Citrus Sinensis ID: 043499

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340-------350-------360-------370-------380-------390------
Protein Sequence
MPEDMHQQLDNFRMLRRLIKIFNEPDPNNRWKLKGASTIKQKFLIQKGLYTTVANNNVKQMAGGNRRAETSHFFKVILPSTVQEKKLRIPRKFVKRFGDELSAVATLNVPNGRVWQVGLRKDGRKIWLQDGWDNFAEYHSIAVGYFLVFKYAKNSTFDVLVFDMTACEIDYPYDYEETESEEGDEMETENSVEILSFTKMNTPPVQENQVKPGSKPEKKKIGGIKLETATNSREKKRCPTHGNEHGKLKKAAYHEVETDSSDGDQVFEEMGIFMSEGHRYLSVEERQSLVTAVRLFKPQNPSFVDILRSKKRYSYMYVPSKFSKKHLIRGTRSIKLQDSDGKEWPAQLTWSSGCGIKGGWPAFSKYKNLKQGHVCVFELIKAKDILLKVSIHASSE
Secondary Structure (PSIPRED)
ccHHHHHHHHHHHHHHHHHHccccccccccccccccccHHHHHHHHccccHHHHHHHHHHHHccccccccccEEEEccccccccccccccHHHHHHHcccccccEEEEcccccEEEEEEEEEccEEEEcccHHHHHHHcccccccEEEEEEccccEEEEEEEccccccccccccccccccccccccccccccEEEccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEEccccccHHHHHHHHHHHHHHcccccccEEEEcccccccccccccHHHHHHHccccccEEEEEEccccEEEEEEEEccccEEccccHHHHHHcccccccEEEEEEEEccccEEEEEEEEccc
Secondary Structure Prediction (SSPRO)
ccHHHHHHHHHHHHHHHHEEEcccccccccccccccccccccEEEcccccccHHHHHHHHHHHHHcccccccEEEEEccccccccccEccHHHHHHHccccccEEEEEcccccEEEEEEEEcccEEEEcccHHHHHHHcccccccEEEEEEcccEEEEEEEEcccccEEEccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHccccccEEEEEEcccccEcEEEccHHHHHHHccccccEEEEEcccccEEEEEEEEccccEEcccHHHHHHHcccccccEEEEEEEccccEEEEEEEEEEcc
Coil and Loop (DISEMBL)
MPEDMHQQLDNFRMLRRLIKIfnepdpnnrwklkgastIKQKFLIQKGLYTTVANNnvkqmaggnrraetSHFFKVilpstvqekklriPRKFVKRFGDELSAVatlnvpngrvwqvglrkdgrkIWLQDGWDNFAEYHSIAVGYFLVFKYAKNSTFDVLVFDMtaceidypydyeeteseegdemetENSVEILSFtkmntppvqenqvkpgskpekkkiggikletatnsrekkrcpthgnehgklKKAAYHevetdssdgdqVFEEMGIFMseghrylsvEERQSLVTAVrlfkpqnpsfvdILRSkkrysymyvpskfskkhlirgtrsiklqdsdgkewpaqltwssgcgikggwpafskyknlkqGHVCVFELIKAKDILLKVSIHASSE
Flexible Loop (DISEMBL)
MPEDMHQQLDNFRMLRRLIKIfnepdpnnrwklkGASTIKQKFLIQKGLYTTVANNNVKQMAGGNRRAETSHFFKvilpstvqekklripRKFVKRFGDELsavatlnvpngrvwqvglrKDGRKIWLQDGWDNFAEYHSIAVGYFLVFKYAKNSTFDVLVFDMTACEIDYPYDYEETESEEGDEMETENSVEILSFtkmntppvqenqvkpgskpekkkiggikletatnsrekkrcpthgnehgklkkaaYHEVETDSSDGDQVFEEMGIFMSEGHRYLSVEERQSLVTavrlfkpqnpsfvdilrskkrYSYMYvpskfskkhlirgtrsiklqdsdgkewPAQLTWSSGCGIKGGWPAFSKYKNLKQGHVCVFELIKAKDILLKVSIHASSE
Low Complexity Region (SEG)
MPEDMHQQLDNFRMLRRLIKIFNEPDPNNRWKLKGASTIKQKFLIQKGLYTTVANNNVKQMAGGNRRAETSHFFKVILPSTVQEKKLRIPRKFVKRFGDELSAVATLNVPNGRVWQVGLRKDGRKIWLQDGWDNFAEYHSIAVGYFLVFKYAKNSTFDVLVFDMTACEIDYPYDYeeteseegdemeteNSVEILSFTKMNTPPVQENQVKPGSKPEKKKIGGIKLETATNSREKKRCPTHGNEHGKLKKAAYHEVETDSSDGDQVFEEMGIFMSEGHRYLSVEERQSLVTAVRLFKPQNPSFVDILRSKKRYSYMYVPSKFSKKHLIRGTRSIKLQDSDGKEWPAQLTWSSGCGIKGGWPAFSKYKNLKQGHVCVFELIKAKDILLKVSIHASSE
Disordered region (IsUnstruct)
**********NFRMLRRLIKIFNEPDPNNRWKLKGASTIKQKFLIQKGLYTTVANNNVKQMAGGNRRAETSHFFKVILPSTVQEKKLRIPRKFVKRFGDELSAVATLNVPNGRVWQVGLRKDGRKIWLQDGWDNFAEYHSIAVGYFLVFKYAKNSTFDVLVFDMTACEIDYPYDY*******************************************************************************************FEEMGIFMSEGHRYLSVEERQSLVTAVRLFKPQNPSFVDILRSKKRYSYMYVPSKFSKKHLIRGTRSIKLQDSDGKEWPAQLTWSSGCGIKGGWPAFSKYKNLKQGHVCVFELIKAKDILLKVSI*****
Disordered Region (DISOPRED)
*********DNFRMLRRLI*******************************TT*******************HFFKVILPSTVQEKKLRIPRKFVKRFGDELSAVATLNVPNGRVWQVGLRKDGRKIWLQDGWDNFAEYHSIAVGYFLVFKYAKNSTFDVLVFDMTACEIDYPYDYEETESE***************FTKMNTPPVQENQVKPGSKPEKKKIGGIKLETATNSREK***PTHGNEHGKLKKAAYHEVETDSSDGDQVFEEMGIFMSEGHRYLSVEERQSLVTAVRLFKPQNPSFVDILRSKKRYSYMYVPSKFSKKHLIRGTRSIKLQDSDGKEWPAQLTWSSGCGIKGGWPAFSKYKNLKQGHVCVFELIKAKDILLKVSIHAS**
Disordered Region (DISEMBL)
MPEDMHQQLDNFRMLRRLIKIFNEPDPNNRWKLKGASTIKQKFLIQKGLYTTVANNNVKQMAGGNRRAETSHFFKVILPSTVQEKKLRIPRKFVKRFGDELSAVATLNVPNGRVWQVGLRKDGRKIWLQDGWDNFAEYHSIAVGYFLVFKYAKNSTFDVLVFDMTACEIDYPYDYE**************SVEILSFTKMNTPP****************IGGIKLETATNSREKKRCPTHGNEHGKLKKAAYHEVETDSSDGDQVFEEMGIFMSEGHRYLSVEERQSLVTAVRLFKPQNPSFVDILRSKKRYSYMYVPSKFSKKHLIRGTRSIKLQDSDGKEWPAQLTWSSGCGIKGGWPAFSKYKNLKQGHVCVFELIKAKDILLKVSIHASSE
Disordered Region (DISPRO)
*PEDMHQQLDNFRMLRRLIKIFNE*DP*NRWKLKGASTIKQKFLIQKGLYTTVANNNVKQMAGGNRRAETSHFFKVILPSTVQEKKLRIPRKFVKRFGDELSAVATLNVPNGRVWQVGLRKDGRKIWLQDGWDNFAEYHSIAVGYFLVFKYAKNSTFDVLVFDMTACEIDYPY********************************************************************************************************HRYLSVEERQSLVTAVRLFKPQNPSFVDILRSKKRYSYMYVPSKFSKKHLIRGTRSIKLQDSDGKEWPAQLTWSSGCGIKGGWPAFSKYKNLKQGHVCVFELIKAKDILLKVSIHASSE
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MPEDMHQQLDNFRMLRRLIKIFNEPDPNNRWKLKGASTIKQKFLIQKGLYTTVANNNVKQMAGGNRRAETSHFFKVILPSTVQEKKLRIPRKFVKRFGDELSAVATLNVPNGRVWQVGLRKDGRKIWLQDGWDNFAEYHSIAVGYFLVFKYAKNSTFDVLVFDMTACEIDYPYDYEETESEEGDEMETENSVEILSFTKMNTPPVQENQVKPGSKPEKKKIGGIKLETATNSREKKRCPTHGNEHGKLKKAAYHEVETDSSDGDQVFEEMGIFMSEGHRYLSVEERQSLVTAVRLFKPQNPSFVDILRSKKRYSYMYVPSKFSKKHLIRGTRSIKLQDSDGKEWPAQLTWSSGCGIKGGWPAFSKYKNLKQGHVCVFELIKAKDILLKVSIHASSE
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	396	2.2.26 [Sep-21-2011]
Q8L3W1	341	B3 domain-containing tran	yes	no	0.795	0.923	0.353	2e-47
Q9ZSH7	190	B3 domain-containing prot	no	no	0.290	0.605	0.460	1e-25
Q84R27	209	B3 domain-containing prot	no	no	0.313	0.593	0.407	2e-25
Q2QMT2	358	B3 domain-containing prot	yes	no	0.739	0.818	0.272	1e-21
Q2R9D2	406	B3 domain-containing prot	yes	no	0.780	0.761	0.256	4e-19
Q9XIB4	190	B3 domain-containing prot	no	no	0.275	0.573	0.409	5e-19
Q2QMT5	334	B3 domain-containing prot	no	no	0.704	0.835	0.261	6e-19
Q10GM3	378	B3 domain-containing prot	no	no	0.712	0.746	0.247	7e-16
Q9XIB5	226	B3 domain-containing prot	no	no	0.358	0.628	0.331	1e-14
Q851V5	1029	Putative B3 domain-contai	no	no	0.636	0.244	0.243	5e-14

>sp|Q8L3W1|VRN1_ARATH B3 domain-containing transcription factor VRN1 OS=Arabidopsis thaliana GN=VRN1 PE=1 SV=1

 Score =  190 bits (482), Expect = 2e-47,   Method: Compositional matrix adjust.
 Identities = 117/331 (35%), Positives = 177/331 (53%), Gaps = 16/331 (4%)

Query: 73  FFKVILPSTVQEKKLRIPRKFVKRFGDELSAVATLNVPNGRVWQVGLRKDGRKIWLQDGW 132
           F K+I  ST+QEK+LR+P KFV +F DELS    L VP+G VW+VGLRK   KIW QDGW
Sbjct: 6   FHKLIFSSTIQEKRLRVPDKFVSKFKDELSVAVALTVPDGHVWRVGLRKADNKIWFQDGW 65

Query: 133 DNFAEYHSIAVGYFLVFKYAKNSTFDVLVFDMTACEIDYP----YDYEETESEEG---DE 185
             F + +SI +GY L+F+Y  NS F V +F+++  EI+Y      D      +     ++
Sbjct: 66  QEFVDRYSIRIGYLLIFRYEGNSAFSVYIFNLSHSEINYHSTGLMDSAHNHFKRARLFED 125

Query: 186 METENSVEILSFTKMNTPPVQENQVKPGSKPEKKKIGGIKLETATNSREKKRCPTHGNEH 245
           +E E++ E++  + +   P+ E+ V P +K                + E    P    + 
Sbjct: 126 LEDEDA-EVIFPSSVYPSPLPESTV-PANKGYASSAIQTLFTGPVKAEEPTPTPKIPKKR 183

Query: 246 GKLKKAAYHEVETDSSDGDQVFEEMGIF---MSEGHRYLSVEERQSLVTAVRLFKPQNPS 302
           G+ KK A  E    S+  D   E    F    S   R ++ EER+  + A + F+P NP 
Sbjct: 184 GRKKKNADPEEINSSAPRDDDPENRSKFYESASARKRTVTAEERERAINAAKTFEPTNPF 243

Query: 303 FVDILRSKKRY--SYMYVPSKFSKKHLIRGTRSIKLQDSDGKEWPAQLTWSSG-CGIKGG 359
           F  +LR    Y    MY+PS F++K+L   +  IK+Q ++ K+WP +  + +G      G
Sbjct: 244 FRVVLRPSYLYRGCIMYLPSGFAEKYLSGISGFIKVQLAE-KQWPVRCLYKAGRAKFSQG 302

Query: 360 WPAFSKYKNLKQGHVCVFELIKAKDILLKVS 390
           W  F+   NL +G VCVFEL++ +D +LKV+
Sbjct: 303 WYEFTLENNLGEGDVCVFELLRTRDFVLKVT 333

Involved in the regulation of vernalization. Acts as transcriptional repressor of FLC, a major target of the vernalization pathway. Binds DNA in vitro in a non-sequence-specific manner.
Arabidopsis thaliana (taxid: 3702)

>sp|Q9ZSH7|Y4158_ARATH B3 domain-containing protein At4g01580 OS=Arabidopsis thaliana GN=At4g01580 PE=2 SV=1

 Score =  117 bits (293), Expect = 1e-25,   Method: Compositional matrix adjust.
 Identities = 53/115 (46%), Positives = 77/115 (66%)

Query: 73  FFKVILPSTVQEKKLRIPRKFVKRFGDELSAVATLNVPNGRVWQVGLRKDGRKIWLQDGW 132
           FFK++LPST+++K +RIP +FVK  G +LS V TL  P G    + L++ G +IW  +GW
Sbjct: 30  FFKLVLPSTMKDKMMRIPPRFVKLQGSKLSEVVTLVTPAGYKRSIKLKRIGEEIWFHEGW 89

Query: 133 DNFAEYHSIAVGYFLVFKYAKNSTFDVLVFDMTACEIDYPYDYEETESEEGDEME 187
             FAE HSI  G+FL+F+Y KNS+F V++F+ +ACE +YP D       + D +E
Sbjct: 90  SEFAEAHSIEEGHFLLFEYKKNSSFRVIIFNASACETNYPLDAVHIIDSDDDVIE 144

Arabidopsis thaliana (taxid: 3702)

>sp|Q84R27|Y3896_ARATH B3 domain-containing protein At3g18960 OS=Arabidopsis thaliana GN=At3g18960 PE=2 SV=1

 Score =  117 bits (292), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 53/130 (40%), Positives = 82/130 (63%), Gaps = 6/130 (4%)

Query: 51  TTVANNNVKQMAGGNRRAE------TSHFFKVILPSTVQEKKLRIPRKFVKRFGDELSAV 104
            T  N   +  +  +RR++         FFK++LPST+++K ++IP +FVK  G +LS V
Sbjct: 2   VTTQNTKARVTSVSHRRSQQDPESPVKKFFKLVLPSTMKDKMMKIPPRFVKLQGSKLSEV 61

Query: 105 ATLNVPNGRVWQVGLRKDGRKIWLQDGWDNFAEYHSIAVGYFLVFKYAKNSTFDVLVFDM 164
            TL  P G    + L++ G +IW  +GW  FAE HSI  G+FL+F+Y +NS+F V++F++
Sbjct: 62  VTLETPAGFKRSIKLKRIGEEIWFHEGWSEFAEAHSIEEGHFLLFEYKENSSFRVIIFNV 121

Query: 165 TACEIDYPYD 174
           +ACE  YP D
Sbjct: 122 SACETKYPLD 131

Arabidopsis thaliana (taxid: 3702)

>sp|Q2QMT2|Y1223_ORYSJ B3 domain-containing protein Os12g0592300 OS=Oryza sativa subsp. japonica GN=Os12g0592300 PE=2 SV=2

 Score =  104 bits (260), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 87/319 (27%), Positives = 149/319 (46%), Gaps = 26/319 (8%)

Query: 87  LRIPRKFVKRFGDELSAVATLNVPNGRVWQVGLRKDGRKIWLQDGWDNFAEYHSIAVGYF 146
           + IP K   RF  +++    L  P+G  W+V + K   ++ L  GW++FA+ H +     
Sbjct: 40  ISIPEKVADRFSGQITKGFNLKAPSGETWRVSVEKVADELILMSGWEDFAKAHELQENDL 99

Query: 147 LVF----KYAKNSTFDVLVFDMTACEIDYPYDYEETESEEGDEMETENSVEI-LSFTKMN 201
           L F    +   + +FDVL+FD + CE    +   +  S  G   +T+N+ +  LS ++  
Sbjct: 100 LFFTCNGRCNGSFSFDVLIFDASGCEKVSCFFIGKKNSIGG---QTQNAEQYHLSDSEDT 156

Query: 202 TPPVQENQVKPGSKPEKKKIGGIKLETATNSREKKRCPTHGNEHGKLKKAAYHEVETDSS 261
           + P       P      KK+ G   +T TN R++   P     H K +     + + D  
Sbjct: 157 STPSTFLVGSPHKASTSKKLNG---KTKTNPRKEPEDPNSSRSHVKHEMIEEEKSDDDDE 213

Query: 262 DGDQVFEEMGIFMSEGHRYLSVEERQSLVTAVRLFKPQNPSFVDILRSKK--RYSYMYVP 319
             D  +E    + S    YL+ EER+ + + V L +P NP FV +L++ +  R   + VP
Sbjct: 214 HAD--YEHADYYYSRFANYLTGEEREEIFSLVSL-QPGNPVFVTVLQAPQIHRKGLLIVP 270

Query: 320 SKFSKKHLIRGTRSIKLQDSDGKE------WPAQLTWSSGCGIKGGWPAFSKYKNLKQGH 373
           S F+  HL   ++ I L   + KE      + A  T    C     W  F +   L++G+
Sbjct: 271 SGFAADHLDSRSQEILLMRPNKKEKWYVKYYHASTTRGFNC---QRWIKFIRENRLREGY 327

Query: 374 VCVFELIK-AKDILLKVSI 391
           +C+FEL+K A+ + + V +
Sbjct: 328 ICIFELMKGARRVTMTVHV 346

Oryza sativa subsp. japonica (taxid: 39947)

>sp|Q2R9D2|Y1176_ORYSJ B3 domain-containing protein Os11g0197600 OS=Oryza sativa subsp. japonica GN=Os11g0197600 PE=2 SV=1

 Score = 95.9 bits (237), Expect = 4e-19,   Method: Compositional matrix adjust.
 Identities = 94/366 (25%), Positives = 151/366 (41%), Gaps = 57/366 (15%)

Query: 73  FFKVILPSTVQE-KKLRIPRKFVKRFGDELSAVATLNVPNGRVWQVGLRKDGRKIWLQDG 131
           FF+V+L  T+Q  ++++IP  F +   ++ + + +L   +G  W   L  D    +   G
Sbjct: 32  FFRVLL--TLQSLERMKIPSSFNQCLQNQPTGMVSLVDRSGNKWSAELTSDSEGFFFVHG 89

Query: 132 WDNFAEYHSIAVGYFLVFKYAKNSTFDVLVFDMTACEIDYPYDYE-------ETESEEGD 184
           W  F   +SI  G FLVF Y K S F V VF+ +  +    +          +TES+EG 
Sbjct: 90  WKEFVRDNSIQCGQFLVFTYDKRSQFSVTVFEPSGIDKISTFSAHPSKNVIIKTESDEGG 149

Query: 185 EMETENSVEILSFTKMNTPPVQENQVKPGSKPE------KKKIGGIKLETATNSREKKRC 238
            +    + E ++      P ++EN    G +        + ++   K  +  N  E  R 
Sbjct: 150 MVTAAITTEKMA------PALKENNGITGKRTRDVDYLMEDRVVVFKKSSEANVCESSRR 203

Query: 239 PTHGNEHGKLKKAAYHEVETD----SSDGDQV-----------------FEEMGIFMSEG 277
              G   GK K  +     T     SSD D                       G  +S+G
Sbjct: 204 KRAGASAGKSKVTSTSHNSTRGSSCSSDEDNSSSKSPNPPFLMRFLSGEVSRRGRCVSKG 263

Query: 278 HRYLSVEERQSLVTA---------VRLFKPQNPSFVDILRSKKRYS--YMYVPSKFSKKH 326
            R L+V  ++  VT           R FK +NP  V I+     Y   +M +P +F ++ 
Sbjct: 264 QRQLTVISQRRPVTEAEKDHALQRAREFKSKNPFAVQIMMESYVYVGFFMNIPCEFVREC 323

Query: 327 LIRGTRSIKLQDSDGKEWPAQLTWSSGCGI---KGGWPAFSKYKNLKQGHVCVFELIKAK 383
           L    + I L D  GK W     + S   +    GGW  F+   NL++  VCVFEL++  
Sbjct: 324 LPHTNKRITLWDPQGKAWEVNYVYYSDRSVGSFSGGWGKFAVGNNLEKFDVCVFELVQKD 383

Query: 384 DILLKV 389
           +I + +
Sbjct: 384 NIKVHI 389

Oryza sativa subsp. japonica (taxid: 39947)

>sp|Q9XIB4|Y1475_ARATH B3 domain-containing protein At1g49475 OS=Arabidopsis thaliana GN=At1g49475 PE=2 SV=2

 Score = 95.9 bits (237), Expect = 5e-19,   Method: Compositional matrix adjust.
 Identities = 45/110 (40%), Positives = 70/110 (63%), Gaps = 1/110 (0%)

Query: 73  FFKVILPSTVQEKKLRIPRKFVKRFGDELSAVATLNVPNGRVWQVGLRKDGRKIWLQDGW 132
           F K+IL S + EK +++P +FV RFG +L+   TL  P G    + +++ G ++W + GW
Sbjct: 34  FIKIILLSRIIEKMMKVPARFV-RFGPKLTDNVTLQTPVGFKRSIRIKRIGDEVWFEKGW 92

Query: 133 DNFAEYHSIAVGYFLVFKYAKNSTFDVLVFDMTACEIDYPYDYEETESEE 182
             FAE HS++ G+FL F Y  +S F V++FD++A EI+YP D  +   EE
Sbjct: 93  SEFAEAHSLSDGHFLFFHYEGDSCFRVVIFDVSASEIEYPLDDTDDNREE 142

Arabidopsis thaliana (taxid: 3702)

>sp|Q2QMT5|Y1209_ORYSJ B3 domain-containing protein LOC_Os12g40090 OS=Oryza sativa subsp. japonica GN=Os12g0591500 PE=2 SV=1

 Score = 95.5 bits (236), Expect = 6e-19,   Method: Compositional matrix adjust.
 Identities = 81/310 (26%), Positives = 144/310 (46%), Gaps = 31/310 (10%)

Query: 87  LRIPRKFVKRFGDELSAVATLNVPNGRVWQVGLRKDGRKIWLQDGWDNFAEYHSIAVGYF 146
           + IP K  + F  +++    L  P+G  W+VG+ K   ++ L+ GW++FA+ H +     
Sbjct: 20  ISIPEKVAEIFSGQITKGFNLKSPSGETWRVGVAKVADELILKSGWEDFAKAHELQENDL 79

Query: 147 LVFKYAKN----STFDVLVFDMTACEIDYPYDYEETES---EEGDEMETENSVEILSFTK 199
           L F    +     +FDVL+FD + CE    +   +  S   +  + +  + + + LS   
Sbjct: 80  LFFTCNGHGNGSCSFDVLIFDASGCEKVSCFFTGKKNSYMCKNFNSIGGQVAGQYLSSDS 139

Query: 200 MNTPPVQENQVKPGSKPEKKKIGGIKLETATNSREKKRCPTHGNEHGKLKKAAYHEVETD 259
            +T         P      KK+ G   +T TN R++   P           + +H +E  
Sbjct: 140 EDTSTPSVLIGSPHKASTSKKLSG---KTKTNPRKEPEDPN---------CSHWHVIEEK 187

Query: 260 SSDGDQVFEEMGIFMSEGHRYLSVEERQSLVTAVRLFKPQNPSFVDILRSK--KRYSYMY 317
           ++D D   E      +    YL+ EER  + + V L +P NP FV +L++   +R + + 
Sbjct: 188 NTDDD---EHADYHYTRFANYLTGEERDEIFSLVSL-QPGNPVFVVVLQTAHVRRRNILI 243

Query: 318 VPSKFSKKHLIRGTRSIKLQDSDGKE-WPAQLTWSSGCGIKG----GWPAFSKYKNLKQG 372
           VP++F+  HL R +  I L   + K+ W  +  + S    +G     W  F +   L++G
Sbjct: 244 VPTRFAADHLERKSHDILLIRPNRKQKWSVKYYYLSNT-TRGFNCHRWIKFIRENRLREG 302

Query: 373 HVCVFELIKA 382
           +VC+FEL+K 
Sbjct: 303 NVCIFELMKG 312

Oryza sativa subsp. japonica (taxid: 39947)

>sp|Q10GM3|Y3222_ORYSJ B3 domain-containing protein Os03g0622200 OS=Oryza sativa subsp. japonica GN=Os03g0622200 PE=2 SV=1

 Score = 85.5 bits (210), Expect = 7e-16,   Method: Compositional matrix adjust.
 Identities = 84/339 (24%), Positives = 140/339 (41%), Gaps = 57/339 (16%)

Query: 70  TSHFFKVILPSTVQEKKLRIPRKFVKRFGDELSAVATLNVPNGRVWQVGL-RKDGRKIWL 128
           + HF K ++    +   + +P +F   F   +S    L  P+G  W +G+   D  ++ L
Sbjct: 29  SKHFLKHMVGDFTE--SMTVPARFANNFNGHISEEVNLRSPSGETWSIGVANSDAGELVL 86

Query: 129 QDGWDNFAEYHSIAVGYFLVFKYAK-NSTFDVLVFDMTACEIDYP-----YDYEETESEE 182
           Q GW  F + + I  G  L+F+Y+  +S+FDVL+FD + CE   P     + +   E+  
Sbjct: 87  QPGWKEFVDGNGIEEGDCLLFRYSGVSSSFDVLIFDPSGCEKASPHFVGSHGFGRAENSA 146

Query: 183 GDEMETENSVEILSFTKMNTPPVQENQVKPGSKPEKKKIGGIKLETATNSREKKRCPTHG 242
           G E    N           TPP+ +     G    +       LE   +    +  P   
Sbjct: 147 GAEQGGRNG--------RRTPPIVD-----GDNGHRH-----HLEMTLHRNSCRSIPR-- 186

Query: 243 NEHGKLKKAAYHEVETDSSDGDQVFEEMGIFMSEGHRY---------------LSVEERQ 287
                 K++ + + ET++ + D   E++ +  +EG RY               L  E+R+
Sbjct: 187 ----ACKRSLFSD-ETEAKENDGEDEDV-VAAAEGGRYGEYYFSRHGRVAEYNLREEDRE 240

Query: 288 SLVTAVRLFKPQNPSFVDILRS----KKRYSYMYVPSKFSKKHLIRGTRSIKLQ-DSDGK 342
            +       +P NP FV ++ S      +Y  + V  +F+ K+L    R + L+  S G 
Sbjct: 241 EISRVPVPVQPGNPVFVQVIHSSHVRSSKYCIVGVSPEFAGKYLGAVEREVVLERASRGG 300

Query: 343 EWPAQLTWSSGC-GIKG-GWPAFSKYKNLKQGHVCVFEL 379
           EW           G  G GW  F+    L    VC+FEL
Sbjct: 301 EWHVPFVHRQNTRGFYGAGWRQFAGDNRLVAHDVCLFEL 339

Oryza sativa subsp. japonica (taxid: 39947)

>sp|Q9XIB5|REM19_ARATH B3 domain-containing protein REM19 OS=Arabidopsis thaliana GN=REM19 PE=2 SV=1

 Score = 81.3 bits (199), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 49/148 (33%), Positives = 78/148 (52%), Gaps = 6/148 (4%)

Query: 254 HEVETDSSDGDQVFEEMGIFMSEG--HRYLSVEERQSLVTAVRLFKPQNPSFVDILRSKK 311
            EV + +  GD        + S     R ++ EER+  V A + F+P NP F  +LR   
Sbjct: 78  EEVNSSTPGGDDSENRSKFYESASARKRTVTAEERERAVNAAKTFEPTNPYFRVVLRPSY 137

Query: 312 RY--SYMYVPSKFSKKHLIRGTRSIKLQDSDGKEWPAQLTWSSG-CGIKGGWPAFSKYKN 368
            Y    MY+PS F++K+L   +  IKLQ  + K+WP +  + +G      GW  F+   N
Sbjct: 138 LYRGCIMYLPSGFAEKYLSGISGFIKLQLGE-KQWPVRCLYKAGRAKFSQGWYEFTLENN 196

Query: 369 LKQGHVCVFELIKAKDILLKVSIHASSE 396
           + +G VCVFEL++ +D +L+V+    +E
Sbjct: 197 IGEGDVCVFELLRTRDFVLEVTAFRVNE 224

Arabidopsis thaliana (taxid: 3702)

>sp|Q851V5|Y3216_ORYSJ Putative B3 domain-containing protein Os03g0621600 OS=Oryza sativa subsp. japonica GN=Os03g0621600 PE=3 SV=1

 Score = 79.3 bits (194), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 77/316 (24%), Positives = 133/316 (42%), Gaps = 64/316 (20%)

Query: 69  ETSHFFKVILPSTVQEKKLRIPRKFVKRFGDELSAVATLNVPNGRVWQVGLRKDGRKIWL 128
           + ++FFKV++      +++ IP KF + F D++     L   NG    V + K   K+ L
Sbjct: 146 QDTYFFKVMIGGF--RRQMTIPYKFAENFRDQIQGTIKLKARNGNTCSVLVDKCSNKLVL 203

Query: 129 QDGWDNFAEYHSIAVGYFLVFKYAKNSTFDVLVFDMTACEIDYPYDY----EETESEEGD 184
             GW  FA  H I +G FLVF+Y  NS F+V +FD + C     ++     +  ++ +GD
Sbjct: 204 TKGWAEFANSHDIKMGDFLVFRYTGNSQFEVKIFDPSGCVKAASHNAVNIGQHAQNMQGD 263

Query: 185 EMETENSVEILSFTKMNTPPVQENQVKPGSKPEKKKIGG----IKLETATNSREKKRCPT 240
                  +EILS +  +    Q    +  ++PEK  I      +K E A++S + +  PT
Sbjct: 264 ------PIEILSCSDEHL-RAQSLTTERQNQPEKDVIDNCNKKMKTEHASSSEDDQETPT 316

Query: 241 HGNEHGKLKKAAYHEVETDSSDGDQVFEEMGIFMSEGHRYLSVEERQSLVTAVRLFKPQN 300
                                             +E HR + VEE       VR     +
Sbjct: 317 ----------------------------------AEVHR-MKVEE------MVRAIHSNH 335

Query: 301 PSFVDILRSK---KRYSYMYVPSKFSKKHLIRGTRSIKLQDSDGKEWPAQLTWSSGC--G 355
           P FV +++     ++  Y+ +  K++ ++   G + + LQ   GK W  +   S      
Sbjct: 336 PVFVAVMKKSNVTRQPCYVAISRKYANEYFPGGDQMLTLQ-RHGKRWQVKFCISKRKLRM 394

Query: 356 IKGGWPAFSKYKNLKQ 371
           +  GW  F++   L+ 
Sbjct: 395 LSKGWRKFTRDNELQH 410

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	396
297741372	355	unnamed protein product [Vitis vinifera]	0.752	0.839	0.376	7e-49
225428645	407	PREDICTED: B3 domain-containing transcri	0.795	0.773	0.349	7e-49
224109350	341	predicted protein [Populus trichocarpa]	0.755	0.876	0.366	1e-46
449471266	412	PREDICTED: B3 domain-containing transcri	0.833	0.800	0.325	2e-46
297834810	341	hypothetical protein ARALYDRAFT_479415 [	0.785	0.912	0.361	2e-46
255556221	333	DNA binding protein, putative [Ricinus c	0.734	0.873	0.367	2e-46
40806799	329	reduced vernalization response 1 [Brassi	0.747	0.899	0.36	3e-46
312282979	341	unnamed protein product [Thellungiella h	0.785	0.912	0.361	5e-46
30685150	341	B3 domain-containing transcription facto	0.795	0.923	0.353	1e-45
224123406	407	predicted protein [Populus trichocarpa]	0.795	0.773	0.357	1e-45

>gi|297741372|emb|CBI32503.3| unnamed protein product [Vitis vinifera]

 Score =  201 bits (510), Expect = 7e-49,   Method: Compositional matrix adjust.
 Identities = 127/337 (37%), Positives = 190/337 (56%), Gaps = 39/337 (11%)

Query: 73  FFKVILPSTVQEKKLRIPRKFVKRFGDELSAVATLNVPNGRVWQVGLRKDGRKIWLQDGW 132
           F+K+I+ S +Q K+LRIP+KFVK+ GD+LSAV TL +PNG VW VGL K   K W   GW
Sbjct: 25  FYKLIVSSVLQAKRLRIPQKFVKKSGDQLSAVTTLTLPNGGVWYVGLTKADNKFWFYHGW 84

Query: 133 DNFAEYHSIAVGYFLVFKYAKNSTFDVLVFDMTACEIDYPYDY----------EETESEE 182
             F EY+SI VGYFL+F+Y  NS F+V +FD+TA EI+YP +           ++  + +
Sbjct: 85  HEFVEYYSIHVGYFLIFRYEGNSNFNVNIFDLTASEINYPSNNLRNSEKTSHGKQCPASD 144

Query: 183 GDEM-ETENSVEILSFTKMNTPPVQENQVKPGSKPEKKKIGGIKLETATNSREKKRCPTH 241
           G+EM + ++SVEIL     +  PV                  ++ +      +++    +
Sbjct: 145 GEEMNDDDDSVEILG----SASPV-----------------SLRSKVFDECIDQQPLGKN 183

Query: 242 GNEHGKLKKAAYHEVET--DSSDGDQVFEEMGIFMSEGHRY--LSVEERQSLVTAVRLFK 297
            NE+  L K A     T   S D    F    +  SE  R+  +++EE++  + A  +F+
Sbjct: 184 YNENLHLAKDANSLQVTIRSSRDIGIQFNSSELTNSECKRWRVVTMEEKKRALHAAEMFQ 243

Query: 298 PQNPSFVDILRSKKRYS--YMYVPSKFSKKHLIRGTRSIKLQDSDGKEWPAQ-LTWSSGC 354
           P NP    ILR    +    +++PS+F++K+L   ++ IKLQ SDGK+W  + L+  S  
Sbjct: 244 PSNPFCRVILRRSYVHERFLLHMPSRFAEKYLNGVSKFIKLQTSDGKQWHVRCLSGESRV 303

Query: 355 GIKGGWPAFSKYKNLKQGHVCVFELIKAKDILLKVSI 391
            +  GW  F K  NL++G VCVFELI  +D++LKVSI
Sbjct: 304 KLSKGWTEFVKDNNLEEGDVCVFELINMEDVVLKVSI 340

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225428645|ref|XP_002281517.1| PREDICTED: B3 domain-containing transcription factor VRN1-like [Vitis vinifera]

 Score =  201 bits (510), Expect = 7e-49,   Method: Compositional matrix adjust.
 Identities = 130/372 (34%), Positives = 198/372 (53%), Gaps = 57/372 (15%)

Query: 73  FFKVILPSTVQEKKLRIPRKFVKRFGDELSAVATLNVPNGRVWQVGLRKDGRKIWLQDGW 132
           F+K+I+ S +Q K+LRIP+KFVK+ GD+LSAV TL +PNG VW VGL K   K W   GW
Sbjct: 25  FYKLIVSSVLQAKRLRIPQKFVKKSGDQLSAVTTLTLPNGGVWYVGLTKADNKFWFYHGW 84

Query: 133 DNFAEYHSIAVGYFLVFKYAKNSTFDVLVFDMTACEIDYPYDY----------EETESEE 182
             F EY+SI VGYFL+F+Y  NS F+V +FD+TA EI+YP +           ++  + +
Sbjct: 85  HEFVEYYSIHVGYFLIFRYEGNSNFNVNIFDLTASEINYPSNNLRNSEKTSHGKQCPASD 144

Query: 183 GDEM-ETENSVEILSFTK------------MNTPPVQEN--------------QVKPGSK 215
           G+EM + ++SVEIL                ++  P+ +N              QV   S 
Sbjct: 145 GEEMNDDDDSVEILGSASPVSLRSKVFDECIDQQPLGKNYNENLHLAKDANSLQVTIRSS 204

Query: 216 PE-------------KKKIGGIKLETATNSREKKRCPTHGNEHGKLKKAAYHEVETDSSD 262
            +             + K+G ++L+ A     + +     NE    +  A H+ E +  D
Sbjct: 205 RDIGIQFNSSELTNSECKVGLLRLDEANGKTYRTKAKRKRNEPDANESPAKHKDEVEMPD 264

Query: 263 GDQVFEEMGIFMSEGHRYLSVEERQSLVTAVRLFKPQNPSFVDILRSKKRYS--YMYVPS 320
                E       +  R +++EE++  + A  +F+P NP    ILR    +    +++PS
Sbjct: 265 LKTSAET----SKQRWRVVTMEEKKRALHAAEMFQPSNPFCRVILRRSYVHERFLLHMPS 320

Query: 321 KFSKKHLIRGTRSIKLQDSDGKEWPAQ-LTWSSGCGIKGGWPAFSKYKNLKQGHVCVFEL 379
           +F++K+L   ++ IKLQ SDGK+W  + L+  S   +  GW  F K  NL++G VCVFEL
Sbjct: 321 RFAEKYLNGVSKFIKLQTSDGKQWHVRCLSGESRVKLSKGWTEFVKDNNLEEGDVCVFEL 380

Query: 380 IKAKDILLKVSI 391
           I  +D++LKVSI
Sbjct: 381 INMEDVVLKVSI 392

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224109350|ref|XP_002315168.1| predicted protein [Populus trichocarpa] gi|222864208|gb|EEF01339.1| predicted protein [Populus trichocarpa]

 Score =  193 bits (491), Expect = 1e-46,   Method: Compositional matrix adjust.
 Identities = 122/333 (36%), Positives = 176/333 (52%), Gaps = 34/333 (10%)

Query: 88  RIPRKFVKRFGDELSAVATLNVPNGRVWQVGLRKDGRKIWLQDGWDNFAEYHSIAVGYFL 147
           RIPRKFV++FG+ LS +A + VPNG  WQVG+ K+   IW  +GW  F E+HSI  GY +
Sbjct: 3   RIPRKFVEKFGEGLSDIAKVAVPNGNEWQVGITKEHNNIWFDEGWQEFVEHHSIGSGYLV 62

Query: 148 VFKYAKNSTFDVLVFDMTACEIDYPY----------DYEETESEEGDEMETENSVEILSF 197
           VF+Y  +S F VL+FDMTACEI Y            D E+    + DEM+ E SVE L  
Sbjct: 63  VFRYRGDSNFSVLIFDMTACEIQYRRMRPTGGEGMNDAEKCSFYDEDEMKDEGSVESLDT 122

Query: 198 -------TKMNTPPVQENQVKPGSKPEKKKIGGIKLETATNSREKKRCPT---------H 241
                  +++     +E     G  P  +     ++    ++ E +R  +         H
Sbjct: 123 HYCRALKSRVFNLNAREGGSSKGRGPSSETTVKNEMTYIDDTSESRRGKSLKKHRMSAPH 182

Query: 242 GNEHGKLKKAAYHEVETDSSDGDQVFEEMGIFMSEGHRYLSVEERQSLVTAVRLFKPQNP 301
           G    K  K+     E +     +  E    F+  G    S E+ +  + A R+FKP++P
Sbjct: 183 GETKAKKSKSKSRLGENELLPECEAIE----FVPRGFAKAS-EKSKRAIHAARMFKPKSP 237

Query: 302 SFVDILRSKKRYS-YMYVPSKFSKKHLIRGTRSIKLQDSDGKEWPAQLTWSSG--CGIKG 358
           SF+ +LR    Y+ ++YVP +F+++HL    R IKLQ SDG+EWP Q+  +      I  
Sbjct: 238 SFMVMLRRYNFYNHFLYVPLEFAQRHLSDAPRCIKLQVSDGREWPIQINRNQCRYLSISK 297

Query: 359 GWPAFSKYKNLKQGHVCVFELIKAKDILLKVSI 391
           GW  FS+  NLK+G VCVFELI  +  +LKV+I
Sbjct: 298 GWNEFSQENNLKEGDVCVFELINKEKFVLKVAI 330

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449471266|ref|XP_004153259.1| PREDICTED: B3 domain-containing transcription factor VRN1-like [Cucumis sativus] gi|449502391|ref|XP_004161627.1| PREDICTED: B3 domain-containing transcription factor VRN1-like [Cucumis sativus]

 Score =  192 bits (489), Expect = 2e-46,   Method: Compositional matrix adjust.
 Identities = 121/372 (32%), Positives = 188/372 (50%), Gaps = 42/372 (11%)

Query: 60  QMAGGNRRAETSHFFKVILPSTVQEKKLRIPRKFVKRFGDELSAVATLNVPNGRVWQVGL 119
           +  G  R+    HF K++L ST+Q +KLRIP  FV+   DELSAVATL VP+G VW+VGL
Sbjct: 8   RTGGFKRKMPRPHFHKLVLTSTIQARKLRIPETFVRMIRDELSAVATLTVPDGHVWRVGL 67

Query: 120 RKDGRKIWLQDGWDNFAEYHSIAVGYFLVFKYAKNSTFDVLVFDMTACEIDYP------- 172
           RK   K W +DGW  F E++SI VGY LVF+Y  NS+F V +F++   EI+Y        
Sbjct: 68  RKADNKFWFEDGWQGFLEHYSIRVGYLLVFRYEGNSSFCVFIFNLNTSEINYQSAALSNN 127

Query: 173 ----YDYEETESEEGDEMETENSVEILSFTKMNTPPVQE---------NQVKPGSKPEKK 219
               Y  +    EE ++ +   +  I S   MN+  ++          +Q K  S  + +
Sbjct: 128 QRNNYSIQNRIFEEMEDYDIPEA--IPSNQSMNSGSLRNKLFGDEWNLHQSKSASTLQAE 185

Query: 220 KIGGIKLETATNSREKK-----------------RCPTHGNEHGKLKKAAYHEVETDSSD 262
            +    +    ++ E K                 R    G++  K++ + +H    +S D
Sbjct: 186 YLSTRDIGVQFSAVEVKKSADEVRFQNLGDDAAHRVKKSGSKKRKIESSEHHPSAHNSED 245

Query: 263 GDQVFEEMGIFMSEGHRYLSVEERQSLVTAVRLFKPQNPSFVDILRSKKRY--SYMYVPS 320
              +        S   R ++ EER+  + + + F+P NP    +LR    Y    MY+PS
Sbjct: 246 LGDIRFRFYESASARKRTVTAEERERAINSAKAFEPGNPFCRVVLRPSYLYRGCIMYLPS 305

Query: 321 KFSKKHLIRGTRSIKLQDSDGKEWPAQLTWSSG-CGIKGGWPAFSKYKNLKQGHVCVFEL 379
            F++K+L   +  IKLQ  DG++WP +  +  G   +  GW  F    NL +G VCVFEL
Sbjct: 306 CFAEKNLSGVSGFIKLQTPDGRQWPVRCLYKVGRAKLSQGWYEFCLENNLGEGDVCVFEL 365

Query: 380 IKAKDILLKVSI 391
           ++ ++I+LKV++
Sbjct: 366 LRMREIVLKVTM 377

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297834810|ref|XP_002885287.1| hypothetical protein ARALYDRAFT_479415 [Arabidopsis lyrata subsp. lyrata] gi|297331127|gb|EFH61546.1| hypothetical protein ARALYDRAFT_479415 [Arabidopsis lyrata subsp. lyrata]

 Score =  192 bits (489), Expect = 2e-46,   Method: Compositional matrix adjust.
 Identities = 121/335 (36%), Positives = 179/335 (53%), Gaps = 24/335 (7%)

Query: 73  FFKVILPSTVQEKKLRIPRKFVKRFGDELSAVATLNVPNGRVWQVGLRKDGRKIWLQDGW 132
           F K+I  ST+QEK+LR+P KFV +F DELS    L VP+G VW+VGLRK   KIW QDGW
Sbjct: 6   FHKLIFSSTIQEKRLRVPDKFVSKFKDELSVAVALTVPDGHVWRVGLRKADNKIWFQDGW 65

Query: 133 DNFAEYHSIAVGYFLVFKYAKNSTFDVLVFDMTACEIDYP----YDYEETESEEG---DE 185
             F + +SI +GY L+F+Y  NS F V +F+++  EI+Y      D      +     ++
Sbjct: 66  QEFVDRYSIRIGYLLIFRYEGNSAFSVYIFNLSHSEINYHSTGLMDSAHNHFKRARLFED 125

Query: 186 METENSVEILSFTKMNTP----PVQENQVKPGSKPEKKKIGGIKLETATNSREKKRCPTH 241
           +E E++  I   +   +P     V  N+   GS  +    G +K E AT +      P  
Sbjct: 126 LEDEDAEFIFPSSVYPSPLPESTVPANKGYAGSAIQSLFTGSVKAEEATPT------PKI 179

Query: 242 GNEHGKLKKAAYHEVETDSSDGDQVFEEMGIF---MSEGHRYLSVEERQSLVTAVRLFKP 298
             + G+ KK A  E    S+  D   E    F    S   R ++ EER+  + A + F+P
Sbjct: 180 PKKRGRKKKNADPEEINSSAPRDDDPENRSKFYESASARKRTVTAEERERAINAAKTFEP 239

Query: 299 QNPSFVDILRSKKRY--SYMYVPSKFSKKHLIRGTRSIKLQDSDGKEWPAQLTWSSG-CG 355
            NP F  +LR    Y    MY+PS F++K+L   +  IK+Q ++ K+WP +  + +G   
Sbjct: 240 TNPFFRVVLRPSYLYRGCIMYLPSGFAEKYLSGISGFIKVQLAE-KQWPVRCLYKAGRAK 298

Query: 356 IKGGWPAFSKYKNLKQGHVCVFELIKAKDILLKVS 390
              GW  F+   NL +G VCVFEL++ +D +LKV+
Sbjct: 299 FSQGWYEFTLENNLGEGDVCVFELLRTRDFVLKVT 333

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255556221|ref|XP_002519145.1| DNA binding protein, putative [Ricinus communis] gi|223541808|gb|EEF43356.1| DNA binding protein, putative [Ricinus communis]

 Score =  192 bits (488), Expect = 2e-46,   Method: Compositional matrix adjust.
 Identities = 124/337 (36%), Positives = 187/337 (55%), Gaps = 46/337 (13%)

Query: 72  HFFKVILPSTVQEKKLRIPRKFVKRFGDELSAVATLNVPNGRVWQVGLRKDGRKIWLQDG 131
           +F K+IL +++++KKLRIP  FVK+FG++LSA   L+VP G VW VGL K   K W ++G
Sbjct: 5   YFHKLILSNSIKDKKLRIPDNFVKKFGNDLSAFGRLSVPGGPVWPVGLIKADDKFWFREG 64

Query: 132 WDNFAEYHSIAVGYFLVFKYAKNSTFDVLVFDMTACEIDYPYDYEETESEEG------DE 185
           W  F E +SI VGYFLVF+Y  +S F V +F+++A EI+Y     ++ +  G      ++
Sbjct: 65  WQEFMERYSIRVGYFLVFRYEGHSVFTVHIFNLSASEINY-----QSNNTAGRRYLLFED 119

Query: 186 METENSVEILSFTKMNTPPVQENQVK-------PGSKPEK-KKIGGIKLETATNSREKKR 237
           ME ++ VE LS    ++P +  N +K       P ++ +K KK G  KL+   N ++   
Sbjct: 120 MEDDDFVEHLS---SSSPCLVPNSLKSDVRYYTPDAEAQKPKKRGRKKLKVDPNQQQ--- 173

Query: 238 CPTHGNEHGKLKKAAYHEVETDSSDGDQVFEEMGIFMSEGHRYLSVEERQSLVTAVRLFK 297
            P+   E              D  D    F E     S   R ++ EER+  +   + F+
Sbjct: 174 -PSAQQE--------------DEVDMRFRFYESA---SARKRTVTAEERERAINTAKTFE 215

Query: 298 PQNPSFVDILRSKKRY--SYMYVPSKFSKKHLIRGTRSIKLQDSDGKEWPAQLTWSSG-C 354
           P NP    +LR    Y    MY+PS F++KHL   +  IKLQ SDGK+WP +  +  G  
Sbjct: 216 PMNPFCRVVLRPSYLYRGCIMYLPSCFAEKHLNGVSGFIKLQSSDGKQWPVRCLYRGGRA 275

Query: 355 GIKGGWPAFSKYKNLKQGHVCVFELIKAKDILLKVSI 391
            +  GW  F+   N+ +G VCVFEL+K++DI+LKV++
Sbjct: 276 KLSQGWYEFTLENNMGEGDVCVFELLKSRDIVLKVTV 312

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|40806799|gb|AAR92199.1| reduced vernalization response 1 [Brassica rapa]

 Score =  192 bits (487), Expect = 3e-46,   Method: Compositional matrix adjust.
 Identities = 126/350 (36%), Positives = 181/350 (51%), Gaps = 54/350 (15%)

Query: 73  FFKVILPSTVQEKKLRIPRKFVKRFGDELSAVATLNVPNGRVWQVGLRK--DGRKIWLQD 130
           F K+I  ST+QEK+LR+P KFV RF DELS    L VP+G VW+VGLRK  +  KIW QD
Sbjct: 6   FHKLIFSSTIQEKRLRVPDKFVSRFKDELSVAVALTVPDGHVWRVGLRKADNNNKIWFQD 65

Query: 131 GWDNFAEYHSIAVGYFLVFKYAKNSTFDVLVFDMTACEIDY-----------------PY 173
           GW  F + +SI +GY L+F+Y  NS F V ++++   EI+Y                 P 
Sbjct: 66  GWQEFVDRYSIRIGYLLIFRYEGNSAFSVCIYNLPQSEINYHSTGLMDSASHNNHFKRPR 125

Query: 174 DYEETESEEGDEMETENSVEILSFTKMNTPPVQENQVKPGSKPEKKKIGGIKLETATNSR 233
            +E+ E E+ + + T  S  I SF    T PV+  +  P               T T+  
Sbjct: 126 LFEDLEDEDAETLHTTASA-IQSFF---TGPVKPEEATP---------------TQTSKV 166

Query: 234 EKKRCPTHGNEHGKLKKAAYHEVETDSS----DGDQVFEEMGIFMSEGHRYLSVEERQSL 289
            KKR        G+ KK A H  E +SS    D  +   +     S   R ++ EER+  
Sbjct: 167 PKKR--------GRKKKNADHPEEVNSSAPRDDDPESRSKFYESASARKRTVNAEERERA 218

Query: 290 VTAVRLFKPQNPSFVDILRSKKRY--SYMYVPSKFSKKHLIRGTRSIKLQDSDGKEWPAQ 347
           V A + F+P NP F  +LR    Y    MY+PS F++K+L   +  IK+Q  + K+WP +
Sbjct: 219 VNAAKTFEPTNPFFRVVLRPSYLYRGCIMYLPSGFAEKYLSGISGFIKVQLGE-KQWPVR 277

Query: 348 LTWSSG-CGIKGGWPAFSKYKNLKQGHVCVFELIKAKDILLKVSIHASSE 396
             + +G      GW  F+   NL +G VCVFEL++ +D +LKV+ +  +E
Sbjct: 278 CLYKAGRAKFSQGWYEFTVENNLGEGDVCVFELLRTRDFVLKVTAYRVNE 327

Source: Brassica rapa

Species: Brassica rapa

Genus: Brassica

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|312282979|dbj|BAJ34355.1| unnamed protein product [Thellungiella halophila]

 Score =  191 bits (485), Expect = 5e-46,   Method: Compositional matrix adjust.
 Identities = 121/335 (36%), Positives = 179/335 (53%), Gaps = 24/335 (7%)

Query: 73  FFKVILPSTVQEKKLRIPRKFVKRFGDELSAVATLNVPNGRVWQVGLRKDGRKIWLQDGW 132
           F K+I  ST+QEK+LR+P KFV +F DELS    L VP+G VW+VGLRK   KIW QDGW
Sbjct: 6   FHKLIFSSTIQEKRLRVPDKFVSKFKDELSVAVALTVPDGHVWRVGLRKAENKIWFQDGW 65

Query: 133 DNFAEYHSIAVGYFLVFKYAKNSTFDVLVFDMTACEIDYP----YDYEETESEEG---DE 185
             F + +SI +GY L+F+Y  NS F V +F+++  EI+Y      D      +     ++
Sbjct: 66  QEFVDRYSIRIGYLLIFRYEGNSAFSVYIFNLSHSEINYHSTGLMDSAHNHFKRARLFED 125

Query: 186 METENSVEILSFTKMNTP----PVQENQVKPGSKPEKKKIGGIKLETATNSREKKRCPTH 241
           +E E++  I   +   +P     V  N+   GS  +    G +K E AT +      P  
Sbjct: 126 LEDEDAEVIYPSSVYPSPLPDSTVPANKGYSGSAIQSLFTGPVKAEEATPT------PKV 179

Query: 242 GNEHGKLKKAAYHEVETDSSDGDQVFEEMGIF---MSEGHRYLSVEERQSLVTAVRLFKP 298
             + G+ KK A  E    S+  D   E    F    S   R ++ EER+  + A + F+P
Sbjct: 180 PKKRGRKKKNADPEEINSSAPRDDDPENRSKFYESASARKRTVTAEERERAINAAKTFEP 239

Query: 299 QNPSFVDILRSKKRY--SYMYVPSKFSKKHLIRGTRSIKLQDSDGKEWPAQLTWSSG-CG 355
            NP F  +LR    Y    MY+PS F++K+L   +  IK+Q ++ K+WP +  + +G   
Sbjct: 240 TNPFFRVVLRPSYLYRGCIMYLPSGFAEKYLSGISGFIKVQLAE-KQWPVRCLYKAGRAK 298

Query: 356 IKGGWPAFSKYKNLKQGHVCVFELIKAKDILLKVS 390
              GW  F+   NL +G VCVFEL++ +D +LKV+
Sbjct: 299 FSQGWYEFTLENNLGEGDVCVFELLRTRDFVLKVT 333

Source: Thellungiella halophila

Species: Eutrema halophilum

Genus: Eutrema

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|30685150|ref|NP_188529.2| B3 domain-containing transcription factor VRN1 [Arabidopsis thaliana] gi|75153628|sp|Q8L3W1.1|VRN1_ARATH RecName: Full=B3 domain-containing transcription factor VRN1; AltName: Full=Protein VERNALIZATION 1 gi|21734794|gb|AAM76972.1|AF289051_1 reduced vernalization response 1 [Arabidopsis thaliana] gi|21734796|gb|AAM76973.1|AF289052_1 reduced vernalization response 1 [Arabidopsis thaliana] gi|89000959|gb|ABD59069.1| At3g18990 [Arabidopsis thaliana] gi|110741272|dbj|BAF02186.1| hypothetical protein [Arabidopsis thaliana] gi|225898655|dbj|BAH30458.1| hypothetical protein [Arabidopsis thaliana] gi|332642657|gb|AEE76178.1| B3 domain-containing transcription factor VRN1 [Arabidopsis thaliana]

 Score =  190 bits (482), Expect = 1e-45,   Method: Compositional matrix adjust.
 Identities = 117/331 (35%), Positives = 177/331 (53%), Gaps = 16/331 (4%)

Query: 73  FFKVILPSTVQEKKLRIPRKFVKRFGDELSAVATLNVPNGRVWQVGLRKDGRKIWLQDGW 132
           F K+I  ST+QEK+LR+P KFV +F DELS    L VP+G VW+VGLRK   KIW QDGW
Sbjct: 6   FHKLIFSSTIQEKRLRVPDKFVSKFKDELSVAVALTVPDGHVWRVGLRKADNKIWFQDGW 65

Query: 133 DNFAEYHSIAVGYFLVFKYAKNSTFDVLVFDMTACEIDYP----YDYEETESEEG---DE 185
             F + +SI +GY L+F+Y  NS F V +F+++  EI+Y      D      +     ++
Sbjct: 66  QEFVDRYSIRIGYLLIFRYEGNSAFSVYIFNLSHSEINYHSTGLMDSAHNHFKRARLFED 125

Query: 186 METENSVEILSFTKMNTPPVQENQVKPGSKPEKKKIGGIKLETATNSREKKRCPTHGNEH 245
           +E E++ E++  + +   P+ E+ V P +K                + E    P    + 
Sbjct: 126 LEDEDA-EVIFPSSVYPSPLPESTV-PANKGYASSAIQTLFTGPVKAEEPTPTPKIPKKR 183

Query: 246 GKLKKAAYHEVETDSSDGDQVFEEMGIF---MSEGHRYLSVEERQSLVTAVRLFKPQNPS 302
           G+ KK A  E    S+  D   E    F    S   R ++ EER+  + A + F+P NP 
Sbjct: 184 GRKKKNADPEEINSSAPRDDDPENRSKFYESASARKRTVTAEERERAINAAKTFEPTNPF 243

Query: 303 FVDILRSKKRY--SYMYVPSKFSKKHLIRGTRSIKLQDSDGKEWPAQLTWSSG-CGIKGG 359
           F  +LR    Y    MY+PS F++K+L   +  IK+Q ++ K+WP +  + +G      G
Sbjct: 244 FRVVLRPSYLYRGCIMYLPSGFAEKYLSGISGFIKVQLAE-KQWPVRCLYKAGRAKFSQG 302

Query: 360 WPAFSKYKNLKQGHVCVFELIKAKDILLKVS 390
           W  F+   NL +G VCVFEL++ +D +LKV+
Sbjct: 303 WYEFTLENNLGEGDVCVFELLRTRDFVLKVT 333

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224123406|ref|XP_002330307.1| predicted protein [Populus trichocarpa] gi|222871342|gb|EEF08473.1| predicted protein [Populus trichocarpa]

 Score =  190 bits (482), Expect = 1e-45,   Method: Compositional matrix adjust.
 Identities = 136/380 (35%), Positives = 193/380 (50%), Gaps = 65/380 (17%)

Query: 72  HFFKVILPSTVQEKKLRIPRKFVKRFGDELSAVATLNVPNGRVWQVGLRKDGRKIWLQDG 131
           HFFK+I  ST+++KKLRIP KF ++FG+ELS VA + +PNG  WQ+GL K    +   DG
Sbjct: 22  HFFKIITQSTLKDKKLRIPNKFARKFGEELSDVAKVVLPNGHSWQIGLTKSNNSVSFDDG 81

Query: 132 WDNFAEYHSIAVGYFLVFKYAKNSTFDVLVFDMTACEIDY----------PYDYEETESE 181
           W  F E HS+  G+ LVF Y   S F+ L+FD TACEI Y            +Y+E  S 
Sbjct: 82  WLQFLEQHSVGYGHLLVFGYRGCSNFNALIFDKTACEIPYHRCRGGTSGGKINYDEKCSP 141

Query: 182 -EGDEMETENSVEILSFTKM--------------------NTPPVQENQV---------- 210
            + D M+ E ++  +                         + PP  EN            
Sbjct: 142 YDVDVMKDEGTIASIDSQYCCALESGVFDEDAGDSRQRHPSKPPPSENNAQERPCFECSG 201

Query: 211 -KPGSKPEKKK-IGGIKLETATNSREKK-----RCP-THGN---------EHGKLKKAAY 253
            K G  P KK+ I   +L+    S+ +K     R P  HG+            K K A  
Sbjct: 202 DKRGKIPVKKELIVMAELDDTDESKRRKLSKKCRLPRPHGSLIDETKVNKGKSKTKFAPS 261

Query: 254 HEVETDSSDGDQVFEEMGIFMSEGHRYLSVEERQSLVTAVRLFKPQNPSFVDILRSKKRY 313
           +  ETD S   +  E+  I +    +  + EE +  + A R+F+P+NPSF+ +LRS  + 
Sbjct: 262 YADETDFS--PRCGEDTDIIVCGFAK--ASEESKKAIHAARMFRPKNPSFMVLLRSYNK- 316

Query: 314 SYMYVPSKFSKKHLIRGTRSIKLQDSDGKEWPAQL--TWSSGCGIKGGWPAFSKYKNLKQ 371
            ++ VP++FSK+HL   +  IKLQ SDG++WP +L  T  +   I  GW  F +  NLK+
Sbjct: 317 CFVAVPAEFSKRHLSGVSEHIKLQVSDGRQWPLRLNKTQRARMIISRGWNEFKRENNLKE 376

Query: 372 GHVCVFELIKAKDILLKVSI 391
           G VCVFELIK K   L+VS+
Sbjct: 377 GDVCVFELIKNKKFSLQVSM 396

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	396
TAIR|locus:2085849	341	VRN1 "REDUCED VERNALIZATION RE	0.813	0.944	0.345	7.9e-46
TAIR|locus:2133362	190	AT4G01580 [Arabidopsis thalian	0.257	0.536	0.5	7.6e-25
TAIR|locus:2085859	209	AT3G18960 [Arabidopsis thalian	0.310	0.588	0.410	2e-24
TAIR|locus:504956318	190	AT1G49475 [Arabidopsis thalian	0.255	0.531	0.421	6.6e-19
TAIR|locus:2010262	226	RTV1 "AT1G49480" [Arabidopsis	0.459	0.805	0.305	5.5e-17
TAIR|locus:2119166	337	AT4G33280 [Arabidopsis thalian	0.247	0.290	0.392	2.1e-15
TAIR|locus:2124879	352	AT4G31640 [Arabidopsis thalian	0.244	0.275	0.330	1.4e-13
TAIR|locus:2124824	462	AT4G31680 [Arabidopsis thalian	0.267	0.229	0.318	2.2e-12
TAIR|locus:2172319	301	AT5G18090 [Arabidopsis thalian	0.265	0.348	0.277	3.6e-11
TAIR|locus:2126016	528	MEE45 "maternal effect embryo	0.237	0.178	0.320	4.2e-10

TAIR|locus:2085849 VRN1 "REDUCED VERNALIZATION RESPONSE 1" [Arabidopsis thaliana (taxid:3702)]

 Score = 481 (174.4 bits), Expect = 7.9e-46, P = 7.9e-46
 Identities = 116/336 (34%), Positives = 172/336 (51%)

Query:    73 FFKVILPSTVQEKKLRIPRKFVKRFGDELSAVATLNVPNGRVWQVGLRKDGRKIWLQDGW 132
             F K+I  ST+QEK+LR+P KFV +F DELS    L VP+G VW+VGLRK   KIW QDGW
Sbjct:     6 FHKLIFSSTIQEKRLRVPDKFVSKFKDELSVAVALTVPDGHVWRVGLRKADNKIWFQDGW 65

Query:   133 DNFAEYHSIAVGYFLVFKYAKNSTFDVLVFDMTACEIDYP----YD--YXXXXXXXXXXX 186
               F + +SI +GY L+F+Y  NS F V +F+++  EI+Y      D  +           
Sbjct:    66 QEFVDRYSIRIGYLLIFRYEGNSAFSVYIFNLSHSEINYHSTGLMDSAHNHFKRARLFED 125

Query:   187 XXXNSVEILSFTKMNTPPVQENQVKPGSKPEKKKIGGIKLETATNSREKKRCPTHGNEHG 246
                   E++  + +   P+ E+ V P +K                + E    P    + G
Sbjct:   126 LEDEDAEVIFPSSVYPSPLPESTV-PANKGYASSAIQTLFTGPVKAEEPTPTPKIPKKRG 184

Query:   247 KLKKAAYHEVETDSSDGDQVFEEMGIFM---SEGHRYLSVEERQSLVTAVRLFKPQNPSF 303
             + KK A  E    S+  D   E    F    S   R ++ EER+  + A + F+P NP F
Sbjct:   185 RKKKNADPEEINSSAPRDDDPENRSKFYESASARKRTVTAEERERAINAAKTFEPTNPFF 244

Query:   304 VDILRSKKRYS--YMYVPSKFSKKHLIRGTRSIKLQDSDGKEWPAQLTWSSG-CGIKGGW 360
               +LR    Y    MY+PS F++K+L   +  IK+Q ++ K+WP +  + +G      GW
Sbjct:   245 RVVLRPSYLYRGCIMYLPSGFAEKYLSGISGFIKVQLAE-KQWPVRCLYKAGRAKFSQGW 303

Query:   361 PAFSKYKNLKQGHVCVFELIKAKDILLKVSIHASSE 396
               F+   NL +G VCVFEL++ +D +LKV+    +E
Sbjct:   304 YEFTLENNLGEGDVCVFELLRTRDFVLKVTAFRVNE 339

GO:0005634 "nucleus" evidence=ISM

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

GO:0003677 "DNA binding" evidence=IDA

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

GO:0005654 "nucleoplasm" evidence=IDA

GO:0010048 "vernalization response" evidence=IMP

TAIR|locus:2133362 AT4G01580 [Arabidopsis thaliana (taxid:3702)]

 Score = 283 (104.7 bits), Expect = 7.6e-25, P = 7.6e-25
 Identities = 51/102 (50%), Positives = 73/102 (71%)

Query:    73 FFKVILPSTVQEKKLRIPRKFVKRFGDELSAVATLNVPNGRVWQVGLRKDGRKIWLQDGW 132
             FFK++LPST+++K +RIP +FVK  G +LS V TL  P G    + L++ G +IW  +GW
Sbjct:    30 FFKLVLPSTMKDKMMRIPPRFVKLQGSKLSEVVTLVTPAGYKRSIKLKRIGEEIWFHEGW 89

Query:   133 DNFAEYHSIAVGYFLVFKYAKNSTFDVLVFDMTACEIDYPYD 174
               FAE HSI  G+FL+F+Y KNS+F V++F+ +ACE +YP D
Sbjct:    90 SEFAEAHSIEEGHFLLFEYKKNSSFRVIIFNASACETNYPLD 131

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

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

GO:0005634 "nucleus" evidence=ISM

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

TAIR|locus:2085859 AT3G18960 [Arabidopsis thaliana (taxid:3702)]

 Score = 279 (103.3 bits), Expect = 2.0e-24, P = 2.0e-24
 Identities = 53/129 (41%), Positives = 82/129 (63%)

Query:    52 TVANNNVKQMAGGNRRAE------TSHFFKVILPSTVQEKKLRIPRKFVKRFGDELSAVA 105
             T  N   +  +  +RR++         FFK++LPST+++K ++IP +FVK  G +LS V 
Sbjct:     3 TTQNTKARVTSVSHRRSQQDPESPVKKFFKLVLPSTMKDKMMKIPPRFVKLQGSKLSEVV 62

Query:   106 TLNVPNGRVWQVGLRKDGRKIWLQDGWDNFAEYHSIAVGYFLVFKYAKNSTFDVLVFDMT 165
             TL  P G    + L++ G +IW  +GW  FAE HSI  G+FL+F+Y +NS+F V++F+++
Sbjct:    63 TLETPAGFKRSIKLKRIGEEIWFHEGWSEFAEAHSIEEGHFLLFEYKENSSFRVIIFNVS 122

Query:   166 ACEIDYPYD 174
             ACE  YP D
Sbjct:   123 ACETKYPLD 131

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

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

GO:0005634 "nucleus" evidence=ISM

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

TAIR|locus:504956318 AT1G49475 [Arabidopsis thaliana (taxid:3702)]

 Score = 230 (86.0 bits), Expect = 6.6e-19, P = 6.6e-19
 Identities = 43/102 (42%), Positives = 67/102 (65%)

Query:    73 FFKVILPSTVQEKKLRIPRKFVKRFGDELSAVATLNVPNGRVWQVGLRKDGRKIWLQDGW 132
             F K+IL S + EK +++P +FV RFG +L+   TL  P G    + +++ G ++W + GW
Sbjct:    34 FIKIILLSRIIEKMMKVPARFV-RFGPKLTDNVTLQTPVGFKRSIRIKRIGDEVWFEKGW 92

Query:   133 DNFAEYHSIAVGYFLVFKYAKNSTFDVLVFDMTACEIDYPYD 174
               FAE HS++ G+FL F Y  +S F V++FD++A EI+YP D
Sbjct:    93 SEFAEAHSLSDGHFLFFHYEGDSCFRVVIFDVSASEIEYPLD 134

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

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

GO:0005634 "nucleus" evidence=ISM

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

TAIR|locus:2010262 RTV1 "AT1G49480" [Arabidopsis thaliana (taxid:3702)]

 Score = 213 (80.0 bits), Expect = 5.5e-17, P = 5.5e-17
 Identities = 58/190 (30%), Positives = 94/190 (49%)

Query:   214 SKPEKKKIGG-IKLETATNSREKKRCPTHGNEHGKLKKAAYHEVETDSSDGDQVFEEMGI 272
             ++P  K  GG   +++     + +  P    + G+ KK    E    S+ G    E    
Sbjct:    36 TEPVNKGYGGSTAIQSFFKESKAEETPKVLKKRGRKKKNPNPEEVNSSTPGGDDSENRSK 95

Query:   273 FM---SEGHRYLSVEERQSLVTAVRLFKPQNPSFVDILRSKKRYS--YMYVPSKFSKKHL 327
             F    S   R ++ EER+  V A + F+P NP F  +LR    Y    MY+PS F++K+L
Sbjct:    96 FYESASARKRTVTAEERERAVNAAKTFEPTNPYFRVVLRPSYLYRGCIMYLPSGFAEKYL 155

Query:   328 IRGTRSIKLQDSDGKEWPAQLTWSSG-CGIKGGWPAFSKYKNLKQGHVCVFELIKAKDIL 386
                +  IKLQ  + K+WP +  + +G      GW  F+   N+ +G VCVFEL++ +D +
Sbjct:   156 SGISGFIKLQLGE-KQWPVRCLYKAGRAKFSQGWYEFTLENNIGEGDVCVFELLRTRDFV 214

Query:   387 LKVSIHASSE 396
             L+V+    +E
Sbjct:   215 LEVTAFRVNE 224

GO:0003677 "DNA binding" evidence=ISS

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

GO:0005634 "nucleus" evidence=ISM;IDA

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

GO:0032880 "regulation of protein localization" evidence=RCA

GO:0005515 "protein binding" evidence=IPI

GO:0005886 "plasma membrane" evidence=IDA

GO:0034613 "cellular protein localization" evidence=IDA

TAIR|locus:2119166 AT4G33280 [Arabidopsis thaliana (taxid:3702)]

 Score = 169 (64.5 bits), Expect = 2.1e-15, Sum P(2) = 2.1e-15
 Identities = 40/102 (39%), Positives = 56/102 (54%)

Query:    69 ETSHFFKVILPSTVQEKKLRIPRKFVKRFGDELSAVATLNVPNGRVWQVGLRKDGRKIW- 127
             +T HF +++LP      +L IPRKF      +L  + TL  P+G  + VG+ +D  K   
Sbjct:    21 QTLHFTQLLLPGF--HNRLVIPRKFSTHCKRKLPQIVTLKSPSGVTYNVGVEEDDEKTMA 78

Query:   128 LQDGWDNFAEYHSIAVGYFLVFKYAKNSTFDVLVFD-MTACE 168
              + GWD F + HS+     LVFK+   S F+VLVFD  T CE
Sbjct:    79 FRFGWDKFVKDHSLEENDLLVFKFHGVSEFEVLVFDGQTLCE 120

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

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

GO:0005634 "nucleus" evidence=ISM

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

GO:0005773 "vacuole" evidence=IDA

TAIR|locus:2124879 AT4G31640 [Arabidopsis thaliana (taxid:3702)]

 Score = 146 (56.5 bits), Expect = 1.4e-13, Sum P(2) = 1.4e-13
 Identities = 35/106 (33%), Positives = 56/106 (52%)

Query:    69 ETSHFFKVILPSTVQEKKLRIPRKFVKRFGD---ELSAVATLNVPNGRVWQVGLRKDGRK 125
             ++ HFF+ ILP    +  ++IP KF  +  +   E + V   + P+ R W+V  + +G K
Sbjct:    10 KSPHFFQPILPGF--KSHIKIPVKFFSKHIEGKHEGNTVYLRSYPSRRTWKV--KMEGHK 65

Query:   126 IWLQDGWDNFAEYHSIAVGYFLVFKYAKNSTFDVLVFDMTACEIDY 171
               L +GW  F E H + VG F+VFK+  +  F V     + CE+ Y
Sbjct:    66 --LTEGWKEFVEAHDLRVGDFVVFKHKGDMLFHVTAIGPSCCEVQY 109

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

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

GO:0005634 "nucleus" evidence=ISM

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

TAIR|locus:2124824 AT4G31680 [Arabidopsis thaliana (taxid:3702)]

 Score = 144 (55.7 bits), Expect = 2.2e-12, Sum P(2) = 2.2e-12
 Identities = 37/116 (31%), Positives = 56/116 (48%)

Query:    61 MAGGNRRAETS-HFFKVILPSTVQEKKLRIPRKFVKRF--GDELSAVATLNVP-NGRVWQ 116
             MA  ++ + T+ HFFK +LP    ++ L IP KF      G        L    + R W+
Sbjct:     1 MANASQLSPTNKHFFKPLLPGF--QRNLNIPVKFFSEHIEGKHEGETVKLRADASKRTWE 58

Query:   117 VGLRKDGRKIWLQDGWDNFAEYHSIAVGYFLVFKYAKNSTFDVLVFDMTACEIDYP 172
             V  + DG +  L +GW  F E H + +  F+VF++  +  F V     + CEI YP
Sbjct:    59 V--KMDGNR--LTEGWKEFVEAHDLRIRDFVVFRHEGDMVFHVTALGPSCCEIQYP 110

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

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

GO:0005634 "nucleus" evidence=ISM

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

TAIR|locus:2172319 AT5G18090 [Arabidopsis thaliana (taxid:3702)]

 Score = 113 (44.8 bits), Expect = 3.6e-11, Sum P(2) = 3.6e-11
 Identities = 30/108 (27%), Positives = 52/108 (48%)

Query:    68 AETSHFFKVILPSTVQEKKLR-IPRKFVKRFGDE-LSAVATLNVPNGRVWQVGLRKDGRK 125
             AE   FFK++  + +  + +R IP  F+K   +E LSA   L V  G  W + + ++   
Sbjct:    13 AENPGFFKILRSADLSSEIMRGIPLNFIKSISEEELSAKMLLKVSWGSSWPIKICRNPSF 72

Query:   126 IWLQD-GWDNFAEYHSIAVGYFLVFKYAKNSTFDVLVFDMTACEIDYP 172
              +++  GWD F   + +    FL F +  N  F V ++ +   E+  P
Sbjct:    73 YFMEKKGWDQFLSDNGLGNDEFLTFTHQGNMCFTVDIYQIDGKELLTP 120

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

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

GO:0005634 "nucleus" evidence=ISM

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

TAIR|locus:2126016 MEE45 "maternal effect embryo arrest 45" [Arabidopsis thaliana (taxid:3702)]

 Score = 117 (46.2 bits), Expect = 4.2e-10, Sum P(2) = 4.2e-10
 Identities = 33/103 (32%), Positives = 48/103 (46%)

Query:    72 HFFKVILPSTVQEKKLRIPRKFVKRF--GDELSAVATLNVP-NGRVWQVGLRKDGRKIWL 128
             HFFK +LP       L IP  F  ++  G      A L    + R W+V +  DG++  L
Sbjct:     5 HFFKPLLPGF--HASLTIPVAFFLKYIEGRYEQKTAKLRSDASKRTWEVKI--DGQR--L 58

Query:   129 QDGWDNFAEYHSIAVGYFLVFKYAKNSTFDVLVFDMTACEIDY 171
              DGW  FA  H + +G  +VF+   +  F V +   + C I Y
Sbjct:    59 TDGWKEFAVSHDLRIGDIVVFRQESDLAFHVTLLGPSCCGIQY 101

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

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

GO:0005634 "nucleus" evidence=ISM

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

GO:0009793 "embryo development ending in seed dormancy" evidence=IMP

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input: GSVIVG00036489001 SubName- Full=Chromosome chr3 scaffold_8, whole genome shotgun sequence; (355 aa) (Vitis vinifera)

Predicted Functional Partners:

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

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	396
cd10017	98	cd10017, B3_DNA, Plant-specific B3-DNA binding dom	1e-19
pfam02362	97	pfam02362, B3, B3 DNA binding domain	6e-18
smart01019	96	smart01019, B3, B3 DNA binding domain	2e-16
cd10017	98	cd10017, B3_DNA, Plant-specific B3-DNA binding dom	9e-14
pfam02362	97	pfam02362, B3, B3 DNA binding domain	5e-10
smart01019	96	smart01019, B3, B3 DNA binding domain	7e-10

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

 Score = 82.4 bits (204), Expect = 1e-19
 Identities = 34/97 (35%), Positives = 48/97 (49%), Gaps = 5/97 (5%)

Query: 72  HFFKVILPSTV-QEKKLRIPRKFVKRFGDE-LSAVATLNVPNGRVWQVGLRKDG--RKIW 127
            FFKV+ PS V    +L +P+KF K           TL  P+G+ W V L+K     ++ 
Sbjct: 2   LFFKVLTPSDVSSLGRLVLPKKFAKAHLPPKEGVEVTLEDPDGKKWTVKLKKRKNSGRMV 61

Query: 128 LQDGWDNFAEYHSIAVGYFLVFKY-AKNSTFDVLVFD 163
           L  GW  F   + +  G FLVF+   +NS F V +F 
Sbjct: 62  LSGGWKEFVRANGLKEGDFLVFELDGRNSKFKVRIFR 98

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

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

 Score = 78.1 bits (193), Expect = 6e-18
 Identities = 34/95 (35%), Positives = 49/95 (51%), Gaps = 4/95 (4%)

Query: 73  FFKVILPSTVQEK-KLRIPRKFVKRFG-DELSAVATLNVPNGRVWQVGLR--KDGRKIWL 128
           F KV+ PS V +  +L +P+KF +  G ++     TL  P+G+ W V LR  K GR+  L
Sbjct: 1   FVKVLTPSDVSKDGRLVLPKKFAEENGLNKKGQEITLLDPDGKSWTVKLRYRKSGRRYLL 60

Query: 129 QDGWDNFAEYHSIAVGYFLVFKYAKNSTFDVLVFD 163
             GW  F + + +  G  LVFK      F V +F 
Sbjct: 61  TSGWKEFVKANGLKAGDSLVFKLDGGGKFVVGIFR 95

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

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

 Score = 73.5 bits (181), Expect = 2e-16
 Identities = 29/95 (30%), Positives = 45/95 (47%), Gaps = 4/95 (4%)

Query: 73  FFKVILPSTVQEK-KLRIPRKFVKRFGDELSAV-ATLNVPNGRVWQVGLRKDGRK--IWL 128
           FFK +  S V +  +L +P++F +  G  L     TL  P+G+ W+V L+  G      L
Sbjct: 1   FFKTLTTSDVSKHGRLVLPKQFAESNGPPLKPKEITLLDPDGKSWKVKLKYRGSSGMFLL 60

Query: 129 QDGWDNFAEYHSIAVGYFLVFKYAKNSTFDVLVFD 163
             GW  F + + +  G  L F+   N  F V +F 
Sbjct: 61  TGGWKEFVKANGLKAGDSLTFELDGNGEFVVSIFR 95

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

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

 Score = 66.2 bits (162), Expect = 9e-14
 Identities = 34/103 (33%), Positives = 47/103 (45%), Gaps = 11/103 (10%)

Query: 294 RLFKPQNPSFVDILRSKKRYSYMYVPSKFSKKHLI-RGTRSIKLQDSDGKEWPAQLTWSS 352
             FK   PS V  L        + +P KF+K HL  +    + L+D DGK+W  +L    
Sbjct: 2   LFFKVLTPSDVSSL------GRLVLPKKFAKAHLPPKEGVEVTLEDPDGKKWTVKLKKRK 55

Query: 353 GCG---IKGGWPAFSKYKNLKQGHVCVFELIKAKDILLKVSIH 392
             G   + GGW  F +   LK+G   VFEL   ++   KV I 
Sbjct: 56  NSGRMVLSGGWKEFVRANGLKEGDFLVFELDG-RNSKFKVRIF 97

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

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

 Score = 55.8 bits (135), Expect = 5e-10
 Identities = 27/98 (27%), Positives = 43/98 (43%), Gaps = 10/98 (10%)

Query: 296 FKPQNPSFVDILRSKKRYSYMYVPSKFSKKH-LIRGTRSIKLQDSDGKEWPAQLTW--SS 352
            K   PS V       +   + +P KF++++ L +  + I L D DGK W  +L +  S 
Sbjct: 2   VKVLTPSDVS------KDGRLVLPKKFAEENGLNKKGQEITLLDPDGKSWTVKLRYRKSG 55

Query: 353 GCGI-KGGWPAFSKYKNLKQGHVCVFELIKAKDILLKV 389
              +   GW  F K   LK G   VF+L      ++ +
Sbjct: 56  RRYLLTSGWKEFVKANGLKAGDSLVFKLDGGGKFVVGI 93

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

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

 Score = 55.4 bits (134), Expect = 7e-10
 Identities = 22/83 (26%), Positives = 37/83 (44%), Gaps = 4/83 (4%)

Query: 312 RYSYMYVPSKFSKKHLI-RGTRSIKLQDSDGKEWPAQLT-WSSGC--GIKGGWPAFSKYK 367
           ++  + +P +F++ +      + I L D DGK W  +L    S     + GGW  F K  
Sbjct: 12  KHGRLVLPKQFAESNGPPLKPKEITLLDPDGKSWKVKLKYRGSSGMFLLTGGWKEFVKAN 71

Query: 368 NLKQGHVCVFELIKAKDILLKVS 390
            LK G    FEL    + ++ + 
Sbjct: 72  GLKAGDSLTFELDGNGEFVVSIF 94

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	396
PF02362	100	B3: B3 DNA binding domain; InterPro: IPR003340 Two	99.84
PF02362	100	B3: B3 DNA binding domain; InterPro: IPR003340 Two	99.84
PF03754	114	DUF313: Domain of unknown function (DUF313) ; Inte	93.39
PF03754	114	DUF313: Domain of unknown function (DUF313) ; Inte	92.48

>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=99.84  E-value=7.6e-21  Score=156.16  Aligned_cols=93  Identities=37%  Similarity=0.732  Sum_probs=68.8

Q ss_pred             EEEEcccccce--eEEEeCHHHHHhhcCC--CCeeEEEEcCCCCEEEEEEEee---cceEeCcCchhhhcccCCCCCCEE
Q 043499          303 FVDILRSKKRY--SYMYVPSKFSKKHLIR--GTRSIKLQDSDGKEWPAQLTWS---SGCGIKGGWPAFSKYKNLKQGHVC  375 (396)
Q Consensus       303 F~~~m~~s~v~--~~L~IP~~F~~~~l~~--~~~~i~L~~~~G~~W~v~l~~~---~~~~~~~GW~~F~~~N~L~~GD~c  375 (396)
                      |+++|.++++.  +.|.||++|+++|...  .+.+|+|+|++|+.|+|++...   ..+.|++||.+||++|+|++||+|
T Consensus         1 F~K~l~~s~~~~~~~l~iP~~f~~~~~~~~~~~~~v~l~~~~g~~W~v~~~~~~~~~~~~l~~GW~~Fv~~n~L~~GD~~   80 (100)
T PF02362_consen    1 FFKVLKPSDVSSSCRLIIPKEFAKKHGGNKRKSREVTLKDPDGRSWPVKLKYRKNSGRYYLTGGWKKFVRDNGLKEGDVC   80 (100)
T ss_dssp             EEEE--TTCCCCTT-EEE-HHHHTTTS--SS--CEEEEEETTTEEEEEEEEEECCTTEEEEETTHHHHHHHCT--TT-EE
T ss_pred             CEEEEEccCcCCCCEEEeCHHHHHHhCCCcCCCeEEEEEeCCCCEEEEEEEEEccCCeEEECCCHHHHHHHcCCCCCCEE
Confidence            78888888776  7899999999999633  5679999999999999999532   247899999999999999999999


Q ss_pred             EEEEeeCcccEEEEEEEecC
Q 043499          376 VFELIKAKDILLKVSIHASS  395 (396)
Q Consensus       376 vFeli~~~~~~~~VhI~r~~  395 (396)
                      +|+++++....+.|||||+.
T Consensus        81 ~F~~~~~~~~~~~v~i~~~~  100 (100)
T PF02362_consen   81 VFELIGNSNFTLKVHIFRKS  100 (100)
T ss_dssp             EEEE-SSSCE-EEEEEE---
T ss_pred             EEEEecCCCceEEEEEEECc
Confidence            99999877678899999974

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.

>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=99.84  E-value=1.6e-20  Score=154.20  Aligned_cols=93  Identities=39%  Similarity=0.720  Sum_probs=70.4

Q ss_pred             EEEEccCCCCcc-ceeecChHHHHHhCCC--CCceEEEEcCCCCEEEEEE--EEECCeEEecccHHHHHhHcCCCCCCEE
Q 043499           73 FFKVILPSTVQE-KKLRIPRKFVKRFGDE--LSAVATLNVPNGRVWQVGL--RKDGRKIWLQDGWDNFAEYHSIAVGYFL  147 (396)
Q Consensus        73 F~kv~~~~~~~~-~~L~IP~~F~~~~~~~--~~~~v~L~~p~G~~W~V~l--~~~~~~~~~~~GW~~F~~~~~L~~GD~l  147 (396)
                      |+|+|++++... ..|.||..|++.|...  .+..|+|++++|+.|.|.+  .+.++.++|++||++||++|+|++||+|
T Consensus         1 F~K~l~~s~~~~~~~l~iP~~f~~~~~~~~~~~~~v~l~~~~g~~W~v~~~~~~~~~~~~l~~GW~~Fv~~n~L~~GD~~   80 (100)
T PF02362_consen    1 FFKVLKPSDVSSSCRLIIPKEFAKKHGGNKRKSREVTLKDPDGRSWPVKLKYRKNSGRYYLTGGWKKFVRDNGLKEGDVC   80 (100)
T ss_dssp             EEEE--TTCCCCTT-EEE-HHHHTTTS--SS--CEEEEEETTTEEEEEEEEEECCTTEEEEETTHHHHHHHCT--TT-EE
T ss_pred             CEEEEEccCcCCCCEEEeCHHHHHHhCCCcCCCeEEEEEeCCCCEEEEEEEEEccCCeEEECCCHHHHHHHcCCCCCCEE
Confidence            899998876544 6899999999999754  5779999999999999999  4556788999999999999999999999


Q ss_pred             EEEEccCceE--EEEEEcCC
Q 043499          148 VFKYAKNSTF--DVLVFDMT  165 (396)
Q Consensus       148 vF~~~g~~~F--~V~If~~s  165 (396)
                      +|++++++.|  .|+||+.|
T Consensus        81 ~F~~~~~~~~~~~v~i~~~~  100 (100)
T PF02362_consen   81 VFELIGNSNFTLKVHIFRKS  100 (100)
T ss_dssp             EEEE-SSSCE-EEEEEE---
T ss_pred             EEEEecCCCceEEEEEEECc
Confidence            9999997766  99999864

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

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

Probab=93.39  E-value=0.36  Score=40.83  Aligned_cols=67  Identities=21%  Similarity=0.328  Sum_probs=45.6

Q ss_pred             cEEEEccCCCCcc--ceeecChHHHHH--------------h----CCCCCceEEEEcCCCCEEEEEEEEECC-----eE
Q 043499           72 HFFKVILPSTVQE--KKLRIPRKFVKR--------------F----GDELSAVATLNVPNGRVWQVGLRKDGR-----KI  126 (396)
Q Consensus        72 ~F~kv~~~~~~~~--~~L~IP~~F~~~--------------~----~~~~~~~v~L~~p~G~~W~V~l~~~~~-----~~  126 (396)
                      .+-|.+..+.+..  .+|.||-.=+..              .    .....-.|+|.+|+++.|.+.+++..-     .+
T Consensus        23 i~~K~L~~tDv~~~qsRLsmP~~qi~~~dFLt~eE~~~i~~~~~~~~~~~Gv~V~lvdp~~~~~~m~lkkW~mg~~~~~Y  102 (114)
T PF03754_consen   23 IIEKTLFKTDVDPHQSRLSMPFNQIIDNDFLTEEEKRIIKEEKKNNDKKKGVEVILVDPSLRKWTMRLKKWNMGNGTSNY  102 (114)
T ss_pred             EEeeeecccCCCCCCceeeccHHHhcccccCCHHHHHHHHHhhccCcccCCceEEEECCcCcEEEEEEEEecccCCceEE
Confidence            4555566655533  567777553311              0    123345799999999999999998643     56


Q ss_pred             EecccHHHHHhH
Q 043499          127 WLQDGWDNFAEY  138 (396)
Q Consensus       127 ~~~~GW~~F~~~  138 (396)
                      .|..||.++|.+
T Consensus       103 vL~~gWn~VV~~  114 (114)
T PF03754_consen  103 VLNSGWNKVVED  114 (114)
T ss_pred             EEEcChHhhccC
Confidence            799999999864

>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=92.48  E-value=0.46  Score=40.19  Aligned_cols=65  Identities=17%  Similarity=0.303  Sum_probs=47.2

Q ss_pred             EEEEEcccccce---eEEEeCHHHHHhh--cC----------------CCCeeEEEEcCCCCEEEEEEE-eec-----ce
Q 043499          302 SFVDILRSKKRY---SYMYVPSKFSKKH--LI----------------RGTRSIKLQDSDGKEWPAQLT-WSS-----GC  354 (396)
Q Consensus       302 ~F~~~m~~s~v~---~~L~IP~~F~~~~--l~----------------~~~~~i~L~~~~G~~W~v~l~-~~~-----~~  354 (396)
                      .+.+.|.+|+|.   .+|.||-.=+..+  |.                ...-.++|.|+.++.|.+++. |..     .|
T Consensus        23 i~~K~L~~tDv~~~qsRLsmP~~qi~~~dFLt~eE~~~i~~~~~~~~~~~Gv~V~lvdp~~~~~~m~lkkW~mg~~~~~Y  102 (114)
T PF03754_consen   23 IIEKTLFKTDVDPHQSRLSMPFNQIIDNDFLTEEEKRIIKEEKKNNDKKKGVEVILVDPSLRKWTMRLKKWNMGNGTSNY  102 (114)
T ss_pred             EEeeeecccCCCCCCceeeccHHHhcccccCCHHHHHHHHHhhccCcccCCceEEEECCcCcEEEEEEEEecccCCceEE
Confidence            355688888887   8899997755222  11                122478999999999999986 322     37


Q ss_pred             EeCcCchhhhcc
Q 043499          355 GIKGGWPAFSKY  366 (396)
Q Consensus       355 ~~~~GW~~F~~~  366 (396)
                      .|..||.+++.+
T Consensus       103 vL~~gWn~VV~~  114 (114)
T PF03754_consen  103 VLNSGWNKVVED  114 (114)
T ss_pred             EEEcChHhhccC
Confidence            899999998864

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	396
4i1k_A	146	Crystal Structure Of Vrn1 (residues 208-341) Length		8e-16
1yel_A	104	Structure Of The Hypothetical Arabidopsis Thaliana		2e-07

>pdb|4I1K|A Chain A, Crystal Structure Of Vrn1 (residues 208-341) Length = 146

Iteration: 1
 Score = 81.3 bits (199), Expect = 8e-16,   Method: Compositional matrix adjust.
 Identities = 45/125 (36%), Positives = 72/125 (57%), Gaps = 4/125 (3%)
Query: 275 SEGHRYLSVEERQSLVTAVRLFKPQNPSFVDILRSKKRY--SYMYVPSKFSKKHLIRGTR 332
           S   R ++ EER+  + A + F+P NP F  +LR    Y    MY+PS F++K+L   + 
Sbjct: 21  SARKRTVTAEERERAINAAKTFEPTNPFFRVVLRPSYLYRGCIMYLPSGFAEKYLSGISG 80
Query: 333 SIKLQDSDGKEWPAQLTWSSG-CGIKGGWPAFSKYKNLKQGHVCVFELIKAKDILLKVSI 391
            IK+Q ++ K+WP +  + +G      GW  F+   NL +G VCVFEL++ +D +LKV+ 
Sbjct: 81  FIKVQLAE-KQWPVRCLYKAGRAKFSQGWYEFTLENNLGEGDVCVFELLRTRDFVLKVTA 139
Query: 392 HASSE 396
              +E
Sbjct: 140 FRVNE 144

>pdb|1YEL|A Chain A, Structure Of The Hypothetical Arabidopsis Thaliana Protein At1g16640.1 Length = 104

Iteration: 1
 Score = 53.5 bits (127), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 27/83 (32%), Positives = 44/83 (53%)
Query: 85  KKLRIPRKFVKRFGDELSAVATLNVPNGRVWQVGLRKDGRKIWLQDGWDNFAEYHSIAVG 144
           K L IP  F + F         L   +GR W V ++K G K++L  GW+NF + +++  G
Sbjct: 22  KSLEIPLGFNEYFPAPFPITVDLLDYSGRSWTVRMKKRGEKVFLTVGWENFVKDNNLEDG 81
Query: 145 YFLVFKYAKNSTFDVLVFDMTAC 167
            +L F Y ++ TF V+++    C
Sbjct: 82  KYLQFIYDRDRTFYVIIYGHNMC 104

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	396
1yel_A	104	AT1G16640; CESG, protein structure initiative, str	4e-38
1yel_A	104	AT1G16640; CESG, protein structure initiative, str	4e-13
1wid_A	130	DNA-binding protein RAV1; DNA-binding domain, stru	7e-07
3k1f_M	197	Transcription initiation factor IIB; RNA polymeras	8e-04

>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 =  132 bits (333), Expect = 4e-38
 Identities = 28/96 (29%), Positives = 47/96 (48%), Gaps = 1/96 (1%)

Query: 72  HFFKVILPSTVQEKKLRIPRKFVKRFGDELSAVATLNVPNGRVWQVGLRKDGRKIWLQDG 131
            F K  +     +  L IP  F + F         L   +GR W V ++K G K++L  G
Sbjct: 10  QFMKPFISEKSSKS-LEIPLGFNEYFPAPFPITVDLLDYSGRSWTVRMKKRGEKVFLTVG 68

Query: 132 WDNFAEYHSIAVGYFLVFKYAKNSTFDVLVFDMTAC 167
           W+NF + +++  G +L F Y ++ TF V+++    C
Sbjct: 69  WENFVKDNNLEDGKYLQFIYDRDRTFYVIIYGHNMC 104

>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 = 64.1 bits (156), Expect = 4e-13
 Identities = 20/102 (19%), Positives = 37/102 (36%), Gaps = 3/102 (2%)

Query: 295 LFKPQNPSFVDILRSKKRYSYMYVPSKFSKKHLIRGTRSIKLQDSDGKEWPAQLTWSSG- 353
           +       F+    S+K    + +P  F++        ++ L D  G+ W  ++      
Sbjct: 3   MADTGEVQFMKPFISEKSSKSLEIPLGFNEYFPAPFPITVDLLDYSGRSWTVRMKKRGEK 62

Query: 354 CGIKGGWPAFSKYKNLKQGHVCVFELIKAKDILLKVSIHASS 395
             +  GW  F K  NL+ G    F     +D    V I+  +
Sbjct: 63  VFLTVGWENFVKDNNLEDGKYLQFIYD--RDRTFYVIIYGHN 102

>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 = 47.0 bits (111), Expect = 7e-07
 Identities = 21/108 (19%), Positives = 41/108 (37%), Gaps = 12/108 (11%)

Query: 296 FKPQNPSFVDILRSK--KRYSYMYVPSKFSKKHLIRGTRS-------IKLQDSDGKEWPA 346
            +     F   +      + + + +P   ++KH    + +       +  +D +GK W  
Sbjct: 7   GRSAEALFEKAVTPSDVGKLNRLVIPKHHAEKHFPLPSSNVSVKGVLLNFEDVNGKVWRF 66

Query: 347 QLTW---SSGCGIKGGWPAFSKYKNLKQGHVCVFELIKAKDILLKVSI 391
           + ++   S    +  GW  F K KNL+ G V  F     +D  L +  
Sbjct: 67  RYSYWNSSQSYVLTKGWSRFVKEKNLRAGDVVSFSRSNGQDQQLYIGW 114

>3k1f_M Transcription initiation factor IIB; RNA polymerase II, TFIIB, transcription factor, DNA-binding, DNA-directed RNA polymerase; 4.30A {Saccharomyces cerevisiae} Length = 197

 Score = 39.3 bits (91), Expect = 8e-04
 Identities = 14/63 (22%), Positives = 21/63 (33%), Gaps = 11/63 (17%)

Query: 214 SKPEKKKIGGIKLETATNSREKKRCPTHGNEHGKLKKAAYHEVETDSSDGDQVFEEMGIF 273
           ++    K  G       N      CP       K+       VE   S+GD V    G+ 
Sbjct: 3   TRESIDKRAG---RRGPNLNIVLTCPECKVYPPKI-------VE-RFSEGDVVCALCGLV 51

Query: 274 MSE 276
           +S+
Sbjct: 52  LSD 54

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	396
4i1k_A	146	B3 domain-containing transcription factor VRN1; B3	99.97
1yel_A	104	AT1G16640; CESG, protein structure initiative, str	99.95
4i1k_A	146	B3 domain-containing transcription factor VRN1; B3	99.87
1yel_A	104	AT1G16640; CESG, protein structure initiative, str	99.87
1wid_A	130	DNA-binding protein RAV1; DNA-binding domain, stru	99.77
1wid_A	130	DNA-binding protein RAV1; DNA-binding domain, stru	99.62

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

Probab=99.97  E-value=2.3e-31  Score=233.03  Aligned_cols=124  Identities=35%  Similarity=0.643  Sum_probs=108.5

Q ss_pred             eeecC--CcccCCHHHHHHHHHHhhhcCCCCCEEEEEcccccce--eEEEeCHHHHHhhcCCCCeeEEEEcCCCCEEEEE
Q 043499          272 IFMSE--GHRYLSVEERQSLVTAVRLFKPQNPSFVDILRSKKRY--SYMYVPSKFSKKHLIRGTRSIKLQDSDGKEWPAQ  347 (396)
Q Consensus       272 ~y~~~--~~~~lt~~ek~~a~~~a~~~~s~~P~F~~~m~~s~v~--~~L~IP~~F~~~~l~~~~~~i~L~~~~G~~W~v~  347 (396)
                      +|++.  .++++|.+|+++|+++|++|+|++|+|+++|++|+++  +.|.||++|+++|||....+|+|+++ |+.|.|+
T Consensus        16 ~~~~~~~~r~~~t~~~k~~a~~~A~~~~s~~P~Fvk~l~~S~v~~~~~L~IP~~Fa~~~lp~~~~~i~L~~~-gk~W~v~   94 (146)
T 4i1k_A           16 FYESASARKRTVTAEERERAINAAKTFEPTNPFFRVVLRPSYLYRGCIMYLPSGFAEKYLSGISGFIKVQLA-EKQWPVR   94 (146)
T ss_dssp             ----------CCCHHHHHHHHHHHHHCCCSSCEEEEECCGGGSSTTCCEECCHHHHHHHCTTCCSEEEEEET-TEEEEEE
T ss_pred             hhhhhccCCCCCCHHHHHHHHHHHHHcCCCCCEEEEEECchhcCCCcEEEeCHHHHHHhCCCCCeEEEEEEC-CcEEEEE
Confidence            45543  4568999999999999999999999999999999998  58999999999999999999999998 5999999


Q ss_pred             EEeec-ceEeCcCchhhhcccCCCCCCEEEEEEeeCcccEEEEEEEecCC
Q 043499          348 LTWSS-GCGIKGGWPAFSKYKNLKQGHVCVFELIKAKDILLKVSIHASSE  396 (396)
Q Consensus       348 l~~~~-~~~~~~GW~~F~~~N~L~~GD~cvFeli~~~~~~~~VhI~r~~e  396 (396)
                      +.... .+.|++||+.||++|+|++||+|+|||++..+++|+|||||+.|
T Consensus        95 ~~~~~~~~~ls~GW~~Fv~dn~L~~GD~cvFeli~~~~~~f~V~IfR~~e  144 (146)
T 4i1k_A           95 CLYKAGRAKFSQGWYEFTLENNLGEGDVCVFELLRTRDFVLKVTAFRVNE  144 (146)
T ss_dssp             EEEETTEEEECTTHHHHHHHTTCCTTCEEEEEECSSSSCEEEEEEECCC-
T ss_pred             EEEeCCcEEECCchHHHHHHcCCCCCCEEEEEEecCCceEEEEEEEeccC
Confidence            87643 47899999999999999999999999999888899999999986

>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=99.95  E-value=2.2e-27  Score=196.34  Aligned_cols=100  Identities=29%  Similarity=0.618  Sum_probs=95.0

Q ss_pred             CCCCccEEEEccCCCCccceeecChHHHHHhCCCCCceEEEEcCCCCEEEEEEEEECCeEEecccHHHHHhHcCCCCCCE
Q 043499           67 RAETSHFFKVILPSTVQEKKLRIPRKFVKRFGDELSAVATLNVPNGRVWQVGLRKDGRKIWLQDGWDNFAEYHSIAVGYF  146 (396)
Q Consensus        67 ~~~~p~F~kv~~~~~~~~~~L~IP~~F~~~~~~~~~~~v~L~~p~G~~W~V~l~~~~~~~~~~~GW~~F~~~~~L~~GD~  146 (396)
                      .+..|+|+|+|++++ ....|.||..|+++|.+..+..|+|++++|++|.|++.+..++++|++||++||.+|+|++||+
T Consensus         5 ~~~~p~F~K~l~~~~-~~~~L~IP~~F~~~~~~~~~~~v~L~~~~G~~W~v~~~~~~~~~~l~~GW~~Fv~~~~L~~GD~   83 (104)
T 1yel_A            5 DTGEVQFMKPFISEK-SSKSLEIPLGFNEYFPAPFPITVDLLDYSGRSWTVRMKKRGEKVFLTVGWENFVKDNNLEDGKY   83 (104)
T ss_dssp             CCCCEEEEEECCHHH-HTTCEECCHHHHTTCCCCCCSEEEEEETTSCEEEEEEEEETTEEEECTTHHHHHHHHTCCTTCE
T ss_pred             CCCCCCEEEEECCCC-ccceEECCHHHHHhcCccCCCEEEEECCCCCEEEEEEEEECCcEEEccChHHHHHHcCCCCCCE
Confidence            578899999999875 3479999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEEEEccCceEEEEEEcCCCc
Q 043499          147 LVFKYAKNSTFDVLVFDMTAC  167 (396)
Q Consensus       147 lvF~~~g~~~F~V~If~~s~c  167 (396)
                      |+|+|+|++.|.|+||+.++|
T Consensus        84 lvF~~~~~~~f~V~If~~s~C  104 (104)
T 1yel_A           84 LQFIYDRDRTFYVIIYGHNMC  104 (104)
T ss_dssp             EEEEECSSSEEEEEEECSSCC
T ss_pred             EEEEEcCCCeEEEEEECCCCC
Confidence            999999999999999999998

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

Probab=99.87  E-value=4.1e-22  Score=174.28  Aligned_cols=121  Identities=17%  Similarity=0.287  Sum_probs=99.4

Q ss_pred             eEeeccceeeeccCchhhhccCCCCCCCccEEEEccCCCCcc-ceeecChHHHHHhCCCCCceEEEEcCCCCEEEEEEEE
Q 043499           43 FLIQKGLYTTVANNNVKQMAGGNRRAETSHFFKVILPSTVQE-KKLRIPRKFVKRFGDELSAVATLNVPNGRVWQVGLRK  121 (396)
Q Consensus        43 ~~~~~g~~~~~~~~~~~~ma~~~~~~~~p~F~kv~~~~~~~~-~~L~IP~~F~~~~~~~~~~~v~L~~p~G~~W~V~l~~  121 (396)
                      +|-.+.-++......++..|. .+++.+|+|+++|+++++.. ..|.||..|++.|++..+..|+|+++ |++|.|.+..
T Consensus        20 ~~~~r~~~t~~~k~~a~~~A~-~~~s~~P~Fvk~l~~S~v~~~~~L~IP~~Fa~~~lp~~~~~i~L~~~-gk~W~v~~~~   97 (146)
T 4i1k_A           20 ASARKRTVTAEERERAINAAK-TFEPTNPFFRVVLRPSYLYRGCIMYLPSGFAEKYLSGISGFIKVQLA-EKQWPVRCLY   97 (146)
T ss_dssp             ------CCCHHHHHHHHHHHH-HCCCSSCEEEEECCGGGSSTTCCEECCHHHHHHHCTTCCSEEEEEET-TEEEEEEEEE
T ss_pred             hccCCCCCCHHHHHHHHHHHH-HcCCCCCEEEEEECchhcCCCcEEEeCHHHHHHhCCCCCeEEEEEEC-CcEEEEEEEE
Confidence            333344444433444444454 57899999999999999865 47999999999999999999999998 5999999998


Q ss_pred             ECCeEEecccHHHHHhHcCCCCCCEEEEEEccCc--eEEEEEEcCC
Q 043499          122 DGRKIWLQDGWDNFAEYHSIAVGYFLVFKYAKNS--TFDVLVFDMT  165 (396)
Q Consensus       122 ~~~~~~~~~GW~~F~~~~~L~~GD~lvF~~~g~~--~F~V~If~~s  165 (396)
                      .+++.+|++||.+||.+|+|++||+|+|+|+++.  .|.|+||+..
T Consensus        98 ~~~~~~ls~GW~~Fv~dn~L~~GD~cvFeli~~~~~~f~V~IfR~~  143 (146)
T 4i1k_A           98 KAGRAKFSQGWYEFTLENNLGEGDVCVFELLRTRDFVLKVTAFRVN  143 (146)
T ss_dssp             ETTEEEECTTHHHHHHHTTCCTTCEEEEEECSSSSCEEEEEEECCC
T ss_pred             eCCcEEECCchHHHHHHcCCCCCCEEEEEEecCCceEEEEEEEecc
Confidence            8888999999999999999999999999999965  8999999874

>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=99.87  E-value=4e-22  Score=164.72  Aligned_cols=97  Identities=20%  Similarity=0.307  Sum_probs=87.1

Q ss_pred             CCCCCEEEEEcccccceeEEEeCHHHHHhhcCCCCeeEEEEcCCCCEEEEEEEeec-ceEeCcCchhhhcccCCCCCCEE
Q 043499          297 KPQNPSFVDILRSKKRYSYMYVPSKFSKKHLIRGTRSIKLQDSDGKEWPAQLTWSS-GCGIKGGWPAFSKYKNLKQGHVC  375 (396)
Q Consensus       297 ~s~~P~F~~~m~~s~v~~~L~IP~~F~~~~l~~~~~~i~L~~~~G~~W~v~l~~~~-~~~~~~GW~~F~~~N~L~~GD~c  375 (396)
                      .++.|.|.++|.+++...+|.||.+|++.|.+..+.+|+|+|++|+.|+|++.... ...|++||++||++|+|++||+|
T Consensus         5 ~~~~p~F~K~l~~~~~~~~L~IP~~F~~~~~~~~~~~v~L~~~~G~~W~v~~~~~~~~~~l~~GW~~Fv~~~~L~~GD~l   84 (104)
T 1yel_A            5 DTGEVQFMKPFISEKSSKSLEIPLGFNEYFPAPFPITVDLLDYSGRSWTVRMKKRGEKVFLTVGWENFVKDNNLEDGKYL   84 (104)
T ss_dssp             CCCCEEEEEECCHHHHTTCEECCHHHHTTCCCCCCSEEEEEETTSCEEEEEEEEETTEEEECTTHHHHHHHHTCCTTCEE
T ss_pred             CCCCCCEEEEECCCCccceEECCHHHHHhcCccCCCEEEEECCCCCEEEEEEEEECCcEEEccChHHHHHHcCCCCCCEE
Confidence            46789999999998744889999999999988888999999999999999997653 46899999999999999999999


Q ss_pred             EEEEeeCcccEEEEEEEecC
Q 043499          376 VFELIKAKDILLKVSIHASS  395 (396)
Q Consensus       376 vFeli~~~~~~~~VhI~r~~  395 (396)
                      +|+|+++.  .|+|+||+.+
T Consensus        85 vF~~~~~~--~f~V~If~~s  102 (104)
T 1yel_A           85 QFIYDRDR--TFYVIIYGHN  102 (104)
T ss_dssp             EEEECSSS--EEEEEEECSS
T ss_pred             EEEEcCCC--eEEEEEECCC
Confidence            99999875  5999999864

>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=99.77  E-value=1.5e-18  Score=148.94  Aligned_cols=99  Identities=21%  Similarity=0.402  Sum_probs=85.2

Q ss_pred             CCCCCEEEEEcccccce--eEEEeCHHHHHhhcCCCC-------eeEEEEcCCCCEEEEEEEee---cceEeCcCchhhh
Q 043499          297 KPQNPSFVDILRSKKRY--SYMYVPSKFSKKHLIRGT-------RSIKLQDSDGKEWPAQLTWS---SGCGIKGGWPAFS  364 (396)
Q Consensus       297 ~s~~P~F~~~m~~s~v~--~~L~IP~~F~~~~l~~~~-------~~i~L~~~~G~~W~v~l~~~---~~~~~~~GW~~F~  364 (396)
                      .+..|+|.++|++|++.  ++|.||+.|+.+|||...       .+|+|+|.+|+.|.+++...   ..+.|++||..||
T Consensus         8 ~~~~~~F~K~Lt~SDv~~~~rL~iPk~~a~~~lP~~~~~~~~~~~~l~l~D~~Gk~W~fr~~~~~~~~~~~Lt~GW~~FV   87 (130)
T 1wid_A            8 RSAEALFEKAVTPSDVGKLNRLVIPKHHAEKHFPLPSSNVSVKGVLLNFEDVNGKVWRFRYSYWNSSQSYVLTKGWSRFV   87 (130)
T ss_dssp             CCCEEEEEEECCTTTTSSSCCEEECHHHHTTTSCCCSSCCSSCCEEEEEEETTTEEEEEEEEEETTTTEEEEESSHHHHH
T ss_pred             CCCcceEEEEEehHHcCCCCEEEeCHHHHHhhCCccccccCCCcEEEEEEeCCCCEEEEEEEEECCCCceEEcCChHHHH
Confidence            46789999999999997  789999999999998765       47899999999999998753   2478999999999


Q ss_pred             cccCCCCCCEEEEEEeeCcccEEEEEEEecC
Q 043499          365 KYKNLKQGHVCVFELIKAKDILLKVSIHASS  395 (396)
Q Consensus       365 ~~N~L~~GD~cvFeli~~~~~~~~VhI~r~~  395 (396)
                      ++|+|++||+|+|++.....-.+.|++.|+.
T Consensus        88 ~~~~L~~GD~~~F~~~~~~~~~l~I~~rr~~  118 (130)
T 1wid_A           88 KEKNLRAGDVVSFSRSNGQDQQLYIGWKSRS  118 (130)
T ss_dssp             HHTTCCTTCEEEEEECCSSSCCEEEEEECCC
T ss_pred             HHcCCCCCCEEEEEEecCCCcEEEEEEEECC
Confidence            9999999999999999865445777777754

>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=99.62  E-value=3.8e-15  Score=127.66  Aligned_cols=98  Identities=20%  Similarity=0.350  Sum_probs=83.7

Q ss_pred             CCCCccEEEEccCCCCcc-ceeecChHHHHHhCCCCC-------ceEEEEcCCCCEEEEEEEEEC--CeEEecccHHHHH
Q 043499           67 RAETSHFFKVILPSTVQE-KKLRIPRKFVKRFGDELS-------AVATLNVPNGRVWQVGLRKDG--RKIWLQDGWDNFA  136 (396)
Q Consensus        67 ~~~~p~F~kv~~~~~~~~-~~L~IP~~F~~~~~~~~~-------~~v~L~~p~G~~W~V~l~~~~--~~~~~~~GW~~F~  136 (396)
                      .+..|.|.|+|+++++.. ..|.||..|+..|++.+.       ..++|+|+.|+.|.+++....  ..++|+.||..||
T Consensus         8 ~~~~~~F~K~Lt~SDv~~~~rL~iPk~~a~~~lP~~~~~~~~~~~~l~l~D~~Gk~W~fr~~~~~~~~~~~Lt~GW~~FV   87 (130)
T 1wid_A            8 RSAEALFEKAVTPSDVGKLNRLVIPKHHAEKHFPLPSSNVSVKGVLLNFEDVNGKVWRFRYSYWNSSQSYVLTKGWSRFV   87 (130)
T ss_dssp             CCCEEEEEEECCTTTTSSSCCEEECHHHHTTTSCCCSSCCSSCCEEEEEEETTTEEEEEEEEEETTTTEEEEESSHHHHH
T ss_pred             CCCcceEEEEEehHHcCCCCEEEeCHHHHHhhCCccccccCCCcEEEEEEeCCCCEEEEEEEEECCCCceEEcCChHHHH
Confidence            466789999999999863 689999999999998665       368899999999999998763  5788999999999


Q ss_pred             hHcCCCCCCEEEEEEccC--ceEEEEEEcC
Q 043499          137 EYHSIAVGYFLVFKYAKN--STFDVLVFDM  164 (396)
Q Consensus       137 ~~~~L~~GD~lvF~~~g~--~~F~V~If~~  164 (396)
                      ++|+|++||+|+|.++.+  ..+.|.+-+.
T Consensus        88 ~~~~L~~GD~~~F~~~~~~~~~l~I~~rr~  117 (130)
T 1wid_A           88 KEKNLRAGDVVSFSRSNGQDQQLYIGWKSR  117 (130)
T ss_dssp             HHTTCCTTCEEEEEECCSSSCCEEEEEECC
T ss_pred             HHcCCCCCCEEEEEEecCCCcEEEEEEEEC
Confidence            999999999999999874  4566665544

---

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	396
d1yela1	102	b.142.1.2 (A:1-102) At1g16640 {Thale cress (Arabid	3e-32
d1yela1	102	b.142.1.2 (A:1-102) At1g16640 {Thale cress (Arabid	4e-18
d1wida_	117	b.142.1.2 (A:) DNA-binding protein RAV1 {Thale cre	8e-09
d1wida_	117	b.142.1.2 (A:) DNA-binding protein RAV1 {Thale cre	2e-05

>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 =  114 bits (288), Expect = 3e-32
 Identities = 29/96 (30%), Positives = 47/96 (48%), Gaps = 1/96 (1%)

Query: 72  HFFKVILPSTVQEKKLRIPRKFVKRFGDELSAVATLNVPNGRVWQVGLRKDGRKIWLQDG 131
            F K  +      K L IP  F + F         L   +GR W V ++K G K++L  G
Sbjct: 8   QFMKPFISEKSS-KSLEIPLGFNEYFPAPFPITVDLLDYSGRSWTVRMKKRGEKVFLTVG 66

Query: 132 WDNFAEYHSIAVGYFLVFKYAKNSTFDVLVFDMTAC 167
           W+NF + +++  G +L F Y ++ TF V+++    C
Sbjct: 67  WENFVKDNNLEDGKYLQFIYDRDRTFYVIIYGHNMC 102

>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 = 76.8 bits (189), Expect = 4e-18
 Identities = 20/98 (20%), Positives = 36/98 (36%), Gaps = 3/98 (3%)

Query: 299 QNPSFVDILRSKKRYSYMYVPSKFSKKHLIRGTRSIKLQDSDGKEWPAQLTWSSGC-GIK 357
               F+    S+K    + +P  F++        ++ L D  G+ W  ++        + 
Sbjct: 5   GEVQFMKPFISEKSSKSLEIPLGFNEYFPAPFPITVDLLDYSGRSWTVRMKKRGEKVFLT 64

Query: 358 GGWPAFSKYKNLKQGHVCVFELIKAKDILLKVSIHASS 395
            GW  F K  NL+ G    F     +D    V I+  +
Sbjct: 65  VGWENFVKDNNLEDGKYLQFIYD--RDRTFYVIIYGHN 100

>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 = 51.1 bits (122), Expect = 8e-09
 Identities = 22/107 (20%), Positives = 40/107 (37%), Gaps = 12/107 (11%)

Query: 297 KPQNPSFVDILRSK--KRYSYMYVPSKFSKKHL-------IRGTRSIKLQDSDGKEWPAQ 347
           +     F   +      + + + +P   ++KH              +  +D +GK W  +
Sbjct: 1   RSAEALFEKAVTPSDVGKLNRLVIPKHHAEKHFPLPSSNVSVKGVLLNFEDVNGKVWRFR 60

Query: 348 LT-WSSG--CGIKGGWPAFSKYKNLKQGHVCVFELIKAKDILLKVSI 391
            + W+S     +  GW  F K KNL+ G V  F     +D  L +  
Sbjct: 61  YSYWNSSQSYVLTKGWSRFVKEKNLRAGDVVSFSRSNGQDQQLYIGW 107

>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 = 41.5 bits (97), Expect = 2e-05
 Identities = 20/105 (19%), Positives = 39/105 (37%), Gaps = 10/105 (9%)

Query: 67  RAETSHFFKVILPSTVQEK-KLRIPRKFVKRFGDELSAVA-------TLNVPNGRVWQVG 118
           R+  + F K + PS V +  +L IP+   ++     S+              NG+VW+  
Sbjct: 1   RSAEALFEKAVTPSDVGKLNRLVIPKHHAEKHFPLPSSNVSVKGVLLNFEDVNGKVWRFR 60

Query: 119 L--RKDGRKIWLQDGWDNFAEYHSIAVGYFLVFKYAKNSTFDVLV 161
                  +   L  GW  F +  ++  G  + F  +      + +
Sbjct: 61  YSYWNSSQSYVLTKGWSRFVKEKNLRAGDVVSFSRSNGQDQQLYI 105

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	396
d1yela1	102	At1g16640 {Thale cress (Arabidopsis thaliana) [Tax	99.94
d1yela1	102	At1g16640 {Thale cress (Arabidopsis thaliana) [Tax	99.86
d1wida_	117	DNA-binding protein RAV1 {Thale cress (Arabidopsis	99.76
d1wida_	117	DNA-binding protein RAV1 {Thale cress (Arabidopsis	99.6
d1na6a1	175	Restriction endonuclease EcoRII, N-terminal domain	97.73
d1na6a1	175	Restriction endonuclease EcoRII, N-terminal domain	97.33

>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=99.94  E-value=2.6e-27  Score=193.38  Aligned_cols=100  Identities=29%  Similarity=0.614  Sum_probs=95.0

Q ss_pred             CCCCccEEEEccCCCCccceeecChHHHHHhCCCCCceEEEEcCCCCEEEEEEEEECCeEEecccHHHHHhHcCCCCCCE
Q 043499           67 RAETSHFFKVILPSTVQEKKLRIPRKFVKRFGDELSAVATLNVPNGRVWQVGLRKDGRKIWLQDGWDNFAEYHSIAVGYF  146 (396)
Q Consensus        67 ~~~~p~F~kv~~~~~~~~~~L~IP~~F~~~~~~~~~~~v~L~~p~G~~W~V~l~~~~~~~~~~~GW~~F~~~~~L~~GD~  146 (396)
                      +...|+|+|++++++. ...|.||..|+++|.+..+++|+|++++|+.|.|++.+.++.++|..||++||++|+|++||+
T Consensus         3 ~~~~~~Ffkv~~~~~~-~~~L~IP~~F~~~~~~~~~~~i~L~d~~G~~W~v~~~~~~~~~~~~~GW~~Fv~~n~L~~GD~   81 (102)
T d1yela1           3 DTGEVQFMKPFISEKS-SKSLEIPLGFNEYFPAPFPITVDLLDYSGRSWTVRMKKRGEKVFLTVGWENFVKDNNLEDGKY   81 (102)
T ss_dssp             CCCCEEEEEECCHHHH-TTCEECCHHHHTTCCCCCCSEEEEEETTSCEEEEEEEEETTEEEECTTHHHHHHHHTCCTTCE
T ss_pred             CCCCCeEEEEEcCccc-CCCEECCHHHHHhCCCCCCCEEEEEcCCCCEEEEEEEEeCCeEEEccCHHHHHHHcCCCcCCE
Confidence            5678999999999754 368999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEEEEccCceEEEEEEcCCCc
Q 043499          147 LVFKYAKNSTFDVLVFDMTAC  167 (396)
Q Consensus       147 lvF~~~g~~~F~V~If~~s~c  167 (396)
                      |+|+|+|++.|.|+||+.++|
T Consensus        82 ~vF~~~~~~~f~V~If~~s~C  102 (102)
T d1yela1          82 LQFIYDRDRTFYVIIYGHNMC  102 (102)
T ss_dssp             EEEEECSSSEEEEEEECSSCC
T ss_pred             EEEEEcCCcEEEEEEeCCCCC
Confidence            999999999999999999998

>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=99.86  E-value=7.4e-22  Score=160.66  Aligned_cols=97  Identities=20%  Similarity=0.307  Sum_probs=86.6

Q ss_pred             CCCCCEEEEEcccccceeEEEeCHHHHHhhcCCCCeeEEEEcCCCCEEEEEEEeec-ceEeCcCchhhhcccCCCCCCEE
Q 043499          297 KPQNPSFVDILRSKKRYSYMYVPSKFSKKHLIRGTRSIKLQDSDGKEWPAQLTWSS-GCGIKGGWPAFSKYKNLKQGHVC  375 (396)
Q Consensus       297 ~s~~P~F~~~m~~s~v~~~L~IP~~F~~~~l~~~~~~i~L~~~~G~~W~v~l~~~~-~~~~~~GW~~F~~~N~L~~GD~c  375 (396)
                      .+..|.|.++|.+++....|.||..|++.|.+..+++|+|+|++|+.|+|++.... ..+|++||++||++|+|++||+|
T Consensus         3 ~~~~~~Ffkv~~~~~~~~~L~IP~~F~~~~~~~~~~~i~L~d~~G~~W~v~~~~~~~~~~~~~GW~~Fv~~n~L~~GD~~   82 (102)
T d1yela1           3 DTGEVQFMKPFISEKSSKSLEIPLGFNEYFPAPFPITVDLLDYSGRSWTVRMKKRGEKVFLTVGWENFVKDNNLEDGKYL   82 (102)
T ss_dssp             CCCCEEEEEECCHHHHTTCEECCHHHHTTCCCCCCSEEEEEETTSCEEEEEEEEETTEEEECTTHHHHHHHHTCCTTCEE
T ss_pred             CCCCCeEEEEEcCcccCCCEECCHHHHHhCCCCCCCEEEEEcCCCCEEEEEEEEeCCeEEEccCHHHHHHHcCCCcCCEE
Confidence            36788999999998766789999999999999889999999999999999987654 36789999999999999999999


Q ss_pred             EEEEeeCcccEEEEEEEecC
Q 043499          376 VFELIKAKDILLKVSIHASS  395 (396)
Q Consensus       376 vFeli~~~~~~~~VhI~r~~  395 (396)
                      +|||.+..  .|.|+||..+
T Consensus        83 vF~~~~~~--~f~V~If~~s  100 (102)
T d1yela1          83 QFIYDRDR--TFYVIIYGHN  100 (102)
T ss_dssp             EEEECSSS--EEEEEEECSS
T ss_pred             EEEEcCCc--EEEEEEeCCC
Confidence            99999965  6999999753

>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=99.76  E-value=9e-19  Score=145.47  Aligned_cols=98  Identities=22%  Similarity=0.410  Sum_probs=83.0

Q ss_pred             CCCCEEEEEcccccce--eEEEeCHHHHHhhcCCCCe-------eEEEEcCCCCEEEEEEEee-c--ceEeCcCchhhhc
Q 043499          298 PQNPSFVDILRSKKRY--SYMYVPSKFSKKHLIRGTR-------SIKLQDSDGKEWPAQLTWS-S--GCGIKGGWPAFSK  365 (396)
Q Consensus       298 s~~P~F~~~m~~s~v~--~~L~IP~~F~~~~l~~~~~-------~i~L~~~~G~~W~v~l~~~-~--~~~~~~GW~~F~~  365 (396)
                      +..|+|.++|++|++.  ++|.||+.|+.+|+|....       .|+++|.+|+.|++++... +  .+.+++||.+||+
T Consensus         2 ~~~~iF~K~Lt~sDv~~~~rL~iP~~~~~~~lp~~~~~~~~~~~~~~~~d~~g~~W~~~~~~~~~~~~~~l~~GW~~Fv~   81 (117)
T d1wida_           2 SAEALFEKAVTPSDVGKLNRLVIPKHHAEKHFPLPSSNVSVKGVLLNFEDVNGKVWRFRYSYWNSSQSYVLTKGWSRFVK   81 (117)
T ss_dssp             CCEEEEEEECCTTTTSSSCCEEECHHHHTTTSCCCSSCCSSCCEEEEEEETTTEEEEEEEEEETTTTEEEEESSHHHHHH
T ss_pred             CCceEEEEEecchhcCCCCEEEECHHHHHHhCCccccccCCCcEEEEEEeCCCCEEEEEEEEECCCCceEEecCHHHHHH
Confidence            4578999999999997  6899999999999886443       5899999999999999753 2  3678999999999


Q ss_pred             ccCCCCCCEEEEEEeeCcccEEEEEEEecC
Q 043499          366 YKNLKQGHVCVFELIKAKDILLKVSIHASS  395 (396)
Q Consensus       366 ~N~L~~GD~cvFeli~~~~~~~~VhI~r~~  395 (396)
                      +|+|++||+|+|++....+..+.|.+.|+.
T Consensus        82 ~~~Lk~GD~~~F~~~~~~~~~~~i~~r~~~  111 (117)
T d1wida_          82 EKNLRAGDVVSFSRSNGQDQQLYIGWKSRS  111 (117)
T ss_dssp             HTTCCTTCEEEEEECCSSSCCEEEEEECCC
T ss_pred             HcCCCCCCEEEEEEEeCCCCEEEEEEEECC
Confidence            999999999999998766555677666654

>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=99.60  E-value=4e-15  Score=123.10  Aligned_cols=99  Identities=19%  Similarity=0.341  Sum_probs=82.1

Q ss_pred             CCCccEEEEccCCCCcc-ceeecChHHHHHhCCCCCc-------eEEEEcCCCCEEEEEEEEE--CCeEEecccHHHHHh
Q 043499           68 AETSHFFKVILPSTVQE-KKLRIPRKFVKRFGDELSA-------VATLNVPNGRVWQVGLRKD--GRKIWLQDGWDNFAE  137 (396)
Q Consensus        68 ~~~p~F~kv~~~~~~~~-~~L~IP~~F~~~~~~~~~~-------~v~L~~p~G~~W~V~l~~~--~~~~~~~~GW~~F~~  137 (396)
                      +..+-|.|+|+++++.+ ..|.||..|++.|++.+..       .+.+.+++|+.|.+.+...  +...+|..||.+||+
T Consensus         2 ~~~~iF~K~Lt~sDv~~~~rL~iP~~~~~~~lp~~~~~~~~~~~~~~~~d~~g~~W~~~~~~~~~~~~~~l~~GW~~Fv~   81 (117)
T d1wida_           2 SAEALFEKAVTPSDVGKLNRLVIPKHHAEKHFPLPSSNVSVKGVLLNFEDVNGKVWRFRYSYWNSSQSYVLTKGWSRFVK   81 (117)
T ss_dssp             CCEEEEEEECCTTTTSSSCCEEECHHHHTTTSCCCSSCCSSCCEEEEEEETTTEEEEEEEEEETTTTEEEEESSHHHHHH
T ss_pred             CCceEEEEEecchhcCCCCEEEECHHHHHHhCCccccccCCCcEEEEEEeCCCCEEEEEEEEECCCCceEEecCHHHHHH
Confidence            34678999999999864 5899999999999876543       4899999999999999875  456789999999999


Q ss_pred             HcCCCCCCEEEEEEccC--ceEEEEEEcCCC
Q 043499          138 YHSIAVGYFLVFKYAKN--STFDVLVFDMTA  166 (396)
Q Consensus       138 ~~~L~~GD~lvF~~~g~--~~F~V~If~~s~  166 (396)
                      +|+|++||.|+|..+..  ..+.|-+...++
T Consensus        82 ~~~Lk~GD~~~F~~~~~~~~~~~i~~r~~~~  112 (117)
T d1wida_          82 EKNLRAGDVVSFSRSNGQDQQLYIGWKSRSG  112 (117)
T ss_dssp             HTTCCTTCEEEEEECCSSSCCEEEEEECCCS
T ss_pred             HcCCCCCCEEEEEEEeCCCCEEEEEEEECCC
Confidence            99999999999999853  456666655543

>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=97.73  E-value=3.9e-05  Score=65.22  Aligned_cols=95  Identities=13%  Similarity=0.072  Sum_probs=71.2

Q ss_pred             CCCCEEEEEcccccce--eE----EEeCHHHHHhhcCCCC--------eeEEEE--cCCCCEEEEEEEe-ec--------
Q 043499          298 PQNPSFVDILRSKKRY--SY----MYVPSKFSKKHLIRGT--------RSIKLQ--DSDGKEWPAQLTW-SS--------  352 (396)
Q Consensus       298 s~~P~F~~~m~~s~v~--~~----L~IP~~F~~~~l~~~~--------~~i~L~--~~~G~~W~v~l~~-~~--------  352 (396)
                      +....|.++|+++++.  ..    ++||+.++.+++|...        +.+.|.  |.+|..|.+++.+ .+        
T Consensus        13 ~~~~~F~K~LtasD~g~tg~HQaG~~IPK~~ae~~FP~l~~~~e~nP~~~l~~~i~d~~g~~w~fR~iYyn~~~~ggTRn   92 (175)
T d1na6a1          13 ENYFVYIKRLSANDTGATGGHQVGLYIPSGIVEKLFPSINHTRELNPSVFLTAHVSSHDCPDSEARAIYYNSAHFGKTRN   92 (175)
T ss_dssp             SSEEEEEEECCHHHHTCC---CCCCCCCHHHHHHHCGGGCCCSSSSCEEEEEEEESSSCCCCEEEEEEEECGGGTTSCCC
T ss_pred             CceEEEEEEcccccccccCCccceeeecHHHHHHhCCCCCcccccCCCceEEEEEecCCCCeeEEEEEEECCccCCCccc
Confidence            4456899999999997  44    9999999999977311        145555  8899999999864 21        


Q ss_pred             ceEeCcCchhhhcccCCCCCCEEEEEEeeCc--ccEEEEEEE
Q 043499          353 GCGIKGGWPAFSKYKNLKQGHVCVFELIKAK--DILLKVSIH  392 (396)
Q Consensus       353 ~~~~~~GW~~F~~~N~L~~GD~cvFeli~~~--~~~~~VhI~  392 (396)
                      -++++++|+.|...+.+..||+.+|-.....  .-.+-|+|.
T Consensus        93 eyRiT~~g~~~~~~~~~n~G~l~i~af~~~~~~~~~~~~~vw  134 (175)
T d1na6a1          93 EKRITRWGRGSPLQDPENTGALTLLAFKLDEQGGDCKEVNIW  134 (175)
T ss_dssp             EEEEECCCTTSGGGCGGGTTCEEEEEEECCTTSCCCCEEEEE
T ss_pred             cEEEEeccccccccCccccccEEEEEeecCCCCCceeEEEEE
Confidence            2789999999999999999999999886332  123445543

>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=97.33  E-value=9.2e-05  Score=62.87  Aligned_cols=83  Identities=8%  Similarity=0.008  Sum_probs=66.8

Q ss_pred             CccEEEEccCCCCcc-ce----eecChHHHHHhCCCCC-----c---eEEEE--cCCCCEEEEEEEEEC--------CeE
Q 043499           70 TSHFFKVILPSTVQE-KK----LRIPRKFVKRFGDELS-----A---VATLN--VPNGRVWQVGLRKDG--------RKI  126 (396)
Q Consensus        70 ~p~F~kv~~~~~~~~-~~----L~IP~~F~~~~~~~~~-----~---~v~L~--~p~G~~W~V~l~~~~--------~~~  126 (396)
                      ...|.|.++++.+.. ..    ++||+.++..+++.+.     +   .+.|.  +.+|..|+++....+        +..
T Consensus        15 ~~~F~K~LtasD~g~tg~HQaG~~IPK~~ae~~FP~l~~~~e~nP~~~l~~~i~d~~g~~w~fR~iYyn~~~~ggTRney   94 (175)
T d1na6a1          15 YFVYIKRLSANDTGATGGHQVGLYIPSGIVEKLFPSINHTRELNPSVFLTAHVSSHDCPDSEARAIYYNSAHFGKTRNEK   94 (175)
T ss_dssp             EEEEEEECCHHHHTCC---CCCCCCCHHHHHHHCGGGCCCSSSSCEEEEEEEESSSCCCCEEEEEEEECGGGTTSCCCEE
T ss_pred             eEEEEEEcccccccccCCccceeeecHHHHHHhCCCCCcccccCCCceEEEEEecCCCCeeEEEEEEECCccCCCccccE
Confidence            457999999876654 23    9999999999987432     1   34444  889999999998764        568


Q ss_pred             EecccHHHHHhHcCCCCCCEEEEEEc
Q 043499          127 WLQDGWDNFAEYHSIAVGYFLVFKYA  152 (396)
Q Consensus       127 ~~~~GW~~F~~~~~L~~GD~lvF~~~  152 (396)
                      .|+.+|+.|...+.+..||+++|-+.
T Consensus        95 RiT~~g~~~~~~~~~n~G~l~i~af~  120 (175)
T d1na6a1          95 RITRWGRGSPLQDPENTGALTLLAFK  120 (175)
T ss_dssp             EEECCCTTSGGGCGGGTTCEEEEEEE
T ss_pred             EEEeccccccccCccccccEEEEEee
Confidence            89999999999999999999999884