||++..+..++.+|+..||.+..+.++.+|+..+....||+||+|+.||+++|+++++.||+..          
T Consensus         2 ~~ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~a~~~~~~~~~dlvi~D~~l~~~~g~~~~~~l~~~~----------   71 (124)
T 1mb3_A            2 KKVLIVEDNELNMKLFHDLLEAQGYETLQTREGLSALSIARENKPDLILMDIQLPEISGLEVTKWLKEDD----------   71 (124)
T ss_dssp             CEEEEECSCHHHHHHHHHHHHHTTCEEEEESCHHHHHHHHHHHCCSEEEEESBCSSSBHHHHHHHHHHST----------
T ss_pred             cEEEEEcCCHHHHHHHHHHHHHcCcEEEEeCCHHHHHHHHhcCCCCEEEEeCCCCCCCHHHHHHHHHcCc----------
Confidence            4799999999999999999999999999999999999999988999999999999999999999999631          


Q ss_pred             hhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHHhhc
Q 039716          940 AGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQYF 1001 (1002)
Q Consensus       940 ~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~~l 1001 (1002)
                                    ..+.+|||++|+....+....++++|+++||.||++.++|...|++.+
T Consensus        72 --------------~~~~~~ii~~s~~~~~~~~~~~~~~g~~~~l~KP~~~~~l~~~i~~~~  119 (124)
T 1mb3_A           72 --------------DLAHIPVVAVTAFAMKGDEERIREGGCEAYISKPISVVHFLETIKRLL  119 (124)
T ss_dssp             --------------TTTTSCEEEEC------CHHHHHHHTCSEEECSSCCHHHHHHHHHHHH
T ss_pred             --------------cccCCcEEEEECCCCHHHHHHHHhCCCCEEEeCCCCHHHHHHHHHHHH
Confidence                          235799999999999999999999999999999999999999998754

>1tmy_A CHEY protein, TMY; chemotaxis, phosphoryl transfer, signal transduction; 1.90A {Thermotoga maritima} SCOP: c.23.1.1 PDB: 2tmy_A 3tmy_A 4tmy_A 1u0s_Y

Probab=99.76  E-value=6.7e-18  Score=159.45  Aligned_cols=116  Identities=26%  Similarity=0.386  Sum_probs=108.3

Q ss_pred             CeEEEEecCHHHHHHHHHHHHhcCCe-EEEEcCHHHHHHHHHcCCCcEEEEcCCCCCCCHHHHHHHHhccccCCCchhhh
Q 039716          860 PKILLVEDNKINVMVAKSMMKQLGHS-IDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDAAA  938 (1002)
Q Consensus       860 ~~ILiVeDn~~n~~~l~~~L~~~g~~-v~~a~~G~eAl~~~~~~~~DlIlmDi~MP~mdG~e~~~~IR~~~~~~~~~~~~  938 (1002)
                      .+||||||++..+..++.+|+..||. +..+.++.+|++.+....||+||+|+.||+++|+++++.||+.          
T Consensus         3 ~~ilivdd~~~~~~~l~~~l~~~g~~vv~~~~~~~~a~~~~~~~~~dlil~D~~l~~~~g~~~~~~l~~~----------   72 (120)
T 1tmy_A            3 KRVLIVDDAAFMRMMLKDIITKAGYEVAGEATNGREAVEKYKELKPDIVTMDITMPEMNGIDAIKEIMKI----------   72 (120)
T ss_dssp             CEEEEECSCHHHHHHHHHHHHHTTCEEEEEESSHHHHHHHHHHHCCSEEEEECSCGGGCHHHHHHHHHHH----------
T ss_pred             ceEEEEcCcHHHHHHHHHHHhhcCcEEEEEECCHHHHHHHHHhcCCCEEEEeCCCCCCcHHHHHHHHHhh----------
Confidence            48999999999999999999999999 5689999999999999999999999999999999999999963          


Q ss_pred             hhhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHHhhc
Q 039716          939 EAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQYF 1001 (1002)
Q Consensus       939 ~~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~~l 1001 (1002)
                                      .+.+|||++|+....+...+++++|+++|+.||++.++|...|++.+
T Consensus        73 ----------------~~~~~ii~~s~~~~~~~~~~~~~~g~~~~l~KP~~~~~l~~~i~~~~  119 (120)
T 1tmy_A           73 ----------------DPNAKIIVCSAMGQQAMVIEAIKAGAKDFIVKPFQPSRVVEALNKVS  119 (120)
T ss_dssp             ----------------CTTCCEEEEECTTCHHHHHHHHHTTCCEEEESSCCHHHHHHHHHHHC
T ss_pred             ----------------CCCCeEEEEeCCCCHHHHHHHHHhCcceeEeCCCCHHHHHHHHHHHh
Confidence                            25689999999999999999999999999999999999999998765

>1jbe_A Chemotaxis protein CHEY; signaling protein; 1.08A {Escherichia coli} SCOP: c.23.1.1 PDB: 3chy_A 1a0o_A 1cey_A 1bdj_A 1eay_A 1f4v_A 1ffg_A 1ffs_A 1ffw_A 1fqw_A 2b1j_A 1chn_A 1djm_A 1kmi_Y* 1d4z_A 3olx_A 3olw_A 1cye_A 2che_A 2chf_A ...

Probab=99.76  E-value=1.2e-17  Score=159.59  Aligned_cols=119  Identities=29%  Similarity=0.531  Sum_probs=109.1

Q ss_pred             CCeEEEEecCHHHHHHHHHHHHhcCC-eEEEEcCHHHHHHHHHcCCCcEEEEcCCCCCCCHHHHHHHHhccccCCCchhh
Q 039716          859 KPKILLVEDNKINVMVAKSMMKQLGH-SIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDAA  937 (1002)
Q Consensus       859 ~~~ILiVeDn~~n~~~l~~~L~~~g~-~v~~a~~G~eAl~~~~~~~~DlIlmDi~MP~mdG~e~~~~IR~~~~~~~~~~~  937 (1002)
                      ..+||||||++..+..++.+|+..|+ .+..+.++.+|++.+....||+||+|+.||+++|+++++.||+..        
T Consensus         4 ~~~ilivdd~~~~~~~l~~~l~~~~~~~v~~~~~~~~a~~~~~~~~~dlvi~D~~l~~~~g~~l~~~l~~~~--------   75 (128)
T 1jbe_A            4 ELKFLVVDDFSTMRRIVRNLLKELGFNNVEEAEDGVDALNKLQAGGYGFVISDWNMPNMDGLELLKTIRAXX--------   75 (128)
T ss_dssp             TCCEEEECSCHHHHHHHHHHHHHTTCCCEEEESSHHHHHHHHTTCCCCEEEEESCCSSSCHHHHHHHHHC----------
T ss_pred             ccEEEEECCCHHHHHHHHHHHHHcCCcEEEeeCCHHHHHHHHHhcCCCEEEEeCCCCCCCHHHHHHHHHhhc--------
Confidence            45799999999999999999999999 799999999999999999999999999999999999999999632        


Q ss_pred             hhhhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHHhhc
Q 039716          938 AEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQYF 1001 (1002)
Q Consensus       938 ~~~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~~l 1001 (1002)
                                      ..+.+|||++|+....+...+++++|+++|+.||++.++|...|++.+
T Consensus        76 ----------------~~~~~~ii~~s~~~~~~~~~~~~~~ga~~~l~KP~~~~~l~~~i~~~~  123 (128)
T 1jbe_A           76 ----------------AMSALPVLMVTAEAKKENIIAAAQAGASGYVVKPFTAATLEEKLNKIF  123 (128)
T ss_dssp             ----------------CCTTCCEEEEESSCCHHHHHHHHHTTCSEEEESSCCHHHHHHHHHHHH
T ss_pred             ----------------ccCCCcEEEEecCccHHHHHHHHHhCcCceeecCCCHHHHHHHHHHHH
Confidence                            235789999999999999999999999999999999999999988753

>3hv2_A Response regulator/HD domain protein; PSI-2, NYSGXRC, structural genomics, protein structure initiative; 1.50A {Pseudomonas fluorescens pf-5}

Probab=99.76  E-value=9.8e-18  Score=166.05  Aligned_cols=119  Identities=20%  Similarity=0.342  Sum_probs=111.5

Q ss_pred             CCCCeEEEEecCHHHHHHHHHHHHhcCCeEEEEcCHHHHHHHHHcCCCcEEEEcCCCCCCCHHHHHHHHhccccCCCchh
Q 039716          857 KPKPKILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDA  936 (1002)
Q Consensus       857 ~~~~~ILiVeDn~~n~~~l~~~L~~~g~~v~~a~~G~eAl~~~~~~~~DlIlmDi~MP~mdG~e~~~~IR~~~~~~~~~~  936 (1002)
                      ....+||||||++..+..+..+|+..||.|..+.++.+|++.+....||+||+|+.||+++|+++++.||..        
T Consensus        12 ~~~~~ILivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~a~~~l~~~~~dlvi~D~~l~~~~g~~~~~~l~~~--------   83 (153)
T 3hv2_A           12 TRRPEILLVDSQEVILQRLQQLLSPLPYTLHFARDATQALQLLASREVDLVISAAHLPQMDGPTLLARIHQQ--------   83 (153)
T ss_dssp             CSCCEEEEECSCHHHHHHHHHHHTTSSCEEEEESSHHHHHHHHHHSCCSEEEEESCCSSSCHHHHHHHHHHH--------
T ss_pred             cCCceEEEECCCHHHHHHHHHHhcccCcEEEEECCHHHHHHHHHcCCCCEEEEeCCCCcCcHHHHHHHHHhH--------
Confidence            346799999999999999999999999999999999999999999999999999999999999999999973        


Q ss_pred             hhhhhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcC-CCEEEeCCCChHHHHHHHHhhc
Q 039716          937 AAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANG-MDSFVSKPVTFQKLKECLEQYF 1001 (1002)
Q Consensus       937 ~~~~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG-~d~~l~KP~~~~~L~~~l~~~l 1001 (1002)
                                        .+.+|||++|+....+...+++.+| +++||.||++..+|...|++.+
T Consensus        84 ------------------~~~~~ii~~s~~~~~~~~~~~~~~g~~~~~l~KP~~~~~l~~~i~~~l  131 (153)
T 3hv2_A           84 ------------------YPSTTRILLTGDPDLKLIAKAINEGEIYRYLSKPWDDQELLLALRQAL  131 (153)
T ss_dssp             ------------------CTTSEEEEECCCCCHHHHHHHHHTTCCSEEECSSCCHHHHHHHHHHHH
T ss_pred             ------------------CCCCeEEEEECCCCHHHHHHHHhCCCcceEEeCCCCHHHHHHHHHHHH
Confidence                              3568999999999999999999999 9999999999999999998754

>3r0j_A Possible two component system response transcript positive regulator PHOP; beta-alpha fold, winged helix-turn-helix; 2.50A {Mycobacterium tuberculosis}

Probab=99.76  E-value=7e-18  Score=181.85  Aligned_cols=118  Identities=25%  Similarity=0.382  Sum_probs=110.7

Q ss_pred             CCCeEEEEecCHHHHHHHHHHHHhcCCeEEEEcCHHHHHHHHHcCCCcEEEEcCCCCCCCHHHHHHHHhccccCCCchhh
Q 039716          858 PKPKILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDAA  937 (1002)
Q Consensus       858 ~~~~ILiVeDn~~n~~~l~~~L~~~g~~v~~a~~G~eAl~~~~~~~~DlIlmDi~MP~mdG~e~~~~IR~~~~~~~~~~~  937 (1002)
                      ...+||||||++..+..++.+|+..||.|..|.||.+|++.+....||+||+|+.||+|||+++++.||+.         
T Consensus        22 ~~~~ILivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~al~~~~~~~~dlvllD~~lp~~~g~~~~~~lr~~---------   92 (250)
T 3r0j_A           22 PEARVLVVDDEANIVELLSVSLKFQGFEVYTATNGAQALDRARETRPDAVILDVXMPGMDGFGVLRRLRAD---------   92 (250)
T ss_dssp             SSCEEEEECSCHHHHHHHHHHHHHTTCEEEEESSHHHHHHHHHHHCCSEEEEESCCSSSCHHHHHHHHHHT---------
T ss_pred             CCceEEEEECCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHHHhCCCCEEEEeCCCCCCCHHHHHHHHHhc---------
Confidence            45799999999999999999999999999999999999999999999999999999999999999999963         


Q ss_pred             hhhhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHHhhc
Q 039716          938 AEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQYF 1001 (1002)
Q Consensus       938 ~~~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~~l 1001 (1002)
                                       .+.+|||++|+..+.+...+|+++|+++||.||++.++|...|+..+
T Consensus        93 -----------------~~~~~ii~lt~~~~~~~~~~~~~~Ga~~yl~Kp~~~~~L~~~i~~~~  139 (250)
T 3r0j_A           93 -----------------GIDAPALFLTARDSLQDKIAGLTLGGDDYVTKPFSLEEVVARLRVIL  139 (250)
T ss_dssp             -----------------TCCCCEEEEECSTTHHHHHHHHTSTTCEEEESSCCHHHHHHHHHHHH
T ss_pred             -----------------CCCCCEEEEECCCCHHHHHHHHHcCCcEEEeCCCCHHHHHHHHHHHH
Confidence                             35689999999999999999999999999999999999999987653

>4e7p_A Response regulator; DNA binding, cytosol, transcription regulator; 1.89A {Streptococcus pneumoniae} PDB: 4e7o_A

Probab=99.76  E-value=9.2e-18  Score=165.67  Aligned_cols=119  Identities=24%  Similarity=0.318  Sum_probs=110.3

Q ss_pred             CCCCeEEEEecCHHHHHHHHHHHHhcC--CeEEEEcCHHHHHHHHHcCCCcEEEEcCCCCCCCHHHHHHHHhccccCCCc
Q 039716          857 KPKPKILLVEDNKINVMVAKSMMKQLG--HSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNW  934 (1002)
Q Consensus       857 ~~~~~ILiVeDn~~n~~~l~~~L~~~g--~~v~~a~~G~eAl~~~~~~~~DlIlmDi~MP~mdG~e~~~~IR~~~~~~~~  934 (1002)
                      ....+||||||++..+..+..+|+..|  +.|..+.++.+|++.+....||+||+|+.||+++|+++++.||+.      
T Consensus        18 ~~m~~iLivdd~~~~~~~l~~~L~~~~~~~~v~~~~~~~~al~~l~~~~~dlii~D~~l~~~~g~~~~~~l~~~------   91 (150)
T 4e7p_A           18 GSHMKVLVAEDQSMLRDAMCQLLTLQPDVESVLQAKNGQEAIQLLEKESVDIAILDVEMPVKTGLEVLEWIRSE------   91 (150)
T ss_dssp             --CEEEEEECSCHHHHHHHHHHHHTSTTEEEEEEESSHHHHHHHHTTSCCSEEEECSSCSSSCHHHHHHHHHHT------
T ss_pred             CCccEEEEEcCCHHHHHHHHHHHHhCCCcEEEEEECCHHHHHHHhhccCCCEEEEeCCCCCCcHHHHHHHHHHh------
Confidence            446799999999999999999999887  789999999999999999999999999999999999999999962      


Q ss_pred             hhhhhhhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHHhhc
Q 039716          935 DAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQYF 1001 (1002)
Q Consensus       935 ~~~~~~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~~l 1001 (1002)
                                          .+.+|||++|+..+.+...+++++|+++||.||++.++|..+|++++
T Consensus        92 --------------------~~~~~ii~ls~~~~~~~~~~~~~~g~~~~l~Kp~~~~~l~~~i~~~~  138 (150)
T 4e7p_A           92 --------------------KLETKVVVVTTFKRAGYFERAVKAGVDAYVLKERSIADLMQTLHTVL  138 (150)
T ss_dssp             --------------------TCSCEEEEEESCCCHHHHHHHHHTTCSEEEETTSCHHHHHHHHHHHH
T ss_pred             --------------------CCCCeEEEEeCCCCHHHHHHHHHCCCcEEEecCCCHHHHHHHHHHHH
Confidence                                36799999999999999999999999999999999999999998764

>1zgz_A Torcad operon transcriptional regulatory protein; two-component system, gene regulation, transcription factor, respiratory system; 1.80A {Escherichia coli} SCOP: c.23.1.1

Probab=99.75  E-value=1.7e-17  Score=157.08  Aligned_cols=115  Identities=27%  Similarity=0.403  Sum_probs=107.8

Q ss_pred             CeEEEEecCHHHHHHHHHHHHhcCCeEEEEcCHHHHHHHHHcCCCcEEEEcCCCCCCCHHHHHHHHhccccCCCchhhhh
Q 039716          860 PKILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDAAAE  939 (1002)
Q Consensus       860 ~~ILiVeDn~~n~~~l~~~L~~~g~~v~~a~~G~eAl~~~~~~~~DlIlmDi~MP~mdG~e~~~~IR~~~~~~~~~~~~~  939 (1002)
                      .+||||||++..+..++.+|+..||.+..+.++.+|+..+....||+||+|+.||+++|+++++.||+            
T Consensus         3 ~~ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~~~~~~~dlvi~d~~l~~~~g~~~~~~l~~------------   70 (122)
T 1zgz_A            3 HHIVIVEDEPVTQARLQSYFTQEGYTVSVTASGAGLREIMQNQSVDLILLDINLPDENGLMLTRALRE------------   70 (122)
T ss_dssp             CEEEEECSSHHHHHHHHHHHHHTTCEEEEESSHHHHHHHHHHSCCSEEEEESCCSSSCHHHHHHHHHT------------
T ss_pred             cEEEEEECCHHHHHHHHHHHHHCCCeEEEecCHHHHHHHHhcCCCCEEEEeCCCCCCChHHHHHHHHh------------
Confidence            47999999999999999999999999999999999999999999999999999999999999999995            


Q ss_pred             hhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHHhhc
Q 039716          940 AGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQYF 1001 (1002)
Q Consensus       940 ~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~~l 1001 (1002)
                                     .+.+|||++|+........+++++|+++|+.||++.++|...|++.+
T Consensus        71 ---------------~~~~~ii~~s~~~~~~~~~~~~~~ga~~~l~Kp~~~~~l~~~i~~~~  117 (122)
T 1zgz_A           71 ---------------RSTVGIILVTGRSDRIDRIVGLEMGADDYVTKPLELRELVVRVKNLL  117 (122)
T ss_dssp             ---------------TCCCEEEEEESSCCHHHHHHHHHHTCSEEEESSCCHHHHHHHHHHHH
T ss_pred             ---------------cCCCCEEEEECCCChhhHHHHHHhCHHHHccCCCCHHHHHHHHHHHH
Confidence                           14589999999999999999999999999999999999999988753

>3i42_A Response regulator receiver domain protein (CHEY- like); structural genomics, PSI-2, protein structure initiative; 2.15A {Methylobacillus flagellatus KT} SCOP: c.23.1.0

Probab=99.75  E-value=4.3e-18  Score=162.64  Aligned_cols=118  Identities=24%  Similarity=0.395  Sum_probs=108.9

Q ss_pred             CCeEEEEecCHHHHHHHHHHHHhcCCeEEEEcCHHHHHHHHHcCCCcEEEEcCCCCCCCHHHHHHHHhccccCCCchhhh
Q 039716          859 KPKILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDAAA  938 (1002)
Q Consensus       859 ~~~ILiVeDn~~n~~~l~~~L~~~g~~v~~a~~G~eAl~~~~~~~~DlIlmDi~MP~mdG~e~~~~IR~~~~~~~~~~~~  938 (1002)
                      ..+||||||++..+..++.+|+..||.|..+.++.+|++.+....||+||+|+.||+++|+++++.||+..         
T Consensus         3 ~~~ilivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~a~~~l~~~~~dlii~D~~l~~~~g~~~~~~l~~~~---------   73 (127)
T 3i42_A            3 LQQALIVEDYQAAAETFKELLEMLGFQADYVMSGTDALHAMSTRGYDAVFIDLNLPDTSGLALVKQLRALP---------   73 (127)
T ss_dssp             CEEEEEECSCHHHHHHHHHHHHHTTEEEEEESSHHHHHHHHHHSCCSEEEEESBCSSSBHHHHHHHHHHSC---------
T ss_pred             cceEEEEcCCHHHHHHHHHHHHHcCCCEEEECCHHHHHHHHHhcCCCEEEEeCCCCCCCHHHHHHHHHhhh---------
Confidence            35899999999999999999999999999999999999999999999999999999999999999999742         


Q ss_pred             hhhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHHhhc
Q 039716          939 EAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQYF 1001 (1002)
Q Consensus       939 ~~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~~l 1001 (1002)
                                     ..+.+|||++|+....+. ..++..|+++||.||++.++|...++.+.
T Consensus        74 ---------------~~~~~~ii~~s~~~~~~~-~~~~~~g~~~~l~KP~~~~~L~~~i~~~~  120 (127)
T 3i42_A           74 ---------------MEKTSKFVAVSGFAKNDL-GKEACELFDFYLEKPIDIASLEPILQSIE  120 (127)
T ss_dssp             ---------------CSSCCEEEEEECC-CTTC-CHHHHHHCSEEEESSCCHHHHHHHHHHHC
T ss_pred             ---------------ccCCCCEEEEECCcchhH-HHHHHHhhHHheeCCCCHHHHHHHHHHhh
Confidence                           246799999999998888 88999999999999999999999998764

>3hdv_A Response regulator; PSI-II, structural genomics, Pro structure initiative, NEW YORK SGX research center for STRU genomics, nysgxrc; 2.09A {Pseudomonas putida} SCOP: c.23.1.0

Probab=99.75  E-value=1.7e-17  Score=160.39  Aligned_cols=119  Identities=27%  Similarity=0.355  Sum_probs=110.4

Q ss_pred             CCCeEEEEecCHHHHHHHHHHHHhcCCeEEEEcCHHHHHHHHHcCC-CcEEEEcCCCCCCCHHHHHHHHhccccCCCchh
Q 039716          858 PKPKILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQN-YDLILMDVCMPVMDGLKATRLIRSFEDTGNWDA  936 (1002)
Q Consensus       858 ~~~~ILiVeDn~~n~~~l~~~L~~~g~~v~~a~~G~eAl~~~~~~~-~DlIlmDi~MP~mdG~e~~~~IR~~~~~~~~~~  936 (1002)
                      ...+||||||++..+..++.+|+..||.|..+.++.+|+..+.... ||+||+|+.||+++|+++++.||+..       
T Consensus         6 ~~~~ilivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~a~~~~~~~~~~dlvi~D~~l~~~~g~~~~~~l~~~~-------   78 (136)
T 3hdv_A            6 ARPLVLVVDDNAVNREALILYLKSRGIDAVGADGAEEARLYLHYQKRIGLMITDLRMQPESGLDLIRTIRASE-------   78 (136)
T ss_dssp             -CCEEEEECSCHHHHHHHHHHHHHTTCCEEEESSHHHHHHHHHHCTTEEEEEECSCCSSSCHHHHHHHHHTST-------
T ss_pred             CCCeEEEECCCHHHHHHHHHHHHHcCceEEEeCCHHHHHHHHHhCCCCcEEEEeccCCCCCHHHHHHHHHhcC-------
Confidence            3568999999999999999999999999999999999999998777 99999999999999999999999631       


Q ss_pred             hhhhhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHHhhc
Q 039716          937 AAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQYF 1001 (1002)
Q Consensus       937 ~~~~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~~l 1001 (1002)
                                        .+.+|||++|+....+...+++++|+++||.||++.++|...|++++
T Consensus        79 ------------------~~~~~ii~~s~~~~~~~~~~~~~~g~~~~l~KP~~~~~l~~~i~~~~  125 (136)
T 3hdv_A           79 ------------------RAALSIIVVSGDTDVEEAVDVMHLGVVDFLLKPVDLGKLLELVNKEL  125 (136)
T ss_dssp             ------------------TTTCEEEEEESSCCHHHHHHHHHTTCSEEEESSCCHHHHHHHHHHHH
T ss_pred             ------------------CCCCCEEEEeCCCChHHHHHHHhCCcceEEeCCCCHHHHHHHHHHHh
Confidence                              36799999999999999999999999999999999999999998864

>1xhf_A DYE resistance, aerobic respiration control protein ARCA; two-component system, gene regulation, transcription factor, anoxic redox control; 2.15A {Escherichia coli} SCOP: c.23.1.1 PDB: 1xhe_A

Probab=99.75  E-value=1.5e-17  Score=157.82  Aligned_cols=115  Identities=22%  Similarity=0.353  Sum_probs=107.9

Q ss_pred             CCeEEEEecCHHHHHHHHHHHHhcCCeEEEEcCHHHHHHHHHcCCCcEEEEcCCCCCCCHHHHHHHHhccccCCCchhhh
Q 039716          859 KPKILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDAAA  938 (1002)
Q Consensus       859 ~~~ILiVeDn~~n~~~l~~~L~~~g~~v~~a~~G~eAl~~~~~~~~DlIlmDi~MP~mdG~e~~~~IR~~~~~~~~~~~~  938 (1002)
                      .++||||||++..+..++.+|+..||.|..+.++.+|++.+....||+||+|+.||+++|+++++.||+.          
T Consensus         3 ~~~ilivdd~~~~~~~l~~~l~~~~~~v~~~~~~~~a~~~~~~~~~dlvi~D~~l~~~~g~~~~~~l~~~----------   72 (123)
T 1xhf_A            3 TPHILIVEDELVTRNTLKSIFEAEGYDVFEATDGAEMHQILSEYDINLVIMDINLPGKNGLLLARELREQ----------   72 (123)
T ss_dssp             CCEEEEECSCHHHHHHHHHHHHTTTCEEEEESSHHHHHHHHHHSCCSEEEECSSCSSSCHHHHHHHHHHH----------
T ss_pred             CceEEEEeCCHHHHHHHHHHHhhCCcEEEEeCCHHHHHHHHhcCCCCEEEEcCCCCCCCHHHHHHHHHhC----------
Confidence            3589999999999999999999999999999999999999999999999999999999999999999962          


Q ss_pred             hhhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHHhh
Q 039716          939 EAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQY 1000 (1002)
Q Consensus       939 ~~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~~ 1000 (1002)
                                       +.+|||++|+........+++++|+++|+.||++.++|...|++.
T Consensus        73 -----------------~~~~ii~~s~~~~~~~~~~~~~~g~~~~l~KP~~~~~l~~~i~~~  117 (123)
T 1xhf_A           73 -----------------ANVALMFLTGRDNEVDKILGLEIGADDYITKPFNPRELTIRARNL  117 (123)
T ss_dssp             -----------------CCCEEEEEESCCSHHHHHHHHHHTCSEEEESSCCHHHHHHHHHHH
T ss_pred             -----------------CCCcEEEEECCCChHHHHHHHhcCcceEEeCCCCHHHHHHHHHHH
Confidence                             358999999999999999999999999999999999999988765

>1p6q_A CHEY2; chemotaxis, signal transduction, response regulator, structural proteomics in europe, spine, structural genomics; NMR {Sinorhizobium meliloti} SCOP: c.23.1.1 PDB: 1p6u_A

Probab=99.75  E-value=9.4e-18  Score=160.56  Aligned_cols=119  Identities=27%  Similarity=0.440  Sum_probs=109.6

Q ss_pred             CCeEEEEecCHHHHHHHHHHHHhcCC-eEEEEcCHHHHHHHHHcCCCcEEEEcCCCCCCCHHHHHHHHhccccCCCchhh
Q 039716          859 KPKILLVEDNKINVMVAKSMMKQLGH-SIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDAA  937 (1002)
Q Consensus       859 ~~~ILiVeDn~~n~~~l~~~L~~~g~-~v~~a~~G~eAl~~~~~~~~DlIlmDi~MP~mdG~e~~~~IR~~~~~~~~~~~  937 (1002)
                      ..+||||||++..+..++.+|+..|| .+..+.++.+|++.+....||+||+|+.||+++|+++++.||+..        
T Consensus         6 ~~~ilivdd~~~~~~~l~~~L~~~g~~~v~~~~~~~~a~~~~~~~~~dlvl~D~~l~~~~g~~~~~~l~~~~--------   77 (129)
T 1p6q_A            6 KIKVLIVDDQVTSRLLLGDALQQLGFKQITAAGDGEQGMKIMAQNPHHLVISDFNMPKMDGLGLLQAVRANP--------   77 (129)
T ss_dssp             CCCEEEECSSHHHHHHHHHHHHTTTCSCEECCSSHHHHHHHHHTSCCSEEEECSSSCSSCHHHHHHHHTTCT--------
T ss_pred             cCeEEEEcCCHHHHHHHHHHHHHCCCcEEEecCCHHHHHHHHHcCCCCEEEEeCCCCCCCHHHHHHHHhcCc--------
Confidence            45899999999999999999999999 799999999999999999999999999999999999999999631        


Q ss_pred             hhhhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHHhhc
Q 039716          938 AEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQYF 1001 (1002)
Q Consensus       938 ~~~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~~l 1001 (1002)
                                      ..+.+|||++|+....+...+++++|+++|+.||++.++|...|++.+
T Consensus        78 ----------------~~~~~~ii~~s~~~~~~~~~~~~~~g~~~~l~KP~~~~~l~~~i~~~~  125 (129)
T 1p6q_A           78 ----------------ATKKAAFIILTAQGDRALVQKAAALGANNVLAKPFTIEKMKAAIEAVF  125 (129)
T ss_dssp             ----------------TSTTCEEEECCSCCCHHHHHHHHHHTCSCEECCCSSHHHHHHHHHHHH
T ss_pred             ----------------cccCCCEEEEeCCCCHHHHHHHHHcCCCEEEECCCCHHHHHHHHHHHH
Confidence                            235799999999999999999999999999999999999999998753

>3lua_A Response regulator receiver protein; two-component signal transduction system, histidine kinase, phosphorelay, receiver domain, nysgxrc; 2.40A {Clostridium thermocellum}

Probab=99.75  E-value=5.1e-18  Score=165.19  Aligned_cols=119  Identities=17%  Similarity=0.236  Sum_probs=111.3

Q ss_pred             CCeEEEEecCHHHHHHHHHHHHh-cCCeEEEEcCHHHHHHHHHc-CCCcEEEEcCCCC-CCCHHHHHHHHhccccCCCch
Q 039716          859 KPKILLVEDNKINVMVAKSMMKQ-LGHSIDVVNNGVEAVHAVQC-QNYDLILMDVCMP-VMDGLKATRLIRSFEDTGNWD  935 (1002)
Q Consensus       859 ~~~ILiVeDn~~n~~~l~~~L~~-~g~~v~~a~~G~eAl~~~~~-~~~DlIlmDi~MP-~mdG~e~~~~IR~~~~~~~~~  935 (1002)
                      ..+||||||++..+..++.+|+. .||.|..+.++.+|++.+.. ..||+||+|+.|| +++|+++++.||+..      
T Consensus         4 ~~~ilivdd~~~~~~~l~~~L~~~~~~~v~~~~~~~~a~~~l~~~~~~dlvi~D~~l~~~~~g~~~~~~l~~~~------   77 (140)
T 3lua_A            4 DGTVLLIDYFEYEREKTKIIFDNIGEYDFIEVENLKKFYSIFKDLDSITLIIMDIAFPVEKEGLEVLSAIRNNS------   77 (140)
T ss_dssp             CCEEEEECSCHHHHHHHHHHHHHHCCCEEEEECSHHHHHTTTTTCCCCSEEEECSCSSSHHHHHHHHHHHHHSG------
T ss_pred             CCeEEEEeCCHHHHHHHHHHHHhccCccEEEECCHHHHHHHHhcCCCCcEEEEeCCCCCCCcHHHHHHHHHhCc------
Confidence            46899999999999999999999 99999999999999999999 9999999999999 999999999999732      


Q ss_pred             hhhhhhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHHhhc
Q 039716          936 AAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQYF 1001 (1002)
Q Consensus       936 ~~~~~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~~l 1001 (1002)
                                        ..+.+|||++|+....+...+++++|+++||.||++.++|...|++++
T Consensus        78 ------------------~~~~~~ii~ls~~~~~~~~~~~~~~g~~~~l~KP~~~~~l~~~i~~~~  125 (140)
T 3lua_A           78 ------------------RTANTPVIIATKSDNPGYRHAALKFKVSDYILKPYPTKRLENSVRSVL  125 (140)
T ss_dssp             ------------------GGTTCCEEEEESCCCHHHHHHHHHSCCSEEEESSCCTTHHHHHHHHHH
T ss_pred             ------------------ccCCCCEEEEeCCCCHHHHHHHHHcCCCEEEECCCCHHHHHHHHHHHH
Confidence                              236799999999999999999999999999999999999999998764

>3hzh_A Chemotaxis response regulator (CHEY-3); phosphatase, complex, response regulator, receiver domain, two-component signal transduction; HET: BFD; 1.96A {Borrelia burgdorferi}

Probab=99.75  E-value=1.1e-17  Score=166.79  Aligned_cols=118  Identities=25%  Similarity=0.417  Sum_probs=111.0

Q ss_pred             CCCeEEEEecCHHHHHHHHHHHHhcCCeEE-EEcCHHHHHHHHHcC--CCcEEEEcCCCCCCCHHHHHHHHhccccCCCc
Q 039716          858 PKPKILLVEDNKINVMVAKSMMKQLGHSID-VVNNGVEAVHAVQCQ--NYDLILMDVCMPVMDGLKATRLIRSFEDTGNW  934 (1002)
Q Consensus       858 ~~~~ILiVeDn~~n~~~l~~~L~~~g~~v~-~a~~G~eAl~~~~~~--~~DlIlmDi~MP~mdG~e~~~~IR~~~~~~~~  934 (1002)
                      ...+||||||++..+..++.+|+..||.+. .+.++.+|++.+...  .|||||+|+.||+++|+++++.||+.      
T Consensus        35 ~~~~Ilivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~~al~~l~~~~~~~dliilD~~l~~~~g~~~~~~lr~~------  108 (157)
T 3hzh_A           35 IPFNVLIVDDSVFTVKQLTQIFTSEGFNIIDTAADGEEAVIKYKNHYPNIDIVTLXITMPKMDGITCLSNIMEF------  108 (157)
T ss_dssp             EECEEEEECSCHHHHHHHHHHHHHTTCEEEEEESSHHHHHHHHHHHGGGCCEEEECSSCSSSCHHHHHHHHHHH------
T ss_pred             CceEEEEEeCCHHHHHHHHHHHHhCCCeEEEEECCHHHHHHHHHhcCCCCCEEEEeccCCCccHHHHHHHHHhh------
Confidence            456999999999999999999999999988 999999999999988  89999999999999999999999973      


Q ss_pred             hhhhhhhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHHhhc
Q 039716          935 DAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQYF 1001 (1002)
Q Consensus       935 ~~~~~~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~~l 1001 (1002)
                                          .+.+|||++|+..+.+...+|+++|+++||.||++.++|...|++++
T Consensus       109 --------------------~~~~~ii~ls~~~~~~~~~~~~~~g~~~~l~KP~~~~~l~~~i~~~l  155 (157)
T 3hzh_A          109 --------------------DKNARVIMISALGKEQLVKDCLIKGAKTFIVKPLDRAKVLQRVMSVF  155 (157)
T ss_dssp             --------------------CTTCCEEEEESCCCHHHHHHHHHTTCSEEEESSCCHHHHHHHHHHTT
T ss_pred             --------------------CCCCcEEEEeccCcHHHHHHHHHcCCCEEEeCCCCHHHHHHHHHHHh
Confidence                                25689999999999999999999999999999999999999999876

>3heb_A Response regulator receiver domain protein (CHEY); NYSGXRC, PSI-II, respose regulator, structure initiative, structural genomics; 2.40A {Rhodospirillum rubrum} SCOP: c.23.1.0

Probab=99.75  E-value=1.8e-17  Score=163.87  Aligned_cols=118  Identities=20%  Similarity=0.481  Sum_probs=108.9

Q ss_pred             CCeEEEEecCHHHHHHHHHHHHhcCC--eEEEEcCHHHHHHHHH---------cCCCcEEEEcCCCCCCCHHHHHHHHhc
Q 039716          859 KPKILLVEDNKINVMVAKSMMKQLGH--SIDVVNNGVEAVHAVQ---------CQNYDLILMDVCMPVMDGLKATRLIRS  927 (1002)
Q Consensus       859 ~~~ILiVeDn~~n~~~l~~~L~~~g~--~v~~a~~G~eAl~~~~---------~~~~DlIlmDi~MP~mdG~e~~~~IR~  927 (1002)
                      +.+||||||++..+..++.+|+..|+  .|..+.++.+|++.+.         ...||+||+|+.||+++|+++++.||.
T Consensus         4 ~~~ILivddd~~~~~~l~~~L~~~g~~~~v~~~~~~~~al~~l~~~~~~~~~~~~~~dliilD~~l~~~~g~~~~~~lr~   83 (152)
T 3heb_A            4 SVTIVMIEDDLGHARLIEKNIRRAGVNNEIIAFTDGTSALNYLFGDDKSGRVSAGRAQLVLLDLNLPDMTGIDILKLVKE   83 (152)
T ss_dssp             -CEEEEECCCHHHHHHHHHHHHHTTCCCCEEEESSHHHHHHHHHCTTSSSGGGTTCBEEEEECSBCSSSBHHHHHHHHHH
T ss_pred             CceEEEEeCCHHHHHHHHHHHHhCCCcceEEEeCCHHHHHHHHhccccccccccCCCCEEEEeCCCCCCcHHHHHHHHHh
Confidence            46899999999999999999999998  8999999999999995         678999999999999999999999997


Q ss_pred             cccCCCchhhhhhhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHHhh
Q 039716          928 FEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQY 1000 (1002)
Q Consensus       928 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~~ 1000 (1002)
                      ..                        ..+.+|||++|+....+...+++++|+++||.||++.++|...|+++
T Consensus        84 ~~------------------------~~~~~pii~~t~~~~~~~~~~~~~~g~~~~l~KP~~~~~l~~~i~~~  132 (152)
T 3heb_A           84 NP------------------------HTRRSPVVILTTTDDQREIQRCYDLGANVYITKPVNYENFANAIRQL  132 (152)
T ss_dssp             ST------------------------TTTTSCEEEEESCCCHHHHHHHHHTTCSEEEECCSSHHHHHHHHHHH
T ss_pred             cc------------------------cccCCCEEEEecCCCHHHHHHHHHCCCcEEEeCCCCHHHHHHHHHHH
Confidence            32                        24679999999999999999999999999999999999999999875

>2a9o_A Response regulator; essential protein, YYCF/YYCG homolog, signaling protein; 1.65A {Streptococcus pneumoniae} SCOP: c.23.1.1 PDB: 1nxo_A 1nxs_A 1nxv_A 1nxw_A 1nxx_A 1nxp_A 2a9p_A 2a9q_A 1nxt_A* 2a9r_A*

Probab=99.75  E-value=1.6e-17  Score=156.58  Aligned_cols=115  Identities=27%  Similarity=0.444  Sum_probs=107.6

Q ss_pred             CeEEEEecCHHHHHHHHHHHHhcCCeEEEEcCHHHHHHHHHcCCCcEEEEcCCCCCCCHHHHHHHHhccccCCCchhhhh
Q 039716          860 PKILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDAAAE  939 (1002)
Q Consensus       860 ~~ILiVeDn~~n~~~l~~~L~~~g~~v~~a~~G~eAl~~~~~~~~DlIlmDi~MP~mdG~e~~~~IR~~~~~~~~~~~~~  939 (1002)
                      .+||||||++..+..++.+|...||.+..+.++.+|++.+....||+||+|+.||+++|+++++.||+.           
T Consensus         2 ~~ilivdd~~~~~~~l~~~l~~~~~~v~~~~~~~~a~~~~~~~~~dlvl~D~~l~~~~g~~~~~~l~~~-----------   70 (120)
T 2a9o_A            2 KKILIVDDEKPISDIIKFNMTKEGYEVVTAFNGREALEQFEAEQPDIIILDLMLPEIDGLEVAKTIRKT-----------   70 (120)
T ss_dssp             CEEEEECSCHHHHHHHHHHHHHTTCEEEEESSHHHHHHHHHHHCCSEEEECSSCSSSCHHHHHHHHHHH-----------
T ss_pred             ceEEEEcCCHHHHHHHHHHHHhcCcEEEEecCHHHHHHHHHhCCCCEEEEeccCCCCCHHHHHHHHHhC-----------
Confidence            379999999999999999999999999999999999999998899999999999999999999999952           


Q ss_pred             hhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHHhhc
Q 039716          940 AGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQYF 1001 (1002)
Q Consensus       940 ~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~~l 1001 (1002)
                                      +.+|||++|+.........++++|+++|+.||++.++|...|++.+
T Consensus        71 ----------------~~~~ii~~s~~~~~~~~~~~~~~g~~~~l~Kp~~~~~l~~~i~~~~  116 (120)
T 2a9o_A           71 ----------------SSVPILMLSAKDSEFDKVIGLELGADDYVTKPFSNRELQARVKALL  116 (120)
T ss_dssp             ----------------CCCCEEEEESCCSHHHHHHHHHHTCSEEEESSCCHHHHHHHHHHHH
T ss_pred             ----------------CCCCEEEEecCCchHHHHHHHhCCHhheEeCCCCHHHHHHHHHHHH
Confidence                            3589999999999999999999999999999999999999988753

>3kto_A Response regulator receiver protein; PSI-II,structural genomics, protein structure initiative; 1.98A {Pseudoalteromonas atlantica T6C} SCOP: c.23.1.0

Probab=99.75  E-value=4.3e-18  Score=165.10  Aligned_cols=117  Identities=15%  Similarity=0.184  Sum_probs=109.9

Q ss_pred             CCeEEEEecCHHHHHHHHHHHHhcCCeEEEEcCHHHHHHHHHcCCCcEEEEcCCCCC--CCHHHHHHHHhccccCCCchh
Q 039716          859 KPKILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPV--MDGLKATRLIRSFEDTGNWDA  936 (1002)
Q Consensus       859 ~~~ILiVeDn~~n~~~l~~~L~~~g~~v~~a~~G~eAl~~~~~~~~DlIlmDi~MP~--mdG~e~~~~IR~~~~~~~~~~  936 (1002)
                      ..+||||||++..+..++.+|+..||.|..+.++.+|++.+....||+||+|+.||+  ++|+++++.||+.        
T Consensus         6 ~~~ilivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~a~~~l~~~~~dlvi~D~~l~~~~~~g~~~~~~l~~~--------   77 (136)
T 3kto_A            6 HPIIYLVDHQKDARAALSKLLSPLDVTIQCFASAESFMRQQISDDAIGMIIEAHLEDKKDSGIELLETLVKR--------   77 (136)
T ss_dssp             -CEEEEECSCHHHHHHHHHHHTTSSSEEEEESSHHHHTTSCCCTTEEEEEEETTGGGBTTHHHHHHHHHHHT--------
T ss_pred             CCeEEEEcCCHHHHHHHHHHHHHCCcEEEEeCCHHHHHHHHhccCCCEEEEeCcCCCCCccHHHHHHHHHhC--------
Confidence            468999999999999999999999999999999999999999999999999999999  9999999999973        


Q ss_pred             hhhhhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHHhhc
Q 039716          937 AAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQYF 1001 (1002)
Q Consensus       937 ~~~~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~~l 1001 (1002)
                                        .+.+|||++|+....+...+|+++|+++||.||++.++|...|++.+
T Consensus        78 ------------------~~~~~ii~~s~~~~~~~~~~~~~~ga~~~l~KP~~~~~l~~~i~~~~  124 (136)
T 3kto_A           78 ------------------GFHLPTIVMASSSDIPTAVRAMRASAADFIEKPFIEHVLVHDVQQII  124 (136)
T ss_dssp             ------------------TCCCCEEEEESSCCHHHHHHHHHTTCSEEEESSBCHHHHHHHHHHHH
T ss_pred             ------------------CCCCCEEEEEcCCCHHHHHHHHHcChHHheeCCCCHHHHHHHHHHHH
Confidence                              36799999999999999999999999999999999999999998753

>1i3c_A Response regulator RCP1; phytochrome, signaling protein; 1.90A {Synechocystis SP} SCOP: c.23.1.1 PDB: 1jlk_A

Probab=99.75  E-value=2e-17  Score=163.16  Aligned_cols=118  Identities=22%  Similarity=0.387  Sum_probs=107.3

Q ss_pred             CCeEEEEecCHHHHHHHHHHHHhcCC--eEEEEcCHHHHHHHHHc-------CCCcEEEEcCCCCCCCHHHHHHHHhccc
Q 039716          859 KPKILLVEDNKINVMVAKSMMKQLGH--SIDVVNNGVEAVHAVQC-------QNYDLILMDVCMPVMDGLKATRLIRSFE  929 (1002)
Q Consensus       859 ~~~ILiVeDn~~n~~~l~~~L~~~g~--~v~~a~~G~eAl~~~~~-------~~~DlIlmDi~MP~mdG~e~~~~IR~~~  929 (1002)
                      ..+||||||++..+..++.+|+..|+  .|..+.+|.+|++.+..       ..||+||+|+.||+|||+++++.||+..
T Consensus         8 ~~~ILivdd~~~~~~~l~~~L~~~~~~~~v~~~~~~~~al~~l~~~~~~~~~~~~dlillD~~lp~~~g~~l~~~l~~~~   87 (149)
T 1i3c_A            8 PKVILLVEDSKADSRLVQEVLKTSTIDHELIILRDGLAAMAFLQQQGEYENSPRPNLILLDLNLPKKDGREVLAEIKQNP   87 (149)
T ss_dssp             CEEEEEECCCHHHHHHHHHHHHSCCSCEEEEEECSHHHHHHHHTTCGGGTTCCCCSEEEECSCCSSSCHHHHHHHHHHCT
T ss_pred             CCeEEEEECCHHHHHHHHHHHHhcCCCccEEEeCCHHHHHHHHHhccccccCCCCCEEEEeCCCCCCcHHHHHHHHHhCc
Confidence            45899999999999999999999887  78999999999999975       5799999999999999999999999631


Q ss_pred             cCCCchhhhhhhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHHhh
Q 039716          930 DTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQY 1000 (1002)
Q Consensus       930 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~~ 1000 (1002)
                                              ..+++|||++|+....+...+++++|+++||.||++.++|...|++.
T Consensus        88 ------------------------~~~~~piiils~~~~~~~~~~~~~~ga~~~l~KP~~~~~L~~~i~~~  134 (149)
T 1i3c_A           88 ------------------------DLKRIPVVVLTTSHNEDDVIASYELHVNCYLTKSRNLKDLFKMVQGI  134 (149)
T ss_dssp             ------------------------TTTTSCEEEEESCCCHHHHHHHHHTTCSEEEECCSSHHHHHHHHHHH
T ss_pred             ------------------------CcCCCeEEEEECCCChHHHHHHHHcCCcEEEECCCCHHHHHHHHHHH
Confidence                                    23579999999999999999999999999999999999999988764

>3grc_A Sensor protein, kinase; protein structure initiative II(PSI II), NYSGXRC, 11025B, structural genomics; 2.21A {Polaromonas SP}

Probab=99.74  E-value=6.9e-18  Score=164.08  Aligned_cols=119  Identities=23%  Similarity=0.377  Sum_probs=109.5

Q ss_pred             CCeEEEEecCHHHHHHHHHHHHhcCCeEEEEcCHHHHHHHHHcCCCcEEEEcCCCCCCCHHHHHHHHhccccCCCchhhh
Q 039716          859 KPKILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDAAA  938 (1002)
Q Consensus       859 ~~~ILiVeDn~~n~~~l~~~L~~~g~~v~~a~~G~eAl~~~~~~~~DlIlmDi~MP~mdG~e~~~~IR~~~~~~~~~~~~  938 (1002)
                      ..+||||||++..+..++.+|+..||.|..+.++.+|++.+....||+||+|+.||+++|+++++.||+..         
T Consensus         6 ~~~iLivdd~~~~~~~l~~~l~~~g~~v~~~~~~~~a~~~l~~~~~dlvi~d~~l~~~~g~~~~~~l~~~~---------   76 (140)
T 3grc_A            6 RPRILICEDDPDIARLLNLMLEKGGFDSDMVHSAAQALEQVARRPYAAMTVDLNLPDQDGVSLIRALRRDS---------   76 (140)
T ss_dssp             CSEEEEECSCHHHHHHHHHHHHHTTCEEEEECSHHHHHHHHHHSCCSEEEECSCCSSSCHHHHHHHHHTSG---------
T ss_pred             CCCEEEEcCCHHHHHHHHHHHHHCCCeEEEECCHHHHHHHHHhCCCCEEEEeCCCCCCCHHHHHHHHHhCc---------
Confidence            46899999999999999999999999999999999999999999999999999999999999999999632         


Q ss_pred             hhhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHH-HHHHcCCCEEEeCCCChHHHHHHHHhhc
Q 039716          939 EAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAE-ECFANGMDSFVSKPVTFQKLKECLEQYF 1001 (1002)
Q Consensus       939 ~~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~-~~~~aG~d~~l~KP~~~~~L~~~l~~~l 1001 (1002)
                                     ..+.+|||++|+........ .++.+|+++||.||++.++|...|++.+
T Consensus        77 ---------------~~~~~~ii~~s~~~~~~~~~~~~~~~g~~~~l~kP~~~~~l~~~i~~~l  125 (140)
T 3grc_A           77 ---------------RTRDLAIVVVSANAREGELEFNSQPLAVSTWLEKPIDENLLILSLHRAI  125 (140)
T ss_dssp             ---------------GGTTCEEEEECTTHHHHHHHHCCTTTCCCEEECSSCCHHHHHHHHHHHH
T ss_pred             ---------------ccCCCCEEEEecCCChHHHHHHhhhcCCCEEEeCCCCHHHHHHHHHHHH
Confidence                           23679999999998887777 8999999999999999999999998754

>3b2n_A Uncharacterized protein Q99UF4; structural genomics, PSI-2, protein structure initiative, NE SGX research center for structural genomics; 2.04A {Staphylococcus aureus}

Probab=99.74  E-value=1.7e-17  Score=160.23  Aligned_cols=116  Identities=22%  Similarity=0.360  Sum_probs=107.3

Q ss_pred             CeEEEEecCHHHHHHHHHHHHhcC--CeEEEEcCHHHHHHHHHcCCCcEEEEcCCCCCCCHHHHHHHHhccccCCCchhh
Q 039716          860 PKILLVEDNKINVMVAKSMMKQLG--HSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDAA  937 (1002)
Q Consensus       860 ~~ILiVeDn~~n~~~l~~~L~~~g--~~v~~a~~G~eAl~~~~~~~~DlIlmDi~MP~mdG~e~~~~IR~~~~~~~~~~~  937 (1002)
                      .+||||||++..+..++.+|+..|  +.+..+.++.+|++.+....||+||+|+.||+++|+++++.||+.         
T Consensus         4 ~~Ilivdd~~~~~~~l~~~l~~~~~~~~v~~~~~~~~al~~~~~~~~dlvilD~~lp~~~g~~~~~~l~~~---------   74 (133)
T 3b2n_A            4 TSLIIAEDQNMLRQAMVQLIKLHGDFEILADTDNGLDAMKLIEEYNPNVVILDIEMPGMTGLEVLAEIRKK---------   74 (133)
T ss_dssp             EEEEEECSCHHHHHHHHHHHHHHSSEEEEEEESCHHHHHHHHHHHCCSEEEECSSCSSSCHHHHHHHHHHT---------
T ss_pred             eEEEEECCCHHHHHHHHHHHhhCCCcEEEEEcCCHHHHHHHHhhcCCCEEEEecCCCCCCHHHHHHHHHHH---------
Confidence            479999999999999999999887  567889999999999998899999999999999999999999962         


Q ss_pred             hhhhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHHhhc
Q 039716          938 AEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQYF 1001 (1002)
Q Consensus       938 ~~~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~~l 1001 (1002)
                                       .+.+|||++|+....+...+++.+|+++||.||++.++|...|++.+
T Consensus        75 -----------------~~~~~ii~ls~~~~~~~~~~~~~~ga~~~l~Kp~~~~~L~~~i~~~~  121 (133)
T 3b2n_A           75 -----------------HLNIKVIIVTTFKRPGYFEKAVVNDVDAYVLKERSIEELVETINKVN  121 (133)
T ss_dssp             -----------------TCSCEEEEEESCCCHHHHHHHHHTTCSEEEETTSCHHHHHHHHHHHH
T ss_pred             -----------------CCCCcEEEEecCCCHHHHHHHHHcCCcEEEECCCCHHHHHHHHHHHH
Confidence                             35799999999999999999999999999999999999999998753

>4dad_A Putative pilus assembly-related protein; response regulator receiver domain, CHEY-related protein, ST genomics; 2.50A {Burkholderia pseudomallei} PDB: 4dn6_A

Probab=99.74  E-value=4.2e-18  Score=167.04  Aligned_cols=119  Identities=12%  Similarity=0.196  Sum_probs=110.1

Q ss_pred             CCCCeEEEEecCHHHHHHHHHHHHhcC-CeEEEEcCHHHHHHHHHc--CCCcEEEEcCCCCCCCHHHHHHHHhccccCCC
Q 039716          857 KPKPKILLVEDNKINVMVAKSMMKQLG-HSIDVVNNGVEAVHAVQC--QNYDLILMDVCMPVMDGLKATRLIRSFEDTGN  933 (1002)
Q Consensus       857 ~~~~~ILiVeDn~~n~~~l~~~L~~~g-~~v~~a~~G~eAl~~~~~--~~~DlIlmDi~MP~mdG~e~~~~IR~~~~~~~  933 (1002)
                      ..+.+||||||++..+..+..+|+..| |.|..+.++.+|+..+..  ..||+||+|+.||+++|+++++.||..     
T Consensus        18 ~~~~~ilivdd~~~~~~~l~~~L~~~g~~~v~~~~~~~~~~~~~~~~~~~~dlvi~D~~l~~~~g~~~~~~l~~~-----   92 (146)
T 4dad_A           18 QGMINILVASEDASRLAHLARLVGDAGRYRVTRTVGRAAQIVQRTDGLDAFDILMIDGAALDTAELAAIEKLSRL-----   92 (146)
T ss_dssp             GGGCEEEEECSCHHHHHHHHHHHHHHCSCEEEEECCCHHHHTTCHHHHTTCSEEEEECTTCCHHHHHHHHHHHHH-----
T ss_pred             CCCCeEEEEeCCHHHHHHHHHHHhhCCCeEEEEeCCHHHHHHHHHhcCCCCCEEEEeCCCCCccHHHHHHHHHHh-----
Confidence            456799999999999999999999999 999999999999988765  899999999999999999999999973     


Q ss_pred             chhhhhhhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHHhhc
Q 039716          934 WDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQYF 1001 (1002)
Q Consensus       934 ~~~~~~~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~~l 1001 (1002)
                                           .+.+|||++|+....+...+|+.+|+++||.||++.++|...|++.+
T Consensus        93 ---------------------~~~~~ii~lt~~~~~~~~~~~~~~ga~~~l~Kp~~~~~L~~~i~~~~  139 (146)
T 4dad_A           93 ---------------------HPGLTCLLVTTDASSQTLLDAMRAGVRDVLRWPLEPRALDDALKRAA  139 (146)
T ss_dssp             ---------------------CTTCEEEEEESCCCHHHHHHHHTTTEEEEEESSCCHHHHHHHHHHHH
T ss_pred             ---------------------CCCCcEEEEeCCCCHHHHHHHHHhCCceeEcCCCCHHHHHHHHHHHH
Confidence                                 25689999999999999999999999999999999999999998764

>3cfy_A Putative LUXO repressor protein; structural genomics, unknown function, uncharacterized protein, signal receiver domain; 2.50A {Vibrio parahaemolyticus rimd 2210633}

Probab=99.74  E-value=1.2e-17  Score=162.54  Aligned_cols=116  Identities=25%  Similarity=0.367  Sum_probs=108.6

Q ss_pred             CeEEEEecCHHHHHHHHHHHHhcCCeEEEEcCHHHHHHHHHcCCCcEEEEcCCCCCCCHHHHHHHHhccccCCCchhhhh
Q 039716          860 PKILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDAAAE  939 (1002)
Q Consensus       860 ~~ILiVeDn~~n~~~l~~~L~~~g~~v~~a~~G~eAl~~~~~~~~DlIlmDi~MP~mdG~e~~~~IR~~~~~~~~~~~~~  939 (1002)
                      .+||||||++..+..++.+|+..||.|..+.++.+|++.+....||+||+|+.||+++|+++++.||+.           
T Consensus         5 ~~ILivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~a~~~l~~~~~dlvllD~~l~~~~g~~l~~~l~~~-----------   73 (137)
T 3cfy_A            5 PRVLLVEDSTSLAILYKQYVKDEPYDIFHVETGRDAIQFIERSKPQLIILDLKLPDMSGEDVLDWINQN-----------   73 (137)
T ss_dssp             CEEEEECSCTTHHHHHHHHTTTSSSEEEEESSHHHHHHHHHHHCCSEEEECSBCSSSBHHHHHHHHHHT-----------
T ss_pred             ceEEEEeCCHHHHHHHHHHHHhcCceEEEeCCHHHHHHHHHhcCCCEEEEecCCCCCCHHHHHHHHHhc-----------
Confidence            379999999999999999999999999999999999999999999999999999999999999999962           


Q ss_pred             hhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHHhhc
Q 039716          940 AGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQYF 1001 (1002)
Q Consensus       940 ~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~~l 1001 (1002)
                                     .+.+|||++|+....+...+++++|+++||.||++.++|...|++.+
T Consensus        74 ---------------~~~~~ii~ls~~~~~~~~~~~~~~ga~~~l~KP~~~~~L~~~i~~~~  120 (137)
T 3cfy_A           74 ---------------DIPTSVIIATAHGSVDLAVNLIQKGAEDFLEKPINADRLKTSVALHL  120 (137)
T ss_dssp             ---------------TCCCEEEEEESSCCHHHHHHHHHTTCSEEEESSCCHHHHHHHHHHHH
T ss_pred             ---------------CCCCCEEEEEecCcHHHHHHHHHCCccEEEeCCCCHHHHHHHHHHHH
Confidence                           25689999999999999999999999999999999999999987653

>3hdg_A Uncharacterized protein; two-component sensor activity, response regulator, PSI-II, 11227F, NYSGXRC, structural genomics; 2.27A {Wolinella succinogenes} SCOP: c.23.1.0

Probab=99.74  E-value=1.3e-17  Score=161.54  Aligned_cols=118  Identities=22%  Similarity=0.256  Sum_probs=110.6

Q ss_pred             CCCeEEEEecCHHHHHHHHHHHHhcCCeEEEEcCHHHHHHHHHcCCCcEEEEcCCCCCCCHHHHHHHHhccccCCCchhh
Q 039716          858 PKPKILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDAA  937 (1002)
Q Consensus       858 ~~~~ILiVeDn~~n~~~l~~~L~~~g~~v~~a~~G~eAl~~~~~~~~DlIlmDi~MP~mdG~e~~~~IR~~~~~~~~~~~  937 (1002)
                      ...+||||||++..+..++.+|+..|+.|..+.++.+|++.+....||+||+|+.||+++|+++++.||+.         
T Consensus         6 ~~~~ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~a~~~l~~~~~dlvi~d~~l~~~~g~~~~~~l~~~---------   76 (137)
T 3hdg_A            6 VALKILIVEDDTDAREWLSTIISNHFPEVWSAGDGEEGERLFGLHAPDVIITDIRMPKLGGLEMLDRIKAG---------   76 (137)
T ss_dssp             -CCCEEEECSCHHHHHHHHHHHHTTCSCEEEESSHHHHHHHHHHHCCSEEEECSSCSSSCHHHHHHHHHHT---------
T ss_pred             cccEEEEEeCCHHHHHHHHHHHHhcCcEEEEECCHHHHHHHHhccCCCEEEEeCCCCCCCHHHHHHHHHhc---------
Confidence            35689999999999999999999999999999999999999999999999999999999999999999963         


Q ss_pred             hhhhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHHhhc
Q 039716          938 AEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQYF 1001 (1002)
Q Consensus       938 ~~~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~~l 1001 (1002)
                                       .+.+|||++|+....+...+++.+|+++||.||++.++|...|++++
T Consensus        77 -----------------~~~~~ii~~s~~~~~~~~~~~~~~g~~~~l~kP~~~~~l~~~i~~~~  123 (137)
T 3hdg_A           77 -----------------GAKPYVIVISAFSEMKYFIKAIELGVHLFLPKPIEPGRLMETLEDFR  123 (137)
T ss_dssp             -----------------TCCCEEEECCCCCCHHHHHHHHHHCCSEECCSSCCHHHHHHHHHHHH
T ss_pred             -----------------CCCCcEEEEecCcChHHHHHHHhCCcceeEcCCCCHHHHHHHHHHHH
Confidence                             35789999999999999999999999999999999999999998764

>2qzj_A Two-component response regulator; 11017X, PSI-II, structural genomics; 2.89A {Clostridium difficile}

Probab=99.74  E-value=1.9e-17  Score=160.79  Aligned_cols=115  Identities=27%  Similarity=0.427  Sum_probs=108.0

Q ss_pred             CCeEEEEecCHHHHHHHHHHHHhcCCeEEEEcCHHHHHHHHHcCCCcEEEEcCCCCCCCHHHHHHHHhccccCCCchhhh
Q 039716          859 KPKILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDAAA  938 (1002)
Q Consensus       859 ~~~ILiVeDn~~n~~~l~~~L~~~g~~v~~a~~G~eAl~~~~~~~~DlIlmDi~MP~mdG~e~~~~IR~~~~~~~~~~~~  938 (1002)
                      ..+||||||++..+..+..+|+..|+.|..+.++.+|++.+....||+||+|+.||+++|+++++.||..          
T Consensus         4 ~~~Ilivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~al~~~~~~~~dlvllD~~l~~~~g~~l~~~l~~~----------   73 (136)
T 2qzj_A            4 QTKILIIDGDKDNCQKLKGFLEEKGISIDLAYNCEEAIGKIFSNKYDLIFLEIILSDGDGWTLCKKIRNV----------   73 (136)
T ss_dssp             CCEEEEECSCHHHHHHHHHHHHTTTCEEEEESSHHHHHHHHHHCCCSEEEEESEETTEEHHHHHHHHHTT----------
T ss_pred             CCeEEEEcCCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHHHhcCCCEEEEeCCCCCCCHHHHHHHHccC----------
Confidence            4589999999999999999999999999999999999999999999999999999999999999999952          


Q ss_pred             hhhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHHhh
Q 039716          939 EAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQY 1000 (1002)
Q Consensus       939 ~~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~~ 1000 (1002)
                                       ..+|||++|+....+...+++++|+++||.||++.++|...|++.
T Consensus        74 -----------------~~~~ii~ls~~~~~~~~~~~~~~ga~~~l~KP~~~~~L~~~l~~~  118 (136)
T 2qzj_A           74 -----------------TTCPIVYMTYINEDQSILNALNSGGDDYLIKPLNLEILYAKVKAI  118 (136)
T ss_dssp             -----------------CCCCEEEEESCCCHHHHHHHHHTTCCEEEESSCCHHHHHHHHHHH
T ss_pred             -----------------CCCCEEEEEcCCCHHHHHHHHHcCCcEEEECCCCHHHHHHHHHHH
Confidence                             258999999999999999999999999999999999999998765

>3ilh_A Two component response regulator; NYSGXRC, PSI-II, protein S initiative, structural genomics; 2.59A {Cytophaga hutchinsonii}

Probab=99.74  E-value=2.6e-17  Score=160.66  Aligned_cols=122  Identities=18%  Similarity=0.315  Sum_probs=111.7

Q ss_pred             CCCeEEEEecCHHHHHHHHHHHHhcCC--eEEEEcCHHHHHHHHHc-----CCCcEEEEcCCCCCCCHHHHHHHHhcccc
Q 039716          858 PKPKILLVEDNKINVMVAKSMMKQLGH--SIDVVNNGVEAVHAVQC-----QNYDLILMDVCMPVMDGLKATRLIRSFED  930 (1002)
Q Consensus       858 ~~~~ILiVeDn~~n~~~l~~~L~~~g~--~v~~a~~G~eAl~~~~~-----~~~DlIlmDi~MP~mdG~e~~~~IR~~~~  930 (1002)
                      ...+||||||++..+..++.+|+..|+  .|..+.++.+|++.+..     ..||+||+|+.||+++|+++++.||+...
T Consensus         8 ~~~~iLivdd~~~~~~~l~~~l~~~~~~~~v~~~~~~~~a~~~l~~~~~~~~~~dlvi~D~~l~~~~g~~~~~~l~~~~~   87 (146)
T 3ilh_A            8 KIDSVLLIDDDDIVNFLNTTIIRMTHRVEEIQSVTSGNAAINKLNELYAAGRWPSIICIDINMPGINGWELIDLFKQHFQ   87 (146)
T ss_dssp             CEEEEEEECSCHHHHHHHHHHHHTTCCEEEEEEESSHHHHHHHHHHHHTSSCCCSEEEEESSCSSSCHHHHHHHHHHHCG
T ss_pred             ccceEEEEeCCHHHHHHHHHHHHhcCCCeeeeecCCHHHHHHHHHHhhccCCCCCEEEEcCCCCCCCHHHHHHHHHHhhh
Confidence            356899999999999999999999999  89999999999999998     89999999999999999999999997321


Q ss_pred             CCCchhhhhhhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcC-CCEEEeCCCChHHHHHHHHhhc
Q 039716          931 TGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANG-MDSFVSKPVTFQKLKECLEQYF 1001 (1002)
Q Consensus       931 ~~~~~~~~~~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG-~d~~l~KP~~~~~L~~~l~~~l 1001 (1002)
                                            ...+.+|||++|+....+...+++.+| +++||.||++.++|..+|++++
T Consensus        88 ----------------------~~~~~~~ii~~t~~~~~~~~~~~~~~g~~~~~l~KP~~~~~L~~~i~~~~  137 (146)
T 3ilh_A           88 ----------------------PMKNKSIVCLLSSSLDPRDQAKAEASDWVDYYVSKPLTANALNNLYNKVL  137 (146)
T ss_dssp             ----------------------GGTTTCEEEEECSSCCHHHHHHHHHCSSCCEEECSSCCHHHHHHHHHHHH
T ss_pred             ----------------------hccCCCeEEEEeCCCChHHHHHHHhcCCcceeeeCCCCHHHHHHHHHHHH
Confidence                                  013678999999999999999999999 9999999999999999999874

>3snk_A Response regulator CHEY-like protein; P-loop containing nucleoside triphosphate hydrolases, struct genomics; 2.02A {Mesorhizobium loti}

Probab=99.74  E-value=1.7e-18  Score=167.61  Aligned_cols=118  Identities=12%  Similarity=0.099  Sum_probs=111.2

Q ss_pred             CCCeEEEEecCHHHHHHHHHHHHhcC-CeEEEEcCHHHHHHHHHcCCCcEEEEcCCCCCCCHHHHHHHHhccccCCCchh
Q 039716          858 PKPKILLVEDNKINVMVAKSMMKQLG-HSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDA  936 (1002)
Q Consensus       858 ~~~~ILiVeDn~~n~~~l~~~L~~~g-~~v~~a~~G~eAl~~~~~~~~DlIlmDi~MP~mdG~e~~~~IR~~~~~~~~~~  936 (1002)
                      ...+||||||++..+..++.+|+..| |.|..+.++.+|++.+....||+||+|+.||+++|+++++.||+..       
T Consensus        13 ~~~~ilivdd~~~~~~~l~~~L~~~g~~~v~~~~~~~~a~~~l~~~~~dlvi~D~~l~~~~g~~~~~~l~~~~-------   85 (135)
T 3snk_A           13 KRKQVALFSSDPNFKRDVATRLDALAIYDVRVSETDDFLKGPPADTRPGIVILDLGGGDLLGKPGIVEARALW-------   85 (135)
T ss_dssp             CCEEEEEECSCHHHHHHHHHHHHHTSSEEEEEECGGGGGGCCCTTCCCSEEEEEEETTGGGGSTTHHHHHGGG-------
T ss_pred             CCcEEEEEcCCHHHHHHHHHHHhhcCCeEEEEeccHHHHHHHHhccCCCEEEEeCCCCCchHHHHHHHHHhhC-------
Confidence            35689999999999999999999999 9999999999999999999999999999999999999999999732       


Q ss_pred             hhhhhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHHhhc
Q 039716          937 AAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQYF 1001 (1002)
Q Consensus       937 ~~~~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~~l 1001 (1002)
                                         +.+|||++|+....+...+++++|+++||.||++.++|...|++++
T Consensus        86 -------------------~~~~ii~~s~~~~~~~~~~~~~~g~~~~l~KP~~~~~L~~~i~~~~  131 (135)
T 3snk_A           86 -------------------ATVPLIAVSDELTSEQTRVLVRMNASDWLHKPLDGKELLNAVTFHD  131 (135)
T ss_dssp             -------------------TTCCEEEEESCCCHHHHHHHHHTTCSEEEESSCCHHHHHHHHHHTC
T ss_pred             -------------------CCCcEEEEeCCCCHHHHHHHHHcCcHhhccCCCCHHHHHHHHHHHh
Confidence                               4689999999999999999999999999999999999999999875

>3kht_A Response regulator; PSI-II, 11023K, structural genomics, Pro structure initiative, NEW YORK SGX research center for STRU genomics, nysgxrc; 2.10A {Hahella chejuensis} SCOP: c.23.1.0

Probab=99.74  E-value=2.6e-17  Score=160.98  Aligned_cols=119  Identities=26%  Similarity=0.507  Sum_probs=110.2

Q ss_pred             CCeEEEEecCHHHHHHHHHHHHhcCCe--EEEEcCHHHHHHHHHcCCCcEEEEcCCCCCCCHHHHHHHHhccccCCCchh
Q 039716          859 KPKILLVEDNKINVMVAKSMMKQLGHS--IDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDA  936 (1002)
Q Consensus       859 ~~~ILiVeDn~~n~~~l~~~L~~~g~~--v~~a~~G~eAl~~~~~~~~DlIlmDi~MP~mdG~e~~~~IR~~~~~~~~~~  936 (1002)
                      ..+||||||++..+..++.+|+..|+.  |..+.++.+|++.+....||+||+|+.||+++|+++++.||+..       
T Consensus         5 ~~~ILivdd~~~~~~~l~~~L~~~~~~~~v~~~~~~~~a~~~l~~~~~dlii~D~~l~~~~g~~~~~~lr~~~-------   77 (144)
T 3kht_A            5 SKRVLVVEDNPDDIALIRRVLDRKDIHCQLEFVDNGAKALYQVQQAKYDLIILDIGLPIANGFEVMSAVRKPG-------   77 (144)
T ss_dssp             CEEEEEECCCHHHHHHHHHHHHHTTCCEEEEEESSHHHHHHHHTTCCCSEEEECTTCGGGCHHHHHHHHHSSS-------
T ss_pred             CCEEEEEeCCHHHHHHHHHHHHhcCCCeeEEEECCHHHHHHHhhcCCCCEEEEeCCCCCCCHHHHHHHHHhcc-------
Confidence            468999999999999999999999987  88999999999999999999999999999999999999999632       


Q ss_pred             hhhhhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCC-ChHHHHHHHHhhc
Q 039716          937 AAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPV-TFQKLKECLEQYF 1001 (1002)
Q Consensus       937 ~~~~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~-~~~~L~~~l~~~l 1001 (1002)
                                       ..+.+|||++|+..+.+...+|+++|+++||.||+ +.++|...|++.+
T Consensus        78 -----------------~~~~~pii~~s~~~~~~~~~~~~~~ga~~~l~Kp~~~~~~l~~~i~~~l  126 (144)
T 3kht_A           78 -----------------ANQHTPIVILTDNVSDDRAKQCMAAGASSVVDKSSNNVTDFYGRIYAIF  126 (144)
T ss_dssp             -----------------TTTTCCEEEEETTCCHHHHHHHHHTTCSEEEECCTTSHHHHHHHHHHHH
T ss_pred             -----------------cccCCCEEEEeCCCCHHHHHHHHHcCCCEEEECCCCcHHHHHHHHHHHH
Confidence                             24679999999999999999999999999999999 9999999887653

>3jte_A Response regulator receiver protein; structural genomics, nysgrc, response regulator receiver DOM target 11226E, PSI-2; 1.90A {Clostridium thermocellum atcc 27405}

Probab=99.74  E-value=3.7e-17  Score=159.52  Aligned_cols=117  Identities=21%  Similarity=0.385  Sum_probs=109.5

Q ss_pred             CCeEEEEecCHHHHHHHHHHHHhcCCeEEEEcCHHHHHHHHH--cCCCcEEEEcCCCCCCCHHHHHHHHhccccCCCchh
Q 039716          859 KPKILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQ--CQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDA  936 (1002)
Q Consensus       859 ~~~ILiVeDn~~n~~~l~~~L~~~g~~v~~a~~G~eAl~~~~--~~~~DlIlmDi~MP~mdG~e~~~~IR~~~~~~~~~~  936 (1002)
                      ..+||||||++..+..++.+|+..|+.|..+.++.+|++.+.  ...||+||+|+.||+++|+++++.||..        
T Consensus         3 ~~~ilivdd~~~~~~~l~~~l~~~g~~v~~~~~~~~a~~~~~~~~~~~dlvi~d~~l~~~~g~~~~~~l~~~--------   74 (143)
T 3jte_A            3 LAKILVIDDESTILQNIKFLLEIDGNEVLTASSSTEGLRIFTENCNSIDVVITDMKMPKLSGMDILREIKKI--------   74 (143)
T ss_dssp             CCEEEEECSCHHHHHHHHHHHHHTTCEEEEESSHHHHHHHHHHTTTTCCEEEEESCCSSSCHHHHHHHHHHH--------
T ss_pred             CCEEEEEcCCHHHHHHHHHHHHhCCceEEEeCCHHHHHHHHHhCCCCCCEEEEeCCCCCCcHHHHHHHHHHh--------
Confidence            458999999999999999999999999999999999999998  6799999999999999999999999963        


Q ss_pred             hhhhhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHHhhc
Q 039716          937 AAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQYF 1001 (1002)
Q Consensus       937 ~~~~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~~l 1001 (1002)
                                        .+.+|||++|+....+...+++++|+++||.||++.++|..+|++.+
T Consensus        75 ------------------~~~~~ii~ls~~~~~~~~~~~~~~g~~~~l~kp~~~~~l~~~l~~~~  121 (143)
T 3jte_A           75 ------------------TPHMAVIILTGHGDLDNAILAMKEGAFEYLRKPVTAQDLSIAINNAI  121 (143)
T ss_dssp             ------------------CTTCEEEEEECTTCHHHHHHHHHTTCSEEEESSCCHHHHHHHHHHHH
T ss_pred             ------------------CCCCeEEEEECCCCHHHHHHHHHhCcceeEeCCCCHHHHHHHHHHHH
Confidence                              35699999999999999999999999999999999999999998753

>3dzd_A Transcriptional regulator (NTRC family); sigma43 activator, AAA+ ATPase, response regulator, transcriptional activator, ATP-binding; HET: ADP; 2.40A {Aquifex aeolicus} PDB: 1zit_A 2jrl_A

Probab=99.73  E-value=5.6e-18  Score=193.17  Aligned_cols=115  Identities=20%  Similarity=0.340  Sum_probs=109.1

Q ss_pred             eEEEEecCHHHHHHHHHHHHhcCCeEEEEcCHHHHHHHHHcCCCcEEEEcCCCCCCCHHHHHHHHhccccCCCchhhhhh
Q 039716          861 KILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDAAAEA  940 (1002)
Q Consensus       861 ~ILiVeDn~~n~~~l~~~L~~~g~~v~~a~~G~eAl~~~~~~~~DlIlmDi~MP~mdG~e~~~~IR~~~~~~~~~~~~~~  940 (1002)
                      +||||||++..+..++.+|+..||.|..|.||.+|++.+....||+||+|+.||+|||+++++.||+.            
T Consensus         2 ~ILiVDDd~~~~~~l~~~L~~~g~~v~~a~~~~eal~~l~~~~~DlvllDi~mP~~dG~ell~~lr~~------------   69 (368)
T 3dzd_A            2 RVLVVDDEESITSSLSAILEEEGYHPDTAKTLREAEKKIKELFFPVIVLDVWMPDGDGVNFIDFIKEN------------   69 (368)
T ss_dssp             EEEEECSCHHHHHHHHHHHHHTTCEEEEESSHHHHHHHHHHBCCSEEEEESEETTEETTTHHHHHHHH------------
T ss_pred             EEEEEeCCHHHHHHHHHHHHHcCCEEEEECCHHHHHHHHHhCCCCEEEEeCCCCCCCHHHHHHHHHhh------------
Confidence            79999999999999999999999999999999999999999999999999999999999999999963            


Q ss_pred             hhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHHhhc
Q 039716          941 GIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQYF 1001 (1002)
Q Consensus       941 ~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~~l 1001 (1002)
                                    .+.+|||++|++.+.+...+|+++|+++||.||++.++|...|++.+
T Consensus        70 --------------~~~~pvI~lT~~~~~~~~~~a~~~Ga~~yl~KP~~~~~L~~~i~~~l  116 (368)
T 3dzd_A           70 --------------SPDSVVIVITGHGSVDTAVKAIKKGAYEFLEKPFSVERFLLTIKHAF  116 (368)
T ss_dssp             --------------CTTCEEEEEECSSCCHHHHHHHHHTCCEEEESSCCHHHHHHHHHHHH
T ss_pred             --------------CCCCeEEEEeCCCCHHHHHHHHhcCcceEEeCCCCHHHHHHHHHHHH
Confidence                          25689999999999999999999999999999999999999988753

>1k68_A Phytochrome response regulator RCPA; phosphorylated aspartate, CHEY homologue, homodimer, (beta/alpha)5, signaling protein; HET: PHD; 1.90A {Tolypothrix SP} SCOP: c.23.1.1

Probab=99.73  E-value=4.8e-17  Score=157.24  Aligned_cols=119  Identities=23%  Similarity=0.388  Sum_probs=109.4

Q ss_pred             CCeEEEEecCHHHHHHHHHHHHhcCC--eEEEEcCHHHHHHHHHc-------CCCcEEEEcCCCCCCCHHHHHHHHhccc
Q 039716          859 KPKILLVEDNKINVMVAKSMMKQLGH--SIDVVNNGVEAVHAVQC-------QNYDLILMDVCMPVMDGLKATRLIRSFE  929 (1002)
Q Consensus       859 ~~~ILiVeDn~~n~~~l~~~L~~~g~--~v~~a~~G~eAl~~~~~-------~~~DlIlmDi~MP~mdG~e~~~~IR~~~  929 (1002)
                      +.+||||||++..+..++.+|+..|+  .|..+.++.+|++.+..       ..||+||+|+.||+++|+++++.||+..
T Consensus         2 ~~~ilivdd~~~~~~~l~~~L~~~~~~~~v~~~~~~~~a~~~l~~~~~~~~~~~~dlvi~d~~~~~~~g~~~~~~l~~~~   81 (140)
T 1k68_A            2 HKKIFLVEDNKADIRLIQEALANSTVPHEVVTVRDGMEAMAYLRQEGEYANASRPDLILLXLNLPKKDGREVLAEIKSDP   81 (140)
T ss_dssp             CCEEEEECCCHHHHHHHHHHHHTCSSCCEEEEECSHHHHHHHHTTCGGGGSCCCCSEEEECSSCSSSCHHHHHHHHHHST
T ss_pred             CCeEEEEeCCHHHHHHHHHHHHhcCCCceEEEECCHHHHHHHHHcccccccCCCCcEEEEecCCCcccHHHHHHHHHcCc
Confidence            45899999999999999999999998  89999999999999987       7899999999999999999999999732


Q ss_pred             cCCCchhhhhhhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHHhhc
Q 039716          930 DTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQYF 1001 (1002)
Q Consensus       930 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~~l 1001 (1002)
                                              ..+.+|||++|+....+...+++++|+++|+.||++.++|...|++++
T Consensus        82 ------------------------~~~~~pii~ls~~~~~~~~~~~~~~g~~~~l~kP~~~~~l~~~i~~~~  129 (140)
T 1k68_A           82 ------------------------TLKRIPVVVLSTSINEDDIFHSYDLHVNCYITKSANLSQLFQIVKGIE  129 (140)
T ss_dssp             ------------------------TGGGSCEEEEESCCCHHHHHHHHHTTCSEEEECCSSHHHHHHHHHHHH
T ss_pred             ------------------------ccccccEEEEecCCcHHHHHHHHHhchhheecCCCCHHHHHHHHHHHH
Confidence                                    125689999999999999999999999999999999999999887653

>3nhm_A Response regulator; protein structure initiative II(PSI II), NYSGXRC, structural genomics; 2.19A {Myxococcus xanthus}

Probab=99.73  E-value=2.4e-17  Score=158.61  Aligned_cols=117  Identities=23%  Similarity=0.288  Sum_probs=103.4

Q ss_pred             CCeEEEEecCHHHHHHHHHHHHhcCCeEEEEcCHHHHHHHHHcCCCcEEEEcCCCCCCCHHHHHHHHhccccCCCchhhh
Q 039716          859 KPKILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDAAA  938 (1002)
Q Consensus       859 ~~~ILiVeDn~~n~~~l~~~L~~~g~~v~~a~~G~eAl~~~~~~~~DlIlmDi~MP~mdG~e~~~~IR~~~~~~~~~~~~  938 (1002)
                      +.+||||||++..+..++.+|+ .|+.|..+.++.+|++.+....||+||+|+.||+++|+++++.||+..         
T Consensus         4 ~~~ilivdd~~~~~~~l~~~l~-~~~~v~~~~~~~~a~~~l~~~~~dlvi~d~~l~~~~g~~~~~~l~~~~---------   73 (133)
T 3nhm_A            4 KPKVLIVENSWTMRETLRLLLS-GEFDCTTAADGASGLQQALAHPPDVLISDVNMDGMDGYALCGHFRSEP---------   73 (133)
T ss_dssp             -CEEEEECSCHHHHHHHHHHHT-TTSEEEEESSHHHHHHHHHHSCCSEEEECSSCSSSCHHHHHHHHHHST---------
T ss_pred             CCEEEEEcCCHHHHHHHHHHHh-CCcEEEEECCHHHHHHHHhcCCCCEEEEeCCCCCCCHHHHHHHHHhCC---------
Confidence            4689999999999999999999 899999999999999999999999999999999999999999999732         


Q ss_pred             hhhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHHhhc
Q 039716          939 EAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQYF 1001 (1002)
Q Consensus       939 ~~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~~l 1001 (1002)
                                     ..+.+|||++|+...... ..++.+|+++||.||++.++|...|++.+
T Consensus        74 ---------------~~~~~pii~~s~~~~~~~-~~~~~~g~~~~l~KP~~~~~l~~~i~~~l  120 (133)
T 3nhm_A           74 ---------------TLKHIPVIFVSGYAPRTE-GPADQPVPDAYLVKPVKPPVLIAQLHALL  120 (133)
T ss_dssp             ---------------TTTTCCEEEEESCCC------TTSCCCSEEEESSCCHHHHHHHHHHHH
T ss_pred             ---------------ccCCCCEEEEeCCCcHhH-HHHhhcCCceEEeccCCHHHHHHHHHHHH
Confidence                           235799999999988877 89999999999999999999999998764

>3eul_A Possible nitrate/nitrite response transcriptional regulatory protein NARL (DNA-binding...; central beta strand flanked by alpha helices; 1.90A {Mycobacterium tuberculosis}

Probab=99.73  E-value=3.6e-17  Score=161.59  Aligned_cols=119  Identities=17%  Similarity=0.264  Sum_probs=109.4

Q ss_pred             CCCCeEEEEecCHHHHHHHHHHHHhcCCe--EEEEcCHHHHHHHHHcCCCcEEEEcCCCCCCCHHHHHHHHhccccCCCc
Q 039716          857 KPKPKILLVEDNKINVMVAKSMMKQLGHS--IDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNW  934 (1002)
Q Consensus       857 ~~~~~ILiVeDn~~n~~~l~~~L~~~g~~--v~~a~~G~eAl~~~~~~~~DlIlmDi~MP~mdG~e~~~~IR~~~~~~~~  934 (1002)
                      ..+.+||||||++..+..++.+|+..|+.  |..+.++.+|++.+....||+||+|+.||+++|+++++.||..      
T Consensus        13 ~~~~~iLivdd~~~~~~~l~~~L~~~~~~~~v~~~~~~~~a~~~l~~~~~dlii~d~~l~~~~g~~~~~~l~~~------   86 (152)
T 3eul_A           13 PEKVRVVVGDDHPLFREGVVRALSLSGSVNVVGEADDGAAALELIKAHLPDVALLDYRMPGMDGAQVAAAVRSY------   86 (152)
T ss_dssp             -CCEEEEEECSSHHHHHHHHHHHHHHSSEEEEEEESSHHHHHHHHHHHCCSEEEEETTCSSSCHHHHHHHHHHT------
T ss_pred             CceEEEEEEcCCHHHHHHHHHHHhhCCCeEEEEEeCCHHHHHHHHHhcCCCEEEEeCCCCCCCHHHHHHHHHhc------
Confidence            45679999999999999999999999954  6689999999999999999999999999999999999999963      


Q ss_pred             hhhhhhhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHHhhc
Q 039716          935 DAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQYF 1001 (1002)
Q Consensus       935 ~~~~~~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~~l 1001 (1002)
                                          .+.+|||++|+..+.+...+++++|+++||.||++.++|..+|++++
T Consensus        87 --------------------~~~~~ii~~s~~~~~~~~~~~~~~g~~~~l~Kp~~~~~l~~~i~~~~  133 (152)
T 3eul_A           87 --------------------ELPTRVLLISAHDEPAIVYQALQQGAAGFLLKDSTRTEIVKAVLDCA  133 (152)
T ss_dssp             --------------------TCSCEEEEEESCCCHHHHHHHHHTTCSEEEETTCCHHHHHHHHHHHH
T ss_pred             --------------------CCCCeEEEEEccCCHHHHHHHHHcCCCEEEecCCCHHHHHHHHHHHH
Confidence                                35789999999999999999999999999999999999999998753

>3c3m_A Response regulator receiver protein; structural genomics, unknown function, PSI-2, protein struct initiative; HET: MSE; 1.70A {Methanoculleus marisnigri JR1}

Probab=99.73  E-value=3.7e-17  Score=158.91  Aligned_cols=118  Identities=26%  Similarity=0.423  Sum_probs=106.5

Q ss_pred             CeEEEEecCHHHHHHHHHHHHhcCCeEEEEcCHHHHHHHHHcCCCcEEEEcCCCCCCCHHHHHHHHhccccCCCchhhhh
Q 039716          860 PKILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDAAAE  939 (1002)
Q Consensus       860 ~~ILiVeDn~~n~~~l~~~L~~~g~~v~~a~~G~eAl~~~~~~~~DlIlmDi~MP~mdG~e~~~~IR~~~~~~~~~~~~~  939 (1002)
                      .+||||||++..+..++.+|+..||.|..+.++.+|++.+....||+||+|+.||+++|+++++.||...          
T Consensus         4 ~~ILivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~al~~l~~~~~dlvi~D~~l~~~~g~~~~~~l~~~~----------   73 (138)
T 3c3m_A            4 YTILVVDDSPMIVDVFVTMLERGGYRPITAFSGEECLEALNATPPDLVLLDIMMEPMDGWETLERIKTDP----------   73 (138)
T ss_dssp             CEEEEECSCHHHHHHHHHHHHHTTCEEEEESSHHHHHHHHHHSCCSEEEEESCCSSSCHHHHHHHHHHST----------
T ss_pred             ceEEEEeCCHHHHHHHHHHHHHcCceEEEeCCHHHHHHHHhccCCCEEEEeCCCCCCCHHHHHHHHHcCc----------
Confidence            5899999999999999999999999999999999999999999999999999999999999999999632          


Q ss_pred             hhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHHhhc
Q 039716          940 AGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQYF 1001 (1002)
Q Consensus       940 ~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~~l 1001 (1002)
                                    ..+.+|||++|+.........++.+|+++||.||++.++|...|++.+
T Consensus        74 --------------~~~~~~ii~ls~~~~~~~~~~~~~~~~~~~l~KP~~~~~L~~~i~~~~  121 (138)
T 3c3m_A           74 --------------ATRDIPVLMLTAKPLTPEEANEYGSYIEDYILKPTTHHQLYEAIEHVL  121 (138)
T ss_dssp             --------------TTTTSCEEEEESSCCCHHHHHHTTTTCSEEEECCCHHHHHHHHHHHHH
T ss_pred             --------------ccCCCCEEEEECCCChHHHHHHhhcCHhheEeCCCCHHHHHHHHHHHH
Confidence                          235799999999887666666777889999999999999999998753

>3f6c_A Positive transcription regulator EVGA; structural genomics, PSI-2, protein structure initiative, PO transcription regulator EVGA; 1.45A {Escherichia coli k-12}

Probab=99.73  E-value=1e-17  Score=161.49  Aligned_cols=116  Identities=19%  Similarity=0.307  Sum_probs=106.1

Q ss_pred             CeEEEEecCHHHHHHHHHHHHhcCCeEE-EEcCHHHHHHHHHcCCCcEEEEcCCCCCCCHHHHHHHHhccccCCCchhhh
Q 039716          860 PKILLVEDNKINVMVAKSMMKQLGHSID-VVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDAAA  938 (1002)
Q Consensus       860 ~~ILiVeDn~~n~~~l~~~L~~~g~~v~-~a~~G~eAl~~~~~~~~DlIlmDi~MP~mdG~e~~~~IR~~~~~~~~~~~~  938 (1002)
                      .+||||||++..+..++.+|++.|+.+. .+.++.+|++.+....||+||+|+.||+++|+++++.||+.          
T Consensus         2 ~~ilivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~~a~~~~~~~~~dlii~d~~l~~~~g~~~~~~l~~~----------   71 (134)
T 3f6c_A            2 LNAIIIDDHPLAIAAIRNLLIKNDIEILAELTEGGSAVQRVETLKPDIVIIDVDIPGVNGIQVLETLRKR----------   71 (134)
T ss_dssp             EEEEEECCCHHHHHHHHHHHHHTTEEEEEEESSSTTHHHHHHHHCCSEEEEETTCSSSCHHHHHHHHHHT----------
T ss_pred             eEEEEEcCCHHHHHHHHHHHhhCCcEEEEEcCCHHHHHHHHHhcCCCEEEEecCCCCCChHHHHHHHHhc----------
Confidence            4899999999999999999999999987 89999999999999999999999999999999999999962          


Q ss_pred             hhhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHHhhc
Q 039716          939 EAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQYF 1001 (1002)
Q Consensus       939 ~~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~~l 1001 (1002)
                                      .+.+|||++|+....+...+++++|+++||.||++.++|..+|++.+
T Consensus        72 ----------------~~~~~ii~~s~~~~~~~~~~~~~~g~~~~l~kp~~~~~l~~~i~~~~  118 (134)
T 3f6c_A           72 ----------------QYSGIIIIVSAKNDHFYGKHCADAGANGFVSKKEGMNNIIAAIEAAK  118 (134)
T ss_dssp             ----------------TCCSEEEEEECC---CTHHHHHHTTCSEEEEGGGCTHHHHHHHHHHH
T ss_pred             ----------------CCCCeEEEEeCCCChHHHHHHHHhCCCEEEeCCCCHHHHHHHHHHHH
Confidence                            35789999999999999999999999999999999999999998754

>1mvo_A PHOP response regulator; phosphate regulon, transcriptional regulatory protein, alpha/beta doubly wound fold, phosphorylation; 1.60A {Bacillus subtilis} SCOP: c.23.1.1

Probab=99.73  E-value=3.9e-17  Score=157.78  Aligned_cols=115  Identities=23%  Similarity=0.400  Sum_probs=107.7

Q ss_pred             CeEEEEecCHHHHHHHHHHHHhcCCeEEEEcCHHHHHHHHHcCCCcEEEEcCCCCCCCHHHHHHHHhccccCCCchhhhh
Q 039716          860 PKILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDAAAE  939 (1002)
Q Consensus       860 ~~ILiVeDn~~n~~~l~~~L~~~g~~v~~a~~G~eAl~~~~~~~~DlIlmDi~MP~mdG~e~~~~IR~~~~~~~~~~~~~  939 (1002)
                      .+||||||++..+..+..+|...||.|..+.++.+|+..+....||+||+|+.||+++|+++++.||+.           
T Consensus         4 ~~ilivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~a~~~~~~~~~dlvl~D~~l~~~~g~~~~~~l~~~-----------   72 (136)
T 1mvo_A            4 KKILVVDDEESIVTLLQYNLERSGYDVITASDGEEALKKAETEKPDLIVLDVMLPKLDGIEVCKQLRQQ-----------   72 (136)
T ss_dssp             CEEEEECSCHHHHHHHHHHHHHTTCEEEEESSHHHHHHHHHHHCCSEEEEESSCSSSCHHHHHHHHHHT-----------
T ss_pred             CEEEEEECCHHHHHHHHHHHHHCCcEEEEecCHHHHHHHHhhcCCCEEEEecCCCCCCHHHHHHHHHcC-----------
Confidence            489999999999999999999999999999999999999998899999999999999999999999963           


Q ss_pred             hhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHHhh
Q 039716          940 AGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQY 1000 (1002)
Q Consensus       940 ~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~~ 1000 (1002)
                                     .+.+|||++|+.........++++|+++||.||++.++|...|++.
T Consensus        73 ---------------~~~~~ii~~s~~~~~~~~~~~~~~g~~~~l~KP~~~~~l~~~i~~~  118 (136)
T 1mvo_A           73 ---------------KLMFPILMLTAKDEEFDKVLGLELGADDYMTKPFSPREVNARVKAI  118 (136)
T ss_dssp             ---------------TCCCCEEEEECTTCCCCHHHHHHTTCCEEEESSCCHHHHHHHHHHH
T ss_pred             ---------------CCCCCEEEEECCCCHHHHHHHHhCCCCEEEECCCCHHHHHHHHHHH
Confidence                           2468999999999988899999999999999999999999998865

>3zxq_A Hypoxia sensor histidine kinase response regulato; transferase; 1.90A {Mycobacterium tuberculosis}

Probab=99.72  E-value=2.9e-17  Score=156.90  Aligned_cols=122  Identities=20%  Similarity=0.282  Sum_probs=93.0

Q ss_pred             CHHHHHHHHHHHHHHHHhhcceeccccCCCCCeeEEccHHHHHHHHHHHHhhhhhcCCCCeeEEEEEecCCCCcccchhh
Q 039716          444 RPREVVKHVLQTAAASLQKILMLEGDIADDVPIEVIGDVLRIRQILTNLISNAIKFTPEGKVGIKLYVVPEPPFAKEGLK  523 (1002)
Q Consensus       444 ~l~~li~~v~~~~~~~~~k~i~l~~~i~~~~p~~v~gD~~rL~QIL~NLlsNAIKfT~~G~I~I~v~~~~~~~~~~~~~~  523 (1002)
                      ++.+.+..++..+   ....+.+...+....+.....+...|.+|+.||++||+||++.|.|.|.+..            
T Consensus         2 ~l~~~l~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~l~~il~nll~Na~k~~~~~~i~i~~~~------------   66 (124)
T 3zxq_A            2 GLRHRLDKVIDQL---AIPALHTTVQYTGPLSVVDTVLANHAEAVLREAVSNAVRHANATSLAINVSV------------   66 (124)
T ss_dssp             CHHHHHHHHHHHH---TTTTSEEEEEEESCGGGCCHHHHHHHHHHHHHHHHHHHTCTTCCEEEEEEEE------------
T ss_pred             cHHHHHHHHHHHH---HhcCceEEEEeeCccccccHHHHHHHHHHHHHHHHHHHHhCCCCEEEEEEEe------------
Confidence            4555666665555   2233444444433333223346889999999999999999998888777642            


Q ss_pred             hhhhhhhcchhhhhhhccCCCCCccCCCCCCCCCCCCCCccCCCCCCCCCCCccCCCCCccccccceEEEEEEEecCCCC
Q 039716          524 QKSKAYQSATDAVKEEKHQPKSQTASDQNGFHDKKHGEGYQDHKHDDDPGTPVSHGNSMDEDLEATVWIRCDVYDTGIGI  603 (1002)
Q Consensus       524 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~i~V~DtGiGI  603 (1002)
                                                                                      ... +.|+|.|+|+||
T Consensus        67 ----------------------------------------------------------------~~~-~~i~v~D~G~gi   81 (124)
T 3zxq_A           67 ----------------------------------------------------------------EDD-VRVEVVDDGVGI   81 (124)
T ss_dssp             ----------------------------------------------------------------EEE-EEEEEEECCCSS
T ss_pred             ----------------------------------------------------------------CCC-EEEEEEECCCCC
Confidence                                                                            112 678999999999


Q ss_pred             CcCcHhhhhhhccCCCccccCcCCCccccHHHHHHHHHHhCCEEEEEeecCCceEEEEEEeCC
Q 039716          604 PENALPTLFRKYMQVSADHARKYGGTGLGLAICKQLVELMGGRLTVTSKVHCGSTFTFILPYQ  666 (1002)
Q Consensus       604 ~~e~l~~IF~pF~q~~~~~~~~~~GtGLGLaI~k~Lve~~gG~I~v~S~~g~GTtF~~~LP~~  666 (1002)
                      +++.                     +||||++|+++++.|||+|++.|.+++||+|+++||+.
T Consensus        82 ~~~~---------------------~GlGL~~~~~~~~~~gG~i~~~~~~~~G~~~~i~lP~~  123 (124)
T 3zxq_A           82 SGDI---------------------TESGLRNLRQRADDAGGEFTVENMPTGGTLLRWSAPLR  123 (124)
T ss_dssp             CGGG---------------------SHHHHHHHHHHHHHHTCEEEEEECTTSSEEEEEEEECC
T ss_pred             Cccc---------------------cccCHHHHHHHHHHhCCEEEEEEcCCCcEEEEEEEecC
Confidence            9865                     39999999999999999999999999999999999974

>1k66_A Phytochrome response regulator RCPB; CHEY homologue, homodimer, APO-protein, (beta/alpha)5, signaling protein; 1.75A {Tolypothrix SP} SCOP: c.23.1.1

Probab=99.72  E-value=6.9e-17  Score=158.07  Aligned_cols=119  Identities=24%  Similarity=0.447  Sum_probs=109.5

Q ss_pred             CCCeEEEEecCHHHHHHHHHHHHhcCC--eEEEEcCHHHHHHHHHc----------CCCcEEEEcCCCCCCCHHHHHHHH
Q 039716          858 PKPKILLVEDNKINVMVAKSMMKQLGH--SIDVVNNGVEAVHAVQC----------QNYDLILMDVCMPVMDGLKATRLI  925 (1002)
Q Consensus       858 ~~~~ILiVeDn~~n~~~l~~~L~~~g~--~v~~a~~G~eAl~~~~~----------~~~DlIlmDi~MP~mdG~e~~~~I  925 (1002)
                      ...+||||||++..+..++.+|+..|+  .|..+.++.+|++.+..          ..||+||+|+.||+++|+++++.|
T Consensus         5 ~~~~iLivdd~~~~~~~l~~~L~~~g~~~~v~~~~~~~~al~~l~~~~~~~~~~~~~~~dlvi~D~~l~~~~g~~~~~~l   84 (149)
T 1k66_A            5 ATQPLLVVEDSDEDFSTFQRLLQREGVVNPIYRCITGDQALDFLYQTGSYCNPDIAPRPAVILLDLNLPGTDGREVLQEI   84 (149)
T ss_dssp             TTSCEEEECCCHHHHHHHHHHHHHTTBCSCEEEECSHHHHHHHHHTCCSSSCGGGCCCCSEEEECSCCSSSCHHHHHHHH
T ss_pred             CCccEEEEECCHHHHHHHHHHHHHcCCCceEEEECCHHHHHHHHHhcccccCcccCCCCcEEEEECCCCCCCHHHHHHHH
Confidence            356899999999999999999999998  89999999999999987          889999999999999999999999


Q ss_pred             hccccCCCchhhhhhhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHHhh
Q 039716          926 RSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQY 1000 (1002)
Q Consensus       926 R~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~~ 1000 (1002)
                      |+..                        ..+.+|||++|+....+....++++|+++||.||++.++|...|+++
T Consensus        85 ~~~~------------------------~~~~~~ii~~t~~~~~~~~~~~~~~g~~~~l~kP~~~~~l~~~i~~~  135 (149)
T 1k66_A           85 KQDE------------------------VLKKIPVVIMTTSSNPKDIEICYSYSISSYIVKPLEIDRLTETVQTF  135 (149)
T ss_dssp             TTST------------------------TGGGSCEEEEESCCCHHHHHHHHHTTCSEEEECCSSHHHHHHHHHHH
T ss_pred             HhCc------------------------ccCCCeEEEEeCCCCHHHHHHHHHCCCCEEEeCCCCHHHHHHHHHHH
Confidence            9631                        12579999999999999999999999999999999999999988765

>3lte_A Response regulator; structural genomics, PSI, protein structure initiative, NYSG YORK structural genomix research consortium, nysgxrc; 2.00A {Bermanella marisrubri}

Probab=99.72  E-value=7.1e-17  Score=155.05  Aligned_cols=119  Identities=18%  Similarity=0.368  Sum_probs=105.3

Q ss_pred             CCCeEEEEecCHHHHHHHHHHHHhcCCeEEEEcCHHHHHHHHHcCCCcEEEEcCCCCCCCHHHHHHHHhccccCCCchhh
Q 039716          858 PKPKILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDAA  937 (1002)
Q Consensus       858 ~~~~ILiVeDn~~n~~~l~~~L~~~g~~v~~a~~G~eAl~~~~~~~~DlIlmDi~MP~mdG~e~~~~IR~~~~~~~~~~~  937 (1002)
                      .+.+||||||++..+..++.+|++.||.|..+.++.+|++.+....||+||+|+.||+++|+++++.||+..        
T Consensus         5 ~~~~ilivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~a~~~l~~~~~dlii~d~~l~~~~g~~~~~~l~~~~--------   76 (132)
T 3lte_A            5 QSKRILVVDDDQAMAAAIERVLKRDHWQVEIAHNGFDAGIKLSTFEPAIMTLDLSMPKLDGLDVIRSLRQNK--------   76 (132)
T ss_dssp             --CEEEEECSCHHHHHHHHHHHHHTTCEEEEESSHHHHHHHHHHTCCSEEEEESCBTTBCHHHHHHHHHTTT--------
T ss_pred             CCccEEEEECCHHHHHHHHHHHHHCCcEEEEeCCHHHHHHHHHhcCCCEEEEecCCCCCCHHHHHHHHHhcC--------
Confidence            356899999999999999999999999999999999999999999999999999999999999999999632        


Q ss_pred             hhhhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHHhhc
Q 039716          938 AEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQYF 1001 (1002)
Q Consensus       938 ~~~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~~l 1001 (1002)
                                      ..+.+|||++|+.... ...+++++|+++||.||++.++|...|++++
T Consensus        77 ----------------~~~~~~ii~~~~~~~~-~~~~~~~~g~~~~l~kP~~~~~l~~~i~~~~  123 (132)
T 3lte_A           77 ----------------VANQPKILVVSGLDKA-KLQQAVTEGADDYLEKPFDNDALLDRIHDLV  123 (132)
T ss_dssp             ----------------CSSCCEEEEECCSCSH-HHHHHHHHTCCEEECSSCCHHHHHHHHHHHH
T ss_pred             ----------------ccCCCeEEEEeCCChH-HHHHHHHhChHHHhhCCCCHHHHHHHHHHHc
Confidence                            1234667777776655 7889999999999999999999999998764

>1dcf_A ETR1 protein; beta-alpha five sandwich, transferase; 2.50A {Arabidopsis thaliana} SCOP: c.23.1.2

Probab=99.72  E-value=5.9e-17  Score=156.76  Aligned_cols=122  Identities=24%  Similarity=0.512  Sum_probs=106.1

Q ss_pred             CCCeEEEEecCHHHHHHHHHHHHhcCCeEEEEcCHHHHHHHHHcCCCcEEEEcCCCCCCCHHHHHHHHhccccCCCchhh
Q 039716          858 PKPKILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDAA  937 (1002)
Q Consensus       858 ~~~~ILiVeDn~~n~~~l~~~L~~~g~~v~~a~~G~eAl~~~~~~~~DlIlmDi~MP~mdG~e~~~~IR~~~~~~~~~~~  937 (1002)
                      .+.+||||||++..+..++.+|+..|+.|..+.+|.+|++.+.... |+||+|+.||+++|+++++.||+....      
T Consensus         6 ~~~~ILivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~a~~~~~~~~-dlvllD~~lp~~~g~~~~~~l~~~~~~------   78 (136)
T 1dcf_A            6 TGLKVLVMDENGVSRMVTKGLLVHLGCEVTTVSSNEECLRVVSHEH-KVVFMDVCMPGVENYQIALRIHEKFTK------   78 (136)
T ss_dssp             TTCEEEEECSCHHHHHHHHHHHHHTTCEEEEESSHHHHHHHCCTTC-SEEEEECCSSTTTTTHHHHHHHHHHC-------
T ss_pred             CCCeEEEEeCCHHHHHHHHHHHHHcCCeEEEeCCHHHHHHHHhccC-CEEEEeCCCCCCcHHHHHHHHHHhhhh------
Confidence            4568999999999999999999999999999999999999987655 999999999999999999999852110      


Q ss_pred             hhhhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHHhhc
Q 039716          938 AEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQYF 1001 (1002)
Q Consensus       938 ~~~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~~l 1001 (1002)
                                     ...+..|||++|+........+|+++|+++||.||++.++|...|++.+
T Consensus        79 ---------------~~~~~~~ii~~s~~~~~~~~~~~~~~ga~~~l~KP~~~~~L~~~l~~~~  127 (136)
T 1dcf_A           79 ---------------QRHQRPLLVALSGNTDKSTKEKCMSFGLDGVLLKPVSLDNIRDVLSDLL  127 (136)
T ss_dssp             ---------------CCSCCCEEEEEESCCSHHHHHHHHHTTCCEEEESSCCHHHHHHHHHHHH
T ss_pred             ---------------ccCCCceEEEEeCCCCHHHHHHHHHcCCCeEEECCCCHHHHHHHHHHHh
Confidence                           0012246889999999999999999999999999999999999998754

>3a10_A Response regulator; phosphoacceptor, signaling protein; HET: MSE PG4; 1.63A {Thermotoga maritima} PDB: 3a0r_B* 3a0u_A*

Probab=99.72  E-value=2.6e-17  Score=154.41  Aligned_cols=114  Identities=31%  Similarity=0.443  Sum_probs=104.7

Q ss_pred             CeEEEEecCHHHHHHHHHHHHhcCCeEEEEcCHHHHHHHHHcCCCcEEEEcCCCCCCCHHHHHHHHhccccCCCchhhhh
Q 039716          860 PKILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDAAAE  939 (1002)
Q Consensus       860 ~~ILiVeDn~~n~~~l~~~L~~~g~~v~~a~~G~eAl~~~~~~~~DlIlmDi~MP~mdG~e~~~~IR~~~~~~~~~~~~~  939 (1002)
                      .+||||||++..+..++.+|+..|+.|..+.++.+|++.+....||+||+|+.||+++|+++++.||+.           
T Consensus         2 ~~ilivdd~~~~~~~l~~~l~~~~~~v~~~~~~~~a~~~~~~~~~dlvl~D~~l~~~~g~~~~~~l~~~-----------   70 (116)
T 3a10_A            2 KRILVVDDEPNIRELLKEELQEEGYEIDTAENGEEALKKFFSGNYDLVILDIEMPGISGLEVAGEIRKK-----------   70 (116)
T ss_dssp             CEEEEECSCHHHHHHHHHHHHHTTCEEEEESSHHHHHHHHHHSCCSEEEECSCCSSSCHHHHHHHHHHH-----------
T ss_pred             cEEEEEeCCHHHHHHHHHHHHHCCCEEEEeCCHHHHHHHHhcCCCCEEEEECCCCCCCHHHHHHHHHcc-----------
Confidence            379999999999999999999999999999999999999999999999999999999999999999963           


Q ss_pred             hhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHHhhc
Q 039716          940 AGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQYF 1001 (1002)
Q Consensus       940 ~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~~l 1001 (1002)
                                     .+.+|||++|+.....  ..++.+|+++|+.||++.++|...|++.+
T Consensus        71 ---------------~~~~~ii~~s~~~~~~--~~~~~~g~~~~l~Kp~~~~~l~~~i~~~~  115 (116)
T 3a10_A           71 ---------------KKDAKIILLTAYSHYR--SDMSSWAADEYVVKSFNFDELKEKVKKLL  115 (116)
T ss_dssp             ---------------CTTCCEEEEESCGGGG--GCGGGGGSSEEEECCSSTHHHHHHHHHHT
T ss_pred             ---------------CCCCeEEEEECCcchH--HHHHhccccceEECCCCHHHHHHHHHHHh
Confidence                           2568999999986554  67889999999999999999999998865

>1zh2_A KDP operon transcriptional regulatory protein KDPE; two-component system, gene regulation, transcription factor, KDP potassium transport system; 2.00A {Escherichia coli} SCOP: c.23.1.1 PDB: 1zh4_A

Probab=99.72  E-value=3.9e-17  Score=154.06  Aligned_cols=114  Identities=21%  Similarity=0.366  Sum_probs=106.8

Q ss_pred             CeEEEEecCHHHHHHHHHHHHhcCCeEEEEcCHHHHHHHHHcCCCcEEEEcCCCCCCCHHHHHHHHhccccCCCchhhhh
Q 039716          860 PKILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDAAAE  939 (1002)
Q Consensus       860 ~~ILiVeDn~~n~~~l~~~L~~~g~~v~~a~~G~eAl~~~~~~~~DlIlmDi~MP~mdG~e~~~~IR~~~~~~~~~~~~~  939 (1002)
                      .+||||||++..+..++.+|+..|+.+..+.++.+|+..+....||+||+|+.||+++|+++++.||.            
T Consensus         2 ~~ilivdd~~~~~~~l~~~l~~~~~~v~~~~~~~~~~~~~~~~~~dlvi~D~~l~~~~g~~~~~~l~~------------   69 (121)
T 1zh2_A            2 TNVLIVEDEQAIRRFLRTALEGDGMRVFEAETLQRGLLEAATRKPDLIILDLGLPDGDGIEFIRDLRQ------------   69 (121)
T ss_dssp             CEEEEECSCHHHHHHHHHHHHTTTCEEEEESSHHHHHHHHHHHCCSEEEEESEETTEEHHHHHHHHHT------------
T ss_pred             cEEEEEeCCHHHHHHHHHHHhcCCCEEEEeCCHHHHHHHHhcCCCCEEEEeCCCCCCcHHHHHHHHHh------------
Confidence            47999999999999999999999999999999999999998889999999999999999999999994            


Q ss_pred             hhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHHhh
Q 039716          940 AGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQY 1000 (1002)
Q Consensus       940 ~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~~ 1000 (1002)
                                     .+.+|||++|+........+++++|+++|+.||++.++|...|++.
T Consensus        70 ---------------~~~~~ii~~s~~~~~~~~~~~~~~g~~~~l~Kp~~~~~l~~~i~~~  115 (121)
T 1zh2_A           70 ---------------WSAVPVIVLSARSEESDKIAALDAGADDYLSKPFGIGELQARLRVA  115 (121)
T ss_dssp             ---------------TCCCCEEEEESCCSHHHHHHHHHHTCSEEEESSCCHHHHHHHHHHH
T ss_pred             ---------------CCCCcEEEEECCCCHHHHHHHHhcCCCeEEeCCcCHHHHHHHHHHH
Confidence                           1458999999999999999999999999999999999999988765

>1dz3_A Stage 0 sporulation protein A; response regulator, domain swapping; 1.65A {Bacillus stearothermophilus} SCOP: c.23.1.1 PDB: 1qmp_A*

Probab=99.72  E-value=2.9e-17  Score=157.68  Aligned_cols=117  Identities=21%  Similarity=0.356  Sum_probs=106.5

Q ss_pred             CeEEEEecCHHHHHHHHHHHHhc-CCeEE-EEcCHHHHHHHHHcCCCcEEEEcCCCCCCCHHHHHHHHhccccCCCchhh
Q 039716          860 PKILLVEDNKINVMVAKSMMKQL-GHSID-VVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDAA  937 (1002)
Q Consensus       860 ~~ILiVeDn~~n~~~l~~~L~~~-g~~v~-~a~~G~eAl~~~~~~~~DlIlmDi~MP~mdG~e~~~~IR~~~~~~~~~~~  937 (1002)
                      .+||||||++..+..++.+|... |+.+. .+.++.+|++.+....||+||+|+.||+++|+++++.||+..        
T Consensus         3 ~~ilivdd~~~~~~~l~~~l~~~~~~~~~~~~~~~~~a~~~~~~~~~dlvllD~~l~~~~g~~~~~~l~~~~--------   74 (130)
T 1dz3_A            3 IKVCIADDNRELVSLLDEYISSQPDMEVIGTAYNGQDCLQMLEEKRPDILLLDIIMPHLDGLAVLERIRAGF--------   74 (130)
T ss_dssp             EEEEEECSCHHHHHHHHHHHHTSTTEEEEEEESSHHHHHHHHHHHCCSEEEEESCCSSSCHHHHHHHHHHHC--------
T ss_pred             eEEEEEcCCHHHHHHHHHHHHhCCCceEEEEeCCHHHHHHHHhcCCCCEEEEecCCCCCCHHHHHHHHHhcC--------
Confidence            47999999999999999999987 88865 899999999999988999999999999999999999999621        


Q ss_pred             hhhhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHHhhc
Q 039716          938 AEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQYF 1001 (1002)
Q Consensus       938 ~~~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~~l 1001 (1002)
                                       .+.+|||++|+....+...+++++|+++||.||++.++|...|++.+
T Consensus        75 -----------------~~~~~ii~ls~~~~~~~~~~~~~~ga~~~l~KP~~~~~l~~~i~~~~  121 (130)
T 1dz3_A           75 -----------------EHQPNVIMLTAFGQEDVTKKAVELGASYFILKPFDMENLAHHIRQVY  121 (130)
T ss_dssp             -----------------SSCCEEEEEEETTCHHHHHHHHHTTCEEEEECSSCCTTHHHHHHHHH
T ss_pred             -----------------CCCCcEEEEecCCCHHHHHHHHHcCCCEEEeCCCCHHHHHHHHHHHh
Confidence                             24579999999999999999999999999999999999999988753

>3h5i_A Response regulator/sensory box protein/ggdef domain protein; structural genomics, transcription, PSI-2; 1.90A {Carboxydothermus hydrogenoformans z-2901}

Probab=99.72  E-value=1.8e-17  Score=161.54  Aligned_cols=116  Identities=28%  Similarity=0.388  Sum_probs=107.5

Q ss_pred             CCeEEEEecCHHHHHHHHHHHHhcCCeEEEEcCHHHHHHHHHc-CCCcEEEEcCCCCC-CCHHHHHHHHhccccCCCchh
Q 039716          859 KPKILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQC-QNYDLILMDVCMPV-MDGLKATRLIRSFEDTGNWDA  936 (1002)
Q Consensus       859 ~~~ILiVeDn~~n~~~l~~~L~~~g~~v~~a~~G~eAl~~~~~-~~~DlIlmDi~MP~-mdG~e~~~~IR~~~~~~~~~~  936 (1002)
                      +.+||||||++..+..++.+|+..||.|..+.++.+|++.+.. ..||+||+|+.||. ++|+++++.||+.        
T Consensus         5 ~~~ilivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~a~~~l~~~~~~dlvi~D~~l~~~~~g~~~~~~l~~~--------   76 (140)
T 3h5i_A            5 DKKILIVEDSKFQAKTIANILNKYGYTVEIALTGEAAVEKVSGGWYPDLILMDIELGEGMDGVQTALAIQQI--------   76 (140)
T ss_dssp             -CEEEEECSCHHHHHHHHHHHHHTTCEEEEESSHHHHHHHHHTTCCCSEEEEESSCSSSCCHHHHHHHHHHH--------
T ss_pred             CcEEEEEeCCHHHHHHHHHHHHHcCCEEEEecChHHHHHHHhcCCCCCEEEEeccCCCCCCHHHHHHHHHhC--------
Confidence            4689999999999999999999999999999999999999987 78999999999995 9999999999962        


Q ss_pred             hhhhhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHHhhc
Q 039716          937 AAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQYF 1001 (1002)
Q Consensus       937 ~~~~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~~l 1001 (1002)
                                         +.+|||++|+....+...+++.+|+++||.||++.++|...|++.+
T Consensus        77 -------------------~~~~ii~ls~~~~~~~~~~~~~~g~~~~l~KP~~~~~l~~~i~~~l  122 (140)
T 3h5i_A           77 -------------------SELPVVFLTAHTEPAVVEKIRSVTAYGYVMKSATEQVLITIVEMAL  122 (140)
T ss_dssp             -------------------CCCCEEEEESSSSCCCCGGGGGSCEEEEEETTCCHHHHHHHHHHHH
T ss_pred             -------------------CCCCEEEEECCCCHHHHHHHHhCCCcEEEeCCCCHHHHHHHHHHHH
Confidence                               4589999999999888899999999999999999999999998754

>3cnb_A DNA-binding response regulator, MERR family; signal receiver domain, DNA binding protein, protein structu initiative, PSI-2; 2.00A {Colwellia psychrerythraea}

Probab=99.72  E-value=1.1e-16  Score=155.66  Aligned_cols=120  Identities=23%  Similarity=0.352  Sum_probs=110.2

Q ss_pred             CCCeEEEEecCHHHHHHHHHHHHh-cCCe-EEEEcCHHHHHHHHHcCCCcEEEEcCCCCCCCHHHHHHHHhccccCCCch
Q 039716          858 PKPKILLVEDNKINVMVAKSMMKQ-LGHS-IDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWD  935 (1002)
Q Consensus       858 ~~~~ILiVeDn~~n~~~l~~~L~~-~g~~-v~~a~~G~eAl~~~~~~~~DlIlmDi~MP~mdG~e~~~~IR~~~~~~~~~  935 (1002)
                      ...+||||||++..+..++.+|+. .||. |..+.++.+|++.+....||+||+|+.||+++|+++++.||...      
T Consensus         7 ~~~~iLivdd~~~~~~~l~~~L~~~~~~~~v~~~~~~~~a~~~l~~~~~dlii~d~~l~~~~g~~~~~~l~~~~------   80 (143)
T 3cnb_A            7 NDFSILIIEDDKEFADMLTQFLENLFPYAKIKIAYNPFDAGDLLHTVKPDVVMLDLMMVGMDGFSICHRIKSTP------   80 (143)
T ss_dssp             --CEEEEECSCHHHHHHHHHHHHHHCTTCEEEEECSHHHHHHHHHHTCCSEEEEETTCTTSCHHHHHHHHHTST------
T ss_pred             CCceEEEEECCHHHHHHHHHHHHhccCccEEEEECCHHHHHHHHHhcCCCEEEEecccCCCcHHHHHHHHHhCc------
Confidence            356899999999999999999999 8999 99999999999999999999999999999999999999999631      


Q ss_pred             hhhhhhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHHhhc
Q 039716          936 AAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQYF 1001 (1002)
Q Consensus       936 ~~~~~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~~l 1001 (1002)
                                        ..+.+|||++|+........+++++|+++||.||++.++|...|++.+
T Consensus        81 ------------------~~~~~~ii~~s~~~~~~~~~~~~~~g~~~~l~kP~~~~~l~~~i~~~~  128 (143)
T 3cnb_A           81 ------------------ATANIIVIAMTGALTDDNVSRIVALGAETCFGKPLNFTLLEKTIKQLV  128 (143)
T ss_dssp             ------------------TTTTSEEEEEESSCCHHHHHHHHHTTCSEEEESSCCHHHHHHHHHHHH
T ss_pred             ------------------cccCCcEEEEeCCCCHHHHHHHHhcCCcEEEeCCCCHHHHHHHHHHHH
Confidence                              246799999999999999999999999999999999999999998753

>1yio_A Response regulatory protein; transcription regulation, DNA binding protein; 2.20A {Pseudomonas fluorescens} SCOP: a.4.6.2 c.23.1.1 PDB: 1zn2_A

Probab=99.72  E-value=2.3e-17  Score=172.15  Aligned_cols=116  Identities=20%  Similarity=0.341  Sum_probs=108.8

Q ss_pred             CCeEEEEecCHHHHHHHHHHHHhcCCeEEEEcCHHHHHHHHHcCCCcEEEEcCCCCCCCHHHHHHHHhccccCCCchhhh
Q 039716          859 KPKILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDAAA  938 (1002)
Q Consensus       859 ~~~ILiVeDn~~n~~~l~~~L~~~g~~v~~a~~G~eAl~~~~~~~~DlIlmDi~MP~mdG~e~~~~IR~~~~~~~~~~~~  938 (1002)
                      .++||||||++..+..+..+|+..||.|..+.+|.+|++.+....||+||+|+.||++||+++++.||..          
T Consensus         4 ~~~ilivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~al~~~~~~~~dlvl~D~~lp~~~g~~~~~~l~~~----------   73 (208)
T 1yio_A            4 KPTVFVVDDDMSVREGLRNLLRSAGFEVETFDCASTFLEHRRPEQHGCLVLDMRMPGMSGIELQEQLTAI----------   73 (208)
T ss_dssp             CCEEEEECSCHHHHHHHHHHHHTTTCEEEEESSHHHHHHHCCTTSCEEEEEESCCSSSCHHHHHHHHHHT----------
T ss_pred             CCEEEEEcCCHHHHHHHHHHHHhCCceEEEcCCHHHHHHhhhccCCCEEEEeCCCCCCCHHHHHHHHHhc----------
Confidence            4589999999999999999999999999999999999999999999999999999999999999999963          


Q ss_pred             hhhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHHhh
Q 039716          939 EAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQY 1000 (1002)
Q Consensus       939 ~~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~~ 1000 (1002)
                                      .+.+|||++|++.+.+...+++++|+++||.||++.++|...|++.
T Consensus        74 ----------------~~~~~ii~ls~~~~~~~~~~a~~~Ga~~~l~Kp~~~~~L~~~i~~~  119 (208)
T 1yio_A           74 ----------------SDGIPIVFITAHGDIPMTVRAMKAGAIEFLPKPFEEQALLDAIEQG  119 (208)
T ss_dssp             ----------------TCCCCEEEEESCTTSCCCHHHHHTTEEEEEESSCCHHHHHHHHHHH
T ss_pred             ----------------CCCCCEEEEeCCCCHHHHHHHHHCCCcEEEeCCCCHHHHHHHHHHH
Confidence                            3569999999999999999999999999999999999999988765

>2jba_A Phosphate regulon transcriptional regulatory PROT; transcription factor, sensory transduction, phosphate regula transcription regulation; 1.45A {Escherichia coli} PDB: 2jba_B 1b00_A 2iyn_A 2jb9_A 1zes_A

Probab=99.71  E-value=1.7e-17  Score=158.06  Aligned_cols=117  Identities=22%  Similarity=0.277  Sum_probs=108.3

Q ss_pred             CeEEEEecCHHHHHHHHHHHHhcCCeEEEEcCHHHHHHHHHcCCCcEEEEcCCCCCCCHHHHHHHHhccccCCCchhhhh
Q 039716          860 PKILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDAAAE  939 (1002)
Q Consensus       860 ~~ILiVeDn~~n~~~l~~~L~~~g~~v~~a~~G~eAl~~~~~~~~DlIlmDi~MP~mdG~e~~~~IR~~~~~~~~~~~~~  939 (1002)
                      .+||||||++..+..++.+|+..|+.+..+.++.+|++.+....||+||+|+.||+++|+++++.||+..          
T Consensus         3 ~~ilivdd~~~~~~~l~~~l~~~g~~v~~~~~~~~a~~~~~~~~~dlvi~D~~l~~~~g~~~~~~l~~~~----------   72 (127)
T 2jba_A            3 RRILVVEDEAPIREMVCFVLEQNGFQPVEAEDYDSAVNQLNEPWPDLILLAWMLPGGSGIQFIKHLRRES----------   72 (127)
T ss_dssp             CEEEEECSCHHHHHHHHHHHHHTTCEEEEECSHHHHHTTCSSSCCSEEEEESEETTEEHHHHHHHHHTST----------
T ss_pred             cEEEEEcCCHHHHHHHHHHHHHCCceEEEeCCHHHHHHHHhccCCCEEEEecCCCCCCHHHHHHHHHhCc----------
Confidence            4799999999999999999999999999999999999999888999999999999999999999999631          


Q ss_pred             hhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHHhh
Q 039716          940 AGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQY 1000 (1002)
Q Consensus       940 ~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~~ 1000 (1002)
                                    ..+.+|||++|+....+...+++++|+++|+.||++.++|...|++.
T Consensus        73 --------------~~~~~~ii~~s~~~~~~~~~~~~~~ga~~~l~Kp~~~~~l~~~i~~~  119 (127)
T 2jba_A           73 --------------MTRDIPVVMLTARGEEEDRVRGLETGADDCITKPFSPKELVARIKAV  119 (127)
T ss_dssp             --------------TTTTSCEEEEEETTHHHHHHTTCCCSCSEEEEESCCHHHHHHHHHHH
T ss_pred             --------------ccCCCCEEEEeCCCCHHHHHHHHhcCCCeEEeCCCCHHHHHHHHHHH
Confidence                          23579999999999888999999999999999999999999988765

>3q9s_A DNA-binding response regulator; DNA binding protein; 2.40A {Deinococcus radiodurans}

Probab=99.71  E-value=5.3e-17  Score=175.18  Aligned_cols=117  Identities=23%  Similarity=0.367  Sum_probs=109.7

Q ss_pred             CCCeEEEEecCHHHHHHHHHHHHhcCCeEEEEcCHHHHHHHHHcCCCcEEEEcCCCCCCCHHHHHHHHhccccCCCchhh
Q 039716          858 PKPKILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDAA  937 (1002)
Q Consensus       858 ~~~~ILiVeDn~~n~~~l~~~L~~~g~~v~~a~~G~eAl~~~~~~~~DlIlmDi~MP~mdG~e~~~~IR~~~~~~~~~~~  937 (1002)
                      ...+||||||++..+..++.+|+..|+.|..+.++.+|++.+....||+||+|+.||++||+++++.||.          
T Consensus        36 ~~~~ILivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~al~~~~~~~~DlvllD~~lp~~~G~~l~~~lr~----------  105 (249)
T 3q9s_A           36 NEQRILVIEDDHDIANVLRMDLTDAGYVVDHADSAMNGLIKAREDHPDLILLDLGLPDFDGGDVVQRLRK----------  105 (249)
T ss_dssp             -CCEEEEECSCHHHHHHHHHHHHTTTCEEEEESSHHHHHHHHHHSCCSEEEEECCSCHHHHHHHHHHHHT----------
T ss_pred             CCCEEEEEECCHHHHHHHHHHHHHCCCEEEEeCCHHHHHHHHhcCCCCEEEEcCCCCCCCHHHHHHHHHc----------
Confidence            3468999999999999999999999999999999999999999999999999999999999999999995          


Q ss_pred             hhhhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHHhhc
Q 039716          938 AEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQYF 1001 (1002)
Q Consensus       938 ~~~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~~l 1001 (1002)
                                       .+.+|||++|+..+.+...+|+++|+++||.||++.++|...|+.++
T Consensus       106 -----------------~~~~~iI~lt~~~~~~~~~~a~~~Ga~~yl~Kp~~~~~L~~~i~~~l  152 (249)
T 3q9s_A          106 -----------------NSALPIIVLTARDTVEEKVRLLGLGADDYLIKPFHPDELLARVKVQL  152 (249)
T ss_dssp             -----------------TCCCCEEEEESCCSHHHHHHHHHHTCSEEEESSCCHHHHHHHHHHHH
T ss_pred             -----------------CCCCCEEEEECCCCHHHHHHHHHCCCcEEEECCCCHHHHHHHHHHHH
Confidence                             14589999999999999999999999999999999999999998754

>1a04_A Nitrate/nitrite response regulator protein NARL; signal transduction protein, response regulators, two- component systems; 2.20A {Escherichia coli} SCOP: a.4.6.2 c.23.1.1 PDB: 1rnl_A

Probab=99.71  E-value=7.1e-17  Score=169.41  Aligned_cols=116  Identities=22%  Similarity=0.341  Sum_probs=107.5

Q ss_pred             CCeEEEEecCHHHHHHHHHHHHhcC-CeE-EEEcCHHHHHHHHHcCCCcEEEEcCCCCCCCHHHHHHHHhccccCCCchh
Q 039716          859 KPKILLVEDNKINVMVAKSMMKQLG-HSI-DVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDA  936 (1002)
Q Consensus       859 ~~~ILiVeDn~~n~~~l~~~L~~~g-~~v-~~a~~G~eAl~~~~~~~~DlIlmDi~MP~mdG~e~~~~IR~~~~~~~~~~  936 (1002)
                      ..+||||||++..+..++.+|+..| +.+ ..+.+|.+|++.+....||+||+|+.||++||+++++.||+.        
T Consensus         5 ~~~ilivdd~~~~~~~l~~~L~~~~~~~vv~~~~~~~~al~~~~~~~~dlvllD~~lp~~~g~~~~~~lr~~--------   76 (215)
T 1a04_A            5 PATILLIDDHPMLRTGVKQLISMAPDITVVGEASNGEQGIELAESLDPDLILLDLNMPGMNGLETLDKLREK--------   76 (215)
T ss_dssp             CEEEEEECSCHHHHHHHHHHHTTCTTEEEEEEESSHHHHHHHHHHHCCSEEEEETTSTTSCHHHHHHHHHHS--------
T ss_pred             ceEEEEECCCHHHHHHHHHHHhcCCCcEEEEEeCCHHHHHHHHHhcCCCEEEEeCCCCCCcHHHHHHHHHHh--------
Confidence            4589999999999999999999875 777 789999999999999999999999999999999999999963        


Q ss_pred             hhhhhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHHhh
Q 039716          937 AAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQY 1000 (1002)
Q Consensus       937 ~~~~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~~ 1000 (1002)
                                        .+.+|||++|+....+...+++.+|+++||.||++.++|...|++.
T Consensus        77 ------------------~~~~~ii~ls~~~~~~~~~~~~~~Ga~~~l~Kp~~~~~L~~~i~~~  122 (215)
T 1a04_A           77 ------------------SLSGRIVVFSVSNHEEDVVTALKRGADGYLLKDMEPEDLLKALHQA  122 (215)
T ss_dssp             ------------------CCCSEEEEEECCCCHHHHHHHHHTTCSEEEETTCCHHHHHHHHHHH
T ss_pred             ------------------CCCCcEEEEECCCCHHHHHHHHHcCCcEEEeCCCCHHHHHHHHHHH
Confidence                              3568999999999999999999999999999999999999999865

>2zay_A Response regulator receiver protein; structural genomics, NYSGXRC, target 11006U, protein structure initiative; 2.00A {Desulfuromonas acetoxidans}

Probab=99.71  E-value=7.1e-17  Score=158.27  Aligned_cols=120  Identities=23%  Similarity=0.344  Sum_probs=110.6

Q ss_pred             CCCeEEEEecCHHHHHHHHHHHHhcCCeEEEEcCHHHHHHHHHcCCCcEEEEcCCCCCCCHHHHHHHHhccccCCCchhh
Q 039716          858 PKPKILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDAA  937 (1002)
Q Consensus       858 ~~~~ILiVeDn~~n~~~l~~~L~~~g~~v~~a~~G~eAl~~~~~~~~DlIlmDi~MP~mdG~e~~~~IR~~~~~~~~~~~  937 (1002)
                      ...+||||||++..+..+..+|...||.|..+.++.+|+..+....||+||+|+.||+++|+++++.||...        
T Consensus         7 ~~~~iLivd~~~~~~~~l~~~L~~~g~~v~~~~~~~~a~~~l~~~~~dlii~d~~l~~~~g~~~~~~l~~~~--------   78 (147)
T 2zay_A            7 KWWRIMLVDTQLPALAASISALSQEGFDIIQCGNAIEAVPVAVKTHPHLIITEANMPKISGMDLFNSLKKNP--------   78 (147)
T ss_dssp             -CEEEEEECTTGGGGHHHHHHHHHHTEEEEEESSHHHHHHHHHHHCCSEEEEESCCSSSCHHHHHHHHHTST--------
T ss_pred             CCceEEEEeCCHHHHHHHHHHHHHcCCeEEEeCCHHHHHHHHHcCCCCEEEEcCCCCCCCHHHHHHHHHcCc--------
Confidence            356899999999999999999999999999999999999999999999999999999999999999999621        


Q ss_pred             hhhhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHHhhc
Q 039716          938 AEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQYF 1001 (1002)
Q Consensus       938 ~~~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~~l 1001 (1002)
                                      ..+.+|||++|+....+...+++++|+++||.||++..+|...|++.+
T Consensus        79 ----------------~~~~~pii~ls~~~~~~~~~~~~~~g~~~~l~kp~~~~~L~~~i~~~~  126 (147)
T 2zay_A           79 ----------------QTASIPVIALSGRATAKEEAQLLDMGFIDFIAKPVNAIRLSARIKRVL  126 (147)
T ss_dssp             ----------------TTTTSCEEEEESSCCHHHHHHHHHHTCSEEEESSCCHHHHHHHHHHHH
T ss_pred             ----------------ccCCCCEEEEeCCCCHHHHHHHHhCCCCEEEeCCCCHHHHHHHHHHHH
Confidence                            246799999999999999999999999999999999999999988653

>2qxy_A Response regulator; regulation of transcription, NYSGXRC, protein structure initiative II (PSI II), structural genomics; 1.95A {Thermotoga maritima}

Probab=99.70  E-value=9.6e-17  Score=156.33  Aligned_cols=116  Identities=20%  Similarity=0.351  Sum_probs=109.0

Q ss_pred             CCeEEEEecCHHHHHHHHHHHHhcCCeEEEEcCHHHHHHHHHcCCCcEEEEcCCCCCCCHHHHHHHHhccccCCCchhhh
Q 039716          859 KPKILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDAAA  938 (1002)
Q Consensus       859 ~~~ILiVeDn~~n~~~l~~~L~~~g~~v~~a~~G~eAl~~~~~~~~DlIlmDi~MP~mdG~e~~~~IR~~~~~~~~~~~~  938 (1002)
                      ..+||||||++..+..++.+|+..||.|..+.++.+|++.+....||+||+|+ ||+++|+++++.||..          
T Consensus         4 ~~~iLivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~a~~~l~~~~~dlvi~d~-~~~~~g~~~~~~l~~~----------   72 (142)
T 2qxy_A            4 TPTVMVVDESRITFLAVKNALEKDGFNVIWAKNEQEAFTFLRREKIDLVFVDV-FEGEESLNLIRRIREE----------   72 (142)
T ss_dssp             CCEEEEECSCHHHHHHHHHHHGGGTCEEEEESSHHHHHHHHTTSCCSEEEEEC-TTTHHHHHHHHHHHHH----------
T ss_pred             CCeEEEEeCCHHHHHHHHHHHHhCCCEEEEECCHHHHHHHHhccCCCEEEEeC-CCCCcHHHHHHHHHHH----------
Confidence            46899999999999999999999999999999999999999999999999999 9999999999999963          


Q ss_pred             hhhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHHhhc
Q 039716          939 EAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQYF 1001 (1002)
Q Consensus       939 ~~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~~l 1001 (1002)
                                      .+.+|||++|+....+...+++.+|+++||.||++.++|...|++.+
T Consensus        73 ----------------~~~~pii~ls~~~~~~~~~~~~~~g~~~~l~kP~~~~~l~~~i~~~~  119 (142)
T 2qxy_A           73 ----------------FPDTKVAVLSAYVDKDLIINSVKAGAVDYILKPFRLDYLLERVKKII  119 (142)
T ss_dssp             ----------------CTTCEEEEEESCCCHHHHHHHHHHTCSCEEESSCCHHHHHHHHHHHH
T ss_pred             ----------------CCCCCEEEEECCCCHHHHHHHHHCCcceeEeCCCCHHHHHHHHHHHH
Confidence                            25699999999999999999999999999999999999999998753

>2rjn_A Response regulator receiver:metal-dependent phosphohydrolase, HD subdomain; structural genomics, oceanospirillum SP. MED92; 2.10A {Neptuniibacter caesariensis}

Probab=99.70  E-value=1.7e-16  Score=157.21  Aligned_cols=118  Identities=19%  Similarity=0.326  Sum_probs=109.8

Q ss_pred             CCCeEEEEecCHHHHHHHHHHHHhcCCeEEEEcCHHHHHHHHHcCCCcEEEEcCCCCCCCHHHHHHHHhccccCCCchhh
Q 039716          858 PKPKILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDAA  937 (1002)
Q Consensus       858 ~~~~ILiVeDn~~n~~~l~~~L~~~g~~v~~a~~G~eAl~~~~~~~~DlIlmDi~MP~mdG~e~~~~IR~~~~~~~~~~~  937 (1002)
                      ...+||||||++..+..+..+|+..||.|..+.++.+|+..+....||+||+|+.||+++|+++++.||..         
T Consensus         6 ~~~~iLivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~a~~~l~~~~~dlvi~d~~l~~~~g~~~~~~l~~~---------   76 (154)
T 2rjn_A            6 KNYTVMLVDDEQPILNSLKRLIKRLGCNIITFTSPLDALEALKGTSVQLVISDMRMPEMGGEVFLEQVAKS---------   76 (154)
T ss_dssp             SCCEEEEECSCHHHHHHHHHHHHTTTCEEEEESCHHHHHHHHTTSCCSEEEEESSCSSSCHHHHHHHHHHH---------
T ss_pred             CCCeEEEEcCCHHHHHHHHHHHHHcCCeEEEeCCHHHHHHHHhcCCCCEEEEecCCCCCCHHHHHHHHHHh---------
Confidence            45689999999999999999999999999999999999999999999999999999999999999999963         


Q ss_pred             hhhhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcC-CCEEEeCCCChHHHHHHHHhhc
Q 039716          938 AEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANG-MDSFVSKPVTFQKLKECLEQYF 1001 (1002)
Q Consensus       938 ~~~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG-~d~~l~KP~~~~~L~~~l~~~l 1001 (1002)
                                       .+.+|||++|+........+++.+| +++||.||++..+|...|++.+
T Consensus        77 -----------------~~~~~ii~ls~~~~~~~~~~~~~~g~~~~~l~kP~~~~~L~~~i~~~~  124 (154)
T 2rjn_A           77 -----------------YPDIERVVISGYADAQATIDAVNRGKISRFLLKPWEDEDVFKVVEKGL  124 (154)
T ss_dssp             -----------------CTTSEEEEEECGGGHHHHHHHHHTTCCSEEEESSCCHHHHHHHHHHHH
T ss_pred             -----------------CCCCcEEEEecCCCHHHHHHHHhccchheeeeCCCCHHHHHHHHHHHH
Confidence                             2569999999999999999999998 9999999999999999987653

>3cu5_A Two component transcriptional regulator, ARAC FAM; structural genomics, protein structure initiative; 2.60A {Clostridium phytofermentans isdg}

Probab=99.70  E-value=5.4e-17  Score=158.58  Aligned_cols=115  Identities=22%  Similarity=0.317  Sum_probs=99.6

Q ss_pred             CeEEEEecCHHHHHHHHHHHHh--cCCeEE-EEcCHHHHHHHHHcCCCcEEEEcCCCCCCCHHHHHHHHhccccCCCchh
Q 039716          860 PKILLVEDNKINVMVAKSMMKQ--LGHSID-VVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDA  936 (1002)
Q Consensus       860 ~~ILiVeDn~~n~~~l~~~L~~--~g~~v~-~a~~G~eAl~~~~~~~~DlIlmDi~MP~mdG~e~~~~IR~~~~~~~~~~  936 (1002)
                      .+||||||++..+..+..+|..  .|+.+. .+.+|.+|++.+....||+||+|+.||+++|+++++.||+.        
T Consensus         3 ~~ILivdd~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~al~~~~~~~~dlvllD~~lp~~~g~~l~~~l~~~--------   74 (141)
T 3cu5_A            3 LRILIVDDEKLTRDGLIANINWKALSFDQIDQADDGINAIQIALKHPPNVLLTDVRMPRMDGIELVDNILKL--------   74 (141)
T ss_dssp             CEEEEECSCHHHHHHHHHHCCGGGSCCSEEEEESSHHHHHHHHTTSCCSEEEEESCCSSSCHHHHHHHHHHH--------
T ss_pred             ceEEEEeCCHHHHHHHHHHHHHccCCcEEeeecccHHHHHHHHhcCCCCEEEEeCCCCCCCHHHHHHHHHhh--------
Confidence            4799999999999999999973  688877 89999999999998999999999999999999999999963        


Q ss_pred             hhhhhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHHhh
Q 039716          937 AAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQY 1000 (1002)
Q Consensus       937 ~~~~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~~ 1000 (1002)
                                        .+.+|||++|+....+...+++++|+++||.||++.++|...|++.
T Consensus        75 ------------------~~~~~ii~ls~~~~~~~~~~~~~~ga~~~l~KP~~~~~L~~~i~~~  120 (141)
T 3cu5_A           75 ------------------YPDCSVIFMSGYSDKEYLKAAIKFRAIRYVEKPIDPSEIMDALKQS  120 (141)
T ss_dssp             ------------------CTTCEEEEECCSTTTCCC------CCCEEECSSCCHHHHHHHHHHH
T ss_pred             ------------------CCCCcEEEEeCCCcHHHHHHHHhCCccEEEeCCCCHHHHHHHHHHH
Confidence                              2568999999999888889999999999999999999999998765

>3eq2_A Probable two-component response regulator; adaptor sigmas, signaling protein; 3.40A {Pseudomonas aeruginosa} PDB: 3f7a_A

Probab=99.70  E-value=4e-17  Score=188.11  Aligned_cols=116  Identities=21%  Similarity=0.413  Sum_probs=104.8

Q ss_pred             CCeEEEEecCHHHHHHHHHHHHhcCCeEEEEcCHHHHHHHHHcCCCcEEEEcCCCCCCCHHHHHHHHhccccCCCchhhh
Q 039716          859 KPKILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDAAA  938 (1002)
Q Consensus       859 ~~~ILiVeDn~~n~~~l~~~L~~~g~~v~~a~~G~eAl~~~~~~~~DlIlmDi~MP~mdG~e~~~~IR~~~~~~~~~~~~  938 (1002)
                      ..+||||||++.++..++.+|+..||.|..+.||.+|++.+....||+||+|++||+|||+++++.||+.          
T Consensus         5 ~~~iLivdD~~~~~~~l~~~L~~~g~~v~~a~~~~~al~~~~~~~~dlvllD~~mp~~~G~~~~~~lr~~----------   74 (394)
T 3eq2_A            5 SATLLIIDDDEVVRESLAAYLEDSNFKVLQALNGLQGLQIFESEQPDLVICDLRMPQIDGLELIRRIRQT----------   74 (394)
T ss_dssp             EEEEEEECSCHHHHHHHHHHHHHTTEEEEECSSHHHHHHHHHHSCCSEEEECCCSSSSCTHHHHHHHHHT----------
T ss_pred             CCEEEEEeCCHHHHHHHHHHHHhCCCEEEEECCHHHHHHHHhhCCCCEEEEcCCCCCCCHHHHHHHHHhh----------
Confidence            3589999999999999999999999999999999999999999999999999999999999999999963          


Q ss_pred             hhhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCC-ChHHHHHHHHhh
Q 039716          939 EAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPV-TFQKLKECLEQY 1000 (1002)
Q Consensus       939 ~~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~-~~~~L~~~l~~~ 1000 (1002)
                                      .+.+|||++|++.+.+...+|+++|+++||.||+ +.+.|...|++.
T Consensus        75 ----------------~~~~pii~lt~~~~~~~~~~a~~~ga~~yl~KP~~~~~~l~~~i~~~  121 (394)
T 3eq2_A           75 ----------------ASETPIIVLSGAGVMSDAVEALRLGAADYLIKPLEDLAVLEHSVRRA  121 (394)
T ss_dssp             ----------------TCCCCEEEC---CHHHHHHHHHHHTCSEECCSSCSCTHHHHHHHHHH
T ss_pred             ----------------CCCCcEEEEEcCCCHHHHHHHHhcChhhEEECCCChHHHHHHHHHHH
Confidence                            3579999999999999999999999999999999 688888777654

>2jk1_A HUPR, hydrogenase transcriptional regulatory protein HU; nucleotide-binding, transcription regulation; 2.10A {Rhodobacter capsulatus} PDB: 2vui_B 2vuh_B

Probab=99.69  E-value=1.4e-16  Score=154.80  Aligned_cols=114  Identities=20%  Similarity=0.265  Sum_probs=104.0

Q ss_pred             CeEEEEecCHHHHHHHHHHHHhcCCeEEEEcCHHHHHHHHHcCCCcEEEEcCCCCCCCHHHHHHHHhccccCCCchhhhh
Q 039716          860 PKILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDAAAE  939 (1002)
Q Consensus       860 ~~ILiVeDn~~n~~~l~~~L~~~g~~v~~a~~G~eAl~~~~~~~~DlIlmDi~MP~mdG~e~~~~IR~~~~~~~~~~~~~  939 (1002)
                      .+||||||++..+..++.+|+.. |.|..+.+|.+|++.+....||+||+|+.||+++|+++++.||..           
T Consensus         2 ~~Ilivdd~~~~~~~l~~~l~~~-~~v~~~~~~~~a~~~~~~~~~dlvl~D~~lp~~~g~~~~~~l~~~-----------   69 (139)
T 2jk1_A            2 PAILLVDDEPHSLAAMKLALEDD-FDVLTAQGAEAAIAILEEEWVQVIICDQRMPGRTGVDFLTEVRER-----------   69 (139)
T ss_dssp             CEEEEECSSHHHHHHHHHHHTTT-SCEEEESSHHHHHHHHHHSCEEEEEEESCCSSSCHHHHHHHHHHH-----------
T ss_pred             CeEEEEcCCHHHHHHHHHHhhcC-ceEEEcCCHHHHHHHHhcCCCCEEEEeCCCCCCcHHHHHHHHHHh-----------
Confidence            47999999999999999999875 999999999999999999999999999999999999999999963           


Q ss_pred             hhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHc-CCCEEEeCCCChHHHHHHHHhh
Q 039716          940 AGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFAN-GMDSFVSKPVTFQKLKECLEQY 1000 (1002)
Q Consensus       940 ~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~a-G~d~~l~KP~~~~~L~~~l~~~ 1000 (1002)
                                     .+.+|||++|+........+++.. |+++||.||++.++|...|++.
T Consensus        70 ---------------~~~~~ii~~s~~~~~~~~~~~~~~~ga~~~l~KP~~~~~L~~~i~~~  116 (139)
T 2jk1_A           70 ---------------WPETVRIIITGYTDSASMMAAINDAGIHQFLTKPWHPEQLLSSARNA  116 (139)
T ss_dssp             ---------------CTTSEEEEEESCTTCHHHHHHHHHTTCCEEEESSCCHHHHHHHHHHH
T ss_pred             ---------------CCCCcEEEEeCCCChHHHHHHHHhhchhhhccCCCCHHHHHHHHHHH
Confidence                           256899999999988888888876 5999999999999999988764

>3n53_A Response regulator receiver modulated diguanylate; diguanylate cyclase, protein structure I II(PSI II), NYSGXRC, structural genomics; 2.20A {Pelobacter carbinolicus} SCOP: c.23.1.0

Probab=99.69  E-value=4.3e-17  Score=158.59  Aligned_cols=118  Identities=17%  Similarity=0.285  Sum_probs=99.4

Q ss_pred             CCeEEEEecCHHHHHHHHHHHHhcCCeEEEEcCHHHHHHHHHcCCCcEEEEcCCCCCCCHHHHHHHHhccccCCCchhhh
Q 039716          859 KPKILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDAAA  938 (1002)
Q Consensus       859 ~~~ILiVeDn~~n~~~l~~~L~~~g~~v~~a~~G~eAl~~~~~~~~DlIlmDi~MP~mdG~e~~~~IR~~~~~~~~~~~~  938 (1002)
                      ..+||||||++..+..+..+|+.. +.|..+.++.+|++.+....||+||+|+.||+++|+++++.||+..         
T Consensus         3 ~~~iLivdd~~~~~~~l~~~l~~~-~~v~~~~~~~~a~~~~~~~~~dlvi~D~~l~~~~g~~~~~~l~~~~---------   72 (140)
T 3n53_A            3 LKKILIIDQQDFSRIELKNFLDSE-YLVIESKNEKEALEQIDHHHPDLVILDMDIIGENSPNLCLKLKRSK---------   72 (140)
T ss_dssp             CCEEEEECSCHHHHHHHHHHHTTT-SEEEEESSHHHHHHHHHHHCCSEEEEETTC------CHHHHHHTST---------
T ss_pred             CCEEEEEeCCHHHHHHHHHHHHhc-ceEEEeCCHHHHHHHHhcCCCCEEEEeCCCCCCcHHHHHHHHHcCc---------
Confidence            458999999999999999999988 9999999999999999999999999999999999999999999632         


Q ss_pred             hhhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHHhhc
Q 039716          939 EAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQYF 1001 (1002)
Q Consensus       939 ~~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~~l 1001 (1002)
                                     ..+.+|||++|+....+...+++++|+++||.||++.++|...|++++
T Consensus        73 ---------------~~~~~~ii~~s~~~~~~~~~~~~~~g~~~~l~KP~~~~~l~~~i~~~~  120 (140)
T 3n53_A           73 ---------------GLKNVPLILLFSSEHKEAIVNGLHSGADDYLTKPFNRNDLLSRIEIHL  120 (140)
T ss_dssp             ---------------TCTTCCEEEEECC----CTTTTTTCCCSEEEESSCCHHHHHHHHHHHH
T ss_pred             ---------------ccCCCCEEEEecCCCHHHHHHHHhcCCCeeeeCCCCHHHHHHHHHHHH
Confidence                           236799999999999999999999999999999999999999998753

>1kgs_A DRRD, DNA binding response regulator D; DNA-binding protein, ALPH-beta sandwich, winged-helix, helix helix, DNA binding protein; HET: DNA MSE; 1.50A {Thermotoga maritima} SCOP: a.4.6.1 c.23.1.1 PDB: 3nnn_A*

Probab=99.69  E-value=1.3e-16  Score=168.44  Aligned_cols=115  Identities=22%  Similarity=0.379  Sum_probs=108.6

Q ss_pred             CeEEEEecCHHHHHHHHHHHHhcCCeEEEEcCHHHHHHHHHcCCCcEEEEcCCCCCCCHHHHHHHHhccccCCCchhhhh
Q 039716          860 PKILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDAAAE  939 (1002)
Q Consensus       860 ~~ILiVeDn~~n~~~l~~~L~~~g~~v~~a~~G~eAl~~~~~~~~DlIlmDi~MP~mdG~e~~~~IR~~~~~~~~~~~~~  939 (1002)
                      .+||||||++..+..+..+|+..|+.|..+.++.+|++.+....||+||+|+.||+++|+++++.||..           
T Consensus         3 ~~ilivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~a~~~~~~~~~dlvllD~~l~~~~g~~~~~~lr~~-----------   71 (225)
T 1kgs_A            3 VRVLVVEDERDLADLITEALKKEMFTVDVCYDGEEGMYMALNEPFDVVILDIMLPVHDGWEILKSMRES-----------   71 (225)
T ss_dssp             CEEEEECSSHHHHHHHHHHHHHTTCEEEEESSHHHHHHHHHHSCCSEEEEESCCSSSCHHHHHHHHHHT-----------
T ss_pred             ceEEEEeCCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHHhcCCCCEEEEeCCCCCCCHHHHHHHHHhc-----------
Confidence            589999999999999999999999999999999999999999999999999999999999999999962           


Q ss_pred             hhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHHhh
Q 039716          940 AGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQY 1000 (1002)
Q Consensus       940 ~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~~ 1000 (1002)
                                     .+.+|||++|+....+....++.+|+++||.||++.++|...|+..
T Consensus        72 ---------------~~~~~ii~ls~~~~~~~~~~~~~~ga~~~l~Kp~~~~~l~~~i~~~  117 (225)
T 1kgs_A           72 ---------------GVNTPVLMLTALSDVEYRVKGLNMGADDYLPKPFDLRELIARVRAL  117 (225)
T ss_dssp             ---------------TCCCCEEEEESSCHHHHHHHTCCCCCSEEEESSCCHHHHHHHHHHH
T ss_pred             ---------------CCCCCEEEEeCCCCHHHHHHHHhCCccEEEeCCCCHHHHHHHHHHH
Confidence                           2579999999999999999999999999999999999999998765

>3kcn_A Adenylate cyclase homolog; SGX, PSI 2, structural genomics, protein structure initiative; 2.45A {Rhodopirellula baltica}

Probab=99.69  E-value=1.9e-16  Score=156.43  Aligned_cols=116  Identities=22%  Similarity=0.357  Sum_probs=107.0

Q ss_pred             CCeEEEEecCHHHHHHHHHHHHhcCCeEEEEcCHHHHHHHHHcCC-CcEEEEcCCCCCCCHHHHHHHHhccccCCCchhh
Q 039716          859 KPKILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQN-YDLILMDVCMPVMDGLKATRLIRSFEDTGNWDAA  937 (1002)
Q Consensus       859 ~~~ILiVeDn~~n~~~l~~~L~~~g~~v~~a~~G~eAl~~~~~~~-~DlIlmDi~MP~mdG~e~~~~IR~~~~~~~~~~~  937 (1002)
                      ..+||||||++..+..+..+|+. |+.|..+.++.+|++.+.... ||+||+|+.||+++|+++++.||..         
T Consensus         4 ~~~ILivdd~~~~~~~l~~~L~~-~~~v~~~~~~~~a~~~l~~~~~~dlvi~D~~l~~~~g~~~~~~l~~~---------   73 (151)
T 3kcn_A            4 NERILLVDDDYSLLNTLKRNLSF-DFEVTTCESGPEALACIKKSDPFSVIMVDMRMPGMEGTEVIQKARLI---------   73 (151)
T ss_dssp             CCEEEEECSCHHHHHHHHHHHTT-TSEEEEESSHHHHHHHHHHSCCCSEEEEESCCSSSCHHHHHHHHHHH---------
T ss_pred             CCeEEEEeCCHHHHHHHHHHhcc-CceEEEeCCHHHHHHHHHcCCCCCEEEEeCCCCCCcHHHHHHHHHhc---------
Confidence            46899999999999999999986 999999999999999998876 6999999999999999999999963         


Q ss_pred             hhhhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcC-CCEEEeCCCChHHHHHHHHhhc
Q 039716          938 AEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANG-MDSFVSKPVTFQKLKECLEQYF 1001 (1002)
Q Consensus       938 ~~~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG-~d~~l~KP~~~~~L~~~l~~~l 1001 (1002)
                                       .+.+|||++|+..+.+...+++.+| +++||.||++.++|...|.+.+
T Consensus        74 -----------------~~~~~ii~~s~~~~~~~~~~~~~~g~~~~~l~KP~~~~~L~~~i~~~l  121 (151)
T 3kcn_A           74 -----------------SPNSVYLMLTGNQDLTTAMEAVNEGQVFRFLNKPCQMSDIKAAINAGI  121 (151)
T ss_dssp             -----------------CSSCEEEEEECGGGHHHHHHHHHHTCCSEEEESSCCHHHHHHHHHHHH
T ss_pred             -----------------CCCcEEEEEECCCCHHHHHHHHHcCCeeEEEcCCCCHHHHHHHHHHHH
Confidence                             3568999999999999999999999 9999999999999999987653

>1s8n_A Putative antiterminator; RV1626, structural genomics, transcriptional antiterminator, component system, PSI; 1.48A {Mycobacterium tuberculosis} SCOP: c.23.1.1 PDB: 1sd5_A

Probab=99.69  E-value=8.4e-17  Score=167.65  Aligned_cols=115  Identities=29%  Similarity=0.417  Sum_probs=106.8

Q ss_pred             CCeEEEEecCHHHHHHHHHHHHhcCCeEE-EEcCHHHHHHHHHcCCCcEEEEcCCCCCCCHHHHHHHHhccccCCCchhh
Q 039716          859 KPKILLVEDNKINVMVAKSMMKQLGHSID-VVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDAA  937 (1002)
Q Consensus       859 ~~~ILiVeDn~~n~~~l~~~L~~~g~~v~-~a~~G~eAl~~~~~~~~DlIlmDi~MP~mdG~e~~~~IR~~~~~~~~~~~  937 (1002)
                      ..+||||||++..+..+..+|...||.|. .+.+|.+|++.+....||+||+|+.||+++|+++++.||..         
T Consensus        13 ~~~iLivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~~al~~~~~~~~dlvi~D~~~p~~~g~~~~~~l~~~---------   83 (205)
T 1s8n_A           13 PRRVLIAEDEALIRMDLAEMLREEGYEIVGEAGDGQEAVELAELHKPDLVIMDVKMPRRDGIDAASEIASK---------   83 (205)
T ss_dssp             CCEEEEECSSHHHHHHHHHHHHHTTCEEEEEESSHHHHHHHHHHHCCSEEEEESSCSSSCHHHHHHHHHHT---------
T ss_pred             CccEEEEECCHHHHHHHHHHHHHCCCEEEEEeCCHHHHHHHHhhcCCCEEEEeCCCCCCChHHHHHHHHhc---------
Confidence            35899999999999999999999999988 89999999999999999999999999999999999999962         


Q ss_pred             hhhhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHHhh
Q 039716          938 AEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQY 1000 (1002)
Q Consensus       938 ~~~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~~ 1000 (1002)
                                        ...|||++|++...+...+++++|+++||.||++.++|...|++.
T Consensus        84 ------------------~~~pii~lt~~~~~~~~~~~~~~ga~~~l~KP~~~~~L~~~i~~~  128 (205)
T 1s8n_A           84 ------------------RIAPIVVLTAFSQRDLVERARDAGAMAYLVKPFSISDLIPAIELA  128 (205)
T ss_dssp             ------------------TCSCEEEEEEGGGHHHHHTTGGGSCEEEEEESCCHHHHHHHHHHH
T ss_pred             ------------------CCCCEEEEecCCCHHHHHHHHhcCCcEEEeCCCCHHHHHHHHHHH
Confidence                              124999999999999999999999999999999999999988764

>3cg0_A Response regulator receiver modulated diguanylate with PAS/PAC sensor; signal receiver domain, diguanylate cyclase; 2.15A {Desulfovibrio desulfuricans subsp}

Probab=99.69  E-value=1.9e-16  Score=153.54  Aligned_cols=117  Identities=24%  Similarity=0.372  Sum_probs=109.0

Q ss_pred             CCCeEEEEecCHHHHHHHHHHHHhcCCeEE-EEcCHHHHHHHHHcCCCcEEEEcCCCC-CCCHHHHHHHHhccccCCCch
Q 039716          858 PKPKILLVEDNKINVMVAKSMMKQLGHSID-VVNNGVEAVHAVQCQNYDLILMDVCMP-VMDGLKATRLIRSFEDTGNWD  935 (1002)
Q Consensus       858 ~~~~ILiVeDn~~n~~~l~~~L~~~g~~v~-~a~~G~eAl~~~~~~~~DlIlmDi~MP-~mdG~e~~~~IR~~~~~~~~~  935 (1002)
                      ...+||||||++..+..++.+|+..||.+. ++.++.+|+..+....||+||+|+.|| +++|+++++.||..       
T Consensus         8 ~~~~iLivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~~a~~~~~~~~~dlii~d~~~~~~~~g~~~~~~l~~~-------   80 (140)
T 3cg0_A            8 DLPGVLIVEDGRLAAATLRIQLESLGYDVLGVFDNGEEAVRCAPDLRPDIALVDIMLCGALDGVETAARLAAG-------   80 (140)
T ss_dssp             CCCEEEEECCBHHHHHHHHHHHHHHTCEEEEEESSHHHHHHHHHHHCCSEEEEESSCCSSSCHHHHHHHHHHH-------
T ss_pred             CCceEEEEECCHHHHHHHHHHHHHCCCeeEEEECCHHHHHHHHHhCCCCEEEEecCCCCCCCHHHHHHHHHhC-------
Confidence            457899999999999999999999999999 599999999999999999999999999 89999999999963       


Q ss_pred             hhhhhhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHHhhc
Q 039716          936 AAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQYF 1001 (1002)
Q Consensus       936 ~~~~~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~~l 1001 (1002)
                                          +.+|||++|+....+....++++|+++||.||++.++|...|++.+
T Consensus        81 --------------------~~~~ii~ls~~~~~~~~~~~~~~g~~~~l~kp~~~~~l~~~i~~~~  126 (140)
T 3cg0_A           81 --------------------CNLPIIFITSSQDVETFQRAKRVNPFGYLAKPVAADTLHRSIEMAI  126 (140)
T ss_dssp             --------------------SCCCEEEEECCCCHHHHHHHHTTCCSEEEEESCCHHHHHHHHHHHH
T ss_pred             --------------------CCCCEEEEecCCCHHHHHHHHhcCCCEEEeCCCCHHHHHHHHHHHH
Confidence                                4589999999999999999999999999999999999999998753

>3cg4_A Response regulator receiver domain protein (CHEY-; structural genomics, unknown function; HET: MSE; 1.61A {Methanospirillum hungatei jf-1}

Probab=99.69  E-value=6.8e-17  Score=157.27  Aligned_cols=120  Identities=20%  Similarity=0.328  Sum_probs=110.7

Q ss_pred             CCCeEEEEecCHHHHHHHHHHHHhcCCeEEEEcCHHHHHHHHHcCCCcEEEEcCCCCCCCHHHHHHHHhccccCCCchhh
Q 039716          858 PKPKILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDAA  937 (1002)
Q Consensus       858 ~~~~ILiVeDn~~n~~~l~~~L~~~g~~v~~a~~G~eAl~~~~~~~~DlIlmDi~MP~mdG~e~~~~IR~~~~~~~~~~~  937 (1002)
                      ...+||||||++..+..+..+|+..||.|..+.++.+|++.+....||+||+|+.||+++|+++++.||...        
T Consensus         6 ~~~~iLivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~a~~~l~~~~~dlii~d~~l~~~~g~~~~~~l~~~~--------   77 (142)
T 3cg4_A            6 HKGDVMIVDDDAHVRIAVKTILSDAGFHIISADSGGQCIDLLKKGFSGVVLLDIMMPGMDGWDTIRAILDNS--------   77 (142)
T ss_dssp             CCCEEEEECSCHHHHHHHHHHHHHTTCEEEEESSHHHHHHHHHTCCCEEEEEESCCSSSCHHHHHHHHHHTT--------
T ss_pred             CCCeEEEEcCCHHHHHHHHHHHHHCCeEEEEeCCHHHHHHHHHhcCCCEEEEeCCCCCCCHHHHHHHHHhhc--------
Confidence            456899999999999999999999999999999999999999999999999999999999999999999621        


Q ss_pred             hhhhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHHhhc
Q 039716          938 AEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQYF 1001 (1002)
Q Consensus       938 ~~~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~~l 1001 (1002)
                                      ..+.+|||++|+....+...+++.+|+++||.||++.++|...|++++
T Consensus        78 ----------------~~~~~pii~~s~~~~~~~~~~~~~~g~~~~l~kp~~~~~l~~~i~~~~  125 (142)
T 3cg4_A           78 ----------------LEQGIAIVMLTAKNAPDAKMIGLQEYVVDYITKPFDNEDLIEKTTFFM  125 (142)
T ss_dssp             ----------------CCTTEEEEEEECTTCCCCSSTTGGGGEEEEEESSCCHHHHHHHHHHHH
T ss_pred             ----------------ccCCCCEEEEECCCCHHHHHHHHhcCccEEEeCCCCHHHHHHHHHHHH
Confidence                            246799999999998888889999999999999999999999988754

>1qkk_A DCTD, C4-dicarboxylate transport transcriptional regulatory protein; receiver domain, 2-component signal transduction; 1.7A {Sinorhizobium meliloti} SCOP: c.23.1.1 PDB: 1l5z_A 1l5y_A

Probab=99.69  E-value=1.7e-16  Score=157.21  Aligned_cols=117  Identities=21%  Similarity=0.362  Sum_probs=109.0

Q ss_pred             CCeEEEEecCHHHHHHHHHHHHhcCCeEEEEcCHHHHHHHHHcCCCcEEEEcCCCCCCCHHHHHHHHhccccCCCchhhh
Q 039716          859 KPKILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDAAA  938 (1002)
Q Consensus       859 ~~~ILiVeDn~~n~~~l~~~L~~~g~~v~~a~~G~eAl~~~~~~~~DlIlmDi~MP~mdG~e~~~~IR~~~~~~~~~~~~  938 (1002)
                      +.+||||||++..+..+..+|...||.|..+.++.+|+..+....||+||+|+.||+++|+++++.||..          
T Consensus         3 ~~~ILivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~a~~~l~~~~~dliild~~l~~~~g~~~~~~l~~~----------   72 (155)
T 1qkk_A            3 APSVFLIDDDRDLRKAMQQTLELAGFTVSSFASATEALAGLSADFAGIVISDIRMPGMDGLALFRKILAL----------   72 (155)
T ss_dssp             -CEEEEECSCHHHHHHHHHHHHHTTCEEEEESCHHHHHHTCCTTCCSEEEEESCCSSSCHHHHHHHHHHH----------
T ss_pred             CCEEEEEeCCHHHHHHHHHHHHHcCcEEEEECCHHHHHHHHHhCCCCEEEEeCCCCCCCHHHHHHHHHhh----------
Confidence            4689999999999999999999999999999999999999999999999999999999999999999963          


Q ss_pred             hhhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHHhhc
Q 039716          939 EAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQYF 1001 (1002)
Q Consensus       939 ~~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~~l 1001 (1002)
                                      .+.+|||++|+....+....++.+|+++||.||++..+|...|++.+
T Consensus        73 ----------------~~~~pii~ls~~~~~~~~~~~~~~g~~~~l~kP~~~~~L~~~i~~~~  119 (155)
T 1qkk_A           73 ----------------DPDLPMILVTGHGDIPMAVQAIQDGAYDFIAKPFAADRLVQSARRAE  119 (155)
T ss_dssp             ----------------CTTSCEEEEECGGGHHHHHHHHHTTCCEEEESSCCHHHHHHHHHHHH
T ss_pred             ----------------CCCCCEEEEECCCChHHHHHHHhcCCCeEEeCCCCHHHHHHHHHHHH
Confidence                            25699999999999999999999999999999999999999987653

>2qr3_A Two-component system response regulator; structural genomics, signal receiver, PSI-2, protein structu initiative; 1.80A {Bacteroides fragilis}

Probab=99.69  E-value=2e-16  Score=153.40  Aligned_cols=117  Identities=24%  Similarity=0.294  Sum_probs=108.8

Q ss_pred             CCeEEEEecCHHHHHHHHHHHHhcCCeEEEEcCHHHHHHHHHcCCCcEEEEcCCCC-----CCCHHHHHHHHhccccCCC
Q 039716          859 KPKILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMP-----VMDGLKATRLIRSFEDTGN  933 (1002)
Q Consensus       859 ~~~ILiVeDn~~n~~~l~~~L~~~g~~v~~a~~G~eAl~~~~~~~~DlIlmDi~MP-----~mdG~e~~~~IR~~~~~~~  933 (1002)
                      ..+||||||++..+..++.+|+..|+.|..+.++.+|++.+....||+||+|+.||     +++|+++++.||..     
T Consensus         3 ~~~ilivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~a~~~l~~~~~dlvi~d~~~~~~~~~~~~g~~~~~~l~~~-----   77 (140)
T 2qr3_A            3 LGTIIIVDDNKGVLTAVQLLLKNHFSKVITLSSPVSLSTVLREENPEVVLLDMNFTSGINNGNEGLFWLHEIKRQ-----   77 (140)
T ss_dssp             CCEEEEECSCHHHHHHHHHHHTTTSSEEEEECCHHHHHHHHHHSCEEEEEEETTTTC-----CCHHHHHHHHHHH-----
T ss_pred             CceEEEEeCCHHHHHHHHHHHHhCCcEEEEeCCHHHHHHHHHcCCCCEEEEeCCcCCCCCCCccHHHHHHHHHhh-----
Confidence            45899999999999999999999999999999999999999999999999999999     99999999999963     


Q ss_pred             chhhhhhhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHHhhc
Q 039716          934 WDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQYF 1001 (1002)
Q Consensus       934 ~~~~~~~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~~l 1001 (1002)
                                           .+.+|||++|+....+...+++++|+++||.||++.++|...|++.+
T Consensus        78 ---------------------~~~~~ii~ls~~~~~~~~~~~~~~g~~~~l~kp~~~~~l~~~l~~~~  124 (140)
T 2qr3_A           78 ---------------------YRDLPVVLFTAYADIDLAVRGIKEGASDFVVKPWDNQKLLETLLNAA  124 (140)
T ss_dssp             ---------------------CTTCCEEEEEEGGGHHHHHHHHHTTCCEEEEESCCHHHHHHHHHHHH
T ss_pred             ---------------------CcCCCEEEEECCCCHHHHHHHHHcCchheeeCCCCHHHHHHHHHHHH
Confidence                                 35789999999999999999999999999999999999999998754

>2qvg_A Two component response regulator; NYSGXRC, PSI-2, structural genomics, protein structure initiative; 1.50A {Legionella pneumophila subsp}

Probab=99.69  E-value=3.3e-16  Score=152.52  Aligned_cols=118  Identities=19%  Similarity=0.361  Sum_probs=108.5

Q ss_pred             CCeEEEEecCHHHHHHHHHHHHhcCC--eEEEEcCHHHHHHHHHc------CCCcEEEEcCCCCCCCHHHHHHHHhcccc
Q 039716          859 KPKILLVEDNKINVMVAKSMMKQLGH--SIDVVNNGVEAVHAVQC------QNYDLILMDVCMPVMDGLKATRLIRSFED  930 (1002)
Q Consensus       859 ~~~ILiVeDn~~n~~~l~~~L~~~g~--~v~~a~~G~eAl~~~~~------~~~DlIlmDi~MP~mdG~e~~~~IR~~~~  930 (1002)
                      ..+||||||++..+..++.+|+..|+  .|..+.++.+|++.+..      ..||+||+|+.||+++|+++++.||+.. 
T Consensus         7 ~~~ILivdd~~~~~~~l~~~L~~~g~~~~v~~~~~~~~a~~~l~~~~~~~~~~~dlii~D~~l~~~~g~~~~~~l~~~~-   85 (143)
T 2qvg_A            7 KVDILYLEDDEVDIQSVERVFHKISSLIKIEIAKSGNQALDMLYGRNKENKIHPKLILLDINIPKMNGIEFLKELRDDS-   85 (143)
T ss_dssp             CCSEEEECCCHHHHHHHHHHHHHHCTTCCEEEESSHHHHHHHHHTCTTCCCCCCSEEEEETTCTTSCHHHHHHHHTTSG-
T ss_pred             CCeEEEEeCCHHHHHHHHHHHHHhCCCceEEEECCHHHHHHHHHhcccccCCCCCEEEEecCCCCCCHHHHHHHHHcCc-
Confidence            46899999999999999999999998  99999999999999987      7899999999999999999999999632 


Q ss_pred             CCCchhhhhhhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHHhh
Q 039716          931 TGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQY 1000 (1002)
Q Consensus       931 ~~~~~~~~~~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~~ 1000 (1002)
                                             ..+.+|||++|+....+...+++++|+++||.||++.++|..++..+
T Consensus        86 -----------------------~~~~~~ii~ls~~~~~~~~~~~~~~g~~~~l~kP~~~~~L~~~~~~~  132 (143)
T 2qvg_A           86 -----------------------SFTDIEVFVLTAAYTSKDKLAFESLNIRGHLIKPLDYGEAIKLFWIL  132 (143)
T ss_dssp             -----------------------GGTTCEEEEEESCCCHHHHHHHTTTTCCEEEESSCCHHHHHHHHHHH
T ss_pred             -----------------------cccCCcEEEEeCCCCHHHHHHHHhcCCCeEEECCCCHHHHHHHHHHH
Confidence                                   12569999999999999999999999999999999999999988754

>1w25_A Stalked-cell differentiation controlling protein; two-component system, ggdef domain, cyclic dinucleotide, cyclic-digmp; HET: C2E; 2.70A {Caulobacter vibrioides} SCOP: c.23.1.1 c.23.1.1 d.58.29.2 PDB: 2v0n_A* 2wb4_A*

Probab=99.68  E-value=1.5e-16  Score=186.96  Aligned_cols=117  Identities=24%  Similarity=0.347  Sum_probs=109.2

Q ss_pred             CeEEEEecCHHHHHHHHHHHHhcCCeEEEEcCHHHHHHHHHcCCCcEEEEcCCCCCCCHHHHHHHHhccccCCCchhhhh
Q 039716          860 PKILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDAAAE  939 (1002)
Q Consensus       860 ~~ILiVeDn~~n~~~l~~~L~~~g~~v~~a~~G~eAl~~~~~~~~DlIlmDi~MP~mdG~e~~~~IR~~~~~~~~~~~~~  939 (1002)
                      .+||||||++.++..++.+|+..||.|..|.+|.+|++.+....||+||+|+.||+|||+++++.||...          
T Consensus         2 ~~iLivdD~~~~~~~l~~~L~~~~~~v~~a~~~~~al~~~~~~~~dlvllD~~mp~~~G~~~~~~l~~~~----------   71 (459)
T 1w25_A            2 ARILVVDDIEANVRLLEAKLTAEYYEVSTAMDGPTALAMAARDLPDIILLDVMMPGMDGFTVCRKLKDDP----------   71 (459)
T ss_dssp             CEEEEECSSTTHHHHHHHHHHHTTCEEEEESSHHHHHHHHHHHCCSEEEEESCCSSSCHHHHHHHHHHST----------
T ss_pred             CeEEEEeCCHHHHHHHHHHHHHcCCEEEEECCHHHHHHHHhcCCCCEEEEcCCCCCCCHHHHHHHHhcCc----------
Confidence            4799999999999999999999999999999999999999999999999999999999999999999632          


Q ss_pred             hhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHHhh
Q 039716          940 AGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQY 1000 (1002)
Q Consensus       940 ~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~~ 1000 (1002)
                                    ..+++|||++|+..+.+...+|+++|+++||.||++..+|...|++.
T Consensus        72 --------------~~~~~pii~lt~~~~~~~~~~a~~~Ga~~~l~KP~~~~~l~~~i~~~  118 (459)
T 1w25_A           72 --------------TTRHIPVVLITALDGRGDRIQGLESGASDFLTKPIDDVMLFARVRSL  118 (459)
T ss_dssp             --------------TTTTSCEEEEECSSCHHHHHHHHHHTCCEEEESSCCHHHHHHHHHHH
T ss_pred             --------------ccCCCCEEEEECCCCHHHHHHHHHcCCCEEEeCCCCHHHHHHHHHHH
Confidence                          23579999999999999999999999999999999999999988764

>3cz5_A Two-component response regulator, LUXR family; structural genomics, protein structure initiative; 2.70A {Aurantimonas SP}

Probab=99.68  E-value=3.6e-16  Score=154.58  Aligned_cols=117  Identities=24%  Similarity=0.344  Sum_probs=109.3

Q ss_pred             CCeEEEEecCHHHHHHHHHHHHh-cCCeEE-EEcCHHHHHHHHHcCCCcEEEEcCCCCCCCHHHHHHHHhccccCCCchh
Q 039716          859 KPKILLVEDNKINVMVAKSMMKQ-LGHSID-VVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDA  936 (1002)
Q Consensus       859 ~~~ILiVeDn~~n~~~l~~~L~~-~g~~v~-~a~~G~eAl~~~~~~~~DlIlmDi~MP~mdG~e~~~~IR~~~~~~~~~~  936 (1002)
                      ..+||||||++..+..++.+|+. .||.+. .+.++.+|++.+....||+||+|+.||+++|+++++.||..        
T Consensus         5 ~~~ILivdd~~~~~~~l~~~L~~~~~~~v~~~~~~~~~a~~~l~~~~~dlii~D~~l~~~~g~~~~~~l~~~--------   76 (153)
T 3cz5_A            5 TARIMLVDDHPIVREGYRRLIERRPGYAVVAEAADAGEAYRLYRETTPDIVVMDLTLPGPGGIEATRHIRQW--------   76 (153)
T ss_dssp             CEEEEEECSCHHHHHHHHHHHTTSTTEEEEEEESSHHHHHHHHHTTCCSEEEECSCCSSSCHHHHHHHHHHH--------
T ss_pred             ccEEEEECCcHHHHHHHHHHHhhCCCcEEEEEeCCHHHHHHHHhcCCCCEEEEecCCCCCCHHHHHHHHHHh--------
Confidence            46899999999999999999998 799988 89999999999999999999999999999999999999973        


Q ss_pred             hhhhhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHHhhc
Q 039716          937 AAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQYF 1001 (1002)
Q Consensus       937 ~~~~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~~l 1001 (1002)
                                        .+.+|||++|+....+...+++.+|+++||.||++.++|...|++++
T Consensus        77 ------------------~~~~~ii~ls~~~~~~~~~~~~~~g~~~~l~kp~~~~~L~~~i~~~~  123 (153)
T 3cz5_A           77 ------------------DGAARILIFTMHQGSAFALKAFEAGASGYVTKSSDPAELVQAIEAIL  123 (153)
T ss_dssp             ------------------CTTCCEEEEESCCSHHHHHHHHHTTCSEEEETTSCTTHHHHHHHHHT
T ss_pred             ------------------CCCCeEEEEECCCCHHHHHHHHHCCCcEEEecCCCHHHHHHHHHHHH
Confidence                              25689999999999999999999999999999999999999998764

>1ny5_A Transcriptional regulator (NTRC family); AAA+ ATPase, sigma54 activator, bacterial transcription, DIM transcription; HET: ADP; 2.40A {Aquifex aeolicus} SCOP: c.23.1.1 c.37.1.20 PDB: 1ny6_A* 3m0e_A* 1zy2_A*

Probab=99.68  E-value=1.6e-16  Score=182.42  Aligned_cols=115  Identities=19%  Similarity=0.413  Sum_probs=108.7

Q ss_pred             eEEEEecCHHHHHHHHHHHHhcCCeEEEEcCHHHHHHHHHcCCCcEEEEcCCCCCCCHHHHHHHHhccccCCCchhhhhh
Q 039716          861 KILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDAAAEA  940 (1002)
Q Consensus       861 ~ILiVeDn~~n~~~l~~~L~~~g~~v~~a~~G~eAl~~~~~~~~DlIlmDi~MP~mdG~e~~~~IR~~~~~~~~~~~~~~  940 (1002)
                      +||||||++..+..++.+|+..||.|..|.+|.+|++.+....||+||+|+.||+|||+++++.||..            
T Consensus         2 ~ILIVDDd~~~~~~l~~~L~~~g~~v~~a~~~~eal~~l~~~~~DlvllD~~mp~~dG~ell~~lr~~------------   69 (387)
T 1ny5_A            2 NVLVIEDDKVFRGLLEEYLSMKGIKVESAERGKEAYKLLSEKHFNVVLLDLLLPDVNGLEILKWIKER------------   69 (387)
T ss_dssp             EEEEECCCHHHHHHHHHHHHHHTCEEEEESSHHHHHHHHHHSCCSEEEEESBCSSSBHHHHHHHHHHH------------
T ss_pred             EEEEEECCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHHHhCCCCEEEEeCCCCCCCHHHHHHHHHhh------------
Confidence            79999999999999999999999999999999999999999999999999999999999999999963            


Q ss_pred             hhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHHhhc
Q 039716          941 GIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQYF 1001 (1002)
Q Consensus       941 ~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~~l 1001 (1002)
                                    .+.+|||++|++.+.+...+|+++|+++||.||++.++|...|++.+
T Consensus        70 --------------~~~~pvIvlT~~~~~~~~~~a~~~Ga~dyl~KP~~~~~L~~~i~~~l  116 (387)
T 1ny5_A           70 --------------SPETEVIVITGHGTIKTAVEAMKMGAYDFLTKPCMLEEIELTINKAI  116 (387)
T ss_dssp             --------------CTTSEEEEEEETTCHHHHHHHHTTTCCEEEEESCCHHHHHHHHHHHH
T ss_pred             --------------CCCCcEEEEeCCCCHHHHHHHHhcCceEEecCCCCHHHHHHHHHHHH
Confidence                          25689999999999999999999999999999999999999887653

>3eqz_A Response regulator; structural genomics, unknown function, PSI-2, protein struct initiative; 2.15A {Colwellia psychrerythraea} SCOP: c.23.1.0

Probab=99.68  E-value=9.8e-17  Score=154.38  Aligned_cols=116  Identities=16%  Similarity=0.275  Sum_probs=106.6

Q ss_pred             CCeEEEEecCHHHHHHHHHHHHhcCCeEEEEcCHHHHHHHHHcCCCcEEEEcCCCCCCCHHHHHHHHhccccCCCchhhh
Q 039716          859 KPKILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDAAA  938 (1002)
Q Consensus       859 ~~~ILiVeDn~~n~~~l~~~L~~~g~~v~~a~~G~eAl~~~~~~~~DlIlmDi~MP~mdG~e~~~~IR~~~~~~~~~~~~  938 (1002)
                      ..+||||||++..+..++.+|+..|+.|..+.++.+|+..+... ||+||+|+.||+++|+++++.||+.          
T Consensus         3 ~~~ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~~~~~-~dlvi~D~~l~~~~g~~~~~~l~~~----------   71 (135)
T 3eqz_A            3 LNRVFIVDDDTLTCNLLKTIVEPIFGNVEAFQHPRAFLTLSLNK-QDIIILDLMMPDMDGIEVIRHLAEH----------   71 (135)
T ss_dssp             CCEEEEECSCHHHHHHHHHHHTTTCSCEEEESCHHHHTTSCCCT-TEEEEEECCTTTTHHHHHHHHHHHT----------
T ss_pred             cceEEEEeCCHHHHHHHHHHHHhhcceeeeecCHHHHHHhhccC-CCEEEEeCCCCCCCHHHHHHHHHhC----------
Confidence            45899999999999999999999988999999999999988888 9999999999999999999999963          


Q ss_pred             hhhhcccCCCCCCCCCCCCccEEEEcCCCCH-----HHHHHHHHcCCCEEEeCCCChHHHHHHHHhhc
Q 039716          939 EAGIEQAMPSSGSSNHFKRIPIIAMTANALS-----ESAEECFANGMDSFVSKPVTFQKLKECLEQYF 1001 (1002)
Q Consensus       939 ~~~~~~~~~~~~~~~~~~~ipIIalTa~~~~-----~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~~l 1001 (1002)
                                      .+.+|||++|+....     +...+++.+|+++||.||++.++|...|++++
T Consensus        72 ----------------~~~~~ii~~s~~~~~~~~~~~~~~~~~~~g~~~~l~KP~~~~~l~~~l~~~~  123 (135)
T 3eqz_A           72 ----------------KSPASLILISGYDSGVLHSAETLALSCGLNVINTFTKPINTEVLTCFLTSLS  123 (135)
T ss_dssp             ----------------TCCCEEEEEESSCHHHHHHHHHHHHHTTCEEEEEEESSCCHHHHHHHHHHHS
T ss_pred             ----------------CCCCCEEEEEeccchhHHHHHHHHHHcCCCcceeeCCCCCHHHHHHHHHHHH
Confidence                            356899999999875     66777999999999999999999999999875

>2pln_A HP1043, response regulator; signaling protein; 1.80A {Helicobacter pylori} PDB: 2hqo_A

Probab=99.67  E-value=7.3e-16  Score=149.22  Aligned_cols=114  Identities=21%  Similarity=0.336  Sum_probs=107.0

Q ss_pred             CCCCeEEEEecCHHHHHHHHHHHHhcCCeEEEEcCHHHHHHHHHcCCCcEEEEcCCCCCCCHHHHHHHHhccccCCCchh
Q 039716          857 KPKPKILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDA  936 (1002)
Q Consensus       857 ~~~~~ILiVeDn~~n~~~l~~~L~~~g~~v~~a~~G~eAl~~~~~~~~DlIlmDi~MP~mdG~e~~~~IR~~~~~~~~~~  936 (1002)
                      ..+.+||||||++..+..++.+|+..||.|..+.++.+|+..+....||+||    ||+++|+++++.||..        
T Consensus        16 ~~~~~ilivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~al~~l~~~~~dlvi----~~~~~g~~~~~~l~~~--------   83 (137)
T 2pln_A           16 RGSMRVLLIEKNSVLGGEIEKGLNVKGFMADVTESLEDGEYLMDIRNYDLVM----VSDKNALSFVSRIKEK--------   83 (137)
T ss_dssp             TTCSEEEEECSCHHHHHHHHHHHHHTTCEEEEESCHHHHHHHHHHSCCSEEE----ECSTTHHHHHHHHHHH--------
T ss_pred             CCCCeEEEEeCCHHHHHHHHHHHHHcCcEEEEeCCHHHHHHHHHcCCCCEEE----EcCccHHHHHHHHHhc--------
Confidence            4567999999999999999999999999999999999999999999999999    9999999999999962        


Q ss_pred             hhhhhhcccCCCCCCCCCCC-CccEEEEcCCCCHHHHHHHHHcCCCEEEeCCC-ChHHHHHHHHhhc
Q 039716          937 AAEAGIEQAMPSSGSSNHFK-RIPIIAMTANALSESAEECFANGMDSFVSKPV-TFQKLKECLEQYF 1001 (1002)
Q Consensus       937 ~~~~~~~~~~~~~~~~~~~~-~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~-~~~~L~~~l~~~l 1001 (1002)
                                         + .+|||++|+....+...+++++|+++||.||+ +.++|...|++.+
T Consensus        84 -------------------~~~~~ii~ls~~~~~~~~~~~~~~g~~~~l~kP~~~~~~l~~~i~~~~  131 (137)
T 2pln_A           84 -------------------HSSIVVLVSSDNPTSEEEVHAFEQGADDYIAKPYRSIKALVARIEARL  131 (137)
T ss_dssp             -------------------STTSEEEEEESSCCHHHHHHHHHTTCSEEEESSCSCHHHHHHHHHHHT
T ss_pred             -------------------CCCccEEEEeCCCCHHHHHHHHHcCCceeeeCCCCCHHHHHHHHHHHH
Confidence                               3 58999999999999999999999999999999 9999999998765

>1ys7_A Transcriptional regulatory protein PRRA; response regulator, DNA binding domain, phosphorylation; 1.58A {Mycobacterium tuberculosis} SCOP: a.4.6.1 c.23.1.1 PDB: 1ys6_A

Probab=99.67  E-value=1.7e-16  Score=168.47  Aligned_cols=117  Identities=21%  Similarity=0.439  Sum_probs=109.3

Q ss_pred             CCeEEEEecCHHHHHHHHHHHHhcCCeEEEEcCHHHHHHHHHcCCCcEEEEcCCCCCCCHHHHHHHHhccccCCCchhhh
Q 039716          859 KPKILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDAAA  938 (1002)
Q Consensus       859 ~~~ILiVeDn~~n~~~l~~~L~~~g~~v~~a~~G~eAl~~~~~~~~DlIlmDi~MP~mdG~e~~~~IR~~~~~~~~~~~~  938 (1002)
                      ..+||||||++..+..+..+|+..||.|..+.++.+|++.+....||+||+|+.||+++|+++++.||..          
T Consensus         7 ~~~ilivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~a~~~~~~~~~dlvllD~~l~~~~g~~~~~~l~~~----------   76 (233)
T 1ys7_A            7 SPRVLVVDDDSDVLASLERGLRLSGFEVATAVDGAEALRSATENRPDAIVLDINMPVLDGVSVVTALRAM----------   76 (233)
T ss_dssp             CCEEEEECSCHHHHHHHHHHHHHTTCEEEEESSHHHHHHHHHHSCCSEEEEESSCSSSCHHHHHHHHHHT----------
T ss_pred             CCeEEEEeCCHHHHHHHHHHHHhCCCEEEEECCHHHHHHHHHhCCCCEEEEeCCCCCCCHHHHHHHHHhc----------
Confidence            4689999999999999999999999999999999999999999999999999999999999999999963          


Q ss_pred             hhhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHHhhc
Q 039716          939 EAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQYF 1001 (1002)
Q Consensus       939 ~~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~~l 1001 (1002)
                                      .+.+|||++|+....+...+++++|+++||.||++.++|...|++.+
T Consensus        77 ----------------~~~~~ii~lt~~~~~~~~~~~~~~ga~~~l~Kp~~~~~L~~~i~~~~  123 (233)
T 1ys7_A           77 ----------------DNDVPVCVLSARSSVDDRVAGLEAGADDYLVKPFVLAELVARVKALL  123 (233)
T ss_dssp             ----------------TCCCCEEEEECCCTTTCCCTTTTTTCSEEEESSCCHHHHHHHHHHHH
T ss_pred             ----------------CCCCCEEEEEcCCCHHHHHHHHHcCCCEEEeCCCCHHHHHHHHHHHH
Confidence                            25699999999999988899999999999999999999999988653

>1mu5_A Type II DNA topoisomerase VI subunit B; GHKL ATPase, helix two-turns helix; 2.00A {Sulfolobus shibatae} SCOP: a.156.1.3 d.14.1.3 d.122.1.2 PDB: 1mx0_A* 1z5b_A* 1z5a_A* 1z59_A* 1z5c_A* 2hkj_A*

Probab=99.67  E-value=1.6e-16  Score=185.42  Aligned_cols=117  Identities=21%  Similarity=0.343  Sum_probs=95.9

Q ss_pred             EEccHHHHHHHHHHHHhhhhhcCCCC----eeEEEEEecCCCCcccchhhhhhhhhhcchhhhhhhccCCCCCccCCCCC
Q 039716          478 VIGDVLRIRQILTNLISNAIKFTPEG----KVGIKLYVVPEPPFAKEGLKQKSKAYQSATDAVKEEKHQPKSQTASDQNG  553 (1002)
Q Consensus       478 v~gD~~rL~QIL~NLlsNAIKfT~~G----~I~I~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  553 (1002)
                      +.+|+.+|.|||.|||.||+||+..|    .|.|.+....                                        
T Consensus        26 ~~~d~~~L~qvl~nLv~NAida~~~gg~~p~I~I~i~~~~----------------------------------------   65 (471)
T 1mu5_A           26 FPNPARALYQTVRELIENSLDATDVHGILPNIKITIDLID----------------------------------------   65 (471)
T ss_dssp             CSSHHHHHHHHHHHHHHHHHHTTGGGTCCCEEEEEEEEEE----------------------------------------
T ss_pred             EeCCHHHHHHHHHHHHHHHHHHhhcCCCceEEEEEEEECC----------------------------------------
Confidence            45688999999999999999999875    4666553210                                        


Q ss_pred             CCCCCCCCCccCCCCCCCCCCCccCCCCCccccccceEEEEEEEecCCCCCcCcHhhhhhhccCCCcccc-CcCCCcccc
Q 039716          554 FHDKKHGEGYQDHKHDDDPGTPVSHGNSMDEDLEATVWIRCDVYDTGIGIPENALPTLFRKYMQVSADHA-RKYGGTGLG  632 (1002)
Q Consensus       554 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~i~V~DtGiGI~~e~l~~IF~pF~q~~~~~~-~~~~GtGLG  632 (1002)
                                                       ....++.|+|.|||+||+++.++++|++|++++.... ...+|+|||
T Consensus        66 ---------------------------------~~~~~~~I~V~DnG~GI~~e~l~~iF~~f~~tsk~~~~~~~gg~GLG  112 (471)
T 1mu5_A           66 ---------------------------------DARQIYKVNVVDNGIGIPPQEVPNAFGRVLYSSKYVNRQTRGMYGLG  112 (471)
T ss_dssp             ---------------------------------TTTTEEEEEEECCSCCCCGGGHHHHHHCCCCC-CCCCSCCSCSCTTT
T ss_pred             ---------------------------------CcCcEEEEEEEECCCCCCHHHHHHHhcccccccccccccCCCCceee
Confidence                                             0012578999999999999999999999987765422 456799999


Q ss_pred             HHHHHHHHHHhCCE-EEEEeecCCce-EEEEEEeCCC
Q 039716          633 LAICKQLVELMGGR-LTVTSKVHCGS-TFTFILPYQV  667 (1002)
Q Consensus       633 LaI~k~Lve~~gG~-I~v~S~~g~GT-tF~~~LP~~~  667 (1002)
                      |++|+.+++.|||. |+|.|..+.|+ +|+|+||+..
T Consensus       113 L~iv~~l~~~~gG~~i~v~S~~~~g~~~~~~~Lpl~~  149 (471)
T 1mu5_A          113 VKAAVLYSQMHQDKPIEIETSPVNSKRIYTFKLKIDI  149 (471)
T ss_dssp             HHHHHHHHHHHCCCCEEEEEECTTCSEEEEEEEEECT
T ss_pred             HHHHHHHHHHhCCCceeEEEecCCCceEEEEEEeccc
Confidence            99999999999999 99999999987 9999998764

>2zbk_B Type 2 DNA topoisomerase 6 subunit B; DNA binding protein, decatenation, ATPase, drug design, DNA-binding, magnesium, metal-binding; HET: RDC; 3.56A {Sulfolobus shibatae}

Probab=99.67  E-value=1.3e-16  Score=187.95  Aligned_cols=77  Identities=22%  Similarity=0.403  Sum_probs=68.1

Q ss_pred             EEEEEEEecCCCCCcCcHhhhhhhccCCCcccc-CcCCCccccHHHHHHHHHHhCCE-EEEEeecCCce-EEEEEEeCCC
Q 039716          591 WIRCDVYDTGIGIPENALPTLFRKYMQVSADHA-RKYGGTGLGLAICKQLVELMGGR-LTVTSKVHCGS-TFTFILPYQV  667 (1002)
Q Consensus       591 ~l~i~V~DtGiGI~~e~l~~IF~pF~q~~~~~~-~~~~GtGLGLaI~k~Lve~~gG~-I~v~S~~g~GT-tF~~~LP~~~  667 (1002)
                      ++.|+|.|||+||+++.++++|++|++++.... ...+|+||||++|+.++++|||. |++.|..+.|+ +|+|.||+..
T Consensus        69 ~~~I~V~DnG~GI~~e~l~~iF~~f~~tsk~~~~~~~gg~GLGLsiv~~l~~~~gG~~I~V~S~~~~g~~~~~~~Lpl~~  148 (530)
T 2zbk_B           69 IYKVNVVDNGIGIPPQEVPNAFGRVLYSSKYVNRQTRGMYGLGVKAAVLYSQMHQDKPIEIETSPVNSKRIYTFKLKIDI  148 (530)
T ss_dssp             EEEEEEECCSCCCCGGGSHHHHTSCCCSCCCCCSCCSCSSSSHHHHHHHHHHHHCCCCEEEEEECTTCSEEEEEEEEEET
T ss_pred             eEEEEEEECCCCCCHHHHHHHhccccccCCcccccCCCCccchHHHHHHHHHHhCCCceEEEEecCCCeEEEEEEEEecc
Confidence            578999999999999999999999987765322 45689999999999999999999 99999999887 8999988754

>3kyj_B CHEY6 protein, putative histidine protein kinase; protein-protein interaction, histidine kinase, response regulator, phosphorylation; 1.40A {Rhodobacter sphaeroides} PDB: 3kyi_B*

Probab=99.67  E-value=1.1e-16  Score=156.69  Aligned_cols=109  Identities=29%  Similarity=0.407  Sum_probs=95.1

Q ss_pred             CCCCeEEEEecCHHHHHHHHHHHHhc-CCeE-EEEcCHHHHHHHHHcC-CCcEEEEcCCCCCCCHHHHHHHHhccccCCC
Q 039716          857 KPKPKILLVEDNKINVMVAKSMMKQL-GHSI-DVVNNGVEAVHAVQCQ-NYDLILMDVCMPVMDGLKATRLIRSFEDTGN  933 (1002)
Q Consensus       857 ~~~~~ILiVeDn~~n~~~l~~~L~~~-g~~v-~~a~~G~eAl~~~~~~-~~DlIlmDi~MP~mdG~e~~~~IR~~~~~~~  933 (1002)
                      ...++||||||++..+..++.+|++. |+.+ ..+.++.+|++.+... .||+||+|+.||+++|+++++.||+.     
T Consensus        11 ~~~~~vlivdd~~~~~~~l~~~L~~~~~~~~v~~~~~~~~al~~l~~~~~~dlvilD~~l~~~~g~~~~~~lr~~-----   85 (145)
T 3kyj_B           11 GSPYNVMIVDDAAMMRLYIASFIKTLPDFKVVAQAANGQEALDKLAAQPNVDLILLDIEMPVMDGMEFLRHAKLK-----   85 (145)
T ss_dssp             CCSEEEEEECSCHHHHHHHHHHHTTCTTEEEEEEESSHHHHHHHHHHCTTCCEEEECTTSCCCTTCHHHHHHHHH-----
T ss_pred             CCCCeEEEEcCCHHHHHHHHHHHHhCCCceEEEEECCHHHHHHHHhcCCCCCEEEEeCCCCCCCHHHHHHHHHhc-----
Confidence            34678999999999999999999998 8885 5899999999999988 89999999999999999999999963     


Q ss_pred             chhhhhhhhcccCCCCCCCCCCCCccEEEEcC--CCCHHHHHHHHHcCCCEEEeCCCChHH
Q 039716          934 WDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTA--NALSESAEECFANGMDSFVSKPVTFQK  992 (1002)
Q Consensus       934 ~~~~~~~~~~~~~~~~~~~~~~~~ipIIalTa--~~~~~~~~~~~~aG~d~~l~KP~~~~~  992 (1002)
                                            ..+|||++|+  ....+...+|+++|+++||.||++..+
T Consensus        86 ----------------------~~~~iiil~~~~~~~~~~~~~~~~~ga~~~l~KP~~~~~  124 (145)
T 3kyj_B           86 ----------------------TRAKICMLSSVAVSGSPHAARARELGADGVVAKPSGTVS  124 (145)
T ss_dssp             ----------------------CCCEEC-CBSSCSTTSSHHHHHHHTTCSCCCBCCCSCC-
T ss_pred             ----------------------CCCCeEEEEEeccCChHHHHHHHhCCCCEEEeCCCCHHH
Confidence                                  1278999987  666677889999999999999999443

>2gkg_A Response regulator homolog; social motility, receiver domain, signalling, high resolutio signaling protein; 1.00A {Myxococcus xanthus} PDB: 2i6f_A 2nt4_A 2nt3_A

Probab=99.67  E-value=3.5e-16  Score=148.45  Aligned_cols=117  Identities=21%  Similarity=0.345  Sum_probs=108.5

Q ss_pred             CeEEEEecCHHHHHHHHHHHHhcCCeEEEEcCHHHHHHHHHcCCCcEEEEcCCCC-CCCHHHHHHHHhccccCCCchhhh
Q 039716          860 PKILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMP-VMDGLKATRLIRSFEDTGNWDAAA  938 (1002)
Q Consensus       860 ~~ILiVeDn~~n~~~l~~~L~~~g~~v~~a~~G~eAl~~~~~~~~DlIlmDi~MP-~mdG~e~~~~IR~~~~~~~~~~~~  938 (1002)
                      .+||||||++..+..+..+|+..||.|..+.++.+|++.+....||+||+|+.|| +++|+++++.||...         
T Consensus         6 ~~ilivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~a~~~~~~~~~dlvi~d~~~~~~~~g~~~~~~l~~~~---------   76 (127)
T 2gkg_A            6 KKILIVESDTALSATLRSALEGRGFTVDETTDGKGSVEQIRRDRPDLVVLAVDLSAGQNGYLICGKLKKDD---------   76 (127)
T ss_dssp             CEEEEECSCHHHHHHHHHHHHHHTCEEEEECCHHHHHHHHHHHCCSEEEEESBCGGGCBHHHHHHHHHHST---------
T ss_pred             CeEEEEeCCHHHHHHHHHHHHhcCceEEEecCHHHHHHHHHhcCCCEEEEeCCCCCCCCHHHHHHHHhcCc---------
Confidence            5899999999999999999999999999999999999999999999999999999 999999999999732         


Q ss_pred             hhhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHHhhc
Q 039716          939 EAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQYF 1001 (1002)
Q Consensus       939 ~~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~~l 1001 (1002)
                                     ..+.+|||++ +....+...+++++|+++|+.||++..+|...|++.+
T Consensus        77 ---------------~~~~~~ii~~-~~~~~~~~~~~~~~g~~~~l~kp~~~~~l~~~i~~~~  123 (127)
T 2gkg_A           77 ---------------DLKNVPIVII-GNPDGFAQHRKLKAHADEYVAKPVDADQLVERAGALI  123 (127)
T ss_dssp             ---------------TTTTSCEEEE-ECGGGHHHHHHSTTCCSEEEESSCCHHHHHHHHHHHH
T ss_pred             ---------------cccCCCEEEE-ecCCchhHHHHHHhCcchheeCCCCHHHHHHHHHHHH
Confidence                           2367999999 8888888999999999999999999999999998764

>1th8_A Anti-sigma F factor; SPOIIAB, SPOIIAA, anti-ANTI-sigma, sporulation, serine kinase, transcription; HET: ADP; 2.40A {Geobacillus stearothermophilus} SCOP: d.122.1.3 PDB: 1thn_A* 1til_A* 1l0o_A* 1tid_A*

Probab=99.66  E-value=3.4e-16  Score=154.05  Aligned_cols=102  Identities=21%  Similarity=0.360  Sum_probs=82.8

Q ss_pred             ccHHHHHHHHHHHHhhhhhcCCC----CeeEEEEEecCCCCcccchhhhhhhhhhcchhhhhhhccCCCCCccCCCCCCC
Q 039716          480 GDVLRIRQILTNLISNAIKFTPE----GKVGIKLYVVPEPPFAKEGLKQKSKAYQSATDAVKEEKHQPKSQTASDQNGFH  555 (1002)
Q Consensus       480 gD~~rL~QIL~NLlsNAIKfT~~----G~I~I~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  555 (1002)
                      .|...+.+|+.||+.||+||+..    |.|.|.+...                                           
T Consensus        35 ~~~~~l~~il~~l~~Nai~h~~~~~~~~~I~i~~~~~-------------------------------------------   71 (145)
T 1th8_A           35 DELTEIKTVVSEAVTNAIIHGYNNDPNGIVSISVIIE-------------------------------------------   71 (145)
T ss_dssp             HHHHHHHHHHHHHHHHHHHTTSTTCTTSEEEEEEEEE-------------------------------------------
T ss_pred             hhHHHHHHHHHHHHHHHHHHhcCCCCCCEEEEEEEEe-------------------------------------------
Confidence            58889999999999999999964    6777766421                                           


Q ss_pred             CCCCCCCccCCCCCCCCCCCccCCCCCccccccceEEEEEEEecCCCCCcCcHhhhhhhccCCCccccCcCCCccccHHH
Q 039716          556 DKKHGEGYQDHKHDDDPGTPVSHGNSMDEDLEATVWIRCDVYDTGIGIPENALPTLFRKYMQVSADHARKYGGTGLGLAI  635 (1002)
Q Consensus       556 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~i~V~DtGiGI~~e~l~~IF~pF~q~~~~~~~~~~GtGLGLaI  635 (1002)
                                                       ..++.|.|.|+|+||+  .++++|++|++.+.    ...|+||||+|
T Consensus        72 ---------------------------------~~~~~i~V~D~G~g~~--~~~~~~~~~~~~~~----~~~~~GlGL~i  112 (145)
T 1th8_A           72 ---------------------------------DGVVHLTVRDEGVGIP--DIEEARQPLFTTKP----ELERSGMGFTI  112 (145)
T ss_dssp             ---------------------------------TTEEEEEEEECSSCCS--CHHHHTCCC-----------CCCSCHHHH
T ss_pred             ---------------------------------CCEEEEEEEECCCCcC--hHHHhhcccccCCC----CCCCCcchHHH
Confidence                                             1148899999999999  89999999997653    33589999999


Q ss_pred             HHHHHHHhCCEEEEEeecCCceEEEEEEeCCC
Q 039716          636 CKQLVELMGGRLTVTSKVHCGSTFTFILPYQV  667 (1002)
Q Consensus       636 ~k~Lve~~gG~I~v~S~~g~GTtF~~~LP~~~  667 (1002)
                      |+++++    .|+++|.+++||+|+++||+..
T Consensus       113 v~~~~~----~i~~~~~~~~Gt~v~~~lp~~~  140 (145)
T 1th8_A          113 MENFMD----EVIVESEVNKGTTVYLKKHGIH  140 (145)
T ss_dssp             HHHHSS----EEEEEEETTTEEEEEEEECCC-
T ss_pred             HHHHHh----eEEEEeCCCCCEEEEEEEeccc
Confidence            999998    8999999999999999999864

>2gwr_A DNA-binding response regulator MTRA; two-component regulatory system, transcription regulation, phosphorylation, OMPR family; 2.10A {Mycobacterium tuberculosis} PDB: 3nhz_A

Probab=99.65  E-value=4.7e-16  Score=166.10  Aligned_cols=115  Identities=24%  Similarity=0.445  Sum_probs=108.5

Q ss_pred             CeEEEEecCHHHHHHHHHHHHhcCCeEEEEcCHHHHHHHHHcCCCcEEEEcCCCCCCCHHHHHHHHhccccCCCchhhhh
Q 039716          860 PKILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDAAAE  939 (1002)
Q Consensus       860 ~~ILiVeDn~~n~~~l~~~L~~~g~~v~~a~~G~eAl~~~~~~~~DlIlmDi~MP~mdG~e~~~~IR~~~~~~~~~~~~~  939 (1002)
                      .+||||||++..+..++.+|+..||.|..+.++.+|++.+....||+||+|+.||+++|+++++.||+.           
T Consensus         6 ~~ILivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~al~~l~~~~~dlvilD~~l~~~~g~~~~~~lr~~-----------   74 (238)
T 2gwr_A            6 QRILVVDDDASLAEMLTIVLRGEGFDTAVIGDGTQALTAVRELRPDLVLLDLMLPGMNGIDVCRVLRAD-----------   74 (238)
T ss_dssp             CEEEEECSCHHHHHHHHHHHHHTTCEEEEECCGGGHHHHHHHHCCSEEEEESSCSSSCHHHHHHHHHTT-----------
T ss_pred             CeEEEEeCCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHHHhCCCCEEEEeCCCCCCCHHHHHHHHHhC-----------
Confidence            589999999999999999999999999999999999999999999999999999999999999999962           


Q ss_pred             hhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHHhhc
Q 039716          940 AGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQYF 1001 (1002)
Q Consensus       940 ~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~~l 1001 (1002)
                                      +.+|||++|+.........++.+|+++||.||++.++|...|+..+
T Consensus        75 ----------------~~~~ii~lt~~~~~~~~~~~~~~Ga~~~l~Kp~~~~~L~~~i~~~~  120 (238)
T 2gwr_A           75 ----------------SGVPIVMLTAKTDTVDVVLGLESGADDYIMKPFKPKELVARVRARL  120 (238)
T ss_dssp             ----------------CCCCEEEEEETTCCSCHHHHHHTTCCEEEEESCCHHHHHHHHHHHC
T ss_pred             ----------------CCCcEEEEeCCCCHHHHHHHHHCCCCEEEeCCCCHHHHHHHHHHHH
Confidence                            2589999999999999999999999999999999999999998764

>2qv0_A Protein MRKE; structural genomics, transcription, PSI-2, protein structure initiative; 2.40A {Klebsiella pneumoniae}

Probab=99.65  E-value=1.3e-15  Score=148.42  Aligned_cols=115  Identities=22%  Similarity=0.347  Sum_probs=102.4

Q ss_pred             CCeEEEEecCHHHHHHHHHHHHhc-CCe-EEEEcCHHHHHHHHHcCCCcEEEEcCCCCCCCHHHHHHHHhccccCCCchh
Q 039716          859 KPKILLVEDNKINVMVAKSMMKQL-GHS-IDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDA  936 (1002)
Q Consensus       859 ~~~ILiVeDn~~n~~~l~~~L~~~-g~~-v~~a~~G~eAl~~~~~~~~DlIlmDi~MP~mdG~e~~~~IR~~~~~~~~~~  936 (1002)
                      ..+||||||++..+..+..+|+.. |+. +..+.++.+|++.+....||+||+|+.||+++|+++++.||..        
T Consensus         9 ~~~iLivdd~~~~~~~l~~~L~~~~~~~~v~~~~~~~~al~~l~~~~~dlvi~d~~l~~~~g~~~~~~l~~~--------   80 (143)
T 2qv0_A            9 KMKVIIVEDEFLAQQELSWLINTHSQMEIVGSFDDGLDVLKFLQHNKVDAIFLDINIPSLDGVLLAQNISQF--------   80 (143)
T ss_dssp             -CEEEEECSCHHHHHHHHHHHHHHSCCEEEEEESCHHHHHHHHHHCCCSEEEECSSCSSSCHHHHHHHHTTS--------
T ss_pred             ceEEEEEcCCHHHHHHHHHHHHhCCCceEEEEeCCHHHHHHHHHhCCCCEEEEecCCCCCCHHHHHHHHHcc--------
Confidence            468999999999999999999986 788 5589999999999999999999999999999999999999962        


Q ss_pred             hhhhhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHHhhc
Q 039716          937 AAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQYF 1001 (1002)
Q Consensus       937 ~~~~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~~l 1001 (1002)
                                        .+.+|||++|+..  +...+++.+|+++||.||++.++|...|++++
T Consensus        81 ------------------~~~~~ii~~s~~~--~~~~~~~~~g~~~~l~KP~~~~~l~~~i~~~~  125 (143)
T 2qv0_A           81 ------------------AHKPFIVFITAWK--EHAVEAFELEAFDYILKPYQESRIINMLQKLT  125 (143)
T ss_dssp             ------------------TTCCEEEEEESCC--TTHHHHHHTTCSEEEESSCCHHHHHHHHHHHH
T ss_pred             ------------------CCCceEEEEeCCH--HHHHHHHhCCcceEEeCCCCHHHHHHHHHHHH
Confidence                              2457899999874  36778999999999999999999999998753

>2j48_A Two-component sensor kinase; pseudo-receiver, circadian clock, transferase, response regulator, histidine protein kinase; NMR {Synechococcus elongatus}

Probab=99.65  E-value=8.9e-16  Score=143.29  Aligned_cols=115  Identities=19%  Similarity=0.216  Sum_probs=105.9

Q ss_pred             CeEEEEecCHHHHHHHHHHHHhcCCeEEEEcCHHHHHHHHHcCCCcEEEEcCCCCCCCHHHHHHHHhccccCCCchhhhh
Q 039716          860 PKILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDAAAE  939 (1002)
Q Consensus       860 ~~ILiVeDn~~n~~~l~~~L~~~g~~v~~a~~G~eAl~~~~~~~~DlIlmDi~MP~mdG~e~~~~IR~~~~~~~~~~~~~  939 (1002)
                      .+||||||++..+..+..+|+..|+.|..+.++.+|+..+....||+||+|+.||+++|+++++.||...          
T Consensus         2 ~~iliv~~~~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~l~~~~~dlii~d~~~~~~~~~~~~~~l~~~~----------   71 (119)
T 2j48_A            2 GHILLLEEEDEAATVVCEMLTAAGFKVIWLVDGSTALDQLDLLQPIVILMAWPPPDQSCLLLLQHLREHQ----------   71 (119)
T ss_dssp             CEEEEECCCHHHHHHHHHHHHHTTCEEEEESCHHHHHHHHHHHCCSEEEEECSTTCCTHHHHHHHHHHTC----------
T ss_pred             CEEEEEeCCHHHHHHHHHHHHhCCcEEEEecCHHHHHHHHHhcCCCEEEEecCCCCCCHHHHHHHHHhcc----------
Confidence            4799999999999999999999999999999999999999999999999999999999999999999732          


Q ss_pred             hhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHHhhc
Q 039716          940 AGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQYF 1001 (1002)
Q Consensus       940 ~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~~l 1001 (1002)
                                    ..+.+|||++|+.....   .++.+|+++|+.||++..+|...|++.+
T Consensus        72 --------------~~~~~~ii~~~~~~~~~---~~~~~g~~~~l~kp~~~~~l~~~l~~~~  116 (119)
T 2j48_A           72 --------------ADPHPPLVLFLGEPPVD---PLLTAQASAILSKPLDPQLLLTTLQGLC  116 (119)
T ss_dssp             --------------CCSSCCCEEEESSCCSS---HHHHHHCSEECSSCSTTHHHHHHHHTTC
T ss_pred             --------------ccCCCCEEEEeCCCCch---hhhhcCHHHhccCCCCHHHHHHHHHHHh
Confidence                          23679999999987766   8999999999999999999999998765

>3c97_A Signal transduction histidine kinase; structural genomics, signaling, PSI-2, protein structure initiative; 1.70A {Aspergillus oryzae RIB40}

Probab=99.65  E-value=4.8e-16  Score=151.24  Aligned_cols=118  Identities=37%  Similarity=0.629  Sum_probs=102.9

Q ss_pred             CeEEEEecCHHHHHHHHHHHHhcCCeEEEEcCHHHHHHHHHcCCCcEEEEcCCCCCCCHHHHHHHHhccccCCCchhhhh
Q 039716          860 PKILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDAAAE  939 (1002)
Q Consensus       860 ~~ILiVeDn~~n~~~l~~~L~~~g~~v~~a~~G~eAl~~~~~~~~DlIlmDi~MP~mdG~e~~~~IR~~~~~~~~~~~~~  939 (1002)
                      .+||||||++..+..++.+|+..|+.+..+.+|.+|++.+....||+||+|+.||+++|+++++.||+....        
T Consensus        11 ~~iLivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~al~~l~~~~~dlvllD~~lp~~~g~~~~~~l~~~~~~--------   82 (140)
T 3c97_A           11 LSVLIAEDNDICRLVAAKALEKCTNDITVVTNGLQALQAYQNRQFDVIIMDIQMPVMDGLEAVSEIRNYERT--------   82 (140)
T ss_dssp             CEEEEECCCHHHHHHHHHHHTTTCSEEEEESSHHHHHHHHHHSCCSEEEECTTCCSSCHHHHHHHHHHHHHH--------
T ss_pred             ceEEEEcCCHHHHHHHHHHHHHcCCceEEECCHHHHHHHHhcCCCCEEEEeCCCCCCcHHHHHHHHHhhhhh--------
Confidence            589999999999999999999999999999999999999999999999999999999999999999963210        


Q ss_pred             hhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHHhhc
Q 039716          940 AGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQYF 1001 (1002)
Q Consensus       940 ~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~~l 1001 (1002)
                                   ...+.+|||++|+........   .+|+++||.||++.++|...|++.+
T Consensus        83 -------------~~~~~~~ii~~s~~~~~~~~~---~~g~~~~l~KP~~~~~L~~~i~~~~  128 (140)
T 3c97_A           83 -------------HNTKRASIIAITADTIDDDRP---GAELDEYVSKPLNPNQLRDVVLTCH  128 (140)
T ss_dssp             -------------HTCCCCCCEEEESSCCSCCCC---CSSCSEEEESSCCHHHHHHHHHHHH
T ss_pred             -------------cCCCceEEEEEeCccchhHHH---hCChhheEeCCCCHHHHHHHHHHHh
Confidence                         013568999999876654433   7899999999999999999998753

>3bre_A Probable two-component response regulator; protein-nucleotide complex, signaling protein; HET: C2E; 2.40A {Pseudomonas aeruginosa} PDB: 3i5a_A*

Probab=99.64  E-value=4e-16  Score=176.97  Aligned_cols=118  Identities=21%  Similarity=0.292  Sum_probs=107.8

Q ss_pred             CCeEEEEecCHHHHHHHHHHHH-hcCCeEEEEcCHHHHHHHHHcCCCcEEEEcCCCCCCCHHHHHHHHhccccCCCchhh
Q 039716          859 KPKILLVEDNKINVMVAKSMMK-QLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDAA  937 (1002)
Q Consensus       859 ~~~ILiVeDn~~n~~~l~~~L~-~~g~~v~~a~~G~eAl~~~~~~~~DlIlmDi~MP~mdG~e~~~~IR~~~~~~~~~~~  937 (1002)
                      ..+||||||++..+..++.+|. ..|+.|..|.||.+|++.+....||+||+|+.||+|||+++++.||...        
T Consensus        18 ~~~ilivdD~~~~~~~l~~~l~~~~~~~v~~~~~~~~al~~~~~~~~dlvl~D~~mp~~~G~~~~~~l~~~~--------   89 (358)
T 3bre_A           18 AVMVLLVDDQAMIGEAVRRSLASEAGIDFHFCSDPQQAVAVANQIKPTVILQDLVMPGVDGLTLLAAYRGNP--------   89 (358)
T ss_dssp             CEEEEEECSCTTHHHHHHTTSSSCTTEEEEEECCHHHHHHHHHHHCCSEEEEESBCSSSBHHHHHHHHTTST--------
T ss_pred             CceEEEEECCHHHHHHHHHHHHhccCcEEEEeCCHHHHHHHHHhCCCCEEEEeCCCCCCCHHHHHHHHhcCc--------
Confidence            4579999999999999999996 4689999999999999999999999999999999999999999999632        


Q ss_pred             hhhhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHHhh
Q 039716          938 AEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQY 1000 (1002)
Q Consensus       938 ~~~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~~ 1000 (1002)
                                      ..+.+|||++|++.+.+...+|+++|+++||.||++..+|...+..+
T Consensus        90 ----------------~~~~~~ii~~s~~~~~~~~~~a~~~Ga~~~l~Kp~~~~~l~~~v~~~  136 (358)
T 3bre_A           90 ----------------ATRDIPIIVLSTKEEPTVKSAAFAAGANDYLVKLPDAIELVARIRYH  136 (358)
T ss_dssp             ----------------TTTTSCEEEEESSCCHHHHHHHHHTTCSEEEESCCCHHHHHHHHHHH
T ss_pred             ----------------ccCCCcEEEEeCCCCHHHHHHHHhcChheEeeccCCHHHHHHHHHHH
Confidence                            23679999999999999999999999999999999999999888754

>2oqr_A Sensory transduction protein REGX3; response regulator, winged-helix-turn-helix, DNA-binding, 3D swapping, two component system; 2.03A {Mycobacterium tuberculosis H37RV}

Probab=99.64  E-value=5.8e-16  Score=164.09  Aligned_cols=115  Identities=23%  Similarity=0.386  Sum_probs=108.1

Q ss_pred             CeEEEEecCHHHHHHHHHHHHhcCCeEEEEcCHHHHHHHHHcCCCcEEEEcCCCCCCCHHHHHHHHhccccCCCchhhhh
Q 039716          860 PKILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDAAAE  939 (1002)
Q Consensus       860 ~~ILiVeDn~~n~~~l~~~L~~~g~~v~~a~~G~eAl~~~~~~~~DlIlmDi~MP~mdG~e~~~~IR~~~~~~~~~~~~~  939 (1002)
                      .+||||||++..+..+..+|+..|+.|..+.++.+|++.+....||+||+|+.||+++|+++++.||..           
T Consensus         5 ~~ilivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~al~~~~~~~~dlvllD~~l~~~~g~~~~~~l~~~-----------   73 (230)
T 2oqr_A            5 TSVLIVEDEESLADPLAFLLRKEGFEATVVTDGPAALAEFDRAGADIVLLDLMLPGMSGTDVCKQLRAR-----------   73 (230)
T ss_dssp             CEEEEECSCHHHHHHHHHHHHHTTCEEEEECSHHHHHHHHHHHCCSEEEEESSCSSSCHHHHHHHHHHH-----------
T ss_pred             CeEEEEeCCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHHhccCCCEEEEECCCCCCCHHHHHHHHHcC-----------
Confidence            589999999999999999999999999999999999999998899999999999999999999999962           


Q ss_pred             hhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHHhhc
Q 039716          940 AGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQYF 1001 (1002)
Q Consensus       940 ~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~~l 1001 (1002)
                                      +.+|||++|+.........++++|+++||.||++.++|...|++.+
T Consensus        74 ----------------~~~~ii~lt~~~~~~~~~~~~~~ga~~~l~Kp~~~~~l~~~i~~~~  119 (230)
T 2oqr_A           74 ----------------SSVPVIMVTARDSEIDKVVGLELGADDYVTKPYSARELIARIRAVL  119 (230)
T ss_dssp             ----------------CSCSEEEEECCHHHHHHHHHHHHCCSCCCCSSCCHHHHHHHHHHHH
T ss_pred             ----------------CCCCEEEEeCCCcHHHHHHHHHcCCCEEEeCCCCHHHHHHHHHHHH
Confidence                            3589999999998888999999999999999999999999998753

>3t8y_A CHEB, chemotaxis response regulator protein-glutamate methylesterase; CHEA, hydrolase; 1.90A {Thermotoga maritima}

Probab=99.64  E-value=1.3e-15  Score=152.99  Aligned_cols=117  Identities=26%  Similarity=0.366  Sum_probs=102.6

Q ss_pred             CCCeEEEEecCHHHHHHHHHHHHhcCC--eEEEEcCHHHHHHHHHcCCCcEEEEcCCCCCCCHHHHHHHHhccccCCCch
Q 039716          858 PKPKILLVEDNKINVMVAKSMMKQLGH--SIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWD  935 (1002)
Q Consensus       858 ~~~~ILiVeDn~~n~~~l~~~L~~~g~--~v~~a~~G~eAl~~~~~~~~DlIlmDi~MP~mdG~e~~~~IR~~~~~~~~~  935 (1002)
                      ...+||||||++..+..++.+|+..|.  .+..+.++.+|++.+....||+||+|+.||+++|+++++.||+.       
T Consensus        24 ~~~~ILivdd~~~~~~~l~~~L~~~~~~~~v~~~~~~~~al~~l~~~~~dlvilD~~l~~~~g~~l~~~lr~~-------   96 (164)
T 3t8y_A           24 RVIRVLVVDDSAFMRMVLKDIIDSQPDMKVVGFAKDGLEAVEKAIELKPDVITMDIEMPNLNGIEALKLIMKK-------   96 (164)
T ss_dssp             CCEEEEEECSCHHHHHHHHHHHHTSTTEEEEEEESSHHHHHHHHHHHCCSEEEECSSCSSSCHHHHHHHHHHH-------
T ss_pred             CccEEEEEcCCHHHHHHHHHHHhcCCCeEEEEecCCHHHHHHHhccCCCCEEEEeCCCCCCCHHHHHHHHHhc-------
Confidence            356899999999999999999998863  35579999999999999999999999999999999999999963       


Q ss_pred             hhhhhhhcccCCCCCCCCCCCCccEEEEcCCCCHH--HHHHHHHcCCCEEEeCCCC---------hHHHHHHHHhhc
Q 039716          936 AAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSE--SAEECFANGMDSFVSKPVT---------FQKLKECLEQYF 1001 (1002)
Q Consensus       936 ~~~~~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~--~~~~~~~aG~d~~l~KP~~---------~~~L~~~l~~~l 1001 (1002)
                                         .+ +|||++|+.....  ...+++.+|+++||.||++         ..+|...|++++
T Consensus        97 -------------------~~-~~ii~~s~~~~~~~~~~~~~~~~ga~~~l~KP~~~~~l~~r~~~~~l~~~i~~~~  153 (164)
T 3t8y_A           97 -------------------AP-TRVIMVSSLTEEGAAITIEALRNGAVDFITKPHGSISLTFRQVAPELLEKIRQAM  153 (164)
T ss_dssp             -------------------SC-CEEEEEESSCCTTCHHHHHHHHTTCCEEEECSSSSSCGGGGGGHHHHHHHHHHHT
T ss_pred             -------------------CC-ceEEEEecCCccchHHHHHHHHcCcCEEEeCCCCHHHHHHHhhhHHHHHHHHHHh
Confidence                               13 7999999977654  6678999999999999999         688888887764

>2rdm_A Response regulator receiver protein; structural genomics, unknown function, PSI-2, protein struct initiative; HET: MSE; 1.76A {Sinorhizobium medicae}

Probab=99.64  E-value=1.6e-15  Score=145.43  Aligned_cols=115  Identities=23%  Similarity=0.355  Sum_probs=105.1

Q ss_pred             CCeEEEEecCHHHHHHHHHHHHhcCCeEEEEcCHHHHHHHHHcC-CCcEEEEcCCCCC-CCHHHHHHHHhccccCCCchh
Q 039716          859 KPKILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQ-NYDLILMDVCMPV-MDGLKATRLIRSFEDTGNWDA  936 (1002)
Q Consensus       859 ~~~ILiVeDn~~n~~~l~~~L~~~g~~v~~a~~G~eAl~~~~~~-~~DlIlmDi~MP~-mdG~e~~~~IR~~~~~~~~~~  936 (1002)
                      ..+||||||++..+..++.+|...||.|..+.++.+|++.+... .||+||+|+.||+ ++|+++++.||..        
T Consensus         5 ~~~ilivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~a~~~l~~~~~~dlvi~d~~l~~~~~g~~~~~~l~~~--------   76 (132)
T 2rdm_A            5 AVTILLADDEAILLLDFESTLTDAGFLVTAVSSGAKAIEMLKSGAAIDGVVTDIRFCQPPDGWQVARVAREI--------   76 (132)
T ss_dssp             SCEEEEECSSHHHHHHHHHHHHHTTCEEEEESSHHHHHHHHHTTCCCCEEEEESCCSSSSCHHHHHHHHHHH--------
T ss_pred             CceEEEEcCcHHHHHHHHHHHHHcCCEEEEECCHHHHHHHHHcCCCCCEEEEeeeCCCCCCHHHHHHHHHhc--------
Confidence            46899999999999999999999999999999999999999987 8999999999997 9999999999973        


Q ss_pred             hhhhhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHHhhc
Q 039716          937 AAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQYF 1001 (1002)
Q Consensus       937 ~~~~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~~l 1001 (1002)
                                        .+.+|||++|+....+....++.+|  +||.||++.++|...|++++
T Consensus        77 ------------------~~~~~ii~~s~~~~~~~~~~~~~~~--~~l~kP~~~~~l~~~i~~~~  121 (132)
T 2rdm_A           77 ------------------DPNMPIVYISGHAALEWASNGVPDS--IILEKPFTSAQLITAVSQLL  121 (132)
T ss_dssp             ------------------CTTCCEEEEESSCCTTHHHHSCTTC--EEEESSCCHHHHHHHHHHHH
T ss_pred             ------------------CCCCCEEEEeCCccHHHHHhhcCCc--ceEeCCCCHHHHHHHHHHHH
Confidence                              2568999999999888888877776  89999999999999998764

>2qsj_A DNA-binding response regulator, LUXR family; structural genomics, PSI-2, protein structure initiative; 2.10A {Silicibacter pomeroyi dss-3}

Probab=99.64  E-value=5.7e-16  Score=153.16  Aligned_cols=117  Identities=18%  Similarity=0.292  Sum_probs=97.8

Q ss_pred             CCeEEEEecCHHHHHHHHHHHHhc-CC-eEEEEcCHHHHHHHHHc-CCCcEEEEcCCCCCCCHHHHHHHHhccccCCCch
Q 039716          859 KPKILLVEDNKINVMVAKSMMKQL-GH-SIDVVNNGVEAVHAVQC-QNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWD  935 (1002)
Q Consensus       859 ~~~ILiVeDn~~n~~~l~~~L~~~-g~-~v~~a~~G~eAl~~~~~-~~~DlIlmDi~MP~mdG~e~~~~IR~~~~~~~~~  935 (1002)
                      ..+||||||++..+..++.+|+.. |+ .|..+.++.+|++.+.. ..||+||+|+.||+++|+++++.||..       
T Consensus         3 ~~~iLivdd~~~~~~~l~~~L~~~~g~~~v~~~~~~~~a~~~l~~~~~~dlvi~d~~l~~~~g~~~~~~l~~~-------   75 (154)
T 2qsj_A            3 LTVVLIVDDHHLIRAGAKNLLEGAFSGMRVEGAETVSDALAFLEADNTVDLILLDVNLPDAEAIDGLVRLKRF-------   75 (154)
T ss_dssp             CEEEEEECSCHHHHHHHHHHHHHHCTTEEEEEESSHHHHHHHHHTTCCCSEEEECC------CHHHHHHHHHH-------
T ss_pred             ccEEEEEcCCHHHHHHHHHHHHhCCCceEEEEecCHHHHHHHHhccCCCCEEEEeCCCCCCchHHHHHHHHHh-------
Confidence            358999999999999999999988 88 68899999999999998 899999999999999999999999973       


Q ss_pred             hhhhhhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHHhhc
Q 039716          936 AAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQYF 1001 (1002)
Q Consensus       936 ~~~~~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~~l 1001 (1002)
                                         .+.+|||++|+....+....++.+|+++||.||++.++|..+|++.+
T Consensus        76 -------------------~~~~~ii~ls~~~~~~~~~~~~~~g~~~~l~kp~~~~~L~~~l~~~~  122 (154)
T 2qsj_A           76 -------------------DPSNAVALISGETDHELIRAALEAGADGFIPKSADPQVLIHAVSLIL  122 (154)
T ss_dssp             -------------------CTTSEEEEC-----CHHHHHHHHTTCCBBCCTTSCHHHHHHHHHHHH
T ss_pred             -------------------CCCCeEEEEeCCCCHHHHHHHHHccCCEEEeCCCCHHHHHHHHHHHH
Confidence                               25689999999999999999999999999999999999999998754

>2b4a_A BH3024; flavodoxin-like fold, structural genomics, joint center for structural genomics, JCSG, protein structure initiative; 2.42A {Bacillus halodurans} SCOP: c.23.1.1

Probab=99.64  E-value=6e-16  Score=150.04  Aligned_cols=115  Identities=15%  Similarity=0.204  Sum_probs=102.5

Q ss_pred             CCCCeEEEEecCHHHHHHHHHHHHhcCCeEEEEcCHHHHHHHHHc-CCCcEEEEcCCCCCCCHHHHHHHHhccccCCCch
Q 039716          857 KPKPKILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQC-QNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWD  935 (1002)
Q Consensus       857 ~~~~~ILiVeDn~~n~~~l~~~L~~~g~~v~~a~~G~eAl~~~~~-~~~DlIlmDi~MP~mdG~e~~~~IR~~~~~~~~~  935 (1002)
                      ....+||||||++..+..++.+|+..||.|..+.++.+|++.+.. ..||+||+|+.||+++|+++++.||..       
T Consensus        13 ~~~~~ilivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~al~~l~~~~~~dlvilD~~l~~~~g~~~~~~l~~~-------   85 (138)
T 2b4a_A           13 MQPFRVTLVEDEPSHATLIQYHLNQLGAEVTVHPSGSAFFQHRSQLSTCDLLIVSDQLVDLSIFSLLDIVKEQ-------   85 (138)
T ss_dssp             -CCCEEEEECSCHHHHHHHHHHHHHTTCEEEEESSHHHHHHTGGGGGSCSEEEEETTCTTSCHHHHHHHHTTS-------
T ss_pred             CCCCeEEEECCCHHHHHHHHHHHHHcCCEEEEeCCHHHHHHHHHhCCCCCEEEEeCCCCCCCHHHHHHHHHhh-------
Confidence            456799999999999999999999999999999999999999998 899999999999999999999999962       


Q ss_pred             hhhhhhhcccCCCCCCCCCCCCccEEEEc-CCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHHhhc
Q 039716          936 AAAEAGIEQAMPSSGSSNHFKRIPIIAMT-ANALSESAEECFANGMDSFVSKPVTFQKLKECLEQYF 1001 (1002)
Q Consensus       936 ~~~~~~~~~~~~~~~~~~~~~~ipIIalT-a~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~~l 1001 (1002)
                                         .+.+|||++| +...... .+++   +++|+.||++.++|...|++.+
T Consensus        86 -------------------~~~~~ii~ls~~~~~~~~-~~~~---~~~~l~KP~~~~~L~~~i~~~~  129 (138)
T 2b4a_A           86 -------------------TKQPSVLILTTGRHELIE-SSEH---NLSYLQKPFAISELRAAIDYHK  129 (138)
T ss_dssp             -------------------SSCCEEEEEESCC--CCC-CSSS---CEEEEESSCCHHHHHHHHHHTC
T ss_pred             -------------------CCCCCEEEEECCCCCHHH-HHHH---HHheeeCCCCHHHHHHHHHHHH
Confidence                               3579999999 8877666 6666   9999999999999999998765

>1p2f_A Response regulator; DRRB, OMPR/PHOB, transcription; HET: MSE; 1.80A {Thermotoga maritima} SCOP: a.4.6.1 c.23.1.1 PDB: 3nns_A*

Probab=99.62  E-value=1.4e-15  Score=160.06  Aligned_cols=113  Identities=23%  Similarity=0.384  Sum_probs=105.4

Q ss_pred             CeEEEEecCHHHHHHHHHHHHhcCCeEEEEcCHHHHHHHHHcCCCcEEEEcCCCCCCCHHHHHHHHhccccCCCchhhhh
Q 039716          860 PKILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDAAAE  939 (1002)
Q Consensus       860 ~~ILiVeDn~~n~~~l~~~L~~~g~~v~~a~~G~eAl~~~~~~~~DlIlmDi~MP~mdG~e~~~~IR~~~~~~~~~~~~~  939 (1002)
                      .+||||||++..+..+..+|+..| .|..+.++.+|++.+  ..||+||+|+.||+++|+++++.||..           
T Consensus         3 ~~ilivdd~~~~~~~l~~~L~~~~-~v~~~~~~~~al~~~--~~~dlvllD~~lp~~~g~~~~~~lr~~-----------   68 (220)
T 1p2f_A            3 WKIAVVDDDKNILKKVSEKLQQLG-RVKTFLTGEDFLNDE--EAFHVVVLDVMLPDYSGYEICRMIKET-----------   68 (220)
T ss_dssp             EEEEEECSCHHHHHHHHHHHTTTE-EEEEESSHHHHHHCC--SCCSEEEEESBCSSSBHHHHHHHHHHH-----------
T ss_pred             ceEEEEeCCHHHHHHHHHHHHhCC-CEEEECCHHHHHHhc--CCCCEEEEeCCCCCCCHHHHHHHHHhc-----------
Confidence            479999999999999999999999 999999999999987  789999999999999999999999963           


Q ss_pred             hhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHHhhc
Q 039716          940 AGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQYF 1001 (1002)
Q Consensus       940 ~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~~l 1001 (1002)
                                     .+.+|||++|+..+.+...+++.+|+++||.||++.++|...|++++
T Consensus        69 ---------------~~~~~ii~lt~~~~~~~~~~~~~~ga~~~l~Kp~~~~~L~~~i~~~~  115 (220)
T 1p2f_A           69 ---------------RPETWVILLTLLSDDESVLKGFEAGADDYVTKPFNPEILLARVKRFL  115 (220)
T ss_dssp             ---------------CTTSEEEEEESCCSHHHHHHHHHHTCSEEEESSCCHHHHHHHHHHHH
T ss_pred             ---------------CCCCcEEEEEcCCCHHHHHHHHHcCCCEEEECCCCHHHHHHHHHHHH
Confidence                           25689999999999999999999999999999999999999998753

>3c3w_A Two component transcriptional regulatory protein; response regulator, two-component regulatory system, DNA-BIN protein; 2.20A {Mycobacterium tuberculosis}

Probab=99.62  E-value=1.8e-16  Score=168.12  Aligned_cols=115  Identities=17%  Similarity=0.246  Sum_probs=106.7

Q ss_pred             CeEEEEecCHHHHHHHHHHHHhcC-Ce-EEEEcCHHHHHHHHHcCCCcEEEEcCCCCCCCHHHHHHHHhccccCCCchhh
Q 039716          860 PKILLVEDNKINVMVAKSMMKQLG-HS-IDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDAA  937 (1002)
Q Consensus       860 ~~ILiVeDn~~n~~~l~~~L~~~g-~~-v~~a~~G~eAl~~~~~~~~DlIlmDi~MP~mdG~e~~~~IR~~~~~~~~~~~  937 (1002)
                      .+||||||++..+..++.+|+..| +. +..+.+|.+|++.+....||+||+|+.||++||+++++.||..         
T Consensus         2 ~~ILivdd~~~~~~~l~~~L~~~~~~~vv~~~~~~~~al~~l~~~~~dlvllD~~lp~~~g~~~~~~lr~~---------   72 (225)
T 3c3w_A            2 VKVFLVDDHEVVRRGLVDLLGADPELDVVGEAGSVAEAMARVPAARPDVAVLDVRLPDGNGIELCRDLLSR---------   72 (225)
T ss_dssp             EEEEEECSCHHHHHHHHHHHHTCTTEEEEEEESSHHHHHHHHHHHCCSEEEECSEETTEEHHHHHHHHHHH---------
T ss_pred             cEEEEEcCCHHHHHHHHHHHhcCCCcEEEEEECCHHHHHHHHhhcCCCEEEEeCCCCCCCHHHHHHHHHHh---------
Confidence            479999999999999999999887 88 4579999999999999899999999999999999999999963         


Q ss_pred             hhhhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHHhh
Q 039716          938 AEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQY 1000 (1002)
Q Consensus       938 ~~~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~~ 1000 (1002)
                                       .+.+|||++|+..+.+...+++++|+++||.||++.++|...|++.
T Consensus        73 -----------------~~~~~ii~lt~~~~~~~~~~~~~~Ga~~~l~Kp~~~~~L~~~i~~~  118 (225)
T 3c3w_A           73 -----------------MPDLRCLILTSYTSDEAMLDAILAGASGYVVKDIKGMELARAVKDV  118 (225)
T ss_dssp             -----------------CTTCEEEEGGGSSSHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHHH
T ss_pred             -----------------CCCCcEEEEECCCCHHHHHHHHHCCCCEEEECCCCHHHHHHHHHHH
Confidence                             3569999999999999999999999999999999999999998765

>3sy8_A ROCR; TIM barrel phosphodiesterase-A, transcription regulator; HET: EPE; 2.50A {Pseudomonas aeruginosa}

Probab=99.62  E-value=5.3e-16  Score=179.22  Aligned_cols=116  Identities=25%  Similarity=0.308  Sum_probs=104.1

Q ss_pred             CeEEEEecCHHHHHHHHHHHHh-cCCeEEEEcCHHHHHHHHHc-CCCcEEEEcCCCCCCCHHHHHHHHhccccCCCchhh
Q 039716          860 PKILLVEDNKINVMVAKSMMKQ-LGHSIDVVNNGVEAVHAVQC-QNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDAA  937 (1002)
Q Consensus       860 ~~ILiVeDn~~n~~~l~~~L~~-~g~~v~~a~~G~eAl~~~~~-~~~DlIlmDi~MP~mdG~e~~~~IR~~~~~~~~~~~  937 (1002)
                      .+||||||++.++..++.+|+. .|+.|..|.||.+|++.+.. ..||+||+|+.||+|||+++++.||..         
T Consensus         4 ~~ILivDD~~~~~~~l~~~L~~~~~~~v~~a~~g~eal~~l~~~~~~DlvllDi~mP~~dG~ell~~l~~~---------   74 (400)
T 3sy8_A            4 LNVLVLEDEPFQRLVAVTALKKVVPGSILEAADGKEAVAILESCGHVDIAICDLQMSGMDGLAFLRHASLS---------   74 (400)
T ss_dssp             EEEEEECSSHHHHHHHHHHHHHHCSEEEEEESSHHHHHHHHHHHSCEEEEEECSSCSSSCHHHHHHHHHHH---------
T ss_pred             ceEEEEcCCHHHHHHHHHHHHhcCCcEEEEecCHHHHHHHHhhCCCCCEEEEeCCCCCCCHHHHHHHHHhc---------
Confidence            5899999999999999999998 57899999999999999988 589999999999999999999999963         


Q ss_pred             hhhhhcccCCCCCCCCCCCCccEEEEcCCCCH-----HHHHHHHHcCCCEEEeCCCChHHHHHHHHhhc
Q 039716          938 AEAGIEQAMPSSGSSNHFKRIPIIAMTANALS-----ESAEECFANGMDSFVSKPVTFQKLKECLEQYF 1001 (1002)
Q Consensus       938 ~~~~~~~~~~~~~~~~~~~~ipIIalTa~~~~-----~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~~l 1001 (1002)
                                       .+.+|||++|+....     ....+|+.+|+++||.||++.++|...|++.+
T Consensus        75 -----------------~~~~~ii~~s~~~~~~~~~~~~~~~a~~~ga~~yl~KP~~~~~L~~~i~~~~  126 (400)
T 3sy8_A           75 -----------------GKVHSVILSSEVDPILRQATISMIECLGLNFLGDLGKPFSLERITALLTRYN  126 (400)
T ss_dssp             -----------------TCEEEEEESCCCCGGGHHHHHHHHHTTTCEEEEECCSSCCHHHHHHHHHHHH
T ss_pred             -----------------CCCceEEEEcCchHHHHHHHHHHHHHcCCeeccCcCCCcCHHHHHHHHHHHH
Confidence                             245778888887766     66778999999999999999999999998753

>3klo_A Transcriptional regulator VPST; REC domain, HTH domain, DNA-binding, transcription regulation; HET: C2E TAR; 2.80A {Vibrio cholerae} PDB: 3kln_A*

Probab=99.62  E-value=2.3e-16  Score=167.04  Aligned_cols=118  Identities=8%  Similarity=0.059  Sum_probs=103.6

Q ss_pred             CCeEEEEecCHHHHHHHHHHHHh-cCCeEEE-EcCHHHHHHH-HHcCCCcEEEEcCCCCCCCHHHHHHHHhccccCCCch
Q 039716          859 KPKILLVEDNKINVMVAKSMMKQ-LGHSIDV-VNNGVEAVHA-VQCQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWD  935 (1002)
Q Consensus       859 ~~~ILiVeDn~~n~~~l~~~L~~-~g~~v~~-a~~G~eAl~~-~~~~~~DlIlmDi~MP~mdG~e~~~~IR~~~~~~~~~  935 (1002)
                      ..+||||||++..+..++.+|+. .|+.+.. +.++.+|+.. +....||+||+|+.||+|||+++++.||+.       
T Consensus         7 ~~~IlivdD~~~~~~~l~~~L~~~~~~~v~~~~~~~~~~~~~~~~~~~~dlvllD~~mp~~~G~~~~~~lr~~-------   79 (225)
T 3klo_A            7 KLNVRMLSDVCMQSRLLKEALESKLPLALEITPFSELWLEENKPESRSIQMLVIDYSRISDDVLTDYSSFKHI-------   79 (225)
T ss_dssp             SEEEEEESCCSHHHHHHHHHHHHHSSEEEEEECGGGHHHHTTCSGGGGCCEEEEEGGGCCHHHHHHHHHHHHH-------
T ss_pred             ceEEEEEcCcHHHHHHHHHHHhhCCCceEEEEeCCcHHHHHHHhhccCCCEEEEeCCCCCCCHHHHHHHHHHh-------
Confidence            46899999999999999999994 6888754 4677777764 678899999999999999999999999961       


Q ss_pred             hhhhhhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHHhhc
Q 039716          936 AAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQYF 1001 (1002)
Q Consensus       936 ~~~~~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~~l 1001 (1002)
                                        ..+.+|||++|++.+......++.+|+++||.||+++++|...|++.+
T Consensus        80 ------------------~~~~~~ii~lt~~~~~~~~~~~~~~Ga~~~l~Kp~~~~~L~~~i~~~~  127 (225)
T 3klo_A           80 ------------------SCPDAKEVIINCPQDIEHKLLFKWNNLAGVFYIDDDMDTLIKGMSKIL  127 (225)
T ss_dssp             ------------------HCTTCEEEEEEECTTCCHHHHTTSTTEEEEEETTCCHHHHHHHHHHHH
T ss_pred             ------------------hCCCCcEEEEECCcchhHHHHHHHhCCCEEEecCCCHHHHHHHHHHHH
Confidence                              025689999999999999999999999999999999999999998753

>1qo0_D AMIR; binding protein, gene regulator, receptor; 2.25A {Pseudomonas aeruginosa} SCOP: c.23.1.3

Probab=99.60  E-value=1.2e-15  Score=157.61  Aligned_cols=111  Identities=10%  Similarity=0.089  Sum_probs=100.9

Q ss_pred             CCeEEEEecCHHHHHHHHHHHHhcCCeEEEEcCHHHHHHHHHcCCCcEEEEcCCCCCCCHHHHHHHHhccccCCCchhhh
Q 039716          859 KPKILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDAAA  938 (1002)
Q Consensus       859 ~~~ILiVeDn~~n~~~l~~~L~~~g~~v~~a~~G~eAl~~~~~~~~DlIlmDi~MP~mdG~e~~~~IR~~~~~~~~~~~~  938 (1002)
                      ..+||||||++..+..+..+|...||.|..+.++.+|+    ...||+||+|+.||+|||+ +++.++..          
T Consensus        12 ~~~iLivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~al----~~~~dlvl~D~~mp~~~g~-l~~~~~~~----------   76 (196)
T 1qo0_D           12 ELQVLVLNPPGEVSDALVLQLIRIGCSVRQCWPPPEAF----DVPVDVVFTSIFQNRHHDE-IAALLAAG----------   76 (196)
T ss_dssp             GCEEEEESCTTHHHHHHHHHHHHHTCEEEEECSCCSSC----SSCCSEEEEECCSSTHHHH-HHHHHHHS----------
T ss_pred             CCeEEEEcCChhHHHHHHHHHHHcCCeEEEecCchhhC----CCCCCEEEEeCCCCccchH-HHHHHhcc----------
Confidence            46899999999999999999999999999999988877    4689999999999999999 99999862          


Q ss_pred             hhhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHHhh
Q 039716          939 EAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQY 1000 (1002)
Q Consensus       939 ~~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~~ 1000 (1002)
                                      .+.+|||++|++.+.+...+|+++|+++||.||++..+|...|+..
T Consensus        77 ----------------~~~~~ii~lt~~~~~~~~~~a~~~ga~~~l~KP~~~~~L~~~l~~~  122 (196)
T 1qo0_D           77 ----------------TPRTTLVALVEYESPAVLSQIIELECHGVITQPLDAHRVLPVLVSA  122 (196)
T ss_dssp             ----------------CTTCEEEEEECCCSHHHHHHHHHHTCSEEEESSCCGGGHHHHHHHH
T ss_pred             ----------------CCCCCEEEEEcCCChHHHHHHHHcCCCeeEecCcCHHHHHHHHHHH
Confidence                            1568999999999999999999999999999999999999888754

>1dc7_A NTRC, nitrogen regulation protein; receiver domain, phosphorylation, signal transduction, conformational rearrangement; NMR {Salmonella typhimurium} SCOP: c.23.1.1 PDB: 1j56_A 1krw_A 1krx_A 1ntr_A 1dc8_A*

Probab=99.60  E-value=4.2e-17  Score=154.33  Aligned_cols=115  Identities=24%  Similarity=0.384  Sum_probs=107.0

Q ss_pred             CeEEEEecCHHHHHHHHHHHHhcCCeEEEEcCHHHHHHHHHcCCCcEEEEcCCCCCCCHHHHHHHHhccccCCCchhhhh
Q 039716          860 PKILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDAAAE  939 (1002)
Q Consensus       860 ~~ILiVeDn~~n~~~l~~~L~~~g~~v~~a~~G~eAl~~~~~~~~DlIlmDi~MP~mdG~e~~~~IR~~~~~~~~~~~~~  939 (1002)
                      .+||||||++..+..+..+|...|+.+..+.++.+|++.+....||+||+|+.||+++|+++++.||..           
T Consensus         4 ~~ilivdd~~~~~~~l~~~l~~~~~~v~~~~~~~~~~~~~~~~~~dlvi~d~~~~~~~g~~~~~~l~~~-----------   72 (124)
T 1dc7_A            4 GIVWVVDDDSSIRWVLERALAGAGLTCTTFENGNEVLAALASKTPDVLLSDIRMPGMDGLALLKQIKQR-----------   72 (124)
T ss_dssp             CCCEEECSSSSHHHHHHHHHTTTTCCCEECCCTTHHHHHSSSCCCSCEEECSCSSHHHHCSTHHHHHHH-----------
T ss_pred             cEEEEEeCCHHHHHHHHHHHHhCCcEEEEeCCHHHHHHHHhcCCCCEEEEeeecCCCCHHHHHHHHHhh-----------
Confidence            479999999999999999999999999999999999999998999999999999999999999999963           


Q ss_pred             hhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHHhh
Q 039716          940 AGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQY 1000 (1002)
Q Consensus       940 ~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~~ 1000 (1002)
                                     .+.+|||++|+....+...+++++|+++|+.||++.++|...|++.
T Consensus        73 ---------------~~~~~ii~~s~~~~~~~~~~~~~~g~~~~l~kp~~~~~l~~~i~~~  118 (124)
T 1dc7_A           73 ---------------HPMLPVIIMTAHSDLDAAVSAYQQGAFDYLPKPFDIDEAVALVERA  118 (124)
T ss_dssp             ---------------CTTSCCCCBCCSTTSTTTTSSCTTCCCCCBCSSCCHHHHHHHHHHH
T ss_pred             ---------------CCCCCEEEEecCCCHHHHHHHHhcCcceEeeCCCCHHHHHHHHHHH
Confidence                           2568999999999888888999999999999999999999998765

>2hqr_A Putative transcriptional regulator; phosporylation-independent response regulator, H. pylori, SY dimer, signaling protein; NMR {Helicobacter pylori}

Probab=99.59  E-value=8.1e-15  Score=154.56  Aligned_cols=111  Identities=22%  Similarity=0.347  Sum_probs=104.4

Q ss_pred             eEEEEecCHHHHHHHHHHHHhcCCeEEEEcCHHHHHHHHHcCCCcEEEEcCCCCCCCHHHHHHHHhccccCCCchhhhhh
Q 039716          861 KILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDAAAEA  940 (1002)
Q Consensus       861 ~ILiVeDn~~n~~~l~~~L~~~g~~v~~a~~G~eAl~~~~~~~~DlIlmDi~MP~mdG~e~~~~IR~~~~~~~~~~~~~~  940 (1002)
                      +||||||++..+..++.+|+..||.|..+.++.+|++.+....||+||    ||+++|+++++.||+.            
T Consensus         2 ~ilivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~al~~l~~~~~dlvi----lp~~~g~~~~~~lr~~------------   65 (223)
T 2hqr_A            2 RVLLIEKNSVLGGEIEKGLNVKGFMADVTESLEDGEYLMDIRNYDLVM----VSDKNALSFVSRIKEK------------   65 (223)
T ss_dssp             CEEEECSCHHHHHHHHHHHGGGTCCEEEESSHHHHHHHHTTSCCSEEE----ECCTTHHHHHHHHHHH------------
T ss_pred             EEEEEcCCHHHHHHHHHHHHHCCcEEEEECCHHHHHHHHhcCCCCEEE----eCCCCHHHHHHHHHhC------------
Confidence            699999999999999999999999999999999999999999999999    9999999999999963            


Q ss_pred             hhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCC-ChHHHHHHHHhhc
Q 039716          941 GIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPV-TFQKLKECLEQYF 1001 (1002)
Q Consensus       941 ~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~-~~~~L~~~l~~~l 1001 (1002)
                                    .+.+|||++|+..+.+....++.+|+++||.||+ +.++|...|++.+
T Consensus        66 --------------~~~~~ii~lt~~~~~~~~~~~~~~Ga~~~l~Kp~~~~~~L~~~i~~~~  113 (223)
T 2hqr_A           66 --------------HSSIVVLVSSDNPTSEEEVHAFEQGADDYIAKPYRSIKALVARIEARL  113 (223)
T ss_dssp             --------------CTTSEEEEEESSCCHHHHHHHHHHTCSEEEETTCSCTHHHHHHHHHHT
T ss_pred             --------------CCCCcEEEEECCCCHHHHHHHHHcCCCEEEECCCCCHHHHHHHHHHHh
Confidence                          1268999999999999999999999999999999 9999999998764

>3luf_A Two-component system response regulator/ggdef domain protein; structural genomics, ASA_2441, PSI-2, protein structure initiative; HET: MSE; 1.76A {Aeromonas salmonicida} PDB: 3mf4_A*

Probab=99.57  E-value=3e-15  Score=162.51  Aligned_cols=102  Identities=24%  Similarity=0.366  Sum_probs=89.7

Q ss_pred             CeEEEEecCHHHHHHHHHHHHhc-CCeEEEEcCHHHHHHHHHcCCCcEEEEcCCCCCCCHHHHHHHHhccccCCCchhhh
Q 039716          860 PKILLVEDNKINVMVAKSMMKQL-GHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDAAA  938 (1002)
Q Consensus       860 ~~ILiVeDn~~n~~~l~~~L~~~-g~~v~~a~~G~eAl~~~~~~~~DlIlmDi~MP~mdG~e~~~~IR~~~~~~~~~~~~  938 (1002)
                      .+||||||++..+..+...|... |+.+. +.+|.+|+..+....||+||+|+.||+|||+++++.||+           
T Consensus         5 ~~ILiVdD~~~~~~~l~~~L~~~~~~~v~-~~~~~~~~~~~~~~~~dlvllD~~mP~~~G~~~~~~lr~-----------   72 (259)
T 3luf_A            5 QKILIVEDSMTIRRMLIQAIAQQTGLEID-AFDTLEGARHCQGDEYVVALVDLTLPDAPSGEAVKVLLE-----------   72 (259)
T ss_dssp             CEEEEECCCHHHHHHHHHHHHHHHCCEEE-EESSTGGGTTCCTTTEEEEEEESCBTTBTTSHHHHHHHH-----------
T ss_pred             CeEEEEECCHHHHHHHHHHHHhcCCeEEE-EeChHHHHHHhhcCCCcEEEEeCCCCCCCHHHHHHHHHh-----------
Confidence            58999999999999999999764 77765 667777887777789999999999999999999999995           


Q ss_pred             hhhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCCh
Q 039716          939 EAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTF  990 (1002)
Q Consensus       939 ~~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~  990 (1002)
                                       ..+|||++|++.+.+...+|+++|+++||.||+..
T Consensus        73 -----------------~~~pvi~lt~~~~~~~~~~a~~~Ga~dyl~Kp~~~  107 (259)
T 3luf_A           73 -----------------RGLPVVILTADISEDKREAWLEAGVLDYVMKDSRH  107 (259)
T ss_dssp             -----------------TTCCEEEEECC-CHHHHHHHHHTTCCEEEECSSHH
T ss_pred             -----------------CCCCEEEEEccCCHHHHHHHHHCCCcEEEeCCchh
Confidence                             13899999999999999999999999999999754

>1a2o_A CHEB methylesterase; bacterial chemotaxis, adaptation, serine hydrolase; 2.40A {Salmonella typhimurium} SCOP: c.23.1.1 c.40.1.1

Probab=99.53  E-value=3.6e-14  Score=160.38  Aligned_cols=114  Identities=19%  Similarity=0.281  Sum_probs=101.1

Q ss_pred             CeEEEEecCHHHHHHHHHHHHhc-CCe-EEEEcCHHHHHHHHHcCCCcEEEEcCCCCCCCHHHHHHHHhccccCCCchhh
Q 039716          860 PKILLVEDNKINVMVAKSMMKQL-GHS-IDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDAA  937 (1002)
Q Consensus       860 ~~ILiVeDn~~n~~~l~~~L~~~-g~~-v~~a~~G~eAl~~~~~~~~DlIlmDi~MP~mdG~e~~~~IR~~~~~~~~~~~  937 (1002)
                      .+||||||++..+..++.+|+.. |+. |..+.|+.+|++.+....||+||+|+.||+|||+++++.||+.         
T Consensus         4 ~rVLIVDD~~~~r~~L~~~L~~~~g~~vv~~a~~~~eAl~~l~~~~pDlVllDi~mp~~dGlell~~l~~~---------   74 (349)
T 1a2o_A            4 IRVLSVDDSALMRQIMTEIINSHSDMEMVATAPDPLVARDLIKKFNPDVLTLDVEMPRMDGLDFLEKLMRL---------   74 (349)
T ss_dssp             EEEEEECSCHHHHHHHHHHHHTSTTEEEEEEESSHHHHHHHHHHHCCSEEEEECCCSSSCHHHHHHHHHHS---------
T ss_pred             CEEEEEECCHHHHHHHHHHHhcCCCcEEEEEeCCHHHHHHHHhccCCCEEEEECCCCCCCHHHHHHHHHhc---------
Confidence            58999999999999999999986 888 6799999999999999999999999999999999999999962         


Q ss_pred             hhhhhcccCCCCCCCCCCCCccEEEEcCCCCH--HHHHHHHHcCCCEEEeCCCCh---------HHHHHHHHhh
Q 039716          938 AEAGIEQAMPSSGSSNHFKRIPIIAMTANALS--ESAEECFANGMDSFVSKPVTF---------QKLKECLEQY 1000 (1002)
Q Consensus       938 ~~~~~~~~~~~~~~~~~~~~ipIIalTa~~~~--~~~~~~~~aG~d~~l~KP~~~---------~~L~~~l~~~ 1000 (1002)
                                       .+ +|||++|+....  +...+++++|+++||.||++.         ++|...|+..
T Consensus        75 -----------------~p-~pVIvlS~~~~~~~~~~~~al~~Ga~d~l~KP~~~~~~~l~~~~~~L~~~I~~~  130 (349)
T 1a2o_A           75 -----------------RP-MPVVMVSSLTGKGSEVTLRALELGAIDFVTKPQLGIREGMLAYSEMIAEKVRTA  130 (349)
T ss_dssp             -----------------SC-CCEEEEECCTHHHHHHHHHHHHHTCCEEEECSSSSCSSCHHHHHHHHHHHHHHH
T ss_pred             -----------------CC-CcEEEEECCCcccHHHHHHHHhCCceEEEECCCCccchhHHHHHHHHHHHHHHH
Confidence                             23 899999998875  447889999999999999983         7777776643

>2vyc_A Biodegradative arginine decarboxylase; pyridoxal phosphate, PLP-dependent E lyase, acid resistance; HET: LLP; 2.4A {Escherichia coli}

Probab=99.45  E-value=6.1e-14  Score=173.91  Aligned_cols=113  Identities=10%  Similarity=0.064  Sum_probs=102.9

Q ss_pred             eEEEEecCH-HH-------HHHHHHHHHhcCCeEEEEcCHHHHHHHHHcCC-CcEEEEcCCCCC----CCHHHHHHHHhc
Q 039716          861 KILLVEDNK-IN-------VMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQN-YDLILMDVCMPV----MDGLKATRLIRS  927 (1002)
Q Consensus       861 ~ILiVeDn~-~n-------~~~l~~~L~~~g~~v~~a~~G~eAl~~~~~~~-~DlIlmDi~MP~----mdG~e~~~~IR~  927 (1002)
                      +||||||++ ..       +..++..|++.||+|..|.||.+|+..+.... ||+||+|++||+    |||+++++.||+
T Consensus         2 ~ILiVdDd~~~~~~~~~~~~~~L~~~L~~~g~~v~~a~~g~~al~~~~~~~~~d~vilDi~lp~~~~~~~G~~ll~~iR~   81 (755)
T 2vyc_A            2 KVLIVESEFLHQDTWVGNAVERLADALSQQNVTVIKSTSFDDGFAILSSNEAIDCLMFSYQMEHPDEHQNVRQLIGKLHE   81 (755)
T ss_dssp             EEEEECCTTSTTSHHHHHHHHHHHHHHHHTTCEEEEESSHHHHHHHHTTTCCCSEEEEECCCCSHHHHHHHHHHHHHHHH
T ss_pred             eEEEEeCCccccccccHHHHHHHHHHHHhCCCEEEEECCHHHHHHHHhcCCCCcEEEEeCCCCcccccccHHHHHHHHHH
Confidence            799999999 78       89999999999999999999999999999874 999999999999    999999999997


Q ss_pred             cccCCCchhhhhhhhcccCCCCCCCCCCCCccEEEEcCCCC-HHHHHHHHHcCCCEEEeCCCChHH-HHHHHHh
Q 039716          928 FEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANAL-SESAEECFANGMDSFVSKPVTFQK-LKECLEQ  999 (1002)
Q Consensus       928 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipIIalTa~~~-~~~~~~~~~aG~d~~l~KP~~~~~-L~~~l~~  999 (1002)
                      .                          ...+|||++|+... .+++...+..|+|||+.||++..+ |...|+.
T Consensus        82 ~--------------------------~~~iPIi~lTa~~~~~~d~~~~l~~gaddyi~kpf~~~efl~~ri~a  129 (755)
T 2vyc_A           82 R--------------------------QQNVPVFLLGDREKALAAMDRDLLELVDEFAWILEDTADFIAGRAVA  129 (755)
T ss_dssp             H--------------------------STTCCEEEEECHHHHHHTCSHHHHHHCSEEEETTTSCHHHHHHHHHH
T ss_pred             h--------------------------CCCCCEEEEecCCcchhhccHhHhhcCCceEeCCCCCHHHHHHHHHH
Confidence            3                          24699999999888 888899999999999999999999 6555543

>2q2e_B Type 2 DNA topoisomerase 6 subunit B; DNA-binding, SPO11, ATPase; 4.00A {Methanosarcina mazei}

Probab=99.42  E-value=1.8e-13  Score=163.39  Aligned_cols=114  Identities=17%  Similarity=0.287  Sum_probs=86.6

Q ss_pred             EEccHHHHHHHHHHHHhhhhhcCCC-C---eeEEEEEecCCCCcccchhhhhhhhhhcchhhhhhhccCCCCCccCCCCC
Q 039716          478 VIGDVLRIRQILTNLISNAIKFTPE-G---KVGIKLYVVPEPPFAKEGLKQKSKAYQSATDAVKEEKHQPKSQTASDQNG  553 (1002)
Q Consensus       478 v~gD~~rL~QIL~NLlsNAIKfT~~-G---~I~I~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  553 (1002)
                      +.+|+.+|.|||.|||.||++|+.. |   .|.|.+...                                         
T Consensus        31 ~~~D~~~L~~Vl~ELV~NAIDa~~~~g~~~~I~V~i~~~-----------------------------------------   69 (621)
T 2q2e_B           31 FDSAPRSLITTVKEAVDNALDACEEAGILPDILVQVERT-----------------------------------------   69 (621)
T ss_dssp             CSSHHHHHHHHHHHHHHHHHHHHTTTSCSCEEEECCEEE-----------------------------------------
T ss_pred             EecCHHHHHHHHHHHHHHHHHHHhhcCCCcEEEEEEEEC-----------------------------------------
Confidence            6689999999999999999999984 5   455543210                                         


Q ss_pred             CCCCCCCCCccCCCCCCCCCCCccCCCCCccccccceEEEEEEEecCCCCCcCcHhhhhhhccCCCcc--ccCcCCCccc
Q 039716          554 FHDKKHGEGYQDHKHDDDPGTPVSHGNSMDEDLEATVWIRCDVYDTGIGIPENALPTLFRKYMQVSAD--HARKYGGTGL  631 (1002)
Q Consensus       554 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~i~V~DtGiGI~~e~l~~IF~pF~q~~~~--~~~~~~GtGL  631 (1002)
                                                        ...++.|+|.|+|+|||++.++++|.+|+.++.-  .....+|+||
T Consensus        70 ----------------------------------~~~~~~I~V~DnG~GIp~e~l~~iF~~~~atskf~~~~~s~Gg~Gl  115 (621)
T 2q2e_B           70 ----------------------------------GPDYVTVIIEDNGPGIVREQIPKVFAKLLYGSRFHALKQSRGQQGI  115 (621)
T ss_dssp             ----------------------------------TTTEEEEEEECCSCCCCGGGHHHHHSCCCCC--CCCCC-CCSSSSH
T ss_pred             ----------------------------------CCcEEEEEEEECCCCCCHHHHHHHhhhhccCCccccccccCCCcee
Confidence                                              0024789999999999999999999887654321  1123479999


Q ss_pred             cHHHHHHHHHHhCCE-EEEEeecCC---ceEEEEEEeCC
Q 039716          632 GLAICKQLVELMGGR-LTVTSKVHC---GSTFTFILPYQ  666 (1002)
Q Consensus       632 GLaI~k~Lve~~gG~-I~v~S~~g~---GTtF~~~LP~~  666 (1002)
                      ||++|+.+++.|||. |+++|..+.   |++|+|.||..
T Consensus       116 GLsiv~~ls~~~gG~~I~V~S~~~gg~~g~~~~~~lp~~  154 (621)
T 2q2e_B          116 GISAAVLYAQMTAGRHTKILSKTSPTAPAHYYELMINTS  154 (621)
T ss_dssp             HHHHHHHHHHHHTCCCCEEEEECSSSSCEEEEECCCCSS
T ss_pred             chhhhhHHHHHhCCCceeEEeeccCCccceEEEEecchh
Confidence            999999999999999 899998874   55555555543

>3p7n_A Sensor histidine kinase; LOV domain, light-activated transcription factor, DNA bindin; HET: FMN; 2.10A {Erythrobacter litoralis}

Probab=99.10  E-value=2.8e-10  Score=122.23  Aligned_cols=176  Identities=11%  Similarity=0.082  Sum_probs=116.3

Q ss_pred             HHHHHHHHHHHHHHHhccCcEEEEecc---cccEEEeeccC---CCCCcccccCCCchhccCccchhhhhHHHHHHHHhC
Q 039716          214 SQILKRADNFLHFVLQNAPVVMGHQDK---ELRYRFIYNHF---PSLHEEDILGKTDVEIFSGAGVKESQDFKREVLEKG  287 (1002)
Q Consensus       214 ~~~l~~~~~~l~~il~~~p~~i~~~d~---~~~~~~~~~~~---~~~~~e~iiGk~~~e~~~~~~~~~~~~~~~~vl~~g  287 (1002)
                      .+.++.++.+++.+++++|.+|+..|.   ++++.++|..|   .|+++++++|++..+++++............++..+
T Consensus        55 ~~~l~~~~~~~~~i~~~~~~~i~~~d~~~~~g~i~~~N~a~~~l~G~~~~el~g~~~~~l~~~~~~~~~~~~~~~~l~~~  134 (258)
T 3p7n_A           55 RVEVQPPAQWVLDLIEASPIASVVSDPRLADNPLIAINQAFTDLTGYSEEECVGRNCRFLAGSGTEPWLTDKIRQGVREH  134 (258)
T ss_dssp             ------CCHHHHHHHHTCSSEEEEECTTSTTCCEEEECHHHHHHHCCCGGGTTTSCGGGGCCTTCCHHHHHHHHHHHHHT
T ss_pred             HHHHHhHHHHHHHHHhcCCccEEEEcCCCCCCcEEEEhHHHHHHcCCCHHHHCCCChhhccCCCCchhHHHHHHHHHHcC
Confidence            344666778899999999999999999   99999999865   588999999999888887766555555666777788


Q ss_pred             CCcceeEEEEEeecCceEEEEEEeeeecCCCCEEEEEEEeechhHHHHH--HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 039716          288 LPAKREITFETELFGSKTFLIYVEPVFSKSGETIGVNYMGMDVTDQVRK--REKMAKLREEIAVQKAKETELNKTIHITE  365 (1002)
Q Consensus       288 ~~~~~e~~~~~~~~~~~~~~~~~~p~~~~~G~~~gi~~~~~DITe~~~~--~~~~~~l~~el~~~~~~~~el~k~~~~~e  365 (1002)
                      .+...++.+....+...++.+.+.|+++.+|.+.|+++++.|||+++..  +..+.+..+.+......+.+....     
T Consensus       135 ~~~~~e~~~~~~dG~~~~~~~~~~pi~d~~g~~~~~v~~~~DITerk~~~~e~~~~~~~~~l~~L~~r~~~i~~~-----  209 (258)
T 3p7n_A          135 KPVLVEILNYKKDGTPFRNAVLVAPIYDDDDELLYFLGSQVEVDDDQPNMGMARRERAAEMLKTLSPRQLEVTTL-----  209 (258)
T ss_dssp             CCEEEEEEEECTTSCEEEEEEEEEEEECTTSCSEEEEEEEEEC-------CHHHHHHHHHHHTTSCHHHHHHHHH-----
T ss_pred             CCeEEEEEEEcCCCCEEEEeeEEEEEEcCCCCEEEEEEEeeecchhhhhhhHHHHHHHHHHHhhcCHHHHHHHHH-----
Confidence            7776676665555555667788999999999999999999999998433  222222222111100111110000     


Q ss_pred             HHHHHHHHHHHhhhccccHHHHHHHHHHHHh
Q 039716          366 ETMRAKQMLATMSHEIRSPLTGVVSMAEILS  396 (1002)
Q Consensus       366 ~~~~~k~fla~iSHELRTPL~~I~g~~elL~  396 (1002)
                        ...+.....++|+|..|++.|......+.
T Consensus       210 --~~~g~~~~eia~~l~~s~~tv~~~l~~i~  238 (258)
T 3p7n_A          210 --VASGLRNKEVAARLGLSEKTVKMHRGLVM  238 (258)
T ss_dssp             --HHTTCCHHHHHHHHTCCHHHHHHHHHHHH
T ss_pred             --HHcCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence              00112346789999999999988877553

>1w25_A Stalked-cell differentiation controlling protein; two-component system, ggdef domain, cyclic dinucleotide, cyclic-digmp; HET: C2E; 2.70A {Caulobacter vibrioides} SCOP: c.23.1.1 c.23.1.1 d.58.29.2 PDB: 2v0n_A* 2wb4_A*

Probab=99.05  E-value=1.4e-09  Score=127.50  Aligned_cols=115  Identities=20%  Similarity=0.317  Sum_probs=99.0

Q ss_pred             CCeEEEEecCHHHHHHHHHHHHhcCCeEEEEcCHHHHHHHHHcCCCcEEEEcCCCCCCCHHHHHHHHhccccCCCchhhh
Q 039716          859 KPKILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDAAA  938 (1002)
Q Consensus       859 ~~~ILiVeDn~~n~~~l~~~L~~~g~~v~~a~~G~eAl~~~~~~~~DlIlmDi~MP~mdG~e~~~~IR~~~~~~~~~~~~  938 (1002)
                      ..+||+|||+..+...+...|.. .+.+..+.++.+++ ......||+|+||+.||+|||+++++.||....        
T Consensus       152 ~~~ilivdd~~~~~~~i~~~L~~-~~~~~~~~~~~~~~-~~~~~~~dlil~D~~mp~~dG~~~~~~ir~~~~--------  221 (459)
T 1w25_A          152 GGRVLIVDDNERQAQRVAAELGV-EHRPVIESDPEKAK-ISAGGPVDLVIVNAAAKNFDGLRFTAALRSEER--------  221 (459)
T ss_dssp             SCEEEEECSCHHHHHHHHHHHTT-TSEEEEECCHHHHH-HHHHSSCSEEEEETTCSSSCHHHHHHHHHTSGG--------
T ss_pred             CCeEEEECCchhhHHHHHHHHhc-ccceeeccCHHHHh-hhccCCCCEEEEecCCCCCcHHHHHHHHHhCcc--------
Confidence            45899999999998888888865 46777888998886 445678999999999999999999999997432        


Q ss_pred             hhhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHHh
Q 039716          939 EAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQ  999 (1002)
Q Consensus       939 ~~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~  999 (1002)
                                      ...+|||++|+....+....|+++|+++|+.||++..++...+..
T Consensus       222 ----------------~~~~pii~lt~~~~~~~~~~~l~~Ga~d~~~kp~~~~~l~~~v~~  266 (459)
T 1w25_A          222 ----------------TRQLPVLAMVDPDDRGRMVKALEIGVNDILSRPIDPQELSARVKT  266 (459)
T ss_dssp             ----------------GTTCCEEEEECTTCHHHHHHHHHTTCCEEEESSCCHHHHHHHHHH
T ss_pred             ----------------ccCCcEEEEcCCCchHHHHHHHhccccccccCCCCHHHHHHHHHH
Confidence                            246899999999999999999999999999999999988776654

>3k3c_A Protein RV1364C/MT1410; sensor, PAS, signal transduction, fatty-acid binding, sigma regulator, signaling protein; HET: PLM; 1.62A {Mycobacterium tuberculosis} PDB: 3k3d_A

Probab=98.99  E-value=6.3e-09  Score=101.80  Aligned_cols=122  Identities=19%  Similarity=0.313  Sum_probs=95.5

Q ss_pred             HHHHHHHHHhccCcEEEEec-ccccEEEeeccC---CCCCcccccCCCchhccCccchhhhhHHHHHHHHhCCCccee-E
Q 039716          220 ADNFLHFVLQNAPVVMGHQD-KELRYRFIYNHF---PSLHEEDILGKTDVEIFSGAGVKESQDFKREVLEKGLPAKRE-I  294 (1002)
Q Consensus       220 ~~~~l~~il~~~p~~i~~~d-~~~~~~~~~~~~---~~~~~e~iiGk~~~e~~~~~~~~~~~~~~~~vl~~g~~~~~e-~  294 (1002)
                      +.++++.+++++|.+|+..| .++++.++|..+   .|+.  +++|++..+++++............++..|.+...+ .
T Consensus        15 ~~~~~~~~~~~~~~~i~~~d~~~~~i~~~N~~~~~~~g~~--~~~G~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~   92 (158)
T 3k3c_A           15 AAEDVRRIFEHIPAILVGLEGPDHRFVAVNAAYRGFSPLL--DTVGQPAREVYPELEGQQIYEMLDRVYQTGEPQSGSEW   92 (158)
T ss_dssp             CHHHHHHHHHHCSSEEEEEETTTTEEEEECHHHHHHCTTC--CSTTSBHHHHSGGGGGTTHHHHHHHHHHHCCCEEEEEE
T ss_pred             HHHHHHHHHhcCCceEEEEECCCcEeHHHHHHHHHHcCCc--hhcCCcHHHhCCchhHHHHHHHHHHHHHhCCcccccce
Confidence            34578899999999999999 999999998865   5666  899999999998766556667778888888775432 3


Q ss_pred             EEEEee----cCceEEEEEEeeeecCCCCEEEEEEEeechhHHHHHHHHHHHH
Q 039716          295 TFETEL----FGSKTFLIYVEPVFSKSGETIGVNYMGMDVTDQVRKREKMAKL  343 (1002)
Q Consensus       295 ~~~~~~----~~~~~~~~~~~p~~~~~G~~~gi~~~~~DITe~~~~~~~~~~l  343 (1002)
                      .+....    +...++.+...|+++.+|.+.|+++++.|||+++++++++..+
T Consensus        93 ~~~~~~~~~~g~~~~~~~~~~pi~~~~g~~~g~~~~~~DITe~k~~e~~l~~~  145 (158)
T 3k3c_A           93 RLQTDYDGSGVEERYFDFVVTPRRRADGSIEGVQLIVDDVTSRVRARQAAEAR  145 (158)
T ss_dssp             EEEEESSSSCEEEEEEEEEEEEEECTTSCEEEEEEEEEECHHHHHHHHHHHHH
T ss_pred             eEEeccCCCCcceEEEEEEEEEeECCCCCEEEEEEEEEehhHHHHHHHHHHHH
Confidence            232221    2236777888999999999999999999999998877665543

>3mxq_A Sensor protein; PSI2, MCSG, structural genomics, protein structure initiativ midwest center for structural genomics; 2.78A {Vibrio cholerae o1 biovar el tor}

Probab=98.93  E-value=2.2e-09  Score=106.48  Aligned_cols=122  Identities=15%  Similarity=0.079  Sum_probs=92.9

Q ss_pred             HHHHHHHHHHHHHHhccCcEEEEecccccEEEeecc---CCCCCcccccCCCchhccCccchhhhhHHHHHHHHhCCCcc
Q 039716          215 QILKRADNFLHFVLQNAPVVMGHQDKELRYRFIYNH---FPSLHEEDILGKTDVEIFSGAGVKESQDFKREVLEKGLPAK  291 (1002)
Q Consensus       215 ~~l~~~~~~l~~il~~~p~~i~~~d~~~~~~~~~~~---~~~~~~e~iiGk~~~e~~~~~~~~~~~~~~~~vl~~g~~~~  291 (1002)
                      .+++.++..++.+++++|.+|+..|.++++.++|..   +.|++.++++|++..+++++ .........+.++..|.+..
T Consensus        15 ~~~~~~~~~l~~il~~~~~gi~v~D~~g~I~~~N~a~~~~~G~~~~eviG~~~~~~~p~-~~~~~~~~l~~vl~~G~~~~   93 (152)
T 3mxq_A           15 NAMAKSRLLLSELLDQLSFALCIVRNDYVIVKVNEYFESRVIFDGETMQGKNILELFPE-SADYLKRKIDTALVIESSSF   93 (152)
T ss_dssp             HHHHHHHHHHHHHHHHHCCEEEEEETTSBEEEECHHHHHTSSSCHHHHTTSBHHHHSGG-GHHHHHHHHHHHHHHTSCEE
T ss_pred             HHHHHHHHHHHHHHhcCCCCEEEEcCCCEEEEECHHHHHHHCcCHHHHCCCCHHHhcCC-hHHHHHHHHHHHHhcCCcee
Confidence            456777888999999999999999999999999875   57888899999999999988 65666667788999887632


Q ss_pred             eeE-------EEE--Ee---ecCceEEEEEEeeeecCCCCEEEEEEEeechhHHHHHH
Q 039716          292 REI-------TFE--TE---LFGSKTFLIYVEPVFSKSGETIGVNYMGMDVTDQVRKR  337 (1002)
Q Consensus       292 ~e~-------~~~--~~---~~~~~~~~~~~~p~~~~~G~~~gi~~~~~DITe~~~~~  337 (1002)
                      ...       .+.  .+   .+...++.+++.|+.+.+|++.|++.+..|||++++++
T Consensus        94 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ti~Pl~d~~G~v~gv~~ii~DVTe~~~a~  151 (152)
T 3mxq_A           94 SSWEQKPHLLPFKSSRPVSGEEEQMYQNLEVIPIHSEDGTIEHVCLCVYDVTIQASQQ  151 (152)
T ss_dssp             EECCSSSCSSCC----------CCEEEEEEEEEEECTTSCEEEEEEEEEEEECC----
T ss_pred             eecccccccccccccCCCCCCCcEEEEEEEEEEEECCCCCEEEEEEEEEECCHHHhcc
Confidence            111       010  11   11233567888999999999999999999999987654

>3cwo_X Beta/alpha-barrel protein based on 1THF and 1TMY; XRAY, CHEY, HISF, half barrel, de novo protein; 3.10A {Thermotoga maritima} PDB: 2lle_A

Probab=98.90  E-value=4.4e-10  Score=118.82  Aligned_cols=91  Identities=26%  Similarity=0.349  Sum_probs=75.5

Q ss_pred             CeEEEEcCHHHHHHHHHcCCCcEEEEcCCCCCCCHHHHHHHHhccccCCCchhhhhhhhcccCCCCCCCCCCCCccEEEE
Q 039716          884 HSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAM  963 (1002)
Q Consensus       884 ~~v~~a~~G~eAl~~~~~~~~DlIlmDi~MP~mdG~e~~~~IR~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipIIal  963 (1002)
                      +.|..+.|+.+|++.+....||+||+|+.||+|+|+++++.||+..                          +..||+++
T Consensus         6 ~~v~~~~~~~~a~~~~~~~~~dlvl~D~~~p~~~g~~~~~~l~~~~--------------------------~~~~i~vi   59 (237)
T 3cwo_X            6 LIVDDATNGREAVEKYKELKPDIVTMDITMPEMNGIDAIKEIMKID--------------------------PNAKIIVC   59 (237)
T ss_dssp             EEEECCCSSSTTHHHHHHHCCSCEEEECCSTTSSHHHHHHHHHHHS--------------------------SSCCEEEE
T ss_pred             EEEEECCCHHHHHHHHHhcCCCEEEEeCCCCCCCHHHHHHHHHHhC--------------------------CCCCEEEE
Confidence            4556689999999999999999999999999999999999999742                          23445555


Q ss_pred             cCCCCHHHHHHHHHcCCCEEEeCC--CChHHHHHHHHhh
Q 039716          964 TANALSESAEECFANGMDSFVSKP--VTFQKLKECLEQY 1000 (1002)
Q Consensus       964 Ta~~~~~~~~~~~~aG~d~~l~KP--~~~~~L~~~l~~~ 1000 (1002)
                      ++....+...+++++|+++|+.||  ++..+|...+.+.
T Consensus        60 ~~~~~~~~~~~~~~~Ga~~~l~kp~~~~~~~l~~~i~~~   98 (237)
T 3cwo_X           60 SAMGQQAMVIEAIKAGAKDFIVNTAAVENPSLITQIAQT   98 (237)
T ss_dssp             CCSSTHHHHHHHHHTTCCEEEESHHHHHCTHHHHHHHHH
T ss_pred             ECCCCHHHHHHHHHCCHHheEeCCcccChHHHHHHHHHH
Confidence            665668899999999999999999  7777887776654

>3mr0_A Sensory box histidine kinase/response regulator; PAS fold, structural genomics, PSI-2; HET: PG5; 1.49A {Burkholderia thailandensis}

Probab=98.88  E-value=1.3e-08  Score=98.47  Aligned_cols=131  Identities=15%  Similarity=0.125  Sum_probs=95.3

Q ss_pred             HHHHHHHHHHHHHHhccCcEEEEecccccEEEeeccC---CCCCcccccCC--CchhccCccchhhhhHHHHHHHHhCCC
Q 039716          215 QILKRADNFLHFVLQNAPVVMGHQDKELRYRFIYNHF---PSLHEEDILGK--TDVEIFSGAGVKESQDFKREVLEKGLP  289 (1002)
Q Consensus       215 ~~l~~~~~~l~~il~~~p~~i~~~d~~~~~~~~~~~~---~~~~~e~iiGk--~~~e~~~~~~~~~~~~~~~~vl~~g~~  289 (1002)
                      ++|++++++++.++++++.+++..|.++...++|..+   .|+.++++.|.  ...+++++.............+..+.+
T Consensus         2 ~aL~~se~rl~~~~~~~~~g~w~~d~~~~~~~~s~~~~~~~G~~~~~~~~~~~~~~~~ihpdD~~~~~~~~~~~~~~~~~   81 (142)
T 3mr0_A            2 NALSASEERFQLAVSGASAGLWDWNPKTGAMYLSPHFKKIMGYEDHELPDEITGHRESIHPDDRARVLAALKAHLEHRDT   81 (142)
T ss_dssp             -------CCHHHHHHHTTCEEEEECTTTCCEEECHHHHHHTTCCGGGSCSEEC---CCBCTTTHHHHHHHHHHHHHHCCC
T ss_pred             hHHHHHHHHHHHHHHhCCcEEEEEEcCCCeEEECHHHHHHhCCCccccCCCHHHHHhhcCHHHHHHHHHHHHHHHhCCCc
Confidence            4577788899999999999999999999988887754   57777777663  345666676666666666677777777


Q ss_pred             cceeEEEEEeecCceEEEEEEeeeecCCCCEEEEEEEeechhHHHHHHHHHHHHHH
Q 039716          290 AKREITFETELFGSKTFLIYVEPVFSKSGETIGVNYMGMDVTDQVRKREKMAKLRE  345 (1002)
Q Consensus       290 ~~~e~~~~~~~~~~~~~~~~~~p~~~~~G~~~gi~~~~~DITe~~~~~~~~~~l~~  345 (1002)
                      ...++.+....+...|+.....|+++.+|.+.+++++..|||+++++++++.+.++
T Consensus        82 ~~~e~r~~~~~G~~~w~~~~~~~~~d~~g~~~~~~G~~~DITerk~~E~~L~~~~~  137 (142)
T 3mr0_A           82 YDVEYRVRTRSGDFRWIQSRGQALWNSAGEPYRMVGWIMDVTDRKRDEDALRVSRE  137 (142)
T ss_dssp             EEEEEEEECTTSCEEEEEEEEEEEECTTSCEEEEEEEEEECHHHHHHHHHHHHHHH
T ss_pred             eEEEEEEECCCCCEEEEEEEEEEEECCCCCEEEEEEEEEcCchHHHHHHHHHHHHH
Confidence            66666665555555677788889999999999999999999999888777655443

>2gj3_A Nitrogen fixation regulatory protein; PAS domain, FAD, redox sensor, atomic resolution, transferase; HET: FAD; 1.04A {Azotobacter vinelandii}

Probab=98.81  E-value=9.2e-09  Score=96.08  Aligned_cols=113  Identities=18%  Similarity=0.193  Sum_probs=86.9

Q ss_pred             HHHHHHHHhccCcEEEEecccccEEEeeccC---CCCCcccccCCCchhccCccchhhhhHHHHHHHHhCCCcceeEEEE
Q 039716          221 DNFLHFVLQNAPVVMGHQDKELRYRFIYNHF---PSLHEEDILGKTDVEIFSGAGVKESQDFKREVLEKGLPAKREITFE  297 (1002)
Q Consensus       221 ~~~l~~il~~~p~~i~~~d~~~~~~~~~~~~---~~~~~e~iiGk~~~e~~~~~~~~~~~~~~~~vl~~g~~~~~e~~~~  297 (1002)
                      +..++.+++++|.+|+..|.++++.++|..|   .|++.++++|++..++.++.............+..+.+...++.+.
T Consensus         4 ~~~~~~~~~~~~~~i~~~d~~g~i~~~N~a~~~~~G~~~~elig~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~   83 (120)
T 2gj3_A            4 PEIFRQTVEHAPIAISITDLKANILYANRAFRTITGYGSEEVLGKNESILSNGTTPRLVYQALWGRLAQKKPWSGVLVNR   83 (120)
T ss_dssp             HHHHHHHHHHCSSEEEEECTTCBEEEECHHHHHHHCCCTTGGGGCBGGGGCCTTSCHHHHHHHHHHHHTTCCEEEEEEEE
T ss_pred             HHHHHHHHHhCCCeEEEECCCCCEEeehHHHHHHHCcCHHHHcCCCHHHcCCCCCCHHHHHHHHHHHHcCCCEEEEEEEE
Confidence            3567789999999999999999999999865   6889999999998887665433332333344556666666666555


Q ss_pred             EeecCceEEEEEEeeeecCCCCEEEEEEEeechhHH
Q 039716          298 TELFGSKTFLIYVEPVFSKSGETIGVNYMGMDVTDQ  333 (1002)
Q Consensus       298 ~~~~~~~~~~~~~~p~~~~~G~~~gi~~~~~DITe~  333 (1002)
                      .+.+...++.+.+.|+++.+|.+.+++++..|||++
T Consensus        84 ~~dG~~~~~~~~~~pi~~~~g~~~~~v~~~~DITe~  119 (120)
T 2gj3_A           84 RKDKTLYLAELTVAPVLNEAGETIYYLGMHRDTSEL  119 (120)
T ss_dssp             CTTSCEEEEEEEEEEEECTTSCEEEEEEEEEECCSC
T ss_pred             cCCCCEEEEEEEEEEEECCCCCEEEEEEEeccCccc
Confidence            555455566788899999999999999999999974

>3ue6_A Aureochrome1; PAS/LOV domain, FMN-binding blue-light photoreceptor, signal protein; HET: FMN; 2.75A {Vaucheria frigida} PDB: 3ulf_A*

Probab=98.80  E-value=9.2e-09  Score=100.89  Aligned_cols=124  Identities=17%  Similarity=0.106  Sum_probs=94.9

Q ss_pred             HHHHHHHHHHHHHHHHhccCcEEEEecc---cccEEEeeccC---CCCCcccccCCCchhccCccchhhhhHHHHHHHHh
Q 039716          213 LSQILKRADNFLHFVLQNAPVVMGHQDK---ELRYRFIYNHF---PSLHEEDILGKTDVEIFSGAGVKESQDFKREVLEK  286 (1002)
Q Consensus       213 ~~~~l~~~~~~l~~il~~~p~~i~~~d~---~~~~~~~~~~~---~~~~~e~iiGk~~~e~~~~~~~~~~~~~~~~vl~~  286 (1002)
                      +.+.++.++.+++.+++++|.+++..|.   ++++.++|..|   .|++.++++|++..+++++.............+..
T Consensus        26 ~~~~l~~~~~~~~~~~~~~~~~i~~~d~~~~~g~i~~~N~~~~~l~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~  105 (166)
T 3ue6_A           26 ANRILEDPDYSLVKALQMAQQNFVITDASLPDNPIVYASRGFLTLTGYSLDQILGRNCRFLQGPETDPRAVDKIRNAITK  105 (166)
T ss_dssp             -----CCCCCHHHHHHHHTTSCEEEEETTSTTCCEEEECHHHHHHHCCCHHHHTTSCGGGGCCTTSCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHhcCCceEEEEEccCCCCcEEEECHHHHHHhCcCHHHHcCCCHhheeCCCCCHHHHHHHHHHHhc
Confidence            3444555667888999999999999999   79999999865   57888999999988887765555555555667777


Q ss_pred             CCCcceeEEEEEeecCceEEEEEEeeeecCCCCEEEEEEEeechhHHHHH
Q 039716          287 GLPAKREITFETELFGSKTFLIYVEPVFSKSGETIGVNYMGMDVTDQVRK  336 (1002)
Q Consensus       287 g~~~~~e~~~~~~~~~~~~~~~~~~p~~~~~G~~~gi~~~~~DITe~~~~  336 (1002)
                      +.+...++.+....+...++.+...|+++.+|.+.|+++++.|||+++.+
T Consensus       106 ~~~~~~e~~~~~~~g~~~~~~~~~~~i~~~~g~~~~~~~~~~DITe~k~~  155 (166)
T 3ue6_A          106 GVDTSVCLLNYRQDGTTFWNLFFVAGLRDSKGNIVNYVGVQSKVSEDYAK  155 (166)
T ss_dssp             TCCEEEEEEEECTTSCEEEEEEEEEEEECTTSCEEEEEEECCBCCHHHHH
T ss_pred             CCceEEEEEEEcCCCCEEEEEEEEEeeeCCCCCEEEEEEEEEechHHHHH
Confidence            77766666655544455566788899999999999999999999987654

>4hia_A LOV protein; PAS, HTH, signaling protein; HET: FMN; 1.95A {Rhodobacter sphaeroides} PDB: 4hnb_A* 4hj4_A* 4hj6_A* 4hj3_A*

Probab=98.80  E-value=1e-08  Score=102.26  Aligned_cols=119  Identities=13%  Similarity=0.050  Sum_probs=96.3

Q ss_pred             HHHHHHHHhccCcEEEEeccc---ccEEEeeccC---CCCCcccccCCCchhccCccchhhhhHHHHHHHHhCCCcceeE
Q 039716          221 DNFLHFVLQNAPVVMGHQDKE---LRYRFIYNHF---PSLHEEDILGKTDVEIFSGAGVKESQDFKREVLEKGLPAKREI  294 (1002)
Q Consensus       221 ~~~l~~il~~~p~~i~~~d~~---~~~~~~~~~~---~~~~~e~iiGk~~~e~~~~~~~~~~~~~~~~vl~~g~~~~~e~  294 (1002)
                      ...++.+++++|.+|+..|.+   +++.++|..|   .|++.++++|++..+++++............++..+.+...++
T Consensus         6 ~~~~~~~~~~~~~~i~~~d~~~~~g~i~~~N~a~~~~~G~~~~e~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~   85 (176)
T 4hia_A            6 FEKIRAVFDRSGVALTLVDMSLPEQPVVLANPPFLRMTGYTEGQILGFNCRFLQRGDENAQARADIRDALKLGRELQVVL   85 (176)
T ss_dssp             HHHHHHHHHHCSSCCEEEETTSTTCCEEEECHHHHHHHTCCHHHHTTSCGGGGCCTTCCHHHHHHHHHHHHHTCCEEEEE
T ss_pred             HHHHHHHHhcCCCcEEEEecCCCCCcEEEECHHHHHHHCcCHHHHcCCCcceeeCCCCCHHHHHHHHHHHHcCCceEEEE
Confidence            356788999999999999999   9999999865   5888999999998888877655555556667777887776666


Q ss_pred             EEEEeecCceEEEEEEeeeecCCCCEEEEEEEeechhHHHHHHHH
Q 039716          295 TFETELFGSKTFLIYVEPVFSKSGETIGVNYMGMDVTDQVRKREK  339 (1002)
Q Consensus       295 ~~~~~~~~~~~~~~~~~p~~~~~G~~~gi~~~~~DITe~~~~~~~  339 (1002)
                      .+....+...++.+...|+++.+|.+.|+++++.|||++++.+++
T Consensus        86 ~~~~~dG~~~~~~~~~~pi~~~~g~~~~~~~~~~DITe~k~~e~~  130 (176)
T 4hia_A           86 RNYRANDEPFDNLLFLHPVGGRPDAPDYFLGSQFELGRSGNSEEA  130 (176)
T ss_dssp             EEECTTCCEEEEEEEEEEESSBTTBCSEEEEEEEEESSSGGGHHH
T ss_pred             EEEcCCCCEEEEEEEEEEeeCCCCCeEEEEEEEEECcHhhHHHHH
Confidence            665555555666788999999999999999999999998776554

>2pr5_A Blue-light photoreceptor; light-oxygen-voltage, LOV, PER-ARNT-SIM, PAS, flavoprotein, protein; HET: FMN; 1.45A {Bacillus subtilis} PDB: 2pr6_A*

Probab=98.77  E-value=5.1e-08  Score=92.63  Aligned_cols=119  Identities=17%  Similarity=0.093  Sum_probs=84.8

Q ss_pred             HHHhccCcEEEEecccc---cEEEeeccC---CCCCcccccCCCchhccCccchhhhhHHHHHHHHhCCCcceeEEEEEe
Q 039716          226 FVLQNAPVVMGHQDKEL---RYRFIYNHF---PSLHEEDILGKTDVEIFSGAGVKESQDFKREVLEKGLPAKREITFETE  299 (1002)
Q Consensus       226 ~il~~~p~~i~~~d~~~---~~~~~~~~~---~~~~~e~iiGk~~~e~~~~~~~~~~~~~~~~vl~~g~~~~~e~~~~~~  299 (1002)
                      .+++++|.+|+..|.++   ++.++|..|   .|++.++++|++...+.++.............+..+.+...++.+..+
T Consensus         3 ~~~~~~~~~i~~~d~~g~~~~i~~~N~a~~~~~G~~~~el~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~k   82 (132)
T 2pr5_A            3 HMLDHVRVGVVITDPALEDNPIVYVNQGFVQMTGYETEEILGKNCRFLQGKHTDPAEVDNIRTALQNKEPVTVQIQNYKK   82 (132)
T ss_dssp             ---CCCCCEEEEECTTSTTCCEEEECHHHHHHHSCCHHHHTTSCGGGGCCTTCCHHHHHHHHHHHHHTCCEEEEEEEECT
T ss_pred             hHHhcCCCcEEEEeCCCCCCcEEEECHHHHHHhCcCHHHHcCCChhhhCCCCCCHHHHHHHHHHHHcCCCeEEEEEEEec
Confidence            47899999999999976   999998765   688999999998877665443333233344556666665556555554


Q ss_pred             ecCceEEEEEEeeeecCCCCEEEEEEEeechhHHHHHHHHHHHHHHH
Q 039716          300 LFGSKTFLIYVEPVFSKSGETIGVNYMGMDVTDQVRKREKMAKLREE  346 (1002)
Q Consensus       300 ~~~~~~~~~~~~p~~~~~G~~~gi~~~~~DITe~~~~~~~~~~l~~e  346 (1002)
                      .+...++.+.+.|+.+.+  +.+++++..|||++++.++++..++++
T Consensus        83 dG~~~~~~~~~~~~~~~~--~~~~~~~~~DITe~k~~e~~l~~~~~~  127 (132)
T 2pr5_A           83 DGTMFWNELNIDPMEIED--KTYFVGIQNDITKQKEYEKLLEDSLTE  127 (132)
T ss_dssp             TSCEEEEEEEEEEEEETT--EEEEEEEEEECHHHHHHHHHHHHHHHH
T ss_pred             CCCeeeeEEEEEeccCCC--eeEEEEEEEeCcHHHHHHHHHHHHHHH
Confidence            444556677888998765  788999999999998887776555443

>3sw1_A Sensory box protein; light-oxygen-voltage, LOV, PAS, signaling protein; HET: FMN; 2.63A {Pseudomonas putida}

Probab=98.76  E-value=2.7e-08  Score=97.27  Aligned_cols=126  Identities=15%  Similarity=0.111  Sum_probs=98.4

Q ss_pred             HHHHHHHHhccCcEEEEecccc---cEEEeeccC---CCCCcccccCCCchhccCccchhhhhHHHHHHHHhCCCcceeE
Q 039716          221 DNFLHFVLQNAPVVMGHQDKEL---RYRFIYNHF---PSLHEEDILGKTDVEIFSGAGVKESQDFKREVLEKGLPAKREI  294 (1002)
Q Consensus       221 ~~~l~~il~~~p~~i~~~d~~~---~~~~~~~~~---~~~~~e~iiGk~~~e~~~~~~~~~~~~~~~~vl~~g~~~~~e~  294 (1002)
                      +.+++.+++++|.+++..|.++   ++.++|..+   .|+..++++|++..+++++............++..+.+...++
T Consensus        24 ~~~~~~i~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~g~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  103 (162)
T 3sw1_A           24 AQLLQSMVDASNDGIVVAEKEGDDTILIYVNAAFEYLTGYSRDEILYQDCRFLQGDDRDQLGRARIRKAMAEGRPCREVL  103 (162)
T ss_dssp             HHHHHHHHHTCSSEEEEEEEETTEEEEEEECHHHHHHHTCCHHHHTTSBGGGGTTTCCCCHHHHHHHHHHHHTCCEEEEE
T ss_pred             HHHHHHHHhhccCcEEEEeCCCCccEEEEECHHHHHHHCCCHHHHcCCCcceecCCCcCHHHHHHHHHHHhcCCCCcceE
Confidence            4678889999999999999999   999998764   5778899999999888876555545555566677777666665


Q ss_pred             EEEEeecCceEEEEEEeeeecCCCCEEEEEEEeechhHHHHHHHHHHHHHHH
Q 039716          295 TFETELFGSKTFLIYVEPVFSKSGETIGVNYMGMDVTDQVRKREKMAKLREE  346 (1002)
Q Consensus       295 ~~~~~~~~~~~~~~~~~p~~~~~G~~~gi~~~~~DITe~~~~~~~~~~l~~e  346 (1002)
                      .+....+...++.+...|+.+.+|.+.|+++++.|||++++.++++.++.++
T Consensus       104 ~~~~~~g~~~~~~~~~~~i~~~~g~~~~~~~~~~DiTe~k~~e~~l~~~~~~  155 (162)
T 3sw1_A          104 RNYRKDGSAFWNELSITPVKSDFDQRTYFIGIQKDVSRQVELERELAELRAR  155 (162)
T ss_dssp             EEECTTCCEEEEEEEEEEEECSSSSCEEEEEEEEECHHHHHHHHHHHHHTC-
T ss_pred             EEECCCCCEEEEEEEEEEeecCCCCEEEEEEEEEeCcHHHHHHHHHHHHHHH
Confidence            5544444556677888999999999999999999999998887766555433

>3kx0_X Uncharacterized protein RV1364C/MT1410; PAS domain, sensory domain, mycobacteium tuberculos molecule binding domain; 2.30A {Mycobacterium tuberculosis}

Probab=98.74  E-value=2.4e-08  Score=101.41  Aligned_cols=119  Identities=19%  Similarity=0.315  Sum_probs=92.9

Q ss_pred             HHHHHHHHHHhccCcEEEEec-ccccEEEeeccC---CCCCcccccCCCchhccCccchhhhhHHHHHHHHhCCCccee-
Q 039716          219 RADNFLHFVLQNAPVVMGHQD-KELRYRFIYNHF---PSLHEEDILGKTDVEIFSGAGVKESQDFKREVLEKGLPAKRE-  293 (1002)
Q Consensus       219 ~~~~~l~~il~~~p~~i~~~d-~~~~~~~~~~~~---~~~~~e~iiGk~~~e~~~~~~~~~~~~~~~~vl~~g~~~~~e-  293 (1002)
                      +++.+++.+++++|.+++..| .++++.++|..+   .|+.  +++|++..+++++............++..|.+...+ 
T Consensus        34 ~~~~~l~~l~~~~~~~i~~~d~~~g~i~~~N~a~~~l~G~~--~~~G~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~  111 (185)
T 3kx0_X           34 GAAEDVRRIFEHIPAILVGLEGPDHRFVAVNAAYRGFSPLL--DTVGQPAREVYPELEGQQIYEMLDRVYQTGEPQSGSE  111 (185)
T ss_dssp             CCHHHHHHHHHHCSSEEEEEETTTTEEEEECHHHHHHCCCC--SCTTSBHHHHCTTSCSSSSHHHHHHHHHHCCCEEEEE
T ss_pred             hhHHHHHHHHhcCCceEEEEECCCcEEEEEcHHHHHHcCCc--cccCCcHHHHCCchhhhhHHHHHHHHHHcCCcccccc
Confidence            345678999999999999999 999999998765   5666  899999999998766655667778888888775432 


Q ss_pred             EEEEEe--e--cCceEEEEEEeeeecCCCCEEEEEEEeechhHHHHHHHH
Q 039716          294 ITFETE--L--FGSKTFLIYVEPVFSKSGETIGVNYMGMDVTDQVRKREK  339 (1002)
Q Consensus       294 ~~~~~~--~--~~~~~~~~~~~p~~~~~G~~~gi~~~~~DITe~~~~~~~  339 (1002)
                      ..+...  .  +...++.+...|+++.+|.+.|+++++.|||++++++++
T Consensus       112 ~~~~~~~~~~gg~~~~~~~~~~pi~~~~g~~~g~~~~~~DITerk~~e~~  161 (185)
T 3kx0_X          112 WRLQTDYDGSGVEERYFDFVVTPRRRADGSIEGVQLIVDDVTSRVRARQA  161 (185)
T ss_dssp             EEEC--------CCEEEEEEEEEEECTTSCEEEEEEEEEECHHHHTTCC-
T ss_pred             eeEEeeccCCCCccEEEEEEEEEEECCCCCEEEEEEEEEeCCHHHHHHHH
Confidence            222211  1  344677888999999999999999999999999887665

>3nja_A Probable ggdef family protein; structural genomics, PSI-2, protein structure initiative, MI center for structural genomics, MCSG; 2.37A {Chromobacterium violaceum}

Probab=98.71  E-value=2.9e-08  Score=91.50  Aligned_cols=118  Identities=10%  Similarity=-0.102  Sum_probs=79.7

Q ss_pred             HHHHHHHHHHHHhccCcEEEEecccccEEEeeccC---CCCCcccccC--CCchhccCccchhhhhHHHHHHHHhCCCcc
Q 039716          217 LKRADNFLHFVLQNAPVVMGHQDKELRYRFIYNHF---PSLHEEDILG--KTDVEIFSGAGVKESQDFKREVLEKGLPAK  291 (1002)
Q Consensus       217 l~~~~~~l~~il~~~p~~i~~~d~~~~~~~~~~~~---~~~~~e~iiG--k~~~e~~~~~~~~~~~~~~~~vl~~g~~~~  291 (1002)
                      |++++.+++.+++++|.+++..|.++++.++|..+   .|+.+++++|  ....+++++............++..+.+..
T Consensus         2 l~~~~~~l~~~~~~~~~~i~~~d~~~~~~~~n~~~~~~~G~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~~   81 (125)
T 3nja_A            2 NAMAEKLLHTAESDAGIGSWVLHMESGRLEWSQAVHDIFGTDSATFDATEDAYFQRVHPDDRARVRRELDRHVLGDRPFD   81 (125)
T ss_dssp             ---------------CCEEEEEETTTTEEEECHHHHHHHTCCTTTCCCBHHHHHHHBCTTTHHHHHHHHHHHHHSCCCEE
T ss_pred             cHHHHHHHHHHHHhCCeeEEEEEcCCCcEEECHHHHHHhCCCcccccccHHHHHhhcChhHHHHHHHHHHHHHhcCCCce
Confidence            45667888999999999999999999999998764   5778888888  455566666666666666677777777765


Q ss_pred             eeEEEEEeecCceEEEEEEeeeecCCCCEEEEEEEeechhHHH
Q 039716          292 REITFETELFGSKTFLIYVEPVFSKSGETIGVNYMGMDVTDQV  334 (1002)
Q Consensus       292 ~e~~~~~~~~~~~~~~~~~~p~~~~~G~~~gi~~~~~DITe~~  334 (1002)
                      .++.+....+...++.+...|+++.+|.+.+++++..|||+++
T Consensus        82 ~e~~~~~~~g~~~~~~~~~~~~~~~~g~~~~~~g~~~DITe~k  124 (125)
T 3nja_A           82 VEYRIVRPDGQVRELLERNHIQRQASGQVDHLWGTVIDMTEHK  124 (125)
T ss_dssp             EEEEEECTTSCEEEEEEEEEEEECTTSCEEEEEEEEEECCC--
T ss_pred             EEEEEECCCCCEEEEEEeeEEEECCCCCEEEEEEEEEeccccc
Confidence            6666655555556777888899999999999999999999875

>3f1p_B ARYL hydrocarbon receptor nuclear translocator; PAS domain, heterodimer, internal cavity, activator, angiogenesis, congenital erythrocytosis; 1.17A {Homo sapiens} SCOP: d.110.3.0 PDB: 3f1o_B* 3f1n_B 3h7w_B* 3h82_B* 1x0o_A 2hv1_A 4h6j_B 2b02_A* 2k7s_A 2a24_B

Probab=98.68  E-value=3.1e-08  Score=92.34  Aligned_cols=112  Identities=14%  Similarity=0.108  Sum_probs=85.7

Q ss_pred             HHHHHHhccCcEEEEecccccEEEeeccC---CCCCcccccCCCchhccCccchhhhhHHHHHHHH-hCCCcceeEEEEE
Q 039716          223 FLHFVLQNAPVVMGHQDKELRYRFIYNHF---PSLHEEDILGKTDVEIFSGAGVKESQDFKREVLE-KGLPAKREITFET  298 (1002)
Q Consensus       223 ~l~~il~~~p~~i~~~d~~~~~~~~~~~~---~~~~~e~iiGk~~~e~~~~~~~~~~~~~~~~vl~-~g~~~~~e~~~~~  298 (1002)
                      |...+++++|.+|+..|.++++.++|..+   .|+++++++|++..+++++............++. .+.+...++.+..
T Consensus         3 ~~~ll~e~~~d~i~~~d~~g~i~~~n~~~~~~~G~~~~el~g~~~~~~i~p~d~~~~~~~~~~~~~~~~~~~~~e~r~~~   82 (121)
T 3f1p_B            3 FKGLNVCQPTRFISRHNIEGIFTFVDHRCVATVGYQPQELLGKNIVEFCHPEDQQLLRDSFQQVVKLKGQVLSVMFRFRS   82 (121)
T ss_dssp             -----CCCCCEEEEEECTTSBEEEECTTHHHHHSCCGGGTTTSBGGGGBCTTTHHHHHHHHHHHTTSTTCCEEEEEEEEC
T ss_pred             cccceecCCCceEEEECCCceEEEECcchhhhhCCChHHHcCCCHHHeECHHHHHHHHHHHHHHHhcCCCcccEEEEEEe
Confidence            45678999999999999999999999865   5889999999999999988776665555555553 4445555666666


Q ss_pred             eecCceEEEEEEeeeecC-CCCEEEEEEEeechhHHH
Q 039716          299 ELFGSKTFLIYVEPVFSK-SGETIGVNYMGMDVTDQV  334 (1002)
Q Consensus       299 ~~~~~~~~~~~~~p~~~~-~G~~~gi~~~~~DITe~~  334 (1002)
                      ..+...++.....|+++. +|.+.+++++..|||+++
T Consensus        83 ~dG~~~w~~~~~~~~~~~~~g~~~~iv~~~~DIT~~k  119 (121)
T 3f1p_B           83 KNQEWLWMRTSSFTFQNPYSDEIEYIICTNTNVKNSS  119 (121)
T ss_dssp             TTSCEEEEEEEEEEECCTTCCCCCEEEEEEEECCCC-
T ss_pred             cCCCEEEEEEEEEEEECCCCCceeEEEEEeEEccccc
Confidence            656666777888899987 889999999999999864

>3luq_A Sensor protein; PAS, histidine, kinase, PSI, MCSG, structural genomics, midwest center for structural genomics; HET: PGE; 2.49A {Geobacter sulfurreducens}

Probab=98.67  E-value=7.8e-08  Score=87.13  Aligned_cols=110  Identities=25%  Similarity=0.303  Sum_probs=81.3

Q ss_pred             HHHHHHHHhccCcEEEEecccccEEEeeccC---CCCCcccccCCCchhccCccchhhhhHHHHHHHHhCCCcceeEEEE
Q 039716          221 DNFLHFVLQNAPVVMGHQDKELRYRFIYNHF---PSLHEEDILGKTDVEIFSGAGVKESQDFKREVLEKGLPAKREITFE  297 (1002)
Q Consensus       221 ~~~l~~il~~~p~~i~~~d~~~~~~~~~~~~---~~~~~e~iiGk~~~e~~~~~~~~~~~~~~~~vl~~g~~~~~e~~~~  297 (1002)
                      +++++.+++++|.+++..|.++++.++|..+   .|+.+++++|++..++++. ...........++..+.....+..+.
T Consensus         2 e~~~~~~~~~~~~~i~~~d~~g~i~~~N~~~~~~~g~~~~~~~g~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~   80 (114)
T 3luq_A            2 DERLRLFTEHAPAALAMFDREMRYLAVSRRWREDYGLGDGDILGMSHYDIFPE-IGEEWKSVHRRGLAGEVIRVEEDCFV   80 (114)
T ss_dssp             CHHHHHHHHTCSSEEEEEETTCBEEEECHHHHHHTTCCSSCCTTCBHHHHCTT-CCHHHHHHHHHHHTTCCEEEEEEEEE
T ss_pred             hHHHHHHHhcCCceEEEEcCCcEEEEECHHHHHHHCCCHHHHcCCcHHHHCCc-cHHHHHHHHHHHhcCCcceeeeeEEE
Confidence            3567889999999999999999999998764   6788899999999998853 33444444555554332222222444


Q ss_pred             EeecCceEEEEEEeeeecCCCCEEEEEEEeechh
Q 039716          298 TELFGSKTFLIYVEPVFSKSGETIGVNYMGMDVT  331 (1002)
Q Consensus       298 ~~~~~~~~~~~~~~p~~~~~G~~~gi~~~~~DIT  331 (1002)
                      ...+...++.+...|+++.+|.+.|+++++.|||
T Consensus        81 ~~~g~~~~~~~~~~p~~~~~g~~~~~~~~~~DIT  114 (114)
T 3luq_A           81 RADGRTQWLRWEVRPWYEGEGRVGGVVIFTEDIT  114 (114)
T ss_dssp             C--CCEEEEEEEEEEEECTTSCEEEEEEEEEECC
T ss_pred             cCCCcEEEEEEEEEEeECCCCCEEEEEEEEeeCC
Confidence            4444556677888999999999999999999997

>3t50_A Blue-light-activated histidine kinase; PAS superfamily, blue-light photoreceptor, FMN binding, TRAN; HET: FMN; 1.64A {Brucella melitensis}

Probab=98.64  E-value=5.4e-08  Score=90.87  Aligned_cols=114  Identities=11%  Similarity=0.064  Sum_probs=86.9

Q ss_pred             HHhccCcEEEEecc---cccEEEeeccC---CCCCcccccCCCchhccCccchhhhhHHHHHHHHhCCCcceeEEEEEee
Q 039716          227 VLQNAPVVMGHQDK---ELRYRFIYNHF---PSLHEEDILGKTDVEIFSGAGVKESQDFKREVLEKGLPAKREITFETEL  300 (1002)
Q Consensus       227 il~~~p~~i~~~d~---~~~~~~~~~~~---~~~~~e~iiGk~~~e~~~~~~~~~~~~~~~~vl~~g~~~~~e~~~~~~~  300 (1002)
                      +++++|.+++..|.   ++++.++|..+   .|+..++++|++..+++++.............+..+.+...++.+....
T Consensus         2 ~~~~~~~~i~~~d~~~~~g~i~~~N~~~~~l~g~~~~e~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~   81 (128)
T 3t50_A            2 ASEFTLMPMLITNPHLPDNPIVFANPAFLKLTGYEADEVMGRNCRFLQGHGTDPAHVRAIKSAIAAEKPIDIDIINYKKS   81 (128)
T ss_dssp             CCCCCSSCEEEECTTSTTCCEEEECHHHHHHHCCCHHHHTTSCGGGGCCTTSCHHHHHHHHHHHHTTCCEEEEEEEECTT
T ss_pred             ccccCcccEEEecCCCCCCcEEEEcHHHHHHhCcCHHHHcCCCHhhhcCCccCHHHHHHHHHHHHcCCCceeEEEEEcCC
Confidence            56889999999999   89999998865   5788899999998888876555545555566677777666666555544


Q ss_pred             cCceEEEEEEeeeecCCCCEEEEEEEeechhHHHHHHHHH
Q 039716          301 FGSKTFLIYVEPVFSKSGETIGVNYMGMDVTDQVRKREKM  340 (1002)
Q Consensus       301 ~~~~~~~~~~~p~~~~~G~~~gi~~~~~DITe~~~~~~~~  340 (1002)
                      +...++.+...|+++.+|.+.|+++++.|||++++++++.
T Consensus        82 g~~~~~~~~~~~i~~~~g~~~~~~~~~~DITe~k~~e~~~  121 (128)
T 3t50_A           82 GEAFWNRLHISPVHNANGRLQHFVSSQLDVTLELVPRGSL  121 (128)
T ss_dssp             CCEEEEEEEEEEEECTTSCEEEEEEEEEECHHHHC-----
T ss_pred             CCEEEEEEEEEEEECCCCCEEEEEEEEEEcchhhhhhhhh
Confidence            5556677889999999999999999999999987765544

>3lyx_A Sensory BOX/ggdef domain protein; structural genomics, PSI- 2, protein structure initiative, northeast structural genomics consortium; 2.00A {Colwellia psychrerythraea}

Probab=98.59  E-value=1.4e-07  Score=85.61  Aligned_cols=115  Identities=9%  Similarity=-0.081  Sum_probs=90.2

Q ss_pred             HHHHHHHHHhccCcEEEEecccccEEEeeccC---CCCCcccccCCCchhccCccchhhhhHHHHHHHHhCCCcceeEEE
Q 039716          220 ADNFLHFVLQNAPVVMGHQDKELRYRFIYNHF---PSLHEEDILGKTDVEIFSGAGVKESQDFKREVLEKGLPAKREITF  296 (1002)
Q Consensus       220 ~~~~l~~il~~~p~~i~~~d~~~~~~~~~~~~---~~~~~e~iiGk~~~e~~~~~~~~~~~~~~~~vl~~g~~~~~e~~~  296 (1002)
                      +..+++.+++++|.+++..|.++++.++|..+   .|+..++++|++...++++............++..+.+...++.+
T Consensus         5 ~~~~~~~~~~~~~~~i~~~d~~~~i~~~N~~~~~~~g~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   84 (124)
T 3lyx_A            5 ILKQRAKAFDYVFDAIVVTDLQGFIIDWNKGSETLYGYSKEQAIGQPVNMLHVPGDTEHITSEVISAVENQGKWTGEIRM   84 (124)
T ss_dssp             HHHHHHHGGGTCSSEEEEEETTCBEEEECHHHHHHHCCCHHHHTTSBGGGGSCTTTHHHHHHHHHHHHHHTSCEEEEEEE
T ss_pred             HHHHHHHHHhhcCceEEEECCCCcEeehhhHHHHHhCCCHHHHcCCCHHHhcCcchhhHHHHHHHHHHHcCCcccceEEE
Confidence            45678889999999999999999999998764   577888999999886666554444444556667777776666665


Q ss_pred             EEeecCceEEEEEEeeeecCCCCEEEEEEEeechhHHH
Q 039716          297 ETELFGSKTFLIYVEPVFSKSGETIGVNYMGMDVTDQV  334 (1002)
Q Consensus       297 ~~~~~~~~~~~~~~~p~~~~~G~~~gi~~~~~DITe~~  334 (1002)
                      ....+...++.+...|+.+.+|.+.|+++++.|||+++
T Consensus        85 ~~~~g~~~~~~~~~~~~~~~~g~~~~~~~~~~Dit~~~  122 (124)
T 3lyx_A           85 LHKDGHIGWIESMCVPIYGENYQMVGALGINRDITKRK  122 (124)
T ss_dssp             ECTTSCEEEEEEEEEEEECSTTCEEEEEEEEEECSCC-
T ss_pred             EccCCCEEEEEEEEEEEECCCCCEEEEEEEEecchhhh
Confidence            55555556777889999999999999999999999864

>3vol_A Aerotaxis transducer AER2; heme, oxygen sensor protein, PAS, HAMP, cyanoMet, CN-bound, protein; HET: HEM; 2.40A {Pseudomonas aeruginosa}

Probab=98.56  E-value=3.8e-07  Score=96.82  Aligned_cols=114  Identities=19%  Similarity=0.312  Sum_probs=85.0

Q ss_pred             HHHHHHHhccCcEEEEecccccEEEeeccC---------------CCCCcccccCCCchhccCccchhhhhHHHHHHHHh
Q 039716          222 NFLHFVLQNAPVVMGHQDKELRYRFIYNHF---------------PSLHEEDILGKTDVEIFSGAGVKESQDFKREVLEK  286 (1002)
Q Consensus       222 ~~l~~il~~~p~~i~~~d~~~~~~~~~~~~---------------~~~~~e~iiGk~~~e~~~~~~~~~~~~~~~~vl~~  286 (1002)
                      .+++.+++++|.+|...|.++++.|+|..+               +|++.++++|++..++++..      ...+.++..
T Consensus        22 ~~l~~iLd~~~~~vii~D~~g~I~~~N~a~~~ll~~~~~~~~~~l~G~~~~eliG~~~~~~~~~~------~~~~~~~~~   95 (233)
T 3vol_A           22 ARIKSALDNVSANVMIADNDLNIIYMNRTVSEMLGRAEADIRKQLPNFDAGRLMGANIDVFHKNP------AHQRHLLAN   95 (233)
T ss_dssp             HHHHHHHTTSSSEEEEEETTSBEEEECHHHHHHHHHTHHHHHTTCTTCCTTSCTTCBGGGGSSSH------HHHHHHHHT
T ss_pred             HHHHHHHhcCCCcEEEECCCCcEEEecHHHHHHHHHHHHHHHhhcCCCCHHHHcCCCHHHHcCCH------HHHHHHHHh
Confidence            456788999999999999999999998754               36788999999988877532      122334443


Q ss_pred             CCCcceeEEEEEeecCceEEEEEEeeeecCCCCEEEEEEEeechhHHHHHHHHHHHHHH
Q 039716          287 GLPAKREITFETELFGSKTFLIYVEPVFSKSGETIGVNYMGMDVTDQVRKREKMAKLRE  345 (1002)
Q Consensus       287 g~~~~~e~~~~~~~~~~~~~~~~~~p~~~~~G~~~gi~~~~~DITe~~~~~~~~~~l~~  345 (1002)
                      ... ..+  .+... +..++.++..|+++.+|++.|++.++.|||++++.++++..+.+
T Consensus        96 ~~~-~~~--~~~~~-~g~~~~~~~~Pi~d~~G~~~g~v~~~~DITe~~~~e~ei~~l~~  150 (233)
T 3vol_A           96 LTG-VHK--AELNL-GGRRFSLDVVPVFNDANERLGSAVQWTDRTEEHRAEQEVSQLVQ  150 (233)
T ss_dssp             CCS-CEE--EEEEE-TTEEEEEEEEEEECTTCCEEEEEEEEEECHHHHHHHHHHHHHHH
T ss_pred             ccc-cee--EEEEE-CCEEEEEEEEEEECCCCCEEEEEEEEehhhHHHHHHHHHHHHHH
Confidence            322 122  22222 45678899999999999999999999999999888776655543

>2z6d_A Phototropin-2; PAS-fold, LOV-fold, alternative splicing, ATP-binding, chromophore, flavoprotein, FMN, kinase, membrane, nucleotide-binding; HET: FMN; 2.00A {Arabidopsis thaliana} PDB: 2z6c_A*

Probab=98.52  E-value=2.2e-07  Score=84.83  Aligned_cols=119  Identities=15%  Similarity=0.095  Sum_probs=87.0

Q ss_pred             HHHHHHHHHHhccCcEEEEec---ccccEEEeeccC---CCCCcccccCCCchhccCccchhhhhHHHHHHHHhCCCcce
Q 039716          219 RADNFLHFVLQNAPVVMGHQD---KELRYRFIYNHF---PSLHEEDILGKTDVEIFSGAGVKESQDFKREVLEKGLPAKR  292 (1002)
Q Consensus       219 ~~~~~l~~il~~~p~~i~~~d---~~~~~~~~~~~~---~~~~~e~iiGk~~~e~~~~~~~~~~~~~~~~vl~~g~~~~~  292 (1002)
                      +++..++.+++++|.+++..|   .++++.++|..+   .|+..++++|++..+++++.............+..+.+...
T Consensus         3 ~~~~~~~~~~~~~~~~i~~~d~~d~~~~i~~~N~~~~~~~g~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   82 (130)
T 2z6d_A            3 RVSQELKTALSTLQQTFVVSDATQPHCPIVYASSGFFTMTGYSSKEIVGRNCRFLQGPDTDKNEVAKIRDCVKNGKSYCG   82 (130)
T ss_dssp             ----CHHHHHHHTTCEEEEEETTSTTCCEEEECHHHHHHHCCCHHHHTTSCGGGGCCTTSCHHHHHHHHHHHHTTCCEEE
T ss_pred             hHHHHHHHHHHhcccceeeeeccCCCCcEEEecHHHHHHhCcCHHHHcCCChhhccCCCCCchHHHHHHHHHHcCCccee
Confidence            345667889999999999999   899999998764   57788899999998887765444444444556666666555


Q ss_pred             eEEEEEeecCceEEEEEEeeeecCCCCEEEEEEEeechhHHHHHH
Q 039716          293 EITFETELFGSKTFLIYVEPVFSKSGETIGVNYMGMDVTDQVRKR  337 (1002)
Q Consensus       293 e~~~~~~~~~~~~~~~~~~p~~~~~G~~~gi~~~~~DITe~~~~~  337 (1002)
                      ++.+....+...++.+...|+.+.+|.+.|+++++.|||++++.+
T Consensus        83 ~~~~~~~~g~~~~~~~~~~~~~~~~g~~~~~~~~~~Dit~~~~~e  127 (130)
T 2z6d_A           83 RLLNYKKDGTPFWNLLTVTPIKDDQGNTIKFIGMQVEVSKYTEGV  127 (130)
T ss_dssp             EEEEECTTSCEEEEEEEEEEEECTTSCEEEEEEEEEECCTTC---
T ss_pred             EEEEEcCCCcEEEEEEEEEEEECCCCCeeEEEEEEecchHHHHhh
Confidence            555444444455677888999999999999999999999876543

>3eeh_A Putative light and redox sensing histidine kinase; structural genomic MCSG, protein structure initiative, midwest center for STRU genomics; HET: PG5; 1.95A {Haloarcula marismortui}

Probab=98.47  E-value=3.1e-07  Score=83.75  Aligned_cols=117  Identities=14%  Similarity=0.080  Sum_probs=82.4

Q ss_pred             HHHHHHHHHHHHHHHhccCcEEEEeccc-ccEEEeeccC---CCCCcccccCCC--chhccCccchhhhhHHHHHHHHhC
Q 039716          214 SQILKRADNFLHFVLQNAPVVMGHQDKE-LRYRFIYNHF---PSLHEEDILGKT--DVEIFSGAGVKESQDFKREVLEKG  287 (1002)
Q Consensus       214 ~~~l~~~~~~l~~il~~~p~~i~~~d~~-~~~~~~~~~~---~~~~~e~iiGk~--~~e~~~~~~~~~~~~~~~~vl~~g  287 (1002)
                      ++.|++++.+++.+++++|.+++..|.+ +++.++|..+   .|+.+++++|+.  ..+.+++............ +..+
T Consensus         3 e~~l~~~~~~~~~~~~~~~~~i~~~d~~~~~i~~~n~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~   81 (125)
T 3eeh_A            3 KQQAAKSERRVRELTEATNDILWEFTADLSEVLVINSAYEDIWGRSVAKLRENPHDFLNGIHPEDRELMKDTMQS-LMDG   81 (125)
T ss_dssp             -------CHHHHHHHSCCCCEEEEEETTSSCEEEECTHHHHHHSSCHHHHHHCGGGGGGGBCHHHHHHHHHHHHH-HHTT
T ss_pred             HHHHHHHHHHHHHHHhcCCceEEEEEcCCCcEEEecHHHHHHHCCCHHHHccCcHHHHHhcCHHHHHHHHHHHHH-HHcC
Confidence            3456677888999999999999999999 9999998764   577888888876  4555555444444443433 3455


Q ss_pred             CCcceeEEEEEeecCceEEEEEEeeeecCCCCEEEEEEEeechh
Q 039716          288 LPAKREITFETELFGSKTFLIYVEPVFSKSGETIGVNYMGMDVT  331 (1002)
Q Consensus       288 ~~~~~e~~~~~~~~~~~~~~~~~~p~~~~~G~~~gi~~~~~DIT  331 (1002)
                      .+...++.+....+...++.+...|+.+.+|.+.++++++.|||
T Consensus        82 ~~~~~e~~~~~~~g~~~~~~~~~~~~~~~~g~~~~~~~~~~DIT  125 (125)
T 3eeh_A           82 ESADVECRVNATEEYQRWVWIQGEPITNDAGETVRVAGFARDIT  125 (125)
T ss_dssp             CCEEEEEEECGGGTTCEEEEEEEEEEECTTSCEEEEEEEEEECC
T ss_pred             CCccEEEEEEcCCCCEEEEEEecEEEECCCCCEEEEEEEEEecC
Confidence            55545555444444567778889999999999999999999997

>4eet_B Phototropin-2; LOV, blue light photoreceptor, signaling protein, flavoprote; HET: FMN; 1.20A {Arabidopsis thaliana} PDB: 4ees_A* 4eer_A* 4eep_A* 4eeu_A* 1jnu_A* 1g28_A*

Probab=98.47  E-value=2.8e-07  Score=83.34  Aligned_cols=107  Identities=15%  Similarity=0.080  Sum_probs=82.6

Q ss_pred             HHhccCcEEEEecc---cccEEEeeccC---CCCCcccccCCCchhccCccchhhhhHHHHHHHHhCCCcceeEEEEEee
Q 039716          227 VLQNAPVVMGHQDK---ELRYRFIYNHF---PSLHEEDILGKTDVEIFSGAGVKESQDFKREVLEKGLPAKREITFETEL  300 (1002)
Q Consensus       227 il~~~p~~i~~~d~---~~~~~~~~~~~---~~~~~e~iiGk~~~e~~~~~~~~~~~~~~~~vl~~g~~~~~e~~~~~~~  300 (1002)
                      .++++|.+++..|.   ++++.++|..+   .|++.++++|++..+++++.............+..+.+...++.+....
T Consensus         2 ~l~~~~~~i~~~d~~~~~g~i~~~N~~~~~~~g~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   81 (115)
T 4eet_B            2 SPEFIEKNFVITDPRLPDNPIIFASDGFLELTEYSREEILGRNARFLQGPETDQATVQKIRDAIRDQRETTVQLINYTKS   81 (115)
T ss_dssp             ---CCCCSEEEECTTSTTCCEEEECHHHHHHHCCCHHHHTTSCGGGGCCTTSCHHHHHHHHHHHHTTCCEEEEEEEECTT
T ss_pred             ccccCCCcEEEEcCCCCCCcEEEEcHHHHHHHCcCHHHHhCCCHHHhcCCCCChHHHHHHHHHHHcCCCcceEEEEecCC
Confidence            46889999999999   99999999865   5788899999998877766554444455566677777666666655444


Q ss_pred             cCceEEEEEEeeeecCCCCEEEEEEEeechhHH
Q 039716          301 FGSKTFLIYVEPVFSKSGETIGVNYMGMDVTDQ  333 (1002)
Q Consensus       301 ~~~~~~~~~~~p~~~~~G~~~gi~~~~~DITe~  333 (1002)
                      +...++.+...|+++.+|.+.|+++++.|||++
T Consensus        82 g~~~~~~~~~~~~~~~~g~~~~~~~~~~DITer  114 (115)
T 4eet_B           82 GKKFWNLLHLQPVRDQKGELQYFIGVQLDGSDH  114 (115)
T ss_dssp             CCEEEEEEEEEEEECTTSCEEEEEEEEEECSCC
T ss_pred             CCEEEEEEEEEEEECCCCCEEEEEEEEEeeccc
Confidence            555566788999999999999999999999975

>1d06_A Nitrogen fixation regulatory protein FIXL; oxygen sensor, histidine kinase, PAS, high-resolution, two-C system, signaling protein; HET: HEM; 1.40A {Sinorhizobium meliloti} SCOP: d.110.3.2 PDB: 1ew0_A*

Probab=98.46  E-value=7.3e-07  Score=84.22  Aligned_cols=120  Identities=13%  Similarity=0.068  Sum_probs=85.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHhccCcEEEEecccccEEEeecc---CCCCCcccccCCCchhccCccchhhhhHHHHHHHHh
Q 039716          210 VEELSQILKRADNFLHFVLQNAPVVMGHQDKELRYRFIYNH---FPSLHEEDILGKTDVEIFSGAGVKESQDFKREVLEK  286 (1002)
Q Consensus       210 ~~~~~~~l~~~~~~l~~il~~~p~~i~~~d~~~~~~~~~~~---~~~~~~e~iiGk~~~e~~~~~~~~~~~~~~~~vl~~  286 (1002)
                      +..+++.|++++..++.+++++|.+|+..|.++++.++|..   +.|++.++++|++..+++++................
T Consensus         4 ~~~~e~~l~~~~~~~~~l~~~~~d~i~~~d~~g~i~~~N~a~~~l~Gy~~~eliG~~~~~l~~~~~~~~~~~~~~~~~~~   83 (130)
T 1d06_A            4 MLETEDVVRARDAHLRSILDTVPDATVVSATDGTIVSFNAAAVRQFGYAEEEVIGQNLRILMPEPYRHEHDGYLQRYMAT   83 (130)
T ss_dssp             HHHHHHHHHHHTSCHHHHHTTCSSEEEEEETTSBEEEECHHHHHHHCCCHHHHTTSBGGGGSCTTHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHhhCcCeEEEECCCCeEEEEcHHHHHHHCCCHHHHcCCcHHHHCCchhHHHHHHHHHHHHhc
Confidence            45667788888889999999999999999999999999876   468899999999988887765433333333444444


Q ss_pred             CCC----cceeEEEEEeecCceEEEEEEeeeecCCCCEEEEEEEeechh
Q 039716          287 GLP----AKREITFETELFGSKTFLIYVEPVFSKSGETIGVNYMGMDVT  331 (1002)
Q Consensus       287 g~~----~~~e~~~~~~~~~~~~~~~~~~p~~~~~G~~~gi~~~~~DIT  331 (1002)
                      +..    ...++....+.+...++.+.+.|+.+.  ...+++++++|||
T Consensus        84 ~~~~~~~~~~e~~~~~kdG~~~~~~~~~~~~~~~--~~~~~~~~~~DIT  130 (130)
T 1d06_A           84 GEKRIIGIDRVVSGQRKDGSTFPMKLAVGEMRSG--GERFFTGFIRDLT  130 (130)
T ss_dssp             CCCSSTTSCEEEEEECTTSCEEEEEEEEEEEEET--TEEEEEEEEEECC
T ss_pred             CCccccCCeeEEEEEeCCCCEEEEEEEEEEEEEC--CeEEEEEEEEECc
Confidence            432    223444444444445566777888763  3345788889997

>2v0u_A NPH1-1, LOV2; kinase, transferase, ATP-binding, serine/threonine-protein kinase, light-induced signal trans phototropin1, nucleotide-binding; HET: FMN; 1.40A {Avena sativa} PDB: 2v0w_A* 2v1b_A* 2v1a_A* 1jnu_A* 1g28_A*

Probab=98.46  E-value=4e-07  Score=85.33  Aligned_cols=112  Identities=16%  Similarity=0.126  Sum_probs=87.0

Q ss_pred             HHHHHhccCcEEEEecc---cccEEEeeccC---CCCCcccccCCCchhccCccchhhhhHHHHHHHHhCCCcceeEEEE
Q 039716          224 LHFVLQNAPVVMGHQDK---ELRYRFIYNHF---PSLHEEDILGKTDVEIFSGAGVKESQDFKREVLEKGLPAKREITFE  297 (1002)
Q Consensus       224 l~~il~~~p~~i~~~d~---~~~~~~~~~~~---~~~~~e~iiGk~~~e~~~~~~~~~~~~~~~~vl~~g~~~~~e~~~~  297 (1002)
                      ++.+++++|.+++..|.   ++++.++|..+   .|+..++++|++..+++++.............+..+.+...++.+.
T Consensus         4 l~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~g~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   83 (146)
T 2v0u_A            4 LATTLERIEKNFVITDPRLPDNPIIFASDSFLQLTEYSREEILGRNCRFLQGPETDRATVRKIRDAIDNQTEVTVQLINY   83 (146)
T ss_dssp             CCCTGGGSSSCEEEECTTSTTCCEEEECHHHHHHHCCCHHHHTTSCGGGGCCTTSCHHHHHHHHHHHHTTCCEEEEEEEE
T ss_pred             HHHHHhcCCCcEEEEcCCCCCceEEEEcHHHHHHHCcCHHHHcCCCHHHhcCCcCChHHHHHHHHHHhcCCCcceEEEEE
Confidence            34578999999999999   99999998764   5778889999998888776554444455556677777665565554


Q ss_pred             EeecCceEEEEEEeeeecCCCCEEEEEEEeechhHHHH
Q 039716          298 TELFGSKTFLIYVEPVFSKSGETIGVNYMGMDVTDQVR  335 (1002)
Q Consensus       298 ~~~~~~~~~~~~~~p~~~~~G~~~gi~~~~~DITe~~~  335 (1002)
                      ...+...++.+...|+++.+|.+.|+++++.|||++++
T Consensus        84 ~~~g~~~~~~~~~~~~~~~~g~~~~~~~~~~Dit~~~~  121 (146)
T 2v0u_A           84 TKSGKKFWNLFHLQPMRDQKGDVQYFIGVQLDGTEHVR  121 (146)
T ss_dssp             CTTCCEEEEEEEEEEEECTTSCEEEEEEEEEEESSCCC
T ss_pred             ecCCcEEEEEEEEEEeECCCCCEEEEEEEEeechHHHH
Confidence            44444567778889999999999999999999998765

>3f1p_A Endothelial PAS domain-containing protein 1; PAS domain, heterodimer, internal cavity, activator, angiogenesis, congenital erythrocytosis; 1.17A {Homo sapiens} SCOP: d.110.3.7 PDB: 3f1o_A* 3f1n_A 3h7w_A* 3h82_A* 1p97_A 2a24_A 4h6j_A

Probab=98.46  E-value=1.6e-07  Score=86.81  Aligned_cols=105  Identities=8%  Similarity=0.178  Sum_probs=87.0

Q ss_pred             ccCcEEEEecccccEEEeeccC---CCCCcccccCCCchhccCccchhhhhHHHHHHHHhCCCcceeEEEEEeecCceEE
Q 039716          230 NAPVVMGHQDKELRYRFIYNHF---PSLHEEDILGKTDVEIFSGAGVKESQDFKREVLEKGLPAKREITFETELFGSKTF  306 (1002)
Q Consensus       230 ~~p~~i~~~d~~~~~~~~~~~~---~~~~~e~iiGk~~~e~~~~~~~~~~~~~~~~vl~~g~~~~~e~~~~~~~~~~~~~  306 (1002)
                      +++..|+..|.++++.++|..+   .|+++++++|++..+++++...+........++..+.+...++.+....+...++
T Consensus         7 ~~~~~i~~~d~~g~i~~~n~~~~~~~Gy~~~el~g~~~~~~~~p~d~~~~~~~~~~~~~~~~~~~~e~r~~~~dG~~~w~   86 (117)
T 3f1p_A            7 DSKTFLSEHSMDMKFTYCDDRITELIGYHPEELLGRSAYEFYHALDSENMTKSHQNLCTKGQVVSGQYRMLAKHGGYVWL   86 (117)
T ss_dssp             GGGEEEEEECTTCBEEEECTHHHHHHCCCHHHHTTSBGGGGBCGGGHHHHHHHHHHHHHHSEEECCCEEEECTTSSEEEE
T ss_pred             CCccEEEEECCCceEEEECcChhhhhCCCHHHHcCCchhheECHHHHHHHHHHHHHHHhCCCeeeeEEEEEecCCCEEEE
Confidence            4577889999999999999865   6889999999999999988877777666777777777666677776666666777


Q ss_pred             EEEEeeeecC-CCCEEEEEEEeechhHHH
Q 039716          307 LIYVEPVFSK-SGETIGVNYMGMDVTDQV  334 (1002)
Q Consensus       307 ~~~~~p~~~~-~G~~~gi~~~~~DITe~~  334 (1002)
                      .....|+++. +|.+.+++++..|||+++
T Consensus        87 ~~~~~~~~d~~~g~~~~iv~~~~DITer~  115 (117)
T 3f1p_A           87 ETQGTVIYNPRNLQPQCIMCVNYVLSEIE  115 (117)
T ss_dssp             EEEEEEEEETTTTEEEEEEEEEEECSCCB
T ss_pred             EEeeEEEECCCCCCceEEEEEeeeccccc
Confidence            7888999997 899999999999999864

>3icy_A Sensor protein; sensory box histidine kinase/response regulator domain, kinase, chlorobium tepidum TLS, PSI-2; 2.68A {Chlorobaculum tepidum}

Probab=98.45  E-value=7.4e-07  Score=81.37  Aligned_cols=112  Identities=13%  Similarity=0.023  Sum_probs=86.7

Q ss_pred             HHHHHHHHHhccCcEEEEecccccEEEeeccC---CCCCcccccCCCc--hhccCccchhhhhHHHHHHHHhCCCcceeE
Q 039716          220 ADNFLHFVLQNAPVVMGHQDKELRYRFIYNHF---PSLHEEDILGKTD--VEIFSGAGVKESQDFKREVLEKGLPAKREI  294 (1002)
Q Consensus       220 ~~~~l~~il~~~p~~i~~~d~~~~~~~~~~~~---~~~~~e~iiGk~~--~e~~~~~~~~~~~~~~~~vl~~g~~~~~e~  294 (1002)
                      +++.++.+++++|.+++..|.++++.++|..+   .|+++++++|+..  .+++++............++..+.+...++
T Consensus         2 s~~~~~~l~~~~~~~i~~~d~~~~~~~~n~~~~~~~G~~~~~~~~~~~~~~~~i~p~d~~~~~~~~~~~~~~~~~~~~e~   81 (118)
T 3icy_A            2 NAEELQALVDNIPAAIYHLDVSGQATIRFRPPAFLKTLVSEHAGTTRLNTLSMIHHDDRHMLSNAYSKLREAKHSLTLVY   81 (118)
T ss_dssp             HHHHHHHHHTTCCCCCEEECTTSCEEECCCCCGGGGGGEEEETTEEEEGGGGGBCGGGHHHHHHHHHHHHHSCCEEEEEE
T ss_pred             cHHHHHHHHhcCCceEEEEEcCCCceEEechhHhhcCCCHHHccCChhHHHHHcCHHHHHHHHHHHHHHHhcCCCceEEE
Confidence            35678899999999999999999999998765   4667778777653  566666666666666666777776655666


Q ss_pred             EEEEeecCceEEEEEEeeeecCCCCEEEEEEEeechh
Q 039716          295 TFETELFGSKTFLIYVEPVFSKSGETIGVNYMGMDVT  331 (1002)
Q Consensus       295 ~~~~~~~~~~~~~~~~~p~~~~~G~~~gi~~~~~DIT  331 (1002)
                      .+....+...++.....|+++.+|.+.+++++..|||
T Consensus        82 r~~~~~g~~~w~~~~~~~~~~~~g~~~~~~g~~~DIT  118 (118)
T 3icy_A           82 RIVTPEGKLHWIEDHMRSSFSDDGLFSGIDGILCEVT  118 (118)
T ss_dssp             EEECTTCCEEEEEEEEEEEECTTSCEEEEEEEEEECC
T ss_pred             EEECCCCCEEEEEEEEEEEECCCCCEEEEEEEEEecC
Confidence            6655555556777888999999999999999999997

>1v9y_A Heme PAS sensor protein; signaling protein; HET: HEM; 1.32A {Escherichia coli} SCOP: d.110.3.2 PDB: 1v9z_A* 1vb6_A* 1s67_L* 1s66_L*

Probab=98.38  E-value=6.2e-07  Score=87.32  Aligned_cols=130  Identities=14%  Similarity=0.092  Sum_probs=73.7

Q ss_pred             hHHHHHHHHHHHHHHHHHHHhccCcEEEEecccccEEEeeccC---CCCCcccccCCCchhccCccchhhhhHHHHHHHH
Q 039716          209 PVEELSQILKRADNFLHFVLQNAPVVMGHQDKELRYRFIYNHF---PSLHEEDILGKTDVEIFSGAGVKESQDFKREVLE  285 (1002)
Q Consensus       209 ~~~~~~~~l~~~~~~l~~il~~~p~~i~~~d~~~~~~~~~~~~---~~~~~e~iiGk~~~e~~~~~~~~~~~~~~~~vl~  285 (1002)
                      .+.+..+.+++++..++.+++++|.+++..|.++++.++|..+   .|+..++++|++..+++++............+..
T Consensus        27 ~~~~~~~~~~~~~~~~~~~l~~~~~~i~~~d~~g~i~~~N~~~~~l~g~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~  106 (167)
T 1v9y_A           27 VIMKLTDADNAADGIFFPALEQNMMGAVLINENDEVMFFNPAAEKLWGYKREEVIGNNIDMLIPRDLRPAHPEYIRHNRE  106 (167)
T ss_dssp             -------------CCHHHHHHTCSSEEEEECTTSBEEEECHHHHHHHSCCGGGTTTSBGGGGSCGGGTTTHHHHHHHHHC
T ss_pred             HHHHHHHHHhhhhHHHHHHHHhCCCCEEEECCCCcEEEECHHHHHHhCCCHHHHcCCChhhccCccccchHHHHHHHHhh
Confidence            3444555667777888999999999999999999999998764   5788899999999888876554444444444544


Q ss_pred             hCCC----cceeEEEEEeecCceEEEEEEeeeecCCCCEEEEEEEeechhHHHHHHHHH
Q 039716          286 KGLP----AKREITFETELFGSKTFLIYVEPVFSKSGETIGVNYMGMDVTDQVRKREKM  340 (1002)
Q Consensus       286 ~g~~----~~~e~~~~~~~~~~~~~~~~~~p~~~~~G~~~gi~~~~~DITe~~~~~~~~  340 (1002)
                      .+..    ...++.+....+...++.+...|+ +..|.+ ++++++.|||++++.++++
T Consensus       107 ~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~-~~~g~~-~~~~~~~DiT~~~~~e~~l  163 (167)
T 1v9y_A          107 GGKARVEGMSRELQLEKKDGSKIWTRFALSKV-SAEGKV-YYLALVRDASVEMAQKEQT  163 (167)
T ss_dssp             ----------CEEEEECTTSCEEEEEEEEEEE-EETTEE-EEEEEEEC-----------
T ss_pred             cCCCcccccceEEEEEcCCCcEEEEEEEEEEE-ecCCCE-EEEEEEecCcHHHHHHHHH
Confidence            4332    223444433334445666777788 556665 4888999999987665443

>1b63_A MUTL; DNA mismatch repair, ATPase; HET: ANP; 1.90A {Escherichia coli K12} SCOP: d.14.1.3 d.122.1.2 PDB: 1nhh_A* 1nhi_A* 1bkn_A 1nhj_A* 1b62_A*

Probab=98.36  E-value=4.9e-07  Score=101.09  Aligned_cols=58  Identities=24%  Similarity=0.275  Sum_probs=44.5

Q ss_pred             EEEEEecCCCCCcCcHhhhhhhccCCCccc------cCcCCCccccHHHHHHHHHHhCCEEEEEeecCC
Q 039716          593 RCDVYDTGIGIPENALPTLFRKYMQVSADH------ARKYGGTGLGLAICKQLVELMGGRLTVTSKVHC  655 (1002)
Q Consensus       593 ~i~V~DtGiGI~~e~l~~IF~pF~q~~~~~------~~~~~GtGLGLaI~k~Lve~~gG~I~v~S~~g~  655 (1002)
                      .|+|.|+|+||+++++..+|.+|++.+...      ....|+.|+||+.+..+     +++.|.|....
T Consensus        55 ~i~V~DnG~Gi~~~~l~~~~~~~~tsK~~~~~d~~~~~~~G~~G~gl~si~~v-----s~l~v~s~~~~  118 (333)
T 1b63_A           55 LIRIRDNGCGIKKDELALALARHATSKIASLDDLEAIISLGFRGEALASISSV-----SRLTLTSRTAE  118 (333)
T ss_dssp             EEEEEECSCCCCGGGHHHHHSTTCCSSCCSHHHHHTCCSSCCSSCHHHHHHTT-----SEEEEEEECTT
T ss_pred             EEEEEEcCCCcCHHHHHHhhhcccccCccccchhhhccccCccccchhhhhcC-----CcEEEEEecCC
Confidence            478999999999999999999998764321      12456799999987554     36888887643

>2qkp_A Uncharacterized protein; structural genomics, unknown function, PSI-2, protein struct initiative; 1.75A {Streptococcus mutans}

Probab=98.35  E-value=2.4e-06  Score=84.34  Aligned_cols=112  Identities=13%  Similarity=0.140  Sum_probs=82.4

Q ss_pred             HHHHHHHhccCcEEEEecccccEEEeecc---CCCC--CcccccCCCchhccCccchhhhhHHHHHHHHhCCCcceeEEE
Q 039716          222 NFLHFVLQNAPVVMGHQDKELRYRFIYNH---FPSL--HEEDILGKTDVEIFSGAGVKESQDFKREVLEKGLPAKREITF  296 (1002)
Q Consensus       222 ~~l~~il~~~p~~i~~~d~~~~~~~~~~~---~~~~--~~e~iiGk~~~e~~~~~~~~~~~~~~~~vl~~g~~~~~e~~~  296 (1002)
                      ..+..+++++|.+|...|.++++.|+|..   +..+  ..++++|++..+++++.... .......++++|.+...++.+
T Consensus        19 ~~l~~IL~~~~~gI~~vD~~g~I~~~N~a~~~~~~i~g~~~~~iGr~v~~~~~~~~~~-~v~~i~~~l~~g~~~~~~~~~   97 (151)
T 2qkp_A           19 EQANLILNHLPLEITFVNKDDIFQYYNDSVPAAEMVFKRTPSQVGRNVELCHPPKVLD-KVKKVFELLRNGQRDKVNMWF   97 (151)
T ss_dssp             HHHHHHHHHSSSEEEEEETTSBEEEECCCSCGGGCSSCCCGGGTTSBGGGSSCHHHHH-HHHHHHHHHHTTSBSEEEEEE
T ss_pred             HHHHHHHHhCCCceEEEcCCCeEEEEeCCCchhhhhcCCCHHHcCCCHHHhCCHHHHH-HHHHHHHHHHcCCccEEEEEE
Confidence            45778999999999999999999999988   4333  35789999999987743222 112234456667765554443


Q ss_pred             EEeecC-ceEEEEEEeeeecCCCCEEEEEEEeechhHHHHH
Q 039716          297 ETELFG-SKTFLIYVEPVFSKSGETIGVNYMGMDVTDQVRK  336 (1002)
Q Consensus       297 ~~~~~~-~~~~~~~~~p~~~~~G~~~gi~~~~~DITe~~~~  336 (1002)
                        ...+ .+.+.+...|+++.+|+++|++.++.|||+.++.
T Consensus        98 --~~~~~~~~v~v~~~Pi~d~~G~~~G~vev~~Dit~l~~l  136 (151)
T 2qkp_A           98 --QSERLGKFVYVTYAAVRDQAGDFQGVLEYVQDIKPFFEL  136 (151)
T ss_dssp             --EETTTTEEEEEEEEEEECTTCCEEEEEEEEEECGGGGGG
T ss_pred             --ecCCCCeEEEEEEEEEECCCCCEEEEEEEEEECHHHHhh
Confidence              2222 5667888899999999999999999999976543

>1kij_A DNA gyrase subunit B; topoisomerase, gyrase B-coumarin complex, isomerase; HET: DNA NOV; 2.30A {Thermus thermophilus} SCOP: d.14.1.3 d.122.1.2

Probab=98.34  E-value=3.6e-07  Score=104.06  Aligned_cols=51  Identities=24%  Similarity=0.346  Sum_probs=39.4

Q ss_pred             EEEEEecCCCCCcCcHhh--------hhhhccCCCcc----ccCcCCCccccHHHHHHHHHHh
Q 039716          593 RCDVYDTGIGIPENALPT--------LFRKYMQVSAD----HARKYGGTGLGLAICKQLVELM  643 (1002)
Q Consensus       593 ~i~V~DtGiGI~~e~l~~--------IF~pF~q~~~~----~~~~~~GtGLGLaI~k~Lve~~  643 (1002)
                      .|+|.|+|+|||++.+++        +|.+|+....-    .....|+.|+||++|+.+++.+
T Consensus        65 ~i~V~DnG~GIp~~~~~~~~~~~~e~if~~~~~~~kf~~~~~~~s~G~~G~Gls~v~als~~~  127 (390)
T 1kij_A           65 SLTVEDNGRGIPVDLMPEEGKPAVEVIYNTLHSGGKFEQGAYKVSGGLHGVGASVVNALSEWT  127 (390)
T ss_dssp             CEEEEECSSCCCCSEETTTTEEHHHHHHHSSCEESGGGGSSCCCCSCSSTTSHHHHHHTEEEE
T ss_pred             EEEEEEcCCCCCHHHhhhccccchhhheeeeeecccccCccccccCCCCCcceeeecccccce
Confidence            378999999999999988        99988765321    1113457999999999999754

>3mqq_A Transcriptional regulator, LUXR family; PAS domain, PSI, MCSG, structural genomics, center for structural genomics; 1.65A {Burkholderia thailandensis} PDB: 3mqo_A

Probab=98.31  E-value=7e-07  Score=82.85  Aligned_cols=111  Identities=6%  Similarity=-0.024  Sum_probs=77.0

Q ss_pred             HHHHHHhccCcEEEEecccccEEEeeccC---CCCCcccccCCCchhccCccch-hhhhHHHHHHHHhCCCcceeEEEEE
Q 039716          223 FLHFVLQNAPVVMGHQDKELRYRFIYNHF---PSLHEEDILGKTDVEIFSGAGV-KESQDFKREVLEKGLPAKREITFET  298 (1002)
Q Consensus       223 ~l~~il~~~p~~i~~~d~~~~~~~~~~~~---~~~~~e~iiGk~~~e~~~~~~~-~~~~~~~~~vl~~g~~~~~e~~~~~  298 (1002)
                      .++.+++++|.+|+ .|.++++.++|..+   .|+++++++|++..+++++... ..........+..+.+...++.+..
T Consensus         4 ~~~~~~~~~~~~i~-~~~~g~i~~~N~a~~~l~G~~~~el~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~   82 (120)
T 3mqq_A            4 DYKTAFHLAPIGLV-LSRDRVIEDCNDELAAIFRCARADLIGRSFEVLYPSSDEFERIGERISPVMIAHGSYADDRIMKR   82 (120)
T ss_dssp             CHHHHHHHCSSEEE-EEETTEEEEECHHHHHHTTSCHHHHTTCBGGGGSSSHHHHHHHHHHHHHHHHHHSCEEEEEEEEC
T ss_pred             hHHHHHhcCCceEE-EecCCEEHHHHHHHHHHhCcCHHHhCCCchhhccCChhhHHHHHHHHHHHHhcCCcceEEEEEEe
Confidence            36789999999996 47899999999865   6888999999998888765322 2233333444555656556666555


Q ss_pred             eecCceEEEEEEeeeecCCCCEEEEEEEeechhHHHH
Q 039716          299 ELFGSKTFLIYVEPVFSKSGETIGVNYMGMDVTDQVR  335 (1002)
Q Consensus       299 ~~~~~~~~~~~~~p~~~~~G~~~gi~~~~~DITe~~~  335 (1002)
                      ..+...+..+...|+ +..|...|+++++.|||++++
T Consensus        83 ~dG~~~~~~~~~~~~-~~~~~~~~~v~~~~DITerk~  118 (120)
T 3mqq_A           83 AGGELFWCHVTGRAL-DRTAPLAAGVWTFEDLSATRR  118 (120)
T ss_dssp             TTSCEEEEEEEEEES-STTSTTSSEEEEEEESCC---
T ss_pred             CCCCEEEEEEEEEEC-CCCCCceeEEEEEEcccHhhc
Confidence            544445556777777 556666788889999999765

>2wkq_A NPH1-1, RAS-related C3 botulinum toxin substrate 1; transferase, cell adhesion, nucleotide-binding, protein engineering, RAS superfamily LOV2; HET: GTP FMN; 1.60A {Avena sativa} PDB: 2wkr_A* 2wkp_A*

Probab=98.28  E-value=2e-06  Score=95.59  Aligned_cols=114  Identities=15%  Similarity=0.126  Sum_probs=90.6

Q ss_pred             HHHhccCcEEEEecc---cccEEEeeccC---CCCCcccccCCCchhccCccchhhhhHHHHHHHHhCCCcceeEEEEEe
Q 039716          226 FVLQNAPVVMGHQDK---ELRYRFIYNHF---PSLHEEDILGKTDVEIFSGAGVKESQDFKREVLEKGLPAKREITFETE  299 (1002)
Q Consensus       226 ~il~~~p~~i~~~d~---~~~~~~~~~~~---~~~~~e~iiGk~~~e~~~~~~~~~~~~~~~~vl~~g~~~~~e~~~~~~  299 (1002)
                      .+++++|.+|+..|.   ++++.++|..+   .|+++++++|++..+++++.............+..+.+...++.+...
T Consensus        15 ~~~~~~~~~i~~~D~~~~~g~i~~~N~a~~~l~G~~~~el~G~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~   94 (332)
T 2wkq_A           15 TTLERIEKNFVITDPRLPDNPIIFASDSFLQLTEYSREEILGRNARFLQGPETDRATVRKIRDAIDNQTEVTVQLINYTK   94 (332)
T ss_dssp             CCGGGCCSEEEEECTTSTTCCEEEECHHHHHHHCCCHHHHTTSCGGGGCCTTCCHHHHHHHHHHHHTTCCEEEEEEEECT
T ss_pred             hHhhcCCCcEEEecCCCCCCCEEEeehHHHHHhCCCHHHHcCCCchhhcCCCCCHHHHHHHHHHHHcCCeeEEEEEEEcC
Confidence            467899999999999   99999999865   688999999999988877655444445556677777776666666555


Q ss_pred             ecCceEEEEEEeeeecCCCCEEEEEEEeechhHHHHHHHH
Q 039716          300 LFGSKTFLIYVEPVFSKSGETIGVNYMGMDVTDQVRKREK  339 (1002)
Q Consensus       300 ~~~~~~~~~~~~p~~~~~G~~~gi~~~~~DITe~~~~~~~  339 (1002)
                      .+...++.+...|+++..|.+.|++++..|||++++.+++
T Consensus        95 dG~~~~~~~~~~pi~d~~g~~~~~v~~~~DITe~k~~e~~  134 (332)
T 2wkq_A           95 SGKKFWNLFHLQPMRDQKGDVQYFIGVQLDGTEHVRDAAE  134 (332)
T ss_dssp             TCCEEEEEEEEEEEECTTSCEEEEEEEEEEESSCCCHHHH
T ss_pred             CCCEEEEeeEEEEeEcCCCCEEEEEEEeccCchhhhhhhh
Confidence            5555677788999999999999999999999997655443

>3ewk_A Sensor protein; PAS domain, alpha/beta fold, kinase, phosphoprotein, transfe flavoprotein; HET: FAD; 2.34A {Methylococcus capsulatus}

Probab=98.27  E-value=3.1e-06  Score=88.69  Aligned_cols=106  Identities=14%  Similarity=0.108  Sum_probs=80.6

Q ss_pred             EEEecccccEEEeeccC---CCCCcccccCCCchhccCccchhhhhHHHHHHHHhCCCcceeEEEEEeecCceEEEEEEe
Q 039716          235 MGHQDKELRYRFIYNHF---PSLHEEDILGKTDVEIFSGAGVKESQDFKREVLEKGLPAKREITFETELFGSKTFLIYVE  311 (1002)
Q Consensus       235 i~~~d~~~~~~~~~~~~---~~~~~e~iiGk~~~e~~~~~~~~~~~~~~~~vl~~g~~~~~e~~~~~~~~~~~~~~~~~~  311 (1002)
                      |+..|.++++.++|..|   .|++.++++|++...+.++...........+.+..+.+...++.+..+.+...++.....
T Consensus         2 i~i~D~~g~i~~~N~a~~~l~Gy~~~el~G~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~dG~~~~~~~~~~   81 (227)
T 3ewk_A            2 VSITDLQGRILYANDNFCAVSRYGREELVGQDHRIVNSGYHGKAYIRDMWRTISRGNIWQGEFCNRRKDGTRYWVDSTIV   81 (227)
T ss_dssp             EEEEETTCBEEEECHHHHHHTTCCHHHHTTSBGGGGCCSCSCHHHHHHHHHHHTTTCCEEEEEEEECSSSCEEEEEEEEE
T ss_pred             EEEECCCCcEEehHHHHHHHHCcCHHHHcCCCHHHcCCCCCCHHHHHHHHHHHHcCCeEEEEEEEEcCCCCEEeeeeEEE
Confidence            56789999999999865   688999999999877766544333333334455667666667766655555566678889


Q ss_pred             eeecCCCCEEEEEEEeechhHHHHHHHHH
Q 039716          312 PVFSKSGETIGVNYMGMDVTDQVRKREKM  340 (1002)
Q Consensus       312 p~~~~~G~~~gi~~~~~DITe~~~~~~~~  340 (1002)
                      |+++.+|.+.+++++..|||+++++++++
T Consensus        82 p~~d~~g~~~~~~~~~~DIT~~k~~e~~l  110 (227)
T 3ewk_A           82 PLMDNAGKPRQYISIRRDITAQKEAEAQL  110 (227)
T ss_dssp             EEECSSSCEEEEEEEEEECTTTTHHHHHH
T ss_pred             EEEcCCCCEEEEEEEEEehhhHHHHHHHH
Confidence            99999999999999999999987766554

>1h7s_A PMS1 protein homolog 2; DNA repair, GHL ATPase, mismatch repair, HNPCC; 1.95A {Homo sapiens} SCOP: d.14.1.3 d.122.1.2 PDB: 1h7u_A* 1ea6_A*

Probab=98.27  E-value=1.6e-06  Score=97.91  Aligned_cols=57  Identities=21%  Similarity=0.180  Sum_probs=35.8

Q ss_pred             EEEEEecCCCCCcCcHhhhhhhccCCCcccc-----CcCCCc-cccHHHHHHHHHHhCCEEEEEeecC
Q 039716          593 RCDVYDTGIGIPENALPTLFRKYMQVSADHA-----RKYGGT-GLGLAICKQLVELMGGRLTVTSKVH  654 (1002)
Q Consensus       593 ~i~V~DtGiGI~~e~l~~IF~pF~q~~~~~~-----~~~~Gt-GLGLaI~k~Lve~~gG~I~v~S~~g  654 (1002)
                      .|+|.|+|+||+++.++++|++|++.+....     ....|. |+||+.+..+    . .+.|.|...
T Consensus        65 ~I~V~DnG~Gi~~~~l~~~f~~~~tsK~~~~~dl~~i~s~G~rG~gl~si~~v----s-~v~v~t~~~  127 (365)
T 1h7s_A           65 LIEVSDNGCGVEEENFEGLTLKHHTSKIQEFADLTQVETFGFRGEALSSLCAL----S-DVTISTCHA  127 (365)
T ss_dssp             EEEEEECSCCCCGGGSGGGGC----------CCTTCSEEESSSSSHHHHHHHH----S-EEEEEEECT
T ss_pred             EEEEEECCCCcCHHHHHHHhhhccccccccccchhcccccCCCCchhhhhhhh----c-cEEEEEccC
Confidence            5789999999999999999999998654321     112244 9999877654    2 677777653

>1n9l_A PHOT-LOV1, putative blue light receptor; phototropin, flavin, electron transport; HET: FMN; 1.90A {Chlamydomonas reinhardtii} SCOP: d.110.3.6 PDB: 1n9n_A* 1n9o_A*

Probab=98.26  E-value=2.8e-06  Score=77.98  Aligned_cols=102  Identities=14%  Similarity=0.091  Sum_probs=75.8

Q ss_pred             cCcEEEEec---ccccEEEeeccC---CCCCcccccCCCchhccCccchhhhhHHHHHHHHhCCCcceeEEEEEeecCce
Q 039716          231 APVVMGHQD---KELRYRFIYNHF---PSLHEEDILGKTDVEIFSGAGVKESQDFKREVLEKGLPAKREITFETELFGSK  304 (1002)
Q Consensus       231 ~p~~i~~~d---~~~~~~~~~~~~---~~~~~e~iiGk~~~e~~~~~~~~~~~~~~~~vl~~g~~~~~e~~~~~~~~~~~  304 (1002)
                      ++.+|+..|   .++++.++|..|   .|++.++++|++...+.++.............+..+.+...++....+.+...
T Consensus         2 ~~~~i~i~d~~~~~g~i~~~N~a~~~l~Gy~~~e~~G~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~kdG~~~   81 (109)
T 1n9l_A            2 LRHTFVVADATLPDCPLVYASEGFYAMTGYGPDEVLGHNCRFLQGEGTDPKEVQKIRDAIKKGEACSVRLLNYRKDGTPF   81 (109)
T ss_dssp             CSCEEEEEETTSTTCCEEEECHHHHHHHCCCHHHHTTSCGGGGCCTTCCHHHHHHHHHHHHHTCCEEEEEEEECTTSCEE
T ss_pred             CccEEEEEcCCCCCCeEEEEchHHHHHHCcCHHHHcCCCchhcCCCCCCHHHHHHHHHHHHcCCcEEEEEEEEcCCCCEE
Confidence            456777788   479999999865   58899999999876655443332233344556677777666666655555556


Q ss_pred             EEEEEEeeeecCCCCEEEEEEEeechhH
Q 039716          305 TFLIYVEPVFSKSGETIGVNYMGMDVTD  332 (1002)
Q Consensus       305 ~~~~~~~p~~~~~G~~~gi~~~~~DITe  332 (1002)
                      +..+.+.|+++.+|.+.+++++..|||+
T Consensus        82 ~~~~~~~pi~d~~G~~~~~v~~~~DITe  109 (109)
T 1n9l_A           82 WNLLTVTPIKTPDGRVSKFVGVQVDVTS  109 (109)
T ss_dssp             EEEEEEEEEECTTSCEEEEEEEEEECCC
T ss_pred             EEEEEEEEEECCCCCEEEEEEEEEeCCC
Confidence            7778899999999999999999999985

>4hi4_A Aerotaxis transducer AER2; PAS domain, diatomic GAS sensor, signaling protein; HET: HEM GOL; 2.30A {Pseudomonas aeruginosa}

Probab=98.26  E-value=6.1e-06  Score=77.19  Aligned_cols=102  Identities=17%  Similarity=0.268  Sum_probs=75.0

Q ss_pred             HHHHHHHhccCcEEEEecccccEEEeeccCC---------------CCCcccccCCCchhccCccchhhhhHHHHHHHHh
Q 039716          222 NFLHFVLQNAPVVMGHQDKELRYRFIYNHFP---------------SLHEEDILGKTDVEIFSGAGVKESQDFKREVLEK  286 (1002)
Q Consensus       222 ~~l~~il~~~p~~i~~~d~~~~~~~~~~~~~---------------~~~~e~iiGk~~~e~~~~~~~~~~~~~~~~vl~~  286 (1002)
                      .+++.+++++|.+|...|.++++.++|.++.               |+..++++|++..++++..      ...+.++..
T Consensus         5 ~rl~~il~~~~~gviv~D~~g~I~~~N~a~~~llg~~~~~i~~~~~g~~~~~~~G~~~~~~~~~~------~~~~~~~~~   78 (121)
T 4hi4_A            5 ARIASALDNVSANVMIADNDLNIIYMNRTVSEMLGRAEADIRKQLPNFDAGRLMGANIDVFHKNP------AHQRHLLAN   78 (121)
T ss_dssp             HHHHHHHTTSSSEEEEEETTCBEEEECHHHHHHHHHTHHHHHHHCTTCCGGGCTTCBGGGGCSSH------HHHHHHHHH
T ss_pred             HHHHHHHhcCCccEEEEcCCCeEEEecHHHHHHHHHHHHHHHHhcCCCChHHhcCCCHHHhcCCH------HHHHHHHhC
Confidence            3578899999999999999999999997643               3677899999988887542      122344554


Q ss_pred             CCCcceeEEEEEeecCceEEEEEEeeeecCCCCEEEEEEEeechhHH
Q 039716          287 GLPAKREITFETELFGSKTFLIYVEPVFSKSGETIGVNYMGMDVTDQ  333 (1002)
Q Consensus       287 g~~~~~e~~~~~~~~~~~~~~~~~~p~~~~~G~~~gi~~~~~DITe~  333 (1002)
                      ... ..+..+  .. +..++.+++.|+++.+|++.|+++++.|||++
T Consensus        79 ~~~-~~~~~~--~~-~~~~~~~~~~pi~~~~g~~~g~v~~~~DiTee  121 (121)
T 4hi4_A           79 LTG-VHKAEL--NL-GGRRFSLDVVPVFNDANARLGSAVQWTDRTEE  121 (121)
T ss_dssp             CSS-CEEEEE--EE-TTEEEEEEEEEEECTTSCEEEEEEEEEECC--
T ss_pred             cCC-CcEEEE--EE-CCEEEEEEEEEEECCCCCEEEEEEEEEEecCC
Confidence            431 112222  22 45677889999999999999999999999973

>3na3_A DNA mismatch repair protein MLH1; MUTL protein homolog 1, DNA damag repair, structural genomics consortium, SGC, protein bindin; HET: DNA ATP; 2.50A {Homo sapiens}

Probab=98.21  E-value=2e-06  Score=95.89  Aligned_cols=58  Identities=22%  Similarity=0.348  Sum_probs=42.0

Q ss_pred             EEEEEecCCCCCcCcHhhhhhhccCCCcccc------CcCCCccccHHHHHHHHHHhCCEEEEEeecCC
Q 039716          593 RCDVYDTGIGIPENALPTLFRKYMQVSADHA------RKYGGTGLGLAICKQLVELMGGRLTVTSKVHC  655 (1002)
Q Consensus       593 ~i~V~DtGiGI~~e~l~~IF~pF~q~~~~~~------~~~~GtGLGLaI~k~Lve~~gG~I~v~S~~g~  655 (1002)
                      .|+|.|+|+||+++.++.+|+||++.+....      ..+|--|.||+-+..+.     .+.|.|....
T Consensus        59 ~I~V~DnG~GI~~~~l~~~~~~~~tsK~~~~~dl~~i~s~GfrGeaL~Si~avs-----~l~v~sr~~~  122 (348)
T 3na3_A           59 LIQIQDNGTGIRKEDLDIVCERFTTSKLQSFEDLASISTYGFRGEALASISHVA-----HVTITTKTAD  122 (348)
T ss_dssp             EEEEEECSCCCCGGGGGTTTSTTCCSSCCCC---------CCTTCHHHHHHHSS-----EEEEEEECTT
T ss_pred             EEEEEECCcCcChHHhhhhhccccccccCcchhhhccccCCcCChHHHHhhccc-----EEEEEEEECC
Confidence            5789999999999999999999998764321      12344578887555442     6899887643

>3fc7_A HTR-like protein, sensor protein; APC87712.1, HTR-like protein,haloarcula marismortui ATCC 430 structural genomics, PSI-2; 2.65A {Haloarcula marismortui}

Probab=98.21  E-value=1.4e-06  Score=80.46  Aligned_cols=105  Identities=10%  Similarity=0.136  Sum_probs=71.1

Q ss_pred             HHHHHHHHHhccCcEEEEecccccEEEeeccC---CCCCcccccCCCchhccCccchhhhhHHHHHHHHhCCCcceeEEE
Q 039716          220 ADNFLHFVLQNAPVVMGHQDKELRYRFIYNHF---PSLHEEDILGKTDVEIFSGAGVKESQDFKREVLEKGLPAKREITF  296 (1002)
Q Consensus       220 ~~~~l~~il~~~p~~i~~~d~~~~~~~~~~~~---~~~~~e~iiGk~~~e~~~~~~~~~~~~~~~~vl~~g~~~~~e~~~  296 (1002)
                      ++.+++.+++++|.+|+..|.++++.++|..+   .|+.+++++|++..+++++............+...+.+.      
T Consensus        17 ~~~~~~~i~~~~~~~i~~~d~~g~i~~~N~~~~~~~g~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~------   90 (125)
T 3fc7_A           17 TRKKFESLVSDSPDGIVHLTTNGTILSVNPSMAGRLGADPDTLVGQQLSAVMDSEAANQRLEAGKSAVENGTAT------   90 (125)
T ss_dssp             ---------CCSCCEEEEEETTSBEEEECHHHHHHHTSCHHHHTTSBGGGSSCHHHHHHHHHHHHHHHHHTSCE------
T ss_pred             HHHHHHHHHhcCCCeEEEEcCCCeEEEECHHHHHHhCCCHHHHcCccHHHhCCHHHHHHHHHHHHHHhcCCCeE------
Confidence            67788999999999999999999999999864   578889999999999885433333333335566666432      


Q ss_pred             EEeecC-ceEEEEEEeeeecCCCCEEEEEEEeechh
Q 039716          297 ETELFG-SKTFLIYVEPVFSKSGETIGVNYMGMDVT  331 (1002)
Q Consensus       297 ~~~~~~-~~~~~~~~~p~~~~~G~~~gi~~~~~DIT  331 (1002)
                      ....+. ..++.+...|+.+. |...|+++++.|||
T Consensus        91 ~~~~~~~~~~~~~~~~p~~~~-~~~~~~~~~~~DIT  125 (125)
T 3fc7_A           91 RSEDAVGGRHYHNQYIPVDSH-RKSDTFQLVSRDIT  125 (125)
T ss_dssp             EEEEEETTEEEEEEEEESSTT-TTTTEEEEEEEECC
T ss_pred             EeEcCCCcEEEEEEEEeEecC-CCeEEEEEEEecCC
Confidence            122233 67788889998765 66678899999997

>3ke6_A Protein RV1364C/MT1410; anti-sigma factor, anti-sigma factor antagonist, phosphatase serine kinase, ATPase, unknown function; 2.60A {Mycobacterium tuberculosis}

Probab=98.21  E-value=2.2e-06  Score=98.40  Aligned_cols=55  Identities=25%  Similarity=0.274  Sum_probs=35.5

Q ss_pred             EEEEEEEecCCCCCcCcHhhhhhhccCCCccccCcCCCccccHHHHHHHHHHhCCEEEEEeecCCceEEEEEEeCCC
Q 039716          591 WIRCDVYDTGIGIPENALPTLFRKYMQVSADHARKYGGTGLGLAICKQLVELMGGRLTVTSKVHCGSTFTFILPYQV  667 (1002)
Q Consensus       591 ~l~i~V~DtGiGI~~e~l~~IF~pF~q~~~~~~~~~~GtGLGLaI~k~Lve~~gG~I~v~S~~g~GTtF~~~LP~~~  667 (1002)
                      .++|+|.|+|+|+++.            .     ...+.|+||.|++.+++.+    .+.+. +.|+++++.+|+..
T Consensus       333 ~l~i~V~D~G~g~~~~------------~-----~~~~~G~GL~lv~~l~~~~----~~~~~-~~G~~v~~~~~~~~  387 (399)
T 3ke6_A          333 NVRASVIDRGQWKDHR------------D-----GARGRGRGLAMAEALVSEA----RIMHG-AGGTTATLTHRLSR  387 (399)
T ss_dssp             EEEEEEEESCBC-----------------------------CHHHHHTTSSEE----EEEEE-TTEEEEEEEEECEE
T ss_pred             EEEEEEEECCCCCCCC------------C-----CCCCCCcHHHHHHHHHHhe----eeEEC-CCcEEEEEEEEcCC
Confidence            4889999999999976            0     1136799999999998754    45554 56999999999753

>2vv6_A FIXL, sensor protein FIXL; signaling protein, transferase, phosphoprotein, nitrogen FIX PER-ARNT-SIM, metal-binding, PAS, iron, heme; HET: HEM; 1.5A {Bradyrhizobium japonicum} PDB: 1xj6_A* 1xj4_A* 2vv7_A* 2vv8_A* 1lsw_A* 1dp8_A* 1dp9_A* 1drm_A* 1lsv_A* 1dp6_A* 1lsx_A* 1lt0_A* 1y28_A* 2cmn_A* 1xj3_A* 1xj2_A* 2owh_A* 2owj_A*

Probab=98.18  E-value=5.5e-06  Score=76.65  Aligned_cols=109  Identities=10%  Similarity=0.018  Sum_probs=67.5

Q ss_pred             ccCcEEEEecccccEEEeeccC---CCCCcccccCCCchhccCccchhhhhHHHHHHHHhCCC----cceeEEEEEeecC
Q 039716          230 NAPVVMGHQDKELRYRFIYNHF---PSLHEEDILGKTDVEIFSGAGVKESQDFKREVLEKGLP----AKREITFETELFG  302 (1002)
Q Consensus       230 ~~p~~i~~~d~~~~~~~~~~~~---~~~~~e~iiGk~~~e~~~~~~~~~~~~~~~~vl~~g~~----~~~e~~~~~~~~~  302 (1002)
                      ++|.+|+..|.++++.++|..+   .|++.++++|++...++++................+..    ...++....+.+.
T Consensus         1 ~~~d~i~~~d~~g~i~~~N~a~~~l~G~~~~el~G~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~dG~   80 (119)
T 2vv6_A            1 TIPDAMIVIDGHGIIQLFSTAAERLFGWSELEAIGQNVNILMPEPDRSRHDSYISRYRTTSDPHIIGIGRIVTGKRRDGT   80 (119)
T ss_dssp             -CCCEEEEEETTSBEEEECHHHHHHHCCCHHHHTTSBGGGGSCTTHHHHHHHHHHHHHHHCCCSSTTTCEEEEEECTTSC
T ss_pred             CCcceEEEECCCCeEEEEhHHHHHHhCCCHHHHcCCCHHHhCCchHHHHHHHHHHHHhcCCCcccCCCceEEEEEeCCCC
Confidence            3688999999999999998764   68899999999988887654433323333444444433    2334444444444


Q ss_pred             ceEEEEEEeeeecCCCCEEEEEEEeechhHHHHHHHHH
Q 039716          303 SKTFLIYVEPVFSKSGETIGVNYMGMDVTDQVRKREKM  340 (1002)
Q Consensus       303 ~~~~~~~~~p~~~~~G~~~gi~~~~~DITe~~~~~~~~  340 (1002)
                      ..++.+.+.|+.+.  ...++++++.|||++++.++++
T Consensus        81 ~~~~~~~~~~~~~~--~~~~~~~~~~DITerk~~e~~l  116 (119)
T 2vv6_A           81 TFPMHLSIGEMQSG--GEPYFTGFVRDLTEHQQTQARL  116 (119)
T ss_dssp             EEEEEEEEEEEEET--TEEEEEEEEEECC---------
T ss_pred             EEEEEEEEEEEEEC--CeEEEEEEEEEcHHHHHHHHHH
Confidence            45566777888763  3346788899999988776654

>2r78_A Sensor protein; sensory box sensor histidine kinase/response regulator, structural genomics, PSI, MCSG; 1.60A {Geobacter sulfurreducens pca}

Probab=98.17  E-value=6.8e-06  Score=76.25  Aligned_cols=109  Identities=16%  Similarity=0.025  Sum_probs=72.1

Q ss_pred             HHHHHHHHHHHHhccCcEEEEecccccEEEeeccC---CCCCcccccCCCchhccCccchhhhhHHHHHHHHhCCCccee
Q 039716          217 LKRADNFLHFVLQNAPVVMGHQDKELRYRFIYNHF---PSLHEEDILGKTDVEIFSGAGVKESQDFKREVLEKGLPAKRE  293 (1002)
Q Consensus       217 l~~~~~~l~~il~~~p~~i~~~d~~~~~~~~~~~~---~~~~~e~iiGk~~~e~~~~~~~~~~~~~~~~vl~~g~~~~~e  293 (1002)
                      |+.++..++.+++++|.+|+..|.++++.++|..+   .|++.++++|++..++.++.......... ..+..+.+...+
T Consensus         6 l~~se~~~~~l~e~~~d~i~~~d~~g~i~~vN~a~~~l~Gy~~~el~g~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~e   84 (117)
T 2r78_A            6 LYFQSNAYRALFEHAIDGIFIMDAEGHYLDVNPAICSAIGYTRDEFLALDWGVLSRGVDSGWAAASL-ARIVGGEPLREE   84 (117)
T ss_dssp             HHHHHHHHHHHHHHCSSEEEEECTTSBEEEECHHHHHHHCCCHHHHTTCBTTTTTTCSTTSHHHHHH-HHHHTTCCEEEE
T ss_pred             HHHhHHHHHHHHhcCCceEEEECCCCCEEEecHHHHHHHCcCHHHHcCCCHHHhCCccchhHHHHHH-HHHHcCCcEEEE
Confidence            56778889999999999999999999999999865   58899999999876554322211111222 334445454455


Q ss_pred             EEEEEeecCceEEEEEEeeeecCCCCEEEEEEEeechh
Q 039716          294 ITFETELFGSKTFLIYVEPVFSKSGETIGVNYMGMDVT  331 (1002)
Q Consensus       294 ~~~~~~~~~~~~~~~~~~p~~~~~G~~~gi~~~~~DIT  331 (1002)
                      ..+..+.+...++.+...|+.  +|.   ++++++|||
T Consensus        85 ~~~~~kdG~~~~v~~~~~~~~--~g~---~~~i~~DIT  117 (117)
T 2r78_A           85 RTVWTRNGDQLTVELSAHLLP--DGK---ILGIARDVS  117 (117)
T ss_dssp             EEEECTTSCEEEEEEEEEECT--TSC---EEEEEEC--
T ss_pred             EEEEecCCCEEEEEEEEEEec--CCe---EEEEEEeCC
Confidence            555444444455556677775  566   456678987

>3mjq_A Uncharacterized protein; NESG, structural genomics, PSI-2, protein structure initiati northeast structural genomics consortium; 2.60A {Desulfitobacterium hafniense}

Probab=98.16  E-value=2.2e-06  Score=79.09  Aligned_cols=113  Identities=11%  Similarity=0.009  Sum_probs=74.7

Q ss_pred             HHHHhccCcEEEEecccccEEEeeccC---CCCCcccccCCCchhccCccchhhhhHHHHHHHHhCCCcceeEEEEEeec
Q 039716          225 HFVLQNAPVVMGHQDKELRYRFIYNHF---PSLHEEDILGKTDVEIFSGAGVKESQDFKREVLEKGLPAKREITFETELF  301 (1002)
Q Consensus       225 ~~il~~~p~~i~~~d~~~~~~~~~~~~---~~~~~e~iiGk~~~e~~~~~~~~~~~~~~~~vl~~g~~~~~e~~~~~~~~  301 (1002)
                      +.+++++|.+++..|.++++.++|..+   .|++.++++|++..+++++............++..+.. ..++.+....+
T Consensus         2 ~~l~~~~~~~i~~~d~~g~i~~~N~~~~~~~g~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~g   80 (126)
T 3mjq_A            2 KNFLETIEDMILIINREGRLLYANTAVPKKLGYTHEELMSMHILTITSAGKMAEGEKILAELFAGKKE-SLPLSLEKKEG   80 (126)
T ss_dssp             CTTGGGCSSEEEEEETTSBEEEECTHHHHHHSCCHHHHHHSBHHHHHCTTCHHHHHHHHHHHHHTCCS-EEEEEEECTTS
T ss_pred             hhHHhhCCceEEEEeCCCcEEEEcHHHHHHHCCCHHHHcCCCHHHHcCchhHHHHHHHHHHHHhCCCc-eeEEEEEccCC
Confidence            457899999999999999999998764   57888999999999988776655555555566655544 44554444433


Q ss_pred             CceEEEEEEeeeecCCCCEEEEEEEeechhHHHHHHHHH
Q 039716          302 GSKTFLIYVEPVFSKSGETIGVNYMGMDVTDQVRKREKM  340 (1002)
Q Consensus       302 ~~~~~~~~~~p~~~~~G~~~gi~~~~~DITe~~~~~~~~  340 (1002)
                      ...++.+...|+..  +...|+++++.|||++++++++.
T Consensus        81 ~~~~~~~~~~~~~~--~~~~~~~~~~~DITe~k~a~~~~  117 (126)
T 3mjq_A           81 TSIPAKARIWQGKW--HNEPCLFAIIKDLSKEERASSPP  117 (126)
T ss_dssp             CEEEEEEEEEEEES--SSSEEEEEEEEECC---------
T ss_pred             CEEEEEEEEEeeeE--CCceEEEEEEEechHHHHhhccc
Confidence            44455555565554  34668889999999987765543

>3h9w_A Diguanylate cyclase with PAS/PAC sensor; alpha-beta protein., structural genomics, PSI-2, protein STR initiative; 1.90A {Marinobacter aquaeolei}

Probab=98.11  E-value=4.7e-06  Score=76.52  Aligned_cols=107  Identities=9%  Similarity=-0.032  Sum_probs=79.7

Q ss_pred             cCcEEEEec-ccccEEEeeccC---CCCCcccccCCC-chhccCccchhhhhHHHHHHHHhCCCcceeEEEEEeecCceE
Q 039716          231 APVVMGHQD-KELRYRFIYNHF---PSLHEEDILGKT-DVEIFSGAGVKESQDFKREVLEKGLPAKREITFETELFGSKT  305 (1002)
Q Consensus       231 ~p~~i~~~d-~~~~~~~~~~~~---~~~~~e~iiGk~-~~e~~~~~~~~~~~~~~~~vl~~g~~~~~e~~~~~~~~~~~~  305 (1002)
                      ++.+++..| .++++.|+|..+   .|+.+++++|.. ..++++++..+.........+..+.+...++.+..+.+...+
T Consensus         2 a~~giw~~d~~~~~~~~~n~~~~~l~G~~~~e~~~~~~~~~~ihpdd~~~~~~~~~~~~~~~~~~~~e~r~~~~dG~~~w   81 (115)
T 3h9w_A            2 TKAIPWKINWQTMAFEYIGPQIEALLGWPQGSWKSVEDWATRMHPEDQEWVVNFCVKQSECGVDHEADYRALHRDGHYVW   81 (115)
T ss_dssp             -CCEEEEEETTTTEEEEECTHHHHHHCSCGGGCCBHHHHHHSBCHHHHHHHHHHHHHHHHTTCCEEEEEEEECTTSCEEE
T ss_pred             cceEEEEEEcCCCcEEEEChhHHHHhCCChHHccCHHHHHHhcCHHHHHHHHHHHHHHHhcCCcccEEEEEEcCCCCEEE
Confidence            567888888 678888888754   578888888832 235666666666666666777777766667666665566677


Q ss_pred             EEEEEeeeecCCCCEEEEEEEeechhHHHHHH
Q 039716          306 FLIYVEPVFSKSGETIGVNYMGMDVTDQVRKR  337 (1002)
Q Consensus       306 ~~~~~~p~~~~~G~~~gi~~~~~DITe~~~~~  337 (1002)
                      +.....|+++.+|.+++++++..|||++++++
T Consensus        82 ~~~~~~~~~d~~G~~~~~~G~~~Dit~~k~~~  113 (115)
T 3h9w_A           82 IRDVVHVVRDDSGEVEALIGFMFDISLEHHHH  113 (115)
T ss_dssp             EEEEEEEEECTTSCEEEEEEEEEECGGGGC--
T ss_pred             EEEEEEEEECCCCCEEEEEEEEeccCcccccc
Confidence            78888999999999999999999999987654

>3ewk_A Sensor protein; PAS domain, alpha/beta fold, kinase, phosphoprotein, transfe flavoprotein; HET: FAD; 2.34A {Methylococcus capsulatus}

Probab=98.05  E-value=2.3e-05  Score=81.92  Aligned_cols=106  Identities=15%  Similarity=0.155  Sum_probs=84.2

Q ss_pred             HHHHHhccCcEEEEecccccEEEeeccC---CCCCcccccCCCchhccCccchhhhhHHHHHHHHhCCCcceeEEEEEee
Q 039716          224 LHFVLQNAPVVMGHQDKELRYRFIYNHF---PSLHEEDILGKTDVEIFSGAGVKESQDFKREVLEKGLPAKREITFETEL  300 (1002)
Q Consensus       224 l~~il~~~p~~i~~~d~~~~~~~~~~~~---~~~~~e~iiGk~~~e~~~~~~~~~~~~~~~~vl~~g~~~~~e~~~~~~~  300 (1002)
                      ++.+++++|.+|+..|.++++.++|..|   .|++.++++|++...+.++...........+.+..+.+...++....+.
T Consensus       113 ~~~~~~~~~~~i~~~d~~g~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~k~  192 (227)
T 3ewk_A          113 LKQAMDANSEMILLTDRAGRIIYANPALCRFSGMAEGELLGQSPSILDSPLADQETLAAMQEALQAGQPWSGRLLNRRRT  192 (227)
T ss_dssp             HHHHHHTCCSEEEEECTTSCEEEECHHHHHHHTCCTHHHHSSCGGGGBCTTSCHHHHHHHHHHHHHTCCEECCEEEEEEC
T ss_pred             HHHHHhcCcCeEEEEcCCCcEEEEchHHHHHhCCCHHHHcCCChhhccCCCCCHHHHHHHHHHHHcCCceeEEEEEECCC
Confidence            3456789999999999999999999865   5889999999998888776555555555666777888877777666554


Q ss_pred             cC------ceEEEEEEeeeecCCCCEEEEEEEeec
Q 039716          301 FG------SKTFLIYVEPVFSKSGETIGVNYMGMD  329 (1002)
Q Consensus       301 ~~------~~~~~~~~~p~~~~~G~~~gi~~~~~D  329 (1002)
                      +.      ..+..+.+.|+++.+|.++|++++..|
T Consensus       193 G~~~~dg~~~~~~~~~~pi~d~~g~~~~~v~i~~D  227 (227)
T 3ewk_A          193 GPAPHDAEDYWAEISTTPIHTDGNGLVGYVQIQHD  227 (227)
T ss_dssp             CSSSSCEEEEEEEEEEEEEECSSSCEEEEEEEEEC
T ss_pred             CCcCcccceEEEEEEEEEEECCCCCEEEEEEEecC
Confidence            43      355668889999999999999999876

>3olo_A Two-component sensor histidine kinase; structural genomics, PSI-2, protein structure initiative, MI center for structural genomics, MCSG, TRA; 2.09A {Nostoc SP}

Probab=98.03  E-value=1.1e-05  Score=73.43  Aligned_cols=107  Identities=7%  Similarity=0.020  Sum_probs=71.5

Q ss_pred             HHHHHHHHHHHhccCcEEEEecccccEEEeeccC---CCCCcccccCCCchhccCccchhhhhHHHHHHHHhCCCcceeE
Q 039716          218 KRADNFLHFVLQNAPVVMGHQDKELRYRFIYNHF---PSLHEEDILGKTDVEIFSGAGVKESQDFKREVLEKGLPAKREI  294 (1002)
Q Consensus       218 ~~~~~~l~~il~~~p~~i~~~d~~~~~~~~~~~~---~~~~~e~iiGk~~~e~~~~~~~~~~~~~~~~vl~~g~~~~~e~  294 (1002)
                      +++..+++.+++++|.+|+..|.++++.++|..+   .|+++++++|++..++++......    ...+ ..+.....+.
T Consensus         9 e~~~~~~~~~~~~~~~~i~~~d~~g~i~~~N~~~~~l~G~~~~el~g~~~~~~~~~~~~~~----~~~~-~~~~~~~~e~   83 (118)
T 3olo_A            9 ELEFKFAHYLINNAVEASFCLGDNWQFLYVNDATCRMTEYSREQLLSMNLQDIDVDFALHD----WEEI-RQKNNYTFKT   83 (118)
T ss_dssp             HHHHHHHHHHHHHCSSEEEEECTTSBEEEECHHHHHHHCCCHHHHTTCBGGGTBTTGGGSC----HHHH-HHHSEEEEEE
T ss_pred             HHHHHHHHHHHhcCCceEEEECCCCcEEEEHHHHHHHHCCCHHHHhCCChhhcccccCHHH----HHHH-HhcCcEEEEE
Confidence            3444567789999999999999999999998864   588999999999998886543332    2222 2333334444


Q ss_pred             EEEEeecCceEEEEEEeeeecCCCCEEEEEEEeechh
Q 039716          295 TFETELFGSKTFLIYVEPVFSKSGETIGVNYMGMDVT  331 (1002)
Q Consensus       295 ~~~~~~~~~~~~~~~~~p~~~~~G~~~gi~~~~~DIT  331 (1002)
                      .+....+...++.+...|+.+.. . .++++++.|||
T Consensus        84 ~~~~~~g~~~~~~~~~~~~~~~~-~-~~~~~~~~DIT  118 (118)
T 3olo_A           84 RYRSQSGRIFLVEMSLTFLEDQE-R-RFSCVFVREKS  118 (118)
T ss_dssp             EEECTTCCEEEEEEEEEEEEETT-E-EEEEEEEEEC-
T ss_pred             EEEccCCCEEEEEEEEEEEEECC-c-cEEEEEEEeCC
Confidence            44444344445556667776543 2 35667889987

>3fg8_A Uncharacterized protein RHA05790; PAS domain, structural genomics, PS protein structure initiative, midwest center for structural genomics, MCSG; HET: 3PB; 1.80A {Rhodococcus SP}

Probab=97.97  E-value=2.3e-06  Score=79.69  Aligned_cols=110  Identities=13%  Similarity=0.080  Sum_probs=77.9

Q ss_pred             HHHHHHHHHHHHHhccCcEEEEecccccEEEeeccC---CCCCcccccCCCchhccCccchhhhhHHHHHHHHhCCCcce
Q 039716          216 ILKRADNFLHFVLQNAPVVMGHQDKELRYRFIYNHF---PSLHEEDILGKTDVEIFSGAGVKESQDFKREVLEKGLPAKR  292 (1002)
Q Consensus       216 ~l~~~~~~l~~il~~~p~~i~~~d~~~~~~~~~~~~---~~~~~e~iiGk~~~e~~~~~~~~~~~~~~~~vl~~g~~~~~  292 (1002)
                      .+....++.+.+++++|.+|+..|.++++.++|..+   .|++.++++|++..+++++...........+++..|.+...
T Consensus         6 ~~~~~~~~~~~il~~~~~~i~~~D~~g~i~~~N~a~~~l~g~~~~e~~G~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   85 (118)
T 3fg8_A            6 HHHHHSSGRENLYFQGGLGFMALDEDLRIIYVNSGCLRHVRRSRDELLGRVVTEVLPETQGSYFDALCRKVLATGREQQT   85 (118)
T ss_dssp             -------CCCCSSSCTTCEEEEECTTCBEEEECHHHHHHHTCCHHHHTTSBHHHHCGGGTTSHHHHHHHHHHHHCCCEEE
T ss_pred             ccccccchHHHHHhhCCceEEEECCCCeEEEECHHHHHHhCCCHHHHcCCcHHHHcCccchHHHHHHHHHHHHcCCceEE
Confidence            345566778889999999999999999999999764   57888999999999999876555555667778888876544


Q ss_pred             eEEEEEeecCceEEEEEEeeeecCCCCEEEEEEEeechhHH
Q 039716          293 EITFETELFGSKTFLIYVEPVFSKSGETIGVNYMGMDVTDQ  333 (1002)
Q Consensus       293 e~~~~~~~~~~~~~~~~~~p~~~~~G~~~gi~~~~~DITe~  333 (1002)
                      ++.....  ...++.+...|+.+      |+++++.|||++
T Consensus        86 ~~~~~~~--~g~~~~~~~~p~~~------g~v~~~~DITer  118 (118)
T 3fg8_A           86 RVDSLYS--PGMTIEVTAAADSG------ALVVHFRDVTAE  118 (118)
T ss_dssp             EEECSSS--TTCEEEEEEEEETT------EEEEEEEECSCC
T ss_pred             EEEEEcC--CCeEEEEEEEEcCC------cEEEEEEeccCC
Confidence            2211111  34667777788753      477788999963

>3bwl_A Sensor protein; structural genomics, APC87707.1, PAS domain, HTR-like protei protein structure initiative; HET: MSE I3A; 1.73A {Haloarcula marismortui atcc 43049}

Probab=97.95  E-value=7.1e-05  Score=69.34  Aligned_cols=114  Identities=14%  Similarity=0.129  Sum_probs=71.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHhccCcEEEEecccccEEEeeccC---CCCCcccc--cCCCchhccCccchhhhhHHHHHHH
Q 039716          210 VEELSQILKRADNFLHFVLQNAPVVMGHQDKELRYRFIYNHF---PSLHEEDI--LGKTDVEIFSGAGVKESQDFKREVL  284 (1002)
Q Consensus       210 ~~~~~~~l~~~~~~l~~il~~~p~~i~~~d~~~~~~~~~~~~---~~~~~e~i--iGk~~~e~~~~~~~~~~~~~~~~vl  284 (1002)
                      .+++++.|++++..++.+++++|.+|+..|.++++.++|..+   .|++++++  +|++..++++ . ..   ... ..+
T Consensus         5 r~~~e~~L~~~~~~~~~l~e~~~~~i~~~d~~g~i~~~N~a~~~~~G~~~~el~g~g~~~~~~~~-~-~~---~~~-~~~   78 (126)
T 3bwl_A            5 RKRREKRLEETSSRLEALFENSPDMIDVLDADGTICEVNQRFCAELGYDESEVLGRSIWEFDLMF-D-AE---DVQ-TQL   78 (126)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHCSSEEEEECTTCBEEEECHHHHHHHTCCGGGTTTSBGGGTBTTC-C-HH---HHH-HHH
T ss_pred             HHHHHHHHHHHHHHHHHHHhhCCcEEEEEcCCCCEEEEcHHHHHHhCCCHHHHhhCCCchhhccC-C-HH---HHH-HHH
Confidence            455667788889999999999999999999999999999865   58889999  5677777665 1 11   111 111


Q ss_pred             Hh---CCCcceeEEEEEeecCceEEEEEEeeeecCCCCEEEEEEEeechh
Q 039716          285 EK---GLPAKREITFETELFGSKTFLIYVEPVFSKSGETIGVNYMGMDVT  331 (1002)
Q Consensus       285 ~~---g~~~~~e~~~~~~~~~~~~~~~~~~p~~~~~G~~~gi~~~~~DIT  331 (1002)
                      ..   +.....+..+..+.+...++.+...|+. ..|.. ++++++.|||
T Consensus        79 ~~~~~~~~~~~e~~~~~~dG~~~~~~~~~~~~~-~~~~~-~~~~~~~DIT  126 (126)
T 3bwl_A           79 SGFSVDERRKFEGLYERRDGSTMSVEVHLLRFN-LEGED-RFLAISRDIT  126 (126)
T ss_dssp             HTCCTTCEEEEEEEEECTTSCEEEEEEEEEEEE-ETTEE-EEEEEEEEC-
T ss_pred             HHHhcCCCcceEEEEEeCCCCEEEEEEEeEEEe-cCCcE-EEEEEEEeCC
Confidence            11   1111222233333333334444445553 34443 5677889997

>2kdk_A ARYL hydrocarbon receptor nuclear translocator-LI 2; circadian clock, PAS domain, transcription, activator, biolo rhythms, DNA-binding, nucleus; NMR {Homo sapiens}

Probab=97.95  E-value=2.8e-05  Score=71.58  Aligned_cols=108  Identities=10%  Similarity=0.026  Sum_probs=79.1

Q ss_pred             HHHhccCcEEEEecccccEEEeecc---CCCCCcccccCCCchhccCccchhhhhHHHHHHHHhCCC-cceeEEEEEeec
Q 039716          226 FVLQNAPVVMGHQDKELRYRFIYNH---FPSLHEEDILGKTDVEIFSGAGVKESQDFKREVLEKGLP-AKREITFETELF  301 (1002)
Q Consensus       226 ~il~~~p~~i~~~d~~~~~~~~~~~---~~~~~~e~iiGk~~~e~~~~~~~~~~~~~~~~vl~~g~~-~~~e~~~~~~~~  301 (1002)
                      .+++++|.+|+..|.++++.++|..   +.|+++++++|++..+++++............++..+.. ...++.+..+.+
T Consensus         7 ~~~~~~~~~i~~~d~~g~i~~~N~~~~~~~G~~~~el~g~~~~~~~~p~d~~~~~~~~~~~~~~~~~~~~~e~r~~~~dG   86 (121)
T 2kdk_A            7 EINVKPTEFITRFAVNGKFVYVDQRATAILGYLPQELLGTSCYEYFHQDDHNNLTDKHKAVLQSKEKILTDSYKFRAKDG   86 (121)
T ss_dssp             CCCCCSSEEEEEECTTSBEEEECTHHHHHTCCCTTTSBTSBTTTTBCSSSHHHHHHHHHHHHTSSSCEEEEEEEEECSSS
T ss_pred             ccccCCccEEEEECCCeeEEEEChhHHHHHCCCHHHHcCCcHHHeeCHHHHHHHHHHHHHHHhCCCCCccEEEEEEEcCC
Confidence            3678899999999999999999876   468899999999998888776655555545555554332 344555555555


Q ss_pred             CceEEEEEEeeeecCC-CCEEEEEEEeechhHH
Q 039716          302 GSKTFLIYVEPVFSKS-GETIGVNYMGMDVTDQ  333 (1002)
Q Consensus       302 ~~~~~~~~~~p~~~~~-G~~~gi~~~~~DITe~  333 (1002)
                      ...++.....|+++.. |.+.+++++..||++.
T Consensus        87 ~~~~~~~~~~~~~d~~~~~~~~~v~~~~~i~~~  119 (121)
T 2kdk_A           87 SFVTLKSQWFSFTNPDTKELEYIVSVNTLVLGH  119 (121)
T ss_dssp             CEEEEEEEEEEEECCSSSCEEEEEEEEECCSSC
T ss_pred             CEEEEEEEEEEEECCCCCeeeEEEEEEEecccc
Confidence            5556667888999875 5666788888888863

>2l0w_A Potassium voltage-gated channel, subfamily H (EAG member 2, isoform CRA_B; HERG, PAS domain, voltage-gated potassium channel, membrane; NMR {Homo sapiens} PDB: 2l1m_A 2l4r_A

Probab=97.89  E-value=3.7e-05  Score=70.98  Aligned_cols=107  Identities=12%  Similarity=0.019  Sum_probs=74.1

Q ss_pred             HHHhccCcEEEEecc---cccEEEeeccC---CCCCcccccCCC--chhccCccchhhhhHHHHHHHHhCCCcceeEEEE
Q 039716          226 FVLQNAPVVMGHQDK---ELRYRFIYNHF---PSLHEEDILGKT--DVEIFSGAGVKESQDFKREVLEKGLPAKREITFE  297 (1002)
Q Consensus       226 ~il~~~p~~i~~~d~---~~~~~~~~~~~---~~~~~e~iiGk~--~~e~~~~~~~~~~~~~~~~vl~~g~~~~~e~~~~  297 (1002)
                      ..++++|.+++..|.   ++++.++|..+   .|+..++++|++  ...+.++.............+..+.+...++.+.
T Consensus        23 ~~~~~~~~~i~~~d~~~~~g~i~~~N~~~~~l~g~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  102 (138)
T 2l0w_A           23 RKFEGQSRKFIIANARVENCAVIYCNDGFCELCGYSRAEVMQRPCTCDFLHGPRTQRRAAAQIAQALLGAEERKVEIAFY  102 (138)
T ss_dssp             HHHTTTTSEEEEEESSSTTCBEEEECSHHHHHHSCCHHHHTTSBTTCGGGCCTTCCHHHHHHHHHHTTCSSCEEEEEEEE
T ss_pred             HHHhcCCCCEEEEecCCCCCEEEEeCHHHHHHhCCCHHHHcCCCCcccccCCcccchhHHHHHHHHHhhcCCceeEEEEE
Confidence            446779999999999   99999998764   577888999998  3334333322222233344444554444444443


Q ss_pred             EeecCceEEEEEEeeeecCCCCEEEEEEEeechhH
Q 039716          298 TELFGSKTFLIYVEPVFSKSGETIGVNYMGMDVTD  332 (1002)
Q Consensus       298 ~~~~~~~~~~~~~~p~~~~~G~~~gi~~~~~DITe  332 (1002)
                      ...+...++.+...|+.+.+|.+.|+++++.|||+
T Consensus       103 ~~~g~~~~~~~~~~~~~~~~g~~~~~~~~~~Dit~  137 (138)
T 2l0w_A          103 RKDGSCFLCLVDVVPVKNEDGAVIMFILNFEVVME  137 (138)
T ss_dssp             CTTSCEEEEEEEEEEEECTTSCEEEEEEEEEEEEE
T ss_pred             CCCCCEEEEEEEEEEEeCCCCCEEEEEEEEEeccC
Confidence            33344456678889999999999999999999996

>3cax_A Uncharacterized protein PF0695; structural genomics, unknown function, PSI-2, protein struct initiative; 2.43A {Pyrococcus furiosus dsm 3638}

Probab=97.88  E-value=0.00011  Score=83.40  Aligned_cols=109  Identities=22%  Similarity=0.269  Sum_probs=83.2

Q ss_pred             HHHHHHHhccCcEEEEecccccEEEeeccCCC--CCcccccCCCchhccCccchhhhhHHHHHHHHhCCCcceeEEEEEe
Q 039716          222 NFLHFVLQNAPVVMGHQDKELRYRFIYNHFPS--LHEEDILGKTDVEIFSGAGVKESQDFKREVLEKGLPAKREITFETE  299 (1002)
Q Consensus       222 ~~l~~il~~~p~~i~~~d~~~~~~~~~~~~~~--~~~e~iiGk~~~e~~~~~~~~~~~~~~~~vl~~g~~~~~e~~~~~~  299 (1002)
                      ..+..+++++|.+|...|.++++.++|.. ..  +..++++|++..+++++...... .....++.+|.+...+..+.  
T Consensus       239 ~~l~~IL~~l~dgIivvD~~g~I~~~N~a-e~i~~~~~e~iGr~v~~~~p~~~~~~~-~~l~~~l~~g~~~~~~~~~~--  314 (369)
T 3cax_A          239 EELKAIFEALPVDVTFIDKDDRVRFFSPG-ERIFTRTPSVLGRPVQLCHPPKSVYVV-NKILKAFKEGRKKEATFWLR--  314 (369)
T ss_dssp             HHHHHHHHHSSSEEEEECTTSBEEEECCS-SCSSCCCGGGTTCBTTTSSCGGGHHHH-HHHHHHHHHTSCSCEEEEEE--
T ss_pred             HHHHHHHHhCCCcEEEECCCCcEEEEcCH-HHccCChHHHcCCcHHHHCChhhHHHH-HHHHHHHHcCCceEEEEEEe--
Confidence            46788999999999999999999999986 44  35678999999998875432222 22345667777655544432  


Q ss_pred             ecCceEEEEEEeeeecCCCCEEEEEEEeechhHHHH
Q 039716          300 LFGSKTFLIYVEPVFSKSGETIGVNYMGMDVTDQVR  335 (1002)
Q Consensus       300 ~~~~~~~~~~~~p~~~~~G~~~gi~~~~~DITe~~~  335 (1002)
                      . +.+++.+...|+++.+|.++|++.++.|||+.++
T Consensus       315 ~-~g~~v~v~~~PI~d~~G~~~G~v~v~~DITe~~~  349 (369)
T 3cax_A          315 L-REKYVYIKYVPLFNEKGEYIGTLEMTMDIAPYKK  349 (369)
T ss_dssp             E-TTEEEEEEEEEEECTTSCEEEEEEEEEECHHHHT
T ss_pred             e-CCEEEEEEEEEEECCCCCEEEEEEEEEcCHHHHH
Confidence            2 2367888899999999999999999999998654

>3zcc_A HAMP, osmolarity sensor protein ENVZ; signaling protein, signal transduction, membrane protein, signalling, chimera; 1.25A {Archaeoglobus fulgidus} PDB: 3zrw_A 3zrv_A 3zrx_A 3zrw_B 2lfr_A 2lfs_A 1joy_A 2l7h_A 2l7i_A 2y20_A 2y21_A 2y0q_A 2y0t_A

Probab=97.87  E-value=4.2e-05  Score=70.17  Aligned_cols=54  Identities=22%  Similarity=0.357  Sum_probs=46.7

Q ss_pred             HHHHHHhhhccccHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 039716          371 KQMLATMSHEIRSPLTGVVSMAEILSNTKLDREQRQLLGVMISSGDLVLQLINDILDLS  429 (1002)
Q Consensus       371 k~fla~iSHELRTPL~~I~g~~elL~~~~l~~~~~~~l~~i~~s~~~L~~LIndlLd~s  429 (1002)
                      ++|++.+||||||||++|.++++++.+.     ..+++..+..++.+|..+|+++|+|.
T Consensus        61 ~~~~~~~shel~tpl~~i~~~~e~l~~~-----~~~~~~~i~~~~~~l~~~i~~ll~~~  114 (114)
T 3zcc_A           61 TLLMAGVSHDLRTPLTRIRLATEMMSEQ-----DGYLAESINKDIEECNAIIEQFIDYL  114 (114)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHTSCGG-----GHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_pred             HHHHHHhhHHHcChHHHHHHHHHHHHHh-----hhHHHHHHHHHHHHHHHHHHHHHhhC
Confidence            4799999999999999999999988542     34456899999999999999999873

>3h4l_A DNA mismatch repair protein PMS1; ATP binding, DNA repair, DNA damage, nucleus, phosphop DNA binding protein, protein binding; HET: DNA ANP; 2.50A {Saccharomyces cerevisiae}

Probab=97.87  E-value=1.1e-05  Score=90.73  Aligned_cols=58  Identities=19%  Similarity=0.171  Sum_probs=38.1

Q ss_pred             EEEEEEecCCCCCcCcHhhhhhhccCCCcccc------CcCCCccccHHHHHHHHHHhCCEEEEEeecC
Q 039716          592 IRCDVYDTGIGIPENALPTLFRKYMQVSADHA------RKYGGTGLGLAICKQLVELMGGRLTVTSKVH  654 (1002)
Q Consensus       592 l~i~V~DtGiGI~~e~l~~IF~pF~q~~~~~~------~~~~GtGLGLaI~k~Lve~~gG~I~v~S~~g  654 (1002)
                      ..|+|.|+|+||+++.+..+|++|++.+....      ..+|--|-||+-+..+     +.+.|.|...
T Consensus        55 ~~i~V~DnG~Gi~~~~l~~~~~~~~tsK~~~~~Dl~~i~t~GfrGeaL~Si~av-----S~l~V~sr~~  118 (367)
T 3h4l_A           55 ESIECSDNGDGIDPSNYEFLALKHYTSKIAKFQDVAKVQTLGFRGEALSSLCGI-----AKLSVITTTS  118 (367)
T ss_dssp             SEEEEEECSCCCCGGGTTTTTCCEEC---------CCCCEEEETTHHHHHHHHS-----SEEEEEEESS
T ss_pred             EEEEEEECCCCcChhHhccceeccccCcCCchhhhhhhhccCccchHHHHhhcc-----CEEEEEEEEC
Confidence            35789999999999999999999998754321      1112236777655443     2688888754

>3b33_A Sensor protein; structural genomics, PAS domain, nitrogen regulation protein APC91440.4, PSI-2; HET: MSE; 1.83A {Vibrio parahaemolyticus rimd 2210633}

Probab=97.64  E-value=0.00019  Score=65.33  Aligned_cols=103  Identities=14%  Similarity=0.089  Sum_probs=74.1

Q ss_pred             HHHHHhccCcEEEEecccccEEEeecc---CCCCCcccccCCCchhccCccchhhhhHHHHHHHHhCCCc-ceeEEEEEe
Q 039716          224 LHFVLQNAPVVMGHQDKELRYRFIYNH---FPSLHEEDILGKTDVEIFSGAGVKESQDFKREVLEKGLPA-KREITFETE  299 (1002)
Q Consensus       224 l~~il~~~p~~i~~~d~~~~~~~~~~~---~~~~~~e~iiGk~~~e~~~~~~~~~~~~~~~~vl~~g~~~-~~e~~~~~~  299 (1002)
                      ...+++++|.+++..|.++++.++|..   +.|++.++++|++..++++...  ........++..+.+. ..++.+. .
T Consensus         9 ~~~il~~~~~~i~~~D~~g~I~~~N~aa~~l~g~~~~~~~g~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~-~   85 (115)
T 3b33_A            9 PSAILNNMVTATLILDDGLAIRYANPAAELLFSQSAKRIVEQSLSQLIQHAS--LDLALLTQPLQSGQSITDSDVTFV-V   85 (115)
T ss_dssp             HHHHHHHCSSEEEEECTTCBEEEECHHHHHHTTSCHHHHTTCBHHHHCSEEE--CCTHHHHHHHHHCCCEEEEEEEEE-E
T ss_pred             HHHHHhhcCceEEEECCCCcEEEECHHHHHHhCCCHHHHhCCCHHHHhCccc--hhhHHHHHHHHcCCcccCCceEEe-c
Confidence            345899999999999999999999875   4678888999999988876432  1233445566666553 2344443 3


Q ss_pred             ecCceEEEEEEeeeecCCCCEEEEEEEeechh
Q 039716          300 LFGSKTFLIYVEPVFSKSGETIGVNYMGMDVT  331 (1002)
Q Consensus       300 ~~~~~~~~~~~~p~~~~~G~~~gi~~~~~DIT  331 (1002)
                      .+...++.+...|+.+ +|. .|++.++.||+
T Consensus        86 ~g~~~~~~~~~~pi~~-~g~-~~~l~~~~Di~  115 (115)
T 3b33_A           86 DGRPLMLEVTVSPITW-QRQ-LMLLVEMRKID  115 (115)
T ss_dssp             TTEEEEEEEEEEEEEE-TTE-EEEEEEEEEC-
T ss_pred             CCCEEEEEEEEEEeec-CCc-eEEEEEEEeCC
Confidence            3334456788899998 787 68889999974

>2wer_A ATP-dependent molecular chaperone HSP82; ATPase, ATP-binding, phosphoprotein, stress respo nucleotide-binding; HET: RDC; 1.60A {Saccharomyces cerevisiae} PDB: 2weq_A* 2wep_A* 1zwh_A* 1zw9_A* 2fxs_A* 3c11_A* 3c0e_A* 2yge_A* 2ygf_A* 2akp_A

Probab=97.59  E-value=2.2e-05  Score=82.50  Aligned_cols=48  Identities=17%  Similarity=0.261  Sum_probs=31.7

Q ss_pred             EEEEEecCCCCCcCcHhhhhhhccCCCc----------cccCcCCCccccHHHHHHHH
Q 039716          593 RCDVYDTGIGIPENALPTLFRKYMQVSA----------DHARKYGGTGLGLAICKQLV  640 (1002)
Q Consensus       593 ~i~V~DtGiGI~~e~l~~IF~pF~q~~~----------~~~~~~~GtGLGLaI~k~Lv  640 (1002)
                      .|.|.|||+||+++++...|..+.+...          ......|..|+|++-|..++
T Consensus        74 ~i~I~DnG~GMs~edl~~~l~~ia~S~~~~f~~k~~~~~~~~~iG~fGiG~~s~~~~~  131 (220)
T 2wer_A           74 VLEIRDSGIGMTKAELINNLGTIAKSGTKAFMEALSAGADVSMIGQFGVGFYSLFLVA  131 (220)
T ss_dssp             EEEEEECSCCCCHHHHHHHTTTSCCTTHHHHHHHHTTTCCGGGGGGGTCGGGGGGGTE
T ss_pred             EEEEEEcCCCCCHHHHHHHHHhHhcccchhHHHHhhccCCcccCCccchhHHHhhhcC
Confidence            4789999999999999888766543210          01112344799997665443

>1byw_A Protein (human ERG potassium channel); PAS domain, potassium channel domain, membrane protein; 2.60A {Homo sapiens} SCOP: d.110.3.6

Probab=97.57  E-value=0.0002  Score=62.65  Aligned_cols=99  Identities=13%  Similarity=0.074  Sum_probs=67.3

Q ss_pred             EEEEecc---cccEEEeeccC---CCCCcccccCCC-chhccC-ccchhhhhHHHHHHHHhCCCcceeEEEEEeecCceE
Q 039716          234 VMGHQDK---ELRYRFIYNHF---PSLHEEDILGKT-DVEIFS-GAGVKESQDFKREVLEKGLPAKREITFETELFGSKT  305 (1002)
Q Consensus       234 ~i~~~d~---~~~~~~~~~~~---~~~~~e~iiGk~-~~e~~~-~~~~~~~~~~~~~vl~~g~~~~~e~~~~~~~~~~~~  305 (1002)
                      +++..|.   ++++.++|..+   .|++.++++|++ ....+. +.............+..+.+...++.+....+...+
T Consensus         3 ~i~i~d~~~~~g~i~~~N~~~~~~~g~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~   82 (110)
T 1byw_A            3 KFIIANARVENCAVIYCNDGFCELCGYSRAEVMQRPCTCDFLHGPCTQRRAAAQIAQALLGAEERKVEIAFYRKDGSCFL   82 (110)
T ss_dssp             EEEEEETTSSSCBEEEECHHHHHHHTCCHHHHTTSBTTCGGGCCTTCCHHHHHHHHHHHHTTCCEEEEEEEECTTSCEEE
T ss_pred             CEEEEeccCCCCcEEEECHHHHHHhCCCHHHHccCCCccccccCCcCCHHHHHHHHHHHhcCCCceEEEEEEcCCCCEEE
Confidence            4555565   59999998764   578889999998 244443 322222233444556666665555555444444556


Q ss_pred             EEEEEeeeecCCCCEEEEEEEeechhH
Q 039716          306 FLIYVEPVFSKSGETIGVNYMGMDVTD  332 (1002)
Q Consensus       306 ~~~~~~p~~~~~G~~~gi~~~~~DITe  332 (1002)
                      +.+...|+.+..|.+.|++++..|||+
T Consensus        83 ~~~~~~~~~~~~g~~~~~~~~~~DiTe  109 (110)
T 1byw_A           83 CLVDVVPVKNEDGAVIMFILNFEVVME  109 (110)
T ss_dssp             EEEEEEEEECTTCCEEEEEEEEEEEEE
T ss_pred             EEEEEEEeecCCCCEEEEEEEEEeccC
Confidence            778889999999999999999999996

>4f3l_A Mclock, circadian locomoter output cycles protein kaput; BHLH, PAS, circadian rhythm proteins, transcription-activato; 2.27A {Mus musculus}

Probab=97.55  E-value=0.00016  Score=81.83  Aligned_cols=105  Identities=8%  Similarity=0.023  Sum_probs=86.1

Q ss_pred             CcEEEEecccccEEEeeccC---CCCCcccccCCCchhccCccchhhhhHHHHHHHHhCCCcceeEEEEEeecCceEEEE
Q 039716          232 PVVMGHQDKELRYRFIYNHF---PSLHEEDILGKTDVEIFSGAGVKESQDFKREVLEKGLPAKREITFETELFGSKTFLI  308 (1002)
Q Consensus       232 p~~i~~~d~~~~~~~~~~~~---~~~~~e~iiGk~~~e~~~~~~~~~~~~~~~~vl~~g~~~~~e~~~~~~~~~~~~~~~  308 (1002)
                      ...+...|.++++.++|..+   .|+.+++++|++..+++++++.+........++..|.....++.+....++..|+..
T Consensus       251 ~~f~~~~~~dg~~~~vn~~~~~ilGY~~eEl~g~~~~~~iHpdD~~~~~~~~~~~l~~g~~~~~eyR~~~kdG~~vWv~~  330 (361)
T 4f3l_A          251 EEFTSRHSLEWKFLFLDHRAPPIIGYLPFEVLGTSGYDYYHVDDLENLAKCHEHLMQYGKGKSCYYRFLTKGQQWIWLQT  330 (361)
T ss_dssp             CEEEEEECTTSBEEEECTTSHHHHCCCHHHHTTSBGGGGBCHHHHHHHHHHHHHHHHHSEEECCCEEEECTTSEEEEEEE
T ss_pred             ceeEEEEcCCceEEEECChhhhhhCcCHHHHcCCCHHHeECHHHHHHHHHHHHHHHhCCCcceEEEEEEecCCCEEEEEE
Confidence            45677789999999999876   589999999999999999887777777777888888665566777666666666777


Q ss_pred             EEeeeecC-CCCEEEEEEEeechhHHHHH
Q 039716          309 YVEPVFSK-SGETIGVNYMGMDVTDQVRK  336 (1002)
Q Consensus       309 ~~~p~~~~-~G~~~gi~~~~~DITe~~~~  336 (1002)
                      ...|+++. +|++.+++++..|||++..+
T Consensus       331 ~~~~v~~~~~g~~~~iv~~~~dITe~~~~  359 (361)
T 4f3l_A          331 HYYITYHQWNSRPEFIVCTHTVVSYAEVR  359 (361)
T ss_dssp             EEEEEECTTTCCEEEEEEEEEECCHHHHH
T ss_pred             EEEEEEcCCCCCeeEEEEEEEECChhHhh
Confidence            78899997 89999999999999987543

>2w0n_A Sensor protein DCUS; signal transduction, two-component regulatory system, PAS, kinase, membrane, transferase, solid state cell inner membrane; NMR {Escherichia coli}

Probab=97.50  E-value=3.3e-05  Score=70.04  Aligned_cols=103  Identities=20%  Similarity=0.166  Sum_probs=74.9

Q ss_pred             HHHHHHHHHHHHhccCcEEEEecccccEEEeeccC---CCC---CcccccCCCchhccCccchhhhhHHHHHHHHhCCCc
Q 039716          217 LKRADNFLHFVLQNAPVVMGHQDKELRYRFIYNHF---PSL---HEEDILGKTDVEIFSGAGVKESQDFKREVLEKGLPA  290 (1002)
Q Consensus       217 l~~~~~~l~~il~~~p~~i~~~d~~~~~~~~~~~~---~~~---~~e~iiGk~~~e~~~~~~~~~~~~~~~~vl~~g~~~  290 (1002)
                      ++++..+++.+++++|.+++..|.++++.++|..+   .|+   ..++++|++..+++++..       ...++..+.+.
T Consensus        10 l~~~~~~~~~il~~~~~~i~~~d~~g~i~~~N~~~~~~~g~~~~~~~~~~g~~~~~~~~~~~-------~~~~~~~~~~~   82 (118)
T 2w0n_A           10 ISTLFEQRQAMLQSIKEGVVAVDDRGEVTLINDAAQELLNYRKSQDDEKLSTLSHSWSQVVD-------VSEVLRDGTPR   82 (118)
T ss_dssp             HCTTHHHHHHHHHCCCCCCEEEBTTTBCCCBCHHHHHHHCSCTTTTTSSCCCTTCCCSCTHH-------HHHHHHTTCCC
T ss_pred             HHHHHHHHHHHHhhccccEEEECCCCcEeehhHHHHHHhCCCccChhhhhccCcccccCchh-------HHHHhccCcee
Confidence            44455667889999999999999999999998764   464   678899999888876532       33455555543


Q ss_pred             ceeEEEEEeecCceEEEEEEeeeecCCCCEEEEEEEeechh
Q 039716          291 KREITFETELFGSKTFLIYVEPVFSKSGETIGVNYMGMDVT  331 (1002)
Q Consensus       291 ~~e~~~~~~~~~~~~~~~~~~p~~~~~G~~~gi~~~~~DIT  331 (1002)
                      .... +  .. +..++.+...|+.+ +|.+.|+++++.|||
T Consensus        83 ~~~~-~--~~-~~~~~~~~~~p~~~-~g~~~g~v~~~~DiT  118 (118)
T 2w0n_A           83 RDEE-I--TI-KDRLLLINTVPVRS-NGVIIGAISTFRDKT  118 (118)
T ss_dssp             CCCC-E--ES-SSCEECCCEECCCC-SSCCCCEEECCCCCC
T ss_pred             ccEE-E--EE-CCEEEEEeeceeee-CCEEEEEEEEEEeCC
Confidence            2211 1  11 33567777889987 888889999999987

>3d72_A Vivid PAS protein VVD; circadian, photoreceptor, blue-light, LOV, signaling protein; HET: FAD; 1.65A {Neurospora crassa} PDB: 3is2_A* 2pd8_A* 3hjk_A* 2pdr_A* 2pd7_A* 2pdt_A* 3hji_A* 3rh8_B*

Probab=97.47  E-value=0.00034  Score=66.76  Aligned_cols=102  Identities=14%  Similarity=0.124  Sum_probs=74.5

Q ss_pred             HHhccCcEEEEec---ccccEEEeeccC---CCCCcccccCCCchhccCccc-----------hhhhhHHHHHHHHhCCC
Q 039716          227 VLQNAPVVMGHQD---KELRYRFIYNHF---PSLHEEDILGKTDVEIFSGAG-----------VKESQDFKREVLEKGLP  289 (1002)
Q Consensus       227 il~~~p~~i~~~d---~~~~~~~~~~~~---~~~~~e~iiGk~~~e~~~~~~-----------~~~~~~~~~~vl~~g~~  289 (1002)
                      ++++ +.+++..|   .++++.++|..+   .|++.++++|++..+++++..           ...........+..+.+
T Consensus        31 ~~~~-~~~i~~~d~~d~~g~i~~~N~a~~~l~G~~~~el~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  109 (149)
T 3d72_A           31 PVDT-SVALILCDLKQKDTPIVYASEAFLYMTGYSNAEVLGRNCRFLQSPDGMVKPKSTRKYVDSNTINTMRKAIDRNAE  109 (149)
T ss_dssp             SCCT-TSCEEEEETTSTTCCEEEECHHHHHHHCCCHHHHTTSCGGGGGSTTSCCCTTCCCSSSCHHHHHHHHHHHHHTCC
T ss_pred             hhcC-CccEEEEeccCCCCcEEEECHHHHHHHCcCHHHHcCCChhHhCCccccccccccccccChHHHHHHHHHHHCCCc
Confidence            4555 47777788   799999998764   688899999999888876542           23333344556666766


Q ss_pred             cceeEEEEEeecCceEEEEEEeeeecCCCCEEEEEEEeec
Q 039716          290 AKREITFETELFGSKTFLIYVEPVFSKSGETIGVNYMGMD  329 (1002)
Q Consensus       290 ~~~e~~~~~~~~~~~~~~~~~~p~~~~~G~~~gi~~~~~D  329 (1002)
                      ...++.+....+...++.+...|+++.+|.+.|++++..|
T Consensus       110 ~~~e~~~~~~dG~~~~~~~~~~~i~~~~g~~~~~v~~~~D  149 (149)
T 3d72_A          110 VQVEVVNFKKNGQRFVNFLTMIPVRDETGEYRYSMGFQCE  149 (149)
T ss_dssp             EEEEEEEECTTCCEEEEEEEEEEEECTTSSEEEEEEECCC
T ss_pred             eEEEEEEECCCCCEEEEEEEEEEEEcCCCCEEEEEEEEeC
Confidence            6666655555455556778889999999999999988766

>1qy5_A Endoplasmin; GRP94, NECA, HSP90, chaperone; HET: NEC; 1.75A {Canis lupus familiaris} SCOP: d.122.1.1 PDB: 1qy8_A* 1qye_A* 1u0y_A* 1yt2_A*

Probab=97.39  E-value=2.2e-05  Score=84.45  Aligned_cols=48  Identities=19%  Similarity=0.272  Sum_probs=30.6

Q ss_pred             EEEEEecCCCCCcCcHhhhhhhccCCCc---------------cccCcCCCccccHHHHHHHH
Q 039716          593 RCDVYDTGIGIPENALPTLFRKYMQVSA---------------DHARKYGGTGLGLAICKQLV  640 (1002)
Q Consensus       593 ~i~V~DtGiGI~~e~l~~IF~pF~q~~~---------------~~~~~~~GtGLGLaI~k~Lv  640 (1002)
                      .|.|.|||+||+++.+...|..+.+...               ......|..|+|++-|..++
T Consensus        76 ~l~I~DnGiGMt~edl~~~l~tia~Sgtk~F~~kl~~~~~~~~~d~~~IG~fGvGfySaf~va  138 (269)
T 1qy5_A           76 LLHVTDTGVGMTREELVKNLGTIAKSGTSEFLNKMTEAQEDGQSTSELIGQFGVGFYSAFLVA  138 (269)
T ss_dssp             EEEEEECSCCCCHHHHHHHHHSCCSHHHHHHHHHHHHHHHHTCCCHHHHHHTTCGGGGGGGTE
T ss_pred             EEEEEECCCCCCHHHHHHHhhhhcccccHHHHHhhhhcccccccchhhcCCccccHHHHhhcc
Confidence            4689999999999998776644322100               01112245799998776554

>1ixm_A SPO0B, protein (sporulation response regulatory protein); phosphotransferase, two component system; 2.60A {Bacillus subtilis} SCOP: d.123.1.1 PDB: 2ftk_A* 1f51_A

Probab=97.38  E-value=0.00073  Score=69.09  Aligned_cols=42  Identities=10%  Similarity=0.096  Sum_probs=29.7

Q ss_pred             HHHHHhhhccccHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHH
Q 039716          372 QMLATMSHEIRSPLTGVVSMAEILSNTKLDREQRQLLGVMISSGDL  417 (1002)
Q Consensus       372 ~fla~iSHELRTPL~~I~g~~elL~~~~l~~~~~~~l~~i~~s~~~  417 (1002)
                      +.+....||+.|=|..|.|++++=    --++..+|+..+....+.
T Consensus        23 ~~LR~qrHdf~NkLqvI~GLlql~----~ydea~~yI~~~~~~~q~   64 (192)
T 1ixm_A           23 HLLGHSRHDWMNKLQLIKGNLSLQ----KYDRVFEMIEEMVIDAKH   64 (192)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHTT----CHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHhHHHHHHHHHHHHHHHcC----CHHHHHHHHHHHHHHHHH
Confidence            467778999999999999998862    224556666655544443

>2ior_A Chaperone protein HTPG; heat shock protein, HSP90; HET: ADP; 1.65A {Escherichia coli}

Probab=97.27  E-value=6.5e-05  Score=79.55  Aligned_cols=48  Identities=13%  Similarity=0.272  Sum_probs=32.3

Q ss_pred             EEEEEecCCCCCcCcHhhhhhhccCCCcc------------ccCcCCCccccHHHHHHHH
Q 039716          593 RCDVYDTGIGIPENALPTLFRKYMQVSAD------------HARKYGGTGLGLAICKQLV  640 (1002)
Q Consensus       593 ~i~V~DtGiGI~~e~l~~IF~pF~q~~~~------------~~~~~~GtGLGLaI~k~Lv  640 (1002)
                      .|.|.|||+||+++++...|..+.+....            .....|..|+||+-|..++
T Consensus        95 ~i~I~DnG~GMs~edl~~~~~~ia~S~~~~f~~~l~~~~~~~~~~iG~fGiG~~S~~~~~  154 (235)
T 2ior_A           95 TLTISDNGVGMTRDEVIDHLGTIAKSGTKSFLESLGSDQAKDSQLIGQFGVGFYSAFIVA  154 (235)
T ss_dssp             EEEEEECSSCCCHHHHHHHHTTCCCTTHHHHHHHCCSCHHHHHHHHTTCCCCGGGGGGTE
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHccccccchhhhhccccccccccCCCCChhHHHHHhCc
Confidence            37899999999999999888665443210            0112356899997664443

>1yc1_A HSP 86, heat shock protein HSP 90-alpha; cell-cycle, cancer, drug design, cell cycle; HET: 4BC; 1.70A {Homo sapiens} SCOP: d.122.1.1 PDB: 1yc3_A* 1yc4_A*

Probab=97.25  E-value=0.00022  Score=76.59  Aligned_cols=56  Identities=21%  Similarity=0.326  Sum_probs=36.3

Q ss_pred             EEEEEecCCCCCcCcHhhhhhhccCCCcc----------ccCcCCCccccHHHHHHHHHHhCCEEEEEee
Q 039716          593 RCDVYDTGIGIPENALPTLFRKYMQVSAD----------HARKYGGTGLGLAICKQLVELMGGRLTVTSK  652 (1002)
Q Consensus       593 ~i~V~DtGiGI~~e~l~~IF~pF~q~~~~----------~~~~~~GtGLGLaI~k~Lve~~gG~I~v~S~  652 (1002)
                      .|.|.|||+||+++++...|..+.+....          .....|..|+|++-|..++    -.+.|.|.
T Consensus       116 ~I~I~DnG~GMs~edL~~~l~~ia~S~~~~f~~~l~~~~d~~~iG~fGiGf~S~f~va----~~v~V~Sr  181 (264)
T 1yc1_A          116 TLTIVDTGIGMTKADLINNLGTIAKSGTKAFMEALQAGADISMIGQFGVGFYSAYLVA----EKVTVITK  181 (264)
T ss_dssp             EEEEEECSCCCCHHHHHHHHHSCTTSCHHHHHHHHHTTCCGGGGGGGTCGGGGHHHHE----EEEEEEEE
T ss_pred             EEEEEECCcCCCHHHHHHHHHhhccccchhhhhhhccccchhhcCCCCCCccccccCC----CEEEEEEe
Confidence            47799999999999998777655433210          1113345799998776654    34555554

>3mfx_A Sensory BOX/ggdef family protein; alpha-beta protein, structural genomics, PSI-2, protein structure initiative; 2.40A {Shewanella oneidensis}

Probab=97.16  E-value=0.00056  Score=65.16  Aligned_cols=107  Identities=10%  Similarity=0.043  Sum_probs=68.7

Q ss_pred             HHHHHHHhccCcEEEEecccccEEEeeccC---CCCCcccccCCCchhccCccchhhhhHHHHHHHHhCC----C---cc
Q 039716          222 NFLHFVLQNAPVVMGHQDKELRYRFIYNHF---PSLHEEDILGKTDVEIFSGAGVKESQDFKREVLEKGL----P---AK  291 (1002)
Q Consensus       222 ~~l~~il~~~p~~i~~~d~~~~~~~~~~~~---~~~~~e~iiGk~~~e~~~~~~~~~~~~~~~~vl~~g~----~---~~  291 (1002)
                      ..++.+++++|.+|...|.+|++.++|..+   .|++.++++|++..+++++................+.    +   ..
T Consensus         7 ~~l~~i~~~~~d~i~~~D~~g~I~~~N~aa~~l~G~~~~el~G~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   86 (129)
T 3mfx_A            7 ETIELFIQHLTEAMILVNANGFIRSCNQRSAELLDCPQVSLKGQDWRNFLTEHHQARYDNLLSHDVQLGTNCGQPVQHPA   86 (129)
T ss_dssp             HHHHHHHTTCSSEEEEEETTSBEEEECHHHHHHTTSCHHHHTTSBGGGGBCTTCCGGGGCTTC----------CCSCEEE
T ss_pred             HHHHHHHhcCCceEEEECCCCEEEeEhHHHHHHHCcCHHHHcCCcHHHHcChHhHHHHHHHHHHHHhcCcccccccCCCc
Confidence            457789999999999999999999998764   6889999999999999887543332222222222221    1   12


Q ss_pred             eeEEEEEeecCceEEEEEEeeeecCCCCEEEEEEEeechh
Q 039716          292 REITFETELFGSKTFLIYVEPVFSKSGETIGVNYMGMDVT  331 (1002)
Q Consensus       292 ~e~~~~~~~~~~~~~~~~~~p~~~~~G~~~gi~~~~~DIT  331 (1002)
                      .++.+..+.+...+..+++.|+.+  +... ++++.+|..
T Consensus        87 ~E~~~~rkdG~~~~velsis~i~~--~~~~-~v~~~~~~~  123 (129)
T 3mfx_A           87 QETTLICASGKAKDVELSISYIPG--HEPM-FVMVMHDLE  123 (129)
T ss_dssp             EEEEEECTTSCEEEEEEEEEEECS--SSCE-EEEEEEEC-
T ss_pred             eEEEEEcCCCCEEEEEEEEEEecC--CCcE-EEEEEechh
Confidence            455555555555666788888873  3333 334455653

>2jhe_A Transcription regulator TYRR; aromatic hydrocarbons catabolism, TYRR protei nucleotide-binding, transcription regulation, activator; HET: PG4; 2.30A {Escherichia coli}

Probab=97.12  E-value=0.0002  Score=72.26  Aligned_cols=105  Identities=14%  Similarity=0.148  Sum_probs=74.6

Q ss_pred             HHHHHHHHHHhccCcEEEEecccccEEEeeccC---CCCCcccccCCCchhccCccchhhhhHHHHHHHHhCCCcceeEE
Q 039716          219 RADNFLHFVLQNAPVVMGHQDKELRYRFIYNHF---PSLHEEDILGKTDVEIFSGAGVKESQDFKREVLEKGLPAKREIT  295 (1002)
Q Consensus       219 ~~~~~l~~il~~~p~~i~~~d~~~~~~~~~~~~---~~~~~e~iiGk~~~e~~~~~~~~~~~~~~~~vl~~g~~~~~e~~  295 (1002)
                      +...+++.+++++|.++...|.++++.++|..+   .++..++++|++..+++++...       ..++..+........
T Consensus        77 ~~~~~l~~il~~~~~gvi~~D~~g~I~~~N~aa~~llg~~~~~~~g~~~~~~~~~~~~-------~~~~~~~~~~~~~~~  149 (190)
T 2jhe_A           77 REHLALSALLEALPEPVLSVDMKSKVDMANPASCQLFGQKLDRLRNHTAAQLINGFNF-------LRWLESEPQDSHNEH  149 (190)
T ss_dssp             HHHHHHHHHHHHCSSCEEEECTTCBEEEECHHHHHHHTSCHHHHTTSBGGGTSTTCCH-------HHHHHTCCCSCEEEE
T ss_pred             HHHHHHHHHHHhCCCcEEEEcCCCCEEEEcHHHHHHhCCCHHHhcCccHHHHhCCCCH-------HHHHhcCCCCCcceE
Confidence            345678899999999999999999999998754   5777788999999998875421       234454432212222


Q ss_pred             EEEeecCceEEEEEEeeeecCCCC----EEEEEEEeechhHH
Q 039716          296 FETELFGSKTFLIYVEPVFSKSGE----TIGVNYMGMDVTDQ  333 (1002)
Q Consensus       296 ~~~~~~~~~~~~~~~~p~~~~~G~----~~gi~~~~~DITe~  333 (1002)
                      +  .. +...+.+...|+++.+|.    +.|++.++.|||+.
T Consensus       150 ~--~~-~g~~~~~~~~pi~~~~~~~~~~~~g~v~~~~DiTe~  188 (190)
T 2jhe_A          150 V--VI-NGQNFLMEITPVYLQDENDQHVLTGAVVMLRSTIRM  188 (190)
T ss_dssp             E--EE-TTEEEEEEEEEETTTTEEEEEEEE-HHHHHHHHTTT
T ss_pred             E--EE-CCeEEEEEEEEEEecCCCCcceEEeEEEEEeccchh
Confidence            2  22 335677888999876665    78888888999974

>4f3l_B BMAL1B; BHLH, PAS, circadian rhythm proteins, transcription-activato; 2.27A {Mus musculus}

Probab=97.10  E-value=0.00064  Score=77.52  Aligned_cols=105  Identities=12%  Similarity=0.090  Sum_probs=80.7

Q ss_pred             ccCcEEEEecccccEEEeeccC---CCCCcccccCCCchhccCccchhhhhHHHHHHHHhCCC-cceeEEEEEeecCceE
Q 039716          230 NAPVVMGHQDKELRYRFIYNHF---PSLHEEDILGKTDVEIFSGAGVKESQDFKREVLEKGLP-AKREITFETELFGSKT  305 (1002)
Q Consensus       230 ~~p~~i~~~d~~~~~~~~~~~~---~~~~~e~iiGk~~~e~~~~~~~~~~~~~~~~vl~~g~~-~~~e~~~~~~~~~~~~  305 (1002)
                      +....+...|.++++.|++..+   .||.++|++|++..+++++++.+........++..+.+ ...++++....++..|
T Consensus       276 ~~~~fi~~~~~dg~~~~vn~~~~~ilGY~~eEl~g~~~~~~iHpdD~~~~~~~~~~~l~~~~~~~~~eyR~~~kdG~~vW  355 (387)
T 4f3l_B          276 KSMEYVSRHAIDGKFVFVDQRATAILAYLPQELLGTSCYEYFHQDDIGHLAECHRQVLQTREKITTNCYKFKIKDGSFIT  355 (387)
T ss_dssp             CCCEEEEEECTTSBEEEECTHHHHHHCCCHHHHTTSBGGGTBCHHHHHHHHHHHHHHTTCSSCEECCCEEEECTTSCEEE
T ss_pred             CCceEEEEECCCCEEEEECCCcccccCCCHHHHcCCcHHHeeCHHHHHHHHHHHHHHHhcCCCeeeEEEEEEccCCCEEE
Confidence            3455778889999999998764   68999999999999999887777666666666655443 3346777776666667


Q ss_pred             EEEEEeeeecC-CCCEEEEEEEeechhHHH
Q 039716          306 FLIYVEPVFSK-SGETIGVNYMGMDVTDQV  334 (1002)
Q Consensus       306 ~~~~~~p~~~~-~G~~~gi~~~~~DITe~~  334 (1002)
                      +.....++++. +|++.+++++..|||+++
T Consensus       356 v~~~~~~~~~~~~g~~~~ivg~~~dIT~Rk  385 (387)
T 4f3l_B          356 LRSRWFSFMNPWTKEVEYIVSTNTVVLANV  385 (387)
T ss_dssp             EEEEEEEEEETTTTEEEEEEEEEEECC---
T ss_pred             EEEEEEEEECCCCCCEEEEEEEEEEcchhh
Confidence            77778889887 899999999999999875

>3zrx_A AF1503 protein, osmolarity sensor protein ENVZ; signaling protein, osmoregulation, OMPR, OMPC; 1.25A {Archaeoglobus fulgidus} PDB: 3zrv_A 3zrw_A 3zrw_B 2lfs_A 2lfr_A 1joy_A 2l7i_A 2y20_A 2l7h_A 2y21_A 2y0t_A 2y0q_A

Probab=96.90  E-value=0.002  Score=58.61  Aligned_cols=55  Identities=22%  Similarity=0.367  Sum_probs=47.2

Q ss_pred             HHHHHHhhhccccHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 039716          371 KQMLATMSHEIRSPLTGVVSMAEILSNTKLDREQRQLLGVMISSGDLVLQLINDILDLSK  430 (1002)
Q Consensus       371 k~fla~iSHELRTPL~~I~g~~elL~~~~l~~~~~~~l~~i~~s~~~L~~LIndlLd~sk  430 (1002)
                      ++|++.+|||||||++.|.++++.+...     ..+....+...+.+|..++++++++++
T Consensus        61 ~~~~~~~shel~~~l~~i~~~~~~l~~~-----~~~~~~~~~~~~~~~~~~~~~l~~~~~  115 (115)
T 3zrx_A           61 TLLMAGVSHDLRTPLTRIRLATEMMSEQ-----DGYLAESINKDIEECNAIIEQFIDYLR  115 (115)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHTSCGG-----GHHHHHHHHHHHHHHHHHHHHHHTTCC
T ss_pred             HHHHHHHHHHHHhhHHHHHHHHHHHHhh-----hHHHHHHHHHHHHHHHHHHHHHHHHhC
Confidence            4799999999999999999999987543     246678889999999999999998764

>2ayx_A Sensor kinase protein RCSC; two independent structural domains, transferase; NMR {Escherichia coli} SCOP: c.23.1.1 c.23.1.6 PDB: 2ayz_A 2ayy_A

Probab=96.88  E-value=0.0011  Score=70.77  Aligned_cols=95  Identities=8%  Similarity=0.096  Sum_probs=70.2

Q ss_pred             CCCCeEEEEecCHHHHHHHHHHHHhcCCeEEEEcCHHHHHHHHHcCCCcEEEEcCCCCCCCHHHHHHHHhccccCCCchh
Q 039716          857 KPKPKILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDA  936 (1002)
Q Consensus       857 ~~~~~ILiVeDn~~n~~~l~~~L~~~g~~v~~a~~G~eAl~~~~~~~~DlIlmDi~MP~mdG~e~~~~IR~~~~~~~~~~  936 (1002)
                      ..+.+|||||||+.++..+..+|...|+.|..+.+       .....||+||+|..||...+.+                
T Consensus         9 l~~~~vlvv~d~~~~~~~l~~~L~~~g~~v~~~~~-------~~~~~~~~ii~d~~~~~~~~~~----------------   65 (254)
T 2ayx_A            9 LSGKRCWLAVRNASLCQFLETSLQRSGIVVTTYEG-------QEPTPEDVLITDEVVSKKWQGR----------------   65 (254)
T ss_dssp             TTTEEEEEECCCHHHHHHHHHHHTTTTEEEEECSS-------CCCCTTCEEEEESSCSCCCCSS----------------
T ss_pred             cCCCEEEEEcCCHHHHHHHHHHHHHCCCEEEEecC-------CCCCcCcEEEEcCCCccccccc----------------
Confidence            45679999999999999999999999999988875       1346799999999999764311                


Q ss_pred             hhhhhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHHhh
Q 039716          937 AAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQY 1000 (1002)
Q Consensus       937 ~~~~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~~ 1000 (1002)
                                            .++.++.......    ...+...++.||+...+|...+.++
T Consensus        66 ----------------------~~i~~~~~~~~~~----~~~~~~~~~~~~~~~~~l~~~l~~~  103 (254)
T 2ayx_A           66 ----------------------AVVTFCRRHIGIP----LEKAPGEWVHSVAAPHELPALLARI  103 (254)
T ss_dssp             ----------------------EEEEECSSCCCSC----CTTSTTEEEECSSCCSHHHHHHHHH
T ss_pred             ----------------------eEEEEecccCCCc----ccccCCceeccccchHHHHHHHHHH
Confidence                                  1444444321100    1235568999999999888888764

>1nwz_A PYP, photoactive yellow protein; PAS, LOV, GAF, domains fold, signaling protein; HET: HC4; 0.82A {Halorhodospira halophila} SCOP: d.110.3.1 PDB: 1kou_A* 1ot9_A* 1otb_A* 1s4r_A* 1s4s_A* 1ts0_A* 1ts6_A* 1ts7_A* 1ts8_A* 1uwn_X* 1uwp_X* 2d01_A* 2phy_A* 2pyp_A* 2pyr_A* 2qj5_A* 2qj7_A* 2qws_A* 2zoh_A* 2zoi_A* ...

Probab=96.77  E-value=0.0059  Score=57.71  Aligned_cols=99  Identities=11%  Similarity=-0.020  Sum_probs=72.0

Q ss_pred             HHHHhccCcEEEEecccccEEEeecc---CCCCCcccccCCCchhcc-CccchhhhhHHHHHHHHhCCCcceeEEEEEee
Q 039716          225 HFVLQNAPVVMGHQDKELRYRFIYNH---FPSLHEEDILGKTDVEIF-SGAGVKESQDFKREVLEKGLPAKREITFETEL  300 (1002)
Q Consensus       225 ~~il~~~p~~i~~~d~~~~~~~~~~~---~~~~~~e~iiGk~~~e~~-~~~~~~~~~~~~~~vl~~g~~~~~e~~~~~~~  300 (1002)
                      ..+++++|.++...|.++++.++|..   ..|+++++++|++.++.+ +......+.....+.+++|. ......+....
T Consensus        20 ~~~ld~l~~Gii~lD~~g~I~~~N~~~e~~sG~~~~eviGk~~f~~~~~~~~~~~f~~rf~~~~~~g~-l~~~~~~v~~~   98 (125)
T 1nwz_A           20 DGQLDGLAFGAIQLDGDGNILQYNAAEGDITGRDPKQVIGKNFFKDVAPCTDSPEFYGKFKEGVASGN-LNTMFEYTFDY   98 (125)
T ss_dssp             HHHHTTCSSEEEEEETTCBEEEECHHHHHHHCCCHHHHTTSBCCCCCCGGGCSTTTHHHHHHHHHHTC-CEEEEEEEECT
T ss_pred             HHHHhccCceEEEECCCCEEEEEHHHHHHHhCCCHHHHcCCchhhhccchhcccHHHHHHHHHHhcCc-eeEEEEEEEcC
Confidence            34799999999999999999998864   468999999999998754 43444555555666666776 44444444222


Q ss_pred             cCceEEEEEEeeeecCCCCEEEEEE
Q 039716          301 FGSKTFLIYVEPVFSKSGETIGVNY  325 (1002)
Q Consensus       301 ~~~~~~~~~~~p~~~~~G~~~gi~~  325 (1002)
                       ......+.+.+..+.+|..+|+..
T Consensus        99 -~~~p~~v~i~l~~~~~~~~~~i~v  122 (125)
T 1nwz_A           99 -QMTPTKVKVHMKKALSGDSYWVFV  122 (125)
T ss_dssp             -TSCCEEEEEEEEECSSSSEEEEEE
T ss_pred             -CCCEEEEEEEEEEcCCCCEEEEEE
Confidence             233677788888899999988764

>3a0s_A Sensor protein; PAS-fold, kinase, phosphoprotein, transferase, two-component regulatory system; HET: PG4 PGE; 1.47A {Thermotoga maritima} PDB: 3a0v_A*

Probab=96.72  E-value=0.0087  Score=50.59  Aligned_cols=92  Identities=20%  Similarity=0.177  Sum_probs=62.7

Q ss_pred             cCcEEEEecccccEEEeeccC---CCCCcccccCCCchhccCccchhhhhHHHHHHHHhCCCcceeEEEEEeecCceEEE
Q 039716          231 APVVMGHQDKELRYRFIYNHF---PSLHEEDILGKTDVEIFSGAGVKESQDFKREVLEKGLPAKREITFETELFGSKTFL  307 (1002)
Q Consensus       231 ~p~~i~~~d~~~~~~~~~~~~---~~~~~e~iiGk~~~e~~~~~~~~~~~~~~~~vl~~g~~~~~e~~~~~~~~~~~~~~  307 (1002)
                      +|.+|+..|.++++.++|..+   .++..++++|++..++ +. . ..........+..+.+.    .+....++..++.
T Consensus         1 ~~~~i~~~d~~g~i~~~N~~~~~l~g~~~~~~~g~~~~~~-~~-~-~~~~~~~~~~~~~~~~~----~~~~~~~~~~~~~   73 (96)
T 3a0s_A            1 METAIITLSKDGRITEWNKKAEQLFGLKKENVLGRRLKDL-PD-F-EEIGSVAESVFENKEPV----FLNFYKFGERYFN   73 (96)
T ss_dssp             CCCEEEEEETTSBEEEECHHHHHHHCCCHHHHTTSBGGGS-TT-C-HHHHHHHHHHHHHTCCE----EEEEEEETTEEEE
T ss_pred             CCceEEEEcCCCCEeehhHHHHHHhCCCHHHhcCCCHHHC-cc-h-HHHHHHHHHHhccCCeE----EEEEEcCCcEEEE
Confidence            367888999999999998764   5778889999998887 32 1 22222334445544432    2333344667788


Q ss_pred             EEEeeeecCCCC-EEEEEEEeec
Q 039716          308 IYVEPVFSKSGE-TIGVNYMGMD  329 (1002)
Q Consensus       308 ~~~~p~~~~~G~-~~gi~~~~~D  329 (1002)
                      +...|+.+.+|. +.|+++++.|
T Consensus        74 ~~~~p~~~~~~~~~~g~v~~~~D   96 (96)
T 3a0s_A           74 IRFSPFRNAKTQLLEGVIITIDD   96 (96)
T ss_dssp             EEEEEEECTTTCCEEEEEEEEEC
T ss_pred             EEEEEeEcCCCCeeeEEEEEecC
Confidence            899999988664 6788887765

>1mzu_A PPR; photoactive yellow protein, PAS, PYP, signaling protein; HET: HC4; 2.00A {Rhodospirillum centenum} SCOP: d.110.3.1

Probab=96.68  E-value=0.0073  Score=57.26  Aligned_cols=98  Identities=7%  Similarity=-0.019  Sum_probs=71.5

Q ss_pred             HHHhccCcEEEEecccccEEEeecc---CCCCCcccccCCCchhcc-CccchhhhhHHHHHHHHhCCCcceeEEEEEeec
Q 039716          226 FVLQNAPVVMGHQDKELRYRFIYNH---FPSLHEEDILGKTDVEIF-SGAGVKESQDFKREVLEKGLPAKREITFETELF  301 (1002)
Q Consensus       226 ~il~~~p~~i~~~d~~~~~~~~~~~---~~~~~~e~iiGk~~~e~~-~~~~~~~~~~~~~~vl~~g~~~~~e~~~~~~~~  301 (1002)
                      .+++++|.++...|.++++.++|..   ..|+++++++|++.++.+ +......+.....+.++.|. ......+.... 
T Consensus        26 ~~ld~l~~GiivlD~dg~I~~~N~~~e~isG~s~eeviGk~~f~~~~p~~~~~~f~grf~~~~~~G~-l~~~~~yv~~~-  103 (129)
T 1mzu_A           26 AEFDALPVGAIQVDGSGVIHRYNRTESRLSGRIPERVIGRNFFTEVAPCTNIPAFSGRFMDGVTSGT-LDARFDFVFDF-  103 (129)
T ss_dssp             TTGGGCSSEEEEEETTCBEEEECHHHHHHHCCCHHHHTTSBCCCCCCGGGCSTTTHHHHHHHHHTSC-CEEEEEEEEEC-
T ss_pred             HHHhccCceEEEECCCCeEEEEHHHHHHHhCCCHHHHcCCchhhhccchhcccHHHHHHHHHHhcCc-eeEEEEEEEcC-
Confidence            3689999999999999999998864   468999999999998754 43444555555666666766 44444444222 


Q ss_pred             CceEEEEEEeeeecCCCCEEEEEE
Q 039716          302 GSKTFLIYVEPVFSKSGETIGVNY  325 (1002)
Q Consensus       302 ~~~~~~~~~~p~~~~~G~~~gi~~  325 (1002)
                      ....+.+.+....+.+|..+|++.
T Consensus       104 ~~~p~~v~i~l~~~~~~~~~~i~v  127 (129)
T 1mzu_A          104 QMAPVRVQIRMQNAGVPDRYWIFV  127 (129)
T ss_dssp             SSCEEEEEEEEEECSSTTEEEEEE
T ss_pred             CCCEEEEEEEEEEcCCCCEEEEEE
Confidence            233677888888899999988764

>2vlg_A Sporulation kinase A; histidine kinase, two-component regulatory system, two-component signal transduction, transferase, phosphorylation, SCOD; 1.7A {Bacillus subtilis}

Probab=96.67  E-value=0.0028  Score=58.55  Aligned_cols=90  Identities=11%  Similarity=0.029  Sum_probs=55.4

Q ss_pred             HHHhccCcEEEEecccccEEEeeccC---CCCCcccccCCCchhccCccchhhhhHHHHHHHHhCCCcceeEEEEEeecC
Q 039716          226 FVLQNAPVVMGHQDKELRYRFIYNHF---PSLHEEDILGKTDVEIFSGAGVKESQDFKREVLEKGLPAKREITFETELFG  302 (1002)
Q Consensus       226 ~il~~~p~~i~~~d~~~~~~~~~~~~---~~~~~e~iiGk~~~e~~~~~~~~~~~~~~~~vl~~g~~~~~e~~~~~~~~~  302 (1002)
                      .++++++.+|+..|.+|++.|+|..+   .|+++++++|++..+++++...+.....   +...+.....+..+..+.+.
T Consensus         3 ~lle~~~d~i~v~d~~G~i~yvn~~~~~~lGy~~~el~G~~~~~~ihp~D~~~~~~~---~~~~~~~~~~e~r~~~kdG~   79 (111)
T 2vlg_A            3 FPLQTKTDIHAVLASNGRIIYISANSKLHLGYLQGEMIGSFLKTFLHEEDQFLVESY---FYNEHHLMPCTFRFIKKDHT   79 (111)
T ss_dssp             ------CCEEEEECTTSBEEEECTTHHHHHSCCHHHHTTSBGGGGBCGGGHHHHHHH---HHCSCCSSCEEEEEECTTSC
T ss_pred             chhhcCCCEEEEEcCCCeEEEEChHHHHHhCCCHHHHcCCcHHHeECHhHHHHHHHH---HhccCCCccEEEEEEcCCCC
Confidence            57899999999999999999999864   6899999999999999887665443322   22222223345555555555


Q ss_pred             ceEEEEEEeeeecCCC
Q 039716          303 SKTFLIYVEPVFSKSG  318 (1002)
Q Consensus       303 ~~~~~~~~~p~~~~~G  318 (1002)
                      ..|+...+.++.+..+
T Consensus        80 ~~wve~~~~~v~~~~~   95 (111)
T 2vlg_A           80 IVWVEAAVEIVTTRAE   95 (111)
T ss_dssp             EEEEEEEEEEC-----
T ss_pred             EEEEEEEEEEEecccC
Confidence            5566677777777544

>1s16_A Topoisomerase IV subunit B; two-domain protein complexed with ADPNP; HET: ANP; 2.10A {Escherichia coli} SCOP: d.14.1.3 d.122.1.2

Probab=96.47  E-value=0.0035  Score=71.18  Aligned_cols=48  Identities=21%  Similarity=0.452  Sum_probs=35.6

Q ss_pred             EEEEecCCCCCcCc--------HhhhhhhccCCCc---cccCcCCC-ccccHHHHHHHHH
Q 039716          594 CDVYDTGIGIPENA--------LPTLFRKYMQVSA---DHARKYGG-TGLGLAICKQLVE  641 (1002)
Q Consensus       594 i~V~DtGiGI~~e~--------l~~IF~pF~q~~~---~~~~~~~G-tGLGLaI~k~Lve  641 (1002)
                      |+|.|+|.|||.+.        ++.+|..|+.+..   ......+| .|.||+.+.-+.+
T Consensus        65 I~V~DnG~GIp~~~~~~~~~~~~e~v~~~lhagsKf~~~~~~~sgGl~GvGls~vnalS~  124 (390)
T 1s16_A           65 LEVIDDGRGMPVDIHPEEGVPAVELILCRLHAGGKFSNKNYQFSGGLHGVGISVVNALSK  124 (390)
T ss_dssp             EEEEECSSCCCCSBCTTTCSBHHHHHHHCTTEESCSSSSSCSSCSCCSSCHHHHHHHTEE
T ss_pred             EEEEECCCCcCcccccccCcchhhheeeeecccCCcCCCcccccCCccccchHHHHHhhc
Confidence            77999999999998        6788988765432   11122344 8999999988874

>3cwo_X Beta/alpha-barrel protein based on 1THF and 1TMY; XRAY, CHEY, HISF, half barrel, de novo protein; 3.10A {Thermotoga maritima} PDB: 2lle_A

Probab=96.28  E-value=0.0075  Score=62.72  Aligned_cols=88  Identities=23%  Similarity=0.273  Sum_probs=67.6

Q ss_pred             EEEcCHHHHHHHHHcC-CCcEEEEcC-CCCCCCHHHHHHHHhccccCCCchhhhhhhhcccCCCCCCCCCCCCccEEEEc
Q 039716          887 DVVNNGVEAVHAVQCQ-NYDLILMDV-CMPVMDGLKATRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMT  964 (1002)
Q Consensus       887 ~~a~~G~eAl~~~~~~-~~DlIlmDi-~MP~mdG~e~~~~IR~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipIIalT  964 (1002)
                      ....+..+.+..+... ..+++++++ .++.|+|+. ++.|+....                        ..++|||+++
T Consensus       127 ~~~~~~~~~i~~~~~~~~~~vli~~~~~~g~~~g~~-~~~i~~~~~------------------------~~~~Pvia~~  181 (237)
T 3cwo_X          127 NTGILLRDWVVEVEKRGAGEILLTSIDRDGTKSGYD-TEMIRFVRP------------------------LTTLPIIASG  181 (237)
T ss_dssp             EEEEEHHHHHHHHHHHTCSEEEEEETTTTTCCSCCC-HHHHHHHGG------------------------GCCSCEEEES
T ss_pred             ccccCHHHHHHHHhhcCCCeEEEEecCCCCcccccc-HHHHHHHHH------------------------hcCCCEEecC
Confidence            3344566666666554 556999997 788888876 555554321                        2368999999


Q ss_pred             CCCCHHHHHHHHHcCCCEEE------eCCCChHHHHHHHHh
Q 039716          965 ANALSESAEECFANGMDSFV------SKPVTFQKLKECLEQ  999 (1002)
Q Consensus       965 a~~~~~~~~~~~~aG~d~~l------~KP~~~~~L~~~l~~  999 (1002)
                      +....++..+|+++|||+++      .+|+++.++...+.+
T Consensus       182 g~~~~~~~~~~~~~G~~~~~vg~a~~~~~~~~~~~~~~l~~  222 (237)
T 3cwo_X          182 GAGKMEHFLEAFLAGADAALAASVFHFREIDVRELKEYLKK  222 (237)
T ss_dssp             CCCSHHHHHHHHHHTCSEEEESHHHHTTSSCHHHHHHHHHT
T ss_pred             CCCCHHHHHHHHHcCcHHHhhhHHHHcCCCCHHHHHHHHHH
Confidence            99999999999999999995      899999999988764

>2ykf_A Pdtas, probable sensor histidine kinase pdtas; transferase, two-component system, GAF domain, PAS domain; 2.00A {Mycobacterium tuberculosis} PDB: 2ykh_A

Probab=95.13  E-value=0.00089  Score=73.78  Aligned_cols=108  Identities=17%  Similarity=0.191  Sum_probs=72.1

Q ss_pred             HHhccCcEEEEecccccEEEeeccCCCC-----CcccccCCCchhccCcc---chh--hhhHHHHHHHHh-CCCcceeEE
Q 039716          227 VLQNAPVVMGHQDKELRYRFIYNHFPSL-----HEEDILGKTDVEIFSGA---GVK--ESQDFKREVLEK-GLPAKREIT  295 (1002)
Q Consensus       227 il~~~p~~i~~~d~~~~~~~~~~~~~~~-----~~e~iiGk~~~e~~~~~---~~~--~~~~~~~~vl~~-g~~~~~e~~  295 (1002)
                      ++++++.+|...|.++++.++|..+..+     ..++++|++..++++..   ...  ........++.. +.+...++.
T Consensus       175 ~~~~~~dGIivvD~~G~Ii~~N~aA~~ll~~lG~~~~~iGk~l~el~~~~~~~~~~~~~~~~~l~~vl~~~~~~~~~ei~  254 (305)
T 2ykf_A          175 SSPRAGDGFIRLDVDGVVSYASPNALSAYHRMGLTTELEGVNLIDATRPLISDPFEAHEVDEHVQDLLAGDGKGMRMEVD  254 (305)
Confidence            5678999999999999999999876443     12688999999887643   110  111222224443 222222211


Q ss_pred             EEEeecCceEEEEEEeeeecCCCCEEEEEEEeechhHHHHHHHHH
Q 039716          296 FETELFGSKTFLIYVEPVFSKSGETIGVNYMGMDVTDQVRKREKM  340 (1002)
Q Consensus       296 ~~~~~~~~~~~~~~~~p~~~~~G~~~gi~~~~~DITe~~~~~~~~  340 (1002)
                           .+..++.+...|+++ +|.+.|++.+++|||+.++.++++
T Consensus       255 -----~~~~~l~v~~~Pi~~-~g~~~G~Vvv~rDITE~~~lE~eL  293 (305)
T 2ykf_A          255 -----AGGATVLLRTLPLVV-AGRNVGAAILIRDVTEVKRRDRAL  293 (305)
Confidence                 134567778889986 588899999999999987766554

>3t0h_A Heat shock protein HSP 90-alpha; chaperone, ATPase; 1.20A {Homo sapiens} SCOP: d.122.1.1 PDB: 3r4m_A 3t0z_A* 3t10_A* 3t1k_A* 3t2s_A* 1uyl_A 1uy7_A* 1uy8_A* 1uy9_A* 1uyc_A* 1uyd_A* 1uye_A* 1uyf_A* 1uyg_A* 1uyh_A* 1uyk_A* 1uy6_A 2cdd_A* 2uwd_A* 2vci_A* ...

Probab=96.12  E-value=0.0011  Score=69.39  Aligned_cols=57  Identities=21%  Similarity=0.304  Sum_probs=35.0

Q ss_pred             EEEEEecCCCCCcCcHhhhhhhccCCCc----------cccCcCCCccccHHHHHHHHHHhCCEEEEEeec
Q 039716          593 RCDVYDTGIGIPENALPTLFRKYMQVSA----------DHARKYGGTGLGLAICKQLVELMGGRLTVTSKV  653 (1002)
Q Consensus       593 ~i~V~DtGiGI~~e~l~~IF~pF~q~~~----------~~~~~~~GtGLGLaI~k~Lve~~gG~I~v~S~~  653 (1002)
                      .|.|.|||+||+++++...|....+...          ......|--|+||+-+-.+.    -++.|.|..
T Consensus        80 ~i~V~DnG~GMs~edl~~~l~~ia~S~~~~f~~~l~~~~~~~~iG~fG~G~~S~~~va----d~v~V~Sr~  146 (228)
T 3t0h_A           80 TLTIVDTGIGMTKADLINNLGTIAKSGTKAFMEALQAGADISMIGQFGVGFYSAYLVA----EKVTVITKH  146 (228)
T ss_dssp             EEEEEECSCCCCHHHHHTGGGSCHHHHHHHHHHHHHTTCCGGGGGGGTCGGGGGGGTE----EEEEEEEEC
T ss_pred             EEEEEeCCCCCCHHHHHHHHHhhccccchhhhhhhcccCCcccCCCCChhHHHHhccC----CEEEEEEec
Confidence            4679999999999998766644322100          11123455689998764432    256666654

>1ll8_A PAS kinase; PAS domain, ligand binding, ligand screening, kinase regulation, transferase; NMR {Homo sapiens} SCOP: d.110.3.5

Probab=95.92  E-value=0.0061  Score=55.17  Aligned_cols=100  Identities=9%  Similarity=0.055  Sum_probs=61.8

Q ss_pred             ccCcEEEEeccc-ccEEEeeccC---CCCCcccccCCCchhccCccchhhhhHHHHHHHH-hCCCc---ceeEEEEEeec
Q 039716          230 NAPVVMGHQDKE-LRYRFIYNHF---PSLHEEDILGKTDVEIFSGAGVKESQDFKREVLE-KGLPA---KREITFETELF  301 (1002)
Q Consensus       230 ~~p~~i~~~d~~-~~~~~~~~~~---~~~~~e~iiGk~~~e~~~~~~~~~~~~~~~~vl~-~g~~~---~~e~~~~~~~~  301 (1002)
                      +++.+|+..|.+ +++.++|..+   .|++.++++|++..+++++........+....+. .+...   ..++.+....+
T Consensus         6 ~~~~~i~~~d~~~g~I~~~N~aa~~l~G~~~~el~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~dG   85 (114)
T 1ll8_A            6 EFNKAIFTVDAKTTEILVANDKACGLLGYSSQDLIGQKLTQFFLRSDSDVVEALSEEHMEADGHAAVVFGTVVDIISRSG   85 (114)
T ss_dssp             TTTCEEEEEETTTCBEEEECTTHHHHHTCCTTTTTTSBGGGGSSCTTTHHHHHTTSSTTSSSSCSSCCCSSSEEECCTTC
T ss_pred             CCCceEEEEECCCCeEEEehHHHHHHhCCCHHHHcCCCHHHhcCcchhHHHHHHHHHhhccCCcceeccCcEEEEEecCC
Confidence            455789999999 9999999864   6889999999999998876432211111100111 11111   23444444444


Q ss_pred             CceEEEEEEeeeecCCCCEEEEEEEeechh
Q 039716          302 GSKTFLIYVEPVFSKSGETIGVNYMGMDVT  331 (1002)
Q Consensus       302 ~~~~~~~~~~p~~~~~G~~~gi~~~~~DIT  331 (1002)
                      ...++.++..|+.+..+.  +++++..|++
T Consensus        86 ~~~~v~~~~~~~~~~~~~--~~v~~~~~~~  113 (114)
T 1ll8_A           86 EKIPVSVWMKRMRQERRL--CCVVVLEPVE  113 (114)
T ss_dssp             CCEEEECCEECCBSSSSB--EEEEEEEECC
T ss_pred             CEEEEEEEEEeeccCCcc--EEEEEEeecC
Confidence            455666778888765543  5566777764

>3peh_A Endoplasmin homolog; structural genomics, structural genomics consortium, SGC, HE protein, chaperone, ATP binding; HET: IBD; 2.75A {Plasmodium falciparum 3D7} PDB: 3pej_A*

Probab=95.73  E-value=0.0041  Score=66.75  Aligned_cols=48  Identities=21%  Similarity=0.302  Sum_probs=29.1

Q ss_pred             EEEEEecCCCCCcCcHhhhhhh--------cc---CCCccccCcCCCccccHHHHHHHH
Q 039716          593 RCDVYDTGIGIPENALPTLFRK--------YM---QVSADHARKYGGTGLGLAICKQLV  640 (1002)
Q Consensus       593 ~i~V~DtGiGI~~e~l~~IF~p--------F~---q~~~~~~~~~~GtGLGLaI~k~Lv  640 (1002)
                      .|.|.|||+||+++.+..-+..        |.   +........-|-.|+|++-|..++
T Consensus        94 tLtI~DNGiGMt~edL~~~LgtIa~Sgtk~f~e~l~~~~~d~~~IGqFGVGFySaf~va  152 (281)
T 3peh_A           94 ILSITDTGIGMTKVDLINNLGTIAKSGTSNFLEAISKSGGDMSLIGQFGVGFYSAFLVA  152 (281)
T ss_dssp             EEEEEECSCCCCHHHHHHHHHHHHHSCHHHHHHHHHHTTCCSTTTTTTTCGGGGGGGTE
T ss_pred             EEEEEeCCCCCCHHHHHHHHHHHHhHhhhhHHHhhhccccccccccccCccchhhcccc
Confidence            4679999999999997653321        21   100111223466799998775543

>3o0i_A HSP90AA1 protein; HSP90 heat-shock proteins, chaperone-inhibitor complex; HET: P54; 1.47A {Homo sapiens} PDB: 2fwz_A* 2fwy_A* 2h55_A*

Probab=95.52  E-value=0.0026  Score=67.54  Aligned_cols=48  Identities=19%  Similarity=0.279  Sum_probs=29.7

Q ss_pred             EEEEEecCCCCCcCcHhhhhhhccCCC----------ccccCcCCCccccHHHHHHHH
Q 039716          593 RCDVYDTGIGIPENALPTLFRKYMQVS----------ADHARKYGGTGLGLAICKQLV  640 (1002)
Q Consensus       593 ~i~V~DtGiGI~~e~l~~IF~pF~q~~----------~~~~~~~~GtGLGLaI~k~Lv  640 (1002)
                      .|.|.|||+||+++++..-|....+..          .......|--|+||+-+..++
T Consensus       108 ~I~I~DnG~GMt~edl~~~l~~ia~S~~~~f~~~L~~~~~~~~iG~fG~Gf~S~f~Va  165 (256)
T 3o0i_A          108 TLTIVDTGIGMTKADLINNLGTIAKSGTKAFMEALQAGADISMIGQFGVGFYSAYLVA  165 (256)
T ss_dssp             EEEEEECSCCCCHHHHHTHHHHHHHHHHHHHHHHHHTTCCGGGGGGGTCGGGGGGGTE
T ss_pred             EEEEecCCCCcCHHHHHHHHHhhccccccchhhhhcccCCccccCCCcchHHHhhccC
Confidence            468999999999999876553321100          011123456789998775443

>2gqp_A Endoplasmin; GRP94, HSP82, HSP90, HTPG, chaperone, ligand, NECA, NPCA, adenosine; HET: PA7 PG4 1PE; 1.50A {Canis lupus familiaris} SCOP: d.122.1.1 PDB: 1tc0_A* 1tbw_A* 1u0z_A* 1u2o_A* 1ysz_A* 1yt0_A* 1yt1_A* 2exl_A* 2fyp_A* 2gfd_A* 1tc6_A* 2h8m_A* 2hch_A* 2hg1_A* 3o2f_A* 2esa_A*

Probab=95.50  E-value=0.0033  Score=66.41  Aligned_cols=58  Identities=22%  Similarity=0.312  Sum_probs=36.9

Q ss_pred             EEEEEecCCCCCcCcHhhhhhhccCCCccc---------------cCcCCCccccHHHHHHHHHHhCCEEEEEeecC
Q 039716          593 RCDVYDTGIGIPENALPTLFRKYMQVSADH---------------ARKYGGTGLGLAICKQLVELMGGRLTVTSKVH  654 (1002)
Q Consensus       593 ~i~V~DtGiGI~~e~l~~IF~pF~q~~~~~---------------~~~~~GtGLGLaI~k~Lve~~gG~I~v~S~~g  654 (1002)
                      .|.|.|||+||+++++...|..+.+.....               ....|..|+|+.-+..++    ..+.|.|...
T Consensus        80 ~i~I~DnG~GMt~edl~~~l~~ia~Sg~~~f~~kl~~~~~~~~~d~~~iG~fGiG~~S~f~va----~~v~V~Sr~~  152 (236)
T 2gqp_A           80 LLHVTDTGVGMTREELVKNLGTIAKSGTSEFLNKMTEAQEDGQSTSELIGQFGVGFYSAFLVA----DKVIVTSKHN  152 (236)
T ss_dssp             EEEEEECSCCCCHHHHHHHHHCC---------------------CHHHHHHTTCGGGGGGGTE----EEEEEEEECT
T ss_pred             EEEEEECCcCCCHHHHHHHHhhhcccccHhHHHHhhccccccccchhhcCCCCcchhhHhhcC----CEEEEEEeCC
Confidence            468999999999999988886554321100               001123689987666554    6788888764

>1y4s_A Chaperone protein HTPG; HSP90, molecular chaperone, ATPase; HET: ADP; 2.90A {Escherichia coli} PDB: 1y4u_A

Probab=95.39  E-value=0.016  Score=68.49  Aligned_cols=72  Identities=18%  Similarity=0.307  Sum_probs=43.9

Q ss_pred             EEEEEecCCCCCcCcHhhhhhhccCCCc------------cccCcCCCccccHHHHHHHHH------Hh-----------
Q 039716          593 RCDVYDTGIGIPENALPTLFRKYMQVSA------------DHARKYGGTGLGLAICKQLVE------LM-----------  643 (1002)
Q Consensus       593 ~i~V~DtGiGI~~e~l~~IF~pF~q~~~------------~~~~~~~GtGLGLaI~k~Lve------~~-----------  643 (1002)
                      .|+|.|||+||+++++..-|....+...            ......|.-|+|++-+..+++      .+           
T Consensus        75 ~I~I~DnGiGMt~edl~~~l~tiA~Sg~~~f~e~l~~~~~~~~~~iG~fGvGfyS~f~VadkV~V~Sr~~~~~~~~~~~w  154 (559)
T 1y4s_A           75 TLTISDNGVGMTRDEVIDHLGTIAKSGTKSFLESLGSDQAKDSQLIGQFGVGFYSAFIVADKVTVRTRAAGEKPENGVFW  154 (559)
T ss_dssp             EEEEEECSSCCCHHHHHHHHSCCSCCCCCCTTCC--------CCCCSSCCCSGGGHHHHEEEEEEEEECSSSCGGGEEEE
T ss_pred             EEEEEECCCCCCHHHHHHHHhhhcccccHHHHHHhhccccccccccCCCCcchhhhhhccCeEEEEEcCCCCCCCeeEEE
Confidence            4679999999999998876654322210            011233566999877766642      11           


Q ss_pred             ----CCEEEEEe--ecCCceEEEEEEe
Q 039716          644 ----GGRLTVTS--KVHCGSTFTFILP  664 (1002)
Q Consensus       644 ----gG~I~v~S--~~g~GTtF~~~LP  664 (1002)
                          ||...+..  ..+.||++++.|.
T Consensus       155 ~s~g~~~~~i~~~~~~~~GT~I~L~Lk  181 (559)
T 1y4s_A          155 ESAGEGEYTVADITKEDRGTEITLHLR  181 (559)
T ss_dssp             EECSSSEEEEEEECCCSCEEEEEEEEC
T ss_pred             EEeCCCeeEEeECCCCCCCeEEEEEEc
Confidence                23444442  3467888888874

>3n75_A LDC, lysine decarboxylase, inducible; pyridoxal-5'-phosphate dependent decarboxylase, acid stress stringent response; HET: LLP G4P P6G; 2.00A {Escherichia coli} PDB: 3q16_A*

Probab=95.27  E-value=0.01  Score=72.48  Aligned_cols=91  Identities=11%  Similarity=0.053  Sum_probs=72.9

Q ss_pred             HHHHHHHHHhcCCeEEEEcCHHHHHHHHHcC-CCcEEEEcCCCCCCCHHHHHHHHhccccCCCchhhhhhhhcccCCCCC
Q 039716          872 VMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQ-NYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDAAAEAGIEQAMPSSG  950 (1002)
Q Consensus       872 ~~~l~~~L~~~g~~v~~a~~G~eAl~~~~~~-~~DlIlmDi~MP~mdG~e~~~~IR~~~~~~~~~~~~~~~~~~~~~~~~  950 (1002)
                      ...|...|++.||+|..+.++.+|+..++.+ .+++|++|+.|+   +.++++.||..                      
T Consensus        19 i~~L~~~Le~~g~~V~~a~s~~Da~~~i~~~~~i~avIld~d~~---~~~ll~~Ir~~----------------------   73 (715)
T 3n75_A           19 IRELHRALERLNFQIVYPNDRDDLLKLIENNARLCGVIFDWDKY---NLELCEEISKM----------------------   73 (715)
T ss_dssp             HHHHHHHHHHTTCEEECCSSHHHHHHHHHHCTTEEEEEEEHHHH---HHHHHHHHHHH----------------------
T ss_pred             HHHHHHHHHHCCcEEEEeCCHHHHHHHHHhCCCceEEEEecccc---HHHHHHHHHHh----------------------
Confidence            3446688999999999999999999999876 499999999997   78999999973                      


Q ss_pred             CCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChH
Q 039716          951 SSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQ  991 (1002)
Q Consensus       951 ~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~  991 (1002)
                          ...+||++++.....++..-..-.++++|+.+..+-.
T Consensus        74 ----~~~iPVFl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  110 (715)
T 3n75_A           74 ----NENLPLYAFANTYSTLDVSLNDLRLQISFFEYALGAA  110 (715)
T ss_dssp             ----CTTCEEEEECCTTCCCCGGGTTSCCEEEEECCCTTCH
T ss_pred             ----CCCCCEEEEecCCcccccchhhhhccCeEEEeCCCCH
Confidence                3579999999886544433222457899999987543

>3rty_A Period circadian protein; PAS domain, signalling, timeless, circadian clock protein; 2.85A {Drosophila melanogaster} PDB: 1wa9_A 3gec_A

Probab=95.18  E-value=0.063  Score=59.72  Aligned_cols=102  Identities=10%  Similarity=0.012  Sum_probs=77.5

Q ss_pred             cCcEEEEecccccEEEeeccC---CCCCcccccCCCchhccCccchhhhhHHHHHHHHhCCCc-----ceeEEEEEeecC
Q 039716          231 APVVMGHQDKELRYRFIYNHF---PSLHEEDILGKTDVEIFSGAGVKESQDFKREVLEKGLPA-----KREITFETELFG  302 (1002)
Q Consensus       231 ~p~~i~~~d~~~~~~~~~~~~---~~~~~e~iiGk~~~e~~~~~~~~~~~~~~~~vl~~g~~~-----~~e~~~~~~~~~  302 (1002)
                      ....+...+.+|++.+++.++   .|+.++|++|++..+++++++..........++..|...     ..++++.+..++
T Consensus       153 ~~~fi~r~~~dG~~~yvn~~~~~lLGY~peELiG~s~~~~vHPdD~~~~~~~~~~~l~~G~~~~~~~~s~~yR~~~kdG~  232 (339)
T 3rty_A          153 SPKFAIRHTATGIISHVDSAAVSALGYLPQDLIGRSIMDFYHHEDLSVMKETYETVMKKGQTAGASFCSKPYRFLIQNGC  232 (339)
T ss_dssp             CCEEEEEEETTCBEEEECTTHHHHHCCCHHHHTTSBGGGGBCGGGHHHHHHHHHHHHHHTTSTTCCCBCCCEEEECTTSC
T ss_pred             CceEEEEECCCCeEEEcChhhhcccCCCHHHHcCCcHHHEECHHHHHHHHHHHHHHHHcCCcccccccceEEEEEccCCC
Confidence            355777789999999998865   689999999999999999988877777777888877642     346777776666


Q ss_pred             ceEEEEEEeeeecC-CCCEEEEEEEeechhH
Q 039716          303 SKTFLIYVEPVFSK-SGETIGVNYMGMDVTD  332 (1002)
Q Consensus       303 ~~~~~~~~~p~~~~-~G~~~gi~~~~~DITe  332 (1002)
                      ..|+.....++++. ++.+..++++...|+.
T Consensus       233 ~vWlet~~~~~~np~s~~~~~II~~h~vi~~  263 (339)
T 3rty_A          233 YVLLETEWTSFVNPWSRKLEFVVGHHRVFQG  263 (339)
T ss_dssp             EEEEEEEEEEEECTTTCSEEEEEEEEEEEEC
T ss_pred             EEEEEEEEEEEECCCCCCeeEEEEEEEECCC
Confidence            66666777888885 5666666666655553

>2cg9_A ATP-dependent molecular chaperone HSP82; chaperone complex, HSP90, heat shock protein, ATP-binding, heat shock, nucleotide-binding, acetylation; HET: ATP; 3.1A {Saccharomyces cerevisiae}

Probab=94.71  E-value=0.016  Score=69.55  Aligned_cols=72  Identities=24%  Similarity=0.367  Sum_probs=42.5

Q ss_pred             EEEEEecCCCCCcCcHhhhhhhccCC---------Cc-cccCcCCCccccHHHHHHHHH------------------HhC
Q 039716          593 RCDVYDTGIGIPENALPTLFRKYMQV---------SA-DHARKYGGTGLGLAICKQLVE------------------LMG  644 (1002)
Q Consensus       593 ~i~V~DtGiGI~~e~l~~IF~pF~q~---------~~-~~~~~~~GtGLGLaI~k~Lve------------------~~g  644 (1002)
                      .|+|.|||+||+++++..-|...-+.         .. .....-|..|+|++-|..+++                  .-|
T Consensus        74 ~I~I~DnGiGMt~edl~~~l~tIA~Sgt~~f~~kl~~~~d~~~IGqFGvGFySaf~vadkV~V~Sk~~~~~~~~W~s~g~  153 (677)
T 2cg9_A           74 VLEIRDSGIGMTKAELINNLGTIAKSGTKAFMEALSAGADVSMIGQFGVGFYSLFLVADRVQVISKSNDDEQYIWESNAG  153 (677)
T ss_dssp             EEEEEECSCCCCHHHHHGGGSSSSSCTTHHHHSCCCSSCCCCCCCCTTCTTGGGGGTEEEEEEEEECTTSCEEEEEECSS
T ss_pred             EEEEEECCCCCCHHHHHHHHHhHhccccHHHHHhhhcccchhhcCCCCchhHHHhhcCcEEEEEEccCCCceEEEEEcCC
Confidence            47899999999999987655332111         00 011234557899876643321                  113


Q ss_pred             CEEEEEe-----ecCCceEEEEEEe
Q 039716          645 GRLTVTS-----KVHCGSTFTFILP  664 (1002)
Q Consensus       645 G~I~v~S-----~~g~GTtF~~~LP  664 (1002)
                      |...+..     ..+.||++++.|.
T Consensus       154 ~~~ti~~~~~~~~~~~GT~I~L~Lk  178 (677)
T 2cg9_A          154 GSFTVTLDEVNERIGRGTILRLFLK  178 (677)
T ss_dssp             SEEEEEECCSSCCCSSEEEEEEEEC
T ss_pred             ceEEEeecCCCCCCCCCeEEEEEEc
Confidence            4555654     2356888888874

>3nmq_A Heat shock protein HSP 90-beta; ATPase, chaperone-chaperone inhibitor complex; HET: 7PP; 2.20A {Homo sapiens} SCOP: d.122.1.1

Probab=94.63  E-value=0.0068  Score=63.69  Aligned_cols=47  Identities=23%  Similarity=0.374  Sum_probs=29.0

Q ss_pred             EEEEEecCCCCCcCcHhhhhh--------hccC---CCccccCcCCCccccHHHHHHHH
Q 039716          593 RCDVYDTGIGIPENALPTLFR--------KYMQ---VSADHARKYGGTGLGLAICKQLV  640 (1002)
Q Consensus       593 ~i~V~DtGiGI~~e~l~~IF~--------pF~q---~~~~~~~~~~GtGLGLaI~k~Lv  640 (1002)
                      .|.|.|||+||+++++..-+.        .|..   ... ....-|--|+|++-|..++
T Consensus        87 ~L~I~DnGiGMt~edL~~~LgtIA~Sgtk~f~e~~~~~~-d~~~IGqFGvGfySaf~va  144 (239)
T 3nmq_A           87 TLTLVDTGIGMTKADLINNLGTIAKSGTKAFMEALQAGA-DISMIGQFGVGFYSAYLVA  144 (239)
T ss_dssp             EEEEEECSCCCCHHHHHTHHHHHHHHHHHHHHHHHHTTC-CGGGGGGGTCGGGGGGGTE
T ss_pred             EEEEEeCCCCCCHHHHHHHHHHHhcccchhhhhhhcccC-CcccccccCcccccccccC
Confidence            468999999999999843221        1211   111 1223456799998876554

>2ioq_A Chaperone protein HTPG; heat shock protein, HSP90; 3.50A {Escherichia coli} PDB: 2iop_A

Probab=94.58  E-value=0.014  Score=69.86  Aligned_cols=48  Identities=13%  Similarity=0.272  Sum_probs=30.5

Q ss_pred             EEEEEecCCCCCcCcHhhhhhhccCCCc------------cccCcCCCccccHHHHHHHH
Q 039716          593 RCDVYDTGIGIPENALPTLFRKYMQVSA------------DHARKYGGTGLGLAICKQLV  640 (1002)
Q Consensus       593 ~i~V~DtGiGI~~e~l~~IF~pF~q~~~------------~~~~~~~GtGLGLaI~k~Lv  640 (1002)
                      .|+|.|||+||+++++..-|....+...            ......|.-|+|++-+..++
T Consensus        75 ~I~I~DnGiGMt~edl~~~l~tiA~Sg~~~f~~~l~~~~~~~~~~iG~fGvGfyS~f~Va  134 (624)
T 2ioq_A           75 TLTISDNGVGMTRDEVIDHLGTIAKSGTKSFLESLGSDQAKDSQLIGQFGVGFYSAFIVA  134 (624)
T ss_dssp             EEEEEECSCCCCHHHHHHHHHHHCC---------------CCTTHHHHHHHHHHHHHHHE
T ss_pred             EEEEEECCCCCCHHHHHHHHHhhcccccHHHHHHhcccccccccccCCCCccHHHHHhcC
Confidence            4679999999999998776654332210            01111234599998777776

>1ei1_A DNA gyrase B, GYRB; ATPase domain, dimer, isomerase; HET: DNA ANP; 2.30A {Escherichia coli} SCOP: d.14.1.3 d.122.1.2

Probab=94.54  E-value=0.045  Score=62.03  Aligned_cols=48  Identities=23%  Similarity=0.438  Sum_probs=32.8

Q ss_pred             EEEEecCCCCCcCc--------HhhhhhhccCCCc---cccCcCCC-ccccHHHHHHHHH
Q 039716          594 CDVYDTGIGIPENA--------LPTLFRKYMQVSA---DHARKYGG-TGLGLAICKQLVE  641 (1002)
Q Consensus       594 i~V~DtGiGI~~e~--------l~~IF~pF~q~~~---~~~~~~~G-tGLGLaI~k~Lve  641 (1002)
                      |+|.|+|.|||.+.        .+-+|..+..+..   ......+| .|.||+.+.-+.+
T Consensus        68 I~V~DnG~GIp~~~~~~~~~~~~elv~~~lhagsKf~~~~~~vSgGl~GvGls~vnalS~  127 (391)
T 1ei1_A           68 VSVQDDGRGIPTGIHPEEGVSAAEVIMTVLHAGGKFDDNSYKVSGGLHGVGVSVVNALSQ  127 (391)
T ss_dssp             EEEEECSSCCCCSBCTTTSSBHHHHHHHSTTEESCSSSSSCSSCSCCSSCHHHHHHHTEE
T ss_pred             EEEEECCCCcccCcccccCcchHHHhheeccccCCcCCCcccccCCccccchHHHHHhcC
Confidence            77999999999998        4457875544321   11112334 7999999888775

>2o1u_A Endoplasmin; GRP94, HSP82, HSP90, HTPG, chaperone, AMP-PNP, GP96; HET: ANP; 2.40A {Canis lupus familiaris} PDB: 2o1v_A* 2o1w_A 2o1t_A

Probab=94.24  E-value=0.014  Score=70.03  Aligned_cols=72  Identities=19%  Similarity=0.311  Sum_probs=37.9

Q ss_pred             EEEEEecCCCCCcCcHhhhhhhccCC---------Cc------cccCcCCCccccHHHHHHHHH----------------
Q 039716          593 RCDVYDTGIGIPENALPTLFRKYMQV---------SA------DHARKYGGTGLGLAICKQLVE----------------  641 (1002)
Q Consensus       593 ~i~V~DtGiGI~~e~l~~IF~pF~q~---------~~------~~~~~~~GtGLGLaI~k~Lve----------------  641 (1002)
                      .|+|.|||+||+++++..-|...-+.         ..      .....-|..|+|++-+-.+++                
T Consensus        93 ~I~I~DnGiGMt~edl~~~l~tIA~SGtk~f~~kl~~~~~~~~~d~~~IGqFGvGfySaf~vAdkV~V~Sr~~~~~~~~W  172 (666)
T 2o1u_A           93 LLHVTDTGVGMTREELVKNLGTIAKSGTSEFLNKMTEAQEDGQSTSELIGQFGVGFYSAFLVADKVIVTSKHNNDTQHIW  172 (666)
T ss_dssp             EEEEEECSCCCCHHHHHHHTTC-------------------------------CTTGGGGGTEEEEEEEEECTTSCCEEE
T ss_pred             EEEEEECCCCCCHHHHHHHHhhhcccccHHHHHHhhhcccccccchhhccCCCcHHHhHHHhcCEEEEEEeeCCCceEEE
Confidence            36799999999999987765432111         00      011123456899876644431                


Q ss_pred             -HhCCEEEEEee-----cCCceEEEEEEe
Q 039716          642 -LMGGRLTVTSK-----VHCGSTFTFILP  664 (1002)
Q Consensus       642 -~~gG~I~v~S~-----~g~GTtF~~~LP  664 (1002)
                       .-||.++++..     .+.||++++.|.
T Consensus       173 ~s~gg~~ti~~~~~~~~~~~GT~I~L~Lk  201 (666)
T 2o1u_A          173 ESDSNEFSVIADPRGNTLGRGTTITLVLK  201 (666)
T ss_dssp             EESSSCCEEEECTTCCSSSSEEEEEEEEC
T ss_pred             EEeCCeEEEEecccCCCCCCCeEEEEEEc
Confidence             11245555543     357888888874

>2yxb_A Coenzyme B12-dependent mutase; alpha/beta, structural genomics, NPPSFA, national project on structural and functional analyses; 1.80A {Aeropyrum pernix}

Probab=93.68  E-value=0.79  Score=45.07  Aligned_cols=117  Identities=11%  Similarity=0.145  Sum_probs=81.8

Q ss_pred             CCCeEEEE----ecCHHHHHHHHHHHHhcCCeEEEE---cCHHHHHHHHHcCCCcEEEEcCCCCCC--CHHHHHHHHhcc
Q 039716          858 PKPKILLV----EDNKINVMVAKSMMKQLGHSIDVV---NNGVEAVHAVQCQNYDLILMDVCMPVM--DGLKATRLIRSF  928 (1002)
Q Consensus       858 ~~~~ILiV----eDn~~n~~~l~~~L~~~g~~v~~a---~~G~eAl~~~~~~~~DlIlmDi~MP~m--dG~e~~~~IR~~  928 (1002)
                      .+++||+.    |-+.+-..++..+|+..||+|...   ...++.++.+....+|+|.+-..|...  .--++++.+|+.
T Consensus        17 ~~~~vlla~~~gd~HdiG~~~va~~l~~~G~eVi~lG~~~p~e~lv~aa~~~~~diV~lS~~~~~~~~~~~~~i~~L~~~   96 (161)
T 2yxb_A           17 RRYKVLVAKMGLDGHDRGAKVVARALRDAGFEVVYTGLRQTPEQVAMAAVQEDVDVIGVSILNGAHLHLMKRLMAKLREL   96 (161)
T ss_dssp             CSCEEEEEEESSSSCCHHHHHHHHHHHHTTCEEECCCSBCCHHHHHHHHHHTTCSEEEEEESSSCHHHHHHHHHHHHHHT
T ss_pred             CCCEEEEEeCCCCccHHHHHHHHHHHHHCCCEEEECCCCCCHHHHHHHHHhcCCCEEEEEeechhhHHHHHHHHHHHHhc
Confidence            45689988    888899999999999999998853   577888999999999999998877631  112344455541


Q ss_pred             ccCCCchhhhhhhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHHhh
Q 039716          929 EDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQY 1000 (1002)
Q Consensus       929 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~~ 1000 (1002)
                                               ..+++||+ +-+....++...+.+.|+|.++..=-+..+....+.++
T Consensus        97 -------------------------g~~~i~v~-vGG~~~~~~~~~l~~~G~d~v~~~~~~~~~~~~~~~~~  142 (161)
T 2yxb_A           97 -------------------------GADDIPVV-LGGTIPIPDLEPLRSLGIREIFLPGTSLGEIIEKVRKL  142 (161)
T ss_dssp             -------------------------TCTTSCEE-EEECCCHHHHHHHHHTTCCEEECTTCCHHHHHHHHHHH
T ss_pred             -------------------------CCCCCEEE-EeCCCchhcHHHHHHCCCcEEECCCCCHHHHHHHHHHH
Confidence                                     11346665 45566666766788999998665444444444444443

>3fv5_A DNA topoisomerase 4 subunit B; topoisomerase IV B subunit complex, antibiotic resistance, ATP-binding, nucleotide-binding; HET: DNA 1EU; 1.80A {Escherichia coli} PDB: 1s14_A*

Probab=93.62  E-value=0.095  Score=53.75  Aligned_cols=47  Identities=21%  Similarity=0.278  Sum_probs=22.1

Q ss_pred             EEEEecCCCCCcCcH--------hhh-hhhccCCCcc---ccCcCCCccccHHHHHHHH
Q 039716          594 CDVYDTGIGIPENAL--------PTL-FRKYMQVSAD---HARKYGGTGLGLAICKQLV  640 (1002)
Q Consensus       594 i~V~DtGiGI~~e~l--------~~I-F~pF~q~~~~---~~~~~~GtGLGLaI~k~Lv  640 (1002)
                      |+|.|+|.|||.+..        +.+ +.+....+-.   .....|=-|.||+.+..+.
T Consensus        51 i~V~DnG~GIp~~~~~~~~~~~~e~i~~~~hatsK~~~~~~~~s~GfrGeglssinalS  109 (201)
T 3fv5_A           51 LEVIDDGRGMPVDIHPEEGVPAVELILCRLHAGGKFSNKNYQFSGGLHGVGISVVNALS  109 (201)
T ss_dssp             EEEEECSSCCCCSBCTTCSSBHHHHHHHCC---------------------CHHHHHTE
T ss_pred             EEEEECCCCcCcccccccCcchhheeeeeeccccCcCCCcccccCcccceecchhhccc
Confidence            679999999999984        343 3333222110   1111222588999887765

>3cwv_A DNA gyrase, B subunit, truncated; structural genomics, unknown function, B-subunit binding, isomerase, nucleotide-binding, topoisomerase; HET: DNA; 1.95A {Myxococcus xanthus}

Probab=92.69  E-value=0.17  Score=56.84  Aligned_cols=20  Identities=10%  Similarity=0.104  Sum_probs=17.0

Q ss_pred             cHHHHHHHHHHHHhhhhhcC
Q 039716          481 DVLRIRQILTNLISNAIKFT  500 (1002)
Q Consensus       481 D~~rL~QIL~NLlsNAIKfT  500 (1002)
                      |+..+..++.-||.|||+..
T Consensus        27 ~~~gl~~~v~ElvdNsiDe~   46 (369)
T 3cwv_A           27 GEYGLHHLVYFLLDVAYEEA   46 (369)
T ss_dssp             SHHHHHHHHHHHHHHHHHHH
T ss_pred             CCchHHHHHHHHHhhhHhHH
Confidence            56789999999999999863

>4dj3_A Period circadian protein homolog 3; PAS domain, circadian rhythm, protein binding; 2.50A {Mus musculus}

Probab=92.63  E-value=0.37  Score=52.98  Aligned_cols=96  Identities=7%  Similarity=-0.051  Sum_probs=71.5

Q ss_pred             cEEEEecccccEEEeeccC---CCCCcccccCCCchhccCccchhhhhHHHHHHHHhCCC---cceeEEEEEeecCceEE
Q 039716          233 VVMGHQDKELRYRFIYNHF---PSLHEEDILGKTDVEIFSGAGVKESQDFKREVLEKGLP---AKREITFETELFGSKTF  306 (1002)
Q Consensus       233 ~~i~~~d~~~~~~~~~~~~---~~~~~e~iiGk~~~e~~~~~~~~~~~~~~~~vl~~g~~---~~~e~~~~~~~~~~~~~  306 (1002)
                      ..+...+.++++.|++.++   .|+.++|++|++..+++++++..........++..+..   ...++++..+.++..|+
T Consensus       175 ~Fitrh~~dG~~~yvs~~~~~lLGY~peELig~s~~~~vHPdD~~~~~~~~~~~l~~~~~~~f~s~~yR~~~kdG~~vwv  254 (317)
T 4dj3_A          175 IFTTTHTPGCVFLEVDERAVPLLGYLPQDLIGTSILTYLHPEDRPLMVAIHQKVLKYAGHPPFEHSPVRFCTQNGEYVIL  254 (317)
T ss_dssp             EEEEEECTTSBEEEECTTHHHHHSCCHHHHTTSBGGGGBCTTTTTHHHHHHHHHHHTTTSCCEECCCEEEECTTSCEEEE
T ss_pred             ceEEEecCCCeEEEEChHHhhhcCcChHHHcCCCHHHeECHHHHHHHHHHHHHHHHcCCCccccceEEEEEccCCCEEEE
Confidence            5677779999999998764   68999999999999999988887777777778876544   34567777666665666


Q ss_pred             EEEEeeeecC-CCCEEEEEEEee
Q 039716          307 LIYVEPVFSK-SGETIGVNYMGM  328 (1002)
Q Consensus       307 ~~~~~p~~~~-~G~~~gi~~~~~  328 (1002)
                      .....++++. ++++..+++...
T Consensus       255 et~~~~~~np~s~~~e~II~~h~  277 (317)
T 4dj3_A          255 DSSWSSFVNPWSRKVSFIIGRHK  277 (317)
T ss_dssp             EEEEEEEECSSSCCEEEEEEEEE
T ss_pred             EEEEEEEECCCCCcccEEEEEEE
Confidence            6666677775 566655555554

>3gdi_A Period circadian protein homolog 2; tandem PAS domains, biological rhythms, cytoplasm, nucleus, phosphoprotein, transcription; 2.40A {Mus musculus}

Probab=91.73  E-value=0.53  Score=51.53  Aligned_cols=99  Identities=9%  Similarity=-0.001  Sum_probs=69.7

Q ss_pred             cEEEEecccccEEEeeccC---CCCCcccccCCCchhccCccchhhhhHHHHHHHHhCC-Ccc-eeEEEEEeecCceEEE
Q 039716          233 VVMGHQDKELRYRFIYNHF---PSLHEEDILGKTDVEIFSGAGVKESQDFKREVLEKGL-PAK-REITFETELFGSKTFL  307 (1002)
Q Consensus       233 ~~i~~~d~~~~~~~~~~~~---~~~~~e~iiGk~~~e~~~~~~~~~~~~~~~~vl~~g~-~~~-~e~~~~~~~~~~~~~~  307 (1002)
                      ..+..-+.++++.|++.++   .|+.++|++|++..+++++++..........++..+. +.. .++++..+.++..|+.
T Consensus       166 ~Fitrh~~dG~~~yvd~~~~~lLGY~peELig~s~~~~iHpdD~~~~~~~~~~~l~~~g~~~~~~~yR~~~kdG~~vwve  245 (309)
T 3gdi_A          166 IFTTTHTPNCLFQAVDERAVPLLGYLPQDLIETPVLVQLHPSDRPLMLAIHKKILQAGGQPFDYSPIRFRTRNGEYITLD  245 (309)
T ss_dssp             EEEEEECTTCBEEEECTTHHHHHSCCHHHHTTSBHHHHBCTTSHHHHHHHHHHHHHTTTCCEEEEEEEEECTTSCEEEEE
T ss_pred             eEEEEecCCCeEEEECcccccccCcCHHHHcCCCHHHhCCHHHHHHHHHHHHHHHhcCCceeeceEEEEEccCCCEEEEE
Confidence            4677779999999998764   6899999999999999998887777777777777543 333 3566666655555555


Q ss_pred             EEEeeeecC-CCCEEEEEEEeechh
Q 039716          308 IYVEPVFSK-SGETIGVNYMGMDVT  331 (1002)
Q Consensus       308 ~~~~p~~~~-~G~~~gi~~~~~DIT  331 (1002)
                      ....++.+. ++++..+++...-++
T Consensus       246 t~~~~~~np~s~~~e~ii~~h~v~~  270 (309)
T 3gdi_A          246 TSWSSFINPWSRKISFIIGRHKVRV  270 (309)
T ss_dssp             EEEEEEECTTTCCEEEEEEEEEEEE
T ss_pred             EEEEEEECCCCCcccEEEEEEEEcc
Confidence            555666664 566655555544433

>3q7r_A Transcriptional regulatory protein; CHXR, receiver domain, transcription factor, OMPR, chlamydia transcription; 1.60A {Chlamydia trachomatis} PDB: 3q7s_A* 3q7t_A

Probab=91.63  E-value=0.31  Score=43.07  Aligned_cols=102  Identities=17%  Similarity=0.245  Sum_probs=76.1

Q ss_pred             eEEEEecCHHHHHHHHHHHHhcCCeEEEEcCHHHHHHHHHcCCCcEEEEcCCC-CCCCHHHHHHHHhccccCCCchhhhh
Q 039716          861 KILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCM-PVMDGLKATRLIRSFEDTGNWDAAAE  939 (1002)
Q Consensus       861 ~ILiVeDn~~n~~~l~~~L~~~g~~v~~a~~G~eAl~~~~~~~~DlIlmDi~M-P~mdG~e~~~~IR~~~~~~~~~~~~~  939 (1002)
                      .||+|-.|-..--.++.++....|.+.+...-.      ....-|+|+|...+ |.        .|++            
T Consensus        14 ~iL~VtEd~~ls~QlKel~~~~eY~~~is~~~~------~e~~AdlIfCEYlLLPe--------~ifS------------   67 (121)
T 3q7r_A           14 HVLLVSEHWDLFFQTKELLNPEEYRCTIGQQYK------QELSADLVVCEYSLLPR--------EIRS------------   67 (121)
T ss_dssp             EEEEECSCHHHHHHHHHHSCTTTEEEEEESSCC------CCTTEEEEEEEGGGSCT--------TCCC------------
T ss_pred             EEEEEecCchhhHHHHHhcCCcceeEEeccccC------CcccceeEEEeeecChH--------HhcC------------
Confidence            588888888777778888877778888775422      13456999999754 42        2332            


Q ss_pred             hhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHHhhc
Q 039716          940 AGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQYF 1001 (1002)
Q Consensus       940 ~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~~l 1001 (1002)
                                  .+.....-+|++-..-+++...+.++.|+. ||..|++..-|..+|+.+|
T Consensus        68 ------------~k~~~~~dliVLfD~F~EEa~v~vLd~Ga~-yLlrPIT~kvldAvIraFL  116 (121)
T 3q7r_A           68 ------------PKSLEGSFVLVLLDFFDEETSVDLLDRGFW-YLIRPITPRILKSAISLFL  116 (121)
T ss_dssp             ------------CTTCCSCEEEEEESSCCHHHHHHHHHTTCE-EEESCCCHHHHHHHHHHHH
T ss_pred             ------------CCCCCcccEEEEehhhchHHHHHHHhCCce-eEeccCcHHHHHHHHHHHH
Confidence                        112233457777777788999999999999 9999999999999998775

>4dj2_A Period circadian protein homolog 1; PAS domains, circadian clock protein, protein binding; 2.75A {Mus musculus}

Probab=91.47  E-value=0.48  Score=52.17  Aligned_cols=100  Identities=12%  Similarity=0.006  Sum_probs=70.8

Q ss_pred             CcEEEEecccccEEEeeccC---CCCCcccccCCCchhccCccchhhhhHHHHHHHHh-CCCc-ceeEEEEEeecCceEE
Q 039716          232 PVVMGHQDKELRYRFIYNHF---PSLHEEDILGKTDVEIFSGAGVKESQDFKREVLEK-GLPA-KREITFETELFGSKTF  306 (1002)
Q Consensus       232 p~~i~~~d~~~~~~~~~~~~---~~~~~e~iiGk~~~e~~~~~~~~~~~~~~~~vl~~-g~~~-~~e~~~~~~~~~~~~~  306 (1002)
                      ...+..-+.+|++.|++..+   .|+.++|++|++..+++++++..........++.. |.+. ..++++..+.++..|+
T Consensus       176 ~~Fitrh~~dG~~~yvd~~~~~lLGY~peELig~s~~~~vHPdD~~~~~~~~~~~l~~~g~~~~~~~yR~~~kdG~~vwv  255 (320)
T 4dj2_A          176 RIFTTRHTPSCLFQDVDERAAPLLGYLPQDLLGAPVLLFLHPEDRPLMLAIHKKILQLAGQPFDHSPIRFCARNGEYVTM  255 (320)
T ss_dssp             CEEEEEECTTCBEEEECTTHHHHHSCCHHHHTTSBGGGGBCGGGHHHHHHHHHHHTTSSSCCEECCCEEEECSSSCEEEE
T ss_pred             ceEEEEecCCceEEEcCcceeccCCcChHHHcCCcHHHhCCHHHHHHHHHHHHHHHhcCCCcccceEEEEEccCCCEEEE
Confidence            34667779999999998764   68999999999999999988877766666677663 4443 2466776666655555


Q ss_pred             EEEEeeeecC-CCCEEEEEEEeechh
Q 039716          307 LIYVEPVFSK-SGETIGVNYMGMDVT  331 (1002)
Q Consensus       307 ~~~~~p~~~~-~G~~~gi~~~~~DIT  331 (1002)
                      .....++.+. ++++..+++.-.-++
T Consensus       256 et~~~~~~np~s~~~e~II~~h~v~~  281 (320)
T 4dj2_A          256 DTSWAGFVHPWSRKVAFVLGRHKVRT  281 (320)
T ss_dssp             ECEEEEEECTTTCSEEEEEEEEEESS
T ss_pred             EEEEEEEECCCCCCccEEEEEEEEcc
Confidence            5555666664 566666666554444

>4duh_A DNA gyrase subunit B; structure-based drug design, antibacterial, DNA gyrase B, GY isomerase-isomerase inhibitor complex; HET: DNA RLI; 1.50A {Escherichia coli} PDB: 1aj6_A* 1kzn_A* 3g7e_A*

Probab=90.08  E-value=0.61  Score=48.37  Aligned_cols=65  Identities=22%  Similarity=0.391  Sum_probs=35.9

Q ss_pred             EEEEecCCCCCcCcH--------hhhhhhccCCC---ccccCcCCC-ccccHHHHHHHHHHhCCEEEEEeecCCceEEEE
Q 039716          594 CDVYDTGIGIPENAL--------PTLFRKYMQVS---ADHARKYGG-TGLGLAICKQLVELMGGRLTVTSKVHCGSTFTF  661 (1002)
Q Consensus       594 i~V~DtGiGI~~e~l--------~~IF~pF~q~~---~~~~~~~~G-tGLGLaI~k~Lve~~gG~I~v~S~~g~GTtF~~  661 (1002)
                      |+|.|+|.|||.+..        +-+|.......   .......+| -|.||+.+.-|.+    .+.|++..+ |..+..
T Consensus        69 i~V~DnGrGIp~~~~~~~~~~~~e~i~t~lhag~Kfd~~~yk~SgGlhGvG~svvNAlS~----~l~v~v~r~-g~~~~~  143 (220)
T 4duh_A           69 VSVQDDGRGIPTGIHPEEGVSAAEVIMTVLHAGGKFDDNSYKVSGGLHGVGVSVVNALSQ----KLELVIQRE-GKIHRQ  143 (220)
T ss_dssp             EEEEECSSCCCCSEETTTTEEHHHHHHHSTTCSSCCCTTC--------CCCHHHHHHTEE----EEEEEEEET-TEEEEE
T ss_pred             EEEEECCcCcccccccccCcchhhheeeecccCCCcCCCccccccCccceecchhccccc----ceEEEEEEC-CEEEEE
Confidence            679999999999975        34553222111   111111223 6899998877654    455655543 455555


Q ss_pred             EE
Q 039716          662 IL  663 (1002)
Q Consensus       662 ~L  663 (1002)
                      .+
T Consensus       144 ~f  145 (220)
T 4duh_A          144 IY  145 (220)
T ss_dssp             EE
T ss_pred             Ee
Confidence            55

>1ccw_A Protein (glutamate mutase); coenzyme B12, radical reaction, TIM-barrel rossman-fold, isomerase; HET: CNC TAR; 1.60A {Clostridium cochlearium} SCOP: c.23.6.1 PDB: 1cb7_A* 1b1a_A 1i9c_A* 1be1_A 1fmf_A 1id8_A*

Probab=89.58  E-value=3.2  Score=39.41  Aligned_cols=116  Identities=10%  Similarity=0.010  Sum_probs=77.0

Q ss_pred             CeEEEE----ecCHHHHHHHHHHHHhcCCeEE---EEcCHHHHHHHHHcCCCcEEEEcCCCCCCC--HHHHHHHHhcccc
Q 039716          860 PKILLV----EDNKINVMVAKSMMKQLGHSID---VVNNGVEAVHAVQCQNYDLILMDVCMPVMD--GLKATRLIRSFED  930 (1002)
Q Consensus       860 ~~ILiV----eDn~~n~~~l~~~L~~~g~~v~---~a~~G~eAl~~~~~~~~DlIlmDi~MP~md--G~e~~~~IR~~~~  930 (1002)
                      ++|++.    |-+.+-..++..+|+..||+|.   .....++.++.+....+|+|.+-..|..-.  --++++.+|+.  
T Consensus         4 ~~vvla~~~~d~HdiG~~~v~~~l~~~G~~Vi~lG~~~p~e~~v~~a~~~~~d~v~lS~~~~~~~~~~~~~i~~l~~~--   81 (137)
T 1ccw_A            4 KTIVLGVIGSDCHAVGNKILDHAFTNAGFNVVNIGVLSPQELFIKAAIETKADAILVSSLYGQGEIDCKGLRQKCDEA--   81 (137)
T ss_dssp             CEEEEEEETTCCCCHHHHHHHHHHHHTTCEEEEEEEEECHHHHHHHHHHHTCSEEEEEECSSTHHHHHTTHHHHHHHT--
T ss_pred             CEEEEEeCCCchhHHHHHHHHHHHHHCCCEEEECCCCCCHHHHHHHHHhcCCCEEEEEecCcCcHHHHHHHHHHHHhc--
Confidence            456654    4556777889999999999988   346889999999999999999988875311  12345555541  


Q ss_pred             CCCchhhhhhhhcccCCCCCCCCCCCCccEEEEcCCC-----CHHHHHHHHHcCCCEEEeCCCChHHHHHHHHhh
Q 039716          931 TGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANA-----LSESAEECFANGMDSFVSKPVTFQKLKECLEQY 1000 (1002)
Q Consensus       931 ~~~~~~~~~~~~~~~~~~~~~~~~~~~ipIIalTa~~-----~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~~ 1000 (1002)
                                             ..++++|++=-+-.     ..+....+.++|+|.|..---+..+....|.+.
T Consensus        82 -----------------------g~~~i~v~vGG~~~~~~~~~~~~~~~~~~~G~d~~~~~g~~~~~~~~~l~~~  133 (137)
T 1ccw_A           82 -----------------------GLEGILLYVGGNIVVGKQHWPDVEKRFKDMGYDRVYAPGTPPEVGIADLKKD  133 (137)
T ss_dssp             -----------------------TCTTCEEEEEESCSSSSCCHHHHHHHHHHTTCSEECCTTCCHHHHHHHHHHH
T ss_pred             -----------------------CCCCCEEEEECCCcCchHhhhhhHHHHHHCCCCEEECCCCCHHHHHHHHHHH
Confidence                                   11246665443221     122255688999999986666666666655543

>1wv2_A Thiazole moeity, thiazole biosynthesis protein THIG; structural genomics, protein structure initiative, PSI; 2.90A {Pseudomonas aeruginosa} SCOP: c.1.31.1

Probab=87.43  E-value=3.2  Score=43.63  Aligned_cols=89  Identities=11%  Similarity=0.120  Sum_probs=62.6

Q ss_pred             cCHHHHHHHHHHHHhcCCeEE--EEcCHHHHHHHHHcCCCcEEEEcCCCCCCCH-----HHHHHHHhccccCCCchhhhh
Q 039716          867 DNKINVMVAKSMMKQLGHSID--VVNNGVEAVHAVQCQNYDLILMDVCMPVMDG-----LKATRLIRSFEDTGNWDAAAE  939 (1002)
Q Consensus       867 Dn~~n~~~l~~~L~~~g~~v~--~a~~G~eAl~~~~~~~~DlIlmDi~MP~mdG-----~e~~~~IR~~~~~~~~~~~~~  939 (1002)
                      |.....+ ....|.+.|+.|.  ++.|...|- .+..-.++.| |.+..|.-.|     +++++.|++.           
T Consensus       120 D~~~tv~-aa~~L~~~Gf~Vlpy~~dd~~~ak-rl~~~G~~aV-mPlg~pIGsG~Gi~~~~lI~~I~e~-----------  185 (265)
T 1wv2_A          120 NVVETLK-AAEQLVKDGFDVMVYTSDDPIIAR-QLAEIGCIAV-MPLAGLIGSGLGICNPYNLRIILEE-----------  185 (265)
T ss_dssp             CHHHHHH-HHHHHHTTTCEEEEEECSCHHHHH-HHHHSCCSEE-EECSSSTTCCCCCSCHHHHHHHHHH-----------
T ss_pred             CHHHHHH-HHHHHHHCCCEEEEEeCCCHHHHH-HHHHhCCCEE-EeCCccCCCCCCcCCHHHHHHHHhc-----------
Confidence            3333333 3456667799977  445555444 4455677877 7776663333     6788888862           


Q ss_pred             hhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEe
Q 039716          940 AGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVS  985 (1002)
Q Consensus       940 ~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~  985 (1002)
                                      .++|||+=-+-..+++...|++.|+|+++.
T Consensus       186 ----------------~~vPVI~eGGI~TPsDAa~AmeLGAdgVlV  215 (265)
T 1wv2_A          186 ----------------AKVPVLVDAGVGTASDAAIAMELGCEAVLM  215 (265)
T ss_dssp             ----------------CSSCBEEESCCCSHHHHHHHHHHTCSEEEE
T ss_pred             ----------------CCCCEEEeCCCCCHHHHHHHHHcCCCEEEE
Confidence                            458999988889999999999999999874

>4emv_A DNA topoisomerase IV, B subunit; protein-inhibitor complex, ATP binding, structure-based drug antimicrobial, virtual screen; HET: DNA 0R9; 1.70A {Streptococcus pneumoniae GA47373} PDB: 4em7_A*

Probab=87.34  E-value=1  Score=46.86  Aligned_cols=65  Identities=22%  Similarity=0.355  Sum_probs=37.0

Q ss_pred             EEEEecCCCCCcCc-------HhhhhhhccCCCc---cccCcCCC-ccccHHHHHHHHHHhCCEEEEEeecCCceEEEEE
Q 039716          594 CDVYDTGIGIPENA-------LPTLFRKYMQVSA---DHARKYGG-TGLGLAICKQLVELMGGRLTVTSKVHCGSTFTFI  662 (1002)
Q Consensus       594 i~V~DtGiGI~~e~-------l~~IF~pF~q~~~---~~~~~~~G-tGLGLaI~k~Lve~~gG~I~v~S~~g~GTtF~~~  662 (1002)
                      |+|.|+|.|||.+.       .+-+|........   ......+| -|.|++.|.-|.+    .+.|++.. .|-.+...
T Consensus        74 i~V~DnG~GIp~~~h~~~~~~~e~v~t~lhag~Kfd~~~yk~SgGlhGvG~svvNALS~----~l~v~v~r-~g~~~~q~  148 (226)
T 4emv_A           74 LTVQDHGRGMPTGMHAMGIPTVEVIFTILHAGGKFGQGGYKTSGGLHGVGSSVVNALSS----WLEVEITR-DGAVYKQR  148 (226)
T ss_dssp             EEEEECSSCCCCSBCGGGCBHHHHHHHCBC--------------CGGGCCHHHHHHTEE----EEEEEEEE-TTEEEEEE
T ss_pred             EEEEEcCCCccccccccCceehheeEEeecccCccCccceEeccccccccchhhhhccc----ceEEEEEe-CCcEEEEE
Confidence            67999999999998       6667743322111   11112223 6899998776654    45566554 35555555


Q ss_pred             E
Q 039716          663 L  663 (1002)
Q Consensus       663 L  663 (1002)
                      +
T Consensus       149 f  149 (226)
T 4emv_A          149 F  149 (226)
T ss_dssp             E
T ss_pred             E
Confidence            5

>1zxm_A TOPO IIA ATPase, DNA topoisomerase II, alpha isozyme; GHKL nucleotide-binding fold; HET: DNA ANP; 1.87A {Homo sapiens} PDB: 1zxn_A*

Probab=87.08  E-value=2.1  Score=48.45  Aligned_cols=48  Identities=23%  Similarity=0.468  Sum_probs=29.4

Q ss_pred             EEEEEecCCCCCcCc--------HhhhhhhccCCC---cc-ccCcCCCccccHHHHHHHH
Q 039716          593 RCDVYDTGIGIPENA--------LPTLFRKYMQVS---AD-HARKYGGTGLGLAICKQLV  640 (1002)
Q Consensus       593 ~i~V~DtGiGI~~e~--------l~~IF~pF~q~~---~~-~~~~~~GtGLGLaI~k~Lv  640 (1002)
                      .|+|.|+|.|||.+.        .+-+|.....+.   .. .....|=.|.||+.|.-+-
T Consensus        87 ~I~V~DnGrGIPv~~h~~~~~~~~e~v~t~lhagsKf~~~~ykvSgGlhGvGlsvVnAlS  146 (400)
T 1zxm_A           87 LISIWNNGKGIPVVEHKVEKMYVPALIFGQLLTSSNYDDDEKKVTGGRNGYGAKLCNIFS  146 (400)
T ss_dssp             EEEEEEESSCCCCSEETTTTEEHHHHHHHSSSEESCCCGGGCCCCSCCSSCHHHHHHHTE
T ss_pred             EEEEEECCCcccCccccccCccchhheeeeecccCCCCCCcccccCCccccceeeeEEec
Confidence            377999999999997        455666322111   11 1112233699999887663

>3ied_A Heat shock protein; HSP90, chaperone, structural genomics, structura genomics consortium, SGC, stress response; HET: AN2; 2.01A {Plasmodium falciparum}

Probab=85.77  E-value=0.27  Score=51.81  Aligned_cols=56  Identities=20%  Similarity=0.344  Sum_probs=33.9

Q ss_pred             EEEEEecCCCCCcCcHhhhhhh--------cc---CCCccccCcCCCccccHHHHHHHHHHhCCEEEEEee
Q 039716          593 RCDVYDTGIGIPENALPTLFRK--------YM---QVSADHARKYGGTGLGLAICKQLVELMGGRLTVTSK  652 (1002)
Q Consensus       593 ~i~V~DtGiGI~~e~l~~IF~p--------F~---q~~~~~~~~~~GtGLGLaI~k~Lve~~gG~I~v~S~  652 (1002)
                      .|+|.|||+||+++.+..-|-.        |.   +........-|-.|+|++-|-.++    -.+.|.|.
T Consensus       131 tLtI~DNGiGMTkeeL~~~LgtIA~SGtk~Fle~l~~~~~d~~~IGqFGVGFySaFmVA----dkV~V~Sk  197 (272)
T 3ied_A          131 TLTITDNGIGMDKSELINNLGTIAQSGTAKFLKQIEEGKADSNLIGQFGVGFYSSFLVS----NRVEVYTK  197 (272)
T ss_dssp             EEEEEECSCCCCHHHHHHHTTCSCCHHHHHHHHHHHTTSSCTTCGGGSCCGGGGGGGTE----EEEEEEEE
T ss_pred             EEEEEeCCCCCCHHHHHHHHHHHhhcchhhHHHHhhcccccccccCcccceeheeeccC----CEEEEEEc
Confidence            4789999999999999875522        21   111011123356799998765443    44555554

>3ttz_A DNA gyrase subunit B; protein-inhibitor complex, ATP-binding, structure-based drug antimicrobial, isomerase-isomerase inhibitor complex; HET: DNA 07N; 1.63A {Staphylococcus aureus} PDB: 3u2d_A* 3u2k_A* 3g75_A* 3g7b_A*

Probab=83.73  E-value=2  Score=43.69  Aligned_cols=29  Identities=7%  Similarity=0.239  Sum_probs=19.0

Q ss_pred             cHHHHHHHHHHHHhhhhhcCC---CCeeEEEE
Q 039716          481 DVLRIRQILTNLISNAIKFTP---EGKVGIKL  509 (1002)
Q Consensus       481 D~~rL~QIL~NLlsNAIKfT~---~G~I~I~v  509 (1002)
                      ++..+.+++.-||.||++..-   ...|.|.+
T Consensus        28 ~~~gl~~~v~Elv~NsiD~~~ag~~~~I~V~i   59 (198)
T 3ttz_A           28 SERGLHHLVWEIVDNSIDEALAGYANQIEVVI   59 (198)
T ss_dssp             SHHHHHHHHHHHHHHHHHHHHTTSCCEEEEEE
T ss_pred             CCcchHHHHHHHHHHHHhHHhcCCCcEEEEEE
Confidence            456788888888888887532   23555544

>4f3l_A Mclock, circadian locomoter output cycles protein kaput; BHLH, PAS, circadian rhythm proteins, transcription-activato; 2.27A {Mus musculus}

Probab=83.19  E-value=1  Score=50.22  Aligned_cols=57  Identities=7%  Similarity=0.071  Sum_probs=48.4

Q ss_pred             HHHHHHHHhccCcEEEEecccccEEEeeccC---CCCCcccccCCCchhccCccchhhhh
Q 039716          221 DNFLHFVLQNAPVVMGHQDKELRYRFIYNHF---PSLHEEDILGKTDVEIFSGAGVKESQ  277 (1002)
Q Consensus       221 ~~~l~~il~~~p~~i~~~d~~~~~~~~~~~~---~~~~~e~iiGk~~~e~~~~~~~~~~~  277 (1002)
                      +++.+.++++++..++..|.+|++.|+|..+   .|+++++++|++..+++++.......
T Consensus        85 ~~~~~~~l~a~~~~i~v~~~~G~i~yvs~~~~~~lGy~~~el~g~~~~~~ihp~D~~~~~  144 (361)
T 4f3l_A           85 EEFTQLMLEALDGFFLAIMTDGSIIYVSESVTSLLEHLPSDLVDQSIFNFIPEGEHSEVY  144 (361)
T ss_dssp             HHHHHHHHHHTTEEEEEEETTSBEEEECTTHHHHHCCCHHHHTTSBGGGGSCGGGHHHHH
T ss_pred             HHHHHHHHHhcCceEEEEcCCccEEEEechhhhhcCCCHHHhcCCcHHHhcCHHHHHHHH
Confidence            4567788999999999999999999998865   58899999999999999887655443

>1oj5_A Steroid receptor coactivator 1A; transcriptional coactivator, complex, LXXLL motif, transcriptional regulation; 2.2A {Mus musculus} SCOP: d.110.3.8

Probab=81.06  E-value=2.6  Score=39.77  Aligned_cols=99  Identities=14%  Similarity=0.095  Sum_probs=62.1

Q ss_pred             cCcEEEEecccccEEEeecc--CCCCCc--ccccCCCchhccCccchh--hhhHHHHHHHHhCCCcceeEEEEEeecCce
Q 039716          231 APVVMGHQDKELRYRFIYNH--FPSLHE--EDILGKTDVEIFSGAGVK--ESQDFKREVLEKGLPAKREITFETELFGSK  304 (1002)
Q Consensus       231 ~p~~i~~~d~~~~~~~~~~~--~~~~~~--e~iiGk~~~e~~~~~~~~--~~~~~~~~vl~~g~~~~~e~~~~~~~~~~~  304 (1002)
                      ..-.+...|.+|.+.++-..  ..++.+  +|++|+...+++.+.+..  ......++|+.+|.....-.+|....++-.
T Consensus         6 ~e~F~sRh~~dGKf~~vDq~~~r~~~~~g~qdLlGrsiy~f~H~~D~~~s~l~~h~~~vl~~Gq~~S~~YRfr~k~g~~V   85 (132)
T 1oj5_A            6 VESFMTKQDTTGKIISIDTSSLRAAGRTGWEDLVRKCIYAFFQPQGREPSYARQLFQEVMTRGTASSPSYRFILNDGTML   85 (132)
T ss_dssp             CCEEEEEECTTCCEEEEECHHHHTTCCSCHHHHHHHHHHHHTSCBTTBCCHHHHHHHHHHHHSEEECCCEEEECTTSCEE
T ss_pred             ceeeEEeecCCCcEEEEecccccccccccHHHHHHHHHHHHhCcccchHHHHHHHHHHHHHcCCccccceEEEecCCcEE
Confidence            34567778999999998663  134444  899999999999988755  677778889988876555556655543322


Q ss_pred             EEEEEE----eeeecCCCCEEEEEEEeec
Q 039716          305 TFLIYV----EPVFSKSGETIGVNYMGMD  329 (1002)
Q Consensus       305 ~~~~~~----~p~~~~~G~~~gi~~~~~D  329 (1002)
                      +.....    .|..++-.-++++..+.++
T Consensus        86 ~~qT~sk~f~np~t~e~e~Ivs~n~v~r~  114 (132)
T 1oj5_A           86 SAHTRCKLCYPQSPDMQPFIMGIHIIDRE  114 (132)
T ss_dssp             EEEEEEEEECC----CCCEEEEEEEEECC
T ss_pred             EEEEEEEEecCCCCCCCCEEEEEEEEEcC
Confidence            222222    2332333445566655544

>2i2x_B MTAC, methyltransferase 1; TIM barrel and helix bundle (MTAB), rossman fold and helix B (MTAC); HET: B13; 2.50A {Methanosarcina barkeri}

Probab=80.67  E-value=16  Score=38.53  Aligned_cols=101  Identities=11%  Similarity=0.090  Sum_probs=71.8

Q ss_pred             CCCeEEEE----ecCHHHHHHHHHHHHhcCCeEEEE---cCHHHHHHHHHcCCCcEEEEcCCCCC-CCH-HHHHHHHhcc
Q 039716          858 PKPKILLV----EDNKINVMVAKSMMKQLGHSIDVV---NNGVEAVHAVQCQNYDLILMDVCMPV-MDG-LKATRLIRSF  928 (1002)
Q Consensus       858 ~~~~ILiV----eDn~~n~~~l~~~L~~~g~~v~~a---~~G~eAl~~~~~~~~DlIlmDi~MP~-mdG-~e~~~~IR~~  928 (1002)
                      .+++||++    |-+.+-..++..+|+..||+|...   ....+.++.+...+||+|.+-..|+. +.. -++++.+|+.
T Consensus       122 ~~~~vlla~~~gd~HdiG~~iva~~L~~~G~~Vi~LG~~vp~e~l~~~~~~~~~d~V~lS~l~~~~~~~~~~~i~~l~~~  201 (258)
T 2i2x_B          122 TKGTVVCHVAEGDVHDIGKNIVTALLRANGYNVVDLGRDVPAEEVLAAVQKEKPIMLTGTALMTTTMYAFKEVNDMLLEN  201 (258)
T ss_dssp             CSCEEEEEECTTCCCCHHHHHHHHHHHHTTCEEEEEEEECCSHHHHHHHHHHCCSEEEEECCCTTTTTHHHHHHHHHHTT
T ss_pred             CCCeEEEEeCCCCccHHHHHHHHHHHHHCCCEEEECCCCCCHHHHHHHHHHcCCCEEEEEeeccCCHHHHHHHHHHHHhc
Confidence            35688888    667788889999999999998643   46777888999999999999987764 332 3455666641


Q ss_pred             ccCCCchhhhhhhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCC
Q 039716          929 EDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKP  987 (1002)
Q Consensus       929 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP  987 (1002)
                                                ..++||++--+....+.   +-..|+|.|-.-+
T Consensus       202 --------------------------~~~~~v~vGG~~~~~~~---~~~igad~~~~da  231 (258)
T 2i2x_B          202 --------------------------GIKIPFACGGGAVNQDF---VSQFALGVYGEEA  231 (258)
T ss_dssp             --------------------------TCCCCEEEESTTCCHHH---HHTSTTEEECSST
T ss_pred             --------------------------CCCCcEEEECccCCHHH---HHHcCCeEEECCH
Confidence                                      23478776655555432   3477998776544

---

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	1002
d1dcfa_	134	c.23.1.2 (A:) Receiver domain of the ethylene rece	1e-24
d2c2aa2	161	d.122.1.3 (A:321-481) Sensor histidine kinase TM08	2e-24
d2c2aa2	161	d.122.1.3 (A:321-481) Sensor histidine kinase TM08	6e-11
d2r25b1	128	c.23.1.1 (B:1087-1214) Response regulator Sin1 {Ba	2e-23
d1ysra1	148	d.122.1.3 (A:299-446) Sensor-type histidine kinase	1e-22
d1ysra1	148	d.122.1.3 (A:299-446) Sensor-type histidine kinase	8e-08
d1dz3a_	123	c.23.1.1 (A:) Sporulation response regulator Spo0A	3e-22
d1u0sy_	118	c.23.1.1 (Y:) CheY protein {Thermotoga maritima [T	3e-22
d1jbea_	128	c.23.1.1 (A:) CheY protein {Escherichia coli [TaxI	4e-22
d1peya_	119	c.23.1.1 (A:) Sporulation response regulator Spo0F	1e-21
d1zesa1	121	c.23.1.1 (A:3-123) PhoB receiver domain {Escherich	3e-21
d1bxda_	161	d.122.1.3 (A:) Histidine kinase domain of the osmo	6e-21
d1bxda_	161	d.122.1.3 (A:) Histidine kinase domain of the osmo	9e-08
d1mb3a_	123	c.23.1.1 (A:) Cell division response regulator Div	3e-20
d2ayxa1	133	c.23.1.1 (A:817-949) Sensor kinase protein RcsC, C	7e-20
d1p6qa_	129	c.23.1.1 (A:) CheY protein {Sinorhizobium meliloti	2e-19
d1i3ca_	144	c.23.1.1 (A:) Response regulator for cyanobacteria	3e-19
d1a04a2	138	c.23.1.1 (A:5-142) Nitrate/nitrite response regula	3e-19
d2b4aa1	118	c.23.1.1 (A:2-119) Hypothetical protein BH3024 {Ba	4e-19
d1k68a_	140	c.23.1.1 (A:) Response regulator for cyanobacteria	5e-19
d1jm6a2	190	d.122.1.4 (A:1177-1366) Pyruvate dehydrogenase kin	9e-19
d1jm6a2	190	d.122.1.4 (A:1177-1366) Pyruvate dehydrogenase kin	5e-10
d1a2oa1	140	c.23.1.1 (A:1-140) Methylesterase CheB, N-terminal	9e-19
d2a9pa1	117	c.23.1.1 (A:2-118) DNA-binding response regulator	1e-18
d1id0a_	146	d.122.1.3 (A:) Histidine kinase PhoQ domain {Esche	1e-18
d1id0a_	146	d.122.1.3 (A:) Histidine kinase PhoQ domain {Esche	1e-07
d1zgza1	120	c.23.1.1 (A:2-121) TorCAD operon transcriptional r	2e-18
d1xhfa1	121	c.23.1.1 (A:2-122) Aerobic respiration control pro	7e-18
d1yioa2	128	c.23.1.1 (A:3-130) Response regulatory protein Sty	2e-17
d1krwa_	123	c.23.1.1 (A:) NTRC receiver domain {Salmonella typ	3e-17
d1qkka_	140	c.23.1.1 (A:) Transcriptional regulatory protein D	7e-17
d1s8na_	190	c.23.1.1 (A:) Probable two-component system transc	1e-16
d1ys7a2	121	c.23.1.1 (A:7-127) Transcriptional regulatory prot	1e-16
d1dbwa_	123	c.23.1.1 (A:) Transcriptional regulatory protein F	7e-16
d1zh2a1	119	c.23.1.1 (A:2-120) Transcriptional regulatory prot	9e-16
d1mvoa_	121	c.23.1.1 (A:) PhoP receiver domain {Bacillus subti	2e-15
d1k66a_	149	c.23.1.1 (A:) Response regulator for cyanobacteria	5e-15
d1ny5a1	137	c.23.1.1 (A:1-137) Transcriptional activator sigm5	5e-15
d2pl1a1	119	c.23.1.1 (A:1-119) PhoP receiver domain {Escherich	1e-14
d1kgsa2	122	c.23.1.1 (A:2-123) PhoB receiver domain {Thermotog	5e-14
d1gkza2	193	d.122.1.4 (A:186-378) Branched-chain alpha-ketoaci	7e-14
d1p2fa2	120	c.23.1.1 (A:1-120) Response regulator DrrB {Thermo	2e-13
d1w25a1	139	c.23.1.1 (A:2-140) Response regulator PleD, receiv	4e-13
d1w25a2	153	c.23.1.1 (A:141-293) Response regulator PleD, rece	6e-13
d1i58a_	189	d.122.1.3 (A:) Histidine kinase CheA {Thermotoga m	8e-13
d1r62a_	156	d.122.1.3 (A:) Nitrogen regulation protein NtrB, C	1e-12
d1r62a_	156	d.122.1.3 (A:) Nitrogen regulation protein NtrB, C	2e-07
d1qo0d_	189	c.23.1.3 (D:) Positive regulator of the amidase op	2e-10
d2c2aa1	89	a.30.2.1 (A:232-320) Sensor histidine kinase TM085	2e-08
d2hkja3	219	d.122.1.2 (A:10-228) Topoisomerase VI-B subunit {A	4e-08
d2hkja3	219	d.122.1.2 (A:10-228) Topoisomerase VI-B subunit {A	2e-04
d1joya_	67	a.30.2.1 (A:) EnvZ histidine kinase {Escherichia c	1e-07
d1th8a_	139	d.122.1.3 (A:) Anti-sigma factor spoIIab {Bacillus	9e-05

>d1dcfa_ c.23.1.2 (A:) Receiver domain of the ethylene receptor {Thale cress (Arabidopsis thaliana) [TaxId: 3702]} Length = 134

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: Receiver domain of the ethylene receptor
domain: Receiver domain of the ethylene receptor
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

 Score = 98.1 bits (244), Expect = 1e-24
 Identities = 29/140 (20%), Positives = 63/140 (45%), Gaps = 22/140 (15%)

Query: 861  KILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLK 920
            K+L++++N ++ MV K ++  LG  +  V++  E +  V    + ++ MDVCMP ++  +
Sbjct: 9    KVLVMDENGVSRMVTKGLLVHLGCEVTTVSSNEECLRVVS-HEHKVVFMDVCMPGVENYQ 67

Query: 921  ATRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGM 980
                I                         +    +R  ++A++ N    + E+C + G+
Sbjct: 68   IALRIHEKF---------------------TKQRHQRPLLVALSGNTDKSTKEKCMSFGL 106

Query: 981  DSFVSKPVTFQKLKECLEQY 1000
            D  + KPV+   +++ L   
Sbjct: 107  DGVLLKPVSLDNIRDVLSDL 126

>d2c2aa2 d.122.1.3 (A:321-481) Sensor histidine kinase TM0853 {Thermotoga maritima [TaxId: 2336]} Length = 161

class: Alpha and beta proteins (a+b)
fold: ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
superfamily: ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
family: Histidine kinase
domain: Sensor histidine kinase TM0853
species: Thermotoga maritima [TaxId: 2336]

 Score = 98.8 bits (246), Expect = 2e-24
 Identities = 32/74 (43%), Positives = 46/74 (62%)

Query: 591 WIRCDVYDTGIGIPENALPTLFRKYMQVSADHARKYGGTGLGLAICKQLVELMGGRLTVT 650
            +   V D GIGIP++A   +F ++ +V +    +  GTGLGLAI K++VEL GGR+ V 
Sbjct: 84  GVLIIVEDNGIGIPDHAKDRIFEQFYRVDSSLTYEVPGTGLGLAITKEIVELHGGRIWVE 143

Query: 651 SKVHCGSTFTFILP 664
           S+V  GS F   +P
Sbjct: 144 SEVGKGSRFFVWIP 157

>d2c2aa2 d.122.1.3 (A:321-481) Sensor histidine kinase TM0853 {Thermotoga maritima [TaxId: 2336]} Length = 161

class: Alpha and beta proteins (a+b)
fold: ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
superfamily: ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
family: Histidine kinase
domain: Sensor histidine kinase TM0853
species: Thermotoga maritima [TaxId: 2336]

 Score = 59.5 bits (144), Expect = 6e-11
 Identities = 14/72 (19%), Positives = 31/72 (43%), Gaps = 1/72 (1%)

Query: 437 KLEAAKFRPREVVKHVLQTAAASL-QKILMLEGDIADDVPIEVIGDVLRIRQILTNLISN 495
           ++   K    ++V+  +           + +  +     P+E   D  RIRQ+L NL++N
Sbjct: 1   QINREKVDLCDLVESAVNAIKEFASSHNVNVLFESNVPCPVEAYIDPTRIRQVLLNLLNN 60

Query: 496 AIKFTPEGKVGI 507
            +K++ +     
Sbjct: 61  GVKYSKKDAPDK 72

>d2r25b1 c.23.1.1 (B:1087-1214) Response regulator Sin1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 128

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: Response regulator Sin1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 94.3 bits (234), Expect = 2e-23
 Identities = 49/146 (33%), Positives = 75/146 (51%), Gaps = 31/146 (21%)

Query: 861  KILLVEDNKINVMVAKSMMKQLG-HSIDVVNNGVEAVHAVQC-----QNYDLILMDVCMP 914
            KIL+VEDN +N  V K M+   G  +I++  +G EA   V+      +NY++I MDV MP
Sbjct: 3    KILVVEDNHVNQEVIKRMLNLEGIENIELACDGQEAFDKVKELTSKGENYNMIFMDVQMP 62

Query: 915  VMDGLKATRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEE 974
             +DGL +T++IR                          +     PI+A+TA A   + +E
Sbjct: 63   KVDGLLSTKMIRR-------------------------DLGYTSPIVALTAFADDSNIKE 97

Query: 975  CFANGMDSFVSKPVTFQKLKECLEQY 1000
            C  +GM+ F+SKP+   KLK  L ++
Sbjct: 98   CLESGMNGFLSKPIKRPKLKTILTEF 123

>d1ysra1 d.122.1.3 (A:299-446) Sensor-type histidine kinase PrrB {Mycobacterium tuberculosis [TaxId: 1773]} Length = 148

class: Alpha and beta proteins (a+b)
fold: ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
superfamily: ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
family: Histidine kinase
domain: Sensor-type histidine kinase PrrB
species: Mycobacterium tuberculosis [TaxId: 1773]

 Score = 92.6 bits (230), Expect = 1e-22
 Identities = 19/74 (25%), Positives = 34/74 (45%), Gaps = 3/74 (4%)

Query: 591 WIRCDVYDTGIGIPENALPTLFRKYMQVSADHARKYGGTGLGLAICKQLVELMGGRLTVT 650
            +   + D G G+PE     +F ++ +        + G+GLGLA+  Q  +L GG  ++ 
Sbjct: 75  GVEIAIDDNGSGVPEGERQVVFERFSRG---STASHSGSGLGLALVAQQAQLHGGTASLE 131

Query: 651 SKVHCGSTFTFILP 664
           +    G+     LP
Sbjct: 132 NSPLGGARLVLRLP 145

>d1ysra1 d.122.1.3 (A:299-446) Sensor-type histidine kinase PrrB {Mycobacterium tuberculosis [TaxId: 1773]} Length = 148

class: Alpha and beta proteins (a+b)
fold: ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
superfamily: ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
family: Histidine kinase
domain: Sensor-type histidine kinase PrrB
species: Mycobacterium tuberculosis [TaxId: 1773]

 Score = 50.3 bits (120), Expect = 8e-08
 Identities = 10/72 (13%), Positives = 24/72 (33%), Gaps = 3/72 (4%)

Query: 439 EAAKFRPREVVKHVLQTAAASLQKILMLEGDIADDVPIEVIGDVLRIRQILTNLISNAIK 498
           +       +++      AA     +   +  +       ++G    +R  + N I+NA+K
Sbjct: 2   DHVPVDITDLLDRAAHDAARIYPDL---DVSLVPSPTCIIVGLPAGLRLAVDNAIANAVK 58

Query: 499 FTPEGKVGIKLY 510
                 V +   
Sbjct: 59  HGGATLVQLSAV 70

>d1dz3a_ c.23.1.1 (A:) Sporulation response regulator Spo0A {Bacillus stearothermophilus [TaxId: 1422]} Length = 123

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: Sporulation response regulator Spo0A
species: Bacillus stearothermophilus [TaxId: 1422]

 Score = 91.0 bits (226), Expect = 3e-22
 Identities = 26/141 (18%), Positives = 52/141 (36%), Gaps = 27/141 (19%)

Query: 861 KILLVEDNKINVMVAKSMMKQLG--HSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDG 918
           K+ + +DN+  V +    +        I    NG + +  ++ +  D++L+D+ MP +DG
Sbjct: 3   KVCIADDNRELVSLLDEYISSQPDMEVIGTAYNGQDCLQMLEEKRPDILLLDIIMPHLDG 62

Query: 919 LKATRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFAN 978
           L     IR                         +    +  +I +TA    +  ++    
Sbjct: 63  LAVLERIR-------------------------AGFEHQPNVIMLTAFGQEDVTKKAVEL 97

Query: 979 GMDSFVSKPVTFQKLKECLEQ 999
           G   F+ KP   + L   + Q
Sbjct: 98  GASYFILKPFDMENLAHHIRQ 118

>d1u0sy_ c.23.1.1 (Y:) CheY protein {Thermotoga maritima [TaxId: 2336]} Length = 118

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: CheY protein
species: Thermotoga maritima [TaxId: 2336]

 Score = 90.7 bits (225), Expect = 3e-22
 Identities = 30/140 (21%), Positives = 51/140 (36%), Gaps = 27/140 (19%)

Query: 861 KILLVEDNKINVMVAKSMMKQLGHS-IDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGL 919
           ++L+V+D     M+ K ++ + G+       NG EAV   +    D++ MD+ MP M+G+
Sbjct: 3   RVLIVDDAAFMRMMLKDIITKAGYEVAGEATNGREAVEKYKELKPDIVTMDITMPEMNGI 62

Query: 920 KATRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANG 979
            A + I                                  II  +A        E    G
Sbjct: 63  DAIKEIMK--------------------------IDPNAKIIVCSAMGQQAMVIEAIKAG 96

Query: 980 MDSFVSKPVTFQKLKECLEQ 999
              F+ KP    ++ E L +
Sbjct: 97  AKDFIVKPFQPSRVVEALNK 116

>d1peya_ c.23.1.1 (A:) Sporulation response regulator Spo0F {Bacillus subtilis [TaxId: 1423]} Length = 119

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: Sporulation response regulator Spo0F
species: Bacillus subtilis [TaxId: 1423]

 Score = 88.8 bits (220), Expect = 1e-21
 Identities = 29/142 (20%), Positives = 62/142 (43%), Gaps = 26/142 (18%)

Query: 861  KILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLK 920
            KIL+V+D     ++   +  + G+      NG++A+  V  +  DL+L+D+ +P MDG++
Sbjct: 3    KILIVDDQSGIRILLNEVFNKEGYQTFQAANGLQALDIVTKERPDLVLLDMKIPGMDGIE 62

Query: 921  ATRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGM 980
              + ++                             + I +I MTA    +  +E    G 
Sbjct: 63   ILKRMKV--------------------------IDENIRVIIMTAYGELDMIQESKELGA 96

Query: 981  DSFVSKPVTFQKLKECLEQYFP 1002
             +  +KP    ++++ +++Y P
Sbjct: 97   LTHFAKPFDIDEIRDAVKKYLP 118

>d1zesa1 c.23.1.1 (A:3-123) PhoB receiver domain {Escherichia coli [TaxId: 562]} Length = 121

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: PhoB receiver domain
species: Escherichia coli [TaxId: 562]

 Score = 87.7 bits (217), Expect = 3e-21
 Identities = 26/139 (18%), Positives = 54/139 (38%), Gaps = 24/139 (17%)

Query: 861 KILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLK 920
           +IL+VED      +   +++Q G       +   AV+ +     DLIL+D  +P   G++
Sbjct: 2   RILVVEDEAPIREMVCFVLEQNGFQPVEAEDYDSAVNQLNEPWPDLILLDWMLPGGSGIQ 61

Query: 921 ATRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGM 980
             + ++    T +                         P++ +TA    E        G 
Sbjct: 62  FIKHLKRESMTRDI------------------------PVVMLTARGEEEDRVRGLETGA 97

Query: 981 DSFVSKPVTFQKLKECLEQ 999
           D +++KP + ++L   ++ 
Sbjct: 98  DDYITKPFSPKELVARIKA 116

>d1bxda_ d.122.1.3 (A:) Histidine kinase domain of the osmosensor EnvZ {Escherichia coli [TaxId: 562]} Length = 161

class: Alpha and beta proteins (a+b)
fold: ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
superfamily: ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
family: Histidine kinase
domain: Histidine kinase domain of the osmosensor EnvZ
species: Escherichia coli [TaxId: 562]

 Score = 88.4 bits (219), Expect = 6e-21
 Identities = 25/86 (29%), Positives = 40/86 (46%), Gaps = 2/86 (2%)

Query: 591 WIRCDVYDTGIGIPENALPTLFRKYMQVSADHARKYGGTGLGLAICKQLVELMGGRLTVT 650
                V D G GI       LF+ +++   D AR   GTGLGLAI +++V+   G L + 
Sbjct: 77  RAWFQVEDDGPGIAPEQRKHLFQPFVR--GDSARTISGTGLGLAIVQRIVDNHNGMLELG 134

Query: 651 SKVHCGSTFTFILPYQVSPIEENSDD 676
           +    G +    LP  V+  +  + +
Sbjct: 135 TSERGGLSIRAWLPVPVTRAQGTTKE 160

>d1bxda_ d.122.1.3 (A:) Histidine kinase domain of the osmosensor EnvZ {Escherichia coli [TaxId: 562]} Length = 161

class: Alpha and beta proteins (a+b)
fold: ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
superfamily: ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
family: Histidine kinase
domain: Histidine kinase domain of the osmosensor EnvZ
species: Escherichia coli [TaxId: 562]

 Score = 50.7 bits (121), Expect = 9e-08
 Identities = 14/78 (17%), Positives = 31/78 (39%), Gaps = 5/78 (6%)

Query: 437 KLEAAKFRPREVVKHVLQTAAASLQKILMLEGDIADDVPIEVIGDVLRIRQILTNLISNA 496
           ++         V+  V+   +   ++I   E  +     IEV    L I++ + N++ NA
Sbjct: 4   EMPMEMADLNAVLGEVIAAESGYEREI---ETALYPG-SIEVKMHPLSIKRAVANMVVNA 59

Query: 497 IKFTPEGKVGIKLYVVPE 514
            ++   G + +     P 
Sbjct: 60  ARYG-NGWIKVSSGTEPN 76

>d1mb3a_ c.23.1.1 (A:) Cell division response regulator DivK {Caulobacter crescentus [TaxId: 155892]} Length = 123

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: Cell division response regulator DivK
species: Caulobacter crescentus [TaxId: 155892]

 Score = 85.1 bits (210), Expect = 3e-20
 Identities = 33/139 (23%), Positives = 67/139 (48%), Gaps = 24/139 (17%)

Query: 861 KILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLK 920
           K+L+VEDN++N+ +   +++  G+       G+ A+   +    DLILMD+ +P + GL+
Sbjct: 3   KVLIVEDNELNMKLFHDLLEAQGYETLQTREGLSALSIARENKPDLILMDIQLPEISGLE 62

Query: 921 ATRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGM 980
            T+ ++  +D                           IP++A+TA A+    E     G 
Sbjct: 63  VTKWLKEDDDL------------------------AHIPVVAVTAFAMKGDEERIREGGC 98

Query: 981 DSFVSKPVTFQKLKECLEQ 999
           ++++SKP++     E +++
Sbjct: 99  EAYISKPISVVHFLETIKR 117

>d2ayxa1 c.23.1.1 (A:817-949) Sensor kinase protein RcsC, C-terminal domain {Escherichia coli [TaxId: 562]} Length = 133

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: Sensor kinase protein RcsC, C-terminal domain
species: Escherichia coli [TaxId: 562]

 Score = 84.4 bits (208), Expect = 7e-20
 Identities = 45/140 (32%), Positives = 70/140 (50%), Gaps = 26/140 (18%)

Query: 861  KILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLK 920
             IL+V+D+ IN  +    +  LG+     N+GV+A++ +   + D++L DV MP MDG +
Sbjct: 10   MILVVDDHPINRRLLADQLGSLGYQCKTANDGVDALNVLSKNHIDIVLSDVNMPNMDGYR 69

Query: 921  ATRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGM 980
             T+ IR                               +P+I +TANAL+E  + C  +GM
Sbjct: 70   LTQRIRQ--------------------------LGLTLPVIGVTANALAEEKQRCLESGM 103

Query: 981  DSFVSKPVTFQKLKECLEQY 1000
            DS +SKPVT   +K+ L  Y
Sbjct: 104  DSCLSKPVTLDVIKQTLTLY 123

>d1p6qa_ c.23.1.1 (A:) CheY protein {Sinorhizobium meliloti, CheY2 [TaxId: 382]} Length = 129

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: CheY protein
species: Sinorhizobium meliloti, CheY2 [TaxId: 382]

 Score = 83.1 bits (205), Expect = 2e-19
 Identities = 32/144 (22%), Positives = 61/144 (42%), Gaps = 25/144 (17%)

Query: 859  KPKILLVEDNKINVMVAKSMMKQLGHS-IDVVNNGVEAVHAVQCQNYDLILMDVCMPVMD 917
            K K+L+V+D   + ++    ++QLG   I    +G + +  +    + L++ D  MP MD
Sbjct: 6    KIKVLIVDDQVTSRLLLGDALQQLGFKQITAAGDGEQGMKIMAQNPHHLVISDFNMPKMD 65

Query: 918  GLKATRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFA 977
            GL   + +R+                            K+   I +TA       ++  A
Sbjct: 66   GLGLLQAVRANPA------------------------TKKAAFIILTAQGDRALVQKAAA 101

Query: 978  NGMDSFVSKPVTFQKLKECLEQYF 1001
             G ++ ++KP T +K+K  +E  F
Sbjct: 102  LGANNVLAKPFTIEKMKAAIEAVF 125

>d1i3ca_ c.23.1.1 (A:) Response regulator for cyanobacterial phytochrome {Synechocystis sp. PCC 6803, RCP1 [TaxId: 1148]} Length = 144

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: Response regulator for cyanobacterial phytochrome
species: Synechocystis sp. PCC 6803, RCP1 [TaxId: 1148]

 Score = 83.2 bits (205), Expect = 3e-19
 Identities = 28/151 (18%), Positives = 62/151 (41%), Gaps = 33/151 (21%)

Query: 858 PKPKILLVEDNKINVMVAKSMMKQLG--HSIDVVNNGVEAVHAVQCQN-------YDLIL 908
           P   ILLVED+K +  + + ++K     H + ++ +G+ A+  +Q Q         +LIL
Sbjct: 2   PPKVILLVEDSKADSRLVQEVLKTSTIDHELIILRDGLAAMAFLQQQGEYENSPRPNLIL 61

Query: 909 MDVCMPVMDGLKATRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANAL 968
           +D+ +P  DG +    I+   D                           IP++ +T +  
Sbjct: 62  LDLNLPKKDGREVLAEIKQNPDLKR------------------------IPVVVLTTSHN 97

Query: 969 SESAEECFANGMDSFVSKPVTFQKLKECLEQ 999
            +     +   ++ +++K    + L + ++ 
Sbjct: 98  EDDVIASYELHVNCYLTKSRNLKDLFKMVQG 128

>d1a04a2 c.23.1.1 (A:5-142) Nitrate/nitrite response regulator (NarL), receiver domain {Escherichia coli [TaxId: 562]} Length = 138

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: Nitrate/nitrite response regulator (NarL), receiver domain
species: Escherichia coli [TaxId: 562]

 Score = 82.6 bits (204), Expect = 3e-19
 Identities = 26/141 (18%), Positives = 51/141 (36%), Gaps = 28/141 (19%)

Query: 861 KILLVEDNKINVMVAKSMMKQLGH--SIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDG 918
            ILL++D+ +     K ++        +   +NG + +   +  + DLIL+D+ MP M+G
Sbjct: 4   TILLIDDHPMLRTGVKQLISMAPDITVVGEASNGEQGIELAESLDPDLILLDLNMPGMNG 63

Query: 919 LKATRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFAN 978
           L+    +R                                 I+  + +   E        
Sbjct: 64  LETLDKLRE--------------------------KSLSGRIVVFSVSNHEEDVVTALKR 97

Query: 979 GMDSFVSKPVTFQKLKECLEQ 999
           G D ++ K +  + L + L Q
Sbjct: 98  GADGYLLKDMEPEDLLKALHQ 118

>d2b4aa1 c.23.1.1 (A:2-119) Hypothetical protein BH3024 {Bacillus halodurans [TaxId: 86665]} Length = 118

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: Hypothetical protein BH3024
species: Bacillus halodurans [TaxId: 86665]

 Score = 81.9 bits (202), Expect = 4e-19
 Identities = 20/143 (13%), Positives = 49/143 (34%), Gaps = 30/143 (20%)

Query: 861  KILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAV-HAVQCQNYDLILMDVCMPVMDGL 919
            ++ LVED   +  + +  + QLG  + V  +G     H  Q    DL+++   +  +   
Sbjct: 4    RVTLVEDEPSHATLIQYHLNQLGAEVTVHPSGSAFFQHRSQLSTCDLLIVSDQLVDLSIF 63

Query: 920  KATRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANG 979
                +++                             K+  ++ +T         E   + 
Sbjct: 64   SLLDIVKE--------------------------QTKQPSVLILTTGR--HELIESSEHN 95

Query: 980  MDSFVSKPVTFQKLKECLEQYFP 1002
            +  ++ KP    +L+  ++ + P
Sbjct: 96   LS-YLQKPFAISELRAAIDYHKP 117

>d1k68a_ c.23.1.1 (A:) Response regulator for cyanobacterial phytochrome {Calothrix sp. pcc 7601, RcpA [TaxId: 1188]} Length = 140

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: Response regulator for cyanobacterial phytochrome
species: Calothrix sp. pcc 7601, RcpA [TaxId: 1188]

 Score = 82.0 bits (202), Expect = 5e-19
 Identities = 29/148 (19%), Positives = 62/148 (41%), Gaps = 33/148 (22%)

Query: 861 KILLVEDNKINVMVAKSMMKQLG--HSIDVVNNGVEAVHAVQCQ-------NYDLILMDV 911
           KI LVEDNK ++ + +  +      H +  V +G+EA+  ++ +         DLIL+D+
Sbjct: 4   KIFLVEDNKADIRLIQEALANSTVPHEVVTVRDGMEAMAYLRQEGEYANASRPDLILLDL 63

Query: 912 CMPVMDGLKATRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSES 971
            +P  DG +    I+S                            KRIP++ ++ +   + 
Sbjct: 64  NLPKKDGREVLAEIKSDPTL------------------------KRIPVVVLSTSINEDD 99

Query: 972 AEECFANGMDSFVSKPVTFQKLKECLEQ 999
               +   ++ +++K     +L + ++ 
Sbjct: 100 IFHSYDLHVNCYITKSANLSQLFQIVKG 127

>d1jm6a2 d.122.1.4 (A:1177-1366) Pyruvate dehydrogenase kinase {Rat (Rattus norvegicus), isozyme 2 [TaxId: 10116]} Length = 190

class: Alpha and beta proteins (a+b)
fold: ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
superfamily: ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
family: alpha-ketoacid dehydrogenase kinase, C-terminal domain
domain: Pyruvate dehydrogenase kinase
species: Rat (Rattus norvegicus), isozyme 2 [TaxId: 10116]

 Score = 83.2 bits (205), Expect = 9e-19
 Identities = 17/88 (19%), Positives = 27/88 (30%), Gaps = 5/88 (5%)

Query: 591 WIRCDVYDTGIGIPENALPTLFRKYMQVSADHARK-----YGGTGLGLAICKQLVELMGG 645
            +   + D G G+P   +  LF      +             G G GL I +   +   G
Sbjct: 99  DLSIKMSDRGGGVPLRKIERLFSYMYSTAPTPQPGTGGTPLAGFGYGLPISRLYAKYFQG 158

Query: 646 RLTVTSKVHCGSTFTFILPYQVSPIEEN 673
            L + S    G+     L    +   E 
Sbjct: 159 DLQLFSMEGFGTDAVIYLKALSTDSVER 186

>d1jm6a2 d.122.1.4 (A:1177-1366) Pyruvate dehydrogenase kinase {Rat (Rattus norvegicus), isozyme 2 [TaxId: 10116]} Length = 190

class: Alpha and beta proteins (a+b)
fold: ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
superfamily: ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
family: alpha-ketoacid dehydrogenase kinase, C-terminal domain
domain: Pyruvate dehydrogenase kinase
species: Rat (Rattus norvegicus), isozyme 2 [TaxId: 10116]

 Score = 57.8 bits (139), Expect = 5e-10
 Identities = 14/68 (20%), Positives = 22/68 (32%), Gaps = 8/68 (11%)

Query: 444 RPREVVKHVLQTA--------AASLQKILMLEGDIADDVPIEVIGDVLRIRQILTNLISN 495
              +VVK     A         AS    +          PI ++     +  +L  L  N
Sbjct: 12  SVSDVVKDAYDMAKLLCDKYYMASPDLEIQEVNATNATQPIHMVYVPSHLYHMLFELFKN 71

Query: 496 AIKFTPEG 503
           A++ T E 
Sbjct: 72  AMRATVES 79

>d1a2oa1 c.23.1.1 (A:1-140) Methylesterase CheB, N-terminal domain {Salmonella typhimurium [TaxId: 90371]} Length = 140

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: Methylesterase CheB, N-terminal domain
species: Salmonella typhimurium [TaxId: 90371]

 Score = 81.5 bits (201), Expect = 9e-19
 Identities = 23/132 (17%), Positives = 45/132 (34%), Gaps = 27/132 (20%)

Query: 859 KPKILLVEDNKINVMVAKSMMKQLG--HSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVM 916
           K ++L V+D+ +   +   ++        +    + + A   ++  N D++ +DV MP M
Sbjct: 3   KIRVLSVDDSALMRQIMTEIINSHSDMEMVATAPDPLVARDLIKKFNPDVLTLDVEMPRM 62

Query: 917 DGLKATRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECF 976
           DGL     +                                + + ++T    SE      
Sbjct: 63  DGLDFLEKLMRL------------------------RPMPVVMVSSLTGKG-SEVTLRAL 97

Query: 977 ANGMDSFVSKPV 988
             G   FV+KP 
Sbjct: 98  ELGAIDFVTKPQ 109

>d2a9pa1 c.23.1.1 (A:2-118) DNA-binding response regulator MicA, N-terminal domain {Streptococcus pneumoniae [TaxId: 1313]} Length = 117

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: DNA-binding response regulator MicA, N-terminal domain
species: Streptococcus pneumoniae [TaxId: 1313]

 Score = 80.8 bits (199), Expect = 1e-18
 Identities = 31/139 (22%), Positives = 60/139 (43%), Gaps = 27/139 (19%)

Query: 861 KILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLK 920
           KIL+V+D K    + K  M + G+ +    NG EA+   + +  D+I++D+ +P +DGL+
Sbjct: 2   KILIVDDEKPISDIIKFNMTKEGYEVVTAFNGREALEQFEAEQPDIIILDLMLPEIDGLE 61

Query: 921 ATRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGM 980
             + IR                               +PI+ ++A             G 
Sbjct: 62  VAKTIRKTSS---------------------------VPILMLSAKDSEFDKVIGLELGA 94

Query: 981 DSFVSKPVTFQKLKECLEQ 999
           D +V+KP + ++L+  ++ 
Sbjct: 95  DDYVTKPFSNRELQARVKA 113

>d1id0a_ d.122.1.3 (A:) Histidine kinase PhoQ domain {Escherichia coli [TaxId: 562]} Length = 146

class: Alpha and beta proteins (a+b)
fold: ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
superfamily: ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
family: Histidine kinase
domain: Histidine kinase PhoQ domain
species: Escherichia coli [TaxId: 562]

 Score = 81.4 bits (201), Expect = 1e-18
 Identities = 18/76 (23%), Positives = 32/76 (42%), Gaps = 4/76 (5%)

Query: 591 WIRCDVYDTGIGIPENALPTLFRKYMQVSADHARKYGGTGLGLAICKQLVELMGGRLTVT 650
            +   V D G GIP +    +F +  +V         G G+GLA+ +++ E   G++   
Sbjct: 74  HLYIVVEDDGPGIPLSKREVIFDRGQRVD----TLRPGQGVGLAVAREITEQYEGKIVAG 129

Query: 651 SKVHCGSTFTFILPYQ 666
             +  G+    I   Q
Sbjct: 130 ESMLGGARMEVIFGRQ 145

>d1id0a_ d.122.1.3 (A:) Histidine kinase PhoQ domain {Escherichia coli [TaxId: 562]} Length = 146

class: Alpha and beta proteins (a+b)
fold: ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
superfamily: ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
family: Histidine kinase
domain: Histidine kinase PhoQ domain
species: Escherichia coli [TaxId: 562]

 Score = 49.8 bits (119), Expect = 1e-07
 Identities = 14/65 (21%), Positives = 32/65 (49%), Gaps = 9/65 (13%)

Query: 446 REV--VKHVLQTAAASLQKI-----LMLEGDIADDVPIEVIGDVLRIRQILTNLISNAIK 498
           RE+  V  +L    ++L K+     + +  DI+ ++    +G+     +++ N++ NA K
Sbjct: 1   RELHPVAPLLDNLTSALNKVYQRKGVNISLDISPEIS--FVGEQNDFVEVMGNVLDNACK 58

Query: 499 FTPEG 503
           +  E 
Sbjct: 59  YCLEF 63

>d1zgza1 c.23.1.1 (A:2-121) TorCAD operon transcriptional regulator TorD, N-terminal domain {Escherichia coli [TaxId: 562]} Length = 120

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: TorCAD operon transcriptional regulator TorD, N-terminal domain
species: Escherichia coli [TaxId: 562]

 Score = 79.7 bits (196), Expect = 2e-18
 Identities = 31/139 (22%), Positives = 56/139 (40%), Gaps = 27/139 (19%)

Query: 861 KILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLK 920
            I++VED  +     +S   Q G+++ V  +G      +Q Q+ DLIL+D+ +P  +GL 
Sbjct: 3   HIVIVEDEPVTQARLQSYFTQEGYTVSVTASGAGLREIMQNQSVDLILLDINLPDENGLM 62

Query: 921 ATRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGM 980
            TR +R                               + II +T  +           G 
Sbjct: 63  LTRALR---------------------------ERSTVGIILVTGRSDRIDRIVGLEMGA 95

Query: 981 DSFVSKPVTFQKLKECLEQ 999
           D +V+KP+  ++L   ++ 
Sbjct: 96  DDYVTKPLELRELVVRVKN 114

>d1xhfa1 c.23.1.1 (A:2-122) Aerobic respiration control protein ArcA, N-terminal domain {Escherichia coli [TaxId: 562]} Length = 121

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: Aerobic respiration control protein ArcA, N-terminal domain
species: Escherichia coli [TaxId: 562]

 Score = 78.5 bits (193), Expect = 7e-18
 Identities = 25/140 (17%), Positives = 50/140 (35%), Gaps = 27/140 (19%)

Query: 860 PKILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGL 919
           P IL+VED  +     KS+ +  G+ +    +G E    +   + +L++MD+ +P  +GL
Sbjct: 3   PHILIVEDELVTRNTLKSIFEAEGYDVFEATDGAEMHQILSEYDINLVIMDINLPGKNGL 62

Query: 920 KATRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANG 979
              R +R                               + ++ +T              G
Sbjct: 63  LLARELR---------------------------EQANVALMFLTGRDNEVDKILGLEIG 95

Query: 980 MDSFVSKPVTFQKLKECLEQ 999
            D +++KP   ++L      
Sbjct: 96  ADDYITKPFNPRELTIRARN 115

>d1yioa2 c.23.1.1 (A:3-130) Response regulatory protein StyR, N-terminal domain {Pseudomonas fluorescens [TaxId: 294]} Length = 128

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: Response regulatory protein StyR, N-terminal domain
species: Pseudomonas fluorescens [TaxId: 294]

 Score = 77.0 bits (189), Expect = 2e-17
 Identities = 23/141 (16%), Positives = 53/141 (37%), Gaps = 26/141 (18%)

Query: 859 KPKILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDG 918
           KP + +V+D+       +++++  G  ++  +     +   + + +  +++D+ MP M G
Sbjct: 2   KPTVFVVDDDMSVREGLRNLLRSAGFEVETFDCASTFLEHRRPEQHGCLVLDMRMPGMSG 61

Query: 919 LKATRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFAN 978
           ++    + +                              IPI+ +TA+            
Sbjct: 62  IELQEQLTA--------------------------ISDGIPIVFITAHGDIPMTVRAMKA 95

Query: 979 GMDSFVSKPVTFQKLKECLEQ 999
           G   F+ KP   Q L + +EQ
Sbjct: 96  GAIEFLPKPFEEQALLDAIEQ 116

>d1krwa_ c.23.1.1 (A:) NTRC receiver domain {Salmonella typhimurium [TaxId: 90371]} Length = 123

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: NTRC receiver domain
species: Salmonella typhimurium [TaxId: 90371]

 Score = 76.7 bits (188), Expect = 3e-17
 Identities = 28/141 (19%), Positives = 56/141 (39%), Gaps = 26/141 (18%)

Query: 859 KPKILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDG 918
           +  + +V+D+     V +  +   G +     NG E + A+  +  D++L D+ MP MDG
Sbjct: 3   RGIVWVVDDDSSIRWVLERALAGAGLTCTTFENGNEVLAALASKTPDVLLSDIRMPGMDG 62

Query: 919 LKATRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFAN 978
           L   + I+                               +P+I MTA++  ++A   +  
Sbjct: 63  LALLKQIK--------------------------QRHPMLPVIIMTAHSDLDAAVSAYQQ 96

Query: 979 GMDSFVSKPVTFQKLKECLEQ 999
           G   ++ KP    +    +E+
Sbjct: 97  GAFDYLPKPFDIDEAVALVER 117

>d1qkka_ c.23.1.1 (A:) Transcriptional regulatory protein DctD, receiver domain {Sinorhizobium meliloti [TaxId: 382]} Length = 140

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: Transcriptional regulatory protein DctD, receiver domain
species: Sinorhizobium meliloti [TaxId: 382]

 Score = 76.2 bits (187), Expect = 7e-17
 Identities = 24/140 (17%), Positives = 53/140 (37%), Gaps = 26/140 (18%)

Query: 860 PKILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGL 919
           P + L++D++      +  ++  G ++    +  EA+  +      +++ D+ MP MDGL
Sbjct: 1   PSVFLIDDDRDLRKAMQQTLELAGFTVSSFASATEALAGLSADFAGIVISDIRMPGMDGL 60

Query: 920 KATRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANG 979
              R I +                              +P+I +T +     A +   +G
Sbjct: 61  ALFRKILA--------------------------LDPDLPMILVTGHGDIPMAVQAIQDG 94

Query: 980 MDSFVSKPVTFQKLKECLEQ 999
              F++KP    +L +   +
Sbjct: 95  AYDFIAKPFAADRLVQSARR 114

>d1s8na_ c.23.1.1 (A:) Probable two-component system transcriptional regulator Rv1626 {Mycobacterium tuberculosis [TaxId: 1773]} Length = 190

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: Probable two-component system transcriptional regulator Rv1626
species: Mycobacterium tuberculosis [TaxId: 1773]

 Score = 76.8 bits (188), Expect = 1e-16
 Identities = 31/135 (22%), Positives = 54/135 (40%), Gaps = 29/135 (21%)

Query: 858 PKPKILLVEDNKINVMVAKSMMKQLGHS-IDVVNNGVEAVHAVQCQNYDLILMDVCMPVM 916
           P+ ++L+ ED  +  M    M+++ G+  +    +G EAV   +    DL++MDV MP  
Sbjct: 3   PR-RVLIAEDEALIRMDLAEMLREEGYEIVGEAGDGQEAVELAELHKPDLVIMDVKMPRR 61

Query: 917 DGLKATRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECF 976
           DG+ A   I S                               PI+ +TA +  +  E   
Sbjct: 62  DGIDAASEIASKRI---------------------------APIVVLTAFSQRDLVERAR 94

Query: 977 ANGMDSFVSKPVTFQ 991
             G  +++ KP +  
Sbjct: 95  DAGAMAYLVKPFSIS 109

>d1ys7a2 c.23.1.1 (A:7-127) Transcriptional regulatory protein PrrA, N-terminal domain {Mycobacterium tuberculosis [TaxId: 1773]} Length = 121

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: Transcriptional regulatory protein PrrA, N-terminal domain
species: Mycobacterium tuberculosis [TaxId: 1773]

 Score = 74.7 bits (183), Expect = 1e-16
 Identities = 24/140 (17%), Positives = 55/140 (39%), Gaps = 26/140 (18%)

Query: 860 PKILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGL 919
           P++L+V+D+   +   +  ++  G  +    +G EA+ +      D I++D+ MPV+DG+
Sbjct: 2   PRVLVVDDDSDVLASLERGLRLSGFEVATAVDGAEALRSATENRPDAIVLDINMPVLDGV 61

Query: 920 KATRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANG 979
                +R+                              +P+  ++A +  +        G
Sbjct: 62  SVVTALRA--------------------------MDNDVPVCVLSARSSVDDRVAGLEAG 95

Query: 980 MDSFVSKPVTFQKLKECLEQ 999
            D ++ KP    +L   ++ 
Sbjct: 96  ADDYLVKPFVLAELVARVKA 115

>d1dbwa_ c.23.1.1 (A:) Transcriptional regulatory protein FixJ, receiver domain {Rhizobium meliloti [TaxId: 382]} Length = 123

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: Transcriptional regulatory protein FixJ, receiver domain
species: Rhizobium meliloti [TaxId: 382]

 Score = 72.8 bits (178), Expect = 7e-16
 Identities = 22/141 (15%), Positives = 46/141 (32%), Gaps = 26/141 (18%)

Query: 859 KPKILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDG 918
              + +V+D +        M+   G ++ +  +    +         +++ D+ MP M G
Sbjct: 3   DYTVHIVDDEEPVRKSLAFMLTMNGFAVKMHQSAEAFLAFAPDVRNGVLVTDLRMPDMSG 62

Query: 919 LKATRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFAN 978
           ++  R +                           +    IP I +T +     A E    
Sbjct: 63  VELLRNLG--------------------------DLKINIPSIVITGHGDVPMAVEAMKA 96

Query: 979 GMDSFVSKPVTFQKLKECLEQ 999
           G   F+ KP     + E +E+
Sbjct: 97  GAVDFIEKPFEDTVIIEAIER 117

>d1zh2a1 c.23.1.1 (A:2-120) Transcriptional regulatory protein KdpE, N-terminal domain {Escherichia coli [TaxId: 562]} Length = 119

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: Transcriptional regulatory protein KdpE, N-terminal domain
species: Escherichia coli [TaxId: 562]

 Score = 72.4 bits (177), Expect = 9e-16
 Identities = 24/139 (17%), Positives = 51/139 (36%), Gaps = 27/139 (19%)

Query: 861 KILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLK 920
            +L+VED +      ++ ++  G  +         +     +  DLI++D+ +P  DG++
Sbjct: 2   NVLIVEDEQAIRRFLRTALEGDGMRVFEAETLQRGLLEAATRKPDLIILDLGLPDGDGIE 61

Query: 921 ATRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGM 980
             R +R                            +  +P+I ++A +           G 
Sbjct: 62  FIRDLR---------------------------QWSAVPVIVLSARSEESDKIAALDAGA 94

Query: 981 DSFVSKPVTFQKLKECLEQ 999
           D ++SKP    +L+  L  
Sbjct: 95  DDYLSKPFGIGELQARLRV 113

>d1mvoa_ c.23.1.1 (A:) PhoP receiver domain {Bacillus subtilis [TaxId: 1423]} Length = 121

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: PhoP receiver domain
species: Bacillus subtilis [TaxId: 1423]

 Score = 71.6 bits (175), Expect = 2e-15
 Identities = 27/141 (19%), Positives = 61/141 (43%), Gaps = 26/141 (18%)

Query: 859 KPKILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDG 918
             KIL+V+D +  V + +  +++ G+ +   ++G EA+   + +  DLI++DV +P +DG
Sbjct: 2   NKKILVVDDEESIVTLLQYNLERSGYDVITASDGEEALKKAETEKPDLIVLDVMLPKLDG 61

Query: 919 LKATRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFAN 978
           ++  + +R                                PI+ +TA             
Sbjct: 62  IEVCKQLR--------------------------QQKLMFPILMLTAKDEEFDKVLGLEL 95

Query: 979 GMDSFVSKPVTFQKLKECLEQ 999
           G D +++KP + +++   ++ 
Sbjct: 96  GADDYMTKPFSPREVNARVKA 116

>d1k66a_ c.23.1.1 (A:) Response regulator for cyanobacterial phytochrome {Calothrix sp. pcc 7601, RcpB [TaxId: 1188]} Length = 149

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: Response regulator for cyanobacterial phytochrome
species: Calothrix sp. pcc 7601, RcpB [TaxId: 1188]

 Score = 71.0 bits (173), Expect = 5e-15
 Identities = 26/152 (17%), Positives = 61/152 (40%), Gaps = 36/152 (23%)

Query: 861  KILLVEDNKINVMVAKSMMKQLG--HSIDVVNNGVEAVHAVQ----------CQNYDLIL 908
             +L+VED+  +    + ++++ G  + I     G +A+  +                +IL
Sbjct: 8    PLLVVEDSDEDFSTFQRLLQREGVVNPIYRCITGDQALDFLYQTGSYCNPDIAPRPAVIL 67

Query: 909  MDVCMPVMDGLKATRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANAL 968
            +D+ +P  DG +  + I+  E                             P++ MT ++ 
Sbjct: 68   LDLNLPGTDGREVLQEIKQDEVLKKI------------------------PVVIMTTSSN 103

Query: 969  SESAEECFANGMDSFVSKPVTFQKLKECLEQY 1000
             +  E C++  + S++ KP+   +L E ++ +
Sbjct: 104  PKDIEICYSYSISSYIVKPLEIDRLTETVQTF 135

>d1ny5a1 c.23.1.1 (A:1-137) Transcriptional activator sigm54 (NtrC1), N-terminal domain {Aquifex aeolicus [TaxId: 63363]} Length = 137

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: Transcriptional activator sigm54 (NtrC1), N-terminal domain
species: Aquifex aeolicus [TaxId: 63363]

 Score = 70.4 bits (172), Expect = 5e-15
 Identities = 22/139 (15%), Positives = 60/139 (43%), Gaps = 26/139 (18%)

Query: 861 KILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLK 920
            +L++ED+K+   + +  +   G  ++    G EA   +  ++++++L+D+ +P ++GL+
Sbjct: 2   NVLVIEDDKVFRGLLEEYLSMKGIKVESAERGKEAYKLLSEKHFNVVLLDLLLPDVNGLE 61

Query: 921 ATRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGM 980
             + I+                                 +I +T +   ++A E    G 
Sbjct: 62  ILKWIKE--------------------------RSPETEVIVITGHGTIKTAVEAMKMGA 95

Query: 981 DSFVSKPVTFQKLKECLEQ 999
             F++KP   ++++  + +
Sbjct: 96  YDFLTKPCMLEEIELTINK 114

>d2pl1a1 c.23.1.1 (A:1-119) PhoP receiver domain {Escherichia coli [TaxId: 562]} Length = 119

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: PhoP receiver domain
species: Escherichia coli [TaxId: 562]

 Score = 69.0 bits (168), Expect = 1e-14
 Identities = 30/139 (21%), Positives = 58/139 (41%), Gaps = 26/139 (18%)

Query: 861 KILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLK 920
           ++L+VEDN +     K  ++  GH +D   +  EA + +     D+ ++D+ +P  DGL 
Sbjct: 2   RVLVVEDNALLRHHLKVQIQDAGHQVDDAEDAKEADYYLNEHIPDIAIVDLGLPDEDGLS 61

Query: 921 ATRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGM 980
             R  RS                          +   +PI+ +TA    +   E  + G 
Sbjct: 62  LIRRWRS--------------------------NDVSLPILVLTARESWQDKVEVLSAGA 95

Query: 981 DSFVSKPVTFQKLKECLEQ 999
           D +V+KP   +++   ++ 
Sbjct: 96  DDYVTKPFHIEEVMARMQA 114

>d1kgsa2 c.23.1.1 (A:2-123) PhoB receiver domain {Thermotoga maritima [TaxId: 2336]} Length = 122

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: PhoB receiver domain
species: Thermotoga maritima [TaxId: 2336]

 Score = 67.4 bits (164), Expect = 5e-14
 Identities = 25/139 (17%), Positives = 58/139 (41%), Gaps = 26/139 (18%)

Query: 861 KILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLK 920
           ++L+VED +    +    +K+   ++DV  +G E ++    + +D++++D+ +PV DG +
Sbjct: 3   RVLVVEDERDLADLITEALKKEMFTVDVCYDGEEGMYMALNEPFDVVILDIMLPVHDGWE 62

Query: 921 ATRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGM 980
             + +R                                P++ +TA +  E   +    G 
Sbjct: 63  ILKSMR--------------------------ESGVNTPVLMLTALSDVEYRVKGLNMGA 96

Query: 981 DSFVSKPVTFQKLKECLEQ 999
           D ++ KP   ++L   +  
Sbjct: 97  DDYLPKPFDLRELIARVRA 115

>d1gkza2 d.122.1.4 (A:186-378) Branched-chain alpha-ketoacid dehydrogenase kinase (BCK) {Rat (Rattus norvegicus) [TaxId: 10116]} Length = 193

class: Alpha and beta proteins (a+b)
fold: ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
superfamily: ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
family: alpha-ketoacid dehydrogenase kinase, C-terminal domain
domain: Branched-chain alpha-ketoacid dehydrogenase kinase (BCK)
species: Rat (Rattus norvegicus) [TaxId: 10116]

 Score = 69.1 bits (168), Expect = 7e-14
 Identities = 15/94 (15%), Positives = 25/94 (26%), Gaps = 20/94 (21%)

Query: 591 WIRCDVYDTGIGIPENALPTLFRKYMQVSADHARKYGG--------------------TG 630
            +   + D G GI    L  +   +   +    +                         G
Sbjct: 93  DLIIRISDRGGGIAHKDLDRVMDYHFTTAEASTQDPRISPLFGHLDMHSGGQSGPMHGFG 152

Query: 631 LGLAICKQLVELMGGRLTVTSKVHCGSTFTFILP 664
            GL   +   E +GG L + S    G+     L 
Sbjct: 153 FGLPTSRAYAEYLGGSLQLQSLQGIGTDVYLRLR 186

>d1p2fa2 c.23.1.1 (A:1-120) Response regulator DrrB {Thermotoga maritima [TaxId: 2336]} Length = 120

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: Response regulator DrrB
species: Thermotoga maritima [TaxId: 2336]

 Score = 65.8 bits (160), Expect = 2e-13
 Identities = 26/141 (18%), Positives = 57/141 (40%), Gaps = 29/141 (20%)

Query: 860  PKILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGL 919
             KI +V+D+K  +      ++QLG  +     G + ++  +   + ++++DV +P   G 
Sbjct: 3    WKIAVVDDDKNILKKVSEKLQQLGR-VKTFLTGEDFLNDEE--AFHVVVLDVMLPDYSGY 59

Query: 920  KATRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANG 979
            +  R+I+                                 +I +T  +  ES  + F  G
Sbjct: 60   EICRMIK--------------------------ETRPETWVILLTLLSDDESVLKGFEAG 93

Query: 980  MDSFVSKPVTFQKLKECLEQY 1000
             D +V+KP   + L   ++++
Sbjct: 94   ADDYVTKPFNPEILLARVKRF 114

>d1w25a1 c.23.1.1 (A:2-140) Response regulator PleD, receiver domain {Caulobacter crescentus [TaxId: 155892]} Length = 139

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: Response regulator PleD, receiver domain
species: Caulobacter crescentus [TaxId: 155892]

 Score = 65.3 bits (158), Expect = 4e-13
 Identities = 28/139 (20%), Positives = 54/139 (38%), Gaps = 24/139 (17%)

Query: 861 KILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLK 920
           +IL+V+D + NV + ++ +    + +    +G  A+        D+IL+DV MP MDG  
Sbjct: 3   RILVVDDIEANVRLLEAKLTAEYYEVSTAMDGPTALAMAARDLPDIILLDVMMPGMDGFT 62

Query: 921 ATRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGM 980
             R ++    T +                         P++ +TA        +   +G 
Sbjct: 63  VCRKLKDDPTTRHI------------------------PVVLITALDGRGDRIQGLESGA 98

Query: 981 DSFVSKPVTFQKLKECLEQ 999
             F++KP+    L   +  
Sbjct: 99  SDFLTKPIDDVMLFARVRS 117

>d1w25a2 c.23.1.1 (A:141-293) Response regulator PleD, receiver domain {Caulobacter crescentus [TaxId: 155892]} Length = 153

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: Response regulator PleD, receiver domain
species: Caulobacter crescentus [TaxId: 155892]

 Score = 65.1 bits (158), Expect = 6e-13
 Identities = 24/139 (17%), Positives = 50/139 (35%), Gaps = 26/139 (18%)

Query: 861 KILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLK 920
           ++L+V+DN+       + +        V+ +  E          DL++++      DGL+
Sbjct: 15  RVLIVDDNERQAQRVAAELGVEHR--PVIESDPEKAKISAGGPVDLVIVNAAAKNFDGLR 72

Query: 921 ATRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGM 980
            T  +RS E T                           P++AM          +    G+
Sbjct: 73  FTAALRSEERTRQL------------------------PVLAMVDPDDRGRMVKALEIGV 108

Query: 981 DSFVSKPVTFQKLKECLEQ 999
           +  +S+P+  Q+L   ++ 
Sbjct: 109 NDILSRPIDPQELSARVKT 127

>d1i58a_ d.122.1.3 (A:) Histidine kinase CheA {Thermotoga maritima [TaxId: 2336]} Length = 189

class: Alpha and beta proteins (a+b)
fold: ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
superfamily: ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
family: Histidine kinase
domain: Histidine kinase CheA
species: Thermotoga maritima [TaxId: 2336]

 Score = 65.9 bits (159), Expect = 8e-13
 Identities = 30/192 (15%), Positives = 55/192 (28%), Gaps = 10/192 (5%)

Query: 474 VPIE-VIGDVLRIRQILTNLISNAIKFTPEGKVGIKLYVVPEPPFAKEGLKQKSKAYQSA 532
           VPI  V     R+ + L   ++  + F   G+      +                     
Sbjct: 5   VPISFVFNRFPRMVRDLAKKMNKEVNFIMRGE---DTELDRTFVEEIGEPLLHLLRNAID 61

Query: 533 TDAVKEEKHQPKSQTASDQNGFHDKKHGEGYQDHKHDDDPGTPVSHGNSMDEDLEATVWI 592
                +E+   K +          +  G        DD  G           +       
Sbjct: 62  HGIEPKEERIAKGKPPIGTLILSARHEGNNVVIEVEDDGRGIDKEKIIRKAIE-----KG 116

Query: 593 RCDVYDTGIGIPENALPTLFRKYMQVSADHARKYGGTGLGLAICKQLVELMGGRLTVTSK 652
             D         +  L  LF        +   +  G G+G+ + K +VE + G +++ S+
Sbjct: 117 LIDESKAATLSDQEILNFLFVPGFST-KEKVSEVSGRGVGMDVVKNVVESLNGSISIESE 175

Query: 653 VHCGSTFTFILP 664
              G+  T  LP
Sbjct: 176 KDKGTKVTIRLP 187

>d1r62a_ d.122.1.3 (A:) Nitrogen regulation protein NtrB, C-terminal domain {Escherichia coli [TaxId: 562]} Length = 156

class: Alpha and beta proteins (a+b)
fold: ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
superfamily: ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
family: Histidine kinase
domain: Nitrogen regulation protein NtrB, C-terminal domain
species: Escherichia coli [TaxId: 562]

 Score = 64.5 bits (156), Expect = 1e-12
 Identities = 26/102 (25%), Positives = 41/102 (40%), Gaps = 7/102 (6%)

Query: 563 YQDHKHDDDPGTPVSHGNSMDEDLEATVWIRCDVYDTGIGIPENALPTLFRKYMQVSADH 622
               +  +      +            +  R DV D G GIP +   TLF   +      
Sbjct: 59  ALGPEGGEIILRTRTAFQLTLHGERYRLAARIDVEDNGPGIPPHLQDTLFYPMVS----- 113

Query: 623 ARKYGGTGLGLAICKQLVELMGGRLTVTSKVHCGSTFTFILP 664
             + GGTGLGL+I + L++   G++  TS     + F+  LP
Sbjct: 114 -GREGGTGLGLSIARNLIDQHSGKIEFTSWPG-HTEFSVYLP 153

>d1r62a_ d.122.1.3 (A:) Nitrogen regulation protein NtrB, C-terminal domain {Escherichia coli [TaxId: 562]} Length = 156

class: Alpha and beta proteins (a+b)
fold: ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
superfamily: ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
family: Histidine kinase
domain: Nitrogen regulation protein NtrB, C-terminal domain
species: Escherichia coli [TaxId: 562]

 Score = 49.4 bits (117), Expect = 2e-07
 Identities = 14/60 (23%), Positives = 27/60 (45%), Gaps = 1/60 (1%)

Query: 446 REVVKHVLQTAAASLQKILMLEGDIADDVPIEVIGDVLRIRQILTNLISNAIKFTPEGKV 505
            +V + V+   +  L   + L  D    +P E+  D  +I Q+L N++ NA++       
Sbjct: 7   HKVAERVVTLVSMELPDNVRLIRDYDPSLP-ELAHDPDQIEQVLLNIVRNALQALGPEGG 65

>d1qo0d_ c.23.1.3 (D:) Positive regulator of the amidase operon AmiR {Pseudomonas aeruginosa [TaxId: 287]} Length = 189

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: Positive regulator of the amidase operon AmiR
domain: Positive regulator of the amidase operon AmiR
species: Pseudomonas aeruginosa [TaxId: 287]

 Score = 58.9 bits (141), Expect = 2e-10
 Identities = 12/142 (8%), Positives = 33/142 (23%), Gaps = 31/142 (21%)

Query: 861  KILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLK 920
            ++L++             + ++G S+       EA         D++   +         
Sbjct: 13   QVLVLNPPGEVSDALVLQLIRIGCSVRQCWPPPEA----FDVPVDVVFTSIFQNRHHDEI 68

Query: 921  ATRLIRSFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGM 980
            A  L                                R  ++A+          +      
Sbjct: 69   AALLAA---------------------------GTPRTTLVALVEYESPAVLSQIIELEC 101

Query: 981  DSFVSKPVTFQKLKECLEQYFP 1002
               +++P+   ++   L     
Sbjct: 102  HGVITQPLDAHRVLPVLVSARR 123

>d2c2aa1 a.30.2.1 (A:232-320) Sensor histidine kinase TM0853 {Thermotoga maritima [TaxId: 2336]} Length = 89

class: All alpha proteins
fold: ROP-like
superfamily: Homodimeric domain of signal transducing histidine kinase
family: Homodimeric domain of signal transducing histidine kinase
domain: Sensor histidine kinase TM0853
species: Thermotoga maritima [TaxId: 2336]

 Score = 50.5 bits (120), Expect = 2e-08
 Identities = 23/83 (27%), Positives = 46/83 (55%), Gaps = 4/83 (4%)

Query: 358 NKTIHITEETMRAK-QMLATMSHEIRSPLTGVVSMAEILSNT---KLDREQRQLLGVMIS 413
           +K +   +   R K + +A +SHE+R+PLT + + AE + N+         ++ L V+I 
Sbjct: 7   SKELERLKRIDRMKTEFIANISHELRTPLTAIKAYAETIYNSLGELDLSTLKEFLEVIID 66

Query: 414 SGDLVLQLINDILDLSKVESGVM 436
             + +  L+N++LD S++E   +
Sbjct: 67  QSNHLENLLNELLDFSRLERKSL 89

>d2hkja3 d.122.1.2 (A:10-228) Topoisomerase VI-B subunit {Archaeon Sulfolobus shibatae [TaxId: 2286]} Length = 219

class: Alpha and beta proteins (a+b)
fold: ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
superfamily: ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
family: DNA gyrase/MutL, N-terminal domain
domain: Topoisomerase VI-B subunit
species: Archaeon Sulfolobus shibatae [TaxId: 2286]

 Score = 52.5 bits (125), Expect = 4e-08
 Identities = 18/97 (18%), Positives = 35/97 (36%), Gaps = 2/97 (2%)

Query: 567 KHDDDPGTPVSHGNSMDEDLEATVWIRCDVYDTGIGIPENALPTLFRKYMQVSADHARKY 626
              D  G   +   ++D   +A    + +V D GIGIP   +P  F + +  S    R+ 
Sbjct: 36  DATDVHGILPNIKITIDLIDDARQIYKVNVVDNGIGIPPQEVPNAFGRVLYSSKYVNRQT 95

Query: 627 G-GTGLGLAICKQLVELMGGR-LTVTSKVHCGSTFTF 661
               GLG+       ++   + + + +          
Sbjct: 96  RGMYGLGVKAAVLYSQMHQDKPIEIETSPVNSKRIYT 132

>d2hkja3 d.122.1.2 (A:10-228) Topoisomerase VI-B subunit {Archaeon Sulfolobus shibatae [TaxId: 2286]} Length = 219

class: Alpha and beta proteins (a+b)
fold: ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
superfamily: ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
family: DNA gyrase/MutL, N-terminal domain
domain: Topoisomerase VI-B subunit
species: Archaeon Sulfolobus shibatae [TaxId: 2286]

 Score = 41.3 bits (96), Expect = 2e-04
 Identities = 5/32 (15%), Positives = 12/32 (37%)

Query: 480 GDVLRIRQILTNLISNAIKFTPEGKVGIKLYV 511
                + Q +  LI N++  T    +   + +
Sbjct: 18  NPARALYQTVRELIENSLDATDVHGILPNIKI 49

>d1joya_ a.30.2.1 (A:) EnvZ histidine kinase {Escherichia coli [TaxId: 562]} Length = 67

class: All alpha proteins
fold: ROP-like
superfamily: Homodimeric domain of signal transducing histidine kinase
family: Homodimeric domain of signal transducing histidine kinase
domain: EnvZ histidine kinase
species: Escherichia coli [TaxId: 562]

 Score = 47.6 bits (113), Expect = 1e-07
 Identities = 11/60 (18%), Positives = 26/60 (43%), Gaps = 5/60 (8%)

Query: 371 KQMLATMSHEIRSPLTGVVSMAEILSNTKLDREQRQLLGVMISSGDLVLQLINDILDLSK 430
             ++A +SH++R+PLT +    E++       +   L   +    +    +I   +D  +
Sbjct: 13  TLLMAGVSHDLRTPLTRIRLATEMM-----SEQDGYLAESINKDIEECNAIIEQFIDYLR 67

>d1th8a_ d.122.1.3 (A:) Anti-sigma factor spoIIab {Bacillus stearothermophilus [TaxId: 1422]} Length = 139

class: Alpha and beta proteins (a+b)
fold: ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
superfamily: ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
family: Histidine kinase
domain: Anti-sigma factor spoIIab
species: Bacillus stearothermophilus [TaxId: 1422]

 Score = 41.3 bits (96), Expect = 9e-05
 Identities = 20/97 (20%), Positives = 38/97 (39%), Gaps = 15/97 (15%)

Query: 565 DHKHDDDPGTPVSHGNSMDEDLEATVWIRCDVYDTGIGIPENALPTLFRKYMQVSADHAR 624
            H +++DP   VS    +++       +   V D G+GIP+        +  Q       
Sbjct: 53  IHGYNNDPNGIVSISVIIEDG-----VVHLTVRDEGVGIPD------IEEARQPLFTTKP 101

Query: 625 KYGGTGLGLAICKQLVELMGGRLTVTSKVHCGSTFTF 661
           +   +G+G  I +         + V S+V+ G+T   
Sbjct: 102 ELERSGMGFTIMENF----MDEVIVESEVNKGTTVYL 134

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	1002
d2c2aa2	161	Sensor histidine kinase TM0853 {Thermotoga maritim	100.0
d1ysra1	148	Sensor-type histidine kinase PrrB {Mycobacterium t	99.96
d1bxda_	161	Histidine kinase domain of the osmosensor EnvZ {Es	99.96
d1id0a_	146	Histidine kinase PhoQ domain {Escherichia coli [Ta	99.96
d1r62a_	156	Nitrogen regulation protein NtrB, C-terminal domai	99.95
d1gkza2	193	Branched-chain alpha-ketoacid dehydrogenase kinase	99.94
d1jm6a2	190	Pyruvate dehydrogenase kinase {Rat (Rattus norvegi	99.94
d1peya_	119	Sporulation response regulator Spo0F {Bacillus sub	99.92
d2r25b1	128	Response regulator Sin1 {Baker's yeast (Saccharomy	99.92
d1ys7a2	121	Transcriptional regulatory protein PrrA, N-termina	99.92
d2pl1a1	119	PhoP receiver domain {Escherichia coli [TaxId: 562	99.92
d1dcfa_	134	Receiver domain of the ethylene receptor {Thale cr	99.91
d1zesa1	121	PhoB receiver domain {Escherichia coli [TaxId: 562	99.91
d2a9pa1	117	DNA-binding response regulator MicA, N-terminal do	99.91
d1mb3a_	123	Cell division response regulator DivK {Caulobacter	99.91
d1dbwa_	123	Transcriptional regulatory protein FixJ, receiver	99.91
d1mvoa_	121	PhoP receiver domain {Bacillus subtilis [TaxId: 14	99.91
d1xhfa1	121	Aerobic respiration control protein ArcA, N-termin	99.9
d1p6qa_	129	CheY protein {Sinorhizobium meliloti, CheY2 [TaxId	99.9
d1zh2a1	119	Transcriptional regulatory protein KdpE, N-termina	99.9
d2ayxa1	133	Sensor kinase protein RcsC, C-terminal domain {Esc	99.9
d1kgsa2	122	PhoB receiver domain {Thermotoga maritima [TaxId:	99.9
d1krwa_	123	NTRC receiver domain {Salmonella typhimurium [TaxI	99.9
d1qkka_	140	Transcriptional regulatory protein DctD, receiver	99.9
d1jbea_	128	CheY protein {Escherichia coli [TaxId: 562]}	99.9
d1u0sy_	118	CheY protein {Thermotoga maritima [TaxId: 2336]}	99.9
d1w25a1	139	Response regulator PleD, receiver domain {Caulobac	99.9
d1ny5a1	137	Transcriptional activator sigm54 (NtrC1), N-termin	99.89
d1zgza1	120	TorCAD operon transcriptional regulator TorD, N-te	99.89
d1k66a_	149	Response regulator for cyanobacterial phytochrome	99.89
d1yioa2	128	Response regulatory protein StyR, N-terminal domai	99.89
d1k68a_	140	Response regulator for cyanobacterial phytochrome	99.89
d1i3ca_	144	Response regulator for cyanobacterial phytochrome	99.88
d1s8na_	190	Probable two-component system transcriptional regu	99.88
d1dz3a_	123	Sporulation response regulator Spo0A {Bacillus ste	99.88
d1w25a2	153	Response regulator PleD, receiver domain {Caulobac	99.87
d1p2fa2	120	Response regulator DrrB {Thermotoga maritima [TaxI	99.87
d1a04a2	138	Nitrate/nitrite response regulator (NarL), receive	99.86
d2b4aa1	118	Hypothetical protein BH3024 {Bacillus halodurans [	99.85
d1a2oa1	140	Methylesterase CheB, N-terminal domain {Salmonella	99.81
d1qo0d_	189	Positive regulator of the amidase operon AmiR {Pse	99.77
d1ixma_	179	Sporulation response regulatory protein Spo0B {Bac	99.7
d2hkja3	219	Topoisomerase VI-B subunit {Archaeon Sulfolobus sh	99.65
d1i58a_	189	Histidine kinase CheA {Thermotoga maritima [TaxId:	99.43
d1th8a_	139	Anti-sigma factor spoIIab {Bacillus stearothermoph	99.41
d2c2aa1	89	Sensor histidine kinase TM0853 {Thermotoga maritim	99.41
d1y8oa2	125	Pyruvate dehydrogenase kinase {Human (Homo sapiens	99.22
d1joya_	67	EnvZ histidine kinase {Escherichia coli [TaxId: 56	99.04
d1ew0a_	130	Histidine kinase FixL heme domain {Rhizobium melil	98.74
d1n9la_	109	Putative blue light receptor, phot-lov1 domain {Gr	98.5
d1p97a_	114	Hypoxia-inducible factor Hif2a, C-terminal domain	98.34
d1jnua_	104	Photoreceptor phy3 flavin-binding domain, lov2 {Ma	98.33
d1bywa_	110	Erg potassium channel, N-terminal domain {Human (H	98.28
d1v9ya_	113	Direct oxygen sensor protein, DOS {Escherichia col	97.88
d1xj3a1	106	Histidine kinase FixL heme domain {Bradyrhizobium	97.57
d1nwza_	125	Photoactive yellow protein, PYP {Ectothiorhodospir	97.49
d1mzua_	110	PYP domain of sensor histidine kinase Ppr {Rhodosp	97.38
d1h7sa2	203	DNA mismatch repair protein PMS2 {Human (Homo sapi	96.4
d1oj5a_	109	PAS domain of steroid receptor coactivator 1A, NCo	95.47
d1b63a2	218	DNA mismatch repair protein MutL {Escherichia coli	95.36
d1ll8a_	114	N-terminal PAS domain of Pas kinase {Human (Homo s	95.07
d1ccwa_	137	Glutamate mutase, small subunit {Clostridium cochl	92.98
d1pvga2	239	DNA topoisomerase II {Baker's yeast (Saccharomyces	86.52
d1ei1a2	219	DNA gyrase B {Escherichia coli [TaxId: 562]}	85.24
d7reqa2	168	Methylmalonyl-CoA mutase alpha subunit, C-terminal	84.52
d2iwxa1	213	HSP90 {Baker's yeast (Saccharomyces cerevisiae) [T	83.39
d1kija2	212	DNA gyrase B {Thermus thermophilus [TaxId: 274]}	80.22

>d2c2aa2 d.122.1.3 (A:321-481) Sensor histidine kinase TM0853 {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a+b)
fold: ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
superfamily: ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
family: Histidine kinase
domain: Sensor histidine kinase TM0853
species: Thermotoga maritima [TaxId: 2336]

Probab=100.00  E-value=8.6e-33  Score=276.36  Aligned_cols=155  Identities=30%  Similarity=0.434  Sum_probs=124.1

Q ss_pred             eEeeecCHHHHHHHHHHHHHHHHh-hcceeccccCCCCCeeEEccHHHHHHHHHHHHhhhhhcCCCCee--EEEEEecCC
Q 039716          438 LEAAKFRPREVVKHVLQTAAASLQ-KILMLEGDIADDVPIEVIGDVLRIRQILTNLISNAIKFTPEGKV--GIKLYVVPE  514 (1002)
Q Consensus       438 l~~~~~~l~~li~~v~~~~~~~~~-k~i~l~~~i~~~~p~~v~gD~~rL~QIL~NLlsNAIKfT~~G~I--~I~v~~~~~  514 (1002)
                      ++.++|++.+++++++..+...+. +.+.+........+..+.+|+.+|+|||.|||+||+|||++|.+  .|.+.+.. 
T Consensus         2 l~~e~v~l~~li~~~~~~~~~~~~~~~i~~~~~~~~~~~~~v~~D~~~l~qvl~NLi~NAik~t~~~~~~~~i~i~~~~-   80 (161)
T d2c2aa2           2 INREKVDLCDLVESAVNAIKEFASSHNVNVLFESNVPCPVEAYIDPTRIRQVLLNLLNNGVKYSKKDAPDKYVKVILDE-   80 (161)
T ss_dssp             CCCEEEEHHHHHHHHHHHHHHHHHHTTCEEEEEESSCSCCEEEECHHHHHHHHHHHHHHHHHTCCTTCTTCEEEEEEEE-
T ss_pred             CccEEECHHHHHHHHHHHHHHHHHHCCCEEEEEeCCCCCEEEEECHHHHHHHHHHHHHHHHHhhhcCCCcceeeEEEEe-
Confidence            456789999999999998887664 56777766665666789999999999999999999999988642  33332210 


Q ss_pred             CCcccchhhhhhhhhhcchhhhhhhccCCCCCccCCCCCCCCCCCCCCccCCCCCCCCCCCccCCCCCccccccceEEEE
Q 039716          515 PPFAKEGLKQKSKAYQSATDAVKEEKHQPKSQTASDQNGFHDKKHGEGYQDHKHDDDPGTPVSHGNSMDEDLEATVWIRC  594 (1002)
Q Consensus       515 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~i  594 (1002)
                                                                                               ...++.|
T Consensus        81 -------------------------------------------------------------------------~~~~~~i   87 (161)
T d2c2aa2          81 -------------------------------------------------------------------------KDGGVLI   87 (161)
T ss_dssp             -------------------------------------------------------------------------ETTEEEE
T ss_pred             -------------------------------------------------------------------------cCCEEEE
Confidence                                                                                     1125889


Q ss_pred             EEEecCCCCCcCcHhhhhhhccCCCccccCcCCCccccHHHHHHHHHHhCCEEEEEeecCCceEEEEEEeCC
Q 039716          595 DVYDTGIGIPENALPTLFRKYMQVSADHARKYGGTGLGLAICKQLVELMGGRLTVTSKVHCGSTFTFILPYQ  666 (1002)
Q Consensus       595 ~V~DtGiGI~~e~l~~IF~pF~q~~~~~~~~~~GtGLGLaI~k~Lve~~gG~I~v~S~~g~GTtF~~~LP~~  666 (1002)
                      +|.|+|+|||++.+++||+||||.+...+++.+|+||||+|||+||+.|||+|+|+|.+|+||+|+|+||..
T Consensus        88 ~V~D~G~GI~~~~~~~iF~~F~~~~~~~~~~~~G~GLGL~i~k~iv~~hgG~i~v~s~~~~Gt~f~i~lP~~  159 (161)
T d2c2aa2          88 IVEDNGIGIPDHAKDRIFEQFYRVDSSLTYEVPGTGLGLAITKEIVELHGGRIWVESEVGKGSRFFVWIPKD  159 (161)
T ss_dssp             EEEECSSCCCGGGTTGGGSTTCCCC---------CCCTHHHHHHHHHHTTCEEEEEEETTTEEEEEEEEECC
T ss_pred             EEEEcCCCCCHHHHHHhhCCcEEcCCCCCCCCCcccHHHHHHHHHHHHCCCEEEEEecCCCeeEEEEEEEcc
Confidence            999999999999999999999999877777788999999999999999999999999999999999999974

>d1ysra1 d.122.1.3 (A:299-446) Sensor-type histidine kinase PrrB {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a+b)
fold: ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
superfamily: ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
family: Histidine kinase
domain: Sensor-type histidine kinase PrrB
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=99.96  E-value=5.2e-30  Score=252.18  Aligned_cols=144  Identities=22%  Similarity=0.290  Sum_probs=112.7

Q ss_pred             eeecCHHHHHHHHHHHHHHHHhhcceeccccCCCCCeeEEccHHHHHHHHHHHHhhhhhcCCCCeeEEEEEecCCCCccc
Q 039716          440 AAKFRPREVVKHVLQTAAASLQKILMLEGDIADDVPIEVIGDVLRIRQILTNLISNAIKFTPEGKVGIKLYVVPEPPFAK  519 (1002)
Q Consensus       440 ~~~~~l~~li~~v~~~~~~~~~k~i~l~~~i~~~~p~~v~gD~~rL~QIL~NLlsNAIKfT~~G~I~I~v~~~~~~~~~~  519 (1002)
                      ..++|+.+++++++..+..... ...+....  ..+..|.+|+.+|+|||.|||+||+||++.|.|.|++...       
T Consensus         3 ~~pvdl~~l~~~~~~~~~~~~~-~~~i~~~~--~~~~~v~~d~~~l~~vl~NLl~NAiky~~~~~I~i~~~~~-------   72 (148)
T d1ysra1           3 HVPVDITDLLDRAAHDAARIYP-DLDVSLVP--SPTCIIVGLPAGLRLAVDNAIANAVKHGGATLVQLSAVSS-------   72 (148)
T ss_dssp             CEEEEHHHHHHHHHHHHHHHST-TCEEEECS--CCCCEEEECHHHHHHHHHHHHHHHHHTTCCSEEEEEEEEE-------
T ss_pred             CCcccHHHHHHHHHHHHHHHcC-CCcEEEec--CCCcEEEECHHHHHHHHHHHHHHHHHhcCCcEEEEEEEec-------
Confidence            4679999999999987765443 23333333  2345799999999999999999999999888877766421       


Q ss_pred             chhhhhhhhhhcchhhhhhhccCCCCCccCCCCCCCCCCCCCCccCCCCCCCCCCCccCCCCCccccccceEEEEEEEec
Q 039716          520 EGLKQKSKAYQSATDAVKEEKHQPKSQTASDQNGFHDKKHGEGYQDHKHDDDPGTPVSHGNSMDEDLEATVWIRCDVYDT  599 (1002)
Q Consensus       520 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~i~V~Dt  599 (1002)
                                                                                           ..++.|+|.|+
T Consensus        73 ---------------------------------------------------------------------~~~~~i~V~D~   83 (148)
T d1ysra1          73 ---------------------------------------------------------------------RAGVEIAIDDN   83 (148)
T ss_dssp             ---------------------------------------------------------------------TTEEEEEEEES
T ss_pred             ---------------------------------------------------------------------CCEEEEEEEEc
Confidence                                                                                 11588999999


Q ss_pred             CCCCCcCcHhhhhhhccCCCccccCcCCCccccHHHHHHHHHHhCCEEEEEeecCCceEEEEEEeC
Q 039716          600 GIGIPENALPTLFRKYMQVSADHARKYGGTGLGLAICKQLVELMGGRLTVTSKVHCGSTFTFILPY  665 (1002)
Q Consensus       600 GiGI~~e~l~~IF~pF~q~~~~~~~~~~GtGLGLaI~k~Lve~~gG~I~v~S~~g~GTtF~~~LP~  665 (1002)
                      |+|||++.+++||+|||+.+.   .+.+|+||||+|||+|++.|||+|+++|.+++||+|+|+||+
T Consensus        84 G~Gi~~~~~~~ife~f~r~~~---~~~~G~GLGL~i~~~iv~~hgG~i~~~s~~~~Gt~f~i~lP~  146 (148)
T d1ysra1          84 GSGVPEGERQVVFERFSRGST---ASHSGSGLGLALVAQQAQLHGGTASLENSPLGGARLVLRLPG  146 (148)
T ss_dssp             SSCCCGGGHHHHHTSCC--------------CCCHHHHHHHHHTTCEEEEEECTTSSEEEEEEEEC
T ss_pred             CCCCCHHHHHHhcCccccCCC---CCCCCccHHHHHHHHHHHHcCCEEEEEEcCCCeEEEEEEEEc
Confidence            999999999999999998643   245799999999999999999999999999999999999996

>d1bxda_ d.122.1.3 (A:) Histidine kinase domain of the osmosensor EnvZ {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a+b)
fold: ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
superfamily: ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
family: Histidine kinase
domain: Histidine kinase domain of the osmosensor EnvZ
species: Escherichia coli [TaxId: 562]

Probab=99.96  E-value=4.6e-29  Score=248.80  Aligned_cols=150  Identities=23%  Similarity=0.344  Sum_probs=120.8

Q ss_pred             eeEeeecCHHHHHHHHHHHHHHHHhhcceeccccCCCCCeeEEccHHHHHHHHHHHHhhhhhcCCCCeeEEEEEecCCCC
Q 039716          437 KLEAAKFRPREVVKHVLQTAAASLQKILMLEGDIADDVPIEVIGDVLRIRQILTNLISNAIKFTPEGKVGIKLYVVPEPP  516 (1002)
Q Consensus       437 ~l~~~~~~l~~li~~v~~~~~~~~~k~i~l~~~i~~~~p~~v~gD~~rL~QIL~NLlsNAIKfT~~G~I~I~v~~~~~~~  516 (1002)
                      ++..+.+|+.+++++++..+.. ..+.+.  ..+.+. +..+.+|+.+|+|||.|||+||+||+ .|.|.|.+...    
T Consensus         4 el~~e~~dl~~ll~e~i~~~~~-~~~~i~--~~~~~~-~~~v~~d~~~l~~vl~NLi~NAik~~-~~~i~i~~~~~----   74 (161)
T d1bxda_           4 EMPMEMADLNAVLGEVIAAESG-YEREIE--TALYPG-SIEVKMHPLSIKRAVANMVVNAARYG-NGWIKVSSGTE----   74 (161)
T ss_dssp             CCCSEEECHHHHHHHHHHHHCS-SSCCEE--EECCSS-CCCEEECHHHHHHHHHHHHHHHHTTC-CSCEEEEEEEE----
T ss_pred             CCCcccCcHHHHHHHHHHHhhc-ccCcEE--EEecCC-CeEEEECHHHHHHHHHHHHHHHHHhC-CCeEEEEEEEe----
Confidence            4556789999999998765432 123333  333333 34689999999999999999999998 56777766431    


Q ss_pred             cccchhhhhhhhhhcchhhhhhhccCCCCCccCCCCCCCCCCCCCCccCCCCCCCCCCCccCCCCCccccccceEEEEEE
Q 039716          517 FAKEGLKQKSKAYQSATDAVKEEKHQPKSQTASDQNGFHDKKHGEGYQDHKHDDDPGTPVSHGNSMDEDLEATVWIRCDV  596 (1002)
Q Consensus       517 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~i~V  596 (1002)
                                                                                              ..++.|+|
T Consensus        75 ------------------------------------------------------------------------~~~~~i~V   82 (161)
T d1bxda_          75 ------------------------------------------------------------------------PNRAWFQV   82 (161)
T ss_dssp             ------------------------------------------------------------------------TTEEEEEE
T ss_pred             ------------------------------------------------------------------------CCEEEEEE
Confidence                                                                                    11478999


Q ss_pred             EecCCCCCcCcHhhhhhhccCCCccccCcCCCccccHHHHHHHHHHhCCEEEEEeecCCceEEEEEEeCCCCC
Q 039716          597 YDTGIGIPENALPTLFRKYMQVSADHARKYGGTGLGLAICKQLVELMGGRLTVTSKVHCGSTFTFILPYQVSP  669 (1002)
Q Consensus       597 ~DtGiGI~~e~l~~IF~pF~q~~~~~~~~~~GtGLGLaI~k~Lve~~gG~I~v~S~~g~GTtF~~~LP~~~~~  669 (1002)
                      .|+|+|||++.+++||+|||+.+..  +..+|+||||+|||+||+.|||+|+++|.+++||+|+|+||+....
T Consensus        83 ~D~G~GI~~e~~~~iF~~F~r~~~~--~~~~g~GLGL~ivk~iv~~hgG~i~v~s~~~~Gt~f~v~lPl~~~~  153 (161)
T d1bxda_          83 EDDGPGIAPEQRKHLFQPFVRGDSA--RTISGTGLGLAIVQRIVDNHNGMLELGTSERGGLSIRAWLPVPVTR  153 (161)
T ss_dssp             EEESSCSCTTGGGCSSCCCCCCSCC--CCCCCCSCCCCTTHHHHHHHTSEEEEEEETTTEEEEEEEECCCSCC
T ss_pred             EEcCCCCCHHHHHHHhCCceECCCC--CcCCCCCchHHHHHHHHHHCCCEEEEEEcCCCcEEEEEEEEeeccc
Confidence            9999999999999999999998643  4567999999999999999999999999999999999999986543

>d1id0a_ d.122.1.3 (A:) Histidine kinase PhoQ domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a+b)
fold: ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
superfamily: ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
family: Histidine kinase
domain: Histidine kinase PhoQ domain
species: Escherichia coli [TaxId: 562]

Probab=99.96  E-value=8.9e-29  Score=242.63  Aligned_cols=141  Identities=22%  Similarity=0.318  Sum_probs=119.2

Q ss_pred             cCHHHHHHHHHHHHHHHHh-hcceeccccCCCCCeeEEccHHHHHHHHHHHHhhhhhcCCCCeeEEEEEecCCCCcccch
Q 039716          443 FRPREVVKHVLQTAAASLQ-KILMLEGDIADDVPIEVIGDVLRIRQILTNLISNAIKFTPEGKVGIKLYVVPEPPFAKEG  521 (1002)
Q Consensus       443 ~~l~~li~~v~~~~~~~~~-k~i~l~~~i~~~~p~~v~gD~~rL~QIL~NLlsNAIKfT~~G~I~I~v~~~~~~~~~~~~  521 (1002)
                      +++.+++++++..+...+. +.+.+..++++.  ..+.+|+.+|.|||.|||+||+|||+++ |.|.+....        
T Consensus         4 ~~l~~ll~~~~~~~~~~~~~k~i~i~~~~~~~--~~~~~d~~~l~~vl~NLl~NAik~~~~~-i~i~~~~~~--------   72 (146)
T d1id0a_           4 HPVAPLLDNLTSALNKVYQRKGVNISLDISPE--ISFVGEQNDFVEVMGNVLDNACKYCLEF-VEISARQTD--------   72 (146)
T ss_dssp             EEHHHHHHHHHHHHHHHTTTTTCEEEEECCTT--CEEESCHHHHHHHHHHHHHHHHHHCSSE-EEEEEEECS--------
T ss_pred             cCHHHHHHHHHHHHHHHHHHCCCEEEEEcCCC--cEEEECHHHHHHHHHHHHHHHHHhhcCC-EEEEEEeeC--------
Confidence            4578899999988877664 667777776654  3589999999999999999999999864 666654211        


Q ss_pred             hhhhhhhhhcchhhhhhhccCCCCCccCCCCCCCCCCCCCCccCCCCCCCCCCCccCCCCCccccccceEEEEEEEecCC
Q 039716          522 LKQKSKAYQSATDAVKEEKHQPKSQTASDQNGFHDKKHGEGYQDHKHDDDPGTPVSHGNSMDEDLEATVWIRCDVYDTGI  601 (1002)
Q Consensus       522 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~i~V~DtGi  601 (1002)
                                                                                          .++.|+|.|+|+
T Consensus        73 --------------------------------------------------------------------~~~~i~V~D~G~   84 (146)
T d1id0a_          73 --------------------------------------------------------------------EHLYIVVEDDGP   84 (146)
T ss_dssp             --------------------------------------------------------------------SCEEEEEEESSS
T ss_pred             --------------------------------------------------------------------CEEEEEEEeeCC
Confidence                                                                                137899999999


Q ss_pred             CCCcCcHhhhhhhccCCCccccCcCCCccccHHHHHHHHHHhCCEEEEEeecCCceEEEEEEeCC
Q 039716          602 GIPENALPTLFRKYMQVSADHARKYGGTGLGLAICKQLVELMGGRLTVTSKVHCGSTFTFILPYQ  666 (1002)
Q Consensus       602 GI~~e~l~~IF~pF~q~~~~~~~~~~GtGLGLaI~k~Lve~~gG~I~v~S~~g~GTtF~~~LP~~  666 (1002)
                      |||++.+++||+|||+.+..    .+|+||||+|||+||+.|||+|+++|.+++||+|++.||.+
T Consensus        85 Gi~~~~~~~iF~~F~r~~~~----~~G~GLGL~I~k~iv~~h~G~i~~~s~~~~Gt~f~i~lP~~  145 (146)
T d1id0a_          85 GIPLSKREVIFDRGQRVDTL----RPGQGVGLAVAREITEQYEGKIVAGESMLGGARMEVIFGRQ  145 (146)
T ss_dssp             CCCGGGTTGGGSCCCCTTCC----CTTCCSCHHHHHHHHHHTTCEEEEEECTTSSEEEEEEECCC
T ss_pred             CCCHHHHHHHcCCcccCCCC----CCCeeHHHHHHHHHHHHcCCEEEEEEcCCCeeEEEEEEeCC
Confidence            99999999999999997643    25999999999999999999999999999999999999964

>d1r62a_ d.122.1.3 (A:) Nitrogen regulation protein NtrB, C-terminal domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a+b)
fold: ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
superfamily: ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
family: Histidine kinase
domain: Nitrogen regulation protein NtrB, C-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=99.95  E-value=2.8e-28  Score=242.17  Aligned_cols=153  Identities=27%  Similarity=0.350  Sum_probs=104.5

Q ss_pred             ecCHHHHHHHHHHHHHHHHhhcceeccccCCCCCeeEEccHHHHHHHHHHHHhhhhhcCCCCeeEEEEEecCCCCcccch
Q 039716          442 KFRPREVVKHVLQTAAASLQKILMLEGDIADDVPIEVIGDVLRIRQILTNLISNAIKFTPEGKVGIKLYVVPEPPFAKEG  521 (1002)
Q Consensus       442 ~~~l~~li~~v~~~~~~~~~k~i~l~~~i~~~~p~~v~gD~~rL~QIL~NLlsNAIKfT~~G~I~I~v~~~~~~~~~~~~  521 (1002)
                      ..++++++++++..+...+++++.+..+++++.| .+.+|+.+|+|||.||+.||+||+..+...+.+........    
T Consensus         3 ~~~i~evie~v~~l~~~~~~~~i~i~~~~~~~~~-~v~~D~~~l~qvl~NLl~NA~~~~~~~~~~~~~~~~~~~~~----   77 (156)
T d1r62a_           3 TESIHKVAERVVTLVSMELPDNVRLIRDYDPSLP-ELAHDPDQIEQVLLNIVRNALQALGPEGGEIILRTRTAFQL----   77 (156)
T ss_dssp             EECHHHHHHHHHHHHTTTCCTTEEEEEECCTTCC-CEEECHHHHHHHHHHHHHHHHHHHGGGCEEEEEEEEEEEEE----
T ss_pred             cccHHHHHHHHHHHHHHHccCCCEEEEEcCCCCC-EEEECHHHHHHHHHHHHHHHHHhhhcCCCceeeecccccee----
Confidence            5689999999998887767778888888887777 58999999999999999999999976543332211100000    


Q ss_pred             hhhhhhhhhcchhhhhhhccCCCCCccCCCCCCCCCCCCCCccCCCCCCCCCCCccCCCCCccccccceEEEEEEEecCC
Q 039716          522 LKQKSKAYQSATDAVKEEKHQPKSQTASDQNGFHDKKHGEGYQDHKHDDDPGTPVSHGNSMDEDLEATVWIRCDVYDTGI  601 (1002)
Q Consensus       522 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~i~V~DtGi  601 (1002)
                                                                                  .........++.|.|.|||+
T Consensus        78 ------------------------------------------------------------~~~~~~~~~~~~i~v~D~G~   97 (156)
T d1r62a_          78 ------------------------------------------------------------TLHGERYRLAARIDVEDNGP   97 (156)
T ss_dssp             ------------------------------------------------------------EETTEEEEEEEEEEEEEECT
T ss_pred             ------------------------------------------------------------eeccccCCceEEEEEecCCC
Confidence                                                                        00001123468999999999


Q ss_pred             CCCcCcHhhhhhhccCCCccccCcCCCccccHHHHHHHHHHhCCEEEEEeecCCceEEEEEEeCC
Q 039716          602 GIPENALPTLFRKYMQVSADHARKYGGTGLGLAICKQLVELMGGRLTVTSKVHCGSTFTFILPYQ  666 (1002)
Q Consensus       602 GI~~e~l~~IF~pF~q~~~~~~~~~~GtGLGLaI~k~Lve~~gG~I~v~S~~g~GTtF~~~LP~~  666 (1002)
                      ||+++.++++|+|||+.      +.+|+||||+|||+||+.|||+|+++|.+| ||+|+|+||++
T Consensus        98 Gi~~~~~~~iF~pf~s~------k~~G~GLGL~i~~~iv~~hgG~i~v~s~~g-Gt~f~i~LPl~  155 (156)
T d1r62a_          98 GIPPHLQDTLFYPMVSG------REGGTGLGLSIARNLIDQHSGKIEFTSWPG-HTEFSVYLPIR  155 (156)
T ss_dssp             TC--------------------------CHHHHHHHHHHHHTTCEEEEEEETT-EEEEEEEEEEE
T ss_pred             CCCHHHHHhhcccceec------CCCCCCchHHHHHHHHHHCCCEEEEEEeCC-cEEEEEEEEec
Confidence            99999999999999964      346999999999999999999999999997 99999999974

>d1gkza2 d.122.1.4 (A:186-378) Branched-chain alpha-ketoacid dehydrogenase kinase (BCK) {Rat (Rattus norvegicus) [TaxId: 10116]}

class: Alpha and beta proteins (a+b)
fold: ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
superfamily: ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
family: alpha-ketoacid dehydrogenase kinase, C-terminal domain
domain: Branched-chain alpha-ketoacid dehydrogenase kinase (BCK)
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=99.94  E-value=2.1e-27  Score=244.34  Aligned_cols=148  Identities=20%  Similarity=0.259  Sum_probs=113.8

Q ss_pred             eecCHHHHHHHHHHHHHHHHhh----cceeccccCCCCCeeEEccHHHHHHHHHHHHhhhhhcCCCCe---------eEE
Q 039716          441 AKFRPREVVKHVLQTAAASLQK----ILMLEGDIADDVPIEVIGDVLRIRQILTNLISNAIKFTPEGK---------VGI  507 (1002)
Q Consensus       441 ~~~~l~~li~~v~~~~~~~~~k----~i~l~~~i~~~~p~~v~gD~~rL~QIL~NLlsNAIKfT~~G~---------I~I  507 (1002)
                      ..+++.++++++++.+...+..    ...+....  +.+..+.+|+.+|+|||.|||.||+|||+++.         |.|
T Consensus         8 t~~~l~~lv~~~~~~~~~~~~~~~~~~~~v~i~~--~~~~~~~~d~~~l~qvl~NLl~NAi~~t~~~~~~~~~~~~~I~i   85 (193)
T d1gkza2           8 TRLSPKKIIEKWVDFARRLCEHKYGNAPRVRING--HVAARFPFIPMPLDYILPELLKNAMRATMESHLDTPYNVPDVVI   85 (193)
T ss_dssp             EEECHHHHHHHHHHHHHHHHHHHHSCCCCEEEEE--STTCCEEECCHHHHHHHHHHHHHHHHHHHHTCTTCTTSCCCEEE
T ss_pred             CCCCHHHHHHHHHHHHHHHHHHhcCCCcEEEecc--CCCceeeecHHHHHHHHHHHHHHHHHhcccCceeeccccceEEE
Confidence            4678999999998876654321    22333333  33456889999999999999999999986432         333


Q ss_pred             EEEecCCCCcccchhhhhhhhhhcchhhhhhhccCCCCCccCCCCCCCCCCCCCCccCCCCCCCCCCCccCCCCCccccc
Q 039716          508 KLYVVPEPPFAKEGLKQKSKAYQSATDAVKEEKHQPKSQTASDQNGFHDKKHGEGYQDHKHDDDPGTPVSHGNSMDEDLE  587 (1002)
Q Consensus       508 ~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  587 (1002)
                      .+.                                                                            .
T Consensus        86 ~~~----------------------------------------------------------------------------~   89 (193)
T d1gkza2          86 TIA----------------------------------------------------------------------------N   89 (193)
T ss_dssp             EEE----------------------------------------------------------------------------E
T ss_pred             EEE----------------------------------------------------------------------------c
Confidence            321                                                                            1


Q ss_pred             cceEEEEEEEecCCCCCcCcHhhhhhhccCCCccccC--------------------cCCCccccHHHHHHHHHHhCCEE
Q 039716          588 ATVWIRCDVYDTGIGIPENALPTLFRKYMQVSADHAR--------------------KYGGTGLGLAICKQLVELMGGRL  647 (1002)
Q Consensus       588 ~~~~l~i~V~DtGiGI~~e~l~~IF~pF~q~~~~~~~--------------------~~~GtGLGLaI~k~Lve~~gG~I  647 (1002)
                      ...++.|+|.|+|+|||++.+++||+|||+++....+                    ...|+||||+|||++|+.|||.|
T Consensus        90 ~~~~v~i~V~D~G~GI~~e~~~~iF~~f~tt~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~GlGL~i~k~ive~~gG~i  169 (193)
T d1gkza2          90 NDVDLIIRISDRGGGIAHKDLDRVMDYHFTTAEASTQDPRISPLFGHLDMHSGGQSGPMHGFGFGLPTSRAYAEYLGGSL  169 (193)
T ss_dssp             CSSEEEEEEECCSCCCCTTTTTTTTSTTCCCC-------------------------CCSCSSCHHHHHHHHHHHTTCEE
T ss_pred             cCCEEEEEEecCCCCCCHHHHHHhcCCceecccccccccccccccccccccccccccccccCCcCHHHHHHHHHHCCCEE
Confidence            1236889999999999999999999999998654322                    23499999999999999999999


Q ss_pred             EEEeecCCceEEEEEEeCC
Q 039716          648 TVTSKVHCGSTFTFILPYQ  666 (1002)
Q Consensus       648 ~v~S~~g~GTtF~~~LP~~  666 (1002)
                      +|+|.+|+||+|+|+||..
T Consensus       170 ~v~S~~g~Gt~f~l~L~~~  188 (193)
T d1gkza2         170 QLQSLQGIGTDVYLRLRHI  188 (193)
T ss_dssp             EEEEETTTEEEEEEEEECS
T ss_pred             EEEecCCCceEEEEEECCC
Confidence            9999999999999999963

>d1jm6a2 d.122.1.4 (A:1177-1366) Pyruvate dehydrogenase kinase {Rat (Rattus norvegicus), isozyme 2 [TaxId: 10116]}

class: Alpha and beta proteins (a+b)
fold: ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
superfamily: ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
family: alpha-ketoacid dehydrogenase kinase, C-terminal domain
domain: Pyruvate dehydrogenase kinase
species: Rat (Rattus norvegicus), isozyme 2 [TaxId: 10116]

Probab=99.94  E-value=7.2e-27  Score=239.33  Aligned_cols=149  Identities=19%  Similarity=0.236  Sum_probs=113.4

Q ss_pred             ecCHHHHHHHHHHHHHHHHh------h--cceeccccCCCCCeeEEccHHHHHHHHHHHHhhhhhcCCCCe--------e
Q 039716          442 KFRPREVVKHVLQTAAASLQ------K--ILMLEGDIADDVPIEVIGDVLRIRQILTNLISNAIKFTPEGK--------V  505 (1002)
Q Consensus       442 ~~~l~~li~~v~~~~~~~~~------k--~i~l~~~i~~~~p~~v~gD~~rL~QIL~NLlsNAIKfT~~G~--------I  505 (1002)
                      .+++.++++++++.......      .  .+..........+..+.+|+.+|+|||.|||.||+||++++.        |
T Consensus        10 ~~~l~~ii~da~e~~r~l~~~~~~~~~~~~i~~~~~~~~~~~~~~~~d~~~l~qvl~NLl~NA~~~~~~~~~~~~~~~~I   89 (190)
T d1jm6a2          10 NCSVSDVVKDAYDMAKLLCDKYYMASPDLEIQEVNATNATQPIHMVYVPSHLYHMLFELFKNAMRATVESHESSLTLPPI   89 (190)
T ss_dssp             EEEHHHHHHHHHHHHHHHHHHHHSCCCCEEEEEEESSSTTSCCEEEECHHHHHHHHHHHHHHHHHHHHHHCSCTTSCCCE
T ss_pred             CCCHHHHHHHHHHHHHHHHHHhhccCcccceEEEeccCCCCCEEEEECHHHHHHHHHHHHHHHHHHhhccCccccccceE
Confidence            45788888888776543221      1  122222334445667899999999999999999999985431        4


Q ss_pred             EEEEEecCCCCcccchhhhhhhhhhcchhhhhhhccCCCCCccCCCCCCCCCCCCCCccCCCCCCCCCCCccCCCCCccc
Q 039716          506 GIKLYVVPEPPFAKEGLKQKSKAYQSATDAVKEEKHQPKSQTASDQNGFHDKKHGEGYQDHKHDDDPGTPVSHGNSMDED  585 (1002)
Q Consensus       506 ~I~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  585 (1002)
                      .|.+..                                                                          
T Consensus        90 ~v~~~~--------------------------------------------------------------------------   95 (190)
T d1jm6a2          90 KIMVAL--------------------------------------------------------------------------   95 (190)
T ss_dssp             EEEEEE--------------------------------------------------------------------------
T ss_pred             EEEEEe--------------------------------------------------------------------------
Confidence            343321                                                                          


Q ss_pred             cccceEEEEEEEecCCCCCcCcHhhhhhhccCCCccccCcC-----CCccccHHHHHHHHHHhCCEEEEEeecCCceEEE
Q 039716          586 LEATVWIRCDVYDTGIGIPENALPTLFRKYMQVSADHARKY-----GGTGLGLAICKQLVELMGGRLTVTSKVHCGSTFT  660 (1002)
Q Consensus       586 ~~~~~~l~i~V~DtGiGI~~e~l~~IF~pF~q~~~~~~~~~-----~GtGLGLaI~k~Lve~~gG~I~v~S~~g~GTtF~  660 (1002)
                        ...++.|+|+|+|+|||++.+++||+|||+++....+..     +|+||||+|||+||+.|||+|+++|.+|+||+|+
T Consensus        96 --~~~~~~i~V~D~G~GI~~~~~~~iF~~f~~~~~~~~~~~~~~~~~G~GLGL~i~k~ive~hgG~I~v~s~~g~Gt~f~  173 (190)
T d1jm6a2          96 --GEEDLSIKMSDRGGGVPLRKIERLFSYMYSTAPTPQPGTGGTPLAGFGYGLPISRLYAKYFQGDLQLFSMEGFGTDAV  173 (190)
T ss_dssp             --CSSEEEEEEEECSCCCCGGGTTGGGCTTCCCSCCC---------CCSSCHHHHHHHHHHHTTCEEEEEEETTTEEEEE
T ss_pred             --CCeEEEEEEeccCCCCCHHHHHHHhCcceecCCcCcCcccccccCCCCccHHHHHHHHHHCCCEEEEEecCCCceEEE
Confidence              112588999999999999999999999999876544332     4999999999999999999999999999999999


Q ss_pred             EEEeCC
Q 039716          661 FILPYQ  666 (1002)
Q Consensus       661 ~~LP~~  666 (1002)
                      |+||..
T Consensus       174 i~lP~~  179 (190)
T d1jm6a2         174 IYLKAL  179 (190)
T ss_dssp             EEEESS
T ss_pred             EEEeCC
Confidence            999964

>d1peya_ c.23.1.1 (A:) Sporulation response regulator Spo0F {Bacillus subtilis [TaxId: 1423]}

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: Sporulation response regulator Spo0F
species: Bacillus subtilis [TaxId: 1423]

Probab=99.92  E-value=3.2e-25  Score=209.50  Aligned_cols=117  Identities=25%  Similarity=0.423  Sum_probs=112.2

Q ss_pred             CeEEEEecCHHHHHHHHHHHHhcCCeEEEEcCHHHHHHHHHcCCCcEEEEcCCCCCCCHHHHHHHHhccccCCCchhhhh
Q 039716          860 PKILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDAAAE  939 (1002)
Q Consensus       860 ~~ILiVeDn~~n~~~l~~~L~~~g~~v~~a~~G~eAl~~~~~~~~DlIlmDi~MP~mdG~e~~~~IR~~~~~~~~~~~~~  939 (1002)
                      .|||||||++.++..++.+|+..||.|..|.||.+|++.++..+||+||+|+.||+|||++++++||+.           
T Consensus         2 krILvVDD~~~~~~~l~~~L~~~g~~v~~a~~g~eal~~~~~~~~dlillD~~mP~~~G~el~~~lr~~-----------   70 (119)
T d1peya_           2 EKILIVDDQSGIRILLNEVFNKEGYQTFQAANGLQALDIVTKERPDLVLLDMKIPGMDGIEILKRMKVI-----------   70 (119)
T ss_dssp             CEEEEECSCHHHHHHHHHHHHHTTCEEEEESSHHHHHHHHHHHCCSEEEEESCCTTCCHHHHHHHHHHH-----------
T ss_pred             CEEEEEeCCHHHHHHHHHHHHHcCCEEEEeCCHHHHHHHHHhCCCCEEEEeccCCCCCHHHHHHHHHHh-----------
Confidence            389999999999999999999999999999999999999999999999999999999999999999973           


Q ss_pred             hhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHHhhcC
Q 039716          940 AGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQYFP 1002 (1002)
Q Consensus       940 ~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~~l~ 1002 (1002)
                                     .+.+|||++|++...+...+|+++|+++||.|||+.++|...|+++||
T Consensus        71 ---------------~~~~pvi~lt~~~~~~~~~~a~~~Ga~~yl~KP~~~~~L~~~v~~~L~  118 (119)
T d1peya_          71 ---------------DENIRVIIMTAYGELDMIQESKELGALTHFAKPFDIDEIRDAVKKYLP  118 (119)
T ss_dssp             ---------------CTTCEEEEEESSCCHHHHHHHHHTTCCEEEESSCCHHHHHHHHHHHSC
T ss_pred             ---------------CCCCcEEEEecCCCHHHHHHHHHCCCCEEEECCCCHHHHHHHHHHHCC
Confidence                           256999999999999999999999999999999999999999999986

>d2r25b1 c.23.1.1 (B:1087-1214) Response regulator Sin1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: Response regulator Sin1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.92  E-value=1.6e-24  Score=207.27  Aligned_cols=118  Identities=42%  Similarity=0.629  Sum_probs=109.0

Q ss_pred             CeEEEEecCHHHHHHHHHHHHhcCCe-EEEEcCHHHHHHHHH-----cCCCcEEEEcCCCCCCCHHHHHHHHhccccCCC
Q 039716          860 PKILLVEDNKINVMVAKSMMKQLGHS-IDVVNNGVEAVHAVQ-----CQNYDLILMDVCMPVMDGLKATRLIRSFEDTGN  933 (1002)
Q Consensus       860 ~~ILiVeDn~~n~~~l~~~L~~~g~~-v~~a~~G~eAl~~~~-----~~~~DlIlmDi~MP~mdG~e~~~~IR~~~~~~~  933 (1002)
                      .||||||||+.++.+++.+|+..|+. |..|.||.+|+++++     ...||+||||++||+|||++++++||+..    
T Consensus         2 irVLvVDD~~~~~~~l~~~L~~~g~~~v~~a~~g~eAl~~l~~~~~~~~~~dlillD~~mP~~dG~el~~~ir~~~----   77 (128)
T d2r25b1           2 VKILVVEDNHVNQEVIKRMLNLEGIENIELACDGQEAFDKVKELTSKGENYNMIFMDVQMPKVDGLLSTKMIRRDL----   77 (128)
T ss_dssp             SCEEEECSCHHHHHHHHHHHHHTTCCCEEEESSHHHHHHHHHHHHHHTCCCSEEEECSCCSSSCHHHHHHHHHHHS----
T ss_pred             eEEEEEeCCHHHHHHHHHHHHHcCCeEEEEEcChHHHHHHHHhhhhccCCCCEEEEEeCCCCCCHHHHHHHHHHcc----
Confidence            48999999999999999999999985 899999999999885     36899999999999999999999999632    


Q ss_pred             chhhhhhhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHHhhcC
Q 039716          934 WDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQYFP 1002 (1002)
Q Consensus       934 ~~~~~~~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~~l~ 1002 (1002)
                                           ...+|||++|++.+.+...+|+++|+++||.|||+.++|..+|++++.
T Consensus        78 ---------------------~~~~piI~lT~~~~~~~~~~~~~~G~~~~l~KP~~~~~L~~~l~~~~~  125 (128)
T d2r25b1          78 ---------------------GYTSPIVALTAFADDSNIKECLESGMNGFLSKPIKRPKLKTILTEFCA  125 (128)
T ss_dssp             ---------------------CCCSCEEEEESCCSHHHHHHHHHTTCSEEEESSCCHHHHHHHHHHHCT
T ss_pred             ---------------------CCCCeEEEEECCCCHHHHHHHHHcCCCEEEECCCCHHHHHHHHHHHHH
Confidence                                 245899999999999999999999999999999999999999999863

>d1ys7a2 c.23.1.1 (A:7-127) Transcriptional regulatory protein PrrA, N-terminal domain {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: Transcriptional regulatory protein PrrA, N-terminal domain
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=99.92  E-value=3.8e-25  Score=209.62  Aligned_cols=116  Identities=21%  Similarity=0.442  Sum_probs=110.7

Q ss_pred             CeEEEEecCHHHHHHHHHHHHhcCCeEEEEcCHHHHHHHHHcCCCcEEEEcCCCCCCCHHHHHHHHhccccCCCchhhhh
Q 039716          860 PKILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDAAAE  939 (1002)
Q Consensus       860 ~~ILiVeDn~~n~~~l~~~L~~~g~~v~~a~~G~eAl~~~~~~~~DlIlmDi~MP~mdG~e~~~~IR~~~~~~~~~~~~~  939 (1002)
                      ||||||||++.++..++.+|+..||.|.+|.||.+|++.++...||+||+|++||+|||++++++||+.           
T Consensus         2 PkILiVDD~~~~~~~l~~~L~~~g~~v~~a~~~~eal~~~~~~~~dlvl~D~~mP~~~G~el~~~ir~~-----------   70 (121)
T d1ys7a2           2 PRVLVVDDDSDVLASLERGLRLSGFEVATAVDGAEALRSATENRPDAIVLDINMPVLDGVSVVTALRAM-----------   70 (121)
T ss_dssp             CEEEEECSCHHHHHHHHHHHHHTTCEEEEESSHHHHHHHHHHSCCSEEEEESSCSSSCHHHHHHHHHHT-----------
T ss_pred             CEEEEEECCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHHHhCCCCEEEEEeeccCcccHHHHHHHHhc-----------
Confidence            589999999999999999999999999999999999999999999999999999999999999999973           


Q ss_pred             hhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHHhhc
Q 039716          940 AGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQYF 1001 (1002)
Q Consensus       940 ~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~~l 1001 (1002)
                                     .+.+|||++|++.+.+...+|+++|+++||+|||+.++|...|++.+
T Consensus        71 ---------------~~~~piI~lt~~~~~~~~~~a~~~Ga~dyl~KP~~~~~L~~~i~~~l  117 (121)
T d1ys7a2          71 ---------------DNDVPVCVLSARSSVDDRVAGLEAGADDYLVKPFVLAELVARVKALL  117 (121)
T ss_dssp             ---------------TCCCCEEEEECCCTTTCCCTTTTTTCSEEEESSCCHHHHHHHHHHHH
T ss_pred             ---------------CCCCEEEEEEeeCCHHHHHHHHHCCCCEEEECCCCHHHHHHHHHHHH
Confidence                           25699999999999999999999999999999999999999998765

>d2pl1a1 c.23.1.1 (A:1-119) PhoP receiver domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: PhoP receiver domain
species: Escherichia coli [TaxId: 562]

Probab=99.92  E-value=1.8e-24  Score=204.32  Aligned_cols=116  Identities=26%  Similarity=0.387  Sum_probs=110.4

Q ss_pred             CeEEEEecCHHHHHHHHHHHHhcCCeEEEEcCHHHHHHHHHcCCCcEEEEcCCCCCCCHHHHHHHHhccccCCCchhhhh
Q 039716          860 PKILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDAAAE  939 (1002)
Q Consensus       860 ~~ILiVeDn~~n~~~l~~~L~~~g~~v~~a~~G~eAl~~~~~~~~DlIlmDi~MP~mdG~e~~~~IR~~~~~~~~~~~~~  939 (1002)
                      .|||||||++.++..++.+|+..||.|.+|.||.+|++.+....||+||+|+.||+|||++++++||+.           
T Consensus         1 mrILvVDDd~~~~~~l~~~L~~~G~~v~~a~~g~eal~~l~~~~~dliilD~~mP~~~G~e~~~~i~~~-----------   69 (119)
T d2pl1a1           1 MRVLVVEDNALLRHHLKVQIQDAGHQVDDAEDAKEADYYLNEHIPDIAIVDLGLPDEDGLSLIRRWRSN-----------   69 (119)
T ss_dssp             CEEEEECSCHHHHHHHHHHHHHTTCEEEEESSHHHHHHHHHHSCCSEEEECSCCSSSCHHHHHHHHHHT-----------
T ss_pred             CEEEEEeCCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHHHhcccceeehhccCCCchhHHHHHHHHhc-----------
Confidence            489999999999999999999999999999999999999999999999999999999999999999973           


Q ss_pred             hhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHHhhc
Q 039716          940 AGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQYF 1001 (1002)
Q Consensus       940 ~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~~l 1001 (1002)
                                     .+.+|||++|+....+...+|+++|+++||.|||+.++|...|++.+
T Consensus        70 ---------------~~~~pvi~lt~~~~~~~~~~a~~~Ga~~yl~KP~~~~~L~~~v~~~l  116 (119)
T d2pl1a1          70 ---------------DVSLPILVLTARESWQDKVEVLSAGADDYVTKPFHIEEVMARMQALM  116 (119)
T ss_dssp             ---------------TCCSCEEEEESCCCHHHHHHHHHTTCSEEEESSCCHHHHHHHHHHHH
T ss_pred             ---------------CcccceEeeeccCCHHHHHHHHHcCCCEEEECCCCHHHHHHHHHHHH
Confidence                           25689999999999999999999999999999999999999998764

>d1dcfa_ c.23.1.2 (A:) Receiver domain of the ethylene receptor {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: Receiver domain of the ethylene receptor
domain: Receiver domain of the ethylene receptor
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=99.91  E-value=1.3e-24  Score=209.78  Aligned_cols=123  Identities=24%  Similarity=0.494  Sum_probs=112.4

Q ss_pred             CCCCeEEEEecCHHHHHHHHHHHHhcCCeEEEEcCHHHHHHHHHcCCCcEEEEcCCCCCCCHHHHHHHHhccccCCCchh
Q 039716          857 KPKPKILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDA  936 (1002)
Q Consensus       857 ~~~~~ILiVeDn~~n~~~l~~~L~~~g~~v~~a~~G~eAl~~~~~~~~DlIlmDi~MP~mdG~e~~~~IR~~~~~~~~~~  936 (1002)
                      ..+.|||||||++.++.+++.+|++.||.|.+|.||.+|++.+. +.||+||+|++||+|||++++++||+....     
T Consensus         5 ~~g~rILvVDD~~~~~~~l~~~L~~~G~~v~~a~~g~eal~~l~-~~~dlillD~~mP~~dG~el~~~ir~~~~~-----   78 (134)
T d1dcfa_           5 FTGLKVLVMDENGVSRMVTKGLLVHLGCEVTTVSSNEECLRVVS-HEHKVVFMDVCMPGVENYQIALRIHEKFTK-----   78 (134)
T ss_dssp             CTTCEEEEECSCHHHHHHHHHHHHHTTCEEEEESSHHHHHHHCC-TTCSEEEEECCSSTTTTTHHHHHHHHHHC------
T ss_pred             CCCCEEEEEeCCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHhh-cCCCeEEEEeccCCCchHHHHHHHHHhccc-----
Confidence            45789999999999999999999999999999999999999875 589999999999999999999999974321     


Q ss_pred             hhhhhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHHhhc
Q 039716          937 AAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQYF 1001 (1002)
Q Consensus       937 ~~~~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~~l 1001 (1002)
                                      ...+.+|||++||+...+...+|+++|+++||.||++.++|..+|.+++
T Consensus        79 ----------------~~~~~~~ii~lT~~~~~~~~~~~~~~G~~~~l~KP~~~~~L~~~l~~~l  127 (134)
T d1dcfa_          79 ----------------QRHQRPLLVALSGNTDKSTKEKCMSFGLDGVLLKPVSLDNIRDVLSDLL  127 (134)
T ss_dssp             ----------------CCSCCCEEEEEESCCSHHHHHHHHHTTCCEEEESSCCHHHHHHHHHHHH
T ss_pred             ----------------ccCCCCeEEEEeCCCCHHHHHHHHHcCCCEEEECCCCHHHHHHHHHHHh
Confidence                            2346789999999999999999999999999999999999999999876

>d1zesa1 c.23.1.1 (A:3-123) PhoB receiver domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: PhoB receiver domain
species: Escherichia coli [TaxId: 562]

Probab=99.91  E-value=2.9e-24  Score=203.56  Aligned_cols=117  Identities=22%  Similarity=0.309  Sum_probs=111.1

Q ss_pred             eEEEEecCHHHHHHHHHHHHhcCCeEEEEcCHHHHHHHHHcCCCcEEEEcCCCCCCCHHHHHHHHhccccCCCchhhhhh
Q 039716          861 KILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDAAAEA  940 (1002)
Q Consensus       861 ~ILiVeDn~~n~~~l~~~L~~~g~~v~~a~~G~eAl~~~~~~~~DlIlmDi~MP~mdG~e~~~~IR~~~~~~~~~~~~~~  940 (1002)
                      ||||||||+.++..+..+|+..||.|..|.||.+|++.++...||+||+|++||+|||+++++.||+..           
T Consensus         2 kILiVDD~~~~~~~l~~~L~~~g~~v~~a~~~~~al~~l~~~~~dlil~D~~mp~~~G~~l~~~lr~~~-----------   70 (121)
T d1zesa1           2 RILVVEDEAPIREMVCFVLEQNGFQPVEAEDYDSAVNQLNEPWPDLILLDWMLPGGSGIQFIKHLKRES-----------   70 (121)
T ss_dssp             EEEEECSCHHHHHHHHHHHHHTTCEEEEECSHHHHHHHSSSSCCSEEEECSSCTTSCHHHHHHHHHHST-----------
T ss_pred             EEEEEeCCHHHHHHHHHHHHHCCCEEEEECChHHHHHHHHccCCCEEEeecCCCCCCHHHHHHHHHhCc-----------
Confidence            799999999999999999999999999999999999999999999999999999999999999999743           


Q ss_pred             hhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHHhhc
Q 039716          941 GIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQYF 1001 (1002)
Q Consensus       941 ~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~~l 1001 (1002)
                                   ..+.+|||++|++.+.+...+|+++|+++|+.|||+.++|...|++.+
T Consensus        71 -------------~~~~~pvi~lt~~~~~~~~~~~~~~G~~d~l~KP~~~~~L~~~v~~~l  118 (121)
T d1zesa1          71 -------------MTRDIPVVMLTARGEEEDRVRGLETGADDYITKPFSPKELVARIKAVM  118 (121)
T ss_dssp             -------------TTTTSCEEEEESCCSHHHHHHHHHHTCSEEEESSCCHHHHHHHHHHHH
T ss_pred             -------------cCCCCeEEEEECCCCHHHHHHHHHCCCCEEEECCCCHHHHHHHHHHHH
Confidence                         346799999999999999999999999999999999999999998764

>d2a9pa1 c.23.1.1 (A:2-118) DNA-binding response regulator MicA, N-terminal domain {Streptococcus pneumoniae [TaxId: 1313]}

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: DNA-binding response regulator MicA, N-terminal domain
species: Streptococcus pneumoniae [TaxId: 1313]

Probab=99.91  E-value=3.6e-24  Score=201.70  Aligned_cols=114  Identities=27%  Similarity=0.450  Sum_probs=109.3

Q ss_pred             eEEEEecCHHHHHHHHHHHHhcCCeEEEEcCHHHHHHHHHcCCCcEEEEcCCCCCCCHHHHHHHHhccccCCCchhhhhh
Q 039716          861 KILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDAAAEA  940 (1002)
Q Consensus       861 ~ILiVeDn~~n~~~l~~~L~~~g~~v~~a~~G~eAl~~~~~~~~DlIlmDi~MP~mdG~e~~~~IR~~~~~~~~~~~~~~  940 (1002)
                      |||||||++.++..++.+|+..||.|..|.||.+|++.++..+||+||+|+.||+|||+++++.||+.            
T Consensus         2 rILiVdDd~~~~~~l~~~L~~~g~~v~~a~~~~eal~~~~~~~~dlillD~~mp~~~G~~~~~~i~~~------------   69 (117)
T d2a9pa1           2 KILIVDDEKPISDIIKFNMTKEGYEVVTAFNGREALEQFEAEQPDIIILDLMLPEIDGLEVAKTIRKT------------   69 (117)
T ss_dssp             EEEEECSCHHHHHHHHHHHHHTTCEEEEESSHHHHHHHHHHHCCSEEEECSSCSSSCHHHHHHHHHTT------------
T ss_pred             EEEEEECCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHHHhcCCCEEEeccccCCCCccHHHHHHHhC------------
Confidence            79999999999999999999999999999999999999999999999999999999999999999952            


Q ss_pred             hhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHHhhc
Q 039716          941 GIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQYF 1001 (1002)
Q Consensus       941 ~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~~l 1001 (1002)
                                     +++|||++|+....+...+|+++|+++||.|||++++|...|++.|
T Consensus        70 ---------------~~~pvI~lt~~~~~~~~~~a~~~Ga~d~l~KP~~~~~L~~~i~~~l  115 (117)
T d2a9pa1          70 ---------------SSVPILMLSAKDSEFDKVIGLELGADDYVTKPFSNRELQARVKALL  115 (117)
T ss_dssp             ---------------CCCCEEEEESCCSHHHHHHHHHHTCSEEEESSCCHHHHHHHHHHHH
T ss_pred             ---------------CCCCEEEEecCCCHHHHHHHHHcCCCEEEECCCCHHHHHHHHHHHh
Confidence                           4589999999999999999999999999999999999999998765

>d1mb3a_ c.23.1.1 (A:) Cell division response regulator DivK {Caulobacter crescentus [TaxId: 155892]}

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: Cell division response regulator DivK
species: Caulobacter crescentus [TaxId: 155892]

Probab=99.91  E-value=2.1e-24  Score=205.27  Aligned_cols=118  Identities=27%  Similarity=0.522  Sum_probs=106.1

Q ss_pred             CeEEEEecCHHHHHHHHHHHHhcCCeEEEEcCHHHHHHHHHcCCCcEEEEcCCCCCCCHHHHHHHHhccccCCCchhhhh
Q 039716          860 PKILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDAAAE  939 (1002)
Q Consensus       860 ~~ILiVeDn~~n~~~l~~~L~~~g~~v~~a~~G~eAl~~~~~~~~DlIlmDi~MP~mdG~e~~~~IR~~~~~~~~~~~~~  939 (1002)
                      .||||||||+.++..++.+|+..||+|..|.||.+|++.++...||+||+|++||+|||+++++.||+..          
T Consensus         2 krILiVDD~~~~~~~l~~~L~~~g~~v~~a~~~~~al~~~~~~~~dlil~D~~mp~~dG~el~~~ir~~~----------   71 (123)
T d1mb3a_           2 KKVLIVEDNELNMKLFHDLLEAQGYETLQTREGLSALSIARENKPDLILMDIQLPEISGLEVTKWLKEDD----------   71 (123)
T ss_dssp             CEEEEECSCHHHHHHHHHHHHHTTCEEEEESCHHHHHHHHHHHCCSEEEEESBCSSSBHHHHHHHHHHST----------
T ss_pred             ceEEEEECCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHHHhCCCCEEEEEeccCCCcHHHHHHHHHhCC----------
Confidence            4899999999999999999999999999999999999999999999999999999999999999999743          


Q ss_pred             hhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHHhhc
Q 039716          940 AGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQYF 1001 (1002)
Q Consensus       940 ~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~~l 1001 (1002)
                                    ..+++|||++|++...++..+|+++|+++||.|||+..+|...|++++
T Consensus        72 --------------~~~~iPii~lt~~~~~~~~~~~~~~G~~~~l~KP~~~~~L~~~i~~~l  119 (123)
T d1mb3a_          72 --------------DLAHIPVVAVTAFAMKGDEERIREGGCEAYISKPISVVHFLETIKRLL  119 (123)
T ss_dssp             --------------TTTTSCEEEEC------CHHHHHHHTCSEEECSSCCHHHHHHHHHHHH
T ss_pred             --------------CcCCCCeEEEEEecCHHHHHHHHHcCCCEEEECCCCHHHHHHHHHHHH
Confidence                          346799999999999999999999999999999999999999998875

>d1dbwa_ c.23.1.1 (A:) Transcriptional regulatory protein FixJ, receiver domain {Rhizobium meliloti [TaxId: 382]}

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: Transcriptional regulatory protein FixJ, receiver domain
species: Rhizobium meliloti [TaxId: 382]

Probab=99.91  E-value=8.6e-24  Score=200.83  Aligned_cols=117  Identities=19%  Similarity=0.239  Sum_probs=111.0

Q ss_pred             CCeEEEEecCHHHHHHHHHHHHhcCCeEEEEcCHHHHHHHHHcCCCcEEEEcCCCCCCCHHHHHHHHhccccCCCchhhh
Q 039716          859 KPKILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDAAA  938 (1002)
Q Consensus       859 ~~~ILiVeDn~~n~~~l~~~L~~~g~~v~~a~~G~eAl~~~~~~~~DlIlmDi~MP~mdG~e~~~~IR~~~~~~~~~~~~  938 (1002)
                      ..+||||||++.++..++.+|+..||.|..|.||.+|++.+...+||+||+|+.||+|||++++++||+.          
T Consensus         3 ~~~ILiVDDd~~~~~~l~~~L~~~g~~v~~a~~~~~al~~~~~~~~dlvi~D~~mp~~~G~e~~~~lr~~----------   72 (123)
T d1dbwa_           3 DYTVHIVDDEEPVRKSLAFMLTMNGFAVKMHQSAEAFLAFAPDVRNGVLVTDLRMPDMSGVELLRNLGDL----------   72 (123)
T ss_dssp             CCEEEEEESSHHHHHHHHHHHHHTTCEEEEESCHHHHHHHGGGCCSEEEEEECCSTTSCHHHHHHHHHHT----------
T ss_pred             CCEEEEEECCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHHhhcCCcEEEEeccCccccchHHHHHHHhc----------
Confidence            4699999999999999999999999999999999999999999999999999999999999999999963          


Q ss_pred             hhhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHHhhc
Q 039716          939 EAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQYF 1001 (1002)
Q Consensus       939 ~~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~~l 1001 (1002)
                                      .+.+|||++|++.+.+...+|+++|+++||.|||+.++|...|++.+
T Consensus        73 ----------------~~~~~iI~lt~~~~~~~~~~a~~~Ga~~yl~KP~~~~~L~~~i~~a~  119 (123)
T d1dbwa_          73 ----------------KINIPSIVITGHGDVPMAVEAMKAGAVDFIEKPFEDTVIIEAIERAS  119 (123)
T ss_dssp             ----------------TCCCCEEEEECTTCHHHHHHHHHTTCSEEEESSCCHHHHHHHHHHHH
T ss_pred             ----------------CCCCeEEEEEeeCCHHHHHHHHHCCCCEEEECCCCHHHHHHHHHHHH
Confidence                            35799999999999999999999999999999999999999988753

>d1mvoa_ c.23.1.1 (A:) PhoP receiver domain {Bacillus subtilis [TaxId: 1423]}

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: PhoP receiver domain
species: Bacillus subtilis [TaxId: 1423]

Probab=99.91  E-value=4.2e-24  Score=202.46  Aligned_cols=116  Identities=23%  Similarity=0.402  Sum_probs=110.1

Q ss_pred             CeEEEEecCHHHHHHHHHHHHhcCCeEEEEcCHHHHHHHHHcCCCcEEEEcCCCCCCCHHHHHHHHhccccCCCchhhhh
Q 039716          860 PKILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDAAAE  939 (1002)
Q Consensus       860 ~~ILiVeDn~~n~~~l~~~L~~~g~~v~~a~~G~eAl~~~~~~~~DlIlmDi~MP~mdG~e~~~~IR~~~~~~~~~~~~~  939 (1002)
                      .||||||||+.++..++.+|++.||+|.+|.||.+|++.++..+||+||+|+.||+|||+++++++|..           
T Consensus         3 krILiVDDd~~~~~~l~~~L~~~g~~v~~a~~~~~al~~l~~~~~dlillD~~mp~~~G~~~~~~~r~~-----------   71 (121)
T d1mvoa_           3 KKILVVDDEESIVTLLQYNLERSGYDVITASDGEEALKKAETEKPDLIVLDVMLPKLDGIEVCKQLRQQ-----------   71 (121)
T ss_dssp             CEEEEECSCHHHHHHHHHHHHHTTCEEEEESSHHHHHHHHHHHCCSEEEEESSCSSSCHHHHHHHHHHT-----------
T ss_pred             CCEEEEECCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHHhcccccEEEecccccCCCCchhhhhhhcc-----------
Confidence            489999999999999999999999999999999999999999999999999999999999999999963           


Q ss_pred             hhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHHhhc
Q 039716          940 AGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQYF 1001 (1002)
Q Consensus       940 ~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~~l 1001 (1002)
                                     .+.+|||++|+....+...+|+++|+++||.|||++++|...|++++
T Consensus        72 ---------------~~~~~ii~lt~~~~~~~~~~~~~~Ga~~yl~KP~~~~~L~~~i~~~l  118 (121)
T d1mvoa_          72 ---------------KLMFPILMLTAKDEEFDKVLGLELGADDYMTKPFSPREVNARVKAIL  118 (121)
T ss_dssp             ---------------TCCCCEEEEECTTCCCCHHHHHHTTCCEEEESSCCHHHHHHHHHHHH
T ss_pred             ---------------CCCCEEEEEEeeCCHHHHHHHHHCCCCEEEECCCCHHHHHHHHHHHH
Confidence                           25689999999999999999999999999999999999999998765

>d1xhfa1 c.23.1.1 (A:2-122) Aerobic respiration control protein ArcA, N-terminal domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: Aerobic respiration control protein ArcA, N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=99.90  E-value=8.3e-24  Score=200.33  Aligned_cols=116  Identities=22%  Similarity=0.356  Sum_probs=110.2

Q ss_pred             CCeEEEEecCHHHHHHHHHHHHhcCCeEEEEcCHHHHHHHHHcCCCcEEEEcCCCCCCCHHHHHHHHhccccCCCchhhh
Q 039716          859 KPKILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDAAA  938 (1002)
Q Consensus       859 ~~~ILiVeDn~~n~~~l~~~L~~~g~~v~~a~~G~eAl~~~~~~~~DlIlmDi~MP~mdG~e~~~~IR~~~~~~~~~~~~  938 (1002)
                      .++|||||||+.++..+..+|++.||+|..|.||.+|++.+...+||+||+|++||+|||+++++.+|+.          
T Consensus         2 tp~ILiVDDd~~~~~~l~~~L~~~g~~v~~a~~~~~al~~l~~~~~dlii~D~~mp~~~G~~~~~~~r~~----------   71 (121)
T d1xhfa1           2 TPHILIVEDELVTRNTLKSIFEAEGYDVFEATDGAEMHQILSEYDINLVIMDINLPGKNGLLLARELREQ----------   71 (121)
T ss_dssp             CCEEEEECSCHHHHHHHHHHHHTTTCEEEEESSHHHHHHHHHHSCCSEEEECSSCSSSCHHHHHHHHHHH----------
T ss_pred             CCEEEEEECCHHHHHHHHHHHHHCCCEEEEECChHHHHHHHHhcCCCEEEeecccCCccCcHHHHHHHhc----------
Confidence            3599999999999999999999999999999999999999999999999999999999999999999962          


Q ss_pred             hhhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHHhhc
Q 039716          939 EAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQYF 1001 (1002)
Q Consensus       939 ~~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~~l 1001 (1002)
                                       +++|||++|++.+.+...+|+++|++|||.|||++++|...+++.+
T Consensus        72 -----------------~~~pii~lt~~~~~~~~~~a~~~Ga~dyl~KP~~~~~L~~~v~~~l  117 (121)
T d1xhfa1          72 -----------------ANVALMFLTGRDNEVDKILGLEIGADDYITKPFNPRELTIRARNLL  117 (121)
T ss_dssp             -----------------CCCEEEEEESCCSHHHHHHHHHHTCSEEEESSCCHHHHHHHHHHHH
T ss_pred             -----------------CCCcEEEEECCCCHHHHHHHHHcCCCEEEeCCCCHHHHHHHHHHHH
Confidence                             4589999999999999999999999999999999999999988764

>d1p6qa_ c.23.1.1 (A:) CheY protein {Sinorhizobium meliloti, CheY2 [TaxId: 382]}

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: CheY protein
species: Sinorhizobium meliloti, CheY2 [TaxId: 382]

Probab=99.90  E-value=4.5e-24  Score=204.56  Aligned_cols=120  Identities=27%  Similarity=0.435  Sum_probs=112.6

Q ss_pred             CCCeEEEEecCHHHHHHHHHHHHhcCCe-EEEEcCHHHHHHHHHcCCCcEEEEcCCCCCCCHHHHHHHHhccccCCCchh
Q 039716          858 PKPKILLVEDNKINVMVAKSMMKQLGHS-IDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDA  936 (1002)
Q Consensus       858 ~~~~ILiVeDn~~n~~~l~~~L~~~g~~-v~~a~~G~eAl~~~~~~~~DlIlmDi~MP~mdG~e~~~~IR~~~~~~~~~~  936 (1002)
                      .+.|||||||++.++..++.+|+..||. |..|.||.+|++.+..+.||+||+|++||+|||+++++.||+..       
T Consensus         5 ~~~kILiVDD~~~~~~~l~~~L~~~g~~~v~~a~~~~~al~~l~~~~~dlii~D~~mP~~~G~el~~~lr~~~-------   77 (129)
T d1p6qa_           5 EKIKVLIVDDQVTSRLLLGDALQQLGFKQITAAGDGEQGMKIMAQNPHHLVISDFNMPKMDGLGLLQAVRANP-------   77 (129)
T ss_dssp             SCCCEEEECSSHHHHHHHHHHHHTTTCSCEECCSSHHHHHHHHHTSCCSEEEECSSSCSSCHHHHHHHHTTCT-------
T ss_pred             CCCEEEEEECCHHHHHHHHHHHHHCCCeEEEEECCHHHHHHHHHhCCCCeEEeeeecCCCChHHHHHHHHhCc-------
Confidence            4578999999999999999999999995 88899999999999999999999999999999999999999743       


Q ss_pred             hhhhhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHHhhc
Q 039716          937 AAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQYF 1001 (1002)
Q Consensus       937 ~~~~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~~l 1001 (1002)
                                       ..+++|||++|++.+.+...+|+++|+++|+.|||+.++|...|+++|
T Consensus        78 -----------------~~~~~pii~lt~~~~~~~~~~a~~~G~~~~l~KP~~~~~L~~~i~~vl  125 (129)
T d1p6qa_          78 -----------------ATKKAAFIILTAQGDRALVQKAAALGANNVLAKPFTIEKMKAAIEAVF  125 (129)
T ss_dssp             -----------------TSTTCEEEECCSCCCHHHHHHHHHHTCSCEECCCSSHHHHHHHHHHHH
T ss_pred             -----------------ccCCCeEEEEEecCCHHHHHHHHHCCCCEEEECCCCHHHHHHHHHHHH
Confidence                             346799999999999999999999999999999999999999999875

>d1zh2a1 c.23.1.1 (A:2-120) Transcriptional regulatory protein KdpE, N-terminal domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: Transcriptional regulatory protein KdpE, N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=99.90  E-value=4.1e-24  Score=201.91  Aligned_cols=114  Identities=21%  Similarity=0.371  Sum_probs=108.8

Q ss_pred             eEEEEecCHHHHHHHHHHHHhcCCeEEEEcCHHHHHHHHHcCCCcEEEEcCCCCCCCHHHHHHHHhccccCCCchhhhhh
Q 039716          861 KILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDAAAEA  940 (1002)
Q Consensus       861 ~ILiVeDn~~n~~~l~~~L~~~g~~v~~a~~G~eAl~~~~~~~~DlIlmDi~MP~mdG~e~~~~IR~~~~~~~~~~~~~~  940 (1002)
                      +|||||||+.++..++.+|++.||+|..|.||.+|++.++...||+||+|++||+|||+++++.||+.            
T Consensus         2 nILiVDDd~~~~~~l~~~L~~~g~~v~~a~~~~eal~~l~~~~~dliilD~~mP~~~G~e~~~~ir~~------------   69 (119)
T d1zh2a1           2 NVLIVEDEQAIRRFLRTALEGDGMRVFEAETLQRGLLEAATRKPDLIILDLGLPDGDGIEFIRDLRQW------------   69 (119)
T ss_dssp             EEEEECSCHHHHHHHHHHHHTTTCEEEEESSHHHHHHHHHHHCCSEEEEESEETTEEHHHHHHHHHTT------------
T ss_pred             EEEEEECCHHHHHHHHHHHHHCCCEEEEeCCHHHHHHHHHhcCCCEEEeccccCCCCCchHHHHHHhc------------
Confidence            69999999999999999999999999999999999999999999999999999999999999999962            


Q ss_pred             hhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHHhhc
Q 039716          941 GIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQYF 1001 (1002)
Q Consensus       941 ~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~~l 1001 (1002)
                                     +.+|||++|+....+...+|+++|+++||.|||+.++|...|++.+
T Consensus        70 ---------------~~~piI~lt~~~~~~~~~~a~~~Ga~dyl~KP~~~~~L~~~i~~~l  115 (119)
T d1zh2a1          70 ---------------SAVPVIVLSARSEESDKIAALDAGADDYLSKPFGIGELQARLRVAL  115 (119)
T ss_dssp             ---------------CCCCEEEEESCCSHHHHHHHHHHTCSEEEESSCCHHHHHHHHHHHH
T ss_pred             ---------------cCCcEEEEeccCCHHHHHHHHHcCCCEEEECCCCHHHHHHHHHHHH
Confidence                           3579999999999999999999999999999999999999998764

>d2ayxa1 c.23.1.1 (A:817-949) Sensor kinase protein RcsC, C-terminal domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: Sensor kinase protein RcsC, C-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=99.90  E-value=4.6e-24  Score=205.56  Aligned_cols=118  Identities=38%  Similarity=0.625  Sum_probs=112.0

Q ss_pred             CCCeEEEEecCHHHHHHHHHHHHhcCCeEEEEcCHHHHHHHHHcCCCcEEEEcCCCCCCCHHHHHHHHhccccCCCchhh
Q 039716          858 PKPKILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDAA  937 (1002)
Q Consensus       858 ~~~~ILiVeDn~~n~~~l~~~L~~~g~~v~~a~~G~eAl~~~~~~~~DlIlmDi~MP~mdG~e~~~~IR~~~~~~~~~~~  937 (1002)
                      ...+|||||||+.++..++.+|+..||.|.+|.||.+|++.+...+||+||+|+.||+|||++++++||+..        
T Consensus         7 ~~~~ILiVDD~~~~~~~l~~~L~~~g~~v~~a~~g~ea~~~~~~~~~dlillD~~mP~~dG~el~~~ir~~~--------   78 (133)
T d2ayxa1           7 DDMMILVVDDHPINRRLLADQLGSLGYQCKTANDGVDALNVLSKNHIDIVLSDVNMPNMDGYRLTQRIRQLG--------   78 (133)
T ss_dssp             CCCEEEEEESSHHHHHHHHHHHHHHTSEEEEECCSHHHHHHHHHSCCSEEEEEESSCSSCCHHHHHHHHHHH--------
T ss_pred             CCCEEEEEECCHHHHHHHHHHHHHcCCEEEEECcHHHHHHHHhccCceEEEEeccCCCCCHHHHHHHHHHhC--------
Confidence            467999999999999999999999999999999999999999999999999999999999999999999742        


Q ss_pred             hhhhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHHhhc
Q 039716          938 AEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQYF 1001 (1002)
Q Consensus       938 ~~~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~~l 1001 (1002)
                                        +.+|||++|++...+...+|+++|+++||+|||+.++|...|.+++
T Consensus        79 ------------------~~~pii~lt~~~~~~~~~~~~~~G~~~~l~KP~~~~~L~~~l~~~~  124 (133)
T d2ayxa1          79 ------------------LTLPVIGVTANALAEEKQRCLESGMDSCLSKPVTLDVIKQTLTLYA  124 (133)
T ss_dssp             ------------------CCSCEEEEESSTTSHHHHHHHHCCCEEEEESSCCHHHHHHHHHHHH
T ss_pred             ------------------CCCCEEEEeccCCHHHHHHHHHcCCCEEEECCCCHHHHHHHHHHHH
Confidence                              4689999999999999999999999999999999999999998764

>d1kgsa2 c.23.1.1 (A:2-123) PhoB receiver domain {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: PhoB receiver domain
species: Thermotoga maritima [TaxId: 2336]

Probab=99.90  E-value=6.6e-24  Score=201.42  Aligned_cols=116  Identities=22%  Similarity=0.378  Sum_probs=110.3

Q ss_pred             CeEEEEecCHHHHHHHHHHHHhcCCeEEEEcCHHHHHHHHHcCCCcEEEEcCCCCCCCHHHHHHHHhccccCCCchhhhh
Q 039716          860 PKILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDAAAE  939 (1002)
Q Consensus       860 ~~ILiVeDn~~n~~~l~~~L~~~g~~v~~a~~G~eAl~~~~~~~~DlIlmDi~MP~mdG~e~~~~IR~~~~~~~~~~~~~  939 (1002)
                      .||||||||+.++..++.+|+..||.|.+|.||.+|++.+....||+||+|+.||+|||+++++.||..           
T Consensus         2 irILiVdDd~~~~~~l~~~L~~~g~~v~~a~~~~~al~~l~~~~~dlillD~~mp~~~g~~~~~~lr~~-----------   70 (122)
T d1kgsa2           2 VRVLVVEDERDLADLITEALKKEMFTVDVCYDGEEGMYMALNEPFDVVILDIMLPVHDGWEILKSMRES-----------   70 (122)
T ss_dssp             CEEEEECSSHHHHHHHHHHHHHTTCEEEEESSHHHHHHHHHHSCCSEEEEESCCSSSCHHHHHHHHHHT-----------
T ss_pred             CEEEEEeCCHHHHHHHHHHHHHCCCEEEEEcchHHHHHHHHhhCccccccccccccchhHHHHHHHHhc-----------
Confidence            589999999999999999999999999999999999999999999999999999999999999999963           


Q ss_pred             hhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHHhhc
Q 039716          940 AGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQYF 1001 (1002)
Q Consensus       940 ~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~~l 1001 (1002)
                                     .+.+|||++|++...+...+|+++|+++||.|||++++|...|++++
T Consensus        71 ---------------~~~~piI~lt~~~~~~~~~~~~~~Ga~~yl~KP~~~~~L~~~i~~~l  117 (122)
T d1kgsa2          71 ---------------GVNTPVLMLTALSDVEYRVKGLNMGADDYLPKPFDLRELIARVRALI  117 (122)
T ss_dssp             ---------------TCCCCEEEEESSCHHHHHHHTCCCCCSEEEESSCCHHHHHHHHHHHH
T ss_pred             ---------------CCCCcEEEEcCCCCHHHHHHHHHcCCceeecCCCCHHHHHHHHHHHH
Confidence                           25689999999999999999999999999999999999999998764

>d1krwa_ c.23.1.1 (A:) NTRC receiver domain {Salmonella typhimurium [TaxId: 90371]}

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: NTRC receiver domain
species: Salmonella typhimurium [TaxId: 90371]

Probab=99.90  E-value=2.5e-24  Score=204.66  Aligned_cols=117  Identities=24%  Similarity=0.388  Sum_probs=111.1

Q ss_pred             CCeEEEEecCHHHHHHHHHHHHhcCCeEEEEcCHHHHHHHHHcCCCcEEEEcCCCCCCCHHHHHHHHhccccCCCchhhh
Q 039716          859 KPKILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDAAA  938 (1002)
Q Consensus       859 ~~~ILiVeDn~~n~~~l~~~L~~~g~~v~~a~~G~eAl~~~~~~~~DlIlmDi~MP~mdG~e~~~~IR~~~~~~~~~~~~  938 (1002)
                      +.+|||||||+.++..++.+|++.||.|.+|.||.+|++.++.+.||+||+|++||+|||++++++||+.          
T Consensus         3 k~~ILIVDDd~~~~~~l~~~L~~~g~~v~~a~~~~~a~~~l~~~~~dlii~D~~mp~~~G~el~~~l~~~----------   72 (123)
T d1krwa_           3 RGIVWVVDDDSSIRWVLERALAGAGLTCTTFENGNEVLAALASKTPDVLLSDIRMPGMDGLALLKQIKQR----------   72 (123)
T ss_dssp             CCEEEEESSSHHHHHHHHHHHHHTTCEEEEESSSHHHHHHHTTCCCSEEEECCSSSSSTTHHHHHHHHHH----------
T ss_pred             CCEEEEEECCHHHHHHHHHHHHHCCCEEEEeCCHHHHHHHHHhCCCCEEEehhhcCCchHHHHHHHHHHh----------
Confidence            4589999999999999999999999999999999999999999999999999999999999999999963          


Q ss_pred             hhhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHHhhc
Q 039716          939 EAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQYF 1001 (1002)
Q Consensus       939 ~~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~~l 1001 (1002)
                                      .+.+|||++|++.+.+...+|+++|+++||.|||+.++|...|++.+
T Consensus        73 ----------------~~~~piI~~t~~~~~~~~~~a~~~Ga~dyl~KP~~~~eL~~~i~~~l  119 (123)
T d1krwa_          73 ----------------HPMLPVIIMTAHSDLDAAVSAYQQGAFDYLPKPFDIDEAVALVERAI  119 (123)
T ss_dssp             ----------------SSSCCEEESCCCSCHHHHHHHHHHTEEEECSSCCHHHHHHHHHHHHH
T ss_pred             ----------------CCCCeEEEEecCCCHHHHHHHHHcCCCeEEeCcCCHHHHHHHHHHHH
Confidence                            35799999999999999999999999999999999999999998764

>d1qkka_ c.23.1.1 (A:) Transcriptional regulatory protein DctD, receiver domain {Sinorhizobium meliloti [TaxId: 382]}

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: Transcriptional regulatory protein DctD, receiver domain
species: Sinorhizobium meliloti [TaxId: 382]

Probab=99.90  E-value=6.6e-24  Score=206.36  Aligned_cols=116  Identities=21%  Similarity=0.366  Sum_probs=110.1

Q ss_pred             CeEEEEecCHHHHHHHHHHHHhcCCeEEEEcCHHHHHHHHHcCCCcEEEEcCCCCCCCHHHHHHHHhccccCCCchhhhh
Q 039716          860 PKILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDAAAE  939 (1002)
Q Consensus       860 ~~ILiVeDn~~n~~~l~~~L~~~g~~v~~a~~G~eAl~~~~~~~~DlIlmDi~MP~mdG~e~~~~IR~~~~~~~~~~~~~  939 (1002)
                      |+||||||++.++..++.+|+..||.|..+.||.+|++.+..+.||+||+|+.||+|||++++++||+.           
T Consensus         1 P~ILiVDDd~~~~~~l~~~L~~~g~~v~~~~~~~~al~~l~~~~~dlil~D~~mP~~~G~el~~~lr~~-----------   69 (140)
T d1qkka_           1 PSVFLIDDDRDLRKAMQQTLELAGFTVSSFASATEALAGLSADFAGIVISDIRMPGMDGLALFRKILAL-----------   69 (140)
T ss_dssp             CEEEEECSCHHHHHHHHHHHHHTTCEEEEESCHHHHHHTCCTTCCSEEEEESCCSSSCHHHHHHHHHHH-----------
T ss_pred             CEEEEEECCHHHHHHHHHHHHHCCCEEEEeCChHHHHHHHhccCcchHHHhhccCCCCHHHHHHHHHHh-----------
Confidence            589999999999999999999999999999999999999999999999999999999999999999973           


Q ss_pred             hhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHHhhc
Q 039716          940 AGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQYF 1001 (1002)
Q Consensus       940 ~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~~l 1001 (1002)
                                     .+.+|||++|++.+.+...+|+++|++|||.||++.++|...+++.+
T Consensus        70 ---------------~~~~pvI~lT~~~~~~~~~~a~~~Ga~dyl~KP~~~~~L~~~i~~~~  116 (140)
T d1qkka_          70 ---------------DPDLPMILVTGHGDIPMAVQAIQDGAYDFIAKPFAADRLVQSARRAE  116 (140)
T ss_dssp             ---------------CTTSCEEEEECGGGHHHHHHHHHTTCCEEEESSCCHHHHHHHHHHHH
T ss_pred             ---------------CCCCcEEEEECCCCHHHHHHHHHcCCCEeecCCCCHHHHHHHHHHHH
Confidence                           35799999999999999999999999999999999999998887653

>d1u0sy_ c.23.1.1 (Y:) CheY protein {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: CheY protein
species: Thermotoga maritima [TaxId: 2336]

Probab=99.90  E-value=1.2e-23  Score=198.30  Aligned_cols=116  Identities=26%  Similarity=0.401  Sum_probs=109.4

Q ss_pred             CCeEEEEecCHHHHHHHHHHHHhcCCeEE-EEcCHHHHHHHHHcCCCcEEEEcCCCCCCCHHHHHHHHhccccCCCchhh
Q 039716          859 KPKILLVEDNKINVMVAKSMMKQLGHSID-VVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDAA  937 (1002)
Q Consensus       859 ~~~ILiVeDn~~n~~~l~~~L~~~g~~v~-~a~~G~eAl~~~~~~~~DlIlmDi~MP~mdG~e~~~~IR~~~~~~~~~~~  937 (1002)
                      +.|||||||++.++..++.+|++.||+|. +|.||.+|++.++..+||+||+|++||+|||++++++||+.         
T Consensus         1 GkrILivDD~~~~~~~l~~~L~~~g~~v~~~a~~~~~al~~~~~~~~dliilD~~mp~~~G~e~~~~ir~~---------   71 (118)
T d1u0sy_           1 GKRVLIVDDAAFMRMMLKDIITKAGYEVAGEATNGREAVEKYKELKPDIVTMDITMPEMNGIDAIKEIMKI---------   71 (118)
T ss_dssp             CCEEEEECSCHHHHHHHHHHHHHTTCEEEEEESSHHHHHHHHHHHCCSEEEEECSCGGGCHHHHHHHHHHH---------
T ss_pred             CCEEEEEeCCHHHHHHHHHHHHHcCCceEEEECCHHHHHHHHHhccCCEEEEecCCCCCCHHHHHHHHHHh---------
Confidence            35899999999999999999999999976 78999999999999999999999999999999999999963         


Q ss_pred             hhhhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHHhh
Q 039716          938 AEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQY 1000 (1002)
Q Consensus       938 ~~~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~~ 1000 (1002)
                                       .+++|||++|++...+...+|+++|+++||.|||+.++|..+|+++
T Consensus        72 -----------------~~~~pvi~ls~~~~~~~~~~a~~~Ga~~yl~KP~~~~~L~~~l~~v  117 (118)
T d1u0sy_          72 -----------------DPNAKIIVCSAMGQQAMVIEAIKAGAKDFIVKPFQPSRVVEALNKV  117 (118)
T ss_dssp             -----------------CTTCCEEEEECTTCHHHHHHHHHTTCCEEEESSCCHHHHHHHHHHH
T ss_pred             -----------------CCCCcEEEEEccCCHHHHHHHHHcCCCEEEECCCCHHHHHHHHHHh
Confidence                             2569999999999999999999999999999999999999999875

>d1w25a1 c.23.1.1 (A:2-140) Response regulator PleD, receiver domain {Caulobacter crescentus [TaxId: 155892]}

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: Response regulator PleD, receiver domain
species: Caulobacter crescentus [TaxId: 155892]

Probab=99.90  E-value=2.1e-23  Score=202.57  Aligned_cols=117  Identities=24%  Similarity=0.347  Sum_probs=110.4

Q ss_pred             CeEEEEecCHHHHHHHHHHHHhcCCeEEEEcCHHHHHHHHHcCCCcEEEEcCCCCCCCHHHHHHHHhccccCCCchhhhh
Q 039716          860 PKILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDAAAE  939 (1002)
Q Consensus       860 ~~ILiVeDn~~n~~~l~~~L~~~g~~v~~a~~G~eAl~~~~~~~~DlIlmDi~MP~mdG~e~~~~IR~~~~~~~~~~~~~  939 (1002)
                      .|||||||++.++..++.+|++.||+|.+|.||.+|++.+..+.|||||+|+.||++||+++++.||...          
T Consensus         2 arILiVDD~~~~~~~l~~~L~~~g~~v~~a~~~~eal~~~~~~~~dlil~D~~~p~~~G~~~~~~ir~~~----------   71 (139)
T d1w25a1           2 ARILVVDDIEANVRLLEAKLTAEYYEVSTAMDGPTALAMAARDLPDIILLDVMMPGMDGFTVCRKLKDDP----------   71 (139)
T ss_dssp             CEEEEECSSTTHHHHHHHHHHHTTCEEEEESSHHHHHHHHHHHCCSEEEEESCCSSSCHHHHHHHHHHST----------
T ss_pred             CEEEEEECCHHHHHHHHHHHHHCCCEEEEEccchhhhhhhhcccceeeeeeccccCCCchHHHHHhhhcc----------
Confidence            4899999999999999999999999999999999999999999999999999999999999999999743          


Q ss_pred             hhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHHhh
Q 039716          940 AGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQY 1000 (1002)
Q Consensus       940 ~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~~ 1000 (1002)
                                    ..+++|||++|++.+.+...+|+++|++|||.|||+..+|...|+.+
T Consensus        72 --------------~~~~~piI~lt~~~~~~~~~~a~~~Ga~dyl~KP~~~~~L~~~i~~~  118 (139)
T d1w25a1          72 --------------TTRHIPVVLITALDGRGDRIQGLESGASDFLTKPIDDVMLFARVRSL  118 (139)
T ss_dssp             --------------TTTTSCEEEEECSSCHHHHHHHHHHTCCEEEESSCCHHHHHHHHHHH
T ss_pred             --------------cccCCCEEEEEcCCCHHHHHHHHHcCCCEEEECCCCHHHHHHHHHHH
Confidence                          34679999999999999999999999999999999999999888754

>d1ny5a1 c.23.1.1 (A:1-137) Transcriptional activator sigm54 (NtrC1), N-terminal domain {Aquifex aeolicus [TaxId: 63363]}

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: Transcriptional activator sigm54 (NtrC1), N-terminal domain
species: Aquifex aeolicus [TaxId: 63363]

Probab=99.89  E-value=1.6e-23  Score=202.80  Aligned_cols=116  Identities=19%  Similarity=0.402  Sum_probs=110.0

Q ss_pred             CeEEEEecCHHHHHHHHHHHHhcCCeEEEEcCHHHHHHHHHcCCCcEEEEcCCCCCCCHHHHHHHHhccccCCCchhhhh
Q 039716          860 PKILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDAAAE  939 (1002)
Q Consensus       860 ~~ILiVeDn~~n~~~l~~~L~~~g~~v~~a~~G~eAl~~~~~~~~DlIlmDi~MP~mdG~e~~~~IR~~~~~~~~~~~~~  939 (1002)
                      .|||||||++.++..++.+|+..||.|..|.||.+|++.+..+.||+||+|+.||+|+|+++++.||+.           
T Consensus         1 mkILiVDDd~~~~~~l~~~L~~~g~~v~~a~~~~eAl~~l~~~~~dlvilD~~mp~~~G~e~~~~lr~~-----------   69 (137)
T d1ny5a1           1 MNVLVIEDDKVFRGLLEEYLSMKGIKVESAERGKEAYKLLSEKHFNVVLLDLLLPDVNGLEILKWIKER-----------   69 (137)
T ss_dssp             CEEEEECCCHHHHHHHHHHHHHHTCEEEEESSHHHHHHHHHHSCCSEEEEESBCSSSBHHHHHHHHHHH-----------
T ss_pred             CEEEEEecCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHhhccccccchHHHhhhhhhHHHHHHHHHHh-----------
Confidence            479999999999999999999999999999999999999999999999999999999999999999963           


Q ss_pred             hhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHHhhc
Q 039716          940 AGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQYF 1001 (1002)
Q Consensus       940 ~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~~l 1001 (1002)
                                     .+.+|||++|++.+.+...+|+++|++|||.||++.++|...|.+.+
T Consensus        70 ---------------~~~~piI~lT~~~~~~~~~~a~~~Ga~dyl~KP~~~~~L~~~i~~~l  116 (137)
T d1ny5a1          70 ---------------SPETEVIVITGHGTIKTAVEAMKMGAYDFLTKPCMLEEIELTINKAI  116 (137)
T ss_dssp             ---------------CTTSEEEEEEETTCHHHHHHHHTTTCCEEEEESCCHHHHHHHHHHHH
T ss_pred             ---------------CCCCCEEEEECCCCHHHHHHHHHcCCCEEEeCCCCHHHHHHHHHHHH
Confidence                           36799999999999999999999999999999999999999887753

>d1zgza1 c.23.1.1 (A:2-121) TorCAD operon transcriptional regulator TorD, N-terminal domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: TorCAD operon transcriptional regulator TorD, N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=99.89  E-value=5.5e-23  Score=194.44  Aligned_cols=115  Identities=27%  Similarity=0.403  Sum_probs=109.3

Q ss_pred             CeEEEEecCHHHHHHHHHHHHhcCCeEEEEcCHHHHHHHHHcCCCcEEEEcCCCCCCCHHHHHHHHhccccCCCchhhhh
Q 039716          860 PKILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDAAAE  939 (1002)
Q Consensus       860 ~~ILiVeDn~~n~~~l~~~L~~~g~~v~~a~~G~eAl~~~~~~~~DlIlmDi~MP~mdG~e~~~~IR~~~~~~~~~~~~~  939 (1002)
                      .|||||||++.++..+..+|++.||.|..|.+|.+|++.+..+.||+||+|+.||+|||+++++.+|..           
T Consensus         2 ~rILiVDDd~~~~~~l~~~L~~~g~~v~~a~~~~~a~~~~~~~~~dliilD~~mp~~~g~~~~~~~~~~-----------   70 (120)
T d1zgza1           2 HHIVIVEDEPVTQARLQSYFTQEGYTVSVTASGAGLREIMQNQSVDLILLDINLPDENGLMLTRALRER-----------   70 (120)
T ss_dssp             CEEEEECSSHHHHHHHHHHHHHTTCEEEEESSHHHHHHHHHHSCCSEEEEESCCSSSCHHHHHHHHHTT-----------
T ss_pred             CEEEEEeCCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHHHhcCCCEEeeehhhccchhHHHHHHHhcc-----------
Confidence            489999999999999999999999999999999999999999999999999999999999999999852           


Q ss_pred             hhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHHhhc
Q 039716          940 AGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQYF 1001 (1002)
Q Consensus       940 ~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~~l 1001 (1002)
                                      +.+|||++|++.+.+...+|+++|++|||+|||++++|...|++.+
T Consensus        71 ----------------~~~piI~lt~~~~~~~~~~a~~~Ga~dyl~KP~~~~~L~~~i~~~l  116 (120)
T d1zgza1          71 ----------------STVGIILVTGRSDRIDRIVGLEMGADDYVTKPLELRELVVRVKNLL  116 (120)
T ss_dssp             ----------------CCCEEEEEESSCCHHHHHHHHHHTCSEEEESSCCHHHHHHHHHHHH
T ss_pred             ----------------CCCeEEEEEccCCHHHHHHHHHCCCCEEEECCCCHHHHHHHHHHHH
Confidence                            4589999999999999999999999999999999999999988764

>d1k66a_ c.23.1.1 (A:) Response regulator for cyanobacterial phytochrome {Calothrix sp. pcc 7601, RcpB [TaxId: 1188]}

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: Response regulator for cyanobacterial phytochrome
species: Calothrix sp. pcc 7601, RcpB [TaxId: 1188]

Probab=99.89  E-value=4.1e-23  Score=202.83  Aligned_cols=119  Identities=24%  Similarity=0.450  Sum_probs=108.6

Q ss_pred             CCeEEEEecCHHHHHHHHHHHHhcCC--eEEEEcCHHHHHHHHHcC----------CCcEEEEcCCCCCCCHHHHHHHHh
Q 039716          859 KPKILLVEDNKINVMVAKSMMKQLGH--SIDVVNNGVEAVHAVQCQ----------NYDLILMDVCMPVMDGLKATRLIR  926 (1002)
Q Consensus       859 ~~~ILiVeDn~~n~~~l~~~L~~~g~--~v~~a~~G~eAl~~~~~~----------~~DlIlmDi~MP~mdG~e~~~~IR  926 (1002)
                      ..+||||||++.++.+++.+|++.|+  .|..|.||.+|++.++..          .||+||+|++||+|||++++++||
T Consensus         6 ~~~ILiVDD~~~~~~~l~~~L~~~g~~~~v~~a~~g~eAl~~l~~~~~~~~~~~~~~pdlillD~~mP~~~G~el~~~ir   85 (149)
T d1k66a_           6 TQPLLVVEDSDEDFSTFQRLLQREGVVNPIYRCITGDQALDFLYQTGSYCNPDIAPRPAVILLDLNLPGTDGREVLQEIK   85 (149)
T ss_dssp             TSCEEEECCCHHHHHHHHHHHHHTTBCSCEEEECSHHHHHHHHHTCCSSSCGGGCCCCSEEEECSCCSSSCHHHHHHHHT
T ss_pred             CCcEEEEECCHHHHHHHHHHHHHcCCceEEEEECChHHHHHHHHhhccccccccccCCCeEEccccccCCCcHHHHHHHH
Confidence            44799999999999999999999997  789999999999999753          699999999999999999999999


Q ss_pred             ccccCCCchhhhhhhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHHhhc
Q 039716          927 SFEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQYF 1001 (1002)
Q Consensus       927 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~~l 1001 (1002)
                      +..                        ..+++|||++|+..+.+...+|+++|+++||.||++..+|...|++++
T Consensus        86 ~~~------------------------~~~~ipiI~lT~~~~~~~~~~~~~~Ga~~~l~KP~~~~~L~~~i~~~l  136 (149)
T d1k66a_          86 QDE------------------------VLKKIPVVIMTTSSNPKDIEICYSYSISSYIVKPLEIDRLTETVQTFI  136 (149)
T ss_dssp             TST------------------------TGGGSCEEEEESCCCHHHHHHHHHTTCSEEEECCSSHHHHHHHHHHHH
T ss_pred             hcc------------------------ccCCCeEEEEeCCCCHHHHHHHHHCCCCEEEECCCCHHHHHHHHHHHH
Confidence            743                        346799999999999999999999999999999999999988887653

>d1yioa2 c.23.1.1 (A:3-130) Response regulatory protein StyR, N-terminal domain {Pseudomonas fluorescens [TaxId: 294]}

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: Response regulatory protein StyR, N-terminal domain
species: Pseudomonas fluorescens [TaxId: 294]

Probab=99.89  E-value=2e-23  Score=199.81  Aligned_cols=117  Identities=20%  Similarity=0.344  Sum_probs=110.8

Q ss_pred             CCeEEEEecCHHHHHHHHHHHHhcCCeEEEEcCHHHHHHHHHcCCCcEEEEcCCCCCCCHHHHHHHHhccccCCCchhhh
Q 039716          859 KPKILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDAAA  938 (1002)
Q Consensus       859 ~~~ILiVeDn~~n~~~l~~~L~~~g~~v~~a~~G~eAl~~~~~~~~DlIlmDi~MP~mdG~e~~~~IR~~~~~~~~~~~~  938 (1002)
                      +|+|||||||+.++..+..+|++.||.|.++.||.+|++.+....||+||+|++||+|||+++++.+|..          
T Consensus         2 kP~ILiVDDd~~~~~~l~~~L~~~g~~v~~a~~~~~al~~~~~~~~dliilD~~mp~~~G~~~~~~i~~~----------   71 (128)
T d1yioa2           2 KPTVFVVDDDMSVREGLRNLLRSAGFEVETFDCASTFLEHRRPEQHGCLVLDMRMPGMSGIELQEQLTAI----------   71 (128)
T ss_dssp             CCEEEEECSCHHHHHHHHHHHHTTTCEEEEESSHHHHHHHCCTTSCEEEEEESCCSSSCHHHHHHHHHHT----------
T ss_pred             CCEEEEEECCHHHHHHHHHHHHHcCCCccccccHHHHHHHHHhcCCCEeehhhhcccchhHHHHHHHHhh----------
Confidence            4699999999999999999999999999999999999999999999999999999999999999999973          


Q ss_pred             hhhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHHhhc
Q 039716          939 EAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQYF 1001 (1002)
Q Consensus       939 ~~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~~l 1001 (1002)
                                      .+.+|||++|++.+.+...+|+++|+++||+|||+.++|...|++.+
T Consensus        72 ----------------~~~~~ii~lt~~~~~~~~~~a~~~Ga~dyl~KP~~~~~L~~~i~~~l  118 (128)
T d1yioa2          72 ----------------SDGIPIVFITAHGDIPMTVRAMKAGAIEFLPKPFEEQALLDAIEQGL  118 (128)
T ss_dssp             ----------------TCCCCEEEEESCTTSCCCHHHHHTTEEEEEESSCCHHHHHHHHHHHH
T ss_pred             ----------------CCCCeEEEEEEECCHHHHHHHHHCCCCEEEECCCCHHHHHHHHHHHH
Confidence                            35689999999999999999999999999999999999999998764

>d1k68a_ c.23.1.1 (A:) Response regulator for cyanobacterial phytochrome {Calothrix sp. pcc 7601, RcpA [TaxId: 1188]}

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: Response regulator for cyanobacterial phytochrome
species: Calothrix sp. pcc 7601, RcpA [TaxId: 1188]

Probab=99.89  E-value=6.3e-23  Score=199.32  Aligned_cols=117  Identities=25%  Similarity=0.439  Sum_probs=106.9

Q ss_pred             CeEEEEecCHHHHHHHHHHHHhcC--CeEEEEcCHHHHHHHHHc-------CCCcEEEEcCCCCCCCHHHHHHHHhcccc
Q 039716          860 PKILLVEDNKINVMVAKSMMKQLG--HSIDVVNNGVEAVHAVQC-------QNYDLILMDVCMPVMDGLKATRLIRSFED  930 (1002)
Q Consensus       860 ~~ILiVeDn~~n~~~l~~~L~~~g--~~v~~a~~G~eAl~~~~~-------~~~DlIlmDi~MP~mdG~e~~~~IR~~~~  930 (1002)
                      .|||||||++.++.+++.+|++.|  |.|..|.||.+|++.++.       ..||+||+|++||+|||++++++||+.. 
T Consensus         3 krILiVDD~~~~~~~l~~~L~~~g~~~~v~~a~~g~eAl~~l~~~~~~~~~~~pdlillD~~mP~~dG~el~~~ir~~~-   81 (140)
T d1k68a_           3 KKIFLVEDNKADIRLIQEALANSTVPHEVVTVRDGMEAMAYLRQEGEYANASRPDLILLDLNLPKKDGREVLAEIKSDP-   81 (140)
T ss_dssp             CEEEEECCCHHHHHHHHHHHHTCSSCCEEEEECSHHHHHHHHTTCGGGGSCCCCSEEEECSSCSSSCHHHHHHHHHHST-
T ss_pred             CcEEEEECCHHHHHHHHHHHHHcCCCeEEEEECCHHHHHHHHHHhHHhhccCCCCEEEEeeccccccChHHHHHHHhCc-
Confidence            489999999999999999999876  689999999999999864       4699999999999999999999999743 


Q ss_pred             CCCchhhhhhhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHHhh
Q 039716          931 TGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQY 1000 (1002)
Q Consensus       931 ~~~~~~~~~~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~~ 1000 (1002)
                                             ..+++|||++|++.+.+...+|+++|+++||+||++.++|...|+++
T Consensus        82 -----------------------~~~~iPvI~ls~~~~~~~~~~a~~~Ga~~yl~KP~~~~~L~~~i~~i  128 (140)
T d1k68a_          82 -----------------------TLKRIPVVVLSTSINEDDIFHSYDLHVNCYITKSANLSQLFQIVKGI  128 (140)
T ss_dssp             -----------------------TGGGSCEEEEESCCCHHHHHHHHHTTCSEEEECCSSHHHHHHHHHHH
T ss_pred             -----------------------ccCCCcEEEEeCCCCHHHHHHHHHCCCCEEEECCCCHHHHHHHHHHH
Confidence                                   34679999999999999999999999999999999999998888763

>d1i3ca_ c.23.1.1 (A:) Response regulator for cyanobacterial phytochrome {Synechocystis sp. PCC 6803, RCP1 [TaxId: 1148]}

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: Response regulator for cyanobacterial phytochrome
species: Synechocystis sp. PCC 6803, RCP1 [TaxId: 1148]

Probab=99.88  E-value=1.2e-22  Score=198.29  Aligned_cols=117  Identities=24%  Similarity=0.423  Sum_probs=106.7

Q ss_pred             CeEEEEecCHHHHHHHHHHHHhcC--CeEEEEcCHHHHHHHHHcC-------CCcEEEEcCCCCCCCHHHHHHHHhcccc
Q 039716          860 PKILLVEDNKINVMVAKSMMKQLG--HSIDVVNNGVEAVHAVQCQ-------NYDLILMDVCMPVMDGLKATRLIRSFED  930 (1002)
Q Consensus       860 ~~ILiVeDn~~n~~~l~~~L~~~g--~~v~~a~~G~eAl~~~~~~-------~~DlIlmDi~MP~mdG~e~~~~IR~~~~  930 (1002)
                      .+||||||++.++.+++.+|++.|  +.|.+|.||.+|++.++..       .||+||+|++||+|||++++++||+.. 
T Consensus         4 k~ILiVdD~~~~~~~l~~~L~~~g~~~~v~~a~~g~~Al~~l~~~~~~~~~~~pdlIllD~~mP~~~G~el~~~ir~~~-   82 (144)
T d1i3ca_           4 KVILLVEDSKADSRLVQEVLKTSTIDHELIILRDGLAAMAFLQQQGEYENSPRPNLILLDLNLPKKDGREVLAEIKQNP-   82 (144)
T ss_dssp             EEEEEECCCHHHHHHHHHHHHSCCSCEEEEEECSHHHHHHHHTTCGGGTTCCCCSEEEECSCCSSSCHHHHHHHHHHCT-
T ss_pred             CEEEEEECCHHHHHHHHHHHHHcCCCeEEEEECCHHHHHHHHHhchhhhccCCCCEEEEECccccccchHHHHHHHhCc-
Confidence            489999999999999999999877  4788999999999999753       599999999999999999999999743 


Q ss_pred             CCCchhhhhhhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHHhh
Q 039716          931 TGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQY 1000 (1002)
Q Consensus       931 ~~~~~~~~~~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~~ 1000 (1002)
                                             ..+++|||++|++.+.+...+|+++|+++||+||++.++|...|+++
T Consensus        83 -----------------------~~~~iPvi~lT~~~~~~~~~~a~~~Ga~~yl~KP~~~~~L~~~i~~l  129 (144)
T d1i3ca_          83 -----------------------DLKRIPVVVLTTSHNEDDVIASYELHVNCYLTKSRNLKDLFKMVQGI  129 (144)
T ss_dssp             -----------------------TTTTSCEEEEESCCCHHHHHHHHHTTCSEEEECCSSHHHHHHHHHHH
T ss_pred             -----------------------ccCCCeEEEEECCCCHHHHHHHHHCCCCEEEECCCCHHHHHHHHHHH
Confidence                                   34679999999999999999999999999999999999998888654

>d1s8na_ c.23.1.1 (A:) Probable two-component system transcriptional regulator Rv1626 {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: Probable two-component system transcriptional regulator Rv1626
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=99.88  E-value=3.2e-23  Score=212.30  Aligned_cols=114  Identities=29%  Similarity=0.431  Sum_probs=107.5

Q ss_pred             CeEEEEecCHHHHHHHHHHHHhcCCeE-EEEcCHHHHHHHHHcCCCcEEEEcCCCCCCCHHHHHHHHhccccCCCchhhh
Q 039716          860 PKILLVEDNKINVMVAKSMMKQLGHSI-DVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDAAA  938 (1002)
Q Consensus       860 ~~ILiVeDn~~n~~~l~~~L~~~g~~v-~~a~~G~eAl~~~~~~~~DlIlmDi~MP~mdG~e~~~~IR~~~~~~~~~~~~  938 (1002)
                      .|||||||++.++..++.+|++.||.| ..|.||.+|++.+....|||||||++||+|||++++++||+.          
T Consensus         4 ~kILiVDD~~~~r~~l~~~L~~~g~~vv~~a~~g~eal~~~~~~~pDlvllDi~mP~~dG~e~~~~ir~~----------   73 (190)
T d1s8na_           4 RRVLIAEDEALIRMDLAEMLREEGYEIVGEAGDGQEAVELAELHKPDLVIMDVKMPRRDGIDAASEIASK----------   73 (190)
T ss_dssp             CEEEEECSSHHHHHHHHHHHHHTTCEEEEEESSHHHHHHHHHHHCCSEEEEESSCSSSCHHHHHHHHHHT----------
T ss_pred             CEEEEEeCCHHHHHHHHHHHHHCCCEEEEEECCHHHHHHHHhcCCCCEEEEeccccCcchHHHHHHHHhc----------
Confidence            489999999999999999999999986 489999999999999999999999999999999999999962          


Q ss_pred             hhhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHHhh
Q 039716          939 EAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQY 1000 (1002)
Q Consensus       939 ~~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~~ 1000 (1002)
                                       +++|||++|++.+.+...+|+++||+|||+||+++++|..+|...
T Consensus        74 -----------------~~~pIi~lTa~~~~~~~~~al~~Ga~~yl~KP~~~~~L~~~i~~~  118 (190)
T d1s8na_          74 -----------------RIAPIVVLTAFSQRDLVERARDAGAMAYLVKPFSISDLIPAIELA  118 (190)
T ss_dssp             -----------------TCSCEEEEEEGGGHHHHHTTGGGSCEEEEEESCCHHHHHHHHHHH
T ss_pred             -----------------CCCCEEEEeCCCCHHHHHHHHHcCCCEeccCCCCHHHHHHHHHHH
Confidence                             348999999999999999999999999999999999999998754

>d1dz3a_ c.23.1.1 (A:) Sporulation response regulator Spo0A {Bacillus stearothermophilus [TaxId: 1422]}

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: Sporulation response regulator Spo0A
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=99.88  E-value=7.3e-23  Score=194.36  Aligned_cols=117  Identities=22%  Similarity=0.361  Sum_probs=106.5

Q ss_pred             CeEEEEecCHHHHHHHHHHHHhcC-C-eEEEEcCHHHHHHHHHcCCCcEEEEcCCCCCCCHHHHHHHHhccccCCCchhh
Q 039716          860 PKILLVEDNKINVMVAKSMMKQLG-H-SIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDAA  937 (1002)
Q Consensus       860 ~~ILiVeDn~~n~~~l~~~L~~~g-~-~v~~a~~G~eAl~~~~~~~~DlIlmDi~MP~mdG~e~~~~IR~~~~~~~~~~~  937 (1002)
                      .|||||||++.++..++.+|+..| + .|..|.||.+|++.++...||+||+|+.||+|||++++++||+..        
T Consensus         2 irILivDD~~~~~~~l~~~L~~~~~~~~v~~a~~g~~al~~~~~~~~dlillD~~mP~~dG~e~~~~ir~~~--------   73 (123)
T d1dz3a_           2 IKVCIADDNRELVSLLDEYISSQPDMEVIGTAYNGQDCLQMLEEKRPDILLLDIIMPHLDGLAVLERIRAGF--------   73 (123)
T ss_dssp             EEEEEECSCHHHHHHHHHHHHTSTTEEEEEEESSHHHHHHHHHHHCCSEEEEESCCSSSCHHHHHHHHHHHC--------
T ss_pred             cEEEEEeCCHHHHHHHHHHHHhCCCcEEEEEECCHHHHHHHHHhcCCCEEEEcCCCCCCCHHHHHHHHHhcC--------
Confidence            489999999999999999999876 3 366899999999999999999999999999999999999999632        


Q ss_pred             hhhhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHHhhc
Q 039716          938 AEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQYF 1001 (1002)
Q Consensus       938 ~~~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~~l 1001 (1002)
                                       ...+|||++|++...+...+|+++|+++||.|||+.++|...|++++
T Consensus        74 -----------------~~~~~ii~~t~~~~~~~~~~a~~~Ga~~~l~KP~~~~~L~~~i~~v~  120 (123)
T d1dz3a_          74 -----------------EHQPNVIMLTAFGQEDVTKKAVELGASYFILKPFDMENLAHHIRQVY  120 (123)
T ss_dssp             -----------------SSCCEEEEEEETTCHHHHHHHHHTTCEEEEECSSCCTTHHHHHHHHH
T ss_pred             -----------------CCCCeEEEEECcCCHHHHHHHHHCCCCEEEECCCCHHHHHHHHHHHH
Confidence                             12357999999999999999999999999999999999999998865

>d1w25a2 c.23.1.1 (A:141-293) Response regulator PleD, receiver domain {Caulobacter crescentus [TaxId: 155892]}

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: Response regulator PleD, receiver domain
species: Caulobacter crescentus [TaxId: 155892]

Probab=99.87  E-value=2.3e-22  Score=198.17  Aligned_cols=118  Identities=19%  Similarity=0.316  Sum_probs=107.0

Q ss_pred             CCCeEEEEecCHHHHHHHHHHHHhcCCeEEEEcCHHHHHHHHHcCCCcEEEEcCCCCCCCHHHHHHHHhccccCCCchhh
Q 039716          858 PKPKILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDAA  937 (1002)
Q Consensus       858 ~~~~ILiVeDn~~n~~~l~~~L~~~g~~v~~a~~G~eAl~~~~~~~~DlIlmDi~MP~mdG~e~~~~IR~~~~~~~~~~~  937 (1002)
                      .+.|||||||++.++..+..+|+..||.|  +.+|.+|+..+....|||||+|++||+|||+++++.||+.+        
T Consensus        12 ~~~rILiVDD~~~~~~~l~~~L~~~g~~v--~~~~~~~~~~~~~~~~DlillD~~mP~~dG~el~~~ir~~~--------   81 (153)
T d1w25a2          12 LGGRVLIVDDNERQAQRVAAELGVEHRPV--IESDPEKAKISAGGPVDLVIVNAAAKNFDGLRFTAALRSEE--------   81 (153)
T ss_dssp             CSCEEEEECSCHHHHHHHHHHHTTTSEEE--EECCHHHHHHHHHSSCSEEEEETTCSSSCHHHHHHHHHTSG--------
T ss_pred             CCCeEEEEeCCHHHHHHHHHHHHHCCCEE--EEccHHHHHHHhcCCCCEEEEECccccccchHHHHHHHhcc--------
Confidence            46799999999999999999999999876  45677888888999999999999999999999999999743        


Q ss_pred             hhhhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHHhhc
Q 039716          938 AEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQYF 1001 (1002)
Q Consensus       938 ~~~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~~l 1001 (1002)
                                      ..+++|||++|++.+.+...+|+++|++|||+|||+..+|...|+.++
T Consensus        82 ----------------~~~~iPiI~lt~~~~~~~~~~a~~~Ga~d~l~KP~~~~~L~~~i~~~l  129 (153)
T d1w25a2          82 ----------------RTRQLPVLAMVDPDDRGRMVKALEIGVNDILSRPIDPQELSARVKTQI  129 (153)
T ss_dssp             ----------------GGTTCCEEEEECTTCHHHHHHHHHTTCCEEEESSCCHHHHHHHHHHHH
T ss_pred             ----------------ccccceeEEeecCCCHHHHHHHHhcCcceEEECCCCHHHHHHHHHHHH
Confidence                            246799999999999999999999999999999999999998887653

>d1p2fa2 c.23.1.1 (A:1-120) Response regulator DrrB {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: Response regulator DrrB
species: Thermotoga maritima [TaxId: 2336]

Probab=99.87  E-value=1.8e-22  Score=190.78  Aligned_cols=113  Identities=23%  Similarity=0.387  Sum_probs=104.8

Q ss_pred             CeEEEEecCHHHHHHHHHHHHhcCCeEEEEcCHHHHHHHHHcCCCcEEEEcCCCCCCCHHHHHHHHhccccCCCchhhhh
Q 039716          860 PKILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDAAAE  939 (1002)
Q Consensus       860 ~~ILiVeDn~~n~~~l~~~L~~~g~~v~~a~~G~eAl~~~~~~~~DlIlmDi~MP~mdG~e~~~~IR~~~~~~~~~~~~~  939 (1002)
                      .|||||||++.++..++.+|++.|+ +.++.+|.+|++  ....||+||+|+.||+|||+++++.+|..           
T Consensus         3 ~kILiVDDd~~~~~~l~~~L~~~g~-v~~~~~~~~al~--~~~~~dlillD~~mP~~~G~~~~~~lr~~-----------   68 (120)
T d1p2fa2           3 WKIAVVDDDKNILKKVSEKLQQLGR-VKTFLTGEDFLN--DEEAFHVVVLDVMLPDYSGYEICRMIKET-----------   68 (120)
T ss_dssp             EEEEEECSCHHHHHHHHHHHTTTEE-EEEESSHHHHHH--CCSCCSEEEEESBCSSSBHHHHHHHHHHH-----------
T ss_pred             CEEEEEECCHHHHHHHHHHHHhCCE-EEEECCHHHHHh--cCCCCCEEEEeCcccccchhHHHHHHhhc-----------
Confidence            4899999999999999999999986 889999999987  45679999999999999999999999963           


Q ss_pred             hhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHHhhc
Q 039716          940 AGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQYF 1001 (1002)
Q Consensus       940 ~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~~l 1001 (1002)
                                     .+.+|||++|+..+.+...+|+++|++|||.|||+.++|...|++++
T Consensus        69 ---------------~~~~~ii~it~~~~~~~~~~a~~~Ga~dyl~KP~~~~~L~~~i~~~l  115 (120)
T d1p2fa2          69 ---------------RPETWVILLTLLSDDESVLKGFEAGADDYVTKPFNPEILLARVKRFL  115 (120)
T ss_dssp             ---------------CTTSEEEEEESCCSHHHHHHHHHHTCSEEEESSCCHHHHHHHHHHHH
T ss_pred             ---------------CCCCcEEEEecCCCHHHHHHHHHCCCCEEEECCCCHHHHHHHHHHHH
Confidence                           25689999999999999999999999999999999999999998865

>d1a04a2 c.23.1.1 (A:5-142) Nitrate/nitrite response regulator (NarL), receiver domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: Nitrate/nitrite response regulator (NarL), receiver domain
species: Escherichia coli [TaxId: 562]

Probab=99.86  E-value=1.1e-21  Score=190.21  Aligned_cols=115  Identities=23%  Similarity=0.344  Sum_probs=107.4

Q ss_pred             CeEEEEecCHHHHHHHHHHHHhcC--CeEEEEcCHHHHHHHHHcCCCcEEEEcCCCCCCCHHHHHHHHhccccCCCchhh
Q 039716          860 PKILLVEDNKINVMVAKSMMKQLG--HSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDAA  937 (1002)
Q Consensus       860 ~~ILiVeDn~~n~~~l~~~L~~~g--~~v~~a~~G~eAl~~~~~~~~DlIlmDi~MP~mdG~e~~~~IR~~~~~~~~~~~  937 (1002)
                      .+||||||++.++..++.+|+..|  +.|..|.||.+|++.+...+||+||+|++||+|||++++++||+.         
T Consensus         3 i~VLiVDD~~~~r~~l~~~L~~~~~~~~v~~a~~~~~al~~~~~~~~DlvllD~~mP~~~G~el~~~ir~~---------   73 (138)
T d1a04a2           3 ATILLIDDHPMLRTGVKQLISMAPDITVVGEASNGEQGIELAESLDPDLILLDLNMPGMNGLETLDKLREK---------   73 (138)
T ss_dssp             EEEEEECSCHHHHHHHHHHHTTCTTEEEEEEESSHHHHHHHHHHHCCSEEEEETTSTTSCHHHHHHHHHHS---------
T ss_pred             CEEEEECCCHHHHHHHHHHHHhCCCcEEEEEECCHHHHHHHHHhcCCCEEEEecCCCCCCHHHHHHHHHhh---------
Confidence            489999999999999999999877  457789999999999999999999999999999999999999963         


Q ss_pred             hhhhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHHhh
Q 039716          938 AEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQY 1000 (1002)
Q Consensus       938 ~~~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~~ 1000 (1002)
                                       .+.+|||++|++.+.+...+|+++|+++||.||++.++|..+|++.
T Consensus        74 -----------------~~~~~vivlt~~~~~~~~~~a~~~Ga~~yl~Kp~~~~~L~~~i~~v  119 (138)
T d1a04a2          74 -----------------SLSGRIVVFSVSNHEEDVVTALKRGADGYLLKDMEPEDLLKALHQA  119 (138)
T ss_dssp             -----------------CCCSEEEEEECCCCHHHHHHHHHTTCSEEEETTCCHHHHHHHHHHH
T ss_pred             -----------------CCCCCEEEEEEECCHHHHHHHHHcCCCEEEECCCCHHHHHHHHHHH
Confidence                             3578999999999999999999999999999999999999999874

>d2b4aa1 c.23.1.1 (A:2-119) Hypothetical protein BH3024 {Bacillus halodurans [TaxId: 86665]}

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: Hypothetical protein BH3024
species: Bacillus halodurans [TaxId: 86665]

Probab=99.85  E-value=1e-21  Score=184.85  Aligned_cols=115  Identities=17%  Similarity=0.278  Sum_probs=101.4

Q ss_pred             CCeEEEEecCHHHHHHHHHHHHhcCCeEEEEcCHHHHHHHHHc-CCCcEEEEcCCCCCCCHHHHHHHHhccccCCCchhh
Q 039716          859 KPKILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQC-QNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDAA  937 (1002)
Q Consensus       859 ~~~ILiVeDn~~n~~~l~~~L~~~g~~v~~a~~G~eAl~~~~~-~~~DlIlmDi~MP~mdG~e~~~~IR~~~~~~~~~~~  937 (1002)
                      ..|||||||++..+..+..+|+..||.|.++.||.+|++.+.+ ..||+||+|+.||+|||+++++.||+.         
T Consensus         2 p~rILvVdDd~~~~~~l~~~L~~~g~~v~~~~~~~~al~~l~~~~~~dliilD~~lp~~~G~el~~~ir~~---------   72 (118)
T d2b4aa1           2 PFRVTLVEDEPSHATLIQYHLNQLGAEVTVHPSGSAFFQHRSQLSTCDLLIVSDQLVDLSIFSLLDIVKEQ---------   72 (118)
T ss_dssp             CCEEEEECSCHHHHHHHHHHHHHTTCEEEEESSHHHHHHTGGGGGSCSEEEEETTCTTSCHHHHHHHHTTS---------
T ss_pred             CCEEEEEECCHHHHHHHHHHHHhcCCCeEEECCHHHHHHHHHhcCCCCEEEEeCCCCCCCHHHHHHHHHhc---------
Confidence            3589999999999999999999999999999999999998754 579999999999999999999999962         


Q ss_pred             hhhhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHHhhcC
Q 039716          938 AEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQYFP 1002 (1002)
Q Consensus       938 ~~~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~~l~ 1002 (1002)
                                       .+++|||++|+....  ..++...|+ |||+|||++++|...|+++.|
T Consensus        73 -----------------~~~~pii~lt~~~~~--~~~~~~~~~-dyl~KP~~~~eL~~~i~~~~p  117 (118)
T d2b4aa1          73 -----------------TKQPSVLILTTGRHE--LIESSEHNL-SYLQKPFAISELRAAIDYHKP  117 (118)
T ss_dssp             -----------------SSCCEEEEEESCC----CCCCSSSCE-EEEESSCCHHHHHHHHHHTCC
T ss_pred             -----------------CCCCcEEEEECCccH--HHHHhhcCC-CEEECCCCHHHHHHHHHHHCc
Confidence                             356999999997654  345666777 899999999999999999876

>d1a2oa1 c.23.1.1 (A:1-140) Methylesterase CheB, N-terminal domain {Salmonella typhimurium [TaxId: 90371]}

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: Methylesterase CheB, N-terminal domain
species: Salmonella typhimurium [TaxId: 90371]

Probab=99.81  E-value=5.1e-20  Score=178.62  Aligned_cols=105  Identities=21%  Similarity=0.283  Sum_probs=89.5

Q ss_pred             CCeEEEEecCHHHHHHHHHHHHhcC--CeEEEEcCHHHHHHHHHcCCCcEEEEcCCCCCCCHHHHHHHHhccccCCCchh
Q 039716          859 KPKILLVEDNKINVMVAKSMMKQLG--HSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDA  936 (1002)
Q Consensus       859 ~~~ILiVeDn~~n~~~l~~~L~~~g--~~v~~a~~G~eAl~~~~~~~~DlIlmDi~MP~mdG~e~~~~IR~~~~~~~~~~  936 (1002)
                      +.|||||||++.++..++.+|++.|  +.|.+|.||.+|++.+..+.||+||+|++||+|||+++++.||+..       
T Consensus         3 kirVLiVDD~~~~r~~l~~~L~~~g~~~~v~~a~~g~~al~~~~~~~pDlvllDi~MP~~dG~e~~~~ir~~~-------   75 (140)
T d1a2oa1           3 KIRVLSVDDSALMRQIMTEIINSHSDMEMVATAPDPLVARDLIKKFNPDVLTLDVEMPRMDGLDFLEKLMRLR-------   75 (140)
T ss_dssp             CEEEEEECSCHHHHHHHHHHHHTSTTEEEEEEESSHHHHHHHHHHHCCSEEEEECCCSSSCHHHHHHHHHHSS-------
T ss_pred             CCEEEEEeCCHHHHHHHHHHHHhCCCeEEEEEECCHHHHHHHHHhcCCCEEEEcCCCCCCCHHHHHHHHHHhC-------
Confidence            4689999999999999999999998  4577899999999999999999999999999999999999999742       


Q ss_pred             hhhhhhcccCCCCCCCCCCCCccEEEEcCCC-CHHHHHHHHHcCCCEEEeCCCC
Q 039716          937 AAEAGIEQAMPSSGSSNHFKRIPIIAMTANA-LSESAEECFANGMDSFVSKPVT  989 (1002)
Q Consensus       937 ~~~~~~~~~~~~~~~~~~~~~ipIIalTa~~-~~~~~~~~~~aG~d~~l~KP~~  989 (1002)
                                         +..+|+++|... ..+...+|+++|+++||.||+.
T Consensus        76 -------------------~~~~i~i~~~~~~~~~~~~~al~~Ga~~yl~KP~~  110 (140)
T d1a2oa1          76 -------------------PMPVVMVSSLTGKGSEVTLRALELGAIDFVTKPQL  110 (140)
T ss_dssp             -------------------CCCEEEEECCTHHHHHHHHHHHHHTCCEEEECSSS
T ss_pred             -------------------CCCcEEEEEecCCChHHHHHHHHcCCCEEEECCCC
Confidence                               233455555443 2356778999999999999974

>d1qo0d_ c.23.1.3 (D:) Positive regulator of the amidase operon AmiR {Pseudomonas aeruginosa [TaxId: 287]}

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: Positive regulator of the amidase operon AmiR
domain: Positive regulator of the amidase operon AmiR
species: Pseudomonas aeruginosa [TaxId: 287]

Probab=99.77  E-value=2.3e-19  Score=182.89  Aligned_cols=112  Identities=11%  Similarity=0.098  Sum_probs=102.4

Q ss_pred             CCCeEEEEecCHHHHHHHHHHHHhcCCeEEEEcCHHHHHHHHHcCCCcEEEEcCCCCCCCHHHHHHHHhccccCCCchhh
Q 039716          858 PKPKILLVEDNKINVMVAKSMMKQLGHSIDVVNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKATRLIRSFEDTGNWDAA  937 (1002)
Q Consensus       858 ~~~~ILiVeDn~~n~~~l~~~L~~~g~~v~~a~~G~eAl~~~~~~~~DlIlmDi~MP~mdG~e~~~~IR~~~~~~~~~~~  937 (1002)
                      ...+||||||++.++..+..+|++.||.|..|.+|.+|++    ..||+||||++||+|+|+.+.+.++.          
T Consensus        10 ~~~~iLvvdd~~~~~~~l~~~L~~~G~~v~~~~~~~~al~----~~~Dlvl~D~~mp~~~~~~~~~~~~~----------   75 (189)
T d1qo0d_          10 RELQVLVLNPPGEVSDALVLQLIRIGCSVRQCWPPPEAFD----VPVDVVFTSIFQNRHHDEIAALLAAG----------   75 (189)
T ss_dssp             GGCEEEEESCTTHHHHHHHHHHHHHTCEEEEECSCCSSCS----SCCSEEEEECCSSTHHHHHHHHHHHS----------
T ss_pred             cCCEEEEEeCCHHHHHHHHHHHHHcCCcceecCCHHHhcc----CCCCEEEEcCCCCCcHHHHHHHHHHc----------
Confidence            4569999999999999999999999999999999999984    58999999999999999877766553          


Q ss_pred             hhhhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEeCCCChHHHHHHHHhh
Q 039716          938 AEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVSKPVTFQKLKECLEQY 1000 (1002)
Q Consensus       938 ~~~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~~ 1000 (1002)
                                       .+++|||++|++.+.+...+|+++|+++||.|||+.++|...|...
T Consensus        76 -----------------~p~~pvI~lta~~~~~~~~~al~~Ga~~yL~KP~~~~~L~~~i~~~  121 (189)
T d1qo0d_          76 -----------------TPRTTLVALVEYESPAVLSQIIELECHGVITQPLDAHRVLPVLVSA  121 (189)
T ss_dssp             -----------------CTTCEEEEEECCCSHHHHHHHHHHTCSEEEESSCCGGGHHHHHHHH
T ss_pred             -----------------CCCCCEEEEeccchHHHHHHHHHcCCcEEEEecchhhHHHHHHhhc
Confidence                             3679999999999999999999999999999999999999988754

>d1ixma_ d.123.1.1 (A:) Sporulation response regulatory protein Spo0B {Bacillus subtilis [TaxId: 1423]}

class: Alpha and beta proteins (a+b)
fold: Sporulation response regulatory protein Spo0B
superfamily: Sporulation response regulatory protein Spo0B
family: Sporulation response regulatory protein Spo0B
domain: Sporulation response regulatory protein Spo0B
species: Bacillus subtilis [TaxId: 1423]

Probab=99.70  E-value=6.1e-18  Score=168.58  Aligned_cols=163  Identities=9%  Similarity=0.026  Sum_probs=88.4

Q ss_pred             HHHHHHhhhccccHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCeeeEeeecCHHHHHH
Q 039716          371 KQMLATMSHEIRSPLTGVVSMAEILSNTKLDREQRQLLGVMISSGDLVLQLINDILDLSKVESGVMKLEAAKFRPREVVK  450 (1002)
Q Consensus       371 k~fla~iSHELRTPL~~I~g~~elL~~~~l~~~~~~~l~~i~~s~~~L~~LIndlLd~skiesg~~~l~~~~~~l~~li~  450 (1002)
                      .+|++.+|||+||||++|.|++++...    .+..+++..+.....+...+++       .            ....+. 
T Consensus        10 ~~~l~~~~Hdl~npL~~I~g~l~L~~~----~~~~~~i~~i~~~~~~~~~~~~-------~------------~~~~~~-   65 (179)
T d1ixma_          10 IHLLGHSRHDWMNKLQLIKGNLSLQKY----DRVFEMIEEMVIDAKHESKLSN-------L------------KTPHLA-   65 (179)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHTTCH----HHHHHHHHHHHHHHHHHHHHHT-------T------------TCHHHH-
T ss_pred             HHHHHHhhHhhcCHHHHHHHHHHcccc----ccchhHHHHHHHhhhccccccc-------c------------cccccc-
Confidence            369999999999999999999986321    2333344433333332222111       0            000000 


Q ss_pred             HHHHHHHHHHhhcceeccccCCCCCeeEEccHHHHHHHHHHHHhhhhhcCCC-C--eeEEEEEecCCCCcccchhhhhhh
Q 039716          451 HVLQTAAASLQKILMLEGDIADDVPIEVIGDVLRIRQILTNLISNAIKFTPE-G--KVGIKLYVVPEPPFAKEGLKQKSK  527 (1002)
Q Consensus       451 ~v~~~~~~~~~k~i~l~~~i~~~~p~~v~gD~~rL~QIL~NLlsNAIKfT~~-G--~I~I~v~~~~~~~~~~~~~~~~~~  527 (1002)
                       ............+.+........ ..+.+|+.++.|||.|||.||++|+.. |  ...|++.+..              
T Consensus        66 -~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~l~qvl~Nll~NAi~~~~~~~~~~~~I~i~~~~--------------  129 (179)
T d1ixma_          66 -FDFLTFNWKTHYMTLEYEVLGEI-KDLSAYDQKLAKLMRKLFHLFDQAVSRESENHLTVSLQTDH--------------  129 (179)
T ss_dssp             -HHHHHGGGSCCSSEEEEEEESSC-CCCTTTHHHHHHHHHHHHHHHHHHBCTTSCCEEEEEEECCC--------------
T ss_pred             -ccccchhhhcccccccccccccc-chhhhhhhhhHHHHHHHHHHHHHHhhhccccchhhhhhhcc--------------
Confidence             00001111122333333333333 346789999999999999999999854 3  2344443211              


Q ss_pred             hhhcchhhhhhhccCCCCCccCCCCCCCCCCCCCCccCCCCCCCCCCCccCCCCCccccccceEEEEEEEecCCCCCcCc
Q 039716          528 AYQSATDAVKEEKHQPKSQTASDQNGFHDKKHGEGYQDHKHDDDPGTPVSHGNSMDEDLEATVWIRCDVYDTGIGIPENA  607 (1002)
Q Consensus       528 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~i~V~DtGiGI~~e~  607 (1002)
                                                                                  ...++.|+|.|+|+||||+.
T Consensus       130 ------------------------------------------------------------~~~~~~i~v~D~G~gi~~e~  149 (179)
T d1ixma_         130 ------------------------------------------------------------PDRQLILYLDFHGAFADPSA  149 (179)
T ss_dssp             ------------------------------------------------------------SSSSCEEEEEEESCBSCGGG
T ss_pred             ------------------------------------------------------------cccEEEEEEEeCCCCcCHHH
Confidence                                                                        11247899999999999999


Q ss_pred             HhhhhhhccCCCcc----ccCcCCCccccH
Q 039716          608 LPTLFRKYMQVSAD----HARKYGGTGLGL  633 (1002)
Q Consensus       608 l~~IF~pF~q~~~~----~~~~~~GtGLGL  633 (1002)
                      +++||++||+....    .+....|+||||
T Consensus       150 l~~if~~~y~~~~~~~~~~~~~~~~~~~~~  179 (179)
T d1ixma_         150 FDDIRQNGYEDVDIMRFEITSHECLIEIGL  179 (179)
T ss_dssp             CC-----------EEEEEECSSEEEEEEEC
T ss_pred             HHHHHHhccccccceEEEeecCceeEeeCC
Confidence            99999999987532    122345777776

>d2hkja3 d.122.1.2 (A:10-228) Topoisomerase VI-B subunit {Archaeon Sulfolobus shibatae [TaxId: 2286]}

class: Alpha and beta proteins (a+b)
fold: ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
superfamily: ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
family: DNA gyrase/MutL, N-terminal domain
domain: Topoisomerase VI-B subunit
species: Archaeon Sulfolobus shibatae [TaxId: 2286]

Probab=99.65  E-value=3.3e-16  Score=162.95  Aligned_cols=73  Identities=21%  Similarity=0.341  Sum_probs=63.5

Q ss_pred             EEEEEEEecCCCCCcCcHhhhhhhccCCCccccCc-CCCccccHHHHHHHHHHhCCE-EEEEeecCCceEEEEEE
Q 039716          591 WIRCDVYDTGIGIPENALPTLFRKYMQVSADHARK-YGGTGLGLAICKQLVELMGGR-LTVTSKVHCGSTFTFIL  663 (1002)
Q Consensus       591 ~l~i~V~DtGiGI~~e~l~~IF~pF~q~~~~~~~~-~~GtGLGLaI~k~Lve~~gG~-I~v~S~~g~GTtF~~~L  663 (1002)
                      ++.|.|.|||+||++++++++|++|++.+....+. +||+||||++|+.++++|+|. |.|.|..++|++++...
T Consensus        60 ~~~i~V~DnG~Gi~~~~~~~~f~~~~~s~~~~~~~~~G~~GlGl~~~~~~s~~~~g~~i~V~S~~~~~~~~~~~~  134 (219)
T d2hkja3          60 IYKVNVVDNGIGIPPQEVPNAFGRVLYSSKYVNRQTRGMYGLGVKAAVLYSQMHQDKPIEIETSPVNSKRIYTFK  134 (219)
T ss_dssp             EEEEEEEECSCCCCGGGHHHHHHCCCSSCCCCCSCCSCSCTTTHHHHHHHHHHHCCCCEEEEEECTTCSEEEEEE
T ss_pred             EEEEEEEcCCCCCCHHHHHhhccceEeccccccccccCccCHHHHHHHHHHHHcCCcEEEEEEEecCCCcEEEEe
Confidence            57899999999999999999999999987655443 678999999999999999997 99999998888755443

>d1i58a_ d.122.1.3 (A:) Histidine kinase CheA {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a+b)
fold: ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
superfamily: ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
family: Histidine kinase
domain: Histidine kinase CheA
species: Thermotoga maritima [TaxId: 2336]

Probab=99.43  E-value=1.6e-14  Score=145.19  Aligned_cols=70  Identities=23%  Similarity=0.381  Sum_probs=62.8

Q ss_pred             EEEecCCCCCcCcHhhhhhhccCCCccccCcCCCccccHHHHHHHHHHhCCEEEEEeecCCceEEEEEEeC
Q 039716          595 DVYDTGIGIPENALPTLFRKYMQVSADHARKYGGTGLGLAICKQLVELMGGRLTVTSKVHCGSTFTFILPY  665 (1002)
Q Consensus       595 ~V~DtGiGI~~e~l~~IF~pF~q~~~~~~~~~~GtGLGLaI~k~Lve~~gG~I~v~S~~g~GTtF~~~LP~  665 (1002)
                      .+.|.|.|++++..+++|++||+... ..+.++|+||||+|||+||++|||+|+|+|++|+||||+|+||+
T Consensus       119 ~~~~~~~~~~~~~~~~~f~~~~~~~~-~~~~~~G~GLGLai~k~ive~hgG~I~v~S~~g~GT~f~i~lPl  188 (189)
T d1i58a_         119 DESKAATLSDQEILNFLFVPGFSTKE-KVSEVSGRGVGMDVVKNVVESLNGSISIESEKDKGTKVTIRLPL  188 (189)
T ss_dssp             CHHHHTTCCHHHHHGGGGSTTCSHHH-HHHGGGTCCCHHHHHHHHHHHTTCEEEEEEETTTEEEEEEEEEC
T ss_pred             eecccccchhhhhhhhhhcccccccc-ccccCCcCccCHHHHHHHHHHCCCEEEEEecCCCCEEEEEEEeC
Confidence            36688888989999999999998654 34467799999999999999999999999999999999999997

>d1th8a_ d.122.1.3 (A:) Anti-sigma factor spoIIab {Bacillus stearothermophilus [TaxId: 1422]}

class: Alpha and beta proteins (a+b)
fold: ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
superfamily: ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
family: Histidine kinase
domain: Anti-sigma factor spoIIab
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=99.41  E-value=4.1e-13  Score=129.06  Aligned_cols=62  Identities=23%  Similarity=0.453  Sum_probs=48.6

Q ss_pred             EEEEEEEecCCCCCcCcHhhhhhhccCCCccccCcCCCccccHHHHHHHHHHhCCEEEEEeecCCceEEEEE
Q 039716          591 WIRCDVYDTGIGIPENALPTLFRKYMQVSADHARKYGGTGLGLAICKQLVELMGGRLTVTSKVHCGSTFTFI  662 (1002)
Q Consensus       591 ~l~i~V~DtGiGI~~e~l~~IF~pF~q~~~~~~~~~~GtGLGLaI~k~Lve~~gG~I~v~S~~g~GTtF~~~  662 (1002)
                      ++.|.|.|+|+|||+  .+++|+||++...    ...|+||||+|+++++    |+|+++|.+|+||+|+++
T Consensus        74 ~l~i~i~D~G~gi~~--~~~~~~~~~~~~~----~~~~~GlGL~iv~~l~----d~i~i~s~~~~Gt~v~i~  135 (139)
T d1th8a_          74 VVHLTVRDEGVGIPD--IEEARQPLFTTKP----ELERSGMGFTIMENFM----DEVIVESEVNKGTTVYLK  135 (139)
T ss_dssp             EEEEEEEECSSCCSC--HHHHTCCC-----------CCCSCHHHHHHHHS----SEEEEEEETTTEEEEEEE
T ss_pred             EEEEEEccccccccc--ccccccccceecc----cCCCchHHHHHHHHhC----CEEEEEEcCCCcEEEEEE
Confidence            588999999999975  7789999987543    2347899999887754    899999999999999886

>d2c2aa1 a.30.2.1 (A:232-320) Sensor histidine kinase TM0853 {Thermotoga maritima [TaxId: 2336]}

class: All alpha proteins
fold: ROP-like
superfamily: Homodimeric domain of signal transducing histidine kinase
family: Homodimeric domain of signal transducing histidine kinase
domain: Sensor histidine kinase TM0853
species: Thermotoga maritima [TaxId: 2336]

Probab=99.41  E-value=1.6e-13  Score=121.45  Aligned_cols=66  Identities=30%  Similarity=0.542  Sum_probs=59.3

Q ss_pred             HHHHHHhhhccccHHHHHHHHHHHHhCC---CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCe
Q 039716          371 KQMLATMSHEIRSPLTGVVSMAEILSNT---KLDREQRQLLGVMISSGDLVLQLINDILDLSKVESGVM  436 (1002)
Q Consensus       371 k~fla~iSHELRTPL~~I~g~~elL~~~---~l~~~~~~~l~~i~~s~~~L~~LIndlLd~skiesg~~  436 (1002)
                      .+|++++||||||||++|.|++++|.+.   ..++.++++++.|..++.+|..+|+++|+|||+|+|++
T Consensus        21 ~~f~~~vsHeLRtPL~~I~~~~~~L~~~~~~~~~~~~~~~l~~i~~~~~rl~~li~~lLd~srle~g~l   89 (89)
T d2c2aa1          21 TEFIANISHELRTPLTAIKAYAETIYNSLGELDLSTLKEFLEVIIDQSNHLENLLNELLDFSRLERKSL   89 (89)
T ss_dssp             HHHHHHHHHHTHHHHHHHHHHHHHHHHTGGGCCTTTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCC
T ss_pred             HHHHHHhhHHHHHHHHHHHHHHHHHHhhccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCC
Confidence            4799999999999999999999998653   23456789999999999999999999999999999974

>d1y8oa2 d.122.1.4 (A:177-301) Pyruvate dehydrogenase kinase {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
superfamily: ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
family: alpha-ketoacid dehydrogenase kinase, C-terminal domain
domain: Pyruvate dehydrogenase kinase
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.22  E-value=1.9e-11  Score=114.37  Aligned_cols=60  Identities=23%  Similarity=0.212  Sum_probs=42.7

Q ss_pred             ecCHHHHHHHHHHHHHHHHhh--------cceeccccCCCCCeeEEccHHHHHHHHHHHHhhhhhcCC
Q 039716          442 KFRPREVVKHVLQTAAASLQK--------ILMLEGDIADDVPIEVIGDVLRIRQILTNLISNAIKFTP  501 (1002)
Q Consensus       442 ~~~l~~li~~v~~~~~~~~~k--------~i~l~~~i~~~~p~~v~gD~~rL~QIL~NLlsNAIKfT~  501 (1002)
                      .+++.++++++++.+......        .........++.+..+.+|+.+|.|||.|||+||+||+.
T Consensus        14 ~~~l~~iv~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~d~~~l~qvl~NLl~NAi~~~~   81 (125)
T d1y8oa2          14 TCNVADVVKDAYETAKMLCEQYYLVAPELEVEEFNAKAPDKPIQVVYVPSHLFHMLFELFKNSMRATV   81 (125)
T ss_dssp             EEEHHHHHHHHHHHHHHHHHHHHSCCCCEEEEEEETTSTTSCCEEEECHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHHHHHhhhhhhhHhhhhhheeeeCCCCCeEEeeCHHHHHHHHHHHHHHHHHhhh
Confidence            457888888887765543221        112222334556678999999999999999999999974

>d1joya_ a.30.2.1 (A:) EnvZ histidine kinase {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: ROP-like
superfamily: Homodimeric domain of signal transducing histidine kinase
family: Homodimeric domain of signal transducing histidine kinase
domain: EnvZ histidine kinase
species: Escherichia coli [TaxId: 562]

Probab=99.04  E-value=4.4e-11  Score=99.24  Aligned_cols=55  Identities=22%  Similarity=0.377  Sum_probs=49.5

Q ss_pred             HHHHHHhhhccccHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 039716          371 KQMLATMSHEIRSPLTGVVSMAEILSNTKLDREQRQLLGVMISSGDLVLQLINDILDLSK  430 (1002)
Q Consensus       371 k~fla~iSHELRTPL~~I~g~~elL~~~~l~~~~~~~l~~i~~s~~~L~~LIndlLd~sk  430 (1002)
                      ++|++++||||||||++|.|+++++.+     +..++++.|..++++|..+|+++|+|||
T Consensus        13 ~~f~~~vsHeLRTPLt~i~~~~e~l~~-----~~~~~~~~i~~~~~rm~~li~dlL~~aR   67 (67)
T d1joya_          13 TLLMAGVSHDLRTPLTRIRLATEMMSE-----QDGYLAESINKDIEECNAIIEQFIDYLR   67 (67)
T ss_dssp             HHHHTTTHHHHHHHHHHHHHHHHHHHH-----HHTHHHHHHHHHHHHHHHHHHHHHTTCC
T ss_pred             HHHHHHhhHHHHHHHHHHHHHHHHhhh-----ccHHHHHHHHHHHHHHHHHHHHHHHhhC
Confidence            479999999999999999999999853     3457888999999999999999999986

>d1ew0a_ d.110.3.2 (A:) Histidine kinase FixL heme domain {Rhizobium meliloti [TaxId: 382]}

class: Alpha and beta proteins (a+b)
fold: Profilin-like
superfamily: PYP-like sensor domain (PAS domain)
family: Heme-binding PAS domain
domain: Histidine kinase FixL heme domain
species: Rhizobium meliloti [TaxId: 382]

Probab=98.74  E-value=1.6e-08  Score=94.15  Aligned_cols=121  Identities=12%  Similarity=0.066  Sum_probs=95.0

Q ss_pred             hHHHHHHHHHHHHHHHHHHHhccCcEEEEecccccEEEeecc---CCCCCcccccCCCchhccCccchhhhhHHHHHHHH
Q 039716          209 PVEELSQILKRADNFLHFVLQNAPVVMGHQDKELRYRFIYNH---FPSLHEEDILGKTDVEIFSGAGVKESQDFKREVLE  285 (1002)
Q Consensus       209 ~~~~~~~~l~~~~~~l~~il~~~p~~i~~~d~~~~~~~~~~~---~~~~~~e~iiGk~~~e~~~~~~~~~~~~~~~~vl~  285 (1002)
                      .+.+.++.|++++++++.+++++|.+|+..|.+|++.++|..   +.|+++++++|++..+++++.............+.
T Consensus         3 ~l~~~e~~l~~~e~~~~~i~~~~~~~i~~~d~~g~i~~~N~~~~~l~Gy~~~el~g~~~~~~~~~~~~~~~~~~~~~~~~   82 (130)
T d1ew0a_           3 HMLETEDVVRARDAHLRSILDTVPDATVVSATDGTIVSFNAAAVRQFGYAEEEVIGQNLRILMPEPYRHEHDGYLQRYMA   82 (130)
T ss_dssp             HHHHHHHHHHHHTSCHHHHHTTCSSEEEEEETTSBEEEECHHHHHHHCCCHHHHTTSBGGGGSCTTTGGGHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHHHHHHHHcCCCeEEEEeCCccEEEEHHHHHHhhcCCHHHhcCCccccccccchhHHHHHHHHHHHH
Confidence            356678889999999999999999999999999999999985   46899999999999888887666666666667777


Q ss_pred             hCCC----cceeEEEEEeecCceEEEEEEeeeecCCCCEEEEEEEeechh
Q 039716          286 KGLP----AKREITFETELFGSKTFLIYVEPVFSKSGETIGVNYMGMDVT  331 (1002)
Q Consensus       286 ~g~~----~~~e~~~~~~~~~~~~~~~~~~p~~~~~G~~~gi~~~~~DIT  331 (1002)
                      .+..    ...++.+..+.+...++.+++.|+.+.++  .+++++.+|||
T Consensus        83 ~~~~~~~~~~~e~~~~~~dG~~~~v~~~~~~i~~~~~--~~~~~i~rDIT  130 (130)
T d1ew0a_          83 TGEKRIIGIDRVVSGQRKDGSTFPMKLAVGEMRSGGE--RFFTGFIRDLT  130 (130)
T ss_dssp             HCCCSSTTSCEEEEEECTTSCEEEEEEEEEEEEETTE--EEEEEEEEECC
T ss_pred             hCCCccccceeeEEEEcCCCCEEEEEEEEEEEEECCe--EEEEEEEEECC
Confidence            6654    34455555555555677788899987544  34678889997

>d1n9la_ d.110.3.6 (A:) Putative blue light receptor, phot-lov1 domain {Green algae (Chlamydomonas reinhardtii) [TaxId: 3055]}

class: Alpha and beta proteins (a+b)
fold: Profilin-like
superfamily: PYP-like sensor domain (PAS domain)
family: Flavin-binding PAS domain
domain: Putative blue light receptor, phot-lov1 domain
species: Green algae (Chlamydomonas reinhardtii) [TaxId: 3055]

Probab=98.50  E-value=1.8e-07  Score=84.53  Aligned_cols=98  Identities=14%  Similarity=0.107  Sum_probs=77.8

Q ss_pred             EEEEec---ccccEEEeeccC---CCCCcccccCCCchhccCccchhhhhHHHHHHHHhCCCcceeEEEEEeecCceEEE
Q 039716          234 VMGHQD---KELRYRFIYNHF---PSLHEEDILGKTDVEIFSGAGVKESQDFKREVLEKGLPAKREITFETELFGSKTFL  307 (1002)
Q Consensus       234 ~i~~~d---~~~~~~~~~~~~---~~~~~e~iiGk~~~e~~~~~~~~~~~~~~~~vl~~g~~~~~e~~~~~~~~~~~~~~  307 (1002)
                      .+...|   +++++.|+|..|   .|++.+|++|++...++++.............++.+.+...|+.+..+.+...+..
T Consensus         5 ~~vi~Da~~pdg~Ii~vN~a~~~~~Gy~~~El~G~~~~~l~~~~~~~~~~~~~~~~l~~~~~~~~e~~~~~kdG~~~w~~   84 (109)
T d1n9la_           5 TFVVADATLPDCPLVYASEGFYAMTGYGPDEVLGHNCRFLQGEGTDPKEVQKIRDAIKKGEACSVRLLNYRKDGTPFWNL   84 (109)
T ss_dssp             EEEEEETTSTTCCEEEECHHHHHHHCCCHHHHTTSCGGGGCCTTCCHHHHHHHHHHHHHTCCEEEEEEEECTTSCEEEEE
T ss_pred             eEEEEeCCCCCCeEEEEcHHHHHHHCcCHHHHcCCcceeeecccCCHHHhhhhhhHhhcCCceeeeEEEEecCCeEEEEE
Confidence            455567   589999999875   58899999999988777665444444555667788888888877766655556677


Q ss_pred             EEEeeeecCCCCEEEEEEEeechh
Q 039716          308 IYVEPVFSKSGETIGVNYMGMDVT  331 (1002)
Q Consensus       308 ~~~~p~~~~~G~~~gi~~~~~DIT  331 (1002)
                      +.+.|+++.+|++.|+++++.|||
T Consensus        85 ~~~~pi~d~~G~v~~~v~~~~DIT  108 (109)
T d1n9la_          85 LTVTPIKTPDGRVSKFVGVQVDVT  108 (109)
T ss_dssp             EEEEEEECTTSCEEEEEEEEEECC
T ss_pred             EEEEEEECCCCCEEEEEEEEEECC
Confidence            899999999999999999999998

>d1p97a_ d.110.3.7 (A:) Hypoxia-inducible factor Hif2a, C-terminal domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Profilin-like
superfamily: PYP-like sensor domain (PAS domain)
family: Hypoxia-inducible factor Hif2a, C-terminal domain
domain: Hypoxia-inducible factor Hif2a, C-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.34  E-value=1.4e-07  Score=85.70  Aligned_cols=104  Identities=8%  Similarity=0.174  Sum_probs=84.7

Q ss_pred             cCcEEEEecccccEEEeeccC---CCCCcccccCCCchhccCccchhhhhHHHHHHHHhCCCcceeEEEEEeecCceEEE
Q 039716          231 APVVMGHQDKELRYRFIYNHF---PSLHEEDILGKTDVEIFSGAGVKESQDFKREVLEKGLPAKREITFETELFGSKTFL  307 (1002)
Q Consensus       231 ~p~~i~~~d~~~~~~~~~~~~---~~~~~e~iiGk~~~e~~~~~~~~~~~~~~~~vl~~g~~~~~e~~~~~~~~~~~~~~  307 (1002)
                      .++.|...|.+|++.|+|.++   .|++.++++|++..+++.++..+........++..+.....++.+....+...|+.
T Consensus         5 ~~~fi~r~~~dG~i~~~N~~~~~~~G~~~~el~g~~~~~~~~~ed~~~~~~~~~~~~~~~~~~~~e~~~~~kdG~~~wv~   84 (114)
T d1p97a_           5 SKTFLSRHSMDMKFTYCDDRITELIGYHPEELLGRSAYEFYHALDSENMTKSHQNLCTKGQVVSGQYRMLAKHGGYVWLE   84 (114)
T ss_dssp             CEEEEEEECTTTSCSEECTTHHHHTSSCHHHHTTSCHHHHSCSSSHHHHHHHHHHHTTTSEEEEEEEEEECTTSCEEEEE
T ss_pred             cCEEEEEECCCCcEEEECHHHHHHcCCCccccccccccccccccccccceeeeeecccccceeecceeeeeecCcceEEE
Confidence            356777789999999999875   68999999999999998888777777777777666655666777776666666777


Q ss_pred             EEEeeeecC-CCCEEEEEEEeechhHHH
Q 039716          308 IYVEPVFSK-SGETIGVNYMGMDVTDQV  334 (1002)
Q Consensus       308 ~~~~p~~~~-~G~~~gi~~~~~DITe~~  334 (1002)
                      +...|+++. +|.+.+++++..|||+++
T Consensus        85 ~~~~~~~~~~~~~~~~ii~~~~dite~k  112 (114)
T d1p97a_          85 TQGTVIYNPRNLQPQCIMCVNYVLSEIE  112 (114)
T ss_dssp             EEEEEEECTTTCSEEEEEEEEEEEEEEE
T ss_pred             EEEEEEEeCCCCCEEEEEEEEEECChhh
Confidence            888999986 799999999999999853

>d1jnua_ d.110.3.6 (A:) Photoreceptor phy3 flavin-binding domain, lov2 {Maidenhair fern (Adiantum capillus-veneris) [TaxId: 13818]}

class: Alpha and beta proteins (a+b)
fold: Profilin-like
superfamily: PYP-like sensor domain (PAS domain)
family: Flavin-binding PAS domain
domain: Photoreceptor phy3 flavin-binding domain, lov2
species: Maidenhair fern (Adiantum capillus-veneris) [TaxId: 13818]

Probab=98.33  E-value=5.1e-07  Score=80.48  Aligned_cols=91  Identities=10%  Similarity=0.062  Sum_probs=79.1

Q ss_pred             ccccEEEeeccC---CCCCcccccCCCchhccCccchhhhhHHHHHHHHhCCCcceeEEEEEeecCceEEEEEEeeeecC
Q 039716          240 KELRYRFIYNHF---PSLHEEDILGKTDVEIFSGAGVKESQDFKREVLEKGLPAKREITFETELFGSKTFLIYVEPVFSK  316 (1002)
Q Consensus       240 ~~~~~~~~~~~~---~~~~~e~iiGk~~~e~~~~~~~~~~~~~~~~vl~~g~~~~~e~~~~~~~~~~~~~~~~~~p~~~~  316 (1002)
                      +|+++.|+|++|   .|++.++++|++..+++++...+.........++.+.+...|+.+..+.++..++.+.+.|+++.
T Consensus        11 pd~~I~y~N~a~~~~~G~s~~e~~G~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~dg~~~~~~~~~~pi~d~   90 (104)
T d1jnua_          11 PDNPIIFASDRFLELTEYTREEVLGNNCRFLQGRGTDRKAVQLIRDAVKEQRDVTVQVLNYTKGGRAFWNLFHLQVMRDE   90 (104)
T ss_dssp             TTCCEEEECHHHHHHHTCCHHHHTTSCGGGGCCTTSCHHHHHHHHHHHHHTCCEEEEEEEECTTSCEEEEEEEEEEECTT
T ss_pred             CCCEEEEEcHHHHHHHCcCHHHHCCccceeccccccchHHHhhhhhhhhcCceeEeEEEEEecccceEEEEEEEEEEECC
Confidence            578999999876   58899999999998888877767777777788888888888888877777777888999999999


Q ss_pred             CCCEEEEEEEeech
Q 039716          317 SGETIGVNYMGMDV  330 (1002)
Q Consensus       317 ~G~~~gi~~~~~DI  330 (1002)
                      +|++.|++++.+||
T Consensus        91 ~G~v~~~i~i~~DI  104 (104)
T d1jnua_          91 NGDVQYFIGVQQEM  104 (104)
T ss_dssp             TSSCCEEEEEEEEC
T ss_pred             CCCEEEEEEEEEcC
Confidence            99999999999997

>d1bywa_ d.110.3.6 (A:) Erg potassium channel, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Profilin-like
superfamily: PYP-like sensor domain (PAS domain)
family: Flavin-binding PAS domain
domain: Erg potassium channel, N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.28  E-value=6.8e-07  Score=80.53  Aligned_cols=94  Identities=15%  Similarity=0.069  Sum_probs=73.8

Q ss_pred             ccccEEEeeccC---CCCCcccccCCCchhccC--ccchhhhhHHHHHHHHhCCCcceeEEEEEeecCceEEEEEEeeee
Q 039716          240 KELRYRFIYNHF---PSLHEEDILGKTDVEIFS--GAGVKESQDFKREVLEKGLPAKREITFETELFGSKTFLIYVEPVF  314 (1002)
Q Consensus       240 ~~~~~~~~~~~~---~~~~~e~iiGk~~~e~~~--~~~~~~~~~~~~~vl~~g~~~~~e~~~~~~~~~~~~~~~~~~p~~  314 (1002)
                      .+..+.|+|.+|   .|++.++++|++..+.+.  +.............++.+.+...++.+....+...++.+.+.|++
T Consensus        12 ~d~~I~~~N~a~~~l~G~~~~eiiG~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~e~~~~~~~g~~~w~~~~~~pi~   91 (110)
T d1bywa_          12 ENCAVIYCNDGFCELCGYSRAEVMQRPCTCDFLHGPCTQRRAAAQIAQALLGAEERKVEIAFYRKDGSCFLCLVDVVPVK   91 (110)
T ss_dssp             SSCBEEEECHHHHHHHTCCHHHHTTSBTTCGGGCCTTCCHHHHHHHHHHHHTTCCEEEEEEEECTTSCEEEEEEEEEEEE
T ss_pred             CCCEEEEEcHHHHHHhCCCHHHhcccCcccccceeeheecccccccchhhcccccccceeeeeecccceeeeeeeEEEEE
Confidence            567899998765   688999999998876542  333344455566777888887777777666666677789999999


Q ss_pred             cCCCCEEEEEEEeechhHH
Q 039716          315 SKSGETIGVNYMGMDVTDQ  333 (1002)
Q Consensus       315 ~~~G~~~gi~~~~~DITe~  333 (1002)
                      |.+|+++|+++++.||||+
T Consensus        92 d~~G~v~~~i~~~~DITer  110 (110)
T d1bywa_          92 NEDGAVIMFILNFEVVMEK  110 (110)
T ss_dssp             CTTCCEEEEEEEEEEEEEC
T ss_pred             CCCCCEEEEEEEEEECCCC
Confidence            9999999999999999974

>d1v9ya_ d.110.3.2 (A:) Direct oxygen sensor protein, DOS {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a+b)
fold: Profilin-like
superfamily: PYP-like sensor domain (PAS domain)
family: Heme-binding PAS domain
domain: Direct oxygen sensor protein, DOS
species: Escherichia coli [TaxId: 562]

Probab=97.88  E-value=2.2e-05  Score=69.89  Aligned_cols=104  Identities=12%  Similarity=0.021  Sum_probs=74.6

Q ss_pred             HHHHHhccCcEEEEecccccEEEeecc---CCCCCcccccCCCchhccCccchhhhhHHHHHHHHhCC----CcceeEEE
Q 039716          224 LHFVLQNAPVVMGHQDKELRYRFIYNH---FPSLHEEDILGKTDVEIFSGAGVKESQDFKREVLEKGL----PAKREITF  296 (1002)
Q Consensus       224 l~~il~~~p~~i~~~d~~~~~~~~~~~---~~~~~~e~iiGk~~~e~~~~~~~~~~~~~~~~vl~~g~----~~~~e~~~  296 (1002)
                      |..+++++|.+|+..|.++++.++|..   +.|++.++++|++...+++..............+..+.    ....+..+
T Consensus         3 ~~~~~e~~~d~i~~~d~~g~i~~~N~~~~~l~Gy~~~e~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~   82 (113)
T d1v9ya_           3 FFPALEQNMMGAVLINENDEVMFFNPAAEKLWGYKREEVIGNNIDMLIPRDLRPAHPEYIRHNREGGKARVEGMSRELQL   82 (113)
T ss_dssp             HHHHHHTCSSEEEEECTTSBEEEECHHHHHHHSCCGGGTTTSBGGGGSCGGGTTTHHHHHHHHHC----------CEEEE
T ss_pred             HHHHHHcCcCcEEEEeCCCCEEEEchhHhhhhccchhhhcCcceecccccccccccccccccccccccccccccceeeee
Confidence            677899999999999999999999985   46899999999999888876655555555555444332    23445556


Q ss_pred             EEeecCceEEEEEEeeeecCCCCEEEEEEEeec
Q 039716          297 ETELFGSKTFLIYVEPVFSKSGETIGVNYMGMD  329 (1002)
Q Consensus       297 ~~~~~~~~~~~~~~~p~~~~~G~~~gi~~~~~D  329 (1002)
                      ..+.+...+..+++.|+.+..|..  ++++.+|
T Consensus        83 ~~~dG~~~~v~~~~~~i~~~~~~~--~~~v~rD  113 (113)
T d1v9ya_          83 EKKDGSKIWTRFALSKVSAEGKVY--YLALVRD  113 (113)
T ss_dssp             ECTTSCEEEEEEEEEEEEETTEEE--EEEEEEC
T ss_pred             ccccceeEEEEEEEEEEEECCeEE--EEEEEEC
Confidence            555556667889999999876544  4555555

>d1xj3a1 d.110.3.2 (A:154-259) Histidine kinase FixL heme domain {Bradyrhizobium japonicum [TaxId: 375]}

class: Alpha and beta proteins (a+b)
fold: Profilin-like
superfamily: PYP-like sensor domain (PAS domain)
family: Heme-binding PAS domain
domain: Histidine kinase FixL heme domain
species: Bradyrhizobium japonicum [TaxId: 375]

Probab=97.57  E-value=0.00011  Score=64.11  Aligned_cols=97  Identities=10%  Similarity=-0.015  Sum_probs=70.5

Q ss_pred             EEEEecccccEEEeeccC---CCCCcccccCCCchhccCccchhhhhHHHHHHHHhCCC----cceeEEEEEeecCceEE
Q 039716          234 VMGHQDKELRYRFIYNHF---PSLHEEDILGKTDVEIFSGAGVKESQDFKREVLEKGLP----AKREITFETELFGSKTF  306 (1002)
Q Consensus       234 ~i~~~d~~~~~~~~~~~~---~~~~~e~iiGk~~~e~~~~~~~~~~~~~~~~vl~~g~~----~~~e~~~~~~~~~~~~~  306 (1002)
                      +|+..|.+|++.++|..+   .|++.++++|++...++++.............+..+..    ...++.+....+...++
T Consensus         2 gi~~~D~~G~I~~~N~a~~~l~Gy~~~el~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~dg~~~~v   81 (106)
T d1xj3a1           2 AMIVIDGHGIIQLFSTAAERLFGWSELEAIGQNVNILMPEPDRSRHDSYISRYRTTSDPHIIGIGRIVTGKRRDGTTFPM   81 (106)
T ss_dssp             CEEEEETTSBEEEECHHHHHHHCCCHHHHTTSBGGGGSCTTHHHHHHHHHHHHHHHCCCSSTTTCEEEEEECTTSCEEEE
T ss_pred             EEEEECCCCcEEEEcHHHHHHhhhchHhhcCCCcccccccccccchhhhhhhhhhhcccccccccceeeeeeccceEEEE
Confidence            577889999999999864   68899999999998888876655555555555554432    23455554445555567


Q ss_pred             EEEEeeeecCCCCEEEEEEEeechhH
Q 039716          307 LIYVEPVFSKSGETIGVNYMGMDVTD  332 (1002)
Q Consensus       307 ~~~~~p~~~~~G~~~gi~~~~~DITe  332 (1002)
                      .+++.|+.+.++.  +++++++||||
T Consensus        82 ~~~~~~~~~~~~~--~~~~~~~DITE  105 (106)
T d1xj3a1          82 HLSIGEMQSGGEP--YFTGFVRDLTE  105 (106)
T ss_dssp             EEEEEEEEETTEE--EEEEEEEECHH
T ss_pred             EEEEEEEEECCeE--EEEEEEEeCCC
Confidence            7889999986554  57788999997

>d1nwza_ d.110.3.1 (A:) Photoactive yellow protein, PYP {Ectothiorhodospira halophila [TaxId: 1053]}

class: Alpha and beta proteins (a+b)
fold: Profilin-like
superfamily: PYP-like sensor domain (PAS domain)
family: PYP-like
domain: Photoactive yellow protein, PYP
species: Ectothiorhodospira halophila [TaxId: 1053]

Probab=97.49  E-value=7.8e-05  Score=68.46  Aligned_cols=100  Identities=9%  Similarity=-0.088  Sum_probs=69.6

Q ss_pred             HHHHHHHHhccCcEEEEecccccEEEeeccC---CCCCcccccCCCchhccCc-cchhhhhHHHHHHHHhCCCcceeEEE
Q 039716          221 DNFLHFVLQNAPVVMGHQDKELRYRFIYNHF---PSLHEEDILGKTDVEIFSG-AGVKESQDFKREVLEKGLPAKREITF  296 (1002)
Q Consensus       221 ~~~l~~il~~~p~~i~~~d~~~~~~~~~~~~---~~~~~e~iiGk~~~e~~~~-~~~~~~~~~~~~vl~~g~~~~~e~~~  296 (1002)
                      ..++..+++++|.+++..|.+|++.++|..+   .|+++++++|++..+++.+ ...........+++.+|.....+...
T Consensus        16 ~~~~d~~ld~~p~gi~~lD~~G~i~~~N~a~~~l~G~~~~e~iG~~~~~~~~p~~~~~~~~~~~~~~~~~g~~~~~~~~~   95 (125)
T d1nwza_          16 AKMDDGQLDGLAFGAIQLDGDGNILQYNAAEGDITGRDPKQVIGKNFFKDVAPCTDSPEFYGKFKEGVASGNLNTMFEYT   95 (125)
T ss_dssp             TTCCHHHHTTCSSEEEEEETTCBEEEECHHHHHHHCCCHHHHTTSBCCCCCCGGGCSTTTHHHHHHHHHHTCCEEEEEEE
T ss_pred             HHHHHHHHhCCCccEEEEeCCCCEEEEcHHHHHhhccchHhhcCCCHHHccCchhhhhheeeeceeeeecCCcceEEEEE
Confidence            3566789999999999999999999999865   6889999999999887754 34455566677788888765443333


Q ss_pred             EEeecCceEEEEEEeeeecCCCCEEE
Q 039716          297 ETELFGSKTFLIYVEPVFSKSGETIG  322 (1002)
Q Consensus       297 ~~~~~~~~~~~~~~~p~~~~~G~~~g  322 (1002)
                      -...+...++.+...+  ..+|...+
T Consensus        96 ~~~~G~~~~v~v~l~~--~~~g~~~~  119 (125)
T d1nwza_          96 FDYQMTPTKVKVHMKK--ALSGDSYW  119 (125)
T ss_dssp             ECTTSCCEEEEEEEEE--CSSSSEEE
T ss_pred             eccCCcEEEEEEEEEE--ecCCCEEE
Confidence            2333334444454444  45565544

>d1mzua_ d.110.3.1 (A:) PYP domain of sensor histidine kinase Ppr {Rhodospirillum centenum [TaxId: 34018]}

class: Alpha and beta proteins (a+b)
fold: Profilin-like
superfamily: PYP-like sensor domain (PAS domain)
family: PYP-like
domain: PYP domain of sensor histidine kinase Ppr
species: Rhodospirillum centenum [TaxId: 34018]

Probab=97.38  E-value=0.00011  Score=66.00  Aligned_cols=99  Identities=9%  Similarity=0.023  Sum_probs=66.0

Q ss_pred             HHHHHHHhccCcEEEEecccccEEEeecc---CCCCCcccccCCCchhccCc-cchhhhhHHHHHHHHhCCCcce-eEEE
Q 039716          222 NFLHFVLQNAPVVMGHQDKELRYRFIYNH---FPSLHEEDILGKTDVEIFSG-AGVKESQDFKREVLEKGLPAKR-EITF  296 (1002)
Q Consensus       222 ~~l~~il~~~p~~i~~~d~~~~~~~~~~~---~~~~~~e~iiGk~~~e~~~~-~~~~~~~~~~~~vl~~g~~~~~-e~~~  296 (1002)
                      .+++.+++++|.+|...|.+|++.++|..   +.|++.++++|++..+++.+ ...+.......+.+.+|..... +..+
T Consensus         3 ~~~~A~ld~~p~gvi~~D~~G~I~~~N~aa~~~~G~~~eellG~~~~~~~~p~~~~~~~~~~~~~~~~~g~~~~~~~~~l   82 (110)
T d1mzua_           3 GMGTAEFDALPVGAIQVDGSGVIHRYNRTESRLSGRIPERVIGRNFFTEVAPCTNIPAFSGRFMDGVTSGTLDARFDFVF   82 (110)
T ss_dssp             ---CTTGGGCSSEEEEEETTCBEEEECHHHHHHHCCCHHHHTTSBCCCCCCGGGCSTTTHHHHHHHHHTSCCEEEEEEEE
T ss_pred             cHHHHHHhCCCcEEEEEcCCCCEEEeHHHHHHHHcCCHHHHcCCCHHHhcCChhhhHHHHHHHHHHHhccccCcceEEEE
Confidence            45678899999999999999999999975   46899999999998876654 3445566677788888865332 3332


Q ss_pred             EEeecCceEEEEEEeeeecCCCCEEEE
Q 039716          297 ETELFGSKTFLIYVEPVFSKSGETIGV  323 (1002)
Q Consensus       297 ~~~~~~~~~~~~~~~p~~~~~G~~~gi  323 (1002)
                       ...+....+.+...+  ...|..+++
T Consensus        83 -~~~G~~~~v~v~~~~--~~~~~~~~i  106 (110)
T d1mzua_          83 -DFQMAPVRVQIRMQN--AGVPDRYWI  106 (110)
T ss_dssp             -ECSSCEEEEEEEEEE--CSSTTEEEE
T ss_pred             -ecCCceEEEEEEEEE--ecCCCEEEE
Confidence             233333333344433  345555544

>d1h7sa2 d.122.1.2 (A:29-231) DNA mismatch repair protein PMS2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
superfamily: ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
family: DNA gyrase/MutL, N-terminal domain
domain: DNA mismatch repair protein PMS2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.40  E-value=0.004  Score=61.74  Aligned_cols=59  Identities=19%  Similarity=0.219  Sum_probs=34.7

Q ss_pred             EEEEEecCCCCCcCcHhhhhhhccCCCccc------cCcCCCccccHHHHHHHHHHhCCEEEEEeecCCc
Q 039716          593 RCDVYDTGIGIPENALPTLFRKYMQVSADH------ARKYGGTGLGLAICKQLVELMGGRLTVTSKVHCG  656 (1002)
Q Consensus       593 ~i~V~DtGiGI~~e~l~~IF~pF~q~~~~~------~~~~~GtGLGLaI~k~Lve~~gG~I~v~S~~g~G  656 (1002)
                      .|.|.|+|.||++++++.+|.++.+.+-..      ...+|.-|.+|+-.   ..  -+.+.+.|....+
T Consensus        37 ~i~V~DnG~Gi~~~dl~~~~~~~~tsk~~~~~~~~~~~t~GfrGeaL~si---~~--~s~~~i~s~~~~~  101 (203)
T d1h7sa2          37 LIEVSDNGCGVEEENFEGLTLKHHTSKIQEFADLTQVETFGFRGEALSSL---CA--LSDVTISTCHASA  101 (203)
T ss_dssp             EEEEEECSCCCCGGGSGGGGC----------CCTTCSEEESSSSSHHHHH---HH--HSEEEEEEECTTC
T ss_pred             EEEEeeCCcccCHHHhhhhhhheeecccccccccccccccCccchhhhhh---hh--ccceEEEeecCCC
Confidence            367999999999999999999987654221      11124446666632   22  2678888875443

>d1oj5a_ d.110.3.8 (A:) PAS domain of steroid receptor coactivator 1A, NCo-A1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Profilin-like
superfamily: PYP-like sensor domain (PAS domain)
family: PAS domain of steroid receptor coactivator 1A, NCo-A1
domain: PAS domain of steroid receptor coactivator 1A, NCo-A1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=95.47  E-value=0.0097  Score=52.57  Aligned_cols=95  Identities=16%  Similarity=0.162  Sum_probs=67.4

Q ss_pred             EEEEecccccEEEeecc---CCCCCc-ccccCCCchhccCccchhh--hhHHHHHHHHhCCCcceeEEEEEeecCceEEE
Q 039716          234 VMGHQDKELRYRFIYNH---FPSLHE-EDILGKTDVEIFSGAGVKE--SQDFKREVLEKGLPAKREITFETELFGSKTFL  307 (1002)
Q Consensus       234 ~i~~~d~~~~~~~~~~~---~~~~~~-e~iiGk~~~e~~~~~~~~~--~~~~~~~vl~~g~~~~~e~~~~~~~~~~~~~~  307 (1002)
                      .+..-|.+|++.+++..   ..|+.+ +|++|++..+++++++.+.  .....+.++..|.....+.++....+...|+.
T Consensus         4 F~trh~~~g~~~~vd~~~~~~~gy~~~eelig~s~~~f~HPeD~~~~~~~~~~~~~~~~g~~~~~~yR~~~kdG~~vWv~   83 (109)
T d1oj5a_           4 FMTKQDTTGKIISIDTSSLRAAGRTGWEDLVRKCIYAFFQPQGREPSYARQLFQEVMTRGTASSPSYRFILNDGTMLSAH   83 (109)
T ss_dssp             EEEEECTTCCEEEEECHHHHTTCCSCHHHHHHHHHHHHTSCBTTBCCHHHHHHHHHHHHSEEECCCEEEECTTSCEEEEE
T ss_pred             EEEEECCCceEEEECHHHhhHhhcCCHHHHcCCcHHHeECcccchHHHhhHHHHHHHhhcccchhhhhhhhccCcEEEEE
Confidence            34566899999999764   467775 8999999999999877543  33445678888888777888877776666677


Q ss_pred             EEEeeeecCCC-C---EEEEEEEee
Q 039716          308 IYVEPVFSKSG-E---TIGVNYMGM  328 (1002)
Q Consensus       308 ~~~~p~~~~~G-~---~~gi~~~~~  328 (1002)
                      ....++++..| +   ++|+..+.+
T Consensus        84 t~~~~~~~~~~~~~~~Ii~~h~i~~  108 (109)
T d1oj5a_          84 TRCKLCYPQSPDMQPFIMGIHIIDR  108 (109)
T ss_dssp             EEEEEECC----CCCEEEEEEEEEC
T ss_pred             EEEEEEECCCCCcccEEEEEEEEec
Confidence            77888887543 2   445554443

>d1ll8a_ d.110.3.5 (A:) N-terminal PAS domain of Pas kinase {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Profilin-like
superfamily: PYP-like sensor domain (PAS domain)
family: N-terminal PAS domain of Pas kinase
domain: N-terminal PAS domain of Pas kinase
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.07  E-value=0.0085  Score=52.94  Aligned_cols=97  Identities=7%  Similarity=0.011  Sum_probs=65.4

Q ss_pred             cEEEEecc-cccEEEeeccC---CCCCcccccCCCchhccCccchhhhhHHHHHHHHhCC----CcceeEEEEEeecCce
Q 039716          233 VVMGHQDK-ELRYRFIYNHF---PSLHEEDILGKTDVEIFSGAGVKESQDFKREVLEKGL----PAKREITFETELFGSK  304 (1002)
Q Consensus       233 ~~i~~~d~-~~~~~~~~~~~---~~~~~e~iiGk~~~e~~~~~~~~~~~~~~~~vl~~g~----~~~~e~~~~~~~~~~~  304 (1002)
                      ..|+..|. +|++.++|.++   .|++.++++|++..+++++.............+..+.    ....++.+.+..+...
T Consensus         9 ~AI~~id~~~G~I~~~N~a~~~l~Gy~~~el~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~G~~~   88 (114)
T d1ll8a_           9 KAIFTVDAKTTEILVANDKACGLLGYSSQDLIGQKLTQFFLRSDSDVVEALSEEHMEADGHAAVVFGTVVDIISRSGEKI   88 (114)
T ss_dssp             CEEEEEETTTCBEEEECTTHHHHHTCCTTTTTTSBGGGGSSCTTTHHHHHTTSSTTSSSSCSSCCCSSSEEECCTTCCCE
T ss_pred             cEEEEEECCCCEEEEECHHHHHhhcCCHHHHcCCCeeeecCcccHHHHHHHHHHHHhcCCCccceeeEEEEEEccCCcEE
Confidence            45677784 69999999875   6889999999999999987655444443334444432    1233566555556666


Q ss_pred             EEEEEEeeeecCCCCEEEEEEEeechh
Q 039716          305 TFLIYVEPVFSKSGETIGVNYMGMDVT  331 (1002)
Q Consensus       305 ~~~~~~~p~~~~~G~~~gi~~~~~DIT  331 (1002)
                      +..+++.++....+ .. ++++..||+
T Consensus        89 pvevs~~~i~~~~~-~~-~l~vi~dV~  113 (114)
T d1ll8a_          89 PVSVWMKRMRQERR-LC-CVVVLEPVE  113 (114)
T ss_dssp             EEECCEECCBSSSS-BE-EEEEEEECC
T ss_pred             EEEEEEEEEEECCe-EE-EEEEEEECc
Confidence            77778888765444 43 467788884

>d1ccwa_ c.23.6.1 (A:) Glutamate mutase, small subunit {Clostridium cochlearium [TaxId: 1494]}

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: Cobalamin (vitamin B12)-binding domain
family: Cobalamin (vitamin B12)-binding domain
domain: Glutamate mutase, small subunit
species: Clostridium cochlearium [TaxId: 1494]

Probab=92.98  E-value=0.53  Score=42.74  Aligned_cols=115  Identities=10%  Similarity=0.019  Sum_probs=82.8

Q ss_pred             CCeEEE--E--ecCHHHHHHHHHHHHhcCCeEEE---EcCHHHHHHHHHcCCCcEEEEcCCCCCCCHHHHHH----HHhc
Q 039716          859 KPKILL--V--EDNKINVMVAKSMMKQLGHSIDV---VNNGVEAVHAVQCQNYDLILMDVCMPVMDGLKATR----LIRS  927 (1002)
Q Consensus       859 ~~~ILi--V--eDn~~n~~~l~~~L~~~g~~v~~---a~~G~eAl~~~~~~~~DlIlmDi~MP~mdG~e~~~----~IR~  927 (1002)
                      +.+||+  +  |-+..-..++..+|+..||+|..   ....++.++++.+.++|+|.+-..|+..  ...++    .+|+
T Consensus         3 k~kVvi~~~~gD~H~lG~~mva~~l~~~G~~V~~LG~~~p~e~iv~a~~~~~~d~v~lS~~~~~~--~~~~~~~~~~l~~   80 (137)
T d1ccwa_           3 KKTIVLGVIGSDCHAVGNKILDHAFTNAGFNVVNIGVLSPQELFIKAAIETKADAILVSSLYGQG--EIDCKGLRQKCDE   80 (137)
T ss_dssp             CCEEEEEEETTCCCCHHHHHHHHHHHHTTCEEEEEEEEECHHHHHHHHHHHTCSEEEEEECSSTH--HHHHTTHHHHHHH
T ss_pred             CCEEEEEecCCChhHHHHHHHHHHHHHCCCeEEecccccCHHHHHHHHHhcCCCEEEEeeccccc--hHHHHHHHHHHHH
Confidence            457777  4  44456778899999999999884   3588999999999999999999999853  34333    3333


Q ss_pred             cccCCCchhhhhhhhcccCCCCCCCCCCCCccEEEEcCC----C-CHHHHHHHHHcCCCEEEeCCCChHHHHHHHHhh
Q 039716          928 FEDTGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTAN----A-LSESAEECFANGMDSFVSKPVTFQKLKECLEQY 1000 (1002)
Q Consensus       928 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipIIalTa~----~-~~~~~~~~~~aG~d~~l~KP~~~~~L~~~l~~~ 1000 (1002)
                      .                         ...++||++=-+-    . .+....+..+.|+|......-++++..+.|++-
T Consensus        81 ~-------------------------~~~~i~iivGG~~~~~~~~~~~~~~~l~~~Gv~~if~~~t~~~~~~~~l~~~  133 (137)
T d1ccwa_          81 A-------------------------GLEGILLYVGGNIVVGKQHWPDVEKRFKDMGYDRVYAPGTPPEVGIADLKKD  133 (137)
T ss_dssp             T-------------------------TCTTCEEEEEESCSSSSCCHHHHHHHHHHTTCSEECCTTCCHHHHHHHHHHH
T ss_pred             h-------------------------ccCCCEEEEeCCcCCCccccHHHHHHHHHcCCCEEECCCCCHHHHHHHHHHH
Confidence            1                         1246887754332    2 244555566889999998888888888888764

>d1pvga2 d.122.1.2 (A:7-245) DNA topoisomerase II {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
superfamily: ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
family: DNA gyrase/MutL, N-terminal domain
domain: DNA topoisomerase II
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=86.52  E-value=0.65  Score=46.29  Aligned_cols=69  Identities=17%  Similarity=0.328  Sum_probs=42.3

Q ss_pred             EEEEEecCCCCCcCcHhh--------hhhhccCCCcc---c-cCcCCCccccHHHHHHHHHHhCCEEEEEee-cCCceEE
Q 039716          593 RCDVYDTGIGIPENALPT--------LFRKYMQVSAD---H-ARKYGGTGLGLAICKQLVELMGGRLTVTSK-VHCGSTF  659 (1002)
Q Consensus       593 ~i~V~DtGiGI~~e~l~~--------IF~pF~q~~~~---~-~~~~~GtGLGLaI~k~Lve~~gG~I~v~S~-~g~GTtF  659 (1002)
                      .|+|.|+|.|||-+..+.        +|.-+.....-   . ....|..|+|+++|.-+.+.    +.++.. ...|-.|
T Consensus        88 si~V~d~GrGIPv~~h~~~~~~~~e~ift~l~ag~nfd~~~~k~sgGlnGvG~~vvNalS~~----f~vev~~~~~g~~~  163 (239)
T d1pvga2          88 TIEVKNDGKGIPIEIHNKENIYIPEMIFGHLLTSSNYDDDEKKVTGGRNGYGAKLCNIFSTE----FILETADLNVGQKY  163 (239)
T ss_dssp             EEEEEEESSCCCCSBCTTTCSBHHHHHHHSSSEESCCCTTSCCCCSCCSSCHHHHHHHTEEE----EEEEEEETTTTEEE
T ss_pred             EEEEEecCcceeeeeccccccchhheeeEeeccccccccccceeeCCeeccceeehhhhhHh----hheeeEEeecCceE
Confidence            378999999999876443        67655443221   1 11235679999987776554    444433 3346777


Q ss_pred             EEEEeC
Q 039716          660 TFILPY  665 (1002)
Q Consensus       660 ~~~LP~  665 (1002)
                      +..+-.
T Consensus       164 ~q~~~~  169 (239)
T d1pvga2         164 VQKWEN  169 (239)
T ss_dssp             EEEEET
T ss_pred             EEEeeC
Confidence            766643

>d1ei1a2 d.122.1.2 (A:2-220) DNA gyrase B {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a+b)
fold: ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
superfamily: ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
family: DNA gyrase/MutL, N-terminal domain
domain: DNA gyrase B
species: Escherichia coli [TaxId: 562]

Probab=85.24  E-value=0.75  Score=45.15  Aligned_cols=66  Identities=20%  Similarity=0.290  Sum_probs=41.4

Q ss_pred             EEEEecCCCCCcCc--------HhhhhhhccCCCc---cc-cCcCCCccccHHHHHHHHHHhCCEEEEEeecCCceEEEE
Q 039716          594 CDVYDTGIGIPENA--------LPTLFRKYMQVSA---DH-ARKYGGTGLGLAICKQLVELMGGRLTVTSKVHCGSTFTF  661 (1002)
Q Consensus       594 i~V~DtGiGI~~e~--------l~~IF~pF~q~~~---~~-~~~~~GtGLGLaI~k~Lve~~gG~I~v~S~~g~GTtF~~  661 (1002)
                      |+|.|+|.|||-+.        .+-||--......   .. ....|.-|+|+++|.-+-+.    +.|++.-+ |-.++.
T Consensus        68 IsV~ddGrGIPv~~h~~~~~~~~e~if~~l~tg~~fd~~~~~~sgG~nGvG~~~~NalS~~----f~v~~~r~-g~~y~q  142 (219)
T d1ei1a2          68 VSVQDDGRGIPTGIHPEEGVSAAEVIMTVLHAGGKFDDNSYKVSGGLHGVGVSVVNALSQK----LELVIQRE-GKIHRQ  142 (219)
T ss_dssp             EEEEECSSCCCCSBCTTTSSBHHHHHHHSTTEESCSSSSSCSSCSCCSSCHHHHHHHTEEE----EEEEEEET-TEEEEE
T ss_pred             EEEEECCccccccccCccCCchhhhhhhhhhhccCCCCCcceeEcCccccceeEEEEeeeE----EEEEEEEC-CEEEEE
Confidence            68999999999876        4566655433221   11 11234579999988877664    45555433 566666


Q ss_pred             EEe
Q 039716          662 ILP  664 (1002)
Q Consensus       662 ~LP  664 (1002)
                      .+-
T Consensus       143 ~f~  145 (219)
T d1ei1a2         143 IYE  145 (219)
T ss_dssp             EEE
T ss_pred             EEe
Confidence            653

>d7reqa2 c.23.6.1 (A:561-728) Methylmalonyl-CoA mutase alpha subunit, C-terminal domain {Propionibacterium freudenreichii, subsp. shermanii [TaxId: 1744]}

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: Cobalamin (vitamin B12)-binding domain
family: Cobalamin (vitamin B12)-binding domain
domain: Methylmalonyl-CoA mutase alpha subunit, C-terminal domain
species: Propionibacterium freudenreichii, subsp. shermanii [TaxId: 1744]

Probab=84.52  E-value=3.7  Score=38.19  Aligned_cols=104  Identities=16%  Similarity=0.153  Sum_probs=73.0

Q ss_pred             CCCeEEEE----ecCHHHHHHHHHHHHhcCCeEEEE---cCHHHHHHHHHcCCCcEEEEcCCCCCCCHHHHHHHHhcccc
Q 039716          858 PKPKILLV----EDNKINVMVAKSMMKQLGHSIDVV---NNGVEAVHAVQCQNYDLILMDVCMPVMDGLKATRLIRSFED  930 (1002)
Q Consensus       858 ~~~~ILiV----eDn~~n~~~l~~~L~~~g~~v~~a---~~G~eAl~~~~~~~~DlIlmDi~MP~mdG~e~~~~IR~~~~  930 (1002)
                      .+++||++    |-+..=..++..+|+..||+|...   ...++.++++.+..+|+|.+-..|..  ..+.++.+...-.
T Consensus        36 r~pkVlla~~g~D~Hd~G~~~va~~l~~~G~eVi~lg~~~~~e~iv~aa~~~~advI~iSs~~~~--~~~~~~~l~~~L~  113 (168)
T d7reqa2          36 RRPRILLAKMGQDGHDRGQKVIATAYADLGFDVDVGPLFQTPEETARQAVEADVHVVGVSSLAGG--HLTLVPALRKELD  113 (168)
T ss_dssp             SCCEEEEECBTTCCCCHHHHHHHHHHHHTTCEEEECCTTBCHHHHHHHHHHHTCSEEEEEECSSC--HHHHHHHHHHHHH
T ss_pred             CCCeEEEEeCCccHHHHHHHHHHHHHHhCCcceecCCCcCcHHHHHHHHHccCCCEEEEecCccc--chHHHHHHHHHHH
Confidence            35688887    446667778899999999998874   48899999999999999999876653  3444444432111


Q ss_pred             CCCchhhhhhhhcccCCCCCCCCCCCCccEEEEcCCCCHHHHHHHHHcCCCEEEe
Q 039716          931 TGNWDAAAEAGIEQAMPSSGSSNHFKRIPIIAMTANALSESAEECFANGMDSFVS  985 (1002)
Q Consensus       931 ~~~~~~~~~~~~~~~~~~~~~~~~~~~ipIIalTa~~~~~~~~~~~~aG~d~~l~  985 (1002)
                      .        .             ..+++||+ +-+....++.....++|++++..
T Consensus       114 ~--------~-------------g~~~v~Vi-vGG~ip~~d~~~l~~~Gv~~iF~  146 (168)
T d7reqa2         114 K--------L-------------GRPDILIT-VGGVIPEQDFDELRKDGAVEIYT  146 (168)
T ss_dssp             H--------T-------------TCTTSEEE-EEESCCGGGHHHHHHHTEEEEEC
T ss_pred             h--------c-------------CCCCeEEE-EeCCCCHHHHHHHHhCCCCEEEC
Confidence            0        0             12456554 55555677788888999999664

>d2iwxa1 d.122.1.1 (A:2-214) HSP90 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
superfamily: ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
family: Heat shock protein 90, HSP90, N-terminal domain
domain: HSP90
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=83.39  E-value=0.36  Score=47.36  Aligned_cols=57  Identities=21%  Similarity=0.320  Sum_probs=35.5

Q ss_pred             EEEEEecCCCCCcCcHhhhhhhccCCCcc----------ccCcCCCccccHHHHHHHHHHhCCEEEEEeec
Q 039716          593 RCDVYDTGIGIPENALPTLFRKYMQVSAD----------HARKYGGTGLGLAICKQLVELMGGRLTVTSKV  653 (1002)
Q Consensus       593 ~i~V~DtGiGI~~e~l~~IF~pF~q~~~~----------~~~~~~GtGLGLaI~k~Lve~~gG~I~v~S~~  653 (1002)
                      .+.|.|||+||+.+.+.+-+-........          ...--|-.|+|++-|--+.+    .|.|.|..
T Consensus        73 ~l~i~DnGiGMt~~~~~~~l~~ia~S~~~~~~~~~~~~~~~~~IGqFGIGfyS~Fmvad----~v~V~trs  139 (213)
T d2iwxa1          73 VLEIRDSGIGMTKAELINNLGTIAKSGTKAFMEALSAGADVSMIGQFGVGFYSLFLVAD----RVQVISKS  139 (213)
T ss_dssp             EEEEEECSSCCCHHHHHHHHTTCCCSTHHHHHHHHHHTCCGGGGGGGTCGGGGGGGTEE----EEEEEEEC
T ss_pred             eeEEecCCccccHHHHHHHHhhhhcccchHHHhhhhhhhhhhhhcccccchhhhhhhcc----ceeEEeec
Confidence            36799999999999988766443322110          00113567899887765544    46666654

>d1kija2 d.122.1.2 (A:9-220) DNA gyrase B {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a+b)
fold: ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
superfamily: ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
family: DNA gyrase/MutL, N-terminal domain
domain: DNA gyrase B
species: Thermus thermophilus [TaxId: 274]

Probab=80.22  E-value=1.7  Score=42.19  Aligned_cols=65  Identities=20%  Similarity=0.262  Sum_probs=38.7

Q ss_pred             EEEEecCCCCCcCcH--------hhhhhhccCCCc----cccCcCCCccccHHHHHHHHHHhCCEEEEEeecCCceEEEE
Q 039716          594 CDVYDTGIGIPENAL--------PTLFRKYMQVSA----DHARKYGGTGLGLAICKQLVELMGGRLTVTSKVHCGSTFTF  661 (1002)
Q Consensus       594 i~V~DtGiGI~~e~l--------~~IF~pF~q~~~----~~~~~~~GtGLGLaI~k~Lve~~gG~I~v~S~~g~GTtF~~  661 (1002)
                      |+|.|+|.|||-+..        +-||.-+.....    ......|.-|+|+++|.-+.+.    +.|+..- .|-.++.
T Consensus        60 i~V~ddG~GIpv~~h~~~~~~~~e~if~~l~~~~~~d~~~~~~sgG~hGvGa~vvNalS~~----~~v~v~r-~~k~~~~  134 (212)
T d1kija2          60 LTVEDNGRGIPVDLMPEEGKPAVEVIYNTLHSGGKFEQGAYKVSGGLHGVGASVVNALSEW----TVVEVFR-EGKHHRI  134 (212)
T ss_dssp             EEEEECSSCCCCSEETTTTEEHHHHHHHSSCEESGGGGSSCCCCSCSSTTSHHHHHHTEEE----EEEEEEE-TTEEEEE
T ss_pred             EEEEECCcccccccccccCcceEEEEEEEEcccccccCCCceecCCCccccceEEEEeccc----eEEEEEE-ecceeee
Confidence            679999999998763        345544433211    1122335679999988877664    4454443 2444555


Q ss_pred             EE
Q 039716          662 IL  663 (1002)
Q Consensus       662 ~L  663 (1002)
                      .+
T Consensus       135 ~f  136 (212)
T d1kija2         135 AF  136 (212)
T ss_dssp             EE
T ss_pred             EE
Confidence            44