Citrus Sinensis ID: 046549

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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-------210-------220-------230-------240-------250
Protein Sequence
MQDPATFNPMKPHFPESEQLKCPRCESTNTKFCYYNNYNLSQPRHFCKNCRRYWTRGGALRNIPIGGGTRKSNTKKRQKPDPDPSRSNPTRKSQETANTQSMLQAAATTSTSSQEPAVTLPGAVARESGTEHDPRRLYGLPLDQDHKMLDITGSFSSLLASNGGLGSVLDGITPNGSGFKMVQMGGFGENFGSDQSLDLISVRGSGSQNQGNNNGGESFMQSGNNDSSCWSGGSNGWPDLAIYTPSSNFQ
Secondary Structure (PSIPRED)
ccccccccccccccccccccccccccccccEEEEEcccccccccHHcccccccccccccEEEcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEccccccc
Secondary Structure Prediction (SSPRO)
ccccccccccccccccHcccccccccccccEEEEEcccccccccHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHcccccccccccccccccccccccEEccccccccccccccccccccccccccccccccccEEEEEccccccccccccccccccEEEccccccc
Coil and Loop (DISEMBL)
mqdpatfnpmkphfpeseqlkcprcestntkfcyynnynlsqprhfckncrrywtrggalrnipigggtrksntkkrqkpdpdpsrsnptrksqeTANTQSMLQAAAttstssqepavtlpgavaresgtehdprrlyglpldqdhkmlditGSFSSLLasngglgsvldgitpngsgfkmvqmggfgenfgsdqsldlisvrgsgsqnqgnnnggesfmqsgnndsscwsggsngwpdlaiytpssnfq
Flexible Loop (DISEMBL)
mqdpatfnpmkphfpeseqlKCPRCESTNTKFCYYnnynlsqprhFCKNCRRYWTRggalrnipigggtrksntkkrqkpdpdpsrsnptrksqetANTQSMLQAAattstssqepaVTLPGAvaresgtehdprrLYGLPLDQDHKMLDITGSFSSLLASNGGLGSVLDGITPNGSGFKMVQMGGFGENFGSDQSLDLISVRGSGSQNQGNNNGGESFMQSGNNDSSCWSGGSNGWPDLAIYTPSSNFQ
Low Complexity Region (SEG)
MQDPATFNPMKPHFPESEQLKCPRCESTNTKFCYYNNYNLSQPRHFCKNCRRYWTRGGALRNIPIGGGTRKSNTKKRQKPDPDPSRSNPTRKSQETANTQSMLQAAATTSTSSQEPAVTLPGAVARESGTEHDPRRLYGLPLDQDHKMLDITgsfssllasngglgsvlDGITPNGSGFKMVQMGGFGENFGSDQSLDLISVRgsgsqnqgnnnggESFMQSGNNDSSCWSGGSNGWPDLAIYTPSSNFQ
Disordered region (IsUnstruct)
***********************RCESTNTKFCYYNNYNLSQPRHFCKNCRRYWTRGGALRNIPI************************************************************************YGLPLD*DHKMLDITGSFSSLLASNGGLGSVLDGITPNGSGFKMVQMGGFG************************************************WPDLAI********
Disordered Region (DISOPRED)
************************CESTNTKFCYYNNYNLSQPRHFCKNCRRYWTRGGALRN*********************************************************************************************************************************************************************SCWSGGSNGWPDLAIYTPS****
Disordered Region (DISEMBL)
********PMKPHFPESEQLKCPRCESTNTKFCYYNNYNLSQPRHFCKNCRRYWTRGGALRNIPIGGGT************************************************VTLPGAVARESGTEHDPRRLYGLPLDQDHKMLDITGSFSSLLASNGGLGSVLDGITPNGSGFKMVQMGGFGENFGSDQSLDLISVRGSGSQNQGNNNGGESFMQSGNNDSSCWSGGSNGWPDLAIYTPSSNFQ
Disordered Region (DISPRO)
************HF***EQLKCPRCESTNTKFCYYNNYNLSQPRHFCKNCRRYWTRGGALRNIPIGG****************************************************************HDPRRLYGLPLDQDHKMLDITGSFSSLLASNGGLGSVLDGITPNGSGFKMVQMGGFGENFGSDQSLDLISVRGSGSQNQGNNNGGESFMQSGNNDSSCWSGGSNGWPDLAIYTPSSNF*
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MQDPATFNPMKPHFPESEQLKCPRCESTNTKFCYYNNYNLSQPRHFCKNCRRYWTRGGALRNIPIGGGTRKSNTKKRQKPDPDPSRSNPTRKSQETANTQSMLQAAATTSTSSQEPAVTLPGAVARESGTEHDPRRLYGLPLDQDHKMLDITGSFSSLLASNGGLGSVLDGITPNGSGFKMVQMGGFGENFGSDQSLDLISVRGSGSQNQGNNNGGESFMQSGNNDSSCWSGGSNGWPDLAIYTPSSNFQ
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	250	2.2.26 [Sep-21-2011]
O82155	194	Dof zinc finger protein D	yes	no	0.536	0.690	0.518	2e-34
Q94AR6	204	Dof zinc finger protein D	no	no	0.588	0.720	0.494	8e-32
Q8LDR0	307	Dof zinc finger protein D	no	no	0.292	0.237	0.671	1e-25
Q9FGD6	225	Dof zinc finger protein D	no	no	0.248	0.275	0.758	1e-25
Q9LSL6	316	Dof zinc finger protein D	no	no	0.256	0.202	0.772	1e-25
Q8L9V6	331	Dof zinc finger protein D	no	no	0.252	0.190	0.730	2e-25
Q39088	253	Dof zinc finger protein D	no	no	0.248	0.245	0.741	5e-25
O80928	330	Dof zinc finger protein D	no	no	0.248	0.187	0.746	8e-25
Q84K52	246	Dof zinc finger protein D	no	no	0.28	0.284	0.7	1e-24
Q9ZV33	340	Dof zinc finger protein D	no	no	0.228	0.167	0.771	2e-24

>sp|O82155|DOF17_ARATH Dof zinc finger protein DOF1.7 OS=Arabidopsis thaliana GN=DOF1.7 PE=2 SV=1

 Score =  146 bits (368), Expect = 2e-34,   Method: Compositional matrix adjust.
 Identities = 83/160 (51%), Positives = 99/160 (61%), Gaps = 26/160 (16%)

Query: 11  KPHFPESEQLKCPRCESTNTKFCYYNNYNLSQPRHFCKNCRRYWTRGGALRNIPIGGGTR 70
           +P  PE EQLKCPRC+S NTKFCYYNNYNLSQPRHFCKNCRRYWT+GGALRNIP+GGGTR
Sbjct: 24  QPELPEQEQLKCPRCDSPNTKFCYYNNYNLSQPRHFCKNCRRYWTKGGALRNIPVGGGTR 83

Query: 71  KSNTKKRQKPDPDPSRSNPTRKSQETANTQSMLQAAATTSTSSQEPAVTLPGAVARESGT 130
           KSN  KR    P  +  N           Q++ +      + S+E          R SG 
Sbjct: 84  KSN--KRSGSSPSSNLKN-----------QTVAEKPDHHGSGSEEKE-------ERVSGQ 123

Query: 131 EHDP-RRLYGLPLDQDHKMLDITGSFSSLLASNGGLGSVL 169
           E +P R LYGLP+   +       SFSSLLASN  +G ++
Sbjct: 124 EMNPTRMLYGLPVGDPN-----GASFSSLLASNMQMGGLV 158

Transcription factor that binds specifically to a 5'-AA[AG]G-3' consensus core sequence.
Arabidopsis thaliana (taxid: 3702)

>sp|Q94AR6|DOF31_ARATH Dof zinc finger protein DOF3.1 OS=Arabidopsis thaliana GN=DOF3.1 PE=2 SV=2

 Score =  137 bits (344), Expect = 8e-32,   Method: Compositional matrix adjust.
 Identities = 83/168 (49%), Positives = 106/168 (63%), Gaps = 21/168 (12%)

Query: 20  LKCPRCESTNTKFCYYNNYNLSQPRHFCKNCRRYWTRGGALRNIPIGGGTRKSNTKKRQK 79
           LKCPRC+S NTKFCYYNNYNLSQPRHFCK+CRRYWT+GGALRN+P+GGG+RK+ TK+   
Sbjct: 29  LKCPRCDSPNTKFCYYNNYNLSQPRHFCKSCRRYWTKGGALRNVPVGGGSRKNATKRSTS 88

Query: 80  PDPDPSRSNPTRKSQETANTQSMLQAAATTSTSSQEPAVTLPGAVARESGTEHDP-RRLY 138
                S  + + ++++T N             +SQ+P +              DP R LY
Sbjct: 89  SSSSASSPSNSSQNKKTKNPD-----PDPDPRNSQKPDL--------------DPTRMLY 129

Query: 139 GLPL-DQDHKMLDITGSFSSLLASNGGLGSVLDGITPNGSGFKMVQMG 185
           G P+ DQD K ++I GSFSSLLA+N  LG    GI  +GSG+    MG
Sbjct: 130 GFPIGDQDVKGMEIGGSFSSLLANNMQLGLGGGGIMLDGSGWDHPGMG 177

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

Arabidopsis thaliana (taxid: 3702)

>sp|Q8LDR0|DOF54_ARATH Dof zinc finger protein DOF5.4 OS=Arabidopsis thaliana GN=DOF5.4 PE=2 SV=2

 Score =  117 bits (292), Expect = 1e-25,   Method: Compositional matrix adjust.
 Identities = 49/73 (67%), Positives = 56/73 (76%)

Query: 18  EQLKCPRCESTNTKFCYYNNYNLSQPRHFCKNCRRYWTRGGALRNIPIGGGTRKSNTKKR 77
           + LKCPRC S NTKFCYYNNYNLSQPRHFCKNCRRYWT+GG LRN+P+GGG RK+   K 
Sbjct: 49  QSLKCPRCNSLNTKFCYYNNYNLSQPRHFCKNCRRYWTKGGVLRNVPVGGGCRKAKRSKT 108

Query: 78  QKPDPDPSRSNPT 90
           ++     S   PT
Sbjct: 109 KQVPSSSSADKPT 121

Transcription factor that binds specifically to a 5'-AA[AG]G-3' consensus core sequence. Enhances the DNA binding of OBF transcription factors to OCS elements.

Arabidopsis thaliana (taxid: 3702)

>sp|Q9FGD6|DOF58_ARATH Dof zinc finger protein DOF5.8 OS=Arabidopsis thaliana GN=DOF5.8 PE=2 SV=1

 Score =  116 bits (291), Expect = 1e-25,   Method: Compositional matrix adjust.
 Identities = 47/62 (75%), Positives = 54/62 (87%)

Query: 16 ESEQLKCPRCESTNTKFCYYNNYNLSQPRHFCKNCRRYWTRGGALRNIPIGGGTRKSNTK 75
          + EQL CPRCESTNTKFCYYNNYN SQPRHFCK+CRRYWT GG LR+IP+GG +RKS+ +
Sbjct: 28 QQEQLSCPRCESTNTKFCYYNNYNFSQPRHFCKSCRRYWTHGGTLRDIPVGGVSRKSSKR 87

Query: 76 KR 77
           R
Sbjct: 88 SR 89

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

Arabidopsis thaliana (taxid: 3702)

>sp|Q9LSL6|DOF57_ARATH Dof zinc finger protein DOF5.7 OS=Arabidopsis thaliana GN=DOF5.7 PE=2 SV=1

 Score =  116 bits (291), Expect = 1e-25,   Method: Compositional matrix adjust.
 Identities = 51/66 (77%), Positives = 57/66 (86%), Gaps = 2/66 (3%)

Query: 16  ESEQLKCPRCESTNTKFCYYNNYNLSQPRHFCKNCRRYWTRGGALRNIPIGGGTRKSNTK 75
           + + LKCPRC S NTKFCYYNNY+LSQPRHFCK+CRRYWTRGGALRN+PIGGG RK  TK
Sbjct: 37  DQQNLKCPRCNSPNTKFCYYNNYSLSQPRHFCKSCRRYWTRGGALRNVPIGGGCRK--TK 94

Query: 76  KRQKPD 81
           K  KP+
Sbjct: 95  KSIKPN 100

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

Arabidopsis thaliana (taxid: 3702)

>sp|Q8L9V6|DOF11_ARATH Dof zinc finger protein DOF1.1 OS=Arabidopsis thaliana GN=DOF1.1 PE=1 SV=2

 Score =  115 bits (289), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 46/63 (73%), Positives = 56/63 (88%)

Query: 15  PESEQLKCPRCESTNTKFCYYNNYNLSQPRHFCKNCRRYWTRGGALRNIPIGGGTRKSNT 74
           P +  LKCPRC+S+NTKFCYYNNYNL+QPRHFCK CRRYWT+GGALRN+P+GGG R++N 
Sbjct: 72  PLAGPLKCPRCDSSNTKFCYYNNYNLTQPRHFCKGCRRYWTQGGALRNVPVGGGCRRNNK 131

Query: 75  KKR 77
           K +
Sbjct: 132 KGK 134

Transcription factor that binds specifically to a 5'-AA[AG]G-3' consensus core sequence. Enhances the DNA binding of OBF transcription factors to OCS elements.

Arabidopsis thaliana (taxid: 3702)

>sp|Q39088|DOF34_ARATH Dof zinc finger protein DOF3.4 OS=Arabidopsis thaliana GN=DOF3.4 PE=1 SV=2

 Score =  114 bits (286), Expect = 5e-25,   Method: Compositional matrix adjust.
 Identities = 46/62 (74%), Positives = 53/62 (85%)

Query: 16 ESEQLKCPRCESTNTKFCYYNNYNLSQPRHFCKNCRRYWTRGGALRNIPIGGGTRKSNTK 75
          + EQL CPRC+S+NTKFCYYNNYN SQPRHFCK CRRYWT GG LR++P+GGGTRKS  +
Sbjct: 26 QQEQLPCPRCDSSNTKFCYYNNYNFSQPRHFCKACRRYWTHGGTLRDVPVGGGTRKSAKR 85

Query: 76 KR 77
           R
Sbjct: 86 SR 87

Transcription factor that binds specifically to a 5'-AA[AG]G-3' consensus core sequence. Enhances the DNA binding of OBF transcription factors to OCS elements.

Arabidopsis thaliana (taxid: 3702)

>sp|O80928|DOF24_ARATH Dof zinc finger protein DOF2.4 OS=Arabidopsis thaliana GN=DOF2.4 PE=2 SV=1

 Score =  114 bits (284), Expect = 8e-25,   Method: Compositional matrix adjust.
 Identities = 47/63 (74%), Positives = 55/63 (87%), Gaps = 1/63 (1%)

Query: 14  FPESEQLKCPRCESTNTKFCYYNNYNLSQPRHFCKNCRRYWTRGGALRNIPIGGGTRKSN 73
            PE+  LKCPRCESTNTKFCY+NNY+L+QPRHFCK CRRYWTRGGALRN+P+GGG R++ 
Sbjct: 84  LPEAA-LKCPRCESTNTKFCYFNNYSLTQPRHFCKTCRRYWTRGGALRNVPVGGGCRRNR 142

Query: 74  TKK 76
             K
Sbjct: 143 RTK 145

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

Arabidopsis thaliana (taxid: 3702)

>sp|Q84K52|DOF47_ARATH Dof zinc finger protein DOF4.7 OS=Arabidopsis thaliana GN=DOF4.7 PE=2 SV=1

 Score =  113 bits (283), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 49/70 (70%), Positives = 54/70 (77%)

Query: 4  PATFNPMKPHFPESEQLKCPRCESTNTKFCYYNNYNLSQPRHFCKNCRRYWTRGGALRNI 63
          P   N  +P       LKCPRC+S NTKFCYYNNY+LSQPRH+CKNCRRYWTRGGALRN+
Sbjct: 25 PRQINNKEPSPATQPVLKCPRCDSVNTKFCYYNNYSLSQPRHYCKNCRRYWTRGGALRNV 84

Query: 64 PIGGGTRKSN 73
          PIGG TR  N
Sbjct: 85 PIGGSTRNKN 94

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

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 =  112 bits (280), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 44/57 (77%), Positives = 50/57 (87%)

Query: 15  PESEQLKCPRCESTNTKFCYYNNYNLSQPRHFCKNCRRYWTRGGALRNIPIGGGTRK 71
           P    LKCPRC+S NTKFCY+NNYNL+QPRHFCK CRRYWTRGGALRN+P+GGG R+
Sbjct: 89  PPEGALKCPRCDSANTKFCYFNNYNLTQPRHFCKACRRYWTRGGALRNVPVGGGCRR 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	250
224134959	235	f-box family protein [Populus trichocarp	0.916	0.974	0.531	3e-63
359482860	216	PREDICTED: dof zinc finger protein DOF1.	0.864	1.0	0.528	1e-56
449458237	202	PREDICTED: dof zinc finger protein DOF1.	0.804	0.995	0.478	2e-54
255587071	250	zinc finger protein, putative [Ricinus c	0.94	0.94	0.516	3e-51
358349226	218	Dof zinc finger protein [Medicago trunca	0.868	0.995	0.486	4e-51
356522204	211	PREDICTED: dof zinc finger protein DOF1.	0.836	0.990	0.492	2e-50
356556684	211	PREDICTED: dof zinc finger protein DOF1.	0.836	0.990	0.503	1e-48
356550464	212	PREDICTED: dof zinc finger protein DOF1.	0.824	0.971	0.484	4e-44
297830826	199	hypothetical protein ARALYDRAFT_898570 [	0.66	0.829	0.489	2e-35
297743110	239	unnamed protein product [Vitis vinifera]	0.32	0.334	0.827	8e-35

>gi|224134959|ref|XP_002327532.1| f-box family protein [Populus trichocarpa] gi|222836086|gb|EEE74507.1| f-box family protein [Populus trichocarpa]

 Score =  247 bits (630), Expect = 3e-63,   Method: Compositional matrix adjust.
 Identities = 136/256 (53%), Positives = 175/256 (68%), Gaps = 27/256 (10%)

Query: 1   MQDPAT-FNPMKPHFPESEQLKCPRCESTNTKFCYYNNYNLSQPRHFCKNCRRYWTRGGA 59
           MQDP+T F+ +KP FPE EQLKCPRC+S NTKFCYYNNYNLSQPRHFCKNC+RYWT+GGA
Sbjct: 1   MQDPSTAFHTIKPQFPEQEQLKCPRCDSNNTKFCYYNNYNLSQPRHFCKNCKRYWTKGGA 60

Query: 60  LRNIPIGGGTRK----SNTKKRQKPDPDPSRSNPTRKSQETANTQSMLQAAATTSTSSQE 115
           LRNIP+GGG+RK    S+  KR  PDP+P    PTR+  +++       ++AT+STS Q+
Sbjct: 61  LRNIPVGGGSRKNTKRSSNTKRANPDPNPDPVKPTRRVADSS------SSSATSSTSGQQ 114

Query: 116 PAVTLPGAVARESGTEHDPRRLYGLPLDQDHKMLDITGSFSSLLASNGGLGSVLDGITPN 175
            A               DP R+YG+  D D K+LD+ GSFSSLLAS+G  GS+ +G+   
Sbjct: 115 LA----------GNGNQDPTRVYGVEADPDRKILDMGGSFSSLLASSGQFGSIFEGLDSG 164

Query: 176 GSGFKMVQMGGFGENFGSDQSLDL-ISVRGSGSQNQGNNNGGESFMQSGNNDSSCWSGGS 234
           GSG KMV+MGGFGE+  +  S +  + ++GS + N  N+ GGES++Q G      W   +
Sbjct: 165 GSGLKMVRMGGFGEDLNAGPSRNPGLDLQGSSNNNTTNDGGGESYLQGGE-----WGNSN 219

Query: 235 NGWPDLAIYTPSSNFQ 250
           NGWP LAIYTP S+FQ
Sbjct: 220 NGWPGLAIYTPGSSFQ 235

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359482860|ref|XP_003632855.1| PREDICTED: dof zinc finger protein DOF1.7-like [Vitis vinifera]

 Score =  225 bits (573), Expect = 1e-56,   Method: Compositional matrix adjust.
 Identities = 132/250 (52%), Positives = 160/250 (64%), Gaps = 34/250 (13%)

Query: 1   MQDPATFNPMKPHFPESEQLKCPRCESTNTKFCYYNNYNLSQPRHFCKNCRRYWTRGGAL 60
           MQDP+TF PMK HFPE E LKCPRCESTNTKFCYYNNYNLSQPRHFCKNCRRYWT+GGAL
Sbjct: 1   MQDPSTFQPMKTHFPEQEHLKCPRCESTNTKFCYYNNYNLSQPRHFCKNCRRYWTKGGAL 60

Query: 61  RNIPIGGGTRKSNTKKRQKPDPDPSRSNPTRKSQETANTQSMLQAAATTSTSSQEPAVTL 120
           RNIP+GGG+RK NTK+                    ++      ++++TS+ S  P  + 
Sbjct: 61  RNIPVGGGSRK-NTKR--------------------SSNPKRPSSSSSTSSVSSPPVSST 99

Query: 121 PGAVARESGTEHDPRRLYGLPLDQDHKMLDITGSFSSLLASNGGLGSVLDGITPNGSGFK 180
             A A++S    +P  +Y    DQD +MLDI+GSFSSLLASNG  GS+L+ + P GS  +
Sbjct: 100 SNAAAQKS----EPSGIYVTAADQDRRMLDISGSFSSLLASNGQFGSLLESLNPTGS-VR 154

Query: 181 MVQMGGFGENFGSDQSLDLISVRGSGSQNQGNNNGGESFMQSGNNDSSCWSGGSNGWPDL 240
            V +  F E   SD      S R    + Q N N  ESF+     DS+CW+GG NGWPDL
Sbjct: 155 GVPLSAFSETPNSD------SGRTPAMELQSNGN-SESFLGIQTGDSNCWNGG-NGWPDL 206

Query: 241 AIYTPSSNFQ 250
           AIYTP S FQ
Sbjct: 207 AIYTPGSTFQ 216

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449458237|ref|XP_004146854.1| PREDICTED: dof zinc finger protein DOF1.7-like [Cucumis sativus] gi|449476907|ref|XP_004154872.1| PREDICTED: dof zinc finger protein DOF1.7-like [Cucumis sativus]

 Score =  218 bits (555), Expect = 2e-54,   Method: Compositional matrix adjust.
 Identities = 120/251 (47%), Positives = 153/251 (60%), Gaps = 50/251 (19%)

Query: 1   MQDPATFNPMKPHFPESEQLKCPRCESTNTKFCYYNNYNLSQPRHFCKNCRRYWTRGGAL 60
           MQDP+TF P+KP FPE EQLKCPRC+STNTKFCYYNNYNLSQPRHFCKNCRRYWT+GGAL
Sbjct: 1   MQDPSTFQPIKPQFPEQEQLKCPRCDSTNTKFCYYNNYNLSQPRHFCKNCRRYWTKGGAL 60

Query: 61  RNIPIGGGTRKSNTKKRQKPDPDPSRSNPTRKSQETANTQSMLQAAATTSTSSQEPAVTL 120
           RNIP+GGGTRK++ +                         + ++   ++++S+    +T+
Sbjct: 61  RNIPVGGGTRKNSKRA----------------------VAATVKRPPSSTSSTHPNTITV 98

Query: 121 PGAVARESGTEHDPRRLYGLPLDQDHKMLDITGSFSSLLASNGGLGSVLDGITPNGSGFK 180
           P         +H+P R YG         LDI GSFSSLLASNG  G++L+G+ PN S  K
Sbjct: 99  P---------DHNPIRGYG-------GGLDIPGSFSSLLASNGQFGNLLEGVDPNQSEVK 142

Query: 181 MVQMGGFGENFGSDQSLDLISVRGSGSQNQGNNNGGESFMQSGNNDSSCWS-GGSNGWPD 239
           MV++G F             S R S ++ Q             N DS+CW+ GGSNGWPD
Sbjct: 143 MVELGEFSG-----------SGRKSAAEEQSAGVPENYLGVLQNGDSNCWNGGGSNGWPD 191

Query: 240 LAIYTPSSNFQ 250
           LAI+TP S++Q
Sbjct: 192 LAIFTPGSSYQ 202

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255587071|ref|XP_002534123.1| zinc finger protein, putative [Ricinus communis] gi|223525818|gb|EEF28260.1| zinc finger protein, putative [Ricinus communis]

 Score =  207 bits (527), Expect = 3e-51,   Method: Compositional matrix adjust.
 Identities = 137/265 (51%), Positives = 169/265 (63%), Gaps = 30/265 (11%)

Query: 1   MQDPAT-FNPMKPHFPESEQLKCPRCESTNTKFCYYNNYNLSQPRHFCKNCRRYWTRGGA 59
           MQDP+T F  MKP FPE EQLKCPRC+S NTKFCYYNNYNLSQPRHFCKNCRRYWT+GGA
Sbjct: 1   MQDPSTAFQQMKPQFPEQEQLKCPRCDSNNTKFCYYNNYNLSQPRHFCKNCRRYWTKGGA 60

Query: 60  LRNIPIGGGTRKSNTKKR---QKPDPDPSRSNPTRKSQETANTQSMLQAAATTSTSSQEP 116
           LRNIP+GGG+RK NTK+    ++ +PDPS  +P R ++   +  S    + TT+TS+   
Sbjct: 61  LRNIPVGGGSRK-NTKRSSNTKRSNPDPS-DDPNRINRRVPDAASSSSTSTTTATSNSH- 117

Query: 117 AVTLPGAVARESGTEHDPRRLYGLPLDQDHKMLDITGSFSSLLASNGGLGSVLDGITPNG 176
                  +   +    DP R+YGL  DQ+ K+LD+ GSFSSLL+SNG  G   DG+ P G
Sbjct: 118 ------LLGNGNSDMVDPTRMYGLEADQERKILDLGGSFSSLLSSNGQYGGFFDGLNPTG 171

Query: 177 SGFKMVQMGGFGENFGSDQSLDL-----------ISVRGSGSQNQGNNNGGESFMQSGNN 225
           S  KMVQ+GGF E+  S Q+ +L                 G    G   G E+++QSG  
Sbjct: 172 SSLKMVQIGGFAEDLNSGQNPNLDVQGSNNNGSGGGGEAGGGGGGGGGGGVENYLQSGE- 230

Query: 226 DSSCWSGGSNGWPDLAIYTPSSNFQ 250
               W G SNGWPDLAIYTP S+FQ
Sbjct: 231 ----W-GNSNGWPDLAIYTPGSSFQ 250

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|358349226|ref|XP_003638640.1| Dof zinc finger protein [Medicago truncatula] gi|355504575|gb|AES85778.1| Dof zinc finger protein [Medicago truncatula]

 Score =  207 bits (526), Expect = 4e-51,   Method: Compositional matrix adjust.
 Identities = 122/251 (48%), Positives = 154/251 (61%), Gaps = 34/251 (13%)

Query: 1   MQDPATFNPMKPHFPESEQLKCPRCESTNTKFCYYNNYNLSQPRHFCKNCRRYWTRGGAL 60
           MQD  TF PMKP+FPE EQLKCPRCES NTKFCYYNNYNLSQPRHFCKNC+RYWT+GGAL
Sbjct: 1   MQDQTTFQPMKPNFPEQEQLKCPRCESNNTKFCYYNNYNLSQPRHFCKNCKRYWTKGGAL 60

Query: 61  RNIPIGGGTRKSNTKKRQKPDPDPSRSNPTRKSQETANTQSMLQAAATTSTSSQEPAVTL 120
           RNIP+GGGTRK   +           SN  R +  ++++ S    +++ +  S       
Sbjct: 61  RNIPVGGGTRKVTKRS----------SNSKRSTTPSSSSPSASTTSSSAAKVSA------ 104

Query: 121 PGAVARESGTEHDPRRLYGLPLDQDHKMLDITGSFSSLLASNGGLGSVLDGITPNGSGFK 180
                  S +E DP +++  P +++       GSFSSLLAS    G++ +G+  NGSG K
Sbjct: 105 -------SVSETDPTQIHVDPAERNFS----GGSFSSLLASTERFGNLFEGLNSNGSGLK 153

Query: 181 MVQMGGFGENFGSDQSLDLISVRGSGSQNQGNNNG-GESFMQSGNNDSSCWSGGSNGWPD 239
           MV+MG FGEN   D       V     QNQG  NG  E F+   N  S+CW+  ++GW D
Sbjct: 154 MVEMGEFGENLNCDP-----VVNTDLGQNQGGRNGESEIFLGLQNGGSNCWN-DNHGWSD 207

Query: 240 LAIYTPSSNFQ 250
           LAIYTPSS +Q
Sbjct: 208 LAIYTPSSTYQ 218

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356522204|ref|XP_003529737.1| PREDICTED: dof zinc finger protein DOF1.7-like [Glycine max]

 Score =  205 bits (521), Expect = 2e-50,   Method: Compositional matrix adjust.
 Identities = 124/252 (49%), Positives = 151/252 (59%), Gaps = 43/252 (17%)

Query: 1   MQDPATFNPMKP-HFPESEQLKCPRCESTNTKFCYYNNYNLSQPRHFCKNCRRYWTRGGA 59
           MQDP  F  +KP  FPE EQLKCPRC+S NTKFCYYNNYNLSQPRHFCKNCRRYWT+GGA
Sbjct: 1   MQDPTAFQGVKPPQFPEQEQLKCPRCDSNNTKFCYYNNYNLSQPRHFCKNCRRYWTKGGA 60

Query: 60  LRNIPIGGGTRKSNTKKRQKPDPDPSRSNPTRKSQETANTQSMLQAAATTSTSSQEPAVT 119
           LRNIP+GGG+RK                                    TT  SS   +  
Sbjct: 61  LRNIPVGGGSRK------------------------------------TTKRSSSTLSKR 84

Query: 120 LPGAVARESGTEHDPRRLYGLPLDQDHKMLDITG-SFSSLLASNGGLGSVLDGITPNGSG 178
                +  + ++ DP R+   P+DQD ++L+I G SFSSLLAS+G  G++L+G+ P+GSG
Sbjct: 85  SSAPSSSSAVSDPDPTRICTNPVDQDQRVLNIGGGSFSSLLASSGHFGTLLEGLNPSGSG 144

Query: 179 FKMVQMGGFGENFGSDQSLDLISVRGSGSQNQGNNNGGESFMQSGNNDSSCWSGGSNGWP 238
            K   MG F E   SD  L+L S      Q Q N N  ESF+   N DSSCW+ G++GW 
Sbjct: 145 LK---MGEFVEGVSSDPGLNLDSGLNPDLQVQSNEN-SESFLGLQNGDSSCWN-GTHGWS 199

Query: 239 DLAIYTPSSNFQ 250
           DLAIYTP  +FQ
Sbjct: 200 DLAIYTPGPSFQ 211

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356556684|ref|XP_003546653.1| PREDICTED: dof zinc finger protein DOF1.7-like [Glycine max]

 Score =  199 bits (505), Expect = 1e-48,   Method: Compositional matrix adjust.
 Identities = 127/252 (50%), Positives = 145/252 (57%), Gaps = 43/252 (17%)

Query: 1   MQDPATFNPMKPHFPESEQLKCPRCESTNTKFCYYNNYNLSQPRHFCKNCRRYWTRGGAL 60
           MQDP  F PMKPHFPE EQLKCPRC+STNTKFCYYNNYNLSQPRHFCKNCRRYWT+GGAL
Sbjct: 1   MQDPTLFQPMKPHFPEQEQLKCPRCDSTNTKFCYYNNYNLSQPRHFCKNCRRYWTKGGAL 60

Query: 61  RNIPIGGGTRKSNTKKRQKPDPDPSRSNPTRKSQETANTQSMLQAAATTSTSSQEPAVTL 120
           RNIP+GGG+RK NTK               R S    NT+    +   +S  + EP    
Sbjct: 61  RNIPVGGGSRK-NTK---------------RSSSSNNNTKRASPSPPVSSAPAPEP---- 100

Query: 121 PGAVARESGTEHDPRRLYGLPLDQDHKMLDITGSFSSLLASNGGLGSVLDGITP--NGSG 178
                       DP R+   P+          GSFSSLLAS+G LG          +GS 
Sbjct: 101 ------------DPTRIGPTPVVGG-------GSFSSLLASSGHLGLGNLLEGLNSSGSN 141

Query: 179 FKMVQMGGFGENFGSDQSLDLISVRGSGSQNQGNNNGGESFMQSGNNDSSCWSGGSNGWP 238
            K VQM  FGEN  S    D  S R  G + Q N N  E+F+   N DSSCW+G S GW 
Sbjct: 142 LKTVQMEEFGENVSSGPVADPDSGRNPGLEMQSNGN-AENFLSLQNGDSSCWNGTS-GWS 199

Query: 239 DLAIYTPSSNFQ 250
            LAI+TP S+FQ
Sbjct: 200 HLAIFTPGSSFQ 211

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356550464|ref|XP_003543607.1| PREDICTED: dof zinc finger protein DOF1.7 [Glycine max]

 Score =  184 bits (466), Expect = 4e-44,   Method: Compositional matrix adjust.
 Identities = 124/256 (48%), Positives = 145/256 (56%), Gaps = 50/256 (19%)

Query: 1   MQDPATFNPMKPHFPESEQLKCPRCESTNTKFCYYNNYNLSQPRHFCKNCRRYWTRGGAL 60
           MQDP  F PMKPHFPE EQLKCPRC+STNTKFCYYNNYNLSQPRHFCKNCRRYWT+GGAL
Sbjct: 1   MQDPTLFQPMKPHFPEQEQLKCPRCDSTNTKFCYYNNYNLSQPRHFCKNCRRYWTKGGAL 60

Query: 61  RNIPIGGGTRKSNTKKRQKPDPDPSRSNPTRKSQETANTQSMLQAAATTSTSSQEPAVTL 120
           RNIP+GGG+RK NTK               R S    NT+    +   +S  +       
Sbjct: 61  RNIPVGGGSRK-NTK---------------RSSSSNNNTKHASPSPPVSSAPA------- 97

Query: 121 PGAVARESGTEHDPRRLYGLPLDQDHKMLDITGSFSSLLASNGGLGSVLDGIT--PNGSG 178
                     E DP R        D   +   GSF SLLAS+G LG          +GS 
Sbjct: 98  ---------PEIDPTRT-------DPNPVGGGGSFRSLLASSGHLGLGNLLEGLNSSGSN 141

Query: 179 FKMVQMGGFGENFGSDQSLDLISVRGSGSQNQG----NNNGGESFMQSGNNDSSCWSGGS 234
            K VQM  FGEN  S      ++V GSG QN G    +N   ESF+   N DS C + G+
Sbjct: 142 LKSVQMEEFGENVSSGTP---VAVPGSG-QNPGLEMQSNGNAESFLSLQNGDSGCCN-GT 196

Query: 235 NGWPDLAIYTPSSNFQ 250
           NGW +LAI+TP S++Q
Sbjct: 197 NGWSNLAIFTPGSSYQ 212

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297830826|ref|XP_002883295.1| hypothetical protein ARALYDRAFT_898570 [Arabidopsis lyrata subsp. lyrata] gi|297329135|gb|EFH59554.1| hypothetical protein ARALYDRAFT_898570 [Arabidopsis lyrata subsp. lyrata]

 Score =  154 bits (390), Expect = 2e-35,   Method: Compositional matrix adjust.
 Identities = 94/192 (48%), Positives = 118/192 (61%), Gaps = 27/192 (14%)

Query: 1   MQDPATF-----NPMKPHFPESEQLKCPRCESTNTKFCYYNNYNLSQPRHFCKNCRRYWT 55
           MQDPA +        +P F E EQLKCPRC+S NTKFCYYNNYNLSQPRHFCK+CRRYWT
Sbjct: 1   MQDPAAYYQTMMAKQQPQFAEQEQLKCPRCDSPNTKFCYYNNYNLSQPRHFCKSCRRYWT 60

Query: 56  RGGALRNIPIGGGTRKSNTKKRQKPDPDPSRSNPTRKSQETANTQSMLQAAATTSTSSQE 115
           +GGALRN+P+GGG+RK+ TK+        S S+ + ++++T N             +SQ 
Sbjct: 61  KGGALRNVPVGGGSRKNATKRSTSSSSSSSPSSNSSQNKKTKNPD-----PDPDPRNSQN 115

Query: 116 PAVTLPGAVARESGTEHDP-RRLYGLPL-DQDHKMLDITGSFSSLLASNGGLGSVLDGIT 173
           P +              DP R LYG P+ D D K ++I GSFSSLLASN  LG +  GI 
Sbjct: 116 PDI--------------DPTRMLYGFPIGDHDVKGMEIGGSFSSLLASNMQLG-LGGGIM 160

Query: 174 PNGSGFKMVQMG 185
            +GSG+    MG
Sbjct: 161 LDGSGWDHPGMG 172

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297743110|emb|CBI35977.3| unnamed protein product [Vitis vinifera]

 Score =  153 bits (386), Expect = 8e-35,   Method: Compositional matrix adjust.
 Identities = 67/81 (82%), Positives = 72/81 (88%), Gaps = 1/81 (1%)

Query: 1  MQDPATFNPMKPHFPESEQLKCPRCESTNTKFCYYNNYNLSQPRHFCKNCRRYWTRGGAL 60
          MQDP+TF PMK HFPE E LKCPRCESTNTKFCYYNNYNLSQPRHFCKNCRRYWT+GGAL
Sbjct: 1  MQDPSTFQPMKTHFPEQEHLKCPRCESTNTKFCYYNNYNLSQPRHFCKNCRRYWTKGGAL 60

Query: 61 RNIPIGGGTRKSNTKKRQKPD 81
          RNIP+GGG+RK NTK+   P 
Sbjct: 61 RNIPVGGGSRK-NTKRSSNPK 80

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	250
TAIR|locus:2074850	253	OBP1 "OBF binding protein 1" [	0.264	0.260	0.712	2.5e-32
TAIR|locus:2017567	194	DOF1 "DOF zinc finger protein	0.312	0.402	0.75	1.6e-31
TAIR|locus:2094746	204	DOF2 "DOF zinc finger protein	0.368	0.450	0.601	8.8e-31
TAIR|locus:2155755	316	AT5G65590 [Arabidopsis thalian	0.296	0.234	0.687	4.7e-29
TAIR|locus:2019499	352	AT1G64620 [Arabidopsis thalian	0.352	0.25	0.577	8.4e-28
TAIR|locus:2159275	307	OBP4 "OBF binding protein 4" [	0.376	0.306	0.591	1.3e-27
TAIR|locus:2039959	369	DAG2 "DOF AFFECTING GERMINATIO	0.22	0.149	0.745	9.4e-27
TAIR|locus:2040746	330	DOF2.4 "DNA binding with one f	0.352	0.266	0.602	1.2e-26
TAIR|locus:2026595	339	OBP2 [Arabidopsis thaliana (ta	0.388	0.286	0.529	1.5e-26
TAIR|locus:2053175	340	AT2G28810 [Arabidopsis thalian	0.4	0.294	0.533	1.5e-26

TAIR|locus:2074850 OBP1 "OBF binding protein 1" [Arabidopsis thaliana (taxid:3702)]

 Score = 288 (106.4 bits), Expect = 2.5e-32, Sum P(3) = 2.5e-32
 Identities = 47/66 (71%), Positives = 54/66 (81%)

Query:    12 PHFPESEQLKCPRCESTNTKFCYYNNYNLSQPRHFCKNCRRYWTRGGALRNIPIGGGTRK 71
             P   + EQL CPRC+S+NTKFCYYNNYN SQPRHFCK CRRYWT GG LR++P+GGGTRK
Sbjct:    22 PISDQQEQLPCPRCDSSNTKFCYYNNYNFSQPRHFCKACRRYWTHGGTLRDVPVGGGTRK 81

Query:    72 SNTKKR 77
             S  + R
Sbjct:    82 SAKRSR 87

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

GO:0005634 "nucleus" evidence=ISM

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

GO:0008270 "zinc ion binding" evidence=IEA

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

GO:0009751 "response to salicylic acid stimulus" evidence=IEP

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

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

GO:0042545 "cell wall modification" evidence=IMP

GO:0045787 "positive regulation of cell cycle" evidence=IMP

GO:0005515 "protein binding" evidence=IPI

TAIR|locus:2017567 DOF1 "DOF zinc finger protein 1" [Arabidopsis thaliana (taxid:3702)]

 Score = 346 (126.9 bits), Expect = 1.6e-31, P = 1.6e-31
 Identities = 60/80 (75%), Positives = 65/80 (81%)

Query:    11 KPHFPESEQLKCPRCESTNTKFCYYNNYNLSQPRHFCKNCRRYWTRGGALRNIPIGGGTR 70
             +P  PE EQLKCPRC+S NTKFCYYNNYNLSQPRHFCKNCRRYWT+GGALRNIP+GGGTR
Sbjct:    24 QPELPEQEQLKCPRCDSPNTKFCYYNNYNLSQPRHFCKNCRRYWTKGGALRNIPVGGGTR 83

Query:    71 KSNTKKRQKPDPDPSRSNPT 90
             KSN  KR    P  +  N T
Sbjct:    84 KSN--KRSGSSPSSNLKNQT 101

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:0010200 "response to chitin" evidence=IEP

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

 Score = 339 (124.4 bits), Expect = 8.8e-31, P = 8.8e-31
 Identities = 62/103 (60%), Positives = 74/103 (71%)

Query:     1 MQDPATF---------NPMKPHFPESEQLKCPRCESTNTKFCYYNNYNLSQPRHFCKNCR 51
             MQDPA +            +P F E EQLKCPRC+S NTKFCYYNNYNLSQPRHFCK+CR
Sbjct:     1 MQDPAAYYQTMMAKQQQQQQPQFAEQEQLKCPRCDSPNTKFCYYNNYNLSQPRHFCKSCR 60

Query:    52 RYWTRGGALRNIPIGGGTRKSNTKKRQKPDPDPSRSNPTRKSQ 94
             RYWT+GGALRN+P+GGG+RK+ TK+        S S+P+  SQ
Sbjct:    61 RYWTKGGALRNVPVGGGSRKNATKR--STSSSSSASSPSNSSQ 101

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

TAIR|locus:2155755 AT5G65590 [Arabidopsis thaliana (taxid:3702)]

 Score = 299 (110.3 bits), Expect = 4.7e-29, Sum P(2) = 4.7e-29
 Identities = 55/80 (68%), Positives = 62/80 (77%)

Query:    16 ESEQLKCPRCESTNTKFCYYNNYNLSQPRHFCKNCRRYWTRGGALRNIPIGGGTRKSNTK 75
             + + LKCPRC S NTKFCYYNNY+LSQPRHFCK+CRRYWTRGGALRN+PIGGG RK  TK
Sbjct:    37 DQQNLKCPRCNSPNTKFCYYNNYSLSQPRHFCKSCRRYWTRGGALRNVPIGGGCRK--TK 94

Query:    76 KRQKPDPD----PSRSNPTR 91
             K  KP+      PS S+  R
Sbjct:    95 KSIKPNSSMNTLPSSSSSQR 114

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:2019499 AT1G64620 [Arabidopsis thaliana (taxid:3702)]

 Score = 289 (106.8 bits), Expect = 8.4e-28, Sum P(2) = 8.4e-28
 Identities = 52/90 (57%), Positives = 63/90 (70%)

Query:     4 PATFNPMKPHFPESEQ-LKCPRCESTNTKFCYYNNYNLSQPRHFCKNCRRYWTRGGALRN 62
             PAT    K   PE +Q L CPRC S NTKFCYYNNY+L+QPR+FCK+CRRYWT GG+LRN
Sbjct:    33 PATPVERKAR-PEKDQALNCPRCNSLNTKFCYYNNYSLTQPRYFCKDCRRYWTAGGSLRN 91

Query:    63 IPIGGGTRKSNTKKRQKPDPDPSRSNPTRK 92
             IP+GGG RK+           PS S+ ++K
Sbjct:    92 IPVGGGVRKNKRSSSNSSSSSPSSSSSSKK 121

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:2159275 OBP4 "OBF binding protein 4" [Arabidopsis thaliana (taxid:3702)]

 Score = 309 (113.8 bits), Expect = 1.3e-27, P = 1.3e-27
 Identities = 58/98 (59%), Positives = 69/98 (70%)

Query:    18 EQLKCPRCESTNTKFCYYNNYNLSQPRHFCKNCRRYWTRGGALRNIPIGGGTRKSNTKKR 77
             + LKCPRC S NTKFCYYNNYNLSQPRHFCKNCRRYWT+GG LRN+P+GGG RK+   KR
Sbjct:    49 QSLKCPRCNSLNTKFCYYNNYNLSQPRHFCKNCRRYWTKGGVLRNVPVGGGCRKA---KR 105

Query:    78 QKPDPDPSRSNPTRKSQETANTQSMLQAAATTSTSSQE 115
              K    PS S+   K   T +   + + ++T S SS E
Sbjct:   106 SKTKQVPSSSSAD-KPTTTQDDHHVEEKSSTGSHSSSE 142

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:2039959 DAG2 "DOF AFFECTING GERMINATION 2" [Arabidopsis thaliana (taxid:3702)]

 Score = 265 (98.3 bits), Expect = 9.4e-27, Sum P(2) = 9.4e-27
 Identities = 41/55 (74%), Positives = 50/55 (90%)

Query:    18 EQLKCPRCESTNTKFCYYNNYNLSQPRHFCKNCRRYWTRGGALRNIPIGGGTRKS 72
             E+L CPRC STNTKFCYYNNY+L+QPR+FCK CRRYWT GG+LRN+P+GG +RK+
Sbjct:    78 EKLNCPRCNSTNTKFCYYNNYSLTQPRYFCKGCRRYWTEGGSLRNVPVGGSSRKN 132

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

GO:0009409 "response to cold" evidence=IMP

GO:0009416 "response to light stimulus" evidence=IMP

GO:0009845 "seed germination" evidence=IMP

GO:0006598 "polyamine catabolic process" evidence=RCA

GO:0009698 "phenylpropanoid metabolic process" evidence=RCA

GO:0042398 "cellular modified amino acid biosynthetic process" evidence=RCA

TAIR|locus:2040746 DOF2.4 "DNA binding with one finger 2.4" [Arabidopsis thaliana (taxid:3702)]

 Score = 300 (110.7 bits), Expect = 1.2e-26, P = 1.2e-26
 Identities = 59/98 (60%), Positives = 70/98 (71%)

Query:    15 PESEQLKCPRCESTNTKFCYYNNYNLSQPRHFCKNCRRYWTRGGALRNIPIGGGTRKSNT 74
             PE+  LKCPRCESTNTKFCY+NNY+L+QPRHFCK CRRYWTRGGALRN+P+GGG R++  
Sbjct:    85 PEAA-LKCPRCESTNTKFCYFNNYSLTQPRHFCKTCRRYWTRGGALRNVPVGGGCRRN-- 141

Query:    75 KKRQKPDPDPSRSNPTRKSQETANTQSMLQA-AATTST 111
              +R K     S SN    S  T+N  S     A+T ST
Sbjct:   142 -RRTK-----SNSNNNNNSTATSNNTSFSSGNASTIST 173

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

GO:0010089 "xylem development" evidence=RCA

GO:0044036 "cell wall macromolecule metabolic process" evidence=RCA

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

 Score = 299 (110.3 bits), Expect = 1.5e-26, P = 1.5e-26
 Identities = 54/102 (52%), Positives = 72/102 (70%)

Query:    15 PESEQLKCPRCESTNTKFCYYNNYNLSQPRHFCKNCRRYWTRGGALRNIPIGGGTRKSNT 74
             P +  LKCPRC+S+NTKFCYYNNYNL+QPRHFCK CRRYWT+GGALRN+P+GGG R++N 
Sbjct:    80 PLAGPLKCPRCDSSNTKFCYYNNYNLTQPRHFCKGCRRYWTQGGALRNVPVGGGCRRNNK 139

Query:    75 KKRQKPDPDPSRSNPTRKSQETANTQSMLQAAATTSTSSQEP 116
             K +   + +   S+ + K   + N QS   ++    T+ Q P
Sbjct:   140 KGK---NGNLKSSSSSSKQSSSVNAQS--PSSGQLRTNHQFP 176

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:2053175 AT2G28810 [Arabidopsis thaliana (taxid:3702)]

 Score = 299 (110.3 bits), Expect = 1.5e-26, P = 1.5e-26
 Identities = 55/103 (53%), Positives = 69/103 (66%)

Query:    15 PESEQLKCPRCESTNTKFCYYNNYNLSQPRHFCKNCRRYWTRGGALRNIPIGGGTRKSNT 74
             P    LKCPRC+S NTKFCY+NNYNL+QPRHFCK CRRYWTRGGALRN+P+GGG R++  
Sbjct:    89 PPEGALKCPRCDSANTKFCYFNNYNLTQPRHFCKACRRYWTRGGALRNVPVGGGCRRN-- 146

Query:    75 KKRQKPDPDPSRSNPTRKSQETANTQSMLQAA-ATTSTSSQEP 116
             KK +  +   S S+  ++S    N  S    +     T+SQ P
Sbjct:   147 KKGKSGNSKSSSSSQNKQSTSMVNATSPTNTSNVQLQTNSQFP 189

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

---

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	250
pfam02701	63	pfam02701, zf-Dof, Dof domain, zinc finger	1e-37

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

 Score =  126 bits (317), Expect = 1e-37
 Identities = 44/63 (69%), Positives = 51/63 (80%)

Query: 15 PESEQLKCPRCESTNTKFCYYNNYNLSQPRHFCKNCRRYWTRGGALRNIPIGGGTRKSNT 74
             + LKCPRC+S NTKFCYYNNYNL+QPR+FCKNCRRYWT GGALRN+P+GGG RK+  
Sbjct: 1  KPDKALKCPRCDSMNTKFCYYNNYNLNQPRYFCKNCRRYWTAGGALRNVPVGGGRRKNKR 60

Query: 75 KKR 77
             
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	250
PF02701	63	zf-Dof: Dof domain, zinc finger; InterPro: IPR0038	100.0
TIGR02159	146	PA_CoA_Oxy4 phenylacetate-CoA oxygenase, PaaJ subu	93.39
PF12760	46	Zn_Tnp_IS1595: Transposase zinc-ribbon domain; Int	93.38
COG3677	129	Transposase and inactivated derivatives [DNA repli	92.08
PF03811	36	Zn_Tnp_IS1: InsA N-terminal domain; InterPro: IPR0	90.16
smart00440	40	ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding mo	89.17
PF01096	39	TFIIS_C: Transcription factor S-II (TFIIS); InterP	86.57
PHA02998	195	RNA polymerase subunit; Provisional	82.69
PF04216	290	FdhE: Protein involved in formate dehydrogenase fo	81.06
TIGR01384	104	TFS_arch transcription factor S, archaeal. There h	80.96
cd00202	54	ZnF_GATA Zinc finger DNA binding domain; binds spe	80.21

>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=1.5e-36  Score=224.89  Aligned_cols=57  Identities=75%  Similarity=1.560  Sum_probs=55.8

Q ss_pred             cccccCCCCCCCCceeeeecccCCCCCcccccccccccccCcccccccCCCcccCCC
Q 046549           17 SEQLKCPRCESTNTKFCYYNNYNLSQPRHFCKNCRRYWTRGGALRNIPIGGGTRKSN   73 (250)
Q Consensus        17 ~~~~~CPRC~S~~TKFcYyNNy~~~QPR~fCk~CrRyWT~GGtlRnVPVGGG~RKnk   73 (250)
                      ++.++||||+|.+|||||||||++.||||||++|+||||+||+|||||||||+||+|
T Consensus         3 ~~~~~CPRC~S~nTKFcYyNNy~~~QPR~~Ck~C~rywT~GG~lRnVPvggg~Rk~k   59 (63)
T PF02701_consen    3 EQPLPCPRCDSTNTKFCYYNNYNLSQPRYFCKSCRRYWTHGGTLRNVPVGGGCRKNK   59 (63)
T ss_pred             ccCCCCCCcCCCCCEEEeecCCCCCCcchhhHHHHHHHHhcceecCCccCCCcccCC
Confidence            478999999999999999999999999999999999999999999999999999998

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=93.39  E-value=0.031  Score=47.05  Aligned_cols=36  Identities=22%  Similarity=0.559  Sum_probs=27.4

Q ss_pred             cccCCCCCCCCceeeeecccCCCCCccccccccccc
Q 046549           19 QLKCPRCESTNTKFCYYNNYNLSQPRHFCKNCRRYW   54 (250)
Q Consensus        19 ~~~CPRC~S~~TKFcYyNNy~~~QPR~fCk~CrRyW   54 (250)
                      ...||||.|.+|+..--=-=+.++.-|+|++|+.=+
T Consensus       105 ~~~cp~c~s~~t~~~s~fg~t~cka~~~c~~c~epf  140 (146)
T TIGR02159       105 SVQCPRCGSADTTITSIFGPTACKALYRCRACKEPF  140 (146)
T ss_pred             CCcCCCCCCCCcEeecCCCChhhHHHhhhhhhCCcH
Confidence            479999999999965322235568889999998644

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.

>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=93.38  E-value=0.068  Score=36.54  Aligned_cols=29  Identities=38%  Similarity=0.824  Sum_probs=23.2

Q ss_pred             ccccCCCCCCCCceeeeecccCCCCCccccccccc
Q 046549           18 EQLKCPRCESTNTKFCYYNNYNLSQPRHFCKNCRR   52 (250)
Q Consensus        18 ~~~~CPRC~S~~TKFcYyNNy~~~QPR~fCk~CrR   52 (250)
                      ++..||+|.+.  ++..+.+    +.++.|++|++
T Consensus        17 ~g~~CP~Cg~~--~~~~~~~----~~~~~C~~C~~   45 (46)
T PF12760_consen   17 DGFVCPHCGST--KHYRLKT----RGRYRCKACRK   45 (46)
T ss_pred             CCCCCCCCCCe--eeEEeCC----CCeEECCCCCC
Confidence            35779999998  6655555    78999999985

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

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

Probab=92.08  E-value=0.11  Score=42.99  Aligned_cols=36  Identities=31%  Similarity=0.670  Sum_probs=28.2

Q ss_pred             cccCCCCCCCCceeeeecccCCCCCccccccccccccc
Q 046549           19 QLKCPRCESTNTKFCYYNNYNLSQPRHFCKNCRRYWTR   56 (250)
Q Consensus        19 ~~~CPRC~S~~TKFcYyNNy~~~QPR~fCk~CrRyWT~   56 (250)
                      ...||+|.+.+  +-=+.-+.....|+.|++|++-|+.
T Consensus        30 ~~~cP~C~s~~--~~k~g~~~~~~qRyrC~~C~~tf~~   65 (129)
T COG3677          30 KVNCPRCKSSN--VVKIGGIRRGHQRYKCKSCGSTFTV   65 (129)
T ss_pred             cCcCCCCCccc--eeeECCccccccccccCCcCcceee
Confidence            47899999999  3334555555999999999999874

>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=90.16  E-value=0.2  Score=33.78  Aligned_cols=31  Identities=39%  Similarity=0.789  Sum_probs=21.4

Q ss_pred             cccCCCCCCCCceeeeecccCC-CCCcccccccc
Q 046549           19 QLKCPRCESTNTKFCYYNNYNL-SQPRHFCKNCR   51 (250)
Q Consensus        19 ~~~CPRC~S~~TKFcYyNNy~~-~QPR~fCk~Cr   51 (250)
                      .+.||+|.+.+.=  |=|-.+. -..||+|++|+
T Consensus         5 ~v~CP~C~s~~~v--~k~G~~~~G~qryrC~~C~   36 (36)
T PF03811_consen    5 DVHCPRCQSTEGV--KKNGKSPSGHQRYRCKDCR   36 (36)
T ss_pred             eeeCCCCCCCCcc--eeCCCCCCCCEeEecCcCC
Confidence            4789999998721  2233333 35899999996

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=89.17  E-value=0.41  Score=32.40  Aligned_cols=37  Identities=22%  Similarity=0.696  Sum_probs=28.0

Q ss_pred             ccCCCCCCCCceeeeecccCCCCC---ccccccccccccc
Q 046549           20 LKCPRCESTNTKFCYYNNYNLSQP---RHFCKNCRRYWTR   56 (250)
Q Consensus        20 ~~CPRC~S~~TKFcYyNNy~~~QP---R~fCk~CrRyWT~   56 (250)
                      .+||+|...+.-|-..+-.....|   -|.|.+|...|..
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            379999877777766666655555   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=86.57  E-value=0.6  Score=31.36  Aligned_cols=36  Identities=28%  Similarity=0.771  Sum_probs=24.6

Q ss_pred             ccCCCCCCCCceeeeecccCCCCCc---ccccccccccc
Q 046549           20 LKCPRCESTNTKFCYYNNYNLSQPR---HFCKNCRRYWT   55 (250)
Q Consensus        20 ~~CPRC~S~~TKFcYyNNy~~~QPR---~fCk~CrRyWT   55 (250)
                      .+||.|...+.-|--.+......|-   |.|.+|..-|+
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            3799999988766655666555553   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 ....

>PHA02998 RNA polymerase subunit; Provisional

Probab=82.69  E-value=1.3  Score=40.01  Aligned_cols=43  Identities=26%  Similarity=0.626  Sum_probs=35.8

Q ss_pred             CCCcccccCCCCCCCCceeeeecccCCCCCc---cccccccccccc
Q 046549           14 FPESEQLKCPRCESTNTKFCYYNNYNLSQPR---HFCKNCRRYWTR   56 (250)
Q Consensus        14 ~pe~~~~~CPRC~S~~TKFcYyNNy~~~QPR---~fCk~CrRyWT~   56 (250)
                      +|+....+||+|...++-|--.|-++-..|-   |.|..|..-|.-
T Consensus       138 lpkkt~v~CPkCg~~~A~f~qlQTRSADEPmT~FYkC~~CG~~wkp  183 (195)
T PHA02998        138 LDEKYNTPCPNCKSKNTTPMMIQTRAADEPPLVRHACRDCKKHFKP  183 (195)
T ss_pred             cCcccCCCCCCCCCCceEEEEEeeccCCCCceEEEEcCCCCCccCC
Confidence            3444679999999999999888888887775   899999999964

>PF04216 FdhE: Protein involved in formate dehydrogenase formation; InterPro: IPR006452 This family of sequences describe an accessory protein required for the assembly of formate dehydrogenase of certain proteobacteria although not present in the final complex []

Probab=81.06  E-value=0.74  Score=41.45  Aligned_cols=37  Identities=27%  Similarity=0.695  Sum_probs=19.0

Q ss_pred             cccCCCCCCCC-ceeeeecc-cCCCCCcccccccccccc
Q 046549           19 QLKCPRCESTN-TKFCYYNN-YNLSQPRHFCKNCRRYWT   55 (250)
Q Consensus        19 ~~~CPRC~S~~-TKFcYyNN-y~~~QPR~fCk~CrRyWT   55 (250)
                      ...||.|...+ .++-||.. -....--+.|..|+.|+-
T Consensus       211 R~~Cp~Cg~~~~~~l~~~~~e~~~~~rve~C~~C~~YlK  249 (290)
T PF04216_consen  211 RIKCPYCGNTDHEKLEYFTVEGEPAYRVEVCESCGSYLK  249 (290)
T ss_dssp             TTS-TTT---SS-EEE--------SEEEEEETTTTEEEE
T ss_pred             CCCCcCCCCCCCcceeeEecCCCCcEEEEECCcccchHH
Confidence            57899999855 55667643 333333499999999983

The exact nature of the function of FdhE in the assembly of the complex is unknown, but considering the presence of selenocysteine, molybdopterin, iron-sulphur clusters and cytochrome b556, it is likely to be involved in the insertion of cofactors. ; GO: 0005737 cytoplasm; PDB: 2FIY_B.

>TIGR01384 TFS_arch transcription factor S, archaeal

Probab=80.96  E-value=2  Score=33.04  Aligned_cols=45  Identities=18%  Similarity=0.612  Sum_probs=31.2

Q ss_pred             CCCCCcccccCCCCCCCCceeeeecccCCCCCc---ccccccccccccC
Q 046549           12 PHFPESEQLKCPRCESTNTKFCYYNNYNLSQPR---HFCKNCRRYWTRG   57 (250)
Q Consensus        12 p~~pe~~~~~CPRC~S~~TKFcYyNNy~~~QPR---~fCk~CrRyWT~G   57 (250)
                      |.+|. -...||+|...+.-|-..+-.+...|-   |.|..|.-.|+.+
T Consensus        56 ~~~~~-~~~~Cp~Cg~~~a~f~~~Q~RsadE~~T~fy~C~~C~~~w~~~  103 (104)
T TIGR01384        56 ETLPT-TRVECPKCGHKEAYYWLLQTRRADEPETRFYKCTKCGYVWREY  103 (104)
T ss_pred             cCCCc-ccCCCCCCCCCeeEEEEeccCCCCCCcEEEEEeCCCCCeeEeC
Confidence            33444 258999998777666555555443343   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.

>cd00202 ZnF_GATA Zinc finger DNA binding domain; binds specifically to DNA consensus sequence [AT]GATA[AG] promoter elements; a subset of family members may also bind protein; zinc-finger consensus topology is C-X(2)-C-X(17)-C-X(2)-C

Probab=80.21  E-value=1.5  Score=31.50  Aligned_cols=41  Identities=27%  Similarity=0.697  Sum_probs=28.5

Q ss_pred             cCCCCCCCCceeeeecccCCCCCcccccccccccccCccccccc
Q 046549           21 KCPRCESTNTKFCYYNNYNLSQPRHFCKNCRRYWTRGGALRNIP   64 (250)
Q Consensus        21 ~CPRC~S~~TKFcYyNNy~~~QPR~fCk~CrRyWT~GGtlRnVP   64 (250)
                      .|-.|...+|..=.-.   ......+|-+|.-||.+.|..|.+-
T Consensus         1 ~C~~C~~~~Tp~WR~g---~~~~~~LCNaCgl~~~k~~~~rp~~   41 (54)
T cd00202           1 ACSNCGTTTTPLWRRG---PSGGSTLCNACGLYWKKHGVMRPLS   41 (54)
T ss_pred             CCCCCCCCCCcccccC---CCCcchHHHHHHHHHHhcCCCCCcc
Confidence            3677777776432221   2467799999999999999665443

---

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	250
3h0g_I	113	DNA-directed RNA polymerases I, II, and III subuni	82.72
1qyp_A	57	RNA polymerase II; transcription, RPB9, Zn ribbon,	82.61
1tfi_A	50	Transcriptional elongation factor SII; transcripti	82.37

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

Probab=82.72  E-value=0.93  Score=35.14  Aligned_cols=44  Identities=23%  Similarity=0.532  Sum_probs=27.8

Q ss_pred             CCCCCcccccCCCCCCCCceeeeecccCCCCCc---cccccccccccc
Q 046549           12 PHFPESEQLKCPRCESTNTKFCYYNNYNLSQPR---HFCKNCRRYWTR   56 (250)
Q Consensus        12 p~~pe~~~~~CPRC~S~~TKFcYyNNy~~~QPR---~fCk~CrRyWT~   56 (250)
                      |.+|... .+||+|...+..|-..+-.....|-   |.|..|..-|..
T Consensus        66 ~tlp~~~-~~Cp~C~~~~a~~~q~q~rsade~mt~fy~C~~C~~~w~~  112 (113)
T 3h0g_I           66 PTLPRSD-KECPRCHQHEAVFYQTHSRRGDTMMTLIYVCVHCGFAFEE  112 (113)
T ss_dssp             SSSCBCC-SCCSSSCCSCEEEECCCCSSCCCCCCCEEEESSSCCCCCC
T ss_pred             ccCCCcc-cCCCCCCCceEEEEEEecccCCCCCeeEEEcCCCCCEEec
Confidence            3445443 8999999876554333333332232   889999999974

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

Probab=82.61  E-value=1.2  Score=30.48  Aligned_cols=38  Identities=18%  Similarity=0.594  Sum_probs=25.6

Q ss_pred             cccCCCCCCCCceeeeecccCCCCC---ccccccccccccc
Q 046549           19 QLKCPRCESTNTKFCYYNNYNLSQP---RHFCKNCRRYWTR   56 (250)
Q Consensus        19 ~~~CPRC~S~~TKFcYyNNy~~~QP---R~fCk~CrRyWT~   56 (250)
                      .++||+|...+..|--.+-.....|   .|.|..|.--|..
T Consensus        15 ~~~Cp~Cg~~~~~~~q~Q~rsadep~T~fy~C~~Cg~~w~~   55 (57)
T 1qyp_A           15 KITCPKCGNDTAYWWEMQTRAGDEPSTIFYKCTKCGHTWRS   55 (57)
T ss_dssp             ECCCTTTCCSEEEEEEECCSSSSCSSEEEEEESSSCCEEEC
T ss_pred             EeECCCCCCCEEEEEEeecccCCCCCcEEEEcCCCCCEecc
Confidence            6889999984444333333333344   3899999999975

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

Probab=82.37  E-value=1.1  Score=30.85  Aligned_cols=38  Identities=18%  Similarity=0.664  Sum_probs=28.7

Q ss_pred             ccccCCCCCCCCceeeeecccCCCCCc---ccccccccccc
Q 046549           18 EQLKCPRCESTNTKFCYYNNYNLSQPR---HFCKNCRRYWT   55 (250)
Q Consensus        18 ~~~~CPRC~S~~TKFcYyNNy~~~QPR---~fCk~CrRyWT   55 (250)
                      ....||+|...+.-|--.+..+...|-   |.|..|..-|.
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            357899999888776666666555554   89999998885

---

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	250
d1twfi2	72	RBP9 subunit of RNA polymerase II {Baker's yeast (	92.08
d1tfia_	50	Transcriptional factor SII, C-terminal domain {Hum	88.81
d1qypa_	57	RBP9 subunit of RNA polymerase II {Archaeon Thermo	82.01

>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=92.08  E-value=0.071  Score=37.92  Aligned_cols=46  Identities=24%  Similarity=0.587  Sum_probs=34.0

Q ss_pred             CCCCCcccccCCCCCCCCceeeeecccCCCCCc---ccccccccccccCc
Q 046549           12 PHFPESEQLKCPRCESTNTKFCYYNNYNLSQPR---HFCKNCRRYWTRGG   58 (250)
Q Consensus        12 p~~pe~~~~~CPRC~S~~TKFcYyNNy~~~QPR---~fCk~CrRyWT~GG   58 (250)
                      |-+|.- ...||+|...+.-|-..+-....-|-   |.|..|.-.|+.-.
T Consensus        17 Ptlp~t-~~~CpkCg~~~a~~~q~QtRsaDE~mT~Fy~C~~C~h~Wr~~~   65 (72)
T d1twfi2          17 PTLPRS-DRECPKCHSRENVFFQSQQRRKDTSMVLFFVCLSCSHIFTSDQ   65 (72)
T ss_dssp             TTSCCC-CCCCTTTCCCCEEEEECSSCCTTCCCCEEEEETTTCCEEECCT
T ss_pred             CCCCcc-CCCCCCCCCCeEEEEEeecCccCCCceEEEEcCCCCCCccccc
Confidence            345554 57999999888777766666554444   89999999998843

>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=88.81  E-value=0.15  Score=34.05  Aligned_cols=37  Identities=19%  Similarity=0.681  Sum_probs=31.4

Q ss_pred             ccccCCCCCCCCceeeeecccCCCCCc---cccccccccc
Q 046549           18 EQLKCPRCESTNTKFCYYNNYNLSQPR---HFCKNCRRYW   54 (250)
Q Consensus        18 ~~~~CPRC~S~~TKFcYyNNy~~~QPR---~fCk~CrRyW   54 (250)
                      ...+||+|.+.+..|--.+..+...|-   +.|..|..-|
T Consensus         8 ~~~~C~kC~~~~~~~~~~QtRSADEp~T~F~~C~~Cg~~W   47 (50)
T d1tfia_           8 DLFTCGKCKKKNCTYTQVQTRSADEPMTTFVVCNECGNRW   47 (50)
T ss_dssp             CCSCCSSSCSSCEEEEEECSSSSSSCCEEEEEESSSCCEE
T ss_pred             CCEECCCCCCCccEEEEEEccCCCCCceEEEEccccCCee
Confidence            457999999999888777777777776   8999999988

>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=82.01  E-value=0.58  Score=31.60  Aligned_cols=43  Identities=19%  Similarity=0.631  Sum_probs=31.9

Q ss_pred             CCCCcccccCCCCCCCCceeeeecccCCCCCc---cccccccccccc
Q 046549           13 HFPESEQLKCPRCESTNTKFCYYNNYNLSQPR---HFCKNCRRYWTR   56 (250)
Q Consensus        13 ~~pe~~~~~CPRC~S~~TKFcYyNNy~~~QPR---~fCk~CrRyWT~   56 (250)
                      .+|.. .+.||+|...+.-|--.+-....-|-   |.|..|.--|..
T Consensus        10 ~~pt~-~~~CpkC~~~~a~~~~~QtRsaDE~~T~fy~C~~Cg~~wre   55 (57)
T d1qypa_          10 TLPTT-KITCPKCGNDTAYWWEMQTRAGDEPSTIFYKCTKCGHTWRS   55 (57)
T ss_dssp             SSCEE-ECCCTTTCCSEEEEEEECCSSSSCSSEEEEEESSSCCEEEC
T ss_pred             cCCcc-cCCCCCCCCCceEEEEeecccccCCCeEEEEeCCCCCccee
Confidence            34443 57999999888887666666555554   899999999863