Citrus Sinensis ID: 043493

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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
MPSESTDRKLARAHNPISTYPPPKVTESLPCPRCESTSTKFCYYNNYNLSQPRHFCKSCRRYWTQGGTLRNIPVGGGTRKNSKRTRISSSSSSGAVVATANSSSCSSAVTHDRVAEPANPVSVLPCGNPEMGLITMTDVNLNDSVGVPGSGSYTTMLNMQIQGQNFLGLGGFHNHGYGIGSGLEELELGFGTARSWDIPGTGYACTGGGSGAATSGCNTWQMMNGDDQGGNDVGEDCFGWSGLAISTPAGKDLK
Secondary Structure (PSIPRED)
cccccHHHHHHccccccccccccccccccccccccccccEEEEEccccccccHHHHHHHHHcccccccEEcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEcccccccc
Secondary Structure Prediction (SSPRO)
cccccccccccccccccccccccccHcccccccccccccEEEEEcccccccccHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEEccccccccccccccccccccEEEcccccccc
Coil and Loop (DISEMBL)
mpsestdrklarahnpistypppkvteslpcprceststkfcyynnynlsqprhfcKSCRrywtqggtlrnipvgggtrknskrtrissssssgavvatanssscssavthdrvaepanpvsvlpcgnpemglITMTdvnlndsvgvpgsgsytTMLNMQIQGqnflglggfhnhgygigsgleelelgfgtarswdipgtgyactgggsgaatsgcntwqmmngddqggndvgedcfgwsglaistpagkdlk
Flexible Loop (DISEMBL)
mpsestdrklarahnpistypppkvteslpCPRCESTSTKFCYYNNYNLSQPRHFCKSCRRYWTqggtlrnipvgggtrknskrtrissssssgavVATANSSSCSSAVTHDRVAEPANPVSVLPCGNPEMGLITMTDVNLNDSVGVPGSGSYTTMLNMQIQGQNFLGLGGFHNHGYGIGSGLEELELGFGTARSWDIPGTGYACTGGGSGAATSGCNTWQMMNGDDQGGNDVGEDCFGWSglaistpagkdlk
Low Complexity Region (SEG)
MPSESTDRKLARAHNPISTYPPPKVTESLPCPRCESTSTKFCYYNNYNLSQPRHFCKSCRRYWTQGGTLRNIPVGGGtrknskrtrissssssgavvatansssCSSAVTHDRVAEPANPVSVLPCGNPEMGLITMTDVNLNDSVGVPGSGSYTTMLNMQIQGQNFLGLGGFHNHgygigsgleelelgfgTARSWDIPgtgyactgggsgaatsgcNTWQMMNGDDQGGNDVGEDCFGWSGLAISTPAGKDLK
Disordered region (IsUnstruct)
*********************************CESTSTKFCYYNNYNLSQPRHFCKSCRRYWTQGGTLRNIPV***********************************************SVLPCGNPEMGLITMTDVNLNDSVGVPGSGSYTTMLNMQIQGQNFLGLGGFHNHGYGIGSGLEELELGFGTARSWDIPGTGYACTGGGSGAATSGCNTWQMMNGDDQGGNDVGEDCFGWSGLAI*********
Disordered Region (DISOPRED)
*******************************PRCESTSTKFCYYNNYNLSQPRHFCKSCRRYWTQGGTLRN***************************************************************************************************************************SW************************************VGEDCFGWSGLAISTPA*****
Disordered Region (DISEMBL)
************AHNPISTYPPPKVTESLPCPRCESTSTKFCYYNNYNLSQPRHFCKSCRRYWTQGGTLRNIPVGG*************************************VAEPANPVSVLPCGNPEMGLITMTDVNLNDSVGVPGSGSYTTMLNMQIQGQNFLGLGGFHNHGYGIGSGLEELELGFGTARSWDIPGTGYACTGGGSGAATSGCNTWQMMNGDDQGGNDVGEDCFGWSGLAISTPAGKDLK
Disordered Region (DISPRO)
**************************ESLPCPRCESTSTKFCYYNNYNLSQPRHFCKSCRRYWTQGGTLRNIPVGG*T*************************************EPANPVSVLPCGNPEMGLITMTDVNLNDSVGVPGSGSYTTMLNMQIQGQNFLGLGGFHNHGYGIGSGLEELELGFGTARSWDIPGTGYACTGGGSGAATSGCNTWQMMNGDDQGGNDVGEDCFGWSGLAISTPA*****
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MPSESTDRKLARAHNPISTYPPPKVTESLPCPRCESTSTKFCYYNNYNLSQPRHFCKSCRRYWTQGGTLRNIPVGGGTRKNSKRTRISSSSSSGAVVATANSSSCSSAVTHDRVAEPANPVSVLPCGNPEMGLITMTDVNLNDSVGVPGSGSYTTMLNMQIQGQNFLGLGGFHNHGYGIGSGLEELELGFGTARSWDIPGTGYACTGGGSGAATSGCNTWQMMNGDDQGGNDVGEDCFGWSGLAISTPAGKDLK
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	254	2.2.26 [Sep-21-2011]
Q9FGD6	225	Dof zinc finger protein D	yes	no	0.397	0.448	0.605	1e-28
Q9SX97	209	Dof zinc finger protein D	no	no	0.307	0.373	0.679	3e-28
O82155	194	Dof zinc finger protein D	no	no	0.602	0.788	0.434	3e-27
Q39088	253	Dof zinc finger protein D	no	no	0.307	0.308	0.670	3e-27
O24463	328	Dof zinc finger protein P	N/A	no	0.330	0.256	0.579	2e-25
Q8LDR0	307	Dof zinc finger protein D	no	no	0.354	0.293	0.567	9e-25
Q8L9V6	331	Dof zinc finger protein D	no	no	0.582	0.447	0.409	2e-24
Q9LSL6	316	Dof zinc finger protein D	no	no	0.708	0.569	0.355	3e-24
Q84TE9	257	Dof zinc finger protein D	no	no	0.326	0.322	0.6	3e-24
Q94AR6	204	Dof zinc finger protein D	no	no	0.633	0.789	0.436	4e-24

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

 Score =  126 bits (317), Expect = 1e-28,   Method: Compositional matrix adjust.
 Identities = 63/104 (60%), Positives = 77/104 (74%), Gaps = 3/104 (2%)

Query: 1   MPSE-STDRKLARAHNPI--STYPPPKVTESLPCPRCESTSTKFCYYNNYNLSQPRHFCK 57
           MPSE S  R++ +  +    S   P    E L CPRCEST+TKFCYYNNYN SQPRHFCK
Sbjct: 1   MPSEFSESRRVPKIPHGQGGSVAIPTDQQEQLSCPRCESTNTKFCYYNNYNFSQPRHFCK 60

Query: 58  SCRRYWTQGGTLRNIPVGGGTRKNSKRTRISSSSSSGAVVATAN 101
           SCRRYWT GGTLR+IPVGG +RK+SKR+R  SS+++ +VV + N
Sbjct: 61  SCRRYWTHGGTLRDIPVGGVSRKSSKRSRTYSSAATTSVVGSRN 104

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

>sp|Q9SX97|DOF16_ARATH Dof zinc finger protein DOF1.6 OS=Arabidopsis thaliana GN=DOF1.6 PE=2 SV=1

 Score =  125 bits (314), Expect = 3e-28,   Method: Compositional matrix adjust.
 Identities = 53/78 (67%), Positives = 62/78 (79%)

Query: 1  MPSESTDRKLARAHNPISTYPPPKVTESLPCPRCESTSTKFCYYNNYNLSQPRHFCKSCR 60
          MPSE    +  R     + YPPP + E LPCPRC ST+TKFCYYNNYNL+QPR++CKSCR
Sbjct: 1  MPSEPNQTRPTRVQPSTAAYPPPNLAEPLPCPRCNSTTTKFCYYNNYNLAQPRYYCKSCR 60

Query: 61 RYWTQGGTLRNIPVGGGT 78
          RYWTQGGTLR++PVGGGT
Sbjct: 61 RYWTQGGTLRDVPVGGGT 78

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

Arabidopsis thaliana (taxid: 3702)

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

 Score =  122 bits (305), Expect = 3e-27,   Method: Compositional matrix adjust.
 Identities = 79/182 (43%), Positives = 102/182 (56%), Gaps = 29/182 (15%)

Query: 27  ESLPCPRCESTSTKFCYYNNYNLSQPRHFCKSCRRYWTQGGTLRNIPVGGGTRKNSKRTR 86
           E L CPRC+S +TKFCYYNNYNLSQPRHFCK+CRRYWT+GG LRNIPVGGGTRK++KR+ 
Sbjct: 31  EQLKCPRCDSPNTKFCYYNNYNLSQPRHFCKNCRRYWTKGGALRNIPVGGGTRKSNKRSG 90

Query: 87  ISSSSS--SGAVVATANSSSCSSAVTHDRVA-EPANPVSVLPCGNPEMGLITMTDVNLND 143
            S SS+  +  V    +     S    +RV+ +  NP  +L       GL          
Sbjct: 91  SSPSSNLKNQTVAEKPDHHGSGSEEKEERVSGQEMNPTRML------YGL---------- 134

Query: 144 SVGVPGSGSYTTMLNMQIQGQNFLGLGGFHNHGYGIGSG-LEELELGFGTARSWDIPGTG 202
            VG P   S++++L   +Q      +GG     Y  GS  L  ++LG G+ R  D   T 
Sbjct: 135 PVGDPNGASFSSLLASNMQ------MGGL---VYESGSRWLPGMDLGLGSVRRSDDTWTD 185

Query: 203 YA 204
            A
Sbjct: 186 LA 187

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

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 =  122 bits (305), Expect = 3e-27,   Method: Compositional matrix adjust.
 Identities = 53/79 (67%), Positives = 65/79 (82%), Gaps = 1/79 (1%)

Query: 8  RKLARAHNPISTYPPPKVTESLPCPRCESTSTKFCYYNNYNLSQPRHFCKSCRRYWTQGG 67
          R++A   N + T P     E LPCPRC+S++TKFCYYNNYN SQPRHFCK+CRRYWT GG
Sbjct: 10 RRIAMKPNGV-TVPISDQQEQLPCPRCDSSNTKFCYYNNYNFSQPRHFCKACRRYWTHGG 68

Query: 68 TLRNIPVGGGTRKNSKRTR 86
          TLR++PVGGGTRK++KR+R
Sbjct: 69 TLRDVPVGGGTRKSAKRSR 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|O24463|PBF_MAIZE Dof zinc finger protein PBF OS=Zea mays GN=PBF PE=1 SV=1

 Score =  115 bits (289), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 51/88 (57%), Positives = 64/88 (72%), Gaps = 4/88 (4%)

Query: 4   ESTDRKLARAHNPI----STYPPPKVTESLPCPRCESTSTKFCYYNNYNLSQPRHFCKSC 59
           E+ D K  RA   I       P P++ E+L CPRC+S +TKFCYYNNY++SQPR+FCK+C
Sbjct: 31  EARDPKQTRAMPQIGGSGERKPRPQLPEALKCPRCDSNNTKFCYYNNYSMSQPRYFCKAC 90

Query: 60  RRYWTQGGTLRNIPVGGGTRKNSKRTRI 87
           RRYWT GGTLRN+P+GGG RKN   +R 
Sbjct: 91  RRYWTHGGTLRNVPIGGGCRKNKHASRF 118

Transcription factor that binds specifically to a 5'-AA[AG]G-3' consensus core sequence. May enhance the DNA binding of the bZIP transcription factor Opaque-2 to O2 binding site elements.

Zea mays (taxid: 4577)

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

 Score =  114 bits (284), Expect = 9e-25,   Method: Compositional matrix adjust.
 Identities = 55/97 (56%), Positives = 67/97 (69%), Gaps = 7/97 (7%)

Query: 7   DRKLARAHNPISTYPPPKVTESLPCPRCESTSTKFCYYNNYNLSQPRHFCKSCRRYWTQG 66
           DR++    N I  +      +SL CPRC S +TKFCYYNNYNLSQPRHFCK+CRRYWT+G
Sbjct: 34  DRRMRAHQNNILNH-----HQSLKCPRCNSLNTKFCYYNNYNLSQPRHFCKNCRRYWTKG 88

Query: 67  GTLRNIPVGGGTR--KNSKRTRISSSSSSGAVVATAN 101
           G LRN+PVGGG R  K SK  ++ SSSS+     T +
Sbjct: 89  GVLRNVPVGGGCRKAKRSKTKQVPSSSSADKPTTTQD 125

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

 Score =  113 bits (282), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 75/183 (40%), Positives = 95/183 (51%), Gaps = 35/183 (19%)

Query: 23  PKVTESLPCPRCESTSTKFCYYNNYNLSQPRHFCKSCRRYWTQGGTLRNIPVGGGTRKNS 82
           P +   L CPRC+S++TKFCYYNNYNL+QPRHFCK CRRYWTQGG LRN+PVGGG R+N+
Sbjct: 71  PPLAGPLKCPRCDSSNTKFCYYNNYNLTQPRHFCKGCRRYWTQGGALRNVPVGGGCRRNN 130

Query: 83  KRTR---ISSSSSSGAVVATANSSSCSSAVTHDRVAEPANPVSVLPCGNPEMGLITMTDV 139
           K+ +   + SSSSS    ++ N+ S SS         P +P                T  
Sbjct: 131 KKGKNGNLKSSSSSSKQSSSVNAQSPSSGQLRTNHQFPFSP----------------TLY 174

Query: 140 NLNDSVGVPGSGSYTTMLNMQIQGQNFLGLGGFHNHGYGIGSGLEELELGFGTARSWDIP 199
           NL    G+               G N     G +N  + IGS L   +LGF   R+   P
Sbjct: 175 NLTQLGGI---------------GLNLAATNG-NNQAHQIGSSLMMSDLGFLHGRNTSTP 218

Query: 200 GTG 202
            TG
Sbjct: 219 MTG 221

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

 Score =  112 bits (280), Expect = 3e-24,   Method: Compositional matrix adjust.
 Identities = 71/200 (35%), Positives = 98/200 (49%), Gaps = 20/200 (10%)

Query: 27  ESLPCPRCESTSTKFCYYNNYNLSQPRHFCKSCRRYWTQGGTLRNIPVGGGTRKNSKRTR 86
           ++L CPRC S +TKFCYYNNY+LSQPRHFCKSCRRYWT+GG LRN+P+GGG RK  K  +
Sbjct: 39  QNLKCPRCNSPNTKFCYYNNYSLSQPRHFCKSCRRYWTRGGALRNVPIGGGCRKTKKSIK 98

Query: 87  ISSSSSSGAVVATANSSSCSSAVTHDRVAEPANPVSVLPCGNPEMGLITMTDVNLNDSVG 146
            +SS ++    +++     S      +   P   +     G   + L  M D+ L     
Sbjct: 99  PNSSMNTLPSSSSSQRFFSSIMEDSSKFFPPPTTMDFQLAG---LSLNKMNDLQL----- 150

Query: 147 VPGSGSYTTMLNMQIQGQNFLGLGGFHNHGYGIGSGLEELELGFGTARSWDIPGTGYACT 206
                    + N ++     +   G  N    +GSGL    +GFG   +   P TG+   
Sbjct: 151 ---------LNNQEVLDLRPMMSSGRENTPVDVGSGLS--LMGFGDFNNNHSP-TGFTTA 198

Query: 207 GGGSGAATSGCNTWQMMNGD 226
           G   G   S   T   +N D
Sbjct: 199 GASDGNLASSIETLSCLNQD 218

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

Arabidopsis thaliana (taxid: 3702)

>sp|Q84TE9|DOF53_ARATH Dof zinc finger protein DOF5.3 OS=Arabidopsis thaliana GN=DOF5.3 PE=2 SV=1

 Score =  112 bits (279), Expect = 3e-24,   Method: Compositional matrix adjust.
 Identities = 51/85 (60%), Positives = 66/85 (77%), Gaps = 2/85 (2%)

Query: 7   DRKLARAHNPISTYPPPKVTESLPCPRCESTSTKFCYYNNYNLSQPRHFCKSCRRYWTQG 66
           D+K       ++   PP++  +L CPRC+ST+TKFCYYNNY+L+QPR+FCKSCRRYWT+G
Sbjct: 35  DQKKPSPATAVTRPQPPEL--ALRCPRCDSTNTKFCYYNNYSLTQPRYFCKSCRRYWTKG 92

Query: 67  GTLRNIPVGGGTRKNSKRTRISSSS 91
           GTLRNIPVGGG RKN + T  ++ S
Sbjct: 93  GTLRNIPVGGGCRKNKRSTSSAARS 117

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 =  111 bits (278), Expect = 4e-24,   Method: Compositional matrix adjust.
 Identities = 75/172 (43%), Positives = 98/172 (56%), Gaps = 11/172 (6%)

Query: 29  LPCPRCESTSTKFCYYNNYNLSQPRHFCKSCRRYWTQGGTLRNIPVGGGTRKNS-KRTRI 87
           L CPRC+S +TKFCYYNNYNLSQPRHFCKSCRRYWT+GG LRN+PVGGG+RKN+ KR+  
Sbjct: 29  LKCPRCDSPNTKFCYYNNYNLSQPRHFCKSCRRYWTKGGALRNVPVGGGSRKNATKRSTS 88

Query: 88  SSSSSSGAVVATANSSSCSSAVTHDRVAEPANPVSVLPCGNPEMGLITMTDVNLNDSVGV 147
           SSSS+S    ++ N  + +     D   +P N  S  P  +P   L     +   D  G+
Sbjct: 89  SSSSASSPSNSSQNKKTKNP----DPDPDPRN--SQKPDLDPTRMLYGFP-IGDQDVKGM 141

Query: 148 PGSGSYTTMLNMQIQGQNFLGLGGFHNHGY---GIGSGLEELELGFGTARSW 196
              GS++++L   +Q     G       G+   G+G GL   E G      W
Sbjct: 142 EIGGSFSSLLANNMQLGLGGGGIMLDGSGWDHPGMGLGLRRTEPGNNNNNPW 193

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	254
224096854	248	predicted protein [Populus trichocarpa]	0.933	0.955	0.475	4e-44
225458485	226	PREDICTED: dof zinc finger protein DOF3.	0.862	0.969	0.490	5e-44
356498503	234	PREDICTED: dof zinc finger protein DOF3.	0.909	0.987	0.447	5e-43
224136656	261	f-box family protein [Populus trichocarp	0.964	0.938	0.447	1e-41
255538444	368	zinc finger protein, putative [Ricinus c	0.921	0.635	0.453	4e-38
224081531	253	predicted protein [Populus trichocarpa]	0.921	0.924	0.416	9e-38
302398785	248	DOF domain class transcription factor [M	0.925	0.947	0.414	8e-37
356559454	236	PREDICTED: dof zinc finger protein DOF3.	0.917	0.987	0.439	7e-36
118486281	264	unknown [Populus trichocarpa]	0.940	0.905	0.415	8e-35
224067288	306	f-box family protein [Populus trichocarp	0.980	0.813	0.434	2e-34

>gi|224096854|ref|XP_002310762.1| predicted protein [Populus trichocarpa] gi|222853665|gb|EEE91212.1| predicted protein [Populus trichocarpa]

 Score =  184 bits (466), Expect = 4e-44,   Method: Compositional matrix adjust.
 Identities = 126/265 (47%), Positives = 150/265 (56%), Gaps = 28/265 (10%)

Query: 1   MPSESTDRKLARAHNPIS----TYP---PPKVTESLPCPRCESTSTKFCYYNNYNLSQPR 53
           MP+E +  + AR     +    T P   PP+  E LPCPRC+ST+TKFCYYNNYN SQPR
Sbjct: 1   MPAELSSSEAARRAQQSTAATLTKPGGAPPQEQEHLPCPRCDSTNTKFCYYNNYNFSQPR 60

Query: 54  HFCKSCRRYWTQGGTLRNIPVGGGTRKNSKRTRISSSSSSGAVVATANSSSCSSAVTHDR 113
           HFCKSCRRYWT GGTLR+IPVGGGTRKN+KR+R S++S        A+     +    D 
Sbjct: 61  HFCKSCRRYWTHGGTLRDIPVGGGTRKNAKRSRTSATSP-------ASFMGPMTGTNIDG 113

Query: 114 VAEPANPVSVLPCGNPEMGLITMTDVNLNDSVGVPGSGSYTTMLNMQIQGQNFLGLGGFH 173
           +  PA PV +LP      GL            G    GS+T++LN Q     FL L GF 
Sbjct: 114 LPLPATPV-LLPL-TANQGLSVHFGGGDGKGNGGGLGGSFTSLLNTQGPA-GFLALNGF- 169

Query: 174 NHGYGIGSGLEELELGFGTARSWDIPGTGY--ACTGGGSGAA-TSGC-NTWQMMNGDDQG 229
             G GIG G+E++    G    W  PG G   A  GG  GAA T+G  NTWQ  NG + G
Sbjct: 170 --GLGIGPGIEDVNFALGRGL-WPFPGMGDVGASVGGNGGAAVTAGLGNTWQFENGQENG 226

Query: 230 GNDVGEDCFGWSGLAISTPAGKDLK 254
              VG DCF W  LAISTP G  LK
Sbjct: 227 --FVGGDCFSWPDLAISTP-GNGLK 248

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225458485|ref|XP_002284108.1| PREDICTED: dof zinc finger protein DOF3.4 [Vitis vinifera]

 Score =  184 bits (466), Expect = 5e-44,   Method: Compositional matrix adjust.
 Identities = 128/261 (49%), Positives = 154/261 (59%), Gaps = 42/261 (16%)

Query: 1   MPSESTDRKLARAHNPISTYPPPKVTESLPCPRCESTSTKFCYYNNYNLSQPRHFCKSCR 60
           MPSES +R++AR    +  +PP   +E LPCPRC+ST+TKFCYYNNYNLSQPRHFCKSCR
Sbjct: 1   MPSESGERRVARPQQ-VGGHPP--QSEHLPCPRCDSTNTKFCYYNNYNLSQPRHFCKSCR 57

Query: 61  RYWTQGGTLRNIPVGGGTRKNSKRTRISSSSSSGAVVATANSSSCSSAVTHDRVAEPANP 120
           RYWTQGGTLRNIPVGGGTRKNSKR+R ++SSSS  +  T                 PANP
Sbjct: 58  RYWTQGGTLRNIPVGGGTRKNSKRSRTATSSSSSTLETT-----------------PANP 100

Query: 121 VSVLPCGNPEMGLITMTDVNLNDSVGVPGSGSYTTMLNMQIQGQNFLGLGGFHNHGYGIG 180
           +SV P    E        ++LN  V    SG +T++LN   QG  FL L GF     G+G
Sbjct: 101 ISVSPVLKAETETPQRNGLSLNGDV----SGGFTSLLNS--QGPGFLALNGFS---LGLG 151

Query: 181 SGLEELELGFGTARS-WDIPGTGYACTGGGSGAATSG------CNTWQMMNGDDQGGNDV 233
            G +  E+GFG A+  W  P  G    GG    +  G      CNTWQ+  G+      V
Sbjct: 152 PGFD--EMGFGPAKGVWSYPDVGDVVLGGDGTGSGGGSASSSICNTWQLSGGEV---GFV 206

Query: 234 GEDCFGWSGLAISTPAGKDLK 254
             DCF W  LAISTP G+ LK
Sbjct: 207 DGDCFAWPDLAISTP-GQGLK 226

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356498503|ref|XP_003518090.1| PREDICTED: dof zinc finger protein DOF3.4 [Glycine max]

 Score =  180 bits (457), Expect = 5e-43,   Method: Compositional matrix adjust.
 Identities = 115/257 (44%), Positives = 153/257 (59%), Gaps = 26/257 (10%)

Query: 1   MPSEST--DRKLARAHNPISTYPPPKVTESLPCPRCESTSTKFCYYNNYNLSQPRHFCKS 58
           MPS ++   R+ ++  +     PPP   E+LPCPRC+ST+TKFCYYNNYN SQPRHFCKS
Sbjct: 1   MPSSNSGESRRASKPQSSGGAAPPPPEQENLPCPRCDSTNTKFCYYNNYNYSQPRHFCKS 60

Query: 59  CRRYWTQGGTLRNIPVGGGTRKNSKRTRISSSSSSGAVVATANSSSCSSAVTHDRVAEPA 118
           CRRYWT GGTLR+IPVGGG+RKN+KR+R    +++ +   ++  +S      H  +A   
Sbjct: 61  CRRYWTHGGTLRDIPVGGGSRKNAKRSRTHHVAATSSSSTSSTMTSAQEHHAHTLLA--- 117

Query: 119 NPVSVLPCGNPEMGLITMTDVNLNDSVGVPGSGSYTTMLNMQIQGQNFLGLGGFHNHGYG 178
            PV+    G  +  +   ++ N N        GS+T++LN    G  FL LGGF     G
Sbjct: 118 -PVASTHYGVLDGDVKQTSNGNGNV------CGSFTSLLN-NTHGSGFLALGGF-----G 164

Query: 179 IGSGLEELELGFGTARS-WDIPGTGYACTGGGSGAATSGCNTWQMMNGDDQGGNDVGEDC 237
           +G G +  ++GFG  RS W  PG       GG+  A+SG NTWQ+ +G+   G  V  DC
Sbjct: 165 LGHGYD--DMGFGIGRSGWAFPGMVDGGNIGGA-VASSGLNTWQLESGE---GGFVSGDC 218

Query: 238 FGWSGLAISTPAGKDLK 254
           F W GLAISTP G  LK
Sbjct: 219 FAWPGLAISTP-GNGLK 234

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224136656|ref|XP_002326913.1| f-box family protein [Populus trichocarpa] gi|222835228|gb|EEE73663.1| f-box family protein [Populus trichocarpa]

 Score =  175 bits (444), Expect = 1e-41,   Method: Compositional matrix adjust.
 Identities = 120/268 (44%), Positives = 156/268 (58%), Gaps = 23/268 (8%)

Query: 1   MPSESTDRKLARAHNPI-STYPPPKVTESLPCPRCESTSTKFCYYNNYNLSQPRHFCKSC 59
           MP+E +      A N + +T+ PPK TE LPCPRC ST+TKFCYYNNYNLSQPRHFCKSC
Sbjct: 1   MPTEISQGHPTEAQNTMGATHQPPKTTEPLPCPRCNSTTTKFCYYNNYNLSQPRHFCKSC 60

Query: 60  RRYWTQGGTLRNIPVGGGTRKNSKRTRISSSSSSGAVVATANSSS------CSSAVTHDR 113
           RRYWTQGGTLR++PVGGGTRKNSKR+R +S++SS    +++NS+S       +   TH+ 
Sbjct: 61  RRYWTQGGTLRDVPVGGGTRKNSKRSRSTSNNSSSISTSSSNSTSSNSATLTAFTTTHEP 120

Query: 114 VAEPANPVSVLPCGNPEMGLITMTDVNLNDSVGVPGS-GSYTTMLNMQIQGQNFLGLGGF 172
            + P    S    G   +       +NLND  G+P   G++ +++N   Q   F GLGG+
Sbjct: 121 ESMPVVLSSTTDSGLAAVKTEVPAGLNLND--GLPSEDGNFISLMNSNDQ-HGFTGLGGY 177

Query: 173 HNHGYGIGSGLEELELGFGTARSWDIPGTGYACTGGGSGAATSGCNTWQMMNGDDQGGND 232
             +  G G G  E+ +GFG   SW  P        GG    TSGC+ WQ+     +GG  
Sbjct: 178 -GYASGFGFGPSEMGIGFGGRGSWSCPVMENVLVNGG----TSGCHPWQLDCDHVEGGGL 232

Query: 233 VG------EDCFG-WSGLAISTPAGKDL 253
                   E+ FG W  L +S PAGK L
Sbjct: 233 QAGFTADTENYFGSWPDLVMSAPAGKGL 260

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255538444|ref|XP_002510287.1| zinc finger protein, putative [Ricinus communis] gi|223550988|gb|EEF52474.1| zinc finger protein, putative [Ricinus communis]

 Score =  164 bits (415), Expect = 4e-38,   Method: Compositional matrix adjust.
 Identities = 121/267 (45%), Positives = 153/267 (57%), Gaps = 33/267 (12%)

Query: 1   MPSESTDRKLARAHNPIS-TYPPPKVTESLPCPRCESTSTKFCYYNNYNLSQPRHFCKSC 59
           MP+EST  +     NP+S ++PPPK+ E LPCPRC+S +TKFCYYNNYNLSQPRHFCK+C
Sbjct: 122 MPTESTPGQ--NNTNPVSHSHPPPKLAEPLPCPRCDSNNTKFCYYNNYNLSQPRHFCKAC 179

Query: 60  RRYWTQGGTLRNIPVGGGTRKNSKRTRISSSSSSGAVVATANSSSCSSAVTHDRVAEPAN 119
           RRYWT GGTLRN+P+GGGTRKNSKR+R  SSS + +   T+ S+  S          P  
Sbjct: 180 RRYWTHGGTLRNVPIGGGTRKNSKRSRSYSSSITTSTTTTSASALSSLNT-------PDQ 232

Query: 120 PVSVLPCGNPEMGLITMTDVNLNDSVG--------VPGSGSYTTMLNMQIQGQNFLGLGG 171
           P   LP       ++T    NL+D+          V  +G++ ++L+ Q QGQ F+G+  
Sbjct: 233 PDQSLPVLAIPESVLTAKSENLSDNWNLNDEKVNLVSQNGNFISLLSSQ-QGQGFMGM-- 289

Query: 172 FHNHGYGIGSGLEELELGFGTAR-SWDIPGTGYACTGGGSGAAT-SGCNTWQMMNGDDQG 229
                  +G G         T R +W  PG  Y   G      T SGCNTWQ +   D G
Sbjct: 290 -------VGYGPGFGYGFCDTGRENWVYPGMAYVNGGDAVEDGTSSGCNTWQQVEVGDAG 342

Query: 230 GNDV-GE-DCFGWSGLAISTPAGKDLK 254
           G  V GE +C  W GLAISTP GK  K
Sbjct: 343 GGLVDGENNCLSWPGLAISTP-GKGFK 368

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224081531|ref|XP_002306448.1| predicted protein [Populus trichocarpa] gi|222855897|gb|EEE93444.1| predicted protein [Populus trichocarpa]

 Score =  162 bits (411), Expect = 9e-38,   Method: Compositional matrix adjust.
 Identities = 110/264 (41%), Positives = 141/264 (53%), Gaps = 30/264 (11%)

Query: 1   MPSESTDRKLARAHNPISTYP--------PPKVTESLPCPRCESTSTKFCYYNNYNLSQP 52
           MP+E +  +  R   P+ST P        PP+  E LPCPRC+ST+TKFCYYNNYN SQP
Sbjct: 1   MPTELSSSEKTR-RPPLSTTPTSNKPGGAPPQEQEHLPCPRCDSTNTKFCYYNNYNFSQP 59

Query: 53  RHFCKSCRRYWTQGGTLRNIPVGGGTRKNSKRTRISSSSSSGAVVATANSSSCSSAVTHD 112
           RHFCKSCRRYWT GGTLR+IPVGGGTRKN+KR+R S+++++       +++        D
Sbjct: 60  RHFCKSCRRYWTHGGTLRDIPVGGGTRKNAKRSRTSATTAASFAGPIIDNNI-------D 112

Query: 113 RVAEPANPVSVLPCGNPEMGL---ITMTDVNLNDSVGVPGSGSYTTMLNMQIQGQNFLGL 169
            +  PA PV V    +    +                    GS+T++LN        L L
Sbjct: 113 NLPLPATPVLVPLTASQGFSVHFGGGSDGKGNGGCGSGALGGSFTSLLNTPGPA-GILAL 171

Query: 170 GGFHNHGYGIGSGLEELELGFGTARSWDIPGTGYACTGGGSGAATSGC----NTWQMMNG 225
           G F   G+G+G GLE++  G G    W  PG G +  G G     +      NTWQ  + 
Sbjct: 172 GRF---GHGLGHGLEDVGCGLGRGL-WSFPGIGDSGAGVGGHGGVTVTAGLDNTWQFGSA 227

Query: 226 DDQGGNDVGEDCFGWSGLAISTPA 249
              G   VG DCF W  LAISTPA
Sbjct: 228 GQNG--FVGGDCFSWPELAISTPA 249

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|302398785|gb|ADL36687.1| DOF domain class transcription factor [Malus x domestica]

 Score =  159 bits (403), Expect = 8e-37,   Method: Compositional matrix adjust.
 Identities = 107/258 (41%), Positives = 144/258 (55%), Gaps = 23/258 (8%)

Query: 1   MPSESTDRKL-----ARAHNPISTYPPPKVTESLPCPRCESTSTKFCYYNNYNLSQPRHF 55
           MP +S D  +      R  + +  +PPP+ TE L CPRC+S +TKFCYYNNYNL+QPRHF
Sbjct: 1   MPFDSADALMQPSMTTRVQHSLG-HPPPQQTEPLHCPRCDSDNTKFCYYNNYNLAQPRHF 59

Query: 56  CKSCRRYWTQGGTLRNIPVGGGTRKNSKRTRISSSSSSGAVVATANSSSCSSAVTHDRVA 115
           CKSCRRYWT GGTLRN+PVGGG+RKN+KR+R S SSSSG+  +++ +   SS       +
Sbjct: 60  CKSCRRYWTHGGTLRNVPVGGGSRKNTKRSRPSCSSSSGSPSSSSLTQEVSSVAPDKPNS 119

Query: 116 EPANPVSVLPCGNPEMGLITMTDVNLNDSVGVPGSGSYTTMLNMQ-IQGQNFLGLGGFHN 174
            P  P        PE        ++LN+S    G+G +T++L+ Q      F+   GF  
Sbjct: 120 FPVEP-------KPETATDHEKLMDLNES--AVGNGGFTSLLSAQGPPASGFMAFSGF-G 169

Query: 175 HGYGIGSGLEEL-----ELGFGTARSWDI-PGTGYACTGGGSGAATSGCNTWQMMNGDDQ 228
           +G G+G G +E+     + G G     D+   T      G     + GCNTWQ+M G D 
Sbjct: 170 YGLGLGQGFDEVGTFGYDGGRGVLAYPDVGDFTNVIHNNGAVSGGSVGCNTWQIMTGGDG 229

Query: 229 GGNDVGEDCFGWSGLAIS 246
           G  +   DCF W  L  S
Sbjct: 230 GIAENNGDCFAWPELETS 247

Source: Malus x domestica

Species: Malus x domestica

Genus: Malus

Family: Rosaceae

Order: Rosales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356559454|ref|XP_003548014.1| PREDICTED: dof zinc finger protein DOF3.4 [Glycine max]

 Score =  156 bits (395), Expect = 7e-36,   Method: Compositional matrix adjust.
 Identities = 113/257 (43%), Positives = 152/257 (59%), Gaps = 24/257 (9%)

Query: 1   MPSEST--DRKLARAHNPISTYPPPKVTESLPCPRCESTSTKFCYYNNYNLSQPRHFCKS 58
           MPS ++   R+ ++ H  ++   PP   E+LPCPRC+S +TKFCYYNNYN SQPRHFCKS
Sbjct: 1   MPSSNSGESRRASKPHRSVAA--PPVEPENLPCPRCDSANTKFCYYNNYNYSQPRHFCKS 58

Query: 59  CRRYWTQGGTLRNIPVGGGTRKNSKRTRISSSSSSGAVVATANSSSCSSAVTHDRVAEPA 118
           CRRYWT GGTLR+IPVGGG+RKN+KR+R   ++++ +  ++ +S++ S+   H+     A
Sbjct: 59  CRRYWTHGGTLRDIPVGGGSRKNAKRSRTHHAAAATSSSSSTSSATTSAHEHHNAHTLTA 118

Query: 119 NPVSVLPCGNPEMGLITMTDVNLNDSVGVPGSGSYTTMLNMQIQGQNFLGLGGFHNHGYG 178
                        G +  T+ N          GSYT++LN      N  G G F   G+G
Sbjct: 119 LAPVTAATHFGHDGDVKQTNGN--------ACGSYTSLLN------NTQGSGFFALGGFG 164

Query: 179 IGSGLEELELGFGTARS-WDIPGTGYACTGGGSGAATSGCNTWQMMNGDDQGGNDVGEDC 237
           +G G    ++GFG  RS W  PG       GG+  A+SG NTWQ+ +G+   G  VG DC
Sbjct: 165 LGLGHGFDDMGFGIGRSGWAFPGMVDNGNIGGA-IASSGVNTWQLESGE---GGFVGGDC 220

Query: 238 FGWSGLAISTPAGKDLK 254
           F W GLAISTP G  LK
Sbjct: 221 FSWPGLAISTP-GNGLK 236

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|118486281|gb|ABK94982.1| unknown [Populus trichocarpa]

 Score =  153 bits (386), Expect = 8e-35,   Method: Compositional matrix adjust.
 Identities = 115/277 (41%), Positives = 153/277 (55%), Gaps = 38/277 (13%)

Query: 1   MPSESTDRKLARAHNPISTYPPP-KVTESLPCPRCESTSTKFCYYNNYNLSQPRHFCKSC 59
           MPSE +      A N + T PPP K TE LPCPRC ST TKFCY+NNYNLSQPR+FCKSC
Sbjct: 1   MPSEISQTHPNEAQNTMGTAPPPPKTTEPLPCPRCNSTITKFCYFNNYNLSQPRYFCKSC 60

Query: 60  RRYWTQGGTLRNIPVGGGTRKNSKRTRISSSSSSGAVVATANSSSCSSAVT-----HDRV 114
           RRYWT+GGTLR++PVGGG+RKNSKR+R SS++SS +  ++ +++S  + +T     H+  
Sbjct: 61  RRYWTKGGTLRDVPVGGGSRKNSKRSRSSSNNSSPSTSSSNSTASNPATLTAFTAIHEPE 120

Query: 115 AEPANPVSVLPCGNPEMGLITMTDVNLNDSVGVPGSGSYTTMLNMQIQGQNFLGLGGFHN 174
           + P    S    G   +       +NLN+  G+  +G++ ++++   Q            
Sbjct: 121 SIPVVVSSTTDSGAAAVKTEMPAGINLNE--GLAENGNFISLISSNDQ------------ 166

Query: 175 HGYGIGSGLE----------ELELGFGTARSWDIPGTGYACTGGGS-GAATSGCNTWQMM 223
           HG+    G            E+ LGFG    W  PG       GG+ G  TSGCNTWQ+ 
Sbjct: 167 HGFNSLGGYGYGSGFGLGPCEVGLGFGARGFWSFPGMENVSVNGGTIGGCTSGCNTWQLQ 226

Query: 224 NGDDQGGNDV------GEDCFG-WSGLAISTPAGKDL 253
               +GG         GE+ FG W GL IS PA K L
Sbjct: 227 GDHVEGGGSQGGFAADGENYFGSWPGLVISAPAEKGL 263

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224067288|ref|XP_002302449.1| f-box family protein [Populus trichocarpa] gi|222844175|gb|EEE81722.1| f-box family protein [Populus trichocarpa]

 Score =  151 bits (382), Expect = 2e-34,   Method: Compositional matrix adjust.
 Identities = 116/267 (43%), Positives = 158/267 (59%), Gaps = 18/267 (6%)

Query: 1   MPSESTDRKLARAHNPISTYPPP-KVTESLPCPRCESTSTKFCYYNNYNLSQPRHFCKSC 59
           MPSE +      A N + T PPP K TE LPCPRC ST TKFCY+NNYNLSQPR+FCKSC
Sbjct: 1   MPSEISQTHPNEAQNTMGTAPPPPKTTEPLPCPRCNSTITKFCYFNNYNLSQPRYFCKSC 60

Query: 60  RRYWTQGGTLRNIPVGGGTRKNSKRTRISSSSSSGAVVATANSSSCSSAVT-----HDRV 114
           RRYWT+GGTLR++PVGGG+RKNSKR+R SS++SS +  ++ +++S  + +T     H+  
Sbjct: 61  RRYWTKGGTLRDVPVGGGSRKNSKRSRSSSNNSSPSTSSSNSTASNPATLTAFTAIHEPE 120

Query: 115 AEPANPVSVLPCGNPEMGLITMTDVNLNDSVGVPGSGSYTTMLNMQIQGQNFLGLGGFHN 174
           + P    S    G   +       +NLN+  G+  +G++ ++++     Q+     G + 
Sbjct: 121 SIPVVVSSTTDSGAAAVKTEMPAGINLNE--GLAENGNFISLISS--NDQHGFNGLGGYG 176

Query: 175 HGYGIGSGLEELELGFGTARSWDIPGTGYACTGGGS-GAATSGCNTWQMMNGDDQGGNDV 233
           +G G G G  E+ LGFG    W  PG       GG+ G  TSGCNTWQ+     +GG   
Sbjct: 177 YGSGFGLGPCEVGLGFGARGFWSFPGMENVSVNGGTIGGCTSGCNTWQLQGDHVEGGGSQ 236

Query: 234 ------GEDCFG-WSGLAISTPAGKDL 253
                 GE+ FG W GL IS PA K++
Sbjct: 237 GGFAADGENYFGSWPGLVISAPAEKEV 263

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

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	254
TAIR|locus:2074850	253	OBP1 "OBF binding protein 1" [	0.299	0.300	0.645	8.6e-30
TAIR|locus:505006172	209	AT1G47655 [Arabidopsis thalian	0.303	0.368	0.675	1.2e-28
TAIR|locus:2026595	339	OBP2 [Arabidopsis thaliana (ta	0.216	0.162	0.763	1.5e-26
TAIR|locus:2094746	204	DOF2 "DOF zinc finger protein	0.531	0.661	0.420	5.3e-24
TAIR|locus:2158078	225	AT5G66940 [Arabidopsis thalian	0.299	0.337	0.658	5.3e-24
TAIR|locus:2039959	369	DAG2 "DOF AFFECTING GERMINATIO	0.196	0.135	0.78	7.9e-24
TAIR|locus:2019499	352	AT1G64620 [Arabidopsis thalian	0.570	0.411	0.403	1.8e-23
TAIR|locus:2144030	257	TMO6 "TARGET OF MONOPTEROS 6"	0.271	0.268	0.647	2.9e-23
TAIR|locus:2085697	245	DOF6 "DOF transcription factor	0.240	0.248	0.721	4.8e-23
TAIR|locus:2159275	307	OBP4 "OBF binding protein 4" [	0.255	0.211	0.680	4.8e-23

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

 Score = 283 (104.7 bits), Expect = 8.6e-30, Sum P(2) = 8.6e-30
 Identities = 51/79 (64%), Positives = 62/79 (78%)

Query:     1 MP-SESTD-RKLARAHNPISTYPPPKVTESLPCPRCESTSTKFCYYNNYNLSQPRHFCKS 58
             MP S+S + R++A   N + T P     E LPCPRC+S++TKFCYYNNYN SQPRHFCK+
Sbjct:     1 MPTSDSGEPRRIAMKPNGV-TVPISDQQEQLPCPRCDSSNTKFCYYNNYNFSQPRHFCKA 59

Query:    59 CRRYWTQGGTLRNIPVGGG 77
             CRRYWT GGTLR++PVGGG
Sbjct:    60 CRRYWTHGGTLRDVPVGGG 78

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:505006172 AT1G47655 [Arabidopsis thaliana (taxid:3702)]

 Score = 319 (117.4 bits), Expect = 1.2e-28, P = 1.2e-28
 Identities = 52/77 (67%), Positives = 61/77 (79%)

Query:     1 MPSESTDRKLARAHNPISTYPPPKVTESLPCPRCESTSTKFCYYNNYNLSQPRHFCKSCR 60
             MPSE    +  R     + YPPP + E LPCPRC ST+TKFCYYNNYNL+QPR++CKSCR
Sbjct:     1 MPSEPNQTRPTRVQPSTAAYPPPNLAEPLPCPRCNSTTTKFCYYNNYNLAQPRYYCKSCR 60

Query:    61 RYWTQGGTLRNIPVGGG 77
             RYWTQGGTLR++PVGGG
Sbjct:    61 RYWTQGGTLRDVPVGGG 77

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:2026595 OBP2 [Arabidopsis thaliana (taxid:3702)]

 Score = 265 (98.3 bits), Expect = 1.5e-26, Sum P(2) = 1.5e-26
 Identities = 42/55 (76%), Positives = 48/55 (87%)

Query:    23 PKVTESLPCPRCESTSTKFCYYNNYNLSQPRHFCKSCRRYWTQGGTLRNIPVGGG 77
             P +   L CPRC+S++TKFCYYNNYNL+QPRHFCK CRRYWTQGG LRN+PVGGG
Sbjct:    79 PPLAGPLKCPRCDSSNTKFCYYNNYNLTQPRHFCKGCRRYWTQGGALRNVPVGGG 133

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

 Score = 275 (101.9 bits), Expect = 5.3e-24, P = 5.3e-24
 Identities = 61/145 (42%), Positives = 75/145 (51%)

Query:    27 ESLPCPRCESTSTKFCYYNNYNLSQPRHFCKSCRRYWTQGGTLRNIPVGGGXXXXXXXXX 86
             E L CPRC+S +TKFCYYNNYNLSQPRHFCKSCRRYWT+GG LRN+PVGGG         
Sbjct:    27 EQLKCPRCDSPNTKFCYYNNYNLSQPRHFCKSCRRYWTKGGALRNVPVGGGSRKNATKRS 86

Query:    87 XXXXXXXXXXXXXXXXXXCSSAVTHDRVAEPANPVSVLPCGNPEMGLITMTDVNLNDSVG 146
                                 +    D   +P N  S  P  +P   L     +   D  G
Sbjct:    87 TSSSSSASSPSNSSQNKKTKNP---DPDPDPRN--SQKPDLDPTRMLYGFP-IGDQDVKG 140

Query:   147 VPGSGSYTTMLNMQIQGQNFLGLGG 171
             +   GS++++L   +Q    LGLGG
Sbjct:   141 MEIGGSFSSLLANNMQ----LGLGG 161

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:2158078 AT5G66940 [Arabidopsis thaliana (taxid:3702)]

 Score = 275 (101.9 bits), Expect = 5.3e-24, P = 5.3e-24
 Identities = 52/79 (65%), Positives = 58/79 (73%)

Query:     1 MPSE-STDRKLARA-HNPISTYP-PPKVTESLPCPRCESTSTKFCYYNNYNLSQPRHFCK 57
             MPSE S  R++ +  H    +   P    E L CPRCEST+TKFCYYNNYN SQPRHFCK
Sbjct:     1 MPSEFSESRRVPKIPHGQGGSVAIPTDQQEQLSCPRCESTNTKFCYYNNYNFSQPRHFCK 60

Query:    58 SCRRYWTQGGTLRNIPVGG 76
             SCRRYWT GGTLR+IPVGG
Sbjct:    61 SCRRYWTHGGTLRDIPVGG 79

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 = 248 (92.4 bits), Expect = 7.9e-24, Sum P(2) = 7.9e-24
 Identities = 39/50 (78%), Positives = 46/50 (92%)

Query:    27 ESLPCPRCESTSTKFCYYNNYNLSQPRHFCKSCRRYWTQGGTLRNIPVGG 76
             E L CPRC ST+TKFCYYNNY+L+QPR+FCK CRRYWT+GG+LRN+PVGG
Sbjct:    78 EKLNCPRCNSTNTKFCYYNNYSLTQPRYFCKGCRRYWTEGGSLRNVPVGG 127

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

 Score = 270 (100.1 bits), Expect = 1.8e-23, P = 1.8e-23
 Identities = 65/161 (40%), Positives = 81/161 (50%)

Query:    16 PISTYPPPKVTESLPCPRCESTSTKFCYYNNYNLSQPRHFCKSCRRYWTQGGTLRNIPVG 75
             P+     P+  ++L CPRC S +TKFCYYNNY+L+QPR+FCK CRRYWT GG+LRNIPVG
Sbjct:    36 PVERKARPEKDQALNCPRCNSLNTKFCYYNNYSLTQPRYFCKDCRRYWTAGGSLRNIPVG 95

Query:    76 GGXXXXXXXXXXXXXXXXXXXXXXXXXXXCSSAVTHDRVAEPANPVSVLPCGNPEMGLIT 135
             GG                            SS+      A    P   LP  NP++G   
Sbjct:    96 GGVRKNKRSSSNSSSSSPSS----------SSSSKKPLFANNNTPTPPLPHLNPKIGEAA 145

Query:   136 MTDV-NLNDSVGVPGSGSYTTMLNMQIQGQNFLGLGGFHNH 175
              T V +L  S G  G+      LN+    Q F G+G  HNH
Sbjct:   146 ATKVQDLTFSQGF-GNAHEVKDLNLAFS-QGF-GIG--HNH 181

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:2144030 TMO6 "TARGET OF MONOPTEROS 6" [Arabidopsis thaliana (taxid:3702)]

 Score = 268 (99.4 bits), Expect = 2.9e-23, P = 2.9e-23
 Identities = 46/71 (64%), Positives = 58/71 (81%)

Query:     7 DRKLARAHNPISTYPPPKVTESLPCPRCESTSTKFCYYNNYNLSQPRHFCKSCRRYWTQG 66
             D+K       ++   PP++  +L CPRC+ST+TKFCYYNNY+L+QPR+FCKSCRRYWT+G
Sbjct:    35 DQKKPSPATAVTRPQPPEL--ALRCPRCDSTNTKFCYYNNYSLTQPRYFCKSCRRYWTKG 92

Query:    67 GTLRNIPVGGG 77
             GTLRNIPVGGG
Sbjct:    93 GTLRNIPVGGG 103

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:0048364 "root development" evidence=IEP

GO:0009855 "determination of bilateral symmetry" evidence=RCA

GO:0009944 "polarity specification of adaxial/abaxial axis" evidence=RCA

GO:0010014 "meristem initiation" evidence=RCA

GO:0010075 "regulation of meristem growth" evidence=RCA

TAIR|locus:2085697 DOF6 "DOF transcription factor 6" [Arabidopsis thaliana (taxid:3702)]

 Score = 266 (98.7 bits), Expect = 4.8e-23, P = 4.8e-23
 Identities = 44/61 (72%), Positives = 52/61 (85%)

Query:    16 PISTYPPPKVTESLPCPRCESTSTKFCYYNNYNLSQPRHFCKSCRRYWTQGGTLRNIPVG 75
             P+S   P    +SL CPRC+ST+TKFCYYNNY+LSQPR+FCKSCRRYWT+GG LRNIP+G
Sbjct:    27 PLSATRPAPPEQSLRCPRCDSTNTKFCYYNNYSLSQPRYFCKSCRRYWTKGGILRNIPIG 86

Query:    76 G 76
             G
Sbjct:    87 G 87

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

 Score = 266 (98.7 bits), Expect = 4.8e-23, P = 4.8e-23
 Identities = 49/72 (68%), Positives = 57/72 (79%)

Query:     7 DRKLARAH-NPISTYPPPKVTESLPCPRCESTSTKFCYYNNYNLSQPRHFCKSCRRYWTQ 65
             DR++ RAH N I  +      +SL CPRC S +TKFCYYNNYNLSQPRHFCK+CRRYWT+
Sbjct:    34 DRRM-RAHQNNILNHH-----QSLKCPRCNSLNTKFCYYNNYNLSQPRHFCKNCRRYWTK 87

Query:    66 GGTLRNIPVGGG 77
             GG LRN+PVGGG
Sbjct:    88 GGVLRNVPVGGG 99

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

---

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

Your Input: eugene3.00070983 hypothetical protein (248 aa) (Populus trichocarpa)

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	254
pfam02701	63	pfam02701, zf-Dof, Dof domain, zinc finger	6e-37

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

 Score =  124 bits (313), Expect = 6e-37
 Identities = 43/63 (68%), Positives = 53/63 (84%)

Query: 24 KVTESLPCPRCESTSTKFCYYNNYNLSQPRHFCKSCRRYWTQGGTLRNIPVGGGTRKNSK 83
          K  ++L CPRC+S +TKFCYYNNYNL+QPR+FCK+CRRYWT GG LRN+PVGGG RKN +
Sbjct: 1  KPDKALKCPRCDSMNTKFCYYNNYNLNQPRYFCKNCRRYWTAGGALRNVPVGGGRRKNKR 60

Query: 84 RTR 86
           + 
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	254
PF02701	63	zf-Dof: Dof domain, zinc finger; InterPro: IPR0038	100.0
TIGR02159	146	PA_CoA_Oxy4 phenylacetate-CoA oxygenase, PaaJ subu	94.47
PF12760	46	Zn_Tnp_IS1595: Transposase zinc-ribbon domain; Int	94.01
COG3677	129	Transposase and inactivated derivatives [DNA repli	93.38
PF03811	36	Zn_Tnp_IS1: InsA N-terminal domain; InterPro: IPR0	92.74
smart00440	40	ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding mo	91.49
PF01096	39	TFIIS_C: Transcription factor S-II (TFIIS); InterP	88.74
PF04216	290	FdhE: Protein involved in formate dehydrogenase fo	84.14
PHA02998	195	RNA polymerase subunit; Provisional	83.1
TIGR01384	104	TFS_arch transcription factor S, archaeal. There h	81.71
PF13453	41	zf-TFIIB: Transcription factor zinc-finger	81.51
cd00202	54	ZnF_GATA Zinc finger DNA binding domain; binds spe	80.55

>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-37  Score=230.70  Aligned_cols=62  Identities=77%  Similarity=1.527  Sum_probs=58.1

Q ss_pred             CCCCCCCCCCCcCCCceeeeeccCCCCCCcccchhcccccccCcccccccCCCccCCCCCCC
Q 043493           24 KVTESLPCPRCESTSTKFCYYNNYNLSQPRHFCKSCRRYWTQGGTLRNIPVGGGTRKNSKRT   85 (254)
Q Consensus        24 ~e~~~~~CPRC~S~nTKFcYyNNy~~~QPR~fCk~CrRYWT~GGtLRnVPVGGG~RKn~krs   85 (254)
                      ++++.++||||+|+||||||||||+++||||||++|+||||+||+|||||||||+||+++++
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            36789999999999999999999999999999999999999999999999999999995443

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=94.47  E-value=0.021  Score=48.09  Aligned_cols=35  Identities=26%  Similarity=0.684  Sum_probs=27.9

Q ss_pred             CCCCCCCcCCCceeeeeccC--CCCCCcccchhcccccc
Q 043493           28 SLPCPRCESTSTKFCYYNNY--NLSQPRHFCKSCRRYWT   64 (254)
Q Consensus        28 ~~~CPRC~S~nTKFcYyNNy--~~~QPR~fCk~CrRYWT   64 (254)
                      ..+||||.|.+|+..  +.|  +.++.-|.|++|+.=|.
T Consensus       105 ~~~cp~c~s~~t~~~--s~fg~t~cka~~~c~~c~epf~  141 (146)
T TIGR02159       105 SVQCPRCGSADTTIT--SIFGPTACKALYRCRACKEPFE  141 (146)
T ss_pred             CCcCCCCCCCCcEee--cCCCChhhHHHhhhhhhCCcHh
Confidence            579999999999964  555  45677899999997543

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=94.01  E-value=0.047  Score=37.38  Aligned_cols=29  Identities=38%  Similarity=0.855  Sum_probs=23.1

Q ss_pred             CCCCCCCCcCCCceeeeeccCCCCCCcccchhccc
Q 043493           27 ESLPCPRCESTSTKFCYYNNYNLSQPRHFCKSCRR   61 (254)
Q Consensus        27 ~~~~CPRC~S~nTKFcYyNNy~~~QPR~fCk~CrR   61 (254)
                      +...||+|.+.  +...+.+    +.+|.|++|++
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            34679999998  6655655    78999999986

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

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

Probab=93.38  E-value=0.054  Score=44.74  Aligned_cols=36  Identities=31%  Similarity=0.631  Sum_probs=28.4

Q ss_pred             CCCCCCCcCCCceeeeeccCCCCCCcccchhccccccc
Q 043493           28 SLPCPRCESTSTKFCYYNNYNLSQPRHFCKSCRRYWTQ   65 (254)
Q Consensus        28 ~~~CPRC~S~nTKFcYyNNy~~~QPR~fCk~CrRYWT~   65 (254)
                      ...||+|.+.+  +-=+.-+.....||.|++|++-|+.
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            46899999999  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=92.74  E-value=0.071  Score=36.02  Aligned_cols=31  Identities=42%  Similarity=0.760  Sum_probs=21.8

Q ss_pred             CCCCCCCcCCCceeeeeccCCCC-CCcccchhcc
Q 043493           28 SLPCPRCESTSTKFCYYNNYNLS-QPRHFCKSCR   60 (254)
Q Consensus        28 ~~~CPRC~S~nTKFcYyNNy~~~-QPR~fCk~Cr   60 (254)
                      .+.||+|.+++.-  |=|-.+.. ..||+|++|+
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            4689999998721  23444443 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=91.49  E-value=0.21  Score=33.92  Aligned_cols=37  Identities=24%  Similarity=0.768  Sum_probs=28.9

Q ss_pred             CCCCCCcCCCceeeeeccCCCCCC---cccchhccccccc
Q 043493           29 LPCPRCESTSTKFCYYNNYNLSQP---RHFCKSCRRYWTQ   65 (254)
Q Consensus        29 ~~CPRC~S~nTKFcYyNNy~~~QP---R~fCk~CrRYWT~   65 (254)
                      .+||+|...+.-|-..+-.+...|   -|.|.+|...|..
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            379999988877766666666666   4999999999963

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=88.74  E-value=0.39  Score=32.34  Aligned_cols=35  Identities=23%  Similarity=0.696  Sum_probs=24.7

Q ss_pred             CCCCCcCCCceeeeeccCCCCCCc---ccchhcccccc
Q 043493           30 PCPRCESTSTKFCYYNNYNLSQPR---HFCKSCRRYWT   64 (254)
Q Consensus        30 ~CPRC~S~nTKFcYyNNy~~~QPR---~fCk~CrRYWT   64 (254)
                      +||.|...+.-|--.+......|-   |.|.+|..-|+
T Consensus         2 ~Cp~Cg~~~a~~~~~Q~rsaDE~~T~fy~C~~C~~~wr   39 (39)
T PF01096_consen    2 KCPKCGHNEAVFFQIQTRSADEPMTLFYVCCNCGHRWR   39 (39)
T ss_dssp             --SSS-SSEEEEEEESSSSSSSSSEEEEEESSSTEEEE
T ss_pred             CCcCCCCCeEEEEEeeccCCCCCCeEEEEeCCCCCeeC
Confidence            799999988776655666555553   99999999885

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 ....

>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=84.14  E-value=0.53  Score=42.45  Aligned_cols=37  Identities=27%  Similarity=0.632  Sum_probs=18.4

Q ss_pred             CCCCCCCcCCC-ceeeeeccCCCCCC-cccchhcccccc
Q 043493           28 SLPCPRCESTS-TKFCYYNNYNLSQP-RHFCKSCRRYWT   64 (254)
Q Consensus        28 ~~~CPRC~S~n-TKFcYyNNy~~~QP-R~fCk~CrRYWT   64 (254)
                      ...||.|..++ .++-||..-....- -+.|.+|+.|+-
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            45899998854 56777743333333 399999999983

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.

>PHA02998 RNA polymerase subunit; Provisional

Probab=83.10  E-value=1.2  Score=40.19  Aligned_cols=39  Identities=26%  Similarity=0.686  Sum_probs=34.1

Q ss_pred             CCCCCCCCcCCCceeeeeccCCCCCCc---ccchhccccccc
Q 043493           27 ESLPCPRCESTSTKFCYYNNYNLSQPR---HFCKSCRRYWTQ   65 (254)
Q Consensus        27 ~~~~CPRC~S~nTKFcYyNNy~~~QPR---~fCk~CrRYWT~   65 (254)
                      ...+||+|...++-|--.|-++-..|-   |.|..|..-|.-
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            568999999999999888888888885   899999999963

>TIGR01384 TFS_arch transcription factor S, archaeal

Probab=81.71  E-value=1.9  Score=33.19  Aligned_cols=39  Identities=18%  Similarity=0.603  Sum_probs=29.3

Q ss_pred             CCCCCCCcCCCceeeeeccCCCCCCc---ccchhcccccccC
Q 043493           28 SLPCPRCESTSTKFCYYNNYNLSQPR---HFCKSCRRYWTQG   66 (254)
Q Consensus        28 ~~~CPRC~S~nTKFcYyNNy~~~QPR---~fCk~CrRYWT~G   66 (254)
                      ..+||+|...+.-|-..+-.+-..|-   |.|..|.-.|+..
T Consensus        62 ~~~Cp~Cg~~~a~f~~~Q~RsadE~~T~fy~C~~C~~~w~~~  103 (104)
T TIGR01384        62 RVECPKCGHKEAYYWLLQTRRADEPETRFYKCTKCGYVWREY  103 (104)
T ss_pred             cCCCCCCCCCeeEEEEeccCCCCCCcEEEEEeCCCCCeeEeC
Confidence            57999998777766655555544443   9999999999864

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=81.51  E-value=0.46  Score=31.78  Aligned_cols=38  Identities=26%  Similarity=0.635  Sum_probs=27.5

Q ss_pred             CCCCCcCCCceeeeeccCCCCCCcccchhcccccccCcccccc
Q 043493           30 PCPRCESTSTKFCYYNNYNLSQPRHFCKSCRRYWTQGGTLRNI   72 (254)
Q Consensus        30 ~CPRC~S~nTKFcYyNNy~~~QPR~fCk~CrRYWT~GGtLRnV   72 (254)
                      +||+|...=...-+     ..-+-+.|.+|.-.|=..+.|..+
T Consensus         1 ~CP~C~~~l~~~~~-----~~~~id~C~~C~G~W~d~~el~~~   38 (41)
T PF13453_consen    1 KCPRCGTELEPVRL-----GDVEIDVCPSCGGIWFDAGELEKL   38 (41)
T ss_pred             CcCCCCcccceEEE-----CCEEEEECCCCCeEEccHHHHHHH
Confidence            69999985444433     235668899999999888776543

>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=80.55  E-value=1.6  Score=31.37  Aligned_cols=41  Identities=27%  Similarity=0.723  Sum_probs=29.5

Q ss_pred             CCCCCcCCCceeeeeccCCCCCCcccchhcccccccCccccccc
Q 043493           30 PCPRCESTSTKFCYYNNYNLSQPRHFCKSCRRYWTQGGTLRNIP   73 (254)
Q Consensus        30 ~CPRC~S~nTKFcYyNNy~~~QPR~fCk~CrRYWT~GGtLRnVP   73 (254)
                      .|-.|...+|..=.-..   .....+|-+|.-||.+.+..|.+-
T Consensus         1 ~C~~C~~~~Tp~WR~g~---~~~~~LCNaCgl~~~k~~~~rp~~   41 (54)
T cd00202           1 ACSNCGTTTTPLWRRGP---SGGSTLCNACGLYWKKHGVMRPLS   41 (54)
T ss_pred             CCCCCCCCCCcccccCC---CCcchHHHHHHHHHHhcCCCCCcc
Confidence            37788887775332222   467899999999999999665543

---

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	254
1qyp_A	57	RNA polymerase II; transcription, RPB9, Zn ribbon,	86.33
1tfi_A	50	Transcriptional elongation factor SII; transcripti	86.24

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

Probab=86.33  E-value=0.47  Score=32.56  Aligned_cols=38  Identities=18%  Similarity=0.588  Sum_probs=26.4

Q ss_pred             CCCCCCCcCCCceeeeeccCCCCCC---cccchhccccccc
Q 043493           28 SLPCPRCESTSTKFCYYNNYNLSQP---RHFCKSCRRYWTQ   65 (254)
Q Consensus        28 ~~~CPRC~S~nTKFcYyNNy~~~QP---R~fCk~CrRYWT~   65 (254)
                      ..+||+|...+..|--.+-.....|   .|.|..|.--|..
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            5789999985444444444444445   3999999999975

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

Probab=86.24  E-value=0.6  Score=32.16  Aligned_cols=38  Identities=16%  Similarity=0.628  Sum_probs=29.5

Q ss_pred             CCCCCCCCcCCCceeeeeccCCCCCCc---ccchhcccccc
Q 043493           27 ESLPCPRCESTSTKFCYYNNYNLSQPR---HFCKSCRRYWT   64 (254)
Q Consensus        27 ~~~~CPRC~S~nTKFcYyNNy~~~QPR---~fCk~CrRYWT   64 (254)
                      ...+||+|...+..|--.+..+...|-   |.|.+|..-|.
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            456899999988777666666665564   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	254
d1twfi2	72	RBP9 subunit of RNA polymerase II {Baker's yeast (	92.16
d1tfia_	50	Transcriptional factor SII, C-terminal domain {Hum	91.16
d1qypa_	57	RBP9 subunit of RNA polymerase II {Archaeon Thermo	84.19

>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=92.16  E-value=0.08  Score=37.69  Aligned_cols=41  Identities=22%  Similarity=0.492  Sum_probs=32.3

Q ss_pred             CCCCCCCcCCCceeeeeccCCCCCCc---ccchhcccccccCcc
Q 043493           28 SLPCPRCESTSTKFCYYNNYNLSQPR---HFCKSCRRYWTQGGT   68 (254)
Q Consensus        28 ~~~CPRC~S~nTKFcYyNNy~~~QPR---~fCk~CrRYWT~GGt   68 (254)
                      ...||+|...+.-|-+.+-.+..-|-   |.|..|.-.|+...+
T Consensus        23 ~~~CpkCg~~~a~~~q~QtRsaDE~mT~Fy~C~~C~h~Wr~~~~   66 (72)
T d1twfi2          23 DRECPKCHSRENVFFQSQQRRKDTSMVLFFVCLSCSHIFTSDQK   66 (72)
T ss_dssp             CCCCTTTCCCCEEEEECSSCCTTCCCCEEEEETTTCCEEECCTT
T ss_pred             CCCCCCCCCCeEEEEEeecCccCCCceEEEEcCCCCCCcccccc
Confidence            46999999988887777766555554   999999999998543

>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=91.16  E-value=0.077  Score=35.60  Aligned_cols=38  Identities=16%  Similarity=0.628  Sum_probs=32.2

Q ss_pred             CCCCCCCCcCCCceeeeeccCCCCCCc---ccchhcccccc
Q 043493           27 ESLPCPRCESTSTKFCYYNNYNLSQPR---HFCKSCRRYWT   64 (254)
Q Consensus        27 ~~~~CPRC~S~nTKFcYyNNy~~~QPR---~fCk~CrRYWT   64 (254)
                      ....||+|.+.+..|--+|..+...|-   +.|.+|..-|-
T Consensus         8 ~~~~C~kC~~~~~~~~~~QtRSADEp~T~F~~C~~Cg~~Wr   48 (50)
T d1tfia_           8 DLFTCGKCKKKNCTYTQVQTRSADEPMTTFVVCNECGNRWK   48 (50)
T ss_dssp             CCSCCSSSCSSCEEEEEECSSSSSSCCEEEEEESSSCCEEE
T ss_pred             CCEECCCCCCCccEEEEEEccCCCCCceEEEEccccCCeee
Confidence            467999999999888878888877776   89999999883

>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=84.19  E-value=0.31  Score=33.10  Aligned_cols=38  Identities=18%  Similarity=0.614  Sum_probs=29.8

Q ss_pred             CCCCCCCcCCCceeeeeccCCCCCCc---ccchhccccccc
Q 043493           28 SLPCPRCESTSTKFCYYNNYNLSQPR---HFCKSCRRYWTQ   65 (254)
Q Consensus        28 ~~~CPRC~S~nTKFcYyNNy~~~QPR---~fCk~CrRYWT~   65 (254)
                      .++||+|...+..|--.|-....-|-   |.|..|..-|..
T Consensus        15 ~~~CpkC~~~~a~~~~~QtRsaDE~~T~fy~C~~Cg~~wre   55 (57)
T d1qypa_          15 KITCPKCGNDTAYWWEMQTRAGDEPSTIFYKCTKCGHTWRS   55 (57)
T ss_dssp             ECCCTTTCCSEEEEEEECCSSSSCSSEEEEEESSSCCEEEC
T ss_pred             cCCCCCCCCCceEEEEeecccccCCCeEEEEeCCCCCccee
Confidence            46899999988887766666655554   899999999863