Citrus Sinensis ID: 013565

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340-------350-------360-------370-------380-------390-------400-------410-------420-------430-------440
Protein Sequence
MIGIDYEMGNIISNTGSNQAVKLHFSTTYASNSSSSPSSASSHHHHYTTQTQQLLPLTTHHQNYNKQQQPQMGSWLLGKTTTTTTAAELEDVSNEEETAAPTKEQAIIMQETKDIIEEGEAEEDRVLISLEKEHMFDKVVTPSDVGKLNRLVIPKQHAEKYFPLDSSSNEKGLLLNFEDRNGKPWRFRYSYWNSSQSYVMTKGWSRFVKDKKLDAGDVVSFHRGVGDLAKGRLFIDWRRRSHPPAAAAASFSRHLPFYRSIPWNPLLMMRPPVLPASMYSQSQINNNFYNRNSISLGGTGNNNNVLSTRTLGSILYLRSQLPAAPATQQPPPPPPPPHTEIGMTKWQQHPIVFDSVPVVQGKATAKRLRLFGVNMDCPITESDDECHILSSSTSIQHATMAIHDQPSQLSSSSQLSLYDATPLLPPFDFLNKGKASMSFD
Secondary Structure (PSIPRED)
cccccHHccccccccccccccccHHHHHHccccccccccccccEEcccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHccccccccccHHHHHHHHccccccEEEEEEEcccccccccEEEEHHHHHHHcccccccccccEEEEEEEcccccEEEEEEEEccccEEEEEccHHHHHHccccccccEEEEEEcccccccccEEEEEEEccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHccccccccccc
Secondary Structure Prediction (SSPRO)
cccEEcHHcHHcccccccHHHHHccccHcccccccccccccEEEEcccccHHHHHHHccccccccccccccccccccccEEEEEEEEEEEccccccEEEEEEEEcccccccccccccccccccccccccccccccEEEEEccccccccccccHHHHHHHHcccccccccccHHHHHHHHHccccEEEEEEEccccccEEEccccEEEEcccEEEcccEEEEEEcccccccccEEEEEEEccccccccccHHHccccccEEEEEccccccccEEEEHHHHHHHHHcccccEEEEEEEccccccccEEEEEEccccccccccccEEEEEcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHcccccccccccccccccccccccccccccccccccccccc
Coil and Loop (DISEMBL)
migidyemgniisntgsnqaVKLHFSTtyasnsssspssasshhhhyttqtqqllpltthhqnynkqqqpqmgswllgkttttttaaeledvsneeetaaptKEQAIIMQETKDIIEEGEAEEDRVLISLEKehmfdkvvtpsdvgklnrlvipkqhaekyfpldsssnekglllnfedrngkpwrfRYSYWNSSQSYVMTKgwsrfvkdkkldagdvvsfhrgvgdlakgrlfidwrrrshppaaaaasfsrhlpfyrsipwnpllmmrppvlpasmysqsqinnnfynrnsislggtgnnnnvlSTRTLGSILYLrsqlpaapatqqpppppppphteigmtkwqqhpivfdsvpvvqgkaTAKRLRLfgvnmdcpitesddechilssstSIQHATMaihdqpsqlssssqlslydatpllppfdflnkgkasmsfd
Flexible Loop (DISEMBL)
MIGIDYEMGNIISNTGSNQAVKLHFSTTYASNSSSSPSSASSHHHHYTTQTQQLLPLTTHHQNYNKQQQPQMGSWLLGKTTTTTTAAEledvsneeetaaptkeqaIIMQETKDIIEEGEAEEDRVLISLEkehmfdkvvtpsdvgklnRLVIPKQHaekyfpldsssnekglllnfEDRNGKPWRFRYSYWNSSQSYVMTKGWSRFVKDKKLDAgdvvsfhrgvgdlakgrlFIDWRRRSHPPAaaaasfsrhlPFYRSIPWNPLLMMRPPVLPASMYSQSQINNNFYNRNSISLGGTGNNNNVLSTRTLGSILYLRSQLPAAPATQQPPPPPPPPHTEIGMTKWQQHPIVFDSVPVVQGKATAKRLRLFGVNMDCPITESDDECHILSSSTSIQHATMAIHDQPSQLSSSSQLSLYDATPLlppfdflnkgkasmsfd
Low Complexity Region (SEG)
MIGIDYEMGNIISNTGSNQAVKLHFsttyasnsssspssasshhhhyttqtqqllpltthhqnYNKQQQPQMGSWLLGKttttttAAELEDVSNEEETAAPTKEQAIIMQETKDIIEEGEAEEDRVLISLEKEHMFDKVVTPSDVGKLNRLVIPKQHAEKYFPLDSSSNEKGLLLNFEDRNGKPWRFRYSYWNSSQSYVMTKGWSRFVKDKKLDAGDVVSFHRGVGDLAKGRLFIDWrrrshppaaaaasfsrhLPFYRSIPWNPLLMMRPPVLPASMYSQSQINNNFYNRNSISLGGTGNNNNVLSTRTLGSILYLRSQLpaapatqqppppppppHTEIGMTKWQQHPIVFDSVPVVQGKATAKRLRLFGVNMDCPITESDDECHILSSSTSIQHATMAIHDQPsqlssssqlslYDATPLLPPFDFLNKGKASMSFD
Disordered region (IsUnstruct)
**************************************************************************************************************************************MFDKVVTPSDVGKLNRLVIPKQHAEKYFP********GLLLNFEDRNGKPWRFRYSYWNSSQSYVMTKGWSRFVKDKKLDAGDVVSFHRGVGDLAKGRLFIDWRRRSHPPAAAAASFSRHLPFYRSIPWNPLLMMRPPVLPASMYSQSQINNNFYNRNSISLGGTGNNNNVLSTRTLGSILYLR************************MTKWQQHPIVFDSVPVVQGKATAKRLRLFGVNMDCPITESDDECHIL***************************************************
Disordered Region (DISOPRED)
**G*************************YA*****************************************MGSWLLGKTTTT**************************************************HMFDKVVTPSDVGKLNRLVIPKQHAEKYFPLDSSSNEKGLLLNFEDRNGKPWRFRYSYWNSSQSYVMTKGWSRFVKDKKLDAGDVVSFHRGVGDLAKGRLFIDWR**************************PLLMMRPPVLPAS********************************************************************************************LFGVNM*****************************************************************
Disordered Region (DISEMBL)
MIGIDYEMGNIISNTGSNQAVKLHFST************************QQLLPLTTHHQNYNKQQQPQMGSWLLGKTTTTTTAAEL***********PTKEQAIIMQETKDIIEEGEAEEDRVLISLEKEHMFDKVVTPSDVGKLNRLVIPKQHAEKYFPLDSSSNEKGLLLNFEDRNGKPWRFRYSYWNSSQSYVMTKGWSRFVKDKKLDAGDVVSFHRGVGDLAKGRLFIDWRRRS********SFSRHLPFYRSIPWNPLLMMRPPVLPASMYSQSQINNNFYNRNSISLGGTGNNNNVLSTRTLGSILYLRSQLP**************PHTEIGMTKWQQHPIVFDSVPVVQGKATAKRLRLFGVNMDCPITESDDECHILSSSTSIQHATMAI************LSLYDATPLLPPFDFLNKGKASMSFD
Disordered Region (DISPRO)
MIGIDYEMGNIISNTGSNQAVKLHFSTTYASNSSSSPSSASSHHHHYTTQTQQLLPLTTHHQNYNKQQQPQMGSWLLGKTTTTTTAAELEDVSNEEETAAPTKEQAII*******************IS**KEHMFDKVVTPSDVGKLNRLVIPKQHAEKYFPLDSSSNEKGLLLNFEDRNGKPWRFRYSYWNSSQSYVMTKGWSRFVKDKKLDAGDVVSFHRGVGDLAKGRLFIDWRRRSHPPAAAAA***RHLPFYRSIPWNPLLMMRPPVLPASMYSQSQINNNFYNRNSISLGGTGNNNNVLSTRTLGSILYLRSQLPAAPATQQPPPP*******IGMTKWQQHPIVFDSVPVVQGKATAKRLRLFGVNMDC**********************************************LPP**************
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MIGIDYEMGNIISNTGSNQAVKLHFSTTYASNSSSSPSSASSHHHHYTTQTQQLLPLTTHHQNYNKQQQPQMGSWLLGKTTTTTTAAELEDVSNEEETAAPTKEQAIIMQETKDIIEEGEAEEDRVLISLEKEHMFDKVVTPSDVGKLNRLVIPKQHAEKYFPLDSSSNEKGLLLNFEDRNGKPWRFRYSYWNSSQSYVMTKGWSRFVKDKKLDAGDVVSFHRGVGDLAKGRLFIDWRRRSHPPAAAAASFSRHLPFYRSIPWNPLLMMRPPVLPASMYSQSQINNNFYNRNSISLGGTGNNNNVLSTRTLGSILYLRSQLPAAPATQQPPPPPPPPHTEIGMTKWQQHPIVFDSVPVVQGKATAKRLRLFGVNMDCPITESDDECHILSSSTSIQHATMAIHDQPSQLSSSSQLSLYDATPLLPPFDFLNKGKASMSFD
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	440	2.2.26 [Sep-21-2011]
Q8LMR9	311	B3 domain-containing prot	yes	no	0.513	0.726	0.496	1e-63
O82799	310	B3 domain-containing tran	yes	no	0.493	0.7	0.511	6e-60
Q6EU30	412	B3 domain-containing prot	no	no	0.536	0.572	0.513	3e-58
Q9MAN1	358	B3 domain-containing tran	no	no	0.470	0.578	0.473	3e-56
Q7F9W2	316	B3 domain-containing prot	no	no	0.254	0.354	0.830	2e-53
Q8LNN8	312	Putative B3 domain-contai	no	no	0.502	0.708	0.449	1e-52
Q9M268	299	B3 domain-containing tran	no	no	0.445	0.655	0.473	2e-51
Q9FNI3	282	B3 domain-containing prot	no	no	0.459	0.716	0.391	5e-43
O82595	333	B3 domain-containing tran	no	no	0.552	0.729	0.406	1e-41
Q8GYJ2	244	B3 domain-containing prot	no	no	0.245	0.442	0.734	1e-41

>sp|Q8LMR9|Y3209_ORYSJ B3 domain-containing protein Os03g0120900 OS=Oryza sativa subsp. japonica GN=Os03g0120900 PE=2 SV=1

 Score =  244 bits (622), Expect = 1e-63,   Method: Compositional matrix adjust.
 Identities = 148/298 (49%), Positives = 179/298 (60%), Gaps = 72/298 (24%)

Query: 119 GEAEED--RVLISLEKEHMFDKVVTPSDVGKLNRLVIPKQHAEKYFPLDSSSNEKGLLLN 176
           GE +E   R L ++EKEHMFDKVVTPSDVGKLNRLVIPKQHAEKYFPLD++SNEKGLLL+
Sbjct: 18  GEVQESGGRSLAAVEKEHMFDKVVTPSDVGKLNRLVIPKQHAEKYFPLDAASNEKGLLLS 77

Query: 177 FEDRNGKPWRFRYSYWNSSQSYVMTKGWSRFVKDKKLDAGDVVSFHRGVGDLAKGRLFID 236
           FEDR GKPWRFRYSYWNSSQSYVMTKGWSRFVK+K+LDAGD VSF RGVG+ A+GRLFID
Sbjct: 78  FEDRTGKPWRFRYSYWNSSQSYVMTKGWSRFVKEKRLDAGDTVSFGRGVGEAARGRLFID 137

Query: 237 WRRRSHPPAAAAAS-----FSRHLPFYRSIPWNPLL------------------MMRPPV 273
           WRRR  P   AA       F+ HLP   SIP+ P                     + PP 
Sbjct: 138 WRRR--PDVVAALQPPTHRFAHHLP--SSIPFAPWAHHHGHGAAAAAAAAAGARFLLPP- 192

Query: 274 LPASMYSQSQINNNFYNRNSISLGGTGNNNNVLSTRTLGSILYLRSQLPAAPATQQPPPP 333
                 S + I ++ + R++ ++G      +  +  T   +L+ R               
Sbjct: 193 ------SSTPIYDH-HRRHAHAVG-----YDAYAAATSRQVLFYR--------------- 225

Query: 334 PPPPHTEIGMTKWQQHP-IVFDSVPVVQGK-------ATAKRLRLFGVNMDCPITESD 383
           P PP         Q HP +V +SVPV           A +KR+RLFGVN+DC  +E D
Sbjct: 226 PLPPQQ-------QHHPAVVLESVPVRMTAGHAEPPSAPSKRVRLFGVNLDCANSEQD 276

Oryza sativa subsp. japonica (taxid: 39947)

>sp|O82799|NGA1_ARATH B3 domain-containing transcription factor NGA1 OS=Arabidopsis thaliana GN=NGA1 PE=1 SV=1

 Score =  231 bits (590), Expect = 6e-60,   Method: Compositional matrix adjust.
 Identities = 138/270 (51%), Positives = 160/270 (59%), Gaps = 53/270 (19%)

Query: 121 AEEDRVLISLEKEHMFDKVVTPSDVGKLNRLVIPKQHAEKYFPLDSSSNEKGLLLNFEDR 180
           AEE+      ++EHMFDKVVTPSDVGKLNRLVIPKQHAE++FPLDSSSNEKGLLLNFED 
Sbjct: 20  AEEEGAREVADREHMFDKVVTPSDVGKLNRLVIPKQHAERFFPLDSSSNEKGLLLNFEDL 79

Query: 181 NGKPWRFRYSYWNSSQSYVMTKGWSRFVKDKKLDAGDVVSFHRGVGDLAK-GRLFIDWRR 239
            GK WRFRYSYWNSSQSYVMTKGWSRFVKDKKLDAGD+VSF R VGD  +  RLFIDWRR
Sbjct: 80  TGKSWRFRYSYWNSSQSYVMTKGWSRFVKDKKLDAGDIVSFQRCVGDSGRDSRLFIDWRR 139

Query: 240 R----SHPPAAAAASFSRHLPFYRSIPWNPLLMMRPPVLPASMYSQSQINNNFYNRNSIS 295
           R     HP  AA A F R   F              P    S+Y+  Q  ++        
Sbjct: 140 RPKVPDHPHFAAGAMFPRFYSF--------------PSTNYSLYNHQQQRHH-------H 178

Query: 296 LGGTGNNNNVLSTRTLGSILYLRSQLPAAPATQQPPPPPPPPHTEIGMTKWQQHPIVFDS 355
            GG  N + +   R  G   ++RS        Q+  P                 P+V +S
Sbjct: 179 SGGGYNYHQI--PREFGYGYFVRS------VDQRNNPAAAVA-----------DPLVIES 219

Query: 356 VPV-VQGKA-------TAKRLRLFGVNMDC 377
           VPV + G+A         KRLRLFGV+M+C
Sbjct: 220 VPVMMHGRANQELVGTAGKRLRLFGVDMEC 249

Regulates lateral organ growth. Functionally redundant with NGA2, NGA3 and NGA4.

Arabidopsis thaliana (taxid: 3702)

>sp|Q6EU30|Y2835_ORYSJ B3 domain-containing protein Os02g0683500 OS=Oryza sativa subsp. japonica GN=Os02g0683500 PE=2 SV=1

 Score =  226 bits (576), Expect = 3e-58,   Method: Compositional matrix adjust.
 Identities = 135/263 (51%), Positives = 164/263 (62%), Gaps = 27/263 (10%)

Query: 130 LEKEHMFDKVVTPSDVGKLNRLVIPKQHAEKYFPLDSSSNEKGLLLNFEDRNGKPWRFRY 189
           +EKEHMFDKVVTPSDVGKLNRLVIPKQ+AEKYFPLD+++NEKGLLLNFEDR GKPWRFRY
Sbjct: 90  VEKEHMFDKVVTPSDVGKLNRLVIPKQYAEKYFPLDAAANEKGLLLNFEDRAGKPWRFRY 149

Query: 190 SYWNSSQSYVMTKGWSRFVKDKKLDAGDVVSFHRGVGD-LAKGRLFIDWRRRSHPPAAAA 248
           SYWNSSQSYVMTKGWSRFVK+K+LDAGD VSF RG+GD  A+ RLFIDW+RR+       
Sbjct: 150 SYWNSSQSYVMTKGWSRFVKEKRLDAGDTVSFSRGIGDEAARHRLFIDWKRRAD--TRDP 207

Query: 249 ASFSRHLPFYRSI-----PW---NPLLMMRPPVLPASMYSQSQINNNFYNRNSISLGGTG 300
               R LP    +     PW           P  PA++Y          +R    L    
Sbjct: 208 LRLPRGLPLPMPLTSHYAPWGIGGGGGFFVQPSPPATLYE---------HRLRQGLDFRA 258

Query: 301 NNNNVLSTRTLGSILYLRSQL-PAAPATQQPPPPPPPPHT---EIGMTKWQQHPIVFDSV 356
            N      R +  +L+  +++ P AP   + P P    +T        +    P+V DSV
Sbjct: 259 FNPAAAMGRQV--LLFGSARIPPQAPLLARAPSPLHHHYTLQPSGDGVRAAGSPVVLDSV 316

Query: 357 PVVQGKAT-AKRLRLFGVNMDCP 378
           PV++   T AKR+RLFGVN+D P
Sbjct: 317 PVIESPTTAAKRVRLFGVNLDNP 339

Oryza sativa subsp. japonica (taxid: 39947)

>sp|Q9MAN1|NGA3_ARATH B3 domain-containing transcription factor NGA3 OS=Arabidopsis thaliana GN=NGA3 PE=2 SV=1

 Score =  219 bits (558), Expect = 3e-56,   Method: Compositional matrix adjust.
 Identities = 134/283 (47%), Positives = 157/283 (55%), Gaps = 76/283 (26%)

Query: 131 EKEHMFDKVVTPSDVGKLNRLVIPKQHAEKYFPLDSSSNEKGLLLNFEDRNGKPWRFRYS 190
           EKEHMFDKVVTPSDVGKLNRLVIPKQHAE+YFPLDSS+N+ G LLNF+DRNGK WRFRYS
Sbjct: 51  EKEHMFDKVVTPSDVGKLNRLVIPKQHAERYFPLDSSNNQNGTLLNFQDRNGKMWRFRYS 110

Query: 191 YWNSSQSYVMTKGWSRFVKDKKLDAGDVVSFHRGVGDLA-KGRLFIDWRRR--------- 240
           YWNSSQSYVMTKGWSRFVK+KKLDAGD+VSF RG+GD + + +L+IDWR R         
Sbjct: 111 YWNSSQSYVMTKGWSRFVKEKKLDAGDIVSFQRGIGDESERSKLYIDWRHRPDMSLVQAH 170

Query: 241 --------SHPPAAAAASFSRH-LPFYRSIPWNPLLMMRPPVLPASMYSQSQINNN---F 288
                    + P  +  S   H LP Y S+P               ++    I N+   +
Sbjct: 171 QFGNFGFNFNFPTTSQYSNRFHPLPEYNSVP---------------IHRGLNIGNHQRSY 215

Query: 289 YNRNSISLGGTGNNNNVLSTRTLGSILYLRSQLPAAPATQQPPPPPPPPHTEIGMTKWQQ 348
           YN       G G  N        G   Y  S               P  H  I  ++   
Sbjct: 216 YNTQRQEFVGYGYGN------LAGRCYYTGS---------------PLDHRNIVGSE--- 251

Query: 349 HPIVFDSVPVVQGKAT--------------AKRLRLFGVNMDC 377
            P+V DSVPVV G+ T               KRLRLFGVNM+C
Sbjct: 252 -PLVIDSVPVVPGRLTPVMLPPLPPPPSTAGKRLRLFGVNMEC 293

Regulates lateral organ growth. Functionally redundant with NGA1, NGA2 and NGA4.

Arabidopsis thaliana (taxid: 3702)

>sp|Q7F9W2|Y4814_ORYSJ B3 domain-containing protein Os04g0581400 OS=Oryza sativa subsp. japonica GN=Os04g0581400 PE=2 SV=2

 Score =  210 bits (535), Expect = 2e-53,   Method: Compositional matrix adjust.
 Identities = 93/112 (83%), Positives = 103/112 (91%)

Query: 130 LEKEHMFDKVVTPSDVGKLNRLVIPKQHAEKYFPLDSSSNEKGLLLNFEDRNGKPWRFRY 189
           +EKEHMFDKVVTPSDVGKLNRLVIPKQHAEKYFPLDS++NEKGLLL+FEDR GK WRFRY
Sbjct: 104 IEKEHMFDKVVTPSDVGKLNRLVIPKQHAEKYFPLDSAANEKGLLLSFEDRTGKLWRFRY 163

Query: 190 SYWNSSQSYVMTKGWSRFVKDKKLDAGDVVSFHRGVGDLAKGRLFIDWRRRS 241
           SYWNSSQSYVMTKGWSRFVK+K+LDAGD VSF RG  +  + RLFIDW+RR+
Sbjct: 164 SYWNSSQSYVMTKGWSRFVKEKRLDAGDTVSFCRGAAEATRDRLFIDWKRRA 215

Oryza sativa subsp. japonica (taxid: 39947)

>sp|Q8LNN8|Y1071_ORYSJ Putative B3 domain-containing protein Os10g0537100 OS=Oryza sativa subsp. japonica GN=Os10g0537100 PE=3 SV=1

 Score =  207 bits (527), Expect = 1e-52,   Method: Compositional matrix adjust.
 Identities = 133/296 (44%), Positives = 161/296 (54%), Gaps = 75/296 (25%)

Query: 116 IEEGEAEEDR---VLISLEKEHMFDKVVTPSDVGKLNRLVIPKQHAEKYFPLDSSSNE-- 170
           +  GE + +R       +EKEHMF+KVVTPSDVGKLNRLVIPKQHAE+YFPLD+++    
Sbjct: 12  VAGGEEDSERGAAAWAVVEKEHMFEKVVTPSDVGKLNRLVIPKQHAERYFPLDAAAGAGG 71

Query: 171 -----------KGLLLNFEDRNGKPWRFRYSYWNSSQSYVMTKGWSRFVKDKKLDAGDVV 219
                      KGL+L+FEDR GK WRFRYSYWNSSQSYVMTKGWSRFVK+K+L AGD V
Sbjct: 72  GGGGGGGGGGGKGLVLSFEDRTGKAWRFRYSYWNSSQSYVMTKGWSRFVKEKRLGAGDTV 131

Query: 220 SFHRGVGDLAKGRLFIDWRRRSH-------PPAAAAASFSRHLPFYRSIPWNPLLMMRPP 272
           SF RG+GD A+GRLFID+RRR         PP AA  S S H       P   +     P
Sbjct: 132 SFGRGLGDAARGRLFIDFRRRRQDAGSFMFPPTAAPPSHSHHHHQRHHPPLPSV-----P 186

Query: 273 VLPASMYSQSQINNNFYNRNSISLGGTGNNNNVLSTRTLGSILYLRSQLPAAPATQQPPP 332
           + P   Y+ +      Y     S   +  +           +L+LR Q+PAA        
Sbjct: 187 LCPWRDYTTAYGGGYGYGYGGGSTPASSRH-----------VLFLRPQVPAA-------- 227

Query: 333 PPPPPHTEIGMTKWQQHPIVFDSVPV-------VQGKATA---KRLRLFGVNMDCP 378
                             +V  SVPV       VQ  AT    KR+RLFGVN+DCP
Sbjct: 228 ------------------VVLKSVPVHVAATSAVQEAATTTRPKRVRLFGVNLDCP 265

Oryza sativa subsp. japonica (taxid: 39947)

>sp|Q9M268|NGA2_ARATH B3 domain-containing transcription factor NGA2 OS=Arabidopsis thaliana GN=NGA2 PE=2 SV=1

 Score =  204 bits (518), Expect = 2e-51,   Method: Compositional matrix adjust.
 Identities = 124/262 (47%), Positives = 150/262 (57%), Gaps = 66/262 (25%)

Query: 129 SLEKEHMFDKVVTPSDVGKLNRLVIPKQHAEKYFPLDSSS---NEKGLLLNFEDRNGKPW 185
           S+E+EHMFDKVVTPSDVGKLNRLVIPKQHAE+YFPLD+S+   + KGLLLNFEDR+G  W
Sbjct: 16  SMEREHMFDKVVTPSDVGKLNRLVIPKQHAERYFPLDNSTTNDSNKGLLLNFEDRSGNSW 75

Query: 186 RFRYSYWNSSQSYVMTKGWSRFVKDKKLDAGDVVSFHRGVGDLAKGRLFIDWRRRSHPPA 245
           RFRYSYWNSSQSYVMTKGWSRFVKDKKLDAGD+VSF R      K +L+IDWRRR   P 
Sbjct: 76  RFRYSYWNSSQSYVMTKGWSRFVKDKKLDAGDIVSFQR--DSCNKDKLYIDWRRRPKIPD 133

Query: 246 AAAASFSRHL-PFYRSIPWNPLLMMRPPVLPASMYSQSQINNNFYNRNSISLGGTGNNNN 304
                F+  + P + + P         P +P +  +     +N Y+R             
Sbjct: 134 HHHQQFAGAMFPRFYTFP--------HPQMPTNYET-----HNLYHR------------- 167

Query: 305 VLSTRTLGSILYLRSQLPAAPATQQPPPPPPPPHTEIGMTKWQQHPIVFDSVPV-VQGKA 363
               R LG   Y+RS   + P                          V +SVPV +Q +A
Sbjct: 168 -FHQRDLGIGYYVRSMERSHPTA------------------------VIESVPVMMQRRA 202

Query: 364 TA--------KRLRLFGVNMDC 377
                     KRLRLFGV+M+C
Sbjct: 203 QVASMASRGEKRLRLFGVDMEC 224

Regulates lateral organ growth. Functionally redundant with NGA1, NGA3 and NGA4.

Arabidopsis thaliana (taxid: 3702)

>sp|Q9FNI3|Y5625_ARATH B3 domain-containing protein At5g06250 OS=Arabidopsis thaliana GN=At5g06250 PE=2 SV=1

 Score =  175 bits (444), Expect = 5e-43,   Method: Compositional matrix adjust.
 Identities = 107/273 (39%), Positives = 144/273 (52%), Gaps = 71/273 (26%)

Query: 132 KEHMFDKVVTPSDVGKLNRLVIPKQHAEKYFPLDS----------SSNEKGLLLNFEDRN 181
           KE +F+K +TPSDVGKLNRLVIPKQHAEKYFPL++          SS+EKG+LL+FED +
Sbjct: 42  KESLFEKSLTPSDVGKLNRLVIPKQHAEKYFPLNAVLVSSAAADTSSSEKGMLLSFEDES 101

Query: 182 GKPWRFRYSYWNSSQSYVMTKGWSRFVKDKKLDAGDVVSFHRGVGDLAKGRLFIDWRRRS 241
           GK WRFRYSYWNSSQSYV+TKGWSRFVKDK+LD GDVV F R   D    RLFI WRRR 
Sbjct: 102 GKSWRFRYSYWNSSQSYVLTKGWSRFVKDKQLDPGDVVFFQRHRSD--SRRLFIGWRRRG 159

Query: 242 HPPAAAAASFSRHLPFYRSIPWNPLLMMRPPVLPASMYSQSQINNNFYNRNSISLGGTGN 301
              +++ A+                                                   
Sbjct: 160 QGSSSSVAA--------------------------------------------------- 168

Query: 302 NNNVLSTRTLGSILYLRSQLPAAPATQQPPPPPPPPHTEIGM-TKWQQHPIVFDSVPVVQ 360
            N+ ++T ++G++ Y   Q+ A      PP      H    + T  + H     S P   
Sbjct: 169 TNSAVNTSSMGALSY--HQIHATSNYSNPPSHSEYSHYGAAVATAAETH-----STPSSS 221

Query: 361 GKATAKRLRLFGVNMDCPITESDDECHILSSST 393
              +++ +RLFGVN++C + E+D +  +  ++T
Sbjct: 222 VVGSSRTVRLFGVNLECQMDENDGDDSVAVATT 254

Arabidopsis thaliana (taxid: 3702)

>sp|O82595|NGA4_ARATH B3 domain-containing transcription factor NGA4 OS=Arabidopsis thaliana GN=NGA4 PE=2 SV=2

 Score =  171 bits (433), Expect = 1e-41,   Method: Compositional matrix adjust.
 Identities = 121/298 (40%), Positives = 155/298 (52%), Gaps = 55/298 (18%)

Query: 110 QETKDIIEEGEAEEDRVLISLEKEHMFDKVVTPSDVGKLNRLVIPKQHAEKYFPLDSSSN 169
           QE  +I        +    S  +EHMFDKV+TPSDVGKLNRLVIPKQHAE +FPL+   N
Sbjct: 10  QELAEIRASSSDHTNYFYSSERREHMFDKVLTPSDVGKLNRLVIPKQHAENFFPLED--N 67

Query: 170 EKGLLLNFEDRNGKPWRFRYSYWNSSQSYVMTKGWSRFVKDKKLDAGDVVSFHRGV---- 225
           + G +L+F+D+NGK WRFRYSYWNSSQSYVMTKGWSRFVK+KKL AGD VSF+RG     
Sbjct: 68  QNGTVLDFQDKNGKMWRFRYSYWNSSQSYVMTKGWSRFVKEKKLFAGDTVSFYRGYIPDD 127

Query: 226 ---GDLAKGRLFIDWRRRSHPPAAAAASFSRHL---PFYRSIPWNPLLMMRPPVLPASMY 279
               +  +  +FIDWR R      A  +F  ++    F    P  P     P     SM 
Sbjct: 128 NAQPERRRKIMFIDWRPR------AEINFVHNINNHNFVFGSPTYPTARFYPVTPEYSMP 181

Query: 280 SQS---QINNNFYNRNSISLG-GTGNNNNVLSTRTLGSILYLRSQLPAAPATQQPPPPPP 335
            +S      N F  R  +  G G   N N       G   Y       +P  Q       
Sbjct: 182 YRSFPPFYQNQFQEREYLGYGYGRVVNGN-------GVRYYA-----GSPLDQ------- 222

Query: 336 PPHTEIGMTKWQQHPIVFDSVPVV-QGK---------ATAKRLRLFGVNMDCPITESD 383
             H +  + +    P+V+DSVPV   G+         +T K+LRLFGV+++   +  D
Sbjct: 223 --HHQWNLGR--SEPLVYDSVPVFPAGRVPPSAPPQPSTTKKLRLFGVDVEESSSSGD 276

Regulates lateral organ growth. Functionally redundant with NGA1, NGA2 and NGA3.

Arabidopsis thaliana (taxid: 3702)

>sp|Q8GYJ2|Y2608_ARATH B3 domain-containing protein At2g36080 OS=Arabidopsis thaliana GN=ARF31 PE=2 SV=1

 Score =  171 bits (432), Expect = 1e-41,   Method: Compositional matrix adjust.
 Identities = 83/113 (73%), Positives = 93/113 (82%), Gaps = 5/113 (4%)

Query: 131 EKEHMFDKVVTPSDVGKLNRLVIPKQHAEKYFPLDSSSN---EKGLLLNFEDRNGKPWRF 187
           EKE +F+K +TPSDVGKLNRLVIPKQHAE+YFPL +++    EKGLLL FED  GKPWRF
Sbjct: 33  EKEALFEKPLTPSDVGKLNRLVIPKQHAERYFPLAAAAADAVEKGLLLCFEDEEGKPWRF 92

Query: 188 RYSYWNSSQSYVMTKGWSRFVKDKKLDAGDVVSFHRGVGDLAKGRLFIDWRRR 240
           RYSYWNSSQSYV+TKGWSR+VK+K LDAGDVV FHR   D   GR FI WRRR
Sbjct: 93  RYSYWNSSQSYVLTKGWSRYVKEKHLDAGDVVLFHRHRSD--GGRFFIGWRRR 143

Arabidopsis thaliana (taxid: 3702)

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	440
225426506	411	PREDICTED: B3 domain-containing protein	0.663	0.710	0.577	5e-88
255555825	406	transcription factor, putative [Ricinus	0.743	0.805	0.504	3e-86
147768788	505	hypothetical protein VITISV_009603 [Viti	0.618	0.538	0.574	1e-82
297742476	380	unnamed protein product [Vitis vinifera]	0.518	0.6	0.573	2e-72
225453662	461	PREDICTED: B3 domain-containing transcri	0.697	0.665	0.493	3e-71
296089028	375	unnamed protein product [Vitis vinifera]	0.534	0.626	0.536	9e-69
125542174	308	hypothetical protein OsI_09772 [Oryza sa	0.522	0.746	0.508	5e-62
115450383	311	Os03g0120900 [Oryza sativa Japonica Grou	0.513	0.726	0.496	8e-62
358347636	624	Maturase K [Medicago truncatula] gi|3555	0.640	0.451	0.470	1e-61
356571279	413	PREDICTED: B3 domain-containing transcri	0.6	0.639	0.468	1e-61

>gi|225426506|ref|XP_002271695.1| PREDICTED: B3 domain-containing protein Os03g0120900-like [Vitis vinifera]

 Score =  331 bits (848), Expect = 5e-88,   Method: Compositional matrix adjust.
 Identities = 187/324 (57%), Positives = 216/324 (66%), Gaps = 32/324 (9%)

Query: 129 SLEKEHMFDKVVTPSDVGKLNRLVIPKQHAEKYFPLDSSSNEKGLLLNFEDRNGKPWRFR 188
           +LE+EHMFDKVVTPSDVGKLNRLVIPKQHAEKYFPLDSS+NEKGLLLNFEDR+GKPWRFR
Sbjct: 105 ALEREHMFDKVVTPSDVGKLNRLVIPKQHAEKYFPLDSSANEKGLLLNFEDRSGKPWRFR 164

Query: 189 YSYWNSSQSYVMTKGWSRFVKDKKLDAGDVVSFHRGVGDLAKGRLFIDWRRRSHPPAAAA 248
           YSYWNSSQSYVMTKGWSRFVK+KKLDAGD+VSF RGVG+  K RL+IDWRRR  P A   
Sbjct: 165 YSYWNSSQSYVMTKGWSRFVKEKKLDAGDIVSFQRGVGESGKDRLYIDWRRR--PDAPEP 222

Query: 249 ASFSRHLPFYRSIPWNPLLMMRPPVLPASMYSQSQIN-------NNFYNRNSISLGGTGN 301
           +S + H  F+RS+PW+PL +  P    A    + Q+        ++   RN    G    
Sbjct: 223 SSLAHHF-FHRSVPWSPLFLQAPVAGGAVSMGRQQVQLAQPNYMSHLGGRNPYGSGAYSY 281

Query: 302 NNNVLSTRTLGSILYLRSQLPAAPATQQPPPPPPPPHTEIGMTKWQQHPIVFDSVPVVQG 361
           NN V      GS+ YLR             P  P     + + +    P+VF+SVPVV G
Sbjct: 282 NNAV--NPCSGSVFYLR-------------PTAPQQVGMVQVQQGGVEPMVFNSVPVVHG 326

Query: 362 KATAKRLRLFGVNMDCPITESDDECHILSSSTSIQHATMA----IHDQPSQLSSSSQLSL 417
           KA AKRLRLFGVNM+CPI+ES DEC IL SSTSI HA +A        PS      QL L
Sbjct: 327 KAAAKRLRLFGVNMECPISES-DECDIL-SSTSIPHAAVASQPPHLSSPSSHHHPLQLRL 384

Query: 418 YDATPL-LPPFDFLNKGKASMSFD 440
           Y+ TPL   P + LNKGK SMSFD
Sbjct: 385 YNGTPLPTLPTNLLNKGKESMSFD 408

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255555825|ref|XP_002518948.1| transcription factor, putative [Ricinus communis] gi|223541935|gb|EEF43481.1| transcription factor, putative [Ricinus communis]

 Score =  325 bits (833), Expect = 3e-86,   Method: Compositional matrix adjust.
 Identities = 205/406 (50%), Positives = 243/406 (59%), Gaps = 79/406 (19%)

Query: 62  QNYNKQQQPQMGSWLLGKTTTTTTAAELEDVSNEEETAAPTKEQAIIMQETKDIIEEGEA 121
           Q Y+K   PQ+GSWL  K           D   E+  +A     A I +E +       +
Sbjct: 50  QIYDKNHHPQVGSWLGSKY----------DPEQEDAGSA-----AGIFEEEE------GS 88

Query: 122 EEDRVLISLEKEHMFDKVVTPSDVGKLNRLVIPKQHAEKYFPLDSSSNEKGLLLNFEDRN 181
            E    + ++KEHMFDKVVTPSDVGKLNRLVIPKQHAEKYFPLDSS+N+KGLLLNFED+ 
Sbjct: 89  GEGECGVVIQKEHMFDKVVTPSDVGKLNRLVIPKQHAEKYFPLDSSTNDKGLLLNFEDKT 148

Query: 182 GKPWRFRYSYWNSSQSYVMTKGWSRFVKDKKLDAGDVVSFHRGVGDLAKGRLFIDWRRRS 241
           GK WRFRYSYWNSSQSYVMTKGWSRFVKDKKLDAGD+VSF RGVG+ AK RL+IDWRRR 
Sbjct: 149 GKAWRFRYSYWNSSQSYVMTKGWSRFVKDKKLDAGDIVSFQRGVGEAAKDRLYIDWRRRP 208

Query: 242 HPPAAAAASFSRHLPFYR-------SIPWNPLLMMRPPVLPASMYSQSQ----INNNFYN 290
             P         H P +R       SIPW+PLL MRPP +P   +  S      ++    
Sbjct: 209 DGP--------HHQPTHRHQQHHLSSIPWSPLL-MRPPPVPRDHFHLSNPNYYNSSGGGG 259

Query: 291 RNSISLGGTG-------NNNNVLSTRTLGSILYLRSQLPAAPATQQPPPPPPPPHTEIGM 343
             S    G G       N N+ + +   G+I+Y+RS                    + GM
Sbjct: 260 GASAYGFGYGYNSSNNYNYNSNVGSSNSGTIIYMRSP------------------QQAGM 301

Query: 344 TKWQQ---------HPIVFDSVPVVQGKATAKRLRLFGVNMDCPITESDDECHILSSSTS 394
            +WQQ          P+VF+SVPVVQGKA AKRLRLFGVNMDCPI++SD EC  LS+ST 
Sbjct: 302 VQWQQAAASSGGFMEPMVFESVPVVQGKAAAKRLRLFGVNMDCPISDSDHECDKLSTSTP 361

Query: 395 IQHATMAIHDQPSQLSSSSQLSLYDATPLLPPFDFLNKGKASMSFD 440
           I  A  A   QPS      QL LY+ TPL  P  FL+KGK+SMS D
Sbjct: 362 IP-AMAAALQQPSH--HPLQLRLYNGTPLPSP-QFLHKGKSSMSLD 403

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147768788|emb|CAN73636.1| hypothetical protein VITISV_009603 [Vitis vinifera]

 Score =  313 bits (801), Expect = 1e-82,   Method: Compositional matrix adjust.
 Identities = 174/303 (57%), Positives = 202/303 (66%), Gaps = 31/303 (10%)

Query: 129 SLEKEHMFDKVVTPSDVGKLNRLVIPKQHAEKYFPLDSSSNEKGLLLNFEDRNGKPWRFR 188
           +LE+EHMFDKVVTPSDVGKLNRLVIPKQHAEKYFPLDSS+NEKGLLLNFEDR+GKPWRFR
Sbjct: 105 ALEREHMFDKVVTPSDVGKLNRLVIPKQHAEKYFPLDSSANEKGLLLNFEDRSGKPWRFR 164

Query: 189 YSYWNSSQSYVMTKGWSRFVKDKKLDAGDVVSFHRGVGDLAKGRLFIDWRRRSHPPAAAA 248
           YSYWNSSQSYVMTKGWSRFVK+KKLDAGD+VSF RGVG+  K RL+IDWRRR  P A   
Sbjct: 165 YSYWNSSQSYVMTKGWSRFVKEKKLDAGDIVSFQRGVGESGKDRLYIDWRRR--PDAPEP 222

Query: 249 ASFSRHLPFYRSIPWNPLLMMRPPVLPASMYSQSQIN-------NNFYNRNSISLGGTGN 301
           +S + H  F+RS+PW+PL +  P    A    + Q+        ++   RN    G    
Sbjct: 223 SSLAHHF-FHRSVPWSPLFLQAPVAGGAVSMGRQQVQLAQPNYMSHLGGRNPYGSGAYSY 281

Query: 302 NNNVLSTRTLGSILYLRSQLPAAPATQQPPPPPPPPHTEIGMTKWQQHPIVFDSVPVVQG 361
           NN V      GS+ YLR             P  P     + + +    P+VF+SVPVV G
Sbjct: 282 NNAV--NPCSGSVFYLR-------------PTAPQQVGMVQVQQGGVEPMVFNSVPVVHG 326

Query: 362 KATAKRLRLFGVNMDCPITESDDECHILSSSTSIQHATMA----IHDQPSQLSSSSQLSL 417
           KA AKRLRLFGVNM+CPI+ES DEC IL SSTSI HA +A        PS      QL L
Sbjct: 327 KAAAKRLRLFGVNMECPISES-DECDIL-SSTSIPHAAVASQPPHLSSPSSHHHPLQLRL 384

Query: 418 YDA 420
           Y+A
Sbjct: 385 YNA 387

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297742476|emb|CBI34625.3| unnamed protein product [Vitis vinifera]

 Score =  279 bits (714), Expect = 2e-72,   Method: Compositional matrix adjust.
 Identities = 153/267 (57%), Positives = 179/267 (67%), Gaps = 39/267 (14%)

Query: 129 SLEKEHMFDKVVTPSDVGKLNRLVIPKQHAEKYFPLDSSSNEKGLLLNFEDRNGKPWRFR 188
           +LE+EHMFDKVVTPSDVGKLNRLVIPKQHAEKYFPLDSS+NEKGLLLNFEDR+GKPWRFR
Sbjct: 150 ALEREHMFDKVVTPSDVGKLNRLVIPKQHAEKYFPLDSSANEKGLLLNFEDRSGKPWRFR 209

Query: 189 YSYWNSSQSYVMTKGWSRFVKDKKLDAGDVVSFHRGVGDLAKGRLFIDWRRRSHPPAAAA 248
           YSYWNSSQSYVMTKGWSRFVK+KKLDAGD+VSF RGVG+  K RL+IDWRRR  P A   
Sbjct: 210 YSYWNSSQSYVMTKGWSRFVKEKKLDAGDIVSFQRGVGESGKDRLYIDWRRR--PDAPEP 267

Query: 249 ASFSRHLPFYRSIPWNPLLMMRPPVLPASMYSQSQINNNFYNRNSISLGGTGNNNNVLST 308
           +S + H  F+RS              P  M       ++   RN    G    NN V   
Sbjct: 268 SSLAHHF-FHRS--------------PNYM-------SHLGGRNPYGSGAYSYNNAV--N 303

Query: 309 RTLGSILYLRSQLPAAPATQQPPPPPPPPHTEIGMTKWQQHPIVFDSVPVVQGKATAKRL 368
              GS+ YLR             P  P     + + +    P+VF+SVPVV GKA AKRL
Sbjct: 304 PCSGSVFYLR-------------PTAPQQVGMVQVQQGGVEPMVFNSVPVVHGKAAAKRL 350

Query: 369 RLFGVNMDCPITESDDECHILSSSTSI 395
           RLFGVNM+CPI+ESD+  + LSS +++
Sbjct: 351 RLFGVNMECPISESDELSNKLSSLSTL 377

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225453662|ref|XP_002268399.1| PREDICTED: B3 domain-containing transcription factor NGA1-like [Vitis vinifera]

 Score =  275 bits (703), Expect = 3e-71,   Method: Compositional matrix adjust.
 Identities = 162/328 (49%), Positives = 202/328 (61%), Gaps = 21/328 (6%)

Query: 131 EKEHMFDKVVTPSDVGKLNRLVIPKQHAEKYFPLDSSSNEKGLLLNFEDRNGKPWRFRYS 190
           E+EHMFDKVVTPSDVGKLNRLVIPKQHAEKYFPLDSS+++KGLLLNFEDR+GKPWRFRYS
Sbjct: 134 EREHMFDKVVTPSDVGKLNRLVIPKQHAEKYFPLDSSASDKGLLLNFEDRDGKPWRFRYS 193

Query: 191 YWNSSQSYVMTKGWSRFVKDKKLDAGDVVSFHRGVGDLAKGRLFIDWRRRSHPPAAAAAS 250
           YWNSSQSYVMTKGWSRFVK+KKLDAGD+VSF RGVG+  K RL+IDWRRR   P   + S
Sbjct: 194 YWNSSQSYVMTKGWSRFVKEKKLDAGDIVSFERGVGESGKDRLYIDWRRRPDAPDPTSLS 253

Query: 251 ---FSRHLPFYRSIPWNPLLMMRPPVLPASMYSQSQINNNFYNRNSISLGGTGNNNNVLS 307
                  LPF +S+ W  L  +  P  P+   +  Q +++    N  S+     +++   
Sbjct: 254 HLHLPTQLPFSQSVRWGRLYSL--PQSPSMSMNMPQGHDHMQQLNYSSIHPYHRHHHHHP 311

Query: 308 T------------RTLGSILYLRSQLPAAPATQQPPPPPPPPHTEIGMTKWQQHPIVFDS 355
                         TLG   +  + + +   +          H    + +    P+V +S
Sbjct: 312 HHHHHHHHHHHQRNTLGGGYHDYNAVTSGSGSLYYLSSSSSSHQIGAVQQGGDAPMVINS 371

Query: 356 VPVVQGKATAKRLRLFGVNMDCPITESDDECHILSSSTSIQHATMAIHDQPSQLSSSSQL 415
           VPVV GK TAKRLRLFGVNM+C   +   EC+IL  ST+I H TMA        SS   L
Sbjct: 372 VPVVHGKTTAKRLRLFGVNMECSTPDDHPECNIL-PSTAIPHVTMASLSPHLPSSSLPPL 430

Query: 416 S--LYDATPLLP-PFDFLNKGKASMSFD 440
              L++ +PL   P +F  KGK S+SFD
Sbjct: 431 QLRLFNGSPLQAVPDEFPKKGKTSLSFD 458

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|296089028|emb|CBI38731.3| unnamed protein product [Vitis vinifera]

 Score =  267 bits (682), Expect = 9e-69,   Method: Compositional matrix adjust.
 Identities = 147/274 (53%), Positives = 175/274 (63%), Gaps = 39/274 (14%)

Query: 131 EKEHMFDKVVTPSDVGKLNRLVIPKQHAEKYFPLDSSSNEKGLLLNFEDRNGKPWRFRYS 190
           E+EHMFDKVVTPSDVGKLNRLVIPKQHAEKYFPLDSS+++KGLLLNFEDR+GKPWRFRYS
Sbjct: 90  EREHMFDKVVTPSDVGKLNRLVIPKQHAEKYFPLDSSASDKGLLLNFEDRDGKPWRFRYS 149

Query: 191 YWNSSQSYVMTKGWSRFVKDKKLDAGDVVSFHRGVGDLAKGRLFIDWRRRSHPPAAAAAS 250
           YWNSSQSYVMTKGWSRFVK+KKLDAGD+VSF RGVG+  K RL+IDWRRR   P   + S
Sbjct: 150 YWNSSQSYVMTKGWSRFVKEKKLDAGDIVSFERGVGESGKDRLYIDWRRRPDAPDPTSLS 209

Query: 251 ---FSRHLPFYRSIPWNPLLMMRPPVLPASMYSQSQINNNFYNRNSISLGGTGNNNNVLS 307
                  LPF +S+ W              +YS  Q  N        +LGG  ++ N ++
Sbjct: 210 HLHLPTQLPFSQSVRW------------GRLYSLPQSPN--------TLGGGYHDYNAVT 249

Query: 308 TRTLGSILYLRSQLPAAPATQQPPPPPPPPHTEIGMTKWQQHPIVFDSVPVVQGKATAKR 367
           + +        S                  H    + +    P+V +SVPVV GK TAKR
Sbjct: 250 SGSGSLYYLSSSSS---------------SHQIGAVQQGGDAPMVINSVPVVHGKTTAKR 294

Query: 368 LRLFGVNMDCPITESDDECHILSSSTSIQHATMA 401
           LRLFGVNM+C   +   EC+IL  ST+I H TMA
Sbjct: 295 LRLFGVNMECSTPDDHPECNIL-PSTAIPHVTMA 327

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|125542174|gb|EAY88313.1| hypothetical protein OsI_09772 [Oryza sativa Indica Group]

 Score =  244 bits (624), Expect = 5e-62,   Method: Compositional matrix adjust.
 Identities = 148/291 (50%), Positives = 177/291 (60%), Gaps = 61/291 (20%)

Query: 119 GEAEED--RVLISLEKEHMFDKVVTPSDVGKLNRLVIPKQHAEKYFPLDSSSNEKGLLLN 176
           GE +E   R L ++EKEHMFDKVVTPSDVGKLNRLVIPKQHAEKYFPLD++SNEKGLLL+
Sbjct: 18  GEVQESGGRSLAAVEKEHMFDKVVTPSDVGKLNRLVIPKQHAEKYFPLDAASNEKGLLLS 77

Query: 177 FEDRNGKPWRFRYSYWNSSQSYVMTKGWSRFVKDKKLDAGDVVSFHRGVGDLAKGRLFID 236
           FEDR GKPWRFRYSYWNSSQSYVMTKGWSRFVK+K+LDAGD VSF RGVG+ A+GRLFID
Sbjct: 78  FEDRTGKPWRFRYSYWNSSQSYVMTKGWSRFVKEKRLDAGDTVSFGRGVGEAARGRLFID 137

Query: 237 WRRRSHPPAAAAAS-----FSRHLPFYRSIPWNPLLMMRPP-----------VLPASMYS 280
           WRRR  P   AA       F+ HLP   SIP+ P                  +LP S   
Sbjct: 138 WRRR--PDVVAALQPPTHRFAHHLP--SSIPFAPWAHHHGHGAAAAAAGARFLLPPS--- 190

Query: 281 QSQINNNFYNRNSISLGGTGNNNNVLSTRTLGSILYLRSQLPAAPATQQPPPPPPPPHTE 340
            S    + + R++ ++G      +  +  T   +L+ R               P PP   
Sbjct: 191 -STPIYDHHRRHAHAVG-----YDAYAAATSRQVLFYR---------------PLPPQQ- 228

Query: 341 IGMTKWQQHP-IVFDSVPVVQGK-------ATAKRLRLFGVNMDCPITESD 383
                 Q HP +V +SVPV           A +KR+RLFGVN+DC  +E D
Sbjct: 229 ------QHHPAVVLESVPVRMTAGHAEPPSAPSKRVRLFGVNLDCANSEQD 273

Source: Oryza sativa Indica Group

Species: Oryza sativa

Genus: Oryza

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|115450383|ref|NP_001048792.1| Os03g0120900 [Oryza sativa Japonica Group] gi|75246354|sp|Q8LMR9.1|Y3209_ORYSJ RecName: Full=B3 domain-containing protein Os03g0120900 gi|21426118|gb|AAM52315.1|AC105363_4 Putative RAV-like B3 domain DNA binding protein [Oryza sativa Japonica Group] gi|108705902|gb|ABF93697.1| B3 DNA binding domain containing protein, expressed [Oryza sativa Japonica Group] gi|113547263|dbj|BAF10706.1| Os03g0120900 [Oryza sativa Japonica Group]

 Score =  244 bits (622), Expect = 8e-62,   Method: Compositional matrix adjust.
 Identities = 148/298 (49%), Positives = 179/298 (60%), Gaps = 72/298 (24%)

Query: 119 GEAEED--RVLISLEKEHMFDKVVTPSDVGKLNRLVIPKQHAEKYFPLDSSSNEKGLLLN 176
           GE +E   R L ++EKEHMFDKVVTPSDVGKLNRLVIPKQHAEKYFPLD++SNEKGLLL+
Sbjct: 18  GEVQESGGRSLAAVEKEHMFDKVVTPSDVGKLNRLVIPKQHAEKYFPLDAASNEKGLLLS 77

Query: 177 FEDRNGKPWRFRYSYWNSSQSYVMTKGWSRFVKDKKLDAGDVVSFHRGVGDLAKGRLFID 236
           FEDR GKPWRFRYSYWNSSQSYVMTKGWSRFVK+K+LDAGD VSF RGVG+ A+GRLFID
Sbjct: 78  FEDRTGKPWRFRYSYWNSSQSYVMTKGWSRFVKEKRLDAGDTVSFGRGVGEAARGRLFID 137

Query: 237 WRRRSHPPAAAAAS-----FSRHLPFYRSIPWNPLL------------------MMRPPV 273
           WRRR  P   AA       F+ HLP   SIP+ P                     + PP 
Sbjct: 138 WRRR--PDVVAALQPPTHRFAHHLP--SSIPFAPWAHHHGHGAAAAAAAAAGARFLLPP- 192

Query: 274 LPASMYSQSQINNNFYNRNSISLGGTGNNNNVLSTRTLGSILYLRSQLPAAPATQQPPPP 333
                 S + I ++ + R++ ++G      +  +  T   +L+ R               
Sbjct: 193 ------SSTPIYDH-HRRHAHAVG-----YDAYAAATSRQVLFYR--------------- 225

Query: 334 PPPPHTEIGMTKWQQHP-IVFDSVPVVQGK-------ATAKRLRLFGVNMDCPITESD 383
           P PP         Q HP +V +SVPV           A +KR+RLFGVN+DC  +E D
Sbjct: 226 PLPPQQ-------QHHPAVVLESVPVRMTAGHAEPPSAPSKRVRLFGVNLDCANSEQD 276

Source: Oryza sativa Japonica Group

Species: Oryza sativa

Genus: Oryza

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|358347636|ref|XP_003637862.1| Maturase K [Medicago truncatula] gi|355503797|gb|AES85000.1| Maturase K [Medicago truncatula]

 Score =  243 bits (621), Expect = 1e-61,   Method: Compositional matrix adjust.
 Identities = 154/327 (47%), Positives = 186/327 (56%), Gaps = 45/327 (13%)

Query: 131 EKEHMFDKVVTPSDVGKLNRLVIPKQHAEKYFPLDSSSNEKGLLLNFEDRNGKPWRFRYS 190
           EKEHMFDK VTPSDVGKLNRLVIPKQHAEKYFPLDS+SNEKGLLLNFEDRNGK WRFRYS
Sbjct: 167 EKEHMFDKAVTPSDVGKLNRLVIPKQHAEKYFPLDSTSNEKGLLLNFEDRNGKLWRFRYS 226

Query: 191 YWNSSQSYVMTKGWSRFVKDKKLDAGDVVSFHRGVGDLAKGRLFIDWRRRS----HPPAA 246
           YWNSSQSYVMTKGWSRFVK+KKLDAGD+VSF RGVG+L + RLFIDWRRRS    H    
Sbjct: 227 YWNSSQSYVMTKGWSRFVKEKKLDAGDIVSFQRGVGELFRHRLFIDWRRRSNHNHHTIDP 286

Query: 247 AAASFSRHLPFY------RSIPW---NPLLMMRPPVLPASMYSQSQ-----INNNF-YNR 291
           ++A+     PF+       SI W   N      P   P  +  Q Q     ++N   +N 
Sbjct: 287 SSATL--FTPFFLPNQQQYSIRWGGANSRFYSLPYPTPQRLQHQQQNHHDPLHNQMNFNH 344

Query: 292 NSISL----GGTGNNNNVLSTRTLGSILYLRSQLPAAPATQQPPPPPPPPHTEIGMTKWQ 347
           N        GG  N+          S+ Y+RS  P++ +  Q          E G     
Sbjct: 345 NMFPFHQYGGGNVNHQYNFHHHDPSSVFYMRSLAPSSMSMPQGSLSTRSQQQEGGGGSNV 404

Query: 348 QHPIVFDSVPV-----------------VQGKATAKRLRLFGVNMDCPITESDDECHILS 390
            + I+ DSVPV                       AKRLRLFGVNM+C  + + D+     
Sbjct: 405 SNMII-DSVPVSHYHHHHGNLTSNATTSTTTNGAAKRLRLFGVNMECGGSSTSDDNLASP 463

Query: 391 SST--SIQHATMAIHDQPSQLSSSSQL 415
           SS   S+QH  +  H++    S+S++ 
Sbjct: 464 SSIVPSLQHLKVPHHEETLSSSTSTRF 490

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356571279|ref|XP_003553806.1| PREDICTED: B3 domain-containing transcription factor NGA1-like [Glycine max]

 Score =  243 bits (620), Expect = 1e-61,   Method: Compositional matrix adjust.
 Identities = 151/322 (46%), Positives = 186/322 (57%), Gaps = 58/322 (18%)

Query: 130 LEKEHMFDKVVTPSDVGKLNRLVIPKQHAEKYFPLDSSSNEKGLLLNFEDRNGKPWRFRY 189
           +EKE+MF+KVVTPSDVGKLNRLVIPKQHAEKYFPLDSSSNEKGLLLNFEDRNGK WRFRY
Sbjct: 84  VEKENMFEKVVTPSDVGKLNRLVIPKQHAEKYFPLDSSSNEKGLLLNFEDRNGKVWRFRY 143

Query: 190 SYWNSSQSYVMTKGWSRFVKDKKLDAGDVVSFHRGVGDLAKGRLFIDWRRRSHPPAAAAA 249
           SYWNSSQSYVMTKGWSRFVK+KKLDAGD+VSF RG+GDL + RL+IDWR+RS  P A   
Sbjct: 144 SYWNSSQSYVMTKGWSRFVKEKKLDAGDIVSFQRGLGDLYRHRLYIDWRKRSAHPHAHHH 203

Query: 250 SFSRHLPFYRSIPWNPLLMMRPPVLPASMYSQSQIN-NNF--YNRNSISLGGT------- 299
           +      F  SI W  L    PP      +    +N NN   + ++   LG         
Sbjct: 204 APDP--LFLPSIRWYSLPPTMPPRYHHDHHFHHHLNYNNLFTFQQHQYQLGAATAAATAA 261

Query: 300 --GNNNNVLSTRTLGSILYLRSQLPAAPATQQPPPPPPPPHTEIGMTKWQQHPIVFDSVP 357
             G+ N+       GS+ YLRS +      Q            +        P++ DSVP
Sbjct: 262 HHGDQNS-----GSGSLYYLRSSMSMGGGDQN-----------LQGRGNNIVPMIIDSVP 305

Query: 358 VVQGK----------------ATAKRLRLFGVNMDCPITESDDE-------CHILSSSTS 394
           V  G                 ++ KRLRLFGVNM+C  +  D +        H+ ++++S
Sbjct: 306 VSVGHHNNRHGNGGITSGGATSSGKRLRLFGVNMECASSAEDSKGLSSGSAAHVTTAASS 365

Query: 395 IQHATMAI---HDQPSQLSSSS 413
             H  + +   H+ P  LSSSS
Sbjct: 366 SLHQRLRLPLPHEDP--LSSSS 385

Source: Glycine max

Species: Glycine max

Genus: Glycine

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	440
TAIR|locus:2041404	310	NGA1 "NGATHA1" [Arabidopsis th	0.286	0.406	0.769	4.2e-55
TAIR|locus:2200950	358	NGA3 "NGATHA3" [Arabidopsis th	0.243	0.298	0.833	1.8e-54
TAIR|locus:2079537	299	NGA2 "NGATHA2" [Arabidopsis th	0.270	0.397	0.733	3.7e-50
TAIR|locus:2039165	244	ABS2 "ABNORMAL SHOOT 2" [Arabi	0.238	0.430	0.727	2e-43
TAIR|locus:2164215	282	DPA4 "DEVELOPMENT-RELATED PcG	0.236	0.368	0.698	4.1e-43
TAIR|locus:2117007	333	NGA4 "NGATHA4" [Arabidopsis th	0.286	0.378	0.614	5.2e-43
TAIR|locus:2080782	267	AT3G11580 [Arabidopsis thalian	0.238	0.393	0.661	1.4e-40
TAIR|locus:2205319	344	RAV1 "related to ABI3/VP1 1" [	0.234	0.299	0.726	8.3e-39
TAIR|locus:2012438	352	RAV2 "related to ABI3/VP1 2" [	0.254	0.318	0.686	8.9e-38
TAIR|locus:2031185	361	TEM1 "TEMPRANILLO 1" [Arabidop	0.268	0.326	0.6	2.2e-36

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

 Score = 507 (183.5 bits), Expect = 4.2e-55, Sum P(2) = 4.2e-55
 Identities = 100/130 (76%), Positives = 108/130 (83%)

Query:   112 TKDIIEEGE---AEEDRVLISLEKEHMFDKVVTPSDVGKLNRLVIPKQHAEKYFPLDSSS 168
             T+D  EE     AEE+      ++EHMFDKVVTPSDVGKLNRLVIPKQHAE++FPLDSSS
Sbjct:     8 TRDEDEEEAKPLAEEEGAREVADREHMFDKVVTPSDVGKLNRLVIPKQHAERFFPLDSSS 67

Query:   169 NEKGLLLNFEDRNGKPWRFRYSYWNSSQSYVMTKGWSRFVKDKKLDAGDVVSFHRGVGDL 228
             NEKGLLLNFED  GK WRFRYSYWNSSQSYVMTKGWSRFVKDKKLDAGD+VSF R VGD 
Sbjct:    68 NEKGLLLNFEDLTGKSWRFRYSYWNSSQSYVMTKGWSRFVKDKKLDAGDIVSFQRCVGDS 127

Query:   229 AK-GRLFIDW 237
              +  RLFIDW
Sbjct:   128 GRDSRLFIDW 137

GO:0003677 "DNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISM

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

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

GO:0009908 "flower development" evidence=IMP

GO:0048366 "leaf development" evidence=IMP

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

 Score = 501 (181.4 bits), Expect = 1.8e-54, Sum P(2) = 1.8e-54
 Identities = 90/108 (83%), Positives = 101/108 (93%)

Query:   131 EKEHMFDKVVTPSDVGKLNRLVIPKQHAEKYFPLDSSSNEKGLLLNFEDRNGKPWRFRYS 190
             EKEHMFDKVVTPSDVGKLNRLVIPKQHAE+YFPLDSS+N+ G LLNF+DRNGK WRFRYS
Sbjct:    51 EKEHMFDKVVTPSDVGKLNRLVIPKQHAERYFPLDSSNNQNGTLLNFQDRNGKMWRFRYS 110

Query:   191 YWNSSQSYVMTKGWSRFVKDKKLDAGDVVSFHRGVGDLA-KGRLFIDW 237
             YWNSSQSYVMTKGWSRFVK+KKLDAGD+VSF RG+GD + + +L+IDW
Sbjct:   111 YWNSSQSYVMTKGWSRFVKEKKLDAGDIVSFQRGIGDESERSKLYIDW 158

GO:0003677 "DNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISM

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

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

GO:0009908 "flower development" evidence=IMP

GO:0048366 "leaf development" evidence=IMP

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

 Score = 469 (170.2 bits), Expect = 3.7e-50, Sum P(2) = 3.7e-50
 Identities = 91/124 (73%), Positives = 103/124 (83%)

Query:   117 EEGEAEEDRVLISLEKEHMFDKVVTPSDVGKLNRLVIPKQHAEKYFPLDSSS-NE--KGL 173
             E+ E   +    S+E+EHMFDKVVTPSDVGKLNRLVIPKQHAE+YFPLD+S+ N+  KGL
Sbjct:     4 EDKEKPIEEASSSMEREHMFDKVVTPSDVGKLNRLVIPKQHAERYFPLDNSTTNDSNKGL 63

Query:   174 LLNFEDRNGKPWRFRYSYWNSSQSYVMTKGWSRFVKDKKLDAGDVVSFHRGVGDLAKGRL 233
             LLNFEDR+G  WRFRYSYWNSSQSYVMTKGWSRFVKDKKLDAGD+VSF R      K +L
Sbjct:    64 LLNFEDRSGNSWRFRYSYWNSSQSYVMTKGWSRFVKDKKLDAGDIVSFQRD--SCNKDKL 121

Query:   234 FIDW 237
             +IDW
Sbjct:   122 YIDW 125

GO:0003677 "DNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISM

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

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

GO:0009908 "flower development" evidence=IMP

GO:0048366 "leaf development" evidence=IMP

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

 Score = 413 (150.4 bits), Expect = 2.0e-43, Sum P(2) = 2.0e-43
 Identities = 80/110 (72%), Positives = 90/110 (81%)

Query:   131 EKEHMFDKVVTPSDVGKLNRLVIPKQHAEKYFPLDSSSN---EKGLLLNFEDRNGKPWRF 187
             EKE +F+K +TPSDVGKLNRLVIPKQHAE+YFPL +++    EKGLLL FED  GKPWRF
Sbjct:    33 EKEALFEKPLTPSDVGKLNRLVIPKQHAERYFPLAAAAADAVEKGLLLCFEDEEGKPWRF 92

Query:   188 RYSYWNSSQSYVMTKGWSRFVKDKKLDAGDVVSFHRGVGDLAKGRLFIDW 237
             RYSYWNSSQSYV+TKGWSR+VK+K LDAGDVV FHR   D   GR FI W
Sbjct:    93 RYSYWNSSQSYVLTKGWSRYVKEKHLDAGDVVLFHRHRSD--GGRFFIGW 140

GO:0003677 "DNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISM

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

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

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

GO:0080167 "response to karrikin" evidence=IEP

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

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

 Score = 404 (147.3 bits), Expect = 4.1e-43, Sum P(2) = 4.1e-43
 Identities = 81/116 (69%), Positives = 91/116 (78%)

Query:   132 KEHMFDKVVTPSDVGKLNRLVIPKQHAEKYFPL----------DSSSNEKGLLLNFEDRN 181
             KE +F+K +TPSDVGKLNRLVIPKQHAEKYFPL          D+SS+EKG+LL+FED +
Sbjct:    42 KESLFEKSLTPSDVGKLNRLVIPKQHAEKYFPLNAVLVSSAAADTSSSEKGMLLSFEDES 101

Query:   182 GKPWRFRYSYWNSSQSYVMTKGWSRFVKDKKLDAGDVVSFHRGVGDLAKGRLFIDW 237
             GK WRFRYSYWNSSQSYV+TKGWSRFVKDK+LD GDVV F R   D    RLFI W
Sbjct:   102 GKSWRFRYSYWNSSQSYVLTKGWSRFVKDKQLDPGDVVFFQRHRSD--SRRLFIGW 155

GO:0003677 "DNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISM

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

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

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

GO:0010073 "meristem maintenance" evidence=IMP

GO:0010358 "leaf shaping" evidence=IGI

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

GO:0048366 "leaf development" evidence=IGI

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

 Score = 411 (149.7 bits), Expect = 5.2e-43, Sum P(2) = 5.2e-43
 Identities = 83/135 (61%), Positives = 98/135 (72%)

Query:   110 QETKDIIEEGEAEEDRVLISLEKEHMFDKVVTPSDVGKLNRLVIPKQHAEKYFPLDSSSN 169
             QE  +I        +    S  +EHMFDKV+TPSDVGKLNRLVIPKQHAE +FPL+   N
Sbjct:    10 QELAEIRASSSDHTNYFYSSERREHMFDKVLTPSDVGKLNRLVIPKQHAENFFPLED--N 67

Query:   170 EKGLLLNFEDRNGKPWRFRYSYWNSSQSYVMTKGWSRFVKDKKLDAGDVVSFHRGV--GD 227
             + G +L+F+D+NGK WRFRYSYWNSSQSYVMTKGWSRFVK+KKL AGD VSF+RG    D
Sbjct:    68 QNGTVLDFQDKNGKMWRFRYSYWNSSQSYVMTKGWSRFVKEKKLFAGDTVSFYRGYIPDD 127

Query:   228 LAKGR-----LFIDW 237
              A+       +FIDW
Sbjct:   128 NAQPERRRKIMFIDW 142

GO:0003677 "DNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISM

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

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

GO:0009908 "flower development" evidence=IMP

GO:0048366 "leaf development" evidence=IMP

TAIR|locus:2080782 AT3G11580 [Arabidopsis thaliana (taxid:3702)]

 Score = 391 (142.7 bits), Expect = 1.4e-40, Sum P(2) = 1.4e-40
 Identities = 78/118 (66%), Positives = 93/118 (78%)

Query:   131 EKEHMFDKVVTPSDVGKLNRLVIPKQHAEKYFPLDSSSN-----------EKGLLLNFED 179
             ++E +F+K +TPSDVGKLNRLVIPKQHAEKYFPL++++N           EKG+LL+FED
Sbjct:    24 QRESLFEKSLTPSDVGKLNRLVIPKQHAEKYFPLNNNNNNGGSGDDVATTEKGMLLSFED 83

Query:   180 RNGKPWRFRYSYWNSSQSYVMTKGWSRFVKDKKLDAGDVVSFHRGVGDLAKGRLFIDW 237
              +GK W+FRYSYWNSSQSYV+TKGWSR+VKDK LDAGDVV F R   DL   RLFI W
Sbjct:    84 ESGKCWKFRYSYWNSSQSYVLTKGWSRYVKDKHLDAGDVVFFQRHRFDLH--RLFIGW 139

GO:0003677 "DNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISM

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

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

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

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

 Score = 393 (143.4 bits), Expect = 8.3e-39, Sum P(2) = 8.3e-39
 Identities = 77/106 (72%), Positives = 87/106 (82%)

Query:   133 EHMFDKVVTPSDVGKLNRLVIPKQHAEKYFPLDSSS-NEKGLLLNFEDRNGKPWRFRYSY 191
             E +F+K VTPSDVGKLNRLVIPK HAEK+FPL SS+ + KG+LLNFED NGK WRFRYSY
Sbjct:   185 EALFEKAVTPSDVGKLNRLVIPKHHAEKHFPLPSSNVSVKGVLLNFEDVNGKVWRFRYSY 244

Query:   192 WNSSQSYVMTKGWSRFVKDKKLDAGDVVSFHRGVGDLAKGRLFIDW 237
             WNSSQSYV+TKGWSRFVK+K L AGDVVSF R  G     +L+I W
Sbjct:   245 WNSSQSYVLTKGWSRFVKEKNLRAGDVVSFSRSNGQ--DQQLYIGW 288

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

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

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

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

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

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

GO:0048366 "leaf development" evidence=IMP

GO:0048527 "lateral root development" evidence=IMP

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

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

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

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

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

 Score = 405 (147.6 bits), Expect = 8.9e-38, P = 8.9e-38
 Identities = 81/118 (68%), Positives = 96/118 (81%)

Query:   122 EEDRVLISLEKEHMFDKVVTPSDVGKLNRLVIPKQHAEKYFPLDSSSNE--KGLLLNFED 179
             + D+VL +  +E +F+K VTPSDVGKLNRLVIPKQHAEK+FPL S S    KG+L+NFED
Sbjct:   176 QNDKVLKT--REVLFEKAVTPSDVGKLNRLVIPKQHAEKHFPLPSPSPAVTKGVLINFED 233

Query:   180 RNGKPWRFRYSYWNSSQSYVMTKGWSRFVKDKKLDAGDVVSFHRGVGDLAKGRLFIDW 237
              NGK WRFRYSYWNSSQSYV+TKGWSRFVK+K L AGDVV+F R  G L + +L+IDW
Sbjct:   234 VNGKVWRFRYSYWNSSQSYVLTKGWSRFVKEKNLRAGDVVTFERSTG-LER-QLYIDW 289

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

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

GO:0005634 "nucleus" evidence=ISM

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

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

GO:0010167 "response to nitrate" evidence=RCA

GO:0010200 "response to chitin" evidence=RCA

GO:0015706 "nitrate transport" evidence=RCA

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

 Score = 371 (135.7 bits), Expect = 2.2e-36, Sum P(2) = 2.2e-36
 Identities = 78/130 (60%), Positives = 91/130 (70%)

Query:   116 IEEGEAEEDRVLISLEKEHMFDKVVTPSDVGKLNRLVIPKQHAEKYFPLDSS-------- 167
             +E      D VL +  +E +F+K VTPSDVGKLNRLVIPKQHAEK+FPL +         
Sbjct:   177 LETATYGNDAVLRA--REVLFEKTVTPSDVGKLNRLVIPKQHAEKHFPLPAMTTAMGMNP 234

Query:   168 SNEKGLLLNFEDRNGKPWRFRYSYWNSSQSYVMTKGWSRFVKDKKLDAGDVVSFHRGVGD 227
             S  KG+L+N EDR GK WRFRYSYWNSSQSYV+TKGWSRFVK+K L AGDVV F R  G 
Sbjct:   235 SPTKGVLINLEDRTGKVWRFRYSYWNSSQSYVLTKGWSRFVKEKNLRAGDVVCFERSTGP 294

Query:   228 LAKGRLFIDW 237
                 +L+I W
Sbjct:   295 --DRQLYIHW 302

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

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

GO:0005634 "nucleus" evidence=ISM

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

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

GO:0048573 "photoperiodism, flowering" evidence=IMP

GO:0030003 "cellular cation homeostasis" evidence=RCA

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

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input: GSVIVG00000473001 SubName- Full=Chromosome chr2 scaffold_105, whole genome shotgun sequence; (383 aa) (Vitis vinifera)

Predicted Functional Partners:

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

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	440
pfam02362	97	pfam02362, B3, B3 DNA binding domain	3e-33
smart01019	96	smart01019, B3, B3 DNA binding domain	1e-26
cd10017	98	cd10017, B3_DNA, Plant-specific B3-DNA binding dom	2e-26
cd10015	109	cd10015, BfiI_C_EcoRII_N_B3, DNA binding domains o	1e-07

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

 Score =  120 bits (302), Expect = 3e-33
 Identities = 41/106 (38%), Positives = 56/106 (52%), Gaps = 9/106 (8%)

Query: 136 FDKVVTPSDVGKLNRLVIPKQHAEKYFPLDSSSNEKGLLLNFEDRNGKPWRFRYSYWNSS 195
           F KV+TPSDV K  RLV+PK+ AE+        N+KG  +   D +GK W  +  Y  S 
Sbjct: 1   FVKVLTPSDVSKDGRLVLPKKFAEENGL-----NKKGQEITLLDPDGKSWTVKLRYRKSG 55

Query: 196 QSYVMTKGWSRFVKDKKLDAGDVVSFHRGVGDLAKGRLFIDWRRRS 241
           + Y++T GW  FVK   L AGD + F    G    G+  +   R+S
Sbjct: 56  RRYLLTSGWKEFVKANGLKAGDSLVFKLDGG----GKFVVGIFRKS 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|214977 smart01019, B3, B3 DNA binding domain

 Score =  102 bits (256), Expect = 1e-26
 Identities = 35/88 (39%), Positives = 46/88 (52%), Gaps = 5/88 (5%)

Query: 136 FDKVVTPSDVGKLNRLVIPKQHAEKYFPLDSSSNEKGLLLNFEDRNGKPWRFRYSYWNSS 195
           F K +T SDV K  RLV+PKQ AE   P       K   +   D +GK W+ +  Y  SS
Sbjct: 1   FFKTLTTSDVSKHGRLVLPKQFAESNGP-----PLKPKEITLLDPDGKSWKVKLKYRGSS 55

Query: 196 QSYVMTKGWSRFVKDKKLDAGDVVSFHR 223
             +++T GW  FVK   L AGD ++F  
Sbjct: 56  GMFLLTGGWKEFVKANGLKAGDSLTFEL 83

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

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

 Score =  102 bits (255), Expect = 2e-26
 Identities = 32/90 (35%), Positives = 49/90 (54%), Gaps = 5/90 (5%)

Query: 134 HMFDKVVTPSDVGKLNRLVIPKQHAEKYFPLDSSSNEKGLLLNFEDRNGKPWRFRYSYWN 193
            +F KV+TPSDV  L RLV+PK+ A+ + P      ++G+ +  ED +GK W  +     
Sbjct: 1   PLFFKVLTPSDVSSLGRLVLPKKFAKAHLPP-----KEGVEVTLEDPDGKKWTVKLKKRK 55

Query: 194 SSQSYVMTKGWSRFVKDKKLDAGDVVSFHR 223
           +S   V++ GW  FV+   L  GD + F  
Sbjct: 56  NSGRMVLSGGWKEFVRANGLKEGDFLVFEL 85

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

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

 Score = 49.2 bits (117), Expect = 1e-07
 Identities = 25/96 (26%), Positives = 43/96 (44%), Gaps = 8/96 (8%)

Query: 136 FDKVVTPSDVGK----LNRLVIPKQHAEKYFPLDSSSNEK--GLLLNFED-RNGKPWRFR 188
             K ++ +D G        L IPK   EK+ P  + + E    + L   D  + + W  R
Sbjct: 3   LIKRLSANDTGATGGHQVGLYIPKGIVEKFPPSINHTREANPSIFLTMHDISDCRDWEAR 62

Query: 189 YSYWNSSQSYV-MTKGWSRFVKDKKLDAGDVVSFHR 223
             ++NS+++   +T+G   FVK   L+ GD+     
Sbjct: 63  AIFYNSNRNEKRLTRGGRGFVKQNPLNTGDLTLIAF 98

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	440
PF02362	100	B3: B3 DNA binding domain; InterPro: IPR003340 Two	99.82
PF03754	114	DUF313: Domain of unknown function (DUF313) ; Inte	98.55
PF09217	156	EcoRII-N: Restriction endonuclease EcoRII, N-termi	98.16

>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=99.82  E-value=9e-20  Score=147.92  Aligned_cols=100  Identities=35%  Similarity=0.562  Sum_probs=76.3

Q ss_pred             EEEecccCCCCCCCcEEeehhchhhhCCCCCCCCCCCeEEEEEeCCCCeEEEEEEEeCCCcceEEecChhhhhhccCCCC
Q 013565          136 FDKVVTPSDVGKLNRLVIPKQHAEKYFPLDSSSNEKGLLLNFEDRNGKPWRFRYSYWNSSQSYVMTKGWSRFVKDKKLDA  215 (440)
Q Consensus       136 F~KvLT~SDV~k~gRLvIPKr~AEk~FPLd~s~~~~g~~L~veD~~GK~W~FRysywn~SrrYVLTkGWs~FVKdKkLka  215 (440)
                      |.|+|+++|+.+.++|.||+++++++..    ....++.|.++|..|+.|++++++++++.+++|++||.+||++++|++
T Consensus         1 F~K~l~~s~~~~~~~l~iP~~f~~~~~~----~~~~~~~v~l~~~~g~~W~v~~~~~~~~~~~~l~~GW~~Fv~~n~L~~   76 (100)
T PF02362_consen    1 FFKVLKPSDVSSSCRLIIPKEFAKKHGG----NKRKSREVTLKDPDGRSWPVKLKYRKNSGRYYLTGGWKKFVRDNGLKE   76 (100)
T ss_dssp             EEEE--TTCCCCTT-EEE-HHHHTTTS------SS--CEEEEEETTTEEEEEEEEEECCTTEEEEETTHHHHHHHCT--T
T ss_pred             CEEEEEccCcCCCCEEEeCHHHHHHhCC----CcCCCeEEEEEeCCCCEEEEEEEEEccCCeEEECCCHHHHHHHcCCCC
Confidence            8999999999998999999999998821    123578999999999999999999988888999999999999999999


Q ss_pred             CCEEEEEeccccCCCCeEEEEEEeCC
Q 013565          216 GDVVSFHRGVGDLAKGRLFIDWRRRS  241 (440)
Q Consensus       216 GDvVvF~R~~~e~~~grLfIgIRRa~  241 (440)
                      ||+|+|++..  ....++.|.|.|+.
T Consensus        77 GD~~~F~~~~--~~~~~~~v~i~~~~  100 (100)
T PF02362_consen   77 GDVCVFELIG--NSNFTLKVHIFRKS  100 (100)
T ss_dssp             T-EEEEEE-S--SSCE-EEEEEE---
T ss_pred             CCEEEEEEec--CCCceEEEEEEECc
Confidence            9999999973  36677799999863

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=98.55  E-value=1.1e-07  Score=83.51  Aligned_cols=81  Identities=23%  Similarity=0.555  Sum_probs=65.8

Q ss_pred             cccceeEEEecccCCCC-CCCcEEeehhchhh--hC-CC---------CCCCCCCCeEEEEEeCCCCeEEEEEEEeCC--
Q 013565          130 LEKEHMFDKVVTPSDVG-KLNRLVIPKQHAEK--YF-PL---------DSSSNEKGLLLNFEDRNGKPWRFRYSYWNS--  194 (440)
Q Consensus       130 ~eke~lF~KvLT~SDV~-k~gRLvIPKr~AEk--~F-PL---------d~s~~~~g~~L~veD~~GK~W~FRysywn~--  194 (440)
                      .....+|+|+|+.|||. ..+||.||......  +| |.         .......|+.+.+.|..++.|.++++.|+.  
T Consensus        18 ~d~kli~~K~L~~tDv~~~qsRLsmP~~qi~~~dFLt~eE~~~i~~~~~~~~~~~Gv~V~lvdp~~~~~~m~lkkW~mg~   97 (114)
T PF03754_consen   18 EDPKLIIEKTLFKTDVDPHQSRLSMPFNQIIDNDFLTEEEKRIIKEEKKNNDKKKGVEVILVDPSLRKWTMRLKKWNMGN   97 (114)
T ss_pred             CCCeEEEeeeecccCCCCCCceeeccHHHhcccccCCHHHHHHHHHhhccCcccCCceEEEECCcCcEEEEEEEEecccC
Confidence            45578999999999999 57899999987743  23 21         112356889999999999999999999965  


Q ss_pred             -CcceEEecChhhhhhc
Q 013565          195 -SQSYVMTKGWSRFVKD  210 (440)
Q Consensus       195 -SrrYVLTkGWs~FVKd  210 (440)
                       .-.|+|..||..+|++
T Consensus        98 ~~~~YvL~~gWn~VV~~  114 (114)
T PF03754_consen   98 GTSNYVLNSGWNKVVED  114 (114)
T ss_pred             CceEEEEEcChHhhccC
Confidence             4689999999999974

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

Probab=98.16  E-value=1.9e-05  Score=73.04  Aligned_cols=90  Identities=20%  Similarity=0.381  Sum_probs=58.4

Q ss_pred             cceeEEEecccCCCCC----CCcEEeehhchhhhCC-CCC-CCCCCCeEEEEEeCCC--CeEEEEEEEeCC------Ccc
Q 013565          132 KEHMFDKVVTPSDVGK----LNRLVIPKQHAEKYFP-LDS-SSNEKGLLLNFEDRNG--KPWRFRYSYWNS------SQS  197 (440)
Q Consensus       132 ke~lF~KvLT~SDV~k----~gRLvIPKr~AEk~FP-Ld~-s~~~~g~~L~veD~~G--K~W~FRysywn~------Srr  197 (440)
                      ....|+|.|++.|++.    ..++.|||..++.+|| +.. ...++.+.|.+++..+  ..|+||++|.|+      ++.
T Consensus         6 ~~~~~~K~LSaNDtGaTGgHQaGiyIpk~~~~~lFp~~~~~~~~Np~~~~~~~~~s~~~~~~~~r~iYYnn~~~~gTRNE   85 (156)
T PF09217_consen    6 SWAIYCKRLSANDTGATGGHQAGIYIPKSAAELLFPSINHTKEENPDIWLKARWQSHFVTDSQVRFIYYNNRLFGGTRNE   85 (156)
T ss_dssp             SEEEEEEE--CCCCTTTSSS--EEEE-HHHHHHH-GGG-SSSSSS-EEEEEEEETTTT---EEEEEEEE-CCCTTSS--E
T ss_pred             ceEEEEEEccCCCCCCcCcccceeEecccHHHHhCCCCCcccccCCceeEEEEECCCCccceeEEEEEEcccccCCCcCc
Confidence            3457999999999994    3599999999999997 332 3566789999998877  569999999977      577


Q ss_pred             eEEecChhhhhhccC-CCCCCEEEEE
Q 013565          198 YVMTKGWSRFVKDKK-LDAGDVVSFH  222 (440)
Q Consensus       198 YVLTkGWs~FVKdKk-LkaGDvVvF~  222 (440)
                      |.||. |.....--+ =.+||.++|.
T Consensus        86 ~RIT~-~G~~~~~~~~~~tGaL~vla  110 (156)
T PF09217_consen   86 YRITR-FGRGFPLQNPENTGALLVLA  110 (156)
T ss_dssp             EEEE----TTSGGG-GGGTT-EEEEE
T ss_pred             eEEee-ecCCCccCCccccccEEEEE
Confidence            99987 876655333 3679999887

All types of enzymes recognise specific short DNA sequences and carry out the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. They differ in their recognition sequence, subunit composition, cleavage position, and cofactor requirements [, ], as summarised below: Type I enzymes (3.1.21.3 from EC) cleave at sites remote from recognition site; require both ATP and S-adenosyl-L-methionine to function; multifunctional protein with both restriction and methylase (2.1.1.72 from EC) activities. Type II enzymes (3.1.21.4 from EC) cleave within or at short specific distances from recognition site; most require magnesium; single function (restriction) enzymes independent of methylase. Type III enzymes (3.1.21.5 from EC) cleave at sites a short distance from recognition site; require ATP (but doesn't hydrolyse it); S-adenosyl-L-methionine stimulates reaction but is not required; exists as part of a complex with a modification methylase methylase (2.1.1.72 from EC). Type IV enzymes target methylated DNA. Type II restriction endonucleases (3.1.21.4 from EC) are components of prokaryotic DNA restriction-modification mechanisms that protect the organism against invading foreign DNA. These site-specific deoxyribonucleases catalyse the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. Of the 3000 restriction endonucleases that have been characterised, most are homodimeric or tetrameric enzymes that cleave target DNA at sequence-specific sites close to the recognition site. For homodimeric enzymes, the recognition site is usually a palindromic sequence 4-8 bp in length. Most enzymes require magnesium ions as a cofactor for catalysis. Although they can vary in their mode of recognition, many restriction endonucleases share a similar structural core comprising four beta-strands and one alpha-helix, as well as a similar mechanism of cleavage, suggesting a common ancestral origin []. However, there is still considerable diversity amongst restriction endonucleases [, ]. The target site recognition process triggers large conformational changes of the enzyme and the target DNA, leading to the activation of the catalytic centres. Like other DNA binding proteins, restriction enzymes are capable of non-specific DNA binding as well, which is the prerequisite for efficient target site location by facilitated diffusion. Non-specific binding usually does not involve interactions with the bases but only with the DNA backbone []. This entry represents the N-terminal effector-binding domain of the type II restriction endonuclease EcoRII, which has a DNA recognition fold, allowing for binding to 5'-CCWGG sequences. It assumes a structure composed of an eight-stranded beta-sheet with the strands in the order of b2, b5, b4, b3, b7, b6, b1 and b8. They are mostly antiparallel to each other except that b3 is parallel to b7. Alternatively, it may also be viewed as consisting of two mini beta-sheets of four antiparallel beta-strands, sheet I from beta-strands b2, b5, b4, b3 and sheet II from strands b7, b6, b1, b8, folded into an open mixed beta-barrel with a novel topology. Sheet I has a simple Greek key motif while sheet II does not []. The domain represented by this entry is only found in bacterial proteins.; PDB: 3HQF_A 1NA6_A.

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	440
1wid_A	130	Solution Structure Of The B3 Dna-Binding Domain Of		3e-37

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

Iteration: 1
 Score =  152 bits (385), Expect = 3e-37,   Method: Compositional matrix adjust.
 Identities = 77/106 (72%), Positives = 87/106 (82%), Gaps = 3/106 (2%)
Query: 133 EHMFDKVVTPSDVGKLNRLVIPKQHAEKYFPLDSSS-NEKGLLLNFEDRNGKPWRFRYSY 191
           E +F+K VTPSDVGKLNRLVIPK HAEK+FPL SS+ + KG+LLNFED NGK WRFRYSY
Sbjct: 11  EALFEKAVTPSDVGKLNRLVIPKHHAEKHFPLPSSNVSVKGVLLNFEDVNGKVWRFRYSY 70
Query: 192 WNSSQSYVMTKGWSRFVKDKKLDAGDVVSFHRGVGDLAKGRLFIDW 237
           WNSSQSYV+TKGWSRFVK+K L AGDVVSF R  G     +L+I W
Sbjct: 71  WNSSQSYVLTKGWSRFVKEKNLRAGDVVSFSRSNGQ--DQQLYIGW 114

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	440
1wid_A	130	DNA-binding protein RAV1; DNA-binding domain, stru	9e-39
1yel_A	104	AT1G16640; CESG, protein structure initiative, str	1e-10
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	2e-06

>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 =  135 bits (341), Expect = 9e-39
 Identities = 79/123 (64%), Positives = 91/123 (73%), Gaps = 3/123 (2%)

Query: 131 EKEHMFDKVVTPSDVGKLNRLVIPKQHAEKYFP-LDSSSNEKGLLLNFEDRNGKPWRFRY 189
             E +F+K VTPSDVGKLNRLVIPK HAEK+FP   S+ + KG+LLNFED NGK WRFRY
Sbjct: 9   SAEALFEKAVTPSDVGKLNRLVIPKHHAEKHFPLPSSNVSVKGVLLNFEDVNGKVWRFRY 68

Query: 190 SYWNSSQSYVMTKGWSRFVKDKKLDAGDVVSFHRGVGDLAKGRLFIDWRRRSHPPAAAAA 249
           SYWNSSQSYV+TKGWSRFVK+K L AGDVVSF R  G     +L+I W+ RS     A+ 
Sbjct: 69  SYWNSSQSYVLTKGWSRFVKEKNLRAGDVVSFSRSNGQ--DQQLYIGWKSRSGSDLDASG 126

Query: 250 SFS 252
             S
Sbjct: 127 PSS 129

>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 = 57.5 bits (139), Expect = 1e-10
 Identities = 23/86 (26%), Positives = 32/86 (37%), Gaps = 10/86 (11%)

Query: 136 FDKVVTPSDVGKLNRLVIPKQHAEKYFPLDSSSNEKGLLLNFEDRNGKPWRFRYSYWNSS 195
           F K        K   L IP     +YFP           ++  D +G+ W  R       
Sbjct: 11  FMKPFISEKSSK--SLEIPLGFN-EYFPAPFPIT-----VDLLDYSGRSWTVRMKK--RG 60

Query: 196 QSYVMTKGWSRFVKDKKLDAGDVVSF 221
           +   +T GW  FVKD  L+ G  + F
Sbjct: 61  EKVFLTVGWENFVKDNNLEDGKYLQF 86

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

 Score = 49.5 bits (117), Expect = 2e-06
 Identities = 52/369 (14%), Positives = 95/369 (25%), Gaps = 135/369 (36%)

Query: 43  HHHHYTTQTQQLLPLTTHHQNYNKQQQPQMGSWLLGKTTTTTTAAELEDVSNEEETAAPT 102
           HHHH   +T +       +Q                           +D+          
Sbjct: 3   HHHHMDFETGEH-----QYQY--------------------------KDI-------LSV 24

Query: 103 KEQAIIMQ-ETKDIIEEGEAEEDRVLISLEKEHMFDKVVTPSDVGKLNRLVI-----PKQ 156
            E A +   + KD+    +     +L   E +H+   +++   V    RL        ++
Sbjct: 25  FEDAFVDNFDCKDV----QDMPKSILSKEEIDHI---IMSKDAVSGTLRLFWTLLSKQEE 77

Query: 157 HAEKYFPLDSSSNEKGLLLNFEDRNGKPWRFRYSY-------WNSSQSYVMTKGW-SRFV 208
             +K+       N K L+   +    +P      Y       +N +Q +   K   SR  
Sbjct: 78  MVQKFVEEVLRINYKFLMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVF--AKYNVSRLQ 135

Query: 209 KDKKL--------DAGDVVSFHRGVGDLAKGRLFIDWRRRSHPPAAAAASFSRHLPFYRS 260
              KL         A +V+    GV    K  +                S+         
Sbjct: 136 PYLKLRQALLELRPAKNVL-ID-GVLGSGKTWV----------ALDVCLSYKVQCKMDFK 183

Query: 261 IPWNPLLMMRPPVLPASMYSQSQINNNFYNRNSISLGGTGNNNNVLSTRTLGSI---LYL 317
           I W                              ++L       N  S  T+  +   L  
Sbjct: 184 IFW------------------------------LNLK------NCNSPETVLEMLQKLLY 207

Query: 318 RSQLPAAPATQQPPPPPPPPHTEIG----MTKWQQHP---IVFDSVPVVQGKATAKRLRL 370
           +        +          H+       + K + +    +V  +V        AK    
Sbjct: 208 QIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVLLNV------QNAKAWNA 261

Query: 371 FGVNMDCPI 379
           F ++  C I
Sbjct: 262 FNLS--CKI 268

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	440
1wid_A	130	DNA-binding protein RAV1; DNA-binding domain, stru	99.97
4i1k_A	146	B3 domain-containing transcription factor VRN1; B3	99.81
1yel_A	104	AT1G16640; CESG, protein structure initiative, str	99.68
1na6_A	404	Ecorii, restriction endonuclease ecorii; site-spec	95.13
1gcc_A	63	Ethylene responsive element binding factor 1; tran	92.53

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

Probab=99.97  E-value=9.4e-31  Score=227.13  Aligned_cols=118  Identities=66%  Similarity=1.066  Sum_probs=104.5

Q ss_pred             cccccceeEEEecccCCCCCCCcEEeehhchhhhCCC-CCCCCCCCeEEEEEeCCCCeEEEEEEEeCCCcceEEecChhh
Q 013565          128 ISLEKEHMFDKVVTPSDVGKLNRLVIPKQHAEKYFPL-DSSSNEKGLLLNFEDRNGKPWRFRYSYWNSSQSYVMTKGWSR  206 (440)
Q Consensus       128 ~~~eke~lF~KvLT~SDV~k~gRLvIPKr~AEk~FPL-d~s~~~~g~~L~veD~~GK~W~FRysywn~SrrYVLTkGWs~  206 (440)
                      ....++++|+|+||+|||+++++|+||+++|++|||. +.....+++.|.++|.+|++|+|+|+||+++++|+|++||+.
T Consensus         6 ~~~~~~~~F~K~Lt~SDv~~~~rL~iPk~~a~~~lP~~~~~~~~~~~~l~l~D~~Gk~W~fr~~~~~~~~~~~Lt~GW~~   85 (130)
T 1wid_A            6 SGRSAEALFEKAVTPSDVGKLNRLVIPKHHAEKHFPLPSSNVSVKGVLLNFEDVNGKVWRFRYSYWNSSQSYVLTKGWSR   85 (130)
T ss_dssp             --CCCEEEEEEECCTTTTSSSCCEEECHHHHTTTSCCCSSCCSSCCEEEEEEETTTEEEEEEEEEETTTTEEEEESSHHH
T ss_pred             CCCCCcceEEEEEehHHcCCCCEEEeCHHHHHhhCCccccccCCCcEEEEEEeCCCCEEEEEEEEECCCCceEEcCChHH
Confidence            3567788999999999999899999999999999994 333356789999999999999999999998899999999999


Q ss_pred             hhhccCCCCCCEEEEEeccccCCCCeEEEEEEeCCCCCccc
Q 013565          207 FVKDKKLDAGDVVSFHRGVGDLAKGRLFIDWRRRSHPPAAA  247 (440)
Q Consensus       207 FVKdKkLkaGDvVvF~R~~~e~~~grLfIgIRRa~~~~~~~  247 (440)
                      ||++|+|++||+|+|++.+  ..+++|+|++||+......+
T Consensus        86 FV~~~~L~~GD~~~F~~~~--~~~~~l~I~~rr~~~~~~~~  124 (130)
T 1wid_A           86 FVKEKNLRAGDVVSFSRSN--GQDQQLYIGWKSRSGSDLDA  124 (130)
T ss_dssp             HHHHTTCCTTCEEEEEECC--SSSCCEEEEEECCCSCSSCC
T ss_pred             HHHHcCCCCCCEEEEEEec--CCCcEEEEEEEECCCCCccc
Confidence            9999999999999999984  46789999999999766444

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

Probab=99.81  E-value=1.3e-19  Score=160.66  Aligned_cols=103  Identities=22%  Similarity=0.278  Sum_probs=89.5

Q ss_pred             ccccceeEEEecccCCCCCCCcEEeehhchhhhCCCCCCCCCCCeEEEEEeCCCCeEEEEEEEeCCCcceEEecChhhhh
Q 013565          129 SLEKEHMFDKVVTPSDVGKLNRLVIPKQHAEKYFPLDSSSNEKGLLLNFEDRNGKPWRFRYSYWNSSQSYVMTKGWSRFV  208 (440)
Q Consensus       129 ~~eke~lF~KvLT~SDV~k~gRLvIPKr~AEk~FPLd~s~~~~g~~L~veD~~GK~W~FRysywn~SrrYVLTkGWs~FV  208 (440)
                      ....+++|.|+|++|||.+.++|.||+++++++||..      ...|.++|. |+.|+|+|+|++.  ++.|++||..||
T Consensus        42 ~~s~~P~Fvk~l~~S~v~~~~~L~IP~~Fa~~~lp~~------~~~i~L~~~-gk~W~v~~~~~~~--~~~ls~GW~~Fv  112 (146)
T 4i1k_A           42 FEPTNPFFRVVLRPSYLYRGCIMYLPSGFAEKYLSGI------SGFIKVQLA-EKQWPVRCLYKAG--RAKFSQGWYEFT  112 (146)
T ss_dssp             CCCSSCEEEEECCGGGSSTTCCEECCHHHHHHHCTTC------CSEEEEEET-TEEEEEEEEEETT--EEEECTTHHHHH
T ss_pred             cCCCCCEEEEEECchhcCCCcEEEeCHHHHHHhCCCC------CeEEEEEEC-CcEEEEEEEEeCC--cEEECCchHHHH
Confidence            4578899999999999998889999999999999853      357788888 6999999999863  799999999999


Q ss_pred             hccCCCCCCEEEEEeccccCCCCeEEEEEEeCCC
Q 013565          209 KDKKLDAGDVVSFHRGVGDLAKGRLFIDWRRRSH  242 (440)
Q Consensus       209 KdKkLkaGDvVvF~R~~~e~~~grLfIgIRRa~~  242 (440)
                      ++|+|++||+|+|....  ..+-.|.|.|.|+.+
T Consensus       113 ~dn~L~~GD~cvFeli~--~~~~~f~V~IfR~~e  144 (146)
T 4i1k_A          113 LENNLGEGDVCVFELLR--TRDFVLKVTAFRVNE  144 (146)
T ss_dssp             HHTTCCTTCEEEEEECS--SSSCEEEEEEECCC-
T ss_pred             HHcCCCCCCEEEEEEec--CCceEEEEEEEeccC
Confidence            99999999999999974  334579999999875

>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=99.68  E-value=1.4e-16  Score=132.22  Aligned_cols=96  Identities=22%  Similarity=0.371  Sum_probs=81.4

Q ss_pred             cceeEEEecccCCCCCCCcEEeehhchhhhCCCCCCCCCCCeEEEEEeCCCCeEEEEEEEeCCCcceEEecChhhhhhcc
Q 013565          132 KEHMFDKVVTPSDVGKLNRLVIPKQHAEKYFPLDSSSNEKGLLLNFEDRNGKPWRFRYSYWNSSQSYVMTKGWSRFVKDK  211 (440)
Q Consensus       132 ke~lF~KvLT~SDV~k~gRLvIPKr~AEk~FPLd~s~~~~g~~L~veD~~GK~W~FRysywn~SrrYVLTkGWs~FVKdK  211 (440)
                      ..+.|.|+|+++|.  ..+|.||+++++.+.+..      ...+.++|.+|+.|++++++++  .+++|++||.+||++|
T Consensus         7 ~~p~F~K~l~~~~~--~~~L~IP~~F~~~~~~~~------~~~v~L~~~~G~~W~v~~~~~~--~~~~l~~GW~~Fv~~~   76 (104)
T 1yel_A            7 GEVQFMKPFISEKS--SKSLEIPLGFNEYFPAPF------PITVDLLDYSGRSWTVRMKKRG--EKVFLTVGWENFVKDN   76 (104)
T ss_dssp             CCEEEEEECCHHHH--TTCEECCHHHHTTCCCCC------CSEEEEEETTSCEEEEEEEEET--TEEEECTTHHHHHHHH
T ss_pred             CCCCEEEEECCCCc--cceEECCHHHHHhcCccC------CCEEEEECCCCCEEEEEEEEEC--CcEEEccChHHHHHHc
Confidence            45789999999994  459999999998775532      3478899999999999999874  5789999999999999


Q ss_pred             CCCCCCEEEEEeccccCCCCeEEEEEEeCC
Q 013565          212 KLDAGDVVSFHRGVGDLAKGRLFIDWRRRS  241 (440)
Q Consensus       212 kLkaGDvVvF~R~~~e~~~grLfIgIRRa~  241 (440)
                      +|++||+|+|...    .+.++.|.|-|+.
T Consensus        77 ~L~~GD~lvF~~~----~~~~f~V~If~~s  102 (104)
T 1yel_A           77 NLEDGKYLQFIYD----RDRTFYVIIYGHN  102 (104)
T ss_dssp             TCCTTCEEEEEEC----SSSEEEEEEECSS
T ss_pred             CCCCCCEEEEEEc----CCCeEEEEEECCC
Confidence            9999999999986    4567888888753

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

Probab=95.13  E-value=0.063  Score=55.13  Aligned_cols=94  Identities=19%  Similarity=0.300  Sum_probs=67.4

Q ss_pred             cccceeEEEecccCCCCC----CCcEEeehhchhhhCC-CCC-CCCCCCeEEEEE--eCCCCeEEEEEEEeC------CC
Q 013565          130 LEKEHMFDKVVTPSDVGK----LNRLVIPKQHAEKYFP-LDS-SSNEKGLLLNFE--DRNGKPWRFRYSYWN------SS  195 (440)
Q Consensus       130 ~eke~lF~KvLT~SDV~k----~gRLvIPKr~AEk~FP-Ld~-s~~~~g~~L~ve--D~~GK~W~FRysywn------~S  195 (440)
                      ......|.|.|++.|++.    ...+.+|+..++.+|| +.. .+.++...+.++  |...-++.++++|.+      ++
T Consensus        15 ~~~~~v~~K~LSAnDtgatgshQ~gi~ipk~~l~~lfp~lg~~~e~~~~~~~~~~l~d~d~p~td~~~twYn~R~~~~tR   94 (404)
T 1na6_A           15 CENYFVYIKRLSANDTGATGGHQVGLYIPSGIVEKLFPSINHTRELNPSVFLTAHVSSHDCPDSEARAIYYNSAHFGKTR   94 (404)
T ss_dssp             HSSEEEEEEECCHHHHTCC---CCCCCCCHHHHHHHCGGGCCCSSSSCEEEEEEEESSSCCCCEEEEEEEECGGGTTSCC
T ss_pred             cccchheeEEcccccCCCCCCcccccCCchHHHHHhcccCCCccccCCcceeEEEeccCCCceEEEEEEEecccccCCCC
Confidence            445679999999999993    4589999987899997 442 233444555443  443455599999996      34


Q ss_pred             cceEEecChh-hhhhccCCCCCCEEEEEec
Q 013565          196 QSYVMTKGWS-RFVKDKKLDAGDVVSFHRG  224 (440)
Q Consensus       196 rrYVLTkGWs-~FVKdKkLkaGDvVvF~R~  224 (440)
                      ..|.|+. |. .+.--+...+||.++|-+.
T Consensus        95 nEyRLt~-~~~~~~~~~~a~~GDLlvia~~  123 (404)
T 1na6_A           95 NEKRITR-WGRGSPLQDPENTGALTLLAFK  123 (404)
T ss_dssp             CEEEEEC-CCTTSGGGCGGGTTCEEEEEEE
T ss_pred             CceEEee-cCCCCcccccCCCCCEEEEEEe
Confidence            6799986 54 3455577889999999876

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

Probab=92.53  E-value=0.013  Score=45.36  Aligned_cols=40  Identities=15%  Similarity=0.043  Sum_probs=31.1

Q ss_pred             eeccccccccccccccc----ccccceeeccCCcccccccccccccc
Q 013565           54 LLPLTTHHQNYNKQQQP----QMGSWLLGKTTTTTTAAELEDVSNEE   96 (440)
Q Consensus        54 ~~p~~~~~~~~~~q~~~----h~~~w~~~~~~~~~~Aa~~~~v~~~~   96 (440)
                      |--.+.|  +|.++|..    ..+.|||+++.++ +||+|||+++..
T Consensus         6 V~~r~~g--kw~A~I~~~~~~g~r~~LGtf~T~e-eAA~AyD~Aa~~   49 (63)
T 1gcc_A            6 VRQRPWG--KFAAEIRDPAKNGARVWLGTFETAE-DAALAYDRAAFR   49 (63)
T ss_dssp             EEEETTT--EEEEEEEETTTTSEEEEEEEESSHH-HHHHHHHHHHHH
T ss_pred             EeeCCCC--cEEEEEccccCCCeEEEeeeCCCHH-HHHHHHHHHHHH
Confidence            4433455  99999975    2588999999998 899999976654

---

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	440
d1wida_	117	b.142.1.2 (A:) DNA-binding protein RAV1 {Thale cre	3e-41
d1na6a1	175	b.142.1.1 (A:4-178) Restriction endonuclease EcoRI	1e-32
d1yela1	102	b.142.1.2 (A:1-102) At1g16640 {Thale cress (Arabid	3e-21

>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 =  140 bits (354), Expect = 3e-41
 Identities = 77/112 (68%), Positives = 88/112 (78%), Gaps = 3/112 (2%)

Query: 131 EKEHMFDKVVTPSDVGKLNRLVIPKQHAEKYFP-LDSSSNEKGLLLNFEDRNGKPWRFRY 189
             E +F+K VTPSDVGKLNRLVIPK HAEK+FP   S+ + KG+LLNFED NGK WRFRY
Sbjct: 2   SAEALFEKAVTPSDVGKLNRLVIPKHHAEKHFPLPSSNVSVKGVLLNFEDVNGKVWRFRY 61

Query: 190 SYWNSSQSYVMTKGWSRFVKDKKLDAGDVVSFHRGVGDLAKGRLFIDWRRRS 241
           SYWNSSQSYV+TKGWSRFVK+K L AGDVVSF R  G     +L+I W+ RS
Sbjct: 62  SYWNSSQSYVLTKGWSRFVKEKNLRAGDVVSFSRSNGQ--DQQLYIGWKSRS 111

>d1na6a1 b.142.1.1 (A:4-178) Restriction endonuclease EcoRII, N-terminal domain {Escherichia coli [TaxId: 562]} Length = 175

class: All beta proteins
fold: DNA-binding pseudobarrel domain
superfamily: DNA-binding pseudobarrel domain
family: Type II restriction endonuclease effector domain
domain: Restriction endonuclease EcoRII, N-terminal domain
species: Escherichia coli [TaxId: 562]

 Score =  119 bits (299), Expect = 1e-32
 Identities = 18/124 (14%), Positives = 38/124 (30%), Gaps = 14/124 (11%)

Query: 131 EKEHMFDKVVTPSDVGKLNR----LVIPKQHAEKYFP-LDSSSNEK---GLLLNFEDRNG 182
           E   ++ K ++ +D G        L IP    EK FP ++ +        L  +    + 
Sbjct: 13  ENYFVYIKRLSANDTGATGGHQVGLYIPSGIVEKLFPSINHTRELNPSVFLTAHVSSHDC 72

Query: 183 KPWRFRYSYWNSS------QSYVMTKGWSRFVKDKKLDAGDVVSFHRGVGDLAKGRLFID 236
                R  Y+NS+          +T+           + G +      + +       ++
Sbjct: 73  PDSEARAIYYNSAHFGKTRNEKRITRWGRGSPLQDPENTGALTLLAFKLDEQGGDCKEVN 132

Query: 237 WRRR 240
               
Sbjct: 133 IWVC 136

>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 = 86.1 bits (213), Expect = 3e-21
 Identities = 22/92 (23%), Positives = 32/92 (34%), Gaps = 10/92 (10%)

Query: 132 KEHMFDKVVTPSDVGKLNRLVIPKQHAEKYFPLDSSSNEKGLLLNFEDRNGKPWRFRYSY 191
            E  F K        K   L IP    E +      +      ++  D +G+ W  R   
Sbjct: 5   GEVQFMKPFISEKSSK--SLEIPLGFNEYFPAPFPIT------VDLLDYSGRSWTVRM-- 54

Query: 192 WNSSQSYVMTKGWSRFVKDKKLDAGDVVSFHR 223
               +   +T GW  FVKD  L+ G  + F  
Sbjct: 55  KKRGEKVFLTVGWENFVKDNNLEDGKYLQFIY 86

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	440
d1wida_	117	DNA-binding protein RAV1 {Thale cress (Arabidopsis	99.96
d1na6a1	175	Restriction endonuclease EcoRII, N-terminal domain	99.78
d1yela1	102	At1g16640 {Thale cress (Arabidopsis thaliana) [Tax	99.59
d1gcca_	63	GCC-box binding domain {Mouse-ear cress (Arabidops	95.88

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

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

Probab=99.96  E-value=3e-29  Score=209.77  Aligned_cols=112  Identities=68%  Similarity=1.113  Sum_probs=102.3

Q ss_pred             ccceeEEEecccCCCCCCCcEEeehhchhhhCC-CCCCCCCCCeEEEEEeCCCCeEEEEEEEeCCCcceEEecChhhhhh
Q 013565          131 EKEHMFDKVVTPSDVGKLNRLVIPKQHAEKYFP-LDSSSNEKGLLLNFEDRNGKPWRFRYSYWNSSQSYVMTKGWSRFVK  209 (440)
Q Consensus       131 eke~lF~KvLT~SDV~k~gRLvIPKr~AEk~FP-Ld~s~~~~g~~L~veD~~GK~W~FRysywn~SrrYVLTkGWs~FVK  209 (440)
                      ..+++|+|+||+|||++.+||+||++++++||| ++...+.+++.|.+.|.+|++|+|+|++|+++++|+|++||..||+
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            467899999999999998999999999999998 5555667899999999999999999999988899999999999999


Q ss_pred             ccCCCCCCEEEEEeccccCCCCeEEEEEEeCCCCC
Q 013565          210 DKKLDAGDVVSFHRGVGDLAKGRLFIDWRRRSHPP  244 (440)
Q Consensus       210 dKkLkaGDvVvF~R~~~e~~~grLfIgIRRa~~~~  244 (440)
                      +|+|++||+|+|+|+.  ..+++|+|++||+....
T Consensus        82 ~~~Lk~GD~~~F~~~~--~~~~~~~i~~r~~~~~~  114 (117)
T d1wida_          82 EKNLRAGDVVSFSRSN--GQDQQLYIGWKSRSGSD  114 (117)
T ss_dssp             HTTCCTTCEEEEEECC--SSSCCEEEEEECCCSCS
T ss_pred             HcCCCCCCEEEEEEEe--CCCCEEEEEEEECCCCC
Confidence            9999999999999973  56789999999998754

>d1na6a1 b.142.1.1 (A:4-178) Restriction endonuclease EcoRII, N-terminal domain {Escherichia coli [TaxId: 562]}

class: All beta proteins
fold: DNA-binding pseudobarrel domain
superfamily: DNA-binding pseudobarrel domain
family: Type II restriction endonuclease effector domain
domain: Restriction endonuclease EcoRII, N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=99.78  E-value=8.8e-20  Score=165.20  Aligned_cols=115  Identities=16%  Similarity=0.182  Sum_probs=96.3

Q ss_pred             cccceeEEEecccCCCCCCCc----EEeehhchhhhCC-CCCCC-CCCCeEEE--EEeCCCCeEEEEEEEeCCC------
Q 013565          130 LEKEHMFDKVVTPSDVGKLNR----LVIPKQHAEKYFP-LDSSS-NEKGLLLN--FEDRNGKPWRFRYSYWNSS------  195 (440)
Q Consensus       130 ~eke~lF~KvLT~SDV~k~gR----LvIPKr~AEk~FP-Ld~s~-~~~g~~L~--veD~~GK~W~FRysywn~S------  195 (440)
                      .+..++|+|+||+|||+++|+    |+|||++||++|| ++..+ .++.+.|.  ++|.+|+.|+|||+|||++      
T Consensus        12 ~~~~~~F~K~LtasD~g~tg~HQaG~~IPK~~ae~~FP~l~~~~e~nP~~~l~~~i~d~~g~~w~fR~iYyn~~~~ggTR   91 (175)
T d1na6a1          12 CENYFVYIKRLSANDTGATGGHQVGLYIPSGIVEKLFPSINHTRELNPSVFLTAHVSSHDCPDSEARAIYYNSAHFGKTR   91 (175)
T ss_dssp             HSSEEEEEEECCHHHHTCC---CCCCCCCHHHHHHHCGGGCCCSSSSCEEEEEEEESSSCCCCEEEEEEEECGGGTTSCC
T ss_pred             CCceEEEEEEcccccccccCCccceeeecHHHHHHhCCCCCcccccCCCceEEEEEecCCCCeeEEEEEEECCccCCCcc
Confidence            456799999999999999886    9999999999998 66544 34666665  5599999999999999874      


Q ss_pred             cceEEecChhhhhhccCCCCCCEEEEEeccccCCCCeEEEEEEeCCCCC
Q 013565          196 QSYVMTKGWSRFVKDKKLDAGDVVSFHRGVGDLAKGRLFIDWRRRSHPP  244 (440)
Q Consensus       196 rrYVLTkGWs~FVKdKkLkaGDvVvF~R~~~e~~~grLfIgIRRa~~~~  244 (440)
                      +.|+||++|+.|+..+.+.+||.++|.+...+......+|+|-.-.+..
T Consensus        92 neyRiT~~g~~~~~~~~~n~G~l~i~af~~~~~~~~~~~~~vwvc~~~~  140 (175)
T d1na6a1          92 NEKRITRWGRGSPLQDPENTGALTLLAFKLDEQGGDCKEVNIWVCASTD  140 (175)
T ss_dssp             CEEEEECCCTTSGGGCGGGTTCEEEEEEECCTTSCCCCEEEEEECCSHH
T ss_pred             ccEEEEeccccccccCccccccEEEEEeecCCCCCceeEEEEEEecCcc
Confidence            8899999999999999999999999999655667778888887776554

>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=99.59  E-value=2.5e-15  Score=123.56  Aligned_cols=95  Identities=23%  Similarity=0.389  Sum_probs=79.5

Q ss_pred             cceeEEEecccCCCCCCCcEEeehhchhhhCCCCCCCCCCCeEEEEEeCCCCeEEEEEEEeCCCcceEEecChhhhhhcc
Q 013565          132 KEHMFDKVVTPSDVGKLNRLVIPKQHAEKYFPLDSSSNEKGLLLNFEDRNGKPWRFRYSYWNSSQSYVMTKGWSRFVKDK  211 (440)
Q Consensus       132 ke~lF~KvLT~SDV~k~gRLvIPKr~AEk~FPLd~s~~~~g~~L~veD~~GK~W~FRysywn~SrrYVLTkGWs~FVKdK  211 (440)
                      ..+-|.|+|.++++..  +|.||+.+++.+.+..      ...+.++|.+|+.|++++...  .....|+.||.+||++|
T Consensus         5 ~~~~Ffkv~~~~~~~~--~L~IP~~F~~~~~~~~------~~~i~L~d~~G~~W~v~~~~~--~~~~~~~~GW~~Fv~~n   74 (102)
T d1yela1           5 GEVQFMKPFISEKSSK--SLEIPLGFNEYFPAPF------PITVDLLDYSGRSWTVRMKKR--GEKVFLTVGWENFVKDN   74 (102)
T ss_dssp             CCEEEEEECCHHHHTT--CEECCHHHHTTCCCCC------CSEEEEEETTSCEEEEEEEEE--TTEEEECTTHHHHHHHH
T ss_pred             CCCeEEEEEcCcccCC--CEECCHHHHHhCCCCC------CCEEEEEcCCCCEEEEEEEEe--CCeEEEccCHHHHHHHc
Confidence            4456889999999876  8999999999876533      357888999999999998764  45678899999999999


Q ss_pred             CCCCCCEEEEEeccccCCCCeEEEEEEeC
Q 013565          212 KLDAGDVVSFHRGVGDLAKGRLFIDWRRR  240 (440)
Q Consensus       212 kLkaGDvVvF~R~~~e~~~grLfIgIRRa  240 (440)
                      +|++||+|+|...    ++.++.|.|.+.
T Consensus        75 ~L~~GD~~vF~~~----~~~~f~V~If~~   99 (102)
T d1yela1          75 NLEDGKYLQFIYD----RDRTFYVIIYGH   99 (102)
T ss_dssp             TCCTTCEEEEEEC----SSSEEEEEEECS
T ss_pred             CCCcCCEEEEEEc----CCcEEEEEEeCC
Confidence            9999999999986    567788877754

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

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

Probab=95.88  E-value=0.00043  Score=52.32  Aligned_cols=45  Identities=16%  Similarity=0.046  Sum_probs=35.7

Q ss_pred             cccCccccceeeeccccccccccccccc----ccccceeeccCCccccccccccccccc
Q 013565           43 HHHHYTTQTQQLLPLTTHHQNYNKQQQP----QMGSWLLGKTTTTTTAAELEDVSNEEE   97 (440)
Q Consensus        43 ~~~~~~~~~~~~~p~~~~~~~~~~q~~~----h~~~w~~~~~~~~~~Aa~~~~v~~~~~   97 (440)
                      ||++       |-..++|  +|.++|..    ..+.|||+...++ +||+|||+++...
T Consensus         2 ~yrG-------Vr~r~~g--kw~A~Ir~~~~~~~r~~LGtf~t~e-eAArAYD~aa~~~   50 (63)
T d1gcca_           2 HYRG-------VRQRPWG--KFAAEIRDPAKNGARVWLGTFETAE-DAALAYDRAAFRM   50 (63)
T ss_dssp             CCTT-------EEEETTT--EEEEEEEETTTTSEEEEEEEESSHH-HHHHHHHHHHHHH
T ss_pred             Ccce-------EeECCCC--CEEEEEecCCCCCcEeccccccCHH-HHHHHHHHHHHHh
Confidence            6778       6666666  99999962    3567999999998 8999999776654