Citrus Sinensis ID: 030575

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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
MEFDSEDAARKFYMGYARRMGFVVRIMQRRRSRTDGTTLARRLGCNKQGFSPNSKGTNGPEKKPRPSAREGCKATILVKMEKSGKWVVTRFIKDHNHPLVVTANGYSTVGDKDKKIEELTLELERQEQLCAAYREKLFNFMNNVEEQTEELSSKIQVIVDNIRKVESEMLKSFLQ
Secondary Structure (PSIPRED)
cccccHHHHHHHHHHHcccccEEEEEEEEEEEcccccEEEEEEEEEcccccccccccccccccccccccccccEEEEEEEEEccEEEEEEEEccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccHHHHHHHHHHHHHHHHHHHHccc
Secondary Structure Prediction (SSPRO)
cccccHHHHHHHHHHHHHHcccEEEEEEcEcEccccEEEEEEEEEccccccccccccccccccccccccccccEEEEEEEccccEEEEEEEEHHcccccccccHHHHccHHHHHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHcHHHHHHHHHHHHHHHHHHHcccccccc
Coil and Loop (DISEMBL)
MEFDSEDAARKFYMGYARRMGFVVRIMQrrrsrtdgttlarrlgcnkqgfspnskgtngpekkprpsaregcKATILVKMEKSGKWVVTRFIkdhnhplvvtangystvgdkdkKIEELTLELERQEQLCAAYREKLFNFMNNVEEQTEELSSKIQVIVDNIRKVESEMLKSFLQ
Flexible Loop (DISEMBL)
MEFDSEDAARKfymgyarrmgfvvrimqrrrsrtdgttlarrlgcnkqgfspnskgtngpekkprpsaregcKATILVKMEKSGKWVVTrfikdhnhplvvtangystvgdkdKKIEELTLELERQEQLCAAYREKLFNFMNNVEEQTEELSSKIQVIVDNIRKVESEMLKSFLQ
Low Complexity Region (SEG)
MEFDSEDAARKFYMGYARRMGFVVRIMQRRRSRTDGTTLARRLGCNKQGFSPNSKGTNGPEKKPRPSAREGCKATILVKMEKSGKWVVTRFIKDHNHPLVVTANGYSTVGDKDKKIeeltlelerqeqlCAAYREKLFNFMNNVEEQTEELSSKIQVIVDNIRKVESEMLKSFLQ
Disordered region (IsUnstruct)
**********KFYMGYARRMGFVVRIMQ*******************************************CKATILVKMEKSGKWVVTRFIKDHNHPLVVTANGYSTVGDKDKKIEELTLELERQEQLCAAYREKLFNFMNNVE*******SKIQVIVDNIR************
Disordered Region (DISOPRED)
MEFDSEDAARKFYMGYARRMGFVVRIMQRRRSRTDGTTLARRLGCNKQGFSPNSKGTNG**KKPRPSAREGCKATILVKMEKSGKWVVTRFIKDHNHPLVVTANGY****************************EKLFNFMNNVEEQTEELSSKIQVIVDNIRKVESE*******
Disordered Region (DISEMBL)
MEFDSEDAARKFYMGYARRMGFVVRIMQRRRSRTDGTTLARRLGCNKQGFSP******************GCKATILVKMEKSGKWVVTRFIKDHNHPLVVTANGYSTVGDKDKKIEELTLELERQEQLCAAYREKLFNFMNNVEEQTEELSSKIQVIVDNIRKVESEMLKSFLQ
Disordered Region (DISPRO)
****SEDAARKFYMGYARRMGFVVRIMQRRRSRTDGTTLARRLGCNKQ********************REGCKATILVKMEKSGKWVVTRFIKDHNHPLVVTANGYSTVGDKDKKIEELTLELERQEQLCAAYREKLFNFMNNVEEQTEELSSKIQVIVDNIRKVESEM****L*
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
oooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MEFDSEDAARKFYMGYARRMGFVVRIMQRRRSRTDGTTLARRLGCNKQGFSPNSKGTNGPEKKPRPSAREGCKATILVKMEKSGKWVVTRFIKDHNHPLVVTANGYSTxxxxxxxxxxxxxxxxxxxxxxxxxxxxLFNFxxxxxxxxxxxxxxxxxxxxxIRKVESEMLKSFLQ
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	175	2.2.26 [Sep-21-2011]
Q9SZL8	788	Protein FAR1-RELATED SEQU	no	no	0.571	0.126	0.529	3e-20
Q3E7I5	788	Protein FAR1-RELATED SEQU	no	no	0.485	0.107	0.454	2e-16
Q9M8J3	764	Protein FAR1-RELATED SEQU	no	no	0.485	0.111	0.444	7e-16
Q3EBQ3	807	Protein FAR1-RELATED SEQU	no	no	0.662	0.143	0.330	7e-13
Q6NQJ7	732	Protein FAR1-RELATED SEQU	no	no	0.582	0.139	0.358	2e-12
Q9SWG3	827	Protein FAR-RED IMPAIRED	no	no	0.565	0.119	0.34	3e-12
Q9LIE5	839	Protein FAR-RED ELONGATED	no	no	0.571	0.119	0.339	5e-11
Q5UBY2	687	Protein FAR1-RELATED SEQU	no	no	0.56	0.142	0.327	4e-10
Q9ZVC9	851	Protein FAR1-RELATED SEQU	no	no	0.48	0.098	0.32	1e-08
Q9S793	725	Protein FAR1-RELATED SEQU	no	no	0.525	0.126	0.350	4e-08

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

 Score = 97.8 bits (242), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 54/102 (52%), Positives = 71/102 (69%), Gaps = 2/102 (1%)

Query: 1   MEFDSEDAARKFYMGYARRMGFVVRIMQRRRSRTDGTTLARRLGCNKQGF-SPNSKGTNG 59
           +EF+SE+AA+ FY  YARR+GF  R+   RRSR DG  + R+  C K+GF + N K T  
Sbjct: 77  LEFESEEAAKAFYNSYARRIGFSTRVSSSRRSRRDGAIIQRQFVCAKEGFRNMNEKRTKD 136

Query: 60  PE-KKPRPSAREGCKATILVKMEKSGKWVVTRFIKDHNHPLV 100
            E K+PR   R GCKA++ VKM+ SGKW+V+ F+KDHNH LV
Sbjct: 137 REIKRPRTITRVGCKASLSVKMQDSGKWLVSGFVKDHNHELV 178

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 = 85.5 bits (210), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 45/99 (45%), Positives = 57/99 (57%), Gaps = 14/99 (14%)

Query: 1   MEFDSEDAARKFYMGYARRMGFVVRIMQRRRSRTDGTTLARRLGCNKQGFSPNSKGTNGP 60
           +EFD+ + AR+FY  YA R GF VR  Q  RSRTDGT  +RR  C+K+GF  NS      
Sbjct: 47  LEFDTAEEAREFYNAYAARTGFKVRTGQLYRSRTDGTVSSRRFVCSKEGFQLNS------ 100

Query: 61  EKKPRPSAREGCKATILVKMEKSGKWVVTRFIKDHNHPL 99
                   R GC A I V+   +GKWV+ +  K+HNH L
Sbjct: 101 --------RTGCTAFIRVQRRDTGKWVLDQIQKEHNHEL 131

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 = 83.6 bits (205), Expect = 7e-16,   Method: Compositional matrix adjust.
 Identities = 44/99 (44%), Positives = 56/99 (56%), Gaps = 14/99 (14%)

Query: 1   MEFDSEDAARKFYMGYARRMGFVVRIMQRRRSRTDGTTLARRLGCNKQGFSPNSKGTNGP 60
           +EFD+ + AR +Y  YA R GF VR  Q  RSRTDGT  +RR  C+K+GF  NS      
Sbjct: 32  LEFDTAEEARDYYNSYATRTGFKVRTGQLYRSRTDGTVSSRRFVCSKEGFQLNS------ 85

Query: 61  EKKPRPSAREGCKATILVKMEKSGKWVVTRFIKDHNHPL 99
                   R GC A I V+   +GKWV+ +  K+HNH L
Sbjct: 86  --------RTGCPAFIRVQRRDTGKWVLDQIQKEHNHDL 116

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 = 73.6 bits (179), Expect = 7e-13,   Method: Compositional matrix adjust.
 Identities = 40/121 (33%), Positives = 66/121 (54%), Gaps = 5/121 (4%)

Query: 1   MEFDSEDAARKFYMGYARRMGFVVRIMQRRRSRTDGTTLARRLGCNKQGFSPNSKGTNGP 60
           M+F+S++AA  FY  YAR +GF + I   RRS+  G  +  ++ C++ G    +K     
Sbjct: 42  MDFESKEAAYYFYREYARSVGFGITIKASRRSKRSGKFIDVKIACSRFG----TKREKAT 97

Query: 61  EKKPRPSAREGCKATILVKMEKSGKWVVTRFIKDHNHPLVVTANGYSTVGDKDKKIEELT 120
              PR   + GCKA + +K ++  KWV+  F+K+HNH  +   + Y +V  K+K    L 
Sbjct: 98  AINPRSCPKTGCKAGLHMKRKEDEKWVIYNFVKEHNHE-ICPDDFYVSVRGKNKPAGALA 156

Query: 121 L 121
           +
Sbjct: 157 I 157

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 = 71.6 bits (174), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 38/106 (35%), Positives = 54/106 (50%), Gaps = 4/106 (3%)

Query: 1   MEFDSEDAARKFYMGYARRMGFVVRIMQRRRSRTDGTTLARRLGCNKQGFSPNSKGTNGP 60
           MEF++ + A  FY  YA+ +GF    +  RRSR     +  +  C + G    SK  +  
Sbjct: 1   MEFETHEDAYLFYKDYAKSVGFGTAKLSSRRSRASKEFIDAKFSCIRYG----SKQQSDD 56

Query: 61  EKKPRPSAREGCKATILVKMEKSGKWVVTRFIKDHNHPLVVTANGY 106
              PR S + GCKA++ VK    GKW V  F+K+HNH L+     Y
Sbjct: 57  AINPRASPKIGCKASMHVKRRPDGKWYVYSFVKEHNHDLLPEQAHY 102

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 = 71.6 bits (174), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 34/100 (34%), Positives = 55/100 (55%), Gaps = 1/100 (1%)

Query: 1   MEFDSEDAARKFYMGYARRMGFVVRIMQRRRSRTDGTTLARRLGCNKQGFSPNSKGTNGP 60
           ++FD+ +AA  FY  YA+ MGF   I   RRS+     +  +  C++ G +P S+ +   
Sbjct: 55  IDFDTHEAAYIFYQEYAKSMGFTTSIKNSRRSKKTKDFIDAKFACSRYGVTPESESSGS- 113

Query: 61  EKKPRPSAREGCKATILVKMEKSGKWVVTRFIKDHNHPLV 100
             +     +  CKA++ VK    GKW++  F+KDHNH L+
Sbjct: 114 SSRRSTVKKTDCKASMHVKRRPDGKWIIHEFVKDHNHELL 153

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

 Score = 67.4 bits (163), Expect = 5e-11,   Method: Compositional matrix adjust.
 Identities = 38/112 (33%), Positives = 54/112 (48%), Gaps = 12/112 (10%)

Query: 1   MEFDSEDAARKFYMGYARRMGFVVRIMQRRRSRTDGTTLARRLGCNKQGFS-PNSKGTNG 59
           MEF+S   A  FY  Y+R MGF   I   RRS+T    +  +  C++ G      K  N 
Sbjct: 74  MEFESHGEAYSFYQEYSRAMGFNTAIQNSRRSKTTREFIDAKFACSRYGTKREYDKSFNR 133

Query: 60  PEKKP-----------RPSAREGCKATILVKMEKSGKWVVTRFIKDHNHPLV 100
           P  +            R  A+  CKA++ VK    GKWV+  F+++HNH L+
Sbjct: 134 PRARQSKQDPENMAGRRTCAKTDCKASMHVKRRPDGKWVIHSFVREHNHELL 185

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

 Score = 63.9 bits (154), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 36/110 (32%), Positives = 55/110 (50%), Gaps = 12/110 (10%)

Query: 2   EFDSEDAARKFYMGYARRMGFVVRIMQRRRSRTDGTTLARRLGCNKQGFSP-------NS 54
           EF+S++ A +FY  YA  +GF   I   RRSR  G  +  +  C + G           +
Sbjct: 26  EFESKEEAFEFYKEYANSVGFTTIIKASRRSRMTGKFIDAKFVCTRYGSKKEDIDTGLGT 85

Query: 55  KGTNGPEKKPR-----PSAREGCKATILVKMEKSGKWVVTRFIKDHNHPL 99
            G N P+ + R      S++  CKA + VK  + G+WVV   +K+HNH +
Sbjct: 86  DGFNIPQARKRGRINRSSSKTDCKAFLHVKRRQDGRWVVRSLVKEHNHEI 135

Putative transcription activator involved in regulating light control of development.

Arabidopsis thaliana (taxid: 3702)

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

 Score = 59.7 bits (143), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 32/100 (32%), Positives = 52/100 (52%), Gaps = 16/100 (16%)

Query: 1   MEFDSEDAARKFYMGYARRMGFVVRIMQRRRSRTDGTTLARRLGCNKQGFSPNSKGTNGP 60
           MEF+SE  A+ FY  Y+R++GF  +++     RTDG+   R   C+              
Sbjct: 53  MEFNSEKEAKSFYDEYSRQLGFTSKLL----PRTDGSVSVREFVCSSS------------ 96

Query: 61  EKKPRPSAREGCKATILVKMEKSGKWVVTRFIKDHNHPLV 100
            K+ +    E C A + ++++   KWVVT+F+K+H 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 = 57.8 bits (138), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 34/97 (35%), Positives = 45/97 (46%), Gaps = 5/97 (5%)

Query: 1   MEFDSEDAARKFYMGYARRMGFVVRIMQRRRSRTDGTTLARRLGCNKQGFSPNSKGTNGP 60
           MEF+S D A  FY  YAR +GF +R+      R         L CN QGF    K     
Sbjct: 99  MEFESYDDAYSFYNSYARELGFAIRVKSSWTKRNSKEKRGAVLCCNCQGF----KLLKDA 154

Query: 61  EKKPRPSAREGCKATILVKMEKSGKWVVTRFIKDHNH 97
             + R   R GC+A I +++    +W V +   DHNH
Sbjct: 155 HSR-RKETRTGCQAMIRLRLIHFDRWKVDQVKLDHNH 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	175
255572674	212	conserved hypothetical protein [Ricinus	0.977	0.806	0.824	6e-78
449502056	209	PREDICTED: protein FAR1-RELATED SEQUENCE	0.988	0.827	0.797	2e-77
449462447	209	PREDICTED: protein FAR1-RELATED SEQUENCE	0.988	0.827	0.797	2e-77
124360619	657	FAR1; Polynucleotidyl transferase, Ribon	0.982	0.261	0.790	2e-77
356567708	219	PREDICTED: protein FAR1-RELATED SEQUENCE	0.977	0.780	0.789	4e-77
224069685	195	predicted protein [Populus trichocarpa]	0.965	0.866	0.795	6e-75
388506702	180	unknown [Lotus japonicus]	0.96	0.933	0.767	6e-74
224129362	167	predicted protein [Populus trichocarpa]	0.925	0.970	0.754	2e-68
147864082	240	hypothetical protein VITISV_030389 [Viti	0.96	0.7	0.609	2e-52
359495410	471	PREDICTED: uncharacterized protein LOC10	0.988	0.367	0.597	2e-52

>gi|255572674|ref|XP_002527270.1| conserved hypothetical protein [Ricinus communis] gi|223533363|gb|EEF35114.1| conserved hypothetical protein [Ricinus communis]

 Score =  295 bits (754), Expect = 6e-78,   Method: Compositional matrix adjust.
 Identities = 141/171 (82%), Positives = 152/171 (88%)

Query: 1   MEFDSEDAARKFYMGYARRMGFVVRIMQRRRSRTDGTTLARRLGCNKQGFSPNSKGTNGP 60
           MEFDSED ARKFY+ YARR+GFVVRIMQRRRS  DG TLARRLGCNKQGFSPN +    P
Sbjct: 37  MEFDSEDDARKFYVDYARRVGFVVRIMQRRRSGIDGKTLARRLGCNKQGFSPNHRNAMRP 96

Query: 61  EKKPRPSAREGCKATILVKMEKSGKWVVTRFIKDHNHPLVVTANGYSTVGDKDKKIEELT 120
           +KKPR SAREGCKATILVKMEKSGKWVVTRF KDHNHPLV+TANG+STVGDKDKKIEEL+
Sbjct: 97  DKKPRSSAREGCKATILVKMEKSGKWVVTRFEKDHNHPLVITANGFSTVGDKDKKIEELS 156

Query: 121 LELERQEQLCAAYREKLFNFMNNVEEQTEELSSKIQVIVDNIRKVESEMLK 171
            ELE QEQLCA YRE+L  FMN+V EQTEELSSKIQVIVDN+RKVESE+ K
Sbjct: 157 RELEHQEQLCAVYRERLLTFMNDVAEQTEELSSKIQVIVDNVRKVESEVKK 207

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449502056|ref|XP_004161531.1| PREDICTED: protein FAR1-RELATED SEQUENCE 5-like [Cucumis sativus]

 Score =  293 bits (749), Expect = 2e-77,   Method: Compositional matrix adjust.
 Identities = 138/173 (79%), Positives = 154/173 (89%)

Query: 1   MEFDSEDAARKFYMGYARRMGFVVRIMQRRRSRTDGTTLARRLGCNKQGFSPNSKGTNGP 60
           MEFDSEDAAR+FY  YAR+MGFVVRIMQRRRS  DG TLARRLGCNKQGFSPN +G  G 
Sbjct: 33  MEFDSEDAARRFYAEYARQMGFVVRIMQRRRSGIDGRTLARRLGCNKQGFSPNHRGIYGL 92

Query: 61  EKKPRPSAREGCKATILVKMEKSGKWVVTRFIKDHNHPLVVTANGYSTVGDKDKKIEELT 120
           +KK RPSAREGCKATILVKMEKSGKWVVTRF+KDHNHPLVV +NG+++ GDKDKKIEEL 
Sbjct: 93  DKKSRPSAREGCKATILVKMEKSGKWVVTRFVKDHNHPLVVCSNGFNSSGDKDKKIEELK 152

Query: 121 LELERQEQLCAAYREKLFNFMNNVEEQTEELSSKIQVIVDNIRKVESEMLKSF 173
           +ELE QEQLC AYREKLFNF++NVEEQTEELSSKIQVI+ N+R+VES M K +
Sbjct: 153 MELEHQEQLCIAYREKLFNFISNVEEQTEELSSKIQVIIGNVRQVESGMQKHY 205

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449462447|ref|XP_004148952.1| PREDICTED: protein FAR1-RELATED SEQUENCE 5-like [Cucumis sativus]

 Score =  293 bits (749), Expect = 2e-77,   Method: Compositional matrix adjust.
 Identities = 138/173 (79%), Positives = 154/173 (89%)

Query: 1   MEFDSEDAARKFYMGYARRMGFVVRIMQRRRSRTDGTTLARRLGCNKQGFSPNSKGTNGP 60
           MEFDSEDAAR+FY  YAR+MGFVVRIMQRRRS  DG TLARRLGCNKQGFSPN +G  G 
Sbjct: 33  MEFDSEDAARRFYAEYARQMGFVVRIMQRRRSGIDGRTLARRLGCNKQGFSPNHRGIYGL 92

Query: 61  EKKPRPSAREGCKATILVKMEKSGKWVVTRFIKDHNHPLVVTANGYSTVGDKDKKIEELT 120
           +KK RPSAREGCKATILVKMEKSGKWVVTRF+KDHNHPLVV +NG+++ GDKDKKIEEL 
Sbjct: 93  DKKSRPSAREGCKATILVKMEKSGKWVVTRFVKDHNHPLVVCSNGFNSSGDKDKKIEELK 152

Query: 121 LELERQEQLCAAYREKLFNFMNNVEEQTEELSSKIQVIVDNIRKVESEMLKSF 173
           +ELE QEQLC AYREKLFNF++NVEEQTEELSSKIQVI+ N+R+VES M K +
Sbjct: 153 MELEHQEQLCIAYREKLFNFISNVEEQTEELSSKIQVIIGNVRQVESGMQKHY 205

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|124360619|gb|ABD33394.2| FAR1; Polynucleotidyl transferase, Ribonuclease H fold [Medicago truncatula]

 Score =  293 bits (749), Expect = 2e-77,   Method: Compositional matrix adjust.
 Identities = 136/172 (79%), Positives = 155/172 (90%)

Query: 1   MEFDSEDAARKFYMGYARRMGFVVRIMQRRRSRTDGTTLARRLGCNKQGFSPNSKGTNGP 60
           MEFDSE+AARKFY  YARR+GFVVR+MQRRRS  DG TLARRLGCNKQGFSPNSKGT G 
Sbjct: 480 MEFDSEEAARKFYAEYARRVGFVVRVMQRRRSGIDGRTLARRLGCNKQGFSPNSKGTLGK 539

Query: 61  EKKPRPSAREGCKATILVKMEKSGKWVVTRFIKDHNHPLVVTANGYSTVGDKDKKIEELT 120
           EK+PRPSAREGC ATILVKMEKSGKWVVTRFIKDHNHPL  TANG+ T  DKDKKI ELT
Sbjct: 540 EKRPRPSAREGCMATILVKMEKSGKWVVTRFIKDHNHPLTATANGFRTEDDKDKKIAELT 599

Query: 121 LELERQEQLCAAYREKLFNFMNNVEEQTEELSSKIQVIVDNIRKVESEMLKS 172
           +ELERQ++LCAAYREKL +F+NN+EEQTEE+S+++Q+I++NIR+ ESEM KS
Sbjct: 600 MELERQDELCAAYREKLLSFINNIEEQTEEMSTRVQLIIENIRRAESEMQKS 651

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356567708|ref|XP_003552059.1| PREDICTED: protein FAR1-RELATED SEQUENCE 7-like [Glycine max]

 Score =  292 bits (747), Expect = 4e-77,   Method: Compositional matrix adjust.
 Identities = 135/171 (78%), Positives = 156/171 (91%)

Query: 1   MEFDSEDAARKFYMGYARRMGFVVRIMQRRRSRTDGTTLARRLGCNKQGFSPNSKGTNGP 60
           MEF SE+ ARKFY+ YARR+GFVVRIMQRRRS  DG TLARRLGCNKQGFSPN+KG  GP
Sbjct: 38  MEFGSEEDARKFYVDYARRVGFVVRIMQRRRSGIDGRTLARRLGCNKQGFSPNNKGILGP 97

Query: 61  EKKPRPSAREGCKATILVKMEKSGKWVVTRFIKDHNHPLVVTANGYSTVGDKDKKIEELT 120
           EKKPRPSAREGCKATILVK EKSGKW+VTRF+KDHNHPL+ TANG+ST GDKDKKI ELT
Sbjct: 98  EKKPRPSAREGCKATILVKFEKSGKWIVTRFVKDHNHPLIATANGFSTAGDKDKKIVELT 157

Query: 121 LELERQEQLCAAYREKLFNFMNNVEEQTEELSSKIQVIVDNIRKVESEMLK 171
           +ELERQ+QLCAAYREKL +F++NVEE+TEELS+KIQ+I++N+R+ ES+M K
Sbjct: 158 MELERQDQLCAAYREKLLSFISNVEEETEELSTKIQLIIENVRRAESDMKK 208

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224069685|ref|XP_002303021.1| predicted protein [Populus trichocarpa] gi|222844747|gb|EEE82294.1| predicted protein [Populus trichocarpa]

 Score =  285 bits (728), Expect = 6e-75,   Method: Compositional matrix adjust.
 Identities = 136/171 (79%), Positives = 154/171 (90%), Gaps = 2/171 (1%)

Query: 1   MEFDSEDAARKFYMGYARRMGFVVRIMQRRRSRTDGTTLARRLGCNKQGFSPNSKGT--N 58
           MEF+SEDAARKFY  YARR+GFVVR+MQRRRS  DG TLARRLGCNKQGFSPN++     
Sbjct: 18  MEFESEDAARKFYSEYARRLGFVVRVMQRRRSGIDGRTLARRLGCNKQGFSPNNRTIVGP 77

Query: 59  GPEKKPRPSAREGCKATILVKMEKSGKWVVTRFIKDHNHPLVVTANGYSTVGDKDKKIEE 118
           GP+KKPRPSAREGCKATILVKM+KSGKWVVTRF KDHNHPLVVTA+G+S+ GDKDKKIEE
Sbjct: 78  GPDKKPRPSAREGCKATILVKMDKSGKWVVTRFEKDHNHPLVVTASGFSSSGDKDKKIEE 137

Query: 119 LTLELERQEQLCAAYREKLFNFMNNVEEQTEELSSKIQVIVDNIRKVESEM 169
           LT ELE Q+ LCA YREKL +FMN++EEQTEEL+SKIQ+IVDN+RKVESE+
Sbjct: 138 LTKELEHQDHLCATYREKLVSFMNSIEEQTEELASKIQLIVDNVRKVESEV 188

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|388506702|gb|AFK41417.1| unknown [Lotus japonicus]

 Score =  281 bits (720), Expect = 6e-74,   Method: Compositional matrix adjust.
 Identities = 129/168 (76%), Positives = 152/168 (90%)

Query: 1   MEFDSEDAARKFYMGYARRMGFVVRIMQRRRSRTDGTTLARRLGCNKQGFSPNSKGTNGP 60
           MEFD E+ ARKFY+ YA+R+GFVVRIMQRRRS  DG TLARRLGCNKQGFS ++KGT GP
Sbjct: 1   MEFDCEEDARKFYVEYAKRVGFVVRIMQRRRSGVDGKTLARRLGCNKQGFSSHNKGTLGP 60

Query: 61  EKKPRPSAREGCKATILVKMEKSGKWVVTRFIKDHNHPLVVTANGYSTVGDKDKKIEELT 120
           EKKPRPSAR+GCKAT+LVK+EKSGKWVVTRF+KDHNHPL+ T NG STVGDKD+KI EL+
Sbjct: 61  EKKPRPSARQGCKATVLVKLEKSGKWVVTRFVKDHNHPLIPTTNGLSTVGDKDEKIAELS 120

Query: 121 LELERQEQLCAAYREKLFNFMNNVEEQTEELSSKIQVIVDNIRKVESE 168
           +ELE Q+QLCAAYREKL +F+N VE+QTEELS+KIQ+IV+N+R+ ESE
Sbjct: 121 MELEHQDQLCAAYREKLLSFINKVEDQTEELSTKIQLIVENVRRAESE 168

Source: Lotus japonicus

Species: Lotus japonicus

Genus: Lotus

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224129362|ref|XP_002320568.1| predicted protein [Populus trichocarpa] gi|222861341|gb|EEE98883.1| predicted protein [Populus trichocarpa]

 Score =  263 bits (671), Expect = 2e-68,   Method: Compositional matrix adjust.
 Identities = 129/171 (75%), Positives = 142/171 (83%), Gaps = 9/171 (5%)

Query: 1   MEFDSEDAARKFYMGYARRMGFVVRIMQRRRSRTDGTTLARRLGCNKQGFSPNSKGTNGP 60
           MEF+SEDAAR+FY  YARR+GF VR+MQRRRS  DG TLARRLGCNKQGFSPN +   GP
Sbjct: 1   MEFESEDAARRFYTEYARRVGFAVRVMQRRRSGIDGRTLARRLGCNKQGFSPNHRTDVGP 60

Query: 61  EKKPRPSAREGCKATILVKMEKSGKWVVTRFIKDHNHPLVVTANGYSTVGDKDKKIEELT 120
           +KKPRP AR+GCKATILVKMEKSGKWVVTRF KDHNHPL         VG KDKKIEELT
Sbjct: 61  DKKPRPGARDGCKATILVKMEKSGKWVVTRFEKDHNHPL---------VGGKDKKIEELT 111

Query: 121 LELERQEQLCAAYREKLFNFMNNVEEQTEELSSKIQVIVDNIRKVESEMLK 171
            ELE QEQLCA YREKL +FMNNV E+ EEL+SKIQVIVD++RKVESE+ K
Sbjct: 112 QELEHQEQLCATYREKLLSFMNNVVEEAEELASKIQVIVDSVRKVESEVQK 162

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  210 bits (535), Expect = 2e-52,   Method: Compositional matrix adjust.
 Identities = 103/169 (60%), Positives = 131/169 (77%), Gaps = 1/169 (0%)

Query: 1   MEFDSEDAARKFYMGYARRMGFVVRIMQRRRSRTDGTTLARRLGCNKQGFSPNSKGTNGP 60
           MEFDSEDAA++FY  YARR+GF++RI Q RRS  D   L+RRL CNKQGF    +   GP
Sbjct: 40  MEFDSEDAAKEFYDEYARRVGFIMRIDQCRRSEVDKRILSRRLSCNKQGFYVKIRDQYGP 99

Query: 61  EKKPRPSAREGCKATILVKMEKSGKWVVTRFIKDHNHPLVV-TANGYSTVGDKDKKIEEL 119
            +KPRPS R+GCKA +LVK+ KSGKWVVTRF+KDH HPLVV +    S++  KD++I+EL
Sbjct: 100 VRKPRPSTRQGCKAMMLVKLNKSGKWVVTRFVKDHTHPLVVSSRPSRSSMDSKDRRIQEL 159

Query: 120 TLELERQEQLCAAYREKLFNFMNNVEEQTEELSSKIQVIVDNIRKVESE 168
           T+E+E Q+QLC  YR +L  F+ NVEEQTE LS+KI+V V+++RKVESE
Sbjct: 160 TMEVEHQDQLCELYRGQLITFLKNVEEQTEVLSTKIEVAVNSVRKVESE 208

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359495410|ref|XP_002270370.2| PREDICTED: uncharacterized protein LOC100248330 [Vitis vinifera]

 Score =  210 bits (535), Expect = 2e-52,   Method: Compositional matrix adjust.
 Identities = 104/174 (59%), Positives = 132/174 (75%), Gaps = 1/174 (0%)

Query: 1   MEFDSEDAARKFYMGYARRMGFVVRIMQRRRSRTDGTTLARRLGCNKQGFSPNSKGTNGP 60
           MEFDSEDAA++FY  YARR+GF++RI Q RRS  D   L+RRL CNKQGF    +   GP
Sbjct: 29  MEFDSEDAAKEFYDEYARRVGFIMRIDQCRRSEVDKRILSRRLSCNKQGFYVKIRDQYGP 88

Query: 61  EKKPRPSAREGCKATILVKMEKSGKWVVTRFIKDHNHPLVV-TANGYSTVGDKDKKIEEL 119
            +KPRPS R+GCKA +LVK+ KSGKWVVTRF+KDH HPLVV +    S++  KD++I+EL
Sbjct: 89  VRKPRPSTRQGCKAMMLVKLNKSGKWVVTRFVKDHTHPLVVSSRPSRSSMDSKDRRIQEL 148

Query: 120 TLELERQEQLCAAYREKLFNFMNNVEEQTEELSSKIQVIVDNIRKVESEMLKSF 173
           T+E+E Q+QLC  YR +L  F+ NVEEQTE LS+KI+V V+++RKVESE    F
Sbjct: 149 TMEVEHQDQLCELYRGQLITFLKNVEEQTEVLSTKIEVAVNSVRKVESEETDHF 202

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	175
TAIR|locus:2135738	183	AT4G12850 "AT4G12850" [Arabido	0.942	0.901	0.529	1.2e-44
TAIR|locus:2041041	206	AT2G43280 [Arabidopsis thalian	0.937	0.796	0.484	5.3e-40
TAIR|locus:2079651	217	AT3G07500 "AT3G07500" [Arabido	0.948	0.764	0.425	8.8e-31
TAIR|locus:2097543	251	AT3G59470 [Arabidopsis thalian	0.931	0.649	0.396	8.2e-28
TAIR|locus:2121060	788	FRS5 "FAR1-related sequence 5"	0.571	0.126	0.529	1.6e-27
TAIR|locus:2144930	788	FRS12 "FAR1-related sequence 1	0.485	0.107	0.454	2e-14
TAIR|locus:2082420	764	FRS7 "FAR1-related sequence 7"	0.485	0.111	0.444	6.4e-14
TAIR|locus:2129665	827	FAR1 "FAR-RED IMPAIRED RESPONS	0.565	0.119	0.35	9.2e-14
TAIR|locus:2062606	807	FRS2 "FAR1-related sequence 2"	0.622	0.135	0.350	6.4e-13
TAIR|locus:2090394	839	FHY3 "far-red elongated hypoco	0.571	0.119	0.348	2.2e-12

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

 Score = 470 (170.5 bits), Expect = 1.2e-44, P = 1.2e-44
 Identities = 90/170 (52%), Positives = 125/170 (73%)

Query:     1 MEFDSEDAARKFYMGYARRMGFVVRIMQRRRSRTDGTTLARRLGCNKQGFSPNSKGTNGP 60
             ++F+SE+ A+ FY+ Y++R+GFVVR+MQRRRS  DG TLARRLGCNKQGF PN++ ++  
Sbjct:    14 LKFESEEEAKDFYVEYSKRLGFVVRMMQRRRSGIDGRTLARRLGCNKQGFGPNNQRSSSS 73

Query:    61 EKKPRPSAREGCKATILVKMEKSGKWVVTRFIKDHNHPL-VVTANGYSTVGDKDKKIXXX 119
                   S+REGCKATILVKMEKSGKWVVTRFIK+HNH L  + ++ Y +  DK++KI   
Sbjct:    74 SS----SSREGCKATILVKMEKSGKWVVTRFIKEHNHSLQFIGSSSYDSFADKERKIKEL 129

Query:   120 XXXXXXXXXXCAAYREKLFNFMNNVEEQTEELSSKIQVIVDNIRKVESEM 169
                       C  YR++L +F++NVE  TEELS K++ IV+N++K+E ++
Sbjct:   130 TEEIECQDRLCDVYRDRLVSFIDNVEHYTEELSLKVRDIVENVKKLECQI 179

GO:0003674 "molecular_function" evidence=ND

GO:0005634 "nucleus" evidence=ISM

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

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

 Score = 426 (155.0 bits), Expect = 5.3e-40, P = 5.3e-40
 Identities = 80/165 (48%), Positives = 113/165 (68%)

Query:     3 FDSEDAARKFYMGYARRMGFVVRIMQRRRSRTDGTTLARRLGCNKQGFSPNSKGTNGPEK 62
             F+SEDAA+ FY  Y+RR+GFV+R+M  RRS  DG  LARR GCNK+G   + +G  G  +
Sbjct:    28 FESEDAAKMFYDDYSRRLGFVMRVMSCRRSEKDGRILARRFGCNKEGHCVSIRGKFGSVR 87

Query:    63 KPRPSAREGCKATILVKMEKSGKWVVTRFIKDHNHPLVVTAN-GYSTVGDKDKKIXXXXX 121
             KPRPS REGCKA I VK ++SGKWV+T+F+K+HNHPLVV+      T+ +KDK+I     
Sbjct:    88 KPRPSTREGCKAMIHVKYDRSGKWVITKFVKEHNHPLVVSPREARHTLDEKDKRIQELTI 147

Query:   122 XXXXXXXXCAAYREKLFNFMNNVEEQTEELSSKIQVIVDNIRKVE 166
                     CAAY+E+L  F   VEE + +++ K++ +V+N+++ E
Sbjct:   148 ELRNKKRLCAAYKEQLDAFAKIVEEHSNQIAKKVENVVNNLKEFE 192

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 = 339 (124.4 bits), Expect = 8.8e-31, P = 8.8e-31
 Identities = 74/174 (42%), Positives = 101/174 (58%)

Query:     1 MEFDSEDAARKFYMGYARRMGFVVRIMQRRRSRTDGTTLARRLGCNKQGFSPNSKGTNGP 60
             MEF+SE+AA+ FY  YA  MGFV+R+   RRS  DGT + RRL CNK+GF   S+     
Sbjct:    37 MEFESEEAAKSFYDNYATCMGFVMRVDAFRRSMRDGTVVWRRLVCNKEGFR-RSRPRRSE 95

Query:    61 EKKPRPSAREGCKATILVKMEKSGKWVVTRFIKDHNHPLV-----VTANGY--STVGDKD 113
              +KPR   REGCKA I+VK EKSG W+VT+F K+HNHPL+     V  N     T  +KD
Sbjct:    96 SRKPRAITREGCKALIVVKREKSGTWLVTKFEKEHNHPLLPLSPNVRRNFQLPQTPDEKD 155

Query:   114 KKIXXXXXXXXXXXXXCAAYREKLFNFMNNVEEQTEELSSKIQVIVDNIRKVES 167
              KI             C A +++L   +  +EE +  L+  I  ++ ++R +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:2097543 AT3G59470 [Arabidopsis thaliana (taxid:3702)]

 Score = 311 (114.5 bits), Expect = 8.2e-28, P = 8.2e-28
 Identities = 67/169 (39%), Positives = 94/169 (55%)

Query:     2 EFDSEDAARKFYMGYARRMGFVVRIMQRRRSRTDGTTLARRLGCNKQGFSPNSKGTNGPE 61
             EF+SE AA  FY  YA ++GFV+R+ +  RSR DG+ + R+L CNK+G+   SK      
Sbjct:    75 EFESEAAAHGFYNAYATKVGFVIRVSKLSRSRHDGSPIGRQLVCNKEGYRLPSK--RDKV 132

Query:    62 KKPRPSAREGCKATILVKMEKSGKWVVTRFIKDHNHPLVV--TANG--YSTVGDKDKKIX 117
              + R   R GCKA IL++ E SGKWV+T+F+K+HNH L+      G  Y    ++  KI 
Sbjct:   133 IRQRAETRVGCKAMILIRKENSGKWVITKFVKEHNHSLMPGRVRRGCIYDQYPNEHDKIQ 192

Query:   118 XXXXXXXXXXXXCAAYREKLFNFMNNVEEQTEELSSKIQVIVDNIRKVE 166
                          A Y+  L      +E+  E LS +IQ IVDN+R +E
Sbjct:   193 ELMQQLAAEKKRAATYKRHLEMLFEQIEQHNESLSKRIQHIVDNVRNLE 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 = 1.6e-27, Sum P(2) = 1.6e-27
 Identities = 54/102 (52%), Positives = 71/102 (69%)

Query:     1 MEFDSEDAARKFYMGYARRMGFVVRIMQRRRSRTDGTTLARRLGCNKQGF-SPNSKGTNG 59
             +EF+SE+AA+ FY  YARR+GF  R+   RRSR DG  + R+  C K+GF + N K T  
Sbjct:    77 LEFESEEAAKAFYNSYARRIGFSTRVSSSRRSRRDGAIIQRQFVCAKEGFRNMNEKRTKD 136

Query:    60 PE-KKPRPSAREGCKATILVKMEKSGKWVVTRFIKDHNHPLV 100
              E K+PR   R GCKA++ VKM+ SGKW+V+ F+KDHNH 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:2144930 FRS12 "FAR1-related sequence 12" [Arabidopsis thaliana (taxid:3702)]

 Score = 196 (74.1 bits), Expect = 2.0e-14, P = 2.0e-14
 Identities = 45/99 (45%), Positives = 57/99 (57%)

Query:     1 MEFDSEDAARKFYMGYARRMGFVVRIMQRRRSRTDGTTLARRLGCNKQGFSPNSKGTNGP 60
             +EFD+ + AR+FY  YA R GF VR  Q  RSRTDGT  +RR  C+K+GF  NS      
Sbjct:    47 LEFDTAEEAREFYNAYAARTGFKVRTGQLYRSRTDGTVSSRRFVCSKEGFQLNS------ 100

Query:    61 EKKPRPSAREGCKATILVKMEKSGKWVVTRFIKDHNHPL 99
                     R GC A I V+   +GKWV+ +  K+HNH L
Sbjct:   101 --------RTGCTAFIRVQRRDTGKWVLDQIQKEHNHEL 131

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

 Score = 191 (72.3 bits), Expect = 6.4e-14, P = 6.4e-14
 Identities = 44/99 (44%), Positives = 56/99 (56%)

Query:     1 MEFDSEDAARKFYMGYARRMGFVVRIMQRRRSRTDGTTLARRLGCNKQGFSPNSKGTNGP 60
             +EFD+ + AR +Y  YA R GF VR  Q  RSRTDGT  +RR  C+K+GF  NS      
Sbjct:    32 LEFDTAEEARDYYNSYATRTGFKVRTGQLYRSRTDGTVSSRRFVCSKEGFQLNS------ 85

Query:    61 EKKPRPSAREGCKATILVKMEKSGKWVVTRFIKDHNHPL 99
                     R GC A I V+   +GKWV+ +  K+HNH L
Sbjct:    86 --------RTGCPAFIRVQRRDTGKWVLDQIQKEHNHDL 116

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 = 190 (71.9 bits), Expect = 9.2e-14, P = 9.2e-14
 Identities = 35/100 (35%), Positives = 57/100 (57%)

Query:     1 MEFDSEDAARKFYMGYARRMGFVVRIMQRRRSRTDGTTLARRLGCNKQGFSPNSKGTNGP 60
             ++FD+ +AA  FY  YA+ MGF   I   RRS+     +  +  C++ G +P S+ ++G 
Sbjct:    55 IDFDTHEAAYIFYQEYAKSMGFTTSIKNSRRSKKTKDFIDAKFACSRYGVTPESE-SSGS 113

Query:    61 EKKPRPSAREGCKATILVKMEKSGKWVVTRFIKDHNHPLV 100
               +     +  CKA++ VK    GKW++  F+KDHNH L+
Sbjct:   114 SSRRSTVKKTDCKASMHVKRRPDGKWIIHEFVKDHNHELL 153

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

 Score = 182 (69.1 bits), Expect = 6.4e-13, P = 6.4e-13
 Identities = 40/114 (35%), Positives = 65/114 (57%)

Query:     1 MEFDSEDAARKFYMGYARRMGFVVRIMQRRRSRTDGTTLARRLGCNKQGFSPNSKGTNGP 60
             M+F+S++AA  FY  YAR +GF + I   RRS+  G  +  ++ C++ G +   K T   
Sbjct:    42 MDFESKEAAYYFYREYARSVGFGITIKASRRSKRSGKFIDVKIACSRFG-TKREKAT--- 97

Query:    61 EKKPRPSAREGCKATILVKMEKSGKWVVTRFIKDHNHPLVVTANGYSTVGDKDK 114
                PR   + GCKA + +K ++  KWV+  F+K+HNH  +   + Y +V  K+K
Sbjct:    98 AINPRSCPKTGCKAGLHMKRKEDEKWVIYNFVKEHNHE-ICPDDFYVSVRGKNK 150

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:2090394 FHY3 "far-red elongated hypocotyls 3" [Arabidopsis thaliana (taxid:3702)]

 Score = 163 (62.4 bits), Expect = 2.2e-12, Sum P(2) = 2.2e-12
 Identities = 39/112 (34%), Positives = 55/112 (49%)

Query:     1 MEFDSEDAARKFYMGYARRMGFVVRIMQRRRSRTDGTTLARRLGCNKQGFSPN-SKGTNG 59
             MEF+S   A  FY  Y+R MGF   I   RRS+T    +  +  C++ G      K  N 
Sbjct:    74 MEFESHGEAYSFYQEYSRAMGFNTAIQNSRRSKTTREFIDAKFACSRYGTKREYDKSFNR 133

Query:    60 PEKK-----P------RPSAREGCKATILVKMEKSGKWVVTRFIKDHNHPLV 100
             P  +     P      R  A+  CKA++ VK    GKWV+  F+++HNH L+
Sbjct:   134 PRARQSKQDPENMAGRRTCAKTDCKASMHVKRRPDGKWVIHSFVREHNHELL 185

GO:0004553 "hydrolase activity, hydrolyzing O-glycosyl compounds" evidence=IEA

GO:0005634 "nucleus" evidence=ISM;IDA

GO:0005975 "carbohydrate metabolic process" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

GO:0009585 "red, far-red light phototransduction" evidence=IMP

GO:0007623 "circadian rhythm" evidence=IMP

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

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

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

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

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

GO:0000956 "nuclear-transcribed mRNA catabolic process" evidence=RCA

GO:0006487 "protein N-linked glycosylation" evidence=RCA

GO:0008284 "positive regulation of cell proliferation" evidence=RCA

GO:0009630 "gravitropism" evidence=RCA

GO:0009639 "response to red or far red light" 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

Fail to connect to STRING server

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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	175
pfam03101	90	pfam03101, FAR1, FAR1 DNA-binding domain	3e-36
PLN03097	846	PLN03097, FHY3, Protein FAR-RED ELONGATED HYPOCOTY	2e-15

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

 Score =  120 bits (304), Expect = 3e-36
 Identities = 45/90 (50%), Positives = 60/90 (66%), Gaps = 1/90 (1%)

Query: 11  KFYMGYARRMGFVVRIMQRRRSRTDGTTLARRLGCNKQGFSPNSKGTNGPEKKPRPSARE 70
            FY  YARR+GF VR  + RRSR DG  + RR  C+K+GF    K +   +++PR S R 
Sbjct: 1   DFYNAYARRVGFSVRKSKSRRSRRDGEIIRRRFVCSKEGFRKERKKSV-RKRRPRASTRT 59

Query: 71  GCKATILVKMEKSGKWVVTRFIKDHNHPLV 100
           GCKA ++VK+   GKWVVT+F+ +HNHPL 
Sbjct: 60  GCKAMMVVKLRSDGKWVVTKFVLEHNHPLA 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 = 72.3 bits (177), Expect = 2e-15
 Identities = 41/112 (36%), Positives = 56/112 (50%), Gaps = 12/112 (10%)

Query: 1   MEFDSEDAARKFYMGYARRMGFVVRIMQRRRSRTDGTTLARRLGCNKQGFS--------- 51
           MEF+S   A  FY  YAR MGF   I   RRS+T    +  +  C++ G           
Sbjct: 78  MEFESHGEAYSFYQEYARSMGFNTAIQNSRRSKTSREFIDAKFACSRYGTKREYDKSFNR 137

Query: 52  PNSKGT-NGPEKKP--RPSAREGCKATILVKMEKSGKWVVTRFIKDHNHPLV 100
           P ++ T   PE     R  A+  CKA++ VK    GKWV+  F+K+HNH L+
Sbjct: 138 PRARQTKQDPENGTGRRSCAKTDCKASMHVKRRPDGKWVIHSFVKEHNHELL 189

Length = 846

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	175
PLN03097	846	FHY3 Protein FAR-RED ELONGATED HYPOCOTYL 3; Provis	99.98
PF03101	91	FAR1: FAR1 DNA-binding domain; InterPro: IPR004330	99.96
PF08731	111	AFT: Transcription factor AFT; InterPro: IPR014842	99.15
PF03108	67	DBD_Tnp_Mut: MuDR family transposase; InterPro: IP	97.73
PF04500	62	FLYWCH: FLYWCH zinc finger domain; InterPro: IPR00	90.36
PF03106	60	WRKY: WRKY DNA -binding domain; InterPro: IPR00365	89.39

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

Probab=99.98  E-value=2.1e-32  Score=257.34  Aligned_cols=104  Identities=36%  Similarity=0.630  Sum_probs=90.2

Q ss_pred             CccCCHHHHHHHHHHHhhhcCeEEEEeeeeeccCCCceEEEEEEeccCCCCCCCCC-C-----------CCCCCCCCCcc
Q 030575            1 MEFDSEDAARKFYMGYARRMGFVVRIMQRRRSRTDGTTLARRLGCNKQGFSPNSKG-T-----------NGPEKKPRPSA   68 (175)
Q Consensus         1 M~F~s~eeA~~FY~~YA~~~GF~ir~~~~~rs~~dg~i~~~~~~CsreG~~~~~~~-~-----------~~~~~~~r~~t   68 (175)
                      |+|+|+||||+|||.||+++||+||+++++|++.+|+|++++|||||||+++.... .           ....+++|+.+
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            89999999999999999999999999999999999999999999999998754211 0           00112457789


Q ss_pred             cccCcceeEEEeeeCCeEEEEEecccCCCCCCCCCC
Q 030575           69 REGCKATILVKMEKSGKWVVTRFIKDHNHPLVVTAN  104 (175)
Q Consensus        69 RtgC~A~~~v~~~~~g~W~V~~~~~eHNH~L~~~~~  104 (175)
                      ||||+|+|+|++..+|+|+|++|++||||||.|+..
T Consensus       158 RtGC~A~m~Vk~~~~gkW~V~~fv~eHNH~L~p~~~  193 (846)
T PLN03097        158 KTDCKASMHVKRRPDGKWVIHSFVKEHNHELLPAQA  193 (846)
T ss_pred             CCCCceEEEEEEcCCCeEEEEEEecCCCCCCCCccc
Confidence            999999999999878999999999999999998654

>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=7.5e-30  Score=180.74  Aligned_cols=91  Identities=42%  Similarity=0.734  Sum_probs=82.7

Q ss_pred             HHHHHHhhhcCeEEEEeeeeeccCCCceEEEEEEeccCCCCCCCCCCCCCCCCCCCcccccCcceeEEEeeeCCeEEEEE
Q 030575           11 KFYMGYARRMGFVVRIMQRRRSRTDGTTLARRLGCNKQGFSPNSKGTNGPEKKPRPSAREGCKATILVKMEKSGKWVVTR   90 (175)
Q Consensus        11 ~FY~~YA~~~GF~ir~~~~~rs~~dg~i~~~~~~CsreG~~~~~~~~~~~~~~~r~~tRtgC~A~~~v~~~~~g~W~V~~   90 (175)
                      +||+.||..+||+||+..+++++.+|.+++..|+|+++|++..........+++++++||||||+|.|++..+|.|.|+.
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            59999999999999999999988899999999999999999765443345678899999999999999987789999999


Q ss_pred             ecccCCCCCCC
Q 030575           91 FIKDHNHPLVV  101 (175)
Q Consensus        91 ~~~eHNH~L~~  101 (175)
                      |++||||||.|
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=99.15  E-value=4.9e-10  Score=82.26  Aligned_cols=90  Identities=22%  Similarity=0.366  Sum_probs=69.8

Q ss_pred             cCCHHHHHHHHHHHhhhcCeEEEEeeeeeccCCCceEEEEEEeccCCCCCCCCCC--------------------CCCCC
Q 030575            3 FDSEDAARKFYMGYARRMGFVVRIMQRRRSRTDGTTLARRLGCNKQGFSPNSKGT--------------------NGPEK   62 (175)
Q Consensus         3 F~s~eeA~~FY~~YA~~~GF~ir~~~~~rs~~dg~i~~~~~~CsreG~~~~~~~~--------------------~~~~~   62 (175)
                      |++.+|...|....++..||+|++-+|..+       ...|.|--.|........                    .....
T Consensus         1 F~~k~~ikpwlq~~~~~~Gi~iVIerSd~~-------ki~FkCk~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~   73 (111)
T PF08731_consen    1 FDDKDEIKPWLQKIFYPQGIGIVIERSDKK-------KIVFKCKNGKRYRHKKKKKGQAQAQQKESTSGNKNKSSKKKKK   73 (111)
T ss_pred             CCchHHHHHHHHHHhhhcCceEEEEecCCc-------eEEEEEecCCCcccccccccccccccccccccccccccccccC
Confidence            899999999999999999999999876532       235889888776443221                    11122


Q ss_pred             CCCCcccccCcceeEEEee-eCCeEEEEEecccCCCCC
Q 030575           63 KPRPSAREGCKATILVKME-KSGKWVVTRFIKDHNHPL   99 (175)
Q Consensus        63 ~~r~~tRtgC~A~~~v~~~-~~g~W~V~~~~~eHNH~L   99 (175)
                      +.-.+..++||++|+.... ...+|-|..+..+|||||
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            2335678899999998875 589999999999999998

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=97.73  E-value=0.00021  Score=47.63  Aligned_cols=59  Identities=19%  Similarity=0.401  Sum_probs=48.7

Q ss_pred             CccCCHHHHHHHHHHHhhhcCeEEEEeeeeeccCCCceEEEEEEeccCCCCCCCCCCCCCCCCCCCcccccCcceeEEEe
Q 030575            1 MEFDSEDAARKFYMGYARRMGFVVRIMQRRRSRTDGTTLARRLGCNKQGFSPNSKGTNGPEKKPRPSAREGCKATILVKM   80 (175)
Q Consensus         1 M~F~s~eeA~~FY~~YA~~~GF~ir~~~~~rs~~dg~i~~~~~~CsreG~~~~~~~~~~~~~~~r~~tRtgC~A~~~v~~   80 (175)
                      |.|+|.+|++.-...||-..||.+++..+.+       .+...+|.  +                    .|||++|..+.
T Consensus         8 ~~F~~~~e~k~av~~yai~~~~~~~v~ksd~-------~r~~~~C~--~--------------------~~C~Wrv~as~   58 (67)
T PF03108_consen    8 QTFPSKEEFKEAVREYAIKNGFEFKVKKSDK-------KRYRAKCK--D--------------------KGCPWRVRASK   58 (67)
T ss_pred             CEECCHHHHHHHHHHHHHhcCcEEEEeccCC-------EEEEEEEc--C--------------------CCCCEEEEEEE
Confidence            7899999999999999999999999876542       46678886  1                    25999999987


Q ss_pred             e-eCCeEEE
Q 030575           81 E-KSGKWVV   88 (175)
Q Consensus        81 ~-~~g~W~V   88 (175)
                      . .++.|.|
T Consensus        59 ~~~~~~~~I   67 (67)
T PF03108_consen   59 RKRSDTFQI   67 (67)
T ss_pred             cCCCCEEEC
Confidence            6 4578876

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

>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=90.36  E-value=0.18  Score=31.99  Aligned_cols=25  Identities=36%  Similarity=0.720  Sum_probs=10.5

Q ss_pred             ccCcceeEEEeeeCCeEEEEEecccCCC
Q 030575           70 EGCKATILVKMEKSGKWVVTRFIKDHNH   97 (175)
Q Consensus        70 tgC~A~~~v~~~~~g~W~V~~~~~eHNH   97 (175)
                      .+|+|++.+. .+++  .|.....+|||
T Consensus        38 ~~C~a~~~~~-~~~~--~~~~~~~~HnH   62 (62)
T PF04500_consen   38 HGCRARLITD-AGDG--RVVRTNGEHNH   62 (62)
T ss_dssp             S----EEEEE---TT--EEEE-S---SS
T ss_pred             CCCeEEEEEE-CCCC--EEEECCCccCC
Confidence            6899999988 2233  45666689999

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.

>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=89.39  E-value=0.5  Score=31.04  Aligned_cols=28  Identities=32%  Similarity=0.617  Sum_probs=21.5

Q ss_pred             cCcceeEEEee-eCCeEEEEEecccCCCC
Q 030575           71 GCKATILVKME-KSGKWVVTRFIKDHNHP   98 (175)
Q Consensus        71 gC~A~~~v~~~-~~g~W~V~~~~~eHNH~   98 (175)
                      ||+|.=.|... +++.-+++-...+||||
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            89999888875 47788889999999997

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.

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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	175
2ayd_A	76	WRKY transcription factor 1; beta strands, zinc fi	92.38
1wj2_A	78	Probable WRKY transcription factor 4; DNA-binding	91.14
2rpr_A	87	Flywch-type zinc finger-containing protein 1; flyw	90.59

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

Probab=92.38  E-value=0.19  Score=33.80  Aligned_cols=32  Identities=22%  Similarity=0.423  Sum_probs=26.3

Q ss_pred             ccCcceeEEEee-eCCeEEEEEecccCCCCCCC
Q 030575           70 EGCKATILVKME-KSGKWVVTRFIKDHNHPLVV  101 (175)
Q Consensus        70 tgC~A~~~v~~~-~~g~W~V~~~~~eHNH~L~~  101 (175)
                      .||+|+=.|... +++.-.++-...+|||++.+
T Consensus        43 ~gC~a~K~Ver~~~d~~~~~~tY~G~H~H~~p~   75 (76)
T 2ayd_A           43 PGCPVKKHVERSSHDTKLLITTYEGKHDHDMPP   75 (76)
T ss_dssp             TTCCCEEEEEECSSSTTEEEEEEESCCSSCCCC
T ss_pred             CCCCceeeEEEECCCCCEEEEEEccCcCCCCCC
Confidence            489999888775 46788888999999999854

>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=91.14  E-value=0.27  Score=33.16  Aligned_cols=31  Identities=35%  Similarity=0.454  Sum_probs=25.9

Q ss_pred             ccCcceeEEEee-eCCeEEEEEecccCCCCCC
Q 030575           70 EGCKATILVKME-KSGKWVVTRFIKDHNHPLV  100 (175)
Q Consensus        70 tgC~A~~~v~~~-~~g~W~V~~~~~eHNH~L~  100 (175)
                      .||+|+=.|... .++.-+++-...+||||+.
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            499999888875 4677888889999999974

>2rpr_A Flywch-type zinc finger-containing protein 1; flywch domain, alternative splicing, DNA-binding, metal- binding, nucleus, metal binding protein; NMR {Homo sapiens}

Probab=90.59  E-value=0.49  Score=31.87  Aligned_cols=23  Identities=17%  Similarity=0.522  Sum_probs=16.5

Q ss_pred             cCcceeEEEeeeCCeEEEEEecccCCCCC
Q 030575           71 GCKATILVKMEKSGKWVVTRFIKDHNHPL   99 (175)
Q Consensus        71 gC~A~~~v~~~~~g~W~V~~~~~eHNH~L   99 (175)
                      +|+|++.....  +   | .+...||||.
T Consensus        51 kCrARi~T~~~--~---~-~~~~~HnH~p   73 (87)
T 2rpr_A           51 GCRSRAITQGH--R---I-MVMRSHCHQP   73 (87)
T ss_dssp             CCCCEEEEETT--E---E-EECSCCSSCC
T ss_pred             CCCEEEEEcCC--C---E-ECCCCcCCCC
Confidence            89999887642  2   3 2567899974

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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	175
d1wj2a_	71	WRKY DNA-binding protein 4 {Thale cress (Arabidops	91.52

>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=91.52  E-value=0.12  Score=32.74  Aligned_cols=31  Identities=35%  Similarity=0.454  Sum_probs=25.2

Q ss_pred             ccCcceeEEEee-eCCeEEEEEecccCCCCCC
Q 030575           70 EGCKATILVKME-KSGKWVVTRFIKDHNHPLV  100 (175)
Q Consensus        70 tgC~A~~~v~~~-~~g~W~V~~~~~eHNH~L~  100 (175)
                      .||+|+=.|-.. +++.-+++-...+||||+.
T Consensus        39 ~~C~a~K~Vqr~~~d~~~~~vtY~G~H~h~~P   70 (71)
T d1wj2a_          39 PGCGVRKHVERAATDPKAVVTTYEGKHNHDLP   70 (71)
T ss_dssp             SSCEEEEEEEEETTTTSEEEEEEESCCSSCCC
T ss_pred             cCCCCcceEEEEcCCCCEEEEEEeeEeCCCCC
Confidence            489999888775 4677788888999999874