Citrus Sinensis ID: 020733

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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-------310-------320--
Protein Sequence
MEEEMLSIISNGETNVIPELSDSISSTPLIPATKRLRHASAVSKFKGVVPQQNGHWGAQIYANHQRIWLGTFKSEKDAAMAYDSAAIRLRGVDSHRNFPWTKITIEEPNFQSHYSTEAVINMIRDGSYSSRQLFQKELTPSDVGKLNRLVIPKKYAVKYFPQISERVEEHAENDKADDVQLVFHDKSMKLWKFRYCYWKSSQSFVFTRGWNRFVKENQLKANDTICFYLCELRDIAKGTKTFGMIDAKKGENSGASAEVSGPYVDMKVDLQLQLGQNKKENKVEEDDNGNEIEATEEVELKAPSSTSDSERKLFKLFGVEIF
Secondary Structure (PSIPRED)
cHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEEcccccHHHHHHHHHHHHcccccccccccccccccccccccccccccHHHHHHHcccccccccccccccccccccccccccccccccccccccccHHHHccccccccccccEEEEEccccccEEEccccccccccEEEEccccccccccccccccEEEEEEcccccccccccEEEEEEcccccccccccccccccccccccHHccccccccccccccccccccccccHHHHcccccccccccccEEEEEcEEcc
Secondary Structure Prediction (SSPRO)
ccHHHHHHcccccccccccccccccccccccccccccEccccccccccccccccccHHHHHHHccEEEEcccccHHHHHHHHHHHHHHHccccccccccccccccHHHHHHHcccHHHHHHHHHccccccHHHcEEEccccccccccccEccHHHHHHHcccccHccccccHHHccccEEEEEEcccccEEEEEEEEcccccEEEEEcccHHHHHHcccccccEEEEEEccccccccccccEEEEEEEcccccccccccccccccccccccccccccccccccccccccccccHHHHHccccccccccccccEEEEEEEEcc
Coil and Loop (DISEMBL)
MEEEMLSIISngetnvipelsdsisstplipatkrlRHASAVskfkgvvpqqnghwgAQIYANHQriwlgtfkseKDAAMAYDSAAIRLrgvdshrnfpwtkitieepnfqshysTEAVINMIRdgsyssrqlfqkeltpsdvgklnrlvipkkyavkyFPQISERVEEhaendkaddvqlVFHDKSMKLWKFRYCYWKSSQSFVFTRGWNRFVKENQLKANDTICFYLCELRDIakgtktfgmidakkgensgasaevsgpyvdMKVDLQLQlgqnkkenkveeddngneieateevelkapsstsdsERKLFKLFGVEIF
Flexible Loop (DISEMBL)
MEEEMLSIISNGETNVIPELSDSISSTPLIPATKRLRHASAVSKFKGVVPQQNGHWGAQIYANHQRIWLGTFKSEKDAAMAYDSAAIRLRGVDSHRNFPWTKitieepnfqshYSTEAVINMIRDGSYSSRQLFQKeltpsdvgklnrlvipkkyaVKYFPQISERVEEHaendkaddvqlvFHDKSMKLWKFRYCYWKSSQSFVFTRGWNRFVKENQLKANDTICFYLCELRDIAKGTKTFGMidakkgensgasAEVSGPYVDMKVDLQLQLgqnkkenkveeddngneieateevelkapsstsdserklfklfgveif
Low Complexity Region (SEG)
MEEEMLSIISNGETNVIPELSDSISSTPLIPATKRLRHASAVSKFKGVVPQQNGHWGAQIYANHQRIWLGTFKSEKDAAMAYDSAAIRLRGVDSHRNFPWTKITIEEPNFQSHYSTEAVINMIRDGSYSSRQLFQKELTPSDVGKLNRLVIPKKYAVKYFPQISERVEEHAENDKADDVQLVFHDKSMKLWKFRYCYWKSSQSFVFTRGWNRFVKENQLKANDTICFYLCELRDIAKGTKTFGMIDAKKGENSGASAEVSGPYVDMKVDLQLQLGQNKKENKVEEDDNGNEIEATEEVELKAPSSTSDSERKLFKLFGVEIF
Disordered region (IsUnstruct)
**************************************ASAVSKFKGVVPQQNGHWGAQIYANHQRIWLGTFKSEKDAAMAYDSAAIRLRGVDSHRNFPWTKITIEEPNFQSHYSTEAVINMIRDGSYSSRQLFQKELTPSDVGKLNRLVIPKKYAVKYFPQISER**********DDVQLVFHDKSMKLWKFRYCYWKSSQSFVFTRGWNRFVKENQLKANDTICFYLCELRDIAKGTKTFGMI*****************************************************************************
Disordered Region (DISOPRED)
****M***********************************************NGHWGAQIYANHQRIWLGTFKSEKDAAMAYDSAAIRLRGVDSHRNFPWTKITIEEPNFQSHYSTEAVINMIRDGSYSSRQ**************************************************FHDKSMKLWKFRYCYWKSSQSFVFTRGWNRFVKENQLKANDTICFYLCELRDIAKGTKTFGMID*********************************************************************LFGVEIF
Disordered Region (DISEMBL)
MEEEMLSIISNGETNVIPELSDSISSTPLIPATKRLRHASAVSKFKGVVPQQNGHWGAQIYANHQRIWLGTFKSEKDAAMAYDSAAIRLRGVDSHRNFPWTKITIEEPNFQSHYSTEAVINMIRDGSYSSRQLFQKELTPSDVGKLNRLVIPKKYAVKYFPQISERVEEHAENDKADDVQLVFHDKSMKLWKFRYCYWKSSQSFVFTRGWNRFVKENQLKANDTICFYLCELRDIAKGTKTFGMIDAKKG********VSGPYVDMKVDLQLQLGQN************NEIEATEE***********SERKLFKLFGVEIF
Disordered Region (DISPRO)
********************************************FKGVVPQQNGHWGAQIYANHQRIWLGTFKSEKDAAMAYDSAAIRLRGVDSHRNFPWTKITIEEPNFQSHYSTEAVINMIRDGSYSSRQLFQKELTPSDVGKLNRLVIPKKYAVKYFPQISERVEEHAE*DKADDVQLVFHDKSMKLWKFRYCYWKSSQSFVFTRGWNRFVKENQLKANDTICFYLCELRDIAKGTKTFGMIDAKKGE***********************************************************RKLFKLFGVEIF
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MEEEMLSIISNGETNVIPELSDSISSTPLIPATKRLRHASAVSKFKGVVPQQNGHWGAQIYANHQRIWLGTFKSEKDAAMAYDSAAIRLRGVDSHRNFPWTKITIEEPNFQSHYSTEAVINMIRDGSYSSRQLFQKELTPSDVGKLNRLVIPKKYAVKYFPQISERVEEHAENDKADDVQLVFHDKSMKLWKFRYCYWKSSQSFVFTRGWNRFVKENQLKANDTICFYLCELRDIAKGTKTFGMIDAKKGENSGASAEVSGPYVDMKVDLQLQLGQNKKENKVEEDDNGNEIEATEEVELKAPSSTSDSERKLFKLFGVEIF
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	322	2.2.26 [Sep-21-2011]
Q9C688	352	AP2/ERF and B3 domain-con	yes	no	0.754	0.690	0.512	2e-76
Q9C6P5	337	AP2/ERF and B3 domain-con	no	no	0.878	0.839	0.464	3e-75
Q9ZWM9	344	AP2/ERF and B3 domain-con	no	no	0.552	0.517	0.432	1e-44
Q9C6M5	361	AP2/ERF and B3 domain-con	no	no	0.565	0.504	0.423	1e-43
Q6L4H4	394	AP2/ERF and B3 domain-con	yes	no	0.621	0.507	0.422	2e-43
Q9LS06	333	AP2/ERF and B3 domain-con	no	no	0.555	0.537	0.444	2e-43
Q8RZX9	393	AP2/ERF and B3 domain-con	no	no	0.562	0.460	0.432	4e-43
P82280	352	AP2/ERF and B3 domain-con	no	no	0.546	0.5	0.427	1e-41
Q9AWS7	317	Putative AP2/ERF and B3 d	no	no	0.636	0.646	0.424	4e-40
Q9AWS0	365	AP2/ERF and B3 domain-con	no	no	0.624	0.550	0.432	7e-40

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

 Score =  285 bits (730), Expect = 2e-76,   Method: Compositional matrix adjust.
 Identities = 149/291 (51%), Positives = 183/291 (62%), Gaps = 48/291 (16%)

Query: 10  SNGETNVIPELSDSISSTPLIPATKRLRHASAVSKFKGVVPQQNGHWGAQIYANHQRIWL 69
           ++G T+ +  L+  +  T +   TK     S  +KFKGVV QQNGHWGAQIYA+H+RIWL
Sbjct: 14  TSGLTDSVLSLTKRMKPTEVTTTTKPA--LSNTTKFKGVVQQQNGHWGAQIYADHRRIWL 71

Query: 70  GTFKSEKDAAMAYDSAAIRLRGVD--SHRNFPWTKITIEEPNFQSHYSTEAVINMIRDGS 127
           GTFKS  +AA AYDSA+I+LR  D  SHRNFPW+  T+ EP+FQ  Y+TEAV+NMIRDGS
Sbjct: 72  GTFKSAHEAAAAYDSASIKLRSFDANSHRNFPWSDFTLHEPDFQECYTTEAVLNMIRDGS 131

Query: 128 Y----------------------------------------SSRQLFQKELTPSDVGKLN 147
           Y                                        S  QLFQKELTPSDVGKLN
Sbjct: 132 YQHKFRDFLRIRSQIVANINIVGSKQVLGGGEGGQESNKCFSCTQLFQKELTPSDVGKLN 191

Query: 148 RLVIPKKYAVKYFPQISERVEEHAENDKADDVQLVFHDKSMKLWKFRYCYWKSSQSFVFT 207
           RLVIPKKYAVKY P IS+   E   ++  +DV++VF+D++M+ WKFRYCYW+SSQSFVFT
Sbjct: 192 RLVIPKKYAVKYMPFISDDQSEKETSEGVEDVEVVFYDRAMRQWKFRYCYWRSSQSFVFT 251

Query: 208 RGWNRFVKENQLKANDTICFYLCELRDIAKG----TKTFGMIDAKKGENSG 254
           RGWN FVKE  LK  D I FY C++ +  K     +KTF MID      +G
Sbjct: 252 RGWNGFVKEKNLKEKDIIVFYTCDVPNNVKTLEGQSKTFLMIDVHHFSGNG 302

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

 Score =  281 bits (720), Expect = 3e-75,   Method: Compositional matrix adjust.
 Identities = 163/351 (46%), Positives = 202/351 (57%), Gaps = 68/351 (19%)

Query: 20  LSDSISSTPLIPATKRLRHASAVSKFKGVVPQQNGHWGAQIYANHQRIWLGTFKSEKDAA 79
           L D   +  ++ ++ +   AS   K+KGVV QQNGHWGAQIYA+H+RIWLGTFKS  +AA
Sbjct: 3   LDDEPENALVVSSSPKTVVASGNVKYKGVVQQQNGHWGAQIYADHKRIWLGTFKSADEAA 62

Query: 80  MAYDSAAIRLRGVD--SHRNFPWTKITIEEPNFQSHYSTEAVINMIRDGSY--------- 128
            AYDSA+I+LR  D  SHRNFPW+ IT+ EP+FQ+ Y+TE V+NMIRDGSY         
Sbjct: 63  TAYDSASIKLRSFDANSHRNFPWSTITLNEPDFQNCYTTETVLNMIRDGSYQHKFRDFLR 122

Query: 129 -----------------------------SSRQLFQKELTPSDVGKLNRLVIPKKYAVKY 159
                                        S  QLFQKELTPSDVGKLNRLVIPKKYAVKY
Sbjct: 123 IRSQIVASINIGGPKQARGEVNQESDKCFSCTQLFQKELTPSDVGKLNRLVIPKKYAVKY 182

Query: 160 FPQISERVEEHAEND---KADDVQLVFHDKSMKLWKFRYCYWKSSQSFVFTRGWNRFVKE 216
            P IS    E  E +     +DV++VF+D++M+ WKFRYCYWKSSQSFVFTRGWN FVKE
Sbjct: 183 MPFISADQSEKEEGEIVGSVEDVEVVFYDRAMRQWKFRYCYWKSSQSFVFTRGWNSFVKE 242

Query: 217 NQLKANDTICFYLCELRDIAKGT----KTFGMIDAKKGENSGA--SAEVSGPYVDMKVDL 270
             LK  D I FY C++ +  K      K F MID     ++G+  + EVS    D  V +
Sbjct: 243 KNLKEKDVIAFYTCDVPNNVKTLEGQRKNFLMIDVHCFSDNGSVVAEEVSMTVHDSSVQV 302

Query: 271 QLQLGQNKKENKVEEDDNGNEIEATEEVELKAPSSTSDSERKLFKLFGVEI 321
           +      K EN V                L+   + S+  +  F LFGV I
Sbjct: 303 K------KTENLVSS-------------MLEDKETKSEENKGGFMLFGVRI 334

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

 Score =  180 bits (456), Expect = 1e-44,   Method: Compositional matrix adjust.
 Identities = 96/222 (43%), Positives = 123/222 (55%), Gaps = 44/222 (19%)

Query: 43  SKFKGVVPQQNGHWGAQIYANHQRIWLGTFKSEKDAAMAYDSAAIRLRGVDSHRNFPWTK 102
           SK+KGVVPQ NG WGAQIY  HQR+WLGTF  E +AA AYD A  R R  D+  NF   K
Sbjct: 60  SKYKGVVPQPNGRWGAQIYEKHQRVWLGTFNEEDEAARAYDVAVHRFRRRDAVTNFKDVK 119

Query: 103 ITIEEPNFQSHYSTEAVINMIRDGSY---------------------------------- 128
           +  +E +F + +S   +++M+R  +Y                                  
Sbjct: 120 MDEDEVDFLNSHSKSEIVDMLRKHTYNEELEQSKRRRNGNGNMTRTLLTSGLSNDGVSTT 179

Query: 129 ---SSRQLFQKELTPSDVGKLNRLVIPKKYAVKYFPQISERVEEHAENDKADDVQLVFHD 185
              S+  LF+K +TPSDVGKLNRLVIPK +A K+FP  S  V           V L F D
Sbjct: 180 GFRSAEALFEKAVTPSDVGKLNRLVIPKHHAEKHFPLPSSNVS-------VKGVLLNFED 232

Query: 186 KSMKLWKFRYCYWKSSQSFVFTRGWNRFVKENQLKANDTICF 227
            + K+W+FRY YW SSQS+V T+GW+RFVKE  L+A D + F
Sbjct: 233 VNGKVWRFRYSYWNSSQSYVLTKGWSRFVKEKNLRAGDVVSF 274

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 =  177 bits (448), Expect = 1e-43,   Method: Compositional matrix adjust.
 Identities = 94/222 (42%), Positives = 126/222 (56%), Gaps = 40/222 (18%)

Query: 43  SKFKGVVPQQNGHWGAQIYANHQRIWLGTFKSEKDAAMAYDSAAIRLRGVDSHRNFPWTK 102
           SK+KGVVPQ NG WGAQIY  HQR+WLGTF  E++AA +YD A  R RG D+  NF   K
Sbjct: 70  SKYKGVVPQPNGRWGAQIYEKHQRVWLGTFNEEEEAASSYDIAVRRFRGRDAVTNF---K 126

Query: 103 ITIE----EPNFQSHYSTEAVINMIRDGSYS-----SRQ--------------------- 132
             ++    E  F   +S   +++M+R  +Y+     SR+                     
Sbjct: 127 SQVDGNDAESAFLDAHSKAEIVDMLRKHTYADEFEQSRRKFVNGDGKRSGLETATYGNDA 186

Query: 133 -------LFQKELTPSDVGKLNRLVIPKKYAVKYFPQISERVEEHAENDKADDVQLVFHD 185
                  LF+K +TPSDVGKLNRLVIPK++A K+FP  +              V +   D
Sbjct: 187 VLRAREVLFEKTVTPSDVGKLNRLVIPKQHAEKHFPLPAMTTAMGMNPSPTKGVLINLED 246

Query: 186 KSMKLWKFRYCYWKSSQSFVFTRGWNRFVKENQLKANDTICF 227
           ++ K+W+FRY YW SSQS+V T+GW+RFVKE  L+A D +CF
Sbjct: 247 RTGKVWRFRYSYWNSSQSYVLTKGWSRFVKEKNLRAGDVVCF 288

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

 Score =  176 bits (446), Expect = 2e-43,   Method: Compositional matrix adjust.
 Identities = 106/251 (42%), Positives = 131/251 (52%), Gaps = 51/251 (20%)

Query: 43  SKFKGVVPQQNGHWGAQIYANHQRIWLGTFKSEKDAAMAYDSAAIRLRGVDSHRNF-PWT 101
           SK+KGVVPQ NG WGAQIY  HQR+WLGTF  E +AA AYD AA R RG D+  NF P  
Sbjct: 67  SKYKGVVPQPNGRWGAQIYERHQRVWLGTFTGEAEAARAYDVAAQRFRGRDAVTNFRPLA 126

Query: 102 KITIE---EPNFQSHYSTEAVINMIRDGSY------------------------------ 128
           +   E   E  F +  S   V++M+R  +Y                              
Sbjct: 127 ESDPEAAVELRFLASRSKAEVVDMLRKHTYLEELTQNKRAFAAISPPPPKHPASSPTSSS 186

Query: 129 -SSRQLFQKELTPSDVGKLNRLVIPKKYAVKYFP----------QISERVEEHAENDKAD 177
            +   LF K +TPSDVGKLNRLVIPK++A K+FP           ++   +  A      
Sbjct: 187 AAREHLFDKTVTPSDVGKLNRLVIPKQHAEKHFPLQLPPPTTTSSVAAAADAAAGGGDCK 246

Query: 178 DVQLVFHDKSMKLWKFRYCYWKSSQSFVFTRGWNRFVKENQLKANDTICFYLCELRDIAK 237
            V L F D + K+WKFRY YW SSQS+V T+GW+RFVKE  L A D + FY    R   K
Sbjct: 247 GVLLNFEDAAGKVWKFRYSYWNSSQSYVLTKGWSRFVKEKGLHAGDAVGFY----RAAGK 302

Query: 238 GTKTFGMIDAK 248
             + F  ID K
Sbjct: 303 NAQLF--IDCK 311

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 =  176 bits (446), Expect = 2e-43,   Method: Compositional matrix adjust.
 Identities = 97/218 (44%), Positives = 122/218 (55%), Gaps = 39/218 (17%)

Query: 43  SKFKGVVPQQNGHWGAQIYANHQRIWLGTFKSEKDAAMAYDSAAIRLRGVDSHRNFPWTK 102
           S+FKGVVPQ NG WGAQIY  HQR+WLGTF  E +AA AYD AA R RG D+  NF  T 
Sbjct: 60  SRFKGVVPQPNGRWGAQIYEKHQRVWLGTFNEEDEAARAYDVAAHRFRGRDAVTNFKDTT 119

Query: 103 ITIEEPNFQSHYSTEAVINMIRDGSY---------------------------------S 129
              EE  F + +S   +++M+R  +Y                                 +
Sbjct: 120 FE-EEVEFLNAHSKSEIVDMLRKHTYKEELDQRKRNRDGNGKETTAFALASMVVMTGFKT 178

Query: 130 SRQLFQKELTPSDVGKLNRLVIPKKYAVKYFPQISERVEEHAENDKADDVQLVFHDKSMK 189
           +  LF+K +TPSDVGKLNRLVIPK  A K+FP     +     N     + L F D + K
Sbjct: 179 AELLFEKTVTPSDVGKLNRLVIPKHQAEKHFP-----LPLGNNNVSVKGMLLNFEDVNGK 233

Query: 190 LWKFRYCYWKSSQSFVFTRGWNRFVKENQLKANDTICF 227
           +W+FRY YW SSQS+V T+GW+RFVKE +L A D I F
Sbjct: 234 VWRFRYSYWNSSQSYVLTKGWSRFVKEKRLCAGDLISF 271

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

 Score =  175 bits (444), Expect = 4e-43,   Method: Compositional matrix adjust.
 Identities = 100/231 (43%), Positives = 125/231 (54%), Gaps = 50/231 (21%)

Query: 43  SKFKGVVPQQNGHWGAQIYANHQRIWLGTFKSEKDAAMAYDSAAIRLRGVDSHRNF-PWT 101
           SKFKGVVPQ NG WGAQIY  HQR+WLGTF  E DAA AYD AA R RG D+  NF P  
Sbjct: 80  SKFKGVVPQPNGRWGAQIYERHQRVWLGTFAGEDDAARAYDVAAQRFRGRDAVTNFRPLA 139

Query: 102 KITIEEP---NFQSHYSTEAVINMIRDGSY------------------------------ 128
           +   +      F +  S   V++M+R  +Y                              
Sbjct: 140 EADPDAAAELRFLATRSKAEVVDMLRKHTYFDELAQSKRTFAASTPSAATTTASLSNGHL 199

Query: 129 -SSR----------QLFQKELTPSDVGKLNRLVIPKKYAVKYFPQISERVEEHAENDKAD 177
            S R           LF K +TPSDVGKLNRLVIPK++A K+FP     ++  +   ++ 
Sbjct: 200 SSPRSPFAPAAARDHLFDKTVTPSDVGKLNRLVIPKQHAEKHFP-----LQLPSAGGESK 254

Query: 178 DVQLVFHDKSMKLWKFRYCYWKSSQSFVFTRGWNRFVKENQLKANDTICFY 228
            V L F D + K+W+FRY YW SSQS+V T+GW+RFVKE  L A D + FY
Sbjct: 255 GVLLNFEDAAGKVWRFRYSYWNSSQSYVLTKGWSRFVKEKGLHAGDVVGFY 305

Oryza sativa subsp. japonica (taxid: 39947)

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

 Score =  170 bits (431), Expect = 1e-41,   Method: Compositional matrix adjust.
 Identities = 95/222 (42%), Positives = 126/222 (56%), Gaps = 46/222 (20%)

Query: 43  SKFKGVVPQQNGHWGAQIYANHQRIWLGTFKSEKDAAMAYDSAAIRLRGVDSHRNFPWTK 102
           SK+KGVVPQ NG WGAQIY  HQR+WLGTF  +++AA +YD AA R RG D+  NF   K
Sbjct: 63  SKYKGVVPQPNGRWGAQIYEKHQRVWLGTFNEQEEAARSYDIAACRFRGRDAVVNF---K 119

Query: 103 ITIEEPN--FQSHYSTEAVINMIRDGSYSS-------RQ--------------------- 132
             +E+ +  F   +S   +++M+R  +Y+        RQ                     
Sbjct: 120 NVLEDGDLAFLEAHSKAEIVDMLRKHTYADELEQNNKRQLFLSVDANGKRNGSSTTQNDK 179

Query: 133 -------LFQKELTPSDVGKLNRLVIPKKYAVKYFPQISERVEEHAENDKADDVQLVFHD 185
                  LF+K +TPSDVGKLNRLVIPK++A K+FP  S              V + F D
Sbjct: 180 VLKTREVLFEKAVTPSDVGKLNRLVIPKQHAEKHFPLPS------PSPAVTKGVLINFED 233

Query: 186 KSMKLWKFRYCYWKSSQSFVFTRGWNRFVKENQLKANDTICF 227
            + K+W+FRY YW SSQS+V T+GW+RFVKE  L+A D + F
Sbjct: 234 VNGKVWRFRYSYWNSSQSYVLTKGWSRFVKEKNLRAGDVVTF 275

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

 Score =  165 bits (418), Expect = 4e-40,   Method: Compositional matrix adjust.
 Identities = 99/233 (42%), Positives = 133/233 (57%), Gaps = 28/233 (12%)

Query: 43  SKFKGVVPQQNGHWGAQIYANHQRIWLGTFKSEKDAAMAYDSAAIRLRGVD--SHRNFPW 100
           S++KGVVPQ NG WGAQIY  H R+WLGTF  E+ AA AYD AA+R RG D  ++R    
Sbjct: 65  SRYKGVVPQPNGRWGAQIYERHARVWLGTFPDEEAAARAYDVAALRFRGRDAVTNRAPAA 124

Query: 101 TKITIEEPNFQSHYSTEAVINMIRDGSY--------------------SSRQLFQKELTP 140
              +  E  F + +S   V++M+R  +Y                    +   LF+K +TP
Sbjct: 125 EGASAGELAFLAAHSKAEVVDMLRKHTYDDELQQGLRRGSRAQPTPRWAREPLFEKAVTP 184

Query: 141 SDVGKLNRLVIPKKYAVKYFPQISERVEEHAENDKADDVQLVFHDKSMKLWKFRYCYWKS 200
           SDVGKLNRLV+PK+ A ++FP    R   H+ +     V L F D   K+W+FRY YW S
Sbjct: 185 SDVGKLNRLVVPKQQAERHFPFPLRR---HSSDAAGKGVLLNFEDGDGKVWRFRYSYWNS 241

Query: 201 SQSFVFTRGWNRFVKENQLKANDTICFYLCELRDIAKGTKTFGMIDAKKGENS 253
           SQS+V T+GW+RFV+E  L+  DT+ F        A GT+   +ID KK E +
Sbjct: 242 SQSYVLTKGWSRFVREKGLRPGDTVAFSRSA---AAWGTEKHLLIDCKKMERN 291

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 =  164 bits (416), Expect = 7e-40,   Method: Compositional matrix adjust.
 Identities = 100/231 (43%), Positives = 132/231 (57%), Gaps = 30/231 (12%)

Query: 44  KFKGVVPQQNGHWGAQIYANHQRIWLGTFKSEKDAAMAYDSAAIRLRGVDSHRNFPWTKI 103
           ++KGVVPQ NG WGAQIY  H R+WLGTF  E+ AA AYD AA+R RG D+  NFP    
Sbjct: 68  RYKGVVPQPNGRWGAQIYERHARVWLGTFPDEEAAARAYDVAALRYRGRDAATNFPGAAA 127

Query: 104 TIEEPNFQSHYSTEAVINMIRDGSYSS--RQ----------------------LFQKELT 139
           +  E  F + +S   +++M+R  +Y+   RQ                      LF+K +T
Sbjct: 128 SAAELAFLAAHSKAEIVDMLRKHTYADELRQGLRRGRGMGARAQPTPSWAREPLFEKAVT 187

Query: 140 PSDVGKLNRLVIPKKYAVKYFP-QISERVEEHAENDKADDVQLVFHDKSMKLWKFRYCYW 198
           PSDVGKLNRLV+PK++A K+FP + +   +  +       V L F D   K+W+FRY YW
Sbjct: 188 PSDVGKLNRLVVPKQHAEKHFPLRRAASSDSASAAATGKGVLLNFEDGEGKVWRFRYSYW 247

Query: 199 KSSQSFVFTRGWNRFVKENQLKANDTICFYLCELRDIAKGTKTFGMIDAKK 249
            SSQS+V T+GW+RFV+E  L+A DTI F        A G      ID KK
Sbjct: 248 NSSQSYVLTKGWSRFVREKGLRAGDTIVFSRS-----AYGPDKLLFIDCKK 293

Oryza sativa subsp. japonica (taxid: 39947)

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	322
225445893	357	PREDICTED: AP2/ERF and B3 domain-contain	0.975	0.879	0.539	1e-101
255587881	349	DNA-binding protein RAV1, putative [Rici	0.956	0.882	0.539	1e-100
224143966	549	AP2 domain-containing transcription fact	0.835	0.489	0.596	7e-96
449457911	339	PREDICTED: AP2/ERF and B3 domain-contain	0.944	0.896	0.540	1e-95
255578178	374	DNA binding protein, putative [Ricinus c	0.987	0.850	0.502	2e-85
449462611	356	PREDICTED: AP2/ERF and B3 domain-contain	0.701	0.634	0.597	2e-82
224088262	324	AP2 domain-containing transcription fact	0.894	0.888	0.491	5e-79
224073210	369	AP2 domain-containing transcription fact	0.838	0.731	0.5	6e-79
15223743	352	RAV-like factor [Arabidopsis thaliana] g	0.754	0.690	0.512	1e-74
297852776	337	hypothetical protein ARALYDRAFT_474200 [	0.838	0.801	0.484	6e-74

>gi|225445893|ref|XP_002276492.1| PREDICTED: AP2/ERF and B3 domain-containing transcription factor At1g51120-like [Vitis vinifera]

 Score =  373 bits (957), Expect = e-101,   Method: Compositional matrix adjust.
 Identities = 196/363 (53%), Positives = 240/363 (66%), Gaps = 49/363 (13%)

Query: 1   MEEEMLSIISNGETNVIPELSDSISSTPLIPATKRLRHASAVS--KFKGVVPQQNGHWGA 58
           MEEE+LS+ISNG TNVI E SDS SS+     +KR +   +VS  +FKGVVPQQNGHWGA
Sbjct: 1   MEEEILSVISNGGTNVIVEASDSNSSSLPFHGSKRTKQGISVSSGRFKGVVPQQNGHWGA 60

Query: 59  QIYANHQRIWLGTFKSEKDAAMAYDSAAIRLRGVDSHRNFPWTKITIEEPNFQSHYSTEA 118
           QIYANHQRIWLGT+KSE +AAMAYDSAAI+LR  D+HRNFPWT +TI+EPNFQS +STE 
Sbjct: 61  QIYANHQRIWLGTYKSETEAAMAYDSAAIKLRSGDNHRNFPWTNLTIQEPNFQSFFSTET 120

Query: 119 VINMIRDGSYSS---------------------------------RQLFQKELTPSDVGK 145
           V+NMI+DGSY S                                 R LFQKELTPSDVGK
Sbjct: 121 VVNMIKDGSYPSKFAEFLKTESQRGETEVLSLDQVGVHRNGRFMCRLLFQKELTPSDVGK 180

Query: 146 LNRLVIPKKYAVKYFPQISERVEEHAENDKADDVQLVFHDKSMKLWKFRYCYWKSSQSFV 205
           LNRLVIPKKYA K+FP ISE  EE+     A D+QLVF+D+ M+LWKFRYCYW+SSQS+V
Sbjct: 181 LNRLVIPKKYATKHFPPISESAEENEVGGAAADMQLVFYDRLMRLWKFRYCYWRSSQSYV 240

Query: 206 FTRGWNRFVKENQLKANDTICFYLCELRDIAKGTKTFGMID-----AKKGENSGASAEVS 260
           FTRGWNRFVK+ +L  ND + FYLCE     K  +TF MID     +  G ++   + V 
Sbjct: 241 FTRGWNRFVKDKELNENDIVTFYLCEYGQGTKEGRTFCMIDVAYDRSTDGRDANNGSFVE 300

Query: 261 GP--YVDMKVDLQLQLGQNKKENKVEEDDNGNEIEATEEVELKAPSSTSDSERKLFKLFG 318
           GP  YV ++++LQ  L QN   NK       +E ++ EE E        + ++K  +LFG
Sbjct: 301 GPNRYVGLQIELQQDLKQNIGYNK-------HERKSQEEEESVGTEPALEGQKKGLRLFG 353

Query: 319 VEI 321
           V+I
Sbjct: 354 VQI 356

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255587881|ref|XP_002534427.1| DNA-binding protein RAV1, putative [Ricinus communis] gi|223525312|gb|EEF27956.1| DNA-binding protein RAV1, putative [Ricinus communis]

 Score =  370 bits (949), Expect = e-100,   Method: Compositional matrix adjust.
 Identities = 193/358 (53%), Positives = 236/358 (65%), Gaps = 50/358 (13%)

Query: 3   EEMLSIISNGETNVIPELSDSISSTPLIPATKRLRHASAV--SKFKGVVPQQNGHWGAQI 60
           EE++S+ISNGET V  E+SDS SST    A+KR+ H S +  S+F+GVVP QNGHWG QI
Sbjct: 4   EEIVSMISNGETAVTEEVSDSNSSTYPALASKRVMHGSNICTSRFRGVVPHQNGHWGCQI 63

Query: 61  YANHQRIWLGTFKSEKDAAMAYDSAAIRLRGVDSHRNFPWTKITIEEPNFQSHYSTEAVI 120
           YANHQRIWLGTFKSEK+AAMAYDSAA++LR  D  RNFP T I++EEP FQS+YSTEAV+
Sbjct: 64  YANHQRIWLGTFKSEKEAAMAYDSAALKLRSGDCRRNFPITNISVEEPKFQSYYSTEAVL 123

Query: 121 NMIRDGSYSSR--------------------------------QLFQKELTPSDVGKLNR 148
            MI+DG+Y S+                                +LFQKELTPSDVGKLNR
Sbjct: 124 KMIKDGTYQSKLAYFSSTSSQSVETELSIKLTKTQRNRSLMCKELFQKELTPSDVGKLNR 183

Query: 149 LVIPKKYAVKYFPQISERVEEHAENDKADDVQLVFHDKSMKLWKFRYCYWKSSQSFVFTR 208
           LVIPK++A+K+F  ISE VE++   +KA+D QL F+DK+MKLWKFRYCYWKSSQS+VFTR
Sbjct: 184 LVIPKRFAIKFFSHISESVEQNIGGNKANDGQLAFYDKAMKLWKFRYCYWKSSQSYVFTR 243

Query: 209 GWNRFVKENQLKANDTICFYLCELRDIAKGTKTFGMIDAKKGENSGASAEVSGPYVDMKV 268
           GWNRFVKE QLKANDTI   LCE R+ A+ T ++ MID K   +S +  E        K+
Sbjct: 244 GWNRFVKEKQLKANDTIAICLCECRENAELTDSYYMIDVKNEGDSSSLLESGSQSETTKM 303

Query: 269 DLQLQLGQNK----KENKVEEDDNGNEIEATEEVELKAPSSTSDSERKLFKLFGVEIF 322
            + L LGQ       +NKVE +             LK      D +RK F+LFG EI 
Sbjct: 304 QVHLHLGQTTACHYNKNKVEGEG------------LKEARPRHDGDRKSFRLFGTEII 349

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224143966|ref|XP_002325139.1| AP2 domain-containing transcription factor [Populus trichocarpa] gi|222866573|gb|EEF03704.1| AP2 domain-containing transcription factor [Populus trichocarpa]

 Score =  356 bits (914), Expect = 7e-96,   Method: Compositional matrix adjust.
 Identities = 185/310 (59%), Positives = 217/310 (70%), Gaps = 41/310 (13%)

Query: 1   MEEEMLSIISNGETNVIPELSDSISSTPLIPATKRLRHASAVS--KFKGVVPQQNGHWGA 58
           ME+E +S+ISNGET+V+ E SDS SST   PA+KR R  S +S  KFKGVVP  NGHWG 
Sbjct: 1   MEDETVSLISNGETSVVEEFSDSNSSTHPFPASKRARSGSNISASKFKGVVPLPNGHWGC 60

Query: 59  QIYANHQRIWLGTFKSEKDAAMAYDSAAIRLRGVDSHRNFPWTKITIEEPNFQSHYSTEA 118
           QIYANHQRIWLGTFKSEK+AAMAYDSAAI+LR  DS RNFP T +T+EEP F+S++STE 
Sbjct: 61  QIYANHQRIWLGTFKSEKEAAMAYDSAAIKLRSGDSRRNFPLTDVTVEEPKFRSYFSTEV 120

Query: 119 VINMIRDGSY--------------------------------SSRQLFQKELTPSDVGKL 146
           V+NMI+DG+Y                                + +QLFQKELTPSDVGKL
Sbjct: 121 VLNMIKDGTYQCKFANFTRTCSQSVETELSLKLMMPQSNQGLTCKQLFQKELTPSDVGKL 180

Query: 147 NRLVIPKKYAVKYFPQISERVEEHAENDKADDVQLVFHDKSMKLWKFRYCYWKSSQSFVF 206
           NR+VIPKKYA+KYFP ISE  EE       D V L F+DKSMKLWKFRYCYWKSSQS+VF
Sbjct: 181 NRIVIPKKYAIKYFPHISESAEE------VDGVMLAFYDKSMKLWKFRYCYWKSSQSYVF 234

Query: 207 TRGWNRFVKENQLKANDTICFYLCELRD-IAKGTKTFGMIDAKKGENSGASAEVSGPYVD 265
           TRGWNRFVKE +LKANDTI F LCE  + +    +TF MID    ENS + +E+S   + 
Sbjct: 235 TRGWNRFVKEKKLKANDTISFSLCERGETVDSAAQTFNMIDVNNRENSSSISELSSQSIA 294

Query: 266 MKVDLQLQLG 275
            KV+LQL  G
Sbjct: 295 SKVELQLNPG 304

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449457911|ref|XP_004146691.1| PREDICTED: AP2/ERF and B3 domain-containing transcription factor At1g50680-like [Cucumis sativus] gi|449503179|ref|XP_004161873.1| PREDICTED: AP2/ERF and B3 domain-containing transcription factor At1g50680-like [Cucumis sativus]

 Score =  355 bits (912), Expect = 1e-95,   Method: Compositional matrix adjust.
 Identities = 192/355 (54%), Positives = 227/355 (63%), Gaps = 51/355 (14%)

Query: 1   MEEEMLSIISNGETNVIPELSDSISSTPLIPATKRLRHA-SAVSKFKGVVPQQNGHWGAQ 59
           M++E  S+IS  +TN + E  DS   T  +P     R   S  SKFKGVVPQQNGHWGAQ
Sbjct: 1   MKQEFSSMISKAKTNAVGETLDSSCITCPLPINGCSRQGRSLTSKFKGVVPQQNGHWGAQ 60

Query: 60  IYANHQRIWLGTFKSEKDAAMAYDSAAIRLRGVDSHRNFPWTKITIEEPNFQSHYSTEAV 119
           IYANHQRIWLGTFKSE +AAMAYDSAAIR+R  D HRNFPWTK+TIEEPNFQ  Y+TE +
Sbjct: 61  IYANHQRIWLGTFKSENEAAMAYDSAAIRIRSGDCHRNFPWTKVTIEEPNFQKLYTTETL 120

Query: 120 INMIRDGSY--------------------------------SSRQLFQKELTPSDVGKLN 147
           +NMI+DGSY                                S +QLFQKELTPSDVGKLN
Sbjct: 121 LNMIKDGSYRTKFSEYLRDRSESTQTSASPSTEKAHNNGGTSIKQLFQKELTPSDVGKLN 180

Query: 148 RLVIPKKYAVKYFPQISERVEEHAEN-DKADDVQLVFHDKSMKLWKFRYCYWKSSQSFVF 206
           RLVIPKKYAVKYFP+IS    E+ E+ D   D+QL+F DK M+ WKFRYCYWKSSQS+VF
Sbjct: 181 RLVIPKKYAVKYFPRISASTTENVEHVDDDRDLQLLFFDKMMRQWKFRYCYWKSSQSYVF 240

Query: 207 TRGWNRFVKENQLKANDTICFYLCELRDIAKGTKTFGMIDAKKGENSGASAEVSGPYVDM 266
           TRGWNRFVKE QLKANDTI FYLCE    +    TF ++D K  +NSG   E      ++
Sbjct: 241 TRGWNRFVKEKQLKANDTIAFYLCEAAKSSDSKTTFCVVDVKNRDNSGGLVENETTCSEL 300

Query: 267 KVDLQLQLGQNKKENKVEEDDNGNEIEATEEVELKAPSSTSDSERKLFKLFGVEI 321
           +++L        +  +VEE  +   I+     ELK      + E K FKLFGV I
Sbjct: 301 QLNL--------RHGEVEESVSPKHIDD----ELK-----DEREVKGFKLFGVHI 338

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255578178|ref|XP_002529958.1| DNA binding protein, putative [Ricinus communis] gi|223530556|gb|EEF32435.1| DNA binding protein, putative [Ricinus communis]

 Score =  322 bits (824), Expect = 2e-85,   Method: Compositional matrix adjust.
 Identities = 189/376 (50%), Positives = 234/376 (62%), Gaps = 58/376 (15%)

Query: 1   MEEEM-LSIISNGET-NVIPELSDSISS-TPLIPATKRLR-----HASAVSKFKGVVPQQ 52
           MEEE   S++SN +  N   E+SDS  S     PA KR R      A+ ++KFKGVVPQQ
Sbjct: 1   MEEEASTSMLSNAKNENGTAEVSDSFDSHCHPFPANKRPRLGNNIGAANLAKFKGVVPQQ 60

Query: 53  NGHWGAQIYANHQRIWLGTFKSEKDAAMAYDSAAIRLRGVDSHRNFPWTKITIEEPNFQS 112
           NGHWGAQIYANHQRIWLGTFKSEK+AAMAYDSAAI+LR  DSHRNFPWT   I EP+FQ+
Sbjct: 61  NGHWGAQIYANHQRIWLGTFKSEKEAAMAYDSAAIKLRSGDSHRNFPWTDKNIPEPDFQT 120

Query: 113 HYSTEAVINMIRDGSYSSR------------------------------------QLFQK 136
            YSTEA++NMIRDGSY  +                                    QLFQK
Sbjct: 121 QYSTEAILNMIRDGSYQPKFADFLRTQSGRQEQAGASFNNQTKVPGSDHGQFSCIQLFQK 180

Query: 137 ELTPSDVGKLNRLVIPKKYAVKYFPQISERVEEHAENDKA---------DDVQLVFHDKS 187
           ELTPSDVGKLNRLVIPKK+AVKYFP IS   EE  E ++          DD++LVF+D+ 
Sbjct: 181 ELTPSDVGKLNRLVIPKKFAVKYFPYISGNGEEEGEEEEEKVVGAPSVLDDIELVFYDRL 240

Query: 188 MKLWKFRYCYWKSSQSFVFTRGWNRFVKENQLKANDTICFYLCELRD--IAKGTKTFGMI 245
           MK WKFRYCYW+SSQSFVFTRGWNRFVKE  LK  D I FY C   D  + +G + F +I
Sbjct: 241 MKCWKFRYCYWRSSQSFVFTRGWNRFVKEKNLKEKDIITFYACASPDNRVQEG-QNFSLI 299

Query: 246 DAKKGENSGASAEVSGPYVDMKVDLQLQLGQNKKENKVEEDDNGNEIEATEEVELKAPSS 305
           D     N     + +    +M+ +L+L+LG   +  ++++DD   EI   +E+E K  ++
Sbjct: 300 DISY-SNGQVVVDGNNQMEEMQKELELRLGHTIRR-RLQKDDRVKEINGLKELESKNNNN 357

Query: 306 TSDSERKLFKLFGVEI 321
            +  + K  +LFGV I
Sbjct: 358 NNKMKGKGLRLFGVRI 373

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449462611|ref|XP_004149034.1| PREDICTED: AP2/ERF and B3 domain-containing transcription factor At1g51120-like [Cucumis sativus] gi|449525498|ref|XP_004169754.1| PREDICTED: AP2/ERF and B3 domain-containing transcription factor At1g51120-like [Cucumis sativus]

 Score =  311 bits (798), Expect = 2e-82,   Method: Compositional matrix adjust.
 Identities = 163/273 (59%), Positives = 187/273 (68%), Gaps = 47/273 (17%)

Query: 1   MEEEMLSIISNGETNVI--PELSDSISSTPLIPATKR------LRHASAVSKFKGVVPQQ 52
           ME+E  S + +   N I   E+SDS  +   IP  KR      L    AV KFKGVVPQQ
Sbjct: 1   MEDEASSSLLSHIKNPILAEEVSDSNFTYYAIPEAKRPRLDNDLNDVMAVGKFKGVVPQQ 60

Query: 53  NGHWGAQIYANHQRIWLGTFKSEKDAAMAYDSAAIRLRGVDSHRNFPWTKITIEEPNFQS 112
           NG WGAQIYANHQRIWLGTFK+EKDAAMAYDSA+I+LR  DSHRNFPWT+ TIEEPNFQ 
Sbjct: 61  NGRWGAQIYANHQRIWLGTFKTEKDAAMAYDSASIKLRTRDSHRNFPWTRRTIEEPNFQI 120

Query: 113 HYSTEAVINMIRDGSYSSR----------------------------------QLFQKEL 138
            +ST+AV++MI+DGSY S+                                   LFQKEL
Sbjct: 121 KFSTDAVLSMIKDGSYYSKFSAYLRTRSQIHDTNIQNPKKIDNGDGDSLFSCSHLFQKEL 180

Query: 139 TPSDVGKLNRLVIPKKYAVKYFPQISERVEEHAENDKADDVQLVFHDKSMKLWKFRYCYW 198
           TPSDVGKLNRLVIPKKYAVK+FP ISE  EE+      DD+++VF+D SMK+WKFRYCYW
Sbjct: 181 TPSDVGKLNRLVIPKKYAVKHFPYISESAEENG-----DDIEIVFYDTSMKIWKFRYCYW 235

Query: 199 KSSQSFVFTRGWNRFVKENQLKANDTICFYLCE 231
           +SSQSFVFTRGWNRFVKE +LKAND I FY  E
Sbjct: 236 RSSQSFVFTRGWNRFVKEKKLKANDIITFYTYE 268

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224088262|ref|XP_002308395.1| AP2 domain-containing transcription factor [Populus trichocarpa] gi|222854371|gb|EEE91918.1| AP2 domain-containing transcription factor [Populus trichocarpa]

 Score =  300 bits (768), Expect = 5e-79,   Method: Compositional matrix adjust.
 Identities = 176/358 (49%), Positives = 216/358 (60%), Gaps = 70/358 (19%)

Query: 1   MEEEMLSIISNGETNVIPELSDSISSTPLIPATKRLRHASAVS--KFKGVVPQQNGHWGA 58
           MEEE +S+I N ET+VI ELSDS SST   P  KR R  S VS  +FKGVVPQ NGHWG 
Sbjct: 1   MEEETVSLILNAETSVIEELSDSNSSTHPFPPNKRARSGSNVSASRFKGVVPQPNGHWGC 60

Query: 59  QIYANHQRIWLGTFKSEKDAAMAYDSAAIRLRGVDSHRNFPWTKITIEEPNFQSHYSTEA 118
           QIYANHQRIWLGTFKSE++AAMAYDSAAI+LR  DS RNFP T IT++EP FQS+YS E 
Sbjct: 61  QIYANHQRIWLGTFKSEREAAMAYDSAAIKLRSGDSRRNFPPTDITVQEPKFQSYYSIEV 120

Query: 119 VINMIRDGSYSSR--------------------------------QLFQKELTPSDVGKL 146
           V+ MI+DG+Y S+                                QLF+KELTPSDVGKL
Sbjct: 121 VLAMIKDGTYQSKFADFIRTCSQSVETALSLKLMMPQSSEGLTCKQLFRKELTPSDVGKL 180

Query: 147 NRLVIPKKYAVKYFPQISERVEEHAENDKADDVQLVFHDKSMKLWKFRYCYWKSSQSFVF 206
           NRLVIPKKYA+KYFP           N KA             L K R     ++QS+VF
Sbjct: 181 NRLVIPKKYAIKYFP-----------NTKA-------------LKKMRRL---TNQSYVF 213

Query: 207 TRGWNRFVKENQLKANDTICFYLCELRD-IAKGTKTFGMIDAKKGENSGASAEVSGPYVD 265
           TRGWNRFVKE +LKAND+I F+LCE  + +    +TF MID    EN    AE S   + 
Sbjct: 214 TRGWNRFVKEKKLKANDSIVFWLCESGETVDSAAQTFQMIDVSNCENISNIAESSNQSIA 273

Query: 266 MKVDLQLQLGQN-KKENKVEEDDNGNEIEATEEVELKAPSSTSDSERKLFKLFGVEIF 322
            KV+LQL  G    +++ V+++         E+  ++A   T D+ +  FKLFG++I 
Sbjct: 274 SKVELQLLQGPGIARDSTVKKN-------VEEDRMVRADKPTHDAVKTGFKLFGIQIM 324

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224073210|ref|XP_002304025.1| AP2 domain-containing transcription factor [Populus trichocarpa] gi|222841457|gb|EEE79004.1| AP2 domain-containing transcription factor [Populus trichocarpa]

 Score =  300 bits (768), Expect = 6e-79,   Method: Compositional matrix adjust.
 Identities = 161/322 (50%), Positives = 207/322 (64%), Gaps = 52/322 (16%)

Query: 42  VSKFKGVVPQQNGHWGAQIYANHQRIWLGTFKSEKDAAMAYDSAAIRLRGVDSHRNFPWT 101
           V+KFKG+VPQ+NGHWGAQIY+NHQRIWLGTFK+EK+AAMAYDSAAI+LR  DSHRNFPW 
Sbjct: 42  VAKFKGIVPQKNGHWGAQIYSNHQRIWLGTFKTEKEAAMAYDSAAIKLRSTDSHRNFPWN 101

Query: 102 KITIEEPNFQSHYSTEAVINMIRDGSY--------------------------------- 128
              ++EP+FQ+ YSTE ++NMIRDGSY                                 
Sbjct: 102 DRNVQEPSFQNQYSTEEILNMIRDGSYQQIFVDFIMKQSQREEIGGSDDPNGRRVHADDE 161

Query: 129 --SSRQLFQKELTPSDVGKLNRLVIPKKYAVKYFPQISERVEEHAENDKA--DDVQLVFH 184
             S  QLFQK+LTPSDVGKLNRLVIPKK+AVKYFP I + VE+    + A  DD +L+F+
Sbjct: 162 QFSCIQLFQKDLTPSDVGKLNRLVIPKKFAVKYFPNIFKDVEDDRVLNAAGVDDTELIFY 221

Query: 185 DKSMKLWKFRYCYWKSSQSFVFTRGWNRFVKENQLKANDTICFYLCE-----LRDIAKGT 239
           D+ MK WKFRYCYW+SSQSFVFT+GWNRFVKE +LK  D I FY C      L    +G 
Sbjct: 222 DRFMKSWKFRYCYWRSSQSFVFTKGWNRFVKEKKLKEKDIIIFYTCACPNKVLEQHGQG- 280

Query: 240 KTFGMIDAKKGENSGASAEVSGPYVDMKVDLQLQLGQNKKENKVEEDDNGNEIEATEEVE 299
           + F MID       G   +      D++ +L + L QN ++ K+++D  G E++  +E  
Sbjct: 281 QYFSMIDVVYCNGQGGKVDGFNQTEDVQRELAVVLRQNMRK-KLQKD--GKELKEEKE-- 335

Query: 300 LKAPSSTSDSERKLFKLFGVEI 321
               +  +  ++K F+LFGV+I
Sbjct: 336 ----TLKNKVKQKGFRLFGVQI 353

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|15223743|ref|NP_175524.1| RAV-like factor [Arabidopsis thaliana] gi|75268188|sp|Q9C688.1|RAVL3_ARATH RecName: Full=AP2/ERF and B3 domain-containing transcription factor At1g51120; AltName: Full=RAV1-like ethylene-responsive transcription factor At1g51120 gi|12320776|gb|AAG50531.1|AC079828_2 DNA-binding protein RAV1, putative [Arabidopsis thaliana] gi|48479358|gb|AAT44950.1| putative AP2/EREBP transcription factor [Arabidopsis thaliana] gi|332194503|gb|AEE32624.1| RAV-like factor [Arabidopsis thaliana]

 Score =  285 bits (730), Expect = 1e-74,   Method: Compositional matrix adjust.
 Identities = 149/291 (51%), Positives = 183/291 (62%), Gaps = 48/291 (16%)

Query: 10  SNGETNVIPELSDSISSTPLIPATKRLRHASAVSKFKGVVPQQNGHWGAQIYANHQRIWL 69
           ++G T+ +  L+  +  T +   TK     S  +KFKGVV QQNGHWGAQIYA+H+RIWL
Sbjct: 14  TSGLTDSVLSLTKRMKPTEVTTTTKPA--LSNTTKFKGVVQQQNGHWGAQIYADHRRIWL 71

Query: 70  GTFKSEKDAAMAYDSAAIRLRGVD--SHRNFPWTKITIEEPNFQSHYSTEAVINMIRDGS 127
           GTFKS  +AA AYDSA+I+LR  D  SHRNFPW+  T+ EP+FQ  Y+TEAV+NMIRDGS
Sbjct: 72  GTFKSAHEAAAAYDSASIKLRSFDANSHRNFPWSDFTLHEPDFQECYTTEAVLNMIRDGS 131

Query: 128 Y----------------------------------------SSRQLFQKELTPSDVGKLN 147
           Y                                        S  QLFQKELTPSDVGKLN
Sbjct: 132 YQHKFRDFLRIRSQIVANINIVGSKQVLGGGEGGQESNKCFSCTQLFQKELTPSDVGKLN 191

Query: 148 RLVIPKKYAVKYFPQISERVEEHAENDKADDVQLVFHDKSMKLWKFRYCYWKSSQSFVFT 207
           RLVIPKKYAVKY P IS+   E   ++  +DV++VF+D++M+ WKFRYCYW+SSQSFVFT
Sbjct: 192 RLVIPKKYAVKYMPFISDDQSEKETSEGVEDVEVVFYDRAMRQWKFRYCYWRSSQSFVFT 251

Query: 208 RGWNRFVKENQLKANDTICFYLCELRDIAKG----TKTFGMIDAKKGENSG 254
           RGWN FVKE  LK  D I FY C++ +  K     +KTF MID      +G
Sbjct: 252 RGWNGFVKEKNLKEKDIIVFYTCDVPNNVKTLEGQSKTFLMIDVHHFSGNG 302

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297852776|ref|XP_002894269.1| hypothetical protein ARALYDRAFT_474200 [Arabidopsis lyrata subsp. lyrata] gi|297340111|gb|EFH70528.1| hypothetical protein ARALYDRAFT_474200 [Arabidopsis lyrata subsp. lyrata]

 Score =  283 bits (725), Expect = 6e-74,   Method: Compositional matrix adjust.
 Identities = 157/324 (48%), Positives = 194/324 (59%), Gaps = 54/324 (16%)

Query: 20  LSDSISSTPLIPATKRLRHASAVSKFKGVVPQQNGHWGAQIYANHQRIWLGTFKSEKDAA 79
           L+D   +  ++ +  +    S   K+KGVV QQNGHWGAQIYA+H+RIWLGTFKS  +AA
Sbjct: 3   LNDEPENALVVSSATKTVVVSGNVKYKGVVQQQNGHWGAQIYADHKRIWLGTFKSAAEAA 62

Query: 80  MAYDSAAIRLRGVD--SHRNFPWTKITIEEPNFQSHYSTEAVINMIRDGSY--------- 128
            AYDSA+I+LR  D  SHRNFPW+ IT+ EP+FQ  Y+TE V+NMIRDGSY         
Sbjct: 63  TAYDSASIKLRSFDANSHRNFPWSNITVHEPDFQDCYTTETVLNMIRDGSYPHKFRDFLR 122

Query: 129 -----------------------------SSRQLFQKELTPSDVGKLNRLVIPKKYAVKY 159
                                        S  QLFQKELTPSDVGKLNRLVIPKKYAVKY
Sbjct: 123 VRSQIVASMNIGGTKQVRGEVNQESDKCFSCTQLFQKELTPSDVGKLNRLVIPKKYAVKY 182

Query: 160 FPQISERVEEHAEND---KADDVQLVFHDKSMKLWKFRYCYWKSSQSFVFTRGWNRFVKE 216
            P IS+   E  + +     +DV++VF+D++M+ WKFRYCYWKSSQSFVFTRGWN FVKE
Sbjct: 183 MPFISDDQSEKEDGEIGGSVEDVEVVFYDRAMRQWKFRYCYWKSSQSFVFTRGWNSFVKE 242

Query: 217 NQLKANDTICFYLCELRDIAKG----TKTFGMIDAKKGENSG--ASAEVSGPYVD----- 265
             LK  D I FY C++ +  K     +KTF MID     ++G   + EVS    D     
Sbjct: 243 KNLKEKDVIVFYTCDVPNNVKTLEGQSKTFLMIDVHYFSDNGTVVAEEVSMTVHDSSEEG 302

Query: 266 MKVDLQLQLGQNKKENKVEEDDNG 289
           MK +  +      KE K EE+  G
Sbjct: 303 MKTENFVSSKSKDKETKTEENKGG 326

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

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	322
TAIR|locus:2026058	352	AT1G51120 [Arabidopsis thalian	0.546	0.5	0.484	8.5e-75
TAIR|locus:2015832	337	AT1G50680 [Arabidopsis thalian	0.527	0.504	0.502	3.7e-74
TAIR|locus:2031185	361	TEM1 "TEMPRANILLO 1" [Arabidop	0.319	0.285	0.490	4.7e-44
TAIR|locus:2164215	282	DPA4 "DEVELOPMENT-RELATED PcG	0.695	0.794	0.321	5.9e-25
TAIR|locus:2012438	352	RAV2 "related to ABI3/VP1 2" [	0.456	0.417	0.395	7.9e-24
TAIR|locus:2080782	267	AT3G11580 [Arabidopsis thalian	0.319	0.385	0.514	2.3e-23
TAIR|locus:2117007	333	NGA4 "NGATHA4" [Arabidopsis th	0.282	0.273	0.528	3.8e-23
TAIR|locus:2205319	344	RAV1 "related to ABI3/VP1 1" [	0.295	0.276	0.529	6.1e-23
TAIR|locus:2079537	299	NGA2 "NGATHA2" [Arabidopsis th	0.298	0.321	0.495	1.3e-22
TAIR|locus:2039165	244	ABS2 "ABNORMAL SHOOT 2" [Arabi	0.350	0.463	0.456	1.6e-22

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

 Score = 411 (149.7 bits), Expect = 8.5e-75, Sum P(2) = 8.5e-75
 Identities = 96/198 (48%), Positives = 125/198 (63%)

Query:   128 YSSRQLFQKELTPSDVGKLNRLVIPKKYAVKYFPQISERVEEHAENDKADDVQLVFHDKS 187
             +S  QLFQKELTPSDVGKLNRLVIPKKYAVKY P IS+   E   ++  +DV++VF+D++
Sbjct:   172 FSCTQLFQKELTPSDVGKLNRLVIPKKYAVKYMPFISDDQSEKETSEGVEDVEVVFYDRA 231

Query:   188 MKLWKFRYCYWKSSQSFVFTRGWNRFVKENQLKANDTICFYLCELRDIAK---G-TKTFG 243
             M+ WKFRYCYW+SSQSFVFTRGWN FVKE  LK  D I FY C++ +  K   G +KTF 
Sbjct:   232 MRQWKFRYCYWRSSQSFVFTRGWNGFVKEKNLKEKDIIVFYTCDVPNNVKTLEGQSKTFL 291

Query:   244 MIDAKKGENSGASAEVSGPYVDMKVDLQLQLGQNKKENKVEEDDNGNEIEATEEVELKAP 303
             MID      SG     +G  V  +V        NK  +++ +++   E   T +VE    
Sbjct:   292 MIDVH--HFSG-----NGFVVPEEV--------NKTVHEISDEEMKTETLFTSKVE---E 333

Query:   304 SSTSDSERKLFKLFGVEI 321
              + S+ ++  F LFGV I
Sbjct:   334 ETKSEEKKGGFMLFGVRI 351

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:2015832 AT1G50680 [Arabidopsis thaliana (taxid:3702)]

 Score = 413 (150.4 bits), Expect = 3.7e-74, Sum P(2) = 3.7e-74
 Identities = 91/181 (50%), Positives = 116/181 (64%)

Query:   120 INMIRDGSYSSRQLFQKELTPSDVGKLNRLVIPKKYAVKYFPQISERVEEHAEND---KA 176
             +N   D  +S  QLFQKELTPSDVGKLNRLVIPKKYAVKY P IS    E  E +     
Sbjct:   143 VNQESDKCFSCTQLFQKELTPSDVGKLNRLVIPKKYAVKYMPFISADQSEKEEGEIVGSV 202

Query:   177 DDVQLVFHDKSMKLWKFRYCYWKSSQSFVFTRGWNRFVKENQLKANDTICFYLCELRDIA 236
             +DV++VF+D++M+ WKFRYCYWKSSQSFVFTRGWN FVKE  LK  D I FY C++ +  
Sbjct:   203 EDVEVVFYDRAMRQWKFRYCYWKSSQSFVFTRGWNSFVKEKNLKEKDVIAFYTCDVPNNV 262

Query:   237 K---GT-KTFGMIDAKKGENSGA--SAEVSGPYVDMKVDLQLQLGQNKKENKVEEDDNGN 290
             K   G  K F MID     ++G+  + EVS    D  V  Q++  +N   + +E+ +  +
Sbjct:   263 KTLEGQRKNFLMIDVHCFSDNGSVVAEEVSMTVHDSSV--QVKKTENLVSSMLEDKETKS 320

Query:   291 E 291
             E
Sbjct:   321 E 321

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

 Score = 270 (100.1 bits), Expect = 4.7e-44, Sum P(2) = 4.7e-44
 Identities = 51/104 (49%), Positives = 69/104 (66%)

Query:   125 DGSYSSRQ-LFQKELTPSDVGKLNRLVIPKKYAVKYFPQISERVEEHAENDKADDVQLVF 183
             D    +R+ LF+K +TPSDVGKLNRLVIPK++A K+FP  +              V +  
Sbjct:   185 DAVLRAREVLFEKTVTPSDVGKLNRLVIPKQHAEKHFPLPAMTTAMGMNPSPTKGVLINL 244

Query:   184 HDKSMKLWKFRYCYWKSSQSFVFTRGWNRFVKENQLKANDTICF 227
              D++ K+W+FRY YW SSQS+V T+GW+RFVKE  L+A D +CF
Sbjct:   245 EDRTGKVWRFRYSYWNSSQSYVLTKGWSRFVKEKNLRAGDVVCF 288

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

 Score = 284 (105.0 bits), Expect = 5.9e-25, P = 5.9e-25
 Identities = 75/233 (32%), Positives = 109/233 (46%)

Query:    93 DSHRNFPWTKITIEEPNFQSHYSTEAVINMIRDGSYSSRQLFQKELTPSDVGKLNRLVIP 152
             D H    W +         S  +T A    + D    S  LF+K LTPSDVGKLNRLVIP
Sbjct:     9 DHHHTLLWQQQQHRHTTDTSETTTTAT--WLHDDLKES--LFEKSLTPSDVGKLNRLVIP 64

Query:   153 KKYAVKYFPQISERVEEHAENDKADD--VQLVFHDKSMKLWKFRYCYWKSSQSFVFTRGW 210
             K++A KYFP  +  V   A +  + +  + L F D+S K W+FRY YW SSQS+V T+GW
Sbjct:    65 KQHAEKYFPLNAVLVSSAAADTSSSEKGMLLSFEDESGKSWRFRYSYWNSSQSYVLTKGW 124

Query:   211 NRFVKENQLKANDTICF--YLCELRDIAKGTKTFGMIDAKKGENSGASAEVSGPYVDMKV 268
             +RFVK+ QL   D + F  +  + R +  G +  G   +     + ++   S        
Sbjct:   125 SRFVKDKQLDPGDVVFFQRHRSDSRRLFIGWRRRGQGSSSSVAATNSAVNTSSMGALSYH 184

Query:   269 DLQLQLGQNKKENKVEEDDNGNEIEATEEVELKAPSSTSDSERKLFKLFGVEI 321
              +      +   +  E    G  +    E     PSS+     +  +LFGV +
Sbjct:   185 QIHATSNYSNPPSHSEYSHYGAAVATAAETH-STPSSSVVGSSRTVRLFGVNL 236

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

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

 Score = 251 (93.4 bits), Expect = 7.9e-24, Sum P(2) = 7.9e-24
 Identities = 66/167 (39%), Positives = 95/167 (56%)

Query:    72 FKSE-KDAAMAYDSAAIRLRGVDSHRNFPWTKITIEEPNFQSHY-STEAVINMIRDGSYS 129
             FK+  +D  +A+  A  +   VD  R   +    +E+ N +  + S +A  N  R+GS +
Sbjct:   118 FKNVLEDGDLAFLEAHSKAEIVDMLRKHTYAD-ELEQNNKRQLFLSVDA--NGKRNGSST 174

Query:   130 SRQ---------LFQKELTPSDVGKLNRLVIPKKYAVKYFPQISERVEEHAENDKADDVQ 180
             ++          LF+K +TPSDVGKLNRLVIPK++A K+FP  S              V 
Sbjct:   175 TQNDKVLKTREVLFEKAVTPSDVGKLNRLVIPKQHAEKHFPLPSPSPAV------TKGVL 228

Query:   181 LVFHDKSMKLWKFRYCYWKSSQSFVFTRGWNRFVKENQLKANDTICF 227
             + F D + K+W+FRY YW SSQS+V T+GW+RFVKE  L+A D + F
Sbjct:   229 INFEDVNGKVWRFRYSYWNSSQSYVLTKGWSRFVKEKNLRAGDVVTF 275

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:2080782 AT3G11580 [Arabidopsis thaliana (taxid:3702)]

 Score = 269 (99.8 bits), Expect = 2.3e-23, P = 2.3e-23
 Identities = 55/107 (51%), Positives = 72/107 (67%)

Query:   125 DGSYSSRQ-LFQKELTPSDVGKLNRLVIPKKYAVKYFPQISERVEEHAENDKADDVQ--- 180
             D + + R+ LF+K LTPSDVGKLNRLVIPK++A KYFP  +      + +D A   +   
Sbjct:    19 DVAIAQRESLFEKSLTPSDVGKLNRLVIPKQHAEKYFPLNNNNNNGGSGDDVATTEKGML 78

Query:   181 LVFHDKSMKLWKFRYCYWKSSQSFVFTRGWNRFVKENQLKANDTICF 227
             L F D+S K WKFRY YW SSQS+V T+GW+R+VK+  L A D + F
Sbjct:    79 LSFEDESGKCWKFRYSYWNSSQSYVLTKGWSRYVKDKHLDAGDVVFF 125

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:0009062 "fatty acid catabolic process" evidence=RCA

TAIR|locus:2117007 NGA4 "NGATHA4" [Arabidopsis thaliana (taxid:3702)]

 Score = 267 (99.0 bits), Expect = 3.8e-23, P = 3.8e-23
 Identities = 55/104 (52%), Positives = 71/104 (68%)

Query:   128 YSSRQ---LFQKELTPSDVGKLNRLVIPKKYAVKYFPQISERVEEHAENDKADDVQLVFH 184
             YSS +   +F K LTPSDVGKLNRLVIPK++A  +FP     +E++      D     F 
Sbjct:    27 YSSERREHMFDKVLTPSDVGKLNRLVIPKQHAENFFP-----LEDNQNGTVLD-----FQ 76

Query:   185 DKSMKLWKFRYCYWKSSQSFVFTRGWNRFVKENQLKANDTICFY 228
             DK+ K+W+FRY YW SSQS+V T+GW+RFVKE +L A DT+ FY
Sbjct:    77 DKNGKMWRFRYSYWNSSQSYVMTKGWSRFVKEKKLFAGDTVSFY 120

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

 Score = 265 (98.3 bits), Expect = 6.1e-23, P = 6.1e-23
 Identities = 54/102 (52%), Positives = 67/102 (65%)

Query:   126 GSYSSRQLFQKELTPSDVGKLNRLVIPKKYAVKYFPQISERVEEHAENDKADDVQLVFHD 185
             G  S+  LF+K +TPSDVGKLNRLVIPK +A K+FP  S  V           V L F D
Sbjct:   180 GFRSAEALFEKAVTPSDVGKLNRLVIPKHHAEKHFPLPSSNVS-------VKGVLLNFED 232

Query:   186 KSMKLWKFRYCYWKSSQSFVFTRGWNRFVKENQLKANDTICF 227
              + K+W+FRY YW SSQS+V T+GW+RFVKE  L+A D + F
Sbjct:   233 VNGKVWRFRYSYWNSSQSYVLTKGWSRFVKEKNLRAGDVVSF 274

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:2079537 NGA2 "NGATHA2" [Arabidopsis thaliana (taxid:3702)]

 Score = 262 (97.3 bits), Expect = 1.3e-22, P = 1.3e-22
 Identities = 50/101 (49%), Positives = 66/101 (65%)

Query:   127 SYSSRQLFQKELTPSDVGKLNRLVIPKKYAVKYFPQISERVEEHAENDKADDVQLVFHDK 186
             S     +F K +TPSDVGKLNRLVIPK++A +YFP     ++    ND    + L F D+
Sbjct:    16 SMEREHMFDKVVTPSDVGKLNRLVIPKQHAERYFP-----LDNSTTNDSNKGLLLNFEDR 70

Query:   187 SMKLWKFRYCYWKSSQSFVFTRGWNRFVKENQLKANDTICF 227
             S   W+FRY YW SSQS+V T+GW+RFVK+ +L A D + F
Sbjct:    71 SGNSWRFRYSYWNSSQSYVMTKGWSRFVKDKKLDAGDIVSF 111

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 = 261 (96.9 bits), Expect = 1.6e-22, P = 1.6e-22
 Identities = 57/125 (45%), Positives = 80/125 (64%)

Query:   133 LFQKELTPSDVGKLNRLVIPKKYAVKYFPQISERVEEHAENDKADDVQLVFHDKSMKLWK 192
             LF+K LTPSDVGKLNRLVIPK++A +YFP ++    +  E      + L F D+  K W+
Sbjct:    37 LFEKPLTPSDVGKLNRLVIPKQHAERYFP-LAAAAADAVEKG----LLLCFEDEEGKPWR 91

Query:   193 FRYCYWKSSQSFVFTRGWNRFVKENQLKANDTICFYLCELRDIAKGTKTF-GMIDAKKGE 251
             FRY YW SSQS+V T+GW+R+VKE  L A D + F+    R  + G + F G    ++G+
Sbjct:    92 FRYSYWNSSQSYVLTKGWSRYVKEKHLDAGDVVLFH----RHRSDGGRFFIGW--RRRGD 145

Query:   252 NSGAS 256
             +S +S
Sbjct:   146 SSSSS 150

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

---

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)
Q9C688	RAVL3_ARATH	No assigned EC number	0.5120	0.7546	0.6903	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

Your Input: GSVIVG00017239001 SubName- Full=Chromosome chr11 scaffold_14, whole genome shotgun sequence; Flags- Fragment; (359 aa) (Vitis vinifera)

Predicted Functional Partners:

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

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	322
cd10017	98	cd10017, B3_DNA, Plant-specific B3-DNA binding dom	2e-24
smart01019	96	smart01019, B3, B3 DNA binding domain	9e-24
pfam02362	97	pfam02362, B3, B3 DNA binding domain	1e-23
cd00018	61	cd00018, AP2, DNA-binding domain found in transcri	3e-23
smart00380	64	smart00380, AP2, DNA-binding domain in plant prote	1e-19
cd10015	109	cd10015, BfiI_C_EcoRII_N_B3, DNA binding domains o	2e-07
pfam03754	112	pfam03754, DUF313, Domain of unknown function (DUF	2e-07
pfam00847	53	pfam00847, AP2, AP2 domain	1e-04

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

 Score = 94.7 bits (236), Expect = 2e-24
 Identities = 35/97 (36%), Positives = 46/97 (47%), Gaps = 13/97 (13%)

Query: 133 LFQKELTPSDVGKLNRLVIPKKYAVKYFPQISERVEEHAENDKADDVQLVFHDKSMKLWK 192
           LF K LTPSDV  L RLV+PKK+A  + P               + V++   D   K W 
Sbjct: 2   LFFKVLTPSDVSSLGRLVLPKKFAKAHLPPK-------------EGVEVTLEDPDGKKWT 48

Query: 193 FRYCYWKSSQSFVFTRGWNRFVKENQLKANDTICFYL 229
            +    K+S   V + GW  FV+ N LK  D + F L
Sbjct: 49  VKLKKRKNSGRMVLSGGWKEFVRANGLKEGDFLVFEL 85

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 = 92.7 bits (231), Expect = 9e-24
 Identities = 36/96 (37%), Positives = 47/96 (48%), Gaps = 13/96 (13%)

Query: 134 FQKELTPSDVGKLNRLVIPKKYAVKYFPQISERVEEHAENDKADDVQLVFHDKSMKLWKF 193
           F K LT SDV K  RLV+PK++A    P +  +             ++   D   K WK 
Sbjct: 1   FFKTLTTSDVSKHGRLVLPKQFAESNGPPLKPK-------------EITLLDPDGKSWKV 47

Query: 194 RYCYWKSSQSFVFTRGWNRFVKENQLKANDTICFYL 229
           +  Y  SS  F+ T GW  FVK N LKA D++ F L
Sbjct: 48  KLKYRGSSGMFLLTGGWKEFVKANGLKAGDSLTFEL 83

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

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

 Score = 92.4 bits (230), Expect = 1e-23
 Identities = 35/98 (35%), Positives = 46/98 (46%), Gaps = 13/98 (13%)

Query: 134 FQKELTPSDVGKLNRLVIPKKYAVKYFPQISERVEEHAENDKADDVQLVFHDKSMKLWKF 193
           F K LTPSDV K  RLV+PKK+A +                     ++   D   K W  
Sbjct: 1   FVKVLTPSDVSKDGRLVLPKKFAEENG-------------LNKKGQEITLLDPDGKSWTV 47

Query: 194 RYCYWKSSQSFVFTRGWNRFVKENQLKANDTICFYLCE 231
           +  Y KS + ++ T GW  FVK N LKA D++ F L  
Sbjct: 48  KLRYRKSGRRYLLTSGWKEFVKANGLKAGDSLVFKLDG 85

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 = 90.4 bits (225), Expect = 3e-23
 Identities = 28/61 (45%), Positives = 41/61 (67%), Gaps = 2/61 (3%)

Query: 43  SKFKGVVPQQNGHWGAQIY--ANHQRIWLGTFKSEKDAAMAYDSAAIRLRGVDSHRNFPW 100
           SK++GV  +  G W A+I   +  +RIWLGTF + ++AA AYD AA++LRG  +  NFP 
Sbjct: 1   SKYRGVRQRPWGKWVAEIRDPSGGRRIWLGTFDTAEEAARAYDRAALKLRGSSAVLNFPD 60

Query: 101 T 101
           +
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 = 81.2 bits (201), Expect = 1e-19
 Identities = 25/58 (43%), Positives = 37/58 (63%), Gaps = 2/58 (3%)

Query: 44 KFKGVVPQQNGHWGAQIY--ANHQRIWLGTFKSEKDAAMAYDSAAIRLRGVDSHRNFP 99
          K++GV  +  G W A+I   +  +R+WLGTF + ++AA AYD AA + RG  +  NFP
Sbjct: 1  KYRGVRQRPWGKWVAEIRDPSKGKRVWLGTFDTAEEAARAYDRAAFKFRGRSARLNFP 58

Length = 64

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

 Score = 48.4 bits (115), Expect = 2e-07
 Identities = 28/102 (27%), Positives = 43/102 (42%), Gaps = 12/102 (11%)

Query: 133 LFQKELTPSDVGK----LNRLVIPKKYAVKYFPQISERVEEHAENDKADDVQLVFHDKSM 188
           +  K L+ +D G        L IPK    K+ P I+   E +        + L  HD S 
Sbjct: 2   VLIKRLSANDTGATGGHQVGLYIPKGIVEKFPPSINHTREAN------PSIFLTMHDISD 55

Query: 189 -KLWKFRYCYWKSSQSFVF-TRGWNRFVKENQLKANDTICFY 228
            + W+ R  ++ S+++    TRG   FVK+N L   D     
Sbjct: 56  CRDWEARAIFYNSNRNEKRLTRGGRGFVKQNPLNTGDLTLIA 97

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|217713 pfam03754, DUF313, Domain of unknown function (DUF313)

 Score = 48.5 bits (116), Expect = 2e-07
 Identities = 27/109 (24%), Positives = 49/109 (44%), Gaps = 8/109 (7%)

Query: 116 TEAVINMIRD--GSYSSRQLFQKELTPSDVGKL-NRLVIPKKYAVKY-F--PQISERVEE 169
            E ++ ++R   G+   + + +K L  +DV    +RL +P    ++  F   +    +EE
Sbjct: 4   PEWLLKVMRKMNGAEDPKLIIEKTLFKTDVDPTQSRLSMPFNQLLRNDFLTEEEKRIIEE 63

Query: 170 HAENDKADDVQLVFHDKSMKLWKFRYCYW--KSSQSFVFTRGWNRFVKE 216
               DK   V ++  D   K W  +   W  KS+ ++V   GWN  V+ 
Sbjct: 64  DKNKDKDIGVGVILVDPESKKWVLKLKKWDMKSTLNYVLVCGWNDVVEA 112

Family of proteins from Arabidopsis thaliana with uncharacterized function. Length = 112

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

 Score = 38.8 bits (91), Expect = 1e-04
 Identities = 21/54 (38%), Positives = 31/54 (57%), Gaps = 6/54 (11%)

Query: 43 SKFKGVV-PQQNGHWGAQIYAN----HQRIWLGTFKSEKDAAMAYDSAAIRLRG 91
          S +KGV   ++ G W A+I        +R  LGTF +E+ AA A  +A ++LRG
Sbjct: 1  SGYKGVRYDKRWGRWVAEIRDPGEKKKKRFSLGTFGTEE-AARAAIAARLKLRG 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	322
cd00018	61	AP2 DNA-binding domain found in transcription regu	99.76
smart00380	64	AP2 DNA-binding domain in plant proteins such as A	99.75
PF02362	100	B3: B3 DNA binding domain; InterPro: IPR003340 Two	99.72
PHA00280	121	putative NHN endonuclease	99.55
PF00847	56	AP2: AP2 domain; InterPro: IPR001471 Pathogenesis-	98.98
PF03754	114	DUF313: Domain of unknown function (DUF313) ; Inte	98.91
PF09217	156	EcoRII-N: Restriction endonuclease EcoRII, N-termi	97.45

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

Probab=99.76  E-value=1.1e-18  Score=128.97  Aligned_cols=59  Identities=47%  Similarity=0.821  Sum_probs=56.6

Q ss_pred             CceEEEEECCCCeEEEEEeeC--CeeEEecCCCCHHHHHHHHHHHHHHhcCCCCCCCCCcc
Q 020733           43 SKFKGVVPQQNGHWGAQIYAN--HQRIWLGTFKSEKDAAMAYDSAAIRLRGVDSHRNFPWT  101 (322)
Q Consensus        43 S~yrGV~~~~~gkw~A~I~~~--~k~~~LG~f~t~eeAa~Ayd~aa~~~~g~~a~~NFp~~  101 (322)
                      |+|+||+++++|+|+|+|+.+  ++++|||+|+|+||||.|||.|+++++|.++.+|||.+
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            799999998889999999998  99999999999999999999999999999999999964

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.

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

Probab=99.75  E-value=3.8e-18  Score=127.38  Aligned_cols=61  Identities=41%  Similarity=0.768  Sum_probs=58.5

Q ss_pred             ceEEEEECCCCeEEEEEee--CCeeEEecCCCCHHHHHHHHHHHHHHhcCCCCCCCCCccccc
Q 020733           44 KFKGVVPQQNGHWGAQIYA--NHQRIWLGTFKSEKDAAMAYDSAAIRLRGVDSHRNFPWTKIT  104 (322)
Q Consensus        44 ~yrGV~~~~~gkw~A~I~~--~~k~~~LG~f~t~eeAa~Ayd~aa~~~~g~~a~~NFp~~~y~  104 (322)
                      +|+||+++++|+|+|+|+.  +++.+|||+|+|+||||.|||.|+++++|..+.+|||.++|+
T Consensus         1 ~~kGV~~~~~gkw~A~I~~~~~~k~~~lG~f~t~eeAa~Ayd~a~~~~~g~~a~~Nf~~~~y~   63 (64)
T smart00380        1 KYRGVRQRPWGKWVAEIRDPSKGKRVWLGTFDTAEEAARAYDRAAFKFRGRSARLNFPNSLYD   63 (64)
T ss_pred             CEeeEEeCCCCeEEEEEEecCCCcEEecCCCCCHHHHHHHHHHHHHHhcCCccccCCCCccCC
Confidence            4899998888999999999  999999999999999999999999999999999999999884

>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=99.72  E-value=2.6e-17  Score=131.48  Aligned_cols=87  Identities=34%  Similarity=0.563  Sum_probs=68.3

Q ss_pred             cccccCccccccccccccchhhHhhcCCCCchhhhhhcccCCCCCeEEEEEeCCCceEEEEEEEeCCCCceEEccChHHH
Q 020733          134 FQKELTPSDVGKLNRLVIPKKYAVKYFPQISERVEEHAENDKADDVQLVFHDKSMKLWKFRYCYWKSSQSFVFTRGWNRF  213 (322)
Q Consensus       134 F~K~LT~SDV~~~~rL~IPk~~a~~~lP~l~~~~~~~~~~~~~~~~~l~~~D~~gk~W~fr~~~~~~~~~yvLt~GW~~F  213 (322)
                      |.|+|++||+...++|.||+++++.|....            ..+..+.+.|..|+.|.+++++++.+.+++|++||..|
T Consensus         1 F~K~l~~s~~~~~~~l~iP~~f~~~~~~~~------------~~~~~v~l~~~~g~~W~v~~~~~~~~~~~~l~~GW~~F   68 (100)
T PF02362_consen    1 FFKVLKPSDVSSSCRLIIPKEFAKKHGGNK------------RKSREVTLKDPDGRSWPVKLKYRKNSGRYYLTGGWKKF   68 (100)
T ss_dssp             EEEE--TTCCCCTT-EEE-HHHHTTTS--S------------S--CEEEEEETTTEEEEEEEEEECCTTEEEEETTHHHH
T ss_pred             CEEEEEccCcCCCCEEEeCHHHHHHhCCCc------------CCCeEEEEEeCCCCEEEEEEEEEccCCeEEECCCHHHH
Confidence            789999999988889999999999973111            24668888999999999999999988889999999999


Q ss_pred             HhhcCCCCCCEEEEEEeec
Q 020733          214 VKENQLKANDTICFYLCEL  232 (322)
Q Consensus       214 V~~k~L~~GD~i~F~~~~~  232 (322)
                      |++|+|++||+|+|+...+
T Consensus        69 v~~n~L~~GD~~~F~~~~~   87 (100)
T PF02362_consen   69 VRDNGLKEGDVCVFELIGN   87 (100)
T ss_dssp             HHHCT--TT-EEEEEE-SS
T ss_pred             HHHcCCCCCCEEEEEEecC
Confidence            9999999999999999865

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.

>PHA00280 putative NHN endonuclease

Probab=99.55  E-value=6.6e-15  Score=123.01  Aligned_cols=71  Identities=15%  Similarity=0.107  Sum_probs=63.9

Q ss_pred             CCCCCCCCcCcccCCCCCCCceEEEEE-CCCCeEEEEEeeCCeeEEecCCCCHHHHHHHHHHHHHHhcCCCCC
Q 020733           24 ISSTPLIPATKRLRHASAVSKFKGVVP-QQNGHWGAQIYANHQRIWLGTFKSEKDAAMAYDSAAIRLRGVDSH   95 (322)
Q Consensus        24 ~~~~~~~~~~~r~~~~~~~S~yrGV~~-~~~gkw~A~I~~~~k~~~LG~f~t~eeAa~Ayd~aa~~~~g~~a~   95 (322)
                      +..+...+..+++.+++|+|||+||++ ++.|||+|+|.++||+++||.|+++|+|+.||+ ++.+|||.+|.
T Consensus        48 r~~T~~eN~~N~~~~~~N~SG~kGV~~~k~~~kw~A~I~~~gK~~~lG~f~~~e~A~~a~~-~~~~lhGeFa~  119 (121)
T PHA00280         48 RLALPKENSWNMKTPKSNTSGLKGLSWSKEREMWRGTVTAEGKQHNFRSRDLLEVVAWIYR-TRRELHGQFAR  119 (121)
T ss_pred             hhcCHHHHhcccCCCCCCCCCCCeeEEecCCCeEEEEEEECCEEEEcCCCCCHHHHHHHHH-HHHHHhhcccc
Confidence            456667788888889999999999987 678999999999999999999999999999997 77899999875

>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=98.98  E-value=1.1e-09  Score=79.07  Aligned_cols=50  Identities=36%  Similarity=0.472  Sum_probs=44.5

Q ss_pred             CceEEEEE-CCCCeEEEEEeeC-----CeeEEecCCCCHHHHHHHHHHHHHHhcCC
Q 020733           43 SKFKGVVP-QQNGHWGAQIYAN-----HQRIWLGTFKSEKDAAMAYDSAAIRLRGV   92 (322)
Q Consensus        43 S~yrGV~~-~~~gkw~A~I~~~-----~k~~~LG~f~t~eeAa~Ayd~aa~~~~g~   92 (322)
                      |+|+||++ +..++|+|+|++.     ++.++||.|+++++|+.|++.++..++|.
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            78999987 5689999999982     49999999999999999999999999873

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=98.91  E-value=5.1e-09  Score=86.89  Aligned_cols=99  Identities=28%  Similarity=0.601  Sum_probs=75.6

Q ss_pred             hhHhhhhhc--CCCccccccccccCcccc-ccccccccchhhHhhcCCCCchh---h--hhhcccCCCCCeEEEEEeCCC
Q 020733          117 EAVINMIRD--GSYSSRQLFQKELTPSDV-GKLNRLVIPKKYAVKYFPQISER---V--EEHAENDKADDVQLVFHDKSM  188 (322)
Q Consensus       117 Eevi~aLR~--gs~s~~~~F~K~LT~SDV-~~~~rL~IPk~~a~~~lP~l~~~---~--~~~~~~~~~~~~~l~~~D~~g  188 (322)
                      +.+.+.++.  +.+....++.|.|+.||| .+++||.||...+.. ..+|...   .  +++.......|+.+.+.|..+
T Consensus         5 ~~l~~~m~~~~g~~d~kli~~K~L~~tDv~~~qsRLsmP~~qi~~-~dFLt~eE~~~i~~~~~~~~~~~Gv~V~lvdp~~   83 (114)
T PF03754_consen    5 EWLKNVMREMNGAEDPKLIIEKTLFKTDVDPHQSRLSMPFNQIID-NDFLTEEEKRIIKEEKKNNDKKKGVEVILVDPSL   83 (114)
T ss_pred             HHHHHHHHHhcCCCCCeEEEeeeecccCCCCCCceeeccHHHhcc-cccCCHHHHHHHHHhhccCcccCCceEEEECCcC
Confidence            344455553  335568899999999999 568999999998866 4555521   1  112233556899999999999


Q ss_pred             ceEEEEEEEeCC---CCceEEccChHHHHhh
Q 020733          189 KLWKFRYCYWKS---SQSFVFTRGWNRFVKE  216 (322)
Q Consensus       189 k~W~fr~~~~~~---~~~yvLt~GW~~FV~~  216 (322)
                      +.|.++++.|..   +..|+|..||+.+|.+
T Consensus        84 ~~~~m~lkkW~mg~~~~~YvL~~gWn~VV~~  114 (114)
T PF03754_consen   84 RKWTMRLKKWNMGNGTSNYVLNSGWNKVVED  114 (114)
T ss_pred             cEEEEEEEEecccCCceEEEEEcChHhhccC
Confidence            999999999987   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=97.45  E-value=0.00025  Score=61.42  Aligned_cols=92  Identities=23%  Similarity=0.380  Sum_probs=57.0

Q ss_pred             cccccccccCcccc----ccccccccchhhHhhcCCCCchhhhhhcccCCCCCeEEEEEeCCC--ceEEEEEEEeCC---
Q 020733          130 SRQLFQKELTPSDV----GKLNRLVIPKKYAVKYFPQISERVEEHAENDKADDVQLVFHDKSM--KLWKFRYCYWKS---  200 (322)
Q Consensus       130 ~~~~F~K~LT~SDV----~~~~rL~IPk~~a~~~lP~l~~~~~~~~~~~~~~~~~l~~~D~~g--k~W~fr~~~~~~---  200 (322)
                      ...+|.|.|++.|+    +++.++.||+..+..+||.+...      ....+.+.|.+.+..+  ..|.||++|.++   
T Consensus         6 ~~~~~~K~LSaNDtGaTGgHQaGiyIpk~~~~~lFp~~~~~------~~~Np~~~~~~~~~s~~~~~~~~r~iYYnn~~~   79 (156)
T PF09217_consen    6 SWAIYCKRLSANDTGATGGHQAGIYIPKSAAELLFPSINHT------KEENPDIWLKARWQSHFVTDSQVRFIYYNNRLF   79 (156)
T ss_dssp             SEEEEEEE--CCCCTTTSSS--EEEE-HHHHHHH-GGG-SS------SSSS-EEEEEEEETTTT---EEEEEEEE-CCCT
T ss_pred             ceEEEEEEccCCCCCCcCcccceeEecccHHHHhCCCCCcc------cccCCceeEEEEECCCCccceeEEEEEEccccc
Confidence            45679999999999    56789999999999999887632      2335788888888766  568899999987   


Q ss_pred             ---CCceEEccChHH-HHhhcCCCCCCEEEEE
Q 020733          201 ---SQSFVFTRGWNR-FVKENQLKANDTICFY  228 (322)
Q Consensus       201 ---~~~yvLt~GW~~-FV~~k~L~~GD~i~F~  228 (322)
                         +.-|-|| .|.. |--.+-=.+||.++|-
T Consensus        80 ~gTRNE~RIT-~~G~~~~~~~~~~tGaL~vla  110 (156)
T PF09217_consen   80 GGTRNEYRIT-RFGRGFPLQNPENTGALLVLA  110 (156)
T ss_dssp             TSS--EEEEE----TTSGGG-GGGTT-EEEEE
T ss_pred             CCCcCceEEe-eecCCCccCCccccccEEEEE
Confidence               4557785 7776 4333334689988886

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	322
1wid_A	130	Solution Structure Of The B3 Dna-Binding Domain Of		6e-24
1gcc_A	63	Solution Nmr Structure Of The Complex Of Gcc-Box Bi		2e-07
2gcc_A	70	Solution Structure Of The Gcc-Box Binding Domain, N		2e-07

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

Iteration: 1
 Score =  107 bits (268), Expect = 6e-24,   Method: Compositional matrix adjust.
 Identities = 52/95 (54%), Positives = 64/95 (67%), Gaps = 7/95 (7%)
Query: 133 LFQKELTPSDVGKLNRLVIPKKYAVKYFPQISERVEEHAENDKADDVQLVFHDKSMKLWK 192
           LF+K +TPSDVGKLNRLVIPK +A K+FP  S  V           V L F D + K+W+
Sbjct: 13  LFEKAVTPSDVGKLNRLVIPKHHAEKHFPLPSSNVS-------VKGVLLNFEDVNGKVWR 65
Query: 193 FRYCYWKSSQSFVFTRGWNRFVKENQLKANDTICF 227
           FRY YW SSQS+V T+GW+RFVKE  L+A D + F
Sbjct: 66  FRYSYWNSSQSYVLTKGWSRFVKEKNLRAGDVVSF 100

>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 = 53.5 bits (127), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 26/58 (44%), Positives = 38/58 (65%), Gaps = 3/58 (5%)
Query: 45 FKGVVPQQNGHWGAQIY---ANHQRIWLGTFKSEKDAAMAYDSAAIRLRGVDSHRNFP 99
          ++GV  +  G + A+I     N  R+WLGTF++ +DAA+AYD AA R+RG  +  NFP
Sbjct: 3  YRGVRQRPWGKFAAEIRDPAKNGARVWLGTFETAEDAALAYDRAAFRMRGSRALLNFP 60

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

Iteration: 1
 Score = 52.8 bits (125), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 26/58 (44%), Positives = 38/58 (65%), Gaps = 3/58 (5%)
Query: 45 FKGVVPQQNGHWGAQIY---ANHQRIWLGTFKSEKDAAMAYDSAAIRLRGVDSHRNFP 99
          ++GV  +  G + A+I     N  R+WLGTF++ +DAA+AYD AA R+RG  +  NFP
Sbjct: 6  YRGVRQRPWGKFAAEIRDPAKNGARVWLGTFETAEDAALAYDRAAFRMRGSRALLNFP 63

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	322
1wid_A	130	DNA-binding protein RAV1; DNA-binding domain, stru	1e-27
1gcc_A	63	Ethylene responsive element binding factor 1; tran	2e-15
1yel_A	104	AT1G16640; CESG, protein structure initiative, str	1e-08
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	6e-08

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

 Score =  104 bits (259), Expect = 1e-27
 Identities = 57/130 (43%), Positives = 74/130 (56%), Gaps = 13/130 (10%)

Query: 133 LFQKELTPSDVGKLNRLVIPKKYAVKYFPQISERVEEHAENDKADDVQLVFHDKSMKLWK 192
           LF+K +TPSDVGKLNRLVIPK +A K+FP  S  V           V L F D + K+W+
Sbjct: 13  LFEKAVTPSDVGKLNRLVIPKHHAEKHFPLPSSNVSVKG-------VLLNFEDVNGKVWR 65

Query: 193 FRYCYWKSSQSFVFTRGWNRFVKENQLKANDTICFYLCELRDIAKGTKTFGM-IDAKKGE 251
           FRY YW SSQS+V T+GW+RFVKE  L+A D + F            +   +   ++ G 
Sbjct: 66  FRYSYWNSSQSYVLTKGWSRFVKEKNLRAGDVVSFSRSN-----GQDQQLYIGWKSRSGS 120

Query: 252 NSGASAEVSG 261
           +  AS   SG
Sbjct: 121 DLDASGPSSG 130

>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 = 68.9 bits (169), Expect = 2e-15
 Identities = 26/59 (44%), Positives = 38/59 (64%), Gaps = 3/59 (5%)

Query: 44 KFKGVVPQQNGHWGAQI---YANHQRIWLGTFKSEKDAAMAYDSAAIRLRGVDSHRNFP 99
           ++GV  +  G + A+I     N  R+WLGTF++ +DAA+AYD AA R+RG  +  NFP
Sbjct: 2  HYRGVRQRPWGKFAAEIRDPAKNGARVWLGTFETAEDAALAYDRAAFRMRGSRALLNFP 60

>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 = 51.0 bits (122), Expect = 1e-08
 Identities = 21/99 (21%), Positives = 29/99 (29%), Gaps = 18/99 (18%)

Query: 129 SSRQLFQKELTPSDVGKLNRLVIPKKYAVKYFPQISERVEEHAENDKADDVQLVFHDKSM 188
           +    F K        K   L IP  +   +       V                 D S 
Sbjct: 6   TGEVQFMKPFISEKSSK--SLEIPLGFNEYFPAPFPITV--------------DLLDYSG 49

Query: 189 KLWKFRYCYWKSSQSFVFTRGWNRFVKENQLKANDTICF 227
           + W  R    K  +    T GW  FVK+N L+    + F
Sbjct: 50  RSWTVRMK--KRGEKVFLTVGWENFVKDNNLEDGKYLQF 86

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 53.3 bits (127), Expect = 6e-08
 Identities = 60/408 (14%), Positives = 113/408 (27%), Gaps = 150/408 (36%)

Query: 1   MEEEMLSIISNGETNVIPELSDSISSTPLIPATKRLRHASAVSKFKGVVPQQNGHW---- 56
           +++   SI+S  E + I    D++S T  +  T   +    V KF   V + N  +    
Sbjct: 38  VQDMPKSILSKEEIDHIIMSKDAVSGTLRLFWTLLSKQEEMVQKFVEEVLRINYKFLMSP 97

Query: 57  ------------------------GAQIYANHQ----------RIWL------------- 69
                                     Q++A +           R  L             
Sbjct: 98  IKTEQRQPSMMTRMYIEQRDRLYNDNQVFAKYNVSRLQPYLKLRQALLELRPAKNVLIDG 157

Query: 70  --GTFKSEKDAAMAYDSAAIRLRGVDSHRNFP--WTKITIEEPNFQSHYSTEAVINMIR- 124
             G+ K+     +A          V    +F   W  + ++  N     S E V+ M++ 
Sbjct: 158 VLGSGKT----WVA--LDVCLSYKVQCKMDFKIFW--LNLKNCN-----SPETVLEMLQK 204

Query: 125 -----DGSYSSR--QLFQKELTPSDV-GKLNRLVIPKKYAVKYFPQISERVEEHAENDKA 176
                D +++SR       +L    +  +L RL+  K Y                     
Sbjct: 205 LLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYE------------------NC 246

Query: 177 ----DDVQLVFHDKSMKLWK-FRY-CYWKSSQSFVFTRGWNRFVKENQLKANDTICFYLC 230
                +VQ    +   K W  F   C     +  + TR                +  +L 
Sbjct: 247 LLVLLNVQ----NA--KAWNAFNLSC-----KILLTTR-------------FKQVTDFL- 281

Query: 231 ELRDIAKGTKTFGMIDAKKGENSGASAEVSGPYVDMKV-DLQLQ-----------LGQNK 278
                A  T    +              +   Y+D +  DL  +           + ++ 
Sbjct: 282 ----SAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTTNPRRLSIIAESI 337

Query: 279 KENKVE----EDDNGNEIEATEEVELKAPSSTSDSERKLFKLFGVEIF 322
           ++        +  N +++    E  L          RK+F      +F
Sbjct: 338 RDGLATWDNWKHVNCDKLTTIIESSLNV--LEPAEYRKMFDRLS--VF 381

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	322
1wid_A	130	DNA-binding protein RAV1; DNA-binding domain, stru	99.95
1gcc_A	63	Ethylene responsive element binding factor 1; tran	99.83
4i1k_A	146	B3 domain-containing transcription factor VRN1; B3	99.77
1yel_A	104	AT1G16640; CESG, protein structure initiative, str	99.59
3igm_B	77	PF14_0633 protein; AP2 domain, specific transcript	90.31
1na6_A	404	Ecorii, restriction endonuclease ecorii; site-spec	88.23

>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=99.95  E-value=5.7e-28  Score=203.27  Aligned_cols=112  Identities=50%  Similarity=0.779  Sum_probs=100.0

Q ss_pred             CccccccccccCccccccccccccchhhHhhcCCCCchhhhhhcccCCCCCeEEEEEeCCCceEEEEEEEeCCCCceEEc
Q 020733          128 YSSRQLFQKELTPSDVGKLNRLVIPKKYAVKYFPQISERVEEHAENDKADDVQLVFHDKSMKLWKFRYCYWKSSQSFVFT  207 (322)
Q Consensus       128 ~s~~~~F~K~LT~SDV~~~~rL~IPk~~a~~~lP~l~~~~~~~~~~~~~~~~~l~~~D~~gk~W~fr~~~~~~~~~yvLt  207 (322)
                      .+..++|.|+||+|||+.+++|+||+++|++|||.++.       .....++.|.+.|.+|+.|+|+|+||+++++|+|+
T Consensus         8 ~~~~~~F~K~Lt~SDv~~~~rL~iPk~~a~~~lP~~~~-------~~~~~~~~l~l~D~~Gk~W~fr~~~~~~~~~~~Lt   80 (130)
T 1wid_A            8 RSAEALFEKAVTPSDVGKLNRLVIPKHHAEKHFPLPSS-------NVSVKGVLLNFEDVNGKVWRFRYSYWNSSQSYVLT   80 (130)
T ss_dssp             CCCEEEEEEECCTTTTSSSCCEEECHHHHTTTSCCCSS-------CCSSCCEEEEEEETTTEEEEEEEEEETTTTEEEEE
T ss_pred             CCCcceEEEEEehHHcCCCCEEEeCHHHHHhhCCcccc-------ccCCCcEEEEEEeCCCCEEEEEEEEECCCCceEEc
Confidence            45678999999999999899999999999999999873       12357899999999999999999999988999999


Q ss_pred             cChHHHHhhcCCCCCCEEEEEEeeccCceecceeEEEEeeeeCCC
Q 020733          208 RGWNRFVKENQLKANDTICFYLCELRDIAKGTKTFGMIDAKKGEN  252 (322)
Q Consensus       208 ~GW~~FV~~k~L~~GD~i~F~~~~~~~~~~~~~~~~~i~~~~~~~  252 (322)
                      +||..||++|+|++||+|+|+++++++.      +++|++++...
T Consensus        81 ~GW~~FV~~~~L~~GD~~~F~~~~~~~~------~l~I~~rr~~~  119 (130)
T 1wid_A           81 KGWSRFVKEKNLRAGDVVSFSRSNGQDQ------QLYIGWKSRSG  119 (130)
T ss_dssp             SSHHHHHHHTTCCTTCEEEEEECCSSSC------CEEEEEECCCS
T ss_pred             CChHHHHHHcCCCCCCEEEEEEecCCCc------EEEEEEEECCC
Confidence            9999999999999999999999886543      58899998763

>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=99.83  E-value=3.8e-21  Score=142.31  Aligned_cols=58  Identities=45%  Similarity=0.829  Sum_probs=55.1

Q ss_pred             ceEEEEECCCCeEEEEEee---CCeeEEecCCCCHHHHHHHHHHHHHHhcCCCCCCCCCcc
Q 020733           44 KFKGVVPQQNGHWGAQIYA---NHQRIWLGTFKSEKDAAMAYDSAAIRLRGVDSHRNFPWT  101 (322)
Q Consensus        44 ~yrGV~~~~~gkw~A~I~~---~~k~~~LG~f~t~eeAa~Ayd~aa~~~~g~~a~~NFp~~  101 (322)
                      +|+||+++++|||+|+|+.   +|+++|||+|+|+||||+|||.|+++++|..+.+|||.+
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            6999999889999999998   579999999999999999999999999999999999964

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

Probab=99.77  E-value=1.2e-18  Score=149.21  Aligned_cols=92  Identities=28%  Similarity=0.432  Sum_probs=80.6

Q ss_pred             CCccccccccccCccccccccccccchhhHhhcCCCCchhhhhhcccCCCCCeEEEEEeCCCceEEEEEEEeCCCCceEE
Q 020733          127 SYSSRQLFQKELTPSDVGKLNRLVIPKKYAVKYFPQISERVEEHAENDKADDVQLVFHDKSMKLWKFRYCYWKSSQSFVF  206 (322)
Q Consensus       127 s~s~~~~F~K~LT~SDV~~~~rL~IPk~~a~~~lP~l~~~~~~~~~~~~~~~~~l~~~D~~gk~W~fr~~~~~~~~~yvL  206 (322)
                      -.+..|.|.|+||+|||...+.|.||+.+++.|||..+            .  .+.+.|. |+.|.++|+++++  ++.|
T Consensus        42 ~~s~~P~Fvk~l~~S~v~~~~~L~IP~~Fa~~~lp~~~------------~--~i~L~~~-gk~W~v~~~~~~~--~~~l  104 (146)
T 4i1k_A           42 FEPTNPFFRVVLRPSYLYRGCIMYLPSGFAEKYLSGIS------------G--FIKVQLA-EKQWPVRCLYKAG--RAKF  104 (146)
T ss_dssp             CCCSSCEEEEECCGGGSSTTCCEECCHHHHHHHCTTCC------------S--EEEEEET-TEEEEEEEEEETT--EEEE
T ss_pred             cCCCCCEEEEEECchhcCCCcEEEeCHHHHHHhCCCCC------------e--EEEEEEC-CcEEEEEEEEeCC--cEEE
Confidence            46788999999999999887899999999999999754            2  4555676 5999999999875  6899


Q ss_pred             ccChHHHHhhcCCCCCCEEEEEEeeccCc
Q 020733          207 TRGWNRFVKENQLKANDTICFYLCELRDI  235 (322)
Q Consensus       207 t~GW~~FV~~k~L~~GD~i~F~~~~~~~~  235 (322)
                      ++||..||++|+|++||+|+|....+.+.
T Consensus       105 s~GW~~Fv~dn~L~~GD~cvFeli~~~~~  133 (146)
T 4i1k_A          105 SQGWYEFTLENNLGEGDVCVFELLRTRDF  133 (146)
T ss_dssp             CTTHHHHHHHTTCCTTCEEEEEECSSSSC
T ss_pred             CCchHHHHHHcCCCCCCEEEEEEecCCce
Confidence            99999999999999999999999887654

>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=99.59  E-value=3.2e-15  Score=120.40  Aligned_cols=87  Identities=22%  Similarity=0.358  Sum_probs=72.7

Q ss_pred             ccccccccccCccccccccccccchhhHhhcCCCCchhhhhhcccCCCCCeEEEEEeCCCceEEEEEEEeCCCCceEEcc
Q 020733          129 SSRQLFQKELTPSDVGKLNRLVIPKKYAVKYFPQISERVEEHAENDKADDVQLVFHDKSMKLWKFRYCYWKSSQSFVFTR  208 (322)
Q Consensus       129 s~~~~F~K~LT~SDV~~~~rL~IPk~~a~~~lP~l~~~~~~~~~~~~~~~~~l~~~D~~gk~W~fr~~~~~~~~~yvLt~  208 (322)
                      +..|.|.|+|+++|.  ..+|.||+.+++.|.|.+.              -.+.+.|..|+.|+++|+++.  .+++|++
T Consensus         6 ~~~p~F~K~l~~~~~--~~~L~IP~~F~~~~~~~~~--------------~~v~L~~~~G~~W~v~~~~~~--~~~~l~~   67 (104)
T 1yel_A            6 TGEVQFMKPFISEKS--SKSLEIPLGFNEYFPAPFP--------------ITVDLLDYSGRSWTVRMKKRG--EKVFLTV   67 (104)
T ss_dssp             CCCEEEEEECCHHHH--TTCEECCHHHHTTCCCCCC--------------SEEEEEETTSCEEEEEEEEET--TEEEECT
T ss_pred             CCCCCEEEEECCCCc--cceEECCHHHHHhcCccCC--------------CEEEEECCCCCEEEEEEEEEC--CcEEEcc
Confidence            356789999999994  4599999999988665433              256678999999999999764  4788999


Q ss_pred             ChHHHHhhcCCCCCCEEEEEEeecc
Q 020733          209 GWNRFVKENQLKANDTICFYLCELR  233 (322)
Q Consensus       209 GW~~FV~~k~L~~GD~i~F~~~~~~  233 (322)
                      ||.+||++|+|++||.|+|....+.
T Consensus        68 GW~~Fv~~~~L~~GD~lvF~~~~~~   92 (104)
T 1yel_A           68 GWENFVKDNNLEDGKYLQFIYDRDR   92 (104)
T ss_dssp             THHHHHHHHTCCTTCEEEEEECSSS
T ss_pred             ChHHHHHHcCCCCCCEEEEEEcCCC
Confidence            9999999999999999999986543

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

Probab=90.31  E-value=0.22  Score=37.33  Aligned_cols=28  Identities=25%  Similarity=0.310  Sum_probs=22.9

Q ss_pred             CCCCceEEEEE-CCCCeEEEEEeeCCeeE
Q 020733           40 SAVSKFKGVVP-QQNGHWGAQIYANHQRI   67 (322)
Q Consensus        40 ~~~S~yrGV~~-~~~gkw~A~I~~~~k~~   67 (322)
                      ..+|||.||++ .+.+.|.|.-..+|++.
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            35699999977 66799999999888764

>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=88.23  E-value=0.23  Score=48.19  Aligned_cols=101  Identities=18%  Similarity=0.229  Sum_probs=68.6

Q ss_pred             hhcCCCccccccccccCcccc----ccccccccchhhHhhcCCCCchhhhhhcccCCCCCeEEEE--EeCCCceEEEEEE
Q 020733          123 IRDGSYSSRQLFQKELTPSDV----GKLNRLVIPKKYAVKYFPQISERVEEHAENDKADDVQLVF--HDKSMKLWKFRYC  196 (322)
Q Consensus       123 LR~gs~s~~~~F~K~LT~SDV----~~~~rL~IPk~~a~~~lP~l~~~~~~~~~~~~~~~~~l~~--~D~~gk~W~fr~~  196 (322)
                      +-.........|.|.|++-|+    +++.++.+|+..+..+||.+.-..      ...+...+.+  -|+..-.+.++++
T Consensus        10 ~~~~~~~~~~v~~K~LSAnDtgatgshQ~gi~ipk~~l~~lfp~lg~~~------e~~~~~~~~~~l~d~d~p~td~~~t   83 (404)
T 1na6_A           10 LLEIACENYFVYIKRLSANDTGATGGHQVGLYIPSGIVEKLFPSINHTR------ELNPSVFLTAHVSSHDCPDSEARAI   83 (404)
T ss_dssp             HHHHHHSSEEEEEEECCHHHHTCC---CCCCCCCHHHHHHHCGGGCCCS------SSSCEEEEEEEESSSCCCCEEEEEE
T ss_pred             HHHhccccchheeEEcccccCCCCCCcccccCCchHHHHHhcccCCCcc------ccCCcceeEEEeccCCCceEEEEEE
Confidence            333445567789999999998    456799999988999998877211      1123333333  3443455599988


Q ss_pred             EeC------CCCceEEccChHH-HHhhcCCCCCCEEEEEEe
Q 020733          197 YWK------SSQSFVFTRGWNR-FVKENQLKANDTICFYLC  230 (322)
Q Consensus       197 ~~~------~~~~yvLt~GW~~-FV~~k~L~~GD~i~F~~~  230 (322)
                      |..      .+.-|-|+ .|.. +.--+...+||.++|-..
T Consensus        84 wYn~R~~~~tRnEyRLt-~~~~~~~~~~~a~~GDLlvia~~  123 (404)
T 1na6_A           84 YYNSAHFGKTRNEKRIT-RWGRGSPLQDPENTGALTLLAFK  123 (404)
T ss_dssp             EECGGGTTSCCCEEEEE-CCCTTSGGGCGGGTTCEEEEEEE
T ss_pred             EecccccCCCCCceEEe-ecCCCCcccccCCCCCEEEEEEe
Confidence            876      23457786 3655 666688899999999876

---

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	322
d1wida_	117	b.142.1.2 (A:) DNA-binding protein RAV1 {Thale cre	4e-29
d1na6a1	175	b.142.1.1 (A:4-178) Restriction endonuclease EcoRI	1e-19
d1gcca_	63	d.10.1.2 (A:) GCC-box binding domain {Mouse-ear cr	5e-18
d1yela1	102	b.142.1.2 (A:1-102) At1g16640 {Thale cress (Arabid	3e-17

>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 =  106 bits (265), Expect = 4e-29
 Identities = 53/103 (51%), Positives = 66/103 (64%), Gaps = 7/103 (6%)

Query: 129 SSRQLFQKELTPSDVGKLNRLVIPKKYAVKYFPQISERVEEHAENDKADDVQLVFHDKSM 188
           S+  LF+K +TPSDVGKLNRLVIPK +A K+FP  S  V           V L F D + 
Sbjct: 2   SAEALFEKAVTPSDVGKLNRLVIPKHHAEKHFPLPSSNVSVK-------GVLLNFEDVNG 54

Query: 189 KLWKFRYCYWKSSQSFVFTRGWNRFVKENQLKANDTICFYLCE 231
           K+W+FRY YW SSQS+V T+GW+RFVKE  L+A D + F    
Sbjct: 55  KVWRFRYSYWNSSQSYVLTKGWSRFVKEKNLRAGDVVSFSRSN 97

>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 = 82.3 bits (203), Expect = 1e-19
 Identities = 17/132 (12%), Positives = 35/132 (26%), Gaps = 18/132 (13%)

Query: 131 RQLFQKELTPSDVGKLNR----LVIPKKYAVKYFPQISERVEEHAENDKADDVQLVFHDK 186
             ++ K L+ +D G        L IP     K FP I+       E + +  +       
Sbjct: 15  YFVYIKRLSANDTGATGGHQVGLYIPSGIVEKLFPSINHT----RELNPSVFLTAHVSSH 70

Query: 187 SMKLWKFRYCYWKSS------QSFVFTRGWNRFVKENQLKANDTICFYLCELRDIAKGTK 240
                + R  Y+ S+           TR       ++                 + +   
Sbjct: 71  DCPDSEARAIYYNSAHFGKTRNEKRITRWGRGSPLQDPENTGALTLLA----FKLDEQGG 126

Query: 241 TFGMIDAKKGEN 252
               ++     +
Sbjct: 127 DCKEVNIWVCAS 138

>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 = 74.7 bits (184), Expect = 5e-18
 Identities = 26/59 (44%), Positives = 38/59 (64%), Gaps = 3/59 (5%)

Query: 44 KFKGVVPQQNGHWGAQIY---ANHQRIWLGTFKSEKDAAMAYDSAAIRLRGVDSHRNFP 99
           ++GV  +  G + A+I     N  R+WLGTF++ +DAA+AYD AA R+RG  +  NFP
Sbjct: 2  HYRGVRQRPWGKFAAEIRDPAKNGARVWLGTFETAEDAALAYDRAAFRMRGSRALLNFP 60

>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 = 73.8 bits (181), Expect = 3e-17
 Identities = 21/101 (20%), Positives = 29/101 (28%), Gaps = 18/101 (17%)

Query: 129 SSRQLFQKELTPSDVGKLNRLVIPKKYAVKYFPQISERVEEHAENDKADDVQLVFHDKSM 188
           +    F K        K   L IP  +   +       V                 D S 
Sbjct: 4   TGEVQFMKPFISEKSSK--SLEIPLGFNEYFPAPFPITV--------------DLLDYSG 47

Query: 189 KLWKFRYCYWKSSQSFVFTRGWNRFVKENQLKANDTICFYL 229
           + W  R    K  +    T GW  FVK+N L+    + F  
Sbjct: 48  RSWTVRM--KKRGEKVFLTVGWENFVKDNNLEDGKYLQFIY 86

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	322
d1wida_	117	DNA-binding protein RAV1 {Thale cress (Arabidopsis	99.94
d1gcca_	63	GCC-box binding domain {Mouse-ear cress (Arabidops	99.83
d1na6a1	175	Restriction endonuclease EcoRII, N-terminal domain	99.67
d1yela1	102	At1g16640 {Thale cress (Arabidopsis thaliana) [Tax	99.48

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

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

Probab=99.94  E-value=2.9e-27  Score=192.92  Aligned_cols=113  Identities=50%  Similarity=0.785  Sum_probs=100.1

Q ss_pred             ccccccccccCccccccccccccchhhHhhcCCCCchhhhhhcccCCCCCeEEEEEeCCCceEEEEEEEeCCCCceEEcc
Q 020733          129 SSRQLFQKELTPSDVGKLNRLVIPKKYAVKYFPQISERVEEHAENDKADDVQLVFHDKSMKLWKFRYCYWKSSQSFVFTR  208 (322)
Q Consensus       129 s~~~~F~K~LT~SDV~~~~rL~IPk~~a~~~lP~l~~~~~~~~~~~~~~~~~l~~~D~~gk~W~fr~~~~~~~~~yvLt~  208 (322)
                      +..++|+|+||+|||+++++|+||+.++++|||+++.       .....++.|.+.|.+|+.|+|+|++|+++++|+|++
T Consensus         2 ~~~~iF~K~Lt~sDv~~~~rL~iP~~~~~~~lp~~~~-------~~~~~~~~~~~~d~~g~~W~~~~~~~~~~~~~~l~~   74 (117)
T d1wida_           2 SAEALFEKAVTPSDVGKLNRLVIPKHHAEKHFPLPSS-------NVSVKGVLLNFEDVNGKVWRFRYSYWNSSQSYVLTK   74 (117)
T ss_dssp             CCEEEEEEECCTTTTSSSCCEEECHHHHTTTSCCCSS-------CCSSCCEEEEEEETTTEEEEEEEEEETTTTEEEEES
T ss_pred             CCceEEEEEecchhcCCCCEEEECHHHHHHhCCcccc-------ccCCCcEEEEEEeCCCCEEEEEEEEECCCCceEEec
Confidence            4678999999999999889999999999999999873       223478999999999999999999999999999999


Q ss_pred             ChHHHHhhcCCCCCCEEEEEEeeccCceecceeEEEEeeeeCCCCC
Q 020733          209 GWNRFVKENQLKANDTICFYLCELRDIAKGTKTFGMIDAKKGENSG  254 (322)
Q Consensus       209 GW~~FV~~k~L~~GD~i~F~~~~~~~~~~~~~~~~~i~~~~~~~~~  254 (322)
                      ||..||++|+|++||+|+|+|+..++.      .++|.+++.++.+
T Consensus        75 GW~~Fv~~~~Lk~GD~~~F~~~~~~~~------~~~i~~r~~~~~~  114 (117)
T d1wida_          75 GWSRFVKEKNLRAGDVVSFSRSNGQDQ------QLYIGWKSRSGSD  114 (117)
T ss_dssp             SHHHHHHHTTCCTTCEEEEEECCSSSC------CEEEEEECCCSCS
T ss_pred             CHHHHHHHcCCCCCCEEEEEEEeCCCC------EEEEEEEECCCCC
Confidence            999999999999999999999876654      3788888777544

>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=99.83  E-value=2.1e-21  Score=141.68  Aligned_cols=58  Identities=45%  Similarity=0.829  Sum_probs=54.2

Q ss_pred             ceEEEEECCCCeEEEEEee---CCeeEEecCCCCHHHHHHHHHHHHHHhcCCCCCCCCCcc
Q 020733           44 KFKGVVPQQNGHWGAQIYA---NHQRIWLGTFKSEKDAAMAYDSAAIRLRGVDSHRNFPWT  101 (322)
Q Consensus        44 ~yrGV~~~~~gkw~A~I~~---~~k~~~LG~f~t~eeAa~Ayd~aa~~~~g~~a~~NFp~~  101 (322)
                      +||||+++++|||.|+|++   +++++|||+|+|+||||+|||.|+++++|.++.+|||..
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            5999998889999999986   668999999999999999999999999999999999963

>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=99.67  E-value=1.7e-17  Score=141.44  Aligned_cols=114  Identities=16%  Similarity=0.099  Sum_probs=90.8

Q ss_pred             CccccccccccCccccccccc----cccchhhHhhcCCCCchhhhhhcccCCCCCeEE--EEEeCCCceEEEEEEEeCCC
Q 020733          128 YSSRQLFQKELTPSDVGKLNR----LVIPKKYAVKYFPQISERVEEHAENDKADDVQL--VFHDKSMKLWKFRYCYWKSS  201 (322)
Q Consensus       128 ~s~~~~F~K~LT~SDV~~~~r----L~IPk~~a~~~lP~l~~~~~~~~~~~~~~~~~l--~~~D~~gk~W~fr~~~~~~~  201 (322)
                      .+...+|.|.||+||++.+++    |+|||.+|+.|||+|+...      ...+.+.|  .+.|.+|..|+|||+||++.
T Consensus        12 ~~~~~~F~K~LtasD~g~tg~HQaG~~IPK~~ae~~FP~l~~~~------e~nP~~~l~~~i~d~~g~~w~fR~iYyn~~   85 (175)
T d1na6a1          12 CENYFVYIKRLSANDTGATGGHQVGLYIPSGIVEKLFPSINHTR------ELNPSVFLTAHVSSHDCPDSEARAIYYNSA   85 (175)
T ss_dssp             HSSEEEEEEECCHHHHTCC---CCCCCCCHHHHHHHCGGGCCCS------SSSCEEEEEEEESSSCCCCEEEEEEEECGG
T ss_pred             CCceEEEEEEcccccccccCCccceeeecHHHHHHhCCCCCccc------ccCCCceEEEEEecCCCCeeEEEEEEECCc
Confidence            445789999999999988876    9999999999999998422      12345555  45599999999999999884


Q ss_pred             ------CceEEccChHHHHhhcCCCCCCEEEEEEeeccCceecceeEEEEeeeeCC
Q 020733          202 ------QSFVFTRGWNRFVKENQLKANDTICFYLCELRDIAKGTKTFGMIDAKKGE  251 (322)
Q Consensus       202 ------~~yvLt~GW~~FV~~k~L~~GD~i~F~~~~~~~~~~~~~~~~~i~~~~~~  251 (322)
                            ..|.||.+|..|+..+.+.+||+++|.+......    .....+++..+.
T Consensus        86 ~~ggTRneyRiT~~g~~~~~~~~~n~G~l~i~af~~~~~~----~~~~~~~vwvc~  137 (175)
T d1na6a1          86 HFGKTRNEKRITRWGRGSPLQDPENTGALTLLAFKLDEQG----GDCKEVNIWVCA  137 (175)
T ss_dssp             GTTSCCCEEEEECCCTTSGGGCGGGTTCEEEEEEECCTTS----CCCCEEEEEECC
T ss_pred             cCCCccccEEEEeccccccccCccccccEEEEEeecCCCC----CceeEEEEEEec
Confidence                  8899999999999999999999999999644443    334566666665

>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=99.48  E-value=5.5e-14  Score=111.20  Aligned_cols=85  Identities=22%  Similarity=0.340  Sum_probs=70.5

Q ss_pred             cccccccccCccccccccccccchhhHhhcCCCCchhhhhhcccCCCCCeEEEEEeCCCceEEEEEEEeCCCCceEEccC
Q 020733          130 SRQLFQKELTPSDVGKLNRLVIPKKYAVKYFPQISERVEEHAENDKADDVQLVFHDKSMKLWKFRYCYWKSSQSFVFTRG  209 (322)
Q Consensus       130 ~~~~F~K~LT~SDV~~~~rL~IPk~~a~~~lP~l~~~~~~~~~~~~~~~~~l~~~D~~gk~W~fr~~~~~~~~~yvLt~G  209 (322)
                      ..+-|.|+|.+++...  +|.||..++..|.+.+.            .  .+.+.|..|+.|++++...  +....|++|
T Consensus         5 ~~~~Ffkv~~~~~~~~--~L~IP~~F~~~~~~~~~------------~--~i~L~d~~G~~W~v~~~~~--~~~~~~~~G   66 (102)
T d1yela1           5 GEVQFMKPFISEKSSK--SLEIPLGFNEYFPAPFP------------I--TVDLLDYSGRSWTVRMKKR--GEKVFLTVG   66 (102)
T ss_dssp             CCEEEEEECCHHHHTT--CEECCHHHHTTCCCCCC------------S--EEEEEETTSCEEEEEEEEE--TTEEEECTT
T ss_pred             CCCeEEEEEcCcccCC--CEECCHHHHHhCCCCCC------------C--EEEEEcCCCCEEEEEEEEe--CCeEEEccC
Confidence            3455889999999765  89999999998776543            2  5667899999999998754  446778999


Q ss_pred             hHHHHhhcCCCCCCEEEEEEeec
Q 020733          210 WNRFVKENQLKANDTICFYLCEL  232 (322)
Q Consensus       210 W~~FV~~k~L~~GD~i~F~~~~~  232 (322)
                      |..||++|+|++||.|+|....+
T Consensus        67 W~~Fv~~n~L~~GD~~vF~~~~~   89 (102)
T d1yela1          67 WENFVKDNNLEDGKYLQFIYDRD   89 (102)
T ss_dssp             HHHHHHHHTCCTTCEEEEEECSS
T ss_pred             HHHHHHHcCCCcCCEEEEEEcCC
Confidence            99999999999999999988654