Citrus Sinensis ID: 028717

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-----
Protein Sequence
MMENVNDQEMAVTKGSSDGEPYLGMEFESEEAAKVFYDAYATHMGFIMRVDAFRRSMRDGKVVWRRLVCNKEGFRKLRPRRSENRKPRAVTREGCKAMIVVKKEKTGKWVVTRFVKEHNHPLVAIPANGRRSVLLSQTPDEKDVKIRELTAELQRERKRSAAYQEQLEMVLRDMENHSHHLSRNIDDIVQSVKQIEAKRIAASHC
Secondary Structure (PSIPRED)
cccccccccccccccccccccccccEEccHHHHHHHHHHHHHHccEEEEEEEEEEEcccccEEEEEEEEccccccccccccccccccccccccccccEEEEEEccccEEEEEEEccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHccccHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHcccc
Secondary Structure Prediction (SSPRO)
ccccccccccccccccccccccccEEEccHHHHHHHHHHHHHHcccEEEEEEEEcEccccEEEEEEEEEcccccccccccccccccccccccccccEEEEEEEcccccEEEEEEEHHcccccccccHHHHHHHHHcccHHHHHHHHHHHHHHHHHHHHHHHccHHHcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccc
Coil and Loop (DISEMBL)
MMENVNDQEMAVtkgssdgepylgmefesEEAAKVFYDAYATHMGFIMRVDAFRRSMRDGKVVWRRLVCnkegfrklrprrsenrkpravtrEGCKAMIVVKKEKTGKWVVTRFVKehnhplvaipangrrsvllsqtpdekdVKIRELTAELQRERKRSAAYQEQLEMVLRDMENHSHHLSRNIDDIVQSVKQIEAKRIAASHC
Flexible Loop (DISEMBL)
mmenvndqemavtkgssdgepYLGMEFESEEAAKVFYDAYATHMGFIMRVDAFRRSMRDGKVVWrrlvcnkegfrklrprrsenrkpravtregckamivvkkektgkwVVTRFVKEhnhplvaipangrrsvllsqtpdekdvkiRELTAELQRERKRSAAYQEQLEMVLRDMENHSHHLSRNIDDIVQSVKQIEAKRIAASHC
Low Complexity Region (SEG)
MMENVNDQEMAVTKGSSDGEPYLGMEFESEEAAKVFYDAYATHMGFIMRVDAFRRSMRDGKVVWRRLVCNKEGFRKLRPRRSENRKPRAVTREGCKAMIVVKKEKTGKWVVTRFVKEHNHPLVAIPANGRRSVLLSQTPDEKDVKIRELTAELQRERKRSAAYQEQLEMVLRDMENHSHHLSRNIDDIVQSVKQIEAKRIAASHC
Disordered region (IsUnstruct)
******************************EAAKVFYDAYATHMGFIMRVDAFRRSMRDGKVVWRRLVCNKEGFR****************REGCKAMIVVKKEKTGKWVVTRFVKEHNHPLVAIPANG****************************************************************************
Disordered Region (DISOPRED)
******************GEPYLGMEFESEEAAKVFYDAYATHMGFIMRVDAFRRSMRDGKVVWRRLVCNKEGFRKLRPRRSENRKPRAVTREGCKAMIVVKKEKTGKWVVTRFVKEHNHPLVAIPANGRRSVLLS*************************AYQEQLEMVLRDMENHSHHLSRNIDDIVQSVKQIEAKRI*****
Disordered Region (DISEMBL)
***************SSDGEPYLGMEFESEEAAKVFYDAYATHMGFIMRVDAFRRSMRDGKVVWRRLVCNKEGFRKLRPR***********REGCKAMIVVKKEKTGKWVVTRFVKEHNHPLVAIPANGRRSVLLSQTPDEKDVKIRELTAELQRERKRSAAYQEQLEMVLRDMENHSHHLSRNIDDIVQSVKQIEAKRIAASHC
Disordered Region (DISPRO)
*****************DGEPYLGMEFESEEAAKVFYDAYATHMGFIMRVDAFRRSMRDGKVVWRRLVCNKEGFR***************TREGCKAMIVVKKEKTGKWVVTRFVKEHNHPLVAIPANGRRSVLLSQTPDEKDVKIRELTAELQRERKRSAAYQEQLEMVLRDMENHSHHLSRNIDDIVQSVKQIEAKRIA****
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
oooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MMENVNDQEMAVTKGSSDGEPYLGMEFESEEAAKVFYDAYATHMGFIMRVDAFRRSMRDGKVVWRRLVCNKEGFRKLRPRRSENRKPRAVTREGCKAMIVVKKEKTGKWVVTRFVKEHNHPLVAIPANGRRSVLLSQTPDEKDVKxxxxxxxxxxxxxxxxxxxxxxxxxxxxMENHSHHLSRNIDDIVQSVKQIEAKRIAASHC
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	205	2.2.26 [Sep-21-2011]
Q9SZL8	788	Protein FAR1-RELATED SEQU	no	no	0.517	0.134	0.550	3e-26
Q9M8J3	764	Protein FAR1-RELATED SEQU	no	no	0.487	0.130	0.424	7e-19
Q3E7I5	788	Protein FAR1-RELATED SEQU	no	no	0.468	0.121	0.440	8e-19
Q3EBQ3	807	Protein FAR1-RELATED SEQU	no	no	0.473	0.120	0.4	3e-15
Q9SWG3	827	Protein FAR-RED IMPAIRED	no	no	0.541	0.134	0.345	8e-14
Q5UBY2	687	Protein FAR1-RELATED SEQU	no	no	0.614	0.183	0.344	6e-13
Q9LIE5	839	Protein FAR-RED ELONGATED	no	no	0.526	0.128	0.355	1e-11
Q6NQJ7	732	Protein FAR1-RELATED SEQU	no	no	0.721	0.202	0.322	2e-11
Q9ZVC9	851	Protein FAR1-RELATED SEQU	no	no	0.521	0.125	0.352	3e-11
Q9SSQ4	703	Protein FAR1-RELATED SEQU	no	no	0.575	0.167	0.315	2e-09

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

 Score =  118 bits (295), Expect = 3e-26,   Method: Compositional matrix adjust.
 Identities = 60/109 (55%), Positives = 81/109 (74%), Gaps = 3/109 (2%)

Query: 18  DGEPYLGMEFESEEAAKVFYDAYATHMGFIMRVDAFRRSMRDGKVVWRRLVCNKEGFRKL 77
           D EPY G+EFESEEAAK FY++YA  +GF  RV + RRS RDG ++ R+ VC KEGFR +
Sbjct: 70  DLEPYDGLEFESEEAAKAFYNSYARRIGFSTRVSSSRRSRRDGAIIQRQFVCAKEGFRNM 129

Query: 78  RPRRSENR---KPRAVTREGCKAMIVVKKEKTGKWVVTRFVKEHNHPLV 123
             +R+++R   +PR +TR GCKA + VK + +GKW+V+ FVK+HNH LV
Sbjct: 130 NEKRTKDREIKRPRTITRVGCKASLSVKMQDSGKWLVSGFVKDHNHELV 178

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 = 93.6 bits (231), Expect = 7e-19,   Method: Compositional matrix adjust.
 Identities = 48/113 (42%), Positives = 66/113 (58%), Gaps = 13/113 (11%)

Query: 10  MAVTKGSSDGEPYLGMEFESEEAAKVFYDAYATHMGFIMRVDAFRRSMRDGKVVWRRLVC 69
           +A  +G S  EPY+G+EF++ E A+ +Y++YAT  GF +R     RS  DG V  RR VC
Sbjct: 17  IAENEGDSGLEPYVGLEFDTAEEARDYYNSYATRTGFKVRTGQLYRSRTDGTVSSRRFVC 76

Query: 70  NKEGFRKLRPRRSENRKPRAVTREGCKAMIVVKKEKTGKWVVTRFVKEHNHPL 122
           +KEGF             +  +R GC A I V++  TGKWV+ +  KEHNH L
Sbjct: 77  SKEGF-------------QLNSRTGCPAFIRVQRRDTGKWVLDQIQKEHNHDL 116

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 = 93.6 bits (231), Expect = 8e-19,   Method: Compositional matrix adjust.
 Identities = 48/109 (44%), Positives = 63/109 (57%), Gaps = 13/109 (11%)

Query: 14  KGSSDGEPYLGMEFESEEAAKVFYDAYATHMGFIMRVDAFRRSMRDGKVVWRRLVCNKEG 73
           +G S  EPY+G+EF++ E A+ FY+AYA   GF +R     RS  DG V  RR VC+KEG
Sbjct: 36  EGGSGVEPYVGLEFDTAEEAREFYNAYAARTGFKVRTGQLYRSRTDGTVSSRRFVCSKEG 95

Query: 74  FRKLRPRRSENRKPRAVTREGCKAMIVVKKEKTGKWVVTRFVKEHNHPL 122
           F             +  +R GC A I V++  TGKWV+ +  KEHNH L
Sbjct: 96  F-------------QLNSRTGCTAFIRVQRRDTGKWVLDQIQKEHNHEL 131

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 = 82.0 bits (201), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 40/100 (40%), Positives = 63/100 (63%), Gaps = 3/100 (3%)

Query: 24  GMEFESEEAAKVFYDAYATHMGFIMRVDAFRRSMRDGKVVWRRLVCNKEGFRKLRPRRSE 83
           GM+FES+EAA  FY  YA  +GF + + A RRS R GK +  ++ C++ G ++    ++ 
Sbjct: 41  GMDFESKEAAYYFYREYARSVGFGITIKASRRSKRSGKFIDVKIACSRFGTKR---EKAT 97

Query: 84  NRKPRAVTREGCKAMIVVKKEKTGKWVVTRFVKEHNHPLV 123
              PR+  + GCKA + +K+++  KWV+  FVKEHNH + 
Sbjct: 98  AINPRSCPKTGCKAGLHMKRKEDEKWVIYNFVKEHNHEIC 137

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 = 77.0 bits (188), Expect = 8e-14,   Method: Compositional matrix adjust.
 Identities = 39/113 (34%), Positives = 59/113 (52%), Gaps = 2/113 (1%)

Query: 15  GSSDGEPYLGMEFESEEAAKVFYDAYATHMGFIMRVDAFRRSMRDGKVVWRRLVCNKEGF 74
           G  D EP  G++F++ EAA +FY  YA  MGF   +   RRS +    +  +  C++ G 
Sbjct: 45  GDLDLEPRNGIDFDTHEAAYIFYQEYAKSMGFTTSIKNSRRSKKTKDFIDAKFACSRYGV 104

Query: 75  RKLRPRRSENRKPRAVTREGCKAMIVVKKEKTGKWVVTRFVKEHNHPLVAIPA 127
                    + +   V +  CKA + VK+   GKW++  FVK+HNH L  +PA
Sbjct: 105 TPESESSGSSSRRSTVKKTDCKASMHVKRRPDGKWIIHEFVKDHNHEL--LPA 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 = 74.3 bits (181), Expect = 6e-13,   Method: Compositional matrix adjust.
 Identities = 50/145 (34%), Positives = 70/145 (48%), Gaps = 19/145 (13%)

Query: 24  GMEFESEEAAKVFYDAYATHMGFIMRVDAFRRSMRDGKVVWRRLVCNKEGFRK------- 76
           G EFES+E A  FY  YA  +GF   + A RRS   GK +  + VC + G +K       
Sbjct: 24  GREFESKEEAFEFYKEYANSVGFTTIIKASRRSRMTGKFIDAKFVCTRYGSKKEDIDTGL 83

Query: 77  ------LRPRRSENRKPRAVTREGCKAMIVVKKEKTGKWVVTRFVKEHNHPLVAIPAN-- 128
                 +   R   R  R+ ++  CKA + VK+ + G+WVV   VKEHNH +    A+  
Sbjct: 84  GTDGFNIPQARKRGRINRSSSKTDCKAFLHVKRRQDGRWVVRSLVKEHNHEIFTGQADSL 143

Query: 129 ----GRRSVLLSQTPDEKDVKIREL 149
               GRR +        K+VK R+L
Sbjct: 144 RELSGRRKLEKLNGAIVKEVKSRKL 168

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 = 69.7 bits (169), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 43/121 (35%), Positives = 59/121 (48%), Gaps = 13/121 (10%)

Query: 20  EPYLGMEFESEEAAKVFYDAYATHMGFIMRVDAFRRSMRDGKVVWRRLVCNKEGFRK--- 76
           EP  GMEFES   A  FY  Y+  MGF   +   RRS    + +  +  C++ G ++   
Sbjct: 69  EPLNGMEFESHGEAYSFYQEYSRAMGFNTAIQNSRRSKTTREFIDAKFACSRYGTKREYD 128

Query: 77  ---LRPR-RSENRKP------RAVTREGCKAMIVVKKEKTGKWVVTRFVKEHNHPLVAIP 126
               RPR R   + P      R   +  CKA + VK+   GKWV+  FV+EHNH L+   
Sbjct: 129 KSFNRPRARQSKQDPENMAGRRTCAKTDCKASMHVKRRPDGKWVIHSFVREHNHELLPAQ 188

Query: 127 A 127
           A
Sbjct: 189 A 189

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

 Score = 68.9 bits (167), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 49/152 (32%), Positives = 75/152 (49%), Gaps = 4/152 (2%)

Query: 25  MEFESEEAAKVFYDAYATHMGFIMRVDAFRRSMRDGKVVWRRLVCNKEGFRKLRPRRSEN 84
           MEFE+ E A +FY  YA  +GF     + RRS    + +  +  C + G ++   +  + 
Sbjct: 1   MEFETHEDAYLFYKDYAKSVGFGTAKLSSRRSRASKEFIDAKFSCIRYGSKQ---QSDDA 57

Query: 85  RKPRAVTREGCKAMIVVKKEKTGKWVVTRFVKEHNHPLVAIPANGRRSVLLSQTPDEKDV 144
             PRA  + GCKA + VK+   GKW V  FVKEHNH L+   A+  RS   ++     D 
Sbjct: 58  INPRASPKIGCKASMHVKRRPDGKWYVYSFVKEHNHDLLPEQAHYFRSHRNTELVKSNDS 117

Query: 145 KIRELTAELQRERKRSAAYQEQLEMVLRDMEN 176
           ++R        + K  +AY + L+ +   M N
Sbjct: 118 RLRRKKNTPLTDCKHLSAYHD-LDFIDGYMRN 148

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 = 68.6 bits (166), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 43/122 (35%), Positives = 62/122 (50%), Gaps = 15/122 (12%)

Query: 3   ENVNDQEMAVTKGSSDGEPYLGMEFESEEAAKVFYDAYATHMGFIMRVDAFRRSMRDGKV 62
           +N  D  + V       EP +GMEF SE+ AK FYD Y+  +GF  ++    R+  DG V
Sbjct: 31  QNNMDNSLGVQDEIGIAEPCVGMEFNSEKEAKSFYDEYSRQLGFTSKL--LPRT--DGSV 86

Query: 63  VWRRLVCNKEGFRKLRPRRSENRKPRAVTREGCKAMIVVKKEKTGKWVVTRFVKEHNHPL 122
             R  VC            S +++ +    E C AM+ ++ +   KWVVT+FVKEH H L
Sbjct: 87  SVREFVC-----------SSSSKRSKRRLSESCDAMVRIELQGHEKWVVTKFVKEHTHGL 135

Query: 123 VA 124
            +
Sbjct: 136 AS 137

Putative transcription activator involved in regulating light control of development.

Arabidopsis thaliana (taxid: 3702)

>sp|Q9SSQ4|FRS6_ARATH Protein FAR1-RELATED SEQUENCE 6 OS=Arabidopsis thaliana GN=FRS6 PE=2 SV=1

 Score = 62.8 bits (151), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 42/133 (31%), Positives = 71/133 (53%), Gaps = 15/133 (11%)

Query: 21  PYLGMEFESEEAAKVFYDAYATHMGFIMRV--DAFRRSMRD--GKVVWRRLVCNKEGFRK 76
           P +GMEFES + A  +Y+ YA+ +GF +RV    F+R  ++  G V    L C+ +GF++
Sbjct: 85  PAVGMEFESYDDAYNYYNCYASEVGFRVRVKNSWFKRRSKEKYGAV----LCCSSQGFKR 140

Query: 77  LRPRRSENRKPRAVTREGCKAMIVVKKEKTGKWVVTRFVKEHNHPL---VAIPANGRRSV 133
           +    ++  + R  TR GC AMI +++  + +W V     +HNH L   +      +R  
Sbjct: 141 I----NDVNRVRKETRTGCPAMIRMRQVDSKRWRVVEVTLDHNHLLGCKLYKSVKRKRKC 196

Query: 134 LLSQTPDEKDVKI 146
           + S   D K +K+
Sbjct: 197 VSSPVSDAKTIKL 209

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	205
255572676	209	conserved hypothetical protein [Ricinus	0.965	0.947	0.863	2e-97
147864083	206	hypothetical protein VITISV_030390 [Viti	0.990	0.985	0.827	5e-96
296088822	305	unnamed protein product [Vitis vinifera]	0.990	0.665	0.827	5e-96
359495408	200	PREDICTED: protein FAR1-RELATED SEQUENCE	0.960	0.985	0.798	7e-90
224132014	171	predicted protein [Populus trichocarpa]	0.829	0.994	0.898	1e-86
449465248	222	PREDICTED: protein FAR-RED IMPAIRED RESP	0.946	0.873	0.762	1e-85
297742884	621	unnamed protein product [Vitis vinifera]	0.775	0.256	0.880	3e-77
30680320	217	far-red impaired responsive 1-like prote	0.960	0.907	0.675	1e-69
359496191	153	PREDICTED: protein FAR1-RELATED SEQUENCE	0.736	0.986	0.840	3e-69
297829302	223	far-red impaired responsive family prote	0.951	0.874	0.680	2e-68

>gi|255572676|ref|XP_002527271.1| conserved hypothetical protein [Ricinus communis] gi|223533364|gb|EEF35115.1| conserved hypothetical protein [Ricinus communis]

 Score =  360 bits (924), Expect = 2e-97,   Method: Compositional matrix adjust.
 Identities = 171/198 (86%), Positives = 187/198 (94%)

Query: 2   MENVNDQEMAVTKGSSDGEPYLGMEFESEEAAKVFYDAYATHMGFIMRVDAFRRSMRDGK 61
           +++ N +E+   + SSD EPY+GMEFESEEAAKVFYDAYAT +GFIMRVDAFRRSMRDGK
Sbjct: 12  VDSSNGKEVTTAEESSDMEPYVGMEFESEEAAKVFYDAYATRLGFIMRVDAFRRSMRDGK 71

Query: 62  VVWRRLVCNKEGFRKLRPRRSENRKPRAVTREGCKAMIVVKKEKTGKWVVTRFVKEHNHP 121
           VVWRRLVCNKEGFRKLRPRRSENRKPRA+TREGCKAMIVVKKEKTGKWVVTRFVKEHNHP
Sbjct: 72  VVWRRLVCNKEGFRKLRPRRSENRKPRAITREGCKAMIVVKKEKTGKWVVTRFVKEHNHP 131

Query: 122 LVAIPANGRRSVLLSQTPDEKDVKIRELTAELQRERKRSAAYQEQLEMVLRDMENHSHHL 181
           LVAIP+NGRRSVLLSQTPDEKDVKIRELTAELQRERKRSAAYQEQL  VLRDME HS+HL
Sbjct: 132 LVAIPSNGRRSVLLSQTPDEKDVKIRELTAELQRERKRSAAYQEQLYTVLRDMEEHSNHL 191

Query: 182 SRNIDDIVQSVKQIEAKR 199
           SRNI+D+VQSV++IE+KR
Sbjct: 192 SRNIEDVVQSVREIESKR 209

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147864083|emb|CAN81120.1| hypothetical protein VITISV_030390 [Vitis vinifera]

 Score =  355 bits (912), Expect = 5e-96,   Method: Compositional matrix adjust.
 Identities = 168/203 (82%), Positives = 188/203 (92%)

Query: 1   MMENVNDQEMAVTKGSSDGEPYLGMEFESEEAAKVFYDAYATHMGFIMRVDAFRRSMRDG 60
           M+E+ N +E+   +G+S+ EP++GMEFESEEAAKVFYD YATH+GFIMRVDAFRRSMRDG
Sbjct: 1   MIESSNGKELVAHEGNSEMEPHVGMEFESEEAAKVFYDTYATHLGFIMRVDAFRRSMRDG 60

Query: 61  KVVWRRLVCNKEGFRKLRPRRSENRKPRAVTREGCKAMIVVKKEKTGKWVVTRFVKEHNH 120
           KVVWRRLVCNKEGFRKLRPRRSENRKPRA+TREGCKAMIVVKKEKTGKWVVTRFVKEHNH
Sbjct: 61  KVVWRRLVCNKEGFRKLRPRRSENRKPRAITREGCKAMIVVKKEKTGKWVVTRFVKEHNH 120

Query: 121 PLVAIPANGRRSVLLSQTPDEKDVKIRELTAELQRERKRSAAYQEQLEMVLRDMENHSHH 180
            LVA PAN RR+VLLSQTPDEKD+KIRELTAELQRERKR AA+QEQL+MVLRDME HS+H
Sbjct: 121 QLVATPANSRRTVLLSQTPDEKDIKIRELTAELQRERKRCAAFQEQLDMVLRDMEEHSNH 180

Query: 181 LSRNIDDIVQSVKQIEAKRIAAS 203
           LSRNID IVQSV++IE+K+I  S
Sbjct: 181 LSRNIDGIVQSVREIESKKIVHS 203

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|296088822|emb|CBI38280.3| unnamed protein product [Vitis vinifera]

 Score =  355 bits (911), Expect = 5e-96,   Method: Compositional matrix adjust.
 Identities = 168/203 (82%), Positives = 188/203 (92%)

Query: 1   MMENVNDQEMAVTKGSSDGEPYLGMEFESEEAAKVFYDAYATHMGFIMRVDAFRRSMRDG 60
           M+E+ N +E+   +G+S+ EP++GMEFESEEAAKVFYD YATH+GFIMRVDAFRRSMRDG
Sbjct: 44  MIESSNGKELVAHEGNSEMEPHVGMEFESEEAAKVFYDTYATHLGFIMRVDAFRRSMRDG 103

Query: 61  KVVWRRLVCNKEGFRKLRPRRSENRKPRAVTREGCKAMIVVKKEKTGKWVVTRFVKEHNH 120
           KVVWRRLVCNKEGFRKLRPRRSENRKPRA+TREGCKAMIVVKKEKTGKWVVTRFVKEHNH
Sbjct: 104 KVVWRRLVCNKEGFRKLRPRRSENRKPRAITREGCKAMIVVKKEKTGKWVVTRFVKEHNH 163

Query: 121 PLVAIPANGRRSVLLSQTPDEKDVKIRELTAELQRERKRSAAYQEQLEMVLRDMENHSHH 180
            LVA PAN RR+VLLSQTPDEKD+KIRELTAELQRERKR AA+QEQL+MVLRDME HS+H
Sbjct: 164 QLVATPANSRRTVLLSQTPDEKDIKIRELTAELQRERKRCAAFQEQLDMVLRDMEEHSNH 223

Query: 181 LSRNIDDIVQSVKQIEAKRIAAS 203
           LSRNID IVQSV++IE+K+I  S
Sbjct: 224 LSRNIDGIVQSVREIESKKIVHS 246

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359495408|ref|XP_003634985.1| PREDICTED: protein FAR1-RELATED SEQUENCE 5-like [Vitis vinifera]

 Score =  335 bits (859), Expect = 7e-90,   Method: Compositional matrix adjust.
 Identities = 162/203 (79%), Positives = 181/203 (89%), Gaps = 6/203 (2%)

Query: 1   MMENVNDQEMAVTKGSSDGEPYLGMEFESEEAAKVFYDAYATHMGFIMRVDAFRRSMRDG 60
           M+E+ N +E+   +G+S+ EP++GMEFESEEAAKVFYD YATH+GFIMRVDAFRRSMRDG
Sbjct: 1   MIESSNGKELVAHEGNSEMEPHVGMEFESEEAAKVFYDTYATHLGFIMRVDAFRRSMRDG 60

Query: 61  KVVWRRLVCNKEGFRKLRPRRSENRKPRAVTREGCKAMIVVKKEKTGKWVVTRFVKEHNH 120
           KVVWRRLVCNKEGFRKLRPRRSENRKPRA+TREGCKAMIVVKKEKTGKWVVTRFVKEHNH
Sbjct: 61  KVVWRRLVCNKEGFRKLRPRRSENRKPRAITREGCKAMIVVKKEKTGKWVVTRFVKEHNH 120

Query: 121 PLVAIPANGRRSVLLSQTPDEKDVKIRELTAELQRERKRSAAYQEQLEMVLRDMENHSHH 180
            LVA PAN RR      T DEKD+KIRELTAELQRERKR AA+QEQL+MVLRDME HS+H
Sbjct: 121 QLVATPANSRR------TLDEKDIKIRELTAELQRERKRCAAFQEQLDMVLRDMEEHSNH 174

Query: 181 LSRNIDDIVQSVKQIEAKRIAAS 203
           LSRNID IVQSV++IE+K+I  S
Sbjct: 175 LSRNIDGIVQSVREIESKKIVHS 197

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224132014|ref|XP_002321234.1| predicted protein [Populus trichocarpa] gi|222862007|gb|EEE99549.1| predicted protein [Populus trichocarpa]

 Score =  324 bits (831), Expect = 1e-86,   Method: Compositional matrix adjust.
 Identities = 159/177 (89%), Positives = 165/177 (93%), Gaps = 7/177 (3%)

Query: 20  EPYLGMEFESEEAAKVFYDAYATHMGFIMRVDAFRRSMRDGKVVWRRLVCNKEGFRKLRP 79
           EP +GMEFESEEAAKVFYDAYATH+GFIMRVDAFRRSMRDGKVVWRRLVCNKEGFRKLRP
Sbjct: 2   EPCVGMEFESEEAAKVFYDAYATHVGFIMRVDAFRRSMRDGKVVWRRLVCNKEGFRKLRP 61

Query: 80  RRSENRKPRAVTREGCKAMIVVKKEKTGKWVVTRFVKEHNHPLVAIPANGRRSVLLSQTP 139
           RRSENRKPRAVTREGCKAMIVVKKEK GKWVVTRFVKEHNHPLV  PANGRR+       
Sbjct: 62  RRSENRKPRAVTREGCKAMIVVKKEKAGKWVVTRFVKEHNHPLVPTPANGRRT------- 114

Query: 140 DEKDVKIRELTAELQRERKRSAAYQEQLEMVLRDMENHSHHLSRNIDDIVQSVKQIE 196
           DEKDVKIRELTAELQRERKRSAAYQEQL+MVLRDME HS+HLSRNIDDIVQSVK+IE
Sbjct: 115 DEKDVKIRELTAELQRERKRSAAYQEQLDMVLRDMEEHSNHLSRNIDDIVQSVKEIE 171

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449465248|ref|XP_004150340.1| PREDICTED: protein FAR-RED IMPAIRED RESPONSE 1-like [Cucumis sativus] gi|449507905|ref|XP_004163163.1| PREDICTED: protein FAR-RED IMPAIRED RESPONSE 1-like [Cucumis sativus]

 Score =  321 bits (822), Expect = 1e-85,   Method: Compositional matrix adjust.
 Identities = 148/194 (76%), Positives = 173/194 (89%)

Query: 11  AVTKGSSDGEPYLGMEFESEEAAKVFYDAYATHMGFIMRVDAFRRSMRDGKVVWRRLVCN 70
           A+T  +SD EP++GMEFESEE+ KVFYDAYA+ +GFIMRVDAFRRSMRDG VVWRRLVCN
Sbjct: 28  AITSNNSDTEPFVGMEFESEESVKVFYDAYASRLGFIMRVDAFRRSMRDGAVVWRRLVCN 87

Query: 71  KEGFRKLRPRRSENRKPRAVTREGCKAMIVVKKEKTGKWVVTRFVKEHNHPLVAIPANGR 130
           KEGFRK +P+RSENRKPRAVTREGCKAM+VVKKEKTGKWVVT+FVK+HNHPL+  PA+ R
Sbjct: 88  KEGFRKFKPKRSENRKPRAVTREGCKAMVVVKKEKTGKWVVTKFVKDHNHPLIVTPASAR 147

Query: 131 RSVLLSQTPDEKDVKIRELTAELQRERKRSAAYQEQLEMVLRDMENHSHHLSRNIDDIVQ 190
           R+VLLS T DEKD KIRELTAELQ+ERKR AAYQEQL M+L DME HS+HL+RNID+I+Q
Sbjct: 148 RNVLLSHTRDEKDAKIRELTAELQQERKRCAAYQEQLAMILGDMEEHSNHLARNIDNIIQ 207

Query: 191 SVKQIEAKRIAASH 204
           SV+ IE++  A S+
Sbjct: 208 SVRDIESENNAFSN 221

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297742884|emb|CBI35674.3| unnamed protein product [Vitis vinifera]

 Score =  293 bits (750), Expect = 3e-77,   Method: Compositional matrix adjust.
 Identities = 140/159 (88%), Positives = 150/159 (94%)

Query: 46  FIMRVDAFRRSMRDGKVVWRRLVCNKEGFRKLRPRRSENRKPRAVTREGCKAMIVVKKEK 105
           FIMRVDAFRRSMRDGKVVWRRLVCNKEGFRKLRPRRSENRKPRA+TREGCKAMIVVKKEK
Sbjct: 461 FIMRVDAFRRSMRDGKVVWRRLVCNKEGFRKLRPRRSENRKPRAITREGCKAMIVVKKEK 520

Query: 106 TGKWVVTRFVKEHNHPLVAIPANGRRSVLLSQTPDEKDVKIRELTAELQRERKRSAAYQE 165
           TGKWVVTRFVKEHNH LVA PAN RR+VLLSQTPDEKD+KIRELTAELQRERKR AA+QE
Sbjct: 521 TGKWVVTRFVKEHNHQLVATPANSRRTVLLSQTPDEKDIKIRELTAELQRERKRCAAFQE 580

Query: 166 QLEMVLRDMENHSHHLSRNIDDIVQSVKQIEAKRIAASH 204
           QL+MVLRDME HS+HLSRNID IVQSV++IE+K+I  S 
Sbjct: 581 QLDMVLRDMEEHSNHLSRNIDGIVQSVREIESKKIVHSQ 619

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|30680320|ref|NP_187406.2| far-red impaired responsive 1-like protein [Arabidopsis thaliana] gi|28393276|gb|AAO42066.1| unknown protein [Arabidopsis thaliana] gi|28827544|gb|AAO50616.1| unknown protein [Arabidopsis thaliana] gi|332641029|gb|AEE74550.1| far-red impaired responsive 1-like protein [Arabidopsis thaliana]

 Score =  268 bits (685), Expect = 1e-69,   Method: Compositional matrix adjust.
 Identities = 133/197 (67%), Positives = 163/197 (82%)

Query: 1   MMENVNDQEMAVTKGSSDGEPYLGMEFESEEAAKVFYDAYATHMGFIMRVDAFRRSMRDG 60
           MMEN +  +    + S   EP++GMEFESEEAAK FYD YAT MGF+MRVDAFRRSMRDG
Sbjct: 13  MMENSDVMKTVTDEASPMVEPFIGMEFESEEAAKSFYDNYATCMGFVMRVDAFRRSMRDG 72

Query: 61  KVVWRRLVCNKEGFRKLRPRRSENRKPRAVTREGCKAMIVVKKEKTGKWVVTRFVKEHNH 120
            VVWRRLVCNKEGFR+ RPRRSE+RKPRA+TREGCKA+IVVK+EK+G W+VT+F KEHNH
Sbjct: 73  TVVWRRLVCNKEGFRRSRPRRSESRKPRAITREGCKALIVVKREKSGTWLVTKFEKEHNH 132

Query: 121 PLVAIPANGRRSVLLSQTPDEKDVKIRELTAELQRERKRSAAYQEQLEMVLRDMENHSHH 180
           PL+ +  N RR+  L QTPDEKD KIREL+AEL RER+R  A Q+QL+MVL++ME HS+H
Sbjct: 133 PLLPLSPNVRRNFQLPQTPDEKDAKIRELSAELSRERRRCTALQQQLDMVLKEMEEHSNH 192

Query: 181 LSRNIDDIVQSVKQIEA 197
           L+ NI+ ++QSV+ IE+
Sbjct: 193 LTININSVIQSVRDIES 209

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359496191|ref|XP_002270413.2| PREDICTED: protein FAR1-RELATED SEQUENCE 1-like [Vitis vinifera]

 Score =  266 bits (681), Expect = 3e-69,   Method: Compositional matrix adjust.
 Identities = 132/157 (84%), Positives = 141/157 (89%), Gaps = 6/157 (3%)

Query: 48  MRVDAFRRSMRDGKVVWRRLVCNKEGFRKLRPRRSENRKPRAVTREGCKAMIVVKKEKTG 107
           MRVDAFRRSMRDGKVVWRRLVCNKEGFRKLRPRRSENRKPRA+TREGCKAMIVVKKEKTG
Sbjct: 1   MRVDAFRRSMRDGKVVWRRLVCNKEGFRKLRPRRSENRKPRAITREGCKAMIVVKKEKTG 60

Query: 108 KWVVTRFVKEHNHPLVAIPANGRRSVLLSQTPDEKDVKIRELTAELQRERKRSAAYQEQL 167
           KWVVTRFVKEHNH LVA PAN RR      T DEKD+KIRELTAELQRERKR AA+QEQL
Sbjct: 61  KWVVTRFVKEHNHQLVATPANSRR------TLDEKDIKIRELTAELQRERKRCAAFQEQL 114

Query: 168 EMVLRDMENHSHHLSRNIDDIVQSVKQIEAKRIAASH 204
           +MVLRDME HS+HLSRNID IVQSV++IE+K+I  S 
Sbjct: 115 DMVLRDMEEHSNHLSRNIDGIVQSVREIESKKIVHSQ 151

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297829302|ref|XP_002882533.1| far-red impaired responsive family protein [Arabidopsis lyrata subsp. lyrata] gi|297328373|gb|EFH58792.1| far-red impaired responsive family protein [Arabidopsis lyrata subsp. lyrata]

 Score =  263 bits (673), Expect = 2e-68,   Method: Compositional matrix adjust.
 Identities = 134/197 (68%), Positives = 163/197 (82%), Gaps = 2/197 (1%)

Query: 1   MMENVNDQEMAVTKGSSDGEPYLGMEFESEEAAKVFYDAYATHMGFIMRVDAFRRSMRDG 60
           MMEN +   M   +     EP++GM+FESEEAAK FYD YA  MGF+MRVDAFRRSMRDG
Sbjct: 21  MMENSDG--MKTVESFPMVEPFIGMKFESEEAAKSFYDNYAICMGFVMRVDAFRRSMRDG 78

Query: 61  KVVWRRLVCNKEGFRKLRPRRSENRKPRAVTREGCKAMIVVKKEKTGKWVVTRFVKEHNH 120
            VVWRRLVCNKEGFR+ RPRRSE+RKPRA+TREGCKA+IVVK+EK+GKWVVT+  KEHNH
Sbjct: 79  TVVWRRLVCNKEGFRRSRPRRSESRKPRAITREGCKALIVVKREKSGKWVVTKLEKEHNH 138

Query: 121 PLVAIPANGRRSVLLSQTPDEKDVKIRELTAELQRERKRSAAYQEQLEMVLRDMENHSHH 180
           PL+ +  N RR+  L QTPDEKD KIREL+AEL RER+R  A Q+QL+MVL++ME HS+H
Sbjct: 139 PLLPLSPNVRRNPPLPQTPDEKDAKIRELSAELSRERRRCTALQQQLDMVLKEMEEHSNH 198

Query: 181 LSRNIDDIVQSVKQIEA 197
           LS NI++++QSV+QIE+
Sbjct: 199 LSVNINNVIQSVRQIES 215

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	205
TAIR|locus:2079651	217	AT3G07500 "AT3G07500" [Arabido	0.960	0.907	0.675	7e-70
TAIR|locus:2097543	251	AT3G59470 [Arabidopsis thalian	0.917	0.749	0.481	8.1e-44
TAIR|locus:2041041	206	AT2G43280 [Arabidopsis thalian	0.907	0.902	0.454	1.9e-42
TAIR|locus:2135738	183	AT4G12850 "AT4G12850" [Arabido	0.829	0.928	0.424	2e-33
TAIR|locus:2121060	788	FRS5 "FAR1-related sequence 5"	0.517	0.134	0.550	7.5e-28
TAIR|locus:2082420	764	FRS7 "FAR1-related sequence 7"	0.487	0.130	0.433	8.2e-17
TAIR|locus:2144930	788	FRS12 "FAR1-related sequence 1	0.468	0.121	0.449	8.6e-17
TAIR|locus:2062606	807	FRS2 "FAR1-related sequence 2"	0.468	0.118	0.404	3.6e-15
TAIR|locus:2129665	827	FAR1 "FAR-RED IMPAIRED RESPONS	0.785	0.194	0.297	2.1e-14
TAIR|locus:2014639	732	FRS4 "FAR1-related sequence 4"	0.760	0.213	0.316	1.5e-12

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

 Score = 708 (254.3 bits), Expect = 7.0e-70, P = 7.0e-70
 Identities = 133/197 (67%), Positives = 163/197 (82%)

Query:     1 MMENVNDQEMAVTKGSSDGEPYLGMEFESEEAAKVFYDAYATHMGFIMRVDAFRRSMRDG 60
             MMEN +  +    + S   EP++GMEFESEEAAK FYD YAT MGF+MRVDAFRRSMRDG
Sbjct:    13 MMENSDVMKTVTDEASPMVEPFIGMEFESEEAAKSFYDNYATCMGFVMRVDAFRRSMRDG 72

Query:    61 KVVWRRLVCNKEGFRKLRPRRSENRKPRAVTREGCKAMIVVKKEKTGKWVVTRFVKEHNH 120
              VVWRRLVCNKEGFR+ RPRRSE+RKPRA+TREGCKA+IVVK+EK+G W+VT+F KEHNH
Sbjct:    73 TVVWRRLVCNKEGFRRSRPRRSESRKPRAITREGCKALIVVKREKSGTWLVTKFEKEHNH 132

Query:   121 PLVAIPANGRRSVLLSQTPDEKDVKIRELTAELQRERKRSAAYQEQLEMVLRDMENHSHH 180
             PL+ +  N RR+  L QTPDEKD KIREL+AEL RER+R  A Q+QL+MVL++ME HS+H
Sbjct:   133 PLLPLSPNVRRNFQLPQTPDEKDAKIRELSAELSRERRRCTALQQQLDMVLKEMEEHSNH 192

Query:   181 LSRNIDDIVQSVKQIEA 197
             L+ NI+ ++QSV+ IE+
Sbjct:   193 LTININSVIQSVRDIES 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 = 462 (167.7 bits), Expect = 8.1e-44, P = 8.1e-44
 Identities = 93/193 (48%), Positives = 129/193 (66%)

Query:    12 VTKGSSDGEPYLGMEFESEEAAKVFYDAYATHMGFIMRVDAFRRSMRDGKVVWRRLVCNK 71
             +T+   D EPY+G EFESE AA  FY+AYAT +GF++RV    RS  DG  + R+LVCNK
Sbjct:    62 MTEAQGD-EPYVGQEFESEAAAHGFYNAYATKVGFVIRVSKLSRSRHDGSPIGRQLVCNK 120

Query:    72 EGFRKLRPRRSENRKPRAVTREGCKAMIVVKKEKTGKWVVTRFVKEHNHPLVAIPANGRR 131
             EG+R L  +R +  + RA TR GCKAMI+++KE +GKWV+T+FVKEHNH L+  P   RR
Sbjct:   121 EGYR-LPSKRDKVIRQRAETRVGCKAMILIRKENSGKWVITKFVKEHNHSLM--PGRVRR 177

Query:   132 SVLLSQTPDEKDVKIRELTAELQRERKRSAAYQEQLEMVLRDMENHSHHLSRNIDDIVQS 191
               +  Q P+E D KI+EL  +L  E+KR+A Y+  LEM+   +E H+  LS+ I  IV +
Sbjct:   178 GCIYDQYPNEHD-KIQELMQQLAAEKKRAATYKRHLEMLFEQIEQHNESLSKRIQHIVDN 236

Query:   192 VKQIEAKRIAASH 204
             V+ +E +    +H
Sbjct:   237 VRNLEQRDHQQNH 249

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 = 449 (163.1 bits), Expect = 1.9e-42, P = 1.9e-42
 Identities = 90/198 (45%), Positives = 136/198 (68%)

Query:     5 VNDQEMAVTKGSSDG-----EPYLGMEFESEEAAKVFYDAYATHMGFIMRVDAFRRSMRD 59
             + D++   TK S++      EP  G+ FESE+AAK+FYD Y+  +GF+MRV + RRS +D
Sbjct:     1 MEDEDDPTTKNSNNTDDFAIEPREGIIFESEDAAKMFYDDYSRRLGFVMRVMSCRRSEKD 60

Query:    60 GKVVWRRLVCNKEGFR-KLRPRRSENRKPRAVTREGCKAMIVVKKEKTGKWVVTRFVKEH 118
             G+++ RR  CNKEG    +R +    RKPR  TREGCKAMI VK +++GKWV+T+FVKEH
Sbjct:    61 GRILARRFGCNKEGHCVSIRGKFGSVRKPRPSTREGCKAMIHVKYDRSGKWVITKFVKEH 120

Query:   119 NHPLVAIPANGRRSVLLSQTPDEKDVKIRELTAELQRERKRSAAYQEQLEMVLRDMENHS 178
             NHPLV  P   R ++      DEKD +I+ELT EL+ +++  AAY+EQL+   + +E HS
Sbjct:   121 NHPLVVSPREARHTL------DEKDKRIQELTIELRNKKRLCAAYKEQLDAFAKIVEEHS 174

Query:   179 HHLSRNIDDIVQSVKQIE 196
             + +++ ++++V ++K+ E
Sbjct:   175 NQIAKKVENVVNNLKEFE 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:2135738 AT4G12850 "AT4G12850" [Arabidopsis thaliana (taxid:3702)]

 Score = 364 (133.2 bits), Expect = 2.0e-33, P = 2.0e-33
 Identities = 76/179 (42%), Positives = 117/179 (65%)

Query:    20 EPYLGMEFESEEAAKVFYDAYATHMGFIMRVDAFRRSMRDGKVVWRRLVCNKEGFRKLRP 79
             EPY+G++FESEE AK FY  Y+  +GF++R+   RRS  DG+ + RRL CNK+GF    P
Sbjct:     9 EPYVGLKFESEEEAKDFYVEYSKRLGFVVRMMQRRRSGIDGRTLARRLGCNKQGFG---P 65

Query:    80 RRSENRKPRAVTREGCKAMIVVKKEKTGKWVVTRFVKEHNHPLVAIPANGRRSVLLSQTP 139
                 +    + +REGCKA I+VK EK+GKWVVTRF+KEHNH L  I ++   S       
Sbjct:    66 NNQRSSSSSSSSREGCKATILVKMEKSGKWVVTRFIKEHNHSLQFIGSSSYDSFA----- 120

Query:   140 DEKDVKIRELTAELQRERKRSAAYQEQLEMVLRDMENHSHHLSRNIDDIVQSVKQIEAK 198
              +K+ KI+ELT E++ + +    Y+++L   + ++E+++  LS  + DIV++VK++E +
Sbjct:   121 -DKERKIKELTEEIECQDRLCDVYRDRLVSFIDNVEHYTEELSLKVRDIVENVKKLECQ 178

GO:0003674 "molecular_function" evidence=ND

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 = 321 (118.1 bits), Expect = 7.5e-28, P = 7.5e-28
 Identities = 60/109 (55%), Positives = 81/109 (74%)

Query:    18 DGEPYLGMEFESEEAAKVFYDAYATHMGFIMRVDAFRRSMRDGKVVWRRLVCNKEGFRKL 77
             D EPY G+EFESEEAAK FY++YA  +GF  RV + RRS RDG ++ R+ VC KEGFR +
Sbjct:    70 DLEPYDGLEFESEEAAKAFYNSYARRIGFSTRVSSSRRSRRDGAIIQRQFVCAKEGFRNM 129

Query:    78 RPRRSENR---KPRAVTREGCKAMIVVKKEKTGKWVVTRFVKEHNHPLV 123
               +R+++R   +PR +TR GCKA + VK + +GKW+V+ FVK+HNH LV
Sbjct:   130 NEKRTKDREIKRPRTITRVGCKASLSVKMQDSGKWLVSGFVKDHNHELV 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:2082420 FRS7 "FAR1-related sequence 7" [Arabidopsis thaliana (taxid:3702)]

 Score = 218 (81.8 bits), Expect = 8.2e-17, P = 8.2e-17
 Identities = 49/113 (43%), Positives = 67/113 (59%)

Query:    10 MAVTKGSSDGEPYLGMEFESEEAAKVFYDAYATHMGFIMRVDAFRRSMRDGKVVWRRLVC 69
             +A  +G S  EPY+G+EF++ E A+ +Y++YAT  GF +R     RS  DG V  RR VC
Sbjct:    17 IAENEGDSGLEPYVGLEFDTAEEARDYYNSYATRTGFKVRTGQLYRSRTDGTVSSRRFVC 76

Query:    70 NKEGFRKLRPRRSENRKPRAVTREGCKAMIVVKKEKTGKWVVTRFVKEHNHPL 122
             +KEGF+        N      +R GC A I V++  TGKWV+ +  KEHNH L
Sbjct:    77 SKEGFQL-------N------SRTGCPAFIRVQRRDTGKWVLDQIQKEHNHDL 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:2144930 FRS12 "FAR1-related sequence 12" [Arabidopsis thaliana (taxid:3702)]

 Score = 218 (81.8 bits), Expect = 8.6e-17, P = 8.6e-17
 Identities = 49/109 (44%), Positives = 64/109 (58%)

Query:    14 KGSSDGEPYLGMEFESEEAAKVFYDAYATHMGFIMRVDAFRRSMRDGKVVWRRLVCNKEG 73
             +G S  EPY+G+EF++ E A+ FY+AYA   GF +R     RS  DG V  RR VC+KEG
Sbjct:    36 EGGSGVEPYVGLEFDTAEEAREFYNAYAARTGFKVRTGQLYRSRTDGTVSSRRFVCSKEG 95

Query:    74 FRKLRPRRSENRKPRAVTREGCKAMIVVKKEKTGKWVVTRFVKEHNHPL 122
             F+        N      +R GC A I V++  TGKWV+ +  KEHNH L
Sbjct:    96 FQL-------N------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

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

 Score = 203 (76.5 bits), Expect = 3.6e-15, P = 3.6e-15
 Identities = 40/99 (40%), Positives = 63/99 (63%)

Query:    24 GMEFESEEAAKVFYDAYATHMGFIMRVDAFRRSMRDGKVVWRRLVCNKEGFRKLRPRRSE 83
             GM+FES+EAA  FY  YA  +GF + + A RRS R GK +  ++ C++ G ++    ++ 
Sbjct:    41 GMDFESKEAAYYFYREYARSVGFGITIKASRRSKRSGKFIDVKIACSRFGTKR---EKAT 97

Query:    84 NRKPRAVTREGCKAMIVVKKEKTGKWVVTRFVKEHNHPL 122
                PR+  + GCKA + +K+++  KWV+  FVKEHNH +
Sbjct:    98 AINPRSCPKTGCKAGLHMKRKEDEKWVIYNFVKEHNHEI 136

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 = 196 (74.1 bits), Expect = 2.1e-14, P = 2.1e-14
 Identities = 50/168 (29%), Positives = 85/168 (50%)

Query:    15 GSSDGEPYLGMEFESEEAAKVFYDAYATHMGFIMRVDAFRRSMRDGKVVWRRLVCNKEGF 74
             G  D EP  G++F++ EAA +FY  YA  MGF   +   RRS +    +  +  C++ G 
Sbjct:    45 GDLDLEPRNGIDFDTHEAAYIFYQEYAKSMGFTTSIKNSRRSKKTKDFIDAKFACSRYGV 104

Query:    75 RKLRPRRSENRKPRAVTREGCKAMIVVKKEKTGKWVVTRFVKEHNHPLV-AIPANGR--R 131
                      + +   V +  CKA + VK+   GKW++  FVK+HNH L+ A+  + R  R
Sbjct:   105 TPESESSGSSSRRSTVKKTDCKASMHVKRRPDGKWIIHEFVKDHNHELLPALAYHFRIQR 164

Query:   132 SVLLSQTPDEKDV--KIRELTAELQRERKR-SAAYQEQLEMVLRDMEN 176
             +V L++  +  D+   + E T ++  E  R S  Y+    ++  D+ +
Sbjct:   165 NVKLAEK-NNIDILHAVSERTKKMYVEMSRQSGGYKNIGSLLQTDVSS 211

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

 Score = 178 (67.7 bits), Expect = 1.5e-12, P = 1.5e-12
 Identities = 51/161 (31%), Positives = 78/161 (48%)

Query:    25 MEFESEEAAKVFYDAYATHMGFIMRVDAFRRSMRDGKVVWRRLVCNKEGFRKLRPRRSEN 84
             MEFE+ E A +FY  YA  +GF     + RRS    + +  +  C + G ++   +  + 
Sbjct:     1 MEFETHEDAYLFYKDYAKSVGFGTAKLSSRRSRASKEFIDAKFSCIRYGSKQ---QSDDA 57

Query:    85 RKPRAVTREGCKAMIVVKKEKTGKWVVTRFVKEHNHPLVAIPANGRRSVLLSQTPDEKDV 144
               PRA  + GCKA + VK+   GKW V  FVKEHNH L+   A+  RS   ++     D 
Sbjct:    58 INPRASPKIGCKASMHVKRRPDGKWYVYSFVKEHNHDLLPEQAHYFRSHRNTELVKSNDS 117

Query:   145 KIRELTAELQRERKRSAAYQEQLEMVLRDMENHSHHLSRNI 185
             ++R        + K  +AY + L+ +   M N  H   R +
Sbjct:   118 RLRRKKNTPLTDCKHLSAYHD-LDFIDGYMRNQ-HDKGRRL 156

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!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	205
pfam03101	90	pfam03101, FAR1, FAR1 DNA-binding domain	3e-38
PLN03097	846	PLN03097, FHY3, Protein FAR-RED ELONGATED HYPOCOTY	3e-17

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

 Score =  127 bits (320), Expect = 3e-38
 Identities = 53/88 (60%), Positives = 64/88 (72%)

Query: 36  FYDAYATHMGFIMRVDAFRRSMRDGKVVWRRLVCNKEGFRKLRPRRSENRKPRAVTREGC 95
           FY+AYA  +GF +R    RRS RDG+++ RR VC+KEGFRK R +    R+PRA TR GC
Sbjct: 2   FYNAYARRVGFSVRKSKSRRSRRDGEIIRRRFVCSKEGFRKERKKSVRKRRPRASTRTGC 61

Query: 96  KAMIVVKKEKTGKWVVTRFVKEHNHPLV 123
           KAM+VVK    GKWVVT+FV EHNHPL 
Sbjct: 62  KAMMVVKLRSDGKWVVTKFVLEHNHPLA 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 = 78.9 bits (194), Expect = 3e-17
 Identities = 46/137 (33%), Positives = 66/137 (48%), Gaps = 13/137 (9%)

Query: 4   NVNDQEMAVTKGSSDGEPYLGMEFESEEAAKVFYDAYATHMGFIMRVDAFRRSMRDGKVV 63
           N    E+   K  ++ EP  GMEFES   A  FY  YA  MGF   +   RRS    + +
Sbjct: 57  NSPTGELVEFKEDTNLEPLSGMEFESHGEAYSFYQEYARSMGFNTAIQNSRRSKTSREFI 116

Query: 64  WRRLVCNKEGFRKL------RPRRSENRKP-------RAVTREGCKAMIVVKKEKTGKWV 110
             +  C++ G ++       RPR  + ++        R+  +  CKA + VK+   GKWV
Sbjct: 117 DAKFACSRYGTKREYDKSFNRPRARQTKQDPENGTGRRSCAKTDCKASMHVKRRPDGKWV 176

Query: 111 VTRFVKEHNHPLVAIPA 127
           +  FVKEHNH L+   A
Sbjct: 177 IHSFVKEHNHELLPAQA 193

Length = 846

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	205
PLN03097	846	FHY3 Protein FAR-RED ELONGATED HYPOCOTYL 3; Provis	100.0
PF03101	91	FAR1: FAR1 DNA-binding domain; InterPro: IPR004330	99.95
PF08731	111	AFT: Transcription factor AFT; InterPro: IPR014842	99.1
PF03108	67	DBD_Tnp_Mut: MuDR family transposase; InterPro: IP	98.19
PF04500	62	FLYWCH: FLYWCH zinc finger domain; InterPro: IPR00	91.17
PF03106	60	WRKY: WRKY DNA -binding domain; InterPro: IPR00365	90.57
COG5470	96	Uncharacterized conserved protein [Function unknow	85.8

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

Probab=100.00  E-value=3.2e-35  Score=286.40  Aligned_cols=123  Identities=34%  Similarity=0.582  Sum_probs=106.2

Q ss_pred             cccccccccccCCCCCCCccCCeeCCHHHHHHHHHHHhhhcCcEEEEcceeeccCCcceEEEEEEecccCccccCCCC--
Q 028717            4 NVNDQEMAVTKGSSDGEPYLGMEFESEEAAKVFYDAYATHMGFIMRVDAFRRSMRDGKVVWRRLVCNKEGFRKLRPRR--   81 (205)
Q Consensus         4 ~~~~~~~~~~e~~~~~~P~~Gm~F~S~eeA~~FY~~YA~~~GF~ir~~~s~rs~~~g~i~~~~fvCsreG~~~~~~~~--   81 (205)
                      ++.+.+.++.+.++..+|++||+|+|+||||+||+.||+++||+||+.+++|++.+|.|++++|+|+|+|+++.+.+.  
T Consensus        57 ~~~~~~~~~~~~~~~~~P~vGMeF~S~eeA~~FYn~YA~~~GFsVRi~~srrsk~~~~ii~r~fvCsreG~~~~~~~~~~  136 (846)
T PLN03097         57 NSPTGELVEFKEDTNLEPLSGMEFESHGEAYSFYQEYARSMGFNTAIQNSRRSKTSREFIDAKFACSRYGTKREYDKSFN  136 (846)
T ss_pred             cccccccccccCCCCccCcCCCeECCHHHHHHHHHHHHhhcCceEEeeceeccCCCCcEEEEEEEEcCCCCCcccccccc
Confidence            344566677888999999999999999999999999999999999999999999999999999999999996432110  


Q ss_pred             -----------CCCCCCCcccccCCccEEEEEEecCCcEEEEEEeecCCcccccCC
Q 028717           82 -----------SENRKPRAVTREGCKAMIVVKKEKTGKWVVTRFVKEHNHPLVAIP  126 (205)
Q Consensus        82 -----------~~~~r~r~~tRtgC~A~m~vk~~~~gkW~V~~~~~eHNH~L~~~~  126 (205)
                                 ...+++|+.+||||+|+|+|++.++|+|+|++|++||||||.|+.
T Consensus       137 ~~~~~~~k~~~~~~~~rR~~tRtGC~A~m~Vk~~~~gkW~V~~fv~eHNH~L~p~~  192 (846)
T PLN03097        137 RPRARQTKQDPENGTGRRSCAKTDCKASMHVKRRPDGKWVIHSFVKEHNHELLPAQ  192 (846)
T ss_pred             cccccccccCcccccccccccCCCCceEEEEEEcCCCeEEEEEEecCCCCCCCCcc
Confidence                       011235778999999999999988899999999999999999764

>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=99.95  E-value=1.3e-28  Score=180.23  Aligned_cols=90  Identities=41%  Similarity=0.757  Sum_probs=82.0

Q ss_pred             HHHHHHhhhcCcEEEEcceeeccCCcceEEEEEEecccCccccCCCC-CCCCCCCcccccCCccEEEEEEecCCcEEEEE
Q 028717           35 VFYDAYATHMGFIMRVDAFRRSMRDGKVVWRRLVCNKEGFRKLRPRR-SENRKPRAVTREGCKAMIVVKKEKTGKWVVTR  113 (205)
Q Consensus        35 ~FY~~YA~~~GF~ir~~~s~rs~~~g~i~~~~fvCsreG~~~~~~~~-~~~~r~r~~tRtgC~A~m~vk~~~~gkW~V~~  113 (205)
                      +||+.||..+||+||+.++++++.+|.+++..|+|+++|+++.+... ...+++++++||||||+|.|++..+|.|.|+.
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            59999999999999999999988899999999999999997665443 45678899999999999999998789999999


Q ss_pred             EeecCCccccc
Q 028717          114 FVKEHNHPLVA  124 (205)
Q Consensus       114 ~~~eHNH~L~~  124 (205)
                      |+++|||||+|
T Consensus        81 ~~~~HNH~L~P   91 (91)
T PF03101_consen   81 FVLEHNHPLCP   91 (91)
T ss_pred             CcCCcCCCCCC
Confidence            99999999986

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=99.10  E-value=8e-10  Score=84.00  Aligned_cols=89  Identities=19%  Similarity=0.367  Sum_probs=69.2

Q ss_pred             eCCHHHHHHHHHHHhhhcCcEEEEcceeeccCCcceEEEEEEecccCccccCCCC--------------------CCCCC
Q 028717           27 FESEEAAKVFYDAYATHMGFIMRVDAFRRSMRDGKVVWRRLVCNKEGFRKLRPRR--------------------SENRK   86 (205)
Q Consensus        27 F~S~eeA~~FY~~YA~~~GF~ir~~~s~rs~~~g~i~~~~fvCsreG~~~~~~~~--------------------~~~~r   86 (205)
                      |++.+|...|....++..||+|++.+|..+       ...|.|--.|..+.....                    ...+.
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            889999999999999999999999988653       347999887774332110                    11122


Q ss_pred             CC-cccccCCccEEEEEEe-cCCcEEEEEEeecCCccc
Q 028717           87 PR-AVTREGCKAMIVVKKE-KTGKWVVTRFVKEHNHPL  122 (205)
Q Consensus        87 ~r-~~tRtgC~A~m~vk~~-~~gkW~V~~~~~eHNH~L  122 (205)
                      ++ .+..++||++|+-... ...+|.|..+..+|||||
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            33 4556999999998876 579999999999999997

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=98.19  E-value=1.1e-05  Score=55.66  Aligned_cols=62  Identities=26%  Similarity=0.416  Sum_probs=52.2

Q ss_pred             ccCCeeCCHHHHHHHHHHHhhhcCcEEEEcceeeccCCcceEEEEEEecccCccccCCCCCCCCCCCcccccCCccEEEE
Q 028717           22 YLGMEFESEEAAKVFYDAYATHMGFIMRVDAFRRSMRDGKVVWRRLVCNKEGFRKLRPRRSENRKPRAVTREGCKAMIVV  101 (205)
Q Consensus        22 ~~Gm~F~S~eeA~~FY~~YA~~~GF~ir~~~s~rs~~~g~i~~~~fvCsreG~~~~~~~~~~~~r~r~~tRtgC~A~m~v  101 (205)
                      .+||.|+|.+|+......||-..||.++..++.+       .+..++|.  +                   .|||++|..
T Consensus         5 ~~G~~F~~~~e~k~av~~yai~~~~~~~v~ksd~-------~r~~~~C~--~-------------------~~C~Wrv~a   56 (67)
T PF03108_consen    5 EVGQTFPSKEEFKEAVREYAIKNGFEFKVKKSDK-------KRYRAKCK--D-------------------KGCPWRVRA   56 (67)
T ss_pred             ccCCEECCHHHHHHHHHHHHHhcCcEEEEeccCC-------EEEEEEEc--C-------------------CCCCEEEEE
Confidence            5799999999999999999999999999987643       36778886  1                   369999999


Q ss_pred             EEec-CCcEEE
Q 028717          102 KKEK-TGKWVV  111 (205)
Q Consensus       102 k~~~-~gkW~V  111 (205)
                      ...+ ++.|.|
T Consensus        57 s~~~~~~~~~I   67 (67)
T PF03108_consen   57 SKRKRSDTFQI   67 (67)
T ss_pred             EEcCCCCEEEC
Confidence            8874 578876

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=91.17  E-value=0.49  Score=30.94  Aligned_cols=25  Identities=40%  Similarity=0.694  Sum_probs=10.7

Q ss_pred             cCCccEEEEEEecCCcEEEEEEeecCCc
Q 028717           93 EGCKAMIVVKKEKTGKWVVTRFVKEHNH  120 (205)
Q Consensus        93 tgC~A~m~vk~~~~gkW~V~~~~~eHNH  120 (205)
                      .+|+|++.+.   ++.-.|.....+|||
T Consensus        38 ~~C~a~~~~~---~~~~~~~~~~~~HnH   62 (62)
T PF04500_consen   38 HGCRARLITD---AGDGRVVRTNGEHNH   62 (62)
T ss_dssp             S----EEEEE-----TTEEEE-S---SS
T ss_pred             CCCeEEEEEE---CCCCEEEECCCccCC
Confidence            6899999987   233345556689999

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=90.57  E-value=1.8  Score=29.41  Aligned_cols=28  Identities=36%  Similarity=0.656  Sum_probs=21.6

Q ss_pred             CCccEEEEEEec-CCcEEEEEEeecCCcc
Q 028717           94 GCKAMIVVKKEK-TGKWVVTRFVKEHNHP  121 (205)
Q Consensus        94 gC~A~m~vk~~~-~gkW~V~~~~~eHNH~  121 (205)
                      ||+|.=.|.+.. ++.-+++...-+||||
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            899998888763 7788899999999997

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.

>COG5470 Uncharacterized conserved protein [Function unknown]

Probab=85.80  E-value=0.46  Score=35.41  Aligned_cols=45  Identities=22%  Similarity=0.229  Sum_probs=34.5

Q ss_pred             ccccccccCCCCCCCccCCeeCCHHHHHHHHHHHhhhcCcEEEEc
Q 028717            7 DQEMAVTKGSSDGEPYLGMEFESEEAAKVFYDAYATHMGFIMRVD   51 (205)
Q Consensus         7 ~~~~~~~e~~~~~~P~~Gm~F~S~eeA~~FY~~YA~~~GF~ir~~   51 (205)
                      |++..+.|++-.-.+.+=++|+|.+.|++|||+=+...=-++|..
T Consensus        40 GG~v~~lEG~w~ptr~vviEFps~~~ar~~y~SpeYq~a~~~Rq~   84 (96)
T COG5470          40 GGEVETLEGEWRPTRNVVIEFPSLEAARDCYNSPEYQAAAAIRQA   84 (96)
T ss_pred             CCCeeeccCCCCcccEEEEEcCCHHHHHHHhcCHHHHHHHHHHhh
Confidence            455677788877678888999999999999998666655555443

---

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	205
2ayd_A	76	WRKY transcription factor 1; beta strands, zinc fi	93.08
2rpr_A	87	Flywch-type zinc finger-containing protein 1; flyw	89.29
1wj2_A	78	Probable WRKY transcription factor 4; DNA-binding	88.31

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

Probab=93.08  E-value=0.42  Score=33.20  Aligned_cols=31  Identities=23%  Similarity=0.497  Sum_probs=26.0

Q ss_pred             cCCccEEEEEEe-cCCcEEEEEEeecCCcccc
Q 028717           93 EGCKAMIVVKKE-KTGKWVVTRFVKEHNHPLV  123 (205)
Q Consensus        93 tgC~A~m~vk~~-~~gkW~V~~~~~eHNH~L~  123 (205)
                      .||+|+=.|.+. ++..-.++-..-+|||++.
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            489999888876 4678888999999999974

>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=89.29  E-value=0.54  Score=32.80  Aligned_cols=24  Identities=17%  Similarity=0.477  Sum_probs=16.8

Q ss_pred             cCCccEEEEEEecCCcEEEEEEeecCCccc
Q 028717           93 EGCKAMIVVKKEKTGKWVVTRFVKEHNHPL  122 (205)
Q Consensus        93 tgC~A~m~vk~~~~gkW~V~~~~~eHNH~L  122 (205)
                      .+|+|++.....  +   |. +...||||.
T Consensus        50 ~kCrARi~T~~~--~---~~-~~~~HnH~p   73 (87)
T 2rpr_A           50 LGCRSRAITQGH--R---IM-VMRSHCHQP   73 (87)
T ss_dssp             SCCCCEEEEETT--E---EE-ECSCCSSCC
T ss_pred             CCCCEEEEEcCC--C---EE-CCCCcCCCC
Confidence            389999887642  2   32 567899974

>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=88.31  E-value=0.62  Score=32.49  Aligned_cols=31  Identities=35%  Similarity=0.494  Sum_probs=25.9

Q ss_pred             cCCccEEEEEEe-cCCcEEEEEEeecCCcccc
Q 028717           93 EGCKAMIVVKKE-KTGKWVVTRFVKEHNHPLV  123 (205)
Q Consensus        93 tgC~A~m~vk~~-~~gkW~V~~~~~eHNH~L~  123 (205)
                      .||+|+=.|.+. .+..-.++-..-+|||++.
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            489999888876 4677888889999999974

---

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	205
d1wj2a_	71	WRKY DNA-binding protein 4 {Thale cress (Arabidops	92.22

>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=92.22  E-value=0.14  Score=33.58  Aligned_cols=31  Identities=35%  Similarity=0.494  Sum_probs=25.2

Q ss_pred             cCCccEEEEEEe-cCCcEEEEEEeecCCcccc
Q 028717           93 EGCKAMIVVKKE-KTGKWVVTRFVKEHNHPLV  123 (205)
Q Consensus        93 tgC~A~m~vk~~-~~gkW~V~~~~~eHNH~L~  123 (205)
                      .||+|+=.|-.. +++.-+++-..-+||||+.
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            489999888876 4677788888999999863