Citrus Sinensis ID: 040084

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------
Protein Sequence
PISPSSPEIPPRFVKAVLPSTLRDQKPRIPNKIVRKFSHELSDVAHITIPNGYVWQVKLKKEGRKVWFDDGWQDFVEAYSTFVGSLVLFEYESNSTFQAHIYDETACEINYPSSNEESHTNGEESHH
Secondary Structure (PSIPRED)
ccccccccccccEEEEccccccccccccccHHHHHHccccccccEEEEcccccEEEEEEEEEccEEEEcccHHHHHHHcccccccEEEEEEccccEEEEEEEcccccEEEccccccccccccccccc
Secondary Structure Prediction (SSPRO)
ccccccccccccEEEEEccccccccccEccHHHHHHHccccccEEEEEcccccEEEEEEEEcccEEEEcccHHHHHHHcccccccEEEEEEcccEEEEEEEEcccccEEEccccccccccccccccc
Coil and Loop (DISEMBL)
pispsspeipprfvkavlpstlrdqkpripnkIVRKFSHELSDVAHITIPNGYVWQVKLKKegrkvwfddGWQDFVEAYSTFVGSLVLFeyesnstfqahiydetaceinypssneeshtngeeshh
Flexible Loop (DISEMBL)
pispsspeipprfvkavlpstlrdqkpripNKIVRKFSHELSDVAHITIPNGYVWQVKLKKEGRKVWFDDGWQDFVEAYSTFVGSLVLFEYESNSTFQAHIYDETACEINYPSSneeshtngeeshh
Low Complexity Region (SEG)
pispsspeippRFVKAVLPSTLRDQKPRIPNKIVRKFSHELSDVAHITIPNGYVWQVKLKKEGRKVWFDDGWQDFVEAYSTFVGSLVLFEYESNSTFQAHIYDETACEINYPSSNEESHTNGEESHH
Disordered region (IsUnstruct)
******************************NKIVRKFSHELSDVAHITIPNGYVWQVKLKKEGRKVWFDDGWQDFVEAYSTFVGSLVLFEYESNSTFQAHIYDETACEINY****************
Disordered Region (DISOPRED)
************FVKAVLPSTLRDQKPRIPNKIVRKFSHELSDVAHITIPNGYVWQVKLKKEGRKVWFDDGWQDFVEAYSTFVGSLVLFEYESNSTFQAHIYDETACEI******************
Disordered Region (DISEMBL)
PISPSSPEIPPRFVKAVLPSTLRDQKPRIPNKIVRKFSHELSDVAHITIPNGYVWQVKLKKEGRKVWFDDGWQDFVEAYSTFVGSLVLFEYESNSTFQAHIYDETACEINYP***************
Disordered Region (DISPRO)
********IPPRFVKAVLPSTLRDQKPRIPNKIVRKFSHELSDVAHITIPNGYVWQVKLKKEGRKVWFDDGWQDFVEAYSTFVGSLVLFEYESNSTFQAHIYDETACEINYPSS*************
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
PISPSSPEIPPRFVKAVLPSTLRDQKPRIPNKIVRKFSHELSDVAHITIPNGYVWQVKLKKEGRKVWFDDGWQDFVEAYSTFVGSLVLFEYESNSTFQAHIYDETACEINYPSSNEESHTNGEESHH
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	127	2.2.26 [Sep-21-2011]
Q8L3W1	341	B3 domain-containing tran	yes	no	0.826	0.307	0.447	8e-24
Q9ZSH7	190	B3 domain-containing prot	no	no	0.866	0.578	0.441	2e-22
Q84R27	209	B3 domain-containing prot	no	no	0.866	0.526	0.414	1e-20
Q9XIB4	190	B3 domain-containing prot	no	no	0.866	0.578	0.345	7e-15
Q2QMT6	490	B3 domain-containing prot	yes	no	0.669	0.173	0.341	7e-10
Q67VL7	393	Putative B3 domain-contai	yes	no	0.803	0.259	0.314	2e-09
Q7XS75	427	Putative B3 domain-contai	yes	no	0.708	0.210	0.326	3e-08
Q7XS74	434	Putative B3 domain-contai	yes	no	0.905	0.264	0.25	7e-08
Q9SB80	352	B3 domain-containing prot	no	no	0.874	0.315	0.32	4e-07
Q851V5	1029	Putative B3 domain-contai	yes	no	0.700	0.086	0.277	6e-07

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

 Score =  108 bits (271), Expect = 8e-24,   Method: Compositional matrix adjust.
 Identities = 47/105 (44%), Positives = 72/105 (68%)

Query: 11  PRFVKAVLPSTLRDQKPRIPNKIVRKFSHELSDVAHITIPNGYVWQVKLKKEGRKVWFDD 70
           P F K +  ST+++++ R+P+K V KF  ELS    +T+P+G+VW+V L+K   K+WF D
Sbjct: 4   PFFHKLIFSSTIQEKRLRVPDKFVSKFKDELSVAVALTVPDGHVWRVGLRKADNKIWFQD 63

Query: 71  GWQDFVEAYSTFVGSLVLFEYESNSTFQAHIYDETACEINYPSSN 115
           GWQ+FV+ YS  +G L++F YE NS F  +I++ +  EINY S+ 
Sbjct: 64  GWQEFVDRYSIRIGYLLIFRYEGNSAFSVYIFNLSHSEINYHSTG 108

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

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

 Score =  103 bits (258), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 49/111 (44%), Positives = 72/111 (64%), Gaps = 1/111 (0%)

Query: 3   SPSSPEIP-PRFVKAVLPSTLRDQKPRIPNKIVRKFSHELSDVAHITIPNGYVWQVKLKK 61
           S   PE P  +F K VLPST++D+  RIP + V+    +LS+V  +  P GY   +KLK+
Sbjct: 19  SQQDPESPVKKFFKLVLPSTMKDKMMRIPPRFVKLQGSKLSEVVTLVTPAGYKRSIKLKR 78

Query: 62  EGRKVWFDDGWQDFVEAYSTFVGSLVLFEYESNSTFQAHIYDETACEINYP 112
            G ++WF +GW +F EA+S   G  +LFEY+ NS+F+  I++ +ACE NYP
Sbjct: 79  IGEEIWFHEGWSEFAEAHSIEEGHFLLFEYKKNSSFRVIIFNASACETNYP 129

Arabidopsis thaliana (taxid: 3702)

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

 Score = 98.2 bits (243), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 46/111 (41%), Positives = 71/111 (63%), Gaps = 1/111 (0%)

Query: 3   SPSSPEIP-PRFVKAVLPSTLRDQKPRIPNKIVRKFSHELSDVAHITIPNGYVWQVKLKK 61
           S   PE P  +F K VLPST++D+  +IP + V+    +LS+V  +  P G+   +KLK+
Sbjct: 19  SQQDPESPVKKFFKLVLPSTMKDKMMKIPPRFVKLQGSKLSEVVTLETPAGFKRSIKLKR 78

Query: 62  EGRKVWFDDGWQDFVEAYSTFVGSLVLFEYESNSTFQAHIYDETACEINYP 112
            G ++WF +GW +F EA+S   G  +LFEY+ NS+F+  I++ +ACE  YP
Sbjct: 79  IGEEIWFHEGWSEFAEAHSIEEGHFLLFEYKENSSFRVIIFNVSACETKYP 129

Arabidopsis thaliana (taxid: 3702)

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

 Score = 79.0 bits (193), Expect = 7e-15,   Method: Compositional matrix adjust.
 Identities = 39/113 (34%), Positives = 68/113 (60%), Gaps = 3/113 (2%)

Query: 12  RFVKAVLPSTLRDQKPRIPNKIVRKFSHELSDVAHITIPNGYVWQVKLKKEGRKVWFDDG 71
           +F+K +L S + ++  ++P + VR F  +L+D   +  P G+   +++K+ G +VWF+ G
Sbjct: 33  KFIKIILLSRIIEKMMKVPARFVR-FGPKLTDNVTLQTPVGFKRSIRIKRIGDEVWFEKG 91

Query: 72  WQDFVEAYSTFVGSLVLFEYESNSTFQAHIYDETACEINYPSSNEESHTNGEE 124
           W +F EA+S   G  + F YE +S F+  I+D +A EI YP   +++  N EE
Sbjct: 92  WSEFAEAHSLSDGHFLFFHYEGDSCFRVVIFDVSASEIEYPL--DDTDDNREE 142

Arabidopsis thaliana (taxid: 3702)

>sp|Q2QMT6|Y1208_ORYSJ B3 domain-containing protein LOC_Os12g40080 OS=Oryza sativa subsp. japonica GN=Os12g0591400 PE=3 SV=1

 Score = 62.8 bits (151), Expect = 7e-10,   Method: Compositional matrix adjust.
 Identities = 29/85 (34%), Positives = 43/85 (50%)

Query: 29  IPNKIVRKFSHELSDVAHITIPNGYVWQVKLKKEGRKVWFDDGWQDFVEAYSTFVGSLVL 88
           IP K  R F  ++S    +   NG  ++V++ KE   +    GW+ F  AY    G +++
Sbjct: 41  IPAKFARNFGGQMSGTVKLETRNGKTYEVQVAKELNNLVLRSGWERFASAYELEKGDILV 100

Query: 89  FEYESNSTFQAHIYDETACEINYPS 113
           F Y  NS F+  IYD +ACE   P 
Sbjct: 101 FIYSGNSHFKVWIYDPSACEKGLPC 125

Oryza sativa subsp. japonica (taxid: 39947)

>sp|Q67VL7|Y6325_ORYSJ Putative B3 domain-containing protein Os06g0632500 OS=Oryza sativa subsp. japonica GN=Os06g0632500 PE=3 SV=1

 Score = 61.2 bits (147), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 34/108 (31%), Positives = 54/108 (50%), Gaps = 6/108 (5%)

Query: 11  PRFVKAVLPSTLRDQKPRIPNKIVRKFSHELSDVAH----ITIPNGYVWQVKLKKEGRKV 66
           PRF+K +    L  +K +IP K V++   E     H    I  P G  W+V+L++E   V
Sbjct: 142 PRFIKLLQQEDL--EKMKIPEKFVQQHLTETYTNNHQNAIIVCPLGKFWRVELQREQPDV 199

Query: 67  WFDDGWQDFVEAYSTFVGSLVLFEYESNSTFQAHIYDETACEINYPSS 114
              DGW  F+ A+    G+++LF YE N  F   ++ +  C   Y ++
Sbjct: 200 LLRDGWAPFLAAHDLSEGNILLFRYEGNMVFTVEVFLQNGCLKEYKTA 247

Oryza sativa subsp. japonica (taxid: 39947)

>sp|Q7XS75|Y4469_ORYSJ Putative B3 domain-containing protein Os04g0346900 OS=Oryza sativa subsp. japonica GN=Os04g0346900 PE=3 SV=2

 Score = 57.4 bits (137), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 31/95 (32%), Positives = 51/95 (53%), Gaps = 5/95 (5%)

Query: 11  PRFVKAVLPSTLRDQKPRIPNKIVRKF---SHELSDVAHITIPNGYVWQVKLKKEGRKVW 67
           P+F+  +LP  +   K RIP+K VR +    +  S++A I  P G  W+V+L K+   V+
Sbjct: 141 PQFLTVLLPGIM--DKMRIPDKFVRDYITGENLNSNMAIILSPLGKSWRVELDKDQSGVF 198

Query: 68  FDDGWQDFVEAYSTFVGSLVLFEYESNSTFQAHIY 102
              GW  F+  +    G +V+F YE N  F+  ++
Sbjct: 199 LGGGWLQFLSFHGISRGDVVIFRYEGNLVFKISVF 233

Oryza sativa subsp. japonica (taxid: 39947)

>sp|Q7XS74|Y4474_ORYSJ Putative B3 domain-containing protein Os04g0347400 OS=Oryza sativa subsp. japonica GN=Os04g0347400 PE=3 SV=3

 Score = 55.8 bits (133), Expect = 7e-08,   Method: Composition-based stats.
 Identities = 30/120 (25%), Positives = 60/120 (50%), Gaps = 5/120 (4%)

Query: 11  PRFVKAVLPSTLRDQKPRIPNKIVRKF---SHELSDVAHITIPNGYVWQVKLKKEGRKVW 67
           P+F++ +LP  +  +K RIP K V+ +    H    +A I  P G  W+++L+K+   ++
Sbjct: 151 PQFLRVLLPGFM--EKMRIPAKFVQHYIAEEHLNIHMASILSPLGKFWRIELEKDELGMF 208

Query: 68  FDDGWQDFVEAYSTFVGSLVLFEYESNSTFQAHIYDETACEINYPSSNEESHTNGEESHH 127
           F  GW  F+  +    G +VL  +E N  F+  ++    C+ +  + ++ +      + H
Sbjct: 209 FKGGWLQFLSFHGISPGDVVLLRHEGNLVFKIKVFGINGCKKDLKTKDDITIQQSARNQH 268

Oryza sativa subsp. japonica (taxid: 39947)

>sp|Q9SB80|REM5_ARATH B3 domain-containing protein REM5 OS=Arabidopsis thaliana GN=REM5 PE=2 SV=1

 Score = 53.5 bits (127), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 40/125 (32%), Positives = 61/125 (48%), Gaps = 14/125 (11%)

Query: 11  PRFVKAVLPSTLRDQKPRIPNKIVRKF---SHELSDVAHITIPNGYVWQVKLKKEGRKVW 67
           P F + +LP        +IP K   K     HE + V   + P+   W+VK+  EG K+ 
Sbjct: 12  PHFFQPILPGF--KSHIKIPVKFFSKHIEGKHEGNTVYLRSYPSRRTWKVKM--EGHKL- 66

Query: 68  FDDGWQDFVEAYSTFVGSLVLFEYESNSTFQAHIYDETACEINYPSS-----NEESHTNG 122
             +GW++FVEA+   VG  V+F+++ +  F       + CE+ Y  S     NEES   G
Sbjct: 67  -TEGWKEFVEAHDLRVGDFVVFKHKGDMLFHVTAIGPSCCEVQYAPSRSHDRNEESDEIG 125

Query: 123 EESHH 127
           E S +
Sbjct: 126 ESSRN 130

Arabidopsis thaliana (taxid: 3702)

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

 Score = 52.8 bits (125), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 25/90 (27%), Positives = 45/90 (50%)

Query: 29  IPNKIVRKFSHELSDVAHITIPNGYVWQVKLKKEGRKVWFDDGWQDFVEAYSTFVGSLVL 88
           IP+K  R F   +S    +   +GY + V++ K+   +    GW+ FV A+   +G  ++
Sbjct: 467 IPDKFARHFKGVISKTIKLEPRSGYTFDVQVTKKLNILVLGSGWESFVNAHDLNMGDFLV 526

Query: 89  FEYESNSTFQAHIYDETACEINYPSSNEES 118
           F+Y  +   Q  I+D + CE +   S E +
Sbjct: 527 FKYNGDFLLQVLIFDPSGCEKSTSCSMENA 556

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	127
255556207	545	hypothetical protein RCOM_0939100 [Ricin	0.960	0.223	0.48	1e-24
255637330	437	unknown [Glycine max]	0.818	0.237	0.471	1e-23
356521114	437	PREDICTED: B3 domain-containing transcri	0.818	0.237	0.471	1e-23
224123406	407	predicted protein [Populus trichocarpa]	0.779	0.243	0.525	3e-23
357490715	274	B3 domain-containing transcription facto	0.921	0.427	0.466	1e-22
357455499	266	B3 domain-containing protein [Medicago t	0.858	0.409	0.468	1e-22
356575102	435	PREDICTED: B3 domain-containing transcri	0.818	0.239	0.461	1e-22
449471266	412	PREDICTED: B3 domain-containing transcri	0.818	0.252	0.5	3e-22
297834810	341	hypothetical protein ARALYDRAFT_479415 [	0.826	0.307	0.447	5e-22
30685150	341	B3 domain-containing transcription facto	0.826	0.307	0.447	5e-22

>gi|255556207|ref|XP_002519138.1| hypothetical protein RCOM_0939100 [Ricinus communis] gi|223541801|gb|EEF43349.1| hypothetical protein RCOM_0939100 [Ricinus communis]

 Score =  117 bits (294), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 60/125 (48%), Positives = 78/125 (62%), Gaps = 3/125 (2%)

Query: 4   PSSP-EIPPR-FVKAVLPSTLRDQKPRIPNKIVRKFSHELSDVAHITIPNGYVWQVKLKK 61
           P SP E P R F K +LPS L D K RIP K VR F +ELSDVA+   PN  +W+V L+K
Sbjct: 18  PHSPAEKPLRHFFKIILPSNLNDMKLRIPTKFVRNFGNELSDVANFITPNCRLWKVGLRK 77

Query: 62  EGRKVWFDDGWQDFVEAYSTFVGSLVLFEYESNSTFQAHIYDETACEINYPSSNEESHTN 121
               +WFDDGW DFV+ +S  +G L++F Y   S F   I+D +ACEI YP  N++   +
Sbjct: 78  VHNDIWFDDGWHDFVKHHSICIGYLLVFGYRGFSDFSVFIFDVSACEIEYP-CNDQGLVH 136

Query: 122 GEESH 126
           GE+  
Sbjct: 137 GEKCR 141

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  114 bits (285), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 49/104 (47%), Positives = 73/104 (70%)

Query: 11  PRFVKAVLPSTLRDQKPRIPNKIVRKFSHELSDVAHITIPNGYVWQVKLKKEGRKVWFDD 70
           P F K VLP+TL+ ++ RIP+  +RK+  +LS +A +T+P+G VW + LKK   ++WF D
Sbjct: 4   PCFDKLVLPTTLQSRQLRIPDNFLRKYGTQLSTIATLTVPDGSVWPIGLKKADNRIWFVD 63

Query: 71  GWQDFVEAYSTFVGSLVLFEYESNSTFQAHIYDETACEINYPSS 114
           GWQDFV+ YS  VG  ++F YE NS+F  HI++ +  E+NY S+
Sbjct: 64  GWQDFVQRYSIGVGYFLVFMYEGNSSFIVHIFNLSTSEVNYQSA 107

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 =  114 bits (285), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 49/104 (47%), Positives = 73/104 (70%)

Query: 11  PRFVKAVLPSTLRDQKPRIPNKIVRKFSHELSDVAHITIPNGYVWQVKLKKEGRKVWFDD 70
           P F K VLP+TL+ ++ RIP+  +RK+  +LS +A +T+P+G VW + LKK   ++WF D
Sbjct: 4   PCFDKLVLPTTLQSRQLRIPDNFLRKYGTQLSTIATLTVPDGSVWPIGLKKADNRIWFVD 63

Query: 71  GWQDFVEAYSTFVGSLVLFEYESNSTFQAHIYDETACEINYPSS 114
           GWQDFV+ YS  VG  ++F YE NS+F  HI++ +  E+NY S+
Sbjct: 64  GWQDFVQRYSIGVGYFLVFMYEGNSSFIVHIFNLSTSEVNYQSA 107

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  113 bits (282), Expect = 3e-23,   Method: Compositional matrix adjust.
 Identities = 52/99 (52%), Positives = 65/99 (65%)

Query: 13  FVKAVLPSTLRDQKPRIPNKIVRKFSHELSDVAHITIPNGYVWQVKLKKEGRKVWFDDGW 72
           F K +  STL+D+K RIPNK  RKF  ELSDVA + +PNG+ WQ+ L K    V FDDGW
Sbjct: 23  FFKIITQSTLKDKKLRIPNKFARKFGEELSDVAKVVLPNGHSWQIGLTKSNNSVSFDDGW 82

Query: 73  QDFVEAYSTFVGSLVLFEYESNSTFQAHIYDETACEINY 111
             F+E +S   G L++F Y   S F A I+D+TACEI Y
Sbjct: 83  LQFLEQHSVGYGHLLVFGYRGCSNFNALIFDKTACEIPY 121

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357490715|ref|XP_003615645.1| B3 domain-containing transcription factor VRN1 [Medicago truncatula] gi|355516980|gb|AES98603.1| B3 domain-containing transcription factor VRN1 [Medicago truncatula]

 Score =  111 bits (277), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 56/120 (46%), Positives = 82/120 (68%), Gaps = 3/120 (2%)

Query: 5   SSPEIPPR-FVKAVLPSTLRDQKPRIPNKIVRKFSHELSDVAHITIPNGYVWQVKLKKEG 63
           SSPE   + F+KA+LPS +  ++ RIP++ + +F +EL++VA IT+P+G VW+++LKK G
Sbjct: 12  SSPEKESKHFMKAILPSPIHSKQIRIPDEFITRFGNELNNVATITVPDGRVWKMELKKRG 71

Query: 64  RKVWFDDGWQDFVEAYSTFVGSLVLFEYESNSTFQAHIYDETACEINYPSSNEESHTNGE 123
             V+F + WQ+FVE YS   G  + F+YE NS F   I+D T+ EI+YP   E   TNGE
Sbjct: 72  ENVFFCNKWQEFVEYYSIGYGCFISFKYEGNSKFSVIIFDATSVEISYPF--ETPSTNGE 129

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357455499|ref|XP_003598030.1| B3 domain-containing protein [Medicago truncatula] gi|357455503|ref|XP_003598032.1| B3 domain-containing protein [Medicago truncatula] gi|355487078|gb|AES68281.1| B3 domain-containing protein [Medicago truncatula] gi|355487080|gb|AES68283.1| B3 domain-containing protein [Medicago truncatula]

 Score =  111 bits (277), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 52/111 (46%), Positives = 74/111 (66%), Gaps = 2/111 (1%)

Query: 13  FVKAVLPSTLRDQKPRIPNKIVRKFSHELSDVAHITIPNGYVWQVKLKKEGRKVWFDDGW 72
           F+KA+LPS + D K RIP++ +++F +EL +VA IT+P+G  W++KLKK G  V+F + W
Sbjct: 21  FMKAILPSAIHDTKLRIPDEFIKRFGNELKNVATITVPDGCDWEMKLKKCGNDVYFCNKW 80

Query: 73  QDFVEAYSTFVGSLVLFEYESNSTFQAHIYDETACEINYPSSNEESHTNGE 123
           Q F E YS   GS + F+YE +S F   I+D T+ EI YP   +   TNGE
Sbjct: 81  QQFAEYYSIGYGSFLCFKYEGDSKFSVFIFDATSIEICYPFKTQS--TNGE 129

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  110 bits (276), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 48/104 (46%), Positives = 73/104 (70%)

Query: 11  PRFVKAVLPSTLRDQKPRIPNKIVRKFSHELSDVAHITIPNGYVWQVKLKKEGRKVWFDD 70
           P F K VLP+TL+ ++ RIP+  +RK+  +LS +A +T+P+G VW++ LKK   ++ F D
Sbjct: 4   PCFHKLVLPTTLQSRQLRIPDNFLRKYGTQLSTIATLTVPDGSVWRIGLKKADNRILFVD 63

Query: 71  GWQDFVEAYSTFVGSLVLFEYESNSTFQAHIYDETACEINYPSS 114
           GWQDFV+ YS  VG  ++F YE NS+F  HI++ +  E+NY S+
Sbjct: 64  GWQDFVQHYSIGVGYFLVFMYEGNSSFIVHIFNLSTSEVNYQSA 107

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

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 =  110 bits (274), Expect = 3e-22,   Method: Compositional matrix adjust.
 Identities = 52/104 (50%), Positives = 69/104 (66%)

Query: 11  PRFVKAVLPSTLRDQKPRIPNKIVRKFSHELSDVAHITIPNGYVWQVKLKKEGRKVWFDD 70
           P F K VL ST++ +K RIP   VR    ELS VA +T+P+G+VW+V L+K   K WF+D
Sbjct: 19  PHFHKLVLTSTIQARKLRIPETFVRMIRDELSAVATLTVPDGHVWRVGLRKADNKFWFED 78

Query: 71  GWQDFVEAYSTFVGSLVLFEYESNSTFQAHIYDETACEINYPSS 114
           GWQ F+E YS  VG L++F YE NS+F   I++    EINY S+
Sbjct: 79  GWQGFLEHYSIRVGYLLVFRYEGNSSFCVFIFNLNTSEINYQSA 122

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 =  109 bits (272), Expect = 5e-22,   Method: Compositional matrix adjust.
 Identities = 47/105 (44%), Positives = 72/105 (68%)

Query: 11  PRFVKAVLPSTLRDQKPRIPNKIVRKFSHELSDVAHITIPNGYVWQVKLKKEGRKVWFDD 70
           P F K +  ST+++++ R+P+K V KF  ELS    +T+P+G+VW+V L+K   K+WF D
Sbjct: 4   PFFHKLIFSSTIQEKRLRVPDKFVSKFKDELSVAVALTVPDGHVWRVGLRKADNKIWFQD 63

Query: 71  GWQDFVEAYSTFVGSLVLFEYESNSTFQAHIYDETACEINYPSSN 115
           GWQ+FV+ YS  +G L++F YE NS F  +I++ +  EINY S+ 
Sbjct: 64  GWQEFVDRYSIRIGYLLIFRYEGNSAFSVYIFNLSHSEINYHSTG 108

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 =  108 bits (271), Expect = 5e-22,   Method: Compositional matrix adjust.
 Identities = 47/105 (44%), Positives = 72/105 (68%)

Query: 11  PRFVKAVLPSTLRDQKPRIPNKIVRKFSHELSDVAHITIPNGYVWQVKLKKEGRKVWFDD 70
           P F K +  ST+++++ R+P+K V KF  ELS    +T+P+G+VW+V L+K   K+WF D
Sbjct: 4   PFFHKLIFSSTIQEKRLRVPDKFVSKFKDELSVAVALTVPDGHVWRVGLRKADNKIWFQD 63

Query: 71  GWQDFVEAYSTFVGSLVLFEYESNSTFQAHIYDETACEINYPSSN 115
           GWQ+FV+ YS  +G L++F YE NS F  +I++ +  EINY S+ 
Sbjct: 64  GWQEFVDRYSIRIGYLLIFRYEGNSAFSVYIFNLSHSEINYHSTG 108

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	127
TAIR|locus:2085849	341	VRN1 "REDUCED VERNALIZATION RE	0.858	0.319	0.423	1.8e-23
TAIR|locus:2133362	190	AT4G01580 [Arabidopsis thalian	0.795	0.531	0.445	1.1e-21
TAIR|locus:2085859	209	AT3G18960 [Arabidopsis thalian	0.795	0.483	0.415	4.4e-20
TAIR|locus:504956318	190	AT1G49475 [Arabidopsis thalian	0.866	0.578	0.345	7.7e-16
TAIR|locus:2124879	352	AT4G31640 [Arabidopsis thalian	0.858	0.309	0.333	1.1e-08
TAIR|locus:2124839	461	AT4G31690 [Arabidopsis thalian	0.637	0.175	0.356	1.1e-08
TAIR|locus:2124824	462	AT4G31680 [Arabidopsis thalian	0.826	0.227	0.318	1.1e-07
TAIR|locus:2017953	134	AT1G16640 [Arabidopsis thalian	0.582	0.552	0.333	1e-06
TAIR|locus:2124794	251	AT4G31660 [Arabidopsis thalian	0.496	0.250	0.347	3.8e-06
TAIR|locus:2126016	528	MEE45 "maternal effect embryo	0.519	0.125	0.3	2.4e-05

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

 Score = 270 (100.1 bits), Expect = 1.8e-23, P = 1.8e-23
 Identities = 47/111 (42%), Positives = 75/111 (67%)

Query:    13 FVKAVLPSTLRDQKPRIPNKIVRKFSHELSDVAHITIPNGYVWQVKLKKEGRKVWFDDGW 72
             F K +  ST+++++ R+P+K V KF  ELS    +T+P+G+VW+V L+K   K+WF DGW
Sbjct:     6 FHKLIFSSTIQEKRLRVPDKFVSKFKDELSVAVALTVPDGHVWRVGLRKADNKIWFQDGW 65

Query:    73 QDFVEAYSTFVGSLVLFEYESNSTFQAHIYDETACEINYPSSN--EESHTN 121
             Q+FV+ YS  +G L++F YE NS F  +I++ +  EINY S+   + +H +
Sbjct:    66 QEFVDRYSIRIGYLLIFRYEGNSAFSVYIFNLSHSEINYHSTGLMDSAHNH 116

GO:0005634 "nucleus" evidence=ISM

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

GO:0003677 "DNA binding" evidence=IDA

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

GO:0005654 "nucleoplasm" evidence=IDA

GO:0010048 "vernalization response" evidence=IMP

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

 Score = 253 (94.1 bits), Expect = 1.1e-21, P = 1.1e-21
 Identities = 45/101 (44%), Positives = 68/101 (67%)

Query:    12 RFVKAVLPSTLRDQKPRIPNKIVRKFSHELSDVAHITIPNGYVWQVKLKKEGRKVWFDDG 71
             +F K VLPST++D+  RIP + V+    +LS+V  +  P GY   +KLK+ G ++WF +G
Sbjct:    29 KFFKLVLPSTMKDKMMRIPPRFVKLQGSKLSEVVTLVTPAGYKRSIKLKRIGEEIWFHEG 88

Query:    72 WQDFVEAYSTFVGSLVLFEYESNSTFQAHIYDETACEINYP 112
             W +F EA+S   G  +LFEY+ NS+F+  I++ +ACE NYP
Sbjct:    89 WSEFAEAHSIEEGHFLLFEYKKNSSFRVIIFNASACETNYP 129

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 = 238 (88.8 bits), Expect = 4.4e-20, P = 4.4e-20
 Identities = 42/101 (41%), Positives = 67/101 (66%)

Query:    12 RFVKAVLPSTLRDQKPRIPNKIVRKFSHELSDVAHITIPNGYVWQVKLKKEGRKVWFDDG 71
             +F K VLPST++D+  +IP + V+    +LS+V  +  P G+   +KLK+ G ++WF +G
Sbjct:    29 KFFKLVLPSTMKDKMMKIPPRFVKLQGSKLSEVVTLETPAGFKRSIKLKRIGEEIWFHEG 88

Query:    72 WQDFVEAYSTFVGSLVLFEYESNSTFQAHIYDETACEINYP 112
             W +F EA+S   G  +LFEY+ NS+F+  I++ +ACE  YP
Sbjct:    89 WSEFAEAHSIEEGHFLLFEYKENSSFRVIIFNVSACETKYP 129

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 = 198 (74.8 bits), Expect = 7.7e-16, P = 7.7e-16
 Identities = 39/113 (34%), Positives = 68/113 (60%)

Query:    12 RFVKAVLPSTLRDQKPRIPNKIVRKFSHELSDVAHITIPNGYVWQVKLKKEGRKVWFDDG 71
             +F+K +L S + ++  ++P + VR F  +L+D   +  P G+   +++K+ G +VWF+ G
Sbjct:    33 KFIKIILLSRIIEKMMKVPARFVR-FGPKLTDNVTLQTPVGFKRSIRIKRIGDEVWFEKG 91

Query:    72 WQDFVEAYSTFVGSLVLFEYESNSTFQAHIYDETACEINYPSSNEESHTNGEE 124
             W +F EA+S   G  + F YE +S F+  I+D +A EI YP   +++  N EE
Sbjct:    92 WSEFAEAHSLSDGHFLFFHYEGDSCFRVVIFDVSASEIEYPL--DDTDDNREE 142

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:2124879 AT4G31640 [Arabidopsis thaliana (taxid:3702)]

 Score = 137 (53.3 bits), Expect = 1.1e-08, P = 1.1e-08
 Identities = 41/123 (33%), Positives = 61/123 (49%)

Query:    13 FVKAVLPSTLRDQKPRIPNKIVRKF---SHELSDVAHITIPNGYVWQVKLKKEGRKVWFD 69
             F + +LP      K  IP K   K     HE + V   + P+   W+VK+  EG K+   
Sbjct:    14 FFQPILPGFKSHIK--IPVKFFSKHIEGKHEGNTVYLRSYPSRRTWKVKM--EGHKL--T 67

Query:    70 DGWQDFVEAYSTFVGSLVLFEYESNSTFQAHIYDETACEINY-PSS----NEESHTNGEE 124
             +GW++FVEA+   VG  V+F+++ +  F       + CE+ Y PS     NEES   GE 
Sbjct:    68 EGWKEFVEAHDLRVGDFVVFKHKGDMLFHVTAIGPSCCEVQYAPSRSHDRNEESDEIGES 127

Query:   125 SHH 127
             S +
Sbjct:   128 SRN 130

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:2124839 AT4G31690 [Arabidopsis thaliana (taxid:3702)]

 Score = 139 (54.0 bits), Expect = 1.1e-08, P = 1.1e-08
 Identities = 31/87 (35%), Positives = 46/87 (52%)

Query:    39 HELSDVAHITIPNGYVWQVKLKKEGRKVWFDDGWQDFVEAYSTFVGSLVLFEYESNSTFQ 98
             HE   V   T  +   W+VK+  EG ++   +GW++FVEA+   +G  V+F +E +  F 
Sbjct:    41 HEGKTVTLRTDASERTWEVKM--EGHRL--TEGWKEFVEAHDLRIGDFVVFRHEGDMVFH 96

Query:    99 AHIYDETACEINYPSSNEESHTNGEES 125
                   + CEI YP S+   H  GEES
Sbjct:    97 VTALGPSCCEIQYPQSSR--HEEGEES 121

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:0009941 "chloroplast envelope" evidence=IDA

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

 Score = 130 (50.8 bits), Expect = 1.1e-07, P = 1.1e-07
 Identities = 37/116 (31%), Positives = 55/116 (47%)

Query:    13 FVKAVLPSTLRDQKPRIPNKIVRKF---SHELSDVAHITIPNGYVWQVKLKKEGRKVWFD 69
             F K +LP   R+    IP K   +     HE   V      +   W+VK+  +G ++   
Sbjct:    14 FFKPLLPGFQRNLN--IPVKFFSEHIEGKHEGETVKLRADASKRTWEVKM--DGNRL--T 67

Query:    70 DGWQDFVEAYSTFVGSLVLFEYESNSTFQAHIYDETACEINYPSSNEESHTNGEES 125
             +GW++FVEA+   +   V+F +E +  F       + CEI YP S   SH  GEES
Sbjct:    68 EGWKEFVEAHDLRIRDFVVFRHEGDMVFHVTALGPSCCEIQYPQSI--SHEEGEES 121

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:2017953 AT1G16640 [Arabidopsis thaliana (taxid:3702)]

 Score = 112 (44.5 bits), Expect = 1.0e-06, P = 1.0e-06
 Identities = 26/78 (33%), Positives = 40/78 (51%)

Query:    51 NGYVWQVKLKKEGRKVWFDDGWQDFVEAYSTFVGSLVLFEYESNSTFQAHIYDETACEI- 109
             +G  W V++KK G KV+   GW++FV+  +   G  + F Y+ + TF   IY    C   
Sbjct:    46 SGRSWTVRMKKRGEKVFLTVGWENFVKDNNLEDGKYLQFIYDRDRTFYVIIYGHNMCSEY 105

Query:   110 -NYPSSNEE--SHTNGEE 124
              ++P    E   + NGEE
Sbjct:   106 RDFPQVAVEVDDYENGEE 123

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:2124794 AT4G31660 [Arabidopsis thaliana (taxid:3702)]

 Score = 111 (44.1 bits), Expect = 3.8e-06, P = 3.8e-06
 Identities = 24/69 (34%), Positives = 41/69 (59%)

Query:    55 WQVKLKKEGRKVWFDDGWQDFVEAYSTFVGSLVLFEYESNSTFQAHIYDETACEINY-PS 113
             WQVK+  +GR++    GW++F  A+   VG +++F +E +  F       + CEI Y PS
Sbjct:    57 WQVKI--QGRRLTV--GWKEFASAHDFRVGDIIVFRHEGSLVFHVTALGPSCCEIQYVPS 112

Query:   114 -SNEESHTN 121
              +N+E+ +N
Sbjct:   113 CNNQENISN 121

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

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

GO:0005634 "nucleus" evidence=ISM

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

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

 Score = 109 (43.4 bits), Expect = 2.4e-05, P = 2.4e-05
 Identities = 21/70 (30%), Positives = 40/70 (57%)

Query:    55 WQVKLKKEGRKVWFDDGWQDFVEAYSTFVGSLVLFEYESNSTFQAHIYDETACEINYPSS 114
             W+VK+  +G+++   DGW++F  ++   +G +V+F  ES+  F   +   + C I Y S 
Sbjct:    49 WEVKI--DGQRL--TDGWKEFAVSHDLRIGDIVVFRQESDLAFHVTLLGPSCCGIQYGSC 104

Query:   115 NEESHTNGEE 124
             + E +  G+E
Sbjct:   105 SVEKNNLGDE 114

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

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

GO:0005634 "nucleus" evidence=ISM

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

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

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

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	127
smart01019	96	smart01019, B3, B3 DNA binding domain	1e-11
pfam02362	97	pfam02362, B3, B3 DNA binding domain	2e-11
cd10017	98	cd10017, B3_DNA, Plant-specific B3-DNA binding dom	2e-11

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

 Score = 56.2 bits (136), Expect = 1e-11
 Identities = 24/95 (25%), Positives = 38/95 (40%), Gaps = 4/95 (4%)

Query: 13  FVKAVLPS-TLRDQKPRIPNKIVRKFSHELSDV-AHITIPNGYVWQVKLKKEGRK--VWF 68
           F K +  S   +  +  +P +        L      +  P+G  W+VKLK  G       
Sbjct: 1   FFKTLTTSDVSKHGRLVLPKQFAESNGPPLKPKEITLLDPDGKSWKVKLKYRGSSGMFLL 60

Query: 69  DDGWQDFVEAYSTFVGSLVLFEYESNSTFQAHIYD 103
             GW++FV+A     G  + FE + N  F   I+ 
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 = 55.8 bits (135), Expect = 2e-11
 Identities = 28/96 (29%), Positives = 45/96 (46%), Gaps = 6/96 (6%)

Query: 13  FVKAVLPS-TLRDQKPRIPNKIVRKFSHELSDVAHITI--PNGYVWQVKLK--KEGRKVW 67
           FVK + PS   +D +  +P K   +          IT+  P+G  W VKL+  K GR+  
Sbjct: 1   FVKVLTPSDVSKDGRLVLPKKFAEENGLNKKGQE-ITLLDPDGKSWTVKLRYRKSGRRYL 59

Query: 68  FDDGWQDFVEAYSTFVGSLVLFEYESNSTFQAHIYD 103
              GW++FV+A     G  ++F+ +    F   I+ 
Sbjct: 60  LTSGWKEFVKANGLKAGDSLVFKLDGGGKFVVGIFR 95

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

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

 Score = 55.8 bits (135), Expect = 2e-11
 Identities = 27/98 (27%), Positives = 43/98 (43%), Gaps = 5/98 (5%)

Query: 11  PRFVKAVLPS-TLRDQKPRIPNKIVRKFS-HELSDVAHITIPNGYVWQVKLKKEG--RKV 66
           P F K + PS      +  +P K  +     +      +  P+G  W VKLKK     ++
Sbjct: 1   PLFFKVLTPSDVSSLGRLVLPKKFAKAHLPPKEGVEVTLEDPDGKKWTVKLKKRKNSGRM 60

Query: 67  WFDDGWQDFVEAYSTFVGSLVLFEYE-SNSTFQAHIYD 103
               GW++FV A     G  ++FE +  NS F+  I+ 
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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	127
PF02362	100	B3: B3 DNA binding domain; InterPro: IPR003340 Two	99.94
PF03754	114	DUF313: Domain of unknown function (DUF313) ; Inte	96.94
PF04014	47	Antitoxin-MazE: Antidote-toxin recognition MazE; I	87.84
PLN03148	167	Blue copper-like protein; Provisional	82.91

>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=99.94  E-value=3.9e-26  Score=150.96  Aligned_cols=93  Identities=30%  Similarity=0.592  Sum_probs=70.1

Q ss_pred             EEEeccCCccC-CCceeccHHHHHhcccC--CCceEEEEcCCCCEEEEEEE--EeCCEEEecccHHHHHhHhCCCCCCEE
Q 040084           13 FVKAVLPSTLR-DQKPRIPNKIVRKFSHE--LSDVAHITIPNGYVWQVKLK--KEGRKVWFDDGWQDFVEAYSTFVGSLV   87 (127)
Q Consensus        13 F~k~i~~~~~~-~~~L~IP~~F~~~~~~~--~~~~v~L~~~~G~~W~V~l~--~~~~~~~~~~GW~~Fv~~~~L~~GD~l   87 (127)
                      |+|+|++++.. .+.|.||..|++.|+..  .+..++|++++|+.|+|++.  +..++++|++||++||++|+|++||+|
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            89999887654 47899999999999754  57799999999999999995  456789999999999999999999999


Q ss_pred             EEEEecCcEE--EEEEECCC
Q 040084           88 LFEYESNSTF--QAHIYDET  105 (127)
Q Consensus        88 vF~~~~~~~F--~V~If~~~  105 (127)
                      +|++++++.|  .|+||+++
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            9999987665  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=96.94  E-value=0.0056  Score=41.78  Aligned_cols=67  Identities=18%  Similarity=0.346  Sum_probs=48.8

Q ss_pred             eEEEeccCCccC--CCceeccHHHHHh--c----------------ccCCCceEEEEcCCCCEEEEEEEEeCC-----EE
Q 040084           12 RFVKAVLPSTLR--DQKPRIPNKIVRK--F----------------SHELSDVAHITIPNGYVWQVKLKKEGR-----KV   66 (127)
Q Consensus        12 ~F~k~i~~~~~~--~~~L~IP~~F~~~--~----------------~~~~~~~v~L~~~~G~~W~V~l~~~~~-----~~   66 (127)
                      -+.|.|..+++.  ..+|.||..=+..  +                .....-.|+|.+|+++.|.+.+++-.-     .+
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            455678888775  3778888664411  1                123356899999999999999998532     67


Q ss_pred             EecccHHHHHhH
Q 040084           67 WFDDGWQDFVEA   78 (127)
Q Consensus        67 ~~~~GW~~Fv~~   78 (127)
                      .|..||.++|++
T Consensus       103 vL~~gWn~VV~~  114 (114)
T PF03754_consen  103 VLNSGWNKVVED  114 (114)
T ss_pred             EEEcChHhhccC
Confidence            899999999864

>PF04014 Antitoxin-MazE: Antidote-toxin recognition MazE; InterPro: IPR007159 This domain is found in AbrB from Bacillus subtilis

Probab=87.84  E-value=2.2  Score=24.00  Aligned_cols=30  Identities=17%  Similarity=0.126  Sum_probs=24.6

Q ss_pred             HHHHhHhCCCCCCEEEEEEecCcEEEEEEE
Q 040084           73 QDFVEAYSTFVGSLVLFEYESNSTFQAHIY  102 (127)
Q Consensus        73 ~~Fv~~~~L~~GD~lvF~~~~~~~F~V~If  102 (127)
                      ++++...+|+.||.+.+...++....+.-+
T Consensus        13 k~~~~~l~l~~Gd~v~i~~~~~g~i~i~p~   42 (47)
T PF04014_consen   13 KEIREKLGLKPGDEVEIEVEGDGKIVIRPV   42 (47)
T ss_dssp             HHHHHHTTSSTTTEEEEEEETTSEEEEEES
T ss_pred             HHHHHHcCCCCCCEEEEEEeCCCEEEEEEC
Confidence            578899999999999999999875555433

The product of the abrB gene is an ambiactive repressor and activator of the transcription of genes expressed during the transition state between vegetative growth and the onset of stationary phase and sporulation []. AbrB is thought to interact directly with the transcription initiation regions of genes under its control []. AbrB contains a helix-turn-helix structure, but this domain ends before the helix-turn-helix begins []. The product of the B. subtilis gene spoVT is another member of this family and is also a transcriptional regulator []. DNA-binding activity in this AbrB homologue requires hexamerisation []. Another family member has been isolated from the Sulfolobus solfataricus and has been identified as a homologue of bacterial repressor-like proteins. The Escherichia coli family member SohA or Prl1F appears to be bifunctional and is able to regulate its own expression as well as relieve the export block imposed by high-level synthesis of beta-galactosidase hybrid proteins [].; PDB: 2L66_A 2GLW_A 3TND_D 2W1T_B 2RO5_B 2FY9_A 2RO3_B 1UB4_C 3ZVK_G 1YFB_B ....

>PLN03148 Blue copper-like protein; Provisional

Probab=82.91  E-value=1.1  Score=32.57  Aligned_cols=38  Identities=18%  Similarity=0.437  Sum_probs=26.4

Q ss_pred             HhHhCCCCCCEEEEEEecC--cEEEEEEECCCCeEEecCC
Q 040084           76 VEAYSTFVGSLVLFEYESN--STFQAHIYDETACEINYPS  113 (127)
Q Consensus        76 v~~~~L~~GD~lvF~~~~~--~~F~V~If~~~~ce~~~~~  113 (127)
                      +..+....||.|+|.|..+  ++.+|.==+-+.|...-|.
T Consensus        41 A~~k~F~VGD~LvF~Y~~~~hnV~~V~~~~Y~~C~~~~pi   80 (167)
T PLN03148         41 ANNQTFYVGDLISFRYQKTQYNVFEVNQTGYDNCTTEGAA   80 (167)
T ss_pred             hcCCCCccCCEEEEEecCCCceEEEEChHHcCcccCCCCc
Confidence            5678889999999999875  5666643333567654443

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	127
1yel_A	104	Structure Of The Hypothetical Arabidopsis Thaliana		6e-05

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

Iteration: 1
 Score = 42.4 bits (98), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 20/57 (35%), Positives = 31/57 (54%)
Query: 51  NGYVWQVKLKKEGRKVWFDDGWQDFVEAYSTFVGSLVLFEYESNSTFQAHIYDETAC 107
           +G  W V++KK G KV+   GW++FV+  +   G  + F Y+ + TF   IY    C
Sbjct: 48  SGRSWTVRMKKRGEKVFLTVGWENFVKDNNLEDGKYLQFIYDRDRTFYVIIYGHNMC 104

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	127
1yel_A	104	AT1G16640; CESG, protein structure initiative, str	2e-29

>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 =  101 bits (253), Expect = 2e-29
 Identities = 25/97 (25%), Positives = 41/97 (42%), Gaps = 1/97 (1%)

Query: 11  PRFVKAVLPSTLRDQKPRIPNKIVRKFSHELSDVAHITIPNGYVWQVKLKKEGRKVWFDD 70
            +F+K  +      +   IP      F         +   +G  W V++KK G KV+   
Sbjct: 9   VQFMKPFISE-KSSKSLEIPLGFNEYFPAPFPITVDLLDYSGRSWTVRMKKRGEKVFLTV 67

Query: 71  GWQDFVEAYSTFVGSLVLFEYESNSTFQAHIYDETAC 107
           GW++FV+  +   G  + F Y+ + TF   IY    C
Sbjct: 68  GWENFVKDNNLEDGKYLQFIYDRDRTFYVIIYGHNMC 104

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	127
1yel_A	104	AT1G16640; CESG, protein structure initiative, str	100.0
4i1k_A	146	B3 domain-containing transcription factor VRN1; B3	99.95
1wid_A	130	DNA-binding protein RAV1; DNA-binding domain, stru	99.83
1yfb_A	59	Transition state regulatory protein ABRB; , homodi	82.66

>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=100.00  E-value=3.4e-34  Score=191.49  Aligned_cols=100  Identities=25%  Similarity=0.485  Sum_probs=95.1

Q ss_pred             CCCCCeEEEeccCCccCCCceeccHHHHHhcccCCCceEEEEcCCCCEEEEEEEEeCCEEEecccHHHHHhHhCCCCCCE
Q 040084            7 PEIPPRFVKAVLPSTLRDQKPRIPNKIVRKFSHELSDVAHITIPNGYVWQVKLKKEGRKVWFDDGWQDFVEAYSTFVGSL   86 (127)
Q Consensus         7 ~~~~p~F~k~i~~~~~~~~~L~IP~~F~~~~~~~~~~~v~L~~~~G~~W~V~l~~~~~~~~~~~GW~~Fv~~~~L~~GD~   86 (127)
                      .++.|+|+|+|++++ ....|.||..|+++|++..+++|+|++++|++|+|++.+..++++|++||++||.+|+|++||+
T Consensus         5 ~~~~p~F~K~l~~~~-~~~~L~IP~~F~~~~~~~~~~~v~L~~~~G~~W~v~~~~~~~~~~l~~GW~~Fv~~~~L~~GD~   83 (104)
T 1yel_A            5 DTGEVQFMKPFISEK-SSKSLEIPLGFNEYFPAPFPITVDLLDYSGRSWTVRMKKRGEKVFLTVGWENFVKDNNLEDGKY   83 (104)
T ss_dssp             CCCCEEEEEECCHHH-HTTCEECCHHHHTTCCCCCCSEEEEEETTSCEEEEEEEEETTEEEECTTHHHHHHHHTCCTTCE
T ss_pred             CCCCCCEEEEECCCC-ccceEECCHHHHHhcCccCCCEEEEECCCCCEEEEEEEEECCcEEEccChHHHHHHcCCCCCCE
Confidence            457899999999877 3599999999999999999999999999999999999998899999999999999999999999


Q ss_pred             EEEEEecCcEEEEEEECCCCe
Q 040084           87 VLFEYESNSTFQAHIYDETAC  107 (127)
Q Consensus        87 lvF~~~~~~~F~V~If~~~~c  107 (127)
                      |+|+|+++++|+|+||++++|
T Consensus        84 lvF~~~~~~~f~V~If~~s~C  104 (104)
T 1yel_A           84 LQFIYDRDRTFYVIIYGHNMC  104 (104)
T ss_dssp             EEEEECSSSEEEEEEECSSCC
T ss_pred             EEEEEcCCCeEEEEEECCCCC
Confidence            999999999999999999998

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

Probab=99.95  E-value=1.4e-26  Score=163.18  Aligned_cols=99  Identities=17%  Similarity=0.309  Sum_probs=90.9

Q ss_pred             CCCCCCeEEEeccCCccCC-CceeccHHHHHhcccCCCceEEEEcCCCCEEEEEEEEeCCEEEecccHHHHHhHhCCCCC
Q 040084            6 SPEIPPRFVKAVLPSTLRD-QKPRIPNKIVRKFSHELSDVAHITIPNGYVWQVKLKKEGRKVWFDDGWQDFVEAYSTFVG   84 (127)
Q Consensus         6 ~~~~~p~F~k~i~~~~~~~-~~L~IP~~F~~~~~~~~~~~v~L~~~~G~~W~V~l~~~~~~~~~~~GW~~Fv~~~~L~~G   84 (127)
                      +.+..|.|+++|+++++.. ..|.||..|++.|++.....|+|+++ |+.|+|++...+++..|++||++||.+|+|++|
T Consensus        42 ~~s~~P~Fvk~l~~S~v~~~~~L~IP~~Fa~~~lp~~~~~i~L~~~-gk~W~v~~~~~~~~~~ls~GW~~Fv~dn~L~~G  120 (146)
T 4i1k_A           42 FEPTNPFFRVVLRPSYLYRGCIMYLPSGFAEKYLSGISGFIKVQLA-EKQWPVRCLYKAGRAKFSQGWYEFTLENNLGEG  120 (146)
T ss_dssp             CCCSSCEEEEECCGGGSSTTCCEECCHHHHHHHCTTCCSEEEEEET-TEEEEEEEEEETTEEEECTTHHHHHHHTTCCTT
T ss_pred             cCCCCCEEEEEECchhcCCCcEEEeCHHHHHHhCCCCCeEEEEEEC-CcEEEEEEEEeCCcEEECCchHHHHHHcCCCCC
Confidence            5578899999999999854 47999999999999988899999998 599999999888899999999999999999999


Q ss_pred             CEEEEEEecCc--EEEEEEECCC
Q 040084           85 SLVLFEYESNS--TFQAHIYDET  105 (127)
Q Consensus        85 D~lvF~~~~~~--~F~V~If~~~  105 (127)
                      |+|+|+++++.  .|+|+||+.+
T Consensus       121 D~cvFeli~~~~~~f~V~IfR~~  143 (146)
T 4i1k_A          121 DVCVFELLRTRDFVLKVTAFRVN  143 (146)
T ss_dssp             CEEEEEECSSSSCEEEEEEECCC
T ss_pred             CEEEEEEecCCceEEEEEEEecc
Confidence            99999999954  8999999875

>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=99.83  E-value=7.4e-20  Score=126.43  Aligned_cols=100  Identities=21%  Similarity=0.275  Sum_probs=84.8

Q ss_pred             CCCCCCeEEEeccCCccC-CCceeccHHHHHhcccCCC-------ceEEEEcCCCCEEEEEEEEe--CCEEEecccHHHH
Q 040084            6 SPEIPPRFVKAVLPSTLR-DQKPRIPNKIVRKFSHELS-------DVAHITIPNGYVWQVKLKKE--GRKVWFDDGWQDF   75 (127)
Q Consensus         6 ~~~~~p~F~k~i~~~~~~-~~~L~IP~~F~~~~~~~~~-------~~v~L~~~~G~~W~V~l~~~--~~~~~~~~GW~~F   75 (127)
                      .....|.|.|+|+++++. ...|.||..|+++|++.+.       ..++|+|+.|+.|++++...  ..+++|+.||..|
T Consensus         7 ~~~~~~~F~K~Lt~SDv~~~~rL~iPk~~a~~~lP~~~~~~~~~~~~l~l~D~~Gk~W~fr~~~~~~~~~~~Lt~GW~~F   86 (130)
T 1wid_A            7 GRSAEALFEKAVTPSDVGKLNRLVIPKHHAEKHFPLPSSNVSVKGVLLNFEDVNGKVWRFRYSYWNSSQSYVLTKGWSRF   86 (130)
T ss_dssp             -CCCEEEEEEECCTTTTSSSCCEEECHHHHTTTSCCCSSCCSSCCEEEEEEETTTEEEEEEEEEETTTTEEEEESSHHHH
T ss_pred             CCCCcceEEEEEehHHcCCCCEEEeCHHHHHhhCCccccccCCCcEEEEEEeCCCCEEEEEEEEECCCCceEEcCChHHH
Confidence            344557999999999985 4789999999999887654       36889999999999999876  3578999999999


Q ss_pred             HhHhCCCCCCEEEEEEecC--cEEEEEEECCC
Q 040084           76 VEAYSTFVGSLVLFEYESN--STFQAHIYDET  105 (127)
Q Consensus        76 v~~~~L~~GD~lvF~~~~~--~~F~V~If~~~  105 (127)
                      |++|+|++||+|+|+++.+  ..+.|.+-++.
T Consensus        87 V~~~~L~~GD~~~F~~~~~~~~~l~I~~rr~~  118 (130)
T 1wid_A           87 VKEKNLRAGDVVSFSRSNGQDQQLYIGWKSRS  118 (130)
T ss_dssp             HHHTTCCTTCEEEEEECCSSSCCEEEEEECCC
T ss_pred             HHHcCCCCCCEEEEEEecCCCcEEEEEEEECC
Confidence            9999999999999999873  57888877665

>1yfb_A Transition state regulatory protein ABRB; , homodimer, bioinformatics, swapped-hairpin barrel, transcription; NMR {Bacillus subtilis} SCOP: b.129.1.3 PDB: 1ysf_A 2k1n_A* 1z0r_A 2ro4_A 2fy9_A 2ro3_A

Probab=82.66  E-value=3.8  Score=23.66  Aligned_cols=36  Identities=6%  Similarity=-0.010  Sum_probs=26.7

Q ss_pred             CCEEEecccHHHHHhHhCCCCCCEEEEEEecCcEEEEEEE
Q 040084           63 GRKVWFDDGWQDFVEAYSTFVGSLVLFEYESNSTFQAHIY  102 (127)
Q Consensus        63 ~~~~~~~~GW~~Fv~~~~L~~GD~lvF~~~~~~~F~V~If  102 (127)
                      .+++.|=   ++..+..+|++||.+.|..+++ ...+.-+
T Consensus        21 kGqItIP---keiR~~Lgi~~Gd~l~i~~~~~-~IiL~p~   56 (59)
T 1yfb_A           21 LGRVVIP---IELRRTLGIAEKDALEIYVDDE-KIILKKY   56 (59)
T ss_dssp             TCEEECC---HHHHHHTTCCTTCEEEEEEETT-EEEEEEC
T ss_pred             CCEEEeC---HHHHHHcCCCCCCEEEEEEECC-EEEEEEC
Confidence            3555555   5788999999999999999887 4444433

---

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	127
d1yela1	102	b.142.1.2 (A:1-102) At1g16640 {Thale cress (Arabid	2e-24

>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 = 87.6 bits (217), Expect = 2e-24
 Identities = 25/97 (25%), Positives = 40/97 (41%), Gaps = 1/97 (1%)

Query: 11  PRFVKAVLPSTLRDQKPRIPNKIVRKFSHELSDVAHITIPNGYVWQVKLKKEGRKVWFDD 70
            +F+K  +          IP      F         +   +G  W V++KK G KV+   
Sbjct: 7   VQFMKPFISEKSSKS-LEIPLGFNEYFPAPFPITVDLLDYSGRSWTVRMKKRGEKVFLTV 65

Query: 71  GWQDFVEAYSTFVGSLVLFEYESNSTFQAHIYDETAC 107
           GW++FV+  +   G  + F Y+ + TF   IY    C
Sbjct: 66  GWENFVKDNNLEDGKYLQFIYDRDRTFYVIIYGHNMC 102

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	127
d1yela1	102	At1g16640 {Thale cress (Arabidopsis thaliana) [Tax	100.0
d1wida_	117	DNA-binding protein RAV1 {Thale cress (Arabidopsis	99.83
d1na6a1	175	Restriction endonuclease EcoRII, N-terminal domain	98.12

>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=100.00  E-value=3.9e-34  Score=189.33  Aligned_cols=99  Identities=25%  Similarity=0.485  Sum_probs=94.5

Q ss_pred             CCCCeEEEeccCCccCCCceeccHHHHHhcccCCCceEEEEcCCCCEEEEEEEEeCCEEEecccHHHHHhHhCCCCCCEE
Q 040084            8 EIPPRFVKAVLPSTLRDQKPRIPNKIVRKFSHELSDVAHITIPNGYVWQVKLKKEGRKVWFDDGWQDFVEAYSTFVGSLV   87 (127)
Q Consensus         8 ~~~p~F~k~i~~~~~~~~~L~IP~~F~~~~~~~~~~~v~L~~~~G~~W~V~l~~~~~~~~~~~GW~~Fv~~~~L~~GD~l   87 (127)
                      +..|+|+|+|++++. +..|.||..|+++|++..+++|+|++++|+.|+|++.+.++.++|..||++||++|+|++||+|
T Consensus         4 ~~~~~Ffkv~~~~~~-~~~L~IP~~F~~~~~~~~~~~i~L~d~~G~~W~v~~~~~~~~~~~~~GW~~Fv~~n~L~~GD~~   82 (102)
T d1yela1           4 TGEVQFMKPFISEKS-SKSLEIPLGFNEYFPAPFPITVDLLDYSGRSWTVRMKKRGEKVFLTVGWENFVKDNNLEDGKYL   82 (102)
T ss_dssp             CCCEEEEEECCHHHH-TTCEECCHHHHTTCCCCCCSEEEEEETTSCEEEEEEEEETTEEEECTTHHHHHHHHTCCTTCEE
T ss_pred             CCCCeEEEEEcCccc-CCCEECCHHHHHhCCCCCCCEEEEEcCCCCEEEEEEEEeCCeEEEccCHHHHHHHcCCCcCCEE
Confidence            467899999999874 4789999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEEEecCcEEEEEEECCCCe
Q 040084           88 LFEYESNSTFQAHIYDETAC  107 (127)
Q Consensus        88 vF~~~~~~~F~V~If~~~~c  107 (127)
                      +|+|+++++|+|+|||.++|
T Consensus        83 vF~~~~~~~f~V~If~~s~C  102 (102)
T d1yela1          83 QFIYDRDRTFYVIIYGHNMC  102 (102)
T ss_dssp             EEEECSSSEEEEEEECSSCC
T ss_pred             EEEEcCCcEEEEEEeCCCCC
Confidence            99999999999999999998

>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=99.83  E-value=6.8e-20  Score=122.54  Aligned_cols=100  Identities=21%  Similarity=0.311  Sum_probs=83.6

Q ss_pred             CCCCeEEEeccCCccCC-CceeccHHHHHhcccCCCc-------eEEEEcCCCCEEEEEEEEe--CCEEEecccHHHHHh
Q 040084            8 EIPPRFVKAVLPSTLRD-QKPRIPNKIVRKFSHELSD-------VAHITIPNGYVWQVKLKKE--GRKVWFDDGWQDFVE   77 (127)
Q Consensus         8 ~~~p~F~k~i~~~~~~~-~~L~IP~~F~~~~~~~~~~-------~v~L~~~~G~~W~V~l~~~--~~~~~~~~GW~~Fv~   77 (127)
                      +..|-|.|+|+++++.. ..|.||..|++.|++.+..       .+++.+.+|+.|+|.+...  ....+|..||.+||.
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            34578999999999854 5899999999999766533       4899999999999999875  467789999999999


Q ss_pred             HhCCCCCCEEEEEEec--CcEEEEEEECCCCe
Q 040084           78 AYSTFVGSLVLFEYES--NSTFQAHIYDETAC  107 (127)
Q Consensus        78 ~~~L~~GD~lvF~~~~--~~~F~V~If~~~~c  107 (127)
                      +|+|++||.|+|+.+.  +..+.|.+-.+++-
T Consensus        82 ~~~Lk~GD~~~F~~~~~~~~~~~i~~r~~~~~  113 (117)
T d1wida_          82 EKNLRAGDVVSFSRSNGQDQQLYIGWKSRSGS  113 (117)
T ss_dssp             HTTCCTTCEEEEEECCSSSCCEEEEEECCCSC
T ss_pred             HcCCCCCCEEEEEEEeCCCCEEEEEEEECCCC
Confidence            9999999999999985  45677777766543

>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=98.12  E-value=9.1e-07  Score=61.32  Aligned_cols=82  Identities=11%  Similarity=0.052  Sum_probs=65.0

Q ss_pred             CeEEEeccCCccCC-Cc----eeccHHHHHhcccCCC------c--eEE--EEcCCCCEEEEEEEEeC--------CEEE
Q 040084           11 PRFVKAVLPSTLRD-QK----PRIPNKIVRKFSHELS------D--VAH--ITIPNGYVWQVKLKKEG--------RKVW   67 (127)
Q Consensus        11 p~F~k~i~~~~~~~-~~----L~IP~~F~~~~~~~~~------~--~v~--L~~~~G~~W~V~l~~~~--------~~~~   67 (127)
                      -.|.|.|++++... ..    +.||+.++.++.+.+.      .  .+.  +.|.+|+.|+++....+        +.+.
T Consensus        16 ~~F~K~LtasD~g~tg~HQaG~~IPK~~ae~~FP~l~~~~e~nP~~~l~~~i~d~~g~~w~fR~iYyn~~~~ggTRneyR   95 (175)
T d1na6a1          16 FVYIKRLSANDTGATGGHQVGLYIPSGIVEKLFPSINHTRELNPSVFLTAHVSSHDCPDSEARAIYYNSAHFGKTRNEKR   95 (175)
T ss_dssp             EEEEEECCHHHHTCC---CCCCCCCHHHHHHHCGGGCCCSSSSCEEEEEEEESSSCCCCEEEEEEEECGGGTTSCCCEEE
T ss_pred             EEEEEEcccccccccCCccceeeecHHHHHHhCCCCCcccccCCCceEEEEEecCCCCeeEEEEEEECCccCCCccccEE
Confidence            37999999987743 33    8999999998865321      1  233  34889999999998742        6889


Q ss_pred             ecccHHHHHhHhCCCCCCEEEEEEe
Q 040084           68 FDDGWQDFVEAYSTFVGSLVLFEYE   92 (127)
Q Consensus        68 ~~~GW~~Fv~~~~L~~GD~lvF~~~   92 (127)
                      |+.+|+.|+..+.+..||+++|-+.
T Consensus        96 iT~~g~~~~~~~~~n~G~l~i~af~  120 (175)
T d1na6a1          96 ITRWGRGSPLQDPENTGALTLLAFK  120 (175)
T ss_dssp             EECCCTTSGGGCGGGTTCEEEEEEE
T ss_pred             EEeccccccccCccccccEEEEEee
Confidence            9999999999999999999999875