Citrus Sinensis ID: 047290

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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
MGNDEEEQGIKLFGKTITLHGRQVKEEQNQRGSDQPQAVVDKRPDKIIPCPRCKSMETKFCYFNNYNVNQPRHFCKGCQRYWTAGGALRNVPVGAGRRKTKPPGRGLPDGCLYDVASGDHHHQLLHHQLDQFDLEGVFVEDWHPAAAAHGYGGFQNAFPVKRRRSNSGGQLC
Secondary Structure (PSIPRED)
cccccHHcccccccccccccccccHHHHHcccccccccccccccccccccccccccccccEEEcccccccccHHcccccccccccccEEccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEcccccccc
Secondary Structure Prediction (SSPRO)
ccccccccccEEccccEEEcccccccccccccccHHHHccccccccccccccccccccEEEEEcccccccccHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEcccccccccccccccccccccccccccccccc
Coil and Loop (DISEMBL)
MGNDEEEQGIKLFGKTITLHgrqvkeeqnqrgsdqpqavvdkrpdkiipcprcksmetkfcyfnnynvnqprhfckgcqrywtaggalrnvpvgagrrktkppgrglpdgclydvasgdhhhQLLHHQldqfdlegvfvedwhpaaaahgyggfqnafpvkrrrsnsggqlc
Flexible Loop (DISEMBL)
MGNDEEEQGIKLFGKTITLHgrqvkeeqnqrgsdqpqavvdkrpdkiiPCPRCKSMETKFCYFNNYNVNQPRHFCKGCQRYWTAGgalrnvpvgagrrktkppgrgLPDGCLYDVASGDHHHQLLHHQLDQFDLEGVFVEDWHPAAAAHGYGGFQNAFPVKRRRSNSGGQLC
Low Complexity Region (SEG)
MGNDEEEQGIKLFGKTITLHGRQVKEEQNQRGSDQPQAVVDKRPDKIIPCPRCKSMETKFCYFNNYNVNQPRHFCKGCQRYWTAGGALRNVPVGAGRRKTKPPGRGLPDGCLYDVASGdhhhqllhhqldqfdlEGVFVEDWHPAAAAHGYGGFQNAFPVKRRRSNSGGQLC
Disordered region (IsUnstruct)
************FGKTI****************************KIIPCPRCKSMETKFCYFNNYNVNQPRHFCKGCQRYWTAGGALRNVPVGA***********LPDGCLYDVASGDHHHQLLHHQLDQFDLEGVFVEDWHPAAAAHGYGGFQNAF**************
Disordered Region (DISOPRED)
***************************************************RCKSMETKFCYFNNYNVNQPRHFCKGCQRYWTAGGALRN**********************************************************************************
Disordered Region (DISEMBL)
********GIKLFGKTITLHGRQ****************VDKRPDKIIPCPRCKSMETKFCYFNNYNVNQPRHFCKGCQRYWTAGGALRNVPVGAGRRKTKPPGRGLPDGCLYDVASGDHHHQLLHHQLDQFDLEGVFVEDWHPAAAAHGYGGFQNAFPVKR**********
Disordered Region (DISPRO)
********GIKL**KTITLH**********************RPDKIIPCPRCKSMETKFCYFNNYNVNQPRHFCKGCQRYWTAGGALRNVPVG*****************************************GVFVEDWHPAAAAHGYGGFQNAFPVK***********
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MGNDEEEQGIKLFGKTITLHGRQVKEEQNQRGSDQPQAVVDKRPDKIIPCPRCKSMETKFCYFNNYNVNQPRHFCKGCQRYWTAGGALRNVPVGAGRRKTKPPGRGLPDGCLYDVASGDHHHQLLHHQLDQFDLEGVFVEDWHPAAAAHGYGGFQNAFPVKRRRSNSGGQLC
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	172	2.2.26 [Sep-21-2011]
P68350	175	Dof zinc finger protein D	yes	no	0.912	0.897	0.540	1e-47
O22967	170	Cyclic dof factor 4 OS=Ar	no	no	0.901	0.911	0.566	8e-47
Q8W1E3	298	Cyclic dof factor 1 OS=Ar	no	no	0.569	0.328	0.580	7e-30
Q93ZL5	457	Cyclic dof factor 2 OS=Ar	no	no	0.587	0.221	0.592	9e-30
Q8LFV3	448	Cyclic dof factor 3 OS=Ar	no	no	0.424	0.162	0.733	4e-29
Q9SEZ3	399	Cyclic dof factor 5 OS=Ar	no	no	0.476	0.205	0.563	1e-26
Q9LQX4	366	Dof zinc finger protein D	no	no	0.401	0.188	0.695	2e-26
P38564	238	Dof zinc finger protein M	N/A	no	0.296	0.214	0.784	2e-20
Q43385	296	Dof zinc finger protein D	no	no	0.389	0.226	0.573	3e-20
Q9ZV33	340	Dof zinc finger protein D	no	no	0.325	0.164	0.714	3e-20

>sp|P68350|DOF15_ARATH Dof zinc finger protein DOF1.5 OS=Arabidopsis thaliana GN=DOF1.5 PE=1 SV=1

 Score =  188 bits (478), Expect = 1e-47,   Method: Compositional matrix adjust.
 Identities = 99/183 (54%), Positives = 117/183 (63%), Gaps = 26/183 (14%)

Query: 5   EEEQGIKLFGKTITLHGRQVKEEQNQRG---------------SDQPQAVVDKRPDKIIP 49
           ++ QGIKLFGKTIT +    +  + +                 S       +KRPDKIIP
Sbjct: 4   QDSQGIKLFGKTITFNANITQTIKKEEQQQQQQPELQATTAVRSPSSDLTAEKRPDKIIP 63

Query: 50  CPRCKSMETKFCYFNNYNVNQPRHFCKGCQRYWTAGGALRNVPVGAGRRKTKPPGRGLPD 109
           CPRCKSMETKFCYFNNYNVNQPRHFCKGCQRYWTAGGALRNVPVGAGRRK+KPPGR    
Sbjct: 64  CPRCKSMETKFCYFNNYNVNQPRHFCKGCQRYWTAGGALRNVPVGAGRRKSKPPGRVGGF 123

Query: 110 GCLYDVASGDHHHQLLHHQLDQFDLEGVFVEDWHPAAAAHGYGGFQNAFPVKRRRSNSGG 169
             L   A+G          +DQ +L+ + VE+W  A A+H  GGF++ FPVKR R  + G
Sbjct: 124 AELLGAATG---------AVDQVELDALLVEEWRAATASH--GGFRHDFPVKRLRCYTDG 172

Query: 170 QLC 172
           Q C
Sbjct: 173 QSC 175

Transcription factor that binds specifically to a 5'-AA[AG]G-3' consensus core sequence. Acts as a negative regulator in the phytochrome-mediated light responses. Controls phyB-mediated end-of-day response and the phyA-mediated anthocyanin accumulation.
Arabidopsis thaliana (taxid: 3702)

>sp|O22967|CDF4_ARATH Cyclic dof factor 4 OS=Arabidopsis thaliana GN=CDF4 PE=2 SV=1

 Score =  186 bits (471), Expect = 8e-47,   Method: Compositional matrix adjust.
 Identities = 102/180 (56%), Positives = 119/180 (66%), Gaps = 25/180 (13%)

Query: 5   EEEQGIKLFGKTITLHGRQVKEEQNQ-----------RGSDQPQAVVDKRPDKIIPCPRC 53
           ++ QGIKLFGKTI  + R +K E+             R S       +KRPDKII CPRC
Sbjct: 4   QDSQGIKLFGKTIAFNTRTIKNEEETHPPEQEATIAVRSSSSSDLTAEKRPDKIIACPRC 63

Query: 54  KSMETKFCYFNNYNVNQPRHFCKGCQRYWTAGGALRNVPVGAGRRKTKPPGRGLPDGCLY 113
           KSMETKFCYFNNYNVNQPRHFCKGC RYWTAGGALRNVPVGAGRRK+KPPGR +  G L 
Sbjct: 64  KSMETKFCYFNNYNVNQPRHFCKGCHRYWTAGGALRNVPVGAGRRKSKPPGR-VVVGMLG 122

Query: 114 DVASGDHHHQLLHHQLDQFDLEGVFVEDW-HPAAAAHGYGGFQNAFPVKRRRSNSGGQLC 172
           D  +G    +L++         G+ VE+W H AAAAH  G F++ FP+KR R  S GQ C
Sbjct: 123 D-GNGVRQVELIN---------GLLVEEWQHAAAAAH--GSFRHDFPMKRLRCYSDGQSC 170

Transcription factor that binds specifically to a 5'-AA[AG]G-3' consensus core sequence.

Arabidopsis thaliana (taxid: 3702)

>sp|Q8W1E3|CDF1_ARATH Cyclic dof factor 1 OS=Arabidopsis thaliana GN=CDF1 PE=1 SV=2

 Score =  129 bits (325), Expect = 7e-30,   Method: Compositional matrix adjust.
 Identities = 61/105 (58%), Positives = 75/105 (71%), Gaps = 7/105 (6%)

Query: 4   DEEEQGIKLFGKTI----TLHGRQVKEEQNQRGSDQPQAVVDK---RPDKIIPCPRCKSM 56
           + ++  IKLFG  I     L     +EE+NQ  +   Q+  DK   +P KI+PCPRC SM
Sbjct: 3   ETKDPAIKLFGMKIPFPTVLEVADEEEEKNQNKTLTDQSEKDKTLKKPTKILPCPRCNSM 62

Query: 57  ETKFCYFNNYNVNQPRHFCKGCQRYWTAGGALRNVPVGAGRRKTK 101
           ETKFCY+NNYNVNQPRHFCK CQRYWT+GG +R+VP+GAGRRK K
Sbjct: 63  ETKFCYYNNYNVNQPRHFCKACQRYWTSGGTMRSVPIGAGRRKNK 107

Transcription factor that binds specifically to a 5'-AA[AG]G-3' consensus core sequence.

Arabidopsis thaliana (taxid: 3702)

>sp|Q93ZL5|CDF2_ARATH Cyclic dof factor 2 OS=Arabidopsis thaliana GN=CDF2 PE=1 SV=2

 Score =  129 bits (324), Expect = 9e-30,   Method: Compositional matrix adjust.
 Identities = 61/103 (59%), Positives = 68/103 (66%), Gaps = 2/103 (1%)

Query: 2   GNDEEEQGIKLFGKTITLHGRQVKEEQNQRGSDQPQAVVDKRPDKIIPCPRCKSMETKFC 61
            ND       +  KT T    +  EE       Q   +  K+PDKI+PCPRC SMETKFC
Sbjct: 94  SNDVTTTTSGITEKTETTKAAKTNEESGGTACSQEGKL--KKPDKILPCPRCNSMETKFC 151

Query: 62  YFNNYNVNQPRHFCKGCQRYWTAGGALRNVPVGAGRRKTKPPG 104
           Y+NNYNVNQPRHFCK CQRYWTAGG +RNVPVGAGRRK K P 
Sbjct: 152 YYNNYNVNQPRHFCKKCQRYWTAGGTMRNVPVGAGRRKNKSPA 194

Transcription factor that binds specifically to a 5'-AA[AG]G-3' consensus core sequence.

Arabidopsis thaliana (taxid: 3702)

>sp|Q8LFV3|CDF3_ARATH Cyclic dof factor 3 OS=Arabidopsis thaliana GN=CDF3 PE=1 SV=2

 Score =  127 bits (319), Expect = 4e-29,   Method: Compositional matrix adjust.
 Identities = 55/75 (73%), Positives = 62/75 (82%), Gaps = 2/75 (2%)

Query: 27  EQNQRGSDQPQAVVDKRPDKIIPCPRCKSMETKFCYFNNYNVNQPRHFCKGCQRYWTAGG 86
           E NQ+ +  P     K+P KI+PCPRCKSMETKFCY+NNYN+NQPRHFCK CQRYWTAGG
Sbjct: 91  EDNQQTT--PDGKTLKKPTKILPCPRCKSMETKFCYYNNYNINQPRHFCKACQRYWTAGG 148

Query: 87  ALRNVPVGAGRRKTK 101
            +RNVPVGAGRRK K
Sbjct: 149 TMRNVPVGAGRRKNK 163

Transcription factor that binds specifically to a 5'-AA[AG]G-3' consensus core sequence.

Arabidopsis thaliana (taxid: 3702)

>sp|Q9SEZ3|CDF5_ARATH Cyclic dof factor 5 OS=Arabidopsis thaliana GN=CDF5 PE=2 SV=1

 Score =  119 bits (297), Expect = 1e-26,   Method: Compositional matrix adjust.
 Identities = 53/94 (56%), Positives = 67/94 (71%), Gaps = 12/94 (12%)

Query: 37  QAVVDKRPDKIIPCPRCKSMETKFCYFNNYNVNQPRHFCKGCQRYWTAGGALRNVPVGAG 96
           ++   K+PDK+IPCPRC+S  TKFCY+NNYNVNQPR+FC+ CQRYWTAGG++RNVPVG+G
Sbjct: 121 KSTALKKPDKLIPCPRCESANTKFCYYNNYNVNQPRYFCRNCQRYWTAGGSMRNVPVGSG 180

Query: 97  RRKTKPPGRGLPDGCLYDVASGDHHHQLLHHQLD 130
           RRK K    G P        S +H+ Q+     D
Sbjct: 181 RRKNK----GWP--------SSNHYLQVTSEDCD 202

Transcription factor that binds specifically to a 5'-AA[AG]G-3' consensus core sequence.

Arabidopsis thaliana (taxid: 3702)

>sp|Q9LQX4|DOF13_ARATH Dof zinc finger protein DOF1.3 OS=Arabidopsis thaliana GN=DOF1.3 PE=2 SV=1

 Score =  118 bits (295), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 48/69 (69%), Positives = 59/69 (85%)

Query: 33  SDQPQAVVDKRPDKIIPCPRCKSMETKFCYFNNYNVNQPRHFCKGCQRYWTAGGALRNVP 92
           S++ +    K+PDKI+PCPRC S +TKFCY+NNYNVNQPRHFC+ CQRYWTAGG++R VP
Sbjct: 90  SEEEKTTELKKPDKILPCPRCNSADTKFCYYNNYNVNQPRHFCRKCQRYWTAGGSMRIVP 149

Query: 93  VGAGRRKTK 101
           VG+GRRK K
Sbjct: 150 VGSGRRKNK 158

Transcription factor that binds specifically to a 5'-AA[AG]G-3' consensus core sequence.

Arabidopsis thaliana (taxid: 3702)

>sp|P38564|MNB1A_MAIZE Dof zinc finger protein MNB1A OS=Zea mays GN=MNB1A PE=1 SV=2

 Score = 98.2 bits (243), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 40/51 (78%), Positives = 44/51 (86%)

Query: 49 PCPRCKSMETKFCYFNNYNVNQPRHFCKGCQRYWTAGGALRNVPVGAGRRK 99
          PCPRC S +TKFCY+NNYN +QPRHFCKGC+RYWT GG LRNVPVG G RK
Sbjct: 48 PCPRCASRDTKFCYYNNYNTSQPRHFCKGCRRYWTKGGTLRNVPVGGGTRK 98

Transcription factor that binds specifically to a 5'-AA[AG]G-3' consensus core sequence at the MNF1-binding site.

Zea mays (taxid: 4577)

>sp|Q43385|DOF37_ARATH Dof zinc finger protein DOF3.7 OS=Arabidopsis thaliana GN=DOF3.7 PE=1 SV=2

 Score = 97.8 bits (242), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 43/75 (57%), Positives = 51/75 (68%), Gaps = 8/75 (10%)

Query: 43  RPDKIIPCPRCKSMETKFCYFNNYNVNQPRHFCKGCQRYWTAGGALRNVPVGAGRRKTK- 101
           RP + + CPRC S  TKFCY+NNY++ QPR+FCKGC+RYWT GG+LRNVPVG   RK K 
Sbjct: 69  RPQEKVNCPRCNSTNTKFCYYNNYSLTQPRYFCKGCRRYWTEGGSLRNVPVGGSSRKNKR 128

Query: 102 -------PPGRGLPD 109
                  P    LPD
Sbjct: 129 SSTPLASPSNPKLPD 143

Transcription factor specifically involved in the maternal control of seed germination. Regulates transcription by binding to a 5'-AA[AG]G-3' consensus core sequence. May ensure the inactivity of a component that would be activated to trigger germination as a consequence of red light perception.

Arabidopsis thaliana (taxid: 3702)

>sp|Q9ZV33|DOF22_ARATH Dof zinc finger protein DOF2.2 OS=Arabidopsis thaliana GN=DOF2.2 PE=2 SV=2

 Score = 97.8 bits (242), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 40/56 (71%), Positives = 45/56 (80%)

Query: 44  PDKIIPCPRCKSMETKFCYFNNYNVNQPRHFCKGCQRYWTAGGALRNVPVGAGRRK 99
           P+  + CPRC S  TKFCYFNNYN+ QPRHFCK C+RYWT GGALRNVPVG G R+
Sbjct: 90  PEGALKCPRCDSANTKFCYFNNYNLTQPRHFCKACRRYWTRGGALRNVPVGGGCRR 145

Transcription factor that binds specifically to a 5'-AA[AG]G-3' consensus core sequence.

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	172
359483726	159	PREDICTED: dof zinc finger protein DOF1.	0.854	0.924	0.645	6e-54
297740502	173	unnamed protein product [Vitis vinifera]	0.854	0.849	0.645	9e-54
255563152	148	hypothetical protein RCOM_1015170 [Ricin	0.825	0.959	0.670	3e-52
224076964	159	f-box family protein [Populus trichocarp	0.877	0.949	0.610	2e-50
224114680	161	f-box family protein [Populus trichocarp	0.883	0.944	0.604	1e-46
15218846	175	Dof zinc finger protein DOF1.5 [Arabidop	0.912	0.897	0.540	6e-46
297851336	173	Dof-type zinc finger domain-containing p	0.906	0.901	0.538	3e-45
333037489	162	Dof-domain transcription factor protein	0.877	0.932	0.579	3e-45
15226224	170	Dof zinc finger protein DOF2.3 [Arabidop	0.901	0.911	0.566	3e-45
351726341	165	uncharacterized protein LOC100527802 [Gl	0.744	0.775	0.586	4e-42

>gi|359483726|ref|XP_002266522.2| PREDICTED: dof zinc finger protein DOF1.5-like [Vitis vinifera]

 Score =  215 bits (547), Expect = 6e-54,   Method: Compositional matrix adjust.
 Identities = 111/172 (64%), Positives = 128/172 (74%), Gaps = 25/172 (14%)

Query: 5   EEEQGIKLFGKTITLHGRQVKEEQNQRGSDQPQAVVDKRPDKIIPCPRCKSMETKFCYFN 64
           ++  GIKLFG TI LHG +VKEE N +G  +     +KRP+KIIPCPRCKSMETKFCYFN
Sbjct: 9   QDAPGIKLFGATIALHGGEVKEEANNKGDHKE----EKRPEKIIPCPRCKSMETKFCYFN 64

Query: 65  NYNVNQPRHFCKGCQRYWTAGGALRNVPVGAGRRKTKPPGRGLP---DGCLYDVASGDHH 121
           NYNVNQPRHFCKGCQRYWTAGGALRNVPVGAGRRK+KPP RG+    + CL+D ++G H 
Sbjct: 65  NYNVNQPRHFCKGCQRYWTAGGALRNVPVGAGRRKSKPPCRGVAGFLESCLFDASAGVH- 123

Query: 122 HQLLHHQLDQFDLEGVFVEDWHPAAAAHGYGGFQNAFPVKRRR-SNSGGQLC 172
                    QFDLEGV VE+WH        GGF++AFP KRRR S+SGGQ C
Sbjct: 124 ---------QFDLEGVVVEEWH-------MGGFRHAFPAKRRRSSSSGGQTC 159

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297740502|emb|CBI30684.3| unnamed protein product [Vitis vinifera]

 Score =  214 bits (545), Expect = 9e-54,   Method: Compositional matrix adjust.
 Identities = 111/172 (64%), Positives = 128/172 (74%), Gaps = 25/172 (14%)

Query: 5   EEEQGIKLFGKTITLHGRQVKEEQNQRGSDQPQAVVDKRPDKIIPCPRCKSMETKFCYFN 64
           ++  GIKLFG TI LHG +VKEE N +G  +     +KRP+KIIPCPRCKSMETKFCYFN
Sbjct: 23  QDAPGIKLFGATIALHGGEVKEEANNKGDHKE----EKRPEKIIPCPRCKSMETKFCYFN 78

Query: 65  NYNVNQPRHFCKGCQRYWTAGGALRNVPVGAGRRKTKPPGRGLP---DGCLYDVASGDHH 121
           NYNVNQPRHFCKGCQRYWTAGGALRNVPVGAGRRK+KPP RG+    + CL+D ++G H 
Sbjct: 79  NYNVNQPRHFCKGCQRYWTAGGALRNVPVGAGRRKSKPPCRGVAGFLESCLFDASAGVH- 137

Query: 122 HQLLHHQLDQFDLEGVFVEDWHPAAAAHGYGGFQNAFPVKRRR-SNSGGQLC 172
                    QFDLEGV VE+WH        GGF++AFP KRRR S+SGGQ C
Sbjct: 138 ---------QFDLEGVVVEEWH-------MGGFRHAFPAKRRRSSSSGGQTC 173

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255563152|ref|XP_002522580.1| hypothetical protein RCOM_1015170 [Ricinus communis] gi|223538271|gb|EEF39880.1| hypothetical protein RCOM_1015170 [Ricinus communis]

 Score =  209 bits (532), Expect = 3e-52,   Method: Compositional matrix adjust.
 Identities = 114/170 (67%), Positives = 130/170 (76%), Gaps = 28/170 (16%)

Query: 1   MGNDEEEQGIKLFGKTITLHGRQ-VKEEQNQRGSDQPQAVVDKRPDKIIPCPRCKSMETK 59
           M N++EE GIKLFG TITLHG+Q VKE+QN+  S          P+KIIPCPRCKSMETK
Sbjct: 1   MANNQEE-GIKLFGTTITLHGKQEVKEDQNKENST---------PEKIIPCPRCKSMETK 50

Query: 60  FCYFNNYNVNQPRHFCKGCQRYWTAGGALRNVPVGAGRRKTKPPGRGLPDGCLYDVASGD 119
           FCYFNNYNVNQPRHFCKGCQRYWTAGGALRNVPVGAGRRKTK PGR  PDGCLYD +SG 
Sbjct: 51  FCYFNNYNVNQPRHFCKGCQRYWTAGGALRNVPVGAGRRKTKLPGR--PDGCLYDGSSG- 107

Query: 120 HHHQLLHHQLDQFDLEG-VFVEDWHPAAAAHGYGGFQNAFPVKRRRSNSG 168
                    +D F+L+G V VE+W  A+    +GGF++ FPVKRRRSN+G
Sbjct: 108 ---------VDPFELDGRVIVEEWQVAS----HGGFRHVFPVKRRRSNTG 144

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224076964|ref|XP_002305070.1| f-box family protein [Populus trichocarpa] gi|222848034|gb|EEE85581.1| f-box family protein [Populus trichocarpa]

 Score =  203 bits (517), Expect = 2e-50,   Method: Compositional matrix adjust.
 Identities = 105/172 (61%), Positives = 125/172 (72%), Gaps = 21/172 (12%)

Query: 6   EEQGIKLFGKTITLHGRQVKEEQNQRGSDQPQAVVDKRPDKIIPCPRCKSMETKFCYFNN 65
           +E+GIKLFG TITLH +Q   E N+   ++     DKRP+K+IPCPRCKSMETKFCYFNN
Sbjct: 4   QEEGIKLFGATITLHDKQ---EGNKEDPNKENPTTDKRPEKVIPCPRCKSMETKFCYFNN 60

Query: 66  YNVNQPRHFCKGCQRYWTAGGALRNVPVGAGRRKTKPPGR----GLPDGCLYDVASGDHH 121
           YNVNQPR+FCKGCQRYWTAGGALRNVPVGAGRRKTKPPGR    G  +GCLYD + G H 
Sbjct: 61  YNVNQPRYFCKGCQRYWTAGGALRNVPVGAGRRKTKPPGRVGLDGYSEGCLYDGSGGVH- 119

Query: 122 HQLLHHQLDQFDLEGVFVEDWHPAAAAHGYGGFQNAFPVKRRRS-NSGGQLC 172
                    +F+L+G+ +E+WH A     +G  ++ FPVKRRRS  SGG  C
Sbjct: 120 ---------RFELDGMVLEEWHLATT---HGSSRHVFPVKRRRSGGSGGHTC 159

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224114680|ref|XP_002316826.1| f-box family protein [Populus trichocarpa] gi|222859891|gb|EEE97438.1| f-box family protein [Populus trichocarpa]

 Score =  191 bits (484), Expect = 1e-46,   Method: Compositional matrix adjust.
 Identities = 104/172 (60%), Positives = 122/172 (70%), Gaps = 20/172 (11%)

Query: 6   EEQGIKLFGKTITLHGRQVKEEQNQRGSDQPQAVVDKRPDKIIPCPRCKSMETKFCYFNN 65
           +E+GIKLFG TITLH  QV  +++Q   ++    +DKRP+KII CPRCKSMETKFCYFNN
Sbjct: 4   QEEGIKLFGATITLHDGQVISKEDQ---NKENPTIDKRPEKIIQCPRCKSMETKFCYFNN 60

Query: 66  YNVNQPRHFCKGCQRYWTAGGALRNVPVGAGRRKTK----PPGRGLPDGCLYDVASGDHH 121
           YNVNQPRHFCKGCQRYWTAGGALRNVPVGAGRRKTK        G  + CL+D + G  H
Sbjct: 61  YNVNQPRHFCKGCQRYWTAGGALRNVPVGAGRRKTKPPGRGGPGGYSEECLFDGSGGVIH 120

Query: 122 HQLLHHQLDQFDLEGVFVEDWHPAAAAHGYGGFQNAFPVKRRRS-NSGGQLC 172
                    QF+L+GV +E+ H A     +GGF+  FPVKRRRS  SGGQ C
Sbjct: 121 ---------QFELDGVVLEELHLATT---HGGFRQVFPVKRRRSGGSGGQNC 160

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|15218846|ref|NP_174211.1| Dof zinc finger protein DOF1.5 [Arabidopsis thaliana] gi|55583799|sp|P68350.1|DOF15_ARATH RecName: Full=Dof zinc finger protein DOF1.5; Short=AtDOF1.5 gi|124300952|gb|ABN04728.1| At1g29160 [Arabidopsis thaliana] gi|225897978|dbj|BAH30321.1| hypothetical protein [Arabidopsis thaliana] gi|332192930|gb|AEE31051.1| Dof zinc finger protein DOF1.5 [Arabidopsis thaliana]

 Score =  188 bits (478), Expect = 6e-46,   Method: Compositional matrix adjust.
 Identities = 99/183 (54%), Positives = 117/183 (63%), Gaps = 26/183 (14%)

Query: 5   EEEQGIKLFGKTITLHGRQVKEEQNQRG---------------SDQPQAVVDKRPDKIIP 49
           ++ QGIKLFGKTIT +    +  + +                 S       +KRPDKIIP
Sbjct: 4   QDSQGIKLFGKTITFNANITQTIKKEEQQQQQQPELQATTAVRSPSSDLTAEKRPDKIIP 63

Query: 50  CPRCKSMETKFCYFNNYNVNQPRHFCKGCQRYWTAGGALRNVPVGAGRRKTKPPGRGLPD 109
           CPRCKSMETKFCYFNNYNVNQPRHFCKGCQRYWTAGGALRNVPVGAGRRK+KPPGR    
Sbjct: 64  CPRCKSMETKFCYFNNYNVNQPRHFCKGCQRYWTAGGALRNVPVGAGRRKSKPPGRVGGF 123

Query: 110 GCLYDVASGDHHHQLLHHQLDQFDLEGVFVEDWHPAAAAHGYGGFQNAFPVKRRRSNSGG 169
             L   A+G          +DQ +L+ + VE+W  A A+H  GGF++ FPVKR R  + G
Sbjct: 124 AELLGAATG---------AVDQVELDALLVEEWRAATASH--GGFRHDFPVKRLRCYTDG 172

Query: 170 QLC 172
           Q C
Sbjct: 173 QSC 175

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297851336|ref|XP_002893549.1| Dof-type zinc finger domain-containing protein [Arabidopsis lyrata subsp. lyrata] gi|297339391|gb|EFH69808.1| Dof-type zinc finger domain-containing protein [Arabidopsis lyrata subsp. lyrata]

 Score =  186 bits (472), Expect = 3e-45,   Method: Compositional matrix adjust.
 Identities = 98/182 (53%), Positives = 116/182 (63%), Gaps = 26/182 (14%)

Query: 5   EEEQGIKLFGKTITLHGRQVKEEQNQRG--------------SDQPQAVVDKRPDKIIPC 50
           ++ QGIKLFGKTIT +    +  + +                S       +KRPDKIIPC
Sbjct: 4   QDSQGIKLFGKTITFNANITQTVKKEEQQQQQPELQATTPVRSSSSDLTAEKRPDKIIPC 63

Query: 51  PRCKSMETKFCYFNNYNVNQPRHFCKGCQRYWTAGGALRNVPVGAGRRKTKPPGRGLPDG 110
           PRCKSMETKFCYFNNYNVNQPRHFCKGCQRYWTAGGALRNVPVGAGRRK+KPPGR     
Sbjct: 64  PRCKSMETKFCYFNNYNVNQPRHFCKGCQRYWTAGGALRNVPVGAGRRKSKPPGRVGGFA 123

Query: 111 CLYDVASGDHHHQLLHHQLDQFDLEGVFVEDWHPAAAAHGYGGFQNAFPVKRRRSNSGGQ 170
            L   A+G          +DQ +L+ + VE+W    AA  +GGF++ FPVKR R  + GQ
Sbjct: 124 ELLGAATG---------AVDQVELDALLVEEWR---AATSHGGFRHDFPVKRLRCYTDGQ 171

Query: 171 LC 172
            C
Sbjct: 172 SC 173

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|333037489|gb|AEF13372.1| Dof-domain transcription factor protein [Platycodon grandiflorus]

 Score =  186 bits (472), Expect = 3e-45,   Method: Compositional matrix adjust.
 Identities = 102/176 (57%), Positives = 118/176 (67%), Gaps = 25/176 (14%)

Query: 3   NDEEEQGIKLFGKTITLHG-RQVKEEQNQRGSDQPQAVVDKRPDKIIPCPRCKSMETKFC 61
           N  +  GIKLFGKTIT+   + +K+E N+   +     ++KRPDKIIPCPRCKSMETKFC
Sbjct: 6   NGHDSPGIKLFGKTITVQVIKDIKDEPNKADEE----ALEKRPDKIIPCPRCKSMETKFC 61

Query: 62  YFNNYNVNQPRHFCKGCQRYWTAGGALRNVPVGAGRRKTKPP-GRGL----PDGCLYDVA 116
           YFNNYNVNQPRHFCKGCQRYWTAGGALRNVPVGAGRRKTKPP GR L     +   +D  
Sbjct: 62  YFNNYNVNQPRHFCKGCQRYWTAGGALRNVPVGAGRRKTKPPIGRELAGTFSENSFFDTP 121

Query: 117 SGDHHHQLLHHQLDQFDLEGVFVEDWHPAAAAHGYGGFQNAFPVKRRRSNSGGQLC 172
                       + Q D +G  VE+W  A    G+G F + FPVKRRRS S GQ C
Sbjct: 122 G-----------IHQLDFDGDQVEEWQVA----GHGDFHHVFPVKRRRSTSSGQSC 162

Source: Platycodon grandiflorus

Species: Platycodon grandiflorus

Genus: Platycodon

Family: Campanulaceae

Order: Asterales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|15226224|ref|NP_180961.1| Dof zinc finger protein DOF2.3 [Arabidopsis thaliana] gi|55583789|sp|O22967.1|DOF23_ARATH RecName: Full=Dof zinc finger protein DOF2.3; Short=AtDOF2.3 gi|2342734|gb|AAB67632.1| putative DOF zinc finger protein [Arabidopsis thaliana] gi|34365615|gb|AAQ65119.1| At2g34140 [Arabidopsis thaliana] gi|62319965|dbj|BAD94068.1| putative DOF zinc finger protein [Arabidopsis thaliana] gi|330253829|gb|AEC08923.1| Dof zinc finger protein DOF2.3 [Arabidopsis thaliana]

 Score =  186 bits (471), Expect = 3e-45,   Method: Compositional matrix adjust.
 Identities = 102/180 (56%), Positives = 119/180 (66%), Gaps = 25/180 (13%)

Query: 5   EEEQGIKLFGKTITLHGRQVKEEQNQ-----------RGSDQPQAVVDKRPDKIIPCPRC 53
           ++ QGIKLFGKTI  + R +K E+             R S       +KRPDKII CPRC
Sbjct: 4   QDSQGIKLFGKTIAFNTRTIKNEEETHPPEQEATIAVRSSSSSDLTAEKRPDKIIACPRC 63

Query: 54  KSMETKFCYFNNYNVNQPRHFCKGCQRYWTAGGALRNVPVGAGRRKTKPPGRGLPDGCLY 113
           KSMETKFCYFNNYNVNQPRHFCKGC RYWTAGGALRNVPVGAGRRK+KPPGR +  G L 
Sbjct: 64  KSMETKFCYFNNYNVNQPRHFCKGCHRYWTAGGALRNVPVGAGRRKSKPPGR-VVVGMLG 122

Query: 114 DVASGDHHHQLLHHQLDQFDLEGVFVEDW-HPAAAAHGYGGFQNAFPVKRRRSNSGGQLC 172
           D  +G    +L++         G+ VE+W H AAAAH  G F++ FP+KR R  S GQ C
Sbjct: 123 D-GNGVRQVELIN---------GLLVEEWQHAAAAAH--GSFRHDFPMKRLRCYSDGQSC 170

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|351726341|ref|NP_001237635.1| uncharacterized protein LOC100527802 [Glycine max] gi|255633246|gb|ACU16979.1| unknown [Glycine max]

 Score =  176 bits (445), Expect = 4e-42,   Method: Compositional matrix adjust.
 Identities = 95/162 (58%), Positives = 107/162 (66%), Gaps = 34/162 (20%)

Query: 8   QGIKLFGKTITLHGRQVKEEQNQRGSDQPQAVVDKRPDKIIPCPRCKSMETKFCYFNNYN 67
           +GIKLFG TITLHGR+ KE++N    D  + +  KRPDKIIPCPRCKSMETKFCYFNNYN
Sbjct: 11  EGIKLFGTTITLHGRERKEDRND-SEDGTEEI--KRPDKIIPCPRCKSMETKFCYFNNYN 67

Query: 68  VNQPRHFCKGCQRYWTAGGALRNVPVGAGRRKTKPPGRGLPDGCLYDVASGDHHHQLLHH 127
           VNQPRHFCKGCQRYWTAGGALRNVPVGAGRRK KP                         
Sbjct: 68  VNQPRHFCKGCQRYWTAGGALRNVPVGAGRRKVKP------------------------- 102

Query: 128 QLDQF-DLEGVFVEDWHPAAAAHGYGGFQNAFPVKRRRSNSG 168
              QF   E + +++WH AA AH  G F+  FP KRRR +S 
Sbjct: 103 ---QFGQEERLALDEWHVAAVAH--GDFRQLFPSKRRRMSSA 139

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

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	172
TAIR|locus:2030006	175	AT1G29160 [Arabidopsis thalian	0.901	0.885	0.562	2.1e-45
TAIR|locus:2055506	170	AT2G34140 [Arabidopsis thalian	0.901	0.911	0.561	1.2e-44
TAIR|locus:2164860	457	CDF2 "cycling DOF factor 2" [A	0.505	0.190	0.662	1e-32
TAIR|locus:2154079	298	CDF1 "AT5G62430" [Arabidopsis	0.569	0.328	0.580	1.6e-29
TAIR|locus:2007151	399	AT1G69570 [Arabidopsis thalian	0.348	0.150	0.783	3.7e-29
TAIR|locus:2079152	448	CDF3 "cycling DOF factor 3" [A	0.424	0.162	0.733	5.6e-29
TAIR|locus:2053175	340	AT2G28810 [Arabidopsis thalian	0.337	0.170	0.706	1.5e-21
TAIR|locus:2026595	339	OBP2 [Arabidopsis thaliana (ta	0.337	0.171	0.689	2.4e-21
TAIR|locus:2019499	352	AT1G64620 [Arabidopsis thalian	0.430	0.210	0.551	3e-21
TAIR|locus:2094746	204	DOF2 "DOF zinc finger protein	0.383	0.323	0.614	4.9e-21

TAIR|locus:2030006 AT1G29160 [Arabidopsis thaliana (taxid:3702)]

 Score = 477 (173.0 bits), Expect = 2.1e-45, P = 2.1e-45
 Identities = 104/185 (56%), Positives = 120/185 (64%)

Query:     5 EEEQGIKLFGKTITLHGR--QV--KEEQNQRGSDQPQAVV-----------DKRPDKIIP 49
             ++ QGIKLFGKTIT +    Q   KEEQ Q+   + QA             +KRPDKIIP
Sbjct:     4 QDSQGIKLFGKTITFNANITQTIKKEEQQQQQQPELQATTAVRSPSSDLTAEKRPDKIIP 63

Query:    50 CPRCKSMETKFCYFNNYNVNQPRHFCKGCQRYWTAGGALRNVPVGAGRRKTKPPGR--GL 107
             CPRCKSMETKFCYFNNYNVNQPRHFCKGCQRYWTAGGALRNVPVGAGRRK+KPPGR  G 
Sbjct:    64 CPRCKSMETKFCYFNNYNVNQPRHFCKGCQRYWTAGGALRNVPVGAGRRKSKPPGRVGGF 123

Query:   108 PDGCLYDVASGXXXXXXXXXXXXXXXXEGVFVEDWHPAAAAHGYGGFQNAFPVKRRRSNS 167
              +  L   A+G                + + VE+W  A A+HG  GF++ FPVKR R  +
Sbjct:   124 AE--LLGAATGAVDQVEL---------DALLVEEWRAATASHG--GFRHDFPVKRLRCYT 170

Query:   168 GGQLC 172
              GQ C
Sbjct:   171 DGQSC 175

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

GO:0005634 "nucleus" evidence=ISM

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

GO:0008270 "zinc ion binding" evidence=IEA

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

TAIR|locus:2055506 AT2G34140 [Arabidopsis thaliana (taxid:3702)]

 Score = 470 (170.5 bits), Expect = 1.2e-44, P = 1.2e-44
 Identities = 101/180 (56%), Positives = 115/180 (63%)

Query:     5 EEEQGIKLFGKTITLHGRQVKEEQNQ-----------RGSDQPQAVVDKRPDKIIPCPRC 53
             ++ QGIKLFGKTI  + R +K E+             R S       +KRPDKII CPRC
Sbjct:     4 QDSQGIKLFGKTIAFNTRTIKNEEETHPPEQEATIAVRSSSSSDLTAEKRPDKIIACPRC 63

Query:    54 KSMETKFCYFNNYNVNQPRHFCKGCQRYWTAGGALRNVPVGAGRRKTKPPGRGLPDGCLY 113
             KSMETKFCYFNNYNVNQPRHFCKGC RYWTAGGALRNVPVGAGRRK+KPPGR +  G L 
Sbjct:    64 KSMETKFCYFNNYNVNQPRHFCKGCHRYWTAGGALRNVPVGAGRRKSKPPGRVVV-GMLG 122

Query:   114 DVASGXXXXXXXXXXXXXXXXEGVFVEDW-HPAAAAHGYGGFQNAFPVKRRRSNSGGQLC 172
             D  +G                 G+ VE+W H AAAAHG   F++ FP+KR R  S GQ C
Sbjct:   123 D-GNGVRQVELI---------NGLLVEEWQHAAAAAHG--SFRHDFPMKRLRCYSDGQSC 170

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

GO:0005634 "nucleus" evidence=ISM

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

GO:0008270 "zinc ion binding" evidence=IEA

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

TAIR|locus:2164860 CDF2 "cycling DOF factor 2" [Arabidopsis thaliana (taxid:3702)]

 Score = 330 (121.2 bits), Expect = 1.0e-32, Sum P(2) = 1.0e-32
 Identities = 59/89 (66%), Positives = 65/89 (73%)

Query:    15 KTITLHGRQVKEEQNQRGSDQPQAVVDKRPDKIIPCPRCKSMETKFCYFNNYNVNQPRHF 74
             KT T    +  EE       Q   +  K+PDKI+PCPRC SMETKFCY+NNYNVNQPRHF
Sbjct:   107 KTETTKAAKTNEESGGTACSQEGKL--KKPDKILPCPRCNSMETKFCYYNNYNVNQPRHF 164

Query:    75 CKGCQRYWTAGGALRNVPVGAGRRKTKPP 103
             CK CQRYWTAGG +RNVPVGAGRRK K P
Sbjct:   165 CKKCQRYWTAGGTMRNVPVGAGRRKNKSP 193

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

GO:0005634 "nucleus" evidence=ISM

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

GO:0008270 "zinc ion binding" evidence=IEA

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

GO:0005515 "protein binding" evidence=IPI

GO:0048510 "regulation of timing of transition from vegetative to reproductive phase" evidence=IMP

TAIR|locus:2154079 CDF1 "AT5G62430" [Arabidopsis thaliana (taxid:3702)]

 Score = 327 (120.2 bits), Expect = 1.6e-29, P = 1.6e-29
 Identities = 61/105 (58%), Positives = 75/105 (71%)

Query:     4 DEEEQGIKLFGKTI----TLHGRQVKEEQNQRGSDQPQAVVDK---RPDKIIPCPRCKSM 56
             + ++  IKLFG  I     L     +EE+NQ  +   Q+  DK   +P KI+PCPRC SM
Sbjct:     3 ETKDPAIKLFGMKIPFPTVLEVADEEEEKNQNKTLTDQSEKDKTLKKPTKILPCPRCNSM 62

Query:    57 ETKFCYFNNYNVNQPRHFCKGCQRYWTAGGALRNVPVGAGRRKTK 101
             ETKFCY+NNYNVNQPRHFCK CQRYWT+GG +R+VP+GAGRRK K
Sbjct:    63 ETKFCYYNNYNVNQPRHFCKACQRYWTSGGTMRSVPIGAGRRKNK 107

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

GO:0005634 "nucleus" evidence=ISM;IDA

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

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

GO:0005515 "protein binding" evidence=IPI

GO:0045892 "negative regulation of transcription, DNA-dependent" evidence=IDA

GO:0048510 "regulation of timing of transition from vegetative to reproductive phase" evidence=IMP

GO:0009658 "chloroplast organization" evidence=IMP

TAIR|locus:2007151 AT1G69570 [Arabidopsis thaliana (taxid:3702)]

 Score = 298 (110.0 bits), Expect = 3.7e-29, Sum P(2) = 3.7e-29
 Identities = 47/60 (78%), Positives = 56/60 (93%)

Query:    42 KRPDKIIPCPRCKSMETKFCYFNNYNVNQPRHFCKGCQRYWTAGGALRNVPVGAGRRKTK 101
             K+PDK+IPCPRC+S  TKFCY+NNYNVNQPR+FC+ CQRYWTAGG++RNVPVG+GRRK K
Sbjct:   126 KKPDKLIPCPRCESANTKFCYYNNYNVNQPRYFCRNCQRYWTAGGSMRNVPVGSGRRKNK 185

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

GO:0005634 "nucleus" evidence=ISM

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

GO:0008270 "zinc ion binding" evidence=IEA

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

TAIR|locus:2079152 CDF3 "cycling DOF factor 3" [Arabidopsis thaliana (taxid:3702)]

 Score = 322 (118.4 bits), Expect = 5.6e-29, P = 5.6e-29
 Identities = 55/75 (73%), Positives = 62/75 (82%)

Query:    27 EQNQRGSDQPQAVVDKRPDKIIPCPRCKSMETKFCYFNNYNVNQPRHFCKGCQRYWTAGG 86
             E NQ+ +  P     K+P KI+PCPRCKSMETKFCY+NNYN+NQPRHFCK CQRYWTAGG
Sbjct:    91 EDNQQTT--PDGKTLKKPTKILPCPRCKSMETKFCYYNNYNINQPRHFCKACQRYWTAGG 148

Query:    87 ALRNVPVGAGRRKTK 101
              +RNVPVGAGRRK K
Sbjct:   149 TMRNVPVGAGRRKNK 163

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

GO:0005634 "nucleus" evidence=ISM

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

GO:0008270 "zinc ion binding" evidence=IEA

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

GO:0005515 "protein binding" evidence=IPI

GO:0048510 "regulation of timing of transition from vegetative to reproductive phase" evidence=IMP

TAIR|locus:2053175 AT2G28810 [Arabidopsis thaliana (taxid:3702)]

 Score = 252 (93.8 bits), Expect = 1.5e-21, P = 1.5e-21
 Identities = 41/58 (70%), Positives = 46/58 (79%)

Query:    44 PDKIIPCPRCKSMETKFCYFNNYNVNQPRHFCKGCQRYWTAGGALRNVPVGAGRRKTK 101
             P+  + CPRC S  TKFCYFNNYN+ QPRHFCK C+RYWT GGALRNVPVG G R+ K
Sbjct:    90 PEGALKCPRCDSANTKFCYFNNYNLTQPRHFCKACRRYWTRGGALRNVPVGGGCRRNK 147

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

GO:0005634 "nucleus" evidence=ISM;IDA

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

GO:0008270 "zinc ion binding" evidence=IEA

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

TAIR|locus:2026595 OBP2 [Arabidopsis thaliana (taxid:3702)]

 Score = 250 (93.1 bits), Expect = 2.4e-21, P = 2.4e-21
 Identities = 40/58 (68%), Positives = 46/58 (79%)

Query:    48 IPCPRCKSMETKFCYFNNYNVNQPRHFCKGCQRYWTAGGALRNVPVGAGRRKTKPPGR 105
             + CPRC S  TKFCY+NNYN+ QPRHFCKGC+RYWT GGALRNVPVG G R+    G+
Sbjct:    85 LKCPRCDSSNTKFCYYNNYNLTQPRHFCKGCRRYWTQGGALRNVPVGGGCRRNNKKGK 142

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

GO:0005634 "nucleus" evidence=ISM;IDA

GO:0008270 "zinc ion binding" evidence=IEA

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

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

GO:0009611 "response to wounding" evidence=IEP

GO:0009625 "response to insect" evidence=IEP

GO:0009753 "response to jasmonic acid stimulus" evidence=IEP

GO:0010439 "regulation of glucosinolate biosynthetic process" evidence=IEP

GO:0000165 "MAPK cascade" evidence=RCA

GO:0006612 "protein targeting to membrane" evidence=RCA

GO:0009595 "detection of biotic stimulus" evidence=RCA

GO:0009697 "salicylic acid biosynthetic process" evidence=RCA

GO:0009862 "systemic acquired resistance, salicylic acid mediated signaling pathway" evidence=RCA

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

GO:0010200 "response to chitin" evidence=RCA

GO:0010310 "regulation of hydrogen peroxide metabolic process" evidence=RCA

GO:0010363 "regulation of plant-type hypersensitive response" evidence=RCA

GO:0019761 "glucosinolate biosynthetic process" evidence=RCA

GO:0031348 "negative regulation of defense response" evidence=RCA

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

GO:0043900 "regulation of multi-organism process" evidence=RCA

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

GO:0003002 "regionalization" evidence=IMP

TAIR|locus:2019499 AT1G64620 [Arabidopsis thaliana (taxid:3702)]

 Score = 249 (92.7 bits), Expect = 3.0e-21, P = 3.0e-21
 Identities = 43/78 (55%), Positives = 56/78 (71%)

Query:    28 QNQRGSDQPQAVVDK--RPDK--IIPCPRCKSMETKFCYFNNYNVNQPRHFCKGCQRYWT 83
             + Q     P   V++  RP+K   + CPRC S+ TKFCY+NNY++ QPR+FCK C+RYWT
Sbjct:    25 KQQSNPPSPATPVERKARPEKDQALNCPRCNSLNTKFCYYNNYSLTQPRYFCKDCRRYWT 84

Query:    84 AGGALRNVPVGAGRRKTK 101
             AGG+LRN+PVG G RK K
Sbjct:    85 AGGSLRNIPVGGGVRKNK 102

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

GO:0005634 "nucleus" evidence=ISM

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

GO:0008270 "zinc ion binding" evidence=IEA

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

TAIR|locus:2094746 DOF2 "DOF zinc finger protein 2" [Arabidopsis thaliana (taxid:3702)]

 Score = 247 (92.0 bits), Expect = 4.9e-21, P = 4.9e-21
 Identities = 43/70 (61%), Positives = 51/70 (72%)

Query:    30 QRGSDQPQAVVDKRPDKIIPCPRCKSMETKFCYFNNYNVNQPRHFCKGCQRYWTAGGALR 89
             Q+   QPQ    ++    + CPRC S  TKFCY+NNYN++QPRHFCK C+RYWT GGALR
Sbjct:    15 QQQQQQPQFAEQEQ----LKCPRCDSPNTKFCYYNNYNLSQPRHFCKSCRRYWTKGGALR 70

Query:    90 NVPVGAGRRK 99
             NVPVG G RK
Sbjct:    71 NVPVGGGSRK 80

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

GO:0005634 "nucleus" evidence=ISM

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

GO:0008270 "zinc ion binding" evidence=IEA

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

GO:0019344 "cysteine biosynthetic process" 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

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
P68350	DOF15_ARATH	No assigned EC number	0.5409	0.9127	0.8971	yes	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input: GSVIVG00035876001 SubName- Full=Chromosome chr10 scaffold_81, whole genome shotgun sequence; (159 aa) (Vitis vinifera)

Predicted Functional Partners:

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

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	172
pfam02701	63	pfam02701, zf-Dof, Dof domain, zinc finger	9e-41

>gnl|CDD|111583 pfam02701, zf-Dof, Dof domain, zinc finger

 Score =  131 bits (331), Expect = 9e-41
 Identities = 46/63 (73%), Positives = 52/63 (82%)

Query: 43  RPDKIIPCPRCKSMETKFCYFNNYNVNQPRHFCKGCQRYWTAGGALRNVPVGAGRRKTKP 102
           +PDK + CPRC SM TKFCY+NNYN+NQPR+FCK C+RYWTAGGALRNVPVG GRRK K 
Sbjct: 1   KPDKALKCPRCDSMNTKFCYYNNYNLNQPRYFCKNCRRYWTAGGALRNVPVGGGRRKNKR 60

Query: 103 PGR 105
              
Sbjct: 61  SSS 63

The Dof domain is a zinc finger DNA-binding domain, that shows resemblance to the Cys2 zinc finger. Length = 63

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	172
PF02701	63	zf-Dof: Dof domain, zinc finger; InterPro: IPR0038	100.0
TIGR02159	146	PA_CoA_Oxy4 phenylacetate-CoA oxygenase, PaaJ subu	93.01
COG3677	129	Transposase and inactivated derivatives [DNA repli	93.0
PF12760	46	Zn_Tnp_IS1595: Transposase zinc-ribbon domain; Int	92.44
PF03811	36	Zn_Tnp_IS1: InsA N-terminal domain; InterPro: IPR0	92.02
smart00440	40	ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding mo	91.3
PF01096	39	TFIIS_C: Transcription factor S-II (TFIIS); InterP	89.9
TIGR01384	104	TFS_arch transcription factor S, archaeal. There h	83.29
PF13453	41	zf-TFIIB: Transcription factor zinc-finger	82.29
PHA02998	195	RNA polymerase subunit; Provisional	80.07

>PF02701 zf-Dof: Dof domain, zinc finger; InterPro: IPR003851 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule

Probab=100.00  E-value=5.7e-39  Score=227.52  Aligned_cols=62  Identities=65%  Similarity=1.393  Sum_probs=60.2

Q ss_pred             CCCCcccCCCCCCCCceeeEeccccCCCCCccccccccccccCcccccccCCCCccCCCCCC
Q 047290           43 RPDKIIPCPRCKSMETKFCYFNNYNVNQPRHFCKGCQRYWTAGGALRNVPVGAGRRKTKPPG  104 (172)
Q Consensus        43 ~p~~~~~CPRC~S~~TKFcYyNNyn~~QPRhfCksCrRYWT~GGtLRnVPVGgG~RKnK~s~  104 (172)
                      +|++.++||||+|++|||||||||+++||||||++|+||||+||+|||||||||+||+|+++
T Consensus         1 ~~~~~~~CPRC~S~nTKFcYyNNy~~~QPR~~Ck~C~rywT~GG~lRnVPvggg~Rk~k~~~   62 (63)
T PF02701_consen    1 KPEQPLPCPRCDSTNTKFCYYNNYNLSQPRYFCKSCRRYWTHGGTLRNVPVGGGCRKNKRSS   62 (63)
T ss_pred             CCccCCCCCCcCCCCCEEEeecCCCCCCcchhhHHHHHHHHhcceecCCccCCCcccCCcCC
Confidence            48899999999999999999999999999999999999999999999999999999999975

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. This entry consists of proteins containing a Dof domain, which is a zinc finger DNA-binding domain that shows resemblance to the Cys2 zinc finger, although it has a longer putative loop where an extra Cys residue is conserved []. AOBP, a DNA-binding protein in pumpkin (Cucurbita maxima), contains a 52 amino acid Dof domain, which is highly conserved in several DNA-binding proteins of higher plants. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003677 DNA binding, 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent

>TIGR02159 PA_CoA_Oxy4 phenylacetate-CoA oxygenase, PaaJ subunit

Probab=93.01  E-value=0.036  Score=44.14  Aligned_cols=34  Identities=24%  Similarity=0.661  Sum_probs=27.1

Q ss_pred             cccCCCCCCCCceeeEeccc--cCCCCCcccccccccc
Q 047290           47 IIPCPRCKSMETKFCYFNNY--NVNQPRHFCKGCQRYW   82 (172)
Q Consensus        47 ~~~CPRC~S~~TKFcYyNNy--n~~QPRhfCksCrRYW   82 (172)
                      ...||+|.|.+|+..  +.+  +.+..-|.|++|+.=+
T Consensus       105 ~~~cp~c~s~~t~~~--s~fg~t~cka~~~c~~c~epf  140 (146)
T TIGR02159       105 SVQCPRCGSADTTIT--SIFGPTACKALYRCRACKEPF  140 (146)
T ss_pred             CCcCCCCCCCCcEee--cCCCChhhHHHhhhhhhCCcH
Confidence            589999999999965  455  4567779999998644

Phenylacetate-CoA oxygenase is comprised of a five gene complex responsible for the hydroxylation of phenylacetate-CoA (PA-CoA) as the second catabolic step in phenylacetic acid (PA) degradation. Although the exact function of this enzyme has not been determined, it has been shown to be required for phenylacetic acid degradation and has been proposed to function in a multicomponent oxygenase acting on phenylacetate-CoA.

>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]

Probab=93.00  E-value=0.071  Score=41.62  Aligned_cols=35  Identities=31%  Similarity=0.668  Sum_probs=28.2

Q ss_pred             ccCCCCCCCCceeeEeccccCCCCCcccccccccccc
Q 047290           48 IPCPRCKSMETKFCYFNNYNVNQPRHFCKGCQRYWTA   84 (172)
Q Consensus        48 ~~CPRC~S~~TKFcYyNNyn~~QPRhfCksCrRYWT~   84 (172)
                      ..||+|.+.+  +-=++-+.....||.|++|.+-|+.
T Consensus        31 ~~cP~C~s~~--~~k~g~~~~~~qRyrC~~C~~tf~~   65 (129)
T COG3677          31 VNCPRCKSSN--VVKIGGIRRGHQRYKCKSCGSTFTV   65 (129)
T ss_pred             CcCCCCCccc--eeeECCccccccccccCCcCcceee
Confidence            6799999999  3444555555999999999999874

>PF12760 Zn_Tnp_IS1595: Transposase zinc-ribbon domain; InterPro: IPR024442 This zinc binding domain is found in a range of transposase proteins such as ISSPO8, ISSOD11, ISRSSP2 etc

Probab=92.44  E-value=0.11  Score=33.56  Aligned_cols=27  Identities=33%  Similarity=0.803  Sum_probs=21.7

Q ss_pred             ccCCCCCCCCceeeEeccccCCCCCcccccccc
Q 047290           48 IPCPRCKSMETKFCYFNNYNVNQPRHFCKGCQR   80 (172)
Q Consensus        48 ~~CPRC~S~~TKFcYyNNyn~~QPRhfCksCrR   80 (172)
                      ..||+|.+.  +...+.+    ..++.|++|++
T Consensus        19 ~~CP~Cg~~--~~~~~~~----~~~~~C~~C~~   45 (46)
T PF12760_consen   19 FVCPHCGST--KHYRLKT----RGRYRCKACRK   45 (46)
T ss_pred             CCCCCCCCe--eeEEeCC----CCeEECCCCCC
Confidence            669999998  6555555    78899999985

It may be a zinc-binding beta ribbon domain that could bind DNA.

>PF03811 Zn_Tnp_IS1: InsA N-terminal domain; InterPro: IPR003220 Insertion elements are mobile elements in DNA, usually encoding proteins required for transposition, for example transposases

Probab=92.02  E-value=0.094  Score=33.56  Aligned_cols=31  Identities=35%  Similarity=0.687  Sum_probs=21.9

Q ss_pred             cccCCCCCCCCceeeEeccccCC-CCCccccccc
Q 047290           47 IIPCPRCKSMETKFCYFNNYNVN-QPRHFCKGCQ   79 (172)
Q Consensus        47 ~~~CPRC~S~~TKFcYyNNyn~~-QPRhfCksCr   79 (172)
                      .+.||+|.|.+.  -|=|-.+.+ ..||.|++|+
T Consensus         5 ~v~CP~C~s~~~--v~k~G~~~~G~qryrC~~C~   36 (36)
T PF03811_consen    5 DVHCPRCQSTEG--VKKNGKSPSGHQRYRCKDCR   36 (36)
T ss_pred             eeeCCCCCCCCc--ceeCCCCCCCCEeEecCcCC
Confidence            478999999872  123444433 5899999996

Protein InsA is absolutely required for transposition of insertion element 1. This entry represents a short zinc binding domain found in IS1 InsA family protein. It is found at the N terminus of the protein and may be a DNA-binding domain.; GO: 0006313 transposition, DNA-mediated

>smart00440 ZnF_C2C2 C2C2 Zinc finger

Probab=91.30  E-value=0.22  Score=31.95  Aligned_cols=37  Identities=27%  Similarity=0.805  Sum_probs=29.1

Q ss_pred             ccCCCCCCCCceeeEeccccCCCC---Ccccccccccccc
Q 047290           48 IPCPRCKSMETKFCYFNNYNVNQP---RHFCKGCQRYWTA   84 (172)
Q Consensus        48 ~~CPRC~S~~TKFcYyNNyn~~QP---RhfCksCrRYWT~   84 (172)
                      .+||.|...+.-|-..+-.+...|   -|.|.+|..-|..
T Consensus         1 ~~Cp~C~~~~a~~~q~Q~RsaDE~mT~fy~C~~C~~~w~~   40 (40)
T smart00440        1 APCPKCGNREATFFQLQTRSADEPMTVFYVCTKCGHRWRE   40 (40)
T ss_pred             CcCCCCCCCeEEEEEEcccCCCCCCeEEEEeCCCCCEeCC
Confidence            379999988887777666666666   3999999999963

Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.

>PF01096 TFIIS_C: Transcription factor S-II (TFIIS); InterPro: IPR001222 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule

Probab=89.90  E-value=0.27  Score=31.31  Aligned_cols=36  Identities=28%  Similarity=0.756  Sum_probs=25.2

Q ss_pred             ccCCCCCCCCceeeEeccccCCCCC---ccccccccccc
Q 047290           48 IPCPRCKSMETKFCYFNNYNVNQPR---HFCKGCQRYWT   83 (172)
Q Consensus        48 ~~CPRC~S~~TKFcYyNNyn~~QPR---hfCksCrRYWT   83 (172)
                      .+||.|.+.+.-|--.+......|-   |.|.+|..-|+
T Consensus         1 ~~Cp~Cg~~~a~~~~~Q~rsaDE~~T~fy~C~~C~~~wr   39 (39)
T PF01096_consen    1 IKCPKCGHNEAVFFQIQTRSADEPMTLFYVCCNCGHRWR   39 (39)
T ss_dssp             S--SSS-SSEEEEEEESSSSSSSSSEEEEEESSSTEEEE
T ss_pred             CCCcCCCCCeEEEEEeeccCCCCCCeEEEEeCCCCCeeC
Confidence            3799999988776666666655554   89999999885

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. This entry represents a zinc finger motif found in transcription factor IIs (TFIIS). In eukaryotes the initiation of transcription of protein encoding genes by polymerase II (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least eight different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, -IIH and -IIS []. During mRNA elongation, Pol II can encounter DNA sequences that cause reverse movement of the enzyme. Such backtracking involves extrusion of the RNA 3'-end into the pore, and can lead to transcriptional arrest. Escape from arrest requires cleavage of the extruded RNA with the help of TFIIS, which induces mRNA cleavage by enhancing the intrinsic nuclease activity of RNA polymerase (Pol) II, past template-encoded pause sites []. TFIIS extends from the polymerase surface via a pore to the internal active site. Two essential and invariant acidic residues in a TFIIS loop complement the Pol II active site and could position a metal ion and a water molecule for hydrolytic RNA cleavage. TFIIS also induces extensive structural changes in Pol II that would realign nucleic acids in the active centre. TFIIS is a protein of about 300 amino acids. It contains three regions: a variable N-terminal domain not required for TFIIS activity; a conserved central domain required for Pol II binding; and a conserved C-terminal C4-type zinc finger essential for RNA cleavage. The zinc finger folds in a conformation termed a zinc ribbon [] characterised by a three-stranded antiparallel beta-sheet and two beta-hairpins. A backbone model for Pol II-TFIIS complex was obtained from X-ray analysis. It shows that a beta hairpin protrudes from the zinc finger and complements the pol II active site []. Some viral proteins also contain the TFIIS zinc ribbon C-terminal domain. The Vaccinia virus protein, unlike its eukaryotic homologue, is an integral RNA polymerase subunit rather than a readily separable transcription factor []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding, 0006351 transcription, DNA-dependent; PDB: 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I 3I4M_I ....

>TIGR01384 TFS_arch transcription factor S, archaeal

Probab=83.29  E-value=1.7  Score=31.49  Aligned_cols=42  Identities=21%  Similarity=0.643  Sum_probs=31.2

Q ss_pred             CCCcccCCCCCCCCceeeEeccccCCCCC---ccccccccccccC
Q 047290           44 PDKIIPCPRCKSMETKFCYFNNYNVNQPR---HFCKGCQRYWTAG   85 (172)
Q Consensus        44 p~~~~~CPRC~S~~TKFcYyNNyn~~QPR---hfCksCrRYWT~G   85 (172)
                      |--...||.|.+.+.-|-..+-.+...|-   |.|.+|.-.|+.+
T Consensus        59 ~~~~~~Cp~Cg~~~a~f~~~Q~RsadE~~T~fy~C~~C~~~w~~~  103 (104)
T TIGR01384        59 PTTRVECPKCGHKEAYYWLLQTRRADEPETRFYKCTKCGYVWREY  103 (104)
T ss_pred             CcccCCCCCCCCCeeEEEEeccCCCCCCcEEEEEeCCCCCeeEeC
Confidence            44458999999877776666655544443   9999999999865

There has been an apparent duplication event in the Halobacteriaceae lineage (Haloarcula, Haloferax, Haloquadratum, Halobacterium and Natromonas). There appears to be a separate duplication in Methanosphaera stadtmanae.

>PF13453 zf-TFIIB: Transcription factor zinc-finger

Probab=82.29  E-value=0.39  Score=30.32  Aligned_cols=37  Identities=24%  Similarity=0.600  Sum_probs=27.1

Q ss_pred             cCCCCCCCCceeeEeccccCCCCCccccccccccccCccccc
Q 047290           49 PCPRCKSMETKFCYFNNYNVNQPRHFCKGCQRYWTAGGALRN   90 (172)
Q Consensus        49 ~CPRC~S~~TKFcYyNNyn~~QPRhfCksCrRYWT~GGtLRn   90 (172)
                      +||+|...=...-+     ..-+-+.|.+|.-.|=..+.+..
T Consensus         1 ~CP~C~~~l~~~~~-----~~~~id~C~~C~G~W~d~~el~~   37 (41)
T PF13453_consen    1 KCPRCGTELEPVRL-----GDVEIDVCPSCGGIWFDAGELEK   37 (41)
T ss_pred             CcCCCCcccceEEE-----CCEEEEECCCCCeEEccHHHHHH
Confidence            59999985554444     23466889999999988877654

>PHA02998 RNA polymerase subunit; Provisional

Probab=80.07  E-value=1.9  Score=37.05  Aligned_cols=39  Identities=28%  Similarity=0.700  Sum_probs=34.3

Q ss_pred             CcccCCCCCCCCceeeEeccccCCCCC---cccccccccccc
Q 047290           46 KIIPCPRCKSMETKFCYFNNYNVNQPR---HFCKGCQRYWTA   84 (172)
Q Consensus        46 ~~~~CPRC~S~~TKFcYyNNyn~~QPR---hfCksCrRYWT~   84 (172)
                      ...+||+|...++-|--.|-.+-..|-   |.|..|..-|.-
T Consensus       142 t~v~CPkCg~~~A~f~qlQTRSADEPmT~FYkC~~CG~~wkp  183 (195)
T PHA02998        142 YNTPCPNCKSKNTTPMMIQTRAADEPPLVRHACRDCKKHFKP  183 (195)
T ss_pred             cCCCCCCCCCCceEEEEEeeccCCCCceEEEEcCCCCCccCC
Confidence            568999999999999999999888875   899999999863

---

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	172
1tfi_A	50	Transcriptional elongation factor SII; transcripti	87.35
1qyp_A	57	RNA polymerase II; transcription, RPB9, Zn ribbon,	85.52
3h0g_I	113	DNA-directed RNA polymerases I, II, and III subuni	83.39

>1tfi_A Transcriptional elongation factor SII; transcription regulation; NMR {Homo sapiens} SCOP: g.41.3.1

Probab=87.35  E-value=0.47  Score=30.92  Aligned_cols=38  Identities=18%  Similarity=0.676  Sum_probs=29.8

Q ss_pred             CcccCCCCCCCCceeeEeccccCCCCC---ccccccccccc
Q 047290           46 KIIPCPRCKSMETKFCYFNNYNVNQPR---HFCKGCQRYWT   83 (172)
Q Consensus        46 ~~~~CPRC~S~~TKFcYyNNyn~~QPR---hfCksCrRYWT   83 (172)
                      ....||+|...+.-|--.+..+...|-   |.|.+|.--|.
T Consensus         8 ~~~~Cp~Cg~~~a~f~q~Q~RsaDE~mT~Fy~C~~Cg~~w~   48 (50)
T 1tfi_A            8 DLFTCGKCKKKNCTYTQVQTRSADEPMTTFVVCNECGNRWK   48 (50)
T ss_dssp             CCSCCSSSCSSCEEEEEECSSSSSSCCEEEEEESSSCCEEE
T ss_pred             CccCCCCCCCCEEEEEEecCcCCCCCceEEEEcCCCCCeEE
Confidence            456899999988877776666666664   89999998885

>1qyp_A RNA polymerase II; transcription, RPB9, Zn ribbon, hyperthermophilic, extremophIle; NMR {Thermococcus celer} SCOP: g.41.3.1

Probab=85.52  E-value=0.48  Score=30.65  Aligned_cols=41  Identities=22%  Similarity=0.595  Sum_probs=27.3

Q ss_pred             CCCcccCCCCCCCCceeeEeccccCCCC---Ccccccccccccc
Q 047290           44 PDKIIPCPRCKSMETKFCYFNNYNVNQP---RHFCKGCQRYWTA   84 (172)
Q Consensus        44 p~~~~~CPRC~S~~TKFcYyNNyn~~QP---RhfCksCrRYWT~   84 (172)
                      |....+||.|...+..|--.+-.+...|   .|.|..|.--|+.
T Consensus        12 ~~~~~~Cp~Cg~~~~~~~q~Q~rsadep~T~fy~C~~Cg~~w~~   55 (57)
T 1qyp_A           12 PTTKITCPKCGNDTAYWWEMQTRAGDEPSTIFYKCTKCGHTWRS   55 (57)
T ss_dssp             CEEECCCTTTCCSEEEEEEECCSSSSCSSEEEEEESSSCCEEEC
T ss_pred             CceEeECCCCCCCEEEEEEeecccCCCCCcEEEEcCCCCCEecc
Confidence            3335789999984444444443344445   3899999999975

>3h0g_I DNA-directed RNA polymerases I, II, and III subunit rpabc5; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe}

Probab=83.39  E-value=1.2  Score=32.51  Aligned_cols=41  Identities=22%  Similarity=0.417  Sum_probs=27.3

Q ss_pred             CCCcccCCCCCCCCceeeEeccccCCCCC---cccccccccccc
Q 047290           44 PDKIIPCPRCKSMETKFCYFNNYNVNQPR---HFCKGCQRYWTA   84 (172)
Q Consensus        44 p~~~~~CPRC~S~~TKFcYyNNyn~~QPR---hfCksCrRYWT~   84 (172)
                      |....+||+|...+..|-..+-.+...|-   |.|..|.--|+.
T Consensus        69 p~~~~~Cp~C~~~~a~~~q~q~rsade~mt~fy~C~~C~~~w~~  112 (113)
T 3h0g_I           69 PRSDKECPRCHQHEAVFYQTHSRRGDTMMTLIYVCVHCGFAFEE  112 (113)
T ss_dssp             CBCCSCCSSSCCSCEEEECCCCSSCCCCCCCEEEESSSCCCCCC
T ss_pred             CCcccCCCCCCCceEEEEEEecccCCCCCeeEEEcCCCCCEEec
Confidence            44448999999877554433333333332   889999999974

---

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	172
d1twfi2	72	RBP9 subunit of RNA polymerase II {Baker's yeast (	92.96
d1tfia_	50	Transcriptional factor SII, C-terminal domain {Hum	92.17
d1qypa_	57	RBP9 subunit of RNA polymerase II {Archaeon Thermo	89.25

>d1twfi2 g.41.3.1 (I:50-121) RBP9 subunit of RNA polymerase II {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Zinc beta-ribbon
family: Transcriptional factor domain
domain: RBP9 subunit of RNA polymerase II
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=92.96  E-value=0.079  Score=35.71  Aligned_cols=44  Identities=23%  Similarity=0.498  Sum_probs=34.3

Q ss_pred             CCCcccCCCCCCCCceeeEeccccCCCCC---ccccccccccccCcc
Q 047290           44 PDKIIPCPRCKSMETKFCYFNNYNVNQPR---HFCKGCQRYWTAGGA   87 (172)
Q Consensus        44 p~~~~~CPRC~S~~TKFcYyNNyn~~QPR---hfCksCrRYWT~GGt   87 (172)
                      |..-..||+|.+.+.-|-..+..+..-|-   |.|.+|.-.|+...+
T Consensus        20 p~t~~~CpkCg~~~a~~~q~QtRsaDE~mT~Fy~C~~C~h~Wr~~~~   66 (72)
T d1twfi2          20 PRSDRECPKCHSRENVFFQSQQRRKDTSMVLFFVCLSCSHIFTSDQK   66 (72)
T ss_dssp             CCCCCCCTTTCCCCEEEEECSSCCTTCCCCEEEEETTTCCEEECCTT
T ss_pred             CccCCCCCCCCCCeEEEEEeecCccCCCceEEEEcCCCCCCcccccc
Confidence            44457999999988887777776655554   899999999998543

>d1tfia_ g.41.3.1 (A:) Transcriptional factor SII, C-terminal domain {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Zinc beta-ribbon
family: Transcriptional factor domain
domain: Transcriptional factor SII, C-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=92.17  E-value=0.05  Score=34.62  Aligned_cols=40  Identities=18%  Similarity=0.640  Sum_probs=33.4

Q ss_pred             CCCcccCCCCCCCCceeeEeccccCCCCC---ccccccccccc
Q 047290           44 PDKIIPCPRCKSMETKFCYFNNYNVNQPR---HFCKGCQRYWT   83 (172)
Q Consensus        44 p~~~~~CPRC~S~~TKFcYyNNyn~~QPR---hfCksCrRYWT   83 (172)
                      +...+.||+|.+.+..|--.+..+...|-   +.|.+|..-|-
T Consensus         6 ~T~~~~C~kC~~~~~~~~~~QtRSADEp~T~F~~C~~Cg~~Wr   48 (50)
T d1tfia_           6 QTDLFTCGKCKKKNCTYTQVQTRSADEPMTTFVVCNECGNRWK   48 (50)
T ss_dssp             ECCCSCCSSSCSSCEEEEEECSSSSSSCCEEEEEESSSCCEEE
T ss_pred             ccCCEECCCCCCCccEEEEEEccCCCCCceEEEEccccCCeee
Confidence            44568999999999888888888877776   89999998883

>d1qypa_ g.41.3.1 (A:) RBP9 subunit of RNA polymerase II {Archaeon Thermococcus celer [TaxId: 2264]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Zinc beta-ribbon
family: Transcriptional factor domain
domain: RBP9 subunit of RNA polymerase II
species: Archaeon Thermococcus celer [TaxId: 2264]

Probab=89.25  E-value=0.15  Score=32.89  Aligned_cols=42  Identities=21%  Similarity=0.587  Sum_probs=32.3

Q ss_pred             CCCCcccCCCCCCCCceeeEeccccCCCCC---cccccccccccc
Q 047290           43 RPDKIIPCPRCKSMETKFCYFNNYNVNQPR---HFCKGCQRYWTA   84 (172)
Q Consensus        43 ~p~~~~~CPRC~S~~TKFcYyNNyn~~QPR---hfCksCrRYWT~   84 (172)
                      .|-..++||+|.+.+.-|--.+.....-|-   |.|.+|.--|..
T Consensus        11 ~pt~~~~CpkC~~~~a~~~~~QtRsaDE~~T~fy~C~~Cg~~wre   55 (57)
T d1qypa_          11 LPTTKITCPKCGNDTAYWWEMQTRAGDEPSTIFYKCTKCGHTWRS   55 (57)
T ss_dssp             SCEEECCCTTTCCSEEEEEEECCSSSSCSSEEEEEESSSCCEEEC
T ss_pred             CCcccCCCCCCCCCceEEEEeecccccCCCeEEEEeCCCCCccee
Confidence            354557999999988887777766655555   899999998853