Citrus Sinensis ID: 021945

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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-------260-------270-------280-------290-------300-----
Protein Sequence
MASNSSSVDLDHDHNLSENGIDAESKKLPSSKYKGVVPQPNGRWGAQIYEKHQRVWLGTFIEEEEAARVYDTAALRFRGQNAITNFRTSLETDDEDDYMEKIFLSSHSKAEIVDMLRKHTYKHELEQSKQNYACVGISCYNNSSGFSDLFGSNCFQETPVEFLFEKVLTPSDVGKLNRMVIPKQQAEKHFALSSEIASKGLLLNFEDSTQKVWRLRYCYWSSSQSYVLTKGWSRFVKEKGVKAGDTVSFWRSNVGSNSKLFIDCKLQQNGNGSGFEEMQSQVPNIGVVRLFGVNILEDPNNLCCR
Secondary Structure (PSIPRED)
cccccccccccccccccccccccccccccccccccccccccccEEEEEEccccEEEEcccccHHHHHHHHHHHHHHHcccccccccccccccccccHHHHHHHccccccHHHHHHHHcccccHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHcccccccccccccEEEEEEccccEEEEEEEEEcccccEEEEccccHHHHHcccccccEEEEEEcccccccEEEEEEEEccccccccccccccccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
ccccccEEEEccccccccccccccccccccccccccccccccccHHHHHHHccEEEEcccccHHHHHHHHHHHHHHHcccccccccccccccccccccHHHHHcccccHHHHHHHHHHcccHHHHHHcHHHHHccccccccccccccccccccccccccccHHHHEEccHccccccccEEEcHHHHHHHcccccccccccEEEEEEEccccEEEEEEEEcccccEEEEEcccHHHHHHcccccccEEEEEEcccccccEEEEEEEEccccccccccccccccccccEEEEEEEcccccccccEEc
Coil and Loop (DISEMBL)
masnsssvdldhdhnlsengidaeskklpsskykgvvpqpngrwgaqIYEKHQRVWLGTFIEEEEAARVYDTAALRFRGQNaitnfrtsletddeddymEKIFLSSHSKAEIVDMLRKHTYKHELEQSKQNYACVGiscynnssgfsdlfgsncfqetpVEFLFEkvltpsdvgklnrmvipkqQAEKHFALSSEIASKGLLLNFEDSTQKVWRLRYCYWSSSQSYVLTKGWSRFVkekgvkagdtvsfwrsnvgsnskLFIDCklqqngngsgfeemqsqvpnigvVRLFgvniledpnnlccr
Flexible Loop (DISEMBL)
masnsssvdldhdhnlsengidaeskklpsskykgVVPQPNGRWGAQIYEKHQRVWLGTFIEEEEAARVYDTAalrfrgqnaitnfrtsletddeddYMEKIFLSSHSKAEIVDMLRKHTYKHELEQSKQNYACVGISCYNNSSGFSDLFGSNCFQETPVEFLFEKVLTPSDVGKLNRMVIPKQQAEKHFALSSEIASKGLLLNFEDSTQKVWRLRYCYWSSSQSYVLTKGWSRFVKEkgvkagdtvsfwrsnvgsnskLFIDCKLQQNGNGSGFEEMQSQVPNIGVVRLFGvniledpnnlccr
Low Complexity Region (SEG)
MASNSSSVDLDHDHNLSENGIDAESKKLPSSKYKGVVPQPNGRWGAQIYEKHQRVWLGTFIEEEEAARVYDTAALRFRGQNAITNFRTSLETDDEDDYMEKIFLSSHSKAEIVDMLRKHTYKHELEQSKQNYACVGISCYNNSSGFSDLFGSNCFQETPVEFLFEKVLTPSDVGKLNRMVIPKQQAEKHFALSSEIASKGLLLNFEDSTQKVWRLRYCYWSSSQSYVLTKGWSRFVKEKGVKAGDTVSFWRSNVGSNSKLFIDCKLQQNGNGSGFEEMQSQVPNIGVVRLFGVNILEDPNNLCCR
Disordered region (IsUnstruct)
****************************************NGRWGAQIYEKHQRVWLGTFIEEEEAARVYDTAALRFRGQNAITNFRTSLETD*EDDYMEKIFLSSHSKAEIVDMLRKHTYKHELEQSKQNYACVGISCYNNSSGFSDLFGSNCFQETPVEFLFEKVLTPSDVGKLNRMVIPKQQAEKHFALSSEIASKGLLLNFEDSTQKVWRLRYCYWSSSQSYVLTKGWSRFVKEKGVKAGDTVSFWRSNVGSNSKLFIDCKLQQN***********QVPNIGVVRLFGVNILEDPNNLC**
Disordered Region (DISOPRED)
************************************VPQPNGRWGAQIYEKHQRVWLGTFIEEEEAARVYDTAALRFRGQNAITNFRTSLETD************************KHTYKHELEQSKQNYACVGISCYNNSSGFSDLFGSNCFQETPVEFLFEKVLTPSDVGKLNRMVIPKQQ*******************FEDSTQKVWRLRYCYWSSSQSYVLTKGWSRFVKEKGVKAGDTVSFWRSNVGSNSKLFIDCK**********************VRLFGVNILEDPNN****
Disordered Region (DISEMBL)
**********DHDHNLSENGIDAESKKLPSSKYKGVVPQPNGRWGAQIYEKHQRVWLGTFIEEEEAARVYDTAALRFRGQNAITNFRTSLETDDEDDYMEKIFLSSHSKAEIVDMLRKHTYKHELEQSKQNYACVGISCYNNSSGFSDLFGSNCFQETPVEFLFEKVLTPSDVGKLNRMVIPKQQAEKHFALSSEIASKGLLLNFEDSTQKVWRLRYCYWSSSQSYVLTKGWSRFVKEKGVKAGDTVSFWRSNVGSNSKLFIDCKLQQNGNGSGFEEMQSQVPNIGVVRLFGVNILEDPNNLCCR
Disordered Region (DISPRO)
********************************YKGVVPQPNGRWGAQIYEKHQRVWLGTFIEEEEAARVYDTAALRFRGQNAITNFRTSLETDDEDDYMEKIFLSSHSKAEIVDMLRKHTYKHELEQSK******************************VEFLFEKVLTPSDVGKLNRMVIPKQQAEKHFALSSEIASKGLLLNFEDSTQKVWRLRYCYWSSSQSYVLTKGWSRFVKEKGVKAGDTVSFWRSNVGSNSKLFIDCKLQQN***************IGVVRLFGVNILEDPNNLCCR
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
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TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MASNSSSVDLDHDHNLSENGIDAESKKLPSSKYKGVVPQPNGRWGAQIYEKHQRVWLGTFIEEEEAARVYDTAALRFRGQNAITNFRTSLETDDEDDYMEKIFLSSHSKAEIVDMLRKHTYKHELEQSKQNYACVGISCYNNSSGFSDLFGSNCFQETPVEFLFEKVLTPSDVGKLNRMVIPKQQAEKHFALSSEIASKGLLLNFEDSTQKVWRLRYCYWSSSQSYVLTKGWSRFVKEKGVKAGDTVSFWRSNVGSNSKLFIDCKLQQNGNGSGFEEMQSQVPNIGVVRLFGVNILEDPNNLCCR
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	305	2.2.26 [Sep-21-2011]
P82280	352	AP2/ERF and B3 domain-con	yes	no	0.921	0.798	0.567	3e-86
Q9ZWM9	344	AP2/ERF and B3 domain-con	no	no	0.875	0.776	0.607	6e-86
Q9C6M5	361	AP2/ERF and B3 domain-con	no	no	0.908	0.767	0.547	2e-85
Q8RZX9	393	AP2/ERF and B3 domain-con	yes	no	0.885	0.687	0.575	2e-84
Q9LS06	333	AP2/ERF and B3 domain-con	no	no	0.862	0.789	0.567	1e-80
Q6L4H4	394	AP2/ERF and B3 domain-con	no	no	0.898	0.695	0.517	7e-79
Q9AWS7	317	Putative AP2/ERF and B3 d	no	no	0.793	0.763	0.557	5e-72
Q9AWS0	365	AP2/ERF and B3 domain-con	no	no	0.796	0.665	0.542	2e-66
Q9C6P5	337	AP2/ERF and B3 domain-con	no	no	0.721	0.652	0.4	2e-41
Q9C688	352	AP2/ERF and B3 domain-con	no	no	0.8	0.693	0.378	1e-38

>sp|P82280|RAV2_ARATH AP2/ERF and B3 domain-containing transcription repressor RAV2 OS=Arabidopsis thaliana GN=RAV2 PE=2 SV=1

 Score =  318 bits (816), Expect = 3e-86,   Method: Compositional matrix adjust.
 Identities = 176/310 (56%), Positives = 207/310 (66%), Gaps = 29/310 (9%)

Query: 1   MASNSSSVDLDHDHNLSENGIDAESKKLPSSKYKGVVPQPNGRWGAQIYEKHQRVWLGTF 60
           M S  SSV LD      ENG++ ES+KLPSSKYKGVVPQPNGRWGAQIYEKHQRVWLGTF
Sbjct: 38  MGSGGSSVVLD-----PENGLETESRKLPSSKYKGVVPQPNGRWGAQIYEKHQRVWLGTF 92

Query: 61  IEEEEAARVYDTAALRFRGQNAITNFRTSLETDDEDDYMEKIFLSSHSKAEIVDMLRKHT 120
            E+EEAAR YD AA RFRG++A+ NF+  LE  D        FL +HSKAEIVDMLRKHT
Sbjct: 93  NEQEEAARSYDIAACRFRGRDAVVNFKNVLEDGD------LAFLEAHSKAEIVDMLRKHT 146

Query: 121 YKHELEQSKQNYACVGISCYNNSSGFSDLFGSNCFQETPVEFLFEKVLTPSDVGKLNRMV 180
           Y  ELEQ+ +    + +      +G S        +    E LFEK +TPSDVGKLNR+V
Sbjct: 147 YADELEQNNKRQLFLSVDANGKRNGSSTTQNDKVLKTR--EVLFEKAVTPSDVGKLNRLV 204

Query: 181 IPKQQAEKHFAL--SSEIASKGLLLNFEDSTQKVWRLRYCYWSSSQSYVLTKGWSRFVKE 238
           IPKQ AEKHF L   S   +KG+L+NFED   KVWR RY YW+SSQSYVLTKGWSRFVKE
Sbjct: 205 IPKQHAEKHFPLPSPSPAVTKGVLINFEDVNGKVWRFRYSYWNSSQSYVLTKGWSRFVKE 264

Query: 239 KGVKAGDTVSFWRSNVGSNSKLFIDCKLQQNGNGSGFEEMQSQVPNIGVVRLFGVNILE- 297
           K ++AGD V+F RS  G   +L+ID K++     SG  E   QV    VVRLFGV+I   
Sbjct: 265 KNLRAGDVVTFERS-TGLERQLYIDWKVR-----SGPRENPVQV----VVRLFGVDIFNV 314

Query: 298 ---DPNNLCC 304
               PN++  
Sbjct: 315 TTVKPNDVVA 324

Probably acts as a transcriptional activator. Binds to the GCC-box pathogenesis-related promoter element. May be involved in the regulation of gene expression by stress factors and by components of stress signal transduction pathways (By similarity). Transcritptional repressor of flowering time on long day plants. Acts directly on FT expression by binding 5'-CAACA-3' and 5'-CACCTG-3 sequences (Probable). Functionally redundant with TEM1.
Arabidopsis thaliana (taxid: 3702)

>sp|Q9ZWM9|RAV1_ARATH AP2/ERF and B3 domain-containing transcription factor RAV1 OS=Arabidopsis thaliana GN=RAV1 PE=1 SV=1

 Score =  317 bits (813), Expect = 6e-86,   Method: Compositional matrix adjust.
 Identities = 178/293 (60%), Positives = 211/293 (72%), Gaps = 26/293 (8%)

Query: 6   SSVDLDHDHNLSENGIDAESKKLPSSKYKGVVPQPNGRWGAQIYEKHQRVWLGTFIEEEE 65
           SSV LD     SENG++AES+KLPSSKYKGVVPQPNGRWGAQIYEKHQRVWLGTF EE+E
Sbjct: 40  SSVVLD-----SENGVEAESRKLPSSKYKGVVPQPNGRWGAQIYEKHQRVWLGTFNEEDE 94

Query: 66  AARVYDTAALRFRGQNAITNFRTSLETDDEDDYMEKIFLSSHSKAEIVDMLRKHTYKHEL 125
           AAR YD A  RFR ++A+TNF+     +DE D     FL+SHSK+EIVDMLRKHTY  EL
Sbjct: 95  AARAYDVAVHRFRRRDAVTNFKDVKMDEDEVD-----FLNSHSKSEIVDMLRKHTYNEEL 149

Query: 126 EQSKQNYACVG-ISCYNNSSGFS-DLFGSNCFQETPVEFLFEKVLTPSDVGKLNRMVIPK 183
           EQSK+     G ++    +SG S D   +  F+    E LFEK +TPSDVGKLNR+VIPK
Sbjct: 150 EQSKRRRNGNGNMTRTLLTSGLSNDGVSTTGFRS--AEALFEKAVTPSDVGKLNRLVIPK 207

Query: 184 QQAEKHFAL-SSEIASKGLLLNFEDSTQKVWRLRYCYWSSSQSYVLTKGWSRFVKEKGVK 242
             AEKHF L SS ++ KG+LLNFED   KVWR RY YW+SSQSYVLTKGWSRFVKEK ++
Sbjct: 208 HHAEKHFPLPSSNVSVKGVLLNFEDVNGKVWRFRYSYWNSSQSYVLTKGWSRFVKEKNLR 267

Query: 243 AGDTVSFWRSNVGSNSKLFIDCKLQQNGNGSGFEEMQSQVPNIGVVRLFGVNI 295
           AGD VSF RSN G + +L+I  K +   +GS  +  +       V+RLFGVNI
Sbjct: 268 AGDVVSFSRSN-GQDQQLYIGWKSR---SGSDLDAGR-------VLRLFGVNI 309

Binds specifically to bipartite recognition sequences composed of two unrelated motifs, 5'-CAACA-3' and 5'-CACCTG-3'. May function as negative regulator of plant growth and development.

Arabidopsis thaliana (taxid: 3702)

>sp|Q9C6M5|RAVL1_ARATH AP2/ERF and B3 domain-containing transcription repressor TEM1 OS=Arabidopsis thaliana GN=TEM1 PE=1 SV=1

 Score =  316 bits (809), Expect = 2e-85,   Method: Compositional matrix adjust.
 Identities = 173/316 (54%), Positives = 207/316 (65%), Gaps = 39/316 (12%)

Query: 1   MASNSSSVDLDHDHNLSENGIDAESKKLPSSKYKGVVPQPNGRWGAQIYEKHQRVWLGTF 60
           M S  SSV LD     SENG++ ES+KLPSSKYKGVVPQPNGRWGAQIYEKHQRVWLGTF
Sbjct: 45  MGSGGSSVVLD-----SENGVETESRKLPSSKYKGVVPQPNGRWGAQIYEKHQRVWLGTF 99

Query: 61  IEEEEAARVYDTAALRFRGQNAITNFRTSLETDDEDDYMEKIFLSSHSKAEIVDMLRKHT 120
            EEEEAA  YD A  RFRG++A+TNF++ ++ +D     E  FL +HSKAEIVDMLRKHT
Sbjct: 100 NEEEEAASSYDIAVRRFRGRDAVTNFKSQVDGND----AESAFLDAHSKAEIVDMLRKHT 155

Query: 121 YKHELEQSKQNYACVGISCYNNSSGFSDLFGSNCFQETPVEFLFEKVLTPSDVGKLNRMV 180
           Y  E EQS++ +    ++     SG       N       E LFEK +TPSDVGKLNR+V
Sbjct: 156 YADEFEQSRRKF----VNGDGKRSGLETATYGNDAVLRAREVLFEKTVTPSDVGKLNRLV 211

Query: 181 IPKQQAEKHFALSSEIA--------SKGLLLNFEDSTQKVWRLRYCYWSSSQSYVLTKGW 232
           IPKQ AEKHF L +           +KG+L+N ED T KVWR RY YW+SSQSYVLTKGW
Sbjct: 212 IPKQHAEKHFPLPAMTTAMGMNPSPTKGVLINLEDRTGKVWRFRYSYWNSSQSYVLTKGW 271

Query: 233 SRFVKEKGVKAGDTVSFWRSNVGSNSKLFIDCKLQQNGNGSGFEEMQSQVPNIGVVRLFG 292
           SRFVKEK ++AGD V F RS  G + +L+I  K++ +             P   VVRLFG
Sbjct: 272 SRFVKEKNLRAGDVVCFERS-TGPDRQLYIHWKVRSS-------------PVQTVVRLFG 317

Query: 293 VNIL----EDPNNLCC 304
           VNI     E PN++  
Sbjct: 318 VNIFNVSNEKPNDVAV 333

Transcritptional repressor of flowering time on long day plants. Acts directly on FT expression by binding 5'-CAACA-3' and 5'-CACCTG-3 sequences. Functionally redundant with TEM2.

Arabidopsis thaliana (taxid: 3702)

>sp|Q8RZX9|Y1934_ORYSJ AP2/ERF and B3 domain-containing protein Os01g0693400 OS=Oryza sativa subsp. japonica GN=Os01g0693400 PE=2 SV=1

 Score =  312 bits (800), Expect = 2e-84,   Method: Compositional matrix adjust.
 Identities = 164/285 (57%), Positives = 198/285 (69%), Gaps = 15/285 (5%)

Query: 27  KLPSSKYKGVVPQPNGRWGAQIYEKHQRVWLGTFIEEEEAARVYDTAALRFRGQNAITNF 86
           KLPSSK+KGVVPQPNGRWGAQIYE+HQRVWLGTF  E++AAR YD AA RFRG++A+TNF
Sbjct: 76  KLPSSKFKGVVPQPNGRWGAQIYERHQRVWLGTFAGEDDAARAYDVAAQRFRGRDAVTNF 135

Query: 87  RTSLETDDEDDYMEKIFLSSHSKAEIVDMLRKHTYKHELEQSKQNYACVGISCYNNSSGF 146
           R  L   D D   E  FL++ SKAE+VDMLRKHTY  EL QSK+ +A    S    ++  
Sbjct: 136 RP-LAEADPDAAAELRFLATRSKAEVVDMLRKHTYFDELAQSKRTFAASTPSAATTTASL 194

Query: 147 SDLFGSNCFQETPV------EFLFEKVLTPSDVGKLNRMVIPKQQAEKHFALSSEIA--- 197
           S+  G      +P       + LF+K +TPSDVGKLNR+VIPKQ AEKHF L    A   
Sbjct: 195 SN--GHLSSPRSPFAPAAARDHLFDKTVTPSDVGKLNRLVIPKQHAEKHFPLQLPSAGGE 252

Query: 198 SKGLLLNFEDSTQKVWRLRYCYWSSSQSYVLTKGWSRFVKEKGVKAGDTVSFWRS--NVG 255
           SKG+LLNFED+  KVWR RY YW+SSQSYVLTKGWSRFVKEKG+ AGD V F+RS  + G
Sbjct: 253 SKGVLLNFEDAAGKVWRFRYSYWNSSQSYVLTKGWSRFVKEKGLHAGDVVGFYRSAASAG 312

Query: 256 SNSKLFIDCKLQQNGNGSGFEEMQSQVPN-IGVVRLFGVNILEDP 299
            + KLFIDCKL ++   +         P+ +  VRLFGV++L  P
Sbjct: 313 DDGKLFIDCKLVRSTGAALASPADQPAPSPVKAVRLFGVDLLTAP 357

Oryza sativa subsp. japonica (taxid: 39947)

>sp|Q9LS06|RAVL4_ARATH AP2/ERF and B3 domain-containing transcription factor ARF14 OS=Arabidopsis thaliana GN=ARF14 PE=2 SV=1

 Score =  300 bits (767), Expect = 1e-80,   Method: Compositional matrix adjust.
 Identities = 169/298 (56%), Positives = 207/298 (69%), Gaps = 35/298 (11%)

Query: 6   SSVDLDHDHNLSENGID----AESKKLPSSKYKGVVPQPNGRWGAQIYEKHQRVWLGTFI 61
           +SV LD     SENG++    AES+KLPSS++KGVVPQPNGRWGAQIYEKHQRVWLGTF 
Sbjct: 36  TSVVLD-----SENGVEVEVEAESRKLPSSRFKGVVPQPNGRWGAQIYEKHQRVWLGTFN 90

Query: 62  EEEEAARVYDTAALRFRGQNAITNFR-TSLETDDEDDYMEKIFLSSHSKAEIVDMLRKHT 120
           EE+EAAR YD AA RFRG++A+TNF+ T+ E + E       FL++HSK+EIVDMLRKHT
Sbjct: 91  EEDEAARAYDVAAHRFRGRDAVTNFKDTTFEEEVE-------FLNAHSKSEIVDMLRKHT 143

Query: 121 YKHELEQSKQNYACVGISCYNNSSGFSDLFGSNCFQETPVEFLFEKVLTPSDVGKLNRMV 180
           YK EL+Q K+N    G      +   + +     F+    E LFEK +TPSDVGKLNR+V
Sbjct: 144 YKEELDQRKRNRDGNGKET--TAFALASMVVMTGFK--TAELLFEKTVTPSDVGKLNRLV 199

Query: 181 IPKQQAEKHFAL---SSEIASKGLLLNFEDSTQKVWRLRYCYWSSSQSYVLTKGWSRFVK 237
           IPK QAEKHF L   ++ ++ KG+LLNFED   KVWR RY YW+SSQSYVLTKGWSRFVK
Sbjct: 200 IPKHQAEKHFPLPLGNNNVSVKGMLLNFEDVNGKVWRFRYSYWNSSQSYVLTKGWSRFVK 259

Query: 238 EKGVKAGDTVSFWRSNVGSNSKLFIDCKLQQNGNGSGFEEMQSQVPNIGVVRLFGVNI 295
           EK + AGD +SF RSN   + K FI  K     + SG +    +     V+RLFGV+I
Sbjct: 260 EKRLCAGDLISFKRSN-DQDQKFFIGWK-----SKSGLDLETGR-----VMRLFGVDI 306

Probably acts as a transcriptional activator. Binds to the GCC-box pathogenesis-related promoter element. May be involved in the regulation of gene expression by stress factors and by components of stress signal transduction pathways.

Arabidopsis thaliana (taxid: 3702)

>sp|Q6L4H4|Y5498_ORYSJ AP2/ERF and B3 domain-containing protein Os05g0549800 OS=Oryza sativa subsp. japonica GN=Os05g0549800 PE=2 SV=1

 Score =  293 bits (751), Expect = 7e-79,   Method: Compositional matrix adjust.
 Identities = 164/317 (51%), Positives = 204/317 (64%), Gaps = 43/317 (13%)

Query: 15  NLSENGIDAESK---------KLPSSKYKGVVPQPNGRWGAQIYEKHQRVWLGTFIEEEE 65
           + +E G +A+S          KLPSSKYKGVVPQPNGRWGAQIYE+HQRVWLGTF  E E
Sbjct: 42  DAAEPGAEADSGGERRGGGGGKLPSSKYKGVVPQPNGRWGAQIYERHQRVWLGTFTGEAE 101

Query: 66  AARVYDTAALRFRGQNAITNFRTSLETDDEDDYMEKIFLSSHSKAEIVDMLRKHTYKHEL 125
           AAR YD AA RFRG++A+TNFR   E+D E   +E  FL+S SKAE+VDMLRKHTY  EL
Sbjct: 102 AARAYDVAAQRFRGRDAVTNFRPLAESDPE-AAVELRFLASRSKAEVVDMLRKHTYLEEL 160

Query: 126 EQSKQNYACVGISCYNNSSGFSDLFGSNCFQETPVEFLFEKVLTPSDVGKLNRMVIPKQQ 185
            Q+K+ +A +      + +       S        E LF+K +TPSDVGKLNR+VIPKQ 
Sbjct: 161 TQNKRAFAAISPPPPKHPA------SSPTSSSAAREHLFDKTVTPSDVGKLNRLVIPKQH 214

Query: 186 AEKHFAL-------SSEIAS-----------KGLLLNFEDSTQKVWRLRYCYWSSSQSYV 227
           AEKHF L       +S +A+           KG+LLNFED+  KVW+ RY YW+SSQSYV
Sbjct: 215 AEKHFPLQLPPPTTTSSVAAAADAAAGGGDCKGVLLNFEDAAGKVWKFRYSYWNSSQSYV 274

Query: 228 LTKGWSRFVKEKGVKAGDTVSFWRSNVGSNSKLFIDCKLQ--------QNGNGSGFEEMQ 279
           LTKGWSRFVKEKG+ AGD V F+R+  G N++LFIDCK++             S      
Sbjct: 275 LTKGWSRFVKEKGLHAGDAVGFYRA-AGKNAQLFIDCKVRAKPTTAAAAAAFLSAVAAAA 333

Query: 280 SQVPNIGVVRLFGVNIL 296
           +  P +  +RLFGV++L
Sbjct: 334 APPPAVKAIRLFGVDLL 350

Oryza sativa subsp. japonica (taxid: 39947)

>sp|Q9AWS7|Y1407_ORYSJ Putative AP2/ERF and B3 domain-containing protein Os01g0140700 OS=Oryza sativa subsp. japonica GN=Os01g0140700 PE=3 SV=1

 Score =  271 bits (693), Expect = 5e-72,   Method: Compositional matrix adjust.
 Identities = 156/280 (55%), Positives = 188/280 (67%), Gaps = 38/280 (13%)

Query: 29  PSSKYKGVVPQPNGRWGAQIYEKHQRVWLGTFIEEEEAARVYDTAALRFRGQNAITNFRT 88
           PSS+YKGVVPQPNGRWGAQIYE+H RVWLGTF +EE AAR YD AALRFRG++A+TN   
Sbjct: 63  PSSRYKGVVPQPNGRWGAQIYERHARVWLGTFPDEEAAARAYDVAALRFRGRDAVTNRAP 122

Query: 89  SLETDDEDDYMEKIFLSSHSKAEIVDMLRKHTYKHELEQSKQNYACVGISCYNNSSGFSD 148
           + E        E  FL++HSKAE+VDMLRKHTY  EL+Q  +                  
Sbjct: 123 AAEGASAG---ELAFLAAHSKAEVVDMLRKHTYDDELQQGLRR----------------- 162

Query: 149 LFGSNCFQETP---VEFLFEKVLTPSDVGKLNRMVIPKQQAEKHFAL-----SSEIASKG 200
             GS   Q TP    E LFEK +TPSDVGKLNR+V+PKQQAE+HF       SS+ A KG
Sbjct: 163 --GSRA-QPTPRWAREPLFEKAVTPSDVGKLNRLVVPKQQAERHFPFPLRRHSSDAAGKG 219

Query: 201 LLLNFEDSTQKVWRLRYCYWSSSQSYVLTKGWSRFVKEKGVKAGDTVSFWRSNV--GSNS 258
           +LLNFED   KVWR RY YW+SSQSYVLTKGWSRFV+EKG++ GDTV+F RS    G+  
Sbjct: 220 VLLNFEDGDGKVWRFRYSYWNSSQSYVLTKGWSRFVREKGLRPGDTVAFSRSAAAWGTEK 279

Query: 259 KLFIDCKLQQNGNGSGFEEMQSQVPNIGVVRLFGVNILED 298
            L IDCK  +  N +  ++  ++V    VV+LFGV+I  D
Sbjct: 280 HLLIDCKKMERNNLATVDD-DARV----VVKLFGVDIAGD 314

Oryza sativa subsp. japonica (taxid: 39947)

>sp|Q9AWS0|Y1410_ORYSJ AP2/ERF and B3 domain-containing protein Os01g0141000 OS=Oryza sativa subsp. japonica GN=Os01g0141000 PE=2 SV=1

 Score =  253 bits (645), Expect = 2e-66,   Method: Compositional matrix adjust.
 Identities = 152/280 (54%), Positives = 176/280 (62%), Gaps = 37/280 (13%)

Query: 32  KYKGVVPQPNGRWGAQIYEKHQRVWLGTFIEEEEAARVYDTAALRFRGQNAITNFRTSLE 91
           +YKGVVPQPNGRWGAQIYE+H RVWLGTF +EE AAR YD AALR+RG++A TNF     
Sbjct: 68  RYKGVVPQPNGRWGAQIYERHARVWLGTFPDEEAAARAYDVAALRYRGRDAATNF----- 122

Query: 92  TDDEDDYMEKIFLSSHSKAEIVDMLRKHTYKHELEQSKQNYACVGISCYNNSSGFSDLFG 151
                   E  FL++HSKAEIVDMLRKHTY  EL Q  +    +G               
Sbjct: 123 PGAAASAAELAFLAAHSKAEIVDMLRKHTYADELRQGLRRGRGMGARA------------ 170

Query: 152 SNCFQETPV---EFLFEKVLTPSDVGKLNRMVIPKQQAEKHFAL---------SSEIASK 199
               Q TP    E LFEK +TPSDVGKLNR+V+PKQ AEKHF L         S+    K
Sbjct: 171 ----QPTPSWAREPLFEKAVTPSDVGKLNRLVVPKQHAEKHFPLRRAASSDSASAAATGK 226

Query: 200 GLLLNFEDSTQKVWRLRYCYWSSSQSYVLTKGWSRFVKEKGVKAGDTVSFWRSNVGSNSK 259
           G+LLNFED   KVWR RY YW+SSQSYVLTKGWSRFV+EKG++AGDT+ F RS  G +  
Sbjct: 227 GVLLNFEDGEGKVWRFRYSYWNSSQSYVLTKGWSRFVREKGLRAGDTIVFSRSAYGPDKL 286

Query: 260 LFIDCK----LQQNGNGSGFEEMQSQVPNIGVVRLFGVNI 295
           LFIDCK           +G E   +      VVRLFGV+I
Sbjct: 287 LFIDCKKNNAAAATTTCAGDERPTTSGAEPRVVRLFGVDI 326

Oryza sativa subsp. japonica (taxid: 39947)

>sp|Q9C6P5|RAVL2_ARATH AP2/ERF and B3 domain-containing transcription factor At1g50680 OS=Arabidopsis thaliana GN=At1g50680 PE=2 SV=1

 Score =  169 bits (428), Expect = 2e-41,   Method: Compositional matrix adjust.
 Identities = 98/245 (40%), Positives = 138/245 (56%), Gaps = 25/245 (10%)

Query: 32  KYKGVVPQPNGRWGAQIYEKHQRVWLGTFIEEEEAARVYDTAALRFRG--QNAITNFRTS 89
           KYKGVV Q NG WGAQIY  H+R+WLGTF   +EAA  YD+A+++ R    N+  NF  S
Sbjct: 27  KYKGVVQQQNGHWGAQIYADHKRIWLGTFKSADEAATAYDSASIKLRSFDANSHRNFPWS 86

Query: 90  LETDDEDDYMEKIFLSSHSKAEIVDMLRKHTYKHE----LEQSKQNYACVGISCYNNSSG 145
             T +E D     F + ++   +++M+R  +Y+H+    L    Q  A + I     + G
Sbjct: 87  TITLNEPD-----FQNCYTTETVLNMIRDGSYQHKFRDFLRIRSQIVASINIGGPKQARG 141

Query: 146 FSDLFGSNCFQETPVEFLFEKVLTPSDVGKLNRMVIPKQQAEKHFALSSEIAS------- 198
             +     CF  T    LF+K LTPSDVGKLNR+VIPK+ A K+    S   S       
Sbjct: 142 EVNQESDKCFSCTQ---LFQKELTPSDVGKLNRLVIPKKYAVKYMPFISADQSEKEEGEI 198

Query: 199 ----KGLLLNFEDSTQKVWRLRYCYWSSSQSYVLTKGWSRFVKEKGVKAGDTVSFWRSNV 254
               + + + F D   + W+ RYCYW SSQS+V T+GW+ FVKEK +K  D ++F+  +V
Sbjct: 199 VGSVEDVEVVFYDRAMRQWKFRYCYWKSSQSFVFTRGWNSFVKEKNLKEKDVIAFYTCDV 258

Query: 255 GSNSK 259
            +N K
Sbjct: 259 PNNVK 263

Probably acts as a transcriptional activator. Binds to the GCC-box pathogenesis-related promoter element. May be involved in the regulation of gene expression by stress factors and by components of stress signal transduction pathways.

Arabidopsis thaliana (taxid: 3702)

>sp|Q9C688|RAVL3_ARATH AP2/ERF and B3 domain-containing transcription factor At1g51120 OS=Arabidopsis thaliana GN=At1g51120 PE=2 SV=1

 Score =  160 bits (405), Expect = 1e-38,   Method: Compositional matrix adjust.
 Identities = 108/285 (37%), Positives = 151/285 (52%), Gaps = 41/285 (14%)

Query: 30  SSKYKGVVPQPNGRWGAQIYEKHQRVWLGTFIEEEEAARVYDTAALRFRG--QNAITNFR 87
           ++K+KGVV Q NG WGAQIY  H+R+WLGTF    EAA  YD+A+++ R    N+  NF 
Sbjct: 44  TTKFKGVVQQQNGHWGAQIYADHRRIWLGTFKSAHEAAAAYDSASIKLRSFDANSHRNFP 103

Query: 88  TSLETDDEDDYMEKIFLSSHSKAEIVDMLRKHTYKHELE-------QSKQNYACVGISCY 140
            S  T  E D+ E      ++   +++M+R  +Y+H+         Q   N   VG S  
Sbjct: 104 WSDFTLHEPDFQE-----CYTTEAVLNMIRDGSYQHKFRDFLRIRSQIVANINIVG-SKQ 157

Query: 141 NNSSGFSDLFGSNCFQETPVEFLFEKVLTPSDVGKLNRMVIPKQQAEKHFALSSEIAS-- 198
               G      + CF  T    LF+K LTPSDVGKLNR+VIPK+ A K+    S+  S  
Sbjct: 158 VLGGGEGGQESNKCFSCTQ---LFQKELTPSDVGKLNRLVIPKKYAVKYMPFISDDQSEK 214

Query: 199 ------KGLLLNFEDSTQKVWRLRYCYWSSSQSYVLTKGWSRFVKEKGVKAGDTVSFWRS 252
                 + + + F D   + W+ RYCYW SSQS+V T+GW+ FVKEK +K  D + F+  
Sbjct: 215 ETSEGVEDVEVVFYDRAMRQWKFRYCYWRSSQSFVFTRGWNGFVKEKNLKEKDIIVFYTC 274

Query: 253 NVGSNSK---------LFIDCKLQQNGNGSGF---EEMQSQVPNI 285
           +V +N K         L ID     + +G+GF   EE+   V  I
Sbjct: 275 DVPNNVKTLEGQSKTFLMIDV---HHFSGNGFVVPEEVNKTVHEI 316

Probably acts as a transcriptional activator. Binds to the GCC-box pathogenesis-related promoter element. May be involved in the regulation of gene expression by stress factors and by components of stress signal transduction pathways.

Arabidopsis thaliana (taxid: 3702)

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	305
164458456	395	RAV2 [Solanum lycopersicum]	0.911	0.703	0.632	3e-93
58982624	399	RAV transcription factor [Capsicum annuu	0.967	0.739	0.596	2e-92
33320073	386	DNA binding protein Rav [Capsicum annuum	0.967	0.764	0.596	3e-92
225423895	358	PREDICTED: AP2/ERF and B3 domain-contain	0.924	0.787	0.611	9e-92
147782990	364	hypothetical protein VITISV_032171 [Viti	0.924	0.774	0.611	1e-91
253560642	362	RAV transcription factor [Camellia sinen	0.891	0.751	0.612	4e-90
292668949	406	AP2 domain class transcription factor [M	0.957	0.719	0.586	1e-89
383932346	357	RAV [Gossypium hirsutum]	0.885	0.756	0.622	1e-89
449434658	344	PREDICTED: AP2/ERF and B3 domain-contain	0.954	0.845	0.588	6e-89
224099325	369	AP2 domain-containing transcription fact	0.895	0.739	0.622	7e-89

>gi|164458456|gb|ABY57635.1| RAV2 [Solanum lycopersicum]

 Score =  347 bits (890), Expect = 3e-93,   Method: Compositional matrix adjust.
 Identities = 186/294 (63%), Positives = 213/294 (72%), Gaps = 16/294 (5%)

Query: 17  SENGIDAESKKLPSSKYKGVVPQPNGRWGAQIYEKHQRVWLGTFIEEEEAARVYDTAALR 76
           +ENG++AESKKLPSS+YKGVVPQPNGRWGAQIYEKHQRVWLGTF EE EAAR YD AA R
Sbjct: 57  AENGVEAESKKLPSSRYKGVVPQPNGRWGAQIYEKHQRVWLGTFNEENEAARAYDIAAQR 116

Query: 77  FRGQNAITNFRTSLETDDEDDYMEKIFLSSHSKAEIVDMLRKHTYKHELEQSKQNYACVG 136
           FRG++A+TNF+  LE  + DD ME  FL+SHSKAEIVD+LRKHTY  ELEQSK+ +    
Sbjct: 117 FRGRDAVTNFKPLLENQESDD-MEIAFLNSHSKAEIVDVLRKHTYIDELEQSKRLFGFTK 175

Query: 137 ISCYNNSSGF--SDLFGS-----NCFQETPVEFLFEKVLTPSDVGKLNRMVIPKQQAEKH 189
                   G   S  FGS     NC      E LFEKV+TPSDVGKLNR+VIPKQ AEKH
Sbjct: 176 DGMIKRKDGLVISSFFGSTNDKVNC---KAREQLFEKVVTPSDVGKLNRLVIPKQHAEKH 232

Query: 190 FALSSEIASKGLLLNFEDSTQKVWRLRYCYWSSSQSYVLTKGWSRFVKEKGVKAGDTVSF 249
           F L +   SKG+LLNFED   KVWR RY YW+SSQSYVLTKGWSRFVKEK +KAGD VSF
Sbjct: 233 FPLQNGNNSKGVLLNFEDLNGKVWRFRYSYWNSSQSYVLTKGWSRFVKEKNLKAGDIVSF 292

Query: 250 WRSNVGSNSKLFIDCKLQQNGNGSGF----EEMQSQVPNIGVVRLFGVNILEDP 299
            RS  G + +L+ID K +  GN S       + Q QVP + +VRLFGVNI + P
Sbjct: 293 QRSTSG-DKQLYIDFKAKNVGNTSMVVTNQVQAQVQVPLVQMVRLFGVNICKVP 345

Source: Solanum lycopersicum

Species: Solanum lycopersicum

Genus: Solanum

Family: Solanaceae

Order: Solanales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|58982624|gb|AAW83473.1| RAV transcription factor [Capsicum annuum]

 Score =  345 bits (885), Expect = 2e-92,   Method: Compositional matrix adjust.
 Identities = 188/315 (59%), Positives = 221/315 (70%), Gaps = 20/315 (6%)

Query: 1   MASNSSSVDLDHDHNLSENGIDAESKKLPSSKYKGVVPQPNGRWGAQIYEKHQRVWLGTF 60
           M S +SSV +D      ENG++AES+KLPSSKYKGVVPQPNGRWGAQIYEKHQRVWLGTF
Sbjct: 47  MGSGTSSVIID-----GENGVEAESRKLPSSKYKGVVPQPNGRWGAQIYEKHQRVWLGTF 101

Query: 61  IEEEEAARVYDTAALRFRGQNAITNFRTSLETDDEDDYMEKIFLSSHSKAEIVDMLRKHT 120
            EE EAAR YD AA RFRG++A+TNF+  LE  + DD +E  FL+SHSKAEIVDMLRKHT
Sbjct: 102 NEENEAARAYDVAAQRFRGRDAVTNFKPLLENQESDDDVEIAFLNSHSKAEIVDMLRKHT 161

Query: 121 YKHELEQSKQ--NYACVGISCYNNSSGFSDL---FGS----NCFQETPVEFLFEKVLTPS 171
           Y  ELEQSK+   Y   G +   N  G  D+   FG     +       E LFEK +TPS
Sbjct: 162 YIDELEQSKKLFGYTKDG-TMAKNKDGLIDISSFFGGGGTIDKVNNKVREQLFEKAVTPS 220

Query: 172 DVGKLNRMVIPKQQAEKHFALSSEIASKGLLLNFEDSTQKVWRLRYCYWSSSQSYVLTKG 231
           DVGKLNR+VIPKQ AEKHF L +   SKG+LLNFED   KVWR RY YW+SSQSYVLTKG
Sbjct: 221 DVGKLNRLVIPKQHAEKHFPLQNGNNSKGVLLNFEDLNGKVWRFRYSYWNSSQSYVLTKG 280

Query: 232 WSRFVKEKGVKAGDTVSFWRSNVGSNSKLFIDCKLQQ----NGNGSGFEEMQSQVPNIGV 287
           WSRFVKEK +KAGD VSF RS  G + +L+ID K +     N   +   + Q QVP + +
Sbjct: 281 WSRFVKEKNLKAGDIVSFQRSTSG-DKQLYIDFKARNMAPTNPVVTNQVQAQVQVPRVQM 339

Query: 288 VRLFGVNILEDPNNL 302
           +RLFGVNI + P  +
Sbjct: 340 MRLFGVNICKIPATI 354

Source: Capsicum annuum

Species: Capsicum annuum

Genus: Capsicum

Family: Solanaceae

Order: Solanales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|33320073|gb|AAQ05799.1|AF478458_1 DNA binding protein Rav [Capsicum annuum]

 Score =  344 bits (882), Expect = 3e-92,   Method: Compositional matrix adjust.
 Identities = 188/315 (59%), Positives = 221/315 (70%), Gaps = 20/315 (6%)

Query: 1   MASNSSSVDLDHDHNLSENGIDAESKKLPSSKYKGVVPQPNGRWGAQIYEKHQRVWLGTF 60
           M S +SSV +D      ENG++AES+KLPSSKYKGVVPQPNGRWGAQIYEKHQRVWLGTF
Sbjct: 34  MGSGTSSVIID-----GENGVEAESRKLPSSKYKGVVPQPNGRWGAQIYEKHQRVWLGTF 88

Query: 61  IEEEEAARVYDTAALRFRGQNAITNFRTSLETDDEDDYMEKIFLSSHSKAEIVDMLRKHT 120
            EE EAAR YD AA RFRG++A+TNF+  LE  + DD +E  FL+SHSKAEIVDMLRKHT
Sbjct: 89  NEENEAARAYDVAAQRFRGRDAVTNFKPLLENQESDDDVEIAFLNSHSKAEIVDMLRKHT 148

Query: 121 YKHELEQSKQ--NYACVGISCYNNSSGFSDL---FGS----NCFQETPVEFLFEKVLTPS 171
           Y  ELEQSK+   Y   G +   N  G  D+   FG     +       E LFEK +TPS
Sbjct: 149 YIDELEQSKKLFGYTKDG-TMAKNKDGLIDISSFFGGGGTIDKVNNKVREQLFEKAVTPS 207

Query: 172 DVGKLNRMVIPKQQAEKHFALSSEIASKGLLLNFEDSTQKVWRLRYCYWSSSQSYVLTKG 231
           DVGKLNR+VIPKQ AEKHF L +   SKG+LLNFED   KVWR RY YW+SSQSYVLTKG
Sbjct: 208 DVGKLNRLVIPKQHAEKHFPLQNGNNSKGVLLNFEDLNGKVWRFRYSYWNSSQSYVLTKG 267

Query: 232 WSRFVKEKGVKAGDTVSFWRSNVGSNSKLFIDCKLQQ----NGNGSGFEEMQSQVPNIGV 287
           WSRFVKEK +KAGD VSF RS  G + +L+ID K +     N   +   + Q QVP + +
Sbjct: 268 WSRFVKEKNLKAGDIVSFQRSTSG-DKQLYIDFKARNMAPTNPVVTNQVQAQVQVPRVQM 326

Query: 288 VRLFGVNILEDPNNL 302
           +RLFGVNI + P  +
Sbjct: 327 MRLFGVNICKIPATI 341

Source: Capsicum annuum

Species: Capsicum annuum

Genus: Capsicum

Family: Solanaceae

Order: Solanales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225423895|ref|XP_002281709.1| PREDICTED: AP2/ERF and B3 domain-containing transcription repressor TEM1-like [Vitis vinifera]

 Score =  342 bits (878), Expect = 9e-92,   Method: Compositional matrix adjust.
 Identities = 181/296 (61%), Positives = 218/296 (73%), Gaps = 14/296 (4%)

Query: 6   SSVDLDHDHNLSENGIDAESKKLPSSKYKGVVPQPNGRWGAQIYEKHQRVWLGTFIEEEE 65
           +SV LD     SE+ I+AES+KLPSS++KGVVPQPNGRWGAQIYEKHQRVWLGTF EEEE
Sbjct: 41  TSVILD-----SESSIEAESRKLPSSRFKGVVPQPNGRWGAQIYEKHQRVWLGTFNEEEE 95

Query: 66  AARVYDTAALRFRGQNAITNFRTSLETDDEDDYMEKIFLSSHSKAEIVDMLRKHTYKHEL 125
           AA+ YD AA RFRG++A+TNF+   ET+++D  +E  FL+SHSKAEIVDMLRKHTY  EL
Sbjct: 96  AAKAYDIAAQRFRGRDAVTNFKPLSETEEDD--IEAAFLNSHSKAEIVDMLRKHTYNDEL 153

Query: 126 EQSKQNYACVGISCYNNSSGFSDLFGSNCFQETPVEFLFEKVLTPSDVGKLNRMVIPKQQ 185
           EQSK+NY        + + G    FGS+   ++  E LFEK +TPSDVGKLNR+VIPKQ 
Sbjct: 154 EQSKRNYGLDANGKRSRAEGLMTPFGSDRVTKS-REQLFEKTVTPSDVGKLNRLVIPKQH 212

Query: 186 AEKHFALSSEIASKGLLLNFEDSTQKVWRLRYCYWSSSQSYVLTKGWSRFVKEKGVKAGD 245
           AEKHF L +   SKG+LLNFED   KVWR RY YW+SSQSYVLTKGWSRFVKEK +KAGD
Sbjct: 213 AEKHFPLQTGTTSKGVLLNFEDMGGKVWRFRYSYWNSSQSYVLTKGWSRFVKEKNLKAGD 272

Query: 246 TVSFWRSNVGSNSKLFIDCKLQQNGNGSGFEEMQSQVPNIGVVRLFGVNILEDPNN 301
            VSF RS  G + +L+ID K +     +G     + V  + +VRLFGVNI + P N
Sbjct: 273 IVSFQRS-TGGDKQLYIDWKAR-----NGPTNQINPVEPVEMVRLFGVNIFKVPVN 322

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147782990|emb|CAN68564.1| hypothetical protein VITISV_032171 [Vitis vinifera]

 Score =  342 bits (877), Expect = 1e-91,   Method: Compositional matrix adjust.
 Identities = 181/296 (61%), Positives = 218/296 (73%), Gaps = 14/296 (4%)

Query: 6   SSVDLDHDHNLSENGIDAESKKLPSSKYKGVVPQPNGRWGAQIYEKHQRVWLGTFIEEEE 65
           +SV LD     SE+ I+AES+KLPSS++KGVVPQPNGRWGAQIYEKHQRVWLGTF EEEE
Sbjct: 41  TSVILD-----SESSIEAESRKLPSSRFKGVVPQPNGRWGAQIYEKHQRVWLGTFNEEEE 95

Query: 66  AARVYDTAALRFRGQNAITNFRTSLETDDEDDYMEKIFLSSHSKAEIVDMLRKHTYKHEL 125
           AA+ YD AA RFRG++A+TNF+   ET+++D  +E  FL+SHSKAEIVDMLRKHTY  EL
Sbjct: 96  AAKAYDIAAQRFRGRDAVTNFKPLSETEEDD--IEAAFLNSHSKAEIVDMLRKHTYNDEL 153

Query: 126 EQSKQNYACVGISCYNNSSGFSDLFGSNCFQETPVEFLFEKVLTPSDVGKLNRMVIPKQQ 185
           EQSK+NY        + + G    FGS+   ++  E LFEK +TPSDVGKLNR+VIPKQ 
Sbjct: 154 EQSKRNYGLDANGKRSRAEGLMTPFGSDRVTKS-REQLFEKTVTPSDVGKLNRLVIPKQH 212

Query: 186 AEKHFALSSEIASKGLLLNFEDSTQKVWRLRYCYWSSSQSYVLTKGWSRFVKEKGVKAGD 245
           AEKHF L +   SKG+LLNFED   KVWR RY YW+SSQSYVLTKGWSRFVKEK +KAGD
Sbjct: 213 AEKHFPLQTGTTSKGVLLNFEDMGGKVWRFRYSYWNSSQSYVLTKGWSRFVKEKNLKAGD 272

Query: 246 TVSFWRSNVGSNSKLFIDCKLQQNGNGSGFEEMQSQVPNIGVVRLFGVNILEDPNN 301
            VSF RS  G + +L+ID K +     +G     + V  + +VRLFGVNI + P N
Sbjct: 273 IVSFQRS-TGGDKQLYIDWKAR-----NGPTNQINPVEPVEMVRLFGVNIFKVPVN 322

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|253560642|gb|ACT33043.1| RAV transcription factor [Camellia sinensis]

 Score =  337 bits (864), Expect = 4e-90,   Method: Compositional matrix adjust.
 Identities = 174/284 (61%), Positives = 212/284 (74%), Gaps = 12/284 (4%)

Query: 18  ENGIDAESKKLPSSKYKGVVPQPNGRWGAQIYEKHQRVWLGTFIEEEEAARVYDTAALRF 77
           E G +AES+KLPSS++KGVVPQPNGRWGAQIYEKHQRVWLGTF EE+EAAR YD AA RF
Sbjct: 55  EGGAEAESRKLPSSRFKGVVPQPNGRWGAQIYEKHQRVWLGTFNEEDEAARAYDIAAQRF 114

Query: 78  RGQNAITNFRTSLETDDEDDYMEKIFLSSHSKAEIVDMLRKHTYKHELEQSKQNYACVGI 137
           RG++A+TNF+  L  ++E D +E +FL+SHSK+EIVDMLRKHTY  E EQS++NY    I
Sbjct: 115 RGRDAVTNFK-PLSENEEQDELETLFLNSHSKSEIVDMLRKHTYNDEPEQSRKNYIGGFI 173

Query: 138 SCYNNSSGFSDLFGSNCFQET--PVEFLFEKVLTPSDVGKLNRMVIPKQQAEKHFALSSE 195
           +   N     +   +  ++      E LFEK +TPSDVGKLNR+VIPKQ AEKHF L SE
Sbjct: 174 NNNGNKKACCNEKSTTNYKNNVKATEQLFEKAVTPSDVGKLNRLVIPKQHAEKHFPLQSE 233

Query: 196 IASKGLLLNFEDSTQKVWRLRYCYWSSSQSYVLTKGWSRFVKEKGVKAGDTVSFWRSNVG 255
             SKG+LLNF+D   KVWR RY YW+SSQSYVLTKGWSRFVKEK +KAGD VSF+RS  G
Sbjct: 234 TTSKGVLLNFKDVAGKVWRFRYSYWNSSQSYVLTKGWSRFVKEKSLKAGDIVSFYRS-TG 292

Query: 256 SNSKLFIDCKLQQNGNGSGFEEMQSQVPNIGVVRLFGVNILEDP 299
           S+++LFID K  +NG+    + +Q       +VRLFGVNI + P
Sbjct: 293 SDNQLFIDWK-PRNGSNPVVQPVQ-------MVRLFGVNIFKVP 328

Source: Camellia sinensis

Species: Camellia sinensis

Genus: Camellia

Family: Theaceae

Order: Ericales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|292668949|gb|ADE41129.1| AP2 domain class transcription factor [Malus x domestica]

 Score =  335 bits (859), Expect = 1e-89,   Method: Compositional matrix adjust.
 Identities = 189/322 (58%), Positives = 223/322 (69%), Gaps = 30/322 (9%)

Query: 1   MASNSSSVDLDHDHNLS--ENGIDAESKKLPSSKYKGVVPQPNGRWGAQIYEKHQRVWLG 58
           + S +SSV LD + + S    G++AES+KLPSS+YKGVVPQPNGRWGAQIYEKHQRVWLG
Sbjct: 44  IGSGASSVILDPELSSSGGTGGVEAESRKLPSSRYKGVVPQPNGRWGAQIYEKHQRVWLG 103

Query: 59  TFIEEEEAARVYDTAALRFRGQNAITNFRTS----LETDDED-DYMEKIFLSSHSKAEIV 113
           TF EE+EAAR YD AA RFRG++A+TNF+ S    + +DDE+ D  E  FLS HSK+EIV
Sbjct: 104 TFNEEDEAARAYDVAAQRFRGRDAVTNFKPSSAEPISSDDEENDDAEAAFLSCHSKSEIV 163

Query: 114 DMLRKHTYKHELEQSKQNYACVGISCYNNSSGFSDLFGS-NCFQETPVEFLFEKVLTPSD 172
           DMLRKHTY  ELEQSK+N +  G    +N  G   LFG+ N       E LFEK +TPSD
Sbjct: 164 DMLRKHTYNDELEQSKRNNSAYGKRSRSN--GSLGLFGTDNSGVPKAREQLFEKAVTPSD 221

Query: 173 VGKLNRMVIPKQQAEKHFAL----------SSEIASKGLLLNFEDSTQKVWRLRYCYWSS 222
           VGKLNR+VIPKQ AEKHF L          S+  A KG+LLNFED   KVWR RY YW+S
Sbjct: 222 VGKLNRLVIPKQHAEKHFPLQSGSAATLTVSASTACKGVLLNFEDVGGKVWRFRYSYWNS 281

Query: 223 SQSYVLTKGWSRFVKEKGVKAGDTVSFWRSNVGSNSKLFIDCKLQQ-----NGNGSGFEE 277
           SQSYVLTKGWSRFVKEK + AGD VSF RS  G + +L+ID K +      N NGS    
Sbjct: 282 SQSYVLTKGWSRFVKEKNLMAGDIVSFQRS-TGPDKQLYIDWKARMSVNNTNNNGSS--- 337

Query: 278 MQSQVPNIGVVRLFGVNILEDP 299
              QV  + +VRLFGVNI + P
Sbjct: 338 -PVQVGPVPMVRLFGVNIFKIP 358

Source: Malus x domestica

Species: Malus x domestica

Genus: Malus

Family: Rosaceae

Order: Rosales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|383932346|gb|AFH57270.1| RAV [Gossypium hirsutum]

 Score =  335 bits (859), Expect = 1e-89,   Method: Compositional matrix adjust.
 Identities = 180/289 (62%), Positives = 214/289 (74%), Gaps = 19/289 (6%)

Query: 17  SENGIDAESKKLPSSKYKGVVPQPNGRWGAQIYEKHQRVWLGTFIEEEEAARVYDTAALR 76
           SE+G++AES+KLPSSKYKGVVPQPNGRWGAQIYEKHQRVWLGTF EE+EAA+ YD AA R
Sbjct: 50  SESGVEAESRKLPSSKYKGVVPQPNGRWGAQIYEKHQRVWLGTFNEEDEAAKAYDIAAQR 109

Query: 77  FRGQNAITNFRTSLETDDEDDYMEKIFLSSHSKAEIVDMLRKHTYKHELEQSKQNYACVG 136
           FRG++A+TNF+   E +D+D  ++  FL+SHSKAEIVDMLRKHTY  ELEQS+++Y   G
Sbjct: 110 FRGRDAVTNFKHLHEMEDDD--IQIAFLNSHSKAEIVDMLRKHTYNDELEQSRRSYGFDG 167

Query: 137 ISCYNNSSGF---SDLFGSNCFQETPVEFLFEKVLTPSDVGKLNRMVIPKQQAEKHFALS 193
                N        D FG+  F+    E LFEK +TPSDVGKLNR+VIPKQ AEK+F L 
Sbjct: 168 -----NGKRIVRKEDGFGTLGFELKAREQLFEKAVTPSDVGKLNRLVIPKQHAEKYFPLQ 222

Query: 194 SEIA-SKGLLLNFEDSTQKVWRLRYCYWSSSQSYVLTKGWSRFVKEKGVKAGDTVSFWRS 252
           S  A SKG+LLNFED T KVWR RY YW+SSQSYVL KGWSRFVKEK +KAGD VSF RS
Sbjct: 223 SGSASSKGVLLNFEDVTGKVWRFRYSYWNSSQSYVLIKGWSRFVKEKNLKAGDIVSFQRS 282

Query: 253 NVGSNSKLFIDCKLQQNGNGSGFEEMQSQVPNIGVVRLFGVNILEDPNN 301
             G+  +L+ID K  + G GSG E        + +VRLFGVNI + P +
Sbjct: 283 -TGTEKQLYIDWK-ARTGLGSGLEN------PVQMVRLFGVNIFKMPGS 323

Source: Gossypium hirsutum

Species: Gossypium hirsutum

Genus: Gossypium

Family: Malvaceae

Order: Malvales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449434658|ref|XP_004135113.1| PREDICTED: AP2/ERF and B3 domain-containing transcription repressor RAV2-like [Cucumis sativus] gi|449529138|ref|XP_004171558.1| PREDICTED: AP2/ERF and B3 domain-containing transcription repressor RAV2-like [Cucumis sativus]

 Score =  333 bits (854), Expect = 6e-89,   Method: Compositional matrix adjust.
 Identities = 180/306 (58%), Positives = 216/306 (70%), Gaps = 15/306 (4%)

Query: 1   MASNSSSVDLDHDHNLSENGIDAESKKLPSSKYKGVVPQPNGRWGAQIYEKHQRVWLGTF 60
           + S  +SV LD D   S  G++AES+KLPSS+YKGVVPQPNGRWGAQIYEKHQRVWLGTF
Sbjct: 26  VGSGVTSVVLDSDS--SGGGVEAESRKLPSSRYKGVVPQPNGRWGAQIYEKHQRVWLGTF 83

Query: 61  IEEEEAARVYDTAALRFRGQNAITNFRTSLETDDEDDYMEKIFLSSHSKAEIVDMLRKHT 120
            EE+EAAR YD AA RFRG++A+TNF+       E+D +   FL+SHSKAEIVDMLRKHT
Sbjct: 84  NEEDEAARAYDVAAQRFRGRDAVTNFKPLTHGGGEEDDIVSAFLNSHSKAEIVDMLRKHT 143

Query: 121 YKHELEQSKQNYACVGISCYNNSSGFSDLFGSNCFQETPVEFLFEKVLTPSDVGKLNRMV 180
           Y  EL QSK+N    G     N      L GS+   ET  E LFEK +TPSDVGKLNR+V
Sbjct: 144 YLDELHQSKRNAGLSGSDRKQNRF----LSGSDDDPETARELLFEKAVTPSDVGKLNRLV 199

Query: 181 IPKQQAEKHFAL--SSEIASKGLLLNFEDSTQKVWRLRYCYWSSSQSYVLTKGWSRFVKE 238
           IPKQ AEK+F L   S  +SKGLLLNFED   KVWR RY YW+SSQSYVLTKGWSRFVKE
Sbjct: 200 IPKQHAEKNFPLQTGSTASSKGLLLNFEDGGGKVWRFRYSYWNSSQSYVLTKGWSRFVKE 259

Query: 239 KGVKAGDTVSFWRSNVGSNSKLFIDCKLQQNGNGSGFEEMQSQVPNIGVVRLFGVNILE- 297
           K +KAGD VSF +S  G + +L+I+ K ++    +G     S +  +   RLFGV+I++ 
Sbjct: 260 KNLKAGDIVSFLKS-TGQDKQLYIEWKARKPSTTTG-----SAINPVQTFRLFGVDIIKV 313

Query: 298 DPNNLC 303
            PN+ C
Sbjct: 314 SPNSGC 319

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224099325|ref|XP_002311438.1| AP2 domain-containing transcription factor [Populus trichocarpa] gi|222851258|gb|EEE88805.1| AP2 domain-containing transcription factor [Populus trichocarpa]

 Score =  333 bits (853), Expect = 7e-89,   Method: Compositional matrix adjust.
 Identities = 180/289 (62%), Positives = 213/289 (73%), Gaps = 16/289 (5%)

Query: 18  ENGIDAESKKLPSSKYKGVVPQPNGRWGAQIYEKHQRVWLGTFIEEEEAARVYDTAALRF 77
           E G++AES+KLPSSKYKGVVPQPNGRWGAQIYEKHQRVWLGTF EE+EAAR YDTAA RF
Sbjct: 56  ELGVEAESRKLPSSKYKGVVPQPNGRWGAQIYEKHQRVWLGTFNEEDEAARAYDTAAQRF 115

Query: 78  RGQNAITNFRTSLETDDEDDYMEKIFLSSHSKAEIVDMLRKHTYKHELEQSKQNYAC--- 134
           RG++A+TNF+   ET  EDD +E  FL +HSKAEIVDMLRKHTY  ELEQSK+N      
Sbjct: 116 RGRDAVTNFKQVNET--EDDEIEAAFLITHSKAEIVDMLRKHTYSDELEQSKRNQRSNNG 173

Query: 135 VGISCYNNSSGF-SDLFGSNCFQETPV-EFLFEKVLTPSDVGKLNRMVIPKQQAEKHFAL 192
           V    Y N++ + S+ +   C +     E LFEK +TPSDVGKLNR+VIPKQ AEKHF L
Sbjct: 174 VNGKQYKNTANYESNSYDHGCGRVLKAREQLFEKAVTPSDVGKLNRLVIPKQHAEKHFPL 233

Query: 193 --SSEIASKGLLLNFEDSTQKVWRLRYCYWSSSQSYVLTKGWSRFVKEKGVKAGDTVSFW 250
             +S  ++KG+LLN ED + KVWR RY YW+SSQSYVLTKGWSRFVKEK +KAGD V F 
Sbjct: 234 QSTSSCSTKGVLLNLEDMSGKVWRFRYSYWNSSQSYVLTKGWSRFVKEKSLKAGDIVCFQ 293

Query: 251 RSNVGSNSKLFIDCKLQQNGNGSGFEEMQSQVPNIGVVRLFGVNILEDP 299
           RS  G + +L+ID K +     SG  ++Q   P I +VRLFGVNI   P
Sbjct: 294 RS-TGPDKQLYIDWKAR-----SGSNQVQPVQP-IQMVRLFGVNIFNVP 335

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

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	305
TAIR|locus:2205319	344	RAV1 "related to ABI3/VP1 1" [	0.881	0.781	0.603	2.6e-79
TAIR|locus:2012438	352	RAV2 "related to ABI3/VP1 2" [	0.891	0.772	0.585	5.4e-79
TAIR|locus:2031185	361	TEM1 "TEMPRANILLO 1" [Arabidop	0.898	0.759	0.549	1.9e-76
TAIR|locus:2085969	333	EDF3 "ethylene response DNA bi	0.819	0.750	0.592	5.1e-74
TAIR|locus:2015832	337	AT1G50680 [Arabidopsis thalian	0.721	0.652	0.404	2.6e-40
TAIR|locus:2026058	352	AT1G51120 [Arabidopsis thalian	0.727	0.630	0.402	3.4e-38
TAIR|locus:2041404	310	NGA1 "NGATHA1" [Arabidopsis th	0.337	0.332	0.666	1.4e-32
TAIR|locus:2039165	244	ABS2 "ABNORMAL SHOOT 2" [Arabi	0.390	0.487	0.552	2.6e-32
TAIR|locus:2200950	358	NGA3 "NGATHA3" [Arabidopsis th	0.459	0.391	0.5	1.6e-31
TAIR|locus:2164215	282	DPA4 "DEVELOPMENT-RELATED PcG	0.396	0.429	0.537	2.3e-31

TAIR|locus:2205319 RAV1 "related to ABI3/VP1 1" [Arabidopsis thaliana (taxid:3702)]

 Score = 797 (285.6 bits), Expect = 2.6e-79, P = 2.6e-79
 Identities = 178/295 (60%), Positives = 212/295 (71%)

Query:     4 NSSSVDLDHDHNLSENGIDAESKKLPSSKYKGVVPQPNGRWGAQIYEKHQRVWLGTFIEE 63
             + SSV LD     SENG++AES+KLPSSKYKGVVPQPNGRWGAQIYEKHQRVWLGTF EE
Sbjct:    38 SGSSVVLD-----SENGVEAESRKLPSSKYKGVVPQPNGRWGAQIYEKHQRVWLGTFNEE 92

Query:    64 EEAARVYDTAALRFRGQNAITNFRTSLETDDEDDYMEKIFLSSHSKAEIVDMLRKHTYKH 123
             +EAAR YD A  RFR ++A+TNF+     +DE D     FL+SHSK+EIVDMLRKHTY  
Sbjct:    93 DEAARAYDVAVHRFRRRDAVTNFKDVKMDEDEVD-----FLNSHSKSEIVDMLRKHTYNE 147

Query:   124 ELEQSKQNYACVG-ISCYNNSSGFS-DLFGSNCFQETPVEFLFEKVLTPSDVGKLNRMVI 181
             ELEQSK+     G ++    +SG S D   +  F+    E LFEK +TPSDVGKLNR+VI
Sbjct:   148 ELEQSKRRRNGNGNMTRTLLTSGLSNDGVSTTGFRSA--EALFEKAVTPSDVGKLNRLVI 205

Query:   182 PKQQAEKHFAL-SSEIASKGLLLNFEDSTQKVWRLRYCYWSSSQSYVLTKGWSRFVKEKG 240
             PK  AEKHF L SS ++ KG+LLNFED   KVWR RY YW+SSQSYVLTKGWSRFVKEK 
Sbjct:   206 PKHHAEKHFPLPSSNVSVKGVLLNFEDVNGKVWRFRYSYWNSSQSYVLTKGWSRFVKEKN 265

Query:   241 VKAGDTVSFWRSNVGSNSKLFIDCKLQQNGNGSGFEEMQSQVPNIGVVRLFGVNI 295
             ++AGD VSF RSN G + +L+I  K +   +GS  +  +       V+RLFGVNI
Sbjct:   266 LRAGDVVSFSRSN-GQDQQLYIGWKSR---SGSDLDAGR-------VLRLFGVNI 309

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

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

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

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

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

GO:0009910 "negative regulation of flower development" evidence=IMP

GO:0048366 "leaf development" evidence=IMP

GO:0048527 "lateral root development" evidence=IMP

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

GO:0006612 "protein targeting to membrane" evidence=RCA

GO:0009963 "positive regulation of flavonoid biosynthetic process" evidence=RCA

GO:0010363 "regulation of plant-type hypersensitive response" evidence=RCA

TAIR|locus:2012438 RAV2 "related to ABI3/VP1 2" [Arabidopsis thaliana (taxid:3702)]

 Score = 794 (284.6 bits), Expect = 5.4e-79, P = 5.4e-79
 Identities = 174/297 (58%), Positives = 203/297 (68%)

Query:     1 MASNSSSVDLDHDHNLSENGIDAESKKLPSSKYKGVVPQPNGRWGAQIYEKHQRVWLGTF 60
             M S  SSV LD      ENG++ ES+KLPSSKYKGVVPQPNGRWGAQIYEKHQRVWLGTF
Sbjct:    38 MGSGGSSVVLD-----PENGLETESRKLPSSKYKGVVPQPNGRWGAQIYEKHQRVWLGTF 92

Query:    61 IEEEEAARVYDTAALRFRGQNAITNFRTSLETDDEDDYMEKIFLSSHSKAEIVDMLRKHT 120
              E+EEAAR YD AA RFRG++A+ NF+  LE  D        FL +HSKAEIVDMLRKHT
Sbjct:    93 NEQEEAARSYDIAACRFRGRDAVVNFKNVLEDGD------LAFLEAHSKAEIVDMLRKHT 146

Query:   121 YKHELEQSKQNYACVGISCYNNSSGFSDLFGSNCFQETPVEFLFEKVLTPSDVGKLNRMV 180
             Y  ELEQ+ +    + +      +G S        +    E LFEK +TPSDVGKLNR+V
Sbjct:   147 YADELEQNNKRQLFLSVDANGKRNGSSTTQNDKVLKTR--EVLFEKAVTPSDVGKLNRLV 204

Query:   181 IPKQQAEKHFALSSE--IASKGLLLNFEDSTQKVWRLRYCYWSSSQSYVLTKGWSRFVKE 238
             IPKQ AEKHF L S     +KG+L+NFED   KVWR RY YW+SSQSYVLTKGWSRFVKE
Sbjct:   205 IPKQHAEKHFPLPSPSPAVTKGVLINFEDVNGKVWRFRYSYWNSSQSYVLTKGWSRFVKE 264

Query:   239 KGVKAGDTVSFWRSNVGSNSKLFIDCKLQQNGNGSGFEEMQSQVPNIGVVRLFGVNI 295
             K ++AGD V+F RS  G   +L+ID K++     SG  E   QV    VVRLFGV+I
Sbjct:   265 KNLRAGDVVTFERST-GLERQLYIDWKVR-----SGPRENPVQV----VVRLFGVDI 311

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

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

GO:0005634 "nucleus" evidence=ISM

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

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

GO:0010167 "response to nitrate" evidence=RCA

GO:0010200 "response to chitin" evidence=RCA

GO:0015706 "nitrate transport" evidence=RCA

TAIR|locus:2031185 TEM1 "TEMPRANILLO 1" [Arabidopsis thaliana (taxid:3702)]

 Score = 770 (276.1 bits), Expect = 1.9e-76, P = 1.9e-76
 Identities = 173/315 (54%), Positives = 213/315 (67%)

Query:     1 MASNSSSVDLDHDHNLSENGIDAESKKLPSSKYKGVVPQPNGRWGAQIYEKHQRVWLGTF 60
             M S  SSV LD     SENG++ ES+KLPSSKYKGVVPQPNGRWGAQIYEKHQRVWLGTF
Sbjct:    45 MGSGGSSVVLD-----SENGVETESRKLPSSKYKGVVPQPNGRWGAQIYEKHQRVWLGTF 99

Query:    61 IEEEEAARVYDTAALRFRGQNAITNFRTSLETDDEDDYMEKIFLSSHSKAEIVDMLRKHT 120
              EEEEAA  YD A  RFRG++A+TNF++ ++ +D     E  FL +HSKAEIVDMLRKHT
Sbjct:   100 NEEEEAASSYDIAVRRFRGRDAVTNFKSQVDGNDA----ESAFLDAHSKAEIVDMLRKHT 155

Query:   121 YKHELEQSKQNYACVGISCYNNSSGFSDL-FGSNCFQETPVEFLFEKVLTPSDVGKLNRM 179
             Y  E EQS++ +    ++     SG     +G++       E LFEK +TPSDVGKLNR+
Sbjct:   156 YADEFEQSRRKF----VNGDGKRSGLETATYGNDAVLRAR-EVLFEKTVTPSDVGKLNRL 210

Query:   180 VIPKQQAEKHF---ALSSEIA-----SKGLLLNFEDSTQKVWRLRYCYWSSSQSYVLTKG 231
             VIPKQ AEKHF   A+++ +      +KG+L+N ED T KVWR RY YW+SSQSYVLTKG
Sbjct:   211 VIPKQHAEKHFPLPAMTTAMGMNPSPTKGVLINLEDRTGKVWRFRYSYWNSSQSYVLTKG 270

Query:   232 WSRFVKEKGVKAGDTVSFWRSNVGSNSKLFIDCKLQQNGNGSGFEEMQSQVPNIGVVRLF 291
             WSRFVKEK ++AGD V F RS  G + +L+I  K++ +             P   VVRLF
Sbjct:   271 WSRFVKEKNLRAGDVVCFERST-GPDRQLYIHWKVRSS-------------PVQTVVRLF 316

Query:   292 GVNIL----EDPNNL 302
             GVNI     E PN++
Sbjct:   317 GVNIFNVSNEKPNDV 331

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

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

GO:0005634 "nucleus" evidence=ISM

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

GO:0009873 "ethylene mediated signaling pathway" evidence=NAS

GO:0048573 "photoperiodism, flowering" evidence=IMP

GO:0030003 "cellular cation homeostasis" evidence=RCA

GO:0070838 "divalent metal ion transport" evidence=RCA

TAIR|locus:2085969 EDF3 "ethylene response DNA binding factor 3" [Arabidopsis thaliana (taxid:3702)]

 Score = 747 (268.0 bits), Expect = 5.1e-74, P = 5.1e-74
 Identities = 157/265 (59%), Positives = 196/265 (73%)

Query:     4 NSSSVDLDHDHNLSENGIDAESKKLPSSKYKGVVPQPNGRWGAQIYEKHQRVWLGTFIEE 63
             + +SV LD ++ + E  ++AES+KLPSS++KGVVPQPNGRWGAQIYEKHQRVWLGTF EE
Sbjct:    34 SGTSVVLDSENGV-EVEVEAESRKLPSSRFKGVVPQPNGRWGAQIYEKHQRVWLGTFNEE 92

Query:    64 EEAARVYDTAALRFRGQNAITNFRTSLETDDEDDYMEKIFLSSHSKAEIVDMLRKHTYKH 123
             +EAAR YD AA RFRG++A+TNF+   +T  E++ +E  FL++HSK+EIVDMLRKHTYK 
Sbjct:    93 DEAARAYDVAAHRFRGRDAVTNFK---DTTFEEE-VE--FLNAHSKSEIVDMLRKHTYKE 146

Query:   124 ELEQSKQNYACVGISCYNNSSGFSDLFGSNCFQETPVEFLFEKVLTPSDVGKLNRMVIPK 183
             EL+Q K+N    G      +   + +     F+    E LFEK +TPSDVGKLNR+VIPK
Sbjct:   147 ELDQRKRNRD--GNGKETTAFALASMVVMTGFKTA--ELLFEKTVTPSDVGKLNRLVIPK 202

Query:   184 QQAEKHFAL---SSEIASKGLLLNFEDSTQKVWRLRYCYWSSSQSYVLTKGWSRFVKEKG 240
              QAEKHF L   ++ ++ KG+LLNFED   KVWR RY YW+SSQSYVLTKGWSRFVKEK 
Sbjct:   203 HQAEKHFPLPLGNNNVSVKGMLLNFEDVNGKVWRFRYSYWNSSQSYVLTKGWSRFVKEKR 262

Query:   241 VKAGDTVSFWRSNVGSNSKLFIDCK 265
             + AGD +SF RSN   + K FI  K
Sbjct:   263 LCAGDLISFKRSN-DQDQKFFIGWK 286

GO:0003677 "DNA binding" evidence=IEA

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

GO:0005634 "nucleus" evidence=ISM

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

GO:0009691 "cytokinin biosynthetic process" evidence=RCA

TAIR|locus:2015832 AT1G50680 [Arabidopsis thaliana (taxid:3702)]

 Score = 429 (156.1 bits), Expect = 2.6e-40, P = 2.6e-40
 Identities = 99/245 (40%), Positives = 142/245 (57%)

Query:    32 KYKGVVPQPNGRWGAQIYEKHQRVWLGTFIEEEEAARVYDTAALRFRG--QNAITNFRTS 89
             KYKGVV Q NG WGAQIY  H+R+WLGTF   +EAA  YD+A+++ R    N+  NF  S
Sbjct:    27 KYKGVVQQQNGHWGAQIYADHKRIWLGTFKSADEAATAYDSASIKLRSFDANSHRNFPWS 86

Query:    90 LETDDEDDYMEKIFLSSHSKAEIVDMLRKHTYKHE----LEQSKQNYACVGISCYNNSSG 145
               T +E D     F + ++   +++M+R  +Y+H+    L    Q  A + I     + G
Sbjct:    87 TITLNEPD-----FQNCYTTETVLNMIRDGSYQHKFRDFLRIRSQIVASINIGGPKQARG 141

Query:   146 FSDLFGSNCFQETPVEFLFEKVLTPSDVGKLNRMVIPKQQAEKHFA-LSSEIASK--GLL 202
               +     CF  T    LF+K LTPSDVGKLNR+VIPK+ A K+   +S++ + K  G +
Sbjct:   142 EVNQESDKCFSCTQ---LFQKELTPSDVGKLNRLVIPKKYAVKYMPFISADQSEKEEGEI 198

Query:   203 LN--------FEDSTQKVWRLRYCYWSSSQSYVLTKGWSRFVKEKGVKAGDTVSFWRSNV 254
             +         F D   + W+ RYCYW SSQS+V T+GW+ FVKEK +K  D ++F+  +V
Sbjct:   199 VGSVEDVEVVFYDRAMRQWKFRYCYWKSSQSFVFTRGWNSFVKEKNLKEKDVIAFYTCDV 258

Query:   255 GSNSK 259
              +N K
Sbjct:   259 PNNVK 263

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

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

GO:0005634 "nucleus" evidence=ISM;ISS

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

TAIR|locus:2026058 AT1G51120 [Arabidopsis thaliana (taxid:3702)]

 Score = 409 (149.0 bits), Expect = 3.4e-38, P = 3.4e-38
 Identities = 99/246 (40%), Positives = 139/246 (56%)

Query:    30 SSKYKGVVPQPNGRWGAQIYEKHQRVWLGTFIEEEEAARVYDTAALRFRG--QNAITNFR 87
             ++K+KGVV Q NG WGAQIY  H+R+WLGTF    EAA  YD+A+++ R    N+  NF 
Sbjct:    44 TTKFKGVVQQQNGHWGAQIYADHRRIWLGTFKSAHEAAAAYDSASIKLRSFDANSHRNFP 103

Query:    88 TSLETDDEDDYMEKIFLSSHSKAEIVDMLRKHTYKHE----LEQSKQNYACVGI--SCYN 141
              S  T  E D+ E      ++   +++M+R  +Y+H+    L    Q  A + I  S   
Sbjct:   104 WSDFTLHEPDFQE-----CYTTEAVLNMIRDGSYQHKFRDFLRIRSQIVANINIVGSKQV 158

Query:   142 NSSGFSDLFGSNCFQETPVEFLFEKVLTPSDVGKLNRMVIPKQQAEKHFAL-----SSEI 196
                G      + CF  T    LF+K LTPSDVGKLNR+VIPK+ A K+        S + 
Sbjct:   159 LGGGEGGQESNKCFSCTQ---LFQKELTPSDVGKLNRLVIPKKYAVKYMPFISDDQSEKE 215

Query:   197 ASKGLL---LNFEDSTQKVWRLRYCYWSSSQSYVLTKGWSRFVKEKGVKAGDTVSFWRSN 253
              S+G+    + F D   + W+ RYCYW SSQS+V T+GW+ FVKEK +K  D + F+  +
Sbjct:   216 TSEGVEDVEVVFYDRAMRQWKFRYCYWRSSQSFVFTRGWNGFVKEKNLKEKDIIVFYTCD 275

Query:   254 VGSNSK 259
             V +N K
Sbjct:   276 VPNNVK 281

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

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

GO:0005634 "nucleus" evidence=ISM;ISS

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

TAIR|locus:2041404 NGA1 "NGATHA1" [Arabidopsis thaliana (taxid:3702)]

 Score = 356 (130.4 bits), Expect = 1.4e-32, P = 1.4e-32
 Identities = 70/105 (66%), Positives = 82/105 (78%)

Query:   161 EFLFEKVLTPSDVGKLNRMVIPKQQAEKHFALSSEIASKGLLLNFEDSTQKVWRLRYCYW 220
             E +F+KV+TPSDVGKLNR+VIPKQ AE+ F L S    KGLLLNFED T K WR RY YW
Sbjct:    32 EHMFDKVVTPSDVGKLNRLVIPKQHAERFFPLDSSSNEKGLLLNFEDLTGKSWRFRYSYW 91

Query:   221 SSSQSYVLTKGWSRFVKEKGVKAGDTVSFWR--SNVGSNSKLFID 263
             +SSQSYV+TKGWSRFVK+K + AGD VSF R   + G +S+LFID
Sbjct:    92 NSSQSYVMTKGWSRFVKDKKLDAGDIVSFQRCVGDSGRDSRLFID 136

GO:0003677 "DNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISM

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

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

GO:0009908 "flower development" evidence=IMP

GO:0048366 "leaf development" evidence=IMP

TAIR|locus:2039165 ABS2 "ABNORMAL SHOOT 2" [Arabidopsis thaliana (taxid:3702)]

 Score = 321 (118.1 bits), Expect = 2.6e-32, Sum P(2) = 2.6e-32
 Identities = 69/125 (55%), Positives = 84/125 (67%)

Query:   161 EFLFEKVLTPSDVGKLNRMVIPKQQAEKHFALSSEIAS---KGLLLNFEDSTQKVWRLRY 217
             E LFEK LTPSDVGKLNR+VIPKQ AE++F L++  A    KGLLL FED   K WR RY
Sbjct:    35 EALFEKPLTPSDVGKLNRLVIPKQHAERYFPLAAAAADAVEKGLLLCFEDEEGKPWRFRY 94

Query:   218 CYWSSSQSYVLTKGWSRFVKEKGVKAGDTVSFWRSNVGSNSKLFIDCKLQQNGNGSG--F 275
              YW+SSQSYVLTKGWSR+VKEK + AGD V F R       + FI  + + + + S   +
Sbjct:    95 SYWNSSQSYVLTKGWSRYVKEKHLDAGDVVLFHRHR-SDGGRFFIGWRRRGDSSSSSDSY 153

Query:   276 EEMQS 280
               +QS
Sbjct:   154 RHVQS 158

GO:0003677 "DNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISM

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

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

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

GO:0080167 "response to karrikin" evidence=IEP

GO:0009062 "fatty acid catabolic process" evidence=RCA

TAIR|locus:2200950 NGA3 "NGATHA3" [Arabidopsis thaliana (taxid:3702)]

 Score = 346 (126.9 bits), Expect = 1.6e-31, P = 1.6e-31
 Identities = 71/142 (50%), Positives = 93/142 (65%)

Query:   124 ELEQSKQNYACVGISCYNNSSGFSDLFGSNCFQETPVEFLFEKVLTPSDVGKLNRMVIPK 183
             E ++ ++  + +G S  +  SG ++            E +F+KV+TPSDVGKLNR+VIPK
Sbjct:    16 EQDRDQELTSNIGASSSSGPSGNNNNLPMMMIPPPEKEHMFDKVVTPSDVGKLNRLVIPK 75

Query:   184 QQAEKHFALSSEIASKGLLLNFEDSTQKVWRLRYCYWSSSQSYVLTKGWSRFVKEKGVKA 243
             Q AE++F L S     G LLNF+D   K+WR RY YW+SSQSYV+TKGWSRFVKEK + A
Sbjct:    76 QHAERYFPLDSSNNQNGTLLNFQDRNGKMWRFRYSYWNSSQSYVMTKGWSRFVKEKKLDA 135

Query:   244 GDTVSFWRS--NVGSNSKLFID 263
             GD VSF R   +    SKL+ID
Sbjct:   136 GDIVSFQRGIGDESERSKLYID 157

GO:0003677 "DNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISM

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

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

GO:0009908 "flower development" evidence=IMP

GO:0048366 "leaf development" evidence=IMP

TAIR|locus:2164215 DPA4 "DEVELOPMENT-RELATED PcG TARGET IN THE APEX 4" [Arabidopsis thaliana (taxid:3702)]

 Score = 322 (118.4 bits), Expect = 2.3e-31, Sum P(2) = 2.3e-31
 Identities = 71/132 (53%), Positives = 86/132 (65%)

Query:   161 EFLFEKVLTPSDVGKLNRMVIPKQQAEKHFALSSEIAS----------KGLLLNFEDSTQ 210
             E LFEK LTPSDVGKLNR+VIPKQ AEK+F L++ + S          KG+LL+FED + 
Sbjct:    43 ESLFEKSLTPSDVGKLNRLVIPKQHAEKYFPLNAVLVSSAAADTSSSEKGMLLSFEDESG 102

Query:   211 KVWRLRYCYWSSSQSYVLTKGWSRFVKEKGVKAGDTVSFWRSNVGSNSKLFIDCKLQQNG 270
             K WR RY YW+SSQSYVLTKGWSRFVK+K +  GD V F R    S  +LFI  + +  G
Sbjct:   103 KSWRFRYSYWNSSQSYVLTKGWSRFVKDKQLDPGDVVFFQRHRSDSR-RLFIGWRRRGQG 161

Query:   271 NGSGFEEMQSQV 282
             + S      S V
Sbjct:   162 SSSSVAATNSAV 173

GO:0003677 "DNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISM

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

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

GO:0009062 "fatty acid catabolic process" evidence=RCA

GO:0010073 "meristem maintenance" evidence=IMP

GO:0010358 "leaf shaping" evidence=IGI

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

GO:0048366 "leaf development" evidence=IGI

---

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)
Q8RZX9	Y1934_ORYSJ	No assigned EC number	0.5754	0.8852	0.6870	yes	no
P82280	RAV2_ARATH	No assigned EC number	0.5677	0.9213	0.7982	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	Length	Definition	E-value
Query	305
pfam02362	97	pfam02362, B3, B3 DNA binding domain	2e-26
cd00018	61	cd00018, AP2, DNA-binding domain found in transcri	4e-26
smart00380	64	smart00380, AP2, DNA-binding domain in plant prote	1e-25
cd10017	98	cd10017, B3_DNA, Plant-specific B3-DNA binding dom	1e-24
smart01019	96	smart01019, B3, B3 DNA binding domain	3e-21
cd10015	109	cd10015, BfiI_C_EcoRII_N_B3, DNA binding domains o	3e-09
pfam00847	53	pfam00847, AP2, AP2 domain	3e-07

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

 Score = 99.7 bits (249), Expect = 2e-26
 Identities = 37/86 (43%), Positives = 51/86 (59%), Gaps = 5/86 (5%)

Query: 164 FEKVLTPSDVGKLNRMVIPKQQAEKHFALSSEIASKGLLLNFEDSTQKVWRLRYCYWSSS 223
           F KVLTPSDV K  R+V+PK+ AE++      +  KG  +   D   K W ++  Y  S 
Sbjct: 1   FVKVLTPSDVSKDGRLVLPKKFAEENG-----LNKKGQEITLLDPDGKSWTVKLRYRKSG 55

Query: 224 QSYVLTKGWSRFVKEKGVKAGDTVSF 249
           + Y+LT GW  FVK  G+KAGD++ F
Sbjct: 56  RRYLLTSGWKEFVKANGLKAGDSLVF 81

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|237985 cd00018, AP2, DNA-binding domain found in transcription regulators in plants such as APETALA2 and EREBP (ethylene responsive element binding protein)

 Score = 97.7 bits (244), Expect = 4e-26
 Identities = 32/61 (52%), Positives = 42/61 (68%), Gaps = 2/61 (3%)

Query: 31 SKYKGVVPQPNGRWGAQIYE--KHQRVWLGTFIEEEEAARVYDTAALRFRGQNAITNFRT 88
          SKY+GV  +P G+W A+I +    +R+WLGTF   EEAAR YD AAL+ RG +A+ NF  
Sbjct: 1  SKYRGVRQRPWGKWVAEIRDPSGGRRIWLGTFDTAEEAARAYDRAALKLRGSSAVLNFPD 60

Query: 89 S 89
          S
Sbjct: 61 S 61

In EREBPs the domain specifically binds to the 11bp GCC box of the ethylene response element (ERE), a promotor element essential for ethylene responsiveness. EREBPs and the C-repeat binding factor CBF1, which is involved in stress response, contain a single copy of the AP2 domain. APETALA2-like proteins, which play a role in plant development contain two copies. Length = 61

>gnl|CDD|197689 smart00380, AP2, DNA-binding domain in plant proteins such as APETALA2 and EREBPs

 Score = 96.6 bits (241), Expect = 1e-25
 Identities = 34/62 (54%), Positives = 43/62 (69%), Gaps = 2/62 (3%)

Query: 32 KYKGVVPQPNGRWGAQIYE--KHQRVWLGTFIEEEEAARVYDTAALRFRGQNAITNFRTS 89
          KY+GV  +P G+W A+I +  K +RVWLGTF   EEAAR YD AA +FRG++A  NF  S
Sbjct: 1  KYRGVRQRPWGKWVAEIRDPSKGKRVWLGTFDTAEEAARAYDRAAFKFRGRSARLNFPNS 60

Query: 90 LE 91
          L 
Sbjct: 61 LY 62

Length = 64

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

 Score = 95.1 bits (237), Expect = 1e-24
 Identities = 38/101 (37%), Positives = 53/101 (52%), Gaps = 7/101 (6%)

Query: 162 FLFEKVLTPSDVGKLNRMVIPKQQAEKHFALSSEIASKGLLLNFEDSTQKVWRLRYCYWS 221
            LF KVLTPSDV  L R+V+PK+ A+ H         +G+ +  ED   K W ++     
Sbjct: 1   PLFFKVLTPSDVSSLGRLVLPKKFAKAHL-----PPKEGVEVTLEDPDGKKWTVKLKKRK 55

Query: 222 SSQSYVLTKGWSRFVKEKGVKAGDTVSFWRSNVGSNSKLFI 262
           +S   VL+ GW  FV+  G+K GD + F     G NSK  +
Sbjct: 56  NSGRMVLSGGWKEFVRANGLKEGDFLVFEL--DGRNSKFKV 94

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|214977 smart01019, B3, B3 DNA binding domain

 Score = 85.8 bits (213), Expect = 3e-21
 Identities = 36/102 (35%), Positives = 52/102 (50%), Gaps = 7/102 (6%)

Query: 164 FEKVLTPSDVGKLNRMVIPKQQAEKHFALSSEIASKGLLLNFEDSTQKVWRLRYCYWSSS 223
           F K LT SDV K  R+V+PKQ AE +         K   +   D   K W+++  Y  SS
Sbjct: 1   FFKTLTTSDVSKHGRLVLPKQFAESNG-----PPLKPKEITLLDPDGKSWKVKLKYRGSS 55

Query: 224 QSYVLTKGWSRFVKEKGVKAGDTVSFWRSNVGSNSKLFIDCK 265
             ++LT GW  FVK  G+KAGD+++F     G+   +    +
Sbjct: 56  GMFLLTGGWKEFVKANGLKAGDSLTFEL--DGNGEFVVSIFR 95

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

>gnl|CDD|197381 cd10015, BfiI_C_EcoRII_N_B3, DNA binding domains of BfiI, EcoRII and plant B3 proteins

 Score = 53.8 bits (129), Expect = 3e-09
 Identities = 24/98 (24%), Positives = 41/98 (41%), Gaps = 8/98 (8%)

Query: 162 FLFEKVLTPSDVGK----LNRMVIPKQQAEKHFALSSEI--ASKGLLLNFED-STQKVWR 214
            +  K L+ +D G        + IPK   EK     +    A+  + L   D S  + W 
Sbjct: 1   VVLIKRLSANDTGATGGHQVGLYIPKGIVEKFPPSINHTREANPSIFLTMHDISDCRDWE 60

Query: 215 LRYCYWSSSQSYV-LTKGWSRFVKEKGVKAGDTVSFWR 251
            R  +++S+++   LT+G   FVK+  +  GD      
Sbjct: 61  ARAIFYNSNRNEKRLTRGGRGFVKQNPLNTGDLTLIAF 98

This family contains the N-terminal DNA binding domain of type IIE restriction endonuclease EcoRII-like proteins, the C-terminal DNA binding domain of type IIS restriction endonuclease BfiI-like proteins and plant-specific B3 proteins. Type II restriction endonucleases are components of restriction modification (RM) systems that protect bacteria and archaea against invading foreign DNA. They usually function as homodimers or homotetramers that cleave DNA at defined sites of 4 to 8 bp in length, and they require Mg2+, not ATP or GTP, for catalysis. EcoRII is specific for the 5'-CCWGG sequence (W stands for A or T). EcoRII consists of 2 domains, the C-terminal catalytic/dimerization domain (EcoRII-C), and the N-terminal effector DNA binding domain (EcoRII-N). BfiI is unique in cleaving DNA at fixed positions downstream of an asymmetric sequence in the absence of Mg2+. BfiI consists of two discrete domains with distinct functions: an N-terminal catalytic domain with non-specific nuclease activity and dimerization function that is more closely related to Nuc, an EDTA-resistant nuclease from the phospholipase D (PLD) superfamily; and a C-terminal domain that specifically recognizes its target sequences, 5'-ACTGGG-3'. B3 proteins are a family of plant-specific transcription factors, involved in a great variety of processes, including seed development and auxin response. Length = 109

>gnl|CDD|216148 pfam00847, AP2, AP2 domain

 Score = 46.5 bits (111), Expect = 3e-07
 Identities = 25/54 (46%), Positives = 29/54 (53%), Gaps = 6/54 (11%)

Query: 31 SKYKGVVPQPN-GRWGAQIYE----KHQRVWLGTFIEEEEAARVYDTAALRFRG 79
          S YKGV      GRW A+I +    K +R  LGTF   EEAAR    A L+ RG
Sbjct: 1  SGYKGVRYDKRWGRWVAEIRDPGEKKKKRFSLGTF-GTEEAARAAIAARLKLRG 53

This 60 amino acid residue domain can bind to DNA and is found in transcription factor proteins. Length = 53

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	305
cd00018	61	AP2 DNA-binding domain found in transcription regu	99.8
PF02362	100	B3: B3 DNA binding domain; InterPro: IPR003340 Two	99.78
smart00380	64	AP2 DNA-binding domain in plant proteins such as A	99.77
PHA00280	121	putative NHN endonuclease	99.66
PF00847	56	AP2: AP2 domain; InterPro: IPR001471 Pathogenesis-	99.1
PF03754	114	DUF313: Domain of unknown function (DUF313) ; Inte	99.04
PF09217	156	EcoRII-N: Restriction endonuclease EcoRII, N-termi	98.28

>cd00018 AP2 DNA-binding domain found in transcription regulators in plants such as APETALA2 and EREBP (ethylene responsive element binding protein)

Probab=99.80  E-value=1e-19  Score=133.26  Aligned_cols=59  Identities=54%  Similarity=0.945  Sum_probs=56.9

Q ss_pred             CceEEeEECCCCeEEEEEEeC--CeEEeecCCCCHHHHHHHHHHHHHhccCCCCCCCCCCC
Q 021945           31 SKYKGVVPQPNGRWGAQIYEK--HQRVWLGTFIEEEEAARVYDTAALRFRGQNAITNFRTS   89 (305)
Q Consensus        31 s~yrGV~~~~~grw~A~I~~~--~k~v~LG~f~t~EeAA~AYD~Aa~~~~G~~a~~NFp~~   89 (305)
                      |+|+||+++++|+|+|+|+.+  ++++|||+|+|+||||+|||.|+++++|.++.+|||++
T Consensus         1 s~~~GV~~~~~gkw~A~I~~~~~gk~~~lG~f~t~eeAa~Ayd~a~~~~~g~~a~~Nf~~~   61 (61)
T cd00018           1 SKYRGVRQRPWGKWVAEIRDPSGGRRIWLGTFDTAEEAARAYDRAALKLRGSSAVLNFPDS   61 (61)
T ss_pred             CCccCEEECCCCcEEEEEEeCCCCceEccCCCCCHHHHHHHHHHHHHHhcCCccccCCCCC
Confidence            789999999899999999999  99999999999999999999999999999999999974

In EREBPs the domain specifically binds to the 11bp GCC box of the ethylene response element (ERE), a promotor element essential for ethylene responsiveness. EREBPs and the C-repeat binding factor CBF1, which is involved in stress response, contain a single copy of the AP2 domain. APETALA2-like proteins, which play a role in plant development contain two copies.

>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=99.78  E-value=2.1e-18  Score=136.59  Aligned_cols=99  Identities=35%  Similarity=0.553  Sum_probs=74.7

Q ss_pred             eeeecccCCCCCCceEEeeHHHHHhcCCCcccccCCCeEEEEEeCCCCEEEEEEEEeCCCCceEEeCCcchhhhhcCCCC
Q 021945          164 FEKVLTPSDVGKLNRMVIPKQQAEKHFALSSEIASKGLLLNFEDSTQKVWRLRYCYWSSSQSYVLTKGWSRFVKEKGVKA  243 (305)
Q Consensus       164 F~K~Lt~SDv~~~~rL~iPk~~ae~~fP~~~~~~~~g~~l~v~D~~Gk~W~fr~~~~~~~~~yvLt~GW~~FV~~k~Lk~  243 (305)
                      |.|+|+++|+...++|.||++++++|...    ...++.|.+.|..|+.|.+++++++.+.+++|++||..||++++|++
T Consensus         1 F~K~l~~s~~~~~~~l~iP~~f~~~~~~~----~~~~~~v~l~~~~g~~W~v~~~~~~~~~~~~l~~GW~~Fv~~n~L~~   76 (100)
T PF02362_consen    1 FFKVLKPSDVSSSCRLIIPKEFAKKHGGN----KRKSREVTLKDPDGRSWPVKLKYRKNSGRYYLTGGWKKFVRDNGLKE   76 (100)
T ss_dssp             EEEE--TTCCCCTT-EEE-HHHHTTTS------SS--CEEEEEETTTEEEEEEEEEECCTTEEEEETTHHHHHHHCT--T
T ss_pred             CEEEEEccCcCCCCEEEeCHHHHHHhCCC----cCCCeEEEEEeCCCCEEEEEEEEEccCCeEEECCCHHHHHHHcCCCC
Confidence            88999999999889999999999997211    13568999999999999999999988888999999999999999999


Q ss_pred             CCEEEEEecccCCCCeEEEEEEec
Q 021945          244 GDTVSFWRSNVGSNSKLFIDCKLQ  267 (305)
Q Consensus       244 GD~I~F~~~~~~~~~~l~i~~r~~  267 (305)
                      ||+|+|+...+ ...++.|.+.++
T Consensus        77 GD~~~F~~~~~-~~~~~~v~i~~~   99 (100)
T PF02362_consen   77 GDVCVFELIGN-SNFTLKVHIFRK   99 (100)
T ss_dssp             T-EEEEEE-SS-SCE-EEEEEE--
T ss_pred             CCEEEEEEecC-CCceEEEEEEEC
Confidence            99999999862 555557776654

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.

>smart00380 AP2 DNA-binding domain in plant proteins such as APETALA2 and EREBPs

Probab=99.77  E-value=1.1e-18  Score=129.11  Aligned_cols=60  Identities=57%  Similarity=0.943  Sum_probs=57.4

Q ss_pred             ceEEeEECCCCeEEEEEEe--CCeEEeecCCCCHHHHHHHHHHHHHhccCCCCCCCCCCCCC
Q 021945           32 KYKGVVPQPNGRWGAQIYE--KHQRVWLGTFIEEEEAARVYDTAALRFRGQNAITNFRTSLE   91 (305)
Q Consensus        32 ~yrGV~~~~~grw~A~I~~--~~k~v~LG~f~t~EeAA~AYD~Aa~~~~G~~a~~NFp~~~~   91 (305)
                      +|+||+++++|||+|+|+.  +++++|||+|+|+||||+|||.|+++++|.++.+|||.+.|
T Consensus         1 ~~kGV~~~~~gkw~A~I~~~~~~k~~~lG~f~t~eeAa~Ayd~a~~~~~g~~a~~Nf~~~~y   62 (64)
T smart00380        1 KYRGVRQRPWGKWVAEIRDPSKGKRVWLGTFDTAEEAARAYDRAAFKFRGRSARLNFPNSLY   62 (64)
T ss_pred             CEeeEEeCCCCeEEEEEEecCCCcEEecCCCCCHHHHHHHHHHHHHHhcCCccccCCCCccC
Confidence            5899999889999999999  99999999999999999999999999999999999999774

>PHA00280 putative NHN endonuclease

Probab=99.66  E-value=1.2e-16  Score=132.26  Aligned_cols=70  Identities=19%  Similarity=0.142  Sum_probs=64.5

Q ss_pred             CCCCcCCcccCCCCCCCCceEEeEECC-CCeEEEEEEeCCeEEeecCCCCHHHHHHHHHHHHHhccCCCCCC
Q 021945           14 HNLSENGIDAESKKLPSSKYKGVVPQP-NGRWGAQIYEKHQRVWLGTFIEEEEAARVYDTAALRFRGQNAIT   84 (305)
Q Consensus        14 ~~~~~n~~n~~~~~~~~s~yrGV~~~~-~grw~A~I~~~~k~v~LG~f~t~EeAA~AYD~Aa~~~~G~~a~~   84 (305)
                      ++.++|..|++.+++|+|||+||++++ .|||+|+|+.+||+++||.|+++|+|+.||+ ++.+|||+++..
T Consensus        50 ~T~~eN~~N~~~~~~N~SG~kGV~~~k~~~kw~A~I~~~gK~~~lG~f~~~e~A~~a~~-~~~~lhGeFa~~  120 (121)
T PHA00280         50 ALPKENSWNMKTPKSNTSGLKGLSWSKEREMWRGTVTAEGKQHNFRSRDLLEVVAWIYR-TRRELHGQFARF  120 (121)
T ss_pred             cCHHHHhcccCCCCCCCCCCCeeEEecCCCeEEEEEEECCEEEEcCCCCCHHHHHHHHH-HHHHHhhccccC
Confidence            456899999999999999999999886 8999999999999999999999999999997 778899998853

>PF00847 AP2: AP2 domain; InterPro: IPR001471 Pathogenesis-related genes transcriptional activator binds to the GCC-box pathogenesis-related promoter element and activates the plant's defence genes

Probab=99.10  E-value=1.4e-10  Score=83.02  Aligned_cols=50  Identities=42%  Similarity=0.508  Sum_probs=45.3

Q ss_pred             CceEEeEECC-CCeEEEEEEeC-----CeEEeecCCCCHHHHHHHHHHHHHhccCC
Q 021945           31 SKYKGVVPQP-NGRWGAQIYEK-----HQRVWLGTFIEEEEAARVYDTAALRFRGQ   80 (305)
Q Consensus        31 s~yrGV~~~~-~grw~A~I~~~-----~k~v~LG~f~t~EeAA~AYD~Aa~~~~G~   80 (305)
                      |+|+||++++ .++|+|+|+..     ++.++||.|++++||++|++.++.+++|+
T Consensus         1 s~~~GV~~~~~~~~W~a~i~~~~~~g~~k~f~~g~fg~~~eA~~~a~~~r~~~~~e   56 (56)
T PF00847_consen    1 SGYKGVSWDKRRGRWRAQIRVWSENGKRKRFSVGKFGFEEEAKRAAIEARKELEGE   56 (56)
T ss_dssp             SSSTTEEEETTTTEEEEEEEECCCTTEEEEEEECCCCCHHHHHHHHHHHHHHCTS-
T ss_pred             CCcEEEEEcCCCCEEEEEEEEcccCcccEEEeCccCCCHHHHHHHHHHHHHHhcCC
Confidence            7899999887 79999999983     49999999999999999999999999874

Ethylene, chemically the simplest plant hormone, participates in a number of stress responses and developmental processes: e.g., fruit ripening, inhibition of stem and root elongation, promotion of seed germination and flowering, senescence of leaves and flowers, and sex determination []. DNA sequence elements that confer ethylene responsiveness have been shown to contain two 11bp GCC boxes, which are necessary and sufficient for transcriptional control by ethylene. Ethylene responsive element binding proteins (EREBPs) have now been identified in a variety of plants. The proteins share a similar domain of around 59 amino acids, which interacts directly with the GCC box in the ERE.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 3IGM_A 3GCC_A 1GCC_A 2GCC_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=99.04  E-value=7.8e-10  Score=90.93  Aligned_cols=79  Identities=27%  Similarity=0.544  Sum_probs=65.2

Q ss_pred             cceeeeeeecccCCCC-CCceEEeeHHHHHhcCCCcccc-------------cCCCeEEEEEeCCCCEEEEEEEEeCC--
Q 021945          159 PVEFLFEKVLTPSDVG-KLNRMVIPKQQAEKHFALSSEI-------------ASKGLLLNFEDSTQKVWRLRYCYWSS--  222 (305)
Q Consensus       159 ~~~~lF~K~Lt~SDv~-~~~rL~iPk~~ae~~fP~~~~~-------------~~~g~~l~v~D~~Gk~W~fr~~~~~~--  222 (305)
                      ....++.|+|+.|||. +++||.||-..+.. ..+|...             ...|+.+.+.|..++.|.++++.|.-  
T Consensus        19 d~kli~~K~L~~tDv~~~qsRLsmP~~qi~~-~dFLt~eE~~~i~~~~~~~~~~~Gv~V~lvdp~~~~~~m~lkkW~mg~   97 (114)
T PF03754_consen   19 DPKLIIEKTLFKTDVDPHQSRLSMPFNQIID-NDFLTEEEKRIIKEEKKNNDKKKGVEVILVDPSLRKWTMRLKKWNMGN   97 (114)
T ss_pred             CCeEEEeeeecccCCCCCCceeeccHHHhcc-cccCCHHHHHHHHHhhccCcccCCceEEEECCcCcEEEEEEEEecccC
Confidence            4588999999999999 78999999777743 2333311             35689999999999999999999965  


Q ss_pred             -CCceEEeCCcchhhhh
Q 021945          223 -SQSYVLTKGWSRFVKE  238 (305)
Q Consensus       223 -~~~yvLt~GW~~FV~~  238 (305)
                       +..|+|..||.++|.+
T Consensus        98 ~~~~YvL~~gWn~VV~~  114 (114)
T PF03754_consen   98 GTSNYVLNSGWNKVVED  114 (114)
T ss_pred             CceEEEEEcChHhhccC
Confidence             5789999999999864

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

Probab=98.28  E-value=1.2e-05  Score=68.97  Aligned_cols=92  Identities=18%  Similarity=0.280  Sum_probs=59.4

Q ss_pred             eeeeeeecccCCCC----CCceEEeeHHHHHhcCCCcccc--cCCCeEEEEEeCCC--CEEEEEEEEeCC------CCce
Q 021945          161 EFLFEKVLTPSDVG----KLNRMVIPKQQAEKHFALSSEI--ASKGLLLNFEDSTQ--KVWRLRYCYWSS------SQSY  226 (305)
Q Consensus       161 ~~lF~K~Lt~SDv~----~~~rL~iPk~~ae~~fP~~~~~--~~~g~~l~v~D~~G--k~W~fr~~~~~~------~~~y  226 (305)
                      ..+|.|.|++.|++    |+.++.|||..++.+||.+...  ..+.+.|.+.+..+  ..|.+|++|.++      +..|
T Consensus         7 ~~~~~K~LSaNDtGaTGgHQaGiyIpk~~~~~lFp~~~~~~~~Np~~~~~~~~~s~~~~~~~~r~iYYnn~~~~gTRNE~   86 (156)
T PF09217_consen    7 WAIYCKRLSANDTGATGGHQAGIYIPKSAAELLFPSINHTKEENPDIWLKARWQSHFVTDSQVRFIYYNNRLFGGTRNEY   86 (156)
T ss_dssp             EEEEEEE--CCCCTTTSSS--EEEE-HHHHHHH-GGG-SSSSSS-EEEEEEEETTTT---EEEEEEEE-CCCTTSS--EE
T ss_pred             eEEEEEEccCCCCCCcCcccceeEecccHHHHhCCCCCcccccCCceeEEEEECCCCccceeEEEEEEcccccCCCcCce
Confidence            46899999999999    7889999999999999876643  45679999999877  568899999966      5779


Q ss_pred             EEeCCcchhhhhcC-CCCCCEEEEEecc
Q 021945          227 VLTKGWSRFVKEKG-VKAGDTVSFWRSN  253 (305)
Q Consensus       227 vLt~GW~~FV~~k~-Lk~GD~I~F~~~~  253 (305)
                      .||. |.....--+ =.+||.++|-...
T Consensus        87 RIT~-~G~~~~~~~~~~tGaL~vlaf~~  113 (156)
T PF09217_consen   87 RITR-FGRGFPLQNPENTGALLVLAFDP  113 (156)
T ss_dssp             EEE----TTSGGG-GGGTT-EEEEEEE-
T ss_pred             EEee-ecCCCccCCccccccEEEEEEcc
Confidence            9994 774444333 3689999987444

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.

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	305
1wid_A	130	Solution Structure Of The B3 Dna-Binding Domain Of		5e-36
1gcc_A	63	Solution Nmr Structure Of The Complex Of Gcc-Box Bi		4e-08
2gcc_A	70	Solution Structure Of The Gcc-Box Binding Domain, N		7e-08

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

Iteration: 1
 Score =  147 bits (372), Expect = 5e-36,   Method: Compositional matrix adjust.
 Identities = 74/107 (69%), Positives = 85/107 (79%), Gaps = 2/107 (1%)
Query: 160 VEFLFEKVLTPSDVGKLNRMVIPKQQAEKHFAL-SSEIASKGLLLNFEDSTQKVWRLRYC 218
            E LFEK +TPSDVGKLNR+VIPK  AEKHF L SS ++ KG+LLNFED   KVWR RY 
Sbjct: 10  AEALFEKAVTPSDVGKLNRLVIPKHHAEKHFPLPSSNVSVKGVLLNFEDVNGKVWRFRYS 69
Query: 219 YWSSSQSYVLTKGWSRFVKEKGVKAGDTVSFWRSNVGSNSKLFIDCK 265
           YW+SSQSYVLTKGWSRFVKEK ++AGD VSF RSN G + +L+I  K
Sbjct: 70  YWNSSQSYVLTKGWSRFVKEKNLRAGDVVSFSRSN-GQDQQLYIGWK 115

>pdb|1GCC|A Chain A, Solution Nmr Structure Of The Complex Of Gcc-Box Binding Domain Of Aterf1 And Gcc-Box Dna, Minimized Average Structure Length = 63

Iteration: 1
 Score = 55.5 bits (132), Expect = 4e-08,   Method: Composition-based stats.
 Identities = 27/57 (47%), Positives = 36/57 (63%), Gaps = 3/57 (5%)
Query: 33 YKGVVPQPNGRWGAQIYEKHQ---RVWLGTFIEEEEAARVYDTAALRFRGQNAITNF 86
          Y+GV  +P G++ A+I +  +   RVWLGTF   E+AA  YD AA R RG  A+ NF
Sbjct: 3  YRGVRQRPWGKFAAEIRDPAKNGARVWLGTFETAEDAALAYDRAAFRMRGSRALLNF 59

>pdb|2GCC|A Chain A, Solution Structure Of The Gcc-Box Binding Domain, Nmr, Minimized Mean Structure Length = 70

Iteration: 1
 Score = 54.7 bits (130), Expect = 7e-08,   Method: Composition-based stats.
 Identities = 27/57 (47%), Positives = 36/57 (63%), Gaps = 3/57 (5%)
Query: 33 YKGVVPQPNGRWGAQIYEKHQ---RVWLGTFIEEEEAARVYDTAALRFRGQNAITNF 86
          Y+GV  +P G++ A+I +  +   RVWLGTF   E+AA  YD AA R RG  A+ NF
Sbjct: 6  YRGVRQRPWGKFAAEIRDPAKNGARVWLGTFETAEDAALAYDRAAFRMRGSRALLNF 62

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	305
1wid_A	130	DNA-binding protein RAV1; DNA-binding domain, stru	7e-34
1gcc_A	63	Ethylene responsive element binding factor 1; tran	2e-20
1yel_A	104	AT1G16640; CESG, protein structure initiative, str	3e-07

>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 =  119 bits (300), Expect = 7e-34
 Identities = 75/125 (60%), Positives = 89/125 (71%), Gaps = 2/125 (1%)

Query: 151 GSNCFQETPVEFLFEKVLTPSDVGKLNRMVIPKQQAEKHFA-LSSEIASKGLLLNFEDST 209
           GS+       E LFEK +TPSDVGKLNR+VIPK  AEKHF   SS ++ KG+LLNFED  
Sbjct: 1   GSSGSSGRSAEALFEKAVTPSDVGKLNRLVIPKHHAEKHFPLPSSNVSVKGVLLNFEDVN 60

Query: 210 QKVWRLRYCYWSSSQSYVLTKGWSRFVKEKGVKAGDTVSFWRSNVGSNSKLFIDCKLQQN 269
            KVWR RY YW+SSQSYVLTKGWSRFVKEK ++AGD VSF RSN G + +L+I  K +  
Sbjct: 61  GKVWRFRYSYWNSSQSYVLTKGWSRFVKEKNLRAGDVVSFSRSN-GQDQQLYIGWKSRSG 119

Query: 270 GNGSG 274
            +   
Sbjct: 120 SDLDA 124

>1gcc_A Ethylene responsive element binding factor 1; transcription factor, protein-DNA complex, ethylene inducible; HET: DNA; NMR {Arabidopsis thaliana} SCOP: d.10.1.2 PDB: 2gcc_A 3gcc_A Length = 63

 Score = 82.0 bits (203), Expect = 2e-20
 Identities = 27/58 (46%), Positives = 35/58 (60%), Gaps = 3/58 (5%)

Query: 32 KYKGVVPQPNGRWGAQIYE---KHQRVWLGTFIEEEEAARVYDTAALRFRGQNAITNF 86
           Y+GV  +P G++ A+I +      RVWLGTF   E+AA  YD AA R RG  A+ NF
Sbjct: 2  HYRGVRQRPWGKFAAEIRDPAKNGARVWLGTFETAEDAALAYDRAAFRMRGSRALLNF 59

>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 = 47.1 bits (112), Expect = 3e-07
 Identities = 19/87 (21%), Positives = 28/87 (32%), Gaps = 10/87 (11%)

Query: 164 FEKVLTPSDVGKLNRMVIPKQQAEKHFALSSEIASKGLLLNFEDSTQKVWRLRYCYWSSS 223
           F K        K   + IP    E   A               D + + W +R       
Sbjct: 11  FMKPFISEKSSK--SLEIPLGFNEYFPAPFPITVD------LLDYSGRSWTVRMKK--RG 60

Query: 224 QSYVLTKGWSRFVKEKGVKAGDTVSFW 250
           +   LT GW  FVK+  ++ G  + F 
Sbjct: 61  EKVFLTVGWENFVKDNNLEDGKYLQFI 87

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	305
1wid_A	130	DNA-binding protein RAV1; DNA-binding domain, stru	99.97
1gcc_A	63	Ethylene responsive element binding factor 1; tran	99.86
4i1k_A	146	B3 domain-containing transcription factor VRN1; B3	99.72
1yel_A	104	AT1G16640; CESG, protein structure initiative, str	99.6
1na6_A	404	Ecorii, restriction endonuclease ecorii; site-spec	94.65
3igm_B	77	PF14_0633 protein; AP2 domain, specific transcript	93.36
1u3e_M	174	HNH homing endonuclease; HNH catalytic motif, heli	91.42

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

Probab=99.97  E-value=3.7e-31  Score=220.79  Aligned_cols=114  Identities=64%  Similarity=1.049  Sum_probs=104.5

Q ss_pred             CCcceeeeeeecccCCCCCCceEEeeHHHHHhcCCCcccc-cCCCeEEEEEeCCCCEEEEEEEEeCCCCceEEeCCcchh
Q 021945          157 ETPVEFLFEKVLTPSDVGKLNRMVIPKQQAEKHFALSSEI-ASKGLLLNFEDSTQKVWRLRYCYWSSSQSYVLTKGWSRF  235 (305)
Q Consensus       157 ~~~~~~lF~K~Lt~SDv~~~~rL~iPk~~ae~~fP~~~~~-~~~g~~l~v~D~~Gk~W~fr~~~~~~~~~yvLt~GW~~F  235 (305)
                      .++++++|.|+||+|||+++++|+||+++|++|||.++.. ..+++.|.++|.+|++|+|+|+||+++++|+|++||..|
T Consensus         7 ~~~~~~~F~K~Lt~SDv~~~~rL~iPk~~a~~~lP~~~~~~~~~~~~l~l~D~~Gk~W~fr~~~~~~~~~~~Lt~GW~~F   86 (130)
T 1wid_A            7 GRSAEALFEKAVTPSDVGKLNRLVIPKHHAEKHFPLPSSNVSVKGVLLNFEDVNGKVWRFRYSYWNSSQSYVLTKGWSRF   86 (130)
T ss_dssp             -CCCEEEEEEECCTTTTSSSCCEEECHHHHTTTSCCCSSCCSSCCEEEEEEETTTEEEEEEEEEETTTTEEEEESSHHHH
T ss_pred             CCCCcceEEEEEehHHcCCCCEEEeCHHHHHhhCCccccccCCCcEEEEEEeCCCCEEEEEEEEECCCCceEEcCChHHH
Confidence            5788999999999999998899999999999999998853 457899999999999999999999988999999999999


Q ss_pred             hhhcCCCCCCEEEEEecccCCCCeEEEEEEeccCCC
Q 021945          236 VKEKGVKAGDTVSFWRSNVGSNSKLFIDCKLQQNGN  271 (305)
Q Consensus       236 V~~k~Lk~GD~I~F~~~~~~~~~~l~i~~r~~~~~~  271 (305)
                      |++|+|++||+|+|+++. ..+++|+|++|++..++
T Consensus        87 V~~~~L~~GD~~~F~~~~-~~~~~l~I~~rr~~~~~  121 (130)
T 1wid_A           87 VKEKNLRAGDVVSFSRSN-GQDQQLYIGWKSRSGSD  121 (130)
T ss_dssp             HHHTTCCTTCEEEEEECC-SSSCCEEEEEECCCSCS
T ss_pred             HHHcCCCCCCEEEEEEec-CCCcEEEEEEEECCCCC
Confidence            999999999999999987 56789999999996544

>1gcc_A Ethylene responsive element binding factor 1; transcription factor, protein-DNA complex, ethylene inducible; HET: DNA; NMR {Arabidopsis thaliana} SCOP: d.10.1.2 PDB: 2gcc_A 3gcc_A

Probab=99.86  E-value=1.8e-22  Score=148.24  Aligned_cols=58  Identities=47%  Similarity=0.828  Sum_probs=55.4

Q ss_pred             ceEEeEECCCCeEEEEEEe---CCeEEeecCCCCHHHHHHHHHHHHHhccCCCCCCCCCCC
Q 021945           32 KYKGVVPQPNGRWGAQIYE---KHQRVWLGTFIEEEEAARVYDTAALRFRGQNAITNFRTS   89 (305)
Q Consensus        32 ~yrGV~~~~~grw~A~I~~---~~k~v~LG~f~t~EeAA~AYD~Aa~~~~G~~a~~NFp~~   89 (305)
                      +||||+++++|||+|+|+.   +++++|||+|+|+||||+|||.|+++++|.++.+|||.+
T Consensus         2 ~yrGV~~r~~gkw~A~I~~~~~~g~r~~LGtf~T~eeAA~AyD~Aa~~~~G~~a~~NFp~~   62 (63)
T 1gcc_A            2 HYRGVRQRPWGKFAAEIRDPAKNGARVWLGTFETAEDAALAYDRAAFRMRGSRALLNFPLR   62 (63)
T ss_dssp             CCTTEEEETTTEEEEEEEETTTTSEEEEEEEESSHHHHHHHHHHHHHHHHSSCCCCSSCTT
T ss_pred             CcccEeeCCCCcEEEEEccccCCCeEEEeeeCCCHHHHHHHHHHHHHHhcCcccccCCCCc
Confidence            6999999889999999999   579999999999999999999999999999999999975

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

Probab=99.72  E-value=4.1e-17  Score=138.40  Aligned_cols=98  Identities=24%  Similarity=0.334  Sum_probs=80.8

Q ss_pred             cceeeeeeecccCCCCCCceEEeeHHHHHhcCCCcccccCCCeEEEEEeCCCCEEEEEEEEeCCCCceEEeCCcchhhhh
Q 021945          159 PVEFLFEKVLTPSDVGKLNRMVIPKQQAEKHFALSSEIASKGLLLNFEDSTQKVWRLRYCYWSSSQSYVLTKGWSRFVKE  238 (305)
Q Consensus       159 ~~~~lF~K~Lt~SDv~~~~rL~iPk~~ae~~fP~~~~~~~~g~~l~v~D~~Gk~W~fr~~~~~~~~~yvLt~GW~~FV~~  238 (305)
                      +..+.|.|+|++|||.+.++|.||++++++|||...      ..|.+.|. |+.|.++|+|++.  ++.|++||..||++
T Consensus        44 s~~P~Fvk~l~~S~v~~~~~L~IP~~Fa~~~lp~~~------~~i~L~~~-gk~W~v~~~~~~~--~~~ls~GW~~Fv~d  114 (146)
T 4i1k_A           44 PTNPFFRVVLRPSYLYRGCIMYLPSGFAEKYLSGIS------GFIKVQLA-EKQWPVRCLYKAG--RAKFSQGWYEFTLE  114 (146)
T ss_dssp             CSSCEEEEECCGGGSSTTCCEECCHHHHHHHCTTCC------SEEEEEET-TEEEEEEEEEETT--EEEECTTHHHHHHH
T ss_pred             CCCCEEEEEECchhcCCCcEEEeCHHHHHHhCCCCC------eEEEEEEC-CcEEEEEEEEeCC--cEEECCchHHHHHH
Confidence            345699999999999987899999999999998754      46778887 5999999999864  69999999999999


Q ss_pred             cCCCCCCEEEEEecccCCCCeEEEEEEe
Q 021945          239 KGVKAGDTVSFWRSNVGSNSKLFIDCKL  266 (305)
Q Consensus       239 k~Lk~GD~I~F~~~~~~~~~~l~i~~r~  266 (305)
                      |+|++||+|+|--..+ .+-.|.|.+-+
T Consensus       115 n~L~~GD~cvFeli~~-~~~~f~V~IfR  141 (146)
T 4i1k_A          115 NNLGEGDVCVFELLRT-RDFVLKVTAFR  141 (146)
T ss_dssp             TTCCTTCEEEEEECSS-SSCEEEEEEEC
T ss_pred             cCCCCCCEEEEEEecC-CceEEEEEEEe
Confidence            9999999999988761 22245454433

>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=99.60  E-value=3.8e-15  Score=118.97  Aligned_cols=91  Identities=21%  Similarity=0.361  Sum_probs=74.7

Q ss_pred             eeeeeeecccCCCCCCceEEeeHHHHHhcCCCcccccCCCeEEEEEeCCCCEEEEEEEEeCCCCceEEeCCcchhhhhcC
Q 021945          161 EFLFEKVLTPSDVGKLNRMVIPKQQAEKHFALSSEIASKGLLLNFEDSTQKVWRLRYCYWSSSQSYVLTKGWSRFVKEKG  240 (305)
Q Consensus       161 ~~lF~K~Lt~SDv~~~~rL~iPk~~ae~~fP~~~~~~~~g~~l~v~D~~Gk~W~fr~~~~~~~~~yvLt~GW~~FV~~k~  240 (305)
                      .+.|.|+|+++|.  ..+|.||+.+++.|.+..      +..+.++|..|+.|.++++++.  .+++|++||..||++++
T Consensus         8 ~p~F~K~l~~~~~--~~~L~IP~~F~~~~~~~~------~~~v~L~~~~G~~W~v~~~~~~--~~~~l~~GW~~Fv~~~~   77 (104)
T 1yel_A            8 EVQFMKPFISEKS--SKSLEIPLGFNEYFPAPF------PITVDLLDYSGRSWTVRMKKRG--EKVFLTVGWENFVKDNN   77 (104)
T ss_dssp             CEEEEEECCHHHH--TTCEECCHHHHTTCCCCC------CSEEEEEETTSCEEEEEEEEET--TEEEECTTHHHHHHHHT
T ss_pred             CCCEEEEECCCCc--cceEECCHHHHHhcCccC------CCEEEEECCCCCEEEEEEEEEC--CcEEEccChHHHHHHcC
Confidence            4589999999984  459999999998865433      2478899999999999998773  47899999999999999


Q ss_pred             CCCCCEEEEEecccCCCCeEEEEE
Q 021945          241 VKAGDTVSFWRSNVGSNSKLFIDC  264 (305)
Q Consensus       241 Lk~GD~I~F~~~~~~~~~~l~i~~  264 (305)
                      |++||.|+|.-..   +..+.|.+
T Consensus        78 L~~GD~lvF~~~~---~~~f~V~I   98 (104)
T 1yel_A           78 LEDGKYLQFIYDR---DRTFYVII   98 (104)
T ss_dssp             CCTTCEEEEEECS---SSEEEEEE
T ss_pred             CCCCCEEEEEEcC---CCeEEEEE
Confidence            9999999998865   45554433

>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=94.65  E-value=0.037  Score=53.29  Aligned_cols=92  Identities=17%  Similarity=0.216  Sum_probs=67.0

Q ss_pred             ceeeeeeecccCCCC----CCceEEeeHHHHHhcCCCcccc--cCCC--eEEEEEeCCCCEEEEEEEEeC------CCCc
Q 021945          160 VEFLFEKVLTPSDVG----KLNRMVIPKQQAEKHFALSSEI--ASKG--LLLNFEDSTQKVWRLRYCYWS------SSQS  225 (305)
Q Consensus       160 ~~~lF~K~Lt~SDv~----~~~rL~iPk~~ae~~fP~~~~~--~~~g--~~l~v~D~~Gk~W~fr~~~~~------~~~~  225 (305)
                      -..+|.|.|++.|++    |+..+.||+..+..+||.+...  ....  ..+.+-|.+.-.+.++++|.+      +...
T Consensus        17 ~~~v~~K~LSAnDtgatgshQ~gi~ipk~~l~~lfp~lg~~~e~~~~~~~~~~l~d~d~p~td~~~twYn~R~~~~tRnE   96 (404)
T 1na6_A           17 NYFVYIKRLSANDTGATGGHQVGLYIPSGIVEKLFPSINHTRELNPSVFLTAHVSSHDCPDSEARAIYYNSAHFGKTRNE   96 (404)
T ss_dssp             SEEEEEEECCHHHHTCC---CCCCCCCHHHHHHHCGGGCCCSSSSCEEEEEEEESSSCCCCEEEEEEEECGGGTTSCCCE
T ss_pred             cchheeEEcccccCCCCCCcccccCCchHHHHHhcccCCCccccCCcceeEEEeccCCCceEEEEEEEecccccCCCCCc
Confidence            356999999999998    6779999998899999887722  1222  333344444455599998885      4467


Q ss_pred             eEEeCCcc-hhhhhcCCCCCCEEEEEec
Q 021945          226 YVLTKGWS-RFVKEKGVKAGDTVSFWRS  252 (305)
Q Consensus       226 yvLt~GW~-~FV~~k~Lk~GD~I~F~~~  252 (305)
                      |-|+. |. .+.-.+...+||.++|-+.
T Consensus        97 yRLt~-~~~~~~~~~~a~~GDLlvia~~  123 (404)
T 1na6_A           97 KRITR-WGRGSPLQDPENTGALTLLAFK  123 (404)
T ss_dssp             EEEEC-CCTTSGGGCGGGTTCEEEEEEE
T ss_pred             eEEee-cCCCCcccccCCCCCEEEEEEe
Confidence            99995 55 4555688899999999765

>3igm_B PF14_0633 protein; AP2 domain, specific transcription FA protein-DNA complex, transcription-DNA complex; 2.20A {Plasmodium falciparum}

Probab=93.36  E-value=0.036  Score=41.21  Aligned_cols=28  Identities=32%  Similarity=0.330  Sum_probs=23.7

Q ss_pred             CCCCceEEeEECC-CCeEEEEEEeCCeEE
Q 021945           28 LPSSKYKGVVPQP-NGRWGAQIYEKHQRV   55 (305)
Q Consensus        28 ~~~s~yrGV~~~~-~grw~A~I~~~~k~v   55 (305)
                      ..+|+|+||+|.+ .+.|.|+-.+++++.
T Consensus         3 ~~~Sg~pGVsw~kR~~~WlA~W~e~g~rr   31 (77)
T 3igm_B            3 HMSSGYPGVSWNKRMCAWLAFFYDGASRR   31 (77)
T ss_dssp             -CCSSSTTEEEETTTTEEEEEEEETTEEE
T ss_pred             CCCCCCCcEEeecCCceEEEEEecCCeEe
Confidence            4679999999987 699999999988754

>1u3e_M HNH homing endonuclease; HNH catalytic motif, helix-turn-helix DNA binding domain, PR complex, DNA binding protein-DNA complex; 2.92A {Bacillus phage SPO1} SCOP: d.4.1.3 d.285.1.1

Probab=91.42  E-value=0.0016  Score=55.73  Aligned_cols=54  Identities=9%  Similarity=-0.163  Sum_probs=36.7

Q ss_pred             CCcCCcccCCCCCCCCceEEeEECCCCeEEEEEEeCCeEEeecCCCCHHHHHHHHH
Q 021945           16 LSENGIDAESKKLPSSKYKGVVPQPNGRWGAQIYEKHQRVWLGTFIEEEEAARVYD   71 (305)
Q Consensus        16 ~~~n~~n~~~~~~~~s~yrGV~~~~~grw~A~I~~~~k~v~LG~f~t~EeAA~AYD   71 (305)
                      .+||..|+.....+.+ .+||.+.+.++|.+.|..+ +..+||.|++.+|||++|.
T Consensus        93 ~~eN~~~~~~~~~~~~-~~g~~~~~~~k~~~vi~~~-~~~~~~~f~s~~eAa~~~G  146 (174)
T 1u3e_M           93 QKINVENQMSRGTLNV-SKAQQIAKIKNQKPIIVIS-PDGIEKEYPSTKCACEELG  146 (174)
T ss_dssp             HHHHHHHHHHHTCCCC-HHHHHHHHHHTCCCEEEEC-TTSCEEEESCHHHHHHHHT
T ss_pred             HHHHhhcccccCcccc-eeeeeeccCCCCceEEEEc-CCceEEeeCCHHHHHHHHC
Confidence            3455555543332222 4577552245688999988 7788999999999999964

---

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	305
d1wida_	117	b.142.1.2 (A:) DNA-binding protein RAV1 {Thale cre	2e-32
d1na6a1	175	b.142.1.1 (A:4-178) Restriction endonuclease EcoRI	5e-24
d1gcca_	63	d.10.1.2 (A:) GCC-box binding domain {Mouse-ear cr	2e-22
d1yela1	102	b.142.1.2 (A:1-102) At1g16640 {Thale cress (Arabid	3e-15

>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 =  113 bits (285), Expect = 2e-32
 Identities = 73/106 (68%), Positives = 84/106 (79%), Gaps = 2/106 (1%)

Query: 161 EFLFEKVLTPSDVGKLNRMVIPKQQAEKHF-ALSSEIASKGLLLNFEDSTQKVWRLRYCY 219
           E LFEK +TPSDVGKLNR+VIPK  AEKHF   SS ++ KG+LLNFED   KVWR RY Y
Sbjct: 4   EALFEKAVTPSDVGKLNRLVIPKHHAEKHFPLPSSNVSVKGVLLNFEDVNGKVWRFRYSY 63

Query: 220 WSSSQSYVLTKGWSRFVKEKGVKAGDTVSFWRSNVGSNSKLFIDCK 265
           W+SSQSYVLTKGWSRFVKEK ++AGD VSF RSN G + +L+I  K
Sbjct: 64  WNSSQSYVLTKGWSRFVKEKNLRAGDVVSFSRSN-GQDQQLYIGWK 108

>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 = 93.9 bits (233), Expect = 5e-24
 Identities = 18/137 (13%), Positives = 37/137 (27%), Gaps = 15/137 (10%)

Query: 158 TPVEFLFEKVLTPSDVGKLNR----MVIPKQQAEKHFALSSEIA----SKGLLLNFEDST 209
               F++ K L+ +D G        + IP    EK F   +       S  L  +     
Sbjct: 12  CENYFVYIKRLSANDTGATGGHQVGLYIPSGIVEKLFPSINHTRELNPSVFLTAHVSSHD 71

Query: 210 QKVWRLRYCYWSSS------QSYVLTKGWSRFVKEKGVKAGDTVSFWR-SNVGSNSKLFI 262
                 R  Y++S+          +T+       +     G         +        +
Sbjct: 72  CPDSEARAIYYNSAHFGKTRNEKRITRWGRGSPLQDPENTGALTLLAFKLDEQGGDCKEV 131

Query: 263 DCKLQQNGNGSGFEEMQ 279
           +  +  + +     E  
Sbjct: 132 NIWVCASTDEEDVIETA 148

>d1gcca_ d.10.1.2 (A:) GCC-box binding domain {Mouse-ear cress (Arabidopsis thaliana) [TaxId: 3702]} Length = 63

class: Alpha and beta proteins (a+b)
fold: DNA-binding domain
superfamily: DNA-binding domain
family: GCC-box binding domain
domain: GCC-box binding domain
species: Mouse-ear cress (Arabidopsis thaliana) [TaxId: 3702]

 Score = 86.3 bits (214), Expect = 2e-22
 Identities = 27/58 (46%), Positives = 35/58 (60%), Gaps = 3/58 (5%)

Query: 32 KYKGVVPQPNGRWGAQIYE---KHQRVWLGTFIEEEEAARVYDTAALRFRGQNAITNF 86
           Y+GV  +P G++ A+I +      RVWLGTF   E+AA  YD AA R RG  A+ NF
Sbjct: 2  HYRGVRQRPWGKFAAEIRDPAKNGARVWLGTFETAEDAALAYDRAAFRMRGSRALLNF 59

>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 = 68.0 bits (166), Expect = 3e-15
 Identities = 20/89 (22%), Positives = 29/89 (32%), Gaps = 10/89 (11%)

Query: 161 EFLFEKVLTPSDVGKLNRMVIPKQQAEKHFALSSEIASKGLLLNFEDSTQKVWRLRYCYW 220
           E  F K        K   + IP    E   A               D + + W +R    
Sbjct: 6   EVQFMKPFISEKSSK--SLEIPLGFNEYFPAPFPITVD------LLDYSGRSWTVRM--K 55

Query: 221 SSSQSYVLTKGWSRFVKEKGVKAGDTVSF 249
              +   LT GW  FVK+  ++ G  + F
Sbjct: 56  KRGEKVFLTVGWENFVKDNNLEDGKYLQF 84

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	305
d1wida_	117	DNA-binding protein RAV1 {Thale cress (Arabidopsis	99.96
d1gcca_	63	GCC-box binding domain {Mouse-ear cress (Arabidops	99.86
d1na6a1	175	Restriction endonuclease EcoRII, N-terminal domain	99.76
d1yela1	102	At1g16640 {Thale cress (Arabidopsis thaliana) [Tax	99.53

>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=99.96  E-value=4.7e-29  Score=201.91  Aligned_cols=110  Identities=66%  Similarity=1.082  Sum_probs=102.0

Q ss_pred             cceeeeeeecccCCCCCCceEEeeHHHHHhcCCCcccc-cCCCeEEEEEeCCCCEEEEEEEEeCCCCceEEeCCcchhhh
Q 021945          159 PVEFLFEKVLTPSDVGKLNRMVIPKQQAEKHFALSSEI-ASKGLLLNFEDSTQKVWRLRYCYWSSSQSYVLTKGWSRFVK  237 (305)
Q Consensus       159 ~~~~lF~K~Lt~SDv~~~~rL~iPk~~ae~~fP~~~~~-~~~g~~l~v~D~~Gk~W~fr~~~~~~~~~yvLt~GW~~FV~  237 (305)
                      .+++||+|+||+|||++++||+||++++++|||.++.. ..+++.|.+.|.+|++|+|+|++|+++++|+|+.||..||+
T Consensus         2 ~~~~iF~K~Lt~sDv~~~~rL~iP~~~~~~~lp~~~~~~~~~~~~~~~~d~~g~~W~~~~~~~~~~~~~~l~~GW~~Fv~   81 (117)
T d1wida_           2 SAEALFEKAVTPSDVGKLNRLVIPKHHAEKHFPLPSSNVSVKGVLLNFEDVNGKVWRFRYSYWNSSQSYVLTKGWSRFVK   81 (117)
T ss_dssp             CCEEEEEEECCTTTTSSSCCEEECHHHHTTTSCCCSSCCSSCCEEEEEEETTTEEEEEEEEEETTTTEEEEESSHHHHHH
T ss_pred             CCceEEEEEecchhcCCCCEEEECHHHHHHhCCccccccCCCcEEEEEEeCCCCEEEEEEEEECCCCceEEecCHHHHHH
Confidence            56789999999999998899999999999999999854 45789999999999999999999998899999999999999


Q ss_pred             hcCCCCCCEEEEEecccCCCCeEEEEEEeccC
Q 021945          238 EKGVKAGDTVSFWRSNVGSNSKLFIDCKLQQN  269 (305)
Q Consensus       238 ~k~Lk~GD~I~F~~~~~~~~~~l~i~~r~~~~  269 (305)
                      +++|++||+|+|+++. .++++++|++|+++.
T Consensus        82 ~~~Lk~GD~~~F~~~~-~~~~~~~i~~r~~~~  112 (117)
T d1wida_          82 EKNLRAGDVVSFSRSN-GQDQQLYIGWKSRSG  112 (117)
T ss_dssp             HTTCCTTCEEEEEECC-SSSCCEEEEEECCCS
T ss_pred             HcCCCCCCEEEEEEEe-CCCCEEEEEEEECCC
Confidence            9999999999999986 678899999999943

>d1gcca_ d.10.1.2 (A:) GCC-box binding domain {Mouse-ear cress (Arabidopsis thaliana) [TaxId: 3702]}

class: Alpha and beta proteins (a+b)
fold: DNA-binding domain
superfamily: DNA-binding domain
family: GCC-box binding domain
domain: GCC-box binding domain
species: Mouse-ear cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=99.86  E-value=1.2e-22  Score=147.20  Aligned_cols=58  Identities=47%  Similarity=0.828  Sum_probs=54.4

Q ss_pred             ceEEeEECCCCeEEEEEEe---CCeEEeecCCCCHHHHHHHHHHHHHhccCCCCCCCCCCC
Q 021945           32 KYKGVVPQPNGRWGAQIYE---KHQRVWLGTFIEEEEAARVYDTAALRFRGQNAITNFRTS   89 (305)
Q Consensus        32 ~yrGV~~~~~grw~A~I~~---~~k~v~LG~f~t~EeAA~AYD~Aa~~~~G~~a~~NFp~~   89 (305)
                      .||||+++++|||+|+|++   +++++|||+|+|+||||+|||.|+++++|+++.+|||..
T Consensus         2 ~yrGVr~r~~gkw~A~Ir~~~~~~~r~~LGtf~t~eeAArAYD~aa~~~~G~~a~~NFP~~   62 (63)
T d1gcca_           2 HYRGVRQRPWGKFAAEIRDPAKNGARVWLGTFETAEDAALAYDRAAFRMRGSRALLNFPLR   62 (63)
T ss_dssp             CCTTEEEETTTEEEEEEEETTTTSEEEEEEEESSHHHHHHHHHHHHHHHHSSCCCCSSCTT
T ss_pred             CcceEeECCCCCEEEEEecCCCCCcEeccccccCHHHHHHHHHHHHHHhcCCCcccCCCcc
Confidence            4999999889999999986   568999999999999999999999999999999999973

>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=99.76  E-value=3.1e-19  Score=151.08  Aligned_cols=110  Identities=15%  Similarity=0.118  Sum_probs=91.6

Q ss_pred             CcceeeeeeecccCCCCCCce----EEeeHHHHHhcCCCccccc--CCCeEE--EEEeCCCCEEEEEEEEeCCC------
Q 021945          158 TPVEFLFEKVLTPSDVGKLNR----MVIPKQQAEKHFALSSEIA--SKGLLL--NFEDSTQKVWRLRYCYWSSS------  223 (305)
Q Consensus       158 ~~~~~lF~K~Lt~SDv~~~~r----L~iPk~~ae~~fP~~~~~~--~~g~~l--~v~D~~Gk~W~fr~~~~~~~------  223 (305)
                      .++.++|.|+||+||++.+++    |+|||++++++||.++...  ++.++|  .+.|.+|+.|+|||+||++.      
T Consensus        12 ~~~~~~F~K~LtasD~g~tg~HQaG~~IPK~~ae~~FP~l~~~~e~nP~~~l~~~i~d~~g~~w~fR~iYyn~~~~ggTR   91 (175)
T d1na6a1          12 CENYFVYIKRLSANDTGATGGHQVGLYIPSGIVEKLFPSINHTRELNPSVFLTAHVSSHDCPDSEARAIYYNSAHFGKTR   91 (175)
T ss_dssp             HSSEEEEEEECCHHHHTCC---CCCCCCCHHHHHHHCGGGCCCSSSSCEEEEEEEESSSCCCCEEEEEEEECGGGTTSCC
T ss_pred             CCceEEEEEEcccccccccCCccceeeecHHHHHHhCCCCCcccccCCCceEEEEEecCCCCeeEEEEEEECCccCCCcc
Confidence            356889999999999998886    9999999999999988542  344444  56699999999999999763      


Q ss_pred             CceEEeCCcchhhhhcCCCCCCEEEEEec-ccCCCCeEEEEEEec
Q 021945          224 QSYVLTKGWSRFVKEKGVKAGDTVSFWRS-NVGSNSKLFIDCKLQ  267 (305)
Q Consensus       224 ~~yvLt~GW~~FV~~k~Lk~GD~I~F~~~-~~~~~~~l~i~~r~~  267 (305)
                      +.|.||.+|..|+..+.+.+||.++|.+. .......++|.+.+.
T Consensus        92 neyRiT~~g~~~~~~~~~n~G~l~i~af~~~~~~~~~~~~~vwvc  136 (175)
T d1na6a1          92 NEKRITRWGRGSPLQDPENTGALTLLAFKLDEQGGDCKEVNIWVC  136 (175)
T ss_dssp             CEEEEECCCTTSGGGCGGGTTCEEEEEEECCTTSCCCCEEEEEEC
T ss_pred             ccEEEEeccccccccCccccccEEEEEeecCCCCCceeEEEEEEe
Confidence            88999999999999999999999999995 445566677777766

>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=99.53  E-value=1.7e-14  Score=113.23  Aligned_cols=91  Identities=22%  Similarity=0.378  Sum_probs=74.3

Q ss_pred             ceeeeeeecccCCCCCCceEEeeHHHHHhcCCCcccccCCCeEEEEEeCCCCEEEEEEEEeCCCCceEEeCCcchhhhhc
Q 021945          160 VEFLFEKVLTPSDVGKLNRMVIPKQQAEKHFALSSEIASKGLLLNFEDSTQKVWRLRYCYWSSSQSYVLTKGWSRFVKEK  239 (305)
Q Consensus       160 ~~~lF~K~Lt~SDv~~~~rL~iPk~~ae~~fP~~~~~~~~g~~l~v~D~~Gk~W~fr~~~~~~~~~yvLt~GW~~FV~~k  239 (305)
                      -++-|-|+|.+++...  +|.||+.++..|.+...      ..|.++|.+|+.|++++...  .....|+.||..||+++
T Consensus         5 ~~~~Ffkv~~~~~~~~--~L~IP~~F~~~~~~~~~------~~i~L~d~~G~~W~v~~~~~--~~~~~~~~GW~~Fv~~n   74 (102)
T d1yela1           5 GEVQFMKPFISEKSSK--SLEIPLGFNEYFPAPFP------ITVDLLDYSGRSWTVRMKKR--GEKVFLTVGWENFVKDN   74 (102)
T ss_dssp             CCEEEEEECCHHHHTT--CEECCHHHHTTCCCCCC------SEEEEEETTSCEEEEEEEEE--TTEEEECTTHHHHHHHH
T ss_pred             CCCeEEEEEcCcccCC--CEECCHHHHHhCCCCCC------CEEEEEcCCCCEEEEEEEEe--CCeEEEccCHHHHHHHc
Confidence            3456889999998766  89999999998765543      46888999999999998654  45678899999999999


Q ss_pred             CCCCCCEEEEEecccCCCCeEEEE
Q 021945          240 GVKAGDTVSFWRSNVGSNSKLFID  263 (305)
Q Consensus       240 ~Lk~GD~I~F~~~~~~~~~~l~i~  263 (305)
                      +|++||.|+|--+.   +..+.+.
T Consensus        75 ~L~~GD~~vF~~~~---~~~f~V~   95 (102)
T d1yela1          75 NLEDGKYLQFIYDR---DRTFYVI   95 (102)
T ss_dssp             TCCTTCEEEEEECS---SSEEEEE
T ss_pred             CCCcCCEEEEEEcC---CcEEEEE
Confidence            99999999997765   5555443