Citrus Sinensis ID: 001353

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---

MGLQGNRETTNSIGGGHNTTPFKSSDAKMKPVNKGKTIIDHYNADAGLLAEFEQSVASGKSFNYSRSVISPPEGVPEEQITAYLSKIQRGGLIQPFGCMLAVEEPTFRIIGYSENCLEMLDLRSRSEDFELNGLIGIDARTLFTPPSGASLAKAAASREISLLNPILVHSNSRSIEKPFYAILHRIDVGIVIDLEPSKSGDPALSLAGAVQSQKLAVSAISRLQALPGGDIGLLCDTVVEDVQKLTGYDRVMLYNFHDDDHGEVVSEIRRSDLEPYLGIHFPANDIPQAARFLFKQNRVRMICDCHAIPVMVIQSKELKQPLCLVNSTLRSPHGCHLQYMTNMGSIASLVMAVIINSKDSMKLWGLVVCHHTSPRYIPFPLRYACEFLVQAFSLQLYMELQVAMQLAEKNILRTQVLLCDMLLRDAPFSIVTQSPSIMDLVKCDGAALYYGGRCWLVGVTPTESQLKDIAWWLLNNHGDCTGLSTDSLAEAGYPGAALLGQAVCGMATARITSKDFLFWFRSHTAKEVKWGGAKHHPEHKDNGGKMHPRSSFKAFLEVVKNRSFPWEVSEINAIHSLQIVMRDSFQEMEEENDSKVQGNTQQNGSKMQGVDELSSVACEMVRLIETATAPIFGVDSSGTINGWNAKVAELTGLPASEAMGKSLIDEVVHEESQGAVENLICRALLGEEDKNVELKLRKFELQKQHSVVYILVNACTSRDYKNNVKGVCFVGQDITHEKVLMDKFIRLQGDYEAIIQSVNPLIPPIFASDENACCSEWNAAMEKVTGWMRHEVIGITGQGTENFPFGFFNRQGQFVEVALTASRRTDAEGKVIGCFCFMQILVPDLQPALEAQGLEDMDIYAKIKELAYIRQEVKNPLNGIRFVHKLLESSSISENQRQYLETSDACERQIMTIIDGMDLRCIEEGNMELKSEEFLLGNILDAVVSQVMVLLRDKNLHLLHDIPEEIKALSLNGDRIRLQLVLSDFLHCVVRHAPSPDGWVEIKVLPGLKLIKDADQFVHVQFRLTHPGEGIPSHLIEDMYNGRNQWTTPEGLGLKLSRKLLIMMNGRVRYVRENSKCYFVIDLELKTRGRQKM

ccccccccccccccccccccccccccccccccccccEEEEEEcccccHHHHHHHcccccccEEEccccccccccccccHHHHHHHccccccccccccEEEEEEccccEEEEEEccHHHHHcccccccccccccccccccHHcccccHHHHHHHHHHcccccccccEEEEEcccccccEEEEEEEEEccEEEEEEEEcccccccccHHHHHHHHHHHHHHHHHHcccccccHHHHHHHHHHHHHHHccccEEEEEEEccccccEEEEEEcccccccccccccccccccHHHHHHHHcccEEEEcccccccccEEccccccccccccccccccccHHHHHHHHHccccEEEEEEEEEEccccccEEEEEEEcccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccHHcccccHHHHHccccEEEEEccEEEEEcccccHHHHHHHHHHHHHccccccEEEEcccccccccccccccccEEEEEEEEEccccEEEEEccccccEEEccccccccccccccccccccccHHHHHHHHHcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccHHHHHHHHHHHHHHHHHHccccccccccccccccHHHHHHHHHcccHHHHHHHHHHHHHHccccHHHHHHHHHHHHcccccccHHHHHHHHccccccccEEEEEcccccccccccccEEEEEEEcccHHHHHHHHHHHccccHHHHHcccccccccEEEEcccccHHHHHHHHHHHHcccccEEEEccccccccccccEEEEcccEEEEEEEccccccccccEEEEEEEEEcccccccHHHHHHcHHHHHHHHHHHHHHHHHHHHHcHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccccHHHHHHHHHHHHHHHcccccEEEEEcccccccccEEEEcHHHHHHHHHHHHHHHHHccccccccEEEEEEEcccccccccEEEEEEEEEEccccccccHHHHHccccccccccccccHHHHHHHHHHHcccEEEEEEEccEEEEEEEEEccccccccc

cccccccccccccccccccccccccccccccccccEEEEEEEEcccEEEEEEEEccccccccccccccccccccccHHHHHHHHHHHHHccccccccEEEEEccccEEEEEEcccHHHHHccccccccccccEEEcccHHHHcccHHHHHHHHHHHHccHcccccEEEEEccccccccEEEEEEEEEEEEEEEcccccccccHHHHHHHHHHHHHHHHHHHHHHccccccHHHHHHHHHHHHHHHccccEEEEEEEccccccEEEEEEcccccccccccccccccHHHHHHHHHHHccEEEEEEcccccEEEEEccccccccEEccccccccccHHHHHHHHHcHHHHHHEEEEEEcccccEEEEEEEEcccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccEEEEcccccHcHEccccEEEEEcccEEEEcccccHHHHHHHHHHHHHHcccccccccHHHHHcccccHHHHccHHcccEEEEEccccEEEEEccccHHHHccccccccccccccccccccccHHHHHHHHHHHccccHHHHHHHHHHHHHHHHHHHHHHHcccccccEEEEccccccccccHHHHHHHHHHHHHHHHHccccEEEEEccccEcccHHHHHHHccccHHHHHcHHHHHHHHHHcHHHHHHHHHHHHHccccHccEEEEEEEcccccccccEEEEEEccccccccccEEEEEEEEEcccccHHHHHHHEEEccccEEEEccccccccccEccccccccHHHHHHHHHHccccHHHEEEcccccccccccccEcccccEEEEEEEEccccccccEEEEEEEEEEcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccHHHHHHHHHccccccHHHHHHHHHHHHHHHHHHHHHHcccHHHHHcccEEEccEEEEHHHHHHHHHHHHHHHHHHcccEEEEcccHHHcccEccccHHHHHHHHHHHHHHHHHcccccccEEEEEEEcccccccccEEEEEEEEEEEcccccccHHHHHHHHccccccccHHHHHHHHHHHHHHHHcccEEEEEEcccEEEEEEEEEcccccccc

mglqgnrettnsiggghnttpfkssdakmkpvnkgkTIIDHYNADAGLLAEFEQsvasgksfnysrsvisppegvpeEQITAYLSKIQrggliqpfgcmlaveeptfriigYSENCLEMLDlrsrsedfelngligidartlftppsgaSLAKAAASREISLLNPilvhsnsrsiekpFYAILHRIDVGividlepsksgdpalsLAGAVQSQKLAVSAISRLqalpggdiglLCDTVVEDVQKltgydrvmlynfhdddhgevvseirrsdlepylgihfpandipQAARFLFKQNRVRMICDCHAIPVMVIQskelkqplclvnstlrsphgchlQYMTNMGSIASLVMAVIINSKDSMKLWGLVvchhtspryipfplRYACEFLVQAFSLQLYMELQVAMQLAEKNILRTQVLLCDMllrdapfsivtqspsimdlvkcdgaalyyggrcwlvgvtptesQLKDIAWWLLNnhgdctglstdslaeagypgaaLLGQAVCGMATARITSKDFLFWFRSHTAkevkwggakhhpehkdnggkmhprsSFKAFLEVVKnrsfpwevsEINAIHSLQIVMRDSFqemeeendskvqgntqqngskmqgvdELSSVACEMVRLIETatapifgvdssgtingWNAKVAEltglpaseamGKSLIDEVVHEESQGAVENLICRALLGEEDKNVELKLRKFELQKQHSVVYILVNACtsrdyknnvkgvcfvgqdithEKVLMDKFIRLQGDYEAIIQsvnplippifasdenaCCSEWNAAMEKVTGWMRHEVIgitgqgtenfpfgffnrqGQFVEVALTasrrtdaegkvigcfcfmqilvpdlqpaleaqgleDMDIYAKIKELAYIRQEVKNPLNGIRFVHKLLESSSISENQRQYLETSDACERQIMTIIDGMDLRCIEEGNMELKSEEFLLGNILDAVVSQVMVLLRDKNLHLLHDIPEEIKALSLNGDRIRLQLVLSDFLHCVvrhapspdgwveikvlpglklikdadQFVHVQFrlthpgegipshliedmyngrnqwttpeglglkLSRKLLIMMNGRVRyvrenskcyfvidlelktrgrqkm

mglqgnrettnsiggghnttpfkssdakmKPVNKGKTIIDHYNADAGLLAEFEQSVASGKSFNYSRSVISPPEGVPEEQITAYLSKIQRGGLIQPFGCMLAVEEPTFRIIGYSENCLEMLDLRSRSEDFELNGLIGIDARTLFTPPSGASLAKAAASREISLLNpilvhsnsrsIEKPFYAILHRIDVGIVIDLEPSKSGDPALSLAGAVQSQKLAVSAISRLQALPGGDIGLLCDTVVEDVQKLTGYDRVMLYNFHDDDHGEVVSEIRRSDLEPYLGIHFPANDIPQAARFLFKQNRVRMICDCHAIPVMVIQSKELKQPLCLVNSTLRSPHGCHLQYMTNMGSIASLVMAVIINSKDSMKLWGLVVCHHTSPRYIPFPLRYACEFLVQAFSLQLYMELQVAMQLAEKNILRTQVLLCDMLLRDAPFsivtqspsimDLVKCDGAALYYGGRCWLVGVTPTESQLKDIAWWLLNNHGDCTGLSTDSLAEAGYPGAALLGQAVCGMATARITSKDFLFWFRSHTAkevkwggakhhpehkdnggkmhpRSSFKAFLEVVKNRSFPWEVSEINAIHSLQIVMRDSFQEMEEENDSkvqgntqqngskmqgVDELSSVACEMVRLIETAtapifgvdsSGTINGWNAKVAELTGLPASEAMGKSLIDEVVHEESQGAVENLICRALLGEEDKNVELKLRkfelqkqhsVVYILVNActsrdyknnVKGVCFVGQDITHEKVLMDKFIRLQGDYEAIIQSVNPLIPPIFASDENACCSEWNAAMEKVTGWMRHEVIGITGQGTENFPFGFFNRQGQFVEVALTASRRTDAEGKVIGCFCFMQILVPDLQPALEAQGLEDMDIYAKIKELAYIRQEVKNPLNGIRFVHKLLesssisenqRQYLETSDACERQIMTIIDGMDLRCIEEGNMELKSEEFLLGNILDAVVSQVMVLLRDKNLHLLHDIPEEIKALSLNGDRIRLQLVLSDFLHCVVRhapspdgwVEIKVLPGLKLIKDADQFVHVQFRLTHPGEGIPSHLIEDMYNGRNQWTTPEGLGLKLSRKLLIMMNGRvryvrenskcyfvidlelktrgrqkm

************************************TIIDHYNADAGLLAEFEQ************************QITAYLSKIQRGGLIQPFGCMLAVEEPTFRIIGYSENCLEMLDLRSRSEDFELNGLIGIDARTLFTPP****LAKAAASREISLLNPILVHSNSRSIEKPFYAILHRIDVGIVIDLE***********AGAVQSQKLAVSAISRLQALPGGDIGLLCDTVVEDVQKLTGYDRVMLYNFHDDDHGEVVSEIRRSDLEPYLGIHFPANDIPQAARFLFKQNRVRMICDCHAIPVMVIQSKELKQPLCLVNSTLRSPHGCHLQYMTNMGSIASLVMAVIINSKDSMKLWGLVVCHHTSPRYIPFPLRYACEFLVQAFSLQLYMELQVAMQLAEKNILRTQVLLCDMLLRDAPFSIVTQSPSIMDLVKCDGAALYYGGRCWLVGVTPTESQLKDIAWWLLNNHGDCTGLSTDSLAEAGYPGAALLGQAVCGMATARITSKDFLFWFRSHTAKEVKWG********************FKAFLEVVKNRSFPWEVSEINAIHSLQIVMR*******************************SSVACEMVRLIETATAPIFGVDSSGTINGWNAKVAELTGLPASEAMGKSLIDEVVHEESQGAVENLICRALLGEEDKNVELKLRKFELQKQHSVVYILVNACTSRDYKNNVKGVCFVGQDITHEKVLMDKFIRLQGDYEAIIQSVNPLIPPIFASDENACCSEWNAAMEKVTGWMRHEVIGITGQGTENFPFGFFNRQGQFVEVALTASRRTDAEGKVIGCFCFMQILVPDLQPALEAQGLEDMDIYAKIKELAYIRQEVKNPLNGIRFVHKLLE*********QYLETSDACERQIMTIIDGMDLRCIEEGNMELKSEEFLLGNILDAVVSQVMVLLRDKNLHLLHDIPEEIKALSLNGDRIRLQLVLSDFLHCVVRHAPSPDGWVEIKVLPGLKLIKDADQFVHVQFRLTHPGEGIPSHLIEDMYNGRNQWTTPEGLGLKLSRKLLIMMNGRVRYVRENSKCYFVIDLEL********

*****************************************YNADAGLLAEFE**************************ITAYLSKIQRGGLIQPFGCMLAVEEPTFRIIGYSENCLEMLDLRSRSEDFELNGLIGIDARTLFTPPSGASLAKAAASREISLLNPILVHSNSRSIEKPFYAILHRIDVGIVIDLEPSKSGDPALSLAGAVQSQKLAVSA***L***PGGDIGLLCDTVVEDVQKLTGYDRVMLYNFHDDDHGEVVSEIRRSDLEPYLGIHFPANDIPQAARFLFKQNRVRMICDCHAIPVMVIQSKELKQPLCLVNSTLRSPHGCHLQYMTNMGSIASLVMAVIINSKDSMKLWGLVVCHHTSPRYIPFPLRYACEFLVQAFSLQLYMELQVAMQLAEKNILRTQVLLCDMLLRDAPFSIVTQSPSIMDLVKCDGAALYYGGRCWLVGVTPTESQLKDIAWWLLNNHGDCTGLSTDSLAEAGYPGAALLGQAVCGMATARITSKDFLFWFRSHTAKEVKWGGAK***************SSFKAFLEVVKNRSFPWEVSEINAIHSLQIVMRDSFQEME********************VDELSSVACEMVRLIETATAPIFGVDSSGTINGWNAKVAELTGLPASEAMGKSLIDEVVHEESQGAVENLICRALLGEEDKNVELKLRK*****QHSVVYILVNACTSRDYKNNVKGVCFVGQDITHEKVLMDKFIRLQGDYEAIIQSVNPLIPPIFASDENACCSEWNAAMEKVTGWMRHEVIGITGQGTENFPFGFFNRQGQFVEVALTASRRTDAEGKVIGCFCFMQILVP*********************ELAYIRQEVKNPLNGIRFVHKLL************************TIIDGMDLRCIEEGNMELKSEEFLLGNILDAVVSQVMVLLRDKNLHLLHDIPEEIKALSLNGDRIRLQLVLSDFLHCVVRHAPSPDGWVEIKVLPGLKLIKDADQFVHVQFRLTHPGEGIPSHLIEDMYNGRNQWTTPEGLGLKLSRKLLIMMNGRVRYVRENSKCYFVIDL**********

**********NSIGGGHNTTPFKSSDAKMKPVNKGKTIIDHYNADAGLLAEFEQSVASGKSFNYSRSVISPPEGVPEEQITAYLSKIQRGGLIQPFGCMLAVEEPTFRIIGYSENCLEMLDLRSRSEDFELNGLIGIDARTLFTPPSGASLAKAAASREISLLNPILVHSNSRSIEKPFYAILHRIDVGIVIDLEPSKSGDPALSLAGAVQSQKLAVSAISRLQALPGGDIGLLCDTVVEDVQKLTGYDRVMLYNFHDDDHGEVVSEIRRSDLEPYLGIHFPANDIPQAARFLFKQNRVRMICDCHAIPVMVIQSKELKQPLCLVNSTLRSPHGCHLQYMTNMGSIASLVMAVIINSKDSMKLWGLVVCHHTSPRYIPFPLRYACEFLVQAFSLQLYMELQVAMQLAEKNILRTQVLLCDMLLRDAPFSIVTQSPSIMDLVKCDGAALYYGGRCWLVGVTPTESQLKDIAWWLLNNHGDCTGLSTDSLAEAGYPGAALLGQAVCGMATARITSKDFLFWFRSHTAKEVKWGGAKHHPEHKDNGGKMHPRSSFKAFLEVVKNRSFPWEVSEINAIHSLQIVMRDSFQ************************DELSSVACEMVRLIETATAPIFGVDSSGTINGWNAKVAELTGLPASEAMGKSLIDEVVHEESQGAVENLICRALLGEEDKNVELKLRKFELQKQHSVVYILVNACTSRDYKNNVKGVCFVGQDITHEKVLMDKFIRLQGDYEAIIQSVNPLIPPIFASDENACCSEWNAAMEKVTGWMRHEVIGITGQGTENFPFGFFNRQGQFVEVALTASRRTDAEGKVIGCFCFMQILVPDLQPALEAQGLEDMDIYAKIKELAYIRQEVKNPLNGIRFVHKLLESSSISENQRQYLETSDACERQIMTIIDGMDLRCIEEGNMELKSEEFLLGNILDAVVSQVMVLLRDKNLHLLHDIPEEIKALSLNGDRIRLQLVLSDFLHCVVRHAPSPDGWVEIKVLPGLKLIKDADQFVHVQFRLTHPGEGIPSHLIEDMYNGRNQWTTPEGLGLKLSRKLLIMMNGRVRYVRENSKCYFVIDLELKTRGRQKM

*********************************KGKTIIDHYNADAGLLAEFEQSV****************EGVPEEQITAYLSKIQRGGLIQPFGCMLAVEEPTFRIIGYSENCLEMLDLRSRSEDFELNGLIGIDARTLFTPPSGASLAKAAASREISLLNPILVHSNSRSIEKPFYAILHRIDVGIVIDLEPSKSGDPALSLAGAVQSQKLAVSAISRLQALPGGDIGLLCDTVVEDVQKLTGYDRVMLYNFHDDDHGEVVSEIRRSDLEPYLGIHFPANDIPQAARFLFKQNRVRMICDCHAIPVMVIQSKELKQPLCLVNSTLRSPHGCHLQYMTNMGSIASLVMAVIINSKDSMKLWGLVVCHHTSPRYIPFPLRYACEFLVQAFSLQLYMELQVAMQLAEKNILRTQVLLCDMLLRDAPFSIVTQSPSIMDLVKCDGAALYYGGRCWLVGVTPTESQLKDIAWWLLNNHGDCTGLSTDSLAEAGYPGAALLGQAVCGMATARITSKDFLFWFRSHTAKEVKWGGAK***********MHPRSSFKAFLEVVKNRSFPWEVSEINAIHSLQIVMRDSFQEMEEENDSKVQGNTQQNGSKMQGVDELSSVACEMVRLIETATAPIFGVDSSGTINGWNAKVAELTGLPASEAMGKSLIDEVVHEESQGAVENLICRALLGEEDKNVELKLRKFELQKQHSVVYILVNACTSRDYKNNVKGVCFVGQDITHEKVLMDKFIRLQGDYEAIIQSVNPLIPPIFASDENACCSEWNAAMEKVTGWMRHEVIGITGQGTENFPFGFFNRQGQFVEVALTASRRTDAEGKVIGCFCFMQILVPDLQPALEAQGLEDMDIYAKIKELAYIRQEVKNPLNGIRFVHKLLESSSISENQRQYLETSDACERQIMTIIDGMDLRCIEEGNMELKSEEFLLGNILDAVVSQVMVLLRDKNLHLLHDIPEEIKALSLNGDRIRLQLVLSDFLHCVVRHAPSPDGWVEIKVLPGLKLIKDADQFVHVQFRLTHPGEGIPSHLIEDMYNGRNQWTTPEGLGLKLSRKLLIMMNGRVRYVRENSKCYFVIDLELKTR*****

ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo

iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo

SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo

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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		1093	2.2.26 [Sep-21-2011]
P55004		1115	Phytochrome E OS=Ipomoea	N/A	no	0.968	0.949	0.699	0.0
P42498		1112	Phytochrome E OS=Arabidop	yes	no	0.957	0.941	0.641	0.0
Q41046		1131	Phytochrome OS=Pinus sylv	N/A	no	0.959	0.927	0.629	0.0
P34094		1130	Phytochrome B OS=Solanum	N/A	no	0.953	0.922	0.630	0.0
P29130		1132	Phytochrome B OS=Nicotian	N/A	no	0.959	0.926	0.623	0.0
Q9ZS62		1131	Phytochrome B1 OS=Solanum	N/A	no	0.973	0.940	0.612	0.0
P14713		1172	Phytochrome B OS=Arabidop	no	no	0.978	0.912	0.589	0.0
P93527		1178	Phytochrome B OS=Sorghum	N/A	no	0.955	0.886	0.599	0.0
A2XFW2		1171	Phytochrome B OS=Oryza sa	N/A	no	0.955	0.891	0.600	0.0
Q10MG9		1171	Phytochrome B OS=Oryza sa	yes	no	0.955	0.891	0.600	0.0

>sp\|P55004\|PHYE_IPONI Phytochrome E OS=Ipomoea nil GN=PHYE PE=2 SV=1	Back alignment and function desciption

 Score = 1583 bits (4100), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 767/1096 (69%), Positives = 901/1096 (82%), Gaps = 37/1096 (3%)

Query: 25   SDAKMKPVNKGKTIIDHYNADAGLLAEFEQSVASGKSFNYSRSVISPPEGVPEEQITAYL 84
            S +    +N GK I   YNADA L+AEFEQS  SGKSF+YSRSVI  P+ V EE++TAYL
Sbjct: 11   SSSATSNLNTGKAIA-QYNADAKLMAEFEQSRESGKSFDYSRSVIHAPQNVTEEEMTAYL 69

Query: 85   SKIQRGGLIQPFGCMLAVEEPTFRIIGYSENCLEMLDLRSRSEDFELNGLIGIDARTLFT 144
            S+IQRGGLIQPFGCMLA+EEP+F+I+G+SENC ++L L+S  E  E   LIGIDARTLFT
Sbjct: 70   SRIQRGGLIQPFGCMLAIEEPSFKIVGFSENCFDLLGLKSGVEPPERMSLIGIDARTLFT 129

Query: 145  PPSGASLAKAAASREISLLNPILVHSNSRSIEKPFYAILHRIDVGIVIDLEPSKSGDPAL 204
              S ASLAKA ASREISLLNPI VHS     +KPFYA+LHRIDVGIVIDLEP+ S DPAL
Sbjct: 130  LSSRASLAKAVASREISLLNPIWVHSKIN--QKPFYAVLHRIDVGIVIDLEPANSADPAL 187

Query: 205  SLAGAVQSQKLAVSAISRLQALPGGDIGLLCDTVVEDVQKLTGYDRVMLYNFHDDDHGEV 264
             LAGAVQSQKLAV AISRLQ+LPGGDIG LCDTVVEDVQKLTGYDRVM+Y FHDD HGEV
Sbjct: 188  LLAGAVQSQKLAVRAISRLQSLPGGDIGTLCDTVVEDVQKLTGYDRVMVYKFHDDSHGEV 247

Query: 265  VSEIRRSDLEPYLGIHFPANDIPQAARFLFKQNRVRMICDCHAIPVMVIQSKELKQPLCL 324
            VSEIRRSDLEPYLG+H+PA DIPQAARFLFKQNRVRMICDC+A PV V+Q +ELKQPLCL
Sbjct: 248  VSEIRRSDLEPYLGLHYPATDIPQAARFLFKQNRVRMICDCNAQPVKVLQCEELKQPLCL 307

Query: 325  VNSTLRSPHGCHLQYMTNMGSIASLVMAVIINSKDSMKLWGLVVCHHTSPRYIPFPLRYA 384
            VNSTLRSPHGCH +YM NMGSIASLVMAV+INS +SMKLWGLVVCHHTSPRY+PFPLRYA
Sbjct: 308  VNSTLRSPHGCHTKYMANMGSIASLVMAVVINSSESMKLWGLVVCHHTSPRYVPFPLRYA 367

Query: 385  CEFLVQAFSLQLYMELQVAMQLAEKNILRTQVLLCDMLLRDAPFSIVTQSPSIMDLVKCD 444
            CEFL+QAFSLQLYMELQ+A QLAEK IL+TQ LLCDMLLRDAPF IVTQ+PSIMDLV+CD
Sbjct: 368  CEFLMQAFSLQLYMELQLASQLAEKKILQTQTLLCDMLLRDAPFGIVTQTPSIMDLVRCD 427

Query: 445  GAALYYGGRCWLVGVTPTESQLKDIAWWLLNNHGDCTGLSTDSLAEAGYPGAALLGQAVC 504
            GAALYY G+CWL+GVTPTE+Q+KDIA WLL+NHGD TGLSTD L++AGYPGA LLG AV 
Sbjct: 428  GAALYYNGKCWLLGVTPTETQVKDIAEWLLHNHGDSTGLSTDCLSDAGYPGAPLLGDAVS 487

Query: 505  GMATARITSKDFLFWFRSHTAKEVKWGGAKHHPEHKDNGGKMHPRSSFKAFLEVVKNRSF 564
            GMATARITSKDFLFWFRSHTAKEVKWGGAKHHPE KD+GG+MHPRSSF AFLEVVK+RS 
Sbjct: 488  GMATARITSKDFLFWFRSHTAKEVKWGGAKHHPEDKDDGGRMHPRSSFIAFLEVVKSRSL 547

Query: 565  PWEVSEINAIHSLQIVMRDSFQEMEEENDSKVQGNTQQNGSKMQGVDELSSVACEMVRLI 624
            PWE SEINAIHSLQ++MRDS Q +  EN  K   + QQN S      ELSS+A E+VRL+
Sbjct: 548  PWEDSEINAIHSLQLIMRDSLQGI-GENYMKSVSSPQQNDSDGVRFYELSSMALELVRLV 606

Query: 625  ETATAPIFGVDSSGTINGWNAKVAELTGLPASEAMGKSLIDEVVHEESQGAVENLICRAL 684
            ETAT PIFGVDSSG INGWNAK+AELTGL A+ A+GK LID+V HE+S    + L+CRAL
Sbjct: 607  ETATVPIFGVDSSGLINGWNAKIAELTGLQANVAIGKYLIDDVTHEDSHETFKALMCRAL 666

Query: 685  LGEEDKNVELKLRKFELQKQHSVVYILVNACTSRDYKNNVKGVCFVGQDITHEKVLMDKF 744
             GEED+NVE+KL KF       VVY++VNACTSRDYKN++ GVCFVGQDIT EK +MDKF
Sbjct: 667  QGEEDRNVEVKLLKFGNHPTKEVVYLVVNACTSRDYKNDIIGVCFVGQDITPEKAVMDKF 726

Query: 745  IRLQGDYEAIIQSVNPLIPPIFASDENACCSEWNAAMEKVTGWMRHEVI----------- 793
            +RLQGDYEAIIQS+NPLIPPIFASDENACCSEWNAAME++TG ++ EVI           
Sbjct: 727  VRLQGDYEAIIQSLNPLIPPIFASDENACCSEWNAAMERLTGLVKCEVIGKRLPGEIFGG 786

Query: 794  -------------------GITGQGTENFPFGFFNRQGQFVEVALTASRRTDAEGKVIGC 834
                               GI+G  TE   FGFF+R+G F++V +TA++RTD  G +IGC
Sbjct: 787  LCRLKGQDALTKFMILLYQGISGHDTEKLSFGFFDRKGNFIDVFITANKRTDERGNIIGC 846

Query: 835  FCFMQILVPDLQPALEAQGLE-DMDIYAKIKELAYIRQEVKNPLNGIRFVHKLLESSSIS 893
            FCF+Q +  D  P + A+ +E D +  + +KE AYI+Q++KNPLNGIRF HKLLE +  S
Sbjct: 847  FCFLQTMAVD-HPQISARDIEDDRECLSTLKEFAYIQQQMKNPLNGIRFTHKLLEGTVTS 905

Query: 894  ENQRQYLETSDACERQIMTIIDGMDLRCIEEGN-MELKSEEFLLGNILDAVVSQVMVLLR 952
            ++Q+Q+LETS+ACE+QI++II+ MD   I +GN +ELK+EEF++GN++DAVVSQVM+ L+
Sbjct: 906  DHQKQFLETSEACEKQILSIIENMDSGGIVDGNRVELKTEEFVIGNVIDAVVSQVMIPLK 965

Query: 953  DKNLHLLHDIPEEIKALSLNGDRIRLQLVLSDFLHCVVRHAPSPDGWVEIKVLPGLKLIK 1012
            +KNL LLHDIP++IK+L + GD+I+LQLVLSDFL  +VRHAPSPDGWVEI+V PGLKLI+
Sbjct: 966  EKNLQLLHDIPDQIKSLPIYGDQIKLQLVLSDFLLSIVRHAPSPDGWVEIRVSPGLKLIQ 1025

Query: 1013 DADQFVHVQFRLTHPGEGIPSHLIEDMYNGRNQWTTPEGLGLKLSRKLLIMMNGRVRYVR 1072
            D + F+H+QFR+THPG+G+PS LIEDM  G  +WTT EG+ L LS+KL+ MMNG V YVR
Sbjct: 1026 DGNVFIHIQFRMTHPGQGLPSALIEDMVRGGTRWTTQEGVVLHLSQKLVRMMNGHVHYVR 1085

Query: 1073 ENSKCYFVIDLELKTR 1088
            E  KCYF+IDL+ KT+
Sbjct: 1086 EQQKCYFLIDLDFKTQ 1101

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.
Ipomoea nil (taxid: 35883)

>sp\|P42498\|PHYE_ARATH Phytochrome E OS=Arabidopsis thaliana GN=PHYE PE=1 SV=2	Back alignment and function description

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

>sp\|P34094\|PHYB_SOLTU Phytochrome B OS=Solanum tuberosum GN=PHYB PE=3 SV=2	Back alignment and function description

>sp\|P29130\|PHYB_TOBAC Phytochrome B OS=Nicotiana tabacum GN=PHYB PE=2 SV=2	Back alignment and function description

>sp\|Q9ZS62\|PHYB1_SOLLC Phytochrome B1 OS=Solanum lycopersicum GN=PHYB1 PE=2 SV=1	Back alignment and function description

>sp\|P14713\|PHYB_ARATH Phytochrome B OS=Arabidopsis thaliana GN=PHYB PE=1 SV=1	Back alignment and function description

>sp\|P93527\|PHYB_SORBI Phytochrome B OS=Sorghum bicolor GN=PHYB PE=3 SV=2	Back alignment and function description

>sp\|A2XFW2\|PHYB_ORYSI Phytochrome B OS=Oryza sativa subsp. indica GN=PHYB PE=3 SV=2	Back alignment and function description

>sp\|Q10MG9\|PHYB_ORYSJ Phytochrome B OS=Oryza sativa subsp. japonica GN=PHYB PE=2 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		1093
255557437		1131	phytochrome B, putative [Ricinus communi	0.989	0.956	0.720	0.0
183239028		1124	phytochrome E [Vitis riparia]	0.980	0.953	0.724	0.0
225463382		1124	PREDICTED: phytochrome E [Vitis vinifera	0.980	0.953	0.722	0.0
147775698		1162	hypothetical protein VITISV_030984 [Viti	0.980	0.922	0.716	0.0
1730566		1115	RecName: Full=Phytochrome E gi\|1145714\|g	0.968	0.949	0.699	0.0
6708129		1137	phytochrome E [Solanum lycopersicum]	0.966	0.928	0.680	0.0
356532946		1120	PREDICTED: phytochrome E-like [Glycine m	0.974	0.950	0.671	0.0
449459392		1134	PREDICTED: phytochrome E-like [Cucumis s	0.954	0.919	0.666	0.0
356556523		1121	PREDICTED: phytochrome E-like [Glycine m	0.971	0.947	0.667	0.0
226234965		1116	phytochrome E [Cardamine nipponica]	0.959	0.939	0.638	0.0

>gi\|255557437\|ref\|XP_002519749.1\| phytochrome B, putative [Ricinus communis] gi\|223541166\|gb\|EEF42722.1\| phytochrome B, putative [Ricinus communis]	Back alignment and taxonomy information

 Score = 1692 bits (4382), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 812/1127 (72%), Positives = 940/1127 (83%), Gaps = 45/1127 (3%)

Query: 1    MGLQGNRETTNSIGGGHNTTPFKSSDAKMKPV---NKGKTIIDHYNADAGLLAEFEQSVA 57
            MG Q  RE          TT   S+ + MKP    ++    I  YNADAGLLAEFEQS  
Sbjct: 1    MGFQNARERGT-------TTLSSSAASSMKPFATNSENTATIAQYNADAGLLAEFEQSGV 53

Query: 58   SGKSFNYSRSVISPPEGVPEEQITAYLSKIQRGGLIQPFGCMLAVEEPTFRIIGYSENCL 117
            SGKSFNYSRSV+S P  VPEEQITAYLS+IQRGGLIQPFGCM+A+EEPTFRII YSENC 
Sbjct: 54   SGKSFNYSRSVLSAPHNVPEEQITAYLSRIQRGGLIQPFGCMVAIEEPTFRIISYSENCF 113

Query: 118  EMLDLRSRS--EDFELNGLIGIDARTLFTPPSGASLAKAAASREISLLNPILVHSNSRSI 175
             +L L + S  E  ++ GLIGID R LFTP SGASL+KAAASREIS+LNPI V+S  R+ 
Sbjct: 114  HLLGLSASSVLESNQVKGLIGIDVRALFTPQSGASLSKAAASREISMLNPIWVYS--RTS 171

Query: 176  EKPFYAILHRIDVGIVIDLEPSKSGDPALSLAGAVQSQKLAVSAISRLQALPGGDIGLLC 235
            +KPFYAILHRIDVGIVIDLEP++SGDP LSLAGAVQSQKLAV AISRLQ+LPGGDIG+LC
Sbjct: 172  QKPFYAILHRIDVGIVIDLEPARSGDPVLSLAGAVQSQKLAVRAISRLQSLPGGDIGMLC 231

Query: 236  DTVVEDVQKLTGYDRVMLYNFHDDDHGEVVSEIRRSDLEPYLGIHFPANDIPQAARFLFK 295
            DTVVEDVQKLTGYDRVM+Y FHDDDHGEV+SEIRRSDLEPYLG+H+PA DIPQAARFLFK
Sbjct: 232  DTVVEDVQKLTGYDRVMVYKFHDDDHGEVLSEIRRSDLEPYLGLHYPATDIPQAARFLFK 291

Query: 296  QNRVRMICDCHAIPVMVIQSKELKQPLCLVNSTLRSPHGCHLQYMTNMGSIASLVMAVII 355
            QNRVRMICDCHA PV VIQS+ELK PLCLVNSTLRSPHGCH QYM NMGSIASLVMAV+I
Sbjct: 292  QNRVRMICDCHANPVRVIQSEELKHPLCLVNSTLRSPHGCHTQYMANMGSIASLVMAVVI 351

Query: 356  NSKDSMKLWGLVVCHHTSPRYIPFPLRYACEFLVQAFSLQLYMELQVAMQLAEKNILRTQ 415
            N  DS KLWGLVVCHHTSPRY+PFPLRYACEFL+QAF LQLYMELQ+A +L EK IL+TQ
Sbjct: 352  NGNDSTKLWGLVVCHHTSPRYVPFPLRYACEFLMQAFGLQLYMELQLAAKLVEKKILQTQ 411

Query: 416  VLLCDMLLRDAPFSIVTQSPSIMDLVKCDGAALYYGGRCWLVGVTPTESQLKDIAWWLLN 475
             LLCDMLLRDAPF IVTQSPSIMDLVKCDGAALYY G+CWL+G+TPTESQ+KDIA WLLN
Sbjct: 412  TLLCDMLLRDAPFGIVTQSPSIMDLVKCDGAALYYRGKCWLLGITPTESQVKDIADWLLN 471

Query: 476  NHGDCTGLSTDSLAEAGYPGAALLGQAVCGMATARITSKDFLFWFRSHTAKEVKWGGAKH 535
            NHGD TGL+TDSLA+AGYPGA LLG AVCGMATARITS+DFLFWFRSHTAKE+KWGGAKH
Sbjct: 472  NHGDSTGLTTDSLADAGYPGALLLGDAVCGMATARITSRDFLFWFRSHTAKEIKWGGAKH 531

Query: 536  HPEHKDNGGKMHPRSSFKAFLEVVKNRSFPWEVSEINAIHSLQIVMRDSFQEMEEENDSK 595
            HPE KD+G +MHPRSSF AFLEVVK+RS PWEVSEINAIHSLQ++MRDSFQ+M E++ SK
Sbjct: 532  HPEDKDDGQRMHPRSSFNAFLEVVKSRSMPWEVSEINAIHSLQLIMRDSFQDM-EDSASK 590

Query: 596  VQGNTQQNGSKMQGVDELSSVACEMVRLIETATAPIFGVDSSGTINGWNAKVAELTGLPA 655
               N QQ  + +QG+DELSSVACEMVRLIETATAPIFGVDS+G++NGWNAK+AELTGL A
Sbjct: 591  AMVNAQQTDTDVQGIDELSSVACEMVRLIETATAPIFGVDSAGSVNGWNAKIAELTGLQA 650

Query: 656  SEAMGKSLIDEVVHEESQGAVENLICRALLGEEDKNVELKLRKFELQKQHSVVYILVNAC 715
            SEAMGKSL+ EVVH++S   VE+L+CRAL GEEDKNVELKLRKF L +Q+S V+++ NAC
Sbjct: 651  SEAMGKSLVREVVHKDSYEFVESLLCRALQGEEDKNVELKLRKFGLHQQNSAVFVVANAC 710

Query: 716  TSRDYKNNVKGVCFVGQDITHEKVLMDKFIRLQGDYEAIIQSVNPLIPPIFASDENACCS 775
            TSRDY NNV GVCFVGQD+T EK++MDKF+RLQGDY+ II+S+NPLIPPIFASDENACC 
Sbjct: 711  TSRDYANNVIGVCFVGQDVTSEKIVMDKFLRLQGDYKVIIESLNPLIPPIFASDENACCC 770

Query: 776  EWNAAMEKVTGWMRHEVI------------------------------GITGQGTENFPF 805
            EWNAAME++TG  R EVI                              G++ Q T+ FPF
Sbjct: 771  EWNAAMERLTGRTRQEVIGKMLPGEIFGGLCRLKDQDTLTKFMILLYRGLSDQDTDKFPF 830

Query: 806  GFFNRQGQFVEVALTASRRTDAEGKVIGCFCFMQILVPDLQPALEAQGLEDMDIYAKIKE 865
            GFFNRQG+FVEV LTA++RTDA+GK IGCFCF+Q++ PDLQ  L+    ED +   K+K+
Sbjct: 831  GFFNRQGKFVEVFLTANKRTDADGKTIGCFCFLQVIGPDLQQTLDEHKQEDQESLLKLKQ 890

Query: 866  LAYIRQEVKNPLNGIRFVHKLLESSSISENQRQYLETSDACERQIMTIIDGMDLRCIEEG 925
            LAYIR+E+K+PL+GIRF HKLLE ++ SE+Q+Q+LETSDACE+QIMTII+ +DL  +EEG
Sbjct: 891  LAYIREEMKSPLSGIRFTHKLLEDTATSEHQKQFLETSDACEKQIMTIIEDIDLAKLEEG 950

Query: 926  NMELKSEEFLLGNILDAVVSQVMVLLRDKNLHLLHDIPEEIKALSLNGDRIRLQLVLSDF 985
             +ELK EEF L N+LDA+VSQ+M+LLR++++ L H+IPEEIK +S+ GD+IRLQLVLSDF
Sbjct: 951  KIELKVEEFFLVNVLDAIVSQIMLLLRERSIQLFHEIPEEIKTVSVYGDQIRLQLVLSDF 1010

Query: 986  LHCVVRHAPSPDGWVEIKVLPGLKLIKDADQFVHVQFRLTHPGEGIPSHLIEDMYNGRNQ 1045
            L  VVRHAPSPDGWVEIKV  GLKL++D+ +F+ VQ R+THPG+G+PS L EDM+   N 
Sbjct: 1011 LLSVVRHAPSPDGWVEIKVSSGLKLMQDSHEFLRVQIRMTHPGQGLPSALTEDMFEEGNC 1070

Query: 1046 WTTPEGLGLKLSRKLLIMMNGRVRYVRENSKCYFVIDLELKTRGRQK 1092
            WTT EGL LKLSRKLL  MNG V Y RE++KC+F+IDLELK + RQK
Sbjct: 1071 WTTQEGLALKLSRKLLHQMNGHVHYTREHNKCFFLIDLELKLKNRQK 1117

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi\|183239028\|gb\|ACC60972.1\| phytochrome E [Vitis riparia]	Back alignment and taxonomy information

>gi\|225463382\|ref\|XP_002271671.1\| PREDICTED: phytochrome E [Vitis vinifera] gi\|183239020\|gb\|ACC60968.1\| phytochrome E [Vitis vinifera]	Back alignment and taxonomy information

>gi\|147775698\|emb\|CAN62723.1\| hypothetical protein VITISV_030984 [Vitis vinifera]	Back alignment and taxonomy information

>gi\|1730566\|sp\|P55004.1\|PHYE_IPONI RecName: Full=Phytochrome E gi\|1145714\|gb\|AAA84970.1\| phytochrome E [Ipomoea nil]	Back alignment and taxonomy information

>gi\|6708129\|gb\|AAF25812.1\|AF178571_1 phytochrome E [Solanum lycopersicum]	Back alignment and taxonomy information

>gi\|356532946\|ref\|XP_003535030.1\| PREDICTED: phytochrome E-like [Glycine max]	Back alignment and taxonomy information

>gi\|449459392\|ref\|XP_004147430.1\| PREDICTED: phytochrome E-like [Cucumis sativus]	Back alignment and taxonomy information

>gi\|356556523\|ref\|XP_003546574.1\| PREDICTED: phytochrome E-like [Glycine max]	Back alignment and taxonomy information

>gi\|226234965\|dbj\|BAH47472.1\| phytochrome E [Cardamine nipponica]	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		1093
TAIR\|locus:2005515		1172	PHYB "AT2G18790" [Arabidopsis	0.719	0.670	0.640	0.0
TAIR\|locus:2005535		1164	PHYD "phytochrome D" [Arabidop	0.688	0.646	0.649	0.0
TAIR\|locus:2005536		1112	PHYE "phytochrome E" [Arabidop	0.893	0.878	0.579	3.4e-299
TAIR\|locus:2165199		1111	PHYC "phytochrome C" [Arabidop	0.675	0.664	0.532	3.6e-275
UNIPROTKB\|P06593		1129	PHYA3 "Phytochrome A type 3" [	0.701	0.679	0.509	6.3e-258
TAIR\|locus:2012300		1122	PHYA "phytochrome A" [Arabidop	0.810	0.789	0.478	1.7e-217
UNIPROTKB\|Q55168		748	cph1 "Phytochrome-like protein	0.440	0.643	0.339	5.1e-64
UNIPROTKB\|Q48G81		745	bphP "Bacteriophytochrome hist	0.471	0.691	0.284	1.7e-49
UNIPROTKB\|Q4K656		746	bphP "Bacteriophytochrome hist	0.442	0.648	0.283	9.4e-49
UNIPROTKB\|Q7CY45		736	Atu1990 "Bacteriophytochrome p	0.364	0.540	0.324	1.2e-45

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

 Score = 2662 (942.1 bits), Expect = 0., Sum P(2) = 0.
 Identities = 521/814 (64%), Positives = 631/814 (77%)

Query:     9 TTNSIGGGHN--TTPFKSSDAKMKPVNKGKTIIDHYNADAGLLAEFEQSVASGKSFNYSR 66
             T N+  GG    ++  KS   +    +  K I   Y  DA L A FEQS  SGKSF+YS+
Sbjct:    27 TPNNRRGGEQAQSSGTKSLRPRSNTESMSKAI-QQYTVDARLHAVFEQSGESGKSFDYSQ 85

Query:    67 SVISPPEG--VPEEQITAYLSKIQRGGLIQPFGCMLAVEEPTFRIIGYSENCLEMLDLRS 124
             S+ +   G  VPE+QITAYLS+IQRGG IQPFGCM+AV+E +FRIIGYSEN  EML +  
Sbjct:    86 SLKTTTYGSSVPEQQITAYLSRIQRGGYIQPFGCMIAVDESSFRIIGYSENAREMLGIMP 145

Query:   125 RS----EDFELNGLIGIDARTLFTPPSGASLAKAAASREISLLNPILVHSNSRSIEKPFY 180
             +S    E  E+  + G D R+LFT  S   L +A  +REI+LLNP+ +HS +    KPFY
Sbjct:   146 QSVPTLEKPEILAM-GTDVRSLFTSSSSILLERAFVAREITLLNPVWIHSKNTG--KPFY 202

Query:   181 AILHRIDVGIVIDLEPSKSGDPALSLAGAVQSQKLAVSAISRLQALPGGDIGLLCDTVVE 240
             AILHRIDVG+VIDLEP+++ DPALS+AGAVQSQKLAV AIS+LQALPGGDI LLCDTVVE
Sbjct:   203 AILHRIDVGVVIDLEPARTEDPALSIAGAVQSQKLAVRAISQLQALPGGDIKLLCDTVVE 262

Query:   241 DVQKLTGYDRVMLYNFHDDDHGEVVSEIRRSDLEPYLGIHFPANDIPQAARFLFKQNRVR 300
              V+ LTGYDRVM+Y FH+D+HGEVV+E +R DLEPY+G+H+PA DIPQA+RFLFKQNRVR
Sbjct:   263 SVRDLTGYDRVMVYKFHEDEHGEVVAESKRDDLEPYIGLHYPATDIPQASRFLFKQNRVR 322

Query:   301 MICDCHAIPVMVIQSKELKQPLCLVNSTLRSPHGCHLQYMTNMGSIASLVMAVIINSKD- 359
             MI DC+A PV+V+Q   L Q +CLV STLR+PHGCH QYM NMGSIASL MAVIIN  + 
Sbjct:   323 MIVDCNATPVLVVQDDRLTQSMCLVGSTLRAPHGCHSQYMANMGSIASLAMAVIINGNED 382

Query:   360 ----------SMKLWGLVVCHHTSPRYIPFPLRYACEFLVQAFSLQLYMELQVAMQLAEK 409
                       SM+LWGLVVCHHTS R IPFPLRYACEFL+QAF LQL MELQ+A+Q++EK
Sbjct:   383 DGSNVASGRSSMRLWGLVVCHHTSSRCIPFPLRYACEFLMQAFGLQLNMELQLALQMSEK 442

Query:   410 NILRTQVLLCDMLLRDAPFSIVTQSPSIMDLVKCDGAALYYGGRCWLVGVTPTESQLKDI 469
              +LRTQ LLCDMLLRD+P  IVTQSPSIMDLVKCDGAA  Y G+ + +GV P+E Q+KD+
Sbjct:   443 RVLRTQTLLCDMLLRDSPAGIVTQSPSIMDLVKCDGAAFLYHGKYYPLGVAPSEVQIKDV 502

Query:   470 AWWLLNNHGDCTGLSTDSLAEAGYPGAALLGQAVCGMATARITSKDFLFWFRSHTAKEVK 529
               WLL NH D TGLSTDSL +AGYPGAA LG AVCGMA A IT +DFLFWFRSHTAKE+K
Sbjct:   503 VEWLLANHADSTGLSTDSLGDAGYPGAAALGDAVCGMAVAYITKRDFLFWFRSHTAKEIK 562

Query:   530 WGGAKHHPEHKDNGGKMHPRSSFKAFLEVVKNRSFPWEVSEINAIHSLQIVMRDSFQEME 589
             WGGAKHHPE KD+G +MHPRSSF+AFLEVVK+RS PWE +E++AIHSLQ+++RDSF+E E
Sbjct:   563 WGGAKHHPEDKDDGQRMHPRSSFQAFLEVVKSRSQPWETAEMDAIHSLQLILRDSFKESE 622

Query:   590 EENDSKVQGNTQQNGSKM---QGVDELSSVACEMVRLIETATAPIFGVDSSGTINGWNAK 646
                +SKV     Q    M   QG+DEL +VA EMVRLIETAT PIF VD+ G INGWNAK
Sbjct:   623 AAMNSKVVDGVVQPCRDMAGEQGIDELGAVAREMVRLIETATVPIFAVDAGGCINGWNAK 682

Query:   647 VAELTGLPASEAMGKSLIDEVVHEESQGAVENLICRALLGEEDKNVELKLRKFELQKQHS 706
             +AELTGL   EAMGKSL+ +++++E++  V  L+ RAL G+E+KNVE+KL+ F  + Q  
Sbjct:   683 IAELTGLSVEEAMGKSLVSDLIYKENEATVNKLLSRALRGDEEKNVEVKLKTFSPELQGK 742

Query:   707 VVYILVNACTSRDYKNNVKGVCFVGQDITHEKVLMDKFIRLQGDYEAIIQSVNPLIPPIF 766
              V+++VNAC+S+DY NN+ GVCFVGQD+T +K++MDKFI +QGDY+AI+ S NPLIPPIF
Sbjct:   743 AVFVVVNACSSKDYLNNIVGVCFVGQDVTSQKIVMDKFINIQGDYKAIVHSPNPLIPPIF 802

Query:   767 ASDENACCSEWNAAMEKVTGWMRHEVIG--ITGQ 798
             A+DEN CC EWN AMEK+TGW R EVIG  I G+
Sbjct:   803 AADENTCCLEWNMAMEKLTGWSRSEVIGKMIVGE 836

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

GO:0004871 "signal transducer activity" evidence=ISS

GO:0005886 "plasma membrane" evidence=ISM

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

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

GO:0005634 "nucleus" evidence=IDA

GO:0005515 "protein binding" evidence=IPI

GO:0009409 "response to cold" evidence=IMP

GO:0009649 "entrainment of circadian clock" evidence=IMP

GO:0009883 "red or far-red light photoreceptor activity" evidence=IMP

GO:0009638 "phototropism" evidence=IMP

GO:0042802 "identical protein binding" evidence=IPI

GO:0009630 "gravitropism" evidence=RCA;IMP

GO:0009687 "abscisic acid metabolic process" evidence=IMP

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

GO:0010161 "red light signaling pathway" evidence=IMP

GO:0010617 "circadian regulation of calcium ion oscillation" evidence=IMP

GO:0009867 "jasmonic acid mediated signaling pathway" evidence=IMP

GO:0031347 "regulation of defense response" evidence=IMP

GO:0010148 "transpiration" evidence=IMP

GO:0010374 "stomatal complex development" evidence=IMP

GO:0015979 "photosynthesis" evidence=IMP

GO:0006325 "chromatin organization" evidence=IMP

GO:0007623 "circadian rhythm" evidence=RCA

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

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

GO:0046685 "response to arsenic-containing substance" evidence=RCA

GO:0046777 "protein autophosphorylation" evidence=RCA

GO:0005829 "cytosol" evidence=IDA

GO:0009640 "photomorphogenesis" evidence=IMP

GO:0016604 "nuclear body" evidence=IDA

GO:0031516 "far-red light photoreceptor activity" evidence=IDA

GO:0031517 "red light photoreceptor activity" evidence=IDA

GO:0010218 "response to far red light" evidence=IMP

GO:0010202 "response to low fluence red light stimulus" evidence=IMP

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

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

TAIR\|locus:2165199 PHYC "phytochrome C" [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:2012300 PHYA "phytochrome A" [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)
P42498	PHYE_ARATH	No assigned EC number	0.6410	0.9579	0.9415	yes	no
P42496	PHY_ADICA	No assigned EC number	0.5425	0.9423	0.9212	N/A	no
P36505	PHY1_PHYPA	No assigned EC number	0.5683	0.9588	0.9257	N/A	no
P55004	PHYE_IPONI	No assigned EC number	0.6998	0.9688	0.9497	N/A	no
Q40762	PHY_PICAB	No assigned EC number	0.5522	0.9505	0.9146	N/A	no
Q41046	PHY_PINSY	No assigned EC number	0.6290	0.9597	0.9274	N/A	no
A2XFW2	PHYB_ORYSI	No assigned EC number	0.6003	0.9551	0.8915	N/A	no
P33529	PHY_MOUSC	No assigned EC number	0.5296	0.9533	0.9270	N/A	no
P29130	PHYB_TOBAC	No assigned EC number	0.6236	0.9597	0.9266	N/A	no
P34094	PHYB_SOLTU	No assigned EC number	0.6302	0.9533	0.9221	N/A	no
P93527	PHYB_SORBI	No assigned EC number	0.5996	0.9551	0.8862	N/A	no
Q01549	PHY1_SELMA	No assigned EC number	0.5834	0.9524	0.9179	N/A	no
Q10MG9	PHYB_ORYSJ	No assigned EC number	0.6003	0.9551	0.8915	yes	no
Q9ZS62	PHYB1_SOLLC	No assigned EC number	0.6122	0.9734	0.9407	N/A	no
Q39557	PHY2_CERPU	No assigned EC number	0.5720	0.9771	0.9527	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

No EC number assignment, probably not an enzyme!

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Alignment Graph	Length	Definition	E-value
Query		1093
COG4251		750	COG4251, COG4251, Bacteriophytochrome (light-regul	1e-106
pfam00360		183	pfam00360, PHY, Phytochrome region	2e-86
pfam08446		107	pfam08446, PAS_2, PAS fold	5e-47
pfam00989		113	pfam00989, PAS, PAS fold	2e-25
smart00065		149	smart00065, GAF, Domain present in phytochromes an	2e-20
pfam01590		143	pfam01590, GAF, GAF domain	7e-20
cd00075		103	cd00075, HATPase_c, Histidine kinase-like ATPases;	5e-13
COG0642		336	COG0642, BaeS, Signal transduction histidine kinas	2e-12
pfam02518		111	pfam02518, HATPase_c, Histidine kinase-, DNA gyras	3e-12
TIGR02956		968	TIGR02956, TMAO_torS, TMAO reductase sytem sensor	8e-12
pfam00989		113	pfam00989, PAS, PAS fold	9e-12
pfam00512		66	pfam00512, HisKA, His Kinase A (phospho-acceptor)	3e-10
PRK15347		921	PRK15347, PRK15347, two component system sensor ki	4e-10
smart00388		66	smart00388, HisKA, His Kinase A (phosphoacceptor)	5e-10
pfam13426		101	pfam13426, PAS_9, PAS domain	1e-09
smart00387		111	smart00387, HATPase_c, Histidine kinase-like ATPas	2e-09
PRK11107		919	PRK11107, PRK11107, hybrid sensory histidine kinas	2e-08
TIGR00229		124	TIGR00229, sensory_box, PAS domain S-box	3e-08
cd00130		103	cd00130, PAS, PAS domain; PAS motifs appear in arc	3e-07
cd00082		65	cd00082, HisKA, Histidine Kinase A (dimerization/p	1e-06
PRK11466		914	PRK11466, PRK11466, hybrid sensory histidine kinas	6e-06
smart00091		67	smart00091, PAS, PAS domain	9e-06
PRK10841		924	PRK10841, PRK10841, hybrid sensory kinase in two-c	6e-05
COG2202		232	COG2202, AtoS, FOG: PAS/PAC domain [Signal transdu	9e-05
COG2205		890	COG2205, KdpD, Osmosensitive K+ channel histidine	1e-04
COG2202		232	COG2202, AtoS, FOG: PAS/PAC domain [Signal transdu	2e-04
pfam08448		110	pfam08448, PAS_4, PAS fold	0.001
TIGR01386		457	TIGR01386, cztS_silS_copS, heavy metal sensor kina	0.002
cd00130		103	cd00130, PAS, PAS domain; PAS motifs appear in arc	0.003

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

 Score =  350 bits (901), Expect = e-106
 Identities = 172/534 (32%), Positives = 260/534 (48%), Gaps = 55/534 (10%)

Query: 91  GLIQPFGCMLAVEEPTFRIIGYSENCLEMLDLRSRSEDFELNGLIGIDARTLFTPPSGAS 150
           G IQP G +L ++E    ++  SENC                 ++G +   L     GA 
Sbjct: 24  GAIQPHGALLVLDEADLMVLQASENC---------------ANILGREPEDLLGRTLGAV 68

Query: 151 LAKAAASREISLLNPI-LVHSNSRSIE----KPFYAILHRIDVGIVIDLEPSKSGDPALS 205
           L         S L    L   N   +       F    HR    ++++ EP+ +G+ A  
Sbjct: 69  LTSEQVPPLQSALTVGGLTTLNPTKMWTRKGGSFDVSAHRSKELLILEFEPAGTGETASF 128

Query: 206 LAGAVQSQKLAVSAISRLQALPGGDIGLLCDTVVEDVQKLTGYDRVMLYNFHDDDHGEVV 265
           L        LA  A++RLQ+    ++  L     ++V+++TG+DRVMLY F +D  GEV+
Sbjct: 129 LGFY----HLAKLAMNRLQSAA--NLRDLLSRTTQEVRRMTGFDRVMLYRFDEDGSGEVI 182

Query: 266 SEIRRSDLEPYLGIHFPANDIPQAARFLFKQNRVRMICDCH--AIPVMVIQSKELKQPLC 323
           +E +R DLE YLG+ +PA+DIPQ AR L+ QN +R+I D     +PV+   + E  +PL 
Sbjct: 183 AEAKREDLESYLGLRYPASDIPQQARALYIQNPLRLIPDVSYTPVPVLPAVNPETNEPLD 242

Query: 324 LVNSTLRSPHGCHLQYMTNMGSIASLVMAVIINSKDSMKLWGLVVCHHTSPRYIPFPLRY 383
           L  S LRS    HL+Y+ NMG  AS+ ++++++     KLWGL+ CHH SP+ IP+ +R 
Sbjct: 243 LSYSVLRSVSPIHLEYLRNMGVGASMSISIVVDG----KLWGLIACHHQSPKVIPYEVRK 298

Query: 384 ACEFLVQAFSLQLYMELQ-----VAMQLAEKNILRTQVLLCDMLLRDAPFSIVTQS-PSI 437
           ACEF  Q  S+++    Q       +QL E        LL  M         +      +
Sbjct: 299 ACEFFGQVLSMEISALEQSEDADYRVQLTE----HHARLLRYMAHAADFVDGLIDHQDDL 354

Query: 438 MDLVKCDGAALYYGGRCWLVGVTPTESQLKDIAWWLLNN-HGDCTGLSTDSLAEAGYPGA 496
           +DL+  DGAAL +GGR  LVG TP    ++ +  WL     GD    +TDSL++  YP A
Sbjct: 355 LDLMPADGAALCFGGRWHLVGETPPRPAVQRLLQWLAEREEGDV--FATDSLSQV-YPDA 411

Query: 497 ALLGQAVCGMATARIT--SKDFLFWFRSHTAKEVKWGGAKHHP-EHKDNGGKMHPRSSFK 553
                   G+    I+    ++L WFR    + V WGG    P E    G ++ PR SF+
Sbjct: 412 EDYASVASGLLAIPISRVKSNYLLWFRPEVVQTVNWGGDPEKPYEAGPMGIRLTPRKSFE 471

Query: 554 AFLEVVKNRSFPWEVSEINAIHSLQ-----IVMRDSFQEMEEENDSKVQGNTQQ 602
            + E V+ +S PW   EI A   L+     IV+R + +E+ +      + N + 
Sbjct: 472 LWKETVRLQSQPWSEVEIEAALELRKAIVGIVLRHA-EELAQLRRELERSNAEL 524

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\|214500 smart00065, GAF, Domain present in phytochromes and cGMP-specific phosphodiesterases	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\|223715 COG0642, BaeS, Signal transduction histidine kinase [Signal transduction mechanisms]	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\|234070 TIGR02956, TMAO_torS, TMAO reductase sytem sensor TorS	Back alignment and domain information

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

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

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

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

>gnl\|CDD\|222120 pfam13426, PAS_9, PAS domain	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\|232884 TIGR00229, sensory_box, PAS domain S-box	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\|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\|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\|182772 PRK10841, PRK10841, hybrid sensory kinase in two-component regulatory system with RcsB and YojN; Provisional	Back alignment and domain information

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

>gnl\|CDD\|219845 pfam08448, PAS_4, PAS fold	Back alignment and domain information

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Alignment Graph	Length	Definition	Probability
Query		1093
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
PRK11073		348	glnL nitrogen regulation protein NR(II); Provision	100.0
PRK10618		894	phosphotransfer intermediate protein in two-compon	100.0
PRK13557		540	histidine kinase; Provisional	100.0
PRK10841		924	hybrid sensory kinase in two-component regulatory	100.0
PRK11360		607	sensory histidine kinase AtoS; Provisional	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
COG2205		890	KdpD Osmosensitive K+ channel histidine kinase [Si	100.0
PF00360		182	PHY: Phytochrome region; InterPro: IPR013515 Phyto	100.0
COG5000		712	NtrY Signal transduction histidine kinase involved	100.0
PRK13559		361	hypothetical protein; Provisional	100.0
PRK09303		380	adaptive-response sensory kinase; Validated	99.98
PRK11086		542	sensory histidine kinase DcuS; Provisional	99.98
COG4191		603	Signal transduction histidine kinase regulating C4	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	99.97
PRK11466		914	hybrid sensory histidine kinase TorS; Provisional	99.96
PRK11107		919	hybrid sensory histidine kinase BarA; Provisional	99.96
PRK10490		895	sensor protein KdpD; Provisional	99.96
PRK13837		828	two-component VirA-like sensor kinase; Provisional	99.96
COG3290		537	CitA Signal transduction histidine kinase regulati	99.95
PRK10364		457	sensor protein ZraS; Provisional	99.95
PRK10815		485	sensor protein PhoQ; Provisional	99.95
PRK10604		433	sensor protein RstB; Provisional	99.95
TIGR03785		703	marine_sort_HK proteobacterial dedicated sortase s	99.94
PRK10549		466	signal transduction histidine-protein kinase BaeS;	99.93
PRK10755		356	sensor protein BasS/PmrB; Provisional	99.93
PRK09835		482	sensor kinase CusS; Provisional	99.93
TIGR01386		457	cztS_silS_copS heavy metal sensor kinase. Members	99.92
TIGR02916		679	PEP_his_kin putative PEP-CTERM system histidine ki	99.92
PRK10337		449	sensor protein QseC; Provisional	99.91
PRK11100		475	sensory histidine kinase CreC; Provisional	99.91
PRK09467		435	envZ osmolarity sensor protein; Provisional	99.91
PRK09470		461	cpxA two-component sensor protein; Provisional	99.91
PF08446		110	PAS_2: PAS fold; InterPro: IPR013654 The PAS fold	99.9
COG0642		336	BaeS Signal transduction histidine kinase [Signal	99.9
PRK09776		1092	putative diguanylate cyclase; Provisional	99.87
PRK09776		1092	putative diguanylate cyclase; Provisional	99.87
COG4192		673	Signal transduction histidine kinase regulating ph	99.87
PRK11644		495	sensory histidine kinase UhpB; Provisional	99.84
TIGR02040		442	PpsR-CrtJ transcriptional regulator PpsR. This mod	99.83
PRK13560		807	hypothetical protein; Provisional	99.81
PRK11359		799	cyclic-di-GMP phosphodiesterase; Provisional	99.74
PF02518		111	HATPase_c: Histidine kinase-, DNA gyrase B-, and H	99.74
TIGR02040		442	PpsR-CrtJ transcriptional regulator PpsR. This mod	99.69
PRK10935		565	nitrate/nitrite sensor protein NarQ; Provisional	99.69
PRK10600		569	nitrate/nitrite sensor protein NarX; Provisional	99.68
COG3920		221	Signal transduction histidine kinase [Signal trans	99.62
PRK10547		670	chemotaxis protein CheA; Provisional	99.61
COG4564		459	Signal transduction histidine kinase [Signal trans	99.47
PF08448		110	PAS_4: PAS fold; InterPro: IPR013656 The PAS fold	99.44
COG4585		365	Signal transduction histidine kinase [Signal trans	99.44
PF00989		113	PAS: PAS fold; InterPro: IPR013767 PAS domains are	99.41
COG3851		497	UhpB Signal transduction histidine kinase, glucose	99.4
PF13426		104	PAS_9: PAS domain; PDB: 3ULF_B 3UE6_E 2Z6D_B 2Z6C_	99.4
PF01590		154	GAF: GAF domain; InterPro: IPR003018 This domain i	99.38
COG3850		574	NarQ Signal transduction histidine kinase, nitrate	99.38
smart00387		111	HATPase_c Histidine kinase-like ATPases. Histidine	99.37
COG0643		716	CheA Chemotaxis protein histidine kinase and relat	99.34
PRK04184		535	DNA topoisomerase VI subunit B; Validated	99.29
PRK14868		795	DNA topoisomerase VI subunit B; Provisional	99.21
cd00075		103	HATPase_c Histidine kinase-like ATPases; This fami	99.17
TIGR01052		488	top6b DNA topoisomerase VI, B subunit. This model	99.15
TIGR01925		137	spIIAB anti-sigma F factor. This model describes t	99.11
PRK11359		799	cyclic-di-GMP phosphodiesterase; Provisional	99.1
smart00065		149	GAF Domain present in phytochromes and cGMP-specif	99.06
PRK03660		146	anti-sigma F factor; Provisional	99.05
KOG0519		786	consensus Sensory transduction histidine kinase [S	99.02
PRK13558		665	bacterio-opsin activator; Provisional	99.01
PRK14867		659	DNA topoisomerase VI subunit B; Provisional	99.0
PF13426		104	PAS_9: PAS domain; PDB: 3ULF_B 3UE6_E 2Z6D_B 2Z6C_	98.99
PF00989		113	PAS: PAS fold; InterPro: IPR013767 PAS domains are	98.98
TIGR00229		124	sensory_box PAS domain S-box. The PAS domain was p	98.98
PRK10060		663	RNase II stability modulator; Provisional	98.98
PRK04069		161	serine-protein kinase RsbW; Provisional	98.97
PRK11091		779	aerobic respiration control sensor protein ArcB; P	98.92
COG3275		557	LytS Putative regulator of cell autolysis [Signal	98.91
PF13596		106	PAS_10: PAS domain; PDB: 3CAX_A 2QKP_D.	98.9
PRK10060		663	RNase II stability modulator; Provisional	98.83
PF00512		68	HisKA: His Kinase A (phospho-acceptor) domain; Int	98.82
PF08448		110	PAS_4: PAS fold; InterPro: IPR013656 The PAS fold	98.82
COG3829		560	RocR Transcriptional regulator containing PAS, AAA	98.81
COG2972		456	Predicted signal transduction protein with a C-ter	98.81
TIGR01924		159	rsbW_low_gc serine-protein kinase RsbW. This model	98.81
COG2203		175	FhlA FOG: GAF domain [Signal transduction mechanis	98.72
PF14501		100	HATPase_c_5: GHKL domain	98.63
PF08447		91	PAS_3: PAS fold; InterPro: IPR013655 The PAS fold	98.59
PRK11360		607	sensory histidine kinase AtoS; Provisional	98.58
PF13492		129	GAF_3: GAF domain; PDB: 3EEA_A 4DMZ_A 4DN0_A 1VHM_	98.53
PF12860		115	PAS_7: PAS fold	98.51
cd00130		103	PAS PAS domain; PAS motifs appear in archaea, euba	98.49
PRK13559		361	hypothetical protein; Provisional	98.49
TIGR02966		333	phoR_proteo phosphate regulon sensor kinase PhoR.	98.46
KOG0787		414	consensus Dehydrogenase kinase [Signal transductio	98.42
PF13581		125	HATPase_c_2: Histidine kinase-like ATPase domain	98.42
PRK13558		665	bacterio-opsin activator; Provisional	98.38
TIGR02938		494	nifL_nitrog nitrogen fixation negative regulator N	98.36
PRK13557		540	histidine kinase; Provisional	98.36
PF13185		148	GAF_2: GAF domain; PDB: 2QYB_A 3KSG_B 3KSF_C 3KSI_	98.36
TIGR00229		124	sensory_box PAS domain S-box. The PAS domain was p	98.28
TIGR01817		534	nifA Nif-specific regulatory protein. This model r	98.24
PRK11006		430	phoR phosphate regulon sensor protein; Provisional	98.23
PRK11388		638	DNA-binding transcriptional regulator DhaR; Provis	98.17
PRK11086		542	sensory histidine kinase DcuS; Provisional	98.16
KOG3558		768	consensus Hypoxia-inducible factor 1/Neuronal PAS	98.15
PRK10820		520	DNA-binding transcriptional regulator TyrR; Provis	98.14
COG1389		538	DNA topoisomerase VI, subunit B [DNA replication,	98.08
COG2202		232	AtoS FOG: PAS/PAC domain [Signal transduction mech	98.07
COG3829		560	RocR Transcriptional regulator containing PAS, AAA	98.05
PRK15429		686	formate hydrogenlyase transcriptional activator Fh	98.04
PRK05022		509	anaerobic nitric oxide reductase transcription reg	97.99
COG3604		550	FhlA Transcriptional regulator containing GAF, AAA	97.98
PF08447		91	PAS_3: PAS fold; InterPro: IPR013655 The PAS fold	97.9
COG2172		146	RsbW Anti-sigma regulatory factor (Ser/Thr protein	97.86
PF14598		111	PAS_11: PAS domain; PDB: 1P97_A 3F1O_A 2A24_A 3H7W	97.83
PRK11061		748	fused phosphoenolpyruvate-protein phosphotransfera	97.82
TIGR00585		312	mutl DNA mismatch repair protein MutL. All protein	97.8
smart00388		66	HisKA His Kinase A (phosphoacceptor) domain. Dimer	97.72
COG3290		537	CitA Signal transduction histidine kinase regulati	97.69
PRK15053		545	dpiB sensor histidine kinase DpiB; Provisional	97.64
COG2202		232	AtoS FOG: PAS/PAC domain [Signal transduction mech	97.6
cd00130		103	PAS PAS domain; PAS motifs appear in archaea, euba	97.58
PF12860		115	PAS_7: PAS fold	97.48
PF13596		106	PAS_10: PAS domain; PDB: 3CAX_A 2QKP_D.	97.45
PF13188		64	PAS_8: PAS domain; PDB: 2JHE_D 3VOL_A.	97.42
PRK11073		348	glnL nitrogen regulation protein NR(II); Provision	97.36
PRK15429		686	formate hydrogenlyase transcriptional activator Fh	97.34
COG5002		459	VicK Signal transduction histidine kinase [Signal	97.16
cd00082		65	HisKA Histidine Kinase A (dimerization/phosphoacce	97.11
PF13589		137	HATPase_c_3: Histidine kinase-, DNA gyrase B-, and	97.09
PRK09959		1197	hybrid sensory histidine kinase in two-component r	97.09
PRK11388		638	DNA-binding transcriptional regulator DhaR; Provis	96.95
PRK00095		617	mutL DNA mismatch repair protein; Reviewed	96.93
PRK10820		520	DNA-binding transcriptional regulator TyrR; Provis	96.9
COG2461		409	Uncharacterized conserved protein [Function unknow	96.86
KOG3559		598	consensus Transcriptional regulator SIM1 [Transcri	96.83
KOG0501		971	consensus K+-channel KCNQ [Inorganic ion transport	96.69
smart00091		67	PAS PAS domain. PAS motifs appear in archaea, euba	96.62
TIGR02373		124	photo_yellow photoactive yellow protein. Members o	96.36
PF13188		64	PAS_8: PAS domain; PDB: 2JHE_D 3VOL_A.	96.31
KOG3560		712	consensus Aryl-hydrocarbon receptor [Transcription	96.15
KOG0501		971	consensus K+-channel KCNQ [Inorganic ion transport	96.06
COG5385		214	Uncharacterized protein conserved in bacteria [Fun	96.03
PF08670		148	MEKHLA: MEKHLA domain; InterPro: IPR013978 The MEK	95.99
KOG3558		768	consensus Hypoxia-inducible factor 1/Neuronal PAS	95.95
PF14598		111	PAS_11: PAS domain; PDB: 1P97_A 3F1O_A 2A24_A 3H7W	95.86
PF10090		182	DUF2328: Uncharacterized protein conserved in bact	95.79
PRK05559		631	DNA topoisomerase IV subunit B; Reviewed	95.74
TIGR02916		679	PEP_his_kin putative PEP-CTERM system histidine ki	95.5
TIGR01055		625	parE_Gneg DNA topoisomerase IV, B subunit, proteob	95.14
COG3283		511	TyrR Transcriptional regulator of aromatic amino a	95.07
PF07568		76	HisKA_2: Histidine kinase; InterPro: IPR011495 Two	94.86
TIGR01059		654	gyrB DNA gyrase, B subunit. This model describes t	94.63
PRK10841		924	hybrid sensory kinase in two-component regulatory	94.49
COG3852		363	NtrB Signal transduction histidine kinase, nitroge	94.48
PRK05644		638	gyrB DNA gyrase subunit B; Validated	94.44
COG0323		638	MutL DNA mismatch repair enzyme (predicted ATPase)	94.29
COG5000		712	NtrY Signal transduction histidine kinase involved	93.87
PRK05218		613	heat shock protein 90; Provisional	93.48
PRK10618		894	phosphotransfer intermediate protein in two-compon	93.29
smart00433		594	TOP2c TopoisomeraseII. Eukaryotic DNA topoisomeras	92.82
KOG1229		775	consensus 3'5'-cyclic nucleotide phosphodiesterase	92.82
KOG0519		786	consensus Sensory transduction histidine kinase [S	92.6
smart00086		43	PAC Motif C-terminal to PAS motifs (likely to cont	92.29
PRK14939		756	gyrB DNA gyrase subunit B; Provisional	92.03
TIGR02851		180	spore_V_T stage V sporulation protein T. Members o	91.53
KOG1229		775	consensus 3'5'-cyclic nucleotide phosphodiesterase	90.97
COG3284		606	AcoR Transcriptional activator of acetoin/glycerol	90.95
PRK14083		601	HSP90 family protein; Provisional	90.5
smart00086		43	PAC Motif C-terminal to PAS motifs (likely to cont	88.71
COG1956		163	GAF domain-containing protein [Signal transduction	88.45
COG5381		184	Uncharacterized protein conserved in bacteria [Fun	87.9
PTZ00272		701	heat shock protein 83 kDa (Hsp83); Provisional	87.55
COG0326		623	HtpG Molecular chaperone, HSP90 family [Posttransl	85.68
smart00091		67	PAS PAS domain. PAS motifs appear in archaea, euba	85.36
TIGR02373		124	photo_yellow photoactive yellow protein. Members o	84.95
KOG3561		803	consensus Aryl-hydrocarbon receptor nuclear transl	84.75
TIGR01058		637	parE_Gpos DNA topoisomerase IV, B subunit, Gram-po	84.36
PTZ00108		1388	DNA topoisomerase 2-like protein; Provisional	83.8
PHA02569		602	39 DNA topoisomerase II large subunit; Provisional	82.37
PF14689		62	SPOB_a: Sensor_kinase_SpoOB-type, alpha-helical do	82.27
PLN03237		1465	DNA topoisomerase 2; Provisional	82.09
COG3887		655	Predicted signaling protein consisting of a modifi	82.03
PRK13837		828	two-component VirA-like sensor kinase; Provisional	81.03

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

Probab=100.00  E-value=8.4e-149  Score=1250.46  Aligned_cols=721  Identities=27%  Similarity=0.456  Sum_probs=624.7

Q ss_pred             hhhHHHH-HhhccCCCCCCccceEEEEeCCCceEEEEecChhhhhCCCCcccccccccccCCccccccCCchHHHHHHHH
Q 001353           77 EEQITAY-LSKIQRGGLIQPFGCMLAVEEPTFRIIGYSENCLEMLDLRSRSEDFELNGLIGIDARTLFTPPSGASLAKAA  155 (1093)
Q Consensus        77 ~~~~~~~-~~~i~~~g~iQp~G~Ll~~~~~~~~i~~~S~N~~~~lg~~~~~~~~~~~~~lg~~~~~~~~~~~~~~~~~~~  155 (1093)
                      ...++.| .+|||+||+||||||||++|+.++.|+|+|+||..+||+.|       +.++|+++.++|+.+....++.++
T Consensus         9 ~v~l~nce~ePIHipG~IQPHG~Llvl~~~~~~Vlq~S~N~~~~LG~~~-------e~l~~~tl~~vl~~~qv~~l~~~l   81 (750)
T COG4251           9 HVTLTNCEREPIHIPGAIQPHGALLVLDEADLMVLQASENCANILGREP-------EDLLGRTLGAVLTSEQVPPLQSAL   81 (750)
T ss_pred             cCcccccccCCccCCCccCCceeEEEeecCCchhhhhhhhHHHHhCCCh-------hhhhcCCHHHhcchhhccHHHHhc
Confidence            4567889 99999999999999999999999999999999999999988       689999999999999999999999


Q ss_pred             hcccccccCceeecccCCCCCccEEEEEeeeCCEEEEEeccCCCCCccchhhhhhHHHHHHHHHHHHhhcCCCCCHHHHH
Q 001353          156 ASREISLLNPILVHSNSRSIEKPFYAILHRIDVGIVIDLEPSKSGDPALSLAGAVQSQKLAVSAISRLQALPGGDIGLLC  235 (1093)
Q Consensus       156 ~~~~~~~~~~~~~~~~~~~~~~~f~~~~hr~~~~~~ie~Ep~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  235 (1093)
                      ........||..+-.  + .+..|++++||+++.+|+||||....+. .   ..+..|+++..++.+||+.+  |+.++|
T Consensus        82 ~~~~~~~~np~~~w~--~-~~~~fDv~~HR~~~llIlEfEp~~t~e~-~---~~l~f~h~~k~a~~~lq~a~--~l~~l~  152 (750)
T COG4251          82 TVGGLTTLNPTKMWT--R-KGGSFDVSAHRSKELLILEFEPAGTGET-A---SFLGFYHLAKLAMNRLQSAA--NLRDLL  152 (750)
T ss_pred             cccCcccCCchhhhh--h-cCCceeEEEEecCcEEEEEEecCccccc-c---cccchHHHHHHHHHHHhcCc--cHHHHH
Confidence            988888888854432  1 2338999999999999999999754432 2   23346788888999999954  999999


Q ss_pred             HHHHHHHHhhhCCCeEEEEeecCCCCceEEEEecCCCCCCccCCccCCCCchHHHHHhHhcCCeEEEecCCCCCccccc-
Q 001353          236 DTVVEDVQKLTGYDRVMLYNFHDDDHGEVVSEIRRSDLEPYLGIHFPANDIPQAARFLFKQNRVRMICDCHAIPVMVIQ-  314 (1093)
Q Consensus       236 ~~~~~~vr~~~~~dRv~iy~f~~d~~G~vvaE~~~~~~~~~lg~~~p~~dip~~~r~l~~~~~~r~i~d~~~~~~~l~~-  314 (1093)
                      +.+++|||++|||||||+|||++||+|+||||+++++++||||+||||||||+|||+||.+|++|+|+|+.|+|||+.| 
T Consensus       153 ~~~tqeVr~~tGfDRVMlYrF~~d~~G~VIAEak~e~LesyLGl~yPaSDIP~qAR~LY~~N~lRlIpD~~~~~vpv~Pa  232 (750)
T COG4251         153 SRTTQEVRRMTGFDRVMLYRFDEDGSGEVIAEAKREDLESYLGLRYPASDIPQQARALYIQNPLRLIPDVSYTPVPVLPA  232 (750)
T ss_pred             HHHHHHHHHhcCCceEEEEeecCCCCccEEeccccccchhhhcccCCcccCCHHHHHHHhcCceeecccccCcccccccc
Confidence            9999999999999999999999999999999999999999999999999999999999999999999999999999999 


Q ss_pred             -ccccCCCccccCccccCCChhHHHHHHhcCceeEEEEEEEEcCCCCcceeEEEEeecCCCCCCCchHHHHHHHHHHHHH
Q 001353          315 -SKELKQPLCLVNSTLRSPHGCHLQYMTNMGSIASLVMAVIINSKDSMKLWGLVVCHHTSPRYIPFPLRYACEFLVQAFS  393 (1093)
Q Consensus       315 -~~~~~~~ldl~~s~lRs~s~~h~~yl~n~~v~asl~~~i~~~~~~~~~LWGl~~~h~~~p~~~~~~~r~~~~~l~~~~~  393 (1093)
                       +|.+++|+|||+|+||||||||++||+||||.||||||||+||    +|||||+|||.+||.+||+.|.+||++||++|
T Consensus       233 vNp~t~~p~DLs~svLRSvSp~H~eYLrNMGV~ASmSISivv~g----~LWGLIACHH~sPk~ip~~vR~acef~gq~~s  308 (750)
T COG4251         233 VNPETNEPLDLSYSVLRSVSPIHLEYLRNMGVGASMSISIVVDG----KLWGLIACHHQSPKVIPYEVRKACEFFGQVLS  308 (750)
T ss_pred             cCcccCCcccchHHHHhccChHHHHHHHhcCcceeeEEEEEECC----eeEEeeeeccCCCccCCHHHHHHHHHHHHHHH
Confidence             7999999999999999999999999999999999999999999    99999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHH-HHHHHhhccCCC-cccccCCcchhhhccCCEEEEEECCeEEEecCCCCHHHHHHHHH
Q 001353          394 LQLYMELQVAMQLAEKNILRTQ-VLLCDMLLRDAP-FSIVTQSPSIMDLVKCDGAALYYGGRCWLVGVTPTESQLKDIAW  471 (1093)
Q Consensus       394 ~~l~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~-~~~~~~~~~~~~l~~a~g~al~~~~~~~~~G~~p~~~~~~~l~~  471 (1093)
                      .+++.+.+.+..-........+ .++..|...+++ .+++...++|++|+.|||++||.+|++.++|.||+..++..|++
T Consensus       309 ~~i~~~e~~~~~d~r~~l~~~~arl~~~ma~~~~~~d~L~~~~~dll~L~~adGaal~fg~~~~~vG~tP~~~~v~~Ll~  388 (750)
T COG4251         309 MEISALEQSEDADYRVQLTEHHARLLRYMAHAADFVDGLIDHQDDLLDLMPADGAALCFGGRWHLVGETPPRPAVQRLLQ  388 (750)
T ss_pred             HHHHHHhhhhhHHHHHHHHHHHHHHHHHHhhhcchhhhhcCCchhhHhhccCCceEEEECCEEEEecCCCChHHHHHHHH
Confidence            9997654333222222222333 334445445554 67888889999999999999999999999999999999999999


Q ss_pred             HHHhccCCCceeeeccccccCCCCccccccccccEEEEeeCC--CcEEEEeecCcCcEEEecCCCCCCcc-CCCCCcccc
Q 001353          472 WLLNNHGDCTGLSTDSLAEAGYPGAALLGQAVCGMATARITS--KDFLFWFRSHTAKEVKWGGAKHHPEH-KDNGGKMHP  548 (1093)
Q Consensus       472 ~l~~~~~~~~~~~t~~l~~~~~p~~~~~~~~~~G~l~~~~~~--~~~l~wfR~e~~~~v~W~G~p~~~~~-~~~~~~l~P  548 (1093)
                      ||.++... .+|+||+|++. ||+++.++..||||||++++.  .+||+|||||.+++|+|||+|+|+++ .+++.|++|
T Consensus       389 wl~~~~~~-~vf~TdsL~q~-yPda~~~~~vAsGlLAI~is~~~s~~llWFRpEvv~tV~WGG~P~k~~e~~~~~~rL~P  466 (750)
T COG4251         389 WLAEREEG-DVFATDSLSQV-YPDAEDYASVASGLLAIPISRVKSNYLLWFRPEVVQTVNWGGDPEKPYEAGPMGIRLTP  466 (750)
T ss_pred             HHhcCCcc-cEEeecccccc-CcchhhhccccceeEEEEeeccccceEEEEchHHheeeccCCCCCCccccCCCCcccCC
Confidence            99887554 79999999985 999999999999999999997  79999999999999999999999976 445789999


Q ss_pred             CchhHHHHHHhhccccccchhhhhhhhHHHHHHHHHHHHhhhhccchhhhccccccchhhhHHHHHHHHHHHHHHHHhcC
Q 001353          549 RSSFKAFLEVVKNRSFPWEVSEINAIHSLQIVMRDSFQEMEEENDSKVQGNTQQNGSKMQGVDELSSVACEMVRLIETAT  628 (1093)
Q Consensus       549 r~SF~~w~e~v~g~s~pW~~~El~aa~sL~liL~~sl~~l~~~~~~~~~~~~~L~~~l~q~~~eL~~~~~~l~~lie~~~  628 (1093)
                      |+||+.|+|+|+++|.||+..|++++..|+..|.+...+-.                     +|+...            
T Consensus       467 RkSFe~WkE~vRl~s~PWs~~ei~~A~~LR~aiv~ivl~~a---------------------eela~l------------  513 (750)
T COG4251         467 RKSFELWKETVRLQSQPWSEVEIEAALELRKAIVGIVLRHA---------------------EELAQL------------  513 (750)
T ss_pred             cccHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHHHHHHH---------------------HHHHHH------------
Confidence            99999999999999999999999999988544432221110                     000000            


Q ss_pred             ccEEEECCCCcEEEecHHHHHhcCCCccccCCCCccccccccccHHHHHHHHHHHHcCCCCceEEEEEEEeeeccCCcEE
Q 001353          629 APIFGVDSSGTINGWNAKVAELTGLPASEAMGKSLIDEVVHEESQGAVENLICRALLGEEDKNVELKLRKFELQKQHSVV  708 (1093)
Q Consensus       629 ~~I~~~D~dG~I~~~N~~~~~llG~~~eeliG~~~~~~lv~~~~~~~~~~~l~~~l~g~~~~~~e~~l~~~~~~kdG~~~  708 (1093)
                                                                                                      
T Consensus       514 --------------------------------------------------------------------------------  513 (750)
T COG4251         514 --------------------------------------------------------------------------------  513 (750)
T ss_pred             --------------------------------------------------------------------------------
Confidence                                                                                            


Q ss_pred             EEEEEEEEeecCCCCEEEEEEEEEecchhHHHHHHHHHHHHHHHHHHHhcCCCCCceEEecCCCcEeechhhhHHHhCCC
Q 001353          709 YILVNACTSRDYKNNVKGVCFVGQDITHEKVLMDKFIRLQGDYEAIIQSVNPLIPPIFASDENACCSEWNAAMEKVTGWM  788 (1093)
Q Consensus       709 ~v~v~~~pi~d~~g~v~gv~~v~~DITerK~aEe~L~~se~~lr~i~~~~~~li~~I~~~D~~g~i~~~N~a~~~l~G~~  788 (1093)
                                                                                                      
T Consensus       514 --------------------------------------------------------------------------------  513 (750)
T COG4251         514 --------------------------------------------------------------------------------  513 (750)
T ss_pred             --------------------------------------------------------------------------------
Confidence                                                                                            


Q ss_pred             cchhccccCCCccceeeEEEccCCcEEEEEEEEeEeecCCCcEEEEEEEEeecccCcHHHHHHHhHHHHHHHHHHHHHHH
Q 001353          789 RHEVIGITGQGTENFPFGFFNRQGQFVEVALTASRRTDAEGKVIGCFCFMQILVPDLQPALEAQGLEDMDIYAKIKELAY  868 (1093)
Q Consensus       789 ~eEliG~~~~~~~~~e~~~~~kdG~~~~v~~~~~~i~d~~G~v~g~i~~~~DITe~k~~e~elq~~~e~~~~~k~~~la~  868 (1093)
                                                                                     .+..++.+....+|...
T Consensus       514 ---------------------------------------------------------------~r~lersn~el~~f~yv  530 (750)
T COG4251         514 ---------------------------------------------------------------RRELERSNAELRAFAYV  530 (750)
T ss_pred             ---------------------------------------------------------------HHHHhhhhHHHHHHHHH
Confidence                                                                           00111111123356677


Q ss_pred             HHHhhhhHHHHHHHHHHHHhcC---CCCHHHHHHHHHHHHHHHHHHHHHhc-ccccccccCccccceeeeeHHHHHHHHH
Q 001353          869 IRQEVKNPLNGIRFVHKLLESS---SISENQRQYLETSDACERQIMTIIDG-MDLRCIEEGNMELKSEEFLLGNILDAVV  944 (1093)
Q Consensus       869 isHELrnPLt~I~g~~~LL~~~---~l~~~~~~~l~~i~~~~~rl~~lI~d-Ldlsrie~g~~~l~~~~v~L~~ll~~v~  944 (1093)
                      ++|++++||..|.++.++|...   .++++.++++..+......|..||++ +.++++.....+  ..+.|+..+++.++
T Consensus       531 ~sHdlqePl~~I~~~a~lL~~~~~~~~d~~~~~~i~~~~~~~~~~~~lidd~l~~s~l~~~~~~--l~~td~~~vv~~vl  608 (750)
T COG4251         531 ASHDLQEPLRQISNYAQLLSERYSDALDEEAKEFITFISRLTSLMQQLIDDLLTYSKLGLTEAP--LQPTDVQKVVDKVL  608 (750)
T ss_pred             hhhhhhHHHHHHHHHHHhhhhccccccChHHHHHHHHHHHHHHHHHHHHHHHhhhhhhccccCC--CCCcchHHHHHHHH
Confidence            8999999999999999999864   67888999999999999999999999 699998655444  45889999999999


Q ss_pred             HHHHHHhccCCeEEEeecCCCccceEEEecHHHHHHHHHHHHHHHHHcCCCCCCeEEEEEEeCCccccCCCceeEEEEEE
Q 001353          945 SQVMVLLRDKNLHLLHDIPEEIKALSLNGDRIRLQLVLSDFLHCVVRHAPSPDGWVEIKVLPGLKLIKDADQFVHVQFRL 1024 (1093)
Q Consensus       945 ~~~~~~~~~~~i~l~~~~~~~lp~~~v~~D~~~L~qVl~nLl~NAik~t~~~~g~I~I~v~~~~~~~~~~~~~~~v~l~V 1024 (1093)
                      ..+.......++.+.+..   +|  .+.+|+.++.||+.||+.||+||..+...+|+|+.....+         .++|.|
T Consensus       609 ~~l~~ri~dtgaei~i~~---lp--~v~~d~~~l~qv~~NLi~Naik~~~~e~~~i~I~~~r~ed---------~~t~sV  674 (750)
T COG4251         609 LELSQRIADTGAEIRIAP---LP--VVAADATQLGQVFQNLIANAIKFGGPENPDIEISAERQED---------EWTFSV  674 (750)
T ss_pred             HhcccccccccceEEecc---cc--eeecCHHHHHHHHHHHHhhheecCCCCCCceEEeeeccCC---------ceEEEe
Confidence            999998888887777654   55  4899999999999999999999987745899999877777         899999


Q ss_pred             ecCCCCCChhhHhhhccCCCC-----CCCCccchHHHHHHHHHHcCCEEEEEeeCCe-eEEEEEEeecCCccC
Q 001353         1025 THPGEGIPSHLIEDMYNGRNQ-----WTTPEGLGLKLSRKLLIMMNGRVRYVRENSK-CYFVIDLELKTRGRQ 1091 (1093)
Q Consensus      1025 ~DnG~GIp~e~~~~IFe~F~~-----~~~GtGLGL~ivr~ive~hgG~I~v~S~~gg-t~F~v~LPlp~~~~~ 1091 (1093)
                      .|||.||+++..++||..|.+     ...|+|+||+|||+|++.|+|+|+++|.+|. +||.+++|.-.+++.
T Consensus       675 ~dng~Gi~~a~~~riF~iFqRl~s~~~y~gtG~GL~I~kkI~e~H~G~i~vEs~~gEgsTF~f~lp~~~~e~~  747 (750)
T COG4251         675 RDNGIGIDPAYFERIFVIFQRLHSRDEYLGTGLGLAICKKIAERHQGRIWVESTPGEGSTFYFTLPVGGEEPG  747 (750)
T ss_pred             cCCCCCcCHHHHHHHHHHHHhcCchhhhcCCCccHHHHHHHHHHhCceEEEeecCCCceeEEEEeecCCcCcc
Confidence            999999999999999999977     6779999999999999999999999999885 999999998766544

>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

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

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

>PRK13557 histidine kinase; 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

>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

>COG2205 KdpD Osmosensitive K+ channel histidine kinase [Signal transduction mechanisms]	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

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

>PRK13559 hypothetical protein; Provisional	Back alignment and domain information

>PRK09303 adaptive-response sensory kinase; Validated	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

>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

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

>PRK10490 sensor protein KdpD; 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

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

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

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

>PRK09835 sensor kinase CusS; Provisional	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

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

>PRK09470 cpxA two-component sensor protein; 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

>COG0642 BaeS Signal transduction histidine kinase [Signal transduction mechanisms]	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

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

>PRK11644 sensory histidine kinase UhpB; Provisional	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

>PRK11359 cyclic-di-GMP phosphodiesterase; Provisional	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

>TIGR02040 PpsR-CrtJ transcriptional regulator PpsR	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

>COG4564 Signal transduction histidine kinase [Signal transduction mechanisms]	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

>COG4585 Signal transduction histidine kinase [Signal transduction mechanisms]	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

>COG3851 UhpB Signal transduction histidine kinase, glucose-6-phosphate specific [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

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

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

>smart00387 HATPase_c Histidine kinase-like ATPases	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

>PRK04184 DNA topoisomerase VI subunit B; Validated	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

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

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

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

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

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

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

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

>PRK14867 DNA topoisomerase VI subunit B; Provisional	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

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

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

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

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

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

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

>PRK10060 RNase II stability modulator; 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

>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

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

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

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

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

>PF14501 HATPase_c_5: GHKL domain	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

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

>PF12860 PAS_7: PAS fold	Back alignment and domain information

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

>PRK13559 hypothetical protein; Provisional	Back alignment and domain information

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

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

>PF13581 HATPase_c_2: Histidine kinase-like ATPase domain	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

>PRK13557 histidine kinase; 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

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

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

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

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

>PRK11086 sensory histidine kinase DcuS; Provisional	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

>PRK10820 DNA-binding transcriptional regulator TyrR; Provisional	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

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

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

>PRK05022 anaerobic nitric oxide reductase transcription regulator; Provisional	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

>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

>COG2172 RsbW Anti-sigma regulatory factor (Ser/Thr protein kinase) [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

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

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

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

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

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

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

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

>PF12860 PAS_7: PAS fold	Back alignment and domain information

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

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

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

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

>COG5002 VicK Signal transduction histidine kinase [Signal transduction mechanisms]	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

>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

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

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

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

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

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

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

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

>smart00091 PAS PAS domain	Back alignment and domain information

>TIGR02373 photo_yellow photoactive yellow protein	Back alignment and domain information

>PF13188 PAS_8: PAS domain; PDB: 2JHE_D 3VOL_A	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

>COG5385 Uncharacterized protein conserved in bacteria [Function unknown]	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

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

>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

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

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

>TIGR01055 parE_Gneg DNA topoisomerase IV, B subunit, proteobacterial	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

>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

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

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

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

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

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

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

>PRK10618 phosphotransfer intermediate protein in two-component regulatory system with RcsBC; Provisional	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

>KOG0519 consensus Sensory transduction histidine kinase [Signal transduction mechanisms]	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

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

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

>KOG1229 consensus 3'5'-cyclic nucleotide phosphodiesterases [Signal transduction mechanisms]	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

>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

>COG1956 GAF domain-containing protein [Signal transduction mechanisms]	Back alignment and domain information

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

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

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

>smart00091 PAS PAS domain	Back alignment and domain information

>TIGR02373 photo_yellow photoactive yellow protein	Back alignment and domain information

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

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

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

>PHA02569 39 DNA topoisomerase II large subunit; Provisional	Back alignment and domain information

>PF14689 SPOB_a: Sensor_kinase_SpoOB-type, alpha-helical domain; PDB: 1F51_C 2FTK_B 1IXM_B	Back alignment and domain information

>PLN03237 DNA topoisomerase 2; Provisional	Back alignment and domain information

>COG3887 Predicted signaling protein consisting of a modified GGDEF domain and a DHH domain [Signal transduction mechanisms]	Back alignment and domain information

>PRK13837 two-component VirA-like sensor kinase; Provisional	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		1093
2vea_A		520	The Complete Sensory Module Of The Cyanobacterial P		5e-66
3zq5_A		520	Structure Of The Y263f Mutant Of The Cyanobacterial		1e-65
4gw9_A		655	Structure Of A Bacteriophytochrome And Light-Stimul		7e-55
3g6o_A		505	Crystal Structure Of P. Aeruginosa Bacteriophytochr		3e-44
3c2w_A		505	Crystal Structure Of The Photosensory Core Domain O		1e-43
3ibr_A		505	Crystal Structure Of P. Aeruginosa Bacteriophytochr		5e-42
2ool_A		337	Crystal Structure Of The Chromophore-Binding Domain		4e-37
4e04_A		327	Rpbphp2 Chromophore-binding Domain Crystallized By		5e-37
2o9b_A		342	Crystal Structure Of Bacteriophytochrome Chromophor		6e-27
3s7n_A		343	Crystal Structure Of The Alternate His 207 Conforma		5e-26
1ztu_A		341	Structure Of The Chromophore Binding Domain Of Bact		7e-26
3s7q_A		343	Crystal Structure Of A Monomeric Infrared Fluoresce		1e-25
2lb5_A		208	Refined Structural Basis For The Photoconversion Of		1e-19
2k2n_A		172	Solution Structure Of A Cyanobacterial Phytochrome		1e-19

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