Citrus Sinensis ID: 030419

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------
Protein Sequence
MEFDSEEAAKIFYDEYARRVGFVMRVMSCRRSERDGRILARRLGCNKEGYCVSIRGKFGPVRKPRPSTREGCKAMIHVKFDKSGKWVITKFVKEHNHPLVVAPREARQTMDEKDKKIQELTVELRNKKRLCALYQEQLTTFMKVVEVHSDHLSKKVQNVINNLKEFESIEKELSRNR
Secondary Structure (PSIPRED)
cccccHHHHHHHHHHHHHHcccEEEEcEEEEccccccEEEEEEEEEcccEEEcccccccccccccccccccccEEEEEEEccccEEEEEEEcccccccccccccccccccHHHHHHHHHHHHHHHHHHHHccccHHHHHHHHHHHHcccccccccHHHHHHHHHHHHHHHHHHHHcc
Secondary Structure Prediction (SSPRO)
cccccHHHHHHHHHHHHHHcccEEEEEEEEcEccccEEEEEEEEEccccccccccccccccccccccccccccEEEEEEEcccccEEEEEEEHHccccccccccccccccHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccc
Coil and Loop (DISEMBL)
MEFDSEEAAKIFYDEYARRVGFVMRVMSCRRSERDGRILARRLgcnkegycvsirgkfgpvrkprpstregCKAMIHVKFDKSGKWVITKFVKehnhplvvaprearqtmDEKDKKIQELTVELRNKKRLCALYQEQLTTFMKVVEVHSDHLSKKVQNVINNLKEFESIEKELSRNR
Flexible Loop (DISEMBL)
mefdseeaakifydeyarrvGFVMRVMscrrserdgrilarrlgcnkegycvsirgkfgpvrkprpstregcKAMIHVKFDKSGKWVITKFvkehnhplvvaprearqtmdekDKKIQELTVELRNKKRLCALYQEQLTTFMKVVEVHSDHLSKKVQNVINnlkefesiekelsrnr
Low Complexity Region (SEG)
MEFDSEEAAKIFYDEYARRVGFVMRVMSCRRSERDGRILARRLGCNKEGYCVSIRGKFGPVRKPRPSTREGCKAMIHVKFDKSGKWVITKFVKEHNHPLVVAPREARQTMDEKDKKIQELTVELRNKKRLCALYQEQLTTFMKVVEVHSDHLSKKVQNVINNLKEFESIEKELSRNR
Disordered region (IsUnstruct)
********AKIFYDEYARRVGFVMRVMSCRRSERDGRILARRLGCNKEGYCVSIRGKFGPV********EGCKAMIHVKFDKSGKWVITKFVKEHNHPLVVA****************ELTVELRNKKRLCALYQEQLTTFMKVVEVHSDHLSKKVQNVINNL**************
Disordered Region (DISOPRED)
MEFDSEEAAKIFYDEYARRVGFVMRVMSCRRSERDGRILARRLGCNKEGYCVSIRGKFGPVRKPRPSTREGCKAMIHVKFDKSGKWVITKFVKEHNHPLVVAPREARQTMDE******************************KVVEVHSDHLSKKVQNVINNLK*************
Disordered Region (DISEMBL)
MEFDSEEAAKIFYDEYARRVGFVMRVMSCRRSERDGRILARRLGCNKEGYCVSIRGKFGPV********EGCKAMIHVKFDKSGKWVITKFVKEHNHPLVVAPREARQTMDEKDKKIQELTVELRNKKRLCALYQEQLTTFMKVVEVHSDHLSKKVQNVINNLKEFES*********
Disordered Region (DISPRO)
****SEEAAKIFYDEYARRVGFVMRVMSCRRSERDGRILARRLGCNKE*******************TREGCKAMIHVKFDKSGKWVITKFVKEHNHPLVVAPREARQTMDEKDKKIQELTVELRNKKRLCALYQEQLTTFMKVVEVHSDHLSKKVQNVINNLKEFESIEKE*****
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
oooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MEFDSEEAAKIFYDEYARRVGFVMRVMSCRRSERDGRILARRLGCNKEGYCVSIRGKFGPVRKPRPSTREGCKAMIHVKFDKSGKWVITKFVKEHNHPLVVAPREARQTxxxxxxxxxxxxxxxxxxxxxxxxxxxxLTTFMKVVEVHSDHLSKKxxxxxxxxxxxxxxxxxxxxxR
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	177	2.2.26 [Sep-21-2011]
Q9SZL8	788	Protein FAR1-RELATED SEQU	no	no	0.564	0.126	0.539	9e-20
Q3EBQ3	807	Protein FAR1-RELATED SEQU	no	no	0.655	0.143	0.385	7e-16
Q9M8J3	764	Protein FAR1-RELATED SEQU	no	no	0.536	0.124	0.376	7e-14
Q3E7I5	788	Protein FAR1-RELATED SEQU	no	no	0.480	0.107	0.393	1e-13
Q6NQJ7	732	Protein FAR1-RELATED SEQU	no	no	0.564	0.136	0.386	2e-13
Q9SWG3	827	Protein FAR-RED IMPAIRED	no	no	0.570	0.122	0.362	1e-12
Q5UBY2	687	Protein FAR1-RELATED SEQU	no	no	0.581	0.149	0.327	2e-11
Q9LIE5	839	Protein FAR-RED ELONGATED	no	no	0.615	0.129	0.355	3e-11
Q9ZVC9	851	Protein FAR1-RELATED SEQU	no	no	0.474	0.098	0.35	3e-10
Q9S793	725	Protein FAR1-RELATED SEQU	no	no	0.508	0.124	0.333	7e-07

>sp|Q9SZL8|FRS5_ARATH Protein FAR1-RELATED SEQUENCE 5 OS=Arabidopsis thaliana GN=FRS5 PE=2 SV=1

 Score = 96.3 bits (238), Expect = 9e-20,   Method: Compositional matrix adjust.
 Identities = 55/102 (53%), Positives = 70/102 (68%), Gaps = 2/102 (1%)

Query: 1   MEFDSEEAAKIFYDEYARRVGFVMRVMSCRRSERDGRILARRLGCNKEGY--CVSIRGKF 58
           +EF+SEEAAK FY+ YARR+GF  RV S RRS RDG I+ R+  C KEG+      R K 
Sbjct: 77  LEFESEEAAKAFYNSYARRIGFSTRVSSSRRSRRDGAIIQRQFVCAKEGFRNMNEKRTKD 136

Query: 59  GPVRKPRPSTREGCKAMIHVKFDKSGKWVITKFVKEHNHPLV 100
             +++PR  TR GCKA + VK   SGKW+++ FVK+HNH LV
Sbjct: 137 REIKRPRTITRVGCKASLSVKMQDSGKWLVSGFVKDHNHELV 178

Putative transcription activator involved in regulating light control of development.
Arabidopsis thaliana (taxid: 3702)

>sp|Q3EBQ3|FRS2_ARATH Protein FAR1-RELATED SEQUENCE 2 OS=Arabidopsis thaliana GN=FRS2 PE=2 SV=1

 Score = 83.2 bits (204), Expect = 7e-16,   Method: Compositional matrix adjust.
 Identities = 47/122 (38%), Positives = 72/122 (59%), Gaps = 6/122 (4%)

Query: 1   MEFDSEEAAKIFYDEYARRVGFVMRVMSCRRSERDGRILARRLGCNKEGYCVSIRGKFGP 60
           M+F+S+EAA  FY EYAR VGF + + + RRS+R G+ +  ++ C++ G   + R K   
Sbjct: 42  MDFESKEAAYYFYREYARSVGFGITIKASRRSKRSGKFIDVKIACSRFG---TKREKATA 98

Query: 61  VRKPRPSTREGCKAMIHVKFDKSGKWVITKFVKEHNHPLVVAPREARQTMDEKDKKIQEL 120
           +  PR   + GCKA +H+K  +  KWVI  FVKEHNH   + P +   ++  K+K    L
Sbjct: 99  I-NPRSCPKTGCKAGLHMKRKEDEKWVIYNFVKEHNHE--ICPDDFYVSVRGKNKPAGAL 155

Query: 121 TV 122
            +
Sbjct: 156 AI 157

Putative transcription activator involved in regulating light control of development.

Arabidopsis thaliana (taxid: 3702)

>sp|Q9M8J3|FRS7_ARATH Protein FAR1-RELATED SEQUENCE 7 OS=Arabidopsis thaliana GN=FRS7 PE=2 SV=1

 Score = 77.0 bits (188), Expect = 7e-14,   Method: Compositional matrix adjust.
 Identities = 41/109 (37%), Positives = 59/109 (54%), Gaps = 14/109 (12%)

Query: 1   MEFDSEEAAKIFYDEYARRVGFVMRVMSCRRSERDGRILARRLGCNKEGYCVSIRGKFGP 60
           +EFD+ E A+ +Y+ YA R GF +R     RS  DG + +RR  C+KEG+ +        
Sbjct: 32  LEFDTAEEARDYYNSYATRTGFKVRTGQLYRSRTDGTVSSRRFVCSKEGFQL-------- 83

Query: 61  VRKPRPSTREGCKAMIHVKFDKSGKWVITKFVKEHNHPLVVAPREARQT 109
                 ++R GC A I V+   +GKWV+ +  KEHNH L     EA+ T
Sbjct: 84  ------NSRTGCPAFIRVQRRDTGKWVLDQIQKEHNHDLGGHIEEAQTT 126

Putative transcription activator involved in regulating light control of development.

Arabidopsis thaliana (taxid: 3702)

>sp|Q3E7I5|FRS12_ARATH Protein FAR1-RELATED SEQUENCE 12 OS=Arabidopsis thaliana GN=FRS12 PE=2 SV=1

 Score = 75.9 bits (185), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 39/99 (39%), Positives = 55/99 (55%), Gaps = 14/99 (14%)

Query: 1   MEFDSEEAAKIFYDEYARRVGFVMRVMSCRRSERDGRILARRLGCNKEGYCVSIRGKFGP 60
           +EFD+ E A+ FY+ YA R GF +R     RS  DG + +RR  C+KEG+ +        
Sbjct: 47  LEFDTAEEAREFYNAYAARTGFKVRTGQLYRSRTDGTVSSRRFVCSKEGFQL-------- 98

Query: 61  VRKPRPSTREGCKAMIHVKFDKSGKWVITKFVKEHNHPL 99
                 ++R GC A I V+   +GKWV+ +  KEHNH L
Sbjct: 99  ------NSRTGCTAFIRVQRRDTGKWVLDQIQKEHNHEL 131

Putative transcription activator involved in regulating light control of development.

Arabidopsis thaliana (taxid: 3702)

>sp|Q6NQJ7|FRS4_ARATH Protein FAR1-RELATED SEQUENCE 4 OS=Arabidopsis thaliana GN=FRS4 PE=2 SV=2

 Score = 75.5 bits (184), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 41/106 (38%), Positives = 57/106 (53%), Gaps = 6/106 (5%)

Query: 1   MEFDSEEAAKIFYDEYARRVGFVMRVMSCRRSERDGRILARRLGCNKEGYCVSIRGKFGP 60
           MEF++ E A +FY +YA+ VGF    +S RRS      +  +  C + G     + +   
Sbjct: 1   MEFETHEDAYLFYKDYAKSVGFGTAKLSSRRSRASKEFIDAKFSCIRYG----SKQQSDD 56

Query: 61  VRKPRPSTREGCKAMIHVKFDKSGKWVITKFVKEHNHPLVVAPREA 106
              PR S + GCKA +HVK    GKW +  FVKEHNH L+  P +A
Sbjct: 57  AINPRASPKIGCKASMHVKRRPDGKWYVYSFVKEHNHDLL--PEQA 100

Putative transcription activator involved in regulating light control of development.

Arabidopsis thaliana (taxid: 3702)

>sp|Q9SWG3|FAR1_ARATH Protein FAR-RED IMPAIRED RESPONSE 1 OS=Arabidopsis thaliana GN=FAR1 PE=1 SV=1

 Score = 72.8 bits (177), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 37/102 (36%), Positives = 57/102 (55%), Gaps = 1/102 (0%)

Query: 1   MEFDSEEAAKIFYDEYARRVGFVMRVMSCRRSERDGRILARRLGCNKEGYCVSIRGKFGP 60
           ++FD+ EAA IFY EYA+ +GF   + + RRS++    +  +  C++ G         G 
Sbjct: 55  IDFDTHEAAYIFYQEYAKSMGFTTSIKNSRRSKKTKDFIDAKFACSRYG-VTPESESSGS 113

Query: 61  VRKPRPSTREGCKAMIHVKFDKSGKWVITKFVKEHNHPLVVA 102
             +     +  CKA +HVK    GKW+I +FVK+HNH L+ A
Sbjct: 114 SSRRSTVKKTDCKASMHVKRRPDGKWIIHEFVKDHNHELLPA 155

Transcription activator that recognizes and binds to the DNA consensus sequence 5'-CACGCGC-3'. Activates the expression of FHY1 and FHL involved in light responses.

Arabidopsis thaliana (taxid: 3702)

>sp|Q5UBY2|FRS1_ARATH Protein FAR1-RELATED SEQUENCE 1 OS=Arabidopsis thaliana GN=FRS1 PE=1 SV=1

 Score = 68.6 bits (166), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 39/119 (32%), Positives = 59/119 (49%), Gaps = 16/119 (13%)

Query: 2   EFDSEEAAKIFYDEYARRVGFVMRVMSCRRSERDGRILARRLGCNK-------------- 47
           EF+S+E A  FY EYA  VGF   + + RRS   G+ +  +  C +              
Sbjct: 26  EFESKEEAFEFYKEYANSVGFTTIIKASRRSRMTGKFIDAKFVCTRYGSKKEDIDTGLGT 85

Query: 48  EGYCVSIRGKFGPVRKPRPSTREGCKAMIHVKFDKSGKWVITKFVKEHNHPLVVAPREA 106
           +G+ +    K G  R  R S++  CKA +HVK  + G+WV+   VKEHNH +     ++
Sbjct: 86  DGFNIPQARKRG--RINRSSSKTDCKAFLHVKRRQDGRWVVRSLVKEHNHEIFTGQADS 142

Putative transcription activator involved in regulating light control of development.

Arabidopsis thaliana (taxid: 3702)

>sp|Q9LIE5|FHY3_ARATH Protein FAR-RED ELONGATED HYPOCOTYL 3 OS=Arabidopsis thaliana GN=FHY3 PE=1 SV=1

 Score = 68.2 bits (165), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 43/121 (35%), Positives = 57/121 (47%), Gaps = 12/121 (9%)

Query: 1   MEFDSEEAAKIFYDEYARRVGFVMRVMSCRRSERDGRILARRLGCNKEGYCVSIRGKFGP 60
           MEF+S   A  FY EY+R +GF   + + RRS+     +  +  C++ G        F  
Sbjct: 74  MEFESHGEAYSFYQEYSRAMGFNTAIQNSRRSKTTREFIDAKFACSRYGTKREYDKSFNR 133

Query: 61  VR----KPRPSTREG--------CKAMIHVKFDKSGKWVITKFVKEHNHPLVVAPREARQ 108
            R    K  P    G        CKA +HVK    GKWVI  FV+EHNH L+ A   + Q
Sbjct: 134 PRARQSKQDPENMAGRRTCAKTDCKASMHVKRRPDGKWVIHSFVREHNHELLPAQAVSEQ 193

Query: 109 T 109
           T
Sbjct: 194 T 194

Transcription activator that recognizes and binds to the DNA consensus sequence 5'-CACGCGC-3'. Activates the expression of FHY1 and FHL involved in light responses. When associated with PHYA, protects it from being recognized and degraded by the COP1/SPA complex.

Arabidopsis thaliana (taxid: 3702)

>sp|Q9ZVC9|FRS3_ARATH Protein FAR1-RELATED SEQUENCE 3 OS=Arabidopsis thaliana GN=FRS3 PE=2 SV=2

 Score = 64.7 bits (156), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 35/100 (35%), Positives = 52/100 (52%), Gaps = 16/100 (16%)

Query: 1   MEFDSEEAAKIFYDEYARRVGFVMRVMSCRRSERDGRILARRLGCNKEGYCVSIRGKFGP 60
           MEF+SE+ AK FYDEY+R++GF  +++       DG +  R   C+              
Sbjct: 53  MEFNSEKEAKSFYDEYSRQLGFTSKLLP----RTDGSVSVREFVCSSS------------ 96

Query: 61  VRKPRPSTREGCKAMIHVKFDKSGKWVITKFVKEHNHPLV 100
            ++ +    E C AM+ ++     KWV+TKFVKEH H L 
Sbjct: 97  SKRSKRRLSESCDAMVRIELQGHEKWVVTKFVKEHTHGLA 136

Putative transcription activator involved in regulating light control of development.

Arabidopsis thaliana (taxid: 3702)

>sp|Q9S793|FRS8_ARATH Protein FAR1-RELATED SEQUENCE 8 OS=Arabidopsis thaliana GN=FRS8 PE=2 SV=2

 Score = 53.5 bits (127), Expect = 7e-07,   Method: Compositional matrix adjust.
 Identities = 33/99 (33%), Positives = 52/99 (52%), Gaps = 9/99 (9%)

Query: 1   MEFDSEEAAKIFYDEYARRVGFVMRVMS--CRRSERDGRILARRLGCNKEGYCVSIRGKF 58
           MEF+S + A  FY+ YAR +GF +RV S   +R+ ++ R     L CN +G+ +      
Sbjct: 99  MEFESYDDAYSFYNSYARELGFAIRVKSSWTKRNSKEKR--GAVLCCNCQGFKL-----L 151

Query: 59  GPVRKPRPSTREGCKAMIHVKFDKSGKWVITKFVKEHNH 97
                 R  TR GC+AMI ++     +W + +   +HNH
Sbjct: 152 KDAHSRRKETRTGCQAMIRLRLIHFDRWKVDQVKLDHNH 190

Putative transcription activator involved in regulating light control of development. May have a role in controlling flowering time.

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	177
255585325	225	conserved hypothetical protein [Ricinus	1.0	0.786	0.875	2e-87
224132740	185	predicted protein [Populus trichocarpa]	0.977	0.935	0.884	1e-86
449437613	227	PREDICTED: protein FAR1-RELATED SEQUENCE	1.0	0.779	0.853	2e-86
449520738	227	PREDICTED: LOW QUALITY PROTEIN: protein	1.0	0.779	0.841	2e-85
356517812	241	PREDICTED: protein FAR1-RELATED SEQUENCE	0.977	0.717	0.843	4e-83
356508152	241	PREDICTED: protein FAR1-RELATED SEQUENCE	0.994	0.730	0.829	7e-83
297824305	206	far-red impaired responsive family prote	1.0	0.859	0.785	4e-81
30689328	206	far-red impaired responsive 1-like prote	0.988	0.849	0.788	3e-80
2289005	171	hypothetical protein [Arabidopsis thalia	0.943	0.976	0.790	2e-76
147864082	240	hypothetical protein VITISV_030389 [Viti	0.949	0.7	0.619	5e-54

>gi|255585325|ref|XP_002533360.1| conserved hypothetical protein [Ricinus communis] gi|223526800|gb|EEF29022.1| conserved hypothetical protein [Ricinus communis]

 Score =  326 bits (835), Expect = 2e-87,   Method: Compositional matrix adjust.
 Identities = 155/177 (87%), Positives = 168/177 (94%)

Query: 1   MEFDSEEAAKIFYDEYARRVGFVMRVMSCRRSERDGRILARRLGCNKEGYCVSIRGKFGP 60
           MEF+SE+AAKIFYDEYARRVGFVMRVMSCRRSERDGRILARRLGCNKEGYCVS+RGKFG 
Sbjct: 49  MEFESEDAAKIFYDEYARRVGFVMRVMSCRRSERDGRILARRLGCNKEGYCVSVRGKFGN 108

Query: 61  VRKPRPSTREGCKAMIHVKFDKSGKWVITKFVKEHNHPLVVAPREARQTMDEKDKKIQEL 120
           VRKPR STREGCKAMIHVKFDKSGKWVITKFVK+HNHPLVVAPREARQTMDEKDK+IQEL
Sbjct: 109 VRKPRASTREGCKAMIHVKFDKSGKWVITKFVKDHNHPLVVAPREARQTMDEKDKRIQEL 168

Query: 121 TVELRNKKRLCALYQEQLTTFMKVVEVHSDHLSKKVQNVINNLKEFESIEKELSRNR 177
           T+ELRNKKRLCA YQ+QLT FMK+VE HS  LSKKVQ+V+ NLKEFESIE+EL ++R
Sbjct: 169 TMELRNKKRLCATYQDQLTAFMKIVEEHSVQLSKKVQDVVRNLKEFESIEQELMQHR 225

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224132740|ref|XP_002327869.1| predicted protein [Populus trichocarpa] gi|222837278|gb|EEE75657.1| predicted protein [Populus trichocarpa]

 Score =  323 bits (829), Expect = 1e-86,   Method: Compositional matrix adjust.
 Identities = 153/173 (88%), Positives = 165/173 (95%)

Query: 1   MEFDSEEAAKIFYDEYARRVGFVMRVMSCRRSERDGRILARRLGCNKEGYCVSIRGKFGP 60
           MEF+SE+AAKIFYDEYARR+GFVMRVMSCRRSERDGRILARRLGCNKEGYCVSIRGKFG 
Sbjct: 9   MEFESEDAAKIFYDEYARRIGFVMRVMSCRRSERDGRILARRLGCNKEGYCVSIRGKFGN 68

Query: 61  VRKPRPSTREGCKAMIHVKFDKSGKWVITKFVKEHNHPLVVAPREARQTMDEKDKKIQEL 120
           VRKPRPSTREGCKAMIHVKFDKSGKWVITKFVK+HNHPLVVAPREARQT+DEKDKKIQEL
Sbjct: 69  VRKPRPSTREGCKAMIHVKFDKSGKWVITKFVKDHNHPLVVAPREARQTLDEKDKKIQEL 128

Query: 121 TVELRNKKRLCALYQEQLTTFMKVVEVHSDHLSKKVQNVINNLKEFESIEKEL 173
           T ELRNKKRLCA YQEQL+ F+K+VE HS+ LSKKV+N + NLKEFESIE+EL
Sbjct: 129 TAELRNKKRLCATYQEQLSAFVKIVEDHSEKLSKKVKNAVENLKEFESIEQEL 181

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449437613|ref|XP_004136586.1| PREDICTED: protein FAR1-RELATED SEQUENCE 5-like [Cucumis sativus]

 Score =  322 bits (826), Expect = 2e-86,   Method: Compositional matrix adjust.
 Identities = 151/177 (85%), Positives = 167/177 (94%)

Query: 1   MEFDSEEAAKIFYDEYARRVGFVMRVMSCRRSERDGRILARRLGCNKEGYCVSIRGKFGP 60
           MEF+SE+AAKIFYD+YAR++GFVMRVMSCRRSE+DGRILARRLGCNKEG+CVSIRGKFG 
Sbjct: 51  MEFESEDAAKIFYDKYARQLGFVMRVMSCRRSEKDGRILARRLGCNKEGHCVSIRGKFGA 110

Query: 61  VRKPRPSTREGCKAMIHVKFDKSGKWVITKFVKEHNHPLVVAPREARQTMDEKDKKIQEL 120
           VRKPRPSTREGCKAMIHVK+DKSGKWVITKFVKEHNHPLVV+PREARQTMDEKDK+IQEL
Sbjct: 111 VRKPRPSTREGCKAMIHVKYDKSGKWVITKFVKEHNHPLVVSPREARQTMDEKDKQIQEL 170

Query: 121 TVELRNKKRLCALYQEQLTTFMKVVEVHSDHLSKKVQNVINNLKEFESIEKELSRNR 177
           T+ELRNKKRLC+ YQEQL  FMK+VE H+D LSKKVQNV+ NLKEFESIE+EL   R
Sbjct: 171 TIELRNKKRLCSTYQEQLAAFMKIVEEHTDQLSKKVQNVVTNLKEFESIEQELLHPR 227

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449520738|ref|XP_004167390.1| PREDICTED: LOW QUALITY PROTEIN: protein FAR1-RELATED SEQUENCE 5-like [Cucumis sativus]

 Score =  320 bits (819), Expect = 2e-85,   Method: Compositional matrix adjust.
 Identities = 149/177 (84%), Positives = 166/177 (93%)

Query: 1   MEFDSEEAAKIFYDEYARRVGFVMRVMSCRRSERDGRILARRLGCNKEGYCVSIRGKFGP 60
           MEF+SE+AAKIFYD+YAR++GFVMRVMSCRRSE+DGRILARRLGCNKEG+CVSIRGKFG 
Sbjct: 51  MEFESEDAAKIFYDKYARQLGFVMRVMSCRRSEKDGRILARRLGCNKEGHCVSIRGKFGA 110

Query: 61  VRKPRPSTREGCKAMIHVKFDKSGKWVITKFVKEHNHPLVVAPREARQTMDEKDKKIQEL 120
           VRKPRPSTREGCKAMIHVK+DKSGKWVITKFVKEHNHPLVV+PREARQTMDEKDK+IQEL
Sbjct: 111 VRKPRPSTREGCKAMIHVKYDKSGKWVITKFVKEHNHPLVVSPREARQTMDEKDKQIQEL 170

Query: 121 TVELRNKKRLCALYQEQLTTFMKVVEVHSDHLSKKVQNVINNLKEFESIEKELSRNR 177
           T+ELRNKKRLC+ YQEQL  FMK+VE H+D L +KVQNV+ NLKEFESIE+EL   R
Sbjct: 171 TIELRNKKRLCSTYQEQLAAFMKIVEEHTDQLXQKVQNVVTNLKEFESIEQELLHPR 227

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356517812|ref|XP_003527580.1| PREDICTED: protein FAR1-RELATED SEQUENCE 5-like [Glycine max]

 Score =  312 bits (799), Expect = 4e-83,   Method: Compositional matrix adjust.
 Identities = 146/173 (84%), Positives = 163/173 (94%)

Query: 1   MEFDSEEAAKIFYDEYARRVGFVMRVMSCRRSERDGRILARRLGCNKEGYCVSIRGKFGP 60
           MEF+SE+AAKIFYDEYARR+GFVMRVMSCRRSERDGRILARRLGCNKEGYCVSIRGKF  
Sbjct: 66  MEFESEDAAKIFYDEYARRLGFVMRVMSCRRSERDGRILARRLGCNKEGYCVSIRGKFSS 125

Query: 61  VRKPRPSTREGCKAMIHVKFDKSGKWVITKFVKEHNHPLVVAPREARQTMDEKDKKIQEL 120
           VRKPR STREGCKAMIH+K++KSGKWVITKFVK+HNHPLVV+PREARQTMDEKDKKIQEL
Sbjct: 126 VRKPRASTREGCKAMIHIKYNKSGKWVITKFVKDHNHPLVVSPREARQTMDEKDKKIQEL 185

Query: 121 TVELRNKKRLCALYQEQLTTFMKVVEVHSDHLSKKVQNVINNLKEFESIEKEL 173
           T ELR+KKRLCA YQEQLT+FMK+VE H++ LS K+ +V+NNLKEFESIE+ L
Sbjct: 186 TAELRHKKRLCATYQEQLTSFMKIVEEHNEKLSAKIHHVVNNLKEFESIEELL 238

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356508152|ref|XP_003522824.1| PREDICTED: protein FAR1-RELATED SEQUENCE 4-like [Glycine max]

 Score =  311 bits (797), Expect = 7e-83,   Method: Compositional matrix adjust.
 Identities = 146/176 (82%), Positives = 163/176 (92%)

Query: 1   MEFDSEEAAKIFYDEYARRVGFVMRVMSCRRSERDGRILARRLGCNKEGYCVSIRGKFGP 60
           MEF+SE+AAK+FYDEYARR+GFVMRVMSCRRSERDGRILARRLGCNKEGYCVSIRGKF  
Sbjct: 66  MEFESEDAAKLFYDEYARRLGFVMRVMSCRRSERDGRILARRLGCNKEGYCVSIRGKFAS 125

Query: 61  VRKPRPSTREGCKAMIHVKFDKSGKWVITKFVKEHNHPLVVAPREARQTMDEKDKKIQEL 120
           VRKPR STREGCKAMIH+K+DKSGKWVITKFVK+HNHPLVV+PREARQTMDEKDKKIQEL
Sbjct: 126 VRKPRASTREGCKAMIHIKYDKSGKWVITKFVKDHNHPLVVSPREARQTMDEKDKKIQEL 185

Query: 121 TVELRNKKRLCALYQEQLTTFMKVVEVHSDHLSKKVQNVINNLKEFESIEKELSRN 176
           T ELR KKRLCA YQEQLT+FMK+VE H++ LS K+ +V+NNLKEFESIE+ L + 
Sbjct: 186 TAELRLKKRLCATYQEQLTSFMKIVEEHNEKLSAKIHHVVNNLKEFESIEELLHQT 241

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297824305|ref|XP_002880035.1| far-red impaired responsive family protein [Arabidopsis lyrata subsp. lyrata] gi|297325874|gb|EFH56294.1| far-red impaired responsive family protein [Arabidopsis lyrata subsp. lyrata]

 Score =  305 bits (781), Expect = 4e-81,   Method: Compositional matrix adjust.
 Identities = 139/177 (78%), Positives = 164/177 (92%)

Query: 1   MEFDSEEAAKIFYDEYARRVGFVMRVMSCRRSERDGRILARRLGCNKEGYCVSIRGKFGP 60
           +EF+SE+AAK+FYD+Y+RR+GFVMRVMSCRRSE+DGRILARR GCNKEG+CVSIRGKFG 
Sbjct: 26  IEFESEDAAKMFYDDYSRRLGFVMRVMSCRRSEKDGRILARRFGCNKEGHCVSIRGKFGS 85

Query: 61  VRKPRPSTREGCKAMIHVKFDKSGKWVITKFVKEHNHPLVVAPREARQTMDEKDKKIQEL 120
           VRKPRPSTREGCKAMIHVK+D+SGKWVITKFVKEHNHPLVV+PREAR T+DEKDK+IQEL
Sbjct: 86  VRKPRPSTREGCKAMIHVKYDRSGKWVITKFVKEHNHPLVVSPREARHTLDEKDKRIQEL 145

Query: 121 TVELRNKKRLCALYQEQLTTFMKVVEVHSDHLSKKVQNVINNLKEFESIEKELSRNR 177
           T+ELRNKKRLCA Y+EQL  F K+VE HS+ ++KKV+NV+NNLKEFE +E  L R++
Sbjct: 146 TIELRNKKRLCAAYKEQLDAFAKIVEEHSNQIAKKVENVVNNLKEFEPLEHALLRSK 202

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|30689328|ref|NP_181857.2| far-red impaired responsive 1-like protein [Arabidopsis thaliana] gi|27754520|gb|AAO22707.1| unknown protein [Arabidopsis thaliana] gi|28393991|gb|AAO42403.1| unknown protein [Arabidopsis thaliana] gi|330255153|gb|AEC10247.1| far-red impaired responsive 1-like protein [Arabidopsis thaliana]

 Score =  302 bits (774), Expect = 3e-80,   Method: Compositional matrix adjust.
 Identities = 138/175 (78%), Positives = 162/175 (92%)

Query: 3   FDSEEAAKIFYDEYARRVGFVMRVMSCRRSERDGRILARRLGCNKEGYCVSIRGKFGPVR 62
           F+SE+AAK+FYD+Y+RR+GFVMRVMSCRRSE+DGRILARR GCNKEG+CVSIRGKFG VR
Sbjct: 28  FESEDAAKMFYDDYSRRLGFVMRVMSCRRSEKDGRILARRFGCNKEGHCVSIRGKFGSVR 87

Query: 63  KPRPSTREGCKAMIHVKFDKSGKWVITKFVKEHNHPLVVAPREARQTMDEKDKKIQELTV 122
           KPRPSTREGCKAMIHVK+D+SGKWVITKFVKEHNHPLVV+PREAR T+DEKDK+IQELT+
Sbjct: 88  KPRPSTREGCKAMIHVKYDRSGKWVITKFVKEHNHPLVVSPREARHTLDEKDKRIQELTI 147

Query: 123 ELRNKKRLCALYQEQLTTFMKVVEVHSDHLSKKVQNVINNLKEFESIEKELSRNR 177
           ELRNKKRLCA Y+EQL  F K+VE HS+ ++KKV+NV+NNLKEFE +E  L R++
Sbjct: 148 ELRNKKRLCAAYKEQLDAFAKIVEEHSNQIAKKVENVVNNLKEFEHLEHALLRSK 202

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|2289005|gb|AAB64334.1| hypothetical protein [Arabidopsis thaliana] gi|20197151|gb|AAM14941.1| hypothetical protein [Arabidopsis thaliana]

 Score =  290 bits (741), Expect = 2e-76,   Method: Compositional matrix adjust.
 Identities = 132/167 (79%), Positives = 154/167 (92%)

Query: 11  IFYDEYARRVGFVMRVMSCRRSERDGRILARRLGCNKEGYCVSIRGKFGPVRKPRPSTRE 70
           +FYD+Y+RR+GFVMRVMSCRRSE+DGRILARR GCNKEG+CVSIRGKFG VRKPRPSTRE
Sbjct: 1   MFYDDYSRRLGFVMRVMSCRRSEKDGRILARRFGCNKEGHCVSIRGKFGSVRKPRPSTRE 60

Query: 71  GCKAMIHVKFDKSGKWVITKFVKEHNHPLVVAPREARQTMDEKDKKIQELTVELRNKKRL 130
           GCKAMIHVK+D+SGKWVITKFVKEHNHPLVV+PREAR T+DEKDK+IQELT+ELRNKKRL
Sbjct: 61  GCKAMIHVKYDRSGKWVITKFVKEHNHPLVVSPREARHTLDEKDKRIQELTIELRNKKRL 120

Query: 131 CALYQEQLTTFMKVVEVHSDHLSKKVQNVINNLKEFESIEKELSRNR 177
           CA Y+EQL  F K+VE HS+ ++KKV+NV+NNLKEFE +E  L R++
Sbjct: 121 CAAYKEQLDAFAKIVEEHSNQIAKKVENVVNNLKEFEHLEHALLRSK 167

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147864082|emb|CAN81119.1| hypothetical protein VITISV_030389 [Vitis vinifera]

 Score =  215 bits (548), Expect = 5e-54,   Method: Compositional matrix adjust.
 Identities = 104/168 (61%), Positives = 139/168 (82%)

Query: 1   MEFDSEEAAKIFYDEYARRVGFVMRVMSCRRSERDGRILARRLGCNKEGYCVSIRGKFGP 60
           MEFDSE+AAK FYDEYARRVGF+MR+  CRRSE D RIL+RRL CNK+G+ V IR ++GP
Sbjct: 40  MEFDSEDAAKEFYDEYARRVGFIMRIDQCRRSEVDKRILSRRLSCNKQGFYVKIRDQYGP 99

Query: 61  VRKPRPSTREGCKAMIHVKFDKSGKWVITKFVKEHNHPLVVAPREARQTMDEKDKKIQEL 120
           VRKPRPSTR+GCKAM+ VK +KSGKWV+T+FVK+H HPLVV+ R +R +MD KD++IQEL
Sbjct: 100 VRKPRPSTRQGCKAMMLVKLNKSGKWVVTRFVKDHTHPLVVSSRPSRSSMDSKDRRIQEL 159

Query: 121 TVELRNKKRLCALYQEQLTTFMKVVEVHSDHLSKKVQNVINNLKEFES 168
           T+E+ ++ +LC LY+ QL TF+K VE  ++ LS K++  +N++++ ES
Sbjct: 160 TMEVEHQDQLCELYRGQLITFLKNVEEQTEVLSTKIEVAVNSVRKVES 207

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

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	177
TAIR|locus:2041041	206	AT2G43280 [Arabidopsis thalian	0.988	0.849	0.788	1e-75
TAIR|locus:2079651	217	AT3G07500 "AT3G07500" [Arabido	0.943	0.769	0.534	1.4e-41
TAIR|locus:2135738	183	AT4G12850 "AT4G12850" [Arabido	0.920	0.890	0.467	4.9e-37
TAIR|locus:2097543	251	AT3G59470 [Arabidopsis thalian	0.909	0.641	0.453	4.7e-32
TAIR|locus:2121060	788	FRS5 "FAR1-related sequence 5"	0.564	0.126	0.539	3e-30
TAIR|locus:2062606	807	FRS2 "FAR1-related sequence 2"	0.751	0.164	0.375	1.5e-16
TAIR|locus:2014639	732	FRS4 "FAR1-related sequence 4"	0.689	0.166	0.348	1.6e-15
TAIR|locus:2129665	827	FAR1 "FAR-RED IMPAIRED RESPONS	0.570	0.122	0.362	1.9e-13
TAIR|locus:2082420	764	FRS7 "FAR1-related sequence 7"	0.536	0.124	0.376	4.3e-12
TAIR|locus:2144930	788	FRS12 "FAR1-related sequence 1	0.480	0.107	0.393	5.7e-12

TAIR|locus:2041041 AT2G43280 [Arabidopsis thaliana (taxid:3702)]

 Score = 763 (273.6 bits), Expect = 1.0e-75, P = 1.0e-75
 Identities = 138/175 (78%), Positives = 162/175 (92%)

Query:     3 FDSEEAAKIFYDEYARRVGFVMRVMSCRRSERDGRILARRLGCNKEGYCVSIRGKFGPVR 62
             F+SE+AAK+FYD+Y+RR+GFVMRVMSCRRSE+DGRILARR GCNKEG+CVSIRGKFG VR
Sbjct:    28 FESEDAAKMFYDDYSRRLGFVMRVMSCRRSEKDGRILARRFGCNKEGHCVSIRGKFGSVR 87

Query:    63 KPRPSTREGCKAMIHVKFDKSGKWVITKFVKEHNHPLVVAPREARQTMDEKDKKIQELTV 122
             KPRPSTREGCKAMIHVK+D+SGKWVITKFVKEHNHPLVV+PREAR T+DEKDK+IQELT+
Sbjct:    88 KPRPSTREGCKAMIHVKYDRSGKWVITKFVKEHNHPLVVSPREARHTLDEKDKRIQELTI 147

Query:   123 ELRNKKRLCALYQEQLTTFMKVVEVHSDHLSKKVQNVINNLKEFESIEKELSRNR 177
             ELRNKKRLCA Y+EQL  F K+VE HS+ ++KKV+NV+NNLKEFE +E  L R++
Sbjct:   148 ELRNKKRLCAAYKEQLDAFAKIVEEHSNQIAKKVENVVNNLKEFEHLEHALLRSK 202

GO:0005634 "nucleus" evidence=ISM

GO:0009639 "response to red or far red light" evidence=ISS

GO:0006301 "postreplication repair" evidence=RCA

TAIR|locus:2079651 AT3G07500 "AT3G07500" [Arabidopsis thaliana (taxid:3702)]

 Score = 441 (160.3 bits), Expect = 1.4e-41, P = 1.4e-41
 Identities = 93/174 (53%), Positives = 122/174 (70%)

Query:     1 MEFDSEEAAKIFYDEYARRVGFVMRVMSCRRSERDGRILARRLGCNKEGYCVSIRGKFGP 60
             MEF+SEEAAK FYD YA  +GFVMRV + RRS RDG ++ RRL CNKEG+  S R +   
Sbjct:    37 MEFESEEAAKSFYDNYATCMGFVMRVDAFRRSMRDGTVVWRRLVCNKEGFRRS-RPRRSE 95

Query:    61 VRKPRPSTREGCKAMIHVKFDKSGKWVITKFVKEHNHPLV-VAPREAR-----QTMDEKD 114
              RKPR  TREGCKA+I VK +KSG W++TKF KEHNHPL+ ++P   R     QT DEKD
Sbjct:    96 SRKPRAITREGCKALIVVKREKSGTWLVTKFEKEHNHPLLPLSPNVRRNFQLPQTPDEKD 155

Query:   115 KKIQELTVELRNKKRLCALYQEQLTTFMKVVEVHSDHLSKKVQNVINNLKEFES 168
              KI+EL+ EL  ++R C   Q+QL   +K +E HS+HL+  + +VI ++++ ES
Sbjct:   156 AKIRELSAELSRERRRCTALQQQLDMVLKEMEEHSNHLTININSVIQSVRDIES 209

GO:0003674 "molecular_function" evidence=ND

GO:0005634 "nucleus" evidence=ISM

GO:0009639 "response to red or far red light" evidence=ISS

TAIR|locus:2135738 AT4G12850 "AT4G12850" [Arabidopsis thaliana (taxid:3702)]

 Score = 398 (145.2 bits), Expect = 4.9e-37, P = 4.9e-37
 Identities = 78/167 (46%), Positives = 118/167 (70%)

Query:     1 MEFDSEEAAKIFYDEYARRVGFVMRVMSCRRSERDGRILARRLGCNKEGYCVSIRGKFGP 60
             ++F+SEE AK FY EY++R+GFV+R+M  RRS  DGR LARRLGCNK+G+  + +     
Sbjct:    14 LKFESEEEAKDFYVEYSKRLGFVVRMMQRRRSGIDGRTLARRLGCNKQGFGPNNQRS--- 70

Query:    61 VRKPRPSTREGCKAMIHVKFDKSGKWVITKFVKEHNHPLVVAPREARQTMDEKDKKIQEL 120
                   S+REGCKA I VK +KSGKWV+T+F+KEHNH L      +  +  +K++KI+EL
Sbjct:    71 -SSSSSSSREGCKATILVKMEKSGKWVVTRFIKEHNHSLQFIGSSSYDSFADKERKIKEL 129

Query:   121 TVELRNKKRLCALYQEQLTTFMKVVEVHSDHLSKKVQNVINNLKEFE 167
             T E+  + RLC +Y+++L +F+  VE +++ LS KV++++ N+K+ E
Sbjct:   130 TEEIECQDRLCDVYRDRLVSFIDNVEHYTEELSLKVRDIVENVKKLE 176

GO:0003674 "molecular_function" evidence=ND

GO:0005634 "nucleus" evidence=ISM

GO:0009639 "response to red or far red light" evidence=ISS

TAIR|locus:2097543 AT3G59470 [Arabidopsis thaliana (taxid:3702)]

 Score = 351 (128.6 bits), Expect = 4.7e-32, P = 4.7e-32
 Identities = 78/172 (45%), Positives = 107/172 (62%)

Query:     2 EFDSEEAAKIFYDEYARRVGFVMRVMSCRRSERDGRILARRLGCNKEGYCVSIRGKFGPV 61
             EF+SE AA  FY+ YA +VGFV+RV    RS  DG  + R+L CNKEGY   +  K   V
Sbjct:    75 EFESEAAAHGFYNAYATKVGFVIRVSKLSRSRHDGSPIGRQLVCNKEGY--RLPSKRDKV 132

Query:    62 RKPRPSTREGCKAMIHVKFDKSGKWVITKFVKEHNHPLVVAPREAR------QTMDEKDK 115
              + R  TR GCKAMI ++ + SGKWVITKFVKEHNH L+  P   R      Q  +E DK
Sbjct:   133 IRQRAETRVGCKAMILIRKENSGKWVITKFVKEHNHSLM--PGRVRRGCIYDQYPNEHDK 190

Query:   116 KIQELTVELRNKKRLCALYQEQLTTFMKVVEVHSDHLSKKVQNVINNLKEFE 167
              IQEL  +L  +K+  A Y+  L    + +E H++ LSK++Q++++N++  E
Sbjct:   191 -IQELMQQLAAEKKRAATYKRHLEMLFEQIEQHNESLSKRIQHIVDNVRNLE 241

GO:0005634 "nucleus" evidence=ISM

GO:0009639 "response to red or far red light" evidence=ISS

TAIR|locus:2121060 FRS5 "FAR1-related sequence 5" [Arabidopsis thaliana (taxid:3702)]

 Score = 278 (102.9 bits), Expect = 3.0e-30, Sum P(2) = 3.0e-30
 Identities = 55/102 (53%), Positives = 70/102 (68%)

Query:     1 MEFDSEEAAKIFYDEYARRVGFVMRVMSCRRSERDGRILARRLGCNKEGY--CVSIRGKF 58
             +EF+SEEAAK FY+ YARR+GF  RV S RRS RDG I+ R+  C KEG+      R K 
Sbjct:    77 LEFESEEAAKAFYNSYARRIGFSTRVSSSRRSRRDGAIIQRQFVCAKEGFRNMNEKRTKD 136

Query:    59 GPVRKPRPSTREGCKAMIHVKFDKSGKWVITKFVKEHNHPLV 100
               +++PR  TR GCKA + VK   SGKW+++ FVK+HNH LV
Sbjct:   137 REIKRPRTITRVGCKASLSVKMQDSGKWLVSGFVKDHNHELV 178

GO:0005634 "nucleus" evidence=ISM

GO:0008270 "zinc ion binding" evidence=IEA

GO:0009639 "response to red or far red light" evidence=ISS

TAIR|locus:2062606 FRS2 "FAR1-related sequence 2" [Arabidopsis thaliana (taxid:3702)]

 Score = 216 (81.1 bits), Expect = 1.5e-16, P = 1.5e-16
 Identities = 54/144 (37%), Positives = 82/144 (56%)

Query:     1 MEFDSEEAAKIFYDEYARRVGFVMRVMSCRRSERDGRILARRLGCNKEGYCVSIRGKFGP 60
             M+F+S+EAA  FY EYAR VGF + + + RRS+R G+ +  ++ C++ G   + R K   
Sbjct:    42 MDFESKEAAYYFYREYARSVGFGITIKASRRSKRSGKFIDVKIACSRFG---TKREKATA 98

Query:    61 VRKPRPSTREGCKAMIHVKFDKSGKWVITKFVKEHNHPLVVAPREARQTMDEKDKKIQEL 120
             +  PR   + GCKA +H+K  +  KWVI  FVKEHNH   + P +   ++  K+K    L
Sbjct:    99 IN-PRSCPKTGCKAGLHMKRKEDEKWVIYNFVKEHNHE--ICPDDFYVSVRGKNKPAGAL 155

Query:   121 TVELRNKKRL-CALYQEQLTTFMK 143
              +    KK L  AL +E L   ++
Sbjct:   156 AI----KKGLQLALEEEDLKLLLE 175

GO:0005634 "nucleus" evidence=ISM

GO:0008270 "zinc ion binding" evidence=IEA

GO:0009639 "response to red or far red light" evidence=ISS

TAIR|locus:2014639 FRS4 "FAR1-related sequence 4" [Arabidopsis thaliana (taxid:3702)]

 Score = 192 (72.6 bits), Expect = 1.6e-15, Sum P(2) = 1.6e-15
 Identities = 45/129 (34%), Positives = 66/129 (51%)

Query:     1 MEFDSEEAAKIFYDEYARRVGFVMRVMSCRRSERDGRILARRLGCNKEGYCVSIRGKFGP 60
             MEF++ E A +FY +YA+ VGF    +S RRS      +  +  C + G     + +   
Sbjct:     1 MEFETHEDAYLFYKDYAKSVGFGTAKLSSRRSRASKEFIDAKFSCIRYGS----KQQSDD 56

Query:    61 VRKPRPSTREGCKAMIHVKFDKSGKWVITKFVKEHNHPLVVAPREARQTMDEKDKK-IQE 119
                PR S + GCKA +HVK    GKW +  FVKEHNH L+  P +A      ++ + ++ 
Sbjct:    57 AINPRASPKIGCKASMHVKRRPDGKWYVYSFVKEHNHDLL--PEQAHYFRSHRNTELVKS 114

Query:   120 LTVELRNKK 128
                 LR KK
Sbjct:   115 NDSRLRRKK 123

GO:0005634 "nucleus" evidence=ISM

GO:0008270 "zinc ion binding" evidence=IEA

GO:0009639 "response to red or far red light" evidence=ISS

TAIR|locus:2129665 FAR1 "FAR-RED IMPAIRED RESPONSE 1" [Arabidopsis thaliana (taxid:3702)]

 Score = 187 (70.9 bits), Expect = 1.9e-13, P = 1.9e-13
 Identities = 37/102 (36%), Positives = 57/102 (55%)

Query:     1 MEFDSEEAAKIFYDEYARRVGFVMRVMSCRRSERDGRILARRLGCNKEGYCVSIRGKFGP 60
             ++FD+ EAA IFY EYA+ +GF   + + RRS++    +  +  C++ G           
Sbjct:    55 IDFDTHEAAYIFYQEYAKSMGFTTSIKNSRRSKKTKDFIDAKFACSRYGVTPESESSGSS 114

Query:    61 VRKPRPSTREGCKAMIHVKFDKSGKWVITKFVKEHNHPLVVA 102
              R+      + CKA +HVK    GKW+I +FVK+HNH L+ A
Sbjct:   115 SRRSTVKKTD-CKASMHVKRRPDGKWIIHEFVKDHNHELLPA 155

GO:0005634 "nucleus" evidence=ISM;IDA

GO:0008270 "zinc ion binding" evidence=IEA

GO:0009639 "response to red or far red light" evidence=IMP

GO:0010017 "red or far-red light signaling pathway" evidence=IMP

GO:0010018 "far-red light signaling pathway" evidence=IMP

GO:0005515 "protein binding" evidence=IPI

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

GO:0010218 "response to far red light" evidence=IMP

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

GO:0042753 "positive regulation of circadian rhythm" evidence=IMP

GO:0000278 "mitotic cell cycle" evidence=RCA

GO:0000724 "double-strand break repair via homologous recombination" evidence=RCA

GO:0006396 "RNA processing" evidence=RCA

GO:0009410 "response to xenobiotic stimulus" evidence=RCA

GO:0009630 "gravitropism" evidence=RCA

GO:0009640 "photomorphogenesis" evidence=RCA

GO:0010212 "response to ionizing radiation" evidence=RCA

GO:0010388 "cullin deneddylation" evidence=RCA

GO:0016567 "protein ubiquitination" evidence=RCA

GO:0016571 "histone methylation" evidence=RCA

GO:0016579 "protein deubiquitination" evidence=RCA

GO:0048522 "positive regulation of cellular process" evidence=RCA

TAIR|locus:2082420 FRS7 "FAR1-related sequence 7" [Arabidopsis thaliana (taxid:3702)]

 Score = 174 (66.3 bits), Expect = 4.3e-12, P = 4.3e-12
 Identities = 41/109 (37%), Positives = 59/109 (54%)

Query:     1 MEFDSEEAAKIFYDEYARRVGFVMRVMSCRRSERDGRILARRLGCNKEGYCVSIRGKFGP 60
             +EFD+ E A+ +Y+ YA R GF +R     RS  DG + +RR  C+KEG+ ++       
Sbjct:    32 LEFDTAEEARDYYNSYATRTGFKVRTGQLYRSRTDGTVSSRRFVCSKEGFQLN------- 84

Query:    61 VRKPRPSTREGCKAMIHVKFDKSGKWVITKFVKEHNHPLVVAPREARQT 109
                    +R GC A I V+   +GKWV+ +  KEHNH L     EA+ T
Sbjct:    85 -------SRTGCPAFIRVQRRDTGKWVLDQIQKEHNHDLGGHIEEAQTT 126

GO:0005634 "nucleus" evidence=ISM

GO:0008270 "zinc ion binding" evidence=IEA

GO:0009639 "response to red or far red light" evidence=ISS

TAIR|locus:2144930 FRS12 "FAR1-related sequence 12" [Arabidopsis thaliana (taxid:3702)]

 Score = 173 (66.0 bits), Expect = 5.7e-12, P = 5.7e-12
 Identities = 39/99 (39%), Positives = 55/99 (55%)

Query:     1 MEFDSEEAAKIFYDEYARRVGFVMRVMSCRRSERDGRILARRLGCNKEGYCVSIRGKFGP 60
             +EFD+ E A+ FY+ YA R GF +R     RS  DG + +RR  C+KEG+ ++       
Sbjct:    47 LEFDTAEEAREFYNAYAARTGFKVRTGQLYRSRTDGTVSSRRFVCSKEGFQLN------- 99

Query:    61 VRKPRPSTREGCKAMIHVKFDKSGKWVITKFVKEHNHPL 99
                    +R GC A I V+   +GKWV+ +  KEHNH L
Sbjct:   100 -------SRTGCTAFIRVQRRDTGKWVLDQIQKEHNHEL 131

GO:0005634 "nucleus" evidence=ISM

GO:0008270 "zinc ion binding" evidence=IEA

GO:0009639 "response to red or far red light" evidence=ISS

---

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!

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Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input: fgenesh4_pg.C_scaffold_64000104 hypothetical protein (185 aa) (Populus trichocarpa)

Predicted Functional Partners:

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

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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	177
pfam03101	90	pfam03101, FAR1, FAR1 DNA-binding domain	7e-33
PLN03097	846	PLN03097, FHY3, Protein FAR-RED ELONGATED HYPOCOTY	1e-15

>gnl|CDD|217369 pfam03101, FAR1, FAR1 DNA-binding domain

 Score =  112 bits (282), Expect = 7e-33
 Identities = 52/89 (58%), Positives = 60/89 (67%), Gaps = 1/89 (1%)

Query: 12  FYDEYARRVGFVMRVMSCRRSERDGRILARRLGCNKEGYCVSIRGKFGPVRKPRPSTREG 71
           FY+ YARRVGF +R    RRS RDG I+ RR  C+KEG+    R K    R+PR STR G
Sbjct: 2   FYNAYARRVGFSVRKSKSRRSRRDGEIIRRRFVCSKEGF-RKERKKSVRKRRPRASTRTG 60

Query: 72  CKAMIHVKFDKSGKWVITKFVKEHNHPLV 100
           CKAM+ VK    GKWV+TKFV EHNHPL 
Sbjct: 61  CKAMMVVKLRSDGKWVVTKFVLEHNHPLA 89

This domain contains a WRKY like fold and is therefore most likely a zinc binding DNA-binding domain. Length = 90

>gnl|CDD|178645 PLN03097, FHY3, Protein FAR-RED ELONGATED HYPOCOTYL 3; Provisional

 Score = 73.5 bits (180), Expect = 1e-15
 Identities = 43/121 (35%), Positives = 56/121 (46%), Gaps = 12/121 (9%)

Query: 1   MEFDSEEAAKIFYDEYARRVGFVMRVMSCRRSERDGRILARRLGCNKEGYCVSIRGKFGP 60
           MEF+S   A  FY EYAR +GF   + + RRS+     +  +  C++ G        F  
Sbjct: 78  MEFESHGEAYSFYQEYARSMGFNTAIQNSRRSKTSREFIDAKFACSRYGTKREYDKSFNR 137

Query: 61  VRKP------------RPSTREGCKAMIHVKFDKSGKWVITKFVKEHNHPLVVAPREARQ 108
            R              R   +  CKA +HVK    GKWVI  FVKEHNH L+ A   + Q
Sbjct: 138 PRARQTKQDPENGTGRRSCAKTDCKASMHVKRRPDGKWVIHSFVKEHNHELLPAQAVSEQ 197

Query: 109 T 109
           T
Sbjct: 198 T 198

Length = 846

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	177
PLN03097	846	FHY3 Protein FAR-RED ELONGATED HYPOCOTYL 3; Provis	100.0
PF03101	91	FAR1: FAR1 DNA-binding domain; InterPro: IPR004330	99.96
PF08731	111	AFT: Transcription factor AFT; InterPro: IPR014842	98.73
PF03108	67	DBD_Tnp_Mut: MuDR family transposase; InterPro: IP	97.03
PF03106	60	WRKY: WRKY DNA -binding domain; InterPro: IPR00365	91.08
PF04500	62	FLYWCH: FLYWCH zinc finger domain; InterPro: IPR00	89.13

>PLN03097 FHY3 Protein FAR-RED ELONGATED HYPOCOTYL 3; Provisional

Probab=100.00  E-value=2.9e-34  Score=271.26  Aligned_cols=166  Identities=25%  Similarity=0.423  Sum_probs=117.7

Q ss_pred             CccCCHHHHHHHHHHHhhhhCceEEEeeeeeccCCCceEEEEEeecCCCcccccCC--CC---------C-CccCCCCCc
Q 030419            1 MEFDSEEAAKIFYDEYARRVGFVMRVMSCRRSERDGRILARRLGCNKEGYCVSIRG--KF---------G-PVRKPRPST   68 (177)
Q Consensus         1 M~F~s~eeA~~FY~~YA~~~GF~vR~~~~~rs~~dg~i~~~~fvCsreG~~~~~~~--~~---------~-~~~r~r~~t   68 (177)
                      |+|+|+||||+||+.||+++||+||++++++++.+|.|+++.|||||||++..+..  ..         + ..+++|+.+
T Consensus        78 MeF~S~eeA~~FYn~YA~~~GFsVRi~~srrsk~~~~ii~r~fvCsreG~~~~~~~~~~~~~~~~~k~~~~~~~~rR~~t  157 (846)
T PLN03097         78 MEFESHGEAYSFYQEYARSMGFNTAIQNSRRSKTSREFIDAKFACSRYGTKREYDKSFNRPRARQTKQDPENGTGRRSCA  157 (846)
T ss_pred             CeECCHHHHHHHHHHHHhhcCceEEeeceeccCCCCcEEEEEEEEcCCCCCcccccccccccccccccCccccccccccc
Confidence            89999999999999999999999999999999999999999999999999754211  00         0 112356789


Q ss_pred             ccccccEEEEEEccCCcEEEEEeccccCccCCCCCcccccCChhHHHHHHHH-HHHhhhhhhhhHHHHHHHHHHHHHHHh
Q 030419           69 REGCKAMIHVKFDKSGKWVITKFVKEHNHPLVVAPREARQTMDEKDKKIQEL-TVELRNKKRLCALYQEQLTTFMKVVEV  147 (177)
Q Consensus        69 R~gC~A~i~v~~~~~g~W~V~~f~~eHNH~L~~~~~~~r~~~d~kdkkI~EL-~~el~~~~k~~~~~r~~l~~~~k~~ee  147 (177)
                      ||||+|+|+|++.++|+|+|++|+++|||||+|+...     +...++|... ...+.....+. .......+.+... .
T Consensus       158 RtGC~A~m~Vk~~~~gkW~V~~fv~eHNH~L~p~~~~-----~~~~r~~~~~~~~~~~~~~~v~-~~~~d~~~~~~~~-r  230 (846)
T PLN03097        158 KTDCKASMHVKRRPDGKWVIHSFVKEHNHELLPAQAV-----SEQTRKMYAAMARQFAEYKNVV-GLKNDSKSSFDKG-R  230 (846)
T ss_pred             CCCCceEEEEEEcCCCeEEEEEEecCCCCCCCCcccc-----chhhhhhHHHHHhhhhcccccc-ccchhhcchhhHH-H
Confidence            9999999999998789999999999999999987642     2233333222 22222111111 0000001111110 0


Q ss_pred             hhhhhhhhHHHHHHHHHHhhhhhhhh
Q 030419          148 HSDHLSKKVQNVINNLKEFESIEKEL  173 (177)
Q Consensus       148 h~~~ls~~v~~~v~~~k~~e~~~~~~  173 (177)
                      .+.-...|++.++++|++++.++|.+
T Consensus       231 ~~~~~~gD~~~ll~yf~~~q~~nP~F  256 (846)
T PLN03097        231 NLGLEAGDTKILLDFFTQMQNMNSNF  256 (846)
T ss_pred             hhhcccchHHHHHHHHHHHHhhCCCc
Confidence            11223579999999999999999976

>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=99.96  E-value=5.1e-30  Score=182.39  Aligned_cols=91  Identities=45%  Similarity=0.748  Sum_probs=82.8

Q ss_pred             HHHHHHhhhhCceEEEeeeeeccCCCceEEEEEeecCCCcccccCCCCCCccCCCCCcccccccEEEEEEccCCcEEEEE
Q 030419           11 IFYDEYARRVGFVMRVMSCRRSERDGRILARRLGCNKEGYCVSIRGKFGPVRKPRPSTREGCKAMIHVKFDKSGKWVITK   90 (177)
Q Consensus        11 ~FY~~YA~~~GF~vR~~~~~rs~~dg~i~~~~fvCsreG~~~~~~~~~~~~~r~r~~tR~gC~A~i~v~~~~~g~W~V~~   90 (177)
                      +||++||..+||+||++++++++.+|.+++..|+|+++|+...........+++++++||||+|+|.|++..+|.|.|+.
T Consensus         1 ~fy~~yA~~~GF~vr~~~s~~~~~~~~~~~~~~~C~r~G~~~~~~~~~~~~~r~~~s~ktgC~a~i~v~~~~~~~w~v~~   80 (91)
T PF03101_consen    1 DFYNSYARRHGFSVRKSSSRKSKKNGEIKRVTFVCSRGGKYKSKKKNEEKRRRNRPSKKTGCKARINVKRRKDGKWRVTS   80 (91)
T ss_pred             CHHHHhcCcCCeEEEEeeeEeCCCCceEEEEEEEECCcccccccccccccccccccccccCCCEEEEEEEccCCEEEEEE
Confidence            59999999999999999999888899999999999999998876543345677899999999999999998789999999


Q ss_pred             eccccCccCCC
Q 030419           91 FVKEHNHPLVV  101 (177)
Q Consensus        91 f~~eHNH~L~~  101 (177)
                      |+.+|||||+|
T Consensus        81 ~~~~HNH~L~P   91 (91)
T PF03101_consen   81 FVLEHNHPLCP   91 (91)
T ss_pred             CcCCcCCCCCC
Confidence            99999999987

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.

>PF08731 AFT: Transcription factor AFT; InterPro: IPR014842 AFT (activator of iron transcription) is an iron regulated transcriptional activator that regulates the expression of genes involved in iron homeostasis

Probab=98.73  E-value=1e-07  Score=70.56  Aligned_cols=90  Identities=21%  Similarity=0.376  Sum_probs=67.4

Q ss_pred             cCCHHHHHHHHHHHhhhhCceEEEeeeeeccCCCceEEEEEeecCCCcccccCCC--------------------CCCcc
Q 030419            3 FDSEEAAKIFYDEYARRVGFVMRVMSCRRSERDGRILARRLGCNKEGYCVSIRGK--------------------FGPVR   62 (177)
Q Consensus         3 F~s~eeA~~FY~~YA~~~GF~vR~~~~~rs~~dg~i~~~~fvCsreG~~~~~~~~--------------------~~~~~   62 (177)
                      |++-+|...|.-..+...||+|-+.+|..    ..   ..|-|--.|........                    .....
T Consensus         1 F~~k~~ikpwlq~~~~~~Gi~iVIerSd~----~k---i~FkCk~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~   73 (111)
T PF08731_consen    1 FDDKDEIKPWLQKIFYPQGIGIVIERSDK----KK---IVFKCKNGKRYRHKKKKKGQAQAQQKESTSGNKNKSSKKKKK   73 (111)
T ss_pred             CCchHHHHHHHHHHhhhcCceEEEEecCC----ce---EEEEEecCCCcccccccccccccccccccccccccccccccC
Confidence            89999999999999999999999986542    22   35889655554333221                    01112


Q ss_pred             CCCCCcccccccEEEEEEc-cCCcEEEEEeccccCccC
Q 030419           63 KPRPSTREGCKAMIHVKFD-KSGKWVITKFVKEHNHPL   99 (177)
Q Consensus        63 r~r~~tR~gC~A~i~v~~~-~~g~W~V~~f~~eHNH~L   99 (177)
                      +.-.+..++||.+|+-... ..++|-|.-+..+|||||
T Consensus        74 k~t~srk~~CPFriRA~yS~k~k~W~lvvvnn~HnH~l  111 (111)
T PF08731_consen   74 KRTKSRKNTCPFRIRANYSKKNKKWTLVVVNNEHNHPL  111 (111)
T ss_pred             CcccccccCCCeEEEEEEEecCCeEEEEEecCCcCCCC
Confidence            2335678999999999876 478999999999999998

This entry includes the paralogous pair of transcription factors AFT1 and AFT2.

>PF03108 DBD_Tnp_Mut: MuDR family transposase; InterPro: IPR004332 The plant MuDR transposase domain is present in plant proteins that are presumed to be the transposases for Mutator transposable elements [, ]

Probab=97.03  E-value=0.0044  Score=41.37  Aligned_cols=59  Identities=29%  Similarity=0.403  Sum_probs=48.2

Q ss_pred             CccCCHHHHHHHHHHHhhhhCceEEEeeeeeccCCCceEEEEEeecCCCcccccCCCCCCccCCCCCcccccccEEEEEE
Q 030419            1 MEFDSEEAAKIFYDEYARRVGFVMRVMSCRRSERDGRILARRLGCNKEGYCVSIRGKFGPVRKPRPSTREGCKAMIHVKF   80 (177)
Q Consensus         1 M~F~s~eeA~~FY~~YA~~~GF~vR~~~~~rs~~dg~i~~~~fvCsreG~~~~~~~~~~~~~r~r~~tR~gC~A~i~v~~   80 (177)
                      |.|+|.+|.......||-..||.++...+.     .  .+...+|.  +                    .||+.+|....
T Consensus         8 ~~F~~~~e~k~av~~yai~~~~~~~v~ksd-----~--~r~~~~C~--~--------------------~~C~Wrv~as~   58 (67)
T PF03108_consen    8 QTFPSKEEFKEAVREYAIKNGFEFKVKKSD-----K--KRYRAKCK--D--------------------KGCPWRVRASK   58 (67)
T ss_pred             CEECCHHHHHHHHHHHHHhcCcEEEEeccC-----C--EEEEEEEc--C--------------------CCCCEEEEEEE
Confidence            789999999999999999999999987553     1  35678885  1                    36999999998


Q ss_pred             cc-CCcEEE
Q 030419           81 DK-SGKWVI   88 (177)
Q Consensus        81 ~~-~g~W~V   88 (177)
                      .+ ++.|.|
T Consensus        59 ~~~~~~~~I   67 (67)
T PF03108_consen   59 RKRSDTFQI   67 (67)
T ss_pred             cCCCCEEEC
Confidence            75 577875

The function of these proteins is unknown. More information about these proteins can be found at Protein of the Month: Transposase [].

>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=91.08  E-value=0.32  Score=32.16  Aligned_cols=28  Identities=39%  Similarity=0.642  Sum_probs=21.8

Q ss_pred             ccccEEEEEEcc-CCcEEEEEeccccCcc
Q 030419           71 GCKAMIHVKFDK-SGKWVITKFVKEHNHP   98 (177)
Q Consensus        71 gC~A~i~v~~~~-~g~W~V~~f~~eHNH~   98 (177)
                      ||+|+-.|.... |+.-+++....+||||
T Consensus        31 ~C~akK~Vqr~~~d~~~~~vtY~G~H~h~   59 (60)
T PF03106_consen   31 GCPAKKQVQRSADDPNIVIVTYEGEHNHP   59 (60)
T ss_dssp             TEEEEEEEEEETTCCCEEEEEEES--SS-
T ss_pred             ChhheeeEEEecCCCCEEEEEEeeeeCCC
Confidence            899999998764 7888888999999997

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.

>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=89.13  E-value=0.26  Score=31.32  Aligned_cols=25  Identities=32%  Similarity=0.581  Sum_probs=10.8

Q ss_pred             cccccEEEEEEccCCcEEEEEeccccCc
Q 030419           70 EGCKAMIHVKFDKSGKWVITKFVKEHNH   97 (177)
Q Consensus        70 ~gC~A~i~v~~~~~g~W~V~~f~~eHNH   97 (177)
                      .+|+|++.+. .  +.-.|.....+|||
T Consensus        38 ~~C~a~~~~~-~--~~~~~~~~~~~HnH   62 (62)
T PF04500_consen   38 HGCRARLITD-A--GDGRVVRTNGEHNH   62 (62)
T ss_dssp             S----EEEEE-----TTEEEE-S---SS
T ss_pred             CCCeEEEEEE-C--CCCEEEECCCccCC
Confidence            6899999998 2  23355555689999

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.

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Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

No hit with e-value below 0.005

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	177
2ayd_A	76	WRKY transcription factor 1; beta strands, zinc fi	93.05
1wj2_A	78	Probable WRKY transcription factor 4; DNA-binding	92.01

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

Probab=93.05  E-value=0.14  Score=34.61  Aligned_cols=31  Identities=29%  Similarity=0.540  Sum_probs=26.4

Q ss_pred             cccccEEEEEEc-cCCcEEEEEeccccCccCC
Q 030419           70 EGCKAMIHVKFD-KSGKWVITKFVKEHNHPLV  100 (177)
Q Consensus        70 ~gC~A~i~v~~~-~~g~W~V~~f~~eHNH~L~  100 (177)
                      .||+|+-.|.+. +|+.-.++-...+|||++.
T Consensus        43 ~gC~a~K~Ver~~~d~~~~~~tY~G~H~H~~p   74 (76)
T 2ayd_A           43 PGCPVKKHVERSSHDTKLLITTYEGKHDHDMP   74 (76)
T ss_dssp             TTCCCEEEEEECSSSTTEEEEEEESCCSSCCC
T ss_pred             CCCCceeeEEEECCCCCEEEEEEccCcCCCCC
Confidence            499999999876 4678888889999999874

>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=92.01  E-value=0.19  Score=34.15  Aligned_cols=31  Identities=35%  Similarity=0.519  Sum_probs=26.1

Q ss_pred             cccccEEEEEEc-cCCcEEEEEeccccCccCC
Q 030419           70 EGCKAMIHVKFD-KSGKWVITKFVKEHNHPLV  100 (177)
Q Consensus        70 ~gC~A~i~v~~~-~~g~W~V~~f~~eHNH~L~  100 (177)
                      .||+|+-.|... .|+.-+++-...+||||+.
T Consensus        46 ~gC~a~K~Ver~~~d~~~~~~tY~G~H~H~~p   77 (78)
T 1wj2_A           46 PGCGVRKHVERAATDPKAVVTTYEGKHNHDLP   77 (78)
T ss_dssp             SSCEEEEEEEEETTTTSEEEEEEESCCSSCCC
T ss_pred             CCCCcEeeEEEEcCCCCEEEEEEeeEcCCCCC
Confidence            499999999875 4677888889999999873

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Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

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

No hit with e-value below 0.005

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	177
d1wj2a_	71	WRKY DNA-binding protein 4 {Thale cress (Arabidops	92.24

>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=92.24  E-value=0.085  Score=33.63  Aligned_cols=30  Identities=37%  Similarity=0.551  Sum_probs=25.1

Q ss_pred             cccccEEEEEEcc-CCcEEEEEeccccCccC
Q 030419           70 EGCKAMIHVKFDK-SGKWVITKFVKEHNHPL   99 (177)
Q Consensus        70 ~gC~A~i~v~~~~-~g~W~V~~f~~eHNH~L   99 (177)
                      .||+|+-.|.... |+.-+++-...+||||+
T Consensus        39 ~~C~a~K~Vqr~~~d~~~~~vtY~G~H~h~~   69 (71)
T d1wj2a_          39 PGCGVRKHVERAATDPKAVVTTYEGKHNHDL   69 (71)
T ss_dssp             SSCEEEEEEEEETTTTSEEEEEEESCCSSCC
T ss_pred             cCCCCcceEEEEcCCCCEEEEEEeeEeCCCC
Confidence            4899999998763 67778888899999986