Citrus Sinensis ID: 006028

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----

MAYVEPNFGCSLSSQGGPGSGDLYRELWKACAGPLVEVPRNGERVYYFPQGHIEQLEASTNQELTHQEPLFDLPSKILCRVVHIELLAEQETDEVYAQITLHPETDQTEPRSPDQCLPEPPKQTVHSFCKILTASDTSTHGGFSVLRKHATECLPPLDMTLATPTQELAAKDLHGYEWRFKHIFRGQPRRHLLTTGWSTFVTSKRLVAGDAFVFLRGENGELRVGVRRLAHQQSSMPSSVISSQSMHLGVLATAAHAVKTSTLFIVYYKPRTSQFIIGLNKYLEAVHHCFSVGMRFKMRFEGEDSPERRFTGTIVGVGDFSEQWPGSKWRSLKIQWDEPATVQRPERVSPWEIEPFVASAPLNLAQPAVKSKRPRSIDIPASASAFWYQGSTQSHDITQVVGATEGQSSESQVVRPMRQKEIDSTIINNNSTDDHRIVAAQSVLSGYASSGRPGNTVIHEEVERGKKSEASLGCWLFGIDLKHNSNTAAPLGRKVVDPTTGTSGVKGSARAASDFDASQNQDLKEVKRGMADVSRKETQNKQGSAASTRTRTKVQMQGIAVGRAVDLTALKGYDDLFDELEKMFEIQGQLRPRDKWAVVFTDDEGDMMLAGDDQWPEFCKMVKKIFIYSTEEVKNMATSSKPIASSVEGEGTAISLDSELKSET

ccccccccccccccccccccccccHHHHHHHccccccccccccEEEEccccHHHHccccccccccccccccccccccEEEEEEEEEccccccHHHHEEEEEcccccccccccccccccccccccccEEEEEEEcccccccccccccccccccccccccccccccccEEEEEEcccccEEEEEEEccccccEEEcccccccccccccccccEEEEEEcccccEEEEEEEEEccccccccccccccccccHHHHHHHHHHHccccEEEEEccccccEEEcHHHHHHHHHcccccccEEEEEEEccccccEEEccEEEEEccccccccccccccEEEEEcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHccccccccccccccccccccccccEEEEEcccEEEEEEEccccccHHHHHHHHHHHHccccccccccccEEEEEcccccEEEcccccHHHHHHcccEEEEEcHHHHHcccccccccccccccccccccccccccccc

ccccccccccccccccccccccccHHHHHHHcccccEccccccEEEEcccccHHHHHccccHcHHHccccccccccEEEEEEEEEEEccccccEEEEEEEEcccccccccccccccccccccccccHHHHEcccccccccccccHHHHHHHHHcccccccccccHHHHHHHHccccEEEEEEEEccccccEEEccccEEEEcccEEEcccEEEEEEcccccEEEEEEEccccccccccccccccccHHHHHHHHHHHHHccccEEEEEccccccEEEEHHHHHHHHHccccEcEEEEEEEcccccccEEEEEEEEEcccccccccccccEEEEEEccccccccccccccccEEEccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEccEEccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEEEEcccEcccEEEEEccccHHHHHHHHHHHHccccccccccccEEEEEcccccEEEEccccHHHHHHHHEEEEEEcHHHHHHccccccccccccccccccccccccccccc

mayvepnfgcslssqggpgsgdLYRELWKACagplvevprngervyyfpqghieqleastnqelthqeplfdlpskilCRVVHIELLAEQETDEVYAQITlhpetdqteprspdqclpeppkqtvhSFCKIltasdtsthgGFSVLRKHateclppldmtlatptqELAAKDLHGYEWRFKhifrgqprrhllttgwstfvtskrlvagdAFVFlrgengelRVGVRRLAhqqssmpssvissqsmHLGVLATAAHAVKTSTLFIVYykprtsqfIIGLNKYLEAVHHCFSVGMRfkmrfegedsperrftgtivgvgdfseqwpgskwrslkiqwdepatvqrpervspweiepfvasaplnlaqpavkskrprsidipasasafwyqgstqshditqvvgategqssesqvvrpmrqkeidstiinnnstddhRIVAAQSVLSgyassgrpgntviheevergkkseaslGCWLFgidlkhnsntaaplgrkvvdpttgtsgvkgsaraasdfdasqnqDLKEVKRGMADvsrketqnkqgsaastrtRTKVQMQGIAVGRAVDLTALKGYDDLFDELEKMFEIQgqlrprdkwavvftddegdmmlagddqwPEFCKMVKKIFIYSTEEVknmatsskpiassvegegtaisldselkset

mayvepnfgcslssqggpGSGDLYRELWKACAGPLVEVPRNGERVYYFPQGHIEQLEASTNQELTHQEPLFDLPSKILCRVVHIELLAEQETDEVYAQITLHpetdqteprspDQCLPEPPKQTVHSFCKILTASDTSTHGGFSVLRKHATECLPPLDMTLATPTQELAAKDLHGYEWRFKHIFRGQPRRHLLTTGWSTFVTSKRLVAGDAFVFLRGENGELRVGVRRLAHQQSSMPSSVISSQSMHLGVLATAAHAVKTSTLFIVYYKPRTSQFIIGLNKYLEAVHHCFSVGMRFKMRFEGEDSPERRFTGTIvgvgdfseqwpgskwrslkiqwdepatvqrpervSPWEIEPFVASAPLNLAQPAVKSKRPRSIDIPASASAFWYQGSTQSHDITQVVGAtegqssesqvvrpMRQKEIDStiinnnstddhRIVAAQSVLSgyassgrpgNTVIHEEVERGKKSEASLGCWLFGIDLKhnsntaaplgrkvvdpttgtsgvkgsaraasdfdasqnqdlkeVKRGmadvsrketqnkqgsaastrtrtkvqmQGIAVGRAVDLTALKGYDDLFDELEKMFeiqgqlrprdkWAVVFTDDEGDMMLAGDDQWPEFCKMVKKIFIYSTEEVKNMATSskpiassvegegtaisldselkset

MAYVEPNFGCSLSSQGGPGSGDLYRELWKACAGPLVEVPRNGERVYYFPQGHIEQLEASTNQELTHQEPLFDLPSKILCRVVHIELLAEQETDEVYAQITLHPETDQTEPRSPDQCLPEPPKQTVHSFCKILTASDTSTHGGFSVLRKHATECLPPLDMTLATPTQELAAKDLHGYEWRFKHIFRGQPRRHLLTTGWSTFVTSKRLVAGDAFVFLRGENGELRVGVRRLAHqqssmpssvissqsMHLGVLATAAHAVKTSTLFIVYYKPRTSQFIIGLNKYLEAVHHCFSVGMRFKMRFEGEDSPERRFTGTIVGVGDFSEQWPGSKWRSLKIQWDEPATVQRPERVSPWEIEPFVASAPLNLAQPAVKSKRPRSIDIPASASAFWYQGSTQSHDITQVVGATEGQSSESQVVRPMRQKEIDSTIINNNSTDDHRIVAAQSVLSGYASSGRPGNTVIHEEVERGKKSEASLGCWLFGIDLKHNSNTAAPLGRKVVDPTTGTSGVKGSARAASDFDASQNQDLKEVKRGMADVSRKETQNKQGSAASTRTRTKVQMQGIAVGRAVDLTALKGYDDLFDELEKMFEIQGQLRPRDKWAVVFTDDEGDMMLAGDDQWPEFCKMVKKIFIYSTEEVKNMATSSKPIASSVEGEGTAISLDSELKSET

*********************DLYRELWKACAGPLVEVPRNGERVYYFPQGHIEQLEA*****LTHQEPLFDLPSKILCRVVHIELLAEQETDEVYAQITL***********************VHSFCKILTASDTSTHGGFSVLRKHATECLPPLDMTLATPTQELAAKDLHGYEWRFKHIFRGQPRRHLLTTGWSTFVTSKRLVAGDAFVFLRGENGELRVGVRRL****************MHLGVLATAAHAVKTSTLFIVYYKPRTSQFIIGL******************************FTGTIVGVGDFSEQWPGSKWRSLKIQWDEPATV*****VSPWEIEPFVASA***********************SAFWYQG********************************************************************************SLGCWLFGIDLKHN***********************************************************************MQGIAVGRAVDLTALKGYDDLFDELEKMFEIQGQLRPRDKWAVVFTDDEGDMMLAGDDQWPEFCKMVKKIFIYSTE*********************************

*************************ELWKACAGPLVEVPRNGERVYYFPQGHIEQLEA**********PLFDLPSKILCRVVHIELLAEQETDEVYAQITLHP***********************SFCKILTASDTSTHGGFSVLRKHATECLPP***********LAAKDLHGYEWRFKHIFRGQPRRHLLTTGWSTFVTSKRLVAGDAFVFLRGENGELRVGVRRLAHQQS*****************ATAAHAVKTSTLFIVYYKPRTSQFIIGLNKYLEAVHHCFSVGMRFKMRFEGEDSPERRFTGTIVGVGDFSEQWPGSKWRSLKIQWDEPATVQRPERVSPWEIEPFVASAPL*********************************DITQVVGATEG******************TIINNNSTDDHRIV*************RPGNTVIHEEVERGKKSEA****************************TTG*************************KRGMADVSRKETQNKQGSAASTRTRTKVQMQGIAVGRAVDLTALKGYDDLFDELEKMFEIQGQLRPRDKWAVVFTDDEGDMMLAGDDQWPEFCKMVKKIFIY************************************

MAYVEPNFGCSLSSQGGPGSGDLYRELWKACAGPLVEVPRNGERVYYFPQGHIEQLEASTNQELTHQEPLFDLPSKILCRVVHIELLAEQETDEVYAQITLHPE********************VHSFCKILTASDTSTHGGFSVLRKHATECLPPLDMTLATPTQELAAKDLHGYEWRFKHIFRGQPRRHLLTTGWSTFVTSKRLVAGDAFVFLRGENGELRVGVRRL*************SQSMHLGVLATAAHAVKTSTLFIVYYKPRTSQFIIGLNKYLEAVHHCFSVGMRFKMRFEGEDSPERRFTGTIVGVGDFSEQWPGSKWRSLKIQWDEPATVQRPERVSPWEIEPFVASAPLNLAQ*********SIDIPASASAFWYQGSTQSHDITQVV****************RQKEIDSTIINNNSTDDHRIVAAQSVLSGYASSGRPGNTVIHEEVERGKKSEASLGCWLFGIDLKHNSNTAAPLGRKVVDPT*****************ASQNQDLKEVK***************************QMQGIAVGRAVDLTALKGYDDLFDELEKMFEIQGQLRPRDKWAVVFTDDEGDMMLAGDDQWPEFCKMVKKIFIYSTEEVKNMATSSKPIASSVEGEGTAISLDSELKSET

********************GDLYRELWKACAGPLVEVPRNGERVYYFPQGHIEQLEASTNQELTHQEPLFDLPSKILCRVVHIELLAEQETDEVYAQITLHPETD****************QTVHSFCKILTASDTSTHGGFSVLRKHATECLPPLDMTLATPTQELAAKDLHGYEWRFKHIFRGQPRRHLLTTGWSTFVTSKRLVAGDAFVFLRGENGELRVGVRRLAH*************SMHLGVLATAAHAVKTSTLFIVYYKPRTSQFIIGLNKYLEAVHHCFSVGMRFKMRFEGEDSPERRFTGTIVGVGDFSEQWPGSKWRSLKIQWDEPATVQRPERVSPWEIEPFVASAPLNLAQPAVKSKRPRSIDI********************************************************************************************LGCWLF*IDLKH****************************************************************TRTRTKVQMQGIAVGRAVDLTALKGYDDLFDELEKMFEIQGQLRPRDKWAVVFTDDEGDMMLAGDDQWPEFCKMVKKIFIYSTEEVKNM****************************

oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo

oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii

ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii

oooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii

xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx

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		664	2.2.26 [Sep-21-2011]
Q9C5W9		602	Auxin response factor 18	yes	no	0.844	0.931	0.595	0.0
Q9ZPY6		622	Auxin response factor 11	no	no	0.875	0.934	0.559	0.0
Q9XED8		638	Auxin response factor 9 O	no	no	0.899	0.935	0.601	0.0
Q6YVY0		678	Auxin response factor 7 O	yes	no	0.894	0.876	0.549	0.0
Q0JCZ4		673	Auxin response factor 9 O	no	no	0.912	0.900	0.533	0.0
Q8L7G0		665	Auxin response factor 1 O	no	no	0.917	0.915	0.526	1e-180
Q5NB85		699	Auxin response factor 1 O	no	no	0.938	0.891	0.500	1e-171
Q9LQE8		605	Putative auxin response f	no	no	0.864	0.948	0.459	1e-155
Q9C8N9		606	Putative auxin response f	no	no	0.850	0.932	0.467	1e-152
Q9LQE3		593	Putative auxin response f	no	no	0.844	0.946	0.460	1e-147

>sp\|Q9C5W9\|ARFR_ARATH Auxin response factor 18 OS=Arabidopsis thaliana GN=ARF18 PE=2 SV=1	Back alignment and function desciption

 Score =  721 bits (1861), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 378/635 (59%), Positives = 439/635 (69%), Gaps = 74/635 (11%)

Query: 23  LYRELWKACAGPLVEVPRNGERVYYFPQGHIEQLEASTNQELTHQE-PLFDLPSKILCRV 81
           LY ELWK CAGPLVEVPR  ERV+YFPQGH+EQL ASTNQ +  +E P+FDLP KILCRV
Sbjct: 22  LYTELWKVCAGPLVEVPRAQERVFYFPQGHMEQLVASTNQGINSEEIPVFDLPPKILCRV 81

Query: 82  VHIELLAEQETDEVYAQITLHPETDQTEPRSPDQCLPEPPKQTVHSFCKILTASDTSTHG 141
           + + L AE ETDEVYAQITL PE DQ+EP S D  +  P KQ  HSF KILTASDTSTHG
Sbjct: 82  LDVTLKAEHETDEVYAQITLQPEEDQSEPTSLDPPIVGPTKQEFHSFVKILTASDTSTHG 141

Query: 142 GFSVLRKHATECLPPLDMTLATPTQELAAKDLHGYEWRFKHIFRGQPRRHLLTTGWSTFV 201
           GFSVLRKHATECLP LDMT ATPTQEL  +DLHG+EWRFKHIFRGQPRRHLLTTGWSTFV
Sbjct: 142 GFSVLRKHATECLPSLDMTQATPTQELVTRDLHGFEWRFKHIFRGQPRRHLLTTGWSTFV 201

Query: 202 TSKRLVAGDAFVFLRGENGELRVGVRRLAHQQSSMPSSVISSQSMHLGVLATAAHAVKTS 261
           +SKRLVAGDAFVFLRGENG+LRVGVRRLA  QS+MP+SVISSQSMHLGVLATA+HAV+T+
Sbjct: 202 SSKRLVAGDAFVFLRGENGDLRVGVRRLARHQSTMPTSVISSQSMHLGVLATASHAVRTT 261

Query: 262 TLFIVYYKPRTSQFIIGLNKYLEAVHHCFSVGMRFKMRFEGEDSPERRFTGTIVGVGDFS 321
           T+F+V+YKPR SQFI+G+NKY+EA+ H FS+G RF+MRFEGE+SPER FTGTIVG GD S
Sbjct: 262 TIFVVFYKPRISQFIVGVNKYMEAIKHGFSLGTRFRMRFEGEESPERIFTGTIVGSGDLS 321

Query: 322 EQWPGSKWRSLKIQWDEPATVQRPERVSPWEIEPFVASAPLNLA--QPAVKSKRPR---- 375
            QWP SKWRSL++QWDEP TVQRP++VSPWEIEPF+A++P++    QP  K KR R    
Sbjct: 322 SQWPASKWRSLQVQWDEPTTVQRPDKVSPWEIEPFLATSPISTPAQQPQSKCKRSRPIEP 381

Query: 376 SIDIPASASAFWYQGSTQSHDITQVVGATEGQSSESQVVRPMRQKEIDSTIINNNSTDDH 435
           S+  PA  S F Y                           P  Q  I++++         
Sbjct: 382 SVKTPAPPS-FLYS-------------------------LPQSQDSINASLKLFQDPSLE 415

Query: 436 RIVAAQSVLSGYASSGRPGNTVIHEEVERGKKSEASLGCWLFGIDLKHNSNTAAPLGRKV 495
           RI    S  + +     P  T              +    LFG DL  NS    P  ++ 
Sbjct: 416 RISGGYSSNNSFKPETPPPPT--------------NCSYRLFGFDLTSNSPAPIPQDKQP 461

Query: 496 VDPTTGTSGVKGSARAASDFDASQNQDLKEVKRGMADVSRKETQNKQGSAASTRTRTKVQ 555
           +D         G+A+                +  +   S  E + +Q S    R+RTKVQ
Sbjct: 462 MD-------TCGAAKC---------------QEPITPTSMSEQKKQQTS----RSRTKVQ 495

Query: 556 MQGIAVGRAVDLTALKGYDDLFDELEKMFEIQGQLRPRDKWAVVFTDDEGDMMLAGDDQW 615
           MQGIAVGRAVDLT LK YD+L DELE+MFEIQGQL  RDKW VVFTDDEGDMMLAGDD W
Sbjct: 496 MQGIAVGRAVDLTLLKSYDELIDELEEMFEIQGQLLARDKWIVVFTDDEGDMMLAGDDPW 555

Query: 616 PEFCKMVKKIFIYSTEEVKNMATSSKPIASSVEGE 650
            EFCKM KKIFIYS++EVK M T  K I+SS+E E
Sbjct: 556 NEFCKMAKKIFIYSSDEVKKMTTKLK-ISSSLENE 589

Auxin response factors (ARFs) are transcriptional factors that binds specifically to the DNA sequence 5'-TGTCTC-3' found in the auxin-responsive promoter elements (AuxREs). Could act as transcriptional activator or repressor. Formation of heterodimers with Aux/IAA proteins may alter their ability to modulate early auxin response genes expression.
Arabidopsis thaliana (taxid: 3702)

>sp\|Q9ZPY6\|ARFK_ARATH Auxin response factor 11 OS=Arabidopsis thaliana GN=ARF11 PE=2 SV=3	Back alignment and function description

>sp\|Q9XED8\|ARFI_ARATH Auxin response factor 9 OS=Arabidopsis thaliana GN=ARF9 PE=1 SV=1	Back alignment and function description

>sp\|Q6YVY0\|ARFG_ORYSJ Auxin response factor 7 OS=Oryza sativa subsp. japonica GN=ARF7 PE=2 SV=1	Back alignment and function description

>sp\|Q0JCZ4\|ARFI_ORYSJ Auxin response factor 9 OS=Oryza sativa subsp. japonica GN=ARF9 PE=2 SV=1	Back alignment and function description

>sp\|Q8L7G0\|ARFA_ARATH Auxin response factor 1 OS=Arabidopsis thaliana GN=ARF1 PE=1 SV=2	Back alignment and function description

>sp\|Q5NB85\|ARFA_ORYSJ Auxin response factor 1 OS=Oryza sativa subsp. japonica GN=ARF1 PE=2 SV=1	Back alignment and function description

>sp\|Q9LQE8\|ARFN_ARATH Putative auxin response factor 14 OS=Arabidopsis thaliana GN=ARF14 PE=3 SV=2	Back alignment and function description

>sp\|Q9C8N9\|ARFU_ARATH Putative auxin response factor 21 OS=Arabidopsis thaliana GN=ARF21 PE=3 SV=2	Back alignment and function description

>sp\|Q9LQE3\|ARFO_ARATH Putative auxin response factor 15 OS=Arabidopsis thaliana GN=ARF15 PE=3 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		664
359489584		764	PREDICTED: auxin response factor 18-like	0.957	0.832	0.680	0.0
302398561		695	ARF domain class transcription factor [M	0.977	0.933	0.658	0.0
297742361		682	unnamed protein product [Vitis vinifera]	0.948	0.923	0.649	0.0
297745485		607	unnamed protein product [Vitis vinifera]	0.881	0.963	0.671	0.0
359473930		693	PREDICTED: auxin response factor 9-like	0.948	0.909	0.638	0.0
255564663		667	Auxin response factor, putative [Ricinus	0.897	0.893	0.699	0.0
449443756		693	PREDICTED: auxin response factor 18-like	0.960	0.920	0.632	0.0
356522502		722	PREDICTED: auxin response factor 7-like	0.995	0.915	0.611	0.0
356560266		799	PREDICTED: auxin response factor 7-like	0.963	0.801	0.629	0.0
255555629		694	hypothetical protein RCOM_1311830 [Ricin	0.969	0.927	0.628	0.0

>gi\|359489584\|ref\|XP_002264072.2\| PREDICTED: auxin response factor 18-like [Vitis vinifera]	Back alignment and taxonomy information

 Score =  929 bits (2400), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 463/680 (68%), Positives = 536/680 (78%), Gaps = 44/680 (6%)

Query: 26  ELWKACAGPLVEVPRNGERVYYFPQGHIEQLEASTNQELTHQEPLFDLPSKILCRVVHIE 85
           +LW+ACAGPLV+VP+  ERV+YFPQGH+EQL+ASTNQ +  + PLF+LPSKILCRVVH  
Sbjct: 86  QLWRACAGPLVDVPKPHERVFYFPQGHMEQLQASTNQGVDQRIPLFNLPSKILCRVVHTR 145

Query: 86  LLAEQETDEVYAQITLHPETDQTEPRSPDQCLPEPPKQTVHSFCKILTASDTSTHGGFSV 145
           LLAEQETDEVYAQITL PE DQTEP+SPD C  E PKQTVHSFCKILTASDTSTHGGFSV
Sbjct: 146 LLAEQETDEVYAQITLQPEADQTEPKSPDSCPDEAPKQTVHSFCKILTASDTSTHGGFSV 205

Query: 146 LRKHATECLPPLDMTLATPTQELAAKDLHGYEWRFKHIFRGQPRRHLLTTGWSTFVTSKR 205
           LRKHA ECLPPLDM+ ATPTQEL A+DLHGYEWRFKHIFRGQPRRHLLTTGWSTFVTSKR
Sbjct: 206 LRKHANECLPPLDMSQATPTQELVARDLHGYEWRFKHIFRGQPRRHLLTTGWSTFVTSKR 265

Query: 206 LVAGDAFVFLRGENGELRVGVRRLAHQQSSMPSSVISSQSMHLGVLATAAHAVKTSTLFI 265
           LVAGDAFVFLRG+NGELRVGVRRLA QQS MPSSVISSQSMHLGVLATA+HAV T TLF+
Sbjct: 266 LVAGDAFVFLRGDNGELRVGVRRLARQQSPMPSSVISSQSMHLGVLATASHAVTTQTLFV 325

Query: 266 VYYKPRTSQFIIGLNKYLEAVHHCFSVGMRFKMRFEGEDSPERRFTGTIVGVGDFSEQWP 325
           VYYKPRTSQFII LNKYLEAV++ F+VGMRFKMRFEGEDSPERRFTGTIVG+GD S QW 
Sbjct: 326 VYYKPRTSQFIISLNKYLEAVNYGFAVGMRFKMRFEGEDSPERRFTGTIVGIGDISPQWS 385

Query: 326 GSKWRSLKIQWDEPATVQRPERVSPWEIEPFVASAPLNLAQPAVKSKRPRSIDIPAS--- 382
            SKWRSLKIQWDEPAT+QRPERVS W+IEPFVASA LNL QP VK KRPR +D+P +   
Sbjct: 386 NSKWRSLKIQWDEPATIQRPERVSSWDIEPFVASASLNLTQPPVKIKRPRPLDLPVAENT 445

Query: 383 ----ASAFWYQGSTQSHDITQVVGATEGQSSESQVVRPMRQKEIDSTIINNNS------- 431
                S FWY GS+ SH++TQ+ G TE QSSESQV  P + KEI+  +I+N++       
Sbjct: 446 SSSVPSPFWYAGSSPSHELTQLGGVTEVQSSESQVHWPPKPKEINGNVIHNSNCGSSIGR 505

Query: 432 ---------------------TDDHRIVAAQSVLSGYAS--SGRPGNTVIHEEVERGKKS 468
                                T+D + V+ +S+LSGY +  S RP N +I ++VE+GK+ 
Sbjct: 506 PEGIWSSSPSVNVSLNLFQDLTEDSKTVSTRSILSGYNTSLSSRPNNGLISDQVEKGKRI 565

Query: 469 EASLGCWLFGIDLKHNSNTAAPLGRKVVDPTTGTSGVKGSARA-ASDFDASQNQDL---- 523
           EAS+GC LFGIDL +NS   A L  ++  P+  +S VKG   A  S+ D  QN D+    
Sbjct: 566 EASIGCRLFGIDLTNNSKATALL--EMSCPSITSSSVKGPISAVVSEADRIQNLDVSKSS 623

Query: 524 KEVKRGMADVSRKETQNKQGSAASTRTRTKVQMQGIAVGRAVDLTALKGYDDLFDELEKM 583
            E K+ + + S+KETQ +Q    S+RTRTKVQMQG+AVGRAVDLTAL+GYD+L  ELEKM
Sbjct: 624 NEQKQVVPEASQKETQGRQSCTPSSRTRTKVQMQGVAVGRAVDLTALEGYDELISELEKM 683

Query: 584 FEIQGQLRPRDKWAVVFTDDEGDMMLAGDDQWPEFCKMVKKIFIYSTEEVKNMATSSKPI 643
           FEI+G+L PR+KW VVFTDDEGDMML GDD W EFCKMV+KIFIYS+EEVK M+   K  
Sbjct: 684 FEIKGELCPRNKWEVVFTDDEGDMMLVGDDPWQEFCKMVRKIFIYSSEEVKKMSPRCKLS 743

Query: 644 ASSVEGEGTAISLDSELKSE 663
            SS++GEGT ISLDSEL++E
Sbjct: 744 TSSLDGEGTVISLDSELRTE 763

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi\|302398561\|gb\|ADL36575.1\| ARF domain class transcription factor [Malus x domestica]	Back alignment and taxonomy information

>gi\|297742361\|emb\|CBI34510.3\| unnamed protein product [Vitis vinifera]	Back alignment and taxonomy information

>gi\|297745485\|emb\|CBI40565.3\| unnamed protein product [Vitis vinifera]	Back alignment and taxonomy information

>gi\|359473930\|ref\|XP_002265162.2\| PREDICTED: auxin response factor 9-like [Vitis vinifera]	Back alignment and taxonomy information

>gi\|255564663\|ref\|XP_002523326.1\| Auxin response factor, putative [Ricinus communis] gi\|223537414\|gb\|EEF39042.1\| Auxin response factor, putative [Ricinus communis]	Back alignment and taxonomy information

>gi\|449443756\|ref\|XP_004139643.1\| PREDICTED: auxin response factor 18-like [Cucumis sativus]	Back alignment and taxonomy information

>gi\|356522502\|ref\|XP_003529885.1\| PREDICTED: auxin response factor 7-like [Glycine max]	Back alignment and taxonomy information

>gi\|356560266\|ref\|XP_003548414.1\| PREDICTED: auxin response factor 7-like [Glycine max]	Back alignment and taxonomy information

>gi\|255555629\|ref\|XP_002518850.1\| hypothetical protein RCOM_1311830 [Ricinus communis] gi\|223541837\|gb\|EEF43383.1\| hypothetical protein RCOM_1311830 [Ricinus communis]	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		664
TAIR\|locus:2076765		602	ARF18 "auxin response factor 1	0.588	0.649	0.681	2.6e-186
TAIR\|locus:2138096		638	ARF9 "auxin response factor 9"	0.906	0.943	0.577	2.7e-178
TAIR\|locus:2039124		622	ARF11 "auxin response factor 1	0.570	0.609	0.696	5.1e-177
TAIR\|locus:2025991		665	ARF1 "auxin response factor 1"	0.558	0.557	0.653	1.4e-161
TAIR\|locus:2174013		859	ARF2 "auxin response factor 2"	0.623	0.481	0.572	4.2e-158
TAIR\|locus:2014731		605	ARF14 "auxin response factor 1	0.567	0.623	0.518	4e-138
TAIR\|locus:2009298		606	ARF21 "auxin response factor 2	0.570	0.625	0.506	1.2e-136
TAIR\|locus:2036288		598	ARF22 "auxin response factor 2	0.558	0.620	0.526	1.2e-132
TAIR\|locus:2206717		590	ARF20 "auxin response factor 2	0.519	0.584	0.529	1.6e-132
TAIR\|locus:2026145		593	ARF12 "auxin response factor 1	0.570	0.639	0.496	2.6e-130

TAIR\|locus:2076765 ARF18 "auxin response factor 18" [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

 Score = 1390 (494.4 bits), Expect = 2.6e-186, Sum P(3) = 2.6e-186
 Identities = 276/405 (68%), Positives = 314/405 (77%)

Query:     1 MAYVE--PNFGCSLSSQGGPGSGDLYRELWKACAGPLVEVPRNGERVYYFPQGHIEQLEA 58
             MA VE   +FG S SS+       LY ELWK CAGPLVEVPR  ERV+YFPQGH+EQL A
Sbjct:     1 MASVEGDDDFGSS-SSRSY--QDQLYTELWKVCAGPLVEVPRAQERVFYFPQGHMEQLVA 57

Query:    59 STNQELTHQE-PLFDLPSKILCRVVHIELLAEQETDEVYAQITLHPETDQTEPRSPDQCL 117
             STNQ +  +E P+FDLP KILCRV+ + L AE ETDEVYAQITL PE DQ+EP S D  +
Sbjct:    58 STNQGINSEEIPVFDLPPKILCRVLDVTLKAEHETDEVYAQITLQPEEDQSEPTSLDPPI 117

Query:   118 PEPPKQTVHSFCKILTASDTSTHGGFSVLRKHATECLPPLDMTLATPTQELAAKDLHGYE 177
               P KQ  HSF KILTASDTSTHGGFSVLRKHATECLP LDMT ATPTQEL  +DLHG+E
Sbjct:   118 VGPTKQEFHSFVKILTASDTSTHGGFSVLRKHATECLPSLDMTQATPTQELVTRDLHGFE 177

Query:   178 WRFKHIFRGQPRRHLLTTGWSTFVTSKRLVAGDAFVFLRGENGELRVGVRRLAHXXXXXX 237
             WRFKHIFRGQPRRHLLTTGWSTFV+SKRLVAGDAFVFLRGENG+LRVGVRRLA       
Sbjct:   178 WRFKHIFRGQPRRHLLTTGWSTFVSSKRLVAGDAFVFLRGENGDLRVGVRRLARHQSTMP 237

Query:   238 XXXXXXXXMHLGVLATAAHAVKTSTLFIVYYKPRTSQFIIGLNKYLEAVHHCFSVGMRFK 297
                     MHLGVLATA+HAV+T+T+F+V+YKPR SQFI+G+NKY+EA+ H FS+G RF+
Sbjct:   238 TSVISSQSMHLGVLATASHAVRTTTIFVVFYKPRISQFIVGVNKYMEAIKHGFSLGTRFR 297

Query:   298 MRFEGEDSPERRFTGTIVGVGDFSEQWPGSKWRSLKIQWDEPATVQRPERVSPWEIEPFV 357
             MRFEGE+SPER FTGTIVG GD S QWP SKWRSL++QWDEP TVQRP++VSPWEIEPF+
Sbjct:   298 MRFEGEESPERIFTGTIVGSGDLSSQWPASKWRSLQVQWDEPTTVQRPDKVSPWEIEPFL 357

Query:   358 ASAPLNLA--QPAVKSKRPR----SIDIPASASAFWYQGSTQSHD 396
             A++P++    QP  K KR R    S+  PA  S F Y    QS D
Sbjct:   358 ATSPISTPAQQPQSKCKRSRPIEPSVKTPAPPS-FLYS-LPQSQD 400

GO:0003677 "DNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISM;IEA

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

GO:0009725 "response to hormone stimulus" evidence=IEA

GO:0046983 "protein dimerization activity" evidence=IEA

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

TAIR\|locus:2138096 ARF9 "auxin response factor 9" [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

TAIR\|locus:2039124 ARF11 "auxin response factor 11" [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

TAIR\|locus:2025991 ARF1 "auxin response factor 1" [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

TAIR\|locus:2174013 ARF2 "auxin response factor 2" [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

TAIR\|locus:2014731 ARF14 "auxin response factor 14" [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

TAIR\|locus:2009298 ARF21 "auxin response factor 21" [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

TAIR\|locus:2036288 ARF22 "auxin response factor 22" [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

TAIR\|locus:2206717 ARF20 "auxin response factor 20" [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

TAIR\|locus:2026145 ARF12 "auxin response factor 12" [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)
Q9C5W9	ARFR_ARATH	No assigned EC number	0.5952	0.8448	0.9318	yes	no
Q6YVY0	ARFG_ORYSJ	No assigned EC number	0.5496	0.8945	0.8761	yes	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

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		664
pfam06507		83	pfam06507, Auxin_resp, Auxin response factor	3e-37
pfam02309		188	pfam02309, AUX_IAA, AUX/IAA family	3e-33
pfam02362		97	pfam02362, B3, B3 DNA binding domain	8e-28
smart01019		96	smart01019, B3, B3 DNA binding domain	5e-25
cd10017		98	cd10017, B3_DNA, Plant-specific B3-DNA binding dom	4e-19

>gnl\|CDD\|191545 pfam06507, Auxin_resp, Auxin response factor	Back alignment and domain information

 Score =  133 bits (336), Expect = 3e-37
 Identities = 50/83 (60%), Positives = 62/83 (74%), Gaps = 3/83 (3%)

Query: 254 AAHAVKTSTLFIVYYKPR--TSQFIIGLNKYLEAVHHCFSVGMRFKMRFEGEDSPERRFT 311
           AAHA  T + F V+Y PR  TS+F++   KYL+A+++ FSVGMRFKMRFE EDS ERRF+
Sbjct: 1   AAHAASTGSPFHVFYNPRASTSEFVVPYAKYLKAMNNPFSVGMRFKMRFETEDSSERRFS 60

Query: 312 GTIVGVGDF-SEQWPGSKWRSLK 333
           GTI GV D    +WP SKWRSL+
Sbjct: 61  GTISGVSDLDPIRWPNSKWRSLQ 83

A conserved region of auxin-responsive transcription factors. Length = 83

>gnl\|CDD\|216968 pfam02309, AUX_IAA, AUX/IAA family	Back alignment and domain information

>gnl\|CDD\|216995 pfam02362, B3, B3 DNA binding domain	Back alignment and domain information

>gnl\|CDD\|214977 smart01019, B3, B3 DNA binding domain	Back alignment and domain information

>gnl\|CDD\|197383 cd10017, B3_DNA, Plant-specific B3-DNA binding 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		664
PF02309		215	AUX_IAA: AUX/IAA family; InterPro: IPR003311 The A	100.0
PF06507		83	Auxin_resp: Auxin response factor; InterPro: IPR01	100.0
PF02362		100	B3: B3 DNA binding domain; InterPro: IPR003340 Two	99.66
KOG0644		1113	consensus Uncharacterized conserved protein, conta	99.54
PF09217		156	EcoRII-N: Restriction endonuclease EcoRII, N-termi	98.37
PF03754		114	DUF313: Domain of unknown function (DUF313) ; Inte	97.52
PF00564		84	PB1: PB1 domain; InterPro: IPR000270 The Phox and	96.86
smart00666		81	PB1 PB1 domain. Phox and Bem1p domain, present in	96.32
cd05992		81	PB1 The PB1 domain is a modular domain mediating s	96.14
cd06398		91	PB1_Joka2 The PB1 domain is present in the Nicotia	96.1
cd06407		82	PB1_NLP A PB1 domain is present in NIN like protei	96.04
cd06396		81	PB1_NBR1 The PB1 domain is an essential part of NB	95.65
cd06403		80	PB1_Par6 The PB1 domain is an essential part of Pa	95.59
cd06401		81	PB1_TFG The PB1 domain found in TFG protein, an on	94.4
cd06409		86	PB1_MUG70 The MUG70 protein is a product of the me	93.28
cd06404		83	PB1_aPKC PB1 domain is an essential modular domain	92.44
cd06408		86	PB1_NoxR The PB1 domain is present in the Epichloe	91.13
cd06402		87	PB1_p62 The PB1 domain is an essential part of p62	90.88
cd06397		82	PB1_UP1 Uncharacterized protein 1. The PB1 domain	89.17

>PF02309 AUX_IAA: AUX/IAA family; InterPro: IPR003311 The Aux/IAA family of genes are key regulators of auxin-modified gene expression []	Back alignment and domain information

Probab=100.00  E-value=4.2e-37  Score=307.11  Aligned_cols=95  Identities=43%  Similarity=0.758  Sum_probs=0.0

Q ss_pred             CCCCCeeEEEecCeeeeeeecCCCCCChHHHHHHHHHHH---hhh----------cc--cCCCCCcEEEEecCCCCeEEe
Q 006028          546 ASTRTRTKVQMQGIAVGRAVDLTALKGYDDLFDELEKMF---EIQ----------GQ--LRPRDKWAVVFTDDEGDMMLA  610 (664)
Q Consensus       546 ~~~~~~vKV~meG~~vGR~vDL~~~~sY~eL~~~L~~MF---~~~----------g~--l~~~~~~~v~Y~D~eGD~mlv  610 (664)
                      +..++||||+|||++|||||||++|+||++|+.+|++||   +|.          +.  |...++|+|||+|+|||||||
T Consensus       106 ~~~~~~vKV~mdG~~igRkVDL~~~~sY~~L~~~L~~MF~~~~i~~~~~~~~~~~~~~~~~~~~~~~l~Y~D~egd~mlv  185 (215)
T PF02309_consen  106 SSSRSYVKVNMDGVPIGRKVDLSAYSSYEELSSALEKMFSCFSIEQCGSHGLNESGLLDLLNGSEYVLVYEDKEGDWMLV  185 (215)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             ccCCceeEEEecCcccceecCHHHhhCHHHHHHHHHHhcCCCCccccccccccchhhccccCCcceeEEEECCCCCEEEe
Confidence            346899999999999999999999999999999999999   665          22  345679999999999999999


Q ss_pred             cCCChHHHHhccceEEEeechhhccccCCC
Q 006028          611 GDDQWPEFCKMVKKIFIYSTEEVKNMATSS  640 (664)
Q Consensus       611 GD~PW~~F~~~vkrl~I~~~~e~~~~~~~~  640 (664)
                      |||||+|||++||||+||+.+|+++|+||+
T Consensus       186 GD~PW~~F~~~vkRl~I~~~~e~~~~~~r~  215 (215)
T PF02309_consen  186 GDVPWEEFVKSVKRLRIMKSSEAKGLAPRA  215 (215)
T ss_dssp             ------------------------------
T ss_pred             cCCCHHHHHHHhhccEEecHHHhcccCCCC
Confidence            999999999999999999999999999974

The plant hormone auxin (indole-3-acetic acid, IAA) regulates diverse cellular and developmental responses in plants, including cell division, expansion, differentiation and patterning of embryo responses []. Auxin can regulate the gene expression of several families, including GH3 and SAUR, as well as Aux/IAA itself. The Aux/IAA proteins act as repressors of auxin-induced gene expression, possibly through modulating the activity of DNA-binding auxin response factors (ARFs) (IPR010525 from INTERPRO). Aux/IAA and ARF are thought to interact through C-terminal protein-protein interaction domains found in both Aux/IAA and ARF. Recent evidence suggests that Aux/IAA proteins can also mediate light responses []. Some members of the AUX/IAA family are longer and contain an N-terminal DNA binding domain [] and may have an early function in the establishment of vascular and body patterns in embryonic and post-embryonic development in some plants.; GO: 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 2P1N_F 2P1Q_C 2P1O_C.

>PF06507 Auxin_resp: Auxin response factor; InterPro: IPR010525 This pattern represents a conserved region of auxin-responsive transcription factors	Back alignment and domain information

>PF02362 B3: B3 DNA binding domain; InterPro: IPR003340 Two DNA binding proteins, RAV1 and RAV2 from Arabidopsis thaliana contain two distinct amino acid sequence domains found only in higher plant species	Back alignment and domain information

>KOG0644 consensus Uncharacterized conserved protein, contains WD40 repeat and BROMO domains [General function prediction only]	Back alignment and domain information

>PF09217 EcoRII-N: Restriction endonuclease EcoRII, N-terminal; InterPro: IPR023372 There are four classes of restriction endonucleases: types I, II,III and IV	Back alignment and domain information

>PF03754 DUF313: Domain of unknown function (DUF313) ; InterPro: IPR005508 This is a family of proteins from Arabidopsis thaliana (Mouse-ear cress) with uncharacterised function	Back alignment and domain information

>PF00564 PB1: PB1 domain; InterPro: IPR000270 The Phox and Bem1p domain, is present in many eukaryotic cytoplasmic signalling proteins	Back alignment and domain information

>smart00666 PB1 PB1 domain	Back alignment and domain information

>cd05992 PB1 The PB1 domain is a modular domain mediating specific protein-protein interactions which play a role in many critical cell processes, such as osteoclastogenesis, angiogenesis, early cardiovascular development, and cell polarity	Back alignment and domain information

>cd06398 PB1_Joka2 The PB1 domain is present in the Nicotiana plumbaginifolia Joka2 protein which interacts with sulfur stress inducible UP9 protein	Back alignment and domain information

>cd06407 PB1_NLP A PB1 domain is present in NIN like proteins (NLP), a key enzyme in a process of establishment of symbiosis betweeen legumes and nitrogen fixing bacteria (Rhizobium)	Back alignment and domain information

>cd06396 PB1_NBR1 The PB1 domain is an essential part of NBR1 protein, next to BRCA1, a scaffold protein mediating specific protein-protein interaction with both titin protein kinase and with another scaffold protein p62	Back alignment and domain information

>cd06403 PB1_Par6 The PB1 domain is an essential part of Par6 protein which in complex with Par3 and aPKC proteins is crucial for establishment of apical-basal polarity of animal cells	Back alignment and domain information

>cd06401 PB1_TFG The PB1 domain found in TFG protein, an oncogenic gene product and fusion partner to nerve growth factor tyrosine kinase receptor TrkA and to the tyrosine kinase ALK	Back alignment and domain information

>cd06409 PB1_MUG70 The MUG70 protein is a product of the meiotically up-regulated gene 70 which has a role in meiosis and harbors a PB1 domain	Back alignment and domain information

>cd06404 PB1_aPKC PB1 domain is an essential modular domain of the atypical protein kinase C (aPKC) which in complex with Par6 and Par3 proteins is crucial for establishment of apical-basal polarity of animal cells	Back alignment and domain information

>cd06408 PB1_NoxR The PB1 domain is present in the Epichloe festucae NoxR protein (NADPH oxidase regulator), a key regulator of NADPH oxidase isoform, NoxA	Back alignment and domain information

>cd06402 PB1_p62 The PB1 domain is an essential part of p62 scaffold protein (alias sequestosome 1,SQSTM) involved in cell signaling, receptor internalization, and protein turnover	Back alignment and domain information

>cd06397 PB1_UP1 Uncharacterized protein 1	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		664
1wid_A		130	Solution Structure Of The B3 Dna-Binding Domain Of		9e-08

>pdb|1WID|A Chain A, Solution Structure Of The B3 Dna-Binding Domain Of Rav1 Length = 130

Back alignment and structure

Iteration: 1

Score = 55.5 bits (132), Expect = 9e-08, Method: Compositional matrix adjust. Identities = 31/100 (31%), Positives = 50/100 (50%), Gaps = 2/100 (2%) Query: 128 FCKILTASDTSTHGGFSVLRKHATECLPPLDMTLATPTQELAAKDLHGYEWRFKHIFRGQ 187 F K +T SD + + HA + P ++ L +D++G WRF++ + Sbjct: 14 FEKAVTPSDVGKLNRLVIPKHHAEKHFPLPSSNVSVKGVLLNFEDVNGKVWRFRYSYWNS 73 Query: 188 PRRHLLTTGWSTFVTSKRLVAGDAFVFLR--GENGELRVG 225 + ++LT GWS FV K L AGD F R G++ +L +G Sbjct: 74 SQSYVLTKGWSRFVKEKNLRAGDVVSFSRSNGQDQQLYIG 113

PyMOL of 1wid

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Alignment Graph	Length	Definition	E-value
Query		664
1wid_A		130	DNA-binding protein RAV1; DNA-binding domain, stru	2e-42

>1wid_A DNA-binding protein RAV1; DNA-binding domain, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Arabidopsis thaliana} SCOP: b.142.1.2 Length = 130	Back alignment and structure

 Score =  148 bits (375), Expect = 2e-42
 Identities = 32/126 (25%), Positives = 55/126 (43%)

Query: 118 PEPPKQTVHSFCKILTASDTSTHGGFSVLRKHATECLPPLDMTLATPTQELAAKDLHGYE 177
               +     F K +T SD        + + HA +  P     ++     L  +D++G  
Sbjct: 4   GSSGRSAEALFEKAVTPSDVGKLNRLVIPKHHAEKHFPLPSSNVSVKGVLLNFEDVNGKV 63

Query: 178 WRFKHIFRGQPRRHLLTTGWSTFVTSKRLVAGDAFVFLRGENGELRVGVRRLAHQQSSMP 237
           WRF++ +    + ++LT GWS FV  K L AGD   F R    + ++ +   +   S + 
Sbjct: 64  WRFRYSYWNSSQSYVLTKGWSRFVKEKNLRAGDVVSFSRSNGQDQQLYIGWKSRSGSDLD 123

Query: 238 SSVISS 243
           +S  SS
Sbjct: 124 ASGPSS 129

PyMOL of 1wid

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Alignment Graph	Length	Definition	Probability
Query		664
1wid_A		130	DNA-binding protein RAV1; DNA-binding domain, stru	99.96
4i1k_A		146	B3 domain-containing transcription factor VRN1; B3	99.62
1yel_A		104	AT1G16640; CESG, protein structure initiative, str	99.39
1wmh_B		86	Partitioning defective-6 homolog alpha; kinase, PB	95.41
1na6_A		404	Ecorii, restriction endonuclease ecorii; site-spec	95.06
1vd2_A		89	Protein kinase C, IOTA type; PB1 domain, OPCA moti	94.6
1q1o_A		98	Cell division control protein 24; PB1 domain, PCCR	90.4
2kkc_A		102	Sequestosome-1; P62, PB1, autophagy, ubiquitin-pro	89.31
2ktr_A		117	Sequestosome-1; autophagy, NF-KB signaling, HOMO-o	85.4
1oey_A		83	P67-PHOX, neutrophil cytosol factor 2; immune syst	84.41

>1wid_A DNA-binding protein RAV1; DNA-binding domain, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Arabidopsis thaliana} SCOP: b.142.1.2	Back alignment and structure

Probab=99.96  E-value=3.5e-29  Score=231.55  Aligned_cols=114  Identities=26%  Similarity=0.445  Sum_probs=104.6

Q ss_pred             CCCCceeeEEEecCccCCCCCCceEEecchhcccCCCCCCCCCCCCeEEEEeeCCCCeEEEEEEEcCCCceeeecccccc
Q 006028          120 PPKQTVHSFCKILTASDTSTHGGFSVLRKHATECLPPLDMTLATPTQELAAKDLHGYEWRFKHIFRGQPRRHLLTTGWST  199 (664)
Q Consensus       120 ~~~~~~~~F~K~LT~SDv~~~grfsVPk~~Ae~~fP~Ld~~~~~p~q~L~~~D~~G~~W~Fr~~yr~~~rr~lLTtGWs~  199 (664)
                      ..++...+|+|+||+|||++++||+||+++|+.|||.++..+..++++|.++|.+|++|+|||+||+++|+|+|++||+.
T Consensus         6 ~~~~~~~~F~K~Lt~SDv~~~~rL~iPk~~a~~~lP~~~~~~~~~~~~l~l~D~~Gk~W~fr~~~~~~~~~~~Lt~GW~~   85 (130)
T 1wid_A            6 SGRSAEALFEKAVTPSDVGKLNRLVIPKHHAEKHFPLPSSNVSVKGVLLNFEDVNGKVWRFRYSYWNSSQSYVLTKGWSR   85 (130)
T ss_dssp             --CCCEEEEEEECCTTTTSSSCCEEECHHHHTTTSCCCSSCCSSCCEEEEEEETTTEEEEEEEEEETTTTEEEEESSHHH
T ss_pred             CCCCCcceEEEEEehHHcCCCCEEEeCHHHHHhhCCccccccCCCcEEEEEEeCCCCEEEEEEEEECCCCceEEcCChHH
Confidence            34567789999999999999999999999999999999987777899999999999999999999999999999999999


Q ss_pred             cccccCCCCCCEEEEEeCCC--CcEEEEEEEccccC
Q 006028          200 FVTSKRLVAGDAFVFLRGEN--GELRVGVRRLAHQQ  233 (664)
Q Consensus       200 FV~~K~L~aGD~VvF~R~~~--G~l~vGiRRa~~~~  233 (664)
                      ||++|+|++||.|+|++.++  +.|+|++||+....
T Consensus        86 FV~~~~L~~GD~~~F~~~~~~~~~l~I~~rr~~~~~  121 (130)
T 1wid_A           86 FVKEKNLRAGDVVSFSRSNGQDQQLYIGWKSRSGSD  121 (130)
T ss_dssp             HHHHTTCCTTCEEEEEECCSSSCCEEEEEECCCSCS
T ss_pred             HHHHcCCCCCCEEEEEEecCCCcEEEEEEEECCCCC
Confidence            99999999999999999764  57999999998654

PyMOL of 1wid

>4i1k_A B3 domain-containing transcription factor VRN1; B3 domain beta-barrel, DNA binding protein; 1.60A {Arabidopsis thaliana}	Back alignment and structure

>1yel_A AT1G16640; CESG, protein structure initiative, structural genomics, center for eukaryotic structural genomics, unknown function; NMR {Arabidopsis thaliana} SCOP: b.142.1.2	Back alignment and structure

>1wmh_B Partitioning defective-6 homolog alpha; kinase, PB1 domain, OPCA motif, APKC, cell polarity, transferase/cell cycle complex; 1.50A {Homo sapiens} SCOP: d.15.2.2	Back alignment and structure

>1na6_A Ecorii, restriction endonuclease ecorii; site-specific restriction, mutation, replication, hydrolase; 2.10A {Escherichia coli} SCOP: b.142.1.1 c.52.1.22 PDB: 3hqg_A 3hqf_A	Back alignment and structure

>1vd2_A Protein kinase C, IOTA type; PB1 domain, OPCA motif, APKC, ZIP/P62, MEK5, molecular recognition, transferase; NMR {Homo sapiens} SCOP: d.15.2.2 PDB: 1wmh_A	Back alignment and structure

>1q1o_A Cell division control protein 24; PB1 domain, PCCR, PC motif, OPCA motif, yeast, cell polarity, protein-protein interaction; NMR {Saccharomyces cerevisiae} SCOP: d.15.2.2 PDB: 2kfj_A 2kfk_B	Back alignment and structure

>2kkc_A Sequestosome-1; P62, PB1, autophagy, ubiquitin-proteasome system, NF-KB signaling, alternative splicing, apoptosis, cytoplasm, differentiation; NMR {Rattus norvegicus} PDB: 2ktr_B	Back alignment and structure

>2ktr_A Sequestosome-1; autophagy, NF-KB signaling, HOMO-oligomer, PB1 dimer, signaling protein, transport protein; NMR {Rattus norvegicus}	Back alignment and structure

>1oey_A P67-PHOX, neutrophil cytosol factor 2; immune system, PB1 heterodimer/complex, NADPH oxidase, PB1 D heterodimerization; 2.0A {Homo sapiens} SCOP: d.15.2.2	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		664
d1wida_		117	b.142.1.2 (A:) DNA-binding protein RAV1 {Thale cre	1e-32
d1na6a1		175	b.142.1.1 (A:4-178) Restriction endonuclease EcoRI	1e-21
d1yela1		102	b.142.1.2 (A:1-102) At1g16640 {Thale cress (Arabid	4e-12

>d1wida_ b.142.1.2 (A:) DNA-binding protein RAV1 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]} Length = 117	Back information, alignment and structure


class: All beta proteins
fold: DNA-binding pseudobarrel domain
superfamily: DNA-binding pseudobarrel domain
family: B3 DNA binding domain
domain: DNA-binding protein RAV1
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

 Score =  120 bits (301), Expect = 1e-32
 Identities = 31/109 (28%), Positives = 52/109 (47%), Gaps = 2/109 (1%)

Query: 122 KQTVHSFCKILTASDTSTHGGFSVLRKHATECLPPLDMTLATPTQELAAKDLHGYEWRFK 181
           +     F K +T SD        + + HA +  P     ++     L  +D++G  WRF+
Sbjct: 1   RSAEALFEKAVTPSDVGKLNRLVIPKHHAEKHFPLPSSNVSVKGVLLNFEDVNGKVWRFR 60

Query: 182 HIFRGQPRRHLLTTGWSTFVTSKRLVAGDAFVFLR--GENGELRVGVRR 228
           + +    + ++LT GWS FV  K L AGD   F R  G++ +L +G + 
Sbjct: 61  YSYWNSSQSYVLTKGWSRFVKEKNLRAGDVVSFSRSNGQDQQLYIGWKS 109

PyMOL of d1wida_

>d1na6a1 b.142.1.1 (A:4-178) Restriction endonuclease EcoRII, N-terminal domain {Escherichia coli [TaxId: 562]} Length = 175	Back information, alignment and structure

>d1yela1 b.142.1.2 (A:1-102) At1g16640 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]} Length = 102	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		664
d1wida_		117	DNA-binding protein RAV1 {Thale cress (Arabidopsis	99.94
d1na6a1		175	Restriction endonuclease EcoRII, N-terminal domain	99.82
d1yela1		102	At1g16640 {Thale cress (Arabidopsis thaliana) [Tax	99.32
d2bkfa1		85	Next to BRCA1 gene 1 protein, NBR1 (KIAA0049) {Hum	95.56
d1ip9a_		85	Bud emergence mediator Bemp1 {Baker's yeast (Sacch	93.98
d1wmhb_		82	Partitioning defective-6 homolog alpha, PAR-6 alph	85.41

>d1wida_ b.142.1.2 (A:) DNA-binding protein RAV1 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}	Back information, alignment and structure

class: All beta proteins
fold: DNA-binding pseudobarrel domain
superfamily: DNA-binding pseudobarrel domain
family: B3 DNA binding domain
domain: DNA-binding protein RAV1
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=99.94  E-value=1e-26  Score=207.80  Aligned_cols=109  Identities=28%  Similarity=0.466  Sum_probs=102.4

Q ss_pred             ceeeEEEecCccCCCCCCceEEecchhcccCCCCCCCCCCCCeEEEEeeCCCCeEEEEEEEcCCCceeeecccccccccc
Q 006028          124 TVHSFCKILTASDTSTHGGFSVLRKHATECLPPLDMTLATPTQELAAKDLHGYEWRFKHIFRGQPRRHLLTTGWSTFVTS  203 (664)
Q Consensus       124 ~~~~F~K~LT~SDv~~~grfsVPk~~Ae~~fP~Ld~~~~~p~q~L~~~D~~G~~W~Fr~~yr~~~rr~lLTtGWs~FV~~  203 (664)
                      ...+|.|+||+|||++++||+||+++|+.|||+++.....++++|.+.|.+|++|.|+|+||++.++|+|++||..||++
T Consensus         3 ~~~iF~K~Lt~sDv~~~~rL~iP~~~~~~~lp~~~~~~~~~~~~~~~~d~~g~~W~~~~~~~~~~~~~~l~~GW~~Fv~~   82 (117)
T d1wida_           3 AEALFEKAVTPSDVGKLNRLVIPKHHAEKHFPLPSSNVSVKGVLLNFEDVNGKVWRFRYSYWNSSQSYVLTKGWSRFVKE   82 (117)
T ss_dssp             CEEEEEEECCTTTTSSSCCEEECHHHHTTTSCCCSSCCSSCCEEEEEEETTTEEEEEEEEEETTTTEEEEESSHHHHHHH
T ss_pred             CceEEEEEecchhcCCCCEEEECHHHHHHhCCccccccCCCcEEEEEEeCCCCEEEEEEEEECCCCceEEecCHHHHHHH
Confidence            45899999999999999999999999999999999988889999999999999999999999988999999999999999


Q ss_pred             cCCCCCCEEEEEeC--CCCcEEEEEEEcccc
Q 006028          204 KRLVAGDAFVFLRG--ENGELRVGVRRLAHQ  232 (664)
Q Consensus       204 K~L~aGD~VvF~R~--~~G~l~vGiRRa~~~  232 (664)
                      ++|++||.|+|+|.  ++|+++|++||+...
T Consensus        83 ~~Lk~GD~~~F~~~~~~~~~~~i~~r~~~~~  113 (117)
T d1wida_          83 KNLRAGDVVSFSRSNGQDQQLYIGWKSRSGS  113 (117)
T ss_dssp             TTCCTTCEEEEEECCSSSCCEEEEEECCCSC
T ss_pred             cCCCCCCEEEEEEEeCCCCEEEEEEEECCCC
Confidence            99999999999996  577999999988643

PyMOL of d1wida_

>d1na6a1 b.142.1.1 (A:4-178) Restriction endonuclease EcoRII, N-terminal domain {Escherichia coli [TaxId: 562]}	Back information, alignment and structure

>d1yela1 b.142.1.2 (A:1-102) At1g16640 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}	Back information, alignment and structure

>d2bkfa1 d.15.2.2 (A:1-85) Next to BRCA1 gene 1 protein, NBR1 (KIAA0049) {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1ip9a_ d.15.2.2 (A:) Bud emergence mediator Bemp1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}	Back information, alignment and structure

>d1wmhb_ d.15.2.2 (B:) Partitioning defective-6 homolog alpha, PAR-6 alpha {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure