Citrus Sinensis ID: 003071

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

MMAVSSGGSRDSRDSGGQKMIMDNGKYVRYTPEQVEALERLYHECPKPSSMRRQQLIRECPILSNIEPKQIKVWFQNRRCREKQRKEASRLQAVNRKLTAMNKLLMEENDRLQKQVSQLVYENTFFRQQTQNAATLATTDTSCESVVTSGQHHLTPQQQHQHPPRDASPAGLLSIAEETLTEFLSKATGTAVEWVQMPGMKPGPDSIGIVAISHGCTGVAARACGLVGLDPTRVAEILKDRPSWYRDCRSVEVVNVLPTGSSGTIELLYMQLYAPTTLAPARDFWLLRYTSVLEDGSLVVCERSLNNTQNGPSMPQAPHFVRAEMLPSGYLIRPCEGGGSIIHIVDHMDLEPWSVPEVLRPLYESSTLIAQKTTMAALRHLRQISQEVSQPSVTGWGRRPAALRALSQRLSRGFNEALNGFTDEGWSMLESDGIDDVTVHVNSSPSKMMGVQLSYVNGFPSMSNAVLCAKASMLLQDVPPAILLRFLREHRSEWADSSIDAYSAAAVKAGPCSLPVPRAGNFGGQVILPLAHTIEHEEFLEVIKLENMAHYREDMIMPSDIFLLQLCSGVDENAVGNCAELVFAPIDASFSDDAPIIPSGFRIIPLDSGKDTPSPNRTLDLASALEVGPTGNKASGDSSTQCGSTKSVITIAFQFAFEMHLQENVASMARQYVRGIIASVQRVALALSPSRFGSNAGLRPPPGSPEAHTLARWICQSYRCYLGAELLKCEGNESILKTLWHHSDAVLCCSLKALPVFTFANQAGLDMLETTLVALQDITLEKIFDDSGRKTLCSEFPQIMQQGFMCLQSGICLSSMGRPISYERAVAWKVLNEEENAHCICFMFINWSFV

cccccccccccccccccccccccccccccccHHHHHHHHHHHHccccccHHHHHHHHHHccccccccccccHHHcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccHHcccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHccccccccccccccccccccccccccccccEEEcccEEEEEccHHHHHHHHcccHHHHHHccccEEEEEEccccccHHHHHHHHHHcccccccccEEEEEEEEEEcccccEEEEEEEccccccccccccccccccEEEcccccEEEEcccccEEEEEEEEcccccccccccHHHHHccHHHHHHHHHHHHHHHHHHHHHHHccccccccccccHHHHHHHHHHHHHHHHHcccccccccccccccccccEEEEEcccccccccccccccccccccccEEEEEEEccccccccHHHHHHHHHHcccccccccHHHHHHHHHccccccccccccccccccEEEEcccccccccEEEEEEEcccccccccccccHHHHHHHHHccccccccccccEEEEEccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEEEEEEcccccccHHHHcHHHHHHHHHHHHHHHHHHHHccccccccccccccccccHHHHHHHHHHHHHHHHHHccccccccccHHHHHHHHccccEEEEcccccccEEEcccHHHHHHHcccHHHHHccccccccccccHHHHHHHHHHHHHHcccccccEEEEccccccEEEccEEEEEEEcccccEEEEEEEEEccEEc

cccEEcccccccccccccccccccccEEcccHHHHHHHHHHHHHcccccHHHHHHHHHHcHHHccccHHHHHHHHHcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHccccccEEcccccccccccccccccccccEEEEEHccEEEEEcHHHHHHHHHccHHHHHHccccEEEEEEccccccEEEEEEEEEccccccccHHHEEEEEEEEEcccccEEEEEEEccccccccccccccccHHcccccccEEEEEcccccEEEEEEEEEccccccHHHHHHHHHHcHHHHHHHHHHHHHHHHHHHHHHHcccccccccccHHHHHHHHHHHHHHHHHHcccccccccEEEcccccccEEEEEEcccccccccccccccccccccccEEEHHHHHHHccccHHHHHHHHHHHHHHHHHHcccHHHHHHHccccccccccccccccEEEEEEcccccccccEEEEEEEccccccccccEccHHHHHHHHccccccccEEEEEEEEEccccccccccccccccccEEEEcccccccccccccccccccccccccccccccccccccccccEEEEEEEEEEccccccHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccHHHHHHHHHHHHHHHHHHcHHHccccccHHHHHHHHccccEEEEEccccccHHHHHcHHHHHHHHHHHHHHHHccHHHHHccccccHHHHHHHHHHHccccEccccEEEccccccccHHHEEEEEEEccccccEEEEEEEEEEccc

mmavssggsrdsrdsggqkmimdngkyvrytPEQVEALERLyhecpkpssmrRQQLIrecpilsniepkqIKVWFQNRRCREKQRKEASRLQAVNRKLTAMNKLLMEENDRLQKQVSQLVYENTFFRQQTQnaatlattdtscesvvtsgqhhltpqqqhqhpprdaspagLLSIAEETLTEFLSKATGTAVEwvqmpgmkpgpdsiGIVAISHGCTGVAARacglvgldptRVAEilkdrpswyrdcrsvevvnvlptgssgtIELLYMQLyapttlaparDFWLLRYTSVLEDGSLVVCERslnntqngpsmpqaphfvraemlpsgylirpcegggsiihivdhmdlepwsvpevlrplyessTLIAQKTTMAALRHLRQISqevsqpsvtgwgrrPAALRALSQRLSRGFNEalngftdegwsmlesdgiddvtvhvnsspskmmgvqlsyvngfpsmSNAVLCAKASMLLQDVPPAILLRFLREHRSEWADSSIDAYSAAAvkagpcslpvpragnfggqvilplahtiehEEFLEVIKLENmahyredmimpsDIFLLQLcsgvdenavgncaelvfapidasfsddapiipsgfriipldsgkdtpspnrtldlasalevgptgnkasgdsstqcgstkSVITIAFQFAFEMHLQENVASMARQYVRGIIASVQRVALAlspsrfgsnaglrpppgspeahTLARWICQSYRCYLgaellkcegNESILKTLWHHSDAVlccslkalpvftfanqAGLDMLETTLVALQDITLEkifddsgrktlcseFPQIMQQGFmclqsgiclssmgrpisYERAVAWKVLNEEENAHCICFmfinwsfv

mmavssggsrdsrdsggqkmimdngkyvRYTPEQVEALERLYhecpkpssmrrQQLIRECpilsniepkqikvwfqNRRCREKQRKEASRLQAVNRKLTAMNKLLMEENDRLQKQVSQLVYENTFFRQQTQNAATLATTDTSCESVVTSGQHHltpqqqhqhpprDASPAGLLSIAEETLTEFLSKATGTAVEWVQMPGMKPGPDSIGIVAISHGCTGVAARACGLVGLDPTRVAEIlkdrpswyrdcrsvEVVNVLPTGSSGTIELLYMQLYAPTTLAPARDFWLLRYTSVLEDGSLVVCERSlnntqngpsmpqAPHFVRAEMLPSGYLIRPCEGGGSIIHIVDHMDLEPWSVPEVLRPLYESSTLIAQKTTMAALRHLRQISqevsqpsvtgwgrRPAALRALSQRLSRGFNEALNGFTDEGWSMLESDGIDDVTVHVNSSPSKMMGVQLSYVNGFPSMSNAVLCAKASMLLQDVPPAILLRFLREHRSEWADSSIDAYSAAAVKAGPCSLPVPRAGNFGGQVILPLAHTIEHEEFLEVIKLENMAHYREDMIMPSDIFLLQLCSGVDENAVGNCAELVFAPIDASFSDDAPIIPSGFRiipldsgkdtpSPNRTLDLASALEvgptgnkasgdsstqcgsTKSVITIAFQFAFEMHLQENVASMARQYVRGIIASVQRVALALSPSRFGSNAGLRPPPGSPEAHTLARWICQSYRCYLGAELLKCEGNESILKTLWHHSDAVLCCSLKALPVFTFANQAGLDMLETTLVALQDITLEKIFDDSGRKTLCSEFPQIMQQGFMCLQSGICLSSMGRPISYERAVAWKVLNEEENAHCICFMFINWSFV

MMAVssggsrdsrdsggQKMIMDNGKYVRYTPEQVEALERLYHECPKPSSMRRQQLIRECPILSNIEPKQIKVWFQNRRCREKQRKEASRLQAVNRKLTAMNKLLMEENDRLQKQVSQLVYENTFFRqqtqnaatlattdtSCESVVTSGqhhltpqqqhqhppRDASPAGLLSIAEETLTEFLSKATGTAVEWVQMPGMKPGPDSIGIVAISHGCTGVAARACGLVGLDPTRVAEILKDRPSWYRDCRSVEVVNVLPTGSSGTIELLYMQLYAPTTLAPARDFWLLRYTSVLEDGSLVVCERSLNNTQNGPSMPQAPHFVRAEMLPSGYLIRPCEGGGSIIHIVDHMDLEPWSVPEVLRPLYESSTLIAQKTTMAALRHLRQISQEVSQPSVTGWGRRPAALRALSQRLSRGFNEALNGFTDEGWSMLESDGIDDVTVHVNSSPSKMMGVQLSYVNGFPSMSNAVLCAKASMLLQDVPPAILLRFLREHRSEWadssidaysaaaVKAGPCSLPVPRAGNFGGQVILPLAHTIEHEEFLEVIKLENMAHYREDMIMPSDIFLLQLCSGVDENAVGNCAELVFAPIDASFSDDAPIIPSGFRIIPLDSGKDTPSPNRTLDLASALEVGPTGNKASGDSSTQCGSTKSVITIAFQFAFEMHLQENVASMARQYVRGIIASVQRVALALSPSRFGSNAGLRPPPGSPEAHTLARWICQSYRCYLGAELLKCEGNESILKTLWHHSDAVLCCSLKALPVFTFANQAGLDMLETTLVALQDITLEKIFDDSGRKTLCSEFPQIMQQGFMCLQSGICLSSMGRPISYERAVAWKVLNEEENAHCICFMFINWSFV

*************************KYVRYTPEQVEALERLYHE**********QLIRECPILSNIEPKQIKVWFQNRRC***********************************VSQLVYENTFFRQQT*******************************************SIAEETLTEFLSKATGTAVEWVQMPGMKPGPDSIGIVAISHGCTGVAARACGLVGLDPTRVAEILKDRPSWYRDCRSVEVVNVLPTGSSGTIELLYMQLYAPTTLAPARDFWLLRYTSVLEDGSLVVCERS***************FVRAEMLPSGYLIRPCEGGGSIIHIVDHMDLEPWSVPEVLRPLYESSTLIAQKTTMAALRHLRQI***********W******************************************************VQLSYVNGFPSMSNAVLCAKASMLLQDVPPAILLRFLREHRSEWADSSIDAYSAAAVKAGPCSLPVPRAGNFGGQVILPLAHTIEHEEFLEVIKLENMAHYREDMIMPSDIFLLQLCSGVDENAVGNCAELVFAPIDASFSDDAPIIPSGFRIIP****************************************KSVITIAFQFAFEMHLQENVASMARQYVRGIIASVQRVALAL********************HTLARWICQSYRCYLGAELLKCEGNESILKTLWHHSDAVLCCSLKALPVFTFANQAGLDMLETTLVALQDITLEKIFDDSGRKTLCSEFPQIMQQGFMCLQSGICLSSMGRPISYERAVAWKVLNEEENAHCICFMFINWSF*

*******************************PEQVEALERLYHE***************CPILSNIEPKQIKVWFQNRR***********LQAVNRKLTAMNKLLMEENDRLQKQVSQ**********************************************************EETLTEFLSKATGTAVEWVQMP*****************CTGVAARACGLVGLDPTRVAEILKDRPSWYRDCRSVEVVNVLPTGSSGTIELLYMQLYAPTTLAPARDFWLLRYTSVLEDGSLVVCERSLNNT*************RAEMLPSGYLIRPCEGGGSIIHIVDHMDLEPWSVPEVLRPLYESSTLIAQKTTMAALRHLRQISQEVS********R*PAALRALSQRLSRGFNEALNGFTDEGWSMLESDGIDDVTVHVNSS****************SMSNAVLCAKASMLLQDVPPAILLRFLREHRSEWADSSIDAYSAAAVKAGPCSL*******FGGQVILPLAHTIEHEEFLEVIKLENMAHYREDMIMPSDIFLLQLCSGVDENAVGNCAELVFAPIDASFSDDAPIIPSGFRIIPLDS***************************************VITIAFQFAFEMHLQENVASMARQYVRGIIASVQRVALALSPSR**********PGSPEAHTLARWICQSYRCYLGAELLKCEGNESILKTLWHHSDAVLCCSLKALPVFTFANQAGLDMLETTLVALQDITLEKI******K**CSEFPQIMQQGFMCLQSGICLSSMGRPISYERAVAWKVLNEEENAHCICFMFINWSFV

****************GQKMIMDNGKYVRYTPEQVEALERLYHECPKPSSMRRQQLIRECPILSNIEPKQIKVWFQNRR***********LQAVNRKLTAMNKLLMEENDRLQKQVSQLVYENTFFRQQTQNA***********************************PAGLLSIAEETLTEFLSKATGTAVEWVQMPGMKPGPDSIGIVAISHGCTGVAARACGLVGLDPTRVAEILKDRPSWYRDCRSVEVVNVLPTGSSGTIELLYMQLYAPTTLAPARDFWLLRYTSVLEDGSLVVCERSLNNTQNGPSMPQAPHFVRAEMLPSGYLIRPCEGGGSIIHIVDHMDLEPWSVPEVLRPLYESSTLIAQKTTMAALRHLRQISQEVSQPSVTGWGRRPAALRALSQRLSRGFNEALNGFTDEGWSMLESDGIDDVTVHVNSSPSKMMGVQLSYVNGFPSMSNAVLCAKASMLLQDVPPAILLRFLREHRSEWADSSIDAYSAAAVKAGPCSLPVPRAGNFGGQVILPLAHTIEHEEFLEVIKLENMAHYREDMIMPSDIFLLQLCSGVDENAVGNCAELVFAPIDASFSDDAPIIPSGFRIIPLDSGKDTPSPNRTLDLASALEVG****************TKSVITIAFQFAFEMHLQENVASMARQYVRGIIASVQRVALALSPSRFGSNAGLRPPPGSPEAHTLARWICQSYRCYLGAELLKCEGNESILKTLWHHSDAVLCCSLKALPVFTFANQAGLDMLETTLVALQDITLEKIFDDSGRKTLCSEFPQIMQQGFMCLQSGICLSSMGRPISYERAVAWKVLNEEENAHCICFMFINWSFV

************************GKYVRYTPEQVEALERLYHECPKPSSMRRQQLIRECPILSNIEPKQIKVWFQNRRCREKQRKEASRLQAVNRKLTAMNKLLMEENDRLQKQVSQLVYENTFFRQ*********************************HPPRDASPAGLLSIAEETLTEFLSKATGTAVEWVQMPGMKPGPDSIGIVAISHGCTGVAARACGLVGLDPTRVAEILKDRPSWYRDCRSVEVVNVLPTGSSGTIELLYMQLYAPTTLAPARDFWLLRYTSVLEDGSLVVCERSLNNTQNGPSMPQAPHFVRAEMLPSGYLIRPCEGGGSIIHIVDHMDLEPWSVPEVLRPLYESSTLIAQKTTMAALRHLRQISQEVSQPSVTGWGRRPAALRALSQRLSRGFNEALNGFTDEGWSMLESDGIDDVTVHVNSSPSKMMGVQLSYVNGFPSMSNAVLCAKASMLLQDVPPAILLRFLREHRSEWADSSIDAYSAAAVKAGPCSLPVPRAGNFGGQVILPLAHTIEHEEFLEVIKLENMAHYREDMIMPSDIFLLQLCSGVDENAVGNCAELVFAPIDASFSDDAPIIPSGFRIIPLDS***********************************STKSVITIAFQFAFEMHLQENVASMARQYVRGIIASVQRVALALSPS**********PPGSPEAHTLARWICQSYRCYLGAELLKCEGNESILKTLWHHSDAVLCCSLKALPVFTFANQAGLDMLETTLVALQDITLEKIFDDSGRKTLCSEFPQIMQQGFMCLQSGICLSSMGRPISYERAVAWKVLNEEENAHCICFMFINWSFV

oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo

iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo

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MMAVSSGGSRDSRDSGGQKMIMDNGKYVRYTPEQVEALERLYHECPKPSSMRRQQLIRECPILSNIEPKQIKVWFQNRRCxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxNTFFRQQTQNAATLATTDTSCESVVTSGQHHLTPQQQHQHPPRDASPAGLLSIAEETLTEFLSKATGTAVEWVQMPGMKPGPDSIGIVAISHGCTGVAARACGLVGLDPTRVAEILKDRPSWYRDCRSVEVVNVLPTGSSGTIELLYMQLYAPTTLAPARDFWLLRYTSVLEDGSLVVCERSLNNTQNGPSMPQAPHFVRAEMLPSGYLIRPCEGGGSIIHIVDHMDLEPWSVPEVLRPLYESSTLIAQKTTMAALRHLRQISQEVSQPSVTGWGRRPAALRALSQRLSRGFNEALNGFTDEGWSMLESDGIDDVTVHVNSSPSKMMGVQLSYVNGFPSMSNAVLCAKASMLLQDVPPAILLRFLREHRSEWADSSIDAYSAAAVKAGPCSLPVPRAGNFGGQVILPLAHTIEHEEFLEVIKLENMAHYREDMIMPSDIFLLQLCSGVDENAVGNCAELVFAPIDASFSDDAPIIPSGFRIIPLDSGKDTPSPNRTLDLASALEVGPTGNKASGDSSTQCGSTKSVITIAFQFAFEMHLQENVASMARQYVRGIIASVQRVALALSPSRFGSNAGLRPPPGSPEAHTLARWICQSYRCYLGAELLKCEGNESILKTLWHHSDAVLCCSLKALPVFTFANQAGLDMLETTLVALQDITLEKIFDDSGRKTLCSEFPQIMQQGFMCLQSGICLSSMGRPISYERAVAWKVLNEEENAHCICFMFINWSFV

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		850	2.2.26 [Sep-21-2011]
Q39123		833	Homeobox-leucine zipper p	yes	no	0.974	0.993	0.812	0.0
Q9ZU11		836	Homeobox-leucine zipper p	no	no	0.970	0.986	0.809	0.0
Q6AST1		859	Homeobox-leucine zipper p	yes	no	0.990	0.980	0.699	0.0
A2XK30		859	Homeobox-leucine zipper p	N/A	no	0.990	0.980	0.699	0.0
Q2QM96		855	Homeobox-leucine zipper p	no	no	0.991	0.985	0.672	0.0
A2ZMN9		855	Homeobox-leucine zipper p	N/A	no	0.991	0.985	0.672	0.0
A2WLR5		861	Homeobox-leucine zipper p	N/A	no	0.964	0.952	0.673	0.0
Q5QMZ9		868	Homeobox-leucine zipper p	no	no	0.971	0.951	0.671	0.0
O04291		852	Homeobox-leucine zipper p	no	no	0.975	0.973	0.665	0.0
A2Z8L4		840	Homeobox-leucine zipper p	N/A	no	0.958	0.970	0.657	0.0

>sp\|Q39123\|ATHB8_ARATH Homeobox-leucine zipper protein ATHB-8 OS=Arabidopsis thaliana GN=ATHB-8 PE=1 SV=1	Back alignment and function desciption

 Score = 1436 bits (3717), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 688/847 (81%), Positives = 770/847 (90%), Gaps = 19/847 (2%)

Query: 7   GGSRDSRDSGGQKMIMDNGKYVRYTPEQVEALERLYHECPKPSSMRRQQLIRECPILSNI 66
           GGS +S +       MDNGKYVRYTPEQVEALERLY++CPKPSSMRRQQLIRECPILSNI
Sbjct: 3   GGSNNSHN-------MDNGKYVRYTPEQVEALERLYNDCPKPSSMRRQQLIRECPILSNI 55

Query: 67  EPKQIKVWFQNRRCREKQRKEASRLQAVNRKLTAMNKLLMEENDRLQKQVSQLVYENTFF 126
           EPKQIKVWFQNRRCREKQRKEASRLQAVNRKLTAMNKLLMEENDRLQKQVS LVYEN++F
Sbjct: 56  EPKQIKVWFQNRRCREKQRKEASRLQAVNRKLTAMNKLLMEENDRLQKQVSHLVYENSYF 115

Query: 127 RQQTQNAATLATTDTSCESVVTSGQHHLTPQQQHQHPPRDASPAGLLSIAEETLTEFLSK 186
           RQ  QN   LATTDTSCESVVTSGQHHLTPQ    H PRDASPAGLLSIA+ETLTEF+SK
Sbjct: 116 RQHPQNQGNLATTDTSCESVVTSGQHHLTPQ----HQPRDASPAGLLSIADETLTEFISK 171

Query: 187 ATGTAVEWVQMPGMKPGPDSIGIVAISHGCTGVAARACGLVGLDPTRVAEILKDRPSWYR 246
           ATGTAVEWVQMPGMKPGPDSIGIVAISHGCTG+AARACGLVGLDPTRVAEILKD+P W R
Sbjct: 172 ATGTAVEWVQMPGMKPGPDSIGIVAISHGCTGIAARACGLVGLDPTRVAEILKDKPCWLR 231

Query: 247 DCRSVEVVNVLPTGSSGTIELLYMQLYAPTTLAPARDFWLLRYTSVLEDGSLVVCERSLN 306
           DCRS+++VNVL T + GT+EL+YMQLYAPTTLAPARDFW+LRYTSV+EDGSLV+CERSLN
Sbjct: 232 DCRSLDIVNVLSTANGGTLELIYMQLYAPTTLAPARDFWMLRYTSVMEDGSLVICERSLN 291

Query: 307 NTQNGPSMPQAPHFVRAEMLPSGYLIRPCEGGGSIIHIVDHMDLEPWSVPEVLRPLYESS 366
           NTQNGPSMP +PHFVRAE+LPSGYLIRPCEGGGSI+HIVDH DLEPWSVPEVLR LYESS
Sbjct: 292 NTQNGPSMPPSPHFVRAEILPSGYLIRPCEGGGSILHIVDHFDLEPWSVPEVLRSLYESS 351

Query: 367 TLIAQKTTMAALRHLRQISQEVSQPSVTGWGRRPAALRALSQRLSRGFNEALNGFTDEGW 426
           TL+AQ+TTMAALR+LRQISQE+SQP+VTGWGRRPAALRALSQRLS+GFNEA+NGF+DEGW
Sbjct: 352 TLLAQRTTMAALRYLRQISQEISQPNVTGWGRRPAALRALSQRLSKGFNEAVNGFSDEGW 411

Query: 427 SMLESDGIDDVTVHVNSSPSKMMGV-QLSYVNGFPSMSNAVLCAKASMLLQDVPPAILLR 485
           S+LESDGIDDVT+ VNSSP+KMM    L + NG+ SM +AVLCAKASMLLQ+VPP+ILLR
Sbjct: 412 SILESDGIDDVTLLVNSSPTKMMMTSSLPFANGYTSMPSAVLCAKASMLLQNVPPSILLR 471

Query: 486 FLREHRSEWADSSIDAYSAAAVKAGPCSLPVPRAGNFGGQVILPLAHTIEHEEFLEVIKL 545
           FLREHR EWAD+SIDAYSAAA+KAGPCSLP+PR G+FGGQVILPLAHTIE+EEF+EVIKL
Sbjct: 472 FLREHRQEWADNSIDAYSAAAIKAGPCSLPIPRPGSFGGQVILPLAHTIENEEFMEVIKL 531

Query: 546 ENMAHYREDMIMPSDIFLLQLCSGVDENAVGNCAELVFAPIDASFSDDAPIIPSGFRIIP 605
           E++ HY+EDM+MP+DIFLLQ+CSGVDENAV +CAEL+FAPIDASFSDDAPIIPSGFRIIP
Sbjct: 532 ESLGHYQEDMMMPADIFLLQMCSGVDENAVESCAELIFAPIDASFSDDAPIIPSGFRIIP 591

Query: 606 LDSGKDTPSPNRTLDLASALEVGPTGNKASGDSSTQCGSTKSVITIAFQFAFEMHLQENV 665
           LDS  +  SPNRTLDLASAL+V   G++ +GDS    G++KSV+TIAFQ AFEMH+QENV
Sbjct: 592 LDSKSEGLSPNRTLDLASALDV---GSRTAGDSCGSRGNSKSVMTIAFQLAFEMHMQENV 648

Query: 666 ASMARQYVRGIIASVQRVALALSPSRFGSNAGLRPPPGSPEAHTLARWICQSYRCYLGAE 725
           ASMARQYVR +IASVQRVALALSPS     +GLRPPP SPEAHTLARWI  SYRCYLG +
Sbjct: 649 ASMARQYVRSVIASVQRVALALSPSSH-QLSGLRPPPASPEAHTLARWISHSYRCYLGVD 707

Query: 726 LLKCEGNESILKTLWHHSDAVLCCSLKAL-PVFTFANQAGLDMLETTLVALQDITLEKIF 784
           LLK  G + +LK+LWHH DAV+CCSLKAL PVFTFANQAGLDMLETTLVALQDITL+KIF
Sbjct: 708 LLKPHGTD-LLKSLWHHPDAVMCCSLKALSPVFTFANQAGLDMLETTLVALQDITLDKIF 766

Query: 785 D-DSGRKTLCSEFPQIMQQGFMCLQSGICLSSMGRPISYERAVAWKVLNEEENAHCICFM 843
           D ++G+KTL SEFPQIMQQGFMC+  GIC+SSMGR ++YE+AV WKVLN++E+ HCICFM
Sbjct: 767 DNNNGKKTLSSEFPQIMQQGFMCMDGGICMSSMGRAVTYEKAVGWKVLNDDEDPHCICFM 826

Query: 844 FINWSFV 850
           F+NWSF+
Sbjct: 827 FLNWSFI 833

Probable transcription factor involved in the regulation of vascular development. May promote differentiation of precambial and cambial cells.
Arabidopsis thaliana (taxid: 3702)

>sp\|Q9ZU11\|ATB15_ARATH Homeobox-leucine zipper protein ATHB-15 OS=Arabidopsis thaliana GN=ATHB-15 PE=1 SV=1	Back alignment and function description

>sp\|Q6AST1\|HOX32_ORYSJ Homeobox-leucine zipper protein HOX32 OS=Oryza sativa subsp. japonica GN=HOX32 PE=2 SV=1	Back alignment and function description

>sp\|A2XK30\|HOX32_ORYSI Homeobox-leucine zipper protein HOX32 OS=Oryza sativa subsp. indica GN=HOX32 PE=2 SV=1	Back alignment and function description

>sp\|Q2QM96\|HOX33_ORYSJ Homeobox-leucine zipper protein HOX33 OS=Oryza sativa subsp. japonica GN=HOX33 PE=2 SV=1	Back alignment and function description

>sp\|A2ZMN9\|HOX33_ORYSI Homeobox-leucine zipper protein HOX33 OS=Oryza sativa subsp. indica GN=HOX33 PE=2 SV=2	Back alignment and function description

>sp\|A2WLR5\|HOX29_ORYSI Homeobox-leucine zipper protein HOX29 OS=Oryza sativa subsp. indica GN=HOX29 PE=2 SV=2	Back alignment and function description

>sp\|Q5QMZ9\|HOX29_ORYSJ Homeobox-leucine zipper protein HOX29 OS=Oryza sativa subsp. japonica GN=HOX29 PE=2 SV=2	Back alignment and function description

>sp\|O04291\|ATB14_ARATH Homeobox-leucine zipper protein ATHB-14 OS=Arabidopsis thaliana GN=ATHB-14 PE=1 SV=1	Back alignment and function description

>sp\|A2Z8L4\|HOX9_ORYSI Homeobox-leucine zipper protein HOX9 OS=Oryza sativa subsp. indica GN=HOX9 PE=2 SV=2	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		850
219879370		829	class III HD-Zip protein 8 [Citrus trifo	0.975	1.0	0.995	0.0
224092274		828	predicted protein [Populus trichocarpa]	0.969	0.995	0.906	0.0
359476025		839	PREDICTED: homeobox-leucine zipper prote	0.972	0.985	0.888	0.0
383930759		840	class III HD-Zip protein 8 [Prunus persi	0.987	0.998	0.877	0.0
206572107		844	putative HB8 HD-ZipIII [Malus x domestic	0.991	0.998	0.880	0.0
147790308		839	hypothetical protein VITISV_009744 [Viti	0.971	0.984	0.876	0.0
302398629		841	BZIP domain class transcription factor [	0.988	0.998	0.870	0.0
224142954		823	predicted protein [Populus trichocarpa]	0.968	1.0	0.884	0.0
356515619		845	PREDICTED: homeobox-leucine zipper prote	0.989	0.995	0.861	0.0
356507931		844	PREDICTED: homeobox-leucine zipper prote	0.989	0.996	0.860	0.0

>gi\|219879370\|gb\|ACL51017.1\| class III HD-Zip protein 8 [Citrus trifoliata]	Back alignment and taxonomy information

 Score = 1719 bits (4452), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 825/829 (99%), Positives = 827/829 (99%)

Query: 22  MDNGKYVRYTPEQVEALERLYHECPKPSSMRRQQLIRECPILSNIEPKQIKVWFQNRRCR 81
           MDNGKYVRYTPEQVEALERLYHECPKPSSMRRQQLIRECPILSNIEPKQIKVWFQ+RRCR
Sbjct: 1   MDNGKYVRYTPEQVEALERLYHECPKPSSMRRQQLIRECPILSNIEPKQIKVWFQDRRCR 60

Query: 82  EKQRKEASRLQAVNRKLTAMNKLLMEENDRLQKQVSQLVYENTFFRQQTQNAATLATTDT 141
           EKQRKEASRLQAVNRKLTAMNKLLMEENDRLQKQVSQLVYENTFFRQQTQNAATLATTDT
Sbjct: 61  EKQRKEASRLQAVNRKLTAMNKLLMEENDRLQKQVSQLVYENTFFRQQTQNAATLATTDT 120

Query: 142 SCESVVTSGQHHLTPQQQHQHPPRDASPAGLLSIAEETLTEFLSKATGTAVEWVQMPGMK 201
           SCESV TSGQHHLTPQQQHQHPPRDASPAGLLSIAEETLTEFLSKATGTAVEWVQMPGMK
Sbjct: 121 SCESVATSGQHHLTPQQQHQHPPRDASPAGLLSIAEETLTEFLSKATGTAVEWVQMPGMK 180

Query: 202 PGPDSIGIVAISHGCTGVAARACGLVGLDPTRVAEILKDRPSWYRDCRSVEVVNVLPTGS 261
           PGPDSIGIVAISHGCTGVAARACGLVGLDPTRVAEILKDRPSWYRDCRSVEVVNVLPTGS
Sbjct: 181 PGPDSIGIVAISHGCTGVAARACGLVGLDPTRVAEILKDRPSWYRDCRSVEVVNVLPTGS 240

Query: 262 SGTIELLYMQLYAPTTLAPARDFWLLRYTSVLEDGSLVVCERSLNNTQNGPSMPQAPHFV 321
           SGTIELLYMQLYAPTTLAPARDFWLLRYTSVLEDGSLVVCERSLNNTQNGPSMPQAPHFV
Sbjct: 241 SGTIELLYMQLYAPTTLAPARDFWLLRYTSVLEDGSLVVCERSLNNTQNGPSMPQAPHFV 300

Query: 322 RAEMLPSGYLIRPCEGGGSIIHIVDHMDLEPWSVPEVLRPLYESSTLIAQKTTMAALRHL 381
           RAEMLPSGYLIRPCEGGGSIIHIVDHMDLEPWSVPEVLRPLYESSTLIAQKTTMAALRHL
Sbjct: 301 RAEMLPSGYLIRPCEGGGSIIHIVDHMDLEPWSVPEVLRPLYESSTLIAQKTTMAALRHL 360

Query: 382 RQISQEVSQPSVTGWGRRPAALRALSQRLSRGFNEALNGFTDEGWSMLESDGIDDVTVHV 441
           RQISQEVSQPSVTGWGRRPAALRALSQRLSRGFNEALNGFTDEGWSMLESDGIDDVTVHV
Sbjct: 361 RQISQEVSQPSVTGWGRRPAALRALSQRLSRGFNEALNGFTDEGWSMLESDGIDDVTVHV 420

Query: 442 NSSPSKMMGVQLSYVNGFPSMSNAVLCAKASMLLQDVPPAILLRFLREHRSEWADSSIDA 501
           NSSPSKMMGVQLSYVNGFPSMSNAVLCAKASMLLQDVPPAILLRFLREHRSEWADSSIDA
Sbjct: 421 NSSPSKMMGVQLSYVNGFPSMSNAVLCAKASMLLQDVPPAILLRFLREHRSEWADSSIDA 480

Query: 502 YSAAAVKAGPCSLPVPRAGNFGGQVILPLAHTIEHEEFLEVIKLENMAHYREDMIMPSDI 561
           YSAAAVKAGPCSLPVPRAGNFGGQVILPLAHTIEHEEFLEVIKLENMAHYREDMIMPSDI
Sbjct: 481 YSAAAVKAGPCSLPVPRAGNFGGQVILPLAHTIEHEEFLEVIKLENMAHYREDMIMPSDI 540

Query: 562 FLLQLCSGVDENAVGNCAELVFAPIDASFSDDAPIIPSGFRIIPLDSGKDTPSPNRTLDL 621
           FLLQLCSGVDENAVGNCAELVFAPIDASFSDDAPIIPSGFRIIPLDSGKDTPSPNRTLDL
Sbjct: 541 FLLQLCSGVDENAVGNCAELVFAPIDASFSDDAPIIPSGFRIIPLDSGKDTPSPNRTLDL 600

Query: 622 ASALEVGPTGNKASGDSSTQCGSTKSVITIAFQFAFEMHLQENVASMARQYVRGIIASVQ 681
           ASALEVGPTGNKASGDSSTQCGS KSVITIAFQFAFEMHLQENVASMARQYVRGIIASVQ
Sbjct: 601 ASALEVGPTGNKASGDSSTQCGSKKSVITIAFQFAFEMHLQENVASMARQYVRGIIASVQ 660

Query: 682 RVALALSPSRFGSNAGLRPPPGSPEAHTLARWICQSYRCYLGAELLKCEGNESILKTLWH 741
           RVALALSPSRFGSNAGLRPPPGSPEAHTLARWICQSYRCYLGAELLKCEGNESILKTLWH
Sbjct: 661 RVALALSPSRFGSNAGLRPPPGSPEAHTLARWICQSYRCYLGAELLKCEGNESILKTLWH 720

Query: 742 HSDAVLCCSLKALPVFTFANQAGLDMLETTLVALQDITLEKIFDDSGRKTLCSEFPQIMQ 801
           HSDAVLCCSLKALPVFTFANQAGLDMLETTLVALQDITLEKIFD+SGRKTLCSEFPQIMQ
Sbjct: 721 HSDAVLCCSLKALPVFTFANQAGLDMLETTLVALQDITLEKIFDESGRKTLCSEFPQIMQ 780

Query: 802 QGFMCLQSGICLSSMGRPISYERAVAWKVLNEEENAHCICFMFINWSFV 850
           QGFMCLQSGICLSSMGRPISYERAVAWKVLNEEENAHCICFMFINWSFV
Sbjct: 781 QGFMCLQSGICLSSMGRPISYERAVAWKVLNEEENAHCICFMFINWSFV 829

Source: Citrus trifoliata

Species: Citrus trifoliata

Genus: Citrus

Family: Rutaceae

Order: Sapindales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi\|224092274\|ref\|XP_002309538.1\| predicted protein [Populus trichocarpa] gi\|60327635\|gb\|AAX19057.1\| class III HD-Zip protein 8 [Populus trichocarpa] gi\|222855514\|gb\|EEE93061.1\| predicted protein [Populus trichocarpa]	Back alignment and taxonomy information

>gi\|359476025\|ref\|XP_002283717.2\| PREDICTED: homeobox-leucine zipper protein ATHB-15-like [Vitis vinifera] gi\|296081833\|emb\|CBI20838.3\| unnamed protein product [Vitis vinifera]	Back alignment and taxonomy information

>gi\|383930759\|gb\|AFH56718.1\| class III HD-Zip protein 8 [Prunus persica]	Back alignment and taxonomy information

>gi\|206572107\|gb\|ACI13686.1\| putative HB8 HD-ZipIII [Malus x domestica]	Back alignment and taxonomy information

>gi\|147790308\|emb\|CAN61201.1\| hypothetical protein VITISV_009744 [Vitis vinifera]	Back alignment and taxonomy information

>gi\|302398629\|gb\|ADL36609.1\| BZIP domain class transcription factor [Malus x domestica]	Back alignment and taxonomy information

>gi\|224142954\|ref\|XP_002324794.1\| predicted protein [Populus trichocarpa] gi\|60327633\|gb\|AAX19056.1\| class III HD-Zip protein 7 [Populus trichocarpa] gi\|222866228\|gb\|EEF03359.1\| predicted protein [Populus trichocarpa]	Back alignment and taxonomy information

>gi\|356515619\|ref\|XP_003526496.1\| PREDICTED: homeobox-leucine zipper protein ATHB-8-like [Glycine max]	Back alignment and taxonomy information

>gi\|356507931\|ref\|XP_003522716.1\| PREDICTED: homeobox-leucine zipper protein ATHB-8-like [Glycine max]	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		850
TAIR\|locus:2134088		833	HB-8 "AT4G32880" [Arabidopsis	0.964	0.984	0.787	0.0
TAIR\|locus:2034086		837	ATHB-15 "AT1G52150" [Arabidops	0.964	0.979	0.787	0.0
TAIR\|locus:2061544		852	PHB "AT2G34710" [Arabidopsis t	0.965	0.963	0.653	3.5e-288
TAIR\|locus:2175856		842	REV "AT5G60690" [Arabidopsis t	0.948	0.957	0.638	5.7e-281
TAIR\|locus:2028140		841	PHV "AT1G30490" [Arabidopsis t	0.955	0.965	0.632	4.7e-277
TAIR\|locus:2119048		762	ATML1 "AT4G21750" [Arabidopsis	0.289	0.322	0.258	2.4e-24
TAIR\|locus:2135368		743	PDF2 "AT4G04890" [Arabidopsis	0.277	0.317	0.264	5.4e-24
TAIR\|locus:2207235		721	HDG2 "AT1G05230" [Arabidopsis	0.081	0.095	0.434	7.7e-20
TAIR\|locus:2127008		802	ANL2 "ANTHOCYANINLESS 2" [Arab	0.324	0.344	0.245	4.5e-17
TAIR\|locus:2098866		808	HDG1 "AT3G61150" [Arabidopsis	0.091	0.096	0.388	6.1e-17

TAIR\|locus:2134088 HB-8 "AT4G32880" [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

 Score = 3435 (1214.2 bits), Expect = 0., P = 0.
 Identities = 655/832 (78%), Positives = 734/832 (88%)

Query:    22 MDNGKYVRYTPEQVEALERLYHECPKPSSMRRQQLIRECPILSNIEPKQIKVWFQNRRCR 81
             MDNGKYVRYTPEQVEALERLY++CPKPSSMRRQQLIRECPILSNIEPKQIKVWFQNRRCR
Sbjct:    11 MDNGKYVRYTPEQVEALERLYNDCPKPSSMRRQQLIRECPILSNIEPKQIKVWFQNRRCR 70

Query:    82 EKQRKEASRLQAVNRKLTAMNKLLMEENDRLQKQVSQLVYENTFFRXXXXXXXXXXXXXX 141
             EKQRKEASRLQAVNRKLTAMNKLLMEENDRLQKQVS LVYEN++FR              
Sbjct:    71 EKQRKEASRLQAVNRKLTAMNKLLMEENDRLQKQVSHLVYENSYFRQHPQNQGNLATTDT 130

Query:   142 SCESVVTSGXXXXXXXXXXXXXXRDASPAGLLSIAEETLTEFLSKATGTAVEWVQMPGMK 201
             SCESVVTSG              RDASPAGLLSIA+ETLTEF+SKATGTAVEWVQMPGMK
Sbjct:   131 SCESVVTSGQHHLTPQHQP----RDASPAGLLSIADETLTEFISKATGTAVEWVQMPGMK 186

Query:   202 PGPDSIGIVAISHGCTGVAARACGLVGLDPTRVAEILKDRPSWYRDCRSVEVVNVLPTGS 261
             PGPDSIGIVAISHGCTG+AARACGLVGLDPTRVAEILKD+P W RDCRS+++VNVL T +
Sbjct:   187 PGPDSIGIVAISHGCTGIAARACGLVGLDPTRVAEILKDKPCWLRDCRSLDIVNVLSTAN 246

Query:   262 SGTIELLYMQLYAPTTLAPARDFWLLRYTSVLEDGSLVVCERSLNNTQNGPSMPQAPHFV 321
              GT+EL+YMQLYAPTTLAPARDFW+LRYTSV+EDGSLV+CERSLNNTQNGPSMP +PHFV
Sbjct:   247 GGTLELIYMQLYAPTTLAPARDFWMLRYTSVMEDGSLVICERSLNNTQNGPSMPPSPHFV 306

Query:   322 RAEMLPSGYLIRPCEGGGSIIHIVDHMDLEPWSVPEVLRPLYESSTLIAQKTTMAALRHL 381
             RAE+LPSGYLIRPCEGGGSI+HIVDH DLEPWSVPEVLR LYESSTL+AQ+TTMAALR+L
Sbjct:   307 RAEILPSGYLIRPCEGGGSILHIVDHFDLEPWSVPEVLRSLYESSTLLAQRTTMAALRYL 366

Query:   382 RQISQEVSQPSVTGWGRRPAALRALSQRLSRGFNEALNGFTDEGWSMLESDGIDDVTVHV 441
             RQISQE+SQP+VTGWGRRPAALRALSQRLS+GFNEA+NGF+DEGWS+LESDGIDDVT+ V
Sbjct:   367 RQISQEISQPNVTGWGRRPAALRALSQRLSKGFNEAVNGFSDEGWSILESDGIDDVTLLV 426

Query:   442 NSSPSKMMGVQ-LSYVNGFPSMSNAVLCAKASMLLQDVPPAILLRFLREHRSEWXXXXXX 500
             NSSP+KMM    L + NG+ SM +AVLCAKASMLLQ+VPP+ILLRFLREHR EW      
Sbjct:   427 NSSPTKMMMTSSLPFANGYTSMPSAVLCAKASMLLQNVPPSILLRFLREHRQEWADNSID 486

Query:   501 XXXXXXVKAGPCSLPVPRAGNFGGQVILPLAHTIEHEEFLEVIKLENMAHYREDMIMPSD 560
                   +KAGPCSLP+PR G+FGGQVILPLAHTIE+EEF+EVIKLE++ HY+EDM+MP+D
Sbjct:   487 AYSAAAIKAGPCSLPIPRPGSFGGQVILPLAHTIENEEFMEVIKLESLGHYQEDMMMPAD 546

Query:   561 IFLLQLCSGVDENAVGNCAELVFAPIDASFSDDAPIIPSGFRIIPLDSGKDTPSPNRTLD 620
             IFLLQ+CSGVDENAV +CAEL+FAPIDASFSDDAPIIPSGFRIIPLDS  +  SPNRTLD
Sbjct:   547 IFLLQMCSGVDENAVESCAELIFAPIDASFSDDAPIIPSGFRIIPLDSKSEGLSPNRTLD 606

Query:   621 LASALEVGPTGNKASGDSSTQCGSTKSVITIAFQFAFEMHLQENVASMARQYVRGIIASV 680
             LASAL+VG   ++ +GDS    G++KSV+TIAFQ AFEMH+QENVASMARQYVR +IASV
Sbjct:   607 LASALDVG---SRTAGDSCGSRGNSKSVMTIAFQLAFEMHMQENVASMARQYVRSVIASV 663

Query:   681 QRVALALSPSRFGSNAGLRPPPGSPEAHTLARWICQSYRCYLGAELLKCEGNESILKTLW 740
             QRVALALSPS     +GLRPPP SPEAHTLARWI  SYRCYLG +LLK  G + +LK+LW
Sbjct:   664 QRVALALSPSSH-QLSGLRPPPASPEAHTLARWISHSYRCYLGVDLLKPHGTD-LLKSLW 721

Query:   741 HHSDAVLCCSLKAL-PVFTFANQAGLDMLETTLVALQDITLEKIFDDS-GRKTLCSEFPQ 798
             HH DAV+CCSLKAL PVFTFANQAGLDMLETTLVALQDITL+KIFD++ G+KTL SEFPQ
Sbjct:   722 HHPDAVMCCSLKALSPVFTFANQAGLDMLETTLVALQDITLDKIFDNNNGKKTLSSEFPQ 781

Query:   799 IMQQGFMCLQSGICLSSMGRPISYERAVAWKVLNEEENAHCICFMFINWSFV 850
             IMQQGFMC+  GIC+SSMGR ++YE+AV WKVLN++E+ HCICFMF+NWSF+
Sbjct:   782 IMQQGFMCMDGGICMSSMGRAVTYEKAVGWKVLNDDEDPHCICFMFLNWSFI 833

GO:0003677 "DNA binding" evidence=ISS

GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=IEA;ISS

GO:0005634 "nucleus" evidence=ISM;ISS;IDA

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

GO:0043565 "sequence-specific DNA binding" evidence=IEA

GO:0008284 "positive regulation of cell proliferation" evidence=IMP

GO:0010089 "xylem development" evidence=RCA;IMP

GO:0045597 "positive regulation of cell differentiation" evidence=IMP

GO:0009733 "response to auxin stimulus" evidence=IEP

GO:0010014 "meristem initiation" evidence=RCA;IMP

GO:0010072 "primary shoot apical meristem specification" evidence=RCA;IMP

GO:0010067 "procambium histogenesis" evidence=IEP

GO:0007062 "sister chromatid cohesion" evidence=RCA

GO:0007155 "cell adhesion" evidence=RCA

GO:0009793 "embryo development ending in seed dormancy" evidence=RCA

GO:0009855 "determination of bilateral symmetry" evidence=RCA

GO:0009880 "embryonic pattern specification" evidence=RCA

GO:0009887 "organ morphogenesis" evidence=RCA

GO:0009888 "tissue development" evidence=RCA

GO:0009944 "polarity specification of adaxial/abaxial axis" evidence=RCA

GO:0010090 "trichome morphogenesis" evidence=RCA

GO:0010228 "vegetative to reproductive phase transition of meristem" evidence=RCA

GO:0010431 "seed maturation" evidence=RCA

GO:0010638 "positive regulation of organelle organization" evidence=RCA

GO:0016049 "cell growth" evidence=RCA

GO:0033044 "regulation of chromosome organization" evidence=RCA

GO:0042546 "cell wall biogenesis" evidence=RCA

GO:0044036 "cell wall macromolecule metabolic process" evidence=RCA

GO:0045010 "actin nucleation" evidence=RCA

GO:0045595 "regulation of cell differentiation" evidence=RCA

GO:0048589 "developmental growth" evidence=RCA

GO:0048765 "root hair cell differentiation" evidence=RCA

GO:0051301 "cell division" evidence=RCA

GO:0071555 "cell wall organization" evidence=RCA

TAIR\|locus:2034086 ATHB-15 "AT1G52150" [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

TAIR\|locus:2061544 PHB "AT2G34710" [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

TAIR\|locus:2175856 REV "AT5G60690" [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

TAIR\|locus:2028140 PHV "AT1G30490" [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

TAIR\|locus:2119048 ATML1 "AT4G21750" [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

TAIR\|locus:2135368 PDF2 "AT4G04890" [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

TAIR\|locus:2207235 HDG2 "AT1G05230" [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

TAIR\|locus:2127008 ANL2 "ANTHOCYANINLESS 2" [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

TAIR\|locus:2098866 HDG1 "AT3G61150" [Arabidopsis thaliana (taxid:3702)]	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)
Q39123	ATHB8_ARATH	No assigned EC number	0.8122	0.9741	0.9939	yes	no
A2WLR5	HOX29_ORYSI	No assigned EC number	0.6735	0.9647	0.9523	N/A	no
Q6AST1	HOX32_ORYSJ	No assigned EC number	0.6991	0.9905	0.9802	yes	no
A2XK30	HOX32_ORYSI	No assigned EC number	0.6991	0.9905	0.9802	N/A	no
Q9ZU11	ATB15_ARATH	No assigned EC number	0.8090	0.9705	0.9868	no	no
A2ZMN9	HOX33_ORYSI	No assigned EC number	0.6724	0.9917	0.9859	N/A	no
A2Z8L4	HOX9_ORYSI	No assigned EC number	0.6578	0.9588	0.9702	N/A	no
A2XBL9	HOX10_ORYSI	No assigned EC number	0.6432	0.98	0.9928	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

Your Input:
	HB8	SubName- Full=Class III HD-Zip protein 8; (828 aa)
		(Populus trichocarpa)
Predicted Functional Partners:
		Sorry, there are no predicted associations at the current settings.

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Alignment Graph	Length	Definition	E-value
Query		850
pfam08670		148	pfam08670, MEKHLA, MEKHLA domain	4e-83
cd08875		229	cd08875, START_ArGLABRA2_like, C-terminal lipid-bi	2e-82
pfam01852		205	pfam01852, START, START domain	5e-55
smart00234		205	smart00234, START, in StAR and phosphatidylcholine	8e-38
cd00177		193	cd00177, START, Lipid-binding START domain of mamm	2e-18
pfam00046		57	pfam00046, Homeobox, Homeobox domain	2e-17
cd00086		59	cd00086, homeodomain, Homeodomain; DNA binding dom	3e-17
smart00389		57	smart00389, HOX, Homeodomain	8e-17
COG5576		156	COG5576, COG5576, Homeodomain-containing transcrip	2e-10
pfam00170		64	pfam00170, bZIP_1, bZIP transcription factor	3e-05
smart00338		65	smart00338, BRLZ, basic region leucin zipper	6e-05
cd08869		197	cd08869, START_RhoGAP, C-terminal lipid-binding ST	7e-05
cd08874		205	cd08874, START_STARD9-like, C-terminal START domai	2e-04
cd08868		208	cd08868, START_STARD1_3_like, Cholesterol-binding	4e-04
cd08907		205	cd08907, START_STARD8-like, C-terminal lipid-bindi	0.004

>gnl\|CDD\|219964 pfam08670, MEKHLA, MEKHLA domain	Back alignment and domain information

 Score =  262 bits (671), Expect = 4e-83
 Identities = 87/148 (58%), Positives = 107/148 (72%), Gaps = 2/148 (1%)

Query: 705 PEAHTLARWICQSYRCYLGAELLKCE--GNESILKTLWHHSDAVLCCSLKALPVFTFANQ 762
           PEA TLARW+CQSYR + G +LL       +S+LK LWHH DAVLC SLKA PVF +ANQ
Sbjct: 1   PEALTLARWLCQSYRRHTGRDLLPSADSSGDSLLKALWHHPDAVLCHSLKADPVFNYANQ 60

Query: 763 AGLDMLETTLVALQDITLEKIFDDSGRKTLCSEFPQIMQQGFMCLQSGICLSSMGRPISY 822
           A LD+LETT V LQD+   K  ++SGRK  CSE  ++MQQGF CL SG+ +SSMGR  S 
Sbjct: 61  AALDLLETTWVELQDLPSRKTAEESGRKERCSELAKVMQQGFACLYSGVRISSMGRRFSI 120

Query: 823 ERAVAWKVLNEEENAHCICFMFINWSFV 850
           E+AVAWK+L+E+   H    MF+NWSF+
Sbjct: 121 EQAVAWKLLDEDGAYHGQAAMFVNWSFL 148

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. Length = 148

>gnl\|CDD\|176884 cd08875, START_ArGLABRA2_like, C-terminal lipid-binding START domain of the Arabidopsis homeobox protein GLABRA 2 and related proteins	Back alignment and domain information

>gnl\|CDD\|216740 pfam01852, START, START domain	Back alignment and domain information

>gnl\|CDD\|214575 smart00234, START, in StAR and phosphatidylcholine transfer protein	Back alignment and domain information

>gnl\|CDD\|176851 cd00177, START, Lipid-binding START domain of mammalian STARD1-STARD15 and related proteins	Back alignment and domain information

>gnl\|CDD\|200956 pfam00046, Homeobox, Homeobox domain	Back alignment and domain information

>gnl\|CDD\|238039 cd00086, homeodomain, Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner	Back alignment and domain information

>gnl\|CDD\|197696 smart00389, HOX, Homeodomain	Back alignment and domain information

>gnl\|CDD\|227863 COG5576, COG5576, Homeodomain-containing transcription factor [Transcription]	Back alignment and domain information

>gnl\|CDD\|201054 pfam00170, bZIP_1, bZIP transcription factor	Back alignment and domain information

>gnl\|CDD\|197664 smart00338, BRLZ, basic region leucin zipper	Back alignment and domain information

>gnl\|CDD\|176878 cd08869, START_RhoGAP, C-terminal lipid-binding START domain of mammalian STARD8, -12, -13 and related proteins, which also have an N-terminal Rho GTPase-activating protein (RhoGAP) domain	Back alignment and domain information

>gnl\|CDD\|176883 cd08874, START_STARD9-like, C-terminal START domain of mammalian STARD9, and related domains; lipid binding	Back alignment and domain information

>gnl\|CDD\|176877 cd08868, START_STARD1_3_like, Cholesterol-binding START domain of mammalian STARD1, -3 and related proteins	Back alignment and domain information

>gnl\|CDD\|176916 cd08907, START_STARD8-like, C-terminal lipid-binding START domain of mammalian STARD8 and related proteins, which also have an N-terminal Rho GTPase-activating protein (RhoGAP) domain	Back alignment and domain information

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Alignment Graph	Length	Definition	Probability
Query		850
cd08875		229	START_ArGLABRA2_like C-terminal lipid-binding STAR	100.0
PF08670		148	MEKHLA: MEKHLA domain; InterPro: IPR013978 The MEK	100.0
PF01852		206	START: START domain; InterPro: IPR002913 START (St	99.73
smart00234		206	START in StAR and phosphatidylcholine transfer pro	99.69
KOG0483		198	consensus Transcription factor HEX, contains HOX a	99.65
KOG0842		307	consensus Transcription factor tinman/NKX2-3, cont	99.51
KOG0487		308	consensus Transcription factor Abd-B, contains HOX	99.5
KOG0488		309	consensus Transcription factor BarH and related HO	99.49
KOG0843		197	consensus Transcription factor EMX1 and related HO	99.46
KOG0489		261	consensus Transcription factor zerknullt and relat	99.46
KOG0850		245	consensus Transcription factor DLX and related pro	99.41
KOG0492		246	consensus Transcription factor MSH, contains HOX d	99.4
KOG0494		332	consensus Transcription factor CHX10 and related H	99.36
KOG0848		317	consensus Transcription factor Caudal, contains HO	99.35
KOG0485		268	consensus Transcription factor NKX-5.1/HMX1, conta	99.35
KOG0484		125	consensus Transcription factor PHOX2/ARIX, contain	99.33
PF00046		57	Homeobox: Homeobox domain not present here.; Inter	99.33
KOG0493		342	consensus Transcription factor Engrailed, contains	99.27
KOG2251		228	consensus Homeobox transcription factor [Transcrip	99.23
cd00177		193	START Lipid-binding START domain of mammalian STAR	99.21
KOG0844		408	consensus Transcription factor EVX1, contains HOX	99.14
smart00389		56	HOX Homeodomain. DNA-binding factors that are invo	99.12
KOG0486		351	consensus Transcription factor PTX1, contains HOX	99.11
cd00086		59	homeodomain Homeodomain; DNA binding domains invol	99.11
TIGR01565		58	homeo_ZF_HD homeobox domain, ZF-HD class. This mod	99.09
COG5576		156	Homeodomain-containing transcription factor [Trans	99.09
KOG0491		194	consensus Transcription factor BSH, contains HOX d	99.08
KOG3802		398	consensus Transcription factor OCT-1, contains POU	99.05
cd08868		208	START_STARD1_3_like Cholesterol-binding START doma	99.01
cd08871		222	START_STARD10-like Lipid-binding START domain of m	98.99
cd08867		206	START_STARD4_5_6-like Lipid-binding START domain o	98.96
KOG0847		288	consensus Transcription factor, contains HOX domai	98.94
cd08904		204	START_STARD6-like Lipid-binding START domain of ma	98.93
KOG4577		383	consensus Transcription factor LIM3, contains LIM	98.9
cd08903		208	START_STARD5-like Lipid-binding START domain of ma	98.81
cd08905		209	START_STARD1-like Cholesterol-binding START domain	98.77
KOG0490		235	consensus Transcription factor, contains HOX domai	98.62
PLN00188		719	enhanced disease resistance protein (EDR2); Provis	98.58
cd08869		197	START_RhoGAP C-terminal lipid-binding START domain	98.53
cd08906		209	START_STARD3-like Cholesterol-binding START domain	98.49
cd08909		205	START_STARD13-like C-terminal lipid-binding START	98.49
KOG0849		354	consensus Transcription factor PRD and related pro	98.41
KOG1168		385	consensus Transcription factor ACJ6/BRN-3, contain	98.31
cd08902		202	START_STARD4-like Lipid-binding START domain of ma	98.18
cd08908		204	START_STARD12-like C-terminal lipid-binding START	98.05
KOG0775		304	consensus Transcription factor SIX and related HOX	98.01
cd08874		205	START_STARD9-like C-terminal START domain of mamma	97.95
PF13426		104	PAS_9: PAS domain; PDB: 3ULF_B 3UE6_E 2Z6D_B 2Z6C_	97.85
cd08910		207	START_STARD2-like Lipid-binding START domain of ma	97.8
cd08870		209	START_STARD2_7-like Lipid-binding START domain of	97.71
cd08907		205	START_STARD8-like C-terminal lipid-binding START d	97.67
cd08872		235	START_STARD11-like Ceramide-binding START domain o	97.61
KOG0774		334	consensus Transcription factor PBX and related HOX	97.6
cd08877		215	START_2 Uncharacterized subgroup of the steroidoge	97.5
cd08876		195	START_1 Uncharacterized subgroup of the steroidoge	97.44
cd08873		235	START_STARD14_15-like Lipid-binding START domain o	97.41
cd08911		207	START_STARD7-like Lipid-binding START domain of ma	97.13
PF05920		40	Homeobox_KN: Homeobox KN domain; InterPro: IPR0084	97.12
cd08913		240	START_STARD14-like Lipid-binding START domain of m	97.07
cd08914		236	START_STARD15-like Lipid-binding START domain of m	96.94
KOG0490		235	consensus Transcription factor, contains HOX domai	96.87
KOG2252		558	consensus CCAAT displacement protein and related h	96.78
PF00989		113	PAS: PAS fold; InterPro: IPR013767 PAS domains are	96.77
PF08448		110	PAS_4: PAS fold; InterPro: IPR013656 The PAS fold	96.18
PRK13557		540	histidine kinase; Provisional	95.99
KOG1146		1406	consensus Homeobox protein [General function predi	95.2
cd08871		222	START_STARD10-like Lipid-binding START domain of m	95.15
PRK13559		361	hypothetical protein; Provisional	94.41
cd08869		197	START_RhoGAP C-terminal lipid-binding START domain	93.98
cd08904		204	START_STARD6-like Lipid-binding START domain of ma	93.57
TIGR00229		124	sensory_box PAS domain S-box. The PAS domain was p	93.33
KOG0773		342	consensus Transcription factor MEIS1 and related H	93.31
cd08907		205	START_STARD8-like C-terminal lipid-binding START d	92.75
PRK11091		779	aerobic respiration control sensor protein ArcB; P	92.42
cd08877		215	START_2 Uncharacterized subgroup of the steroidoge	92.17
PRK09413		121	IS2 repressor TnpA; Reviewed	91.9
TIGR02938		494	nifL_nitrog nitrogen fixation negative regulator N	91.78
cd00130		103	PAS PAS domain; PAS motifs appear in archaea, euba	91.35
cd08874		205	START_STARD9-like C-terminal START domain of mamma	90.57
PF11569		56	Homez: Homeodomain leucine-zipper encoding, Homez;	90.52
PF00170		64	bZIP_1: bZIP transcription factor cAMP response el	90.25
cd08864		208	SRPBCC_DUF3074 DUF3074, an uncharacterized ligand-	89.47
TIGR02040		442	PpsR-CrtJ transcriptional regulator PpsR. This mod	89.28
cd00177		193	START Lipid-binding START domain of mammalian STAR	89.11
KOG4005		292	consensus Transcription factor XBP-1 [Transcriptio	88.94
PRK13560		807	hypothetical protein; Provisional	88.8
PRK13558		665	bacterio-opsin activator; Provisional	88.78
KOG2761		219	consensus START domain-containing proteins involve	87.84
PF13188		64	PAS_8: PAS domain; PDB: 2JHE_D 3VOL_A.	87.68
TIGR02040		442	PpsR-CrtJ transcriptional regulator PpsR. This mod	87.57
KOG4196		135	consensus bZIP transcription factor MafK [Transcri	86.07
cd08868		208	START_STARD1_3_like Cholesterol-binding START doma	85.78
cd08909		205	START_STARD13-like C-terminal lipid-binding START	85.13
smart00338		65	BRLZ basic region leucin zipper.	83.76
cd08906		209	START_STARD3-like Cholesterol-binding START domain	82.93
cd08908		204	START_STARD12-like C-terminal lipid-binding START	82.9
smart00234		206	START in StAR and phosphatidylcholine transfer pro	82.25
PRK11359		799	cyclic-di-GMP phosphodiesterase; Provisional	82.22
PRK11073		348	glnL nitrogen regulation protein NR(II); Provision	81.43
PRK09776		1092	putative diguanylate cyclase; Provisional	80.54

>cd08875 START_ArGLABRA2_like C-terminal lipid-binding START domain of the Arabidopsis homeobox protein GLABRA 2 and related proteins	Back alignment and domain information

Probab=100.00  E-value=1.4e-75  Score=606.02  Aligned_cols=211  Identities=36%  Similarity=0.618  Sum_probs=194.7

Q ss_pred             chhhHHHHHHHHHHHHHHhcCCCcceEeCCCCCC---CCCccceeec------cCCCccceecceeEEeeChhhHHHHhc
Q 003071          169 PAGLLSIAEETLTEFLSKATGTAVEWVQMPGMKP---GPDSIGIVAI------SHGCTGVAARACGLVGLDPTRVAEILK  239 (850)
Q Consensus       169 ~~~l~~lA~~am~El~~la~~~~plWi~~~g~~~---g~~~~~~~~~------~~~~~~EASR~~glV~m~~~~LVe~lm  239 (850)
                      ++++++||++||+||++||++++|+|++++|+|+   ++|.++..++      ..||.+||||+||+|+||+.+|||+||
T Consensus         1 k~~~~~lA~~am~Ell~~a~~~~plWi~~~~~~~~~l~~dey~~~f~~~~~~~~~~~~~eASR~~glV~m~~~~lVe~lm   80 (229)
T cd08875           1 KSGLLELAEEAMDELLKLAQGGEPLWIKSPGMKPEILNPDEYERMFPRHGGSKPGGFTTEASRACGLVMMNAIKLVEILM   80 (229)
T ss_pred             ChHHHHHHHHHHHHHHHHhccCCCCceecCCCCccccCHHHHhhcccCcCCCCCCCCeEEEEeeeEEEecCHHHHHHHHh
Confidence            3589999999999999999999999999999877   7777754332      235999999999999999999999999


Q ss_pred             CchhhhhhCCcc----eEEeeccCCC----cchHHHHHHHhhccccccCCceeeEEeeceeeCCCcEEEEEeecCCCCCC
Q 003071          240 DRPSWYRDCRSV----EVVNVLPTGS----SGTIELLYMQLYAPTTLAPARDFWLLRYTSVLEDGSLVVCERSLNNTQNG  311 (850)
Q Consensus       240 D~~~W~~~f~~~----~~l~~~~~g~----~GalqLm~aE~~v~SPLVp~Re~~fLRyckq~~~G~waVvDvSld~~~~~  311 (850)
                      |+++|.++||++    +|+.++++|+    ||+|||||+|||+||||||+|||||||||||++||+|||||||+|+.+. 
T Consensus        81 D~~kW~~~Fp~iv~~a~tl~vistg~~g~~~G~lqlmyael~~pSpLVp~Re~~fLRyc~~l~dG~w~VvdvSld~~~~-  159 (229)
T cd08875          81 DVNKWSELFPGIVSKAKTLQVISTGNGGNRNGTLQLMYAELQVPSPLVPTREFYFLRYCKQLEDGLWAVVDVSIDGVQT-  159 (229)
T ss_pred             ChhhhhhhhhhhcceeeEEEEeeCCCCCCCCceehhhhhhcccCcccccCCeEEEEEEEEEeCCCeEEEEEEeeccccc-
Confidence            999999999876    9999999996    7899999999999999999999999999999999999999999998763 


Q ss_pred             CCCCCCCCccceeecCcceEEeeCCCCceEEEEEEeeeccCCCccccchhhhchhHHHHHHHHHHHH-HHHh
Q 003071          312 PSMPQAPHFVRAEMLPSGYLIRPCEGGGSIIHIVDHMDLEPWSVPEVLRPLYESSTLIAQKTTMAAL-RHLR  382 (850)
Q Consensus       312 ~~~~~~~~~~r~rrlPSGclIq~~~nG~skVtwVeH~e~d~~~vh~lyRpl~~Sg~afgar~w~~aL-r~~e  382 (850)
                        .++.++|+||||+|||||||||+|||||||||||+|||++.+|.+||++++||+||||+||+++| ||||
T Consensus       160 --~p~~~~~~r~~~~PSGcLIq~~~nG~SkVtwVeH~e~d~~~~~~l~~~l~~sg~AfgA~rw~a~lqRqce  229 (229)
T cd08875         160 --APPPASFVRCRRLPSGCLIQDMPNGYSKVTWVEHVEVDEKPVHLLYRYLVSSGLAFGATRWVATLQRQCE  229 (229)
T ss_pred             --CCCCCCccEEEEecCcEEEEECCCCceEEEEEEEEeccCCcccccchhhhhhhHHHHHHHHHHHHHHhcC
Confidence              33455789999999999999999999999999999999999999999999999999999999999 7997

This subfamily includes the steroidogenic acute regulatory protein (StAR)-related lipid transfer (START) domains of the Arabidopsis homeobox protein GLABRA 2 and related proteins. The START domain family belongs to the SRPBCC (START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain superfamily of proteins that bind hydrophobic ligands. SRPBCC domains have a deep hydrophobic ligand-binding pocket. Most proteins in this subgroup contain an N-terminal homeobox DNA-binding domain, some contain a leucine zipper. ArGLABRA2 plays a role in the differentiation of hairless epidermal cells of the Arabidopsis root. It acts in a cell-position-dependent manner to suppress root hair formation in those cells.

>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

>PF01852 START: START domain; InterPro: IPR002913 START (StAR-related lipid-transfer) is a lipid-binding domain in StAR, HD-ZIP and signalling proteins []	Back alignment and domain information

>smart00234 START in StAR and phosphatidylcholine transfer protein	Back alignment and domain information

>KOG0483 consensus Transcription factor HEX, contains HOX and HALZ domains [Transcription]	Back alignment and domain information

>KOG0842 consensus Transcription factor tinman/NKX2-3, contains HOX domain [Transcription]	Back alignment and domain information

>KOG0487 consensus Transcription factor Abd-B, contains HOX domain [Transcription]	Back alignment and domain information

>KOG0488 consensus Transcription factor BarH and related HOX domain proteins [General function prediction only]	Back alignment and domain information

>KOG0843 consensus Transcription factor EMX1 and related HOX domain proteins [Transcription]	Back alignment and domain information

>KOG0489 consensus Transcription factor zerknullt and related HOX domain proteins [General function prediction only]	Back alignment and domain information

>KOG0850 consensus Transcription factor DLX and related proteins with LIM Zn-binding and HOX domains [Transcription]	Back alignment and domain information

>KOG0492 consensus Transcription factor MSH, contains HOX domain [General function prediction only]	Back alignment and domain information

>KOG0494 consensus Transcription factor CHX10 and related HOX domain proteins [General function prediction only]	Back alignment and domain information

>KOG0848 consensus Transcription factor Caudal, contains HOX domain [Transcription]	Back alignment and domain information

>KOG0485 consensus Transcription factor NKX-5	Back alignment and domain information

>KOG0484 consensus Transcription factor PHOX2/ARIX, contains HOX domain [Transcription]	Back alignment and domain information

>PF00046 Homeobox: Homeobox domain not present here	Back alignment and domain information

>KOG0493 consensus Transcription factor Engrailed, contains HOX domain [General function prediction only]	Back alignment and domain information

>KOG2251 consensus Homeobox transcription factor [Transcription]	Back alignment and domain information

>cd00177 START Lipid-binding START domain of mammalian STARD1-STARD15 and related proteins	Back alignment and domain information

>KOG0844 consensus Transcription factor EVX1, contains HOX domain [Transcription]	Back alignment and domain information

>smart00389 HOX Homeodomain	Back alignment and domain information

>KOG0486 consensus Transcription factor PTX1, contains HOX domain [Transcription]	Back alignment and domain information

>cd00086 homeodomain Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner	Back alignment and domain information

>TIGR01565 homeo_ZF_HD homeobox domain, ZF-HD class	Back alignment and domain information

>COG5576 Homeodomain-containing transcription factor [Transcription]	Back alignment and domain information

>KOG0491 consensus Transcription factor BSH, contains HOX domain [General function prediction only]	Back alignment and domain information

>KOG3802 consensus Transcription factor OCT-1, contains POU and HOX domains [Transcription]	Back alignment and domain information

>cd08868 START_STARD1_3_like Cholesterol-binding START domain of mammalian STARD1, -3 and related proteins	Back alignment and domain information

>cd08871 START_STARD10-like Lipid-binding START domain of mammalian STARD10 and related proteins	Back alignment and domain information

>cd08867 START_STARD4_5_6-like Lipid-binding START domain of mammalian STARD4, -5, -6, and related proteins	Back alignment and domain information

>KOG0847 consensus Transcription factor, contains HOX domain [Transcription]	Back alignment and domain information

>cd08904 START_STARD6-like Lipid-binding START domain of mammalian STARD6 and related proteins	Back alignment and domain information

>KOG4577 consensus Transcription factor LIM3, contains LIM and HOX domains [Transcription]	Back alignment and domain information

>cd08903 START_STARD5-like Lipid-binding START domain of mammalian STARD5 and related proteins	Back alignment and domain information

>cd08905 START_STARD1-like Cholesterol-binding START domain of mammalian STARD1 and related proteins	Back alignment and domain information

>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]	Back alignment and domain information

>PLN00188 enhanced disease resistance protein (EDR2); Provisional	Back alignment and domain information

>cd08869 START_RhoGAP C-terminal lipid-binding START domain of mammalian STARD8, -12, -13 and related proteins, which also have an N-terminal Rho GTPase-activating protein (RhoGAP) domain	Back alignment and domain information

>cd08906 START_STARD3-like Cholesterol-binding START domain of mammalian STARD3 and related proteins	Back alignment and domain information

>cd08909 START_STARD13-like C-terminal lipid-binding START domain of mammalian STARD13 and related proteins, which also have an N-terminal Rho GTPase-activating protein (RhoGAP) domain	Back alignment and domain information

>KOG0849 consensus Transcription factor PRD and related proteins, contain PAX and HOX domains [Transcription]	Back alignment and domain information

>KOG1168 consensus Transcription factor ACJ6/BRN-3, contains POU and HOX domains [Transcription]	Back alignment and domain information

>cd08902 START_STARD4-like Lipid-binding START domain of mammalian STARD4 and related proteins	Back alignment and domain information

>cd08908 START_STARD12-like C-terminal lipid-binding START domain of mammalian STARD12 and related proteins, which also have an N-terminal Rho GTPase-activating protein (RhoGAP) domain	Back alignment and domain information

>KOG0775 consensus Transcription factor SIX and related HOX domain proteins [Transcription]	Back alignment and domain information

>cd08874 START_STARD9-like C-terminal START domain of mammalian STARD9, and related domains; lipid binding	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

>cd08910 START_STARD2-like Lipid-binding START domain of mammalian STARD2 and related proteins	Back alignment and domain information

>cd08870 START_STARD2_7-like Lipid-binding START domain of mammalian STARD2, -7, and related proteins	Back alignment and domain information

>cd08907 START_STARD8-like C-terminal lipid-binding START domain of mammalian STARD8 and related proteins, which also have an N-terminal Rho GTPase-activating protein (RhoGAP) domain	Back alignment and domain information

>cd08872 START_STARD11-like Ceramide-binding START domain of mammalian STARD11 and related domains	Back alignment and domain information

>KOG0774 consensus Transcription factor PBX and related HOX domain proteins [Transcription]	Back alignment and domain information

>cd08877 START_2 Uncharacterized subgroup of the steroidogenic acute regulatory protein (StAR)-related lipid transfer (START) domain family	Back alignment and domain information

>cd08876 START_1 Uncharacterized subgroup of the steroidogenic acute regulatory protein (StAR)-related lipid transfer (START) domain family	Back alignment and domain information

>cd08873 START_STARD14_15-like Lipid-binding START domain of mammalian STARDT14, -15, and related proteins	Back alignment and domain information

>cd08911 START_STARD7-like Lipid-binding START domain of mammalian STARD7 and related proteins	Back alignment and domain information

>PF05920 Homeobox_KN: Homeobox KN domain; InterPro: IPR008422 This entry represents a homeobox transcription factor KN domain conserved from fungi to human and plants []	Back alignment and domain information

>cd08913 START_STARD14-like Lipid-binding START domain of mammalian STARDT14 and related proteins	Back alignment and domain information

>cd08914 START_STARD15-like Lipid-binding START domain of mammalian STARD15 and related proteins	Back alignment and domain information

>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]	Back alignment and domain information

>KOG2252 consensus CCAAT displacement protein and related homeoproteins [Transcription]	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

>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

>PRK13557 histidine kinase; Provisional	Back alignment and domain information

>KOG1146 consensus Homeobox protein [General function prediction only]	Back alignment and domain information

>cd08871 START_STARD10-like Lipid-binding START domain of mammalian STARD10 and related proteins	Back alignment and domain information

>PRK13559 hypothetical protein; Provisional	Back alignment and domain information

>cd08869 START_RhoGAP C-terminal lipid-binding START domain of mammalian STARD8, -12, -13 and related proteins, which also have an N-terminal Rho GTPase-activating protein (RhoGAP) domain	Back alignment and domain information

>cd08904 START_STARD6-like Lipid-binding START domain of mammalian STARD6 and related proteins	Back alignment and domain information

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

>KOG0773 consensus Transcription factor MEIS1 and related HOX domain proteins [Transcription]	Back alignment and domain information

>cd08907 START_STARD8-like C-terminal lipid-binding START domain of mammalian STARD8 and related proteins, which also have an N-terminal Rho GTPase-activating protein (RhoGAP) domain	Back alignment and domain information

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

>cd08877 START_2 Uncharacterized subgroup of the steroidogenic acute regulatory protein (StAR)-related lipid transfer (START) domain family	Back alignment and domain information

>PRK09413 IS2 repressor TnpA; Reviewed	Back alignment and domain information

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

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

>cd08874 START_STARD9-like C-terminal START domain of mammalian STARD9, and related domains; lipid binding	Back alignment and domain information

>PF11569 Homez: Homeodomain leucine-zipper encoding, Homez; PDB: 2YS9_A	Back alignment and domain information

>PF00170 bZIP_1: bZIP transcription factor cAMP response element binding (CREB) protein signature fos transforming protein signature jun transcription factor signature; InterPro: IPR011616 The basic-leucine zipper (bZIP) transcription factors [, ] of eukaryotic are proteins that contain a basic region mediating sequence-specific DNA-binding followed by a leucine zipper region (see IPR002158 from INTERPRO) required for dimerization

Back alignment and domain information

>cd08864 SRPBCC_DUF3074 DUF3074, an uncharacterized ligand-binding domain of the SRPBCC domain superfamily	Back alignment and domain information

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

>cd00177 START Lipid-binding START domain of mammalian STARD1-STARD15 and related proteins	Back alignment and domain information

>KOG4005 consensus Transcription factor XBP-1 [Transcription]	Back alignment and domain information

>PRK13560 hypothetical protein; Provisional	Back alignment and domain information

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

>KOG2761 consensus START domain-containing proteins involved in steroidogenesis/phosphatidylcholine transfer [Lipid transport and metabolism]	Back alignment and domain information

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

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

>KOG4196 consensus bZIP transcription factor MafK [Transcription]	Back alignment and domain information

>cd08868 START_STARD1_3_like Cholesterol-binding START domain of mammalian STARD1, -3 and related proteins	Back alignment and domain information

>cd08909 START_STARD13-like C-terminal lipid-binding START domain of mammalian STARD13 and related proteins, which also have an N-terminal Rho GTPase-activating protein (RhoGAP) domain	Back alignment and domain information

>smart00338 BRLZ basic region leucin zipper	Back alignment and domain information

>cd08906 START_STARD3-like Cholesterol-binding START domain of mammalian STARD3 and related proteins	Back alignment and domain information

>cd08908 START_STARD12-like C-terminal lipid-binding START domain of mammalian STARD12 and related proteins, which also have an N-terminal Rho GTPase-activating protein (RhoGAP) domain	Back alignment and domain information

>smart00234 START in StAR and phosphatidylcholine transfer protein	Back alignment and domain information

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

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

>PRK09776 putative diguanylate cyclase; 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		850
1bw5_A		66	The Nmr Solution Structure Of The Homeodomain Of Th		1e-05
2dmu_A		70	Solution Structure Of The Homeobox Domain Of Homeob		2e-04
2m0c_A		75	Solution Nmr Structure Of Homeobox Domain Of Human		8e-04

>pdb|1BW5|A Chain A, The Nmr Solution Structure Of The Homeodomain Of The Rat Insulin Gene Enhancer Protein Isl-1, 50 Structures Length = 66

Back alignment and structure

Iteration: 1
 Score = 48.9 bits (115), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 18/53 (33%), Positives = 35/53 (66%), Gaps = 4/53 (7%)
Query: 33 EQVEALERLYHECPKPSSMRRQQLIRECPILSNIEPKQIKVWFQNRRCREKQR 85
          +Q+  L   Y   P+P ++ ++QL+     ++ + P+ I+VWFQN+RC++K+R
Sbjct: 13 KQLHTLRTCYAANPRPDALMKEQLVE----MTGLSPRVIRVWFQNKRCKDKKR 61

PyMOL of 1bw5

>pdb|2DMU|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox Protein Goosecoid Length = 70

Back alignment and structure

>pdb|2M0C|A Chain A, Solution Nmr Structure Of Homeobox Domain Of Human Alx4, Northeast Structural Genomics Consortium (Nesg) Target Hr4490c Length = 75

Back alignment and structure

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Alignment Graph	Length	Definition	E-value
Query		850
2pso_A		237	STAR-related lipid transfer protein 13; alpha and	7e-26
2r55_A		231	STAR-related lipid transfer protein 5; alpha and b	8e-25
1jss_A		224	Stard4, cholesterol-regulated start protein 4; sta	7e-23
3fo5_A		258	Thioesterase, adipose associated, isoform BFIT2; o	2e-17
3qsz_A		189	STAR-related lipid transfer protein; structural ge	5e-17
1akh_A		61	Protein (mating-type protein A-1); complex (TWO DN	1e-16
3p0l_A		221	Steroidogenic acute regulatory protein, mitochond;	4e-14
2dn0_A		76	Zinc fingers and homeoboxes protein 3; triple home	1e-13
2da1_A		70	Alpha-fetoprotein enhancer binding protein; homeob	6e-13
1em2_A		229	MLN64 protein; beta barrel, lipid binding protein;	7e-13
2ecb_A		89	Zinc fingers and homeoboxes protein 1; homeobox do	8e-13
2da5_A		75	Zinc fingers and homeoboxes protein 3; homeobox do	2e-12
2da3_A		80	Alpha-fetoprotein enhancer binding protein; homeob	3e-12
2dmp_A		89	Zinc fingers and homeoboxes protein 2; homeobox do	4e-12
2xsd_C		164	POU domain, class 3, transcription factor 1; trans	1e-11
1e3o_C		160	Octamer-binding transcription factor 1; transcript	1e-11
3nau_A		66	Zinc fingers and homeoboxes protein 2; ZHX2, corep	1e-11
2d5v_A		164	Hepatocyte nuclear factor 6; transcription factor,	2e-11
3d1n_I		151	POU domain, class 6, transcription factor 1; prote	3e-11
1au7_A		146	Protein PIT-1, GHF-1; complex (DNA-binding protein	5e-11
1bw5_A		66	ISL-1HD, insulin gene enhancer protein ISL-1; DNA-	2e-10
1ln1_A		214	PC-TP, phosphatidylcholine transfer protein; start	4e-10
2cuf_A		95	FLJ21616 protein; homeobox domain, hepatocyte tran	6e-10
2cqx_A		72	LAG1 longevity assurance homolog 5; homeodomain, D	6e-10
1wi3_A		71	DNA-binding protein SATB2; homeodomain, helix-turn	1e-09
2da2_A		70	Alpha-fetoprotein enhancer binding protein; homeob	4e-09
3l1p_A		155	POU domain, class 5, transcription factor 1; POU,	1e-08
3nar_A		96	ZHX1, zinc fingers and homeoboxes protein 1; corep	6e-08
2hi3_A		73	Homeodomain-only protein; transcription; NMR {Mus	1e-07
2l9r_A		69	Homeobox protein NKX-3.1; structural genomics, nor	1e-07
2djn_A		70	Homeobox protein DLX-5; structural genomics, NPPSF	2e-07
2hdd_A		61	Protein (engrailed homeodomain Q50K); DNA binding,	3e-07
2dmq_A		80	LIM/homeobox protein LHX9; homeobox domain, three	5e-07
1vt4_I		1221	APAF-1 related killer DARK; drosophila apoptosome,	5e-07
1vt4_I		1221	APAF-1 related killer DARK; drosophila apoptosome,	2e-06
1x2m_A		64	LAG1 longevity assurance homolog 6; homeobox domai	6e-07
2k40_A		67	Homeobox expressed in ES cells 1; thermostable hom	1e-06
2vi6_A		62	Homeobox protein nanog; homeodomain, DNA-binding,	1e-06
1nk2_P		77	Homeobox protein VND; homeodomain, DNA-binding pro	1e-06
2ecc_A		76	Homeobox and leucine zipper protein homez; homeobo	2e-06
2kt0_A		84	Nanog, homeobox protein nanog; homeodomain, struct	2e-06
1lfb_A		99	Liver transcription factor (LFB1); transcription r	2e-06
3a01_A		93	Homeodomain-containing protein; homeodomain, prote	2e-06
1jgg_A		60	Segmentation protein EVEN-skipped; homeodomain, pr	2e-06
2cra_A		70	Homeobox protein HOX-B13; DNA-binding, transcripti	2e-06
3a03_A		56	T-cell leukemia homeobox protein 2; homeodomain, d	2e-06
2cue_A		80	Paired box protein PAX6; homeobox domain, transcri	3e-06
1ic8_A		194	Hepatocyte nuclear factor 1-alpha; transcription r	3e-06
1ftt_A		68	TTF-1 HD, thyroid transcription factor 1 homeodoma	3e-06
2l7z_A		73	Homeobox protein HOX-A13; gene regulation; NMR {Ho	3e-06
2dmt_A		80	Homeobox protein BARH-like 1; homeobox domain, thr	4e-06
2h8r_A		221	Hepatocyte nuclear factor 1-beta; trasncription fa	6e-06
1zq3_P		68	PRD-4, homeotic bicoid protein; protein-DNA comple	6e-06
1ig7_A		58	Homeotic protein MSX-1; helix-turn-helix, transcri	6e-06
1yz8_P		68	Pituitary homeobox 2; DNA binding protein, transcr	7e-06
2e1o_A		70	Homeobox protein PRH; DNA binding protein, structu	8e-06
2dmu_A		70	Homeobox protein goosecoid; homeobox domain, three	9e-06
1ci6_A		63	Transcription factor ATF-4; BZIP; 2.60A {Homo sapi	1e-05
3rkq_A		58	Homeobox protein NKX-2.5; helix-turn-helix, DNA bi	1e-05
3a02_A		60	Homeobox protein aristaless; homeodomain, developm	1e-05
2dms_A		80	Homeobox protein OTX2; homeobox domain, three heli	2e-05
1uhs_A		72	HOP, homeodomain only protein; structural genomics	2e-05
1t2k_D		61	Cyclic-AMP-dependent transcription factor ATF-2; p	2e-05
1puf_A		77	HOX-1.7, homeobox protein HOX-A9; homeodomian, pro	3e-05
1ahd_P		68	Antennapedia protein mutant; DNA binding protein/D	3e-05
1fjl_A		81	Paired protein; DNA-binding protein, paired BOX, t	3e-05
2h1k_A		63	IPF-1, pancreatic and duodenal homeobox 1, homeodo	4e-05
2wt7_A		63	Proto-oncogene protein C-FOS; transcription, trans	5e-05
1jnm_A		62	Proto-oncogene C-JUN; BZIP, protein-DNA complex, t	6e-05
3a5t_A		107	Transcription factor MAFG; protein-DNA complex, BZ	7e-05
2wt7_B		90	Transcription factor MAFB; transcription, transcri	9e-05
1b8i_A		81	Ultrabithorax, protein (ultrabithorax homeotic pro	1e-04
1b72_A		97	Protein (homeobox protein HOX-B1); homeodomain, DN	1e-04
1gu4_A		78	CAAT/enhancer binding protein beta; transcription/	1e-04
3lvg_D		190	LCB, clathrin light chain B; SELF assembly, coated	2e-04
1hjb_A		87	Ccaat/enhancer binding protein beta; transcription	2e-04
1gd2_E		70	Transcription factor PAP1; basic leucine zipper, p	2e-04
2r5y_A		88	Homeotic protein sex combs reduced; homeodomain; H	2e-04
2da4_A		80	Hypothetical protein DKFZP686K21156; homeobox doma	4e-04

>2pso_A STAR-related lipid transfer protein 13; alpha and beta protein, lipid binding, helix swapping, struc genomics, structural genomics consortium, SGC; 2.80A {Homo sapiens} SCOP: d.129.3.2 Length = 237	Back alignment and structure

 Score =  106 bits (265), Expect = 7e-26
 Identities = 48/231 (20%), Positives = 78/231 (33%), Gaps = 19/231 (8%)

Query: 151 QHHLTPQQQHQHPPRDASPAGLLSIAEETLTEFLSKATGTAVEWVQMPGMKPGPDSIGIV 210
                  +       + S A   +     +     +A      WV           +   
Sbjct: 9   SGVDLGTENLYFQSMEESGATFHTYLNHLIQGLQKEAKEKFKGWVTCSSTDNT--DLAFK 66

Query: 211 AISHGCTGVAARACGLVGLDPTRVAE-ILKDRPSWYRDCRSVEVVNVLPTGSSGTIELLY 269
            +  G      +A   V   P+ V   +L++R  W  D    +VV  L        E+  
Sbjct: 67  KVGDGNPLKLWKASVEVEAPPSVVLNRVLRERHLWDEDFVQWKVVETL----DRQTEIYQ 122

Query: 270 MQLYAPTTLAPARDFWLLRYTSV-LEDGSLVVCERSLNNTQNGPSMPQAPHFVRAEMLPS 328
             L +     P+RDF +LR     L  G   +   S+ +        Q    VRA ++ S
Sbjct: 123 YVLNSMAPH-PSRDFVVLRTWKTDLPKGMCTLVSLSVEH-----EEAQLLGGVRAVVMDS 176

Query: 329 GYLIRPCEGGGSIIHIVDHMDLEPWSVPEVLRPLYESSTLIAQKTTMAALR 379
            YLI PC  G S +  +  +DL+    PE     +    L A +  +A +R
Sbjct: 177 QYLIEPCGSGKSRLTHICRIDLKGH-SPEWYSKGF--GHLCAAE--VARIR 222

PyMOL of 2pso

>2r55_A STAR-related lipid transfer protein 5; alpha and beta protein, cholesterol binding, structural GENO structural genomics consortium, SGC; 2.50A {Homo sapiens} Length = 231	Back alignment and structure

>1jss_A Stard4, cholesterol-regulated start protein 4; start domain, structural genomics, PSI, protein structure initiative; 2.20A {Mus musculus} SCOP: d.129.3.2 Length = 224	Back alignment and structure

>3fo5_A Thioesterase, adipose associated, isoform BFIT2; orthogonal bundle, consortium, lipid transport; HET: 1PE TCE; 2.00A {Homo sapiens} Length = 258	Back alignment and structure

>3qsz_A STAR-related lipid transfer protein; structural genomics, PSI-biology; 2.39A {Xanthomonas axonopodis PV} Length = 189	Back alignment and structure

>1akh_A Protein (mating-type protein A-1); complex (TWO DNA-binding proteins/DNA), complex, DNA- binding protein, DNA; HET: DNA; 2.50A {Saccharomyces cerevisiae} SCOP: a.4.1.1 PDB: 1f43_A 1yrn_A* Length = 61	Back alignment and structure

>3p0l_A Steroidogenic acute regulatory protein, mitochond; structural genomics consortium, SGC, start domain, cholester transport, cholesterol; 3.40A {Homo sapiens} Length = 221	Back alignment and structure

>2dn0_A Zinc fingers and homeoboxes protein 3; triple homeobox 1 protein, KIAA0395, TIX1, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 76	Back alignment and structure

>2da1_A Alpha-fetoprotein enhancer binding protein; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics; NMR {Homo sapiens} Length = 70	Back alignment and structure

>1em2_A MLN64 protein; beta barrel, lipid binding protein; HET: TAR; 2.20A {Homo sapiens} SCOP: d.129.3.2 Length = 229	Back alignment and structure

>2ecb_A Zinc fingers and homeoboxes protein 1; homeobox domain, transcription factor, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: a.4.1.1 Length = 89	Back alignment and structure

>2da5_A Zinc fingers and homeoboxes protein 3; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 75	Back alignment and structure

>2da3_A Alpha-fetoprotein enhancer binding protein; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics; NMR {Homo sapiens} Length = 80	Back alignment and structure

>2dmp_A Zinc fingers and homeoboxes protein 2; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 89	Back alignment and structure

>2xsd_C POU domain, class 3, transcription factor 1; transcription-DNA complex, SOX; 2.05A {Mus musculus} Length = 164	Back alignment and structure

>1e3o_C Octamer-binding transcription factor 1; transcription factor, POU domain, dimer, DNA binding; 1.9A {Homo sapiens} SCOP: a.4.1.1 a.35.1.1 PDB: 1gt0_C 1hf0_A* 1cqt_A* 1o4x_A 1oct_C* 1pou_A 1pog_A 1hdp_A Length = 160	Back alignment and structure

>3nau_A Zinc fingers and homeoboxes protein 2; ZHX2, corepressor, homeodomain, domain swapping, structural oxford protein production facility, OPPF; 2.70A {Homo sapiens} Length = 66	Back alignment and structure

>2d5v_A Hepatocyte nuclear factor 6; transcription factor, transcription-DNA complex; 2.00A {Rattus norvegicus} PDB: 1s7e_A Length = 164	Back alignment and structure

>3d1n_I POU domain, class 6, transcription factor 1; protein-DNA complex, helix-turn-helix (HTH), DNA-binding, homeobox, nucleus, transcription regulation; 2.51A {Homo sapiens} Length = 151	Back alignment and structure

>1au7_A Protein PIT-1, GHF-1; complex (DNA-binding protein/DNA), pituitary, CPHD, POU domain, transcription factor, transcription/DNA complex; HET: DNA; 2.30A {Rattus norvegicus} SCOP: a.4.1.1 a.35.1.1 Length = 146	Back alignment and structure

>1bw5_A ISL-1HD, insulin gene enhancer protein ISL-1; DNA-binding protein, homeodomain, LIM domain; NMR {Rattus norvegicus} SCOP: a.4.1.1 Length = 66	Back alignment and structure

>1ln1_A PC-TP, phosphatidylcholine transfer protein; start domain, lipid binding protein; HET: DLP; 2.40A {Homo sapiens} SCOP: d.129.3.2 PDB: 1ln2_A* 1ln3_A* Length = 214	Back alignment and structure

>2cuf_A FLJ21616 protein; homeobox domain, hepatocyte transcription factor, structural genomics, loop insertion, NPPSFA; NMR {Homo sapiens} SCOP: a.4.1.1 Length = 95	Back alignment and structure

>2cqx_A LAG1 longevity assurance homolog 5; homeodomain, DNA binding domain, transcription, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: a.4.1.1 Length = 72	Back alignment and structure

>1wi3_A DNA-binding protein SATB2; homeodomain, helix-turn-helix, riken structural genomics/proteomics initiative, RSGI, structural genomics; NMR {Homo sapiens} SCOP: a.4.1.1 Length = 71	Back alignment and structure

>2da2_A Alpha-fetoprotein enhancer binding protein; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics; NMR {Homo sapiens} Length = 70	Back alignment and structure

>3l1p_A POU domain, class 5, transcription factor 1; POU, transcription factor DNA complex, pore, stem cells; HET: DNA; 2.80A {Mus musculus} PDB: 1ocp_A Length = 155	Back alignment and structure

>3nar_A ZHX1, zinc fingers and homeoboxes protein 1; corepressor, homeodomain, structural genomics, oxford production facility, OPPF, transcription; 2.60A {Homo sapiens} Length = 96	Back alignment and structure

>2hi3_A Homeodomain-only protein; transcription; NMR {Mus musculus} SCOP: a.4.1.1 Length = 73	Back alignment and structure

>2l9r_A Homeobox protein NKX-3.1; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative; NMR {Homo sapiens} Length = 69	Back alignment and structure

>2djn_A Homeobox protein DLX-5; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 70	Back alignment and structure

>2hdd_A Protein (engrailed homeodomain Q50K); DNA binding, complex (DNA binding protein/DNA), transcription/DNA complex; HET: DNA; 1.90A {Drosophila melanogaster} SCOP: a.4.1.1 PDB: 1hdd_C* 2jwt_A 3hdd_A 1p7j_A* 1p7i_A* 2hos_A 2hot_A 1du0_A* 1ztr_A 1enh_A 2p81_A Length = 61	Back alignment and structure

>2dmq_A LIM/homeobox protein LHX9; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 80	Back alignment and structure

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221	Back alignment and structure

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221	Back alignment and structure

>1x2m_A LAG1 longevity assurance homolog 6; homeobox domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: a.4.1.1 Length = 64	Back alignment and structure

>2k40_A Homeobox expressed in ES cells 1; thermostable homeodomain variant, DNA binding protein, developmental protein, disease mutation, DNA-binding; NMR {Homo sapiens} Length = 67	Back alignment and structure

>2vi6_A Homeobox protein nanog; homeodomain, DNA-binding, transcription, transcription facto developmental protein, transcription regulation, NUC homeobox; 2.6A {Mus musculus} Length = 62	Back alignment and structure

>1nk2_P Homeobox protein VND; homeodomain, DNA-binding protein, embryonic development, complex (homeodomain/DNA); HET: DNA; NMR {Drosophila melanogaster} SCOP: a.4.1.1 PDB: 1nk3_P* 1vnd_A 1qry_A Length = 77	Back alignment and structure

>2ecc_A Homeobox and leucine zipper protein homez; homeobox domain, transcription factor, leucine zipper- containing factor, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: a.4.1.1 Length = 76	Back alignment and structure

>2kt0_A Nanog, homeobox protein nanog; homeodomain, structural genomics, protein structure initiative, PSI, center for eukaryotic structural genomics; NMR {Homo sapiens} Length = 84	Back alignment and structure

>1lfb_A Liver transcription factor (LFB1); transcription regulation; 2.80A {Rattus norvegicus} SCOP: a.4.1.1 PDB: 2lfb_A Length = 99	Back alignment and structure

>3a01_A Homeodomain-containing protein; homeodomain, protein-DNA complex, DNA-binding, homeobox, NUC developmental protein; 2.70A {Drosophila melanogaster} Length = 93	Back alignment and structure

>1jgg_A Segmentation protein EVEN-skipped; homeodomain, protein-DNA complex, transcription/DNA complex; 2.00A {Drosophila melanogaster} SCOP: a.4.1.1 Length = 60	Back alignment and structure

>2cra_A Homeobox protein HOX-B13; DNA-binding, transcription regulation, helix-turn-helix, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: a.4.1.1 Length = 70	Back alignment and structure

>3a03_A T-cell leukemia homeobox protein 2; homeodomain, developmental protein, DNA-binding, N gene regulation; 1.54A {Homo sapiens} Length = 56	Back alignment and structure

>2cue_A Paired box protein PAX6; homeobox domain, transcription factor, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: a.4.1.1 Length = 80	Back alignment and structure

>1ic8_A Hepatocyte nuclear factor 1-alpha; transcription regulation, DNA-binding, POU domain, diabetes, disease mutation, MODY3, transcription/DNA comple; 2.60A {Homo sapiens} SCOP: a.4.1.1 a.35.1.1 Length = 194	Back alignment and structure

>1ftt_A TTF-1 HD, thyroid transcription factor 1 homeodomain; DNA binding protein; NMR {Rattus norvegicus} SCOP: a.4.1.1 Length = 68	Back alignment and structure

>2l7z_A Homeobox protein HOX-A13; gene regulation; NMR {Homo sapiens} PDB: 2ld5_A* Length = 73	Back alignment and structure

>2dmt_A Homeobox protein BARH-like 1; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 80	Back alignment and structure

>2h8r_A Hepatocyte nuclear factor 1-beta; trasncription factor, POU, homeo, protein-DNA, human disease; 3.20A {Homo sapiens} Length = 221	Back alignment and structure

>1zq3_P PRD-4, homeotic bicoid protein; protein-DNA complex, double helix, helix-turn-helix; NMR {Drosophila melanogaster} SCOP: a.4.1.1 Length = 68	Back alignment and structure

>1ig7_A Homeotic protein MSX-1; helix-turn-helix, transcription/DNA complex; 2.20A {Mus musculus} SCOP: a.4.1.1 Length = 58	Back alignment and structure

>1yz8_P Pituitary homeobox 2; DNA binding protein, transcription/DNA complex; NMR {Homo sapiens} SCOP: a.4.1.1 PDB: 2l7f_P 2lkx_A* 2l7m_P Length = 68	Back alignment and structure

>2e1o_A Homeobox protein PRH; DNA binding protein, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: a.4.1.1 Length = 70	Back alignment and structure

>2dmu_A Homeobox protein goosecoid; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 70	Back alignment and structure

>1ci6_A Transcription factor ATF-4; BZIP; 2.60A {Homo sapiens} SCOP: h.1.3.1 Length = 63	Back alignment and structure

>3rkq_A Homeobox protein NKX-2.5; helix-turn-helix, DNA binding, nucleus, transcription-DNA CO; 1.70A {Homo sapiens} Length = 58	Back alignment and structure

>3a02_A Homeobox protein aristaless; homeodomain, developmental protein, DNA-binding, N gene regulation; 1.00A {Drosophila melanogaster} PDB: 3lnq_A 3cmy_A Length = 60	Back alignment and structure

>2dms_A Homeobox protein OTX2; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics, NPPSFA; NMR {Mus musculus} Length = 80	Back alignment and structure

>1uhs_A HOP, homeodomain only protein; structural genomics, cardiac development, riken structural genomics/proteomics initiative, RSGI, transcription; NMR {Mus musculus} SCOP: a.4.1.1 Length = 72	Back alignment and structure

>1t2k_D Cyclic-AMP-dependent transcription factor ATF-2; protein DNA complex, transcription/DNA complex; 3.00A {Homo sapiens} SCOP: h.1.3.1 Length = 61	Back alignment and structure

>1puf_A HOX-1.7, homeobox protein HOX-A9; homeodomian, protein-DNA complex, HOX hexapeptide, TALE homeodomain, homeodomain interaction; 1.90A {Mus musculus} SCOP: a.4.1.1 PDB: 1san_A Length = 77	Back alignment and structure

>1ahd_P Antennapedia protein mutant; DNA binding protein/DNA; HET: DNA; NMR {Drosophila melanogaster} SCOP: a.4.1.1 PDB: 2hoa_A 1hom_A 1ftz_A Length = 68	Back alignment and structure

>1fjl_A Paired protein; DNA-binding protein, paired BOX, transcription regulation; HET: DNA; 2.00A {Drosophila melanogaster} SCOP: a.4.1.1 PDB: 3a01_B Length = 81	Back alignment and structure

>2h1k_A IPF-1, pancreatic and duodenal homeobox 1, homeodomain; protein-DNA complex, transcription/DNA complex; 2.42A {Mesocricetus auratus} Length = 63	Back alignment and structure

>2wt7_A Proto-oncogene protein C-FOS; transcription, transcription regulation, nucleus, activator, repressor, DNA-binding, phosphoprotein, differentiation; 2.30A {Mus musculus} PDB: 1fos_E* 1a02_F* 1s9k_D Length = 63	Back alignment and structure

>1jnm_A Proto-oncogene C-JUN; BZIP, protein-DNA complex, transcription/DNA complex; 2.20A {Homo sapiens} SCOP: h.1.3.1 PDB: 1fos_F 2h7h_A 1t2k_C 1a02_J* 1s9k_E 1jun_A Length = 62	Back alignment and structure

>3a5t_A Transcription factor MAFG; protein-DNA complex, BZIP factor, acetylation, DNA-binding, isopeptide bond, nucleus; 2.80A {Mus musculus} Length = 107	Back alignment and structure

>2wt7_B Transcription factor MAFB; transcription, transcription regulation, nucleus, activator, repressor, DNA-binding, phosphoprotein, differentiation; 2.30A {Mus musculus} PDB: 2wty_A* 1k1v_A Length = 90	Back alignment and structure

>1b8i_A Ultrabithorax, protein (ultrabithorax homeotic protein IV); DNA binding, homeodomain, homeotic proteins, development, specificity; HET: DNA; 2.40A {Drosophila melanogaster} SCOP: a.4.1.1 PDB: 9ant_A* Length = 81	Back alignment and structure

>1b72_A Protein (homeobox protein HOX-B1); homeodomain, DNA, complex, DNA-binding protein, protein/DNA complex; HET: DNA; 2.35A {Homo sapiens} SCOP: a.4.1.1 Length = 97	Back alignment and structure

>1gu4_A CAAT/enhancer binding protein beta; transcription/DNA, protein-DNA complex, transcription factor, BZIP, C/EBP; 1.80A {Homo sapiens} SCOP: h.1.3.1 PDB: 1gtw_A 1gu5_A 1h88_A 1h8a_A 1io4_A 2e43_A* 2e42_A* 1h89_A 1ci6_B 1nwq_A Length = 78	Back alignment and structure

>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic vesicle, membrane, Ca structural protein; 7.94A {Bos taurus} Length = 190	Back alignment and structure

>1hjb_A Ccaat/enhancer binding protein beta; transcription/DNA, protein-DNA complex; HET: DNA; 3.0A {Homo sapiens} SCOP: h.1.3.1 Length = 87	Back alignment and structure

>1gd2_E Transcription factor PAP1; basic leucine zipper, protein-DNA complex, transcription/DNA complex; HET: DNA; 2.00A {Schizosaccharomyces pombe} SCOP: h.1.3.1 Length = 70	Back alignment and structure

>2r5y_A Homeotic protein sex combs reduced; homeodomain; HET: DNA; 2.60A {Drosophila melanogaster} PDB: 2r5z_A* Length = 88	Back alignment and structure

>2da4_A Hypothetical protein DKFZP686K21156; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 80	Back alignment and structure

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Alignment Graph	Length	Definition	Probability
Query		850
2r55_A		231	STAR-related lipid transfer protein 5; alpha and b	99.8
2dmt_A		80	Homeobox protein BARH-like 1; homeobox domain, thr	99.63
2da3_A		80	Alpha-fetoprotein enhancer binding protein; homeob	99.61
1wh5_A		80	ZF-HD homeobox family protein; structural genomics	99.6
1wh7_A		80	ZF-HD homeobox family protein; homeobox domain, st	99.58
2cue_A		80	Paired box protein PAX6; homeobox domain, transcri	99.58
1nk2_P		77	Homeobox protein VND; homeodomain, DNA-binding pro	99.57
2e1o_A		70	Homeobox protein PRH; DNA binding protein, structu	99.55
2dmq_A		80	LIM/homeobox protein LHX9; homeobox domain, three	99.55
2kt0_A		84	Nanog, homeobox protein nanog; homeodomain, struct	99.55
2dmu_A		70	Homeobox protein goosecoid; homeobox domain, three	99.55
2cra_A		70	Homeobox protein HOX-B13; DNA-binding, transcripti	99.55
2dms_A		80	Homeobox protein OTX2; homeobox domain, three heli	99.55
3a01_A		93	Homeodomain-containing protein; homeodomain, prote	99.55
2da2_A		70	Alpha-fetoprotein enhancer binding protein; homeob	99.54
2h1k_A		63	IPF-1, pancreatic and duodenal homeobox 1, homeodo	99.54
1ig7_A		58	Homeotic protein MSX-1; helix-turn-helix, transcri	99.54
1puf_A		77	HOX-1.7, homeobox protein HOX-A9; homeodomian, pro	99.53
1fjl_A		81	Paired protein; DNA-binding protein, paired BOX, t	99.53
2djn_A		70	Homeobox protein DLX-5; structural genomics, NPPSF	99.53
2da1_A		70	Alpha-fetoprotein enhancer binding protein; homeob	99.53
2hdd_A		61	Protein (engrailed homeodomain Q50K); DNA binding,	99.52
2vi6_A		62	Homeobox protein nanog; homeodomain, DNA-binding,	99.52
1ahd_P		68	Antennapedia protein mutant; DNA binding protein/D	99.52
1zq3_P		68	PRD-4, homeotic bicoid protein; protein-DNA comple	99.51
1uhs_A		72	HOP, homeodomain only protein; structural genomics	99.51
1jgg_A		60	Segmentation protein EVEN-skipped; homeodomain, pr	99.51
1ftt_A		68	TTF-1 HD, thyroid transcription factor 1 homeodoma	99.51
2l7z_A		73	Homeobox protein HOX-A13; gene regulation; NMR {Ho	99.5
1yz8_P		68	Pituitary homeobox 2; DNA binding protein, transcr	99.5
3a02_A		60	Homeobox protein aristaless; homeodomain, developm	99.5
2da5_A		75	Zinc fingers and homeoboxes protein 3; homeobox do	99.5
2hi3_A		73	Homeodomain-only protein; transcription; NMR {Mus	99.5
2da4_A		80	Hypothetical protein DKFZP686K21156; homeobox doma	99.49
3rkq_A		58	Homeobox protein NKX-2.5; helix-turn-helix, DNA bi	99.49
1b8i_A		81	Ultrabithorax, protein (ultrabithorax homeotic pro	99.48
3a03_A		56	T-cell leukemia homeobox protein 2; homeodomain, d	99.48
2r5y_A		88	Homeotic protein sex combs reduced; homeodomain; H	99.48
1akh_A		61	Protein (mating-type protein A-1); complex (TWO DN	99.48
1bw5_A		66	ISL-1HD, insulin gene enhancer protein ISL-1; DNA-	99.48
2ecc_A		76	Homeobox and leucine zipper protein homez; homeobo	99.48
2k40_A		67	Homeobox expressed in ES cells 1; thermostable hom	99.48
2m0c_A		75	Homeobox protein aristaless-like 4; structural gen	99.48
2cuf_A		95	FLJ21616 protein; homeobox domain, hepatocyte tran	99.47
3nar_A		96	ZHX1, zinc fingers and homeoboxes protein 1; corep	99.47
1b72_A		97	Protein (homeobox protein HOX-B1); homeodomain, DN	99.45
1x2n_A		73	Homeobox protein pknox1; homeobox domain, structur	99.45
2ly9_A		74	Zinc fingers and homeoboxes protein 1; structural	99.44
2ecb_A		89	Zinc fingers and homeoboxes protein 1; homeobox do	99.44
2dmp_A		89	Zinc fingers and homeoboxes protein 2; homeobox do	99.43
2dn0_A		76	Zinc fingers and homeoboxes protein 3; triple home	99.43
1k61_A		60	Mating-type protein alpha-2; protein-DNA complex,	99.41
2cqx_A		72	LAG1 longevity assurance homolog 5; homeodomain, D	99.41
1puf_B		73	PRE-B-cell leukemia transcription factor-1; homeod	99.4
1b72_B		87	Protein (PBX1); homeodomain, DNA, complex, DNA-bin	99.4
2dmn_A		83	Homeobox protein TGIF2LX; TGFB-induced factor 2-li	99.39
1au7_A		146	Protein PIT-1, GHF-1; complex (DNA-binding protein	99.39
1du6_A		64	PBX1, homeobox protein PBX1; homeodomain, gene reg	99.39
1e3o_C		160	Octamer-binding transcription factor 1; transcript	99.38
1mnm_C		87	Protein (MAT alpha-2 transcriptional repressor); t	99.37
1wi3_A		71	DNA-binding protein SATB2; homeodomain, helix-turn	99.37
3nau_A		66	Zinc fingers and homeoboxes protein 2; ZHX2, corep	99.36
1le8_B		83	Mating-type protein alpha-2; matalpha2, isothermal	99.36
2l9r_A		69	Homeobox protein NKX-3.1; structural genomics, nor	99.35
3d1n_I		151	POU domain, class 6, transcription factor 1; prote	99.35
2da6_A		102	Hepatocyte nuclear factor 1-beta; homeobox domain,	99.35
1lfb_A		99	Liver transcription factor (LFB1); transcription r	99.35
2xsd_C		164	POU domain, class 3, transcription factor 1; trans	99.34
2pso_A		237	STAR-related lipid transfer protein 13; alpha and	99.33
2e19_A		64	Transcription factor 8; homeobox domain, structura	99.32
1em2_A		229	MLN64 protein; beta barrel, lipid binding protein;	99.3
3l1p_A		155	POU domain, class 5, transcription factor 1; POU,	99.3
3p0l_A		221	Steroidogenic acute regulatory protein, mitochond;	99.3
1x2m_A		64	LAG1 longevity assurance homolog 6; homeobox domai	99.29
2d5v_A		164	Hepatocyte nuclear factor 6; transcription factor,	99.25
3k2a_A		67	Homeobox protein MEIS2; homeobox domain, DNA-bindi	99.19
1ic8_A		194	Hepatocyte nuclear factor 1-alpha; transcription r	99.12
2lk2_A		89	Homeobox protein TGIF1; NESG, structural genomics,	98.95
1ln1_A		214	PC-TP, phosphatidylcholine transfer protein; start	98.95
2h8r_A		221	Hepatocyte nuclear factor 1-beta; trasncription fa	98.91
3fo5_A		258	Thioesterase, adipose associated, isoform BFIT2; o	98.88
2da7_A		71	Zinc finger homeobox protein 1B; homeobox domain,	98.87
1jss_A		224	Stard4, cholesterol-regulated start protein 4; sta	98.86
1mh3_A		421	Maltose binding-A1 homeodomain protein chimera; MA	98.77
2e3n_A		255	Lipid-transfer protein CERT; ceramide transfer, li	98.39
3qsz_A		189	STAR-related lipid transfer protein; structural ge	98.38
2nzz_A		37	Penetratin conjugated GAS (374-394) peptide; confo	98.22
3t50_A		128	Blue-light-activated histidine kinase; PAS superfa	97.52
4eet_B		115	Phototropin-2; LOV, blue light photoreceptor, sign	97.5
3lyx_A		124	Sensory BOX/ggdef domain protein; structural genom	97.45
3ue6_A		166	Aureochrome1; PAS/LOV domain, FMN-binding blue-lig	97.44
1n9l_A		109	PHOT-LOV1, putative blue light receptor; phototrop	97.31
4hia_A		176	LOV protein; PAS, HTH, signaling protein; HET: FMN	97.26
2gj3_A		120	Nitrogen fixation regulatory protein; PAS domain,	97.22
3luq_A		114	Sensor protein; PAS, histidine, kinase, PSI, MCSG,	97.16
3p7n_A		258	Sensor histidine kinase; LOV domain, light-activat	97.16
2z6d_A		130	Phototropin-2; PAS-fold, LOV-fold, alternative spl	97.12
3sw1_A		162	Sensory box protein; light-oxygen-voltage, LOV, PA	97.08
1byw_A		110	Protein (human ERG potassium channel); PAS domain,	97.05
3d72_A		149	Vivid PAS protein VVD; circadian, photoreceptor, b	96.94
3f1p_A		117	Endothelial PAS domain-containing protein 1; PAS d	96.92
3mqq_A		120	Transcriptional regulator, LUXR family; PAS domain	96.85
2pr5_A		132	Blue-light photoreceptor; light-oxygen-voltage, LO	96.7
1d06_A		130	Nitrogen fixation regulatory protein FIXL; oxygen	96.64
2r78_A		117	Sensor protein; sensory box sensor histidine kinas	96.6
3kx0_X		185	Uncharacterized protein RV1364C/MT1410; PAS domain	96.47
3k3c_A		158	Protein RV1364C/MT1410; sensor, PAS, signal transd	96.47
2v0u_A		146	NPH1-1, LOV2; kinase, transferase, ATP-binding, se	96.45
2l0w_A		138	Potassium voltage-gated channel, subfamily H (EAG	96.4
2r55_A		231	STAR-related lipid transfer protein 5; alpha and b	96.39
3f1p_B		121	ARYL hydrocarbon receptor nuclear translocator; PA	96.34
2wkq_A		332	NPH1-1, RAS-related C3 botulinum toxin substrate 1	96.27
3olo_A		118	Two-component sensor histidine kinase; structural	96.12
2vv6_A		119	FIXL, sensor protein FIXL; signaling protein, tran	95.93
3ewk_A		227	Sensor protein; PAS domain, alpha/beta fold, kinas	95.92
3b33_A		115	Sensor protein; structural genomics, PAS domain, n	95.88
3mxq_A		152	Sensor protein; PSI2, MCSG, structural genomics, p	95.8
3mjq_A		126	Uncharacterized protein; NESG, structural genomics	95.78
3ewk_A		227	Sensor protein; PAS domain, alpha/beta fold, kinas	95.73
3eeh_A		125	Putative light and redox sensing histidine kinase;	95.72
2kdk_A		121	ARYL hydrocarbon receptor nuclear translocator-LI	95.47
3fc7_A		125	HTR-like protein, sensor protein; APC87712.1, HTR-	95.45
3nja_A		125	Probable ggdef family protein; structural genomics	95.33
3mfx_A		129	Sensory BOX/ggdef family protein; alpha-beta prote	95.12
3icy_A		118	Sensor protein; sensory box histidine kinase/respo	94.97
3bwl_A		126	Sensor protein; structural genomics, APC87707.1, P	94.52
2pso_A		237	STAR-related lipid transfer protein 13; alpha and	94.48
1v9y_A		167	Heme PAS sensor protein; signaling protein; HET: H	94.32
1ll8_A		114	PAS kinase; PAS domain, ligand binding, ligand scr	94.22
3fo5_A		258	Thioesterase, adipose associated, isoform BFIT2; o	93.88
1jss_A		224	Stard4, cholesterol-regulated start protein 4; sta	93.51
3qsz_A		189	STAR-related lipid transfer protein; structural ge	93.17
3a0s_A		96	Sensor protein; PAS-fold, kinase, phosphoprotein,	92.9
3p0l_A		221	Steroidogenic acute regulatory protein, mitochond;	92.67
4hi4_A		121	Aerotaxis transducer AER2; PAS domain, diatomic GA	92.65
1ln1_A		214	PC-TP, phosphatidylcholine transfer protein; start	92.09
3h9w_A		115	Diguanylate cyclase with PAS/PAC sensor; alpha-bet	91.5
3fg8_A		118	Uncharacterized protein RHA05790; PAS domain, stru	91.32
2d4r_A		147	Hypothetical protein TTHA0849; start domain, struc	90.56
3vol_A		233	Aerotaxis transducer AER2; heme, oxygen sensor pro	90.43
1hjb_A		87	Ccaat/enhancer binding protein beta; transcription	90.29
1gu4_A		78	CAAT/enhancer binding protein beta; transcription/	88.47
1ci6_A		63	Transcription factor ATF-4; BZIP; 2.60A {Homo sapi	87.98
2w0n_A		118	Sensor protein DCUS; signal transduction, two-comp	86.51
1em2_A		229	MLN64 protein; beta barrel, lipid binding protein;	86.51
2vlg_A		111	Sporulation kinase A; histidine kinase, two-compon	86.13
2jhe_A		190	Transcription regulator TYRR; aromatic hydrocarbon	86.04
2wt7_A		63	Proto-oncogene protein C-FOS; transcription, trans	85.78
4f3l_A		361	Mclock, circadian locomoter output cycles protein	85.69
1t2k_D		61	Cyclic-AMP-dependent transcription factor ATF-2; p	85.68
4eho_A		635	Bacteriophytochrome, PAS/PAC sensor; photoreceptor	83.64
1t2k_D		61	Cyclic-AMP-dependent transcription factor ATF-2; p	81.51

>2r55_A STAR-related lipid transfer protein 5; alpha and beta protein, cholesterol binding, structural GENO structural genomics consortium, SGC; 2.50A {Homo sapiens}	Back alignment and structure

Probab=99.80  E-value=6.3e-19  Score=181.78  Aligned_cols=199  Identities=21%  Similarity=0.251  Sum_probs=160.3

Q ss_pred             CchhhHHHHHHHHHHHHHHhcCCCcceEeCCCCCCCCCccceeec-cCCCccceecceeEEeeChhhHHHHhcC-----c
Q 003071          168 SPAGLLSIAEETLTEFLSKATGTAVEWVQMPGMKPGPDSIGIVAI-SHGCTGVAARACGLVGLDPTRVAEILKD-----R  241 (850)
Q Consensus       168 ~~~~l~~lA~~am~El~~la~~~~plWi~~~g~~~g~~~~~~~~~-~~~~~~EASR~~glV~m~~~~LVe~lmD-----~  241 (850)
                      .++.++++|++||+|++++++.+ ..|..... +.|   +.++-. ..+..+.+.|..|+|.+++.+|++.||+     +
T Consensus        20 ~~~~y~~~a~~~~~~~l~~~~~~-~~W~~~~~-~~g---v~v~~~~~~~~~~~~~k~~~~v~~~~~~v~~~l~~~d~~~r   94 (231)
T 2r55_A           20 FQSMAAQMSEAVAEKMLQYRRDT-AGWKICRE-GNG---VSVSWRPSVEFPGNLYRGEGIVYGTLEEVWDCVKPAVGGLR   94 (231)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHCC-SSCEEEEC-CSS---EEEEEEECSSSSSEEEEEEEEESSCHHHHHHHHCC--CCSH
T ss_pred             hHHHHHHHHHHHHHHHHHHhcCC-CCCEEEEe-CCC---EEEEEEccCCCCCcEEEEEEEECCCHHHHHHHHHhhCcchh
Confidence            36689999999999999999754 68987532 222   222221 1244568899999999999999999977     8


Q ss_pred             hhhhhhCCcceEEeeccCCCcchHHHHHHHhh--ccccccCCceeeEEeeceeeCCCcEEEEEeecCCCCCCCCCCCCCC
Q 003071          242 PSWYRDCRSVEVVNVLPTGSSGTIELLYMQLY--APTTLAPARDFWLLRYTSVLEDGSLVVCERSLNNTQNGPSMPQAPH  319 (850)
Q Consensus       242 ~~W~~~f~~~~~l~~~~~g~~GalqLm~aE~~--v~SPLVp~Re~~fLRyckq~~~G~waVvDvSld~~~~~~~~~~~~~  319 (850)
                      .+|-..|...++|..+...  .  .++| ++.  .++++|++|||.++||+++.++|.|+|+.+|++.    +..|+...
T Consensus        95 ~~Wd~~~~~~~vle~i~~~--~--~i~~-~~~~~~~~~~v~~RDfv~~r~~~~~~~g~~vi~~~Sv~~----~~~P~~~~  165 (231)
T 2r55_A           95 VKWDENVTGFEIIQSITDT--L--CVSR-TSTPSAAMKLISPRDFVDLVLVKRYEDGTISSNATHVEH----PLCPPKPG  165 (231)
T ss_dssp             HHHCTTCSEEEEEEECSSS--E--EEEE-EECCCBTTTTBCCEEEEEEEEEEECTTSCEEEEEEECCC----TTSCCCTT
T ss_pred             hhhccccceeEEEEEcCCC--E--EEEE-EEeccccCCccCCCeEEEEEEEEEcCCCEEEEEEEeccC----CCCCCCCC
Confidence            9999999999999988632  1  1222 222  3456899999999999999999999999999984    33556678


Q ss_pred             ccceeecCcceEEeeCC--CCceEEEEEEeeeccCCCccccchhhhchhHHHHHHHHHHHHH-HHhhh
Q 003071          320 FVRAEMLPSGYLIRPCE--GGGSIIHIVDHMDLEPWSVPEVLRPLYESSTLIAQKTTMAALR-HLRQI  384 (850)
Q Consensus       320 ~~r~rrlPSGclIq~~~--nG~skVtwVeH~e~d~~~vh~lyRpl~~Sg~afgar~w~~aLr-~~e~l  384 (850)
                      ++|++.++|||+|++++  +|.|+|||+.|+|..-+ +|   +.++++.+..+...+++.|| +|+.+
T Consensus       166 ~VR~~~~~~g~~i~p~~~~~~~t~vt~~~~~Dp~G~-iP---~~lvn~~~~~~~~~~~~~Lr~~~~~~  229 (231)
T 2r55_A          166 FVRGFNHPCGCFCEPLPGEPTKTNLVTFFHTDLSGY-LP---QNVVDSFFPRSMTRFYANLQKAVKQF  229 (231)
T ss_dssp             CEEEEECSEEEEEEECC--CCCEEEEEEECEECCSS-CC---HHHHHHHHHHHHHHHHHHHHHHHHGG
T ss_pred             CEEEEEEeeEEEEEEeCCCCCcEEEEEEEEeCCCCC-cc---HHHHHHHHhHhHHHHHHHHHHHHHHh
Confidence            99999999999999998  78999999999998865 66   58899999999999999996 88765

PyMOL of 2r55

>2dmt_A Homeobox protein BARH-like 1; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens}	Back alignment and structure

>2da3_A Alpha-fetoprotein enhancer binding protein; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics; NMR {Homo sapiens}	Back alignment and structure

>1wh5_A ZF-HD homeobox family protein; structural genomics, zinc finger homeobox family protein, riken structural genomics/proteomics initiative; NMR {Arabidopsis thaliana} SCOP: a.4.1.1	Back alignment and structure

>1wh7_A ZF-HD homeobox family protein; homeobox domain, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Arabidopsis thaliana} SCOP: a.4.1.1	Back alignment and structure

>2cue_A Paired box protein PAX6; homeobox domain, transcription factor, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: a.4.1.1	Back alignment and structure

>1nk2_P Homeobox protein VND; homeodomain, DNA-binding protein, embryonic development, complex (homeodomain/DNA); HET: DNA; NMR {Drosophila melanogaster} SCOP: a.4.1.1 PDB: 1nk3_P* 1vnd_A 1qry_A	Back alignment and structure

>2e1o_A Homeobox protein PRH; DNA binding protein, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: a.4.1.1	Back alignment and structure

>2dmq_A LIM/homeobox protein LHX9; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens}	Back alignment and structure

>2kt0_A Nanog, homeobox protein nanog; homeodomain, structural genomics, protein structure initiative, PSI, center for eukaryotic structural genomics; NMR {Homo sapiens}	Back alignment and structure

>2dmu_A Homeobox protein goosecoid; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens}	Back alignment and structure

>2cra_A Homeobox protein HOX-B13; DNA-binding, transcription regulation, helix-turn-helix, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: a.4.1.1	Back alignment and structure

>2dms_A Homeobox protein OTX2; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics, NPPSFA; NMR {Mus musculus}	Back alignment and structure

>3a01_A Homeodomain-containing protein; homeodomain, protein-DNA complex, DNA-binding, homeobox, NUC developmental protein; 2.70A {Drosophila melanogaster}	Back alignment and structure

>2da2_A Alpha-fetoprotein enhancer binding protein; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics; NMR {Homo sapiens}	Back alignment and structure

>2h1k_A IPF-1, pancreatic and duodenal homeobox 1, homeodomain; protein-DNA complex, transcription/DNA complex; 2.42A {Mesocricetus auratus}	Back alignment and structure

>1ig7_A Homeotic protein MSX-1; helix-turn-helix, transcription/DNA complex; 2.20A {Mus musculus} SCOP: a.4.1.1	Back alignment and structure

>1puf_A HOX-1.7, homeobox protein HOX-A9; homeodomian, protein-DNA complex, HOX hexapeptide, TALE homeodomain, homeodomain interaction; 1.90A {Mus musculus} SCOP: a.4.1.1 PDB: 1san_A	Back alignment and structure

>1fjl_A Paired protein; DNA-binding protein, paired BOX, transcription regulation; HET: DNA; 2.00A {Drosophila melanogaster} SCOP: a.4.1.1 PDB: 3a01_B	Back alignment and structure

>2djn_A Homeobox protein DLX-5; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}	Back alignment and structure

>2da1_A Alpha-fetoprotein enhancer binding protein; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics; NMR {Homo sapiens}	Back alignment and structure

>2hdd_A Protein (engrailed homeodomain Q50K); DNA binding, complex (DNA binding protein/DNA), transcription/DNA complex; HET: DNA; 1.90A {Drosophila melanogaster} SCOP: a.4.1.1 PDB: 1hdd_C* 2jwt_A 3hdd_A 1p7j_A* 1p7i_A* 2hos_A 2hot_A 1du0_A* 1ztr_A 1enh_A 2p81_A	Back alignment and structure

>2vi6_A Homeobox protein nanog; homeodomain, DNA-binding, transcription, transcription facto developmental protein, transcription regulation, NUC homeobox; 2.6A {Mus musculus}	Back alignment and structure

>1ahd_P Antennapedia protein mutant; DNA binding protein/DNA; HET: DNA; NMR {Drosophila melanogaster} SCOP: a.4.1.1 PDB: 2hoa_A 1hom_A 1ftz_A	Back alignment and structure

>1zq3_P PRD-4, homeotic bicoid protein; protein-DNA complex, double helix, helix-turn-helix; NMR {Drosophila melanogaster} SCOP: a.4.1.1	Back alignment and structure

>1uhs_A HOP, homeodomain only protein; structural genomics, cardiac development, riken structural genomics/proteomics initiative, RSGI, transcription; NMR {Mus musculus} SCOP: a.4.1.1	Back alignment and structure

>1jgg_A Segmentation protein EVEN-skipped; homeodomain, protein-DNA complex, transcription/DNA complex; 2.00A {Drosophila melanogaster} SCOP: a.4.1.1	Back alignment and structure

>1ftt_A TTF-1 HD, thyroid transcription factor 1 homeodomain; DNA binding protein; NMR {Rattus norvegicus} SCOP: a.4.1.1	Back alignment and structure

>2l7z_A Homeobox protein HOX-A13; gene regulation; NMR {Homo sapiens} PDB: 2ld5_A*	Back alignment and structure

>1yz8_P Pituitary homeobox 2; DNA binding protein, transcription/DNA complex; NMR {Homo sapiens} SCOP: a.4.1.1 PDB: 2l7f_P 2lkx_A* 2l7m_P	Back alignment and structure

>3a02_A Homeobox protein aristaless; homeodomain, developmental protein, DNA-binding, N gene regulation; 1.00A {Drosophila melanogaster} PDB: 3lnq_A 3cmy_A	Back alignment and structure

>2da5_A Zinc fingers and homeoboxes protein 3; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens}	Back alignment and structure

>2hi3_A Homeodomain-only protein; transcription; NMR {Mus musculus} SCOP: a.4.1.1	Back alignment and structure

>2da4_A Hypothetical protein DKFZP686K21156; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens}	Back alignment and structure

>3rkq_A Homeobox protein NKX-2.5; helix-turn-helix, DNA binding, nucleus, transcription-DNA CO; 1.70A {Homo sapiens}	Back alignment and structure

>1b8i_A Ultrabithorax, protein (ultrabithorax homeotic protein IV); DNA binding, homeodomain, homeotic proteins, development, specificity; HET: DNA; 2.40A {Drosophila melanogaster} SCOP: a.4.1.1 PDB: 9ant_A*	Back alignment and structure

>3a03_A T-cell leukemia homeobox protein 2; homeodomain, developmental protein, DNA-binding, N gene regulation; 1.54A {Homo sapiens}	Back alignment and structure

>2r5y_A Homeotic protein sex combs reduced; homeodomain; HET: DNA; 2.60A {Drosophila melanogaster} PDB: 2r5z_A*	Back alignment and structure

>1akh_A Protein (mating-type protein A-1); complex (TWO DNA-binding proteins/DNA), complex, DNA- binding protein, DNA; HET: DNA; 2.50A {Saccharomyces cerevisiae} SCOP: a.4.1.1 PDB: 1f43_A 1yrn_A*	Back alignment and structure

>1bw5_A ISL-1HD, insulin gene enhancer protein ISL-1; DNA-binding protein, homeodomain, LIM domain; NMR {Rattus norvegicus} SCOP: a.4.1.1	Back alignment and structure

>2ecc_A Homeobox and leucine zipper protein homez; homeobox domain, transcription factor, leucine zipper- containing factor, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: a.4.1.1	Back alignment and structure

>2k40_A Homeobox expressed in ES cells 1; thermostable homeodomain variant, DNA binding protein, developmental protein, disease mutation, DNA-binding; NMR {Homo sapiens}	Back alignment and structure

>2m0c_A Homeobox protein aristaless-like 4; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative; NMR {Homo sapiens}	Back alignment and structure

>2cuf_A FLJ21616 protein; homeobox domain, hepatocyte transcription factor, structural genomics, loop insertion, NPPSFA; NMR {Homo sapiens} SCOP: a.4.1.1	Back alignment and structure

>3nar_A ZHX1, zinc fingers and homeoboxes protein 1; corepressor, homeodomain, structural genomics, oxford production facility, OPPF, transcription; 2.60A {Homo sapiens}	Back alignment and structure

>1b72_A Protein (homeobox protein HOX-B1); homeodomain, DNA, complex, DNA-binding protein, protein/DNA complex; HET: DNA; 2.35A {Homo sapiens} SCOP: a.4.1.1	Back alignment and structure

>1x2n_A Homeobox protein pknox1; homeobox domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: a.4.1.1	Back alignment and structure

>2ly9_A Zinc fingers and homeoboxes protein 1; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative; NMR {Homo sapiens}	Back alignment and structure

>2ecb_A Zinc fingers and homeoboxes protein 1; homeobox domain, transcription factor, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: a.4.1.1	Back alignment and structure

>2dmp_A Zinc fingers and homeoboxes protein 2; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens}	Back alignment and structure

>2dn0_A Zinc fingers and homeoboxes protein 3; triple homeobox 1 protein, KIAA0395, TIX1, structural genomics, NPPSFA; NMR {Homo sapiens}	Back alignment and structure

>1k61_A Mating-type protein alpha-2; protein-DNA complex, homeodomain, hoogsteen base PAIR, transcription/DNA complex; HET: 5IU; 2.10A {Synthetic} SCOP: a.4.1.1	Back alignment and structure

>2cqx_A LAG1 longevity assurance homolog 5; homeodomain, DNA binding domain, transcription, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: a.4.1.1	Back alignment and structure

>1puf_B PRE-B-cell leukemia transcription factor-1; homeodomian, protein-DNA complex, HOX hexapeptide, TALE homeodomain, homeodomain interaction; 1.90A {Homo sapiens} SCOP: a.4.1.1 PDB: 1b8i_B* 2r5y_B* 2r5z_B*	Back alignment and structure

>1b72_B Protein (PBX1); homeodomain, DNA, complex, DNA-binding protein, protein/DNA complex; HET: DNA; 2.35A {Homo sapiens} SCOP: a.4.1.1 PDB: 1lfu_P	Back alignment and structure

>2dmn_A Homeobox protein TGIF2LX; TGFB-induced factor 2-like protein, X-linked TGF(beta) induced transcription factor 2-like protein, TGIF-like on the X; NMR {Homo sapiens}	Back alignment and structure

>1au7_A Protein PIT-1, GHF-1; complex (DNA-binding protein/DNA), pituitary, CPHD, POU domain, transcription factor, transcription/DNA complex; HET: DNA; 2.30A {Rattus norvegicus} SCOP: a.4.1.1 a.35.1.1	Back alignment and structure

>1du6_A PBX1, homeobox protein PBX1; homeodomain, gene regulation; NMR {Mus musculus} SCOP: a.4.1.1	Back alignment and structure

>1e3o_C Octamer-binding transcription factor 1; transcription factor, POU domain, dimer, DNA binding; 1.9A {Homo sapiens} SCOP: a.4.1.1 a.35.1.1 PDB: 1gt0_C 1hf0_A* 1cqt_A* 1o4x_A 1oct_C* 1pou_A 1pog_A 1hdp_A	Back alignment and structure

>1mnm_C Protein (MAT alpha-2 transcriptional repressor); transcription regulation, transcriptional repression, DNA- binding protein; HET: DNA; 2.25A {Saccharomyces cerevisiae} SCOP: a.4.1.1	Back alignment and structure

>1wi3_A DNA-binding protein SATB2; homeodomain, helix-turn-helix, riken structural genomics/proteomics initiative, RSGI, structural genomics; NMR {Homo sapiens} SCOP: a.4.1.1	Back alignment and structure

>3nau_A Zinc fingers and homeoboxes protein 2; ZHX2, corepressor, homeodomain, domain swapping, structural oxford protein production facility, OPPF; 2.70A {Homo sapiens}	Back alignment and structure

>1le8_B Mating-type protein alpha-2; matalpha2, isothermal titration calorimetry, protein-DNA complex, transcription/DNA complex; 2.30A {Saccharomyces cerevisiae} SCOP: a.4.1.1 PDB: 1akh_B* 1apl_C* 1yrn_B*	Back alignment and structure

>2l9r_A Homeobox protein NKX-3.1; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative; NMR {Homo sapiens}	Back alignment and structure

>3d1n_I POU domain, class 6, transcription factor 1; protein-DNA complex, helix-turn-helix (HTH), DNA-binding, homeobox, nucleus, transcription regulation; 2.51A {Homo sapiens}	Back alignment and structure

>2da6_A Hepatocyte nuclear factor 1-beta; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens}	Back alignment and structure

>1lfb_A Liver transcription factor (LFB1); transcription regulation; 2.80A {Rattus norvegicus} SCOP: a.4.1.1 PDB: 2lfb_A	Back alignment and structure

>2xsd_C POU domain, class 3, transcription factor 1; transcription-DNA complex, SOX; 2.05A {Mus musculus}	Back alignment and structure

>2pso_A STAR-related lipid transfer protein 13; alpha and beta protein, lipid binding, helix swapping, struc genomics, structural genomics consortium, SGC; 2.80A {Homo sapiens} SCOP: d.129.3.2	Back alignment and structure

>2e19_A Transcription factor 8; homeobox domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}	Back alignment and structure

>1em2_A MLN64 protein; beta barrel, lipid binding protein; HET: TAR; 2.20A {Homo sapiens} SCOP: d.129.3.2	Back alignment and structure

>3l1p_A POU domain, class 5, transcription factor 1; POU, transcription factor DNA complex, pore, stem cells; HET: DNA; 2.80A {Mus musculus} PDB: 1ocp_A	Back alignment and structure

>3p0l_A Steroidogenic acute regulatory protein, mitochond; structural genomics consortium, SGC, start domain, cholester transport, cholesterol; 3.40A {Homo sapiens}	Back alignment and structure

>1x2m_A LAG1 longevity assurance homolog 6; homeobox domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: a.4.1.1	Back alignment and structure

>2d5v_A Hepatocyte nuclear factor 6; transcription factor, transcription-DNA complex; 2.00A {Rattus norvegicus} PDB: 1s7e_A	Back alignment and structure

>3k2a_A Homeobox protein MEIS2; homeobox domain, DNA-binding, transcription, nucleus, phosphoprotein, DNA bindi protein; 1.95A {Homo sapiens} SCOP: a.4.1.1	Back alignment and structure

>1ic8_A Hepatocyte nuclear factor 1-alpha; transcription regulation, DNA-binding, POU domain, diabetes, disease mutation, MODY3, transcription/DNA comple; 2.60A {Homo sapiens} SCOP: a.4.1.1 a.35.1.1	Back alignment and structure

>2lk2_A Homeobox protein TGIF1; NESG, structural genomics, northeast structural genomics CON PSI-biology, transcription; NMR {Homo sapiens}	Back alignment and structure

>1ln1_A PC-TP, phosphatidylcholine transfer protein; start domain, lipid binding protein; HET: DLP; 2.40A {Homo sapiens} SCOP: d.129.3.2 PDB: 1ln2_A* 1ln3_A*	Back alignment and structure

>2h8r_A Hepatocyte nuclear factor 1-beta; trasncription factor, POU, homeo, protein-DNA, human disease; 3.20A {Homo sapiens}	Back alignment and structure

>3fo5_A Thioesterase, adipose associated, isoform BFIT2; orthogonal bundle, consortium, lipid transport; HET: 1PE TCE; 2.00A {Homo sapiens}	Back alignment and structure

>2da7_A Zinc finger homeobox protein 1B; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens}	Back alignment and structure

>1jss_A Stard4, cholesterol-regulated start protein 4; start domain, structural genomics, PSI, protein structure initiative; 2.20A {Mus musculus} SCOP: d.129.3.2	Back alignment and structure

>1mh3_A Maltose binding-A1 homeodomain protein chimera; MATA1, binding cooperativity, maltose binding protein, MBP, sugar binding, DNA binding protein; 2.10A {Escherichia coli} SCOP: a.4.1.1 c.94.1.1 PDB: 1mh4_A 1le8_A	Back alignment and structure

>2e3n_A Lipid-transfer protein CERT; ceramide transfer, lipid transport; HET: 6CM; 1.40A {Homo sapiens} PDB: 2e3m_A* 2e3o_A* 2e3p_A* 2e3q_A* 2e3r_A* 2e3s_A 2z9y_A* 3h3q_A* 3h3r_A* 3h3s_A* 3h3t_A* 2z9z_A*	Back alignment and structure

>3qsz_A STAR-related lipid transfer protein; structural genomics, PSI-biology; 2.39A {Xanthomonas axonopodis PV}	Back alignment and structure

>2nzz_A Penetratin conjugated GAS (374-394) peptide; conformational analysis, G protein, GAS subunit, A2A adenosine receptor, cell-penetrating peptides; NMR {Synthetic} PDB: 2o00_A	Back alignment and structure

>3t50_A Blue-light-activated histidine kinase; PAS superfamily, blue-light photoreceptor, FMN binding, TRAN; HET: FMN; 1.64A {Brucella melitensis}	Back alignment and structure

>4eet_B Phototropin-2; LOV, blue light photoreceptor, signaling protein, flavoprote; HET: FMN; 1.20A {Arabidopsis thaliana} PDB: 4ees_A* 4eer_A* 4eep_A* 4eeu_A* 1jnu_A* 1g28_A*	Back alignment and structure

>3lyx_A Sensory BOX/ggdef domain protein; structural genomics, PSI- 2, protein structure initiative, northeast structural genomics consortium; 2.00A {Colwellia psychrerythraea}	Back alignment and structure

>3ue6_A Aureochrome1; PAS/LOV domain, FMN-binding blue-light photoreceptor, signal protein; HET: FMN; 2.75A {Vaucheria frigida} PDB: 3ulf_A*	Back alignment and structure

>1n9l_A PHOT-LOV1, putative blue light receptor; phototropin, flavin, electron transport; HET: FMN; 1.90A {Chlamydomonas reinhardtii} SCOP: d.110.3.6 PDB: 1n9n_A* 1n9o_A*	Back alignment and structure

>4hia_A LOV protein; PAS, HTH, signaling protein; HET: FMN; 1.95A {Rhodobacter sphaeroides} PDB: 4hnb_A* 4hj4_A* 4hj6_A* 4hj3_A*	Back alignment and structure

>2gj3_A Nitrogen fixation regulatory protein; PAS domain, FAD, redox sensor, atomic resolution, transferase; HET: FAD; 1.04A {Azotobacter vinelandii}	Back alignment and structure

>3luq_A Sensor protein; PAS, histidine, kinase, PSI, MCSG, structural genomics, midwest center for structural genomics; HET: PGE; 2.49A {Geobacter sulfurreducens}	Back alignment and structure

>3p7n_A Sensor histidine kinase; LOV domain, light-activated transcription factor, DNA bindin; HET: FMN; 2.10A {Erythrobacter litoralis}	Back alignment and structure

>2z6d_A Phototropin-2; PAS-fold, LOV-fold, alternative splicing, ATP-binding, chromophore, flavoprotein, FMN, kinase, membrane, nucleotide-binding; HET: FMN; 2.00A {Arabidopsis thaliana} PDB: 2z6c_A*	Back alignment and structure

>3sw1_A Sensory box protein; light-oxygen-voltage, LOV, PAS, signaling protein; HET: FMN; 2.63A {Pseudomonas putida}	Back alignment and structure

>1byw_A Protein (human ERG potassium channel); PAS domain, potassium channel domain, membrane protein; 2.60A {Homo sapiens} SCOP: d.110.3.6	Back alignment and structure

>3d72_A Vivid PAS protein VVD; circadian, photoreceptor, blue-light, LOV, signaling protein; HET: FAD; 1.65A {Neurospora crassa} PDB: 3is2_A* 2pd8_A* 3hjk_A* 2pdr_A* 2pd7_A* 2pdt_A* 3hji_A* 3rh8_B*	Back alignment and structure

>3f1p_A Endothelial PAS domain-containing protein 1; PAS domain, heterodimer, internal cavity, activator, angiogenesis, congenital erythrocytosis; 1.17A {Homo sapiens} SCOP: d.110.3.7 PDB: 3f1o_A* 3f1n_A 3h7w_A* 3h82_A* 1p97_A 2a24_A 4h6j_A	Back alignment and structure

>3mqq_A Transcriptional regulator, LUXR family; PAS domain, PSI, MCSG, structural genomics, center for structural genomics; 1.65A {Burkholderia thailandensis} PDB: 3mqo_A	Back alignment and structure

>2pr5_A Blue-light photoreceptor; light-oxygen-voltage, LOV, PER-ARNT-SIM, PAS, flavoprotein, protein; HET: FMN; 1.45A {Bacillus subtilis} PDB: 2pr6_A*	Back alignment and structure

>1d06_A Nitrogen fixation regulatory protein FIXL; oxygen sensor, histidine kinase, PAS, high-resolution, two-C system, signaling protein; HET: HEM; 1.40A {Sinorhizobium meliloti} SCOP: d.110.3.2 PDB: 1ew0_A*	Back alignment and structure

>2r78_A Sensor protein; sensory box sensor histidine kinase/response regulator, structural genomics, PSI, MCSG; 1.60A {Geobacter sulfurreducens pca}	Back alignment and structure

>3kx0_X Uncharacterized protein RV1364C/MT1410; PAS domain, sensory domain, mycobacteium tuberculos molecule binding domain; 2.30A {Mycobacterium tuberculosis}	Back alignment and structure

>3k3c_A Protein RV1364C/MT1410; sensor, PAS, signal transduction, fatty-acid binding, sigma regulator, signaling protein; HET: PLM; 1.62A {Mycobacterium tuberculosis} PDB: 3k3d_A	Back alignment and structure

>2v0u_A NPH1-1, LOV2; kinase, transferase, ATP-binding, serine/threonine-protein kinase, light-induced signal trans phototropin1, nucleotide-binding; HET: FMN; 1.40A {Avena sativa} PDB: 2v0w_A* 2v1b_A* 2v1a_A* 1jnu_A* 1g28_A*	Back alignment and structure

>2l0w_A Potassium voltage-gated channel, subfamily H (EAG member 2, isoform CRA_B; HERG, PAS domain, voltage-gated potassium channel, membrane; NMR {Homo sapiens} PDB: 2l1m_A 2l4r_A	Back alignment and structure

>2r55_A STAR-related lipid transfer protein 5; alpha and beta protein, cholesterol binding, structural GENO structural genomics consortium, SGC; 2.50A {Homo sapiens}	Back alignment and structure

>3f1p_B ARYL hydrocarbon receptor nuclear translocator; PAS domain, heterodimer, internal cavity, activator, angiogenesis, congenital erythrocytosis; 1.17A {Homo sapiens} SCOP: d.110.3.0 PDB: 3f1o_B* 3f1n_B 3h7w_B* 3h82_B* 1x0o_A 2hv1_A 4h6j_B 2b02_A* 2k7s_A 2a24_B	Back alignment and structure

>2wkq_A NPH1-1, RAS-related C3 botulinum toxin substrate 1; transferase, cell adhesion, nucleotide-binding, protein engineering, RAS superfamily LOV2; HET: GTP FMN; 1.60A {Avena sativa} PDB: 2wkr_A* 2wkp_A*	Back alignment and structure

>3olo_A Two-component sensor histidine kinase; structural genomics, PSI-2, protein structure initiative, MI center for structural genomics, MCSG, TRA; 2.09A {Nostoc SP}	Back alignment and structure

>2vv6_A FIXL, sensor protein FIXL; signaling protein, transferase, phosphoprotein, nitrogen FIX PER-ARNT-SIM, metal-binding, PAS, iron, heme; HET: HEM; 1.5A {Bradyrhizobium japonicum} PDB: 1xj6_A* 1xj4_A* 2vv7_A* 2vv8_A* 1lsw_A* 1dp8_A* 1dp9_A* 1drm_A* 1lsv_A* 1dp6_A* 1lsx_A* 1lt0_A* 1y28_A* 2cmn_A* 1xj3_A* 1xj2_A* 2owh_A* 2owj_A*	Back alignment and structure

>3ewk_A Sensor protein; PAS domain, alpha/beta fold, kinase, phosphoprotein, transfe flavoprotein; HET: FAD; 2.34A {Methylococcus capsulatus}	Back alignment and structure

>3b33_A Sensor protein; structural genomics, PAS domain, nitrogen regulation protein APC91440.4, PSI-2; HET: MSE; 1.83A {Vibrio parahaemolyticus rimd 2210633}	Back alignment and structure

>3mxq_A Sensor protein; PSI2, MCSG, structural genomics, protein structure initiativ midwest center for structural genomics; 2.78A {Vibrio cholerae o1 biovar el tor}	Back alignment and structure

>3mjq_A Uncharacterized protein; NESG, structural genomics, PSI-2, protein structure initiati northeast structural genomics consortium; 2.60A {Desulfitobacterium hafniense}	Back alignment and structure

>3ewk_A Sensor protein; PAS domain, alpha/beta fold, kinase, phosphoprotein, transfe flavoprotein; HET: FAD; 2.34A {Methylococcus capsulatus}	Back alignment and structure

>3eeh_A Putative light and redox sensing histidine kinase; structural genomic MCSG, protein structure initiative, midwest center for STRU genomics; HET: PG5; 1.95A {Haloarcula marismortui}	Back alignment and structure

>2kdk_A ARYL hydrocarbon receptor nuclear translocator-LI 2; circadian clock, PAS domain, transcription, activator, biolo rhythms, DNA-binding, nucleus; NMR {Homo sapiens}	Back alignment and structure

>3fc7_A HTR-like protein, sensor protein; APC87712.1, HTR-like protein,haloarcula marismortui ATCC 430 structural genomics, PSI-2; 2.65A {Haloarcula marismortui}	Back alignment and structure

>3nja_A Probable ggdef family protein; structural genomics, PSI-2, protein structure initiative, MI center for structural genomics, MCSG; 2.37A {Chromobacterium violaceum}	Back alignment and structure

>3mfx_A Sensory BOX/ggdef family protein; alpha-beta protein, structural genomics, PSI-2, protein structure initiative; 2.40A {Shewanella oneidensis}	Back alignment and structure

>3icy_A Sensor protein; sensory box histidine kinase/response regulator domain, kinase, chlorobium tepidum TLS, PSI-2; 2.68A {Chlorobaculum tepidum}	Back alignment and structure

>3bwl_A Sensor protein; structural genomics, APC87707.1, PAS domain, HTR-like protei protein structure initiative; HET: MSE I3A; 1.73A {Haloarcula marismortui atcc 43049}	Back alignment and structure

>2pso_A STAR-related lipid transfer protein 13; alpha and beta protein, lipid binding, helix swapping, struc genomics, structural genomics consortium, SGC; 2.80A {Homo sapiens} SCOP: d.129.3.2	Back alignment and structure

>1v9y_A Heme PAS sensor protein; signaling protein; HET: HEM; 1.32A {Escherichia coli} SCOP: d.110.3.2 PDB: 1v9z_A* 1vb6_A* 1s67_L* 1s66_L*	Back alignment and structure

>1ll8_A PAS kinase; PAS domain, ligand binding, ligand screening, kinase regulation, transferase; NMR {Homo sapiens} SCOP: d.110.3.5	Back alignment and structure

>3fo5_A Thioesterase, adipose associated, isoform BFIT2; orthogonal bundle, consortium, lipid transport; HET: 1PE TCE; 2.00A {Homo sapiens}	Back alignment and structure

>1jss_A Stard4, cholesterol-regulated start protein 4; start domain, structural genomics, PSI, protein structure initiative; 2.20A {Mus musculus} SCOP: d.129.3.2	Back alignment and structure

>3qsz_A STAR-related lipid transfer protein; structural genomics, PSI-biology; 2.39A {Xanthomonas axonopodis PV}	Back alignment and structure

>3a0s_A Sensor protein; PAS-fold, kinase, phosphoprotein, transferase, two-component regulatory system; HET: PG4 PGE; 1.47A {Thermotoga maritima} PDB: 3a0v_A*	Back alignment and structure

>3p0l_A Steroidogenic acute regulatory protein, mitochond; structural genomics consortium, SGC, start domain, cholester transport, cholesterol; 3.40A {Homo sapiens}	Back alignment and structure

>4hi4_A Aerotaxis transducer AER2; PAS domain, diatomic GAS sensor, signaling protein; HET: HEM GOL; 2.30A {Pseudomonas aeruginosa}	Back alignment and structure

>1ln1_A PC-TP, phosphatidylcholine transfer protein; start domain, lipid binding protein; HET: DLP; 2.40A {Homo sapiens} SCOP: d.129.3.2 PDB: 1ln2_A* 1ln3_A*	Back alignment and structure

>3h9w_A Diguanylate cyclase with PAS/PAC sensor; alpha-beta protein., structural genomics, PSI-2, protein STR initiative; 1.90A {Marinobacter aquaeolei}	Back alignment and structure

>3fg8_A Uncharacterized protein RHA05790; PAS domain, structural genomics, PS protein structure initiative, midwest center for structural genomics, MCSG; HET: 3PB; 1.80A {Rhodococcus SP}	Back alignment and structure

>2d4r_A Hypothetical protein TTHA0849; start domain, structural genomics, riken structural genomics/proteomics initiative, RSGI, unknown function; 2.40A {Thermus thermophilus} SCOP: d.129.3.6	Back alignment and structure

>3vol_A Aerotaxis transducer AER2; heme, oxygen sensor protein, PAS, HAMP, cyanoMet, CN-bound, protein; HET: HEM; 2.40A {Pseudomonas aeruginosa}	Back alignment and structure

>1hjb_A Ccaat/enhancer binding protein beta; transcription/DNA, protein-DNA complex; HET: DNA; 3.0A {Homo sapiens} SCOP: h.1.3.1	Back alignment and structure

>1gu4_A CAAT/enhancer binding protein beta; transcription/DNA, protein-DNA complex, transcription factor, BZIP, C/EBP; 1.80A {Homo sapiens} SCOP: h.1.3.1 PDB: 1gtw_A 1gu5_A 1h88_A 1h8a_A 1io4_A 2e43_A* 2e42_A* 1h89_A 1ci6_B 1nwq_A	Back alignment and structure

>1ci6_A Transcription factor ATF-4; BZIP; 2.60A {Homo sapiens} SCOP: h.1.3.1	Back alignment and structure

>2w0n_A Sensor protein DCUS; signal transduction, two-component regulatory system, PAS, kinase, membrane, transferase, solid state cell inner membrane; NMR {Escherichia coli}	Back alignment and structure

>1em2_A MLN64 protein; beta barrel, lipid binding protein; HET: TAR; 2.20A {Homo sapiens} SCOP: d.129.3.2	Back alignment and structure

>2vlg_A Sporulation kinase A; histidine kinase, two-component regulatory system, two-component signal transduction, transferase, phosphorylation, SCOD; 1.7A {Bacillus subtilis}	Back alignment and structure

>2jhe_A Transcription regulator TYRR; aromatic hydrocarbons catabolism, TYRR protei nucleotide-binding, transcription regulation, activator; HET: PG4; 2.30A {Escherichia coli}	Back alignment and structure

>2wt7_A Proto-oncogene protein C-FOS; transcription, transcription regulation, nucleus, activator, repressor, DNA-binding, phosphoprotein, differentiation; 2.30A {Mus musculus} PDB: 1fos_E* 1a02_F* 1s9k_D	Back alignment and structure

>4f3l_A Mclock, circadian locomoter output cycles protein kaput; BHLH, PAS, circadian rhythm proteins, transcription-activato; 2.27A {Mus musculus}	Back alignment and structure

>1t2k_D Cyclic-AMP-dependent transcription factor ATF-2; protein DNA complex, transcription/DNA complex; 3.00A {Homo sapiens} SCOP: h.1.3.1	Back alignment and structure

>1t2k_D Cyclic-AMP-dependent transcription factor ATF-2; protein DNA complex, transcription/DNA complex; 3.00A {Homo sapiens} SCOP: h.1.3.1	Back alignment and structure

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

Original result of RPS-BLAST against SCOP70(version1.75) database

ID	Alignment Graph	Length	Definition	E-value
Query		850
d1pufa_		77	a.4.1.1 (A:) Homeobox protein hox-a9 {Mouse (Mus m	1e-18
d2e1oa1		57	a.4.1.1 (A:8-64) Homeobox protein prh {Human (Homo	4e-17
d9anta_		56	a.4.1.1 (A:) Antennapedia Homeodomain {Drosophila	5e-17
d2cuea1		68	a.4.1.1 (A:7-74) Paired box protein pax6 {Human (H	1e-15
d1le8a_		53	a.4.1.1 (A:) Mating type protein A1 Homeodomain {B	2e-15
d1bw5a_		66	a.4.1.1 (A:) Insulin gene enhancer protein isl-1 {	2e-15
d2ecba1		76	a.4.1.1 (A:8-83) Zinc fingers and homeoboxes prote	3e-15
d1ftta_		68	a.4.1.1 (A:) Thyroid transcription factor 1 homeod	4e-15
d1au7a1		58	a.4.1.1 (A:103-160) Pit-1 POU homeodomain {Rat (Ra	1e-14
d1k61a_		60	a.4.1.1 (A:) mat alpha2 Homeodomain {Baker's yeast	1e-14
d1zq3p1		67	a.4.1.1 (P:2-68) Homeotic bicoid protein {Fruit fl	1e-14
d1b72a_		88	a.4.1.1 (A:) Homeobox protein hox-b1 {Human (Homo	1e-14
d2craa1		58	a.4.1.1 (A:7-64) Homeobox protein hox-b13 {Human (	2e-14
d1jgga_		57	a.4.1.1 (A:) Even-skipped homeodomain {Fruit fly (	2e-14
d2psoa1		197	d.129.3.2 (A:908-1104) Star-related lipid transfer	4e-14
d1fjla_		65	a.4.1.1 (A:) Paired protein {Fruit fly (Drosophila	4e-14
d2cufa1		82	a.4.1.1 (A:8-89) Homeobox-containing protein 1, HM	5e-14
d1s7ea1		50	a.4.1.1 (A:103-152) Hepatocyte nuclear factor 6 {M	6e-14
d1p7ia_		53	a.4.1.1 (A:) Engrailed Homeodomain {Drosophila mel	8e-14
d1wh7a_		80	a.4.1.1 (A:) ZF-HD homeobox protein At4g24660 {Tha	3e-13
d1x2ma1		52	a.4.1.1 (A:8-59) Lag1 longevity assurance homolog	3e-13
d1ig7a_		58	a.4.1.1 (A:) Msx-1 homeodomain {Mouse (Mus musculu	7e-13
d1yz8p1		60	a.4.1.1 (P:1-60) Pituitary homeobox 2 {Human (Homo	7e-13
d1lfba_		78	a.4.1.1 (A:) Hepatocyte nuclear factor 1a (LFB1/HN	8e-13
d1ocpa_		67	a.4.1.1 (A:) Oct-3 POU Homeodomain {Mouse (Mus mus	2e-12
d1vnda_		77	a.4.1.1 (A:) VND/NK-2 protein {Fruit fly (Drosophi	2e-12
d1x2na1		62	a.4.1.1 (A:6-67) Homeobox protein pknox1 {Human (H	3e-12
d2cqxa1		59	a.4.1.1 (A:8-66) LAG1 longevity assurance homolog	4e-12
d1pufb_		73	a.4.1.1 (B:) pbx1 {Human (Homo sapiens) [TaxId: 96	4e-12
d1uhsa_		72	a.4.1.1 (A:) Homeodomain-only protein, Hop {Mouse	2e-11
d1e3oc1		57	a.4.1.1 (C:104-160) Oct-1 POU Homeodomain {Human (	3e-11
d2ecca1		76	a.4.1.1 (A:1-76) Homeobox-leucine zipper protein H	3e-10
d1wi3a_		71	a.4.1.1 (A:) DNA-binding protein SATB2 {Human (Hom	5e-10
d1em2a_		214	d.129.3.2 (A:) Lipid transport domain of Mln64 {Hu	8e-07
d1ln1a_		203	d.129.3.2 (A:) Phosphatidylcholine transfer protei	7e-06

>d1pufa_ a.4.1.1 (A:) Homeobox protein hox-a9 {Mouse (Mus musculus) [TaxId: 10090]} Length = 77	Back information, alignment and structure


class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Homeobox protein hox-a9
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 78.3 bits (193), Expect = 1e-18
 Identities = 20/66 (30%), Positives = 33/66 (50%), Gaps = 5/66 (7%)

Query: 26 KYVRYTPEQVEALERLYHECPKPSSMRRQQLIRECPILSNIEPKQIKVWFQNRRCREK-Q 84
          K   YT  Q   LE+ +      +  RR ++ R      N+  +Q+K+WFQNRR + K  
Sbjct: 16 KRCPYTKHQTLELEKEFLFNMYLTRDRRYEVARLL----NLTERQVKIWFQNRRMKMKKI 71

Query: 85 RKEASR 90
           K+ ++
Sbjct: 72 NKDRAK 77

PyMOL of d1pufa_

>d2e1oa1 a.4.1.1 (A:8-64) Homeobox protein prh {Human (Homo sapiens) [TaxId: 9606]} Length = 57	Back information, alignment and structure

>d9anta_ a.4.1.1 (A:) Antennapedia Homeodomain {Drosophila melanogaster [TaxId: 7227]} Length = 56	Back information, alignment and structure

>d2cuea1 a.4.1.1 (A:7-74) Paired box protein pax6 {Human (Homo sapiens) [TaxId: 9606]} Length = 68	Back information, alignment and structure

>d1le8a_ a.4.1.1 (A:) Mating type protein A1 Homeodomain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 53	Back information, alignment and structure

>d1bw5a_ a.4.1.1 (A:) Insulin gene enhancer protein isl-1 {Rat (Rattus norvegicus) [TaxId: 10116]} Length = 66	Back information, alignment and structure

>d2ecba1 a.4.1.1 (A:8-83) Zinc fingers and homeoboxes protein 1, ZHX1 {Human (Homo sapiens) [TaxId: 9606]} Length = 76	Back information, alignment and structure

>d1ftta_ a.4.1.1 (A:) Thyroid transcription factor 1 homeodomain {Rat (Rattus norvegicus) [TaxId: 10116]} Length = 68	Back information, alignment and structure

>d1au7a1 a.4.1.1 (A:103-160) Pit-1 POU homeodomain {Rat (Rattus norvegicus) [TaxId: 10116]} Length = 58	Back information, alignment and structure

>d1k61a_ a.4.1.1 (A:) mat alpha2 Homeodomain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 60	Back information, alignment and structure

>d1zq3p1 a.4.1.1 (P:2-68) Homeotic bicoid protein {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Length = 67	Back information, alignment and structure

>d1b72a_ a.4.1.1 (A:) Homeobox protein hox-b1 {Human (Homo sapiens) [TaxId: 9606]} Length = 88	Back information, alignment and structure

>d2craa1 a.4.1.1 (A:7-64) Homeobox protein hox-b13 {Human (Homo sapiens) [TaxId: 9606]} Length = 58	Back information, alignment and structure

>d1jgga_ a.4.1.1 (A:) Even-skipped homeodomain {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Length = 57	Back information, alignment and structure

>d2psoa1 d.129.3.2 (A:908-1104) Star-related lipid transfer protein 13 {Human (Homo sapiens) [TaxId: 9606]} Length = 197	Back information, alignment and structure

>d1fjla_ a.4.1.1 (A:) Paired protein {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Length = 65	Back information, alignment and structure

>d2cufa1 a.4.1.1 (A:8-89) Homeobox-containing protein 1, HMBOX1 (Flj21616) {Human (Homo sapiens) [TaxId: 9606]} Length = 82	Back information, alignment and structure

>d1s7ea1 a.4.1.1 (A:103-152) Hepatocyte nuclear factor 6 {Mouse (Mus musculus) [TaxId: 10090]} Length = 50	Back information, alignment and structure

>d1p7ia_ a.4.1.1 (A:) Engrailed Homeodomain {Drosophila melanogaster [TaxId: 7227]} Length = 53	Back information, alignment and structure

>d1wh7a_ a.4.1.1 (A:) ZF-HD homeobox protein At4g24660 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]} Length = 80	Back information, alignment and structure

>d1x2ma1 a.4.1.1 (A:8-59) Lag1 longevity assurance homolog 6, LASS6 {Mouse (Mus musculus) [TaxId: 10090]} Length = 52	Back information, alignment and structure

>d1ig7a_ a.4.1.1 (A:) Msx-1 homeodomain {Mouse (Mus musculus) [TaxId: 10090]} Length = 58	Back information, alignment and structure

>d1yz8p1 a.4.1.1 (P:1-60) Pituitary homeobox 2 {Human (Homo sapiens) [TaxId: 9606]} Length = 60	Back information, alignment and structure

>d1lfba_ a.4.1.1 (A:) Hepatocyte nuclear factor 1a (LFB1/HNF1) {Rat (Rattus rattus) [TaxId: 10117]} Length = 78	Back information, alignment and structure

>d1ocpa_ a.4.1.1 (A:) Oct-3 POU Homeodomain {Mouse (Mus musculus) [TaxId: 10090]} Length = 67	Back information, alignment and structure

>d1vnda_ a.4.1.1 (A:) VND/NK-2 protein {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Length = 77	Back information, alignment and structure

>d1x2na1 a.4.1.1 (A:6-67) Homeobox protein pknox1 {Human (Homo sapiens) [TaxId: 9606]} Length = 62	Back information, alignment and structure

>d2cqxa1 a.4.1.1 (A:8-66) LAG1 longevity assurance homolog 5, LASS5 {Mouse (Mus musculus) [TaxId: 10090]} Length = 59	Back information, alignment and structure

>d1pufb_ a.4.1.1 (B:) pbx1 {Human (Homo sapiens) [TaxId: 9606]} Length = 73	Back information, alignment and structure

>d1uhsa_ a.4.1.1 (A:) Homeodomain-only protein, Hop {Mouse (Mus musculus) [TaxId: 10090]} Length = 72	Back information, alignment and structure

>d1e3oc1 a.4.1.1 (C:104-160) Oct-1 POU Homeodomain {Human (Homo sapiens) [TaxId: 9606]} Length = 57	Back information, alignment and structure

>d2ecca1 a.4.1.1 (A:1-76) Homeobox-leucine zipper protein Homez {Human (Homo sapiens) [TaxId: 9606]} Length = 76	Back information, alignment and structure

>d1wi3a_ a.4.1.1 (A:) DNA-binding protein SATB2 {Human (Homo sapiens) [TaxId: 9606]} Length = 71	Back information, alignment and structure

>d1em2a_ d.129.3.2 (A:) Lipid transport domain of Mln64 {Human (Homo sapiens) [TaxId: 9606]} Length = 214	Back information, alignment and structure

>d1ln1a_ d.129.3.2 (A:) Phosphatidylcholine transfer protein {Human (Homo sapiens) [TaxId: 9606]} Length = 203	Back information, alignment and structure

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Alignment Graph	Length	Definition	Probability
Query		850
d2craa1		58	Homeobox protein hox-b13 {Human (Homo sapiens) [Ta	99.65
d2e1oa1		57	Homeobox protein prh {Human (Homo sapiens) [TaxId:	99.64
d1pufa_		77	Homeobox protein hox-a9 {Mouse (Mus musculus) [Tax	99.63
d1ig7a_		58	Msx-1 homeodomain {Mouse (Mus musculus) [TaxId: 10	99.63
d9anta_		56	Antennapedia Homeodomain {Drosophila melanogaster	99.62
d1jgga_		57	Even-skipped homeodomain {Fruit fly (Drosophila me	99.61
d1zq3p1		67	Homeotic bicoid protein {Fruit fly (Drosophila mel	99.61
d1b72a_		88	Homeobox protein hox-b1 {Human (Homo sapiens) [Tax	99.59
d1fjla_		65	Paired protein {Fruit fly (Drosophila melanogaster	99.59
d1p7ia_		53	Engrailed Homeodomain {Drosophila melanogaster [Ta	99.58
d2cuea1		68	Paired box protein pax6 {Human (Homo sapiens) [Tax	99.58
d1vnda_		77	VND/NK-2 protein {Fruit fly (Drosophila melanogast	99.57
d1uhsa_		72	Homeodomain-only protein, Hop {Mouse (Mus musculus	99.57
d1ftta_		68	Thyroid transcription factor 1 homeodomain {Rat (R	99.56
d1yz8p1		60	Pituitary homeobox 2 {Human (Homo sapiens) [TaxId:	99.56
d2cufa1		82	Homeobox-containing protein 1, HMBOX1 (Flj21616) {	99.51
d1le8a_		53	Mating type protein A1 Homeodomain {Baker's yeast	99.51
d1wh7a_		80	ZF-HD homeobox protein At4g24660 {Thale cress (Ara	99.5
d1au7a1		58	Pit-1 POU homeodomain {Rat (Rattus norvegicus) [Ta	99.49
d1bw5a_		66	Insulin gene enhancer protein isl-1 {Rat (Rattus n	99.49
d1wi3a_		71	DNA-binding protein SATB2 {Human (Homo sapiens) [T	99.49
d1ocpa_		67	Oct-3 POU Homeodomain {Mouse (Mus musculus) [TaxId	99.48
d1e3oc1		57	Oct-1 POU Homeodomain {Human (Homo sapiens) [TaxId	99.46
d1s7ea1		50	Hepatocyte nuclear factor 6 {Mouse (Mus musculus)	99.41
d2ecba1		76	Zinc fingers and homeoboxes protein 1, ZHX1 {Human	99.39
d1pufb_		73	pbx1 {Human (Homo sapiens) [TaxId: 9606]}	99.37
d2ecca1		76	Homeobox-leucine zipper protein Homez {Human (Homo	99.37
d1lfba_		78	Hepatocyte nuclear factor 1a (LFB1/HNF1) {Rat (Rat	99.3
d1x2ma1		52	Lag1 longevity assurance homolog 6, LASS6 {Mouse (	99.3
d1k61a_		60	mat alpha2 Homeodomain {Baker's yeast (Saccharomyc	99.29
d2cqxa1		59	LAG1 longevity assurance homolog 5, LASS5 {Mouse (	99.23
d1x2na1		62	Homeobox protein pknox1 {Human (Homo sapiens) [Tax	99.19
d1jssa_		199	Cholesterol-regulated Start protein 4 (Stard4). {M	98.75
d2psoa1		197	Star-related lipid transfer protein 13 {Human (Hom	98.58
d1em2a_		214	Lipid transport domain of Mln64 {Human (Homo sapie	98.43
d1ln1a_		203	Phosphatidylcholine transfer protein {Human (Homo	98.12
d1jnua_		104	Photoreceptor phy3 flavin-binding domain, lov2 {Ma	98.07
d1n9la_		109	Putative blue light receptor, phot-lov1 domain {Gr	97.7
d1mzua_		110	PYP domain of sensor histidine kinase Ppr {Rhodosp	97.18
d1bywa_		110	Erg potassium channel, N-terminal domain {Human (H	97.18
d1ew0a_		130	Histidine kinase FixL heme domain {Rhizobium melil	97.12
d1v9ya_		113	Direct oxygen sensor protein, DOS {Escherichia col	97.0
d1p97a_		114	Hypoxia-inducible factor Hif2a, C-terminal domain	96.62
d1nwza_		125	Photoactive yellow protein, PYP {Ectothiorhodospir	96.24
d1xj3a1		106	Histidine kinase FixL heme domain {Bradyrhizobium	96.1
d1ll8a_		114	N-terminal PAS domain of Pas kinase {Human (Homo s	95.81
d2psoa1		197	Star-related lipid transfer protein 13 {Human (Hom	93.67
d1ln1a_		203	Phosphatidylcholine transfer protein {Human (Homo	92.83
d1em2a_		214	Lipid transport domain of Mln64 {Human (Homo sapie	87.53
d2d4ra1		146	Hypothetical protein TTHA0849 {Thermus thermophilu	83.52

>d2craa1 a.4.1.1 (A:7-64) Homeobox protein hox-b13 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Homeobox protein hox-b13
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.65  E-value=8.6e-18  Score=137.53  Aligned_cols=58  Identities=31%  Similarity=0.558  Sum_probs=55.3

Q ss_pred             CCCCcccCCHHHHHHHHHhHhcCCCCCHHHHHHHHHhcCccCCCCcceEEeecccchhHHHH
Q 003071           23 DNGKYVRYTPEQVEALERLYHECPKPSSMRRQQLIRECPILSNIEPKQIKVWFQNRRCREKQ   84 (850)
Q Consensus        23 ~rr~R~r~T~~Ql~~LE~~F~~~~~Ps~~~r~~LA~~L~~~~gL~~rQVkvWFQNRRak~Kr   84 (850)
                      ++|+|++||++|+..||..|..++||+..+|.+||..|    ||+++||++||||||+|+||
T Consensus         1 Grr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l----~l~~~qV~vWFqNrR~k~kk   58 (58)
T d2craa1           1 GRKKRIPYSKGQLRELEREYAANKFITKDKRRKISAAT----SLSERQITIWFQNRRVKEKK   58 (58)
T ss_dssp             CCCSCCCSCHHHHHHHHHHHHHCSSCCHHHHHHHHHHT----CCCHHHHHHHHHHHHHTTTS
T ss_pred             CCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHc----CCCHHHeeecccchhhhccC
Confidence            36788999999999999999999999999999999999    99999999999999999874

PyMOL of d2craa1

>d2e1oa1 a.4.1.1 (A:8-64) Homeobox protein prh {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1pufa_ a.4.1.1 (A:) Homeobox protein hox-a9 {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d1ig7a_ a.4.1.1 (A:) Msx-1 homeodomain {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d9anta_ a.4.1.1 (A:) Antennapedia Homeodomain {Drosophila melanogaster [TaxId: 7227]}	Back information, alignment and structure

>d1jgga_ a.4.1.1 (A:) Even-skipped homeodomain {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}	Back information, alignment and structure

>d1zq3p1 a.4.1.1 (P:2-68) Homeotic bicoid protein {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}	Back information, alignment and structure

>d1b72a_ a.4.1.1 (A:) Homeobox protein hox-b1 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1fjla_ a.4.1.1 (A:) Paired protein {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}	Back information, alignment and structure

>d1p7ia_ a.4.1.1 (A:) Engrailed Homeodomain {Drosophila melanogaster [TaxId: 7227]}	Back information, alignment and structure

>d2cuea1 a.4.1.1 (A:7-74) Paired box protein pax6 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1vnda_ a.4.1.1 (A:) VND/NK-2 protein {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}	Back information, alignment and structure

>d1uhsa_ a.4.1.1 (A:) Homeodomain-only protein, Hop {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d1ftta_ a.4.1.1 (A:) Thyroid transcription factor 1 homeodomain {Rat (Rattus norvegicus) [TaxId: 10116]}	Back information, alignment and structure

>d1yz8p1 a.4.1.1 (P:1-60) Pituitary homeobox 2 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2cufa1 a.4.1.1 (A:8-89) Homeobox-containing protein 1, HMBOX1 (Flj21616) {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1le8a_ a.4.1.1 (A:) Mating type protein A1 Homeodomain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}	Back information, alignment and structure

>d1wh7a_ a.4.1.1 (A:) ZF-HD homeobox protein At4g24660 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}	Back information, alignment and structure

>d1au7a1 a.4.1.1 (A:103-160) Pit-1 POU homeodomain {Rat (Rattus norvegicus) [TaxId: 10116]}	Back information, alignment and structure

>d1bw5a_ a.4.1.1 (A:) Insulin gene enhancer protein isl-1 {Rat (Rattus norvegicus) [TaxId: 10116]}	Back information, alignment and structure

>d1wi3a_ a.4.1.1 (A:) DNA-binding protein SATB2 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1ocpa_ a.4.1.1 (A:) Oct-3 POU Homeodomain {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d1e3oc1 a.4.1.1 (C:104-160) Oct-1 POU Homeodomain {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1s7ea1 a.4.1.1 (A:103-152) Hepatocyte nuclear factor 6 {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d2ecba1 a.4.1.1 (A:8-83) Zinc fingers and homeoboxes protein 1, ZHX1 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1pufb_ a.4.1.1 (B:) pbx1 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2ecca1 a.4.1.1 (A:1-76) Homeobox-leucine zipper protein Homez {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1lfba_ a.4.1.1 (A:) Hepatocyte nuclear factor 1a (LFB1/HNF1) {Rat (Rattus rattus) [TaxId: 10117]}	Back information, alignment and structure

>d1x2ma1 a.4.1.1 (A:8-59) Lag1 longevity assurance homolog 6, LASS6 {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d1k61a_ a.4.1.1 (A:) mat alpha2 Homeodomain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}	Back information, alignment and structure

>d2cqxa1 a.4.1.1 (A:8-66) LAG1 longevity assurance homolog 5, LASS5 {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d1x2na1 a.4.1.1 (A:6-67) Homeobox protein pknox1 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1jssa_ d.129.3.2 (A:) Cholesterol-regulated Start protein 4 (Stard4). {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d2psoa1 d.129.3.2 (A:908-1104) Star-related lipid transfer protein 13 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1em2a_ d.129.3.2 (A:) Lipid transport domain of Mln64 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1ln1a_ d.129.3.2 (A:) Phosphatidylcholine transfer protein {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1jnua_ d.110.3.6 (A:) Photoreceptor phy3 flavin-binding domain, lov2 {Maidenhair fern (Adiantum capillus-veneris) [TaxId: 13818]}	Back information, alignment and structure

>d1n9la_ d.110.3.6 (A:) Putative blue light receptor, phot-lov1 domain {Green algae (Chlamydomonas reinhardtii) [TaxId: 3055]}	Back information, alignment and structure

>d1mzua_ d.110.3.1 (A:) PYP domain of sensor histidine kinase Ppr {Rhodospirillum centenum [TaxId: 34018]}	Back information, alignment and structure

>d1bywa_ d.110.3.6 (A:) Erg potassium channel, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1ew0a_ d.110.3.2 (A:) Histidine kinase FixL heme domain {Rhizobium meliloti [TaxId: 382]}	Back information, alignment and structure

>d1v9ya_ d.110.3.2 (A:) Direct oxygen sensor protein, DOS {Escherichia coli [TaxId: 562]}	Back information, alignment and structure

>d1p97a_ d.110.3.7 (A:) Hypoxia-inducible factor Hif2a, C-terminal domain {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1nwza_ d.110.3.1 (A:) Photoactive yellow protein, PYP {Ectothiorhodospira halophila [TaxId: 1053]}	Back information, alignment and structure

>d1xj3a1 d.110.3.2 (A:154-259) Histidine kinase FixL heme domain {Bradyrhizobium japonicum [TaxId: 375]}	Back information, alignment and structure

>d1ll8a_ d.110.3.5 (A:) N-terminal PAS domain of Pas kinase {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2psoa1 d.129.3.2 (A:908-1104) Star-related lipid transfer protein 13 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1ln1a_ d.129.3.2 (A:) Phosphatidylcholine transfer protein {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1em2a_ d.129.3.2 (A:) Lipid transport domain of Mln64 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2d4ra1 d.129.3.6 (A:2-147) Hypothetical protein TTHA0849 {Thermus thermophilus [TaxId: 274]}	Back information, alignment and structure