Citrus Sinensis ID: 018533

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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----
Protein Sequence
MPRPYFHKLILASTIRDKRLRIPENFVRNFKDDLSAAATLIVPNGMVSRVGLRRLDNKVWFYDGWQEFMERYFIRIGYFLVFRYEGNSAFNVYIFNLPSSEINYQPNALSNFEVPNHSKQYHIFAEMEDDDSEHVDQPTVNKTFNPPSFQNLLNSSKLSNSINGAGEANLQRLKVKLYSQDGETPKLKKPGRKRKIDPNVQASSAQEVHDGEMQFRFYESASARKRTVTAEERERAINAAKAFEPSNPFCRVVLRPSYLYKGCIMYLPSCFAEKHLNGVCGFIKLQLSDGKQWPVRCLYRGGRAKFSQGWYEFTVENRLGEGDVCVFEVLRAREFVLKVTVFRVSESAGFMSRH
Secondary Structure (PSIPRED)
cccccEEEEEcccccccccccccHHHHHHccccccccEEEEcccccEEEEEEEEEccEEEEcccHHHHHHHHccccccEEEEEEccccEEEEEEEccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHccccccccccccccccccccccccccccccccccccccEEEEcccccccccccHHHHHHHHHHHHHccccccEEEEEcccccccccccccccHHHHHHcccccccEEEEEEccccEEEEEEEEEccEEEEcccHHHHHHHcccccccEEEEEEEEccEEEEEEEEEEEcccccccccc
Secondary Structure Prediction (SSPRO)
cccccEEEEEccccccccccEccHHHHHHHccccccEEEEEcccccEEEEEEEEcccEEEEcccHHHHHHHcccccccEEEEEEcccEEEEEEEEcccccEEEccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEcccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHccccccEEEEEEEccccccccEEEEcHHHHHHHccccccEEEEEcccccEEEEEEEEccccEEEcccHHHHHHHcccccccEEEEEEEcccEEEEEEEEEEEcccccccccc
Coil and Loop (DISEMBL)
MPRPYFHKLILASTirdkrlripenfVRNFKDDLSAAATlivpngmvsrvglrrldnkvwfYDGWQEFMERYFIRIGYFLVFRYEGNSAFNVYIFnlpsseinyqpnalsnfevpnhskqyhifaemedddsehvdqptvnktfnppsfqnllnssklsnsingAGEANLQRLKVKLYsqdgetpklkkpgrkrkidpnvqassaqevhdgemqFRFYESASARKRTVTAEERERAINAakafepsnpfcrvvlrpsylykgcimylpscfaekhlnGVCGFIklqlsdgkqwpvrclyrggrakfsqgWYEFTVenrlgegdvcVFEVLRAREFVLKVTVFRvsesagfmsrh
Flexible Loop (DISEMBL)
mprpyfhklilastirdkrlriPENFVRNFKDdlsaaatlivpngmvsrvglrrldnKVWFYDGWQEFMERYFIRIGYFLVFRYEGNSAFNVYIFNLPSSEINYQPNALSNFEVPNHSKQYHIFAEMEDDDSEHVDQPTVNKTFNPPSFQNLLNSSKLSNSINGAGEANLQRLKVKLYSqdgetpklkkpgrkrkidpnvqassaqevhdgemQFRFYESASARKRTVTAEERERAInaakafepsnpfcrVVLRPSYLYKGCIMYLPSCFAEKHLNGVCGFIKLQLSDGKQWPVRCLYRGGRAKFSQGWYEFTVENRLGEGDVCVFEVLRAREFVLKVTVfrvsesagfmsrh
Low Complexity Region (SEG)
MPRPYFHKLILASTIRDKRLRIPENFVRNFKDDLSAAATLIVPNGMVSRVGLRRLDNKVWFYDGWQEFMERYFIRIGYFLVFRYEGNSAFNVYIFNLPSSEINYQPNALSNFEVPNHSKQYHIFAEMEDDDSEHVDQPTVNKTFNPPSFQnllnssklsnsinGAGEANLQRLKVKLYSQDGETPKLKKPGRKRKIDPNVQASSAQEVHDGEMQFRFYESASARKRTVTAEERERAINAAKAFEPSNPFCRVVLRPSYLYKGCIMYLPSCFAEKHLNGVCGFIKLQLSDGKQWPVRCLYRGGRAKFSQGWYEFTVENRLGEGDVCVFEVLRAREFVLKVTVFRVSESAGFMSRH
Disordered region (IsUnstruct)
****YFHKLILASTIRDKRLRIPENFVRNFKDDLSAAATLIVPNGMVSRVGLRRLDNKVWFYDGWQEFMERYFIRIGYFLVFRYEGNSAFNVYIFNLPSSEINYQPNALSNFEV*****QYHIF**********************************************************************************************************************FEPSNPFCRVVLRPSYLYKGCIMYLPSCFAEKHLNGVCGFIKLQLSDGKQWPVRCLYRGGRAKFSQGWYEFTVENRLGEGDVCVFEVLRAREFVLKVTVFRVS*********
Disordered Region (DISOPRED)
*PRPYFHKLILASTIRDKRLRIPENFVRNFKDDLSAAATLIVPNGMVSRVGLRRLDNKVWFYDGWQEFMERYFIRIGYFLVFRYEGNSAFNVYIFNLPSSEINYQPNALSNFE***************************NKTFNPPSFQNLLNSSKLSNSINGAGEANLQRLKVKLYSQDGETPKLKKPGRKRKIDPNVQASSAQEVHDGEMQFRFYESASARKRTVTAEERERAINAAKAFEPSNPFCRVVLRPSYLYKGCIMYLPSCFAEKHLNGVCGFIKLQLSDGKQWPVRCLYRGGRAKFSQGWYEFTVENRLGEGDVCVFEVLRAREFVLKVTVF************
Disordered Region (DISEMBL)
MPRPYFHKLILASTIRDKRLRIPENFVRNFKDDLSAAATLIVPNGMVSRVGLRRLDNKVWFYDGWQEFMERYFIRIGYFLVFRYEGNSAFNVYIFNLPSSEINYQPNALSNFEVPNHSKQYHIFAEMEDDDSEHVDQPTVNKTFNPPSFQNLLNSSKLSNSINGAGEANLQRLKVKLYSQDGETPKLKKPGRKRKIDPNVQASSAQEVHDGEMQFRFYESA***********RERAINAAKAFEPSNPFCRVVLRPSYLYKGCIMYLPSCFAEKHLNGVCGFIKLQLSDGKQWPVRCLYRGGRAKFSQGWYEFTVENRLGEGDVCVFEVLRAREFVLKVTVFRVSE********
Disordered Region (DISPRO)
**RPYFHKLILASTIRDKRLRIPENFVRNFKDDLSAAATLIVPNGMVSRVGLRRLDNKVWFYDGWQEFMERYFIRIGYFLVFRYEGNSAFNVYIFNLPSSEINYQPNA***********************************************************************************************************************VTAEERERAINAAKAFEPSNPFCRVVLRPSYLYKGCIMYLPSCFAEKHLNGVCGFIKLQLSDGKQWPVRCLYRGGRAKFSQGWYEFTVENRLGEGDVCVFEVLRAREFVLKVTVFRVSE********
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MPRPYFHKLILASTIRDKRLRIPENFVRNFKDDLSAAATLIVPNGMVSRVGLRRLDNKVWFYDGWQEFMERYFIRIGYFLVFRYEGNSAFNVYIFNLPSSEINYQPNALSNFEVPNHSKQYHIFAEMEDDDSEHVDQPTVNKTFNPPSFQNLLNSSKLSNSINGAGEANLQRLKVKLYSQDGETPKLKKPGRKRKIDPNVQASSAQEVHDGEMQFRFYESASARKRTVTAEERERAINAAKAFEPSNPFCRVVLRPSYLYKGCIMYLPSCFAEKHLNGVCGFIKLQLSDGKQWPVRCLYRGGRAKFSQGWYEFTVENRLGEGDVCVFEVLRAREFVLKVTVFRVSESAGFMSRH
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	354	2.2.26 [Sep-21-2011]
Q8L3W1	341	B3 domain-containing tran	yes	no	0.946	0.982	0.605	1e-114
Q9XIB5	226	B3 domain-containing prot	no	no	0.468	0.734	0.719	1e-63
Q8S2E6	402	B3 domain-containing prot	yes	no	0.960	0.845	0.276	7e-24
Q2R9D2	406	B3 domain-containing prot	yes	no	0.929	0.810	0.239	2e-20
Q9ZSH7	190	B3 domain-containing prot	no	no	0.305	0.568	0.425	3e-20
Q84R27	209	B3 domain-containing prot	no	no	0.293	0.497	0.407	4e-19
Q9XIB4	190	B3 domain-containing prot	no	no	0.367	0.684	0.390	3e-17
Q2QMT2	358	B3 domain-containing prot	no	no	0.836	0.826	0.241	1e-14
Q10GM3	378	B3 domain-containing prot	no	no	0.802	0.751	0.263	1e-12
Q851V5	1029	Putative B3 domain-contai	no	no	0.731	0.251	0.240	1e-12

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

 Score =  412 bits (1060), Expect = e-114,   Method: Compositional matrix adjust.
 Identities = 212/350 (60%), Positives = 260/350 (74%), Gaps = 15/350 (4%)

Query: 1   MPRPYFHKLILASTIRDKRLRIPENFVRNFKDDLSAAATLIVPNGMVSRVGLRRLDNKVW 60
           MPRP+FHKLI +STI++KRLR+P+ FV  FKD+LS A  L VP+G V RVGLR+ DNK+W
Sbjct: 1   MPRPFFHKLIFSSTIQEKRLRVPDKFVSKFKDELSVAVALTVPDGHVWRVGLRKADNKIW 60

Query: 61  FYDGWQEFMERYFIRIGYFLVFRYEGNSAFNVYIFNLPSSEINYQPNALSNFEVPNHSKQ 120
           F DGWQEF++RY IRIGY L+FRYEGNSAF+VYIFNL  SEINY    L +    NH K+
Sbjct: 61  FQDGWQEFVDRYSIRIGYLLIFRYEGNSAFSVYIFNLSHSEINYHSTGLMD-SAHNHFKR 119

Query: 121 YHIFAEMEDDDSEHVDQPTVNKTFNPPSFQNLLNSSKLSNSINGAGEANLQRLKVKLYSQ 180
             +F ++ED+D+E +   +V   +  P  ++ + ++K      G   + +Q L       
Sbjct: 120 ARLFEDLEDEDAEVIFPSSV---YPSPLPESTVPANK------GYASSAIQTLFTGPVKA 170

Query: 181 DGETPKLKKP---GRKRK-IDPNVQASSAQEVHDGEMQFRFYESASARKRTVTAEERERA 236
           +  TP  K P   GRK+K  DP    SSA    D E + +FYESASARKRTVTAEERERA
Sbjct: 171 EEPTPTPKIPKKRGRKKKNADPEEINSSAPRDDDPENRSKFYESASARKRTVTAEERERA 230

Query: 237 INAAKAFEPSNPFCRVVLRPSYLYKGCIMYLPSCFAEKHLNGVCGFIKLQLSDGKQWPVR 296
           INAAK FEP+NPF RVVLRPSYLY+GCIMYLPS FAEK+L+G+ GFIK+QL++ KQWPVR
Sbjct: 231 INAAKTFEPTNPFFRVVLRPSYLYRGCIMYLPSGFAEKYLSGISGFIKVQLAE-KQWPVR 289

Query: 297 CLYRGGRAKFSQGWYEFTVENRLGEGDVCVFEVLRAREFVLKVTVFRVSE 346
           CLY+ GRAKFSQGWYEFT+EN LGEGDVCVFE+LR R+FVLKVT FRV+E
Sbjct: 290 CLYKAGRAKFSQGWYEFTLENNLGEGDVCVFELLRTRDFVLKVTAFRVNE 339

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

 Score =  243 bits (621), Expect = 1e-63,   Method: Compositional matrix adjust.
 Identities = 123/171 (71%), Positives = 144/171 (84%), Gaps = 5/171 (2%)

Query: 179 SQDGETPK-LKKPGRKRKIDPNVQA--SSAQEVHDGEMQFRFYESASARKRTVTAEERER 235
           S+  ETPK LKK GRK+K +PN +   SS     D E + +FYESASARKRTVTAEERER
Sbjct: 56  SKAEETPKVLKKRGRKKK-NPNPEEVNSSTPGGDDSENRSKFYESASARKRTVTAEERER 114

Query: 236 AINAAKAFEPSNPFCRVVLRPSYLYKGCIMYLPSCFAEKHLNGVCGFIKLQLSDGKQWPV 295
           A+NAAK FEP+NP+ RVVLRPSYLY+GCIMYLPS FAEK+L+G+ GFIKLQL + KQWPV
Sbjct: 115 AVNAAKTFEPTNPYFRVVLRPSYLYRGCIMYLPSGFAEKYLSGISGFIKLQLGE-KQWPV 173

Query: 296 RCLYRGGRAKFSQGWYEFTVENRLGEGDVCVFEVLRAREFVLKVTVFRVSE 346
           RCLY+ GRAKFSQGWYEFT+EN +GEGDVCVFE+LR R+FVL+VT FRV+E
Sbjct: 174 RCLYKAGRAKFSQGWYEFTLENNIGEGDVCVFELLRTRDFVLEVTAFRVNE 224

Arabidopsis thaliana (taxid: 3702)

>sp|Q8S2E6|Y1235_ORYSJ B3 domain-containing protein Os01g0723500 OS=Oryza sativa subsp. japonica GN=Os01g0723500 PE=2 SV=1

 Score =  111 bits (278), Expect = 7e-24,   Method: Compositional matrix adjust.
 Identities = 103/373 (27%), Positives = 158/373 (42%), Gaps = 33/373 (8%)

Query: 3   RPYFHKLILASTIRDKRLRIPENFVRNFK----------DDLSAAATLIVPNGMVSRVGL 52
           RP+F K+++      +RL+IP NF ++             + S AATL  P+G    V +
Sbjct: 18  RPHFFKVLVGDF--KQRLKIPPNFCKHIPWEESRKAKGLKEASMAATLEGPSGRTWLVVI 75

Query: 53  RRLDNKVWFYDGWQEFMERYFIRIGYFLVFRYEGNSAFNVYIFNLPSSEINYQPNALSNF 112
           RR     +F  GW +F++   +R   F+VFRY+GN+ F   +F+  + E           
Sbjct: 76  RRTAEGTFFTSGWPKFVQDQALRELEFVVFRYDGNTRFTAMVFDRTACEREDLMGGGGGD 135

Query: 113 EVPNHSKQYHIFAEMED---DDSEHVDQPTVNKTFNPPSFQNL--LNSSKLSNSINGA-- 165
                  +    A   D      + V +  V    +P   Q L  ++SS      + A  
Sbjct: 136 RPRKKRGRPRTAAASRDAARPKKDSVGKEMVTYRASPSGGQPLQIVDSSWTPEPGSTAVK 195

Query: 166 GEANLQRLKVKLYSQDGETPKLKKPGRKRKIDPNVQ---ASSAQEVHDG------EMQFR 216
            E +   L V        +P    P      D       A+  + + D           R
Sbjct: 196 NEEDADELPVCELPASSASPPRHVPEGALDADGGAARRGAAKTRSLQDDLALASIPPSIR 255

Query: 217 FYESASARKRTVTAEERERAINAAKAFEPSNPFCRVVLRPSYLYKGCIMYLPSCFAEKHL 276
            Y+   +R+R V   ER+RA   A AF    P+C + +   ++Y   +M  P+ F+ +HL
Sbjct: 256 RYKGYVSRRRAVATAERQRATEIAHAFRSPLPYCVIRMSTMHVYYSFMMRFPTGFSRQHL 315

Query: 277 NGVCGFIKLQLSDGKQWPVRCLY-RGGRAKFSQGWYEFTVENRLGEGDVCVFEVLRAREF 335
                 + L+   GK W V  LY    R + S+GW  F   N L EGD CVFE++ A EF
Sbjct: 316 PRERTDVVLRDPGGKVWSV--LYIPNTRDRLSRGWCAFARGNCLEEGDYCVFELVAAAEF 373

Query: 336 VLKVTVFRVSESA 348
             +V +FRV E A
Sbjct: 374 --RVHIFRVVEPA 384

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 =  100 bits (248), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 90/376 (23%), Positives = 156/376 (41%), Gaps = 47/376 (12%)

Query: 3   RPYFHKLILASTIRDKRLRIPENFVRNFKDDLSAAATLIVPNGMVSRVGLRRLDNKVWFY 62
           R +F  L+   ++  +R++IP +F +  ++  +   +L+  +G      L       +F 
Sbjct: 30  RSFFRVLLTLQSL--ERMKIPSSFNQCLQNQPTGMVSLVDRSGNKWSAELTSDSEGFFFV 87

Query: 63  DGWQEFMERYFIRIGYFLVFRYEGNSAFNVYIFNLPSSEINYQPNALSNFEVPNHSKQYH 122
            GW+EF+    I+ G FLVF Y+  S F+V +F         +P+ +      +     +
Sbjct: 88  HGWKEFVRDNSIQCGQFLVFTYDKRSQFSVTVF---------EPSGIDKISTFSAHPSKN 138

Query: 123 IFAEMEDDDSEHVDQPTVNKTFNPPSFQNLLNSSKLSNSINGAGEANLQRLKVKLYSQDG 182
           +  + E D+   V      +   P   +N   + K +  ++   E  +   K    +   
Sbjct: 139 VIIKTESDEGGMVTAAITTEKMAPALKENNGITGKRTRDVDYLMEDRVVVFKKSSEANVC 198

Query: 183 ETPKLKKPGR---KRKIDP----NVQASSAQEVHDGEMQ--------FRFYESASAR--- 224
           E+ + K+ G    K K+      + + SS     D             RF     +R   
Sbjct: 199 ESSRRKRAGASAGKSKVTSTSHNSTRGSSCSSDEDNSSSKSPNPPFLMRFLSGEVSRRGR 258

Query: 225 --------------KRTVTAEERERAINAAKAFEPSNPFCRVVLRPSYLYKGCIMYLPSC 270
                         +R VT  E++ A+  A+ F+  NPF   ++  SY+Y G  M +P  
Sbjct: 259 CVSKGQRQLTVISQRRPVTEAEKDHALQRAREFKSKNPFAVQIMMESYVYVGFFMNIPCE 318

Query: 271 FAEKHLNGVCGFIKLQLSDGKQWPVRCLYRGGRA--KFSQGWYEFTVENRLGEGDVCVFE 328
           F  + L      I L    GK W V  +Y   R+   FS GW +F V N L + DVCVFE
Sbjct: 319 FVRECLPHTNKRITLWDPQGKAWEVNYVYYSDRSVGSFSGGWGKFAVGNNLEKFDVCVFE 378

Query: 329 VLRAREFVLKVTVFRV 344
           +++     +KV ++RV
Sbjct: 379 LVQKDN--IKVHIYRV 392

Oryza sativa subsp. japonica (taxid: 39947)

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

 Score = 99.8 bits (247), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 46/108 (42%), Positives = 67/108 (62%)

Query: 2   PRPYFHKLILASTIRDKRLRIPENFVRNFKDDLSAAATLIVPNGMVSRVGLRRLDNKVWF 61
           P   F KL+L ST++DK +RIP  FV+     LS   TL+ P G    + L+R+  ++WF
Sbjct: 26  PVKKFFKLVLPSTMKDKMMRIPPRFVKLQGSKLSEVVTLVTPAGYKRSIKLKRIGEEIWF 85

Query: 62  YDGWQEFMERYFIRIGYFLVFRYEGNSAFNVYIFNLPSSEINYQPNAL 109
           ++GW EF E + I  G+FL+F Y+ NS+F V IFN  + E NY  +A+
Sbjct: 86  HEGWSEFAEAHSIEEGHFLLFEYKKNSSFRVIIFNASACETNYPLDAV 133

Arabidopsis thaliana (taxid: 3702)

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

 Score = 95.9 bits (237), Expect = 4e-19,   Method: Compositional matrix adjust.
 Identities = 44/108 (40%), Positives = 66/108 (61%)

Query: 2   PRPYFHKLILASTIRDKRLRIPENFVRNFKDDLSAAATLIVPNGMVSRVGLRRLDNKVWF 61
           P   F KL+L ST++DK ++IP  FV+     LS   TL  P G    + L+R+  ++WF
Sbjct: 26  PVKKFFKLVLPSTMKDKMMKIPPRFVKLQGSKLSEVVTLETPAGFKRSIKLKRIGEEIWF 85

Query: 62  YDGWQEFMERYFIRIGYFLVFRYEGNSAFNVYIFNLPSSEINYQPNAL 109
           ++GW EF E + I  G+FL+F Y+ NS+F V IFN+ + E  Y  +A+
Sbjct: 86  HEGWSEFAEAHSIEEGHFLLFEYKENSSFRVIIFNVSACETKYPLDAV 133

Arabidopsis thaliana (taxid: 3702)

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

 Score = 90.1 bits (222), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 52/133 (39%), Positives = 75/133 (56%), Gaps = 3/133 (2%)

Query: 6   FHKLILASTIRDKRLRIPENFVRNFKDDLSAAATLIVPNGMVSRVGLRRLDNKVWFYDGW 65
           F K+IL S I +K +++P  FVR F   L+   TL  P G    + ++R+ ++VWF  GW
Sbjct: 34  FIKIILLSRIIEKMMKVPARFVR-FGPKLTDNVTLQTPVGFKRSIRIKRIGDEVWFEKGW 92

Query: 66  QEFMERYFIRIGYFLVFRYEGNSAFNVYIFNLPSSEINYQPNALSN--FEVPNHSKQYHI 123
            EF E + +  G+FL F YEG+S F V IF++ +SEI Y  +   +   EV +  +Q   
Sbjct: 93  SEFAEAHSLSDGHFLFFHYEGDSCFRVVIFDVSASEIEYPLDDTDDNREEVMDDDEQGFT 152

Query: 124 FAEMEDDDSEHVD 136
             E  DDD E VD
Sbjct: 153 GFESSDDDGEVVD 165

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 = 81.3 bits (199), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 81/335 (24%), Positives = 147/335 (43%), Gaps = 39/335 (11%)

Query: 20  LRIPENFVRNFKDDLSAAATLIVPNGMVSRVGLRRLDNKVWFYDGWQEFMERYFIRIGYF 79
           + IPE     F   ++    L  P+G   RV + ++ +++    GW++F + + ++    
Sbjct: 40  ISIPEKVADRFSGQITKGFNLKAPSGETWRVSVEKVADELILMSGWEDFAKAHELQENDL 99

Query: 80  LVF----RYEGNSAFNVYIFNLPSSE-----INYQPNALSNFEVPNHSKQYHIFAEMEDD 130
           L F    R  G+ +F+V IF+    E        + N++       +++QYH+       
Sbjct: 100 LFFTCNGRCNGSFSFDVLIFDASGCEKVSCFFIGKKNSIGG--QTQNAEQYHL------S 151

Query: 131 DSEHVDQPTVNKTFNPPSFQNLLNSSKLSNSINGAGEANLQRLKVKLYSQDGETPKLKKP 190
           DSE    P+     +P       + +  S  +NG  + N ++        + E P   + 
Sbjct: 152 DSEDTSTPSTFLVGSP-------HKASTSKKLNGKTKTNPRK--------EPEDPNSSRS 196

Query: 191 GRKRKIDPNVQASSAQEVHDGEMQFRFYESASARKRTVTAEERERAINAAKAFEPSNPFC 250
             K ++    ++    E  D E    +Y   S     +T EERE  I +  + +P NP  
Sbjct: 197 HVKHEMIEEEKSDDDDEHADYEHADYYY---SRFANYLTGEEREE-IFSLVSLQPGNPVF 252

Query: 251 RVVLRPSYLYKGCIMYLPSCFAEKHLNGVCGFIKLQLSDGKQ-WPVRCLYRGGRAKFS-Q 308
             VL+   +++  ++ +PS FA  HL+     I L   + K+ W V+  +      F+ Q
Sbjct: 253 VTVLQAPQIHRKGLLIVPSGFAADHLDSRSQEILLMRPNKKEKWYVKYYHASTTRGFNCQ 312

Query: 309 GWYEFTVENRLGEGDVCVFEVLR-AREFVLKVTVF 342
            W +F  ENRL EG +C+FE+++ AR   + V V 
Sbjct: 313 RWIKFIRENRLREGYICIFELMKGARRVTMTVHVI 347

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 = 74.7 bits (182), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 85/322 (26%), Positives = 136/322 (42%), Gaps = 38/322 (11%)

Query: 20  LRIPENFVRNFKDDLSAAATLIVPNGMVSRVGLRRLD-NKVWFYDGWQEFMERYFIRIGY 78
           + +P  F  NF   +S    L  P+G    +G+   D  ++    GW+EF++   I  G 
Sbjct: 44  MTVPARFANNFNGHISEEVNLRSPSGETWSIGVANSDAGELVLQPGWKEFVDGNGIEEGD 103

Query: 79  FLVFRYEG-NSAFNVYIFNLPSSEINYQPNALSNFEVPNHSKQYHIFAEMEDDDSEHVDQ 137
            L+FRY G +S+F+V IF+ PS      P+ + +          H F   E  +S   +Q
Sbjct: 104 CLLFRYSGVSSSFDVLIFD-PSGCEKASPHFVGS----------HGFGRAE--NSAGAEQ 150

Query: 138 PTVNKTFNPP------SFQNLLNSSKLSNSINGAGEANLQRLKVKLYSQDGETPKLKKPG 191
              N    PP        ++ L  +   NS      A     K  L+S   ET   +  G
Sbjct: 151 GGRNGRRTPPIVDGDNGHRHHLEMTLHRNSCRSIPRA----CKRSLFSD--ETEAKENDG 204

Query: 192 RKRKIDPNVQASSAQEVHDGEMQFRFYESASARKRTVTAEERERAINAAKAFEPSNPFCR 251
               +      ++A+    GE  + F       +  +  E+RE         +P NP   
Sbjct: 205 EDEDV-----VAAAEGGRYGE--YYFSRHGRVAEYNLREEDREEISRVPVPVQPGNPVFV 257

Query: 252 VVLRPSYL--YKGCIMYLPSCFAEKHLNGVCGFIKLQ-LSDGKQWPVRCLYR-GGRAKFS 307
            V+  S++   K CI+ +   FA K+L  V   + L+  S G +W V  ++R   R  + 
Sbjct: 258 QVIHSSHVRSSKYCIVGVSPEFAGKYLGAVEREVVLERASRGGEWHVPFVHRQNTRGFYG 317

Query: 308 QGWYEFTVENRLGEGDVCVFEV 329
            GW +F  +NRL   DVC+FE+
Sbjct: 318 AGWRQFAGDNRLVAHDVCLFEL 339

Oryza sativa subsp. japonica (taxid: 39947)

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

 Score = 73.9 bits (180), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 76/316 (24%), Positives = 121/316 (38%), Gaps = 57/316 (18%)

Query: 5   YFHKLILASTIRDKRLRIPENFVRNFKDDLSAAATLIVPNGMVSRVGLRRLDNKVWFYDG 64
           YF K+++    R  ++ IP  F  NF+D +     L   NG    V + +  NK+    G
Sbjct: 149 YFFKVMIGGFRR--QMTIPYKFAENFRDQIQGTIKLKARNGNTCSVLVDKCSNKLVLTKG 206

Query: 65  WQEFMERYFIRIGYFLVFRYEGNSAFNVYIFNLPSSEINYQPNALSNFEVPNHSKQYHIF 124
           W EF   + I++G FLVFRY GNS F V IF+ PS  +    +   N      + Q    
Sbjct: 207 WAEFANSHDIKMGDFLVFRYTGNSQFEVKIFD-PSGCVKAASHNAVNIGQHAQNMQGDPI 265

Query: 125 AEMEDDDSEHVDQPTVNKTFNPPSFQNLLNSSKLSNSINGAGEANLQRLKVKLYSQDGET 184
             +   D     Q    +  N P    + N +K   + + +   +           D ET
Sbjct: 266 EILSCSDEHLRAQSLTTERQNQPEKDVIDNCNKKMKTEHASSSED-----------DQET 314

Query: 185 PKLKKPGRKRKIDPNVQASSAQEVHDGEMQFRFYESASARKRTVTAEERERAINAAKAFE 244
           P                     EVH                  +  EE  RAI++     
Sbjct: 315 P-------------------TAEVH-----------------RMKVEEMVRAIHSNHPV- 337

Query: 245 PSNPFCRVVLRPSYLYKGCIMYLPSCFAEKHLNGVCGFIKLQLSDGKQWPVR-CLYRGGR 303
               F  V+ + +   + C + +   +A ++  G    + LQ   GK+W V+ C+ +   
Sbjct: 338 ----FVAVMKKSNVTRQPCYVAISRKYANEYFPGGDQMLTLQ-RHGKRWQVKFCISKRKL 392

Query: 304 AKFSQGWYEFTVENRL 319
              S+GW +FT +N L
Sbjct: 393 RMLSKGWRKFTRDNEL 408

Oryza sativa subsp. japonica (taxid: 39947)

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	354
255556221	333	DNA binding protein, putative [Ricinus c	0.909	0.966	0.630	1e-121
449471266	412	PREDICTED: B3 domain-containing transcri	0.971	0.834	0.587	1e-116
449455216	415	PREDICTED: B3 domain-containing transcri	0.971	0.828	0.583	1e-114
297834810	341	hypothetical protein ARALYDRAFT_479415 [	0.949	0.985	0.610	1e-113
30685150	341	B3 domain-containing transcription facto	0.946	0.982	0.605	1e-113
312282979	341	unnamed protein product [Thellungiella h	0.951	0.988	0.612	1e-112
356575102	435	PREDICTED: B3 domain-containing transcri	0.994	0.809	0.532	1e-110
356521114	437	PREDICTED: B3 domain-containing transcri	0.991	0.803	0.530	1e-110
255637330	437	unknown [Glycine max]	0.991	0.803	0.528	1e-109
357473115	429	B3 domain-containing transcription facto	0.985	0.813	0.53	1e-109

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

 Score =  439 bits (1130), Expect = e-121,   Method: Compositional matrix adjust.
 Identities = 224/355 (63%), Positives = 263/355 (74%), Gaps = 33/355 (9%)

Query: 1   MPRPYFHKLILASTIRDKRLRIPENFVRNFKDDLSAAATLIVPNGMVSRVGLRRLDNKVW 60
           MPRPYFHKLIL+++I+DK+LRIP+NFV+ F +DLSA   L VP G V  VGL + D+K W
Sbjct: 1   MPRPYFHKLILSNSIKDKKLRIPDNFVKKFGNDLSAFGRLSVPGGPVWPVGLIKADDKFW 60

Query: 61  FYDGWQEFMERYFIRIGYFLVFRYEGNSAFNVYIFNLPSSEINYQPNALSNFEVPNHSKQ 120
           F +GWQEFMERY IR+GYFLVFRYEG+S F V+IFNL +SEINYQ N  +        ++
Sbjct: 61  FREGWQEFMERYSIRVGYFLVFRYEGHSVFTVHIFNLSASEINYQSNNTAG-------RR 113

Query: 121 YHIFAEMEDDD-SEHVDQPTVNKTFNPPSFQNLLNSSKLSNSINGAGEANLQRLKVKLYS 179
           Y +F +MEDDD  EH+   +      P    N L S                   V+ Y+
Sbjct: 114 YLLFEDMEDDDFVEHLSSSS------PCLVPNSLKSD------------------VRYYT 149

Query: 180 QDGETPKLKKPGRKR-KIDPNVQASSAQEVHDGEMQFRFYESASARKRTVTAEERERAIN 238
            D E  K KK GRK+ K+DPN Q  SAQ+  + +M+FRFYESASARKRTVTAEERERAIN
Sbjct: 150 PDAEAQKPKKRGRKKLKVDPNQQQPSAQQEDEVDMRFRFYESASARKRTVTAEERERAIN 209

Query: 239 AAKAFEPSNPFCRVVLRPSYLYKGCIMYLPSCFAEKHLNGVCGFIKLQLSDGKQWPVRCL 298
            AK FEP NPFCRVVLRPSYLY+GCIMYLPSCFAEKHLNGV GFIKLQ SDGKQWPVRCL
Sbjct: 210 TAKTFEPMNPFCRVVLRPSYLYRGCIMYLPSCFAEKHLNGVSGFIKLQSSDGKQWPVRCL 269

Query: 299 YRGGRAKFSQGWYEFTVENRLGEGDVCVFEVLRAREFVLKVTVFRVSESAGFMSR 353
           YRGGRAK SQGWYEFT+EN +GEGDVCVFE+L++R+ VLKVTVFRV E AG M++
Sbjct: 270 YRGGRAKLSQGWYEFTLENNMGEGDVCVFELLKSRDIVLKVTVFRVLEGAGRMTQ 324

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

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 =  424 bits (1089), Expect = e-116,   Method: Compositional matrix adjust.
 Identities = 224/381 (58%), Positives = 267/381 (70%), Gaps = 37/381 (9%)

Query: 1   MPRPYFHKLILASTIRDKRLRIPENFVRNFKDDLSAAATLIVPNGMVSRVGLRRLDNKVW 60
           MPRP+FHKL+L STI+ ++LRIPE FVR  +D+LSA ATL VP+G V RVGLR+ DNK W
Sbjct: 16  MPRPHFHKLVLTSTIQARKLRIPETFVRMIRDELSAVATLTVPDGHVWRVGLRKADNKFW 75

Query: 61  FYDGWQEFMERYFIRIGYFLVFRYEGNSAFNVYIFNLPSSEINYQPNALSNFEVPNHSKQ 120
           F DGWQ F+E Y IR+GY LVFRYEGNS+F V+IFNL +SEINYQ  ALSN +  N+S Q
Sbjct: 76  FEDGWQGFLEHYSIRVGYLLVFRYEGNSSFCVFIFNLNTSEINYQSAALSNNQRNNYSIQ 135

Query: 121 YHIFAEMEDDDSEHVDQPTVNKTFNPPSFQNLL-------NSSKLSNSING--------- 164
             IF EMED D    +    N++ N  S +N L       + SK ++++           
Sbjct: 136 NRIFEEMEDYDIP--EAIPSNQSMNSGSLRNKLFGDEWNLHQSKSASTLQAEYLSTRDIG 193

Query: 165 -----------AGEANLQRLKVKLYSQDGETPKLKKPG-RKRKIDPNVQASSAQEVHD-G 211
                      A E   Q L       D    ++KK G +KRKI+ +    SA    D G
Sbjct: 194 VQFSAVEVKKSADEVRFQNLG------DDAAHRVKKSGSKKRKIESSEHHPSAHNSEDLG 247

Query: 212 EMQFRFYESASARKRTVTAEERERAINAAKAFEPSNPFCRVVLRPSYLYKGCIMYLPSCF 271
           +++FRFYESASARKRTVTAEERERAIN+AKAFEP NPFCRVVLRPSYLY+GCIMYLPSCF
Sbjct: 248 DIRFRFYESASARKRTVTAEERERAINSAKAFEPGNPFCRVVLRPSYLYRGCIMYLPSCF 307

Query: 272 AEKHLNGVCGFIKLQLSDGKQWPVRCLYRGGRAKFSQGWYEFTVENRLGEGDVCVFEVLR 331
           AEK+L+GV GFIKLQ  DG+QWPVRCLY+ GRAK SQGWYEF +EN LGEGDVCVFE+LR
Sbjct: 308 AEKNLSGVSGFIKLQTPDGRQWPVRCLYKVGRAKLSQGWYEFCLENNLGEGDVCVFELLR 367

Query: 332 AREFVLKVTVFRVSESAGFMS 352
            RE VLKVT+FRV E  G M+
Sbjct: 368 MREIVLKVTMFRVIEEGGRMA 388

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449455216|ref|XP_004145349.1| PREDICTED: B3 domain-containing transcription factor VRN1-like [Cucumis sativus]

 Score =  419 bits (1077), Expect = e-114,   Method: Compositional matrix adjust.
 Identities = 224/384 (58%), Positives = 267/384 (69%), Gaps = 40/384 (10%)

Query: 1   MPRPYFHKLILAST---IRDKRLRIPENFVRNFKDDLSAAATLIVPNGMVSRVGLRRLDN 57
           MPRP+FHKL+L ST   I+ ++LRIPE FVR  +D+LSA ATL VP+G V RVGLR+ DN
Sbjct: 16  MPRPHFHKLVLTSTTSTIQARKLRIPETFVRMIRDELSAVATLTVPDGHVWRVGLRKADN 75

Query: 58  KVWFYDGWQEFMERYFIRIGYFLVFRYEGNSAFNVYIFNLPSSEINYQPNALSNFEVPNH 117
           K WF DGWQ F+E Y IR+GY LVFRYEGNS+F V+IFNL +SEINYQ  ALSN +  N+
Sbjct: 76  KFWFEDGWQGFLEHYSIRVGYLLVFRYEGNSSFCVFIFNLNTSEINYQSAALSNNQRNNY 135

Query: 118 SKQYHIFAEMEDDDSEHVDQPTVNKTFNPPSFQNLL-------NSSKLSNSING------ 164
           S Q  IF EMED D    +    N++ N  S +N L       + SK ++++        
Sbjct: 136 SIQNRIFEEMEDYDIP--EAIPSNQSMNSGSLRNKLFGDEWNLHQSKSASTLQAEYLSTR 193

Query: 165 --------------AGEANLQRLKVKLYSQDGETPKLKKPG-RKRKIDPNVQASSAQEVH 209
                         A E   Q L       D    ++KK G +KRKI+ +    SA    
Sbjct: 194 DIGVQFSAVEVKKSADEVRFQNLG------DDAAHRVKKSGSKKRKIESSEHHPSAHNSE 247

Query: 210 D-GEMQFRFYESASARKRTVTAEERERAINAAKAFEPSNPFCRVVLRPSYLYKGCIMYLP 268
           D G+++FRFYESASARKRTVTAEERERAIN+AKAFEP NPFCRVVLRPSYLY+GCIMYLP
Sbjct: 248 DLGDIRFRFYESASARKRTVTAEERERAINSAKAFEPGNPFCRVVLRPSYLYRGCIMYLP 307

Query: 269 SCFAEKHLNGVCGFIKLQLSDGKQWPVRCLYRGGRAKFSQGWYEFTVENRLGEGDVCVFE 328
           SCFAEK+L+GV GFIKLQ  DG+QWPVRCLY+ GRAK SQGWYEF +EN LGEGDVCVFE
Sbjct: 308 SCFAEKNLSGVSGFIKLQTPDGRQWPVRCLYKVGRAKLSQGWYEFCLENNLGEGDVCVFE 367

Query: 329 VLRAREFVLKVTVFRVSESAGFMS 352
           +LR RE VLKVT+FRV E  G M+
Sbjct: 368 LLRMREIVLKVTMFRVIEEGGRMA 391

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 =  415 bits (1066), Expect = e-113,   Method: Compositional matrix adjust.
 Identities = 213/349 (61%), Positives = 261/349 (74%), Gaps = 13/349 (3%)

Query: 1   MPRPYFHKLILASTIRDKRLRIPENFVRNFKDDLSAAATLIVPNGMVSRVGLRRLDNKVW 60
           MPRP+FHKLI +STI++KRLR+P+ FV  FKD+LS A  L VP+G V RVGLR+ DNK+W
Sbjct: 1   MPRPFFHKLIFSSTIQEKRLRVPDKFVSKFKDELSVAVALTVPDGHVWRVGLRKADNKIW 60

Query: 61  FYDGWQEFMERYFIRIGYFLVFRYEGNSAFNVYIFNLPSSEINYQPNALSNFEVPNHSKQ 120
           F DGWQEF++RY IRIGY L+FRYEGNSAF+VYIFNL  SEINY    L +    NH K+
Sbjct: 61  FQDGWQEFVDRYSIRIGYLLIFRYEGNSAFSVYIFNLSHSEINYHSTGLMD-SAHNHFKR 119

Query: 121 YHIFAEMEDDDSEHVDQPTVNKTFNPPSFQNLLNSSKLSNSINGAGEANLQRLKVKLYSQ 180
             +F ++ED+D+E +   +V        + + L  S +  +   AG A        + ++
Sbjct: 120 ARLFEDLEDEDAEFIFPSSV--------YPSPLPESTVPANKGYAGSAIQSLFTGSVKAE 171

Query: 181 DGE-TPKL-KKPGRKRK-IDPNVQASSAQEVHDGEMQFRFYESASARKRTVTAEERERAI 237
           +   TPK+ KK GRK+K  DP    SSA    D E + +FYESASARKRTVTAEERERAI
Sbjct: 172 EATPTPKIPKKRGRKKKNADPEEINSSAPRDDDPENRSKFYESASARKRTVTAEERERAI 231

Query: 238 NAAKAFEPSNPFCRVVLRPSYLYKGCIMYLPSCFAEKHLNGVCGFIKLQLSDGKQWPVRC 297
           NAAK FEP+NPF RVVLRPSYLY+GCIMYLPS FAEK+L+G+ GFIK+QL++ KQWPVRC
Sbjct: 232 NAAKTFEPTNPFFRVVLRPSYLYRGCIMYLPSGFAEKYLSGISGFIKVQLAE-KQWPVRC 290

Query: 298 LYRGGRAKFSQGWYEFTVENRLGEGDVCVFEVLRAREFVLKVTVFRVSE 346
           LY+ GRAKFSQGWYEFT+EN LGEGDVCVFE+LR R+FVLKVT FRV+E
Sbjct: 291 LYKAGRAKFSQGWYEFTLENNLGEGDVCVFELLRTRDFVLKVTAFRVNE 339

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

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 =  412 bits (1060), Expect = e-113,   Method: Compositional matrix adjust.
 Identities = 212/350 (60%), Positives = 260/350 (74%), Gaps = 15/350 (4%)

Query: 1   MPRPYFHKLILASTIRDKRLRIPENFVRNFKDDLSAAATLIVPNGMVSRVGLRRLDNKVW 60
           MPRP+FHKLI +STI++KRLR+P+ FV  FKD+LS A  L VP+G V RVGLR+ DNK+W
Sbjct: 1   MPRPFFHKLIFSSTIQEKRLRVPDKFVSKFKDELSVAVALTVPDGHVWRVGLRKADNKIW 60

Query: 61  FYDGWQEFMERYFIRIGYFLVFRYEGNSAFNVYIFNLPSSEINYQPNALSNFEVPNHSKQ 120
           F DGWQEF++RY IRIGY L+FRYEGNSAF+VYIFNL  SEINY    L +    NH K+
Sbjct: 61  FQDGWQEFVDRYSIRIGYLLIFRYEGNSAFSVYIFNLSHSEINYHSTGLMD-SAHNHFKR 119

Query: 121 YHIFAEMEDDDSEHVDQPTVNKTFNPPSFQNLLNSSKLSNSINGAGEANLQRLKVKLYSQ 180
             +F ++ED+D+E +   +V   +  P  ++ + ++K      G   + +Q L       
Sbjct: 120 ARLFEDLEDEDAEVIFPSSV---YPSPLPESTVPANK------GYASSAIQTLFTGPVKA 170

Query: 181 DGETPKLKKP---GRKRK-IDPNVQASSAQEVHDGEMQFRFYESASARKRTVTAEERERA 236
           +  TP  K P   GRK+K  DP    SSA    D E + +FYESASARKRTVTAEERERA
Sbjct: 171 EEPTPTPKIPKKRGRKKKNADPEEINSSAPRDDDPENRSKFYESASARKRTVTAEERERA 230

Query: 237 INAAKAFEPSNPFCRVVLRPSYLYKGCIMYLPSCFAEKHLNGVCGFIKLQLSDGKQWPVR 296
           INAAK FEP+NPF RVVLRPSYLY+GCIMYLPS FAEK+L+G+ GFIK+QL++ KQWPVR
Sbjct: 231 INAAKTFEPTNPFFRVVLRPSYLYRGCIMYLPSGFAEKYLSGISGFIKVQLAE-KQWPVR 289

Query: 297 CLYRGGRAKFSQGWYEFTVENRLGEGDVCVFEVLRAREFVLKVTVFRVSE 346
           CLY+ GRAKFSQGWYEFT+EN LGEGDVCVFE+LR R+FVLKVT FRV+E
Sbjct: 290 CLYKAGRAKFSQGWYEFTLENNLGEGDVCVFELLRTRDFVLKVTAFRVNE 339

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  411 bits (1057), Expect = e-112,   Method: Compositional matrix adjust.
 Identities = 213/348 (61%), Positives = 261/348 (75%), Gaps = 11/348 (3%)

Query: 1   MPRPYFHKLILASTIRDKRLRIPENFVRNFKDDLSAAATLIVPNGMVSRVGLRRLDNKVW 60
           MPRP+FHKLI +STI++KRLR+P+ FV  FKD+LS A  L VP+G V RVGLR+ +NK+W
Sbjct: 1   MPRPFFHKLIFSSTIQEKRLRVPDKFVSKFKDELSVAVALTVPDGHVWRVGLRKAENKIW 60

Query: 61  FYDGWQEFMERYFIRIGYFLVFRYEGNSAFNVYIFNLPSSEINYQPNALSNFEVPNHSKQ 120
           F DGWQEF++RY IRIGY L+FRYEGNSAF+VYIFNL  SEINY    L +    NH K+
Sbjct: 61  FQDGWQEFVDRYSIRIGYLLIFRYEGNSAFSVYIFNLSHSEINYHSTGLMD-SAHNHFKR 119

Query: 121 YHIFAEMEDDDSEHVDQPTVNKTFNPPSFQNLLNSSKLSNSINGAGEANLQRLKVKLYSQ 180
             +F ++ED+D+E +   +V  +  P S      +   +   +G+   +L    VK   +
Sbjct: 120 ARLFEDLEDEDAEVIYPSSVYPSPLPDS------TVPANKGYSGSAIQSLFTGPVKA-EE 172

Query: 181 DGETPKL-KKPGRKRK-IDPNVQASSAQEVHDGEMQFRFYESASARKRTVTAEERERAIN 238
              TPK+ KK GRK+K  DP    SSA    D E + +FYESASARKRTVTAEERERAIN
Sbjct: 173 ATPTPKVPKKRGRKKKNADPEEINSSAPRDDDPENRSKFYESASARKRTVTAEERERAIN 232

Query: 239 AAKAFEPSNPFCRVVLRPSYLYKGCIMYLPSCFAEKHLNGVCGFIKLQLSDGKQWPVRCL 298
           AAK FEP+NPF RVVLRPSYLY+GCIMYLPS FAEK+L+G+ GFIK+QL++ KQWPVRCL
Sbjct: 233 AAKTFEPTNPFFRVVLRPSYLYRGCIMYLPSGFAEKYLSGISGFIKVQLAE-KQWPVRCL 291

Query: 299 YRGGRAKFSQGWYEFTVENRLGEGDVCVFEVLRAREFVLKVTVFRVSE 346
           Y+ GRAKFSQGWYEFT+EN LGEGDVCVFE+LR R+FVLKVT FRV+E
Sbjct: 292 YKAGRAKFSQGWYEFTLENNLGEGDVCVFELLRTRDFVLKVTAFRVNE 339

Source: Thellungiella halophila

Species: Eutrema halophilum

Genus: Eutrema

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356575102|ref|XP_003555681.1| PREDICTED: B3 domain-containing transcription factor VRN1-like [Glycine max]

 Score =  405 bits (1041), Expect = e-110,   Method: Compositional matrix adjust.
 Identities = 214/402 (53%), Positives = 271/402 (67%), Gaps = 50/402 (12%)

Query: 1   MPRPYFHKLILASTIRDKRLRIPENFVRNFKDDLSAAATLIVPNGMVSRVGLRRLDNKVW 60
           MPRP FHKL+L +T++ ++LRIP+NF+R +   LS  ATL VP+G V R+GL++ DN++ 
Sbjct: 1   MPRPCFHKLVLPTTLQSRQLRIPDNFLRKYGTQLSTIATLTVPDGSVWRIGLKKADNRIL 60

Query: 61  FYDGWQEFMERYFIRIGYFLVFRYEGNSAFNVYIFNLPSSEINYQPNALSNFEVPNHSKQ 120
           F DGWQ+F++ Y I +GYFLVF YEGNS+F V+IFNL +SE+NYQ    +  E    +  
Sbjct: 61  FVDGWQDFVQHYSIGVGYFLVFMYEGNSSFIVHIFNLSTSEVNYQSAIRNRNEGSCLANY 120

Query: 121 YHIFAEMEDDDS----------------------EHVDQPTVNKTFNPPSFQNLLNS-SK 157
           +HIF EMED DS                        VDQ T  K+ + P+ QNL N  SK
Sbjct: 121 HHIFDEMEDVDSLDLSDLSPQYLTPGSLQNKGCVGSVDQLTPGKS-HTPALQNLFNGGSK 179

Query: 158 L-------------SNSINGAGEANLQRLKVKL----YSQDGETPKL---------KKPG 191
           L             S + N  G  + + + V+     + +  E  KL         K   
Sbjct: 180 LNRINWGDGGSAFSSKNANSQGNQSTRDIGVQFNANEFKRSTEELKLRYSNEETVNKTAK 239

Query: 192 RKRKIDPNVQASSAQEVHDGEMQFRFYESASARKRTVTAEERERAINAAKAFEPSNPFCR 251
           +KRK +P  +  S +   + EM++RFYESASARKRTVTAEERERAINA+K FEP+NPFCR
Sbjct: 240 KKRKSEPYGEEPSGENEEEAEMRYRFYESASARKRTVTAEERERAINASKTFEPTNPFCR 299

Query: 252 VVLRPSYLYKGCIMYLPSCFAEKHLNGVCGFIKLQLSDGKQWPVRCLYRGGRAKFSQGWY 311
           VVLRPSYLY+GCIMYLPSCFAEK+LNGV GFIKLQLS+G+QW VRCLYRGGRAK SQGW+
Sbjct: 300 VVLRPSYLYRGCIMYLPSCFAEKNLNGVSGFIKLQLSNGRQWSVRCLYRGGRAKLSQGWF 359

Query: 312 EFTVENRLGEGDVCVFEVLRAREFVLKVTVFRVSESAGFMSR 353
           EFTVEN LGEGDVCVFE+LR +E VL+VTVFRV+E AG +++
Sbjct: 360 EFTVENNLGEGDVCVFELLRTKEVVLQVTVFRVTEDAGLLNQ 401

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356521114|ref|XP_003529203.1| PREDICTED: B3 domain-containing transcription factor VRN1-like [Glycine max]

 Score =  405 bits (1040), Expect = e-110,   Method: Compositional matrix adjust.
 Identities = 215/405 (53%), Positives = 270/405 (66%), Gaps = 54/405 (13%)

Query: 1   MPRPYFHKLILASTIRDKRLRIPENFVRNFKDDLSAAATLIVPNGMVSRVGLRRLDNKVW 60
           MPRP F KL+L +T++ ++LRIP+NF+R +   LS  ATL VP+G V  +GL++ DN++W
Sbjct: 1   MPRPCFDKLVLPTTLQSRQLRIPDNFLRKYGTQLSTIATLTVPDGSVWPIGLKKADNRIW 60

Query: 61  FYDGWQEFMERYFIRIGYFLVFRYEGNSAFNVYIFNLPSSEINYQPNALSNFEVPNHSKQ 120
           F DGWQ+F++RY I +GYFLVF YEGNS+F V+IFNL +SE+NYQ    ++ E    +  
Sbjct: 61  FVDGWQDFVQRYSIGVGYFLVFMYEGNSSFIVHIFNLSTSEVNYQSAMRNHNEGSCFANY 120

Query: 121 YHIFAEMEDDDS----------------------EHVDQPTVNKTFNPPSFQNLLNSSKL 158
           +HIF EMED DS                        VDQ T  K+ + P+ QNL N    
Sbjct: 121 HHIFDEMEDVDSLGLSDLSPQYLTPGALQSKGFAGSVDQLTPGKS-HTPALQNLFNGGSK 179

Query: 159 SNSIN-GAG-------EANLQ----------------------RLKVKLYSQDGETPKLK 188
            N +N G G       +AN Q                       LK++ YS   E    K
Sbjct: 180 LNRVNWGDGGSAFSLKDANSQGNQSTRDIGVQFNAVEFKRSTEELKLR-YSNSNEEAVNK 238

Query: 189 KPGRKRKIDPNVQASSAQEVHDGEMQFRFYESASARKRTVTAEERERAINAAKAFEPSNP 248
              +KRK +P  +  S +   + EM++RFYESASARKRTVTAEERERAINA+K FEP+NP
Sbjct: 239 TAKKKRKSEPYGEEPSGENEEEAEMRYRFYESASARKRTVTAEERERAINASKTFEPTNP 298

Query: 249 FCRVVLRPSYLYKGCIMYLPSCFAEKHLNGVCGFIKLQLSDGKQWPVRCLYRGGRAKFSQ 308
           FCRVVLRPSYLY+GCIMYLPS FAEK+LNGV GFIKLQLS+G+QW VRCLYRGGRAK SQ
Sbjct: 299 FCRVVLRPSYLYRGCIMYLPSTFAEKNLNGVSGFIKLQLSNGRQWSVRCLYRGGRAKLSQ 358

Query: 309 GWYEFTVENRLGEGDVCVFEVLRAREFVLKVTVFRVSESAGFMSR 353
           GW+EFTVEN LGEGDVCVFE+LR +E VL+VTVFRV+E AG +++
Sbjct: 359 GWFEFTVENNLGEGDVCVFELLRMKEVVLQVTVFRVTEDAGLLNQ 403

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255637330|gb|ACU18995.1| unknown [Glycine max]

 Score =  402 bits (1032), Expect = e-109,   Method: Compositional matrix adjust.
 Identities = 214/405 (52%), Positives = 269/405 (66%), Gaps = 54/405 (13%)

Query: 1   MPRPYFHKLILASTIRDKRLRIPENFVRNFKDDLSAAATLIVPNGMVSRVGLRRLDNKVW 60
           MPRP F KL+L +T++ ++LRIP+NF+R +   LS  ATL VP+G V  +GL++ DN++W
Sbjct: 1   MPRPCFDKLVLPTTLQSRQLRIPDNFLRKYGTQLSTIATLTVPDGSVWPIGLKKADNRIW 60

Query: 61  FYDGWQEFMERYFIRIGYFLVFRYEGNSAFNVYIFNLPSSEINYQPNALSNFEVPNHSKQ 120
           F DGWQ+F++RY I +GYFLVF YEGNS+F V+IFNL +SE+NYQ    ++ E    +  
Sbjct: 61  FVDGWQDFVQRYSIGVGYFLVFMYEGNSSFIVHIFNLSTSEVNYQSAMRNHNEGSCFANY 120

Query: 121 YHIFAEMEDDDS----------------------EHVDQPTVNKTFNPPSFQNLLNSSKL 158
           +HIF EMED DS                        VDQ T  K+ + P+ QNL N    
Sbjct: 121 HHIFDEMEDVDSLGLSDLSPQYLTPGALQSKGFAGSVDQLTPGKS-HTPALQNLFNGGSK 179

Query: 159 SNSIN-GAG-------EANLQ----------------------RLKVKLYSQDGETPKLK 188
            N +N G G       +AN Q                       LK++ YS   E    K
Sbjct: 180 LNRVNWGDGGSAFSLKDANSQGNQSTRDIGVQFNAVEFKRSTEELKLR-YSNSNEEAVNK 238

Query: 189 KPGRKRKIDPNVQASSAQEVHDGEMQFRFYESASARKRTVTAEERERAINAAKAFEPSNP 248
              +KRK +P  +  S +   + EM++RFYESASARKRTVTAEERERAINA+K FEP+NP
Sbjct: 239 TAKKKRKSEPYGEEPSGENEEEAEMRYRFYESASARKRTVTAEERERAINASKTFEPTNP 298

Query: 249 FCRVVLRPSYLYKGCIMYLPSCFAEKHLNGVCGFIKLQLSDGKQWPVRCLYRGGRAKFSQ 308
           FCRVVLRPSYLY+GCIMYLPS FAEK+LNGV GFIKLQLS+G+ W VRCLYRGGRAK SQ
Sbjct: 299 FCRVVLRPSYLYRGCIMYLPSTFAEKNLNGVSGFIKLQLSNGRPWSVRCLYRGGRAKLSQ 358

Query: 309 GWYEFTVENRLGEGDVCVFEVLRAREFVLKVTVFRVSESAGFMSR 353
           GW+EFTVEN LGEGDVCVFE+LR +E VL+VTVFRV+E AG +++
Sbjct: 359 GWFEFTVENNLGEGDVCVFELLRMKEVVLQVTVFRVTEDAGLLNQ 403

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357473115|ref|XP_003606842.1| B3 domain-containing transcription factor VRN1 [Medicago truncatula] gi|355507897|gb|AES89039.1| B3 domain-containing transcription factor VRN1 [Medicago truncatula]

 Score =  400 bits (1027), Expect = e-109,   Method: Compositional matrix adjust.
 Identities = 212/400 (53%), Positives = 261/400 (65%), Gaps = 51/400 (12%)

Query: 1   MPRPYFHKLILASTIRDKRLRIPENFVRNFKDDLSAAATLIVPNGMVSRVGLRRLDNKVW 60
           MP P FHKL+L ST++ K+LR+P++F+R +  D+S   TL VP+G V RV ++++DNK W
Sbjct: 1   MPSPSFHKLVLPSTLQAKQLRLPDDFMRKYGGDISPTVTLTVPDGSVWRVIMKKVDNKFW 60

Query: 61  FYDGWQEFMERYFIRIGYFLVFRYEGNSAFNVYIFNLPSSEINYQPNALSNFEVPNHSKQ 120
           F DGW EF++ Y I  GY LVF+YEG S F V IF+LP+SEINYQ  A  + E     K+
Sbjct: 61  FLDGWNEFVQNYSISTGYLLVFKYEGKSHFTVNIFSLPTSEINYQSPAQRSNEASLFGKR 120

Query: 121 YHIFAEMEDDDSEHV----------------------DQPTVNKTFNPPSFQNLLNSSKL 158
             IF EMED+DS  +                      D+ T  K+  PP+ QNL N SKL
Sbjct: 121 LTIFEEMEDEDSVEIMESSPTKLTPSLLQNKAVSGSADKLTPGKSRPPPALQNLFNGSKL 180

Query: 159 SNSIN-GAGEANLQR----------------LKVKLYSQDGETPKL---------KKPGR 192
            NSIN G G     R                  V  + +  E  KL         K   +
Sbjct: 181 -NSINWGEGGNTPSRNDNSVDNQLTRDIGLQFNVVEFKKSNEELKLRAATDEKVKKTAVK 239

Query: 193 KRKIDPNVQASSAQEVHDGEMQFRFYESASARKRTVTAEERERAINAAKAFEPSNPFCRV 252
           KRK D  VQ   ++   + EM+ RFYESASARKRT TAEERE+AINAAK FEPSNPFCRV
Sbjct: 240 KRKSD--VQEPPSEHEDEVEMRNRFYESASARKRTATAEEREKAINAAKTFEPSNPFCRV 297

Query: 253 VLRPSYLYKGCIMYLPSCFAEKHLNGVCGFIKLQLSDGKQWPVRCLYRGGRAKFSQGWYE 312
           VLRPSYLY+GCIMYLPSCFAEK+LNGV G IKLQ+SDG+QWPVRCLYRGGRAK SQGW+E
Sbjct: 298 VLRPSYLYRGCIMYLPSCFAEKNLNGVSGIIKLQISDGRQWPVRCLYRGGRAKLSQGWFE 357

Query: 313 FTVENRLGEGDVCVFEVLRAREFVLKVTVFRVSESAGFMS 352
           F++EN LGEGDVCVFE++  +E VL+VTVFR++E  G +S
Sbjct: 358 FSLENNLGEGDVCVFELVATKEVVLQVTVFRITEDEGPLS 397

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	354
TAIR|locus:2085849	341	VRN1 "REDUCED VERNALIZATION RE	0.943	0.979	0.612	1.5e-106
TAIR|locus:2010262	226	RTV1 "AT1G49480" [Arabidopsis	0.468	0.734	0.719	7.1e-61
TAIR|locus:2133362	190	AT4G01580 [Arabidopsis thalian	0.305	0.568	0.425	1.7e-20
TAIR|locus:2085859	209	AT3G18960 [Arabidopsis thalian	0.305	0.516	0.407	3.1e-19
TAIR|locus:504956318	190	AT1G49475 [Arabidopsis thalian	0.384	0.715	0.381	6.5e-19
TAIR|locus:2119166	337	AT4G33280 [Arabidopsis thalian	0.330	0.347	0.288	1.7e-12
TAIR|locus:2161533	307	VDD "VERDANDI" [Arabidopsis th	0.387	0.446	0.237	4.9e-10
TAIR|locus:2172319	301	AT5G18090 [Arabidopsis thalian	0.254	0.299	0.265	8e-10
TAIR|locus:2086082	302	REM22 "REPRODUCTIVE MERISTEM 2	0.474	0.556	0.255	6.6e-09
TAIR|locus:2124824	462	AT4G31680 [Arabidopsis thalian	0.370	0.283	0.280	2.5e-08

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

 Score = 1054 (376.1 bits), Expect = 1.5e-106, P = 1.5e-106
 Identities = 215/351 (61%), Positives = 259/351 (73%)

Query:     1 MPRPYFHKLILASTIRDKRLRIPENFVRNFKDDLSAAATLIVPNGMVSRVGLRRLDNKVW 60
             MPRP+FHKLI +STI++KRLR+P+ FV  FKD+LS A  L VP+G V RVGLR+ DNK+W
Sbjct:     1 MPRPFFHKLIFSSTIQEKRLRVPDKFVSKFKDELSVAVALTVPDGHVWRVGLRKADNKIW 60

Query:    61 FYDGWQEFMERYFIRIGYFLVFRYEGNSAFNVYIFNLPSSEINYQPNALSNFEVPNHSKQ 120
             F DGWQEF++RY IRIGY L+FRYEGNSAF+VYIFNL  SEINY    L +    NH K+
Sbjct:    61 FQDGWQEFVDRYSIRIGYLLIFRYEGNSAFSVYIFNLSHSEINYHSTGLMD-SAHNHFKR 119

Query:   121 YHIFAEMEDDDSEHVDQPTVNKTFNPPSFQXXXXXXXXXXXXXGAGEANLQRL---KVKL 177
               +F ++ED+D+E +   +V  +  P S               G   + +Q L    VK 
Sbjct:   120 ARLFEDLEDEDAEVIFPSSVYPSPLPES---------TVPANKGYASSAIQTLFTGPVKA 170

Query:   178 YSQDGETPKL-KKPGRKRK-IDPNVQASSAQEVHDGEMQFRFYESASARKRTVTAEERER 235
               +   TPK+ KK GRK+K  DP    SSA    D E + +FYESASARKRTVTAEERER
Sbjct:   171 -EEPTPTPKIPKKRGRKKKNADPEEINSSAPRDDDPENRSKFYESASARKRTVTAEERER 229

Query:   236 AINAAKAFEPSNPFCRVVLRPSYLYKGCIMYLPSCFAEKHLNGVCGFIKLQLSDGKQWPV 295
             AINAAK FEP+NPF RVVLRPSYLY+GCIMYLPS FAEK+L+G+ GFIK+QL++ KQWPV
Sbjct:   230 AINAAKTFEPTNPFFRVVLRPSYLYRGCIMYLPSGFAEKYLSGISGFIKVQLAE-KQWPV 288

Query:   296 RCLYRGGRAKFSQGWYEFTVENRLGEGDVCVFEVLRAREFVLKVTVFRVSE 346
             RCLY+ GRAKFSQGWYEFT+EN LGEGDVCVFE+LR R+FVLKVT FRV+E
Sbjct:   289 RCLYKAGRAKFSQGWYEFTLENNLGEGDVCVFELLRTRDFVLKVTAFRVNE 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:2010262 RTV1 "AT1G49480" [Arabidopsis thaliana (taxid:3702)]

 Score = 623 (224.4 bits), Expect = 7.1e-61, P = 7.1e-61
 Identities = 123/171 (71%), Positives = 144/171 (84%)

Query:   179 SQDGETPK-LKKPGRKRKIDPNVQA--SSAQEVHDGEMQFRFYESASARKRTVTAEERER 235
             S+  ETPK LKK GRK+K +PN +   SS     D E + +FYESASARKRTVTAEERER
Sbjct:    56 SKAEETPKVLKKRGRKKK-NPNPEEVNSSTPGGDDSENRSKFYESASARKRTVTAEERER 114

Query:   236 AINAAKAFEPSNPFCRVVLRPSYLYKGCIMYLPSCFAEKHLNGVCGFIKLQLSDGKQWPV 295
             A+NAAK FEP+NP+ RVVLRPSYLY+GCIMYLPS FAEK+L+G+ GFIKLQL + KQWPV
Sbjct:   115 AVNAAKTFEPTNPYFRVVLRPSYLYRGCIMYLPSGFAEKYLSGISGFIKLQLGE-KQWPV 173

Query:   296 RCLYRGGRAKFSQGWYEFTVENRLGEGDVCVFEVLRAREFVLKVTVFRVSE 346
             RCLY+ GRAKFSQGWYEFT+EN +GEGDVCVFE+LR R+FVL+VT FRV+E
Sbjct:   174 RCLYKAGRAKFSQGWYEFTLENNIGEGDVCVFELLRTRDFVLEVTAFRVNE 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:2133362 AT4G01580 [Arabidopsis thaliana (taxid:3702)]

 Score = 242 (90.2 bits), Expect = 1.7e-20, P = 1.7e-20
 Identities = 46/108 (42%), Positives = 67/108 (62%)

Query:     2 PRPYFHKLILASTIRDKRLRIPENFVRNFKDDLSAAATLIVPNGMVSRVGLRRLDNKVWF 61
             P   F KL+L ST++DK +RIP  FV+     LS   TL+ P G    + L+R+  ++WF
Sbjct:    26 PVKKFFKLVLPSTMKDKMMRIPPRFVKLQGSKLSEVVTLVTPAGYKRSIKLKRIGEEIWF 85

Query:    62 YDGWQEFMERYFIRIGYFLVFRYEGNSAFNVYIFNLPSSEINYQPNAL 109
             ++GW EF E + I  G+FL+F Y+ NS+F V IFN  + E NY  +A+
Sbjct:    86 HEGWSEFAEAHSIEEGHFLLFEYKKNSSFRVIIFNASACETNYPLDAV 133

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 = 230 (86.0 bits), Expect = 3.1e-19, P = 3.1e-19
 Identities = 44/108 (40%), Positives = 66/108 (61%)

Query:     2 PRPYFHKLILASTIRDKRLRIPENFVRNFKDDLSAAATLIVPNGMVSRVGLRRLDNKVWF 61
             P   F KL+L ST++DK ++IP  FV+     LS   TL  P G    + L+R+  ++WF
Sbjct:    26 PVKKFFKLVLPSTMKDKMMKIPPRFVKLQGSKLSEVVTLETPAGFKRSIKLKRIGEEIWF 85

Query:    62 YDGWQEFMERYFIRIGYFLVFRYEGNSAFNVYIFNLPSSEINYQPNAL 109
             ++GW EF E + I  G+FL+F Y+ NS+F V IFN+ + E  Y  +A+
Sbjct:    86 HEGWSEFAEAHSIEEGHFLLFEYKENSSFRVIIFNVSACETKYPLDAV 133

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 = 227 (85.0 bits), Expect = 6.5e-19, P = 6.5e-19
 Identities = 53/139 (38%), Positives = 77/139 (55%)

Query:     6 FHKLILASTIRDKRLRIPENFVRNFKDDLSAAATLIVPNGMVSRVGLRRLDNKVWFYDGW 65
             F K+IL S I +K +++P  FVR F   L+   TL  P G    + ++R+ ++VWF  GW
Sbjct:    34 FIKIILLSRIIEKMMKVPARFVR-FGPKLTDNVTLQTPVGFKRSIRIKRIGDEVWFEKGW 92

Query:    66 QEFMERYFIRIGYFLVFRYEGNSAFNVYIFNLPSSEINYQPNALSNF--EVPNHSKQYHI 123
              EF E + +  G+FL F YEG+S F V IF++ +SEI Y  +   +   EV +  +Q   
Sbjct:    93 SEFAEAHSLSDGHFLFFHYEGDSCFRVVIFDVSASEIEYPLDDTDDNREEVMDDDEQGFT 152

Query:   124 FAEMEDDDSEHVDQPTVNK 142
               E  DDD E VD   + K
Sbjct:   153 GFESSDDDGEVVDMDELLK 171

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:2119166 AT4G33280 [Arabidopsis thaliana (taxid:3702)]

 Score = 121 (47.7 bits), Expect = 1.7e-12, Sum P(2) = 1.7e-12
 Identities = 36/125 (28%), Positives = 63/125 (50%)

Query:   228 VTAEERERAINAAK-AFEPSNPFCRVVLRPSYLYKGCIMYLPSCFAEKHLNGVCGFIKLQ 286
             ++A   ++A++ AK A  P   F  V ++ S++   C + +P  +  K++      + +Q
Sbjct:   202 ISAGSNKKALSLAKRAISPDG-FL-VFMKRSHVVSKCFLTIPYKWCVKNMLITRQEVVMQ 259

Query:   287 LSDGKQWPVRCLYRGGRAK--FSQGWYEFTVENRLGEGDVCVFEVLRA--REFVLKVTVF 342
             + D  +W ++    G R     S GW +F  +N L EGDVCVFE   +  +   L V +F
Sbjct:   260 V-DQTKWEMKFNIFGARGSGGISTGWKKFVQDNNLREGDVCVFEPANSETKPLHLNVYIF 318

Query:   343 RVSES 347
             R  E+
Sbjct:   319 RGEET 323

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:2161533 VDD "VERDANDI" [Arabidopsis thaliana (taxid:3702)]

 Score = 111 (44.1 bits), Expect = 4.9e-10, Sum P(2) = 4.9e-10
 Identities = 34/143 (23%), Positives = 67/143 (46%)

Query:   201 QASSAQEVHDGEMQFRFYESASARKRTVTAEER-ERAINAAKAFEPSN-PFCRVVLRPSY 258
             +++S +     E+  R  E+    K   + +++ E   N ++A   S  P  ++ ++ S+
Sbjct:   166 ESTSGRLTQKQELNLRKKEADKTEKSKTSKKKKVETVSNDSEAGTSSLIPEFKLTIKKSH 225

Query:   259 LYKGCIMYLPSCFAEKHLNGVCGFIKLQLSDGKQ-WPVRCLYRGGRAKFSQGWYEFTVEN 317
             L     + +P  F + H+       K+    GK+ W V  +    +++FS GW     E 
Sbjct:   226 LL---FLGIPKKFVDMHMPTETTMFKIHYPRGKKSWDVTYVVTDVQSRFSGGWSRLAKEL 282

Query:   318 RLGEGDVCVFEVLRAREFVLKVT 340
              L  GDVC F++++  E  +KV+
Sbjct:   283 GLLVGDVCTFKLIKPTEMRVKVS 305

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:0009553 "embryo sac development" evidence=IMP

GO:0009567 "double fertilization forming a zygote and endosperm" evidence=IMP

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

 Score = 108 (43.1 bits), Expect = 8.0e-10, Sum P(2) = 8.0e-10
 Identities = 25/94 (26%), Positives = 44/94 (46%)

Query:   248 PFCRVVLRPSYLYKGCIMYLPSCFAEKHLNGVCGFIKLQLSDGKQ-WPVRCLYRGGRAKF 306
             P   + ++ SYL     + +P  F E H+       K+   +GK+ W V   +   + +F
Sbjct:   210 PEFTLTIKKSYLI---FLGIPKMFEELHMPTEATMFKIHDPEGKRSWDVMYKFSNNQTRF 266

Query:   307 SQGWYEFTVENRLGEGDVCVFEVLRAREFVLKVT 340
               GW     E  L  GDVC F +++  E +++V+
Sbjct:   267 CAGWIRLAKELGLEIGDVCTFTLIKPTEMLVRVS 300

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:2086082 REM22 "REPRODUCTIVE MERISTEM 22" [Arabidopsis thaliana (taxid:3702)]

 Score = 137 (53.3 bits), Expect = 6.6e-09, Sum P(2) = 6.6e-09
 Identities = 45/176 (25%), Positives = 79/176 (44%)

Query:   167 EAN-LQRLKVKLYSQDGETPKLKKP-GRKRKIDPNVQASSAQEVHDGEMQFR---FYESA 221
             E N L+  K + +   G +  +KK  G    ID   +  S +     E   R     +S 
Sbjct:   114 EQNGLEMRKPRKFQTMGPSSGIKKEEGENSLIDVKKEEESDESPGRAEFLVRKKKTEDSK 173

Query:   222 SARKRTVTAEERERAINAAKAFEPSNPFCRVVLRPSYLYKGCIMYLPSCFAEKHLNGVCG 281
             S++K+    + ++++ + +K      P  ++ +R SYL     + +P  F + H+     
Sbjct:   174 SSKKKMTRNKVKKKSKSKSKQVLDGVPEFKITIRKSYLK---FLAIPKHFVDDHIPNKSK 230

Query:   282 FIKLQLSDGKQWPVRCLYRGGRAKFSQGWYEFTVENRLGEGDVCVFEVLRAREFVL 337
                ++  +G  W V CL R  R  FS G+ +   E  L  GD C F++++  EFVL
Sbjct:   231 IFTIRHPNGGSWKVLCLVREIRTIFSGGYSKLAREFPLMVGDKCTFKLIKPFEFVL 286

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:0010093 "specification of floral organ identity" evidence=RCA

GO:0048440 "carpel development" evidence=RCA

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

 Score = 112 (44.5 bits), Expect = 2.5e-08, Sum P(2) = 2.5e-08
 Identities = 39/139 (28%), Positives = 68/139 (48%)

Query:     5 YFHKLILASTIRDKRLRIPENFVRNFKDDLSAAATLIVPNGMVSRVGLRRLD-NKVWFYD 63
             +F K +L    R+  L IP  F     +      T+ +      R    ++D N++   +
Sbjct:    13 HFFKPLLPGFQRN--LNIPVKFFSEHIEGKHEGETVKLRADASKRTWEVKMDGNRLT--E 68

Query:    64 GWQEFMERYFIRIGYFLVFRYEGNSAFNVYIFNLPSSEINYQPNALSNFEVPNHSKQYHI 123
             GW+EF+E + +RI  F+VFR+EG+  F+V        EI Y P ++S+ E    S +  I
Sbjct:    69 GWKEFVEAHDLRIRDFVVFRHEGDMVFHVTALGPSCCEIQY-PQSISH-EEGEESGEVEI 126

Query:   124 FA-EMEDDDSEHVDQPTVN 141
                E+E++  +  DQ + +
Sbjct:   127 SEREVEENLQKEYDQSSAD 145

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

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q8L3W1	VRN1_ARATH	No assigned EC number	0.6057	0.9463	0.9824	yes	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	354
cd10017	98	cd10017, B3_DNA, Plant-specific B3-DNA binding dom	4e-20
smart01019	96	smart01019, B3, B3 DNA binding domain	1e-17
pfam02362	97	pfam02362, B3, B3 DNA binding domain	7e-17
cd10017	98	cd10017, B3_DNA, Plant-specific B3-DNA binding dom	1e-13
smart01019	96	smart01019, B3, B3 DNA binding domain	8e-12
pfam02362	97	pfam02362, B3, B3 DNA binding domain	8e-11

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

 Score = 83.5 bits (207), Expect = 4e-20
 Identities = 40/99 (40%), Positives = 48/99 (48%), Gaps = 4/99 (4%)

Query: 248 PFCRVVLRPSYLYKGCIMYLPSCFAEKHLNGVCG-FIKLQLSDGKQWPVRCLYRG--GRA 304
           P    VL PS +     + LP  FA+ HL    G  + L+  DGK+W V+   R   GR 
Sbjct: 1   PLFFKVLTPSDVSSLGRLVLPKKFAKAHLPPKEGVEVTLEDPDGKKWTVKLKKRKNSGRM 60

Query: 305 KFSQGWYEFTVENRLGEGDVCVFEVLRAREFVLKVTVFR 343
             S GW EF   N L EGD  VFE L  R    KV +FR
Sbjct: 61  VLSGGWKEFVRANGLKEGDFLVFE-LDGRNSKFKVRIFR 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|214977 smart01019, B3, B3 DNA binding domain

 Score = 76.6 bits (189), Expect = 1e-17
 Identities = 32/91 (35%), Positives = 41/91 (45%), Gaps = 3/91 (3%)

Query: 252 VVLRPSYLYKGCIMYLPSCFAEKHLNGV-CGFIKLQLSDGKQWPVRCLYRG--GRAKFSQ 308
             L  S + K   + LP  FAE +   +    I L   DGK W V+  YRG  G    + 
Sbjct: 3   KTLTTSDVSKHGRLVLPKQFAESNGPPLKPKEITLLDPDGKSWKVKLKYRGSSGMFLLTG 62

Query: 309 GWYEFTVENRLGEGDVCVFEVLRAREFVLKV 339
           GW EF   N L  GD   FE+    EFV+ +
Sbjct: 63  GWKEFVKANGLKAGDSLTFELDGNGEFVVSI 93

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

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

 Score = 74.7 bits (184), Expect = 7e-17
 Identities = 39/96 (40%), Positives = 49/96 (51%), Gaps = 5/96 (5%)

Query: 253 VLRPSYLYKGCIMYLPSCFAEKH-LNGVCGFIKLQLSDGKQWPVRCLYR--GGRAKFSQG 309
           VL PS + K   + LP  FAE++ LN     I L   DGK W V+  YR  G R   + G
Sbjct: 4   VLTPSDVSKDGRLVLPKKFAEENGLNKKGQEITLLDPDGKSWTVKLRYRKSGRRYLLTSG 63

Query: 310 WYEFTVENRLGEGDVCVFEVLRAREFVLKVTVFRVS 345
           W EF   N L  GD  VF++    +FV  V +FR S
Sbjct: 64  WKEFVKANGLKAGDSLVFKLDGGGKFV--VGIFRKS 97

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

 Score = 65.8 bits (161), Expect = 1e-13
 Identities = 31/98 (31%), Positives = 47/98 (47%), Gaps = 5/98 (5%)

Query: 4  PYFHKLILAS-TIRDKRLRIPENFVR-NFKDDLSAAATLIVPNGMVSRVGLRRLDN--KV 59
          P F K++  S      RL +P+ F + +         TL  P+G    V L++  N  ++
Sbjct: 1  PLFFKVLTPSDVSSLGRLVLPKKFAKAHLPPKEGVEVTLEDPDGKKWTVKLKKRKNSGRM 60

Query: 60 WFYDGWQEFMERYFIRIGYFLVFRYEG-NSAFNVYIFN 96
              GW+EF+    ++ G FLVF  +G NS F V IF 
Sbjct: 61 VLSGGWKEFVRANGLKEGDFLVFELDGRNSKFKVRIFR 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|214977 smart01019, B3, B3 DNA binding domain

 Score = 60.8 bits (148), Expect = 8e-12
 Identities = 27/95 (28%), Positives = 44/95 (46%), Gaps = 3/95 (3%)

Query: 5  YFHKLILASTIRDKRLRIPENFVRNFKDDLSAA-ATLIVPNGMVSRVGLRRLDNKVWFY- 62
          +F  L  +   +  RL +P+ F  +    L     TL+ P+G   +V L+   +   F  
Sbjct: 1  FFKTLTTSDVSKHGRLVLPKQFAESNGPPLKPKEITLLDPDGKSWKVKLKYRGSSGMFLL 60

Query: 63 -DGWQEFMERYFIRIGYFLVFRYEGNSAFNVYIFN 96
            GW+EF++   ++ G  L F  +GN  F V IF 
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|216995 pfam02362, B3, B3 DNA binding domain

 Score = 57.7 bits (140), Expect = 8e-11
 Identities = 29/95 (30%), Positives = 45/95 (47%), Gaps = 4/95 (4%)

Query: 6  FHKLILAS-TIRDKRLRIPENFVR-NFKDDLSAAATLIVPNGMVSRVGLRRL--DNKVWF 61
          F K++  S   +D RL +P+ F   N  +      TL+ P+G    V LR      +   
Sbjct: 1  FVKVLTPSDVSKDGRLVLPKKFAEENGLNKKGQEITLLDPDGKSWTVKLRYRKSGRRYLL 60

Query: 62 YDGWQEFMERYFIRIGYFLVFRYEGNSAFNVYIFN 96
            GW+EF++   ++ G  LVF+ +G   F V IF 
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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	354
PF02362	100	B3: B3 DNA binding domain; InterPro: IPR003340 Two	99.89
PF02362	100	B3: B3 DNA binding domain; InterPro: IPR003340 Two	99.85
PF03754	114	DUF313: Domain of unknown function (DUF313) ; Inte	94.64
PF03754	114	DUF313: Domain of unknown function (DUF313) ; Inte	91.44

>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=99.89  E-value=8.4e-23  Score=163.44  Aligned_cols=96  Identities=42%  Similarity=0.763  Sum_probs=73.0

Q ss_pred             EEEEccCCCCCCCceEEcCHHHHHhhCCC--CCeeEEEEeCCCCeEEEEEEEe--CCeeeecccHHHhhhhcCCCCCcEE
Q 018533          250 CRVVLRPSYLYKGCIMYLPSCFAEKHLNG--VCGFIKLQLSDGKQWPVRCLYR--GGRAKFSQGWYEFTVENRLGEGDVC  325 (354)
Q Consensus       250 F~~~m~~s~v~~~~~L~iP~~f~~~~l~~--~~~~i~L~~~~Gr~W~v~~~~~--~~~~~l~~GW~~F~~~n~Lk~GD~c  325 (354)
                      |+++|+++++...+.|.||++|+++|...  .+.+|+|+|++|+.|+|++.+.  ++++.|++||.+||++|+|++||+|
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            78999999998877899999999999643  5679999999999999999643  4678999999999999999999999


Q ss_pred             EEEEecCceeEEEEEEEeec
Q 018533          326 VFEVLRAREFVLKVTVFRVS  345 (354)
Q Consensus       326 vFel~~~~~~~~~V~Ifr~~  345 (354)
                      +|+++++....+.|+|||+.
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            99999876778899999963

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=99.85  E-value=6.1e-21  Score=152.61  Aligned_cols=93  Identities=31%  Similarity=0.521  Sum_probs=70.6

Q ss_pred             EEEeecccccc-cceeecchHHHHHhcCC--CCCcEEEEcCCCCEEEEEE--EEEcCeEEEcccHHHHHhHcCCCCCcEE
Q 018533            6 FHKLILASTIR-DKRLRIPENFVRNFKDD--LSAAATLIVPNGMVSRVGL--RRLDNKVWFYDGWQEFMERYFIRIGYFL   80 (354)
Q Consensus         6 F~k~~~~~~~~-~~~l~IP~~F~~~~~~~--~~~~v~L~~~~G~~W~V~l--~k~~~~~~~~~GW~~F~~~~~L~~gd~l   80 (354)
                      |+|+|+++... .+.|.||..|++.|+..  .+..|+|++++|+.|.|.+  .+..+..+|++||++||++|+|++||+|
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            89999877553 46799999999999754  5779999999999999999  5566889999999999999999999999


Q ss_pred             EEEEeccceE--EEEEEcCC
Q 018533           81 VFRYEGNSAF--NVYIFNLP   98 (354)
Q Consensus        81 vF~~~g~s~F--~V~if~~~   98 (354)
                      +|++++++.|  .|.||+.+
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            9999987777  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=94.64  E-value=0.19  Score=41.14  Aligned_cols=68  Identities=12%  Similarity=0.089  Sum_probs=48.1

Q ss_pred             eEEEEccCCCCCC-CceEEcCHHHHHh--hC----------------CCCCeeEEEEeCCCCeEEEEEEEeCC-----ee
Q 018533          249 FCRVVLRPSYLYK-GCIMYLPSCFAEK--HL----------------NGVCGFIKLQLSDGKQWPVRCLYRGG-----RA  304 (354)
Q Consensus       249 ~F~~~m~~s~v~~-~~~L~iP~~f~~~--~l----------------~~~~~~i~L~~~~Gr~W~v~~~~~~~-----~~  304 (354)
                      .+.+.|.+|+|.. ..+|.||-.=...  +|                ....-.|+|.|+.++.|.+++.+-..     .+
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            4556788888864 2478899764422  12                12345799999999999999875322     47


Q ss_pred             eecccHHHhhhh
Q 018533          305 KFSQGWYEFTVE  316 (354)
Q Consensus       305 ~l~~GW~~F~~~  316 (354)
                      .|..||..+|.+
T Consensus       103 vL~~gWn~VV~~  114 (114)
T PF03754_consen  103 VLNSGWNKVVED  114 (114)
T ss_pred             EEEcChHhhccC
Confidence            899999998864

>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=91.44  E-value=0.86  Score=37.28  Aligned_cols=66  Identities=17%  Similarity=0.328  Sum_probs=45.5

Q ss_pred             EEEeecccccc--cceeecchHHHHHh------------------cCCCCCcEEEEcCCCCEEEEEEEEEcC-----eEE
Q 018533            6 FHKLILASTIR--DKRLRIPENFVRNF------------------KDDLSAAATLIVPNGMVSRVGLRRLDN-----KVW   60 (354)
Q Consensus         6 F~k~~~~~~~~--~~~l~IP~~F~~~~------------------~~~~~~~v~L~~~~G~~W~V~l~k~~~-----~~~   60 (354)
                      +-|.+..+.+.  +.+|.||-.=+...                  .....-.|.|.+|.++.|.+.|++=.-     ...
T Consensus        24 ~~K~L~~tDv~~~qsRLsmP~~qi~~~dFLt~eE~~~i~~~~~~~~~~~Gv~V~lvdp~~~~~~m~lkkW~mg~~~~~Yv  103 (114)
T PF03754_consen   24 IEKTLFKTDVDPHQSRLSMPFNQIIDNDFLTEEEKRIIKEEKKNNDKKKGVEVILVDPSLRKWTMRLKKWNMGNGTSNYV  103 (114)
T ss_pred             EeeeecccCCCCCCceeeccHHHhcccccCCHHHHHHHHHhhccCcccCCceEEEECCcCcEEEEEEEEecccCCceEEE
Confidence            44666666663  46788886644111                  112345899999999999999997422     455


Q ss_pred             EcccHHHHHhH
Q 018533           61 FYDGWQEFMER   71 (354)
Q Consensus        61 ~~~GW~~F~~~   71 (354)
                      |..||..+|++
T Consensus       104 L~~gWn~VV~~  114 (114)
T PF03754_consen  104 LNSGWNKVVED  114 (114)
T ss_pred             EEcChHhhccC
Confidence            99999999864

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	354
4i1k_A	146	Crystal Structure Of Vrn1 (residues 208-341) Length		2e-60

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

Iteration: 1
 Score =  229 bits (583), Expect = 2e-60,   Method: Compositional matrix adjust.
 Identities = 108/131 (82%), Positives = 122/131 (93%), Gaps = 1/131 (0%)
Query: 216 RFYESASARKRTVTAEERERAINAAKAFEPSNPFCRVVLRPSYLYKGCIMYLPSCFAEKH 275
           +FYESASARKRTVTAEERERAINAAK FEP+NPF RVVLRPSYLY+GCIMYLPS FAEK+
Sbjct: 15  KFYESASARKRTVTAEERERAINAAKTFEPTNPFFRVVLRPSYLYRGCIMYLPSGFAEKY 74
Query: 276 LNGVCGFIKLQLSDGKQWPVRCLYRGGRAKFSQGWYEFTVENRLGEGDVCVFEVLRAREF 335
           L+G+ GFIK+QL++ KQWPVRCLY+ GRAKFSQGWYEFT+EN LGEGDVCVFE+LR R+F
Sbjct: 75  LSGISGFIKVQLAE-KQWPVRCLYKAGRAKFSQGWYEFTLENNLGEGDVCVFELLRTRDF 133
Query: 336 VLKVTVFRVSE 346
           VLKVT FRV+E
Sbjct: 134 VLKVTAFRVNE 144

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	354
1yel_A	104	AT1G16640; CESG, protein structure initiative, str	2e-30
1yel_A	104	AT1G16640; CESG, protein structure initiative, str	2e-15
1wid_A	130	DNA-binding protein RAV1; DNA-binding domain, stru	9e-16

>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 =  111 bits (278), Expect = 2e-30
 Identities = 24/94 (25%), Positives = 39/94 (41%), Gaps = 1/94 (1%)

Query: 3   RPYFHKLILASTIRDKRLRIPENFVRNFKDDLSAAATLIVPNGMVSRVGLRRLDNKVWFY 62
              F K  + S    K L IP  F   F         L+  +G    V +++   KV+  
Sbjct: 8   EVQFMKPFI-SEKSSKSLEIPLGFNEYFPAPFPITVDLLDYSGRSWTVRMKKRGEKVFLT 66

Query: 63  DGWQEFMERYFIRIGYFLVFRYEGNSAFNVYIFN 96
            GW+ F++   +  G +L F Y+ +  F V I+ 
Sbjct: 67  VGWENFVKDNNLEDGKYLQFIYDRDRTFYVIIYG 100

>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 = 70.2 bits (172), Expect = 2e-15
 Identities = 23/97 (23%), Positives = 36/97 (37%), Gaps = 5/97 (5%)

Query: 249 FCRVVLRPSYLYKGCIMYLPSCFAEKHLNGVCGFIKLQLSDGKQWPVRCLYRGGRAKFSQ 308
           F +  +      K   + +P  F E         + L    G+ W VR   RG +   + 
Sbjct: 11  FMKPFI-SEKSSKS--LEIPLGFNEYFPAPFPITVDLLDYSGRSWTVRMKKRGEKVFLTV 67

Query: 309 GWYEFTVENRLGEGDVCVFEVLRAREFVLKVTVFRVS 345
           GW  F  +N L +G    F   R R F   V ++  +
Sbjct: 68  GWENFVKDNNLEDGKYLQFIYDRDRTF--YVIIYGHN 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 = 72.1 bits (176), Expect = 9e-16
 Identities = 25/119 (21%), Positives = 41/119 (34%), Gaps = 9/119 (7%)

Query: 238 NAAKAFEPSNPFCRVVLRPSYLYKGCIMYLPSCFAEKHLNGVCGF-------IKLQLSDG 290
           ++  +   +       + PS + K   + +P   AEKH              +  +  +G
Sbjct: 2   SSGSSGRSAEALFEKAVTPSDVGKLNRLVIPKHHAEKHFPLPSSNVSVKGVLLNFEDVNG 61

Query: 291 KQWPVRCLYRGG--RAKFSQGWYEFTVENRLGEGDVCVFEVLRAREFVLKVTVFRVSES 347
           K W  R  Y         ++GW  F  E  L  GDV  F     ++  L +     S S
Sbjct: 62  KVWRFRYSYWNSSQSYVLTKGWSRFVKEKNLRAGDVVSFSRSNGQDQQLYIGWKSRSGS 120

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	354
4i1k_A	146	B3 domain-containing transcription factor VRN1; B3	100.0
1yel_A	104	AT1G16640; CESG, protein structure initiative, str	99.95
1yel_A	104	AT1G16640; CESG, protein structure initiative, str	99.91
1wid_A	130	DNA-binding protein RAV1; DNA-binding domain, stru	99.85
4i1k_A	146	B3 domain-containing transcription factor VRN1; B3	99.84
1wid_A	130	DNA-binding protein RAV1; DNA-binding domain, stru	99.56

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

Probab=100.00  E-value=6.2e-36  Score=254.33  Aligned_cols=133  Identities=81%  Similarity=1.356  Sum_probs=114.1

Q ss_pred             cccchhccccccccCCHHHHHHHHHHHHhcCCCCCeEEEEccCCCCCCCceEEcCHHHHHhhCCCCCeeEEEEeCCCCeE
Q 018533          214 QFRFYESASARKRTVTAEERERAINAAKAFEPSNPFCRVVLRPSYLYKGCIMYLPSCFAEKHLNGVCGFIKLQLSDGKQW  293 (354)
Q Consensus       214 ~~~~~~~~~~~~~~~t~~e~~~a~~~a~~~~s~~P~F~~~m~~s~v~~~~~L~iP~~f~~~~l~~~~~~i~L~~~~Gr~W  293 (354)
                      ...||+++++++++||.+|+++|+++|++|+|++|+|+++|++|++++++.|.||++|+++|||....+|+|+++ |+.|
T Consensus        13 ~~~~~~~~~~~r~~~t~~~k~~a~~~A~~~~s~~P~Fvk~l~~S~v~~~~~L~IP~~Fa~~~lp~~~~~i~L~~~-gk~W   91 (146)
T 4i1k_A           13 RSKFYESASARKRTVTAEERERAINAAKTFEPTNPFFRVVLRPSYLYRGCIMYLPSGFAEKYLSGISGFIKVQLA-EKQW   91 (146)
T ss_dssp             -------------CCCHHHHHHHHHHHHHCCCSSCEEEEECCGGGSSTTCCEECCHHHHHHHCTTCCSEEEEEET-TEEE
T ss_pred             hhhhhhhhccCCCCCCHHHHHHHHHHHHHcCCCCCEEEEEECchhcCCCcEEEeCHHHHHHhCCCCCeEEEEEEC-CcEE
Confidence            346888999999999999999999999999999999999999999998888999999999999999999999999 5999


Q ss_pred             EEEEEEeCCeeeecccHHHhhhhcCCCCCcEEEEEEecCceeEEEEEEEeecCC
Q 018533          294 PVRCLYRGGRAKFSQGWYEFTVENRLGEGDVCVFEVLRAREFVLKVTVFRVSES  347 (354)
Q Consensus       294 ~v~~~~~~~~~~l~~GW~~F~~~n~Lk~GD~cvFel~~~~~~~~~V~Ifr~~~~  347 (354)
                      .|++.+.+++..|++||..||++|+|++||+|||||+++.+++|+|||||++|+
T Consensus        92 ~v~~~~~~~~~~ls~GW~~Fv~dn~L~~GD~cvFeli~~~~~~f~V~IfR~~e~  145 (146)
T 4i1k_A           92 PVRCLYKAGRAKFSQGWYEFTLENNLGEGDVCVFELLRTRDFVLKVTAFRVNEY  145 (146)
T ss_dssp             EEEEEEETTEEEECTTHHHHHHHTTCCTTCEEEEEECSSSSCEEEEEEECCC--
T ss_pred             EEEEEEeCCcEEECCchHHHHHHcCCCCCCEEEEEEecCCceEEEEEEEeccCC
Confidence            999988888999999999999999999999999999998788999999999986

>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-28  Score=196.62  Aligned_cols=98  Identities=23%  Similarity=0.420  Sum_probs=93.5

Q ss_pred             CCCeEEEeecccccccceeecchHHHHHhcCCCCCcEEEEcCCCCEEEEEEEEEcCeEEEcccHHHHHhHcCCCCCcEEE
Q 018533            2 PRPYFHKLILASTIRDKRLRIPENFVRNFKDDLSAAATLIVPNGMVSRVGLRRLDNKVWFYDGWQEFMERYFIRIGYFLV   81 (354)
Q Consensus         2 ~~p~F~k~~~~~~~~~~~l~IP~~F~~~~~~~~~~~v~L~~~~G~~W~V~l~k~~~~~~~~~GW~~F~~~~~L~~gd~lv   81 (354)
                      .+|+|||+|+++.. ...|.||..|+++|.+.++.+|+|++++|++|+|.+.+.+++++|++||++||.+|+|++||+|+
T Consensus         7 ~~p~F~K~l~~~~~-~~~L~IP~~F~~~~~~~~~~~v~L~~~~G~~W~v~~~~~~~~~~l~~GW~~Fv~~~~L~~GD~lv   85 (104)
T 1yel_A            7 GEVQFMKPFISEKS-SKSLEIPLGFNEYFPAPFPITVDLLDYSGRSWTVRMKKRGEKVFLTVGWENFVKDNNLEDGKYLQ   85 (104)
T ss_dssp             CCEEEEEECCHHHH-TTCEECCHHHHTTCCCCCCSEEEEEETTSCEEEEEEEEETTEEEECTTHHHHHHHHTCCTTCEEE
T ss_pred             CCCCEEEEECCCCc-cceEECCHHHHHhcCccCCCEEEEECCCCCEEEEEEEEECCcEEEccChHHHHHHcCCCCCCEEE
Confidence            47899999998863 57899999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEEeccceEEEEEEcCCCC
Q 018533           82 FRYEGNSAFNVYIFNLPSS  100 (354)
Q Consensus        82 F~~~g~s~F~V~if~~~~~  100 (354)
                      |+|+|++.|.|+||+.++|
T Consensus        86 F~~~~~~~f~V~If~~s~C  104 (104)
T 1yel_A           86 FIYDRDRTFYVIIYGHNMC  104 (104)
T ss_dssp             EEECSSSEEEEEEECSSCC
T ss_pred             EEEcCCCeEEEEEECCCCC
Confidence            9999999999999999998

>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=99.91  E-value=4e-24  Score=171.73  Aligned_cols=99  Identities=20%  Similarity=0.272  Sum_probs=89.7

Q ss_pred             cCCCCCeEEEEccCCCCCCCceEEcCHHHHHhhCCCCCeeEEEEeCCCCeEEEEEEEeCCeeeecccHHHhhhhcCCCCC
Q 018533          243 FEPSNPFCRVVLRPSYLYKGCIMYLPSCFAEKHLNGVCGFIKLQLSDGKQWPVRCLYRGGRAKFSQGWYEFTVENRLGEG  322 (354)
Q Consensus       243 ~~s~~P~F~~~m~~s~v~~~~~L~iP~~f~~~~l~~~~~~i~L~~~~Gr~W~v~~~~~~~~~~l~~GW~~F~~~n~Lk~G  322 (354)
                      ..+++|.|.++|.+++.  ...|.||.+|++.|++..+.+|+|++++|+.|.|++.+.+++..|++||++||++|+|++|
T Consensus         4 ~~~~~p~F~K~l~~~~~--~~~L~IP~~F~~~~~~~~~~~v~L~~~~G~~W~v~~~~~~~~~~l~~GW~~Fv~~~~L~~G   81 (104)
T 1yel_A            4 ADTGEVQFMKPFISEKS--SKSLEIPLGFNEYFPAPFPITVDLLDYSGRSWTVRMKKRGEKVFLTVGWENFVKDNNLEDG   81 (104)
T ss_dssp             CCCCCEEEEEECCHHHH--TTCEECCHHHHTTCCCCCCSEEEEEETTSCEEEEEEEEETTEEEECTTHHHHHHHHTCCTT
T ss_pred             CCCCCCCEEEEECCCCc--cceEECCHHHHHhcCccCCCEEEEECCCCCEEEEEEEEECCcEEEccChHHHHHHcCCCCC
Confidence            46789999999999873  3479999999999988888999999999999999998888899999999999999999999


Q ss_pred             cEEEEEEecCceeEEEEEEEeec
Q 018533          323 DVCVFEVLRAREFVLKVTVFRVS  345 (354)
Q Consensus       323 D~cvFel~~~~~~~~~V~Ifr~~  345 (354)
                      |+|+|+++++.  .|+|+||+..
T Consensus        82 D~lvF~~~~~~--~f~V~If~~s  102 (104)
T 1yel_A           82 KYLQFIYDRDR--TFYVIIYGHN  102 (104)
T ss_dssp             CEEEEEECSSS--EEEEEEECSS
T ss_pred             CEEEEEEcCCC--eEEEEEECCC
Confidence            99999999764  6999999963

>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=99.85  E-value=7.2e-21  Score=158.59  Aligned_cols=104  Identities=24%  Similarity=0.348  Sum_probs=91.2

Q ss_pred             CCCCCeEEEEccCCCCCCCceEEcCHHHHHhhCCCCC-------eeEEEEeCCCCeEEEEEEEeC--CeeeecccHHHhh
Q 018533          244 EPSNPFCRVVLRPSYLYKGCIMYLPSCFAEKHLNGVC-------GFIKLQLSDGKQWPVRCLYRG--GRAKFSQGWYEFT  314 (354)
Q Consensus       244 ~s~~P~F~~~m~~s~v~~~~~L~iP~~f~~~~l~~~~-------~~i~L~~~~Gr~W~v~~~~~~--~~~~l~~GW~~F~  314 (354)
                      .+..|.|.++|++|+|...+.|.||++||++|||...       ..|+|+|.+|+.|.+++.+++  .++.|++||..||
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            4778999999999999876789999999999998765       578999999999999998764  4688999999999


Q ss_pred             hhcCCCCCcEEEEEEecCceeEEEEEEEeecCC
Q 018533          315 VENRLGEGDVCVFEVLRAREFVLKVTVFRVSES  347 (354)
Q Consensus       315 ~~n~Lk~GD~cvFel~~~~~~~~~V~Ifr~~~~  347 (354)
                      ++|+|++||+|+|+++.+.+..+.|.+.|....
T Consensus        88 ~~~~L~~GD~~~F~~~~~~~~~l~I~~rr~~~~  120 (130)
T 1wid_A           88 KEKNLRAGDVVSFSRSNGQDQQLYIGWKSRSGS  120 (130)
T ss_dssp             HHTTCCTTCEEEEEECCSSSCCEEEEEECCCSC
T ss_pred             HHcCCCCCCEEEEEEecCCCcEEEEEEEECCCC
Confidence            999999999999999986555688888888644

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

Probab=99.84  E-value=2.9e-20  Score=157.68  Aligned_cols=96  Identities=18%  Similarity=0.289  Sum_probs=88.0

Q ss_pred             CCCeEEEeecccccccc-eeecchHHHHHhcCCCCCcEEEEcCCCCEEEEEEEEEcCeEEEcccHHHHHhHcCCCCCcEE
Q 018533            2 PRPYFHKLILASTIRDK-RLRIPENFVRNFKDDLSAAATLIVPNGMVSRVGLRRLDNKVWFYDGWQEFMERYFIRIGYFL   80 (354)
Q Consensus         2 ~~p~F~k~~~~~~~~~~-~l~IP~~F~~~~~~~~~~~v~L~~~~G~~W~V~l~k~~~~~~~~~GW~~F~~~~~L~~gd~l   80 (354)
                      .+|+|+++|+++++... .|.||..|++.|.+....+|+|+++ |+.|.|.+...+++.+|++||.+||.+|+|++||+|
T Consensus        45 ~~P~Fvk~l~~S~v~~~~~L~IP~~Fa~~~lp~~~~~i~L~~~-gk~W~v~~~~~~~~~~ls~GW~~Fv~dn~L~~GD~c  123 (146)
T 4i1k_A           45 TNPFFRVVLRPSYLYRGCIMYLPSGFAEKYLSGISGFIKVQLA-EKQWPVRCLYKAGRAKFSQGWYEFTLENNLGEGDVC  123 (146)
T ss_dssp             SSCEEEEECCGGGSSTTCCEECCHHHHHHHCTTCCSEEEEEET-TEEEEEEEEEETTEEEECTTHHHHHHHTTCCTTCEE
T ss_pred             CCCEEEEEECchhcCCCcEEEeCHHHHHHhCCCCCeEEEEEEC-CcEEEEEEEEeCCcEEECCchHHHHHHcCCCCCCEE
Confidence            47999999999998543 6999999999999988999999999 599999998888889999999999999999999999


Q ss_pred             EEEEeccc--eEEEEEEcCC
Q 018533           81 VFRYEGNS--AFNVYIFNLP   98 (354)
Q Consensus        81 vF~~~g~s--~F~V~if~~~   98 (354)
                      +|+|+++.  .|.|+||+..
T Consensus       124 vFeli~~~~~~f~V~IfR~~  143 (146)
T 4i1k_A          124 VFELLRTRDFVLKVTAFRVN  143 (146)
T ss_dssp             EEEECSSSSCEEEEEEECCC
T ss_pred             EEEEecCCceEEEEEEEecc
Confidence            99999965  8999999765

>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=99.56  E-value=2.6e-14  Score=118.80  Aligned_cols=96  Identities=19%  Similarity=0.229  Sum_probs=79.8

Q ss_pred             CCCeEEEeecccccc-cceeecchHHHHHhcCCCC-------CcEEEEcCCCCEEEEEEEEE--cCeEEEcccHHHHHhH
Q 018533            2 PRPYFHKLILASTIR-DKRLRIPENFVRNFKDDLS-------AAATLIVPNGMVSRVGLRRL--DNKVWFYDGWQEFMER   71 (354)
Q Consensus         2 ~~p~F~k~~~~~~~~-~~~l~IP~~F~~~~~~~~~-------~~v~L~~~~G~~W~V~l~k~--~~~~~~~~GW~~F~~~   71 (354)
                      ..|.|.|+|+++++. ...|.||..|++.|.+.+.       ..++|+|+.|+.|.+.+...  ....+|+.||..||++
T Consensus        10 ~~~~F~K~Lt~SDv~~~~rL~iPk~~a~~~lP~~~~~~~~~~~~l~l~D~~Gk~W~fr~~~~~~~~~~~Lt~GW~~FV~~   89 (130)
T 1wid_A           10 AEALFEKAVTPSDVGKLNRLVIPKHHAEKHFPLPSSNVSVKGVLLNFEDVNGKVWRFRYSYWNSSQSYVLTKGWSRFVKE   89 (130)
T ss_dssp             CEEEEEEECCTTTTSSSCCEEECHHHHTTTSCCCSSCCSSCCEEEEEEETTTEEEEEEEEEETTTTEEEEESSHHHHHHH
T ss_pred             CcceEEEEEehHHcCCCCEEEeCHHHHHhhCCccccccCCCcEEEEEEeCCCCEEEEEEEEECCCCceEEcCChHHHHHH
Confidence            356899999999885 3689999999999887665       36889999999999998754  3567899999999999


Q ss_pred             cCCCCCcEEEEEEecc--ceEEEEEEcC
Q 018533           72 YFIRIGYFLVFRYEGN--SAFNVYIFNL   97 (354)
Q Consensus        72 ~~L~~gd~lvF~~~g~--s~F~V~if~~   97 (354)
                      |+|++||.|+|..+.+  ..+.|.+...
T Consensus        90 ~~L~~GD~~~F~~~~~~~~~l~I~~rr~  117 (130)
T 1wid_A           90 KNLRAGDVVSFSRSNGQDQQLYIGWKSR  117 (130)
T ss_dssp             TTCCTTCEEEEEECCSSSCCEEEEEECC
T ss_pred             cCCCCCCEEEEEEecCCCcEEEEEEEEC
Confidence            9999999999999864  4666666544

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

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

ID	Length	Definition	E-value
Query	354
d1yela1	102	b.142.1.2 (A:1-102) At1g16640 {Thale cress (Arabid	6e-23
d1yela1	102	b.142.1.2 (A:1-102) At1g16640 {Thale cress (Arabid	1e-19
d1wida_	117	b.142.1.2 (A:) DNA-binding protein RAV1 {Thale cre	5e-17

>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 = 89.9 bits (223), Expect = 6e-23
 Identities = 23/94 (24%), Positives = 39/94 (41%), Gaps = 1/94 (1%)

Query: 3  RPYFHKLILASTIRDKRLRIPENFVRNFKDDLSAAATLIVPNGMVSRVGLRRLDNKVWFY 62
             F K  ++     K L IP  F   F         L+  +G    V +++   KV+  
Sbjct: 6  EVQFMKPFISEKSS-KSLEIPLGFNEYFPAPFPITVDLLDYSGRSWTVRMKKRGEKVFLT 64

Query: 63 DGWQEFMERYFIRIGYFLVFRYEGNSAFNVYIFN 96
           GW+ F++   +  G +L F Y+ +  F V I+ 
Sbjct: 65 VGWENFVKDNNLEDGKYLQFIYDRDRTFYVIIYG 98

>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 = 80.7 bits (199), Expect = 1e-19
 Identities = 22/93 (23%), Positives = 33/93 (35%), Gaps = 4/93 (4%)

Query: 253 VLRPSYLYKGCIMYLPSCFAEKHLNGVCGFIKLQLSDGKQWPVRCLYRGGRAKFSQGWYE 312
                   K   + +P  F E         + L    G+ W VR   RG +   + GW  
Sbjct: 12  PFISEKSSKS--LEIPLGFNEYFPAPFPITVDLLDYSGRSWTVRMKKRGEKVFLTVGWEN 69

Query: 313 FTVENRLGEGDVCVFEVLRAREFVLKVTVFRVS 345
           F  +N L +G    F   R R F   V ++  +
Sbjct: 70  FVKDNNLEDGKYLQFIYDRDRTF--YVIIYGHN 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 = 73.9 bits (181), Expect = 5e-17
 Identities = 25/110 (22%), Positives = 38/110 (34%), Gaps = 9/110 (8%)

Query: 247 NPFCRVVLRPSYLYKGCIMYLPSCFAEKHL-------NGVCGFIKLQLSDGKQWPVRCLY 299
                  + PS + K   + +P   AEKH        +     +  +  +GK W  R  Y
Sbjct: 4   EALFEKAVTPSDVGKLNRLVIPKHHAEKHFPLPSSNVSVKGVLLNFEDVNGKVWRFRYSY 63

Query: 300 R--GGRAKFSQGWYEFTVENRLGEGDVCVFEVLRAREFVLKVTVFRVSES 347
                    ++GW  F  E  L  GDV  F     ++  L +     S S
Sbjct: 64  WNSSQSYVLTKGWSRFVKEKNLRAGDVVSFSRSNGQDQQLYIGWKSRSGS 113

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	354
d1yela1	102	At1g16640 {Thale cress (Arabidopsis thaliana) [Tax	99.96
d1yela1	102	At1g16640 {Thale cress (Arabidopsis thaliana) [Tax	99.89
d1wida_	117	DNA-binding protein RAV1 {Thale cress (Arabidopsis	99.84
d1wida_	117	DNA-binding protein RAV1 {Thale cress (Arabidopsis	99.56
d1na6a1	175	Restriction endonuclease EcoRII, N-terminal domain	98.27
d1na6a1	175	Restriction endonuclease EcoRII, N-terminal domain	97.15

>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=99.96  E-value=4.7e-29  Score=197.73  Aligned_cols=98  Identities=23%  Similarity=0.420  Sum_probs=93.9

Q ss_pred             CCCeEEEeecccccccceeecchHHHHHhcCCCCCcEEEEcCCCCEEEEEEEEEcCeEEEcccHHHHHhHcCCCCCcEEE
Q 018533            2 PRPYFHKLILASTIRDKRLRIPENFVRNFKDDLSAAATLIVPNGMVSRVGLRRLDNKVWFYDGWQEFMERYFIRIGYFLV   81 (354)
Q Consensus         2 ~~p~F~k~~~~~~~~~~~l~IP~~F~~~~~~~~~~~v~L~~~~G~~W~V~l~k~~~~~~~~~GW~~F~~~~~L~~gd~lv   81 (354)
                      .+|+|||+++++.. .+.|.||..|+++|++.++++|+|++++|+.|.|.+.+.++.++|..||++||++|+|++||+|+
T Consensus         5 ~~~~Ffkv~~~~~~-~~~L~IP~~F~~~~~~~~~~~i~L~d~~G~~W~v~~~~~~~~~~~~~GW~~Fv~~n~L~~GD~~v   83 (102)
T d1yela1           5 GEVQFMKPFISEKS-SKSLEIPLGFNEYFPAPFPITVDLLDYSGRSWTVRMKKRGEKVFLTVGWENFVKDNNLEDGKYLQ   83 (102)
T ss_dssp             CCEEEEEECCHHHH-TTCEECCHHHHTTCCCCCCSEEEEEETTSCEEEEEEEEETTEEEECTTHHHHHHHHTCCTTCEEE
T ss_pred             CCCeEEEEEcCccc-CCCEECCHHHHHhCCCCCCCEEEEEcCCCCEEEEEEEEeCCeEEEccCHHHHHHHcCCCcCCEEE
Confidence            36899999999975 47899999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEEeccceEEEEEEcCCCC
Q 018533           82 FRYEGNSAFNVYIFNLPSS  100 (354)
Q Consensus        82 F~~~g~s~F~V~if~~~~~  100 (354)
                      |+|+|+++|.|+|||.++|
T Consensus        84 F~~~~~~~f~V~If~~s~C  102 (102)
T d1yela1          84 FIYDRDRTFYVIIYGHNMC  102 (102)
T ss_dssp             EEECSSSEEEEEEECSSCC
T ss_pred             EEEcCCcEEEEEEeCCCCC
Confidence            9999999999999999998

>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=99.89  E-value=2.4e-23  Score=164.47  Aligned_cols=97  Identities=21%  Similarity=0.268  Sum_probs=88.6

Q ss_pred             CCCCCeEEEEccCCCCCCCceEEcCHHHHHhhCCCCCeeEEEEeCCCCeEEEEEEEeCCeeeecccHHHhhhhcCCCCCc
Q 018533          244 EPSNPFCRVVLRPSYLYKGCIMYLPSCFAEKHLNGVCGFIKLQLSDGKQWPVRCLYRGGRAKFSQGWYEFTVENRLGEGD  323 (354)
Q Consensus       244 ~s~~P~F~~~m~~s~v~~~~~L~iP~~f~~~~l~~~~~~i~L~~~~Gr~W~v~~~~~~~~~~l~~GW~~F~~~n~Lk~GD  323 (354)
                      .+..|.|.++|.+++...  .|.||..|++.|.+..+++|+|+|++|+.|+|++...++..+|+.||.+||++|+|++||
T Consensus         3 ~~~~~~Ffkv~~~~~~~~--~L~IP~~F~~~~~~~~~~~i~L~d~~G~~W~v~~~~~~~~~~~~~GW~~Fv~~n~L~~GD   80 (102)
T d1yela1           3 DTGEVQFMKPFISEKSSK--SLEIPLGFNEYFPAPFPITVDLLDYSGRSWTVRMKKRGEKVFLTVGWENFVKDNNLEDGK   80 (102)
T ss_dssp             CCCCEEEEEECCHHHHTT--CEECCHHHHTTCCCCCCSEEEEEETTSCEEEEEEEEETTEEEECTTHHHHHHHHTCCTTC
T ss_pred             CCCCCeEEEEEcCcccCC--CEECCHHHHHhCCCCCCCEEEEEcCCCCEEEEEEEEeCCeEEEccCHHHHHHHcCCCcCC
Confidence            567899999999987653  699999999999999999999999999999999988888899999999999999999999


Q ss_pred             EEEEEEecCceeEEEEEEEee
Q 018533          324 VCVFEVLRAREFVLKVTVFRV  344 (354)
Q Consensus       324 ~cvFel~~~~~~~~~V~Ifr~  344 (354)
                      +|+||+.++  ..|.|+||+.
T Consensus        81 ~~vF~~~~~--~~f~V~If~~   99 (102)
T d1yela1          81 YLQFIYDRD--RTFYVIIYGH   99 (102)
T ss_dssp             EEEEEECSS--SEEEEEEECS
T ss_pred             EEEEEEcCC--cEEEEEEeCC
Confidence            999999975  4799999974

>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=99.84  E-value=1.4e-20  Score=152.20  Aligned_cols=104  Identities=24%  Similarity=0.345  Sum_probs=87.8

Q ss_pred             CCCCeEEEEccCCCCCCCceEEcCHHHHHhhCCCCC-------eeEEEEeCCCCeEEEEEEEe--CCeeeecccHHHhhh
Q 018533          245 PSNPFCRVVLRPSYLYKGCIMYLPSCFAEKHLNGVC-------GFIKLQLSDGKQWPVRCLYR--GGRAKFSQGWYEFTV  315 (354)
Q Consensus       245 s~~P~F~~~m~~s~v~~~~~L~iP~~f~~~~l~~~~-------~~i~L~~~~Gr~W~v~~~~~--~~~~~l~~GW~~F~~  315 (354)
                      +..|.|.++|++|+|.+.+.|.||++|+++|+|...       ..|.+.|.+|+.|++++.++  +.++.|+.||.+||+
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            567899999999999876689999999999987654       35999999999999999865  346789999999999


Q ss_pred             hcCCCCCcEEEEEEecCceeEEEEEEEeecCCC
Q 018533          316 ENRLGEGDVCVFEVLRAREFVLKVTVFRVSESA  348 (354)
Q Consensus       316 ~n~Lk~GD~cvFel~~~~~~~~~V~Ifr~~~~~  348 (354)
                      +|+|++||+|+|+.....+..+.|.+.++.+..
T Consensus        82 ~~~Lk~GD~~~F~~~~~~~~~~~i~~r~~~~~~  114 (117)
T d1wida_          82 EKNLRAGDVVSFSRSNGQDQQLYIGWKSRSGSD  114 (117)
T ss_dssp             HTTCCTTCEEEEEECCSSSCCEEEEEECCCSCS
T ss_pred             HcCCCCCCEEEEEEEeCCCCEEEEEEEECCCCC
Confidence            999999999999998766556777776665543

>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=99.56  E-value=1.4e-14  Score=116.25  Aligned_cols=97  Identities=19%  Similarity=0.254  Sum_probs=79.8

Q ss_pred             CCeEEEeeccccccc-ceeecchHHHHHhcCCCCC-------cEEEEcCCCCEEEEEEEEE--cCeEEEcccHHHHHhHc
Q 018533            3 RPYFHKLILASTIRD-KRLRIPENFVRNFKDDLSA-------AATLIVPNGMVSRVGLRRL--DNKVWFYDGWQEFMERY   72 (354)
Q Consensus         3 ~p~F~k~~~~~~~~~-~~l~IP~~F~~~~~~~~~~-------~v~L~~~~G~~W~V~l~k~--~~~~~~~~GW~~F~~~~   72 (354)
                      .|-|.|+|+++++.. .+|.||..|++.|.+.+..       .+.+.|+.|+.|++.+...  ....+|..||.+||.+|
T Consensus         4 ~~iF~K~Lt~sDv~~~~rL~iP~~~~~~~lp~~~~~~~~~~~~~~~~d~~g~~W~~~~~~~~~~~~~~l~~GW~~Fv~~~   83 (117)
T d1wida_           4 EALFEKAVTPSDVGKLNRLVIPKHHAEKHFPLPSSNVSVKGVLLNFEDVNGKVWRFRYSYWNSSQSYVLTKGWSRFVKEK   83 (117)
T ss_dssp             EEEEEEECCTTTTSSSCCEEECHHHHTTTSCCCSSCCSSCCEEEEEEETTTEEEEEEEEEETTTTEEEEESSHHHHHHHT
T ss_pred             ceEEEEEecchhcCCCCEEEECHHHHHHhCCccccccCCCcEEEEEEeCCCCEEEEEEEEECCCCceEEecCHHHHHHHc
Confidence            456999999998853 5799999999999876543       4899999999999999864  45667999999999999


Q ss_pred             CCCCCcEEEEEEec--cceEEEEEEcCCC
Q 018533           73 FIRIGYFLVFRYEG--NSAFNVYIFNLPS   99 (354)
Q Consensus        73 ~L~~gd~lvF~~~g--~s~F~V~if~~~~   99 (354)
                      +|++||.|+|..+.  +..|.|.+...++
T Consensus        84 ~Lk~GD~~~F~~~~~~~~~~~i~~r~~~~  112 (117)
T d1wida_          84 NLRAGDVVSFSRSNGQDQQLYIGWKSRSG  112 (117)
T ss_dssp             TCCTTCEEEEEECCSSSCCEEEEEECCCS
T ss_pred             CCCCCCEEEEEEEeCCCCEEEEEEEECCC
Confidence            99999999999874  4567776665543

>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=98.27  E-value=3.7e-07  Score=75.39  Aligned_cols=86  Identities=13%  Similarity=0.123  Sum_probs=69.2

Q ss_pred             CCCCeEEEEccCCCCCCCce----EEcCHHHHHhhCCCCC--------eeEEEE--eCCCCeEEEEEEEeCC--------
Q 018533          245 PSNPFCRVVLRPSYLYKGCI----MYLPSCFAEKHLNGVC--------GFIKLQ--LSDGKQWPVRCLYRGG--------  302 (354)
Q Consensus       245 s~~P~F~~~m~~s~v~~~~~----L~iP~~f~~~~l~~~~--------~~i~L~--~~~Gr~W~v~~~~~~~--------  302 (354)
                      ...-.|.+.|+++++.....    ++||++++.+++|...        +.+.|.  |.+|..|.+++.|.++        
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            44668999999999876433    9999999999987321        245544  7789999999987543        


Q ss_pred             eeeecccHHHhhhhcCCCCCcEEEEEEe
Q 018533          303 RAKFSQGWYEFTVENRLGEGDVCVFEVL  330 (354)
Q Consensus       303 ~~~l~~GW~~F~~~n~Lk~GD~cvFel~  330 (354)
                      .++|+++|+.|...+.+..||+.+|...
T Consensus        93 eyRiT~~g~~~~~~~~~n~G~l~i~af~  120 (175)
T d1na6a1          93 EKRITRWGRGSPLQDPENTGALTLLAFK  120 (175)
T ss_dssp             EEEEECCCTTSGGGCGGGTTCEEEEEEE
T ss_pred             cEEEEeccccccccCccccccEEEEEee
Confidence            3789999999999999999999999885

>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=97.15  E-value=0.00059  Score=55.85  Aligned_cols=81  Identities=12%  Similarity=0.016  Sum_probs=64.3

Q ss_pred             eEEEeeccccccc-ce----eecchHHHHHhcCCCC-----C---cEEEE--cCCCCEEEEEEEEEc--------CeEEE
Q 018533            5 YFHKLILASTIRD-KR----LRIPENFVRNFKDDLS-----A---AATLI--VPNGMVSRVGLRRLD--------NKVWF   61 (354)
Q Consensus         5 ~F~k~~~~~~~~~-~~----l~IP~~F~~~~~~~~~-----~---~v~L~--~~~G~~W~V~l~k~~--------~~~~~   61 (354)
                      -|.|+++++.... .+    +.||+.++..+.+.+.     +   .+.|+  |.+|..|+......+        +...|
T Consensus        17 ~F~K~LtasD~g~tg~HQaG~~IPK~~ae~~FP~l~~~~e~nP~~~l~~~i~d~~g~~w~fR~iYyn~~~~ggTRneyRi   96 (175)
T d1na6a1          17 VYIKRLSANDTGATGGHQVGLYIPSGIVEKLFPSINHTRELNPSVFLTAHVSSHDCPDSEARAIYYNSAHFGKTRNEKRI   96 (175)
T ss_dssp             EEEEECCHHHHTCC---CCCCCCCHHHHHHHCGGGCCCSSSSCEEEEEEEESSSCCCCEEEEEEEECGGGTTSCCCEEEE
T ss_pred             EEEEEcccccccccCCccceeeecHHHHHHhCCCCCcccccCCCceEEEEEecCCCCeeEEEEEEECCccCCCccccEEE
Confidence            4889999987743 22    9999999999887321     1   34444  889999999887532        67789


Q ss_pred             cccHHHHHhHcCCCCCcEEEEEEe
Q 018533           62 YDGWQEFMERYFIRIGYFLVFRYE   85 (354)
Q Consensus        62 ~~GW~~F~~~~~L~~gd~lvF~~~   85 (354)
                      +++|+.|.....+..||+++|-+.
T Consensus        97 T~~g~~~~~~~~~n~G~l~i~af~  120 (175)
T d1na6a1          97 TRWGRGSPLQDPENTGALTLLAFK  120 (175)
T ss_dssp             ECCCTTSGGGCGGGTTCEEEEEEE
T ss_pred             EeccccccccCccccccEEEEEee
Confidence            999999999999999999999884