Citrus Sinensis ID: 033576

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110------
Protein Sequence
MDRRVHRLVLPEDGYEWKKYGQKFIKNIRKFRSYFKCQESSCMAKKRAEWCTSDPTNVRIVYDGVHSHTHHGSSPSSADQPRRGSSNTSSNGNQYNLLTQVFGDQSSNAPPASRRN
Secondary Structure (PSIPRED)
cccccccccccccccccccccccccccccccccEEEccccccccccEEEEcccccccEEEEEEccccccccccccccccccccccccccccccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
ccccccccEcccccccHHHcccEEEccccccccEEEcccccccccEEEEEccccccEEEEEEcccccccccccccccccccccccccccccccccccccccccccccccccccccc
Coil and Loop (DISEMBL)
mdrrvhrlvlpedgyEWKKYGQKFIKNIRKFRSYFkcqesscmakkraewctsdptnvrivydgvhshthhgsspssadqprrgssntssngnqyNLLTQvfgdqssnappasrrn
Flexible Loop (DISEMBL)
mdrrvhrlvlpedgyewkkYGQKFIKNIRKFRSYFKCQESSCMAkkraewctsdpTNVRIVYDGVHSHTHhgsspssadqprRGSSNTSSNGNQYNLLTqvfgdqssnappasrrn
Low Complexity Region (SEG)
MDRRVHRLVLPEDGYEWKKYGQKFIKNIRKFRSYFKCQESSCMAKKRAEWCTSDPTNVRIVYDGVhshthhgsspssADQPRRGssntssngnqynLLTQVFGDQSSNAPPASRRN
Disordered region (IsUnstruct)
******RLVLPEDGYEWKKYGQKFIKNIRKFRSYFKCQESSCMAKKRAEWCTSDPTNVRIVYDGVH**************************************************
Disordered Region (DISOPRED)
*****HR**LPEDGYEWKKYGQKFIKNIRKFRSYFKCQESSCMAKKRAEWCTSDPTNVRIVYDGVHS*************************************************
Disordered Region (DISEMBL)
MDRRVHRLVLPEDGYEWKKYGQKFIKNIRKFRSYFKCQESSCMAKKRAEWCTSDPTNVRIVYDGVH***********************SNGNQYNLLTQVFGDQ***********
Disordered Region (DISPRO)
******RLVLPEDGYEWKKYGQKFIKNIRKFRSYFKCQESSCMAKKRAEWCTSDPTNVRIVYDGVH**************************************************
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
oooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MDRRVHRLVLPEDGYEWKKYGQKFIKNIRKFRSYFKCQESSCMAKKRAEWCTSDPTNVRIVYDGVHSHTHHGSSPSSADQPRRGSSNTSSNGNQYNLLTQVFGDQSSNAPPASRRN
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	116	2.2.26 [Sep-21-2011]
Q9C983	287	Probable WRKY transcripti	yes	no	0.491	0.198	0.508	5e-11
O22900	337	Probable WRKY transcripti	no	no	0.491	0.169	0.508	9e-11
Q9SVB7	304	Probable WRKY transcripti	no	no	0.5	0.190	0.465	1e-10
Q9FGZ4	399	Probable WRKY transcripti	no	no	0.491	0.142	0.473	2e-10
Q8VWJ2	318	Probable WRKY transcripti	no	no	0.491	0.179	0.508	2e-10
Q93WV4	282	Probable WRKY transcripti	no	no	0.491	0.202	0.491	7e-10
Q93WV6	277	Probable WRKY transcripti	no	no	0.612	0.256	0.410	1e-09
Q9FL26	326	Probable WRKY transcripti	no	no	0.491	0.174	0.491	1e-09
Q8VWQ4	195	Probable WRKY transcripti	no	no	0.491	0.292	0.456	2e-09
Q9XI90	514	Probable WRKY transcripti	no	no	0.5	0.112	0.440	2e-09

>sp|Q9C983|WRK57_ARATH Probable WRKY transcription factor 57 OS=Arabidopsis thaliana GN=WRKY57 PE=2 SV=1

 Score = 66.2 bits (160), Expect = 5e-11,   Method: Compositional matrix adjust.
 Identities = 29/57 (50%), Positives = 36/57 (63%)

Query: 12  EDGYEWKKYGQKFIKNIRKFRSYFKCQESSCMAKKRAEWCTSDPTNVRIVYDGVHSH 68
           EDGY W+KYGQK +KN    RSY++C  S C  KKR E  + DP+ V   Y+G H H
Sbjct: 147 EDGYRWRKYGQKAVKNSPFPRSYYRCTNSRCTVKKRVERSSDDPSIVITTYEGQHCH 203

Transcription factor. Interacts specifically with the W box (5'-(T)TGAC[CT]-3'), a frequently occurring elicitor-responsive cis-acting element.
Arabidopsis thaliana (taxid: 3702)

>sp|O22900|WRK23_ARATH Probable WRKY transcription factor 23 OS=Arabidopsis thaliana GN=WRKY23 PE=2 SV=1

 Score = 65.5 bits (158), Expect = 9e-11,   Method: Compositional matrix adjust.
 Identities = 29/57 (50%), Positives = 37/57 (64%)

Query: 12  EDGYEWKKYGQKFIKNIRKFRSYFKCQESSCMAKKRAEWCTSDPTNVRIVYDGVHSH 68
           EDGY W+KYGQK +KN    RSY++C  +SC  KKR E    DP+ V   Y+G H+H
Sbjct: 174 EDGYRWRKYGQKAVKNSPFPRSYYRCTTASCNVKKRVERSFRDPSTVVTTYEGQHTH 230

Transcription factor. Interacts specifically with the W box (5'-(T)TGAC[CT]-3'), a frequently occurring elicitor-responsive cis-acting element.

Arabidopsis thaliana (taxid: 3702)

>sp|Q9SVB7|WRK13_ARATH Probable WRKY transcription factor 13 OS=Arabidopsis thaliana GN=WRKY13 PE=2 SV=1

 Score = 65.1 bits (157), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 27/58 (46%), Positives = 36/58 (62%)

Query: 12  EDGYEWKKYGQKFIKNIRKFRSYFKCQESSCMAKKRAEWCTSDPTNVRIVYDGVHSHT 69
           +DGY W+KYGQK +KN +  RSY++C +  C  KKR E    DP  V   Y+G H H+
Sbjct: 223 DDGYRWRKYGQKVVKNTQHPRSYYRCTQDKCRVKKRVERLADDPRMVITTYEGRHLHS 280

Transcription factor. Interacts specifically with the W box (5'-(T)TGAC[CT]-3'), a frequently occurring elicitor-responsive cis-acting element.

Arabidopsis thaliana (taxid: 3702)

>sp|Q9FGZ4|WRK48_ARATH Probable WRKY transcription factor 48 OS=Arabidopsis thaliana GN=WRKY48 PE=2 SV=1

 Score = 64.7 bits (156), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 27/57 (47%), Positives = 36/57 (63%)

Query: 12  EDGYEWKKYGQKFIKNIRKFRSYFKCQESSCMAKKRAEWCTSDPTNVRIVYDGVHSH 68
           +DGY W+KYGQK +KN    RSY++C    C  KKR E  + DP+ V   Y+G H+H
Sbjct: 221 DDGYRWRKYGQKAVKNSPYPRSYYRCTTVGCGVKKRVERSSDDPSIVMTTYEGQHTH 277

Transcription factor. Interacts specifically with the W box (5'-(T)TGAC[CT]-3'), a frequently occurring elicitor-responsive cis-acting element.

Arabidopsis thaliana (taxid: 3702)

>sp|Q8VWJ2|WRK28_ARATH Probable WRKY transcription factor 28 OS=Arabidopsis thaliana GN=WRKY28 PE=2 SV=1

 Score = 64.3 bits (155), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 29/57 (50%), Positives = 35/57 (61%)

Query: 12  EDGYEWKKYGQKFIKNIRKFRSYFKCQESSCMAKKRAEWCTSDPTNVRIVYDGVHSH 68
           EDGY W+KYGQK +KN    RSY++C    C  KKR E    DPT V   Y+G H+H
Sbjct: 172 EDGYRWRKYGQKAVKNSPYPRSYYRCTTQKCNVKKRVERSFQDPTVVITTYEGQHNH 228

Transcription factor. Interacts specifically with the W box (5'-(T)TGAC[CT]-3'), a frequently occurring elicitor-responsive cis-acting element.

Arabidopsis thaliana (taxid: 3702)

>sp|Q93WV4|WRK71_ARATH Probable WRKY transcription factor 71 OS=Arabidopsis thaliana GN=WRKY71 PE=2 SV=1

 Score = 62.4 bits (150), Expect = 7e-10,   Method: Compositional matrix adjust.
 Identities = 28/57 (49%), Positives = 35/57 (61%)

Query: 12  EDGYEWKKYGQKFIKNIRKFRSYFKCQESSCMAKKRAEWCTSDPTNVRIVYDGVHSH 68
           EDGY W+KYGQK +KN    RSY++C    C  KKR E    DP+ V   Y+G H+H
Sbjct: 136 EDGYRWRKYGQKAVKNSPYPRSYYRCTTQKCNVKKRVERSFQDPSIVITTYEGKHNH 192

Transcription factor. Interacts specifically with the W box (5'-(T)TGAC[CT]-3'), a frequently occurring elicitor-responsive cis-acting element.

Arabidopsis thaliana (taxid: 3702)

>sp|Q93WV6|WRK68_ARATH Probable WRKY transcription factor 68 OS=Arabidopsis thaliana GN=WRKY68 PE=2 SV=1

 Score = 62.0 bits (149), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 32/78 (41%), Positives = 46/78 (58%), Gaps = 7/78 (8%)

Query: 12  EDGYEWKKYGQKFIKNIRKFRSYFKCQESSCMAKKRAEWCTSDPTNVRIVYDGVHSHTH- 70
           +DGY+W+KYGQK +K+    R+Y++C  + C  KKR E   SDP++V   Y+G H+H   
Sbjct: 118 DDGYKWRKYGQKPVKDSPFPRNYYRCTTTWCDVKKRVERSFSDPSSVITTYEGQHTHPRP 177

Query: 71  ------HGSSPSSADQPR 82
                  GSSPS+    R
Sbjct: 178 LLIMPKEGSSPSNGSASR 195

Transcription factor. Interacts specifically with the W box (5'-(T)TGAC[CT]-3'), a frequently occurring elicitor-responsive cis-acting element.

Arabidopsis thaliana (taxid: 3702)

>sp|Q9FL26|WRKY8_ARATH Probable WRKY transcription factor 8 OS=Arabidopsis thaliana GN=WRKY8 PE=2 SV=1

 Score = 62.0 bits (149), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 28/57 (49%), Positives = 34/57 (59%)

Query: 12  EDGYEWKKYGQKFIKNIRKFRSYFKCQESSCMAKKRAEWCTSDPTNVRIVYDGVHSH 68
           EDGY W+KYGQK +KN    RSY++C    C  KKR E    DPT V   Y+  H+H
Sbjct: 183 EDGYRWRKYGQKAVKNSPYPRSYYRCTTQKCNVKKRVERSYQDPTVVITTYESQHNH 239

Transcription factor. Interacts specifically with the W box (5'-(T)TGAC[CT]-3'), a frequently occurring elicitor-responsive cis-acting element.

Arabidopsis thaliana (taxid: 3702)

>sp|Q8VWQ4|WRK56_ARATH Probable WRKY transcription factor 56 OS=Arabidopsis thaliana GN=WRKY56 PE=2 SV=1

 Score = 61.2 bits (147), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 26/57 (45%), Positives = 36/57 (63%)

Query: 12  EDGYEWKKYGQKFIKNIRKFRSYFKCQESSCMAKKRAEWCTSDPTNVRIVYDGVHSH 68
           +DGY W+KYGQK +KN    RSY++C   +C  KK+ +    DP  V   Y+GVH+H
Sbjct: 114 DDGYRWRKYGQKSVKNNAHPRSYYRCTYHTCNVKKQVQRLAKDPNVVVTTYEGVHNH 170

Transcription factor. Interacts specifically with the W box (5'-(T)TGAC[CT]-3'), a frequently occurring elicitor-responsive cis-acting element.

Arabidopsis thaliana (taxid: 3702)

>sp|Q9XI90|WRKY4_ARATH Probable WRKY transcription factor 4 OS=Arabidopsis thaliana GN=WRKY4 PE=1 SV=2

 Score = 61.2 bits (147), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 26/59 (44%), Positives = 34/59 (57%)

Query: 10  LPEDGYEWKKYGQKFIKNIRKFRSYFKCQESSCMAKKRAEWCTSDPTNVRIVYDGVHSH 68
           L +DGY W+KYGQK +K     RSY+KC    C  +K  E   +DP  V   Y+G H+H
Sbjct: 407 LLDDGYRWRKYGQKVVKGNPYPRSYYKCTTPGCGVRKHVERAATDPKAVVTTYEGKHNH 465

Transcription factor. Interacts specifically with the W box (5'-(T)TGAC[CT]-3'), a frequently occurring elicitor-responsive cis-acting element.

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	116
359478811	189	PREDICTED: probable WRKY transcription f	0.879	0.539	0.579	2e-29
346456284	92	WRKY transcription factor 60 [Dimocarpus	0.793	1.0	0.638	2e-26
31415959	148	putative DNA-binding protein [Oryza sati	0.784	0.614	0.571	5e-24
297601419	142	Os03g0657400 [Oryza sativa Japonica Grou	0.784	0.640	0.571	5e-24
48374975	140	putative DNA-binding protein [Zea mays]	0.767	0.635	0.536	2e-21
224073122	116	predicted protein [Populus trichocarpa]	0.827	0.827	0.530	8e-21
357115687	130	PREDICTED: probable WRKY transcription f	0.775	0.692	0.505	6e-19
18483229	178	putative DNA-binding protein homolog [So	0.827	0.539	0.489	2e-18
226533036	99	uncharacterized protein LOC100277808 [Ze	0.836	0.979	0.494	2e-18
410443449	136	WRKY transcript factor 48 [Hordeum vulga	0.775	0.661	0.520	1e-17

>gi|359478811|ref|XP_003632174.1| PREDICTED: probable WRKY transcription factor 2-like [Vitis vinifera]

 Score =  132 bits (332), Expect = 2e-29,   Method: Compositional matrix adjust.
 Identities = 62/107 (57%), Positives = 77/107 (71%), Gaps = 5/107 (4%)

Query: 2   DRRVHRLVLPEDGYEWKKYGQKFIKNIRKFRSYFKCQESSCMAKKRAEWCTSDPTNVRIV 61
           +R  +RLVLP DGYEWKKYGQKFIKNI KFRSYFKCQ + C AKK+AEW  ++P+++++ 
Sbjct: 81  ERSSYRLVLPADGYEWKKYGQKFIKNIGKFRSYFKCQRTGCGAKKKAEWTPTEPSDIKVK 140

Query: 62  YDGVHSHTHHGSSPSSADQPRRGSSNTSSNGNQYNLLTQVFGDQSSN 108
           YDG H+H     S  S      G+S  S+  NQYNL TQVFGDQ S+
Sbjct: 141 YDGKHTHDSWAYSVQS-----EGNSTASTATNQYNLFTQVFGDQDSS 182

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|346456284|gb|AEO31504.1| WRKY transcription factor 60 [Dimocarpus longan]

 Score =  122 bits (307), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 60/94 (63%), Positives = 68/94 (72%), Gaps = 2/94 (2%)

Query: 7   RLVLPEDGYEWKKYGQKFIKNIRKFRSYFKCQESSCMAKKRAEWCTSDPTNVRIVYDGVH 66
           RLVLPEDGYEWKKYGQKFIKNI KFRSYFKCQ   C AKK+AEW   +  ++RIVY+GVH
Sbjct: 1   RLVLPEDGYEWKKYGQKFIKNIGKFRSYFKCQREKCTAKKKAEWSNIESGDMRIVYEGVH 60

Query: 67  SHTHHGSSPSSADQPRRGSSNTSSNGNQYNLLTQ 100
           +H       SSA   +  SS  S+N NQYNLL Q
Sbjct: 61  THGSMTDQNSSAGSSQGTSS--SANANQYNLLNQ 92

Source: Dimocarpus longan

Species: Dimocarpus longan

Genus: Dimocarpus

Family: Sapindaceae

Order: Sapindales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|31415959|gb|AAP50979.1| putative DNA-binding protein [Oryza sativa Japonica Group] gi|108710185|gb|ABF97980.1| DNA-binding protein, putative, expressed [Oryza sativa Japonica Group]

 Score =  115 bits (287), Expect = 5e-24,   Method: Compositional matrix adjust.
 Identities = 56/98 (57%), Positives = 72/98 (73%), Gaps = 7/98 (7%)

Query: 7   RLVLPEDGYEWKKYGQKFIKNIRKFRSYFKCQESSCMAKKRAEWCTSDP-TNVRIVYDGV 65
           +LV+PEDGYEWKKYGQKFIKNI+K RSYF+C++  C AKK+ EW   DP  N+R+VYDG 
Sbjct: 49  QLVMPEDGYEWKKYGQKFIKNIQKNRSYFRCRDQRCGAKKKVEWHPHDPGLNLRVVYDGA 108

Query: 66  HSHTHHGSSPSSADQPRRGSSNTSSNGNQYNLLTQVFG 103
           H   HHGS  S+A +   G ++ ++  NQY+L TQ FG
Sbjct: 109 H---HHGSPSSAAGE---GGTSAAAAANQYDLSTQYFG 140

Source: Oryza sativa Japonica Group

Species: Oryza sativa

Genus: Oryza

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297601419|ref|NP_001050814.2| Os03g0657400 [Oryza sativa Japonica Group] gi|46394374|tpg|DAA05125.1| TPA_inf: WRKY transcription factor 60 [Oryza sativa (indica cultivar-group)] gi|125545112|gb|EAY91251.1| hypothetical protein OsI_12866 [Oryza sativa Indica Group] gi|255674758|dbj|BAF12728.2| Os03g0657400 [Oryza sativa Japonica Group]

 Score =  114 bits (286), Expect = 5e-24,   Method: Compositional matrix adjust.
 Identities = 56/98 (57%), Positives = 72/98 (73%), Gaps = 7/98 (7%)

Query: 7   RLVLPEDGYEWKKYGQKFIKNIRKFRSYFKCQESSCMAKKRAEWCTSDP-TNVRIVYDGV 65
           +LV+PEDGYEWKKYGQKFIKNI+K RSYF+C++  C AKK+ EW   DP  N+R+VYDG 
Sbjct: 43  QLVMPEDGYEWKKYGQKFIKNIQKNRSYFRCRDQRCGAKKKVEWHPHDPGLNLRVVYDGA 102

Query: 66  HSHTHHGSSPSSADQPRRGSSNTSSNGNQYNLLTQVFG 103
           H   HHGS  S+A +   G ++ ++  NQY+L TQ FG
Sbjct: 103 H---HHGSPSSAAGE---GGTSAAAAANQYDLSTQYFG 134

Source: Oryza sativa Japonica Group

Species: Oryza sativa

Genus: Oryza

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|48374975|gb|AAT42172.1| putative DNA-binding protein [Zea mays] gi|413933532|gb|AFW68083.1| putative WRKY DNA-binding domain superfamily protein [Zea mays]

 Score =  105 bits (263), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 52/97 (53%), Positives = 67/97 (69%), Gaps = 8/97 (8%)

Query: 8   LVLPEDGYEWKKYGQKFIKNIRKFRSYFKCQESSCMAKKRAEWCTSDPT-NVRIVYDGVH 66
           +V+PEDGYEWKKYGQKFIKNI+K RSYF+C+   C AKK+ EW   DP+  +R+VYDG H
Sbjct: 44  MVVPEDGYEWKKYGQKFIKNIQKIRSYFRCRHRLCGAKKKVEWHPRDPSAALRVVYDGAH 103

Query: 67  SHTHHGSSPSSADQPRRGSSNTSSNGNQYNLLTQVFG 103
               HG++P +A  P +G    +S  N+Y L  Q FG
Sbjct: 104 ---QHGAAPPAA--PEQGGGGGAS--NRYELGAQYFG 133

Source: Zea mays

Species: Zea mays

Genus: Zea

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224073122|ref|XP_002303982.1| predicted protein [Populus trichocarpa] gi|222841414|gb|EEE78961.1| predicted protein [Populus trichocarpa]

 Score =  104 bits (259), Expect = 8e-21,   Method: Compositional matrix adjust.
 Identities = 60/113 (53%), Positives = 73/113 (64%), Gaps = 17/113 (15%)

Query: 2   DRRVHRLVLPEDGYEWKKYGQKFIKNIRKFRSYFKCQESSCMAKKRAEWCTSDPTNVRIV 61
           DR   RLV PEDG+ WKKYGQKFIK I KFRSYFKCQ+ +C+AKKR EW  S+P  +RI 
Sbjct: 15  DRGGQRLVPPEDGHGWKKYGQKFIKKIGKFRSYFKCQKQNCVAKKRVEW--SNPDYIRIW 72

Query: 62  YDGVHSHTHHGSSPSSADQPRRGSSNTSSNGNQYNLLTQVFGDQSSNAPPASR 114
           Y+G H+H       +S+ Q       +SS  NQ +L  QVFG   S+ P ASR
Sbjct: 73  YEGSHNH-------ASSTQ-----GTSSSAANQDSLYAQVFG---SDQPAASR 110

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357115687|ref|XP_003559618.1| PREDICTED: probable WRKY transcription factor 71-like [Brachypodium distachyon]

 Score = 98.2 bits (243), Expect = 6e-19,   Method: Compositional matrix adjust.
 Identities = 49/97 (50%), Positives = 64/97 (65%), Gaps = 7/97 (7%)

Query: 7   RLVLPEDGYEWKKYGQKFIKNIRKFRSYFKCQESSCMAKKRAEWCTSDPTNVRIVYDGVH 66
           +LV+PEDGYEWKKYGQKFIKNI++ RSYF+C++  C AKK+ EW   DP+ +R+VY+G H
Sbjct: 36  QLVMPEDGYEWKKYGQKFIKNIQRIRSYFRCRDKRCGAKKKVEWQPGDPS-LRVVYEGAH 94

Query: 67  SHTHHGSSPSSADQPRRGSSNTSSNGNQYNLLTQVFG 103
            H    SS S       G++      N+Y L  Q FG
Sbjct: 95  QHGSPSSSSSCTGAGHDGAA------NRYELSAQYFG 125

Source: Brachypodium distachyon

Species: Brachypodium distachyon

Genus: Brachypodium

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|18483229|gb|AAL73973.1|AF466201_2 putative DNA-binding protein homolog [Sorghum bicolor]

 Score = 96.7 bits (239), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 48/98 (48%), Positives = 65/98 (66%), Gaps = 2/98 (2%)

Query: 7   RLVLPEDGYEWKKYGQKFIKNIRKFRSYFKCQESSCMAKKRAEWCTSDPT-NVRIVYDGV 65
           +LV+PEDGYEWKKYGQKFIKNI+K RSYF+C+   C AKK+ EW   DP+ ++RIVY+G 
Sbjct: 76  QLVMPEDGYEWKKYGQKFIKNIQKIRSYFRCRHKLCGAKKKVEWHPRDPSGDLRIVYEGA 135

Query: 66  HSHTHHGSSPSSADQPRRGSSNTSSNGNQYNLLTQVFG 103
           H H    ++ +      +     +S+ N+Y L  Q FG
Sbjct: 136 HQHGAP-AAAAPPGPGGQHHGGGASDFNRYELGAQYFG 172

Source: Sorghum bicolor

Species: Sorghum bicolor

Genus: Sorghum

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|226533036|ref|NP_001144756.1| uncharacterized protein LOC100277808 [Zea mays] gi|48374985|gb|AAT42181.1| putative DNA-binding protein [Zea mays] gi|195646566|gb|ACG42751.1| hypothetical protein [Zea mays] gi|414872049|tpg|DAA50606.1| TPA: putative WRKY DNA-binding domain superfamily protein [Zea mays]

 Score = 96.7 bits (239), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 49/99 (49%), Positives = 61/99 (61%), Gaps = 2/99 (2%)

Query: 10  LPEDGYEWKKYGQKFIKNIRKFRSYFKCQESSCMAKKRAEWCTSDP-TNVRIVYDGVHSH 68
           +PEDGYEWKKYGQKFIKNI+K RSYF+C+   C AKK+ EW   DP  ++RIVYDG H H
Sbjct: 1   MPEDGYEWKKYGQKFIKNIQKMRSYFRCRHRLCGAKKKVEWHPRDPGGDLRIVYDGAHQH 60

Query: 69  THHGSSPSSADQPRRGSSNTSSNGNQYNLLTQVFGDQSS 107
                  +      +     +S+ N+Y L TQ FG   S
Sbjct: 61  GPP-PLAAPPGGHGQMQGGGASDSNRYELCTQYFGGARS 98

Source: Zea mays

Species: Zea mays

Genus: Zea

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|410443449|gb|AFV67804.1| WRKY transcript factor 48 [Hordeum vulgare]

 Score = 93.6 bits (231), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 50/96 (52%), Positives = 62/96 (64%), Gaps = 6/96 (6%)

Query: 8   LVLPEDGYEWKKYGQKFIKNIRKFRSYFKCQESSCMAKKRAEWCTSDPTNVRIVYDGVHS 67
           LV+PEDGY+WKKYGQKFIKNI+K RSYF+C++  C AKK+ EW   DP+ +R+VYDG H 
Sbjct: 38  LVMPEDGYQWKKYGQKFIKNIQKIRSYFRCRDRRCGAKKKVEWQPGDPS-LRVVYDGAHQ 96

Query: 68  HTHHGSSPSSADQPRRGSSNTSSNGNQYNLLTQVFG 103
           H    SS S              +GN+Y L  Q FG
Sbjct: 97  HGSPSSSSSHGG-----GGGQDGDGNRYELSAQYFG 127

Source: Hordeum vulgare

Species: Hordeum vulgare

Genus: Hordeum

Family: Poaceae

Order: Poales

Class: Liliopsida

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	116
TAIR|locus:2122496	304	WRKY13 "WRKY DNA-binding prote	0.456	0.174	0.471	2.8e-10
TAIR|locus:2007081	287	WRKY57 "AT1G69310" [Arabidopsi	0.456	0.184	0.509	3.1e-10
TAIR|locus:2065124	337	WRKY23 "WRKY DNA-binding prote	0.456	0.157	0.509	6.2e-10
TAIR|locus:2141872	318	WRKY28 "WRKY DNA-binding prote	0.456	0.166	0.509	9e-10
TAIR|locus:505006317	218	WRKY12 "WRKY DNA-binding prote	0.456	0.243	0.452	1.8e-09
TAIR|locus:2019382	282	WRKY71 "WRKY DNA-binding prote	0.456	0.187	0.490	1.8e-09
TAIR|locus:2024583	195	WRKY56 "WRKY DNA-binding prote	0.465	0.276	0.444	2.2e-09
TAIR|locus:2170403	326	WRKY8 "WRKY DNA-binding protei	0.448	0.159	0.5	4.4e-09
TAIR|locus:2179739	173	WRKY50 "WRKY DNA-binding prote	0.456	0.306	0.433	4.7e-09
TAIR|locus:2157829	399	WRKY48 "WRKY DNA-binding prote	0.456	0.132	0.471	5.2e-09

TAIR|locus:2122496 WRKY13 "WRKY DNA-binding protein 13" [Arabidopsis thaliana (taxid:3702)]

 Score = 150 (57.9 bits), Expect = 2.8e-10, P = 2.8e-10
 Identities = 25/53 (47%), Positives = 33/53 (62%)

Query:    12 EDGYEWKKYGQKFIKNIRKFRSYFKCQESSCMAKKRAEWCTSDPTNVRIVYDG 64
             +DGY W+KYGQK +KN +  RSY++C +  C  KKR E    DP  V   Y+G
Sbjct:   223 DDGYRWRKYGQKVVKNTQHPRSYYRCTQDKCRVKKRVERLADDPRMVITTYEG 275

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;ISS

GO:0043565 "sequence-specific DNA binding" evidence=IEA

TAIR|locus:2007081 WRKY57 "AT1G69310" [Arabidopsis thaliana (taxid:3702)]

 Score = 149 (57.5 bits), Expect = 3.1e-10, P = 3.1e-10
 Identities = 27/53 (50%), Positives = 34/53 (64%)

Query:    12 EDGYEWKKYGQKFIKNIRKFRSYFKCQESSCMAKKRAEWCTSDPTNVRIVYDG 64
             EDGY W+KYGQK +KN    RSY++C  S C  KKR E  + DP+ V   Y+G
Sbjct:   147 EDGYRWRKYGQKAVKNSPFPRSYYRCTNSRCTVKKRVERSSDDPSIVITTYEG 199

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

GO:0005634 "nucleus" evidence=ISM

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

GO:0006970 "response to osmotic stress" evidence=IMP

GO:0009414 "response to water deprivation" evidence=IMP

GO:0009651 "response to salt stress" evidence=IMP

TAIR|locus:2065124 WRKY23 "WRKY DNA-binding protein 23" [Arabidopsis thaliana (taxid:3702)]

 Score = 148 (57.2 bits), Expect = 6.2e-10, P = 6.2e-10
 Identities = 27/53 (50%), Positives = 34/53 (64%)

Query:    12 EDGYEWKKYGQKFIKNIRKFRSYFKCQESSCMAKKRAEWCTSDPTNVRIVYDG 64
             EDGY W+KYGQK +KN    RSY++C  +SC  KKR E    DP+ V   Y+G
Sbjct:   174 EDGYRWRKYGQKAVKNSPFPRSYYRCTTASCNVKKRVERSFRDPSTVVTTYEG 226

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;ISS

GO:0043565 "sequence-specific DNA binding" evidence=IEA

GO:0009624 "response to nematode" evidence=IEP

GO:0009733 "response to auxin stimulus" evidence=IEP

TAIR|locus:2141872 WRKY28 "WRKY DNA-binding protein 28" [Arabidopsis thaliana (taxid:3702)]

 Score = 146 (56.5 bits), Expect = 9.0e-10, P = 9.0e-10
 Identities = 27/53 (50%), Positives = 32/53 (60%)

Query:    12 EDGYEWKKYGQKFIKNIRKFRSYFKCQESSCMAKKRAEWCTSDPTNVRIVYDG 64
             EDGY W+KYGQK +KN    RSY++C    C  KKR E    DPT V   Y+G
Sbjct:   172 EDGYRWRKYGQKAVKNSPYPRSYYRCTTQKCNVKKRVERSFQDPTVVITTYEG 224

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

GO:0005634 "nucleus" evidence=ISM

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

GO:0043565 "sequence-specific DNA binding" evidence=IEA;IDA

GO:0006865 "amino acid transport" evidence=RCA

GO:0009407 "toxin catabolic process" evidence=RCA

GO:0010583 "response to cyclopentenone" evidence=RCA

TAIR|locus:505006317 WRKY12 "WRKY DNA-binding protein 12" [Arabidopsis thaliana (taxid:3702)]

 Score = 138 (53.6 bits), Expect = 1.8e-09, P = 1.8e-09
 Identities = 24/53 (45%), Positives = 34/53 (64%)

Query:    12 EDGYEWKKYGQKFIKNIRKFRSYFKCQESSCMAKKRAEWCTSDPTNVRIVYDG 64
             +DGY+W+KYGQK +KN    RSY++C  ++C  KKR E  + D   V   Y+G
Sbjct:   145 DDGYKWRKYGQKVVKNSLHPRSYYRCTHNNCRVKKRVERLSEDCRMVITTYEG 197

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;ISS

GO:0043565 "sequence-specific DNA binding" evidence=IEA

GO:0009718 "anthocyanin-containing compound biosynthetic process" evidence=RCA

TAIR|locus:2019382 WRKY71 "WRKY DNA-binding protein 71" [Arabidopsis thaliana (taxid:3702)]

 Score = 142 (55.0 bits), Expect = 1.8e-09, P = 1.8e-09
 Identities = 26/53 (49%), Positives = 32/53 (60%)

Query:    12 EDGYEWKKYGQKFIKNIRKFRSYFKCQESSCMAKKRAEWCTSDPTNVRIVYDG 64
             EDGY W+KYGQK +KN    RSY++C    C  KKR E    DP+ V   Y+G
Sbjct:   136 EDGYRWRKYGQKAVKNSPYPRSYYRCTTQKCNVKKRVERSFQDPSIVITTYEG 188

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;ISS

GO:0043565 "sequence-specific DNA binding" evidence=IEA

TAIR|locus:2024583 WRKY56 "WRKY DNA-binding protein 56" [Arabidopsis thaliana (taxid:3702)]

 Score = 137 (53.3 bits), Expect = 2.2e-09, P = 2.2e-09
 Identities = 24/54 (44%), Positives = 33/54 (61%)

Query:    12 EDGYEWKKYGQKFIKNIRKFRSYFKCQESSCMAKKRAEWCTSDPTNVRIVYDGV 65
             +DGY W+KYGQK +KN    RSY++C   +C  KK+ +    DP  V   Y+GV
Sbjct:   114 DDGYRWRKYGQKSVKNNAHPRSYYRCTYHTCNVKKQVQRLAKDPNVVVTTYEGV 167

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;ISS

GO:0043565 "sequence-specific DNA binding" evidence=IEA

TAIR|locus:2170403 WRKY8 "WRKY DNA-binding protein 8" [Arabidopsis thaliana (taxid:3702)]

 Score = 140 (54.3 bits), Expect = 4.4e-09, P = 4.4e-09
 Identities = 26/52 (50%), Positives = 31/52 (59%)

Query:    12 EDGYEWKKYGQKFIKNIRKFRSYFKCQESSCMAKKRAEWCTSDPTNVRIVYD 63
             EDGY W+KYGQK +KN    RSY++C    C  KKR E    DPT V   Y+
Sbjct:   183 EDGYRWRKYGQKAVKNSPYPRSYYRCTTQKCNVKKRVERSYQDPTVVITTYE 234

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

GO:0005634 "nucleus" evidence=ISM;IDA

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

GO:0043565 "sequence-specific DNA binding" evidence=IEA

GO:0009737 "response to abscisic acid stimulus" evidence=IEP

GO:0042742 "defense response to bacterium" evidence=IMP

GO:0050832 "defense response to fungus" evidence=IMP

GO:0070301 "cellular response to hydrogen peroxide" evidence=IEP

TAIR|locus:2179739 WRKY50 "WRKY DNA-binding protein 50" [Arabidopsis thaliana (taxid:3702)]

 Score = 134 (52.2 bits), Expect = 4.7e-09, P = 4.7e-09
 Identities = 23/53 (43%), Positives = 33/53 (62%)

Query:    12 EDGYEWKKYGQKFIKNIRKFRSYFKCQESSCMAKKRAEWCTSDPTNVRIVYDG 64
             +DG++W+KYG+K +KN    R+Y+KC    C  KKR E    DP+ V   Y+G
Sbjct:   113 DDGFKWRKYGKKMVKNSPHPRNYYKCSVDGCPVKKRVERDRDDPSFVITTYEG 165

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;ISS

GO:0043565 "sequence-specific DNA binding" evidence=IEA

GO:0009867 "jasmonic acid mediated signaling pathway" evidence=IGI

GO:0050832 "defense response to fungus" evidence=IGI

TAIR|locus:2157829 WRKY48 "WRKY DNA-binding protein 48" [Arabidopsis thaliana (taxid:3702)]

 Score = 141 (54.7 bits), Expect = 5.2e-09, P = 5.2e-09
 Identities = 25/53 (47%), Positives = 33/53 (62%)

Query:    12 EDGYEWKKYGQKFIKNIRKFRSYFKCQESSCMAKKRAEWCTSDPTNVRIVYDG 64
             +DGY W+KYGQK +KN    RSY++C    C  KKR E  + DP+ V   Y+G
Sbjct:   221 DDGYRWRKYGQKAVKNSPYPRSYYRCTTVGCGVKKRVERSSDDPSIVMTTYEG 273

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

GO:0005634 "nucleus" evidence=ISM;IDA

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

GO:0043565 "sequence-specific DNA binding" evidence=IEA

GO:0010200 "response to chitin" evidence=IEP;RCA

GO:0003677 "DNA binding" evidence=IDA

GO:0009617 "response to bacterium" evidence=IEP

GO:0042742 "defense response to bacterium" evidence=IMP

GO:0045893 "positive regulation of transcription, DNA-dependent" evidence=IDA

GO:0002679 "respiratory burst involved in defense response" evidence=RCA

GO:0006865 "amino acid transport" evidence=RCA

GO:0015824 "proline transport" evidence=RCA

GO:0035556 "intracellular signal transduction" evidence=RCA

GO:0052542 "defense response by callose deposition" 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: GSVIVG00024838001 SubName- Full=Chromosome chr6 scaffold_3, whole genome shotgun sequence; (134 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	116
smart00774	59	smart00774, WRKY, DNA binding domain	1e-21
pfam03106	60	pfam03106, WRKY, WRKY DNA -binding domain	8e-17

>gnl|CDD|214815 smart00774, WRKY, DNA binding domain

 Score = 80.2 bits (199), Expect = 1e-21
 Identities = 26/59 (44%), Positives = 37/59 (62%), Gaps = 1/59 (1%)

Query: 11 PEDGYEWKKYGQKFIKNIRKFRSYFKC-QESSCMAKKRAEWCTSDPTNVRIVYDGVHSH 68
           +DGY+W+KYGQK IK     RSY++C     C AKK+ +    DP+ V + Y+G H+H
Sbjct: 1  LDDGYQWRKYGQKVIKGSPYPRSYYRCTYTQGCPAKKQVQRSDDDPSVVEVTYEGEHTH 59

The WRKY domain is a DNA binding domain found in one or two copies in a superfamily of plant transcription factors. These transcription factors are involved in the regulation of various physiological programs that are unique to plants, including pathogen defense, senescence and trichome development. The domain is a 60 amino acid region that is defined by the conserved amino acid sequence WRKYGQK at its N-terminal end, together with a novel zinc-finger-like motif. It binds specifically to the DNA sequence motif (T)(T)TGAC(C/T), which is known as the W box. The invariant TGAC core is essential for function and WRKY binding. Length = 59

>gnl|CDD|145969 pfam03106, WRKY, WRKY DNA -binding domain

 Score = 68.4 bits (168), Expect = 8e-17
 Identities = 26/58 (44%), Positives = 35/58 (60%)

Query: 11 PEDGYEWKKYGQKFIKNIRKFRSYFKCQESSCMAKKRAEWCTSDPTNVRIVYDGVHSH 68
           +DGY W+KYGQK +K     RSY++C    C  KK+ E  + DP  V I Y+G H+H
Sbjct: 1  LDDGYNWRKYGQKPVKGSPFPRSYYRCTSPGCPVKKQVERSSDDPQIVEITYEGEHNH 58

Length = 60

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	116
PF03106	60	WRKY: WRKY DNA -binding domain; InterPro: IPR00365	100.0
smart00774	59	WRKY DNA binding domain. The WRKY domain is a DNA	100.0
PF04500	62	FLYWCH: FLYWCH zinc finger domain; InterPro: IPR00	93.34
PF03101	91	FAR1: FAR1 DNA-binding domain; InterPro: IPR004330	85.59

>PF03106 WRKY: WRKY DNA -binding domain; InterPro: IPR003657 The WRKY domain is a 60 amino acid region that is defined by the conserved amino acid sequence WRKYGQK at its N-terminal end, together with a novel zinc-finger- like motif

Probab=100.00  E-value=4.1e-37  Score=198.54  Aligned_cols=60  Identities=43%  Similarity=0.861  Sum_probs=52.6

Q ss_pred             CCCCchhhhhccccccCCCCCCCccccccccccchhhhhhccCCCCeEEEEEeccCCCCC
Q 033576           11 PEDGYEWKKYGQKFIKNIRKFRSYFKCQESSCMAKKRAEWCTSDPTNVRIVYDGVHSHTH   70 (116)
Q Consensus        11 ~~DGy~WRKYGQK~ikg~~~pR~YyrCt~~~C~akK~Vqr~~~d~~~~~vtY~G~H~h~~   70 (116)
                      ++|||.|||||||.|+|+++||+||||++.+|+|+|+|||+.+|+.+|+|||+|+|||+.
T Consensus         1 ~~Dgy~WRKYGqK~i~g~~~pRsYYrCt~~~C~akK~Vqr~~~d~~~~~vtY~G~H~h~k   60 (60)
T PF03106_consen    1 LDDGYRWRKYGQKNIKGSPYPRSYYRCTHPGCPAKKQVQRSADDPNIVIVTYEGEHNHPK   60 (60)
T ss_dssp             --SSS-EEEEEEEEETTTTCEEEEEEEECTTEEEEEEEEEETTCCCEEEEEEES--SS--
T ss_pred             CCCCCchhhccCcccCCCceeeEeeeccccChhheeeEEEecCCCCEEEEEEeeeeCCCC
Confidence            489999999999999999999999999999999999999999999999999999999973

The WRKY domain is found in one or two copies in a superfamily of plant transcription factors involved in the regulation of various physiological programs that are unique to plants, including pathogen defence, senescence, trichome development and the biosynthesis of secondary metabolites. The WRKY domain binds specifically to the DNA sequence motif (T)(T)TGAC(C/T), which is known as the W box. The invariant TGAC core of the W box is essential for function and WRKY binding []. Some proteins known to contain a WRKY domain include Arabidopsis thaliana ZAP1 (Zinc-dependent Activator Protein-1) and AtWRKY44/TTG2, a protein involved in trichome development and anthocyanin pigmentation; and wild oat ABF1-2, two proteins involved in the gibberelic acid-induced expression of the alpha-Amy2 gene. Structural studies indicate that this domain is a four-stranded beta-sheet with a zinc binding pocket, forming a novel zinc and DNA binding structure []. The WRKYGQK residues correspond to the most N-terminal beta-strand, which enables extensive hydrophobic interactions, contributing to the structural stability of the beta-sheet.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2AYD_A 1WJ2_A 2LEX_A.

>smart00774 WRKY DNA binding domain

Probab=100.00  E-value=7.4e-36  Score=192.51  Aligned_cols=58  Identities=45%  Similarity=0.912  Sum_probs=56.5

Q ss_pred             CCCCchhhhhccccccCCCCCCCcccccc-ccccchhhhhhccCCCCeEEEEEeccCCC
Q 033576           11 PEDGYEWKKYGQKFIKNIRKFRSYFKCQE-SSCMAKKRAEWCTSDPTNVRIVYDGVHSH   68 (116)
Q Consensus        11 ~~DGy~WRKYGQK~ikg~~~pR~YyrCt~-~~C~akK~Vqr~~~d~~~~~vtY~G~H~h   68 (116)
                      ++|||.|||||||.|+|+++||+||||++ ++|+|+|+||++++|+.+|+|||+|+|||
T Consensus         1 ~~DGy~WRKYGQK~ikgs~~pRsYYrCt~~~~C~a~K~Vq~~~~d~~~~~vtY~g~H~h   59 (59)
T smart00774        1 LDDGYQWRKYGQKVIKGSPFPRSYYRCTYSQGCPAKKQVQRSDDDPSVVEVTYEGEHTH   59 (59)
T ss_pred             CCCcccccccCcEecCCCcCcceEEeccccCCCCCcccEEEECCCCCEEEEEEeeEeCC
Confidence            48999999999999999999999999999 89999999999999999999999999998

The WRKY domain is a DNA binding domain found in one or two copies in a superfamily of plant transcription factors. These transcription factors are involved in the regulation of various physiological programs that are unique to plants, including pathogen defense, senescence and trichome development. The domain is a 60 amino acid region that is defined by the conserved amino acid sequence WRKYGQK at its N-terminal end, together with a novel zinc-finger-like motif. It binds specifically to the DNA sequence motif (T)(T)TGAC(C/T), which is known as the W box. The invariant TGAC core is essential for function and WRKY binding.

>PF04500 FLYWCH: FLYWCH zinc finger domain; InterPro: IPR007588 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule

Probab=93.34  E-value=0.026  Score=34.15  Aligned_cols=49  Identities=24%  Similarity=0.536  Sum_probs=24.1

Q ss_pred             CCCCCchhhhhccccccCCCCCCCccccccc---cccchhhhhhccCCCCeEEEEEeccCCC
Q 033576           10 LPEDGYEWKKYGQKFIKNIRKFRSYFKCQES---SCMAKKRAEWCTSDPTNVRIVYDGVHSH   68 (116)
Q Consensus        10 ~~~DGy~WRKYGQK~ikg~~~pR~YyrCt~~---~C~akK~Vqr~~~d~~~~~vtY~G~H~h   68 (116)
                      +.-|||.-.+....      ....|++|+..   +|+|+-.+.  . +...+ +...++|||
T Consensus        11 L~~~Gy~y~~~~~~------~~~~~WrC~~~~~~~C~a~~~~~--~-~~~~~-~~~~~~HnH   62 (62)
T PF04500_consen   11 LVYDGYRYYFNKRN------DGKTYWRCSRRRSHGCRARLITD--A-GDGRV-VRTNGEHNH   62 (62)
T ss_dssp             EEETTEEEEEEEE-------SS-EEEEEGGGTTS----EEEEE-----TTEE-EE-S---SS
T ss_pred             EEECCeEEECcCCC------CCcEEEEeCCCCCCCCeEEEEEE--C-CCCEE-EECCCccCC
Confidence            45677776655444      34589999986   599987776  2 22333 334599998

Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. C2H2-type (classical) zinc fingers (Znf) were the first class to be characterised. They contain a short beta hairpin and an alpha helix (beta/beta/alpha structure), where a single zinc atom is held in place by Cys(2)His(2) (C2H2) residues in a tetrahedral array. C2H2 Znf's can be divided into three groups based on the number and pattern of fingers: triple-C2H2 (binds single ligand), multiple-adjacent-C2H2 (binds multiple ligands), and separated paired-C2H2 []. C2H2 Znf's are the most common DNA-binding motifs found in eukaryotic transcription factors, and have also been identified in prokaryotes []. Transcription factors usually contain several Znf's (each with a conserved beta/beta/alpha structure) capable of making multiple contacts along the DNA, where the C2H2 Znf motifs recognise DNA sequences by binding to the major groove of DNA via a short alpha-helix in the Znf, the Znf spanning 3-4 bases of the DNA []. C2H2 Znf's can also bind to RNA and protein targets []. This entry represents a potential FLYWCH Zn-finger domain found in a number of eukaryotic proteins. FLYWCH is a C2H2-type zinc finger characterised by five conserved hydrophobic residues, containing the conserved sequence motif: F/Y-X(n)-L-X(n)-F/Y-X(n)-WXCX(6-12)CX(17-22)HXH where X indicates any amino acid. This domain was first characterised in Drosophila Modifier of mdg4 proteins, Mod(mgd4), putative chromatin modulators involved in higher order chromatin domains. Mod(mdg4) proteins share a common N-terminal BTB/POZ domain, but differ in their C-terminal region, most containing C-terminal FLYWCH zinc finger motifs []. The FLYWCH domain in Mod(mdg4) proteins has a putative role in protein-protein interactions; for example, Mod(mdg4)-67.2 interacts with DNA-binding protein Su(Hw) via its FLYWCH domain. FLYWCH domains have been described in other proteins as well, including suppressor of killer of prune, Su(Kpn), which contains 4 terminal FLYWCH zinc finger motifs in a tandem array and a C-terminal glutathione SH-transferase (GST) domain []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 2RPR_A.

>PF03101 FAR1: FAR1 DNA-binding domain; InterPro: IPR004330 Phytochrome A is the primary photoreceptor for mediating various far-red light-induced responses in higher plants

Probab=85.59  E-value=0.51  Score=30.87  Aligned_cols=30  Identities=17%  Similarity=0.126  Sum_probs=25.1

Q ss_pred             cccchhhhhhccCCCCeEEEEEeccCCCCCC
Q 033576           41 SCMAKKRAEWCTSDPTNVRIVYDGVHSHTHH   71 (116)
Q Consensus        41 ~C~akK~Vqr~~~d~~~~~vtY~G~H~h~~p   71 (116)
                      +|+|+=.|-+.. |+...++.+..+|||+.-
T Consensus        61 gC~a~i~v~~~~-~~~w~v~~~~~~HNH~L~   90 (91)
T PF03101_consen   61 GCKARINVKRRK-DGKWRVTSFVLEHNHPLC   90 (91)
T ss_pred             CCCEEEEEEEcc-CCEEEEEECcCCcCCCCC
Confidence            499988888776 788888899999999863

It has been found that the proteins governing this response, which include FAR-RED ELONGATED HYPOCOTYL3 (FHY3) and FAR-RED-IMPAIRED RESPONSE1 (FAR1), are a pair of homologous proteins sharing significant sequence homology to mutator-like transposases. These proteins appear to be novel transcription factors, which are essential for activating the expression of FHY1 and FHL (for FHY1-like) and related genes, whose products are required for light-induced phytochrome A nuclear accumulation and subsequent light responses in plants. The FRS (FAR1 Related Sequences) family of proteins share a similar domain structure to mutator-like transposases, including an N-terminal C2H2 zinc finger domain, a central putative core transposase domain, and a C-terminal SWIM motif (named after SWI2/SNF and MuDR transposases). It seems plausible that the FRS family represent transcription factors derived from mutator-like transposases [, ]. This entry represents a domain found in FAR1 and FRS proteins. It contains a WRKY like fold and is therefore most likely a zinc binding DNA-binding domain.

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Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	116
1wj2_A	78	Solution Structure Of The C-Terminal Wrky Domain Of		2e-08
2ayd_A	76	Crystal Structure Of The C-Terminal Wrky Domainof A		4e-06

>pdb|1WJ2|A Chain A, Solution Structure Of The C-Terminal Wrky Domain Of Atwrky4 Length = 78

Iteration: 1
 Score = 53.9 bits (128), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 24/55 (43%), Positives = 31/55 (56%)
Query: 10 LPEDGYEWKKYGQKFIKNIRKFRSYFKCQESSCMAKKRAEWCTSDPTNVRIVYDG 64
          L +DGY W+KYGQK +K     RSY+KC    C  +K  E   +DP  V   Y+G
Sbjct: 16 LLDDGYRWRKYGQKVVKGNPYPRSYYKCTTPGCGVRKHVERAATDPKAVVTTYEG 70

>pdb|2AYD|A Chain A, Crystal Structure Of The C-Terminal Wrky Domainof Atwrky1, An Sa-Induced And Partially Npr1-Dependent Transcription Factor Length = 76

Iteration: 1
 Score = 46.6 bits (109), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 21/52 (40%), Positives = 28/52 (53%)
Query: 13 DGYEWKKYGQKFIKNIRKFRSYFKCQESSCMAKKRAEWCTSDPTNVRIVYDG 64
          DGY W+KYGQK +K     RSY++C    C  KK  E  + D   +   Y+G
Sbjct: 16 DGYRWRKYGQKSVKGSPYPRSYYRCSSPGCPVKKHVERSSHDTKLLITTYEG 67

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	116
1wj2_A	78	Probable WRKY transcription factor 4; DNA-binding	3e-19
2ayd_A	76	WRKY transcription factor 1; beta strands, zinc fi	4e-19

>1wj2_A Probable WRKY transcription factor 4; DNA-binding domain, zinc-binding, structural genomics; NMR {Arabidopsis thaliana} SCOP: g.79.1.1 PDB: 2lex_A* Length = 78

 Score = 74.4 bits (183), Expect = 3e-19
 Identities = 26/59 (44%), Positives = 34/59 (57%)

Query: 10 LPEDGYEWKKYGQKFIKNIRKFRSYFKCQESSCMAKKRAEWCTSDPTNVRIVYDGVHSH 68
          L +DGY W+KYGQK +K     RSY+KC    C  +K  E   +DP  V   Y+G H+H
Sbjct: 16 LLDDGYRWRKYGQKVVKGNPYPRSYYKCTTPGCGVRKHVERAATDPKAVVTTYEGKHNH 74

>2ayd_A WRKY transcription factor 1; beta strands, zinc finger; 1.60A {Arabidopsis thaliana} Length = 76

 Score = 74.0 bits (182), Expect = 4e-19
 Identities = 23/59 (38%), Positives = 31/59 (52%)

Query: 10 LPEDGYEWKKYGQKFIKNIRKFRSYFKCQESSCMAKKRAEWCTSDPTNVRIVYDGVHSH 68
          +  DGY W+KYGQK +K     RSY++C    C  KK  E  + D   +   Y+G H H
Sbjct: 13 IVNDGYRWRKYGQKSVKGSPYPRSYYRCSSPGCPVKKHVERSSHDTKLLITTYEGKHDH 71

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	116
2ayd_A	76	WRKY transcription factor 1; beta strands, zinc fi	100.0
1wj2_A	78	Probable WRKY transcription factor 4; DNA-binding	100.0

>2ayd_A WRKY transcription factor 1; beta strands, zinc finger; 1.60A {Arabidopsis thaliana}

Probab=100.00  E-value=6e-39  Score=215.01  Aligned_cols=68  Identities=34%  Similarity=0.646  Sum_probs=65.5

Q ss_pred             ccccCCCCCCchhhhhccccccCCCCCCCccccccccccchhhhhhccCCCCeEEEEEeccCCCCCCC
Q 033576            5 VHRLVLPEDGYEWKKYGQKFIKNIRKFRSYFKCQESSCMAKKRAEWCTSDPTNVRIVYDGVHSHTHHG   72 (116)
Q Consensus         5 ~~~~~~~~DGy~WRKYGQK~ikg~~~pR~YyrCt~~~C~akK~Vqr~~~d~~~~~vtY~G~H~h~~p~   72 (116)
                      .+++++++|||.|||||||.|||++|||+||||++.+|+|+|+|||+++|+.+|+|||+|+|||+.|.
T Consensus         8 ~~~~~~~~DGy~WRKYGQK~ikgs~~PRsYYrCt~~gC~a~K~Ver~~~d~~~~~~tY~G~H~H~~p~   75 (76)
T 2ayd_A            8 QTLFDIVNDGYRWRKYGQKSVKGSPYPRSYYRCSSPGCPVKKHVERSSHDTKLLITTYEGKHDHDMPP   75 (76)
T ss_dssp             ECSSSCCCCSSCEEEEEEECCTTCSSCEEEEEECSTTCCCEEEEEECSSSTTEEEEEEESCCSSCCCC
T ss_pred             cCCCCcCCCCchhhhCcccccCCCCCceeEeEcCCCCCCceeeEEEECCCCCEEEEEEccCcCCCCCC
Confidence            46788999999999999999999999999999999999999999999999999999999999999886

>1wj2_A Probable WRKY transcription factor 4; DNA-binding domain, zinc-binding, structural genomics; NMR {Arabidopsis thaliana} SCOP: g.79.1.1 PDB: 2lex_A*

Probab=100.00  E-value=1.3e-38  Score=214.31  Aligned_cols=69  Identities=38%  Similarity=0.742  Sum_probs=65.6

Q ss_pred             cccccCCCCCCchhhhhccccccCCCCCCCccccccccccchhhhhhccCCCCeEEEEEeccCCCCCCC
Q 033576            4 RVHRLVLPEDGYEWKKYGQKFIKNIRKFRSYFKCQESSCMAKKRAEWCTSDPTNVRIVYDGVHSHTHHG   72 (116)
Q Consensus         4 ~~~~~~~~~DGy~WRKYGQK~ikg~~~pR~YyrCt~~~C~akK~Vqr~~~d~~~~~vtY~G~H~h~~p~   72 (116)
                      ..+++++++|||.|||||||.|||++|||+||||++++|+|+|+|||+.+|+.+|+|||+|+|||+.|.
T Consensus        10 t~s~~~~~dDGy~WRKYGQK~ikgs~~PRsYYrCt~~gC~a~K~Ver~~~d~~~~~~tY~G~H~H~~p~   78 (78)
T 1wj2_A           10 TTSEVDLLDDGYRWRKYGQKVVKGNPYPRSYYKCTTPGCGVRKHVERAATDPKAVVTTYEGKHNHDLPA   78 (78)
T ss_dssp             CCCCCCCCCSSSCBCCCEEECCTTCSSCEEEEEEECSSCEEEEEEEEETTTTSEEEEEEESCCSSCCCC
T ss_pred             ccCCCCcCCCCchhhhCcccccCCCcCeeEEeecCcCCCCcEeeEEEEcCCCCEEEEEEeeEcCCCCCC
Confidence            447788999999999999999999999999999999999999999999999999999999999999874

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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	116
d1wj2a_	71	g.79.1.1 (A:) WRKY DNA-binding protein 4 {Thale cr	3e-20

>d1wj2a_ g.79.1.1 (A:) WRKY DNA-binding protein 4 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]} Length = 71

class: Small proteins
fold: WRKY DNA-binding domain
superfamily: WRKY DNA-binding domain
family: WRKY DNA-binding domain
domain: WRKY DNA-binding protein 4
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

 Score = 75.6 bits (186), Expect = 3e-20
 Identities = 26/59 (44%), Positives = 34/59 (57%)

Query: 10 LPEDGYEWKKYGQKFIKNIRKFRSYFKCQESSCMAKKRAEWCTSDPTNVRIVYDGVHSH 68
          L +DGY W+KYGQK +K     RSY+KC    C  +K  E   +DP  V   Y+G H+H
Sbjct: 9  LLDDGYRWRKYGQKVVKGNPYPRSYYKCTTPGCGVRKHVERAATDPKAVVTTYEGKHNH 67

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	116
d1wj2a_	71	WRKY DNA-binding protein 4 {Thale cress (Arabidops	100.0

>d1wj2a_ g.79.1.1 (A:) WRKY DNA-binding protein 4 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}

class: Small proteins
fold: WRKY DNA-binding domain
superfamily: WRKY DNA-binding domain
family: WRKY DNA-binding domain
domain: WRKY DNA-binding protein 4
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=100.00  E-value=8.3e-40  Score=215.06  Aligned_cols=70  Identities=37%  Similarity=0.739  Sum_probs=66.4

Q ss_pred             ccccccCCCCCCchhhhhccccccCCCCCCCccccccccccchhhhhhccCCCCeEEEEEeccCCCCCCC
Q 033576            3 RRVHRLVLPEDGYEWKKYGQKFIKNIRKFRSYFKCQESSCMAKKRAEWCTSDPTNVRIVYDGVHSHTHHG   72 (116)
Q Consensus         3 r~~~~~~~~~DGy~WRKYGQK~ikg~~~pR~YyrCt~~~C~akK~Vqr~~~d~~~~~vtY~G~H~h~~p~   72 (116)
                      +..+++++++|||.|||||||.|+|++|||+||||++++|+|+|+|||+++|+.+|+|||+|+|||+.|.
T Consensus         2 ~t~~~~~~~dDGy~WRKYGQK~ikgs~~pRsYYrCt~~~C~a~K~Vqr~~~d~~~~~vtY~G~H~h~~Ps   71 (71)
T d1wj2a_           2 QTTSEVDLLDDGYRWRKYGQKVVKGNPYPRSYYKCTTPGCGVRKHVERAATDPKAVVTTYEGKHNHDLPA   71 (71)
T ss_dssp             CCCCCCCCCCSSSCBCCCEEECCTTCSSCEEEEEEECSSCEEEEEEEEETTTTSEEEEEEESCCSSCCCC
T ss_pred             ccccccccCCCCcEecccCceeccCCCCceEEEEccccCCCCcceEEEEcCCCCEEEEEEeeEeCCCCCC
Confidence            3567889999999999999999999999999999999999999999999999999999999999998874