Citrus Sinensis ID: 005491

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----

MANRLGSLSQPSSNSDDLYRELWKACAGPLVDVPKQGQRVYYFPQGHMEQLEASTNQELNQRIPLFRLPSKILCRVVNIHLMAEQETDEVYAQITLLPEPSQNEPTTPDPCPADSPRPKVHSFSKVLTASDTSTHGGFSVLRKHATECLPPLDMNQSTPTQELVAKDLHGYEWRFKHIFRGQPRRHLLTTGWSTFVTSKRLVAGDTFVFLRGENGELHVGVRCLARQQSSMPSSVISSQSMHLGVLATASHAVATQTMFVVYYKPRIITRTSQFIISLNKYLEAVNNKFAVGMRYKMRFEGEDSPERRFSGTVVGVEDFSPHWKDSKWRSLKVQWDEPASITRPDRVSPWEIEPFVASATPNLVQPVLAKNKRPRLSMEVPPLDLPSAASAPWSARLAQSHNLTQLSVTAEDKRIDNHVAWHHKHSDFSSNSNFMSRTQSDGEWLTSPRVKFSQQLFQEAIDDNKNISAWPAHSGHSTPHPSKPNNDTLLEQVETGRKTETGTSCRLFGIELINHATSSAPSEKVPVSSLTTEGHIISTISAAADSDGKSDIAKEFKEKKQEQVQVSPKESQSKQSCLTSNRSRTKVQMQGVAVGRALDLTTLVGYDHLIDELEEMFDIKGQLHTRTKWEIVYTDDEGDMMLVGDDPWHEFCNMVKRIFICSSQDVKKMSPGSKLPMFSIEGEDILLSSDSAEK

cccccccccccccccccccHHHHHHHccccccccccccEEEEccccHHHHHcccccHHHHccccccccccccEEEEEEEEEEcccccHHHHEEEEEcccccccccccccccccccccccccEEEEEEEcccccccccccccccccccccccccccccccccEEEEEEcccccEEEEEEEccccccEEEcccccccccccccccccEEEEEEcccccEEEEEEEEEEccccccccccccccccccHHHHHHHHHHccccEEEEEEcccccccccEEEEHHHHHHHHccccccccEEEEEEcccccccEEEEEEEEEEccccccccccccccEEEEEcccccccccccccccEEEccccccccccccccccccccccccccccccccccccccccHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHccccccccccccccccccccccccEEEEEEccEEEEEEcccccccHHHHHHHHHHHHccccccccccccEEEEEcccccEEEcccccHHHHHHcccEEEEEccccccccccccccccccccccccccccccccc

cccccccccccccccccccHHHHHHHcccccEccccccEEEEEccccHHHHHccccccHHcccccccccccEEEEEEEEEEEccccccEEEEEEEEcccccccccccccccccccccccccHHHHEcccccccccccccHHHHHHHHHcccccccccccHHHHHHHHccccEEEEEEEEccccccEEEccccEEEEcccEEEcccEEEEEEcccccEEEEEEEccccccccccccccccccHHHHHHHHHHHHHccccEEEEEcccEccccccEEEEHHHHHHHHHccccEcEEEEEEEcccccccEEEEEEEEEcccccccccccccEEEEEEccccccccccccccccEEcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEccccEccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEEEEcccccccEEEEEccccHHHHHHHHHHHHccccccccccccEEEEEcccccEEEEccccHHHHHHHHEEEEEEcHHHHHHcccccccccccccccccccccccccc

manrlgslsqpssnsddLYRELWKAcagplvdvpkqgqrvyyfpqghmeqlEASTNQelnqriplfrlpskILCRVVNIHLMAEQETDEVYAQItllpepsqnepttpdpcpadsprpkvhsfskvltasdtsthgGFSVLRKHateclppldmnqstptqELVAKDLHGYEWRFKhifrgqprrhllttgwstfvtskrlvagdtfvflrgengelhVGVRCLarqqssmpssvissqsmhLGVLATASHAVATQTMFVVYYKPRIITRTSQFIISLNKYLEAVNNKFAVGMRYKmrfegedsperrfsgtvvgvedfsphwkdskwrslkvqwdepasitrpdrvspweiepfvasatpnlvqpvlaknkrprlsmevppldlpsaasapwsarlaqshnltqlsvtaedkridnhvawhhkhsdfssnsnfmsrtqsdgewltsprvkFSQQLFQEAIddnknisawpahsghstphpskpnndtLLEQVETgrktetgtscRLFGIELINhatssapsekvpvsslttegHIISTIsaaadsdgkSDIAKEFKEKKqeqvqvspkesqskqscltsnrsrtKVQMQGVAVGRALDLTTLVGYDHLIDELEEMFDIKgqlhtrtkweivytddegdmmlvgddpwhEFCNMVKRIFIcssqdvkkmspgsklpmfsiegedillssdsaek

manrlgslsqpssnSDDLYRELWKACAGPLVDVPKQGQRVYYFPQGHMEQLEASTNQELNQRIPLFRLPSKILCRVVNIHLMAEQETDEVYAQITLLPEPSQNEPTTPDPCPADSPRPKVHSFSKVLTASDTSTHGGFSVLRKHATECLPPLDMNQSTPTQELVAKDLHGYEWRFKHIfrgqprrhlLTTGWSTFVTSKRLVAGDTFVFLRGENGELHVGVRCLARQQSSMPSSVISSQSMHLGVLATASHAVATQTMFVVYYKPRIITRTSQFIISLNKYLEAVNNKFAVGMRYKMRFegedsperrfsgtvvgvedfsphwkdskwrslkvqwdepasitrpdrvspWEIEPFvasatpnlvqpvlAKNKRPRLSMEVPPLDLPSAASAPWSARLAQSHNLTQLSVTAEDKRIDNHVAWHhkhsdfssnsnfMSRTQSDGEWLTSPRVKFSQQLFQEAIDDNKNISAWPAHSghstphpskpnnDTLLEQVETGRKTETGTSCRLFGIELINhatssapsekVPVSSLTTEGHIISTisaaadsdgKSDIAKEFKEkkqeqvqvspkesqskqscltsnrsrtkvqmqgvAVGRALDLTTLVGYDHLIDELEEMFdikgqlhtrtKWEIVYTDDEGDMMLVGDDPWHEFCNMVKRIFICSSQDVKKMspgsklpmfsiegedillssdsaek

MANRLGSLSQPSSNSDDLYRELWKACAGPLVDVPKQGQRVYYFPQGHMEQLEASTNQELNQRIPLFRLPSKILCRVVNIHLMAEQETDEVYAQITLLPEPSQNEPTTPDPCPADSPRPKVHSFSKVLTASDTSTHGGFSVLRKHATECLPPLDMNQSTPTQELVAKDLHGYEWRFKHIFRGQPRRHLLTTGWSTFVTSKRLVAGDTFVFLRGENGELHVGVRCLARqqssmpssvissqsMHLGVLATASHAVATQTMFVVYYKPRIITRTSQFIISLNKYLEAVNNKFAVGMRYKMRFEGEDSPERRFSGTVVGVEDFSPHWKDSKWRSLKVQWDEPASITRPDRVSPWEIEPFVASATPNLVQPVLAKNKRPRLSMEVppldlpsaasapwsarlaQSHNLTQLSVTAEDKRIDNHVAWHHKHSDFSSNSNFMSRTQSDGEWLTSPRVKFSQQLFQEAIDDNKNISAWPAHSGHSTPHPSKPNNDTLLEQVETGRKTETGTSCRLFGIELINHATSSAPSEKVPVSSLTTEGHIISTISAAADSDGKSDIAkefkekkqeqvqvSPKESQSKQSCLTSNRSRTKVQMQGVAVGRALDLTTLVGYDHLIDELEEMFDIKGQLHTRTKWEIVYTDDEGDMMLVGDDPWHEFCNMVKRIFICSSQDVKKMSPGSKLPMFSIEGEDILLSSDSAEK

*****************LYRELWKACAGPLVDVPKQGQRVYYFPQGHME********ELNQRIPLFRLPSKILCRVVNIHLMAEQETDEVYAQITL******************************************SVLR**A**C*************ELVAKDLHGYEWRFKHIFRGQPRRHLLTTGWSTFVTSKRLVAGDTFVFLRGENGELHVGVRCLA***************MHLGVLATASHAVATQTMFVVYYKPRIITRTSQFIISLNKYLEAVNNKFAVGMRYKMRFE********FSGTVVGVEDFSPHWKDSKWRSLKVQWDEPASITRPDRVSPWEIEPFVASATPNLV****************************************************NHVAWH*********************************************************************************SCRLFGIELINH*************************************************************************MQGVAVGRALDLTTLVGYDHLIDELEEMFDIKGQLHTRTKWEIVYTDDEGDMMLVGDDPWHEFCNMVKRIFICSS*******************************

********************ELWKACAGPLVDVPKQGQRVYYFPQGHMEQLE************LFRLPSKILCRVVNIHLMAEQETDEVYAQITL*************************SFSKVLTASDTSTHGGFSVLRKHATECLPP************VAKDLHGYEWRFKHIFRGQPRRHLLTTGWSTFVTSKRLVAGDTFVFLRGENGELHVGVRCLAR**********************ASHAVATQTMFVVYYKPRIITRTSQFIISLNKYLEAVNNKFAVGMRYKMRFEGEDSPERRFSGTVVGVEDFSPHWKDSKWRSLKVQWDEPASITRPDRVSPWEIEPFVASA********************************PWSARLAQSHNLT*************************************************************************************************************************************************************************************KVQMQGVAVGRALDLTTLVGYDHLIDELEEMFDIKGQLHTRTKWEIVYTDDEGDMMLVGDDPWHEFCNMVKRIFIC*********************************

****************DLYRELWKACAGPLVDVPKQGQRVYYFPQGHMEQLEASTNQELNQRIPLFRLPSKILCRVVNIHLMAEQETDEVYAQITLLPEP*********************SFSKVLTASDTSTHGGFSVLRKHATECLPPLDMNQSTPTQELVAKDLHGYEWRFKHIFRGQPRRHLLTTGWSTFVTSKRLVAGDTFVFLRGENGELHVGVRCLA************SQSMHLGVLATASHAVATQTMFVVYYKPRIITRTSQFIISLNKYLEAVNNKFAVGMRYKMRFEGEDSPERRFSGTVVGVEDFSPHWKDSKWRSLKVQWDEPASITRPDRVSPWEIEPFVASATPNLVQPVLAKNKRPRLSMEVPPLDLPSAASAPWSARLAQSHNLTQLSVTAEDKRIDNHVAWHHKHSDFSSNSNFMSRTQSDGEWLTSPRVKFSQQLFQEAIDDNKNISAWP***********KPNNDTLLEQVETGRKTETGTSCRLFGIELINHAT*************TTEGHIISTISAAADSDGKSDIAKEF********************************MQGVAVGRALDLTTLVGYDHLIDELEEMFDIKGQLHTRTKWEIVYTDDEGDMMLVGDDPWHEFCNMVKRIFICSSQDVKKMSPGSKLPMFSIEGEDILLSSDSAEK

***************DDLYRELWKACAGPLVDVPKQGQRVYYFPQGHMEQLEASTNQELNQRIPLFRLPSKILCRVVNIHLMAEQETDEVYAQITLLPEP*****************PKVHSFSKVLTASDTSTHGGFSVLRKHATECLPPLDMNQSTPTQELVAKDLHGYEWRFKHIFRGQPRRHLLTTGWSTFVTSKRLVAGDTFVFLRGENGELHVGVRCLARQQ**MP********MHLGVLATASHAVATQTMFVVYYKPRIITRTSQFIISLNKYLEAVNNKFAVGMRYKMRFEGEDSPERRFSGTVVGVEDFSPHWKDSKWRSLKVQWDEPASITRPDRVSPWEIEPFVASATPNLVQPV*****************************************************************************************************************************************CRLF*IELIN******************************************************************NRSRTKVQMQGVAVGRALDLTTLVGYDHLIDELEEMFDIKGQLHTRTKWEIVYTDDEGDMMLVGDDPWHEFCNMVKRIFICSSQDVKKM*************************

oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo

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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		694	2.2.26 [Sep-21-2011]
Q9XED8		638	Auxin response factor 9 O	yes	no	0.893	0.971	0.609	0.0
Q6YVY0		678	Auxin response factor 7 O	yes	no	0.893	0.914	0.541	0.0
Q0JCZ4		673	Auxin response factor 9 O	no	no	0.903	0.931	0.541	0.0
Q8L7G0		665	Auxin response factor 1 O	no	no	0.877	0.915	0.524	0.0
Q5NB85		699	Auxin response factor 1 O	no	no	0.913	0.907	0.482	1e-170
Q9C8N9		606	Putative auxin response f	no	no	0.821	0.940	0.473	1e-161
Q9LQE3		593	Putative auxin response f	no	no	0.804	0.940	0.465	1e-159
Q9C8N7		598	Auxin response factor 22	no	no	0.804	0.933	0.476	1e-158
Q9LQE8		605	Putative auxin response f	no	no	0.821	0.942	0.457	1e-158
Q9XID4		593	Auxin response factor 12	no	no	0.806	0.944	0.473	1e-157

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

 Score =  767 bits (1981), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 419/687 (60%), Positives = 501/687 (72%), Gaps = 67/687 (9%)

Query: 1   MANRLGSLSQPSSNSDDLYRELWKACAGPLVDVPKQGQRVYYFPQGHMEQLEASTNQ-EL 59
           MANR G           LY ELWK CAGPLVDVP+  +RVYYFPQGHMEQLEAST Q +L
Sbjct: 1   MANRGGEY---------LYDELWKLCAGPLVDVPQAQERVYYFPQGHMEQLEASTQQVDL 51

Query: 60  NQRIPLFRLPSKILCRVVNIHLMAEQETDEVYAQITLLPEPSQ-NEPTTPDPCPADSPRP 118
           N   PLF LP KILC V+N+ L AE++TDEVYAQITL+P  ++ +EP +PDP P +  RP
Sbjct: 52  NTMKPLFVLPPKILCNVMNVSLQAEKDTDEVYAQITLIPVGTEVDEPMSPDPSPPELQRP 111

Query: 119 KVHSFSKVLTASDTSTHGGFSVLRKHATECLPPLDMNQSTPTQELVAKDLHGYEWRFKHI 178
           KVHSFSKVLTASDTSTHGGFSVLRKHATECLPPLDM Q TPTQELVA+D+HGY+W+FKHI
Sbjct: 112 KVHSFSKVLTASDTSTHGGFSVLRKHATECLPPLDMTQQTPTQELVAEDVHGYQWKFKHI 171

Query: 179 FRGQPRRHLLTTGWSTFVTSKRLVAGDTFVFLRGENGELHVGVRCLARQQSSMPSSVISS 238
           FRGQPRRHLLTTGWSTFVTSKRLVAGDTFVFLRGENGEL VGVR    QQSSMPSSVISS
Sbjct: 172 FRGQPRRHLLTTGWSTFVTSKRLVAGDTFVFLRGENGELRVGVRRANLQQSSMPSSVISS 231

Query: 239 QSMHLGVLATASHAVATQTMFVVYYKPRIITRTSQFIISLNKYLEAVNNKFAVGMRYKMR 298
            SMHLGVLATA HA  T+TMF+VYYKPR    TSQFIISLNKYLEA++NKF+VGMR+KMR
Sbjct: 232 HSMHLGVLATARHATQTKTMFIVYYKPR----TSQFIISLNKYLEAMSNKFSVGMRFKMR 287

Query: 299 FEGEDSPERRFSGTVVGVEDFSPHWKDSKWRSLKVQWDEPASITRPDRVSPWEIEPFVAS 358
           FEGEDSPERR+SGTV+GV+D SPHWKDSKWR L+V WDEPASI+RP++VSPWEIEPFV S
Sbjct: 288 FEGEDSPERRYSGTVIGVKDCSPHWKDSKWRCLEVHWDEPASISRPNKVSPWEIEPFVNS 347

Query: 359 ATPNLVQPVLAKNKRPRLSMEVPPLDLPSAASAPWSARLAQSHNLTQLSVTAEDKRIDNH 418
              N+ + V+ KNKRPR   EV  LD+   AS  WS+ L Q H   Q  +T++       
Sbjct: 348 E--NVPKSVMLKNKRPRQVSEVSALDVGITASNLWSSVLTQPHEFAQSCITSQ------- 398

Query: 419 VAWHHKHSDFSSNSNFMSRTQSDGEWLTSPRVKFSQQLFQEAIDDNKNISAWPAHSGHST 478
                                    W +SP     QQ  ++A +D K  S W  ++ +S 
Sbjct: 399 -------------------------W-SSP-----QQCHRDANEDAKK-SDW-LNNSYSV 425

Query: 479 PHPSKPN--NDTLLEQVETGRKTETGTSCRLFGIELINHATSSAPSEKVPVSSLTTEGHI 536
            + +K +  ND ++  VE  +K ET  + RLFGI+L++ + +    +  P+  +      
Sbjct: 426 SNVAKDSTLNDQMVSPVEQ-KKPETTANYRLFGIDLMSSSLAVPEEKTAPMRPIN----- 479

Query: 537 ISTISAAADSDGKSDIAKEFKEKKQEQVQVSPKESQSKQSCLTSNRSRTKVQMQGVAVGR 596
           IS  +  + SD KS+I+K  +EKKQE  + SPKE QSKQS  +S RSRTKVQMQGV VGR
Sbjct: 480 ISKPTMDSHSDPKSEISKVSEEKKQEPAEGSPKEVQSKQS--SSTRSRTKVQMQGVPVGR 537

Query: 597 ALDLTTLVGYDHLIDELEEMFDIKGQLHTRTKWEIVYTDDEGDMMLVGDDPWHEFCNMVK 656
           A+DL  L GY+ LID++E++FDIKG+L +R +WEIV+TDDEGDMMLVGDDPW EFCNMVK
Sbjct: 538 AVDLNALKGYNELIDDIEKLFDIKGELRSRNQWEIVFTDDEGDMMLVGDDPWPEFCNMVK 597

Query: 657 RIFICSSQDVKKMSPGSKLPMFSIEGE 683
           RIFI S ++VKKM+PG++L M   E E
Sbjct: 598 RIFIWSKEEVKKMTPGNQLRMLLREVE 624

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\|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\|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

>sp\|Q9C8N7\|ARFV_ARATH Auxin response factor 22 OS=Arabidopsis thaliana GN=ARF22 PE=2 SV=2	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\|Q9XID4\|ARFL_ARATH Auxin response factor 12 OS=Arabidopsis thaliana GN=ARF12 PE=2 SV=2	Back alignment and function description

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Alignment Graph	Length	Definition	Q cover	H cover	Identity	E-value
Query		694
255555629		694	hypothetical protein RCOM_1311830 [Ricin	0.982	0.982	0.771	0.0
297742361		682	unnamed protein product [Vitis vinifera]	0.958	0.975	0.721	0.0
359473930		693	PREDICTED: auxin response factor 9-like	0.952	0.953	0.71	0.0
356504356		691	PREDICTED: auxin response factor 9-like	0.956	0.960	0.700	0.0
356496084		692	PREDICTED: auxin response factor 9-like	0.958	0.960	0.699	0.0
357469307		666	Auxin response factor [Medicago truncatu	0.923	0.962	0.684	0.0
356520917		664	PREDICTED: auxin response factor 9-like	0.932	0.974	0.677	0.0
356567961		664	PREDICTED: auxin response factor 9-like	0.932	0.974	0.672	0.0
359489584		764	PREDICTED: auxin response factor 18-like	0.966	0.878	0.630	0.0
449533118		669	PREDICTED: LOW QUALITY PROTEIN: auxin re	0.943	0.979	0.638	0.0

>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

 Score = 1073 bits (2775), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 541/701 (77%), Positives = 601/701 (85%), Gaps = 19/701 (2%)

Query: 2   ANRLGSLSQPSSNS---DDLYRELWKACAGPLVDVPKQGQRVYYFPQGHMEQLEASTNQE 58
           ANR+GS SQ +S     DDLY ELWKACAGPLVDVPK G+RV+YFPQGHMEQLEASTNQE
Sbjct: 3   ANRVGSFSQGNSEGSCGDDLYTELWKACAGPLVDVPKDGERVFYFPQGHMEQLEASTNQE 62

Query: 59  LNQRIPLFRLPSKILCRVVNIHLMAEQETDEVYAQITLLPEPSQNEPTTPDPCPAD-SPR 117
           LNQR+PLF LPSKILCRV+NIHL+AEQ+TDEVYAQITLLPE  Q EPT+PDP PA+ S R
Sbjct: 63  LNQRVPLFNLPSKILCRVINIHLLAEQDTDEVYAQITLLPESDQTEPTSPDPSPAEPSRR 122

Query: 118 PKVHSFSKVLTASDTSTHGGFSVLRKHATECLPPLDMNQSTPTQELVAKDLHGYEWRFKH 177
           P VHSF KVLTASDTSTHGGFSVLRKHATECLP LDM Q TPTQELVAKDLHGYEWRFKH
Sbjct: 123 PAVHSFCKVLTASDTSTHGGFSVLRKHATECLPQLDMTQPTPTQELVAKDLHGYEWRFKH 182

Query: 178 IFRGQPRRHLLTTGWSTFVTSKRLVAGDTFVFLRGENGELHVGVRCLARQQSSMPSSVIS 237
           IFRGQPRRHLLTTGWSTFVTSKRLVAGD+FVFLRGENGEL VGVR LARQQSSMPSSVIS
Sbjct: 183 IFRGQPRRHLLTTGWSTFVTSKRLVAGDSFVFLRGENGELRVGVRRLARQQSSMPSSVIS 242

Query: 238 SQSMHLGVLATASHAVATQTMFVVYYKPRIITRTSQFIISLNKYLEAVNNKFAVGMRYKM 297
           SQSMHLGVLATASHAVATQT+FVVYYKPR    TSQFIISLNKYLEA+NNKF+VGMR+KM
Sbjct: 243 SQSMHLGVLATASHAVATQTLFVVYYKPR----TSQFIISLNKYLEAINNKFSVGMRFKM 298

Query: 298 RFEGEDSPERRFSGTVVGVEDFSPHWKDSKWRSLKVQWDEPASITRPDRVSPWEIEPFVA 357
           RFEGEDSPERRFSGT+VGVEDFSPHW DSKWR LKVQWDEPASI RPD+VSPWEIEPF A
Sbjct: 299 RFEGEDSPERRFSGTIVGVEDFSPHWLDSKWRQLKVQWDEPASIPRPDKVSPWEIEPFSA 358

Query: 358 SATPNLVQPVLAKNKRPRLSMEVPPLDLPSAASAPWSARLAQSHNLTQLSVTAEDKRIDN 417
           SA  N+ QPV  KNKRPR  +EVP LDL S AS  W++RL QSH+LTQLSVTAE KR +N
Sbjct: 359 SAPSNISQPVPLKNKRPRPPIEVPTLDLSSTASPLWNSRLTQSHDLTQLSVTAEGKRNEN 418

Query: 418 HVAWHHKHSDFSSNSNFMSRTQSDGEWLTSPRVKFSQQLFQEAIDDNKNISAWPAHSGHS 477
           H+ WHHK +D +S+SN +SRTQ++G WL+SP V  SQ LFQE  +D+K++S WP  SG+S
Sbjct: 419 HIMWHHKQNDINSHSNSISRTQTEGGWLSSPLVNVSQHLFQEVTEDSKSVSNWPVVSGYS 478

Query: 478 TPHPSKPNNDTLLEQVETGRKTETGTSCRLFGIELINHATSSAPSEKVP-----VSSLTT 532
           TP  SK  ND++L+ VE GRK++  TS RLFGIELINH+ SS P+EK P     VSS TT
Sbjct: 479 TPQSSK-LNDSILDPVEKGRKSDVATSYRLFGIELINHSASSLPTEKAPAQPLSVSSGTT 537

Query: 533 EGHIISTISAAADSDGKSDIAKEFKEKKQEQVQVSPKESQSKQSCLTSNRSRTKVQMQGV 592
           E H++ST+S AADSD KSDI+   KE+K EQ+ VSPK++QS+QS   S RSRTKVQMQGV
Sbjct: 538 EAHVVSTLS-AADSDQKSDIS---KERKPEQLHVSPKDAQSRQSS-ASTRSRTKVQMQGV 592

Query: 593 AVGRALDLTTLVGYDHLIDELEEMFDIKGQLHTRTKWEIVYTDDEGDMMLVGDDPWHEFC 652
           AVGRA+DLT + GY+ L+DELEEMFDIKGQLH R KWEIVYTDDEGDMMLVGDDPW EFC
Sbjct: 593 AVGRAIDLTMIKGYNQLLDELEEMFDIKGQLHPRDKWEIVYTDDEGDMMLVGDDPWPEFC 652

Query: 653 NMVKRIFICSSQDVKKMSPGSKLPMFSIEGEDILLSSDSAE 693
           NMV+RIFICSSQDVKKM PGSKLPMFS EGE  ++SSDSA+
Sbjct: 653 NMVRRIFICSSQDVKKMMPGSKLPMFSTEGEGTVISSDSAD 693

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi\|297742361\|emb\|CBI34510.3\| 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\|356504356\|ref\|XP_003520962.1\| PREDICTED: auxin response factor 9-like [Glycine max]	Back alignment and taxonomy information

>gi\|356496084\|ref\|XP_003516900.1\| PREDICTED: auxin response factor 9-like [Glycine max]	Back alignment and taxonomy information

>gi\|357469307\|ref\|XP_003604938.1\| Auxin response factor [Medicago truncatula] gi\|355505993\|gb\|AES87135.1\| Auxin response factor [Medicago truncatula]	Back alignment and taxonomy information

>gi\|356520917\|ref\|XP_003529106.1\| PREDICTED: auxin response factor 9-like [Glycine max]	Back alignment and taxonomy information

>gi\|356567961\|ref\|XP_003552183.1\| PREDICTED: auxin response factor 9-like [Glycine max]	Back alignment and taxonomy information

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

>gi\|449533118\|ref\|XP_004173524.1\| PREDICTED: LOW QUALITY PROTEIN: auxin response factor 9-like, partial [Cucumis sativus]	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		694
TAIR\|locus:2138096		638	ARF9 "auxin response factor 9"	0.602	0.655	0.652	3.2e-197
TAIR\|locus:2039124		622	ARF11 "auxin response factor 1	0.523	0.583	0.686	1.2e-171
TAIR\|locus:2076765		602	ARF18 "auxin response factor 1	0.521	0.601	0.669	1.9e-171
TAIR\|locus:2025991		665	ARF1 "auxin response factor 1"	0.515	0.538	0.658	3.1e-164
TAIR\|locus:2174013		859	ARF2 "auxin response factor 2"	0.508	0.410	0.642	6.2e-157
TAIR\|locus:2036288		598	ARF22 "auxin response factor 2	0.507	0.588	0.559	2.7e-145
TAIR\|locus:2009298		606	ARF21 "auxin response factor 2	0.501	0.574	0.557	1.3e-143
TAIR\|locus:2014731		605	ARF14 "auxin response factor 1	0.510	0.585	0.548	2.7e-143
TAIR\|locus:2026145		593	ARF12 "auxin response factor 1	0.510	0.596	0.548	2.4e-142
TAIR\|locus:2206717		590	ARF20 "auxin response factor 2	0.498	0.586	0.551	2.1e-141

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

 Score = 1424 (506.3 bits), Expect = 3.2e-197, Sum P(2) = 3.2e-197
 Identities = 280/429 (65%), Positives = 321/429 (74%)

Query:    18 LYRELWKACAGPLVDVPKQGQRVYYFPQGHMEQLEASTNQ-ELNQRIPLFRLPSKILCRV 76
             LY ELWK CAGPLVDVP+  +RVYYFPQGHMEQLEAST Q +LN   PLF LP KILC V
Sbjct:     9 LYDELWKLCAGPLVDVPQAQERVYYFPQGHMEQLEASTQQVDLNTMKPLFVLPPKILCNV 68

Query:    77 VNIHLMAEQETDEVYAQITLLPEPSQ-NEPTTPDPCPADSPRPKVHSFSKVLTASDTSTH 135
             +N+ L AE++TDEVYAQITL+P  ++ +EP +PDP P +  RPKVHSFSKVLTASDTSTH
Sbjct:    69 MNVSLQAEKDTDEVYAQITLIPVGTEVDEPMSPDPSPPELQRPKVHSFSKVLTASDTSTH 128

Query:   136 GGFSVLRKHATECLPPLDMNQSTPTQELVAKDLHGYEWRFKHIFRGQPRRHLLTTGWSTF 195
             GGFSVLRKHATECLPPLDM Q TPTQELVA+D+HGY+W+FKHIFRGQPRRHLLTTGWSTF
Sbjct:   129 GGFSVLRKHATECLPPLDMTQQTPTQELVAEDVHGYQWKFKHIFRGQPRRHLLTTGWSTF 188

Query:   196 VTSKRLVAGDTFVFLRGENGELHVGVRCLARXXXXXXXXXXXXXXMHLGVLATASHAVAT 255
             VTSKRLVAGDTFVFLRGENGEL VGVR                  MHLGVLATA HA  T
Sbjct:   189 VTSKRLVAGDTFVFLRGENGELRVGVRRANLQQSSMPSSVISSHSMHLGVLATARHATQT 248

Query:   256 QTMFVVYYKPRIITRTSQFIISLNKYLEAVNNKFAVGMRYKMRFEGEDSPERRFSGTVVG 315
             +TMF+VYYKPR    TSQFIISLNKYLEA++NKF+VGMR+KMRFEGEDSPERR+SGTV+G
Sbjct:   249 KTMFIVYYKPR----TSQFIISLNKYLEAMSNKFSVGMRFKMRFEGEDSPERRYSGTVIG 304

Query:   316 VEDFSPHWKDSKWRSLKVQWDEPASITRPDRVSPWEIEPFVASATPNLVQPVLAKNKRPR 375
             V+D SPHWKDSKWR L+V WDEPASI+RP++VSPWEIEPFV S   N+ + V+ KNKRPR
Sbjct:   305 VKDCSPHWKDSKWRCLEVHWDEPASISRPNKVSPWEIEPFVNSE--NVPKSVMLKNKRPR 362

Query:   376 LSMEVXXXXXXXXXXXXXXXXXXQSHNLTQLSVTAE---DKRIDNHVAWHHKHSDFSSNS 432
                EV                  Q H   Q  +T++    ++         K SD+ +NS
Sbjct:   363 QVSEVSALDVGITASNLWSSVLTQPHEFAQSCITSQWSSPQQCHRDANEDAKKSDWLNNS 422

Query:   433 NFMSRTQSD 441
               +S    D
Sbjct:   423 YSVSNVAKD 431

GO:0005634 "nucleus" evidence=ISM;IEA

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

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

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

GO:0005515 "protein binding" evidence=IPI

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

TAIR\|locus:2076765 ARF18 "auxin response factor 18" [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:2036288 ARF22 "auxin response factor 22" [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:2014731 ARF14 "auxin response factor 14" [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

TAIR\|locus:2206717 ARF20 "auxin response factor 20" [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)
Q9XED8	ARFI_ARATH	No assigned EC number	0.6098	0.8933	0.9717	yes	no
Q6YVY0	ARFG_ORYSJ	No assigned EC number	0.5419	0.8933	0.9144	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		694
pfam06507		83	pfam06507, Auxin_resp, Auxin response factor	4e-38
pfam02309		188	pfam02309, AUX_IAA, AUX/IAA family	2e-35
pfam02362		97	pfam02362, B3, B3 DNA binding domain	6e-28
smart01019		96	smart01019, B3, B3 DNA binding domain	3e-25
cd10017		98	cd10017, B3_DNA, Plant-specific B3-DNA binding dom	8e-20

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

 Score =  135 bits (343), Expect = 4e-38
 Identities = 49/85 (57%), Positives = 63/85 (74%), Gaps = 3/85 (3%)

Query: 249 ASHAVATQTMFVVYYKPRIITRTSQFIISLNKYLEAVNNKFAVGMRYKMRFEGEDSPERR 308
           A+HA +T + F V+Y PR    TS+F++   KYL+A+NN F+VGMR+KMRFE EDS ERR
Sbjct: 1   AAHAASTGSPFHVFYNPR--ASTSEFVVPYAKYLKAMNNPFSVGMRFKMRFETEDSSERR 58

Query: 309 FSGTVVGVEDFSP-HWKDSKWRSLK 332
           FSGT+ GV D  P  W +SKWRSL+
Sbjct: 59  FSGTISGVSDLDPIRWPNSKWRSLQ 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		694
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	99.69
KOG0644		1113	consensus Uncharacterized conserved protein, conta	99.52
PF09217		156	EcoRII-N: Restriction endonuclease EcoRII, N-termi	98.17
PF03754		114	DUF313: Domain of unknown function (DUF313) ; Inte	97.58
PF00564		84	PB1: PB1 domain; InterPro: IPR000270 The Phox and	96.87
smart00666		81	PB1 PB1 domain. Phox and Bem1p domain, present in	96.4
cd06407		82	PB1_NLP A PB1 domain is present in NIN like protei	96.2
cd05992		81	PB1 The PB1 domain is a modular domain mediating s	96.19
cd06398		91	PB1_Joka2 The PB1 domain is present in the Nicotia	96.18
cd06396		81	PB1_NBR1 The PB1 domain is an essential part of NB	95.7
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	94.34
cd06409		86	PB1_MUG70 The MUG70 protein is a product of the me	93.64
cd06404		83	PB1_aPKC PB1 domain is an essential modular domain	93.05
cd06402		87	PB1_p62 The PB1 domain is an essential part of p62	91.91
cd06408		86	PB1_NoxR The PB1 domain is present in the Epichloe	91.9
cd06397		82	PB1_UP1 Uncharacterized protein 1. The PB1 domain	89.95

>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=2.6e-37  Score=310.89  Aligned_cols=94  Identities=46%  Similarity=0.802  Sum_probs=0.0

Q ss_pred             CCcceeEEEecCceeeeeecCCCCCChHHHHHHHHHHh---hhc----------cc--ccCCCceeEEEecCCCCeEEcc
Q 005491          580 SNRSRTKVQMQGVAVGRALDLTTLVGYDHLIDELEEMF---DIK----------GQ--LHTRTKWEIVYTDDEGDMMLVG  644 (694)
Q Consensus       580 ~~~~~vKV~m~G~~vgR~vDL~~~~sY~eL~~~L~~MF---~~~----------g~--l~~~~~~~v~Y~D~eGD~mlvG  644 (694)
                      ..++||||+|||++|||||||++|+||++|+.+|++||   +|.          +.  |..+++|+|||+|+||||||||
T Consensus       107 ~~~~~vKV~mdG~~igRkVDL~~~~sY~~L~~~L~~MF~~~~i~~~~~~~~~~~~~~~~~~~~~~~l~Y~D~egd~mlvG  186 (215)
T PF02309_consen  107 SSRSYVKVNMDGVPIGRKVDLSAYSSYEELSSALEKMFSCFSIEQCGSHGLNESGLLDLLNGSEYVLVYEDKEGDWMLVG  186 (215)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             cCCceeEEEecCcccceecCHHHhhCHHHHHHHHHHhcCCCCccccccccccchhhccccCCcceeEEEECCCCCEEEec
Confidence            46899999999999999999999999999999999999   665          22  3456799999999999999999


Q ss_pred             CCChHHHHhcceEEEEeeccccccCCCCC
Q 005491          645 DDPWHEFCNMVKRIFICSSQDVKKMSPGS  673 (694)
Q Consensus       645 D~PW~~F~~~vkrl~I~~~~e~~~~~~~~  673 (694)
                      ||||+|||++||||+||+.+|++||+||+
T Consensus       187 D~PW~~F~~~vkRl~I~~~~e~~~~~~r~  215 (215)
T PF02309_consen  187 DVPWEEFVKSVKRLRIMKSSEAKGLAPRA  215 (215)
T ss_dssp             -----------------------------
T ss_pred             CCCHHHHHHHhhccEEecHHHhcccCCCC
Confidence            99999999999999999999999999975

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

>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

>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

>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

>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

>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

>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		694
1wid_A		130	Solution Structure Of The B3 Dna-Binding Domain Of		1e-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 = 58.9 bits (141), Expect = 1e-08, Method: Compositional matrix adjust. Identities = 33/103 (32%), Positives = 52/103 (50%), Gaps = 2/103 (1%) Query: 123 FSKVLTASDTSTHGGFSVLRKHATECLPPLDMNQSTPTQELVAKDLHGYEWRFKHIFRGQ 182 F K +T SD + + HA + P N S L +D++G WRF++ + Sbjct: 14 FEKAVTPSDVGKLNRLVIPKHHAEKHFPLPSSNVSVKGVLLNFEDVNGKVWRFRYSYWNS 73 Query: 183 PRRHLLTTGWSTFVTSKRLVAGDTFVFLR--GENGELHVGVRC 223 + ++LT GWS FV K L AGD F R G++ +L++G + Sbjct: 74 SQSYVLTKGWSRFVKEKNLRAGDVVSFSRSNGQDQQLYIGWKS 116 Database: pdbaa

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		694
1wid_A		130	DNA-binding protein RAV1; DNA-binding domain, stru	6e-44
1vt4_I		1221	APAF-1 related killer DARK; drosophila apoptosome,	8e-08

>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 =  152 bits (386), Expect = 6e-44
 Identities = 37/127 (29%), Positives = 56/127 (44%)

Query: 112 PADSPRPKVHSFSKVLTASDTSTHGGFSVLRKHATECLPPLDMNQSTPTQELVAKDLHGY 171
              S R     F K +T SD        + + HA +  P    N S     L  +D++G 
Sbjct: 3   SGSSGRSAEALFEKAVTPSDVGKLNRLVIPKHHAEKHFPLPSSNVSVKGVLLNFEDVNGK 62

Query: 172 EWRFKHIFRGQPRRHLLTTGWSTFVTSKRLVAGDTFVFLRGENGELHVGVRCLARQQSSM 231
            WRF++ +    + ++LT GWS FV  K L AGD   F R    +  + +   +R  S +
Sbjct: 63  VWRFRYSYWNSSQSYVLTKGWSRFVKEKNLRAGDVVSFSRSNGQDQQLYIGWKSRSGSDL 122

Query: 232 PSSVISS 238
            +S  SS
Sbjct: 123 DASGPSS 129

PyMOL of 1wid

>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

No hit with probability above 80.00

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		694
d1wida_		117	b.142.1.2 (A:) DNA-binding protein RAV1 {Thale cre	1e-33
d1na6a1		175	b.142.1.1 (A:4-178) Restriction endonuclease EcoRI	3e-22
d1yela1		102	b.142.1.2 (A:1-102) At1g16640 {Thale cress (Arabid	6e-14

>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 =  122 bits (308), Expect = 1e-33
 Identities = 36/119 (30%), Positives = 57/119 (47%), Gaps = 4/119 (3%)

Query: 117 RPKVHSFSKVLTASDTSTHGGFSVLRKHATECLPPLDMNQSTPTQELVAKDLHGYEWRFK 176
           R     F K +T SD        + + HA +  P    N S     L  +D++G  WRF+
Sbjct: 1   RSAEALFEKAVTPSDVGKLNRLVIPKHHAEKHFPLPSSNVSVKGVLLNFEDVNGKVWRFR 60

Query: 177 HIFRGQPRRHLLTTGWSTFVTSKRLVAGDTFVFLR--GENGELHVGVRCLARQQSSMPS 233
           + +    + ++LT GWS FV  K L AGD   F R  G++ +L++G +   R  S + +
Sbjct: 61  YSYWNSSQSYVLTKGWSRFVKEKNLRAGDVVSFSRSNGQDQQLYIGWKS--RSGSDLDA 117

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		694
d1wida_		117	DNA-binding protein RAV1 {Thale cress (Arabidopsis	99.94
d1na6a1		175	Restriction endonuclease EcoRII, N-terminal domain	99.84
d1yela1		102	At1g16640 {Thale cress (Arabidopsis thaliana) [Tax	99.45
d2bkfa1		85	Next to BRCA1 gene 1 protein, NBR1 (KIAA0049) {Hum	95.5
d1ip9a_		85	Bud emergence mediator Bemp1 {Baker's yeast (Sacch	94.47

>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=1.8e-26  Score=185.12  Aligned_cols=109  Identities=29%  Similarity=0.473  Sum_probs=102.1

Q ss_pred             CCEEEEEECCCCCCCCCCCEEEECCCHHHCCCCCCCCCCCCCEEEEEEECCCCEEEEEEEEECCCCCEEECCCCHHHHCC
Q ss_conf             30079996262569998941671110300199999999999329999857998489999993999702432450113202
Q 005491          119 KVHSFSKVLTASDTSTHGGFSVLRKHATECLPPLDMNQSTPTQELVAKDLHGYEWRFKHIFRGQPRRHLLTTGWSTFVTS  198 (694)
Q Consensus       119 ~~~~F~K~LT~SDv~~~grlsVPk~~Ae~~fP~Ld~~~~~p~q~L~~~D~~G~~W~Fr~~~rg~prr~lLTtGWs~FV~~  198 (694)
                      ..++|.|+||+|||++++||+||+.++++|||+++.....++++|.+.|.+|++|.|+|++|+..++|+|++||..||++
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
T ss_conf             76479999111200898889977899997389543456777079999959999999999998899834774577998887


Q ss_pred             CCCCCCCEEEEEEC--CCCCEEEEEEECCCC
Q ss_conf             67888989999976--897389999972223
Q 005491          199 KRLVAGDTFVFLRG--ENGELHVGVRCLARQ  227 (694)
Q Consensus       199 K~L~aGD~VvF~r~--~~G~l~VGIRRa~~~  227 (694)
                      ++|++||+|+|+++  ++++++|++||+...
T Consensus        83 ~~Lk~GD~~~F~~~~~~~~~~~i~~r~~~~~  113 (117)
T d1wida_          83 KNLRAGDVVSFSRSNGQDQQLYIGWKSRSGS  113 (117)
T ss_dssp             TTCCTTCEEEEEECCSSSCCEEEEEECCCSC
T ss_pred             CCCCCCCEEEEEEEECCCCEEEEEEEECCCC
T ss_conf             4999799999999818998899999999999

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