Citrus Sinensis ID: 001215

Local Sequence Feature Prediction

Prediction and (Method)	Result

Residue Number Marker

Protein Sequence

Secondary Structure (PSIPRED)

Secondary Structure Prediction (SSPRO)

Coil and Loop (DISEMBL)

Flexible Loop (DISEMBL)

Low Complexity Region (SEG)

Disordered region (IsUnstruct)

Disordered Region (DISOPRED)

Disordered Region (DISEMBL)

Disordered Region (DISPRO)

Transmembrane Helix (TMHMM)

Transmembrane Helix (HMMTOP)

Transmembrane Helix (MEMSAT)

TM Helix, Signal Peptide (MEMSAT_SVM)

TM Helix, Signal Peptide (Phobius)

Signal Peptide (SignalP HMM Mode)

Signal Peptide (SignalP NN Mode)

Coiled Coils (COILS)

Positional Conservation

--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340-------350-------360-------370-------380-------390-------400-------410-------420-------430-------440-------450-------460-------470-------480-------490-------500-------510-------520-------530-------540-------550-------560-------570-------580-------590-------600-------610-------620-------630-------640-------650-------660-------670-------680-------690-------700-------710-------720-------730-------740-------750-------760-------770-------780-------790-------800-------810-------820-------830-------840-------850-------860-------870-------880-------890-------900-------910-------920-------930-------940-------950-------960-------970-------980-------990------1000------1010------1020------1030------1040------1050------1060------1070------1080------1090------1100------1110------1120--

MSSKSTNKTNYSRSSSARSKQNARVAAQTSIDAKLAEDFDESDFDYSTSVNISSSTSNVPSSTVSAYLQRVQRGRLIQPFGCMIAVDEQNFTVLGYSENAPEMLDLAPHAVPNIEQQDALTLGIDVRTLFTSSGAAALQKAANFGEVNLLNPILIHCKTSGKPFYAILHRIDVGLVIDLEPVNPDDVPVTAAGALKSYKLAAKAISRLQSLPSGNISLLCDVLVNEVSDLTGYDRVMVYKFHEDEHGEVVAECRRPDLEPYLGFHYPATDIPQASRFLIMKNKVRMICDCLAPPVKVIQDKKLDQPLSLCGSTLRAPHGCHARYMENMGSIASLVMSVTINEAEDELDNDQEQGRKLWGLVVCHHTSPRFVPFPLRYACEFLIQVFGVQVNKEVELSAQLREKHILRTQTVLCDMLLRDSPVGIVTQTPNVMDLVKCDGAALYYRGKLWLLGVTPTEEQIKDIAEWLLEYHRGSTGLSTDSLVEAGYPGALALGDAVCGIAAVKITSKDFLFWFRSHTAKEIKWGGAKHDSGGKDGGRKMHPRSSFKAFLEVVKQRSLPWEDVEMDAIHSLQLILRGSLQDEVAEDSKMIVNVPSVDDRIEKIDELRIITNEMVRLIETAAVPILAVDASGNVNGWNSKAAELTGLTVDQAIGTALVDLVAGDSVDVVKNMLSSAFLGIEERNVEIKLRAFGPRETSGPVILVVNACCTQDTKENVIGVCFVGQDITGQKLVMDKYTRIQGDYVGIVSSPSALIPPIFMTDEDGRCLEWNDGMEKLSGLKREEAIERMLIGEVFTVKNFGCRVKNHDTLTKLRIVMNKVISGQDADKILFGFFDQQGKYVEALLSANKRTNAEGKISGILCFLHVASPELQYALQVQRISEQAAANSLNKLEYIRREIRKPLNGIAFMQNLMGTSDLSEEQKQLLKTSVLCQEQLTNIVDDTDIESIEECYMVLKSGEFNLGEALDAVMTQVMIPSREHQVQFIRDLPAEVSTMNLHGDKLRLQQVLSDFLTNALIFTPAFEGSSIAFRVIPQKERIGKNIHIVHLEFRITHPAPGIPEKLIHDMFYHSQGASREGLGLYISQKLVKLMNGTVQYIREAERSSFLILIEFPLAHQKDADKTK

ccccccccccccccccccccccHHHHHccccccccccccccccccccccEEccccccccccccccHHHcccccccccccccEEEEEEccccEEEEEcccHHHHHcccccccccccccccccccccHHHHccHHHHHHHHHHHccccccccccEEEEEcccccEEEEEEEEEccEEEEEEEEcccccccccHHHHHHHHHHHHHHHHHHcccccccHHHHHHHHHHHHHHHHcccEEEEEEEccccccEEEEEEEccccccccccccccccccHHHHHHHHHccEEEEcccccccccEEccccccccccccccccccccHHHHHHHHHccccEEEEEEEEEEcccccccccccccccEEEEEEccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccHHHHccccEEEEEEccEEEEccccccHHHHHHHHHHHHHHccccEEEEEcccccccccccccccccccEEEEEEcccccEEEEEccccccEEEcccccccccccccccccccccHHHHHHHHHHcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccHHHHcHHHHHHHHHHHHHHHHHccccccccccccHHHHHHHHHHHHccccccccccccccccccccHHHHHHHHHHHHHcccccccEEEEEcccccccccccEEEEEEccccccccccEEEEEEEEEEccccEEEEHHHHcccccEEEEEEccccccccEEEEcccccccccHHHHHHHccccHHHHHHHccccEEccccccccccccccccHHHHHHHHHccccccccEEEEEEEEccccEEEEEEEccccccccccEEEEEEEEEEccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcHHHHHHHHHHHHccccccHHHHHHHHHHHHHHHHHHHHHHHccccHHHccccccccccccHHHHHHHHHHHHcccccccccEEEEEccccccccEEEccHHHHHHHHHHHHHHHHHccccccccEEEEEEEEccccccccEEEEEEEEEEEcccccccHHHHHHHcccccccccccHHHHHHHHHHHHcccEEEEEEEccEEEEEEEEEccccccccccccc

cccccccccccccccccccccccEEEEEEccccEEEEEEEcccccccccEEcccccccccHHHHHHHHHHHHHccccccccEEEEEEcccEEEEEEcccHHHHHccccccccccccccEEEEcccHHHHcccHHHHHHHHHHHHHHHcccccEEEEEccccccEEEEEEEEEEEEEEEccccccccccHHHHHHHHHHHHHHHHHHHHHccccccHHHHHHHHHHHHHHHccccEEEEEEEccccccEEEEEEcccccccccccccccccHHHHHHHHHHHccEEEEEEcccccEEEEEccccccccEEccccccccccHHHHHHHHHcHHHHHHEEEEEEccccccccccccccEEEEEEEEcccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccEEEEcccccHcHEccccEEEEEcccEEEEcccccHHHHHHHHHHHHHHcccccccccHHHHHcccccHHHHccHHcccEEEEEccccEEEEEccccHHHHccccccccccccccccccccccHHHHHHHHHHHccccHHHHHHHHHHHHHHHHHHHHHccccccccEEEEccccccccccHHHHHHHHHHHHHHHHHccccEEEEEccccEcccHHHHHHHccccHHHHHcHHHHHHHHHcHHHHHHHHHHHHHccccHccEEEEEEEcccccccccEEEEEEccccccccccEEEEEEEEEcccccHHHHHHHEEEccccEEEEccccccccccEccccccccHHHHHHHHHHccccHHHHHHHHccHHHHcccccccccccHHHHHHHHHHHHHHcccccccccccccEcccccEEEEEEEEcccccccccEEEEEEEEEcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccHHHHHHHHHccccccHHHHHHHHHHHHHHHHHHHHHHcccHHHHHcccEEEccEEEEHHHHHHHHHHHHHHHHHHcccEEEEcccHHHcccEccccHHHHHHHHHHHHHHHHHccccccccEEEEEEEcccccccccEEEEEEEEEEEcccccccHHHHHHHHcccccccHHHHHHHHHHHHHHHHcccEEEEEEcccEEEEEEEEEcccccccccccc

msskstnktnysrsssARSKQNARVAAQTSIDAklaedfdesdfdystsvnissstsnvpsstVSAYLQRVQRgrliqpfgcmiavdeqnftvlgysenapemldlaphavpnieqqdaltlgidvrtlfTSSGAAALQKAAnfgevnllnpilihcktsgkpfyAILHRIDVGlvidlepvnpddvpvtaaGALKSYKLAAKAISRlqslpsgnisLLCDVLVNEvsdltgydrVMVYKFhedehgevvaecrrpdlepylgfhypatdipqasRFLIMKNKVRMIcdclappvkviqdkkldqplslcgstlraphgchaRYMENMGSIASLVMSVTINEaedeldndqeqGRKLWGLVVchhtsprfvpfpLRYACEFLIQVFGVQVNKEVELSAQLREKHILRTQTVLCDMllrdspvgivtqtpnvmdlvkcdgaalyyrgklwllgvtpteEQIKDIAEWLLEYhrgstglstdslveagypgalaLGDAVCGIAAVKITSKDFLFWFRSHTAKeikwggakhdsggkdggrkmhprsSFKAFLEVVKqrslpwedvEMDAIHSLQLILRGSLQDEVAEDSKmivnvpsvddrIEKIDELRIITNEMVRLIETAAVpilavdasgnvngwnskaaeltgLTVDQAIGTALVDLVAGDSVDVVKNMLSSAFLGIEERNVEIKlrafgpretsgpVILVVNACctqdtkenvigvcfvgqditgqklVMDKYTRIQGdyvgivsspsalippifmtdedgrclewndgmeklsglKREEAIERMLIGEVftvknfgcrvknhdtLTKLRIVMNKvisgqdadKILFGFFDQQGKYVEALLSANkrtnaegkISGILCFLHVASPELQYALQVQRISEQAAANSLNKLEYIRREIRKPLNGIAFMQNLMGTSDLSEEQKQLLKTSVLCQEQltnivddtdiESIEECYMVLKSGEFNLGEALDAVMtqvmipsreHQVQFIRDLPAEVSTMNLHGDKLRLQQVLSDFLTNAliftpafegssiafrvipqkerigknihiVHLEfrithpapgipeklIHDMfyhsqgasreglGLYISQKLVKLMNGTVQYIREAERSSFLILIEfplahqkdadktk

msskstnktnysrsssarskqnARVAAQTSIDAKLAEDFDESDFDYSTSVnissstsnvpsstVSAYLQRVQRGRLIQPFGCMIAVDEQNFTVLGYSENAPEMLDLAPHAVPNIEQQDALTLGIDVRTLFTSSGAAALQKAANFGEVNLLNPILIHCKTSGKPFYAILHRIDVGLVIDLEPVNPDDVPVTAAGALKSYKLAAKAISRLQSLPSGNISLLCDVLVNEVSDLTGYDRVMVYKFHEDEHGEVVAECRRPDLEPYLGFHYPATDIPQASRFLIMKNKVRMICDCLAPPVKVIQDKKLDQPLSLCGSTLRAPHGCHARYMENMGSIASLVMSVTINEAEDELDNDQEQGRKLWGLVVCHHTSPRFVPFPLRYACEFLIQVFGVQVNKEVELSAQLREKHILRTQTVLCDMLLRDSPVgivtqtpnvmdLVKCDGAALYYRGKLWLLGVTPTEEQIKDIAEWLLEYHRGSTGLSTDSLVEAGYPGALALGDAVCGIAAVKITSKDFLFWFRSHTakeikwggakhdsggkdggrkmhprSSFKAFLEVVKQRSLPWEDVEMDAIHSLQLILRGSLQDEVAEDSkmivnvpsvddrieKIDELRIITNEMVRLIETAAVPILAVDASGNVNGWNSKAAELTGLTVDQAIGTALVDLVAGDSVDVVKNMLSsaflgieernVEIKLRafgpretsgpVILVVNACCTQDTKENVIGVCFVGQDITGQKLVMDKYTRIQGDYVGIVSSPSALIPPIFMTDEDGRCLEWNDGMEKLSGLKREEAIERMLIGevftvknfgcrvknhdtltkLRIVMNKVISGQDADKILFGFFDQQGKYVEALLSANKRTNAEGKISGILCFLHVASPELQYALQVQRISEQAAANSLNKLEYIRREIRKPLNGIAFMQNLMGTSDLSEEQKQLLKTSVLCQEQltnivddtdiESIEECYMVLKSGEFNLGEALDAVMTQVMIPSREHQVQFIRDLPAEVSTMNLHGDKLRLQQVLSDFLTNALIFtpafegssiAFRVIPQKERIGKNIHIVHLEFRITHPAPGIPEKLIHDMFYHSQGASREGLGLYISQKLVKLMNGTVQYIREAERSSFLILIefplahqkdadktk

MSSKSTNKTNYSRSSSARSKQNARVAAQTSIDAKLAEDFDESDFDYstsvnissstsnvpsstvsAYLQRVQRGRLIQPFGCMIAVDEQNFTVLGYSENAPEMLDLAPHAVPNIEQQDALTLGIDVRTLFTSSGAAALQKAANFGEVNLLNPILIHCKTSGKPFYAILHRIDVGLVIDLEPVNPDDVPVTAAGALKSYKLAAKAISRLQSLPSGNISLLCDVLVNEVSDLTGYDRVMVYKFHEDEHGEVVAECRRPDLEPYLGFHYPATDIPQASRFLIMKNKVRMICDCLAPPVKVIQDKKLDQPLSLCGSTLRAPHGCHARYMENMGSIASLVMSVTINEAEDELDNDQEQGRKLWGLVVCHHTSPRFVPFPLRYACEFLIQVFGVQVNKEVELSAQLREKHILRTQTVLCDMLLRDSPVGIVTQTPNVMDLVKCDGAALYYRGKLWLLGVTPTEEQIKDIAEWLLEYHRGSTGLSTDSLVEAGYPGALALGDAVCGIAAVKITSKDFLFWFRSHTAKEIKWGGAKHDSGGKDGGRKMHPRSSFKAFLEVVKQRSLPWEDVEMDAIHSLQLILRGSLQDEVAEDSKMIVNVPSVDDRIEKIDELRIITNEMVRLIETAAVPILAVDASGNVNGWNSKAAELTGLTVDQAIGTALVDLVAGDSVDVVKNMLSSAFLGIEERNVEIKLRAFGPRETSGPVILVVNACCTQDTKENVIGVCFVGQDITGQKLVMDKYTRIQGDYVGIVSSPSALIPPIFMTDEDGRCLEWNDGMEKLSGLKREEAIERMLIGEVFTVKNFGCRVKNHDTLTKLRIVMNKVISGQDADKILFGFFDQQGKYVEALLSANKRTNAEGKISGILCFLHVASPELQYALQVQRISEQAAANSLNKLEYIRREIRKPLNGIAFMQNLMGTSDLSEEQKQLLKTSVLCQEQLTNIVDDTDIESIEECYMVLKSGEFNLGEALDAVMTQVMIPSREHQVQFIRDLPAEVSTMNLHGDKLRLQQVLSDFLTNALIFTPAFEGSSIAFRVIPQKERIGKNIHIVHLEFRITHPAPGIPEKLIHDMFYHSQGASREGLGLYISQKLVKLMNGTVQYIREAERSSFLILIEFPLAHQKDADKTK

****************************************************************SAYLQRVQRGRLIQPFGCMIAVDEQNFTVLGYSENAPEMLDLAPHAVPNIEQQDALTLGIDVRTLFTSSGAAALQKAANFGEVNLLNPILIHCKTSGKPFYAILHRIDVGLVIDLEPVNPDDVPVTAAGALKSYKLAAKAISRLQSLPSGNISLLCDVLVNEVSDLTGYDRVMVYKFHEDEHGEVVAECRRPDLEPYLGFHYPATDIPQASRFLIMKNKVRMICDCLAPPVKVIQDKKLDQPLSLCGSTLRAPHGCHARYMENMGSIASLVMSVTIN************GRKLWGLVVCHHTSPRFVPFPLRYACEFLIQVFGVQVNKEVELSAQLREKHILRTQTVLCDMLLRDSPVGIVTQTPNVMDLVKCDGAALYYRGKLWLLGVTPTEEQIKDIAEWLLEYHRGSTGLSTDSLVEAGYPGALALGDAVCGIAAVKITSKDFLFWFRSHTAKEIKWG********************FKAFLEVVKQRSLPWEDVEMDAIHSLQLILRGSLQDEVAEDSKMIVNVPSVDDRIEKIDELRIITNEMVRLIETAAVPILAVDASGNVNGWNSKAAELTGLTVDQAIGTALVDLVAGDSVDVVKNMLSSAFLGIEERNVEIKLRAFGPRETSGPVILVVNACCTQDTKENVIGVCFVGQDITGQKLVMDKYTRIQGDYVGIVSSPSALIPPIFMTDEDGRCLEWNDGMEKLSGLKREEAIERMLIGEVFTVKNFGCRVKNHDTLTKLRIVMNKVISGQDADKILFGFFDQQGKYVEALLSANKRTNAEGKISGILCFLHVASPELQYALQVQRISEQAAANSLNKLEYIRREIRKPLNGIAFMQNLMGT********QLLKTSVLCQEQLTNIVDDTDIESIEECYMVLKSGEFNLGEALDAVMTQVMIPSREHQVQFIRDLPAEVSTMNLHGDKLRLQQVLSDFLTNALIFTPAFEGSSIAFRVIPQKERIGKNIHIVHLEFRITHPAPGIPEKLIHDMFYHSQGASREGLGLYISQKLVKLMNGTVQYIREAERSSFLILIEFPLA*********

******************************IDAKLAED************************TVSAYLQRVQRGRLIQPFGCMIAVDEQNFTVLGYSENAPEMLDLAPHAVPNIEQQDALTLGIDVRTLFTSSGAAALQKAANFGEVNLLNPILIHCKTSGKPFYAILHRIDVGLVIDLEPVNPDDV*VTAAGALKSYKLAAKAIS******SGNISLLCDVLVNEVSDLTGYDRVMVYKFHEDEHGEVVAECRRPDLEPYLGFHYPATDIPQASRFLIMKNKVRMICDCLAPPVKVIQDKKLDQPLSLCGSTLRAPHGCHARYMENMGSIASLVMSVTIN***************LWGLVVCHHTSPRFVPFPLRYACEFLIQVFGVQVNKEVELSAQLREKHILRTQTVLCDMLLRDSPVGIVTQTPNVMDLVKCDGAALYYRGKLWLLGVTPTEEQIKDIAEWLLEYHRGSTGLSTDSLVEAGYPGALALGDAVCGIAAVKITSKDFLFWFRSHTAKEIKWGGAK**************RSSFKAFLEVVKQRSLPWEDVEMDAIHSLQLILRGSLQDEVA********************ELRIITNEMVRLIETAAVPILAVDASGNVNGWNSKAAELTGLTVDQAIGTALVDLVAGDSVDVVKNMLSSAFLGIEERNVEIKLRAFGPRETSGPVILVVNACCTQDTKENVIGVCFVGQDITGQKLVMD*YTRIQGDYVGIVSSPSALIPPIFMTDEDGRCLEWNDGMEKLSGLKREEAIERMLIGEVFTVKNFGCRVKNHDTLTKLRIVMNKVISGQDADKILFGFFDQQGKYVEALLSANKRTNAEGKISGILCFLHVASP*****************NSLNKLEYIRREIRKPLNGIAFMQNLM******************CQEQLTNIVDDTDIESIEECYMVLKSGEFNLGEALDAVMTQVMIPSREHQVQFIRDLPAEVSTMNLHGDKLRLQQVLSDFLTNALIFTPAFEGSSIAFRVIPQKERIGKNIHIVHLEFRITHPAPGIPEKLIHDM*********EGLGLYISQKLVKLMNGTVQYIREAERSSFLILIE*************

****************************TSIDAKLAEDFDESDFDYSTS**************VSAYLQRVQRGRLIQPFGCMIAVDEQNFTVLGYSENAPEMLDLAPHAVPNIEQQDALTLGIDVRTLFTSSGAAALQKAANFGEVNLLNPILIHCKTSGKPFYAILHRIDVGLVIDLEPVNPDDVPVTAAGALKSYKLAAKAISRLQSLPSGNISLLCDVLVNEVSDLTGYDRVMVYKFHEDEHGEVVAECRRPDLEPYLGFHYPATDIPQASRFLIMKNKVRMICDCLAPPVKVIQDKKLDQPLSLCGSTLRAPHGCHARYMENMGSIASLVMSVTINEAEDELDNDQEQGRKLWGLVVCHHTSPRFVPFPLRYACEFLIQVFGVQVNKEVELSAQLREKHILRTQTVLCDMLLRDSPVGIVTQTPNVMDLVKCDGAALYYRGKLWLLGVTPTEEQIKDIAEWLLEYHRGSTGLSTDSLVEAGYPGALALGDAVCGIAAVKITSKDFLFWFRSHTAKEIKW*****************PRSSFKAFLEVVKQRSLPWEDVEMDAIHSLQLILRGSLQDEVAEDSKMIVNVPSVDDRIEKIDELRIITNEMVRLIETAAVPILAVDASGNVNGWNSKAAELTGLTVDQAIGTALVDLVAGDSVDVVKNMLSSAFLGIEERNVEIKLRAFGPRETSGPVILVVNACCTQDTKENVIGVCFVGQDITGQKLVMDKYTRIQGDYVGIVSSPSALIPPIFMTDEDGRCLEWNDGMEKLSGLKREEAIERMLIGEVFTVKNFGCRVKNHDTLTKLRIVMNKVISGQDADKILFGFFDQQGKYVEALLSANKRTNAEGKISGILCFLHVASPELQYALQVQRISEQAAANSLNKLEYIRREIRKPLNGIAFMQNLMGTSDLSEEQKQLLKTSVLCQEQLTNIVDDTDIESIEECYMVLKSGEFNLGEALDAVMTQVMIPSREHQVQFIRDLPAEVSTMNLHGDKLRLQQVLSDFLTNALIFTPAFEGSSIAFRVIPQKERIGKNIHIVHLEFRITHPAPGIPEKLIHDMFYHSQGASREGLGLYISQKLVKLMNGTVQYIREAERSSFLILIEFPLAH********

*********************NARVAAQTSIDAKLAEDFDESDFDYSTSVNISSSTSNVPSSTVSAYLQRVQRGRLIQPFGCMIAVDEQNFTVLGYSENAPEMLDLAPHAVPNIEQQDALTLGIDVRTLFTSSGAAALQKAANFGEVNLLNPILIHCKTSGKPFYAILHRIDVGLVIDLEPVNPDDVPVTAAGALKSYKLAAKAISRLQSLPSGNISLLCDVLVNEVSDLTGYDRVMVYKFHEDEHGEVVAECRRPDLEPYLGFHYPATDIPQASRFLIMKNKVRMICDCLAPPVKVIQDKKLDQPLSLCGSTLRAPHGCHARYMENMGSIASLVMSVTINEAE*******EQGRKLWGLVVCHHTSPRFVPFPLRYACEFLIQVFGVQVNKEVELSAQLREKHILRTQTVLCDMLLRDSPVGIVTQTPNVMDLVKCDGAALYYRGKLWLLGVTPTEEQIKDIAEWLLEYHRGSTGLSTDSLVEAGYPGALALGDAVCGIAAVKITSKDFLFWFRSHTAKEIKWGGAK***********MHPRSSFKAFLEVVKQRSLPWEDVEMDAIHSLQLILRGSLQDEVAEDSKMIVNVPSVDDRIEKIDELRIITNEMVRLIETAAVPILAVDASGNVNGWNSKAAELTGLTVDQAIGTALVDLVAGDSVDVVKNMLSSAFLGIEERNVEIKLRAFGPRETSGPVILVVNACCTQDTKENVIGVCFVGQDITGQKLVMDKYTRIQGDYVGIVSSPSALIPPIFMTDEDGRCLEWNDGMEKLSGLKREEAIERMLIGEVFTVKNFGCRVKNHDTLTKLRIVMNKVISGQDADKILFGFFDQQGKYVEALLSANKRTNAEGKISGILCFLHVASPELQYALQVQRISEQAAANSLNKLEYIRREIRKPLNGIAFMQNLMGTSDLSEEQKQLLKTSVLCQEQLTNIVDDTDIESIEECYMVLKSGEFNLGEALDAVMTQVMIPSREHQVQFIRDLPAEVSTMNLHGDKLRLQQVLSDFLTNALIFTPAFEGSSIAFRVIPQKERIGKNIHIVHLEFRITHPAPGIPEKLIHDMFYHSQGASREGLGLYISQKLVKLMNGTVQYIREAERSSFLILIEFPLA*********

oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo

oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii

SSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo

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no confident homologs detected

Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Alignment graph	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query		1122	2.2.26 [Sep-21-2011]
Q10CQ8		1137	Phytochrome C OS=Oryza sa	yes	no	0.990	0.977	0.693	0.0
A2XM23		1137	Phytochrome C OS=Oryza sa	N/A	no	0.990	0.977	0.693	0.0
P93528		1135	Phytochrome C OS=Sorghum	N/A	no	0.991	0.979	0.689	0.0
P14714		1111	Phytochrome C OS=Arabidop	yes	no	0.980	0.990	0.644	0.0
Q40762		1136	Phytochrome OS=Picea abie	N/A	no	0.974	0.962	0.662	0.0
Q39557		1121	Phytochrome 2 OS=Ceratodo	N/A	no	0.989	0.990	0.614	0.0
Q01549		1134	Phytochrome 1 OS=Selagine	N/A	no	0.992	0.982	0.613	0.0
P36505		1132	Phytochrome 1 OS=Physcomi	N/A	no	0.971	0.962	0.613	0.0
Q41046		1131	Phytochrome OS=Pinus sylv	N/A	no	0.975	0.967	0.594	0.0
P93673		1124	Phytochrome type A OS=Lat	N/A	no	0.988	0.986	0.573	0.0

>sp\|Q10CQ8\|PHYC_ORYSJ Phytochrome C OS=Oryza sativa subsp. japonica GN=PHYC PE=2 SV=1	Back alignment and function desciption

 Score = 1641 bits (4249), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 780/1124 (69%), Positives = 936/1124 (83%), Gaps = 13/1124 (1%)

Query: 2    SSKSTNKTNYSRSSSARSKQNARVAAQTSIDAKLAEDFDESD--FDYSTSVNISSSTSNV 59
            SS+S N+   SRSSSARSK +ARV AQT +DA+L  +F+ S   FDYS+SV  +++ S  
Sbjct: 3    SSRSNNRATCSRSSSARSKHSARVVAQTPMDAQLHAEFEGSQRHFDYSSSVG-AANRSGA 61

Query: 60   PSSTVSAYLQRVQRGRLIQPFGCMIAVDEQNFTVLGYSENAPEMLDLAPHAVPNIEQQDA 119
             +S VSAYLQ +QRGR +QPFGC++AV  + F +L YSENA EMLDL PHAVP I+Q++A
Sbjct: 62   TTSNVSAYLQNMQRGRFVQPFGCLLAVHPETFALLAYSENAAEMLDLTPHAVPTIDQREA 121

Query: 120  LTLGIDVRTLFTSSGAAALQKAANFGEVNLLNPILIHCKTSGKPFYAILHRIDVGLVIDL 179
            L +G DVRTLF S    ALQKAA FG+VNLLNPIL+H +TSGKPFYAI+HRIDVGLVIDL
Sbjct: 122  LAVGTDVRTLFRSHSFVALQKAATFGDVNLLNPILVHARTSGKPFYAIMHRIDVGLVIDL 181

Query: 180  EPVNPDDVPVTAAGALKSYKLAAKAISRLQSLPSGNISLLCDVLVNEVSDLTGYDRVMVY 239
            EPVNP D+PVTA GA+KSYKLAA+AI+RLQSLPSGN+SLLCDVLV EVS+LTGYDRVM Y
Sbjct: 182  EPVNPVDLPVTATGAIKSYKLAARAIARLQSLPSGNLSLLCDVLVREVSELTGYDRVMAY 241

Query: 240  KFHEDEHGEVVAECRRPDLEPYLGFHYPATDIPQASRFLIMKNKVRMICDCLAPPVKVIQ 299
            KFHEDEHGEV+AEC+R DLEPYLG HYPATDIPQASRFL MKNKVRMICDC A PVK+IQ
Sbjct: 242  KFHEDEHGEVIAECKRSDLEPYLGLHYPATDIPQASRFLFMKNKVRMICDCSATPVKIIQ 301

Query: 300  DKKLDQPLSLCGSTLRAPHGCHARYMENMGSIASLVMSVTINEAEDELDN----DQEQGR 355
            D  L QP+S+CGSTLRAPHGCHA+YM +MGS+ASLVMSVTINE ED+  +     Q +GR
Sbjct: 302  DDSLTQPISICGSTLRAPHGCHAQYMASMGSVASLVMSVTINEDEDDDGDTGSDQQPKGR 361

Query: 356  KLWGLVVCHHTSPRFVPFPLRYACEFLIQVFGVQVNKEVELSAQLREKHILRTQTVLCDM 415
            KLWGL+VCHHTSPRFVPFPLRYACEFL+QVFG+Q+NKEVEL+AQ +E+HILRTQT+LCDM
Sbjct: 362  KLWGLMVCHHTSPRFVPFPLRYACEFLLQVFGIQINKEVELAAQAKERHILRTQTLLCDM 421

Query: 416  LLRDSPVGIVTQTPNVMDLVKCDGAALYYRGKLWLLGVTPTEEQIKDIAEWLLEYHRGST 475
            LLRD+PVGI TQ+PNVMDLVKCDGAALYY+ +LW+LG TP+E +IK+I  WL EYH GST
Sbjct: 422  LLRDAPVGIFTQSPNVMDLVKCDGAALYYQNQLWVLGSTPSEAEIKNIVAWLQEYHDGST 481

Query: 476  GLSTDSLVEAGYPGALALGDAVCGIAAVKITSKDFLFWFRSHTAKEIKWGGAKHDS-GGK 534
            GLSTDSLVEAGYPGA ALGD VCG+AA+KI+SKDF+FWFRSHTAKEIKWGGAKH+     
Sbjct: 482  GLSTDSLVEAGYPGAAALGDVVCGMAAIKISSKDFIFWFRSHTAKEIKWGGAKHEPIDAD 541

Query: 535  DGGRKMHPRSSFKAFLEVVKQRSLPWEDVEMDAIHSLQLILRGSLQDEVAE---DSKMIV 591
            D GRKMHPRSSFKAFLEVVK RS+PWEDVEMDAIHSLQLILRGSLQDE A    ++K IV
Sbjct: 542  DNGRKMHPRSSFKAFLEVVKWRSVPWEDVEMDAIHSLQLILRGSLQDEDANKNNNAKSIV 601

Query: 592  NVPSVD-DRIEKIDELRIITNEMVRLIETAAVPILAVDASGNVNGWNSKAAELTGLTVDQ 650
              PS D  +I+ + ELR +TNEMVRLIETA  PILAVD +G++NGWN+KAAELTGL V +
Sbjct: 602  TAPSDDMKKIQGLLELRTVTNEMVRLIETATAPILAVDITGSINGWNNKAAELTGLPVME 661

Query: 651  AIGTALVDLVAGDSVDVVKNMLSSAFLGIEERNVEIKLRAFGPRETSGPVILVVNACCTQ 710
            AIG  LVDLV  DSV+VVK +L+SA  GIEE+N++IKL+ F  +E +GPVIL+VNACC++
Sbjct: 662  AIGKPLVDLVIDDSVEVVKQILNSALQGIEEQNLQIKLKTFNHQENNGPVILMVNACCSR 721

Query: 711  DTKENVIGVCFVGQDITGQKLVMDKYTRIQGDYVGIVSSPSALIPPIFMTDEDGRCLEWN 770
            D  E V+GVCFV QD+TGQ ++MDKYTRIQGDYV IV +PS LIPPIFM ++ G CLEWN
Sbjct: 722  DLSEKVVGVCFVAQDMTGQNIIMDKYTRIQGDYVAIVKNPSELIPPIFMINDLGSCLEWN 781

Query: 771  DGMEKLSGLKREEAIERMLIGEVFTVKNFGCRVKNHDTLTKLRIVMNKVISGQDADKILF 830
            + M+K++G+KRE+A++++LIGEVFT   +GCRVK+H TLTKL I+MN VISGQD +K+LF
Sbjct: 782  EAMQKITGIKREDAVDKLLIGEVFTHHEYGCRVKDHGTLTKLSILMNTVISGQDPEKLLF 841

Query: 831  GFFDQQGKYVEALLSANKRTNAEGKISGILCFLHVASPELQYALQVQRISEQAAANSLNK 890
            GFF+  GKY+E+L++A KRT+AEGKI+G LCFLHVASPELQ+ALQVQ++SEQAA NS  +
Sbjct: 842  GFFNTDGKYIESLMTATKRTDAEGKITGALCFLHVASPELQHALQVQKMSEQAAMNSFKE 901

Query: 891  LEYIRREIRKPLNGIAFMQNLMGTSDLSEEQKQLLKTSVLCQEQLTNIVDDTDIESIEEC 950
            L YIR+E+R PLNG+ F +NL+  SDL+EEQ++LL ++VLCQEQL  I+ DTD+ESIE+C
Sbjct: 902  LTYIRQELRNPLNGMQFTRNLLEPSDLTEEQRKLLASNVLCQEQLKKILHDTDLESIEQC 961

Query: 951  YMVLKSGEFNLGEALDAVMTQVMIPSREHQVQFIRDLPAEVSTMNLHGDKLRLQQVLSDF 1010
            Y  + + +FNL EAL+ V+ Q M  S+E Q+   RD PAEVS M+L GD LRLQQVL+DF
Sbjct: 962  YTEMSTVDFNLEEALNTVLMQAMPQSKEKQISIDRDWPAEVSCMHLCGDNLRLQQVLADF 1021

Query: 1011 LTNALIFTPAFEGSSIAFRVIPQKERIGKNIHIVHLEFRITHPAPGIPEKLIHDMFYHSQ 1070
            L   L FT   EG  I  +VIP+ E IG  + I HLEFR+ HPAPG+PE LI +MF HS 
Sbjct: 1022 LACMLQFTQPAEG-PIVLQVIPRMENIGSGMQIAHLEFRLVHPAPGVPEALIQEMFRHSP 1080

Query: 1071 GASREGLGLYISQKLVKLMNGTVQYIREAERSSFLILIEFPLAH 1114
            GASREGLGLYISQKLVK M+GTVQY+RE+E SSF++L+EFP+A 
Sbjct: 1081 GASREGLGLYISQKLVKTMSGTVQYLRESESSSFIVLVEFPVAQ 1124

Regulatory photoreceptor which exists in two forms that are reversibly interconvertible by light: the Pr form that absorbs maximally in the red region of the spectrum and the Pfr form that absorbs maximally in the far-red region. Photoconversion of Pr to Pfr induces an array of morphogenic responses, whereas reconversion of Pfr to Pr cancels the induction of those responses. Pfr controls the expression of a number of nuclear genes including those encoding the small subunit of ribulose-bisphosphate carboxylase, chlorophyll A/B binding protein, protochlorophyllide reductase, rRNA, etc. It also controls the expression of its own gene(s) in a negative feedback fashion.
Oryza sativa subsp. japonica (taxid: 39947)

>sp\|A2XM23\|PHYC_ORYSI Phytochrome C OS=Oryza sativa subsp. indica GN=PHYC PE=2 SV=2	Back alignment and function description

>sp\|P93528\|PHYC_SORBI Phytochrome C OS=Sorghum bicolor GN=PHYC PE=2 SV=1	Back alignment and function description

>sp\|P14714\|PHYC_ARATH Phytochrome C OS=Arabidopsis thaliana GN=PHYC PE=1 SV=1	Back alignment and function description

>sp\|Q40762\|PHY_PICAB Phytochrome OS=Picea abies PE=2 SV=1	Back alignment and function description

>sp\|Q39557\|PHY2_CERPU Phytochrome 2 OS=Ceratodon purpureus GN=PHY2 PE=3 SV=1	Back alignment and function description

>sp\|Q01549\|PHY1_SELMA Phytochrome 1 OS=Selaginella martensii GN=PHY1 PE=3 SV=1	Back alignment and function description

>sp\|P36505\|PHY1_PHYPA Phytochrome 1 OS=Physcomitrella patens subsp. patens GN=PHY1 PE=2 SV=1	Back alignment and function description

>sp\|Q41046\|PHY_PINSY Phytochrome OS=Pinus sylvestris PE=2 SV=1	Back alignment and function description

>sp\|P93673\|PHYA_LATSA Phytochrome type A OS=Lathyrus sativus GN=PHYA PE=3 SV=1	Back alignment and function description

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Alignment Graph	Length	Definition	Q cover	H cover	Identity	E-value
Query		1122
183239026		1123	phytochrome C [Vitis riparia]	0.996	0.995	0.803	0.0
225447543		1118	PREDICTED: phytochrome C [Vitis vinifera	0.992	0.996	0.808	0.0
183239018		1118	phytochrome C [Vitis vinifera]	0.992	0.996	0.806	0.0
449453752		1119	PREDICTED: phytochrome C-like [Cucumis s	0.988	0.991	0.732	0.0
449506938		1119	PREDICTED: LOW QUALITY PROTEIN: phytochr	0.988	0.991	0.732	0.0
6671484		1118	phytochrome F [Solanum lycopersicum]	0.991	0.995	0.720	0.0
7672696		1137	phytochrome C [Oryza sativa Indica Group	0.990	0.977	0.694	0.0
115455391		1137	Os03g0752100 [Oryza sativa Japonica Grou	0.990	0.977	0.693	0.0
158513185		1137	RecName: Full=Phytochrome C	0.990	0.977	0.693	0.0
51556875		1139	phytochrome C [Triticum aestivum] gi\|515	0.990	0.975	0.689	0.0

>gi\|183239026\|gb\|ACC60971.1\| phytochrome C [Vitis riparia]	Back alignment and taxonomy information

 Score = 1920 bits (4975), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 902/1122 (80%), Positives = 1017/1122 (90%), Gaps = 4/1122 (0%)

Query: 1    MSSKSTNKTNYSRSSSARSKQNARVAAQTSIDAKLAEDFDESD--FDYSTSV--NISSST 56
            MSSKSTNKTN SRSSSARSK  ARV AQT IDA+L  +F+ES+  FDYS S+  NISSST
Sbjct: 1    MSSKSTNKTNCSRSSSARSKHGARVVAQTPIDAQLHVNFEESERHFDYSASIDFNISSST 60

Query: 57   SNVPSSTVSAYLQRVQRGRLIQPFGCMIAVDEQNFTVLGYSENAPEMLDLAPHAVPNIEQ 116
             +VPSSTVSAYLQ++QRG LIQPFGCMIAVDEQN TVL YSENAPEMLDLAPHAVP+IEQ
Sbjct: 61   GDVPSSTVSAYLQKMQRGNLIQPFGCMIAVDEQNLTVLAYSENAPEMLDLAPHAVPSIEQ 120

Query: 117  QDALTLGIDVRTLFTSSGAAALQKAANFGEVNLLNPILIHCKTSGKPFYAILHRIDVGLV 176
            Q+AL +G DVRTLF SSGAAALQKAANFGEVNLLNPIL+HC+ SGKPFYAILHRIDVGL+
Sbjct: 121  QEALAIGTDVRTLFRSSGAAALQKAANFGEVNLLNPILVHCRNSGKPFYAILHRIDVGLI 180

Query: 177  IDLEPVNPDDVPVTAAGALKSYKLAAKAISRLQSLPSGNISLLCDVLVNEVSDLTGYDRV 236
            IDLEPVNP DVP+TAAGALKSYKLAAKAISRLQSLPSGNISLLCDVLV E S+LTGYDRV
Sbjct: 181  IDLEPVNPADVPITAAGALKSYKLAAKAISRLQSLPSGNISLLCDVLVKEASELTGYDRV 240

Query: 237  MVYKFHEDEHGEVVAECRRPDLEPYLGFHYPATDIPQASRFLIMKNKVRMICDCLAPPVK 296
            MVYKFHEDEHGEV+AECR+PDLEPYLG HYPATDIPQASRFL MKNKVRMICDCLAPPVK
Sbjct: 241  MVYKFHEDEHGEVIAECRKPDLEPYLGLHYPATDIPQASRFLFMKNKVRMICDCLAPPVK 300

Query: 297  VIQDKKLDQPLSLCGSTLRAPHGCHARYMENMGSIASLVMSVTINEAEDELDNDQEQGRK 356
            VIQ+K+L QPLSLCGSTLR+PHGCHA+YM NMGS+ASLVMSVTINE +D+ +++Q++GRK
Sbjct: 301  VIQNKRLAQPLSLCGSTLRSPHGCHAQYMANMGSVASLVMSVTINEEDDDTESEQQKGRK 360

Query: 357  LWGLVVCHHTSPRFVPFPLRYACEFLIQVFGVQVNKEVELSAQLREKHILRTQTVLCDML 416
            LWGLVVCH+TSPRFVPFPLRYACEFL+QVFGVQ++KE+EL+AQ++EKHIL+TQTVLCDML
Sbjct: 361  LWGLVVCHNTSPRFVPFPLRYACEFLVQVFGVQISKEMELAAQMKEKHILQTQTVLCDML 420

Query: 417  LRDSPVGIVTQTPNVMDLVKCDGAALYYRGKLWLLGVTPTEEQIKDIAEWLLEYHRGSTG 476
            LRD+PVGIVTQ+PNVMDLV+CDGAALYY+ K WLLGVTPTE QI+DI EWLLEYH GSTG
Sbjct: 421  LRDAPVGIVTQSPNVMDLVRCDGAALYYQKKFWLLGVTPTEAQIRDIVEWLLEYHSGSTG 480

Query: 477  LSTDSLVEAGYPGALALGDAVCGIAAVKITSKDFLFWFRSHTAKEIKWGGAKHDSGGKDG 536
            LSTDSL+EAGYP AL LGDAVCGIAAVKI S DFLFWFRSHTAKEIKWGGAKHD   KD 
Sbjct: 481  LSTDSLMEAGYPAALVLGDAVCGIAAVKINSNDFLFWFRSHTAKEIKWGGAKHDPDDKDD 540

Query: 537  GRKMHPRSSFKAFLEVVKQRSLPWEDVEMDAIHSLQLILRGSLQDEVAEDSKMIVNVPSV 596
            GRKMHPRSSFKAFLEVVK+RSLPWEDVEMDAIHSLQLILRGSLQD+ A+DSKMIVNVPSV
Sbjct: 541  GRKMHPRSSFKAFLEVVKRRSLPWEDVEMDAIHSLQLILRGSLQDKSADDSKMIVNVPSV 600

Query: 597  DDRIEKIDELRIITNEMVRLIETAAVPILAVDASGNVNGWNSKAAELTGLTVDQAIGTAL 656
            D  I+  D+LRI+TNEMVRLIETA+VPILAVDA+G +NGWN+KAAELTGL + QAIG  L
Sbjct: 601  DASIKMADDLRIVTNEMVRLIETASVPILAVDAAGCINGWNNKAAELTGLIMQQAIGMPL 660

Query: 657  VDLVAGDSVDVVKNMLSSAFLGIEERNVEIKLRAFGPRETSGPVILVVNACCTQDTKENV 716
            +DLV  DS D+VK MLS A  GIEE+NVEIKL+ FGP+E +GPVILVVNACC++D K+NV
Sbjct: 661  IDLVENDSADMVKKMLSMALQGIEEQNVEIKLKTFGPQENNGPVILVVNACCSRDIKDNV 720

Query: 717  IGVCFVGQDITGQKLVMDKYTRIQGDYVGIVSSPSALIPPIFMTDEDGRCLEWNDGMEKL 776
            +GVCFVGQDITGQK+VMDKYTRIQGDYVGIV +PSALIPPIFM DE GRCLEWND M+ L
Sbjct: 721  VGVCFVGQDITGQKMVMDKYTRIQGDYVGIVRNPSALIPPIFMMDEHGRCLEWNDAMQNL 780

Query: 777  SGLKREEAIERMLIGEVFTVKNFGCRVKNHDTLTKLRIVMNKVISGQDADKILFGFFDQQ 836
            SGLKREEA +RML+GEVFTV NFGC+VK+HDTLTKLRI++N  I+GQDA K+LFGFFDQ 
Sbjct: 781  SGLKREEATDRMLLGEVFTVNNFGCQVKDHDTLTKLRILLNGAIAGQDAQKLLFGFFDQH 840

Query: 837  GKYVEALLSANKRTNAEGKISGILCFLHVASPELQYALQVQRISEQAAANSLNKLEYIRR 896
            GKY+EALLSANKRT+AEGKI+G+LCFLHVASPELQ+A+QVQRISEQAAA+SL KL YIR+
Sbjct: 841  GKYIEALLSANKRTDAEGKITGVLCFLHVASPELQHAMQVQRISEQAAADSLKKLAYIRQ 900

Query: 897  EIRKPLNGIAFMQNLMGTSDLSEEQKQLLKTSVLCQEQLTNIVDDTDIESIEECYMVLKS 956
            +IRKPLNGI F+QNLM +S+LS++QK+ L+TS++CQEQLT IVDDTD+ESIEECYM L S
Sbjct: 901  QIRKPLNGIMFIQNLMDSSELSQDQKKFLRTSMMCQEQLTKIVDDTDLESIEECYMELNS 960

Query: 957  GEFNLGEALDAVMTQVMIPSREHQVQFIRDLPAEVSTMNLHGDKLRLQQVLSDFLTNALI 1016
             EFNLGE L+ V++Q MI SRE +V+ I D PAEVS+M L+GD LRLQQVLSDFLTNAL+
Sbjct: 961  AEFNLGEVLEVVISQAMILSRERRVEIIYDSPAEVSSMFLYGDNLRLQQVLSDFLTNALL 1020

Query: 1017 FTPAFEGSSIAFRVIPQKERIGKNIHIVHLEFRITHPAPGIPEKLIHDMFYHSQGASREG 1076
            FTPAFEGSS+A RVIP++E IG  +HIVHLEFRI HPAPGIPE LI  MF+H QG SREG
Sbjct: 1021 FTPAFEGSSVALRVIPRRESIGTKVHIVHLEFRIAHPAPGIPEDLIQQMFHHRQGVSREG 1080

Query: 1077 LGLYISQKLVKLMNGTVQYIREAERSSFLILIEFPLAHQKDA 1118
            LGLYI+QKLVK+MNGTVQY+REA+ SSF+ILIEFPLAHQ  +
Sbjct: 1081 LGLYINQKLVKIMNGTVQYLREAQGSSFIILIEFPLAHQNSS 1122

Source: Vitis riparia

Species: Vitis riparia

Genus: Vitis

Family: Vitaceae

Order: Vitales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi\|225447543\|ref\|XP_002268724.1\| PREDICTED: phytochrome C [Vitis vinifera]	Back alignment and taxonomy information

>gi\|183239018\|gb\|ACC60967.1\| phytochrome C [Vitis vinifera]	Back alignment and taxonomy information

>gi\|449453752\|ref\|XP_004144620.1\| PREDICTED: phytochrome C-like [Cucumis sativus]	Back alignment and taxonomy information

>gi\|449506938\|ref\|XP_004162889.1\| PREDICTED: LOW QUALITY PROTEIN: phytochrome C-like [Cucumis sativus]	Back alignment and taxonomy information

>gi\|6671484\|gb\|AAC49301.2\| phytochrome F [Solanum lycopersicum]	Back alignment and taxonomy information

>gi\|7672696\|gb\|AAF66603.1\|AF141942_1 phytochrome C [Oryza sativa Indica Group]	Back alignment and taxonomy information

>gi|115455391|ref|NP_001051296.1| Os03g0752100 [Oryza sativa Japonica Group] gi|122246759|sp|Q10CQ8.1|PHYC_ORYSJ RecName: Full=Phytochrome C gi|21070927|gb|AAM34402.1|AF377947_8 phytochrome C [Oryza sativa Japonica Group] gi|4190974|dbj|BAA74448.1| phytochrome C [Oryza sativa Japonica Group] gi|31712054|gb|AAP68360.1| phytochrome C [Oryza sativa Japonica Group] gi|40538982|gb|AAR87239.1| phytochrome C [Oryza sativa Japonica Group] gi|108711120|gb|ABF98915.1| Phytochrome C, putative, expressed [Oryza sativa Japonica Group] gi|113549767|dbj|BAF13210.1| Os03g0752100 [Oryza sativa Japonica Group] gi|125587941|gb|EAZ28605.1| hypothetical protein OsJ_12592 [Oryza sativa Japonica Group]

Back alignment and taxonomy information

>gi\|158513185\|sp\|A2XM23.2\|PHYC_ORYSI RecName: Full=Phytochrome C	Back alignment and taxonomy information

>gi\|51556875\|gb\|AAU06208.1\| phytochrome C [Triticum aestivum] gi\|51556889\|gb\|AAU06215.1\| phytochrome C [Triticum aestivum]	Back alignment and taxonomy information

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Alignment graph	Length	Definition	Q cover	H cover	Identity	E-value
Query		1122
TAIR\|locus:2165199		1111	PHYC "phytochrome C" [Arabidop	0.980	0.990	0.635	0.0
TAIR\|locus:2012300		1122	PHYA "phytochrome A" [Arabidop	0.988	0.988	0.564	0.0
TAIR\|locus:2005515		1172	PHYB "AT2G18790" [Arabidopsis	0.979	0.937	0.555	0.0
TAIR\|locus:2005535		1164	PHYD "phytochrome D" [Arabidop	0.982	0.946	0.539	3.59999944711e-318
UNIPROTKB\|P06593		1129	PHYA3 "Phytochrome A type 3" [	0.977	0.971	0.536	3.29999982256e-317
TAIR\|locus:2005536		1112	PHYE "phytochrome E" [Arabidop	0.794	0.801	0.510	6.5e-241
UNIPROTKB\|Q55168		748	cph1 "Phytochrome-like protein	0.521	0.782	0.298	4.5e-66
UNIPROTKB\|Q48G81		745	bphP "Bacteriophytochrome hist	0.354	0.534	0.296	1.1e-48
UNIPROTKB\|Q4K656		746	bphP "Bacteriophytochrome hist	0.411	0.619	0.274	3.1e-46
UNIPROTKB\|Q7CY45		736	Atu1990 "Bacteriophytochrome p	0.452	0.690	0.279	6.7e-39

TAIR\|locus:2165199 PHYC "phytochrome C" [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

 Score = 3750 (1325.1 bits), Expect = 0., P = 0.
 Identities = 707/1112 (63%), Positives = 898/1112 (80%)

Query:     9 TNYSRSSSARSKQNARVAAQTSIDAKLAEDFDESD--FDYXXXXXXXXXXXXXX--XXXX 64
             +N SRS S RS+QN+RV++Q  +DAKL  +F+ES+  FDY                    
Sbjct:     3 SNTSRSCSTRSRQNSRVSSQVLVDAKLHGNFEESERLFDYSASINLNMPSSSCEIPSSAV 62

Query:    65 XAYLQRVQRGRLIQPFGCMIAVDEQNFTVLGYSENAPEMLDLAPHAVPNIEQQDALTLGI 124
               YLQ++QRG LIQPFGC+I VDE+N  V+ +SEN  EML L PH VP++EQ++ALT+G 
Sbjct:    63 STYLQKIQRGMLIQPFGCLIVVDEKNLKVIAFSENTQEMLGLIPHTVPSMEQREALTIGT 122

Query:   125 DVRTLFTSSGAAALQKAANFGEVNLLNPILIHCKTSGKPFYAILHRIDVGLVIDLEPVNP 184
             DV++LF S G +AL+KA +FGE+++LNPI +HC++S KPFYAILHRI+ GLVIDLEPV+P
Sbjct:   123 DVKSLFLSPGCSALEKAVDFGEISILNPITLHCRSSSKPFYAILHRIEEGLVIDLEPVSP 182

Query:   185 DDVPVTAAGALKSYKLAAKAISRLQSLPSGNISLLCDVLVNEVSDLTGYDRVMVYKFHED 244
             D+VPVTAAGAL+SYKLAAK+ISRLQ+LPSGN+ LLCD LV EVS+LTGYDRVMVYKFHED
Sbjct:   183 DEVPVTAAGALRSYKLAAKSISRLQALPSGNMLLLCDALVKEVSELTGYDRVMVYKFHED 242

Query:   245 EHGEVVAECRRPDLEPYLGFHYPATDIPQASRFLIMKNKVRMICDCLAPPVKVIQDKKLD 304
              HGEV+AEC R D+EPYLG HY ATDIPQASRFL M+NKVRMICDC A PVKV+QDK L 
Sbjct:   243 GHGEVIAECCREDMEPYLGLHYSATDIPQASRFLFMRNKVRMICDCSAVPVKVVQDKSLS 302

Query:   305 QPLSLCGSTLRAPHGCHARYMENMGSIASLVMSVTINEAE-DELDNDQEQGRKLWGLVVC 363
             QP+SL GSTLRAPHGCHA+YM NMGS+ASLVMSVTIN ++ DE++ D + GR LWGLVVC
Sbjct:   303 QPISLSGSTLRAPHGCHAQYMSNMGSVASLVMSVTINGSDSDEMNRDLQTGRHLWGLVVC 362

Query:   364 HHTSPRFVPFPLRYACEFLIQVFGVQVNKEVELSAQLREKHILRTQTVLCDMLLRDSPVG 423
             HH SPRFVPFPLRYACEFL QVFGVQ+NKE E +  L+EK IL+TQ+VLCDML R++P+G
Sbjct:   363 HHASPRFVPFPLRYACEFLTQVFGVQINKEAESAVLLKEKRILQTQSVLCDMLFRNAPIG 422

Query:   424 IVTQTPNVMDLVKCDGAALYYRGKLWLLGVTPTEEQIKDIAEWLLEYHRGSTGLSTDSLV 483
             IVTQ+PN+MDLVKCDGAALYYR  LW LGVTPTE QI+D+ +W+L+ H G+TG +T+SL+
Sbjct:   423 IVTQSPNIMDLVKCDGAALYYRDNLWSLGVTPTETQIRDLIDWVLKSHGGNTGFTTESLM 482

Query:   484 EAGYPGALALGDAVCGIAAVKITSKDFLFWFRSHTAKEIKWGGAKHDSGGKDGGRKMHPR 543
             E+GYP A  LG+++CG+AAV I+ KDFLFWFRS TAK+IKWGGA+HD   +DG ++MHPR
Sbjct:   483 ESGYPDASVLGESICGMAAVYISEKDFLFWFRSSTAKQIKWGGARHDPNDRDG-KRMHPR 541

Query:   544 SSFKAFLEVVKQRSLPWEDVEMDAIHSLQLILRGSLQDEVAEDSKMIVNVPSVDDRIEKI 603
             SSFKAF+E+V+ +S+PW+D+EMDAI+SLQLI++GSLQ+E    SK +V+VP VD+R++K+
Sbjct:   542 SSFKAFMEIVRWKSVPWDDMEMDAINSLQLIIKGSLQEE---HSKTVVDVPLVDNRVQKV 598

Query:   604 DELRIITNEMVRLIETAAVPILAVDASGNVNGWNSKAAELTGLTVDQAIGTALVDLVAGD 663
             DEL +I NEMVRLI+TAAVPI AVDASG +NGWNSKAAE+TGL V+QAIG  + DLV  D
Sbjct:   599 DELCVIVNEMVRLIDTAAVPIFAVDASGVINGWNSKAAEVTGLAVEQAIGKPVSDLVEDD 658

Query:   664 SVDVVKNMLSSAFLGIEERNVEIKLRAFGPRETSGPVILVVNACCTQDTKENVIGVCFVG 723
             SV+ VKNML+ A  G EER  EI++RAFGP+  S PV LVVN CC++D   NV+GVCF+G
Sbjct:   659 SVETVKNMLALALEGSEERGAEIRIRAFGPKRKSSPVELVVNTCCSRDMTNNVLGVCFIG 718

Query:   724 QDITGQKLVMDKYTRIQGDYVGIVSSPSALIPPIFMTDEDGRCLEWNDGMEKLSGLKREE 783
             QD+TGQK + + Y+R++GDY  I+ SPS LIPPIF+T+E+G C EWN+ M+KLSG+KREE
Sbjct:   719 QDVTGQKTLTENYSRVKGDYARIMWSPSTLIPPIFITNENGVCSEWNNAMQKLSGIKREE 778

Query:   784 AIERMLIGEVFTVKNFGCRVKNHDTLTKLRIVMNKVISGQ-DADKILFGFFDQQGKYVEA 842
              + ++L+GEVFT  ++GC +K+HDTLTKLRI  N VISGQ + +K+LFGF+ + G ++EA
Sbjct:   779 VVNKILLGEVFTTDDYGCCLKDHDTLTKLRIGFNAVISGQKNIEKLLFGFYHRDGSFIEA 838

Query:   843 LLSANKRTNAEGKISGILCFLHVASPELQYALQVQRISEQAAANSLNKLEYIRREIRKPL 902
             LLSANKRT+ EGK++G+LCFL V SPELQYALQVQ+ISE A A +LNKL Y+R E++ P 
Sbjct:   839 LLSANKRTDIEGKVTGVLCFLQVPSPELQYALQVQQISEHAIACALNKLAYLRHEVKDPE 898

Query:   903 NGIAFMQNLMGTSDLSEEQKQLLKTSVLCQEQLTNIVDDTDIESIEECYMVLKSGEFNLG 962
               I+F+Q+L+ +S LSE+QK+LL+TSVLC+EQL  ++ D+DIE IEE Y+ L   EF L 
Sbjct:   899 KAISFLQDLLHSSGLSEDQKRLLRTSVLCREQLAKVISDSDIEGIEEGYVELDCSEFGLQ 958

Query:   963 EALDAVMTQVMIPSREHQVQFIRDLPAEVSTMNLHGDKLRLQQVLSDFLTNALIFTPAFE 1022
             E+L+AV+ QVM  S E +VQ   D P EVS+M L+GD LRLQQ+LS+ L +++ FTPA  
Sbjct:   959 ESLEAVVKQVMELSIERKVQISCDYPQEVSSMRLYGDNLRLQQILSETLLSSIRFTPALR 1018

Query:  1023 GSSIAFRVIPQKERIGKNIHIVHLEFRITHPAPGIPEKLIHDMFYH-SQGASREGLGLYI 1081
             G  ++F+VI + E IGK +  V LEFRI HPAPG+PE L+ +MF    +G SREGLGL+I
Sbjct:  1019 GLCVSFKVIARIEAIGKRMKRVELEFRIIHPAPGLPEDLVREMFQPLRKGTSREGLGLHI 1078

Query:  1082 SQKLVKLMN-GTVQYIREAERSSFLILIEFPL 1112
             +QKLVKLM  GT++Y+RE+E S+F+IL EFPL
Sbjct:  1079 TQKLVKLMERGTLRYLRESEMSAFVILTEFPL 1110

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

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

GO:0004871 "signal transducer activity" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

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

GO:0007165 "signal transduction" evidence=IEA

GO:0008020 "G-protein coupled photoreceptor activity" evidence=IEA

GO:0009584 "detection of visible light" evidence=IEA

GO:0009585 "red, far-red light phototransduction" evidence=IEA

GO:0009881 "photoreceptor activity" evidence=IEA

GO:0016020 "membrane" evidence=IEA

GO:0017006 "protein-tetrapyrrole linkage" evidence=IEA

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

GO:0018298 "protein-chromophore linkage" evidence=IEA

GO:0042803 "protein homodimerization activity" evidence=IEA

GO:0005515 "protein binding" evidence=IPI

GO:0007623 "circadian rhythm" evidence=RCA

GO:0009630 "gravitropism" evidence=RCA

GO:0010017 "red or far-red light signaling pathway" evidence=RCA

GO:0010155 "regulation of proton transport" evidence=RCA

GO:0046777 "protein autophosphorylation" evidence=RCA

TAIR\|locus:2012300 PHYA "phytochrome A" [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

TAIR\|locus:2005515 PHYB "AT2G18790" [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

TAIR\|locus:2005535 PHYD "phytochrome D" [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

UNIPROTKB\|P06593 PHYA3 "Phytochrome A type 3" [Avena sativa (taxid:4498)]	Back alignment and assigned GO terms

TAIR\|locus:2005536 PHYE "phytochrome E" [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

UNIPROTKB\|Q55168 cph1 "Phytochrome-like protein cph1" [Synechocystis sp. PCC 6803 substr. Kazusa (taxid:1111708)]	Back alignment and assigned GO terms

UNIPROTKB\|Q48G81 bphP "Bacteriophytochrome histidine kinase" [Pseudomonas syringae pv. phaseolicola 1448A (taxid:264730)]	Back alignment and assigned GO terms

UNIPROTKB\|Q4K656 bphP "Bacteriophytochrome histidine kinase" [Pseudomonas protegens Pf-5 (taxid:220664)]	Back alignment and assigned GO terms

UNIPROTKB\|Q7CY45 Atu1990 "Bacteriophytochrome protein" [Agrobacterium fabrum str. C58 (taxid:176299)]	Back alignment and assigned GO terms

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
P30733	PHYA_SOLTU	No assigned EC number	0.5746	0.9732	0.9723	N/A	no
A2XLG5	PHYA_ORYSI	No assigned EC number	0.5383	0.9714	0.9663	N/A	no
P42496	PHY_ADICA	No assigned EC number	0.5691	0.9723	0.9758	N/A	no
P36505	PHY1_PHYPA	No assigned EC number	0.6138	0.9714	0.9628	N/A	no
P55141	PHYA_PETCR	No assigned EC number	0.5446	0.9786	0.9725	N/A	no
Q40762	PHY_PICAB	No assigned EC number	0.6627	0.9741	0.9621	N/A	no
Q41046	PHY_PINSY	No assigned EC number	0.5942	0.9750	0.9672	N/A	no
A2XFW2	PHYB_ORYSI	No assigned EC number	0.5576	0.9732	0.9325	N/A	no
P33529	PHY_MOUSC	No assigned EC number	0.5524	0.9705	0.9688	N/A	no
A2XM23	PHYC_ORYSI	No assigned EC number	0.6930	0.9901	0.9771	N/A	no
P15001	PHYA_PEA	No assigned EC number	0.5686	0.9884	0.9866	N/A	no
P14714	PHYC_ARATH	No assigned EC number	0.6447	0.9803	0.9900	yes	no
Q10CQ8	PHYC_ORYSJ	No assigned EC number	0.6939	0.9901	0.9771	yes	no
P29130	PHYB_TOBAC	No assigned EC number	0.5737	0.9795	0.9708	N/A	no
P34094	PHYB_SOLTU	No assigned EC number	0.5734	0.9777	0.9707	N/A	no
P06592	PHYA_CUCPE	No assigned EC number	0.5735	0.9714	0.9697	N/A	no
P93528	PHYC_SORBI	No assigned EC number	0.6895	0.9910	0.9797	N/A	no
P06593	PHYA3_AVESA	No assigned EC number	0.5406	0.9705	0.9645	N/A	no
P06594	PHYA4_AVESA	No assigned EC number	0.5425	0.9688	0.9627	N/A	no
O49934	PHYA_POPTM	No assigned EC number	0.5723	0.9696	0.9671	N/A	no
P55004	PHYE_IPONI	No assigned EC number	0.5344	0.9607	0.9668	N/A	no
P93527	PHYB_SORBI	No assigned EC number	0.5558	0.9616	0.9159	N/A	no
P93526	PHYA_SORBI	No assigned EC number	0.5352	0.9705	0.9628	N/A	no
P33530	PHYA1_TOBAC	No assigned EC number	0.5776	0.9759	0.9741	N/A	no
Q01549	PHY1_SELMA	No assigned EC number	0.6139	0.9928	0.9823	N/A	no
P93673	PHYA_LATSA	No assigned EC number	0.5730	0.9884	0.9866	N/A	no
P19862	PHYA1_MAIZE	No assigned EC number	0.5344	0.9688	0.9610	N/A	no
Q9ZS62	PHYB1_SOLLC	No assigned EC number	0.5609	0.9875	0.9796	N/A	no
Q39557	PHY2_CERPU	No assigned EC number	0.6142	0.9893	0.9901	N/A	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	2.7.13.3	0.737
3rd Layer	2.7.11	0.921

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input:
	PHYC	SubName- Full=Chromosome chr12 scaffold_47, whole genome shotgun sequence; (1118 aa)
		(Vitis vinifera)
Predicted Functional Partners:
		Sorry, there are no predicted associations at the current settings.

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Alignment Graph	Length	Definition	E-value
Query		1122
COG4251		750	COG4251, COG4251, Bacteriophytochrome (light-regul	9e-99
pfam00360		183	pfam00360, PHY, Phytochrome region	3e-93
pfam08446		107	pfam08446, PAS_2, PAS fold	9e-50
pfam00989		113	pfam00989, PAS, PAS fold	2e-19
PRK15347		921	PRK15347, PRK15347, two component system sensor ki	1e-18
pfam01590		143	pfam01590, GAF, GAF domain	4e-18
cd00075		103	cd00075, HATPase_c, Histidine kinase-like ATPases;	2e-17
pfam02518		111	pfam02518, HATPase_c, Histidine kinase-, DNA gyras	2e-17
pfam00989		113	pfam00989, PAS, PAS fold	5e-17
COG0642		336	COG0642, BaeS, Signal transduction histidine kinas	8e-17
smart00387		111	smart00387, HATPase_c, Histidine kinase-like ATPas	1e-16
PRK11107		919	PRK11107, PRK11107, hybrid sensory histidine kinas	3e-15
TIGR02956		968	TIGR02956, TMAO_torS, TMAO reductase sytem sensor	8e-15
smart00065		149	smart00065, GAF, Domain present in phytochromes an	1e-13
COG2205		890	COG2205, KdpD, Osmosensitive K+ channel histidine	1e-12
PRK10841		924	PRK10841, PRK10841, hybrid sensory kinase in two-c	1e-11
PRK11091		779	PRK11091, PRK11091, aerobic respiration control se	9e-10
cd00130		103	cd00130, PAS, PAS domain; PAS motifs appear in arc	7e-08
TIGR01386		457	TIGR01386, cztS_silS_copS, heavy metal sensor kina	3e-07
PRK11360		607	PRK11360, PRK11360, sensory histidine kinase AtoS;	7e-07
cd00130		103	cd00130, PAS, PAS domain; PAS motifs appear in arc	1e-06
pfam00512		66	pfam00512, HisKA, His Kinase A (phospho-acceptor)	1e-06
COG5002		459	COG5002, VicK, Signal transduction histidine kinas	1e-06
pfam13426		101	pfam13426, PAS_9, PAS domain	1e-06
smart00091		67	smart00091, PAS, PAS domain	1e-06
smart00388		66	smart00388, HisKA, His Kinase A (phosphoacceptor)	2e-06
TIGR00229		124	TIGR00229, sensory_box, PAS domain S-box	1e-05
COG3829		560	COG3829, RocR, Transcriptional regulator containin	2e-05
COG2202		232	COG2202, AtoS, FOG: PAS/PAC domain [Signal transdu	2e-05
PRK11100		475	PRK11100, PRK11100, sensory histidine kinase CreC;	6e-05
PRK11466		914	PRK11466, PRK11466, hybrid sensory histidine kinas	8e-05
smart00091		67	smart00091, PAS, PAS domain	1e-04
TIGR00229		124	TIGR00229, sensory_box, PAS domain S-box	1e-04
COG3852		363	COG3852, NtrB, Signal transduction histidine kinas	1e-04
PRK11360		607	PRK11360, PRK11360, sensory histidine kinase AtoS;	2e-04
pfam13426		101	pfam13426, PAS_9, PAS domain	2e-04
PRK10549		466	PRK10549, PRK10549, signal transduction histidine-	2e-04
PRK10490		895	PRK10490, PRK10490, sensor protein KdpD; Provision	3e-04
cd00082		65	cd00082, HisKA, Histidine Kinase A (dimerization/p	0.002
COG3290		537	COG3290, CitA, Signal transduction histidine kinas	0.004

>gnl\|CDD\|226702 COG4251, COG4251, Bacteriophytochrome (light-regulated signal transduction histidine kinase) [Signal transduction mechanisms]	Back alignment and domain information

 Score =  329 bits (846), Expect = 9e-99
 Identities = 176/514 (34%), Positives = 259/514 (50%), Gaps = 49/514 (9%)

Query: 76  LIQPFGCMIAVDEQNFTVLGYSENAPEMLDLAPHAVPNIEQQDALTLGIDVRTLFTSSGA 135
            IQP G ++ +DE +  VL  SEN   +L   P      E     TLG     + TS   
Sbjct: 25  AIQPHGALLVLDEADLMVLQASENCANILGREP------EDLLGRTLG----AVLTSEQV 74

Query: 136 AALQKAANFGEVNLLNPILIHCKTSGKPFYAILHRIDVGLVIDLEPVNPDDVPVTAAGAL 195
             LQ A   G +  LNP  +  +  G  F    HR    L+++ EP    +     A  L
Sbjct: 75  PPLQSALTVGGLTTLNPTKMWTR-KGGSFDVSAHRSKELLILEFEPAGTGE----TASFL 129

Query: 196 KSYKLAAKAISRLQSLPSGNISLLCDVLVNEVSDLTGYDRVMVYKFHEDEHGEVVAECRR 255
             Y LA  A++RLQS    N+  L      EV  +TG+DRVM+Y+F ED  GEV+AE +R
Sbjct: 130 GFYHLAKLAMNRLQSAA--NLRDLLSRTTQEVRRMTGFDRVMLYRFDEDGSGEVIAEAKR 187

Query: 256 PDLEPYLGFHYPATDIPQASRFLIMKNKVRMICDCLAPPVKVIQ--DKKLDQPLSLCGST 313
            DLE YLG  YPA+DIPQ +R L ++N +R+I D    PV V+   + + ++PL L  S 
Sbjct: 188 EDLESYLGLRYPASDIPQQARALYIQNPLRLIPDVSYTPVPVLPAVNPETNEPLDLSYSV 247

Query: 314 LRAPHGCHARYMENMGSIASLVMSVTINEAEDELDNDQEQGRKLWGLVVCHHTSPRFVPF 373
           LR+    H  Y+ NMG  AS+ +S+ ++              KLWGL+ CHH SP+ +P+
Sbjct: 248 LRSVSPIHLEYLRNMGVGASMSISIVVDG-------------KLWGLIACHHQSPKVIPY 294

Query: 374 PLRYACEFLIQVFGVQVNKE-----VELSAQLREKHILRTQTVLCDMLLRDSPV-GIVTQ 427
            +R ACEF  QV  ++++        +   QL E H      +L  M      V G++  
Sbjct: 295 EVRKACEFFGQVLSMEISALEQSEDADYRVQLTEHHAR----LLRYMAHAADFVDGLIDH 350

Query: 428 TPNVMDLVKCDGAALYYRGKLWLLGVTPTEEQIKDIAEWLLEYHRGSTGLSTDSLVEAGY 487
             +++DL+  DGAAL + G+  L+G TP    ++ + +WL E   G    +TDSL +  Y
Sbjct: 351 QDDLLDLMPADGAALCFGGRWHLVGETPPRPAVQRLLQWLAEREEGDV-FATDSLSQV-Y 408

Query: 488 PGALALGDAVCGIAAVKIT--SKDFLFWFRSHTAKEIKWGG--AKHDSGGKDGGRKMHPR 543
           P A        G+ A+ I+    ++L WFR    + + WGG   K    G  G R + PR
Sbjct: 409 PDAEDYASVASGLLAIPISRVKSNYLLWFRPEVVQTVNWGGDPEKPYEAGPMGIR-LTPR 467

Query: 544 SSFKAFLEVVKQRSLPWEDVEMDAIHSLQLILRG 577
            SF+ + E V+ +S PW +VE++A   L+  + G
Sbjct: 468 KSFELWKETVRLQSQPWSEVEIEAALELRKAIVG 501

Length = 750

>gnl\|CDD\|215877 pfam00360, PHY, Phytochrome region	Back alignment and domain information

>gnl\|CDD\|203947 pfam08446, PAS_2, PAS fold	Back alignment and domain information

>gnl\|CDD\|216228 pfam00989, PAS, PAS fold	Back alignment and domain information

>gnl\|CDD\|237951 PRK15347, PRK15347, two component system sensor kinase SsrA; Provisional	Back alignment and domain information

>gnl\|CDD\|216590 pfam01590, GAF, GAF domain	Back alignment and domain information

>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	Back alignment and domain information

>gnl\|CDD\|217081 pfam02518, HATPase_c, Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase	Back alignment and domain information

>gnl\|CDD\|216228 pfam00989, PAS, PAS fold	Back alignment and domain information

>gnl\|CDD\|223715 COG0642, BaeS, Signal transduction histidine kinase [Signal transduction mechanisms]	Back alignment and domain information

>gnl\|CDD\|214643 smart00387, HATPase_c, Histidine kinase-like ATPases	Back alignment and domain information

>gnl\|CDD\|236848 PRK11107, PRK11107, hybrid sensory histidine kinase BarA; Provisional	Back alignment and domain information

>gnl\|CDD\|234070 TIGR02956, TMAO_torS, TMAO reductase sytem sensor TorS	Back alignment and domain information

>gnl\|CDD\|214500 smart00065, GAF, Domain present in phytochromes and cGMP-specific phosphodiesterases	Back alignment and domain information

>gnl\|CDD\|225115 COG2205, KdpD, Osmosensitive K+ channel histidine kinase [Signal transduction mechanisms]	Back alignment and domain information

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

>gnl\|CDD\|236842 PRK11091, PRK11091, aerobic respiration control sensor protein ArcB; Provisional	Back alignment and domain information

>gnl\|CDD\|238075 cd00130, PAS, PAS domain; PAS motifs appear in archaea, eubacteria and eukarya	Back alignment and domain information

>gnl\|CDD\|233391 TIGR01386, cztS_silS_copS, heavy metal sensor kinase	Back alignment and domain information

>gnl\|CDD\|236901 PRK11360, PRK11360, sensory histidine kinase AtoS; Provisional	Back alignment and domain information

>gnl\|CDD\|238075 cd00130, PAS, PAS domain; PAS motifs appear in archaea, eubacteria and eukarya	Back alignment and domain information

>gnl\|CDD\|215963 pfam00512, HisKA, His Kinase A (phospho-acceptor) domain	Back alignment and domain information

>gnl\|CDD\|227335 COG5002, VicK, Signal transduction histidine kinase [Signal transduction mechanisms]	Back alignment and domain information

>gnl\|CDD\|222120 pfam13426, PAS_9, PAS domain	Back alignment and domain information

>gnl\|CDD\|214512 smart00091, PAS, PAS domain	Back alignment and domain information

>gnl\|CDD\|214644 smart00388, HisKA, His Kinase A (phosphoacceptor) domain	Back alignment and domain information

>gnl\|CDD\|232884 TIGR00229, sensory_box, PAS domain S-box	Back alignment and domain information

>gnl\|CDD\|226350 COG3829, RocR, Transcriptional regulator containing PAS, AAA-type ATPase, and DNA-binding domains [Transcription / Signal transduction mechanisms]	Back alignment and domain information

>gnl\|CDD\|225112 COG2202, AtoS, FOG: PAS/PAC domain [Signal transduction mechanisms]	Back alignment and domain information

>gnl\|CDD\|236846 PRK11100, PRK11100, sensory histidine kinase CreC; Provisional	Back alignment and domain information

>gnl\|CDD\|236914 PRK11466, PRK11466, hybrid sensory histidine kinase TorS; Provisional	Back alignment and domain information

>gnl\|CDD\|214512 smart00091, PAS, PAS domain	Back alignment and domain information

>gnl\|CDD\|232884 TIGR00229, sensory_box, PAS domain S-box	Back alignment and domain information

>gnl\|CDD\|226370 COG3852, NtrB, Signal transduction histidine kinase, nitrogen specific [Signal transduction mechanisms]	Back alignment and domain information

>gnl\|CDD\|236901 PRK11360, PRK11360, sensory histidine kinase AtoS; Provisional	Back alignment and domain information

>gnl\|CDD\|222120 pfam13426, PAS_9, PAS domain	Back alignment and domain information

>gnl\|CDD\|182539 PRK10549, PRK10549, signal transduction histidine-protein kinase BaeS; Provisional	Back alignment and domain information

>gnl\|CDD\|236701 PRK10490, PRK10490, sensor protein KdpD; Provisional	Back alignment and domain information

>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	Back alignment and domain information

>gnl\|CDD\|225827 COG3290, CitA, Signal transduction histidine kinase regulating citrate/malate metabolism [Signal transduction mechanisms]	Back alignment and domain information

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Alignment Graph	Length	Definition	Probability
Query		1122
COG4251		750	Bacteriophytochrome (light-regulated signal transd	100.0
TIGR02938		494	nifL_nitrog nitrogen fixation negative regulator N	100.0
PRK13560		807	hypothetical protein; Provisional	100.0
PRK11091		779	aerobic respiration control sensor protein ArcB; P	100.0
COG5002		459	VicK Signal transduction histidine kinase [Signal	100.0
PRK11006		430	phoR phosphate regulon sensor protein; Provisional	100.0
COG3852		363	NtrB Signal transduction histidine kinase, nitroge	100.0
PRK13557		540	histidine kinase; Provisional	100.0
PRK10618		894	phosphotransfer intermediate protein in two-compon	100.0
PRK10841		924	hybrid sensory kinase in two-component regulatory	100.0
PRK11360		607	sensory histidine kinase AtoS; Provisional	100.0
PRK11073		348	glnL nitrogen regulation protein NR(II); Provision	100.0
TIGR02966		333	phoR_proteo phosphate regulon sensor kinase PhoR.	100.0
PRK09959		1197	hybrid sensory histidine kinase in two-component r	100.0
PF00360		182	PHY: Phytochrome region; InterPro: IPR013515 Phyto	100.0
COG2205		890	KdpD Osmosensitive K+ channel histidine kinase [Si	100.0
PRK13559		361	hypothetical protein; Provisional	100.0
PRK11086		542	sensory histidine kinase DcuS; Provisional	100.0
COG4191		603	Signal transduction histidine kinase regulating C4	99.98
COG5000		712	NtrY Signal transduction histidine kinase involved	99.97
PRK09303		380	adaptive-response sensory kinase; Validated	99.97
PRK15053		545	dpiB sensor histidine kinase DpiB; Provisional	99.97
TIGR02956		968	TMAO_torS TMAO reductase sytem sensor TorS. This p	99.97
PRK15347		921	two component system sensor kinase SsrA; Provision	99.96
PRK11466		914	hybrid sensory histidine kinase TorS; Provisional	99.96
PRK10490		895	sensor protein KdpD; Provisional	99.96
PRK11107		919	hybrid sensory histidine kinase BarA; Provisional	99.96
PRK13837		828	two-component VirA-like sensor kinase; Provisional	99.95
COG3290		537	CitA Signal transduction histidine kinase regulati	99.95
PRK10364		457	sensor protein ZraS; Provisional	99.95
PRK10815		485	sensor protein PhoQ; Provisional	99.94
PRK10604		433	sensor protein RstB; Provisional	99.94
PRK10755		356	sensor protein BasS/PmrB; Provisional	99.93
PRK10549		466	signal transduction histidine-protein kinase BaeS;	99.93
TIGR03785		703	marine_sort_HK proteobacterial dedicated sortase s	99.92
PRK09776		1092	putative diguanylate cyclase; Provisional	99.92
PRK09776		1092	putative diguanylate cyclase; Provisional	99.91
PRK09835		482	sensor kinase CusS; Provisional	99.91
PF08446		110	PAS_2: PAS fold; InterPro: IPR013654 The PAS fold	99.91
TIGR01386		457	cztS_silS_copS heavy metal sensor kinase. Members	99.91
TIGR02916		679	PEP_his_kin putative PEP-CTERM system histidine ki	99.91
PRK10337		449	sensor protein QseC; Provisional	99.9
PRK11100		475	sensory histidine kinase CreC; Provisional	99.9
PRK09470		461	cpxA two-component sensor protein; Provisional	99.9
PRK09467		435	envZ osmolarity sensor protein; Provisional	99.9
COG0642		336	BaeS Signal transduction histidine kinase [Signal	99.88
COG4192		673	Signal transduction histidine kinase regulating ph	99.88
TIGR02040		442	PpsR-CrtJ transcriptional regulator PpsR. This mod	99.87
PRK13560		807	hypothetical protein; Provisional	99.86
PRK11644		495	sensory histidine kinase UhpB; Provisional	99.82
PRK11359		799	cyclic-di-GMP phosphodiesterase; Provisional	99.8
TIGR02040		442	PpsR-CrtJ transcriptional regulator PpsR. This mod	99.77
PF02518		111	HATPase_c: Histidine kinase-, DNA gyrase B-, and H	99.7
PRK10935		565	nitrate/nitrite sensor protein NarQ; Provisional	99.7
PRK10600		569	nitrate/nitrite sensor protein NarX; Provisional	99.66
COG3920		221	Signal transduction histidine kinase [Signal trans	99.56
PRK10547		670	chemotaxis protein CheA; Provisional	99.54
PF08448		110	PAS_4: PAS fold; InterPro: IPR013656 The PAS fold	99.46
PF13426		104	PAS_9: PAS domain; PDB: 3ULF_B 3UE6_E 2Z6D_B 2Z6C_	99.44
PF00989		113	PAS: PAS fold; InterPro: IPR013767 PAS domains are	99.42
COG3850		574	NarQ Signal transduction histidine kinase, nitrate	99.36
PRK11091		779	aerobic respiration control sensor protein ArcB; P	99.35
COG4585		365	Signal transduction histidine kinase [Signal trans	99.34
PF13426		104	PAS_9: PAS domain; PDB: 3ULF_B 3UE6_E 2Z6D_B 2Z6C_	99.34
COG3851		497	UhpB Signal transduction histidine kinase, glucose	99.29
smart00387		111	HATPase_c Histidine kinase-like ATPases. Histidine	99.28
PF00989		113	PAS: PAS fold; InterPro: IPR013767 PAS domains are	99.28
PF01590		154	GAF: GAF domain; InterPro: IPR003018 This domain i	99.27
PF08448		110	PAS_4: PAS fold; InterPro: IPR013656 The PAS fold	99.24
PRK04184		535	DNA topoisomerase VI subunit B; Validated	99.23
COG4564		459	Signal transduction histidine kinase [Signal trans	99.23
COG0643		716	CheA Chemotaxis protein histidine kinase and relat	99.21
KOG0519		786	consensus Sensory transduction histidine kinase [S	99.16
PRK10060		663	RNase II stability modulator; Provisional	99.14
PRK13559		361	hypothetical protein; Provisional	99.11
PRK14868		795	DNA topoisomerase VI subunit B; Provisional	99.1
cd00075		103	HATPase_c Histidine kinase-like ATPases; This fami	99.1
PRK13558		665	bacterio-opsin activator; Provisional	99.07
PRK13557		540	histidine kinase; Provisional	99.05
PRK10060		663	RNase II stability modulator; Provisional	99.03
TIGR01052		488	top6b DNA topoisomerase VI, B subunit. This model	99.02
TIGR00229		124	sensory_box PAS domain S-box. The PAS domain was p	99.01
COG3275		557	LytS Putative regulator of cell autolysis [Signal	98.99
TIGR01925		137	spIIAB anti-sigma F factor. This model describes t	98.99
PRK03660		146	anti-sigma F factor; Provisional	98.97
smart00065		149	GAF Domain present in phytochromes and cGMP-specif	98.96
COG3829		560	RocR Transcriptional regulator containing PAS, AAA	98.95
PRK11359		799	cyclic-di-GMP phosphodiesterase; Provisional	98.88
PRK04069		161	serine-protein kinase RsbW; Provisional	98.88
PRK14867		659	DNA topoisomerase VI subunit B; Provisional	98.85
PF00512		68	HisKA: His Kinase A (phospho-acceptor) domain; Int	98.85
COG2972		456	Predicted signal transduction protein with a C-ter	98.84
PF13596		106	PAS_10: PAS domain; PDB: 3CAX_A 2QKP_D.	98.83
PRK13558		665	bacterio-opsin activator; Provisional	98.79
TIGR02938		494	nifL_nitrog nitrogen fixation negative regulator N	98.78
PF14501		100	HATPase_c_5: GHKL domain	98.78
TIGR00229		124	sensory_box PAS domain S-box. The PAS domain was p	98.76
PF08447		91	PAS_3: PAS fold; InterPro: IPR013655 The PAS fold	98.75
TIGR01924		159	rsbW_low_gc serine-protein kinase RsbW. This model	98.74
PF08447		91	PAS_3: PAS fold; InterPro: IPR013655 The PAS fold	98.65
PRK11360		607	sensory histidine kinase AtoS; Provisional	98.65
cd00130		103	PAS PAS domain; PAS motifs appear in archaea, euba	98.6
KOG3558		768	consensus Hypoxia-inducible factor 1/Neuronal PAS	98.55
TIGR02966		333	phoR_proteo phosphate regulon sensor kinase PhoR.	98.51
COG5002		459	VicK Signal transduction histidine kinase [Signal	98.51
PF12860		115	PAS_7: PAS fold	98.5
COG2203		175	FhlA FOG: GAF domain [Signal transduction mechanis	98.45
PRK11388		638	DNA-binding transcriptional regulator DhaR; Provis	98.39
PF13492		129	GAF_3: GAF domain; PDB: 3EEA_A 4DMZ_A 4DN0_A 1VHM_	98.37
PRK11073		348	glnL nitrogen regulation protein NR(II); Provision	98.33
cd00130		103	PAS PAS domain; PAS motifs appear in archaea, euba	98.31
COG2202		232	AtoS FOG: PAS/PAC domain [Signal transduction mech	98.3
PRK11006		430	phoR phosphate regulon sensor protein; Provisional	98.29
PF13581		125	HATPase_c_2: Histidine kinase-like ATPase domain	98.26
KOG0787		414	consensus Dehydrogenase kinase [Signal transductio	98.23
PF13596		106	PAS_10: PAS domain; PDB: 3CAX_A 2QKP_D.	98.22
COG3829		560	RocR Transcriptional regulator containing PAS, AAA	98.15
PRK10820		520	DNA-binding transcriptional regulator TyrR; Provis	98.14
PF13185		148	GAF_2: GAF domain; PDB: 2QYB_A 3KSG_B 3KSF_C 3KSI_	98.12
PF12860		115	PAS_7: PAS fold	98.08
TIGR01817		534	nifA Nif-specific regulatory protein. This model r	98.02
PRK11086		542	sensory histidine kinase DcuS; Provisional	98.02
PF14598		111	PAS_11: PAS domain; PDB: 1P97_A 3F1O_A 2A24_A 3H7W	97.99
COG1389		538	DNA topoisomerase VI, subunit B [DNA replication,	97.9
COG2202		232	AtoS FOG: PAS/PAC domain [Signal transduction mech	97.88
PF14598		111	PAS_11: PAS domain; PDB: 1P97_A 3F1O_A 2A24_A 3H7W	97.85
smart00388		66	HisKA His Kinase A (phosphoacceptor) domain. Dimer	97.76
COG2172		146	RsbW Anti-sigma regulatory factor (Ser/Thr protein	97.74
COG3604		550	FhlA Transcriptional regulator containing GAF, AAA	97.74
PRK05022		509	anaerobic nitric oxide reductase transcription reg	97.7
PRK15429		686	formate hydrogenlyase transcriptional activator Fh	97.68
COG5000		712	NtrY Signal transduction histidine kinase involved	97.54
PF13188		64	PAS_8: PAS domain; PDB: 2JHE_D 3VOL_A.	97.51
PRK15053		545	dpiB sensor histidine kinase DpiB; Provisional	97.5
TIGR00585		312	mutl DNA mismatch repair protein MutL. All protein	97.43
COG3290		537	CitA Signal transduction histidine kinase regulati	97.41
PRK10820		520	DNA-binding transcriptional regulator TyrR; Provis	97.37
KOG3559		598	consensus Transcriptional regulator SIM1 [Transcri	97.36
PRK11061		748	fused phosphoenolpyruvate-protein phosphotransfera	97.35
KOG3560		712	consensus Aryl-hydrocarbon receptor [Transcription	97.24
KOG0501		971	consensus K+-channel KCNQ [Inorganic ion transport	97.22
PRK09959		1197	hybrid sensory histidine kinase in two-component r	97.21
cd00082		65	HisKA Histidine Kinase A (dimerization/phosphoacce	97.2
PRK11388		638	DNA-binding transcriptional regulator DhaR; Provis	97.16
KOG0501		971	consensus K+-channel KCNQ [Inorganic ion transport	97.02
PF13589		137	HATPase_c_3: Histidine kinase-, DNA gyrase B-, and	96.97
smart00091		67	PAS PAS domain. PAS motifs appear in archaea, euba	96.89
PRK15429		686	formate hydrogenlyase transcriptional activator Fh	96.86
COG2461		409	Uncharacterized conserved protein [Function unknow	96.39
PF13188		64	PAS_8: PAS domain; PDB: 2JHE_D 3VOL_A.	96.36
PRK00095		617	mutL DNA mismatch repair protein; Reviewed	96.18
PRK05559		631	DNA topoisomerase IV subunit B; Reviewed	96.01
PF10090		182	DUF2328: Uncharacterized protein conserved in bact	95.66
PF08670		148	MEKHLA: MEKHLA domain; InterPro: IPR013978 The MEK	95.65
COG5385		214	Uncharacterized protein conserved in bacteria [Fun	95.61
KOG3558		768	consensus Hypoxia-inducible factor 1/Neuronal PAS	95.33
TIGR02373		124	photo_yellow photoactive yellow protein. Members o	95.32
KOG1229		775	consensus 3'5'-cyclic nucleotide phosphodiesterase	95.28
TIGR02916		679	PEP_his_kin putative PEP-CTERM system histidine ki	95.0
TIGR02373		124	photo_yellow photoactive yellow protein. Members o	94.92
COG3283		511	TyrR Transcriptional regulator of aromatic amino a	94.78
COG2461		409	Uncharacterized conserved protein [Function unknow	94.76
KOG3753		1114	consensus Circadian clock protein period [Signal t	94.61
COG3852		363	NtrB Signal transduction histidine kinase, nitroge	94.52
TIGR01059		654	gyrB DNA gyrase, B subunit. This model describes t	94.21
PRK05644		638	gyrB DNA gyrase subunit B; Validated	94.08
PRK10841		924	hybrid sensory kinase in two-component regulatory	93.98
TIGR01055		625	parE_Gneg DNA topoisomerase IV, B subunit, proteob	93.96
smart00433		594	TOP2c TopoisomeraseII. Eukaryotic DNA topoisomeras	93.77
KOG1229		775	consensus 3'5'-cyclic nucleotide phosphodiesterase	93.58
PF08670		148	MEKHLA: MEKHLA domain; InterPro: IPR013978 The MEK	93.17
smart00091		67	PAS PAS domain. PAS motifs appear in archaea, euba	93.13
COG3284		606	AcoR Transcriptional activator of acetoin/glycerol	93.06
TIGR02851		180	spore_V_T stage V sporulation protein T. Members o	92.92
PRK05218		613	heat shock protein 90; Provisional	92.86
PF07568		76	HisKA_2: Histidine kinase; InterPro: IPR011495 Two	92.5
smart00086		43	PAC Motif C-terminal to PAS motifs (likely to cont	91.88
KOG0519		786	consensus Sensory transduction histidine kinase [S	91.5
COG0323		638	MutL DNA mismatch repair enzyme (predicted ATPase)	91.25
PRK14939		756	gyrB DNA gyrase subunit B; Provisional	91.2
PRK10618		894	phosphotransfer intermediate protein in two-compon	90.52
PRK14083		601	HSP90 family protein; Provisional	89.04
smart00086		43	PAC Motif C-terminal to PAS motifs (likely to cont	87.58
TIGR01058		637	parE_Gpos DNA topoisomerase IV, B subunit, Gram-po	86.9
PTZ00272		701	heat shock protein 83 kDa (Hsp83); Provisional	85.77
COG5381		184	Uncharacterized protein conserved in bacteria [Fun	85.29
PF07310		137	PAS_5: PAS domain; InterPro: IPR009922 This family	84.25
COG0326		623	HtpG Molecular chaperone, HSP90 family [Posttransl	83.16
PTZ00108		1388	DNA topoisomerase 2-like protein; Provisional	82.85
KOG3561		803	consensus Aryl-hydrocarbon receptor nuclear transl	82.56
KOG3560		712	consensus Aryl-hydrocarbon receptor [Transcription	81.44

>COG4251 Bacteriophytochrome (light-regulated signal transduction histidine kinase) [Signal transduction mechanisms]	Back alignment and domain information

Probab=100.00  E-value=4.7e-154  Score=1295.08  Aligned_cols=717  Identities=29%  Similarity=0.506  Sum_probs=623.7

Q ss_pred             chhhHHH-HhhccCCCCCCccceEEEEecCCcEEEEecCChhhhhCCCCCCCCCcccccccccCcchhhccCchhHHHHH
Q 001215           61 SSTVSAY-LQRVQRGRLIQPFGCMIAVDEQNFTVLGYSENAPEMLDLAPHAVPNIEQQDALTLGIDVRTLFTSSGAAALQ  139 (1122)
Q Consensus        61 ~~~~~~~-~~~i~~~g~iQp~G~ll~~~~~~~~i~~~S~N~~~~lg~~~~~~~~~~~~~~~~lg~~~~~~~~~~~~~~~~  139 (1122)
                      ...++.| .+|||+||+||||||||++|+.++.|+|+|+||..+||+.|+.+          +|+++.++|+.+....|+
T Consensus         9 ~v~l~nce~ePIHipG~IQPHG~Llvl~~~~~~Vlq~S~N~~~~LG~~~e~l----------~~~tl~~vl~~~qv~~l~   78 (750)
T COG4251           9 HVTLTNCEREPIHIPGAIQPHGALLVLDEADLMVLQASENCANILGREPEDL----------LGRTLGAVLTSEQVPPLQ   78 (750)
T ss_pred             cCcccccccCCccCCCccCCceeEEEeecCCchhhhhhhhHHHHhCCChhhh----------hcCCHHHhcchhhccHHH
Confidence            4677889 99999999999999999999999999999999999999999874          899999999999999999


Q ss_pred             HHhccCCCCCCCcEEEeecCCCcceEEEEeecCceEEEEeeecCCCCCccchhhhhhHHHHHHHHHHHhhcCCCCCHHHH
Q 001215          140 KAANFGEVNLLNPILIHCKTSGKPFYAILHRIDVGLVIDLEPVNPDDVPVTAAGALKSYKLAAKAISRLQSLPSGNISLL  219 (1122)
Q Consensus       140 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~h~~~~~~i~e~Ep~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  219 (1122)
                      .++..+.....||..+-.+. +..|++++||+++.+|+||||+...+. .   ..+.+|+++..++.+||+.+  |+.++
T Consensus        79 ~~l~~~~~~~~np~~~w~~~-~~~fDv~~HR~~~llIlEfEp~~t~e~-~---~~l~f~h~~k~a~~~lq~a~--~l~~l  151 (750)
T COG4251          79 SALTVGGLTTLNPTKMWTRK-GGSFDVSAHRSKELLILEFEPAGTGET-A---SFLGFYHLAKLAMNRLQSAA--NLRDL  151 (750)
T ss_pred             HhccccCcccCCchhhhhhc-CCceeEEEEecCcEEEEEEecCccccc-c---cccchHHHHHHHHHHHhcCc--cHHHH
Confidence            99999888888885552222 337999999999999999999754432 1   23357888888999999966  99999


Q ss_pred             HHHHHHHHHhhcCCCEEEEEeecCCCCceEEEEecCCCCCCccCCCCCCCCccHHHHHHHHhCCeEEeecCCCCcceeec
Q 001215          220 CDVLVNEVSDLTGYDRVMVYKFHEDEHGEVVAECRRPDLEPYLGFHYPATDIPQASRFLIMKNKVRMICDCLAPPVKVIQ  299 (1122)
Q Consensus       220 ~~~~~~~vr~~~~~dRv~iy~f~~d~~g~vvaE~~~~~~~~~lg~~~pa~dip~~~r~l~~~~~~r~i~d~~~~~~~~~~  299 (1122)
                      |+.+++|||++|||||||+|||++||+|+||||+++++++||||+||||||||+|||+||.+|++|+|+|+.|+|||+.|
T Consensus       152 ~~~~tqeVr~~tGfDRVMlYrF~~d~~G~VIAEak~e~LesyLGl~yPaSDIP~qAR~LY~~N~lRlIpD~~~~~vpv~P  231 (750)
T COG4251         152 LSRTTQEVRRMTGFDRVMLYRFDEDGSGEVIAEAKREDLESYLGLRYPASDIPQQARALYIQNPLRLIPDVSYTPVPVLP  231 (750)
T ss_pred             HHHHHHHHHHhcCCceEEEEeecCCCCccEEeccccccchhhhcccCCcccCCHHHHHHHhcCceeecccccCccccccc
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             --CCCCCCCCcccCccccCCChhHHHHHHhcCceeEEEEEEEEeCCcccccccccccCceeeEEEeecCCCCCCChhhHH
Q 001215          300 --DKKLDQPLSLCGSTLRAPHGCHARYMENMGSIASLVMSVTINEAEDELDNDQEQGRKLWGLVVCHHTSPRFVPFPLRY  377 (1122)
Q Consensus       300 --~~~~~~~ldl~~~~lr~~sp~h~~yl~n~~v~a~l~~~i~~~~~~~~~~~~~~~~~~lWGl~~~h~~~pr~~~~~~r~  377 (1122)
                        +|.+++|+|||+|.||||||||++||+||||.||||||||+|             |+|||||+|||.|||++||++|.
T Consensus       232 avNp~t~~p~DLs~svLRSvSp~H~eYLrNMGV~ASmSISivv~-------------g~LWGLIACHH~sPk~ip~~vR~  298 (750)
T COG4251         232 AVNPETNEPLDLSYSVLRSVSPIHLEYLRNMGVGASMSISIVVD-------------GKLWGLIACHHQSPKVIPYEVRK  298 (750)
T ss_pred             ccCcccCCcccchHHHHhccChHHHHHHHhcCcceeeEEEEEEC-------------CeeEEeeeeccCCCccCCHHHHH
Confidence              589999999999999999999999999999999999999999             99999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHhhccCC-CcccccCCcchhhhccCCeEEEEECCeEEEecCCC
Q 001215          378 ACEFLIQVFGVQVNKEVELSAQLREKHILRTQ-TVLCDMLLRDS-PVGIVTQTPNVMDLVKCDGAALYYRGKLWLLGVTP  455 (1122)
Q Consensus       378 ~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~-~~~~~~~~~~~~~l~~~~g~al~~~~~~~~~G~~p  455 (1122)
                      ||||+||++|.+|+.+.+.+..-........+ .++..|...++ ..+++...++|++|++||||||+.+|++.++|.||
T Consensus       299 acef~gq~~s~~i~~~e~~~~~d~r~~l~~~~arl~~~ma~~~~~~d~L~~~~~dll~L~~adGaal~fg~~~~~vG~tP  378 (750)
T COG4251         299 ACEFFGQVLSMEISALEQSEDADYRVQLTEHHARLLRYMAHAADFVDGLIDHQDDLLDLMPADGAALCFGGRWHLVGETP  378 (750)
T ss_pred             HHHHHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHhhhcchhhhhcCCchhhHhhccCCceEEEECCEEEEecCCC
Confidence            99999999999998765533222222222222 35555665555 57888889999999999999999999999999999


Q ss_pred             CHHHHHHHHHHHHhccCCCeEEeeccccccCCCCccccccccceEEEEEcCC--CCeEEEeccccceEEeecCCCCCCCC
Q 001215          456 TEEQIKDIAEWLLEYHRGSTGLSTDSLVEAGYPGALALGDAVCGIAAVKITS--KDFLFWFRSHTAKEIKWGGAKHDSGG  533 (1122)
Q Consensus       456 ~~~~~~~l~~~l~~~~~~~~~~~t~~l~~~~~p~~~~~~~~~~g~l~~~i~~--~~~l~wfR~~~~~~v~WaG~p~~~~~  533 (1122)
                      +..++..|+.||.++... .+|+||+|+.. ||+++.|+..|||||||+|+.  .+||+|||||.++||+|||||+|++.
T Consensus       379 ~~~~v~~Ll~wl~~~~~~-~vf~TdsL~q~-yPda~~~~~vAsGlLAI~is~~~s~~llWFRpEvv~tV~WGG~P~k~~e  456 (750)
T COG4251         379 PRPAVQRLLQWLAEREEG-DVFATDSLSQV-YPDAEDYASVASGLLAIPISRVKSNYLLWFRPEVVQTVNWGGDPEKPYE  456 (750)
T ss_pred             ChHHHHHHHHHHhcCCcc-cEEeecccccc-CcchhhhccccceeEEEEeeccccceEEEEchHHheeeccCCCCCCccc
Confidence            999999999999888544 79999999984 999999999999999999997  89999999999999999999999975


Q ss_pred             -CCCCCccccCchHHHHHHHhcccccccchhHHHHHHHHHHHHHhhhhhhhhcccceeeeccchhhhHHHHHHHHHHHHH
Q 001215          534 -KDGGRKMHPRSSFKAFLEVVKQRSLPWEDVEMDAIHSLQLILRGSLQDEVAEDSKMIVNVPSVDDRIEKIDELRIITNE  612 (1122)
Q Consensus       534 -~~~~~~l~PR~SF~~w~e~v~g~s~pW~~~El~aa~~L~liL~~~l~~~~~~~~~~~~~~r~~~~~~~~~~eL~~~e~~  612 (1122)
                       ++++.||+||+||+.|+|+|+++|.||+..|++++..|+..+.+..-.-                    -+++.     
T Consensus       457 ~~~~~~rL~PRkSFe~WkE~vRl~s~PWs~~ei~~A~~LR~aiv~ivl~~--------------------aeela-----  511 (750)
T COG4251         457 AGPMGIRLTPRKSFELWKETVRLQSQPWSEVEIEAALELRKAIVGIVLRH--------------------AEELA-----  511 (750)
T ss_pred             cCCCCcccCCcccHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHHHHHH--------------------HHHHH-----
Confidence             4567899999999999999999999999999999999943333222100                    00000     


Q ss_pred             HHHHHHhcCccEEEecCCCcEEeccHHHHHHcCCCchhhcCCcccccccCCchHHHHHHHHHHHcCCcceeEEEEEEEeC
Q 001215          613 MVRLIETAAVPILAVDASGNVNGWNSKAAELTGLTVDQAIGTALVDLVAGDSVDVVKNMLSSAFLGIEERNVEIKLRAFG  692 (1122)
Q Consensus       613 l~~lie~a~~gI~~~D~dG~Iv~~N~~~~~l~G~s~eeliG~~~~dl~~~~~~~~~~~~l~~~l~g~~~~~~e~~l~~~~  692 (1122)
                                                                                                      
T Consensus       512 --------------------------------------------------------------------------------  511 (750)
T COG4251         512 --------------------------------------------------------------------------------  511 (750)
T ss_pred             --------------------------------------------------------------------------------
Confidence                                                                                            


Q ss_pred             CCCCCCeEEEEEEEEEecCCCCCEEEEEEEEEcchhhHHHHHHHHhHhhhhhhhhcCCCCCCCCeEEecCCCCeeeeehh
Q 001215          693 PRETSGPVILVVNACCTQDTKENVIGVCFVGQDITGQKLVMDKYTRIQGDYVGIVSSPSALIPPIFMTDEDGRCLEWNDG  772 (1122)
Q Consensus       693 ~~~dG~~~~v~v~~~pi~d~~G~v~gvv~v~~DITerK~aE~~L~~se~~l~~l~e~~~~li~~I~~~D~dg~ii~~N~a  772 (1122)
                                                                                                      
T Consensus       512 --------------------------------------------------------------------------------  511 (750)
T COG4251         512 --------------------------------------------------------------------------------  511 (750)
T ss_pred             --------------------------------------------------------------------------------
Confidence                                                                                            


Q ss_pred             HHHhcCCChHHHhhhhccccccccccccccccCcchHHHHHHHHHHHhcCCCcceeEEEEEccCCCEEEEEEEEeeeeCC
Q 001215          773 MEKLSGLKREEAIERMLIGEVFTVKNFGCRVKNHDTLTKLRIVMNKVISGQDADKILFGFFDQQGKYVEALLSANKRTNA  852 (1122)
Q Consensus       773 ~~~l~G~~~eeliGk~l~~~i~~~~~~~~~l~~~d~~~~~~~~l~~~l~g~~~~~~e~~~~~~dG~~~~v~~~~~pv~d~  852 (1122)
                                                                                                      
T Consensus       512 --------------------------------------------------------------------------------  511 (750)
T COG4251         512 --------------------------------------------------------------------------------  511 (750)
T ss_pred             --------------------------------------------------------------------------------
Confidence                                                                                            


Q ss_pred             CCCEEEEEEeeecccHHHHHHHHHHHHHHHHHHHHHhHHHHHHHhhhhHHHHHHHHHHHhcCC---CCCHHHHHHHHHHH
Q 001215          853 EGKISGILCFLHVASPELQYALQVQRISEQAAANSLNKLEYIRREIRKPLNGIAFMQNLMGTS---DLSEEQKQLLKTSV  929 (1122)
Q Consensus       853 ~G~i~gvv~~l~DITerkq~e~~L~~~ae~~~~~k~~fLa~isHELrnPLt~I~g~~~lL~~~---~l~~~~~~~L~~i~  929 (1122)
                                            ++++..++.+....+|...++|++++||+.|.+++++|...   .++++.++++..+.
T Consensus       512 ----------------------~l~r~lersn~el~~f~yv~sHdlqePl~~I~~~a~lL~~~~~~~~d~~~~~~i~~~~  569 (750)
T COG4251         512 ----------------------QLRRELERSNAELRAFAYVASHDLQEPLRQISNYAQLLSERYSDALDEEAKEFITFIS  569 (750)
T ss_pred             ----------------------HHHHHHhhhhHHHHHHHHHhhhhhhHHHHHHHHHHHhhhhccccccChHHHHHHHHHH
Confidence                                  00111222233334556678999999999999999999654   57889999999999


Q ss_pred             HHHHHHHHHHhhh-cccccccccceeeeEEeehHHHHHHHHHHhccccccCCcEEEeecCCCCcceEEEecHHHHHHHHH
Q 001215          930 LCQEQLTNIVDDT-DIESIEECYMVLKSGEFNLGEALDAVMTQVMIPSREHQVQFIRDLPAEVSTMNLHGDKLRLQQVLS 1008 (1122)
Q Consensus       930 ~~~~rl~~iI~dL-d~srie~g~~~l~~~~~dL~~vi~~v~~~~~~~~~~~~i~l~~~~~~~~~~~~v~~D~~~L~QVL~ 1008 (1122)
                      +....|..||+++ .++++  |.......+.|+.++++.++..+.....+.++++.+..   +|  .+.+|+.++.||++
T Consensus       570 ~~~~~~~~lidd~l~~s~l--~~~~~~l~~td~~~vv~~vl~~l~~ri~dtgaei~i~~---lp--~v~~d~~~l~qv~~  642 (750)
T COG4251         570 RLTSLMQQLIDDLLTYSKL--GLTEAPLQPTDVQKVVDKVLLELSQRIADTGAEIRIAP---LP--VVAADATQLGQVFQ  642 (750)
T ss_pred             HHHHHHHHHHHHHhhhhhh--ccccCCCCCcchHHHHHHHHHhcccccccccceEEecc---cc--eeecCHHHHHHHHH
Confidence            9999999999997 99998  56666777999999999999999999999999998765   44  78999999999999


Q ss_pred             HHHHHHhhcCCCCCCCeEEEEEEecccccCccceeEEEEEEEEcCCCCCChhhhhhhcCCC------CCCCCccchHHHH
Q 001215         1009 DFLTNALIFTPAFEGSSIAFRVIPQKERIGKNIHIVHLEFRITHPAPGIPEKLIHDMFYHS------QGASREGLGLYIS 1082 (1122)
Q Consensus      1009 NLL~NAik~t~~~~g~~I~I~v~~~~~~~~~~~~~~~v~~~V~D~G~GI~~e~~~~iF~~f------~~~~GtGLGL~I~ 1082 (1122)
                      ||+.||+||..+ +.++|+|+....++         .+.|.|.|||+||++.+.+++|..|      .++.|+|+||+||
T Consensus       643 NLi~Naik~~~~-e~~~i~I~~~r~ed---------~~t~sV~dng~Gi~~a~~~riF~iFqRl~s~~~y~gtG~GL~I~  712 (750)
T COG4251         643 NLIANAIKFGGP-ENPDIEISAERQED---------EWTFSVRDNGIGIDPAYFERIFVIFQRLHSRDEYLGTGLGLAIC  712 (750)
T ss_pred             HHHhhheecCCC-CCCceEEeeeccCC---------ceEEEecCCCCCcCHHHHHHHHHHHHhcCchhhhcCCCccHHHH
Confidence            999999999975 45799999887777         8899999999999999999999988      4778999999999


Q ss_pred             HHHHHHcCcEEEEEecCC-ceEEEEEEEecCCCC
Q 001215         1083 QKLVKLMNGTVQYIREAE-RSSFLILIEFPLAHQ 1115 (1122)
Q Consensus      1083 r~ive~~gG~I~v~s~~g-g~tF~~~l~LP~~~~ 1115 (1122)
                      |+|++.|+|+||++|.+| |+||.|+  ||....
T Consensus       713 kkI~e~H~G~i~vEs~~gEgsTF~f~--lp~~~~  744 (750)
T COG4251         713 KKIAERHQGRIWVESTPGEGSTFYFT--LPVGGE  744 (750)
T ss_pred             HHHHHHhCceEEEeecCCCceeEEEE--eecCCc
Confidence            999999999999999977 5666664  476554

>TIGR02938 nifL_nitrog nitrogen fixation negative regulator NifL	Back alignment and domain information

>PRK13560 hypothetical protein; Provisional	Back alignment and domain information

>PRK11091 aerobic respiration control sensor protein ArcB; Provisional	Back alignment and domain information

>COG5002 VicK Signal transduction histidine kinase [Signal transduction mechanisms]	Back alignment and domain information

>PRK11006 phoR phosphate regulon sensor protein; Provisional	Back alignment and domain information

>COG3852 NtrB Signal transduction histidine kinase, nitrogen specific [Signal transduction mechanisms]	Back alignment and domain information

>PRK13557 histidine kinase; Provisional	Back alignment and domain information

>PRK10618 phosphotransfer intermediate protein in two-component regulatory system with RcsBC; Provisional	Back alignment and domain information

>PRK10841 hybrid sensory kinase in two-component regulatory system with RcsB and YojN; Provisional	Back alignment and domain information

>PRK11360 sensory histidine kinase AtoS; Provisional	Back alignment and domain information

>PRK11073 glnL nitrogen regulation protein NR(II); Provisional	Back alignment and domain information

>TIGR02966 phoR_proteo phosphate regulon sensor kinase PhoR	Back alignment and domain information

>PRK09959 hybrid sensory histidine kinase in two-component regulatory system with EvgA; Provisional	Back alignment and domain information

>PF00360 PHY: Phytochrome region; InterPro: IPR013515 Phytochrome belongs to a family of plant photoreceptors that mediate physiological and developmental responses to changes in red and far-red light conditions []	Back alignment and domain information

>COG2205 KdpD Osmosensitive K+ channel histidine kinase [Signal transduction mechanisms]	Back alignment and domain information

>PRK13559 hypothetical protein; Provisional	Back alignment and domain information

>PRK11086 sensory histidine kinase DcuS; Provisional	Back alignment and domain information

>COG4191 Signal transduction histidine kinase regulating C4-dicarboxylate transport system [Signal transduction mechanisms]	Back alignment and domain information

>COG5000 NtrY Signal transduction histidine kinase involved in nitrogen fixation and metabolism regulation [Signal transduction mechanisms]	Back alignment and domain information

>PRK09303 adaptive-response sensory kinase; Validated	Back alignment and domain information

>PRK15053 dpiB sensor histidine kinase DpiB; Provisional	Back alignment and domain information

>TIGR02956 TMAO_torS TMAO reductase sytem sensor TorS	Back alignment and domain information

>PRK15347 two component system sensor kinase SsrA; Provisional	Back alignment and domain information

>PRK11466 hybrid sensory histidine kinase TorS; Provisional	Back alignment and domain information

>PRK10490 sensor protein KdpD; Provisional	Back alignment and domain information

>PRK11107 hybrid sensory histidine kinase BarA; Provisional	Back alignment and domain information

>PRK13837 two-component VirA-like sensor kinase; Provisional	Back alignment and domain information

>COG3290 CitA Signal transduction histidine kinase regulating citrate/malate metabolism [Signal transduction mechanisms]	Back alignment and domain information

>PRK10364 sensor protein ZraS; Provisional	Back alignment and domain information

>PRK10815 sensor protein PhoQ; Provisional	Back alignment and domain information

>PRK10604 sensor protein RstB; Provisional	Back alignment and domain information

>PRK10755 sensor protein BasS/PmrB; Provisional	Back alignment and domain information

>PRK10549 signal transduction histidine-protein kinase BaeS; Provisional	Back alignment and domain information

>TIGR03785 marine_sort_HK proteobacterial dedicated sortase system histidine kinase	Back alignment and domain information

>PRK09776 putative diguanylate cyclase; Provisional	Back alignment and domain information

>PRK09776 putative diguanylate cyclase; Provisional	Back alignment and domain information

>PRK09835 sensor kinase CusS; Provisional	Back alignment and domain information

>PF08446 PAS_2: PAS fold; InterPro: IPR013654 The PAS fold corresponds to the structural domain that has previously been defined as PAS and PAC motifs []	Back alignment and domain information

>TIGR01386 cztS_silS_copS heavy metal sensor kinase	Back alignment and domain information

>TIGR02916 PEP_his_kin putative PEP-CTERM system histidine kinase	Back alignment and domain information

>PRK10337 sensor protein QseC; Provisional	Back alignment and domain information

>PRK11100 sensory histidine kinase CreC; Provisional	Back alignment and domain information

>PRK09470 cpxA two-component sensor protein; Provisional	Back alignment and domain information

>PRK09467 envZ osmolarity sensor protein; Provisional	Back alignment and domain information

>COG0642 BaeS Signal transduction histidine kinase [Signal transduction mechanisms]	Back alignment and domain information

>COG4192 Signal transduction histidine kinase regulating phosphoglycerate transport system [Signal transduction mechanisms]	Back alignment and domain information

>TIGR02040 PpsR-CrtJ transcriptional regulator PpsR	Back alignment and domain information

>PRK13560 hypothetical protein; Provisional	Back alignment and domain information

>PRK11644 sensory histidine kinase UhpB; Provisional	Back alignment and domain information

>PRK11359 cyclic-di-GMP phosphodiesterase; Provisional	Back alignment and domain information

>TIGR02040 PpsR-CrtJ transcriptional regulator PpsR	Back alignment and domain information

>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	Back alignment and domain information

>PRK10935 nitrate/nitrite sensor protein NarQ; Provisional	Back alignment and domain information

>PRK10600 nitrate/nitrite sensor protein NarX; Provisional	Back alignment and domain information

>COG3920 Signal transduction histidine kinase [Signal transduction mechanisms]	Back alignment and domain information

>PRK10547 chemotaxis protein CheA; Provisional	Back alignment and domain information

>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 []	Back alignment and domain information

>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	Back alignment and domain information

>PF00989 PAS: PAS fold; InterPro: IPR013767 PAS domains are involved in many signalling proteins where they are used as a signal sensor domain []	Back alignment and domain information

>COG3850 NarQ Signal transduction histidine kinase, nitrate/nitrite-specific [Signal transduction mechanisms]	Back alignment and domain information

>PRK11091 aerobic respiration control sensor protein ArcB; Provisional	Back alignment and domain information

>COG4585 Signal transduction histidine kinase [Signal transduction mechanisms]	Back alignment and domain information

>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	Back alignment and domain information

>COG3851 UhpB Signal transduction histidine kinase, glucose-6-phosphate specific [Signal transduction mechanisms]	Back alignment and domain information

>smart00387 HATPase_c Histidine kinase-like ATPases	Back alignment and domain information

>PF00989 PAS: PAS fold; InterPro: IPR013767 PAS domains are involved in many signalling proteins where they are used as a signal sensor domain []	Back alignment and domain information

>PF01590 GAF: GAF domain; InterPro: IPR003018 This domain is present in phytochromes and cGMP-specific phosphodiesterases	Back alignment and domain information

>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 []	Back alignment and domain information

>PRK04184 DNA topoisomerase VI subunit B; Validated	Back alignment and domain information

>COG4564 Signal transduction histidine kinase [Signal transduction mechanisms]	Back alignment and domain information

>COG0643 CheA Chemotaxis protein histidine kinase and related kinases [Cell motility and secretion / Signal transduction mechanisms]	Back alignment and domain information

>KOG0519 consensus Sensory transduction histidine kinase [Signal transduction mechanisms]	Back alignment and domain information

>PRK10060 RNase II stability modulator; Provisional	Back alignment and domain information

>PRK13559 hypothetical protein; Provisional	Back alignment and domain information

>PRK14868 DNA topoisomerase VI subunit B; Provisional	Back alignment and domain information

>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	Back alignment and domain information

>PRK13558 bacterio-opsin activator; Provisional	Back alignment and domain information

>PRK13557 histidine kinase; Provisional	Back alignment and domain information

>PRK10060 RNase II stability modulator; Provisional	Back alignment and domain information

>TIGR01052 top6b DNA topoisomerase VI, B subunit	Back alignment and domain information

>TIGR00229 sensory_box PAS domain S-box	Back alignment and domain information

>COG3275 LytS Putative regulator of cell autolysis [Signal transduction mechanisms]	Back alignment and domain information

>TIGR01925 spIIAB anti-sigma F factor	Back alignment and domain information

>PRK03660 anti-sigma F factor; Provisional	Back alignment and domain information

>smart00065 GAF Domain present in phytochromes and cGMP-specific phosphodiesterases	Back alignment and domain information

>COG3829 RocR Transcriptional regulator containing PAS, AAA-type ATPase, and DNA-binding domains [Transcription / Signal transduction mechanisms]	Back alignment and domain information

>PRK11359 cyclic-di-GMP phosphodiesterase; Provisional	Back alignment and domain information

>PRK04069 serine-protein kinase RsbW; Provisional	Back alignment and domain information

>PRK14867 DNA topoisomerase VI subunit B; Provisional	Back alignment and domain information

>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 []	Back alignment and domain information

>COG2972 Predicted signal transduction protein with a C-terminal ATPase domain [Signal transduction mechanisms]	Back alignment and domain information

>PF13596 PAS_10: PAS domain; PDB: 3CAX_A 2QKP_D	Back alignment and domain information

>PRK13558 bacterio-opsin activator; Provisional	Back alignment and domain information

>TIGR02938 nifL_nitrog nitrogen fixation negative regulator NifL	Back alignment and domain information

>PF14501 HATPase_c_5: GHKL domain	Back alignment and domain information

>TIGR00229 sensory_box PAS domain S-box	Back alignment and domain information

>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 []	Back alignment and domain information

>TIGR01924 rsbW_low_gc serine-protein kinase RsbW	Back alignment and domain information

>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 []	Back alignment and domain information

>PRK11360 sensory histidine kinase AtoS; Provisional	Back alignment and domain information

>cd00130 PAS PAS domain; PAS motifs appear in archaea, eubacteria and eukarya	Back alignment and domain information

>KOG3558 consensus Hypoxia-inducible factor 1/Neuronal PAS domain protein NPAS1 [Signal transduction mechanisms; Transcription]	Back alignment and domain information

>TIGR02966 phoR_proteo phosphate regulon sensor kinase PhoR	Back alignment and domain information

>COG5002 VicK Signal transduction histidine kinase [Signal transduction mechanisms]	Back alignment and domain information

>PF12860 PAS_7: PAS fold	Back alignment and domain information

>COG2203 FhlA FOG: GAF domain [Signal transduction mechanisms]	Back alignment and domain information

>PRK11388 DNA-binding transcriptional regulator DhaR; Provisional	Back alignment and domain information

>PF13492 GAF_3: GAF domain; PDB: 3EEA_A 4DMZ_A 4DN0_A 1VHM_A	Back alignment and domain information

>PRK11073 glnL nitrogen regulation protein NR(II); Provisional	Back alignment and domain information

>cd00130 PAS PAS domain; PAS motifs appear in archaea, eubacteria and eukarya	Back alignment and domain information

>COG2202 AtoS FOG: PAS/PAC domain [Signal transduction mechanisms]	Back alignment and domain information

>PRK11006 phoR phosphate regulon sensor protein; Provisional	Back alignment and domain information

>PF13581 HATPase_c_2: Histidine kinase-like ATPase domain	Back alignment and domain information

>KOG0787 consensus Dehydrogenase kinase [Signal transduction mechanisms]	Back alignment and domain information

>PF13596 PAS_10: PAS domain; PDB: 3CAX_A 2QKP_D	Back alignment and domain information

>COG3829 RocR Transcriptional regulator containing PAS, AAA-type ATPase, and DNA-binding domains [Transcription / Signal transduction mechanisms]	Back alignment and domain information

>PRK10820 DNA-binding transcriptional regulator TyrR; Provisional	Back alignment and domain information

>PF13185 GAF_2: GAF domain; PDB: 2QYB_A 3KSG_B 3KSF_C 3KSI_A 3KSH_A 3MMH_A 3RFB_B 1F5M_A 3KO6_B 3HCY_A	Back alignment and domain information

>PF12860 PAS_7: PAS fold	Back alignment and domain information

>TIGR01817 nifA Nif-specific regulatory protein	Back alignment and domain information

>PRK11086 sensory histidine kinase DcuS; Provisional	Back alignment and domain information

>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	Back alignment and domain information

>COG1389 DNA topoisomerase VI, subunit B [DNA replication, recombination, and repair]	Back alignment and domain information

>COG2202 AtoS FOG: PAS/PAC domain [Signal transduction mechanisms]	Back alignment and domain information

>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	Back alignment and domain information

>smart00388 HisKA His Kinase A (phosphoacceptor) domain	Back alignment and domain information

>COG2172 RsbW Anti-sigma regulatory factor (Ser/Thr protein kinase) [Signal transduction mechanisms]	Back alignment and domain information

>COG3604 FhlA Transcriptional regulator containing GAF, AAA-type ATPase, and DNA binding domains [Transcription / Signal transduction mechanisms]	Back alignment and domain information

>PRK05022 anaerobic nitric oxide reductase transcription regulator; Provisional	Back alignment and domain information

>PRK15429 formate hydrogenlyase transcriptional activator FhlA; Provisional	Back alignment and domain information

>COG5000 NtrY Signal transduction histidine kinase involved in nitrogen fixation and metabolism regulation [Signal transduction mechanisms]	Back alignment and domain information

>PF13188 PAS_8: PAS domain; PDB: 2JHE_D 3VOL_A	Back alignment and domain information

>PRK15053 dpiB sensor histidine kinase DpiB; Provisional	Back alignment and domain information

>TIGR00585 mutl DNA mismatch repair protein MutL	Back alignment and domain information

>COG3290 CitA Signal transduction histidine kinase regulating citrate/malate metabolism [Signal transduction mechanisms]	Back alignment and domain information

>PRK10820 DNA-binding transcriptional regulator TyrR; Provisional	Back alignment and domain information

>KOG3559 consensus Transcriptional regulator SIM1 [Transcription]	Back alignment and domain information

>PRK11061 fused phosphoenolpyruvate-protein phosphotransferase PtsP/GAF domain; Provisional	Back alignment and domain information

>KOG3560 consensus Aryl-hydrocarbon receptor [Transcription]	Back alignment and domain information

>KOG0501 consensus K+-channel KCNQ [Inorganic ion transport and metabolism]	Back alignment and domain information

>PRK09959 hybrid sensory histidine kinase in two-component regulatory system with EvgA; Provisional	Back alignment and domain information

>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	Back alignment and domain information

>PRK11388 DNA-binding transcriptional regulator DhaR; Provisional	Back alignment and domain information

>KOG0501 consensus K+-channel KCNQ [Inorganic ion transport and metabolism]	Back alignment and domain information

>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	Back alignment and domain information

>smart00091 PAS PAS domain	Back alignment and domain information

>PRK15429 formate hydrogenlyase transcriptional activator FhlA; Provisional	Back alignment and domain information

>COG2461 Uncharacterized conserved protein [Function unknown]	Back alignment and domain information

>PF13188 PAS_8: PAS domain; PDB: 2JHE_D 3VOL_A	Back alignment and domain information

>PRK00095 mutL DNA mismatch repair protein; Reviewed	Back alignment and domain information

>PRK05559 DNA topoisomerase IV subunit B; Reviewed	Back alignment and domain information

>PF10090 DUF2328: Uncharacterized protein conserved in bacteria (DUF2328); InterPro: IPR018762 Members of this family of hypothetical bacterial proteins have no known function	Back alignment and domain information

>PF08670 MEKHLA: MEKHLA domain; InterPro: IPR013978 The MEKHLA domain shares similarity with the PAS domain and is found in the 3' end of plant HD-ZIP III homeobox genes, and bacterial proteins	Back alignment and domain information

>COG5385 Uncharacterized protein conserved in bacteria [Function unknown]	Back alignment and domain information

>KOG3558 consensus Hypoxia-inducible factor 1/Neuronal PAS domain protein NPAS1 [Signal transduction mechanisms; Transcription]	Back alignment and domain information

>TIGR02373 photo_yellow photoactive yellow protein	Back alignment and domain information

>KOG1229 consensus 3'5'-cyclic nucleotide phosphodiesterases [Signal transduction mechanisms]	Back alignment and domain information

>TIGR02916 PEP_his_kin putative PEP-CTERM system histidine kinase	Back alignment and domain information

>TIGR02373 photo_yellow photoactive yellow protein	Back alignment and domain information

>COG3283 TyrR Transcriptional regulator of aromatic amino acids metabolism [Transcription / Amino acid transport and metabolism]	Back alignment and domain information

>COG2461 Uncharacterized conserved protein [Function unknown]	Back alignment and domain information

>KOG3753 consensus Circadian clock protein period [Signal transduction mechanisms]	Back alignment and domain information

>COG3852 NtrB Signal transduction histidine kinase, nitrogen specific [Signal transduction mechanisms]	Back alignment and domain information

>TIGR01059 gyrB DNA gyrase, B subunit	Back alignment and domain information

>PRK05644 gyrB DNA gyrase subunit B; Validated	Back alignment and domain information

>PRK10841 hybrid sensory kinase in two-component regulatory system with RcsB and YojN; Provisional	Back alignment and domain information

>TIGR01055 parE_Gneg DNA topoisomerase IV, B subunit, proteobacterial	Back alignment and domain information

>smart00433 TOP2c TopoisomeraseII	Back alignment and domain information

>KOG1229 consensus 3'5'-cyclic nucleotide phosphodiesterases [Signal transduction mechanisms]	Back alignment and domain information

>PF08670 MEKHLA: MEKHLA domain; InterPro: IPR013978 The MEKHLA domain shares similarity with the PAS domain and is found in the 3' end of plant HD-ZIP III homeobox genes, and bacterial proteins	Back alignment and domain information

>smart00091 PAS PAS domain	Back alignment and domain information

>COG3284 AcoR Transcriptional activator of acetoin/glycerol metabolism [Secondary metabolites biosynthesis, transport, and catabolism / Transcription]	Back alignment and domain information

>TIGR02851 spore_V_T stage V sporulation protein T	Back alignment and domain information

>PRK05218 heat shock protein 90; Provisional	Back alignment and domain information

>PF07568 HisKA_2: Histidine kinase; InterPro: IPR011495 Two-component signal transduction systems enable bacteria to sense, respond, and adapt to a wide range of environments, stressors, and growth conditions []	Back alignment and domain information

>smart00086 PAC Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain)	Back alignment and domain information

>KOG0519 consensus Sensory transduction histidine kinase [Signal transduction mechanisms]	Back alignment and domain information

>COG0323 MutL DNA mismatch repair enzyme (predicted ATPase) [DNA replication, recombination, and repair]	Back alignment and domain information

>PRK14939 gyrB DNA gyrase subunit B; Provisional	Back alignment and domain information

>PRK10618 phosphotransfer intermediate protein in two-component regulatory system with RcsBC; Provisional	Back alignment and domain information

>PRK14083 HSP90 family protein; Provisional	Back alignment and domain information

>smart00086 PAC Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain)	Back alignment and domain information

>TIGR01058 parE_Gpos DNA topoisomerase IV, B subunit, Gram-positive	Back alignment and domain information

>PTZ00272 heat shock protein 83 kDa (Hsp83); Provisional	Back alignment and domain information

>COG5381 Uncharacterized protein conserved in bacteria [Function unknown]	Back alignment and domain information

>PF07310 PAS_5: PAS domain; InterPro: IPR009922 This family contains a number of hypothetical bacterial proteins of unknown function approximately 200 residues long	Back alignment and domain information

>COG0326 HtpG Molecular chaperone, HSP90 family [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

>PTZ00108 DNA topoisomerase 2-like protein; Provisional	Back alignment and domain information

>KOG3561 consensus Aryl-hydrocarbon receptor nuclear translocator [Transcription]	Back alignment and domain information

>KOG3560 consensus Aryl-hydrocarbon receptor [Transcription]	Back alignment and domain information

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Alignment Graph	Length	Definition	E-value
Query		1122
2vea_A		520	The Complete Sensory Module Of The Cyanobacterial P		1e-70
3zq5_A		520	Structure Of The Y263f Mutant Of The Cyanobacterial		3e-70
4gw9_A		655	Structure Of A Bacteriophytochrome And Light-Stimul		2e-51
3g6o_A		505	Crystal Structure Of P. Aeruginosa Bacteriophytochr		3e-45
3c2w_A		505	Crystal Structure Of The Photosensory Core Domain O		9e-45
3ibr_A		505	Crystal Structure Of P. Aeruginosa Bacteriophytochr		7e-43
2ool_A		337	Crystal Structure Of The Chromophore-Binding Domain		7e-37
4e04_A		327	Rpbphp2 Chromophore-binding Domain Crystallized By		7e-34
2o9b_A		342	Crystal Structure Of Bacteriophytochrome Chromophor		3e-27
3s7q_A		343	Crystal Structure Of A Monomeric Infrared Fluoresce		1e-26
1ztu_A		341	Structure Of The Chromophore Binding Domain Of Bact		2e-26
3s7n_A		343	Crystal Structure Of The Alternate His 207 Conforma		3e-26
2lb5_A		208	Refined Structural Basis For The Photoconversion Of		3e-17
2k2n_A		172	Solution Structure Of A Cyanobacterial Phytochrome		3e-17
3a0r_A		349	Crystal Structure Of Histidine Kinase Thka (Tm1359)		2e-05
3sl2_A		177	Atp Forms A Stable Complex With The Essential Histi		6e-05

>pdb|2VEA|A Chain A, The Complete Sensory Module Of The Cyanobacterial Phytochrome Cph1 In The Pr-State Length = 520