Citrus Sinensis ID: 038793

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Local Sequence Feature Prediction

Residue Number Marker
--------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-
Protein Sequence
ETIDAPSETETDDLNSTEISDEDDCEGEIETDDLIFTEISDKDDDYNLLLWQAFAGPPPSLPKKGDLVVYFPQGHLEYSAPASVSKAPPTFDLKPEIICRVADVRYLVSKKTDKVYTKMTLLPLPEMVGENFKGKELQDLVVDNKRDGEGSTANSTPPLFYKKLRASDQSKKKIVIRAKDAENVFPFLAHLDYKKQINYSVIAKDVHGVAWKFNFVDGKSRRHYLTVGWKYFVRQKNLVPGDTVIFIRYAY
Secondary Structure (PSIPRED)
cccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHccccccccccccEEEEEcccccccccccccccccccccccccEEEEEEEEEEEEEccccEEEEEcccccccccccccccccccccccccccccccccccccccccEEEEEEccccccccEEEEHHHHHHcccccccccccccccEEEEEEEccccEEEEEEEEcccccEEEcccHHHHHHHcccccccEEEEEEccc
Secondary Structure Prediction (SSPRO)
cccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHccccccccccccEEEEcccccHHHHHccccccccccccccccEEEEEEEEEEEccccccEEEEEEEEcccccccccccccHHHcccccccccccccccccccccHHEEEEcccccccccccHHHHHHHHHccccccccccccccHHHHHHHHcccEEEEEEEccccccEEEccccEEEEcccEEEcccEEEEEEccc
Coil and Loop (DISEMBL)
etidapsetetddlnsteisdeddcegeietddlifteisdkdddYNLLLWQafagpppslpkkgdlvvyfpqghleysapasvskapptfdlkpeiicRVADVRYLVSKKtdkvytkmtllplpemvgenfkgkelqDLVVDnkrdgegstanstpplfyKKLRASDQSKKKIVIRAKDaenvfpflahldykkqinYSVIAkdvhgvawkfnfvdgksrrhYLTVGWKYFVRqknlvpgdtVIFIRYAY
Flexible Loop (DISEMBL)
etidapsetetddlnsteisdeddcegeIETDDLIFTEISDKDDDYNLLLWQAFAGPPPSLPKKGDLVVYFPQGHLEYSAPASVSKAPPTFDLKPEIICRVADvrylvskktdkvytkmtllplpemvgenfkgkeLQDLVVDnkrdgegstanstpplfykklrasdqsKKKIVIRAKDAENVFPFLAHLDYKKQINYSVIAKDVHGVAWKFNFVDGKSRRHYLTVGWkyfvrqknlvpgdtvIFIRYAY
Low Complexity Region (SEG)
ETIDAPSETETDDLNSTEISDEDDCEGEIETDDLIFTEISDKDDDYNLLLWQAFAGPPPSLPKKGDLVVYFPQGHLEYSAPASVSKAPPTFDLKPEIICRVADVRYLVSKKTDKVYTKMTLLPLPEMVGENFKGKELQDLVVDNKRDGEGSTANSTPPLFYKKLRASDQSKKKIVIRAKDAENVFPFLAHLDYKKQINYSVIAKDVHGVAWKFNFVDGKSRRHYLTVGWKYFVRQKNLVPGDTVIFIRYAY
Disordered region (IsUnstruct)
*****************************ETDDLIFTEISDKDDDYNLLLWQAFAGPPPSLPKKGDLVVYFPQGHLEYSAPA*****PPTFDLKPEIICRVADVRYLVSKKTDKVYTKMTLLPLPEMVGENFKG**************************************KIVIRAKDAENVFPFLAHLDYKKQINYSVIAKDVHGVAWKFNFVDGKSRRHYLTVGWKYFVRQKNLVPGDTVIFIRYA*
Disordered Region (DISOPRED)
******S***************************************NLLLWQAFAGPPPSLPKKGDLVVYFPQGHLEYSA*********TFDLKPEIICRVADVRYLVSKKTDKVYTKMTLLPLP*********************************LFYKKLRASDQSKKKIVIRAKDAENVFPF*************VIAKDVHGVAWKFNFVDGKSRRHYLTVGWKYFVRQKNLVPGDTVIFIRYAY
Disordered Region (DISEMBL)
**************************GEIETDDLIFTEISDKDDDYNLLLWQAFAGPPPSLPKKGDLVVYFPQGHLEYSAPASVSKAPPTFDLKPEIICRVADVRYLVSKKTDKVYTKMTLLPLPEMVGENFKGKELQDLVVDNKRDGEGSTANSTPPLFYKKLRASDQSKKKIVIRAKDAENVFPFLAHLDYKKQINYSVIAKDVHGVAWKFNFVDGKSRRHYLTVGWKYFVRQKNLVPGDTVIFIRYAY
Disordered Region (DISPRO)
******************************************DDDYNLLLWQAFAGPPPSLPKKGDLVVYFPQGHLEYSAPASVSKAPPTFDLKPEIICRVADVRYLVSKKTDKVYTKMTLLPLP*******K*********************STPPLFYKKLRASDQSKKKIVIRAKDAENVFPFLAHLDYKKQINYSVIAKDVHGVAWKFNFVDGKSRRHYLTVGWKYFVRQKNLVPGDTVIFIRYAY
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
oooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
ETIDAPSETETDDLNSTEISDEDDCEGEIETDDLIFTEISDKDDDYNLLLWQAFAGPPPSLPKKGDLVVYFPQGHLEYSAPASVSKAPPTFDLKPEIICRVADVRYLVSKKTDKVYTKMTLLPLPEMVGENFKGKELQDLVVDNKRDGEGSTANSTPPLFYKKLRASDQSKKKIVIRAKDAENVFPFLAHLDYKKQINYSVIAKDVHGVAWKFNFVDGKSRRHYLTVGWKYFVRQKNLVPGDTVIFIRYAY
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	251	2.2.26 [Sep-21-2011]
Q9ZTX9	788	Auxin response factor 4 O	yes	no	0.760	0.242	0.495	6e-46
O23661	608	Auxin response factor 3 O	no	no	0.752	0.310	0.386	6e-32
Q0JKI9	718	Auxin response factor 2 O	yes	no	0.760	0.266	0.399	6e-30
Q5JMM1	731	Auxin response factor 3 O	no	no	0.768	0.264	0.364	3e-28
Q9FGV1	811	Auxin response factor 8 O	no	no	0.745	0.230	0.409	1e-27
Q6H6V4	908	Auxin response factor 6 O	no	no	0.776	0.214	0.380	3e-27
A2X1A1	908	Auxin response factor 6 O	N/A	no	0.776	0.214	0.380	3e-27
Q9SKN5	693	Auxin response factor 10	no	no	0.709	0.256	0.373	3e-27
Q8S985	712	Auxin response factor 15	no	no	0.760	0.268	0.392	4e-27
A2YG67	917	Auxin response factor 17	N/A	no	0.741	0.202	0.406	8e-27

>sp|Q9ZTX9|ARFD_ARATH Auxin response factor 4 OS=Arabidopsis thaliana GN=ARF4 PE=1 SV=1

 Score =  184 bits (466), Expect = 6e-46,   Method: Compositional matrix adjust.
 Identities = 103/208 (49%), Positives = 135/208 (64%), Gaps = 17/208 (8%)

Query: 50  LWQAFAGPPPSLPKKGDLVVYFPQGHLE------YSAPASVSKAPPTFDLKPEIICRVAD 103
           LW A AGP   LPKKG++VVYFPQGHLE      YS+P  +    P FDL P+I+CRV +
Sbjct: 66  LWHACAGPLTCLPKKGNVVVYFPQGHLEQDAMVSYSSPLEI----PKFDLNPQIVCRVVN 121

Query: 104 VRYLVSKKTDKVYTKMTLLPLPEMVGENFKGKELQDLVVDNKRDGEGSTANSTPPLFYKK 163
           V+ L +K TD+VYT++TLLPL E    N +GKE+++L  + +R+G  S+   TP +F K 
Sbjct: 122 VQLLANKDTDEVYTQVTLLPLQEFSMLNGEGKEVKELGGEEERNGS-SSVKRTPHMFCKT 180

Query: 164 LRASDQSKK-KIVIRAKDAENVFPFLAHLDYKKQI-NYSVIAKDVHGVAWKFNFV-DGKS 220
           L ASD S      +  + AE+ F   A LDYK+Q  +  +IAKD+HGV WKF  +  G+ 
Sbjct: 181 LTASDTSTHGGFSVPRRAAEDCF---APLDYKQQRPSQELIAKDLHGVEWKFRHIYRGQP 237

Query: 221 RRHYLTVGWKYFVRQKNLVPGDTVIFIR 248
           RRH LT GW  FV QKNLV GD V+F+R
Sbjct: 238 RRHLLTTGWSIFVSQKNLVSGDAVLFLR 265

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|O23661|ARFC_ARATH Auxin response factor 3 OS=Arabidopsis thaliana GN=ARF3 PE=1 SV=2

 Score =  137 bits (346), Expect = 6e-32,   Method: Compositional matrix adjust.
 Identities = 80/207 (38%), Positives = 121/207 (58%), Gaps = 18/207 (8%)

Query: 48  LLLWQAFAGPPPSLPKKGDLVVYFPQGHLEYSAPASVSKAPPTFDLKPEIICRVADVRYL 107
           L LW A AGP  SLPK+G LV+YFPQGHLE +   S +     + L P + CR+ DV+  
Sbjct: 53  LELWHACAGPLISLPKRGSLVLYFPQGHLEQAPDFSAA----IYGLPPHVFCRILDVKLH 108

Query: 108 VSKKTDKVYTKMTLLPLPEMVGENFKGKELQDLVVD---NKRDGEGSTANSTPPLFYKKL 164
               TD+VY +++LLP  E +      +++++ ++D    + D E    ++TP +F K L
Sbjct: 109 AETTTDEVYAQVSLLPESEDI-----ERKVREGIIDVDGGEEDYEVLKRSNTPHMFCKTL 163

Query: 165 RASDQSKK-KIVIRAKDAENVFPFLAHLDYKK-QINYSVIAKDVHGVAWKFNFV-DGKSR 221
            ASD S      +  + AE+ FP    LDY + + +  ++A+D+HG+ W+F  +  G+ R
Sbjct: 164 TASDTSTHGGFSVPRRAAEDCFP---PLDYSQPRPSQELLARDLHGLEWRFRHIYRGQPR 220

Query: 222 RHYLTVGWKYFVRQKNLVPGDTVIFIR 248
           RH LT GW  FV +K LV GD V+F+R
Sbjct: 221 RHLLTTGWSAFVNKKKLVSGDAVLFLR 247

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. Involved in the establishment or elaboration of tissue patterning during gynoecial development.

Arabidopsis thaliana (taxid: 3702)

>sp|Q0JKI9|ARFB_ORYSJ Auxin response factor 2 OS=Oryza sativa subsp. japonica GN=ARF2 PE=2 SV=1

 Score =  131 bits (329), Expect = 6e-30,   Method: Compositional matrix adjust.
 Identities = 83/208 (39%), Positives = 109/208 (52%), Gaps = 17/208 (8%)

Query: 48  LLLWQAFAGPPPSLPKKGDLVVYFPQGHLEYSAPASVSKAPPTFDLKPEIICRVADVRYL 107
           L LW A AGP   LP+KG  VVY PQGHLE+   A  S   P   + P + CRV DV   
Sbjct: 38  LELWHACAGPVAPLPRKGSAVVYLPQGHLEHLGAAPGSG--PGAAVPPHVFCRVVDVSLH 95

Query: 108 VSKKTDKVYTKMTLLPLPEMVGENFKGKELQDLVVDNKRDGEGSTA----NSTPPLFYKK 163
               TD+VY +++L+   E V      +E +D       DGEG  A       P +F K 
Sbjct: 96  ADAATDEVYAQVSLVADNEEVERRM--REGEDGAAC---DGEGEDAVKRPARIPHMFCKT 150

Query: 164 LRASDQSKK-KIVIRAKDAENVFPFLAHLDYKKQINYS-VIAKDVHGVAWKFNFV-DGKS 220
           L ASD S      +  + AE+ FP    LDY  Q  +  ++AKD+HG  W+F  +  G+ 
Sbjct: 151 LTASDTSTHGGFSVPRRAAEDCFP---PLDYSLQRPFQELVAKDLHGTEWRFRHIYRGQP 207

Query: 221 RRHYLTVGWKYFVRQKNLVPGDTVIFIR 248
           RRH LT GW  F+ +K LV GD V+F+R
Sbjct: 208 RRHLLTTGWSGFINKKKLVSGDAVLFLR 235

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).

Oryza sativa subsp. japonica (taxid: 39947)

>sp|Q5JMM1|ARFC_ORYSJ Auxin response factor 3 OS=Oryza sativa subsp. japonica GN=ARF3 PE=2 SV=1

 Score =  125 bits (314), Expect = 3e-28,   Method: Compositional matrix adjust.
 Identities = 74/203 (36%), Positives = 101/203 (49%), Gaps = 10/203 (4%)

Query: 50  LWQAFAGPPPSLPKKGDLVVYFPQGHLEYSAPASVSKAPPTFDLKPEIICRVADVRYLVS 109
           LW A AGP  SLP++G  VVY PQGHL  +      +      L P + CRV DV     
Sbjct: 83  LWHACAGPVVSLPRRGSAVVYLPQGHLSAAGAGGGIRGEVAVALPPHVACRVVDVELCAD 142

Query: 110 KKTDKVYTKMTLLPLPEMVGENFKGKELQDLVVDNKRDGEGSTANSTPPLFYKKLRASDQ 169
             TD+VY ++ L    E+   N  G  ++          +    +    +F K L ASD 
Sbjct: 143 AATDEVYARLALRAEGEVFERNLHGGGIEREDDMEDG--DEERKSRMLHMFCKTLTASDT 200

Query: 170 SKK-KIVIRAKDAENVFPFLAHLDYKKQINYS--VIAKDVHGVAWKFNFV-DGKSRRHYL 225
           S      +  + AE+ FP L H    KQ+  S  ++AKD+HG  W+F  +  G+ RRH L
Sbjct: 201 STHGGFSVPRRAAEDCFPPLDH----KQLRPSQELVAKDLHGAKWRFRHIYRGQPRRHLL 256

Query: 226 TVGWKYFVRQKNLVPGDTVIFIR 248
           T GW  FV +K LV GD V+F+R
Sbjct: 257 TTGWSSFVNKKKLVSGDAVLFLR 279

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).

Oryza sativa subsp. japonica (taxid: 39947)

>sp|Q9FGV1|ARFH_ARATH Auxin response factor 8 OS=Arabidopsis thaliana GN=ARF8 PE=2 SV=2

 Score =  123 bits (308), Expect = 1e-27,   Method: Composition-based stats.
 Identities = 86/210 (40%), Positives = 106/210 (50%), Gaps = 23/210 (10%)

Query: 47  NLLLWQAFAGPPPSLPKKGDLVVYFPQGHLEYSAPASVSKA----PPTFDLKPEIICRVA 102
           N  LW A AGP  SLP  G  VVYFPQGH E  A  +  +     P    L P++IC++ 
Sbjct: 20  NSELWHACAGPLVSLPSSGSRVVYFPQGHSEQVAATTNKEVDGHIPNYPSLPPQLICQLH 79

Query: 103 DVRYLVSKKTDKVYTKMTLLPL-PEMVGENFKGKELQDLVVDNKRDGEGSTANSTPPLFY 161
           +V      +TD+VY +MTL PL PE   E F   EL            G  +      F 
Sbjct: 80  NVTMHADVETDEVYAQMTLQPLTPEEQKETFVPIEL------------GIPSKQPSNYFC 127

Query: 162 KKLRASDQSKKK-IVIRAKDAENVFPFLAHLDYKKQI-NYSVIAKDVHGVAWKFNFV-DG 218
           K L ASD S      +  + AE VFP    LDY  Q     +IA+D+H V WKF  +  G
Sbjct: 128 KTLTASDTSTHGGFSVPRRAAEKVFP---PLDYTLQPPAQELIARDLHDVEWKFRHIFRG 184

Query: 219 KSRRHYLTVGWKYFVRQKNLVPGDTVIFIR 248
           + +RH LT GW  FV  K LV GD+VIFIR
Sbjct: 185 QPKRHLLTTGWSVFVSAKRLVAGDSVIFIR 214

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). Seems to act as transcriptional activator. Formation of heterodimers with Aux/IAA proteins may alter their ability to modulate early auxin response genes expression. Regulates both stamen and gynoecium maturation. Promotes jasmonic acid production. Partially redundant with ARF6. Involved in fruit initiation. Acts as an inhibitor to stop further carpel development in the absence of fertilization and the generation of signals required to initiate fruit and seed development.

Arabidopsis thaliana (taxid: 3702)

>sp|Q6H6V4|ARFF_ORYSJ Auxin response factor 6 OS=Oryza sativa subsp. japonica GN=ARF6 PE=1 SV=1

 Score =  122 bits (306), Expect = 3e-27,   Method: Composition-based stats.
 Identities = 83/218 (38%), Positives = 116/218 (53%), Gaps = 23/218 (10%)

Query: 38  EISDKDDDYNLLLWQAFAGPPPSLPKKGDLVVYFPQGHLEYSAPAS----VSKAPPTFDL 93
           E++++    N  LW A AGP  SLP  G  VVYFPQGH E  A ++     S+ P   +L
Sbjct: 19  EVAEEQKCLNSELWHACAGPLVSLPAVGSRVVYFPQGHSEQVAASTNKEMESQIPNYPNL 78

Query: 94  KPEIICRVADVRYLVSKKTDKVYTKMTLLPL-PEMVGENFKGKELQDLVVDNKRDGEGST 152
            P++IC++ +V      +TD+VY +MTL PL P+ + + F   EL            G+ 
Sbjct: 79  PPQLICQLHNVTMHADAETDEVYAQMTLQPLSPQELKDPFLPAEL------------GTA 126

Query: 153 ANSTPPLFYKKLRASDQSKK-KIVIRAKDAENVFPFLAHLDYKKQ-INYSVIAKDVHGVA 210
           +      F K L ASD S      +  + AE VFP    LD+ +Q     ++AKD+HG  
Sbjct: 127 SKQPTNYFCKTLTASDTSTHGGFSVPRRAAEKVFP---PLDFTQQPPAQELMAKDLHGNE 183

Query: 211 WKFNFV-DGKSRRHYLTVGWKYFVRQKNLVPGDTVIFI 247
           WKF  +  G+ +RH LT GW  FV  K LV GD+V+FI
Sbjct: 184 WKFRHIFRGQPKRHLLTTGWSVFVSAKRLVAGDSVLFI 221

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).

Oryza sativa subsp. japonica (taxid: 39947)

>sp|A2X1A1|ARFF_ORYSI Auxin response factor 6 OS=Oryza sativa subsp. indica GN=ARF6 PE=2 SV=1

 Score =  122 bits (306), Expect = 3e-27,   Method: Composition-based stats.
 Identities = 83/218 (38%), Positives = 116/218 (53%), Gaps = 23/218 (10%)

Query: 38  EISDKDDDYNLLLWQAFAGPPPSLPKKGDLVVYFPQGHLEYSAPAS----VSKAPPTFDL 93
           E++++    N  LW A AGP  SLP  G  VVYFPQGH E  A ++     S+ P   +L
Sbjct: 19  EVAEEQKCLNSELWHACAGPLVSLPAVGSRVVYFPQGHSEQVAASTNKEMESQIPNYPNL 78

Query: 94  KPEIICRVADVRYLVSKKTDKVYTKMTLLPL-PEMVGENFKGKELQDLVVDNKRDGEGST 152
            P++IC++ +V      +TD+VY +MTL PL P+ + + F   EL            G+ 
Sbjct: 79  PPQLICQLHNVTMHADAETDEVYAQMTLQPLSPQELKDPFLPAEL------------GTA 126

Query: 153 ANSTPPLFYKKLRASDQSKK-KIVIRAKDAENVFPFLAHLDYKKQ-INYSVIAKDVHGVA 210
           +      F K L ASD S      +  + AE VFP    LD+ +Q     ++AKD+HG  
Sbjct: 127 SKQPTNYFCKTLTASDTSTHGGFSVPRRAAEKVFP---PLDFTQQPPAQELMAKDLHGNE 183

Query: 211 WKFNFV-DGKSRRHYLTVGWKYFVRQKNLVPGDTVIFI 247
           WKF  +  G+ +RH LT GW  FV  K LV GD+V+FI
Sbjct: 184 WKFRHIFRGQPKRHLLTTGWSVFVSAKRLVAGDSVLFI 221

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).

Oryza sativa subsp. indica (taxid: 39946)

>sp|Q9SKN5|ARFJ_ARATH Auxin response factor 10 OS=Arabidopsis thaliana GN=ARF10 PE=2 SV=1

 Score =  122 bits (305), Expect = 3e-27,   Method: Compositional matrix adjust.
 Identities = 80/214 (37%), Positives = 106/214 (49%), Gaps = 36/214 (16%)

Query: 50  LWQAFAGPPPSLPKKGDLVVYFPQGHLEYSAPASVSKAPPTFD---LKPEIICRVADVRY 106
           LW A AG    +P     V YF QGH E++       APP F    + P I+CRV  V++
Sbjct: 11  LWHACAGSMVQIPSLNSTVFYFAQGHTEHA------HAPPDFHAPRVPPLILCRVVSVKF 64

Query: 107 LVSKKTDKVYTKMTLLPLPEMVGENFKGKELQDLVVDN---------KRDGEGSTANSTP 157
           L   +TD+V+ K+TLLPLP             DL ++N           DG G+     P
Sbjct: 65  LADAETDEVFAKITLLPLPG-----------NDLDLENDAVLGLTPPSSDGNGN-GKEKP 112

Query: 158 PLFYKKLRASDQSKKK-IVIRAKDAENVFPFLAHLDYKKQINY-SVIAKDVHGVAWKFNF 215
             F K L  SD +      +    AE +FP    LDY  +    +VIAKD+HG  WKF  
Sbjct: 113 ASFAKTLTQSDANNGGGFSVPRYCAETIFP---RLDYSAEPPVQTVIAKDIHGETWKFRH 169

Query: 216 V-DGKSRRHYLTVGWKYFVRQKNLVPGDTVIFIR 248
           +  G  RRH LT GW  FV QK L+ GD+++F+R
Sbjct: 170 IYRGTPRRHLLTTGWSTFVNQKKLIAGDSIVFLR 203

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|Q8S985|ARFO_ORYSJ Auxin response factor 15 OS=Oryza sativa subsp. japonica GN=ARF15 PE=2 SV=1

 Score =  121 bits (304), Expect = 4e-27,   Method: Compositional matrix adjust.
 Identities = 80/204 (39%), Positives = 108/204 (52%), Gaps = 13/204 (6%)

Query: 48  LLLWQAFAGPPPSLPKKGDLVVYFPQGHLEYSAPASVSKAPPTFDLKPEIICRVADVRYL 107
           L LW A AGP   LP+KG +VVY PQGHLE+   A  + A     + P + CRV DV  L
Sbjct: 37  LELWHACAGPVAPLPRKGGVVVYLPQGHLEHLGDAPAAAA-AAAAVPPHVFCRVVDVTLL 95

Query: 108 VSKKTDKVYTKMTLLPLPEMVGENFKGKELQDLVVDNKRDGEGSTANSTPPLFYKKLRAS 167
               TD+VY +++L+P  E V       E +D     +R          P +F K L AS
Sbjct: 96  ADAATDEVYAQLSLVPEKEEVARRADDGEGEDGDGMKQRFAR------MPHMFCKTLTAS 149

Query: 168 DQSKK-KIVIRAKDAENVFPFLAHLDYKKQI-NYSVIAKDVHGVAWKFNFV-DGKSRRHY 224
           D S      +  + AE+ FP    LDY +Q  +  ++AKD+H   W+F  +  G+ RRH 
Sbjct: 150 DTSTHGGFSVPRRAAEDCFP---PLDYSQQRPSQELVAKDLHSTEWRFRHIYRGQPRRHL 206

Query: 225 LTVGWKYFVRQKNLVPGDTVIFIR 248
           LT GW  FV +K LV GD V+F+R
Sbjct: 207 LTTGWSAFVNKKKLVSGDAVLFLR 230

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).

Oryza sativa subsp. japonica (taxid: 39947)

>sp|A2YG67|ARFQ_ORYSI Auxin response factor 17 OS=Oryza sativa subsp. indica GN=ARF17 PE=2 SV=1

 Score =  120 bits (301), Expect = 8e-27,   Method: Composition-based stats.
 Identities = 85/209 (40%), Positives = 112/209 (53%), Gaps = 23/209 (11%)

Query: 47  NLLLWQAFAGPPPSLPKKGDLVVYFPQGHLEYSAPAS----VSKAPPTFDLKPEIICRVA 102
           N  LW A AGP  SLP  G  VVYFPQGH E  A ++     S+ P   +L P++IC++ 
Sbjct: 28  NSELWHACAGPLVSLPAVGSRVVYFPQGHSEQVAASTNKEMESQIPNYPNLPPQLICQLH 87

Query: 103 DVRYLVSKKTDKVYTKMTLLPLPEMVGENFKGKELQDLVVDNKRDGEGSTANSTPP-LFY 161
           +V      +TD+VY +MTL PL          +EL+D  +      E  +AN  P   F 
Sbjct: 88  NVTMHADAETDEVYAQMTLQPLSP--------QELKDPYL----PAELGSANKQPTNYFC 135

Query: 162 KKLRASDQSKK-KIVIRAKDAENVFPFLAHLDYKKQ-INYSVIAKDVHGVAWKFNFV-DG 218
           K L ASD S      +  + AE VFP    LD+ +Q     +IAKD+HG  WKF  +  G
Sbjct: 136 KTLTASDTSTHGGFSVPRRAAEKVFP---PLDFTQQPPAQELIAKDLHGNEWKFRHIFRG 192

Query: 219 KSRRHYLTVGWKYFVRQKNLVPGDTVIFI 247
           + +RH LT GW  FV  K LV GD+V+FI
Sbjct: 193 QPKRHLLTTGWSVFVSAKRLVAGDSVLFI 221

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).

Oryza sativa subsp. indica (taxid: 39946)

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	251
224104665	713	predicted protein [Populus trichocarpa]	0.784	0.276	0.504	1e-47
255570833	810	Auxin response factor, putative [Ricinus	0.784	0.243	0.514	1e-47
147769056	744	hypothetical protein VITISV_000577 [Viti	0.776	0.262	0.514	3e-46
359479063	798	PREDICTED: auxin response factor 4-like	0.776	0.244	0.514	5e-46
356543436	793	PREDICTED: auxin response factor 4-like	0.944	0.298	0.426	6e-45
379323198	758	auxin response factor 4 [Brassica rapa s	0.776	0.257	0.504	3e-44
15239335	788	auxin response factor 4 [Arabidopsis tha	0.760	0.242	0.495	3e-44
259027688	808	putative ARF4 protein [Petunia x hybrida	0.776	0.241	0.485	1e-43
356544621	791	PREDICTED: auxin response factor 4-like	0.784	0.249	0.5	1e-43
449524944	802	PREDICTED: auxin response factor 4-like	0.788	0.246	0.475	5e-43

>gi|224104665|ref|XP_002313521.1| predicted protein [Populus trichocarpa] gi|222849929|gb|EEE87476.1| predicted protein [Populus trichocarpa]

 Score =  196 bits (497), Expect = 1e-47,   Method: Compositional matrix adjust.
 Identities = 104/206 (50%), Positives = 139/206 (67%), Gaps = 9/206 (4%)

Query: 48  LLLWQAFAGPPPSLPKKGDLVVYFPQGHLEYSAPAS--VSKAPPTFDLKPEIICRVADVR 105
           L LW A AGP  SLPKKG++VVYFPQGHLE  A +S    +  P FDL P+I C+V +V+
Sbjct: 40  LELWHACAGPLTSLPKKGNVVVYFPQGHLEQLASSSPFSHRDMPNFDLHPQIFCKVVNVQ 99

Query: 106 YLVSKKTDKVYTKMTLLPLPEMVGENFKGKELQDLVVDNKRDGEGSTANSTPPLFYKKLR 165
            L +++ D+VYT++TLLP PE+VG++ +GKELQ+L VD + D + S   STP +F K L 
Sbjct: 100 LLANRENDEVYTRLTLLPQPEVVGQDLEGKELQELGVDGEGD-DASPTKSTPHMFCKTLT 158

Query: 166 ASDQSKK-KIVIRAKDAENVFPFLAHLDYKKQI-NYSVIAKDVHGVAWKFNFV-DGKSRR 222
           ASD S      +  + AE+ FP    LDYK+Q  +  ++AKD+HGV W+F  +  G+ RR
Sbjct: 159 ASDTSTHGGFSVPRRAAEDCFP---SLDYKQQRPSQELLAKDLHGVEWRFRHIYRGQPRR 215

Query: 223 HYLTVGWKYFVRQKNLVPGDTVIFIR 248
           H LT GW  FV QKNLV GD V+F+R
Sbjct: 216 HLLTTGWSIFVSQKNLVSGDAVLFLR 241

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255570833|ref|XP_002526369.1| Auxin response factor, putative [Ricinus communis] gi|223534328|gb|EEF36040.1| Auxin response factor, putative [Ricinus communis]

 Score =  195 bits (496), Expect = 1e-47,   Method: Compositional matrix adjust.
 Identities = 106/206 (51%), Positives = 138/206 (66%), Gaps = 9/206 (4%)

Query: 48  LLLWQAFAGPPPSLPKKGDLVVYFPQGHLEYSAPAS--VSKAPPTFDLKPEIICRVADVR 105
           L LW A AGP  SLPKKG++VVYFPQGHLE  AP+S       PTFDL+P+I C+V +V+
Sbjct: 46  LELWHACAGPLTSLPKKGNVVVYFPQGHLEQVAPSSPFSPMEMPTFDLQPQIFCKVVNVQ 105

Query: 106 YLVSKKTDKVYTKMTLLPLPEMVGENFKGKELQDLVVDNKRDGEGSTANSTPPLFYKKLR 165
            L +K+ D+VYT++ LLP PE+VG N + KEL++L VD +  G G  A STP +F K L 
Sbjct: 106 LLANKENDEVYTQLALLPQPELVGPNLEVKELEELGVD-EEGGGGLPAKSTPHMFCKTLT 164

Query: 166 ASDQSKK-KIVIRAKDAENVFPFLAHLDYKKQI-NYSVIAKDVHGVAWKFNFV-DGKSRR 222
           ASD S      +  + AE+ FP    LDYK+Q  +  ++AKD+HGV W+F  +  G+ RR
Sbjct: 165 ASDTSTHGGFSVPRRAAEDCFP---PLDYKQQRPSQELVAKDLHGVEWRFRHIYRGQPRR 221

Query: 223 HYLTVGWKYFVRQKNLVPGDTVIFIR 248
           H LT GW  FV QKNLV GD V+F+R
Sbjct: 222 HLLTTGWSIFVSQKNLVSGDAVLFLR 247

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147769056|emb|CAN70219.1| hypothetical protein VITISV_000577 [Vitis vinifera]

 Score =  191 bits (484), Expect = 3e-46,   Method: Compositional matrix adjust.
 Identities = 107/208 (51%), Positives = 136/208 (65%), Gaps = 13/208 (6%)

Query: 48  LLLWQAFAGPPPSLPKKGDLVVYFPQGHLEYSAPASVSKAPP----TFDLKPEIICRVAD 103
           L LW   AG   SLPKKG++VVYFPQGHLE +A  S S  PP    TFDL P+I CRV +
Sbjct: 54  LELWHVCAGRLTSLPKKGNVVVYFPQGHLEQAA--SSSPFPPMDISTFDLPPQIFCRVVN 111

Query: 104 VRYLVSKKTDKVYTKMTLLPLPEMVGENFKGKELQDLVVDNKRDGEGSTANSTPPLFYKK 163
           V+ L +K+ D+VYT++TLLP PE+ G N +GKEL+ L VD +  G GS   STP +F K 
Sbjct: 112 VQLLANKENDEVYTQVTLLPQPELAGINLEGKELEGLGVD-EEGGGGSPTKSTPHMFCKT 170

Query: 164 LRASDQSKK-KIVIRAKDAENVFPFLAHLDYKKQI-NYSVIAKDVHGVAWKFNFV-DGKS 220
           L ASD S      +  + AE+ FP    LDYK+Q  +  ++AKD+HGV W+F  +  G+ 
Sbjct: 171 LTASDTSTHGGFSVPRRAAEDCFP---PLDYKQQRPSQELVAKDLHGVEWRFRHIYRGQP 227

Query: 221 RRHYLTVGWKYFVRQKNLVPGDTVIFIR 248
           RRH LT GW  FV QKNLV GD V+F+R
Sbjct: 228 RRHLLTTGWSIFVSQKNLVSGDAVLFLR 255

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359479063|ref|XP_002285019.2| PREDICTED: auxin response factor 4-like [Vitis vinifera] gi|297746231|emb|CBI16287.3| unnamed protein product [Vitis vinifera]

 Score =  190 bits (482), Expect = 5e-46,   Method: Compositional matrix adjust.
 Identities = 107/208 (51%), Positives = 136/208 (65%), Gaps = 13/208 (6%)

Query: 48  LLLWQAFAGPPPSLPKKGDLVVYFPQGHLEYSAPASVSKAPP----TFDLKPEIICRVAD 103
           L LW   AG   SLPKKG++VVYFPQGHLE +A  S S  PP    TFDL P+I CRV +
Sbjct: 54  LELWHVCAGRLTSLPKKGNVVVYFPQGHLEQAA--SSSPFPPMDISTFDLPPQIFCRVVN 111

Query: 104 VRYLVSKKTDKVYTKMTLLPLPEMVGENFKGKELQDLVVDNKRDGEGSTANSTPPLFYKK 163
           V+ L +K+ D+VYT++TLLP PE+ G N +GKEL+ L VD +  G GS   STP +F K 
Sbjct: 112 VQLLANKENDEVYTQVTLLPQPELAGINLEGKELEGLGVD-EEGGGGSPTKSTPHMFCKT 170

Query: 164 LRASDQSKK-KIVIRAKDAENVFPFLAHLDYKKQI-NYSVIAKDVHGVAWKFNFV-DGKS 220
           L ASD S      +  + AE+ FP    LDYK+Q  +  ++AKD+HGV W+F  +  G+ 
Sbjct: 171 LTASDTSTHGGFSVPRRAAEDCFP---PLDYKQQRPSQELVAKDLHGVEWRFRHIYRGQP 227

Query: 221 RRHYLTVGWKYFVRQKNLVPGDTVIFIR 248
           RRH LT GW  FV QKNLV GD V+F+R
Sbjct: 228 RRHLLTTGWSIFVSQKNLVSGDAVLFLR 255

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356543436|ref|XP_003540166.1| PREDICTED: auxin response factor 4-like [Glycine max]

 Score =  186 bits (473), Expect = 6e-45,   Method: Compositional matrix adjust.
 Identities = 108/253 (42%), Positives = 148/253 (58%), Gaps = 16/253 (6%)

Query: 8   ETETDDLNSTEISDEDDCEGEIETDDLIFTEISDKDDDYN-------LLLWQAFAGPPPS 60
           E + +D  ++E      C GE E    + +         +       + LW A AGP  S
Sbjct: 2   EIDLNDAVTSEAEKSASCNGECEKGAALSSPTCSSSGSSSTRVSSSYIELWHACAGPLTS 61

Query: 61  LPKKGDLVVYFPQGHLEYSAPAS--VSKAPPTFDLKPEIICRVADVRYLVSKKTDKVYTK 118
           LPKKG++VVYFPQGHLE +A  S       PT+DL+P+I CRV +++ L +K+ D+VYT+
Sbjct: 62  LPKKGNVVVYFPQGHLEQAASFSPFSPMEMPTYDLQPQIFCRVVNIQLLANKENDEVYTQ 121

Query: 119 MTLLPLPEMVGENFKGKELQDLVVDNKRDGEGSTANSTPPLFYKKLRASDQSKK-KIVIR 177
           +TLLP  E+ G   +GKEL+ L  D + + E +   STP +F K L ASD S      + 
Sbjct: 122 VTLLPQAELAGMYMEGKELEKLGADEEGN-ETTPTKSTPHMFCKTLTASDTSTHGGFSVP 180

Query: 178 AKDAENVFPFLAHLDYKKQI-NYSVIAKDVHGVAWKFNFV-DGKSRRHYLTVGWKYFVRQ 235
            + AE+ FP    LDYKKQ  +  ++AKD+HGV WKF  +  G+ RRH LT GW  FV Q
Sbjct: 181 RRAAEDCFP---PLDYKKQRPSQELVAKDLHGVEWKFRHIYRGQPRRHLLTTGWSIFVSQ 237

Query: 236 KNLVPGDTVIFIR 248
           KNLV GD V+F+R
Sbjct: 238 KNLVSGDAVLFLR 250

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|379323198|gb|AFD01298.1| auxin response factor 4 [Brassica rapa subsp. pekinensis]

 Score =  184 bits (467), Expect = 3e-44,   Method: Compositional matrix adjust.
 Identities = 103/204 (50%), Positives = 134/204 (65%), Gaps = 9/204 (4%)

Query: 50  LWQAFAGPPPSLPKKGDLVVYFPQGHLEYSAPASVSKAP--PTFDLKPEIICRVADVRYL 107
           LW A AGP  SLPKKG++VVYFPQGHLE  A  S S     P  DL P+I CRVA+V  L
Sbjct: 54  LWHACAGPLTSLPKKGNVVVYFPQGHLEQGAMVSYSSPLDIPKLDLSPQIFCRVANVHLL 113

Query: 108 VSKKTDKVYTKMTLLPLPEMVGENFKGKELQDLVVDNKRDGEGSTANSTPPLFYKKLRAS 167
            +K+TD+VYT++TLLPL E+   N +GKE+++L  D +++G  S+   TP +F K L AS
Sbjct: 114 ANKETDEVYTQVTLLPLQELSVLNGEGKEVRELGGDEEKNGS-SSVKKTPHMFCKTLTAS 172

Query: 168 DQSKK-KIVIRAKDAENVFPFLAHLDYKKQI-NYSVIAKDVHGVAWKFNFV-DGKSRRHY 224
           D S      +  + AE+ F   A LDYK+Q  +  +IAKD+HGV WKF  +  G+ RRH 
Sbjct: 173 DTSTHGGFSVPRRAAEDCF---APLDYKQQRPSQELIAKDLHGVEWKFRHIYRGQPRRHL 229

Query: 225 LTVGWKYFVRQKNLVPGDTVIFIR 248
           LT GW  FV QK+LV GD V+F+R
Sbjct: 230 LTTGWSIFVSQKSLVSGDAVLFLR 253

Source: Brassica rapa subsp. pekinensis

Species: Brassica rapa

Genus: Brassica

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|15239335|ref|NP_200853.1| auxin response factor 4 [Arabidopsis thaliana] gi|46396060|sp|Q9ZTX9.1|ARFD_ARATH RecName: Full=Auxin response factor 4 gi|12744969|gb|AAK06864.1|AF344313_1 auxin response factor 4 [Arabidopsis thaliana] gi|4102598|gb|AAD01512.1| auxin response factor 4 [Arabidopsis thaliana] gi|9757747|dbj|BAB08228.1| auxin response factor 4 [Arabidopsis thaliana] gi|19424051|gb|AAL87308.1| auxin response factor ARF4 [Arabidopsis thaliana] gi|21280887|gb|AAM45025.1| auxin response factor ARF4 [Arabidopsis thaliana] gi|332009949|gb|AED97332.1| auxin response factor 4 [Arabidopsis thaliana]

 Score =  184 bits (466), Expect = 3e-44,   Method: Compositional matrix adjust.
 Identities = 103/208 (49%), Positives = 135/208 (64%), Gaps = 17/208 (8%)

Query: 50  LWQAFAGPPPSLPKKGDLVVYFPQGHLE------YSAPASVSKAPPTFDLKPEIICRVAD 103
           LW A AGP   LPKKG++VVYFPQGHLE      YS+P  +    P FDL P+I+CRV +
Sbjct: 66  LWHACAGPLTCLPKKGNVVVYFPQGHLEQDAMVSYSSPLEI----PKFDLNPQIVCRVVN 121

Query: 104 VRYLVSKKTDKVYTKMTLLPLPEMVGENFKGKELQDLVVDNKRDGEGSTANSTPPLFYKK 163
           V+ L +K TD+VYT++TLLPL E    N +GKE+++L  + +R+G  S+   TP +F K 
Sbjct: 122 VQLLANKDTDEVYTQVTLLPLQEFSMLNGEGKEVKELGGEEERNGS-SSVKRTPHMFCKT 180

Query: 164 LRASDQSKK-KIVIRAKDAENVFPFLAHLDYKKQI-NYSVIAKDVHGVAWKFNFV-DGKS 220
           L ASD S      +  + AE+ F   A LDYK+Q  +  +IAKD+HGV WKF  +  G+ 
Sbjct: 181 LTASDTSTHGGFSVPRRAAEDCF---APLDYKQQRPSQELIAKDLHGVEWKFRHIYRGQP 237

Query: 221 RRHYLTVGWKYFVRQKNLVPGDTVIFIR 248
           RRH LT GW  FV QKNLV GD V+F+R
Sbjct: 238 RRHLLTTGWSIFVSQKNLVSGDAVLFLR 265

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|259027688|gb|ACV91105.1| putative ARF4 protein [Petunia x hybrida]

 Score =  182 bits (462), Expect = 1e-43,   Method: Compositional matrix adjust.
 Identities = 100/206 (48%), Positives = 133/206 (64%), Gaps = 11/206 (5%)

Query: 50  LWQAFAGPPPSLPKKGDLVVYFPQGHLEYSAPAS----VSKAPPTFDLKPEIICRVADVR 105
           LW A AGP   LPKKG++VVYFPQGH+E +A +S    +    PTF L P+I CRV DV+
Sbjct: 62  LWYACAGPLTCLPKKGNVVVYFPQGHMEEAASSSPFSPMKMDLPTFGLHPQIFCRVDDVQ 121

Query: 106 YLVSKKTDKVYTKMTLLPLPEMVGENFKGKELQDLVVDNKRDGEGSTANSTPPLFYKKLR 165
            L +K+ D+VYT+++LLPLPE V  + +GKE +D  +D +R+G  +   S   +F K L 
Sbjct: 122 LLANKENDEVYTQLSLLPLPESVAISLEGKEHEDFGIDEERNGV-NPGKSASHMFCKTLT 180

Query: 166 ASDQSKK-KIVIRAKDAENVFPFLAHLDYKKQI-NYSVIAKDVHGVAWKFNFV-DGKSRR 222
           ASD S      +  + AE+ FP    LDYK+Q  +  +IAKD+HGV WKF  +  G+ RR
Sbjct: 181 ASDTSTHGGFSVPRRAAEDCFP---PLDYKEQRPSQELIAKDLHGVEWKFRHIYRGQPRR 237

Query: 223 HYLTVGWKYFVRQKNLVPGDTVIFIR 248
           H LT GW  FV QKNLV GD V+F+R
Sbjct: 238 HLLTTGWSIFVSQKNLVSGDAVLFLR 263

Source: Petunia x hybrida

Species: Petunia x hybrida

Genus: Petunia

Family: Solanaceae

Order: Solanales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356544621|ref|XP_003540747.1| PREDICTED: auxin response factor 4-like [Glycine max]

 Score =  182 bits (462), Expect = 1e-43,   Method: Compositional matrix adjust.
 Identities = 103/206 (50%), Positives = 133/206 (64%), Gaps = 9/206 (4%)

Query: 48  LLLWQAFAGPPPSLPKKGDLVVYFPQGHLEYSAPAS--VSKAPPTFDLKPEIICRVADVR 105
           L LW A AGP  SL KKG++VVYFPQGHLE  A  S       PT+DL+P+I CRV +V+
Sbjct: 53  LELWHACAGPLTSLLKKGNVVVYFPQGHLEQVASFSPFTPLEIPTYDLQPQIFCRVVNVQ 112

Query: 106 YLVSKKTDKVYTKMTLLPLPEMVGENFKGKELQDLVVDNKRDGEGSTANSTPPLFYKKLR 165
            L +K+ D+VYT++TLLP PE+ G   +GKEL++L  +   D E S   STP +F K L 
Sbjct: 113 LLANKENDEVYTQVTLLPQPELEGMYSEGKELEELGAEEDGD-ERSPTKSTPHMFCKTLT 171

Query: 166 ASDQSKK-KIVIRAKDAENVFPFLAHLDYKKQI-NYSVIAKDVHGVAWKFNFV-DGKSRR 222
           ASD S      +  + AE+ FP    LDYK+Q  +  ++AKD+HGV WKF  +  G+ RR
Sbjct: 172 ASDTSTHGGFSVPRRAAEDCFP---PLDYKQQRPSQELVAKDLHGVEWKFRHIYRGQPRR 228

Query: 223 HYLTVGWKYFVRQKNLVPGDTVIFIR 248
           H LT GW  FV QKNLV GD V+F+R
Sbjct: 229 HLLTTGWSIFVSQKNLVSGDAVLFLR 254

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449524944|ref|XP_004169481.1| PREDICTED: auxin response factor 4-like isoform 1 [Cucumis sativus]

 Score =  180 bits (456), Expect = 5e-43,   Method: Compositional matrix adjust.
 Identities = 99/208 (47%), Positives = 130/208 (62%), Gaps = 10/208 (4%)

Query: 48  LLLWQAFAGPPPSLPKKGDLVVYFPQGHLEYSAPAS--VSKAPPTFDLKPEIICRVADVR 105
           L LW A AGP  SLPKKG++VVYFPQGHLE  A AS        TFDL+P I+CRV +V 
Sbjct: 53  LELWHACAGPLTSLPKKGNVVVYFPQGHLEQIASASPFSPMEMRTFDLQPHILCRVINVH 112

Query: 106 YLVSKKTDKVYTKMTLLPLPEMVGENFKGKELQDLVVDNKRDGEGST--ANSTPPLFYKK 163
            L +K+ D+VYT++TL PLPE++G    GKEL++L ++             STP +F K 
Sbjct: 113 LLANKENDEVYTQLTLRPLPELLGTGVAGKELEELALNGADGDGSGGSPTRSTPHMFCKT 172

Query: 164 LRASDQSKK-KIVIRAKDAENVFPFLAHLDYKK-QINYSVIAKDVHGVAWKFNFV-DGKS 220
           L ASD S      +  + AE+ FP    LDY + + +  +IAKD+HGV W+F  +  G+ 
Sbjct: 173 LTASDTSTHGGFSVPRRAAEDCFP---PLDYTQLRPSQELIAKDLHGVEWRFRHIYRGQP 229

Query: 221 RRHYLTVGWKYFVRQKNLVPGDTVIFIR 248
           RRH LT GW  FV QKNL+ GD V+F+R
Sbjct: 230 RRHLLTTGWSIFVSQKNLISGDAVLFLR 257

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	251
TAIR|locus:2175098	788	ARF4 "auxin response factor 4"	0.772	0.246	0.507	1.1e-43
TAIR|locus:2057609	608	ETT "ETTIN" [Arabidopsis thali	0.756	0.312	0.417	2.4e-31
TAIR|locus:2057517	693	ARF10 "auxin response factor 1	0.745	0.269	0.380	5.2e-27
TAIR|locus:2152642	811	ARF8 "auxin response factor 8"	0.745	0.230	0.409	3.3e-26
TAIR|locus:2126460	670	ARF16 "auxin response factor 1	0.737	0.276	0.364	1.5e-24
TAIR|locus:2039124	622	ARF11 "auxin response factor 1	0.772	0.311	0.353	8.9e-24
TAIR|locus:2204237	935	ARF6 "auxin response factor 6"	0.776	0.208	0.376	9.8e-24
TAIR|locus:2202205	1086	ARF19 "auxin response factor 1	0.741	0.171	0.371	3.3e-23
TAIR|locus:2025991	665	ARF1 "auxin response factor 1"	0.733	0.276	0.356	1.6e-22
TAIR|locus:2138096	638	ARF9 "auxin response factor 9"	0.737	0.289	0.349	1.9e-22

TAIR|locus:2175098 ARF4 "auxin response factor 4" [Arabidopsis thaliana (taxid:3702)]

 Score = 467 (169.5 bits), Expect = 1.1e-43, P = 1.1e-43
 Identities = 104/205 (50%), Positives = 135/205 (65%)

Query:    50 LWQAFAGPPPSLPKKGDLVVYFPQGHLEYSAPASVSKAP---PTFDLKPEIICRVADVRY 106
             LW A AGP   LPKKG++VVYFPQGHLE  A  S S +P   P FDL P+I+CRV +V+ 
Sbjct:    66 LWHACAGPLTCLPKKGNVVVYFPQGHLEQDAMVSYS-SPLEIPKFDLNPQIVCRVVNVQL 124

Query:   107 LVSKKTDKVYTKMTLLPLPEMVGENFKGKELQDLVVDNKRDGEGSTANSTPPLFYKKLRA 166
             L +K TD+VYT++TLLPL E    N +GKE+++L  + +R+G  S+   TP +F K L A
Sbjct:   125 LANKDTDEVYTQVTLLPLQEFSMLNGEGKEVKELGGEEERNGS-SSVKRTPHMFCKTLTA 183

Query:   167 SDQSKKK-IVIRAKDAENVFPFLAHLDYKKQI-NYSVIAKDVHGVAWKFNFV-DGKSRRH 223
             SD S      +  + AE+ F   A LDYK+Q  +  +IAKD+HGV WKF  +  G+ RRH
Sbjct:   184 SDTSTHGGFSVPRRAAEDCF---APLDYKQQRPSQELIAKDLHGVEWKFRHIYRGQPRRH 240

Query:   224 YLTVGWKYFVRQKNLVPGDTVIFIR 248
              LT GW  FV QKNLV GD V+F+R
Sbjct:   241 LLTTGWSIFVSQKNLVSGDAVLFLR 265

GO:0005634 "nucleus" evidence=ISM;IEA

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

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

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

GO:0010158 "abaxial cell fate specification" evidence=IGI

GO:0010050 "vegetative phase change" evidence=IGI

GO:0005515 "protein binding" evidence=IPI

TAIR|locus:2057609 ETT "ETTIN" [Arabidopsis thaliana (taxid:3702)]

 Score = 350 (128.3 bits), Expect = 2.4e-31, P = 2.4e-31
 Identities = 86/206 (41%), Positives = 122/206 (59%)

Query:    48 LLLWQAFAGPPPSLPKKGDLVVYFPQGHLEYSAPASVSKAPPTFDLKPEIICRVADVRYL 107
             L LW A AGP  SLPK+G LV+YFPQGHLE  AP   S A   + L P + CR+ DV+  
Sbjct:    53 LELWHACAGPLISLPKRGSLVLYFPQGHLE-QAP-DFSAA--IYGLPPHVFCRILDVKLH 108

Query:   108 VSKKTDKVYTKMTLLPLPEMVGENFKGKELQDLV-VDN-KRDGEGSTANSTPPLFYKKLR 165
                 TD+VY +++LLP  E   E+ + K  + ++ VD  + D E    ++TP +F K L 
Sbjct:   109 AETTTDEVYAQVSLLP--E--SEDIERKVREGIIDVDGGEEDYEVLKRSNTPHMFCKTLT 164

Query:   166 ASDQSKKK-IVIRAKDAENVFPFLAHLDYKK-QINYSVIAKDVHGVAWKFNFV-DGKSRR 222
             ASD S      +  + AE+ FP    LDY + + +  ++A+D+HG+ W+F  +  G+ RR
Sbjct:   165 ASDTSTHGGFSVPRRAAEDCFP---PLDYSQPRPSQELLARDLHGLEWRFRHIYRGQPRR 221

Query:   223 HYLTVGWKYFVRQKNLVPGDTVIFIR 248
             H LT GW  FV +K LV GD V+F+R
Sbjct:   222 HLLTTGWSAFVNKKKLVSGDAVLFLR 247

GO:0003677 "DNA binding" evidence=IEA;ISS

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;TAS

GO:0009850 "auxin metabolic process" evidence=TAS

GO:0010158 "abaxial cell fate specification" evidence=IGI

GO:0010050 "vegetative phase change" evidence=IGI;RCA;IMP

GO:0007389 "pattern specification process" evidence=RCA

GO:0009616 "virus induced gene silencing" evidence=RCA

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

GO:0009887 "organ morphogenesis" evidence=RCA

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

GO:0048438 "floral whorl development" evidence=RCA

GO:0048439 "flower morphogenesis" evidence=RCA

GO:0048519 "negative regulation of biological process" evidence=RCA

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

TAIR|locus:2057517 ARF10 "auxin response factor 10" [Arabidopsis thaliana (taxid:3702)]

 Score = 312 (114.9 bits), Expect = 5.2e-27, P = 5.2e-27
 Identities = 78/205 (38%), Positives = 106/205 (51%)

Query:    50 LWQAFAGPPPSLPKKGDLVVYFPQGHLEYSAPASVSKAPPTFD---LKPEIICRVADVRY 106
             LW A AG    +P     V YF QGH E++       APP F    + P I+CRV  V++
Sbjct:    11 LWHACAGSMVQIPSLNSTVFYFAQGHTEHA------HAPPDFHAPRVPPLILCRVVSVKF 64

Query:   107 LVSKKTDKVYTKMTLLPLPEMVGENFKGKELQDLVVDNKRDGEGSTANSTPPLFYKKLRA 166
             L   +TD+V+ K+TLLPLP     + +   +  L   +  DG G+     P  F K L  
Sbjct:    65 LADAETDEVFAKITLLPLPGN-DLDLENDAVLGLTPPSS-DGNGN-GKEKPASFAKTLTQ 121

Query:   167 SDQSKKK-IVIRAKDAENVFPFLAHLDYKKQINY-SVIAKDVHGVAWKFNFV-DGKSRRH 223
             SD +      +    AE +FP    LDY  +    +VIAKD+HG  WKF  +  G  RRH
Sbjct:   122 SDANNGGGFSVPRYCAETIFP---RLDYSAEPPVQTVIAKDIHGETWKFRHIYRGTPRRH 178

Query:   224 YLTVGWKYFVRQKNLVPGDTVIFIR 248
              LT GW  FV QK L+ GD+++F+R
Sbjct:   179 LLTTGWSTFVNQKKLIAGDSIVFLR 203

GO:0003677 "DNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISM;IEA

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

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

GO:0035198 "miRNA binding" evidence=ISS

GO:0007389 "pattern specification process" evidence=IDA

GO:0048829 "root cap development" evidence=IGI;IMP

GO:0051301 "cell division" evidence=IGI

GO:0009734 "auxin mediated signaling pathway" evidence=IMP

GO:0009738 "abscisic acid mediated signaling pathway" evidence=IMP

GO:0009743 "response to carbohydrate stimulus" evidence=IMP

GO:0010154 "fruit development" evidence=IMP

GO:0031540 "regulation of anthocyanin biosynthetic process" evidence=IMP

GO:0048366 "leaf development" evidence=IMP

GO:0048441 "petal development" evidence=IMP

GO:0048442 "sepal development" evidence=IMP

GO:0048589 "developmental growth" evidence=IMP

TAIR|locus:2152642 ARF8 "auxin response factor 8" [Arabidopsis thaliana (taxid:3702)]

 Score = 306 (112.8 bits), Expect = 3.3e-26, P = 3.3e-26
 Identities = 86/210 (40%), Positives = 107/210 (50%)

Query:    47 NLLLWQAFAGPPPSLPKKGDLVVYFPQGHLEYSAPASVSKAP---PTF-DLKPEIICRVA 102
             N  LW A AGP  SLP  G  VVYFPQGH E  A  +  +     P +  L P++IC++ 
Sbjct:    20 NSELWHACAGPLVSLPSSGSRVVYFPQGHSEQVAATTNKEVDGHIPNYPSLPPQLICQLH 79

Query:   103 DVRYLVSKKTDKVYTKMTLLPL-PEMVGENFKGKELQDLVVDNKRDGEGSTANSTPPLFY 161
             +V      +TD+VY +MTL PL PE   E F   EL            G  +      F 
Sbjct:    80 NVTMHADVETDEVYAQMTLQPLTPEEQKETFVPIEL------------GIPSKQPSNYFC 127

Query:   162 KKLRASDQSKKK-IVIRAKDAENVFPFLAHLDYKKQIN-YSVIAKDVHGVAWKFNFV-DG 218
             K L ASD S      +  + AE VFP    LDY  Q     +IA+D+H V WKF  +  G
Sbjct:   128 KTLTASDTSTHGGFSVPRRAAEKVFP---PLDYTLQPPAQELIARDLHDVEWKFRHIFRG 184

Query:   219 KSRRHYLTVGWKYFVRQKNLVPGDTVIFIR 248
             + +RH LT GW  FV  K LV GD+VIFIR
Sbjct:   185 QPKRHLLTTGWSVFVSAKRLVAGDSVIFIR 214

GO:0003677 "DNA binding" evidence=IEA

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:0046983 "protein dimerization activity" evidence=IEA

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

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

GO:0009908 "flower development" evidence=IGI

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

GO:0009886 "post-embryonic morphogenesis" evidence=RCA

GO:0009887 "organ morphogenesis" evidence=RCA

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

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

GO:0048439 "flower morphogenesis" evidence=RCA

GO:0048481 "ovule development" evidence=RCA

GO:0048507 "meristem development" evidence=RCA

GO:0048519 "negative regulation of biological process" evidence=RCA

TAIR|locus:2126460 ARF16 "auxin response factor 16" [Arabidopsis thaliana (taxid:3702)]

 Score = 289 (106.8 bits), Expect = 1.5e-24, P = 1.5e-24
 Identities = 74/203 (36%), Positives = 102/203 (50%)

Query:    50 LWQAFAGPPPSLPKKGDLVVYFPQGHLEYSAPASVSKAPPTFDLKPEIICRVADVRYLVS 109
             LW A AG    +P     V YFPQGH E +A   V        + P ++CRV  ++Y+  
Sbjct:    20 LWHACAGGMVRMPPMNSKVFYFPQGHAE-NAYDCVDFG--NLPIPPMVLCRVLAIKYMAD 76

Query:   110 KKTDKVYTKMTLLPLPEMVGENFKGKELQDLVVDNKRDGEGSTANSTP-PLFYKKLRASD 168
              ++D+V+ K+ L+PL        K  E  D    +  D  G  +NS   P F K L  SD
Sbjct:    77 AESDEVFAKLRLIPL--------KDDEYVDHEYGDGEDSNGFESNSEKTPSFAKTLTQSD 128

Query:   169 QSKKK-IVIRAKDAENVFPFLAHLDYKKQINY-SVIAKDVHGVAWKFNFV-DGKSRRHYL 225
              +      +    AE +FP    LDY  +    +++AKDVHG  WKF  +  G  RRH L
Sbjct:   129 ANNGGGFSVPRYCAETIFP---RLDYNAEPPVQTILAKDVHGDVWKFRHIYRGTPRRHLL 185

Query:   226 TVGWKYFVRQKNLVPGDTVIFIR 248
             T GW  FV QK LV GD+++F+R
Sbjct:   186 TTGWSNFVNQKKLVAGDSIVFMR 208

GO:0003677 "DNA binding" evidence=IEA

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

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

GO:0035198 "miRNA binding" evidence=ISS

GO:0007389 "pattern specification process" evidence=IDA

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

GO:0048829 "root cap development" evidence=IGI;IMP

GO:0051301 "cell division" evidence=IGI

TAIR|locus:2039124 ARF11 "auxin response factor 11" [Arabidopsis thaliana (taxid:3702)]

 Score = 281 (104.0 bits), Expect = 8.9e-24, P = 8.9e-24
 Identities = 77/218 (35%), Positives = 109/218 (50%)

Query:    39 ISDKDDDYNLLLWQAFAGPPPSLPKKGDLVVYFPQGHLEYSAPAS----VSKAPPTFDLK 94
             +   DD+    LW+A AGP   +P+ G+ V YFPQGH+E    ++    V +  P F+L 
Sbjct:    32 LGSNDDELYTELWKACAGPLVEVPRYGERVFYFPQGHMEQLVASTNQGVVDQEIPVFNLP 91

Query:    95 PEIICRVADVRYLVSKKTDKVYTKMTLLPLPEMVGENFKGKELQDLVVDNKRDGEGSTAN 154
             P+I+CRV  V      +TD+VY ++TL P  E   +  +   L   +V+         A 
Sbjct:    92 PKILCRVLSVTLKAEHETDEVYAQITLQP-EE---DQSEPTSLDPPLVE--------PAK 139

Query:   155 STPPLFYKKLRASDQSKKK--IVIRAKDAENVFPFLAHLDYKKQI-NYSVIAKDVHGVAW 211
              T   F K L ASD S      V+R K A    P    LD  +      ++A+D+HG  W
Sbjct:   140 PTVDSFVKILTASDTSTHGGFSVLR-KHATECLP---SLDMTQPTPTQELVARDLHGYEW 195

Query:   212 KFNFV-DGKSRRHYLTVGWKYFVRQKNLVPGDTVIFIR 248
             +F  +  G+ RRH LT GW  FV  K LV GD  +F+R
Sbjct:   196 RFKHIFRGQPRRHLLTTGWSTFVTSKRLVAGDAFVFLR 233

GO:0003677 "DNA binding" evidence=IEA

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

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:0009506 "plasmodesma" evidence=IDA

TAIR|locus:2204237 ARF6 "auxin response factor 6" [Arabidopsis thaliana (taxid:3702)]

 Score = 284 (105.0 bits), Expect = 9.8e-24, P = 9.8e-24
 Identities = 82/218 (37%), Positives = 112/218 (51%)

Query:    38 EISDKDDDYNLLLWQAFAGPPPSLPKKGDLVVYFPQGHLEYSAPASVSKAP----PTF-D 92
             E++ +    N  LW A AGP  SLP  G  VVYFPQGH E  A AS +K      P +  
Sbjct:    14 EVTGEKRVLNSELWHACAGPLVSLPPVGSRVVYFPQGHSEQVA-ASTNKEVDAHIPNYPS 72

Query:    93 LKPEIICRVADVRYLVSKKTDKVYTKMTLLPLPEMVGENFKGKELQDLVVDNKRDGEGST 152
             L P++IC++ +V      +TD+VY +MTL PL          +E +D  +  +    G  
Sbjct:    73 LHPQLICQLHNVTMHADVETDEVYAQMTLQPL--------NAQEQKDPYLPAEL---GVP 121

Query:   153 ANSTPPLFYKKLRASDQSKKK-IVIRAKDAENVFPFLAHLDYKKQIN-YSVIAKDVHGVA 210
             +      F K L ASD S      +  + AE VFP    LDY +Q     ++A+D+H   
Sbjct:   122 SRQPTNYFCKTLTASDTSTHGGFSVPRRAAEKVFP---PLDYSQQPPAQELMARDLHDNE 178

Query:   211 WKFNFV-DGKSRRHYLTVGWKYFVRQKNLVPGDTVIFI 247
             WKF  +  G+ +RH LT GW  FV  K LV GD+V+FI
Sbjct:   179 WKFRHIFRGQPKRHLLTTGWSVFVSAKRLVAGDSVLFI 216

GO:0005634 "nucleus" evidence=ISM;IDA

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

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

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

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

GO:0009908 "flower development" evidence=IGI

GO:0005515 "protein binding" evidence=IPI

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

GO:0009886 "post-embryonic morphogenesis" evidence=RCA

GO:0009887 "organ morphogenesis" evidence=RCA

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

GO:0010014 "meristem initiation" evidence=RCA

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

GO:0010073 "meristem maintenance" evidence=RCA

GO:0048439 "flower morphogenesis" evidence=RCA

GO:0048481 "ovule development" evidence=RCA

GO:0048507 "meristem development" evidence=RCA

GO:0048519 "negative regulation of biological process" evidence=RCA

TAIR|locus:2202205 ARF19 "auxin response factor 19" [Arabidopsis thaliana (taxid:3702)]

 Score = 280 (103.6 bits), Expect = 3.3e-23, P = 3.3e-23
 Identities = 78/210 (37%), Positives = 105/210 (50%)

Query:    47 NLLLWQAFAGPPPSLPKKGDLVVYFPQGHLEYSAPASVSKAP---PTF-DLKPEIICRVA 102
             N  LW A AGP  SLP  G LVVYFPQGH E  A AS+ K     P + +L  ++IC + 
Sbjct:    21 NSQLWHACAGPLVSLPPVGSLVVYFPQGHSEQVA-ASMQKQTDFIPNYPNLPSKLICLLH 79

Query:   103 DVRYLVSKKTDKVYTKMTLLPLPEMVGENFKGKELQDLVVDNKRDGEGSTANSTPPLFY- 161
              V      +TD+VY +MTL P+ +   E     ++            G   N  P  F+ 
Sbjct:    80 SVTLHADTETDEVYAQMTLQPVNKYDREALLASDM------------GLKLNRQPTEFFC 127

Query:   162 KKLRASDQSKKK-IVIRAKDAENVFPFLAHLDYKKQIN-YSVIAKDVHGVAWKFNFV-DG 218
             K L ASD S      +  + AE +FP    LD+  Q     ++AKD+H   W F  +  G
Sbjct:   128 KTLTASDTSTHGGFSVPRRAAEKIFP---PLDFSMQPPAQEIVAKDLHDTTWTFRHIYRG 184

Query:   219 KSRRHYLTVGWKYFVRQKNLVPGDTVIFIR 248
             + +RH LT GW  FV  K L  GD+V+F+R
Sbjct:   185 QPKRHLLTTGWSVFVSTKRLFAGDSVLFVR 214

GO:0005634 "nucleus" evidence=ISM;IEA;IDA;TAS

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

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

GO:0009733 "response to auxin stimulus" evidence=RCA;IMP;NAS

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

GO:0048366 "leaf development" evidence=IGI

GO:0048527 "lateral root development" evidence=IGI;RCA

GO:0009723 "response to ethylene stimulus" evidence=IMP

GO:0003677 "DNA binding" evidence=IDA

GO:0010311 "lateral root formation" evidence=IGI

GO:0007155 "cell adhesion" evidence=RCA

GO:0009741 "response to brassinosteroid stimulus" evidence=RCA

GO:0010090 "trichome morphogenesis" evidence=RCA

GO:0010583 "response to cyclopentenone" evidence=RCA

GO:0045010 "actin nucleation" evidence=RCA

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

GO:0071555 "cell wall organization" evidence=RCA

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

GO:0046983 "protein dimerization activity" evidence=IDA

TAIR|locus:2025991 ARF1 "auxin response factor 1" [Arabidopsis thaliana (taxid:3702)]

 Score = 270 (100.1 bits), Expect = 1.6e-22, P = 1.6e-22
 Identities = 73/205 (35%), Positives = 109/205 (53%)

Query:    50 LWQAFAGPPPSLPKKGDLVVYFPQGH---LEYSAPASVSKAPPTFDLKPEIICRVADVRY 106
             LW A AGP  +LP++G+ V YFP+GH   LE S    + +  P+F+L  +I+C+V +++ 
Sbjct:    23 LWHACAGPLVTLPREGERVYYFPEGHMEQLEASMHQGLEQQMPSFNLPSKILCKVINIQR 82

Query:   107 LVSKKTDKVYTKMTLLPLPEMVGENFKGKELQDLVVDNKRDGEGSTANSTPPLFYKKLRA 166
                 +TD+VY ++TLLP  E+   +       D  V   ++ E  T +S    F K L A
Sbjct:    83 RAEPETDEVYAQITLLP--EL---DQSEPTSPDAPV---QEPEKCTVHS----FCKTLTA 130

Query:   167 SDQSKKK-IVIRAKDAENVFPFLAHLDYKKQINYS-VIAKDVHGVAWKFNFV-DGKSRRH 223
             SD S      +  + A++  P    LD  +Q  +  ++A D+H   W F  +  G+ RRH
Sbjct:   131 SDTSTHGGFSVLRRHADDCLP---PLDMSQQPPWQELVATDLHNSEWHFRHIFRGQPRRH 187

Query:   224 YLTVGWKYFVRQKNLVPGDTVIFIR 248
              LT GW  FV  K LV GD  IF+R
Sbjct:   188 LLTTGWSVFVSSKKLVAGDAFIFLR 212

GO:0003677 "DNA binding" evidence=IEA;IDA;IPI

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

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

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;TAS

GO:0010150 "leaf senescence" evidence=IGI

GO:0045892 "negative regulation of transcription, DNA-dependent" evidence=IEP

GO:0005515 "protein binding" evidence=IPI

GO:0006306 "DNA methylation" evidence=RCA

GO:0006342 "chromatin silencing" evidence=RCA

GO:0006346 "methylation-dependent chromatin silencing" evidence=RCA

GO:0007267 "cell-cell signaling" evidence=RCA

GO:0009616 "virus induced gene silencing" evidence=RCA

GO:0010267 "production of ta-siRNAs involved in RNA interference" evidence=RCA

GO:0016246 "RNA interference" evidence=RCA

GO:0035196 "production of miRNAs involved in gene silencing by miRNA" evidence=RCA

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

TAIR|locus:2138096 ARF9 "auxin response factor 9" [Arabidopsis thaliana (taxid:3702)]

 Score = 269 (99.8 bits), Expect = 1.9e-22, P = 1.9e-22
 Identities = 72/206 (34%), Positives = 101/206 (49%)

Query:    50 LWQAFAGPPPSLPKKGDLVVYFPQGHLEY----SAPASVSKAPPTFDLKPEIICRVADVR 105
             LW+  AGP   +P+  + V YFPQGH+E     +    ++   P F L P+I+C V +V 
Sbjct:    13 LWKLCAGPLVDVPQAQERVYYFPQGHMEQLEASTQQVDLNTMKPLFVLPPKILCNVMNVS 72

Query:   106 YLVSKKTDKVYTKMTLLPLPEMVGENFKGKELQDLVVDNKRDGEGSTANSTPPLFYKKLR 165
                 K TD+VY ++TL+P+         G E+ + +  +    E          F K L 
Sbjct:    73 LQAEKDTDEVYAQITLIPV---------GTEVDEPMSPDPSPPE--LQRPKVHSFSKVLT 121

Query:   166 ASDQSKKK-IVIRAKDAENVFPFLAHLDYKKQI-NYSVIAKDVHGVAWKFNFV-DGKSRR 222
             ASD S      +  K A    P    LD  +Q     ++A+DVHG  WKF  +  G+ RR
Sbjct:   122 ASDTSTHGGFSVLRKHATECLP---PLDMTQQTPTQELVAEDVHGYQWKFKHIFRGQPRR 178

Query:   223 HYLTVGWKYFVRQKNLVPGDTVIFIR 248
             H LT GW  FV  K LV GDT +F+R
Sbjct:   179 HLLTTGWSTFVTSKRLVAGDTFVFLR 204

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

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

No confident hit for EC number transfering in SWISSPROT detected by BLAST

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input: fgenesh4_pg.C_LG_IX001438 hypothetical protein (713 aa) (Populus trichocarpa)

Predicted Functional Partners:

Sorry, there are no predicted associations at the current settings.

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	251
cd10017	98	cd10017, B3_DNA, Plant-specific B3-DNA binding dom	1e-12
pfam02362	97	pfam02362, B3, B3 DNA binding domain	1e-11
smart01019	96	smart01019, B3, B3 DNA binding domain	3e-10

>gnl|CDD|197383 cd10017, B3_DNA, Plant-specific B3-DNA binding domain

 Score = 62.0 bits (151), Expect = 1e-12
 Identities = 29/91 (31%), Positives = 39/91 (42%), Gaps = 10/91 (10%)

Query: 158 PLFYKKLRASDQ-SKKKIVIRAKDAENVFPFLAHLDYKKQINYSVIAKDVHGVAWKFNF- 215
           PLF+K L  SD  S  ++V+  K A+   P         +    V  +D  G  W     
Sbjct: 1   PLFFKVLTPSDVSSLGRLVLPKKFAKAHLPP--------KEGVEVTLEDPDGKKWTVKLK 52

Query: 216 VDGKSRRHYLTVGWKYFVRQKNLVPGDTVIF 246
               S R  L+ GWK FVR   L  GD ++F
Sbjct: 53  KRKNSGRMVLSGGWKEFVRANGLKEGDFLVF 83

The plant-specific B3 DNA binding domain superfamily includes the well-characterized auxin response factor (ARF) and the LAV (Leafy cotyledon2 [LEC2]-Abscisic acid insensitive3 [ABI3]-VAL) families, as well as the RAV (Related to ABI3 and VP1) and REM (REproductive Meristem) families. LEC2 and ABI3 have been shown to be involved in seed development, while other members of the LAV family seem to have a more general role, being expressed in many organs during plant development. Members of the ARF family bind to the auxin response element and depending on presence of an activation or repression domain, they activate or repress transcription. RAV and REM families are less studied B3 protein famillies. Length = 98

>gnl|CDD|216995 pfam02362, B3, B3 DNA binding domain

 Score = 59.3 bits (144), Expect = 1e-11
 Identities = 30/91 (32%), Positives = 41/91 (45%), Gaps = 10/91 (10%)

Query: 160 FYKKLRASDQSKK-KIVIRAKDAENVFPFLAHLDYKKQINYSVIAKDVHGVAWKFNF-VD 217
           F K L  SD SK  ++V+  K AE        L+ K Q    +   D  G +W       
Sbjct: 1   FVKVLTPSDVSKDGRLVLPKKFAEENG-----LNKKGQ---EITLLDPDGKSWTVKLRYR 52

Query: 218 GKSRRHYLTVGWKYFVRQKNLVPGDTVIFIR 248
              RR+ LT GWK FV+   L  GD+++F  
Sbjct: 53  KSGRRYLLTSGWKEFVKANGLKAGDSLVFKL 83

This is a family of plant transcription factors with various roles in development, the aligned region corresponds the B3 DNA binding domain as described in this domain is found in VP1/AB13 transcription factors. Some proteins also have a second AP2 DNA binding domain pfam00847 such as RAV1. DNA binding activity was demonstrated by. Length = 97

>gnl|CDD|214977 smart01019, B3, B3 DNA binding domain

 Score = 55.4 bits (134), Expect = 3e-10
 Identities = 30/91 (32%), Positives = 42/91 (46%), Gaps = 10/91 (10%)

Query: 160 FYKKLRASDQSKK-KIVIRAKDAENVFPFLAHLDYKKQINYSVIAKDVHGVAWKFNF-VD 217
           F+K L  SD SK  ++V+  + AE+  P    L  K+     +   D  G +WK      
Sbjct: 1   FFKTLTTSDVSKHGRLVLPKQFAESNGP---PLKPKE-----ITLLDPDGKSWKVKLKYR 52

Query: 218 GKSRRHYLTVGWKYFVRQKNLVPGDTVIFIR 248
           G S    LT GWK FV+   L  GD++ F  
Sbjct: 53  GSSGMFLLTGGWKEFVKANGLKAGDSLTFEL 83

Two DNA binding proteins, RAV1 and RAV2 from Arabidopsis thaliana contain two distinct amino acid sequence domains found only in higher plant species. The N-terminal regions of RAV1 and RAV2 are homologous to the AP2 DNA-binding domain (see ) present in a family of transcription factors, while the C-terminal region exhibits homology to the highly conserved C-terminal domain, designated B3, of VP1/ABI3 transcription factors. The AP2 and B3-like domains of RAV1 bind autonomously to the CAACA and CACCTG motifs, respectively, and together achieve a high affinity and specificity of binding. It has been suggested that the AP2 and B3-like domains of RAV1 are connected by a highly flexible structure enabling the two domains to bind to the CAACA and CACCTG motifs in various spacings and orientations. Length = 96

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	251
PF02362	100	B3: B3 DNA binding domain; InterPro: IPR003340 Two	99.74
PF03754	114	DUF313: Domain of unknown function (DUF313) ; Inte	97.75
PF09217	156	EcoRII-N: Restriction endonuclease EcoRII, N-termi	97.6
KOG0644	1113	consensus Uncharacterized conserved protein, conta	81.6

>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

Probab=99.74  E-value=1.2e-17  Score=127.68  Aligned_cols=83  Identities=34%  Similarity=0.483  Sum_probs=65.9

Q ss_pred             EEEecccCCCCCCC-EEEehhhhhhhCCCCccccccCCCCeEEEEEeCCCCeEEEEE-EeCCCCceEEcccHHHHhhhcC
Q 038793          160 FYKKLRASDQSKKK-IVIRAKDAENVFPFLAHLDYKKQINYSVIAKDVHGVAWKFNF-VDGKSRRHYLTVGWKYFVRQKN  237 (251)
Q Consensus       160 F~K~LT~SDv~~~g-lsVPk~~Ae~~FP~l~~Ld~~~~~p~~L~~~D~~G~~W~Fr~-yr~~srrhlLTtGWs~FVr~K~  237 (251)
                      |.|+|++||+.+.+ |.||+++++.+...     .  ..++.+.+.|..|+.|.+++ +++.+++++|++||..||++++
T Consensus         1 F~K~l~~s~~~~~~~l~iP~~f~~~~~~~-----~--~~~~~v~l~~~~g~~W~v~~~~~~~~~~~~l~~GW~~Fv~~n~   73 (100)
T PF02362_consen    1 FFKVLKPSDVSSSCRLIIPKEFAKKHGGN-----K--RKSREVTLKDPDGRSWPVKLKYRKNSGRYYLTGGWKKFVRDNG   73 (100)
T ss_dssp             EEEE--TTCCCCTT-EEE-HHHHTTTS-------S--S--CEEEEEETTTEEEEEEEEEECCTTEEEEETTHHHHHHHCT
T ss_pred             CEEEEEccCcCCCCEEEeCHHHHHHhCCC-----c--CCCeEEEEEeCCCCEEEEEEEEEccCCeEEECCCHHHHHHHcC
Confidence            89999999999877 99999999987311     1  11268999999999999999 8988888999999999999999


Q ss_pred             CCCCCEEEEEec
Q 038793          238 LVPGDTVIFIRY  249 (251)
Q Consensus       238 L~aGD~VvF~R~  249 (251)
                      |++||.|+|+..
T Consensus        74 L~~GD~~~F~~~   85 (100)
T PF02362_consen   74 LKEGDVCVFELI   85 (100)
T ss_dssp             --TT-EEEEEE-
T ss_pred             CCCCCEEEEEEe
Confidence            999999999853

The N-terminal regions of RAV1 and RAV2 are homologous to the AP2 DNA-binding domain (see IPR001471 from INTERPRO) present in a family of transcription factors, while the C-terminal region exhibits homology to the highly conserved C-terminal domain, designated B3, of VP1/ABI3 transcription factors []. The AP2 and B3-like domains of RAV1 bind autonomously to the CAACA and CACCTG motifs, respectively, and together achieve a high affinity and specificity of binding. It has been suggested that the AP2 and B3-like domains of RAV1 are connected by a highly flexible structure enabling the two domains to bind to the CAACA and CACCTG motifs in various spacings and orientations [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1WID_A 1YEL_A.

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

Probab=97.75  E-value=8.6e-05  Score=60.86  Aligned_cols=79  Identities=18%  Similarity=0.254  Sum_probs=57.7

Q ss_pred             CCCeEEEecccCCCCCCC--EEEehhhhhhhCCCCcc-----c----cc-cCCCCeEEEEEeCCCCeEEEEE-EeCC---
Q 038793          156 TPPLFYKKLRASDQSKKK--IVIRAKDAENVFPFLAH-----L----DY-KKQINYSVIAKDVHGVAWKFNF-VDGK---  219 (251)
Q Consensus       156 ~~~~F~K~LT~SDv~~~g--lsVPk~~Ae~~FP~l~~-----L----d~-~~~~p~~L~~~D~~G~~W~Fr~-yr~~---  219 (251)
                      ....|.|+|++||+..+-  |+||-..-.. ..+|..     +    .. .....+.+.+.|..++.|..++ .|..   
T Consensus        20 ~kli~~K~L~~tDv~~~qsRLsmP~~qi~~-~dFLt~eE~~~i~~~~~~~~~~~Gv~V~lvdp~~~~~~m~lkkW~mg~~   98 (114)
T PF03754_consen   20 PKLIIEKTLFKTDVDPHQSRLSMPFNQIID-NDFLTEEEKRIIKEEKKNNDKKKGVEVILVDPSLRKWTMRLKKWNMGNG   98 (114)
T ss_pred             CeEEEeeeecccCCCCCCceeeccHHHhcc-cccCCHHHHHHHHHhhccCcccCCceEEEECCcCcEEEEEEEEecccCC
Confidence            457899999999998764  9999875532 233110     1    00 1122288999999999999999 8866   


Q ss_pred             CCceEEcccHHHHhhh
Q 038793          220 SRRHYLTVGWKYFVRQ  235 (251)
Q Consensus       220 srrhlLTtGWs~FVr~  235 (251)
                      ...|+|.+||..+|.+
T Consensus        99 ~~~YvL~~gWn~VV~~  114 (114)
T PF03754_consen   99 TSNYVLNSGWNKVVED  114 (114)
T ss_pred             ceEEEEEcChHhhccC
Confidence            4579999999999863

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

Probab=97.60  E-value=0.00026  Score=60.91  Aligned_cols=89  Identities=18%  Similarity=0.173  Sum_probs=52.7

Q ss_pred             CCCeEEEecccCCCCCCC-----EEEehhhhhhhCCCCccccccCCCC-eEEEEEeCCC--CeEEEEE-EeCC------C
Q 038793          156 TPPLFYKKLRASDQSKKK-----IVIRAKDAENVFPFLAHLDYKKQIN-YSVIAKDVHG--VAWKFNF-VDGK------S  220 (251)
Q Consensus       156 ~~~~F~K~LT~SDv~~~g-----lsVPk~~Ae~~FP~l~~Ld~~~~~p-~~L~~~D~~G--~~W~Fr~-yr~~------s  220 (251)
                      ....|+|.|++.|++..|     +.||+..++..||.+.  ..+..+| ..|.+++..|  ..|+||+ |.|+      .
T Consensus         6 ~~~~~~K~LSaNDtGaTGgHQaGiyIpk~~~~~lFp~~~--~~~~~Np~~~~~~~~~s~~~~~~~~r~iYYnn~~~~gTR   83 (156)
T PF09217_consen    6 SWAIYCKRLSANDTGATGGHQAGIYIPKSAAELLFPSIN--HTKEENPDIWLKARWQSHFVTDSQVRFIYYNNRLFGGTR   83 (156)
T ss_dssp             SEEEEEEE--CCCCTTTSSS--EEEE-HHHHHHH-GGG---SSSSSS-EEEEEEEETTTT---EEEEEEEE-CCCTTSS-
T ss_pred             ceEEEEEEccCCCCCCcCcccceeEecccHHHHhCCCCC--cccccCCceeEEEEECCCCccceeEEEEEEcccccCCCc
Confidence            345799999999996643     9999999999999843  2355677 9999999988  5687888 6655      2


Q ss_pred             CceEEcccHHHHhh-hcCCCCCCEEEEE
Q 038793          221 RRHYLTVGWKYFVR-QKNLVPGDTVIFI  247 (251)
Q Consensus       221 rrhlLTtGWs~FVr-~K~L~aGD~VvF~  247 (251)
                      +-+-|| +|...-. .+-=..||-+||.
T Consensus        84 NE~RIT-~~G~~~~~~~~~~tGaL~vla  110 (156)
T PF09217_consen   84 NEYRIT-RFGRGFPLQNPENTGALLVLA  110 (156)
T ss_dssp             -EEEEE----TTSGGG-GGGTT-EEEEE
T ss_pred             CceEEe-eecCCCccCCccccccEEEEE
Confidence            335665 3332222 2222478888886

All types of enzymes recognise specific short DNA sequences and carry out the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. They differ in their recognition sequence, subunit composition, cleavage position, and cofactor requirements [, ], as summarised below: Type I enzymes (3.1.21.3 from EC) cleave at sites remote from recognition site; require both ATP and S-adenosyl-L-methionine to function; multifunctional protein with both restriction and methylase (2.1.1.72 from EC) activities. Type II enzymes (3.1.21.4 from EC) cleave within or at short specific distances from recognition site; most require magnesium; single function (restriction) enzymes independent of methylase. Type III enzymes (3.1.21.5 from EC) cleave at sites a short distance from recognition site; require ATP (but doesn't hydrolyse it); S-adenosyl-L-methionine stimulates reaction but is not required; exists as part of a complex with a modification methylase methylase (2.1.1.72 from EC). Type IV enzymes target methylated DNA. Type II restriction endonucleases (3.1.21.4 from EC) are components of prokaryotic DNA restriction-modification mechanisms that protect the organism against invading foreign DNA. These site-specific deoxyribonucleases catalyse the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. Of the 3000 restriction endonucleases that have been characterised, most are homodimeric or tetrameric enzymes that cleave target DNA at sequence-specific sites close to the recognition site. For homodimeric enzymes, the recognition site is usually a palindromic sequence 4-8 bp in length. Most enzymes require magnesium ions as a cofactor for catalysis. Although they can vary in their mode of recognition, many restriction endonucleases share a similar structural core comprising four beta-strands and one alpha-helix, as well as a similar mechanism of cleavage, suggesting a common ancestral origin []. However, there is still considerable diversity amongst restriction endonucleases [, ]. The target site recognition process triggers large conformational changes of the enzyme and the target DNA, leading to the activation of the catalytic centres. Like other DNA binding proteins, restriction enzymes are capable of non-specific DNA binding as well, which is the prerequisite for efficient target site location by facilitated diffusion. Non-specific binding usually does not involve interactions with the bases but only with the DNA backbone []. This entry represents the N-terminal effector-binding domain of the type II restriction endonuclease EcoRII, which has a DNA recognition fold, allowing for binding to 5'-CCWGG sequences. It assumes a structure composed of an eight-stranded beta-sheet with the strands in the order of b2, b5, b4, b3, b7, b6, b1 and b8. They are mostly antiparallel to each other except that b3 is parallel to b7. Alternatively, it may also be viewed as consisting of two mini beta-sheets of four antiparallel beta-strands, sheet I from beta-strands b2, b5, b4, b3 and sheet II from strands b7, b6, b1, b8, folded into an open mixed beta-barrel with a novel topology. Sheet I has a simple Greek key motif while sheet II does not []. The domain represented by this entry is only found in bacterial proteins.; PDB: 3HQF_A 1NA6_A.

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

Probab=81.60  E-value=0.99  Score=48.35  Aligned_cols=64  Identities=28%  Similarity=0.472  Sum_probs=43.8

Q ss_pred             CCCCCCCeEEEecCCccccccCCCCCCCCCCC-----CCCCcceEEEEEEEEeecCCcCceeEEEEEeec
Q 038793           60 SLPKKGDLVVYFPQGHLEYSAPASVSKAPPTF-----DLKPEIICRVADVRYLVSKKTDKVYTKMTLLPL  124 (251)
Q Consensus        60 ~lP~~gs~V~YFPqGH~Eq~~~s~~~~~~p~~-----~lp~~i~C~V~~V~l~Ad~~TDEVyA~i~L~P~  124 (251)
                      -||..|+.|.||-|||-|.+.+..-. .++.-     ++-..=.|.|..+..--=+-...---+|.|.=.
T Consensus       872 yipQmgDEViyfrQghqeyl~~~~~n-~~~~~~~~p~~~~~v~~~kv~kl~~~~y~~~~~s~c~m~l~~i  940 (1113)
T KOG0644|consen  872 YIPQMGDEVIYFRQGHQEYLEAVRLN-NIELNNKEPWNKMAVEICKVEKLVYITYPGSGDSCCKMKLAVI  940 (1113)
T ss_pred             ccccccceeehhhhhhHHHHhhhhhc-cccccccCcccccchhhheeeeeeeeeccCCCcchheeeeeee
Confidence            68999999999999999999986421 12211     232334688888877666666666666666544

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	251
1wid_A	130	Solution Structure Of The B3 Dna-Binding Domain Of		3e-05

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

Iteration: 1
 Score = 45.4 bits (106), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 34/92 (36%), Positives = 47/92 (51%), Gaps = 4/92 (4%)
Query: 159 LFYKKLRASDQSK-KKIVIRAKDAENVFPFLAHLDYKKQINYSVIAKDVHGVAWKFNFVD 217
           LF K +  SD  K  ++VI    AE  FP  +     K +  +   +DV+G  W+F +  
Sbjct: 13  LFEKAVTPSDVGKLNRLVIPKHHAEKHFPLPSSNVSVKGVLLNF--EDVNGKVWRFRYSY 70
Query: 218 GKSRRHY-LTVGWKYFVRQKNLVPGDTVIFIR 248
             S + Y LT GW  FV++KNL  GD V F R
Sbjct: 71  WNSSQSYVLTKGWSRFVKEKNLRAGDVVSFSR 102

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	251
1wid_A	130	DNA-binding protein RAV1; DNA-binding domain, stru	5e-17
1yel_A	104	AT1G16640; CESG, protein structure initiative, str	3e-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

 Score = 74.0 bits (181), Expect = 5e-17
 Identities = 36/102 (35%), Positives = 50/102 (49%), Gaps = 4/102 (3%)

Query: 149 EGSTANSTPPLFYKKLRASDQSKKK-IVIRAKDAENVFPFLAHLDYKKQINYSVIAKDVH 207
            GS+  S   LF K +  SD  K   +VI    AE  FP  +     K +   +  +DV+
Sbjct: 3   SGSSGRSAEALFEKAVTPSDVGKLNRLVIPKHHAEKHFPLPSSNVSVKGVL--LNFEDVN 60

Query: 208 GVAWKFNFVD-GKSRRHYLTVGWKYFVRQKNLVPGDTVIFIR 248
           G  W+F +     S+ + LT GW  FV++KNL  GD V F R
Sbjct: 61  GKVWRFRYSYWNSSQSYVLTKGWSRFVKEKNLRAGDVVSFSR 102

>1yel_A AT1G16640; CESG, protein structure initiative, structural genomics, center for eukaryotic structural genomics, unknown function; NMR {Arabidopsis thaliana} SCOP: b.142.1.2 Length = 104

 Score = 49.4 bits (118), Expect = 3e-08
 Identities = 25/97 (25%), Positives = 41/97 (42%), Gaps = 11/97 (11%)

Query: 150 GSTANSTPPLFYKKLRASDQSKKKIVIRAKDAENVFPFLAHLDYKKQINYSVIAKDVHGV 209
           GS A++    F K    S++S K + I          F  +  +      +V   D  G 
Sbjct: 1   GSMADTGEVQFMKPFI-SEKSSKSLEIPLG-------FNEY--FPAPFPITVDLLDYSGR 50

Query: 210 AWKFNFVDGKSRRHYLTVGWKYFVRQKNLVPGDTVIF 246
           +W    +  +  + +LTVGW+ FV+  NL  G  + F
Sbjct: 51  SWTVR-MKKRGEKVFLTVGWENFVKDNNLEDGKYLQF 86

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	251
1wid_A	130	DNA-binding protein RAV1; DNA-binding domain, stru	99.96
4i1k_A	146	B3 domain-containing transcription factor VRN1; B3	99.78
1yel_A	104	AT1G16640; CESG, protein structure initiative, str	99.63
1na6_A	404	Ecorii, restriction endonuclease ecorii; site-spec	87.45

>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

Probab=99.96  E-value=1.2e-28  Score=200.95  Aligned_cols=96  Identities=34%  Similarity=0.548  Sum_probs=86.1

Q ss_pred             CCCCCCCeEEEecccCCCCCCC-EEEehhhhhhhCCCCccccccCCCC-eEEEEEeCCCCeEEEEE-EeCCCCceEEccc
Q 038793          152 TANSTPPLFYKKLRASDQSKKK-IVIRAKDAENVFPFLAHLDYKKQIN-YSVIAKDVHGVAWKFNF-VDGKSRRHYLTVG  228 (251)
Q Consensus       152 ~~~~~~~~F~K~LT~SDv~~~g-lsVPk~~Ae~~FP~l~~Ld~~~~~p-~~L~~~D~~G~~W~Fr~-yr~~srrhlLTtG  228 (251)
                      ..++..++|.|+||+|||++++ |+||+++|+.|||.   ++.++..+ +.|.++|.+|++|+|+| ||+++++|+|++|
T Consensus         6 ~~~~~~~~F~K~Lt~SDv~~~~rL~iPk~~a~~~lP~---~~~~~~~~~~~l~l~D~~Gk~W~fr~~~~~~~~~~~Lt~G   82 (130)
T 1wid_A            6 SGRSAEALFEKAVTPSDVGKLNRLVIPKHHAEKHFPL---PSSNVSVKGVLLNFEDVNGKVWRFRYSYWNSSQSYVLTKG   82 (130)
T ss_dssp             --CCCEEEEEEECCTTTTSSSCCEEECHHHHTTTSCC---CSSCCSSCCEEEEEEETTTEEEEEEEEEETTTTEEEEESS
T ss_pred             CCCCCcceEEEEEehHHcCCCCEEEeCHHHHHhhCCc---cccccCCCcEEEEEEeCCCCEEEEEEEEECCCCceEEcCC
Confidence            3466788999999999999877 99999999999999   66554444 89999999999999999 9999999999999


Q ss_pred             HHHHhhhcCCCCCCEEEEEecc
Q 038793          229 WKYFVRQKNLVPGDTVIFIRYA  250 (251)
Q Consensus       229 Ws~FVr~K~L~aGD~VvF~R~~  250 (251)
                      |+.||++|+|++||+|+|+|.+
T Consensus        83 W~~FV~~~~L~~GD~~~F~~~~  104 (130)
T 1wid_A           83 WSRFVKEKNLRAGDVVSFSRSN  104 (130)
T ss_dssp             HHHHHHHTTCCTTCEEEEEECC
T ss_pred             hHHHHHHcCCCCCCEEEEEEec
Confidence            9999999999999999999864

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

Probab=99.78  E-value=6e-19  Score=146.68  Aligned_cols=83  Identities=22%  Similarity=0.290  Sum_probs=74.1

Q ss_pred             CCCCCeEEEecccCCCCCCC-EEEehhhhhhhCCCCccccccCCCCeEEEEEeCCCCeEEEEE-EeCCCCceEEcccHHH
Q 038793          154 NSTPPLFYKKLRASDQSKKK-IVIRAKDAENVFPFLAHLDYKKQINYSVIAKDVHGVAWKFNF-VDGKSRRHYLTVGWKY  231 (251)
Q Consensus       154 ~~~~~~F~K~LT~SDv~~~g-lsVPk~~Ae~~FP~l~~Ld~~~~~p~~L~~~D~~G~~W~Fr~-yr~~srrhlLTtGWs~  231 (251)
                      ++..++|.|+||+||+.+.. |+||+++++.+||.   .+      ..+.+.|. |+.|.|++ |++.  ++.|++||+.
T Consensus        43 ~s~~P~Fvk~l~~S~v~~~~~L~IP~~Fa~~~lp~---~~------~~i~L~~~-gk~W~v~~~~~~~--~~~ls~GW~~  110 (146)
T 4i1k_A           43 EPTNPFFRVVLRPSYLYRGCIMYLPSGFAEKYLSG---IS------GFIKVQLA-EKQWPVRCLYKAG--RAKFSQGWYE  110 (146)
T ss_dssp             CCSSCEEEEECCGGGSSTTCCEECCHHHHHHHCTT---CC------SEEEEEET-TEEEEEEEEEETT--EEEECTTHHH
T ss_pred             CCCCCEEEEEECchhcCCCcEEEeCHHHHHHhCCC---CC------eEEEEEEC-CcEEEEEEEEeCC--cEEECCchHH
Confidence            45678999999999998876 99999999999998   33      46888888 69999999 9874  7899999999


Q ss_pred             HhhhcCCCCCCEEEEEe
Q 038793          232 FVRQKNLVPGDTVIFIR  248 (251)
Q Consensus       232 FVr~K~L~aGD~VvF~R  248 (251)
                      ||++|+|++||+|+|..
T Consensus       111 Fv~dn~L~~GD~cvFel  127 (146)
T 4i1k_A          111 FTLENNLGEGDVCVFEL  127 (146)
T ss_dssp             HHHHTTCCTTCEEEEEE
T ss_pred             HHHHcCCCCCCEEEEEE
Confidence            99999999999999975

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

Probab=99.63  E-value=9.3e-16  Score=119.49  Aligned_cols=82  Identities=28%  Similarity=0.407  Sum_probs=69.2

Q ss_pred             CCCeEEEecccCCCCCCCEEEehhhhhhhCCCCccccccCCCCeEEEEEeCCCCeEEEEE-EeCCCCceEEcccHHHHhh
Q 038793          156 TPPLFYKKLRASDQSKKKIVIRAKDAENVFPFLAHLDYKKQINYSVIAKDVHGVAWKFNF-VDGKSRRHYLTVGWKYFVR  234 (251)
Q Consensus       156 ~~~~F~K~LT~SDv~~~glsVPk~~Ae~~FP~l~~Ld~~~~~p~~L~~~D~~G~~W~Fr~-yr~~srrhlLTtGWs~FVr  234 (251)
                      ..+.|.|+|+++| ....|.||+++++.+.+.   +.      ..+.++|..|+.|++++ .++  ++.+|++||..||+
T Consensus         7 ~~p~F~K~l~~~~-~~~~L~IP~~F~~~~~~~---~~------~~v~L~~~~G~~W~v~~~~~~--~~~~l~~GW~~Fv~   74 (104)
T 1yel_A            7 GEVQFMKPFISEK-SSKSLEIPLGFNEYFPAP---FP------ITVDLLDYSGRSWTVRMKKRG--EKVFLTVGWENFVK   74 (104)
T ss_dssp             CCEEEEEECCHHH-HTTCEECCHHHHTTCCCC---CC------SEEEEEETTSCEEEEEEEEET--TEEEECTTHHHHHH
T ss_pred             CCCCEEEEECCCC-ccceEECCHHHHHhcCcc---CC------CEEEEECCCCCEEEEEEEEEC--CcEEEccChHHHHH
Confidence            4579999999999 333599999999886655   22      47899999999999999 764  46799999999999


Q ss_pred             hcCCCCCCEEEEEec
Q 038793          235 QKNLVPGDTVIFIRY  249 (251)
Q Consensus       235 ~K~L~aGD~VvF~R~  249 (251)
                      +|+|++||.|+|...
T Consensus        75 ~~~L~~GD~lvF~~~   89 (104)
T 1yel_A           75 DNNLEDGKYLQFIYD   89 (104)
T ss_dssp             HHTCCTTCEEEEEEC
T ss_pred             HcCCCCCCEEEEEEc
Confidence            999999999999753

>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

Probab=87.45  E-value=0.59  Score=44.61  Aligned_cols=89  Identities=12%  Similarity=0.035  Sum_probs=59.7

Q ss_pred             CCCeEEEecccCCCCCC-----CEEEehhhhhhhCCCCccccc-cCCCC-eEEE--EEeCCCCeEEEEE-EeC----CCC
Q 038793          156 TPPLFYKKLRASDQSKK-----KIVIRAKDAENVFPFLAHLDY-KKQIN-YSVI--AKDVHGVAWKFNF-VDG----KSR  221 (251)
Q Consensus       156 ~~~~F~K~LT~SDv~~~-----glsVPk~~Ae~~FP~l~~Ld~-~~~~p-~~L~--~~D~~G~~W~Fr~-yr~----~sr  221 (251)
                      ....|+|.|++-|++..     |+.+|+.....+||.   ++. ...++ +.+.  +-|...-++.++. |.+    +++
T Consensus        17 ~~~v~~K~LSAnDtgatgshQ~gi~ipk~~l~~lfp~---lg~~~e~~~~~~~~~~l~d~d~p~td~~~twYn~R~~~~t   93 (404)
T 1na6_A           17 NYFVYIKRLSANDTGATGGHQVGLYIPSGIVEKLFPS---INHTRELNPSVFLTAHVSSHDCPDSEARAIYYNSAHFGKT   93 (404)
T ss_dssp             SEEEEEEECCHHHHTCC---CCCCCCCHHHHHHHCGG---GCCCSSSSCEEEEEEEESSSCCCCEEEEEEEECGGGTTSC
T ss_pred             cchheeEEcccccCCCCCCcccccCCchHHHHHhccc---CCCccccCCcceeEEEeccCCCceEEEEEEEecccccCCC
Confidence            34689999999999654     399999778999998   552 23344 4443  3344344558888 544    233


Q ss_pred             --ceEEc--ccHHHHhhhcCCCCCCEEEEEec
Q 038793          222 --RHYLT--VGWKYFVRQKNLVPGDTVIFIRY  249 (251)
Q Consensus       222 --rhlLT--tGWs~FVr~K~L~aGD~VvF~R~  249 (251)
                        -|-||  ++  .+.-.....+||.++|-+.
T Consensus        94 RnEyRLt~~~~--~~~~~~~a~~GDLlvia~~  123 (404)
T 1na6_A           94 RNEKRITRWGR--GSPLQDPENTGALTLLAFK  123 (404)
T ss_dssp             CCEEEEECCCT--TSGGGCGGGTTCEEEEEEE
T ss_pred             CCceEEeecCC--CCcccccCCCCCEEEEEEe
Confidence              36776  33  4566688899999999764

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

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

ID	Length	Definition	E-value
Query	251
d1wida_	117	b.142.1.2 (A:) DNA-binding protein RAV1 {Thale cre	7e-18
d1yela1	102	b.142.1.2 (A:1-102) At1g16640 {Thale cress (Arabid	1e-10
d1na6a1	175	b.142.1.1 (A:4-178) Restriction endonuclease EcoRI	4e-09

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

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 = 74.6 bits (183), Expect = 7e-18
 Identities = 34/97 (35%), Positives = 48/97 (49%), Gaps = 4/97 (4%)

Query: 155 STPPLFYKKLRASDQSKK-KIVIRAKDAENVFPFLAHLDYKKQINYSVIAKDVHGVAWKF 213
           S   LF K +  SD  K  ++VI    AE  FP  +     K +   +  +DV+G  W+F
Sbjct: 2   SAEALFEKAVTPSDVGKLNRLVIPKHHAEKHFPLPSSNVSVKGVL--LNFEDVNGKVWRF 59

Query: 214 NF-VDGKSRRHYLTVGWKYFVRQKNLVPGDTVIFIRY 249
            +     S+ + LT GW  FV++KNL  GD V F R 
Sbjct: 60  RYSYWNSSQSYVLTKGWSRFVKEKNLRAGDVVSFSRS 96

>d1yela1 b.142.1.2 (A:1-102) At1g16640 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]} Length = 102

class: All beta proteins
fold: DNA-binding pseudobarrel domain
superfamily: DNA-binding pseudobarrel domain
family: B3 DNA binding domain
domain: At1g16640
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

 Score = 54.9 bits (132), Expect = 1e-10
 Identities = 23/96 (23%), Positives = 37/96 (38%), Gaps = 11/96 (11%)

Query: 153 ANSTPPLFYKKLRASDQSKKKIVIRAKDAENVFPFLAHLDYKKQINYSVIAKDVHGVAWK 212
           A++    F K   +   S K + I          F  +  +      +V   D  G +W 
Sbjct: 2   ADTGEVQFMKPFISEK-SSKSLEIPLG-------FNEY--FPAPFPITVDLLDYSGRSWT 51

Query: 213 FNFVDGKSRRHYLTVGWKYFVRQKNLVPGDTVIFIR 248
                 +  + +LTVGW+ FV+  NL  G  + FI 
Sbjct: 52  VRMK-KRGEKVFLTVGWENFVKDNNLEDGKYLQFIY 86

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

class: All beta proteins
fold: DNA-binding pseudobarrel domain
superfamily: DNA-binding pseudobarrel domain
family: Type II restriction endonuclease effector domain
domain: Restriction endonuclease EcoRII, N-terminal domain
species: Escherichia coli [TaxId: 562]

 Score = 52.3 bits (125), Expect = 4e-09
 Identities = 15/104 (14%), Positives = 31/104 (29%), Gaps = 13/104 (12%)

Query: 159 LFYKKLRASDQSK-----KKIVIRAKDAENVFPFLAHLD-YKKQINYSVIAKDVHGVAWK 212
           ++ K+L A+D          + I +   E +FP + H       +  +           +
Sbjct: 17  VYIKRLSANDTGATGGHQVGLYIPSGIVEKLFPSINHTRELNPSVFLTAHVSSHDCPDSE 76

Query: 213 FNFV------DGKSRRHY-LTVGWKYFVRQKNLVPGDTVIFIRY 249
              +       GK+R    +T   +    Q     G   +    
Sbjct: 77  ARAIYYNSAHFGKTRNEKRITRWGRGSPLQDPENTGALTLLAFK 120

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	251
d1wida_	117	DNA-binding protein RAV1 {Thale cress (Arabidopsis	99.94
d1na6a1	175	Restriction endonuclease EcoRII, N-terminal domain	99.78
d1yela1	102	At1g16640 {Thale cress (Arabidopsis thaliana) [Tax	99.56

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

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=1.1e-26  Score=182.56  Aligned_cols=92  Identities=35%  Similarity=0.556  Sum_probs=84.4

Q ss_pred             CCCeEEEecccCCCCCCC-EEEehhhhhhhCCCCccccccCCCC-eEEEEEeCCCCeEEEEE-EeCCCCceEEcccHHHH
Q 038793          156 TPPLFYKKLRASDQSKKK-IVIRAKDAENVFPFLAHLDYKKQIN-YSVIAKDVHGVAWKFNF-VDGKSRRHYLTVGWKYF  232 (251)
Q Consensus       156 ~~~~F~K~LT~SDv~~~g-lsVPk~~Ae~~FP~l~~Ld~~~~~p-~~L~~~D~~G~~W~Fr~-yr~~srrhlLTtGWs~F  232 (251)
                      ..++|.|+||+|||++++ |+||+++++.|||+   ++...... +.|.+.|.+|++|+|+| +|+++++|+|++||..|
T Consensus         3 ~~~iF~K~Lt~sDv~~~~rL~iP~~~~~~~lp~---~~~~~~~~~~~~~~~d~~g~~W~~~~~~~~~~~~~~l~~GW~~F   79 (117)
T d1wida_           3 AEALFEKAVTPSDVGKLNRLVIPKHHAEKHFPL---PSSNVSVKGVLLNFEDVNGKVWRFRYSYWNSSQSYVLTKGWSRF   79 (117)
T ss_dssp             CEEEEEEECCTTTTSSSCCEEECHHHHTTTSCC---CSSCCSSCCEEEEEEETTTEEEEEEEEEETTTTEEEEESSHHHH
T ss_pred             CceEEEEEecchhcCCCCEEEECHHHHHHhCCc---cccccCCCcEEEEEEeCCCCEEEEEEEEECCCCceEEecCHHHH
Confidence            457999999999999877 99999999999999   66665555 99999999999999999 99888899999999999


Q ss_pred             hhhcCCCCCCEEEEEecc
Q 038793          233 VRQKNLVPGDTVIFIRYA  250 (251)
Q Consensus       233 Vr~K~L~aGD~VvF~R~~  250 (251)
                      |++|+|++||+|+|+|..
T Consensus        80 v~~~~Lk~GD~~~F~~~~   97 (117)
T d1wida_          80 VKEKNLRAGDVVSFSRSN   97 (117)
T ss_dssp             HHHTTCCTTCEEEEEECC
T ss_pred             HHHcCCCCCCEEEEEEEe
Confidence            999999999999999864

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

class: All beta proteins
fold: DNA-binding pseudobarrel domain
superfamily: DNA-binding pseudobarrel domain
family: Type II restriction endonuclease effector domain
domain: Restriction endonuclease EcoRII, N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=99.78  E-value=3.3e-20  Score=156.87  Aligned_cols=92  Identities=13%  Similarity=0.052  Sum_probs=81.7

Q ss_pred             CCCCeEEEecccCCCCCCC-----EEEehhhhhhhCCCCccccccCC-CC-eEEEEE--eCCCCeEEEEE-EeCCC----
Q 038793          155 STPPLFYKKLRASDQSKKK-----IVIRAKDAENVFPFLAHLDYKKQ-IN-YSVIAK--DVHGVAWKFNF-VDGKS----  220 (251)
Q Consensus       155 ~~~~~F~K~LT~SDv~~~g-----lsVPk~~Ae~~FP~l~~Ld~~~~-~p-~~L~~~--D~~G~~W~Fr~-yr~~s----  220 (251)
                      ++.++|+|.||+|||+++|     |+|||++|+.+||+   |+++++ +| +.|.++  |.+|.+|+||| |||+.    
T Consensus        13 ~~~~~F~K~LtasD~g~tg~HQaG~~IPK~~ae~~FP~---l~~~~e~nP~~~l~~~i~d~~g~~w~fR~iYyn~~~~gg   89 (175)
T d1na6a1          13 ENYFVYIKRLSANDTGATGGHQVGLYIPSGIVEKLFPS---INHTRELNPSVFLTAHVSSHDCPDSEARAIYYNSAHFGK   89 (175)
T ss_dssp             SSEEEEEEECCHHHHTCC---CCCCCCCHHHHHHHCGG---GCCCSSSSCEEEEEEEESSSCCCCEEEEEEEECGGGTTS
T ss_pred             CceEEEEEEcccccccccCCccceeeecHHHHHHhCCC---CCcccccCCCceEEEEEecCCCCeeEEEEEEECCccCCC
Confidence            4678999999999999876     99999999999999   887764 46 888765  99999999999 99873    


Q ss_pred             --CceEEcccHHHHhhhcCCCCCCEEEEEec
Q 038793          221 --RRHYLTVGWKYFVRQKNLVPGDTVIFIRY  249 (251)
Q Consensus       221 --rrhlLTtGWs~FVr~K~L~aGD~VvF~R~  249 (251)
                        +.|.||++|+.|+..+.+.+||.++|.|.
T Consensus        90 TRneyRiT~~g~~~~~~~~~n~G~l~i~af~  120 (175)
T d1na6a1          90 TRNEKRITRWGRGSPLQDPENTGALTLLAFK  120 (175)
T ss_dssp             CCCEEEEECCCTTSGGGCGGGTTCEEEEEEE
T ss_pred             ccccEEEEeccccccccCccccccEEEEEee
Confidence              56899999999999999999999999884

>d1yela1 b.142.1.2 (A:1-102) At1g16640 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}

class: All beta proteins
fold: DNA-binding pseudobarrel domain
superfamily: DNA-binding pseudobarrel domain
family: B3 DNA binding domain
domain: At1g16640
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=99.56  E-value=3.2e-15  Score=115.10  Aligned_cols=81  Identities=27%  Similarity=0.391  Sum_probs=68.5

Q ss_pred             CCeEEEecccCCCCCCCEEEehhhhhhhCCCCccccccCCCCeEEEEEeCCCCeEEEEE-EeCCCCceEEcccHHHHhhh
Q 038793          157 PPLFYKKLRASDQSKKKIVIRAKDAENVFPFLAHLDYKKQINYSVIAKDVHGVAWKFNF-VDGKSRRHYLTVGWKYFVRQ  235 (251)
Q Consensus       157 ~~~F~K~LT~SDv~~~glsVPk~~Ae~~FP~l~~Ld~~~~~p~~L~~~D~~G~~W~Fr~-yr~~srrhlLTtGWs~FVr~  235 (251)
                      .+.|.|+|.+++++ ..|.||++++..+.+.   +      +.++.++|.+|+.|.+++ .+  +++.+|+.||..||++
T Consensus         6 ~~~Ffkv~~~~~~~-~~L~IP~~F~~~~~~~---~------~~~i~L~d~~G~~W~v~~~~~--~~~~~~~~GW~~Fv~~   73 (102)
T d1yela1           6 EVQFMKPFISEKSS-KSLEIPLGFNEYFPAP---F------PITVDLLDYSGRSWTVRMKKR--GEKVFLTVGWENFVKD   73 (102)
T ss_dssp             CEEEEEECCHHHHT-TCEECCHHHHTTCCCC---C------CSEEEEEETTSCEEEEEEEEE--TTEEEECTTHHHHHHH
T ss_pred             CCeEEEEEcCcccC-CCEECCHHHHHhCCCC---C------CCEEEEEcCCCCEEEEEEEEe--CCeEEEccCHHHHHHH
Confidence            45799999999874 3599999999987766   2      147889999999999999 44  3567899999999999


Q ss_pred             cCCCCCCEEEEEec
Q 038793          236 KNLVPGDTVIFIRY  249 (251)
Q Consensus       236 K~L~aGD~VvF~R~  249 (251)
                      ++|++||.|+|...
T Consensus        74 n~L~~GD~~vF~~~   87 (102)
T d1yela1          74 NNLEDGKYLQFIYD   87 (102)
T ss_dssp             HTCCTTCEEEEEEC
T ss_pred             cCCCcCCEEEEEEc
Confidence            99999999999653