Citrus Sinensis ID: 018549

---

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-------330-------340-------350----
Protein Sequence
MEEEMLSIISNGETNVIPELSDSISSTPLIPATKRLRHASAVSKFKGVVPQQNGHWGAQIYANHQRIWLGTFKSEKDAAMAYDSAAIRLRGVDSHRNFPWTKITIEEPNFQSHYSTEAVINMIRDGSYSSRFADFLRSHSRTLEEDVIFTQMRAGTDGWMMCRQLFQKELTPSDVGKLNRLVIPKKYAVKYFPQISERVEEHAENDKADDVQLVFHDKSMKLWKFRYCYWKSSQSFVFTRGWNRFVKENQLKANDTICFYLCELRDIAKGTKTFGMIDAKKGENSGASAEVSGPYVDMKVDLQLQLGQNKKENKVEEDDNGNEIEATEEVELKAPSSTSDSERKLFKLFGVEIF
Secondary Structure (PSIPRED)
cccccccccccccccccccccccccccccccHHHHccccccccccccccccccccEEEEEEccccEEEEcccccHHHHHHHHHHHHHHcccccccccccccccccccccccccccHHHHHHHcccccccccccccccccccccHHHHHHHccccccccccHHHHccccccccccccccccccccccccccccccccHHHHcccccccccccEEEEcccccccEEEccccccccccEEEEcccHHHHcccccccccEEEEEEcccccccccccEEEEEEcEEcccccccccccccccccccccccccccccccccccccccccccccHHHHHcccccccccccccEEEEEEEEcc
Secondary Structure Prediction (SSPRO)
cccHEEEEEccccccccHHHcccccccccccccccccEccccccccccccccccccHHHHHHHccEEEEcccccHHHHHHHHHHHHHHHccccccccccccccccHHHHHHHHccHHHHHHHHHccccHHHHHHHHHcccccccccccccccccccccccccccHHEEEcccccccccccEEccHHHHHHHccccccccccccHccccccEEEEEEEccccEEEEEEEEEccccEEEEEccccHHHHHcccccccEEEEEEccccccccccccEEEEEEEEcccccccccccccccccccccHcccccccccccccccccccccccccccccccccccccccccEEEEEccccc
Coil and Loop (DISEMBL)
MEEEMLSIISngetnvipelsdsisstplipatkrlRHASAVskfkgvvpqqnghwgAQIYANHQriwlgtfkseKDAAMAYDSAAIRLrgvdshrnfpwtkitieepnfqshysTEAVINMIrdgsyssrFADFLRSHSRTLEEDVIFTQMRAGTDGWMMCRQLFqkeltpsdvgklnrlvipkkyavkyFPQISERVEEhaendkaddvqlVFHDKSMKLWKFRYCYWKSSQSFVFTRGWNRFVKENQLKANDTICFYLCELRDIakgtktfgmidakkgensgasaevsgpyvdMKVDLQLQlgqnkkenkveeddngneieateevelkapsstsdsERKLFKLFGVEIF
Flexible Loop (DISEMBL)
MEEEMLSIISNGETNVIPELSDSISSTPLIPATKRLRHASAVSKFKGVVPQQNGHWGAQIYANHQRIWLGTFKSEKDAAMAYDSAAIRLRGVDSHRNFPWTKitieepnfqshYSTEAVINMIRDGSYSSRFADFLRShsrtleedVIFTQMRAGTDGWMMCRQLFQKeltpsdvgklnrlvipkkyaVKYFPQISERVEEHaendkaddvqlvFHDKSMKLWKFRYCYWKSSQSFVFTRGWNRFVKENQLKANDTICFYLCELRDIAKGTKTFGMidakkgensgasAEVSGPYVDMKVDLQLQLgqnkkenkveeddngneieateevelkapsstsdserklfklfgveif
Low Complexity Region (SEG)
MEEEMLSIISNGETNVIPELSDSISSTPLIPATKRLRHASAVSKFKGVVPQQNGHWGAQIYANHQRIWLGTFKSEKDAAMAYDSAAIRLRGVDSHRNFPWTKITIEEPNFQSHYSTEAVINMIRDGSYSSRFADFLRSHSRTLEEDVIFTQMRAGTDGWMMCRQLFQKELTPSDVGKLNRLVIPKKYAVKYFPQISERVEEHAENDKADDVQLVFHDKSMKLWKFRYCYWKSSQSFVFTRGWNRFVKENQLKANDTICFYLCELRDIAKGTKTFGMIDAKKGENSGASAEVSGPYVDMKVDLQLQLGQNKKENKVEEDDNGNEIEATEEVELKAPSSTSDSERKLFKLFGVEIF
Disordered region (IsUnstruct)
**************************************ASAVSKFKGVVPQQNGHWGAQIYANHQRIWLGTFKSEKDAAMAYDSAAIRLRGVDSHRNFPWTKITIEEPNFQSHYSTEAVINMIRDGSYSSRFADFLRSHSRTLEEDVIFTQMRAGTDGWMMCRQLFQKELTPSDVGKLNRLVIPKKYAVKYFPQISERV********ADDVQLVFHDKSMKLWKFRYCYWKSSQSFVFTRGWNRFVKENQLKANDTICFYLCELRDIAKGTKTFGMI*****************************************************************************
Disordered Region (DISOPRED)
************************************************VPQQNGHWGAQIYANHQRIWLGTFKSEKDAAMAYDSAAIRLRGVDSHRNFPWTKITIEEPNFQSHYSTEAVINMIRDGSYSSRFADFLRSHSRTLEEDVIFTQMRAGTDGWMMCRQLFQKE********************************************VFHDKSMKLWKFRYCYWKSSQSFVFTRGWNRFVKENQLKANDTICFYLCELRDIAKGTKTFGMID*********************************************************************LFGVEIF
Disordered Region (DISEMBL)
MEEEMLSIISNGETNVIPELSDSISSTPLIPATKRLRHASAVSKFKGVVPQQNGHWGAQIYANHQRIWLGTFKSEKDAAMAYDSAAIRLRGVDSHRNFPWTKITIEEPNFQSHYSTEAVINMIRDGSYSSRFADFLRSHSRTLEEDVIFTQMRAGTDGWMMCRQLFQKELTPSDVGKLNRLVIPKKYAVKYFPQISERVEEHAENDKADDVQLVFHDKSMKLWKFRYCYWKSSQSFVFTRGWNRFVKENQLKANDTICFYLCELRDIAKGTKTFGMIDAKKG********VSGPYVDMKVDLQLQLGQN************NEIEATEE***********SERKLFKLFGVEIF
Disordered Region (DISPRO)
*********SN*********************************FKGVVPQQNGHWGAQIYANHQRIWLGTFKSEKDAAMAYDSAAIRLRGVDSHRNFPWTKITIEEPNFQSHYSTEAVINMIRDGSYSSRFADFLRS**********************MCRQLFQKELTPSDVGKLNRLVIPKKYAVKYFPQISERV*******KADDVQLVFHDKSMKLWKFRYCYWKSSQSFVFTRGWNRFVKENQLKANDTICFYLCELRDIAKGTKTFGMIDAKKGE************************************************************KLF******IF
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MEEEMLSIISNGETNVIPELSDSISSTPLIPATKRLRHASAVSKFKGVVPQQNGHWGAQIYANHQRIWLGTFKSEKDAAMAYDSAAIRLRGVDSHRNFPWTKITIEEPNFQSHYSTEAVINMIRDGSYSSRFADFLRSHSRTLEEDVIFTQMRAGTDGWMMCRQLFQKELTPSDVGKLNRLVIPKKYAVKYFPQISERVEEHAENDKADDVQLVFHDKSMKLWKFRYCYWKSSQSFVFTRGWNRFVKENQLKANDTICFYLCELRDIAKGTKTFGMIDAKKGENSGASAEVSGPYVDMKVDLQLQLGQNKKENKVEEDDNGNEIEATEEVELKAPSSTSDSERKLFKLFGVEIF
Positional Conservation
no confident homologs detected

---

Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	354	2.2.26 [Sep-21-2011]
Q9C688	352	AP2/ERF and B3 domain-con	yes	no	0.776	0.781	0.546	6e-84
Q9C6P5	337	AP2/ERF and B3 domain-con	no	no	0.889	0.934	0.490	2e-82
Q9ZWM9	344	AP2/ERF and B3 domain-con	no	no	0.587	0.604	0.450	8e-48
Q9C6M5	361	AP2/ERF and B3 domain-con	no	no	0.604	0.592	0.436	4e-47
Q9LS06	333	AP2/ERF and B3 domain-con	no	no	0.593	0.630	0.470	3e-46
Q8RZX9	393	AP2/ERF and B3 domain-con	yes	no	0.601	0.541	0.441	2e-45
P82280	352	AP2/ERF and B3 domain-con	no	no	0.579	0.582	0.444	3e-44
Q6L4H4	394	AP2/ERF and B3 domain-con	no	no	0.652	0.586	0.428	1e-43
Q9AWS7	317	Putative AP2/ERF and B3 d	no	no	0.635	0.709	0.428	1e-41
Q9AWS0	365	AP2/ERF and B3 domain-con	no	no	0.635	0.616	0.443	5e-41

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

 Score =  311 bits (796), Expect = 6e-84,   Method: Compositional matrix adjust.
 Identities = 159/291 (54%), Positives = 198/291 (68%), Gaps = 16/291 (5%)

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 YSSRFADFLRSHSRTLEEDVIF--TQMRAGTDG------WMMCRQLFQKELTPSDVGKLN 179
           Y  +F DFLR  S+ +    I    Q+  G +G         C QLFQKELTPSDVGKLN
Sbjct: 132 YQHKFRDFLRIRSQIVANINIVGSKQVLGGGEGGQESNKCFSCTQLFQKELTPSDVGKLN 191

Query: 180 RLVIPKKYAVKYFPQISERVEEHAENDKADDVQLVFHDKSMKLWKFRYCYWKSSQSFVFT 239
           RLVIPKKYAVKY P IS+   E   ++  +DV++VF+D++M+ WKFRYCYW+SSQSFVFT
Sbjct: 192 RLVIPKKYAVKYMPFISDDQSEKETSEGVEDVEVVFYDRAMRQWKFRYCYWRSSQSFVFT 251

Query: 240 RGWNRFVKENQLKANDTICFYLCELRDIAKG----TKTFGMIDAKKGENSG 286
           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 =  306 bits (783), Expect = 2e-82,   Method: Compositional matrix adjust.
 Identities = 172/351 (49%), Positives = 216/351 (61%), Gaps = 36/351 (10%)

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

Query: 80  MAYDSAAIRLRGVD--SHRNFPWTKITIEEPNFQSHYSTEAVINMIRDGSYSSRFADFLR 137
            AYDSA+I+LR  D  SHRNFPW+ IT+ EP+FQ+ Y+TE V+NMIRDGSY  +F DFLR
Sbjct: 63  TAYDSASIKLRSFDANSHRNFPWSTITLNEPDFQNCYTTETVLNMIRDGSYQHKFRDFLR 122

Query: 138 SHSRTLEEDVIFTQMRAG------TDGWMMCRQLFQKELTPSDVGKLNRLVIPKKYAVKY 191
             S+ +    I    +A       +D    C QLFQKELTPSDVGKLNRLVIPKKYAVKY
Sbjct: 123 IRSQIVASINIGGPKQARGEVNQESDKCFSCTQLFQKELTPSDVGKLNRLVIPKKYAVKY 182

Query: 192 FPQISERVEEHAEND---KADDVQLVFHDKSMKLWKFRYCYWKSSQSFVFTRGWNRFVKE 248
            P IS    E  E +     +DV++VF+D++M+ WKFRYCYWKSSQSFVFTRGWN FVKE
Sbjct: 183 MPFISADQSEKEEGEIVGSVEDVEVVFYDRAMRQWKFRYCYWKSSQSFVFTRGWNSFVKE 242

Query: 249 NQLKANDTICFYLCELRDIAKGT----KTFGMIDAKKGENSGA--SAEVSGPYVDMKVDL 302
             LK  D I FY C++ +  K      K F MID     ++G+  + EVS    D  V +
Sbjct: 243 KNLKEKDVIAFYTCDVPNNVKTLEGQRKNFLMIDVHCFSDNGSVVAEEVSMTVHDSSVQV 302

Query: 303 QLQLGQNKKENKVEEDDNGNEIEATEEVELKAPSSTSDSERKLFKLFGVEI 353
           +      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 =  191 bits (485), Expect = 8e-48,   Method: Compositional matrix adjust.
 Identities = 101/224 (45%), Positives = 133/224 (59%), Gaps = 16/224 (7%)

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 ITIEEPNFQSHYSTEAVINMIRDGSYSSRFADFLRSHSRTLEEDVIFTQMRAG------- 155
           +  +E +F + +S   +++M+R  +Y+       R   R    ++  T + +G       
Sbjct: 120 MDEDEVDFLNSHSKSEIVDMLRKHTYNEELEQSKR--RRNGNGNMTRTLLTSGLSNDGVS 177

Query: 156 TDGWMMCRQLFQKELTPSDVGKLNRLVIPKKYAVKYFPQISERVEEHAENDKADDVQLVF 215
           T G+     LF+K +TPSDVGKLNRLVIPK +A K+FP  S  V           V L F
Sbjct: 178 TTGFRSAEALFEKAVTPSDVGKLNRLVIPKHHAEKHFPLPSSNVS-------VKGVLLNF 230

Query: 216 HDKSMKLWKFRYCYWKSSQSFVFTRGWNRFVKENQLKANDTICF 259
            D + K+W+FRY YW SSQS+V T+GW+RFVKE  L+A D + F
Sbjct: 231 EDVNGKVWRFRYSYWNSSQSYVLTKGWSRFVKEKNLRAGDVVSF 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 =  189 bits (479), Expect = 4e-47,   Method: Compositional matrix adjust.
 Identities = 97/222 (43%), Positives = 131/222 (59%), Gaps = 8/222 (3%)

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----EPNFQSHYSTEAVINMIRDGSYSSRFADFLRSHSRTLEEDVIFTQMRAGTDG 158
             ++    E  F   +S   +++M+R  +Y+  F    R       +         G D 
Sbjct: 127 SQVDGNDAESAFLDAHSKAEIVDMLRKHTYADEFEQSRRKFVNGDGKRSGLETATYGNDA 186

Query: 159 WMMCRQ-LFQKELTPSDVGKLNRLVIPKKYAVKYFPQISERVEEHAENDKADDVQLVFHD 217
            +  R+ LF+K +TPSDVGKLNRLVIPK++A K+FP  +              V +   D
Sbjct: 187 VLRAREVLFEKTVTPSDVGKLNRLVIPKQHAEKHFPLPAMTTAMGMNPSPTKGVLINLED 246

Query: 218 KSMKLWKFRYCYWKSSQSFVFTRGWNRFVKENQLKANDTICF 259
           ++ 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|Q9LS06|RAVL4_ARATH AP2/ERF and B3 domain-containing transcription factor ARF14 OS=Arabidopsis thaliana GN=ARF14 PE=2 SV=1

 Score =  186 bits (471), Expect = 3e-46,   Method: Compositional matrix adjust.
 Identities = 103/219 (47%), Positives = 129/219 (58%), Gaps = 9/219 (4%)

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 ITIEEPNFQSHYSTEAVINMIRDGSYSSRFADFLRSHSRTLEEDVIF--TQMRAGTDGWM 160
              EE  F + +S   +++M+R  +Y        R+     +E   F    M   T G+ 
Sbjct: 120 FE-EEVEFLNAHSKSEIVDMLRKHTYKEELDQRKRNRDGNGKETTAFALASMVVMT-GFK 177

Query: 161 MCRQLFQKELTPSDVGKLNRLVIPKKYAVKYFPQISERVEEHAENDKADDVQLVFHDKSM 220
               LF+K +TPSDVGKLNRLVIPK  A K+FP     +     N     + L F D + 
Sbjct: 178 TAELLFEKTVTPSDVGKLNRLVIPKHQAEKHFP-----LPLGNNNVSVKGMLLNFEDVNG 232

Query: 221 KLWKFRYCYWKSSQSFVFTRGWNRFVKENQLKANDTICF 259
           K+W+FRY YW SSQS+V T+GW+RFVKE +L A D I F
Sbjct: 233 KVWRFRYSYWNSSQSYVLTKGWSRFVKEKRLCAGDLISF 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 =  182 bits (463), Expect = 2e-45,   Method: Compositional matrix adjust.
 Identities = 102/231 (44%), Positives = 131/231 (56%), Gaps = 18/231 (7%)

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---NFQSHYSTEAVINMIRDGSYSSRFADFLRSHSRTLEEDVIFT-------- 150
           +   +      F +  S   V++M+R  +Y    A   R+ + +       T        
Sbjct: 140 EADPDAAAELRFLATRSKAEVVDMLRKHTYFDELAQSKRTFAASTPSAATTTASLSNGHL 199

Query: 151 -QMRAGTDGWMMCRQLFQKELTPSDVGKLNRLVIPKKYAVKYFPQISERVEEHAENDKAD 209
              R+          LF K +TPSDVGKLNRLVIPK++A K+FP     ++  +   ++ 
Sbjct: 200 SSPRSPFAPAAARDHLFDKTVTPSDVGKLNRLVIPKQHAEKHFP-----LQLPSAGGESK 254

Query: 210 DVQLVFHDKSMKLWKFRYCYWKSSQSFVFTRGWNRFVKENQLKANDTICFY 260
            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 =  179 bits (454), Expect = 3e-44,   Method: Compositional matrix adjust.
 Identities = 100/225 (44%), Positives = 138/225 (61%), Gaps = 20/225 (8%)

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--FQSHYSTEAVINMIRDGSYSSRFADFLRSHSRTLEEDVIFTQMRAGT---- 156
             +E+ +  F   +S   +++M+R  +Y+    +  +++ R L   V     R G+    
Sbjct: 120 NVLEDGDLAFLEAHSKAEIVDMLRKHTYAD---ELEQNNKRQLFLSVDANGKRNGSSTTQ 176

Query: 157 -DGWMMCRQ-LFQKELTPSDVGKLNRLVIPKKYAVKYFPQISERVEEHAENDKADDVQLV 214
            D  +  R+ LF+K +TPSDVGKLNRLVIPK++A K+FP  S              V + 
Sbjct: 177 NDKVLKTREVLFEKAVTPSDVGKLNRLVIPKQHAEKHFPLPS------PSPAVTKGVLIN 230

Query: 215 FHDKSMKLWKFRYCYWKSSQSFVFTRGWNRFVKENQLKANDTICF 259
           F D + K+W+FRY YW SSQS+V T+GW+RFVKE  L+A D + F
Sbjct: 231 FEDVNGKVWRFRYSYWNSSQSYVLTKGWSRFVKEKNLRAGDVVTF 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|Q6L4H4|Y5498_ORYSJ AP2/ERF and B3 domain-containing protein Os05g0549800 OS=Oryza sativa subsp. japonica GN=Os05g0549800 PE=2 SV=1

 Score =  177 bits (449), Expect = 1e-43,   Method: Compositional matrix adjust.
 Identities = 108/252 (42%), Positives = 136/252 (53%), Gaps = 21/252 (8%)

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---EPNFQSHYSTEAVINMIRDGSYSSRFADFLRSHSRTLEEDVIFTQMRAGTDG 158
           +   E   E  F +  S   V++M+R  +Y        R+ +  +          + T  
Sbjct: 127 ESDPEAAVELRFLASRSKAEVVDMLRKHTYLEELTQNKRAFA-AISPPPPKHPASSPTSS 185

Query: 159 WMMCRQLFQKELTPSDVGKLNRLVIPKKYAVKYFP----------QISERVEEHAENDKA 208
                 LF K +TPSDVGKLNRLVIPK++A K+FP           ++   +  A     
Sbjct: 186 SAAREHLFDKTVTPSDVGKLNRLVIPKQHAEKHFPLQLPPPTTTSSVAAAADAAAGGGDC 245

Query: 209 DDVQLVFHDKSMKLWKFRYCYWKSSQSFVFTRGWNRFVKENQLKANDTICFYLCELRDIA 268
             V L F D + K+WKFRY YW SSQS+V T+GW+RFVKE  L A D + FY    R   
Sbjct: 246 KGVLLNFEDAAGKVWKFRYSYWNSSQSYVLTKGWSRFVKEKGLHAGDAVGFY----RAAG 301

Query: 269 KGTKTFGMIDAK 280
           K  + F  ID K
Sbjct: 302 KNAQLF--IDCK 311

Oryza sativa subsp. japonica (taxid: 39947)

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

 Score =  171 bits (432), Expect = 1e-41,   Method: Compositional matrix adjust.
 Identities = 105/245 (42%), Positives = 138/245 (56%), Gaps = 20/245 (8%)

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 TKITIEEPNFQSHYSTEAVINMIRDGSYSSRFADFLRSHSRTLEEDVIFTQMRAGTDGWM 160
              +  E  F + +S   V++M+R  +Y       LR  SR              T  W 
Sbjct: 125 EGASAGELAFLAAHSKAEVVDMLRKHTYDDELQQGLRRGSRAQP-----------TPRWA 173

Query: 161 MCRQLFQKELTPSDVGKLNRLVIPKKYAVKYFPQISERVEEHAENDKADDVQLVFHDKSM 220
               LF+K +TPSDVGKLNRLV+PK+ A ++FP    R   H+ +     V L F D   
Sbjct: 174 R-EPLFEKAVTPSDVGKLNRLVVPKQQAERHFPFPLRR---HSSDAAGKGVLLNFEDGDG 229

Query: 221 KLWKFRYCYWKSSQSFVFTRGWNRFVKENQLKANDTICFYLCELRDIAKGTKTFGMIDAK 280
           K+W+FRY YW SSQS+V T+GW+RFV+E  L+  DT+ F        A GT+   +ID K
Sbjct: 230 KVWRFRYSYWNSSQSYVLTKGWSRFVREKGLRPGDTVAFSRSA---AAWGTEKHLLIDCK 286

Query: 281 KGENS 285
           K E +
Sbjct: 287 KMERN 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 =  168 bits (426), Expect = 5e-41,   Method: Compositional matrix adjust.
 Identities = 106/239 (44%), Positives = 137/239 (57%), Gaps = 14/239 (5%)

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

Query: 104 TIEEPNFQSHYSTEAVINMIRDGSYSSRFADFLRSHSRTLEEDVIFTQMRAGTDGWMMCR 163
           +  E  F + +S   +++M+R  +Y    AD LR   R         Q    T  W    
Sbjct: 128 SAAELAFLAAHSKAEIVDMLRKHTY----ADELRQGLRRGRGMGARAQP---TPSWAR-E 179

Query: 164 QLFQKELTPSDVGKLNRLVIPKKYAVKYFP-QISERVEEHAENDKADDVQLVFHDKSMKL 222
            LF+K +TPSDVGKLNRLV+PK++A K+FP + +   +  +       V L F D   K+
Sbjct: 180 PLFEKAVTPSDVGKLNRLVVPKQHAEKHFPLRRAASSDSASAAATGKGVLLNFEDGEGKV 239

Query: 223 WKFRYCYWKSSQSFVFTRGWNRFVKENQLKANDTICFYLCELRDIAKGTKTFGMIDAKK 281
           W+FRY YW SSQS+V T+GW+RFV+E  L+A DTI F        A G      ID KK
Sbjct: 240 WRFRYSYWNSSQSYVLTKGWSRFVREKGLRAGDTIVFSRS-----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	354
225445893	357	PREDICTED: AP2/ERF and B3 domain-contain	0.977	0.969	0.570	1e-111
255587881	349	DNA-binding protein RAV1, putative [Rici	0.960	0.974	0.555	1e-107
224143966	549	AP2 domain-containing transcription fact	0.850	0.548	0.622	1e-106
449457911	339	PREDICTED: AP2/ERF and B3 domain-contain	0.949	0.991	0.554	1e-103
255578178	374	DNA binding protein, putative [Ricinus c	0.988	0.935	0.534	4e-94
224088262	324	AP2 domain-containing transcription fact	0.903	0.987	0.516	1e-89
449462611	356	PREDICTED: AP2/ERF and B3 domain-contain	0.728	0.724	0.622	1e-89
224073210	369	AP2 domain-containing transcription fact	0.850	0.815	0.523	4e-84
15223743	352	RAV-like factor [Arabidopsis thaliana] g	0.776	0.781	0.546	4e-82
297847474	353	hypothetical protein ARALYDRAFT_474227 [	0.731	0.733	0.565	2e-81

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

 Score =  408 bits (1049), Expect = e-111,   Method: Compositional matrix adjust.
 Identities = 207/363 (57%), Positives = 260/363 (71%), Gaps = 17/363 (4%)

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 VINMIRDGSYSSRFADFLRSHSRTLEEDVI-FTQMRAGTDGWMMCRQLFQKELTPSDVGK 177
           V+NMI+DGSY S+FA+FL++ S+  E +V+   Q+    +G  MCR LFQKELTPSDVGK
Sbjct: 121 VVNMIKDGSYPSKFAEFLKTESQRGETEVLSLDQVGVHRNGRFMCRLLFQKELTPSDVGK 180

Query: 178 LNRLVIPKKYAVKYFPQISERVEEHAENDKADDVQLVFHDKSMKLWKFRYCYWKSSQSFV 237
           LNRLVIPKKYA K+FP ISE  EE+     A D+QLVF+D+ M+LWKFRYCYW+SSQS+V
Sbjct: 181 LNRLVIPKKYATKHFPPISESAEENEVGGAAADMQLVFYDRLMRLWKFRYCYWRSSQSYV 240

Query: 238 FTRGWNRFVKENQLKANDTICFYLCELRDIAKGTKTFGMID-----AKKGENSGASAEVS 292
           FTRGWNRFVK+ +L  ND + FYLCE     K  +TF MID     +  G ++   + V 
Sbjct: 241 FTRGWNRFVKDKELNENDIVTFYLCEYGQGTKEGRTFCMIDVAYDRSTDGRDANNGSFVE 300

Query: 293 GP--YVDMKVDLQLQLGQNKKENKVEEDDNGNEIEATEEVELKAPSSTSDSERKLFKLFG 350
           GP  YV ++++LQ  L QN   NK       +E ++ EE E        + ++K  +LFG
Sbjct: 301 GPNRYVGLQIELQQDLKQNIGYNK-------HERKSQEEEESVGTEPALEGQKKGLRLFG 353

Query: 351 VEI 353
           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 =  395 bits (1016), Expect = e-107,   Method: Compositional matrix adjust.
 Identities = 199/358 (55%), Positives = 252/358 (70%), Gaps = 18/358 (5%)

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 NMIRDGSYSSRFADFLRSHSRTLEEDVIFTQMRAGTDGWMMCRQLFQKELTPSDVGKLNR 180
            MI+DG+Y S+ A F  + S+++E ++     +   +  +MC++LFQKELTPSDVGKLNR
Sbjct: 124 KMIKDGTYQSKLAYFSSTSSQSVETELSIKLTKTQRNRSLMCKELFQKELTPSDVGKLNR 183

Query: 181 LVIPKKYAVKYFPQISERVEEHAENDKADDVQLVFHDKSMKLWKFRYCYWKSSQSFVFTR 240
           LVIPK++A+K+F  ISE VE++   +KA+D QL F+DK+MKLWKFRYCYWKSSQS+VFTR
Sbjct: 184 LVIPKRFAIKFFSHISESVEQNIGGNKANDGQLAFYDKAMKLWKFRYCYWKSSQSYVFTR 243

Query: 241 GWNRFVKENQLKANDTICFYLCELRDIAKGTKTFGMIDAKKGENSGASAEVSGPYVDMKV 300
           GWNRFVKE QLKANDTI   LCE R+ A+ T ++ MID K   +S +  E        K+
Sbjct: 244 GWNRFVKEKQLKANDTIAICLCECRENAELTDSYYMIDVKNEGDSSSLLESGSQSETTKM 303

Query: 301 DLQLQLGQNK----KENKVEEDDNGNEIEATEEVELKAPSSTSDSERKLFKLFGVEIF 354
            + 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 =  390 bits (1001), Expect = e-106,   Method: Compositional matrix adjust.
 Identities = 193/310 (62%), Positives = 235/310 (75%), Gaps = 9/310 (2%)

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 VINMIRDGSYSSRFADFLRSHSRTLEEDVIFTQMRAGTDGWMMCRQLFQKELTPSDVGKL 178
           V+NMI+DG+Y  +FA+F R+ S+++E ++    M   ++  + C+QLFQKELTPSDVGKL
Sbjct: 121 VLNMIKDGTYQCKFANFTRTCSQSVETELSLKLMMPQSNQGLTCKQLFQKELTPSDVGKL 180

Query: 179 NRLVIPKKYAVKYFPQISERVEEHAENDKADDVQLVFHDKSMKLWKFRYCYWKSSQSFVF 238
           NR+VIPKKYA+KYFP ISE  EE       D V L F+DKSMKLWKFRYCYWKSSQS+VF
Sbjct: 181 NRIVIPKKYAIKYFPHISESAEE------VDGVMLAFYDKSMKLWKFRYCYWKSSQSYVF 234

Query: 239 TRGWNRFVKENQLKANDTICFYLCELRD-IAKGTKTFGMIDAKKGENSGASAEVSGPYVD 297
           TRGWNRFVKE +LKANDTI F LCE  + +    +TF MID    ENS + +E+S   + 
Sbjct: 235 TRGWNRFVKEKKLKANDTISFSLCERGETVDSAAQTFNMIDVNNRENSSSISELSSQSIA 294

Query: 298 MKVDLQLQLG 307
            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 =  380 bits (976), Expect = e-103,   Method: Compositional matrix adjust.
 Identities = 197/355 (55%), Positives = 242/355 (68%), Gaps = 19/355 (5%)

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 INMIRDGSYSSRFADFLRSHSRTLEEDVIFTQMRAGTDGWMMCRQLFQKELTPSDVGKLN 179
           +NMI+DGSY ++F+++LR  S + +     +  +A  +G    +QLFQKELTPSDVGKLN
Sbjct: 121 LNMIKDGSYRTKFSEYLRDRSESTQTSASPSTEKAHNNGGTSIKQLFQKELTPSDVGKLN 180

Query: 180 RLVIPKKYAVKYFPQISERVEEHAEN-DKADDVQLVFHDKSMKLWKFRYCYWKSSQSFVF 238
           RLVIPKKYAVKYFP+IS    E+ E+ D   D+QL+F DK M+ WKFRYCYWKSSQS+VF
Sbjct: 181 RLVIPKKYAVKYFPRISASTTENVEHVDDDRDLQLLFFDKMMRQWKFRYCYWKSSQSYVF 240

Query: 239 TRGWNRFVKENQLKANDTICFYLCELRDIAKGTKTFGMIDAKKGENSGASAEVSGPYVDM 298
           TRGWNRFVKE QLKANDTI FYLCE    +    TF ++D K  +NSG   E      ++
Sbjct: 241 TRGWNRFVKEKQLKANDTIAFYLCEAAKSSDSKTTFCVVDVKNRDNSGGLVENETTCSEL 300

Query: 299 KVDLQLQLGQNKKENKVEEDDNGNEIEATEEVELKAPSSTSDSERKLFKLFGVEI 353
           +++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 =  350 bits (899), Expect = 4e-94,   Method: Compositional matrix adjust.
 Identities = 201/376 (53%), Positives = 250/376 (66%), Gaps = 26/376 (6%)

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 HYSTEAVINMIRDGSYSSRFADFLRSHS-RTLEEDVIF---TQMRAGTDGWMMCRQLFQK 168
            YSTEA++NMIRDGSY  +FADFLR+ S R  +    F   T++     G   C QLFQK
Sbjct: 121 QYSTEAILNMIRDGSYQPKFADFLRTQSGRQEQAGASFNNQTKVPGSDHGQFSCIQLFQK 180

Query: 169 ELTPSDVGKLNRLVIPKKYAVKYFPQISERVEEHAENDKA---------DDVQLVFHDKS 219
           ELTPSDVGKLNRLVIPKK+AVKYFP IS   EE  E ++          DD++LVF+D+ 
Sbjct: 181 ELTPSDVGKLNRLVIPKKFAVKYFPYISGNGEEEGEEEEEKVVGAPSVLDDIELVFYDRL 240

Query: 220 MKLWKFRYCYWKSSQSFVFTRGWNRFVKENQLKANDTICFYLCELRD--IAKGTKTFGMI 277
           MK WKFRYCYW+SSQSFVFTRGWNRFVKE  LK  D I FY C   D  + +G + F +I
Sbjct: 241 MKCWKFRYCYWRSSQSFVFTRGWNRFVKEKNLKEKDIITFYACASPDNRVQEG-QNFSLI 299

Query: 278 DAKKGENSGASAEVSGPYVDMKVDLQLQLGQNKKENKVEEDDNGNEIEATEEVELKAPSS 337
           D     N     + +    +M+ +L+L+LG   +  ++++DD   EI   +E+E K  ++
Sbjct: 300 DISY-SNGQVVVDGNNQMEEMQKELELRLGHTIRR-RLQKDDRVKEINGLKELESKNNNN 357

Query: 338 TSDSERKLFKLFGVEI 353
            +  + K  +LFGV I
Sbjct: 358 NNKMKGKGLRLFGVRI 373

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

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 =  335 bits (860), Expect = 1e-89,   Method: Compositional matrix adjust.
 Identities = 185/358 (51%), Positives = 234/358 (65%), Gaps = 38/358 (10%)

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 VINMIRDGSYSSRFADFLRSHSRTLEEDVIFTQMRAGTDGWMMCRQLFQKELTPSDVGKL 178
           V+ MI+DG+Y S+FADF+R+ S+++E  +    M   +   + C+QLF+KELTPSDVGKL
Sbjct: 121 VLAMIKDGTYQSKFADFIRTCSQSVETALSLKLMMPQSSEGLTCKQLFRKELTPSDVGKL 180

Query: 179 NRLVIPKKYAVKYFPQISERVEEHAENDKADDVQLVFHDKSMKLWKFRYCYWKSSQSFVF 238
           NRLVIPKKYA+KYFP           N KA             L K R     ++QS+VF
Sbjct: 181 NRLVIPKKYAIKYFP-----------NTKA-------------LKKMRRL---TNQSYVF 213

Query: 239 TRGWNRFVKENQLKANDTICFYLCELRD-IAKGTKTFGMIDAKKGENSGASAEVSGPYVD 297
           TRGWNRFVKE +LKAND+I F+LCE  + +    +TF MID    EN    AE S   + 
Sbjct: 214 TRGWNRFVKEKKLKANDSIVFWLCESGETVDSAAQTFQMIDVSNCENISNIAESSNQSIA 273

Query: 298 MKVDLQLQLGQN-KKENKVEEDDNGNEIEATEEVELKAPSSTSDSERKLFKLFGVEIF 354
            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|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 =  335 bits (860), Expect = 1e-89,   Method: Compositional matrix adjust.
 Identities = 170/273 (62%), Positives = 202/273 (73%), Gaps = 15/273 (5%)

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 HYSTEAVINMIRDGSYSSRFADFLRSHSRTLEEDVIFTQMRAGTDG--WMMCRQLFQKEL 170
            +ST+AV++MI+DGSY S+F+ +LR+ S+  + ++   +     DG     C  LFQKEL
Sbjct: 121 KFSTDAVLSMIKDGSYYSKFSAYLRTRSQIHDTNIQNPKKIDNGDGDSLFSCSHLFQKEL 180

Query: 171 TPSDVGKLNRLVIPKKYAVKYFPQISERVEEHAENDKADDVQLVFHDKSMKLWKFRYCYW 230
           TPSDVGKLNRLVIPKKYAVK+FP ISE  EE+      DD+++VF+D SMK+WKFRYCYW
Sbjct: 181 TPSDVGKLNRLVIPKKYAVKHFPYISESAEEN-----GDDIEIVFYDTSMKIWKFRYCYW 235

Query: 231 KSSQSFVFTRGWNRFVKENQLKANDTICFYLCE 263
           +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|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 =  318 bits (814), Expect = 4e-84,   Method: Compositional matrix adjust.
 Identities = 169/323 (52%), Positives = 220/323 (68%), Gaps = 22/323 (6%)

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

Query: 102 KITIEEPNFQSHYSTEAVINMIRDGSYSSRFADFLRSHSRTLE----EDVIFTQMRAGTD 157
              ++EP+FQ+ YSTE ++NMIRDGSY   F DF+   S+  E    +D    ++ A  D
Sbjct: 102 DRNVQEPSFQNQYSTEEILNMIRDGSYQQIFVDFIMKQSQREEIGGSDDPNGRRVHA-DD 160

Query: 158 GWMMCRQLFQKELTPSDVGKLNRLVIPKKYAVKYFPQISERVEEHAENDKA--DDVQLVF 215
               C QLFQK+LTPSDVGKLNRLVIPKK+AVKYFP I + VE+    + A  DD +L+F
Sbjct: 161 EQFSCIQLFQKDLTPSDVGKLNRLVIPKKFAVKYFPNIFKDVEDDRVLNAAGVDDTELIF 220

Query: 216 HDKSMKLWKFRYCYWKSSQSFVFTRGWNRFVKENQLKANDTICFYLCE-----LRDIAKG 270
           +D+ MK WKFRYCYW+SSQSFVFT+GWNRFVKE +LK  D I FY C      L    +G
Sbjct: 221 YDRFMKSWKFRYCYWRSSQSFVFTKGWNRFVKEKKLKEKDIIIFYTCACPNKVLEQHGQG 280

Query: 271 TKTFGMIDAKKGENSGASAEVSGPYVDMKVDLQLQLGQNKKENKVEEDDNGNEIEATEEV 330
            + F MID       G   +      D++ +L + L QN ++ K+++D  G E++  +E 
Sbjct: 281 -QYFSMIDVVYCNGQGGKVDGFNQTEDVQRELAVVLRQNMRK-KLQKD--GKELKEEKE- 335

Query: 331 ELKAPSSTSDSERKLFKLFGVEI 353
                +  +  ++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 =  311 bits (796), Expect = 4e-82,   Method: Compositional matrix adjust.
 Identities = 159/291 (54%), Positives = 198/291 (68%), Gaps = 16/291 (5%)

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 YSSRFADFLRSHSRTLEEDVIF--TQMRAGTDG------WMMCRQLFQKELTPSDVGKLN 179
           Y  +F DFLR  S+ +    I    Q+  G +G         C QLFQKELTPSDVGKLN
Sbjct: 132 YQHKFRDFLRIRSQIVANINIVGSKQVLGGGEGGQESNKCFSCTQLFQKELTPSDVGKLN 191

Query: 180 RLVIPKKYAVKYFPQISERVEEHAENDKADDVQLVFHDKSMKLWKFRYCYWKSSQSFVFT 239
           RLVIPKKYAVKY P IS+   E   ++  +DV++VF+D++M+ WKFRYCYW+SSQSFVFT
Sbjct: 192 RLVIPKKYAVKYMPFISDDQSEKETSEGVEDVEVVFYDRAMRQWKFRYCYWRSSQSFVFT 251

Query: 240 RGWNRFVKENQLKANDTICFYLCELRDIAKG----TKTFGMIDAKKGENSG 286
           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|297847474|ref|XP_002891618.1| hypothetical protein ARALYDRAFT_474227 [Arabidopsis lyrata subsp. lyrata] gi|297337460|gb|EFH67877.1| hypothetical protein ARALYDRAFT_474227 [Arabidopsis lyrata subsp. lyrata]

 Score =  308 bits (789), Expect = 2e-81,   Method: Compositional matrix adjust.
 Identities = 155/274 (56%), Positives = 189/274 (68%), Gaps = 15/274 (5%)

Query: 28  PLIPATKRLRHA-SAVSKFKGVVPQQNGHWGAQIYANHQRIWLGTFKSEKDAAMAYDSAA 86
           P +  T  ++ A S  +K+KGVV QQNGHWGAQIYA H+RIWLGTFKS  +AA AYDSA+
Sbjct: 30  PTLVTTTTIKPALSNTTKYKGVVQQQNGHWGAQIYAEHKRIWLGTFKSAPEAAAAYDSAS 89

Query: 87  IRLRGVD--SHRNFPWTKITIEEPNFQSHYSTEAVINMIRDGSYSSRFADFLRSHSRTLE 144
           I+LR  D  SHRNFPW+  T+ EP+FQ  YSTEAV+NMIRDGSY  +F DFLR  S+ + 
Sbjct: 90  IKLRSFDANSHRNFPWSDFTVHEPDFQECYSTEAVLNMIRDGSYQHKFRDFLRIRSQIVA 149

Query: 145 EDVIF--TQMRAGTDG------WMMCRQLFQKELTPSDVGKLNRLVIPKKYAVKYFPQIS 196
              I    Q+R G  G         C QLFQKELTPSDVGKLNRLVIPKKYAVKY P IS
Sbjct: 150 NINIVGSKQVRGGEGGAQESNKCFSCTQLFQKELTPSDVGKLNRLVIPKKYAVKYMPFIS 209

Query: 197 ERVEEHAENDKADDVQLVFHDKSMKLWKFRYCYWKSSQSFVFTRGWNRFVKENQLKANDT 256
           +   E   ++  +DV++VF+D++M+ WKFRYCYW+SSQSFVFTRGWN FVKE  LK  D 
Sbjct: 210 DDQSEKETSEGVEDVEVVFYDRAMRQWKFRYCYWRSSQSFVFTRGWNGFVKEKNLKEKDI 269

Query: 257 ICFYLCE----LRDIAKGTKTFGMIDAKKGENSG 286
           I FY C+    ++ +   +K F MID      +G
Sbjct: 270 IVFYTCDVPSNVKTLEGQSKNFLMIDVHYFSGNG 303

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	354
TAIR|locus:2026058	352	AT1G51120 [Arabidopsis thalian	0.915	0.920	0.491	4.8e-78
TAIR|locus:2015832	337	AT1G50680 [Arabidopsis thalian	0.853	0.896	0.517	3.1e-76
TAIR|locus:2205319	344	RAV1 "related to ABI3/VP1 1" [	0.590	0.607	0.452	7.1e-45
TAIR|locus:2031185	361	TEM1 "TEMPRANILLO 1" [Arabidop	0.610	0.598	0.436	1.2e-44
TAIR|locus:2085969	333	EDF3 "ethylene response DNA bi	0.593	0.630	0.470	1.9e-44
TAIR|locus:2012438	352	RAV2 "related to ABI3/VP1 2" [	0.579	0.582	0.444	3.7e-44
TAIR|locus:2164215	282	DPA4 "DEVELOPMENT-RELATED PcG	0.531	0.666	0.347	1.6e-24
TAIR|locus:2080782	267	AT3G11580 [Arabidopsis thalian	0.268	0.355	0.540	3.8e-23
TAIR|locus:2117007	333	NGA4 "NGATHA4" [Arabidopsis th	0.242	0.258	0.541	7.8e-23
TAIR|locus:2039165	244	ABS2 "ABNORMAL SHOOT 2" [Arabi	0.319	0.463	0.456	1.6e-22

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

 Score = 785 (281.4 bits), Expect = 4.8e-78, P = 4.8e-78
 Identities = 176/358 (49%), Positives = 231/358 (64%)

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 YSSRFADFLRSHSRTLEE-DVIFT-QMRAGTDGWM------MCRQLFQKELTPSDVGKLN 179
             Y  +F DFLR  S+ +   +++ + Q+  G +G         C QLFQKELTPSDVGKLN
Sbjct:   132 YQHKFRDFLRIRSQIVANINIVGSKQVLGGGEGGQESNKCFSCTQLFQKELTPSDVGKLN 191

Query:   180 RLVIPKKYAVKYFPQISERVEEHAENDKADDVQLVFHDKSMKLWKFRYCYWKSSQSFVFT 239
             RLVIPKKYAVKY P IS+   E   ++  +DV++VF+D++M+ WKFRYCYW+SSQSFVFT
Sbjct:   192 RLVIPKKYAVKYMPFISDDQSEKETSEGVEDVEVVFYDRAMRQWKFRYCYWRSSQSFVFT 251

Query:   240 RGWNRFVKENQLKANDTICFYLCELRDIAK---G-TKTFGMIDAKKGENSGASAEVSGPY 295
             RGWN FVKE  LK  D I FY C++ +  K   G +KTF MID      SG     +G  
Sbjct:   252 RGWNGFVKEKNLKEKDIIVFYTCDVPNNVKTLEGQSKTFLMIDVH--HFSG-----NGFV 304

Query:   296 VDMKVDLQLQLGQNKKENKVEEDDNGNEIEATEEVELKAPSSTSDSERKLFKLFGVEI 353
             V  +V        NK  +++ +++   E   T +VE     + S+ ++  F LFGV I
Sbjct:   305 VPEEV--------NKTVHEISDEEMKTETLFTSKVE---EETKSEEKKGGFMLFGVRI 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 = 768 (275.4 bits), Expect = 3.1e-76, P = 3.1e-76
 Identities = 166/321 (51%), Positives = 212/321 (66%)

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

Query:    80 MAYDSAAIRLRGVD--SHRNFPWTKITIEEPNFQSHYSTEAVINMIRDGSYSSRFADFLR 137
              AYDSA+I+LR  D  SHRNFPW+ IT+ EP+FQ+ Y+TE V+NMIRDGSY  +F DFLR
Sbjct:    63 TAYDSASIKLRSFDANSHRNFPWSTITLNEPDFQNCYTTETVLNMIRDGSYQHKFRDFLR 122

Query:   138 SHSRTLEEDVIFTQMRA-G-----TDGWMMCRQLFQKELTPSDVGKLNRLVIPKKYAVKY 191
               S+ +    I    +A G     +D    C QLFQKELTPSDVGKLNRLVIPKKYAVKY
Sbjct:   123 IRSQIVASINIGGPKQARGEVNQESDKCFSCTQLFQKELTPSDVGKLNRLVIPKKYAVKY 182

Query:   192 FPQISERVEEHAEND---KADDVQLVFHDKSMKLWKFRYCYWKSSQSFVFTRGWNRFVKE 248
              P IS    E  E +     +DV++VF+D++M+ WKFRYCYWKSSQSFVFTRGWN FVKE
Sbjct:   183 MPFISADQSEKEEGEIVGSVEDVEVVFYDRAMRQWKFRYCYWKSSQSFVFTRGWNSFVKE 242

Query:   249 NQLKANDTICFYLCELRDIAK---GT-KTFGMIDAKKGENSGA--SAEVSGPYVDMKVDL 302
               LK  D I FY C++ +  K   G  K F MID     ++G+  + EVS    D  V  
Sbjct:   243 KNLKEKDVIAFYTCDVPNNVKTLEGQRKNFLMIDVHCFSDNGSVVAEEVSMTVHDSSV-- 300

Query:   303 QLQLGQNKKENKVEEDDNGNE 323
             Q++  +N   + +E+ +  +E
Sbjct:   301 QVKKTENLVSSMLEDKETKSE 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:2205319 RAV1 "related to ABI3/VP1 1" [Arabidopsis thaliana (taxid:3702)]

 Score = 472 (171.2 bits), Expect = 7.1e-45, P = 7.1e-45
 Identities = 101/223 (45%), Positives = 131/223 (58%)

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 ITIEEPNFQSHYSTEAVINMIRDGSYSSRFADFLRSHS------RTLEEDVIFTQMRAGT 156
             +  +E +F + +S   +++M+R  +Y+       R  +      RTL    +       T
Sbjct:   120 MDEDEVDFLNSHSKSEIVDMLRKHTYNEELEQSKRRRNGNGNMTRTLLTSGLSND-GVST 178

Query:   157 DGWMMCRQLFQKELTPSDVGKLNRLVIPKKYAVKYFPQISERVEEHAENDKADDVQLVFH 216
              G+     LF+K +TPSDVGKLNRLVIPK +A K+FP  S  V           V L F 
Sbjct:   179 TGFRSAEALFEKAVTPSDVGKLNRLVIPKHHAEKHFPLPSSNVS-------VKGVLLNFE 231

Query:   217 DKSMKLWKFRYCYWKSSQSFVFTRGWNRFVKENQLKANDTICF 259
             D + K+W+FRY YW SSQS+V T+GW+RFVKE  L+A D + F
Sbjct:   232 DVNGKVWRFRYSYWNSSQSYVLTKGWSRFVKEKNLRAGDVVSF 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:2031185 TEM1 "TEMPRANILLO 1" [Arabidopsis thaliana (taxid:3702)]

 Score = 470 (170.5 bits), Expect = 1.2e-44, P = 1.2e-44
 Identities = 96/220 (43%), Positives = 131/220 (59%)

Query:    43 SKFKGVVPQQNGHWGAQIYANHQRIWLGTFKSEKDAAMAYDSAAIRLRGVDSHRNFPWTK 102
             SK+KGVVPQ NG WGAQIY  HQR+WLGTF  E++AA +YD A  R RG D+  NF  ++
Sbjct:    70 SKYKGVVPQPNGRWGAQIYEKHQRVWLGTFNEEEEAASSYDIAVRRFRGRDAVTNFK-SQ 128

Query:   103 I--TIEEPNFQSHYSTEAVINMIRDGSYSSRFADFLRSHSRTLEEDVIFTQMRAGTDGWM 160
             +     E  F   +S   +++M+R  +Y+  F    R       +         G D  +
Sbjct:   129 VDGNDAESAFLDAHSKAEIVDMLRKHTYADEFEQSRRKFVNGDGKRSGLETATYGNDAVL 188

Query:   161 MCRQ-LFQKELTPSDVGKLNRLVIPKKYAVKYFPQISERVEEHAENDKADDVQLVFHDKS 219
               R+ LF+K +TPSDVGKLNRLVIPK++A K+FP  +              V +   D++
Sbjct:   189 RAREVLFEKTVTPSDVGKLNRLVIPKQHAEKHFPLPAMTTAMGMNPSPTKGVLINLEDRT 248

Query:   220 MKLWKFRYCYWKSSQSFVFTRGWNRFVKENQLKANDTICF 259
              K+W+FRY YW SSQS+V T+GW+RFVKE  L+A D +CF
Sbjct:   249 GKVWRFRYSYWNSSQSYVLTKGWSRFVKEKNLRAGDVVCF 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:2085969 EDF3 "ethylene response DNA binding factor 3" [Arabidopsis thaliana (taxid:3702)]

 Score = 468 (169.8 bits), Expect = 1.9e-44, P = 1.9e-44
 Identities = 103/219 (47%), Positives = 129/219 (58%)

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 ITIEEPNFQSHYSTEAVINMIRDGSYSSRFADFLRSHSRTLEEDVIFT--QMRAGTDGWM 160
                EE  F + +S   +++M+R  +Y        R+     +E   F    M   T G+ 
Sbjct:   120 FE-EEVEFLNAHSKSEIVDMLRKHTYKEELDQRKRNRDGNGKETTAFALASMVVMT-GFK 177

Query:   161 MCRQLFQKELTPSDVGKLNRLVIPKKYAVKYFPQISERVEEHAENDKADDVQLVFHDKSM 220
                 LF+K +TPSDVGKLNRLVIPK  A K+FP     +     N     + L F D + 
Sbjct:   178 TAELLFEKTVTPSDVGKLNRLVIPKHQAEKHFP-----LPLGNNNVSVKGMLLNFEDVNG 232

Query:   221 KLWKFRYCYWKSSQSFVFTRGWNRFVKENQLKANDTICF 259
             K+W+FRY YW SSQS+V T+GW+RFVKE +L A D I F
Sbjct:   233 KVWRFRYSYWNSSQSYVLTKGWSRFVKEKRLCAGDLISF 271

GO:0003677 "DNA binding" evidence=IEA

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

GO:0005634 "nucleus" evidence=ISM

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

GO:0009691 "cytokinin biosynthetic process" evidence=RCA

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

 Score = 445 (161.7 bits), Expect = 3.7e-44, Sum P(2) = 3.7e-44
 Identities = 100/225 (44%), Positives = 137/225 (60%)

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--FQSHYSTEAVINMIRDGSYSSRFADFLRSHSRTLEEDVIFTQMRAGT---- 156
               +E+ +  F   +S   +++M+R  +Y+       +++ R L   V     R G+    
Sbjct:   120 NVLEDGDLAFLEAHSKAEIVDMLRKHTYADELE---QNNKRQLFLSVDANGKRNGSSTTQ 176

Query:   157 -DGWMMCRQ-LFQKELTPSDVGKLNRLVIPKKYAVKYFPQISERVEEHAENDKADDVQLV 214
              D  +  R+ LF+K +TPSDVGKLNRLVIPK++A K+FP  S              V + 
Sbjct:   177 NDKVLKTREVLFEKAVTPSDVGKLNRLVIPKQHAEKHFPLPSPSPAV------TKGVLIN 230

Query:   215 FHDKSMKLWKFRYCYWKSSQSFVFTRGWNRFVKENQLKANDTICF 259
             F D + K+W+FRY YW SSQS+V T+GW+RFVKE  L+A D + F
Sbjct:   231 FEDVNGKVWRFRYSYWNSSQSYVLTKGWSRFVKEKNLRAGDVVTF 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:2164215 DPA4 "DEVELOPMENT-RELATED PcG TARGET IN THE APEX 4" [Arabidopsis thaliana (taxid:3702)]

 Score = 280 (103.6 bits), Expect = 1.6e-24, P = 1.6e-24
 Identities = 67/193 (34%), Positives = 98/193 (50%)

Query:   165 LFQKELTPSDVGKLNRLVIPKKYAVKYFPQISERVEEHAENDKADD--VQLVFHDKSMKL 222
             LF+K LTPSDVGKLNRLVIPK++A KYFP  +  V   A +  + +  + L F D+S K 
Sbjct:    45 LFEKSLTPSDVGKLNRLVIPKQHAEKYFPLNAVLVSSAAADTSSSEKGMLLSFEDESGKS 104

Query:   223 WKFRYCYWKSSQSFVFTRGWNRFVKENQLKANDTICF--YLCELRDIAKGTKTFGMIDAK 280
             W+FRY YW SSQS+V T+GW+RFVK+ QL   D + F  +  + R +  G +  G   + 
Sbjct:   105 WRFRYSYWNSSQSYVLTKGWSRFVKDKQLDPGDVVFFQRHRSDSRRLFIGWRRRGQGSSS 164

Query:   281 KGENSGASAEVSGPYVDMKVDLQLQLGQNKKENKVEEDDNGNEIEATEEVELKAPSSTSD 340
                 + ++   S         +      +   +  E    G  +    E     PSS+  
Sbjct:   165 SVAATNSAVNTSSMGALSYHQIHATSNYSNPPSHSEYSHYGAAVATAAETH-STPSSSVV 223

Query:   341 SERKLFKLFGVEI 353
                +  +LFGV +
Sbjct:   224 GSSRTVRLFGVNL 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:2080782 AT3G11580 [Arabidopsis thaliana (taxid:3702)]

 Score = 267 (99.0 bits), Expect = 3.8e-23, P = 3.8e-23
 Identities = 53/98 (54%), Positives = 67/98 (68%)

Query:   165 LFQKELTPSDVGKLNRLVIPKKYAVKYFPQISERVEEHAENDKADDVQ---LVFHDKSMK 221
             LF+K LTPSDVGKLNRLVIPK++A KYFP  +      + +D A   +   L F D+S K
Sbjct:    28 LFEKSLTPSDVGKLNRLVIPKQHAEKYFPLNNNNNNGGSGDDVATTEKGMLLSFEDESGK 87

Query:   222 LWKFRYCYWKSSQSFVFTRGWNRFVKENQLKANDTICF 259
              WKFRY YW SSQS+V T+GW+R+VK+  L A D + F
Sbjct:    88 CWKFRYSYWNSSQSYVLTKGWSRYVKDKHLDAGDVVFF 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 = 264 (98.0 bits), Expect = 7.8e-23, P = 7.8e-23
 Identities = 52/96 (54%), Positives = 67/96 (69%)

Query:   165 LFQKELTPSDVGKLNRLVIPKKYAVKYFPQISERVEEHAENDKADDVQLVFHDKSMKLWK 224
             +F K LTPSDVGKLNRLVIPK++A  +FP     +E++      D     F DK+ K+W+
Sbjct:    35 MFDKVLTPSDVGKLNRLVIPKQHAENFFP-----LEDNQNGTVLD-----FQDKNGKMWR 84

Query:   225 FRYCYWKSSQSFVFTRGWNRFVKENQLKANDTICFY 260
             FRY YW SSQS+V T+GW+RFVKE +L A DT+ FY
Sbjct:    85 FRYSYWNSSQSYVMTKGWSRFVKEKKLFAGDTVSFY 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: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:   165 LFQKELTPSDVGKLNRLVIPKKYAVKYFPQISERVEEHAENDKADDVQLVFHDKSMKLWK 224
             LF+K LTPSDVGKLNRLVIPK++A +YFP ++    +  E      + L F D+  K W+
Sbjct:    37 LFEKPLTPSDVGKLNRLVIPKQHAERYFP-LAAAAADAVEKG----LLLCFEDEEGKPWR 91

Query:   225 FRYCYWKSSQSFVFTRGWNRFVKENQLKANDTICFYLCELRDIAKGTKTF-GMIDAKKGE 283
             FRY YW SSQS+V T+GW+R+VKE  L A D + F+    R  + G + F G    ++G+
Sbjct:    92 FRYSYWNSSQSYVLTKGWSRYVKEKHLDAGDVVLFH----RHRSDGGRFFIGW--RRRGD 145

Query:   284 NSGAS 288
             +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	0.5463	0.7768	0.7812	yes	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	354
cd10017	98	cd10017, B3_DNA, Plant-specific B3-DNA binding dom	6e-24
smart01019	96	smart01019, B3, B3 DNA binding domain	2e-23
pfam02362	97	pfam02362, B3, B3 DNA binding domain	4e-23
cd00018	61	cd00018, AP2, DNA-binding domain found in transcri	9e-23
smart00380	64	smart00380, AP2, DNA-binding domain in plant prote	2e-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-05
pfam00847	53	pfam00847, AP2, AP2 domain	2e-04

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

 Score = 93.9 bits (234), Expect = 6e-24
 Identities = 35/97 (36%), Positives = 46/97 (47%), Gaps = 13/97 (13%)

Query: 165 LFQKELTPSDVGKLNRLVIPKKYAVKYFPQISERVEEHAENDKADDVQLVFHDKSMKLWK 224
           LF K LTPSDV  L RLV+PKK+A  + P               + V++   D   K W 
Sbjct: 2   LFFKVLTPSDVSSLGRLVLPKKFAKAHLPPK-------------EGVEVTLEDPDGKKWT 48

Query: 225 FRYCYWKSSQSFVFTRGWNRFVKENQLKANDTICFYL 261
            +    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 = 92.4 bits (230), Expect = 2e-23
 Identities = 36/96 (37%), Positives = 47/96 (48%), Gaps = 13/96 (13%)

Query: 166 FQKELTPSDVGKLNRLVIPKKYAVKYFPQISERVEEHAENDKADDVQLVFHDKSMKLWKF 225
           F K LT SDV K  RLV+PK++A    P +  +             ++   D   K WK 
Sbjct: 1   FFKTLTTSDVSKHGRLVLPKQFAESNGPPLKPK-------------EITLLDPDGKSWKV 47

Query: 226 RYCYWKSSQSFVFTRGWNRFVKENQLKANDTICFYL 261
           +  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 = 92.0 bits (229), Expect = 4e-23
 Identities = 35/98 (35%), Positives = 46/98 (46%), Gaps = 13/98 (13%)

Query: 166 FQKELTPSDVGKLNRLVIPKKYAVKYFPQISERVEEHAENDKADDVQLVFHDKSMKLWKF 225
           F K LTPSDV K  RLV+PKK+A +                     ++   D   K W  
Sbjct: 1   FVKVLTPSDVSKDGRLVLPKKFAEENG-------------LNKKGQEITLLDPDGKSWTV 47

Query: 226 RYCYWKSSQSFVFTRGWNRFVKENQLKANDTICFYLCE 263
           +  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 = 89.6 bits (223), Expect = 9e-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 = 80.8 bits (200), Expect = 2e-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: 165 LFQKELTPSDVGK----LNRLVIPKKYAVKYFPQISERVEEHAENDKADDVQLVFHDKSM 220
           +  K L+ +D G        L IPK    K+ P I+   E +        + L  HD S 
Sbjct: 2   VLIKRLSANDTGATGGHQVGLYIPKGIVEKFPPSINHTREAN------PSIFLTMHDISD 55

Query: 221 -KLWKFRYCYWKSSQSFVF-TRGWNRFVKENQLKANDTICFY 260
            + 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 = 42.7 bits (101), Expect = 2e-05
 Identities = 24/92 (26%), Positives = 41/92 (44%), Gaps = 6/92 (6%)

Query: 163 RQLFQKELTPSDVGKL-NRLVIPKKYAVKY-F--PQISERVEEHAENDKADDVQLVFHDK 218
           + + +K L  +DV    +RL +P    ++  F   +    +EE    DK   V ++  D 
Sbjct: 21  KLIIEKTLFKTDVDPTQSRLSMPFNQLLRNDFLTEEEKRIIEEDKNKDKDIGVGVILVDP 80

Query: 219 SMKLWKFRYCYW--KSSQSFVFTRGWNRFVKE 248
             K W  +   W  KS+ ++V   GWN  V+ 
Sbjct: 81  ESKKWVLKLKKWDMKSTLNYVLVCGWNDVVEA 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 = 2e-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	354
cd00018	61	AP2 DNA-binding domain found in transcription regu	99.77
smart00380	64	AP2 DNA-binding domain in plant proteins such as A	99.76
PF02362	100	B3: B3 DNA binding domain; InterPro: IPR003340 Two	99.67
PHA00280	121	putative NHN endonuclease	99.55
PF03754	114	DUF313: Domain of unknown function (DUF313) ; Inte	99.35
PF00847	56	AP2: AP2 domain; InterPro: IPR001471 Pathogenesis-	98.96
PF09217	156	EcoRII-N: Restriction endonuclease EcoRII, N-termi	98.18

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

Probab=99.77  E-value=7.7e-19  Score=132.02  Aligned_cols=59  Identities=47%  Similarity=0.821  Sum_probs=56.6

Q ss_pred             CceEEeEECCCCeEEEEEEeC--CeEEEecCCCCHHHHHHHHHHHHHHhcCCCCCCCCCCC
Q 018549           43 SKFKGVVPQQNGHWGAQIYAN--HQRIWLGTFKSEKDAAMAYDSAAIRLRGVDSHRNFPWT  101 (354)
Q Consensus        43 SgyrGV~~~~~gkw~A~I~~~--~k~~~LG~f~t~EeAa~Ayd~aa~~~~g~~a~~NFp~~  101 (354)
                      |+|+||+++++|+|+|+|++.  ++++|||+|+|+||||.|||.|+++++|..+.+|||.+
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            789999988889999999998  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=99.76  E-value=1.7e-18  Score=131.62  Aligned_cols=61  Identities=41%  Similarity=0.768  Sum_probs=58.7

Q ss_pred             ceEEeEECCCCeEEEEEEe--CCeEEEecCCCCHHHHHHHHHHHHHHhcCCCCCCCCCCCccc
Q 018549           44 KFKGVVPQQNGHWGAQIYA--NHQRIWLGTFKSEKDAAMAYDSAAIRLRGVDSHRNFPWTKIT  104 (354)
Q Consensus        44 gyrGV~~~~~gkw~A~I~~--~~k~~~LG~f~t~EeAa~Ayd~aa~~~~g~~a~~NFp~~~y~  104 (354)
                      +|+||+++++|+|+|+|++  +++++|||+|+|+||||.|||.|+++++|..+.+|||.++|+
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            4899988889999999999  999999999999999999999999999999999999999986

>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=99.67  E-value=4.4e-16  Score=126.24  Aligned_cols=87  Identities=36%  Similarity=0.583  Sum_probs=68.9

Q ss_pred             eeeeccccccCCCCceeechhhhhhcCCCCchhhhhhccccCCCCeEEEEEeCCCceEEEEEEEeCCCCeeeEccChHHH
Q 018549          166 FQKELTPSDVGKLNRLVIPKKYAVKYFPQISERVEEHAENDKADDVQLVFHDKSMKLWKFRYCYWKSSQSFVFTRGWNRF  245 (354)
Q Consensus       166 F~K~LT~SDv~~~~rL~IPk~~a~~~fP~l~~~~~~~~~~~~~~gv~v~v~D~~g~~W~fr~~~~~~sr~yvLt~GW~~F  245 (354)
                      |.|+|+++|+...++|.||++.+.+|...            ...++.+.+.|..|+.|.+++++++.+.+|+|++||..|
T Consensus         1 F~K~l~~s~~~~~~~l~iP~~f~~~~~~~------------~~~~~~v~l~~~~g~~W~v~~~~~~~~~~~~l~~GW~~F   68 (100)
T PF02362_consen    1 FFKVLKPSDVSSSCRLIIPKEFAKKHGGN------------KRKSREVTLKDPDGRSWPVKLKYRKNSGRYYLTGGWKKF   68 (100)
T ss_dssp             EEEE--TTCCCCTT-EEE-HHHHTTTS--------------SS--CEEEEEETTTEEEEEEEEEECCTTEEEEETTHHHH
T ss_pred             CEEEEEccCcCCCCEEEeCHHHHHHhCCC------------cCCCeEEEEEeCCCCEEEEEEEEEccCCeEEECCCHHHH
Confidence            78999999999889999999999988211            135678999999999999999999998889999999999


Q ss_pred             HhhcCCCCCCEEEEEEeec
Q 018549          246 VKENQLKANDTICFYLCEL  264 (354)
Q Consensus       246 Vr~k~Lk~GD~I~F~r~~~  264 (354)
                      |++++|++||.|+|+...+
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=6.2e-15  Score=125.52  Aligned_cols=70  Identities=16%  Similarity=0.115  Sum_probs=62.2

Q ss_pred             CCCCCCCCcccCCCCCCCceEEeEE-CCCCeEEEEEEeCCeEEEecCCCCHHHHHHHHHHHHHHhcCCCCCC
Q 018549           26 STPLIPATKRLRHASAVSKFKGVVP-QQNGHWGAQIYANHQRIWLGTFKSEKDAAMAYDSAAIRLRGVDSHR   96 (354)
Q Consensus        26 ~~~~~~~~~r~~~~~~~SgyrGV~~-~~~gkw~A~I~~~~k~~~LG~f~t~EeAa~Ayd~aa~~~~g~~a~~   96 (354)
                      .|..++..+++.+++|+|||+||++ +..|||+|+|.++||+++||.|+++|+|+.||+ ++.++||.+|+.
T Consensus        50 ~T~~eN~~N~~~~~~N~SG~kGV~~~k~~~kw~A~I~~~gK~~~lG~f~~~e~A~~a~~-~~~~lhGeFa~~  120 (121)
T PHA00280         50 ALPKENSWNMKTPKSNTSGLKGLSWSKEREMWRGTVTAEGKQHNFRSRDLLEVVAWIYR-TRRELHGQFARF  120 (121)
T ss_pred             cCHHHHhcccCCCCCCCCCCCeeEEecCCCeEEEEEEECCEEEEcCCCCCHHHHHHHHH-HHHHHhhccccC
Confidence            4566778888889999999999965 568999999999999999999999999999997 778999999853

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

Probab=99.35  E-value=1.8e-12  Score=109.43  Aligned_cols=104  Identities=25%  Similarity=0.473  Sum_probs=83.1

Q ss_pred             cccccccccccCCCCcccccceeeeeccccccCC-CCceeechhhhhhcCCCCchhh-----hhhccccCCCCeEEEEEe
Q 018549          144 EEDVIFTQMRAGTDGWMMCRQLFQKELTPSDVGK-LNRLVIPKKYAVKYFPQISERV-----EEHAENDKADDVQLVFHD  217 (354)
Q Consensus       144 et~~~~~~~~~~~~~~~~~~~lF~K~LT~SDv~~-~~rL~IPk~~a~~~fP~l~~~~-----~~~~~~~~~~gv~v~v~D  217 (354)
                      +.|+|+..++..+.+..+..++++|+|++|||.+ ++||+||...+.. ..+|..+.     +++.......|+.|.++|
T Consensus         2 e~P~~l~~~m~~~~g~~d~kli~~K~L~~tDv~~~qsRLsmP~~qi~~-~dFLt~eE~~~i~~~~~~~~~~~Gv~V~lvd   80 (114)
T PF03754_consen    2 ELPEWLKNVMREMNGAEDPKLIIEKTLFKTDVDPHQSRLSMPFNQIID-NDFLTEEEKRIIKEEKKNNDKKKGVEVILVD   80 (114)
T ss_pred             CchHHHHHHHHHhcCCCCCeEEEeeeecccCCCCCCceeeccHHHhcc-cccCCHHHHHHHHHhhccCcccCCceEEEEC
Confidence            5678888888877666677999999999999987 9999999888755 24444211     112234567899999999


Q ss_pred             CCCceEEEEEEEeCC---CCeeeEccChHHHHhh
Q 018549          218 KSMKLWKFRYCYWKS---SQSFVFTRGWNRFVKE  248 (354)
Q Consensus       218 ~~g~~W~fr~~~~~~---sr~yvLt~GW~~FVr~  248 (354)
                      ..++.|.++++.|..   +..|+|+.||+++|+.
T Consensus        81 p~~~~~~m~lkkW~mg~~~~~YvL~~gWn~VV~~  114 (114)
T PF03754_consen   81 PSLRKWTMRLKKWNMGNGTSNYVLNSGWNKVVED  114 (114)
T ss_pred             CcCcEEEEEEEEecccCCceEEEEEcChHhhccC
Confidence            999999999999987   6689999999999863

>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=98.96  E-value=1.4e-09  Score=79.80  Aligned_cols=50  Identities=36%  Similarity=0.468  Sum_probs=44.4

Q ss_pred             CceEEeEEC-CCCeEEEEEEeC-----CeEEEecCCCCHHHHHHHHHHHHHHhcCC
Q 018549           43 SKFKGVVPQ-QNGHWGAQIYAN-----HQRIWLGTFKSEKDAAMAYDSAAIRLRGV   92 (354)
Q Consensus        43 SgyrGV~~~-~~gkw~A~I~~~-----~k~~~LG~f~t~EeAa~Ayd~aa~~~~g~   92 (354)
                      |+|+||++. ..++|+|+|++.     ++.++||.|++++||++||+.++..++|+
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            789999765 589999999982     49999999999999999999999999874

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

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

Probab=98.18  E-value=3.8e-06  Score=74.04  Aligned_cols=93  Identities=19%  Similarity=0.305  Sum_probs=58.9

Q ss_pred             cceeeeeccccccCC----CCceeechhhhhhcCCCCchhhhhhccccCCCCeEEEEEeCCC--ceEEEEEEEeCC----
Q 018549          163 RQLFQKELTPSDVGK----LNRLVIPKKYAVKYFPQISERVEEHAENDKADDVQLVFHDKSM--KLWKFRYCYWKS----  232 (354)
Q Consensus       163 ~~lF~K~LT~SDv~~----~~rL~IPk~~a~~~fP~l~~~~~~~~~~~~~~gv~v~v~D~~g--~~W~fr~~~~~~----  232 (354)
                      -.+|+|.|++.|++.    +.++.|||..+..+||.+..      ..+.++.+.|.+.+..+  ..|+||++|.++    
T Consensus         7 ~~~~~K~LSaNDtGaTGgHQaGiyIpk~~~~~lFp~~~~------~~~~Np~~~~~~~~~s~~~~~~~~r~iYYnn~~~~   80 (156)
T PF09217_consen    7 WAIYCKRLSANDTGATGGHQAGIYIPKSAAELLFPSINH------TKEENPDIWLKARWQSHFVTDSQVRFIYYNNRLFG   80 (156)
T ss_dssp             EEEEEEE--CCCCTTTSSS--EEEE-HHHHHHH-GGG-S------SSSSS-EEEEEEEETTTT---EEEEEEEE-CCCTT
T ss_pred             eEEEEEEccCCCCCCcCcccceeEecccHHHHhCCCCCc------ccccCCceeEEEEECCCCccceeEEEEEEcccccC
Confidence            358999999999975    78899999999999999874      23346889999988766  568899999987    


Q ss_pred             --CCeeeEccChHHHHhhcC-CCCCCEEEEEEe
Q 018549          233 --SQSFVFTRGWNRFVKENQ-LKANDTICFYLC  262 (354)
Q Consensus       233 --sr~yvLt~GW~~FVr~k~-Lk~GD~I~F~r~  262 (354)
                        ...|.|| +|.....--+ =.+||.++|-=.
T Consensus        81 gTRNE~RIT-~~G~~~~~~~~~~tGaL~vlaf~  112 (156)
T PF09217_consen   81 GTRNEYRIT-RFGRGFPLQNPENTGALLVLAFD  112 (156)
T ss_dssp             SS--EEEEE----TTSGGG-GGGTT-EEEEEEE
T ss_pred             CCcCceEEe-eecCCCccCCccccccEEEEEEc
Confidence              4559997 7877433222 468998888744

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	354
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		3e-07

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

Iteration: 1
 Score =  108 bits (269), Expect = 6e-24,   Method: Compositional matrix adjust.
 Identities = 52/95 (54%), Positives = 64/95 (67%), Gaps = 7/95 (7%)
Query: 165 LFQKELTPSDVGKLNRLVIPKKYAVKYFPQISERVEEHAENDKADDVQLVFHDKSMKLWK 224
           LF+K +TPSDVGKLNRLVIPK +A K+FP  S  V           V L F D + K+W+
Sbjct: 13  LFEKAVTPSDVGKLNRLVIPKHHAEKHFPLPSSNVS-------VKGVLLNFEDVNGKVWR 65
Query: 225 FRYCYWKSSQSFVFTRGWNRFVKENQLKANDTICF 259
           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 = 53.1 bits (126), 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 = 3e-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	354
1wid_A	130	DNA-binding protein RAV1; DNA-binding domain, stru	2e-27
1gcc_A	63	Ethylene responsive element binding factor 1; tran	3e-15
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	1e-09
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	4e-04
1yel_A	104	AT1G16640; CESG, protein structure initiative, str	3e-08

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

 Score =  104 bits (259), Expect = 2e-27
 Identities = 57/133 (42%), Positives = 74/133 (55%), Gaps = 13/133 (9%)

Query: 162 CRQLFQKELTPSDVGKLNRLVIPKKYAVKYFPQISERVEEHAENDKADDVQLVFHDKSMK 221
              LF+K +TPSDVGKLNRLVIPK +A K+FP  S  V           V L F D + K
Sbjct: 10  AEALFEKAVTPSDVGKLNRLVIPKHHAEKHFPLPSSNVSVKG-------VLLNFEDVNGK 62

Query: 222 LWKFRYCYWKSSQSFVFTRGWNRFVKENQLKANDTICFYLCELRDIAKGTKTFGM-IDAK 280
           +W+FRY YW SSQS+V T+GW+RFVKE  L+A D + F            +   +   ++
Sbjct: 63  VWRFRYSYWNSSQSYVLTKGWSRFVKEKNLRAGDVVSFSRSN-----GQDQQLYIGWKSR 117

Query: 281 KGENSGASAEVSG 293
            G +  AS   SG
Sbjct: 118 SGSDLDASGPSSG 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 = 68.5 bits (168), Expect = 3e-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

>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 = 59.1 bits (142), Expect = 1e-09
 Identities = 60/394 (15%), Positives = 118/394 (29%), Gaps = 90/394 (22%)

Query: 1   MEEEMLSIISNGETNVIPELSDSISSTPLIPATKRLRHASAVSKFKGVVPQQNGHWGAQI 60
           +++   SI+S  E + I    D++S T  +  T   +    V KF   V + N       
Sbjct: 38  VQDMPKSILSKEEIDHIIMSKDAVSGTLRLFWTLLSKQEEMVQKFVEEVLRIN------- 90

Query: 61  YANHQRIWLGT-FKSE-KDAAM---AYDSAAIRLRGVDSHRNFPWTKITIEEPNFQSHYS 115
           Y      +L +  K+E +  +M    Y     RL   D+   F    ++  +P  +    
Sbjct: 91  YK-----FLMSPIKTEQRQPSMMTRMYIEQRDRLYN-DNQV-FAKYNVSRLQPYLKLR-- 141

Query: 116 TEAVINMIRDGSY-----------SSRFADFLRSHSRTLE-EDVIFTQMRAGTDGWMMCR 163
            +A++ + R               +    D   S+    + +  IF         W+  +
Sbjct: 142 -QALLEL-RPAKNVLIDGVLGSGKTWVALDVCLSYKVQCKMDFKIF---------WLNLK 190

Query: 164 QLFQKELTPSDVGKLNRLVIPKKYAVKYFPQISERVEEHAENDKADDVQLVFHDKSMKLW 223
                E     + KL   + P   +       S  ++    + +A+  +L      +K  
Sbjct: 191 NCNSPETVLEMLQKLLYQIDPNWTSR---SDHSSNIKLRIHSIQAELRRL------LKSK 241

Query: 224 KFRYCYWKSSQSFVFTRGWNRFVKENQLKANDTICFYLCELRDI-------AKGTKTFGM 276
            +  C        V     N         A +  C  L   R         A  T    +
Sbjct: 242 PYENCL------LVLLNVQNAKA----WNAFNLSCKILLTTRFKQVTDFLSAATTTHISL 291

Query: 277 IDAKKGENSGASAEVSGPYVDMKV-DLQLQ-----------LGQNKKENKVE----EDDN 320
                         +   Y+D +  DL  +           + ++ ++        +  N
Sbjct: 292 DHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTTNPRRLSIIAESIRDGLATWDNWKHVN 351

Query: 321 GNEIEATEEVELKAPSSTSDSERKLFKLFGVEIF 354
            +++    E  L          RK+F      +F
Sbjct: 352 CDKLTTIIESSLNV--LEPAEYRKMFDRLS--VF 381

>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 = 41.4 bits (96), Expect = 4e-04
 Identities = 43/268 (16%), Positives = 76/268 (28%), Gaps = 73/268 (27%)

Query: 103 ITIEEPNFQSHYSTEAVINMIRDGSYSSRFADFLRSHSRTLEEDVIFTQMRAGTDGWMMC 162
           +++ E  F  ++  + V +M +           + S         +F         W + 
Sbjct: 22  LSVFEDAFVDNFDCKDVQDMPKSILSKEEIDHIIMSKDAVSGTLRLF---------WTLL 72

Query: 163 RQLFQKELTPSDVGKLNRLVIPKKYAVKYFPQISERVEEHAENDK---ADDVQLVFHDKS 219
            +  Q+E                   V+ F      VEE    +       ++      S
Sbjct: 73  SK--QEE------------------MVQKF------VEEVLRINYKFLMSPIKTEQRQPS 106

Query: 220 MKLWKFRYCY---WKSSQSFVFTRGWNRFVKENQLKANDTICFYLCELRDIAKGTKTFGM 276
           M    +       +  +Q F      +R     +L+        L ELR  AK     G+
Sbjct: 107 MMTRMYIEQRDRLYNDNQVFA-KYNVSRLQPYLKLRQA------LLELRP-AKNVLIDGV 158

Query: 277 IDAKKGENSGASAEVSGPYVDMKVDLQ-------LQLGQNKKENKVEE---------DDN 320
                G  SG +       +  KV  +       L L        V E         D N
Sbjct: 159 ----LG--SGKTWVALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQIDPN 212

Query: 321 GNE-IEATEEVELKAPSSTSDSERKLFK 347
                + +  ++L+   S     R+L K
Sbjct: 213 WTSRSDHSSNIKLRI-HSIQAELRRLLK 239

>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 = 50.2 bits (120), Expect = 3e-08
 Identities = 21/94 (22%), Positives = 28/94 (29%), Gaps = 18/94 (19%)

Query: 166 FQKELTPSDVGKLNRLVIPKKYAVKYFPQISERVEEHAENDKADDVQLVFHDKSMKLWKF 225
           F K        K   L IP  +   +       V                 D S + W  
Sbjct: 11  FMKPFISEKSSK--SLEIPLGFNEYFPAPFPITV--------------DLLDYSGRSWTV 54

Query: 226 RYCYWKSSQSFVFTRGWNRFVKENQLKANDTICF 259
           R    K  +    T GW  FVK+N L+    + F
Sbjct: 55  RMK--KRGEKVFLTVGWENFVKDNNLEDGKYLQF 86

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	354
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	99.63
1yel_A	104	AT1G16640; CESG, protein structure initiative, str	99.45
1na6_A	404	Ecorii, restriction endonuclease ecorii; site-spec	94.97
3igm_B	77	PF14_0633 protein; AP2 domain, specific transcript	89.08

>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

Probab=99.95  E-value=1e-27  Score=205.16  Aligned_cols=111  Identities=50%  Similarity=0.773  Sum_probs=100.1

Q ss_pred             ccccceeeeeccccccCCCCceeechhhhhhcCCCCchhhhhhccccCCCCeEEEEEeCCCceEEEEEEEeCCCCeeeEc
Q 018549          160 MMCRQLFQKELTPSDVGKLNRLVIPKKYAVKYFPQISERVEEHAENDKADDVQLVFHDKSMKLWKFRYCYWKSSQSFVFT  239 (354)
Q Consensus       160 ~~~~~lF~K~LT~SDv~~~~rL~IPk~~a~~~fP~l~~~~~~~~~~~~~~gv~v~v~D~~g~~W~fr~~~~~~sr~yvLt  239 (354)
                      ..+.++|.|+||+|||++++||+||+.+|++|||.++.       .+..+++.|.++|.+|+.|+|+|+||+++++|+|+
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            35578999999999999899999999999999999983       22468899999999999999999999999999999


Q ss_pred             cChHHHHhhcCCCCCCEEEEEEeecCCccccceeEEEEEeeecC
Q 018549          240 RGWNRFVKENQLKANDTICFYLCELRDIAKGTKTFGMIDAKKGE  283 (354)
Q Consensus       240 ~GW~~FVr~k~Lk~GD~I~F~r~~~g~~~~~~~~~~~i~~~~~~  283 (354)
                      +||..||++|+|++||+|+|+++.+++.      +++|++++..
T Consensus        81 ~GW~~FV~~~~L~~GD~~~F~~~~~~~~------~l~I~~rr~~  118 (130)
T 1wid_A           81 KGWSRFVKEKNLRAGDVVSFSRSNGQDQ------QLYIGWKSRS  118 (130)
T ss_dssp             SSHHHHHHHTTCCTTCEEEEEECCSSSC------CEEEEEECCC
T ss_pred             CChHHHHHHcCCCCCCEEEEEEecCCCc------EEEEEEEECC
Confidence            9999999999999999999999885543      4899999986

>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=3e-21  Score=145.59  Aligned_cols=58  Identities=45%  Similarity=0.829  Sum_probs=55.1

Q ss_pred             ceEEeEECCCCeEEEEEEe---CCeEEEecCCCCHHHHHHHHHHHHHHhcCCCCCCCCCCC
Q 018549           44 KFKGVVPQQNGHWGAQIYA---NHQRIWLGTFKSEKDAAMAYDSAAIRLRGVDSHRNFPWT  101 (354)
Q Consensus        44 gyrGV~~~~~gkw~A~I~~---~~k~~~LG~f~t~EeAa~Ayd~aa~~~~g~~a~~NFp~~  101 (354)
                      +|+||+++++|||+|+|++   +++++|||+|+|+||||+|||.|+++++|..+.+|||.+
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            6999998889999999999   589999999999999999999999999999999999964

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

Probab=99.63  E-value=2.1e-15  Score=131.25  Aligned_cols=87  Identities=30%  Similarity=0.454  Sum_probs=76.7

Q ss_pred             cceeeeeccccccCCCCceeechhhhhhcCCCCchhhhhhccccCCCCeEEEEEeCCCceEEEEEEEeCCCCeeeEccCh
Q 018549          163 RQLFQKELTPSDVGKLNRLVIPKKYAVKYFPQISERVEEHAENDKADDVQLVFHDKSMKLWKFRYCYWKSSQSFVFTRGW  242 (354)
Q Consensus       163 ~~lF~K~LT~SDv~~~~rL~IPk~~a~~~fP~l~~~~~~~~~~~~~~gv~v~v~D~~g~~W~fr~~~~~~sr~yvLt~GW  242 (354)
                      .+.|.|+||+|||....+|.||+.++.+|||..+              ..+.+.|. |+.|.++++|++.  +++|++||
T Consensus        46 ~P~Fvk~l~~S~v~~~~~L~IP~~Fa~~~lp~~~--------------~~i~L~~~-gk~W~v~~~~~~~--~~~ls~GW  108 (146)
T 4i1k_A           46 NPFFRVVLRPSYLYRGCIMYLPSGFAEKYLSGIS--------------GFIKVQLA-EKQWPVRCLYKAG--RAKFSQGW  108 (146)
T ss_dssp             SCEEEEECCGGGSSTTCCEECCHHHHHHHCTTCC--------------SEEEEEET-TEEEEEEEEEETT--EEEECTTH
T ss_pred             CCEEEEEECchhcCCCcEEEeCHHHHHHhCCCCC--------------eEEEEEEC-CcEEEEEEEEeCC--cEEECCch
Confidence            5689999999999887789999999999999764              25667777 5999999999864  68999999


Q ss_pred             HHHHhhcCCCCCCEEEEEEeecCC
Q 018549          243 NRFVKENQLKANDTICFYLCELRD  266 (354)
Q Consensus       243 ~~FVr~k~Lk~GD~I~F~r~~~g~  266 (354)
                      ..||++++|++||+|+|-...+.+
T Consensus       109 ~~Fv~dn~L~~GD~cvFeli~~~~  132 (146)
T 4i1k_A          109 YEFTLENNLGEGDVCVFELLRTRD  132 (146)
T ss_dssp             HHHHHHTTCCTTCEEEEEECSSSS
T ss_pred             HHHHHHcCCCCCCEEEEEEecCCc
Confidence            999999999999999999987654

>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=99.45  E-value=2.8e-13  Score=110.87  Aligned_cols=85  Identities=22%  Similarity=0.359  Sum_probs=71.8

Q ss_pred             cceeeeeccccccCCCCceeechhhhhhcCCCCchhhhhhccccCCCCeEEEEEeCCCceEEEEEEEeCCCCeeeEccCh
Q 018549          163 RQLFQKELTPSDVGKLNRLVIPKKYAVKYFPQISERVEEHAENDKADDVQLVFHDKSMKLWKFRYCYWKSSQSFVFTRGW  242 (354)
Q Consensus       163 ~~lF~K~LT~SDv~~~~rL~IPk~~a~~~fP~l~~~~~~~~~~~~~~gv~v~v~D~~g~~W~fr~~~~~~sr~yvLt~GW  242 (354)
                      .+.|-|+|+++|.  ..+|.||+..+..+.|.+.              ..+.+.|..|+.|.+++.++.  ..++|++||
T Consensus         8 ~p~F~K~l~~~~~--~~~L~IP~~F~~~~~~~~~--------------~~v~L~~~~G~~W~v~~~~~~--~~~~l~~GW   69 (104)
T 1yel_A            8 EVQFMKPFISEKS--SKSLEIPLGFNEYFPAPFP--------------ITVDLLDYSGRSWTVRMKKRG--EKVFLTVGW   69 (104)
T ss_dssp             CEEEEEECCHHHH--TTCEECCHHHHTTCCCCCC--------------SEEEEEETTSCEEEEEEEEET--TEEEECTTH
T ss_pred             CCCEEEEECCCCc--cceEECCHHHHHhcCccCC--------------CEEEEECCCCCEEEEEEEEEC--CcEEEccCh
Confidence            4689999999994  4699999999987655433              367889999999999999863  578999999


Q ss_pred             HHHHhhcCCCCCCEEEEEEeecC
Q 018549          243 NRFVKENQLKANDTICFYLCELR  265 (354)
Q Consensus       243 ~~FVr~k~Lk~GD~I~F~r~~~g  265 (354)
                      ..||++++|++||.|+|....+.
T Consensus        70 ~~Fv~~~~L~~GD~lvF~~~~~~   92 (104)
T 1yel_A           70 ENFVKDNNLEDGKYLQFIYDRDR   92 (104)
T ss_dssp             HHHHHHHTCCTTCEEEEEECSSS
T ss_pred             HHHHHHcCCCCCCEEEEEEcCCC
Confidence            99999999999999999986543

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

Probab=94.97  E-value=0.022  Score=56.44  Aligned_cols=93  Identities=19%  Similarity=0.251  Sum_probs=67.3

Q ss_pred             cceeeeeccccccCC----CCceeechhhhhhcCCCCchhhhhhccccCCCCeEEE--EEeCCCceEEEEEEEeC-----
Q 018549          163 RQLFQKELTPSDVGK----LNRLVIPKKYAVKYFPQISERVEEHAENDKADDVQLV--FHDKSMKLWKFRYCYWK-----  231 (354)
Q Consensus       163 ~~lF~K~LT~SDv~~----~~rL~IPk~~a~~~fP~l~~~~~~~~~~~~~~gv~v~--v~D~~g~~W~fr~~~~~-----  231 (354)
                      ...|.|.|++.|++.    +.++.+|+..+..+||.|+-..      ..++.+.+.  +-|+..-.+.++++|.+     
T Consensus        18 ~~v~~K~LSAnDtgatgshQ~gi~ipk~~l~~lfp~lg~~~------e~~~~~~~~~~l~d~d~p~td~~~twYn~R~~~   91 (404)
T 1na6_A           18 YFVYIKRLSANDTGATGGHQVGLYIPSGIVEKLFPSINHTR------ELNPSVFLTAHVSSHDCPDSEARAIYYNSAHFG   91 (404)
T ss_dssp             EEEEEEECCHHHHTCC---CCCCCCCHHHHHHHCGGGCCCS------SSSCEEEEEEEESSSCCCCEEEEEEEECGGGTT
T ss_pred             chheeEEcccccCCCCCCcccccCCchHHHHHhcccCCCcc------ccCCcceeEEEeccCCCceEEEEEEEecccccC
Confidence            568999999999964    7789999977888999987211      113334443  34454556699999997     


Q ss_pred             -CCCeeeEccChHH-HHhhcCCCCCCEEEEEEe
Q 018549          232 -SSQSFVFTRGWNR-FVKENQLKANDTICFYLC  262 (354)
Q Consensus       232 -~sr~yvLt~GW~~-FVr~k~Lk~GD~I~F~r~  262 (354)
                       ....|.|+ .|.. +.=.....+||.++|-+.
T Consensus        92 ~tRnEyRLt-~~~~~~~~~~~a~~GDLlvia~~  123 (404)
T 1na6_A           92 KTRNEKRIT-RWGRGSPLQDPENTGALTLLAFK  123 (404)
T ss_dssp             SCCCEEEEE-CCCTTSGGGCGGGTTCEEEEEEE
T ss_pred             CCCCceEEe-ecCCCCcccccCCCCCEEEEEEe
Confidence             23459998 4654 455577899999999986

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

Probab=89.08  E-value=0.29  Score=37.49  Aligned_cols=28  Identities=25%  Similarity=0.273  Sum_probs=22.8

Q ss_pred             CCCceEEeEE-CCCCeEEEEEEeCCeEEE
Q 018549           41 AVSKFKGVVP-QQNGHWGAQIYANHQRIW   68 (354)
Q Consensus        41 ~~SgyrGV~~-~~~gkw~A~I~~~~k~~~   68 (354)
                      .+|||.||++ ++.+.|.|.-..+|++..
T Consensus         4 ~~Sg~pGVsw~kR~~~WlA~W~e~g~rrs   32 (77)
T 3igm_B            4 MSSGYPGVSWNKRMCAWLAFFYDGASRRS   32 (77)
T ss_dssp             CCSSSTTEEEETTTTEEEEEEEETTEEEE
T ss_pred             CCCCCCcEEeecCCceEEEEEecCCeEee
Confidence            4699999955 568999999998887653

---

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	354
d1wida_	117	b.142.1.2 (A:) DNA-binding protein RAV1 {Thale cre	5e-29
d1na6a1	175	b.142.1.1 (A:4-178) Restriction endonuclease EcoRI	2e-19
d1gcca_	63	d.10.1.2 (A:) GCC-box binding domain {Mouse-ear cr	1e-17
d1yela1	102	b.142.1.2 (A:1-102) At1g16640 {Thale cress (Arabid	3e-16

>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 = 5e-29
 Identities = 52/102 (50%), Positives = 64/102 (62%), Gaps = 7/102 (6%)

Query: 162 CRQLFQKELTPSDVGKLNRLVIPKKYAVKYFPQISERVEEHAENDKADDVQLVFHDKSMK 221
              LF+K +TPSDVGKLNRLVIPK +A K+FP  S  V           V L F D + K
Sbjct: 3   AEALFEKAVTPSDVGKLNRLVIPKHHAEKHFPLPSSNVSVK-------GVLLNFEDVNGK 55

Query: 222 LWKFRYCYWKSSQSFVFTRGWNRFVKENQLKANDTICFYLCE 263
           +W+FRY YW SSQS+V T+GW+RFVKE  L+A D + F    
Sbjct: 56  VWRFRYSYWNSSQSYVLTKGWSRFVKEKNLRAGDVVSFSRSN 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 = 2e-19
 Identities = 17/132 (12%), Positives = 35/132 (26%), Gaps = 18/132 (13%)

Query: 163 RQLFQKELTPSDVGKLNR----LVIPKKYAVKYFPQISERVEEHAENDKADDVQLVFHDK 218
             ++ K L+ +D G        L IP     K FP I+       E + +  +       
Sbjct: 15  YFVYIKRLSANDTGATGGHQVGLYIPSGIVEKLFPSINHT----RELNPSVFLTAHVSSH 70

Query: 219 SMKLWKFRYCYWKSS------QSFVFTRGWNRFVKENQLKANDTICFYLCELRDIAKGTK 272
                + R  Y+ S+           TR       ++                 + +   
Sbjct: 71  DCPDSEARAIYYNSAHFGKTRNEKRITRWGRGSPLQDPENTGALTLLA----FKLDEQGG 126

Query: 273 TFGMIDAKKGEN 284
               ++     +
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 = 74.4 bits (183), Expect = 1e-17
 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 = 71.4 bits (175), Expect = 3e-16
 Identities = 21/96 (21%), Positives = 28/96 (29%), Gaps = 18/96 (18%)

Query: 166 FQKELTPSDVGKLNRLVIPKKYAVKYFPQISERVEEHAENDKADDVQLVFHDKSMKLWKF 225
           F K        K   L IP  +   +       V                 D S + W  
Sbjct: 9   FMKPFISEKSSK--SLEIPLGFNEYFPAPFPITV--------------DLLDYSGRSWTV 52

Query: 226 RYCYWKSSQSFVFTRGWNRFVKENQLKANDTICFYL 261
           R    K  +    T GW  FVK+N L+    + F  
Sbjct: 53  RM--KKRGEKVFLTVGWENFVKDNNLEDGKYLQFIY 86

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	354
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	99.77
d1yela1	102	At1g16640 {Thale cress (Arabidopsis thaliana) [Tax	99.32

>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=4e-27  Score=195.19  Aligned_cols=114  Identities=49%  Similarity=0.762  Sum_probs=101.2

Q ss_pred             cccceeeeeccccccCCCCceeechhhhhhcCCCCchhhhhhccccCCCCeEEEEEeCCCceEEEEEEEeCCCCeeeEcc
Q 018549          161 MCRQLFQKELTPSDVGKLNRLVIPKKYAVKYFPQISERVEEHAENDKADDVQLVFHDKSMKLWKFRYCYWKSSQSFVFTR  240 (354)
Q Consensus       161 ~~~~lF~K~LT~SDv~~~~rL~IPk~~a~~~fP~l~~~~~~~~~~~~~~gv~v~v~D~~g~~W~fr~~~~~~sr~yvLt~  240 (354)
                      ++..||.|+||+|||+.++||+||+.++++|||+++.       ....+++.|.+.|.+|+.|.|+|++|+++++|+|++
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            3578999999999999889999999999999999983       334689999999999999999999999999999999


Q ss_pred             ChHHHHhhcCCCCCCEEEEEEeecCCccccceeEEEEEeeecCCCCC
Q 018549          241 GWNRFVKENQLKANDTICFYLCELRDIAKGTKTFGMIDAKKGENSGA  287 (354)
Q Consensus       241 GW~~FVr~k~Lk~GD~I~F~r~~~g~~~~~~~~~~~i~~~~~~~s~~  287 (354)
                      ||..||++++|++||+|+|||+..++.      .++|.+++.++.+.
T Consensus        75 GW~~Fv~~~~Lk~GD~~~F~~~~~~~~------~~~i~~r~~~~~~~  115 (117)
T d1wida_          75 GWSRFVKEKNLRAGDVVSFSRSNGQDQ------QLYIGWKSRSGSDL  115 (117)
T ss_dssp             SHHHHHHHTTCCTTCEEEEEECCSSSC------CEEEEEECCCSCSS
T ss_pred             CHHHHHHHcCCCCCCEEEEEEEeCCCC------EEEEEEEECCCCCC
Confidence            999999999999999999999876654      27899998875443

>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=1.5e-21  Score=145.28  Aligned_cols=58  Identities=45%  Similarity=0.829  Sum_probs=54.4

Q ss_pred             ceEEeEECCCCeEEEEEEe---CCeEEEecCCCCHHHHHHHHHHHHHHhcCCCCCCCCCCC
Q 018549           44 KFKGVVPQQNGHWGAQIYA---NHQRIWLGTFKSEKDAAMAYDSAAIRLRGVDSHRNFPWT  101 (354)
Q Consensus        44 gyrGV~~~~~gkw~A~I~~---~~k~~~LG~f~t~EeAa~Ayd~aa~~~~g~~a~~NFp~~  101 (354)
                      .||||+++++|||.|+|++   +++++|||+|+|+||||+|||+|+++++|.++.+|||+.
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            4999988889999999986   678999999999999999999999999999999999964

>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=99.77  E-value=1.6e-19  Score=157.17  Aligned_cols=113  Identities=16%  Similarity=0.100  Sum_probs=93.9

Q ss_pred             cccceeeeeccccccCCCCc----eeechhhhhhcCCCCchhhhhhccccCCCCeEEE--EEeCCCceEEEEEEEeCCC-
Q 018549          161 MCRQLFQKELTPSDVGKLNR----LVIPKKYAVKYFPQISERVEEHAENDKADDVQLV--FHDKSMKLWKFRYCYWKSS-  233 (354)
Q Consensus       161 ~~~~lF~K~LT~SDv~~~~r----L~IPk~~a~~~fP~l~~~~~~~~~~~~~~gv~v~--v~D~~g~~W~fr~~~~~~s-  233 (354)
                      ...++|+|.||+|||++++|    |+|||.+|+++||+|+..      ...++.+.|.  +.|.+|..|+|||+||++. 
T Consensus        13 ~~~~~F~K~LtasD~g~tg~HQaG~~IPK~~ae~~FP~l~~~------~e~nP~~~l~~~i~d~~g~~w~fR~iYyn~~~   86 (175)
T d1na6a1          13 ENYFVYIKRLSANDTGATGGHQVGLYIPSGIVEKLFPSINHT------RELNPSVFLTAHVSSHDCPDSEARAIYYNSAH   86 (175)
T ss_dssp             SSEEEEEEECCHHHHTCC---CCCCCCCHHHHHHHCGGGCCC------SSSSCEEEEEEEESSSCCCCEEEEEEEECGGG
T ss_pred             CceEEEEEEcccccccccCCccceeeecHHHHHHhCCCCCcc------cccCCCceEEEEEecCCCCeeEEEEEEECCcc
Confidence            44789999999999999886    999999999999999842      1224666665  5599999999999999874 


Q ss_pred             -----CeeeEccChHHHHhhcCCCCCCEEEEEEeecCCccccceeEEEEEeeecC
Q 018549          234 -----QSFVFTRGWNRFVKENQLKANDTICFYLCELRDIAKGTKTFGMIDAKKGE  283 (354)
Q Consensus       234 -----r~yvLt~GW~~FVr~k~Lk~GD~I~F~r~~~g~~~~~~~~~~~i~~~~~~  283 (354)
                           ..|+||+.|..|+..+.+.+||.++|.+......    ..+.++++..+.
T Consensus        87 ~ggTRneyRiT~~g~~~~~~~~~n~G~l~i~af~~~~~~----~~~~~~~vwvc~  137 (175)
T d1na6a1          87 FGKTRNEKRITRWGRGSPLQDPENTGALTLLAFKLDEQG----GDCKEVNIWVCA  137 (175)
T ss_dssp             TTSCCCEEEEECCCTTSGGGCGGGTTCEEEEEEECCTTS----CCCCEEEEEECC
T ss_pred             CCCccccEEEEeccccccccCccccccEEEEEeecCCCC----CceeEEEEEEec
Confidence                 7799999999999999999999999999755554    556788888876

>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=99.32  E-value=2.7e-12  Score=103.02  Aligned_cols=86  Identities=23%  Similarity=0.380  Sum_probs=70.7

Q ss_pred             cceeeeeccccccCCCCceeechhhhhhcCCCCchhhhhhccccCCCCeEEEEEeCCCceEEEEEEEeCCCCeeeEccCh
Q 018549          163 RQLFQKELTPSDVGKLNRLVIPKKYAVKYFPQISERVEEHAENDKADDVQLVFHDKSMKLWKFRYCYWKSSQSFVFTRGW  242 (354)
Q Consensus       163 ~~lF~K~LT~SDv~~~~rL~IPk~~a~~~fP~l~~~~~~~~~~~~~~gv~v~v~D~~g~~W~fr~~~~~~sr~yvLt~GW  242 (354)
                      ..-|-|+|.++++..  +|.||+..+..+.+.+.              ..+.+.|..|+.|.+++...  +...+|+.||
T Consensus         6 ~~~Ffkv~~~~~~~~--~L~IP~~F~~~~~~~~~--------------~~i~L~d~~G~~W~v~~~~~--~~~~~~~~GW   67 (102)
T d1yela1           6 EVQFMKPFISEKSSK--SLEIPLGFNEYFPAPFP--------------ITVDLLDYSGRSWTVRMKKR--GEKVFLTVGW   67 (102)
T ss_dssp             CEEEEEECCHHHHTT--CEECCHHHHTTCCCCCC--------------SEEEEEETTSCEEEEEEEEE--TTEEEECTTH
T ss_pred             CCeEEEEEcCcccCC--CEECCHHHHHhCCCCCC--------------CEEEEEcCCCCEEEEEEEEe--CCeEEEccCH
Confidence            345789999999754  89999999997766543              36788999999999997764  4567889999


Q ss_pred             HHHHhhcCCCCCCEEEEEEeecCC
Q 018549          243 NRFVKENQLKANDTICFYLCELRD  266 (354)
Q Consensus       243 ~~FVr~k~Lk~GD~I~F~r~~~g~  266 (354)
                      ..||++++|++||.|+|-.+.+..
T Consensus        68 ~~Fv~~n~L~~GD~~vF~~~~~~~   91 (102)
T d1yela1          68 ENFVKDNNLEDGKYLQFIYDRDRT   91 (102)
T ss_dssp             HHHHHHHTCCTTCEEEEEECSSSE
T ss_pred             HHHHHHcCCCcCCEEEEEEcCCcE
Confidence            999999999999999998865443