Citrus Sinensis ID: 004383

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-------

MNKLLMEENDRLQKQVSHLVYENGYMRQQLHSAPATTTDNSCESVVMSGQHQQQQNPTPQHPQRDASNPAGLLAVAEETLAEFLSKATGTAVDWVQMIGMKPGPDSIGIVAVSRNCSGVAARACGLVSLDPTKIAEILKDCPSWFRDCRCLDVLSVIPTGNGGTIELIYMQTYAPTTLAAARDFWLLRYSTSLEDGSLVVCERSLTSSTGGPTGPPPSSFVRAEMLASGFLIRPCEGGGSIIHIVDHVDLDAWSVPEVLRPLYESSKILAQKMTMAAMRHIRQIAQETSGEIQYGGGRQPAVLRTFSQRLSRGFNDAINGFLDDGWSLLSSDGGEDVTVAINSSPNKFLGSQYNWSMLPAFGGVLCAKASMLLQNVPPALLVRFLREHRSEWADYGVDAYSAACLKASPYAVPCARPGGFPSSHVILPLAHTVEHEEFLEVVRLEGHAFSPEDVALARDMYLLQLCSGIDENTVGACAQLVFAPIDESFADDAPLLASGFRVIPLDSKAAMQQDGPAASRTLDLASALEVGSGGARPAGGTELSNYNSRSVLTIAFQFTFENHMRDNVAAMARQYVRSVVGSVQRVAMAISPSRLGPHAGPKALPGSPEALTLARWISRSYRIHTGGELLRADSLTGDALLKQLWHHSDAIMCCSLKTNASPVFTFANQAGLDMLETTLVALQDIMLDKILDEAGRKILCTEFAKIMQQGFAYLPGGMCVSSMGRAVSYEQAVAWKVLDDDDSNHCLAFMFMNWSFV

ccHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHcccccccEEEccccccccccccccccccccccEEEcEEEEEEEccccHHHHHccccHHHHcccEEEEEEEEEcccccHHHHHHHHHHccccccccEEEEEEEEEEEcccccEEEEEEccccccccccccccccccEEEEccccEEEEEcccccEEEEEEEEEEccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccHHHHHHHHHHHHHHHHHHcccccccccccccccccccEEEEEEccccccccccccccccccccEEEEEEEccccccccHHHHHHHHHHccccccccccccccccccccccccccccccccccccEEEEEcccccccccEEEEEEEccccccccHHHHHccEEEEEccccccccccccccEEEEEcccccccccccccccccEEccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHccccccHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccHHHHHHHHHHHHHHHHHHccccccccccccHHHHHHHHHccccEEEEEcccccccEEEEHHHHHHHHHcccHHHHHccHHHHcccHHHHHHHHHHHHHHHHHcccccccEEEEcccccEEEEccEEEEEEEcccccEEEEEEEEcccccc

ccHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccEEccccccccccccccccccccccHHHHHHHHHHHHHHHHHHccccccEEEEccccccccccccEEEccccccEEEHHccEEEEEcHHHHHHHHHcccHHHHHHccHHHEcccccccccHEEEEHEEEccccccccHHHEEEEEEEEEcccccEEEEEEEccccccccccccccccEHEccccccEEEEEcccccEEEEEEEEEccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccHHHHHHHHHHHHHHHHHHccccccccccEEcccccccEEEEEEccccccccccccccccccccEEEEEHEEEEcccccHHHHHHHHHHHHHHHHcccccEHcccccccccccccccccccccccEEEEEcccccccccEEEEEEEEccccccccccccccEEEEEEcccccccccccccEEEEEEccccccccccccccccEEEEcccccccccccccccccccccccccccccccccccccccccccccEEEEEEEEEEccccccHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccHHHHHHHHHHHHHHHHHHcHHHccccccccHHHHHHHHccccEEEEEccccccccHHHHHcHHHHHHHHHHHHHHHHccHHHHHccccccHHHHHHHHHHHccccEccccEEEccccccccHHHEEEEEEEccccccEEEEEEEEEEEcc

MNKLLMEENDRLQKQVSHLVYENGymrqqlhsapatttdnscesvvmsgqhqqqqnptpqhpqrdasnpagLLAVAEETLAEFLSKATGTAVDWVQMigmkpgpdsIGIVAVSRNCSGVaaracglvsldpTKIAEILkdcpswfrdcrcldvlsviptgnggtIELIYMQTYAPTTLAAARDFWLLRYstsledgslVVCErsltsstggptgpppssFVRAEMLASgflirpcegggsiihivdhvdldawsvpevlrpLYESSKILAQKMTMAAMRHIRQIAQEtsgeiqygggrqpaVLRTFSQRLSRGFNDAINGFlddgwsllssdggedVTVAINsspnkflgsqynwsmlpafGGVLCAKASMLLQNVPPALLVRFLREHRSEWADYGVDAYSAAClkaspyavpcarpggfpsshvilplahtveheEFLEVVRleghafspeDVALARDMYLLQLCsgidentvGACAQLvfapidesfaddapllasgfrvipldskaamqqdgpaasRTLDLASAlevgsggarpaggtelsnynsRSVLTIAFQFTFENHMRDNVAAMARQYVRSVVGSVQRVAmaispsrlgphagpkalpgspeaLTLARWISRSYRihtggellradsltGDALLKQLWHhsdaimccslktnaspvftfANQAGLDMLETTLVALQDIMLDKILDEAGRKILCTEFAKIMQQGfaylpggmcvssmgRAVSYEQAVAWKvlddddsnhcLAFMFMNWSFV

MNKLLMEENDRLQKQVSHLVYENGYMRQQLHSAPATTTDNSCESVVMSGQHQQQQNPTPQHPQRDASNPAGLLAVAEETLAEFLSKATGTAVDWVQMIGMKPGPDSIGIVAVSRNCSGVAARACGLVSLDPTKIAEILKDCPSWFRDCRCLDVLSVIPTGNGGTIELIYMQTYAPTTLAAARDFWLLRYSTSLEDGSLVVCERSltsstggptgpppSSFVRAEMLASGFLIRPCEGGGSIIHIVDHVDLDAWSVPEVLRPLYESSKILAQKMTMAAMRHIRQIAQETSGEIQYGGGRQPAVLRTFSQRLSRGFNDAINGFLDDGWSLLSSDGGEDVTVAINSSPNKFLGSQYNWSMLPAFGGVLCAKASMLLQNVPPALLVRFLREHRSEWADYGVDAYSAACLKASPYAVPCARPGGFPSSHVILPLAHTVEHEEFLEVVRLEGHAFSPEDVALARDMYLLQLCSGIDENTVGACAQLVFAPIDESFADDAPLLASGFRVIPLDSKAAMQQDGPAASRTLDLASALEVGsggarpaggtelsnynsRSVLTIAFQFTFENHMRDNVAAMARQYVRSVVGSVQRVAMAISpsrlgphagpkalpgsPEALTLARWISRSYRIHTGGELLRADSLTGDALLKQLWHHSDAIMCCSLKTNASPVFTFANQAGLDMLETTLVALQDIMLDKILDEAGRKILCTEFAKIMQQGFAYLPGGMCVSSMGRAVSYEQAVAWKVLDDDDSNHCLAFMFMNWSFV

MNKLLMEENDRLQKQVSHLVYENGYMRQQLHSAPATTTDNSCESVVMSGqhqqqqnptpqhpqRDASNPAGLLAVAEETLAEFLSKATGTAVDWVQMIGMKPGPDSIGIVAVSRNCSGVAARACGLVSLDPTKIAEILKDCPSWFRDCRCLDVLSVIPTGNGGTIELIYMQTYAPTTLAAARDFWLLRYSTSLEDGSLVVCERSLtsstggptgpppssFVRAEMLASGFLIRPCEGGGSIIHIVDHVDLDAWSVPEVLRPLYESSKILAQKMTMAAMRHIRQIAQETSGEIQYGGGRQPAVLRTFSQRLSRGFNDAINGFLDDGWSLLSSDGGEDVTVAINSSPNKFLGSQYNWSMLPAFGGVLCAKASMLLQNVPPALLVRFLREHRSEWADYGVDAYSAACLKASPYAVPCARPGGFPSSHVILPLAHTVEHEEFLEVVRLEGHAFSPEDVALARDMYLLQLCSGIDENTVGACAQLVFAPIDESFADDAPLLASGFRVIPLDSKAAMQQDGPAASRTLDLASALEVGSGGARPAGGTELSNYNSRSVLTIAFQFTFENHMRDNVAAMARQYVRSVVGSVQRVAMAISPSRLGPHAGPKALPGSPEALTLARWISRSYRIHTGGELLRADSLTGDALLKQLWHHSDAIMCCSLKTNASPVFTFANQAGLDMLETTLVALQDIMLDKILDEAGRKILCTEFAKIMQQGFAYLPGGMCVSSMGRAVSYEQAVAWKVLDDDDSNHCLAFMFMNWSFV

******************LVYE*************************************************LLAVAEETLAEFLSKATGTAVDWVQMIGMKPGPDSIGIVAVSRNCSGVAARACGLVSLDPTKIAEILKDCPSWFRDCRCLDVLSVIPTGNGGTIELIYMQTYAPTTLAAARDFWLLRYSTSLEDGSLVVCE******************VRAEMLASGFLIRPCEGGGSIIHIVDHVDLDAWSVPEVLRPLYESSKILAQKMTMAAMRHIRQIAQETSGEIQYGGGRQPAVLRTFSQRLSRGFNDAINGFLDDGWSLLSSDGGEDVTVAINSSPNKFLGSQYNWSMLPAFGGVLCAKASMLLQNVPPALLVRFLREHRSEWADYGVDAYSAACLKASPYAVPCARPGGFPSSHVILPLAHTVEHEEFLEVVRLEGHAFSPEDVALARDMYLLQLCSGIDENTVGACAQLVFAPIDESFADDAPLLASGFRVIPL****************************************YNSRSVLTIAFQFTFENHMRDNVAAMARQYVRSVVGSVQRVAMAI*******************ALTLARWISRSYRIHTGGELLRADSLTGDALLKQLWHHSDAIMCCSLKTNASPVFTFANQAGLDMLETTLVALQDIMLDKILDEAGRKILCTEFAKIMQQGFAYLPGGMCVSSMGRAVSYEQAVAWKVLDDDDSNHCLAFMFMNWSF*

*NKLLMEENDRLQKQVSHLV***************************************************LLAVAEETLAEFLSKATGTAVDWVQMIGMKPGPDSI**********GVAARACGLVSLDPTKIAEILKDCPSWFRDCRCLDVLSVIPTGNGGTIELIYMQTYAPTTLAAARDFWLLRYSTSLEDGSLVVCERSLTSS***********FVRAEMLASGFLIRPCEGGGSIIHIVDHVDLDAWSVPEVLRPLYESSKILAQKMTMAAMRHIRQIAQ****************LRTFSQRLSRGFNDAINGFLDDGWSLLSSDGGEDVTVAINSSP************LPAFGGVLCAKASMLLQNVPPALLVRFLREHRSEWADYGVDAYSAACLKASPYA*********PS*HVILPLAHTVEHEEFLEVVRLEGHAFSPEDVALARDMYLLQLCSGIDENTVGACAQLVFAPIDESFADDAPLLASGFRVI***********************************************VLTIAFQFTFENHMRDNVA*MARQYVRSVVGSVQRVAMAISP**************SPEALTLARWISRSYRIHTGGELLRADSLTGDALLKQLWHHSDAIMCCSLKTNASPVFTFANQAGLDMLETTLVALQDIMLD***********CTEFAKIMQQGFAYLPGGMCVSSMGRAVSYEQAVAWKVLDDDDSNHCLAFMFMNWSFV

********NDRLQKQVSHLVYENGYMRQQL************************************SNPAGLLAVAEETLAEFLSKATGTAVDWVQMIGMKPGPDSIGIVAVSRNCSGVAARACGLVSLDPTKIAEILKDCPSWFRDCRCLDVLSVIPTGNGGTIELIYMQTYAPTTLAAARDFWLLRYSTSLEDGSLVVCER*************PSSFVRAEMLASGFLIRPCEGGGSIIHIVDHVDLDAWSVPEVLRPLYESSKILAQKMTMAAMRHIRQIAQETSGEIQYGGGRQPAVLRTFSQRLSRGFNDAINGFLDDGWSLLSSDGGEDVTVAINSSPNKFLGSQYNWSMLPAFGGVLCAKASMLLQNVPPALLVRFLREHRSEWADYGVDAYSAACLKASPYAVPCARPGGFPSSHVILPLAHTVEHEEFLEVVRLEGHAFSPEDVALARDMYLLQLCSGIDENTVGACAQLVFAPIDESFADDAPLLASGFRVIPLDSKA**********RTLDLASALEVGSGGARPAGGTELSNYNSRSVLTIAFQFTFENHMRDNVAAMARQYVRSVVGSVQRVAMAISPSRLGPHAGPKALPGSPEALTLARWISRSYRIHTGGELLRADSLTGDALLKQLWHHSDAIMCCSLKTNASPVFTFANQAGLDMLETTLVALQDIMLDKILDEAGRKILCTEFAKIMQQGFAYLPGGMCVSSMGRAVSYEQAVAWKVLDDDDSNHCLAFMFMNWSFV

*NKLLMEENDRLQKQVSHLVYENGYMRQQLHS*********************************ASNPAGLLAVAEETLAEFLSKATGTAVDWVQMIGMKPGPDSIGIVAVSRNCSGVAARACGLVSLDPTKIAEILKDCPSWFRDCRCLDVLSVIPTGNGGTIELIYMQTYAPTTLAAARDFWLLRYSTSLEDGSLVVCERSLTSS***PT***PSSFVRAEMLASGFLIRPCEGGGSIIHIVDHVDLDAWSVPEVLRPLYESSKILAQKMTMAAMRHIRQIAQETSGEIQYGGGRQPAVLRTFSQRLSRGFNDAINGFLDDGWSLLSSDGGEDVTVAINSSPNKF*******SMLPAFGGVLCAKASMLLQNVPPALLVRFLREHRSEWADYGVDAYSAACLKASPYAVPCARPGGFPSSHVILPLAHTVEHEEFLEVVRLEGHAFSPEDVALARDMYLLQLCSGIDENTVGACAQLVFAPIDESFADDAPLLASGFRVIPLDS***************************************NSRSVLTIAFQFTFENHMRDNVAAMARQYVRSVVGSVQRVAMAISPS**********LPGSPEALTLARWISRSYRIHTGGELLRADSLTGDALLKQLWHHSDAIMCCSLKTNASPVFTFANQAGLDMLETTLVALQDIMLDKILDEAGRKILCTEFAKIMQQGFAYLPGGMCVSSMGRAVSYEQAVAWKVLDDDDSNHCLAFMFMNWSFV

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no confident homologs detected

Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Alignment graph	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query		757	2.2.26 [Sep-21-2011]
Q6AST1		859	Homeobox-leucine zipper p	yes	no	0.992	0.874	0.795	0.0
A2XK30		859	Homeobox-leucine zipper p	N/A	no	0.992	0.874	0.795	0.0
O04291		852	Homeobox-leucine zipper p	yes	no	0.992	0.881	0.799	0.0
O04292		841	Homeobox-leucine zipper p	no	no	0.980	0.882	0.781	0.0
Q2QM96		855	Homeobox-leucine zipper p	no	no	0.988	0.874	0.760	0.0
A2ZMN9		855	Homeobox-leucine zipper p	N/A	no	0.988	0.874	0.760	0.0
Q9SE43		842	Homeobox-leucine zipper p	no	no	0.973	0.875	0.682	0.0
A2Z8L4		840	Homeobox-leucine zipper p	N/A	no	0.973	0.877	0.677	0.0
Q9AV49		840	Homeobox-leucine zipper p	no	no	0.973	0.877	0.677	0.0
Q9ZU11		836	Homeobox-leucine zipper p	no	no	0.977	0.885	0.648	0.0

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

 Score = 1245 bits (3222), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 604/759 (79%), Positives = 662/759 (87%), Gaps = 8/759 (1%)

Query: 1   MNKLLMEENDRLQKQVSHLVYENGYMRQQLHSAPATTTDNSCESVVMSGQHQQQQNPTPQ 60
           MNKLLMEENDRLQKQVS LVYENGYMRQQLH+    TTD SCESVV SGQH QQQNP   
Sbjct: 107 MNKLLMEENDRLQKQVSRLVYENGYMRQQLHNPSVATTDTSCESVVTSGQHHQQQNPAAT 166

Query: 61  HPQRDASNPAGLLAVAEETLAEFLSKATGTAVDWVQMIGMKPGPDSIGIVAVSRNCSGVA 120
            PQRDA+NPAGLLA+AEETLAEFLSKATGTAVDWVQM+GMKPGPDSIGI+AVS NCSGVA
Sbjct: 167 RPQRDANNPAGLLAIAEETLAEFLSKATGTAVDWVQMVGMKPGPDSIGIIAVSHNCSGVA 226

Query: 121 ARACGLVSLDPTKIAEILKDCPSWFRDCRCLDVLSVIPTGNGGTIELIYMQTYAPTTLAA 180
           ARACGLVSL+PTK+AEILKD PSW+RDCRC+DVL VIPTGNGGTIELIYMQTYAPTTLAA
Sbjct: 227 ARACGLVSLEPTKVAEILKDRPSWYRDCRCVDVLHVIPTGNGGTIELIYMQTYAPTTLAA 286

Query: 181 ARDFWLLRYSTSLEDGSLVVCERSLTSSTGGPTGPPPSSFVRAEMLASGFLIRPCEGGGS 240
            RDFW+LRY++ LEDGSLV+CERSLT STGGP+GP   +FVRAE+L SG+LIRPCEGGGS
Sbjct: 287 PRDFWILRYTSGLEDGSLVICERSLTQSTGGPSGPNTPNFVRAEVLPSGYLIRPCEGGGS 346

Query: 241 IIHIVDHVDLDAWSVPEVLRPLYESSKILAQKMTMAAMRHIRQIAQETSGEIQYGGGRQP 300
           +IHIVDHVDLDAWSVPEVLRPLYES KILAQKMT+AA+RHIRQIA E+SGE+ YGGGRQP
Sbjct: 347 MIHIVDHVDLDAWSVPEVLRPLYESPKILAQKMTIAALRHIRQIAHESSGEMPYGGGRQP 406

Query: 301 AVLRTFSQRLSRGFNDAINGFLDDGWSLLSSDGGEDVTVAINSSPNKFLGSQYNWSMLPA 360
           AVLRTFSQRLSRGFNDA+NGF DDGWSL+SSDG EDVT+A NSSPNK +GS  N S L +
Sbjct: 407 AVLRTFSQRLSRGFNDAVNGFPDDGWSLMSSDGAEDVTIAFNSSPNKLVGSHVNSSQLFS 466

Query: 361 F--GGVLCAKASMLLQNVPPALLVRFLREHRSEWADYGVDAYSAACLKASPYAVPCARPG 418
              GG+LCAKASMLLQNVPPALLVRFLREHRSEWAD GVDAYSAA L+ASPYAVP  R G
Sbjct: 467 AIGGGILCAKASMLLQNVPPALLVRFLREHRSEWADPGVDAYSAAALRASPYAVPGLRAG 526

Query: 419 GFPSSHVILPLAHTVEHEEFLEVVRLEGHAFSPEDVALARDMYLLQLCSGIDENTVGACA 478
           GF  S VILPLAHT+EHEEFLEV+RLEGH+   ++V L+RDMYLLQLCSG+DEN  GACA
Sbjct: 527 GFMGSQVILPLAHTLEHEEFLEVIRLEGHSLCHDEVVLSRDMYLLQLCSGVDENAAGACA 586

Query: 479 QLVFAPIDESFADDAPLLASGFRVIPLDSKAAMQQDGPAASRTLDLASALEVGSGGARPA 538
           QLVFAPIDESFADDAPLL SGFRVIPLD K     D P+A+RTLDLAS LEVGSGG   A
Sbjct: 587 QLVFAPIDESFADDAPLLPSGFRVIPLDGKT----DAPSATRTLDLASTLEVGSGGTTRA 642

Query: 539 GGTELSNYNSRSVLTIAFQFTFENHMRDNVAAMARQYVRSVVGSVQRVAMAISPSRLGPH 598
                S  N+RSVLTIAFQF++ENH+R++VAAMARQYVR+VV SVQRVAMAI+PSRLG  
Sbjct: 643 SSDTSSTCNTRSVLTIAFQFSYENHLRESVAAMARQYVRTVVASVQRVAMAIAPSRLGGQ 702

Query: 599 AGPKALPGSPEALTLARWISRSYRIHTGGELLRADSLTGDALLKQLWHHSDAIMCCSLKT 658
              K  PGSPEA TLARWI RSYR HTG +LLR DS + D+ LK +W HSD+IMCCSLK 
Sbjct: 703 IETKNPPGSPEAHTLARWIGRSYRFHTGADLLRTDSQSTDSSLKAMWQHSDSIMCCSLK- 761

Query: 659 NASPVFTFANQAGLDMLETTLVALQDIMLDKILDEAGRKILCTEFAKIMQQGFAYLPGGM 718
            A+PVFTFANQAGLDMLETTL+ALQDI L+KILD+ GRK LCTEF KIMQQGFAYLPGG+
Sbjct: 762 -AAPVFTFANQAGLDMLETTLIALQDISLEKILDDDGRKALCTEFPKIMQQGFAYLPGGV 820

Query: 719 CVSSMGRAVSYEQAVAWKVLDDDDSNHCLAFMFMNWSFV 757
           CVSSMGR VSYEQAVAWKVL DDD+ HCLAFMF+NWSFV
Sbjct: 821 CVSSMGRPVSYEQAVAWKVLSDDDTPHCLAFMFVNWSFV 859

Probable transcription factor.
Oryza sativa subsp. japonica (taxid: 39947)

>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\|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\|O04292\|ATBH9_ARATH Homeobox-leucine zipper protein ATHB-9 OS=Arabidopsis thaliana GN=ATHB-9 PE=1 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\|Q9SE43\|REV_ARATH Homeobox-leucine zipper protein REVOLUTA OS=Arabidopsis thaliana GN=REV PE=1 SV=2	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

>sp\|Q9AV49\|HOX9_ORYSJ Homeobox-leucine zipper protein HOX9 OS=Oryza sativa subsp. japonica GN=HOX9 PE=2 SV=1	Back alignment and function description

>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

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		757
359483940		845	PREDICTED: homeobox-leucine zipper prote	0.994	0.891	0.887	0.0
359483942		859	PREDICTED: homeobox-leucine zipper prote	0.994	0.876	0.871	0.0
224056521		844	predicted protein [Populus trichocarpa]	0.994	0.892	0.893	0.0
359483944		862	PREDICTED: homeobox-leucine zipper prote	0.997	0.875	0.864	0.0
224113651		843	predicted protein [Populus trichocarpa]	0.994	0.893	0.877	0.0
356555875		846	PREDICTED: homeobox-leucine zipper prote	0.993	0.888	0.857	0.0
356533043		846	PREDICTED: homeobox-leucine zipper prote	0.993	0.888	0.852	0.0
45479746		843	PHAVOLUTA-like HD-ZIPIII protein [Nicoti	0.993	0.892	0.844	0.0
206572101		783	putative PHV HD-ZIPIII [Malus x domestic	0.993	0.960	0.846	0.0
356528394		849	PREDICTED: homeobox-leucine zipper prote	0.993	0.885	0.826	0.0

>gi\|359483940\|ref\|XP_002281868.2\| PREDICTED: homeobox-leucine zipper protein HOX32-like isoform 1 [Vitis vinifera] gi\|147820218\|emb\|CAN73584.1\| hypothetical protein VITISV_033098 [Vitis vinifera] gi\|297740817\|emb\|CBI30999.3\| unnamed protein product [Vitis vinifera]	Back alignment and taxonomy information

 Score = 1405 bits (3637), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 673/758 (88%), Positives = 707/758 (93%), Gaps = 5/758 (0%)

Query: 1   MNKLLMEENDRLQKQVSHLVYENGYMRQQLHSAPATTTDNSCESVVMSGQHQQQQNPTPQ 60
           MNKLLMEENDRLQKQVS LVYENGYMRQQL SA   TTD SCESVVMSGQHQQQQNPTPQ
Sbjct: 92  MNKLLMEENDRLQKQVSQLVYENGYMRQQLQSASTATTDTSCESVVMSGQHQQQQNPTPQ 151

Query: 61  HPQRDASNPAGLLAVAEETLAEFLSKATGTAVDWVQMIGMKPGPDSIGIVAVSRNCSGVA 120
           HPQRDASNPAGLLA+AEETLAEFLSKATGTAVDWVQMIGMKPGPDSIGIVAVSRNCSGVA
Sbjct: 152 HPQRDASNPAGLLAIAEETLAEFLSKATGTAVDWVQMIGMKPGPDSIGIVAVSRNCSGVA 211

Query: 121 ARACGLVSLDPTKIAEILKDCPSWFRDCRCLDVLSVIPTGNGGTIELIYMQTYAPTTLAA 180
           ARACGLVSL+PTK+AEILKD PSWFRDCRCLDVLSVIPTGNGGTIELIYMQTYAPTTLA+
Sbjct: 212 ARACGLVSLEPTKVAEILKDRPSWFRDCRCLDVLSVIPTGNGGTIELIYMQTYAPTTLAS 271

Query: 181 ARDFWLLRYSTSLEDGSLVVCERSLTSSTGGPTGPPPSSFVRAEMLASGFLIRPCEGGGS 240
           ARDFW LRY+TSLEDGSLV+CERSLTSSTGGPTGPP SS++RAEML SG+LIRPCEGGGS
Sbjct: 272 ARDFWTLRYTTSLEDGSLVICERSLTSSTGGPTGPPASSYIRAEMLPSGYLIRPCEGGGS 331

Query: 241 IIHIVDHVDLDAWSVPEVLRPLYESSKILAQKMTMAAMRHIRQIAQETSGEIQYGGGRQP 300
           IIHIVDHVDLDAWSVPEVLRPLYESSKILAQK T+AA+RHIRQIAQETSGEIQYGGGRQP
Sbjct: 332 IIHIVDHVDLDAWSVPEVLRPLYESSKILAQKTTVAALRHIRQIAQETSGEIQYGGGRQP 391

Query: 301 AVLRTFSQRLSRGFNDAINGFLDDGWSLLSSDGGEDVTVAINSSPNKFLGSQYNWSMLPA 360
           AVLRTFSQRL RGFNDA+NGF DDGWSL+ SDG EDVT+ INSSP+KFLG QYN +M P 
Sbjct: 392 AVLRTFSQRLCRGFNDAVNGFADDGWSLMGSDGVEDVTIVINSSPSKFLGPQYNSTMFPT 451

Query: 361 F-GGVLCAKASMLLQNVPPALLVRFLREHRSEWADYGVDAYSAACLKASPYAVPCARPGG 419
           F GGVLCAKASMLLQNVPPALLVRFLREHRSEWADYGVDAYSAACLKASPY VPCARPGG
Sbjct: 452 FGGGVLCAKASMLLQNVPPALLVRFLREHRSEWADYGVDAYSAACLKASPYEVPCARPGG 511

Query: 420 FPSSHVILPLAHTVEHEEFLEVVRLEGHAFSPEDVALARDMYLLQLCSGIDENTVGACAQ 479
           FPSS VILPLAHTVEHEEFLEVVRLEGHAFSPEDVAL RDMYLLQLCSG+DEN  GACAQ
Sbjct: 512 FPSSQVILPLAHTVEHEEFLEVVRLEGHAFSPEDVALTRDMYLLQLCSGVDENAAGACAQ 571

Query: 480 LVFAPIDESFADDAPLLASGFRVIPLDSKAAMQQDGPAASRTLDLASALEVGSGGARPAG 539
           LVFAPIDESFADDAPLL SGFRVIPLD K     DGPAA+RTLDLAS LEVG+GGARPA 
Sbjct: 572 LVFAPIDESFADDAPLLPSGFRVIPLDPKT----DGPAATRTLDLASTLEVGAGGARPAN 627

Query: 540 GTELSNYNSRSVLTIAFQFTFENHMRDNVAAMARQYVRSVVGSVQRVAMAISPSRLGPHA 599
            ++L+NYN RSVLTIAFQFTFENH+RDNVAAMARQYVRSV+ SVQRVAMAI+PSRL  H 
Sbjct: 628 ESDLNNYNLRSVLTIAFQFTFENHVRDNVAAMARQYVRSVMASVQRVAMAIAPSRLSSHM 687

Query: 600 GPKALPGSPEALTLARWISRSYRIHTGGELLRADSLTGDALLKQLWHHSDAIMCCSLKTN 659
           G K LPGSPEALTLARWI RSYRIHTGGELLR DS  GDA+LK LW+HSDAIMCCSLKTN
Sbjct: 688 GLKPLPGSPEALTLARWICRSYRIHTGGELLRVDSQGGDAVLKLLWNHSDAIMCCSLKTN 747

Query: 660 ASPVFTFANQAGLDMLETTLVALQDIMLDKILDEAGRKILCTEFAKIMQQGFAYLPGGMC 719
           ASPVFTFANQAGLDMLETTLVALQDIMLDKILDEAGRKILC+EF+KIMQQGFAYLP G+C
Sbjct: 748 ASPVFTFANQAGLDMLETTLVALQDIMLDKILDEAGRKILCSEFSKIMQQGFAYLPAGIC 807

Query: 720 VSSMGRAVSYEQAVAWKVLDDDDSNHCLAFMFMNWSFV 757
            SSMGR VSYEQA+AWKVL+D+DSNHCLAFMF+NWSFV
Sbjct: 808 TSSMGRPVSYEQAIAWKVLNDEDSNHCLAFMFINWSFV 845

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi\|359483942\|ref\|XP_003633040.1\| PREDICTED: homeobox-leucine zipper protein HOX32-like isoform 2 [Vitis vinifera]	Back alignment and taxonomy information

>gi\|224056521\|ref\|XP_002298892.1\| predicted protein [Populus trichocarpa] gi\|60327627\|gb\|AAX19053.1\| class III HD-Zip protein 4 [Populus trichocarpa] gi\|222846150\|gb\|EEE83697.1\| predicted protein [Populus trichocarpa]	Back alignment and taxonomy information

>gi\|359483944\|ref\|XP_003633041.1\| PREDICTED: homeobox-leucine zipper protein HOX32-like isoform 3 [Vitis vinifera]	Back alignment and taxonomy information

>gi\|224113651\|ref\|XP_002332526.1\| predicted protein [Populus trichocarpa] gi\|60327625\|gb\|AAX19052.1\| class III HD-Zip protein 3 [Populus trichocarpa] gi\|222832638\|gb\|EEE71115.1\| predicted protein [Populus trichocarpa]	Back alignment and taxonomy information

>gi\|356555875\|ref\|XP_003546255.1\| PREDICTED: homeobox-leucine zipper protein ATHB-14-like [Glycine max]	Back alignment and taxonomy information

>gi\|356533043\|ref\|XP_003535078.1\| PREDICTED: homeobox-leucine zipper protein ATHB-14-like [Glycine max]	Back alignment and taxonomy information

>gi\|45479746\|gb\|AAS66760.1\| PHAVOLUTA-like HD-ZIPIII protein [Nicotiana sylvestris]	Back alignment and taxonomy information

>gi\|206572101\|gb\|ACI13683.1\| putative PHV HD-ZIPIII [Malus x domestica]	Back alignment and taxonomy information

>gi\|356528394\|ref\|XP_003532788.1\| PREDICTED: homeobox-leucine zipper protein HOX32-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		757
TAIR\|locus:2061544		852	PHB "AT2G34710" [Arabidopsis t	0.992	0.881	0.772	4.29999999891e-315
TAIR\|locus:2028140		841	PHV "AT1G30490" [Arabidopsis t	0.981	0.883	0.756	4.4e-306
TAIR\|locus:2175856		842	REV "AT5G60690" [Arabidopsis t	0.973	0.875	0.673	1.6e-269
TAIR\|locus:2034086		837	ATHB-15 "AT1G52150" [Arabidops	0.978	0.885	0.636	1e-256
TAIR\|locus:2134088		833	HB-8 "AT4G32880" [Arabidopsis	0.973	0.884	0.633	2.3e-252
TAIR\|locus:2119048		762	ATML1 "AT4G21750" [Arabidopsis	0.335	0.333	0.256	4.7e-07
UNIPROTKB\|Q60B73		157	MCA0608 "Putative uncharacteri	0.178	0.859	0.263	2.4e-06
TAIR\|locus:2135368		743	PDF2 "AT4G04890" [Arabidopsis	0.336	0.343	0.254	2.6e-06
TAIR\|locus:2207235		721	HDG2 "AT1G05230" [Arabidopsis	0.335	0.352	0.270	2.3e-05

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

 Score = 3022 (1068.9 bits), Expect = 4.3e-315, P = 4.3e-315
 Identities = 586/759 (77%), Positives = 648/759 (85%)

Query:     1 MNKLLMEENDRLQKQVSHLVYENGYMRQQLHSAPATTTDNSCESVVMSGXXXXXXXXXXX 60
             MNKLLMEENDRLQKQVS+LVYENG+M+ QLH+A  TTTDNSCESVV+SG           
Sbjct:   100 MNKLLMEENDRLQKQVSNLVYENGHMKHQLHTASGTTTDNSCESVVVSGQQHQQQNPNPQ 159

Query:    61 XXXRDASNPAGLLAVAEETLAEFLSKATGTAVDWVQMIGMKPGPDSIGIVAVSRNCSGVA 120
                RDA+NPAGLL++AEE LAEFLSKATGTAVDWVQMIGMKPGPDSIGIVA+SRNCSG+A
Sbjct:   160 HQQRDANNPAGLLSIAEEALAEFLSKATGTAVDWVQMIGMKPGPDSIGIVAISRNCSGIA 219

Query:   121 ARACGLVSLDPTKIAEILKDCPSWFRDCRCLDVLSVIPTGNGGTIELIYMQTYAPTTLAA 180
             ARACGLVSL+P K+AEILKD PSW RDCR +D LSVIP GNGGTIELIY Q YAPTTLAA
Sbjct:   220 ARACGLVSLEPMKVAEILKDRPSWLRDCRSVDTLSVIPAGNGGTIELIYTQMYAPTTLAA 279

Query:   181 ARDFWLLRYSTSLEDGSLVVCERSLXXXXXXXXXXXXXXFVRAEMLASGFLIRPCEGGGS 240
             ARDFW LRYST LEDGS VVCERSL              FVRAEM  SGFLIRPC+GGGS
Sbjct:   280 ARDFWTLRYSTCLEDGSYVVCERSLTSATGGPTGPPSSNFVRAEMKPSGFLIRPCDGGGS 339

Query:   241 IIHIVDHVDLDAWSVPEVLRPLYESSKILAQKMTMAAMRHIRQIAQETSGEIQYGGGRQP 300
             I+HIVDHVDLDAWSVPEV+RPLYESSKILAQKMT+AA+RH+RQIAQETSGE+QYGGGRQP
Sbjct:   340 ILHIVDHVDLDAWSVPEVMRPLYESSKILAQKMTVAALRHVRQIAQETSGEVQYGGGRQP 399

Query:   301 AVLRTFSQRLSRGFNDAINGFLDDGWSLLSSDGGEDVTVAINSSPNKFLGSQYNWSMLPA 360
             AVLRTFSQRL RGFNDA+NGF+DDGWS + SDG EDVTV IN SP KF GSQY  S LP+
Sbjct:   400 AVLRTFSQRLCRGFNDAVNGFVDDGWSPMGSDGAEDVTVMINLSPGKFGGSQYGNSFLPS 459

Query:   361 FG-GVLCAKASMLLQNVPPALLVRFLREHRSEWADYGVDAYSAACLKASPYAVPCARPGG 419
             FG GVLCAKASMLLQNVPPA+LVRFLREHRSEWADYGVDAY+AA L+ASP+AVPCAR GG
Sbjct:   460 FGSGVLCAKASMLLQNVPPAVLVRFLREHRSEWADYGVDAYAAASLRASPFAVPCARAGG 519

Query:   420 FPSSHVILPLAHTVEHEEFLEVVRLEGHAFSPEDVALARDMYLLQLCSGIDENTVGACAQ 479
             FPS+ VILPLA TVEHEE LEVVRLEGHA+SPED+ LARDMYLLQLCSG+DEN VG CAQ
Sbjct:   520 FPSNQVILPLAQTVEHEESLEVVRLEGHAYSPEDMGLARDMYLLQLCSGVDENVVGGCAQ 579

Query:   480 LVFAPIDESFADDAPLLASGFRVIPLDSKAAMQQDGPAASRTLDLASALEVGSGGARPAG 539
             LVFAPIDESFADDAPLL SGFR+IPL+ K+    +G +A+RTLDLASALE   G  R AG
Sbjct:   580 LVFAPIDESFADDAPLLPSGFRIIPLEQKST--PNGASANRTLDLASALE---GSTRQAG 634

Query:   540 GTELSNYNSRSVLTIAFQFTFENHMRDNVAAMARQYVRSVVGSVQRVAMAISPSRLGPHA 599
               + +  N RSVLTIAFQFTF+NH RD+VA+MARQYVRS+VGS+QRVA+AI+P R G + 
Sbjct:   635 EADPNGCNFRSVLTIAFQFTFDNHSRDSVASMARQYVRSIVGSIQRVALAIAP-RPGSNI 693

Query:   600 GPKALPGSPEALTLARWISRSYRIHTGGELLRADSLT-GDALLKQLWHHSDAIMCCSLKT 658
              P ++P SPEALTL RWISRSY +HTG +L  +DS T GD LL QLW+HSDAI+CCSLKT
Sbjct:   694 SPISVPTSPEALTLVRWISRSYSLHTGADLFGSDSQTSGDTLLHQLWNHSDAILCCSLKT 753

Query:   659 NASPVFTFANQAGLDMLETTLVALQDIMLDKILDEAGRKILCTEFAKIMQQGFAYLPGGM 718
             NASPVFTFANQ GLDMLETTLVALQDIMLDK LDE GRK LC+EF KIMQQG+A+LP G+
Sbjct:   754 NASPVFTFANQTGLDMLETTLVALQDIMLDKTLDEPGRKALCSEFPKIMQQGYAHLPAGV 813

Query:   719 CVSSMGRAVSYEQAVAWKVLDDDDSNHCLAFMFMNWSFV 757
             C SSMGR VSYEQA  WKVL+DD+SNHCLAFMF+NWSFV
Sbjct:   814 CASSMGRMVSYEQATVWKVLEDDESNHCLAFMFVNWSFV 852

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:0009855 "determination of bilateral symmetry" evidence=RCA;IMP

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

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

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

GO:0080060 "integument development" evidence=IGI

GO:0007062 "sister chromatid cohesion" evidence=RCA

GO:0007131 "reciprocal meiotic recombination" evidence=RCA

GO:0007155 "cell adhesion" evidence=RCA

GO:0009640 "photomorphogenesis" evidence=RCA

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

GO:0009845 "seed germination" evidence=RCA

GO:0009880 "embryonic pattern specification" evidence=RCA

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

GO:0009933 "meristem structural organization" evidence=RCA

GO:0009965 "leaf morphogenesis" evidence=RCA

GO:0010051 "xylem and phloem pattern formation" evidence=RCA

GO:0010073 "meristem maintenance" evidence=RCA

GO:0010075 "regulation of meristem growth" evidence=RCA

GO:0010090 "trichome morphogenesis" evidence=RCA

GO:0010162 "seed dormancy process" evidence=RCA

GO:0010182 "sugar mediated signaling pathway" evidence=RCA

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

GO:0010431 "seed maturation" evidence=RCA

GO:0010564 "regulation of cell cycle process" evidence=RCA

GO:0016049 "cell growth" evidence=RCA

GO:0016567 "protein ubiquitination" evidence=RCA

GO:0019915 "lipid storage" evidence=RCA

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

GO:0042138 "meiotic DNA double-strand break formation" evidence=RCA

GO:0045010 "actin nucleation" evidence=RCA

GO:0045132 "meiotic chromosome segregation" evidence=RCA

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

GO:0048366 "leaf development" evidence=RCA

GO:0048589 "developmental growth" evidence=RCA

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

GO:0048825 "cotyledon development" evidence=RCA

GO:0050826 "response to freezing" evidence=RCA

GO:0051301 "cell division" evidence=RCA

GO:0071555 "cell wall organization" evidence=RCA

GO:0009955 "adaxial/abaxial pattern specification" evidence=IMP

TAIR\|locus:2028140 PHV "AT1G30490" [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:2034086 ATHB-15 "AT1G52150" [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

TAIR\|locus:2134088 HB-8 "AT4G32880" [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

UNIPROTKB\|Q60B73 MCA0608 "Putative uncharacterized protein" [Methylococcus capsulatus str. Bath (taxid:243233)]	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

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)
A2WLR5	HOX29_ORYSI	No assigned EC number	0.5800	0.9854	0.8664	N/A	no
Q6AST1	HOX32_ORYSJ	No assigned EC number	0.7957	0.9920	0.8742	yes	no
A2XK30	HOX32_ORYSI	No assigned EC number	0.7957	0.9920	0.8742	N/A	no
A2ZMN9	HOX33_ORYSI	No assigned EC number	0.7608	0.9881	0.8748	N/A	no
A2Z8L4	HOX9_ORYSI	No assigned EC number	0.6776	0.9735	0.8773	N/A	no
Q2QM96	HOX33_ORYSJ	No assigned EC number	0.7608	0.9881	0.8748	no	no
O04292	ATBH9_ARATH	No assigned EC number	0.7818	0.9801	0.8822	no	no
O04291	ATB14_ARATH	No assigned EC number	0.7997	0.9920	0.8814	yes	no
A2XBL9	HOX10_ORYSI	No assigned EC number	0.6530	0.9735	0.8784	N/A	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Alignment Graph	Length	Definition	E-value
Query		757
pfam08670		148	pfam08670, MEKHLA, MEKHLA domain	1e-77
cd08875		229	cd08875, START_ArGLABRA2_like, C-terminal lipid-bi	4e-70
pfam01852		205	pfam01852, START, START domain	3e-53
smart00234		205	smart00234, START, in StAR and phosphatidylcholine	3e-41
cd00177		193	cd00177, START, Lipid-binding START domain of mamm	8e-14
cd08869		197	cd08869, START_RhoGAP, C-terminal lipid-binding ST	2e-04
cd08868		208	cd08868, START_STARD1_3_like, Cholesterol-binding	0.003

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

 Score =  245 bits (629), Expect = 1e-77
 Identities = 91/150 (60%), Positives = 113/150 (75%), Gaps = 2/150 (1%)

Query: 608 PEALTLARWISRSYRIHTGGELLRADSLTGDALLKQLWHHSDAIMCCSLKTNASPVFTFA 667
           PEALTLARW+ +SYR HTG +LL +   +GD+LLK LWHH DA++C SLK  A PVF +A
Sbjct: 1   PEALTLARWLCQSYRRHTGRDLLPSADSSGDSLLKALWHHPDAVLCHSLK--ADPVFNYA 58

Query: 668 NQAGLDMLETTLVALQDIMLDKILDEAGRKILCTEFAKIMQQGFAYLPGGMCVSSMGRAV 727
           NQA LD+LETT V LQD+   K  +E+GRK  C+E AK+MQQGFA L  G+ +SSMGR  
Sbjct: 59  NQAALDLLETTWVELQDLPSRKTAEESGRKERCSELAKVMQQGFACLYSGVRISSMGRRF 118

Query: 728 SYEQAVAWKVLDDDDSNHCLAFMFMNWSFV 757
           S EQAVAWK+LD+D + H  A MF+NWSF+
Sbjct: 119 SIEQAVAWKLLDEDGAYHGQAAMFVNWSFL 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\|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\|176877 cd08868, START_STARD1_3_like, Cholesterol-binding START domain of mammalian STARD1, -3 and related proteins	Back alignment and domain information

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Alignment Graph	Length	Definition	Probability
Query		757
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	99.83
smart00234		206	START in StAR and phosphatidylcholine transfer pro	99.8
cd00177		193	START Lipid-binding START domain of mammalian STAR	99.46
cd08871		222	START_STARD10-like Lipid-binding START domain of m	99.27
cd08868		208	START_STARD1_3_like Cholesterol-binding START doma	99.27
cd08867		206	START_STARD4_5_6-like Lipid-binding START domain o	99.21
cd08904		204	START_STARD6-like Lipid-binding START domain of ma	99.14
cd08903		208	START_STARD5-like Lipid-binding START domain of ma	99.08
cd08905		209	START_STARD1-like Cholesterol-binding START domain	99.06
cd08909		205	START_STARD13-like C-terminal lipid-binding START	98.91
cd08869		197	START_RhoGAP C-terminal lipid-binding START domain	98.9
PLN00188		719	enhanced disease resistance protein (EDR2); Provis	98.88
cd08906		209	START_STARD3-like Cholesterol-binding START domain	98.81
cd08902		202	START_STARD4-like Lipid-binding START domain of ma	98.62
cd08908		204	START_STARD12-like C-terminal lipid-binding START	98.61
cd08874		205	START_STARD9-like C-terminal START domain of mamma	98.55
cd08907		205	START_STARD8-like C-terminal lipid-binding START d	98.37
cd08910		207	START_STARD2-like Lipid-binding START domain of ma	98.34
cd08870		209	START_STARD2_7-like Lipid-binding START domain of	98.33
cd08877		215	START_2 Uncharacterized subgroup of the steroidoge	98.15
cd08876		195	START_1 Uncharacterized subgroup of the steroidoge	98.11
cd08873		235	START_STARD14_15-like Lipid-binding START domain o	98.1
cd08872		235	START_STARD11-like Ceramide-binding START domain o	97.93
PF13426		104	PAS_9: PAS domain; PDB: 3ULF_B 3UE6_E 2Z6D_B 2Z6C_	97.92
cd08911		207	START_STARD7-like Lipid-binding START domain of ma	97.87
cd08914		236	START_STARD15-like Lipid-binding START domain of m	97.72
cd08913		240	START_STARD14-like Lipid-binding START domain of m	97.61
PF00989		113	PAS: PAS fold; InterPro: IPR013767 PAS domains are	97.06
PF08448		110	PAS_4: PAS fold; InterPro: IPR013656 The PAS fold	96.76
PRK13557		540	histidine kinase; Provisional	96.26
KOG2761		219	consensus START domain-containing proteins involve	95.46
cd08864		208	SRPBCC_DUF3074 DUF3074, an uncharacterized ligand-	95.02
PRK13559		361	hypothetical protein; Provisional	94.94
TIGR00229		124	sensory_box PAS domain S-box. The PAS domain was p	94.65
cd08904		204	START_STARD6-like Lipid-binding START domain of ma	94.46
cd08871		222	START_STARD10-like Lipid-binding START domain of m	93.71
cd08869		197	START_RhoGAP C-terminal lipid-binding START domain	93.62
PRK11091		779	aerobic respiration control sensor protein ArcB; P	93.47
cd08874		205	START_STARD9-like C-terminal START domain of mamma	93.02
cd00130		103	PAS PAS domain; PAS motifs appear in archaea, euba	92.64
cd08907		205	START_STARD8-like C-terminal lipid-binding START d	92.31
TIGR02040		442	PpsR-CrtJ transcriptional regulator PpsR. This mod	91.6
TIGR02938		494	nifL_nitrog nitrogen fixation negative regulator N	91.28
cd00177		193	START Lipid-binding START domain of mammalian STAR	91.14
PRK13558		665	bacterio-opsin activator; Provisional	90.03
TIGR02040		442	PpsR-CrtJ transcriptional regulator PpsR. This mod	89.94
PRK13560		807	hypothetical protein; Provisional	89.84
PF15058		200	Speriolin_N: Speriolin N terminus	89.83
PF13188		64	PAS_8: PAS domain; PDB: 2JHE_D 3VOL_A.	89.44
cd08866		144	SRPBCC_11 Ligand-binding SRPBCC domain of an uncha	89.26
cd08877		215	START_2 Uncharacterized subgroup of the steroidoge	87.58
cd08868		208	START_STARD1_3_like Cholesterol-binding START doma	86.83
cd08875		229	START_ArGLABRA2_like C-terminal lipid-binding STAR	86.3
smart00234		206	START in StAR and phosphatidylcholine transfer pro	86.22
cd08909		205	START_STARD13-like C-terminal lipid-binding START	85.4
cd07819		140	SRPBCC_2 Ligand-binding SRPBCC domain of an unchar	85.3
cd05018		144	CoxG Carbon monoxide dehydrogenase subunit G (CoxG	84.66
PF08447		91	PAS_3: PAS fold; InterPro: IPR013655 The PAS fold	84.2
PRK10060		663	RNase II stability modulator; Provisional	84.07
PRK11073		348	glnL nitrogen regulation protein NR(II); Provision	83.06
PRK11359		799	cyclic-di-GMP phosphodiesterase; Provisional	82.99
cd08913		240	START_STARD14-like Lipid-binding START domain of m	82.78
cd08860		146	TcmN_ARO-CYC_like N-terminal aromatase/cyclase dom	81.92
cd08876		195	START_1 Uncharacterized subgroup of the steroidoge	80.7
cd08906		209	START_STARD3-like Cholesterol-binding START domain	80.58
cd07813		138	COQ10p_like Coenzyme Q-binding protein COQ10p and	80.19

>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=4.2e-77  Score=608.77  Aligned_cols=211  Identities=36%  Similarity=0.595  Sum_probs=198.0

Q ss_pred             hhHHHHHHHHHHHHHHHhhcCCCcceeecCCCCC---CCCccceeeecC------CCceeeeeeeeEEeeChhhhhhhhc
Q 004383           69 PAGLLAVAEETLAEFLSKATGTAVDWVQMIGMKP---GPDSIGIVAVSR------NCSGVAARACGLVSLDPTKIAEILK  139 (757)
Q Consensus        69 ~~~ll~iAe~am~Efl~~At~~~plWv~~pg~k~---gpdsig~~~~~~------~~~~eAsRa~glV~m~~~~LVe~lm  139 (757)
                      +++|++||++||+||++|||+++|+|+++||||+   ++|+++....++      ||++|||||||+|.||+.+|||+||
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            4789999999999999999999999999999998   899998655433      5999999999999999999999999


Q ss_pred             CcchhhhhCccc----eeeeeeccCC----CCeeeeeeehhcccccccccceeEEEEeeeeeCCCcEEEEEeecCCCCCC
Q 004383          140 DCPSWFRDCRCL----DVLSVIPTGN----GGTIELIYMQTYAPTTLAAARDFWLLRYSTSLEDGSLVVCERSLTSSTGG  211 (757)
Q Consensus       140 D~~~W~~~f~~i----~vl~~~~~g~----~G~lqLm~~e~~v~SpLvp~Re~~fLRYckql~~G~wvVvDvSld~~~~~  211 (757)
                      |+++|.++||++    +|++++++|+    ||+|||||+|||+||||||+|||||||||||++||+|||||||+|+.+. 
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            999999988776    9999999997    7899999999999999999999999999999999999999999998752 


Q ss_pred             CCCCCCCccceeeecccceeeeecCCCceEEEEEEeeeecCCcccccchhhhchhHHHHHHHHHHHH-HHHh
Q 004383          212 PTGPPPSSFVRAEMLASGFLIRPCEGGGSIIHIVDHVDLDAWSVPEVLRPLYESSKILAQKMTMAAM-RHIR  282 (757)
Q Consensus       212 ~~~~~~~~f~r~~rlPSGcLIq~~~nG~SkVtwVeH~e~d~~~V~el~RpL~~Sg~afgarrw~aaL-r~~e  282 (757)
                        .++.++|+||||+|||||||||+|||||||||||+|||++.+|.+||+++.||+||||+||+++| ||||
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              33456799999999999999999999999999999999999999999999999999999999999 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

>cd00177 START Lipid-binding START domain of mammalian STARD1-STARD15 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

>cd08868 START_STARD1_3_like Cholesterol-binding START domain of mammalian STARD1, -3 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

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

>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

>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

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

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

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

>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

>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

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

>cd08911 START_STARD7-like Lipid-binding START domain of mammalian STARD7 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

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

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

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

>PRK13559 hypothetical protein; Provisional	Back alignment and domain information

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

>cd08904 START_STARD6-like Lipid-binding START domain of mammalian STARD6 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

>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

>PRK11091 aerobic respiration control sensor protein ArcB; Provisional	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

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

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

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

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

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

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

>PRK13560 hypothetical protein; Provisional	Back alignment and domain information

>PF15058 Speriolin_N: Speriolin N terminus	Back alignment and domain information

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

>cd08866 SRPBCC_11 Ligand-binding SRPBCC domain of an uncharacterized subfamily of proteins	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

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

>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

>smart00234 START in StAR and phosphatidylcholine transfer protein	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

>cd07819 SRPBCC_2 Ligand-binding SRPBCC domain of an uncharacterized subfamily of proteins	Back alignment and domain information

>cd05018 CoxG Carbon monoxide dehydrogenase subunit G (CoxG)	Back alignment and domain information

>PF08447 PAS_3: PAS fold; InterPro: IPR013655 The PAS fold corresponds to the structural domain that has previously been defined as PAS and PAC motifs []	Back alignment and domain information

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

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

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

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

>cd08860 TcmN_ARO-CYC_like N-terminal aromatase/cyclase domain of the multifunctional protein tetracenomycin (TcmN) and related domains	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

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

>cd07813 COQ10p_like Coenzyme Q-binding protein COQ10p and similar proteins	Back alignment and domain information

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Alignment Graph	Length	Definition	E-value
Query		757
2r55_A		231	STAR-related lipid transfer protein 5; alpha and b	8e-25
2pso_A		237	STAR-related lipid transfer protein 13; alpha and	9e-25
1jss_A		224	Stard4, cholesterol-regulated start protein 4; sta	5e-20
3qsz_A		189	STAR-related lipid transfer protein; structural ge	9e-17
3fo5_A		258	Thioesterase, adipose associated, isoform BFIT2; o	6e-14
3p0l_A		221	Steroidogenic acute regulatory protein, mitochond;	2e-12
1em2_A		229	MLN64 protein; beta barrel, lipid binding protein;	4e-11
1ln1_A		214	PC-TP, phosphatidylcholine transfer protein; start	4e-10
1vt4_I		1221	APAF-1 related killer DARK; drosophila apoptosome,	2e-05
1vt4_I		1221	APAF-1 related killer DARK; drosophila apoptosome,	6e-04

>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

 Score =  102 bits (256), Expect = 8e-25
 Identities = 42/249 (16%), Positives = 76/249 (30%), Gaps = 33/249 (13%)

Query: 50  QHQQQQNPTPQHPQRDASNPAGLLAVAEETLAEFLSKATGTAVDWVQMIGMKPGPDSIGI 109
            H    +        +    +    ++E    + L     TA  W      K   +  G+
Sbjct: 2   HHHHHHSSGVDLGTENLYFQSMAAQMSEAVAEKMLQYRRDTA-GW------KICREGNGV 54

Query: 110 VAVSR---NCSGVAARACGLVSLDPTKIAEILKD-----CPSWFRDCRCLDVLSVIPTGN 161
               R      G   R  G+V     ++ + +K         W  +    +++  I    
Sbjct: 55  SVSWRPSVEFPGNLYRGEGIVYGTLEEVWDCVKPAVGGLRVKWDENVTGFEIIQSI---- 110

Query: 162 GGTIELIYMQT-YAPTTLAAARDFWLLRYSTSLEDGSLVVCERSLTSSTGGPTGPPPSSF 220
             T+ +    T  A   L + RDF  L      EDG++      +      P  PP   F
Sbjct: 111 TDTLCVSRTSTPSAAMKLISPRDFVDLVLVKRYEDGTISSNATHVEH----PLCPPKPGF 166

Query: 221 VRAEMLASGFLIRPCEGGGSIIHI--VDHVDLDAWSVPEVLRPLYESSKILAQKMTMAAM 278
           VR      G    P  G  +  ++    H DL  +       P         + MT    
Sbjct: 167 VRGFNHPCGCFCEPLPGEPTKTNLVTFFHTDLSGYL------PQNVVDSFFPRSMTR-FY 219

Query: 279 RHIRQIAQE 287
            ++++  ++
Sbjct: 220 ANLQKAVKQ 228

PyMOL of 2r55

>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

>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

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

>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

>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

>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

>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

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Alignment Graph	Length	Definition	Probability
Query		757
2r55_A		231	STAR-related lipid transfer protein 5; alpha and b	99.88
2pso_A		237	STAR-related lipid transfer protein 13; alpha and	99.58
1em2_A		229	MLN64 protein; beta barrel, lipid binding protein;	99.54
3p0l_A		221	Steroidogenic acute regulatory protein, mitochond;	99.52
1ln1_A		214	PC-TP, phosphatidylcholine transfer protein; start	99.25
1jss_A		224	Stard4, cholesterol-regulated start protein 4; sta	99.18
3fo5_A		258	Thioesterase, adipose associated, isoform BFIT2; o	99.17
3qsz_A		189	STAR-related lipid transfer protein; structural ge	98.79
2e3n_A		255	Lipid-transfer protein CERT; ceramide transfer, li	98.77
4eet_B		115	Phototropin-2; LOV, blue light photoreceptor, sign	97.64
3t50_A		128	Blue-light-activated histidine kinase; PAS superfa	97.63
3lyx_A		124	Sensory BOX/ggdef domain protein; structural genom	97.61
3ue6_A		166	Aureochrome1; PAS/LOV domain, FMN-binding blue-lig	97.52
1n9l_A		109	PHOT-LOV1, putative blue light receptor; phototrop	97.41
4hia_A		176	LOV protein; PAS, HTH, signaling protein; HET: FMN	97.37
2gj3_A		120	Nitrogen fixation regulatory protein; PAS domain,	97.36
3p7n_A		258	Sensor histidine kinase; LOV domain, light-activat	97.28
3sw1_A		162	Sensory box protein; light-oxygen-voltage, LOV, PA	97.26
2z6d_A		130	Phototropin-2; PAS-fold, LOV-fold, alternative spl	97.25
1byw_A		110	Protein (human ERG potassium channel); PAS domain,	97.23
3d72_A		149	Vivid PAS protein VVD; circadian, photoreceptor, b	97.21
3f1p_A		117	Endothelial PAS domain-containing protein 1; PAS d	97.14
3mqq_A		120	Transcriptional regulator, LUXR family; PAS domain	97.07
3luq_A		114	Sensor protein; PAS, histidine, kinase, PSI, MCSG,	97.02
2l0w_A		138	Potassium voltage-gated channel, subfamily H (EAG	96.92
3kx0_X		185	Uncharacterized protein RV1364C/MT1410; PAS domain	96.88
3k3c_A		158	Protein RV1364C/MT1410; sensor, PAS, signal transd	96.85
2r78_A		117	Sensor protein; sensory box sensor histidine kinas	96.82
1d06_A		130	Nitrogen fixation regulatory protein FIXL; oxygen	96.73
2v0u_A		146	NPH1-1, LOV2; kinase, transferase, ATP-binding, se	96.71
2pr5_A		132	Blue-light photoreceptor; light-oxygen-voltage, LO	96.61
2wkq_A		332	NPH1-1, RAS-related C3 botulinum toxin substrate 1	96.53
3f1p_B		121	ARYL hydrocarbon receptor nuclear translocator; PA	96.53
2r55_A		231	STAR-related lipid transfer protein 5; alpha and b	96.44
3olo_A		118	Two-component sensor histidine kinase; structural	96.4
3fc7_A		125	HTR-like protein, sensor protein; APC87712.1, HTR-	96.29
3eeh_A		125	Putative light and redox sensing histidine kinase;	96.28
3ewk_A		227	Sensor protein; PAS domain, alpha/beta fold, kinas	96.26
2vv6_A		119	FIXL, sensor protein FIXL; signaling protein, tran	96.17
3ewk_A		227	Sensor protein; PAS domain, alpha/beta fold, kinas	96.08
3b33_A		115	Sensor protein; structural genomics, PAS domain, n	96.06
3mxq_A		152	Sensor protein; PSI2, MCSG, structural genomics, p	96.05
3mjq_A		126	Uncharacterized protein; NESG, structural genomics	95.94
2kdk_A		121	ARYL hydrocarbon receptor nuclear translocator-LI	95.79
3nja_A		125	Probable ggdef family protein; structural genomics	95.65
3bwl_A		126	Sensor protein; structural genomics, APC87707.1, P	95.46
3icy_A		118	Sensor protein; sensory box histidine kinase/respo	95.46
1v9y_A		167	Heme PAS sensor protein; signaling protein; HET: H	94.92
3mfx_A		129	Sensory BOX/ggdef family protein; alpha-beta prote	94.89
2d4r_A		147	Hypothetical protein TTHA0849; start domain, struc	94.78
3h9w_A		115	Diguanylate cyclase with PAS/PAC sensor; alpha-bet	94.59
1ll8_A		114	PAS kinase; PAS domain, ligand binding, ligand scr	94.47
2pso_A		237	STAR-related lipid transfer protein 13; alpha and	94.46
3a0s_A		96	Sensor protein; PAS-fold, kinase, phosphoprotein,	94.42
1jss_A		224	Stard4, cholesterol-regulated start protein 4; sta	94.28
3p0l_A		221	Steroidogenic acute regulatory protein, mitochond;	94.1
3fo5_A		258	Thioesterase, adipose associated, isoform BFIT2; o	94.08
4hi4_A		121	Aerotaxis transducer AER2; PAS domain, diatomic GA	93.78
3qsz_A		189	STAR-related lipid transfer protein; structural ge	93.25
3fg8_A		118	Uncharacterized protein RHA05790; PAS domain, stru	91.38
1ln1_A		214	PC-TP, phosphatidylcholine transfer protein; start	91.36
1em2_A		229	MLN64 protein; beta barrel, lipid binding protein;	90.67
4f3l_A		361	Mclock, circadian locomoter output cycles protein	90.4
3vol_A		233	Aerotaxis transducer AER2; heme, oxygen sensor pro	87.75
3p9v_A		161	Uncharacterized protein; structural genomics, PSI-	87.64
2w0n_A		118	Sensor protein DCUS; signal transduction, two-comp	87.46
3tfz_A		172	Cyclase; helix-GRIP, BET V1-like superfamily, bios	87.43
2vlg_A		111	Sporulation kinase A; histidine kinase, two-compon	86.64
4eho_A		635	Bacteriophytochrome, PAS/PAC sensor; photoreceptor	84.73
2jhe_A		190	Transcription regulator TYRR; aromatic hydrocarbon	82.25
1t17_A		148	Conserved hypothetical protein; beta-alpha-beta-BE	82.24
3mr0_A		142	Sensory box histidine kinase/response regulator; P	80.39

>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=99.88  E-value=3.3e-21  Score=193.88  Aligned_cols=209  Identities=18%  Similarity=0.226  Sum_probs=164.2

Q ss_pred             CCCCCCCCCChhHHHHHHHHHHHHHHHhhcCCCcceeecCCCCCCCCccceeee-cCCCceeeeeeeeEEeeChhhhhhh
Q 004383           59 PQHPQRDASNPAGLLAVAEETLAEFLSKATGTAVDWVQMIGMKPGPDSIGIVAV-SRNCSGVAARACGLVSLDPTKIAEI  137 (757)
Q Consensus        59 ~~~~~~d~~~~~~ll~iAe~am~Efl~~At~~~plWv~~pg~k~gpdsig~~~~-~~~~~~eAsRa~glV~m~~~~LVe~  137 (757)
                      |-|+..+...++.++++|+++|+||+++++.+ ..|..... +   +-+-++.. ..+..+.+-|+.|+|...+.+|++.
T Consensus        11 ~~~~~~~~~~~~~y~~~a~~~~~~~l~~~~~~-~~W~~~~~-~---~gv~v~~~~~~~~~~~~~k~~~~v~~~~~~v~~~   85 (231)
T 2r55_A           11 VDLGTENLYFQSMAAQMSEAVAEKMLQYRRDT-AGWKICRE-G---NGVSVSWRPSVEFPGNLYRGEGIVYGTLEEVWDC   85 (231)
T ss_dssp             ---------CHHHHHHHHHHHHHHHHHHHHCC-SSCEEEEC-C---SSEEEEEEECSSSSSEEEEEEEEESSCHHHHHHH
T ss_pred             CCCCCCCchhHHHHHHHHHHHHHHHHHHhcCC-CCCEEEEe-C---CCEEEEEEccCCCCCcEEEEEEEECCCHHHHHHH
Confidence            33444455558999999999999999999765 68998632 1   11222221 2345678899999999999999999


Q ss_pred             hcC-----cchhhhhCccceeeeeeccCCCCeeeeeee-hhcccccccccceeEEEEeeeeeCCCcEEEEEeecCCCCCC
Q 004383          138 LKD-----CPSWFRDCRCLDVLSVIPTGNGGTIELIYM-QTYAPTTLAAARDFWLLRYSTSLEDGSLVVCERSLTSSTGG  211 (757)
Q Consensus       138 lmD-----~~~W~~~f~~i~vl~~~~~g~~G~lqLm~~-e~~v~SpLvp~Re~~fLRYckql~~G~wvVvDvSld~~~~~  211 (757)
                      ||+     +.+|-..|...++|+.++.    .-.++|. ....+++++++|||.++||+++.++|.|+|+.+|++.    
T Consensus        86 l~~~d~~~r~~Wd~~~~~~~vle~i~~----~~~i~~~~~~~~~~~~v~~RDfv~~r~~~~~~~g~~vi~~~Sv~~----  157 (231)
T 2r55_A           86 VKPAVGGLRVKWDENVTGFEIIQSITD----TLCVSRTSTPSAAMKLISPRDFVDLVLVKRYEDGTISSNATHVEH----  157 (231)
T ss_dssp             HCC--CCSHHHHCTTCSEEEEEEECSS----SEEEEEEECCCBTTTTBCCEEEEEEEEEEECTTSCEEEEEEECCC----
T ss_pred             HHhhCcchhhhhccccceeEEEEEcCC----CEEEEEEEeccccCCccCCCeEEEEEEEEEcCCCEEEEEEEeccC----
Confidence            977     8999999999999999863    2344442 2234457999999999999999999999999999984    


Q ss_pred             CCCCCCCccceeeecccceeeeecC--CCceEEEEEEeeeecCCcccccchhhhchhHHHHHHHHHHHHH-HHhhh
Q 004383          212 PTGPPPSSFVRAEMLASGFLIRPCE--GGGSIIHIVDHVDLDAWSVPEVLRPLYESSKILAQKMTMAAMR-HIRQI  284 (757)
Q Consensus       212 ~~~~~~~~f~r~~rlPSGcLIq~~~--nG~SkVtwVeH~e~d~~~V~el~RpL~~Sg~afgarrw~aaLr-~~erl  284 (757)
                      |..|+...|+|++.++|||+|||++  +|.|+|||+.|+|...| +|   +.++++.+..+...|++.|| +|+..
T Consensus       158 ~~~P~~~~~VR~~~~~~g~~i~p~~~~~~~t~vt~~~~~Dp~G~-iP---~~lvn~~~~~~~~~~~~~Lr~~~~~~  229 (231)
T 2r55_A          158 PLCPPKPGFVRGFNHPCGCFCEPLPGEPTKTNLVTFFHTDLSGY-LP---QNVVDSFFPRSMTRFYANLQKAVKQF  229 (231)
T ss_dssp             TTSCCCTTCEEEEECSEEEEEEECC--CCCEEEEEEECEECCSS-CC---HHHHHHHHHHHHHHHHHHHHHHHHGG
T ss_pred             CCCCCCCCCEEEEEEeeEEEEEEeCCCCCcEEEEEEEEeCCCCC-cc---HHHHHHHHhHhHHHHHHHHHHHHHHh
Confidence            4456667899999999999999998  78999999999999876 66   68888999999999999996 88764

PyMOL of 2r55

>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

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

>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

>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

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

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

>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

>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

>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

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

>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

>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

>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

>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

>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

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

>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

>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

>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

>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

>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

>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

>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

>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

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

>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

>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

>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

>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

>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

>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

>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

>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

>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

>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

>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

>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

>3p0l_A Steroidogenic acute regulatory protein, mitochond; structural genomics consortium, SGC, start domain, cholester transport, cholesterol; 3.40A {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

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

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

>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

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

>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

>3p9v_A Uncharacterized protein; structural genomics, PSI-biology, protein structure initiati northeast structural genomics consortium, NESG; 1.78A {Marinobacter aquaeolei}	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

>3tfz_A Cyclase; helix-GRIP, BET V1-like superfamily, biosynthetic protein; HET: CXS; 2.39A {Streptomyces SP}	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

>1t17_A Conserved hypothetical protein; beta-alpha-beta-BETA-beta-BETA-beta-BETA-helix, structural G protein structure initiative, PSI, NESG; NMR {Caulobacter crescentus} SCOP: d.129.3.6	Back alignment and structure

>3mr0_A Sensory box histidine kinase/response regulator; PAS fold, structural genomics, PSI-2; HET: PG5; 1.49A {Burkholderia thailandensis}	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		757
d2psoa1		197	d.129.3.2 (A:908-1104) Star-related lipid transfer	1e-14
d1em2a_		214	d.129.3.2 (A:) Lipid transport domain of Mln64 {Hu	2e-07
d1ln1a_		203	d.129.3.2 (A:) Phosphatidylcholine transfer protei	4e-07

>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


class: Alpha and beta proteins (a+b)
fold: TBP-like
superfamily: Bet v1-like
family: STAR domain
domain: Star-related lipid transfer protein 13
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 70.8 bits (173), Expect = 1e-14
 Identities = 33/164 (20%), Positives = 58/164 (35%), Gaps = 15/164 (9%)

Query: 112 VSRNCSGVAARACGLVSLDPTKI-AEILKDCPSWFRDCRCLDVLSVIPTGNGGTIELIYM 170
           V         +A   V   P+ +   +L++   W  D     V+  +        E+   
Sbjct: 37  VGDGNPLKLWKASVEVEAPPSVVLNRVLRERHLWDEDFVQWKVVETL----DRQTEIYQY 92

Query: 171 QTYAPTTLAAARDFWLLR-YSTSLEDGSLVVCERSLTSSTGGPTGPPPSSFVRAEMLASG 229
              +     + RDF +LR + T L  G   +   S+               VRA ++ S 
Sbjct: 93  VLNSMAPHPS-RDFVVLRTWKTDLPKGMCTLVSLSVEHEE-----AQLLGGVRAVVMDSQ 146

Query: 230 FLIRPCEGGGSIIHIVDHVDLDAWSVPEVLRPLYESSKILAQKM 273
           +LI PC  G S +  +  +DL     PE     +    + A ++
Sbjct: 147 YLIEPCGSGKSRLTHICRIDLKGH-SPEWYSKGF--GHLCAAEV 187

PyMOL of d2psoa1

>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		757
d1jssa_		199	Cholesterol-regulated Start protein 4 (Stard4). {M	99.11
d2psoa1		197	Star-related lipid transfer protein 13 {Human (Hom	98.99
d1em2a_		214	Lipid transport domain of Mln64 {Human (Homo sapie	98.78
d1ln1a_		203	Phosphatidylcholine transfer protein {Human (Homo	98.59
d1jnua_		104	Photoreceptor phy3 flavin-binding domain, lov2 {Ma	98.12
d1n9la_		109	Putative blue light receptor, phot-lov1 domain {Gr	97.82
d1bywa_		110	Erg potassium channel, N-terminal domain {Human (H	97.38
d1v9ya_		113	Direct oxygen sensor protein, DOS {Escherichia col	97.3
d1ew0a_		130	Histidine kinase FixL heme domain {Rhizobium melil	97.28
d1mzua_		110	PYP domain of sensor histidine kinase Ppr {Rhodosp	97.27
d1p97a_		114	Hypoxia-inducible factor Hif2a, C-terminal domain	96.95
d1xj3a1		106	Histidine kinase FixL heme domain {Bradyrhizobium	96.82
d1nwza_		125	Photoactive yellow protein, PYP {Ectothiorhodospir	96.47
d1ll8a_		114	N-terminal PAS domain of Pas kinase {Human (Homo s	96.44
d2psoa1		197	Star-related lipid transfer protein 13 {Human (Hom	94.63
d1ln1a_		203	Phosphatidylcholine transfer protein {Human (Homo	92.92
d2d4ra1		146	Hypothetical protein TTHA0849 {Thermus thermophilu	91.04
d1jssa_		199	Cholesterol-regulated Start protein 4 (Stard4). {M	90.91
d1em2a_		214	Lipid transport domain of Mln64 {Human (Homo sapie	89.07
d2rera1		155	Multifunctional enzyme TcmN, cyclase/aromatase dom	80.06

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

class: Alpha and beta proteins (a+b)
fold: TBP-like
superfamily: Bet v1-like
family: STAR domain
domain: Cholesterol-regulated Start protein 4 (Stard4).
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.11  E-value=9.8e-10  Score=105.06  Aligned_cols=167  Identities=17%  Similarity=0.268  Sum_probs=123.1

Q ss_pred             HHHHHHHHHHHHhhcCCCcceeecCCCCCCCCccceeee-cCCCceeeeeeeeEEeeChhhhhhhhcCcch---hhhhCc
Q 004383           74 AVAEETLAEFLSKATGTAVDWVQMIGMKPGPDSIGIVAV-SRNCSGVAARACGLVSLDPTKIAEILKDCPS---WFRDCR  149 (757)
Q Consensus        74 ~iAe~am~Efl~~At~~~plWv~~pg~k~gpdsig~~~~-~~~~~~eAsRa~glV~m~~~~LVe~lmD~~~---W~~~f~  149 (757)
                      ++|.+..++|++.++..+-.|-..- .+.|   +-+... ..+.....-|+.++|...+.++++.|.|.+.   |...|.
T Consensus         2 ~~~~~~~~~l~~~~~~~~~~W~~~~-~~~~---v~v~~~~~~~~~~~~~r~~~~i~~~~~~v~~~l~d~~~~~~Wd~~~~   77 (199)
T d1jssa_           2 SISTKLQNTLIQYHSIEEDEWRVAK-KAKD---VTVWRKPSEEFNGYLYKAQGVMDDVVNNVIDHIRPGPWRLDWDRLMT   77 (199)
T ss_dssp             THHHHHHHHHHHHTTSCGGGCEEEE-EETT---EEEEEEECSSSSSEEEEEEEEESSCHHHHHHHHSSSTTHHHHCSSEE
T ss_pred             cHHHHHHHHHHHhcCcCcCCCeEEE-ecCC---EEEEEEEcCCCCcEEEEEEEEeCCCHHHHHHHHhChhhhhhcccchh
Confidence            4789999999999999999998751 1111   111111 2344556789999999999999999998555   555555


Q ss_pred             cceeeeeeccCCCCeeeeeeehh-cccccccccceeEEEEeeeeeCCCcEEEEEeecCCCCCCCCCCCCCccceeeeccc
Q 004383          150 CLDVLSVIPTGNGGTIELIYMQT-YAPTTLAAARDFWLLRYSTSLEDGSLVVCERSLTSSTGGPTGPPPSSFVRAEMLAS  228 (757)
Q Consensus       150 ~i~vl~~~~~g~~G~lqLm~~e~-~v~SpLvp~Re~~fLRYckql~~G~wvVvDvSld~~~~~~~~~~~~~f~r~~rlPS  228 (757)
                      ..++|+.+..   + ..++|.-+ -.+-|++..|||.++|++...++|. +++.+|.+.      .|..+.++|++++.+
T Consensus        78 ~~~~le~~~~---~-~~i~~~~~~~~~~~~v~~RD~v~~~~~~~~~~~~-~~~~~~~~~------~p~~~~~VR~~~~~~  146 (199)
T d1jssa_          78 SLDVLEHFEE---N-CCVMRYTTAGQLLNIISPREFVDFSYTVGYEEGL-LSCGVSVEW------SETRPEFVRGYNHPC  146 (199)
T ss_dssp             EEEEEEECST---T-EEEEEEEECCBTTTTBCCEEEEEEEEEEEETTEE-EEEEEECCC------CCCCTTSEECEECSE
T ss_pred             eEEEEEEcCC---C-cEEEEEEEcccCCCCcCCcEEEEEEEEEEcCCcE-EEEEEecCC------CCCCCceEEEEEeee
Confidence            5566665542   2 23344333 2467889999999999999998885 455677653      233457999999999


Q ss_pred             ceeeeecCCC--ceEEEEEEeeeecCCccc
Q 004383          229 GFLIRPCEGG--GSIIHIVDHVDLDAWSVP  256 (757)
Q Consensus       229 GcLIq~~~nG--~SkVtwVeH~e~d~~~V~  256 (757)
                      |++|+|.++|  +|+|+++-|+|..-+ +|
T Consensus       147 ~~~i~p~~~~~~~t~vt~~~~~Dp~G~-iP  175 (199)
T d1jssa_         147 GWFCVPLKDSPSQSLLTGYIQTDLRGM-IP  175 (199)
T ss_dssp             EEEEEEETTEEEEEEEEEEECEECCSC-CC
T ss_pred             eEEEEEcCCCCCcEEEEEEEEcCCCCC-Cc
Confidence            9999999988  899999999998754 55

PyMOL of d1jssa_

>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

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

>d1ew0a_ d.110.3.2 (A:) Histidine kinase FixL heme domain {Rhizobium meliloti [TaxId: 382]}	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

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

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

>d2d4ra1 d.129.3.6 (A:2-147) Hypothetical protein TTHA0849 {Thermus thermophilus [TaxId: 274]}	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

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

>d2rera1 d.129.3.6 (A:1-155) Multifunctional enzyme TcmN, cyclase/aromatase domain {Streptomyces glaucescens [TaxId: 1907]}	Back information, alignment and structure